Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D01
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: 64473564
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1880000 characters in sequence are not A, C, G, or T
File 196 of 213
Found at i:58842799 original size:15 final size:15
Alignment explanation
Indices: 58842779--58842812 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
58842769 TATTTATTCT
58842779 TAAACCTCAAAACCC
1 TAAACCTCAAAACCC
* *
58842794 TAAACCTTAAAACTC
1 TAAACCTCAAAACCC
58842809 TAAA
1 TAAA
58842813 TCATAAACCA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.50, C:0.29, G:0.00, T:0.21
Consensus pattern (15 bp):
TAAACCTCAAAACCC
Found at i:58842803 original size:22 final size:22
Alignment explanation
Indices: 58842777--58842827 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
58842767 CCTATTTATT
*
58842777 CTTAAACCTCAAAACCCTAAAC
1 CTTAAACCTCAAAACCATAAAC
* * *
58842799 CTTAAAACTCTAAATCATAAAC
1 CTTAAACCTCAAAACCATAAAC
*
58842821 CATAAAC
1 CTTAAAC
58842828 TATTAACCCT
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.49, C:0.29, G:0.00, T:0.22
Consensus pattern (22 bp):
CTTAAACCTCAAAACCATAAAC
Found at i:58844864 original size:74 final size:71
Alignment explanation
Indices: 58844740--58844881 Score: 176
Period size: 74 Copynumber: 2.0 Consensus size: 71
58844730 ACTTTTGCTA
* * * *
58844740 AAGCGCCGCAAAAAACTAAGCACAACGACGCCGTTTTCTAAGCTTCCGGGGGGGTTTATCGGCGT
1 AAGCGCCGCAAAAAACTAAACACAACGACACCGTTTTCTAAGCTTCC--GGGGGTTTAGCGGCAT
58844805 TTTTATGG
64 TTTTATGG
* * ** *
58844813 AAGCGCCGCAAAAAAATTAAACCCAACGACACCGTTTTCTTTGCTTTCGGGGGTTTAGCGGCATT
1 AAGCGCCGC-AAAAAACTAAACACAACGACACCGTTTTCTAAGCTTCCGGGGGTTTAGCGGCATT
58844878 TTTA
65 TTTA
58844882 GTAAAGCGTC
Statistics
Matches: 59, Mismatches: 9, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
72 19 0.32
73 9 0.15
74 31 0.53
ACGTcount: A:0.26, C:0.23, G:0.24, T:0.27
Consensus pattern (71 bp):
AAGCGCCGCAAAAAACTAAACACAACGACACCGTTTTCTAAGCTTCCGGGGGTTTAGCGGCATTT
TTATGG
Found at i:58844940 original size:112 final size:113
Alignment explanation
Indices: 58844805--58845009 Score: 349
Period size: 113 Copynumber: 1.8 Consensus size: 113
58844795 TTATCGGCGT
* * *
58844805 TTTTATGGAAGCGCCGC-AAAAAAATTAAACCCAACGACACCGTTTTCTTTGCTTTCGGGGGTTT
1 TTTTATGAAAGCGCCGCAAAAAAAATTAAACCCAACGACACCGTTTTCTTAGCTTTCAGGGGTTT
* *
58844869 AGCGGCATTTTTAGTAAAGCGTCGCTAATGCTGGGTTTTTAGCGGCTC
66 AGCGGCATTTTTAATAAAGCGCCGCTAATGCTGGGTTTTTAGCGGCTC
58844917 TTTTATGAAAGCGCCGCAAAAAAAATTAAACCCAACGACACCGTTTTCTTAGCTTTCAGGGGTTT
1 TTTTATGAAAGCGCCGCAAAAAAAATTAAACCCAACGACACCGTTTTCTTAGCTTTCAGGGGTTT
*
58844982 AGCGGCGTTTTTAATAAAGCGCCGCTAA
66 AGCGGCATTTTTAATAAAGCGCCGCTAA
58845010 CGCTCAGGGA
Statistics
Matches: 86, Mismatches: 6, Indels: 1
0.92 0.06 0.01
Matches are distributed among these distances:
112 16 0.19
113 70 0.81
ACGTcount: A:0.27, C:0.21, G:0.22, T:0.30
Consensus pattern (113 bp):
TTTTATGAAAGCGCCGCAAAAAAAATTAAACCCAACGACACCGTTTTCTTAGCTTTCAGGGGTTT
AGCGGCATTTTTAATAAAGCGCCGCTAATGCTGGGTTTTTAGCGGCTC
Found at i:58845249 original size:21 final size:21
Alignment explanation
Indices: 58845225--58845269 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
58845215 TTAAGGTTCA
* *
58845225 AGGTTTTATGGTTTAAGGGTT
1 AGGTGTTATGATTTAAGGGTT
*
58845246 AGGTGTTATGATTTAGGGGTT
1 AGGTGTTATGATTTAAGGGTT
58845267 AGG
1 AGG
58845270 AGGATTTAGG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.20, C:0.00, G:0.38, T:0.42
Consensus pattern (21 bp):
AGGTGTTATGATTTAAGGGTT
Found at i:58845375 original size:14 final size:14
Alignment explanation
Indices: 58845329--58845375 Score: 58
Period size: 14 Copynumber: 3.4 Consensus size: 14
58845319 TGGTTTTACA
*
58845329 GTTTAGGGTTTAAG
1 GTTTATGGTTTAAG
* *
58845343 GGTTATGCTTTAAG
1 GTTTATGGTTTAAG
58845357 GTTTATGGTTTAAG
1 GTTTATGGTTTAAG
*
58845371 ATTTA
1 GTTTA
58845376 AGAATTACAA
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
14 27 1.00
ACGTcount: A:0.23, C:0.02, G:0.28, T:0.47
Consensus pattern (14 bp):
GTTTATGGTTTAAG
Found at i:58848630 original size:52 final size:52
Alignment explanation
Indices: 58848558--58848762 Score: 177
Period size: 52 Copynumber: 4.1 Consensus size: 52
58848548 GTATATAACT
*
58848558 TAATACATAATAACACAATACATAA-TTGGTATATAAGCTTGCATAACTTACA
1 TAATACATAATAACACAATACATAACTT-ATATATAAGCTTGCATAACTTACA
* *
58848610 TAATACATAATAACATAATACATAACTTATATATAAGCTTGTATAACTTACA
1 TAATACATAATAACACAATACATAACTTATATATAAGCTTGCATAACTTACA
* * * *
58848662 TAATA-ACT--T----C----CGTAACTGATATATAATCTGAT-AAT-ACATTACA
1 TAATACA-TAATAACACAATACATAACTTATATATAAGCT--TGCATAAC-TTACA
* *
58848705 TAATACATAATAACATAATACATAACTTATATTATAATCTTGCATAACTTACA
1 TAATACATAATAACACAATACATAACTTATA-TATAAGCTTGCATAACTTACA
58848758 TAATA
1 TAATA
58848763 ACTTACATAT
Statistics
Matches: 122, Mismatches: 12, Indels: 37
0.71 0.07 0.22
Matches are distributed among these distances:
42 18 0.15
43 13 0.11
44 2 0.02
45 1 0.01
50 1 0.01
51 1 0.01
52 53 0.43
53 23 0.19
54 10 0.08
ACGTcount: A:0.46, C:0.15, G:0.05, T:0.34
Consensus pattern (52 bp):
TAATACATAATAACACAATACATAACTTATATATAAGCTTGCATAACTTACA
Found at i:58848707 original size:12 final size:14
Alignment explanation
Indices: 58848692--58848728 Score: 51
Period size: 15 Copynumber: 2.7 Consensus size: 14
58848682 ATATAATCTG
58848692 ATAATACAT-T-AC
1 ATAATACATATAAC
58848704 ATAATACATAATAAC
1 ATAATACAT-ATAAC
58848719 ATAATACATA
1 ATAATACATA
58848729 ACTTATATTA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
12 9 0.41
14 2 0.09
15 11 0.50
ACGTcount: A:0.57, C:0.14, G:0.00, T:0.30
Consensus pattern (14 bp):
ATAATACATATAAC
Found at i:58848722 original size:8 final size:7
Alignment explanation
Indices: 58848692--58848729 Score: 53
Period size: 7 Copynumber: 5.6 Consensus size: 7
58848682 ATATAATCTG
58848692 ATAATAC
1 ATAATAC
58848699 AT--TAC
1 ATAATAC
58848704 ATAATAC
1 ATAATAC
58848711 ATAATAAC
1 ATAAT-AC
58848719 ATAATAC
1 ATAATAC
58848726 ATAA
1 ATAA
58848730 CTTATATTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
5 5 0.18
7 16 0.57
8 7 0.25
ACGTcount: A:0.58, C:0.13, G:0.00, T:0.29
Consensus pattern (7 bp):
ATAATAC
Found at i:58848763 original size:22 final size:21
Alignment explanation
Indices: 58848692--58848771 Score: 67
Period size: 22 Copynumber: 3.7 Consensus size: 21
58848682 ATATAATCTG
58848692 ATAAT-ACATTACATAA--TAC
1 ATAATAAC-TTACATAACTTAC
*
58848711 ATAATAACATAATACATAACTTAT
1 ATAATAAC-T--TACATAACTTAC
* *
58848735 ATTATAATCTTGCATAACTTAC
1 ATAATAA-CTTACATAACTTAC
58848757 ATAATAACTTACATA
1 ATAATAACTTACATA
58848772 TATTCATTTA
Statistics
Matches: 49, Mismatches: 6, Indels: 10
0.75 0.09 0.15
Matches are distributed among these distances:
19 5 0.10
20 4 0.08
21 7 0.14
22 23 0.47
24 9 0.18
25 1 0.02
ACGTcount: A:0.49, C:0.15, G:0.01, T:0.35
Consensus pattern (21 bp):
ATAATAACTTACATAACTTAC
Found at i:58851677 original size:21 final size:21
Alignment explanation
Indices: 58851653--58851721 Score: 111
Period size: 21 Copynumber: 3.3 Consensus size: 21
58851643 TAACAACTTA
58851653 AAGCAGAGGCAGCAACGAGAG
1 AAGCAGAGGCAGCAACGAGAG
* *
58851674 AAGCAGAGGCCGCAGCGAGAG
1 AAGCAGAGGCAGCAACGAGAG
*
58851695 AAGCAGAGGCTGCAACGAGAG
1 AAGCAGAGGCAGCAACGAGAG
58851716 AAGCAG
1 AAGCAG
58851722 CGATAGAAGC
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 44 1.00
ACGTcount: A:0.39, C:0.20, G:0.39, T:0.01
Consensus pattern (21 bp):
AAGCAGAGGCAGCAACGAGAG
Found at i:58851965 original size:19 final size:20
Alignment explanation
Indices: 58851927--58851965 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
58851917 GTAAAGAAAA
* *
58851927 ATATGAATTCAATTTTATTT
1 ATATCAATTCAATATTATTT
58851947 ATATCAATT-AATATTATTT
1 ATATCAATTCAATATTATTT
58851966 TAGTTATTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.38, C:0.05, G:0.03, T:0.54
Consensus pattern (20 bp):
ATATCAATTCAATATTATTT
Found at i:58852231 original size:42 final size:42
Alignment explanation
Indices: 58852163--58852359 Score: 136
Period size: 42 Copynumber: 4.6 Consensus size: 42
58852153 TGCGTTGCTA
*
58852163 AAAGAATACTACTTTTAGCGGCGTTTTTAAAC-AAGCGCCGCT
1 AAAGAACA-TACTTTTAGCGGCGTTTTTAAACTAAGCGCCGCT
* ***
58852205 ATAGAACAGTACTTTTAGCGGCGTTTTTGTCCTAAGCGCCGCT
1 AAAGAACA-TACTTTTAGCGGCGTTTTTAAACTAAGCGCCGCT
* * * *
58852248 AAAGAACATGCTCTTTAGTGGCGTTTATT--TCTTAGCGCCGCT
1 AAAGAACATACT-TTTAGCGGCGTTT-TTAAACTAAGCGCCGCT
** * ** *
58852290 AAAGAACATGGTCTTTAGTGGCGTTTATT--TTTTAGCGCCGCT
1 AAAGAACATACT-TTTAGCGGCGTTT-TTAAACTAAGCGCCGCT
*
58852332 AAAGAACATGA-TCTTTAGTGGCGTTTTT
1 AAAGAACAT-ACT-TTTAGCGGCGTTTTT
58852360 TCCTGTAAGC
Statistics
Matches: 137, Mismatches: 14, Indels: 9
0.86 0.09 0.06
Matches are distributed among these distances:
41 2 0.01
42 104 0.76
43 29 0.21
44 2 0.01
ACGTcount: A:0.24, C:0.19, G:0.22, T:0.35
Consensus pattern (42 bp):
AAAGAACATACTTTTAGCGGCGTTTTTAAACTAAGCGCCGCT
Found at i:58854677 original size:43 final size:43
Alignment explanation
Indices: 58854598--58854688 Score: 110
Period size: 43 Copynumber: 2.1 Consensus size: 43
58854588 TTGCTAACTG
* * * ** *
58854598 CTAAAGAACATGACCTTTAGCGGCGTTATTGGGAAAAGCGCCA
1 CTAAAGAAAATGACATTTAGCAGCGTTATTAAGAAAAGCACCA
* *
58854641 CTAAAGAAAATGACATTTAGCAGCGTTTTTAAGAAAAGCACCG
1 CTAAAGAAAATGACATTTAGCAGCGTTATTAAGAAAAGCACCA
58854684 CTAAA
1 CTAAA
58854689 AGTCATGTTC
Statistics
Matches: 40, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
43 40 1.00
ACGTcount: A:0.38, C:0.19, G:0.21, T:0.22
Consensus pattern (43 bp):
CTAAAGAAAATGACATTTAGCAGCGTTATTAAGAAAAGCACCA
Found at i:58854703 original size:43 final size:41
Alignment explanation
Indices: 58854656--58854755 Score: 110
Period size: 42 Copynumber: 2.3 Consensus size: 41
58854646 GAAAATGACA
*
58854656 TTTAGCAGCGTTTTTAAGAAAAGCACCGCTAAAAGTCATGTTC
1 TTTAGC-GCGTTTGTAAGAAAAGCACCG-TAAAAGTCATGTTC
* ** * *
58854699 TTTAGCGTTGTTTGTGGGAAAAGCATCGTAAAGGTCATGTTC
1 TTTAGCG-CGTTTGTAAGAAAAGCACCGTAAAAGTCATGTTC
58854741 TTTAGCGGCGTTTGT
1 TTTAGC-GCGTTTGT
58854756 GGGGAAAGTG
Statistics
Matches: 48, Mismatches: 7, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
42 26 0.54
43 22 0.46
ACGTcount: A:0.25, C:0.15, G:0.25, T:0.35
Consensus pattern (41 bp):
TTTAGCGCGTTTGTAAGAAAAGCACCGTAAAAGTCATGTTC
Found at i:58854761 original size:43 final size:42
Alignment explanation
Indices: 58854673--58854914 Score: 206
Period size: 43 Copynumber: 5.7 Consensus size: 42
58854663 GCGTTTTTAA
* **
58854673 GAAAAGCACCGCTAAAAGTCATGTTCTTTAGCGTTGTTTGTGG
1 GAAAAGCA-CGCTAAAGGTCATGTTCTTTAGCGGCGTTTGTGG
58854716 GAAAAGCATCG-TAAAGGTCATGTTCTTTAGCGGCGTTTGTGG
1 GAAAAGCA-CGCTAAAGGTCATGTTCTTTAGCGGCGTTTGTGG
* ** *
58854758 GGAAAGTGCTGCTAAAGGTCATG----TTAGTGGCGTTTGTGG
1 GAAAAGCAC-GCTAAAGGTCATGTTCTTTAGCGGCGTTTGTGG
* * * * *
58854797 GAAAAGTGACGTTAAAGGTCATGTTCTATAACGGCATTTGTGG
1 GAAAAG-CACGCTAAAGGTCATGTTCTTTAGCGGCGTTTGTGG
** * * *
58854840 GGTAAGCGCCACTGAAGGTCATGTTCTTTAGCGGCGTTTGTGG
