Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01003775.1 Kokia drynarioides strain JFW-HI SEQ_116753, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 276273
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 2 characters in sequence are not A, C, G, or T
Found at i:413 original size:162 final size:162
Alignment explanation
Indices: 1--2448 Score: 2644
Period size: 162 Copynumber: 15.3 Consensus size: 162
* * *
1 GAAATAATGACATATTCATGATAAAGCGCGGGAATTTGTTTAGTTAAATATAACATTTGTAAACT
1 GAAATAATGTCATATTCGTGATAAAGCGCGGGAATTTGTTTAGTTAAATATAAAATTTGTAAACT
* * ** *
66 TATCAACTCAAGTACAAAAGCATGCAAATTTATTTAGATAAACATAAACTTTAAACTTAACAATT
66 TATCAATTCAAGTACAAAAACGCGCAAATTTATTTAGATAAACATAAGCTTTAAACTTAACAATT
* * *
131 CAAATATGATATCATTTTAAAAAGAAGGCGT-
131 CAAATATGATAACATATTAATAAGAAGGCGTA
** * * *
162 -AAA-AA--T-AT-TT-AAGATAAAACGCGAGAATTTGTTTAGTTAAATGTAAAATTTGTAAACT
1 GAAATAATGTCATATTCGTGATAAAGCGCGGGAATTTGTTTAGTTAAATATAAAATTTGTAAACT
* * * * **
220 TATCAATTCGAA-TACAGAACCAG-GTAAATTTATTTAGATAAACGTAAGCTTTAAACTCGACAA
66 TATCAATTC-AAGTACAAAAAC-GCGCAAATTTATTTAGATAAACATAAGCTTTAAACTTAACAA
* *
283 TTCAAATATGATAATATATTAATAAAAAGGCGTA
129 TTCAAATATGATAACATATTAATAAGAAGGCGTA
* * **
317 AAAATAATGTCATATTCGTGATAAAACGCAAGAATTTGTTTAGTTAAATATAAAATTTGTAAACT
1 GAAATAATGTCATATTCGTGATAAAGCGCGGGAATTTGTTTAGTTAAATATAAAATTTGTAAACT
* * * *
382 TATCAATTCAAGTACAAAAACGCACAAATTTATTTATATAAACATATGCTTTAAACTTAACTATT
66 TATCAATTCAAGTACAAAAACGCGCAAATTTATTTAGATAAACATAAGCTTTAAACTTAACAATT
*
447 CAAATATGATAGCATATTAATAAGAAGGCGTA
131 CAAATATGATAACATATTAATAAGAAGGCGTA
* * * ** * *
479 TAAATAATGACATATTTGTGATAAAGCGCAAGAATTTGTTTAGTTAAATATAATATTTGTAAAGT
1 GAAATAATGTCATATTCGTGATAAAGCGCGGGAATTTGTTTAGTTAAATATAAAATTTGTAAACT
* * * * *
544 TATCAACTCAAGTACAAAAGCTCGCGAATTTATTTAGATTAACATCAA-CTTTAAACTTAACAAT
66 TATCAATTCAAGTACAAAAACGCGCAAATTTATTTAGATAAACAT-AAGCTTTAAACTTAACAAT
* * * * *
608 TCAAATATGAGAGA-ATTTTAGTAAGAAGACATA
130 TCAAATATGATA-ACATATTAATAAGAAGGCGTA
* * * ** *
641 GAAATAATGACATATTCGTGATATAGCGCGAGAATTTGTTTAGTTAAATATAACGTTCGTAAACT
1 GAAATAATGTCATATTCGTGATAAAGCGCGGGAATTTGTTTAGTTAAATATAAAATTTGTAAACT
* * * * *
706 TATCAACTCAAGTACAAAAGCACGCGAATTTATTTAGATAAACATCAA-CTTTAAACTTAACAGT
66 TATCAATTCAAGTACAAAAACGCGCAAATTTATTTAGATAAACAT-AAGCTTTAAACTTAACAAT
* * *
770 TCAACTATGATAGCATATTAATAAGAAGACGT-
130 TCAAATATGATAACATATTAATAAGAAGGCGTA
* * * * *
802 -AAA-AA--T-AT-TT-ATGATAAAGCGCGAGAATCTGTTTAGTTAAATATAAAATTTTTAAATT
1 GAAATAATGTCATATTCGTGATAAAGCGCGGGAATTTGTTTAGTTAAATATAAAATTTGTAAACT
* ** **
860 TATCAATTCAAATGTAAATGCAG-GCAAATTTATTTA-ACTAAACATAAGCTTTAAACTTAACAA
66 TATCAATTCAAGTACAAAAAC-GCGCAAATTTATTTAGA-TAAACATAAGCTTTAAACTTAACAA
*
923 TTCAAATATGATAATATATTAATAAGAAGGCGTA
129 TTCAAATATGATAACATATTAATAAGAAGGCGTA
* *
957 AAAATAATGTCATATTCATGATAAAGCGCGGGAATTTGTTTAGTTAAATAT-AAATTTGTAAACT
1 GAAATAATGTCATATTCGTGATAAAGCGCGGGAATTTGTTTAGTTAAATATAAAATTTGTAAACT
** * *
1021 TATCAATTCAAGTACAAAAATACGCAAATTTATTTAGATAAACATATGCTTTAAACTTAACTATT
66 TATCAATTCAAGTACAAAAACGCGCAAATTTATTTAGATAAACATAAGCTTTAAACTTAACAATT
*
1086 CAAATATGATAGCATATTAATAAGAAGGCGTA
131 CAAATATGATAACATATTAATAAGAAGGCGTA
** ** * * *
1118 GAAATAATAACATATTCGTGATAAAGTACAGGAGTTTGTTTAGTTAAATATAACATTTGTAAACT
1 GAAATAATGTCATATTCGTGATAAAGCGCGGGAATTTGTTTAGTTAAATATAAAATTTGTAAACT
* * * *
1183 TATCAATTCAAGTACAAAAGCACGCGAATTTATTTAGATCAACATCAA-CTTTAAACTTAACAAT
66 TATCAATTCAAGTACAAAAACGCGCAAATTTATTTAGATAAACAT-AAGCTTTAAACTTAACAAT
* *
1247 TCAAATATGATAGCATAATAATAAGAAGGCGTA
130 TCAAATATGATAACATATTAATAAGAAGGCGTA
* * *
1280 CAAAT-AT-T--TA----TGATAAAGCGTGGGAATTTGTTTAGTTAAATATAAAATTTGTAAATT
1 GAAATAATGTCATATTCGTGATAAAGCGCGGGAATTTGTTTAGTTAAATATAAAATTTGTAAACT
* *
1337 TATCAATTCAAGTACAAAAGCAG-GTAAATTTATTTAGATTTATTTAGATAAACATAAGCTTTAA
66 TATCAATTCAAGTACAAAAAC-GCG------CA---A-ATTTATTTAGATAAACATAAGCTTTAA
*
1401 ACTTAACAATTCAAATATGATAATATATTAATAAGAAGGCGTA
120 ACTTAACAATTCAAATATGATAACATATTAATAAGAAGGCGTA
* *** * * * *
1444 AAAATAATGTCATATTAAAGATAAAGTGCTGGAATTTGTTTAATTAACTATAAAATTTGTAAACT
1 GAAATAATGTCATATTCGTGATAAAGCGCGGGAATTTGTTTAGTTAAATATAAAATTTGTAAACT
* *
1509 TATCAATTCAAGTACAAAAGTA-G-ACAAATTTATTTAAATAAACATAAGCTTTAAACTTAACAA
66 TATCAATTCAAGTACAAAA--ACGCGCAAATTTATTTAGATAAACATAAGCTTTAAACTTAACAA
*
1572 TTCAAATATGATAACATATTAATAAAAAGGCGTA
129 TTCAAATATGATAACATATTAATAAGAAGGCGTA
* ** *
1606 G--A-AA--T-AT-TT-GTGATAAAACGCGACAATTTGTTTAGTTAAATATAAAACTTGTAAACT
1 GAAATAATGTCATATTCGTGATAAAGCGCGGGAATTTGTTTAGTTAAATATAAAATTTGTAAACT
* * * * * * *
1663 TATCGATTCAATTACAACAGTA-G-GCAAATTTATTTAGGA-AAACATAAGTTTTGAATTTTACA
66 TATCAATTCAAGTACAA-A-AACGCGCAAATTTATTTA-GATAAACATAAGCTTTAAACTTAACA
* *
1725 ATTCAAATATGATAATATATAAATAAGAAGGCGTA
128 ATTCAAATATGATAACATATTAATAAGAAGGCGTA
* * * *
1760 GAAATAATGTCATATTCGTGATAATGCGTGGTAATTTGTTTAGTTAAATATAACATTTGTAAACT
1 GAAATAATGTCATATTCGTGATAAAGCGCGGGAATTTGTTTAGTTAAATATAAAATTTGTAAACT
* * * * *
1825 TATCAACTCAAGTACAAAAGCACGCGAATTTATTTAGATAAACATTAA-TTTTAAACTTAACAAT
66 TATCAATTCAAGTACAAAAACGCGCAAATTTATTTAGATAAACA-TAAGCTTTAAACTTAACAAT
* * *
1889 TCAAATATGATAGCATACTAATAAGAAGGCATA
130 TCAAATATGATAACATATTAATAAGAAGGCGTA
* *
1922 G--A-AA--T-AT-TT-GTGATAAAGCGCGAGAATTTGTTTAGTTAAATATAAAACTTGTAAACT
1 GAAATAATGTCATATTCGTGATAAAGCGCGGGAATTTGTTTAGTTAAATATAAAATTTGTAAACT
* * *
1979 TATCAATTCAAGTACAACAGTA-G-GTAAATTTATTTAAATAAACATAAGCTTTAAACTTAACAA
66 TATCAATTCAAGTACAA-A-AACGCGCAAATTTATTTAGATAAACATAAGCTTTAAACTTAACAA
* * *
2042 TTCAAAGATGATAATATATTAATAAGAAGGCATA
129 TTCAAATATGATAACATATTAATAAGAAGGCGTA
* * *
2076 GAAATAATGTCATATTTGTGATAAAGCGCAGGATTTTGTTTAGTTAAATATAAAATTTGTAAACT
1 GAAATAATGTCATATTCGTGATAAAGCGCGGGAATTTGTTTAGTTAAATATAAAATTTGTAAACT
*
2141 TATCAATTCAAGTACAAAAGAACGCG--AATTTATTTAGATAAACATAAACTTTAAACTTAACAA
66 TATCAATTCAAGTAC-AAA-AACGCGCAAATTTATTTAGATAAACATAAGCTTTAAACTTAACAA
* * * * *
2204 TTCAAATTTGAGAGCATATTAGTAAGAAGACGTA
129 TTCAAATATGATAACATATTAATAAGAAGGCGTA
* * * *
2238 GAAATAATGACATATTCATGATAAAGCGCGGGAATTTATTTAGTTAAATATAACATTTGTAAACT
1 GAAATAATGTCATATTCGTGATAAAGCGCGGGAATTTGTTTAGTTAAATATAAAATTTGTAAACT
* * * * * * *
2303 TATCAACTCAAGTACAAAAGCACGCGAATTTATTTAGATCAACATCAA-CTTTGAACTAAACAAT
66 TATCAATTCAAGTACAAAAACGCGCAAATTTATTTAGATAAACAT-AAGCTTTAAACTTAACAAT
* **
2367 TCAAATATGATAGCATATTAATAAGAAGATGTA
130 TCAAATATGATAACATATTAATAAGAAGGCGTA
* * *
2400 GAAATAAT-TACATATTTGTGATAAAGCGCGGTAATTTATTTAGTTAAAT
1 GAAATAATGT-CATATTCGTGATAAAGCGCGGGAATTTGTTTAGTTAAAT
2449 CAAGTACAAA
Statistics
Matches: 1946, Mismatches: 256, Indels: 169
0.82 0.11 0.07
Matches are distributed among these distances:
153 6 0.00
154 541 0.28
155 13 0.01
156 16 0.01
157 10 0.01
158 2 0.00
159 12 0.01
160 20 0.01
161 156 0.08
162 1022 0.53
163 14 0.01
164 68 0.03
165 2 0.00
166 2 0.00
168 2 0.00
172 60 0.03
ACGTcount: A:0.44, C:0.10, G:0.13, T:0.33
Consensus pattern (162 bp):
GAAATAATGTCATATTCGTGATAAAGCGCGGGAATTTGTTTAGTTAAATATAAAATTTGTAAACT
TATCAATTCAAGTACAAAAACGCGCAAATTTATTTAGATAAACATAAGCTTTAAACTTAACAATT
CAAATATGATAACATATTAATAAGAAGGCGTA
Found at i:904 original size:478 final size:473
Alignment explanation
Indices: 2--2685 Score: 2773
Period size: 478 Copynumber: 5.6 Consensus size: 473
1 G
* *
2 AAATAATGACATATTCATGATAAAGCGCGGGAATTTGTTTAGTTAAATATAACATTTGTAAACTT
1 AAATAATGACATATTTATGATAAAGCGCGGGAATTTGTTTAGTTAAATATAAAATTTGTAAACTT
* *
67 ATCAACTCAAGTACAAAAGCATGCAAATTTATTTAGATAAACATAAACTTTAAACTTAACAATTC
66 ATCAATTCAAGTACAAAAGTA-GCAAATTTATTTAGATAAACAT-AACTTTAAACTTAACAATTC
* * * ** *
132 AAATATGATATCATTTTAAAAAGAAGGCGT--AAA-AAT-AT-TTAAGATAAAACGCGAGAATTT
129 AAATATGATA-AATATTAATAAGAAGGCGTAGAAATAATCATATTGTGATAAAGCGCGAGAATTT
* * * * * **
192 GTTTAGTTAAATGTAAAATTTGTAAACTTATCAATTCGAA-TACAGAACCAGGTAAATTTATTTA
193 GTTTAGTTAAATATAACATTTGTAAACTTATCAATTC-AAGTACAAAAGCACGCGAATTTATTTA
* ** ** *
256 GATAAACGTAAGCTTTAAACTCGACAATTCAAATATGATAATATATTAATAAAAAGGCGTAAAAA
257 GATAAACATAA-CTTTAAACTTAACAATTCAAATATGATAGCATATTAATAAGAAGGCGTAAAAA
* * *
321 TAATGTCATATTCGTGATAAAACGCAAGAATTTGTTTAGTTAAATATAAAATTTGTAAACTTATC
321 T-A----ATATT-ATGATAAAGCGCGAGAATTTGTTTAGTTAAATATAAAATTTGTAAACTTATC
* * * * *
386 AATTCAAGTACAAAAACGCACAAATTTATTTATATAAACATATGCTTTAAACTTAACTATTCAAA
380 AATTCAAGTACAAAAGCACGCAAATTTATTTATATAAACATAAGCTTTAAACTTAACAATTCAAA
*
451 TATGATAGCATATTAATAAGAAGGCGTAT
445 TATGATAGCATATTAATAAGAAGGCGTAA
* ** * *
480 AAATAATGACATATTTGTGATAAAGCGCAAGAATTTGTTTAGTTAAATATAATATTTGTAAAGTT
1 AAATAATGACATATTTATGATAAAGCGCGGGAATTTGTTTAGTTAAATATAAAATTTGTAAACTT
* * * *
545 ATCAACTCAAGTACAAAAGCTCGCGAATTTATTTAGATTAACATCAACTTTAAACTTAACAATTC
66 ATCAATTCAAGTACAAAAG-TAGCAAATTTATTTAGATAAACAT-AACTTTAAACTTAACAATTC
* * * * * *
610 AAATATGAGAGAATTTTAGTAAGAAGACATAGAAATAATGACATATTCGTGATATAGCGCGAGAA
129 AAATATGATA-AATATTAATAAGAAGGCGTAGAAATAAT--CATATT-GTGATAAAGCGCGAGAA
* * *
675 TTTGTTTAGTTAAATATAACGTTCGTAAACTTATCAACTCAAGTACAAAAGCACGCGAATTTATT
190 TTTGTTTAGTTAAATATAACATTTGTAAACTTATCAATTCAAGTACAAAAGCACGCGAATTTATT
* * *
740 TAGATAAACATCAACTTTAAACTTAACAGTTCAACTATGATAGCATATTAATAAGAAGACGTAAA
255 TAGATAAACAT-AACTTTAAACTTAACAATTCAAATATGATAGCATATTAATAAGAAGGCGTAAA
* * *
805 AAT-AT-TTATGATAAAGCGCGAGAATCTGTTTAGTTAAATATAAAATTTTTAAATTTATCAATT
319 AATAATATTATGATAAAGCGCGAGAATTTGTTTAGTTAAATATAAAATTTGTAAACTTATCAATT
* ** * *
868 CAAATGTAAATGCAGGCAAATTTATTTA-ACTAAACATAAGCTTTAAACTTAACAATTCAAATAT
384 CAAGTACAAAAGCACGCAAATTTATTTATA-TAAACATAAGCTTTAAACTTAACAATTCAAATAT
**
932 GATAATATATTAATAAGAAGGCGTAA
448 GATAGCATATTAATAAGAAGGCGTAA
* *
958 AAATAATGTCATATTCATGATAAAGCGCGGGAATTTGTTTAGTTAAATAT-AAATTTGTAAACTT
1 AAATAATGACATATTTATGATAAAGCGCGGGAATTTGTTTAGTTAAATATAAAATTTGTAAACTT
* * *
1022 ATCAATTCAAGTACAAAAATACGCAAATTTATTTAGATAAACATATGCTTTAAACTTAACTATTC
66 ATCAATTCAAGTACAAAAGTA-GCAAATTTATTTAGATAAACATA-ACTTTAAACTTAACAATTC
* **
1087 AAATATGATAGCATATTAATAAGAAGGCGTAGAAATAATAACATATTCGTGATAAAGTAC-AGGA
129 AAATATGATA-AATATTAATAAGAAGGCGTAGAAATAAT--CATATT-GTGATAAAGCGCGA-GA
*
1151 GTTTGTTTAGTTAAATATAACATTTGTAAACTTATCAATTCAAGTACAAAAGCACGCGAATTTAT
189 ATTTGTTTAGTTAAATATAACATTTGTAAACTTATCAATTCAAGTACAAAAGCACGCGAATTTAT
* * *
1216 TTAGATCAACATCAACTTTAAACTTAACAATTCAAATATGATAGCATAATAATAAGAAGGCGTAC
254 TTAGATAAACAT-AACTTTAAACTTAACAATTCAAATATGATAGCATATTAATAAGAAGGCGTAA
* * *
1281 AAAT-AT-TTATGATAAAGCGTGGGAATTTGTTTAGTTAAATATAAAATTTGTAAATTTATCAAT
318 AAATAATATTATGATAAAGCGCGAGAATTTGTTTAGTTAAATATAAAATTTGTAAACTTATCAAT
* *
1344 TCAAGTACAAAAGCAGGTAAATTTATTTAGATTTATTTAGATAAACATAAGCTTTAAACTTAACA
383 TCAAGTACAAAAGCACG-CAA---ATTT--ATTTA--T--ATAAACATAAGCTTTAAACTTAACA
**
1409 ATTCAAATATGATAATATATTAATAAGAAGGCGTAA
438 ATTCAAATATGATAGCATATTAATAAGAAGGCGTAA
