Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr10
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: 21822658
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.32
Warning! 1067834 characters in sequence are not A, C, G, or T
File 5 of 59
Found at i:1325866 original size:2 final size:2
Alignment explanation
Indices: 1325861--1325901 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
1325851 TCTCTCAGGT
1325861 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1325902 TGTTTATGAT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:1332190 original size:18 final size:19
Alignment explanation
Indices: 1332167--1332205 Score: 71
Period size: 19 Copynumber: 2.1 Consensus size: 19
1332157 TCTTTTTAAG
1332167 TCCCAATAA-TCCTCATTA
1 TCCCAATAACTCCTCATTA
1332185 TCCCAATAACTCCTCATTA
1 TCCCAATAACTCCTCATTA
1332204 TC
1 TC
1332206 TCTCTTTCAT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 9 0.45
19 11 0.55
ACGTcount: A:0.31, C:0.36, G:0.00, T:0.33
Consensus pattern (19 bp):
TCCCAATAACTCCTCATTA
Found at i:1335738 original size:17 final size:18
Alignment explanation
Indices: 1335706--1335739 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
1335696 CATATATTAT
*
1335706 AATCGAACTGACCGAATC
1 AATCGAACTAACCGAATC
1335724 AATCGAA-TAACCGAAT
1 AATCGAACTAACCGAAT
1335740 TAAGGTTCAT
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:0.44, C:0.24, G:0.15, T:0.18
Consensus pattern (18 bp):
AATCGAACTAACCGAATC
Found at i:1336579 original size:2 final size:2
Alignment explanation
Indices: 1336566--1336635 Score: 77
Period size: 2 Copynumber: 34.0 Consensus size: 2
1336556 TTTCTCAGAA
* ** **
1336566 AT AT AT AA AT AT AT AT AT AT AT AT CAT NNN NN AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT -AT -AT AT AT AT AT AT AT AT
1336610 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
1336636 TTTTTTTTTT
Statistics
Matches: 60, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
2 58 0.97
3 2 0.03
ACGTcount: A:0.47, C:0.01, G:0.00, T:0.44
Consensus pattern (2 bp):
AT
Found at i:1354059 original size:19 final size:19
Alignment explanation
Indices: 1354037--1354074 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
1354027 TTCTCCTTGT
1354037 CTTTTTCTTCTTTT-ATTTA
1 CTTTTT-TTCTTTTCATTTA
*
1354056 CTTTTTTTTTTTTCATTTA
1 CTTTTTTTCTTTTCATTTA
1354075 TGTGACTAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.11, C:0.13, G:0.00, T:0.76
Consensus pattern (19 bp):
CTTTTTTTCTTTTCATTTA
Found at i:1365839 original size:2 final size:2
Alignment explanation
Indices: 1365832--1365866 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1365822 ATTAGACCAC
1365832 TA TA TA TA TA 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 TA TA TA TA TA T
1365867 TTATTTATTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1376700 original size:124 final size:124
Alignment explanation
Indices: 1376457--1376701 Score: 271
Period size: 124 Copynumber: 2.0 Consensus size: 124
1376447 AAGATTTGAG
* * * * * * *
1376457 TTTATTTTAATATTAAATATCATGACTCGAAATTTAAATTCAATTTCGTGCAAGTTGAACTTTAA
1 TTTATTTTAATATCAAATATCATGAATCGAAACTTAAATTCAATCTCATGCAAGTTAAACTATAA
* * * *
1376522 AAATAAAATTTAAGTAAATTTATAAATCTTGAGTTTATGTTTTCAACTTAAAAAATAAA
66 AAATAAAATTTAAGTAAATTTATAAATATTGAGTCTATATTCTCAACTTAAAAAATAAA
* * *
1376581 TTTATTTTGATATCAAATGTCATGAATCGAAACTTAAATTCAATCTCATGTAA-TCTCAAACTAT
1 TTTATTTTAATATCAAATATCATGAATCGAAACTTAAATTCAATCTCATGCAAGT-T-AAACTAT
* ** *
1376645 -AAAATAGAATTTATTTAAATTTATAAATAATTGA-TCTATATTCTCAATTTTAAAAAA
64 AAAAATAAAATTTAAGTAAATTTATAAAT-ATTGAGTCTATATTCTCAA-CTTAAAAAA
1376702 AACCTAATAG
Statistics
Matches: 99, Mismatches: 18, Indels: 7
0.80 0.15 0.06
Matches are distributed among these distances:
123 1 0.01
124 81 0.82
125 17 0.17
ACGTcount: A:0.43, C:0.09, G:0.07, T:0.41
Consensus pattern (124 bp):
TTTATTTTAATATCAAATATCATGAATCGAAACTTAAATTCAATCTCATGCAAGTTAAACTATAA
AAATAAAATTTAAGTAAATTTATAAATATTGAGTCTATATTCTCAACTTAAAAAATAAA
Found at i:1400299 original size:2 final size:2
Alignment explanation
Indices: 1400292--1400344 Score: 106
Period size: 2 Copynumber: 26.5 Consensus size: 2
1400282 CTTTCATAAC
1400292 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1400334 AT AT AT AT AT A
1 AT AT AT AT AT A
1400345 GGTGCTATTG
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1402447 original size:27 final size:27
Alignment explanation
Indices: 1402409--1402463 Score: 101
Period size: 27 Copynumber: 2.0 Consensus size: 27
1402399 TTACCCAGAG
*
1402409 AACTTGTTTGGAGGATTGCAAAAAATA
1 AACTAGTTTGGAGGATTGCAAAAAATA
1402436 AACTAGTTTGGAGGATTGCAAAAAATA
1 AACTAGTTTGGAGGATTGCAAAAAATA
1402463 A
1 A
1402464 TCTTAATTGG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.44, C:0.07, G:0.22, T:0.27
Consensus pattern (27 bp):
AACTAGTTTGGAGGATTGCAAAAAATA
Found at i:1402861 original size:2 final size:2
Alignment explanation
Indices: 1402854--1402880 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1402844 TAAGACAAAA
1402854 CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT C
1402881 CACTGAACTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:1403901 original size:2 final size:2
Alignment explanation
Indices: 1403894--1403930 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
1403884 TATGAATGTT
1403894 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1403931 TCCATGTTCT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:1414619 original size:21 final size:21
Alignment explanation
Indices: 1414595--1414637 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
1414585 ACAATTTTTG
*
1414595 TTAAGTTGTGTATGAATAAGA
1 TTAAATTGTGTATGAATAAGA
*
1414616 TTAAATTGTGTTTGAATAAGA
1 TTAAATTGTGTATGAATAAGA
1414637 T
1 T
1414638 CGTTTTTATA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.37, C:0.00, G:0.21, T:0.42
Consensus pattern (21 bp):
TTAAATTGTGTATGAATAAGA
Found at i:1414924 original size:3 final size:3
Alignment explanation
Indices: 1414916--1414942 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
1414906 AAACCCTTAC
1414916 TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT
1414943 GAAGATCGAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:1416875 original size:23 final size:23
Alignment explanation
Indices: 1416846--1416897 Score: 79
Period size: 23 Copynumber: 2.3 Consensus size: 23
1416836 ATAAGAAGAA
1416846 AAAAAGGGAAGAAA-AAAAAAAG
1 AAAAAGGGAAGAAACAAAAAAAG
*
1416868 AAGAAAGGGAAGAAACAAAGAAAG
1 AA-AAAGGGAAGAAACAAAAAAAG
1416892 AAAAAG
1 AAAAAG
1416898 AAAATTGGGG
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
22 2 0.07
23 16 0.59
24 9 0.33
ACGTcount: A:0.73, C:0.02, G:0.25, T:0.00
Consensus pattern (23 bp):
AAAAAGGGAAGAAACAAAAAAAG
Found at i:1416898 original size:27 final size:24
Alignment explanation
Indices: 1416838--1416900 Score: 65
Period size: 23 Copynumber: 2.5 Consensus size: 24
1416828 CCCCACTCAT
*
1416838 AAGAAGAAAAAAAGGGAAGAAAAAA
1 AAGAA-AAAGAAAGGGAAGAAAAAA
*
1416863 AA-AAGAAGAAAGGGAAGAAACAAAGA
1 AAGAAAAAGAAAGGGAAG-AA-AAA-A
1416889 AAGAAAAAGAAA
1 AAGAAAAAGAAA
1416901 ATTGGGGGGG
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
23 11 0.35
24 4 0.13
25 5 0.16
26 3 0.10
27 8 0.26
ACGTcount: A:0.75, C:0.02, G:0.24, T:0.00
Consensus pattern (24 bp):
AAGAAAAAGAAAGGGAAGAAAAAA
Found at i:1420601 original size:60 final size:60
Alignment explanation
Indices: 1420433--1420602 Score: 182
Period size: 60 Copynumber: 2.8 Consensus size: 60
1420423 ATATTCTGGG
* * * * * * *
1420433 TAGGTAAAGGGAGACTTGAAGCGCCGATTTATATATGGTGGA-GTGGGTAATTTCCACGAG
1 TAGGTAAAGGGGGACTTGAAGCCCCGATTTATATTTGAT-GATGTGGGTAGTTCCCACGAC
** * * * *
1420493 TAAATAAAGGGGGACCTGAAGTCCCGATTTATATTTGATGACT-TGGGTAGTTCCCGCTAC
1 TAGGTAAAGGGGGACTTGAAGCCCCGATTTATATTTGATGA-TGTGGGTAGTTCCCACGAC
*
1420553 TAGGTAAAGGGGGACTTGAAGCCCCGATTTATATTTGATGATGCGGGTAG
1 TAGGTAAAGGGGGACTTGAAGCCCCGATTTATATTTGATGATGTGGGTAG
1420603 GGGGTCCTGA
Statistics
Matches: 89, Mismatches: 18, Indels: 6
0.79 0.16 0.05
Matches are distributed among these distances:
59 3 0.03
60 86 0.97
ACGTcount: A:0.27, C:0.14, G:0.31, T:0.28
Consensus pattern (60 bp):
TAGGTAAAGGGGGACTTGAAGCCCCGATTTATATTTGATGATGTGGGTAGTTCCCACGAC
Found at i:1420642 original size:41 final size:41
Alignment explanation
Indices: 1420560--1420643 Score: 114
Period size: 41 Copynumber: 2.0 Consensus size: 41
1420550 TACTAGGTAA
* * *
1420560 AGGGGGACTTGAAGCCCCGATTTATATTTGATGATGCGGGT
1 AGGGGGACCTGAAGCCCCGATTTATATTTGATAACGCGGGT
* * *
1420601 AGGGGGTCCTGAAGCCCCGATTTATATTTGGTAACGTGGGT
1 AGGGGGACCTGAAGCCCCGATTTATATTTGATAACGCGGGT
1420642 AG
1 AG
1420644 TTCTCACGAG
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
41 37 1.00
ACGTcount: A:0.21, C:0.15, G:0.35, T:0.29
Consensus pattern (41 bp):
AGGGGGACCTGAAGCCCCGATTTATATTTGATAACGCGGGT
Found at i:1420675 original size:101 final size:101
Alignment explanation
Indices: 1420500--1420703 Score: 300
Period size: 101 Copynumber: 2.0 Consensus size: 101
1420490 GAGTAAATAA
* * * * * *
1420500 AGGGGGACCTGAAGTCCCGATTTATATTTGATGACTTGGGTAGTTCCCGCTACTAGGTAAAGGGG
1 AGGGGGACCTGAAGCCCCGATTTATATTTGATAACGTGGGTAGTTCCCACGACTAGGTAAAGGGA
*
1420565 GACTTGAAGCCCCGATTTATATTTGATGATGCGGGT
66 GACCTGAAGCCCCGATTTATATTTGATGATGCGGGT
* * * *
1420601 AGGGGGTCCTGAAGCCCCGATTTATATTTGGTAACGTGGGTAGTTCTCACGAGTAGGTAAAGGGA
1 AGGGGGACCTGAAGCCCCGATTTATATTTGATAACGTGGGTAGTTCCCACGACTAGGTAAAGGGA
*
1420666 GACCTGAAGCCCCGATTTATATTTGGTGATGCGGGT
66 GACCTGAAGCCCCGATTTATATTTGATGATGCGGGT
1420702 AG
1 AG
1420704 TTCTCACGAG
Statistics
Matches: 91, Mismatches: 12, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
101 91 1.00
ACGTcount: A:0.23, C:0.17, G:0.32, T:0.28
Consensus pattern (101 bp):
AGGGGGACCTGAAGCCCCGATTTATATTTGATAACGTGGGTAGTTCCCACGACTAGGTAAAGGGA
GACCTGAAGCCCCGATTTATATTTGATGATGCGGGT
Found at i:1420702 original size:60 final size:60
Alignment explanation
Indices: 1420608--1420929 Score: 423
Period size: 60 Copynumber: 5.3 Consensus size: 60
1420598 GGTAGGGGGT
* *
1420608 CCTGAAGCCCCGATTTATATTTGGTAACGTGGGTAGTTCTCACGAGTAGGTAAAGGGAGA
1 CCTGAAGCCCCGATTTATATTTGGTGACGTGGGTAGTTCCCACGAGTAGGTAAAGGGAGA
* * * *
1420668 CCTGAAGCCCCGATTTATATTTGGTGATGCGGGTAGTTCTCACGAGTAGGTAAAGGGGGA
1 CCTGAAGCCCCGATTTATATTTGGTGACGTGGGTAGTTCCCACGAGTAGGTAAAGGGAGA
* * *
1420728 CCTGAAGCCTCGATTTATATTTGGTGACGTAGGTAGTTCCCACGAATAGGTAAAGGGAGGGA
1 CCTGAAGCCCCGATTTATATTTGGTGACGTGGGTAGTTCCCACGAGTAGGTAAAGGGA--GA
* * *
1420790 CCTAAAGCCCCGATTTATATTTGATGACGTGGGTAGTTCCCACGAGCAGGTAAAAGGGA-A
1 CCTGAAGCCCCGATTTATATTTGGTGACGTGGGTAGTTCCCACGAGTAGGT-AAAGGGAGA
* * * *
1420850 CTTAAAACCCCGATTTATATTTGGTGACGTGGGTAATTCCCACGAGTAGGTAAA-GGAGGA
1 CCTGAAGCCCCGATTTATATTTGGTGACGTGGGTAGTTCCCACGAGTAGGTAAAGGGA-GA