1 GAAAAGC-ACGCTAAAGGTCATGTTCTTTAGCGGCGTTTGTGG
* * * *
58854883 GAAAAGCGCCGCTATATGTCATGTTCTATAGC
1 GAAAAGC-ACGCTAAAGGTCATGTTCTTTAGC
58854915 AGTGTTTTTC
Statistics
Matches: 158, Mismatches: 33, Indels: 16
0.76 0.16 0.08
Matches are distributed among these distances:
39 32 0.20
40 1 0.01
41 1 0.01
42 34 0.22
43 90 0.57
ACGTcount: A:0.24, C:0.15, G:0.30, T:0.31
Consensus pattern (42 bp):
GAAAAGCACGCTAAAGGTCATGTTCTTTAGCGGCGTTTGTGG
Found at i:58854803 original size:39 final size:39
Alignment explanation
Indices: 58854708--58854821 Score: 117
Period size: 39 Copynumber: 2.8 Consensus size: 39
58854698 CTTTAGCGTT
*
58854708 GTTTGTGGGAAAAG-CATCG-TAAAGGTCATGTTCTTTAGCGGC
1 GTTTGTGGGAAAAGTGA-CGCTAAAGGTCATG----TTAGCGGC
* *
58854750 GTTTGTGGGGAAAGTG-CTGCTAAAGGTCATGTTAGTGGC
1 GTTTGTGGGAAAAGTGAC-GCTAAAGGTCATGTTAGCGGC
*
58854789 GTTTGTGGGAAAAGTGACGTTAAAGGTCATGTT
1 GTTTGTGGGAAAAGTGACGCTAAAGGTCATGTT
58854822 CTATAACGGC
Statistics
Matches: 63, Mismatches: 5, Indels: 11
0.80 0.06 0.14
Matches are distributed among these distances:
39 36 0.57
40 1 0.02
41 1 0.02
42 14 0.22
43 11 0.17
ACGTcount: A:0.24, C:0.11, G:0.34, T:0.32
Consensus pattern (39 bp):
GTTTGTGGGAAAAGTGACGCTAAAGGTCATGTTAGCGGC
Found at i:58854837 original size:82 final size:81
Alignment explanation
Indices: 58854699--58854912 Score: 214
Period size: 82 Copynumber: 2.6 Consensus size: 81
58854689 AGTCATGTTC
** * * * *
58854699 TTTAGCGTTGTTTGTGGGAAAAGCATCGTAAAGGTCATGTTCTTTAGCGGCGTTTGTGGGGAAAG
1 TTTAGCGGCGTTTGTGGGAAAAGGA-CGTAAAGGTCATGTTCTATAACGGCATTTGTGGGGAAAG
* **
58854764 TGCTGCTAAAGGTCATG
65 CGCCACTAAAGGTCATG
* *
58854781 -TTAGTGGCGTTTGTGGGAAAAGTGACGTTAAAGGTCATGTTCTATAACGGCATTTGTGGGGTAA
1 TTTAGCGGCGTTTGTGGGAAAAG-GACG-TAAAGGTCATGTTCTATAACGGCATTTGTGGGGAAA
*
58854845 GCGCCACTGAAGGTCATG
64 GCGCCACTAAAGGTCATG
* * *
58854863 TTCTTTAGCGGCGTTTGTGGGAAAAGCGCCGCTATATGTCATGTTCTATA
1 ---TTTAGCGGCGTTTGTGGGAAAAG-GACG-TAAAGGTCATGTTCTATA
58854913 GCAGTGTTTT
Statistics
Matches: 108, Mismatches: 18, Indels: 8
0.81 0.13 0.06
Matches are distributed among these distances:
81 21 0.19
82 47 0.44
86 40 0.37
ACGTcount: A:0.22, C:0.14, G:0.31, T:0.32
Consensus pattern (81 bp):
TTTAGCGGCGTTTGTGGGAAAAGGACGTAAAGGTCATGTTCTATAACGGCATTTGTGGGGAAAGC
GCCACTAAAGGTCATG
Found at i:58854989 original size:30 final size:30
Alignment explanation
Indices: 58854955--58855013 Score: 118
Period size: 30 Copynumber: 2.0 Consensus size: 30
58854945 TAGCGGTGTT
58854955 GTCTATAGCAGCGTTTTTTGCGGCGCTTAC
1 GTCTATAGCAGCGTTTTTTGCGGCGCTTAC
58854985 GTCTATAGCAGCGTTTTTTGCGGCGCTTA
1 GTCTATAGCAGCGTTTTTTGCGGCGCTTA
58855014 TCAAATCGCC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.14, C:0.22, G:0.27, T:0.37
Consensus pattern (30 bp):
GTCTATAGCAGCGTTTTTTGCGGCGCTTAC
Found at i:58855819 original size:13 final size:13
Alignment explanation
Indices: 58855798--58855830 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
58855788 ATTACACGTA
58855798 CACTTTTAC-TTT
1 CACTTTTACATTT
58855810 CACATTTTACATTT
1 CAC-TTTTACATTT
58855824 CACTTTT
1 CACTTTT
58855831 GTAGTCCTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
12 3 0.16
13 10 0.53
14 6 0.32
ACGTcount: A:0.21, C:0.24, G:0.00, T:0.55
Consensus pattern (13 bp):
CACTTTTACATTT
Found at i:58859390 original size:18 final size:19
Alignment explanation
Indices: 58859356--58859391 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
58859346 AGTAGGGTTG
58859356 TATTTAAATTATATTTTTT
1 TATTTAAATTATATTTTTT
58859375 TATTTAAATT-TATTTTT
1 TATTTAAATTATATTTTT
58859392 AATCAAAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (19 bp):
TATTTAAATTATATTTTTT
Found at i:58859701 original size:28 final size:25
Alignment explanation
Indices: 58859657--58859708 Score: 59
Period size: 27 Copynumber: 2.0 Consensus size: 25
58859647 AAATATATTC
* *
58859657 TTTTTTTTTATTCTTTCATCTTCTTTA
1 TTTTTTTTCATTATTTC-TC-TCTTTA
58859684 TTTTTTTTACATTATTTCTCTCTTT
1 TTTTTTTT-CATTATTTCTCTCTTT
58859709 GTTTCATTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
26 5 0.23
27 10 0.45
28 7 0.32
ACGTcount: A:0.12, C:0.15, G:0.00, T:0.73
Consensus pattern (25 bp):
TTTTTTTTCATTATTTCTCTCTTTA
Found at i:58866430 original size:3 final size:3
Alignment explanation
Indices: 58866422--58866466 Score: 56
Period size: 3 Copynumber: 15.0 Consensus size: 3
58866412 TAATATTTTC
* *
58866422 ATT ATT ATT ATT GTT ATT ATT ATT ATT ATT ACTC A-T ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A-TT ATT ATT ATT ATT
58866467 GATACTATTA
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
2 1 0.03
3 33 0.92
4 2 0.06
ACGTcount: A:0.31, C:0.04, G:0.02, T:0.62
Consensus pattern (3 bp):
ATT
Found at i:58866440 original size:15 final size:15
Alignment explanation
Indices: 58866422--58866477 Score: 58
Period size: 15 Copynumber: 3.5 Consensus size: 15
58866412 TAATATTTTC
58866422 ATTATTATTATTGTT
1 ATTATTATTATTGTT
*
58866437 ATTATTATTATTATT
1 ATTATTATTATTGTT
*
58866452 ACTCATATTATTATTGAT
1 A-T--TATTATTATTGTT
*
58866470 ACTATTAT
1 ATTATTAT
58866478 ATTTAGTTAT
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
15 21 0.62
16 1 0.03
18 12 0.35
ACGTcount: A:0.32, C:0.05, G:0.04, T:0.59
Consensus pattern (15 bp):
ATTATTATTATTGTT
Found at i:58868990 original size:16 final size:17
Alignment explanation
Indices: 58868965--58869013 Score: 55
Period size: 16 Copynumber: 2.8 Consensus size: 17
58868955 CCCCTTTAAG
*
58868965 TTTTTCAAATTT-TTTC
1 TTTTTAAAATTTATTTC
58868981 TTTTTAAAATTTGATTTC
1 TTTTTAAAATTT-ATTTC
*
58868999 TTTTATAGAATTTAT
1 TTTT-TAAAATTTAT
58869014 AATTTGTATG
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
16 11 0.39
18 10 0.36
19 7 0.25
ACGTcount: A:0.27, C:0.06, G:0.04, T:0.63
Consensus pattern (17 bp):
TTTTTAAAATTTATTTC
Found at i:58878651 original size:30 final size:31
Alignment explanation
Indices: 58878596--58878654 Score: 102
Period size: 31 Copynumber: 1.9 Consensus size: 31
58878586 CAACGCAGTA
*
58878596 ACTTAAATGAAAACTTTCGAATAATTCAATG
1 ACTTAAATGAAAACTTTCAAATAATTCAATG
58878627 ACTTAAATGAAAACTTT-AAATAATTCAA
1 ACTTAAATGAAAACTTTCAAATAATTCAA
58878655 CGACCATTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
30 10 0.37
31 17 0.63
ACGTcount: A:0.49, C:0.12, G:0.07, T:0.32
Consensus pattern (31 bp):
ACTTAAATGAAAACTTTCAAATAATTCAATG
Found at i:58883169 original size:90 final size:87
Alignment explanation
Indices: 58883029--58883220 Score: 242
Period size: 90 Copynumber: 2.2 Consensus size: 87
58883019 TAATAATAAT
* * * **
58883029 AATTAAGTCCCTCCTTTTTTTTTGCACTTAGTTGAGCACTTAAACTTTCAAAATGCATCAAAAAA
1 AATTAAGCCCCTGCTTTTTTTTTGCACTCAACTGAGCACTTAAACTTTCAAAATGCAT-AAAAAA
*
58883094 GGTACTCAAACTTCTTCAAAAAAAGC
65 -G-ACTCAAAATTCTTC-AAAAAAGC
* * * *
58883120 AATTAAGGCCCTGCTTTTTTTTT-CACTCAACTGGGTACTTGAACTTTCAAAATGCATAAAAAAG
1 AATTAAGCCCCTGCTTTTTTTTTGCACTCAACTGAGCACTTAAACTTTCAAAATGCATAAAAAAG
*
58883184 ACTCAAAATTTTTCAAAAAAGC
66 ACTCAAAATTCTTCAAAAAAGC
58883206 AATTAAGCCCCTGCT
1 AATTAAGCCCCTGCT
58883221 CTTATTAAAA
Statistics
Matches: 90, Mismatches: 11, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
86 22 0.24
87 12 0.13
88 1 0.01
89 6 0.07
90 28 0.31
91 21 0.23
ACGTcount: A:0.36, C:0.21, G:0.11, T:0.32
Consensus pattern (87 bp):
AATTAAGCCCCTGCTTTTTTTTTGCACTCAACTGAGCACTTAAACTTTCAAAATGCATAAAAAAG
ACTCAAAATTCTTCAAAAAAGC
Found at i:58883273 original size:18 final size:19
Alignment explanation
Indices: 58883246--58883298 Score: 65
Period size: 19 Copynumber: 2.8 Consensus size: 19
58883236 AAAAATTATA
58883246 AATAATAAATAATAAATTTT
1 AATAA-AAATAATAAATTTT
*
58883266 AA-AAAAATTATTAAATTTT
1 AATAAAAA-TAATAAATTTT
58883285 AATAAAAAT-ATAAA
1 AATAAAAATAATAAA
58883299 AAATTTAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
18 7 0.24
19 15 0.52
20 7 0.24
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (19 bp):
AATAAAAATAATAAATTTT
Found at i:58883289 original size:32 final size:30
Alignment explanation
Indices: 58883226--58883309 Score: 84
Period size: 32 Copynumber: 2.8 Consensus size: 30
58883216 CTGCTCTTAT
58883226 TAAAAA-TTAAAAAAATTATAAATAATAAA
1 TAAAAATTTAAAAAAATTATAAATAATAAA
* *
58883255 TAATAAATTTTAAAAAAATTATTAAAT-TTTAA
1 TAA-AAA-TTTAAAAAAATTA-TAAATAATAAA
* *
58883287 TAAAAATATAAAAAATTTA-AAAT
1 TAAAAATTTAAAAAAATTATAAAT
58883310 TTATTAAAAA
Statistics
Matches: 47, Mismatches: 4, Indels: 9
0.78 0.07 0.15
Matches are distributed among these distances:
28 4 0.09
29 3 0.06
30 14 0.30
31 3 0.06
32 18 0.38
33 5 0.11
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (30 bp):
TAAAAATTTAAAAAAATTATAAATAATAAA
Found at i:58883307 original size:27 final size:29
Alignment explanation
Indices: 58883267--58883320 Score: 76
Period size: 27 Copynumber: 1.9 Consensus size: 29
58883257 ATAAATTTTA
*
58883267 AAAAAATTATTAAATTTTAATAAAAATAT
1 AAAAAATTATTAAAATTTAATAAAAATAT
*
58883296 AAAAAA-T-TTAAAATTTATTAAAAAT
1 AAAAAATTATTAAAATTTAATAAAAAT
58883321 TGGAATTTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 16 0.70
28 1 0.04
29 6 0.26
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (29 bp):
AAAAAATTATTAAAATTTAATAAAAATAT
Found at i:58883481 original size:10 final size:10
Alignment explanation
Indices: 58883463--58883504 Score: 50
Period size: 10 Copynumber: 4.2 Consensus size: 10
58883453 GAAAAATGAT
*
58883463 AAATAAATAA
1 AAATTAATAA
58883473 AAATTAATAA
1 AAATTAATAA
*
58883483 AAATTATAGAA
1 AAATTA-ATAA
58883494 AAATT-ATAA
1 AAATTAATAA
58883503 AA
1 AA
58883505 TACTTCTTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
9 5 0.18
10 15 0.54
11 8 0.29
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.26
Consensus pattern (10 bp):
AAATTAATAA
Found at i:58883552 original size:20 final size:20
Alignment explanation
Indices: 58883527--58883583 Score: 55
Period size: 20 Copynumber: 2.9 Consensus size: 20
58883517 TACGATAATT
58883527 TTTATAATTTTTTTACGAAA
1 TTTATAATTTTTTTACGAAA
* **
58883547 TTTAT-ATTTCTTTAC-ATT
1 TTTATAATTTTTTTACGAAA
*
58883565 TTGTATAATTTTCTTACGA
1 TT-TATAATTTTTTTACGA
58883584 CTTTATCAAA
Statistics
Matches: 29, Mismatches: 5, Indels: 5
0.74 0.13 0.13
Matches are distributed among these distances:
18 3 0.10
19 12 0.41
20 13 0.45
21 1 0.03
ACGTcount: A:0.28, C:0.09, G:0.05, T:0.58
Consensus pattern (20 bp):
TTTATAATTTTTTTACGAAA
Found at i:58883628 original size:29 final size:28
Alignment explanation
Indices: 58883591--58883672 Score: 78
Period size: 29 Copynumber: 2.9 Consensus size: 28
58883581 CGACTTTATC
58883591 AAAATTTATAAATTTTTTTATATTTCTAT
1 AAAA-TTATAAATTTTTTTATATTTCTAT
* * *
58883620 ATATATTATAAA-TATTTTATGATTTTTAT
1 A-AAATTATAAATTTTTTTAT-ATTTCTAT
*
58883649 AAAATTTTACAATTTTTTT-TATTT
1 AAAATTATA-AATTTTTTTATATTT
58883673 TTTTACGATT
Statistics
Matches: 43, Mismatches: 6, Indels: 9
0.74 0.10 0.16
Matches are distributed among these distances:
28 17 0.40
29 19 0.44
30 7 0.16
ACGTcount: A:0.37, C:0.02, G:0.01, T:0.60
Consensus pattern (28 bp):
