Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032245.1 Gossypioides kirkii chromosome KI_2_4
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: 41238926
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 6100 characters in sequence are not A, C, G, or T
File 1 of 132
Found at i:12 original size:7 final size:7
Alignment explanation
Indices: 1--311 Score: 192
Period size: 7 Copynumber: 44.9 Consensus size: 7
1 CCCGAAG
1 CCCGAAG
8 CCCGAAG
1 CCCGAAG
15 CCCGAAG
1 CCCGAAG
*
22 CCCTAAG
1 CCCGAAG
*
29 CCCTAAG
1 CCCGAAG
*
36 CCCTAAG
1 CCCGAAG
*
43 CCCTAAG
1 CCCGAAG
*
50 CCCTAAG
1 CCCGAAG
*
57 CCCTAAG
1 CCCGAAG
*
64 CCCTAAG
1 CCCGAAG
*
71 CCCTAAG
1 CCCGAAG
*
78 CCCTAAG
1 CCCGAAG
*
85 CCCTAAG
1 CCCGAAG
*
92 CCCTAAG
1 CCCGAAG
*
99 CCCTAAG
1 CCCGAAG
*
106 CCCTAAG
1 CCCGAAG
*
113 CCCTAAG
1 CCCGAAG
*
120 CCCTAAG
1 CCCGAAG
*
127 CCCTAAG
1 CCCGAAG
*
134 CCCTAAG
1 CCCGAAG
*
141 CCCTAAAG
1 CCC-GAAG
* *
149 CCCTAAAC
1 CCC-GAAG
157 CCCG-AG
1 CCCGAAG
163 -CCG-AG
1 CCCGAAG
168 CCCCG-AG
1 -CCCGAAG
175 CCCCG-AG
1 -CCCGAAG
182 CCCCCG-AG
1 --CCCGAAG
*
190 CCCCGAAC
1 -CCCGAAG
*
198 CCCGAAC
1 CCCGAAG
*
205 CCCGAAC
1 CCCGAAG
*
212 CCCGAAC
1 CCCGAAG
*
219 CCCGAAC
1 CCCGAAG
*
226 CCCGAAC
1 CCCGAAG
233 CCCGAA-
1 CCCGAAG
*
239 CCCGAAC
1 CCCGAAG
*
246 CCCGAAA
1 CCCGAAG
*
253 CCCGAAC
1 CCCGAAG
*
260 CCCGAAC
1 CCCGAAG
267 CCCGAA-
1 CCCGAAG
*
273 CCCGAAC
1 CCCGAAG
280 CCCGAA-
1 CCCGAAG
*
286 CCCGAAA
1 CCCGAAG
*
293 CCCGAAA
1 CCCGAAG
300 CCCGAA-
1 CCCGAAG
306 CCCGAA
1 CCCGAA
312 CCCCAAACCC
Statistics
Matches: 288, Mismatches: 8, Indels: 17
0.92 0.03 0.05
Matches are distributed among these distances:
5 5 0.02
6 25 0.09
7 237 0.82
8 21 0.07
ACGTcount: A:0.29, C:0.48, G:0.17, T:0.06
Consensus pattern (7 bp):
CCCGAAG
Found at i:1592 original size:7 final size:7
Alignment explanation
Indices: 284--1595 Score: 1524
Period size: 7 Copynumber: 190.7 Consensus size: 7
274 CCGAACCCCG
*
284 AACCCGA
1 AACCCTA
*
291 AACCCGA
1 AACCCTA
*
298 AACCC-G
1 AACCCTA
*
304 AACCC-G
1 AACCCTA
*
310 AACCCCA
1 AACCCTA
317 AACCC-A
1 AACCCTA
*
323 AACCCCA
1 AACCCTA
330 AACCC-A
1 AACCCTA
*
336 AACCCCA
1 AACCCTA
343 AACCC-A
1 AACCCTA
*
349 AACCCCA
1 AACCCTA
*
356 AACCCCA
1 AACCCTA
*
363 AACCCCA
1 AACCCTA
*
370 AACCCCA
1 AACCCTA
*
377 AACCCCA
1 AACCCTA
*
384 AACCCCA
1 AACCCTA
*
391 AACCCCA
1 AACCCTA
*
398 AACCCCA
1 AACCCTA
*
405 AACCCCA
1 AACCCTA
*
412 AACCCCA
1 AACCCTA
*
419 AACCCCA
1 AACCCTA
*
426 AACCCCA
1 AACCCTA
*
433 AACCCCA
1 AACCCTA
440 AACCCTA
1 AACCCTA
447 AACCCTA
1 AACCCTA
454 AACCCTA
1 AACCCTA
461 AACCCTA
1 AACCCTA
468 AACCCTA
1 AACCCTA
475 AA-CCTA
1 AACCCTA
481 AACCCTA
1 AACCCTA
488 AACCCTA
1 AACCCTA
495 AACCCTA
1 AACCCTA
502 AACCCTA
1 AACCCTA
509 AACCCTA
1 AACCCTA
516 AACCCTA
1 AACCCTA
523 AACCCTA
1 AACCCTA
530 AACCCTA
1 AACCCTA
537 AACCCTA
1 AACCCTA
544 AACCCTAA
1 AACCCT-A
552 AACCCTA
1 AACCCTA
559 AACCCTA
1 AACCCTA
566 AACCCTA
1 AACCCTA
573 AACCCTA
1 AACCCTA
580 AACCCTA
1 AACCCTA
587 AACCCTA
1 AACCCTA
594 AACCCT-
1 AACCCTA
600 AACCCTA
1 AACCCTA
607 AACCCTA
1 AACCCTA
614 AACCCTA
1 AACCCTA
621 AACCCTA
1 AACCCTA
628 AACCCTA
1 AACCCTA
635 AACCCTA
1 AACCCTA
642 AACCCTA
1 AACCCTA
649 AACCCTA
1 AACCCTA
656 AACCCTA
1 AACCCTA
663 AACCCT-
1 AACCCTA
669 AACCCTA
1 AACCCTA
676 AACCCTA
1 AACCCTA
683 AACCCTA
1 AACCCTA
690 AACCCTA
1 AACCCTA
697 AACCCTA
1 AACCCTA
704 AACCCTA
1 AACCCTA
711 AACCCTA
1 AACCCTA
718 AACCCTA
1 AACCCTA
725 AACCCTA
1 AACCCTA
732 AACCCTA
1 AACCCTA
739 AACCCTA
1 AACCCTA
746 AACCCTA
1 AACCCTA
753 AACCCTA
1 AACCCTA
760 AACCCTA
1 AACCCTA
767 AACCCTA
1 AACCCTA
774 AACCCTA
1 AACCCTA
781 AACCCTA
1 AACCCTA
788 AA-CCTA
1 AACCCTA
794 AACCCTA
1 AACCCTA
801 AACCCTA
1 AACCCTA
808 AACCCTA
1 AACCCTA
815 AACCCTA
1 AACCCTA
822 AACCCTA
1 AACCCTA
829 AACCC-A
1 AACCCTA
835 AACCCTA
1 AACCCTA
842 AA-CCTA
1 AACCCTA
848 AACCCTA
1 AACCCTA
855 AACCCTA
1 AACCCTA
862 AACCCTA
1 AACCCTA
869 AACCCTA
1 AACCCTA
876 AA-CCTA
1 AACCCTA
882 AACCCTA
1 AACCCTA
889 AACCCTA
1 AACCCTA
896 AACCCTA
1 AACCCTA
903 AACCCTA
1 AACCCTA
910 AACCCTA
1 AACCCTA
917 AACCCTA
1 AACCCTA
924 AACCCTA
1 AACCCTA
931 AACCCTA
1 AACCCTA
938 AACCC-A
1 AACCCTA
944 AACCC-A
1 AACCCTA
*
950 AACCCCAA
1 AA-CCCTA
*
958 AACCCCA
1 AACCCTA
965 AACCC-A
1 AACCCTA
971 AACCC-A
1 AACCCTA
977 AACCC-A
1 AACCCTA
*
983 AACCCCA
1 AACCCTA
*
990 AACCCCA
1 AACCCTA
*
997 AACCCCA
1 AACCCTA
*
1004 AACCCCA
1 AACCCTA
*
1011 AACCCCA
1 AACCCTA
*
1018 AACCCCA
1 AACCCTA
*
1025 AACCCCAA
1 AA-CCCTA
*
1033 AACCCCA
1 AACCCTA
1040 AACCC-A
1 AACCCTA
*
1046 AACCCCA
1 AACCCTA
*
1053 AACCC-C
1 AACCCTA
*
1059 AACCCCA
1 AACCCTA
*
1066 AACCCCA
1 AACCCTA
*
1073 AACCCCA
1 AACCCTA
*
1080 AACCCCA
1 AACCCTA
*
1087 AACCCCA
1 AACCCTA
*
1094 AACCCCA
1 AACCCTA
*
1101 AACCCCA
1 AACCCTA
*
1108 AACCCCA
1 AACCCTA
*
1115 AACCCCA
1 AACCCTA
*
1122 AACCCCA
1 AACCCTA
*
1129 AACCCCA
1 AACCCTA
1136 AACCC-A
1 AACCCTA
*
1142 AACCC-C
1 AACCCTA
*
1148 AACCCCA
1 AACCCTA
*
1155 AACCCCA
1 AACCCTA
*
1162 AACCCCA
1 AACCCTA
*
1169 AACCCCA
1 AACCCTA
1176 AACCC-A
1 AACCCTA
*
1182 AACCCCA
1 AACCCTA
*
1189 AACCCCA
1 AACCCTA
*
1196 AACCCCA
1 AACCCTA
*
1203 AACCCCA
1 AACCCTA
*
1210 AACCCCA
1 AACCCTA
*
1217 AACCCCA
1 AACCCTA
*
1224 AACCCCA
1 AACCCTA
*
1231 AACCCCA
1 AACCCTA
*
1238 AACCCCA
1 AACCCTA
*
1245 AACCCCA
1 AACCCTA
*
1252 AACCCCA
1 AACCCTA
*
1259 AACCCCA
1 AACCCTA
*
1266 AACCCCA
1 AACCCTA
*
1273 AACCCCA
1 AACCCTA
*
1280 AACCCCA
1 AACCCTA
*
1287 AACCCCA
1 AACCCTA
1294 AACCC-A
1 AACCCTA
1300 AACCC-A
1 AACCCTA
1306 AACCC-A
1 AACCCTA
*
1312 AACCCCA
1 AACCCTA
1319 AACCC-A
1 AACCCTA
*
1325 AACCCCA
1 AACCCTA
*
1332 AACCCCA
1 AACCCTA
*
1339 AACCCCA
1 AACCCTA
*
1346 AACCCCA
1 AACCCTA
*
1353 AACCCCA
1 AACCCTA
*
1360 AACCCCA
1 AACCCTA
*
1367 AACCCGA
1 AACCCTA
* *
1374 AGCCCGA
1 AACCCTA
* *
1381 AGCCCGA
1 AACCCTA
*
1388 AGCCCTA
1 AACCCTA
*
1395 AGCCCTA
1 AACCCTA
*
1402 AGCCCTA
1 AACCCTA
*
1409 AGCCCTA
1 AACCCTA
*
1416 AGCCCTA
1 AACCCTA
*
1423 AGCCCTA
1 AACCCTA
*
1430 AGCCCTA
1 AACCCTA
*
1437 AGCCCTA
1 AACCCTA
*
1444 AGCCCTA
1 AACCCTA
*
1451 AGCCCTA
1 AACCCTA
*
1458 AGCCCTA
1 AACCCTA
*
1465 AGCCCTA
1 AACCCTA
*
1472 AGCCCTA
1 AACCCTA
*
1479 AGCCCTA
1 AACCCTA
*
1486 AGCCCTA
1 AACCCTA
*
1493 AGCCCTA
1 AACCCTA
*
1500 AGCCCTA
1 AACCCTA
*
1507 AGCCCTA
1 AACCCTA
*
1514 AGCCCTA
1 AACCCTA
*
1521 AGCCCTA
1 AACCCTA
*
1528 AGCCCTA
1 AACCCTA
*
1535 AGCCCTA
1 AACCCTA
*
1542 AGCCCTA
1 AACCCTA
1549 AACCCTA
1 AACCCTA
1556 AACCCTA
1 AACCCTA
1563 AACCCTA
1 AACCCTA
1570 AACCCTA
1 AACCCTA
1577 AACCCTA
1 AACCCTA
1584 AACCCTA
1 AACCCTA
1591 AACCC
1 AACCC
1596 CGAGCCCCGA
Statistics
Matches: 1269, Mismatches: 14, Indels: 44
0.96 0.01 0.03
Matches are distributed among these distances:
6 150 0.12
7 1103 0.87
8 16 0.01
ACGTcount: A:0.41, C:0.48, G:0.02, T:0.08
Consensus pattern (7 bp):
AACCCTA
Found at i:1603 original size:7 final size:7
Alignment explanation
Indices: 1593--1631 Score: 78
Period size: 7 Copynumber: 5.6 Consensus size: 7
1583 AAACCCTAAA
1593 CCCCGAG
1 CCCCGAG
1600 CCCCGAG
1 CCCCGAG
1607 CCCCGAG
1 CCCCGAG
1614 CCCCGAG
1 CCCCGAG
1621 CCCCGAG
1 CCCCGAG
1628 CCCC
1 CCCC
1632 AAACCCCAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 32 1.00
ACGTcount: A:0.13, C:0.62, G:0.26, T:0.00
Consensus pattern (7 bp):
CCCCGAG
Found at i:1638 original size:14 final size:14
Alignment explanation
Indices: 1593--1665 Score: 83
Period size: 14 Copynumber: 5.2 Consensus size: 14
1583 AAACCCTAAA
*
1593 CCCCGAGCCCCGAG
1 CCCCGAGCCCCAAG
*
1607 CCCCGAGCCCCGAG
1 CCCCGAGCCCCAAG
*
1621 CCCCGAGCCCCAAA
1 CCCCGAGCCCCAAG
* *
1635 CCCCAAACCCCAAG
1 CCCCGAGCCCCAAG
* *
1649 CCACGAGCCTCAAG
1 CCCCGAGCCCCAAG
1663 CCC
1 CCC
1666 TCAAACCTAA
Statistics
Matches: 49, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
14 49 1.00
ACGTcount: A:0.23, C:0.56, G:0.19, T:0.01
Consensus pattern (14 bp):
CCCCGAGCCCCAAG
Found at i:1638 original size:28 final size:28
Alignment explanation
Indices: 985--1672 Score: 260
Period size: 28 Copynumber: 24.6 Consensus size: 28
975 CAAACCCAAA
* * * *
985 CCCCAAACCCCAAACCCCAAACCCCAAA
1 CCCCAAGCCCCAAACCCCAAGCCCCGAG
* * *
1013 CCCCAAACCCCAAACCCCAAAACCCC-AA
1 CCCCAAGCCCCAAACCCC-AAGCCCCGAG
* * * *
1041 ACCCAAACCCCAAACCCCAA-CCCCAAA
1 CCCCAAGCCCCAAACCCCAAGCCCCGAG
* * * *
1068 CCCCAAACCCCAAACCCCAAACCCCAAA
1 CCCCAAGCCCCAAACCCCAAGCCCCGAG
* * * *
1096 CCCCAAACCCCAAACCCCAAACCCCAAA
1 CCCCAAGCCCCAAACCCCAAGCCCCGAG
* * *
1124 CCCCAAACCCCAAA-CCCAAACCCC-AA
1 CCCCAAGCCCCAAACCCCAAGCCCCGAG
* * *
1150 CCCCAAACCCCAAACCCCAAACCCC-AA
1 CCCCAAGCCCCAAACCCCAAGCCCCGAG
* * * * *
1177 ACCCAAACCCCAAACCCCAAACCCCAAA
1 CCCCAAGCCCCAAACCCCAAGCCCCGAG
* * * *
1205 CCCCAAACCCCAAACCCCAAACCCCAAA
1 CCCCAAGCCCCAAACCCCAAGCCCCGAG
* * * *
1233 CCCCAAACCCCAAACCCCAAACCCCAAA
1 CCCCAAGCCCCAAACCCCAAGCCCCGAG
* * * *
1261 CCCCAAACCCCAAACCCCAAACCCCAAA
1 CCCCAAGCCCCAAACCCCAAGCCCCGAG
* * * *
1289 CCCCAA-ACCCAAA-CCCAA-ACCCAAA
1 CCCCAAGCCCCAAACCCCAAGCCCCGAG
* * * *
1314 CCCCAA-ACCCAAACCCCAAACCCCAAA
1 CCCCAAGCCCCAAACCCCAAGCCCCGAG
* *
1341 CCCCAAACCCCAAACCCCAAACCCCAAACCCGAAG
1 CCCCAAGCCCCAAACCCC-AA--GC---CCCG-AG
* * * * **
1376 CCCGAAGCCCGAAGCCCTAAGCCCTAAG
1 CCCCAAGCCCCAAACCCCAAGCCCCGAG
* * * * **
1404 CCCTAAGCCCTAAGCCCTAAGCCCTAAG
1 CCCCAAGCCCCAAACCCCAAGCCCCGAG
* * * * **
1432 CCCTAAGCCCTAAGCCCTAAGCCCTAAG
1 CCCCAAGCCCCAAACCCCAAGCCCCGAG
* * * * **
1460 CCCTAAGCCCTAAGCCCTAAGCCCTAAG
1 CCCCAAGCCCCAAACCCCAAGCCCCGAG
* * * * **
1488 CCCTAAGCCCTAAGCCCTAAGCCCTAAG
1 CCCCAAGCCCCAAACCCCAAGCCCCGAG
* * * * **
1516 CCCTAAGCCCTAAGCCCTAAGCCCTAAG
1 CCCCAAGCCCCAAACCCCAAGCCCCGAG
* * * * * ** *
1544 CCCTAAACCCTAAACCCTAAACCCTAAA
1 CCCCAAGCCCCAAACCCCAAGCCCCGAG
* * * * *
1572 CCCTAAACCCTAAACCCTAAACCCCGAG
1 CCCCAAGCCCCAAACCCCAAGCCCCGAG
* * * *
1600 CCCCGAGCCCCGAGCCCCGAGCCCCGAG
1 CCCCAAGCCCCAAACCCCAAGCCCCGAG
* *
1628 CCCCAAACCCCAAACCCCAAGCCACGAG
1 CCCCAAGCCCCAAACCCCAAGCCCCGAG
*
1656 CCTCAAGCCCTCAAACC
1 CCCCAAGCCC-CAAACC
1673 TAAACCCTCA
Statistics
Matches: 599, Mismatches: 45, Indels: 31
0.89 0.07 0.05
Matches are distributed among these distances:
25 19 0.03
26 30 0.05
27 87 0.15
28 425 0.71
29 17 0.03
31 1 0.00
32 1 0.00
34 5 0.01
35 14 0.02
ACGTcount: A:0.38, C:0.52, G:0.06, T:0.05
Consensus pattern (28 bp):
CCCCAAGCCCCAAACCCCAAGCCCCGAG
Found at i:1645 original size:21 final size:21
Alignment explanation
Indices: 1590--1638 Score: 80
Period size: 21 Copynumber: 2.3 Consensus size: 21
1580 CCTAAACCCT
1590 AAACCCCGAGCCCCGAGCCCC
1 AAACCCCGAGCCCCGAGCCCC
* *
1611 GAGCCCCGAGCCCCGAGCCCC
1 AAACCCCGAGCCCCGAGCCCC
1632 AAACCCC
1 AAACCCC
1639 AAACCCCAAG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.22, C:0.57, G:0.20, T:0.00
Consensus pattern (21 bp):
AAACCCCGAGCCCCGAGCCCC
Found at i:1650 original size:21 final size:21
Alignment explanation
Indices: 1548--1647 Score: 56
Period size: 21 Copynumber: 4.8 Consensus size: 21
1538 CCTAAGCCCT
* * *
1548 AAACCCTAAACCCTAAACCCT
1 AAACCCCAAACCCCAAACCCC
* * *
1569 AAACCCTAAACCCTAAACCCT
1 AAACCCCAAACCCCAAACCCC
* * * *
1590 AAACCCCGAGCCCCGAGCCCC
1 AAACCCCAAACCCCAAACCCC
* * * * * *
1611 GAGCCCCGAGCCCCGAGCCCC
1 AAACCCCAAACCCCAAACCCC
1632 AAACCCCAAACCCCAA
1 AAACCCCAAACCCCAA
1648 GCCACGAGCC
Statistics
Matches: 65, Mismatches: 14, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 65 1.00
ACGTcount: A:0.34, C:0.50, G:0.10, T:0.06
Consensus pattern (21 bp):
AAACCCCAAACCCCAAACCCC
Found at i:1665 original size:35 final size:35
Alignment explanation
Indices: 1607--1714 Score: 94
Period size: 35 Copynumber: 3.1 Consensus size: 35
1597 GAGCCCCGAG
* * * *
1607 CCCCGAGCCCCGAGCCCCGAGCCCCAAACCCCAAA
1 CCCCAAGCCACGAGCCTCAAGCCCCAAACCCCAAA
*
1642 CCCCAAGCCACGAGCCTCAAGCCCTCAAA-CCTAAA
1 CCCCAAGCCACGAGCCTCAAGCCC-CAAACCCCAAA
* * ** *
1677 CCCTCAA-CCTCGAGCTTCAAGCCTTAAACCCCGAA
1 CCC-CAAGCCACGAGCCTCAAGCCCCAAACCCCAAA
1712 CCC
1 CCC
1715 TAAACCATAG
Statistics
Matches: 59, Mismatches: 11, Indels: 6
0.78 0.14 0.08
Matches are distributed among these distances:
34 3 0.05
35 49 0.83
36 7 0.12
ACGTcount: A:0.29, C:0.50, G:0.13, T:0.08
Consensus pattern (35 bp):
CCCCAAGCCACGAGCCTCAAGCCCCAAACCCCAAA
Found at i:1700 original size:42 final size:42
Alignment explanation
Indices: 1654--1773 Score: 154