* * *
1420910 CTTGAAGTCCCGATTCATAT
1 CCTGAAGCCCCGATTTATAT
1420930 GGTGGCGCAG
Statistics
Matches: 231, Mismatches: 26, Indels: 10
0.87 0.10 0.04
Matches are distributed among these distances:
58 3 0.01
59 3 0.01
60 171 0.74
62 47 0.20
63 7 0.03
ACGTcount: A:0.27, C:0.18, G:0.29, T:0.26
Consensus pattern (60 bp):
CCTGAAGCCCCGATTTATATTTGGTGACGTGGGTAGTTCCCACGAGTAGGTAAAGGGAGA
Found at i:1420721 original size:161 final size:161
Alignment explanation
Indices: 1420449--1420750 Score: 412
Period size: 161 Copynumber: 1.9 Consensus size: 161
1420439 AAGGGAGACT
* * *
1420449 TGAAGCGCCGATTTATATATGGTGGAGTGGGTAATTTCCACGAGTAAATAAAGGGGGACCTGAAG
1 TGAAGCCCCGATTTATATATGGTGAAGTGGGTAATTTCCACGAGTAAATAAAGGGAGACCTGAAG
* * * * *
1420514 TCCCGATTTATATTTGATGACTTGGGTAGTTCCCGCTACTAGGTAAAGGGGGACTTGAAGCCCCG
66 CCCCGATTTATATTTGATGACTCGGGTAGTTCCCACGACTAGGTAAAGGGGGACCTGAAGCCCCG
1420579 ATTTATATTTGATGATGCGGGTAGGGGGTCC
131 ATTTATATTTGATGATGCGGGTAGGGGGTCC
* * **
1420610 TGAAGCCCCGATTTATATTTGGT-AACGTGGGT-AGTTCTCACGAGTAGGTAAAGGGAGACCTGA
1 TGAAGCCCCGATTTATATATGGTGAA-GTGGGTAATTTC-CACGAGTAAATAAAGGGAGACCTGA
* * *
1420673 AGCCCCGATTTATATTTGGTGA-TGCGGGTAGTTCTCACGAGTAGGTAAAGGGGGACCTGAAGCC
64 AGCCCCGATTTATATTTGATGACT-CGGGTAGTTCCCACGACTAGGTAAAGGGGGACCTGAAGCC
*
1420737 TCGATTTATATTTG
128 CCGATTTATATTTG
1420751 GTGACGTAGG
Statistics
Matches: 122, Mismatches: 16, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
160 6 0.05
161 116 0.95
ACGTcount: A:0.25, C:0.16, G:0.30, T:0.29
Consensus pattern (161 bp):
TGAAGCCCCGATTTATATATGGTGAAGTGGGTAATTTCCACGAGTAAATAAAGGGAGACCTGAAG
CCCCGATTTATATTTGATGACTCGGGTAGTTCCCACGACTAGGTAAAGGGGGACCTGAAGCCCCG
ATTTATATTTGATGATGCGGGTAGGGGGTCC
Found at i:1420864 original size:122 final size:120
Alignment explanation
Indices: 1420615--1420905 Score: 411
Period size: 122 Copynumber: 2.4 Consensus size: 120
1420605 GGTCCTGAAG
* * *
1420615 CCCCGATTTATATTTGGTAACGTGGGTAGTTCTCACGAGTAGGTAAAGGGAGACCTGAAGCCCCG
1 CCCCGATTTATATTTGGTGACGTGGGTAGTTCCCACGAGTAGGTAAAGGGAGACCTAAAGCCCCG
* * * * * * * *
1420680 ATTTATATTTGGTGATGCGGGTAGTTCTCACGAGTAGGTAAAGGGGGACCTGAAG
66 ATTTATATTTGATGACGCGGGTAGTTCCCACGAGCAGGTAAAAGGGAACCTAAAA
* * *
1420735 CCTCGATTTATATTTGGTGACGTAGGTAGTTCCCACGAATAGGTAAAGGGAGGGACCTAAAGCCC
1 CCCCGATTTATATTTGGTGACGTGGGTAGTTCCCACGAGTAGGTAAAGGGA--GACCTAAAGCCC
* *
1420800 CGATTTATATTTGATGACGTGGGTAGTTCCCACGAGCAGGTAAAAGGGAACTTAAAA
64 CGATTTATATTTGATGACGCGGGTAGTTCCCACGAGCAGGTAAAAGGGAACCTAAAA
*
1420857 CCCCGATTTATATTTGGTGACGTGGGTAATTCCCACGAGTAGGTAAAGG
1 CCCCGATTTATATTTGGTGACGTGGGTAGTTCCCACGAGTAGGTAAAGG
1420906 AGGACTTGAA
Statistics
Matches: 149, Mismatches: 20, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
120 46 0.31
122 103 0.69
ACGTcount: A:0.27, C:0.17, G:0.29, T:0.26
Consensus pattern (120 bp):
CCCCGATTTATATTTGGTGACGTGGGTAGTTCCCACGAGTAGGTAAAGGGAGACCTAAAGCCCCG
ATTTATATTTGATGACGCGGGTAGTTCCCACGAGCAGGTAAAAGGGAACCTAAAA
Found at i:1422688 original size:22 final size:22
Alignment explanation
Indices: 1422663--1422720 Score: 71
Period size: 22 Copynumber: 2.6 Consensus size: 22
1422653 AACTAACAGC
1422663 AAATCACTCACAAACGAATAAT
1 AAATCACTCACAAACGAATAAT
* * * *
1422685 AAATCTCTCATAAACTAGTAAT
1 AAATCACTCACAAACGAATAAT
*
1422707 AAATCACCCACAAA
1 AAATCACTCACAAA
1422721 TCGGTAGCAA
Statistics
Matches: 29, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.52, C:0.24, G:0.03, T:0.21
Consensus pattern (22 bp):
AAATCACTCACAAACGAATAAT
Found at i:1432337 original size:2 final size:2
Alignment explanation
Indices: 1432330--1432363 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
1432320 CTATTTCATT
1432330 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1432364 TATATATATA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:1435279 original size:94 final size:94
Alignment explanation
Indices: 1435118--1435304 Score: 311
Period size: 94 Copynumber: 2.0 Consensus size: 94
1435108 TAGTTTGCCC
* * *
1435118 GATTGCTGATGCGGAAACATGGGATATGTTGAGTCATTTGTGGTCTGATGAATCTGATGCAATAT
1 GATTGCTGATGCAGAAACATGGGATATGCTGAGTCATTTGTGGTCTGATGAATCTGATGCAACAT
*
1435183 TTTTCCTTTGGGATTCTTTTCTTTTTTTG
66 TTTTCCGTTGGGATTCTTTTCTTTTTTTG
*
1435212 GATTGCTGATGCAGAAACATGGGATATGCTGTGTCATTTGTGGTCTGATGAATCTGATGCAACAT
1 GATTGCTGATGCAGAAACATGGGATATGCTGAGTCATTTGTGGTCTGATGAATCTGATGCAACAT
* *
1435277 TTTTTCGTTGGGATTCTTTTTTTTTTTT
66 TTTTCCGTTGGGATTCTTTTCTTTTTTT
1435305 TGAAAGTTAG
Statistics
Matches: 86, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
94 86 1.00
ACGTcount: A:0.19, C:0.12, G:0.24, T:0.45
Consensus pattern (94 bp):
GATTGCTGATGCAGAAACATGGGATATGCTGAGTCATTTGTGGTCTGATGAATCTGATGCAACAT
TTTTCCGTTGGGATTCTTTTCTTTTTTTG
Found at i:1441813 original size:22 final size:22
Alignment explanation
Indices: 1441785--1441872 Score: 63
Period size: 22 Copynumber: 4.0 Consensus size: 22
1441775 CATCACATCT
1441785 CTCACAAACTAATAGTAAATCA
1 CTCACAAACTAATAGTAAATCA
* **
1441807 CTCACAAACCAATCA-TAAATTT
1 CTCACAAACTAAT-AGTAAATCA
* ** *
1441829 CTCATAAACTAGCAATAAATCA
1 CTCACAAACTAATAGTAAATCA
* *
1441851 CCCACAAA-TCAGTAGTAAATCA
1 CTCACAAACT-AATAGTAAATCA
1441873 GTAATAAATA
Statistics
Matches: 50, Mismatches: 13, Indels: 6
0.72 0.19 0.09
Matches are distributed among these distances:
21 2 0.04
22 47 0.94
23 1 0.02
ACGTcount: A:0.48, C:0.25, G:0.05, T:0.23
Consensus pattern (22 bp):
CTCACAAACTAATAGTAAATCA
Found at i:1442840 original size:19 final size:20
Alignment explanation
Indices: 1442805--1442842 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
1442795 GAATAAAGTA
1442805 AAAATGAAAAAACAAAAGAG
1 AAAATGAAAAAACAAAAGAG
1442825 AAAA-GAAAGAAA-AAAAGA
1 AAAATGAAA-AAACAAAAGA
1442843 AAGAGAGAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.79, C:0.03, G:0.16, T:0.03
Consensus pattern (20 bp):
AAAATGAAAAAACAAAAGAG
Found at i:1449954 original size:2 final size:2
Alignment explanation
Indices: 1449947--1449972 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1449937 TTGAGATAAT
1449947 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
1449973 ACCGTTAGTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1451660 original size:15 final size:15
Alignment explanation
Indices: 1451640--1451673 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
1451630 GTTTCACCCT
1451640 TTGGCAGAAAAGAGA
1 TTGGCAGAAAAGAGA
* *
1451655 TTGGCAGAACAGATA
1 TTGGCAGAAAAGAGA
1451670 TTGG
1 TTGG
1451674 GATCCAGATT
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:0.38, C:0.09, G:0.32, T:0.21
Consensus pattern (15 bp):
TTGGCAGAAAAGAGA
Found at i:1451690 original size:27 final size:27
Alignment explanation
Indices: 1451652--1451705 Score: 99
Period size: 27 Copynumber: 2.0 Consensus size: 27
1451642 GGCAGAAAAG
*
1451652 AGATTGGCAGAACAGATATTGGGATCC
1 AGATTGGCAGAAAAGATATTGGGATCC
1451679 AGATTGGCAGAAAAGATATTGGGATCC
1 AGATTGGCAGAAAAGATATTGGGATCC
1451706 TTTTCGTTAT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.35, C:0.13, G:0.30, T:0.22
Consensus pattern (27 bp):
AGATTGGCAGAAAAGATATTGGGATCC
Found at i:1453446 original size:97 final size:96
Alignment explanation
Indices: 1453275--1453459 Score: 318
Period size: 97 Copynumber: 1.9 Consensus size: 96
1453265 TAGTTTGCCC
*
1453275 GATTGCTGATGCGGAAACATGGGATATGTTGAGTCATTTGTGGTCTGATGAATCTGATGCAATAT
1 GATTGCTGATGCAGAAACATGGGATATGTTGAGTCATTTGTGGTCTGATGAATCTGATGCAATAT
1453340 TTTTCCTTTGGGATTCTTTTTTTTTTTTTTTG
66 TTTTCCTTTGGGATT-TTTTTTTTTTTTTTTG
* *
1453372 GATTTCTGATGCAGAAACATGGGATATGTTGTGTCATTTGTGGTCTGATGAATCTGATGCAATAT
1 GATTGCTGATGCAGAAACATGGGATATGTTGAGTCATTTGTGGTCTGATGAATCTGATGCAATAT
1453437 GTTTT-CTTTGGGATTTTTTTTTT
66 -TTTTCCTTTGGGATTTTTTTTTT
1453460 AATTGAAAGT
Statistics
Matches: 84, Mismatches: 3, Indels: 3
0.93 0.03 0.03
Matches are distributed among these distances:
96 8 0.10
97 72 0.86
98 4 0.05
ACGTcount: A:0.19, C:0.10, G:0.24, T:0.47
Consensus pattern (96 bp):
GATTGCTGATGCAGAAACATGGGATATGTTGAGTCATTTGTGGTCTGATGAATCTGATGCAATAT
TTTTCCTTTGGGATTTTTTTTTTTTTTTTTG
Found at i:1464366 original size:16 final size:16
Alignment explanation
Indices: 1464345--1464375 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
1464335 GGCAGAGAAG
1464345 GTTTAATAATGAGGCA
1 GTTTAATAATGAGGCA
1464361 GTTTAATAATGAGGC
1 GTTTAATAATGAGGC
1464376 CAAGTTTGGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.35, C:0.06, G:0.26, T:0.32
Consensus pattern (16 bp):
GTTTAATAATGAGGCA
Found at i:1470540 original size:18 final size:19
Alignment explanation
Indices: 1470514--1470550 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
1470504 TTTATATTAA
1470514 TTTATTTTGGTTTATGTAT
1 TTTATTTTGGTTTATGTAT
*
1470533 TTTA-TTTGTTTTATGTAT
1 TTTATTTTGGTTTATGTAT
1470551 AATTGAGTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 13 0.76
19 4 0.24
ACGTcount: A:0.16, C:0.00, G:0.14, T:0.70
Consensus pattern (19 bp):
TTTATTTTGGTTTATGTAT
Found at i:1473945 original size:3 final size:3
Alignment explanation
Indices: 1473939--1473971 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
1473929 CAACCACCAG
1473939 ACC ACC ACC ACC ACC ACC ACC ACC ACC ACC ACC
1 ACC ACC ACC ACC ACC ACC ACC ACC ACC ACC ACC
1473972 TTCCACACTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.33, C:0.67, G:0.00, T:0.00
Consensus pattern (3 bp):
ACC
Found at i:1481063 original size:21 final size:21
Alignment explanation
Indices: 1481037--1481161 Score: 88
Period size: 21 Copynumber: 5.5 Consensus size: 21
1481027 TCTTTGGTTG
1481037 TGGGCCTTGTTGGGCTTAATT
1 TGGGCCTTGTTGGGCTTAATT
*** *
1481058 TGGGCCTTGTAAGTTATCATTGATTT
1 TGGGCCTTGT---TGGGC-TT-AATT
1481084 TGGGCCTTGTTGGGCTTAATT
1 TGGGCCTTGTTGGGCTTAATT
*** *
1481105 TGGGCCTTGTAAGTTATCATTGATTT
1 TGGGCCTTGT---TGGGC-TT-AATT
1481131 TGGGCCTTGTTGGGCTTAATT
1 TGGGCCTTGTTGGGCTTAATT
1481152 TGGGCCTTGT
1 TGGGCCTTGT
1481162 ATGTGTACTG
Statistics
Matches: 78, Mismatches: 16, Indels: 20
0.68 0.14 0.18
Matches are distributed among these distances:
21 36 0.46
22 4 0.05
23 4 0.05
24 4 0.05
25 4 0.05
26 26 0.33
ACGTcount: A:0.13, C:0.14, G:0.30, T:0.44
Consensus pattern (21 bp):
TGGGCCTTGTTGGGCTTAATT
Found at i:1481086 original size:26 final size:26
Alignment explanation
Indices: 1481056--1481140 Score: 99
Period size: 26 Copynumber: 3.5 Consensus size: 26
1481046 TTGGGCTTAA
1481056 TTTGGGCCTTGTAAGTTATCATTGAT
1 TTTGGGCCTTGTAAGTTATCATTGAT
*** *
1481082 TTTGGGCCTTGT---TGGGC-TT-AA
1 TTTGGGCCTTGTAAGTTATCATTGAT
1481103 TTTGGGCCTTGTAAGTTATCATTGAT
1 TTTGGGCCTTGTAAGTTATCATTGAT
1481129 TTTGGGCCTTGT
1 TTTGGGCCTTGT
1481141 TGGGCTTAAT
Statistics
Matches: 46, Mismatches: 8, Indels: 10
0.72 0.12 0.16
Matches are distributed among these distances:
21 13 0.28
22 2 0.04
23 2 0.04
24 2 0.04
25 2 0.04
26 25 0.54
