GapOverlap: Difference between revisions

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Revision as of 14:37, 17 April 2017

methods

The measurements are taken from the gapOverlap.bed[.gz] file in /hive/data/genomes/<db>/bed/gapOverlap/gapOverlap.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 calculated from: end - start + 2 * score

The size of the duplicated sequence is between 30 bases and 1000 bases, we are not checking for sizes outside that range.

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 gaps involved.

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

These ends were found by taking 1,000 bases on each side of any run of N's in the sequence, thus any gap, and aligned with the blat command: 

 blat -q=dna -minIdentity=95 -repMatch=10 upstream.fa downstream.fa

Filtering the PSL output for a perfect match, no mis-matches, and therefore of equal size matching sequence, where the alignment ends exactly at the end of the upstream sequence before the gap and begins exactly at the start of the downstream sequence after the gap.


gapOverlap table statistics

count year dbName item

count

item

median

item

total

  gap

median

gap

total

example item

dup size, gap size, link

001 2013 CHM1 85 86 10897   88 65164 319, 10, chr6:108876987-108877634
002 2014 acaChl1 5 170 1250   188 2340 722, 188, KK833582:5976-7607
005 2009 ailMel1 48 104 10594   1193 82504 75, 1, GL192694.1:348745-348895
006 2012 allMis1 1151 83 273934   1 74939 999, 1, JH739280:136433-138431
007 2013 allSin1 95 125 26114   2265 261774 69, 10, KE696011:2095494-2095641
008 2013 amaVit1 10099 81 1392334   172 2756641 492, 13, KB238901:2710-3706
009 2013 anaPla1 31 251 10663   1660 94318 99, 1, KB742632:907264-907462
010 2014 ancCey1 805 154 171926   1 85569 981, 1, JARK01000206v1:43215-45177
011 2014 angJap1 4539 91 477038   1 610535 588, 1, KI304555:142639-143815
012 2007 anoCar1 20 383.5 8167   537.5 23338 965, 100, scaffold_84:3853690-3855719
013 2010 anoCar2 25 240 6694   258 26105 318, 100, chr4:54548520-54549255
014 2003 anoGam1 7 528 3139   1000 21041 1000, 384, chr2L:5019927-5022310
015 2013 apaSpi1 607 61 34340   100 56961 86, 10, KB929338:2579176-2579357
017 2004 apiMel1 216 50 12150   10 24454 64, 1, Group14.17:517485-517613
018 2005 apiMel2 133 50 7371   50 19757 168, 50, Group4:4855105-4855490
019 2005 apiMel3 199 62 16045   50 27354 198, 50, Group15:1672512-1672957
020 2010 apiMel4 226 52.5 13378   50 24561 167, 50, Group14:1674117-1674500
021 2008 aplCal1 25 77 3383   100 16863 390, 100, scaffold_1802:24095-24974
022 2014 aptFor1 109 147 26798   1575 323838 779, 98, KL225582:135043-136698
023 2015 aptMan1 15742 124 4653010   1 3331011 1000, 1, NW_013987125v1:2508272-2510272
024 2014 aquChr1 4592 43 201248   65 16118238 65, 1, KK850461:8872-9002
025 2014 aquChr2 326 82.5 31349   1 143600 1000, 1, KN265664v1:16826772-16828772
026 2013 araMac1 120 48.5 7929   33 27135 241, 2, KE047968:4314-4797
027 1880 araTha1 1 289 289   60 60 289, 60, chr3:13855281-13855918
028 2012 ascSuu1 9 404 3688   555 6481 1000, 247, JH879107v1:69728-71974
029 2013 astMex1 1385 78 137888   100 1964877 647, 1, KB872443:19678-20972
030 2013 balAcu1 211 149 57860   821 371511 926, 15, KI537556:2252563-2254429
031 2014 balPav1 5 270 1303   216 1098 391, 46, KL482982:8685-9512
032 2014 bisBis1 8184 72 712109   100 947641 933, 100, KN265089v1:519297-521262
034 2011 bosMut1 139 83 27917   1274 256420 71, 14, JH880933:479978-480133
035 2004 bosTau1 6550 40 289123   50 609155 200, 50, SCAFFOLD51732:9156-9605
036 2005 bosTau2 4361 105 564259   50 2525381 997, 50, scaffold4383:34413-36456
037 2006 bosTau3 411 51 38673   50 270212 1000, 50, chr10:68862764-68864813
038 2007 bosTau4 437 53 52814   50 376407 1000, 50, chr10:75537624-75539673
039 2009 bosTau5 435 53 51742   50 376650 1000, 50, chr10:75464684-75466733