Period size: 42 Copynumber: 2.9 Consensus size: 42
1644 CCAAGCCACG
* *
1654 AGCCTCAAGCCCTC-AAACCTAAACCCTCA-ACCTCGAGCTTCA
1 AGCCTCAAACCC-CGAAACCTAAACCAT-AGACCTCGAGCTTCA
* *
1696 AGCCTTAAACCCCGAACCCTAAACCATAGACCTCGAGCTTCA
1 AGCCTCAAACCCCGAAACCTAAACCATAGACCTCGAGCTTCA
* *
1738 AGCCTTAAACCCCGAACCCTAAACCATAGACCTCGA
1 AGCCTCAAACCCCGAAACCTAAACCATAGACCTCGA
1774 ACCCCGAGAC
Statistics
Matches: 72, Mismatches: 4, Indels: 4
0.90 0.05 0.05
Matches are distributed among these distances:
41 2 0.03
42 70 0.97
ACGTcount: A:0.33, C:0.40, G:0.11, T:0.16
Consensus pattern (42 bp):
AGCCTCAAACCCCGAAACCTAAACCATAGACCTCGAGCTTCA
Found at i:1706 original size:21 final size:21
Alignment explanation
Indices: 1682--1748 Score: 64
Period size: 21 Copynumber: 3.2 Consensus size: 21
1672 CTAAACCCTC
1682 AACCTCGAGCTTCAAGCCTTA
1 AACCTCGAGCTTCAAGCCTTA
* * * * *
1703 AACCCCGAAC-CCTAAACCATA
1 AACCTCGAGCTTC-AAGCCTTA
*
1724 GACCTCGAGCTTCAAGCCTTA
1 AACCTCGAGCTTCAAGCCTTA
1745 AACC
1 AACC
1749 CCGAACCCTA
Statistics
Matches: 32, Mismatches: 12, Indels: 4
0.67 0.25 0.08
Matches are distributed among these distances:
20 1 0.03
21 30 0.94
22 1 0.03
ACGTcount: A:0.33, C:0.37, G:0.12, T:0.18
Consensus pattern (21 bp):
AACCTCGAGCTTCAAGCCTTA
Found at i:1715 original size:35 final size:35
Alignment explanation
Indices: 1632--1762 Score: 104
Period size: 42 Copynumber: 3.5 Consensus size: 35
1622 CCCGAGCCCC
* * *
1632 AAACCCCAAACCC-CAAGCCACGAGCCTCAAGCCCTC
1 AAACCCCAAACCCTCAA-CCTCGAGCTTCAAG-CCTT
*
1668 AAA-CCTAAACCCTCAACCTCGAGCTTCAAGCCTT
1 AAACCCCAAACCCTCAACCTCGAGCTTCAAGCCTT
*
1702 AAACCCCGAACCCTAAACCATAGACCTCGAGCTTCAAGCCTT
1 AAACCCCAAACCCT----C--A-ACCTCGAGCTTCAAGCCTT
* *
1744 AAACCCCGAACCCTAAACC
1 AAACCCCAAACCCTCAACC
1763 ATAGACCTCG
Statistics
Matches: 79, Mismatches: 7, Indels: 19
0.75 0.07 0.18
Matches are distributed among these distances:
34 6 0.08
35 31 0.39
36 7 0.09
39 1 0.01
41 1 0.01
42 33 0.42
ACGTcount: A:0.34, C:0.43, G:0.10, T:0.13
Consensus pattern (35 bp):
AAACCCCAAACCCTCAACCTCGAGCTTCAAGCCTT
Found at i:1776 original size:21 final size:21
Alignment explanation
Indices: 1708--1777 Score: 70
Period size: 21 Copynumber: 3.3 Consensus size: 21
1698 CCTTAAACCC
1708 CGAACCCTAAACCATAGACCT
1 CGAACCCTAAACCATAGACCT
* * * * * *
1729 CG-AGCTTCAAGCCTTAAACCC
1 CGAACCCT-AAACCATAGACCT
1750 CGAACCCTAAACCATAGACCT
1 CGAACCCTAAACCATAGACCT
1771 CGAACCC
1 CGAACCC
1778 CGAGACCCTT
Statistics
Matches: 35, Mismatches: 12, Indels: 4
0.69 0.24 0.08
Matches are distributed among these distances:
20 3 0.09
21 29 0.83
22 3 0.09
ACGTcount: A:0.34, C:0.40, G:0.11, T:0.14
Consensus pattern (21 bp):
CGAACCCTAAACCATAGACCT
Found at i:1827 original size:21 final size:21
Alignment explanation
Indices: 1780--1828 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
1770 TCGAACCCCG
* *
1780 AGACCCTTGACCCAAGACTCA
1 AGACCTTTGACCCAAAACTCA
*
1801 AGACCTTTGACTCAAAACTCA
1 AGACCTTTGACCCAAAACTCA
1822 AGACCTT
1 AGACCTT
1829 AAACTCGAGA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.35, C:0.33, G:0.12, T:0.20
Consensus pattern (21 bp):
AGACCTTTGACCCAAAACTCA
Found at i:1832 original size:14 final size:14
Alignment explanation
Indices: 1815--1846 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
1805 CTTTGACTCA
1815 AAACTCAAGACCTT
1 AAACTCAAGACCTT
*
1829 AAACTCGAGACCTT
1 AAACTCAAGACCTT
1843 AAAC
1 AAAC
1847 CCTAAACTCT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.44, C:0.28, G:0.09, T:0.19
Consensus pattern (14 bp):
AAACTCAAGACCTT
Found at i:1859 original size:14 final size:14
Alignment explanation
Indices: 1824--1902 Score: 52
Period size: 14 Copynumber: 5.6 Consensus size: 14
1814 AAAACTCAAG
* * *
1824 ACCTTAAACTCGAG
1 ACCTTAAACCCTAA
1838 ACCTTAAACCCTAA
1 ACCTTAAACCCTAA
* *
1852 A-CTCTAAATCTTAA
1 ACCT-TAAACCCTAA
*
1866 ACCTTGAACCCTAA
1 ACCTTAAACCCTAA
* * *
1880 ACCTCAAATCCAAA
1 ACCTTAAACCCTAA
*
1894 ATCTTAAAC
1 ACCTTAAAC
1903 TCTATACCCA
Statistics
Matches: 48, Mismatches: 15, Indels: 4
0.72 0.22 0.06
Matches are distributed among these distances:
13 2 0.04
14 44 0.92
15 2 0.04
ACGTcount: A:0.42, C:0.30, G:0.04, T:0.24
Consensus pattern (14 bp):
ACCTTAAACCCTAA
Found at i:1879 original size:21 final size:21
Alignment explanation
Indices: 1840--1880 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
1830 AACTCGAGAC
*
1840 CTTAAACCCTAAACTCTAAAT
1 CTTAAACCCTAAACCCTAAAT
* *
1861 CTTAAACCTTGAACCCTAAA
1 CTTAAACCCTAAACCCTAAA
1881 CCTCAAATCC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.41, C:0.29, G:0.02, T:0.27
Consensus pattern (21 bp):
CTTAAACCCTAAACCCTAAAT
Found at i:2551 original size:18 final size:18
Alignment explanation
Indices: 2528--2656 Score: 143
Period size: 18 Copynumber: 7.2 Consensus size: 18
2518 AGTTAACGTG
2528 CTCTATAAGCCTGGTGAA
1 CTCTATAAGCCTGGTGAA
* **
2546 CTCTATAAGCTTGGAAAA
1 CTCTATAAGCCTGGTGAA
*
2564 GTCTATAAGCCT-GTCGAA
1 CTCTATAAGCCTGGT-GAA
*
2582 GTCTATAAGCCTGGTGAA
1 CTCTATAAGCCTGGTGAA
* *
2600 CTCTATAAGGCTGGTAAA
1 CTCTATAAGCCTGGTGAA
*
2618 ATCTATAAGCCTGGTGAA
1 CTCTATAAGCCTGGTGAA
* * *
2636 GTCTTTAAGCCTGGCGAA
1 CTCTATAAGCCTGGTGAA
2654 CTC
1 CTC
2657 ACAATAAGTG
Statistics
Matches: 92, Mismatches: 17, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
17 1 0.01
18 89 0.97
19 2 0.02
ACGTcount: A:0.29, C:0.20, G:0.22, T:0.28
Consensus pattern (18 bp):
CTCTATAAGCCTGGTGAA
Found at i:2623 original size:54 final size:54
Alignment explanation
Indices: 2529--2656 Score: 190
Period size: 54 Copynumber: 2.4 Consensus size: 54
2519 GTTAACGTGC
2529 TCTATAAGCCTGGTGAACTCTATAAGCTTGGAAAAGTCTATAAGCCT-GTCGAAG
1 TCTATAAGCCTGGTGAACTCTATAAGCTTGGAAAAGTCTATAAGCCTGGT-GAAG
2583 TCTATAAGCCTGGTGAACTCTATAAGGC-TGGTAAAA-TCTATAAGCCTGGTGAAG
1 TCTATAAGCCTGGTGAACTCTATAA-GCTTGG-AAAAGTCTATAAGCCTGGTGAAG
* *
2637 TCTTTAAGCCTGGCGAACTC
1 TCTATAAGCCTGGTGAACTC
2657 ACAATAAGTG
Statistics
Matches: 69, Mismatches: 2, Indels: 6
0.90 0.03 0.08
Matches are distributed among these distances:
54 61 0.88
55 8 0.12
ACGTcount: A:0.30, C:0.20, G:0.23, T:0.28
Consensus pattern (54 bp):
TCTATAAGCCTGGTGAACTCTATAAGCTTGGAAAAGTCTATAAGCCTGGTGAAG
Found at i:29932 original size:19 final size:20
Alignment explanation
Indices: 29905--29948 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
29895 GTGACTTGTA
*
29905 ATTTGAAAACT-GCAACATT
1 ATTTTAAAACTGGCAACATT
*
29924 ATTTTAAAATTGGCAACATT
1 ATTTTAAAACTGGCAACATT
29944 ATTTT
1 ATTTT
29949 TTGCAGTCCT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 9 0.41
20 13 0.59
ACGTcount: A:0.39, C:0.11, G:0.09, T:0.41
Consensus pattern (20 bp):
ATTTTAAAACTGGCAACATT
Found at i:38216 original size:67 final size:67
Alignment explanation
Indices: 38111--38238 Score: 195
Period size: 67 Copynumber: 1.9 Consensus size: 67
38101 ACATCCACAC
* * *
38111 ATGTTTATAATTTAATCTATAAATTCACTAGTACGATATTTGATATTTTGAGAACTTAAATCCAC
1 ATGTTTATAATTTAACCTATAAATTCACTAGTACGATATTTGATATTTTAAGAACTCAAATCCAC
38176 GT
66 GT
* *
38178 ATGTTTATAATTTAACCTATAAATTGA-TCAGTATGATATTTGATATTTTAAGAACTCAAAT
1 ATGTTTATAATTTAACCTATAAATTCACT-AGTACGATATTTGATATTTTAAGAACTCAAAT
38239 AAAATATTTT
Statistics
Matches: 55, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
66 1 0.02
67 54 0.98
ACGTcount: A:0.38, C:0.10, G:0.10, T:0.42
Consensus pattern (67 bp):
ATGTTTATAATTTAACCTATAAATTCACTAGTACGATATTTGATATTTTAAGAACTCAAATCCAC
GT
Found at i:42118 original size:17 final size:17
Alignment explanation
Indices: 42083--42114 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
42073 TATTTAATTT
42083 AAATATAATTGAATTAG
1 AAATATAATTGAATTAG
42100 AAATATAA-TGAATTA
1 AAATATAATTGAATTA
42115 AGAAGCAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.56, C:0.00, G:0.09, T:0.34
Consensus pattern (17 bp):
AAATATAATTGAATTAG
Found at i:51612 original size:3 final size:3
Alignment explanation
Indices: 51604--51651 Score: 96
Period size: 3 Copynumber: 16.0 Consensus size: 3
51594 CAGAACTCTC
51604 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
51652 CACAAGAGTG
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 45 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:56260 original size:6 final size:6
Alignment explanation
Indices: 56249--56302 Score: 90
Period size: 6 Copynumber: 9.0 Consensus size: 6
56239 CGATTCATTC
* *
56249 CATTGT CATTGT CATTGT CATTGT CATTGT CATTGT CATTGC CATTGC
1 CATTGT CATTGT CATTGT CATTGT CATTGT CATTGT CATTGT CATTGT
56297 CATTGT
1 CATTGT
56303 TATCATGCTA
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 46 1.00
ACGTcount: A:0.17, C:0.20, G:0.17, T:0.46
Consensus pattern (6 bp):
CATTGT
Found at i:57421 original size:32 final size:31
Alignment explanation
Indices: 57362--57421 Score: 75
Period size: 32 Copynumber: 1.9 Consensus size: 31
57352 TTTTAAAATC
* * **
57362 AATAAAAAATATTGATAATTTTTTAAAACAT
1 AATAAAAAATACTGATAATATCATAAAACAT
57393 AATATAAAAATACTGATAATATCATAAAA
1 AATA-AAAAATACTGATAATATCATAAAA
57422 TTTATTTAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
31 4 0.17
32 20 0.83
ACGTcount: A:0.58, C:0.05, G:0.03, T:0.33
Consensus pattern (31 bp):
AATAAAAAATACTGATAATATCATAAAACAT
Found at i:58757 original size:21 final size:22
Alignment explanation
Indices: 58714--58754 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
58704 ATGAGATGGG
*
58714 TAACTTTAAATCTCATGACAAT
1 TAACTTGAAATCTCATGACAAT
58736 TAACTTGAAAT-TCAT-ACAA
1 TAACTTGAAATCTCATGACAA
58755 ATTTATCATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 4 0.22
21 4 0.22
22 10 0.56
ACGTcount: A:0.44, C:0.17, G:0.05, T:0.34
Consensus pattern (22 bp):
TAACTTGAAATCTCATGACAAT
Found at i:59067 original size:19 final size:19
Alignment explanation
Indices: 59021--59071 Score: 50
Period size: 19 Copynumber: 2.7 Consensus size: 19
59011 TGCGTATCGA
* *
59021 TATAATATAGTTTTCTCATG
1 TATAA-ATAATTTACTCATG
* *
59041 TGTTAATAATTTACTCATG
1 TATAAATAATTTACTCATG
59060 TATAAAT-ATTTA
1 TATAAATAATTTA
59072 TAGTTTACAA
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
18 5 0.20
19 17 0.68
20 3 0.12
ACGTcount: A:0.35, C:0.08, G:0.08, T:0.49
Consensus pattern (19 bp):
TATAAATAATTTACTCATG
Found at i:59534 original size:23 final size:23
Alignment explanation
Indices: 59491--59535 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
59481 TCTTTAGAAA
59491 AAAAAACAATGTTTGAGTTTGAG
1 AAAAAACAATGTTTGAGTTTGAG
*
59514 AAAAAAGAATAGTTTGA-TTTGA
1 AAAAAACAAT-GTTTGAGTTTGA
59536 TTGGGGTTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 14 0.70
24 6 0.30
ACGTcount: A:0.47, C:0.02, G:0.20, T:0.31
Consensus pattern (23 bp):
AAAAAACAATGTTTGAGTTTGAG
Found at i:62194 original size:24 final size:23
Alignment explanation
Indices: 62164--62220 Score: 96
Period size: 24 Copynumber: 2.4 Consensus size: 23
62154 ATATGCTCTC
62164 TTTTACTCTCTCATTCTCTTTGTT
1 TTTTACTCTCTCATTCTCTTT-TT
62188 TTTTACTCTCTCATTCTCTTTTT
1 TTTTACTCTCTCATTCTCTTTTT
62211 TCTTTACTCT
1 T-TTTACTCT
62221 TTGTCCTTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
23 3 0.09
24 29 0.91
ACGTcount: A:0.09, C:0.26, G:0.02, T:0.63
Consensus pattern (23 bp):
TTTTACTCTCTCATTCTCTTTTT
Found at i:71035 original size:6 final size:6
Alignment explanation
Indices: 71024--71048 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
71014 CATCAGGTTC
71024 TTTTCA TTTTCA TTTTCA TTTTCA T
1 TTTTCA TTTTCA TTTTCA TTTTCA T
71049 CTGAATTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.16, G:0.00, T:0.68
Consensus pattern (6 bp):
TTTTCA
Found at i:73490 original size:5 final size:5
Alignment explanation
Indices: 73477--73506 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
73467 TCAACTCAGG
*
73477 ACCCC ACCCT ACCCC ACCCC ACCCC ACCCC
1 ACCCC ACCCC ACCCC ACCCC ACCCC ACCCC
73507 CCACTTTTTC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.20, C:0.77, G:0.00, T:0.03
Consensus pattern (5 bp):
ACCCC
Found at i:75185 original size:169 final size:169
Alignment explanation
Indices: 74900--75237 Score: 550
Period size: 169 Copynumber: 2.0 Consensus size: 169
74890 AGAATAACAT
*
74900 ATCTTAGATCCAAATCAATTTGATGATCAATATCGGTGATTGGAGAAGAAATTTGTTTGAATTTT
1 ATCTTAGATCCAAATCAATTTGATGATCAATATCGGTGATTGGAGAAGAAAATTGTTTGAATTTT
** * * *
74965 GGTTCACAGCTTTCTAACATTTAAAGCTGTTTCATTAAAAAATTGAACTGTAGAAAAGAAGGGGA