* * * * * * *
1445 AAATAATGTCATATTAAAGATAAAGTGCTGGAATTTGTTTAATTAACTATAAAATTTGTAAACTT
1 AAATAATGACATATTTATGATAAAGCGCGGGAATTTGTTTAGTTAAATATAAAATTTGTAAACTT
*
1510 ATCAATTCAAGTACAAAAGTAGACAAATTTATTTAAATAAACATAAGCTTTAAACTTAACAATTC
66 ATCAATTCAAGTACAAAAGTAG-CAAATTTATTTAGATAAACATAA-CTTTAAACTTAACAATTC
* * *
1575 AAATATGATAACATATTAATAAAAAGGCGTAG--A-AAT-AT-TTGTGATAAAACGCGACAATTT
129 AAATATGATAA-ATATTAATAAGAAGGCGTAGAAATAATCATATTGTGATAAAGCGCGAGAATTT
* * * * * * * *
1635 GTTTAGTTAAATATAAAACTTGTAAACTTATCGATTCAATTACAACAGTAGGCAAATTTATTTAG
193 GTTTAGTTAAATATAACATTTGTAAACTTATCAATTCAAGTACAAAAGCACGCGAATTTATTTA-
* * * * ** *
1700 GA-AAACATAAGTTTTGAATTTTACAATTCAAATATGATAATATATAAATAAGAAGGCGTAGAAA
257 GATAAACATAA-CTTTAAACTTAACAATTCAAATATGATAGCATATTAATAAGAAGGCGT--AAA
* * * * *
1764 TAATGTCATATTCGTGATAATGCGTG-GTAATTTGTTTAGTTAAATATAACATTTGTAAACTTAT
319 -AA--TAATATT-ATGATAAAGCGCGAG-AATTTGTTTAGTTAAATATAAAATTTGTAAACTTAT
* * * *
1828 CAACTCAAGTACAAAAGCACGCGAATTTATTTAGATAAACATTAA-TTTTAAACTTAACAATTCA
379 CAATTCAAGTACAAAAGCACGCAAATTTATTTATATAAACA-TAAGCTTTAAACTTAACAATTCA
*
1892 AATATGATAGCATACTAATAAGAAGGC----
443 AATATGATAGCATATTAATAAGAAGGCGTAA
* * * *
1919 --AT-A-GAAATATTTGTGATAAAGCGCGAGAATTTGTTTAGTTAAATATAAAACTTGTAAACTT
1 AAATAATGACATATTTATGATAAAGCGCGGGAATTTGTTTAGTTAAATATAAAATTTGTAAACTT
* * *
1980 ATCAATTCAAGTACAACAGTAGGTAAATTTATTTAAATAAACATAAGCTTTAAACTTAACAATTC
66 ATCAATTCAAGTACAAAAGTA-GCAAATTTATTTAGATAAACATAA-CTTTAAACTTAACAATTC
* *
2045 AAAGATGATAATATATTAATAAGAAGGCATAGAAATAATGTCATATTTGTGATAAAGCGC-AGGA
129 AAATATGATAA-ATATTAATAAGAAGGCGTAGAAATAA--TCATA-TTGTGATAAAGCGCGA-GA
* * *
2109 TTTTGTTTAGTTAAATATAAAATTTGTAAACTTATCAATTCAAGTACAAAAGAACGCGAATTTAT
189 ATTTGTTTAGTTAAATATAACATTTGTAAACTTATCAATTCAAGTACAAAAGCACGCGAATTTAT
* * * *
2174 TTAGATAAACATAAACTTTAAACTTAACAATTCAAATTTGAGAGCATATTAGTAAGAAGACGTAG
254 TTAGATAAACAT-AACTTTAAACTTAACAATTCAAATATGATAGCATATTAATAAGAAGGCGT--
* * *
2239 AAATAATGACATATTCATGATAAAGCGCGGGAATTTATTTAGTTAAATATAACATTTGTAAACTT
316 AAA-AAT-A-ATATT-ATGATAAAGCGCGAGAATTTGTTTAGTTAAATATAAAATTTGTAAACTT
* * * * * *
2304 ATCAACTCAAGTACAAAAGCACGCGAATTTATTTAGATCAACATCAA-CTTTGAACTAAACAATT
377 ATCAATTCAAGTACAAAAGCACGCAAATTTATTTATATAAACAT-AAGCTTTAAACTTAACAATT
** *
2368 CAAATATGATAGCATATTAATAAGAAGATGTAG
441 CAAATATGATAGCATATTAATAAGAAGGCGTAA
* * * * *
2401 AAATAATTACATATTTGTGATAAAGCGCGGTAATTTATTTAGTT-AA-AT-CAA---G------T
1 AAATAATGACATATTTATGATAAAGCGCGGGAATTTGTTTAGTTAAATATAAAATTTGTAAACTT
* * * * *
2454 A-CAA---AAG--C----G-CGCAAATTTATTTAGATAAACAGATGCTTTAAACTTAGCAATTAA
66 ATCAATTCAAGTACAAAAGTAGCAAATTTATTTAGATAAACATA-ACTTTAAACTTAACAATTCA
* * * ** *
2508 AATATGATACCAGATTAATAAGAAGG-GTTAGAAATAATGACATATTCATGATAAAGCATGGGAA
130 AATATGATA-AATATTAATAAGAAGGCG-TAGAAATAAT--CATATT-GTGATAAAGCGCGAGAA
* * * * *
2572 TTTATTTAGTTAAATATAAAATTTATAAACTTATCAATTCAAGTACATAA--ACGCTTAAATTTA
190 TTTGTTTAGTTAAATATAACATTTGTAAACTTATCAATTCAAGTACAAAAGCACGC--GAATTTA
* * *
2635 TTTAAATAAACAAAAACTTTAAACTTAACAATTCAAATATAATAGCATATT
253 TTTAGATAAAC-ATAACTTTAAACTTAACAATTCAAATATGATAGCATATT
2686 TGTGACAACA
Statistics
Matches: 1897, Mismatches: 232, Indels: 170
0.83 0.10 0.07
Matches are distributed among these distances:
460 5 0.00
461 2 0.00
462 180 0.09
463 1 0.00
464 1 0.00
468 1 0.00
470 139 0.07
471 2 0.00
472 3 0.00
473 5 0.00
474 2 0.00
475 1 0.00
476 6 0.00
477 315 0.17
478 620 0.33
479 10 0.01
480 120 0.06
481 12 0.01
482 9 0.00
483 9 0.00
484 10 0.01
485 11 0.01
486 156 0.08
487 111 0.06
488 166 0.09
ACGTcount: A:0.44, C:0.11, G:0.12, T:0.33
Consensus pattern (473 bp):
AAATAATGACATATTTATGATAAAGCGCGGGAATTTGTTTAGTTAAATATAAAATTTGTAAACTT
ATCAATTCAAGTACAAAAGTAGCAAATTTATTTAGATAAACATAACTTTAAACTTAACAATTCAA
ATATGATAAATATTAATAAGAAGGCGTAGAAATAATCATATTGTGATAAAGCGCGAGAATTTGTT
TAGTTAAATATAACATTTGTAAACTTATCAATTCAAGTACAAAAGCACGCGAATTTATTTAGATA
AACATAACTTTAAACTTAACAATTCAAATATGATAGCATATTAATAAGAAGGCGTAAAAATAATA
TTATGATAAAGCGCGAGAATTTGTTTAGTTAAATATAAAATTTGTAAACTTATCAATTCAAGTAC
AAAAGCACGCAAATTTATTTATATAAACATAAGCTTTAAACTTAACAATTCAAATATGATAGCAT
ATTAATAAGAAGGCGTAA
Found at i:996 original size:316 final size:313
Alignment explanation
Indices: 2--2685 Score: 2615
Period size: 316 Copynumber: 8.5 Consensus size: 313
1 G
* *
2 AAATAATGACATATTCATGATAAAGCGCGGGAATTTGTTTAGTTAAATATAACATTTGTAAACTT
1 AAATAATGTCATATTCATGATAAAGCGCGAGAATTTGTTTAGTTAAATATAACATTTGTAAACTT
* *
67 ATCAACTCAAGTACAAAAGCATGCAAATTTATTTAGATAAACATAAACTTTAAACTTAACAATTC
66 ATCAATTCAAGTACAAAAGCACGCAAATTTATTTAGATAAACAT-AACTTTAAACTTAACAATTC
* * * ** *
132 AAATATGATATCATTTTAAAAAGAAGGCGTAAAAATATTTAAGATAAAACGCGAGAATTTGTTTA
130 AAATATGATAGCATATTAATAAGAAGGCGTAAAAATATTTGTGATAAAGCGCGAGAATTTGTTTA
* * * * **
197 GTTAAATGTAAAATTTGTAAACTTATCAATTCGAA-TACAGAACCAGGTAAATTTATTTAGATAA
195 GTTAAATATAAAATTTGTAAACTTATCAATTC-AAGTACAAAAGCACGCGAATTTATTTAGATAA
* ** * *
261 ACGTAAGCTTTAAACTCGACAATTCAAATATGATAATATATTAATAAAAAGGCGTAA
259 ACATAA-CTTTAAACTTAACAATTCAAATATGATAACATATTAATAAGAAGGCGT-A
* * * *
318 AAATAATGTCATATTCGTGATAAAACGCAAGAATTTGTTTAGTTAAATATAAAATTTGTAAACTT
1 AAATAATGTCATATTCATGATAAAGCGCGAGAATTTGTTTAGTTAAATATAACATTTGTAAACTT
* * * * * *
383 ATCAATTCAAGTACAAAAACGCACAAATTTATTTATATAAACATATGCTTTAAACTTAACTATTC
66 ATCAATTCAAGTACAAAAGCACGCAAATTTATTTAGATAAACATA-ACTTTAAACTTAACAATTC
*
448 AAATATGATAGCATATTAATAAGAAGGCGTATAAATAATGACATATTTGTGATAAAGCGCAAGAA
130 AAATATGATAGCATATTAATAAGAAGGCG--T--A-AA--A-ATATTTGTGATAAAGCGCGAGAA
* * * *
513 TTTGTTTAGTTAAATATAATATTTGTAAAGTTATCAACTCAAGTACAAAAGCTCGCGAATTTATT
187 TTTGTTTAGTTAAATATAAAATTTGTAAACTTATCAATTCAAGTACAAAAGCACGCGAATTTATT
* * * * * *
578 TAGATTAACATCAACTTTAAACTTAACAATTCAAATATGAGAGA-ATTTTAGTAAGAAGACATA
252 TAGATAAACAT-AACTTTAAACTTAACAATTCAAATATGATA-ACATATTAATAAGAAGGCGTA
* * * * *
641 GAAATAATGACATATTCGTGATATAGCGCGAGAATTTGTTTAGTTAAATATAACGTTCGTAAACT
1 -AAATAATGTCATATTCATGATAAAGCGCGAGAATTTGTTTAGTTAAATATAACATTTGTAAACT
* * *
706 TATCAACTCAAGTACAAAAGCACGCGAATTTATTTAGATAAACATCAACTTTAAACTTAACAGTT
65 TATCAATTCAAGTACAAAAGCACGCAAATTTATTTAGATAAACAT-AACTTTAAACTTAACAATT
* * * *
771 CAACTATGATAGCATATTAATAAGAAGACGTAAAAATATTTATGATAAAGCGCGAGAATCTGTTT
129 CAAATATGATAGCATATTAATAAGAAGGCGTAAAAATATTTGTGATAAAGCGCGAGAATTTGTTT
* * * ** * * *
836 AGTTAAATATAAAATTTTTAAATTTATCAATTCAAATGTAAATGCAGGCAAATTTATTTA-ACTA
194 AGTTAAATATAAAATTTGTAAACTTATCAATTCAAGTACAAAAGCACGCGAATTTATTTAGA-TA
*
900 AACATAAGCTTTAAACTTAACAATTCAAATATGATAATATATTAATAAGAAGGCGTAA
258 AACATAA-CTTTAAACTTAACAATTCAAATATGATAACATATTAATAAGAAGGCGT-A
*
958 AAATAATGTCATATTCATGATAAAGCGCGGGAATTTGTTTAGTTAAATATAA-ATTTGTAAACTT
1 AAATAATGTCATATTCATGATAAAGCGCGAGAATTTGTTTAGTTAAATATAACATTTGTAAACTT
** * *
1022 ATCAATTCAAGTACAAAAATACGCAAATTTATTTAGATAAACATATGCTTTAAACTTAACTATTC
66 ATCAATTCAAGTACAAAAGCACGCAAATTTATTTAGATAAACATA-ACTTTAAACTTAACAATTC
**
1087 AAATATGATAGCATATTAATAAGAAGGCGTAGAAATAATAACATATTCGTGATAAAGTAC-AGGA
130 AAATATGATAGCATATTAATAAGAAGGCGT--AAA-AAT---AT-TT-GTGATAAAGCGCGA-GA
* *
1151 GTTTGTTTAGTTAAATATAACATTTGTAAACTTATCAATTCAAGTACAAAAGCACGCGAATTTAT
186 ATTTGTTTAGTTAAATATAAAATTTGTAAACTTATCAATTCAAGTACAAAAGCACGCGAATTTAT
* * *
1216 TTAGATCAACATCAACTTTAAACTTAACAATTCAAATATGATAGCATAATAATAAGAAGGCGT-
251 TTAGATAAACAT-AACTTTAAACTTAACAATTCAAATATGATAACATATTAATAAGAAGGCGTA
* * * * *
1279 ACA-AA--T-AT-TT-ATGATAAAGCGTGGGAATTTGTTTAGTTAAATATAAAATTTGTAAATTT
1 AAATAATGTCATATTCATGATAAAGCGCGAGAATTTGTTTAGTTAAATATAACATTTGTAAACTT
* *
1338 ATCAATTCAAGTACAAAAGCAGGTAAATTTATTTAGATTTATTTAGATAAACATAAGCTTTAAAC
66 ATCAATTCAAGTACAAAAGCACG------CA---A-ATTTATTTAGATAAACATAA-CTTTAAAC
** *
1403 TTAACAATTCAAATATGATAATATATTAATAAGAAGGCGTAAAAATAATGTCATATTAAAGATAA
120 TTAACAATTCAAATATGATAGCATATTAATAAGAAGGCGTAAAAAT-AT-T--T-GT---GATAA
* * * *
1468 AGTGCTG-GAATTTGTTTAATTAACTATAAAATTTGTAAACTTATCAATTCAAGTACAAAAGTA-
177 AGCGC-GAGAATTTGTTTAGTTAAATATAAAATTTGTAAACTTATCAATTCAAGTACAAAAGCAC
* *
1531 GACAAATTTATTTAAATAAACATAAGCTTTAAACTTAACAATTCAAATATGATAACATATTAATA
241 G-CGAATTTATTTAGATAAACATAA-CTTTAAACTTAACAATTCAAATATGATAACATATTAATA
*
1596 AAAAGGCGT-
304 AGAAGGCGTA
* * * * * *
1605 AGA-AA--T-AT-TT-GTGATAAAACGCGACAATTTGTTTAGTTAAATATAAAACTTGTAAACTT
1 AAATAATGTCATATTCATGATAAAGCGCGAGAATTTGTTTAGTTAAATATAACATTTGTAAACTT
* * * * * * * * *
1664 ATCGATTCAATTACAACAGTAGGCAAATTTATTTAGGA-AAACATAAGTTTTGAATTTTACAATT
66 ATCAATTCAAGTACAAAAGCACGCAAATTTATTTA-GATAAACATAA-CTTTAAACTTAACAATT
** * * *
1728 CAAATATGATAATATATAAATAAGAAGGCGTAGAAATAATGTCATATTCGTGATAATGCGTG-GT
129 CAAATATGATAGCATATTAATAAGAAGGCGT--AAA-AA--T-AT-TT-GTGATAAAGCGCGAG-
* *
1792 AATTTGTTTAGTTAAATATAACATTTGTAAACTTATCAACTCAAGTACAAAAGCACGCGAATTTA
185 AATTTGTTTAGTTAAATATAAAATTTGTAAACTTATCAATTCAAGTACAAAAGCACGCGAATTTA
* * * *
1857 TTTAGATAAACATTAATTTTAAACTTAACAATTCAAATATGATAGCATACTAATAAGAAGGCAT-
250 TTTAGATAAACA-TAACTTTAAACTTAACAATTCAAATATGATAACATATTAATAAGAAGGCGTA
* * * *
1921 AGA-AA--T-AT-TT-GTGATAAAGCGCGAGAATTTGTTTAGTTAAATATAAAACTTGTAAACTT
1 AAATAATGTCATATTCATGATAAAGCGCGAGAATTTGTTTAGTTAAATATAACATTTGTAAACTT
* * * * *
1980 ATCAATTCAAGTACAACAGTAGGTAAATTTATTTAAATAAACATAAGCTTTAAACTTAACAATTC
66 ATCAATTCAAGTACAAAAGCACGCAAATTTATTTAGATAAACATAA-CTTTAAACTTAACAATTC
* ** *
2045 AAAGATGATAATATATTAATAAGAAGGCATAGAAATAATGTCATATTTGTGATAAAGCGC-AGGA
130 AAATATGATAGCATATTAATAAGAAGGC---GTAA-AA----ATATTTGTGATAAAGCGCGA-GA
* *
2109 TTTTGTTTAGTTAAATATAAAATTTGTAAACTTATCAATTCAAGTACAAAAGAACGCGAATTTAT
186 ATTTGTTTAGTTAAATATAAAATTTGTAAACTTATCAATTCAAGTACAAAAGCACGCGAATTTAT
* * * * *
2174 TTAGATAAACATAAACTTTAAACTTAACAATTCAAATTTGAGAGCATATTAGTAAGAAGACGTA
251 TTAGATAAACAT-AACTTTAAACTTAACAATTCAAATATGATAACATATTAATAAGAAGGCGTA
* * *
2238 GAAATAATGACATATTCATGATAAAGCGCGGGAATTTATTTAGTTAAATATAACATTTGTAAACT
1 -AAATAATGTCATATTCATGATAAAGCGCGAGAATTTGTTTAGTTAAATATAACATTTGTAAACT
* * * * *
2303 TATCAACTCAAGTACAAAAGCACGCGAATTTATTTAGATCAACATCAACTTTGAACTAAACAATT
65 TATCAATTCAAGTACAAAAGCACGCAAATTTATTTAGATAAACAT-AACTTTAAACTTAACAATT
** * * ** *** * * * **
2368 CAAATATGATAGCATATTAATAAGAAGATGTAGAAATAATT-ACAT-ATTTGTGATAA--AG-CG
129 CAAATATGATAGCATATTAATAAGAAGGCGTAAAAATATTTGTGATAAAGCGCGAGAATTTGTTT
* * * * * *
2428 CGGT-AAT-T--TA-TT-T--AGTTA--AA-TCAAGTACAAAAGCGCGCAAATTTATTTAGATAA
194 AGTTAAATATAAAATTTGTAAACTTATCAATTCAAGTACAAAAGCACGCGAATTTATTTAGATAA
* * * * * *
2482 ACAGATGCTTTAAACTTAGCAATTAAAATATGATACCAGATTAATAAGAAGG-GTTA
259 ACATA-ACTTTAAACTTAACAATTCAAATATGATAACATATTAATAAGAAGGCG-TA
* ** * * * *
2538 GAAATAATGACATATTCATGATAAAGCATGGGAATTTATTTAGTTAAATATAAAATTTATAAACT
1 -AAATAATGTCATATTCATGATAAAGCGCGAGAATTTGTTTAGTTAAATATAACATTTGTAAACT
* * *
2603 TATCAATTCAAGTACATAA--ACGCTTAAATTTATTTAAATAAACAAAAACTTTAAACTTAACAA
