GapOverlap: Difference between revisions

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== BUGS ==
There is something wrong with the ''median'' calculation.  It is not correct.
== methods ==
== methods ==


Line 13: Line 16:
The ''gap total'' is the sum of the sizes of all the gaps
The ''gap total'' is the sum of the sizes of all the gaps
involved.
involved.
== table features==
== table features==
The table columns can be sorted, click on the up/down arrow icon
The table columns can be sorted, click on the up/down arrow icon

Revision as of 14:56, 16 April 2017

BUGS

There is something wrong with the median calculation. It is not correct.

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 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.

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

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

001 2013 CHM1 85 86 10897   88 65164 319 10 chr6:108876987-108877634
002 2014 acaChl1 5 17 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   166 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 24 6694   258 26105 318 100 chr4:54548520-54549255
014 2003 anoGam1 7 528 3139   1 21041 1000 384 chr2L:5019927-5022310
015 2013 apaSpi1 607 61 34340   1 56961 86 10 KB929338:2579176-2579357
017 2004 apiMel1 216 5 12150   1 24454 64 1 Group14.17:517485-517613
018 2005 apiMel2 133 5 7371   5 19757 168 50 Group4:4855105-4855490
019 2005 apiMel3 199 62 16045   5 27354 198 50 Group15:1672512-1672957
020 2010 apiMel4 226 52.5 13378   5 24561 167 50 Group14:1674117-1674500
021 2008 aplCal1 25 77 3383   1 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   6 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   1 1964877 647 1 KB872443:19678-20972
030 2013 balAcu1 211 149 57860   821 371511 926 15 KI537556:2252563-2254429
031 2014 balPav1 5 27 1303   216 1098 391 46 KL482982:8685-9512
032 2014 bisBis1 8184 72 712109   1 947641 933 100 KN265089v1:519297-521262
034 2011 bosMut1 139 83 27917   1274 256420 71 14 JH880933:479978-480133
035 2004 bosTau1 6550 4 289123   5 609155 200 50 SCAFFOLD51732:9156-9605
036 2005 bosTau2 4361 105 564259   5 2525381 997 50 scaffold4383:34413-36456
037 2006 bosTau3 411 51 38673   5 270212 1000 50 chr10:68862764-68864813
038 2007 bosTau4 437 53 52814   5 376407 1000 50 chr10:75537624-75539673
039 2009 bosTau5 435 53 51742   5 376650 1000 50 chr10:75464684-75466733
040 2009 bosTau6 789 67 463109   1 87080 923 1 chr22:31476636-31478482
041 2011 bosTau7 413 55 39706   5 141131 1000 50 chr10:75201034-75203083
042 2014 bosTau8 789 67 463109   1 87080 923 1 chr22:31476636-31478482
043 2009 bosTauMd3 789 67 463109   1 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   281 47557 587 472 chrUn_JH977260:73788-75433
047 2007 bruMal1 55 5 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   1 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   2 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 5 5760   197.5 14178 460 10 chrUn:27560772-27561701
066 2007 caeRem4 46 5 5760   197.5 14178 460 10 Crem_Contig253:25277-26206
067 2010 caeSp111 4 194.5 760   2 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   1 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   1 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   1 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   1 166667 986 100 scaffold_291164:123135-125206
085 2008 cavPor3 3 145 552   1 961 313 100 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   1 270005 815 100 JH767775:6384924-6386653
101 2014 chaVoc1 47 2 13700   1514 133699 780 257 KL409415:13594818-13596634
102 2014 chaVoc2 47 2 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 7 101029   1 267937 996 100 JH721987:2542897-2544988
105 2013 chlSab1 23634 81 2123928   1 396229 923 1 chrX:117110178-117112024
106 2014 chlSab2 23631 81 2123656   1 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   1 720504 991 100 JH823765:402000-404081
110 2011 chrPic1 7555 79 738667   5 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   5 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   5 9493 597 50 chrUn_NW_004190451v1:5050-6293
115 2003 cioSav1 8 124 1554   1 2755 296 100 ps_146:263977-264668
116 2005 cioSav2 6 402.5 2394   2 1668 636 10 reftig_72:2536022-2537303
117 2015 colAng1 5690 77 626146   5 1472786 996 50 NW_012119888v1:35718-37759
118 2013 colLiv1 19 116 3824   129 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   1 233431 924 100 JH655880:49229854-49231801
121 2014 corBra1 41 9 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   1 322061 1000 10 chr25:16217228-16219237
130 2014 danRer10 575 174 105525   1 17550 484 10 chr5:1032421-1033398
131 2004 danRer2 1150 58 191859   1 223764 1000 10 chr10:26174984-26176993
132 2005 danRer3 819 58 88143   1 121196 776 10 chrUn:112388525-112390086
133 2006 danRer4 726 65.5 121967   14 135012 705 11 chr25:30060270-30061690
134 2007 danRer5 1559 17 288298   1 155702 73 1 chr21:35548773-35548919
135 2008 danRer6 1421 133 225674   1 142101 1000 100 Zv8_scaffold431:54613-56712
