TandemDups

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methods

These are measurements of identical paired sequences with a separation between the pairs of at least one nucleotide. The smallest size sequence in this survey is 30 bases, the largest separation considered was 20,000 bases.

The procedure to find these sequences is as follows:

  • generate 29 base kmers for the entire genome, allow only
 kmers with bases: A C T G, no N's allowed.
  • pair up identical kmers with at least one base separation
 and up to 20,000 bases separation.  This separation sequence
 is referred to here as the gap in this document.
  • collapse overlapping kmer pairs when they are the same size
 of sequence and the same spacing between the pairs.  This procedure
 preserves the definition of duplicated identical pairs.
  • the resulting pairs can now be longer sequences with smaller
 separation then the constituent pairs
  • final result selects sizes of 30 bases or more for the size
 of the paired sequence, and at least one base remaining as
 a separation gap.
  • collapsed pairs that close the gap are discarded. They appear to
 indicate simple repeat sequences when this happens.  It would
 be interesting to have this result available, but that is not
 available at this time.

The reason for starting with 29 base sized pairs and then selecting results of at least 30 base sized pairs results in a reasonable number of 30 base pairs. If the procedure starts with 30 base sized pairs, it produces way too many 30 base kmer pairs for a reasonable count.

The measurements are taken from the resulting db.tandemDups.bed[.gz] file in /hive/data/genomes/<db>/bed/tandemDups/db.tandemDups.bed[.gz] The score column in the bed file (column 5) is the size of the duplicated sequence. The gap size between the duplicated sequence is thus calculated from: end - start + 2 * score

This data is also available in the tandemDups table for sequences with genome browser databases. Not all sequences measured here have genome browser databases.

The item total is the sum of the sizes of the duplicated sequences. Not both sides though, just one side. This indicates how much sequence is duplicated. Multiply this by 2 to see total amount of sequence involved in these repeats for both sides.

The gap total is the sum of the sizes of all the separation gaps between the paired sequences.

table features

The table columns can be sorted, click on the up/down arrow icon in the column header. The 'year' is what we have in the dbDb table as indicated from the assembly information files for the date of the assembly. A few do not have dates (set to 1880), and do not have database genome browsers The example item is a worst case example, where the ratio of dup sequence size to gap size is the highest, i.e. smallest gap with largest dup size