65 TATCAATTCAAGTACAAAAGCACGC--AAATTTATTTAGATAAAC-ATAACTTTAAACTTAACAA
*
2666 TTCAAATATAATAGCATATT
127 TTCAAATATGATAGCATATT
2686 TGTGACAACA
Statistics
Matches: 2013, Mismatches: 268, Indels: 190
0.81 0.11 0.08
Matches are distributed among these distances:
298 4 0.00
299 2 0.00
300 200 0.10
301 3 0.00
303 4 0.00
305 1 0.00
306 2 0.00
307 1 0.00
309 1 0.00
310 3 0.00
311 2 0.00
312 1 0.00
314 4 0.00
315 141 0.07
316 792 0.39
317 20 0.01
318 13 0.01
319 10 0.00
320 7 0.00
321 16 0.01
322 7 0.00
323 130 0.06
324 382 0.19
325 10 0.00
326 257 0.13
ACGTcount: A:0.44, C:0.11, G:0.12, T:0.33
Consensus pattern (313 bp):
AAATAATGTCATATTCATGATAAAGCGCGAGAATTTGTTTAGTTAAATATAACATTTGTAAACTT
ATCAATTCAAGTACAAAAGCACGCAAATTTATTTAGATAAACATAACTTTAAACTTAACAATTCA
AATATGATAGCATATTAATAAGAAGGCGTAAAAATATTTGTGATAAAGCGCGAGAATTTGTTTAG
TTAAATATAAAATTTGTAAACTTATCAATTCAAGTACAAAAGCACGCGAATTTATTTAGATAAAC
ATAACTTTAAACTTAACAATTCAAATATGATAACATATTAATAAGAAGGCGTA
Found at i:2525 original size:138 final size:138
Alignment explanation
Indices: 2310--2586 Score: 360
Period size: 138 Copynumber: 2.0 Consensus size: 138
2300 ACTTATCAAC
* * * *
2310 TCAAGTACAAAAGCACGCGAATTTATTTAGATCAACATCAACTTTGAACTAAACAATTCAAATAT
1 TCAAGTACAAAAGCACGCAAATTTATTTAGATAAACATCAACTTTAAACTAAACAATTAAAATAT
* * * * ** * *
2375 GATAGCATATTAATAAGAA-GATGTAGAAATAATTACATATTTGTGATAAAGCGCGGTAATTTAT
66 GATACCAGATTAATAAGAAGGGT-TAGAAATAATGACATATTCATGATAAAGCACGGGAATTTAT
2439 TTAGTTAAA
130 TTAGTTAAA
* * * * *
2448 TCAAGTACAAAAGCGCGCAAATTTATTTAGATAAACA-GATGCTTTAAACTTAGCAATTAAAATA
1 TCAAGTACAAAAGCACGCAAATTTATTTAGATAAACATCA-ACTTTAAACTAAACAATTAAAATA
*
2512 TGATACCAGATTAATAAGAAGGGTTAGAAATAATGACATATTCATGATAAAGCATGGGAATTTAT
65 TGATACCAGATTAATAAGAAGGGTTAGAAATAATGACATATTCATGATAAAGCACGGGAATTTAT
2577 TTAGTTAAA
130 TTAGTTAAA
2586 T
1 T
2587 ATAAAATTTA
Statistics
Matches: 119, Mismatches: 18, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
137 1 0.01
138 116 0.97
139 2 0.02
ACGTcount: A:0.44, C:0.11, G:0.15, T:0.31
Consensus pattern (138 bp):
TCAAGTACAAAAGCACGCAAATTTATTTAGATAAACATCAACTTTAAACTAAACAATTAAAATAT
GATACCAGATTAATAAGAAGGGTTAGAAATAATGACATATTCATGATAAAGCACGGGAATTTATT
TAGTTAAA
Found at i:5020 original size:248 final size:247
Alignment explanation
Indices: 4544--6174 Score: 1772
Period size: 248 Copynumber: 6.6 Consensus size: 247
4534 ATTTATTTTG
* * * *
4544 TTTTTTAAATAATGTTTGCAAGTGTTCGGCAAAAAATCATTCTATCATATTTAACTTTTCTTTTA
1 TTTTTT-AATAATGTTTGCACGTGTTCGACAAAAAATCATTCTACCATGTTTAACTTTTCTTTTA
* * * * *
4609 ACAATA-TCTGCATGTGTCTGACAAAAAAAT-ATTTAATTGTATTGCAGTTATGATCGATATTGA
65 ACAATATTC-GCACGTGTCTGAC-AAAAATTCATTCAATTGTATTGTAGTTATGATCGACATTGA
* * * *
4672 ACTACTTCTTTACATGACATGTCTGTGTTTCTAAATATATCCTAATCATATTTTGCCCAAATTTA
128 ACTACTTCTTTACATGACGTGTCTGTGTTTCTAAATATGTCCTAATCATATTTTGTCCACATTTA
* * * *** *
4737 -ATTTTTTTCACAATGCCTACGTGTGTTTGACAAAGATTTATTTTATTGTGTTTAAA
193 TA-GTTTTTCACAATGTCTGCGTGTGTCCAACAAAGATTTATTTTGTTGTGTTT-AA
* * *
4793 TCTTTTTAAT-ATGGTTGCATGTATTCGACAAAAAATCATTCTACCATGTTTAACTTTTCTTTTA
1 T-TTTTTAATAATGTTTGCACGTGTTCGACAAAAAATCATTCTACCATGTTTAACTTTTCTTTTA
* ** * * **
4857 ACAATATTGGCTTGTGTCCGACCAAAATTCATTCAATTGTATTGTAGTTATGATCGGTATTGAAC
65 ACAATATTCGCACGTGTCTGACAAAAATTCATTCAATTGTATTGTAGTTATGATCGACATTGAAC
* * * * *
4922 TACTTCTTTATATGACGTGTTTGTGTTACTAAATATGTCCTACTCATATTTTGTCCACGTTTATA
130 TACTTCTTTACATGACGTGTCTGTGTTTCTAAATATGTCCTAATCATATTTTGTCCACATTTATA
*
4987 GTTTTTCACAATGTCTGCGTGTGTCCAACAAAGATTTAATTTGTTGTGTTTAA
195 GTTTTTCACAATGTCTGCGTGTGTCCAACAAAGATTTATTTTGTTGTGTTTAA
* * * * *
5040 TTTTTT-CTAGTATGTTTTCACGTATTCGACAAAAAATCGTTCTACCATGTTTAATTTTTCTTTT
1 TTTTTTAATA--ATGTTTGCACGTGTTCGACAAAAAATCATTCTACCATGTTTAACTTTTCTTTT
* * * * *
5104 AACAATATTCACACGTGTTTGACAAAAATTCATTCAATTGTATTGCAATTATGATCGAGATTGAA
64 AACAATATTCGCACGTGTCTGACAAAAATTCATTCAATTGTATTGTAGTTATGATCGACATTGAA
** * *
5169 CTACTTCTTTA-A--A--T-T-AATGTTTCTAAATATGTCCTAATCATATTTTGAT-CGCGTTTA
129 CTACTTCTTTACATGACGTGTCTGTGTTTCTAAATATGTCCTAATCATATTTTG-TCCACATTTA
* * * * *
5226 CAGTTTTCCACAATATCTGCATGTGTCCGAA-AAAGATTTATTTTGCTGTGTTTAA
193 TAGTTTTTCACAATGTCTGCGTGTGTCC-AACAAAGATTTATTTTGTTGTGTTTAA
* * *
5281 TTTTTTTTATAATGTTTGCATGTGTTCGACAAAAAATCATTGTACCATGTTTAACTTTTCTTTTA
1 -TTTTTTAATAATGTTTGCACGTGTTCGACAAAAAATCATTCTACCATGTTTAACTTTTCTTTTA
* * *
5346 ACAATATTCGCACCTGTCCGACAAAAATTCATTCAACTGTATTGTAGTTATGATCGACATTGAAC
65 ACAATATTCGCACGTGTCTGACAAAAATTCATTCAATTGTATTGTAGTTATGATCGACATTGAAC
** * * * *
5411 TGTTTCTTTAGATGACGTGTCTGTGTTTCTAAATATATTCTAATTATATTTTGTCCACATTTATA
130 TACTTCTTTACATGACGTGTCTGTGTTTCTAAATATGTCCTAATCATATTTTGTCCACATTTATA
* * * * * *
5476 GATGTTCACAATGACTACGTGTGTCCGACAAAGATTTATTTTGTTGTGTTTACC
195 GTTTTTCACAATGTCTGCGTGTGTCCAACAAAGATTTATTTTGTTGTGTTTA-A
* * *
5530 TTTTTTTATAATGTTTGCACGTGTTCGACAAAAAATCATTCTACCATGTTTAACATTCCTTTTAA
1 TTTTTTAATAATGTTTGCACGTGTTCGACAAAAAATCATTCTACCATGTTTAACTTTTCTTTTAA
* * * * * *
5595 CAATATCCACACGTGTCTGGCAAAAATTCATTCAACTGTATTGTAGTTATGAACGACATTAAACT
66 CAATATTCGCACGTGTCTGACAAAAATTCATTCAATTGTATTGTAGTTATGATCGACATTGAACT
** * *
5660 ACTTCTTTAGTTGATGTGTCTGTGTTTCTAAATATGTCCTAATCATATTTTATCCACATTTATTT
131 ACTTCTTTACATGACGTGTCTGTGTTTCTAAATATGTCCTAATCATATTTTGTCCACATTTA--T
* ** ** *
5725 A-TTTTTCACAATGTCTGTGTGTGTCTGACAATTATATATTTTGTTGTGTTTAA
194 AGTTTTTCACAATGTCTGCGTGTGTCCAACAAAGATTTATTTTGTTGTGTTTAA
* *
5778 TTTTTTAAATAATGTTTGCACGTGTCCGGCAAAAAATCATTCTACCATGTTTAACTTTTCTTTTA
1 TTTTTT-AATAATGTTTGCACGTGTTCGACAAAAAATCATTCTACCATGTTTAACTTTTCTTTTA
* * * * *
5843 ACAATATTTGCACATGT-TCGACAAAAATTCGTTCAATTGTATTGCAGTTATGATTGACATTGAA
65 ACAATATTCGCACGTGTCT-GACAAAAATTCATTCAATTGTATTGTAGTTATGATCGACATTGAA
* * * * * *
5907 GTACTTCTTTACATGACATGTTTGTGTTTCTAAATATGTCCTAATCATATTTTTTCCACGTTTAC
129 CTACTTCTTTACATGACGTGTCTGTGTTTCTAAATATGTCCTAATCATATTTTGTCCACATTTAT
* * * * * * * * *
5972 A-TTTTT-ACATGATGTTTGCGCGTGTTCTAA-AAAAATCTATTCTATTGTGATTATT
194 AGTTTTTCACA--ATGTCTGCGTGTG-TCCAACAAAGATTTATTTTGTTGTGTTTA-A
* * * * ** *
6027 TATTTTTAATAATGTTTGCAAGTGTTCGACAAAAATTCATTCTATCACGTTTAGGTTTTCTTCTA
1 T-TTTTTAATAATGTTTGCACGTGTTCGACAAAAAATCATTCTACCATGTTTAACTTTTCTTTTA
* * * *
6092 ACAATA-TCTGCACGTGTCTGACAAAACTTCATTCAATTGTGTTATAGTTATGATCGACATTGAG
65 ACAATATTC-GCACGTGTCTGACAAAAATTCATTCAATTGTATTGTAGTTATGATCGACATTGAA
* *
6156 TTACTTTTTTTACATGACG
129 CTAC-TTCTTTACATGACG
6175 AGTGTGTTTC
Statistics
Matches: 1169, Mismatches: 180, Indels: 65
0.83 0.13 0.05
Matches are distributed among these distances:
241 194 0.17
242 11 0.01
243 3 0.00
244 1 0.00
245 2 0.00
246 9 0.01
247 18 0.02
248 590 0.50
249 316 0.27
250 25 0.02
ACGTcount: A:0.28, C:0.15, G:0.13, T:0.43
Consensus pattern (247 bp):
TTTTTTAATAATGTTTGCACGTGTTCGACAAAAAATCATTCTACCATGTTTAACTTTTCTTTTAA
CAATATTCGCACGTGTCTGACAAAAATTCATTCAATTGTATTGTAGTTATGATCGACATTGAACT
ACTTCTTTACATGACGTGTCTGTGTTTCTAAATATGTCCTAATCATATTTTGTCCACATTTATAG
TTTTTCACAATGTCTGCGTGTGTCCAACAAAGATTTATTTTGTTGTGTTTAA
Found at i:5499 original size:489 final size:491
Alignment explanation
Indices: 4552--6154 Score: 1780
Period size: 489 Copynumber: 3.2 Consensus size: 491
4542 TGTTTTTTAA
* * * * *
4552 ATAATGTTTGCAAGTGTTCGGCAAAAAATCATTCTATCATATTTAACTTTTCTTTTAACAATA-T
1 ATAATGTTTGCACGTATTCGACAAAAAATCATTCTACCATGTTTAACTTTTCTTTTAACAATATT
* * * * *
4616 CTGCATGTGTCTGACAAAAAAAT-ATTTAATTGTATTGCAGTTATGATCGATATTGAACTACTTC
66 C-ACACGTGTCTGAC-AAAAATTCATTCAATTGTATTGCAGTTATGATCGACATTGAACTACTTC
* ** *
4680 TTTACATGACATGTCTGTGTTTCTAAATATATCCTAATCATATTTTGCCCAAATTTAATTTTTTT
129 TTT--A-GACATGTCTGTGTTTCTAAATATGTCCTAATCATATTTTGATCACATTTAA--TTTTT
* * * * * * *
4745 CACAATGCCTACGTGTGTTTGACAAAGATTTATTTTATTGTGTTTAAATCTTTTTA-ATATGGTT
189 CACAATGTCTGCGTGTGTCTGACAAAGATTTATTTTGTTGTGTTTAATTTTTTTTATA-ATGTTT
* * ***
4809 GCATGTATTCGACAAAAAATCATTCTACCATGTTTAACTTTTCTTTTAACAATATTGGCTTGTGT
253 GCATGTGTTCGACAAAAAATCATTCTACCATGTTTAACTTTTCTTTTAACAATATTCGCACATGT
* ** *
4874 CCGACCAAAATTCATTCAATTGTATTGTAGTTATGATCGGTATTGAACTACTTCTTTATATGACG
318 CCGACAAAAATTCATTCAATTGTATTGTAGTTATGATCGACATTGAACTACTTCTTTACATGACG
* * * * * *
4939 TGTTTGTGTTACTAAATATGTCCTACTCATATTTTGTCCACGTTTATAGTTTTTCACAATGTCTG
383 TGTTTGTGTTTCTAAATATGTCCTAATCATATTTTGTCCACGTTTATAGATGTTCACAATGACTA
5004 CGTGTGTCCAACAAAGATTTAATTTGTTGTGTTTA-ATTTTTTCT
448 CGTGTGTCCAACAAAGATTTAATTTGTTGTGTTTACATTTTTT-T
* * *
5048 AGT-ATGTTTTCACGTATTCGACAAAAAATCGTTCTACCATGTTTAATTTTTCTTTTAACAATAT
1 A-TAATGTTTGCACGTATTCGACAAAAAATCATTCTACCATGTTTAACTTTTCTTTTAACAATAT
* * *
5112 TCACACGTGTTTGACAAAAATTCATTCAATTGTATTGCAATTATGATCGAGATTGAACTACTTCT
65 TCACACGTGTCTGACAAAAATTCATTCAATTGTATTGCAGTTATGATCGACATTGAACTACTTCT
** * * *
5177 TTA-A-AT-T-AATGTTTCTAAATATGTCCTAATCATATTTTGATCGCGTTTACAGTTTTCCACA
130 TTAGACATGTCTGTGTTTCTAAATATGTCCTAATCATATTTTGATCACATTTA-A-TTTTTCACA
* * * * *
5238 ATATCTGCATGTGTCCGAAAAAGATTTATTTTGCTGTGTTTAATTTTTTTTATAATGTTTGCATG
193 ATGTCTGCGTGTGTCTGACAAAGATTTATTTTGTTGTGTTTAATTTTTTTTATAATGTTTGCATG
* *
5303 TGTTCGACAAAAAATCATTGTACCATGTTTAACTTTTCTTTTAACAATATTCGCACCTGTCCGAC
258 TGTTCGACAAAAAATCATTCTACCATGTTTAACTTTTCTTTTAACAATATTCGCACATGTCCGAC
* ** * *
5368 AAAAATTCATTCAACTGTATTGTAGTTATGATCGACATTGAACTGTTTCTTTAGATGACGTGTCT
323 AAAAATTCATTCAATTGTATTGTAGTTATGATCGACATTGAACTACTTCTTTACATGACGTGTTT
* * * *
5433 GTGTTTCTAAATATATTCTAATTATATTTTGTCCACATTTATAGATGTTCACAATGACTACGTGT
388 GTGTTTCTAAATATGTCCTAATCATATTTTGTCCACGTTTATAGATGTTCACAATGACTACGTGT
* * *
5498 GTCCGACAAAGATTTATTTTGTTGTGTTTACCTTTTTTT
453 GTCCAACAAAGATTTAATTTGTTGTGTTTACATTTTTTT
* * * *
5537 ATAATGTTTGCACGTGTTCGACAAAAAATCATTCTACCATGTTTAACATTCCTTTTAACAATATC
1 ATAATGTTTGCACGTATTCGACAAAAAATCATTCTACCATGTTTAACTTTTCTTTTAACAATATT
* * * * *
5602 CACACGTGTCTGGCAAAAATTCATTCAACTGTATTGTAGTTATGAACGACATTAAACTACTTCTT
66 CACACGTGTCTGACAAAAATTCATTCAATTGTATTGCAGTTATGATCGACATTGAACTACTTCTT
**
5667 TAGTTGATGTGTCTGTGTTTCTAAATATGTCCTAATCATATTTT-ATCCACATTTATTTATTTTT
131 TA---GACATGTCTGTGTTTCTAAATATGTCCTAATCATATTTTGAT-CACATTTA---ATTTTT
* ** * **
5731 CACAATGTCTGTGTGTGTCTGACAATTATATATTTTGTTGTGTTTAATTTTTTAAATAATGTTTG
189 CACAATGTCTGCGTGTGTCTGACAAAGATTTATTTTGTTGTGTTTAATTTTTTTTATAATGTTTG
* * * * *
5796 CACGTGTCCGGCAAAAAATCATTCTACCATGTTTAACTTTTCTTTTAACAATATTTGCACATGTT
254 CATGTGTTCGACAAAAAATCATTCTACCATGTTTAACTTTTCTTTTAACAATATTCGCACATGTC
* * * * *
5861 CGACAAAAATTCGTTCAATTGTATTGCAGTTATGATTGACATTGAAGTACTTCTTTACATGACAT
319 CGACAAAAATTCATTCAATTGTATTGTAGTTATGATCGACATTGAACTACTTCTTTACATGACGT
* * * * **
5926 GTTTGTGTTTCTAAATATGTCCTAATCATATTTTTTCCACG-TT-TACATTTTTACATGATGTTT
384 GTTTGTGTTTCTAAATATGTCCTAATCATATTTTGTCCACGTTTATAGATGTTCACA--ATGACT
* * * * * * * *
