Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032254.1 Gossypioides kirkii chromosome KI_12
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: 43711324
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 1700 characters in sequence are not A, C, G, or T
File 52 of 135
Found at i:18365183 original size:123 final size:122
Alignment explanation
Indices: 18364914--18365187 Score: 320
Period size: 123 Copynumber: 2.2 Consensus size: 122
18364904 ATGTTTCGAG
* * * * *
18364914 ATGAGCATGAGATTATATTAAAGGAAGACTCATGTCTCGAGATGAGCATGAGATTATATTAAAGG
1 ATGAGCATAAGATTTTA-TAAAGGAAGACTCATGACTCAAAATGAGCATGAGATTATATTAAAGG
* * *
18364979 AAGACTCATGACTCGAAATGAGCATGAGATTATATTAAAGGAAGACTCGTGACTCAAA
65 AAGACTCATGACTCGAAATGAGCACGAGATTATATTAAAGAAAGACTCATGACTCAAA
* * *
18365037 ATGAGCATGAGATTTTATTAAAGGAAGACTCGTGACTCAAAATGAGCATGAGATTTTATTAAAGG
1 ATGAGCATAAGATTTTA-TAAAGGAAGACTCATGACTCAAAATGAGCATGAGATTATATTAAAGG
* * * ***
18365102 AAGACTCGTGACTC-AGGATGAGCACGAGATTATATTTAAAGAAAGACTTATGACTCGGT
65 AAGACTCATGACTCGA-AATGAGCACGAGATTATA-TTAAAGAAAGACTCATGACTCAAA
18365161 A-GAGCATAAGATTGTTGA-AAAGGAAGA
1 ATGAGCATAAGATT-TT-ATAAAGGAAGA
18365188 TCTACGACTC
Statistics
Matches: 131, Mismatches: 16, Indels: 8
0.85 0.10 0.05
Matches are distributed among these distances:
122 1 0.01
123 108 0.82
124 21 0.16
125 1 0.01
ACGTcount: A:0.39, C:0.11, G:0.24, T:0.26
Consensus pattern (122 bp):
ATGAGCATAAGATTTTATAAAGGAAGACTCATGACTCAAAATGAGCATGAGATTATATTAAAGGA
AGACTCATGACTCGAAATGAGCACGAGATTATATTAAAGAAAGACTCATGACTCAAA
Found at i:18382129 original size:16 final size:18
Alignment explanation
Indices: 18382108--18382140 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
18382098 TTAAACATAA
18382108 AATTAA-AC-AAATTTAC
1 AATTAACACTAAATTTAC
18382124 AATTAACACTAAATTTA
1 AATTAACACTAAATTTA
18382141 TTCTTAACAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
17 2 0.13
18 7 0.47
ACGTcount: A:0.55, C:0.12, G:0.00, T:0.33
Consensus pattern (18 bp):
AATTAACACTAAATTTAC
Found at i:18383333 original size:26 final size:27
Alignment explanation
Indices: 18383281--18383335 Score: 76
Period size: 26 Copynumber: 2.1 Consensus size: 27
18383271 AACCAATTTT
* *
18383281 TTTTAATTTTAAATATATTTTTTATTA
1 TTTTAATTTTAAATAAATTTTTAATTA
*
18383308 TTTTAATTTT-TATAAATTTTTAATTA
1 TTTTAATTTTAAATAAATTTTTAATTA
18383334 TT
1 TT
18383336 AATTTAATTA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
26 15 0.60
27 10 0.40
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (27 bp):
TTTTAATTTTAAATAAATTTTTAATTA
Found at i:18385348 original size:17 final size:17
Alignment explanation
Indices: 18385326--18385358 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
18385316 AAACTGATCC
18385326 TTCTCTATATGGTTCAT
1 TTCTCTATATGGTTCAT
18385343 TTCTCTATATGGTTCA
1 TTCTCTATATGGTTCA
18385359 AAGCTCAAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.18, C:0.18, G:0.12, T:0.52
Consensus pattern (17 bp):
TTCTCTATATGGTTCAT
Found at i:18390809 original size:18 final size:18
Alignment explanation
Indices: 18390786--18390828 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
18390776 TTTTCAGTTG
18390786 TAATTAATTTAAAATT-TT
1 TAATTAA-TTAAAATTATT
*
18390804 TAATTAATTAAATTTATT
1 TAATTAATTAAAATTATT
18390822 TAATTAA
1 TAATTAA
18390829 CAATTTATTC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 7 0.30
18 16 0.70
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
TAATTAATTAAAATTATT
Found at i:18407597 original size:10 final size:9
Alignment explanation
Indices: 18407570--18407652 Score: 65
Period size: 8 Copynumber: 9.9 Consensus size: 9
18407560 TGGATACAAT
18407570 GAAGAAAAA
1 GAAGAAAAA
* *
18407579 CAAATAAAAA
1 -GAAGAAAAA
18407589 CGAAGAAAAA
1 -GAAGAAAAA
18407599 GAA-AAAAA
1 GAAGAAAAA
18407607 G-AGAAAAA
1 GAAGAAAAA
18407615 -AAGAAAAA
1 GAAGAAAAA
18407623 -AA-AAAAA
1 GAAGAAAAA
*
18407630 AAAG-AAAA
1 GAAGAAAAA
18407638 GAA-AAAAA
1 GAAGAAAAA
18407646 -AAGAAAA
1 GAAGAAAA
18407653 GAAAAGGAGA
Statistics
Matches: 62, Mismatches: 5, Indels: 14
0.77 0.06 0.17
Matches are distributed among these distances:
7 8 0.13
8 36 0.58
9 3 0.05
10 15 0.24
ACGTcount: A:0.83, C:0.02, G:0.13, T:0.01
Consensus pattern (9 bp):
GAAGAAAAA
Found at i:18407598 original size:1 final size:1
Alignment explanation
Indices: 18407594--18407657 Score: 56
Period size: 1 Copynumber: 64.0 Consensus size: 1
18407584 AAAAACGAAG
* * * * * * * *
18407594 AAAAAGAAAAAAAGAGAAAAAAAGAAAAAAAAAAAAAAAGAAAAGAAAAAAAAAGAAAAGAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
18407658 GGAGAGGTCG
Statistics
Matches: 47, Mismatches: 16, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
1 47 1.00
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (1 bp):
A
Found at i:18407611 original size:16 final size:16
Alignment explanation
Indices: 18407584--18407657 Score: 82
Period size: 15 Copynumber: 4.6 Consensus size: 16
18407574 AAAAACAAAT
18407584 AAAAACGAAGAAAAAGAA-
1 AAAAA-GAA-AAAAA-AAG
*
18407602 AAAAAGAGAAAAAAAG
1 AAAAAGAAAAAAAAAG
*
18407618 AAAAAAAAAAAAAAAG
1 AAAAAGAAAAAAAAAG
18407634 -AAAAGAAAAAAAAAG
1 AAAAAGAAAAAAAAAG
18407649 -AAAAGAAAA
1 AAAAAGAAAA
18407658 GGAGAGGTCG
Statistics
Matches: 51, Mismatches: 4, Indels: 5
0.85 0.07 0.08
Matches are distributed among these distances:
15 25 0.49
16 19 0.37
17 2 0.04
18 5 0.10
ACGTcount: A:0.85, C:0.01, G:0.14, T:0.00
Consensus pattern (16 bp):
AAAAAGAAAAAAAAAG
Found at i:18407625 original size:20 final size:20
Alignment explanation
Indices: 18407595--18407658 Score: 87
Period size: 20 Copynumber: 3.2 Consensus size: 20
18407585 AAAACGAAGA
*
18407595 AAAAGAAAAAAAGAG-AAA-
1 AAAAGAAAAAAAAAGAAAAG
*
18407613 AAAAGAAAAAAAAAAAAAAAG
1 AAAAG-AAAAAAAAAGAAAAG
18407634 AAAAGAAAAAAAAAGAAAAG
1 AAAAGAAAAAAAAAGAAAAG
18407654 AAAAG
1 AAAAG
18407659 GAGAGGTCGA
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
18 5 0.12
19 8 0.20
20 22 0.55
21 5 0.12
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (20 bp):
AAAAGAAAAAAAAAGAAAAG
Found at i:18407627 original size:24 final size:25
Alignment explanation
Indices: 18407591--18407658 Score: 84
Period size: 24 Copynumber: 2.7 Consensus size: 25
18407581 AATAAAAACG
*
18407591 AAGAAAAAGAAAAAAAGAGAAAA-A
1 AAGAAAAAAAAAAAAAGAGAAAAGA
*
18407615 AAGAAAAAAAAAAAAAAAGAAAAGA
1 AAGAAAAAAAAAAAAAGAGAAAAGA
*
18407640 AAAAAAAAGAAAAGAAAAG
1 AAGAAAAA-AAAA-AAAAG
18407659 GAGAGGTCGA
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
24 21 0.57
25 8 0.22
26 4 0.11
27 4 0.11
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (25 bp):
AAGAAAAAAAAAAAAAGAGAAAAGA
Found at i:18407658 original size:10 final size:9
Alignment explanation
Indices: 18407574--18407657 Score: 75
Period size: 10 Copynumber: 9.1 Consensus size: 9
18407564 TACAATGAAG
*
18407574 AAAAACAAA
1 AAAAAGAAA
*
18407583 TAAAAACGAAG
1 -AAAAA-GAAA
18407594 AAAAAG-AA
1 AAAAAGAAA
18407602 AAAAAGAGAA
1 AAAAAGA-AA
18407612 AAAAAG-AA
1 AAAAAGAAA
18407620 AAAAA-AAA
1 AAAAAGAAA
18407628 AAAAAGAAA
1 AAAAAGAAA
*
18407637 AGAAAAAAAA
1 A-AAAAGAAA
18407647 AGAAAAGAAA
1 A-AAAAGAAA
18407657 A
1 A
18407658 GGAGAGGTCG
Statistics
Matches: 63, Mismatches: 5, Indels: 12
0.79 0.06 0.15
Matches are distributed among these distances:
8 21 0.33
9 5 0.08
10 35 0.56
11 2 0.03
ACGTcount: A:0.85, C:0.02, G:0.12, T:0.01
Consensus pattern (9 bp):
AAAAAGAAA
Found at i:18409005 original size:50 final size:50
Alignment explanation
Indices: 18408869--18409005 Score: 127
Period size: 50 Copynumber: 2.7 Consensus size: 50
18408859 AAAACACGAC
* * *
18408869 GGGAAAGATCTAAGACCATAACGGAGGATCCAGTACCGCAAAGATACAAAA
1 GGGAAAGATCTAAGAACACAACGGCGGATCCAGTACCGCAAAGATA-AAAA
* * * ** * *
18408920 GGGAAAGGTCTAAG-TCACAACGACGGATCGTGTACCTCAAAAGCAT-GAAA
1 GGGAAAGATCTAAGAACACAACGGCGGATCCAGTACCGC-AAAG-ATAAAAA
*
18408970 -GGAAAGATCTAAGAACACAATGGCGGATCCAGTACC
1 GGGAAAGATCTAAGAACACAACGGCGGATCCAGTACC
18409006 ACGAAGATTT
Statistics
Matches: 68, Mismatches: 15, Indels: 7
0.76 0.17 0.08
Matches are distributed among these distances:
49 12 0.18
50 37 0.54
51 17 0.25
52 2 0.03
ACGTcount: A:0.41, C:0.20, G:0.25, T:0.14
Consensus pattern (50 bp):
GGGAAAGATCTAAGAACACAACGGCGGATCCAGTACCGCAAAGATAAAAA
Found at i:18409288 original size:92 final size:92
Alignment explanation
Indices: 18409125--18410187 Score: 1857
Period size: 92 Copynumber: 11.6 Consensus size: 92
18409115 TCAGATCAAA
*
18409125 ATAGCAAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAACTTCAAACATCAATTCCT
1 ATAGCAAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAGCTTCAAACATCAATTCCT
*
18409190 ATCCTCTTAAAGTTGTAGTAAAGTTGG
66 ATCCTCTTGAAGTTGTAGTAAAGTTGG
* *
18409217 ATAACAAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGTAAGATGAAGCTTCAAACATCAA-TCCT
1 ATAGCAAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAGCTTCAAACATCAATTCC-
*
18409281 TACCCTCTTGAAGTTGTAGTAAAGTTGG
65 TATCCTCTTGAAGTTGTAGTAAAGTTGG
*
18409309 ATAGCAAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGTAAGATGAAGCTTCAAACATCAATTCCT
1 ATAGCAAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAGCTTCAAACATCAATTCCT
18409374 ATCCTCTTGAAGTTGTAGTAAAGTTGG
66 ATCCTCTTGAAGTTGTAGTAAAGTTGG
18409401 ATAGCAAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAGCTTCAAACATCAATTCCT
1 ATAGCAAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAGCTTCAAACATCAATTCCT
*
18409466 ATCCTCTTAAAGTTGTAGTAAAGTTGG
66 ATCCTCTTGAAGTTGTAGTAAAGTTGG
* *
18409493 ATAGCAAGTCTTTATCTCTCAGAAGTTGTAGTAAGAGTAAGATGAAGCTTCAAACATCAA-TCCT
1 ATAGCAAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAGCTTCAAACATCAATTCC-
*
18409557 TATCCTCTTGAAGTTGCAGTAAAGTTGG
65 TATCCTCTTGAAGTTGTAGTAAAGTTGG
*
18409585 ATAGCAAGTCTTTATCTCTCTGAAGTTGTAGTAAGACCAAGATGAAGCTTCAAACATCAA-TCCT
1 ATAGCAAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAGCTTCAAACATCAATTCC-
18409649 TATCCTCTTGAAGTTGTAGTAAAGTTGG
65 TATCCTCTTGAAGTTGTAGTAAAGTTGG
18409677 ATAGCAAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAGCTTCAAACATCAATTCCT
1 ATAGCAAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAGCTTCAAACATCAATTCCT
* *
18409742 ATCCTCTTAAAGTTGCAGTAAAGTTGG
66 ATCCTCTTGAAGTTGTAGTAAAGTTGG
* *
18409769 ATAGCAAGTCTTTATCTCTCTGAAGTTGTAGCAAGAGTAAGATGAAGCTTCAAACATCAA-TCCT
1 ATAGCAAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAGCTTCAAACATCAATTCC-
*
18409833 TATCCTCTTTAAGTTGTAGTAAAGTTGG
65 TATCCTCTTGAAGTTGTAGTAAAGTTGG
*
18409861 ATAGCAAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGGAAGATGAAGCTTCAAACATCAATTCCT
1 ATAGCAAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAGCTTCAAACATCAATTCCT
*
18409926 ATCCTCTTGAAGTTGCAGTAAAGTTGG
66 ATCCTCTTGAAGTTGTAGTAAAGTTGG
*
18409953 ATAGCAAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGTAAGATGAAGCTTCAAACATCAA-TCCT
1 ATAGCAAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAGCTTCAAACATCAATTCC-
18410017 TATCCTCTTGAAGTTGTAGTAAAGTTGG
65 TATCCTCTTGAAGTTGTAGTAAAGTTGG
18410045 ATAGCAAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAGCTTCAAACATCAATTCCT
1 ATAGCAAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAGCTTCAAACATCAATTCCT
*
18410110 ATCCTCTTGAAGTTGCAGTAAAGTTGG
66 ATCCTCTTGAAGTTGTAGTAAAGTTGG
*
18410137 ATAGCAAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATAAAGCTTC
1 ATAGCAAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAGCTTC
18410188 GGTACCAAAT
Statistics
Matches: 930, Mismatches: 33, Indels: 16
0.95 0.03 0.02
Matches are distributed among these distances:
91 12 0.01
92 906 0.97
93 12 0.01
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.32
Consensus pattern (92 bp):
ATAGCAAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAGCTTCAAACATCAATTCCT
ATCCTCTTGAAGTTGTAGTAAAGTTGG
Found at i:18410833 original size:11 final size:11
Alignment explanation
Indices: 18410791--18410831 Score: 64
Period size: 11 Copynumber: 3.7 Consensus size: 11
18410781 TCAATTAGAG
18410791 TTTAAATTGAT
1 TTTAAATTGAT
18410802 TTTAAATTGAT
1 TTTAAATTGAT
* *
18410813 TTTAAATTTAC