66 GGTTCACAAATTCCTAACATTTAAAGCTGTTTCATGAAAAAATTAAACTGTAGAAAAGAAGGGGA
* * * **
75030 TGAGAGCTTTCGATTGATATAGGCAGTGCGAGCGAAGAA
131 TGAGAACTTTCAATTGATACAAACAGTGCGAGCGAAGAA
75069 ATCTTAGATCCAAATCAATTTGATGATCAATATCGGTGATTGGAGAAGAAAATTGTTTGAATTTT
1 ATCTTAGATCCAAATCAATTTGATGATCAATATCGGTGATTGGAGAAGAAAATTGTTTGAATTTT
* *
75134 GGTTCACAAATTCCTAACATTTAAAGTTGTTTCATGAAAAAATTAAACTGTAGAAAATAAGGGGA
66 GGTTCACAAATTCCTAACATTTAAAGCTGTTTCATGAAAAAATTAAACTGTAGAAAAGAAGGGGA
*
75199 TGAGAACTTTCAATTGATACAAATAGTGCGAGCGAAGAA
131 TGAGAACTTTCAATTGATACAAACAGTGCGAGCGAAGAA
75238 GACCATACAA
Statistics
Matches: 155, Mismatches: 14, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
169 155 1.00
ACGTcount: A:0.37, C:0.11, G:0.21, T:0.31
Consensus pattern (169 bp):
ATCTTAGATCCAAATCAATTTGATGATCAATATCGGTGATTGGAGAAGAAAATTGTTTGAATTTT
GGTTCACAAATTCCTAACATTTAAAGCTGTTTCATGAAAAAATTAAACTGTAGAAAAGAAGGGGA
TGAGAACTTTCAATTGATACAAACAGTGCGAGCGAAGAA
Found at i:78222 original size:6 final size:6
Alignment explanation
Indices: 78213--78262 Score: 64
Period size: 6 Copynumber: 8.3 Consensus size: 6
78203 GGAGAGGGAG
* * * *
78213 CGAGAA CGAGAA AGAGAA CGAGTA CGAGAA CGGGAA CGAGAA CGTGAA
1 CGAGAA CGAGAA CGAGAA CGAGAA CGAGAA CGAGAA CGAGAA CGAGAA
78261 CG
1 CG
78263 TTTGCGCATC
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
6 37 1.00
ACGTcount: A:0.44, C:0.16, G:0.36, T:0.04
Consensus pattern (6 bp):
CGAGAA
Found at i:78305 original size:18 final size:18
Alignment explanation
Indices: 78282--78316 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
78272 CTTGGAGCGA
78282 CGGGAGAAGGAAAGAGAG
1 CGGGAGAAGGAAAGAGAG
*
78300 CGGGAGAAGGAGAGAGA
1 CGGGAGAAGGAAAGAGA
78317 ACGAGAGCGC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.43, C:0.06, G:0.51, T:0.00
Consensus pattern (18 bp):
CGGGAGAAGGAAAGAGAG
Found at i:84167 original size:45 final size:45
Alignment explanation
Indices: 84111--84198 Score: 122
Period size: 45 Copynumber: 2.0 Consensus size: 45
84101 ATGATTGTGA
*
84111 CCAAGGAAGAAACTACCGCAGATCAAGTTGAGGAGCCAAAGATGG
1 CCAAGGAAGAAACTAACGCAGATCAAGTTGAGGAGCCAAAGATGG
* * ** *
84156 CCAATGAAGAAACTAATGTTGATCATGTTGAGGAGCCAAAGAT
1 CCAAGGAAGAAACTAACGCAGATCAAGTTGAGGAGCCAAAGAT
84199 AAAAGATGAA
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
45 37 1.00
ACGTcount: A:0.40, C:0.17, G:0.26, T:0.17
Consensus pattern (45 bp):
CCAAGGAAGAAACTAACGCAGATCAAGTTGAGGAGCCAAAGATGG
Found at i:87037 original size:18 final size:16
Alignment explanation
Indices: 87016--87050 Score: 52
Period size: 18 Copynumber: 2.1 Consensus size: 16
87006 TTTTAATAGA
87016 ATGAATTTAATGTTAATT
1 ATGAATTT-AT-TTAATT
87034 ATGAATTTATTTAATT
1 ATGAATTTATTTAATT
87050 A
1 A
87051 GTTAAATACA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.41
17 2 0.12
18 8 0.47
ACGTcount: A:0.40, C:0.00, G:0.09, T:0.51
Consensus pattern (16 bp):
ATGAATTTATTTAATT
Found at i:105590 original size:22 final size:22
Alignment explanation
Indices: 105542--105593 Score: 70
Period size: 22 Copynumber: 2.4 Consensus size: 22
105532 AGCACGTAAA
* *
105542 GTGCTCTCTGTTTAGCATATTT
1 GTGCTCTCTGTTTAGCATACTC
105564 GTGCTCTCTGTTTAGCAT-CTC
1 GTGCTCTCTGTTTAGCATACTC
105585 GATGCTCTC
1 G-TGCTCTC
105594 CGTTCATTTG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
21 2 0.07
22 25 0.93
ACGTcount: A:0.12, C:0.25, G:0.19, T:0.44
Consensus pattern (22 bp):
GTGCTCTCTGTTTAGCATACTC
Found at i:107175 original size:16 final size:16
Alignment explanation
Indices: 107145--107174 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
107135 TTCATTTTAA
107145 TAATAAGTTTTAAAAT
1 TAATAAGTTTTAAAAT
107161 TAATAA-TTTTAAAA
1 TAATAAGTTTTAAAA
107175 AAATATTATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.43
Consensus pattern (16 bp):
TAATAAGTTTTAAAAT
Found at i:108326 original size:32 final size:32
Alignment explanation
Indices: 108274--108336 Score: 81
Period size: 32 Copynumber: 2.0 Consensus size: 32
108264 TTGAATACTA
* * * *
108274 ATTATAATTTTATTTCATTACAGCTTTATTCC
1 ATTACAATCTTATTTCATTACAACTCTATTCC
*
108306 ATTACAATCTTATTTTATTACAACTCTATTC
1 ATTACAATCTTATTTCATTACAACTCTATTC
108337 AATTCCAGTG
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
32 26 1.00
ACGTcount: A:0.30, C:0.17, G:0.02, T:0.51
Consensus pattern (32 bp):
ATTACAATCTTATTTCATTACAACTCTATTCC
Found at i:115183 original size:16 final size:16
Alignment explanation
Indices: 115164--115217 Score: 90
Period size: 16 Copynumber: 3.4 Consensus size: 16
115154 TTTGGTTCAT
*
115164 TGTAATGGAATAGAGG
1 TGTAATGGAATAGAGC
*
115180 TGTAATGAAATAGAGC
1 TGTAATGGAATAGAGC
115196 TGTAATGGAATAGAGC
1 TGTAATGGAATAGAGC
115212 TGTAAT
1 TGTAAT
115218 CAGTAATTCA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 35 1.00
ACGTcount: A:0.39, C:0.04, G:0.30, T:0.28
Consensus pattern (16 bp):
TGTAATGGAATAGAGC
Found at i:115417 original size:16 final size:16
Alignment explanation
Indices: 115398--115491 Score: 50
Period size: 16 Copynumber: 6.0 Consensus size: 16
115388 GATTATTATT
115398 AAATATAATTTAATAA
1 AAATATAATTTAATAA
**
115414 AAATATTAA-TTAATTT
1 AAATA-TAATTTAATAA
* * *
115430 AATTATATTTTAATAT
1 AAATATAATTTAATAA
* * *
115446 AATTATTATTAAAT-A
1 AAATATAATTTAATAA
* **
115461 AAATTTAATAAAAT-A
1 AAATATAATTTAATAA
*
115476 ATATATAATTTAATAA
1 AAATATAATTTAATAA
115492 TATTTTTAAT
Statistics
Matches: 58, Mismatches: 17, Indels: 6
0.72 0.21 0.07
Matches are distributed among these distances:
15 23 0.40
16 32 0.55
17 3 0.05
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (16 bp):
AAATATAATTTAATAA
Found at i:115420 original size:26 final size:26
Alignment explanation
Indices: 115380--115525 Score: 94
Period size: 32 Copynumber: 5.1 Consensus size: 26
115370 CTTATTAAAT
*
115380 TTTAATAAGATTATTATTAAATATAA
1 TTTAATAAAATTATTATTAAATATAA
* *
115406 TTTAATAAAAATATTAATTAATTTAATTATAT
1 TTTAAT--AAA-ATT-ATT-A-TTAAATATAA
* *
115438 TTTAATATAATTATTATTAAATAAAA
1 TTTAATAAAATTATTATTAAATATAA
* *
115464 TTTAATAAAATAATATATAATTTAATAATATT
1 TTTAATAAAAT--TAT-T-ATTAAAT-ATA-A
*
115496 TTTAATATAATTATTATTAAAATATGAA
1 TTTAATAAAATTATTATT-AAATAT-AA
115524 TT
1 TT
115526 AGTAAAAATT
Statistics
Matches: 92, Mismatches: 14, Indels: 26
0.70 0.11 0.20
Matches are distributed among these distances:
26 23 0.25
27 1 0.01
28 15 0.16
29 12 0.13
30 14 0.15
31 3 0.03
32 24 0.26
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.48
Consensus pattern (26 bp):
TTTAATAAAATTATTATTAAATATAA
Found at i:115451 original size:58 final size:58
Alignment explanation
Indices: 115373--115543 Score: 206
Period size: 58 Copynumber: 2.9 Consensus size: 58
115363 GATTATTCTT
* *
115373 ATTAAATTTTAATA-AGATTATTATTAAATATAATTTAATAAAAATATTA-ATTAATTTA
1 ATTATATTTTAATATA-ATTATTATTAAATATAATTTAATAAAAATAATATA-TAATTTA
*
115431 ATTATATTTTAATATAATTATTATTAAATAAAATTTAAT-AAAATAATATATAATTTA
1 ATTATATTTTAATATAATTATTATTAAATATAATTTAATAAAAATAATATATAATTTA
* * *
115488 ATAATATTTTTAATATAATTATTATTAAAATATGAA-TTAGTAAAAATTATAATATA
1 ATTATA-TTTTAATATAATTATTATT-AAATAT-AATTTAATAAAAATAAT-ATATA
115544 TAATATTAGA
Statistics
Matches: 99, Mismatches: 7, Indels: 11
0.85 0.06 0.09
Matches are distributed among these distances:
57 20 0.20
58 55 0.56
59 10 0.10
60 9 0.09
61 5 0.05
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (58 bp):
ATTATATTTTAATATAATTATTATTAAATATAATTTAATAAAAATAATATATAATTTA
Found at i:115510 original size:15 final size:15
Alignment explanation
Indices: 115423--115515 Score: 52
Period size: 15 Copynumber: 6.3 Consensus size: 15
115413 AAAATATTAA
*
115423 TTAATTTAATTATATT
1 TTAATATAATTAT-TT
*
115439 TTAATATAATTATTA
1 TTAATATAATTATTT
*
115454 TTAA-ATAA-AATTT
1 TTAATATAATTATTT
* * *
115467 AATAAAATAATATATAAT
1 -TTAATATAAT-TAT-TT
115485 TT-A-ATAA-TATTT
1 TTAATATAATTATTT
*
115497 TTAATATAATTATTA
1 TTAATATAATTATTT
115512 TTAA
1 TTAA
115516 AATATGAATT
Statistics
Matches: 59, Mismatches: 10, Indels: 17
0.69 0.12 0.20
Matches are distributed among these distances:
12 3 0.05
13 7 0.12
14 11 0.19
15 21 0.36
16 13 0.22
17 3 0.05
18 1 0.02
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (15 bp):
TTAATATAATTATTT
Found at i:133442 original size:12 final size:12
Alignment explanation
Indices: 133400--133446 Score: 51
Period size: 12 Copynumber: 3.8 Consensus size: 12
133390 TTTAGTATTG
133400 TTTTTAAGAAGTA
1 TTTTTAA-AAGTA
133413 TTTTGTAAAAGTGA
1 TTTT-TAAAAGT-A
*
133427 -TTTTGAAAGTA
1 TTTTTAAAAGTA
133438 TTTTTAAAA
1 TTTTTAAAA
133447 AGTTTGGTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 7
0.76 0.05 0.18
Matches are distributed among these distances:
11 1 0.03
12 13 0.45
13 11 0.38
14 4 0.14
ACGTcount: A:0.38, C:0.00, G:0.15, T:0.47
Consensus pattern (12 bp):
TTTTTAAAAGTA
Found at i:135919 original size:21 final size:20
Alignment explanation
Indices: 135877--135919 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 20
135867 TTTTTCAATA
*
135877 TTTTTTAAATTTTTATTCTT
1 TTTTTTAAATTTTAATTCTT
135897 TTTTTTGAAATTTATAATT-TT
1 TTTTTT-AAATTT-TAATTCTT
135918 TT
1 TT
135920 AAAATAAGAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
20 6 0.30
21 10 0.50
22 4 0.20
ACGTcount: A:0.23, C:0.02, G:0.02, T:0.72
Consensus pattern (20 bp):
TTTTTTAAATTTTAATTCTT
Found at i:141127 original size:16 final size:16
Alignment explanation
Indices: 141102--141140 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
141092 TTTATAAGTC
**
141102 TTTTTATTTTTTTATA
1 TTTTTATTTTTAAATA
*
141118 TTTTTGTTTTTAAATA
1 TTTTTATTTTTAAATA
141134 TTTTTAT
1 TTTTTAT
141141 AAATTTTAAA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.21, C:0.00, G:0.03, T:0.77
Consensus pattern (16 bp):
TTTTTATTTTTAAATA
Found at i:147959 original size:17 final size:18
Alignment explanation
Indices: 147937--147970 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
147927 TGGAACCCAC
*
147937 AATTAATAC-AATTAAAA
1 AATTAAAACAAATTAAAA
147954 AATTAAAACAAATTAAA
1 AATTAAAACAAATTAAA
147971 CACTAGCAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.68, C:0.06, G:0.00, T:0.26
Consensus pattern (18 bp):
AATTAAAACAAATTAAAA
Found at i:154508 original size:23 final size:23
Alignment explanation
Indices: 154482--154525 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
154472 ATGTCTTAAA
154482 AAATAATAAAATTGA-ACTTTTCG
1 AAATAATAAAATT-ATACTTTTCG
* *
154505 AAATTATAGAATTATACTTTT
1 AAATAATAAAATTATACTTTT
154526 ATTTTTTAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 1 0.06
23 17 0.94
ACGTcount: A:0.45, C:0.07, G:0.07, T:0.41
Consensus pattern (23 bp):
AAATAATAAAATTATACTTTTCG
Found at i:157026 original size:12 final size:11
Alignment explanation
Indices: 157007--157044 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
156997 AATGAGGTAT
157007 TTTATATA-AA
1 TTTATATATAA
157017 TTTATATATAA
1 TTTATATATAA
*
157028 TTAATATATTAA
1 TTTATATA-TAA
157040 TTTAT
1 TTTAT
157045 CGTTTGAATC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
10 8 0.33
11 9 0.38
12 7 0.29
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (11 bp):
TTTATATATAA
Found at i:162354 original size:24 final size:23
Alignment explanation
Indices: 162306--162354 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
162296 CACAAGGCAG
* *
162306 AAGCGTGCCACAATGCAGAGGAA
1 AAGCGTGCCACAAGGCAGAGAAA
*
162329 AAGCGTGCCACAAAGGCAGATAAA
1 AAGCGTGCCAC-AAGGCAGAGAAA
162353 AA
1 AA
162355 CTAAAAGAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
23 11 0.50
24 11 0.50
ACGTcount: A:0.45, C:0.20, G:0.27, T:0.08
Consensus pattern (23 bp):
AAGCGTGCCACAAGGCAGAGAAA
Found at i:168269 original size:17 final size:17
Alignment explanation
Indices: 168235--168276 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 17
168225 TTATGGGACA
*
168235 AAAATGAGAATGATGTG
1 AAAATGAGAATGAAGTG
168252 AAAAT-AGAATTGAAGTG
1 AAAATGAGAA-TGAAGTG
168269 AAATATGA
1 AAA-ATGA
168277 TTTTTACCCC
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
16 4 0.19
17 14 0.67
18 2 0.10
19 1 0.05
ACGTcount: A:0.52, C:0.00, G:0.24, T:0.24
Consensus pattern (17 bp):
AAAATGAGAATGAAGTG
Found at i:173067 original size:28 final size:26
Alignment explanation
Indices: 173014--173067 Score: 63
Period size: 28 Copynumber: 2.0 Consensus size: 26