5989 GCGCGTGTTCTAA-AAAAATCT-ATTCTATTGTGATTA-TTTATTTTT
447 ACGTGTG-TCCAACAAAGATTTAATT-TGTTGTGTTTACATT-TTTTT
* * * * * ** *
6034 AATAATGTTTGCAAGTGTTCGACAAAAATTCATTCTATCACGTTTAGGTTTTCTTCTAACAATA-
1 -ATAATGTTTGCACGTATTCGACAAAAAATCATTCTACCATGTTTAACTTTTCTTTTAACAATAT
* * * **
6098 TCTGCACGTGTCTGACAAAACTTCATTCAATTGTGTTATAGTTATGATCGACATTGA
65 TC-ACACGTGTCTGACAAAAATTCATTCAATTGTATTGCAGTTATGATCGACATTGA
6155 GTTACTTTTT
Statistics
Matches: 931, Mismatches: 152, Indels: 46
0.82 0.13 0.04
Matches are distributed among these distances:
488 1 0.00
489 408 0.44
490 9 0.01
491 2 0.00
492 1 0.00
493 1 0.00
494 2 0.00
495 18 0.02
496 145 0.16
497 240 0.26
498 104 0.11
ACGTcount: A:0.28, C:0.15, G:0.13, T:0.43
Consensus pattern (491 bp):
ATAATGTTTGCACGTATTCGACAAAAAATCATTCTACCATGTTTAACTTTTCTTTTAACAATATT
CACACGTGTCTGACAAAAATTCATTCAATTGTATTGCAGTTATGATCGACATTGAACTACTTCTT
TAGACATGTCTGTGTTTCTAAATATGTCCTAATCATATTTTGATCACATTTAATTTTTCACAATG
TCTGCGTGTGTCTGACAAAGATTTATTTTGTTGTGTTTAATTTTTTTTATAATGTTTGCATGTGT
TCGACAAAAAATCATTCTACCATGTTTAACTTTTCTTTTAACAATATTCGCACATGTCCGACAAA
AATTCATTCAATTGTATTGTAGTTATGATCGACATTGAACTACTTCTTTACATGACGTGTTTGTG
TTTCTAAATATGTCCTAATCATATTTTGTCCACGTTTATAGATGTTCACAATGACTACGTGTGTC
CAACAAAGATTTAATTTGTTGTGTTTACATTTTTTT
Found at i:8377 original size:24 final size:24
Alignment explanation
Indices: 8318--8385 Score: 84
Period size: 24 Copynumber: 2.8 Consensus size: 24
8308 ATTTTTTAGT
*
8318 TAAACTCTA-TTTAATTGTTTCAAA
1 TAAACTC-AGTTTATTTGTTTCAAA
* *
8342 TAAACTCTGTTTATTTGTTTCAAT
1 TAAACTCAGTTTATTTGTTTCAAA
*
8366 TAAACTGAGTTTATTTGTTT
1 TAAACTCAGTTTATTTGTTT
8386 GAGTCAAACT
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
24 38 1.00
ACGTcount: A:0.29, C:0.10, G:0.09, T:0.51
Consensus pattern (24 bp):
TAAACTCAGTTTATTTGTTTCAAA
Found at i:8394 original size:24 final size:24
Alignment explanation
Indices: 8327--8395 Score: 68
Period size: 24 Copynumber: 2.9 Consensus size: 24
8317 TTAAACTCTA
* **
8327 TTTAATTGTTTCAAAT-AAACTCTG
1 TTTATTTGTTTC-AATCAAACTGAG
*
8351 TTTATTTGTTTCAATTAAACTGAG
1 TTTATTTGTTTCAATCAAACTGAG
* *
8375 TTTATTTGTTTGAGTCAAACT
1 TTTATTTGTTTCAATCAAACT
8396 ATTATTAGTC
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
23 3 0.08
24 35 0.92
ACGTcount: A:0.29, C:0.10, G:0.12, T:0.49
Consensus pattern (24 bp):
TTTATTTGTTTCAATCAAACTGAG
Found at i:10361 original size:24 final size:24
Alignment explanation
Indices: 10299--10369 Score: 88
Period size: 24 Copynumber: 3.0 Consensus size: 24
10289 AGAAATAATC
* * * *
10299 TTTCAGTTAAACTCCGTTTAATTG
1 TTTCAATTAAACTCTGATTATTTG
*
10323 TTTCAAATAAACTCTGATTATTTG
1 TTTCAATTAAACTCTGATTATTTG
*
10347 TTTCAATTAAACTCTGCTTATTT
1 TTTCAATTAAACTCTGATTATTT
10370 ATTTGAGTCA
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 40 1.00
ACGTcount: A:0.28, C:0.15, G:0.08, T:0.48
Consensus pattern (24 bp):
TTTCAATTAAACTCTGATTATTTG
Found at i:10382 original size:24 final size:24
Alignment explanation
Indices: 10323--10390 Score: 66
Period size: 24 Copynumber: 2.8 Consensus size: 24
10313 CGTTTAATTG
*
10323 TTTCAAAT-AAACTCTGATTATTTG
1 TTTC-AATCAAACTCTGATTATTTA
* *
10347 TTTCAATTAAACTCTGCTTATTTA
1 TTTCAATCAAACTCTGATTATTTA
* * *
10371 TTTGAGTCAAACTCTTATTA
1 TTTCAATCAAACTCTGATTA
10391 GTATAGATTA
Statistics
Matches: 36, Mismatches: 7, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
23 3 0.08
24 33 0.92
ACGTcount: A:0.31, C:0.15, G:0.07, T:0.47
Consensus pattern (24 bp):
TTTCAATCAAACTCTGATTATTTA
Found at i:11912 original size:15 final size:16
Alignment explanation
Indices: 11886--11919 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
11876 TAAAAATTAA
*
11886 ATTTTTATAAATGTTT
1 ATTTTTATAAATGCTT
11902 ATTTTTA-AAATGCTT
1 ATTTTTATAAATGCTT
11917 ATT
1 ATT
11920 ATATTATGCA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 10 0.59
16 7 0.41
ACGTcount: A:0.32, C:0.03, G:0.06, T:0.59
Consensus pattern (16 bp):
ATTTTTATAAATGCTT
Found at i:12308 original size:90 final size:90
Alignment explanation
Indices: 12155--12336 Score: 355
Period size: 90 Copynumber: 2.0 Consensus size: 90
12145 TTCTTTAAAA
12155 CTCAATTTTTATTCCTAATTTTGCACCACTAATATCTACTTGTTACAACACTTGATTATGAGGTC
1 CTCAATTTTTATTCCTAATTTTGCACCACTAATATCTACTTGTTACAACACTTGATTATGAGGTC
12220 ATTGTGGTAAGTGTGATAATTATTG
66 ATTGTGGTAAGTGTGATAATTATTG
*
12245 CTCAATTTTTATTCCTAATTTTGCACCACTAGTATCTACTTGTTACAACACTTGATTATGAGGTC
1 CTCAATTTTTATTCCTAATTTTGCACCACTAATATCTACTTGTTACAACACTTGATTATGAGGTC
12310 ATTGTGGTAAGTGTGATAATTATTG
66 ATTGTGGTAAGTGTGATAATTATTG
12335 CT
1 CT
12337 TGTCTGTCGC
Statistics
Matches: 91, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
90 91 1.00
ACGTcount: A:0.27, C:0.16, G:0.15, T:0.42
Consensus pattern (90 bp):
CTCAATTTTTATTCCTAATTTTGCACCACTAATATCTACTTGTTACAACACTTGATTATGAGGTC
ATTGTGGTAAGTGTGATAATTATTG
Found at i:15706 original size:25 final size:23
Alignment explanation
Indices: 15636--15738 Score: 106
Period size: 23 Copynumber: 4.4 Consensus size: 23
15626 ACTATAGCGC
15636 GCCCTCTGT-TTAGCACGTT-TCGT
1 GCCCTCTGTATTAGCAC-TTGT-GT
*
15659 GCCCTCTGT-TCAGCACTGTGTGT
1 GCCCTCTGTATTAGCACT-TGTGT
15682 GCCCTCTGTTATTAGCACTTCGTGT
1 GCCCTCTG-TATTAGCACTT-GTGT
*
15707 GCCATCTG-ATTAGCACTTTGTGT
1 GCCCTCTGTATTAGCAC-TTGTGT
15730 GCCCTCTGT
1 GCCCTCTGT
15739 TACCCAACAC
Statistics
Matches: 69, Mismatches: 4, Indels: 13
0.80 0.05 0.15
Matches are distributed among these distances:
22 1 0.01
23 45 0.65
24 5 0.07
25 18 0.26
ACGTcount: A:0.11, C:0.29, G:0.22, T:0.38
Consensus pattern (23 bp):
GCCCTCTGTATTAGCACTTGTGT
Found at i:20792 original size:16 final size:16
Alignment explanation
Indices: 20771--20810 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
20761 GGATCAAATT
20771 GAAGAGAAAGGAAAAA
1 GAAGAGAAAGGAAAAA
* **
20787 GAAGAGTAAGGAGTAA
1 GAAGAGAAAGGAAAAA
20803 GAAGAGAA
1 GAAGAGAA
20811 GAATATCAAC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.60, C:0.00, G:0.35, T:0.05
Consensus pattern (16 bp):
GAAGAGAAAGGAAAAA
Found at i:29250 original size:18 final size:18
Alignment explanation
Indices: 29227--29264 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
29217 ACTAATGAGT
*
29227 AAAATGCAGTGACAAATA
1 AAAATGCAATGACAAATA
*
29245 AAAATGCAATGACAACTA
1 AAAATGCAATGACAAATA
29263 AA
1 AA
29265 TGATATGCAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.58, C:0.13, G:0.13, T:0.16
Consensus pattern (18 bp):
AAAATGCAATGACAAATA
Found at i:41289 original size:22 final size:23
Alignment explanation
Indices: 41251--41293 Score: 79
Period size: 22 Copynumber: 1.9 Consensus size: 23
41241 TTTTTCTCTT
41251 TTTCTTAGGTTTTAGTTATTTTC
1 TTTCTTAGGTTTTAGTTATTTTC
41274 TTTCTTAGG-TTTAGTTATTT
1 TTTCTTAGGTTTTAGTTATTT
41294 CATTTTGTTC
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
22 11 0.55
23 9 0.45
ACGTcount: A:0.14, C:0.07, G:0.14, T:0.65
Consensus pattern (23 bp):
TTTCTTAGGTTTTAGTTATTTTC
Found at i:45186 original size:41 final size:41
Alignment explanation
Indices: 45132--45216 Score: 125
Period size: 41 Copynumber: 2.1 Consensus size: 41
45122 TGACATGTTG
* * **
45132 TGTTGTGACATAGGGGGTTTGTTGTGACATAGACATTCCTA
1 TGTTGTAACATAGGGGGTTGGTTGCAACATAGACATTCCTA
*
45173 TGTTGTAACATAGGGGGTTGGTTGCAACATAGACATTTCTA
1 TGTTGTAACATAGGGGGTTGGTTGCAACATAGACATTCCTA
45214 TGT
1 TGT
45217 CGCGACGAAG
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
41 39 1.00
ACGTcount: A:0.24, C:0.12, G:0.28, T:0.36
Consensus pattern (41 bp):
TGTTGTAACATAGGGGGTTGGTTGCAACATAGACATTCCTA
Found at i:51015 original size:16 final size:16
Alignment explanation
Indices: 50994--51024 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
50984 TTGTGGATCC
50994 CATTTTACCTTTATTA
1 CATTTTACCTTTATTA
*
51010 CATTTTATCTTTATT
1 CATTTTACCTTTATT
51025 TTTACATTAC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.23, C:0.16, G:0.00, T:0.61
Consensus pattern (16 bp):
CATTTTACCTTTATTA
Found at i:54169 original size:151 final size:151
Alignment explanation
Indices: 53895--54184 Score: 517
Period size: 151 Copynumber: 1.9 Consensus size: 151
53885 TAGTATACAA
* *
53895 TAAATGTGGTATTGATTGATATAATTCAGGATTTAAAGCATGATTCTAGCATTGATGAAGTTGCA
1 TAAATGTGGTATTGATAGATATAATTCAGGATTTAAAGCATGATGCTAGCATTGATGAAGTTGCA
* * *
53960 ATTTTAGTTATTCATATCTATAAATTGTCGGTGGAACATTCTGTCATGTGAATGTAATTCATACA
66 ATTTTAGTTATTCATATCTATAAATTATCGGTGCAACATTCTGTCATGTGAATATAATTCATACA
54025 TTAGGATTTAAGGTTTAGGGT
131 TTAGGATTTAAGGTTTAGGGT
* *
54046 TAAATGTTGTATTGATAGGTATAATTCAGGATTTAAAGCATGATGCTAGCATTGATGAAGTTGCA
1 TAAATGTGGTATTGATAGATATAATTCAGGATTTAAAGCATGATGCTAGCATTGATGAAGTTGCA
54111 ATTTTAGTTATTCATATCTATAAATTATCGGTGCAACATTCTGTCATGTGAATATAATTCATACA
66 ATTTTAGTTATTCATATCTATAAATTATCGGTGCAACATTCTGTCATGTGAATATAATTCATACA
54176 TTAGGATTT
131 TTAGGATTT
54185 TAGAAGATTC
Statistics
Matches: 132, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
151 132 1.00
ACGTcount: A:0.32, C:0.09, G:0.19, T:0.40
Consensus pattern (151 bp):
TAAATGTGGTATTGATAGATATAATTCAGGATTTAAAGCATGATGCTAGCATTGATGAAGTTGCA
ATTTTAGTTATTCATATCTATAAATTATCGGTGCAACATTCTGTCATGTGAATATAATTCATACA
TTAGGATTTAAGGTTTAGGGT
Found at i:55598 original size:16 final size:16
Alignment explanation
Indices: 55577--55607 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
55567 TTGTGGATCC
55577 CATTTTACCTTTATTA
1 CATTTTACCTTTATTA
*
55593 CATTTTATCTTTATT
1 CATTTTACCTTTATT
55608 TCATATTATT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.23, C:0.16, G:0.00, T:0.61
Consensus pattern (16 bp):
CATTTTACCTTTATTA
Found at i:66369 original size:3 final size:3
Alignment explanation
Indices: 66332--66357 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
66322 GAAGGAAAAT
66332 GAA GAA GAA GAA GAA GAA GAA GAA GA
1 GAA GAA GAA GAA GAA GAA GAA GAA GA
66358 GCATGAGAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:77197 original size:26 final size:26
Alignment explanation
Indices: 77168--77224 Score: 87
Period size: 26 Copynumber: 2.2 Consensus size: 26
77158 AGGCTTTGAG
*
77168 CGGTGTATATTTAGTAAGCCTCGAGC
1 CGGTGTATATTTAGCAAGCCTCGAGC
* *
77194 CGGTGTATATTTAGCAGGCTTCGAGC
1 CGGTGTATATTTAGCAAGCCTCGAGC
77220 CGGTG
1 CGGTG
77225 AATGTTTTGC
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.19, C:0.19, G:0.32, T:0.30
Consensus pattern (26 bp):
CGGTGTATATTTAGCAAGCCTCGAGC
Found at i:79427 original size:21 final size:21
Alignment explanation
Indices: 79403--79444 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
79393 ACCTGAGTCG
79403 TGTAAGGAGTTTATGGTTTAC
1 TGTAAGGAGTTTATGGTTTAC
79424 TGTAAGGAGTTTATGGTTTAC
1 TGTAAGGAGTTTATGGTTTAC