tandemDups table statistics

count year dbName ncbiAsmId assembly method item

count

item

median

item

total

  gap

median

gap

total

example item

dup size, gap size, link

scatter plot

dup size vs. gap size

019 2014 acaChl1 GCF_000695815.1 SOAPdenovo v. 1.6 69222 38 3687159   479 270396956 448, 1, KK830956:17007-17903 plot acaChl1
020 2012 aciBauTYTH_1 GCF_000302575.1 tbd 175 43 11650   1165 777735 35, 1, chr_CP003856:2714351-2714421 plot aciBauTYTH_1
021 2006 afrOth13 tbd tbd 63170 39 3109998   1833 319093167 126, 1, 3-3:1498405-1498657 plot afrOth13
022 2009 ailMel1 GCF_000004335.2 tbd 252804 36 12081062   7914 2120476903 1357, 2, GL194066.1:206322-209037 plot ailMel1
023 2012 allMis1 GCF_000281125.1 Allpaths v. R41313; manual scaffolding 77832 39 8850601   2629 379690780 2771, 1, JH736852:249449-254991 plot allMis1
024 2013 allSin1 GCF_000455745.1 SOAPdenovo v. 1.05 116160 39 11500145   3510 624671088 5451, 1, KE696051:101233-112135 plot allSin1
025 2013 amaVit1 GCA_000332375.1 Ray software v. 3 37254 46 10717950   256 63766115 5218, 14, KB272082:90533-100982 plot amaVit1
026 2013 anaPla1 GCF_000355885.1 SOAPdenovo Release v. 1.03 27792 43 2580234   401 91882502 1258, 1, KB745735:2510-5026 plot anaPla1
027 2014 ancCey1 GCA_000688135.1 Velvet v. 1.2.05; BGI GapCloser v. 1.12 (release_2011); HaploMerger v. 20111230; ERANGE v. 3.2 55040 40 3358224   389.5 157542766 4183, 1, JARK01001394v1:846761-855127 plot ancCey1
028 2014 angJap1 GCA_000470695.1 CLC NGS Cell v. 3.2; CLC NGS Cell v. 4.0beta 546983 44 32365612   800 580570188 1181, 1, KI307522:56201-58563 plot angJap1
029 2007 anoCar1 tbd tbd 751544 38 40990303   2923 4158391303 351, 1, scaffold_31:2142294-2142996 plot anoCar1
030 2010 anoCar2 GCF_000090745.1 Arachne v. 3.0.0 674365 37 36071400   3201 3874056176 392, 1, chr4:7395659-7396443 plot anoCar2
031 2003 anoGam1 tbd tbd 75957 43 5353295   2383 356254048 1175, 1, chrX:14717656-14720006 plot anoGam1
032 2013 apaSpi1 GCA_000385615.1 SOAPdenovo v. 1.0.5 78831 41 3668114   120 236011041 453, 2, KB928133:814324-815231 plot apaSpi1
033 2014 apaVit1 GCF_000703405.1 SOAPdenovo v. 1.6 24291 35 1216678   112 56084043 453, 1, KL385068:59340-60246 plot apaVit1
034 2004 apiMel1 tbd tbd 83149 38 3897116   280 81345069 203, 1, GroupUn.6971:896-1302 plot apiMel1
035 2005 apiMel2 tbd tbd 91284 38 4467103   295 110415978 234, 1, Group8:8120781-8121249 plot apiMel2
036 2005 apiMel3 tbd tbd 100380 38 5142600   318 146199642 234, 1, Group8:9788059-9788527 plot apiMel3
037 2010 apiMel4 GCF_000002195.4 Atlas assembly system v. before 2011 101842 38 5017659   328 182902657 234, 1, Group8:11123745-11124213 plot apiMel4
038 2008 aplCal1 tbd tbd 362965 33 14931570   1162 1691576982 254, 1, scaffold_486:233208-233716 plot aplCal1
039 2014 aptFor1 GCF_000699145.1 SOAPdenovo v. 1.6 107781 59 13547646   120 162744750 2370, 1, KL225745:613720-618460 plot aptFor1
040 2015 aptMan1 GCF_001039765.1 tbd 282012 72 84603242   159 396269019 13772, 1, NW_013987314v1:1452350-1479894 plot aptMan1
041 2014 aquChr1 GCA_000696035.1 ABySS v. 1.3.6 91231 42 4160856   43 70439237 98, 1, KK848043:4630547-4630743 plot aquChr1
042 2014 aquChr2 GCA_000766835.1 AllPaths-LG v. August 2013 27433 39 1833575   548 117223799 6351, 4, KN265844v1:264833-277538 plot aquChr2
043 2013 araMac1 GCA_000400695.1 CLC Genomics Workbench v. 4.9 20437 44 1789638   1788 35728109 241, 2, KE047968:4314-4797 plot araMac1
044 1880 araTha1 GCF_000001735.3 tbd 42547 40 2336394   4141 237921318 415, 1, chr3:12226092-12226922 plot araTha1
045 2012 ascSuu1 GCA_000298755.1 SOAPdenovo v. 1.04 26863 62 2864530   136 30068625 680, 1, JH878990v1:516922-518282 plot ascSuu1
046 2013 astMex1 GCF_000372685.1 AllPathsLG v. Jan-2013 300773 36 13069886   344 878056894 647, 1, KB872443:19678-20972 plot astMex1
047 2013 balAcu1 GCF_000493695.1 SOAPdenovo v. 16-Mar-2012 317691 37 19886322   7511 2584004816 5160, 1, KI537228:6365-16685 plot balAcu1
048 2014 balPav1 GCA_000709895.1 SOAPdenovo v. 1.6 17941 37 1027192   127 51713556 375, 1, KL478702:45795-46545 plot balPav1
049 2006 borEut13 tbd tbd 95035 35 3952633   847 394283618 125, 1, chr4:75059497-75059747 plot borEut13
050 2004 bosTau1 tbd tbd 288698 36 12358995   3236 1418202012 332, 1, SCAFFOLD225782:8549-9213 plot bosTau1
051 2009 bosTau6 GCF_000003055.5 UMD Overlapper v. 2009; additional processing 1243148 37 57730762   8928 11394478150 923, 1, chr22:31476636-31478482 plot bosTau6
052 2014 bosTau8 GCF_000003055.5 UMD Overlapper v. 2009; additional processing 1243008 37 57724227   8930 11394290218 923, 1, chr22:31476636-31478482 plot bosTau8
053 2009 bosTauMd3 tbd tbd 1211279 37 56451996   9197 11353955385 923, 1, chr22:31476636-31478482 plot bosTauMd3
054 2008 braFlo2 tbd tbd 335984 40 21237833   1088 1244816809 1512, 1, Bf_V2_32:3091839-3094863 plot braFlo2
055 1880 braRap1 GCF_000309985.1 SOAPdenovo v. 1.04 74411 41 5348931   2750 314357742 1288, 2, chrA5:13328835-13331412 plot braRap1
056 2007 bruMal1 tbd tbd 70008 37 3314327   264 46555408 321, 1, Bmal_supercontigDegenerate10576:240-882 plot bruMal1
057 2014 bruMal2 tbd tbd 72743 38 3759073   402 111607550 453, 1, Bmal_v3_scaffold8088:119-1025 plot bruMal2
058 2014 bucRhi1 GCF_000710305.1 SOAPdenovo v. 1.6 43210 56 3393282   73 48672532 715, 1, KL533494:44624-46054 plot bucRhi1
060 2011 burXyl1 tbd tbd 12719 36 772590   1694 51888226 134, 1, scaffold01254:876286-876554 plot burXyl1
061 2010 caeAng1 GCA_000165025.1 Velvet v. 0.7.56 100045 42 4176946   305 156635287 71, 1, scafRNAPATHr22140:12806-12948 plot caeAng1
062 2012 caeAng2 tbd tbd 148180 41 6380576   369 202631392 131, 1, Cang_2012_03_13_00262:54689-54951 plot caeAng2
063 2008 caeJap1 tbd tbd 54911 37 2702441   669 184995823 179, 1, chrUn:91344286-91344644 plot caeJap1