ACGTcount: A:0.14, C:0.13, G:0.27, T:0.46
Consensus pattern (26 bp):
TTTGGGCCTTGTAAGTTATCATTGAT
Found at i:1481088 original size:47 final size:47
Alignment explanation
Indices: 1481005--1481162 Score: 271
Period size: 47 Copynumber: 3.4 Consensus size: 47
1480995 TTTTAATTAT
* * * * *
1481005 TTAATTTGGGCCTTGCAAGTGATCTTTGGTTGTGGGCCTTGTTGGGC
1 TTAATTTGGGCCTTGTAAGTTATCATTGATTTTGGGCCTTGTTGGGC
1481052 TTAATTTGGGCCTTGTAAGTTATCATTGATTTTGGGCCTTGTTGGGC
1 TTAATTTGGGCCTTGTAAGTTATCATTGATTTTGGGCCTTGTTGGGC
1481099 TTAATTTGGGCCTTGTAAGTTATCATTGATTTTGGGCCTTGTTGGGC
1 TTAATTTGGGCCTTGTAAGTTATCATTGATTTTGGGCCTTGTTGGGC
1481146 TTAATTTGGGCCTTGTA
1 TTAATTTGGGCCTTGTA
1481163 TGTGTACTGG
Statistics
Matches: 106, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
47 106 1.00
ACGTcount: A:0.14, C:0.13, G:0.29, T:0.44
Consensus pattern (47 bp):
TTAATTTGGGCCTTGTAAGTTATCATTGATTTTGGGCCTTGTTGGGC
Found at i:1485266 original size:150 final size:151
Alignment explanation
Indices: 1484646--1485298 Score: 567
Period size: 154 Copynumber: 4.4 Consensus size: 151
1484636 TGAGCTCGCC
* * *
1484646 CCGAAACAAATATTTACTGTTTAATGCTTACATATAATGTGTAACAAATACTCAAGATGTGGAGT
1 CCGAAACAAATATTTACTGTTTAATACTTACATATAATGTGTAACAAATAATCAAGATATGGAGT
* * ** * *
1484711 AATGATTTCAAGCAAATCATG--AC---A-C--GTTCTTAAAAAAAATCAATTATTTACTCCAAA
66 AACGATTCCATTCAAATCATGACACATAATCATGTTATTAAAAAAAATCAATTTTTTACTCCAAA
* * * *
1484768 ACTCATTAATATGAGCTC-AA
131 AATCGTTAATATCAACTCTAA
* * * * * **
1484788 CTTGAAACAAATATTTACCGTTTAATGCTTATATATAATGTGTAACAAATAATCGAGACGTGGAG
1 C-CGAAACAAATATTTACTGTTTAATACTTACATATAATGTGTAACAAATAATCAAGATATGGAG
* * * ** * *
1484853 TAACAATTCTATTCAAATCATGACACAAAATCATGTTATGCAAAAAAATCAA-TTTTTATTTCAA
65 TAACGATTCCATTCAAATCATGACACATAATCATGTTATTAAAAAAAATCAATTTTTTACTCCAA
* ** *
1484917 AAATCGTTAACATGTACT-TGA
130 AAATCGTTAATATCAACTCTAA
* * * ** ** * *
1484938 CCGAAACAAATATTTACTGCTTAATACTTAAATGTAATGTGTAACAAATAATTGAGACGTAGAGC
1 CCGAAACAAATATTTACTGTTTAATACTTACATATAATGTGTAACAAATAATCAAGATATGGAGT
* * * *
1485003 AACGATTCCATTCATATCATGAAACATAATCATGTTATTAGAAAAAAAAAGTCAATTGTTTACTT
66 AACGATTCCATTCAAATCATGACACATAATCATGTTATT---AAAAAAAA-TCAATTTTTTACTC
* * * * **
1485068 TAAAAATTGTTTATATGAACT-TGG
127 CAAAAATCGTTAATATCAACTCTAA
*** * * *
1485092 CCGAAACAAATATTTACCAATTAATACTTACATATAATGTGCAACAAATAATCAAAATATGAAGT
1 CCGAAACAAATATTTACTGTTTAATACTTACATATAATGTGTAACAAATAATCAAGATATGGAGT
* ** * * ** *
1485157 AACGGTTTTATTCAAATCAGGACACGTAATCACATTCTTAAAAAAAATCAATTTTTTACTCCAAA
66 AACGATTCCATTCAAATCATGACACATAATCATGTTATTAAAAAAAATCAATTTTTTACTCCAAA
*
1485222 AATCGTTAAT-TCAAATCTAA
131 AATCGTTAATATCAACTCTAA
* *
1485242 TCGAAACAAATATTTACTGTTTAATACTTACATAAAATGTGTAACAAATAATCAAGA
1 CCGAAACAAATATTTACTGTTTAATACTTACATATAATGTGTAACAAATAATCAAGA
1485299 CGTAAAGTAA
Statistics
Matches: 407, Mismatches: 88, Indels: 24
0.78 0.17 0.05
Matches are distributed among these distances:
142 1 0.00
143 73 0.18
145 2 0.00
148 1 0.00
149 93 0.23
150 98 0.24
151 23 0.06
152 7 0.02
153 4 0.01
154 105 0.26
ACGTcount: A:0.43, C:0.15, G:0.11, T:0.32
Consensus pattern (151 bp):
CCGAAACAAATATTTACTGTTTAATACTTACATATAATGTGTAACAAATAATCAAGATATGGAGT
AACGATTCCATTCAAATCATGACACATAATCATGTTATTAAAAAAAATCAATTTTTTACTCCAAA
AATCGTTAATATCAACTCTAA
Found at i:1492876 original size:31 final size:31
Alignment explanation
Indices: 1492838--1492929 Score: 123
Period size: 31 Copynumber: 3.0 Consensus size: 31
1492828 TTTTATCTAT
1492838 TTGTTTCAGTATAAATTGTTCAGAAGTGTCA
1 TTGTTTCAGTATAAATTGTTCAGAAGTGTCA
* **
1492869 TTGTTTCAGTAT-AAGTCATCGAGAAGTGTCA
1 TTGTTTCAGTATAAATTGTTC-AGAAGTGTCA
* *
1492900 TTGTTTCAGTTTAAGTTGTTCAGAAGTGTC
1 TTGTTTCAGTATAAATTGTTCAGAAGTGTC
1492930 CCTGAATTGC
Statistics
Matches: 51, Mismatches: 8, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
30 5 0.10
31 42 0.82
32 4 0.08
ACGTcount: A:0.26, C:0.11, G:0.22, T:0.41
Consensus pattern (31 bp):
TTGTTTCAGTATAAATTGTTCAGAAGTGTCA
Found at i:1500801 original size:2 final size:2
Alignment explanation
Indices: 1500796--1500825 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1500786 GCCCCCCCTG
1500796 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1500826 TTCCTATCCA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:1503738 original size:2 final size:2
Alignment explanation
Indices: 1503733--1503767 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1503723 CTAACAATAC
1503733 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1503768 AAAGAAAACG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1506900 original size:239 final size:239
Alignment explanation
Indices: 1506349--1507417 Score: 1751
Period size: 239 Copynumber: 4.4 Consensus size: 239
1506339 CTTCTATTCT
1506349 ATTCTTTGACTTGAACCCTAAATTTGAGTTATGAAAAAAGGG-AAAAAAAACTATTGCATGTTTA
1 ATTCTTTGACTTGAACCC-AAATTTGAGTTATGAAAAAAGGGAAAAAAAAACTATTGCATGTTTA
*
1506413 GATTCAATTCTTGAATTTCTTGCTATGCTTTGTGTTAGATTATATGTATATATATATTAATTCTT
65 GATTCAATTCTTGGATTTCTTGCTATGCTTTGTGTTAG----TATGTATATATATATTAATTCTT
1506478 TGACTTGAACCCAAATTTGAGTTATGAAAAAAGGGAAAAAAAATACTATTGCATGTTTAGATTCA
126 TGACTTGAACCCAAATTTGAGTTATGAAAAAAGGG-AAAAAAATACTATTGCATGTTTAGATTCA
1506543 ATTCTTGGATTTCTTGCTATGCTTTGTGTTAG--AT-TATATATATATTA
190 ATTCTTGGATTTCTTGCTATGCTTTGTGTTAGATATATATATATATATTA
* * * *
1506590 ATTCTTTGACTTGAACTCAAATTTGAGTTATGAAAAAGGGGAATAAAATACTATTGCATGTTTAG
1 ATTCTTTGACTTGAACCCAAATTTGAGTTATGAAAAAAGGGAAAAAAAAACTATTGCATGTTTAG
1506655 ATTCAATTCTTGGATTTCTTGCTATGCTTTGTGTTAG-AT-TATATATATATTAATTCTTTGACT
66 ATTCAATTCTTGGATTTCTTGCTATGCTTTGTGTTAGTATGTATATATATATTAATTCTTTGACT
1506718 TGAACCCAAATTTGAGTTATGAAAAAAGGGAAAAAAATTACTATTGCATGTTTAGATTCAATTCT
131 TGAACCCAAATTTGAGTTATGAAAAAAGGGAAAAAAA-TACTATTGCATGTTTAGATTCAATTCT
1506783 TGGATTTCTTGCTATGCTTTGTGTTAGATTATATATATATATATTA
195 TGGATTTCTTGCTATGCTTTGTGTTAGA-TATATATATATATATTA
* * *
1506829 ATTCTTTTACTTGAACCCAAATTTAAGTTATGAAAAAAGGGAAAAAAAAACTATTGCATGTTTAC
1 ATTCTTTGACTTGAACCCAAATTTGAGTTATGAAAAAAGGGAAAAAAAAACTATTGCATGTTTAG
1506894 ATTCAATTCTTGGATTTCTTGCTATGCTTTGTGTTAGATTATATGTATATATATATTAATTCTTT
66 ATTCAATTCTTGGATTTCTTGCTATGCTTTGTGTTAG----TATGTATATATATATTAATTCTTT
*
1506959 GACTTGAACCCAAATTTGAGTTATGAAAAAGGGGAAAAAAATACTATTGCATGTTTAGATTCAAT
127 GACTTGAACCCAAATTTGAGTTATGAAAAAAGGGAAAAAAATACTATTGCATGTTTAGATTCAAT
1507024 TCTTGGATTTCTTGCTATGCTTTGTGTTAGAT-TATATATATATA-T-
192 TCTTGGATTTCTTGCTATGCTTTGTGTTAGATATATATATATATATTA
*
1507069 ATTCTTTGACTTGAACCCAAATTTGAGTTATGAAAAAAGGGAAAAAAATTACTATTGCATGTTTA
1 ATTCTTTGACTTGAACCCAAATTTGAGTTATGAAAAAAGGGAAAAAAA-AACTATTGCATGTTTA
* *
1507134 GATTCAATTCTTGGATTTCTTGCTATGCTTTGTGTTAGATTATATATATATATATTAATTCTTTT
65 GATTCAATTCTTGGATTTCTTGCTATGCTTTGTGTTAG--TATGTATATATATATTAATTCTTTG
* * *
1507199 ACTTGAACCCAAATTTAAGTTATGAAAAAAGGGAAAAAAAAACTATTGCATGTTTACATTCAATT
128 ACTTGAACCCAAATTTGAGTTATGAAAAAAGGGAAAAAAATACTATTGCATGTTTAGATTCAATT
1507264 CTTGGATTTCTTGCTATGCTTTGTGTTAGATTATATGTATATATATATTA
193 CTTGGATTTCTTGCTATGCTTTGTGTTAGA-TATA--TATATATATATTA
1507314 ATTCTTTGACTTGAACCCCAAATTTGAGTTATGAAAAAAGGGAAAAAAAATACTATTGCATGTTT
1 ATTCTTTGACTTGAA-CCCAAATTTGAGTTATGAAAAAAGGGAAAAAAAA-ACTATTGCATGTTT
*
1507379 AGATTCAATTCTTGGATTTCTTGCTACGCTTTGTGTTAG
64 AGATTCAATTCTTGGATTTCTTGCTATGCTTTGTGTTAG
1507418 ATCACACACA
Statistics
Matches: 780, Mismatches: 27, Indels: 37
0.92 0.03 0.04
Matches are distributed among these distances:
234 7 0.01
235 108 0.14
236 2 0.00
238 2 0.00
239 222 0.28
240 69 0.09
241 129 0.17
242 12 0.02
243 11 0.01
244 58 0.07
245 75 0.10
246 85 0.11
ACGTcount: A:0.33, C:0.10, G:0.15, T:0.41
Consensus pattern (239 bp):
ATTCTTTGACTTGAACCCAAATTTGAGTTATGAAAAAAGGGAAAAAAAAACTATTGCATGTTTAG
ATTCAATTCTTGGATTTCTTGCTATGCTTTGTGTTAGTATGTATATATATATTAATTCTTTGACT
TGAACCCAAATTTGAGTTATGAAAAAAGGGAAAAAAATACTATTGCATGTTTAGATTCAATTCTT
GGATTTCTTGCTATGCTTTGTGTTAGATATATATATATATATTA
Found at i:1506981 original size:123 final size:122
Alignment explanation
Indices: 1506349--1507419 Score: 1791
Period size: 118 Copynumber: 8.9 Consensus size: 122
1506339 CTTCTATTCT
1506349 ATTCTTTGACTTGAACCCTAAATTTGAGTTATGAAAAAAGGG-AAAAAAAACTATTGCATGTTTA
1 ATTCTTTGACTTGAACCC-AAATTTGAGTTATGAAAAAAGGGAAAAAAAAACTATTGCATGTTTA
*
1506413 GATTCAATTCTTGAATTTCTTGCTATGCTTTGTGTTAGATTATATGTATATATATATTA
65 GATTCAATTCTTGGATTTCTTGCTATGCTTTGTGTTAGATTATAT-TATATATATATTA
1506472 ATTCTTTGACTTGAACCCAAATTTGAGTTATGAAAAAAGGGAAAAAAAATACTATTGCATGTTTA
1 ATTCTTTGACTTGAACCCAAATTTGAGTTATGAAAAAAGGGAAAAAAAA-ACTATTGCATGTTTA
1506537 GATTCAATTCTTGGATTTCTTGCTATGCTTTGTGTTAG-----ATTATATATATATTA
65 GATTCAATTCTTGGATTTCTTGCTATGCTTTGTGTTAGATTATATTATATATATATTA
* * * *
1506590 ATTCTTTGACTTGAACTCAAATTTGAGTTATGAAAAAGGGGAATAAAATACTATTGCATGTTTAG
1 ATTCTTTGACTTGAACCCAAATTTGAGTTATGAAAAAAGGGAAAAAAAAACTATTGCATGTTTAG
1506655 ATTCAATTCTTGGATTTCTTGCTATGCTTTGTGTTAG-----ATTATATATATATTA
66 ATTCAATTCTTGGATTTCTTGCTATGCTTTGTGTTAGATTATATTATATATATATTA
*
1506707 ATTCTTTGACTTGAACCCAAATTTGAGTTATGAAAAAAGGGAAAAAAATTACTATTGCATGTTTA
1 ATTCTTTGACTTGAACCCAAATTTGAGTTATGAAAAAAGGGAAAAAAA-AACTATTGCATGTTTA
1506772 GATTCAATTCTTGGATTTCTTGCTATGCTTTGTGTTAGATTATA-TATATATATATTA
65 GATTCAATTCTTGGATTTCTTGCTATGCTTTGTGTTAGATTATATTATATATATATTA
* * *
1506829 ATTCTTTTACTTGAACCCAAATTTAAGTTATGAAAAAAGGGAAAAAAAAACTATTGCATGTTTAC
1 ATTCTTTGACTTGAACCCAAATTTGAGTTATGAAAAAAGGGAAAAAAAAACTATTGCATGTTTAG
1506894 ATTCAATTCTTGGATTTCTTGCTATGCTTTGTGTTAGATTATATGTATATATATATTA
66 ATTCAATTCTTGGATTTCTTGCTATGCTTTGTGTTAGATTATAT-TATATATATATTA
* *
1506952 ATTCTTTGACTTGAACCCAAATTTGAGTTATGAAAAAGGGGAAAAAAATACTATTGCATGTTTAG
1 ATTCTTTGACTTGAACCCAAATTTGAGTTATGAAAAAAGGGAAAAAAAAACTATTGCATGTTTAG
1507017 ATTCAATTCTTGGATTTCTTGCTATGCTTTGTGTTAGA-T-TA-TATATATATA-T-
66 ATTCAATTCTTGGATTTCTTGCTATGCTTTGTGTTAGATTATATTATATATATATTA
*
1507069 ATTCTTTGACTTGAACCCAAATTTGAGTTATGAAAAAAGGGAAAAAAATTACTATTGCATGTTTA
1 ATTCTTTGACTTGAACCCAAATTTGAGTTATGAAAAAAGGGAAAAAAA-AACTATTGCATGTTTA
1507134 GATTCAATTCTTGGATTTCTTGCTATGCTTTGTGTTAGATTATA-TATATATATATTA
65 GATTCAATTCTTGGATTTCTTGCTATGCTTTGTGTTAGATTATATTATATATATATTA
* * *
1507191 ATTCTTTTACTTGAACCCAAATTTAAGTTATGAAAAAAGGGAAAAAAAAACTATTGCATGTTTAC
1 ATTCTTTGACTTGAACCCAAATTTGAGTTATGAAAAAAGGGAAAAAAAAACTATTGCATGTTTAG
1507256 ATTCAATTCTTGGATTTCTTGCTATGCTTTGTGTTAGATTATATGTATATATATATTA
66 ATTCAATTCTTGGATTTCTTGCTATGCTTTGTGTTAGATTATAT-TATATATATATTA
1507314 ATTCTTTGACTTGAACCCCAAATTTGAGTTATGAAAAAAGGGAAAAAAAATACTATTGCATGTTT
1 ATTCTTTGACTTGAA-CCCAAATTTGAGTTATGAAAAAAGGGAAAAAAAA-ACTATTGCATGTTT
*
1507379 AGATTCAATTCTTGGATTTCTTGCTACGCTTTGTGTTAGAT
64 AGATTCAATTCTTGGATTTCTTGCTATGCTTTGTGTTAGAT
1507420 CACACACACA
Statistics
Matches: 903, Mismatches: 26, Indels: 36
0.94 0.03 0.04
Matches are distributed among these distances:
117 160 0.18
118 168 0.19
119 13 0.01
120 12 0.01