040 2009 bosTau6 789 670 463109   100 87080 923, 1, chr22:31476636-31478482
041 2011 bosTau7 413 55 39706   50 141131 1000, 50, chr10:75201034-75203083
042 2014 bosTau8 789 670 463109   100 87080 923, 1, chr22:31476636-31478482
043 2009 bosTauMd3 789 670 463109   100 87080 923, 1, chr22:31476636-31478482
044 2006 braFlo1 31 484 14260   417 12668 375, 1, chrUn:879323570-879324320
045 2008 braFlo2 22 439 8529   411 9064 36, 1, Bf_V2_248:1229532-1229604
046 1880 braRap1 12 104 3193   2810 47557 587, 472, chrUn_JH977260:73788-75433
047 2007 bruMal1 55 50 6093   1 18780 87, 1, Bmal_supercontig14387:293-467
048 2014 bruMal2 46 124.5 12221   431.5 63506 1000, 20, Bmal_v3_scaffold83:22898-24917
049 2013 bubBub1 2383 163 395268   100 251657 990, 100, KI418684:2409965-2412044
050 2014 bucRhi1 31 114 5089   78 3263 327, 10, KL526600:8925-9588
052 2011 burXyl1 65 601 33110   301 19553 977, 300, scaffold00460:102617-104870
053 2010 caeAng1 414 41 16726   2 1802 46, 2, scafRNAPATH105:2285-2378
054 2012 caeAng2 461 46 19505   2 1495 46, 2, Cang_2012_03_13_00008:384957-385050
055 2008 caeJap1 135 58 10431   186 27893 687, 10, chrUn:37794313-37795696
056 2009 caeJap2 765 103 130030   1018 891958 707, 10, chrUn:150512438-150513861
057 1880 caeJap2a 764 103 129273   1018 890958 707, 10, Cjap_Contig4853:3969-5392
059 2010 caeJap4 16 98.5 3188   20 1468 1000, 20, Scaffold17129:65445-67464
060 2007 caePb1 115 44 9160   164 37674 476, 10, chrUn:52430125-52431086
061 2008 caePb2 83 37 3814   222 63681 230, 10, chrUn:74484521-74484990
062 2010 caePb3 89 37 4915   222 74680 230, 10, Scfld02_75:384084-384553
063 2005 caeRem1 58 96 10213   133.5 11238 678, 10, SuperCont3:723391-724756
064 2006 caeRem2 58 96 10213   133.5 11238 678, 10, chrUn:13919319-13920684
065 2007 caeRem3 46 50 5760   197.5 14178 460, 10, chrUn:27560772-27561701
066 2007 caeRem4 46 50 5760   197.5 14178 460, 10, Crem_Contig253:25277-26206
067 2010 caeSp111 4 194.5 760   20 80 333, 20, Scaffold629:32984714-32985399
068 2012 caeSp51 14 34 730   12.5 894 201, 3, Csp5_scaffold_09411:792-1196
069 2010 caeSp71 535 47 30250   213 312209 162, 20, Scaffold11:29462-29805
070 2010 caeSp91 26 217.5 7172   8745 180575 1000, 20, Scaffold7498:303469-305488
071 2014 calAnn1 89 127 16337   1006 168943 440, 38, KL218155:301090-302007
072 2007 calJac1 1597 42 129367   182 377725 937, 10, Contig4771:110891-112774
073 2009 calJac3 1516 43 116646   183.5 452860 807, 10, chr3:111956760-111958383
074 2013 calMil1 31 123 8335   100 70257 1000, 100, KI635945:3331497-3333596
075 2011 camFer1 11 205 2059   129 2031 237, 2, KB018701:319294-319769
076 2004 canFam1 12 153 2669   210.5 8118 104, 1, chr18:45376349-45376557
077 2005 canFam2 32 199.5 8095   1 5245 746, 1, chrUn:76334072-76335564
078 2011 canFam3 34 175.5 8234   10 4545 746, 10, chrUn_JH374132:3424-4925
081 2014 capCar1 4 105 618   48 354 139, 26, KL359104:23556-23859
082 2012 capHir1 627 41 71810   100 546475 988, 16, chr16:40339512-40341503
083 2014 carCri1 4 161 644   210.5 878 52, 13, KK509558:67998-68114
084 2005 cavPor2 393 427 164744   100 166667 986, 100, scaffold_291164:123135-125206
085 2008 cavPor3 3 145 552   100 961 313, 100, scaffold_799:9280-10005
086 2002 cb1 81 163 20408   145 39126 645, 10, chrUn:51532611-51533910
087 2005 cb2 86 153 21033   163.5 42461 645, 10, chrI:9244132-9245431
088 2007 cb3 80 148.5 19176   166.5 39580 645, 10, chrI:9355978-9357277
089 2011 cb4 86 153 20969   151.5 40114 645, 10, chrI:11247250-11248549
100 2012 cerSim1 1818 68 129697   100 270005 815, 100, JH767775:6384924-6386653
101 2014 chaVoc1 47 200 13700   1514 133699 780, 257, KL409415:13594818-13596634
102 2014 chaVoc2 47 200 13700   1514 133699 780, 257, KL873469:13594818-13596634
103 2013 cheMyd1 129 204 37111   798 277853 314, 27, KB535131:1778822-1779476
104 2012 chiLan1 1183 70 101029   100 267937 996, 100, JH721987:2542897-2544988
105 2013 chlSab1 23634 81 2123928   10 396229 923, 1, chrX:117110178-117112024
