Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr2
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: 41236440
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 2030548 characters in sequence are not A, C, G, or T
File 56 of 106
Found at i:21037623 original size:74 final size:74
Alignment explanation
Indices: 21037538--21037728 Score: 258
Period size: 74 Copynumber: 2.6 Consensus size: 74
21037528 GACGAGTGCC
* *
21037538 CTTAGTGGACTAACTATGCTTCTTAGTCGATTAAGTCTTCTCTATCTTGAAATTGAGATCTCTGA
1 CTTAGTTGACTAACTATGCTTCTTAGTCGATTAAGTCTTCTCTATCTTGAAATTGAAATCTCTGA
21037603 TAGTGAGCT
66 TAGTGAGCT
* * * *
21037612 CTTAGTTGACTAACTGTGCTTTTTAGTCGATTAAGT-TCTCTTTGTCTTGAAATTGAAATCTCTG
1 CTTAGTTGACTAACTATGCTTCTTAGTCGATTAAGTCT-TCTCTATCTTGAAATTGAAATCTCTG
* *
21037676 GTAGTGTGCT
65 ATAGTGAGCT
* * * *
21037686 CTTTGTTGACTAGCTATGCTTCTTAGTTGACTAAGTCTTCTCT
1 CTTAGTTGACTAACTATGCTTCTTAGTCGATTAAGTCTTCTCT
21037729 GTTTCATAAT
Statistics
Matches: 100, Mismatches: 15, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
73 1 0.01
74 98 0.98
75 1 0.01
ACGTcount: A:0.21, C:0.17, G:0.19, T:0.43
Consensus pattern (74 bp):
CTTAGTTGACTAACTATGCTTCTTAGTCGATTAAGTCTTCTCTATCTTGAAATTGAAATCTCTGA
TAGTGAGCT
Found at i:21038490 original size:23 final size:23
Alignment explanation
Indices: 21038460--21038509 Score: 91
Period size: 23 Copynumber: 2.2 Consensus size: 23
21038450 TCCTAAATTA
*
21038460 CCCTAAATTACTTCTACTTTCTC
1 CCCTAAATTACTTCAACTTTCTC
21038483 CCCTAAATTACTTCAACTTTCTC
1 CCCTAAATTACTTCAACTTTCTC
21038506 CCCT
1 CCCT
21038510 TTTTTATCAT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.22, C:0.38, G:0.00, T:0.40
Consensus pattern (23 bp):
CCCTAAATTACTTCAACTTTCTC
Found at i:21047978 original size:19 final size:19
Alignment explanation
Indices: 21047954--21048017 Score: 58
Period size: 19 Copynumber: 3.4 Consensus size: 19
21047944 TGCCCGTGTG
21047954 CACGATGTGGGGGGATGTA
1 CACGATGTGGGGGGATGTA
**** *
21047973 CACGATG-GCACTGATTGTG
1 CACGATGTGGGGGGA-TGTA
*
21047992 CACGATGTGGGGGGATGCA
1 CACGATGTGGGGGGATGTA
21048011 CACGATG
1 CACGATG
21048018 GCGCCAGCTA
Statistics
Matches: 32, Mismatches: 11, Indels: 4
0.68 0.23 0.09
Matches are distributed among these distances:
18 3 0.09
19 26 0.81
20 3 0.09
ACGTcount: A:0.22, C:0.17, G:0.41, T:0.20
Consensus pattern (19 bp):
CACGATGTGGGGGGATGTA
Found at i:21047992 original size:38 final size:40
Alignment explanation
Indices: 21047950--21048050 Score: 143
Period size: 38 Copynumber: 2.6 Consensus size: 40
21047940 ATAGTGCCCG
*
21047950 TGTGCACGATGTGGGGGGATGTACACGATGGC-ACTGAT-
1 TGTGCACGATGTGGGGGGATGTACACGATGGCGACAGATA
* * *
21047988 TGTGCACGATGTGGGGGGATGCACACGATGGCGCCAGCTA
1 TGTGCACGATGTGGGGGGATGTACACGATGGCGACAGATA
*
21048028 TGTGCATGATGTGGGGGGATGTA
1 TGTGCACGATGTGGGGGGATGTA
21048051 TATGAGCCGG
Statistics
Matches: 55, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
38 31 0.56
39 3 0.05
40 21 0.38
ACGTcount: A:0.20, C:0.16, G:0.42, T:0.23
Consensus pattern (40 bp):
TGTGCACGATGTGGGGGGATGTACACGATGGCGACAGATA
Found at i:21049542 original size:19 final size:19
Alignment explanation
Indices: 21049518--21049558 Score: 82
Period size: 19 Copynumber: 2.2 Consensus size: 19
21049508 GATATTATTT
21049518 TTACAAGGCACAAATATCC
1 TTACAAGGCACAAATATCC
21049537 TTACAAGGCACAAATATCC
1 TTACAAGGCACAAATATCC
21049556 TTA
1 TTA
21049559 TTGTGATTTG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.41, C:0.24, G:0.10, T:0.24
Consensus pattern (19 bp):
TTACAAGGCACAAATATCC
Found at i:21051443 original size:20 final size:20
Alignment explanation
Indices: 21051418--21051455 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
21051408 GTCCTGCCAA
**
21051418 GAATGTATTGATACATTTAG
1 GAATGTATCAATACATTTAG
21051438 GAATGTATCAATACATTT
1 GAATGTATCAATACATTT
21051456 TCCCCTATAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.37, C:0.08, G:0.16, T:0.39
Consensus pattern (20 bp):
GAATGTATCAATACATTTAG
Found at i:21054314 original size:25 final size:25
Alignment explanation
Indices: 21054281--21054340 Score: 93
Period size: 25 Copynumber: 2.4 Consensus size: 25
21054271 GTGGTCGCAA
* *
21054281 CCACGTATATCAACTTGTGGCCTAG
1 CCACATATATCAACCTGTGGCCTAG
*
21054306 CCACATATATCAACCTGTGGCCTTG
1 CCACATATATCAACCTGTGGCCTAG
21054331 CCACATATAT
1 CCACATATAT
21054341 ATATCACAGA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 32 1.00
ACGTcount: A:0.27, C:0.30, G:0.15, T:0.28
Consensus pattern (25 bp):
CCACATATATCAACCTGTGGCCTAG
Found at i:21056908 original size:25 final size:25
Alignment explanation
Indices: 21056880--21056930 Score: 93
Period size: 25 Copynumber: 2.0 Consensus size: 25
21056870 ATAGCACCTT
*
21056880 TTTAACTCCATAACTTCGACCTCAA
1 TTTAACTCCACAACTTCGACCTCAA
21056905 TTTAACTCCACAACTTCGACCTCAA
1 TTTAACTCCACAACTTCGACCTCAA
21056930 T
1 T
21056931 AAGATATTTG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.31, C:0.33, G:0.04, T:0.31
Consensus pattern (25 bp):
TTTAACTCCACAACTTCGACCTCAA
Found at i:21061419 original size:19 final size:19
Alignment explanation
Indices: 21061395--21061432 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
21061385 TCATCTCTAG
*
21061395 ATCGTGTGTAGGATAGTTC
1 ATCGTGCGTAGGATAGTTC
21061414 ATCGTGCGTAGGATAGTTC
1 ATCGTGCGTAGGATAGTTC
21061433 TACTCACGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.21, C:0.13, G:0.32, T:0.34
Consensus pattern (19 bp):
ATCGTGCGTAGGATAGTTC
Found at i:21066618 original size:20 final size:20
Alignment explanation
Indices: 21066592--21066637 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 20
21066582 AATCTTACCT
* *
21066592 TTTTTCACTTGTTTCCTTGAA
1 TTTTACACTT-TTCCCTTGAA
21066613 TTTTCACACTTTTCCCTTGAA
1 TTTT-ACACTTTTCCCTTGAA
21066634 TTTT
1 TTTT
21066638 TCTACCTAGA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 17 0.77
22 5 0.23
ACGTcount: A:0.15, C:0.22, G:0.07, T:0.57
Consensus pattern (20 bp):
TTTTACACTTTTCCCTTGAA
Found at i:21066639 original size:22 final size:22
Alignment explanation
Indices: 21066597--21066637 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
21066587 TACCTTTTTT
*
21066597 CACTTGTTTCCTTGAATTTTCA
1 CACTTGTTCCCTTGAATTTTCA
21066619 CACTT-TTCCCTTGAATTTT
1 CACTTGTTCCCTTGAATTTT
21066638 TCTACCTAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.17, C:0.24, G:0.07, T:0.51
Consensus pattern (22 bp):
CACTTGTTCCCTTGAATTTTCA
Found at i:21068742 original size:82 final size:82
Alignment explanation
Indices: 21068601--21068765 Score: 314
Period size: 82 Copynumber: 2.0 Consensus size: 82
21068591 TTTGATAAAT
21068601 TGTATCTATGTGTGACATGTGGCTGTTATGGATTGTTGTATTACTACATTATGTTGATATATATA
1 TGTATCTATGTGTGACATGTGGCTGTTATGGATTGTTGTATTACTACATTATGTTGATATATATA
21068666 TATATATAT-AATAATG
66 TATATATATAAATAATG
21068682 TGTANTCTATGTGTGACATGTGGCTGTTATGGATTGTTGTATTACTACATTATGTTGATATATAT
1 TGTA-TCTATGTGTGACATGTGGCTGTTATGGATTGTTGTATTACTACATTATGTTGATATATAT
21068747 ATATATATATAAATAATG
65 ATATATATATAAATAATG
21068765 T
1 T
21068766 TGTGTAATGA
Statistics
Matches: 82, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
81 4 0.05
82 70 0.85
83 8 0.10
ACGTcount: A:0.30, C:0.06, G:0.18, T:0.45
Consensus pattern (82 bp):
TGTATCTATGTGTGACATGTGGCTGTTATGGATTGTTGTATTACTACATTATGTTGATATATATA
TATATATATAAATAATG
Found at i:21068838 original size:42 final size:42
Alignment explanation
Indices: 21068787--21068904 Score: 164
Period size: 42 Copynumber: 2.8 Consensus size: 42
21068777 ATTGACCCAC
* *
21068787 CTATGTGCGAGTAGGAGTGTGCATAAGCCGATGCTGACCAGG
1 CTATGTGCGAGTGGGAGTGTGCATAAGCCGATGCTGACCAGA
* * * * *
21068829 TTATGTGCGAATGGGAGTGCGCATAAGTCGATGCTGACCTGA
1 CTATGTGCGAGTGGGAGTGTGCATAAGCCGATGCTGACCAGA
*
21068871 CTATGTGCGAGTGGGAGTGTACATAAGCCGATGC
1 CTATGTGCGAGTGGGAGTGTGCATAAGCCGATGC
21068905 ATATGAGCTA
Statistics
Matches: 64, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
42 64 1.00
ACGTcount: A:0.24, C:0.18, G:0.35, T:0.24
Consensus pattern (42 bp):
CTATGTGCGAGTGGGAGTGTGCATAAGCCGATGCTGACCAGA
Found at i:21072839 original size:22 final size:22
Alignment explanation
Indices: 21072813--21072855 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
21072803 AATTTTTTTG
21072813 TTGATACCAAAAATTAAGGAAT
1 TTGATACCAAAAATTAAGGAAT
* * *
21072835 TTGATTCCTAAAATTATGGAA
1 TTGATACCAAAAATTAAGGAA
21072856 GTCAAAAATA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.44, C:0.09, G:0.14, T:0.33
Consensus pattern (22 bp):
TTGATACCAAAAATTAAGGAAT
Found at i:21073796 original size:57 final size:57
Alignment explanation
Indices: 21073678--21073796 Score: 179
Period size: 57 Copynumber: 2.1 Consensus size: 57
21073668 CATAATCATC
* *
21073678 CAAAGTAGTTTGCATGTGATAGATTTTTTTATGGAATTTAATAAATGCTATGCAATT
1 CAAAGTAGTATGCATGTGATAGATTTTTTTATGGAATTTAATAAATGCTATGCAATG
*
21073735 CAAAGTAGTATGCATGTGATAGATTTATTTTATGTG-ATTTAATAAATGCTATG-TATG
1 CAAAGTAGTATGCATGTGATAGATTT-TTTTATG-GAATTTAATAAATGCTATGCAATG
21073792 CAAAG
1 CAAAG
21073797 ATGAGACCTT
Statistics
Matches: 57, Mismatches: 3, Indels: 4
0.89 0.05 0.06
Matches are distributed among these distances:
57 32 0.56
58 24 0.42
59 1 0.02
ACGTcount: A:0.34, C:0.07, G:0.18, T:0.40
Consensus pattern (57 bp):
CAAAGTAGTATGCATGTGATAGATTTTTTTATGGAATTTAATAAATGCTATGCAATG
Found at i:21078795 original size:11 final size:11
Alignment explanation
Indices: 21078779--21078806 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