121 119 0.13
122 129 0.14
123 164 0.18
124 85 0.09
125 53 0.06
ACGTcount: A:0.34, C:0.10, G:0.15, T:0.41
Consensus pattern (122 bp):
ATTCTTTGACTTGAACCCAAATTTGAGTTATGAAAAAAGGGAAAAAAAAACTATTGCATGTTTAG
ATTCAATTCTTGGATTTCTTGCTATGCTTTGTGTTAGATTATATTATATATATATTA
Found at i:1507030 original size:362 final size:362
Alignment explanation
Indices: 1506348--1507419 Score: 1946
Period size: 362 Copynumber: 3.0 Consensus size: 362
1506338 TCTTCTATTC
1506348 TATTCTTTGACTTGAACCCTAAATTTGAGTTATGAAAAAAGGGAAAAAAA--ACTATTGCATGTT
1 TATTCTTTGACTTGAACCC-AAATTTGAGTTATGAAAAAAGGGAAAAAAATTACTATTGCATGTT
*
1506411 TAGATTCAATTCTTGAATTTCTTGCTATGCTTTGTGTTAGATTATATGTATATATATATTAATTC
65 TAGATTCAATTCTTGGATTTCTTGCTATGCTTTGTGTTAGATTATA--TATATATATATTAATTC
* * *
1506476 TTTGACTTGAACCCAAATTTGAGTTATGAAAAAAGGGAAAAAAAATACTATTGCATGTTTAGATT
128 TTTTACTTGAACCCAAATTTAAGTTATGAAAAAAGGGAAAAAAAA-ACTATTGCATGTTTACATT
1506541 CAATTCTTGGATTTCTTGCTATGCTTTGTGTTAG-----AT-TATATATATATTAATTCTTTGAC
192 CAATTCTTGGATTTCTTGCTATGCTTTGTGTTAGATTATATGTATATATATATTAATTCTTTGAC
* *
1506600 TTGAACTCAAATTTGAGTTATGAAAAAGGGGAATAAAATACTATTGCATGTTTAGATTCAATTCT
257 TTGAACCCAAATTTGAGTTATGAAAAAGGGGAAAAAAATACTATTGCATGTTTAGATTCAATTCT
1506665 TGGATTTCTTGCTATGCTTTGTGTTAGATTATATATATAT-
322 TGGATTTCTTGCTATGCTTTGTGTTAGATTATATATATATA
1506705 TAATTCTTTGACTTGAACCCAAATTTGAGTTATGAAAAAAGGGAAAAAAATTACTATTGCATGTT
1 T-ATTCTTTGACTTGAACCCAAATTTGAGTTATGAAAAAAGGGAAAAAAATTACTATTGCATGTT
1506770 TAGATTCAATTCTTGGATTTCTTGCTATGCTTTGTGTTAGATTATATATATATATATTAATTCTT
65 TAGATTCAATTCTTGGATTTCTTGCTATGCTTTGTGTTAGATTATATATATATATATTAATTCTT
1506835 TTACTTGAACCCAAATTTAAGTTATGAAAAAAGGGAAAAAAAAACTATTGCATGTTTACATTCAA
130 TTACTTGAACCCAAATTTAAGTTATGAAAAAAGGGAAAAAAAAACTATTGCATGTTTACATTCAA
1506900 TTCTTGGATTTCTTGCTATGCTTTGTGTTAGATTATATGTATATATATATTAATTCTTTGACTTG
195 TTCTTGGATTTCTTGCTATGCTTTGTGTTAGATTATATGTATATATATATTAATTCTTTGACTTG
1506965 AACCCAAATTTGAGTTATGAAAAAGGGGAAAAAAATACTATTGCATGTTTAGATTCAATTCTTGG
260 AACCCAAATTTGAGTTATGAAAAAGGGGAAAAAAATACTATTGCATGTTTAGATTCAATTCTTGG
1507030 ATTTCTTGCTATGCTTTGTGTTAGATTATATATATATA
325 ATTTCTTGCTATGCTTTGTGTTAGATTATATATATATA
1507068 TATTCTTTGACTTGAACCCAAATTTGAGTTATGAAAAAAGGGAAAAAAATTACTATTGCATGTTT
1 TATTCTTTGACTTGAACCCAAATTTGAGTTATGAAAAAAGGGAAAAAAATTACTATTGCATGTTT
1507133 AGATTCAATTCTTGGATTTCTTGCTATGCTTTGTGTTAGATTATATATATATATATTAATTCTTT
66 AGATTCAATTCTTGGATTTCTTGCTATGCTTTGTGTTAGATTATATATATATATATTAATTCTTT
1507198 TACTTGAACCCAAATTTAAGTTATGAAAAAAGGGAAAAAAAAACTATTGCATGTTTACATTCAAT
131 TACTTGAACCCAAATTTAAGTTATGAAAAAAGGGAAAAAAAAACTATTGCATGTTTACATTCAAT
1507263 TCTTGGATTTCTTGCTATGCTTTGTGTTAGATTATATGTATATATATATTAATTCTTTGACTTGA
196 TCTTGGATTTCTTGCTATGCTTTGTGTTAGATTATATGTATATATATATTAATTCTTTGACTTGA
*
1507328 ACCCCAAATTTGAGTTATGAAAAAAGGGAAAAAAAATACTATTGCATGTTTAGATTCAATTCTTG
261 A-CCCAAATTTGAGTTATG-AAAAAGGGGAAAAAAATACTATTGCATGTTTAGATTCAATTCTTG
*
1507393 GATTTCTTGCTACGCTTTGTGTTAGAT
324 GATTTCTTGCTATGCTTTGTGTTAGAT
1507420 CACACACACA
Statistics
Matches: 695, Mismatches: 8, Indels: 17
0.97 0.01 0.02
Matches are distributed among these distances:
356 52 0.07
357 91 0.13
358 18 0.03
359 58 0.08
361 2 0.00
362 386 0.56
363 18 0.03
364 70 0.10
ACGTcount: A:0.33, C:0.10, G:0.15, T:0.41
Consensus pattern (362 bp):
TATTCTTTGACTTGAACCCAAATTTGAGTTATGAAAAAAGGGAAAAAAATTACTATTGCATGTTT
AGATTCAATTCTTGGATTTCTTGCTATGCTTTGTGTTAGATTATATATATATATATTAATTCTTT
TACTTGAACCCAAATTTAAGTTATGAAAAAAGGGAAAAAAAAACTATTGCATGTTTACATTCAAT
TCTTGGATTTCTTGCTATGCTTTGTGTTAGATTATATGTATATATATATTAATTCTTTGACTTGA
ACCCAAATTTGAGTTATGAAAAAGGGGAAAAAAATACTATTGCATGTTTAGATTCAATTCTTGGA
TTTCTTGCTATGCTTTGTGTTAGATTATATATATATA
Found at i:1507156 original size:118 final size:121
Alignment explanation
Indices: 1506349--1507419 Score: 1817
Period size: 117 Copynumber: 8.9 Consensus size: 121
1506339 CTTCTATTCT
1506349 ATTCTTTGACTTGAACCCTAAATTTGAGTTATGAAAAAAGGGAAAAAAA-ACTATTGCATGTTTA
1 ATTCTTTGACTTGAACCC-AAATTTGAGTTATGAAAAAAGGGAAAAAAATACTATTGCATGTTTA
*
1506413 GATTCAATTCTTGAATTTCTTGCTATGCTTTGTGTTAGATTATATGTATATATATATTA
65 GATTCAATTCTTGGATTTCTTGCTATGCTTTGTGTTAGATTATA--TATATATATATTA
1506472 ATTCTTTGACTTGAACCCAAATTTGAGTTATGAAAAAAGGGAAAAAAAATACTATTGCATGTTTA
1 ATTCTTTGACTTGAACCCAAATTTGAGTTATGAAAAAAGGG-AAAAAAATACTATTGCATGTTTA
1506537 GATTCAATTCTTGGATTTCTTGCTATGCTTTGTGTTAG---AT-TATATATATATTA
65 GATTCAATTCTTGGATTTCTTGCTATGCTTTGTGTTAGATTATATATATATATATTA
* * *
1506590 ATTCTTTGACTTGAACTCAAATTTGAGTTATGAAAAAGGGGAATAAAATACTATTGCATGTTTAG
1 ATTCTTTGACTTGAACCCAAATTTGAGTTATGAAAAAAGGGAAAAAAATACTATTGCATGTTTAG
1506655 ATTCAATTCTTGGATTTCTTGCTATGCTTTGTGTTAG---AT-TATATATATATTA
66 ATTCAATTCTTGGATTTCTTGCTATGCTTTGTGTTAGATTATATATATATATATTA
1506707 ATTCTTTGACTTGAACCCAAATTTGAGTTATGAAAAAAGGGAAAAAAATTACTATTGCATGTTTA
1 ATTCTTTGACTTGAACCCAAATTTGAGTTATGAAAAAAGGGAAAAAAA-TACTATTGCATGTTTA
1506772 GATTCAATTCTTGGATTTCTTGCTATGCTTTGTGTTAGATTATATATATATATATTA
65 GATTCAATTCTTGGATTTCTTGCTATGCTTTGTGTTAGATTATATATATATATATTA
* * * *
1506829 ATTCTTTTACTTGAACCCAAATTTAAGTTATGAAAAAAGGGAAAAAAAAACTATTGCATGTTTAC
1 ATTCTTTGACTTGAACCCAAATTTGAGTTATGAAAAAAGGGAAAAAAATACTATTGCATGTTTAG
1506894 ATTCAATTCTTGGATTTCTTGCTATGCTTTGTGTTAGATTATATGTATATATATATTA
66 ATTCAATTCTTGGATTTCTTGCTATGCTTTGTGTTAGATTATA--TATATATATATTA
*
1506952 ATTCTTTGACTTGAACCCAAATTTGAGTTATGAAAAAGGGGAAAAAAATACTATTGCATGTTTAG
1 ATTCTTTGACTTGAACCCAAATTTGAGTTATGAAAAAAGGGAAAAAAATACTATTGCATGTTTAG
1507017 ATTCAATTCTTGGATTTCTTGCTATGCTTTGTGTTAGA-T-TATATATATATA-T-
66 ATTCAATTCTTGGATTTCTTGCTATGCTTTGTGTTAGATTATATATATATATATTA
1507069 ATTCTTTGACTTGAACCCAAATTTGAGTTATGAAAAAAGGGAAAAAAATTACTATTGCATGTTTA
1 ATTCTTTGACTTGAACCCAAATTTGAGTTATGAAAAAAGGGAAAAAAA-TACTATTGCATGTTTA
1507134 GATTCAATTCTTGGATTTCTTGCTATGCTTTGTGTTAGATTATATATATATATATTA
65 GATTCAATTCTTGGATTTCTTGCTATGCTTTGTGTTAGATTATATATATATATATTA
* * * *
1507191 ATTCTTTTACTTGAACCCAAATTTAAGTTATGAAAAAAGGGAAAAAAAAACTATTGCATGTTTAC
1 ATTCTTTGACTTGAACCCAAATTTGAGTTATGAAAAAAGGGAAAAAAATACTATTGCATGTTTAG
1507256 ATTCAATTCTTGGATTTCTTGCTATGCTTTGTGTTAGATTATATGTATATATATATTA
66 ATTCAATTCTTGGATTTCTTGCTATGCTTTGTGTTAGATTATA--TATATATATATTA
1507314 ATTCTTTGACTTGAACCCCAAATTTGAGTTATGAAAAAAGGGAAAAAAAATACTATTGCATGTTT
1 ATTCTTTGACTTGAA-CCCAAATTTGAGTTATGAAAAAAGGG-AAAAAAATACTATTGCATGTTT
*
1507379 AGATTCAATTCTTGGATTTCTTGCTACGCTTTGTGTTAGAT
64 AGATTCAATTCTTGGATTTCTTGCTATGCTTTGTGTTAGAT
1507420 CACACACACA
Statistics
Matches: 904, Mismatches: 26, Indels: 34
0.94 0.03 0.04
Matches are distributed among these distances:
117 167 0.18
118 162 0.18
119 11 0.01
120 12 0.01
121 123 0.14
122 129 0.14
123 163 0.18
124 77 0.09
125 60 0.07
ACGTcount: A:0.34, C:0.10, G:0.15, T:0.41
Consensus pattern (121 bp):
ATTCTTTGACTTGAACCCAAATTTGAGTTATGAAAAAAGGGAAAAAAATACTATTGCATGTTTAG
ATTCAATTCTTGGATTTCTTGCTATGCTTTGTGTTAGATTATATATATATATATTA
Found at i:1520946 original size:2 final size:2
Alignment explanation
Indices: 1520939--1520978 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
1520929 ACATACATAC
1520939 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1520979 TATTGGTCAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1535503 original size:3 final size:3
Alignment explanation
Indices: 1535495--1535536 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
1535485 GCAACACACA
1535495 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1535537 TATTATTATT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:1535952 original size:54 final size:51
Alignment explanation
Indices: 1535888--1536139 Score: 208
Period size: 45 Copynumber: 5.0 Consensus size: 51
1535878 CAAGGTGAGG
* *
1535888 AAGGTGACCAGGGCTATCAGGGCTTTGTGCTACCAAAGTTTACTCCAAACGGTC
1 AAGGTGACCA-GGC-ACCAGGGCTTTGTGCTGCCAAAGTTTAC-CCAAACGGTC
* * *
1535942 AAGGT------G-ACCAGGGCTTTATGCCGCCAGAGTTTACCTCAAACGGTC
1 AAGGTGACCAGGCACCAGGGCTTTGTGCTGCCAAAGTTTACC-CAAACGGTC
* *
1535987 AAGGTGACCATGGTGACCAGGGCTTTGTGCTGCCAAACTTTACCCCAAACGGTC
1 AAGGTGACCA-GG-CACCAGGGCTTTGTGCTGCCAAAGTTTA-CCCAAACGGTC
*
1536041 -AGG-G--C--G-ACCAGGGCTTTGTGCTGCCAATGTTTAACCCAAACGGTC
1 AAGGTGACCAGGCACCAGGGCTTTGTGCTGCCAAAGTTT-ACCCAAACGGTC
* * *
1536086 AAGGTGACCAGGGCGACCAGGGCTTTGTGCTACCAAGGTATACCCCAAACGGTC
1 AAGGTGACCA-GGC-ACCAGGGCTTTGTGCTGCCAAAGTTTA-CCCAAACGGTC
1536140 TTGTGATCAC
Statistics
Matches: 162, Mismatches: 14, Indels: 44
0.74 0.06 0.20
Matches are distributed among these distances:
44 1 0.01
45 72 0.44
46 4 0.02
47 3 0.02
49 1 0.01
50 1 0.01
52 3 0.02
53 4 0.02
54 71 0.44
55 2 0.01
ACGTcount: A:0.25, C:0.27, G:0.27, T:0.21
Consensus pattern (51 bp):
AAGGTGACCAGGCACCAGGGCTTTGTGCTGCCAAAGTTTACCCAAACGGTC
Found at i:1536073 original size:99 final size:99
Alignment explanation
Indices: 1535888--1536139 Score: 348
Period size: 99 Copynumber: 2.5 Consensus size: 99
1535878 CAAGGTGAGG
* * *
1535888 AAGGTGACCAGGGCT-ATCAGGGCTTTGTGCTACCAAAGTTTACTCCAAACGGTCAAGGTGACCA
1 AAGGTGACCAGGG-TGACCAGGGCTTTGTGCTACCAAAGTTTACCCCAAACGGTCAAGGCGACCA
1535952 GGGCTTTATGCCGCCAGAGTTT-ACCTCAAACGGTC
65 GGGCTTTATGCCGCCAGAGTTTAACC-CAAACGGTC
* * * *
1535987 AAGGTGACCATGGTGACCAGGGCTTTGTGCTGCCAAACTTTACCCCAAACGGTCAGGGCGACCAG
1 AAGGTGACCAGGGTGACCAGGGCTTTGTGCTACCAAAGTTTACCCCAAACGGTCAAGGCGACCAG
* *
1536052 GGCTTTGTGCTGCCA-ATGTTTAACCCAAACGGTC
66 GGCTTTATGCCGCCAGA-GTTTAACCCAAACGGTC
* * *
1536086 AAGGTGACCAGGGCGACCAGGGCTTTGTGCTACCAAGGTATACCCCAAACGGTC
1 AAGGTGACCAGGGTGACCAGGGCTTTGTGCTACCAAAGTTTACCCCAAACGGTC
1536140 TTGTGATCAC
Statistics
Matches: 135, Mismatches: 15, Indels: 6
0.87 0.10 0.04
Matches are distributed among these distances:
98 2 0.01
99 130 0.96
100 3 0.02
ACGTcount: A:0.25, C:0.27, G:0.27, T:0.21
Consensus pattern (99 bp):
AAGGTGACCAGGGTGACCAGGGCTTTGTGCTACCAAAGTTTACCCCAAACGGTCAAGGCGACCAG
GGCTTTATGCCGCCAGAGTTTAACCCAAACGGTC
Found at i:1537537 original size:51 final size:51
Alignment explanation
Indices: 1537378--1537584 Score: 290
Period size: 51 Copynumber: 4.0 Consensus size: 51
1537368 CAAACTTGTC
** * *
1537378 CAATGCCTCCTTACGTTGTATATCCTGATTCAACATCTGTACTTCCAAGGT
1 CAATGCCTCCTTACAATGCATATCCTGATTCAACATCTGGACTTCCAAGGT
* *
1537429 CGATGCCTCCTTACAATGCATATGCTGCTGATTCAACATCTGTACTTCTC-AGGT
1 CAATGCCTCCTTACAATGCATAT-C--CTGATTCAACATCTGGACTTC-CAAGGT
* *
1537483 CAATGCCTCCTTACAATGCATATTCTGATTCAACATCTGGACTTCCAAGTT
1 CAATGCCTCCTTACAATGCATATCCTGATTCAACATCTGGACTTCCAAGGT
*
1537534 CAATGCCTCCTTACAATGCATATCCTGATTCACCATCTGGACTTCCAAGGT
1 CAATGCCTCCTTACAATGCATATCCTGATTCAACATCTGGACTTCCAAGGT
1537585 TTCCTGAATC
Statistics
Matches: 140, Mismatches: 11, Indels: 10
0.87 0.07 0.06
Matches are distributed among these distances:
50 1 0.01
51 90 0.64
52 1 0.01
54 47 0.34
55 1 0.01
ACGTcount: A:0.25, C:0.29, G:0.14, T:0.33
Consensus pattern (51 bp):
CAATGCCTCCTTACAATGCATATCCTGATTCAACATCTGGACTTCCAAGGT