064 2009 caeJap2 tbd tbd 61394 38 3566172   1128.5 219090212 153, 1, chrUn:143662847-143663153 plot caeJap2
065 1880 caeJap2a tbd tbd 59499 38 3480262   973 192672580 153, 1, Cjap_Contig3098:12088-12394 plot caeJap2a
066 2010 caeJap3 tbd tbd 47394 36 2103165   360 75708219 176, 1, ABLE03028834:844-1196 plot caeJap3
067 2010 caeJap4 GCA_000147155.1 Celera assembler v. 6.0 66567 37 3336966   815 226847582 176, 1, Scaffold17893:329482-329834 plot caeJap4
068 2007 caePb1 tbd tbd 67100 38 3590813   2009 281616954 168, 1, chrUn:161968878-161969214 plot caePb1
069 2008 caePb2 tbd tbd 71710 39 3958202   3788.5 420907669 239, 1, chrUn:97561553-97562031 plot caePb2
070 2010 caePb3 GCA_000143925.2 PCAP v. 9/3/04 71721 39 3951441   3770 420080585 239, 1, Scfld02_132:346628-347106 plot caePb3
071 2005 caeRem1 tbd tbd 78288 40 4264984   1786 318215569 193, 1, SuperCont3184:2552-2938 plot caeRem1
072 2006 caeRem2 tbd tbd 102926 41 5484074   859 350685995 193, 1, chrUn:145434398-145434784 plot caeRem2
073 2007 caeRem3 tbd tbd 69306 40 3736990   2408 318941600 181, 1, chrUn:147913992-147914354 plot caeRem3
074 2007 caeRem4 GCF_000149515.1 tbd 70702 39 3779779   2320 319257206 181, 1, Crem_Contig169:93478-93840 plot caeRem4
075 2010 caeSp111 GCA_000186765.1 Celera assembler v. 6.0 16576 36 783303   2230.5 70961296 161, 1, Scaffold630:3047861-3048183 plot caeSp111
076 2012 caeSp51 tbd tbd 20559 36 877191   1869 57741956 109, 1, Csp5_scaffold_04217:6885-7103 plot caeSp51
077 2010 caeSp91 tbd tbd 67737 36 3110776   1418 221671479 195, 1, Scaffold7109:118818-119208 plot caeSp91
078 2014 calAnn1 GCF_000699085.1 SOAPdenovo v. 1.6 115073 39 9049123   590 450885170 1104, 1, KL218440:2851016-2853224 plot calAnn1
079 2013 calMil1 GCF_000165045.1 Celera v. 6.1 365912 35 15637123   1428 1794921679 144, 1, KI635985:586597-586885 plot calMil1
080 2011 camFer1 GCF_000311805.1 SOAPdenovo v. V1.05 101845 33 6622167   162 292517673 934, 1, KB017230:2215149-2217017 plot camFer1
081 2004 canFam1 tbd tbd 708312 35 27662849   8269 6176862199 292, 1, chr7:79846479-79847063 plot canFam1
082 2005 canFam2 tbd tbd 953541 35 38683290   7862 8147344317 746, 1, chrUn:76334072-76335564 plot canFam2
083 2011 canFam3 GCF_000002285.3 Arachne v. April 2010 971687 35 40018993   7312 7976595682 292, 1, chr7:77369247-77369831 plot canFam3
085 2005 canHg12 tbd tbd 33765 35 1344552   617 139440788 121, 1, 12:76878573-76878815 plot canHg12
086 2014 capCar1 GCF_000700745.1 SOAPdenovo v. 1.6 63810 36 3017510   389.5 221999357 1265, 2, KL360999:16916-19447 plot capCar1
087 2012 capHir1 GCF_000317765.1 SOAPdenovo v. 1.03 620672 36 27059872   6750 4701845701 4915, 1, chr24:61180186-61190016 plot capHir1
088 2014 carCri1 GCF_000690535.1 SOAPdenovo v. 1.6 20461 37 1163337   68 30549622 529, 1, KK515247:46620-47678 plot carCri1
089 2008 cavPor3 GCF_000151735.1 unknown v. before 2008 423409 39 22453984   5720 3122228393 260, 1, scaffold_239:788868-789388 plot cavPor3
090 2002 cb1 tbd tbd 36051 37 2442691   558 98718219 191, 1, chrUn:90311348-90311730 plot cb1
091 2005 cb2 tbd tbd 35978 37 2444306   560 98588417 317, 1, chrIII:126724-127358 plot cb2
092 2007 cb3 tbd tbd 35990 37 2451574   568.5 99618994 317, 1, chrIII:11646590-11647224 plot cb3
093 2011 cb4 tbd tbd 36155 37 2519414   578 100960462 317, 1, chrIII:76433-77067 plot cb4
094 2010 ce10 tbd tbd 33806 38 1760308   427 82769023 1500, 1, chrIV:5554976-5557976 plot ce10
095 2013 ce11 GCF_000002985.6 tbd 33816 38 1760641   427 82800067 1500, 1, chrIV:5554985-5557985 plot ce11
096 2004 ce2 tbd tbd 33799 38 1759889   427 82752389 1500, 1, chrIV:5554978-5557978 plot ce2
097 2005 ce3 tbd tbd 33799 38 1759889   427 82752398 1500, 1, chrIV:5554972-5557972 plot ce3
098 2007 ce4 tbd tbd 33792 38 1759610   427 82743753 1500, 1, chrIV:5554972-5557972 plot ce4
099 2007 ce5 tbd tbd 33794 38 1759781   427 82743927 1500, 1, chrIV:5554972-5557972 plot ce5
100 2008 ce6 tbd tbd 33794 38 1759781   427 82743927 1500, 1, chrIV:5554972-5557972 plot ce6
101 2009 ce7 tbd tbd 33806 38 1760308   427 82769007 1500, 1, chrIV:5554972-5557972 plot ce7
102 2009 ce8 tbd tbd 33806 38 1760308   427 82769007 1500, 1, chrIV:5554972-5557972 plot ce8
103 2010 ce9 tbd tbd 33806 38 1760308   427 82769007 1500, 1, chrIV:5554972-5557972 plot ce9
104 2012 cerSim1 GCF_000283155.1 ALLPATHS v. R41370 182565 35 7975290   7694 1503937586 217, 1, JH767741:19156533-19156967 plot cerSim1
105 2014 chaVoc1 GCF_000708025.1 SOAPdenovo v. 1.6 53439 41 4896801   1813 256127930 1729, 2, KL408233:1252791-1256250 plot chaVoc1
106 2014 chaVoc2 GCF_000708025.1 SOAPdenovo v. 1.6 53430 41 4896157   1812 256095280 1729, 2, KL871243:1252791-1256250 plot chaVoc2
107 2013 cheMyd1 GCF_000344595.1 SOAPdenovo v. 1.05 338286 38 27175756   2112 1711904320 2073, 1, KB534909:887250-891396 plot cheMyd1
108 2012 chiLan1 GCA_000276665.1 ALLPATHS v. R40776 162447 34 8332343   5673 1154905940 274, 1, JH721868:33430685-33431233 plot chiLan1
109 2013 chlSab1 tbd tbd 933660 34 44465888   4819 6164212406 1783, 1, chrY:1553648-1557214 plot chlSab1
110 2014 chlSab2 GCF_000409795.2 ALLPATHS and Newbler v. 13-Feb-2013 934123 34 44534038   4823 6168422847 1783, 1, chrY:1553648-1557214 plot chlSab2
111 2014 chlUnd1 GCF_000695195.1 SOAPdenovo v. 1.6 28454 43 1824188   165 94696650 497, 1, KK750077:105999-106993 plot chlUnd1
112 2014 chrPic2 GCA_000241765.2 Newbler v. 2.6 313473 43 18318992   1246 1347589030 269, 1, chrUn_KK085497v1:1941-2479 plot chrPic2
113 2002 ci1 GCA_000183065.1 tbd 48663 39 2653274   626 122189601 486, 1, Scaffold_604:30085-31057 plot ci1
114 2005 ci2 tbd tbd 119965 43 8287326   1961 566064667 358, 1, scaffold_83:159982-160698 plot ci2
115 2011 ci3 GCF_000224145.1 tbd 48178 39 2574684   692 149951145 486, 1, chrUn_NW_004190340v1:65099-66071 plot ci3
116 2003 cioSav1 tbd tbd 123843 39 6363601   2503 618224769 189, 1, ps_297:30448-30826 plot cioSav1
