| DupID | ChrA | StartA | EndA | StrA | ChrD | StartD | EndD | StrD | LineType | Note |
|---|---|---|---|---|---|---|---|---|---|---|
| 1 | 4552368 | 4553168 | + | 8 | 27612965 | 27613768 | - | L1MdF_I | Complete. Short LINE. Annotated deletion [Keane 2011]. SNPs and deletions in TSD. "AAGAAAAAAAAATAC" in SPRET. Annotated deletion [Keane 2011] | |
| 1 | 93448775 | 93449169 | + | 1 | 8234652 | 8235043 | - | L1MdA_V | Complete. 3rd of 3 duplications. (1st dup [Event 2002] 2nd dup [Event 3002]) Annotated deletion [Keane 2011]. | |
| X | 72350969 | 72351202 | + | 1 | 19805850 | 19806083 | + | L1MdGf_I | Complete. Annotated deletion [Keane 2011]. Absent in CAST, and has variants in TSD region. (Dup also missing in PWK, SPRET, & AKR) | |
| 1 | 20662667 | 20664794 | + | 5 | 90532982 | 90535109 | - | L1MdTf_III | Complete. Large Dup. Similar absence probe on Chr 3. Annotated deletion [Pezer 2015] [Quinlan 2010] [Keane 2011] [Wong2012] | |
| 1 | 22323806 | 22324614 | + | 2 | 53299662 | 53300473 | + | L1MdF_I | Complete. Overlaps annotated deletion [Henrichsen 2009]. Dup in CAST, PWK, WSB. | |
| 1 | 86949877 | 86951028 | - | 8 | 98282889 | 98284045 | - | L1MdTf_II | Complete. Annotated deletion [Henrichsen 2007] [Pezer 2015] [Keane 2011] | |
| 1 | 24356776 | 24357229 | + | 4 | 31892113 | 31892584 | - | L1MdA_II | Complete. Annotated deletion [Keane 2011] | |
| 1 | 30652098 | 30652819 | + | 3 | 44558794 | 44559517 | - | L1MdA_II | Complete. 2nd of 2 duplications. (1st dup [Event 2011]) Annotated deletion [Pezer 2015] [Keane 2011]. Ancestral includes high count region. | |
| 1 | 35100027 | 35100254 | + | 8 | 6887457 | 6887684 | - | L1MdTf_II | Complete. Short LINE. Annotated deletion [Keane 2011]. Insertion of T and C/t SNP in absense probe | |
| 1 | 41959930 | 41960269 | - | 6 | 42130105 | 42130444 | + | L1MdGf_I | Complete. Annotated deletion [Henrichsen 2009] [Pezer 2015] [Wong 2012] [Keane 2011] | |
| 3 | 118335387 | 118335534 | + | 1 | 42341037 | 42341184 | + | L1MdTf_II | Complete. Annotated deletion [Pezer 2015] [Keane 2011] [Wong 2012]. Inserted into LINE-1 (L1Lx_III) | |
| 4 | 111734131 | 111734729 | + | 1 | 44368255 | 44368841 | - | L1MdA_I | Complete. Duplication inserted in an ERVK. Annotated deletion [Pezer 2015] [Keane 2011] | |
| 1 | 45276916 | 45277606 | - | 3 | 29917267 | 29917958 | + | L1MdGf_II | Complete. GAA deletion in absence probe. Annotated deletion [Keane 2011] | |
| 1 | 45295674 | 45296057 | + | 15 | 40878115 | 40878498 | - | L1MdF_I | Complete. Short LINE. No absent strain identified. Overlaps annotated deletion [Pezer 2015] | |
| 16 | 34303544 | 34304246 | - | 1 | 48708383 | 48709084 | - | L1MdTf_III | Complete. Annotated deletion [Pezer 2015] [Keane 2011]. | |
| 1 | 50676732 | 50677308 | - | 8 | 116816518 | 116817094 | + | L1MdTf_III | Complete. Annotated deletion [Pezer 2015] [Keane 2011]. | |
| 1 | 53170939 | 53171181 | + | 17 | 20634179 | 20634422 | + | L1MdGf_II | Complete. CAST has G/t SNP in TSD. Annotated deletion [Keane 2011] | |
| 1 | 56585785 | 56587112 | - | 2 | 66706863 | 66708188 | + | L1MdF_I | Complete. Annotated deletion [Pezer 2015] [Keane 2011] | |
| 4 | 90247105 | 90247649 | - | 1 | 55174932 | 55175471 | - | L1MdGf_II | Complete. Annotated deletion [Keane 2011] | |
| 1 | 57938488 | 57938739 | + | 8 | 97794550 | 97794801 | + | L1MdA_IV | Complete. No deletion annotated. LIMeD in SPRET | |
| 4 | 29431138 | 29432141 | - | 11 | 40795038 | 40796039 | - | L1MdGf_I | Complete. 2nd of 2 duplications. (1st dup [Event 2025]) Large TSD. Inserted into a LINE-1 (L1MdF_I ). Overlaps annotated deletion [Henrichsen 2009] [Pezer 2015]. | |
| 1 | 66058717 | 66059031 | - | 13 | 103787728 | 103788042 | - | L1MdGf_II | Complete. Annotated deletion [Keane 2011]. | |
| 6 | 25727035 | 25727566 | + | 1 | 71450771 | 71451299 | - | L1MdTf_I | Complete. Short "TAAAACA" TSD. Annotated deletion [Pezer 2015] [Keane 2011] | |
| 8 | 77797126 | 77797674 | - | 1 | 73548600 | 73549151 | - | L1MdA_II | Complete. Absence probe has C/g SNP. Annotated deletion [Keane 2011] | |
| 1 | 73700282 | 73700853 | + | 2 | 63383893 | 63384461 | + | L1MdGf_II | Complete. Annotated deletion [Cahan 2009]. Dup in CAST & PWK. Tiny AAAG TSD | |
| 1 | 73783225 | 73783425 | + | 18 | 40418493 | 40418693 | + | L1MdA_I | Complete. Short LINE. Annotated deletion [Quinlan 2010] [Wong 2012] [Keane 2011] | |
| 4 | 22998313 | 22998760 | - | 1 | 78835125 | 78835587 | - | L1MdA_II | Complete. Annotated deletion [Keane 2011] [Wong 2012] | |
| 5 | 79711240 | 79711582 | + | 1 | 81511651 | 81512020 | - | L1MdA_III | Complete. Annotated deletion [Keane 2011]. Short TSD | |
| 1 | 23393674 | 23394005 | - | 10 | 65165873 | 65166204 | - | L1MdTf_II | Complete. 2nd of 2 duplications (1st dup [Event 2036]). Annotated deletion [Pezer 2015] [Keane 2011] (A inserted in proximal TSD) | |
| 10 | 64433745 | 64433963 | - | 1 | 97055956 | 97056185 | - | L1MdF_II | Complete. Annotated deletion [Pezer 2015]. Deletion rather than TSD | |
| 1 | 98016629 | 98017123 | + | 6 | 79040987 | 79041483 | + | L1MdA_III | Complete. T/c SNP in absence probe. Annotated deletion [Pezer 2015] [Keane 2011] | |
| 9 | 38370593 | 38370821 | - | 1 | 98800495 | 98800728 | + | L1MdA_II | Complete. Deletion in prox. TSD. | |
| 2 | 103765014 | 103765765 | - | 1 | 99189601 | 99190350 | + | L1MdA_I | Complete. Annotated deletion [Pezer 2015] [Keane 2011] | |
| 3 | 148268203 | 148268778 | + | 1 | 100435139 | 100435713 | + | L1MdF_II | Complete. Annotated deletion [Keane 2011]. | |
| 13 | 85016548 | 85017634 | + | 1 | 103255685 | 103256784 | - | L1MdTf_II | Complete. Annotated deletion [Henrichsen 2007] [Pezer 2015] [Keane 2011] | |
| 19 | 15953864 | 15954430 | + | 1 | 104224090 | 104224665 | + | L1MdTf_II | Complete. Annotated deletion [Pezer 2015] [Keane 2011] | |
| 1 | 110128073 | 110128271 | - | 3 | 41336667 | 41336864 | - | L1MdA_I | Complete. Annotated deletion [Pezer 2015] [Keane 2011] | |
| 8 | 112633703 | 112634772 | - | 1 | 111573675 | 111574744 | - | L1MdGf_I | Complete. C/G SNP difference in TSDs. Annotated deletion [Pezer 2015] [Keane 2011] [Wong 2012] | |
| X | 66891410 | 66892159 | - | 1 | 112582717 | 112583454 | + | L1MdTf_III | Complete. Annotated deletion [Pezer 2015] [Keane 2011] | |
| X | 82376030 | 82376523 | - | 1 | 114482196 | 114482689 | - | L1MdTf_II | Complete. Annotated deletion [Pezer 2015] [Keane 2011] | |
| 1 | 114947300 | 114947862 | - | 15 | 56254220 | 56254783 | - | L1MdGf_II | Complete. 2nd of 2 duplications (1st dup [Event 2050]) Annotated deletion [Keane 2011]. CAST has an insertion (Bfar retrogene) within its Ancestral Seq. | |
| 15 | 50568630 | 50569407 | - | 1 | 118165019 | 118165779 | + | L1MdF_I | No TSD identified. LiMeD is inserted into LINE-1, thus absence probe will be difficult. Overlaps annotated deletion [Pezer 2015] from 118145424-118228673. | |
| 5 | 41701337 | 41701734 | + | 1 | 122093060 | 122093457 | + | L1MdTf_II | Complete. Annotated deletion [Pezer 2015] [Keane 2011] [Wong 2012] | |
| X | 137081768 | 137082504 | + | 1 | 122875252 | 122875989 | + | L1MdTf_II | Complete. Short LINE (1620bp). Annotated deletion [Keane 2011] [Pezer 2015] | |
| 11 | 55893885 | 55894242 | + | 1 | 123594320 | 123594677 | - | L1MdTf_II/L1MdGf_I | Weird Case. Absence probe is on different strands 1: -123594256 to 1:123589151. Could be a subsequent SV or an assembly error. Also in NOD | |
| 16 | 74874523 | 74874715 | + | 1 | 124965746 | 124965938 | - | L1MdTf_II | Complete. Annotated deletion [Pezer 2015] [Yasuda 2012] [Keane 2011] [Wong 2012] | |
| 10 | 118657810 | 118658340 | + | 1 | 79038735 | 79039254 | - | L1MdGf_II | Complete. Annotated deletion [Henrichsen 2009] [Pezer 2015] [Keane 2011]. In CAST 'AAAAAGCCT_GT' | |
| 6 | 110310998 | 110311362 | + | 1 | 144479175 | 144479539 | - | L1MdA_II | Short LINE. Annotated deletion [Henrichsen 2009] | |
| 2 | 62551395 | 62551810 | + | 1 | 146382205 | 146382620 | + | L1MdA_I | Complete. Short LINE. Annotated deletion [Pezer 2015] [Keane 2011] [Cahan 2009] | |
| 1 | 148372323 | 148372597 | - | 14 | 14004621 | 14004895 | + | L1MdGf_I | Complete. Annotated deletion [Quinlan 2010] [Keane 2011] [Pezer 2015] | |
| 1 | 149069284 | 149069481 | - | 9 | 26886773 | 26886970 | + | L1MdTf_II | Complete. Short LINE. Annotated deletion [Keane 2011] | |