Found at i:1543524 original size:24 final size:23
Alignment explanation
Indices: 1543467--1543512 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
1543457 ATACAATAAC
**
1543467 CTTATCCTAATTTAATTAGGAAT
1 CTTATCCTAATAGAATTAGGAAT
1543490 CTTATCCTAATAGAATTAGGAAT
1 CTTATCCTAATAGAATTAGGAAT
1543513 TGTTATTCTA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.37, C:0.13, G:0.11, T:0.39
Consensus pattern (23 bp):
CTTATCCTAATAGAATTAGGAAT
Found at i:1546998 original size:23 final size:23
Alignment explanation
Indices: 1546972--1547017 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
1546962 ATACAATAAC
*
1546972 CTTATCCTAATATAATTAGGAAT
1 CTTATCCTAATAGAATTAGGAAT
1546995 CTTATCCTAATAGAATTAGGAAT
1 CTTATCCTAATAGAATTAGGAAT
1547018 TGTTATTCTA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.39, C:0.13, G:0.11, T:0.37
Consensus pattern (23 bp):
CTTATCCTAATAGAATTAGGAAT
Found at i:1555707 original size:23 final size:23
Alignment explanation
Indices: 1555669--1555727 Score: 73
Period size: 23 Copynumber: 2.5 Consensus size: 23
1555659 GCGTTCTTTT
*
1555669 TATTTTCAATAGATGTGTCTGTAC
1 TATTTT-AACAGATGTGTCTGTAC
**
1555693 TATTTTAACAGATGTGTCTGTTG
1 TATTTTAACAGATGTGTCTGTAC
*
1555716 TATTTCAACAGA
1 TATTTTAACAGA
1555728 CGTATCTATA
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
23 25 0.81
24 6 0.19
ACGTcount: A:0.27, C:0.12, G:0.17, T:0.44
Consensus pattern (23 bp):
TATTTTAACAGATGTGTCTGTAC
Found at i:1556305 original size:24 final size:23
Alignment explanation
Indices: 1556273--1556320 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 23
1556263 GCACTAAATG
1556273 TTCTAGAATGAGGCTATTTGAATA
1 TTCTAGAATGAGGCTATTT-AATA
1556297 TTCTAGAATGAGGCTATTTAATA
1 TTCTAGAATGAGGCTATTTAATA
1556320 T
1 T
1556321 AAAATTCAGT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 5 0.21
24 19 0.79
ACGTcount: A:0.33, C:0.08, G:0.19, T:0.40
Consensus pattern (23 bp):
TTCTAGAATGAGGCTATTTAATA
Found at i:1560559 original size:15 final size:15
Alignment explanation
Indices: 1560539--1560570 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
1560529 AGTTGTTGCC
1560539 TACTATGGGGATTCG
1 TACTATGGGGATTCG
1560554 TACTATGGGGATTCG
1 TACTATGGGGATTCG
1560569 TA
1 TA
1560571 GACAATGACT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.22, C:0.12, G:0.31, T:0.34
Consensus pattern (15 bp):
TACTATGGGGATTCG
Found at i:1560734 original size:23 final size:23
Alignment explanation
Indices: 1560703--1560811 Score: 177
Period size: 23 Copynumber: 4.7 Consensus size: 23
1560693 TTTTTTTTAT
*
1560703 TTTCAACAGATGTGTCTGTACTGT-
1 TTTCAACAGATGTATCTGT--TGTA
1560727 TTT-AACAGATGTATCTGTTGTA
1 TTTCAACAGATGTATCTGTTGTA
1560749 TTTCAACAGATGTATCTGTTGTA
1 TTTCAACAGATGTATCTGTTGTA
1560772 TTTCAACAGATGTATCTGTTGTA
1 TTTCAACAGATGTATCTGTTGTA
1560795 TTTCAACAGATGTATCT
1 TTTCAACAGATGTATCT
1560812 ATAACTTTCA
Statistics
Matches: 82, Mismatches: 1, Indels: 5
0.93 0.01 0.06
Matches are distributed among these distances:
21 3 0.04
22 3 0.04
23 73 0.89
24 3 0.04
ACGTcount: A:0.26, C:0.14, G:0.17, T:0.43
Consensus pattern (23 bp):
TTTCAACAGATGTATCTGTTGTA
Found at i:1565849 original size:6 final size:6
Alignment explanation
Indices: 1565838--1565870 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
1565828 GTAAGCACTT
*
1565838 GACCTC GACCTC GACCTT GACCTC GACCTC GAC
1 GACCTC GACCTC GACCTC GACCTC GACCTC GAC
1565871 TTTTGACAGT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.18, C:0.45, G:0.18, T:0.18
Consensus pattern (6 bp):
GACCTC
Found at i:1565858 original size:18 final size:18
Alignment explanation
Indices: 1565835--1565870 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
1565825 GATGTAAGCA
1565835 CTTGACCTCGACCTCGAC
1 CTTGACCTCGACCTCGAC
1565853 CTTGACCTCGACCTCGAC
1 CTTGACCTCGACCTCGAC
1565871 TTTTGACAGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.17, C:0.44, G:0.17, T:0.22
Consensus pattern (18 bp):
CTTGACCTCGACCTCGAC
Found at i:1570511 original size:42 final size:42
Alignment explanation
Indices: 1570452--1570532 Score: 135
Period size: 42 Copynumber: 1.9 Consensus size: 42
1570442 AAACTTGGAC
*
1570452 ATAATCATCAGTCTTCTTCCAAACGTGTATATTCTAGAAAAA
1 ATAATCATCAGTCTTCTTCCAAACGTATATATTCTAGAAAAA
**
1570494 ATAATCATCAGTCTTCTTCCAAATTTATATATTCTAGAA
1 ATAATCATCAGTCTTCTTCCAAACGTATATATTCTAGAA
1570533 GTGGAAAGTG
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 36 1.00
ACGTcount: A:0.37, C:0.19, G:0.07, T:0.37
Consensus pattern (42 bp):
ATAATCATCAGTCTTCTTCCAAACGTATATATTCTAGAAAAA
Found at i:1589994 original size:31 final size:31
Alignment explanation
Indices: 1589959--1590017 Score: 118
Period size: 31 Copynumber: 1.9 Consensus size: 31
1589949 TAGGTTTATT
1589959 TGGTTTGTGTTTCTTAGTAGAGACTAATCTC
1 TGGTTTGTGTTTCTTAGTAGAGACTAATCTC
1589990 TGGTTTGTGTTTCTTAGTAGAGACTAAT
1 TGGTTTGTGTTTCTTAGTAGAGACTAAT
1590018 TTCTTTCTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.20, C:0.10, G:0.24, T:0.46
Consensus pattern (31 bp):
TGGTTTGTGTTTCTTAGTAGAGACTAATCTC
Found at i:1594221 original size:24 final size:25
Alignment explanation
Indices: 1594177--1594250 Score: 73
Period size: 24 Copynumber: 3.0 Consensus size: 25
1594167 AAAATATTAT
* *
1594177 TGTTACACGTTATA-TGCAAAAATA-
1 TGTTACACGTTATAGT-TAAAAAAAG
1594201 TGTTACACGTTATAGTTAAAAAAAG
1 TGTTACACGTTATAGTTAAAAAAAG
*
1594226 TTGTTACATGTTAT-GTTGAAAAAAA
1 -TGTTACACGTTATAGTT-AAAAAAA
1594251 AAATATTATT
Statistics
Matches: 43, Mismatches: 3, Indels: 6
0.83 0.06 0.12
Matches are distributed among these distances:
24 20 0.47
25 4 0.09
26 19 0.44
ACGTcount: A:0.42, C:0.08, G:0.15, T:0.35
Consensus pattern (25 bp):
TGTTACACGTTATAGTTAAAAAAAG
Found at i:1594230 original size:26 final size:25
Alignment explanation
Indices: 1594175--1594250 Score: 77
Period size: 26 Copynumber: 3.0 Consensus size: 25
1594165 AAAAAATATT
**
1594175 ATTGTTACACGTTATA--TGCAAAA
1 ATTGTTACACGTTATAGTTAAAAAA
1594198 ATATGTTACACGTTATAGTTAAAAAA
1 AT-TGTTACACGTTATAGTTAAAAAA
*
1594224 AGTTGTTACATGTTAT-GTTGAAAAAA
1 A-TTGTTACACGTTATAGTT-AAAAAA
1594250 A
1 A
1594251 AAATATTATT
Statistics
Matches: 45, Mismatches: 3, Indels: 7
0.82 0.05 0.13
Matches are distributed among these distances:
23 2 0.04
24 14 0.31
25 3 0.07
26 25 0.56
27 1 0.02
ACGTcount: A:0.42, C:0.08, G:0.14, T:0.36
Consensus pattern (25 bp):
ATTGTTACACGTTATAGTTAAAAAA
Found at i:1594264 original size:83 final size:80
Alignment explanation
Indices: 1594163--1594457 Score: 317
Period size: 80 Copynumber: 3.6 Consensus size: 80
1594153 ACGCCATGTT
* * * * *
1594163 AAAAAAAATATTATTGTTACACGTTATATGCAAAAATATGTTACACGTTATAGTTAAAAAAAGTT
1 AAAAAAAATATTATTGTTACACGTCATATACAAAAATATATTACACGTCATAATTAAAAAAAGTT
*
1594228 GTTACATGTTATGTTGAA
66 GTTACATGTCAT-TT--A
* * * * * * *
1594246 AAAAAAAATATTATTGTTACACGTCATGTATAAAAACATGTTATACATCATAATTAAAAAATGTT
1 AAAAAAAATATTATTGTTACACGTCATATACAAAAATATATTACACGTCATAATTAAAAAAAGTT
1594311 GTTACATGTCATATTA
66 GTTACATGTCAT-TTA
* * * *
1594327 AAAAAAAA-ATTGTTGTTACACGTCATGTACAAAAATATATTACATGGT-ATAATTAAAAAAGGT
1 AAAAAAAATATTATTGTTACACGTCATATACAAAAATATATTACA-CGTCATAATTAAAAAAAGT
*
1594390 TGTTACACGTCATTCTA
65 TGTTACATGTCATT-TA
* * *
1594407 AAAAAAAATATTGTTGTTACAC-ACTATATACAAAAGTATATTACACGTCAT
1 AAAAAAAATATTATTGTTACACGTC-ATATACAAAAATATATTACACGTCAT
1594458 GTTGAAAAAA
Statistics
Matches: 182, Mismatches: 25, Indels: 12
0.83 0.11 0.05
Matches are distributed among these distances:
79 1 0.01
80 70 0.38
81 43 0.24
83 68 0.37
ACGTcount: A:0.45, C:0.10, G:0.11, T:0.34
Consensus pattern (80 bp):
AAAAAAAATATTATTGTTACACGTCATATACAAAAATATATTACACGTCATAATTAAAAAAAGTT
GTTACATGTCATTTA
Found at i:1594316 original size:24 final size:23
Alignment explanation
Indices: 1594276--1594331 Score: 60
Period size: 24 Copynumber: 2.3 Consensus size: 23
1594266 ACGTCATGTA
1594276 TAAAAACATGTTATACA-TCATAAT
1 TAAAAA-ATGTTATACAGTCAT-AT
*
1594300 TAAAAAATGTTGTTACATGTCATAT
1 TAAAAAATGTT-ATACA-GTCATAT
1594325 TAAAAAA
1 TAAAAAA
1594332 AAAATTGTTG
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
23 5 0.18
24 10 0.36
25 9 0.32
26 4 0.14
ACGTcount: A:0.50, C:0.09, G:0.07, T:0.34
Consensus pattern (23 bp):
TAAAAAATGTTATACAGTCATAT
Found at i:1594332 original size:26 final size:25
Alignment explanation
Indices: 1594259--1594332 Score: 64
Period size: 26 Copynumber: 2.9 Consensus size: 25
1594249 AAAAATATTA
* *
1594259 TTGTTACACGTCATGTATAAAAACATG
1 TTGTTACA-GTCATAT-TAAAAAAATG
*
1594286 TT-ATACA-TCATAATT-AAAAAATG
1 TTGTTACAGTCAT-ATTAAAAAAATG
1594309 TTGTTACATGTCATATTAAAAAAA
1 TTGTTACA-GTCATATTAAAAAAA
1594333 AAATTGTTGT
Statistics
Matches: 38, Mismatches: 4, Indels: 11
0.72 0.08 0.21
Matches are distributed among these distances:
23 9 0.24
24 9 0.24
25 4 0.11
26 14 0.37
27 2 0.05
ACGTcount: A:0.45, C:0.11, G:0.09, T:0.35
Consensus pattern (25 bp):
TTGTTACAGTCATATTAAAAAAATG
Found at i:1594361 original size:30 final size:29
Alignment explanation
Indices: 1594301--1594361 Score: 79
Period size: 30 Copynumber: 2.1 Consensus size: 29
1594291 CATCATAATT
* *
1594301 AAAAAATGTTGTTACATGTCATATTAAAA
1 AAAAAATGTTGTTACACGTCATAGTAAAA
*
1594330 AAAAAATTGTTGTTACACGTCAT-GTACAA
1 AAAAAA-TGTTGTTACACGTCATAGTAAAA
1594359 AAA
1 AAA
1594362 TATATTACAT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
29 13 0.46
30 15 0.54
ACGTcount: A:0.48, C:0.10, G:0.11, T:0.31
Consensus pattern (29 bp):
AAAAAATGTTGTTACACGTCATAGTAAAA
Found at i:1594481 original size:30 final size:30
Alignment explanation
Indices: 1594445--1594528 Score: 84
Period size: 30 Copynumber: 2.8 Consensus size: 30
1594435 TACAAAAGTA
1594445 TATTACACGTCATGTTGAAAAAAATGTTAT
1 TATTACACGTCATGTTGAAAAAAATGTTAT
* * * *
1594475 TATTACACGCCATATTAGAAAAACATTGTTGT
1 TATTACACGTCATGTT-GAAAAA-AATGTTAT
*
1594507 TA-TACA--TCATGTTTAAAAAAAT
1 TATTACACGTCATGTTGAAAAAAAT
1594529 TTGATTACAC
Statistics
Matches: 44, Mismatches: 8, Indels: 7
0.75 0.14 0.12
Matches are distributed among these distances:
27 2 0.05
28 5 0.11
29 5 0.11
30 14 0.32
31 10 0.23
32 8 0.18
ACGTcount: A:0.42, C:0.12, G:0.11, T:0.36
Consensus pattern (30 bp):
TATTACACGTCATGTTGAAAAAAATGTTAT
Found at i:1601083 original size:12 final size:12
Alignment explanation
Indices: 1601066--1601093 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
1601056 GCATATTAAA
1601066 AAAAAAAAAAAG
1 AAAAAAAAAAAG
1601078 AAAAAAAAAAAG
1 AAAAAAAAAAAG
1601090 AAAA
1 AAAA
1601094 GGAATGGGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.93, C:0.00, G:0.07, T:0.00
Consensus pattern (12 bp):
AAAAAAAAAAAG
Found at i:1612223 original size:37 final size:37
Alignment explanation
Indices: 1612181--1612256 Score: 134
Period size: 37 Copynumber: 2.1 Consensus size: 37
1612171 ATTCATTTTC