1 TTTAAATTGAT
18410824 TTTAAATT
1 TTTAAATT
18410832 TAAAATAATA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
11 28 1.00
ACGTcount: A:0.37, C:0.02, G:0.05, T:0.56
Consensus pattern (11 bp):
TTTAAATTGAT
Found at i:18412857 original size:31 final size:29
Alignment explanation
Indices: 18412787--18412903 Score: 110
Period size: 30 Copynumber: 3.9 Consensus size: 29
18412777 CTCTAGAGGT
* ** *
18412787 CCCTAAACTATTCAAAAATTTTATTTTTAC
1 CCCTAAACT-TCCAAAAATTACATTTTTAA
* *
18412817 CCCTGAACTTCTCCAAAATTACATTTTTAA
1 CCCTAAACTTC-CAAAAATTACATTTTTAA
*
18412847 CCCTAAAACTTCCAAAAATTACATTTTT-G
1 CCCT-AAACTTCCAAAAATTACATTTTTAA
* *
18412876 CCCTCGAACTTCCAAAAATTCCATTTTT
1 CCCT-AAACTTCCAAAAATTACATTTTT
18412904 GGACCTCGAC
Statistics
Matches: 73, Mismatches: 12, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
29 26 0.36
30 41 0.56
31 6 0.08
ACGTcount: A:0.34, C:0.26, G:0.03, T:0.38
Consensus pattern (29 bp):
CCCTAAACTTCCAAAAATTACATTTTTAA
Found at i:18412904 original size:29 final size:30
Alignment explanation
Indices: 18412799--18412927 Score: 122
Period size: 30 Copynumber: 4.3 Consensus size: 30
18412789 CTAAACTATT
** *
18412799 CAAAAATTTTATTTTTACCCCT-GAACTTC
1 CAAAAATTACATTTTTAACCCTCGAACTTC
* **
18412828 TCCAAAATTACATTTTTAACCCTAAAACTTC
1 -CAAAAATTACATTTTTAACCCTCGAACTTC
*
18412859 CAAAAATTACATTTTT-GCCCTCGAACTTC
1 CAAAAATTACATTTTTAACCCTCGAACTTC
* *
18412888 CAAAAATTCCATTTTTGGA-CCTCGACACTTC
1 CAAAAATTACATTTTT-AACCCTCGA-ACTTC
18412919 C-AAAATTAC
1 CAAAAATTAC
18412928 CGTTTTACCA
Statistics
Matches: 83, Mismatches: 12, Indels: 8
0.81 0.12 0.08
Matches are distributed among these distances:
29 25 0.30
30 46 0.55
31 12 0.14
ACGTcount: A:0.34, C:0.26, G:0.05, T:0.35
Consensus pattern (30 bp):
CAAAAATTACATTTTTAACCCTCGAACTTC
Found at i:18412924 original size:30 final size:29
Alignment explanation
Indices: 18412799--18412970 Score: 118
Period size: 30 Copynumber: 5.8 Consensus size: 29
18412789 CTAAACTATT
** *
18412799 CAAAAATTTTATTTTT-ACCCCTGAACTTC
1 CAAAAATTACATTTTTGACCTC-GAACTTC
* * **
18412828 TCCAAAATTACATTTTTAACCCTAAAACTTC
1 -CAAAAATTACATTTTTGA-CCTCGAACTTC
*
18412859 CAAAAATTACATTTTTGCCCTCGAACTTC
1 CAAAAATTACATTTTTGACCTCGAACTTC
*
18412888 CAAAAATTCCATTTTTGGACCTCGACACTTC
1 CAAAAATTACATTTTT-GACCTCGA-ACTTC
** *
18412919 C-AAAATTACCGTTTT-ACCACCGAA-TATC
1 CAAAAATTACATTTTTGACC-TCGAACT-TC
* * *
18412947 CAAAAATTCCGTTTTTGATCTCGA
1 CAAAAATTACATTTTTGACCTCGA
18412971 TTTTTCTAAA
Statistics
Matches: 112, Mismatches: 22, Indels: 17
0.74 0.15 0.11
Matches are distributed among these distances:
27 1 0.01
28 7 0.06
29 41 0.37
30 48 0.43
31 13 0.12
32 2 0.02
ACGTcount: A:0.33, C:0.26, G:0.06, T:0.35
Consensus pattern (29 bp):
CAAAAATTACATTTTTGACCTCGAACTTC
Found at i:18412983 original size:59 final size:59
Alignment explanation
Indices: 18412920--18413053 Score: 198
Period size: 59 Copynumber: 2.3 Consensus size: 59
18412910 CGACACTTCC
18412920 AAAATTACCGTTTTACCACCGAATATCCAAAAATTCCGTTTTTG-ATCTCGATTTTTCTA
1 AAAATTACCGTTTTACCACCGAATATCCAAAAATTCCGTTTTTGAATCT-GATTTTTCTA
* * * * * *
18412979 AAAATTATCATTTTACCCCCGGATGTCCAAAAATTTCGTTTTTGAATCTGATTTTTCTA
1 AAAATTACCGTTTTACCACCGAATATCCAAAAATTCCGTTTTTGAATCTGATTTTTCTA
18413038 AAAATTACCGTTTTAC
1 AAAATTACCGTTTTAC
18413054 ACTCGGATTT
Statistics
Matches: 66, Mismatches: 8, Indels: 2
0.87 0.11 0.03
Matches are distributed among these distances:
59 62 0.94
60 4 0.06
ACGTcount: A:0.31, C:0.20, G:0.09, T:0.40
Consensus pattern (59 bp):
AAAATTACCGTTTTACCACCGAATATCCAAAAATTCCGTTTTTGAATCTGATTTTTCTA
Found at i:18413061 original size:59 final size:57
Alignment explanation
Indices: 18412920--18413079 Score: 187
Period size: 59 Copynumber: 2.7 Consensus size: 57
18412910 CGACACTTCC
* *
18412920 AAAATTACCGTTTTACCACCGAATATCCAAAAATTCCGTTTTTGATCTCGATTTTTCTA
1 AAAATTACCGTTTTA-CACCGGAT-TCCAAAAATTTCGTTTTTGATCTCGATTTTTCTA
* * *
18412979 AAAATTATCATTTTACCCCCGGATGTCCAAAAATTTCGTTTTTGAATCT-GATTTTTCTA
1 AAAATTACCGTTTTA-CACCGGAT-TCCAAAAATTTCGTTTTTG-ATCTCGATTTTTCTA
* * *
18413038 AAAATTACCGTTTTACACTCGGATTTCTAAAATTTCATTTTT
1 AAAATTACCGTTTTACAC-CGGATTCCAAAAATTTCGTTTTT
18413080 AACCCTAAAT
Statistics
Matches: 87, Mismatches: 12, Indels: 5
0.84 0.12 0.05
Matches are distributed among these distances:
58 17 0.20
59 66 0.76
60 4 0.05
ACGTcount: A:0.30, C:0.19, G:0.09, T:0.42
Consensus pattern (57 bp):
AAAATTACCGTTTTACACCGGATTCCAAAAATTTCGTTTTTGATCTCGATTTTTCTA
Found at i:18413092 original size:59 final size:59
Alignment explanation
Indices: 18412920--18413109 Score: 156
Period size: 59 Copynumber: 3.2 Consensus size: 59
18412910 CGACACTTCC
* * * * * * *
18412920 AAAATTACCGTTTTAC-CACCGAATATCCAAAAATTCCGTTTTTG-ATCTCGATTTTTCTA
1 AAAATTACCATTTTACAC-CCGGATGTCCAAAAATTTCATTTTTGAACCT-AATTTTTCTA
* * * * *
18412979 AAAATTATCATTTTACCCCCGGATGTCCAAAAATTTCGTTTTTGAATCTGATTTTTCTA
1 AAAATTACCATTTTACACCCGGATGTCCAAAAATTTCATTTTTGAACCTAATTTTTCTA
* * * * *
18413038 AAAATTACCGTTTTACACTCGGAT-TTCTAAAATTTCATTTTT-AACCCTAAATTTTCCT-
1 AAAATTACCATTTTACACCCGGATGTCCAAAAATTTCATTTTTGAA-CCT-AATTTTTCTA
18413096 AAAATTACCATTTT
1 AAAATTACCATTTT
18413110 GCCCCCAAGT
Statistics
Matches: 111, Mismatches: 16, Indels: 9
0.82 0.12 0.07
Matches are distributed among these distances:
57 2 0.02
58 30 0.27
59 74 0.67
60 5 0.05
ACGTcount: A:0.31, C:0.20, G:0.07, T:0.42
Consensus pattern (59 bp):
AAAATTACCATTTTACACCCGGATGTCCAAAAATTTCATTTTTGAACCTAATTTTTCTA
Found at i:18415637 original size:15 final size:16
Alignment explanation
Indices: 18415610--18415644 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
18415600 TTATTATTTT
18415610 AATAATAAATTTTAAA
1 AATAATAAATTTTAAA
*
18415626 AATAAT-AATTTTAAT
1 AATAATAAATTTTAAA
18415641 AATA
1 AATA
18415645 TTCTTCATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 12 0.67
16 6 0.33
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (16 bp):
AATAATAAATTTTAAA
Found at i:18415698 original size:15 final size:15
Alignment explanation
Indices: 18415678--18415729 Score: 50
Period size: 15 Copynumber: 3.2 Consensus size: 15
18415668 ATTCAATGTT
18415678 AATATTTTAATAATA
1 AATATTTTAATAATA
*
18415693 AATATTTATTATAATTA
1 AATATTT-TAATAA-TA
*
18415710 TAATTATATTAATAATA
1 -AA-TATTTTAATAATA
18415727 AAT
1 AAT
18415730 TCTTTGTAGT
Statistics
Matches: 30, Mismatches: 3, Indels: 8
0.73 0.07 0.20
Matches are distributed among these distances:
15 8 0.27
16 7 0.23
17 4 0.13
18 7 0.23
19 4 0.13
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
AATATTTTAATAATA
Found at i:18418175 original size:29 final size:30
Alignment explanation
Indices: 18418120--18418189 Score: 79
Period size: 29 Copynumber: 2.3 Consensus size: 30
18418110 GTCTAATGTG
* * *
18418120 CAATTGTATACATGAACTTTGATTTTG-TA
1 CAATTTTATACATGAAATTTGAATTTGATA
* *
18418149 CAATTTTATACATGAAATTTTAATTTGATC
1 CAATTTTATACATGAAATTTGAATTTGATA
18418179 CAATTCTTATA
1 CAATT-TTATA
18418190 AATTATTAAC
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
29 23 0.68
30 6 0.18
31 5 0.15
ACGTcount: A:0.34, C:0.11, G:0.09, T:0.46
Consensus pattern (30 bp):
CAATTTTATACATGAAATTTGAATTTGATA
Found at i:18425571 original size:26 final size:27
Alignment explanation
Indices: 18425521--18425572 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
18425511 GGTTAGATTG
18425521 TTAAAATAAATAGGAATAAATAAAATA
1 TTAAAATAAATAGGAATAAATAAAATA
*
18425548 TTAAAATAATTA-GAATTAAA-AAAAT
1 TTAAAATAAATAGGAA-TAAATAAAAT
18425573 TAGGTTAAGA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
26 8 0.35
27 15 0.65
ACGTcount: A:0.65, C:0.00, G:0.06, T:0.29
Consensus pattern (27 bp):
TTAAAATAAATAGGAATAAATAAAATA
Found at i:18426861 original size:24 final size:24
Alignment explanation
Indices: 18426826--18426872 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
18426816 AATCTTCCAG
* **
18426826 TTAAACTTTATTTTTTTGTTTCAA
1 TTAAACTCTATTAATTTGTTTCAA
18426850 TTAAACTCTATTAATTTGTTTCA
1 TTAAACTCTATTAATTTGTTTCA
18426873 GTCAAAGTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.28, C:0.11, G:0.04, T:0.57
Consensus pattern (24 bp):
TTAAACTCTATTAATTTGTTTCAA
Found at i:18429070 original size:8 final size:8
Alignment explanation
Indices: 18429057--18429081 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
18429047 ATTTGTGTGT
18429057 TCAATTTC
1 TCAATTTC
18429065 TCAATTTC
1 TCAATTTC
18429073 TCAATTTC
1 TCAATTTC
18429081 T
1 T
18429082 TTCGCTATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.24, C:0.24, G:0.00, T:0.52
Consensus pattern (8 bp):
TCAATTTC
Found at i:18431465 original size:58 final size:57
Alignment explanation
Indices: 18431350--18431481 Score: 146
Period size: 58 Copynumber: 2.3 Consensus size: 57
18431340 TCATTTAAAC
* * *
18431350 AACATACATATCAATCTCCGTA-AAGCCATCCAAACACCCACAAATCCAATATCTTT
1 AACATACATATCAATCTCCGTACAATCCACCCAAACACCCACAAAGCCAATATCTTT
**
18431406 AACATACATATCAATTCTCCGTACAATCCACCCAAAC-CTCCGGAAAGCCAATA-CTTTT
1 AACATACATATCAA-TCTCCGTACAATCCACCCAAACAC-CCACAAAGCCAATATC-TTT
* *
18431464 AACACACACATCAA-CTCC
1 AACATACATATCAATCTCC
18431482 TCATACAATC
Statistics
Matches: 65, Mismatches: 7, Indels: 8
0.81 0.09 0.10
Matches are distributed among these distances:
56 18 0.28
57 10 0.15
58 37 0.57
ACGTcount: A:0.39, C:0.34, G:0.05, T:0.22
Consensus pattern (57 bp):
AACATACATATCAATCTCCGTACAATCCACCCAAACACCCACAAAGCCAATATCTTT
Found at i:18440358 original size:7 final size:7
Alignment explanation
Indices: 18440328--18440389 Score: 79
Period size: 7 Copynumber: 8.9 Consensus size: 7
18440318 TCTTGAACTC
18440328 TAAACCT
1 TAAACCT
* *
18440335 TGAACCA
1 TAAACCT
* *
18440342 TGAACAT
1 TAAACCT
18440349 TAAACCT
1 TAAACCT
18440356 TAAACCT
1 TAAACCT
18440363 TAAACCT
1 TAAACCT
18440370 TAAACCT
1 TAAACCT
*
18440377 TGAACCT
1 TAAACCT
18440384 TAAACC
1 TAAACC
18440390 ATCGAGCCTA
Statistics
Matches: 47, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
7 47 1.00
ACGTcount: A:0.42, C:0.27, G:0.05, T:0.26
Consensus pattern (7 bp):
TAAACCT
Found at i:18440389 original size:14 final size:14
Alignment explanation
Indices: 18440319--18440389 Score: 81
Period size: 14 Copynumber: 5.1 Consensus size: 14
18440309 GACCATCGAT
18440319 CTTGAA-CTCTAAAC
1 CTTGAACCT-TAAAC
* *
18440333 CTTGAACCATGAAC
1 CTTGAACCTTAAAC
* *
18440347 ATTAAACCTTAAAC
1 CTTGAACCTTAAAC
*
18440361 CTTAAACCTTAAAC
1 CTTGAACCTTAAAC
18440375 CTTGAACCTTAAAC
1 CTTGAACCTTAAAC
18440389 C
1 C
18440390 ATCGAGCCTA
Statistics
Matches: 48, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
14 47 0.98
15 1 0.02
ACGTcount: A:0.39, C:0.28, G:0.06, T:0.27
Consensus pattern (14 bp):
CTTGAACCTTAAAC
Found at i:18440389 original size:21 final size:21
Alignment explanation
Indices: 18440328--18440389 Score: 88
Period size: 21 Copynumber: 3.0 Consensus size: 21
18440318 TCTTGAACTC
* * *
18440328 TAAACCTTGAACCATGAACAT
1 TAAACCTTGAACCTTAAACCT
*
18440349 TAAACCTTAAACCTTAAACCT
1 TAAACCTTGAACCTTAAACCT
18440370 TAAACCTTGAACCTTAAACC
1 TAAACCTTGAACCTTAAACC
18440390 ATCGAGCCTA
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 36 1.00
ACGTcount: A:0.42, C:0.27, G:0.05, T:0.26
Consensus pattern (21 bp):
TAAACCTTGAACCTTAAACCT
Found at i:18453374 original size:2 final size:2
Alignment explanation
Indices: 18453367--18453392 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
18453357 AGCTATCTGC
18453367 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
18453393 GTGTGTGTGT
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):
AT
Found at i:18458467 original size:28 final size:24
Alignment explanation
Indices: 18458410--18458460 Score: 93
Period size: 24 Copynumber: 2.1 Consensus size: 24
18458400 AGAAATAATC
*
18458410 TTTCAGTTAAACTCTATTTATTTG
1 TTTCAATTAAACTCTATTTATTTG
18458434 TTTCAATTAAACTCTATTTATTTG
1 TTTCAATTAAACTCTATTTATTTG
18458458 TTT
1 TTT
18458461 GAGTCAACCT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.25, C:0.12, G:0.06, T:0.57
Consensus pattern (24 bp):
TTTCAATTAAACTCTATTTATTTG