173004 CTTTAAAAAA
* *
173014 TAAAAGATTTTTATTATTAACATTAT
1 TAAAAGATTTTAATTAATAACATTAT
*
173040 TAAAAGATATATTAATTAATAATATTAT
1 TAAAAGAT-T-TTAATTAATAACATTAT
173068 AATAAATAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
26 8 0.35
27 1 0.04
28 14 0.61
ACGTcount: A:0.48, C:0.02, G:0.04, T:0.46
Consensus pattern (26 bp):
TAAAAGATTTTAATTAATAACATTAT
Found at i:173490 original size:17 final size:17
Alignment explanation
Indices: 173456--173497 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 17
173446 TTATGGGACA
*
173456 AAAATGAGAATGATGTG
1 AAAATGAGAATGAAGTG
173473 AAAAT-AGAATTGAAGTG
1 AAAATGAGAA-TGAAGTG
173490 AAATATGA
1 AAA-ATGA
173498 TTTTTACCCC
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
16 4 0.19
17 14 0.67
18 2 0.10
19 1 0.05
ACGTcount: A:0.52, C:0.00, G:0.24, T:0.24
Consensus pattern (17 bp):
AAAATGAGAATGAAGTG
Found at i:177384 original size:33 final size:33
Alignment explanation
Indices: 177323--177385 Score: 83
Period size: 33 Copynumber: 1.9 Consensus size: 33
177313 TTTTTAAGTT
**
177323 AATGATTATTTTTAATTGTGTTTATTTATTAGG
1 AATGATTATTTTTAAAAGTGTTTATTTATTAGG
*
177356 AATGATTTTTTTTAAAAAGTGTTT-TTTATT
1 AATGATTATTTTT-AAAAGTGTTTATTTATT
177386 TTTAAAATGA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
33 18 0.69
34 8 0.31
ACGTcount: A:0.29, C:0.00, G:0.13, T:0.59
Consensus pattern (33 bp):
AATGATTATTTTTAAAAGTGTTTATTTATTAGG
Found at i:186925 original size:56 final size:56
Alignment explanation
Indices: 186859--186970 Score: 179
Period size: 56 Copynumber: 2.0 Consensus size: 56
186849 TACAATAACT
* **
186859 ATTATTATTGTTATTTCATGGTTACATGTGTTAAAAATGCTATGTTAGAATGTTTG
1 ATTATTATTGTTATTTCAGGGTTACATGTGTTAAAAACACTATGTTAGAATGTTTG
* *
186915 ATTATTATTGTTATTTCAGGGTTATATGTGTTAAAGACACTATGTTAGAATGTTTG
1 ATTATTATTGTTATTTCAGGGTTACATGTGTTAAAAACACTATGTTAGAATGTTTG
186971 CTTAAGAATT
Statistics
Matches: 51, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
56 51 1.00
ACGTcount: A:0.29, C:0.05, G:0.19, T:0.47
Consensus pattern (56 bp):
ATTATTATTGTTATTTCAGGGTTACATGTGTTAAAAACACTATGTTAGAATGTTTG
Found at i:190675 original size:17 final size:18
Alignment explanation
Indices: 190642--190675 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
190632 TAAAAAGTTA
*
190642 AAATTTTAGTCGGGTTTT
1 AAATTTTAATCGGGTTTT
190660 AAATTTTAAT-GGGTTT
1 AAATTTTAATCGGGTTT
190676 GGATTTTTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.26, C:0.03, G:0.21, T:0.50
Consensus pattern (18 bp):
AAATTTTAATCGGGTTTT
Found at i:193985 original size:25 final size:25
Alignment explanation
Indices: 193911--193985 Score: 64
Period size: 25 Copynumber: 3.0 Consensus size: 25
193901 ATCATAAATC
193911 CAAGTAAACAACATAAATCCAAGATT
1 CAAGTAAACAACATAAATCCAAG-TT
* * * * *
193937 -ATAATAAAAAAAAT-AAGCAAAAGTT
1 CA-AGTAAACAACATAAATC-CAAGTT
193962 CAAGTAAACAACATAAATCCAAGT
1 CAAGTAAACAACATAAATCCAAGT
193986 AACAACAATA
Statistics
Matches: 35, Mismatches: 10, Indels: 9
0.65 0.19 0.17
Matches are distributed among these distances:
25 19 0.54
26 16 0.46
ACGTcount: A:0.59, C:0.15, G:0.08, T:0.19
Consensus pattern (25 bp):
CAAGTAAACAACATAAATCCAAGTT
Found at i:194016 original size:70 final size:71
Alignment explanation
Indices: 193903--194035 Score: 195
Period size: 70 Copynumber: 1.9 Consensus size: 71
193893 CTTATTTTAT
193903 CATAAATCCAAGTAAACAACATAAATCCAAGATTATAATAAAAAAA-ATAAGCAAAAGTTCAAGT
1 CATAAATCCAAGTAAACAACATAAATCCAAGATTATAATAAAAAAACATAAGCAAAAGTTCAAGT
193967 AAACAA
66 AAACAA
193973 CATAAATCCAAGT-AACAACAATAACA-CAACAAGATTAT-A-AAAAAAACATAAGCAAAAGTTC
1 CATAAATCCAAGTAAACAAC-ATAA-ATC--CAAGATTATAATAAAAAAACATAAGCAAAAGTTC
194034 AA
62 AA
194036 AATACAGTAA
Statistics
Matches: 58, Mismatches: 0, Indels: 9
0.87 0.00 0.13
Matches are distributed among these distances:
69 6 0.10
70 25 0.43
71 18 0.31
72 9 0.16
ACGTcount: A:0.60, C:0.16, G:0.07, T:0.17
Consensus pattern (71 bp):
CATAAATCCAAGTAAACAACATAAATCCAAGATTATAATAAAAAAACATAAGCAAAAGTTCAAGT
AAACAA
Found at i:194280 original size:10 final size:10
Alignment explanation
Indices: 194265--194289 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
194255 TAACCATAAT
194265 AATAATAAAC
1 AATAATAAAC
194275 AATAATAAAC
1 AATAATAAAC
194285 AATAA
1 AATAA
194290 ATTTAGACGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.72, C:0.08, G:0.00, T:0.20
Consensus pattern (10 bp):
AATAATAAAC
Found at i:194666 original size:23 final size:23
Alignment explanation
Indices: 194623--194667 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
194613 AAAAAAATTC
**
194623 AACTCGATTCGTTTAACTCGAAT
1 AACTCGATTCGAATAACTCGAAT
*
194646 AACTCGATTCGAATAATTCGAA
1 AACTCGATTCGAATAACTCGAA
194668 ATTCGAAAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.36, C:0.20, G:0.13, T:0.31
Consensus pattern (23 bp):
AACTCGATTCGAATAACTCGAAT
Found at i:195544 original size:46 final size:46
Alignment explanation
Indices: 195475--195640 Score: 217
Period size: 46 Copynumber: 3.6 Consensus size: 46
195465 TCAAGACAAG
* *
195475 TTGTCTTCCACAATTTTAGGGATTTGTTTGACTAAAGTATAGACAT
1 TTGTCTTCCACAATTTCAGGGATTTGTTTGACTAAACTATAGACAT
* * * *
195521 TTGTCTCCCACAATTCTCA-GGATTTGTTTGACTAAATTGTAGGCAT
1 TTGTCTTCCACAATT-TCAGGGATTTGTTTGACTAAACTATAGACAT
* * *
195567 TTGTCTTCCATAATTTCAGGAATTTGTTTGGCTAAACTATAGACAT
1 TTGTCTTCCACAATTTCAGGGATTTGTTTGACTAAACTATAGACAT
* *
195613 TTATCTTCCACAATTTTAGGGATTTGTT
1 TTGTCTTCCACAATTTCAGGGATTTGTT
195641 GTAACACTCA
Statistics
Matches: 102, Mismatches: 16, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
45 3 0.03
46 97 0.95
47 2 0.02
ACGTcount: A:0.26, C:0.16, G:0.16, T:0.42
Consensus pattern (46 bp):
TTGTCTTCCACAATTTCAGGGATTTGTTTGACTAAACTATAGACAT
Found at i:196866 original size:52 final size:52
Alignment explanation
Indices: 196810--196967 Score: 244
Period size: 52 Copynumber: 3.0 Consensus size: 52
196800 TACAATCTTG
* * *
196810 GGACCTCATAATCCGAAAAGGATTCATATACTCACAATTACACATAGTCATC
1 GGACCTCATAATCCGTAAAGGATTCATATACTCACGATAACACATAGTCATC
* *
196862 GGACCTTATAATCCGTAAAGGATTCATATACTCATGATAACACATAGTCATC
1 GGACCTCATAATCCGTAAAGGATTCATATACTCACGATAACACATAGTCATC
* * *
196914 GGACCTCATAATCTGTAAAGGATTTATATACTCACGATGACACATAGTCATC
1 GGACCTCATAATCCGTAAAGGATTCATATACTCACGATAACACATAGTCATC
196966 GG
1 GG
196968 GCTTTTTGCA
Statistics
Matches: 96, Mismatches: 10, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
52 96 1.00
ACGTcount: A:0.36, C:0.22, G:0.15, T:0.27
Consensus pattern (52 bp):
GGACCTCATAATCCGTAAAGGATTCATATACTCACGATAACACATAGTCATC
Found at i:202248 original size:11 final size:11
Alignment explanation
Indices: 202232--202280 Score: 57
Period size: 11 Copynumber: 4.5 Consensus size: 11
202222 TCATCATTTG
202232 AAAATTATAAA
1 AAAATTATAAA
202243 AAAATTATAAA
1 AAAATTATAAA
*
202254 AAAA-TAT-AG
1 AAAATTATAAA
*
202263 AAATTTATTAAA
1 AAAATTA-TAAA
202275 AAAATT
1 AAAATT
202281 GTGACATCAT
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
9 4 0.13
10 5 0.16
11 16 0.52
12 6 0.19
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (11 bp):
AAAATTATAAA
Found at i:202261 original size:21 final size:21
Alignment explanation
Indices: 202232--202279 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 21
202222 TCATCATTTG
*
202232 AAAATTATAAAAAAATTA-TAA
1 AAAAATAT-AAAAAATTATTAA
* *
202253 AAAAATATAGAAATTTATTAA
1 AAAAATATAAAAAATTATTAA
202274 AAAAAT
1 AAAAAT
202280 TGTGACATCA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
20 7 0.30
21 16 0.70
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29
Consensus pattern (21 bp):
AAAAATATAAAAAATTATTAA
Found at i:202788 original size:45 final size:44
Alignment explanation
Indices: 202729--202827 Score: 128
Period size: 45 Copynumber: 2.2 Consensus size: 44
202719 ATGCTTATAA
* *
202729 TAAAAATTCAAAATAATTGATATTATATTTATATTAA-ATAATATAT
1 TAAAAATT-AAAATAATTAAAATTATATTTATATTAAGA-AAT-TAT
* *
202775 TATAAATTAAAATAATTAAAATTGTATTTATATTAAGAAATTAT
1 TAAAAATTAAAATAATTAAAATTATATTTATATTAAGAAATTAT
202819 TAAAAATTA
1 TAAAAATTA
202828 TATTTACATT
Statistics
Matches: 47, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
44 11 0.23
45 28 0.60
46 8 0.17
ACGTcount: A:0.54, C:0.01, G:0.03, T:0.42
Consensus pattern (44 bp):
TAAAAATTAAAATAATTAAAATTATATTTATATTAAGAAATTAT
Found at i:202789 original size:20 final size:18
Alignment explanation
Indices: 202752--202790 Score: 51
Period size: 20 Copynumber: 2.1 Consensus size: 18
202742 TAATTGATAT
*
202752 TATATTTATATTAAATAA
1 TATATTTAAATTAAATAA
202770 TATATTATAAATTAAAATAA
1 TATATT-TAAATT-AAATAA
202790 T
1 T
202791 TAAAATTGTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 6 0.33
19 5 0.28
20 7 0.39
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (18 bp):
TATATTTAAATTAAATAA
Found at i:208610 original size:18 final size:19
Alignment explanation
Indices: 208570--208608 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
208560 ATTTTAGTGC
*
208570 TTCAAATAACAATGGTTTT
1 TTCAAATAACAATAGTTTT
208589 TTCAAATAACAATAGTTTT
1 TTCAAATAACAATAGTTTT
208608 T
1 T
208609 CATAAGAACT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.38, C:0.10, G:0.08, T:0.44
Consensus pattern (19 bp):
TTCAAATAACAATAGTTTT
Found at i:211377 original size:29 final size:30
Alignment explanation
Indices: 211343--211407 Score: 89
Period size: 29 Copynumber: 2.2 Consensus size: 30
211333 AATTTTTTAT
211343 TTTTATAATTTTTAAA-AATTAAATTA-AA
1 TTTTATAATTTTTAAAGAATTAAATTATAA
* *
211371 TTCTTATTATTTTTAAAGAGTTAAATTATAA
1 TT-TTATAATTTTTAAAGAATTAAATTATAA
211402 TTTTAT
1 TTTTAT
211408 TTTTATTAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
28 2 0.06
29 13 0.41
30 13 0.41
31 4 0.12
ACGTcount: A:0.42, C:0.02, G:0.03, T:0.54
Consensus pattern (30 bp):
TTTTATAATTTTTAAAGAATTAAATTATAA
Found at i:211397 original size:30 final size:29
Alignment explanation
Indices: 211343--211416 Score: 89
Period size: 30 Copynumber: 2.5 Consensus size: 29
211333 AATTTTTTAT
*
211343 TTTTATAATTTTTAAAAATTAAATTA-AA
1 TTTTATTATTTTTAAAAATTAAATTATAA
*
211371 TTCTTATTATTTTTAAAGAGTTAAATTATAA
1 TT-TTATTATTTTTAAA-AATTAAATTATAA
211402 TTTTATT-TTTATTAA
1 TTTTATTATTT-TTAA
211417 TTTAAAGTTT
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
28 2 0.05
29 16 0.40
30 18 0.45
31 4 0.10
ACGTcount: A:0.41, C:0.01, G:0.03, T:0.55
Consensus pattern (29 bp):
TTTTATTATTTTTAAAAATTAAATTATAA
Found at i:225774 original size:15 final size:15
Alignment explanation
Indices: 225742--225775 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
225732 GACAAAGACA
*
225742 ACGACAACGACAACG
1 ACGACAACGACAAAG
*
225757 ACGACAACGATAAAG
1 ACGACAACGACAAAG
225772 ACGA
1 ACGA
225776 GCTACTTCGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.50, C:0.26, G:0.21, T:0.03
Consensus pattern (15 bp):
ACGACAACGACAAAG
Found at i:227832 original size:34 final size:34
Alignment explanation
Indices: 227785--227850 Score: 82
Period size: 34 Copynumber: 1.9 Consensus size: 34
227775 AACCACATAA
227785 ATCCAAATCTAAAATTAACTCAAACTC-AAAATTT
1 ATCCAAATCTAAAA-TAACTCAAACTCGAAAATTT
* *
227819 ATCCAAAAT-TAAAATAATTTAAACTCGAAAAT
1 ATCC-AAATCTAAAATAACTCAAACTCGAAAAT
227851 GATAAAAATA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
33 10 0.36
34 14 0.50
35 4 0.14
ACGTcount: A:0.53, C:0.17, G:0.02, T:0.29
Consensus pattern (34 bp):
ATCCAAATCTAAAATAACTCAAACTCGAAAATTT
Found at i:228492 original size:14 final size:14
Alignment explanation
Indices: 228475--228508 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
228465 TATAATATCC
228475 AAATAATAACAATA
1 AAATAATAACAATA
*
228489 AAATAATATCAATA
1 AAATAATAACAATA
*
228503 TAATAA
1 AAATAA
228509 CAAAATGGTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.68, C:0.06, G:0.00, T:0.26
Consensus pattern (14 bp):
AAATAATAACAATA
Found at i:228557 original size:22 final size:22
Alignment explanation
Indices: 228502--228545 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
228492 TAATATCAAT
*
228502 ATAATAACAAAATGGTAGCAAA
1 ATAATATCAAAATGGTAGCAAA
228524 ATAATATCAAAATGGTAGCAAA
1 ATAATATCAAAATGGTAGCAAA
228546 CATCAATGAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.57, C:0.09, G:0.14, T:0.20
Consensus pattern (22 bp):
ATAATATCAAAATGGTAGCAAA
Found at i:230801 original size:22 final size:22