21078769 AGCTTTTGGG
21078779 TTTAAAGTTGT
1 TTTAAAGTTGT
21078790 TTTAAAGTTGT
1 TTTAAAGTTGT
21078801 TTTAAA
1 TTTAAA
21078807 AACTACAGTG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.32, C:0.00, G:0.14, T:0.54
Consensus pattern (11 bp):
TTTAAAGTTGT
Found at i:21091976 original size:13 final size:13
Alignment explanation
Indices: 21091958--21091982 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
21091948 ATTTTCAAAA
21091958 ATTTTATAAAATT
1 ATTTTATAAAATT
21091971 ATTTTATAAAAT
1 ATTTTATAAAAT
21091983 CCCATTTTCC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (13 bp):
ATTTTATAAAATT
Found at i:21093184 original size:28 final size:29
Alignment explanation
Indices: 21093136--21093199 Score: 76
Period size: 28 Copynumber: 2.2 Consensus size: 29
21093126 GTAAATTTTT
** *
21093136 AAAAATTACACTTTTACCCCCGTAAAGTG
1 AAAAATTACACTTTTACCCCCAAAAACTG
**
21093165 AAAAATTACA-TTTTTGCCCCAAAAACTG
1 AAAAATTACACTTTTACCCCCAAAAACTG
21093193 AAAAATT
1 AAAAATT
21093200 GCCCATAGAC
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
28 20 0.67
29 10 0.33
ACGTcount: A:0.44, C:0.20, G:0.08, T:0.28
Consensus pattern (29 bp):
AAAAATTACACTTTTACCCCCAAAAACTG
Found at i:21096749 original size:13 final size:13
Alignment explanation
Indices: 21096731--21096755 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
21096721 ATTTTCAAAA
21096731 ATTTTATAAAATT
1 ATTTTATAAAATT
21096744 ATTTTATAAAAT
1 ATTTTATAAAAT
21096756 CCCATTTTAC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (13 bp):
ATTTTATAAAATT
Found at i:21097972 original size:28 final size:30
Alignment explanation
Indices: 21097907--21097975 Score: 88
Period size: 30 Copynumber: 2.4 Consensus size: 30
21097897 GAGTAAATTC
*
21097907 TTAAAAATTACACTTTTGCCCCCGTAAAAG
1 TTAAAAATTACACTTTTGCCCCCGAAAAAG
* * *
21097937 TGAAAAATTACATTTTTG-CCCC-AAAAAT
1 TTAAAAATTACACTTTTGCCCCCGAAAAAG
21097965 TTAAAAATTAC
1 TTAAAAATTAC
21097976 CAAAATGCAT
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
28 14 0.41
29 4 0.12
30 16 0.47
ACGTcount: A:0.42, C:0.19, G:0.07, T:0.32
Consensus pattern (30 bp):
TTAAAAATTACACTTTTGCCCCCGAAAAAG
Found at i:21100960 original size:2 final size:2
Alignment explanation
Indices: 21100953--21100992 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
21100943 TCGATCCAAA
21100953 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
21100993 TATTTATANC
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:21101117 original size:2 final size:2
Alignment explanation
Indices: 21101110--21101145 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
21101100 TCGATCCAAA
21101110 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
21101146 TGTTTATAAC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:21101131 original size:157 final size:156
Alignment explanation
Indices: 21100845--21101145 Score: 593
Period size: 157 Copynumber: 1.9 Consensus size: 156
21100835 TCGTAATTCT
21100845 CAACTATAAGTATTTCAGTAATATACTATGGCAACCAAATACTTACATTGTTATCATCCCAAAAT
1 CAACTATAAGTATTTCAGTAATATACTATGGCAACCAAATACTTACATTGTTATCATCCCAAAAT
21100910 AATGTCATCCATTGCCAACTCATAGTGGCATCATCGATCCAAAATATATATATATATATATATAT
66 AATGTCATCCATTGCCAACTCATAGTGGCATCATCGATCCAAAATATATATATATATATATATAT
21100975 ATATATATATATATATATTATTTATA
131 ATATATATATATATATATTATTTATA
21101001 NCAACTATAAGTATTTCAGTAATATACTATGGCAACCAAATACTTACATTGTTATCATCCCAAAA
1 -CAACTATAAGTATTTCAGTAATATACTATGGCAACCAAATACTTACATTGTTATCATCCCAAAA
21101066 TAATGTCATCCATTGCCAACTCATAGTGGCATCATCGATCCAAAATATATATATATATATATATA
65 TAATGTCATCCATTGCCAACTCATAGTGGCATCATCGATCCAAAATATATATATATATATATATA
21101131 TATATATATATATAT
130 TATATATATATATAT
21101146 TGTTTATAAC
Statistics
Matches: 144, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
157 144 1.00
ACGTcount: A:0.40, C:0.17, G:0.07, T:0.36
Consensus pattern (156 bp):
CAACTATAAGTATTTCAGTAATATACTATGGCAACCAAATACTTACATTGTTATCATCCCAAAAT
AATGTCATCCATTGCCAACTCATAGTGGCATCATCGATCCAAAATATATATATATATATATATAT
ATATATATATATATATATTATTTATA
Found at i:21101674 original size:62 final size:61
Alignment explanation
Indices: 21101570--21101793 Score: 277
Period size: 62 Copynumber: 3.6 Consensus size: 61
21101560 CAAGACAGAG
* * * *
21101570 AGTTTCTCACTACGGCGAGAATCAAATTTGGCTGCGGCGAGAATAGTGACTCCCCAAGGTAGAA
1 AGTTTCTCACCACGGCGA-AATC-AATTTGGCTGCGGCGAGAACAGTAACT-CCAAAGGTAGAA
* * * * * *
21101634 AGTTTCTCGCTACGGCGAAATCAATTTTGCTGCGACGAGAACAGTAACTCCTAAGGCAGAA
1 AGTTTCTCACCACGGCGAAATCAATTTGGCTGCGGCGAGAACAGTAACTCCAAAGGTAGAA
*
21101695 AGTTTCTCACCACGGCGAAAATCAATTTGGCTGCGGCGAGAACAATAACTCCAAAGGTAGAA
1 AGTTTCTCACCACGGCG-AAATCAATTTGGCTGCGGCGAGAACAGTAACTCCAAAGGTAGAA
* * *
21101757 AGTTTCTCGCCACGACAAAAATCAATTTGGCTGCGGC
1 AGTTTCTCACCACGGC-GAAATCAATTTGGCTGCGGC
21101794 AAAAATGAAG
Statistics
Matches: 141, Mismatches: 17, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
61 25 0.18
62 95 0.67
63 4 0.03
64 17 0.12
ACGTcount: A:0.31, C:0.23, G:0.24, T:0.22
Consensus pattern (61 bp):
AGTTTCTCACCACGGCGAAATCAATTTGGCTGCGGCGAGAACAGTAACTCCAAAGGTAGAA
Found at i:21101791 original size:124 final size:125
Alignment explanation
Indices: 21101565--21101791 Score: 332
Period size: 124 Copynumber: 1.8 Consensus size: 125
21101555 CCAAACAAGA
* * * * * * *
21101565 CAGAGAGTTTCTCACTACGGCGAGAATCAAATTTGGCTGCGGCGAGAATAGTGACTCCCCAAGGT
1 CAGAAAGTTTCTCACCACGGCGAAAATCAAATTTGGCTGCGGCGAGAACAATAACTCCCAAAGGT
* * * *
21101630 AGAAAGTTTCTCGCTACGGCGAAATCAATTTTGCTGCGACGAGAACAGTAACTCCTAAGG
66 AGAAAGTTTCTCGCCACGACAAAATCAATTTGGCTGCGACGAGAACAGTAACTCCTAAGG
21101690 CAGAAAGTTTCTCACCACGGCGAAAATC-AATTTGGCTGCGGCGAGAACAATAACT-CCAAAGGT
1 CAGAAAGTTTCTCACCACGGCGAAAATCAAATTTGGCTGCGGCGAGAACAATAACTCCCAAAGGT
21101753 AGAAAGTTTCTCGCCACGACAAAAATCAATTTGGCTGCG
66 AGAAAGTTTCTCGCCACGAC-AAAATCAATTTGGCTGCG
21101792 GCAAAAATGA
Statistics
Matches: 90, Mismatches: 11, Indels: 3
0.87 0.11 0.03
Matches are distributed among these distances:
123 25 0.28
124 40 0.44
125 25 0.28
ACGTcount: A:0.32, C:0.23, G:0.24, T:0.22
Consensus pattern (125 bp):
CAGAAAGTTTCTCACCACGGCGAAAATCAAATTTGGCTGCGGCGAGAACAATAACTCCCAAAGGT
AGAAAGTTTCTCGCCACGACAAAATCAATTTGGCTGCGACGAGAACAGTAACTCCTAAGG
Found at i:21104952 original size:40 final size:40
Alignment explanation
Indices: 21104897--21104978 Score: 119
Period size: 40 Copynumber: 2.0 Consensus size: 40
21104887 ATGTTGAAAG
* **
21104897 ATGGAACCTAAAGAAAACCTATCGAAATCCTCAAGCAAAA
1 ATGGAACCTAAAGAAAACCAATCGAAATCCAAAAGCAAAA
* *
21104937 ATGGAACCTCAAGAAAGCCAATCGAAATCCAAAAGCAAAA
1 ATGGAACCTAAAGAAAACCAATCGAAATCCAAAAGCAAAA
21104977 AT
1 AT
21104979 AAAATCCTGC
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
40 37 1.00
ACGTcount: A:0.51, C:0.22, G:0.13, T:0.13
Consensus pattern (40 bp):
ATGGAACCTAAAGAAAACCAATCGAAATCCAAAAGCAAAA
Found at i:21105579 original size:5 final size:5
Alignment explanation
Indices: 21105569--21105622 Score: 51
Period size: 5 Copynumber: 11.2 Consensus size: 5
21105559 ATTTTTGTAC
* * *
21105569 TTTCT TTTCT TTTCT TTTC- TTTCT TCTT-T ATTCT TTTCT CTT-T TTTCC
1 TTTCT TTTCT TTTCT TTTCT TTTCT T-TTCT TTTCT TTTCT TTTCT TTTCT
21105617 TTTCT T
1 TTTCT T
21105623 CTTTTTCCTT
Statistics
Matches: 39, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
4 9 0.23
5 28 0.72
6 2 0.05
ACGTcount: A:0.02, C:0.22, G:0.00, T:0.76
Consensus pattern (5 bp):
TTTCT
Found at i:21105590 original size:19 final size:19
Alignment explanation
Indices: 21105568--21105622 Score: 60
Period size: 19 Copynumber: 2.9 Consensus size: 19
21105558 AATTTTTGTA
21105568 CTTTCTTTTCTTTTCTTTT
1 CTTTCTTTTCTTTTCTTTT
*
21105587 CTTTCTTCTT-TATTCTTTT
1 CTTTCTT-TTCTTTTCTTTT
*
21105606 CTCTT-TTTTCCTTTCTT
1 CT-TTCTTTTCTTTTCTT
21105623 CTTTTTCCTT
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
18 2 0.07
19 24 0.80
20 4 0.13
ACGTcount: A:0.02, C:0.24, G:0.00, T:0.75
Consensus pattern (19 bp):
CTTTCTTTTCTTTTCTTTT
Found at i:21105591 original size:14 final size:13
Alignment explanation
Indices: 21105569--21105642 Score: 51
Period size: 14 Copynumber: 5.2 Consensus size: 13
21105559 ATTTTTGTAC
21105569 TTTCTTTTCTTTTCT
1 TTTCTTTTC--TTCT
21105584 TTTC-TTTCTTCTT
1 TTTCTTTTCTTC-T
*
21105597 TATTCTTTTCTCTTT
1 T-TTCTTTTCT-TCT
*
21105612 TTTCCTTTCTTCTT
1 TTTCTTTTCTTC-T
21105626 TTTCCTTTATCTTCT
1 TTT-CTTT-TCTTCT
21105641 TT
1 TT
21105643 ATTCGTTTTT
Statistics
Matches: 48, Mismatches: 4, Indels: 14
0.73 0.06 0.21
Matches are distributed among these distances:
12 3 0.06
13 3 0.06
14 19 0.40
15 17 0.35
16 6 0.12
ACGTcount: A:0.03, C:0.23, G:0.00, T:0.74
Consensus pattern (13 bp):
TTTCTTTTCTTCT
Found at i:21105602 original size:29 final size:29
Alignment explanation
Indices: 21105570--21105626 Score: 89
Period size: 29 Copynumber: 2.0 Consensus size: 29
21105560 TTTTTGTACT
*
21105570 TTCTTTTCT-TTTCTTTTCTTTCTTCTTTA
1 TTCTTTTCTCTTT-TTTCCTTTCTTCTTTA
21105599 TTCTTTTCTCTTTTTTCCTTTCTTCTTT
1 TTCTTTTCTCTTTTTTCCTTTCTTCTTT
21105627 TTCCTTTATC
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
29 23 0.88
30 3 0.12
ACGTcount: A:0.02, C:0.23, G:0.00, T:0.75
Consensus pattern (29 bp):
TTCTTTTCTCTTTTTTCCTTTCTTCTTTA
Found at i:21110953 original size:24 final size:24
Alignment explanation
Indices: 21110917--21110970 Score: 83
Period size: 24 Copynumber: 2.3 Consensus size: 24
21110907 ACAGTCACAC
* *
21110917 TGAATATTTTAGAATGAGGTTATT