AAAATTATAAATTTTTTTATATTTCTAT
Found at i:58883663 original size:19 final size:20
Alignment explanation
Indices: 58883625--58883665 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 20
58883615 TCTATATATA
**
58883625 TTATAAATATTTTATGATTT
1 TTATAAATATTTTACAATTT
58883645 TTATAAA-ATTTTACAATTT
1 TTATAAATATTTTACAATTT
58883664 TT
1 TT
58883666 TTTATTTTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 12 0.63
20 7 0.37
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.59
Consensus pattern (20 bp):
TTATAAATATTTTACAATTT
Found at i:58883888 original size:91 final size:91
Alignment explanation
Indices: 58883793--58884010 Score: 252
Period size: 91 Copynumber: 2.4 Consensus size: 91
58883783 AAAAGCATGA
* * * *
58883793 GCTTAATTGCTTTT-TTGGAAAAAAGTTTGAG-GGTCTTTTTT-ATGCATTTTGAAAGTTTAAGT
1 GCTTAATTACTTTTCTT-G-AAAAAGTTTGAGAGCT-TTTTTTGATGAATTTTGAAAGTTTAAAT
* * *
58883855 ATCCAATTGAGTGCAAAAAAAAAGTCAGG
63 ACCCAAATAAGTGCAAAAAAAAAGTCAGG
58883884 GCTTAATTACTTTTCTTGAAAAAGTTTGAGAGCTTTTTTTGATGAATTTTGAAAGTTTAAATACC
1 GCTTAATTACTTTTCTTGAAAAAGTTTGAGAGCTTTTTTTGATGAATTTTGAAAGTTTAAATACC
*
58883949 CAAATAAGTGC-AAAAAAAAG--GGG
66 CAAATAAGTGCAAAAAAAAAGTCAGG
* *
58883972 GCTTAATTATTTTTTTTTGAAAACA-TTTGAGAGCTTTTT
1 GCTTAATTA-CTTTTCTTGAAAA-AGTTTGAGAGCTTTTT
58884011 GCACCATTAA
Statistics
Matches: 112, Mismatches: 10, Indels: 12
0.84 0.07 0.09
Matches are distributed among these distances:
88 11 0.10
89 25 0.22
90 28 0.25
91 46 0.41
92 2 0.02
ACGTcount: A:0.33, C:0.09, G:0.18, T:0.39
Consensus pattern (91 bp):
GCTTAATTACTTTTCTTGAAAAAGTTTGAGAGCTTTTTTTGATGAATTTTGAAAGTTTAAATACC
CAAATAAGTGCAAAAAAAAAGTCAGG
Found at i:58886738 original size:26 final size:26
Alignment explanation
Indices: 58886706--58886759 Score: 81
Period size: 26 Copynumber: 2.1 Consensus size: 26
58886696 CCCCATTTTT
* * *
58886706 AAATAAATATTAAAAAATTATTTTAA
1 AAATAAAAAATAAAAAAATATTTTAA
58886732 AAATAAAAAATAAAAAAATATTTTAA
1 AAATAAAAAATAAAAAAATATTTTAA
58886758 AA
1 AA
58886760 GTATTTTAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (26 bp):
AAATAAAAAATAAAAAAATATTTTAA
Found at i:58886753 original size:37 final size:37
Alignment explanation
Indices: 58886705--58886785 Score: 108
Period size: 37 Copynumber: 2.2 Consensus size: 37
58886695 GCCCCATTTT
* *
58886705 TAAATAAATATTAAAAAATTATTTTAAAAATAAAAAA
1 TAAAAAAATATTAAAAAAGTATTTTAAAAATAAAAAA
** * *
58886742 TAAAAAAATATTTTAAAAGTATTTTAAAATTAAAAAT
1 TAAAAAAATATTAAAAAAGTATTTTAAAAATAAAAAA
58886779 TAAAAAA
1 TAAAAAA
58886786 TAAAAATAAA
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.65, C:0.00, G:0.01, T:0.33
Consensus pattern (37 bp):
TAAAAAAATATTAAAAAAGTATTTTAAAAATAAAAAA
Found at i:58886796 original size:37 final size:37
Alignment explanation
Indices: 58886719--58886796 Score: 86
Period size: 36 Copynumber: 2.1 Consensus size: 37
58886709 TAAATATTAA
* ***
58886719 AAAATTATTTTAAAAATAAAAAATAAAAAAATATTTT
1 AAAAGTATTTTAAAAATAAAAAATAAAAAAATAAAAT
* *
58886756 AAAAGTATTTT-AAAATTAAAAATTAAAAAATAAAAAT
1 AAAAGTATTTTAAAAATAAAAAATAAAAAAAT-AAAAT
58886793 AAAA
1 AAAA
58886797 AAAATATTTA
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
36 18 0.53
37 16 0.47
ACGTcount: A:0.68, C:0.00, G:0.01, T:0.31
Consensus pattern (37 bp):
AAAAGTATTTTAAAAATAAAAAATAAAAAAATAAAAT
Found at i:58893900 original size:9 final size:9
Alignment explanation
Indices: 58893888--58894200 Score: 70
Period size: 9 Copynumber: 34.8 Consensus size: 9
58893878 TTACTTTTAT
58893888 TAAAAATTA
1 TAAAAATTA
58893897 TAAAAA--A
1 TAAAAATTA
* *
58893904 TTAAAATCAA
1 TAAAAAT-TA
*
58893914 TAAAAAATA
1 TAAAAATTA
* *
58893923 TAAATATGA
1 TAAAAATTA
**
58893932 TTAAATTTTAA
1 -TAAAAATT-A
58893943 TAAAAAATT-
1 T-AAAAATTA
*
58893952 TCAAATATTA
1 T-AAAAATTA
58893962 -AAA-ATTA
1 TAAAAATTA
*
58893969 GAAAAA-T-
1 TAAAAATTA
**
58893976 TAAAAATGG
1 TAAAAATTA
58893985 TAAAAA-TA
1 TAAAAATTA
*
58893993 TAAAAAATTG
1 T-AAAAATTA
**
58894003 TAAACTTTTA
1 TAAAAAT-TA
58894013 TAAAAATTA
1 TAAAAATTA
58894022 TAAAAATTA
1 TAAAAATTA
58894031 TAAAAA-TA
1 TAAAAATTA
*
58894039 CAAAAAATTA
1 -TAAAAATTA
58894049 T-AAAA-T-
1 TAAAAATTA
*
58894055 T-AAAATCAA
1 TAAAAAT-TA
*
58894064 TAAAAAGTA
1 TAAAAATTA
*
58894073 TAAATATTA
1 TAAAAATTA
**
58894082 TTAAATTTTAA
1 -TAAAAATT-A
58894093 TAAAAAAATTA
1 T--AAAAATTA
58894104 -AAAAA-T-
1 TAAAAATTA
58894110 TAAAAATTA
1 TAAAAATTA
*
58894119 GAAAAA-T-
1 TAAAAATTA
**
58894126 TAAAAATCG
1 TAAAAATTA
*
58894135 TAAAAAATA
1 TAAAAATTA
* *
58894144 TAAAAAACTG
1 T-AAAAATTA
*
58894154 TAAAATTTTTA
1 TAAAA--ATTA
*
58894165 TAAAAATCA
1 TAAAAATTA
58894174 TAAAAAGATTA
1 T-AAAA-ATTA
58894185 T-AAAATATA
1 TAAAAAT-TA
58894194 TAAAAAT
1 TAAAAAT
58894201 ACAAAAAAAA
Statistics
Matches: 221, Mismatches: 47, Indels: 71
0.65 0.14 0.21
Matches are distributed among these distances:
6 5 0.02
7 27 0.12
8 23 0.10
9 92 0.42
10 51 0.23
11 18 0.08
12 5 0.02
ACGTcount: A:0.64, C:0.03, G:0.03, T:0.31
Consensus pattern (9 bp):
TAAAAATTA
Found at i:58893966 original size:16 final size:16
Alignment explanation
Indices: 58893945--58894132 Score: 64
Period size: 16 Copynumber: 11.4 Consensus size: 16
58893935 AATTTTAATA
* *
58893945 AAAAATTTCAAATATT
1 AAAAATTACAAAAATT
*
58893961 AAAAATTAGAAAAATT
1 AAAAATTACAAAAATT
*
58893977 AAAAATGGTA-AAAATATA
1 AAAAAT--TACAAAA-ATT
** **
58893995 AAAAATTGTAAACTTTTAT
1 AAAAATTACAAA--AAT-T
*
58894014 AAAAATTATAAAAATT
1 AAAAATTACAAAAATT
*
58894030 ATAAAAATACAAAAAATT
1 A-AAAATTAC-AAAAATT
58894048 ATAAAATTA-AAATCAA-T
1 A-AAAATTACAAA--AATT
* * *
58894065 AAAAAGTATAAATATT
1 AAAAATTACAAAAATT
* ** *
58894081 ATTAAATTTTAATAA--
1 A-AAAATTACAAAAATT
58894096 AAAAATTA-AAAAATT
1 AAAAATTACAAAAATT
*
58894111 AAAAATTAGAAAAATT
1 AAAAATTACAAAAATT
58894127 AAAAAT
1 AAAAAT
58894133 CGTAAAAAAT
Statistics
Matches: 131, Mismatches: 24, Indels: 34
0.69 0.13 0.18
Matches are distributed among these distances:
13 4 0.03
14 5 0.04
15 10 0.08
16 46 0.35
17 27 0.21
18 28 0.21
19 11 0.08
ACGTcount: A:0.64, C:0.02, G:0.03, T:0.30
Consensus pattern (16 bp):
AAAAATTACAAAAATT
Found at i:58893966 original size:29 final size:29
Alignment explanation
Indices: 58893912--58893967 Score: 69
Period size: 29 Copynumber: 1.9 Consensus size: 29
58893902 AATTAAAATC
*
58893912 AATAAAAAATATAAATATGATTAAATTTT
1 AATAAAAAATATAAATATGATAAAATTTT
* *
58893941 AATAAAAAATTTCAAATATTA-AAAATT
1 AATAAAAAATAT-AAATATGATAAAATT
58893968 AGAAAAATTA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
29 16 0.70
30 7 0.30
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.36
Consensus pattern (29 bp):
AATAAAAAATATAAATATGATAAAATTTT
Found at i:58894012 original size:71 final size:70
Alignment explanation
Indices: 58893886--58894170 Score: 215
Period size: 72 Copynumber: 3.9 Consensus size: 70
58893876 CATTACTTTT
* * *
58893886 ATTAAAAATTATAAAAAATT-AAAATCAATAAAAAATAT-AAATA-TGATTAAATTTTAATAAAA
1 ATTAAAAATTA-GAAAAATTAAAAAT-AGTAAAAAATATAAAAAATTG--TAAATTTTAATAAAA
*
58893948 AATTTCAAAT
62 AATTT-AAAA
*
58893958 ATTAAAAATTAGAAAAATTAAAAATGGT-AAAAATATAAAAAATTGTAAACTTTT-AT-AAAAAT
1 ATTAAAAATTAGAAAAATTAAAAATAGTAAAAAATATAAAAAATTGTAAA-TTTTAATAAAAAAT
58894020 TATAAAA
65 T-TAAAA
* * * * *
58894027 ATTATAAAAATACAAAAAATTATAAAATTAAAATCAATAAAA-AGTATAAATATTATTAAATTTT
1 ATTA-AAAATTA-GAAAAATTA-AAAA-T--AGT-AA-AAAATA-TA-AAAAATT-GTAAATTTT
*
58894091 AATAAAAAAATTAAAAA
55 AAT-AAAAAATTTAAAA
* * *
58894108 ATTAAAAATTAGAAAAATTAAAAATCGTAAAAAATATAAAAAACTGTAAAATTTTTATAAAAA
1 ATTAAAAATTAGAAAAATTAAAAATAGTAAAAAATATAAAAAATTGT-AAATTTTAATAAAAA
58894171 TCATAAAAAG
Statistics
Matches: 171, Mismatches: 20, Indels: 45
0.72 0.08 0.19
Matches are distributed among these distances:
69 14 0.08
70 21 0.12
71 30 0.18
72 36 0.21
73 7 0.04
74 3 0.02
75 2 0.01
77 3 0.02
78 10 0.06
79 18 0.11
80 12 0.07
81 8 0.05
82 7 0.04
ACGTcount: A:0.64, C:0.02, G:0.03, T:0.31
Consensus pattern (70 bp):
ATTAAAAATTAGAAAAATTAAAAATAGTAAAAAATATAAAAAATTGTAAATTTTAATAAAAAATT
TAAAA
Found at i:58894085 original size:150 final size:156
Alignment explanation
Indices: 58893889--58894199 Score: 481
Period size: 150 Copynumber: 2.0 Consensus size: 156
58893879 TACTTTTATT
* *
58893889 AAAAATTATAAAAAATTAAAATCAATAAAAAATATAAATATGATTAAATTTTAATAAAAAATTTC
1 AAAAATTAT-AAAAATTAAAATCAATAAAAAATATAAATATGATTAAATTTTAATAAAAAAATTA
* * *
58893954 AAATATTAAAAATTAGAAAAATTAAAAATGGT-AAAAATATAAAAAATTGT-AAACTTTTATAAA
65 AAAAATTAAAAATTAGAAAAATTAAAAATCGTAAAAAATATAAAAAACTGTAAAACTTTTATAAA
*
58894017 AATTAT-AAAA-ATTATAAAA-ATACA
130 AATCATAAAAAGATTATAAAATATACA
* *
58894041 AAAAATTAT-AAAATTAAAATCAATAAAAAGTATAAATATTATTAAATTTTAATAAAAAAATTAA
1 AAAAATTATAAAAATTAAAATCAATAAAAAATATAAATATGATTAAATTTTAATAAAAAAATTAA
*
58894105 AAAATTAAAAATTAGAAAAATTAAAAATCGTAAAAAATATAAAAAACTGTAAAATTTTTATAAAA
66 AAAATTAAAAATTAGAAAAATTAAAAATCGTAAAAAATATAAAAAACTGTAAAACTTTTATAAAA
*
58894170 ATCATAAAAAGATTATAAAATATATA
131 ATCATAAAAAGATTATAAAATATACA
58894196 AAAA
1 AAAA
58894200 TACAAAAAAA
Statistics
Matches: 144, Mismatches: 10, Indels: 7
0.89 0.06 0.04
Matches are distributed among these distances:
150 80 0.56
151 17 0.12
152 26 0.18
153 4 0.03
154 9 0.06
155 8 0.06
ACGTcount: A:0.64, C:0.03, G:0.03, T:0.30
Consensus pattern (156 bp):
AAAAATTATAAAAATTAAAATCAATAAAAAATATAAATATGATTAAATTTTAATAAAAAAATTAA
AAAATTAAAAATTAGAAAAATTAAAAATCGTAAAAAATATAAAAAACTGTAAAACTTTTATAAAA
ATCATAAAAAGATTATAAAATATACA
Found at i:58894140 original size:16 final size:16
Alignment explanation
Indices: 58894096--58894132 Score: 67
Period size: 16 Copynumber: 2.4 Consensus size: 16
58894086 ATTTTAATAA
58894096 AAAAATTA-AAAAATT
1 AAAAATTAGAAAAATT
58894111 AAAAATTAGAAAAATT
1 AAAAATTAGAAAAATT
58894127 AAAAAT
1 AAAAAT
58894133 CGTAAAAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 8 0.38
16 13 0.62
ACGTcount: A:0.73, C:0.00, G:0.03, T:0.24
Consensus pattern (16 bp):
AAAAATTAGAAAAATT
Found at i:58894185 original size:20 final size:20
Alignment explanation
Indices: 58894162--58894199 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
58894152 TGTAAAATTT
58894162 TTATAAAA-ATCATAAAAAGA
1 TTATAAAATAT-ATAAAAAGA
58894182 TTATAAAATATATAAAAA
1 TTATAAAATATATAAAAA
58894200 TACAAAAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
20 15 0.88
21 2 0.12
ACGTcount: A:0.66, C:0.03, G:0.03, T:0.29
Consensus pattern (20 bp):
TTATAAAATATATAAAAAGA
Found at i:58894195 original size:29 final size:27
Alignment explanation
Indices: 58894014--58894245 Score: 119
Period size: 30 Copynumber: 8.4 Consensus size: 27
58894004 AAACTTTTAT
*
58894014 AAAAATTATAAAAATTATAAAAAT-ACA
1 AAAAATTAT-AAAATTATAAAAATCATA
58894041 AAAAATTATAAAA-T-T-AAAATCA-A
1 AAAAATTATAAAATTATAAAAATCATA
* ** *
58894064 TAAAAAGTATAAATATTATTAAATTTTAATAA
1 -AAAAATTATAAA-ATTA-TAAA-AATCAT-A
*
58894096 AAAAATTA-AAAAAT-TAAAAAT--TA
1 AAAAATTATAAAATTATAAAAATCATA
58894119 GAAAAATTA-AAAATCGTA-AAAAAT-ATA
1 -AAAAATTATAAAAT--TATAAAAATCATA
* *
58894146 AAAAACTGTAAAATTTTTATAAAAATCATA
1 AAAAATTATAAAA---TTATAAAAATCATA
