Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D03
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: 53248092
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1300000 characters in sequence are not A, C, G, or T
File 98 of 175
Found at i:31296033 original size:23 final size:23
Alignment explanation
Indices: 31295993--31296039 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 23
31295983 ACTCGCATAC
*
31295993 ACAAAGAAAATAATAAACCAAAT
1 ACAAAGAAAATAAAAAACCAAAT
31296016 ACAAA-AAAATATAAAAACCAAAT
1 ACAAAGAAAATA-AAAAACCAAAT
31296039 A
1 A
31296040 AATAAAGCCC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 6 0.27
23 16 0.73
ACGTcount: A:0.72, C:0.13, G:0.02, T:0.13
Consensus pattern (23 bp):
ACAAAGAAAATAAAAAACCAAAT
Found at i:31297373 original size:3 final size:3
Alignment explanation
Indices: 31297365--31297405 Score: 57
Period size: 3 Copynumber: 14.0 Consensus size: 3
31297355 ACTTCGTTAA
* *
31297365 TAT TAT TAT TAC TAT TAT TAT TTT TAT TAT TAT TAT T-T TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
31297406 AGTTTTCATT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
2 2 0.06
3 31 0.94
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:31301711 original size:20 final size:20
Alignment explanation
Indices: 31301662--31301712 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
31301652 CCTGGAGCAA
*
31301662 ATTTGACTTGTTTGAAAATC
1 ATTTGACTTGGTTGAAAATC
*
31301682 ATTTTAACTTGGTT-AAAATC
1 A-TTTGACTTGGTTGAAAATC
31301702 ATTTGCACTTG
1 ATTTG-ACTTG
31301713 ATTTTAAAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
19 3 0.12
20 13 0.50
21 10 0.38
ACGTcount: A:0.29, C:0.12, G:0.14, T:0.45
Consensus pattern (20 bp):
ATTTGACTTGGTTGAAAATC
Found at i:31304971 original size:15 final size:15
Alignment explanation
Indices: 31304951--31304981 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
31304941 GAATCTCTAT
31304951 TTTTTCTTCTTCTTC
1 TTTTTCTTCTTCTTC
31304966 TTTTTCTTCTTCTTC
1 TTTTTCTTCTTCTTC
31304981 T
1 T
31304982 ACTGTCTAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (15 bp):
TTTTTCTTCTTCTTC
Found at i:31316691 original size:50 final size:50
Alignment explanation
Indices: 31316634--31316735 Score: 204
Period size: 50 Copynumber: 2.0 Consensus size: 50
31316624 TAATTGACAC
31316634 GTATTTGATATTTTAGGTAATAAAGAAAAAGGTATGAGACGGTGAGGTTT
1 GTATTTGATATTTTAGGTAATAAAGAAAAAGGTATGAGACGGTGAGGTTT
31316684 GTATTTGATATTTTAGGTAATAAAGAAAAAGGTATGAGACGGTGAGGTTT
1 GTATTTGATATTTTAGGTAATAAAGAAAAAGGTATGAGACGGTGAGGTTT
31316734 GT
1 GT
31316736 GCGAAGAGAC
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 52 1.00
ACGTcount: A:0.35, C:0.02, G:0.28, T:0.34
Consensus pattern (50 bp):
GTATTTGATATTTTAGGTAATAAAGAAAAAGGTATGAGACGGTGAGGTTT
Found at i:31322930 original size:125 final size:124
Alignment explanation
Indices: 31322741--31322978 Score: 354
Period size: 125 Copynumber: 1.9 Consensus size: 124
31322731 AAATAGTGGG
** * * * * *
31322741 AAATCGCTTCTACTAGGATGTTATTTAAGAAGAAATTGTGAAATAGTGGCCTCGTGGACGCGATT
1 AAATCGCTGATACCAGGATGCTATATAAGAAGAAATTGTGAAATAGCGCCCTCGTGGACGCGATT
31322806 TCGCTACAG-TGGTCATGT-GAGAAATAATTTTTTTTTGACGTTTTCTGAGGAAATAGTATA
66 TCGCTACAGTTGGTCATGTAG-GAAATAA-TTTTTTTTGACG-TTTCTGAGGAAATAGTATA
* *
31322866 AAATCGCTGATACCAGGATGCTATATGAGAAGAAATTGTGAAATCGCGCCCTCGTGGACGCGATT
1 AAATCGCTGATACCAGGATGCTATATAAGAAGAAATTGTGAAATAGCGCCCTCGTGGACGCGATT
31322931 TCGCTACAGTTGGTCATGTAGGAAATAATTTTTTTTGACGTTTCTGAG
66 TCGCTACAGTTGGTCATGTAGGAAATAATTTTTTTTGACGTTTCTGAG
31322979 CAAACAGTGT
Statistics
Matches: 102, Mismatches: 9, Indels: 5
0.88 0.08 0.04
Matches are distributed among these distances:
124 8 0.08
125 77 0.75
126 16 0.16
127 1 0.01
ACGTcount: A:0.29, C:0.14, G:0.24, T:0.33
Consensus pattern (124 bp):
AAATCGCTGATACCAGGATGCTATATAAGAAGAAATTGTGAAATAGCGCCCTCGTGGACGCGATT
TCGCTACAGTTGGTCATGTAGGAAATAATTTTTTTTGACGTTTCTGAGGAAATAGTATA
Found at i:31323897 original size:18 final size:16
Alignment explanation
Indices: 31323868--31323916 Score: 53
Period size: 16 Copynumber: 2.9 Consensus size: 16
31323858 GCCATTGTTG
*
31323868 AAAATATTAAAATTTA
1 AAAATTTTAAAATTTA
**
31323884 AAAATTATTTAAAAAATA
1 AAAA-T-TTTAAAATTTA
31323902 AAAATTTTAAAATTT
1 AAAATTTTAAAATTT
31323917 CTTAAAAATG
Statistics
Matches: 26, Mismatches: 5, Indels: 4
0.74 0.14 0.11
Matches are distributed among these distances:
16 12 0.46
17 2 0.08
18 12 0.46
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (16 bp):
AAAATTTTAAAATTTA
Found at i:31323997 original size:22 final size:22
Alignment explanation
Indices: 31323967--31324008 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
31323957 ATTTGGAGAT
*
31323967 TTTTTGAAGGAAATTGAGAGGA
1 TTTTGGAAGGAAATTGAGAGGA
*
31323989 TTTTGGAAGGAATTTGAGAG
1 TTTTGGAAGGAAATTGAGAG
31324009 TTTGAGAGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.33, C:0.00, G:0.33, T:0.33
Consensus pattern (22 bp):
TTTTGGAAGGAAATTGAGAGGA
Found at i:31324090 original size:22 final size:22
Alignment explanation
Indices: 31324010--31324093 Score: 118
Period size: 22 Copynumber: 3.9 Consensus size: 22
31324000 ATTTGAGAGT
*
31324010 TTGAGAG-AATTTTGGAAGGAA
1 TTGAGAGAAATTTTGAAAGGAA
*
31324031 TTGATG-GAAATTTTGAAGGGAA
1 TTGA-GAGAAATTTTGAAAGGAA
31324053 TTGAGAGAAATTTTGAAAGGAA
1 TTGAGAGAAATTTTGAAAGGAA
*
31324075 TTGAGAGAATTTTTGAAAG
1 TTGAGAGAAATTTTGAAAG
31324094 AAAATGATAT
Statistics
Matches: 56, Mismatches: 4, Indels: 5
0.86 0.06 0.08
Matches are distributed among these distances:
21 6 0.11
22 50 0.89
ACGTcount: A:0.39, C:0.00, G:0.30, T:0.31
Consensus pattern (22 bp):
TTGAGAGAAATTTTGAAAGGAA
Found at i:31336358 original size:23 final size:23
Alignment explanation
Indices: 31336328--31336376 Score: 89
Period size: 23 Copynumber: 2.1 Consensus size: 23
31336318 TTCGAAGGTT
31336328 AACCAACCTCATGGAAATCAACC
1 AACCAACCTCATGGAAATCAACC
*
31336351 AACCAACCTCATGGAAATTAACC
1 AACCAACCTCATGGAAATCAACC
31336374 AAC
1 AAC
31336377 TACTGTCTGT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.45, C:0.33, G:0.08, T:0.14
Consensus pattern (23 bp):
AACCAACCTCATGGAAATCAACC
Found at i:31338839 original size:21 final size:21
Alignment explanation
Indices: 31338815--31338902 Score: 79
Period size: 21 Copynumber: 4.2 Consensus size: 21
31338805 AGCTTTCACA
* *
31338815 AGTTTCTGTTTAACTCATATG
1 AGTTTCCGTTTAACTCTTATG
31338836 AGTTTCCGTTTAAC-CTTATG
1 AGTTTCCGTTTAACTCTTATG
* * * *
31338856 GGTTTCCGTTCAGCTCTTTTG
1 AGTTTCCGTTTAACTCTTATG
* * *
31338877 AGCTTCTGTTTAACCCTTATG
1 AGTTTCCGTTTAACTCTTATG
*
31338898 GGTTT
1 AGTTT
31338903 TCATTCAGCT
Statistics
Matches: 51, Mismatches: 15, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
20 16 0.31
21 35 0.69
ACGTcount: A:0.16, C:0.19, G:0.18, T:0.47
Consensus pattern (21 bp):
AGTTTCCGTTTAACTCTTATG
Found at i:31338902 original size:42 final size:42
Alignment explanation
Indices: 31338832--31338970 Score: 172
Period size: 42 Copynumber: 3.3 Consensus size: 42
31338822 GTTTAACTCA
* *
31338832 TATGAGTTTCCGTTTAA-CCTTATGGGTTTCCGTTCAGCTCT
1 TATGAGCTTCTGTTTAACCCTTATGGGTTTCCGTTCAGCTCT
* * *
31338873 TTTGAGCTTCTGTTTAACCCTTATGGGTTTTCATTCAGCTCT
1 TATGAGCTTCTGTTTAACCCTTATGGGTTTCCGTTCAGCTCT
* * * * *
31338915 TACGAGCTTTTGTTCAACCCTTACGGGTTTCCGTTTAGCTCT
1 TATGAGCTTCTGTTTAACCCTTATGGGTTTCCGTTCAGCTCT
*
31338957 CATGAGCTTCTGTT
1 TATGAGCTTCTGTT
31338971 CAGCCTTCGG
Statistics
Matches: 81, Mismatches: 16, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
41 14 0.17
42 67 0.83
ACGTcount: A:0.14, C:0.23, G:0.19, T:0.44
Consensus pattern (42 bp):
TATGAGCTTCTGTTTAACCCTTATGGGTTTCCGTTCAGCTCT
Found at i:31338930 original size:21 final size:21
Alignment explanation
Indices: 31338906--31338974 Score: 50
Period size: 21 Copynumber: 3.3 Consensus size: 21
31338896 TGGGTTTTCA
31338906 TTCAGCTCTTACGAGCTTTTG
1 TTCAGCTCTTACGAGCTTTTG
* * * *
31338927 TTCAACCCTTACG-GGTTTCCG
1 TTCAGCTCTTACGAGCTTT-TG
* * * *
31338948 TTTAGCTCTCATGAGCTTCTG
1 TTCAGCTCTTACGAGCTTTTG
31338969 TTCAGC
1 TTCAGC
31338975 CTTCGGGCTT
Statistics
Matches: 33, Mismatches: 13, Indels: 4
0.66 0.26 0.08
Matches are distributed among these distances:
20 4 0.12
21 26 0.79
22 3 0.09
ACGTcount: A:0.14, C:0.28, G:0.19, T:0.39
Consensus pattern (21 bp):
TTCAGCTCTTACGAGCTTTTG
Found at i:31345103 original size:77 final size:77
Alignment explanation
Indices: 31344976--31345137 Score: 306
Period size: 77 Copynumber: 2.1 Consensus size: 77
31344966 TGAGACAATC
*
31344976 TTAAAGTGTTATGTCAATAAAATTTTATATATTTCAAGTTCAAAGATTAAAATATATCTAATTGT
1 TTAAAGTGTTATGCCAATAAAATTTTATATATTTCAAGTTCAAAGATTAAAATATATCTAATTGT
31345041 CAAGTTCAATTA
66 CAAGTTCAATTA
31345053 TTAAAGTGTTATGCCAATAAAATTTTATATATTTCAAGTTCAAAGATTAAAATATATCTAATTGT
1 TTAAAGTGTTATGCCAATAAAATTTTATATATTTCAAGTTCAAAGATTAAAATATATCTAATTGT
*
31345118 CAAGTTTAATTA
66 CAAGTTCAATTA
31345130 TTAAAGTG
1 TTAAAGTG
31345138 GACAAAAAAT
Statistics
Matches: 83, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
77 83 1.00
ACGTcount: A:0.41, C:0.07, G:0.10, T:0.41
Consensus pattern (77 bp):
TTAAAGTGTTATGCCAATAAAATTTTATATATTTCAAGTTCAAAGATTAAAATATATCTAATTGT
CAAGTTCAATTA
Found at i:31345523 original size:24 final size:24
Alignment explanation
Indices: 31345496--31345573 Score: 58
Period size: 26 Copynumber: 3.3 Consensus size: 24
31345486 TATATATTTT
31345496 TTATTAAATTATATTTAATAATAA
1 TTATTAAATTATATTTAATAATAA
* *
31345520 TTATTTTAAATTAT-TATTAA-ATTAT
1 TTA--TTAAATTATAT-TTAATAATAA
* *
31345545 TTATT-ATTTATA-TTAATAAT-C
1 TTATTAAATTATATTTAATAATAA
31345566 TTATTAAA
1 TTATTAAA
31345574 ATTTAATAAC
Statistics
Matches: 42, Mismatches: 6, Indels: 14