1 TGAATATTCTAGAATGAGGCTATT
21110941 TGAATATTCTAGAATGAGGCTATT
1 TGAATATTCTAGAATGAGGCTATT
21110965 T-AATAT
1 TGAATAT
21110971 AAAAAATTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
23 5 0.18
24 23 0.82
ACGTcount: A:0.35, C:0.04, G:0.19, T:0.43
Consensus pattern (24 bp):
TGAATATTCTAGAATGAGGCTATT
Found at i:21114037 original size:28 final size:28
Alignment explanation
Indices: 21114000--21114080 Score: 128
Period size: 28 Copynumber: 2.9 Consensus size: 28
21113990 ATGTCCTAGT
* *
21114000 GGTGG-AAAATTACAATTTTGCCCCTGA
1 GGTGGCAAAATTACCATTTTACCCCTGA
21114027 GGTGGCAAAATTACCATTTTACCCCTGA
1 GGTGGCAAAATTACCATTTTACCCCTGA
*
21114055 GGTGACAAAATTACCATTTTACCCCT
1 GGTGGCAAAATTACCATTTTACCCCT
21114081 ATACACCAAA
Statistics
Matches: 50, Mismatches: 3, Indels: 1
0.93 0.06 0.02
Matches are distributed among these distances:
27 5 0.10
28 45 0.90
ACGTcount: A:0.30, C:0.23, G:0.17, T:0.30
Consensus pattern (28 bp):
GGTGGCAAAATTACCATTTTACCCCTGA
Found at i:21114148 original size:19 final size:19
Alignment explanation
Indices: 21114124--21114161 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
21114114 ACTTCTAAAC
21114124 CTCAAATCATACTCCAATA
1 CTCAAATCATACTCCAATA
21114143 CTCAAATCATACTCCAATA
1 CTCAAATCATACTCCAATA
21114162 AGTCAAATGG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.42, C:0.32, G:0.00, T:0.26
Consensus pattern (19 bp):
CTCAAATCATACTCCAATA
Found at i:21118928 original size:24 final size:24
Alignment explanation
Indices: 21118892--21118944 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
21118882 ATAGTCACAC
* * * *
21118892 TGAATATTTTAGAATGAGGTTATT
1 TGAATACTCTAGAATAAGGCTATT
21118916 TGAATACTCTAGAATAAGGCTATT
1 TGAATACTCTAGAATAAGGCTATT
21118940 T-AATA
1 TGAATA
21118945 TAAAAAATTT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
23 4 0.16
24 21 0.84
ACGTcount: A:0.38, C:0.06, G:0.17, T:0.40
Consensus pattern (24 bp):
TGAATACTCTAGAATAAGGCTATT
Found at i:21124004 original size:29 final size:29
Alignment explanation
Indices: 21123970--21124067 Score: 101
Period size: 29 Copynumber: 3.3 Consensus size: 29
21123960 TTATAAAGAT
*
21123970 TTATTTGATTGAAAATAAAAGTATAAGGC
1 TTATTTGAATGAAAATAAAAGTATAAGGC
* * *
21123999 TTATTTGACTCAAAATAAAAATATAAGAGC
1 TTATTTGAATGAAAATAAAAGTATAAG-GC
* *
21124029 TTGA-TTGAATG-TAATAAAAGTATAAAAGC
1 TT-ATTTGAATGAAAATAAAAGTAT-AAGGC
21124058 TTATTTGAAT
1 TTATTTGAAT
21124068 TTTTTTGAAT
Statistics
Matches: 57, Mismatches: 8, Indels: 8
0.78 0.11 0.11
Matches are distributed among these distances:
28 1 0.02
29 44 0.77
30 11 0.19
31 1 0.02
ACGTcount: A:0.46, C:0.05, G:0.14, T:0.35
Consensus pattern (29 bp):
TTATTTGAATGAAAATAAAAGTATAAGGC
Found at i:21128409 original size:2 final size:2
Alignment explanation
Indices: 21128402--21128426 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
21128392 ATATTGATAC
21128402 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 A
21128427 AATAATGTTG
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:21128515 original size:42 final size:42
Alignment explanation
Indices: 21128450--21128573 Score: 176
Period size: 42 Copynumber: 3.0 Consensus size: 42
21128440 AATGATATTA
* * *
21128450 ACCCGACTATGTGCGAGTAGGAGTGTGCATAAGCTGATGCTG
1 ACCCGACTATGTGCGAGTGGGAGTGCGCATAAGCCGATGCTG
**
21128492 ACCCTCCTATGTGCGAGTGGGAGTGCGCATAAGCCGATGCTG
1 ACCCGACTATGTGCGAGTGGGAGTGCGCATAAGCCGATGCTG
** *
21128534 ACCCGACTATGTGTAAGTGGGAGTGCACATAAGCCGATGC
1 ACCCGACTATGTGCGAGTGGGAGTGCGCATAAGCCGATGC
21128574 ATATGAGCTG
Statistics
Matches: 72, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 72 1.00
ACGTcount: A:0.23, C:0.23, G:0.32, T:0.22
Consensus pattern (42 bp):
ACCCGACTATGTGCGAGTGGGAGTGCGCATAAGCCGATGCTG
Found at i:21128619 original size:2 final size:2
Alignment explanation
Indices: 21128614--21128654 Score: 73
Period size: 2 Copynumber: 20.0 Consensus size: 2
21128604 ATGATGATTG
21128614 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT ANT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT
21128655 GGTATATGGT
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 36 0.95
3 2 0.05
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:21130016 original size:57 final size:58
Alignment explanation
Indices: 21129873--21130026 Score: 166
Period size: 61 Copynumber: 2.6 Consensus size: 58
21129863 ATATTTGATT
* * * * * *
21129873 GTAAAGGGAGACTTGAAGCCTCGATTCATATTAGGTGGCGTGGGCAGTTTCCACGAGTAA
1 GTAAAGGGGGACTTGAAGCCTCGATTCATATTTGGTGGCATAGGCAATTCCCACGAG--A
* * * * *
21129933 GTAAAAGGGGGACCTGAAGCCCCGATTCGTATTTGGTGGCATAGGTAATTCCCATGAG-
1 GT-AAAGGGGGACTTGAAGCCTCGATTCATATTTGGTGGCATAGGCAATTCCCACGAGA
*
21129991 GTAAAGGGGGACTTGAAGCCTCGATTTATATTTGGT
1 GTAAAGGGGGACTTGAAGCCTCGATTCATATTTGGT
21130027 AGTGTTGTTC
Statistics
Matches: 78, Mismatches: 15, Indels: 5
0.80 0.15 0.05
Matches are distributed among these distances:
57 30 0.38
58 2 0.03
60 2 0.03
61 44 0.56
ACGTcount: A:0.26, C:0.16, G:0.31, T:0.27
Consensus pattern (58 bp):
GTAAAGGGGGACTTGAAGCCTCGATTCATATTTGGTGGCATAGGCAATTCCCACGAGA
Found at i:21131535 original size:74 final size:74
Alignment explanation
Indices: 21131406--21131599 Score: 264
Period size: 74 Copynumber: 2.6 Consensus size: 74
21131396 GGAGATTGTG
* * * * *
21131406 AGACAGAGAAGACTTAGTCGACCAAGAAGCATGGTTAGTCAACTAAGAGCACACTACTAAAGATT
1 AGACAAAGAAGACTTAATCGACTAAGAAGCATGGTTAGTCAACTAAAAGCACACTACCAAAGATT
*
21131471 TTAATTTCA
66 TCAATTTCA
* *
21131480 AGACAAAG-AGAACTTAATCGACTAAGAAGCATGGTTAGTCAACTAAAAGCTCACTACCAGAGAT
1 AGACAAAGAAG-ACTTAATCGACTAAGAAGCATGGTTAGTCAACTAAAAGCACACTACCAAAGAT
21131544 TTCAATTTCA
65 TTCAATTTCA
* * * *
21131554 AGATAGAGAAGACTTAATCGACTAAGAAGCATAGTTAGTTAACTAA
1 AGACAAAGAAGACTTAATCGACTAAGAAGCATGGTTAGTCAACTAA
21131600 GATCACTCTG
Statistics
Matches: 106, Mismatches: 12, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
73 2 0.02
74 102 0.96
75 2 0.02
ACGTcount: A:0.42, C:0.16, G:0.18, T:0.23
Consensus pattern (74 bp):
AGACAAAGAAGACTTAATCGACTAAGAAGCATGGTTAGTCAACTAAAAGCACACTACCAAAGATT
TCAATTTCA
Found at i:21131638 original size:74 final size:72
Alignment explanation
Indices: 21131412--21131639 Score: 233
Period size: 74 Copynumber: 3.1 Consensus size: 72
21131402 TGTGAGACAG
* * *
21131412 AGAAGACTTAGTCGACCAAGAAGCATGGTTAGTCAACTAAGAGCACACTACTAAAGATTTTAATT
1 AGAAGACTTAATCGACTAAGAAGCATGGTTAGTCAACTAAGAGCACACTACTAAAGATTTCAATT
21131477 TCAAGAC-
66 TCAAG-CT
* * * * *
21131484 AAAGAGAACTTAATCGACTAAGAAGCATGGTTAGTCAACTAAAAGCTCACTACCAGAGATTTCAA
1 AGA-AG-ACTTAATCGACTAAGAAGCATGGTTAGTCAACTAAGAGCACACTACTAAAGATTTCAA
*
21131549 TTTCAAGAT
64 TTTCAAGCT
* * * * * * *
21131558 AGAGAAGACTTAATCGACTAAGAAGCATAGTTAGTTAACTAAGATCACTCTGTCTAAAAATTTGA
1 --AGAAGACTTAATCGACTAAGAAGCATGGTTAGTCAACTAAGAGCACACT-ACTAAAGATTTCA
*
21131623 ATTTGAATGCT
63 ATTTCAA-GCT
21131634 AGAAGA
1 AGAAGA
21131640 TAGACTAATA
Statistics
Matches: 126, Mismatches: 23, Indels: 12
0.78 0.14 0.07
Matches are distributed among these distances:
72 2 0.02
73 2 0.02
74 102 0.81
75 16 0.13
76 4 0.03
ACGTcount: A:0.41, C:0.16, G:0.18, T:0.25
Consensus pattern (72 bp):
AGAAGACTTAATCGACTAAGAAGCATGGTTAGTCAACTAAGAGCACACTACTAAAGATTTCAATT
TCAAGCT
Found at i:21135709 original size:19 final size:19
Alignment explanation
Indices: 21135614--21135712 Score: 65
Period size: 19 Copynumber: 5.1 Consensus size: 19
21135604 ACTCGGCTCA
21135614 TGTACATCCCCCCACATCG
1 TGTACATCCCCCCACATCG
* * ** *
21135633 TGCACATAGCCGGCACCATTG
1 TGTACAT-CCCCCCA-CATCG
*
21135654 TGTGCATCCCCCCACATCG
1 TGTACATCCCCCCACATCG
* ****
21135673 TGCACAATCAGTGC-CATCG
1 TGTAC-ATCCCCCCACATCG
21135692 TGTACATCCCCCCACATCG
1 TGTACATCCCCCCACATCG
21135711 TG
1 TG
21135713 CACACTGACA
Statistics
Matches: 54, Mismatches: 22, Indels: 8
0.64 0.26 0.10
Matches are distributed among these distances:
18 4 0.07
19 29 0.54
20 12 0.22
21 9 0.17
ACGTcount: A:0.21, C:0.40, G:0.17, T:0.21
Consensus pattern (19 bp):
TGTACATCCCCCCACATCG
Found at i:21135709 original size:38 final size:39
Alignment explanation
Indices: 21135614--21135716 Score: 138
Period size: 38 Copynumber: 2.6 Consensus size: 39
21135604 ACTCGGCTCA
* *
21135614 TGTACATCCCCCCACATCGTGCACATAGCCGGCACCATTG
1 TGTACATCCCCCCACATCGTGCACATAGCAGG-ACCATCG
* *
21135654 TGTGCATCCCCCCACATCGTGCACA-ATCAGTG-CCATCG
1 TGTACATCCCCCCACATCGTGCACATAGCAG-GACCATCG
21135692 TGTACATCCCCCCACATCGTGCACA
1 TGTACATCCCCCCACATCGTGCACA
21135717 CTGACACTAT
Statistics
Matches: 57, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
38 29 0.51
39 3 0.05
40 25 0.44
ACGTcount: A:0.22, C:0.41, G:0.17, T:0.20
Consensus pattern (39 bp):
TGTACATCCCCCCACATCGTGCACATAGCAGGACCATCG
Found at i:21135838 original size:2 final size:2
Alignment explanation
Indices: 21135831--21135867 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
21135821 ATCATGCATA
21135831 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
21135868 TATATATATA
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:0.51, C:0.49, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:21138488 original size:66 final size:65
Alignment explanation
Indices: 21138382--21138511 Score: 224
Period size: 66 Copynumber: 2.0 Consensus size: 65
21138372 TTACTATCGA
21138382 ATGCCAGACACATACCCAGGAGATGAACTACGGGAACTCCTCGATCTAGGGTCCAACAATCACCC
1 ATGCCAGACACATACCCAGGAGATGAACTACGGGAACTCCTCGATCTAGGGTCCAACAATCACCC
* * *