Alignment explanation
Indices: 230774--230815 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
230764 TTTTGCCTTT
* *
230774 TTCTGATTTTGCTGTTATTATC
1 TTCTGATTCTGCTGCTATTATC
230796 TTCTGATTCTGCTGCTATTA
1 TTCTGATTCTGCTGCTATTA
230816 ATTCTGAATA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.14, C:0.17, G:0.14, T:0.55
Consensus pattern (22 bp):
TTCTGATTCTGCTGCTATTATC
Found at i:233375 original size:31 final size:32
Alignment explanation
Indices: 233340--233410 Score: 99
Period size: 32 Copynumber: 2.2 Consensus size: 32
233330 TTTGGTGCAC
* *
233340 TTTAATTTA-TCAATTTTAGTTTTTGTATTTT
1 TTTAAATTAGTCAATTTTAGTTTTTATATTTT
*
233371 TTTAAATTAGTTAATTTTAGTTTTTATATTTT
1 TTTAAATTAGTCAATTTTAGTTTTTATATTTT
*
233403 TTGAAATT
1 TTTAAATT
233411 TAAAATTTTA
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
31 8 0.23
32 27 0.77
ACGTcount: A:0.27, C:0.01, G:0.07, T:0.65
Consensus pattern (32 bp):
TTTAAATTAGTCAATTTTAGTTTTTATATTTT
Found at i:233418 original size:31 final size:31
Alignment explanation
Indices: 233351--233425 Score: 89
Period size: 32 Copynumber: 2.4 Consensus size: 31
233341 TTAATTTATC
* * *
233351 AATTTTAGTTTTTGTATTTTTTTAAATTAGTT
1 AATTTTAGTTTTTATATTTTTTGAAATTAG-A
233383 AATTTTAGTTTTTATATTTTTTGAAATTTA-A
1 AATTTTAGTTTTTATATTTTTTGAAA-TTAGA
*
233414 AATTTTAATTTT
1 AATTTTAGTTTT
233426 AACCCAAATG
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
31 11 0.29
32 24 0.63
33 3 0.08
ACGTcount: A:0.29, C:0.00, G:0.07, T:0.64
Consensus pattern (31 bp):
AATTTTAGTTTTTATATTTTTTGAAATTAGA
Found at i:237344 original size:9 final size:9
Alignment explanation
Indices: 237330--237443 Score: 72
Period size: 9 Copynumber: 11.8 Consensus size: 9
237320 GCAAATGATT
237330 TTAAAATTA
1 TTAAAATTA
237339 TTAAAATTA
1 TTAAAATTA
*
237348 GTTTTTAAAAATA
1 ----TTAAAATTA
237361 -TAAAATTA
1 TTAAAATTA
237369 TTAAAATTA
1 TTAAAATTA
** *
237378 TTTTTTAATAA
1 --TTAAAATTA
237389 TATAAAATTA
1 T-TAAAATTA
237399 TTAAAATTA
1 TTAAAATTA
237408 TTTTAAAATTAA
1 --TTAAAATT-A
237420 TTTAAAA-TA
1 -TTAAAATTA
237429 -TAAAATTA
1 TTAAAATTA
237437 TTAAAAT
1 TTAAAAT
237444 AATCATCATT
Statistics
Matches: 84, Mismatches: 8, Indels: 26
0.71 0.07 0.22
Matches are distributed among these distances:
7 5 0.06
8 9 0.11
9 33 0.39
10 7 0.08
11 21 0.25
12 1 0.01
13 8 0.10
ACGTcount: A:0.54, C:0.00, G:0.01, T:0.46
Consensus pattern (9 bp):
TTAAAATTA
Found at i:237353 original size:22 final size:21
Alignment explanation
Indices: 237328--237368 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
237318 CAGCAAATGA
*
237328 TTTTAAAATTATTAAAATTAGT
1 TTTTAAAAATA-TAAAATTAGT
237350 TTTTAAAAATATAAAATTA
1 TTTTAAAAATATAAAATTA
237369 TTAAAATTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 8 0.44
22 10 0.56
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.46
Consensus pattern (21 bp):
TTTTAAAAATATAAAATTAGT
Found at i:237367 original size:30 final size:29
Alignment explanation
Indices: 237331--237438 Score: 139
Period size: 30 Copynumber: 3.7 Consensus size: 29
237321 CAAATGATTT
237331 TAAAATTATTAAAATTAGTTTTTAAAAATA
1 TAAAATTATTAAAATTA-TTTTTAAAAATA
*
237361 TAAAATTATTAAAATTATTTTTTAATAATA
1 TAAAATTATTAAAATTA-TTTTTAAAAATA
* *
237391 TAAAATTATTAAAATTATTTTAAAATTAATT
1 TAAAATTATTAAAATTATTTTTAAA--AATA
237422 TAAAA-TA-TAAAATTATT
1 TAAAATTATTAAAATTATT
237439 AAAATAATCA
Statistics
Matches: 71, Mismatches: 5, Indels: 5
0.88 0.06 0.06
Matches are distributed among these distances:
29 16 0.23
30 47 0.66
31 8 0.11
ACGTcount: A:0.53, C:0.00, G:0.01, T:0.46
Consensus pattern (29 bp):
TAAAATTATTAAAATTATTTTTAAAAATA
Found at i:237494 original size:14 final size:14
Alignment explanation
Indices: 237477--237504 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
237467 TTTTTTTTTA
237477 CCCTTCCCTTTCCC
1 CCCTTCCCTTTCCC
237491 CCCTTCCCTTTCCC
1 CCCTTCCCTTTCCC
237505 GTCCTTGATG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.00, C:0.64, G:0.00, T:0.36
Consensus pattern (14 bp):
CCCTTCCCTTTCCC
Found at i:238147 original size:18 final size:18
Alignment explanation
Indices: 238110--238150 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
238100 CCCTAAACAG
*
238110 AAGGGAAAGGGAAAGGGA
1 AAGGGAAAGGGAAAGAGA
238128 AAGGGAAAGGGGAAA-AGA
1 AAGGGAAA-GGGAAAGAGA
238146 AAGGG
1 AAGGG
238151 GGGAAGGGGA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 15 0.71
19 6 0.29
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (18 bp):
AAGGGAAAGGGAAAGAGA
Found at i:238161 original size:6 final size:6
Alignment explanation
Indices: 238110--238138 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
238100 CCCTAAACAG
238110 AAGGGA AAGGGA AAGGGA AAGGGA AAGGG
1 AAGGGA AAGGGA AAGGGA AAGGGA AAGGG
238139 GAAAAGAAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (6 bp):
AAGGGA
Found at i:238210 original size:9 final size:9
Alignment explanation
Indices: 238196--238267 Score: 54
Period size: 9 Copynumber: 8.8 Consensus size: 9
238186 AATGATGATT
238196 ATTTTAATA
1 ATTTTAATA
238205 ATTTT-AT-
1 ATTTTAATA
238212 ATTTTAAATTA
1 ATTTT-AA-TA
238223 ATTTTAA-A
1 ATTTTAATA
238231 ATTTT-ATA
1 ATTTTAATA
*
238239 TTTTTAA-A
1 ATTTTAATA
238247 A----AATA
1 ATTTTAATA
238252 ATTTTAATA
1 ATTTTAATA
238261 ATTTTAA
1 ATTTTAA
238268 AATCATTTGG
Statistics
Matches: 50, Mismatches: 2, Indels: 22
0.68 0.03 0.30
Matches are distributed among these distances:
4 2 0.04
5 2 0.04
7 6 0.12
8 14 0.28
9 18 0.36
10 3 0.06
11 5 0.10
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (9 bp):
ATTTTAATA
Found at i:238222 original size:26 final size:28
Alignment explanation
Indices: 238193--238266 Score: 91
Period size: 26 Copynumber: 2.6 Consensus size: 28
238183 TAAAATGATG
238193 ATTATTTTAATAATTTTATA-TTTT-AA
1 ATTATTTTAATAATTTTATATTTTTAAA
238219 ATTAATTTTAA-AATTTTATATTTTTAAAAA
1 ATT-ATTTTAATAATTTTATATTTTT--AAA
*
238249 ATAATTTTAATAATTTTA
1 ATTATTTTAATAATTTTA
238267 AAATCATTTG
Statistics
Matches: 41, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
26 12 0.29
27 11 0.27
29 7 0.17
30 11 0.27
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (28 bp):
ATTATTTTAATAATTTTATATTTTTAAA
Found at i:238226 original size:18 final size:16
Alignment explanation
Indices: 238195--238242 Score: 54
Period size: 12 Copynumber: 3.4 Consensus size: 16
238185 AAATGATGAT
238195 TATTTTAATAATTTTA
1 TATTTTAATAATTTTA
238211 TATTTT-A-AA--TTA
1 TATTTTAATAATTTTA
238223 -ATTTTAA-AATTTTA
1 TATTTTAATAATTTTA
238237 TATTTT
1 TATTTT
238243 TAAAAAATAA
Statistics
Matches: 28, Mismatches: 0, Indels: 9
0.76 0.00 0.24
Matches are distributed among these distances:
11 5 0.18
12 6 0.21
14 5 0.18
15 6 0.21
16 6 0.21
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (16 bp):
TATTTTAATAATTTTA
Found at i:238245 original size:16 final size:15
Alignment explanation
Indices: 238195--238247 Score: 60
Period size: 16 Copynumber: 3.7 Consensus size: 15
238185 AAATGATGAT
238195 TATTTTAATAATTTTA
1 TATTTTAA-AATTTTA
238211 TATTTT-AAA--TTA
1 TATTTTAAAATTTTA
238223 -ATTTTAAAATTTTA
1 TATTTTAAAATTTTA
238237 TATTTTTAAAA
1 TA-TTTTAAAA
238248 AATAATTTTA
Statistics
Matches: 32, Mismatches: 0, Indels: 10
0.76 0.00 0.24
Matches are distributed among these distances:
11 5 0.16
12 6 0.19
14 5 0.16
15 2 0.06
16 14 0.44
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (15 bp):
TATTTTAAAATTTTA
Found at i:257573 original size:2 final size:2
Alignment explanation
Indices: 257566--257590 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
257556 GGTTTACCTT
257566 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
257591 TACATATTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:261767 original size:2 final size:2
Alignment explanation
Indices: 261756--261815 Score: 104
Period size: 2 Copynumber: 30.5 Consensus size: 2
261746 TCTTCTAAAT
*
261756 TA TA TA -A TA TA TA CA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
261797 TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA T
261816 TGCTTCATAT
Statistics
Matches: 55, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
1 1 0.02
2 54 0.98
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:261989 original size:221 final size:220
Alignment explanation
Indices: 261579--261993 Score: 581
Period size: 221 Copynumber: 1.9 Consensus size: 220
261569 AATTATAAAT
* *
261579 TATATATATATAAATTTGCTTCATATCAAAACAAATTTAACTATTATAAAGCTCAAAGCTAAAGG
1 TATATATATATAAATTTGCTTCATATCAAAACAAAGTTAACTATTATAAAGCTCAAAGCTAAAAG
* * *
261644 TTCAAAAACACTAAAACCTTTTCCATTATCATATAAAATATCATTTGACCTTAAACAATACAATG
66 TTCAAAAACACTAAAACCTTTTCCATTATAATACAAAATATCATTTGACCTTAAACAAGACAATG
* *
261709 AAATATAATCTTTCCTATCCTACAAACCTCATTGCATTCTTCTAAATTATATAATATATACATAT
131 AAATATAATCTTTCCTATCCTACAAACCCCATTGCATGCTTCTAAATTATATAATATATACATAT
261774 ATATATATATATATATATATATATA
196 ATATATATATATATATATATATATA
* * * *
261799 TATATATATATATATATTGCTTCATATTAAAACAAAGTTCACTATTATAAAGTTCAAAGCTAAAA
1 TATATATATATAAAT-TTGCTTCATATCAAAACAAAGTTAACTATTATAAAGCTCAAAGCTAAAA
** * * * *
261864 GTTCAAAAACACTAAAACCTTCTT-TGTTATAATACAAAATATCATTTGACCTTGAACTAGGCTA
65 GTTCAAAAACACTAAAACCTT-TTCCATTATAATACAAAATATCATTTGACCTTAAACAAGACAA
* * *
261928 TGAAGTATAATCTTTCCTATCTTAC-AACTCCCATTGCATGCTT-TAAA-TAT-T-ATATATATA
129 TGAAATATAATCTTTCCTATCCTACAAAC-CCCATTGCATGCTTCTAAATTATATAATATATACA
261988 TATATA
193 TATATA
261994 CATAGTTAAC
Statistics
Matches: 172, Mismatches: 20, Indels: 9
0.86 0.10 0.04
Matches are distributed among these distances:
217 14 0.08
218 1 0.01
219 3 0.02
220 21 0.12
221 131 0.76
222 2 0.01
ACGTcount: A:0.42, C:0.15, G:0.05, T:0.37
Consensus pattern (220 bp):
TATATATATATAAATTTGCTTCATATCAAAACAAAGTTAACTATTATAAAGCTCAAAGCTAAAAG
TTCAAAAACACTAAAACCTTTTCCATTATAATACAAAATATCATTTGACCTTAAACAAGACAATG
AAATATAATCTTTCCTATCCTACAAACCCCATTGCATGCTTCTAAATTATATAATATATACATAT
ATATATATATATATATATATATATA
Found at i:271044 original size:90 final size:89
Alignment explanation
Indices: 270876--271045 Score: 196
Period size: 90 Copynumber: 1.9 Consensus size: 89
270866 TTCTTTTTTC
* * ***
270876 AAGTTAATTCTTGAATTTAATAATTGTTCTCATATTAGGCTTGAACTAGACAATTATTTTTACAT
1 AAGTTAATTCATGAATTTAATAATTGTTCTCATATTAAGCTTGAACTAGACAATTATTCACACAT
***
270941 TGAAGTTTGAACTTTTTCTTGTCT
66 TGAAACCTGAACTTTTTCTTGTCT
* * * * * * *
270965 AAGTTAGTTCATGAATTTAATAGTTGTTTTCATATTGAAGCTTGAACTTGATAATTGTTCACACC
1 AAGTTAATTCATGAATTTAATAATTGTTCTCATATT-AAGCTTGAACTAGACAATTATTCACACA
271030 TTGAAACCTGAACTTT
65 TTGAAACCTGAACTTT
271046 AATGTTTTCA
Statistics
Matches: 65, Mismatches: 15, Indels: 1
0.80 0.19 0.01
Matches are distributed among these distances:
89 32 0.49
90 33 0.51
ACGTcount: A:0.30, C:0.12, G:0.14, T:0.44
Consensus pattern (89 bp):
AAGTTAATTCATGAATTTAATAATTGTTCTCATATTAAGCTTGAACTAGACAATTATTCACACAT
TGAAACCTGAACTTTTTCTTGTCT
Found at i:271413 original size:137 final size:137
Alignment explanation
Indices: 271167--271451 Score: 570
Period size: 137 Copynumber: 2.1 Consensus size: 137
271157 CGATGTGTGT
271167 ATAATTGTCAAGTTTGAAGTTAACTTGGATAAAAAAAGTTTAAACCTCAATAAATTTAACTATTA
1 ATAATTGTCAAGTTTGAAGTTAACTTGGATAAAAAAAGTTTAAACCTCAATAAATTTAACTATTA
271232 ATCTGGGGTGTTCTTTTGTTACCTAACACAAGTCACAATTGGAAGCAGACTTAAGCAAACGATGC
66 ATCTGGGGTGTTCTTTTGTTACCTAACACAAGTCACAATTGGAAGCAGACTTAAGCAAACGATGC
271297 CAAGAAA
131 CAAGAAA
271304 ATAATTGTCAAGTTTGAAGTTAACTTGGATAAAAAAAGTTTAAACCTCAATAAATTTAACTATTA
1 ATAATTGTCAAGTTTGAAGTTAACTTGGATAAAAAAAGTTTAAACCTCAATAAATTTAACTATTA
271369 ATCTGGGGTGTTCTTTTGTTACCTAACACAAGTCACAATTGGAAGCAGACTTAAGCAAACGATGC
66 ATCTGGGGTGTTCTTTTGTTACCTAACACAAGTCACAATTGGAAGCAGACTTAAGCAAACGATGC
271434 CAAGAAA
131 CAAGAAA
271441 ATAATTGTCAA
1 ATAATTGTCAA
271452 ATTAAGAGTA
Statistics
Matches: 148, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
137 148 1.00
ACGTcount: A:0.40, C:0.14, G:0.16, T:0.30
Consensus pattern (137 bp):
ATAATTGTCAAGTTTGAAGTTAACTTGGATAAAAAAAGTTTAAACCTCAATAAATTTAACTATTA
ATCTGGGGTGTTCTTTTGTTACCTAACACAAGTCACAATTGGAAGCAGACTTAAGCAAACGATGC
CAAGAAA
Found at i:278956 original size:27 final size:27
Alignment explanation
Indices: 278918--278971 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
278908 CTTAACTTCT
278918 ATTCGCACATCTACATTCGAGCTAAGA
1 ATTCGCACATCTACATTCGAGCTAAGA