106 2014 chlSab2 23631 81 2123656   10 396199 923, 1, chrX:117110178-117112024
107 2014 chlUnd1 5 293 1223   129 617 310, 65, KK747264:28313-28997
108 2008 choHof1 104 54.5 14520   145.5 33892 986, 100, scaffold_56240:3133-5204
109 2012 chrAsi1 3416 76 339291   100 720504 991, 100, JH823765:402000-404081
110 2011 chrPic1 7555 79 738667   50 1230115 64, 1, JH584466:5301285-5301413
111 2014 chrPic2 6315 77 629230   206 2593694 1000, 10, chrUn_KK083066v1:1300793-1302802
112 2002 ci1 28 311.5 8955   50 11060 833, 50, Scaffold_7:289989-291704
113 2005 ci2 2 472.5 945   173 346 843, 296, scaffold_403:40134-42115
114 2011 ci3 22 258.5 6455   50 9493 597, 50, chrUn_NW_004190451v1:5050-6293
115 2003 cioSav1 8 124 1554   100 2755 296, 100, ps_146:263977-264668
116 2005 cioSav2 6 402.5 2394   200 1668 636, 10, reftig_72:2536022-2537303
117 2015 colAng1 5690 77 626146   50 1472786 996, 50, NW_012119888v1:35718-37759
118 2013 colLiv1 19 116 3824   1290 32865 33, 57, KB379196:2050-2172
119 2014 colStr1 5 161 910   308 1203 362, 113, KK530485:3407-4243
120 2012 conCri1 1110 72 108033   100 233431 924, 100, JH655880:49229854-49231801
121 2014 corBra1 41 90 7520   1445 112176 259, 28, KK718436:193091-193636
122 2014 corCor1 21 81 2189   1027 27602 81, 1, KL997637:955359-955521
123 2013 cotJap1 1122 33 38101   68 67651 214, 1, DF262918:84572-85000
124 2013 criGri1 588 217 196516   1481.5 1359815 422, 10, KE379019:554914-555767
125 2011 criGriChoV1 213 162 53736   1526 472877 369, 10, NW_003615838v1:158557-159304
126 2014 cucCan1 113 242 41656   972 203191 961, 69, KL448150:311854-313844
127 2014 cynSem1 78 311.5 27891   935.5 165198 568, 38, chr11:13981930-13983103
128 2014 cypVar1 3240 89 423504   1 2210432 1000, 1, KL653732:89449-91449
129 2003 danRer1 1280 57 186413   10 322061 1000, 10, chr25:16217228-16219237
130 2014 danRer10 575 174 105525   10 17550 484, 10, chr5:1032421-1033398
131 2004 danRer2 1150 58 191859   10 223764 1000, 10, chr10:26174984-26176993
132 2005 danRer3 819 58 88143   10 121196 776, 10, chrUn:112388525-112390086
133 2006 danRer4 726 65.5 121967   14 135012 705, 11, chr25:30060270-30061690
134 2007 danRer5 1559 170 288298   100 155702 73, 1, chr21:35548773-35548919
135 2008 danRer6 1421 133 225674   100 142101 1000, 100, Zv8_scaffold431:54613-56712
136 2010 danRer7 1245 164 217595   100 124500 900, 100, chr22:2241720-2243619
137 2005 dasNov1 55 123 12971   111 31368 681, 100, scaffold_3005:3743-5204
138 2008 dasNov2 109 136 25865   100 58752 836, 100, scaffold_3394:70496-72267
139 2011 dasNov3 239 46 16270   50 94236 677, 50, JH564516:24848-26251
140 2014 dicLab1 275 423 116519   203 134149 994, 20, HG916850:2956140-2958147
141 2008 dipOrd1 219 46 46012   379 102683 1000, 100, scaffold_2463:9467-11566
142 2013 dirImm1 505 175 132528   2 32073 999, 1, nDi_2_2_scaf00035:47420-49418
143 2003 dm1 9 252 2984   20 1237 604, 20, chrU:5250525-5251752
144 2004 dm2 8 362 2818   20 1217 604, 20, chrU:5250525-5251752
145 2006 dm3 20 286 4907   100 423940 276, 20, chrU:4943122-4943693
146 2014 dm6 15 333 4828   100 1340 276, 20, chrUn_DS483709v1:12934-13505
147 2003 dp2 113 64 11633   10 9049 784, 10, Contig4969_Contig4496:202614-204191
148 2004 dp3 136 79.5 17354   79.5 14988 485, 11, chrU:7044759-7045739
149 2006 dp4 183 81 19720   50 18528 798, 50, chrXL_group1e:8376310-8377955
150 2012 droAlb1 4360 30 131320   22 152454 76, 1, JH853217:889-1041
151 2004 droAna1 103 252 28853   100 10300 943, 100, 2448822:95133-97118
152 2005 droAna2 32 160 7905   701 72786 791, 25, scaffold_13266:420335-421941
153 2006 droAna3 35 143 8663   671 75001 707, 25, scaffold_13230:483470-484908
154 2013 droBia2 14 116.5 2103   20 294 447, 20, KB462730:148150-149063
155 2013 droBip2 26 103.5 3925   20 520 409, 20, KB464242:790791-791628
156 2013 droEle2 22 205 4879   20 440 480, 20, KB458480:1051747-1052726