0.68 0.10 0.23
Matches are distributed among these distances:
21 9 0.21
22 8 0.19
23 2 0.05
24 3 0.07
25 7 0.17
26 13 0.31
ACGTcount: A:0.44, C:0.01, G:0.00, T:0.55
Consensus pattern (24 bp):
TTATTAAATTATATTTAATAATAA
Found at i:31345537 original size:56 final size:57
Alignment explanation
Indices: 31345428--31345560 Score: 155
Period size: 56 Copynumber: 2.3 Consensus size: 57
31345418 TATATTATTA
* *
31345428 TATATTATGATTTTAGTAAATTAATATAAGAATAATTATATTAAGAATTTTATTAAAT
1 TATA-TATTATTTTATTAAATTAATATAAGAATAATTATATTAAGAATTTTATTAAAT
* * *
31345486 TATATATT-TTTTATTAAATTATATTTAATAATAATTAT-TTTA-AATTATTATTAAAT
1 TATATATTATTTTATTAAATTA-ATATAAGAATAATTATATTAAGAATT-TTATTAAAT
*
31345542 TATTTATTATTTATATTAA
1 TATATATTATTT-TATTAA
31345561 TAATCTTATT
Statistics
Matches: 65, Mismatches: 6, Indels: 8
0.82 0.08 0.10
Matches are distributed among these distances:
55 4 0.06
56 31 0.48
57 20 0.31
58 10 0.15
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (57 bp):
TATATATTATTTTATTAAATTAATATAAGAATAATTATATTAAGAATTTTATTAAAT
Found at i:31345545 original size:11 final size:11
Alignment explanation
Indices: 31345518--31345550 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
31345508 ATTTAATAAT
31345518 AATTATT-TTA
1 AATTATTATTA
31345528 AATTATTATTA
1 AATTATTATTA
31345539 AATTATTTATTA
1 AATTA-TTATTA
31345551 TTTATATTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
10 7 0.33
11 8 0.38
12 6 0.29
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (11 bp):
AATTATTATTA
Found at i:31345724 original size:44 final size:45
Alignment explanation
Indices: 31345675--31345764 Score: 112
Period size: 45 Copynumber: 2.0 Consensus size: 45
31345665 TCTCTATTCT
31345675 ATTCAACCAAACATAAT-AA-TACTATTACGCCTCTATTCCATTAC
1 ATTCAACCAAACA-AATGAATTACTATTACGCCTCTATTCCATTAC
* * ** *
31345719 ATTCAACTAAACAATTGAATTGTTATTACGCCTTTATTCCATTAC
1 ATTCAACCAAACAAATGAATTACTATTACGCCTCTATTCCATTAC
31345764 A
1 A
31345765 GCGAACCAAA
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
43 2 0.05
44 14 0.36
45 23 0.59
ACGTcount: A:0.37, C:0.23, G:0.04, T:0.36
Consensus pattern (45 bp):
ATTCAACCAAACAAATGAATTACTATTACGCCTCTATTCCATTAC
Found at i:31346439 original size:6 final size:6
Alignment explanation
Indices: 31346428--31346454 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
31346418 CAAAAGGTGA
31346428 AGAATC AGAATC AGAATC AGAATC AGA
1 AGAATC AGAATC AGAATC AGAATC AGA
31346455 GCAACATTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.52, C:0.15, G:0.19, T:0.15
Consensus pattern (6 bp):
AGAATC
Found at i:31354917 original size:5 final size:5
Alignment explanation
Indices: 31354907--31354934 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
31354897 GCATAAGTTA
31354907 TTTAT TTTAT TTTAT TTTAT TTTAT TTT
1 TTTAT TTTAT TTTAT TTTAT TTTAT TTT
31354935 TACATAATAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (5 bp):
TTTAT
Found at i:31367518 original size:19 final size:18
Alignment explanation
Indices: 31367502--31367537 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
31367492 TTATAAAATT
31367502 TATTTTAAAATTAAAAAA
1 TATTTTAAAATTAAAAAA
*
31367520 TATTTTTAAATTAAAAAA
1 TATTTTAAAATTAAAAAA
31367538 GTTATGTAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (18 bp):
TATTTTAAAATTAAAAAA
Found at i:31370620 original size:6 final size:6
Alignment explanation
Indices: 31370609--31370673 Score: 58
Period size: 7 Copynumber: 9.8 Consensus size: 6
31370599 TTAGATTTAT
* *
31370609 TTAAAA TTAAAA TATTAAA TTAAAA TTAAAA TTTAAAA TGTAAAA TAAAAAA
1 TTAAAA TTAAAA T-TAAAA TTAAAA TTAAAA -TTAAAA T-TAAAA T-TAAAA
31370661 TTATAATA TTAAA
1 TTA-AA-A TTAAA
31370674 TATTTAAATA
Statistics
Matches: 49, Mismatches: 5, Indels: 9
0.78 0.08 0.14
Matches are distributed among these distances:
6 19 0.39
7 26 0.53
8 4 0.08
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (6 bp):
TTAAAA
Found at i:31370630 original size:13 final size:12
Alignment explanation
Indices: 31370609--31370673 Score: 58
Period size: 13 Copynumber: 4.9 Consensus size: 12
31370599 TTAGATTTAT
31370609 TTAAAATTAAAA
1 TTAAAATTAAAA
*
31370621 TATTAAATTAAAA
1 T-TAAAATTAAAA
31370634 TTAAAATTTAAAA
1 TTAAAA-TTAAAA
*
31370647 TGTAAAATAAAAAA
1 T-TAAAAT-TAAAA
31370661 TTATAATATTAAA
1 TTA-AA-ATTAAA
31370674 TATTTAAATA
Statistics
Matches: 43, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
12 5 0.12
13 21 0.49
14 15 0.35
15 2 0.05
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (12 bp):
TTAAAATTAAAA
Found at i:31370633 original size:19 final size:19
Alignment explanation
Indices: 31370609--31370663 Score: 69
Period size: 19 Copynumber: 2.9 Consensus size: 19
31370599 TTAGATTTAT
31370609 TTAAAATTAAAATATTAAA
1 TTAAAATTAAAATATTAAA
31370628 TTAAAATTAAAAT-TTAAAA
1 TTAAAATTAAAATATT-AAA
*
31370647 TGTAAAA-TAAAAAATTA
1 T-TAAAATTAAAATATTA
31370664 TAATATTAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
18 2 0.06
19 23 0.72
20 7 0.22
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.35
Consensus pattern (19 bp):
TTAAAATTAAAATATTAAA
Found at i:31370644 original size:7 final size:7
Alignment explanation
Indices: 31370607--31370681 Score: 52
Period size: 7 Copynumber: 11.0 Consensus size: 7
31370597 AGTTAGATTT
31370607 ATTTAAA
1 ATTTAAA
31370614 A-TTAAA
1 ATTTAAA
31370620 ATATT-AA
1 AT-TTAAA
31370627 A-TTAAA
1 ATTTAAA
31370633 A-TTAAA
1 ATTTAAA
31370639 ATTTAAA
1 ATTTAAA
*
31370646 ATGTAAA
1 ATTTAAA
*
31370653 A-TAAAA
1 ATTTAAA
* *
31370659 AATTATA
1 ATTTAAA
31370666 ATATTAAA
1 AT-TTAAA
31370674 TATTTAAA
1 -ATTTAAA
31370682 TAATTAAAAA
Statistics
Matches: 54, Mismatches: 7, Indels: 13
0.73 0.09 0.18
Matches are distributed among these distances:
5 2 0.04
6 19 0.35
7 20 0.37
8 11 0.20
9 2 0.04
ACGTcount: A:0.61, C:0.00, G:0.01, T:0.37
Consensus pattern (7 bp):
ATTTAAA
Found at i:31371080 original size:22 final size:21
Alignment explanation
Indices: 31371047--31371090 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 21
31371037 ATTTTTATAA
*
31371047 AAAAATATTTTTA-AACATTTT
1 AAAAATAGTTTTACAA-ATTTT
31371068 AAAAATAAGTTTTACAAATTTT
1 AAAAAT-AGTTTTACAAATTTT
31371090 A
1 A
31371091 CAATTTTTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
21 6 0.30
22 12 0.60
23 2 0.10
ACGTcount: A:0.50, C:0.05, G:0.02, T:0.43
Consensus pattern (21 bp):
AAAAATAGTTTTACAAATTTT
Found at i:31371197 original size:13 final size:14
Alignment explanation
Indices: 31371163--31371195 Score: 66
Period size: 14 Copynumber: 2.4 Consensus size: 14
31371153 ATTTATTGTA
31371163 AATTTTATTTTTAT
1 AATTTTATTTTTAT
31371177 AATTTTATTTTTAT
1 AATTTTATTTTTAT
31371191 AATTT
1 AATTT
31371196 ATATATATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (14 bp):
AATTTTATTTTTAT
Found at i:31376169 original size:28 final size:27
Alignment explanation
Indices: 31376125--31376178 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
31376115 TTAACAAGAA
*
31376125 GACAAAAAAAACAAGAAA-AAAGAATTT
1 GACAAAAAAAAAAAGAAACAAA-AATTT
31376152 GACAAAAAAAAAAGAGAAACAAAAATT
1 GACAAAAAAAAAA-AGAAACAAAAATT
31376179 GACGTTCAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
27 12 0.50
28 9 0.38
29 3 0.12
ACGTcount: A:0.72, C:0.07, G:0.11, T:0.09
Consensus pattern (27 bp):
GACAAAAAAAAAAAGAAACAAAAATTT
Found at i:31376862 original size:7 final size:7
Alignment explanation
Indices: 31376850--31376901 Score: 86
Period size: 7 Copynumber: 7.4 Consensus size: 7
31376840 GTTATTACAT
31376850 TTTATTA
1 TTTATTA
31376857 TTTATTA
1 TTTATTA
31376864 TTTATTA
1 TTTATTA
31376871 TTTATTA
1 TTTATTA
31376878 TTTATTA
1 TTTATTA
*
31376885 TATATTA
1 TTTATTA
*
31376892 TATATTA
1 TTTATTA
31376899 TTT
1 TTT
31376902 TTAAACAAAC
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 43 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (7 bp):
TTTATTA
Found at i:31385861 original size:12 final size:15
Alignment explanation
Indices: 31385829--31385858 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
31385819 TATATTTTGT
31385829 ATAATTTCAAAAATA
1 ATAATTTCAAAAATA
31385844 ATAATTT-AAAAATA
1 ATAATTTCAAAAATA
31385858 A
1 A
31385859 ATTCCATGTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.53
15 7 0.47
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.33
Consensus pattern (15 bp):
ATAATTTCAAAAATA
Found at i:31390246 original size:24 final size:24
Alignment explanation
Indices: 31390218--31390277 Score: 75
Period size: 24 Copynumber: 2.5 Consensus size: 24
31390208 ATTAGGTAAG
**
31390218 TTTTAAATTATTTTTGAATTTTTA
1 TTTTAAATTATTTTTGAATTAGTA
**
31390242 TTTTATTTTATTTTTGAATTAGTA
1 TTTTAAATTATTTTTGAATTAGTA
*
31390266 ATTTAAATTATT
1 TTTTAAATTATT
31390278 ATGCAACTAA
Statistics
Matches: 29, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.30, C:0.00, G:0.05, T:0.65
Consensus pattern (24 bp):
TTTTAAATTATTTTTGAATTAGTA
Found at i:31392766 original size:22 final size:21
Alignment explanation
Indices: 31392736--31392777 Score: 66
Period size: 22 Copynumber: 2.0 Consensus size: 21
31392726 TTAGAAAAGT
31392736 AAAAATATATATATATATATA
1 AAAAATATATATATATATATA
*
31392757 AAAAAGTATATATATGTATAT
1 AAAAA-TATATATATATATAT
31392778 TATTTAAAAC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 5 0.26
22 14 0.74
ACGTcount: A:0.57, C:0.00, G:0.05, T:0.38
Consensus pattern (21 bp):
AAAAATATATATATATATATA
Found at i:31392771 original size:28 final size:27
Alignment explanation
Indices: 31392730--31392786 Score: 69
Period size: 28 Copynumber: 2.1 Consensus size: 27
31392720 TAAATGTTAG
31392730 AAAAGTAAAAATATATATATATATATAA
1 AAAAGTAAAAATATATATAT-TATATAA
* * * *