| 13 | 116209210 | 116209384 | + | 1 | 150239448 | 150239622 | + | L1MdTf_II | Complete. Annotated deletion [Quinlan 2010] [Yasuda 2012] [Pezer 2015] [Keane 2011] | |
| 1 | 152385528 | 152385889 | - | 18 | 49119265 | 49119626 | - | L1MdA_I | Complete. Short LINE. No polyAs (PolyTs distal to LINE). Annotated deletion [Keane 2011] | |
| 1 | 168875814 | 168876343 | - | 15 | 13846462 | 13846995 | - | L1MdA_III | Complete. Annotated deletion [Keane 2011] | |
| 1 | 177233052 | 177233763 | + | 4 | 99814200 | 99814910 | - | L1MdA_II | Complete. Annotated deletion [Keane 2011] | |
| 1 | 177855425 | 177855976 | - | 13 | 40411401 | 40411952 | + | L1MdGf_I | Complete. Short LINE. Annotated deletion [Keane 2011] | |
| 12 | 58898382 | 58899459 | + | 1 | 192625201 | 192626282 | - | L1MdF_II | Complete. Annotated deletion [Henrichsen 2007] [Pezer 2015] [Keane 2011] | |
| 12 | 45047842 | 45048601 | + | 1 | 193076929 | 193077683 | + | L1MdTf_II | Complete. Annotated deletion [Quinlan 2010] [Pezer 2015] [Keane 2011] | |
| 7 | 50027520 | 50027878 | - | 2 | 8937586 | 8937944 | - | L1MdA_IV | LiMeD is in SPRET and wild derived strains, not in M. Caroli, but can't find TSD | |
| 2 | 9092309 | 9092593 | + | 7 | 121800174 | 121800458 | - | L1MdA_I | Complete. A/g SNP in absence probe. Annotated deletion [Keane 2011] | |
| 2 | 10125344 | 10125725 | + | 3 | 72704816 | 72705196 | + | L1MdTf_III | Complete. Annotated deletion [Keane 2011] | |
| 13 | 14932973 | 14932998 | - | 2 | 12130754 | 12130779 | + | L1MdA_I | Complete. 2nd of 2 duplications. (2nd dup. [Event 2084]) No TSD. Annotated deletion [Pezer 2015] [Keane 2011]. | |
| 8 | 57110747 | 57111317 | + | 2 | 13181845 | 13182415 | + | L1MdTf_II | Complete. Annotated deletion [Pezer 2015] [Keane 2011] | |
| 2 | 13299763 | 13299968 | + | 5 | 99163186 | 99163390 | - | L1MdTf_II | Complete. Annotated deletion [Keane 2011]. Short TSD (Need to adjust TE/polyA/Dup boundries) | |
| 3 | 85412820 | 85413818 | - | 2 | 14302437 | 14303448 | + | L1MdTf_III | Complete. Annotated deletion [Pezer 2015] [Keane 2011] | |
| 2 | 14481349 | 14481903 | - | 7 | 76525947 | 76526498 | - | L1MdA_IV | Complete. Annotated deletion [Pezer 2015] | |
| 2 | 19573301 | 19573980 | - | 3 | 78610421 | 78611099 | + | L1MdA_III | Weird case. Looks like a normal LINE-1 insertion (TSD: "AAGACAAAGGCC") followed by a duplication w/TSD and no LINE. But, NZO is missing both the dup and L1. Second absence probe for LINE is "AGGCTCCTTTAAGACAAAGGCCTAGTGAACAGAC" | |
| 3 | 53915364 | 53916052 | + | 2 | 24116648 | 24117336 | - | L1MdGf_I | Complete. Annotated deletion [Keane 2011] | |
| 3 | 24452797 | 24453301 | + | 2 | 34201179 | 34201684 | + | L1MdA_I | Complete. Annotated deletion [Keane 2011] | |
| 2 | 42602676 | 42604014 | + | 6 | 148368259 | 148369595 | + | L1MdF_I | Complete. Annotated deletion [Keane 2011] | |
| 3 | 33796299 | 33796502 | + | 2 | 47122593 | 47122796 | - | L1MdTf_II | Complete. Annotated deletion [Wong 2012] [Pezer 2015] [Keane 2011]. TSD is A"s | |
| X | 68955251 | 68956618 | + | 2 | 47729431 | 47730802 | + | L1MdA_III | No deletion annotated. Distal LINE (L1MdN_I) | |
| 2 | 54463793 | 54464799 | - | 12 | 81387517 | 81388538 | - | L1MdF_II | Complete. (2nd dup [Event 2099]) No deletion annotated. Inserted near duplication on 8 (-): 83485561 | |
| 15 | 44928302 | 44928998 | - | 2 | 55677561 | 55678243 | + | L1MdTf_II | Complete. Potential 2nd dup location not identified "TAAATAAATCATA". Annotated deletion [Pezer 2015] [Keane 2011] [Wong 2012] | |
| 1 | 149698935 | 149699304 | + | 6 | 30237615 | 30237984 | + | L1MdTf_III | Complete. Tiny LINE inserted in a SINE (B1_Mus1). Annotated deletion [Henrichsen 2009] [Keane 2011] | |
| 2 | 56541481 | 56541897 | + | 14 | 24324401 | 24324818 | + | L1MdTf_II | No proximal Poly-As. Overlaps annotated deletion [Pezer 2015] from 24289779-24326378. | |
| 19 | 43009744 | 43009941 | - | 2 | 64151283 | 64151480 | + | L1MdA_I | Complete. Annotated deletion [Pezer 2015] [Keane 2011] | |
| 2 | 64222523 | 64223188 | + | 4 | 26656461 | 26657128 | - | L1MdA_I | Complete. 2nd dup of 2 duplications. (1st dup [Event 2107]) Annotated deletion [Henrichsen 2009] [Pezer 2015] [Keane 2011] | |
| 11 | 63305829 | 63306782 | - | 2 | 64795226 | 64796205 | + | L1MdTf_III | Complete. Annotated deletion [Keane 2011] | |
| 14 | 111032702 | 111032951 | - | 2 | 72097838 | 72098087 | + | L1MdA_I | Complete. Short LINE. Annotated deletion [Keane 2011] [Wong 2012] | |
| 5 | 54661013 | 54661542 | + | 2 | 77121857 | 77122386 | + | L1MdTf_II | Complete. LINE L1MdTf_I distal to event. Annotated deletion [Pezer 2015] [Keane 2011]. | |
| 16 | 59469566 | 59469719 | - | 2 | 78511269 | 78511422 | + | L1MdTf_I | Complete. 3rd of 3 duplications. (1st dup [Event 3113], 2nd dup [Event 2113]) Overlaps annotated deletion [Pezer 2015] [Wong 2012]. | |
| 2 | 80871454 | 80872696 | - | 4 | 79102043 | 79103236 | + | L1MdF_II | Complete. LiMeD is In CAST & PWK. | |
| 2 | 81798584 | 81798827 | + | 11 | 7860367 | 7860610 | - | L1MdA_I | Complete. Annotated deletion [Keane 2011] | |
| 2 | 82959766 | 82960527 | - | 9 | 91268209 | 91268970 | + | L1MdTf_I | Complete. Annotated deletion [Pezer 2015] [Keane 2011] | |
| 4 | 28116056 | 28116204 | - | 2 | 83436789 | 83436937 | + | L1MdTf_I | Complete. Annotated deletion [Pezer 2015] [Keane 2011] [Wong 2012] | |
| 2 | 84106563 | 84108589 | + | 3 | 81695819 | 81697874 | + | L1MdTf_II | Complete. Annotated deletion [Henrichsen 2007] [Pezer 2015] [Keane 2011]. Deleted in many strains. | |
| 18 | 49381531 | 49381724 | + | 2 | 84400411 | 84400604 | + | L1MdA_II | Complete. Annotated deletion [Keane 2011]. to-do absence probe. | |
| 15 | 49223395 | 49223880 | - | 2 | 86849528 | 86850013 | + | L1MdA_I | Complete. Annotated deletion [Pezer 2015] [Keane 2011] | |
| 2 | 87856696 | 87857391 | - | 5 | 75141345 | 75142040 | + | L1MdGf_II | Complete. Annotated deletion [Keane 2011] | |
| 3 | 29060523 | 29061596 | - | 2 | 87926271 | 87927346 | - | L1MdTf_III | Complete. Annotated deletion [Quinlan 2010] [Keane 2011] [Wong 2012] | |
| 2 | 89720896 | 89721234 | - | 19 | 35591056 | 35591395 | + | L1MdGf_II | Complete. Two G/a SNPs in absence probe. Annotated deletion [Keane 2011] | |
| X | 156911671 | 156912401 | + | 2 | 89736523 | 89737254 | + | L1MdGf_II | Complete. | |
| 16 | 75426417 | 75426566 | + | 2 | 100540033 | 100540182 | - | L1MdGf_I | Complete. Multiple dups. 1st dup is part of another LINE-1 (L1MdA_VII). Annotated deletion [Pezer 2015]. | |
| 15 | 96478932 | 96479445 | + | 2 | 101126426 | 101126936 | - | L1MdTf_II | Complete. 2nd dup [2129] Inserted into LINE (L1MdA_VI). Annotated deletion [Pezer 2015]. | |
| 9 | 30324085 | 30325136 | + | 2 | 106240705 | 106241757 | - | L1MdGf_II | Extra "GTCTGTTT" at boundary of absence sequence (deleted distal TSD?) | |
| 2 | 106771630 | 106772100 | + | 12 | 39019619 | 39020091 | - | L1MdA_V | no dist. poly-A's. TSD not identified. No deletion annotated. Chr. 12 (-) 39021346 == Chr.2 (-)106771591. | |
| 13 | 78955256 | 78955635 | + | 2 | 111761922 | 111762299 | + | L1MdF_I | Complete. 2 dups. Chr13 (-): 78955684-78955766. Note, it is nearby and from other strand. REANNOTATE, as 2320. Old, SPRET has Dup. Inserted into LTR/ERVL-MaLR. | |
| 2 | 116261851 | 116262290 | - | 8 | 24757981 | 24758411 | + | L1MdGf_II | Complete. 2nd of 2 duplications (1st dup [Event 2134]) Annotated deletion [Keane 2011]. Many mutations in absence probe. | |
| 18 | 21859649 | 21859828 | - | 2 | 117893227 | 117893406 | - | L1MdTf_III | Complete. 2nd of 2 duplications (1st dup [Event 2135]) Annotated deletion [Keane 2011]. | |
| 2 | 123053388 | 123053958 | + | 12 | 39863216 | 39863786 | - | L1MdF_II | Complete. Annotated deletion [Keane 2011]. (39863971-39865231 L1MdA_III). | |
| 2 | 134209641 | 134210988 | + | 5 | 71532421 | 71533768 | + | L1MdGf_I | Complete. Annotated deletion [Pezer 2015] [Keane 2011]. | |
| 2 | 135762008 | 135762557 | - | 11 | 17674379 | 17674927 | + | L1MdGf_I | Complete. Annotated deletion [Pezer 2015] [Keane 2011] [Wong 2012] | |
| 2 | 136349432 | 136349774 | - | 17 | 40280130 | 40280473 | + | L1MdA_I | Complete. Deletion not annotated. | |