117 2005 cioSav2 tbd tbd 157468 38 7731855   2875 819500559 280, 1, reftig_238:125039-125599 plot cioSav2
118 2013 colLiv1 GCF_000337935.1 SOAPdenovo v. 2.0 139510 33 6394287   112 419571584 3080, 2, KB375367:1029739-1035900 plot colLiv1
119 2014 colStr1 GCF_000690715.1 SOAPdenovo v. 1.6 55406 40 3066780   131 154687137 309, 1, KK533057:6873-7491 plot colStr1
120 2012 conCri1 GCF_000260355.1 AllPaths v. 2012 253120 35 11854934   7807 2109955223 265, 1, JH655888:40209348-40209878 plot conCri1
121 2014 corBra1 GCF_000691975.1 SOAPdenovo v. 1.6 91630 37 6371852   297 248570100 1583, 1, KK718913:5901493-5904659 plot corBra1
122 2014 corCor1 GCF_000738735.1 AllPaths v. Allpaths-LG version 41687 58556 36 3043376   370 184023111 1935, 1, KL997525:15617964-15621834 plot corCor1
123 2013 cotJap1 GCA_000511605.1 Soapdenovo v. 1.0.5b; bwa v. 0.5.9; SSPACE v. 1.2 7329 33 280548   75 2914174 214, 1, DF262918:84572-85000 plot cotJap1
124 2013 criGri1 GCF_000419365.1 SOAPdenovo v. 2.2 392434 34 24519809   4676 2562035140 2419, 1, KE383702:1200830-1205668 plot criGri1
125 2011 criGriChoV1 GCF_000223135.1 SOAPdenovo v. 1.05 399488 34 20807116   3409 2361128543 2346, 1, NW_003614503v1:231537-236229 plot criGriChoV1
126 2014 cucCan1 GCF_000709325.1 SOAPdenovo v. 1.6 126008 42 16101261   2142 633238955 2278, 1, KL448309:4464943-4469499 plot cucCan1
127 2014 cynSem1 GCF_000523025.1 SOAPdenovo v. April-2011 83655 37 6369004   261 184971677 1536, 1, chr1:16715796-16718868 plot cynSem1
128 2014 cypVar1 GCA_000732505.1 AllPaths v. May 2014 136313 39 9823682   1299 502219020 2138, 1, KL652705:564642-568918 plot cypVar1
129 2014 danRer10 GCF_000002035.5 tbd 830199 36 39955973   1138 3506165088 829, 1, chr7:19536660-19538318 plot danRer10
130 2006 danRer4 tbd tbd 967867 37 3554929771106085888   1483 -5209059568647030784 829, 1, chr7:22863126-22864784 plot danRer4
131 2007 danRer5 tbd tbd 878638 36 43432292   1103 3637100049 829, 1, chr7:21951036-21952694 plot danRer5
132 2008 danRer6 tbd tbd 1054071 36 55306251   1381 4517471825 2083, 1, chr10:31284766-31288932 plot danRer6
133 2010 danRer7 GCF_000002035.4 tbd 910457 36 43398798   1289 3925402743 829, 1, chr7:20946224-20947882 plot danRer7
134 2014 dicLab1 GCA_000689215.1 tbd 204757 36 11489728   924 691437386 841, 1, HG916851:32290203-32291885 plot dicLab1
135 2008 dipOrd1 GCA_000151885.1 tbd 1877441 35 85259926   2185 7963556509 183, 1, scaffold_30074:4167-4533 plot dipOrd1
136 2013 dirImm1 tbd tbd 3309 36 316992   58 1820327 1613, 1, nDi_2_2_scaf00284:19002-22228 plot dirImm1
137 2003 dm1 tbd tbd 12199 50 1260685   3445 60460276 3882, 2, chr2L:1894810-1902575 plot dm1
138 2004 dm2 tbd tbd 13213 51 1372092   3723 67342596 3882, 2, chr2L:1893145-1900910 plot dm2
139 2006 dm3 tbd tbd 113222 40 6787673   2412 622002007 3882, 2, chr2L:1893145-1900910 plot dm3
140 2014 dm6 GCF_000001215.4 tbd 48031 48 4403254   3448 254474999 3882, 2, chr2L:1893145-1900910 plot dm6
141 2003 dp2 tbd tbd 16790 44 1110948   926 42217528 227, 1, Contig7446_Contig2444:1979445-1979899 plot dp2
142 2004 dp3 tbd tbd 20334 44 1389766   1239 62703720 312, 1, chrU:9357988-9358612 plot dp3
143 2006 dp4 tbd tbd 53060 46 3495255   2437 228127096 312, 1, Unknown_singleton_2460:32411-33035 plot dp4
144 2012 droAlb1 GCA_000298335.1 SOAPdenovo v. 1.04 126521 30 3970849   70 35343627 76, 1, JH853217:889-1041 plot droAlb1
145 2004 droAna1 tbd tbd 67882 40 3659056   697 196198368 572, 1, 2446670:645-1789 plot droAna1
146 2005 droAna2 tbd tbd 248263 42 14624595   918 748771139 572, 1, scaffold_13499:1095908-1097052 plot droAna2
147 2006 droAna3 GCF_000005115.1 tbd 246334 42 14515690   927 745835855 572, 1, scaffold_13499:1092668-1093812 plot droAna3
148 2013 droBia2 GCA_000233415.2 Celera Assembler v. 6.1; BWA v. 0.6.0; Samtools v. 0.1.14; GATK v. 1.1-9; Indel_call_and_upgrade.pl v. 1.0 46906 42 2807408   2591 175612579 2241, 3, AFFD02006372:54233-58717 plot droBia2
149 2013 droBip2 GCA_000236285.2 Celera Assembler v. 6.1; BWA v. 0.6.0; Samtools v. 0.1.14; GATK v. 1.1-9; Indel_calland_upgrade.pl v. 1.0 54693 39 2946335   1371 204354268 179, 1, KB463958:131929-132287 plot droBip2
150 2013 droEle2 GCA_000224195.2 Celera Assembler v. 6.1; BWA v. 0.6.0; Samtools v. 0.1.14; GATKv. 1.1-9; Indel_call_and_upgrade.pl v. 1.0 34862 41 2092385   2187 135919965 270, 1, KB458613:1953986-1954526 plot droEle2
151 2005 droEre1 tbd tbd 96336 44 5585722   674 191777516 359, 1, scaffold_1301:371-1089 plot droEre1
152 2006 droEre2 GCF_000005135.1 tbd 95081 44 5535640   676 190524603 359, 1, scaffold_1301:371-1089 plot droEre2
153 2013 droEug2 GCA_000236325.2 Celera Assembler v. 6.1; BWA v. 0.6.0; Samtools v. 0.1.14; GATK v. 1.1-9; Indel_call_and_upgrade.pl v. 1.0 59111 40 3495099   1518 181127987 141, 1, KB464979:6084-6366 plot droEug2
154 2013 droFic2 GCA_000220665.2 Celera Assembler v. 6.1; BWA v. 0.6.0; Samtools v. 0.1.14; GATK v. 1.1-9; Indel_call_and_upgrade.pl v. 1.0 21964 44 1418464   2380.5 83742114 190, 1, AFFG02001364:4041-4421 plot droFic2
155 2005 droGri1 tbd tbd 458551 40 21432909   509 538034457 491, 1, scaffold_2211:899-1881 plot droGri1
156 2006 droGri2 GCF_000005155.2 tbd 302510 40 14467041   522 418546843 188, 1, scaffold_6592:1167-1543 plot droGri2
157 2013 droKik2 GCA_000224215.2 Celera Assembler v. 6.1; BWA v. 0.6.0; Samtools v. 0.1.14; GATK v. 1.1-9; Indel_call_and_upgrade.pl v. 1.0 31358 41 1855833   1533.5 112074726 117, 1, KB459586:778466-778700 plot droKik2
158 2013 droMir2 GCA_000269505.2 Newbler v. 2.6 18368 45 1204033   1747 75101816 140, 1, chr2:3040735-3041015 plot droMir2
159 2004 droMoj1 tbd tbd 69928 38 3220037   310 78711524 225, 1, contig_34282:247-697 plot droMoj1
160 2005 droMoj2 tbd tbd 102140 41 5658627   1086 363630258 202, 1, scaffold_6540:14391223-14391627 plot droMoj2