136 2010 danRer7 1245 164 217595   1 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   1 58752 836 100 scaffold_3394:70496-72267
139 2011 dasNov3 239 46 16270   5 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   2 1237 604 20 chrU:5250525-5251752
144 2004 dm2 8 362 2818   2 1217 604 20 chrU:5250525-5251752
145 2006 dm3 20 286 4907   1 423940 276 20 chrU:4943122-4943693
146 2014 dm6 15 333 4828   1 1340 276 20 chrUn_DS483709v1:12934-13505
147 2003 dp2 113 64 11633   1 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   5 18528 798 50 chrXL_group1e:8376310-8377955
150 2012 droAlb1 4360 3 131320   22 152454 76 1 JH853217:889-1041
151 2004 droAna1 103 252 28853   1 10300 943 100 2448822:95133-97118
152 2005 droAna2 32 16 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   2 294 447 20 KB462730:148150-149063
155 2013 droBip2 26 103.5 3925   2 520 409 20 KB464242:790791-791628
156 2013 droEle2 22 205 4879   2 440 480 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   2 237 72 1 AFPQ02002129:815-959
160 2013 droFic2 11 352 3277   2 220 424 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   2 1721 361 20 KB458730:24774-25515
164 2013 droMir2 122 72 16465   1 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   1 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   2 1286 454 20 KB451407:7018-7945
171 2005 droSec1 17 399 6822   1 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   1 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   2 260 472 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   133 51159 759 50 scaffold_181150:697726-699293
180 2006 droWil2 23 248 8712   133 51159 759 50 CH964291:697726-699293
181 2004 droYak1 65 34 25549   25 24358 955 50 chrU:40768288-40770247
182 2005 droYak2 99 17 26922   54 37713 684 10 chr2L:22155365-22156742
183 2006 droYak3 85 143 20479   1 23713 684 10 chr2L:22155365-22156742
187 2005 echTel1 89 83 17114   1 22024 805 100 scaffold_272928:13200-14909
188 2012 echTel2 3871 93 620444   1 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   1 311199 1000 100 JH947463:2106240-2108339
192 2012 eptFus1 1641 75 188916   1 378407 988 100 JH977647:11513546-11515621
193 2007 equCab1 17 457 5982   1 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   1 209198 1000 100 scaffold_366352:52823-54922
197 2012 eriEur2 3596 7 265454   1 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   1 9398414 1000 10 chrA2:8725380-8727389
207 2011 felCat5 27 72 6437   2 100569 488 20 chrB2:22462351-22463346
208 2014 felCat8 630 55 50300   1 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   5 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   27 70748 51 1 CAEA01526699:46-148
215 2004 galGal2 114 4 12930   124 17674 778 21 chr3:68417113-68418689
216 2006 galGal3 729 37 34199   5 325853 479 10 chrUn_random:55035794-55036761
217 2011 galGal4 55 401 22946   1 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   5 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   1 499615 1000 10 chr10_101645027_418909:206049-208058
227 2011 gorGor3 6926 246 2475426   1 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   1 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   37 3807 466 102 KK641449:26277-27310
233 2014 halLeu1 14 28 4342   95 1676 194 10 KL869356:8708537-8708934
234 2011 hapBur1 965 95 135908   2 374038 975 20 JH425754:7557-9526
235 2011 hetBac1 3 228 1282   2 60 1000 20 GL996479v1:885362-887381
236 2011 hetGla1 743 313 285174   1994 2914751 785 43 JH165660:4306-5918
237 2012 hetGla2 595 7 44604   1 201552 1000 100 JH602085:17402968-17405067
238 2009 hg19 1 2 200   3 3000000 200 3000000 chrY:10104354-13104753
243 2013 hg38 12 78 974   44 56689 125 20 chrUn_KI270442v1:175618-175887
252 2012 jacJac1 2666 63 196366   1 569918 1000 100 JH725440:52488719-52490818
253 2011 latCha1 2038 77 159059   1 504858 955 100 JH127253:476850-478859
255 2014 lepDis1 1 5 50   229 229 50 229 KK681583:9399-9727
256 2011 lepOcu1 2079 95 232474   1 466733 1000 100 chrLG4:37780111-37782210
257 2013 lepWed1 2022 63 135843   1 1218867 1000 100 KB715312:1023296-1025395
258 2013 letCam1 1453 69 123952   1 739039 280 39 KE994354:70338-70936
259 1880 linHum0 179 48 10176   1 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   1 562759 146 1 Scaffold27901:25044-25336
266 2009 macEug2 11689 55 752361   5 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   5 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   1 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   1 661041 169 1 chr3:54352580-54352918
275 2014 melGal5 84 181 17431   1 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   1 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   78 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 9 85250   5 267164 999 25 KQ057470v1:2292330-2294352
286 2017 micMur3 325 95 73918   5 262987 898 10 chr2:108635511-108637316
287 2012 micOch1 6788 65 483435   1 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   1 76884 921 100 chr6:132460596-132462537