1612181 AAAAATACAAATTAAACTTTCAAACAATCAAAAAGCA
1 AAAAATACAAATTAAACTTTCAAACAATCAAAAAGCA
**
1612218 AAAAATACAAATTAAACTTTCAAACAATTGAAAAGCA
1 AAAAATACAAATTAAACTTTCAAACAATCAAAAAGCA
1612255 AA
1 AA
1612257 TCCAGGTGAT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.62, C:0.14, G:0.04, T:0.20
Consensus pattern (37 bp):
AAAAATACAAATTAAACTTTCAAACAATCAAAAAGCA
Found at i:1622497 original size:92 final size:92
Alignment explanation
Indices: 1622379--1622595 Score: 258
Period size: 92 Copynumber: 2.4 Consensus size: 92
1622369 CTCCCATATC
* * * * *
1622379 ATTTTTCAGTGCTGAATGTAACTAATGTAAATTGGTATATATCAGCTAG-CTAAAATA-AGGTTT
1 ATTTTTCAGTGTTAAATGTAATTAATGTAAAGTGGTATATATCAGCTAGCCAAAAATAGA-GTTT
1622442 TGAGAGAGACTGAGTTACAACATATTCT
65 TGAGAGAGACTGAGTTACAACATATTCT
* * *
1622470 ATTTTTCAAGTGTTAAATGTAATTAATGTTAAGTGGTGTATATCAGTTAGCCAAAAATAGAGTTT
1 ATTTTTC-AGTGTTAAATGTAATTAATGTAAAGTGGTATATATCAGCTAGCCAAAAATAGAGTTT
* * * *
1622535 TGATAGAGATTGAGTTACTACATATTTT
65 TGAGAGAGACTGAGTTACAACATATTCT
* * * *
1622563 ATTTTTTAGCGTTAAATGCAATTAATGAAAAGT
1 ATTTTTCAGTGTTAAATGTAATTAATGTAAAGT
1622596 TATGCAGATC
Statistics
Matches: 106, Mismatches: 17, Indels: 5
0.83 0.13 0.04
Matches are distributed among these distances:
91 7 0.07
92 57 0.54
93 41 0.39
94 1 0.01
ACGTcount: A:0.35, C:0.08, G:0.18, T:0.38
Consensus pattern (92 bp):
ATTTTTCAGTGTTAAATGTAATTAATGTAAAGTGGTATATATCAGCTAGCCAAAAATAGAGTTTT
GAGAGAGACTGAGTTACAACATATTCT
Found at i:1622678 original size:12 final size:13
Alignment explanation
Indices: 1622661--1622691 Score: 55
Period size: 12 Copynumber: 2.5 Consensus size: 13
1622651 TCTAATATAA
1622661 GTTTTAAGA-TTT
1 GTTTTAAGATTTT
1622673 GTTTTAAGATTTT
1 GTTTTAAGATTTT
1622686 GTTTTA
1 GTTTTA
1622692 TCGTGAAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 9 0.50
13 9 0.50
ACGTcount: A:0.23, C:0.00, G:0.16, T:0.61
Consensus pattern (13 bp):
GTTTTAAGATTTT
Found at i:1624862 original size:23 final size:23
Alignment explanation
Indices: 1624832--1624882 Score: 93
Period size: 23 Copynumber: 2.2 Consensus size: 23
1624822 CCAGTTCTAC
1624832 AAGGACCTAGTCAATCAAAGGGG
1 AAGGACCTAGTCAATCAAAGGGG
1624855 AAGGACCTAGTCAATCAAAGGGG
1 AAGGACCTAGTCAATCAAAGGGG
*
1624878 GAGGA
1 AAGGA
1624883 GAGAAGAAAC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.39, C:0.16, G:0.33, T:0.12
Consensus pattern (23 bp):
AAGGACCTAGTCAATCAAAGGGG
Found at i:1635270 original size:13 final size:12
Alignment explanation
Indices: 1635252--1635281 Score: 51
Period size: 13 Copynumber: 2.4 Consensus size: 12
1635242 AGTAGTAATT
1635252 ATAAATTCGTAA
1 ATAAATTCGTAA
1635264 CATAAATTCGTAA
1 -ATAAATTCGTAA
1635277 ATAAA
1 ATAAA
1635282 CAAACAAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 5 0.29
13 12 0.71
ACGTcount: A:0.53, C:0.10, G:0.07, T:0.30
Consensus pattern (12 bp):
ATAAATTCGTAA
Found at i:1649574 original size:137 final size:136
Alignment explanation
Indices: 1649409--1649681 Score: 521
Period size: 137 Copynumber: 2.0 Consensus size: 136
1649399 TTTTTTTAAA
1649409 TAATAATATGGTCAAAATAGAAGATTAAATTAAAAAAAAAAAACTAAGTTTTTG-CAAACCGAAG
1 TAATAATATGGTCAAAATAGAAGATTAAATTAAAAAAAAAAAACT-AGTTTTTGTCAAACCGAAG
1649473 GAAATTTGGAGGAAGCTAAGCTAACATGAAACATGTTCCAAGTATTATTATTTTATACCCATTAG
65 GAAATTTGGAGGAAGCTAAGCTAACATGAAACATGTTCCAAGTATTATTATTTTATACCCATTAG
1649538 TGATCAT
130 TGATCAT
1649545 NTAATAATATGGTCAAAATAGAAGATTAAATTAAAAAAAAAAAACTAGTTTTTGTCAAACCGAAG
1 -TAATAATATGGTCAAAATAGAAGATTAAATTAAAAAAAAAAAACTAGTTTTTGTCAAACCGAAG
1649610 GAAATTTGGAGGAAGCTAAGCTAACATGAAACATGTTCCAAGTATTATTATTTTATACCCATTAG
65 GAAATTTGGAGGAAGCTAAGCTAACATGAAACATGTTCCAAGTATTATTATTTTATACCCATTAG
1649675 TGATCAT
130 TGATCAT
1649682 GATTGTAGTG
Statistics
Matches: 135, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
136 8 0.06
137 127 0.94
ACGTcount: A:0.44, C:0.11, G:0.15, T:0.30
Consensus pattern (136 bp):
TAATAATATGGTCAAAATAGAAGATTAAATTAAAAAAAAAAAACTAGTTTTTGTCAAACCGAAGG
AAATTTGGAGGAAGCTAAGCTAACATGAAACATGTTCCAAGTATTATTATTTTATACCCATTAGT
GATCAT
Found at i:1649960 original size:180 final size:174
Alignment explanation
Indices: 1649546--1650004 Score: 519
Period size: 180 Copynumber: 2.6 Consensus size: 174
1649536 AGTGATCATN
* * * *
1649546 TAATAATATGGTCAAAATAGAAGATTAAATTAAAAAAAAAAAACTAGTTTTTGTCAAACCGAAGG
1 TAAT-ATATGGTCAAAATAGAAGATTAAATT--AAAAAGAATACTAGTTTTTGTGAAACCAAAGG
* ** *
1649611 AAATTTGGAGGAAGCTAAGCTAACATGAAACATGTTCCAAGTATTATTATTTTATACCCATTAGT
63 AAATTTGGA-G-A---AAGCTAACATGAAACATCTTCCAAGTACGATTATTTTATAACCATTAGT
* *
1649676 GATCATGATTGTAGTGCGGGCTACTCCCATTTCTTTTTTTTTTTTTTAAAGA
123 GATCATGATTGTAGTGCGGGCTACTCCCATTTATTTATTTTTTTTTTAAAGA
* * * *
1649728 T-A-ATATGGCCAAAATAGAAGATTAAATTAAAAAGAATACAAGCTCTTGTGAAACCAAAAGGAA
1 TAATATATGGTCAAAATAGAAGATTAAATTAAAAAGAATACTAGTTTTTGTGAAACC-AAAGGAA
* * *
1649791 ATTTGGAGAAAGCTAACATGAAACATTTTCCAAGTACGATTATTTTATATACCGTTAGTGGTCAT
65 ATTTGGAGAAAGCTAACATGAAACATCTTCCAAGTACGATTATTTTATA-ACCATTAGTGATCAT
* *
1649856 GATTGTAGTGTGGGCTGCTCCCACTTTATATATATTTTTTTTTTAAA-A
129 GATTGTAGTGCGGGCTACTCCCA-TTTAT-T-TATTTTTTTTTTAAAGA
* * * *
1649904 TCAATATTATGGTCAACATAGAATATTAAATTAAAAAGAATACTAGTTTTTGTGAAACTGAGAGG
1 T-AATA-TATGGTCAAAATAGAAGATTAAATTAAAAAGAATACTAGTTTTTGTGAAAC-CAAAGG
* * *
1649969 AAATTTGGAGGAAGCTAACACGAAACGTCTTCCAAG
63 AAATTTGGAGAAAGCTAACATGAAACATCTTCCAAG
1650005 CTACTCCCAC
Statistics
Matches: 237, Mismatches: 30, Indels: 22
0.82 0.10 0.08
Matches are distributed among these distances:
173 37 0.16
174 33 0.14
175 4 0.02
176 4 0.02
177 36 0.15
178 14 0.06
179 26 0.11
180 81 0.34
181 1 0.00
182 1 0.00
ACGTcount: A:0.38, C:0.12, G:0.17, T:0.33
Consensus pattern (174 bp):
TAATATATGGTCAAAATAGAAGATTAAATTAAAAAGAATACTAGTTTTTGTGAAACCAAAGGAAA
TTTGGAGAAAGCTAACATGAAACATCTTCCAAGTACGATTATTTTATAACCATTAGTGATCATGA
TTGTAGTGCGGGCTACTCCCATTTATTTATTTTTTTTTTAAAGA
Found at i:1650237 original size:36 final size:36
Alignment explanation
Indices: 1650190--1650284 Score: 181
Period size: 36 Copynumber: 2.6 Consensus size: 36
1650180 GTATATATTT
*
1650190 TTAAAAAAAAATCAATAATATGGCCGACTTAGAAGA
1 TTAAATAAAAATCAATAATATGGCCGACTTAGAAGA
1650226 TTAAATAAAAATCAATAATATGGCCGACTTAGAAGA
1 TTAAATAAAAATCAATAATATGGCCGACTTAGAAGA
1650262 TTAAATAAAAATCAATAATATGG
1 TTAAATAAAAATCAATAATATGG
1650285 TCAAAAATAT
Statistics
Matches: 58, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
36 58 1.00
ACGTcount: A:0.53, C:0.09, G:0.13, T:0.25
Consensus pattern (36 bp):
TTAAATAAAAATCAATAATATGGCCGACTTAGAAGA
Found at i:1656808 original size:2 final size:2
Alignment explanation
Indices: 1656801--1656846 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
1656791 AGTCAAAACA
1656801 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1656843 AT AT
1 AT AT
1656847 CAGGGCTAAC
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1671274 original size:21 final size:21
Alignment explanation
Indices: 1671235--1671275 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
1671225 TTTTATTATA
* *
1671235 TTTAATTAAATTTATAAATTT
1 TTTAATTAAATTAAAAAATTT
*
1671256 TTTATTTAAATTAAAAAATT
1 TTTAATTAAATTAAAAAATT
1671276 ATTATAACTA
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:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (21 bp):
TTTAATTAAATTAAAAAATTT
Found at i:1673967 original size:15 final size:16
Alignment explanation
Indices: 1673930--1673969 Score: 57
Period size: 17 Copynumber: 2.6 Consensus size: 16
1673920 ATATAATGGC
1673930 TAAAT-ATATAAATAG
1 TAAATAATATAAATAG
1673945 TTAAATAATATAAATAG
1 -TAAATAATATAAATAG
1673962 -AAATAATA
1 TAAATAATA
1673970 AGATAAAAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 8 0.35
16 5 0.22
17 10 0.43
ACGTcount: A:0.62, C:0.00, G:0.05, T:0.33
Consensus pattern (16 bp):
TAAATAATATAAATAG
Found at i:1673975 original size:18 final size:17
Alignment explanation
Indices: 1673948--1673981 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
1673938 TAAATAGTTA
*
1673948 AATAATATAAATAGAAAT
1 AATAAGATAAA-AGAAAT
1673966 AATAAGATAAAAGAAA
1 AATAAGATAAAAGAAA
1673982 CCTTAATTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.71, C:0.00, G:0.09, T:0.21
Consensus pattern (17 bp):
AATAAGATAAAAGAAAT
Found at i:1674280 original size:46 final size:50
Alignment explanation
Indices: 1674230--1674328 Score: 125
Period size: 50 Copynumber: 2.1 Consensus size: 50
1674220 ATTAATATTA
* *
1674230 AAATAAAAT-AT-TATTTTGAGA-GAACAATT-AAAAATATATAATAAAT
1 AAATAAAATCATAAATTTTGAAAGGAACAATTAAAAAATATATAATAAAT
** *
1674276 AAATAATTTCATAAATTTTGAAAGGAACTATTAAAAAATATATAATAAAT
1 AAATAAAATCATAAATTTTGAAAGGAACAATTAAAAAATATATAATAAAT
1674326 AAA
1 AAA
1674329 AACTTCTAAA
Statistics
Matches: 44, Mismatches: 5, Indels: 4
0.83 0.09 0.08
Matches are distributed among these distances:
46 7 0.16
47 2 0.05
48 8 0.18
49 7 0.16
50 20 0.45
ACGTcount: A:0.59, C:0.03, G:0.06, T:0.32
Consensus pattern (50 bp):
AAATAAAATCATAAATTTTGAAAGGAACAATTAAAAAATATATAATAAAT
Found at i:1674320 original size:50 final size:49
Alignment explanation
Indices: 1674242--1674350 Score: 141
Period size: 50 Copynumber: 2.2 Consensus size: 49
1674232 ATAAAATATT
* * *
1674242 ATTTTGAGA-GAACAATTAAAAATATATAATAAATAAATAATTTC-ATAA
1 ATTTTGAAAGGAACAATTAAAAATATATAATAAATAAA-AACTTCTAAAA
*
1674290 ATTTTGAAAGGAACTATTAAAAAATATATAATAAATAAAAACTTCTAAAA
1 ATTTTGAAAGGAACAATT-AAAAATATATAATAAATAAAAACTTCTAAAA
*
1674340 ATTTTAAAAGG
1 ATTTTGAAAGG
1674351 GTCGTTAATA
Statistics
Matches: 53, Mismatches: 5, Indels: 4
0.85 0.08 0.06
Matches are distributed among these distances:
48 8 0.15
49 12 0.23
50 33 0.62
ACGTcount: A:0.56, C:0.05, G:0.07, T:0.32
Consensus pattern (49 bp):
ATTTTGAAAGGAACAATTAAAAATATATAATAAATAAAAACTTCTAAAA
Found at i:1674365 original size:2 final size:2
Alignment explanation
Indices: 1674358--1674388 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1674348 AGGGTCGTTA
1674358 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1674389 ATAAATAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1674677 original size:2 final size:2
Alignment explanation
Indices: 1674670--1674703 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
1674660 TTATTTTAAG
1674670 TA TA TA TA 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
1674704 AAATAAAAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1675936 original size:29 final size:29
Alignment explanation
Indices: 1675875--1675948 Score: 80
Period size: 29 Copynumber: 2.6 Consensus size: 29
1675865 ATCATTAAGT
* *
1675875 ATAAAAATTTATTTAATTCAAAATAAGAT
1 ATAAAAATTTAATTAATTCAAAATAAGAA
1675904 ATAAAAATTTAATTAATT-ATAATATAA-AA
1 ATAAAAATTTAATTAATTCA-AA-ATAAGAA
* *
1675933 ATAAATACTTAATTAA
1 ATAAAAATTTAATTAA
1675949 ATTTTTTTGT
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
28 1 0.03