157 2005 droEre1 8 86.5 1545   731 6855 773, 25, scaffold_4784:23686196-23687766
158 2006 droEre2 14 221 4384   239 7433 763, 25, scaffold_4784:18133045-18134595
159 2013 droEug2 17 52 1627   20 237 72, 1, AFPQ02002129:815-959
160 2013 droFic2 11 352 3277   20 220 424, 20, KB457328:1582-2449
161 2005 droGri1 17 76 2908   444 11143 734, 312, scaffold_24659:1579-3358
162 2006 droGri2 48 60.5 5904   430.5 52107 774, 25, scaffold_15245:16809148-16810720
163 2013 droKik2 12 102 1812   20 1721 361, 20, KB458730:24774-25515
164 2013 droMir2 122 72 16465   10 57520 1000, 10, chr2:9770771-9772780
166 2005 droMoj2 22 219.5 7748   366.5 30847 969, 25, scaffold_6496:4573125-4575087
167 2006 droMoj3 16 343 6118   426 29359 859, 25, scaffold_6496:14181729-14183471
168 2005 droPer1 28 402 10502   100 10914 937, 100, super_12:105769-107742
169 2013 droPse3 12 51 1309   86 3307 718, 50, chr3:13529933-13531418
170 2013 droRho2 35 167 7228   20 1286 454, 20, KB451407:7018-7945
171 2005 droSec1 17 399 6822   100 5318 765, 100, super_59:77146-78775
172 2005 droSim1 109 106 23001   298 40703 801, 10, chr2L:4623692-4625303
173 2014 droSim2 104 58 5999   10 1818 359, 8, chr2R:7425888-7426613
174 2013 droSuz1 71 185 16489   1565 196054 364, 76, KI420423:11753-12556
175 2013 droTak2 13 102 2070   20 260 472, 20, KB461286:709634-710597
176 2004 droVir1 48 328.5 15839   25 16648 698, 25, scaffold_10:2740496-2741916
177 2005 droVir2 13 232 3421   1415 46365 503, 25, scaffold_13324:149342-150372
178 2006 droVir3 12 341 4206   1536.5 45200 423, 25, scaffold_13324:149231-150101
179 2006 droWil1 23 248 8712   1330 51159 759, 50, scaffold_181150:697726-699293
180 2006 droWil2 23 248 8712   1330 51159 759, 50, CH964291:697726-699293
181 2004 droYak1 65 340 25549   250 24358 955, 50, chrU:40768288-40770247
182 2005 droYak2 99 170 26922   54 37713 684, 10, chr2L:22155365-22156742
183 2006 droYak3 85 143 20479   10 23713 684, 10, chr2L:22155365-22156742
187 2005 echTel1 89 83 17114   100 22024 805, 100, scaffold_272928:13200-14909
188 2012 echTel2 3871 93 620444   100 656358 998, 100, JH980317:1376657-1378752
189 2014 egrGar1 112 213.5 33121   1093.5 229589 998, 134, KK502338:445846-447975
190 2013 eidHel1 27 45 1294   1 186 68, 1, KE769079:2720-2856
191 2012 eleEdw1 1643 71 141553   100 311199 1000, 100, JH947463:2106240-2108339
192 2012 eptFus1 1641 75 188916   100 378407 988, 100, JH977647:11513546-11515621
193 2007 equCab1 17 457 5982   100 6200 715, 100, chr2:10720193-10721722
194 2007 equCab2 4 160.5 610   1909 18507 258, 295, chr22:17653073-17653883
195 2014 equPrz1 39 49 5163   49 12408 78, 11, KK955445:38997-39163
196 2006 eriEur1 343 435 146738   100 209198 1000, 100, scaffold_366352:52823-54922
197 2012 eriEur2 3596 70 265454   100 1205265 1000, 100, JH835375:3514396-3516495
198 2014 esoLuc1 9785 81 734131   15 1227519 950, 10, LG19:14032217-14034126
200 2014 eurHel1 2 89.5 179   436 872 113, 451, KK569808:53808-54484
202 2013 falChe1 27 206 7614   685 35918 51, 10, KB397780:7020361-7020472
203 2013 falPer1 6 48.5 530   631.5 4836 36, 10, KB391040:3398436-3398517
204 1880 felCat1 1343 353 504058   874 2708782 1000, 100, scaffold_217423:45453-47552
205 2006 felCat3 1343 353 504058   874 2708782 1000, 100, scaffold_217423:45453-47552
206 2008 felCat4 9736 503 4582767   10 9398414 1000, 10, chrA2:8725380-8727389
207 2011 felCat5 27 72 6437   20 100569 488, 20, chrB2:22462351-22463346
208 2014 felCat8 630 55 50300   10 89447 895, 14, chrB3:27250577-27252380
209 2013 ficAlb2 632 77 75592   40.5 206854 982, 1, chr7:28154426-28156390
210 2002 fr1 76 155.5 19306   50 16684 71, 1, chrUn:149577204-149577346
211 2004 fr2 5 313 1682   512 2231 47, 1, chrUn:336404518-336404612
212 2011 fr3 6 229 1827   286 2291 47, 1, HE592038:5063-5157
213 2014 fulGla1 8 336.5 2583   103.5 1637 450, 20, KK597768:8602-9521
214 2010 gadMor1 168 53 11363   270 70748 51, 1, CAEA01526699:46-148