*
58894176 AAAAGATTATAAAATATATAAAAATACAAA
1 AAAA-ATTATAAAAT-TATAAAAAT-CATA
* *
58894206 AAAAATTTATAAAATTTTATAAAATCGTA
1 AAAAA-TTATAAAATTATA-AAAATCATA
58894235 AGAAAATTATA
1 A-AAAATTATA
58894246 TATGTAAAGA
Statistics
Matches: 161, Mismatches: 17, Indels: 52
0.70 0.07 0.23
Matches are distributed among these distances:
23 7 0.04
24 26 0.16
25 2 0.01
26 19 0.12
27 19 0.12
28 4 0.02
29 31 0.19
30 38 0.24
31 14 0.09
32 1 0.01
ACGTcount: A:0.64, C:0.03, G:0.03, T:0.30
Consensus pattern (27 bp):
AAAAATTATAAAATTATAAAAATCATA
Found at i:58894496 original size:10 final size:10
Alignment explanation
Indices: 58894481--58894526 Score: 51
Period size: 10 Copynumber: 4.8 Consensus size: 10
58894471 TAAAAATTTC
58894481 TAATTTTTAA
1 TAATTTTTAA
58894491 TAATTTTT-A
1 TAATTTTTAA
*
58894500 T-ATTTTTAT
1 TAATTTTTAA
**
58894509 TAAAATTTAA
1 TAATTTTTAA
58894519 TAATTTTT
1 TAATTTTT
58894527 CTAAAATTTA
Statistics
Matches: 28, Mismatches: 6, Indels: 4
0.74 0.16 0.11
Matches are distributed among these distances:
8 6 0.21
9 3 0.11
10 19 0.68
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (10 bp):
TAATTTTTAA
Found at i:58894498 original size:40 final size:37
Alignment explanation
Indices: 58894427--58894526 Score: 96
Period size: 38 Copynumber: 2.6 Consensus size: 37
58894417 TTTTTTATTA
** *
58894427 TTTTTATAAAATTTTAATTTTTTTTATTTTTTACAAT
1 TTTTTATAAAATTTTAATTTTTAATAATTTTTACAAT
*
58894464 TTTTGTATAAAAATTTCTAATTTTTAATAATTTTTA-TA-
1 TTTT-TAT-AAAATTT-TAATTTTTAATAATTTTTACAAT
58894502 TTTTTATTAAAATTTAATAATTTTT
1 TTTTTA-TAAAATTT--TAATTTTT
58894527 CTAAAATTTA
Statistics
Matches: 53, Mismatches: 5, Indels: 9
0.79 0.07 0.13
Matches are distributed among these distances:
37 13 0.25
38 16 0.30
39 8 0.15
40 16 0.30
ACGTcount: A:0.34, C:0.02, G:0.01, T:0.63
Consensus pattern (37 bp):
TTTTTATAAAATTTTAATTTTTAATAATTTTTACAAT
Found at i:58894506 original size:8 final size:9
Alignment explanation
Indices: 58894418--58894553 Score: 51
Period size: 9 Copynumber: 14.6 Consensus size: 9
58894408 GGTCATTAAT
*
58894418 TTTTTATTA
1 TTTTTATAA
58894427 TTTTTATAAA
1 TTTTTAT-AA
* *
58894437 ATTTTA-AT
1 TTTTTATAA
* *
58894445 TTTTTTTAT
1 TTTTTATAA
*
58894454 TTTTTACAA
1 TTTTTATAA
58894463 TTTTTGTATAAA
1 -TTTT-TAT-AA
** *
58894475 AATTTCTAA
1 TTTTTATAA
58894484 TTTTTAATAA
1 TTTTT-ATAA
58894494 TTTTTAT-A
1 TTTTTATAA
58894502 TTTTTATTAAA
1 TTTTTA-T-AA
* *
58894513 ATTTAATAA
1 TTTTTATAA
*
58894522 TTTTTCTAA
1 TTTTTATAA
** **
58894531 AATTTATTG
1 TTTTTATAA
58894540 TTTTTATAA
1 TTTTTATAA
58894549 TTTTT
1 TTTTT
58894554 TTTCTAATTT
Statistics
Matches: 89, Mismatches: 29, Indels: 18
0.65 0.21 0.13
Matches are distributed among these distances:
8 12 0.13
9 45 0.51
10 21 0.24
11 9 0.10
12 2 0.02
ACGTcount: A:0.32, C:0.02, G:0.01, T:0.64
Consensus pattern (9 bp):
TTTTTATAA
Found at i:58894513 original size:38 final size:37
Alignment explanation
Indices: 58894418--58894526 Score: 105
Period size: 40 Copynumber: 2.9 Consensus size: 37
58894408 GGTCATTAAT
* ** *
58894418 TTTTTATTATTTTTA-TAAAATTTTAATTTTTTTTAT
1 TTTTTACTATTTTTATTAAAATTTTAATTTTTAATAA
* *
58894454 TTTTTACAATTTTTGTATAAAAATTTCTAATTTTTAATAA
1 TTTTTACTA-TTTT-TATTAAAATTT-TAATTTTTAATAA
58894494 TTTTTA-TATTTTTATTAAAATTTAATAATTTTT
1 TTTTTACTATTTTTATTAAAATTT--TAATTTTT
58894527 CTAAAATTTA
Statistics
Matches: 59, Mismatches: 9, Indels: 8
0.78 0.12 0.11
Matches are distributed among these distances:
36 7 0.12
37 14 0.24
38 14 0.24
39 8 0.14
40 16 0.27
ACGTcount: A:0.33, C:0.02, G:0.01, T:0.64
Consensus pattern (37 bp):
TTTTTACTATTTTTATTAAAATTTTAATTTTTAATAA
Found at i:58894517 original size:18 final size:19
Alignment explanation
Indices: 58894420--58894537 Score: 64
Period size: 18 Copynumber: 6.3 Consensus size: 19
58894410 TCATTAATTT
*
58894420 TTTATTATTTTT-ATAAAA
1 TTTATAATTTTTAATAAAA
** ***
58894438 TTT-TAATTTTTTTTATTT
1 TTTATAATTTTTAATAAAA
* *
58894456 TTTACAATTTTTGTATAAAAA
1 TTTATAATTTTT-AAT-AAAA
* **
58894477 TTTCTAATTTTTAATAATT
1 TTTATAATTTTTAATAAAA
*
58894496 TTTAT-ATTTTTATTAAAA
1 TTTATAATTTTTAATAAAA
*
58894514 TTTAATAATTTTT-CTAAAA
1 TTT-ATAATTTTTAATAAAA
58894533 TTTAT
1 TTTAT
58894538 TGTTTTTATA
Statistics
Matches: 74, Mismatches: 20, Indels: 12
0.70 0.19 0.11
Matches are distributed among these distances:
17 7 0.09
18 23 0.31
19 23 0.31
20 10 0.14
21 11 0.15
ACGTcount: A:0.35, C:0.03, G:0.01, T:0.62
Consensus pattern (19 bp):
TTTATAATTTTTAATAAAA
Found at i:58900258 original size:14 final size:14
Alignment explanation
Indices: 58900220--58900262 Score: 54
Period size: 13 Copynumber: 3.1 Consensus size: 14
58900210 CAAAATGTAC
58900220 AATATAATTAAA-T
1 AATATAATTAAATT
58900233 AATATAAATTAAATT
1 AATAT-AATTAAATT
*
58900248 AA-ATAATTTAATT
1 AATATAATTAAATT
58900261 AA
1 AA
58900263 CTGTTTACTC
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
13 15 0.56
14 9 0.33
15 3 0.11
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (14 bp):
AATATAATTAAATT
Found at i:58902691 original size:3 final size:3
Alignment explanation
Indices: 58902683--58902730 Score: 69
Period size: 3 Copynumber: 16.0 Consensus size: 3
58902673 TAAAACAATT
** *
58902683 TAA TAA TAA TAA TAA TAA TAA TGG TAA TAA TAA TAA TAA CAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
58902731 AAATCTTAAA
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.62, C:0.02, G:0.04, T:0.31
Consensus pattern (3 bp):
TAA
Found at i:58902795 original size:17 final size:18
Alignment explanation
Indices: 58902753--58902793 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
58902743 TAAAAATTAT
*
58902753 ATAAAAGGATATAGATAA
1 ATAAAATGATATAGATAA
58902771 ATAAAATGATATA-ATAAA
1 ATAAAATGATATAGAT-AA
58902789 ATAAA
1 ATAAA
58902794 TGTATTTAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 2 0.10
18 19 0.90
ACGTcount: A:0.66, C:0.00, G:0.10, T:0.24
Consensus pattern (18 bp):
ATAAAATGATATAGATAA
Found at i:58907189 original size:57 final size:59
Alignment explanation
Indices: 58907074--58907221 Score: 185
Period size: 57 Copynumber: 2.5 Consensus size: 59
58907064 AATTAACGGT
58907074 AAAAAGGATCTAGCCCGGACGGGTGATCCTATCCTAATATAGCCCTCCCGAAGAATATGTGTG
1 AAAAA-GATCTAGCCCGGACGGGTGATCC-AT-CTAATATAGCCCTCCCGAAGAATATGTG-G
* *
58907137 AAAAAGATCTAGCCCGGACGGGTGAT-C-T-TGATATAGCCCTCCTGAAGAATATGTGG
1 AAAAAGATCTAGCCCGGACGGGTGATCCATCTAATATAGCCCTCCCGAAGAATATGTGG
* * *
58907193 AAAATGAATTTAGCCCGGACGGGTAATCC
1 AAAAAG-ATCTAGCCCGGACGGGTGATCC
58907222 GAATTAGGGT
Statistics
Matches: 78, Mismatches: 5, Indels: 9
0.85 0.05 0.10
Matches are distributed among these distances:
56 6 0.08
57 43 0.55
58 1 0.01
59 1 0.01
61 1 0.01
62 21 0.27
63 5 0.06
ACGTcount: A:0.31, C:0.22, G:0.25, T:0.22
Consensus pattern (59 bp):
AAAAAGATCTAGCCCGGACGGGTGATCCATCTAATATAGCCCTCCCGAAGAATATGTGG
Found at i:58917412 original size:44 final size:47
Alignment explanation
Indices: 58917364--58917482 Score: 154
Period size: 49 Copynumber: 2.6 Consensus size: 47
58917354 TTCAGTTTAT
* *
58917364 TCCACTGTGACTTTAGGGAGATAAGACTAGT-G-G-CTTCAATCTGC
1 TCCACTGTAACTTCAGGGAGATAAGACTAGTAGCGTCTTCAATCTGC
* * *
58917408 TCCACTGCAACTTCAGGGAGATAAGATTTGTAGCCCGTCTTCAATCTGC
1 TCCACTGTAACTTCAGGGAGATAAGACTAGTAG--CGTCTTCAATCTGC
58917457 TCCACTGTAACTTCAGGGAGATAAGA
1 TCCACTGTAACTTCAGGGAGATAAGA
58917483 TTGATTTATT
Statistics
Matches: 64, Mismatches: 6, Indels: 5
0.85 0.08 0.07
Matches are distributed among these distances:
44 26 0.41
45 1 0.02
48 1 0.02
49 36 0.56
ACGTcount: A:0.27, C:0.23, G:0.23, T:0.28
Consensus pattern (47 bp):
TCCACTGTAACTTCAGGGAGATAAGACTAGTAGCGTCTTCAATCTGC
Found at i:58917557 original size:87 final size:87
Alignment explanation
Indices: 58917451--58917894 Score: 306
Period size: 87 Copynumber: 4.9 Consensus size: 87
58917441 CCCGTCTTCA
* * *
58917451 ATCTGCTCCACTGTAACTTCAGGGAGATAAGATTGATTTATTTTTAACCTGTTCCACTGCAACTT
1 ATCTGCTCTACTGCAACTTCAGGGAGATAAGATTGATTTATCTTTAACCTGTTCCACTGCAACTT
*
58917516 CAAGGAGATAAGGTTTGAT-ATG
66 C-AGGAGATAAGATTTGATAATG
* * ** *
58917538 ATCTGCTCTGCTGCAACTTCAGAGAGATAAGATCTGTAATTTATAGCTTTAATATGTTCCATTGC
1 ATCTGCTCTACTGCAACTTCAGGGAGATAAGAT-TG--ATTTAT--CTTTAACCTGTTCCACTGC
* ** *
58917603 AACTTCAGGGAGATAAGATTGGTATCTTCA
61 AACTTCA-GGAGATAAGATTTG-ATAAT-G
* * * * * ** * * *
58917633 ACCTGCTCTATTGTAACTTCAGGGAGATAAGGTT--TGTGGCTTTAATCTGCTCCACTGTAACTT
1 ATCTGCTCTACTGCAACTTCAGGGAGATAAGATTGATTTATCTTTAACCTGTTCCACTGCAACTT
**
58917696 CA-GTTATAAGATTT-ATAACTTG
66 CAGGAGATAAGATTTGATAA--TG
* * * * *
58917718 TCTTCATTTTGCTCCACTGCAACTTCAGGGAGATAAGATTGGTTTATTTTTAACCTGTTCCACTA
1 -----A-TCTGCTCTACTGCAACTTCAGGGAGATAAGATTGATTTATCTTTAACCTGTTCCACTG
*
58917783 CAACTTCAGGAAGATAAGGTTTGAT-ATG
60 CAACTTCAGG-AGATAAGATTTGATAATG
* * *
58917811 ATCTGCTCTACTGCAACTTCAGAGAGATAAGATCTGTAATTTATAGCTTCAATCTGTTCCACTGC
1 ATCTGCTCTACTGCAACTTCAGGGAGATAAGAT-TG--ATTTAT--CTTTAACCTGTTCCACTGC
* * *
58917876 AGCTTTAGGAAATAAGATT
61 AACTTCAGGAGATAAGATT
58917895 CGCTATCTTC
Statistics
Matches: 270, Mismatches: 60, Indels: 50
0.71 0.16 0.13
Matches are distributed among these distances:
84 2 0.01
86 10 0.04
87 58 0.21
88 27 0.10
90 14 0.05
91 36 0.13
92 55 0.20
93 27 0.10
94 3 0.01
95 36 0.13
96 2 0.01
ACGTcount: A:0.28, C:0.18, G:0.18, T:0.35
Consensus pattern (87 bp):
ATCTGCTCTACTGCAACTTCAGGGAGATAAGATTGATTTATCTTTAACCTGTTCCACTGCAACTT
CAGGAGATAAGATTTGATAATG
Found at i:58917565 original size:136 final size:135
Alignment explanation
Indices: 58917402--58917936 Score: 499
Period size: 136 Copynumber: 3.9 Consensus size: 135
58917392 AGTGGCTTCA
* * * ** * *
58917402 ATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGTAGCCCGTCTTCAATCTGCTCCACTGTAA
1 ATCTGCTCCACTGCAACTTCAGAGAGATAAGATCTGTAACTTGTCTTCAATATGCTCCACTGCAA
58917467 CTTCAGGGAGATAAGATTGATTTATTTTTAACCTGTTCCACTGCAACTTCAAGGAGATAAGGTTT
66 CTTCAGGGAGATAAGATTG-TTTATTTTTAACCTGTTCCACTGCAACTTCAAGGAGATAAGGTTT
58917532 GATATG
130 GATATG
** * * * * *
58917538 ATCTGCTCTGCTGCAACTTCAGAGAGATAAGATCTGTAATTTATAGCTTTAATATGTTCCATTGC
1 ATCTGCTCCACTGCAACTTCAGAGAGATAAGATCTGTAACTTGT--CTTCAATATGCTCCACTGC
* * * * * * * *
58917603 AACTTCAGGGAGATAAGATTG-GTATCTTCAACCTGCTCTATTGTAACTTCAGGGAGATAAGGTT
64 AACTTCAGGGAGATAAGATTGTTTATTTTTAACCTGTTCCACTGCAACTTCAAGGAGATAAGG-T
* * *
58917667 TGTGGCTTTA
128 T-T-GATATG
* ** * * * *
58917677 ATCTGCTCCACTGTAACTTC--AGTTATAAGATTTATAACTTGTCTTCATTTTGCTCCACTGCAA
1 ATCTGCTCCACTGCAACTTCAGAGAGATAAGATCTGTAACTTGTCTTCAATATGCTCCACTGCAA
*
58917740 CTTCAGGGAGATAAGATTGGTTTATTTTTAACCTGTTCCACTACAACTTC-AGGAAGATAAGGTT
66 CTTCAGGGAGATAAGATT-GTTTATTTTTAACCTGTTCCACTGCAACTTCAAGG-AGATAAGGTT
58917804 TGATATG
129 TGATATG
* * * * *
58917811 ATCTGCTCTACTGCAACTTCAGAGAGATAAGATCTGTAATTTATAGCTTCAATCTGTTCCACTGC
1 ATCTGCTCCACTGCAACTTCAGAGAGATAAGATCTGTAACTTGT--CTTCAATATGCTCCACTGC
* * * * * * **
58917876 AGCTTTA-GGAAATAAGATTCG-CTATCTTCAGTCTGTTCCACTGCAACTTC-AGGAAGATAAG
64 AACTTCAGGGAGATAAGATT-GTTTATTTTTAACCTGTTCCACTGCAACTTCAAGG-AGATAAG
58917937 ACTAGTAACT