Found at i:18460479 original size:21 final size:23
Alignment explanation
Indices: 18460455--18460507 Score: 65
Period size: 21 Copynumber: 2.3 Consensus size: 23
18460445 CAACTTCTAT
* *
18460455 CGATACAAGTATTCT-A-ACTAC
1 CGATACAAATATGCTCAGACTAC
18460476 CGATACAAATATGCTCAGTACTAC
1 CGATACAAATATGCTCAG-ACTAC
18460500 CGATACAA
1 CGATACAA
18460508 CTTAAGTCAG
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
21 13 0.48
22 1 0.04
24 13 0.48
ACGTcount: A:0.40, C:0.25, G:0.11, T:0.25
Consensus pattern (23 bp):
CGATACAAATATGCTCAGACTAC
Found at i:18461127 original size:41 final size:41
Alignment explanation
Indices: 18461037--18461305 Score: 259
Period size: 41 Copynumber: 6.5 Consensus size: 41
18461027 TTATGCTCTA
* * * * * *
18461037 TCGAGTCATAAGTCTTCCTTTAACCATATTCTCATTCTCATC
1 TCGAGACATGAGTCTTCC-TTAATCAAAATCTCATTCTCATT
18461079 TCGAGACATGAGTCTTCCTTAATCAAAATCTCATTCTCATT
1 TCGAGACATGAGTCTTCCTTAATCAAAATCTCATTCTCATT
** *
18461120 TATAGACATGAGTCTTCCTTAATCAAAACCTCATTCTCATT
1 TCGAGACATGAGTCTTCCTTAATCAAAATCTCATTCTCATT
* * * *
18461161 TCCAGACATGAGTATTCCTTATTCAAAACCTCATTCTCATT
1 TCGAGACATGAGTCTTCCTTAATCAAAATCTCATTCTCATT
* * * * * * *
18461202 TCGGGATACGAGTCTTCCTTATTCATAGTCTCATTCTCATC
1 TCGAGACATGAGTCTTCCTTAATCAAAATCTCATTCTCATT
* * ** * **
18461243 TCGAGACACGAGTCTTCCATTTATACAATTTCTCATGCTCAAC
1 TCGAGACATGAGTCTTCC-TTAAT-CAAAATCTCATTCTCATT
*
18461286 CCGAGACATGAGTCTTCCTT
1 TCGAGACATGAGTCTTCCTT
18461306 TCTATACACC
Statistics
Matches: 192, Mismatches: 33, Indels: 4
0.84 0.14 0.02
Matches are distributed among these distances:
41 142 0.74
42 21 0.11
43 29 0.15
ACGTcount: A:0.26, C:0.27, G:0.10, T:0.36
Consensus pattern (41 bp):
TCGAGACATGAGTCTTCCTTAATCAAAATCTCATTCTCATT
Found at i:18461291 original size:43 final size:44
Alignment explanation
Indices: 18461230--18461313 Score: 116
Period size: 43 Copynumber: 1.9 Consensus size: 44
18461220 TTATTCATAG
* * *
18461230 TCTCATTCTCATCTCGAGACACGAGTCTTCCATT-TATACAATT
1 TCTCATGCTCAACCCGAGACACGAGTCTTCCATTCTATACAATT
* *
18461273 TCTCATGCTCAACCCGAGACATGAGTCTTCCTTTCTATACA
1 TCTCATGCTCAACCCGAGACACGAGTCTTCCATTCTATACA
18461314 CCAAGTATTC
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
43 29 0.83
44 6 0.17
ACGTcount: A:0.25, C:0.30, G:0.11, T:0.35
Consensus pattern (44 bp):
TCTCATGCTCAACCCGAGACACGAGTCTTCCATTCTATACAATT
Found at i:18462152 original size:22 final size:22
Alignment explanation
Indices: 18462105--18462154 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
18462095 GACTTTCATA
*
18462105 ATTAA-CTTAATTAATCATCTT
1 ATTAATCTTAATTAATCATATT
* * *
18462126 TTTAATCTTAATTTATCCTATT
1 ATTAATCTTAATTAATCATATT
18462148 ATTAATC
1 ATTAATC
18462155 AATATTTGTC
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
21 4 0.17
22 19 0.83
ACGTcount: A:0.34, C:0.14, G:0.00, T:0.52
Consensus pattern (22 bp):
ATTAATCTTAATTAATCATATT
Found at i:18462770 original size:24 final size:24
Alignment explanation
Indices: 18462742--18462792 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
18462732 AGAAATAATC
* *
18462742 TTTCAGCTAAACTCTATTTATTTG
1 TTTCAACTAAACTCTATTCATTTG
* *
18462766 TTTCAATTAAACTCTGTTCATTTG
1 TTTCAACTAAACTCTATTCATTTG
18462790 TTT
1 TTT
18462793 AAGTCAAACT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.24, C:0.16, G:0.08, T:0.53
Consensus pattern (24 bp):
TTTCAACTAAACTCTATTCATTTG
Found at i:18462801 original size:24 final size:24
Alignment explanation
Indices: 18462750--18462804 Score: 67
Period size: 24 Copynumber: 2.3 Consensus size: 24
18462740 TCTTTCAGCT
* *
18462750 AAACTCTATTTATTTGTTTCAATT
1 AAACTCTATTCATTTGTTTCAATC
*
18462774 AAACTCTGTTCATTTGTTT-AAGTC
1 AAACTCTATTCATTTGTTTCAA-TC
18462798 AAACTCT
1 AAACTCT
18462805 TATTAGTCTA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
23 2 0.07
24 25 0.93
ACGTcount: A:0.29, C:0.16, G:0.07, T:0.47
Consensus pattern (24 bp):
AAACTCTATTCATTTGTTTCAATC
Found at i:18465004 original size:19 final size:19
Alignment explanation
Indices: 18464969--18465024 Score: 64
Period size: 19 Copynumber: 3.1 Consensus size: 19
18464959 TTTTAAAAAA
*
18464969 TATAAAT-TTTGGAATTTT
1 TATAAATATTTTGAATTTT
18464987 TATAAATATTTTGAATTTT
1 TATAAATATTTTGAATTTT
*
18465006 GA-AAATTATTTT-AATTTT
1 TATAAA-TATTTTGAATTTT
18465024 T
1 T
18465025 TTGTAATTTT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
18 16 0.48
19 17 0.52
ACGTcount: A:0.36, C:0.00, G:0.07, T:0.57
Consensus pattern (19 bp):
TATAAATATTTTGAATTTT
Found at i:18469660 original size:21 final size:21
Alignment explanation
Indices: 18469631--18469678 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
18469621 GAATAATTTT
* * *
18469631 ACTTGAATTTGATTTGACTAG
1 ACTTAAATTTGATTTCACTAA
*
18469652 ACTTAAATTTTATTTCACTAA
1 ACTTAAATTTGATTTCACTAA
18469673 ACTTAA
1 ACTTAA
18469679 TCCGAAAGAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.35, C:0.12, G:0.08, T:0.44
Consensus pattern (21 bp):
ACTTAAATTTGATTTCACTAA
Found at i:18471193 original size:26 final size:28
Alignment explanation
Indices: 18471164--18471222 Score: 72
Period size: 26 Copynumber: 2.2 Consensus size: 28
18471154 AATATTTATA
18471164 TTATATTA-TTTTAATATTT--AATATTT
1 TTATATTATTTTTAATATTTGAAAT-TTT
*
18471190 TTATA-TATTTTTATTATTTGAAATTTT
1 TTATATTATTTTTAATATTTGAAATTTT
18471217 TTATAT
1 TTATAT
18471223 GGCCATCTTA
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
25 2 0.07
26 15 0.54
27 8 0.29
28 3 0.11
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (28 bp):
TTATATTATTTTTAATATTTGAAATTTT
Found at i:18484414 original size:13 final size:13
Alignment explanation
Indices: 18484396--18484425 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
18484386 AAGAATAATA
18484396 TTAATATATATTT
1 TTAATATATATTT
18484409 TTAATATATATTT
1 TTAATATATATTT
18484422 TTAA
1 TTAA
18484426 AATTTTAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (13 bp):
TTAATATATATTT
Found at i:18501183 original size:17 final size:17
Alignment explanation
Indices: 18501142--18501183 Score: 54
Period size: 15 Copynumber: 2.6 Consensus size: 17
18501132 GACGATCTAC
18501142 ATGTTATAAAAAAATTT
1 ATGTTATAAAAAAATTT
18501159 AT-TT-TAAAAAAATATT
1 ATGTTATAAAAAAAT-TT
18501175 -TGTTATAAA
1 ATGTTATAAA
18501184 TGTGTTATAA
Statistics
Matches: 22, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
15 10 0.45
16 6 0.27
17 6 0.27
ACGTcount: A:0.52, C:0.00, G:0.05, T:0.43
Consensus pattern (17 bp):
ATGTTATAAAAAAATTT
Found at i:18507885 original size:17 final size:17
Alignment explanation
Indices: 18507865--18507951 Score: 104
Period size: 17 Copynumber: 5.1 Consensus size: 17
18507855 CCAATTTTAA
18507865 ATTTTAAAATTTAAA-TT
1 ATTTT-AAATTTAAATTT
* *
18507882 ATTTTAAGTTTAAACTT
1 ATTTTAAATTTAAATTT
* *
18507899 ATTTTTGAGTTTAAATTT
1 A-TTTTAAATTTAAATTT
18507917 ATTTTAAATTTAAATTT
1 ATTTTAAATTTAAATTT
*
18507934 ATTTTGAATTTAAATTT
1 ATTTTAAATTTAAATTT
18507951 A
1 A
18507952 AAATTTAATT
Statistics
Matches: 62, Mismatches: 6, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
16 8 0.13
17 39 0.63
18 15 0.24
ACGTcount: A:0.38, C:0.01, G:0.05, T:0.56
Consensus pattern (17 bp):
ATTTTAAATTTAAATTT
Found at i:18507928 original size:6 final size:6
Alignment explanation
Indices: 18507860--18507959 Score: 55
Period size: 6 Copynumber: 16.8 Consensus size: 6
18507850 TGAACCCAAT
* * * ** * *
18507860 TTTAAA TTTTAAAA TTTAAA -TT-AT TTTAAG TTTAAA CTTATT TTTGAG
1 TTTAAA -TTT-AAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
* * *
18507908 TTTAAA TTT-AT TTTAAA TTTAAA TTT-AT TTTGAA TTTAAA TTTAAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTT-AAA
18507955 TTTAA
1 TTTAA
18507960 TTAAAAGTCC
Statistics
Matches: 70, Mismatches: 17, Indels: 13
0.70 0.17 0.13
Matches are distributed among these distances:
4 1 0.01
5 12 0.17
6 42 0.60
7 12 0.17
8 3 0.04
ACGTcount: A:0.40, C:0.01, G:0.04, T:0.55
Consensus pattern (6 bp):
TTTAAA
Found at i:18507950 original size:34 final size:35
Alignment explanation
Indices: 18507872--18507951 Score: 119
Period size: 34 Copynumber: 2.3 Consensus size: 35
18507862 TAAATTTTAA
*
18507872 AATTTAAA-TTATTTTAAGTTTAAACTTATTTTTG
1 AATTTAAATTTATTTTAAATTTAAACTTATTTTTG
* *
18507906 AGTTTAAATTTATTTTAAATTTAAATTTA-TTTTG
1 AATTTAAATTTATTTTAAATTTAAACTTATTTTTG
18507940 AATTTAAATTTA
1 AATTTAAATTTA
18507952 AAATTTAATT
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
34 23 0.56
35 18 0.44
ACGTcount: A:0.38, C:0.01, G:0.05, T:0.56
Consensus pattern (35 bp):
AATTTAAATTTATTTTAAATTTAAACTTATTTTTG
Found at i:18508548 original size:10 final size:10
Alignment explanation
Indices: 18508535--18508582 Score: 62
Period size: 10 Copynumber: 4.8 Consensus size: 10
18508525 CAAAACGTTT
18508535 TTAATATATA
1 TTAATATATA
18508545 TTAATATAT-
1 TTAATATATA
*
18508554 TTAATATTTA
1 TTAATATATA
*
18508564 TTTATTATATA
1 -TTAATATATA
18508575 TTAATATA
1 TTAATATA
18508583 GTTATTAATT
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
9 8 0.25
10 16 0.50
11 8 0.25
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (10 bp):
TTAATATATA
Found at i:18508558 original size:19 final size:20
Alignment explanation
Indices: 18508534--18508582 Score: 64
Period size: 19 Copynumber: 2.5 Consensus size: 20
18508524 TCAAAACGTT
18508534 TTTAATATATA-TTAATATA
1 TTTAATATATATTTAATATA
* *
18508553 TTTAATATTTATTTATTATA
1 TTTAATATATATTTAATATA
18508573 TATTAATATA
1 T-TTAATATA
18508583 GTTATTAATT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
19 10 0.40
20 8 0.32
21 7 0.28
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (20 bp):
TTTAATATATATTTAATATA
Found at i:18508589 original size:19 final size:19
Alignment explanation
Indices: 18508534--18508589 Score: 53
Period size: 19 Copynumber: 2.8 Consensus size: 19
18508524 TCAAAACGTT
18508534 TTTAATATA-TATTAATATA
1 TTTAATATATTATT-ATATA
18508553 TTTAATAT-TTATTTATTATA
1 TTTAATATATTA-TTA-TATA
18508573 TATTAATATAGTTATTA
1 T-TTAATATA-TTATTA
18508590 ATTACTGTTA
Statistics
Matches: 31, Mismatches: 0, Indels: 9
0.77 0.00 0.22
Matches are distributed among these distances:
19 11 0.35
20 7 0.23
21 7 0.23
22 3 0.10
23 3 0.10
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (19 bp):
TTTAATATATTATTATATA
Found at i:18509675 original size:30 final size:29
Alignment explanation
Indices: 18509641--18509874 Score: 215
Period size: 30 Copynumber: 7.9 Consensus size: 29
18509631 CCTAGAAGAT
*
18509641 CCCTAAACTTCTTTAAAATTACATTTTGAC
1 CCCTAAACTT-TTAAAAATTACATTTTGAC
*
18509671 CCCTAAACTTTTCCAAAATTACATTTTGAC
1 CCCTAAACTTTT-AAAAATTACATTTTGAC
** *
18509701 CTTTAAACTTTTCTAAAATTACATTTTGA-
1 CCCTAAACTTTT-AAAAATTACATTTTGAC
* *
18509730 CCCTAAAACTTTTCCAAAATTATATTTTGAC
1 CCCT-AAACTTTT-AAAAATTACATTTTGAC
* * **
18509761 TCCTAAACTTTCCAAAAATTATGTTTTGA-
1 CCCTAAACTTT-TAAAAATTACATTTTGAC
*
18509790 CCCTAAACTTTCTAAAAATTACATTTT-AA
1 CCCTAAACTTT-TAAAAATTACATTTTGAC
* * *
18509819 CCCTCAAACTTCTAAAAATCACATTTTCAC
1 CCCT-AAACTTTTAAAAATTACATTTTGAC
*
18509849 CCC-AAACTTCTCAAAAATTACATTTT
1 CCCTAAACTT-TTAAAAATTACATTTT
18509875 TTCCTTGAAC
Statistics
Matches: 174, Mismatches: 22, Indels: 17
0.82 0.10 0.08
Matches are distributed among these distances:
28 7 0.04
29 58 0.33
30 106 0.61
31 3 0.02
ACGTcount: A:0.36, C:0.23, G:0.03, T:0.38
Consensus pattern (29 bp):
CCCTAAACTTTTAAAAATTACATTTTGAC
Found at i:18509720 original size:60 final size:59
Alignment explanation
Indices: 18509644--18509874 Score: 238
Period size: 60 Copynumber: 3.9 Consensus size: 59
18509634 AGAAGATCCC
*
18509644 TAAACTTCTT-TAAAATTACATTTTGACCCCTAAACTTTTCCAAAATTACATTTTGACCTT
1 TAAACTT-TTCTAAAATTACATTTTGA-CCCTAAACTTTTCAAAAATTACATTTTGACCTT
* * *
18509704 TAAACTTTTCTAAAATTACATTTTGACCCTAAAACTTTTCCAAAATTATATTTTGA-CTCC
1 TAAACTTTTCTAAAATTACATTTTGACCCT-AAACTTTTCAAAAATTACATTTTGACCT-T
* * ** * *
18509764 TAAACTTTCCAAAAATTATGTTTTGACCCTAAAC-TTTCTAAAAATTACATTTTAACCCT
1 TAAACTTTTCTAAAATTACATTTTGACCCTAAACTTTTC-AAAAATTACATTTTGACCTT
* * * * *
18509823 CAAAC--TTCTAAAAATCACATTTTCACCCCAAACTTCTCAAAAATTACATTTT