215 2004 galGal2 114 40 12930   124 17674 778, 21, chr3:68417113-68418689
216 2006 galGal3 729 37 34199   500 325853 479, 10, chrUn_random:55035794-55036761
217 2011 galGal4 55 401 22946   100 31537 805, 100, chr19:3903221-3904930
218 2015 galGal5 1 33 33   795 795 33, 795, chrUn_NT_465606v1:9086-9946
219 2014 galVar1 58964 61 5626241   419 24866346 997, 1, NW_007727116v1:311725-313719
220 2006 gasAcu1 8 46.5 1970   117.5 2520 841, 100, chrUn:38727446-38729227
222 2009 gavGan0 30236 134 5187944   5000 145799649 915, 10, scaffold24725:12789-14628
223 2014 gavSte1 5 164 848   318 2312 269, 245, KK640233:828-1610
224 2012 geoFor1 32 105.5 4877   945.5 51025 617, 11, JH739922:1318693-1319937
226 2009 gorGor2 6585 247 2365617   10 499615 1000, 10, chr10_101645027_418909:206049-208058
227 2011 gorGor3 6926 246 2475426   10 533805 1000, 10, chr10:101539188-101541197
228 2014 gorGor4 8691 94 1514940   25 982883 246, 1, chr9:24397320-24397812
230 2009 haeCon1 25 39 1031   10 1745 58, 10, Hcon_Contig0056815:13389-13514
231 2013 haeCon2 5378 149 831727   55 351011 700, 1, scaffold_63:260903-262303
232 2014 halAlb1 11 126 1936   370 3807 466, 102, KK641449:26277-27310
233 2014 halLeu1 14 280 4342   95 1676 194, 10, KL869356:8708537-8708934
234 2011 hapBur1 965 95 135908   20 374038 975, 20, JH425754:7557-9526
235 2011 hetBac1 3 228 1282   20 60 1000, 20, GL996479v1:885362-887381
236 2011 hetGla1 743 313 285174   1994 2914751 785, 43, JH165660:4306-5918
237 2012 hetGla2 595 70 44604   100 201552 1000, 100, JH602085:17402968-17405067
238 2009 hg19 1 200 200   3000000 3000000 200, 3000000, chrY:10104354-13104753
243 2013 hg38 12 78 974   440 56689 125, 20, chrUn_KI270442v1:175618-175887
252 2012 jacJac1 2666 63 196366   100 569918 1000, 100, JH725440:52488719-52490818
253 2011 latCha1 2038 77 159059   100 504858 955, 100, JH127253:476850-478859
255 2014 lepDis1 1 50 50   229 229 50, 229, KK681583:9399-9727
256 2011 lepOcu1 2079 95 232474   100 466733 1000, 100, chrLG4:37780111-37782210
257 2013 lepWed1 2022 63 135843   100 1218867 1000, 100, KB715312:1023296-1025395
258 2013 letCam1 1453 69 123952   100 739039 280, 39, KE994354:70338-70936
259 1880 linHum0 179 48 10176   100 20986 480, 100, NW_012159984:28893-29952
260 2013 lipVex1 292 92 66483   985.5 386576 876, 10, KE557659:158624-160385
261 2012 loaLoa1 376 382 123384   215 94547 604, 20, JH712068v1:803529-804756
262 2005 loxAfr1 79 44 11426   206 80801 687, 284, scaffold_10531:71539-73196
263 2008 loxAfr2 78 165.5 20735   1078 180887 989, 100, scaffold_3386:17920-19997
264 2009 loxAfr3 11 45 1924   398 9784 731, 100, scaffold_211:333226-334787
265 2007 macEug1 7319 57 504656   10 562759 146, 1, Scaffold27901:25044-25336
266 2009 macEug2 11689 55 752361   50 1102638 146, 1, GL058785:13153-13445
267 2013 macFas5 1138 106.5 145024   204.5 1039415 849, 10, chr14:81860376-81862083
268 2015 macNem1 1828 95 237662   50 834836 982, 25, NW_012016132v1:18826350-18828338
269 2014 manPen1 37129 101 5536376   1 13090743 1000, 1, KN006700:349054-351054
270 2014 manVit1 25 231 8844   1303 65245 701, 296, KK732740:655429-657126
272 2012 mayZeb1 1831 95 241336   100 682313 1000, 100, JH720538:3252564-3254663
273 2013 megLyr1 33 38 1716   1 185 83, 1, KI087181:1999-2165
274 2009 melGal1 834 127 136229   100 661041 169, 1, chr3:54352580-54352918
275 2014 melGal5 84 181 17431   100 76065 724, 100, chrZ:7873702-7875249
278 2008 melInc2 3 77 211   201 513 98, 201, MiV1ctg3:286050-286446
279 2011 melUnd1 39 89 5925   41 36796 334, 20, JH556232:114057-114744
280 2014 merNub1 2 154.5 309   361 722 245, 311, KK701714:10568-11368
281 2013 mesAur1 3589 71 248381   100 755166 212, 100, KB708269:3930600-3931123
282 2014 mesUni1 4 347 1434   124.5 451 332, 23, KK817080:7082-7768
283 1880 micMur0 295 256 90483   780 749299 997, 100, GeneScaffold_4747:166512-168605
284 2007 micMur1 124 124.5 33320   952.5 207469 969, 100, scaffold_5185:107104-109141