21138447 NATGCCAGACACATACCCAGGAGATGCACTACGGGGACTCCTCGATCTAGGGTCCAACAGTCACC
1 -ATGCCAGACACATACCCAGGAGATGAACTACGGGAACTCCTCGATCTAGGGTCCAACAATCACC
21138512 TAATTTGAAA
Statistics
Matches: 61, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
66 61 1.00
ACGTcount: A:0.30, C:0.32, G:0.22, T:0.15
Consensus pattern (65 bp):
ATGCCAGACACATACCCAGGAGATGAACTACGGGAACTCCTCGATCTAGGGTCCAACAATCACCC
Found at i:21139192 original size:64 final size:64
Alignment explanation
Indices: 21139095--21139362 Score: 387
Period size: 64 Copynumber: 4.2 Consensus size: 64
21139085 TCCCCACTTT
* ** * *
21139095 GCACATGCACGGTAGTAATTATCACAACCTTTATCATTAAATCGGTGTTTGTACTTTCCACTCC
1 GCACATGCACGGTCGTAATTATCACAACCTTTATCATTAAATCGGCATTTGCACTTCCCACTCC
*
21139159 GCACATGCACGGTCGTAATTATCACAACTTTTATCATTAAA-CAGGCATTTGCACTTCCCACTCC
1 GCACATGCACGGTCGTAATTATCACAACCTTTATCATTAAATC-GGCATTTGCACTTCCCACTCC
* * **
21139223 GCACATGCACGATCGTAATTATCACAACCTTTATCATTAAACCAACATTTGCACTTCCCACTCC
1 GCACATGCACGGTCGTAATTATCACAACCTTTATCATTAAATCGGCATTTGCACTTCCCACTCC
* * * *
21139287 GCACATGCACGGTCGTAATTATCACATCCTTTATCATTCAATTGGCA-TTGCACTTCCCACTCT
1 GCACATGCACGGTCGTAATTATCACAACCTTTATCATTAAATCGGCATTTGCACTTCCCACTCC
21139350 GCACATGCACGGT
1 GCACATGCACGGT
21139363 TGCATCAATT
Statistics
Matches: 184, Mismatches: 18, Indels: 5
0.89 0.09 0.02
Matches are distributed among these distances:
63 29 0.16
64 154 0.84
65 1 0.01
ACGTcount: A:0.27, C:0.29, G:0.13, T:0.31
Consensus pattern (64 bp):
GCACATGCACGGTCGTAATTATCACAACCTTTATCATTAAATCGGCATTTGCACTTCCCACTCC
Found at i:21142341 original size:37 final size:37
Alignment explanation
Indices: 21142300--21142373 Score: 148
Period size: 37 Copynumber: 2.0 Consensus size: 37
21142290 GTTGTGTGAG
21142300 GATGTTGAAGTGTGCGAGTAGGGAGTGCACACATGAT
1 GATGTTGAAGTGTGCGAGTAGGGAGTGCACACATGAT
21142337 GATGTTGAAGTGTGCGAGTAGGGAGTGCACACATGAT
1 GATGTTGAAGTGTGCGAGTAGGGAGTGCACACATGAT
21142374 AATGAATGCA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.27, C:0.11, G:0.38, T:0.24
Consensus pattern (37 bp):
GATGTTGAAGTGTGCGAGTAGGGAGTGCACACATGAT
Found at i:21144237 original size:19 final size:19
Alignment explanation
Indices: 21144197--21144238 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
21144187 GGTGGCAAGG
*
21144197 TGAAAATGGCATGGAAGTT
1 TGAAAATGGCATGGAAGCT
*
21144216 TGAAAATGGCATGGGAGCT
1 TGAAAATGGCATGGAAGCT
21144235 TGAA
1 TGAA
21144239 GGAGAAAATG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.36, C:0.07, G:0.33, T:0.24
Consensus pattern (19 bp):
TGAAAATGGCATGGAAGCT
Found at i:21151075 original size:19 final size:20
Alignment explanation
Indices: 21151035--21151077 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
21151025 TTTCTTTGTT
21151035 CCTTTGGTAGTGGCACCTTA
1 CCTTTGGTAGTGGCACCTTA
*
21151055 CCTTTGGTAGTGGTA-CTTA
1 CCTTTGGTAGTGGCACCTTA
21151074 CCTT
1 CCTT
21151078 GTATTCAAAC
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 8 0.36
20 14 0.64
ACGTcount: A:0.14, C:0.23, G:0.23, T:0.40
Consensus pattern (20 bp):
CCTTTGGTAGTGGCACCTTA
Found at i:21156814 original size:20 final size:21
Alignment explanation
Indices: 21156772--21156815 Score: 54
Period size: 20 Copynumber: 2.1 Consensus size: 21
21156762 AGGTATATAT
* *
21156772 ATGAATATATGTTTTGTATTG
1 ATGAATATATGTTGTGTACTG
*
21156793 ATGAATA-ATGTTGTGTGCTG
1 ATGAATATATGTTGTGTACTG
21156813 ATG
1 ATG
21156816 TTGAAGTGTG
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 13 0.65
21 7 0.35
ACGTcount: A:0.27, C:0.02, G:0.25, T:0.45
Consensus pattern (21 bp):
ATGAATATATGTTGTGTACTG
Found at i:21156861 original size:37 final size:38
Alignment explanation
Indices: 21156818--21156929 Score: 183
Period size: 37 Copynumber: 3.0 Consensus size: 38
21156808 TGCTGATGTT
21156818 GAAGTGTGCGAGTAGGGAGTGCACACATGATGATGATA
1 GAAGTGTGCGAGTAGGGAGTGCACACATGATGATGATA
*
21156856 G-AGTGTGCGAGTAGGGAGTGCACACATGATGATG-TT
1 GAAGTGTGCGAGTAGGGAGTGCACACATGATGATGATA
* *
21156892 GAAGTGTGAGAGTAAGGAGTGCACACATGATGATGATA
1 GAAGTGTGCGAGTAGGGAGTGCACACATGATGATGATA
21156930 TTGCATTGAG
Statistics
Matches: 68, Mismatches: 4, Indels: 4
0.89 0.05 0.05
Matches are distributed among these distances:
36 2 0.03
37 64 0.94
38 2 0.03
ACGTcount: A:0.31, C:0.10, G:0.37, T:0.22
Consensus pattern (38 bp):
GAAGTGTGCGAGTAGGGAGTGCACACATGATGATGATA
Found at i:21159047 original size:18 final size:18
Alignment explanation
Indices: 21159024--21159081 Score: 57
Period size: 18 Copynumber: 3.3 Consensus size: 18
21159014 TTAAAATTGT
21159024 TTAATTAAATTATTGGGC
1 TTAATTAAATTATTGGGC
* *
21159042 TTAATT-AATTAATT-TGT
1 TTAATTAAATT-ATTGGGC
*
21159059 TTAATTAAGTTATTGGGC
1 TTAATTAAATTATTGGGC
*
21159077 CTAAT
1 TTAAT
21159082 CAATTAAATT
Statistics
Matches: 31, Mismatches: 6, Indels: 6
0.72 0.14 0.14
Matches are distributed among these distances:
17 14 0.45
18 17 0.55
ACGTcount: A:0.33, C:0.05, G:0.14, T:0.48
Consensus pattern (18 bp):
TTAATTAAATTATTGGGC
Found at i:21159059 original size:35 final size:35
Alignment explanation
Indices: 21159020--21159088 Score: 111
Period size: 35 Copynumber: 2.0 Consensus size: 35
21159010 TTGATTAAAA
* *
21159020 TTGTTTAATTAAATTATTGGGCTTAATTAATTAAT
1 TTGTTTAATTAAATTATTGGGCCTAATCAATTAAT
*
21159055 TTGTTTAATTAAGTTATTGGGCCTAATCAATTAA
1 TTGTTTAATTAAATTATTGGGCCTAATCAATTAA
21159089 ATTAAATAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 31 1.00
ACGTcount: A:0.33, C:0.06, G:0.13, T:0.48
Consensus pattern (35 bp):
TTGTTTAATTAAATTATTGGGCCTAATCAATTAAT
Found at i:21159099 original size:35 final size:35
Alignment explanation
Indices: 21159025--21159112 Score: 104
Period size: 35 Copynumber: 2.5 Consensus size: 35
21159015 TAAAATTGTT
* * * * ***
21159025 TAATTAAATTATTGGGCTTAATTAATTAATTTGTT
1 TAATTAAGTTATTGGGCCTAATCAATTAAATTAAA
21159060 TAATTAAGTTATTGGGCCTAATCAATTAAATTAAA
1 TAATTAAGTTATTGGGCCTAATCAATTAAATTAAA
21159095 TAATTAAGTTAATTGGGC
1 TAATTAAGTT-ATTGGGC
21159113 TTCTTAAGGA
Statistics
Matches: 45, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
35 38 0.84
36 7 0.16
ACGTcount: A:0.38, C:0.06, G:0.14, T:0.43
Consensus pattern (35 bp):
TAATTAAGTTATTGGGCCTAATCAATTAAATTAAA
Found at i:21159142 original size:13 final size:13
Alignment explanation
Indices: 21159124--21159157 Score: 59
Period size: 13 Copynumber: 2.6 Consensus size: 13
21159114 TCTTAAGGAC
21159124 TTAATTAAATTAT
1 TTAATTAAATTAT
21159137 TTAATTAAATTAT
1 TTAATTAAATTAT
*
21159150 TAAATTAA
1 TTAATTAA
21159158 TTGGCAATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (13 bp):
TTAATTAAATTAT
Found at i:21164204 original size:12 final size:12
Alignment explanation
Indices: 21164182--21164222 Score: 50
Period size: 11 Copynumber: 3.5 Consensus size: 12
21164172 ATGGTTGGCC
21164182 ATAAG-GAGAAA
1 ATAAGAGAGAAA
21164193 ATAAGAGAGAAA
1 ATAAGAGAGAAA
*
21164205 AT-AGAGAGGAA
1 ATAAGAGAGAAA
21164216 ATGAAGA
1 AT-AAGA
21164223 AAAGAGAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
11 15 0.58
12 8 0.31
13 3 0.12
ACGTcount: A:0.61, C:0.00, G:0.29, T:0.10
Consensus pattern (12 bp):
ATAAGAGAGAAA
Found at i:21181544 original size:32 final size:32
Alignment explanation
Indices: 21181507--21181669 Score: 116
Period size: 32 Copynumber: 4.9 Consensus size: 32
21181497 CCTTTAGCAA
* *
21181507 TGGTTTTCCACGGGATCAACCAAAACCCAAAG
1 TGGTTTTTCACGGGCTCAACCAAAACCCAAAG
** *
21181539 TGGTTTTTCAAAGGCTCAACCACAACCTTTCACAA-
1 TGGTTTTTCACGGGCTCAACCAAAACC---CA-AAG
**
21181574 TAATTTTTCACGGGCTCAACCAAAACCCAAAG
1 TGGTTTTTCACGGGCTCAACCAAAACCCAAAG
** * *
21181606 TGGTTTTTCAAAGGCTCAA-CATAACCTACAACAA
1 TGGTTTTTCACGGGCTCAACCAAAACC--CAA-AG
* *
21181640 TGGTTTTT-ACCGAGATCAACCAAAACCCAA
1 TGGTTTTTCA-CGGGCTCAACCAAAACCCAA
21181670 CAACCAACTT
Statistics
Matches: 100, Mismatches: 21, Indels: 19
0.71 0.15 0.14
Matches are distributed among these distances:
31 8 0.08
32 39 0.39
33 7 0.07
34 14 0.14
35 30 0.30
36 2 0.02
ACGTcount: A:0.36, C:0.27, G:0.13, T:0.24
Consensus pattern (32 bp):
TGGTTTTTCACGGGCTCAACCAAAACCCAAAG
Found at i:21181566 original size:67 final size:65
Alignment explanation
Indices: 21181483--21181669 Score: 232
Period size: 67 Copynumber: 2.8 Consensus size: 65
21181473 GGCTTTTTAC
*
21181483 AGGCTCAGCCACAACCTTTAGCAATGGTTTTCCACGGGATCAACCAAAACCCAAAGTGGTTTTTC
1 AGGCTCAACCACAACCTTTA-CAATGGTTTT-CACGGGATCAACCAAAACCCAAAGTGGTTTTTC
21181548 AA
64 AA
** *
21181550 AGGCTCAACCACAACCTTTCACAATAATTTTTCACGGGCTCAACCAAAACCCAAAGTGGTTTTTC
1 AGGCTCAACCACAACCTTT-ACAAT-GGTTTTCACGGGATCAACCAAAACCCAAAGTGGTTTTTC
21181615 AA
64 AA
* ** * *
21181617 AGGCTCAA-CATAACCTACAACAATGGTTTTTACCGAGATCAACCAAAACCCAA
1 AGGCTCAACCACAACCT-TTACAATGGTTTTCA-CGGGATCAACCAAAACCCAA
21181670 CAACCAACTT
Statistics
Matches: 104, Mismatches: 12, Indels: 9
0.83 0.10 0.07
Matches are distributed among these distances:
65 5 0.05
66 30 0.29
67 64 0.62
68 5 0.05
ACGTcount: A:0.35, C:0.28, G:0.14, T:0.23
Consensus pattern (65 bp):
AGGCTCAACCACAACCTTTACAATGGTTTTCACGGGATCAACCAAAACCCAAAGTGGTTTTTCAA
Found at i:21183496 original size:42 final size:42
Alignment explanation
Indices: 21183320--21183497 Score: 234
Period size: 42 Copynumber: 4.2 Consensus size: 42
21183310 TACCATCCCA
* * *
21183320 TCATTATCAGCTCATATGCACTTCCCACTCGCACATAGCTAGG
1 TCATCATCAGCTCATGTGCAC-TCCCACACGCACATAGCTAGG
* *
21183363 TCATCA-CTAGCTCATGTGCACT-CCACACCGCACATAGTTGGG
1 TCATCATC-AGCTCATGTGCACTCCCACA-CGCACATAGCTAGG
* *