| 2 | 138190820 | 138191453 | - | 13 | 14748119 | 14748671 | + | L1MdGf_II | Complete. 2nd of 2 duplications(1st dup [Event 2141]) Annotated deletion [Keane 2011] | |
| 8 | 49361046 | 49361198 | + | 2 | 139079200 | 139079352 | - | L1MdGf_II | Complete. Old event, SPRET has dup. Mus caroli does not. | |
| 2 | 143413395 | 143414285 | - | 12 | 45303131 | 45304021 | + | L1MdGf_I | Complete. Annotated deletion [Wong 2012] [Pezer 2015] [Keane 2011] | |
| 2 | 143478304 | 143479691 | - | 8 | 16926670 | 16928044 | + | L1MdA_I | Complete. Annotated deletion [Pezer 2015] [Keane 2011]. High counts in dup. to-do absence probe | |
| 2 | 148946128 | 148946337 | - | 4 | 77973178 | 77973387 | - | L1MdTf_II | Complete. Annotated deletion [Keane 2011] | |
| 2 | 159801913 | 159802081 | - | 16 | 47747585 | 47747753 | - | L1MdTf_II | Complete. Annotated deletion [Wong 2012] [Pezer 2015] [Yalcin 2012] [Keane 2011] | |
| 5 | 59157914 | 59159401 | + | 2 | 161804115 | 161805659 | + | L1MdA_I | Complete. Annotated deletion [Henrichsen 2007] [Pezer 2015] [Keane 2011] [Quinlan 2010] [Wong 2012]. TSD is unclear or absent. | |
| 2 | 163072624 | 163072915 | + | 17 | 16669897 | 16670188 | - | L1MdTf_I | Multiple dups from Chr2 with gaps and no intermediate polyAs [2:163069488-163069616, 2:163075636-163075775, 2:163077782-163077881] | |
| 9 | 87864766 | 87864925 | - | 3 | 17902658 | 17902817 | - | L1MdA_I | Complete. Annotated deletion [Quinlan 2010] [Keane 2011] | |
| 17 | 91172612 | 91172845 | - | 3 | 18383037 | 18383270 | + | L1MdA_I | Complete. Annotated deletion [Keane 2011] | |
| 3 | 19132148 | 19132702 | - | 18 | 23897770 | 23898325 | + | L1MdA_VI | Old event, SPRET and Mus caroli have derived. | |
| 3 | 19951920 | 19952780 | + | 6 | 135617760 | 135618618 | - | L1MdF_I | Complete. Annotated deletion [Keane 2011] | |
| 3 | 22320201 | 22321471 | - | 17 | 39497847 | 39499109 | - | L1MdGf_II | Overlaps annotated deletion [Henrichsen 2009]. | |
| 5 | 22762872 | 22763270 | + | 3 | 22422379 | 22422777 | + | L1MdGf_II | Complete. 3rd of 3 duplications (2nd dup [Event 2159] 1st dup [Event 3159]). Annotated deletion [Pezer 2015] [Keane 2011]. SDP=11111001 | |
| 3 | 25509110 | 25509593 | + | 17 | 82148195 | 82148678 | - | L1MdGf_II | Complete. Short LINE. Annotated deletion [Keane 2011]. to-do absence probe. | |
| X | 14757739 | 14758955 | - | 3 | 28520689 | 28521901 | + | L1MdTf_I | Complete. Annotated deletion [Pezer 2015] [Keane 2011] | |
| 12 | 47978269 | 47979212 | - | 3 | 31476765 | 31477710 | + | L1MdA_II | Complete. Annotated deletion [Pezer 2015] [Keane 2011] [Quinlan 2010] | |
| 3 | 34127238 | 34128304 | - | 15 | 7855591 | 7856659 | + | L1MdTf_II | Complete. Annotated deletion [Pezer 2015] [Keane 2011] | |
| 3 | 40053591 | 40054215 | - | 12 | 95829325 | 95829949 | + | L1MdTf_II | Complete. Annotated deletion [Wong 2012] [Pezer 2015] [Keane 2011] | |
| 14 | 49702814 | 49703056 | - | 3 | 43111107 | 43111339 | + | L1MdTf_II | Complete. Annotated deletion [Keane 2011] [Pezer 2015]. Has deletion instead of TSD. 11 bp deletion at L1 insertion. | |
| 3 | 45460914 | 45461271 | + | 5 | 56404302 | 56404659 | + | L1MdTf_I | 2nd dup [Event 2166] Annotated deletion [Pezer 2015]. TSD or absence probe not identified. | |
| 16 | 68028629 | 68028913 | + | 3 | 46310509 | 46310793 | + | L1MdTf_I | Complete. Annotated deletion [Pezer 2015] [Quinlan 2010] [Keane 2011] [Wong 2012] | |
| 7 | 90701696 | 90702047 | + | 3 | 47411065 | 47411417 | - | L1MdA_II | No prox. poly-A or TSD identified | |
| 3 | 56873932 | 56874359 | + | 12 | 43591319 | 43591746 | + | L1MdTf_II | Complete. Annotated deletion [Keane 2011]. Has deletion instead of TSD | |
| 18 | 73406051 | 73406727 | + | 3 | 60374462 | 60375138 | - | L1MdTf_III | Complete. Annotated deletion [Keane 2011] | |
| 3 | 67111720 | 67112067 | - | 4 | 7605445 | 7605792 | + | L1MdTf_I | Complete. Potential 2nd dup location not identified "GAACCCCCCAGCAAAGAGT". Annotated deletion [Pezer 2015] [Keane 2011] | |
| 3 | 70296942 | 70297456 | + | 17 | 22654708 | 22655222 | + | L1MdTf_III | Complete. Annotated deletion [Henrichsen 2007] [Graubert 2007] [Pezer 2015] [Keane 2011] | |
| X | 150821877 | 150822213 | - | 3 | 73414518 | 73414854 | - | L1MdA_I | Complete. Annotated deletion [Cutler 2007] [Keane 2011]. | |
| X | 75228426 | 75229229 | - | 3 | 73875937 | 73876734 | + | L1MdGf_II | Complete. Annotated deletion [Henrichsen 2007] [Keane 2011]. Multiple tiny dups? (+)2:5413664-5413697 [Camk1d] and (+)5:116904338-116904358 | |
| 6 | 75957228 | 75957436 | - | 3 | 81070239 | 81070447 | - | L1MdA_I | Complete. Annotated deletion [Pezer 2015] [Quinlan 2010] [Keane 2011] [Wong 2012] | |
| 3 | 81138173 | 81138526 | + | 12 | 44892457 | 44892810 | + | L1MdA_I | Complete. Annotated deletion [Quinlan 2010] [Pezer 2015] [Keane 2011]. | |
| 3 | 82442550 | 82444001 | - | 4 | 14129503 | 14130967 | - | L1MdF_II | Old dup in PWK and SPRET. | |
| 3 | 85904978 | 85905454 | + | 11 | 3275677 | 3276152 | + | L1MdF_II | LINE is probably inserted in repeat. | |
| 19 | 43129740 | 43132747 | + | 3 | 91118467 | 91121354 | - | L1MdF_II | Dup is in SPRET. Need to find TSD | |
| 6 | 6670791 | 6672032 | - | 3 | 91308627 | 91309865 | + | L1MdF_II | Annotated deletion [Henrichsen 2007] Insertion is in CAST&PWK&WSB | |
| 3 | 99294358 | 99295042 | - | 14 | 106148921 | 106149589 | + | L1MdF_I | Complete. LINE appears to be inserted within a repeated element. A/g and G/a SNPs in absence probe. | |
| X | 89816679 | 89816871 | + | 3 | 102989957 | 102990149 | + | L1MdTf_I | Complete. Annotated deletion [Wong 2012] [Pezer 2015] [Keane 2011] | |
| 4 | 111198742 | 111198919 | + | 3 | 104163373 | 104163550 | + | L1MdGf_II | Complete. Annotated deletion [Keane 2011] | |
| 3 | 114816811 | 114817504 | + | 6 | 17010799 | 17011492 | + | L1MdF_I | Complete. [A/t] SNP in absence probe. | |
| 10 | 4674338 | 4675881 | - | 3 | 124288401 | 124289919 | + | L1MdTf_III | Complete. Annotated deletion [Pezer 2015] [Keane 2011] | |
| 6 | 58827786 | 58828035 | - | 3 | 125208414 | 125208663 | - | L1MdA_I | Complete. Annotated deletion [Pezer 2015] [Keane 2011] | |
| 3 | 126646050 | 126647876 | - | 16 | 48969470 | 48971295 | + | L1MdTf_II | Complete. Annotated deletion [Pezer 2015] [Keane 2011] | |
| 19 | 11105301 | 11105683 | + | 3 | 129018247 | 129018629 | + | L1MdGf_I | Complete. Annotated deletion [Keane 2011] | |
| 3 | 130320879 | 130321893 | - | 5 | 9303683 | 9304700 | - | L1MdA_I | Complete. Potential 2nd dup location not identified. "GACACCAGG" | |
| 3 | 130331873 | 130332126 | - | 7 | 103549733 | 103549986 | - | L1MdGf_II | Complete. Small TSD. Potential 2nd dup location not identified "TAGATATG" Annotated deletion [Pezer 2015] [Keane 2011] [Henrichsen 2009] SPRET has dup. Ref is spretus at dup. | |
| 3 | 141551294 | 141551627 | - | 6 | 107606544 | 107606875 | - | L1MdGf_II | Complete. TSD is short and has INDEL "AGAcAGAG" | |
| 3 | 156325644 | 156325995 | + | 10 | 51221902 | 51222253 | - | L1MdA_I | Complete. 2nd of 2 duplications (1st dup [Event 2204]) Annotated deletion [Pezer 2015] [Keane 2011] | |
| 14 | 99741763 | 99741970 | + | 3 | 158780509 | 158780716 | - | L1MdGf_I | Inserted into a SINE. Dup in PWK, but not in CAST. | |
| 4 | 6100802 | 6102766 | + | 9 | 6634078 | 6636041 | + | L1MdTf_II | Dup appears to be inserted into a repetitive element. Hard to find TSD | |
| 18 | 20203499 | 20203693 | + | 4 | 10101777 | 10101972 | - | L1MdA_I | Complete. Annotated deletion [Wong 2012] [Pezer 2015] [Keane 2011] | |
| 4 | 15181797 | 15182043 | + | 8 | 28063356 | 28063602 | - | L1MdA_I | Complete. Annotated deletion [Quinlan 2010] [Pezer 2015] [Keane 2011] | |
| 8 | 15214294 | 15215449 | - | 4 | 16325979 | 16327138 | + | L1MdA_II | Complete. Annotated deletion [Keane 2011] | |
| 16 | 87642710 | 87643245 | - | 4 | 16680548 | 16681083 | + | L1MdA_I | Complete. Annotated deletion [Wong 2012] [Pezer 2015] [Keane 2011]. | |
| 13 | 116112074 | 116112536 | + | 4 | 23851131 | 23851593 | - | L1MdA_I | Complete. Annotated deletion [Henrichsen 2007] [Pezer 2015] [Keane 2011] | |
| X | 89683232 | 89683462 | - | 4 | 24200976 | 24201185 | + | L1MdTf_II | Complete. Annotated deletion [Pezer 2015] [Keane 2011] [Wong 2012] | |
| 5 | 55303345 | 55303636 | + | 4 | 25566586 | 25566877 | + | L1MdGf_I | Complete. Annotated deletion [Pezer 2015] [Keane 2011] [Wong 2012] | |