285 2015 micMur2 774 90 85250   50 267164 999, 25, KQ057470v1:2292330-2294352
286 2017 micMur3 325 95 73918   50 262987 898, 10, chr2:108635511-108637316
287 2012 micOch1 6788 65 483435   100 1507707 993, 100, chr6:54381083-54383168
288 2011 mm10 2 390.5 781   25879.5 51759 477, 1759, chrX_GL456233_random:239940-242652
292 1880 mm5 204 48.5 30180   100 76884 921, 100, chr6:132460596-132462537
293 2005 mm6 117 48 17647   100 48212 768, 100, chr14:100566071-100567706
294 2005 mm7 45 48 5475   100 64491 451, 100, chr15:68974498-68975499
295 2006 mm8 6 161 1257   162.5 50878 520, 353, chr14:87009574-87010966
296 2007 mm9 2 390.5 781   25879.5 51759 477, 1759, chrX_random:239940-242652
297 2004 monDom1 18 53.5 1891   127 11341 696, 100, scaffold_14754:178069-179560
298 2005 monDom2 5 428 2012   100 520 870, 100, scaffold_38:23849795-23851634
299 2006 monDom4 9 183 3070   1000 21732 870, 1, chr1:400420041-400421781
300 2006 monDom5 9 183 3070   1000 21732 870, 1, chr1:424248968-424250708
301 2013 musDom2 1284 85 165577   1 473996 1000, 1, KB855954:134298-136298
302 2011 musFur1 1009 84 107706   44 286510 1000, 20, GL897138:9717-11736
303 2013 myoBra1 356 119 85889   1109 766318 1000, 31, KE163605:2655193-2657223
304 2012 myoDav1 303 151 56967   1283 942238 502, 19, KB106370:3092722-3093744
305 2006 myoLuc1 42 47 6392   1551 125787 388, 100, scaffold_150441:136761-137636
306 2010 myoLuc2 7 39 357   410 3363 75, 119, GL429781:8032929-8033197
307 2014 nanGal1 730 126 149781   902.5 980462 740, 12, KL200152:4088120-4089611
308 2015 nanPar1 1716 194 477991   974 2590489 552, 12, KN907832v1:31307-32422
309 2014 nasLar1 614 43 93736   7 126885 117, 1, chr1:6190345-6190579
310 2013 necAme1 459 54 28538   100 92887 366, 100, KI657476v1:37386-38217
311 2007 nemVec1 25 378 10288   829 17106 769, 1, scaffold_3968:6459-7997
312 2011 neoBri1 5040 95 1321574   20 665865 998, 20, JH422308:3325010-3327025
313 2014 nipNip1 41 154 11937   1090 77358 514, 15, KL411148:2104426-2105468
314 2010 nomLeu1 859 141 220161   532 1139352 999, 100, GL397299:16863535-16865632
315 2011 nomLeu2 859 141 220161   532 1139352 999, 100, GL397299:16863535-16865632
316 2012 nomLeu3 861 141 220464   519 1139552 999, 100, chr5:41669854-41671951
317 2014 notCor1 174 91.5 17942   51 21717 407, 1, KL665414:596304-597118
318 1880 ochPri0 569 101 138948   1065 1840608 994, 100, GeneScaffold_4726:276480-278567
319 2008 ochPri2 313 55 35317   1365 1110261 967, 100, scaffold_3914:61889-63922
320 2012 ochPri3 1958 69 148238   100 499781 890, 100, JH802177:1348834-1350713
321 2012 octDeg1 2582 68 231489   100 464548 985, 100, JH651571:12809669-12811738
322 2013 odoRosDiv1 2581 68 180258   50 263661 970, 50, KB229427:1083192-1085181
323 2013 oncVol1 10 89.5 2046   1 18211 739, 1, HG738137v1:12037947-12039425
324 2014 opiHoa1 80 170.5 23360   1723.5 216549 855, 28, KK733898:82987-84724
325 2013 orcOrc1 2677 66 181922   50 357696 943, 50, NW_004438742v1:126518-128453
326 2011 oreNil1 1903 93 208888   20 734264 969, 20, GL831201:3474999-3476956
327 2007 ornAna1 793 49 70053   103 148119 718, 10, Contig3645:38619-40064
328 2007 ornAna2 793 49 70053   103 148119 718, 10, chrUn_DS182721v1:38619-40064
329 2012 oryAfe1 3595 65 293465   100 691489 998, 100, JH863829:9451309-9453404
330 2005 oryCun1 122 278.5 44566   462.5 91832 978, 100, scaffold_172390:787-2842
331 2009 oryCun2 12 44.5 836   446 9055 327, 185, chr13:6520795-6521633
332 2006 oryLat1 141 144 25310   10 215389 561, 10, chrUn:20300712-20301843
333 2005 oryLat2 141 144 25310   10 253399 445, 10, ultracontig221:437957-438856
335 2011 otoGar3 3569 86 332700   39 663694 985, 20, GL873641:2218538-2220527
336 2010 oviAri1 5934 53 394316   37 1966190 264, 1, chr15:8985870-8986398
337 2012 oviAri3 149 193 51933   215 178445 46, 3, chr3:3466521-3466615
338 2015 oxyTri2 523 37 30028   50 25856 186, 1, chrMACsb310:15510646-15511018