1 TAAACTTTTCT-AAAATTACATTTTGACCCTAAACTTTTCAAAAATTACATTTT
18509875 TTCCTTGAAC
Statistics
Matches: 144, Mismatches: 20, Indels: 16
0.80 0.11 0.09
Matches are distributed among these distances:
57 2 0.01
58 36 0.25
59 32 0.22
60 74 0.51
ACGTcount: A:0.36, C:0.22, G:0.03, T:0.39
Consensus pattern (59 bp):
TAAACTTTTCTAAAATTACATTTTGACCCTAAACTTTTCAAAAATTACATTTTGACCTT
Found at i:18509794 original size:29 final size:29
Alignment explanation
Indices: 18509655--18509965 Score: 244
Period size: 29 Copynumber: 10.6 Consensus size: 29
18509645 AAACTTCTTT
18509655 AAAATTACATTTTGACCCCTAAACTTTTCC-
1 AAAATTACATTTTGA-CCCTAAAC-TTTCCA
* * *
18509685 AAAATTACATTTTGACCTTTAAACTTTTCT
1 AAAATTACATTTTGACC-CTAAACTTTCCA
18509715 AAAATTACATTTTGACCCTAAAACTTTTCC-
1 AAAATTACATTTTGACCCT-AAAC-TTTCCA
*
18509745 AAAATTATATTTTGACTCCTAAACTTTCCA
1 AAAATTACATTTTGAC-CCTAAACTTTCCA
** *
18509775 AAAATTATGTTTTGACCCTAAACTTTCTA
1 AAAATTACATTTTGACCCTAAACTTTCCA
* *
18509804 AAAATTACATTTTAACCCTCAAAC-TTCTA
1 AAAATTACATTTTGACCCT-AAACTTTCCA
* * *
18509833 AAAATCACATTTTCACCCCAAAC-TTCTCA
1 AAAATTACATTTTGACCCTAAACTTTC-CA
** * * *
18509862 AAAATTACATTTTTTCCTTGAACATT-CA
1 AAAATTACATTTTGACCCTAAACTTTCCA
* *
18509890 AAAATTACCATTTTG-CCCTTGAAC-ATCCA
1 AAAATTA-CATTTTGACCC-TAAACTTTCCA
* *
18509919 AAAATTACCATTTTG-CCCTCGAA-TTTTCA
1 AAAATTA-CATTTTGACCCT-AAACTTTCCA
*
18509948 AAAATCACATTTTCGACC
1 AAAATTACATTTT-GACC
18509966 TCAAATTTTC
Statistics
Matches: 239, Mismatches: 26, Indels: 32
0.80 0.09 0.11
Matches are distributed among these distances:
28 26 0.11
29 123 0.51
30 83 0.35
31 7 0.03
ACGTcount: A:0.36, C:0.23, G:0.04, T:0.37
Consensus pattern (29 bp):
AAAATTACATTTTGACCCTAAACTTTCCA
Found at i:18509967 original size:29 final size:29
Alignment explanation
Indices: 18509917--18509975 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 29
18509907 CTTGAACATC
* * *
18509917 CAAAAATTACCATTTTGCCCTCGAATTTT
1 CAAAAATCACCATTTTGACCTCAAATTTT
18509946 CAAAAATCA-CATTTTCGACCTCAAATTTT
1 CAAAAATCACCATTTT-GACCTCAAATTTT
18509975 C
1 C
18509976 CATAATTTCG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
28 6 0.23
29 20 0.77
ACGTcount: A:0.34, C:0.25, G:0.05, T:0.36
Consensus pattern (29 bp):
CAAAAATCACCATTTTGACCTCAAATTTT
Found at i:18515504 original size:17 final size:16
Alignment explanation
Indices: 18515468--18515518 Score: 57
Period size: 17 Copynumber: 3.0 Consensus size: 16
18515458 GGATTCATTG
*
18515468 AAGAAAAAATAAATAAAA
1 AAGAAAAAA-AGA-AAAA
18515486 AAGAAAGAAAAGAAAAA
1 AAGAAA-AAAAGAAAAA
*
18515503 AAGAAAAAAGGAAAAA
1 AAGAAAAAAAGAAAAA
18515519 GAAAATAGAA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
16 9 0.30
17 10 0.33
18 8 0.27
19 3 0.10
ACGTcount: A:0.82, C:0.00, G:0.14, T:0.04
Consensus pattern (16 bp):
AAGAAAAAAAGAAAAA
Found at i:18515506 original size:8 final size:8
Alignment explanation
Indices: 18515468--18515518 Score: 57
Period size: 8 Copynumber: 6.0 Consensus size: 8
18515458 GGATTCATTG
18515468 AAGAAAAA
1 AAGAAAAA
*
18515476 ATAAATAAAA
1 A-AGA-AAAA
18515486 AAGAAAGAA
1 AAGAAA-AA
18515495 AAGAAAAA
1 AAGAAAAA
18515503 AAGAAAAA
1 AAGAAAAA
*
18515511 AGGAAAAA
1 AAGAAAAA
18515519 GAAAATAGAA
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
8 20 0.54
9 12 0.32
10 5 0.14
ACGTcount: A:0.82, C:0.00, G:0.14, T:0.04
Consensus pattern (8 bp):
AAGAAAAA
Found at i:18515509 original size:7 final size:7
Alignment explanation
Indices: 18515468--18515545 Score: 70
Period size: 7 Copynumber: 11.0 Consensus size: 7
18515458 GGATTCATTG
18515468 AAGAAAA
1 AAGAAAA
*
18515475 AATAAATA
1 AAGAAA-A
18515483 AA-AAAGA
1 AAGAAA-A
18515490 AAGAAAA
1 AAGAAAA
*
18515497 GA-AAAA
1 AAGAAAA
18515503 AAGAAAA
1 AAGAAAA
*
18515510 AAGGAAA
1 AAGAAAA
18515517 AAGAAAA
1 AAGAAAA
*
18515524 TAGAAAA
1 AAGAAAA
*
18515531 AATGGAAA
1 AA-GAAAA
18515539 AAGAAAA
1 AAGAAAA
18515546 GGAGAGGTCG
Statistics
Matches: 57, Mismatches: 10, Indels: 8
0.76 0.13 0.11
Matches are distributed among these distances:
6 5 0.09
7 40 0.70
8 12 0.21
ACGTcount: A:0.79, C:0.00, G:0.15, T:0.05
Consensus pattern (7 bp):
AAGAAAA
Found at i:18515537 original size:22 final size:21
Alignment explanation
Indices: 18515493--18515545 Score: 79
Period size: 22 Copynumber: 2.4 Consensus size: 21
18515483 AAAAAGAAAG
18515493 AAAAGAAAAAAAGAAAAAAGGA
1 AAAAG-AAAAAAGAAAAAAGGA
*
18515515 AAAAGAAAATAGAAAAAATGGA
1 AAAAGAAAAAAGAAAAAA-GGA
18515537 AAAAGAAAA
1 AAAAGAAAA
18515546 GGAGAGGTCG
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
21 12 0.41
22 17 0.59
ACGTcount: A:0.79, C:0.00, G:0.17, T:0.04
Consensus pattern (21 bp):
AAAAGAAAAAAGAAAAAAGGA
Found at i:18516143 original size:12 final size:12
Alignment explanation
Indices: 18516126--18516153 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
18516116 TAAATAATAC
18516126 AAGGACCTGAAA
1 AAGGACCTGAAA
18516138 AAGGACCTGAAA
1 AAGGACCTGAAA
18516150 AAGG
1 AAGG
18516154 GTCTTGAAAC
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:0.50, C:0.14, G:0.29, T:0.07
Consensus pattern (12 bp):
AAGGACCTGAAA
Found at i:18516506 original size:50 final size:50
Alignment explanation
Indices: 18516430--18516774 Score: 301
Period size: 50 Copynumber: 7.0 Consensus size: 50
18516420 GAGAAAACAT
* * * * **
18516430 GAAGATATGAAGGGAAAGGTTAAGGCCGCAACGGGGAACCCAATACCTTA
1 GAAGATGTGATGGGAAAGGTTGAGGCCGCAACGGCGAACCCGGTACCTTA
* * *
18516480 GAAGAAGTGACGGGAAAGGTTGAGGCCGCAACGGCGAACCCGGTACCAT-
1 GAAGATGTGATGGGAAAGGTTGAGGCCGCAACGGCGAACCCGGTACCTTA
* * *
18516529 GAAGATTTGGA-GGGAAAGGTTGAGGCCGCAATGGCGAACCCAGTACCTTA
1 GAAGATGT-GATGGGAAAGGTTGAGGCCGCAACGGCGAACCCGGTACCTTA
* * ** *** *
18516579 GAAGATGTGATGGG-AAGGATTAAGGCCGTAACGATGAATTTGGTACCAT-
1 GAAGATGTGATGGGAAAGG-TTGAGGCCGCAACGGCGAACCCGGTACCTTA
*
18516628 GAA-ATATGATGGGAAAGGTTGAGGCCGCAACGGCGAACCCGGTACCTTA
1 GAAGATGTGATGGGAAAGGTTGAGGCCGCAACGGCGAACCCGGTACCTTA
* * * ** * * *
18516677 GACGATGTGATGGG-GAGGATTGAGGCCGCAATGGTAAATCCGGTTCCAT-
1 GAAGATGTGATGGGAAAGG-TTGAGGCCGCAACGGCGAACCCGGTACCTTA
* ** * *
18516726 GAA-ATGTAATGGGAAAGGTTGAGGCAACAACGGTGAACCCGATACCTTA
1 GAAGATGTGATGGGAAAGGTTGAGGCCGCAACGGCGAACCCGGTACCTTA
18516775 AAAAAACATG
Statistics
Matches: 232, Mismatches: 53, Indels: 21
0.76 0.17 0.07
Matches are distributed among these distances:
48 62 0.27
49 64 0.28
50 106 0.46
ACGTcount: A:0.32, C:0.17, G:0.33, T:0.18
Consensus pattern (50 bp):
GAAGATGTGATGGGAAAGGTTGAGGCCGCAACGGCGAACCCGGTACCTTA
Found at i:18516673 original size:98 final size:99
Alignment explanation
Indices: 18516427--18516774 Score: 398
Period size: 98 Copynumber: 3.5 Consensus size: 99
18516417 GCCGAGAAAA
* * * * *
18516427 CATGAAGATATGAAGGGAAAGGTTAAGGCCGCAACGGGGAACCCAATACCTTAGAAGAAGTGACG
1 CATGAAGATATGATGGGAAAGGTTGAGGCCGCAACGGCGAACCCAATACCTTAGAAGATGTGATG
* *
18516492 GGAAAGG-TTGAGGCCGCAACGGCGAACCCGGTAC
66 GG-AAGGATTGAGGCCGCAACGGTGAATCCGGTAC
* * *
18516526 CATGAAGATTTGGA-GGGAAAGGTTGAGGCCGCAATGGCGAACCCAGTACCTTAGAAGATGTGAT
1 CATGAAGATAT-GATGGGAAAGGTTGAGGCCGCAACGGCGAACCCAATACCTTAGAAGATGTGAT
* * * **
18516590 GGGAAGGATTAAGGCCGTAACGATGAATTTGGTAC
65 GGGAAGGATTGAGGCCGCAACGGTGAATCCGGTAC
** *
18516625 CATGAA-ATATGATGGGAAAGGTTGAGGCCGCAACGGCGAACCCGGTACCTTAGACGATGTGATG
1 CATGAAGATATGATGGGAAAGGTTGAGGCCGCAACGGCGAACCCAATACCTTAGAAGATGTGATG
* * * *
18516689 GGGAGGATTGAGGCCGCAATGGTAAATCCGGTTC
66 GGAAGGATTGAGGCCGCAACGGTGAATCCGGTAC
* * ** * *
18516723 CATGAA-ATGTAATGGGAAAGGTTGAGGCAACAACGGTGAACCCGATACCTTA
1 CATGAAGATATGATGGGAAAGGTTGAGGCCGCAACGGCGAACCCAATACCTTA
18516775 AAAAAACATG
Statistics
Matches: 213, Mismatches: 33, Indels: 7
0.84 0.13 0.03
Matches are distributed among these distances:
97 2 0.01
98 126 0.59
99 83 0.39
100 2 0.01
ACGTcount: A:0.32, C:0.18, G:0.33, T:0.18
Consensus pattern (99 bp):
CATGAAGATATGATGGGAAAGGTTGAGGCCGCAACGGCGAACCCAATACCTTAGAAGATGTGATG
GGAAGGATTGAGGCCGCAACGGTGAATCCGGTAC
Found at i:18516804 original size:197 final size:198
Alignment explanation
Indices: 18516427--18516808 Score: 432
Period size: 197 Copynumber: 1.9 Consensus size: 198
18516417 GCCGAGAAAA
*
18516427 CATGAAGATATGAAGGGAAAGGTTAAGGCCGCAACGGGGAACCCAATACCTTAGAAGAAGTGACG
1 CATGAAGATATGAAGGGAAAGGTTAAGGCCGCAACGGCGAACCCAATACCTTAGAAGAAGTGACG
* * * **
18516492 GGAAAGGTTGAGGCCGCAACGGCGAACCCGGTACCATGAAGATTTGGAGGGAAAGGTTGAGGCCG
66 GGAAAGGTTGAGGCCGCAACGGCAAACCCGGTACCATGAAGATGTGAAGGGAAAGGTTGAGGCAA
* * * ** * * **
18516557 CAATGGCGAACCCAGTACCTTAGAAGATGTGATGGGAAGGATTAAGGCCGTAACGATGAATTTGG
131 CAACGGCGAACCCAGTACCTTAAAAAACATGACGAGAAAAATTAAGGCCGTAACGATGAATTTGG
18516622 TAC
196 TAC
* * ** * * *
18516625 CATGAA-ATATGATGGGAAAGGTTGAGGCCGCAACGGCGAACCCGGTACCTTAGACGATGTGATG
1 CATGAAGATATGAAGGGAAAGGTTAAGGCCGCAACGGCGAACCCAATACCTTAGAAGAAGTGACG
* * * * *
18516689 GG-GAGGATTGAGGCCGCAATGGTAAATCCGGTTCCATGAA-ATGT-AATGGGAAAGGTTGAGGC
66 GGAAAGG-TTGAGGCCGCAACGGCAAACCCGGTACCATGAAGATGTGAA-GGGAAAGGTTGAGGC
* *
18516751 AACAACGGTGAACCC-GATACCTTAAAAAAACATGACGAGAAAAATTGAGGCCGTAACG
129 AACAACGGCGAACCCAG-TACCTT-AAAAAACATGACGAGAAAAATTAAGGCCGTAACG
18516809 GTGAGTCTTA
Statistics
Matches: 151, Mismatches: 29, Indels: 9
0.80 0.15 0.05
Matches are distributed among these distances:
195 2 0.01
196 38 0.25
197 105 0.70
198 6 0.04
ACGTcount: A:0.34, C:0.17, G:0.32, T:0.17
Consensus pattern (198 bp):
CATGAAGATATGAAGGGAAAGGTTAAGGCCGCAACGGCGAACCCAATACCTTAGAAGAAGTGACG
GGAAAGGTTGAGGCCGCAACGGCAAACCCGGTACCATGAAGATGTGAAGGGAAAGGTTGAGGCAA
CAACGGCGAACCCAGTACCTTAAAAAACATGACGAGAAAAATTAAGGCCGTAACGATGAATTTGG
TAC
Found at i:18517158 original size:39 final size:37
Alignment explanation
Indices: 18517052--18517591 Score: 188
Period size: 39 Copynumber: 13.9 Consensus size: 37
18517042 AATTGAAGAT
* *
18517052 TTCGATCTTTTACCCTGAGCCTGGGGGCAGA-TCACCA
1 TTCGATCTTTTACCCCGAGCCT-AGGGCAGATTCACCA
* ** * *
18517089 -TCAGCCAATCTCTTACCCTAAGCTTGGGGCAGATTGCAGCCA
1 TTC-G---ATCTTTTACCCCGAGCCTAGGGCAGATT-CA-CCA
*
18517131 TTCGATCTTTTACCCCGAGCCTAGGGCA-AATCACTATCA
1 TTCGATCTTTTACCCCGAGCCTAGGGCAGATTCAC---CA
** * * * * *
18517170 ACCAATCTCTTACACCGAGCCT-GAGGCAGATTACAATCG
1 TTCGATCTTTTACCCCGAGCCTAG-GGCAGATT-C-ACCA
** * *
18517209 TTAAATCTTTTACCCCGAGCCTGGGGTAGA-TCACCA
1 TTCGATCTTTTACCCCGAGCCTAGGGCAGATTCACCA
* * * * *
18517245 -TCAGCCAATCTCTTACCCCGAGCCTAAGGTAGATTGTAGTCA
1 TTC-G---ATCTTTTACCCCGAGCCTAGGGCAGATT-CA-CCA
* * * *
18517287 TCCGATCTTTTACTCCGAGCATAGGGCAG-GTCACCA
1 TTCGATCTTTTACCCCGAGCCTAGGGCAGATTCACCA
* * *
18517323 -TCAGCCAATCTCTTACCCCAAG-CTTGAGGCAGATTGCAGCCA
1 TTC-G---ATCTTTTACCCCGAGCCTAG-GGCAGATT-CA-CCA
* * *
18517365 TTCGATCTTTTACCTCGAGCCTGGGGCAGA-TCACCGT
1 TTCGATCTTTTACCCCGAGCCTAGGGCAGATTCACC-A
* * * *
18517402 TTGCCAATCTCTTACCCCGAGCCTGGGGCAGATCACAGCCA
1 TT--CGATCTTTTACCCCGAGCCTAGGGCAGAT-TCA-CCA
18517443 TTCGATCTTTTACCCCGAGCCTAGGGCAGA-TCACCATCA
1 TTCGATCTTTTACCCCGAGCCTAGGGCAGATTCA-C--CA
* * * **
18517482 TTTGATCTTTTACCCCGAGCTTGGGGCAGATTGCAGTTA
1 TTCGATCTTTTACCCCGAGCCTAGGGCAGATT-CA-CCA
* * *
18517521 CTCGATCTTTTACCCTGAGCAT-GAGGCAGA-TCACCA
1 TTCGATCTTTTACCCCGAGCCTAG-GGCAGATTCACCA
* * *
18517557 TTAGCCAATCTCTTACCCCGAGCCAAGGGCAGATT
1 TT---CGATCTTTTACCCCGAGCCTAGGGCAGATT
18517592 GCAACCATCC
Statistics
Matches: 372, Mismatches: 81, Indels: 97
0.68 0.15 0.18
Matches are distributed among these distances:
35 2 0.01
36 12 0.03
37 14 0.04
38 10 0.03
39 276 0.74
40 27 0.07
41 12 0.03
42 14 0.04
43 5 0.01
ACGTcount: A:0.24, C:0.30, G:0.21, T:0.26
Consensus pattern (37 bp):
TTCGATCTTTTACCCCGAGCCTAGGGCAGATTCACCA
Found at i:18517181 original size:78 final size:78
Alignment explanation
Indices: 18517052--18517599 Score: 596
Period size: 78 Copynumber: 7.0 Consensus size: 78
18517042 AATTGAAGAT
* * ** * *
18517052 TTCGATCTTTTACCCTGAGCCTGGGGGCAGATCACCATCAGCCAATCTCTTACCCTAAGCTTGGG
1 TTCGATCTTTTACCCCGAGCCT-AGGGCAGATCACCATCAGCCAATCTCTTACCCCGAGCCTGAG
18517117 GCAGATTGCAGCCA
65 GCAGATTGCAGCCA
* * * *
18517131 TTCGATCTTTTACCCCGAGCCTAGGGCAAATCACTATCAACCAATCTCTTACACCGAGCCTGAGG
1 TTCGATCTTTTACCCCGAGCCTAGGGCAGATCACCATCAGCCAATCTCTTACCCCGAGCCTGAGG