161 2006 droMoj3 GCF_000005175.2 tbd 101230 41 5606832   1114 361818537 202, 1, scaffold_6540:14384339-14384743 plot droMoj3
162 2005 droPer1 GCF_000005195.2 tbd 75046 45 5536401   2595 325634621 580, 2, super_62:246420-247581 plot droPer1
163 2013 droPse3 GCF_000001765.3 PBJelly v. 12.8.2; Atlas genome assembly 53481 45 3494617   2480 231367590 312, 1, chrUn_CH674897_1:32411-33035 plot droPse3
164 2013 droRho2 GCA_000236305.2 Celera Assembler v. 6.1; BWA v. 0.6.0; Samtools v. 0.1.14; GATK v. 1.1-9; Indel_call_and_upgrade.pl v. 1.0 68118 41 4002283   1672 235074913 205, 1, AFPP02028413:1419-1829 plot droRho2
165 2005 droSec1 GCA_000005215.1 tbd 127886 38 6652375   465 177925676 360, 1, super_6483:1086-1806 plot droSec1
166 2005 droSim1 tbd tbd 47915 42 2874159   1400 171101666 217, 1, chr3R_random:168062-168496 plot droSim1
167 2014 droSim2 GCF_000754195.2 Velvet v. 1.1.04 10385 40 551061   466 26120972 217, 1, chrUn_NW_015496898v1:4674-5108 plot droSim2
168 2013 droSuz1 GCA_000472105.1 SOAPdenovo v. 2 117859 46 12342639   2277 517597655 4939, 1, KI419149:2637663-2647541 plot droSuz1
169 2013 droTak2 GCA_000224235.2 Celera Assembler v. 6.1; BWA v. 0.6.0; Samtools v. 0.1.14; GATK v. 1.1-9; Indel_call_and_upgrade.pl v. 1.0 48870 41 2816693   2013 202395837 306, 1, AFFI02002878:4290-4902 plot droTak2
170 2004 droVir1 tbd tbd 147648 35 6630839   429 239695710 244, 1, scaffold_0:5707381-5707869 plot droVir1
171 2005 droVir2 tbd tbd 432783 30 17539885   481 757905036 244, 1, scaffold_13049:18877549-18878037 plot droVir2
172 2006 droVir3 GCF_000005245.1 tbd 407188 30 16757243   495 747769004 244, 1, scaffold_13049:18848863-18849351 plot droVir3
173 2006 droWil1 GCF_000005925.1 tbd 118355 42 7234894   1695 472632964 954, 1, scaffold_181130:9135849-9137757 plot droWil1
174 2006 droWil2 GCF_000005925.1 tbd 118240 42 7228999   1695 472142234 954, 1, CH964272:9135849-9137757 plot droWil2
175 2004 droYak1 tbd tbd 81563 43 6228480   3752 459910434 851, 1, chr3L:24830341-24832043 plot droYak1
176 2005 droYak2 tbd tbd 93441 45 6941572   3518 501527798 1122, 2, chrU:731511-733756 plot droYak2
177 2006 droYak3 GCF_000005975.2 tbd 85136 46 6497582   2641 404384429 1122, 2, chrUn_CH892674_1:731511-733756 plot droYak3
180 2014 egrGar1 GCF_000687185.1 SOAPdenovo v. 1.6 74371 43 9954381   893 271113520 2791, 1, KK500861:718810-724392 plot egrGar1
181 2013 eidHel1 GCA_000465285.1 CLC NGS Cell v. 3.20.50819; SOAPdenovo v. 1.05 33439 35 1366001   126 36481318 7647, 43, AWHC01288168:1-15337 plot eidHel1
182 2012 eptFus1 GCF_000308155.1 ALLPATHS v. R40371 222087 35 13225570   2177 1173955475 211, 1, JH977672:6077044-6077466 plot eptFus1
183 2007 equCab2 tbd tbd 393206 37 17857641   2842 2161091933 526, 1, chr14:85222625-85223677 plot equCab2
184 2014 equPrz1 GCA_000696695.1 SOAPdenovo v. 1.05 276230 49 14219094   107 801082402 1923, 1, KK950139:433764-437610 plot equPrz1
185 2012 eriEur2 GCF_000296755.1 allpaths v. R41008 861216 34 39995023   7216 6808639747 13780, 5, JH835378:10400-37964 plot eriEur2
186 2014 esoLuc1 GCA_000721915.1 AllPaths v. 43500 309026 36 12717997   109 633934424 1803, 1, KL593524:286555-290161 plot esoLuc1
187 2006 euaGli13 tbd tbd 85054 35 3561209   981 360128068 95, 1, 4-7:24024058-24024248 plot euaGli13
188 2014 eurHel1 GCF_000690775.1 SOAPdenovo v. 1.6 48033 41 2646849   3690 271468700 462, 1, KK561721:27808-28732 plot eurHel1
189 2006 eutHer13 tbd tbd 75114 37 3312319   1220 345926827 125, 1, 5-6:21163986-21164236 plot eutHer13
190 2013 falChe1 GCF_000337975.1 SOAPdenovo v. 1.4 33448 36 3028131   144 71160661 1589, 1, KB397979:787306-790484 plot falChe1
191 2013 falPer1 GCF_000337955.1 SOAPdenovo v. 1.4 32904 38 2747346   156 69981752 1888, 1, KB390863:6987566-6991342 plot falPer1
192 2011 felCat5 GCF_000181335.1 Celera Assembler v. 6.1 453806 34 18818004   7873 3800500393 238, 1, chrB2:9942275-9942751 plot felCat5
193 2002 fr1 tbd tbd 65564 35 3413218   165 124234021 304, 1, chrUn:169005183-169005791 plot fr1
194 2004 fr2 tbd tbd 104956 35 5519798   156 261084207 151, 1, chrUn:356162839-356163141 plot fr2
195 2011 fr3 GCF_000180615.1 tbd 105765 35 5702900   157 257018230 151, 1, HE592488:202-504 plot fr3
196 2014 fulGla1 GCF_000690835.1 SOAPdenovo v. 1.6 20338 37 1197675   93 36399474 576, 1, KK595554:8470-9622 plot fulGla1
197 2010 gadMor1 GCA_000231765.1 tbd 523023 30 17042881   24 573821154 131, 1, HE571852:62524-62786 plot gadMor1
198 2004 galGal2 tbd tbd 157813 51 15224008   3723 846924205 208, 1, chr2:94743278-94743694 plot galGal2
199 2006 galGal3 tbd tbd 243371 62 25066425   3004 1138149811 208, 1, chr2:97262115-97262531 plot galGal3
200 2011 galGal4 GCF_000002315.3 Celera Assembler v. 5.4 78961 39 4732239   2968 493569103 17591, 16, chrZ:21320544-21355741 plot galGal4
201 2015 galGal5 GCF_000002315.4 MHAP/PBcR v. 8.2beta 985564 36 47990278   1925 3490824745 17591, 16, chrZ:21461674-21496871 plot galGal5
202 2006 gasAcu1 tbd tbd 131262 39 7836949   3635 770629287 296, 1, chrUn:59780312-59780904 plot gasAcu1
203 1880 gasAsc0 GCA_000180675.1 tbd 116031 39 6613325   1417 518945407 316, 1, contig_16726:674-1306 plot gasAsc0
204 2009 gavGan0 tbd tbd 140159 79 22649136   5005 732648585 2263, 10, scaffold7460:20241-24776 plot gavGan0
205 2014 gavSte1 GCF_000690875.1 SOAPdenovo v. 1.6 24295 36 1352476   75 47417993 302, 1, KK611813:2739-3343 plot gavSte1
206 2012 geoFor1 GCF_000277835.1 SOAPdenovo v. 2.01 113187 37 6785044   204 268468600 1013, 1, JH739970:2776008-2778034 plot geoFor1
207 2006 gliRes13 tbd tbd 31976 36 1385928   1661 143989628 95, 1, 4-7:15697982-15698172 plot gliRes13
208 2016 gorGor5 tbd tbd 3555119 33 133654191   4102 21270991545 338, 1, CYUI01005848v1:13590-14266 plot gorGor5
209 2009 haeCon1 tbd tbd 109810 42 5802860   1251.5 319005845 196, 1, Hcon_Contig0025586:3955-4347 plot haeCon1