21183405 TCATCATTAGCTCATGTGCACTCCCACACGCACATAGTTAGG
1 TCATCATCAGCTCATGTGCACTCCCACACGCACATAGCTAGG
* *
21183447 TCATCATCAGCTCATGTGCACTCCCACATGCACATAGCTGGG
1 TCATCATCAGCTCATGTGCACTCCCACACGCACATAGCTAGG
21183489 TCATCATCA
1 TCATCATCA
21183498 TCTAAAAAAA
Statistics
Matches: 120, Mismatches: 11, Indels: 9
0.86 0.08 0.06
Matches are distributed among these distances:
41 4 0.03
42 94 0.78
43 22 0.18
ACGTcount: A:0.25, C:0.33, G:0.16, T:0.26
Consensus pattern (42 bp):
TCATCATCAGCTCATGTGCACTCCCACACGCACATAGCTAGG
Found at i:21185106 original size:42 final size:42
Alignment explanation
Indices: 21184955--21185107 Score: 173
Period size: 42 Copynumber: 3.6 Consensus size: 42
21184945 TCATCAGGTC
* * * *
21184955 ATGTGCACTCCCCACTAGCACATGGCTAGGTCAACATCGGCTT
1 ATGTGCACT-CCTACTCGCACATAGCTAGGTCATCATCGGCTT
* * *
21184998 ATGTGCACTCTTACTCTCACATAG-TACGGTCATTATCGGCTT
1 ATGTGCACTCCTACTCGCACATAGCTA-GGTCATCATCGGCTT
* * * *
21185040 ATGTGCACTCCTACTCCCACATAGCCAGGTCATCATTGGCGT
1 ATGTGCACTCCTACTCGCACATAGCTAGGTCATCATCGGCTT
*
21185082 ATGCGCACTCCTACTCGCACATAGCT
1 ATGTGCACTCCTACTCGCACATAGCT
21185108 GGGCGTACAT
Statistics
Matches: 92, Mismatches: 16, Indels: 5
0.81 0.14 0.04
Matches are distributed among these distances:
41 2 0.02
42 80 0.87
43 10 0.11
ACGTcount: A:0.22, C:0.32, G:0.18, T:0.27
Consensus pattern (42 bp):
ATGTGCACTCCTACTCGCACATAGCTAGGTCATCATCGGCTT
Found at i:21191808 original size:2 final size:2
Alignment explanation
Indices: 21191803--21191921 Score: 139
Period size: 2 Copynumber: 58.0 Consensus size: 2
21191793 ATGTGCAAAC
*
21191803 AT AT AT GT 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
* * * ** * *
21191845 AT AT AT AT ACT AC ACC ANT GT GC AA AC AT AT AT AT AT AT AT AT
1 AT AT AT AT A-T AT A-T A-T AT AT AT AT AT AT AT AT AT AT AT AT
21191888 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
21191922 CCATCACCAT
Statistics
Matches: 104, Mismatches: 11, Indels: 4
0.87 0.09 0.03
Matches are distributed among these distances:
2 100 0.96
3 4 0.04
ACGTcount: A:0.47, C:0.05, G:0.03, T:0.45
Consensus pattern (2 bp):
AT
Found at i:21205171 original size:20 final size:20
Alignment explanation
Indices: 21205124--21205175 Score: 63
Period size: 21 Copynumber: 2.6 Consensus size: 20
21205114 TAATATTATC
21205124 AATTAATT-AA-TTTAAATG
1 AATTAATTCAATTTTAAATG
* *
21205142 AATCATATTCAATTTTAAATT
1 AATTA-ATTCAATTTTAAATG
21205163 AATTAATTCAATT
1 AATTAATTCAATT
21205176 CCATAGACTA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
18 4 0.14
19 3 0.11
20 10 0.36
21 11 0.39
ACGTcount: A:0.46, C:0.06, G:0.02, T:0.46
Consensus pattern (20 bp):
AATTAATTCAATTTTAAATG
Found at i:21214627 original size:15 final size:15
Alignment explanation
Indices: 21214604--21214634 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
21214594 CAACTCATTT
*
21214604 TTTATTAGTCAAGAC
1 TTTACTAGTCAAGAC
21214619 TTTACTAGTCAAGAC
1 TTTACTAGTCAAGAC
21214634 T
1 T
21214635 AAATATTGAG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.32, C:0.16, G:0.13, T:0.39
Consensus pattern (15 bp):
TTTACTAGTCAAGAC
Found at i:21216105 original size:51 final size:51
Alignment explanation
Indices: 21216042--21216163 Score: 235
Period size: 51 Copynumber: 2.4 Consensus size: 51
21216032 TACATTCAAG
*
21216042 AATGTACTGATAGATTTGAACAAGGATGAACATCTATTGATACATTGTCCA
1 AATGTATTGATAGATTTGAACAAGGATGAACATCTATTGATACATTGTCCA
21216093 AATGTATTGATAGATTTGAACAAGGATGAACATCTATTGATACATTGTCCA
1 AATGTATTGATAGATTTGAACAAGGATGAACATCTATTGATACATTGTCCA
21216144 AATGTATTGATAGATTTGAA
1 AATGTATTGATAGATTTGAA
21216164 ATAAAGAGCA
Statistics
Matches: 70, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
51 70 1.00
ACGTcount: A:0.38, C:0.11, G:0.18, T:0.34
Consensus pattern (51 bp):
AATGTATTGATAGATTTGAACAAGGATGAACATCTATTGATACATTGTCCA
Found at i:21222070 original size:54 final size:54
Alignment explanation
Indices: 21221983--21222091 Score: 191
Period size: 54 Copynumber: 2.0 Consensus size: 54
21221973 TACATCATAT
* *
21221983 ACACAATCTTATAGTATACATCATGCATGCTTAATCACCTCATATGGTATATGG
1 ACACAATCTTAGAGTATACATCATGCATACTTAATCACCTCATATGGTATATGG
*
21222037 ACACAATCTTGGAGTATACATCATGCATACTTAATCACCTCATATGGTATATGG
1 ACACAATCTTAGAGTATACATCATGCATACTTAATCACCTCATATGGTATATGG
21222091 A
1 A
21222092 ATTTACATCA
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
54 52 1.00
ACGTcount: A:0.34, C:0.20, G:0.14, T:0.32
Consensus pattern (54 bp):
ACACAATCTTAGAGTATACATCATGCATACTTAATCACCTCATATGGTATATGG
Found at i:21222125 original size:68 final size:68
Alignment explanation
Indices: 21222049--21222175 Score: 245
Period size: 68 Copynumber: 1.9 Consensus size: 68
21222039 ACAATCTTGG
21222049 AGTATACATCATGCATACTTAATCACCTCATATGGTATATGGAATTTACATCATATACACAATCA
1 AGTATACATCATGCATACTTAATCACCTCATATGGTATATGGAATTTACATCATATACACAATCA
21222114 TAT
66 TAT
*
21222117 AGTATACATCATGCATACTTAATCATCTCATATGGTATATGGAATTTACATCATATACA
1 AGTATACATCATGCATACTTAATCACCTCATATGGTATATGGAATTTACATCATATACA
21222176 TTTACATCAT
Statistics
Matches: 58, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
68 58 1.00
ACGTcount: A:0.38, C:0.18, G:0.09, T:0.35
Consensus pattern (68 bp):
AGTATACATCATGCATACTTAATCACCTCATATGGTATATGGAATTTACATCATATACACAATCA
TAT
Found at i:21222140 original size:28 final size:28
Alignment explanation
Indices: 21222109--21222225 Score: 82
Period size: 28 Copynumber: 4.2 Consensus size: 28
21222099 TCATATACAC
21222109 AATCATATAGTATACATCATGCATACTT
1 AATCATATAGTATACATCATGCATACTT
* ** * *
21222137 AATCATCTCA-TATGGTAT-ATGGA-ATTT
1 AATCATAT-AGTAT-ACATCATGCATACTT
* * **
21222164 ACATCATATACATTTACATCAT--ATACAC
1 A-ATCATATA-GTATACATCATGCATACTT
21222192 AATCATATAGTATACATCATGCATACTT
1 AATCATATAGTATACATCATGCATACTT
21222220 AATCAT
1 AATCAT
21222226 CTCATATGGT
Statistics
Matches: 64, Mismatches: 16, Indels: 18
0.65 0.16 0.18
Matches are distributed among these distances:
26 9 0.14
27 14 0.22
28 34 0.53
29 7 0.11
ACGTcount: A:0.39, C:0.18, G:0.07, T:0.36
Consensus pattern (28 bp):
AATCATATAGTATACATCATGCATACTT
Found at i:21222151 original size:122 final size:122
Alignment explanation
Indices: 21221934--21222159 Score: 407
Period size: 122 Copynumber: 1.9 Consensus size: 122
21221924 GTCGTGACAT
* *
21221934 ATCATGCATACTCAATCACTTCATATGGTATATGGAATTTACATCATATACACAATCTTATAGTA
1 ATCATGCATACTCAATCACCTCATATGGTATATGGAATTTACATCATATACACAATCATATAGTA
*
21221999 TACATCATGCATGCTTAATCACCTCATATGGTATATGGACACAATCTTGGAGTATAC
66 TACATCATGCATACTTAATCACCTCATATGGTATATGGACACAATCTTGGAGTATAC
*
21222056 ATCATGCATACTTAATCACCTCATATGGTATATGGAATTTACATCATATACACAATCATATAGTA
1 ATCATGCATACTCAATCACCTCATATGGTATATGGAATTTACATCATATACACAATCATATAGTA
*
21222121 TACATCATGCATACTTAATCATCTCATATGGTATATGGA
66 TACATCATGCATACTTAATCACCTCATATGGTATATGGA
21222160 ATTTACATCA
Statistics
Matches: 99, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
122 99 1.00
ACGTcount: A:0.35, C:0.19, G:0.12, T:0.34
Consensus pattern (122 bp):
ATCATGCATACTCAATCACCTCATATGGTATATGGAATTTACATCATATACACAATCATATAGTA
TACATCATGCATACTTAATCACCTCATATGGTATATGGACACAATCTTGGAGTATAC
Found at i:21222180 original size:15 final size:15
Alignment explanation
Indices: 21222160--21222190 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
21222150 GGTATATGGA
21222160 ATTTACATCATATAC
1 ATTTACATCATATAC
21222175 ATTTACATCATATAC
1 ATTTACATCATATAC
21222190 A
1 A
21222191 CAATCATATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.42, C:0.19, G:0.00, T:0.39
Consensus pattern (15 bp):
ATTTACATCATATAC
Found at i:21222193 original size:83 final size:83
Alignment explanation
Indices: 21222092--21222259 Score: 336
Period size: 83 Copynumber: 2.0 Consensus size: 83
21222082 GGTATATGGA
21222092 ATTTACATCATATACACAATCATATAGTATACATCATGCATACTTAATCATCTCATATGGTATAT
1 ATTTACATCATATACACAATCATATAGTATACATCATGCATACTTAATCATCTCATATGGTATAT
21222157 GGAATTTACATCATATAC
66 GGAATTTACATCATATAC
21222175 ATTTACATCATATACACAATCATATAGTATACATCATGCATACTTAATCATCTCATATGGTATAT
1 ATTTACATCATATACACAATCATATAGTATACATCATGCATACTTAATCATCTCATATGGTATAT
21222240 GGAATTTACATCATATAC
66 GGAATTTACATCATATAC
21222258 AT
1 AT
21222260 AATCTTATGG
Statistics
Matches: 85, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
83 85 1.00
ACGTcount: A:0.39, C:0.18, G:0.07, T:0.36
Consensus pattern (83 bp):
ATTTACATCATATACACAATCATATAGTATACATCATGCATACTTAATCATCTCATATGGTATAT
GGAATTTACATCATATAC
Found at i:21225231 original size:42 final size:43
Alignment explanation
Indices: 21225153--21225234 Score: 130
Period size: 42 Copynumber: 1.9 Consensus size: 43
21225143 CCACACTCCA
* * *
21225153 CTCATGTGCACTCCCTACTCGCACATACCTGGGTCATCATCAG
1 CTCATGTGCACTCCCTACACGCACATAACTAGGTCATCATCAG
21225196 CTCATGTGCACTCCC-ACACGCACATAACTAGGTCATCAT
1 CTCATGTGCACTCCCTACACGCACATAACTAGGTCATCAT
21225235 TATCTCACAA
Statistics
Matches: 36, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
42 21 0.58
43 15 0.42
ACGTcount: A:0.24, C:0.37, G:0.15, T:0.24
Consensus pattern (43 bp):
CTCATGTGCACTCCCTACACGCACATAACTAGGTCATCATCAG
Found at i:21229783 original size:24 final size:24
Alignment explanation
Indices: 21229751--21229799 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
21229741 AAATTTACAG
21229751 TGTCAGTGTGGCCCCAAGTTAAGT
1 TGTCAGTGTGGCCCCAAGTTAAGT
*
21229775 TGTCAGTGTGGTCCCAAGTTAAGT
1 TGTCAGTGTGGCCCCAAGTTAAGT
21229799 T
1 T