Statistics
Matches: 315, Mismatches: 72, Indels: 24
0.77 0.18 0.06
Matches are distributed among these distances:
134 21 0.07
135 35 0.11
136 123 0.39
137 59 0.19
138 57 0.18
139 20 0.06
ACGTcount: A:0.28, C:0.19, G:0.19, T:0.34
Consensus pattern (135 bp):
ATCTGCTCCACTGCAACTTCAGAGAGATAAGATCTGTAACTTGTCTTCAATATGCTCCACTGCAA
CTTCAGGGAGATAAGATTGTTTATTTTTAACCTGTTCCACTGCAACTTCAAGGAGATAAGGTTTG
ATATG
Found at i:58917683 original size:44 final size:44
Alignment explanation
Indices: 58917364--58917698 Score: 163
Period size: 44 Copynumber: 7.4 Consensus size: 44
58917354 TTCAGTTTAT
* * * * * * *
58917364 TCCACTGTGACTTTAGGGAGATAAGACTAGTGGCTTCAATCTGC
1 TCCATTGTAACTTCAGGGAGATAAGATTGGTAGCTTTAATCTGC
* * *
58917408 TCCACTGCAACTTCAGGGAGATAAGATTTGTAGCCCGTCTTCAATCTGC
1 TCCATTGTAACTTCAGGGAGATAAGATTGGTAG--C-T-TT-AATCTGC
* * ** * *
58917457 TCCACTGTAACTTCAGGGAGATAAGATTGATTTATTTTTAACCTGT
1 TCCATTGTAACTTCAGGGAGATAAGATTG--GTAGCTTTAATCTGC
* * * * * * *
58917503 TCCACTGCAACTTCAAGGAGATAAGGTT--T-GATATGATCTGC
1 TCCATTGTAACTTCAGGGAGATAAGATTGGTAGCTTTAATCTGC
*** * * * * *
58917544 TCTGCTGCAACTTCAGAGAGATAAGATCTGTAATTTATAGCTTTAATATGT
1 TCCATTGTAACTTCAGGGAGATAAGAT-TG------GTAGCTTTAATCTGC
* * * *
58917595 TCCATTGCAACTTCAGGGAGATAAGATTGGTATCTTCAACCTGC
1 TCCATTGTAACTTCAGGGAGATAAGATTGGTAGCTTTAATCTGC
* * * *
58917639 TCTATTGTAACTTCAGGGAGATAAGGTTTGTGGCTTTAATCTGC
1 TCCATTGTAACTTCAGGGAGATAAGATTGGTAGCTTTAATCTGC
*
58917683 TCCACTGTAACTTCAG
1 TCCATTGTAACTTCAG
58917699 TTATAAGATT
Statistics
Matches: 221, Mismatches: 53, Indels: 34
0.72 0.17 0.11
Matches are distributed among these distances:
41 28 0.13
42 2 0.01
44 86 0.39
46 31 0.14
47 3 0.01
48 2 0.01
49 34 0.15
50 3 0.01
51 32 0.14
ACGTcount: A:0.27, C:0.19, G:0.21, T:0.33
Consensus pattern (44 bp):
TCCATTGTAACTTCAGGGAGATAAGATTGGTAGCTTTAATCTGC
Found at i:58917751 original size:273 final size:274
Alignment explanation
Indices: 58917373--58917979 Score: 815
Period size: 273 Copynumber: 2.2 Consensus size: 274
58917363 TTCCACTGTG
* *
58917373 ACTTTAGGGAGATAAGACTAGTGGCTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTG
1 ACTTCAGGGAGATAAGACTAGTGGCTTCAATCTGCTCCACTGCAACTTCA-GGAGATAAGATTTA
* *
58917438 TAGCCCGTCTTCAATCTGCTCCACTGTAACTTCAGGGAGATAAGATTGATTTATTTTTAACCTGT
65 TAACCCGTCTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTGATTTATTTTTAACCTGT
* *
58917503 TCCACTGCAACTTCAAGG-AGATAAGGTTTGATATGATCTGCTCTGCTGCAACTTCAGAGAGATA
130 TCCACTACAACTTC-AGGAAGATAAGGTTTGATATGATCTGCTCTACTGCAACTTCAGAGAGATA
* * * *
58917567 AGATCTGTAATTTATAGCTTTAATATGTTCCATTGCAACTTCAGGGAGATAAGATT-GGTATCTT
194 AGATCTGTAATTTATAGCTTCAATATGTTCCACTGCAACTTCA-GGAAATAAGATTCGCTATCTT
58917631 CAACCTGCTCTATTGTA
258 CAACCTGCTCTATTGTA
** * * * **
58917648 ACTTCAGGGAGATAAGGTTTGTGGCTTTAATCTGCTCCACTGTAACTTCA-GTTATAAGATTTAT
1 ACTTCAGGGAGATAAGACTAGTGGCTTCAATCTGCTCCACTGCAACTTCAGGAGATAAGATTTAT
** * * *
58917712 AACTTGTCTTCATTTTGCTCCACTGCAACTTCAGGGAGATAAGATTGGTTTATTTTTAACCTGTT
66 AACCCGTCTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTGATTTATTTTTAACCTGTT
58917777 CCACTACAACTTCAGGAAGATAAGGTTTGATATGATCTGCTCTACTGCAACTTCAGAGAGATAAG
131 CCACTACAACTTCAGGAAGATAAGGTTTGATATGATCTGCTCTACTGCAACTTCAGAGAGATAAG
* * * *
58917842 ATCTGTAATTTATAGCTTCAATCTGTTCCACTGCAGCTTTAGGAAATAAGATTCGCTATCTTCAG
196 ATCTGTAATTTATAGCTTCAATATGTTCCACTGCAACTTCAGGAAATAAGATTCGCTATCTTCAA
* * * * *
58917907 TCTGTTCCACTGCA
261 CCTGCTCTATTGTA
* ** * * * *
58917921 ACTTCAGGAAGATAAGACTAGTAACTTCAACCTACTTCACTACAACTTCAGGGAGATAA
1 ACTTCAGGGAGATAAGACTAGTGGCTTCAATCTGCTCCACTGCAACTTCA-GGAGATAA
58917980 AGTTTGTTAT
Statistics
Matches: 283, Mismatches: 45, Indels: 8
0.84 0.13 0.02
Matches are distributed among these distances:
272 14 0.05
273 220 0.78
275 49 0.17
ACGTcount: A:0.29, C:0.19, G:0.19, T:0.33
Consensus pattern (274 bp):
ACTTCAGGGAGATAAGACTAGTGGCTTCAATCTGCTCCACTGCAACTTCAGGAGATAAGATTTAT
AACCCGTCTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTGATTTATTTTTAACCTGTT
CCACTACAACTTCAGGAAGATAAGGTTTGATATGATCTGCTCTACTGCAACTTCAGAGAGATAAG
ATCTGTAATTTATAGCTTCAATATGTTCCACTGCAACTTCAGGAAATAAGATTCGCTATCTTCAA
CCTGCTCTATTGTA
Found at i:58917949 original size:44 final size:44
Alignment explanation
Indices: 58917857--58917972 Score: 119
Period size: 44 Copynumber: 2.6 Consensus size: 44
58917847 TAATTTATAG
* * * * *
58917857 CTTCAATCTGTTCCACTGCAGCTTTAGGAAATAAGATTCGCTAT
1 CTTCAATCTGTTCCACTGCAACTTCAGGAAATAAGACTAGCTAA
*
58917901 CTTCAGTCTGTTCCACTGCAACTTCAGGAAGATAAGACTAG-TAA
1 CTTCAATCTGTTCCACTGCAACTTCAGGAA-ATAAGACTAGCTAA
* * *
58917945 CTTCAACCTACTT-CACTACAACTTCAGG
1 CTTCAATCT-GTTCCACTGCAACTTCAGG
58917973 GAGATAAAGT
Statistics
Matches: 60, Mismatches: 10, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
44 50 0.83
45 10 0.17
ACGTcount: A:0.29, C:0.26, G:0.15, T:0.30
Consensus pattern (44 bp):
CTTCAATCTGTTCCACTGCAACTTCAGGAAATAAGACTAGCTAA
Found at i:58918950 original size:14 final size:15
Alignment explanation
Indices: 58918927--58918959 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
58918917 ATCAACACTT
*
58918927 TTCCATATAAGA-CC
1 TTCCACATAAGATCC
58918941 TTCCACATAAGATCC
1 TTCCACATAAGATCC
58918956 TTCC
1 TTCC
58918960 TAGTTTGACA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 11 0.65
15 6 0.35
ACGTcount: A:0.30, C:0.33, G:0.06, T:0.30
Consensus pattern (15 bp):
TTCCACATAAGATCC
Found at i:58929926 original size:16 final size:17
Alignment explanation
Indices: 58929896--58929928 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
58929886 TTTTATAATA
*
58929896 TAAAAATTATATAAAAT
1 TAAAAAATATATAAAAT
58929913 TAAAAAATAT-TAAAAT
1 TAAAAAATATATAAAAT
58929929 ATTAAAGTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (17 bp):
TAAAAAATATATAAAAT
Found at i:58929941 original size:13 final size:13
Alignment explanation
Indices: 58929923--58929947 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
58929913 TAAAAAATAT
58929923 TAAAATATTAAAG
1 TAAAATATTAAAG
58929936 TAAAATATTAAA
1 TAAAATATTAAA
58929948 CCATGTTTCT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.64, C:0.00, G:0.04, T:0.32
Consensus pattern (13 bp):
TAAAATATTAAAG
Found at i:58937744 original size:23 final size:22
Alignment explanation
Indices: 58937692--58937744 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
58937682 TCCACGTCTT
*
58937692 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
58937714 -TTCATTTTCTCTTCTTTCTTC-AA
1 TTTC-TTTTCT-TTCTTT-TTCTAA
58937737 TTTCTTTT
1 TTTCTTTT
58937745 TCACTCTCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 3 0.12
22 5 0.19
23 12 0.46
24 6 0.23
ACGTcount: A:0.09, C:0.19, G:0.02, T:0.70
Consensus pattern (22 bp):
TTTCTTTTCTTTCTTTTTCTAA
Found at i:58951688 original size:16 final size:16
Alignment explanation
Indices: 58951655--58951688 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
58951645 TCAAGTTGTT
* *
58951655 AACATTAATGGGAGAC
1 AACATTAATGGCAAAC
58951671 AACATTAATGGCAAAC
1 AACATTAATGGCAAAC
58951687 AA
1 AA
58951689 TACAAAGTGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.15, G:0.18, T:0.18
Consensus pattern (16 bp):
AACATTAATGGCAAAC
Found at i:58954515 original size:21 final size:21
Alignment explanation
Indices: 58954489--58954529 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
58954479 AGACGAGCAA
* *
58954489 TACTCCACAGCAGGTGGAGTG
1 TACTCCAAAACAGGTGGAGTG
58954510 TACTCCAAAACAGGTGGAGT
1 TACTCCAAAACAGGTGGAGT
58954530 TTGAGCAGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.22, G:0.29, T:0.20
Consensus pattern (21 bp):
TACTCCAAAACAGGTGGAGTG
Found at i:58956468 original size:16 final size:16
Alignment explanation
Indices: 58956435--58956468 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
58956425 GGAGATTGTT
* *
58956435 AACATTAATGGGAGAC
1 AACATTAATGGCAAAC
58956451 AACATTAATGGCAAAC
1 AACATTAATGGCAAAC
58956467 AA
1 AA
58956469 TACAAAGTGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.15, G:0.18, T:0.18
Consensus pattern (16 bp):
AACATTAATGGCAAAC
Found at i:58958918 original size:29 final size:30
Alignment explanation
Indices: 58958856--58958924 Score: 104
Period size: 29 Copynumber: 2.3 Consensus size: 30
58958846 TATCAAAACT
58958856 ATACATAAACTTTGATTTAATGTGTAATGTC
1 ATACATAAACTTTGATTT-ATGTGTAATGTC
* *
58958887 ATACATAAACTTTGATTT-TGTGTGATTTC
1 ATACATAAACTTTGATTTATGTGTAATGTC
58958916 ATACATAAA
1 ATACATAAA
58958925 ATTTTAATTT
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
29 18 0.50
31 18 0.50
ACGTcount: A:0.36, C:0.10, G:0.12, T:0.42
Consensus pattern (30 bp):
ATACATAAACTTTGATTTATGTGTAATGTC
Found at i:58958935 original size:29 final size:29
Alignment explanation
Indices: 58958856--58958935 Score: 79
Period size: 29 Copynumber: 2.7 Consensus size: 29
58958846 TATCAAAACT
* *
58958856 ATACATAAACTTTGATTTAATGTGTAATGTC
1 ATACATAAAATTTGAATT--TGTGTAATGTC
* * * *
58958887 ATACATAAACTTTGATTTTGTGTGATTTC
1 ATACATAAAATTTGAATTTGTGTAATGTC
*
58958916 ATACATAAAATTTTAATTTG
1 ATACATAAAATTTGAATTTG
58958936 ATTCAGTTTT
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
29 26 0.59
31 18 0.41
ACGTcount: A:0.35, C:0.09, G:0.11, T:0.45
Consensus pattern (29 bp):
ATACATAAAATTTGAATTTGTGTAATGTC
Found at i:58959413 original size:12 final size:13
Alignment explanation
Indices: 58959396--58959425 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
58959386 GTTAATAGTA
58959396 TATTTTTA-TTTT
1 TATTTTTATTTTT
58959408 TATTTTTATTTTT
1 TATTTTTATTTTT
58959421 TATTT
1 TATTT
58959426 CAAGTCAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 8 0.47
13 9 0.53
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (13 bp):
TATTTTTATTTTT
Found at i:58959414 original size:7 final size:6
Alignment explanation
Indices: 58959396--58959425 Score: 51
Period size: 6 Copynumber: 4.8 Consensus size: 6
58959386 GTTAATAGTA
58959396 TATTTT TATTTT TATTTT TATTTTT TATTT
1 TATTTT TATTTT TATTTT TA-TTTT TATTT
58959426 CAAGTCAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 17 0.74
7 6 0.26
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (6 bp):
TATTTT
Found at i:58960189 original size:3 final size:3
Alignment explanation
Indices: 58960181--58960222 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
58960171 CATGTTTTAG
58960181 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA
58960223 ATATAGTCTG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.33, C:0.33, G:0.00, T:0.33
Consensus pattern (3 bp):
TCA
Found at i:58961662 original size:36 final size:37
Alignment explanation
Indices: 58961572--58961667 Score: 94
Period size: 36 Copynumber: 2.7 Consensus size: 37
58961562 AATTTTAAAA
*
58961572 AAAACACGAAAATTT-TGAAACAC-G--AGATTTCTTT
1 AAAACACGAAAATTTATGAAAAACGGTCA-ATTTCTTT
* *
58961606 GAAACACGAAAATTTATGAAACACGGTCAATTTC-TT
1 AAAACACGAAAATTTATGAAAAACGGTCAATTTCTTT
* * *
58961642 AAAACGCGAAAGTTTTTGAAAAACGG
1 AAAACACGAAAATTTATGAAAAACGG
58961668 GAATTTTTTT
Statistics
Matches: 52, Mismatches: 6, Indels: 6