| 4 | 28152353 | 28152625 | + | 17 | 37640761 | 37641033 | - | L1MdF_II | Complete. Annotated deletion [Pezer 2015] [Keane 2011] | |
| 4 | 43277854 | 43279237 | + | 6 | 66817512 | 66818893 | - | L1MdF_I | Poly-T"s instead of Poly-A"s proximal to LINE | |
| 4 | 45396063 | 45396975 | - | 7 | 128158350 | 128159266 | + | L1MdA_VII | Dup is in SPRET | |
| 4 | 47566072 | 47567469 | - | 12 | 42098642 | 42100047 | + | L1MdF_III | No deletion annotated. TTTA microsatelite just distal of insertion. CAST&PWK have dup. | |
| X | 104055462 | 104056096 | - | 4 | 50518070 | 50518705 | - | L1MdA_III | Complete. Annotated deletion [Pezer 2015] [Keane 2011]. SNP in absence probe | |
| 4 | 58038850 | 58039292 | - | 9 | 25872396 | 25872838 | + | L1MdA_III | Complete. Annotated deletion [Henrichsen 2007] [Keane 2011]. Small TSD | |
| 15 | 10825437 | 10825816 | - | 4 | 58567746 | 58568125 | + | L1MdTf_III | Complete. Short LINE. Annotated deletion [Keane 2011] | |
| 6 | 103544046 | 103544582 | + | 4 | 64950083 | 64950619 | + | L1MdF_II | Complete. 2nd of 2 duplications. (1st dup [Event 2228]) Annotated deletion [Keane 2011]. | |
| 4 | 67567876 | 67568109 | + | 17 | 52043790 | 52044023 | + | L1MdA_I | Complete. Annotated deletion [Wong 2012] [Keane 2011]. to-do absence probe | |
| 4 | 68737384 | 68738179 | + | 5 | 55450090 | 55450885 | - | L1MdA_I | Complete. Annotated deletion [Quinlan 2010] [Pezer 2015] [Keane 2011] [Wong 2012] | |
| 6 | 31875383 | 31876406 | - | 4 | 71892390 | 71893417 | + | L1MdF_I | Possible 2nd dup from (-) 2:100078763 | |
| 4 | 73949662 | 73949933 | - | 6 | 15691005 | 15691276 | + | L1MdTf_III | Complete. Annotated deletion [Keane 2011] | |
| 4 | 76643618 | 76644397 | + | 5 | 91551652 | 91552431 | + | L1MdA_III | Complete. Annotated deletion [Keane 2011] | |
| 4 | 84985470 | 84985678 | - | 12 | 15032464 | 15032672 | + | L1MdGf_I | Complete. Annotated deletion [Pezer 2015] [Keane 2011]. | |
| 15 | 17885157 | 17885561 | - | 4 | 87571903 | 87572308 | - | L1MdA_III | Complete. Annotated deletion [Keane 2011] | |
| 4 | 90225851 | 90226505 | + | 8 | 42074398 | 42075038 | - | L1MdA_III | Dup is in SPRET | |
| 4 | 92215019 | 92215355 | - | 5 | 15726589 | 15726925 | + | L1MdTf_III | Complete. Annotated deletion [Keane 2011] | |
| 4 | 93203500 | 93204438 | - | 14 | 38787238 | 38788175 | + | L1MdF_I | Complete. Annotated deletion [Keane 2011] | |
| 12 | 102460298 | 102460896 | + | 4 | 93435083 | 93435681 | + | L1MdGf_II | Complete. Annotated deletion [Keane 2011] | |
| X | 19376221 | 19376416 | + | 4 | 95833937 | 95834132 | - | L1MdA_I | Complete. | |
| 11 | 105729912 | 105730241 | + | 4 | 96708858 | 96709187 | + | L1MdTf_II | Need to BLAT/BLAST; CHANGED 2020-09-25 distal derived boundary | |
| 4 | 109598209 | 109598582 | + | 8 | 101864986 | 101865359 | + | L1MdTf_I | Complete. 2nd of 2 duplications. (1st dup [Event 2247]). Annotated deletion [Pezer 2015] [Keane 2011] [Wong 2012]. "TATATT" deletion rather than TSD. | |
| 4 | 110436027 | 110436376 | + | 14 | 94325494 | 94325844 | - | L1MdF_I | Complete. Annotated deletion [Keane 2011] | |
| X | 69591930 | 69592737 | + | 4 | 113749793 | 113750615 | - | L1MdTf_II | Potential 2nd dup location not identified. | |
| 4 | 148043422 | 148044071 | - | 5 | 78474488 | 78475151 | - | L1MdN_I | no poly-As; Is dup longer with a deletion? | |
| 6 | 9013704 | 9014054 | - | 5 | 7130286 | 7130635 | - | L1MdGf_II | Overlaps annotated deletion [Pezer 2015]. TSD not identified. | |
| 10 | 85315063 | 85315582 | - | 5 | 8869118 | 8869636 | - | L1MdA_IV | Truncated Line, extra insertion | |
| 13 | 85381033 | 85381339 | + | 5 | 9626605 | 9626911 | + | L1MdA_III | Complete. Annotated deletion [Henrichsen 2007] | |
| 17 | 3666357 | 3666667 | - | 5 | 10565722 | 10566054 | - | L1MdA_I | Complete. Annotated deletion [Pezer 2015] [Keane 2011] | |
| 11 | 7432939 | 7433348 | - | 5 | 12008993 | 12009402 | + | L1MdA_IV | 2nd dup with simple seq? | |
| 5 | 14171337 | 14172866 | + | 14 | 18513770 | 18515298 | - | L1MdA_II | poly-A"s not clear | |
| 12 | 90776232 | 90776904 | - | 5 | 14304189 | 14304849 | - | L1MdF_II | Annotated deletion [Pezer 2015] | |
| 5 | 14732257 | 14732722 | - | 12 | 6077486 | 6077950 | - | L1MdGf_II | Complete. Annotated deletion [Pezer 2015] [Keane 2011] | |
| 8 | 99985079 | 99985376 | + | 5 | 18281337 | 18281634 | + | L1MdA_II | Complete. Annotated deletion [Pezer 2015] [Keane 2011] | |
| 5 | 20984761 | 20985119 | + | 18 | 86902171 | 86902528 | + | L1MdTf_II | Complete. SNP in CAST probe. Annotated deletion [Pezer 2015] [Keane 2011] | |
| 6 | 21135774 | 21136741 | - | 5 | 40351398 | 40352365 | + | L1MdTf_I | Complete. Annotated deletion [Pezer 2015] [Keane 2011] [Wong 2012] [Quinlan 2010]. No TSD. CHANGED 2020-09-24 derived distal boundary | |
| 5 | 52053119 | 52054815 | + | 17 | 89613239 | 89614915 | + | L1MdGf_II | Complete. Short LINE. Short TSD. G/c and T/a SNPs in absence probe. Annotated deletion [Keane 2011] | |
| 11 | 93749520 | 93749704 | - | 5 | 57555632 | 57555816 | - | L1MdGf_I | Complete. Annotated deletion [Keane 2011] | |
| X | 60857186 | 60858702 | + | 5 | 57982821 | 57984394 | + | L1MdTf_II | Complete. Annotated deletion [Pezer 2015] [Keane 2011] | |
| 16 | 43490489 | 43490761 | - | 5 | 60010224 | 60010496 | - | L1MdA_IV | Large TSD (probably larger than annotated should include "AGATATGTATAGAGATTAGATG"). Annotated deletion [Pezer 2015]. | |
| 6 | 15205074 | 15205430 | + | 5 | 63399472 | 63399828 | - | L1MdA_III | Short LINE | |
| 11 | 16135960 | 16136931 | + | 5 | 70203025 | 70203987 | - | L1MdTf_II | Complete. Annotated deletion [Pezer 2015] [Keane 2011] | |
| 11 | 46729343 | 46730427 | - | 5 | 71838497 | 71839541 | + | L1MdTf_I | Complete. Annotated deletion [Pezer 2015] [Keane 2011] | |
| 9 | 76167785 | 76168203 | + | 5 | 72362655 | 72363066 | - | L1MdGf_II | Complete. Annotated deletion [Henrichsen 2007] [Keane 2011] SNP in absence probe | |
| 13 | 89563435 | 89564276 | + | 5 | 79039341 | 79040182 | + | L1MdTf_II | Complete. Annotated deletion [Pezer 2015] [Keane 2011]. 2nd small dup? | |
| 8 | 31671084 | 31671468 | - | 5 | 85326717 | 85327106 | - | L1MdTf_III | Complete. Annotated deletion [Henrichsen 2007] [Keane 2011] | |
| 5 | 85833792 | 85834421 | + | 12 | 39418590 | 39419219 | - | L1MdGf_II | Proximal poly-A? | |
| 5 | 86641202 | 86641766 | + | 7 | 76016623 | 76017195 | - | L1MdA_I | Complete. Annotated deletion [Keane 2011] [Wong 2012] | |
| 5 | 86977242 | 86978322 | + | 12 | 52215547 | 52216630 | - | L1MdA_II | Complete. Annotated deletion [Pezer 2015] [Keane 2011]. 2nd small dup? (Chr 3:78305492) | |
| 5 | 87124364 | 87124671 | - | 7 | 9192927 | 9193234 | - | L1MdTf_II | Complete. Annotated deletion [Pezer 2015]. WSB has both absence and dup versions. | |
| 5 | 90743974 | 90744933 | - | 12 | 94018503 | 94019475 | - | L1MdA_VI | No annotated deletion. | |
| 5 | 91821934 | 91822678 | + | 9 | 3690295 | 3691039 | - | L1MdF_II | Complete. Annotated deletion [Pezer 2015]. In SPRET | |
| 5 | 98858862 | 98859274 | - | 16 | 65457052 | 65457464 | - | L1MdTf_II | Complete. Annotated deletion [Pezer 2015] [Keane 2011]. 2nd dup location(14: 96016097 [No LINE] or 10: - 57326898 [Similar LINE]) | |
| 19 | 16028915 | 16030306 | + | 6 | 3620241 | 3621655 | + | L1MdV_I | seems odd | |
| 10 | 112680990 | 112681372 | + | 6 | 16595134 | 16595516 | - | L1MdTf_II | Annotated deletion [Keane 2011] | |
| 6 | 18501168 | 18501740 | - | 10 | 19137071 | 19137643 | + | L1MdGf_II | Complete. Annotated deletion [Keane 2011] | |
| 9 | 91128681 | 91128906 | + | 6 | 19701611 | 19701836 | + | L1MdTf_II | Short LINE. Need to BLAST/BLAT | |
| 6 | 23920196 | 23920677 | - | 19 | 50755683 | 50756163 | + | L1MdGf_II | Complete. T/g SNP in absence probe. Annotated deletion [Yalcin 2012] [Keane 2011] [Wong 2012] | |
| 6 | 35736133 | 35736733 | - | 13 | 25975791 | 25976384 | + | L1MdA_II | Complete. Annotated deletion [Keane 2011]. No TSD. SNP and 11bp deletion in absence probe. | |
| 13 | 48579277 | 48579851 | - | 6 | 41253656 | 41254228 | + | L1MdF_I | Complete. Annotated deletion [Henrichsen 2007] [Keane 2011]. 2nd dup on same Chr. 13: - 48580803 and - 48583157 (spliced transcript?) | |