* ** *
18517196 CAGATTACAATCG
66 CAGATTGCAGCCA
** * * *
18517209 TTAAATCTTTTACCCCGAGCCTGGGGTAGATCACCATCAGCCAATCTCTTACCCCGAGCCTAAGG
1 TTCGATCTTTTACCCCGAGCCTAGGGCAGATCACCATCAGCCAATCTCTTACCCCGAGCCTGAGG
* * *
18517274 TAGATTGTAGTCA
66 CAGATTGCAGCCA
* * * * * *
18517287 TCCGATCTTTTACTCCGAGCATAGGGCAGGTCACCATCAGCCAATCTCTTACCCCAAGCTTGAGG
1 TTCGATCTTTTACCCCGAGCCTAGGGCAGATCACCATCAGCCAATCTCTTACCCCGAGCCTGAGG
18517352 CAGATTGCAGCCA
66 CAGATTGCAGCCA
* * * ** *
18517365 TTCGATCTTTTACCTCGAGCCTGGGGCAGATCACCGTTTGCCAATCTCTTACCCCGAGCCTGGGG
1 TTCGATCTTTTACCCCGAGCCTAGGGCAGATCACCATCAGCCAATCTCTTACCCCGAGCCTGAGG
**
18517430 CAGATCACAGCCA
66 CAGATTGCAGCCA
**** * * *
18517443 TTCGATCTTTTACCCCGAGCCTAGGGCAGATCACCATCATTTGATCTTTTACCCCGAGCTTGGGG
1 TTCGATCTTTTACCCCGAGCCTAGGGCAGATCACCATCAGCCAATCTCTTACCCCGAGCCTGAGG
**
18517508 CAGATTGCAGTTA
66 CAGATTGCAGCCA
* * * * *
18517521 CTCGATCTTTTACCCTGAGCAT-GAGGCAGATCACCATTAGCCAATCTCTTACCCCGAGCC-AAG
1 TTCGATCTTTTACCCCGAGCCTAG-GGCAGATCACCATCAGCCAATCTCTTACCCCGAGCCTGA-
*
18517584 GGCAGATTGCAACCA
64 GGCAGATTGCAGCCA
18517599 T
1 T
18517600 CCAATAAAAA
Statistics
Matches: 380, Mismatches: 87, Indels: 5
0.81 0.18 0.01
Matches are distributed among these distances:
77 1 0.00
78 358 0.94
79 21 0.06
ACGTcount: A:0.24, C:0.30, G:0.20, T:0.25
Consensus pattern (78 bp):
TTCGATCTTTTACCCCGAGCCTAGGGCAGATCACCATCAGCCAATCTCTTACCCCGAGCCTGAGG
CAGATTGCAGCCA
Found at i:18518114 original size:17 final size:17
Alignment explanation
Indices: 18518094--18518180 Score: 104
Period size: 17 Copynumber: 5.1 Consensus size: 17
18518084 ATTGAACCCA
18518094 ATTTTAAATTTTAAA-TT
1 ATTTTAAA-TTTAAATTT
*
18518111 ATTTTAAGTTTAAATTT
1 ATTTTAAATTTAAATTT
*
18518128 ATTTTAAATTTAAACTT
1 ATTTTAAATTTAAATTT
* *
18518145 ATTTTTGAGTTTAAATTT
1 A-TTTTAAATTTAAATTT
*
18518163 ATTTTGAATTTAAATTT
1 ATTTTAAATTTAAATTT
18518180 A
1 A
18518181 AAATTTAATT
Statistics
Matches: 61, Mismatches: 7, Indels: 4
0.85 0.10 0.06
Matches are distributed among these distances:
16 6 0.10
17 41 0.67
18 14 0.23
ACGTcount: A:0.37, C:0.01, G:0.05, T:0.57
Consensus pattern (17 bp):
ATTTTAAATTTAAATTT
Found at i:18518128 original size:6 final size:6
Alignment explanation
Indices: 18518096--18518188 Score: 50
Period size: 6 Copynumber: 15.8 Consensus size: 6
18518086 TGAACCCAAT
* * *
18518096 TTTAAA TTTTAAA -TT-AT TTTAAG TTTAAA TTT-AT TTTAAA TTTAAA
1 TTTAAA -TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
* ** * * * *
18518142 CTTATT TTTGAG TTTAAA TTT-AT TTTGAA TTTAAA TTTAAAA TTTAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTT-AAA TTTAA
18518189 TTAAAAGTCT
Statistics
Matches: 64, Mismatches: 17, Indels: 11
0.70 0.18 0.12
Matches are distributed among these distances:
4 1 0.02
5 12 0.19
6 39 0.61
7 12 0.19
ACGTcount: A:0.39, C:0.01, G:0.04, T:0.56
Consensus pattern (6 bp):
TTTAAA
Found at i:18518163 original size:35 final size:33
Alignment explanation
Indices: 18518094--18518178 Score: 125
Period size: 35 Copynumber: 2.5 Consensus size: 33
18518084 ATTGAACCCA
18518094 ATTTTAAATTTTAAATTATTTTAAGTTTAAATTT
1 ATTTTAAA-TTTAAATTATTTTAAGTTTAAATTT
*
18518128 ATTTTAAATTTAAACTTATTTTTGAGTTTAAATTT
1 ATTTTAAATTTAAA-TTA-TTTTAAGTTTAAATTT
*
18518163 ATTTTGAATTTAAATT
1 ATTTTAAATTTAAATT
18518179 TAAAATTTAA
Statistics
Matches: 47, Mismatches: 2, Indels: 4
0.89 0.04 0.08
Matches are distributed among these distances:
33 6 0.13
34 13 0.28
35 28 0.60
ACGTcount: A:0.36, C:0.01, G:0.05, T:0.58
Consensus pattern (33 bp):
ATTTTAAATTTAAATTATTTTAAGTTTAAATTT
Found at i:18518780 original size:10 final size:10
Alignment explanation
Indices: 18518767--18518814 Score: 62
Period size: 10 Copynumber: 4.8 Consensus size: 10
18518757 CAAAATGTTT
18518767 TTAATATATA
1 TTAATATATA
18518777 TTAATATAT-
1 TTAATATATA
*
18518786 TTAATATTTA
1 TTAATATATA
*
18518796 TTTATTATATA
1 -TTAATATATA
18518807 TTAATATA
1 TTAATATA
18518815 GTTATTAATT
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
9 8 0.25
10 16 0.50
11 8 0.25
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (10 bp):
TTAATATATA
Found at i:18518790 original size:19 final size:20
Alignment explanation
Indices: 18518766--18518814 Score: 64
Period size: 19 Copynumber: 2.5 Consensus size: 20
18518756 TCAAAATGTT
18518766 TTTAATATATA-TTAATATA
1 TTTAATATATATTTAATATA
* *
18518785 TTTAATATTTATTTATTATA
1 TTTAATATATATTTAATATA
18518805 TATTAATATA
1 T-TTAATATA
18518815 GTTATTAATT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
19 10 0.40
20 8 0.32
21 7 0.28
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (20 bp):
TTTAATATATATTTAATATA
Found at i:18518821 original size:19 final size:19
Alignment explanation
Indices: 18518766--18518821 Score: 53
Period size: 19 Copynumber: 2.8 Consensus size: 19
18518756 TCAAAATGTT
18518766 TTTAATATA-TATTAATATA
1 TTTAATATATTATT-ATATA
18518785 TTTAATAT-TTATTTATTATA
1 TTTAATATATTA-TTA-TATA
18518805 TATTAATATAGTTATTA
1 T-TTAATATA-TTATTA
18518822 ATTACTGTTA
Statistics
Matches: 31, Mismatches: 0, Indels: 9
0.77 0.00 0.22
Matches are distributed among these distances:
19 11 0.35
20 7 0.23
21 7 0.23
22 3 0.10
23 3 0.10
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (19 bp):
TTTAATATATTATTATATA
Found at i:18519960 original size:30 final size:29
Alignment explanation
Indices: 18519917--18520203 Score: 251
Period size: 30 Copynumber: 9.7 Consensus size: 29
18519907 AAGGTCTCTG
* *
18519917 AACTTCTCTAAAATTGCATTTTGACCCCTA
1 AACTT-TCAAAAATTACATTTTGACCCCTA
18519947 AACATTTCAAAAATTACA-TTTGACCCCTA
1 AAC-TTTCAAAAATTACATTTTGACCCCTA
* * **
18519976 AACTTCTCTAAAATTACATTTTAACCTTTA
1 AACTT-TCAAAAATTACATTTTGACCCCTA
*
18520006 AACTTTTCTAAAATTACATTTTGACCCCTA
1 AAC-TTTCAAAAATTACATTTTGACCCCTA
* *
18520036 AACTTCTCTAAAATTATATTTTGACCCCTA
1 AACTT-TCAAAAATTACATTTTGACCCCTA
* *
18520066 AACTTTCCAAAAATTATATTTTGACCTCTA
1 AACTTT-CAAAAATTACATTTTGACCCCTA
* * *
18520096 AACTTTCTAAAAGTTACATTTT-AACCTTAA
1 AACTTTC-AAAAATTACATTTTGACCCCT-A
* *
18520126 AACTTTTCGAAAATTACA-TTTAACCGCC-A
1 AAC-TTTCAAAAATTACATTTTGACC-CCTA
* * * * *
18520155 AACTTCCAAAAGTCACATTTTTACCCC-G
1 AACTTTCAAAAATTACATTTTGACCCCTA
18520183 AACTTCTCAAAAATTACATTT
1 AACTT-TCAAAAATTACATTT
18520204 ATGCCCTGAA
Statistics
Matches: 214, Mismatches: 30, Indels: 27
0.79 0.11 0.10
Matches are distributed among these distances:
28 19 0.09
29 57 0.27
30 129 0.60
31 9 0.04
ACGTcount: A:0.36, C:0.23, G:0.04, T:0.37
Consensus pattern (29 bp):
AACTTTCAAAAATTACATTTTGACCCCTA
Found at i:18520049 original size:60 final size:60
Alignment explanation
Indices: 18519917--18520203 Score: 320
Period size: 60 Copynumber: 4.8 Consensus size: 60
18519907 AAGGTCTCTG
* * *
18519917 AACTTCTCTAAAATTGCATTTTGACCCCTAAACATTTCAAAAATTACA-TTTGACCCCTA
1 AACTTCTCTAAAATTACATTTTAACCCCTAAACTTTTCAAAAATTACATTTTGACCCCTA
** *
18519976 AACTTCTCTAAAATTACATTTTAACCTTTAAACTTTTCTAAAATTACATTTTGACCCCTA
1 AACTTCTCTAAAATTACATTTTAACCCCTAAACTTTTCAAAAATTACATTTTGACCCCTA
* * * * *
18520036 AACTTCTCTAAAATTATATTTTGACCCCTAAACTTTCCAAAAATTATATTTTGACCTCTA
1 AACTTCTCTAAAATTACATTTTAACCCCTAAACTTTTCAAAAATTACATTTTGACCCCTA
* * *
18520096 AACTT-TCTAAAAGTTACATTTTAA-CCTTAAAACTTTTCGAAAATTACA-TTTAACCGCC-A
1 AACTTCTCTAAAA-TTACATTTTAACCCCT-AAACTTTTCAAAAATTACATTTTGACC-CCTA
* * * *
18520155 AACTTC-C-AAAAGTCACATTTTTACCCC-GAACTTCTCAAAAATTACATTT
1 AACTTCTCTAAAA-TTACATTTTAACCCCTAAACTTTTCAAAAATTACATTT
18520204 ATGCCCTGAA
Statistics
Matches: 193, Mismatches: 28, Indels: 15
0.82 0.12 0.06
Matches are distributed among these distances:
57 16 0.08
58 16 0.08
59 67 0.35
60 94 0.49
ACGTcount: A:0.36, C:0.23, G:0.04, T:0.37
Consensus pattern (60 bp):
AACTTCTCTAAAATTACATTTTAACCCCTAAACTTTTCAAAAATTACATTTTGACCCCTA
Found at i:18520129 original size:90 final size:90
Alignment explanation
Indices: 18519912--18520203 Score: 278
Period size: 89 Copynumber: 3.3 Consensus size: 90
18519902 CTCAGAAGGT
* * * * *
18519912 CTCTGAACTTCTCTAAAATTGCATTTTGACCCCTAAACATT-TCAAAAATTACA-TTTGACCCCT
1 CTCTAAACTTTTCTAAAATTACATTTTGAACCCTAAAC-TTCTCGAAAATTACATTTTGACCCCT
*
18519975 AAACTTCTCTAAAATTACATTTTAAC
65 AAACTTCTCAAAAATTACATTTTAAC
* * * *
18520001 CTTTAAACTTTTCTAAAATTACATTTTGACCCCTAAACTTCTCTAAAATTATATTTTGACCCCTA
1 CTCTAAACTTTTCTAAAATTACATTTTGAACCCTAAACTTCTCGAAAATTACATTTTGACCCCTA
* *
18520066 AACTT-TCCAAAAATTATATTTTGAC
66 AACTTCT-CAAAAATTACATTTTAAC
* * *
18520091 CTCTAAAC-TTTCTAAAAGTTACATTTT-AACCTTAAAACTTTTCGAAAATTACA-TTTAACCGC
1 CTCTAAACTTTTCTAAAA-TTACATTTTGAACCCT-AAACTTCTCGAAAATTACATTTTGACC-C
* * *
18520153 C-AAACTTC-CAAAAGTCACATTTTTAC
63 CTAAACTTCTCAAAAATTACATTTTAAC
** * *
18520179 C-CCGAACTTCTCAAAAATTACATTT
1 CTCTAAACTTTTCTAAAATTACATTT
18520204 ATGCCCTGAA
Statistics
Matches: 171, Mismatches: 24, Indels: 18
0.80 0.11 0.08
Matches are distributed among these distances:
87 12 0.07
88 24 0.14
89 70 0.41
90 65 0.38
ACGTcount: A:0.36, C:0.23, G:0.04, T:0.37
Consensus pattern (90 bp):
CTCTAAACTTTTCTAAAATTACATTTTGAACCCTAAACTTCTCGAAAATTACATTTTGACCCCTA
AACTTCTCAAAAATTACATTTTAAC
Found at i:18520186 original size:28 final size:28
Alignment explanation
Indices: 18520135--18520236 Score: 84
Period size: 28 Copynumber: 3.6 Consensus size: 28
18520125 AAACTTTTCG
* *
18520135 AAAATTACATTTA-ACCGCCAAACTTCCA
1 AAAATCACATTTATACC-CCGAACTTCCA
* *
18520163 AAAGTCACATTTTTACCCCGAACTTCTCA
1 AAAATCACATTTATACCCCGAACTTC-CA
* * * *
18520192 AAAATTACATTTATGCCCTGAACATCCA
1 AAAATCACATTTATACCCCGAACTTCCA
18520220 AAAAT-ACCATTT-TACCC
1 AAAATCA-CATTTATACCC
18520237 TCTAAGATCT
Statistics
Matches: 60, Mismatches: 11, Indels: 7
0.77 0.14 0.09
Matches are distributed among these distances:
27 5 0.08
28 30 0.50
29 25 0.42
ACGTcount: A:0.38, C:0.28, G:0.05, T:0.28
Consensus pattern (28 bp):
AAAATCACATTTATACCCCGAACTTCCA
Found at i:18520214 original size:29 final size:28
Alignment explanation
Indices: 18519917--18520237 Score: 170
Period size: 30 Copynumber: 11.0 Consensus size: 28
18519907 AAGGTCTCTG
* *
18519917 AACTTCTCTAAAATTGCATTTTGACCCCTA
1 AACTTCTCAAAAATTACATTTTG--CCCTA
18519947 AACATT-TCAAAAATTACA-TTTGACCCCTA
1 AAC-TTCTCAAAAATTACATTTTG--CCCTA
* * *
18519976 AACTTCTCTAAAATTACATTTTAACCTTTA
1 AACTTCTCAAAAATTACATTTT-GCC-CTA
* *
18520006 AACTTTTCTAAAATTACATTTTGACCCCTA
1 AACTTCTCAAAAATTACATTTTG--CCCTA
* *
18520036 AACTTCTCTAAAATTATATTTTGACCCCTA
1 AACTTCTCAAAAATTACATTTTG--CCCTA
*
18520066 AACTT-TCCAAAAATTATATTTTGACCTCTA
1 AACTTCT-CAAAAATTACATTTTG-CC-CTA
* * *
18520096 AACTT-TCTAAAAGTTACATTTTAACCTTAA
1 AACTTCTC-AAAAATTACATTTT-GCCCT-A
* * ** *
18520126 AACTTTTCGAAAATTACATTTAACCGCCA
1 AACTTCTCAAAAATTACATTTTGCC-CTA
* * * **
18520155 AACTTC-CAAAAGTCACATTTTTACCCCG
1 AACTTCTCAAAAATTACA-TTTTGCCCTA
*
18520183 AACTTCTCAAAAATTACATTTATGCCCTG
1 AACTTCTCAAAAATTACATTT-TGCCCTA
* *
18520212 AACATC-CAAAAA-TACCATTTTACCCT
1 AACTTCTCAAAAATTA-CATTTTGCCCT
18520238 CTAAGATCTA
Statistics
Matches: 240, Mismatches: 33, Indels: 39
0.77 0.11 0.12
Matches are distributed among these distances:
27 7 0.03
28 32 0.13
29 66 0.28
30 129 0.54
31 6 0.03
ACGTcount: A:0.36, C:0.24, G:0.04, T:0.36
Consensus pattern (28 bp):
AACTTCTCAAAAATTACATTTTGCCCTA
Found at i:18520279 original size:29 final size:28
Alignment explanation
Indices: 18520173--18520280 Score: 94
Period size: 29 Copynumber: 3.8 Consensus size: 28
18520163 AAAGTCACAT
* *
18520173 TTTTACCCCGAACTTCTCAAAAATTA-CA
1 TTTTACCCTGAACATC-CAAAAATTACCA
*
18520201 TTTATGCCCTGAACATCCAAAAA-TACCA
1 TTT-TACCCTGAACATCCAAAAATTACCA
* * *
18520229 TTTTACCCTCTAAGATCTAAAAATTACCA
1 TTTTACCCT-GAACATCCAAAAATTACCA
**
18520258 TTTTACCCTTGAATTTCCAAAAA
1 TTTTACCC-TGAACATCCAAAAA
18520281 ACACATTTTC
Statistics
Matches: 64, Mismatches: 11, Indels: 9
0.76 0.13 0.11
Matches are distributed among these distances:
27 7 0.11
28 24 0.38
29 32 0.50
30 1 0.02
ACGTcount: A:0.37, C:0.26, G:0.05, T:0.32
Consensus pattern (28 bp):
TTTTACCCTGAACATCCAAAAATTACCA
Found at i:18523234 original size:60 final size:59
Alignment explanation
Indices: 18523141--18523343 Score: 283