0.81 0.09 0.09
Matches are distributed among these distances:
34 14 0.27
35 8 0.15
36 24 0.46
37 5 0.10
38 1 0.02
ACGTcount: A:0.44, C:0.15, G:0.16, T:0.26
Consensus pattern (37 bp):
AAAACACGAAAATTTATGAAAAACGGTCAATTTCTTT
Found at i:58961696 original size:21 final size:21
Alignment explanation
Indices: 58961654--58961696 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
58961644 AACGCGAAAG
** *
58961654 TTTTTGAAAAACGGGAATTTT
1 TTTTTGAAAAACGAAAAATTT
*
58961675 TTTTTGAAACACGAAAAATTT
1 TTTTTGAAAAACGAAAAATTT
58961696 T
1 T
58961697 GAAACACTGG
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.37, C:0.07, G:0.14, T:0.42
Consensus pattern (21 bp):
TTTTTGAAAAACGAAAAATTT
Found at i:58961868 original size:17 final size:17
Alignment explanation
Indices: 58961848--58961923 Score: 55
Period size: 18 Copynumber: 4.2 Consensus size: 17
58961838 ATTGGAATTT
*
58961848 TTTTGAAAACACGAGAAT
1 TTTTGAAAACACGA-AAA
*
58961866 TTTTGAAAAACATGAAAA
1 TTTTG-AAAACACGAAAA
* * *
58961884 TTTTTG-CAACACGGGAAT
1 -TTTTGAAAACAC-GAAAA
58961902 TTTTGAAAACACGAAAAA
1 TTTTGAAAACACG-AAAA
58961920 TTTT
1 TTTT
58961924 CCGATTTTTT
Statistics
Matches: 44, Mismatches: 9, Indels: 10
0.70 0.14 0.16
Matches are distributed among these distances:
17 10 0.23
18 21 0.48
19 13 0.30
ACGTcount: A:0.43, C:0.11, G:0.14, T:0.32
Consensus pattern (17 bp):
TTTTGAAAACACGAAAA
Found at i:58961875 original size:19 final size:18
Alignment explanation
Indices: 58961572--58961915 Score: 165
Period size: 17 Copynumber: 19.5 Consensus size: 18
58961562 AATTTTAAAA
*
58961572 AAAACACGA-AAATTTTG
1 AAAACACGAGAATTTTTG
*
58961589 -AAACACGAGATTTCTTTG
1 AAAACACGAGAATT-TTTG
* *
58961607 -AAACACGAAAATTTATG
1 AAAACACGAGAATTTTTG
58961624 -AAACACG-GTCAATTTCTT-
1 AAAACACGAG--AATTT-TTG
*
58961642 AAAACGCGA-AAGTTTTTG
1 AAAACACGAGAA-TTTTTG
*
58961660 AAAA-ACGGGAATTTTTTTTTG
1 AAAACACGAGAA----TTTTTG
* *
58961681 -AAACACGAAAAATTTTG
1 AAAACACGAGAATTTTTG
58961698 -AAACACTG-GAA-TTTTG
1 AAAACAC-GAGAATTTTTG
*
58961714 AAAACACGAGGATTTTT-
1 AAAACACGAGAATTTTTG
* **
58961731 -AAATACGA-AAAATTTG
1 AAAACACGAGAATTTTTG
* *
58961747 AAAACAAGAAAATTTTT-
1 AAAACACGAGAATTTTTG
* * *
58961764 AAAATACGAAAATTTTAG
1 AAAACACGAGAATTTTTG
*
58961782 -AAACACGAAAATTTTTG
1 AAAACACGAGAATTTTTG
58961799 -AAACAC-AGAAGTTTTTAG
1 AAAACACGAGAA-TTTTT-G
* *
58961817 AAAACACGAAAAATTTTG
1 AAAACACGAGAATTTTTG
**
58961835 AAAA-TTG-GAATTTTTTTG
1 AAAACACGAGAA--TTTTTG
58961853 AAAACACGAGAATTTTTG
1 AAAACACGAGAATTTTTG
* *
58961871 AAAAACATGAAAATTTTTG
1 -AAAACACGAGAATTTTTG
* *
58961890 -CAACACGGGAATTTTTG
1 AAAACACGAGAATTTTTG
58961907 AAAACACGA
1 AAAACACGA
58961916 AAAATTTTCC
Statistics
Matches: 249, Mismatches: 46, Indels: 63
0.70 0.13 0.18
Matches are distributed among these distances:
15 4 0.02
16 26 0.10
17 99 0.40
18 66 0.27
19 34 0.14
20 9 0.04
21 11 0.04
ACGTcount: A:0.45, C:0.11, G:0.15, T:0.29
Consensus pattern (18 bp):
AAAACACGAGAATTTTTG
Found at i:58961895 original size:36 final size:35
Alignment explanation
Indices: 58961855--58961923 Score: 102
Period size: 35 Copynumber: 1.9 Consensus size: 35
58961845 TTTTTTTGAA
* *
58961855 AACACGAGAATTTTTGAAAAACATGAAAATTTTTGC
1 AACACGAGAATTTTTG-AAAACACGAAAAATTTTGC
*
58961891 AACACGGGAATTTTTGAAAACACGAAAAATTTT
1 AACACGAGAATTTTTGAAAACACGAAAAATTTT
58961924 CCGATTTTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
35 15 0.50
36 15 0.50
ACGTcount: A:0.45, C:0.12, G:0.14, T:0.29
Consensus pattern (35 bp):
AACACGAGAATTTTTGAAAACACGAAAAATTTTGC
Found at i:58962055 original size:21 final size:20
Alignment explanation
Indices: 58962029--58962070 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 20
58962019 TGTTACCTTA
58962029 TTTTTGAAAACACGAGAAATT
1 TTTTTGAAAACACGA-AAATT
*
58962050 TTTTTGAAGACACGAAAATT
1 TTTTTGAAAACACGAAAATT
58962070 T
1 T
58962071 CGAAACCCGA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 6 0.30
21 14 0.70
ACGTcount: A:0.40, C:0.10, G:0.14, T:0.36
Consensus pattern (20 bp):
TTTTTGAAAACACGAAAATT
Found at i:58962254 original size:11 final size:11
Alignment explanation
Indices: 58962234--58962266 Score: 57
Period size: 11 Copynumber: 3.0 Consensus size: 11
58962224 TTAAAATTAT
*
58962234 TTAAAATAAAA
1 TTAAATTAAAA
58962245 TTAAATTAAAA
1 TTAAATTAAAA
58962256 TTAAATTAAAA
1 TTAAATTAAAA
58962267 ATATAAATAC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (11 bp):
TTAAATTAAAA
Found at i:58962255 original size:16 final size:16
Alignment explanation
Indices: 58962225--58962265 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
58962215 CCTTATTTAT
*
58962225 TAAAATT-ATTTAAAA
1 TAAAATTAAATTAAAA
58962240 TAAAATTAAATTAAAA
1 TAAAATTAAATTAAAA
*
58962256 TTAAATTAAA
1 TAAAATTAAA
58962266 AATATAAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 7 0.30
16 16 0.70
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (16 bp):
TAAAATTAAATTAAAA
Found at i:58962447 original size:8 final size:8
Alignment explanation
Indices: 58962434--58962519 Score: 113
Period size: 8 Copynumber: 11.0 Consensus size: 8
58962424 TGAAACTCTT
58962434 TTTTTTTC
1 TTTTTTTC
58962442 TTTTTTTC
1 TTTTTTTC
*
58962450 TTTTTTCC
1 TTTTTTTC
58962458 TTTTTTTC
1 TTTTTTTC
*
58962466 -TCTTTTC
1 TTTTTTTC
58962473 TTTTTTTC
1 TTTTTTTC
*
58962481 -TTCTTTC
1 TTTTTTTC
58962488 TTTTTTTC
1 TTTTTTTC
58962496 TTTTTTTC
1 TTTTTTTC
* *
58962504 TTTCTCTC
1 TTTTTTTC
58962512 TTTTTTTC
1 TTTTTTTC
58962520 CTGGCCTGCT
Statistics
Matches: 66, Mismatches: 10, Indels: 4
0.82 0.12 0.05
Matches are distributed among these distances:
7 12 0.18
8 54 0.82
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (8 bp):
TTTTTTTC
Found at i:58962455 original size:15 final size:15
Alignment explanation
Indices: 58962435--58962517 Score: 112
Period size: 15 Copynumber: 5.4 Consensus size: 15
58962425 GAAACTCTTT
58962435 TTTTTTCTTTTTTTC
1 TTTTTTCTTTTTTTC
58962450 TTTTTTCCTTTTTTTC
1 TTTTTT-CTTTTTTTC
*
58962466 TCTTTTCTTTTTTTC
1 TTTTTTCTTTTTTTC
*
58962481 TTCTTTCTTTTTTTC
1 TTTTTTCTTTTTTTC
* *
58962496 TTTTTTTCTTTCTCTC
1 -TTTTTTCTTTTTTTC
58962512 TTTTTT
1 TTTTTT
58962518 TCCTGGCCTG
Statistics
Matches: 60, Mismatches: 6, Indels: 4
0.86 0.09 0.06
Matches are distributed among these distances:
15 34 0.57
16 26 0.43
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (15 bp):
TTTTTTCTTTTTTTC
Found at i:58962632 original size:15 final size:14
Alignment explanation
Indices: 58962612--58962665 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 14
58962602 GGCCTGCTTC
*
58962612 TTTTTTCTGGGCTG
1 TTTTTTTTGGGCTG
58962626 TTTTTTTTTGGGTCT-
1 -TTTTTTTTGGG-CTG
58962641 TTTCTTTTTGGGCTG
1 TTT-TTTTTGGGCTG
58962656 CTTTTTTTTG
1 -TTTTTTTTG
58962666 CTTTGGTTTT
Statistics
Matches: 34, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
14 5 0.15
15 24 0.71
16 5 0.15
ACGTcount: A:0.00, C:0.11, G:0.22, T:0.67
Consensus pattern (14 bp):
TTTTTTTTGGGCTG
Found at i:58962680 original size:31 final size:33
Alignment explanation
Indices: 58962640--58962714 Score: 91
Period size: 31 Copynumber: 2.3 Consensus size: 33
58962630 TTTTTGGGTC
*
58962640 TTTTCTTTTTGGGCTGCTTT-TTTTTGCTTTG-G
1 TTTT-TTTTTGGGCTGATTTGTTTTTGCTTTGTG
**
58962672 TTTTTTTTTGGGCTGATTTGTTTTTTTTTTGTG
1 TTTTTTTTTGGGCTGATTTGTTTTTGCTTTGTG
58962705 TTGTTTTTTT
1 TT-TTTTTTT
58962715 TTAATTGTTT
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
31 14 0.38
32 13 0.35
33 3 0.08
34 7 0.19
ACGTcount: A:0.01, C:0.07, G:0.20, T:0.72
Consensus pattern (33 bp):
TTTTTTTTTGGGCTGATTTGTTTTTGCTTTGTG
Found at i:58962713 original size:14 final size:14
Alignment explanation
Indices: 58962690--58962730 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 14
58962680 TGGGCTGATT
58962690 TGTT-TTTTTTTTG
1 TGTTGTTTTTTTTG
58962703 TGTTGTTTTTTTT-
1 TGTTGTTTTTTTTG
*
58962716 TAATTGTTTTTTTTG
1 T-GTTGTTTTTTTTG
58962731 GGCTGTTGGG
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
13 5 0.21
14 19 0.79
ACGTcount: A:0.05, C:0.00, G:0.15, T:0.80
Consensus pattern (14 bp):
TGTTGTTTTTTTTG
Found at i:58962837 original size:3 final size:3
Alignment explanation
Indices: 58962831--58962865 Score: 61
Period size: 3 Copynumber: 11.3 Consensus size: 3
58962821 TTTTTTTTCT
58962831 TTC TTC TTC TTTC TTC TTC TTC TTC TTC TTC TTC T
1 TTC TTC TTC -TTC TTC TTC TTC TTC TTC TTC TTC T
58962866 CCTCCTACAC
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 28 0.90
4 3 0.10
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:58962842 original size:19 final size:19
Alignment explanation
Indices: 58962818--58962865 Score: 64
Period size: 19 Copynumber: 2.6 Consensus size: 19
58962808 TTAAATTTTT
*
58962818 TTCTTT-TTTTTCTTTCTTC
1 TTCTTTCTTCTTC-TTCTTC
58962837 TTCTTTCTTCTTCTTCTTC
1 TTCTTTCTTCTTCTTCTTC
58962856 TTC-TTCTTCT
1 TTCTTTCTTCT
58962866 CCTCCTACAC
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
18 7 0.26
19 15 0.56
20 5 0.19
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (19 bp):
TTCTTTCTTCTTCTTCTTC
Found at i:58962966 original size:10 final size:10
Alignment explanation
Indices: 58962931--58962980 Score: 59
Period size: 10 Copynumber: 5.2 Consensus size: 10
58962921 ACGCTGATAC
58962931 TCTT-TCTTT
1 TCTTCTCTTT
* *
58962940 TCTTCTCCTC
1 TCTTCTCTTT
58962950 T-TTCTCTTT
1 TCTTCTCTTT
58962959 TCTTCTCTTT
1 TCTTCTCTTT
*
58962969 TCTTCTTTTT
1 TCTTCTCTTT
58962979 TC
1 TC
58962981 CTTCGAAAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
9 11 0.32
10 23 0.68
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (10 bp):
TCTTCTCTTT
Found at i:58962978 original size:19 final size:19
Alignment explanation
Indices: 58962935--58962977 Score: 63
Period size: 19 Copynumber: 2.3 Consensus size: 19
58962925 TGATACTCTT
58962935 TCTTTTCTTCTCCTCTTTC
1 TCTTTTCTTCTCCTCTTTC
58962954 TCTTTTCTTCT-CT-TTTC
1 TCTTTTCTTCTCCTCTTTC
58962971 TTCTTTT
1 -TCTTTT
58962978 TTCCTTCGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 4 0.17
18 8 0.35
19 11 0.48
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (19 bp):
TCTTTTCTTCTCCTCTTTC
Found at i:58963262 original size:29 final size:30
Alignment explanation
Indices: 58963229--58963345 Score: 105
Period size: 30 Copynumber: 3.9 Consensus size: 30
58963219 TGTAATTTTT
*
58963229 AGAAAATTT-AGGATTAAAATGAAATTTAA
1 AGAAAATTTAAGGGTTAAAATGAAATTTAA
* * *
58963258 TGAAAGTTTAAGGGTCT-AAGTGAAATTTAA
1 AGAAAATTTAAGGGT-TAAAATGAAATTTAA
* *
58963288 AGAAAGTTTAAGGGTCAAAATGAAATTT-A
1 AGAAAATTTAAGGGTTAAAATGAAATTTAA
* * * *
58963317 GGAAAAGTTTAGGGGTCAAAATGTAATTT
1 AGAAAA-TTTAAGGGTTAAAATGAAATTT
58963346 TTATTTTTAA
Statistics
Matches: 73, Mismatches: 11, Indels: 7
0.80 0.12 0.08
Matches are distributed among these distances:
29 12 0.16
30 60 0.82
31 1 0.01
ACGTcount: A:0.45, C:0.03, G:0.21, T:0.31
Consensus pattern (30 bp):
AGAAAATTTAAGGGTTAAAATGAAATTTAA
Found at i:58963284 original size:30 final size:30
Alignment explanation
Indices: 58963244--58963345 Score: 134