| 16 | 44482445 | 44482926 | - | 6 | 42205924 | 42206405 | - | L1MdGf_II | Complete. Annotated deletion [Henrichsen 2009] [Pezer 2015] [Keane 2011] | |
| 6 | 45468654 | 45469205 | - | 8 | 42579037 | 42579586 | - | L1MdA_I | Complete. Annotated deletion [Wong 2012] [Pezer 2015] [Keane 2011] | |
| 10 | 98585904 | 98587554 | - | 6 | 46813338 | 46814981 | + | L1MdTf_II | Complete. Annotated deletion [Pezer 2015] [Wong 2012] | |
| 14 | 25434949 | 25435293 | + | 6 | 49013928 | 49014275 | - | L1MdF_I | Complete. Annotated deletion [Keane 2011] | |
| 6 | 57932392 | 57933021 | - | 18 | 6631175 | 6631803 | + | L1MdA_I | Complete. Annotated deletion [Keane 2011] | |
| X | 111733710 | 111733969 | - | 6 | 60938026 | 60938284 | + | to do | uncertain LINE - L1MdF_III or L1MdF_I | |
| 14 | 60548421 | 60548722 | + | 6 | 66695899 | 66696200 | - | L1MdA_II | Complete. Annotated deletion [Henrichsen 2007] [Keane 2011] | |
| 12 | 41475060 | 41476579 | + | 6 | 69164033 | 69165352 | + | L1MdGf_II | Complete. 2nd of 2 duplications (1st dup [Event 2309]) B1_Mus2 in ancestral seq only. | |
| 16 | 77608520 | 77609406 | - | 6 | 69381629 | 69382508 | + | L1MdA_III | Complete. Annotated deletion [Henrichsen 2007] [Pezer 2015] [Cutler 2007] [Cahan 2008] | |
| X | 56305243 | 56305718 | + | 6 | 69686513 | 69686985 | - | L1MdTf_II | Short LINE | |
| 6 | 74842694 | 74843819 | + | 10 | 6742171 | 6743321 | + | L1MdF_II | Complete. Short LINE. Annotated deletion [Keane 2011]. | |
| 6 | 75757752 | 75757980 | - | 14 | 71553918 | 71554146 | - | L1MdTf_II | Complete. C/t SNP in absence probe. Annotated deletion [Henrichsen 2007] [Keane 2011] [Wong 2012] | |
| X | 104944392 | 104944697 | + | 6 | 75966612 | 75966917 | + | L1MdTf_II | Annotated deletion [Keane 2011] | |
| 9 | 9697022 | 9697500 | + | 6 | 88674958 | 88675425 | + | L1MdA_I | No dist. A's | |
| 9 | 37290411 | 37290907 | - | 6 | 102704342 | 102704837 | - | L1MdF_II | Duplication in PWK and SPRET | |
| 6 | 105518886 | 105519497 | - | 7 | 13996503 | 13997113 | + | L1MdGf_II | Annotated deletion [Henrichsen 2009] [Cutler 2007] [Keane 2011]. Inserted into a CNV? CHANGE 2020-09-25 adjusted L1-PolyA-Derived boundaries | |
| 8 | 39529126 | 39529789 | - | 6 | 107096286 | 107096949 | - | L1MdF_II | Complete. Annotated deletion [Wong 2012] [Pezer 2015] [Keane 2011] | |
| 14 | 104165264 | 104166006 | + | 6 | 109092463 | 109093198 | - | L1MdA_II | Annotated deletion [Henrichsen 2007] [Pezer 2015] | |
| 16 | 79063180 | 79063423 | + | 6 | 120328015 | 120328258 | + | L1MdGf_II | Complete. Annotated deletion [Keane 2011]. to-do absence probe. | |
| 15 | 31455899 | 31456590 | - | 6 | 123693289 | 123693981 | + | L1MdF_II | Complete. Annotated deletion [Henrichsen 2007] | |
| 13 | 80515690 | 80516723 | + | 6 | 130918997 | 130920027 | + | L1MdA_II | adjusted dist. poly-A | |
| 16 | 8060729 | 8060966 | - | 6 | 134328001 | 134328238 | + | L1MdTf_III | Complete. 2nd of 2 duplications (1st dup [Event 2326]) Deletion at insert instead of TSD | |
| 7 | 6476275 | 6476524 | - | 15 | 62686580 | 62686829 | - | L1MdTf_II | Complete. Annotated deletion [Pezer 2015] [Keane 2011] [Quinlan 2010] Varint near distal TSD | |
| 17 | 3725175 | 3725889 | + | 7 | 12081092 | 12081806 | - | L1MdGf_II | TSD not identified. Absent strain not identified. Overlapping deletion [Henrichsen 2009] [Pezer 2015]. | |
| 7 | 13208669 | 13208906 | - | 18 | 54232759 | 54232996 | + | L1MdF_II | Complete Example. Annotated deletion [Pezer 2015] [Keane 2011] | |
| 9 | 122071773 | 122072731 | + | 7 | 26058191 | 26059149 | - | L1MdGf_II | Insertion is in a duplicated region. Need to BLAST/BLAT | |
| 7 | 41445241 | 41445695 | + | 16 | 78994341 | 78994795 | + | L1MdTf_II | Complete. T/c SNP in absence probe. Annotated deletion [Pezer 2015] [Keane 2011] | |
| X | 88522873 | 88523247 | - | 7 | 47276757 | 47277132 | - | L1MdGf_II | Annotated deletion [Henrichsen 2007] [Pezer 2015] | |
| 13 | 111252331 | 111252605 | - | 7 | 47505595 | 47505871 | - | L1MdA_I | Complete. Annotated deletion [Henrichsen 2007] [Pezer 2015] [Keane 2011] [Kazmi 2013] [Cahan 2009] [Cutler 2007] | |
| 16 | 51074661 | 51075007 | + | 7 | 50108754 | 50109090 | - | L1MdGf_I | Complete. Annotated deletion [Keane 2011] | |
| X | 107209480 | 107209655 | + | 7 | 50243245 | 50243420 | - | L1MdGf_II | Complete. Annotated deletion [Keane 2011] | |
| 10 | 26981285 | 26981656 | - | 7 | 53079574 | 53079943 | - | L1MdGf_II | Weird. 2nd of 2 duplications (1st dup [Event 2342]) No poly-A between dups. | |
| 14 | 28678139 | 28678355 | + | 7 | 53386159 | 53386374 | - | L1MdGf_II | Complete. Annotated deletion [Henrichsen 2007] [Pezer 2015] [Keane 2011] | |
| 15 | 95724483 | 95724712 | + | 7 | 55121118 | 55121365 | + | L1MdTf_II | Complete. Annotated deletion [Henrichsen 2007] [Keane 2011] | |
| 14 | 104321971 | 104323344 | + | 7 | 56609862 | 56611154 | - | L1MdTf_III | Complete. 2nd dup (17:55645070) | |
| 16 | 55082751 | 55083603 | - | 7 | 58107070 | 58107922 | + | L1MdTf_II | Complete. Annotated deletion [Quinlan 2010] [Pezer 2015] [Keane 2011] | |
| 7 | 58647812 | 58648569 | + | 16 | 70366665 | 70367395 | - | L1MdA_I | Complete. Annotated deletion [Henrichsen 2007] [Pezer 2015] [Keane 2011] | |
| 9 | 8438571 | 8439586 | - | 7 | 60531046 | 60532064 | - | L1MdGf_I | Complete. Annotated deletion [Quinlan 2010] [Henrichsen 2009] [Cahan 2009] [Wong 2012] [Cutler 2007] [Pezer 2015] [Keane 2011] | |
| 11 | 71153965 | 71154167 | - | 7 | 61176992 | 61177194 | + | L1MdA_II | Complete.INDEL in absence probe at proximal TSD boundary. Small 2nd duplication (ACAATAGAAACAAACAAACA) in PolyA between LINE-1 and dup. Maps 3 other places, all in genes. | |
| 7 | 67204082 | 67205362 | - | 8 | 65510290 | 65511559 | + | L1MdF_III | Annotated deletion [Pezer 2015] | |
| 7 | 68592029 | 68592537 | - | 10 | 85842345 | 85842849 | + | L1MdGf_II | Complete. Short LINE. Probe is skewed proximal because CAST & WSB have a SNP distal. Annotated deletion [Quinlan 2010] [Henrichsen 2009] [Pezer 2015] [Keane 2010] | |
| X | 146688738 | 146689606 | - | 7 | 75188681 | 75189549 | + | L1MdTf_I | Annotated deletion [Pezer 2015] [Keane 2011] | |
| 7 | 77063618 | 77065060 | - | 13 | 100240713 | 100242142 | + | L1MdA_I | Complete. Annotated deletion [Henrichsen 2009] [Cahan 2009] [Cutler 2007][Pezer 2015] [Keane 2011] | |
| 7 | 92156712 | 92157260 | - | 17 | 73214643 | 73215194 | - | L1MdA_I | Complete. Annotated deletion [Keane 2011] | |
| 7 | 94181325 | 94182172 | - | 12 | 66213349 | 66214196 | - | L1MdA_II | Complete. Annotated deletion [Pezer 2015] [Keane 2011]. | |
| 7 | 113977669 | 113978328 | - | 8 | 99116521 | 99117186 | + | L1MdF_I | Unclear Line/dup boundary | |
| 13 | 116532544 | 116533025 | - | 7 | 118125216 | 118125697 | + | L1MdTf_II | Complete. Annotated Deletion [Quinlan 2010] [Henrichsen 2009] [Keane 2011]. Short LINE. Fernando absence probe. | |
| 8 | 76439302 | 76439599 | - | 7 | 119335297 | 119335594 | - | L1MdA_II | Complete. Short LINE. Annotated deletion [Henrichsen 2007] [Pezer 2015] [Keane 2011] | |
| 12 | 35888694 | 35888932 | + | 7 | 120594966 | 120595204 | - | L1MdA_I | Complete. 2nd of 2 duplications (1st dup [Event 2366]) Annotated deletion [Keane 2011] | |
| 7 | 125429114 | 125429489 | + | 12 | 66504408 | 66504775 | + | L1MdA_II | Complete. Annotated deletion [Cahan 2009] [Keane 2011]. | |
| 8 | 9637558 | 9637759 | - | 18 | 31354535 | 31354736 | - | L1MdTf_III | Complete. Annotated deletion [Keane 2011] [Wong 2012]. Inserted in Lx5 LINE-1 | |
| 12 | 53429557 | 53430020 | + | 8 | 20974314 | 20974777 | - | L1MdA_IV | Complete. Annotated deletion [Quinlan 2010] [Pezer 2015] [Keane 2011] C/T SNP in TSD | |
| X | 85952393 | 85952629 | + | 8 | 27507711 | 27507947 | - | L1MdTf_II | Complete Example. Annotated deletion [Pezer 2015] [Keane 2011] | |
| 8 | 28321010 | 28321441 | - | 17 | 61261973 | 61262405 | - | L1MdA_I | Complete. Long absence probe is needed distinguish from 9:20218208. Annotated deletion [Pezer 2015] | |
| 8 | 33719406 | 33719660 | + | 14 | 110520655 | 110520909 | - | L1MdGf_I | Complete. No TSD (has 2-base target site deletion) | |
| 10 | 52697705 | 52698407 | + | 8 | 38271327 | 38272031 | - | L1MdGf_II | Complete. C/a SNP in absence probe. Annotated deletion [Henrichsen 2009] [Pezer 2015] [Keane 2011] [Wong 2012] | |