293 2005 mm6 117 48 17647   1 48212 768 100 chr14:100566071-100567706
294 2005 mm7 45 48 5475   1 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   1 520 870 100 scaffold_38:23849795-23851634
299 2006 monDom4 9 183 3070   1 21732 870 1 chr1:400420041-400421781
300 2006 monDom5 9 183 3070   1 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   41 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   1 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   2 665865 998 20 JH422308:3325010-3327025
313 2014 nipNip1 41 154 11937   109 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   1 499781 890 100 JH802177:1348834-1350713
321 2012 octDeg1 2582 68 231489   1 464548 985 100 JH651571:12809669-12811738
322 2013 odoRosDiv1 2581 68 180258   5 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   5 357696 943 50 NW_004438742v1:126518-128453
326 2011 oreNil1 1903 93 208888   2 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   1 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   1 215389 561 10 chrUn:20300712-20301843
333 2005 oryLat2 141 144 25310   1 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   5 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   2 22114 33 1 JH650468:842203-842269
341 2015 panPan2 70 16 13388   2 1045522 35 1 chr4:127787143-127787213
342 2013 panRed1 123 56 6626   1 3069 62 10 KB454926:42673-42806
343 2013 panTig1 59 111 12591   7 69429 398 9 KE721804:6447970-6448774
344 2003 panTro1 5719 388 2244063   1 3504041 998 100 chr6:137473031-137475126
345 2006 panTro2 692 52 62006   24 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   1 3625772 199 10 chr12_NW_015974005v1_random:1130-1537
349 2012 papAnu2 727 138 144060   5 96682 46 1 chr4:20965571-20965663
350 2008 papHam1 22041 56 1338445   5 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 8 846184   5 1552640 1000 50 KI615759:2266069-2268118
354 2007 petMar1 542 47 48234   1 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   31 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   1 130377 1000 1 KI402232:538054-540054
360 2014 picPub1 59 83 12175   97 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 4 90824   133.5 275853 662 10 Contig208:1185633-1186966
364 2007 ponAbe2 2239 54 444541   1 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   1 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   72 720 282 720 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   2 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   5 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   5 425043 72 1 chr4:1247786-1247930
390 2004 rn4 567 141 142452   5 424693 72 1 chr4:1247786-1247930
391 2012 rn5 64 516 32231   5 28921 712 1 chr3:45275318-45276742
392 2014 rn6 719 29 280406   5 1258566 712 1 chr3:40184108-40185532
393 2006 rodEnt13 1 65 65   -40333062 -40333062 65 -40333062 1:40332999-66
398 2011 saiBol1 1541 77 139356   1 303093 1000 100 JH378136:528784-530883
400 2011 sarHar1 17494 22 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   2 33876 971 1 HG009242:4536330-4538272
404 2006 sorAra1 229 33 79670   1 75086 895 100 scaffold_247593:25660-27549
405 2008 sorAra2 3389 75 359891   1 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   1 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   5 238579 89 1 Scaffold16400:576-754
412 2006 strPur2 367 55 25281   5 79238 35 1 Scaffold12735:108654-108724
413 2009 strPur3 989 56 64991   96 187408 35 1 Scaffold740:110486-110556
414 2011 strPur4 1612 1 326953   5 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   1 66500 986 100 chr2:139016697-139018768
419 2009 susScr2 371 43 34151   1 66500 986 100 chr2:139016697-139018768
420 2011 susScr3 643 76 67571   -5721 -21397319 86 1 chr7:8729166-8729338
421 1880 taeGut0 212 45 20495   442 116920 624 10 Contig233:50949-52206
422 2008 taeGut1 223 45 22373   1 22300 689 100 chr21_random:54357-55834
423 2013 taeGut2 219 44 21273   1 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   44 56689 125 20 chrUn_KI270442v1:175618-175887
427 2008 tarSyr1 331 7 45530   191 102767 892 100 scaffold_111889:3660-5543
428 2013 tarSyr2 189 56 17645   2 9572 1000 20 KE939253v1:939796-941815
429 2014 tauEry1 1 5 50   394 394 50 394 KL466072:20829-21322
430 2004 tetNig1 64 272.5 21868   1 53904 336 59 chr5:807217-807947
431 2007 tetNig2 70 298 25569   5 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 1 8201   5 6900 214 50 Contig5855_Contig1469:226794-227271
435 2005 triCas2 63 62 5442   5 313244 412 50 chrUn_46:283716-284589
436 2011 triMan1 5748 75 527972   1 726640 1000 100 JH594622:8537918-8540017
437 2011 triSpi1 3 55 806   1 230 705 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 7 466776   188.5 1979352 44 1 JH496197:2095-2183
443 2014 tytAlb1 2 17 340   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   1 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   1 99243 775 100 chrUn_NW_016684502v1:7377-9026
455 2012 xipMac1 548 5 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=23971"