21229800 AAGTTAAGTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.20, C:0.18, G:0.29, T:0.33
Consensus pattern (24 bp):
TGTCAGTGTGGCCCCAAGTTAAGT
Found at i:21241860 original size:37 final size:37
Alignment explanation
Indices: 21241820--21241938 Score: 177
Period size: 37 Copynumber: 3.2 Consensus size: 37
21241810 TGATGTTGTG
*
21241820 TGATGATGTTGAAGTGTGTGAGTAGGGAGTGCACACG
1 TGATGATGTTGAAGTGTGTGAGTAGGGAGTGCACACA
* **
21241857 TGATGATGATAGAA-TGTGTGAGTAAAGAGTGCACACA
1 TGATGATG-TTGAAGTGTGTGAGTAGGGAGTGCACACA
*
21241894 TGATGATGTTGAAGTGTGCGAGTAGGGAGTGCACACA
1 TGATGATGTTGAAGTGTGTGAGTAGGGAGTGCACACA
21241931 TGATGATG
1 TGATGATG
21241939 ATATTACATT
Statistics
Matches: 72, Mismatches: 8, Indels: 4
0.86 0.10 0.05
Matches are distributed among these distances:
36 4 0.06
37 64 0.89
38 4 0.06
ACGTcount: A:0.29, C:0.08, G:0.36, T:0.26
Consensus pattern (37 bp):
TGATGATGTTGAAGTGTGTGAGTAGGGAGTGCACACA
Found at i:21245238 original size:20 final size:20
Alignment explanation
Indices: 21245213--21245252 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
21245203 GCATAAATAT
21245213 CTCATTTCTCTAGTACCTTC
1 CTCATTTCTCTAGTACCTTC
* *
21245233 CTCATTTTTCTAGTAGCTTC
1 CTCATTTCTCTAGTACCTTC
21245253 TTCTTCTTCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.15, C:0.30, G:0.07, T:0.47
Consensus pattern (20 bp):
CTCATTTCTCTAGTACCTTC
Found at i:21246094 original size:43 final size:43
Alignment explanation
Indices: 21246035--21246164 Score: 224
Period size: 43 Copynumber: 3.0 Consensus size: 43
21246025 TTGTGTGATA
*
21246035 ATGATGACCCAACTATGTGCGGTGTGGGAGTGCACATGAGCTG
1 ATGATGACCCAGCTATGTGCGGTGTGGGAGTGCACATGAGCTG
* *
21246078 ATGATGACCCAGCTATGTGCGGTATGGGAGTGCACATGAGTTG
1 ATGATGACCCAGCTATGTGCGGTGTGGGAGTGCACATGAGCTG
*
21246121 ATGATGACCCAGCTATGTGCAGTGTGGGAGTGCACATGAGCTG
1 ATGATGACCCAGCTATGTGCGGTGTGGGAGTGCACATGAGCTG
21246164 A
1 A
21246165 GTGTGGTGGG
Statistics
Matches: 81, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
43 81 1.00
ACGTcount: A:0.24, C:0.18, G:0.35, T:0.24
Consensus pattern (43 bp):
ATGATGACCCAGCTATGTGCGGTGTGGGAGTGCACATGAGCTG
Found at i:21246323 original size:24 final size:24
Alignment explanation
Indices: 21246279--21246326 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
21246269 AATTGCTCCC
*
21246279 AAATTGCTTTTCATTTAAACAAGA
1 AAATTGCTTTTCATGTAAACAAGA
*
21246303 AAATTGCTTTTTGATGT-AACAAGA
1 AAATTGC-TTTTCATGTAAACAAGA
21246327 CCCCTTTTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 14 0.67
25 7 0.33
ACGTcount: A:0.40, C:0.10, G:0.12, T:0.38
Consensus pattern (24 bp):
AAATTGCTTTTCATGTAAACAAGA
Found at i:21255791 original size:26 final size:26
Alignment explanation
Indices: 21255755--21255816 Score: 106
Period size: 26 Copynumber: 2.4 Consensus size: 26
21255745 TTGCATATGA
21255755 GATGATGATGATGGGATGATGTGCAT
1 GATGATGATGATGGGATGATGTGCAT
*
21255781 GATGATGATGATGGGATGGTGTGCAT
1 GATGATGATGATGGGATGATGTGCAT
*
21255807 GTTGATGATG
1 GATGATGATG
21255817 GGTATATGGT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 34 1.00
ACGTcount: A:0.24, C:0.03, G:0.40, T:0.32
Consensus pattern (26 bp):
GATGATGATGATGGGATGATGTGCAT
Found at i:21256878 original size:18 final size:19
Alignment explanation
Indices: 21256857--21256896 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
21256847 CAAGTGAAAA
*
21256857 ATTTTA-GAATCAAATAAT
1 ATTTTATGAATAAAATAAT
*
21256875 ATTTTATTAATAAAATAAT
1 ATTTTATGAATAAAATAAT
21256894 ATT
1 ATT
21256897 AAAATATTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 6 0.32
19 13 0.68
ACGTcount: A:0.50, C:0.03, G:0.03, T:0.45
Consensus pattern (19 bp):
ATTTTATGAATAAAATAAT
Found at i:21258047 original size:54 final size:53
Alignment explanation
Indices: 21257965--21258073 Score: 155
Period size: 54 Copynumber: 2.0 Consensus size: 53
21257955 AACTTGATAA
21257965 ATATCCTTAGAAAAAACTAATATATGTGCTAGAGTCATAAACAAGTTGCCAGT
1 ATATCCTTAGAAAAAACTAATATATGTGCTAGAGTCATAAACAAGTTGCCAGT
* * * * * *
21258018 NATATCCTTAGACAAGATTTATATATGTGCTAGAGTCATAAATAAGTTGTCAGT
1 -ATATCCTTAGAAAAAACTAATATATGTGCTAGAGTCATAAACAAGTTGCCAGT
21258072 AT
1 AT
21258074 GTCAAGCCCG
Statistics
Matches: 49, Mismatches: 6, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
53 2 0.04
54 47 0.96
ACGTcount: A:0.39, C:0.13, G:0.16, T:0.32
Consensus pattern (53 bp):
ATATCCTTAGAAAAAACTAATATATGTGCTAGAGTCATAAACAAGTTGCCAGT
Found at i:21261146 original size:5 final size:5
Alignment explanation
Indices: 21261136--21261165 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
21261126 AGTGTGGCCC
*
21261136 AAGTT AAGTT ATGTT AAGTT AAGTT AAGTT
1 AAGTT AAGTT AAGTT AAGTT AAGTT AAGTT
21261166 TGATATAATA
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:0.37, C:0.00, G:0.20, T:0.43
Consensus pattern (5 bp):
AAGTT
Found at i:21268735 original size:35 final size:35
Alignment explanation
Indices: 21268696--21268765 Score: 95
Period size: 35 Copynumber: 2.0 Consensus size: 35
21268686 GGAGTGCGTG
*
21268696 TGATGGTATTGAAATGTACGTGTAGGGAGTGCACA
1 TGATGATATTGAAATGTACGTGTAGGGAGTGCACA
*** *
21268731 TGATGATATTGCCTTGTGCGTGTAGGGAGTGCACA
1 TGATGATATTGAAATGTACGTGTAGGGAGTGCACA
21268766 AAAGTTGATG
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
35 30 1.00
ACGTcount: A:0.24, C:0.11, G:0.34, T:0.30
Consensus pattern (35 bp):
TGATGATATTGAAATGTACGTGTAGGGAGTGCACA
Found at i:21268836 original size:21 final size:21
Alignment explanation
Indices: 21268805--21268860 Score: 69
Period size: 21 Copynumber: 2.7 Consensus size: 21
21268795 TTTATATATT
* *
21268805 CATAAGCTATAGAGACGTTTA
1 CATATGCTATAGAAACGTTTA
* *
21268826 TATATGCTATAGAAATGTTTA
1 CATATGCTATAGAAACGTTTA
21268847 CATATGCTAT-GAAA
1 CATATGCTATAGAAA
21268861 AAGTTAAGAA
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
20 4 0.13
21 26 0.87
ACGTcount: A:0.39, C:0.11, G:0.16, T:0.34
Consensus pattern (21 bp):
CATATGCTATAGAAACGTTTA
Found at i:21273224 original size:54 final size:54
Alignment explanation
Indices: 21273150--21273311 Score: 243
Period size: 54 Copynumber: 3.0 Consensus size: 54
21273140 ATAAGCACAT
**
21273150 ACACCACCATCTCATGCAGCTCATGTGCATCCCCCCACATCGTGCACATAGCCAG
1 ACACC-CCATCTCACCCAGCTCATGTGCATCCCCCCACATCGTGCACATAGCCAG
* **
21273205 ACATCCCATCTCACCCAGCTCATGTGCATCCCCCCACATCGTGCACATAGCTGG
1 ACACCCCATCTCACCCAGCTCATGTGCATCCCCCCACATCGTGCACATAGCCAG
* * *
21273259 ACACCCCATCTCACCCAACTCATGTTCATCCCCCCACATCGTGTACATAGCCA
1 ACACCCCATCTCACCCAGCTCATGTGCATCCCCCCACATCGTGCACATAGCCA
21273312 AAGTCATAGT
Statistics
Matches: 96, Mismatches: 11, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
54 92 0.96
55 4 0.04
ACGTcount: A:0.25, C:0.43, G:0.12, T:0.20
Consensus pattern (54 bp):
ACACCCCATCTCACCCAGCTCATGTGCATCCCCCCACATCGTGCACATAGCCAG
Found at i:21274385 original size:19 final size:20
Alignment explanation
Indices: 21274347--21274385 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
21274337 AGGAAGAAGA
* *
21274347 AGAAGTTGCTGGAGAAATAT
1 AGAAGCTGCTGGAAAAATAT
21274367 AGAAGCTGCT-GAAAAATAT
1 AGAAGCTGCTGGAAAAATAT
21274386 GAGATCTTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.44, C:0.08, G:0.26, T:0.23
Consensus pattern (20 bp):
AGAAGCTGCTGGAAAAATAT
Found at i:21281163 original size:40 final size:38
Alignment explanation
Indices: 21281108--21281213 Score: 140
Period size: 38 Copynumber: 2.7 Consensus size: 38
21281098 CACACCCGGC
* *
21281108 TCATGTACATCCCCCCACATCGTGCACATTGCTGATGCCA
1 TCATGTACATCCCCCCACATCGTGCACAAT-C-AATGCCA
* * *
21281148 TCATGTGCATCCCCCCACATCCTGTACAATCAATGCCA
1 TCATGTACATCCCCCCACATCGTGCACAATCAATGCCA
*
21281186 TCATGTACATCCCCCCACATAGTGCACA
1 TCATGTACATCCCCCCACATCGTGCACA
21281214 CGGGCACTAG
Statistics
Matches: 57, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
38 30 0.53
39 1 0.02
40 26 0.46
ACGTcount: A:0.25, C:0.39, G:0.12, T:0.24
Consensus pattern (38 bp):
TCATGTACATCCCCCCACATCGTGCACAATCAATGCCA
Found at i:21281197 original size:38 final size:40
Alignment explanation
Indices: 21281108--21281205 Score: 137
Period size: 40 Copynumber: 2.5 Consensus size: 40
21281098 CACACCCGGC
* * *
21281108 TCATGTACATCCCCCCACATCGTGCACATTGCTGATGCCA
1 TCATGTACATCCCCCCACATCCTGCACAATGCTAATGCCA
* *
21281148 TCATGTGCATCCCCCCACATCCTGTACAAT-C-AATGCCA
1 TCATGTACATCCCCCCACATCCTGCACAATGCTAATGCCA
21281186 TCATGTACATCCCCCCACAT
1 TCATGTACATCCCCCCACAT
21281206 AGTGCACACG
Statistics
Matches: 52, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
38 25 0.48
39 1 0.02
40 26 0.50
ACGTcount: A:0.24, C:0.40, G:0.11, T:0.24
Consensus pattern (40 bp):
TCATGTACATCCCCCCACATCCTGCACAATGCTAATGCCA
Found at i:21281935 original size:24 final size:24
Alignment explanation
Indices: 21281889--21281936 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
21281879 TTCTAAATAA
* *
21281889 TTTCCACCCAAATCCATCTTATAT
1 TTTCCACACAAATCCATCATATAT
21281913 TTTCCACACATAATCCA-CATATAT
1 TTTCCACACA-AATCCATCATATAT
21281937 GGCAAAAACA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 15 0.71
25 6 0.29
ACGTcount: A:0.33, C:0.31, G:0.00, T:0.35
Consensus pattern (24 bp):
TTTCCACACAAATCCATCATATAT
Found at i:21282524 original size:13 final size:14
Alignment explanation
Indices: 21282506--21282536 Score: 55
Period size: 13 Copynumber: 2.3 Consensus size: 14
21282496 AAAGGCAATG
21282506 GAAAGAAAAT-AAA
1 GAAAGAAAATAAAA
21282519 GAAAGAAAATAAAA
1 GAAAGAAAATAAAA
21282533 GAAA
1 GAAA