| 8 | 42483964 | 42484464 | - | 18 | 37540553 | 37541053 | + | L1MdGf_II | Complete. Short LINE. Annotated deletion [Pezer 2015] [Keane 2011] | |
| 8 | 54838876 | 54839392 | - | 15 | 4114041 | 4114559 | - | L1MdGf_II | No annotated deletions | |
| 8 | 56392231 | 56392766 | + | 13 | 76635380 | 76635915 | - | L1MdGf_II | Complete. Annotated deletion [Keane 2011] [Wong 2012] | |
| 16 | 79411337 | 79411752 | - | 8 | 62562313 | 62562725 | - | L1MdA_II | Complete. Annotated deletion [Pezer 2015] [Keane 2011] | |
| 8 | 64241854 | 64242209 | - | 17 | 70111489 | 70111844 | - | L1MdGf_I | Complete. 2nd of 2 duplications (1st dup [Event 2393]). Annotated deletion [Pezer 2015] [Keane 2011] | |
| 8 | 67348197 | 67348716 | - | 13 | 61412681 | 61413198 | + | L1MdGf_II | Overlaps annotated deletion [Henrichsen 2009] [Pezer 2015] [Keane 2011] (inserted into repeat??) | |
| 19 | 35603452 | 35604136 | - | 8 | 71221148 | 71221832 | - | L1MdF_I | Annotated deletion [Henrichsen 2007] [Pezer 2015] | |
| 8 | 72783895 | 72784520 | - | 12 | 38890498 | 38891123 | + | L1MdF_I | No Poly-As, Annotated deletion [Keane 2011] | |
| 14 | 89215226 | 89215763 | - | 8 | 75332612 | 75333149 | - | L1MdTf_III | Complete. Annotated deletion [Keane 2011] [Wong 2012] | |
| 8 | 79808048 | 79808934 | - | 9 | 74036649 | 74037537 | - | L1MdGf_II | Complete. Annotated deletion [Keane 2011] | |
| 8 | 102437210 | 102437586 | - | 11 | 92916883 | 92917260 | - | L1MdGf_II | Complete. G/c SNP in absence probe. Annotated deletion [Keane 2011] | |
| 14 | 104118289 | 104118873 | - | 9 | 17197186 | 17197770 | - | L1MdA_I | First of multiple dups? | |
| 18 | 30644434 | 30645240 | - | 9 | 17298753 | 17299559 | + | L1MdTf_III | Complete. Annotated deletion [Pezer 2015]. Absence probe is a LINE-1. Needs a long absence probe. | |
| 16 | 63522193 | 63522902 | + | 9 | 23892991 | 23893696 | - | L1MdGf_II | Complete. Annotated deletion [Keane 2011] | |
| 9 | 30506418 | 30507164 | - | 13 | 34513796 | 34514542 | - | L1MdTf_II | Complete. Annotated deletion [Pezer 2015] [Keane 2011] | |
| X | 20247967 | 20249682 | - | 9 | 51612345 | 51614064 | - | L1MdTf_II | Complete. Annotated deletion [Pezer 2015] [Keane 2011] [Wong 2012] [Quinlan 2010] | |
| X | 77476318 | 77476534 | + | 9 | 79279692 | 79279908 | + | L1MdF_I | Short LINE. No annotation. | |
| 9 | 80773714 | 80774502 | + | 12 | 81523051 | 81523839 | + | L1MdTf_II | Complete. 2nd of 2 duplications (1st dup [Event 2414]). Inserted into repeated element. Annotated deletion [Pezer 2015] | |
| 9 | 91064995 | 91066364 | + | 13 | 21599004 | 21600331 | - | L1MdF_I | Annotated deletion [Pezer 2015] [Wong 2012]. Likely inserted into a LINE-1, based on CAST & SPRET which have one copy of ancestral seq | |
| X | 47530749 | 47531264 | + | 9 | 104067530 | 104068041 | - | L1MdF_V | Complete. Annotated gain [Kazmi 2013] [Cahan 2009] [Cutler 2007], SPRET has dup, not in caroli. | |
| 12 | 49568665 | 49568902 | + | 9 | 111970995 | 111971232 | + | L1MdGf_II | Complete. B6 has INDEL aaaatgtcatCTGT in both TSDs. Annotated deletion [Keane 2011] | |
| 17 | 17992302 | 17993141 | - | 10 | 64201297 | 64202103 | - | L1MdGf_II | Complete. Annotated deletion [Yalcin 2012] [Keane 2011]. | |
| 19 | 27128152 | 27128586 | + | 11 | 92700975 | 92701409 | + | L1MdGf_I | Complete. Annotated deletion [Henrichsen 2007] [Pezer 2015] [Keane 2011] [Wong 2012] | |
| 14 | 117526005 | 117526947 | + | 11 | 16380693 | 16381628 | - | L1MdF_I | difficult to distinguish distal poly-A"s | |
| 18 | 18731236 | 18731982 | - | 11 | 27298619 | 27299365 | + | L1MdF_II | Complete. C/t SNP in absence probe. Annotated deletion [Henrichsen 2007] [Keane 2011] | |
| 18 | 71552604 | 71552937 | + | 11 | 27308127 | 27308459 | - | L1MdGf_II | Has two duplications. Second is at 16: - 45409600 (is TSD a coincidence?) | |
| 15 | 90473566 | 90473942 | + | 11 | 28233691 | 28234067 | - | L1MdTf_III | Complete. Annotated deletion [Henrichsen 2007] [Keane 2011]. Derived region appears to have been deleted in AJ postinsertion. | |
| 16 | 49034792 | 49035332 | - | 11 | 30476286 | 30476824 | - | L1MdF_V | Complete. No annotated deletion. | |
| 11 | 30976626 | 30976814 | + | 12 | 41542149 | 41542337 | - | L1MdGf_II | Complete. Tiny all A TSD. T/a SNP in absence probe. Annotated deletion [Keane 2011] | |
| 11 | 40454983 | 40455929 | + | 12 | 27896155 | 27897101 | - | L1MdGf_I | Complete. Annotated deletion [Pezer 2015] [Keane 2011] [Wong 2012] [Quinlan 2010] | |
| 16 | 51140162 | 51140485 | + | 11 | 42671046 | 42671369 | - | L1MdTf_III | Complete. Short LINE. Annotated deletion [Henrichsen 2007] [Quinlan 2010] [Keane 2011] | |
| 16 | 64295456 | 64295884 | + | 11 | 70796013 | 70796441 | - | L1MdA_I | Complete. Annotated deletion [Quinlan 2010] [Pezer 2015] [Keane 2011] [Wong 2012] | |
| 11 | 85756987 | 85757310 | - | 18 | 58916308 | 58916631 | - | L1MdTf_II | Complete. Annotated deletion [Keane 2011] | |
| 13 | 39872861 | 39873136 | + | 11 | 91043882 | 91044157 | - | L1MdA_I | Complete. Short LINE. Annotated deletion [Keane 2011] | |
| 14 | 124591052 | 124592068 | + | 12 | 6241505 | 6242522 | + | L1MdTf_III | Complete. Annotated deletion [Keane 2011] | |
| 12 | 27821439 | 27821702 | - | 14 | 9377955 | 9378218 | + | L1MdGf_II | Complete. A/g SNP in absence probe. Annotated deletion [Quinlan 2010] [Keane 2011] | |
| 12 | 34469099 | 34469967 | - | 14 | 53943056 | 53943962 | + | L1MdGf_II | Complete. Annotated deletion [Pezer 2015] [Quinlan 2010] [Keane 2011] G/C variant in proximal TSD. | |
| 18 | 45243644 | 45244136 | - | 12 | 44673883 | 44674375 | - | L1MdTf_II | Complete. Annotated deletion [Keane 2011]. Has small second duplication | |
| 12 | 59286161 | 59286508 | - | 15 | 59938216 | 59938558 | - | L1MdF_I | No annotated deletion. | |
| 14 | 61732185 | 61732445 | - | 12 | 61756445 | 61756705 | - | L1MdGf_I | Complete. Annotated deletion [Pezer 2015] [Keane 2011] | |
| 13 | 96540612 | 96540918 | - | 12 | 63320261 | 63320567 | - | L1MdTf_II | Line-dup inserted in a tandem duplication on 12 | |
| 12 | 63825045 | 63825727 | - | 14 | 124422129 | 124422809 | + | L1MdA_II | Complete. Annotated deletion [Pezer 2015] [Keane 2011] | |
| 18 | 84995256 | 84996095 | - | 12 | 92358080 | 92358919 | - | L1MdA_III | Complete. [2nd dup location not clear 7: - 47299255 OR 7: - 47860679] Annotated deletion [Henrichsen 2007] [Quinlan 2010] [Keane 2011] [Wong 2012] | |
| 18 | 30687093 | 30688141 | + | 12 | 92761122 | 92762171 | + | L1MdTf_I | extend LINE. | |
| 15 | 48213964 | 48214224 | + | 12 | 119122177 | 119122437 | - | L1MdF_I | Complete. A/g and G/a SNPs in absence probe. Annotated deletion [Pezer 2015] | |
| 13 | 6107629 | 6108535 | - | 18 | 89038031 | 89038936 | - | L1MdA_II | Complete. T/c SNP in TSD. Annotated deletion [Keane 2011] [Wong 2012] | |
| 13 | 17419318 | 17420364 | + | 17 | 62385211 | 62386257 | - | L1MdTf_II | Complete. Annotated deletion [Pezer 2015] [Keane 2011]. TSD:"AAAGTAAGGCTTC" to-do absence probe. | |
| 13 | 17496301 | 17496849 | + | 15 | 67306173 | 67306720 | - | L1MdA_I | Complete. Annotated deletion [Pezer 2015] [Keane 2011] | |
| 14 | 105592372 | 105593121 | + | 13 | 26359278 | 26360027 | - | L1MdTf_II | middle of ancestral seq. is not duplicated | |
| 16 | 40867682 | 40868286 | - | 13 | 53973620 | 53974226 | + | L1MdGf_I | Complete. Very short LINE. Annotated deletion [Pezer 2015] [Keane 2011] | |
| 13 | 56497462 | 56498829 | - | 17 | 79216873 | 79218226 | - | L1MdA_I | Complete. Short LINE. Annotated deletion [Henrichsen 2009] [Pezer 2015] [Wong 2012] [Keane 2011] | |
| 13 | 68511942 | 68513006 | + | 16 | 59904999 | 59906064 | + | L1MdGf_II | No distal Poly-A"s | |
| 15 | 57178248 | 57179168 | - | 13 | 79181309 | 79182230 | + | L1MdGf_I | TSD Not Identified. | |
| X | 122807374 | 122807619 | - | 13 | 82369576 | 82369821 | + | L1MdA_III | Complete. Short LINE. Annotated deletion [Keane 2011] | |
| 18 | 51515070 | 51516420 | + | 14 | 35796836 | 35798285 | - | L1MdTf_I | Complete.Short LINE. Annotated deletion [Keane 2011] | |
| X | 157304071 | 157304364 | + | 14 | 41511692 | 41511985 | + | L1MdA_I | Annotated deletion [Pezer 2015] [Quinlan 2010] Duplication inserted into repeat? | |
| 17 | 52815936 | 52816351 | - | 14 | 71391432 | 71391847 | - | L1MdTf_I | Complete. Annotated deletion [Henrichsen 2007] [Wong 2012] [Keane 2011] | |