278945 ATTCGCACATCTACATTCGAGCTAAGA
1 ATTCGCACATCTACATTCGAGCTAAGA
278972 CTCAATGTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.33, C:0.26, G:0.15, T:0.26
Consensus pattern (27 bp):
ATTCGCACATCTACATTCGAGCTAAGA
Found at i:281614 original size:286 final size:283
Alignment explanation
Indices: 280513--282880 Score: 2812
Period size: 285 Copynumber: 8.4 Consensus size: 283
280503 GGATAAATTT
* * * * * * *
280513 TTTA-TTTTTATATATGTAGATTAAAGTATTTATCTTTCAGTTTTTCATTACGTTTGTTCTCTGA
1 TTTATTTTTTAGACATGTAGATTAAAGTATTTACCTTTCGGTTCTTCATTATGTTT-TTCTCCGA
** * * *
280577 ACCTGTAATCGTACTTAAAATAAAAATAGATAAAGAAATAAATAAATCATTTAATTATTTTCTCT
65 ACCTGTTGTCGTACCTAAAATAAAAACAGAT----AAATAAACAAATCATTTAATTATTTTCTCT
* *
280642 AGT-AGTA-GCATATTAAATTGATTTGTTTAAAATATG-TTTTTTAATAATTTCGTCTTC-TCCT
126 AGTGA-TACG-ATATTAAACTGATTTGTTTAAAATATGTTTTTTTAATAATTTCATCTTCAT-CT
* * * * * *
280703 AGTTAAACTGTTTTTGTTTTTGTTTTTTATTTAATATGCAATATGATATGAGAACTTTAATT-TA
188 AGTTAAACTGTTTTTATTTTTATTTTTGATTTAATATGCAATATGATATAAGAATTTTAATTCAA
* **
280767 AATTTCTAGCAATGTAAATTCGGTTAAAATAA
253 AATTT-TAACAATGTAAATTCGACTAAAATAA
** * ** * * * *
280799 TTTATAATTTAAATGTGTAGATTAAGGTATTTACCTTTCGGTTTTTCATTACGTTTTTCCTCTGA
1 TTTATTTTTTAGACATGTAGATTAAAGTATTTACCTTTCGGTTCTTCATTATGTTTTT-CTCCGA
* ** * * *
280864 ACTTGTAATCGTACATAAAATAAAAATAAATAAATAAAC---T-ATTTAATTATTTTCTCCT-GT
65 ACCTGTTGTCGTACCTAAAATAAAAACAGATAAATAAACAAATCATTTAATTATTTTCT-CTAGT
* *
280924 GATATC-ATATTAAACTGATTTGTTTAAAATATATTTTTCTAATAATTTCATCTTCATCTAGTTA
129 GATA-CGATATTAAACTGATTTGTTTAAAATATGTTTTTTTAATAATTTCATCTTCATCTAGTTA
** * * * *
280988 AACCATTTTTATTTTTGATTTTTGATTTAATATGCAATATGATTTGAGAATTTTATTTCAAATTT
193 AACTGTTTTTATTTTT-ATTTTTGATTTAATATGCAATATGATATAAGAATTTTAATTCAAA-AT
* *
281053 TTTAACTATGTAAATTCGATTAAAATAA
256 TTTAACAATGTAAATTCGACTAAAATAA
* * * *
281081 TTTATTTTTTAGATATGTAGATTAAAATATTTACCTTTCGATTTTTCATTATGCTTTTTCTCCGA
1 TTTATTTTTTAGACATGTAGATTAAAGTATTTACCTTTCGGTTCTTCATTATG-TTTTTCTCCGA
* *
281146 ACCTGTTGTCGTACCTAAAATAAAAACAAATAAATAAA-TAATCATTTAATTATTTTCTCTAGTG
65 ACCTGTTGTCGTACCTAAAATAAAAACAGATAAATAAACAAATCATTTAATTATTTTCTCTAGTG
*
281210 ATACGATGTTAAACTGATTTGTTTAAAATATGTTTTTTTAAATAATTTCATCTTCATCTAGTTAA
130 ATACGATATTAAACTGATTTGTTTAAAATATGTTTTTTT-AATAATTTCATCTTCATCTAGTTAA
* *
281275 ATTGTTTTTATTTTTATTTTTGATTTAATATGCAATATGATATAAAAATTTTAATTCAAAATTTT
194 ACTGTTTTTATTTTTATTTTTGATTTAATATGCAATATGATATAAGAATTTTAATTCAAAATTTT
* *
281340 AATAATGTAAATTTGACTAAAATAA
259 AACAATGTAAATTCGACTAAAATAA
*
281365 TTTATTTTTTAGACATGTAGATTAAAGTATTTACCTTCCGGTTCTTCATTATGTATTTTCTCCGA
1 TTTATTTTTTAGACATGTAGATTAAAGTATTTACCTTTCGGTTCTTCATTATGT-TTTTCTCCGA
* *
281430 ACCTGTTGTCGTACCCAAAATAAAAACAGATAAATAAACAAATCATTTAATTATTTTCTCTAGTA
65 ACCTGTTGTCGTACCTAAAATAAAAACAGATAAATAAACAAATCATTTAATTATTTTCTCTAGTG
* *
281495 ATACGATGTTAAACTGATTTGTTTAAAATATGTTTTTTTTAAATAATTTCATTTTCATCTAGTTA
130 ATACGATATTAAACTGATTTGTTTAAAATATG-TTTTTTT-AATAATTTCATCTTCATCTAGTTA
* *
281560 AATTGTTTTTGTTTTTATTTTTGATTTAATATGCAATATGATATAAGAATTTTAATTCAAAATTT
193 AACTGTTTTTATTTTTATTTTTGATTTAATATGCAATATGATATAAGAATTTTAATTCAAAATTT
* *
281625 TAATAATGTAAATTTGACTAAAATAA
258 TAACAATGTAAATTCGACTAAAATAA
* * *
281651 TTTATTTCTTAGACATGTAGATTAAAGTATTTACCTTTCGGTACTTCATTATGTATTTTTTCCGA
1 TTTATTTTTTAGACATGTAGATTAAAGTATTTACCTTTCGGTTCTTCATTATGT-TTTTCTCCGA
*
281716 ACCTGTTGTCATACCTAAAATAAAAACAGATAAATAAACAAATCATTTAATTATTTTCTCTAGTG
65 ACCTGTTGTCGTACCTAAAATAAAAACAGATAAATAAACAAATCATTTAATTATTTTCTCTAGTG
* *
281781 ATACGATGTTGAACTGATTTGTTTAAAATATGTTTTTTTAAATAATTTCATCTTCATCTAGTTAA
130 ATACGATATTAAACTGATTTGTTTAAAATATGTTTTTTT-AATAATTTCATCTTCATCTAGTTAA
* *
281846 ATTGTTTTTATTTTTATTTTTGATTTAATATGCAATATAATATAAGAATTTTAATTCAAAATTTT
194 ACTGTTTTTATTTTTATTTTTGATTTAATATGCAATATGATATAAGAATTTTAATTCAAAATTTT
*
281911 AACAATGTAAATTTGACTAAAATAA
259 AACAATGTAAATTCGACTAAAATAA
* * * * *
281936 TTTATTTTTTAGACGTGTAGAGTAAGGTATTTACCTTTTGGTTCTTCATTATGTATTTCCTCCGA
1 TTTATTTTTTAGACATGTAGATTAAAGTATTTACCTTTCGGTTCTTCATTATGT-TTTTCTCCGA
* * * * * * *
282001 ACC---TGT-ATACATAAAATAAAAATAGATAAAT----AAATTATTTAATTATTTGCTCCAATG
65 ACCTGTTGTCGTACCTAAAATAAAAACAGATAAATAAACAAATCATTTAATTATTTTCTCTAGTG
* * *
282058 ATATC-ATATTAAATTGATTTGTTTAAAATATGTTTTTTTAATAATTTCATCTTCACCTAATT-A
130 ATA-CGATATTAAACTGATTTGTTTAAAATATGTTTTTTTAATAATTTCATCTTCATCTAGTTAA
** * * * * *
282121 A-----TCCATTTTTATTTTTGATTTAGTATGCAATATGACATGAGAACTTTAATTCAAATTTTT
194 ACTGTTTTTATTTTTATTTTTGATTTAATATGCAATATGATATAAGAATTTTAATTCAAAATTTT
*
282181 AACAATGTAAATTTGACTAAAATAA
259 AACAATGTAAATTCGACTAAAATAA
* * * * *
282206 TTTATATTTTAGACGTGTAGATTAAGGTATTTACTTTTCGGTTCTTCATTACGTTTTTTCTCCGA
1 TTTATTTTTTAGACATGTAGATTAAAGTATTTACCTTTCGGTTCTTCATTATG-TTTTTCTCCGA
* ** * **
282271 ATCTGTAATCGTACATAAAAT--AAA-A-ATAAAT----AAATCATTTGCTTATTTTCTCCT-GT
65 ACCTGTTGTCGTACCTAAAATAAAAACAGATAAATAAACAAATCATTTAATTATTTTCT-CTAGT
* * *
282327 GAAATC-ATATTAAACTGATTTGTTTAAAATATGTTTTTCTAATAATTTCACCTTCATCTAGTTA
129 GATA-CGATATTAAACTGATTTGTTTAAAATATGTTTTTTTAATAATTTCATCTTCATCTAGTTA
** * * *
282391 AACCATTTTCATTTTTTATTTTTGATTTAATATGCAATATGATATGAGAATTTTATTTC-AAATT
193 AACTGTTTTTA-TTTTTATTTTTGATTTAATATGCAATATGATATAAGAATTTTAATTCAAAATT
* *
282455 TCTAACGACGTAAATTCGACTAAAATAA
257 T-TAACAATGTAAATTCGACTAAAATAA
* * *
282483 TTTATTTTTTAGATATGTAGATTAAAATATTTACCTTTCGGTTCTTCATTACGTTTTTTCTCCGA
1 TTTATTTTTTAGACATGTAGATTAAAGTATTTACCTTTCGGTTCTTCATTATG-TTTTTCTCCGA
* * * *
282548 ACCTGATATCGTACCTAAAATAAAAACAGATAAATAACCAAATCATTTAATTATTTTCTCTAATG
65 ACCTGTTGTCGTACCTAAAATAAAAACAGATAAATAAACAAATCATTTAATTATTTTCTCTAGTG
* * * *
282613 ATACGATGTTAAACTGATTTGTTTAAAATAT-TTTTTTTAATAATTTCATCTTCACCTA-ATCAA
130 ATACGATATTAAACTGATTTGTTTAAAATATGTTTTTTTAATAATTTCATCTTCATCTAGTTAAA
** * *
282676 -----TCCATTTTTATTTTTGATTTAATATGCAATATGACATAAGAATTTTAATTCAAATTTTTA
195 CTGTTTTTATTTTTATTTTTGATTTAATATGCAATATGATATAAGAATTTTAATTCAAAATTTTA
**
282736 ACAATGTAAATTCGGTTAAAATAA
260 ACAATGTAAATTCGACTAAAATAA
* * *
282760 TTTATTTTTTAGACACGTAGATTAAGGTATTTACCTTTCGGTTCTTCAATATGTTTTTCCTCCGA
1 TTTATTTTTTAGACATGTAGATTAAAGTATTTACCTTTCGGTTCTTCATTATGTTTTT-CTCCGA
* * * * * **
282825 ACGTATTGTAGTACCTAAAATAAAAACAAATAATTAATTAAATCATTTAATTATTT
65 ACCTGTTGTCGTACCTAAAATAAAAACAGATAAATAAACAAATCATTTAATTATTT
282881 AGGTGGTGGC
Statistics
Matches: 1850, Mismatches: 183, Indels: 107
0.86 0.09 0.05
Matches are distributed among these distances:
270 215 0.12
271 5 0.00
272 3 0.00
273 1 0.00
274 10 0.01
275 2 0.00
276 34 0.02
277 364 0.20
278 9 0.00
279 47 0.03
280 44 0.02
281 66 0.04
282 111 0.06
283 19 0.01
284 150 0.08
285 375 0.20
286 317 0.17
287 78 0.04
ACGTcount: A:0.35, C:0.11, G:0.09, T:0.45
Consensus pattern (283 bp):
TTTATTTTTTAGACATGTAGATTAAAGTATTTACCTTTCGGTTCTTCATTATGTTTTTCTCCGAA
CCTGTTGTCGTACCTAAAATAAAAACAGATAAATAAACAAATCATTTAATTATTTTCTCTAGTGA
TACGATATTAAACTGATTTGTTTAAAATATGTTTTTTTAATAATTTCATCTTCATCTAGTTAAAC
TGTTTTTATTTTTATTTTTGATTTAATATGCAATATGATATAAGAATTTTAATTCAAAATTTTAA
CAATGTAAATTCGACTAAAATAA
Found at i:284082 original size:274 final size:277
Alignment explanation
Indices: 283400--284101 Score: 826
Period size: 274 Copynumber: 2.5 Consensus size: 277
283390 TTATCTTCTC
* * * * *
283400 TAACAATCTAAATTAGGCTAAAATAATTTATTTTTTAGGCTTGTAGATTAAGGTCTTTACCTTTC
1 TAACAATGTAAATTCGGCTAAAATAATTTATTTTTTAGACATGTAGATTAAGGTATTTACCTTTC
* * * ** * *
283465 GGTTCTTCATTACATTTTTCCTCCAAAACTATTGTCTTATTTAAAATAAAAATAGATAAAGAAAT
66 GGTTCTTCATTACGTTTTTCCT-CAGAACTATTGTCGTACCTAAAAT--AAA-A-ACAAATAAAT
* * * **
283530 AAAGAAATCATCTAACTATTTTCTCCGGTGATAGCATATTAAACTGATTTGTTTAAAATATATGT
126 AAACAAATCATTTAATTATTTTCTCCAATGATAGCATATTAAACTGATTTGTTTAAAATATATGT
* * * *
283595 TTTTTAATAATTTTATCTTCACCTAGTTAAACCATTTTTATTTCGGTTTAATAAGCAATATGATA
191 TTTTTAATAATTTCATCTTCACCTAATTAAACCATTTTTATTTCGATTTAATAAGCAATATGACA
* * *
283660 TGAGGATTTTAATTCAGATTTT
256 TAAGAATTTTAATTCAGAATTT
* * **
283682 TAATAATGTAAATTCGACTAAAATAATTTATTTTTTAGACATGTAGATTAAAATATTTACCTTTC
1 TAACAATGTAAATTCGGCTAAAATAATTTATTTTTTAGACATGTAGATTAAGGTATTTACCTTTC
* * *
283747 GGTTCTTCATTACGTCTTTT-CTCCGAACCTGA-TATCGTACCTAAAATAAAAACAGATAAATAA
66 GGTTCTTCATTACGT-TTTTCCTCAGAA-CT-ATTGTCGTACCTAAAATAAAAACAAATAAATAA
* * *
283810 CCAAATCATTTAATTATTTTCTCTAATGATA-CGATGTTAAACTGATTTGTTTAAAATAT-T-TT
128 ACAAATCATTTAATTATTTTCTCCAATGATAGC-ATATTAAACTGATTTGTTTAAAATATATGTT
* * *
283872 TTTTAATAATTTCATCTTCACCTAATTAATCCATTTTTATTTTTGATTTAATATGCAATATGACA
192 TTTTAATAATTTCATCTTCACCTAATTAAACCATTTTTA-TTTCGATTTAATAAGCAATATGACA
*
283937 TAAGAATTTTTATTCA-AATTT
256 TAAGAATTTTAATTCAGAATTT
* *
283958 TAACAATGTAAATTCGGTTAAAATAA-TT-TTTTTTAGACACGTAGATTAAGGTATTTACCTTTC
1 TAACAATGTAAATTCGGCTAAAATAATTTATTTTTTAGACATGTAGATTAAGGTATTTACCTTTC
* * * * * **
284021 GATTCTTCAATATGTTTTTCCTCTGAACGTATTGTAGTACCTAAAATAAAAACAAATAAATAATT
66 GGTTCTTCATTACGTTTTTCCTCAGAAC-TATTGTCGTACCTAAAATAAAAACAAATAAATAAAC
284086 AAATCATTTAATTATT
130 AAATCATTTAATTATT
284102 CAGGTGGCGG
Statistics
Matches: 359, Mismatches: 53, Indels: 24
0.82 0.12 0.06
Matches are distributed among these distances:
273 6 0.02
274 95 0.26
275 2 0.01
276 65 0.18
277 36 0.10
278 58 0.16
279 1 0.00
280 3 0.01
281 3 0.01
282 85 0.24
283 5 0.01
ACGTcount: A:0.36, C:0.12, G:0.09, T:0.42
Consensus pattern (277 bp):
TAACAATGTAAATTCGGCTAAAATAATTTATTTTTTAGACATGTAGATTAAGGTATTTACCTTTC
GGTTCTTCATTACGTTTTTCCTCAGAACTATTGTCGTACCTAAAATAAAAACAAATAAATAAACA
AATCATTTAATTATTTTCTCCAATGATAGCATATTAAACTGATTTGTTTAAAATATATGTTTTTT
AATAATTTCATCTTCACCTAATTAAACCATTTTTATTTCGATTTAATAAGCAATATGACATAAGA
ATTTTAATTCAGAATTT
Found at i:287467 original size:25 final size:23
Alignment explanation
Indices: 287439--287505 Score: 82
Period size: 25 Copynumber: 2.8 Consensus size: 23
287429 TCAAAACATT
287439 ATATTATACATTTTAAACATAATTC
1 ATATTATA-ATTTTAAA-ATAATTC
*
287464 ATATATATATATTTTGAAATAATTC
1 ATAT-TATA-ATTTTAAAATAATTC
287489 ATA-TATAATTTTAAAAT
1 ATATTATAATTTTAAAAT
287506 TTATCTCGAA
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
22 9 0.24
23 4 0.11
25 14 0.37
26 11 0.29
ACGTcount: A:0.46, C:0.06, G:0.01, T:0.46
Consensus pattern (23 bp):
ATATTATAATTTTAAAATAATTC
Found at i:287505 original size:22 final size:24
Alignment explanation
Indices: 287443--287505 Score: 76
Period size: 26 Copynumber: 2.6 Consensus size: 24
287433 AACATTATAT
287443 TATACATTTTAAACATAATTCATATA
1 TATACATTTTAAA-ATAATTCA-ATA
* *
287469 TATATATTTTGAAATAATTC-ATA
1 TATACATTTTAAAATAATTCAATA
287492 TATA-ATTTTAAAAT
1 TATACATTTTAAAAT
287506 TTATCTCGAA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
22 9 0.26
23 7 0.21
25 7 0.21
26 11 0.32
ACGTcount: A:0.46, C:0.06, G:0.02, T:0.46
Consensus pattern (24 bp):
TATACATTTTAAAATAATTCAATA
Found at i:288279 original size:18 final size:18
Alignment explanation
Indices: 288236--288276 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
288226 TTGTCCTACC
288236 TAAATTAAAAAAAATACA
1 TAAATTAAAAAAAATACA
* *
288254 TTAATTAAAAAAAA-ATA
1 TAAATTAAAAAAAATACA
288271 TAAATT
1 TAAATT
288277 TAATCAAAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.29
Consensus pattern (18 bp):
TAAATTAAAAAAAATACA
Found at i:288658 original size:162 final size:162
Alignment explanation
Indices: 288110--288683 Score: 523
Period size: 162 Copynumber: 3.4 Consensus size: 162
288100 ATATTAAACA
** * *
288110 AAATTTAATTGAAATTTATATATAATTTCAAAATTTTATCCCCAAAAACATATATTAACCGATAT
1 AAATTTAATCAAAATTCATATATAATTTCAAAATTTTATCCCCAAAAACATATATTAACCAATAT
*
288175 TAATATAAATGTAGATTAAAGTTTTACCTTTCATTGCCTCTTTAAGTTGTGTTGTCCTACCTAAA
66 TAATATAAATGTAGATTAAAGTTTTACCTTTCATTGCCTCTTTAAGTTGTGTTGTCATACCTAAA
* *
288240 TTAAAAAAAATACATTAATTAAAAAAAAATAT
131 TTAAAAAAAATACATTAGTTAAAAAATAATAT
**
288272 AAATTTAATCAAAATTCATATATAATTTC-AAATTTTATCCCCATAAAAACATATATTAAATGAA
1 AAATTTAATCAAAATTCATATATAATTTCAAAATTTTATCCCC--AAAAACATATATT-AA-CCA
* * * * * ** *
288336 ATTGATGAAAATAAAGTGTAGATTAGAGTTTTTACTTTTCGATT--CT-TTCGAACATGT-TTCT
62 A-T-ATTAATATAAA-TGTAGATTAAAG-TTTTACCTTTC-ATTGCCTCTT-TAAGTTGTGTTGT
* * * *** *
288397 -ATACCTAAAATAAAAAACAAATAAATAAATCGTCTCATTATTTTCTATAGTGAT
121 CATACCT-AAATTAAAAA-AAATACAT---TAGT-T-A--A---AAAATAAT-AT
* * *
288451 ATCATATTAAACAAAATTTAATTGAAATTTATATATAATTTCAAAATTTTATCCCCAAAAACATA
1 A-AAT-TTAATC-AAA----------ATTCATATATAATTTCAAAATTTTATCCCCAAAAACATA