79445 AATGATACGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.24, C:0.05, G:0.29, T:0.43
Consensus pattern (21 bp):
TGTAAGGAGTTTATGGTTTAC
Found at i:80572 original size:19 final size:20
Alignment explanation
Indices: 80545--80582 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
80535 GAGATGTTAC
80545 AATTCTCTCCCTC-AAAATA
1 AATTCTCTCCCTCGAAAATA
*
80564 AATTTTCTCCCTCGAAAAT
1 AATTCTCTCCCTCGAAAAT
80583 CTTACCAAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 12 0.71
20 5 0.29
ACGTcount: A:0.34, C:0.29, G:0.03, T:0.34
Consensus pattern (20 bp):
AATTCTCTCCCTCGAAAATA
Found at i:82879 original size:16 final size:16
Alignment explanation
Indices: 82858--82888 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
82848 TTATGGATCC
82858 CATTTTACCTTTATTA
1 CATTTTACCTTTATTA
*
82874 CATTTTATCTTTATT
1 CATTTTACCTTTATT
82889 TTCGCATTAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.23, C:0.16, G:0.00, T:0.61
Consensus pattern (16 bp):
CATTTTACCTTTATTA
Found at i:83139 original size:282 final size:285
Alignment explanation
Indices: 82615--83182 Score: 955
Period size: 282 Copynumber: 2.0 Consensus size: 285
82605 GACAGTTTAA
* ** *
82615 ACTAATAAGCAAGACAACGGAAGTTGCTTGGGGATTGAAGGACTTTGGTCCACTTGTTCTTAAGT
1 ACTAACAAGCAAGACAACGGAAGTTGCTTAAGGATTGAAGGAATTTGGTCCACTTGTTCTTAAGT
*
82680 GTGTTGCATTGCCAGCACTGAAAGGTATGGTTAGTGTGCATACTAAAGTCATAGGTCTAATAGAA
66 GTGTTGCATTGCCAGCAATGAAAGGTATGGTTAGTGTGCATACTAAAGTCATA-GTCTAATAGAA
*
82745 AAGCCAAGTTTGGTTTGATGTTCATCGCACTTCATTGCGTCGACAAATTACCTGTTATTCTTAAC
130 AAGCAAAGTTTGGTTTGATGTTCATCGCACTTCATTGCGTCGACAAATTACCTGTTATTCTTAAC
* *
82810 CTTGTAGACCACACTTAGTTTTTTGCTGACTATTCACGTTATGGATCCCATTTTACCTTTATTAC
195 CTTGTAGACCACACTTAGTTTTCTGCTGACTATTCACATTATGGATCCCATTTTACCTTTATTAC
*
82875 A-TTTTATCTTTATTTTCGCATTATT
260 ATTTTTATCTTTATTTTCACATTATT
*
82900 ACTAACAAGTAAGACAACGGAAGTTGCTTAAGGATTGAAGGAATTTGGTCCACTTGTTCTTAAGT
1 ACTAACAAGCAAGACAACGGAAGTTGCTTAAGGATTGAAGGAATTTGGTCCACTTGTTCTTAAGT
* *
82965 GTGTTGCATTGCCAGCAATGGAAGGTATGGTTAGTGTGC-TACTAAATTCAT-GTCTAATAGAAA
66 GTGTTGCATTGCCAGCAATGAAAGGTATGGTTAGTGTGCATACTAAAGTCATAGTCTAATAGAAA
*
83028 AGCAAAGTTTGGTTTGATGTTCATTGCACTTCATTGCGTCGACAAATTACCTGTTATTCTTAACC
131 AGCAAAGTTTGGTTTGATGTTCATCGCACTTCATTGCGTCGACAAATTACCTGTTATTCTTAACC
*
83093 TTGTA-AGCCACACTTAGTTTTCTGCTGACTATTCACATTGTGGATCCCATTTTACCTTTATTAC
196 TTGTAGA-CCACACTTAGTTTTCTGCTGACTATTCACATTATGGATCCCATTTTACCTTTATTAC
*
83157 ATTTTTTTCTTTATTTTCACATTATT
260 ATTTTTATCTTTATTTTCACATTATT
83183 GCTCCAACAA
Statistics
Matches: 266, Mismatches: 15, Indels: 6
0.93 0.05 0.02
Matches are distributed among these distances:
281 1 0.00
282 135 0.51
283 22 0.08
284 11 0.04
285 97 0.36
ACGTcount: A:0.26, C:0.17, G:0.18, T:0.38
Consensus pattern (285 bp):
ACTAACAAGCAAGACAACGGAAGTTGCTTAAGGATTGAAGGAATTTGGTCCACTTGTTCTTAAGT
GTGTTGCATTGCCAGCAATGAAAGGTATGGTTAGTGTGCATACTAAAGTCATAGTCTAATAGAAA
AGCAAAGTTTGGTTTGATGTTCATCGCACTTCATTGCGTCGACAAATTACCTGTTATTCTTAACC
TTGTAGACCACACTTAGTTTTCTGCTGACTATTCACATTATGGATCCCATTTTACCTTTATTACA
TTTTTATCTTTATTTTCACATTATT
Found at i:86733 original size:37 final size:38
Alignment explanation
Indices: 86650--86737 Score: 108
Period size: 38 Copynumber: 2.3 Consensus size: 38
86640 TGCACCCAAG
* * *
86650 ACTATCGTTGCATAAATATTCTTCAAATTCCATCCTGA
1 ACTATCGCTGCATAAATATTCTTCAAATTACATCCAGA
*
86688 ACTATCGCTGCATAAGTATTCTTC-AATTACATCCAAGA
1 ACTATCGCTGCATAAATATTCTTCAAATTACATCC-AGA
*
86726 A-TGTCGCTGCAT
1 ACTATCGCTGCAT
86738 GAACATGTCA
Statistics
Matches: 44, Mismatches: 5, Indels: 3
0.85 0.10 0.06
Matches are distributed among these distances:
37 19 0.43
38 25 0.57
ACGTcount: A:0.31, C:0.24, G:0.11, T:0.34
Consensus pattern (38 bp):
ACTATCGCTGCATAAATATTCTTCAAATTACATCCAGA
Found at i:99309 original size:52 final size:52
Alignment explanation
Indices: 99231--99520 Score: 431
Period size: 52 Copynumber: 5.6 Consensus size: 52
99221 ATTTCATTTA
* * * *
99231 ATACTGACAATGACACATAGTCATCAGACCTCTTAATCCGTAAAGGATCCAT
1 ATACTCACGATGACACATAGTCATCAGACCTCATAATCCGTAAAGGATTCAT
* *
99283 ATACTCATGATCG-CACATAGTCATCAGACCTCATAATCCAT-AAGGATTCAT
1 ATACTCACGAT-GACACATAGTCATCAGACCTCATAATCCGTAAAGGATTCAT
* ** *
99334 ATACTCACGATGACACATAGTCATCGGACCTCATAATCAATAATGGATTCAT
1 ATACTCACGATGACACATAGTCATCAGACCTCATAATCCGTAAAGGATTCAT
* *
99386 ATACTCACGATGAAAAATAGTCATCAGACCTCATAATCCGTAAAGGATTCAT
1 ATACTCACGATGACACATAGTCATCAGACCTCATAATCCGTAAAGGATTCAT
99438 ATACTCACGATGACACATAGTCATCAGACCTCATAATCCGTAAAGGATTCAT
1 ATACTCACGATGACACATAGTCATCAGACCTCATAATCCGTAAAGGATTCAT
* *
99490 ATACTCACGATGACACAAAATCATCAGACCT
1 ATACTCACGATGACACATAGTCATCAGACCT
99521 TTACATTTAC
Statistics
Matches: 215, Mismatches: 20, Indels: 6
0.89 0.08 0.02
Matches are distributed among these distances:
50 1 0.00
51 45 0.21
52 168 0.78
53 1 0.00
ACGTcount: A:0.38, C:0.24, G:0.13, T:0.25
Consensus pattern (52 bp):
ATACTCACGATGACACATAGTCATCAGACCTCATAATCCGTAAAGGATTCAT
Found at i:101160 original size:21 final size:21
Alignment explanation
Indices: 101136--101175 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
101126 TAGTGCAGAC
*
101136 TTCTATCGATACAAGTGACAG
1 TTCTACCGATACAAGTGACAG
* *
101157 TTCTACCGTTATAAGTGAC
1 TTCTACCGATACAAGTGAC
101176 TCTTTTACCA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.30, C:0.20, G:0.17, T:0.33
Consensus pattern (21 bp):
TTCTACCGATACAAGTGACAG
Found at i:102017 original size:52 final size:52
Alignment explanation
Indices: 101947--102078 Score: 228
Period size: 52 Copynumber: 2.5 Consensus size: 52
101937 TCATTTAATG
* *
101947 CTCACGATGGCACATAGTCATCGGACCTCATAATCCGTAAAGGATTCATATA
1 CTCACGATGACACATAGTCATCGGACCTCATAATCCATAAAGGATTCATATA
* *
101999 CTCACGATGACACGTAGTCATCAGACCTCATAATCCATAAAGGATTCATATA
1 CTCACGATGACACATAGTCATCGGACCTCATAATCCATAAAGGATTCATATA
102051 CTCACGATGACACATAGTCATCGGACCT
1 CTCACGATGACACATAGTCATCGGACCT
102079 ATTTCATTTA
Statistics
Matches: 74, Mismatches: 6, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
52 74 1.00
ACGTcount: A:0.33, C:0.27, G:0.16, T:0.24
Consensus pattern (52 bp):
CTCACGATGACACATAGTCATCGGACCTCATAATCCATAAAGGATTCATATA
Found at i:104481 original size:12 final size:12
Alignment explanation
Indices: 104460--104488 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
104450 GAGATGAAGG
104460 TTTT-GGAGTGT
1 TTTTGGGAGTGT
104471 TTTTGGGAGTGT
1 TTTTGGGAGTGT
104483 TTTTGG
1 TTTTGG
104489 ATGCACGAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 4 0.24
12 13 0.76
ACGTcount: A:0.07, C:0.00, G:0.38, T:0.55
Consensus pattern (12 bp):
TTTTGGGAGTGT
Found at i:127182 original size:21 final size:20
Alignment explanation
Indices: 127143--127183 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
127133 TTCAATTCTT
* *
127143 TTTATCTATTTTCCCTTGGA
1 TTTAACTATTTTACCTTGGA
127163 TTTAACTATTTTGACCTTGGA
1 TTTAACTATTTT-ACCTTGGA
127184 AGTGCAATTG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 11 0.61
21 7 0.39
ACGTcount: A:0.20, C:0.17, G:0.12, T:0.51
Consensus pattern (20 bp):
TTTAACTATTTTACCTTGGA
Found at i:129223 original size:52 final size:52
Alignment explanation
Indices: 129134--129320 Score: 257
Period size: 52 Copynumber: 3.6 Consensus size: 52
129124 ATTTCATTTA
* * * ** * *
129134 ATACTCACGACGACACATAGTCATCGAACCTTTTAATCCATAAAGGAATCAT
1 ATACTCAAGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCAT
*
129186 ATACTAAAGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCAT
1 ATACTCAAGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCAT
* *
129238 ATACTCATGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCAA
1 ATACTCAAGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCAT
* * *
129290 ATACTCACGGTGACATATAGTCATCGGACCT
1 ATACTCAAGATGACACATAGTCATCGGACCT
129321 ATTTCATTTA
Statistics
Matches: 121, Mismatches: 14, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
52 121 1.00
ACGTcount: A:0.36, C:0.24, G:0.15, T:0.25
Consensus pattern (52 bp):
ATACTCAAGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCAT
Found at i:132587 original size:26 final size:27
Alignment explanation
Indices: 132530--132616 Score: 106
Period size: 26 Copynumber: 3.3 Consensus size: 27
132520 TCTTAATTCT
* *
132530 GGCTCGATAAGAGCGTAAACTCTGTCTA
1 GGCTCGATATGAGC-TAAACTCTGTCTG
* *
132558 GGCTCGA-ATGAGCTAAACTTTGTTTG
1 GGCTCGATATGAGCTAAACTCTGTCTG
132584 GGCTC-ATATGAGCTAAACTCTGTCTG
1 GGCTCGATATGAGCTAAACTCTGTCTG
*
132610 GTCTCGA
1 GGCTCGA
132617 ATGTGTTAAA
Statistics
Matches: 50, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
25 1 0.02
26 36 0.72
27 6 0.12
28 7 0.14
ACGTcount: A:0.24, C:0.21, G:0.25, T:0.30
Consensus pattern (27 bp):
GGCTCGATATGAGCTAAACTCTGTCTG
Found at i:140401 original size:21 final size:21
Alignment explanation
Indices: 140341--140412 Score: 74
Period size: 21 Copynumber: 3.4 Consensus size: 21
140331 GGAGTTTTTA
* *
140341 GTATCGGTA-AATGCATGACTT
1 GTATCGGTAGAA-CCATCACTT
* **
140362 GTTTCGGTAGAACTGTCACTT
1 GTATCGGTAGAACCATCACTT
*
140383 GTATCGGTAGAACCATCACTA
1 GTATCGGTAGAACCATCACTT
140404 GTATCGGTA
1 GTATCGGTA
140413 AAAGTCAGCT
Statistics
Matches: 41, Mismatches: 9, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
21 39 0.95
22 2 0.05
ACGTcount: A:0.26, C:0.18, G:0.24, T:0.32
Consensus pattern (21 bp):
GTATCGGTAGAACCATCACTT
Found at i:141450 original size:26 final size:26
Alignment explanation
Indices: 141421--141494 Score: 112
Period size: 26 Copynumber: 2.8 Consensus size: 26
141411 CATAAATTGT
*
141421 GTCTGGGCTCGAACGAGCTAAACTCG
1 GTCTGGGCTCGAATGAGCTAAACTCG
* *
141447 GTCTGGGCTCGAATGATCTAAACTCT
1 GTCTGGGCTCGAATGAGCTAAACTCG
*
141473 GTCTGGGCTTGAATGAGCTAAA
1 GTCTGGGCTCGAATGAGCTAAA
141495 TTTTTGTATC
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 43 1.00
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.26
Consensus pattern (26 bp):
GTCTGGGCTCGAATGAGCTAAACTCG
Found at i:145539 original size:24 final size:24
Alignment explanation
Indices: 145512--145557 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
145502 TTTAACTAAC
145512 ATTCAAACAACAACACTAAGTTTA
1 ATTCAAACAACAACACTAAGTTTA
* *
145536 ATTCAAATAACAACATTAAGTT
1 ATTCAAACAACAACACTAAGTT
145558 GCTCACTGAG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.50, C:0.17, G:0.04, T:0.28
Consensus pattern (24 bp):
ATTCAAACAACAACACTAAGTTTA
Found at i:148314 original size:20 final size:20
Alignment explanation
Indices: 148289--148331 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
148279 ATTCTACCTA
*
148289 AAGCATTAAACCCTTCATTT
1 AAGCATTAAACCCTCCATTT
*
148309 AAGCATTGAACCCTCCATTT
1 AAGCATTAAACCCTCCATTT
148329 AAG
1 AAG