29 34 0.87
30 4 0.10
ACGTcount: A:0.58, C:0.03, G:0.01, T:0.38
Consensus pattern (29 bp):
ATAAAAATTTAATTAATTCAAAATAAGAA
Found at i:1680842 original size:25 final size:23
Alignment explanation
Indices: 1680776--1680848 Score: 74
Period size: 25 Copynumber: 3.0 Consensus size: 23
1680766 TAATTTTCAA
*
1680776 TTATTTTTTTATTTTCAATGTAAT
1 TTATTTTTTTAATTTCAAT-TAAT
* *
1680800 ATATTTTTAATAATTTTCAATTAAT
1 TTATTTTT-TTAA-TTTCAATTAAT
1680825 GGTTATTTTTTTAATTTCAATTAA
1 --TTATTTTTTTAATTTCAATTAA
1680849 AAGAGTCTCA
Statistics
Matches: 40, Mismatches: 5, Indels: 7
0.77 0.10 0.13
Matches are distributed among these distances:
24 7 0.17
25 16 0.40
26 10 0.25
27 7 0.17
ACGTcount: A:0.32, C:0.04, G:0.04, T:0.60
Consensus pattern (23 bp):
TTATTTTTTTAATTTCAATTAAT
Found at i:1682335 original size:2 final size:2
Alignment explanation
Indices: 1682328--1682374 Score: 55
Period size: 2 Copynumber: 24.5 Consensus size: 2
1682318 CCGTGGCGAT
1682328 AG AG AG AG AG AG AG AG -G AG -G AG A- AG NAG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG -AG AG AG AG AG AG AG
*
1682368 AG GG AG A
1 AG AG AG A
1682375 AGAAACACTG
Statistics
Matches: 39, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
1 3 0.08
2 34 0.87
3 2 0.05
ACGTcount: A:0.47, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1682362 original size:24 final size:23
Alignment explanation
Indices: 1682328--1682377 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 23
1682318 CCGTGGCGAT
1682328 AGAGAGAGAGAGAGAG-GAGGAGA
1 AGAGAGAGAGAGAGAGAG-GGAGA
1682351 AGNAGAGAGAGAGAGAGAGGGAGA
1 AG-AGAGAGAGAGAGAGAGGGAGA
1682375 AGA
1 AGA
1682378 AACACTGAGT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
23 3 0.12
24 21 0.84
25 1 0.04
ACGTcount: A:0.48, C:0.00, G:0.50, T:0.00
Consensus pattern (23 bp):
AGAGAGAGAGAGAGAGAGGGAGA
Found at i:1684422 original size:139 final size:138
Alignment explanation
Indices: 1684243--1684513 Score: 373
Period size: 139 Copynumber: 1.9 Consensus size: 138
1684233 TTGTGAGTTG
* *
1684243 ATGTCTCTTTATATCAGCCTGGATCAATGCTATCCCTTTCTGCCTACGGTAATCTTATCTAATGC
1 ATGTCTCTTTATATCAACCTGGATCAATGCTATCCCTTTCTGCCTAAGGTAATCTTATCTAATGC
*
1684308 TAGAATGAAAA-TCTTCACCAAAAGTAGAAGCTTAATCTTAGGAGGCTGTACGAATACATTCTAT
66 TAGAATGAAAAGTCTTCACCAAAAGTAGAAGCTTAATCTTAGGAGGCTGTACCAATACATTCTAT
1684372 GTGTTTTC
131 GTGTTTTC
* * * *
1684380 ATGTCTCTTTATTTCAATACCTGGATCCATGCTATCCCTTTCTGGCTAAGGTACTCTTATCTAAT
1 ATGTCTCTTTATATC-A-ACCTGGATCAATGCTATCCCTTTCTGCCTAAGGTAATCTTATCTAAT
* * *
1684445 GTTAGAATGAAAAGTGCTGTTCTTCATCATAAGTAGAAGCTTAATCTTAGGAGGCTGTACCAATA
64 GCTAGAATGAAAA-----G-TCTTCACCAAAAGTAGAAGCTTAATCTTAGGAGGCTGTACCAATA
1684510 CATT
123 CATT
1684514 TTAATGGATC
Statistics
Matches: 115, Mismatches: 10, Indels: 9
0.86 0.07 0.07
Matches are distributed among these distances:
137 14 0.12
138 1 0.01
139 54 0.47
146 46 0.40
ACGTcount: A:0.28, C:0.20, G:0.16, T:0.36
Consensus pattern (138 bp):
ATGTCTCTTTATATCAACCTGGATCAATGCTATCCCTTTCTGCCTAAGGTAATCTTATCTAATGC
TAGAATGAAAAGTCTTCACCAAAAGTAGAAGCTTAATCTTAGGAGGCTGTACCAATACATTCTAT
GTGTTTTC
Found at i:1700854 original size:22 final size:21
Alignment explanation
Indices: 1700829--1700893 Score: 61
Period size: 22 Copynumber: 3.3 Consensus size: 21
1700819 TTATGCTCAG
1700829 TTTAACTGAACTTTCTTTGCTT
1 TTTAACTGAA-TTTCTTTGCTT
*
1700851 TTTAA-TGAA-AT-TTTG---
1 TTTAACTGAATTTCTTTGCTT
1700866 TTTAACTGAATTTTCTTTGCTT
1 TTTAACTGAA-TTTCTTTGCTT
1700888 TTTAAC
1 TTTAAC
1700894 GAGATTTTAT
Statistics
Matches: 34, Mismatches: 2, Indels: 14
0.68 0.04 0.28
Matches are distributed among these distances:
15 5 0.15
16 4 0.12
18 5 0.15
19 5 0.15
21 4 0.12
22 11 0.32
ACGTcount: A:0.23, C:0.12, G:0.09, T:0.55
Consensus pattern (21 bp):
TTTAACTGAATTTCTTTGCTT
Found at i:1700870 original size:37 final size:37
Alignment explanation
Indices: 1700828--1700901 Score: 121
Period size: 37 Copynumber: 2.0 Consensus size: 37
1700818 TTTATGCTCA
*
1700828 GTTTAACTGAACTTTCTTTGCTTTTTAATGAAATTTT
1 GTTTAACTGAACTTTCTTTGCTTTTTAACGAAATTTT
* *
1700865 GTTTAACTGAATTTTCTTTGCTTTTTAACGAGATTTT
1 GTTTAACTGAACTTTCTTTGCTTTTTAACGAAATTTT
1700902 ATAATCAAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
37 34 1.00
ACGTcount: A:0.23, C:0.11, G:0.12, T:0.54
Consensus pattern (37 bp):
GTTTAACTGAACTTTCTTTGCTTTTTAACGAAATTTT
Found at i:1701087 original size:18 final size:17
Alignment explanation
Indices: 1701062--1701095 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
1701052 ATTTTAAAAA
1701062 ATATAAATTATATAAAT
1 ATATAAATTATATAAAT
*
1701079 ATATGAAATTATGTAAA
1 ATAT-AAATTATATAAA
1701096 ATTTAAAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.56, C:0.00, G:0.06, T:0.38
Consensus pattern (17 bp):
ATATAAATTATATAAAT
Found at i:1701107 original size:89 final size:89
Alignment explanation
Indices: 1700952--1701158 Score: 290
Period size: 89 Copynumber: 2.3 Consensus size: 89
1700942 AGATGAGATT
* * * * * *
1700952 TTATAGTCAAAATTTACAAAATATAAATTCTATAAAAAATATGAAATTATGTGAAATTTAATAAT
1 TTATAATCAAATTTTAAAAAATATAAATTATATAAAAAATATGAAATTATGTAAAATTTAAAAAT
** *
1701017 TGTCTTATATTCAAATAAAAATTAC
66 TGTCCCATATACAAAT-AAAATTAC
*
1701042 TTATAATCAAATTTTAAAAAATATAAATTATAT-AAATATATGAAATTATGTAAAATTTAAAAAT
1 TTATAATCAAATTTTAAAAAATATAAATTATATAAAAAATATGAAATTATGTAAAATTTAAAAAT
1701106 TGTCCCATATACAAATAAAATTAC
66 TGTCCCATATACAAATAAAATTAC
*
1701130 TTATAATAAAATTTTAAAAAATATGAAAT
1 TTATAATCAAATTTTAAAAAATAT-AAAT
1701159 AAAAATCGTC
Statistics
Matches: 105, Mismatches: 11, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
88 31 0.30
89 45 0.43
90 29 0.28
ACGTcount: A:0.53, C:0.06, G:0.04, T:0.37
Consensus pattern (89 bp):
TTATAATCAAATTTTAAAAAATATAAATTATATAAAAAATATGAAATTATGTAAAATTTAAAAAT
TGTCCCATATACAAATAAAATTAC
Found at i:1701272 original size:56 final size:54
Alignment explanation
Indices: 1701183--1701295 Score: 165
Period size: 56 Copynumber: 2.1 Consensus size: 54
1701173 TTTTACTAAA
* * *
1701183 TTTTCTTTGCTTTTTTTTATGTTCATTTTAAGATGAGATTTTATAATCAAATTT
1 TTTTATTTGCTTTTTTTTATGTTCATTTTAAGATGAAATTTTATAATCAAAATT
1701237 TTTTATTTGC-TTTTTTTATGCTCATCATTTTAAGATGAAATTTTATAATCAAAATT
1 TTTTATTTGCTTTTTTTTATG-T--TCATTTTAAGATGAAATTTTATAATCAAAATT
1701293 TTT
1 TTT
1701296 AAAAAAATAT
Statistics
Matches: 53, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
53 10 0.19
54 10 0.19
56 33 0.62
ACGTcount: A:0.27, C:0.08, G:0.08, T:0.58
Consensus pattern (54 bp):
TTTTATTTGCTTTTTTTTATGTTCATTTTAAGATGAAATTTTATAATCAAAATT
Found at i:1703068 original size:22 final size:22
Alignment explanation
Indices: 1703040--1703084 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
1703030 CCTCATCTAG
1703040 TCAAGTTAGCTTTTCTGATTGA
1 TCAAGTTAGCTTTTCTGATTGA
1703062 TCAAGTTAGCTTTTCTGATTGA
1 TCAAGTTAGCTTTTCTGATTGA
1703084 T
1 T
1703085 ATATATATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.22, C:0.13, G:0.18, T:0.47
Consensus pattern (22 bp):
TCAAGTTAGCTTTTCTGATTGA
Found at i:1719554 original size:37 final size:37
Alignment explanation
Indices: 1719513--1719584 Score: 117
Period size: 37 Copynumber: 1.9 Consensus size: 37
1719503 CGTTTTTTCA
* *
1719513 ATGTGGGATAATGCAATAATATAAGTTTTTTTTTTTG
1 ATGTGGGATAATGCAAGAATATAAGTGTTTTTTTTTG
*
1719550 ATGTGGGATAATGCAAGAATATGAGTGTTTTTTTT
1 ATGTGGGATAATGCAAGAATATAAGTGTTTTTTTT
1719585 AAAAAAAAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
37 32 1.00
ACGTcount: A:0.29, C:0.03, G:0.22, T:0.46
Consensus pattern (37 bp):
ATGTGGGATAATGCAAGAATATAAGTGTTTTTTTTTG
Found at i:1721018 original size:47 final size:47
Alignment explanation
Indices: 1720967--1721058 Score: 132
Period size: 47 Copynumber: 2.0 Consensus size: 47
1720957 GTGAAATTTA
*
1720967 ATAATTGTCATATATACAAATAAAAA-TGACTTATAATCAAATTTTTT
1 ATAATTGTCACATATACAAATAAAAATTG-CTTATAATCAAATTTTTT
** *
1721014 ATAATTGTTGCGTATACAAATAAAAATTGCTTATAATCAAATTTT
1 ATAATTGTCACATATACAAATAAAAATTGCTTATAATCAAATTTT
1721059 AAAAAATATA
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
47 38 0.95
48 2 0.05
ACGTcount: A:0.45, C:0.09, G:0.07, T:0.40
Consensus pattern (47 bp):
ATAATTGTCACATATACAAATAAAAATTGCTTATAATCAAATTTTTT
Found at i:1733167 original size:18 final size:18
Alignment explanation
Indices: 1733140--1733175 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
1733130 AAATGCAATT
1733140 AAAATCTTTA-TTATAAA
1 AAAATCTTTATTTATAAA
1733157 AAAACTCTTTATTTATAAA
1 AAAA-TCTTTATTTATAAA
1733176 GATTATATAC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 4 0.24
18 6 0.35
19 7 0.41
ACGTcount: A:0.50, C:0.08, G:0.00, T:0.42
Consensus pattern (18 bp):
AAAATCTTTATTTATAAA
Found at i:1740596 original size:2 final size:2
Alignment explanation
Indices: 1740591--1740616 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1740581 ATATATATAT
1740591 AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG
1740617 TGNTATATAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1740642 original size:2 final size:2
Alignment explanation
Indices: 1740637--1740664 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1740627 ATATATATAT
1740637 AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1740665 TTGTGTGAAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1742092 original size:9 final size:10
Alignment explanation
Indices: 1742073--1742102 Score: 51
Period size: 10 Copynumber: 2.9 Consensus size: 10
1742063 AATTGGAGAG
1742073 AAAAATAAAA
1 AAAAATAAAA
1742083 AAAAATAAAA
1 AAAAATAAAA
1742093 AAAAACTAAA
1 AAAAA-TAAA
1742103 GGCTACAAGG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 15 0.79
11 4 0.21
ACGTcount: A:0.87, C:0.03, G:0.00, T:0.10
Consensus pattern (10 bp):
AAAAATAAAA
Found at i:1745216 original size:26 final size:26
Alignment explanation
Indices: 1745185--1745237 Score: 97
Period size: 26 Copynumber: 2.0 Consensus size: 26
1745175 AGTTTTGGGA
*
1745185 TCTGTAATTTGATTTGTTCAATTTTC
1 TCTGTAATTTGATTGGTTCAATTTTC
1745211 TCTGTAATTTGATTGGTTCAATTTTC
1 TCTGTAATTTGATTGGTTCAATTTTC
1745237 T
1 T
1745238 TTCTTTTAAC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.19, C:0.11, G:0.13, T:0.57
Consensus pattern (26 bp):
TCTGTAATTTGATTGGTTCAATTTTC
Found at i:1770269 original size:19 final size:18
Alignment explanation
Indices: 1770245--1770380 Score: 86
Period size: 19 Copynumber: 7.5 Consensus size: 18
1770235 GTTAAATGGT
1770245 ATTATCATTTACTTTTATA
1 ATTATCATTTACTTTT-TA
1770264 ATTATCATTTACTTTTT-
1 ATTATCATTTACTTTTTA
**
1770281 ATTATCCA--T-GGTTTTA
1 ATTAT-CATTTACTTTTTA
** *
1770297 ATTATCATTATGGTTTATA
1 ATTATCATT-TACTTTTTA
1770316 ATTATCATTTAC-TTTTA
1 ATTATCATTTACTTTTTA
** **
1770333 ATTATCCATGGTTAAATGGT-
1 ATTAT-CAT--TTACTTTTTA
1770353 ATTATCATTTACTTTTATA
1 ATTATCATTTACTTTT-TA
1770372 ATTATCATT