31392758 AAAAGTATATATATGTATATTATTTAA
1 AAAAGTAAAAATATATATATTATATAA
31392785 AA
1 AA
31392787 CATGCGTATA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
27 8 0.32
28 17 0.68
ACGTcount: A:0.58, C:0.00, G:0.05, T:0.37
Consensus pattern (27 bp):
AAAAGTAAAAATATATATATTATATAA
Found at i:31392814 original size:3 final size:3
Alignment explanation
Indices: 31392806--31392852 Score: 60
Period size: 3 Copynumber: 15.7 Consensus size: 3
31392796 ATATGTGCAG
* *
31392806 TAA TAA TAA TGA TAA TAT TAA TAA TAA TAA TAA TAA T-A TGAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA
31392851 TA
1 TA
31392853 TCAAAAAATA
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
2 2 0.05
3 34 0.89
4 2 0.05
ACGTcount: A:0.60, C:0.00, G:0.04, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:31394535 original size:92 final size:89
Alignment explanation
Indices: 31394374--31394639 Score: 338
Period size: 92 Copynumber: 3.0 Consensus size: 89
31394364 AAGACTTGTA
* *
31394374 TCTTCGATCTACTTCGCCACCAGTAT-GGAACGACAAGATCTGTTATCATTGATCTACTTCACGC
1 TCTTCGATCTACTTCACCACCAGTATGGGAA-GACAAGATCTGTTATCTTTGATCTACTTCACGC
* * *
31394438 TAGTACATGAAGACAAGATTTGTTT
65 CAGTACATGAAGACAAGATCTATTT
* * * * *
31394463 TCTCAGTCGATCTGCTTCACCACCAGTATGGGAAGGCTAGATTTGTTACCTTTGATCTACTTCAC
1 TCT---TCGATCTACTTCACCACCAGTATGGGAAGACAAGATCTGTTATCTTTGATCTACTTCAC
31394528 GCCAGTACATGAAGACAAGATCTATTT
63 GCCAGTACATGAAGACAAGATCTATTT
* * *
31394555 TCTTCGATCTACTCCACCACCAGTATGGGGAGACAAGATCTGCTT-TCTTCGATCTACTTCACGC
1 TCTTCGATCTACTTCACCACCAGTATGGGAAGACAAGATCTG-TTATCTTTGATCTACTTCACGC
* *
31394619 CAATACATGAGGACAAGATCT
65 CAGTACATGAAGACAAGATCT
31394640 GCTTTTTCAA
Statistics
Matches: 152, Mismatches: 20, Indels: 10
0.84 0.11 0.05
Matches are distributed among these distances:
89 72 0.47
90 2 0.01
92 74 0.49
93 4 0.03
ACGTcount: A:0.27, C:0.25, G:0.18, T:0.30
Consensus pattern (89 bp):
TCTTCGATCTACTTCACCACCAGTATGGGAAGACAAGATCTGTTATCTTTGATCTACTTCACGCC
AGTACATGAAGACAAGATCTATTT
Found at i:31394644 original size:44 final size:44
Alignment explanation
Indices: 31394405--31394644 Score: 159
Period size: 44 Copynumber: 5.3 Consensus size: 44
31394395 AGTATGGAAC
* *
31394405 GACAAGATCTG-TTATCATT-GATCTACTTCACGCTAGTACATGAA
1 GACAAGATCTGCTT-TC-TTCGATCTACTTCACGCCAGTACATGAG
* * * * ***
31394449 GACAAGATTTGTTTTCTCAGTCGATCTGCTTCACCACCAGTATGGGAAG
1 GACAAGATCTGCTTTCT---TCGATCTACTTCA-CGCCAGTACATG-AG
* * * * *
31394498 G-CTAGATTTG-TTACCTTTGATCTACTTCACGCCAGTACATGAA
1 GACAAGATCTGCTT-TCTTCGATCTACTTCACGCCAGTACATGAG
** * * *
31394541 GACAAGATCTATTTTCTTCGATCTACTCCACCACCAGT--ATGGGG
1 GACAAGATCTGCTTTCTTCGATCTACTTCA-CGCCAGTACAT-GAG
*
31394585 AGACAAGATCTGCTTTCTTCGATCTACTTCACGCCAATACATGAG
1 -GACAAGATCTGCTTTCTTCGATCTACTTCACGCCAGTACATGAG
31394630 GACAAGATCTGCTTT
1 GACAAGATCTGCTTT
31394645 TTCAATCAAT
Statistics
Matches: 149, Mismatches: 32, Indels: 30
0.71 0.15 0.14
Matches are distributed among these distances:
43 5 0.03
44 60 0.40
45 50 0.34
46 3 0.02
47 12 0.08
48 17 0.11
49 2 0.01
ACGTcount: A:0.27, C:0.24, G:0.18, T:0.31
Consensus pattern (44 bp):
GACAAGATCTGCTTTCTTCGATCTACTTCACGCCAGTACATGAG
Found at i:31394909 original size:100 final size:100
Alignment explanation
Indices: 31394805--31394989 Score: 293
Period size: 100 Copynumber: 1.9 Consensus size: 100
31394795 AATGTCGGGG
* * *
31394805 AAACCAGATCCGTCGTCGTGGCTTCAATCTGTTCCACCGCACCG-TTAGAGAAGTAAGA-TCTGC
1 AAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCCACCGCACCGCTAAG-GAAGTAAGATTC-GC
31394868 CGTTGTGGCTTCAATCTTTTTAATTGCAATATCAGGA
64 CGTTGTGGCTTCAATCTTTTTAATTGCAATATCAGGA
* *
31394905 AAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCCACTGCACTGCTAAGGAAGTAAGATTCGCCG
1 AAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCCACCGCACCGCTAAGGAAGTAAGATTCGCCG
31394970 TTGTGGCTTCAATCTTTTTA
66 TTGTGGCTTCAATCTTTTTA
31394990 CTTTTCAACC
Statistics
Matches: 78, Mismatches: 5, Indels: 4
0.90 0.06 0.05
Matches are distributed among these distances:
100 73 0.94
101 5 0.06
ACGTcount: A:0.24, C:0.25, G:0.21, T:0.30
Consensus pattern (100 bp):
AAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCCACCGCACCGCTAAGGAAGTAAGATTCGCCG
TTGTGGCTTCAATCTTTTTAATTGCAATATCAGGA
Found at i:31406853 original size:2 final size:2
Alignment explanation
Indices: 31406846--31406887 Score: 50
Period size: 2 Copynumber: 21.0 Consensus size: 2
31406836 GAAAAGTAAA
* *
31406846 AT AT AT AT AT AT AT AT AT AT AT A- AA AGT AT AT AT AT GT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT
31406888 TATTTAAAAC
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
1 1 0.03
2 33 0.94
3 1 0.03
ACGTcount: A:0.50, C:0.00, G:0.05, T:0.45
Consensus pattern (2 bp):
AT
Found at i:31406924 original size:3 final size:3
Alignment explanation
Indices: 31406916--31406965 Score: 66
Period size: 3 Copynumber: 16.7 Consensus size: 3
31406906 ATATGTGCAG
* *
31406916 TAA TAA TAA TGA TAA TAT TAA TAA TAA TAA TAA TAA TAA T-A TGAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA
31406961 TAA TA
1 TAA TA
31406966 TCAAAAAATA
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
2 2 0.05
3 37 0.90
4 2 0.05
ACGTcount: A:0.60, C:0.00, G:0.04, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:31408298 original size:20 final size:22
Alignment explanation
Indices: 31408258--31408299 Score: 61
Period size: 20 Copynumber: 2.0 Consensus size: 22
31408248 AAATTTAATA
*
31408258 TAATAAATATAATTTATTATTT
1 TAATAAATATAATTTAATATTT
31408280 TAATAAAT-T-ATTTAATATTT
1 TAATAAATATAATTTAATATTT
31408300 AAATTTTATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 10 0.53
21 1 0.05
22 8 0.42
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (22 bp):
TAATAAATATAATTTAATATTT
Found at i:31408363 original size:15 final size:15
Alignment explanation
Indices: 31408343--31408399 Score: 51
Period size: 15 Copynumber: 3.5 Consensus size: 15
31408333 ACTCAATATC
31408343 AATATTTTAATAATA
1 AATATTTTAATAATA
*
31408358 AATATTTATTACAATTATA
1 AATA-TT-TT--AATAATA
*
31408377 AATATATTAATAATA
1 AATATTTTAATAATA
*
31408392 AATGTTTT
1 AATATTTT
31408400 TAGTATAAAG
Statistics
Matches: 33, Mismatches: 5, Indels: 8
0.72 0.11 0.17
Matches are distributed among these distances:
15 16 0.48
16 2 0.06
17 4 0.12
18 1 0.03
19 10 0.30
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (15 bp):
AATATTTTAATAATA
Found at i:31409448 original size:96 final size:96
Alignment explanation
Indices: 31409251--31409473 Score: 261
Period size: 96 Copynumber: 2.3 Consensus size: 96
31409241 TTTAAAGGTC
* * * * * * *
31409251 ATGGCCAGACTACCCAATGCCACAGCCAAACTGGAAGCCATCACACCCATGGGCAGACTGTTCAA
1 ATGGGCAGACTGCCCAATGCCATAGCCAAACGGGAACCCACCACACCCATGGGCAGACTGTCCAA
* *
31409316 TGCCATGGCCAAACAGGAACCCTCCACGCCT
66 TGCCATGGCCAAACAGGAACCCACCACCCCT
* ** *
31409347 ATGGGCAGATTGTTCAATGCCATAGCCAAACGGGAACCCACCACACTCATGGGCAGACTG-CCAA
1 ATGGGCAGACTGCCCAATGCCATAGCCAAACGGGAACCCACCACACCCATGGGCAGACTGTCC-A
* * **
31409411 ATGCCATGGTCAAACCGGAAGTCACCACACCCT
65 ATGCCATGGCCAAACAGGAACCCACCAC-CCCT
31409444 -TGGGCAGACTGCCCAATGCCATAGCCAAAC
1 ATGGGCAGACTGCCCAATGCCATAGCCAAAC
31409474 CCCAGGACAC
Statistics
Matches: 105, Mismatches: 20, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
95 1 0.01
96 101 0.96
97 3 0.03
ACGTcount: A:0.30, C:0.34, G:0.21, T:0.14
Consensus pattern (96 bp):
ATGGGCAGACTGCCCAATGCCATAGCCAAACGGGAACCCACCACACCCATGGGCAGACTGTCCAA
TGCCATGGCCAAACAGGAACCCACCACCCCT
Found at i:31409474 original size:48 final size:48
Alignment explanation
Indices: 31409250--31409474 Score: 234
Period size: 48 Copynumber: 4.7 Consensus size: 48
31409240 CTTTAAAGGT
* * * * * *
31409250 CATGGCCAGACTACCCAATGCCACAGCCAAACTGGAAGCCATCACACC
1 CATGGGCAGACTGCCCAATGCCATAGCCAAACCGGAACCCACCACACC
** * * * *
31409298 CATGGGCAGACTGTTCAATGCCATGGCCAAACAGGAACCCTCCACGCC
1 CATGGGCAGACTGCCCAATGCCATAGCCAAACCGGAACCCACCACACC
* * ** * *
31409346 TATGGGCAGATTGTTCAATGCCATAGCCAAACGGGAACCCACCACACT
1 CATGGGCAGACTGCCCAATGCCATAGCCAAACCGGAACCCACCACACC
* * * **
31409394 CATGGGCAGACTGCCAAATGCCATGGTCAAACCGGAAGTCACCACACC
1 CATGGGCAGACTGCCCAATGCCATAGCCAAACCGGAACCCACCACACC
*
31409442 CTTGGGCAGACTGCCCAATGCCATAGCCAAACC
1 CATGGGCAGACTGCCCAATGCCATAGCCAAACC
31409475 CCAGGACACT
Statistics
Matches: 144, Mismatches: 33, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
48 144 1.00
ACGTcount: A:0.30, C:0.35, G:0.21, T:0.14
Consensus pattern (48 bp):
CATGGGCAGACTGCCCAATGCCATAGCCAAACCGGAACCCACCACACC
Found at i:31415099 original size:18 final size:18
Alignment explanation
Indices: 31415063--31415101 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 18
31415053 CAATCAATTC
31415063 AATTTTATAATTTAACAAT
1 AATTTTAT-ATTTAACAAT
31415082 AATTTTAT-TTTCAACAAT
1 AATTTTATATTT-AACAAT
31415100 AA
1 AA
31415102 ATATGAATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 3 0.16
18 8 0.42
19 8 0.42
ACGTcount: A:0.46, C:0.08, G:0.00, T:0.46
Consensus pattern (18 bp):
AATTTTATATTTAACAAT
Found at i:31416883 original size:13 final size:13
Alignment explanation
Indices: 31416865--31416890 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
31416855 CATTGGTAGC
31416865 ATGAAAAGATGAA
1 ATGAAAAGATGAA
31416878 ATGAAAAGATGAA
1 ATGAAAAGATGAA
31416891 GAGAATTCTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.62, C:0.00, G:0.23, T:0.15
Consensus pattern (13 bp):
ATGAAAAGATGAA
Found at i:31417722 original size:28 final size:28
Alignment explanation
Indices: 31417672--31417736 Score: 94
Period size: 28 Copynumber: 2.3 Consensus size: 28
31417662 AATGCATCTA
31417672 ATTTATATTACAAAGTTTGTATTTTTGC
1 ATTTATATTACAAAGTTTGTATTTTTGC
* * * *