148332 TTTCATTTTG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.35, C:0.26, G:0.09, T:0.30
Consensus pattern (20 bp):
AAGCATTAAACCCTCCATTT
Found at i:157104 original size:28 final size:28
Alignment explanation
Indices: 157067--157121 Score: 110
Period size: 28 Copynumber: 2.0 Consensus size: 28
157057 TCAGTCTAAT
157067 TTTTGTTTCTTTTTTCTTCATGACATAA
1 TTTTGTTTCTTTTTTCTTCATGACATAA
157095 TTTTGTTTCTTTTTTCTTCATGACATA
1 TTTTGTTTCTTTTTTCTTCATGACATA
157122 CTTTAAGCCT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.16, C:0.15, G:0.07, T:0.62
Consensus pattern (28 bp):
TTTTGTTTCTTTTTTCTTCATGACATAA
Found at i:157174 original size:96 final size:95
Alignment explanation
Indices: 157033--157223 Score: 337
Period size: 96 Copynumber: 2.0 Consensus size: 95
157023 ATCTATAGAT
*
157033 CCTGAAGCAACAACACTCATCTCATCAGTCTAATTTTTGTTTCTTTTTTCTTCATGACATAATTT
1 CCTGAAGCAACAACACTCATCTCATCAATCTAATTTTTGTTTCTTTTTTCTTCATGACATAATTT
157098 TGTTTCTTTTTTCTTCATGACATACTTTAAG
66 TGTTTC-TTTTTCTTCATGACATACTTTAAG
* * *
157129 CCTGAAGCAACAACACTCATGTCATCAATCTAGTTTTTGTTTCTTTTTTCTTCATGACATACTTT
1 CCTGAAGCAACAACACTCATCTCATCAATCTAATTTTTGTTTCTTTTTTCTTCATGACATAATTT
157194 TGTTTCTTTTTCTTCATGACATACTTTAAG
66 TGTTTCTTTTTCTTCATGACATACTTTAAG
157224 GTAGAATGGT
Statistics
Matches: 91, Mismatches: 4, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
95 24 0.26
96 67 0.74
ACGTcount: A:0.24, C:0.21, G:0.09, T:0.47
Consensus pattern (95 bp):
CCTGAAGCAACAACACTCATCTCATCAATCTAATTTTTGTTTCTTTTTTCTTCATGACATAATTT
TGTTTCTTTTTCTTCATGACATACTTTAAG
Found at i:157211 original size:27 final size:28
Alignment explanation
Indices: 157163--157220 Score: 109
Period size: 27 Copynumber: 2.1 Consensus size: 28
157153 TCAATCTAGT
157163 TTTTGTTTCTTTTTTCTTCATGACATAC
1 TTTTGTTTCTTTTTTCTTCATGACATAC
157191 TTTTGTTTC-TTTTTCTTCATGACATAC
1 TTTTGTTTCTTTTTTCTTCATGACATAC
157218 TTT
1 TTT
157221 AAGGTAGAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
27 21 0.70
28 9 0.30
ACGTcount: A:0.14, C:0.17, G:0.07, T:0.62
Consensus pattern (28 bp):
TTTTGTTTCTTTTTTCTTCATGACATAC
Found at i:159533 original size:20 final size:20
Alignment explanation
Indices: 159500--159562 Score: 65
Period size: 20 Copynumber: 3.1 Consensus size: 20
159490 ACAATTTTAA
* *
159500 AAATCAAGTTAAAATGATTTT
1 AAATAAAGTCAAAAT-ATTTT
*
159521 AAAT-AAGTCAAAATAATTT
1 AAATAAAGTCAAAATATTTT
*
159540 GAATAAAGTCAAAATCATTTT
1 AAATAAAGTCAAAAT-ATTTT
159561 AA
1 AA
159563 CACTTCAAAA
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
19 7 0.20
20 19 0.54
21 9 0.26
ACGTcount: A:0.52, C:0.06, G:0.08, T:0.33
Consensus pattern (20 bp):
AAATAAAGTCAAAATATTTT
Found at i:159675 original size:21 final size:21
Alignment explanation
Indices: 159651--159697 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
159641 CAAACAATTT
*
159651 AACACCTCAAAAT-CATTTTCA
1 AACAACTCAAAATAC-TTTTCA
*
159672 AACAAGTCAAAATACTTTTCA
1 AACAACTCAAAATACTTTTCA
159693 AACAA
1 AACAA
159698 TTTAATCTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 22 0.96
22 1 0.04
ACGTcount: A:0.49, C:0.23, G:0.02, T:0.26
Consensus pattern (21 bp):
AACAACTCAAAATACTTTTCA
Found at i:161964 original size:35 final size:36
Alignment explanation
Indices: 161883--161965 Score: 107
Period size: 36 Copynumber: 2.3 Consensus size: 36
161873 TGACATTCTA
* * *
161883 CATGTTAAGCATGTTATTATTTTGATTTTTTATTCG
1 CATGTTAAGCATGTCATTATTTTGATTTCTGATTCG
161919 CATGTTAAGCATGTCATTATTTTGA-TTCTGA-TCTG
1 CATGTTAAGCATGTCATTATTTTGATTTCTGATTC-G
*
161954 CATGTGAAGCAT
1 CATGTTAAGCAT
161966 CCCACTGTGT
Statistics
Matches: 42, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
34 2 0.05
35 16 0.38
36 24 0.57
ACGTcount: A:0.24, C:0.12, G:0.17, T:0.47
Consensus pattern (36 bp):
CATGTTAAGCATGTCATTATTTTGATTTCTGATTCG
Found at i:164968 original size:9 final size:9
Alignment explanation
Indices: 164914--164968 Score: 58
Period size: 9 Copynumber: 6.1 Consensus size: 9
164904 TTGAAAAATC
*
164914 TTTTATAAT
1 TTTTATATT
164923 TTTTATACTT
1 TTTTATA-TT
*
164933 TTTTATACT
1 TTTTATATT
164942 TTTTAT-TT
1 TTTTATATT
* *
164950 TTTAAAATT
1 TTTTATATT
164959 TTTTATATT
1 TTTTATATT
164968 T
1 T
164969 AAAAAATTAA
Statistics
Matches: 37, Mismatches: 7, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
8 5 0.14
9 24 0.65
10 8 0.22
ACGTcount: A:0.25, C:0.04, G:0.00, T:0.71
Consensus pattern (9 bp):
TTTTATATT
Found at i:167278 original size:14 final size:14
Alignment explanation
Indices: 167229--167277 Score: 55
Period size: 15 Copynumber: 3.4 Consensus size: 14
167219 AGATCTGTAT
*
167229 ATAAAACTATAATAA
1 ATAAAATTAT-ATAA
167244 ATAAAATTAT-TAA
1 ATAAAATTATATAA
167257 ATTAAAATTAATATAA
1 A-TAAAATT-ATATAA
167273 ATAAA
1 ATAAA
167278 TAATTTTTAA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
13 4 0.13
14 7 0.23
15 15 0.50
16 4 0.13
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (14 bp):
ATAAAATTATATAA
Found at i:171522 original size:7 final size:7
Alignment explanation
Indices: 171510--171547 Score: 51
Period size: 7 Copynumber: 5.6 Consensus size: 7
171500 AAAATATATT
171510 TATAATA
1 TATAATA
*
171517 TATAATT
1 TATAATA
171524 TATAATA
1 TATAATA
*
171531 TATAAAA
1 TATAATA
171538 TA-AATA
1 TATAATA
171544 TATA
1 TATA
171548 TTATTCAAGC
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
6 5 0.19
7 21 0.81
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (7 bp):
TATAATA
Found at i:175616 original size:46 final size:46
Alignment explanation
Indices: 175537--175625 Score: 124
Period size: 46 Copynumber: 1.9 Consensus size: 46
175527 ATTTGTAGTA
** * *
175537 CACATGATAACTACAATATTTTCCTAGTACATAACTAGTATTATAC
1 CACATGATAACTACAATATCGTCCAAGTACATAACTAATATTATAC
* *
175583 CACATGATAAGTACAATATCGTCCAAGTGCATAACTAATATTA
1 CACATGATAACTACAATATCGTCCAAGTACATAACTAATATTA
175626 CAAATTAGTA
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
46 37 1.00
ACGTcount: A:0.40, C:0.19, G:0.09, T:0.31
Consensus pattern (46 bp):
CACATGATAACTACAATATCGTCCAAGTACATAACTAATATTATAC
Found at i:175644 original size:59 final size:59
Alignment explanation
Indices: 175572--175686 Score: 176
Period size: 59 Copynumber: 1.9 Consensus size: 59
175562 AGTACATAAC
* * * *
175572 TAGTATTATACCACATGATAAGTACAATATCGTCCAAGTGCATAACTAATATTACAAAT
1 TAGTAGTACACCACATGATAACTAAAATATCGTCCAAGTGCATAACTAATATTACAAAT
* *
175631 TAGTAGTACACCACATGATAACTAAAATATTGTCCAAGTGCATAACTAGTATTACA
1 TAGTAGTACACCACATGATAACTAAAATATCGTCCAAGTGCATAACTAATATTACA
175687 CCAAATAATT
Statistics
Matches: 50, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
59 50 1.00
ACGTcount: A:0.42, C:0.17, G:0.11, T:0.30
Consensus pattern (59 bp):
TAGTAGTACACCACATGATAACTAAAATATCGTCCAAGTGCATAACTAATATTACAAAT
Found at i:175699 original size:19 final size:19
Alignment explanation
Indices: 175672--175708 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
175662 GTCCAAGTGC
*
175672 ATAACTAGTATTACACCAA
1 ATAACTAGTACTACACCAA
*
175691 ATAATTAGTACTACACCA
1 ATAACTAGTACTACACCA
175709 CATTAAAGAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.46, C:0.22, G:0.05, T:0.27
Consensus pattern (19 bp):
ATAACTAGTACTACACCAA
Found at i:176705 original size:32 final size:32
Alignment explanation
Indices: 176664--176739 Score: 109
Period size: 32 Copynumber: 2.4 Consensus size: 32
176654 CAACCATTTA
*
176664 AATATCCAACAAGC-TTGAAACATAATAAATTC
1 AATATCCAACAA-CTTTAAAACATAATAAATTC
*
176696 AATATCCAACAACTTTAAAACATAATAATTTC
1 AATATCCAACAACTTTAAAACATAATAAATTC
*
176728 AAAATCCAACAA
1 AATATCCAACAA
176740 AATAATTTCA
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
31 1 0.03
32 39 0.98
ACGTcount: A:0.53, C:0.20, G:0.03, T:0.25
Consensus pattern (32 bp):
AATATCCAACAACTTTAAAACATAATAAATTC
Found at i:180555 original size:25 final size:23
Alignment explanation
Indices: 180527--180573 Score: 67
Period size: 25 Copynumber: 2.0 Consensus size: 23
180517 AGTTGGATCC
180527 GAATTAAATTCTAAAAAGATAATTA
1 GAATTAAA-TCTAAAAA-ATAATTA
*
180552 GAATTAAATCTAAATAATAATT
1 GAATTAAATCTAAAAAATAATT
180574 CCCTAATTTG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 6 0.29
24 7 0.33
25 8 0.38
ACGTcount: A:0.55, C:0.04, G:0.06, T:0.34
Consensus pattern (23 bp):
GAATTAAATCTAAAAAATAATTA
Found at i:181907 original size:14 final size:14
Alignment explanation
Indices: 181871--181916 Score: 56
Period size: 14 Copynumber: 3.1 Consensus size: 14
181861 TTAAAAACCC
*
181871 AAACATAATTCTTA
1 AAACACAATTCTTA
181885 AAACCCACAATTCTTA
1 AAA--CACAATTCTTA
*
181901 AAACACAATTATTA
1 AAACACAATTCTTA
181915 AA
1 AA
181917 GCCAGGTCAA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
14 15 0.54
16 13 0.46
ACGTcount: A:0.52, C:0.20, G:0.00, T:0.28
Consensus pattern (14 bp):
AAACACAATTCTTA
Found at i:185682 original size:20 final size:18
Alignment explanation
Indices: 185657--185708 Score: 59
Period size: 20 Copynumber: 2.7 Consensus size: 18
185647 TCAATATTTA
185657 AATCAAGTTAAAATGGTTTC
1 AATCAAGTTAAAAT--TTTC
*
185677 AATCAAGTAAGAAATTTTC
1 AATCAAGTTA-AAATTTTC
185696 AATCAAAGTTAAA
1 AATC-AAGTTAAA
185709 TTGTTTTTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
19 10 0.36
20 14 0.50
21 4 0.14
ACGTcount: A:0.48, C:0.10, G:0.12, T:0.31
Consensus pattern (18 bp):
AATCAAGTTAAAATTTTC
Found at i:191408 original size:178 final size:178
Alignment explanation
Indices: 191106--191463 Score: 619
Period size: 178 Copynumber: 2.0 Consensus size: 178
191096 CTCGTACTTG
* * *
191106 TTCTTAGTTTGTGGGGAAGGGTTGTCTGCTCTTTTTCGTTTAGGTGTGGCAAACAGAAGTTTGAA
1 TTCTTAGTTTGTGAGGAAGGGTTGTCTGCTCTTTTACGTTTAGCTGTGGCAAACAGAAGTTTGAA
*
191171 AGGGTACCAAATCAATAGATATGCTCTTTTAGTGACACACCTTTTCTTCACAGATGATAGTCTCA
66 AGGGTACCAAATCAATAGATATGCTCTTTTAGTGACACACCTTTTCTTCACAAATGATAGTCTCA
191236 TCTTTGGAGAGGCTACGGTTAAAGGGGCAAATGGTTTAAAGAATTGTC
131 TCTTTGGAGAGGCTACGGTTAAAGGGGCAAATGGTTTAAAGAATTGTC
191284 TTCTTAGTTTGTGAGGAAGGGTTGTCTGCTCTTTTACGTTT-GACTGTGGCAAACAGAAGTTTGA
1 TTCTTAGTTTGTGAGGAAGGGTTGTCTGCTCTTTTACGTTTAG-CTGTGGCAAACAGAAGTTTGA
* **
191348 AAGGGTACCGAATCAATAGATATGCTCTTTTAGTGACACACCTTTTCTTCGTAAATGATAGTCTC
65 AAGGGTACCAAATCAATAGATATGCTCTTTTAGTGACACACCTTTTCTTCACAAATGATAGTCTC
* *
191413 ATCTTTGGAGAGGCTATGGTTGAAGGGGCAAATGGTTTAAAGAATTGTC
130 ATCTTTGGAGAGGCTACGGTTAAAGGGGCAAATGGTTTAAAGAATTGTC
191462 TT
1 TT
191464 AATTCTTATG
Statistics
Matches: 170, Mismatches: 9, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
177 1 0.01
178 169 0.99
ACGTcount: A:0.26, C:0.14, G:0.25, T:0.35
Consensus pattern (178 bp):
TTCTTAGTTTGTGAGGAAGGGTTGTCTGCTCTTTTACGTTTAGCTGTGGCAAACAGAAGTTTGAA