339 2013 panHod1 321 129 65178   1092 702884 628, 10, KE118776:1218541-1219806
340 2012 panPan1 63 133 11209   20 22114 33, 1, JH650468:842203-842269
341 2015 panPan2 70 160 13388   20 1045522 35, 1, chr4:127787143-127787213
342 2013 panRed1 123 56 6626   10 3069 62, 10, KB454926:42673-42806
343 2013 panTig1 59 111 12591   700 69429 398, 9, KE721804:6447970-6448774
344 2003 panTro1 5719 388 2244063   100 3504041 998, 100, chr6:137473031-137475126
345 2006 panTro2 692 52 62006   240 238273 717, 10, chr10_random:5205395-5206838
346 2010 panTro3 472 54 44241   238.5 180280 908, 10, chr2B:124438762-124440587
347 2011 panTro4 472 54 44241   238.5 180280 908, 10, chr2B:124438762-124440587
348 2016 panTro5 2937 199 537385   100 3625772 199, 10, chr12_NW_015974005v1_random:1130-1537
349 2012 papAnu2 727 138 144060   50 96682 46, 1, chr4:20965571-20965663
350 2008 papHam1 22041 56 1338445   50 2303596 376, 50, scaffold4259:86690-87491
351 2014 pelCri1 3 72 517   186 808 386, 173, KK471910:16412-17356
352 2011 pelSin1 126 138 35062   411.5 167243 398, 10, JH212629:287260-288065
353 2013 perManBai1 7908 80 846184   50 1552640 1000, 50, KI615759:2266069-2268118
354 2007 petMar1 542 47 48234   10 42185 746, 10, Contig3178:18125-19626
355 2010 petMar2 31 86 5681   732 39461 617, 100, GL479790:15647-16980
356 2014 phaCar1 2 206 412   79 158 261, 100, KL416242:66648-67269
357 2014 phaLep1 14 179 2930   310 4227 343, 85, KK448216:3226-3996
358 2014 phoRub1 4 288.5 1016   195.5 823 373, 83, KK425162:48893-49721
359 2013 phyCat1 684 82.5 86555   100 130377 1000, 1, KI402232:538054-540054
360 2014 picPub1 59 83 12175   970 106482 111, 28, KL217012:74310-74559
361 2013 poeFor1 848 75 84492   1 328834 972, 1, KI520524:847-2791
362 2014 poeRet1 1124 87 157426   1 421252 988, 1, chrLG12:26078504-26080480
363 1880 ponAbe1 1528 40 90824   133.5 275853 662, 10, Contig208:1185633-1186966
364 2007 ponAbe2 2239 54 444541   100 829820 769, 1, chr11:46659515-46661053
365 2014 priExs1 49 121 12100   1773 95166 181, 38, scaffold470:42605-43004
366 2007 priPac1 121 49 10688   209 31254 90, 1, chrUn:114913780-114913960
368 2014 priPac3 168 49.5 13153   274.5 50322 90, 1, Ppa_Contig2432:805-985
369 2008 proCap1 116 38 5205   534.5 65619 53, 100, scaffold_8867:32393-32598
370 2013 pseHum1 775 142 173055   10 547111 1000, 10, KB221227:5459003-5461012
371 2012 pteAle1 97 127 19728   1023 161616 421, 16, KB031157:14150143-14151000
372 2014 pteGut1 1 282 282   720 720 282, 720, KL237369:530-1813
373 2013 ptePar1 3 31 102   1 3 40, 1, KE827285:1815-1895
374 2008 pteVam1 68 43.5 9173   301.5 27212 971, 100, scaffold_4327:120126-122167
375 2011 punNye1 1574 95 242736   20 332782 992, 20, JH419321:67178-69181
376 2014 pygAde1 42 113 7740   1160.5 93198 78, 17, KL224983:2418932-2419104
377 2013 pytBiv1 21222 101 2315791   99 2845128 649, 10, KE957835:3697-5004
382 2005 rheMac1 2816 39 116369   50 214725 205, 50, SCAFFOLD120616:17732-18191
383 2010 rheMac3 288 192.5 71777   1140.5 887215 949, 27, chr15:33329332-33331256
384 2015 rheMac8 80 99.5 20122   917 437685 823, 20, chr7:1436259-1437924
385 2016 rhiBie1 4262 228 1007049   1 2148972 965, 1, NW_016817388v1:689035-690965
386 2013 rhiFer1 2 42.5 85   1 2 45, 1, KI143993:8550-8640
387 2014 rhiRox1 187 158 50999   529 184770 584, 11, KN296100v1:378785-379963
388 1880 ricCom1 41 332 13808   738 38675 787, 3, EQ973819:99412-100988
389 2003 rn3 574 143 146802   50 425043 72, 1, chr4:1247786-1247930
390 2004 rn4 567 141 142452   50 424693 72, 1, chr4:1247786-1247930
391 2012 rn5 64 516 32231   50 28921 712, 1, chr3:45275318-45276742
392 2014 rn6 719 290 280406   50 1258566 712, 1, chr3:40184108-40185532
398 2011 saiBol1 1541 77 139356   100 303093 1000, 100, JH378136:528784-530883
400 2011 sarHar1 17494 220 2993318   158 6574378 958, 10, chr1_GL834475_random:882665-884590
401 2013 sebNig1 168 55.5 11782   54.5 11235 82, 2, KI499294:4621-4786