288516 TATTAACCAATATTAATATAAATGTAGATTAAAGTTTTACCTTTCATTGCCTCTTTAAGTTGTGT
53 TATTAACCAATATTAATATAAATGTAGATTAAAGTTTTACCTTTCATTGCCTCTTTAAGTTGTGT
288581 TGTCATACCTAAATTAAAAAAAATACATTAGTTAAAAAATAATAT
118 TGTCATACCTAAATTAAAAAAAATACATTAGTTAAAAAATAATAT
288626 AAATTTAATCAAAATTCATATATAATTTCAAAA-TTTATCCCCATAAAACATATATTAA
1 AAATTTAATCAAAATTCATATATAATTTCAAAATTTTATCCCCA-AAAACATATATTAA
288684 ATGAAATTGA
Statistics
Matches: 322, Mismatches: 47, Indels: 86
0.71 0.10 0.19
Matches are distributed among these distances:
161 23 0.07
162 59 0.18
163 13 0.04
164 2 0.01
165 1 0.00
166 6 0.02
167 23 0.07
168 25 0.08
169 10 0.03
170 3 0.01
171 2 0.01
172 4 0.01
173 6 0.02
174 2 0.01
175 4 0.01
176 4 0.01
178 3 0.01
179 4 0.01
180 2 0.01
181 6 0.02
182 4 0.01
183 3 0.01
184 3 0.01
185 10 0.03
186 25 0.08
187 23 0.07
188 7 0.02
189 2 0.01
190 2 0.01
191 13 0.04
192 15 0.05
193 13 0.04
ACGTcount: A:0.44, C:0.12, G:0.06, T:0.38
Consensus pattern (162 bp):
AAATTTAATCAAAATTCATATATAATTTCAAAATTTTATCCCCAAAAACATATATTAACCAATAT
TAATATAAATGTAGATTAAAGTTTTACCTTTCATTGCCTCTTTAAGTTGTGTTGTCATACCTAAA
TTAAAAAAAATACATTAGTTAAAAAATAATAT
Found at i:289303 original size:280 final size:279
Alignment explanation
Indices: 288956--290482 Score: 1578
Period size: 275 Copynumber: 5.5 Consensus size: 279
288946 AATTGGATAA
* * * * * * *
288956 AATTTATTTTTTATATATGCAGATTAA-AGTGTTTACCTTTCAGTTTTTCATTACGTTTGGT-CT
1 AATTTATTTTTTAAACATGTAGATTAAGA-TATTTACCTTTCGGTTCTTCATTACGTTT-TTCCT
*
289019 CTGAACCTGTAGTCGTACCTAAAATAAAAATAGATAAAGAAATAAATAAATCATTTAATTATTTT
64 CTGAACCTGTAGTCGTACCTAAAAT-AAAATA-ATAAATAAATAAATAAATCATTTAATTATTTT
* * * *
289084 CTCTAGTGGTAGCATGTTAAATTGATTTGTTTAAAATATGATTTTTTAATAATTTCATGTTCACC
127 CTCTAGTGATATCATATTAAATTGATTTGTTTAAAATATGATTTTTTAATAATTTCATCTTCACC
* * *
289149 TAGTTAAACTGTTTGTTA-TTT-ATTTAATATGCAATATGATATGAGAACTTTAATTCAAATTTC
192 TAGTTAAACTTTTTTTTATTTTGATTTAATATGCAATATGATATGAGAATTTTAATTCAAATTT-
* *
289212 TAGCAACGTAAATTCGGTTAAAAT
256 TAACAATGTAAATTCGGTTAAAAT
* ** *
289236 AATTTATATTTTAAATGTGTAGATTAAGATATTTACCTTTCGGTTATTCATTACGTTTTTCCTCT
1 AATTTATTTTTTAAACATGTAGATTAAGATATTTACCTTTCGGTTCTTCATTACGTTTTTCCTCT
** * *
289301 GAAATTGTAATC--A--T-ACATAAAATAA-AAATAAATAAATAAATCATTTAATTATTTTCTCC
66 GAACCTGTAGTCGTACCTAAAATAAAATAATAAATAAATAAATAAATCATTTAATTATTTTCT-C
*
289360 T-GTGATATCATATTAAATTGATTTGTTTAAAATATG-TTTTTGTAATAATTTCATCTTCATCTA
130 TAGTGATATCATATTAAATTGATTTGTTTAAAATATGATTTTT-TAATAATTTCATCTTCACCTA
*
289423 GTTAAACCATTTTCTTTTTTTATTTTTGATTTAATATGCAATATGATATGAGAATTTTATTTCAA
194 GTTAAA-C----T-TTTTTTTA-TTTTGATTTAATATGCAATATGATATGAGAATTTTAATTCAA
* * *
289488 ATTTTTAACGATGTAAATTCGGCTAAATT
252 A-TTTTAACAATGTAAATTCGGTTAAAAT
* *
289517 AATTTATTTTTTAGAA-ATGTAAATTAA-AGTATTTACCTTTCGGTTCTTCATTACGTTTTTTCT
1 AATTTATTTTTTA-AACATGTAGATTAAGA-TATTTACCTTTCGGTTCTTCATTACGTTTTTCCT
* * * * * *
289580 CTGAATCTGTTGTTGTACCTAAAAT-AAA-AACAGATAAATAAACAAATCATTTAATTATTTTCT
64 CTGAACCTGTAGTCGTACCTAAAATAAAATAATAAATAAATAAATAAATCATTTAATTATTTTCT
* * * *
289643 CCAGTGATA-CGATGTTAAATTGATTTATTTAAAATAT-ATATTTTTAAATAATTTCATCTTCAT
129 CTAGTGATATC-ATATTAAATTGATTTGTTTAAAATATGAT-TTTTT-AATAATTTCATCTTCAC
* *
289706 CTAGTT-AA-TTTTTTTTATTTTTCATTTAATATGCAATATGATATAAGAATTTTAATTCAAAAT
191 CTAGTTAAACTTTTTTTTA-TTTTGATTTAATATGCAATATGATATGAGAATTTTAATTC-AAAT
* *
289769 TTTAACAATGTAAATTTGACTT-AAAT
254 TTTAACAATGTAAATTCG-GTTAAAAT
* * * * * * * * *
289795 AATTTATTTTTTAGACGTGTAGAGTAAGGTATTTACCTTTCGATTTTTTATTATGTTTTTCCTCC
1 AATTTATTTTTTAAACATGTAGATTAAGATATTTACCTTTCGGTTCTTCATTACGTTTTTCCTCT
* * *
289860 GAACCTGTAGTC-T---T-ACATAAAATAA-AAACAGATAAATAAATCATTTAATTATTTGT-TC
66 GAACCTGTAGTCGTACCTAAAATAAAATAATAAATAAATAAATAAATCATTTAATTATTT-TCTC
* *
289918 TAGTGATATCATATTAAACTGATTTGTTTAAAATATGTTTTTTTTAATAATTTCATCTTCACCTA
130 TAGTGATATCATATTAAATTGATTTGTTTAAAATATG-ATTTTTTAATAATTTCATCTTCACCTA
* ** * * *
289983 GTTAATC-CATTTTTATTTTTGATTTAATATGTAATATGACACGAGAATTTTAATTCAAATTTTT
194 GTTAAACTTTTTTTTA-TTTTGATTTAATATGCAATATGATATGAGAATTTTAATTCAAA-TTTT
*
290047 AACAATGTAAATTCGGTCAAAAT
257 AACAATGTAAATTCGGTTAAAAT
* * * * * * *
290070 AATTTTTTTTTTAGACACGTAGATTAAGATATTTACTTTTCGGTTCTTCAATATGTTTTTCCTCC
1 AATTTATTTTTTAAACATGTAGATTAAGATATTTACCTTTCGGTTCTTCATTACGTTTTTCCTCT
* * * * * * *
290135 AAACCTATTGTAGTACCTAAAAT-AAA-AACAAATAAATAAACAAATCATTTAATTATTTTCTCC
66 GAACCTGTAGTCGTACCTAAAATAAAATAATAAATAAATAAATAAATCATTTAATTATTTTCTCT
* *
290198 AGTGATATCATATTAAATTGATTTGTTTAAAATAT-TTTTTTTAATAAATT-AGTCTTCACCTAG
131 AGTGATATCATATTAAATTGATTTGTTTAAAATATGATTTTTTAATAATTTCA-TCTTCACCTAG
290261 TTAAACAATTTTTATTTTTATTTTTGATTTAATATGCAATATGATATGAGAATTTTAATTCAAAA
195 TTAAAC----TTT-TTTTTA-TTTTGATTTAATATGCAATATGATATGAGAATTTTAATTC-AAA
*
290326 TTTTAACAATGTAAATTCAGTTAAAAT
253 TTTTAACAATGTAAATTCGGTTAAAAT
* * * * ** * * *
290353 AA--T-TTTTTTAAACGTGTAGATTAAGGTCTTTATCTTTTAGTTCTTCATTATGTTTTTCTTTT
1 AATTTATTTTTTAAACATGTAGATTAAGATATTTACCTTTCGGTTCTTCATTACGTTTTTCCTCT
* * * * * *
290415 GAGCTTATAGTCGTACCTAAAATAAAAATGGATAAATAAATAAATAAATCATTCAATTATTTTAT
66 GAACCTGTAGTCGTACCTAAAAT-AAAAT-AATAAATAAATAAATAAATCATTTAATTATTTTCT
290480 CTA
129 CTA
290483 ACAATGTAAA
Statistics
Matches: 1047, Mismatches: 140, Indels: 116
0.80 0.11 0.09
Matches are distributed among these distances:
271 5 0.00
272 88 0.08
273 7 0.01
274 93 0.09
275 140 0.13
276 4 0.00
277 33 0.03
278 136 0.13
279 72 0.07
280 133 0.13
281 119 0.11
282 8 0.01
283 72 0.07
284 39 0.04
285 68 0.06
286 30 0.03
ACGTcount: A:0.35, C:0.10, G:0.09, T:0.45
Consensus pattern (279 bp):
AATTTATTTTTTAAACATGTAGATTAAGATATTTACCTTTCGGTTCTTCATTACGTTTTTCCTCT
GAACCTGTAGTCGTACCTAAAATAAAATAATAAATAAATAAATAAATCATTTAATTATTTTCTCT
AGTGATATCATATTAAATTGATTTGTTTAAAATATGATTTTTTAATAATTTCATCTTCACCTAGT
TAAACTTTTTTTTATTTTGATTTAATATGCAATATGATATGAGAATTTTAATTCAAATTTTAACA
ATGTAAATTCGGTTAAAAT
Found at i:289855 original size:559 final size:553
Alignment explanation
Indices: 288956--290389 Score: 1826
Period size: 553 Copynumber: 2.6 Consensus size: 553
288946 AATTGGATAA
* * * * * * **
288956 AATTTATTTTTTATATATGCAGATTAAAGTGTTTACCTTTCAGTTTTTCATTACGTTTGGTCTCT
1 AATTTATTTTTTAGAAATGTAGATTAAAGTATTTACCTTTCGGTTCTTCATTACGTTTTTTCTCT
* * * *
289021 GAACCTGTAGTCGTACCTAAAATAAAAATAGATAAAGAAATAAATAAATCATTTAATTATTTTCT
66 GAACCTGTTGTAGTACCTAAAATAAAAACAGAT----AAATAAACAAATCATTTAATTATTTTCT
* * *
289086 CTAGTGGTA-GCATGTTAAATTGATTTGTTTAAAATATGATTTTTTAATAATTTCATGTTCACCT
127 CCAGTGATACG-ATGTTAAATTGATTTGTTTAAAATAT-ATTTTTTAATAATTTCATCTTCACCT
* * * *
289150 AGTTAAACTGTTTGTTA--TTTATTTAATATGCAATATGATATGAGAACTTTAATTC-AAATTTC
190 AGTTAAATTTTTTTTTATTTTTATTTAATATGCAATATGATATGAGAATTTTAATTCAAAATTT-
* * * * * *
289212 TAGCAACGTAAATTCG-GTTAAAATAATTTATATTTTAAATGTGTAGATTAAGATATTTACCTTT
254 TAACAATGTAAATTTGAGTTAAAATAATTTATTTTTTAAACGTGTAGATTAAGGTATTTACCTTT
* * * *
289276 CGGTTATTCATTACGTTTTTCCTCTGAAATTGTAATCATACATAAAATAAAAATAAATAAATAAA
319 CGATTATTCATTACGTTTTTCCTCCGAAACTGTAATCATACATAAAATAAAAACAAATAAATAAA
*
289341 TCATTTAATTATTT-TCTCCT-GTGATATCATATTAAATTGATTTGTTTAAAATATG-TTTTTGT
384 TCATTTAATTATTTGT-T-CTAGTGATATCATATTAAACTGATTTGTTTAAAATATGTTTTTTGT
*
289403 AATAATTTCATCTTCATCTAGTTAAACCATTTTCTTTTTTTATTTTTGATTTAATATGCAATATG
447 AATAATTTCATCTTCACCTAGTTAAACCA-------TTTTTATTTTTGATTTAATATGCAATATG
* * * * *
289468 ATATGAGAATTTTATTTCAAATTTTTAACGATGTAAATTCGG-CTAAATT
505 ACACGAGAATTTTAATTCAAATTTTTAACAATGTAAATTCGGTC-AAAAT
*
289517 AATTTATTTTTTAGAAATGTAAATTAAAGTATTTACCTTTCGGTTCTTCATTACGTTTTTTCTCT
1 AATTTATTTTTTAGAAATGTAGATTAAAGTATTTACCTTTCGGTTCTTCATTACGTTTTTTCTCT
* *
289582 GAATCTGTTGTTGTACCTAAAATAAAAACAGATAAATAAACAAATCATTTAATTATTTTCTCCAG
66 GAACCTGTTGTAGTACCTAAAATAAAAACAGATAAATAAACAAATCATTTAATTATTTTCTCCAG
* *
289647 TGATACGATGTTAAATTGATTTATTTAAAATATATATTTTTAAATAATTTCATCTTCATCTAGTT
131 TGATACGATGTTAAATTGATTTGTTTAAAATATAT-TTTTT-AATAATTTCATCTTCACCTAGTT
*
289712 -AA-TTTTTTTTATTTTTCATTTAATATGCAATATGATATAAGAATTTTAATTCAAAATTTTAAC
194 AAATTTTTTTTTATTTTT-ATTTAATATGCAATATGATATGAGAATTTTAATTCAAAATTTTAAC
* * *
289775 AATGTAAATTTGACTT-AAATAATTTATTTTTTAGACGTGTAGAGTAAGGTATTTACCTTTCGAT
258 AATGTAAATTTGAGTTAAAATAATTTATTTTTTAAACGTGTAGATTAAGGTATTTACCTTTCGAT
* * * * * * *
289839 TTTTTATTATGTTTTTCCTCCGAACCTGTAGTCTTACATAAAATAAAAACAGATAAATAAATCAT
323 TATTCATTACGTTTTTCCTCCGAAACTGTAATCATACATAAAATAAAAACAAATAAATAAATCAT
*
289904 TTAATTATTTGTTCTAGTGATATCATATTAAACTGATTTGTTTAAAATATGTTTTTTTTAATAAT
388 TTAATTATTTGTTCTAGTGATATCATATTAAACTGATTTGTTTAAAATATGTTTTTTGTAATAAT
* *
289969 TTCATCTTCACCTAGTTAATCCATTTTTATTTTTGATTTAATATGTAATATGACACGAGAATTTT
453 TTCATCTTCACCTAGTTAAACCATTTTTATTTTTGATTTAATATGCAATATGACACGAGAATTTT
290034 AATTCAAATTTTTAACAATGTAAATTCGGTCAAAAT
518 AATTCAAATTTTTAACAATGTAAATTCGGTCAAAAT
* * * * * * *
290070 AATTTTTTTTTTAGACACGTAGATT-AAGATATTTACTTTTCGGTTCTTCAATATGTTTTTCCTC
1 AATTTATTTTTTAGAAATGTAGATTAAAG-TATTTACCTTTCGGTTCTTCATTACGTTTTTTCTC
** * *
290134 CAAACCTATTGTAGTACCTAAAATAAAAACAAATAAATAAACAAATCATTTAATTATTTTCTCCA
65 TGAACCTGTTGTAGTACCTAAAATAAAAACAGATAAATAAACAAATCATTTAATTATTTTCTCCA
* * *
290199 GTGATATC-ATATTAAATTGATTTGTTTAAAATATTTTTTTTAATAAATT-AGTCTTCACCTAGT
130 GTGATA-CGATGTTAAATTGATTTGTTTAAAATATATTTTTTAATAATTTCA-TCTTCACCTAGT
290262 TAAACAATTTTTATTTTTATTTTTGATTTAATATGCAATATGATATGAGAATTTTAATTCAAAAT
193 T--A-AA-TTTT-TTTTTATTTTT-ATTTAATATGCAATATGATATGAGAATTTTAATTCAAAAT
* * *
290327 TTTAACAATGTAAA-TTCAGTTAAAATAA--T-TTTTTTAAACGTGTAGATTAAGGTCTTTATCT
252 TTTAACAATGTAAATTTGAGTTAAAATAATTTATTTTTTAAACGTGTAGATTAAGGTATTTACCT
290388 TT
317 TT
290390 TAGTTCTTCA
Statistics
Matches: 770, Mismatches: 80, Indels: 52
0.85 0.09 0.06
Matches are distributed among these distances:
550 1 0.00
551 19 0.02
552 8 0.01
553 212 0.28
554 2 0.00
555 32 0.04
556 10 0.01
557 74 0.10
558 97 0.13
559 188 0.24
560 42 0.05
561 85 0.11
ACGTcount: A:0.35, C:0.10, G:0.09, T:0.45
Consensus pattern (553 bp):
AATTTATTTTTTAGAAATGTAGATTAAAGTATTTACCTTTCGGTTCTTCATTACGTTTTTTCTCT
GAACCTGTTGTAGTACCTAAAATAAAAACAGATAAATAAACAAATCATTTAATTATTTTCTCCAG
TGATACGATGTTAAATTGATTTGTTTAAAATATATTTTTTAATAATTTCATCTTCACCTAGTTAA
ATTTTTTTTTATTTTTATTTAATATGCAATATGATATGAGAATTTTAATTCAAAATTTTAACAAT
GTAAATTTGAGTTAAAATAATTTATTTTTTAAACGTGTAGATTAAGGTATTTACCTTTCGATTAT
TCATTACGTTTTTCCTCCGAAACTGTAATCATACATAAAATAAAAACAAATAAATAAATCATTTA
ATTATTTGTTCTAGTGATATCATATTAAACTGATTTGTTTAAAATATGTTTTTTGTAATAATTTC
ATCTTCACCTAGTTAAACCATTTTTATTTTTGATTTAATATGCAATATGACACGAGAATTTTAAT
TCAAATTTTTAACAATGTAAATTCGGTCAAAAT
Found at i:290611 original size:155 final size:152
Alignment explanation
Indices: 290329--290621 Score: 399
Period size: 155 Copynumber: 1.9 Consensus size: 152
290319 TTCAAAATTT
* * *
290329 TAACAATGTAAATTCAGTTAAAATAATTTTTTTAAACGTGTAGATTAAGGTCTTTATCTTTTAGT
1 TAACAATGTAAATTCAGCTAAAATAATTTTTTTAAACGTGTAGATTAAGGTCTTTACCTTTCAGT
** ** * * *
290394 TCTTCATTATGTTTTTCTTTTGAGCTTATAGTCGTACCTAAAATAAAAATGGATAAATAAATAAA
66 TCTTCATTACATTTTTCTTCCGAACTTATAGTCGTACCTAAAATAAAAATAGATAAAGAAATAAA
*
290459 TAAATCATTCAATTATTTTATC
131 GAAATCATTCAATTATTTTATC
* *
290481 TAACAATGTAAATTCGGCTAAAATAATTTATTTTTTAGACGTGTAGATTAAGGTCTTTACCTTTC
1 TAACAATGTAAATTCAGCTAAAATAA--T-TTTTTTAAACGTGTAGATTAAGGTCTTTACCTTTC
* * *
290546 GGTTCTTCATTACATTTTTCTTCCGAAAC-TATTGTCGTACTTAAAATAAAAATAGATAAAGAAA
63 AGTTCTTCATTACATTTTTCTTCCG-AACTTATAGTCGTACCTAAAATAAAAATAGATAAAGAAA
290610 TAAAGAAATCAT
127 TAAAGAAATCAT
290622 CTAAGTATTT
Statistics
Matches: 121, Mismatches: 16, Indels: 5
0.85 0.11 0.04
Matches are distributed among these distances:
152 24 0.20
154 1 0.01
155 94 0.78
156 2 0.02
ACGTcount: A:0.37, C:0.11, G:0.11, T:0.41
Consensus pattern (152 bp):
TAACAATGTAAATTCAGCTAAAATAATTTTTTTAAACGTGTAGATTAAGGTCTTTACCTTTCAGT
TCTTCATTACATTTTTCTTCCGAACTTATAGTCGTACCTAAAATAAAAATAGATAAAGAAATAAA
GAAATCATTCAATTATTTTATC
Found at i:291159 original size:6 final size:6
Alignment explanation
Indices: 291148--291172 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
291138 TTGCCACACC
291148 TAAAAT TAAAAT TAAAAT TAAAAT T
1 TAAAAT TAAAAT TAAAAT TAAAAT T
291173 CCATACGTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (6 bp):
TAAAAT
Found at i:292684 original size:27 final size:27
Alignment explanation
Indices: 292654--292705 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
292644 ATATTTATAA