1 ATTATCATT
1770381 CTTATATTTT
Statistics
Matches: 91, Mismatches: 14, Indels: 24
0.71 0.11 0.19
Matches are distributed among these distances:
15 6 0.07
16 6 0.07
17 18 0.20
18 9 0.10
19 42 0.46
20 8 0.09
21 2 0.02
ACGTcount: A:0.29, C:0.10, G:0.06, T:0.54
Consensus pattern (18 bp):
ATTATCATTTACTTTTTA
Found at i:1770275 original size:56 final size:57
Alignment explanation
Indices: 1770157--1770380 Score: 261
Period size: 56 Copynumber: 4.0 Consensus size: 57
1770147 TCACTTACTT
* * * * * ** *
1770157 TTTAATTTTTATTATCCATGGTTTAATGATCATTATGGTTTATGCTTTATAATTATCC
1 TTTACTTTTAATTATCCATGGTTAAATGGTAATTATCATTTATG-TTTATAATTATCA
1770215 TTTACTTTTAATTATCCATGGTTAAATGGT-ATTATCATTTACT-TTTATAATTATCA
1 TTTACTTTTAATTATCCATGGTTAAATGGTAATTATCATTTA-TGTTTATAATTATCA
*
1770271 TTTACTTTTTATTATCCATGGTT---T--TAATTATCA-TTATGGTTTATAATTATCA
1 TTTACTTTTAATTATCCATGGTTAAATGGTAATTATCATTTAT-GTTTATAATTATCA
1770323 TTTACTTTTAATTATCCATGGTTAAATGGT-ATTATCATTTACT-TTTATAATTATCA
1 TTTACTTTTAATTATCCATGGTTAAATGGTAATTATCATTTA-TGTTTATAATTATCA
1770379 TT
1 TT
1770381 CTTATATTTT
Statistics
Matches: 146, Mismatches: 9, Indels: 24
0.82 0.05 0.13
Matches are distributed among these distances:
50 1 0.01
51 4 0.03
52 42 0.29
53 1 0.01
55 1 0.01
56 56 0.38
57 13 0.09
58 28 0.19
ACGTcount: A:0.28, C:0.10, G:0.08, T:0.54
Consensus pattern (57 bp):
TTTACTTTTAATTATCCATGGTTAAATGGTAATTATCATTTATGTTTATAATTATCA
Found at i:1779930 original size:51 final size:52
Alignment explanation
Indices: 1779835--1779937 Score: 181
Period size: 51 Copynumber: 2.0 Consensus size: 52
1779825 ATGGAAGTTG
*
1779835 GAAAGAAGTAGGTATTGTTGATTTAATAGTACAATATAACAGGTTCGAAATT
1 GAAAGAAGTAGGCATTGTTGATTTAATAGTACAATATAACAGGTTCGAAATT
*
1779887 GAAAGAAGTAGGCATTGTTGA-TTAATAGTACAATTTAACAGGTTCGAAATT
1 GAAAGAAGTAGGCATTGTTGATTTAATAGTACAATATAACAGGTTCGAAATT
1779938 CTCATTCTTT
Statistics
Matches: 49, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
51 29 0.59
52 20 0.41
ACGTcount: A:0.40, C:0.07, G:0.21, T:0.32
Consensus pattern (52 bp):
GAAAGAAGTAGGCATTGTTGATTTAATAGTACAATATAACAGGTTCGAAATT
Found at i:1789326 original size:18 final size:18
Alignment explanation
Indices: 1789279--1789327 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 18
1789269 TGTAAAAAAT
* *
1789279 ATTAATATATTATAATGA
1 ATTAATATAATATAATAA
*
1789297 ATT-AT-T-ACATAATAA
1 ATTAATATAATATAATAA
1789312 ATTAATATAATATAAT
1 ATTAATATAATATAAT
1789328 GATATAATCA
Statistics
Matches: 24, Mismatches: 4, Indels: 6
0.71 0.12 0.18
Matches are distributed among these distances:
15 9 0.38
16 3 0.12
17 3 0.12
18 9 0.38
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.43
Consensus pattern (18 bp):
ATTAATATAATATAATAA
Found at i:1796016 original size:24 final size:23
Alignment explanation
Indices: 1795983--1796042 Score: 59
Period size: 24 Copynumber: 2.5 Consensus size: 23
1795973 TATAAAAAAT
*
1795983 AATTAAAAATTAAT-TATTATATAA
1 AATTATAAATTAATATATT-T-TAA
*
1796007 AATTATAAATTTATATATTTTAA
1 AATTATAAATTAATATATTTTAA
*
1796030 AATTTATATATTA
1 AA-TTATAAATTA
1796043 TAATTAAAGA
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
23 5 0.17
24 21 0.70
25 4 0.13
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (23 bp):
AATTATAAATTAATATATTTTAA
Found at i:1798252 original size:12 final size:13
Alignment explanation
Indices: 1798230--1798255 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1798220 GGGATAATTT
1798230 GGGCGGGGGGGGG
1 GGGCGGGGGGGGG
1798243 GGGCGGGGGGGGG
1 GGGCGGGGGGGGG
1798256 AAGGAAACAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.00, C:0.08, G:0.92, T:0.00
Consensus pattern (13 bp):
GGGCGGGGGGGGG
Found at i:1804784 original size:24 final size:25
Alignment explanation
Indices: 1804757--1804813 Score: 73
Period size: 24 Copynumber: 2.4 Consensus size: 25
1804747 TAATTTAAAA
*
1804757 AATTTAAATAATTTTTTAT-TTTTT
1 AATTTAAATAATTTTTTATATCTTT
*
1804781 AATTTTAA-AATTTTTTATATCTTT
1 AATTTAAATAATTTTTTATATCTTT
*
1804805 ATTTTAAAT
1 AATTTAAAT
1804814 TAAATAAAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
23 10 0.37
24 17 0.63
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (25 bp):
AATTTAAATAATTTTTTATATCTTT
Found at i:1804796 original size:23 final size:24
Alignment explanation
Indices: 1804757--1804812 Score: 71
Period size: 23 Copynumber: 2.4 Consensus size: 24
1804747 TAATTTAAAA
* *
1804757 AATTTAAATAATTTTTTAT-TTTTT
1 AATTTTAA-AATTTTTTATATCTTT
1804781 AATTTTAAAATTTTTTATATCTTT
1 AATTTTAAAATTTTTTATATCTTT
1804805 -ATTTTAAA
1 AATTTTAAA
1804813 TTAAATAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
23 18 0.62
24 11 0.38
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (24 bp):
AATTTTAAAATTTTTTATATCTTT
Found at i:1810507 original size:15 final size:16
Alignment explanation
Indices: 1810483--1810515 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
1810473 CCCTTCATAC
*
1810483 TTTTTAATTATTATTA
1 TTTTTAATTACTATTA
1810499 TTTTT-ATTACTATTA
1 TTTTTAATTACTATTA
1810514 TT
1 TT
1810516 ATTGATTAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 11 0.69
16 5 0.31
ACGTcount: A:0.27, C:0.03, G:0.00, T:0.70
Consensus pattern (16 bp):
TTTTTAATTACTATTA
Found at i:1812326 original size:32 final size:32
Alignment explanation
Indices: 1812286--1812350 Score: 121
Period size: 32 Copynumber: 2.0 Consensus size: 32
1812276 AAAGAAAGAA
1812286 TATTATTTGTCAATTCTGGCTTTTTATAGTCT
1 TATTATTTGTCAATTCTGGCTTTTTATAGTCT
*
1812318 TATTATTTGTCAATTTTGGCTTTTTATAGTCT
1 TATTATTTGTCAATTCTGGCTTTTTATAGTCT
1812350 T
1 T
1812351 TACAAGGTGC
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.18, C:0.11, G:0.12, T:0.58
Consensus pattern (32 bp):
TATTATTTGTCAATTCTGGCTTTTTATAGTCT
Found at i:1821581 original size:18 final size:18
Alignment explanation
Indices: 1821558--1821592 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
1821548 CATCTTGCCC
1821558 TTATTTT-ATTTTATTTCA
1 TTATTTTAATTTT-TTTCA
1821576 TTATTTTAATTTTTTTC
1 TTATTTTAATTTTTTTC
1821593 GGATCACTCA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 11 0.69
19 5 0.31
ACGTcount: A:0.20, C:0.06, G:0.00, T:0.74
Consensus pattern (18 bp):
TTATTTTAATTTTTTTCA
Found at i:1828382 original size:15 final size:15
Alignment explanation
Indices: 1828362--1828393 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
1828352 TGATCCAAAG
1828362 TTTGCAGTTAGACAA
1 TTTGCAGTTAGACAA
1828377 TTTGCAGTTAGACAA
1 TTTGCAGTTAGACAA
1828392 TT
1 TT
1828394 ATAACTTGTG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.31, C:0.12, G:0.19, T:0.38
Consensus pattern (15 bp):
TTTGCAGTTAGACAA
Found at i:1830517 original size:39 final size:39
Alignment explanation
Indices: 1830463--1830564 Score: 152
Period size: 39 Copynumber: 2.6 Consensus size: 39
1830453 TCAACTCAAC
*
1830463 TCATGTGCACTCCCACACAGCACATGGCATATATCATCA
1 TCATGTGCTCTCCCACACAGCACATGGCATATATCATCA
*
1830502 TCATGTGCTCTCCCACA-ACGCACATGGCATATATCATCG
1 TCATGTGCTCTCCCACACA-GCACATGGCATATATCATCA
* *
1830541 GCATGTGCTCTCCCACACCGCACA
1 TCATGTGCTCTCCCACACAGCACA
1830565 CTATCGACAC
Statistics
Matches: 57, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
38 1 0.02
39 56 0.98
ACGTcount: A:0.26, C:0.36, G:0.15, T:0.23
Consensus pattern (39 bp):
TCATGTGCTCTCCCACACAGCACATGGCATATATCATCA
Found at i:1831733 original size:20 final size:20
Alignment explanation
Indices: 1831702--1831748 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
1831692 CCTCCGAGCT
1831702 TTTCTCTTCCTTT-TTCCTTTC
1 TTTCT-TTCCTTTCTT-CTTTC
1831723 TTTCTTTCCTTTCTTCTTTC
1 TTTCTTTCCTTTCTTCTTTC
1831743 -TTCTTT
1 TTTCTTT
1831749 TCTCTCTCCT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
19 6 0.24
20 12 0.48
21 7 0.28
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (20 bp):
TTTCTTTCCTTTCTTCTTTC
Found at i:1832931 original size:19 final size:19
Alignment explanation
Indices: 1832907--1832945 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
1832897 CCCCCTAAAC
1832907 TTTTAAAATTCAATAATTT
1 TTTTAAAATTCAATAATTT
**
1832926 TTTTAAAATTTGATAATTT
1 TTTTAAAATTCAATAATTT
1832945 T
1 T
1832946 ATTCTCTATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.38, C:0.03, G:0.03, T:0.56
Consensus pattern (19 bp):
TTTTAAAATTCAATAATTT
Found at i:1839093 original size:21 final size:21
Alignment explanation
Indices: 1839067--1839131 Score: 67
Period size: 21 Copynumber: 3.0 Consensus size: 21
1839057 ACTTAATCAC
*
1839067 TATGTGACTGATTTTTGGTAT
1 TATGTGACTGATTTTTGGCAT
* * *
1839088 TATGTGATTGGTTTTAGGCAT
1 TATGTGACTGATTTTTGGCAT
**
1839109 TGCGTGACTGATTTTTAGGCAT
1 TATGTGACTGATTTTT-GGCAT
1839131 T
1 T
1839132 GCGTTACTAG
Statistics
Matches: 34, Mismatches: 9, Indels: 1
0.77 0.20 0.02
Matches are distributed among these distances:
21 28 0.82
22 6 0.18
ACGTcount: A:0.18, C:0.08, G:0.26, T:0.48
Consensus pattern (21 bp):
TATGTGACTGATTTTTGGCAT
Found at i:1839206 original size:22 final size:22
Alignment explanation
Indices: 1839178--1839238 Score: 95
Period size: 23 Copynumber: 2.7 Consensus size: 22
1839168 ATCCCTTACT
*
1839178 AACTAGTCACGCAATATATATC
1 AACTAGTCACACAATATATATC
*
1839200 AACTAGTCACACAATGCTATATC
1 AACTAGTCACACAAT-ATATATC
1839223 AACTAGTCACACAATA
1 AACTAGTCACACAATA
1839239 CTTAAAAACT
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
22 14 0.40
23 21 0.60
ACGTcount: A:0.43, C:0.25, G:0.08, T:0.25
Consensus pattern (22 bp):
AACTAGTCACACAATATATATC
Found at i:1839251 original size:22 final size:23
Alignment explanation
Indices: 1839178--1839254 Score: 104
Period size: 22 Copynumber: 3.4 Consensus size: 23
1839168 ATCCCTTACT
*
1839178 AACTAGTCACGCAATA-TATATC
1 AACTAGTCACACAATACTATATC
*
1839200 AACTAGTCACACAATGCTATATC
1 AACTAGTCACACAATACTATATC
**
1839223 AACTAGTCACACAATACT-TAAA
1 AACTAGTCACACAATACTATATC
1839245 AACTAGTCAC
1 AACTAGTCAC
1839255 GTAATGTCCA
Statistics
Matches: 49, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
22 26 0.53
23 23 0.47
ACGTcount: A:0.43, C:0.25, G:0.08, T:0.25
Consensus pattern (23 bp):
AACTAGTCACACAATACTATATC
Found at i:1839275 original size:21 final size:21
Alignment explanation
Indices: 1839249--1839334 Score: 84
Period size: 21 Copynumber: 4.0 Consensus size: 21
1839239 CTTAAAAACT
*
1839249 AGTCACGTAATGTCCAAAGTC
1 AGTCACGTAATATCCAAAGTC
* * **
1839270 AGTCACATAAT-GCCTAAAAAC
1 AGTCACGTAATATCC-AAAGTC
*
1839291 TAGTCACGTAATATCTAAAGTC
1 -AGTCACGTAATATCCAAAGTC
*
1839313 AGTCACGCAATATCCAAAGTC
1 AGTCACGTAATATCCAAAGTC
1839334 A
1 A
1839335 ATCATGAATG
Statistics
Matches: 51, Mismatches: 11, Indels: 6
0.75 0.16 0.09
Matches are distributed among these distances:
20 2 0.04
21 34 0.67
22 14 0.27
23 1 0.02
ACGTcount: A:0.40, C:0.23, G:0.14, T:0.23
Consensus pattern (21 bp):
AGTCACGTAATATCCAAAGTC
Done.