31417700 ATTTATATTATAAATTTTTTATTTTTTC
1 ATTTATATTACAAAGTTTGTATTTTTGC
31417728 ATTTATATT
1 ATTTATATT
31417737 TTTGCATGTA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 33 1.00
ACGTcount: A:0.29, C:0.05, G:0.05, T:0.62
Consensus pattern (28 bp):
ATTTATATTACAAAGTTTGTATTTTTGC
Found at i:31420068 original size:17 final size:16
Alignment explanation
Indices: 31420037--31420070 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
31420027 AATGTAATAC
*
31420037 AAATAAGTATTACAAT
1 AAATAAGTATAACAAT
31420053 AAATATAGTATAACAAT
1 AAATA-AGTATAACAAT
31420070 A
1 A
31420071 TCATTACAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 5 0.31
17 11 0.69
ACGTcount: A:0.59, C:0.06, G:0.06, T:0.29
Consensus pattern (16 bp):
AAATAAGTATAACAAT
Found at i:31420620 original size:31 final size:31
Alignment explanation
Indices: 31420580--31420658 Score: 88
Period size: 31 Copynumber: 2.5 Consensus size: 31
31420570 TCTTTTTTTA
*
31420580 AACCCTAAACAAAA-CTCTCTAATCCTTTTCT
1 AACCCTAAACAAAATC-CCCTAATCCTTTTCT
* *
31420611 AACCTTAAACAAAATCCCCTAATCCTTTTTTT
1 AACCCTAAACAAAATCCCCTAATCC-TTTTCT
31420643 ATACCCTAATACAAAA
1 A-ACCCTAA-ACAAAA
31420659 CTTTTAAGCT
Statistics
Matches: 40, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
31 21 0.52
32 7 0.17
33 6 0.15
34 6 0.15
ACGTcount: A:0.39, C:0.29, G:0.00, T:0.32
Consensus pattern (31 bp):
AACCCTAAACAAAATCCCCTAATCCTTTTCT
Found at i:31420767 original size:19 final size:21
Alignment explanation
Indices: 31420745--31420789 Score: 51
Period size: 19 Copynumber: 2.2 Consensus size: 21
31420735 ATTTTTTCGG
*
31420745 TTCTCAT-TTCTTCTT-TCTC
1 TTCTCATCTTCTCCTTATCTC
31420764 TTCT-ATCTTCTCCTTCATCTC
1 TTCTCATCTTCTCCTT-ATCTC
31420785 TTCTC
1 TTCTC
31420790 TATTCTGCAA
Statistics
Matches: 21, Mismatches: 1, Indels: 5
0.78 0.04 0.19
Matches are distributed among these distances:
18 2 0.10
19 11 0.52
21 8 0.38
ACGTcount: A:0.07, C:0.36, G:0.00, T:0.58
Consensus pattern (21 bp):
TTCTCATCTTCTCCTTATCTC
Found at i:31422779 original size:17 final size:18
Alignment explanation
Indices: 31422745--31422790 Score: 64
Period size: 17 Copynumber: 2.8 Consensus size: 18
31422735 CCGTTATGTC
31422745 CGCGACCGCGA-C--AAA
1 CGCGACCGCGACCGAAAA
31422760 CGCGA-CGCGACCGAAAA
1 CGCGACCGCGACCGAAAA
31422777 CGCGACCGCGACCG
1 CGCGACCGCGACCG
31422791 CAATTTAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
14 5 0.19
15 6 0.22
17 8 0.30
18 8 0.30
ACGTcount: A:0.28, C:0.41, G:0.30, T:0.00
Consensus pattern (18 bp):
CGCGACCGCGACCGAAAA
Found at i:31428339 original size:69 final size:69
Alignment explanation
Indices: 31428261--31428519 Score: 220
Period size: 69 Copynumber: 3.8 Consensus size: 69
31428251 AAGGGTCGGG
* * * *
31428261 AAGAGTCACATGTTGAAGCCGGAGGAAAGACCGATAGTGGAGAAGGTGATAATGTGCAAAAGGCT
1 AAGAATCACATGTTGAAGCCGGAGGAAAGACAGATAGTGGAAAAGGTGATAATGAGCAAAAGGCT
31428326 AAGC
66 AAGC
* * * * * *
31428330 AAGAATCACATTTTGATGCCGGAGGAAAGGCAGATGGTGGAAAAGGTGATAATGAGCACAAGGGT
1 AAGAATCACATGTTGAAGCCGGAGGAAAGACAGATAGTGGAAAAGGTGATAATGAGCAAAAGGCT
*
31428395 AAGG
66 AAGC
* * * ** * ** *
31428399 ACGAATCGC-GGTTTGAAGCCGGAGGAAA-AGTGGACAGTACAAAAGGTGATAACGAGCAAAAGG
1 AAGAATCACATG-TTGAAGCCGGAGGAAAGA-CAGATAGTGGAAAAGGTGATAATGAGCAAAAGG
* *
31428462 GTAAGG
64 CTAAGC
* * * *
31428468 AAGAATCGCA-GTTTGAAGCCAGG-GGAAAGGCAGATGGTGGAAAAGGCGATAA
1 AAGAATCACATG-TTGAAGCC-GGAGGAAAGACAGATAGTGGAAAAGGTGATAA
31428520 GGAGGGTCAG
Statistics
Matches: 151, Mismatches: 34, Indels: 10
0.77 0.17 0.05
Matches are distributed among these distances:
69 149 0.99
70 2 0.01
ACGTcount: A:0.38, C:0.12, G:0.35, T:0.15
Consensus pattern (69 bp):
AAGAATCACATGTTGAAGCCGGAGGAAAGACAGATAGTGGAAAAGGTGATAATGAGCAAAAGGCT
AAGC
Found at i:31430745 original size:16 final size:16
Alignment explanation
Indices: 31430714--31430747 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
31430704 AATTTAAATA
31430714 TAAAATATTTATTCTT
1 TAAAATATTTATTCTT
31430730 TAAAGATATTTA-TCTT
1 TAAA-ATATTTATTCTT
31430746 TA
1 TA
31430748 TATGACAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 10 0.59
17 7 0.41
ACGTcount: A:0.38, C:0.06, G:0.03, T:0.53
Consensus pattern (16 bp):
TAAAATATTTATTCTT
Found at i:31435656 original size:19 final size:18
Alignment explanation
Indices: 31435634--31435669 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
31435624 TATAAATGCA
31435634 AAATTAAATAATCGAAATT
1 AAATTAAATAATC-AAATT
*
31435653 AAATTAGATAATCAAAT
1 AAATTAAATAATCAAAT
31435670 GTGCGAATTC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 4 0.25
19 12 0.75
ACGTcount: A:0.58, C:0.06, G:0.06, T:0.31
Consensus pattern (18 bp):
AAATTAAATAATCAAATT
Found at i:31437256 original size:9 final size:9
Alignment explanation
Indices: 31437242--31437273 Score: 55
Period size: 9 Copynumber: 3.6 Consensus size: 9
31437232 ACATATTTTT
31437242 TATTATATA
1 TATTATATA
31437251 TATTATATA
1 TATTATATA
*
31437260 TATTTTATA
1 TATTATATA
31437269 TATTA
1 TATTA
31437274 ACATAACATA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (9 bp):
TATTATATA
Found at i:31443919 original size:21 final size:22
Alignment explanation
Indices: 31443895--31443935 Score: 75
Period size: 21 Copynumber: 1.9 Consensus size: 22
31443885 CCACTTCACT
31443895 TTCAAATTCTTT-ATTATTTCA
1 TTCAAATTCTTTAATTATTTCA
31443916 TTCAAATTCTTTAATTATTT
1 TTCAAATTCTTTAATTATTT
31443936 TAATATATTA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 12 0.63
22 7 0.37
ACGTcount: A:0.29, C:0.12, G:0.00, T:0.59
Consensus pattern (22 bp):
TTCAAATTCTTTAATTATTTCA
Found at i:31444865 original size:26 final size:26
Alignment explanation
Indices: 31444829--31444882 Score: 90
Period size: 26 Copynumber: 2.1 Consensus size: 26
31444819 AAAACTAAAA
31444829 ATTTTCAATACAGAAGTCAGACGGCC
1 ATTTTCAATACAGAAGTCAGACGGCC
* *
31444855 ATTTTCAATACAGAGGTTAGACGGCC
1 ATTTTCAATACAGAAGTCAGACGGCC
31444881 AT
1 AT
31444883 GTGTCCAGAC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.33, C:0.20, G:0.20, T:0.26
Consensus pattern (26 bp):
ATTTTCAATACAGAAGTCAGACGGCC
Found at i:31451171 original size:71 final size:72
Alignment explanation
Indices: 31451084--31451227 Score: 209
Period size: 74 Copynumber: 2.0 Consensus size: 72
31451074 CTGTCGTATT
* * *
31451084 TTGGACTTTTGCTTATGTTTTTTTCTTATAATC-TTGTTATGTTGTTGTTTACTTCAACTCATGT
1 TTGGACTTTTGATTATGTTATTTTATTATAATCTTTGTTATGTTGTTGTTTACTTCAACTCATGT
31451148 TGTTTAC
66 TGTTTAC
* **
31451155 TTGGACTTTTGATTATGTTATTTTATTATAATCTTGTTGTTTTGTTGTTGTTTACTTGGACTCAT
1 TTGGACTTTTGATTATGTTATTTTATTATAATC-T-TTGTTATGTTGTTGTTTACTTCAACTCAT
31451220 GTTGTTTA
64 GTTGTTTA
31451228 TTTAGACTGA
Statistics
Matches: 64, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
71 30 0.47
74 34 0.53
ACGTcount: A:0.16, C:0.10, G:0.16, T:0.58
Consensus pattern (72 bp):
TTGGACTTTTGATTATGTTATTTTATTATAATCTTTGTTATGTTGTTGTTTACTTCAACTCATGT
TGTTTAC
Found at i:31451224 original size:19 final size:19
Alignment explanation
Indices: 31451200--31451243 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
31451190 GTTGTTTTGT
*
31451200 TGTTGTTTACTTGGACTCA
1 TGTTGTTTACTTAGACTCA
* *
31451219 TGTTGTTTATTTAGACTGA
1 TGTTGTTTACTTAGACTCA
31451238 TGTTGT
1 TGTTGT
31451244 GTTGCTTTTA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.16, C:0.09, G:0.23, T:0.52
Consensus pattern (19 bp):
TGTTGTTTACTTAGACTCA
Found at i:31460097 original size:18 final size:19
Alignment explanation
Indices: 31460074--31460110 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
31460064 TGGTTTAAGT
31460074 CTAAATT-TTTAATTTCTC
1 CTAAATTATTTAATTTCTC
*
31460092 CTAAATTATTTACTTTCTC
1 CTAAATTATTTAATTTCTC
31460111 TTCTACAGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.27, C:0.19, G:0.00, T:0.54
Consensus pattern (19 bp):
CTAAATTATTTAATTTCTC
Found at i:31462188 original size:22 final size:22
Alignment explanation
Indices: 31462163--31462205 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
31462153 TAATTTTAAG
31462163 TTTA-AATTTGTACTAACTATTC
1 TTTATAATTTGT-CTAACTATTC
**
31462185 TTTATTTTTTGTCTAACTATT
1 TTTATAATTTGTCTAACTATT
31462206 GTAATACATA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 13 0.72
23 5 0.28
ACGTcount: A:0.26, C:0.12, G:0.05, T:0.58
Consensus pattern (22 bp):
TTTATAATTTGTCTAACTATTC
Found at i:31463135 original size:15 final size:15
Alignment explanation
Indices: 31463115--31463166 Score: 50
Period size: 15 Copynumber: 3.2 Consensus size: 15
31463105 GCTGAAAAAC
31463115 ATTTATTATTAATAT
1 ATTTATTATTAATAT
*
31463130 ATTTATAATTGTAATAAAT
1 ATTTATTA-T-TAAT--AT
*
31463149 ATTTATTATTAAAAT
1 ATTTATTATTAATAT
31463164 ATT
1 ATT
31463167 AATATGTGAA
Statistics
Matches: 30, Mismatches: 3, Indels: 8
0.73 0.07 0.20
Matches are distributed among these distances:
15 12 0.40
16 1 0.03
17 7 0.23
18 1 0.03
19 9 0.30
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (15 bp):
ATTTATTATTAATAT
Found at i:31463250 original size:17 final size:18
Alignment explanation
Indices: 31463202--31463252 Score: 52
Period size: 17 Copynumber: 2.9 Consensus size: 18
31463192 TTATTATTTG
31463202 TAAAATTTATTAT-TAAAA
1 TAAAA-TTATTATATAAAA
* **
31463220 TAAAATCAAAATATAAAA
1 TAAAATTATTATATAAAA
31463238 T-AAATTATTATATAA
1 TAAAATTATTATATAA
31463253 CTAAATATGT
Statistics
Matches: 26, Mismatches: 6, Indels: 3
0.74 0.17 0.09
Matches are distributed among these distances:
17 15 0.58
18 11 0.42
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (18 bp):
TAAAATTATTATATAAAA
Found at i:31468057 original size:25 final size:24
Alignment explanation
Indices: 31468033--31468096 Score: 67
Period size: 26 Copynumber: 2.6 Consensus size: 24