| 14 | 88308890 | 88309241 | - | 16 | 49260266 | 49260617 | + | L1MdTf_I | Complete. Annotated deletion [Pezer 2015] [Keane 2011] | |
| 19 | 31567869 | 31569006 | + | 15 | 50489776 | 50490937 | + | L1MdA_II | Complete. LINE inserted into LTR/ERVL-MaLR. Annotated deletion [Pezer 2015] [Keane 2011] | |
| 18 | 11460787 | 11461508 | + | 14 | 106858211 | 106858932 | + | L1MdTf_II | distal A"s | |
| 14 | 114956744 | 114957096 | - | 15 | 30087366 | 30087718 | - | L1MdGf_I | Complete. Annotated deletion [Quinlan 2010] [Pezer 2015] [Keane 2011] | |
| 3 | 29863213 | 29863232 | - | 15 | 19274747 | 19274766 | + | L1MdTf_II | Complete. 2nd of 2 duplications (1st dup [Event 2484]) Annotated deletion [Keane 2011]. Note: SWAPPED 484 and 2484 | |
| 19 | 35057013 | 35057231 | - | 15 | 21268256 | 21268474 | + | L1MdTf_II | Complete. Annotated deletion [Keane 2011] | |
| 18 | 14838306 | 14838970 | - | 15 | 21335434 | 21336098 | - | L1MdTf_II | Complete. Annotated deletion [Pezer 2015] [Keane 2011] | |
| 18 | 83886016 | 83886212 | + | 15 | 32389423 | 32389619 | - | L1MdTf_II | Complete. Overlaps annotated duplication [Kazmi 2013]. Annotated deletion [Pezer 2015] [Wong 2012] [Keane 2011]. to-do absence probe. | |
| 15 | 46072709 | 46073184 | + | 18 | 83414221 | 83414694 | + | L1MdGf_I | LINE is inserted into a LINE (L1MdF_V). No proximal Poly-A"s. No absence probe. Annotated deletion in 129P2OlaHsd [Keane 2011]. | |
| X | 66521421 | 66522267 | - | 16 | 20914891 | 20915737 | - | L1MdTf_II | Complete. Annotated deletion [Pezer 2015] [Keane 2011] | |
| 16 | 29020628 | 29020854 | + | 18 | 71637602 | 71637828 | + | L1MdTf_II | Complete. LINE may have ERV/LTR insertion. Annotated deletion [Pezer 2015] [Keane 2011] | |
| X | 84551484 | 84551814 | + | 16 | 34315904 | 34316234 | + | L1MdA_II | Complete. Very short LINE. Annotated deletion [Quinlan 2010] [Keane 2011] | |
| X | 87746841 | 87747219 | + | 16 | 69899615 | 69899993 | + | L1MdTf_II | Complete. Annotated deletion [Pezer 2015] [Keane 2011] [Wong 2012] [Quinlan 2010] | |
| 19 | 17401740 | 17402778 | + | 17 | 42138422 | 42139466 | + | L1MdGf_II | SNP in distal TSD. Annotated deletion [Keane 2011] | |
| 19 | 18340347 | 18340693 | + | 17 | 59052353 | 59052699 | + | L1MdA_II | Complete. Annotated deletion [Pezer 2015] [Keane 2011] | |
| 17 | 64814050 | 64814326 | + | 18 | 60235812 | 60236088 | - | L1MdTf_III | Complete. Annotated deletion [Henrichsen 2009] [Keane 2011] | |
| 18 | 48768368 | 48768715 | - | 17 | 70156925 | 70157265 | + | L1MdTf_II | Complete. 2nd of 2 duplications (1st dup [Event 2502]). LINE is inserted within a repeated element. Annotated deletion [Pezer 2015] [Keane 2011] | |
| X | 132239344 | 132239744 | - | 17 | 93553671 | 93554071 | + | L1MdGf_I | Complete. Annotated deletion [Keane 2011], No TSD | |
| 1 | 30442000 | 30442800 | - | 1 | 33272168 | 33272974 | - | L1MdGf_I | Complete. Annotated deletion [Pezer 2015][Henrichsen 2009][Keane 2011] | |
| 1 | 30185842 | 30186531 | - | 1 | 61361485 | 61362213 | - | L1MdA_II | Complete. Annotated deletion [Keane 2011] | |
| 1 | 104056061 | 104056434 | - | 1 | 174422347 | 174422722 | + | L1MdGf_I | 2nd duplication. Annotated deletion [Wong 2010] [Yasuda 2012] [Henrichsen 2009] [Pezer 2015] [Keane 2011] [Quinlan 2010] | |
| 2 | 81159602 | 81159879 | + | 2 | 179816278 | 179816555 | + | L1MdA_I | Annotated deletion [Henrichsen 2009] [Quinlan 2010] [Wong 2012] [Keane 2011]. TSD:AAAAACCAAGCAGC | |
| 3 | 26538309 | 26538801 | + | 3 | 112185441 | 112185933 | - | L1MdTf_III | Complete. Annotated deletion [Pezer 2015] [Keane 2011]. | |
| 3 | 72927573 | 72928361 | + | 3 | 49650834 | 49651624 | - | L1MdA_II | Annotated deletion [Quinlan 2010] [Wong 2012] [Pezer 2015] [Keane 2011] | |
| 3 | 111637228 | 111637724 | - | 3 | 106929126 | 106929618 | + | L1MdA_III | Annotated deletion [Pezer 2015] [Keane 2011] | |
| 3 | 26538309 | 26538796 | + | 3 | 112185446 | 112185933 | - | L1MdTf_III | Annotated deletion [Pezer 2015] [Keane 2011] | |
| 5 | 7100456 | 7100786 | - | 5 | 8704403 | 8704733 | - | L1MdTf_I | Complete. Annotated deletion [Pezer 2015] [Keane 2011] | |
| 5 | 34080018 | 34081076 | - | 5 | 98012202 | 98013255 | + | L1MdTf_II | Is the sequence without the duplication duplicated in 129S1? LINE appears to also have an ERV insertion. Annotated deletion [Keane 2011] | |
| 5 | 23058869 | 23059397 | + | 5 | 47249380 | 47249904 | - | L1MdA_I | Annotated deletion [Wong 2012] [Pezer 2015] [Keane 2011]. TSD only As? | |
| 6 | 71331705 | 71332132 | - | 6 | 3814320 | 3814747 | - | L1MdTf_I | Complete. Annotated deletion [Keane 2011] | |
| 8 | 36912609 | 36912996 | - | 8 | 41506948 | 41507335 | - | L1MdTf_III | Complete. Inserted into LINE (L1MdF_IV) Annotated deletion [Henrichsen 2007] [Pezer 2015] | |
| 8 | 80594509 | 80595194 | + | 8 | 43582550 | 43583236 | + | L1MdTf_III | Complete. Annotated deletion [Pezer 2015] [Keane 2011]. Looks like there is a post-insertion duplication 8:80594509-80595193. | |
| 13 | 76151071 | 76151882 | - | 13 | 113458159 | 113458971 | + | L1MdA_III | Complete. Annotated deletion [Pezer 2015] [Keane 2011] [Wong 2012]. | |
| 13 | 116112925 | 116113349 | + | 13 | 84202039 | 84202462 | + | L1MdA_I | Complete. Annotated deletion [Keane 2011] | |
| 14 | 55433357 | 55433711 | - | 14 | 53929177 | 53929531 | - | L1MdTf_III | Complete. Annotated deletion [Pezer 2015] [Quinlan 2010] [Keane 2011] [Wong 2012] | |
| 16 | 56672857 | 56673186 | - | 16 | 54842945 | 54843274 | + | L1MdA_III | Complete. Annotated deletion [Keane 2011]. Absence probe has SNP in CAST | |
| 17 | 66030998 | 66031317 | + | 17 | 9811670 | 9811990 | + | L1MdA_I | Complete. Annotated deletion [Keane 2011] | |
| 5 | 23014970 | 23015059 | - | 18 | 37583282 | 37583371 | + | L1MdGf_II/L1MdA_III | Complete. 2nd of 2 duplications (1st dup [Event 2708]). Two T/c SNPs in Absence Probe. Annotated deletion [Pezer 2015] [Keane 2011] | |
| X | 163183435 | 163184190 | - | X | 46108444 | 46109199 | + | L1MdF_II | Complete. Inserted into LINE-1. No duplication in SPRET. | |
| 14 | 51418897 | 51419384 | + | 14 | 74629664 | 74630151 | - | L1MdGf_II | ||
| 8 | 7173106 | 7173219 | + | 9 | 4765346 | 4765459 | - | L1MdTf_II | Complete. Annotated deletion [Pezer 2015] [Keane 2011] SDP=11011000 | |
| 11 | 80743926 | 80744071 | - | 2 | 43665431 | 43665576 | - | L1MdGf_II | Complete. Annotated deletion [Keane 2011] | |
| X | 45125946 | 45126122 | + | 12 | 40524444 | 40524620 | + | L1MdGf_I | Complete. Annotated deletion [Keane 2011] [Wong 2012] | |
| 13 | 84118040 | 84118385 | + | X | 50004703 | 50005030 | + | L1MdTf_II | Complete. 2nd of 2 duplications (1st dup [2003]). Inserted in LTR/ERVK. Not in WSB | |
| 2 | 9219282 | 9219407 | + | X | 56903108 | 56903234 | - | L1MdTf_I | Complete. Annotated deletion [Keane 2011] [Wong 2012] | |
| X | 71840292 | 71840443 | - | 16 | 16093806 | 16093957 | + | L1MdA_II | Complete. Annotated deletion [Keane 2011] [Wong 2012] | |
| 10 | 36635052 | 36635738 | - | 3 | 40038612 | 40039296 | + | L1MdA_III | Annotated deletion [Pezer 2015] [Keane 2011] | |
| 12 | 8112342 | 8112554 | + | 9 | 88666079 | 88666291 | - | L1MdA_I | Inserted into a LINE-1 | |
| 8 | 67348197 | 67348715 | - | 13 | 61412682 | 61413198 | + | L1MdGf_II | Complete. Annotated deletion [Keane 2011]. Inserted in LINE-1 | |
| 8 | 75843525 | 75843707 | - | 4 | 19776719 | 19776901 | + | L1MdTf_I | Complete. Annotated deletion [Quinlan 2010] [Keane 2011] [Wong 2012] | |
| 2 | 41092948 | 41093086 | + | 4 | 66290100 | 66290238 | - | L1MdA_I | Complete. 2nd of 2 duplications (1st dup [Event 2010]) Annotated deletion [Keane2011] | |
| 5 | 38846569 | 38846678 | + | 7 | 123899612 | 123899721 | - | L1MdTf_II | Complete. Annotated deletion [Henrichsen 2007] [Wong 2012] [Keane 2011] | |
| 4 | 73963529 | 73963622 | - | X | 66458357 | 66458450 | + | L1MdTf_I | Complete. Annotated deletion [Keane 2011] | |
| 3 | 117998669 | 117998761 | - | 19 | 48983422 | 48983514 | + | L1MdGf_II | Complete. T/c SNP in absence probe. Annotated deletion [Keane 2011] | |
| 14 | 97698531 | 97698971 | - | 1 | 183258698 | 183259144 | - | L1MdA_II | TSD appears 3 times (183258467-183258482) | |