AGGGTACCAAATCAATAGATATGCTCTTTTAGTGACACACCTTTTCTTCACAAATGATAGTCTCA
TCTTTGGAGAGGCTACGGTTAAAGGGGCAAATGGTTTAAAGAATTGTC
Found at i:195152 original size:101 final size:100
Alignment explanation
Indices: 195011--195226 Score: 243
Period size: 101 Copynumber: 2.1 Consensus size: 100
195001 TTCTAGTTTT
** * *
195011 AGGAGTATAAGATTCGCCTTTGCAGCTTCAATCTACCCCTCTACAGCTTTAGGTGTATGATATTC
1 AGGAGTATAAGATTCGCCCATGCAGCTTCAATCTACCCCTCTACAGCTTTAAGTGTATGAGATTC
* *
195076 ACCATTGCGGATTTAATCTACCCCTCTTTCAGCTTC
66 ACCATTGCGGATTCAATCTACCCCTC-TACAGCTTC
** * * ** *
195112 AGGAGTATAAGATTCGCCCATGTGGCTTTAGTCTGTCCCTCTATAGCTTTAAGTGTATGAGATTC
1 AGGAGTATAAGATTCGCCCATGCAGCTTCAATCTACCCCTCTACAGCTTTAAGTGTATGAGATTC
* ** * * *
195177 ATCATTGTTGCTTCAATCTACCCCTCTACAGTTTT
66 ACCATTGCGGATTCAATCTACCCCTCTACAGCTTC
*
195212 AGGGGTATAAGATTC
1 AGGAGTATAAGATTC
195227 ATTGTTTTGT
Statistics
Matches: 95, Mismatches: 20, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
100 20 0.21
101 75 0.79
ACGTcount: A:0.23, C:0.23, G:0.18, T:0.36
Consensus pattern (100 bp):
AGGAGTATAAGATTCGCCCATGCAGCTTCAATCTACCCCTCTACAGCTTTAAGTGTATGAGATTC
ACCATTGCGGATTCAATCTACCCCTCTACAGCTTC
Found at i:195228 original size:50 final size:50
Alignment explanation
Indices: 195008--195227 Score: 190
Period size: 50 Copynumber: 4.4 Consensus size: 50
194998 TTTTTCTAGT
* * *
195008 TTTAGGAGTATAAGATTCGCCTTTGCAGCTTCAATCTACCCCTCTACAGC
1 TTTAGGAGTATAAGATTCACCATTGCGGCTTCAATCTACCCCTCTACAGC
* * * * * *
195058 TTTAGGTGTATGATATTCACCATTGCGGATTTAATCTACCCCTCTTTCAGC
1 TTTAGGAGTATAAGATTCACCATTGCGGCTTCAATCTACCCCTC-TACAGC
* * * * * ** *
195109 TTCAGGAGTATAAGATTCGCCCA-TGTGGCTTTAGTCTGTCCCTCTATAGC
1 TTTAGGAGTATAAGATTC-ACCATTGCGGCTTCAATCTACCCCTCTACAGC
* * * * ** *
195159 TTTAAGTGTATGAGATTCATCATTGTTGCTTCAATCTACCCCTCTACAGT
1 TTTAGGAGTATAAGATTCACCATTGCGGCTTCAATCTACCCCTCTACAGC
*
195209 TTTAGGGGTATAAGATTCA
1 TTTAGGAGTATAAGATTCA
195228 TTGTTTTGTC
Statistics
Matches: 130, Mismatches: 37, Indels: 6
0.75 0.21 0.03
Matches are distributed among these distances:
49 2 0.02
50 90 0.69
51 35 0.27
52 3 0.02
ACGTcount: A:0.23, C:0.23, G:0.18, T:0.36
Consensus pattern (50 bp):
TTTAGGAGTATAAGATTCACCATTGCGGCTTCAATCTACCCCTCTACAGC
Found at i:201355 original size:12 final size:12
Alignment explanation
Indices: 201335--201367 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
201325 GGCCTTATAA
201335 GCCCTTTCTGAT
1 GCCCTTTCTGAT
*
201347 GCTCTTTCTGAT
1 GCCCTTTCTGAT
201359 GCCCTTTCT
1 GCCCTTTCT
201368 TCAGAAGTAC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.06, C:0.33, G:0.15, T:0.45
Consensus pattern (12 bp):
GCCCTTTCTGAT
Found at i:209159 original size:34 final size:34
Alignment explanation
Indices: 209110--209194 Score: 125
Period size: 34 Copynumber: 2.5 Consensus size: 34
209100 ACTGAATTTT
* *
209110 CGAATTTTTGAATTTTTATAACATTGTTTTATAC
1 CGAATTTTCGGATTTTTATAACATTGTTTTATAC
* *
209144 CGGATTTTCGGATTTTTATAACATTTTTTTATAC
1 CGAATTTTCGGATTTTTATAACATTGTTTTATAC
*
209178 CGAATTTTTGGATTTTT
1 CGAATTTTCGGATTTTT
209195 CGGTGTGAAT
Statistics
Matches: 45, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
34 45 1.00
ACGTcount: A:0.25, C:0.09, G:0.12, T:0.54
Consensus pattern (34 bp):
CGAATTTTCGGATTTTTATAACATTGTTTTATAC
Found at i:212196 original size:24 final size:25
Alignment explanation
Indices: 212149--212197 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
212139 GATAAAAATT
* * *
212149 GATTTAATTTTTTGAAAATTATAAA
1 GATTTAAGTTATTGAAAATGATAAA
212174 GATTTAAGTTATT-AAAATGATAAA
1 GATTTAAGTTATTGAAAATGATAAA
212198 ATTGTATTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
24 10 0.48
25 11 0.52
ACGTcount: A:0.47, C:0.00, G:0.10, T:0.43
Consensus pattern (25 bp):
GATTTAAGTTATTGAAAATGATAAA
Found at i:217561 original size:33 final size:33
Alignment explanation
Indices: 217485--217561 Score: 93
Period size: 32 Copynumber: 2.4 Consensus size: 33
217475 CCTATTTACT
* * * * *
217485 TAAAATAAATAATTTTAGTCAAAATAAAATTAG
1 TAAAATAAACAAATTTAATCAAAACAAAATTAA
*
217518 GAAAAT-AACAAATTTAATCAAAACAAAATTAA
1 TAAAATAAACAAATTTAATCAAAACAAAATTAA
217550 TAAAATAAACAA
1 TAAAATAAACAA
217562 CTTTGACTAA
Statistics
Matches: 36, Mismatches: 7, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
32 26 0.72
33 10 0.28
ACGTcount: A:0.64, C:0.06, G:0.04, T:0.26
Consensus pattern (33 bp):
TAAAATAAACAAATTTAATCAAAACAAAATTAA
Found at i:238092 original size:91 final size:87
Alignment explanation
Indices: 237951--238279 Score: 231
Period size: 91 Copynumber: 3.7 Consensus size: 87
237941 GTTTATACTT
* * * *
237951 ACTTGGATACATAAACTTTCACAATGCGTTGAAAAGACCCTCAAACTTTTTCAAAAAAAAAATTG
1 ACTTGGATACTTAAACTTTCAAAATGCATAGAAAAGACCCTCAAACTTTTTCAAAAAAAAAA---
* *
238016 ATTAAGCCCCTATATTTTTTTCACTC-
63 ACTAAGCCCC--TATTTTTTGCACTCA
* * * ** *
238042 ACTTGGATACTTAAACTTTCATAATGCATA-AGAAATACCTTCAATTTTTTTCAAAAAAAGAAAC
1 ACTTGGATACTTAAACTTTCAAAATGCATAGA-AAAGACCCTCAAACTTTTTCAAAAAAAAAAAC
238106 TAAGCCCCTATTTTTTGCACTCA
65 TAAGCCCCTATTTTTTGCACTCA
* * * * ****
238129 ATTTGG-TACTTGAACTTTCAAAATGTATCAAAAAAG-CCCTCAAACTTAAAAAAAAAAAAAAAG
1 ACTTGGATACTTAAACTTTCAAAATGCAT-AGAAAAGACCCTCAAACTTTTTCAAAAAAAAAAA-
*
238192 CAATTAAGCTCATGCT-TTTGTTTGCACTC-
64 C---TAAGC-C--CCTATTT-TTTGCACTCA
* * * ** *
238221 ACTTGAATACTTAAACTTTTACAATAAATA-AAAAAACCCTCAAACTTTTTCAAAAAAAA
1 ACTTGGATACTTAAACTTTCAAAATGCATAGAAAAGACCCTCAAACTTTTTCAAAAAAAA
238280 GCAATTAAGC
Statistics
Matches: 187, Mismatches: 37, Indels: 27
0.75 0.15 0.11
Matches are distributed among these distances:
86 50 0.27
87 10 0.05
88 10 0.05
90 6 0.03
91 56 0.30
92 27 0.14
93 28 0.15
ACGTcount: A:0.42, C:0.19, G:0.08, T:0.32
Consensus pattern (87 bp):
ACTTGGATACTTAAACTTTCAAAATGCATAGAAAAGACCCTCAAACTTTTTCAAAAAAAAAAACT
AAGCCCCTATTTTTTGCACTCA
Found at i:238232 original size:93 final size:93
Alignment explanation
Indices: 238131--238469 Score: 325
Period size: 93 Copynumber: 3.6 Consensus size: 93
238121 TGCACTCAAT
* *
238131 TTGG-TACTTGAACTTTCAAAATGTATCAAAAAAG-CCCTCAAACTTAAAAAAAAAAAAAAAGCA
1 TTGGATACTTGAACTTTCACAATGCATCAAAAAAGACCCTCAAACTTAAAAAAAAAAAAAAAGCA
*
238194 ATTAAGCTCATGCTTTTGTTTGCACTCAC
66 ATTAAGC-CATGCTTTTGTTTGAACTCAC
* * * ** ****
238223 TTGAATACTTAAACTTTTACAATAAAT-AAAAAA-ACCCTCAAACTT---TTTCAAAAAAAAGCA
1 TTGGATACTTGAACTTTCACAATGCATCAAAAAAGACCCTCAAACTTAAAAAAAAAAAAAAAGCA
* * *
238283 ATTAAGCCCTTGCTTTTTCTTTTTTAAACTCAC
66 ATTAAG-CCATGC---TT-TTGTTTGAACTCAC
* *
238316 TTGGGTATTTGAACTTTCACAATGCATC-AAAAAGACCCTCAAACTTAAAAAAAAAAAAAAAAGA
1 TTGGATACTTGAACTTTCACAATGCATCAAAAAAGACCCTCAAACTT---AAAAAAAAAAAAA-A
*
238380 AGCAATTAAGCCATTGATTTTGTTTGAACTCAC
62 AGCAATTAAGCCA-TGCTTTTGTTTGAACTCAC
* * * *
238413 TTGGATACTTGAAGTTTCACAATGCATTAAAAAAGACCCTCAAAATTTAAAAAAAAA
1 TTGGATACTTGAACTTTCACAATGCATCAAAAAAGACCCTCAAACTTAAAAAAAAAA
238470 TCAATTAAGC
Statistics
Matches: 194, Mismatches: 35, Indels: 33
0.74 0.13 0.13
Matches are distributed among these distances:
89 21 0.11
90 1 0.01
92 22 0.11
93 53 0.27
94 12 0.06
95 9 0.05
97 36 0.19
98 19 0.10
100 8 0.04
101 13 0.07
ACGTcount: A:0.44, C:0.17, G:0.09, T:0.29
Consensus pattern (93 bp):
TTGGATACTTGAACTTTCACAATGCATCAAAAAAGACCCTCAAACTTAAAAAAAAAAAAAAAGCA
ATTAAGCCATGCTTTTGTTTGAACTCAC
Found at i:238468 original size:190 final size:185
Alignment explanation
Indices: 238124--238481 Score: 470
Period size: 190 Copynumber: 1.9 Consensus size: 185
238114 TATTTTTTGC
* *
238124 ACTCAATTTGGTACTTGAACTTTCAAAATGTATCAAAAAAGCCCTCAAACTTAAAAAAAAAAAAA
1 ACTCAATTGGGTACTTGAACTTTCAAAATGCATCAAAAAAGCCCTCAAACTTAAAAAAAAAAAAA
* * *
238189 AAGCAATTAAGCTCATGCTTTTGTTTGCACTCACTTGAATACTTAAACTTTTACAATAAATAAAA
66 AAGCAATTAAGCTCATGATTTTGTTTGAACTCACTTGAATACTTAAACTTTCACAATAAATAAAA
* *
238254 AAACCCTCAAACTTTTTCAAAAAAAAGCAATTAAGCCCTTGCTTTTTCTTTTTTAA
131 AAACCCTCAAAC-ATTTAAAAAAAAAGCAATTAAGCCCTTGCTTTTTCTTTTTTAA
* * *
238310 ACTCACTTGGGTATTTGAACTTTCACAATGCATC-AAAAAGACCCTCAAACTTAAAAAAAAAAAA
1 ACTCAATTGGGTACTTGAACTTTCAAAATGCATCAAAAAAG-CCCTCAAACTT---AAAAAAAAA
* * * *
238374 AAAAGAAGCAATTAAGC-CATTGATTTTGTTTGAACTCACTTGGATACTTGAAGTTTCACAATGC
62 AAAA-AAGCAATTAAGCTCA-TGATTTTGTTTGAACTCACTTGAATACTTAAACTTTCACAAT-A
* *
238438 ATTAAAAAAGACCCTCAAA-ATTTAAAAAAAAATCAATTAAGCCC
124 AATAAAAAA-ACCCTCAAACATTTAAAAAAAAAGCAATTAAGCCC
238482 CTACTATAAC
Statistics
Matches: 148, Mismatches: 16, Indels: 12
0.84 0.09 0.07
Matches are distributed among these distances:
185 6 0.04
186 40 0.27
189 15 0.10
190 70 0.47
191 8 0.05
192 9 0.06
ACGTcount: A:0.43, C:0.18, G:0.09, T:0.29
Consensus pattern (185 bp):
ACTCAATTGGGTACTTGAACTTTCAAAATGCATCAAAAAAGCCCTCAAACTTAAAAAAAAAAAAA
AAGCAATTAAGCTCATGATTTTGTTTGAACTCACTTGAATACTTAAACTTTCACAATAAATAAAA
AAACCCTCAAACATTTAAAAAAAAAGCAATTAAGCCCTTGCTTTTTCTTTTTTAA
Found at i:241752 original size:91 final size:90
Alignment explanation
Indices: 241441--241776 Score: 379
Period size: 90 Copynumber: 3.7 Consensus size: 90
241431 TACACCTACT
* * *
241441 TTTTTTTGCACCCACTTGGGTACTTGAACTTTCACAATGCATCAAAAATACGCTTAAACTTAAAA
1 TTTTTTTGCACCCACTTGGGTACTTGAACTTTCACAATGCATAAAAAAGACCCTTAAACTTAAAA
* *
241506 AAAAAAAAAATGCAACTAAGCCCT-T
66 AAAAAAAAAA-GCAATTAAGCCCTGC
* * * ** * **
241531 TTTTTTTGCACCCAATTGGGTATTTGAACTTTCAAAATGCATAAAAAAGGTCCTCAAACTTTTTC
1 TTTTTTTGCACCCACTTGGGTACTTGAACTTTCACAATGCATAAAAAAGACCCTTAAAC--TTAA
** *
241596 AAAAAAAAAAAAGTTATTAAGCTTCTGC
64 AAAAAAAAAAAAGCAATTAAGC-CCTGC
* ** * * *
241624 TTTTGTTTGTACTTATTTGGGTACTTGAACTTTCACAATGCATCAAAAACACCCTTAAACTTAAA
1 TTTT-TTTGCACCCACTTGGGTACTTGAACTTTCACAATGCATAAAAAAGACCCTTAAACTTAAA
241689 AAAAAAAAAAAGCAATTAAGCCCATGC
65 AAAAAAAAAAAGCAATTAAGCCC-TGC
* *
241716 TTTTTTTGCACTCACTTGAGTACTTGAACTTTCACAATGCATAAAAAAGA-CCTTCAAACTT
1 TTTTTTTGCACCCACTTGGGTACTTGAACTTTCACAATGCATAAAAAAGACCCTT-AAACTT
241777 TTTCACAAAA
Statistics
Matches: 201, Mismatches: 38, Indels: 13
0.80 0.15 0.05
Matches are distributed among these distances:
90 54 0.27
91 54 0.27
92 45 0.22
93 4 0.02
94 44 0.22
ACGTcount: A:0.38, C:0.19, G:0.11, T:0.32
Consensus pattern (90 bp):
TTTTTTTGCACCCACTTGGGTACTTGAACTTTCACAATGCATAAAAAAGACCCTTAAACTTAAAA
AAAAAAAAAAGCAATTAAGCCCTGC
Found at i:241897 original size:88 final size:85
Alignment explanation
Indices: 241531--241916 Score: 234
Period size: 88 Copynumber: 4.3 Consensus size: 85
241521 CTAAGCCCTT
* * * ***
241531 TTTTTTTGCACCCAATTGGGTATTTGAACTTTCAAAATGCATAAAAAAGGTCCTCAAACTTTTTC
1 TTTTTTTGCACTC-ATTGGGTACTTAAACTTTCAAAATGCATAAAAAAAACCCTCAAACTTTTTC
* * *
241596 AAAAAAAAAAAAGTTATTAAGCTTCTGC
65 --AAAAAAAGAA---ATTAA-C-GCTAC
* * * * * * *
241624 TTTTGTTTGTACTTATTTGGGTACTTGAACTTTCACAATGCATCAAAAACACCCTTAAACTTAAA