210 2013 haeCon2 tbd tbd 53818 43 3892613   570 187299643 2147, 1, scaffold_1557:10532-14826 plot haeCon2
211 2014 halAlb1 GCF_000691405.1 SOAPdenovo v. 1.6 13685 36 754065   301 41720730 548, 2, KK653364:30569-31666 plot halAlb1
212 2014 halLeu1 GCF_000737465.1 SOAPdenovo2 v. May 2014 16099 40 1241068   4586 98353830 79, 1, KL869431:1084034-1084192 plot halLeu1
213 2011 hapBur1 GCF_000239415.1 ALLPATHS-LG v. R35951 34584 37 2342045   3524.5 202958431 10390, 20, JH425331:1373378-1394177 plot hapBur1
214 2011 hetBac1 GCA_000223415.1 Celera assembler v. 6.0 3302 51 353946   673 12041725 317, 1, GL996135v1:102345-102979 plot hetBac1
215 2012 hetGla2 GCF_000247695.1 AllPaths v. R39605 103053 34 6024624   6941 791605735 158, 1, JH602100:6973404-6973720 plot hetGla2
216 2006 homIni14 tbd tbd 986594 33 36270527   7838 8265721353 294, 1, chr20:9839450-9840038 plot homIni14
217 1880 homNea0 tbd tbd 148 30 4725   14.5 2669 37, 1, 151586_3339_2553:20-94 plot homNea0
219 2006 lauRas13 tbd tbd 43311 36 1891314   1493 210427636 125, 1, 5-6:22761072-22761322 plot lauRas13
220 2014 lepDis1 GCF_000691785.1 SOAPdenovo v. 1.6 16795 33 749994   94 31438992 199, 1, JJRK01010260:4452-4850 plot lepDis1
221 2011 lepOcu1 GCF_000242695.1 AllPaths v. R38293 77276 37 4579890   1084 350156295 488, 2, chrLG5:14840992-14841969 plot lepOcu1
222 2013 letCam1 GCA_000466285.1 Newbler v. 2.7 768187 35 32420899   153 1525909318 207, 1, KE997215:997-1411 plot letCam1
223 1880 linHum0 GCF_000217595.1 CABOG v. 5.3 42080 41 2313367   5018 259661061 101, 1, NW_012160424:64875-65077 plot linHum0
224 2013 lipVex1 GCF_000442215.1 SOAPdenovo v. 2.01 514863 35 27315468   8421 4503138248 6076, 1, KE559913:905157-917309 plot lipVex1
225 2012 loaLoa1 GCA_000183805.3 Newbler v. 2.1-PreRelease-4/28/2009 15889 37 1294459   188 16478676 109, 1, JH717180v1:404-622 plot loaLoa1
226 2014 manPen1 GCA_000738955.1 SOAPdenovo v. May 2014 304420 55 33766689   853 887951462 4944, 1, KN012191:2418-12306 plot manPen1
227 2014 manVit1 GCF_000692015.1 SOAPdenovo v. 1.6 75103 35 4570292   206 245456943 5268, 1, KK733349:4046063-4056599 plot manVit1
229 2012 mayZeb1 GCF_000238955.1 AllPaths v. R37043 48899 38 3205287   4159 307830483 9605, 105, JH720664:938440-957754 plot mayZeb1
230 2013 megLyr1 GCA_000465345.1 CLC NGS Cell v. 3.20.50819; SOAPdenovo v. 1.05 25192 34 1014702   112 35852812 149, 1, KI041466:2479-2777 plot megLyr1
231 2009 melGal1 tbd tbd 25253 45 1794885   2825 133788059 169, 1, chr3:54352580-54352918 plot melGal1
232 2014 melGal5 GCF_000146605.2 MaSuRCA v. 1.9.2 101903 36 4643970   197 188019328 173, 1, chrUn_NW_011217171v1:1-347 plot melGal5
233 2008 melHap1 GCA_000172435.1 tbd 12515 41 832837   375 21806223 157, 1, MhA1_Contig2844:850-1164 plot melHap1
234 2008 melInc1 GCA_000180415.1 tbd 19330 40 1244828   558 47252172 183, 1, Minc_Contig6373:3669-4035 plot melInc1
235 2008 melInc2 tbd tbd 22743 41 1594354   1067 83086394 183, 1, MiV1ctg2756:3669-4035 plot melInc2
236 2011 melUnd1 GCF_000238935.1 Celera v. 6.1 99875 41 5463070   6271 754338919 120, 1, JH556605:5210251-5210491 plot melUnd1
237 2014 merNub1 GCF_000691845.1 SOAPdenovo v. 1.6 37279 43 2280064   174 103616988 543, 1, KK705997:21022-22108 plot merNub1
238 2013 mesAur1 GCF_000349665.1 allpaths v. R44683 254929 34 11386675   3099 1465851012 529, 2, KB708261:1360324-1361383 plot mesAur1
239 2014 mesUni1 GCF_000695765.1 SOAPdenovo v. 1.6 52863 36 2585696   257 120590969 271, 1, JJRI01098248:16372-16914 plot mesUni1
240 2015 micMur2 GCF_000165445.1 AllPathsLG v. 41070; Atlas Link v. 1.0; Atlas GapFill v. 2.0; PBJelly2 v. 14.9.9 1102998 38 61135566   7563 8957944918 3388, 3, KQ058422v1:91440-98218 plot micMur2
241 2017 micMur3 GCF_000165445.2 AllPathsLG v. 41070; Atlas Link v. 1.0; Atlas GapFill v. 2.0; PBJelly2 v. 14.9.9; Lachesis v. shendurelab-LACHESIS-2151de9; BioNano IrysSolve v. 2.1 1168691 38 66907392   7729 9630726519 185, 1, chr5:43933509-43933879 plot micMur3
242 2012 micOch1 GCF_000317375.1 allpaths v. R41985 HAPLOIDIFY=True SPRS_WRITE_SEPS=True 335553 35 15776999   2433 1838809952 278, 1, chrLG5:33413026-33413582 plot micOch1
243 2006 mm8 tbd tbd 818602 36 37812754   6175 5992918402 499, 1, chr11:108226617-108227615 plot mm8
244 2007 mm9 tbd tbd 841682 36 38909060   6202 6169636600 499, 1, chr11:108271841-108272839 plot mm9
245 2013 musDom2 GCF_000371365.1 AllPathsLG v. September 2012 575203 36 27589830   1941 2513509860 2028, 1, KB856326:64184-68240 plot musDom2
246 2011 musFur1 GCA_000215625.1 ALLPATHS-LG v. R36167 309552 34 12256854   8370 2709245222 446, 1, GL896951:5218180-5219072 plot musFur1
247 2013 myoBra1 GCF_000412655.1 SOAP de novo v. 2.04 508698 38 40839066   1070 2100859228 3719, 1, KE163224:7566116-7573554 plot myoBra1
248 2012 myoDav1 GCF_000327345.1 SOAPdenovo v. 1.06 303669 37 20701160   2186 1562115676 595, 1, KB109238:3742816-3744006 plot myoDav1
249 2010 myoLuc2 GCF_000147115.1 Arachne v. Dev. Jan 2010 404463 36 18255536   5420 2827568613 312, 1, GL430179:150290-150914 plot myoLuc2
250 2015 nanPar1 GCA_000935625.1 SOAPdenovo v. 1.06 725822 37 53289164   248 1815148366 7565, 1, KN905954v1:74233-89363 plot nanPar1
251 2013 necAme1 GCF_000507365.1 Newbler v. MapAsmResearch-04/19/2010-patch-08/17/2010 30870 43 1735538   1580 123448969 93, 1, KI659398v1:132-318 plot necAme1
252 2007 nemVec1 tbd tbd 540729 40 30645450   589 1501673463 353, 1, scaffold_201:423580-424286 plot nemVec1
253 2011 neoBri1 GCF_000239395.1 ALLPATHS-LG v. R36800 62939 46 6697998   1655 274117853 8242, 20, JH422273:8382583-8399086 plot neoBri1
254 2014 nipNip1 GCF_000708225.1 SOAPdenovo v. 1.6 32623 43 3676893   251 104452416 1496, 1, KL409846:432608-435600 plot nipNip1
255 2014 notCor1 GCF_000735185.1 Celera Assembler v. 7.0 164483 34 7109993   199 393266432 407, 1, KL665414:596304-597118 plot notCor1