| 18 | 9298970 | 9299073 | - | 10 | 3101146 | 3101249 | + | L1MdF_I | Beginning of LINE sequence unknown (Ns) | |
| 18 | 43709180 | 43709300 | - | 6 | 33485813 | 33485934 | - | L1MdGf_I | Complete. Annotated deletion [Keane 2011] [Wong 2012] | |
| 3 | 124767596 | 124767744 | + | 2 | 133272704 | 133272852 | + | L1MdA_III | Complete. Annotated deletion [Keane 2011] | |
| 10 | 90813188 | 90813280 | - | 5 | 29174008 | 29174103 | + | L1MdA_II | Complete. Annotated deletion [Keane 2011] | |
| 6 | 12169946 | 12170037 | + | 13 | 16598367 | 16598458 | - | L1MdA_I | Complete. Annotated deletion [Keane 2011] [Wong 2012] | |
| 15 | 41027938 | 41028083 | + | 3 | 104194080 | 104194225 | - | L1MdA_II | Complete. Annotated deletion [Keane 2011] | |
| 6 | 94633478 | 94633562 | - | 6 | 17078989 | 17079073 | + | L1MdA_I | Complete. TSD is HUGE, but consistent with absence probe (single copy). | |
| 4 | 11984597 | 11984715 | + | 3 | 81524881 | 81525000 | + | L1MdA_I | Complete. Annotated deletion [Henrichsen 2007] [Quinlan 2010] [Keane 2011] [Wong 2012] | |
| 8 | 56006570 | 56006687 | + | 16 | 60934645 | 60934762 | + | L1MdA_I | Complete. Annotated deletion [Pezer 2015] [Keane 2011]. Very short LINE-1 | |
| 2 | 22283855 | 22283952 | + | 8 | 28434227 | 28434324 | - | L1MdTf_III | Complete. Annotated deletion [Keane 2011] | |
| 7 | 109103205 | 109103362 | - | 7 | 97272938 | 97273099 | - | L1MdN_I | Complete | |
| 5 | 46212153 | 46212386 | - | 1 | 8235048 | 8235281 | - | L1MdA_V | Complete. 2nd of 3 duplications (3rd dup [Event 2], 1st dup [Event 3002]) | |
| 3 | 115878890 | 115878962 | - | X | 50004607 | 50004679 | + | L1MdTf_II | Complete. 1st of 2 duplications (2nd dup [Event 1003]) | |
| 1 | 143264851 | 143264875 | - | 4 | 66290251 | 66290275 | - | L1MdA_I | Complete. 1st of 2 duplications (2nd dup [Event 1010]) Small duplication with low mapping confidence. | |
| 6 | 26194768 | 26194792 | + | 3 | 44559520 | 44559544 | - | L1MdA_II | Complete. 1st of 2 duplications (2nd dup [Event 11]) | |
| 1 | 58128514 | 58128912 | - | 11 | 40796061 | 40796459 | - | L1MdGf_I | Complete. 1st of 2 duplications (2nd dup [Event 25]) | |
| 10 | 107119172 | 107119225 | + | 10 | 65166219 | 65166272 | - | L1MdTf_II | Complete. 1st of 2 duplications (2nd dup [Event 36]) | |
| 2 | 16335015 | 16335047 | + | 15 | 56254788 | 56254820 | - | L1MdGf_II | Complete. 1st of 2 duplications (2nd dup [Event 50]) | |
| X | 100157332 | 100157522 | - | 2 | 12130539 | 12130729 | + | L1MdA_I | Complete. 1st of 2 duplications (1st dup [Event 84]). No TSD. | |
| 1 | 125253324 | 125253740 | + | 12 | 81388547 | 81388975 | - | L1MdF_II | Complete. 1st of 2 duplicates. (2nd dup [Event 99]) | |
| 11 | 12240751 | 12240884 | + | 4 | 26657137 | 26657270 | - | L1MdA_I | Complete. 1st of 2 duplications (2nd dup [Event 107]) | |
| 14 | 73703434 | 73703598 | + | 2 | 78511079 | 78511243 | + | L1MdTf_II | Complete. 2nd of 3 duplications. ([Event 113] 3rd dup. [Event 3113] 1st dup.) | |
| 7 | 103225677 | 103226113 | + | 2 | 101126961 | 101127395 | - | L1MdTf_II | Complete. 1st of 2 duplications (2nd duplicate [Event 129]) | |
| 11 | 11357024 | 11357050 | + | 8 | 24757937 | 24757963 | + | L1MdGf_II | Complete. 1st of 2 duplications (2nd dup [Event 134]) | |
| 13 | 35166368 | 35166402 | + | 2 | 117893409 | 117893443 | - | L1MdTf_III | Complete. 1st of 2 duplications (2nd dup [Event 135]) | |
| 14 | 84046911 | 84047015 | + | 13 | 14748006 | 14748112 | + | L1MdGf_II | Complete. 1st of 2 duplications (2nd dup [Event 141]) | |
| 5 | 85639849 | 85640163 | - | 3 | 22422058 | 22422372 | + | L1MdGf_II | Complete. 2nd of 3 duplications (3rd dup [Event 159] 1st dup [Event 2159]) SDP=11111001 | |
| 2 | 97815476 | 97815513 | - | 5 | 56404238 | 56404275 | + | L1MdTf_I | [Event 166] 2nd duplicate | |
| 2 | 57544955 | 57545740 | - | 10 | 51222262 | 51223047 | - | L1MdA_I | Complete. 1st of 2 duplications (2nd dup [Event 204]) | |
| 5 | 16559032 | 16559257 | - | 4 | 64949849 | 64950074 | + | L1MdF_II | Complete 1st of 2 duplications. (2nd dup [Event 228]) | |
| 7 | 71750511 | 71750611 | - | 8 | 101864871 | 101864971 | + | L1MdTf_I | Complete.1st of 2 duplications. (2nd dup [Event 247]) | |
| X | 129336698 | 129336767 | + | 6 | 69163956 | 69164025 | + | L1MdGf_II | Complete. 1st of 2 duplications (1st dup [Event 309]) | |
| 7 | 106640469 | 106640517 | + | 6 | 134327945 | 134327993 | + | L1MdTf_III | Complete. 1st of 2 duplications (1st dup [Event 326]) | |
| 10 | 26989316 | 26989787 | - | 7 | 53080294 | 53080764 | - | L1MdGf_II | Weird. 1st of 2 duplications (1st dup [Event 342]) | |
| 2 | 8701359 | 8701428 | - | 7 | 120595207 | 120595276 | - | L1MdA_I | Complete. 1st of 2 duplications (2nd dup [Event 366]) | |
| 16 | 82493903 | 82493985 | - | 17 | 70111845 | 70111927 | - | L1MdGf_I | Complete. 1st of 2 duplications (2nd dup [Event 393]) | |
| 6 | 110058818 | 110058861 | + | 12 | 81522999 | 81523042 | + | L1MdTf_II | Complete. 1st of 2 duplications (2nd dup [Event 414]) | |
| X | 18879037 | 18879246 | + | 15 | 19274519 | 19274728 | + | L1MdTf_II | Complete. 1st of 2 duplications (2nd dup [Event 484]). Annotated deletion [Keane 2011]. Note: SWAPPED 484 and 2484 | |
| 1 | 155457433 | 155457469 | - | 17 | 70156868 | 70156904 | + | L1MdTf_II | Complete. 1st of 2 duplications. (2nd dup [Event 502]) | |
| 18 | 74226833 | 74227925 | - | 18 | 37582174 | 37583268 | + | L1MdGf_II/L1MdA_III | Complete. 1st of 2 duplications. (2nd dup [Event 708]) Two T/c SNPs in Absence Probe. Annotated deletion [Pezer 2015] [Keane 2011] | |
| 18 | 6104954 | 6105458 | + | 1 | 8235287 | 8235781 | - | L1MdA_V | Complete. 1st of 3 duplications (2nd dup [Event 2002], 3rd dup [Event 2]) | |
| 9 | 17955997 | 17956019 | - | 2 | 78511027 | 78511049 | + | L1MdTf_I | Complete. 1st of 3 duplications. (2nd dup [Event 2113] 3rd dup [Event 113]) | |
| 18 | 28889657 | 28889681 | + | 3 | 22422026 | 22422050 | + | L1MdGf_II | Complete. 1st of 3 duplications (2nd dup [Event 2159] 3rd dup [Event 159]) SDP=11111001 | |
| 10 | 26984288 | 26984516 | - | 7 | 53079937 | 53080165 | - | L1MdGf_II | [Event 342] 3rd duplicate, 2nd dup [Event 2342] | |
| 9 | 35347355 | 35347463 | + | 3 | 91708515 | 91708623 | + | L1MdTf_III | 2nd of 2 duplications. (1st dup [Event 5020]) Annotated deletion (Pezer 2015) (Henrichsen 2009). | |
| 1 | 50677083 | 50677308 | - | 3 | 91708264 | 91708489 | + | L1MdTf_III | 1st of 2 duplications (2nd dup [Event4020]) Same duplication as Event20. Annotated deletion (Pezer 2015) (Henrichsen 2009). | |
| 16 | 45409146 | 45409685 | - | 11 | 27307590 | 27308111 | - | L1MdGf_II | Experiment | |
| 9 | 26400171 | 26400492 | - | 9 | 91625401 | 91625722 | + | L1MdTf_I | DNA transduction. Annotated deletion [Pezer 2015] [ Keane 2011]. TSD of ancestral L1: "AAAGAGTAACTGA" at (-)9:26400479 and (-)9:26408415 | |
| 12 | 59326207 | 59327104 | - | 1 | 41078363 | 41079265 | + | L1MdTf_III | TSD is typical of an L-1 insertion near a 2X duplication. No poly-A"s surrounding either end of dup. Derived 2X is not in PWK or SPRET. Could be 2 events. | |
| 13 | 16195643 | 16195924 | - | 1 | 29758132 | 29758412 | - | L1MdGf_II | Interesting case. Looks like L1 is inserted into the middle of a 2X duplication that appears before and after. TSDs are hard to reconcile. | |
| 1 | 107500928 | 107501513 | + | 6 | 73743754 | 73744340 | + | MT2_Mm | no proximal As LTR/ERV | |
| 1 | 156006235 | 156006803 | + | 6 | 122193663 | 122194231 | - | MERVL | No poly-As.Near a duplication on same chromosome (-122024310) | |
| 1 | 168875814 | 168876350 | - | 15 | 13846465 | 13847002 | - | L1MdA_III | Remove (Same as event 67) Annotated deletion [Keane 2011] | |
| 4 | 28116056 | 28116204 | - | 2 | 83436789 | 83436937 | + | to do | Remove | |
| 6 | 103544046 | 103544582 | + | 4 | 64950083 | 64950619 | + | L1MdA_III | DELETE this one (same as 228) | |
| 14 | 19325429 | 19327506 | + | 5 | 77849599 | 77851689 | + | L1MdTf_III | to proximal or distal poly-A, extended prox. end | |
| 8 | 31671091 | 31671468 | - | 5 | 85326730 | 85327106 | - | L1MdTf_III | DELETE this one (same as 279) | |
| 9 | 37290411 | 37290907 | - | 6 | 102704342 | 102704836 | - | L1MdF_II | Remove | |
| 6 | 48660502 | 48660737 | - | 6 | 104848536 | 104848772 | - | L1MdA_III | Remove. Not an event, LINE inserted into dup (GAAAAAAGTT) |
447 duplications