Period size: 30 Copynumber: 3.4 Consensus size: 30
58963234 ATTTAGGATT
*
58963244 AAAATGAAATTTAATGAAAGTTTAAGGGTC
1 AAAATGAAATTTAAAGAAAGTTTAAGGGTC
* *
58963274 TAAGTGAAATTTAAAGAAAGTTTAAGGGTC
1 AAAATGAAATTTAAAGAAAGTTTAAGGGTC
* *
58963304 AAAATGAAATTT-AGGAAAAGTTTAGGGGTC
1 AAAATGAAATTTAAAG-AAAGTTTAAGGGTC
*
58963334 AAAATGTAATTT
1 AAAATGAAATTT
58963346 TTATTTTTAA
Statistics
Matches: 63, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
29 2 0.03
30 61 0.97
ACGTcount: A:0.45, C:0.03, G:0.22, T:0.30
Consensus pattern (30 bp):
AAAATGAAATTTAAAGAAAGTTTAAGGGTC
Found at i:58963345 original size:60 final size:59
Alignment explanation
Indices: 58963216--58963345 Score: 145
Period size: 60 Copynumber: 2.2 Consensus size: 59
58963206 TTCTGGGGCT
** * * *
58963216 AAATGTAATTTTTAGAAAATTTAGGATTAAAATGAAATTTAATGAAAGTTTAAGGGTCT
1 AAATGTAATTTAAAGAAAATTTAGGATCAAAATGAAATTTAAGGAAAGTTTAAGGGTCA
* * * * *
58963275 AAGTGAAATTTAAAGAAAGTTTAAGGGTCAAAATGAAATTT-AGGAAAAGTTTAGGGGTCA
1 AAATGTAATTTAAAGAAAATTT-AGGATCAAAATGAAATTTAAGG-AAAGTTTAAGGGTCA
58963335 AAATGTAATTT
1 AAATGTAATTT
58963346 TTATTTTTAA
Statistics
Matches: 57, Mismatches: 12, Indels: 3
0.79 0.17 0.04
Matches are distributed among these distances:
59 19 0.33
60 38 0.67
ACGTcount: A:0.45, C:0.02, G:0.20, T:0.33
Consensus pattern (59 bp):
AAATGTAATTTAAAGAAAATTTAGGATCAAAATGAAATTTAAGGAAAGTTTAAGGGTCA
Found at i:58963366 original size:14 final size:15
Alignment explanation
Indices: 58963341--58963375 Score: 54
Period size: 14 Copynumber: 2.4 Consensus size: 15
58963331 GTCAAAATGT
58963341 AATTTTTATTTTTAA
1 AATTTTTATTTTTAA
*
58963356 AATTTTT-TTTTTGA
1 AATTTTTATTTTTAA
58963370 AATTTT
1 AATTTT
58963376 GAAAATTAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 12 0.63
15 7 0.37
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.69
Consensus pattern (15 bp):
AATTTTTATTTTTAA
Found at i:58963584 original size:13 final size:13
Alignment explanation
Indices: 58963566--58963601 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
58963556 AATTGACTCT
* *
58963566 TTAAAACTAGACA
1 TTAAAAATAGAAA
58963579 TTAAAAATAGAAA
1 TTAAAAATAGAAA
58963592 TTAAAAATAG
1 TTAAAAATAG
58963602 CTCAGCACGT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.61, C:0.06, G:0.08, T:0.25
Consensus pattern (13 bp):
TTAAAAATAGAAA
Found at i:58963803 original size:54 final size:54
Alignment explanation
Indices: 58963617--58963887 Score: 410
Period size: 54 Copynumber: 5.1 Consensus size: 54
58963607 CACGTGAGCC
* * * *
58963617 AAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTG-AAAACAGAATTTGCAA
1 AAGGCTCAACTCACCTCTCGCAATATGAGTTGGTTTTTGAAAAATAGAAATT--AA
*
58963672 AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAAATAG--A--AA
1 AAGGCTCAACTCACCTCTCGCAATATGAGTTG-GTTTTTGAAAAATAGAAATTAA
58963723 AAGGCTCAACTCACCTCTCGCAATATGAGTTGGTTTTTGAAAAATAGAAATTAA
1 AAGGCTCAACTCACCTCTCGCAATATGAGTTGGTTTTTGAAAAATAGAAATTAA
58963777 AAGGCTCAACTCACCTCTCGCAATATGAGTTGGTTTTTGAAAAATAGAAATTAA
1 AAGGCTCAACTCACCTCTCGCAATATGAGTTGGTTTTTGAAAAATAGAAATTAA
*
58963831 AAGGCTCAACTCACCTCTCGCAATATGAGTT-GATTTTGAAAAATAGAAATTGAA
1 AAGGCTCAACTCACCTCTCGCAATATGAGTTGGTTTTTGAAAAATAGAAATT-AA
58963885 AAG
1 AAG
58963888 TAGAAATTGA
Statistics
Matches: 203, Mismatches: 6, Indels: 15
0.91 0.03 0.07
Matches are distributed among these distances:
50 14 0.07
51 34 0.17
52 1 0.00
53 19 0.09
54 92 0.45
55 31 0.15
56 6 0.03
57 6 0.03
ACGTcount: A:0.37, C:0.17, G:0.17, T:0.29
Consensus pattern (54 bp):
AAGGCTCAACTCACCTCTCGCAATATGAGTTGGTTTTTGAAAAATAGAAATTAA
Found at i:58963885 original size:14 final size:14
Alignment explanation
Indices: 58963866--58963900 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
58963856 TGAGTTGATT
58963866 TTGAAAAATAGAAA
1 TTGAAAAATAGAAA
*
58963880 TTGAAAAGTAGAAA
1 TTGAAAAATAGAAA
58963894 TTGAAAA
1 TTGAAAA
58963901 TACCTCAGCG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.60, C:0.00, G:0.17, T:0.23
Consensus pattern (14 bp):
TTGAAAAATAGAAA
Found at i:58964136 original size:85 final size:87
Alignment explanation
Indices: 58963992--58964239 Score: 308
Period size: 85 Copynumber: 2.8 Consensus size: 87
58963982 AACAGAAATT
* * *
58963992 AAAAACAGAATTTGAAAAAACCTCAGCGTGTGGCCTGAGACTCAACTCACCTCTTGCAATATGAG
1 AAAAACAGAAATTGAAAATACCTCAGC-TGTGGCCTGAGGCTCAACTCACCTCTTGCAATATGAG
*
58964057 TTGATTTGAAAAG-TAGAATT-AG
65 TTGATTTGAAAAGATAG-ATTGAA
* * * *
58964079 TAAAGCAGAAATTGAAAATACCTCAGC-GT-GCCTTGAGGCTCAACTCACCTCTCGCAATATAAG
1 AAAAACAGAAATTGAAAATACCTCAGCTGTGGCC-TGAGGCTCAACTCACCTCTTGCAATATGAG
58964142 TTGATTTTTGAAAAGCATAGATTGAA
65 TTGA--TTTGAAAAG-ATAGATTGAA
*
58964168 AAAAACATAAATTGAAAATACCTCAGCATGTGAGCC-GAGGCTCAACTCACCTCTTGCAATATGA
1 AAAAACAGAAATTGAAAATACCTCAGC-TGTG-GCCTGAGGCTCAACTCACCTCTTGCAATATGA
58964232 GTTGATTT
64 GTTGATTT
58964240 TTGAAAAACA
Statistics
Matches: 138, Mismatches: 13, Indels: 18
0.82 0.08 0.11
Matches are distributed among these distances:
84 3 0.02
85 33 0.24
87 32 0.23
88 3 0.02
89 31 0.22
91 33 0.24
93 3 0.02
ACGTcount: A:0.37, C:0.19, G:0.18, T:0.26
Consensus pattern (87 bp):
AAAAACAGAAATTGAAAATACCTCAGCTGTGGCCTGAGGCTCAACTCACCTCTTGCAATATGAGT
TGATTTGAAAAGATAGATTGAA
Found at i:58964185 original size:15 final size:16
Alignment explanation
Indices: 58964152--58964185 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
58964142 TTGATTTTTG
* *
58964152 AAAAGCATAGATTGAA
1 AAAAACATAAATTGAA
58964168 AAAAACATAAATTGAA
1 AAAAACATAAATTGAA
58964184 AA
1 AA
58964186 TACCTCAGCA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.65, C:0.06, G:0.12, T:0.18
Consensus pattern (16 bp):
AAAAACATAAATTGAA
Found at i:58964227 original size:91 final size:88
Alignment explanation
Indices: 58963992--58964246 Score: 324
Period size: 91 Copynumber: 2.9 Consensus size: 88
58963982 AACAGAAATT
* * *
58963992 AAAAACAGAATTTGAAAAAACCTCAGCGTGTGGCCTGAGACTCAACTCACCTCTTGCAATATGAG
1 AAAAACAGAAATTGAAAATACCTCAGC-TGTGGCCTGAGGCTCAACTCACCTCTTGCAATATGAG
*
58964057 TTGA--TTTGAAAAGTAGAATTAG
65 TTGATTTTTGAAAAGTAGAATTAA
* * * *
58964079 TAAAGCAGAAATTGAAAATACCTCAGC-GT-GCCTTGAGGCTCAACTCACCTCTCGCAATATAAG
1 AAAAACAGAAATTGAAAATACCTCAGCTGTGGCC-TGAGGCTCAACTCACCTCTTGCAATATGAG
58964142 TTGATTTTTGAAAAGCATAG-ATTGAA
65 TTGATTTTTGAAAAG--TAGAATT-AA
*
58964168 AAAAACATAAATTGAAAATACCTCAGCATGTGAGCC-GAGGCTCAACTCACCTCTTGCAATATGA
1 AAAAACAGAAATTGAAAATACCTCAGC-TGTG-GCCTGAGGCTCAACTCACCTCTTGCAATATGA
58964232 GTTGATTTTTGAAAA
64 GTTGATTTTTGAAAA
58964247 ACAAAAATTA
Statistics
Matches: 145, Mismatches: 13, Indels: 16
0.83 0.07 0.09
Matches are distributed among these distances:
84 3 0.02
85 33 0.23
87 32 0.22
88 3 0.02
89 28 0.19
91 43 0.30
93 3 0.02
ACGTcount: A:0.37, C:0.18, G:0.18, T:0.26
Consensus pattern (88 bp):
AAAAACAGAAATTGAAAATACCTCAGCTGTGGCCTGAGGCTCAACTCACCTCTTGCAATATGAGT
TGATTTTTGAAAAGTAGAATTAA
Found at i:58964688 original size:192 final size:192
Alignment explanation
Indices: 58964204--58965010 Score: 1488
Period size: 192 Copynumber: 4.2 Consensus size: 192
58964194 CATGTGAGCC
** *
58964204 GAGGCTCAACTCACCTCTTGCAATATGAGTTGATTTTTGAAAAACAAAAATTAAAAGGCTTAACT
1 GAGGCTCAACTCATTTCTCGCAATATGAGTTGA-TTTTGAAAAACAAAAATTAAAAGGCTTAACT
58964269 CACCTCTCGCAATATGAGTCAATTTAAAACATAAACTAAAAATACCTCGGCGTGCCCCGAGGCTC
65 CACCTCTCGCAATATGAGTCAATTTAAAACATAAACTAAAAATACCTCGGCGTGCCCCGAGGCTC
* ***
58964334 AACTCATTTCTCGCAATATGAGTTGATTTTTTTTTTAAATTTAAAAATACCTCAACGTGTCTT
130 AACTCACTTCTCGCAATATGAGTTGATTTTTTTAAAAAATTTAAAAATACCTCAACGTGTCTT
58964397 GATGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTGAAAAACAAAAATTAAAAGGCTTAACT
1 GA-GGCTCAACTCATTTCTCGCAATATGAGTTGATTTTGAAAAACAAAAATTAAAAGGCTTAACT
* *
58964462 CACCTCTCGCAACATGAGTCAATTTAAAACATAAACTAAACATACCTCGGCGTGCCCCGAGGCTC
65 CACCTCTCGCAATATGAGTCAATTTAAAACATAAACTAAAAATACCTCGGCGTGCCCCGAGGCTC
58964527 AACTCACTTCTCGCAATATGAGTTGATTTTTTTAAAAAATTTAAAAATACCTCAACGTGTCTT
130 AACTCACTTCTCGCAATATGAGTTGATTTTTTTAAAAAATTTAAAAATACCTCAACGTGTCTT
*
58964590 GAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTGAAAAACAAAAATTAAAAGACTTAACTC
1 GAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTGAAAAACAAAAATTAAAAGGCTTAACTC
*
58964655 ACCTCTCGCAATATGAGTCAATTTAAAACATAAACTAAAAATACCTCTGCGTGCCCCGAGGCTCA
66 ACCTCTCGCAATATGAGTCAATTTAAAACATAAACTAAAAATACCTCGGCGTGCCCCGAGGCTCA
*
58964720 ACTCACTTCTCGCAATATGAGTTGATTTTTTTTAAAAATTTAAAAATACCTCAACGTGTCTT
131 ACTCACTTCTCGCAATATGAGTTGATTTTTTTAAAAAATTTAAAAATACCTCAACGTGTCTT
58964782 GAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTGAAAAACAAAAATTAAAAGGCTTAACTC
1 GAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTGAAAAACAAAAATTAAAAGGCTTAACTC
58964847 ACCTCTCGCAATATGAGTCAATTTAAAACATAAACTAAAAATACCTCGGCGTGCCCCGAGGCTCA
66 ACCTCTCGCAATATGAGTCAATTTAAAACATAAACTAAAAATACCTCGGCGTGCCCCGAGGCTCA
58964912 ACTCACTTCTCGCAATATGAGTTGATTTTTTTAAAAAATTTAAAAATACCTCAACGTGTCTT
131 ACTCACTTCTCGCAATATGAGTTGATTTTTTTAAAAAATTTAAAAATACCTCAACGTGTCTT
58964974 GAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTT
1 GAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTT
58965011 CCTTGGAAAG
Statistics
Matches: 596, Mismatches: 17, Indels: 3
0.97 0.03 0.00
Matches are distributed among these distances:
192 411 0.69
193 157 0.26
194 28 0.05
ACGTcount: A:0.35, C:0.21, G:0.14, T:0.31
Consensus pattern (192 bp):
GAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTGAAAAACAAAAATTAAAAGGCTTAACTC
ACCTCTCGCAATATGAGTCAATTTAAAACATAAACTAAAAATACCTCGGCGTGCCCCGAGGCTCA
ACTCACTTCTCGCAATATGAGTTGATTTTTTTAAAAAATTTAAAAATACCTCAACGTGTCTT
Found at i:58975410 original size:15 final size:15
Alignment explanation
Indices: 58975390--58975442 Score: 52
Period size: 15 Copynumber: 3.3 Consensus size: 15
58975380 ACTTTTTCCT
58975390 TTTTTTAAACACGAA
1 TTTTTTAAACACGAA
*
58975405 TTTTTTAAAATACAAGAA
1 TTTTTT--AA-ACACGAA
**
58975423 TTTTAGAAACACGAA
1 TTTTTTAAACACGAA
58975438 TTTTT
1 TTTTT
58975443 AAAAAAAACA
Statistics
Matches: 30, Mismatches: 5, Indels: 6
0.73 0.12 0.15
Matches are distributed among these distances:
15 16 0.53
16 2 0.07
17 2 0.07
18 10 0.33
ACGTcount: A:0.42, C:0.09, G:0.08, T:0.42
Consensus pattern (15 bp):
TTTTTTAAACACGAA
Found at i:58975502 original size:17 final size:17
Alignment explanation
Indices: 58975448--58975798 Score: 203
Period size: 17 Copynumber: 19.9 Consensus size: 17
58975438 TTTTTAAAAA
58975448 AAACACGAAAA-TTTTG
1 AAACACGAAAATTTTTG
* *
58975464 AAACACGAGATTTCTTTG
1 AAACACGAAAATT-TTTG
*
58975482 AAACACGAAAATTTATG
1 AAACACGAAAATTTTTG
** *
58975499 AAACACGGTCAATTTCTTA
1 AAACAC-GAAAATTT-TTG
* *
58975518 AAACGCGAAAGTTTTTG
1 AAACACGAAAATTTTTG
* **
58975535 AAAAACGGGAATTTTTTTTTG
1 AAACAC--GAA--AATTTTTG
*
58975556 AAACACGAAAAATTTTG
1 AAACACGAAAATTTTTG
*
58975573 AAACACTG-GAA-TTTTG
1 AAACAC-GAAAATTTTTG
** *
58975589 AAAACACGAGGATTTTTT
1 -AAACACGAAAATTTTTG
* *
58975607 AAATACGAAAA-ATTTG
1 AAACACGAAAATTTTTG
*
58975623 AAAACAAGAAAATTTTTG
1 -AAACACGAAAATTTTTG
* *
58975641 AAATACGAAAATTTTAG