256 2012 ochPri3 GCF_000292845.1 Allpaths v. R41206 269479 35 14417226   6664 2042363947 5916, 11, JH802070:23930294-23942136 plot ochPri3
257 2013 odoRosDiv1 GCA_000321225.1 AllPaths v. 41070; Atlas-link v. 1.0; Atlas-gapfill v. 2.2 386270 34 17141224   7248 3092233269 336, 1, KB228946:1914846-1915518 plot odoRosDiv1
258 2013 oncVol1 GCA_000499405.1 tbd 5247 39 423838   2124 28089581 739, 1, HG738137v1:12037947-12039425 plot oncVol1
259 2014 opiHoa1 GCF_000692075.1 SOAPdenovo v. 1.6 75782 40 6783674   4083 456471575 1119, 1, KK734928:246587-248825 plot opiHoa1
260 2013 orcOrc1 GCF_000331955.2 AllPaths v. 41070; ATLAS-link v. 1.0; ATLAS-gapfill v. 2.2 355274 35 15657594   8151 3040130649 4550, 14, NW_004438537v1:3574224-3583337 plot orcOrc1
261 2011 oreNil1 tbd tbd 80799 39 4892346   6067 586359236 9755, 32, GL831139:3510855-3530396 plot oreNil1
262 2007 ornAna1 GCF_000002275.2 tbd 843770 36 52838231   2857 4750437899 279, 1, Contig10711:4568-5126 plot ornAna1
263 2007 ornAna2 GCA_000002275.2 tbd 843770 36 52838231   2857 4750437899 279, 1, chrUn_DS187984v1:4568-5126 plot ornAna2
264 2009 oryCun2 GCF_000003625.3 tbd 1022805 35 43458140   7982 8671655620 355, 1, chrX:61423000-61423710 plot oryCun2
265 2006 oryLat1 tbd tbd 191645 40 12487530   1210 620191379 379, 1, chr9:5041681-5042439 plot oryLat1
266 2005 oryLat2 tbd tbd 189087 40 12356700   1234 592910738 379, 1, chr9:5041681-5042439 plot oryLat2
267 2011 otoGar3 GCF_000181295.1 ALLPATHS-LG v. R35710 400962 34 16217113   5408 2796782144 7275, 20, GL873525:45030822-45045391 plot otoGar3
268 2012 oviAri3 GCF_000298735.1 SOAPdenovo v. 1.03 786369 35 35783861   7004 6099422199 7782, 1, chr21:31441666-31457230 plot oviAri3
269 2013 panHod1 GCF_000400835.1 SOAPdenovo v. 2.1 521516 35 25591307   8191 4466818919 3120, 1, KE108970:1986445-1992685 plot panHod1
270 2013 panRed1 GCA_000341325.1 Velvet v. 1.2.07 23300 42 1084666   1396 66559726 101, 1, KB454925:8492-8694 plot panRed1
271 2013 panTig1 GCF_000464555.1 SOAPdenovo v. 08-Jul-2011 289892 33 13318045   7625 2368098055 1135, 1, KE721593:7259595-7261865 plot panTig1
272 2014 pelCri1 GCF_000687375.1 SOAPdenovo v. 1.6 42891 37 2053042   265 127612523 574, 1, KK474798:35527-36675 plot pelCri1
273 2011 pelSin1 GCF_000230535.1 SOAPdenovo v. 1.05 282804 42 32017871   2114.5 1334725849 4166, 1, JH210925:2745573-2753905 plot pelSin1
274 2013 perManBai1 GCF_000500345.1 Newbler v. 2.3 and 2.5; AllPaths v. 41070; ATLAS-gapfill v. 2.2; ATLAS-link v. 1.0 806105 37 49741488   3501 4676973953 266, 1, KI615341:3157564-3158096 plot perManBai1
275 2007 petMar1 tbd tbd 855653 36 38339527   201 932728649 362, 1, Contig99174:237-961 plot petMar1
276 2010 petMar2 GCA_000148955.1 Arachne v. 3.2 836219 37 38092404   692 2324558773 363, 1, GL498477:1987-2713 plot petMar2
277 2014 phaCar1 GCF_000708925.1 SOAPdenovo v. 1.6 41541 34 1992939   36 26355615 779, 1, KL418261:30029-31587 plot phaCar1
278 2014 phaLep1 GCF_000687285.1 SOAPdenovo v. 1.6 26611 38 1718609   216 85779441 1077, 1, KK455387:47187-49341 plot phaLep1
279 2014 phoRub1 GCA_000687265.1 SOAPdenovo v. 1.6 17140 43 1055248   135 39934970 526, 1, KK424259:7588-8640 plot phoRub1
280 2013 phyCat1 GCF_000472045.1 AllPaths-LG v. January 2013 261153 35 10801080   8197 2241115729 5565, 1, KI411098:797892-809022 plot phyCat1
281 2014 picPub1 GCF_000699005.1 SOAPdenovo v. 1.6 397798 36 17968999   7796 3299119050 4915, 3, KL215520:252741-262573 plot picPub1
282 2013 poeFor1 GCF_000485575.1 AllPaths-LG v. July 2013 161806 52 28441594   4650 990605574 1886, 1, KI520679:7484-11256 plot poeFor1
283 2014 poeRet1 tbd tbd 71291 38 4816409   1511 343849361 8790, 4, chrLG5:27506035-27523618 plot poeRet1
284 2014 priExs1 tbd tbd 33878 44 2639333   1128 98936342 1626, 1, scaffold830:51430-54682 plot priExs1
285 2007 priPac1 tbd tbd 29257 43 1929264   448 80615899 500, 1, chrUn:71534792-71535792 plot priPac1
286 2008 priPac2 GCA_000180635.1 tbd 19318 39 1050200   259 25863820 500, 1, ABKE01002096:3239-4239 plot priPac2
287 2014 priPac3 tbd tbd 36759 40 2176431   321 82136541 500, 1, Ppa_Contig5:941324-942324 plot priPac3
288 2013 pseHum1 GCF_000331425.1 SOAPdenovo v. 1.5 140033 36 7836448   130 200423267 7517, 10, KB221191:4083820-4098863 plot pseHum1
289 2012 pteAle1 GCA_000325575.1 SOAPdenovo v. 1.06 114693 37 9365161   223 316324647 1333, 1, KB031158:55901168-55903834 plot pteAle1
290 2014 pteGut1 GCF_000699245.1 SOAPdenovo v. 1.6 41594 36 2007893   100 106772284 534, 1, JMFR01060883:1891-2959 plot pteGut1
291 2013 ptePar1 GCA_000465405.1 CLC NGS Cell v. 3.20.50819; SOAPdenovo v. 1.05 21621 32 935645   268 31185376 1327, 6, AWGZ01430664:1-2660 plot ptePar1
292 2008 pteVam1 GCA_000151845.1 tbd 266592 43 16837304   1547 867093676 194, 1, scaffold_275:208852-209240 plot pteVam1
293 2011 punNye1 GCF_000239375.1 ALLPATHS-LG v. R37016 36249 38 2385815   3630 214952201 5131, 20, JH419262:1608400-1618681 plot punNye1
294 2014 pygAde1 GCA_000699105.1 SOAPdenovo v. 1.6 38534 46 4145677   2165.5 202245057 2147, 1, KL225502:93242-97536 plot pygAde1
295 2013 pytBiv1 GCF_000186305.1 Soap deNovo v. March 2012 167510 47 14323626   217 396468667 235, 1, KE953144:259222-259692 plot pytBiv1
296 2012 repBase0 tbd tbd 54 39 2426   81.5 7619 70, 1, MER51A:232-372 plot repBase0
297 2012 repBase1 tbd tbd 73 39 3249   77 9691 70, 1, MER51A:232-372 plot repBase1
298 1880 repBase2 tbd tbd 51 40 2203   79 6907 70, 1, MER51A:232-372 plot repBase2
300 2013 rhiFer1 GCA_000465495.1 CLC NGS Cell v. 3.20.50819; SOAPdenovo v. 1.05 30159 33 1238560   174 41741562 172, 1, AWHA01239258:1699-2043 plot rhiFer1
301 1880 ricCom1 GCF_000151685.1 tbd 430308 35 18638247   2948 2156357980 460, 1, EQ974418:17730-18650 plot ricCom1
302 2003 rn3 tbd tbd 1202899 39 66661811   5386 8488809019 230, 1, chr1:37917795-37918255 plot rn3