1 TTTT-TTTGCACTCA-TTGGGTACTTAAACTTTCAAAATGCATAAAAAAAACCCTCAAACTT---
**** * * *
241689 AAAAAAAAAAAGCAATTAAGCCCATGC
61 TTTCAAAAAAAGAAATTAA-CGC-TAC
* * * * *
241716 TTTTTTTGCACTCACTTGAGTACTTGAACTTTCACAATGCATAAAAAAGACCTTCAAACTTTTTC
1 TTTTTTTGCACTCA-TTGGGTACTTAAACTTTCAAAATGCATAAAAAAAACCCTCAAACTTTTTC
* ***
241781 ACAAAATTCAATTAAGCCGCTAC
65 AAAAAAAGAAATTAA--CGCTAC
* *
241804 TTTTTTTGCACTCGATTGGGTACTTAAACTTTCAAAATGTATAAAAAAAAAACCCTCAATCTTTT
1 TTTTTTTGCACTC-ATTGGGTACTTAAACTTTCAAAATGCAT--AAAAAAAACCCTCAAACTTTT
241869 TCAAAAAAAGAAATTAA-GCTAC
63 TCAAAAAAAGAAATTAACGCTAC
* *
241891 TGTTTTTTTCATTCAATTGGGTACTT
1 T-TTTTTTGCACTC-ATTGGGTACTT
241917 GAATCATCCT
Statistics
Matches: 233, Mismatches: 49, Indels: 27
0.75 0.16 0.09
Matches are distributed among these distances:
87 6 0.03
88 71 0.30
89 3 0.01
90 31 0.13
91 50 0.21
92 14 0.06
93 5 0.02
94 45 0.19
95 8 0.03
ACGTcount: A:0.37, C:0.18, G:0.11, T:0.35
Consensus pattern (85 bp):
TTTTTTTGCACTCATTGGGTACTTAAACTTTCAAAATGCATAAAAAAAACCCTCAAACTTTTTCA
AAAAAAGAAATTAACGCTAC
Found at i:242072 original size:31 final size:31
Alignment explanation
Indices: 242037--242110 Score: 100
Period size: 30 Copynumber: 2.4 Consensus size: 31
242027 AAATTTTAAT
*
242037 AAAAAATATT-TAAAAT-TATTAGAAAT-TAG
1 AAAAAAAATTATAAAATATA-TAGAAATATAG
242066 AAAAAAAATTATAAAATATATAGAAATATAG
1 AAAAAAAATTATAAAATATATAGAAATATAG
242097 AAAAAAAAATTATA
1 -AAAAAAAATTATA
242111 CAATTTTATA
Statistics
Matches: 40, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
29 9 0.22
30 13 0.32
31 5 0.12
32 13 0.32
ACGTcount: A:0.66, C:0.00, G:0.05, T:0.28
Consensus pattern (31 bp):
AAAAAAAATTATAAAATATATAGAAATATAG
Found at i:242107 original size:32 final size:30
Alignment explanation
Indices: 242037--242115 Score: 99
Period size: 32 Copynumber: 2.6 Consensus size: 30
242027 AAATTTTAAT
*
242037 AAAAAATATT-TAAAATTATTAGAAATTAG
1 AAAAAAAATTATAAAATTATTAGAAATTAG
242066 AAAAAAAATTATAAAA-TATATAGAAATATAG
1 AAAAAAAATTATAAAATTAT-TAGAAAT-TAG
*
242097 AAAAAAAAATTATACAATT
1 -AAAAAAAATTATAAAATT
242116 TTATAAAGGT
Statistics
Matches: 43, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
29 12 0.28
30 12 0.28
31 3 0.07
32 15 0.35
33 1 0.02
ACGTcount: A:0.65, C:0.01, G:0.05, T:0.29
Consensus pattern (30 bp):
AAAAAAAATTATAAAATTATTAGAAATTAG
Found at i:242158 original size:19 final size:19
Alignment explanation
Indices: 242125--242181 Score: 71
Period size: 19 Copynumber: 2.9 Consensus size: 19
242115 TTTATAAAGG
242125 TGTAAGAAAATTATAAAAAA
1 TGTAA-AAAATTATAAAAAA
**
242145 TGTAAAGAAA-TATAAAATT
1 TGTAAA-AAATTATAAAAAA
242164 TGTAAAAAATTATAAAAA
1 TGTAAAAAATTATAAAAA
242182 TTATCGTACT
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
18 3 0.09
19 21 0.66
20 8 0.25
ACGTcount: A:0.63, C:0.00, G:0.09, T:0.28
Consensus pattern (19 bp):
TGTAAAAAATTATAAAAAA
Found at i:243329 original size:168 final size:168
Alignment explanation
Indices: 243051--243388 Score: 658
Period size: 168 Copynumber: 2.0 Consensus size: 168
243041 GAAAAACAAT
243051 ATCCTACTTAGAATAAGACTAGGGTAGACAACACACCCTAGTATTCCTACTAGGGTTGTCGCCCC
1 ATCCTACTTAGAATAAGACTAGGGTAGACAACACACCCTAGTATTCCTACTAGGGTTGTCGCCCC
243116 CTTCATGTCAATGAGGGGTTTTTGGGTTTTTCTCACATCGGGTCCAATTATGAGTATTTCTTGGA
66 CTTCATGTCAATGAGGGGTTTTTGGGTTTTTCTCACATCGGGTCCAATTATGAGTATTTCTTGGA
243181 CCTTTTTGACCTAGTACTTTGTAATATGATCCAACCTG
131 CCTTTTTGACCTAGTACTTTGTAATATGATCCAACCTG
*
243219 ATCCTACTTAGAATAAGACTAGGGTAGACAACACACCCTAGTATTCTTACTAGGGTTGTCGCCCC
1 ATCCTACTTAGAATAAGACTAGGGTAGACAACACACCCTAGTATTCCTACTAGGGTTGTCGCCCC
243284 CTTCATGTCAATGAGGGGTTTTTGGGTTTTTCTCACATCGGGTCCAATTATGAGTATTTCTTGGA
66 CTTCATGTCAATGAGGGGTTTTTGGGTTTTTCTCACATCGGGTCCAATTATGAGTATTTCTTGGA
*
243349 CCTTTTTGACCTAGTACTTTGTAATATGATTCAACCTG
131 CCTTTTTGACCTAGTACTTTGTAATATGATCCAACCTG
243387 AT
1 AT
243389 TCAGTTTTTT
Statistics
Matches: 168, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
168 168 1.00
ACGTcount: A:0.24, C:0.21, G:0.20, T:0.35
Consensus pattern (168 bp):
ATCCTACTTAGAATAAGACTAGGGTAGACAACACACCCTAGTATTCCTACTAGGGTTGTCGCCCC
CTTCATGTCAATGAGGGGTTTTTGGGTTTTTCTCACATCGGGTCCAATTATGAGTATTTCTTGGA
CCTTTTTGACCTAGTACTTTGTAATATGATCCAACCTG
Found at i:243487 original size:26 final size:26
Alignment explanation
Indices: 243451--243507 Score: 78
Period size: 26 Copynumber: 2.2 Consensus size: 26
243441 TTTCATCCCT
*
243451 ATTTTACCCCTAGTAAAAATTTGACG
1 ATTTTACCCCTAGTAAAAATTTGACA
* * *
243477 ATTTTATCCCTGGTAAAATTTTGACA
1 ATTTTACCCCTAGTAAAAATTTGACA
243503 ATTTT
1 ATTTT
243508 GTCCTTGATA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.32, C:0.16, G:0.11, T:0.42
Consensus pattern (26 bp):
ATTTTACCCCTAGTAAAAATTTGACA
Found at i:243523 original size:26 final size:26
Alignment explanation
Indices: 243451--243526 Score: 73
Period size: 26 Copynumber: 2.9 Consensus size: 26
243441 TTTCATCCCT
* * *
243451 ATTTTACCCCT-AGTAAAAATTTGACG
1 ATTTTATCCCTGA-TAAAATTTTGACA
*
243477 ATTTTATCCCTGGTAAAATTTTGACA
1 ATTTTATCCCTGATAAAATTTTGACA
* * *
243503 ATTTTGTCCTTGATAACATTTTGA
1 ATTTTATCCCTGATAAAATTTTGA
243527 GAAAATATGT
Statistics
Matches: 41, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
26 41 1.00
ACGTcount: A:0.30, C:0.16, G:0.12, T:0.42
Consensus pattern (26 bp):
ATTTTATCCCTGATAAAATTTTGACA
Found at i:246218 original size:24 final size:24
Alignment explanation
Indices: 246172--246218 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 24
246162 ATAGCCTGAT
** *
246172 TAGTAGTGATATATTATCTTTGAA
1 TAGTAGTGATATACGATCCTTGAA
*
246196 TAGTAGTGCTATACGATCCTTGA
1 TAGTAGTGATATACGATCCTTGA
246219 CTATATAGGC
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.30, C:0.11, G:0.19, T:0.40
Consensus pattern (24 bp):
TAGTAGTGATATACGATCCTTGAA
Found at i:247679 original size:30 final size:32
Alignment explanation
Indices: 247611--247672 Score: 83
Period size: 32 Copynumber: 2.0 Consensus size: 32
247601 ATCTGTCAAC
* *
247611 ACTATTAACAGTGTTATCAGTCAGCAGTTAAT
1 ACTATTAACAGTGTTAACAGTCAGCAATTAAT
*
247643 ACTATTAACATTG-TAACAGT-AGCAATTAAT
1 ACTATTAACAGTGTTAACAGTCAGCAATTAAT
247673 GTTATTAGCG
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
30 9 0.33
31 6 0.22
32 12 0.44
ACGTcount: A:0.39, C:0.15, G:0.13, T:0.34
Consensus pattern (32 bp):
ACTATTAACAGTGTTAACAGTCAGCAATTAAT
Found at i:260506 original size:32 final size:32
Alignment explanation
Indices: 260470--260550 Score: 162
Period size: 32 Copynumber: 2.5 Consensus size: 32
260460 CAATAGTGAT
260470 AATATCTTACCAAAAAGTTTTGTCAAAAAAAA
1 AATATCTTACCAAAAAGTTTTGTCAAAAAAAA
260502 AATATCTTACCAAAAAGTTTTGTCAAAAAAAA
1 AATATCTTACCAAAAAGTTTTGTCAAAAAAAA
260534 AATATCTTACCAAAAAG
1 AATATCTTACCAAAAAG
260551 GGATTTGATG
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 49 1.00
ACGTcount: A:0.53, C:0.14, G:0.06, T:0.27
Consensus pattern (32 bp):
AATATCTTACCAAAAAGTTTTGTCAAAAAAAA
Found at i:261081 original size:71 final size:71
Alignment explanation
Indices: 260965--261108 Score: 288
Period size: 71 Copynumber: 2.0 Consensus size: 71
260955 CTTCATCATA
260965 TCTGCTTTGCTTAGAAATTTGATTTCAATAATTTAAGATACATACAGAAATATAACATTGTTGAA
1 TCTGCTTTGCTTAGAAATTTGATTTCAATAATTTAAGATACATACAGAAATATAACATTGTTGAA
261030 GAGAGG
66 GAGAGG
261036 TCTGCTTTGCTTAGAAATTTGATTTCAATAATTTAAGATACATACAGAAATATAACATTGTTGAA
1 TCTGCTTTGCTTAGAAATTTGATTTCAATAATTTAAGATACATACAGAAATATAACATTGTTGAA
261101 GAGAGG
66 GAGAGG
261107 TC
1 TC
261109 GGTCTCGCTC
Statistics
Matches: 73, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
71 73 1.00
ACGTcount: A:0.38, C:0.10, G:0.17, T:0.35
Consensus pattern (71 bp):
TCTGCTTTGCTTAGAAATTTGATTTCAATAATTTAAGATACATACAGAAATATAACATTGTTGAA
GAGAGG
Found at i:265646 original size:8 final size:9
Alignment explanation
Indices: 265629--265653 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
265619 TGCTTTTATA
265629 TAATTTTTT
1 TAATTTTTT
265638 TAATTTTTT
1 TAATTTTTT
265647 TAATTTT
1 TAATTTT
265654 GGTCAATTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (9 bp):
TAATTTTTT
Found at i:267172 original size:197 final size:202
Alignment explanation
Indices: 266938--267310 Score: 580
Period size: 208 Copynumber: 1.8 Consensus size: 202
266928 TTCTAATCCT
* * *
266938 TAGGAGGATAAATATTTTCAATATTTTTATTTTAATAGTTAAAAATATCTATTATATTTGAAATT
1 TAGGAAGATAAACATTTTCAATATTTTTATTTTAATAGCTAAAAATATCTATTATATTTGAAATT
*
267003 AATATA-AA-A-T-T-AGT-TTTTTTTTTCCTTTTTTGATATATATGTTAAAATTTTTAAGTATT
66 AATATACAATATTATAAATATTTTTTTTTCC-TTTTTGATATATATGTTAAAATTTTTAAGTATT
267062 TCTTTTCTTAAGTAAAAATTTTAAATAAATTTATTACATTTTTTTATACAATGTCTAAAATCCTA
130 TCTTTTCTTAAGTAAAAATTTTAAATAAATTTATTA-ATTTTTTTATACAATGTCTAAAATCCTA
267127 ATCCTTAAA
194 ATCCTTAAA
*
267136 TAGGAAGATAAACATTTTCAATA-TTTTATTTTAATAGCTAAAAATATTTATTATATTTGAAATT
1 TAGGAAGATAAACATTTTCAATATTTTTATTTTAATAGCTAAAAATATCTATTATATTTGAAATT
267200 AATATACAATTAGTTTATAAAAAATATTTTTTTTTCCTTTTTGATATATATGTTAAAATTTTTAA
66 AATATACAA-TA--TTAT---AAATATTTTTTTTTCCTTTTTGATATATATGTTAAAATTTTTAA
267265 GTATTTCTTTTCTTAAGTAAAAATTTTAAATAAATTTATTAATTTT
125 GTATTTCTTTTCTTAAGTAAAAATTTTAAATAAATTTATTAATTTT
267311 AATATTGTAT
Statistics
Matches: 158, Mismatches: 5, Indels: 15
0.89 0.03 0.08
Matches are distributed among these distances:
197 45 0.28
198 23 0.15
200 1 0.01
203 1 0.01
204 1 0.01
207 5 0.03
208 71 0.45
209 11 0.07
ACGTcount: A:0.38, C:0.06, G:0.06, T:0.50
Consensus pattern (202 bp):
TAGGAAGATAAACATTTTCAATATTTTTATTTTAATAGCTAAAAATATCTATTATATTTGAAATT
AATATACAATATTATAAATATTTTTTTTTCCTTTTTGATATATATGTTAAAATTTTTAAGTATTT
CTTTTCTTAAGTAAAAATTTTAAATAAATTTATTAATTTTTTTATACAATGTCTAAAATCCTAAT
CCTTAAA
Found at i:270726 original size:17 final size:17
Alignment explanation
Indices: 270691--270741 Score: 68
Period size: 17 Copynumber: 2.9 Consensus size: 17
270681 TTAATGGACT
*
270691 TTTATATTTTGTATTTTA
1 TTTAT-TTTTGGATTTTA
270709 TTTATTTATTGG-TTTTA
1 TTTATTT-TTGGATTTTA
270726 TTTATTTTTGGATTTT
1 TTTATTTTTGGATTTT
270742 TTGGTTAGGC
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
16 4 0.13
17 18 0.60
18 8 0.27
ACGTcount: A:0.18, C:0.00, G:0.10, T:0.73
Consensus pattern (17 bp):
TTTATTTTTGGATTTTA
Found at i:272851 original size:20 final size:20
Alignment explanation
Indices: 272826--272875 Score: 100
Period size: 20 Copynumber: 2.5 Consensus size: 20
272816 TCTCCTCAAA
272826 TATCGATACTCGTATTAAGG
1 TATCGATACTCGTATTAAGG
272846 TATCGATACTCGTATTAAGG
1 TATCGATACTCGTATTAAGG
272866 TATCGATACT
1 TATCGATACT
272876 AACAAGAAGA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.30, C:0.16, G:0.18, T:0.36
Consensus pattern (20 bp):
TATCGATACTCGTATTAAGG
Done.