402 2013 sebRub1 119 55 9711   51 8253 142, 1, KI444651:3586-3870
403 2014 serCan1 213 97 36640   20 33876 971, 1, HG009242:4536330-4538272
404 2006 sorAra1 229 330 79670   100 75086 895, 100, scaffold_247593:25660-27549
405 2008 sorAra2 3389 75 359891   100 822102 992, 100, JH798160:15867029-15869112
406 2008 speTri1 99 46 12167   879 197520 835, 100, scaffold_1259:158788-160557
407 2011 speTri2 2964 95 353556   100 565083 1000, 100, JH393486:3045059-3047158
408 2014 stePar1 554 65 47063   1 120402 952, 1, KK580894:321554-323458
409 1880 strCam0 20 243 7267   836.5 40260 184, 13, superscaffold45:7169362-7169742
410 2014 strCam1 19 246 7125   759 39346 184, 13, KL206666:4120006-4120386
411 2005 strPur1 1291 153 303896   50 238579 89, 1, Scaffold16400:576-754
412 2006 strPur2 367 55 25281   50 79238 35, 1, Scaffold12735:108654-108724
413 2009 strPur3 989 56 64991   96 187408 35, 1, Scaffold740:110486-110556
414 2011 strPur4 1612 100 326953   50 206009 425, 3, Scaffold112:361603-362455
416 2014 strRat2 2 54.5 109   6 12 67, 1, chrUn_LN609483v1:243-377
418 2009 susScr1 371 43 34151   100 66500 986, 100, chr2:139016697-139018768
419 2009 susScr2 371 43 34151   100 66500 986, 100, chr2:139016697-139018768
421 1880 taeGut0 212 45 20495   442 116920 624, 10, Contig233:50949-52206
422 2008 taeGut1 223 45 22373   100 22300 689, 100, chr21_random:54357-55834
423 2013 taeGut2 219 44 21273   100 21900 624, 100, chr27:56676-58023
425 2013 takFla1 365 241 91817   788 407496 503, 1, KE121297:329-1335
426 2013 tarIhg38 12 78 974   440 56689 125, 20, chrUn_KI270442v1:175618-175887
427 2008 tarSyr1 331 70 45530   191 102767 892, 100, scaffold_111889:3660-5543
428 2013 tarSyr2 189 56 17645   20 9572 1000, 20, KE939253v1:939796-941815
429 2014 tauEry1 1 50 50   394 394 50, 394, KL466072:20829-21322
430 2004 tetNig1 64 272.5 21868   1000 53904 336, 59, chr5:807217-807947
431 2007 tetNig2 70 298 25569   500 32404 336, 59, chr5:799217-799947
432 2014 tinGut1 18 96 3855   1086 21982 519, 68, KL400865:236113-237218
433 2014 tinGut2 18 96 3855   1086 21982 519, 68, KL895544:236113-237218
434 2005 triCas1 75 100 8201   50 6900 214, 50, Contig5855_Contig1469:226794-227271
435 2005 triCas2 63 62 5442   50 313244 412, 50, chrUn_46:283716-284589
436 2011 triMan1 5748 75 527972   100 726640 1000, 100, JH594622:8537918-8540017
437 2011 triSpi1 3 55 806   10 230 705, 10, GL622790v1:172202-173621
438 2014 triSui1 37 138 7959   1449 82883 120, 68, KL363219v1:83933-84240
440 2013 tupChi1 914 220.5 290632   987.5 1823897 861, 16, KB320907:3306581-3308318
441 2008 turTru1 112 41.5 15556   388 52461 993, 100, scaffold_108458:6669-8754
442 2011 turTru2 5612 70 466776   188.5 1979352 44, 1, JH496197:2095-2183
443 2014 tytAlb1 2 170 340   326 652 289, 220, KK379918:2163-2960
444 2014 ursMar1 205 41 12130   3384 708704 711, 49, KK498595:3401141-3402611
445 2007 venter1 64 411.5 26995   100 64592 862, 20, chr2:102870978-102872721
446 2008 vicPac1 221 251 71912   276 310711 993, 100, scaffold_812:411693-413778
447 2013 vicPac2 1245 69 115488   369 430947 685, 20, KB632527:971889-973278
448 1880 vicVic1 218 252.5 71401   263 309237 993, 100, scaffold_812:411693-413778
449 2016 xenLae2 2660 43 112843   265 1906995 50, 10, chr6S:105116072-105116181
450 2004 xenTro1 140 177.5 37717   889.5 437093 94, 1, scaffold_26179:153-341
451 2005 xenTro2 116 229.5 33928   806.5 320973 83, 1, scaffold_13788:6263-6429
452 2009 xenTro3 116 229.5 33928   806.5 320973 83, 1, GL185958:6263-6429
453 2012 xenTro7 98 82.5 16149   201 69741 775, 100, KB022861:7377-9026
454 2016 xenTro9 172 105.5 27368   100 99243 775, 100, chrUn_NW_016684502v1:7377-9026
455 2012 xipMac1 548 50 32896   131 334271 30, 1, JH556915:15756-15816
457 2013 zonAlb1 538 79 50834   1 134738 990, 1, KB913055:7474487-7476467
Retrieved from "https://genomewiki.ucsc.edu/index.php?title=GapOverlap&oldid=23973"