21282537 ATTAAGTTTC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.59
14 7 0.41
ACGTcount: A:0.77, C:0.00, G:0.16, T:0.06
Consensus pattern (14 bp):
GAAAGAAAATAAAA
Found at i:21294782 original size:19 final size:19
Alignment explanation
Indices: 21294760--21294797 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
21294750 GCCCACGTGT
21294760 CATTGTAAATTAAATTACA
1 CATTGTAAATTAAATTACA
21294779 CATTGTAAATTAAATTACA
1 CATTGTAAATTAAATTACA
21294798 TACCTTGACA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.47, C:0.11, G:0.05, T:0.37
Consensus pattern (19 bp):
CATTGTAAATTAAATTACA
Found at i:21298108 original size:21 final size:22
Alignment explanation
Indices: 21298083--21298123 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
21298073 CCTAGGTGGA
*
21298083 AAAATTCAAGGGAA-AAGTGTG
1 AAAATTCAAGGAAACAAGTGTG
21298104 AAAATTCAAGGAAACAAGTG
1 AAAATTCAAGGAAACAAGTG
21298124 AAAAAAAGGT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.51, C:0.07, G:0.24, T:0.17
Consensus pattern (22 bp):
AAAATTCAAGGAAACAAGTGTG
Found at i:21298124 original size:20 final size:21
Alignment explanation
Indices: 21298083--21298127 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 21
21298073 CCTAGGTGGA
*
21298083 AAAATTCAAGGGAAAAGTGTG
1 AAAATTCAAGGGAAAAGAGTG
21298104 AAAATTCAA-GGAAACA-AGTG
1 AAAATTCAAGGGAAA-AGAGTG
21298124 AAAA
1 AAAA
21298128 AAAGGTAAGA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
20 12 0.55
21 10 0.45
ACGTcount: A:0.56, C:0.07, G:0.22, T:0.16
Consensus pattern (21 bp):
AAAATTCAAGGGAAAAGAGTG
Found at i:21298128 original size:21 final size:20
Alignment explanation
Indices: 21298081--21298128 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 20
21298071 ACCCTAGGTG
*
21298081 GAAAAATTCAAGGGAAAAGT
1 GAAAAATTCAAGGAAAAAGT
*
21298101 GTGAAAATTCAAGGAAACAAGT
1 G-AAAAATTCAAGGAAA-AAGT
21298123 GAAAAA
1 GAAAAA
21298129 AAGGTAAGAT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
20 1 0.04
21 17 0.74
22 5 0.22
ACGTcount: A:0.56, C:0.06, G:0.23, T:0.15
Consensus pattern (20 bp):
GAAAAATTCAAGGAAAAAGT
Found at i:21302344 original size:42 final size:42
Alignment explanation
Indices: 21302270--21302368 Score: 119
Period size: 42 Copynumber: 2.4 Consensus size: 42
21302260 GTAATGATAT
* * **
21302270 TGACCCAGCTATGTGTGAGTAGGAGTGTGCATAAGTTGATGC
1 TGACCCAGCTATGTGCGAGTAGGAGTGCGCATAAGCCGATGC
* *
21302312 TGACCC-GACTATGTGCGAGTGGGTGTGCGCATAAGCCGATGC
1 TGACCCAG-CTATGTGCGAGTAGGAGTGCGCATAAGCCGATGC
*
21302354 TGACCCAGCCATGTG
1 TGACCCAGCTATGTG
21302369 TTAATGGGAG
Statistics
Matches: 48, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
41 1 0.02
42 46 0.96
43 1 0.02
ACGTcount: A:0.21, C:0.21, G:0.33, T:0.24
Consensus pattern (42 bp):
TGACCCAGCTATGTGCGAGTAGGAGTGCGCATAAGCCGATGC
Found at i:21302465 original size:2 final size:2
Alignment explanation
Indices: 21302422--21302454 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
21302412 ATGATGATTG
21302422 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 A
21302455 ATAACATATA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:21306097 original size:5 final size:5
Alignment explanation
Indices: 21306058--21306093 Score: 63
Period size: 5 Copynumber: 7.2 Consensus size: 5
21306048 AGTATGGCCG
*
21306058 AAGTT AAGTT AAGTT AAGTT AAGTT AAGTT AGGTT A
1 AAGTT AAGTT AAGTT AAGTT AAGTT AAGTT AAGTT A
21306094 GGTTGAATAT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
5 30 1.00
ACGTcount: A:0.39, C:0.00, G:0.22, T:0.39
Consensus pattern (5 bp):
AAGTT
Found at i:21312028 original size:13 final size:13
Alignment explanation
Indices: 21312010--21312034 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
21312000 TTTCAGAAAA
21312010 TTTATAAAATCAT
1 TTTATAAAATCAT
21312023 TTTATAAAATCA
1 TTTATAAAATCA
21312035 CAATTTCTCC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.08, G:0.00, T:0.44
Consensus pattern (13 bp):
TTTATAAAATCAT
Found at i:21318585 original size:35 final size:35
Alignment explanation
Indices: 21318484--21318564 Score: 126
Period size: 35 Copynumber: 2.3 Consensus size: 35
21318474 GGAGTGCGTG
* * **
21318484 TGATGGTATTGAAATGTGCGTGTAACGAGTGCACA
1 TGATGATATTGAAATGTGCATGTAGGGAGTGCACA
21318519 TGATGATATTGAAATGTGCATGTAGGGAGTGCACA
1 TGATGATATTGAAATGTGCATGTAGGGAGTGCACA
21318554 TGATGATATTG
1 TGATGATATTG
21318565 CCTTGTGTGT
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 42 1.00
ACGTcount: A:0.30, C:0.09, G:0.31, T:0.31
Consensus pattern (35 bp):
TGATGATATTGAAATGTGCATGTAGGGAGTGCACA
Found at i:21318659 original size:21 final size:21
Alignment explanation
Indices: 21318633--21318683 Score: 77
Period size: 21 Copynumber: 2.5 Consensus size: 21
21318623 ATATTCATAC
* *
21318633 GCTATATAGATGTTTATATAT
1 GCTATAGAAATGTTTATATAT
21318654 GCTATAGAAATGTTTATATAT
1 GCTATAGAAATGTTTATATAT
21318675 GCTAT-GAAA
1 GCTATAGAAA
21318684 AAGTTAAGGA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
20 4 0.14
21 24 0.86
ACGTcount: A:0.37, C:0.06, G:0.16, T:0.41
Consensus pattern (21 bp):
GCTATAGAAATGTTTATATAT
Found at i:21325362 original size:19 final size:19
Alignment explanation
Indices: 21325314--21325362 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 19
21325304 AAATGGCATG
*
21325314 GGAGCATGAAAATGGCGTTA
1 GGAGCATG-AAATGGCGTCA
* **
21325334 GGTGGGTGAAATGGCGTCA
1 GGAGCATGAAATGGCGTCA
21325353 GGAGCATGAA
1 GGAGCATGAA
21325363 GGTGGAGGAG
Statistics
Matches: 22, Mismatches: 7, Indels: 1
0.73 0.23 0.03
Matches are distributed among these distances:
19 17 0.77
20 5 0.23
ACGTcount: A:0.31, C:0.10, G:0.41, T:0.18
Consensus pattern (19 bp):
GGAGCATGAAATGGCGTCA
Found at i:21326933 original size:20 final size:20
Alignment explanation
Indices: 21326888--21326933 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
21326878 CTCAATGATG
* *
21326888 TATCAATACATTTGGCAATG
1 TATCAATACATTTGCCAATA
*
21326908 TATCAATACATTTGCCCATA
1 TATCAATACATTTGCCAATA
*
21326928 TTTCAA
1 TATCAA
21326934 ATAAATGTAC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.35, C:0.20, G:0.09, T:0.37
Consensus pattern (20 bp):
TATCAATACATTTGCCAATA
Found at i:21331913 original size:35 final size:35
Alignment explanation
Indices: 21331865--21331933 Score: 120
Period size: 35 Copynumber: 2.0 Consensus size: 35
21331855 AACAAGTTAA
*
21331865 AACATCCTTTAAGACTAAAAAGATTGTGTCAACAG
1 AACATCCTCTAAGACTAAAAAGATTGTGTCAACAG
*
21331900 AACATCCTCTAAGACTAAGAAGATTGTGTCAACA
1 AACATCCTCTAAGACTAAAAAGATTGTGTCAACA
21331934 ACTAGATCTC
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 32 1.00
ACGTcount: A:0.42, C:0.19, G:0.14, T:0.25
Consensus pattern (35 bp):
AACATCCTCTAAGACTAAAAAGATTGTGTCAACAG
Found at i:21333756 original size:42 final size:42
Alignment explanation
Indices: 21333682--21333764 Score: 105
Period size: 42 Copynumber: 2.0 Consensus size: 42
21333672 CATCTCATAT
* *
21333682 GCAATGGCTTATGTGCACTCTCACTCACACATAGCCGGGTCA
1 GCAACGGCTTAGGTGCACTCTCACTCACACATAGCCGGGTCA
** *
21333724 GCAACGGCTTAGGTGCACTACT-ACTCGTACATAGTCGGGTC
1 GCAACGGCTTAGGTGCACT-CTCACTCACACATAGCCGGGTC
21333765 CACATCAACA
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
42 33 0.94
43 2 0.06
ACGTcount: A:0.23, C:0.29, G:0.24, T:0.24
Consensus pattern (42 bp):
GCAACGGCTTAGGTGCACTCTCACTCACACATAGCCGGGTCA
Found at i:21334562 original size:19 final size:19
Alignment explanation
Indices: 21334534--21334570 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
21334524 AGAACAAGAC
*
21334534 AAGCTGCTAGAAATTCAAA
1 AAGCTACTAGAAATTCAAA
21334553 AAGCTACTAGAAATTCAA
1 AAGCTACTAGAAATTCAA
21334571 GATATTTTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.49, C:0.16, G:0.14, T:0.22
Consensus pattern (19 bp):
AAGCTACTAGAAATTCAAA
Found at i:21337051 original size:20 final size:19
Alignment explanation
Indices: 21337026--21337070 Score: 65
Period size: 20 Copynumber: 2.4 Consensus size: 19
21337016 TAGAAGGCAC
21337026 TTAGTCAACTAAAGAGAATT
1 TTAGTCAACTAAA-AGAATT
*
21337046 TTAGTCAACTAAAAGTATT
1 TTAGTCAACTAAAAGAATT
21337065 TT-GTCA
1 TTAGTCA
21337071 TCTTTAAATA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
18 4 0.17
19 7 0.29
20 13 0.54
ACGTcount: A:0.40, C:0.11, G:0.13, T:0.36
Consensus pattern (19 bp):
TTAGTCAACTAAAAGAATT
Found at i:21342193 original size:20 final size:20
Alignment explanation
Indices: 21342168--21342213 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
21342158 TTTAGGCCCC
* *
21342168 ATTTGACTTATTGGAGTATG
1 ATTTGACTAATTGAAGTATG
*
21342188 ATTTGAGTAATTGAAGTATG
1 ATTTGACTAATTGAAGTATG
21342208 ATTTGA
1 ATTTGA
21342214 GGTTCAGAAG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.30, C:0.02, G:0.24, T:0.43
Consensus pattern (20 bp):
ATTTGACTAATTGAAGTATG
Found at i:21342214 original size:20 final size:20
Alignment explanation
Indices: 21342177--21342214 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
21342167 CATTTGACTT
*
21342177 ATTGGAGTATGATTTGAGTA
1 ATTGAAGTATGATTTGAGTA
21342197 ATTGAAGTATGATTTGAG
1 ATTGAAGTATGATTTGAG
21342215 GTTCAGAAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.32, C:0.00, G:0.29, T:0.39
Consensus pattern (20 bp):
ATTGAAGTATGATTTGAGTA
Found at i:21343453 original size:13 final size:13
Alignment explanation
Indices: 21343435--21343460 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
21343425 AGGAGAAATT
21343435 ATGATTTTATAAA
1 ATGATTTTATAAA