Period size: 60 Copynumber: 3.5 Consensus size: 59
18523131 CTAAATGAAG
18523141 AAGTAAACTTCTATTTTATTAAATGAT-GCAATATAAAAAGAATGTGTACAAAAATATTCA
1 AAGTAAACTTCTATTTTATTAAATGATAG-AATATAAAAA-AATGTGTACAAAAATATTCA
18523201 AAGTAAACTTCTATTTTATTAAATGATAGAATATAAAAATAATGTGTAC-AAAATATTCA
1 AAGTAAACTTCTATTTTATTAAATGATAGAATATAAAAA-AATGTGTACAAAAATATTCA
* ** * *
18523260 AA--AGAACTTTTATTTGGTTAAATGATACAATAT--AAAAATGTGTACAAAAAAATTCA
1 AAGTA-AACTTCTATTTTATTAAATGATAGAATATAAAAAAATGTGTACAAAAATATTCA
18523316 AAGTAAACTTCTATTTTATTAAATGATA
1 AAGTAAACTTCTATTTTATTAAATGATA
18523344 AAGGCTTAAA
Statistics
Matches: 129, Mismatches: 9, Indels: 13
0.85 0.06 0.09
Matches are distributed among these distances:
55 9 0.07
56 14 0.11
57 21 0.16
58 26 0.20
59 12 0.09
60 46 0.36
61 1 0.01
ACGTcount: A:0.48, C:0.07, G:0.09, T:0.35
Consensus pattern (59 bp):
AAGTAAACTTCTATTTTATTAAATGATAGAATATAAAAAAATGTGTACAAAAATATTCA
Found at i:18523364 original size:40 final size:40
Alignment explanation
Indices: 18523320--18523401 Score: 164
Period size: 40 Copynumber: 2.0 Consensus size: 40
18523310 AATTCAAAGT
18523320 AAACTTCTATTTTATTAAATGATAAAGGCTTAAACAACAA
1 AAACTTCTATTTTATTAAATGATAAAGGCTTAAACAACAA
18523360 AAACTTCTATTTTATTAAATGATAAAGGCTTAAACAACAA
1 AAACTTCTATTTTATTAAATGATAAAGGCTTAAACAACAA
18523400 AA
1 AA
18523402 TGGTACTTAA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 42 1.00
ACGTcount: A:0.49, C:0.12, G:0.07, T:0.32
Consensus pattern (40 bp):
AAACTTCTATTTTATTAAATGATAAAGGCTTAAACAACAA
Found at i:18525146 original size:21 final size:21
Alignment explanation
Indices: 18525122--18525175 Score: 63
Period size: 21 Copynumber: 2.6 Consensus size: 21
18525112 TGGGAAGGTC
*
18525122 CTACCTATACAAGTATGACTA
1 CTACCAATACAAGTATGACTA
* * * *
18525143 CTACCGATACAATTATTACTT
1 CTACCAATACAAGTATGACTA
18525164 CTACCAATACAA
1 CTACCAATACAA
18525176 CAAACTCCAG
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.39, C:0.26, G:0.06, T:0.30
Consensus pattern (21 bp):
CTACCAATACAAGTATGACTA
Found at i:18526078 original size:120 final size:120
Alignment explanation
Indices: 18525861--18526098 Score: 386
Period size: 120 Copynumber: 2.0 Consensus size: 120
18525851 TTCCACAAGC
* * *
18525861 TATAATCCATAATTTCATCCTCATGTCTAAATCAACTTTGTTACCAGTATACGATGCTGCTCACA
1 TATAATCCAAAATTTAATCCTCATGTCTAAATCAACTTTGTTACCAGTATACAATGCTGCTCACA
* *
18525926 CGAGCTATCGAGGACTCGCAACATATGTGGTACCTCAACCATCGATACGGTATGA
66 CGAGCTATCAAGGACTCGCAACATATGCGGTACCTCAACCATCGATACGGTATGA
* **
18525981 TATAATCCAAAATTTAATTCTCATGTCTGTATCAACTTTGTTACCAGTATACAATGCTGCTCACA
1 TATAATCCAAAATTTAATCCTCATGTCTAAATCAACTTTGTTACCAGTATACAATGCTGCTCACA
* *
18526046 CGAGCTGTCAAGGACTCGCAATATATGCGGTACCTCAACCATCGATACGGTAT
66 CGAGCTATCAAGGACTCGCAACATATGCGGTACCTCAACCATCGATACGGTAT
18526099 CTGTGCTTAT
Statistics
Matches: 108, Mismatches: 10, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
120 108 1.00
ACGTcount: A:0.30, C:0.24, G:0.16, T:0.30
Consensus pattern (120 bp):
TATAATCCAAAATTTAATCCTCATGTCTAAATCAACTTTGTTACCAGTATACAATGCTGCTCACA
CGAGCTATCAAGGACTCGCAACATATGCGGTACCTCAACCATCGATACGGTATGA
Found at i:18529055 original size:23 final size:25
Alignment explanation
Indices: 18529029--18529074 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
18529019 CCAATTAGGG
18529029 AATTAT-TGTTTAG-ATTTAATTCT
1 AATTATCTGTTTAGAATTTAATTCT
*
18529052 AATTATCTTTTTAGAATTTAATT
1 AATTATCTGTTTAGAATTTAATT
18529075 TGGATCCAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 6 0.30
25 8 0.40
ACGTcount: A:0.33, C:0.04, G:0.07, T:0.57
Consensus pattern (25 bp):
AATTATCTGTTTAGAATTTAATTCT
Found at i:18532981 original size:19 final size:18
Alignment explanation
Indices: 18532939--18532981 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 18
18532929 AACCCGAGTG
18532939 TTTTTATTTTTATTTATA
1 TTTTTATTTTTATTTATA
*
18532957 TATTTA-TTTTACTTTCATA
1 TTTTTATTTTTA-TTT-ATA
18532976 TTTTTA
1 TTTTTA
18532982 AAAAAATTGA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
17 5 0.24
18 8 0.38
19 8 0.38
ACGTcount: A:0.23, C:0.05, G:0.00, T:0.72
Consensus pattern (18 bp):
TTTTTATTTTTATTTATA
Found at i:18532996 original size:10 final size:10
Alignment explanation
Indices: 18532981--18533025 Score: 72
Period size: 10 Copynumber: 4.4 Consensus size: 10
18532971 TCATATTTTT
18532981 AAAAAAATTG
1 AAAAAAATTG
*
18532991 AAAAAAATTA
1 AAAAAAATTG
18533001 AAAAAAATTG
1 AAAAAAATTG
18533011 AAAAAAATTTG
1 AAAAAAA-TTG
18533022 AAAA
1 AAAA
18533026 GTGCAAAAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
10 25 0.78
11 7 0.22
ACGTcount: A:0.73, C:0.00, G:0.07, T:0.20
Consensus pattern (10 bp):
AAAAAAATTG
Found at i:18533076 original size:11 final size:11
Alignment explanation
Indices: 18533045--18533079 Score: 52
Period size: 11 Copynumber: 3.1 Consensus size: 11
18533035 AATTAGTATA
*
18533045 TTTATTTTCAT
1 TTTATTTTAAT
18533056 TTTATTTTTAAT
1 TTTA-TTTTAAT
18533068 TTTATTTTAAT
1 TTTATTTTAAT
18533079 T
1 T
18533080 ATGTAATATT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
11 12 0.55
12 10 0.45
ACGTcount: A:0.23, C:0.03, G:0.00, T:0.74
Consensus pattern (11 bp):
TTTATTTTAAT
Found at i:18534024 original size:21 final size:20
Alignment explanation
Indices: 18533987--18534035 Score: 62
Period size: 21 Copynumber: 2.4 Consensus size: 20
18533977 TTATTATTTA
**
18533987 AAAAAAAATCAAGAAAATCG
1 AAAAAAAATCAAGAAAAAAG
*
18534007 AAAAAAAATTAAGAAAAAAAG
1 AAAAAAAATCAAG-AAAAAAG
18534028 AAAAAAAA
1 AAAAAAAA
18534036 GACAAAAGTG
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
20 12 0.48
21 13 0.52
ACGTcount: A:0.80, C:0.04, G:0.08, T:0.08
Consensus pattern (20 bp):
AAAAAAAATCAAGAAAAAAG
Found at i:18535097 original size:23 final size:25
Alignment explanation
Indices: 18535071--18535116 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
18535061 CCAATTAGGG
18535071 AATTAT-TGTTTAG-ATTTAATTCT
1 AATTATCTGTTTAGAATTTAATTCT
*
18535094 AATTATCTTTTTAGAATTTAATT
1 AATTATCTGTTTAGAATTTAATT
18535117 TGGATCCAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 6 0.30
25 8 0.40
ACGTcount: A:0.33, C:0.04, G:0.07, T:0.57
Consensus pattern (25 bp):
AATTATCTGTTTAGAATTTAATTCT
Found at i:18538282 original size:28 final size:28
Alignment explanation
Indices: 18538250--18538544 Score: 122
Period size: 28 Copynumber: 11.1 Consensus size: 28
18538240 GTATATGTGC
*
18538250 ATAAGCTGGCGAGTGTAAACACATA-GAT
1 ATAAGCTGGCGAGCGTAAACACATATG-T
* * *
18538278 ATAAGTTGACGAGCGT-AA-AC--GTGT
1 ATAAGCTGGCGAGCGTAAACACATATGT
* *
18538302 ACAAGCTGGCGAGCGTAAACTCATATGT
1 ATAAGCTGGCGAGCGTAAACACATATGT
* * * *
18538330 ATAAGCCGGCGAGCATAAACGCAAATGT
1 ATAAGCTGGCGAGCGTAAACACATATGT
* *
18538358 ATAAGCTGACGAGCGT-AA-AC--GTGT
1 ATAAGCTGGCGAGCGTAAACACATATGT
** * * * *
18538382 GCAAGATGGTGAGTGTAGACACATATGT
1 ATAAGCTGGCGAGCGTAAACACATATGT
** * *
18538410 ATAAGCTAACGAGTGTAAACGCA-AGTGT
1 ATAAGCTGGCGAGCGTAAACACATA-TGT
* * * *
18538438 TTAAGCTGACAAGCGT-AA-AC--GTGT
1 ATAAGCTGGCGAGCGTAAACACATATGT
** * *
18538462 GCAAGCTGGCAAGCGTAAACGCATATGT
1 ATAAGCTGGCGAGCGTAAACACATATGT
* *
18538490 ATAAGATGACGAGCGT-AA-AC--ATGT
1 ATAAGCTGGCGAGCGTAAACACATATGT
** * *
18538514 GCAAGCTGGCGAGCGTAAACGCATATTT
1 ATAAGCTGGCGAGCGTAAACACATATGT
18538542 ATA
1 ATA
18538545 CATATTTACG
Statistics
Matches: 189, Mismatches: 60, Indels: 36
0.66 0.21 0.13
Matches are distributed among these distances:
24 59 0.31
25 8 0.04
26 10 0.05
27 9 0.05
28 103 0.54
ACGTcount: A:0.35, C:0.17, G:0.27, T:0.21
Consensus pattern (28 bp):
ATAAGCTGGCGAGCGTAAACACATATGT
Found at i:18538343 original size:52 final size:52
Alignment explanation
Indices: 18538252--18538544 Score: 202
Period size: 52 Copynumber: 5.6 Consensus size: 52
18538242 ATATGTGCAT
* * *
18538252 AAGCTGGCGAGTGTAAACACATA-GATATAAGTTGACGAGCGTAAACGTGTAC
1 AAGCTGGCGAGCGTAAACGCATATG-TATAAGATGACGAGCGTAAACGTGTAC
* ** * * *
18538304 AAGCTGGCGAGCGTAAACTCATATGTATAAGCCGGCGAGCATAAACGCAAATGTAT
1 AAGCTGGCGAGCGTAAACGCATATGTATAAGATGACGAGCGTAAACG----TGTAC
* ** ** * * *
18538360 AAGCTGACGAGCGTAAACG----TGTGCAAGATGGTGAGTGTAGACACATATGTAT
1 AAGCTGGCGAGCGTAAACGCATATGTATAAGATGACGAGCGTA-A-AC--GTGTAC
** * * * * *
18538412 AAGCTAACGAGTGTAAACGCA-AGTGTTTAAGCTGACAAGCGTAAACGTGTGC
1 AAGCTGGCGAGCGTAAACGCATA-TGTATAAGATGACGAGCGTAAACGTGTAC
* * *
18538464 AAGCTGGCAAGCGTAAACGCATATGTATAAGATGACGAGCGTAAACATGTGC
1 AAGCTGGCGAGCGTAAACGCATATGTATAAGATGACGAGCGTAAACGTGTAC
*
18538516 AAGCTGGCGAGCGTAAACGCATATTTATA
1 AAGCTGGCGAGCGTAAACGCATATGTATA
18538545 CATATTTACG
Statistics
Matches: 188, Mismatches: 39, Indels: 28
0.74 0.15 0.11
Matches are distributed among these distances:
52 146 0.78
53 3 0.02
54 4 0.02
55 1 0.01
56 34 0.18
ACGTcount: A:0.35, C:0.17, G:0.27, T:0.21
Consensus pattern (52 bp):
AAGCTGGCGAGCGTAAACGCATATGTATAAGATGACGAGCGTAAACGTGTAC
Found at i:18538502 original size:80 final size:80
Alignment explanation
Indices: 18538250--18538509 Score: 306
Period size: 80 Copynumber: 3.2 Consensus size: 80
18538240 GTATATGTGC
* * * * * *
18538250 ATAAGCTGGCGAGTGTAAACACATA-GATATAAGTTGACGAGCGTAAACGTGTACAAGCTGGCGA
1 ATAAGCTGACGAGCGTAAACGCAAATG-TATAAGCTGACGAGCGTAAACGTGTGCAAGCTGGCGA
*
18538314 GCGTAAACTCATATGT
65 GCGTAAACACATATGT
* * * * *
18538330 ATAAGCCGGCGAGCATAAACGCAAATGTATAAGCTGACGAGCGTAAACGTGTGCAAGATGGTGAG
1 ATAAGCTGACGAGCGTAAACGCAAATGTATAAGCTGACGAGCGTAAACGTGTGCAAGCTGGCGAG
* *
18538395 TGTAGACACATATGT
66 CGTAAACACATATGT
* * * * * *
18538410 ATAAGCTAACGAGTGTAAACGCAAGTGTTTAAGCTGACAAGCGTAAACGTGTGCAAGCTGGCAAG
1 ATAAGCTGACGAGCGTAAACGCAAATGTATAAGCTGACGAGCGTAAACGTGTGCAAGCTGGCGAG
*
18538475 CGTAAACGCATATGT
66 CGTAAACACATATGT
*
18538490 ATAAGATGACGAGCGTAAAC
1 ATAAGCTGACGAGCGTAAAC
18538510 ATGTGCAAGC
Statistics
Matches: 150, Mismatches: 29, Indels: 2
0.83 0.16 0.01
Matches are distributed among these distances:
80 149 0.99
81 1 0.01
ACGTcount: A:0.36, C:0.17, G:0.27, T:0.21
Consensus pattern (80 bp):
ATAAGCTGACGAGCGTAAACGCAAATGTATAAGCTGACGAGCGTAAACGTGTGCAAGCTGGCGAG
CGTAAACACATATGT
Found at i:18545918 original size:59 final size:59
Alignment explanation
Indices: 18545785--18546246 Score: 556
Period size: 59 Copynumber: 7.8 Consensus size: 59
18545775 TTGTTTAAGC
* * *
18545785 AAATAATAAAATATAAAAATAATGTGTACAAAAAAAATTC-AAAGTAAACTTCTCTTTTATT
1 AAATGATACAATATAAAAATAATGTGTAC-AAAAAAATTCAAAAG--AACTTCTATTTTATT
* * * * * *
18545846 TAATGAGAGAATATAAAAATAATGTGTACAAAAATATTCAAAAGAGCTTTTATTTTATT
1 AAATGATACAATATAAAAATAATGTGTACAAAAAAATTCAAAAGAACTTCTATTTTATT
*
18545905 AAATGATACAATATAAAAATAATATGTAC-AAAAAATTC-AAAGCAAACTTCTATTTTATT
1 AAATGATACAATATAAAAATAATGTGTACAAAAAAATTCAAAAG--AACTTCTATTTTATT
* * * * * * *
18545964 AAATGATAGAATATAAAAATAATCTGTACAAAAATATTCAATAGAATTTTTATTTTGTT
1 AAATGATACAATATAAAAATAATGTGTACAAAAAAATTCAAAAGAACTTCTATTTTATT
* *
18546023 AAATGATACAATATAAAAATAATGTGGACAAAAAAATTC-AAAGTAAACTTCTATTTTGTT
1 AAATGATACAATATAAAAATAATGTGTACAAAAAAATTCAAAAG--AACTTCTATTTTATT
* * * * **
18546083 AAATGATAGAATATAAAAATAATGCGTACAAAAATATTTAAAAGATTTTCTATTTTATT
1 AAATGATACAATATAAAAATAATGTGTACAAAAAAATTCAAAAGAACTTCTATTTTATT
* * * *
18546142 TAATGATACAATATAAAAATGATGTGTACAAGAACATTCAAAAGAACTTCTA-TTTATT
1 AAATGATACAATATAAAAATAATGTGTACAAAAAAATTCAAAAGAACTTCTATTTTATT
*
18546200 AAATGATATAATATAAAAATAATGTGTACAAAAAAATTCAAAAGAAC
1 AAATGATACAATATAAAAATAATGTGTACAAAAAAATTCAAAAGAAC
18546247 ATCAATGCAT
Statistics
Matches: 342, Mismatches: 51, Indels: 19
0.83 0.12 0.05
Matches are distributed among these distances:
57 4 0.01
58 59 0.17
59 179 0.52
60 64 0.19
61 36 0.11
ACGTcount: A:0.51, C:0.07, G:0.08, T:0.33
Consensus pattern (59 bp):
AAATGATACAATATAAAAATAATGTGTACAAAAAAATTCAAAAGAACTTCTATTTTATT
Found at i:18546115 original size:119 final size:119
Alignment explanation
Indices: 18545785--18546245 Score: 646
Period size: 118 Copynumber: 3.9 Consensus size: 119
18545775 TTGTTTAAGC
* * * *
18545785 AAATAATAAAATATAAAAATAATGTGTACAAAAAAAATTCAAAGTAAACTTCTCTTTTATTTAAT
1 AAATGATACAATATAAAAATAATGTGTAC-AAAAAAATTCAAAGTAAACTTCTATTTTATTAAAT