31468023 TTTAGTATAT
31468033 TATTAATTATTTTAAAAAATAATA
1 TATTAATTATTTTAAAAAATAATA
* * *
31468057 TATTATTATATTTCTTAAAAATATTA
1 TATTAAT-TATTT-TAAAAAATAATA
31468083 -ATTTAATTATTTTA
1 TA-TTAATTATTTTA
31468097 GAAACAATTC
Statistics
Matches: 32, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
24 7 0.22
25 11 0.34
26 14 0.44
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (24 bp):
TATTAATTATTTTAAAAAATAATA
Found at i:31468059 original size:27 final size:26
Alignment explanation
Indices: 31468028--31468096 Score: 74
Period size: 25 Copynumber: 2.7 Consensus size: 26
31468018 AAATTTTTAG
31468028 TATATTATTAATTATTTTAAAAAATAA
1 TATATTATTAATTATTTTAAAAAAT-A
*
31468055 TATATTATT-A-TATTTCTTAAAAATA
1 TATATTATTAATTATTT-TAAAAAATA
*
31468080 T-TAAT-TTAATTATTTTA
1 TATATTATTAATTATTTTA
31468097 GAAACAATTC
Statistics
Matches: 36, Mismatches: 3, Indels: 9
0.75 0.06 0.19
Matches are distributed among these distances:
23 2 0.06
24 5 0.14
25 12 0.33
26 8 0.22
27 9 0.25
ACGTcount: A:0.45, C:0.01, G:0.00, T:0.54
Consensus pattern (26 bp):
TATATTATTAATTATTTTAAAAAATA
Found at i:31471887 original size:3 final size:3
Alignment explanation
Indices: 31471879--31471908 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
31471869 ACAATGTAAG
31471879 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
31471909 TTTAAAAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
CTT
Found at i:31477650 original size:9 final size:9
Alignment explanation
Indices: 31477636--31477693 Score: 62
Period size: 9 Copynumber: 6.4 Consensus size: 9
31477626 TTTGGTTAAA
31477636 AATTAACCG
1 AATTAACCG
*
31477645 AATTAATCG
1 AATTAACCG
31477654 AATTAACCG
1 AATTAACCG
* * *
31477663 GATTACCCA
1 AATTAACCG
*
31477672 AATTACCCG
1 AATTAACCG
*
31477681 AATTACCCG
1 AATTAACCG
31477690 AATT
1 AATT
31477694 GAATCACTAA
Statistics
Matches: 42, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
9 42 1.00
ACGTcount: A:0.40, C:0.24, G:0.10, T:0.26
Consensus pattern (9 bp):
AATTAACCG
Found at i:31477889 original size:27 final size:27
Alignment explanation
Indices: 31477858--31477912 Score: 101
Period size: 27 Copynumber: 2.0 Consensus size: 27
31477848 CCTAAAAACA
31477858 AAATGTGTAATTGGGTAGATACTTAAG
1 AAATGTGTAATTGGGTAGATACTTAAG
*
31477885 AAATGTGTAATTGGGTAGATATTTAAG
1 AAATGTGTAATTGGGTAGATACTTAAG
31477912 A
1 A
31477913 GTTAGACTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.38, C:0.02, G:0.25, T:0.35
Consensus pattern (27 bp):
AAATGTGTAATTGGGTAGATACTTAAG
Found at i:31477959 original size:38 final size:39
Alignment explanation
Indices: 31477915--31477992 Score: 140
Period size: 38 Copynumber: 2.0 Consensus size: 39
31477905 ATTTAAGAGT
*
31477915 TAGACTTTAGTTTTATTTTTATTGGGTT-GGTAATTGGG
1 TAGACTTTAGTTTTAGTTTTATTGGGTTGGGTAATTGGG
31477953 TAGACTTTAGTTTTAGTTTTATTGGGTTGGGTAATTGGG
1 TAGACTTTAGTTTTAGTTTTATTGGGTTGGGTAATTGGG
31477992 T
1 T
31477993 TGGGTTGGAT
Statistics
Matches: 38, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
38 27 0.71
39 11 0.29
ACGTcount: A:0.18, C:0.03, G:0.28, T:0.51
Consensus pattern (39 bp):
TAGACTTTAGTTTTAGTTTTATTGGGTTGGGTAATTGGG
Found at i:31477991 original size:13 final size:13
Alignment explanation
Indices: 31477973--31477997 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
31477963 TTTTAGTTTT
31477973 ATTGGGTTGGGTA
1 ATTGGGTTGGGTA
31477986 ATTGGGTTGGGT
1 ATTGGGTTGGGT
31477998 TGGATAATTT
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:0.12, C:0.00, G:0.48, T:0.40
Consensus pattern (13 bp):
ATTGGGTTGGGTA
Found at i:31479166 original size:32 final size:32
Alignment explanation
Indices: 31479116--31479177 Score: 81
Period size: 32 Copynumber: 1.9 Consensus size: 32
31479106 ATCACAAGTT
* *
31479116 GGATTTTCGTTCTCAGCTACGTACATTTTTGG
1 GGATTTTCATTCTCAGCTACGCACATTTTTGG
*
31479148 GGATTTTCATTC-CTAGCTATGCACATTTTT
1 GGATTTTCATTCTC-AGCTACGCACATTTTT
31479178 AGGATATAGT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
31 1 0.04
32 25 0.96
ACGTcount: A:0.18, C:0.19, G:0.18, T:0.45
Consensus pattern (32 bp):
GGATTTTCATTCTCAGCTACGCACATTTTTGG
Found at i:31480586 original size:19 final size:19
Alignment explanation
Indices: 31480558--31480621 Score: 101
Period size: 19 Copynumber: 3.3 Consensus size: 19
31480548 AATTTTCGAG
*
31480558 GATATACAATCTTAGATAT
1 GATATGCAATCTTAGATAT
31480577 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
31480596 GATATATGCAATCTTAGATAT
1 G--ATATGCAATCTTAGATAT
31480617 GATAT
1 GATAT
31480622 ATACAATCTT
Statistics
Matches: 42, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
19 23 0.55
21 19 0.45
ACGTcount: A:0.39, C:0.09, G:0.14, T:0.38
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:31480640 original size:19 final size:21
Alignment explanation
Indices: 31480559--31480634 Score: 120
Period size: 21 Copynumber: 3.7 Consensus size: 21
31480549 ATTTTCGAGG
31480559 ATATACAATCTTAGATATG--
1 ATATACAATCTTAGATATGAT
*
31480578 ATATGCAATCTTAGATATGAT
1 ATATACAATCTTAGATATGAT
*
31480599 ATATGCAATCTTAGATATGAT
1 ATATACAATCTTAGATATGAT
31480620 ATATACAATCTTAGA
1 ATATACAATCTTAGA
31480635 AGATATGATT
Statistics
Matches: 53, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
19 18 0.34
21 35 0.66
ACGTcount: A:0.41, C:0.11, G:0.12, T:0.37
Consensus pattern (21 bp):
ATATACAATCTTAGATATGAT
Found at i:31480670 original size:21 final size:23
Alignment explanation
Indices: 31480626--31480670 Score: 58
Period size: 21 Copynumber: 2.0 Consensus size: 23
31480616 TGATATATAC
*
31480626 AATCTTAGAAGATATGATTTTGT
1 AATCTTAGAAGATATGAATTTGT
*
31480649 AATCTTA-AAGAT-TTAATTTGT
1 AATCTTAGAAGATATGAATTTGT
31480670 A
1 A
31480671 GATACCCTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 8 0.40
22 5 0.25
23 7 0.35
ACGTcount: A:0.38, C:0.04, G:0.13, T:0.44
Consensus pattern (23 bp):
AATCTTAGAAGATATGAATTTGT
Found at i:31480851 original size:19 final size:21
Alignment explanation
Indices: 31480827--31480865 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 21
31480817 GGCTTACTGT
*
31480827 TTTTTTTCTT-TTT-CGATTA
1 TTTTTTACTTATTTACGATTA
31480846 TTTTTTACTTATTTACGATT
1 TTTTTTACTTATTTACGATT
31480866 TTAAAAAAGG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 9 0.53
20 3 0.18
21 5 0.29
ACGTcount: A:0.15, C:0.10, G:0.05, T:0.69
Consensus pattern (21 bp):
TTTTTTACTTATTTACGATTA
Found at i:31481095 original size:3 final size:3
Alignment explanation
Indices: 31481087--31481126 Score: 55
Period size: 3 Copynumber: 13.3 Consensus size: 3
31481077 ATTAATTTTG
*
31481087 TTA TTA TTA TTT TTA TTA TTA -TA TTA TATA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA T
31481127 ACCTACATAT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
2 2 0.06
3 28 0.85
4 3 0.09
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:31481095 original size:15 final size:15
Alignment explanation
Indices: 31481071--31481125 Score: 53
Period size: 15 Copynumber: 3.7 Consensus size: 15
31481061 GTTTTTAGTC
31481071 TATT-TTATTAATTT
1 TATTATTATTAATTT
* *
31481085 TGTTATTATTATTTT
1 TATTATTATTAATTT
31481100 TATTATTA-T-ATTAT
1 TATTATTATTAATT-T
31481114 ATATTATTATTA
1 -TATTATTATTA
31481126 TACCTACATA
Statistics
Matches: 32, Mismatches: 4, Indels: 7
0.74 0.09 0.16
Matches are distributed among these distances:
13 2 0.06
14 5 0.16
15 24 0.75
16 1 0.03
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (15 bp):
TATTATTATTAATTT
Found at i:31481102 original size:12 final size:12
Alignment explanation
Indices: 31481073--31481124 Score: 52
Period size: 12 Copynumber: 4.1 Consensus size: 12
31481063 TTTTAGTCTA
31481073 TTTTATTAATT-T
1 TTTTATT-ATTAT
*
31481085 TGTTATTATTAT
1 TTTTATTATTAT
31481097 TTTTATTATTAT
1 TTTTATTATTAT
31481109 ATTATATATTATTAT
1 -TT-T-TATTATTAT
31481124 T
1 T
31481125 ATACCTACAT
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
11 3 0.09
12 18 0.53
13 2 0.06
14 2 0.06
15 9 0.26
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (12 bp):
TTTTATTATTAT
Found at i:31481502 original size:51 final size:48
Alignment explanation
Indices: 31481383--31481503 Score: 118
Period size: 51 Copynumber: 2.4 Consensus size: 48
31481373 ATTTTCCACG
* **
31481383 TTTTATATTATAATTATATATTTCATTTTTTTGTAAATGCATGAATATA
1 TTTTATATTAT-ATTTTATATTTCATTTTTTCATAAATGCATGAATATA
* * *
31481432 TTTTATATGTATATATTTATATTTTCCTTGTTTTCATAAATGCAT-TATGTA
1 TTTTATAT-TATAT-TTTATA-TTTCATT-TTTTCATAAATGCATGAATATA
31481483 TTTTATATATATAGTTTTATA
1 TTTTATAT-TATA-TTTTATA
31481504 ACCCAAAATT
Statistics
Matches: 60, Mismatches: 7, Indels: 8
0.80 0.09 0.11
Matches are distributed among these distances:
49 10 0.17
50 8 0.13
51 28 0.47
52 14 0.23
ACGTcount: A:0.31, C:0.05, G:0.07, T:0.57
Consensus pattern (48 bp):
TTTTATATTATATTTTATATTTCATTTTTTCATAAATGCATGAATATA
Found at i:31487759 original size:17 final size:17
Alignment explanation
Indices: 31487737--31487776 Score: 62
Period size: 17 Copynumber: 2.4 Consensus size: 17
31487727 ACTTTGAGTC
**
31487737 GAAAAAAATGACGAAAT
1 GAAAAAAATGAAAAAAT
31487754 GAAAAAAATGAAAAAAT
1 GAAAAAAATGAAAAAAT
31487771 GAAAAA
1 GAAAAA
31487777 TGAAAAAGTA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.72, C:0.03, G:0.15, T:0.10
Consensus pattern (17 bp):
GAAAAAAATGAAAAAAT
Found at i:31487767 original size:8 final size:8
Alignment explanation
Indices: 31487739--31487783 Score: 56
Period size: 8 Copynumber: 5.6 Consensus size: 8
31487729 TTTGAGTCGA
31487739 AAAAAATG
1 AAAAAATG
**
31487747 ACGAAATG
1 AAAAAATG
31487755 AAAAAAATG
1 -AAAAAATG
31487764 AAAAAATG
1 AAAAAATG
31487772 -AAAAATG
1 AAAAAATG
31487779 AAAAA
1 AAAAA