21343448 ATGATTTTATAAA
1 ATGATTTTATAAA
21343461 TTTTCTGGAA
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:0.46, C:0.00, G:0.08, T:0.46
Consensus pattern (13 bp):
ATGATTTTATAAA
Found at i:21345656 original size:27 final size:27
Alignment explanation
Indices: 21345621--21345703 Score: 148
Period size: 27 Copynumber: 3.1 Consensus size: 27
21345611 TCAATGTTGT
**
21345621 GTTAATGGTTTATATAAATTGATCTGA
1 GTTAATGGTTTATATAAATTGATCCAA
21345648 GTTAATGGTTTATATAAATTGATCCAA
1 GTTAATGGTTTATATAAATTGATCCAA
21345675 GTTAATGGTTTATATAAATTGATCCAA
1 GTTAATGGTTTATATAAATTGATCCAA
21345702 GT
1 GT
21345704 AGCTTGCACA
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 54 1.00
ACGTcount: A:0.35, C:0.06, G:0.17, T:0.42
Consensus pattern (27 bp):
GTTAATGGTTTATATAAATTGATCCAA
Found at i:21352812 original size:64 final size:64
Alignment explanation
Indices: 21352717--21352998 Score: 343
Period size: 64 Copynumber: 4.4 Consensus size: 64
21352707 TTTCATACAA
* * ** * ** * *
21352717 TGTGAGGCAAACATTCCACACGTGGCAAATGCGTCTAGTATGATGGATAATGGTGTTTCAC-TCA
1 TGTGAGG-TAACATTCCACATGTGGTGAATGCGTCTAGTATGATGGATGATGGCATTCCACAT-G
21352781 G
64 G
21352782 TGTGAGGTAACATTCCACATGTGGTGAATGCGTCTAGTATGATGGATGATGGCATTCCACATGG
1 TGTGAGGTAACATTCCACATGTGGTGAATGCGTCTAGTATGATGGATGATGGCATTCCACATGG
* *
21352846 TGTGAGGTAACATTCCACATGTGGTGAATGCGTCTAGTAGGACGGATGATGGCATTCCACATGG
1 TGTGAGGTAACATTCCACATGTGGTGAATGCGTCTAGTATGATGGATGATGGCATTCCACATGG
* * ** * * * * *
21352910 TGTGAGGTAAGATTCGACATAAGGTAAATGTGTCTA-TATGATGGATGATAGCTTTCCACATTG
1 TGTGAGGTAACATTCCACATGTGGTGAATGCGTCTAGTATGATGGATGATGGCATTCCACATGG
*
21352973 TGTGAGGTAATATTCCACATGTGGTG
1 TGTGAGGTAACATTCCACATGTGGTG
21352999 CCAATGCCCA
Statistics
Matches: 189, Mismatches: 27, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
63 43 0.23
64 138 0.73
65 8 0.04
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (64 bp):
TGTGAGGTAACATTCCACATGTGGTGAATGCGTCTAGTATGATGGATGATGGCATTCCACATGG
Found at i:21356266 original size:19 final size:19
Alignment explanation
Indices: 21356230--21356266 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
21356220 AGGTTTGGTG
*
21356230 AGAAACCCTTGGCCAGTTA
1 AGAAACCCTCGGCCAGTTA
*
21356249 AGAAACCCTCGGCTAGTT
1 AGAAACCCTCGGCCAGTT
21356267 GATAATTTAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.30, C:0.27, G:0.22, T:0.22
Consensus pattern (19 bp):
AGAAACCCTCGGCCAGTTA
Found at i:21358136 original size:80 final size:80
Alignment explanation
Indices: 21357988--21358140 Score: 202
Period size: 80 Copynumber: 1.9 Consensus size: 80
21357978 CATCATTATT
* * *
21357988 ATGCTTAGCCCATAGTGTATATGAATATCTCAACACATATATCTCATCGCAGGCATTTCATAACC
1 ATGCTTAGCCCATAGTATATATGAATATCTCAACACATACATCTCATCGCAGGCATTTCACAACC
21358053 TCATAAATCACTCAC
66 TCATAAATCACTCAC
* * * *
21358068 ATGCTTAAG-CCATAGTATATATGACTATCTTAACACATACATCTCATGGCATGCATGTT-ACAA
1 ATGCTT-AGCCCATAGTATATATGAATATCTCAACACATACATCTCATCGCAGGCAT-TTCACAA
*
21358131 TCTCATAAAT
64 CCTCATAAAT
21358141 GGAACTCATG
Statistics
Matches: 63, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
80 59 0.94
81 4 0.06
ACGTcount: A:0.35, C:0.24, G:0.10, T:0.31
Consensus pattern (80 bp):
ATGCTTAGCCCATAGTATATATGAATATCTCAACACATACATCTCATCGCAGGCATTTCACAACC
TCATAAATCACTCAC
Found at i:21364448 original size:37 final size:37
Alignment explanation
Indices: 21364414--21364565 Score: 182
Period size: 37 Copynumber: 4.0 Consensus size: 37
21364404 ATTATCATTG
*
21364414 TGTGTGCACTCCCTAGTCGCACACT-TCAACATCATCA
1 TGTGTGCACTCCCTACTCGCACACTCT-AACATCATCA
* * *
21364451 TGTGTGCACTCCCTACTCGCACACTCTATCATGATCG
1 TGTGTGCACTCCCTACTCGCACACTCTAACATCATCA
* *
21364488 TGTGTGCACGCACTCCTTACTCGCACACTCTATCATCATCA
1 TGTGT----GCACTCCCTACTCGCACACTCTAACATCATCA
21364529 TGTGTGCACTCCCTACTCGCACACT-TCAACATCATCA
1 TGTGTGCACTCCCTACTCGCACACTCT-AACATCATCA
21364566 CACAACATTA
Statistics
Matches: 100, Mismatches: 9, Indels: 12
0.83 0.07 0.10
Matches are distributed among these distances:
36 1 0.01
37 64 0.64
38 1 0.01
41 34 0.34
ACGTcount: A:0.22, C:0.36, G:0.13, T:0.28
Consensus pattern (37 bp):
TGTGTGCACTCCCTACTCGCACACTCTAACATCATCA
Found at i:21381649 original size:35 final size:34
Alignment explanation
Indices: 21381594--21381699 Score: 115
Period size: 35 Copynumber: 3.1 Consensus size: 34
21381584 CACTCAGCCA
* *
21381594 ATGTGCACTCCTTACACGCACAAGGCACA-ATCATC
1 ATGTGCACTCCCTACTCGCACAA-GCA-ATATCATC
* * **
21381629 ATGTGCACTTCCTCCTCGCACATTTCAATATCATC
1 ATGTGCACTCCCTACTCGCACA-AGCAATATCATC
*
21381664 GTGTGCACTCCCTACTCGCACAAGCAATATCATC
1 ATGTGCACTCCCTACTCGCACAAGCAATATCATC
21381698 AT
1 AT
21381700 CCGAACTTCC
Statistics
Matches: 57, Mismatches: 12, Indels: 5
0.77 0.16 0.07
Matches are distributed among these distances:
34 12 0.21
35 45 0.79
ACGTcount: A:0.27, C:0.34, G:0.12, T:0.26
Consensus pattern (34 bp):
ATGTGCACTCCCTACTCGCACAAGCAATATCATC
Found at i:21400228 original size:19 final size:19
Alignment explanation
Indices: 21400179--21400228 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
21400169 GGAAGGAAAA
21400179 AGAAGAAGAAGAAACTACT
1 AGAAGAAGAAGAAACTACT
* *
21400198 -GGAGAATGAAGAAGCTACT
1 AGAAGAA-GAAGAAACTACT
*
21400217 AGAAGAAAAAGA
1 AGAAGAAGAAGA
21400229 TGTTTATAGT
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
18 5 0.20
19 15 0.60
20 5 0.20
ACGTcount: A:0.56, C:0.08, G:0.26, T:0.10
Consensus pattern (19 bp):
AGAAGAAGAAGAAACTACT
Found at i:21405542 original size:37 final size:38
Alignment explanation
Indices: 21405475--21405584 Score: 159
Period size: 38 Copynumber: 2.9 Consensus size: 38
21405465 AATTGTGGGT
* **
21405475 AATGATATTGCTTGCGCACGATGTTAGGGGATGCACAC
1 AATGATATTGCTTGTGCACGATGTGGGGGGATGCACAC
*
21405513 AATGATATTGCTT-TGCACGATGTGGGGGGATGCACAT
1 AATGATATTGCTTGTGCACGATGTGGGGGGATGCACAC
* *
21405550 GATGATATTGCTTGTGCACGATATGGGGGGATGCA
1 AATGATATTGCTTGTGCACGATGTGGGGGGATGCA
21405585 TATGAGCTGA
Statistics
Matches: 65, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
37 32 0.49
38 33 0.51
ACGTcount: A:0.25, C:0.15, G:0.33, T:0.28
Consensus pattern (38 bp):
AATGATATTGCTTGTGCACGATGTGGGGGGATGCACAC
Found at i:21411053 original size:80 final size:80
Alignment explanation
Indices: 21410932--21411151 Score: 307
Period size: 80 Copynumber: 2.8 Consensus size: 80
21410922 TGCTTAACTG
*
21410932 ATAGTGTATATGACTATCTCAACACATACATCTCATCGCATGCATTTTATAACCTCAAAAATCAC
1 ATAGTGTATATGACTATCTCAACACATACATCTCATGGCATGCATTTTATAACCTCAAAAATCAC
21410997 TCACATGCTTA-GCC
66 TCACATGCTTAGGCC
* * * * * *
21411011 TATAGTGTAAATGACTGTCTCAAAACATACATCTCATGGCATGCATTTCATAACCTCATAAGTCA
1 -ATAGTGTATATGACTATCTCAACACATACATCTCATGGCATGCATTTTATAACCTCAAAAATCA
21411076 CTCACATGCTTAGGCC
65 CTCACATGCTTAGGCC
* * * * * *
21411092 GTAGTATATATGACTATCTCGACACATACATCTCATGGCATGCATGTTACAATCTCAAAA
1 ATAGTGTATATGACTATCTCAACACATACATCTCATGGCATGCATTTTATAACCTCAAAA
21411152 TAGGAACTCA
Statistics
Matches: 121, Mismatches: 18, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
80 118 0.98
81 3 0.02
ACGTcount: A:0.34, C:0.25, G:0.12, T:0.30
Consensus pattern (80 bp):
ATAGTGTATATGACTATCTCAACACATACATCTCATGGCATGCATTTTATAACCTCAAAAATCAC
TCACATGCTTAGGCC
Found at i:21416102 original size:42 final size:42
Alignment explanation
Indices: 21416056--21416174 Score: 132
Period size: 42 Copynumber: 2.8 Consensus size: 42
21416046 TATTGACCTG
*
21416056 GCTATGTGTGAGTAGGAGTGCACATAAGCCGTTGCTGACCCA
1 GCTATGTGTGAGTGGGAGTGCACATAAGCCGTTGCTGACCCA
* * ** * **
21416098 GCTATGT-TCAAGTGGGAGTACACATAAGCCGTTATTGATCTG
1 GCTATGTGT-GAGTGGGAGTGCACATAAGCCGTTGCTGACCCA
* *
21416140 GCTATGTGTGAGTGGGGGTGCGCATAAGCCGTTGC
1 GCTATGTGTGAGTGGGAGTGCACATAAGCCGTTGC
21416175 ATATGAGATG
Statistics
Matches: 61, Mismatches: 14, Indels: 4
0.77 0.18 0.05
Matches are distributed among these distances:
41 1 0.02
42 59 0.97
43 1 0.02
ACGTcount: A:0.22, C:0.18, G:0.33, T:0.27
Consensus pattern (42 bp):
GCTATGTGTGAGTGGGAGTGCACATAAGCCGTTGCTGACCCA
Found at i:21416222 original size:2 final size:2
Alignment explanation
Indices: 21416215--21416255 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
21416205 ATGATGATTG
21416215 AT AT AT 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 AT AT AT A
21416256 NNNNNNNNNN
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:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:21416304 original size:2 final size:2
Alignment explanation
Indices: 21416287--21416346 Score: 102
Period size: 2 Copynumber: 29.0 Consensus size: 2
21416277 NNNNNNNNNG
21416287 TA TA GTA TA GTA 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 TA TA TA TA
21416331 TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA
21416347 CGTACATGGT
Statistics
Matches: 56, Mismatches: 0, Indels: 4
0.93 0.00 0.07
Matches are distributed among these distances:
2 52 0.93
3 4 0.07
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
TA
Found at i:21424149 original size:20 final size:20
Alignment explanation
Indices: 21424123--21424168 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 20
21424113 AATCTTACCT
* *
21424123 TTTTTCACTTGTTTCCTTGAA
1 TTTTACACTT-TTCCCTTGAA
21424144 TTTTCACACTTTTCCCTTGAA
1 TTTT-ACACTTTTCCCTTGAA
21424165 TTTT
1 TTTT
21424169 TCCACCTAGG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 17 0.77
22 5 0.23
ACGTcount: A:0.15, C:0.22, G:0.07, T:0.57
Consensus pattern (20 bp):
TTTTACACTTTTCCCTTGAA
Done.