* * **
18545850 GAGAGAATATAAAAATAATGTGTACAAAAATATTCAAAAGAGCTTTTATTTTATT
65 GATAGAATATAAAAATAATGCGTACAAAAATATTCAAAAGAATTTTTATTTTATT
* *
18545905 AAATGATACAATATAAAAATAATATGTAC-AAAAAATTCAAAGCAAACTTCTATTTTATTAAATG
1 AAATGATACAATATAAAAATAATGTGTACAAAAAAATTCAAAGTAAACTTCTATTTTATTAAATG
* *
18545969 ATAGAATATAAAAATAAT-CTGTACAAAAATATTCAATAGAATTTTTATTTTGTT
66 ATAGAATATAAAAATAATGC-GTACAAAAATATTCAAAAGAATTTTTATTTTATT
* *
18546023 AAATGATACAATATAAAAATAATGTGGACAAAAAAATTCAAAGTAAACTTCTATTTTGTTAAATG
1 AAATGATACAATATAAAAATAATGTGTACAAAAAAATTCAAAGTAAACTTCTATTTTATTAAATG
*
18546088 ATAGAATATAAAAATAATGCGTACAAAAATATTTAAAAG-ATTTTCTATTTTATT
66 ATAGAATATAAAAATAATGCGTACAAAAATATTCAAAAGAATTTT-TATTTTATT
* * * *
18546142 TAATGATACAATATAAAAATGATGTGTACAAGAACATTCAAA--AGAACTTCTA-TTTATTAAAT
1 AAATGATACAATATAAAAATAATGTGTACAAAAAAATTCAAAGTA-AACTTCTATTTTATTAAAT
* * *
18546204 GATATAATATAAAAATAATGTGTACAAAAAAATTCAAAAGAA
65 GATAGAATATAAAAATAATGCGTACAAAAATATTCAAAAGAA
18546246 CATCAATGCA
Statistics
Matches: 306, Mismatches: 29, Indels: 14
0.88 0.08 0.04
Matches are distributed among these distances:
117 46 0.15
118 120 0.39
119 113 0.37
120 27 0.09
ACGTcount: A:0.51, C:0.07, G:0.08, T:0.33
Consensus pattern (119 bp):
AAATGATACAATATAAAAATAATGTGTACAAAAAAATTCAAAGTAAACTTCTATTTTATTAAATG
ATAGAATATAAAAATAATGCGTACAAAAATATTCAAAAGAATTTTTATTTTATT
Found at i:18547271 original size:7 final size:7
Alignment explanation
Indices: 18547259--18547283 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
18547249 TTATATACAT
18547259 AATATTA
1 AATATTA
18547266 AATATTA
1 AATATTA
18547273 AATATTA
1 AATATTA
18547280 AATA
1 AATA
18547284 CAAAATCGAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (7 bp):
AATATTA
Found at i:18549027 original size:26 final size:26
Alignment explanation
Indices: 18548951--18549036 Score: 82
Period size: 26 Copynumber: 3.2 Consensus size: 26
18548941 AATTTATAAA
* *
18548951 AAAAATAGAGAAAAATATTAAAAATTGTA
1 AAAAATA-A-AAAAATA-TAAAAATTATG
* * *
18548980 AAAAATAATAAATTATATAAATTATG
1 AAAAATAAAAAAATATAAAAATTATG
* *
18549006 AAAAATAAAAAAATGTAAAAATAATG
1 AAAAATAAAAAAATATAAAAATTATG
18549032 AAAAA
1 AAAAA
18549037 AATGTTTAAA
Statistics
Matches: 47, Mismatches: 10, Indels: 3
0.78 0.17 0.05
Matches are distributed among these distances:
26 34 0.72
27 5 0.11
28 1 0.02
29 7 0.15
ACGTcount: A:0.69, C:0.00, G:0.07, T:0.24
Consensus pattern (26 bp):
AAAAATAAAAAAATATAAAAATTATG
Found at i:18549432 original size:19 final size:18
Alignment explanation
Indices: 18549391--18549425 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
18549381 AAAAAGTTGT
18549391 TTTTATATTTTTCTTATA
1 TTTTATATTTTTCTTATA
*
18549409 TTTTA-ATTTTTTTTATA
1 TTTTATATTTTTCTTATA
18549426 ACTTTTATGC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.23, C:0.03, G:0.00, T:0.74
Consensus pattern (18 bp):
TTTTATATTTTTCTTATA
Found at i:18549464 original size:19 final size:20
Alignment explanation
Indices: 18549442--18549487 Score: 62
Period size: 19 Copynumber: 2.4 Consensus size: 20
18549432 ATGCTTCTTA
18549442 TAATATTT-T-ATAAATTTAT
1 TAATATTTCTAATAAATTT-T
18549461 TAATATTTCTAATAAATTTT
1 TAATATTTCTAATAAATTTT
18549481 T-ATATTT
1 TAATATTT
18549488 AAAAAAAATA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
19 14 0.56
20 3 0.12
21 8 0.32
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (20 bp):
TAATATTTCTAATAAATTTT
Found at i:18549578 original size:19 final size:20
Alignment explanation
Indices: 18549551--18549595 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
18549541 TAATATATAT
*
18549551 ATTTTTTAA-TATATTTAAA
1 ATTTATTAATTATATTTAAA
*
18549570 ATTTATTAATTATTTTTAAA
1 ATTTATTAATTATATTTAAA
18549590 ATTTAT
1 ATTTAT
18549596 ATATTTTTCA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 8 0.35
20 15 0.65
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (20 bp):
ATTTATTAATTATATTTAAA
Found at i:18549598 original size:35 final size:35
Alignment explanation
Indices: 18549559--18549636 Score: 86
Period size: 35 Copynumber: 2.2 Consensus size: 35
18549549 ATATTTTTTA
*
18549559 ATATATTTAAAATTTATTAATTATTTTTA-AAATTT
1 ATATATTTAAAATTTA-TAATGATTTTTATAAATTT
*** *
18549594 ATATATTTTTCATTTATAATGATTTTTATAATTTT
1 ATATATTTAAAATTTATAATGATTTTTATAAATTT
*
18549629 CTATATTT
1 ATATATTT
18549637 TTATAATTTT
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
34 11 0.31
35 25 0.69
ACGTcount: A:0.36, C:0.03, G:0.01, T:0.60
Consensus pattern (35 bp):
ATATATTTAAAATTTATAATGATTTTTATAAATTT
Found at i:18549627 original size:34 final size:36
Alignment explanation
Indices: 18549570--18549638 Score: 97
Period size: 35 Copynumber: 2.0 Consensus size: 36
18549560 TATATTTAAA
*
18549570 ATTTATTAATTATTTTTAAAA-TTTATATATTTTTC
1 ATTTATTAATGATTTTTAAAATTTTATATATTTTTC
* *
18549605 ATTTA-TAATGATTTTTATAATTTTCTATATTTTT
1 ATTTATTAATGATTTTTAAAATTTTATATATTTTT
18549639 ATAATTTTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
34 13 0.43
35 17 0.57
ACGTcount: A:0.32, C:0.03, G:0.01, T:0.64
Consensus pattern (36 bp):
ATTTATTAATGATTTTTAAAATTTTATATATTTTTC
Found at i:18549641 original size:8 final size:9
Alignment explanation
Indices: 18549615--18549674 Score: 54
Period size: 9 Copynumber: 6.7 Consensus size: 9
18549605 ATTTATAATG
18549615 ATTTTTATA
1 ATTTTTATA
18549624 ATTTTCTAT-
1 ATTTT-TATA
18549633 ATTTTTATA
1 ATTTTTATA
*
18549642 ATTTTT-TGC
1 ATTTTTAT-A
*
18549651 ACTTTTAT-
1 ATTTTTATA
18549659 ATTTTTATA
1 ATTTTTATA
18549668 ATATTTT
1 AT-TTTT
18549675 TTATGATATT
Statistics
Matches: 42, Mismatches: 3, Indels: 11
0.75 0.05 0.20
Matches are distributed among these distances:
8 11 0.26
9 23 0.55
10 8 0.19
ACGTcount: A:0.27, C:0.05, G:0.02, T:0.67
Consensus pattern (9 bp):
ATTTTTATA
Found at i:18549648 original size:28 final size:29
Alignment explanation
Indices: 18549616--18549714 Score: 87
Period size: 30 Copynumber: 3.4 Consensus size: 29
18549606 TTTATAATGA
18549616 TTTTTATAATTTTCTATATTTTTAT-AAT
1 TTTTTATAATTTTCTATATTTTTATAAAT
** *
18549644 TTTTT-GCACTTT-TATATTTTTATAATAT
1 TTTTTATAATTTTCTATATTTTTATAA-AT
* * * * *
18549672 TTTTTATGATATTCTATAGTTTCTATGATT
1 TTTTTATAATTTTCTATA-TTTTTATAAAT
18549702 TTTTTATAATTTT
1 TTTTTATAATTTT
18549715 TAATGGCTTT
Statistics
Matches: 54, Mismatches: 12, Indels: 8
0.73 0.16 0.11
Matches are distributed among these distances:
26 11 0.20
27 5 0.09
28 12 0.22
29 3 0.06
30 16 0.30
31 7 0.13
ACGTcount: A:0.25, C:0.05, G:0.04, T:0.66
Consensus pattern (29 bp):
TTTTTATAATTTTCTATATTTTTATAAAT
Found at i:18560771 original size:17 final size:17
Alignment explanation
Indices: 18560751--18560787 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
18560741 ACGCCAAAAG
18560751 AAAGAATCAA-AGAAGAC
1 AAAGAATCAAGA-AAGAC
18560768 AAAGAATCAAGAAAGAC
1 AAAGAATCAAGAAAGAC
18560785 AAA
1 AAA
18560788 AGCCACAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 18 0.95
18 1 0.05
ACGTcount: A:0.68, C:0.11, G:0.16, T:0.05
Consensus pattern (17 bp):
AAAGAATCAAGAAAGAC
Found at i:18561649 original size:26 final size:26
Alignment explanation
Indices: 18561592--18561660 Score: 77
Period size: 26 Copynumber: 2.6 Consensus size: 26
18561582 TTTCACATAA
* *
18561592 ATAAATAATTCAAAAATTAAAATAAT
1 ATAAAAAATTCAAAAATTAAAAAAAT
18561618 ATTAAAAAATTC-AAAATTAAAAAAAT
1 A-TAAAAAATTCAAAAATTAAAAAAAT
* *
18561644 CATAAAAATTTAAAAAA
1 -ATAAAAAATTCAAAAA
18561661 ACAAACATGA
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
26 22 0.61
27 14 0.39
ACGTcount: A:0.68, C:0.04, G:0.00, T:0.28
Consensus pattern (26 bp):
ATAAAAAATTCAAAAATTAAAAAAAT
Found at i:18566724 original size:24 final size:24
Alignment explanation
Indices: 18566692--18566762 Score: 79
Period size: 24 Copynumber: 3.0 Consensus size: 24
18566682 ACTCAATCAT
* * * *
18566692 GTTTCTGCTTGTCAGCTAATGTAC
1 GTTTATGCTCGTCAGCCAATATAC
*
18566716 GTTTATGCTCGTCAGCCACTATAC
1 GTTTATGCTCGTCAGCCAATATAC
* *
18566740 GTTTATGCTCGCCAGCCACTATA
1 GTTTATGCTCGTCAGCCAATATA
18566763 AGAAACACTT
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 41 1.00
ACGTcount: A:0.20, C:0.27, G:0.18, T:0.35
Consensus pattern (24 bp):
GTTTATGCTCGTCAGCCAATATAC
Found at i:18570649 original size:36 final size:37
Alignment explanation
Indices: 18570608--18570723 Score: 96
Period size: 36 Copynumber: 3.1 Consensus size: 37
18570598 ACAAAATCAT
* *
18570608 AAAAATATAAAA-TATCAAAAATTT-ATATAAACTTAC
1 AAAAATAAAAAATTAT-AAAAATTTCATAAAAACTTAC
* *
18570644 AAAAATAAAAAATTATAAGAATTTCATAAAAACTTAT
1 AAAAATAAAAAATTATAAAAATTTCATAAAAACTTAC
* * * *
18570681 AAATATTGTAAAAACTTATAAAAAATT-ATAAAAA-TTAT
1 AAA-A--ATAAAAAATTATAAAAATTTCATAAAAACTTAC
18570719 AAAAA
1 AAAAA
18570724 AATTATAATA
Statistics
Matches: 66, Mismatches: 9, Indels: 11
0.77 0.10 0.13
Matches are distributed among these distances:
36 18 0.27
37 17 0.26
38 8 0.12
39 7 0.11
40 16 0.24
ACGTcount: A:0.63, C:0.05, G:0.02, T:0.30
Consensus pattern (37 bp):
AAAAATAAAAAATTATAAAAATTTCATAAAAACTTAC
Found at i:18570703 original size:9 final size:9
Alignment explanation
Indices: 18570600--18570754 Score: 95
Period size: 10 Copynumber: 16.4 Consensus size: 9
18570590 AAAAAATCAC
*
18570600 AAAATCATA
1 AAAATTATA
18570609 AAAA-TAT-
1 AAAATTATA
18570616 AAAA-TATCA
1 AAAATTAT-A
18570625 AAAATTTATA
1 AAAA-TTATA
* *
18570635 TAAACTTACA
1 -AAAATTATA
18570645 AAAA-TA-A
1 AAAATTATA
18570652 AAAATTATA
1 AAAATTATA
*
18570661 AGAATTTCATA
1 A-AAATT-ATA
18570672 AAAACTTATA
1 AAAA-TTATA
* *
18570682 AATATTGTA
1 AAAATTATA
18570691 AAAACTTATAA
1 AAAA-TTAT-A
18570702 AAAATTATA
1 AAAATTATA
18570711 AAAATTATAAA
1 AAAATTAT--A
18570722 AAAATTATA
1 AAAATTATA
* *
18570731 ATAAGTTCTA
1 A-AAATTATA
18570741 ATAAATTATA
1 A-AAATTATA
18570751 AAAA
1 AAAA
18570755 ACTATAATTT
Statistics
Matches: 117, Mismatches: 14, Indels: 30
0.73 0.09 0.19
Matches are distributed among these distances:
7 12 0.10
8 6 0.05
9 34 0.29
10 39 0.33
11 26 0.22
ACGTcount: A:0.62, C:0.05, G:0.02, T:0.31
Consensus pattern (9 bp):
AAAATTATA
Found at i:18570725 original size:50 final size:50
Alignment explanation
Indices: 18570648--18570761 Score: 128
Period size: 50 Copynumber: 2.3 Consensus size: 50
18570638 ACTTACAAAA
* * *
18570648 ATAAAAAATTATAAGAATTTCATAAAAACTTATAA-ATA-TTGTAA-AAACTT
1 ATAAAAAATTATAAAAATTTCA-AAAAAATTATAATA-AGTTCTAATAAA-TT
18570698 ATAAAAAATTATAAAAATTAT-AAAAAAATTATAATAAGTTCTAATAAATT
1 ATAAAAAATTATAAAAATT-TCAAAAAAATTATAATAAGTTCTAATAAATT
*
18570748 ATAAAAAACTATAA
1 ATAAAAAATTATAA
18570762 TTTTTAATAA
Statistics
Matches: 56, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
49 12 0.21
50 40 0.71
51 4 0.07
ACGTcount: A:0.61, C:0.04, G:0.03, T:0.32
Consensus pattern (50 bp):
ATAAAAAATTATAAAAATTTCAAAAAAATTATAATAAGTTCTAATAAATT
Found at i:18570760 original size:10 final size:10
Alignment explanation
Indices: 18570648--18570761 Score: 97
Period size: 10 Copynumber: 11.4 Consensus size: 10
18570638 ACTTACAAAA
18570648 ATAAAAAATT
1 ATAAAAAATT
* *
18570658 ATAAGAATTT
1 ATAAAAAATT
*
18570668 CATAAAAACTT
1 -ATAAAAAATT
*
18570679 AT-AAATATT
1 ATAAAAAATT
* *
18570688 GTAAAAACTT
1 ATAAAAAATT
18570698 ATAAAAAATT
1 ATAAAAAATT
18570708 AT-AAAAATT
1 ATAAAAAATT
18570717 ATAAAAAAATT
1 AT-AAAAAATT
* *
18570728 ATAATAAGTT
1 ATAAAAAATT
* *
18570738 CTAATAAATT
1 ATAAAAAATT
*
18570748 ATAAAAAACT
1 ATAAAAAATT
18570758 ATAA
1 ATAA
18570762 TTTTTAATAA
Statistics
Matches: 82, Mismatches: 18, Indels: 8
0.76 0.17 0.07
Matches are distributed among these distances:
9 15 0.18
10 50 0.61
11 17 0.21
ACGTcount: A:0.61, C:0.04, G:0.03, T:0.32
Consensus pattern (10 bp):
ATAAAAAATT
Found at i:18571570 original size:46 final size:45
Alignment explanation
Indices: 18571518--18571659 Score: 149
Period size: 46 Copynumber: 3.2 Consensus size: 45
18571508 TATTAGAATT
18571518 TTTTATTATTTATAAGTTTTTATAGTATTTAAATATTTTAAATATG
1 TTTTATTATTTATAAGTTTTTATA-TATTTAAATATTTTAAATATG
*
18571564 TTTTATTAATTTTATAAATTTTTATA-ATTT--ATA----AGAAT-T-
1 TTTTATT-A-TTTATAAGTTTTTATATATTTAAATATTTTA-AATATG
*