31487784 GTAAAATGGA
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
7 7 0.23
8 18 0.58
9 6 0.19
ACGTcount: A:0.73, C:0.02, G:0.13, T:0.11
Consensus pattern (8 bp):
AAAAAATG
Found at i:31489264 original size:44 final size:44
Alignment explanation
Indices: 31489216--31489410 Score: 112
Period size: 44 Copynumber: 4.4 Consensus size: 44
31489206 GAGTAGGTTG
*
31489216 AAGATTGTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCA
1 AAGATTGCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCA
* * * * **
31489260 AAGATGGCAAATCTTATCTTTCC-AAG-A-TAGTGGGAAGCAAATTT
1 AAGATTGCAGATCTTATC-TCCCTAAGCAGTAGT-GG-AGCAGATCA
** * * * * * * * **
31489304 AAG-TCACCA-AGCCTTGTCTCCCTGAGCAGCAGCGGAGTAGGTTG
1 AAGAT-TGCAGA-TCTTATCTCCCTAAGCAGTAGTGGAGCAGATCA
*
31489348 AAGATTGTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCA
1 AAGATTGCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCA
** *
31489392 AAGACGGCAAATCTTATCT
1 AAGATTGCAGATCTTATCT
31489411 TTCCAAGATA
Statistics
Matches: 106, Mismatches: 35, Indels: 20
0.66 0.22 0.12
Matches are distributed among these distances:
42 4 0.04
43 8 0.08
44 84 0.79
45 8 0.08
46 2 0.02
ACGTcount: A:0.31, C:0.19, G:0.23, T:0.26
Consensus pattern (44 bp):
AAGATTGCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCA
Found at i:31489298 original size:132 final size:132
Alignment explanation
Indices: 31489049--31489446 Score: 654
Period size: 132 Copynumber: 3.0 Consensus size: 132
31489039 GTGATACACT
* * * * *
31489049 AAGCCTTGTCTCCCTGAGCAACAGCGAAGTAGGTTGAGGATCGTAGATCTTATCT-CCTTAGCAG
1 AAGCCTTGTCTCCCTGAGCAGCAGCGGAGTAGGTTGAAGATTGTAGATCTTATCTCCCTAAGCAG
* * * *
31489113 TAGTGGAGTAGATCGAGGACGACAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCA
66 TAGTGGAGCAGATCAAAGACGGCAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCA
31489178 CC
131 CC
31489180 AAGCCTTGTCTCCCTGAGCAGCAGCGGAGTAGGTTGAAGATTGTAGATCTTATCTCCCTAAGCAG
1 AAGCCTTGTCTCCCTGAGCAGCAGCGGAGTAGGTTGAAGATTGTAGATCTTATCTCCCTAAGCAG
* * *
31489245 TAGTGGAGCAGATCAAAGATGGCAAATCTTATCTTTCCAAGATAGTGGGAAGCAAATTTAAGTCA
66 TAGTGGAGCAGATCAAAGACGGCAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCA
31489310 CC
131 CC
31489312 AAGCCTTGTCTCCCTGAGCAGCAGCGGAGTAGGTTGAAGATTGTAGATCTTATCTCCCTAAGCAG
1 AAGCCTTGTCTCCCTGAGCAGCAGCGGAGTAGGTTGAAGATTGTAGATCTTATCTCCCTAAGCAG
* *
31489377 TAGTGGAGCAGATCAAAGACGGCAAATCTTATCTTTCCAAGATAGTGAGAAGAAGATTTAAGCCA
66 TAGTGGAGCAGATCAAAGACGGCAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCA
*
31489442 GC
131 CC
31489444 AAG
1 AAG
31489447 TCTTATCCTC
Statistics
Matches: 248, Mismatches: 18, Indels: 1
0.93 0.07 0.00
Matches are distributed among these distances:
131 51 0.21
132 197 0.79
ACGTcount: A:0.30, C:0.20, G:0.25, T:0.25
Consensus pattern (132 bp):
AAGCCTTGTCTCCCTGAGCAGCAGCGGAGTAGGTTGAAGATTGTAGATCTTATCTCCCTAAGCAG
TAGTGGAGCAGATCAAAGACGGCAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCA
CC
Found at i:31489757 original size:21 final size:21
Alignment explanation
Indices: 31489732--31489788 Score: 78
Period size: 21 Copynumber: 2.7 Consensus size: 21
31489722 ATTTTCGAGG
*
31489732 ATATGCAATCTTAGGTATGAT
1 ATATGCAATCTTAGATATGAT
*
31489753 ATATGGAATCTTAGATATGAT
1 ATATGCAATCTTAGATATGAT
* *
31489774 ATATACAATATTAGA
1 ATATGCAATCTTAGA
31489789 AGATATGATT
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.40, C:0.07, G:0.16, T:0.37
Consensus pattern (21 bp):
ATATGCAATCTTAGATATGAT
Found at i:31490006 original size:19 final size:21
Alignment explanation
Indices: 31489982--31490020 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 21
31489972 GGCTTACTAT
*
31489982 TTTTTTTCTT-TTT-CGATTA
1 TTTTTTACTTATTTACGATTA
31490001 TTTTTTACTTATTTACGATT
1 TTTTTTACTTATTTACGATT
31490021 TTAAAAAAGG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 9 0.53
20 3 0.18
21 5 0.29
ACGTcount: A:0.15, C:0.10, G:0.05, T:0.69
Consensus pattern (21 bp):
TTTTTTACTTATTTACGATTA
Found at i:31490251 original size:3 final size:3
Alignment explanation
Indices: 31490243--31490285 Score: 61
Period size: 3 Copynumber: 14.3 Consensus size: 3
31490233 ATTAATTTTG
*
31490243 TTA TTA TTA TTT TTA TTA TTA -TA TTA TATA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA TTA T
31490286 ACCTACATAT
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
2 2 0.06
3 31 0.86
4 3 0.08
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:31490251 original size:15 final size:15
Alignment explanation
Indices: 31490227--31490284 Score: 55
Period size: 15 Copynumber: 3.7 Consensus size: 15
31490217 GTTTTTAGTC
31490227 TATT-TTATTAATTT
1 TATTATTATTAATTT
* *
31490241 TGTTATTATTATTTT
1 TATTATTATTAATTT
*
31490256 TATTATTATATTATATAT
1 TATTA-T-TATTA-ATTT
31490274 TATTATTATTA
1 TATTATTATTA
31490285 TACCTACATA
Statistics
Matches: 35, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
14 3 0.09
15 13 0.37
16 6 0.17
17 6 0.17
18 7 0.20
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (15 bp):
TATTATTATTAATTT
Found at i:31498891 original size:39 final size:43
Alignment explanation
Indices: 31498790--31498898 Score: 136
Period size: 45 Copynumber: 2.6 Consensus size: 43
31498780 GATTAGAGGC
31498790 GTAATGGAATAGAGGTGTAATAGCAAATCAACTGTTTGGTTGAAT
1 GTAATGGAATAGAGGTGTAATAGCAAATCAACTGTTTGGTT--AT
* ***
31498835 GTAATGGAATAGAGGTGTAATAG-TAATCTTGTGTTTGG-T-T
1 GTAATGGAATAGAGGTGTAATAGCAAATCAACTGTTTGGTTAT
31498875 G-AATGGAATAGAGGTGTAATAGCA
1 GTAATGGAATAGAGGTGTAATAGCA
31498899 TAATAGAAAA
Statistics
Matches: 58, Mismatches: 5, Indels: 7
0.83 0.07 0.10
Matches are distributed among these distances:
39 21 0.36
40 2 0.03
43 1 0.02
44 11 0.19
45 23 0.40
ACGTcount: A:0.34, C:0.05, G:0.29, T:0.32
Consensus pattern (43 bp):
GTAATGGAATAGAGGTGTAATAGCAAATCAACTGTTTGGTTAT
Found at i:31499072 original size:14 final size:15
Alignment explanation
Indices: 31499033--31499074 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
31499023 TTTTAACAGA
*
31499033 ATTATTATTAAATAT
1 ATTATAATTAAATAT
31499048 ATTATAATTAAA-AT
1 ATTATAATTAAATAT
*
31499062 A-TATAATTTAATA
1 ATTATAATTAAATA
31499075 AAATTCTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 9 0.38
14 4 0.17
15 11 0.46
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
ATTATAATTAAATAT
Found at i:31499250 original size:47 final size:46
Alignment explanation
Indices: 31499181--31499439 Score: 184
Period size: 47 Copynumber: 5.7 Consensus size: 46
31499171 TTAATTAAAA
*
31499181 TATATG-ATTTAATAAAATTTAAAATAATTATAACTAATAAATTTTCT
1 TATATGAATTT-ATATAATTTAAAATAATTATAA-TAATAAATTTTCT
* * **
31499228 TATATGAATTTGTATAATTTAAAATAATTATTATTAATTATAA-TTTAA
1 TATATGAATTTATATAATTTAAAATAATTA-TAATAA-TA-AATTTTCT
* * *
31499276 TA-AT-AA--TATATTATTTCATAA-AATTATTGATAATAAATTTTCT
1 TATATGAATTTATATAATTT-AAAATAATTA-TAATAATAAATTTTCT
* * *
31499319 TATATGAATTTATATAATTTAAAATAA-T-CAATATTAAATATAAT-T
1 TATATGAATTTATATAATTTAAAATAATTATAATAATAAAT-T-TTCT
* * * *
31499364 TA-AT-AATGATATATAATTTCATAA-AATTCTTGATAATAAATTTTCT
1 TATATGAAT-TTATATAATTT-AAAATAATT-ATAATAATAAATTTTCT
31499410 TATATGAATTTATATAATTTAAAATAATTA
1 TATATGAATTTATATAATTTAAAATAATTA
31499440 ATATTAAATA
Statistics
Matches: 163, Mismatches: 27, Indels: 45
0.69 0.11 0.19
Matches are distributed among these distances:
42 2 0.01
43 10 0.06
44 42 0.26
45 14 0.09
46 14 0.09
47 63 0.39
48 16 0.10
49 2 0.01
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (46 bp):
TATATGAATTTATATAATTTAAAATAATTATAATAATAAATTTTCT
Found at i:31499296 original size:26 final size:25
Alignment explanation
Indices: 31499241--31499296 Score: 69
Period size: 26 Copynumber: 2.2 Consensus size: 25
31499231 ATGAATTTGT
*
31499241 ATAATTTAAAATAATTATTATTAATT
1 ATAATTTAAAATAATTATTATT-ATC
31499267 ATAATTTAATAATAATATATTATT-TC
1 ATAATTTAA-AATAAT-TATTATTATC
31499293 ATAA
1 ATAA
31499297 AATTATTGAT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
26 14 0.52
27 6 0.22
28 7 0.26
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (25 bp):
ATAATTTAAAATAATTATTATTATC
Found at i:31499310 original size:91 final size:91
Alignment explanation
Indices: 31499215--31499460 Score: 429
Period size: 91 Copynumber: 2.7 Consensus size: 91
31499205 TAATTATAAC
* * *
31499215 TAATAAATTTTCTTATATGAATTTGTATAATTTAAAATAATTATTATTAATTATAATTTAATAAT
1 TAATAAATTTTCTTATATGAATTTATATAATTTAAAATAATTAATATTAAATATAATTTAATAAT
*
31499280 AATATATTATTTCATAAAATTATTGA
66 AATATATAATTTCATAAAATTATTGA
*
31499306 TAATAAATTTTCTTATATGAATTTATATAATTTAAAATAATCAATATTAAATATAATTTAATAAT
1 TAATAAATTTTCTTATATGAATTTATATAATTTAAAATAATTAATATTAAATATAATTTAATAAT
* *
31499371 GATATATAATTTCATAAAATTCTTGA
66 AATATATAATTTCATAAAATTATTGA
31499397 TAATAAATTTTCTTATATGAATTTATATAATTTAAAATAATTAATATTAAATATAATTTAATAA
1 TAATAAATTTTCTTATATGAATTTATATAATTTAAAATAATTAATATTAAATATAATTTAATAA
31499461 CGAACGATCA
Statistics
Matches: 147, Mismatches: 8, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
91 147 1.00
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (91 bp):
TAATAAATTTTCTTATATGAATTTATATAATTTAAAATAATTAATATTAAATATAATTTAATAAT
AATATATAATTTCATAAAATTATTGA
Found at i:31499749 original size:23 final size:23
Alignment explanation
Indices: 31499702--31499745 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 23
31499692 ATATATGTAA
31499702 TATTATTAAAATAATATTTTTAT
1 TATTATTAAAATAATATTTTTAT
*
31499725 TATTATTTAAA-AATATTTTTA
1 TATTATTAAAATAATATTTTTA
31499746 ATTAATGCGG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 10 0.50
23 10 0.50
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (23 bp):
TATTATTAAAATAATATTTTTAT
Found at i:31500856 original size:23 final size:23
Alignment explanation