303 2016 rouAeg1 GCF_001466805.2 SparseAssembler v. OCTOBER-2015; DBG2OLC v. OCTOBER-2015; LINKS v. 1.5.1; L_RNA_Scaffolder v. OCTOBER-2015; SSPACE v. 3.0 74090 36 4591683   5517 522939887 410, 2, NW_015493119v1:122550-123371 plot rouAeg1
304 2003 sacCer1 tbd tbd 666 45 76615   1914.5 2711249 50, 1, chr7:519107-519207 plot sacCer1
305 2008 sacCer2 tbd tbd 669 45 76812   1868 2711600 71, 1, chrX:120898-121040 plot sacCer2
306 2011 sacCer3 GCF_000146045.2 tbd 669 45 78716   1868 2711582 1988, 10, chrVIII:212266-216251 plot sacCer3
307 2011 saiBol1 GCA_000235385.1 AllPaths v. R37830 526235 34 21114308   7999 4457057956 278, 1, JH378108:18778847-18779403 plot saiBol1
308 2013 sebNig1 GCA_000475235.1 tbd 344468 43 18020844   94 249080272 492, 1, AUPR01114153:357-1341 plot sebNig1
309 2013 sebRub1 GCA_000475215.1 SOAPdenovo v. 1.05 299208 38 14417679   139 352997550 408, 1, KI445670:61530-62346 plot sebRub1
310 2014 serCan1 GCF_000534875.1 tbd 201507 36 9350381   157 357279352 3222, 1, HG009216:7215262-7221706 plot serCan1
311 2008 sorAra2 GCF_000181275.1 Allpaths v. R41070 410333 34 17425137   5940 2962830748 236, 1, JH798205:592464-592936 plot sorAra2
312 2011 speTri2 GCF_000236235.1 ALLPATHS v. R37591 213421 34 10318652   2662 1156742500 204, 1, JH393366:4794989-4795397 plot speTri2
313 2014 stePar1 GCF_000690725.1 ALLPATHS-LG v. August 2013 96483 40 8151514   3673 549500672 2624, 1, KK581067:134955-140203 plot stePar1
314 1880 strCam0 tbd tbd 23662 45 2730974   666 94888209 1134, 1, superscaffold9:6014874-6017142 plot strCam0
315 2014 strCam1 GCF_000698965.1 SOAPdenovo v. 1.6 23599 45 2718563   646 93976596 1134, 1, KL206988:717376-719644 plot strCam1
316 2005 strPur1 tbd tbd 658932 40 35574440   847.5 1824767726 956, 1, Scaffold18311:2619-4531 plot strPur1
317 2006 strPur2 tbd tbd 611722 39 30968979   1453 2323533345 956, 1, Scaffold47464:201872-203784 plot strPur2
318 2009 strPur3 tbd tbd 689739 40 35781206   1763 2733632009 956, 1, Scaffold85:237230-239142 plot strPur3
319 2011 strPur4 GCF_000002235.3 Atlas v. WGS for Sanger Assembly, Atlas-Link and Atlas-GapFill for SOLiD and Illumina improvement 888256 42 54558021   2360 3918297070 956, 1, Scaffold382:244159-246071 plot strPur4
320 2011 strRat1 tbd tbd 9910 40 540468   1077 26058414 113, 1, RATTI_contig_57682:4110-4336 plot strRat1
321 2014 strRat2 GCA_001040885.1 tbd 8546 41 482721   2233 37502032 67, 1, chrUn_LN609483v1:243-377 plot strRat2
323 1880 taeGut0 tbd tbd 597003 49 43955858   3833 2936709220 209, 1, Contig47:5328655-5329073 plot taeGut0
324 2008 taeGut1 tbd tbd 602657 49 44658308   3557 2849213000 209, 1, chrZ:28813941-28814359 plot taeGut1
325 2013 taeGut2 GCF_000151805.1 PCAP v. 2008 602028 49 44591081   3541 2830875406 209, 1, chrZ:28813941-28814359 plot taeGut2
327 2013 takFla1 GCA_000400755.1 HAPs v. 0.2.2 97724 36 6776388   184 251435705 503, 1, KE121297:329-1335 plot takFla1
328 2014 tauEry1 GCF_000709365.1 SOAPdenovo v. 1.6 58294 35 2621924   2194 291694166 227, 1, JNOY01082112:3268-3722 plot tauEry1
329 2004 tetNig1 tbd tbd 132260 38 9178877   3055 661840431 413, 1, chrUn_random:43732955-43733781 plot tetNig1
330 2007 tetNig2 tbd tbd 130250 38 9072570   3013 657839855 413, 1, chrUn_random:35610230-35611056 plot tetNig2
331 2014 tinGut1 GCF_000705375.1 SOAPdenovo v. 1.6 43221 38 2742653   279 110109614 416, 1, KL400833:106660-107492 plot tinGut1
332 2014 tinGut2 GCF_000705375.1 SOAPdenovo v. 1.6 43210 38 2741340   279 110101482 416, 1, KL895505:106660-107492 plot tinGut2
333 2005 triCas1 tbd tbd 78796 41 4117576   794 170185880 307, 1, Reptig797:115-729 plot triCas1
334 2005 triCas2 tbd tbd 77889 41 4122780   885 196279053 192, 1, singleUn_1374:29986-30370 plot triCas2
335 2011 triSpi1 GCF_000181795.1 PCAP v. January 12, 2007 11343 54 1176023   4572 74727382 98, 1, GL622792v1:5540185-5540381 plot triSpi1
336 2014 triSui1 GCA_000701005.1 SOAPdenovo v. 2 17372 45 1593967   2042.5 75416120 501, 1, KL363185v1:221782-222784 plot triSui1
337 2008 turTru1 tbd tbd 563956 39 29728359   4334 3598266237 726, 1, scaffold_99142:224631-226083 plot turTru1
338 2011 turTru2 GCF_000151865.2 Atlas, Atlas-Link, Atlas-GapFill v. June 2011 776833 45 45568301   691 2466469760 652, 1, JH474081:172050-173354 plot turTru2
339 2014 tytAlb1 GCF_000687205.1 SOAPdenovo v. 1.6 15140 33 776246   81 23744286 199, 1, JJRD01024771:5513-5911 plot tytAlb1
340 2014 ursMar1 GCF_000687225.1 SOAPdenovo v. 1.05 311409 35 14157428   7601 2530787255 5007, 6, KK498603:22100903-22110922 plot ursMar1
341 2007 venter1 tbd tbd 930808 33 34824482   7414 7568565462 475, 1, chr14:54149213-54150163 plot venter1
342 2013 vicPac2 GCF_000164845.1 Newbler v. May-2012 171221 45 11863115   873 480695662 170, 1, KB632444:13257033-13257373 plot vicPac2
343 2004 xenTro1 tbd tbd 1073717 40 65548900   216 2854287515 347, 1, scaffold_3418:6326-7020 plot xenTro1
344 2005 xenTro2 tbd tbd 1034566 40 64677537   219 2820134241 548, 1, scaffold_68:2539823-2540919 plot xenTro2
345 2009 xenTro3 tbd tbd 1034357 40 64662644   219 2819484140 548, 1, GL172704:2539823-2540919 plot xenTro3
346 2012 xenTro7 GCF_000004195.2 ARACHNE v. 20071016_modified 1100470 39 53428011   229 2808691507 3560, 2, KB021656:75384527-75391648 plot xenTro7
347 2016 xenTro9 GCF_000004195.3 Meraculous v. May-2013 967829 39 47452193   241 2585384269 3560, 2, chr6:35780447-35787568 plot xenTro9
348 2012 xipMac1 GCF_000241075.1 PCAP v. 3/30/09; Newbler v. MapAsmResearch-02/17/2010 39708 35 1764516   506 136874274 119, 1, JH557910:3615-3853 plot xipMac1
350 2013 zonAlb1 GCF_000385455.1 Allpaths-LG v. Feb-2013 220251 35 9228906   369 407868591 2060, 1, KB913045:8123897-8128017 plot zonAlb1

assemblies with zero duplicate gap sequences

count year dbName ncbiAsmId number of gaps assembly method
Retrieved from "https://genomewiki.ucsc.edu/index.php?title=TandemDups&oldid=24086"