18571603 TTTTATCATTTATAAGTTTTTATAATATTTAAATATTTTAAATATG
1 TTTTATTATTTATAAGTTTTTAT-ATATTTAAATATTTTAAATATG
*
18571649 CTTTATTATTT
1 TTTTATTATTT
18571660 TTATAAATTT
Statistics
Matches: 78, Mismatches: 5, Indels: 26
0.72 0.05 0.24
Matches are distributed among these distances:
37 14 0.18
38 2 0.03
39 10 0.13
40 2 0.03
41 6 0.08
44 6 0.08
45 2 0.03
46 20 0.26
47 1 0.01
48 15 0.19
ACGTcount: A:0.35, C:0.01, G:0.04, T:0.59
Consensus pattern (45 bp):
TTTTATTATTTATAAGTTTTTATATATTTAAATATTTTAAATATG
Found at i:18571578 original size:48 final size:46
Alignment explanation
Indices: 18571518--18571680 Score: 143
Period size: 48 Copynumber: 3.7 Consensus size: 46
18571508 TATTAGAATT
*
18571518 TTTTATT-ATTTATAAGTTTTTATAGTATTTAAATATTTTAAATATG
1 TTTTATTAATTTATAAATTTTTATA-TATTTAAATATTTTAAATATG
18571564 TTTTATTAATTTTATAAATTTTTATA-ATTT--ATA----AGAAT-T-
1 TTTTATTAA-TTTATAAATTTTTATATATTTAAATATTTTA-AATATG
* *
18571603 TTTTA-TCATTTATAAGTTTTTATAATATTTAAATATTTTAAATATG
1 TTTTATTAATTTATAAATTTTTAT-ATATTTAAATATTTTAAATATG
* *
18571649 CTTTATTATTTTTATAAATTTTT-TATAATTTA
1 TTTTATTA-ATTTATAAATTTTTATAT-ATTTA
18571681 TTAGAATTTT
Statistics
Matches: 94, Mismatches: 7, Indels: 31
0.71 0.05 0.23
Matches are distributed among these distances:
37 14 0.15
38 3 0.03
39 9 0.10
40 2 0.02
41 6 0.06
44 6 0.06
45 2 0.02
46 17 0.18
47 8 0.09
48 27 0.29
ACGTcount: A:0.36, C:0.01, G:0.04, T:0.60
Consensus pattern (46 bp):
TTTTATTAATTTATAAATTTTTATATATTTAAATATTTTAAATATG
Found at i:18571602 original size:85 final size:86
Alignment explanation
Indices: 18571506--18571712 Score: 330
Period size: 85 Copynumber: 2.4 Consensus size: 86
18571496 ATAACATTAT
* *
18571506 TTTATTAGAATTTTTTATTATTTATAAGTTTTTATAGTATTTAAATATTTTAAATATGTTTTATT
1 TTTATTAGAATTTTTTATTATTTATAAGTTTTTATAATATTTAAATATTTTAAATATGCTTTATT
18571571 AATTTTATAAA-TTTTTATAA
66 AATTTTATAAATTTTTTATAA
* *
18571591 TTTATAAGAATTTTTTATCATTTATAAGTTTTTATAATATTTAAATATTTTAAATATGCTTTATT
1 TTTATTAGAATTTTTTATTATTTATAAGTTTTTATAATATTTAAATATTTTAAATATGCTTTATT
*
18571656 ATTTTTATAAATTTTTTATAA
66 AATTTTATAAATTTTTTATAA
18571677 TTTATTAGAATTTTTTAATT-TTTATATA-TTTTTATA
1 TTTATTAGAATTTTTT-ATTATTTATA-AGTTTTTATA
18571713 TTTTTATGAG
Statistics
Matches: 112, Mismatches: 7, Indels: 5
0.90 0.06 0.04
Matches are distributed among these distances:
85 71 0.63
86 38 0.34
87 3 0.03
ACGTcount: A:0.35, C:0.01, G:0.04, T:0.60
Consensus pattern (86 bp):
TTTATTAGAATTTTTTATTATTTATAAGTTTTTATAATATTTAAATATTTTAAATATGCTTTATT
AATTTTATAAATTTTTTATAA
Found at i:18571632 original size:19 final size:18
Alignment explanation
Indices: 18571517--18571633 Score: 67
Period size: 17 Copynumber: 6.8 Consensus size: 18
18571507 TTATTAGAAT
18571517 TTTTTAT-TATTTATAAG
1 TTTTTATATATTTATAAG
18571534 TTTTTATAGTATTTA-AA-
1 TTTTTATA-TATTTATAAG
* *
18571551 TATTTTAAATATGT-T---
1 T-TTTTATATATTTATAAG
* *
18571566 TTATTA-AT-TTTATAAA
1 TTTTTATATATTTATAAG
18571582 TTTTTATA-ATTTATAAG
1 TTTTTATATATTTATAAG
18571599 AATTTTT-TATCATTTATAAG
1 --TTTTTATAT-ATTTATAAG
18571619 TTTTTATAATATTTA
1 TTTTTAT-ATATTTA
18571634 AATATTTTAA
Statistics
Matches: 78, Mismatches: 6, Indels: 30
0.68 0.05 0.26
Matches are distributed among these distances:
12 2 0.03
13 3 0.04
14 4 0.05
15 1 0.01
16 5 0.06
17 20 0.26
18 15 0.19
19 17 0.22
20 11 0.14
ACGTcount: A:0.35, C:0.01, G:0.04, T:0.60
Consensus pattern (18 bp):
TTTTTATATATTTATAAG
Found at i:18571641 original size:37 final size:39
Alignment explanation
Indices: 18571535--18571641 Score: 109
Period size: 37 Copynumber: 2.8 Consensus size: 39
18571525 ATTTATAAGT
* *
18571535 TTTTAT-AGTATTTA-AATATTTTAAATATGTTTTATTAA
1 TTTTATAAGTTTTTATAATA-TTTAAATATTTTTTATTAA
* *
18571573 TTTTATAAATTTTTATAAT-TTATAAGA-ATTTTTTA-TCA
1 TTTTATAAGTTTTTATAATATT-TAA-ATATTTTTTATTAA
18571611 -TTTATAAGTTTTTATAATATTTAAATATTTT
1 TTTTATAAGTTTTTATAATATTTAAATATTTT
18571642 AAATATGCTT
Statistics
Matches: 58, Mismatches: 5, Indels: 13
0.76 0.07 0.17
Matches are distributed among these distances:
36 1 0.02
37 25 0.43
38 12 0.21
39 16 0.28
40 4 0.07
ACGTcount: A:0.36, C:0.01, G:0.04, T:0.59
Consensus pattern (39 bp):
TTTTATAAGTTTTTATAATATTTAAATATTTTTTATTAA
Found at i:18571698 original size:8 final size:9
Alignment explanation
Indices: 18571514--18571719 Score: 99
Period size: 9 Copynumber: 22.0 Consensus size: 9
18571504 ATTTTATTAG
18571514 AATTTTT-T
1 AATTTTTAT
18571522 -ATTATTTAT
1 AATT-TTTAT
18571531 AAGTTTTTAT
1 AA-TTTTTAT
* *
18571541 AGTATTTA-
1 AATTTTTAT
*
18571549 AATATTTTAA
1 AAT-TTTTAT
18571559 ATATGTTTTATT
1 A-AT-TTTTA-T
18571571 AA-TTTTAT
1 AATTTTTAT
18571579 AAATTTTTAT
1 -AATTTTTAT
* *
18571589 AATTTATAAG
1 AATTT-TTAT
18571599 AATTTTT-T
1 AATTTTTAT
*
18571607 -ATCATTTAT
1 AAT-TTTTAT
18571616 AAGTTTTTAT
1 AA-TTTTTAT
*
18571626 AATATTTA-
1 AATTTTTAT
18571634 AATATTTTA-
1 AAT-TTTTAT
18571643 AATATGCTTTAT
1 AAT-T--TTTAT
*
18571655 TATTTTTAT
1 AATTTTTAT
18571664 AAATTTTTTAT
1 -AA-TTTTTAT
*
18571675 AATTTATTAG
1 AATTT-TTAT
18571685 AATTTTT-T
1 AATTTTTAT
18571693 AATTTTTAT
1 AATTTTTAT
18571702 ATATTTTTAT
1 A-ATTTTTAT
18571712 -ATTTTTAT
1 AATTTTTAT
18571720 GAGAAAATAT
Statistics
Matches: 156, Mismatches: 18, Indels: 48
0.70 0.08 0.22
Matches are distributed among these distances:
7 5 0.03
8 27 0.17
9 50 0.32
10 48 0.31
11 23 0.15
12 3 0.02
ACGTcount: A:0.34, C:0.01, G:0.03, T:0.61
Consensus pattern (9 bp):
AATTTTTAT
Found at i:18571713 original size:10 final size:10
Alignment explanation
Indices: 18571553--18571717 Score: 63
Period size: 10 Copynumber: 17.3 Consensus size: 10
18571543 TATTTAAATA
*
18571553 TTTTAAATAT
1 TTTTATATAT
*
18571563 GTTTTAT-TAA
1 -TTTTATATAT
*
18571573 TTTTATAAAT
1 TTTTATATAT
18571583 TTTTATA-AT
1 TTTTATATAT
* *
18571592 TTATA-AGAAT
1 TTTTATA-TAT
18571602 TTTT-TATCA-
1 TTTTATAT-AT
18571611 -TTTATA-AGT
1 TTTTATATA-T
18571620 TTTTATA-AT
1 TTTTATATAT
* *
18571629 ATTTAAATA-
1 TTTTATATAT
*
18571638 TTTTAAATAT
1 TTTTATATAT
*
18571648 GCTTTAT-TAT
1 -TTTTATATAT
*
18571658 TTTTATAAAT
1 TTTTATATAT
18571668 TTTT-TATAAT
1 TTTTATAT-AT
*
18571678 TTATTAGA-AT
1 TT-TTATATAT
18571688 TTTT-TA-AT
1 TTTTATATAT
18571696 TTTTATATAT
1 TTTTATATAT
18571706 TTTTATAT-T
1 TTTTATATAT
18571715 TTT
1 TTT
18571718 ATGAGAAAAT
Statistics
Matches: 119, Mismatches: 17, Indels: 38
0.68 0.10 0.22
Matches are distributed among these distances:
7 1 0.01
8 11 0.09
9 43 0.36
10 52 0.44
11 11 0.09
12 1 0.01
ACGTcount: A:0.34, C:0.01, G:0.03, T:0.62
Consensus pattern (10 bp):
TTTTATATAT
Found at i:18573891 original size:235 final size:235
Alignment explanation
Indices: 18573480--18573950 Score: 924
Period size: 235 Copynumber: 2.0 Consensus size: 235
18573470 TGATGTGGGC
18573480 TACGGCTATAGGGTTGTTGTTTCAGTTGTTGGCTGCAAGGCTTGGTGTGGCAACAGGGAAACACT
1 TACGGCTATAGGGTTGTTGTTTCAGTTGTTGGCTGCAAGGCTTGGTGTGGCAACAGGGAAACACT
18573545 TGGTTGAGCTTTGTAGCGAAGAGTACCCGACTAGGGCTAGGATGGTTTTGTAGGTGATGGCAAAG
66 TGGTTGAGCTTTGTAGCGAAGAGTACCCGACTAGGGCTAGGATGGTTTTGTAGGTGATGGCAAAG
18573610 CTGGCTTTGATTGGAGCTGATATACAGGAAGTTAGGGGTGTTCATAATTGGGTACCCGCGATTTC
131 CTGGCTTTGATTGGAGCTGATATACAGGAAGTTAGGGGTGTTCATAATTGGGTACCCGCGATTTC
18573675 AGGTATTAAAAATGTCGGTCTGTGACCCAACCCTTGAATA
196 AGGTATTAAAAATGTCGGTCTGTGACCCAACCCTTGAATA
* *
18573715 TACGGCTATAGGGTTGTTGTTTTAGTTGTTGGCTGCAAGGTTTGGTGTGGCAACAGGGAAACACT
1 TACGGCTATAGGGTTGTTGTTTCAGTTGTTGGCTGCAAGGCTTGGTGTGGCAACAGGGAAACACT
18573780 TGGTTGAGCTTTGTAGCGAAGAGTACCCGACTAGGGCTAGGATGGTTTTGTAGGTGATGGCAAAG
66 TGGTTGAGCTTTGTAGCGAAGAGTACCCGACTAGGGCTAGGATGGTTTTGTAGGTGATGGCAAAG
18573845 CTGGCTTTGATTGGAGCTGATATACAGGAAGTTAGGGGTGTTCATAATTGGGTACCCGCGATTTC
131 CTGGCTTTGATTGGAGCTGATATACAGGAAGTTAGGGGTGTTCATAATTGGGTACCCGCGATTTC
18573910 AGGTATTAAAAATGTCGGTCTGTGACCCAACCCTTGAATA
196 AGGTATTAAAAATGTCGGTCTGTGACCCAACCCTTGAATA
18573950 T
1 T
18573951 CGGGTACCTA
Statistics
Matches: 234, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
235 234 1.00
ACGTcount: A:0.23, C:0.15, G:0.31, T:0.30
Consensus pattern (235 bp):
TACGGCTATAGGGTTGTTGTTTCAGTTGTTGGCTGCAAGGCTTGGTGTGGCAACAGGGAAACACT
TGGTTGAGCTTTGTAGCGAAGAGTACCCGACTAGGGCTAGGATGGTTTTGTAGGTGATGGCAAAG
CTGGCTTTGATTGGAGCTGATATACAGGAAGTTAGGGGTGTTCATAATTGGGTACCCGCGATTTC
AGGTATTAAAAATGTCGGTCTGTGACCCAACCCTTGAATA
Found at i:18574135 original size:21 final size:21
Alignment explanation
Indices: 18574107--18574157 Score: 75
Period size: 21 Copynumber: 2.4 Consensus size: 21
18574097 ATAATAGCAT
18574107 AATCCAAATATAAAGTTTAAA
1 AATCCAAATATAAAGTTTAAA
* * *
18574128 AATTCAAACATAAAGTTTATA
1 AATCCAAATATAAAGTTTAAA
18574149 AATCCAAAT
1 AATCCAAAT
18574158 TACATAATAC
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.55, C:0.12, G:0.04, T:0.29
Consensus pattern (21 bp):
AATCCAAATATAAAGTTTAAA
Found at i:18575705 original size:25 final size:24
Alignment explanation
Indices: 18575664--18575711 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 24
18575654 TTGTAAATCA
*
18575664 GAAAAATATCTCTAGAGATTTTTT
1 GAAAAATATCTCTAGAGAATTTTT
18575688 GAAATAATATCT-TCAGAGAATTTT
1 GAAA-AATATCTCT-AGAGAATTTT
18575712 CTCTCTGCAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 5 0.24
25 16 0.76
ACGTcount: A:0.40, C:0.08, G:0.12, T:0.40
Consensus pattern (24 bp):
GAAAAATATCTCTAGAGAATTTTT
Found at i:18581272 original size:21 final size:21
Alignment explanation
Indices: 18581248--18581322 Score: 66
Period size: 21 Copynumber: 3.6 Consensus size: 21
18581238 CAATGCAGAT
18581248 TTCTACCAATACAAGTGATAG
1 TTCTACCAATACAAGTGATAG
*
18581269 TTCTA-CAGATACAAGTG-TCAC
1 TTCTACCA-ATACAAGTGAT-AG
* * *
18581290 TTCTACCGACACAAGTCAT-G
1 TTCTACCAATACAAGTGATAG
18581310 CTTCTACCAATAC
1 -TTCTACCAATAC
18581323 TAAAAACTCT
Statistics
Matches: 42, Mismatches: 7, Indels: 10
0.71 0.12 0.17
Matches are distributed among these distances:
20 3 0.07
21 37 0.88
22 2 0.05
ACGTcount: A:0.33, C:0.27, G:0.12, T:0.28
Consensus pattern (21 bp):
TTCTACCAATACAAGTGATAG
Found at i:18589004 original size:30 final size:29
Alignment explanation
Indices: 18588942--18589036 Score: 110
Period size: 27 Copynumber: 3.4 Consensus size: 29
18588932 ACCCGAGATA
18588942 TTTTTCAGAAC-CAATC--GTCAAAATTAT
1 TTTTTCAGAACTC-ATCTTGTCAAAATTAT
18588969 TTTTTCAGAACTCATCTTGTCAAAATTAGT
1 TTTTTCAGAACTCATCTTGTCAAAATTA-T
* *
18588999 TTTTTCAGAACTAATATTGTC-AAATTA-
1 TTTTTCAGAACTCATCTTGTCAAAATTAT
*
18589026 TTGTTCAGAAC
1 TTTTTCAGAAC
18589037 CCTTGAACCC
Statistics
Matches: 61, Mismatches: 3, Indels: 8
0.85 0.04 0.11
Matches are distributed among these distances:
27 24 0.39
28 1 0.02
29 16 0.26
30 20 0.33
ACGTcount: A:0.34, C:0.16, G:0.09, T:0.41
Consensus pattern (29 bp):
TTTTTCAGAACTCATCTTGTCAAAATTAT
Found at i:18589144 original size:23 final size:22
Alignment explanation
Indices: 18589118--18589194 Score: 70
Period size: 23 Copynumber: 3.5 Consensus size: 22
18589108 TCTTAAAACT
*
18589118 TTAAAACCCTAATTAATAAACAC
1 TTAAAA-CATAATTAATAAACAC
*
18589141 TTAAAA-AT--TAAATAAAACAC
1 TTAAAACATAATTAAT-AAACAC
*
18589161 TAAAAATCATAATTAATAAACAC
1 TTAAAA-CATAATTAATAAACAC
*
18589184 TTAAAATATAA
1 TTAAAACATAA
18589195 ATAAAACCTT
Statistics
Matches: 43, Mismatches: 6, Indels: 11
0.72 0.10 0.18
Matches are distributed among these distances:
19 4 0.09
20 11 0.26
21 1 0.02
22 6 0.14
23 17 0.40
24 4 0.09
ACGTcount: A:0.60, C:0.13, G:0.00, T:0.27
Consensus pattern (22 bp):
TTAAAACATAATTAATAAACAC
Found at i:18589151 original size:18 final size:19
Alignment explanation
Indices: 18589135--18589201 Score: 62
Period size: 23 Copynumber: 3.2 Consensus size: 19
18589125 CCTAATTAAT
18589135 AAACACTTAAAAATTAAATA
1 AAACAC-TAAAAATTAAATA
*
18589155 AAACACTAAAAATCATAATTAA
1 AAACACTAAAAAT--TAAAT-A
*
18589177 TAAACACTTAAAATATAAATA
1 -AAACACTAAAAAT-TAAATA
18589198 AAAC
1 AAAC
18589202 CTTAATTTAA
Statistics
Matches: 40, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
19 7 0.17
20 10 0.25
21 5 0.12
22 6 0.15
23 12 0.30
ACGTcount: A:0.64, C:0.12, G:0.00, T:0.24
Consensus pattern (19 bp):
AAACACTAAAAATTAAATA
Done.