1 AAACACGAAAATTTTTG
58975658 AAACACGAAAATTTTTG
1 AAACACGAAAATTTTTG
*
58975675 AAACAC-AGAAGTTTTTAG
1 AAACACGA-AAATTTTT-G
*
58975693 AAAACACGAAAAATTTTG
1 -AAACACGAAAATTTTTG
* **
58975711 AAA-ATTGGAATTTTTTTG
1 AAACA--CGAAAATTTTTG
*
58975729 AAAACACGAGAATTTTTG
1 -AAACACGAAAATTTTTG
*
58975747 AAAAACATGAAAATTTTTG
1 --AAACACGAAAATTTTTG
* *
58975766 CAACACG-GAATTTTTG
1 AAACACGAAAATTTTTG
58975782 AAAACACGAAAAATTTT
1 -AAACACG-AAAATTTT
58975799 CCGATTTTTT
Statistics
Matches: 253, Mismatches: 56, Indels: 49
0.71 0.16 0.14
Matches are distributed among these distances:
16 28 0.11
17 110 0.43
18 53 0.21
19 49 0.19
20 2 0.01
21 11 0.04
ACGTcount: A:0.45, C:0.11, G:0.14, T:0.30
Consensus pattern (17 bp):
AAACACGAAAATTTTTG
Found at i:58975537 original size:36 final size:37
Alignment explanation
Indices: 58975447--58975542 Score: 94
Period size: 36 Copynumber: 2.7 Consensus size: 37
58975437 ATTTTTAAAA
*
58975447 AAAACACGAAAATTT-TGAAACAC-G--AGATTTCTTT
1 AAAACACGAAAATTTATGAAAAACGGTCA-ATTTCTTT
* *
58975481 GAAACACGAAAATTTATGAAACACGGTCAATTTC-TT
1 AAAACACGAAAATTTATGAAAAACGGTCAATTTCTTT
* * *
58975517 AAAACGCGAAAGTTTTTGAAAAACGG
1 AAAACACGAAAATTTATGAAAAACGG
58975543 GAATTTTTTT
Statistics
Matches: 52, Mismatches: 6, Indels: 6
0.81 0.09 0.09
Matches are distributed among these distances:
34 14 0.27
35 8 0.15
36 24 0.46
37 5 0.10
38 1 0.02
ACGTcount: A:0.44, C:0.15, G:0.16, T:0.26
Consensus pattern (37 bp):
AAAACACGAAAATTTATGAAAAACGGTCAATTTCTTT
Found at i:58975571 original size:21 final size:21
Alignment explanation
Indices: 58975529--58975571 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
58975519 AACGCGAAAG
** *
58975529 TTTTTGAAAAACGGGAATTTT
1 TTTTTGAAAAACGAAAAATTT
*
58975550 TTTTTGAAACACGAAAAATTT
1 TTTTTGAAAAACGAAAAATTT
58975571 T
1 T
58975572 GAAACACTGG
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.37, C:0.07, G:0.14, T:0.42
Consensus pattern (21 bp):
TTTTTGAAAAACGAAAAATTT
Found at i:58975759 original size:55 final size:54
Alignment explanation
Indices: 58975667--58975790 Score: 141
Period size: 55 Copynumber: 2.3 Consensus size: 54
58975657 GAAACACGAA
*
58975667 AATTTTTG-AAACAC-AGAAGTTTTTAGAAAACACGAAAAATTTTG-AAAATTGG
1 AATTTTTGAAAACACGAGAAGTTTTTAGAAAACACGAAAAATTTTGCAAAA-CGG
* * *
58975719 AATTTTTTTGAAAACACGAGAA-TTTTT-GAAAAACATGAAAATTTTTGCAACACGG
1 AA--TTTTTGAAAACACGAGAAGTTTTTAG-AAAACACGAAAAATTTTGCAAAACGG
58975774 AATTTTTGAAAACACGA
1 AATTTTTGAAAACACGA
58975791 AAAATTTTCC
Statistics
Matches: 62, Mismatches: 4, Indels: 11
0.81 0.05 0.14
Matches are distributed among these distances:
52 2 0.03
53 15 0.24
54 7 0.11
55 31 0.50
56 7 0.11
ACGTcount: A:0.44, C:0.10, G:0.15, T:0.31
Consensus pattern (54 bp):
AATTTTTGAAAACACGAGAAGTTTTTAGAAAACACGAAAAATTTTGCAAAACGG
Found at i:58975930 original size:21 final size:20
Alignment explanation
Indices: 58975904--58975945 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 20
58975894 TGTTACCTTA
58975904 TTTTTGAAAACACGAGAAATT
1 TTTTTGAAAACACGA-AAATT
*
58975925 TTTTTGAAGACACGAAAATT
1 TTTTTGAAAACACGAAAATT
58975945 T
1 T
58975946 CGAAACCCGA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 6 0.30
21 14 0.70
ACGTcount: A:0.40, C:0.10, G:0.14, T:0.36
Consensus pattern (20 bp):
TTTTTGAAAACACGAAAATT
Found at i:58976320 original size:8 final size:8
Alignment explanation
Indices: 58976307--58976376 Score: 90
Period size: 8 Copynumber: 9.0 Consensus size: 8
58976297 TTGAAACTCT
58976307 TTTTTTTC
1 TTTTTTTC
58976315 TTTTTTTC
1 TTTTTTTC
*
58976323 -TCTTTTC
1 TTTTTTTC
58976330 TTTTTTTC
1 TTTTTTTC
*
58976338 -TTCTTTC
1 TTTTTTTC
58976345 TTTTTTTC
1 TTTTTTTC
58976353 TTTTTTTC
1 TTTTTTTC
* *
58976361 TTTCTCTC
1 TTTTTTTC
58976369 TTTTTTTC
1 TTTTTTTC
58976377 CTGGCCTGCT
Statistics
Matches: 52, Mismatches: 8, Indels: 4
0.81 0.12 0.06
Matches are distributed among these distances:
7 12 0.23
8 40 0.77
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (8 bp):
TTTTTTTC
Found at i:58976337 original size:23 final size:22
Alignment explanation
Indices: 58976309--58976376 Score: 61
Period size: 21 Copynumber: 3.0 Consensus size: 22
58976299 GAAACTCTTT
58976309 TTTTTCTTTTTTTCTCTTTTCTT-
1 TTTTTCTTTTTTTCT-TTTT-TTC
*
58976332 TTTTTC-TTCTTTCTTTTTTTC
1 TTTTTCTTTTTTTCTTTTTTTC
58976353 TTTTT-TTCTTTCTCTCTTTTTTTC
1 TTTTTCTT-TTT-T-TCTTTTTTTC
58976377 CTGGCCTGCT
Statistics
Matches: 38, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
20 2 0.05
21 10 0.26
22 9 0.24
23 7 0.18
24 10 0.26
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (22 bp):
TTTTTCTTTTTTTCTTTTTTTC
Found at i:58976372 original size:15 final size:15
Alignment explanation
Indices: 58976308--58976374 Score: 89
Period size: 15 Copynumber: 4.4 Consensus size: 15
58976298 TGAAACTCTT
58976308 TTTTTTCTTTTTTTC
1 TTTTTTCTTTTTTTC
*
58976323 TCTTTTCTTTTTTTC
1 TTTTTTCTTTTTTTC
*
58976338 TTCTTTCTTTTTTTC
1 TTTTTTCTTTTTTTC
* *
58976353 TTTTTTTCTTTCTCTC
1 -TTTTTTCTTTTTTTC
58976369 TTTTTT
1 TTTTTT
58976375 TCCTGGCCTG
Statistics
Matches: 45, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
15 33 0.73
16 12 0.27
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (15 bp):
TTTTTTCTTTTTTTC
Found at i:58976489 original size:15 final size:15
Alignment explanation
Indices: 58976468--58976522 Score: 51
Period size: 15 Copynumber: 3.6 Consensus size: 15
58976458 TGGCCTGCTT
*
58976468 CTTTTTTCTGGGCTG
1 CTTTTTTTTGGGCTG
*
58976483 TTTTTTTTTTGGGC--
1 -CTTTTTTTTGGGCTG
58976497 CTTTTCTTTTTGGGCTG
1 C-TTT-TTTTTGGGCTG
58976514 CTTTTTTTT
1 CTTTTTTTT
58976523 TGCTTTGGTT
Statistics
Matches: 32, Mismatches: 3, Indels: 9
0.73 0.07 0.20
Matches are distributed among these distances:
14 3 0.09
15 14 0.44
16 14 0.44
17 1 0.03
ACGTcount: A:0.00, C:0.15, G:0.20, T:0.65
Consensus pattern (15 bp):
CTTTTTTTTGGGCTG
Found at i:58976491 original size:17 final size:16
Alignment explanation
Indices: 58976469--58976558 Score: 83
Period size: 16 Copynumber: 5.5 Consensus size: 16
58976459 GGCCTGCTTC
*
58976469 TTTTTTCTGGGCTGTT
1 TTTTTTTTGGGCTGTT
*
58976485 TTTTTTTTGGGC-CTT
1 TTTTTTTTGGGCTGTT
* *
58976500 TTCTTTTTGGGCTGCT
1 TTTTTTTTGGGCTGTT
***
58976516 TTTTTTTTGCTTTGGTT
1 TTTTTTTTGGGCT-GTT
58976533 TTTTTTTTGGGCTGATT
1 TTTTTTTTGGGCTG-TT
58976550 TGTTTTTTT
1 T-TTTTTTT
58976559 TTGTGTTGTT
Statistics
Matches: 57, Mismatches: 13, Indels: 6
0.75 0.17 0.08
Matches are distributed among these distances:
15 13 0.23
16 22 0.39
17 15 0.26
18 7 0.12
ACGTcount: A:0.01, C:0.10, G:0.21, T:0.68
Consensus pattern (16 bp):
TTTTTTTTGGGCTGTT
Found at i:58976571 original size:33 final size:32
Alignment explanation
Indices: 58976503--58976573 Score: 90
Period size: 33 Copynumber: 2.2 Consensus size: 32
58976493 GGGCCTTTTC
* *
58976503 TTTTTGGGCTGCTTTTTTTTTGCTTTGGTTTTT
1 TTTTTGGGCTGATTTTTTTTT-CTTTGGTTGTT
58976536 TTTTTGGGCTGATTTGTTTTTT-TTTGTGTTGTT
1 TTTTTGGGCTGATTT-TTTTTTCTTTG-GTTGTT
58976569 TTTTT
1 TTTTT
58976574 TAATTAATTT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
32 4 0.12
33 24 0.71
34 6 0.18
ACGTcount: A:0.01, C:0.06, G:0.21, T:0.72
Consensus pattern (32 bp):
TTTTTGGGCTGATTTTTTTTTCTTTGGTTGTT
Found at i:58976572 original size:17 final size:17
Alignment explanation
Indices: 58976515--58976574 Score: 50
Period size: 17 Copynumber: 3.4 Consensus size: 17
58976505 TTTGGGCTGC
*
58976515 TTTTTTTTTGCT-TTGGT
1 TTTTTTTTTG-TGTTGTT
* *
58976532 TTTTTTTTTGGGCTGATTT
1 TTTTTTTTTGTGTTG--TT
58976551 GTTTTTTTTTGTGTTGTT
1 -TTTTTTTTTGTGTTGTT
58976569 TTTTTT
1 TTTTTT
58976575 AATTAATTTT
Statistics
Matches: 34, Mismatches: 5, Indels: 8
0.72 0.11 0.17
Matches are distributed among these distances:
17 18 0.53
18 2 0.06
19 1 0.03
20 13 0.38
ACGTcount: A:0.02, C:0.03, G:0.18, T:0.77
Consensus pattern (17 bp):
TTTTTTTTTGTGTTGTT
Found at i:58976684 original size:7 final size:7
Alignment explanation
Indices: 58976676--58976725 Score: 54
Period size: 7 Copynumber: 7.6 Consensus size: 7
58976666 TTAAATTTTT
58976676 TTCTTT-
1 TTCTTTC
*
58976682 TTTTTTC
1 TTCTTTC
58976689 TT-TCTTC
1 TTCT-TTC
58976696 TTCTTTC
1 TTCTTTC
58976703 TTCTTTC
1 TTCTTTC
58976710 TTC-TTC
1 TTCTTTC
58976716 TTC-TTC
1 TTCTTTC
58976722 TTCT
1 TTCT
58976726 CCTCCTACAC
Statistics
Matches: 39, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
6 18 0.46
7 20 0.51
8 1 0.03
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (7 bp):
TTCTTTC
Found at i:58976696 original size:3 final size:3
Alignment explanation
Indices: 58976690--58976725 Score: 54
Period size: 3 Copynumber: 11.3 Consensus size: 3
58976680 TTTTTTTTCT
58976690 TTC TTC TTC TTTC TTC TTTC TTC TTC TTC TTC TTC T
1 TTC TTC TTC -TTC TTC -TTC TTC TTC TTC TTC TTC T
58976726 CCTCCTACAC
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
3 25 0.81
4 6 0.19
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:58976706 original size:17 final size:17
Alignment explanation
Indices: 58976676--58976723 Score: 71
Period size: 17 Copynumber: 2.9 Consensus size: 17
58976666 TTAAATTTTT
* *
58976676 TTCTTTTTTTTTCTTTC
1 TTCTTCTTTCTTCTTTC
58976693 TTCTTCTTTCTTCTTTC
1 TTCTTCTTTCTTCTTTC
58976710 TTCTTC-TTCTTCTT
1 TTCTTCTTTCTTCTT
58976724 CTCCTCCTAC
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
16 8 0.28
17 21 0.72
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (17 bp):
TTCTTCTTTCTTCTTTC
Found at i:58976713 original size:10 final size:10
Alignment explanation
Indices: 58976676--58976725 Score: 59
Period size: 10 Copynumber: 5.1 Consensus size: 10
58976666 TTAAATTTTT
* *
58976676 TTCTTTTTTT
1 TTCTTTCTTC
58976686 TTCTTTCTTC
1 TTCTTTCTTC
58976696 TTCTTTCTTC
1 TTCTTTCTTC
58976706 TT-TCTTCTTC
1 TTCT-TTCTTC
58976716 TTC-TTCTTC
1 TTCTTTCTTC
58976725 T
1 T
58976726 CCTCCTACAC
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
9 8 0.22
10 28 0.78
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (10 bp):
TTCTTTCTTC
Found at i:58976826 original size:10 final size:10
Alignment explanation
Indices: 58976791--58976840 Score: 59
Period size: 10 Copynumber: 5.2 Consensus size: 10
58976781 ACGCCGGTAC
58976791 TCTT-TCTTT
1 TCTTCTCTTT
* *
58976800 TCTTCTCCTC
1 TCTTCTCTTT
58976810 T-TTCTCTTT
1 TCTTCTCTTT
58976819 TCTTCTCTTT
1 TCTTCTCTTT
*
58976829 TCTTCTTTTT
1 TCTTCTCTTT
58976839 TC
1 TC
58976841 CTTCAAAAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
9 11 0.32
10 23 0.68
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (10 bp):
TCTTCTCTTT
Found at i:58976838 original size:19 final size:19
Alignment explanation
Indices: 58976795--58976837 Score: 63
Period size: 19 Copynumber: 2.3 Consensus size: 19
58976785 CGGTACTCTT
58976795 TCTTTTCTTCTCCTCTTTC
1 TCTTTTCTTCTCCTCTTTC
58976814 TCTTTTCTTCT-CT-TTTC
1 TCTTTTCTTCTCCTCTTTC
58976831 TTCTTTT
1 -TCTTTT
58976838 TTCCTTCAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 4 0.17
18 8 0.35
19 11 0.48
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (19 bp):
TCTTTTCTTCTCCTCTTTC
Done.