292654 TTTAATTT-TTAATAAGTTTATATATTT
1 TTTAATTTATTAA-AAGTTTATATATTT
* *
292681 TTTAATTTATTGAAATTTTATATAT
1 TTTAATTTATTAAAAGTTTATATAT
292706 AATCAACTTG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
27 19 0.86
28 3 0.14
ACGTcount: A:0.35, C:0.00, G:0.04, T:0.62
Consensus pattern (27 bp):
TTTAATTTATTAAAAGTTTATATATTT
Found at i:298314 original size:28 final size:28
Alignment explanation
Indices: 298283--298460 Score: 87
Period size: 28 Copynumber: 6.1 Consensus size: 28
298273 AAAACGGGAC
298283 TTTTGGATATTCGGGGGTAAAATGGTAA
1 TTTTGGATATTCGGGGGTAAAATGGTAA
* *
298311 TTTTGGACT-TACGGGGGCAAAATGGTAA
1 TTTTGGA-TATTCGGGGGTAAAATGGTAA
* * *
298339 TTTTCGG-TGAAATC-GGGGTCAAAAAGGAAA
1 TTTT-GGAT--ATTCGGGGGT-AAAATGGTAA
* * * *
298369 TTTTGGAAAATTTGAGGGTAAAATAGTAA
1 TTTTGG-ATATTCGGGGGTAAAATGGTAA
* * *
298398 TTTTTGG-TGAAATCGAGGTTAAAAATGG-AA
1 -TTTTGGAT--ATTCGGGGGT-AAAATGGTAA
* **
298428 TTTTGGAAAGTTTAGGGGTAAAATGGTAA
1 TTTTGGATA-TTCGGGGGTAAAATGGTAA
298457 TTTT
1 TTTT
298461 TGGTGAAATC
Statistics
Matches: 109, Mismatches: 25, Indels: 31
0.66 0.15 0.19
Matches are distributed among these distances:
27 1 0.01
28 36 0.33
29 34 0.31
30 32 0.29
31 6 0.06
ACGTcount: A:0.34, C:0.04, G:0.29, T:0.33
Consensus pattern (28 bp):
TTTTGGATATTCGGGGGTAAAATGGTAA
Found at i:298362 original size:30 final size:28
Alignment explanation
Indices: 298296--298480 Score: 112
Period size: 30 Copynumber: 6.3 Consensus size: 28
298286 TGGATATTCG
**
298296 GGGGTAAAATGGTAATTTT-G-GACTTAC
1 GGGGTAAAATGGTAATTTTGGTGAAAT-C
*
298323 GGGGGCAAAATGGTAATTTTCGGTGAAATC
1 -GGGGTAAAATGGTAATTTT-GGTGAAATC
* * * *
298353 GGGGTCAAAAAGGAAATTTTGG-AAAATTT
1 GGGGT-AAAATGGTAATTTTGGTGAAA-TC
*
298382 GAGGGTAAAATAGTAATTTTTGGTGAAATC
1 G-GGGTAAAATGGTAA-TTTTGGTGAAATC
* *
298412 GAGGTTAAAAATGG-AATTTT-G-GAAAGTTTA
1 G-GGGT-AAAATGGTAATTTTGGTGAAA---TC
298442 GGGGTAAAATGGTAATTTTTGGTGAAATC
1 GGGGTAAAATGGTAA-TTTTGGTGAAATC
298471 GGGGTTAAAA
1 GGGG-TAAAA
298481 ATATGATTTC
Statistics
Matches: 122, Mismatches: 18, Indels: 32
0.71 0.10 0.19
Matches are distributed among these distances:
27 4 0.03
28 29 0.24
29 29 0.24
30 43 0.35
31 13 0.11
32 4 0.03
ACGTcount: A:0.35, C:0.04, G:0.30, T:0.31
Consensus pattern (28 bp):
GGGGTAAAATGGTAATTTTGGTGAAATC
Found at i:298399 original size:29 final size:29
Alignment explanation
Indices: 298367--298460 Score: 77
Period size: 29 Copynumber: 3.2 Consensus size: 29
298357 TCAAAAAGGA
298367 AATTTTGGAAAATTTGAGGGTAAAATAGT
1 AATTTTGGAAAATTTGAGGGTAAAATAGT
* * * *
298396 AATTTTTGGTGAAA-TCGAGGTTAAAA-ATGG
1 AA-TTTTGG-AAAATTTGAGGGTAAAATA-GT
* *
298426 AATTTTGGAAAGTTT-AGGGGTAAAATGGT
1 AATTTTGGAAAATTTGA-GGGTAAAATAGT
298455 AATTTT
1 AATTTT
298461 TGGTGAAATC
Statistics
Matches: 49, Mismatches: 10, Indels: 12
0.69 0.14 0.17
Matches are distributed among these distances:
28 3 0.06
29 24 0.49
30 19 0.39
31 3 0.06
ACGTcount: A:0.37, C:0.01, G:0.26, T:0.36
Consensus pattern (29 bp):
AATTTTGGAAAATTTGAGGGTAAAATAGT
Found at i:298407 original size:59 final size:59
Alignment explanation
Indices: 298324--298522 Score: 244
Period size: 59 Copynumber: 3.4 Consensus size: 59
298314 TGGACTTACG
* * *
298324 GGGGCAAAATGGTAATTTTCGGTGAAATCGGGGTCAAAAA-GGAAATTTTGGAAAATTT-
1 GGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGG-AATTTTGGAAAATTTA
* * *
298382 GAGGGTAAAATAGTAATTTTTGGTGAAATCGAGGTTAAAAATGGAATTTTGGAAAGTTTA
1 G-GGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAATTTA
* * *
298442 GGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATATG-A-TTTCGAAAAGTTTG
1 GGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAAT-GGAATTTTGGAAAA-TTTA
*
298501 GGGGTAAAATGTTAATTTTTGG
1 GGGGTAAAATGGTAATTTTTGG
298523 ATAGTTCAGG
Statistics
Matches: 123, Mismatches: 13, Indels: 9
0.85 0.09 0.06
Matches are distributed among these distances:
58 8 0.07
59 111 0.90
60 4 0.03
ACGTcount: A:0.35, C:0.04, G:0.29, T:0.33
Consensus pattern (59 bp):
GGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAATTTA
Found at i:298986 original size:24 final size:22
Alignment explanation
Indices: 298935--298987 Score: 63
Period size: 22 Copynumber: 2.3 Consensus size: 22
298925 ATGGGTCATA
298935 TAAATATTATTTTTCAGTTTTTT
1 TAAAT-TTATTTTTCAGTTTTTT
*
298958 T-AATTTATTTTTTCATTTTTTT
1 TAAATTTA-TTTTTCAGTTTTTT
298980 TGAAATTT
1 T-AAATTT
298988 CATCCCCCCT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
21 3 0.12
22 17 0.65
23 1 0.04
24 5 0.19
ACGTcount: A:0.25, C:0.04, G:0.04, T:0.68
Consensus pattern (22 bp):
TAAATTTATTTTTCAGTTTTTT
Found at i:299511 original size:17 final size:17
Alignment explanation
Indices: 299468--299524 Score: 71
Period size: 17 Copynumber: 3.3 Consensus size: 17
299458 GCTTTTTAAT
*
299468 TTTAATTTTAAAAT-TA
1 TTTAATTTTAAAATAAA
*
299484 TTTCAAATTTAAAATAAA
1 TTT-AATTTTAAAATAAA
299502 TTTAATTTTAGAAATAAA
1 TTTAATTTTA-AAATAAA
299520 TTTAA
1 TTTAA
299525 AAATCATTTT
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
16 3 0.09
17 16 0.46
18 16 0.46
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (17 bp):
TTTAATTTTAAAATAAA
Found at i:303568 original size:63 final size:63
Alignment explanation
Indices: 303469--303596 Score: 256
Period size: 63 Copynumber: 2.0 Consensus size: 63
303459 CTAGGTGTGA
303469 TAATATCCCTCTCACATCACATGTGTCCACACATCCCCAGCCACCTATATTGTAGCAAAGATT
1 TAATATCCCTCTCACATCACATGTGTCCACACATCCCCAGCCACCTATATTGTAGCAAAGATT
303532 TAATATCCCTCTCACATCACATGTGTCCACACATCCCCAGCCACCTATATTGTAGCAAAGATT
1 TAATATCCCTCTCACATCACATGTGTCCACACATCCCCAGCCACCTATATTGTAGCAAAGATT
303595 TA
1 TA
303597 TGCTTATCAT
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
63 65 1.00
ACGTcount: A:0.30, C:0.33, G:0.09, T:0.27
Consensus pattern (63 bp):
TAATATCCCTCTCACATCACATGTGTCCACACATCCCCAGCCACCTATATTGTAGCAAAGATT
Found at i:310085 original size:21 final size:22
Alignment explanation
Indices: 310059--310101 Score: 61
Period size: 24 Copynumber: 1.9 Consensus size: 22
310049 GGTCGGGGAA
310059 GGCGGAAA-TGGCGGCGGAGAC
1 GGCGGAAAGTGGCGGCGGAGAC
310080 GGCGGAAACGGTGGCGGCGGAG
1 GGCGGAAA--GTGGCGGCGGAG
310102 GGTTTTGGGA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 8 0.42
24 11 0.58
ACGTcount: A:0.21, C:0.19, G:0.56, T:0.05
Consensus pattern (22 bp):
GGCGGAAAGTGGCGGCGGAGAC
Found at i:318204 original size:23 final size:24
Alignment explanation
Indices: 318178--318248 Score: 90
Period size: 24 Copynumber: 2.9 Consensus size: 24
318168 AATAACAATC
*
318178 AAAACAGCAACAAAAAT-AATAGA
1 AAAACAGCAACAAAAATAAAAAGA
*
318201 AAAACAGCAACAAAAATAAAAATA
1 AAAACAGCAACAAAAATAAAAAGA
*
318225 AAAACAGCACCAAAATAGTAAAAA
1 AAAACAGCAACAAAA-A-TAAAAA
318249 AATAACACAA
Statistics
Matches: 42, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
23 17 0.40
24 18 0.43
25 1 0.02
26 6 0.14
ACGTcount: A:0.70, C:0.14, G:0.07, T:0.08
Consensus pattern (24 bp):
AAAACAGCAACAAAAATAAAAAGA
Found at i:318250 original size:23 final size:23
Alignment explanation
Indices: 318178--318250 Score: 69
Period size: 23 Copynumber: 3.1 Consensus size: 23
318168 AATAACAATC
*
318178 AAAACAGCAACAAAA-ATAATAGA
1 AAAACAGCACCAAAATATAA-AGA
* * *
318201 AAAACAGCAACAAAAATAAAAATA
1 AAAACAGC-ACCAAAATATAAAGA
318225 AAAACAGCACCAAAATAGTAAA-A
1 AAAACAGCACCAAAATA-TAAAGA
318248 AAA
1 AAA
318251 TAACACAAAA
Statistics
Matches: 41, Mismatches: 6, Indels: 6
0.77 0.11 0.11
Matches are distributed among these distances:
23 20 0.49
24 18 0.44
25 3 0.07
ACGTcount: A:0.71, C:0.14, G:0.07, T:0.08
Consensus pattern (23 bp):
AAAACAGCACCAAAATATAAAGA
Found at i:318250 original size:34 final size:34
Alignment explanation
Indices: 318201--318284 Score: 98
Period size: 34 Copynumber: 2.4 Consensus size: 34
318191 AAATAATAGA
* *
318201 AAAACAGCAACAAAAATAAAAATAAAAACAGC-ACC
1 AAAACAGTAA-AAAAATAAA-ACAAAAACAGCAACC
* * *
318236 AAAATAGTAAAAAAATAACACAAAAATAGCAACC
1 AAAACAGTAAAAAAATAAAACAAAAACAGCAACC
318270 AAAACAGTAAAAAAA
1 AAAACAGTAAAAAAA
318285 ACACCAAAAC
Statistics
Matches: 42, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
33 9 0.21
34 25 0.60
35 8 0.19
ACGTcount: A:0.70, C:0.15, G:0.06, T:0.08
Consensus pattern (34 bp):
AAAACAGTAAAAAAATAAAACAAAAACAGCAACC
Found at i:318261 original size:57 final size:53
Alignment explanation
Indices: 318189--318308 Score: 132
Period size: 57 Copynumber: 2.2 Consensus size: 53
318179 AAACAGCAAC
* * * *
318189 AAAAATAATAGAAAAACAGCAACAAAAATAAAAATAAAAACAGCACCAAAATAGTAA
1 AAAAATAACACAAAAACAGCAACAAAAACAAAAA-AAAAA-A-CACCAAAACAGT-A
* * **
318246 AAAAATAACACAAAAATAGCAACCAAAACAGTAAAAAAAACACCAAAACAGTA
1 AAAAATAACACAAAAACAGCAACAAAAACAAAAAAAAAAACACCAAAACAGTA
318299 AAAAATAACA
1 AAAAATAACA
318309 ATCAAAGCAG
Statistics
Matches: 55, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
53 11 0.20
54 11 0.20
55 1 0.02
56 5 0.09
57 27 0.49
ACGTcount: A:0.70, C:0.15, G:0.06, T:0.09
Consensus pattern (53 bp):
AAAAATAACACAAAAACAGCAACAAAAACAAAAAAAAAAACACCAAAACAGTA
Found at i:318281 original size:20 final size:20
Alignment explanation
Indices: 318267--318327 Score: 77
Period size: 20 Copynumber: 3.0 Consensus size: 20
318257 AAAAATAGCA
318267 ACCAAAACAGTAAAAAAAAC
1 ACCAAAACAGTAAAAAAAAC
318287 ACCAAAACAGTAAAAAATAAC
1 ACCAAAACAGTAAAAAA-AAC
* * *
318308 AATCAAAGCAGCAAAAAAAA
1 -ACCAAAACAGTAAAAAAAA
318328 AAAACCAAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
20 17 0.47
21 5 0.14
22 14 0.39
ACGTcount: A:0.69, C:0.18, G:0.07, T:0.07
Consensus pattern (20 bp):
ACCAAAACAGTAAAAAAAAC
Found at i:318282 original size:22 final size:22
Alignment explanation
Indices: 318257--318339 Score: 98
Period size: 22 Copynumber: 3.9 Consensus size: 22
318247 AAAATAACAC
*
318257 AAAAATAGCAACCAAAACAGTA
1 AAAAATAACAACCAAAACAGTA
318279 AAAAA-AAC-ACCAAAACAGTA
1 AAAAATAACAACCAAAACAGTA
* * *
318299 AAAAATAACAATCAAAGCAGCA
1 AAAAATAACAACCAAAACAGTA
* *
318321 AAAAAAAAAAACCAAAACA
1 AAAAATAACAACCAAAACA
318340 ACAATATAAT
Statistics
Matches: 51, Mismatches: 8, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
20 17 0.33
21 5 0.10
22 29 0.57
ACGTcount: A:0.70, C:0.18, G:0.06, T:0.06
Consensus pattern (22 bp):
AAAAATAACAACCAAAACAGTA
Found at i:320770 original size:18 final size:17
Alignment explanation
Indices: 320719--320767 Score: 57
Period size: 17 Copynumber: 2.9 Consensus size: 17
320709 TTTTTTTTCT
320719 ATTTTT-ATAACTTTT-A
1 ATTTTTAATAA-TTTTAA
*
320735 CTTTTTAATCAATTTTAA
1 ATTTTTAAT-AATTTTAA
320753 ATTTTTAATAATTTT
1 ATTTTTAATAATTTT
320768 TAATAAATTT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
16 5 0.18
17 12 0.43
18 11 0.39
ACGTcount: A:0.33, C:0.06, G:0.00, T:0.61
Consensus pattern (17 bp):
ATTTTTAATAATTTTAA
Found at i:320816 original size:21 final size:20
Alignment explanation
Indices: 320753--320858 Score: 58
Period size: 21 Copynumber: 5.2 Consensus size: 20
320743 TCAATTTTAA
320753 ATTTTTA-ATAATTTTTA-AT
1 ATTTTTATA-AATTTTTATAT
* ** *
320772 AAATTTTATAAAAATTTACAT
1 -ATTTTTATAAATTTTTATAT
*
320793 -TTTTTA-ATATTTTTATAT
1 ATTTTTATAAATTTTTATAT
*
320811 CATTTTCTATAACTTTTTATAT
1 -ATTTT-TATAAATTTTTATAT
* * *
320833 TTTTTTGTAAAATTTTAATAT
1 ATTTTTAT-AAATTTTTATAT
320854 ATTTT
1 ATTTT
320859 CAATAATTTT
Statistics
Matches: 64, Mismatches: 15, Indels: 13
0.70 0.16 0.14
Matches are distributed among these distances:
18 8 0.12
19 5 0.08
20 18 0.28
21 23 0.36
22 10 0.16
ACGTcount: A:0.35, C:0.04, G:0.01, T:0.60
Consensus pattern (20 bp):
ATTTTTATAAATTTTTATAT
Found at i:320858 original size:20 final size:19
Alignment explanation
Indices: 320753--320870 Score: 60
Period size: 20 Copynumber: 5.8 Consensus size: 19
320743 TCAATTTTAA
*
320753 ATTTTTAATAATTTTTAATAA
1 ATTTTTAA-AA-TTTTAATAT
* *
320774 ATTTTATAAAAATTT-ACAT
1 ATTTT-TAAAATTTTAATAT
* *
320793 -TTTTTAATATTTTTATAT
1 ATTTTTAAAATTTTAATAT
* *
320811 CATTTTCTATAACTTTTTATATT
1 -ATTTT-TA-AAATTTTAATA-T
*
320834 TTTTTGTAAAATTTTAATAT
1 ATTTT-TAAAATTTTAATAT
*
320854 ATTTTCAATAATTTTAA
1 ATTTTTAA-AATTTTAA
320871 AAAAATTATA
Statistics
Matches: 75, Mismatches: 14, Indels: 17
0.71 0.13 0.16
Matches are distributed among these distances:
17 7 0.09
18 7 0.09
19 4 0.05
20 20 0.27
21 18 0.24
22 18 0.24
23 1 0.01
ACGTcount: A:0.36, C:0.04, G:0.01, T:0.58
Consensus pattern (19 bp):
ATTTTTAAAATTTTAATAT
Done.