Indices: 31500826--31500886 Score: 104
Period size: 23 Copynumber: 2.7 Consensus size: 23
31500816 TGGACAAATG
31500826 AAGGCCATGTTCCTGTTTTTATT
1 AAGGCCATGTTCCTGTTTTTATT
31500849 AAGGCCATGTTCCTGTTTTTATT
1 AAGGCCATGTTCCTGTTTTTATT
**
31500872 GTGGCCATGTTCCTG
1 AAGGCCATGTTCCTG
31500887 AGTTGAACAA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.15, C:0.20, G:0.21, T:0.44
Consensus pattern (23 bp):
AAGGCCATGTTCCTGTTTTTATT
Found at i:31505222 original size:21 final size:21
Alignment explanation
Indices: 31505198--31505251 Score: 74
Period size: 20 Copynumber: 2.6 Consensus size: 21
31505188 TAATACCAGA
* **
31505198 AAATGTATCGATAATTTTTTT
1 AAATTTATCGATAATTCATTT
31505219 AAATTTATCGAT-ATTCATTT
1 AAATTTATCGATAATTCATTT
31505239 AAATTTATCGATA
1 AAATTTATCGATA
31505252 CTTGGCAAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
20 18 0.62
21 11 0.38
ACGTcount: A:0.37, C:0.07, G:0.07, T:0.48
Consensus pattern (21 bp):
AAATTTATCGATAATTCATTT
Found at i:31506152 original size:41 final size:41
Alignment explanation
Indices: 31506107--31506244 Score: 197
Period size: 41 Copynumber: 3.4 Consensus size: 41
31506097 CAACGACACT
* *
31506107 TAGCCTGCTAGACTTATAGCCTGATTTAGATCACCGGCACG
1 TAGCCTGCTAGACTTATAACCTGATTCAGATCACCGGCACG
**
31506148 TAGCCTGCTAGGTTTATAACCTGATTCAGATCACCGGCACG
1 TAGCCTGCTAGACTTATAACCTGATTCAGATCACCGGCACG
* * **
31506189 TAGCCTGCTAG-GTTATAACCTAATTCAGATCACCGGCAAT
1 TAGCCTGCTAGACTTATAACCTGATTCAGATCACCGGCACG
31506229 TAGCCTGCTAGACTTA
1 TAGCCTGCTAGACTTA
31506245 AAGTCTGAAA
Statistics
Matches: 87, Mismatches: 9, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
40 36 0.41
41 51 0.59
ACGTcount: A:0.26, C:0.26, G:0.20, T:0.28
Consensus pattern (41 bp):
TAGCCTGCTAGACTTATAACCTGATTCAGATCACCGGCACG
Found at i:31523886 original size:21 final size:21
Alignment explanation
Indices: 31523862--31523915 Score: 74
Period size: 20 Copynumber: 2.6 Consensus size: 21
31523852 TAATACCAGA
* **
31523862 AAATGTATCGATAATTTTTTT
1 AAATTTATCGATAATTCATTT
31523883 AAATTTATCGAT-ATTCATTT
1 AAATTTATCGATAATTCATTT
31523903 AAATTTATCGATA
1 AAATTTATCGATA
31523916 CTTGGCAAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
20 18 0.62
21 11 0.38
ACGTcount: A:0.37, C:0.07, G:0.07, T:0.48
Consensus pattern (21 bp):
AAATTTATCGATAATTCATTT
Found at i:31524815 original size:41 final size:41
Alignment explanation
Indices: 31524770--31524908 Score: 197
Period size: 41 Copynumber: 3.4 Consensus size: 41
31524760 CAACGACACT
* *
31524770 TAGCCTGCTAGACTTATAGCCTGATTTAGATCACCGGCACG
1 TAGCCTGCTAGACTTATAACCTGATTCAGATCACCGGCACG
**
31524811 TAGCCTGCTAGGTTTATAACCTGATTCAGATCACCGGCACG
1 TAGCCTGCTAGACTTATAACCTGATTCAGATCACCGGCACG
** * **
31524852 TAGCCTGCTAGGTTTATAACCTAATTCAGATCACCGGCAAT
1 TAGCCTGCTAGACTTATAACCTGATTCAGATCACCGGCACG
31524893 TAGCCTGCTAGACTTA
1 TAGCCTGCTAGACTTA
31524909 AAGTCTGAAA
Statistics
Matches: 89, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
41 89 1.00
ACGTcount: A:0.26, C:0.26, G:0.20, T:0.28
Consensus pattern (41 bp):
TAGCCTGCTAGACTTATAACCTGATTCAGATCACCGGCACG
Found at i:31532491 original size:41 final size:41
Alignment explanation
Indices: 31532437--31532550 Score: 138
Period size: 41 Copynumber: 2.8 Consensus size: 41
31532427 TTAATTAAAA
* * *
31532437 CAGATTCAACGGCACTTAGCTTGCTAGACTTATAGCCTGATT
1 CAGA-TCACCGGCACTTAGCCTGCTAGACTTATAACCTGATT
* * **
31532479 TAGATCACCGGCACGTAGCCTGCTAGGTTTATAACCTGATT
1 CAGATCACCGGCACTTAGCCTGCTAGACTTATAACCTGATT
* *
31532520 CAGATTACCGGCAATTAGCCTGCTAGACTTA
1 CAGATCACCGGCACTTAGCCTGCTAGACTTA
31532551 AAGTCTGAAA
Statistics
Matches: 59, Mismatches: 13, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
41 56 0.95
42 3 0.05
ACGTcount: A:0.26, C:0.25, G:0.20, T:0.29
Consensus pattern (41 bp):
CAGATCACCGGCACTTAGCCTGCTAGACTTATAACCTGATT
Found at i:31533436 original size:114 final size:114
Alignment explanation
Indices: 31533234--31533525 Score: 539
Period size: 114 Copynumber: 2.6 Consensus size: 114
31533224 ATACATTCGC
31533234 TTTTAAGAAAGCGCCGCTAATGCTCAGGGCTTTAGCGGCGTTTTTGGGAAAGCGCCGCAAAAAAA
1 TTTTAAGAAAGCGCCGCTAATGCTCAGGGCTTTAGCGGCGTTTTTGGGAAAGCGCCGCAAAAAAA
*
31533299 CCTAAGCCCAACGACGCCGTTTTCTGAGCTTTCAGAGATTTAGCGGCGT
66 CCTAAGCCCAACGACGCCATTTTCTGAGCTTTCAGAGATTTAGCGGCGT
31533348 TTTTAAGAAAGCGCCGCTAATGCTCAGGGCTTTAGCGGCGTTTTTGGGAAAGCGCCGCAAAAAAA
1 TTTTAAGAAAGCGCCGCTAATGCTCAGGGCTTTAGCGGCGTTTTTGGGAAAGCGCCGCAAAAAAA
* *
31533413 CCTAAGCCCAACGACGCCATTTTCTGAGCTTTCGGGGATTTAGCGGCGT
66 CCTAAGCCCAACGACGCCATTTTCTGAGCTTTCAGAGATTTAGCGGCGT
* *
31533462 TTTTAAGAAAGCGCCGCTAATGCTTAGGGCTTTAGCGGCGTTTTTGGGAAAGCGCCGCTAAAAA
1 TTTTAAGAAAGCGCCGCTAATGCTCAGGGCTTTAGCGGCGTTTTTGGGAAAGCGCCGCAAAAAA
31533526 TATTTTATCT
Statistics
Matches: 173, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
114 173 1.00
ACGTcount: A:0.25, C:0.23, G:0.27, T:0.25
Consensus pattern (114 bp):
TTTTAAGAAAGCGCCGCTAATGCTCAGGGCTTTAGCGGCGTTTTTGGGAAAGCGCCGCAAAAAAA
CCTAAGCCCAACGACGCCATTTTCTGAGCTTTCAGAGATTTAGCGGCGT
Found at i:31533839 original size:15 final size:15
Alignment explanation
Indices: 31533816--31533854 Score: 60
Period size: 15 Copynumber: 2.6 Consensus size: 15
31533806 GTTGAGATTT
*
31533816 AAGGTTTAGGGGTTA
1 AAGGGTTAGGGGTTA
*
31533831 AAGGGTTAGGGGTTT
1 AAGGGTTAGGGGTTA
31533846 AAGGGTTAG
1 AAGGGTTAG
31533855 ACGTGCTAGG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.26, C:0.00, G:0.44, T:0.31
Consensus pattern (15 bp):
AAGGGTTAGGGGTTA
Found at i:31534085 original size:15 final size:15
Alignment explanation
Indices: 31534067--31534118 Score: 63
Period size: 14 Copynumber: 3.5 Consensus size: 15
31534057 ATTTAGGAAG
31534067 TATGGATTTAAGGAT
1 TATGGATTTAAGGAT
* *
31534082 TAT-GAATTAGGGAT
1 TATGGATTTAAGGAT
31534096 TATGG-TTTAAGGGAT
1 TATGGATTTAA-GGAT
31534111 TATGGATT
1 TATGGATT
31534119 AGGGGTTGAG
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
14 15 0.50
15 13 0.43
16 2 0.07
ACGTcount: A:0.31, C:0.00, G:0.29, T:0.40
Consensus pattern (15 bp):
TATGGATTTAAGGAT
Found at i:31534099 original size:29 final size:29
Alignment explanation
Indices: 31534067--31534122 Score: 87
Period size: 29 Copynumber: 1.9 Consensus size: 29
31534057 ATTTAGGAAG
31534067 TATGGATTTAA-GGATTATGAATTAGGGAT
1 TATGG-TTTAAGGGATTATGAATTAGGGAT
*
31534096 TATGGTTTAAGGGATTATGGATTAGGG
1 TATGGTTTAAGGGATTATGAATTAGGG
31534123 GTTGAGATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
28 5 0.20
29 20 0.80
ACGTcount: A:0.30, C:0.00, G:0.32, T:0.38
Consensus pattern (29 bp):
TATGGTTTAAGGGATTATGAATTAGGGAT
Found at i:31534133 original size:29 final size:29
Alignment explanation
Indices: 31534071--31534136 Score: 82
Period size: 29 Copynumber: 2.3 Consensus size: 29
31534061 AGGAAGTATG
31534071 GATTTAA-GGATTATGAATTAGGGATTAT
1 GATTTAAGGGATTATGAATTAGGGATTAT
* * *
31534099 GGTTTAAGGGATTATGGATTAGGGGTTGA-
1 GATTTAAGGGATTATGAATTAGGGATT-AT
31534128 GATTTAAGG
1 GATTTAAGG
31534137 TTTAGGGGTT
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
28 6 0.19
29 25 0.78
30 1 0.03
ACGTcount: A:0.30, C:0.00, G:0.33, T:0.36
Consensus pattern (29 bp):
GATTTAAGGGATTATGAATTAGGGATTAT
Found at i:31534156 original size:15 final size:15
Alignment explanation
Indices: 31534133--31534171 Score: 60
Period size: 15 Copynumber: 2.6 Consensus size: 15
31534123 GTTGAGATTT
*
31534133 AAGGTTTAGGGGTTA
1 AAGGGTTAGGGGTTA
*
31534148 AAGGGTTAGGGGTTT
1 AAGGGTTAGGGGTTA
31534163 AAGGGTTAG
1 AAGGGTTAG
31534172 ACGTGCTAGG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.26, C:0.00, G:0.44, T:0.31
Consensus pattern (15 bp):
AAGGGTTAGGGGTTA
Found at i:31534363 original size:317 final size:317
Alignment explanation
Indices: 31533772--31534425 Score: 1283
Period size: 317 Copynumber: 2.1 Consensus size: 317
31533762 ATTTTAATGT
* *
31533772 TTAGGGAGTAGGGTTT-AGGGATTATGGATTAGGGGTTGAGATTTAAGGTTTAGGGGTTAAAGGG
1 TTAGGGATTATGGTTTAAGGGATTATGGATTAGGGGTTGAGATTTAAGGTTTAGGGGTTAAAGGG
31533836 TTAGGGGTTTAAGGGTTAGACGTGCTAGGGGTTAAAAGTTAGGGATTTAGGGGTTGAGTTAGGGT
66 TTAGGGGTTTAAGGGTTAGACGTGCTAGGGGTTAAAAGTTAGGGATTTAGGGGTTGAGTTAGGGT
31533901 TTTGGGTTTAGATTAATTATTTTTTAATTTATATTTTAAATATGTTCTTATATAATTGTAAAAGA
131 TTTGGGTTTAGATTAATTATTTTTTAATTTATATTTTAAATATGTTCTTATATAATTGTAAAAGA
31533966 GATAATAATAAATTTGTTTAGGGTTTTTAGTTTAGGGTATATGATTAATTTAAGATTTAAGGCCG
196 GATAATAATAAATTTGTTTAGGGTTTTTAGTTTAGGGTATATGATTAATTTAAGATTTAAGGCCG
31534031 GTTTAGGAGTTCATATTTTAAGGTTAATTTAGGAAGTATGGATTTAAGGATTATGAA
261 GTTTAGGAGTTCATATTTTAAGGTTAATTTAGGAAGTATGGATTTAAGGATTATGAA
31534088 TTAGGGATTATGGTTTAAGGGATTATGGATTAGGGGTTGAGATTTAAGGTTTAGGGGTTAAAGGG
1 TTAGGGATTATGGTTTAAGGGATTATGGATTAGGGGTTGAGATTTAAGGTTTAGGGGTTAAAGGG
31534153 TTAGGGGTTTAAGGGTTAGACGTGCTAGGGGTTAAAAGTTAGGGATTTAGGGGTTGAGTTAGGGT
66 TTAGGGGTTTAAGGGTTAGACGTGCTAGGGGTTAAAAGTTAGGGATTTAGGGGTTGAGTTAGGGT
31534218 TTTGGGTTTAGATTAATTATTTTTTAATTTATATTTTAAATATGTTCTTATATAATTGTAAAAGA
131 TTTGGGTTTAGATTAATTATTTTTTAATTTATATTTTAAATATGTTCTTATATAATTGTAAAAGA
31534283 GATAATAATAAATTTGTTTAGGGTTTTTAGTTTAGGGTATATGATTAATTTAAGATTTAAGGCCG
196 GATAATAATAAATTTGTTTAGGGTTTTTAGTTTAGGGTATATGATTAATTTAAGATTTAAGGCCG
31534348 GTTTAGGAGTTCATATTTTAAGGTTAATTTAGGAAGTATGGATTTAAGGATTATGAA
261 GTTTAGGAGTTCATATTTTAAGGTTAATTTAGGAAGTATGGATTTAAGGATTATGAA
31534405 TTAGGGATTATGGTTTAAGGG
1 TTAGGGATTATGGTTTAAGGG
31534426 TTGAGATTTA
Statistics
Matches: 335, Mismatches: 2, Indels: 1
0.99 0.01 0.00
Matches are distributed among these distances:
316 14 0.04
317 321 0.96
ACGTcount: A:0.29, C:0.02, G:0.28, T:0.41
Consensus pattern (317 bp):
TTAGGGATTATGGTTTAAGGGATTATGGATTAGGGGTTGAGATTTAAGGTTTAGGGGTTAAAGGG
TTAGGGGTTTAAGGGTTAGACGTGCTAGGGGTTAAAAGTTAGGGATTTAGGGGTTGAGTTAGGGT
TTTGGGTTTAGATTAATTATTTTTTAATTTATATTTTAAATATGTTCTTATATAATTGTAAAAGA
GATAATAATAAATTTGTTTAGGGTTTTTAGTTTAGGGTATATGATTAATTTAAGATTTAAGGCCG
GTTTAGGAGTTCATATTTTAAGGTTAATTTAGGAAGTATGGATTTAAGGATTATGAA
Found at i:31534465 original size:14 final size:14
Alignment explanation
Indices: 31534440--31534480 Score: 57
Period size: 14 Copynumber: 2.9 Consensus size: 14
31534430 GATTTAAGGT
*
31534440 TTAAGGGTTAGGGG
1 TTAAGAGTTAGGGG
31534454 TT-AGATGTTAGGGG
1 TTAAGA-GTTAGGGG
31534468 TTAAGAGTTAGGG
1 TTAAGAGTTAGGG
31534481 ATTTAAGGTT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
13 2 0.08
14 19 0.79
15 3 0.12
ACGTcount: A:0.24, C:0.00, G:0.44, T:0.32
Consensus pattern (14 bp):
TTAAGAGTTAGGGG
Found at i:31535239 original size:241 final size:241
Alignment explanation
Indices: 31534758--31535800 Score: 1711
Period size: 241 Copynumber: 4.3 Consensus size: 241
31534748 TTAATTTTAT
**
31534758 AAAA-AAATCAATTTAT-AAAAA-AAAATAAAAAATTTTTAGCATAGCAAAATAGCGTCATTTTG
1 AAAATAAATCAATTTATAAAAAATAAAATAAAAAA-TTTTAGCATAGCAAAACGGCGTCATTTTG
* *
31534820 TTCAAAATGAAATA-ATATTTTGCGGCATTTTT-ATGAAAAACACCGCAAATAATAAATCAATTA
65 TTCAAAATGAAATAGA-A----GC-G--TTTTTGAT-AAAAACGCCGCAAAAAATAAATCAATTA
* ****
31534883 ATAAAAACCAAAATAGCAAAACGGCGTCATTTTGTTCAAAATGAAAAAAAAAATTTGTGGCGTTT
121 ATAAAAACCAAAATAGCAAAACGGCGTCATTTTGTTCAAAATG--GAAACTTTTTTGTGGCGTTT
*
31534948 TTAATAAAAACGCCGCAAAAGATAAGCAATAGCGGCGTTTTTATAAAAAGCACCACAA
184 TTAATAAAAACGCCGCAAAAGATAAGCAATAGCGGCGTTTTTATAAAAAGCGCCACAA
31535006 AAAATAAATCAATTTATAAAAAATAAAATAAAAAATTTTAGCATAGCAAAACGGCGTCATTTTGT
1 AAAATAAATCAATTTATAAAAAATAAAATAAAAAATTTTAGCATAGCAAAACGGCGTCATTTTGT
31535071 TCAAAATGAAATAGAAGCGTTTTTGATAAAAACGCCGCAAAAAATAAATCAATTAATAAAAACCA
66 TCAAAATGAAATAGAAGCGTTTTTGATAAAAACGCCGCAAAAAATAAATCAATTAATAAAAACCA
31535136 AAATAGCAAAACGGCGTCATTTTGTTCAAAATGGAAACTTTTTTGTGGCGTTTTTAATAAAAACG
131 AAATAGCAAAACGGCGTCATTTTGTTCAAAATGGAAACTTTTTTGTGGCGTTTTTAATAAAAACG
*
31535201 CCGCAAAAGATAAGCAATAGCGGCGTTTTTATAAAAAGCGCCGCAA
196 CCGCAAAAGATAAGCAATAGCGGCGTTTTTATAAAAAGCGCCACAA
*
31535247 AAAATAAATCAATTTATAAAAACTAAAATAAAAAATTTTAGCATAGCAAAACGGCGTCATTTTGT
1 AAAATAAATCAATTTATAAAAAATAAAATAAAAAATTTTAGCATAGCAAAACGGCGTCATTTTGT
**
31535312 TCAAAATGAAATAGCGGCGTTTTTGATAAAAACGCCGCAAAAAATAAATCAATTAATAAAAACCA
66 TCAAAATGAAATAGAAGCGTTTTTGATAAAAACGCCGCAAAAAATAAATCAATTAATAAAAACCA
31535377 AAATAGCAAAACGGCGTCATTTTGTTCAAAATGGAAACTTTTTTGTGGCGTTTTTAATAAAAACG
131 AAATAGCAAAACGGCGTCATTTTGTTCAAAATGGAAACTTTTTTGTGGCGTTTTTAATAAAAACG
*
31535442 CCGCAAAAGATAAGCAATAGCGGCGTTTTTATAAAAAGCGTCACAA
196 CCGCAAAAGATAAGCAATAGCGGCGTTTTTATAAAAAGCGCCACAA
* *
31535488 AAAATAAATCAATTTATAAAAAAATAAAATAAAAAATTTTAGCATAGCAAAACAGCATCATTTTG
1 AAAATAAATCAATTTAT-AAAAAATAAAATAAAAAATTTTAGCATAGCAAAACGGCGTCATTTTG
** * *
31535553 TTCAAAATGAAATAGCGGCATTTTTGAT-AAAATGCCGCAAAAAATAAATCAATTAATAAAAACC
65 TTCAAAATGAAATAGAAGCGTTTTTGATAAAAACGCCGCAAAAAATAAATCAATTAATAAAAACC
*
31535617 AAAATAGCAAAACGGCGTCATTTTGTTCAAAATAGAAACTTTTTTGTGGCGTTTTTAATAAAAAC
130 AAAATAGCAAAACGGCGTCATTTTGTTCAAAATGGAAACTTTTTTGTGGCGTTTTTAATAAAAAC
31535682 GCCGCAAAAGATAAGCAATAGCGGCGTTTTTATAAAAAGCGCCACAA
195 GCCGCAAAAGATAAGCAATAGCGGCGTTTTTATAAAAAGCGCCACAA
*
31535729 AAAATAAATCAATTTATAAAAAAATAAAATAAAAAATTTTAGCATAGCAAAATGGCGTCATTTTG
1 AAAATAAATCAATTTAT-AAAAAATAAAATAAAAAATTTTAGCATAGCAAAACGGCGTCATTTTG
31535794 TTCAAAA
65 TTCAAAA
31535801 GCAAAAAATA
Statistics
Matches: 763, Mismatches: 26, Indels: 19
0.94 0.03 0.02
Matches are distributed among these distances:
241 538 0.71
242 71 0.09
243 74 0.10
244 2 0.00
245 1 0.00
246 2 0.00
248 4 0.01
249 12 0.02
250 47 0.06
251 12 0.02
ACGTcount: A:0.47, C:0.13, G:0.13, T:0.27
Consensus pattern (241 bp):
AAAATAAATCAATTTATAAAAAATAAAATAAAAAATTTTAGCATAGCAAAACGGCGTCATTTTGT
TCAAAATGAAATAGAAGCGTTTTTGATAAAAACGCCGCAAAAAATAAATCAATTAATAAAAACCA
AAATAGCAAAACGGCGTCATTTTGTTCAAAATGGAAACTTTTTTGTGGCGTTTTTAATAAAAACG
CCGCAAAAGATAAGCAATAGCGGCGTTTTTATAAAAAGCGCCACAA
Found at i:31535956 original size:212 final size:213
Alignment explanation
Indices: 31535589--31536013 Score: 789
Period size: 212 Copynumber: 2.0 Consensus size: 213
31535579 ATAAAATGCC
31535589 GCAAAAAATAAATCAATTAATAAAAACCAAAATAGCAAAACGGCGTCATTTTGTTCAAAATAGAA
1 GCAAAAAATAAATCAATTAATAAAAACCAAAATAGCAAAACGGCGTCATTTTGTTCAAAATAGAA
31535654 ACTTTTTTGTGGCGTTTTTAATAAAAACGCCGCAAAAGATAAGCAATAGCGGCGTTTTTATAAAA
66 ACTTTTTTGTGGCGTTTTTAATAAAAACGCCGCAAAAGATAAGCAATAGCGGCGTTTTTATAAAA
*
31535719 AGCGCCACAAAAAATAAATCAATTTATAAAAAAATAAAATAAAAAA-TTTTAGCATAGCAAAATG
131 AGCGCCACAAAAAATAAATCAATTTATAAAAAAATAAAATAAAAAATTTTTAGCATAGCAAAACG
*
31535783 GCGTCATTTTGTTCAAAA
196 GCGTCATTTTATTCAAAA
*
31535801 GCAAAAAATAAATCAATTAATAAAAACCAAAATAGCAAAACGGCGTCATTTTGTTCAAAATGGAA
1 GCAAAAAATAAATCAATTAATAAAAACCAAAATAGCAAAACGGCGTCATTTTGTTCAAAATAGAA
* *
31535866 ACTTTTTTGTGGCGTTTTTAATAAAAACGCCGTAAAAGATAAGTAATAGCGGCGTTTTTATAAAA
66 ACTTTTTTGTGGCGTTTTTAATAAAAACGCCGCAAAAGATAAGCAATAGCGGCGTTTTTATAAAA
*
31535931 AGCGCCGCAAAAAATAAATCAATTTATAAAAAAATAAAATAAAAAATTTTTAGCATAGCAAAACG
131 AGCGCCACAAAAAATAAATCAATTTATAAAAAAATAAAATAAAAAATTTTTAGCATAGCAAAACG
31535996 GCGTCATTTTATTCAAAA
196 GCGTCATTTTATTCAAAA
31536014 TGATTGAATT
Statistics
Matches: 206, Mismatches: 6, Indels: 1
0.97 0.03 0.00
Matches are distributed among these distances:
212 172 0.83
213 34 0.17
ACGTcount: A:0.47, C:0.13, G:0.13, T:0.27
Consensus pattern (213 bp):
GCAAAAAATAAATCAATTAATAAAAACCAAAATAGCAAAACGGCGTCATTTTGTTCAAAATAGAA
ACTTTTTTGTGGCGTTTTTAATAAAAACGCCGCAAAAGATAAGCAATAGCGGCGTTTTTATAAAA
AGCGCCACAAAAAATAAATCAATTTATAAAAAAATAAAATAAAAAATTTTTAGCATAGCAAAACG
GCGTCATTTTATTCAAAA
Found at i:31536201 original size:55 final size:55
Alignment explanation
Indices: 31536117--31536228 Score: 215
Period size: 55 Copynumber: 2.0 Consensus size: 55
31536107 ATACCAAAAC
31536117 GGTGTCGTTTTCTTCCCCAAATCAAATTTGACTTAAAAAAACTTAAAACTGAGCG
1 GGTGTCGTTTTCTTCCCCAAATCAAATTTGACTTAAAAAAACTTAAAACTGAGCG
*
31536172 GGTGTCGTTTTCTTCCCCAAATCAGATTTGACTTAAAAAAACTTAAAACTGAGCG
1 GGTGTCGTTTTCTTCCCCAAATCAAATTTGACTTAAAAAAACTTAAAACTGAGCG
31536227 GG
1 GG
31536229 GTTTTGTATT
Statistics
Matches: 56, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
55 56 1.00
ACGTcount: A:0.33, C:0.20, G:0.17, T:0.30
Consensus pattern (55 bp):
GGTGTCGTTTTCTTCCCCAAATCAAATTTGACTTAAAAAAACTTAAAACTGAGCG
Found at i:31538651 original size:94 final size:94
Alignment explanation
Indices: 31538469--31538658 Score: 254
Period size: 95 Copynumber: 2.0 Consensus size: 94
31538459 TTAGCCTGAG
* * *
31538469 TGCTTCCTCTTTCATTGCCTCTACGCGCTTCCCTTTTTGTTTTTGAATTTTTAAAGCTGGCAATA
1 TGCTTCCTCTTTCATTGCCTCTACGCGCTTCCCTTTTTGTTTTTAAAGTTCTAAAGCTGGCAATA
* * *
31538534 CCATTCTTGCAGTAGGTACCTTTTTCTCA
66 CCATTATTGCAGCACGTACCTTTTTCTCA
* * * **
31538563 TGCTTCCTCTTTCATTGCCTCTATGCGCTTCCCTTTTTTGTTTTTAAAGTTCTAGAGTTGGTGAT
1 TGCTTCCTCTTTCATTGCCTCTACGCGCTTCCC-TTTTTGTTTTTAAAGTTCTAAAGCTGGCAAT
*
31538628 ACCATTATTGCAGCACGTACTTTTTTTCTCA
65 ACCATTATTGCAGCACGTAC-CTTTTTCTCA
31538659 ATTATTATAA
Statistics
Matches: 82, Mismatches: 12, Indels: 2
0.85 0.12 0.02
Matches are distributed among these distances:
94 32 0.39
95 41 0.50
96 9 0.11
ACGTcount: A:0.16, C:0.24, G:0.14, T:0.46
Consensus pattern (94 bp):
TGCTTCCTCTTTCATTGCCTCTACGCGCTTCCCTTTTTGTTTTTAAAGTTCTAAAGCTGGCAATA
CCATTATTGCAGCACGTACCTTTTTCTCA
Found at i:31540003 original size:43 final size:43
Alignment explanation
Indices: 31539954--31540243 Score: 245
Period size: 43 Copynumber: 6.7 Consensus size: 43
31539944 CCATAAATGA
* *
31539954 CGCTAAAGAAT-TGTACTTTTAGCGGCGTTTATGATAAAAGCGC
1 CGCTAAAGAATATGTTC-TTTAGCGGCGTTTATGATAAAAGCAC
* * * *
31539997 CGCTAAAGAGCATAT-TT-TTTAGCGGCATTTGTGATAAAAACGC
1 CGCTAAAGA--ATATGTTCTTTAGCGGCGTTTATGATAAAAGCAC
* * * *
31540040 TGCTAAAG-ATCATGTTCTTTAGCGGCATTTGTGATAAAAACAC
1 CGCTAAAGAAT-ATGTTCTTTAGCGGCGTTTATGATAAAAGCAC
* * *
31540083 TGCTAAAG-ATCATGTTCTTTAGTGGCGTTTGTGATAAAAGCAC
1 CGCTAAAGAAT-ATGTTCTTTAGCGGCGTTTATGATAAAAGCAC
* *
31540126 TGCTAAAG-ATCATGTTCTTTAGCGGCGTTTATAGGT-AAAGCAC
1 CGCTAAAGAAT-ATGTTCTTTAGCGGCGTTTAT-GATAAAAGCAC
* ** *
31540169 CGCTAAAGAACATGTTCTTTAGCGGCGTTT-TGATTTTAAGCGC
1 CGCTAAAGAATATGTTCTTTAGCGGCGTTTATGA-TAAAAGCAC
* ** *
31540212 CGCTAAAGAACATGACCTTTAGCGGAGTTTAT
1 CGCTAAAGAATATGTTCTTTAGCGGCGTTTAT
31540244 TTCTGTAAAC
Statistics
Matches: 216, Mismatches: 20, Indels: 21
0.84 0.08 0.08
Matches are distributed among these distances:
40 2 0.01
41 3 0.01
42 4 0.02
43 199 0.92
44 4 0.02
45 3 0.01
46 1 0.00
ACGTcount: A:0.29, C:0.17, G:0.22, T:0.32
Consensus pattern (43 bp):
CGCTAAAGAATATGTTCTTTAGCGGCGTTTATGATAAAAGCAC
Found at i:31540185 original size:129 final size:128
Alignment explanation
Indices: 31539971--31540202 Score: 306
Period size: 129 Copynumber: 1.8 Consensus size: 128
31539961 GAATTGTACT
* * *
31539971 TTTAGCGGCGTTTATGATAAAAGCGCCGCTAAAGAGCATATTTTTTAGCGGCATTTGTGATAAAA
1 TTTAGCGGCGTTTATGATAAAAGCACCGCTAAAGAGCATATTCTTTAGCGGCATTTATGATAAAA
*
31540036 ACGCTGCTAAAGATCATGTTCTTTAGCGGCATTTGTGATAAAAACACTGCTAAAGATCATGTTC
66 ACGCTGCTAAAGAACATGTTCTTTAGCGGCATTT-TGATAAAAACACTGCTAAAGATCATGTTC
* * * * * * *
31540100 TTTAGTGGCGTTTGTGATAAAAGCACTGCTAAAGATCATGTTCTTTAGCGGCGTTTATAGGTAAA
1 TTTAGCGGCGTTTATGATAAAAGCACCGCTAAAGAGCATATTCTTTAGCGGCATTTAT-GATAAA
* *
31540165 GCAC-C-GCTAAAGAACATGTTCTTTAGCGGCGTTTTGAT
65 -AACGCTGCTAAAGAACATGTTCTTTAGCGGCATTTTGAT
31540203 TTTAAGCGCC
Statistics
Matches: 88, Mismatches: 13, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
128 4 0.05
129 76 0.86
130 6 0.07
131 2 0.02
ACGTcount: A:0.29, C:0.16, G:0.22, T:0.33
Consensus pattern (128 bp):
TTTAGCGGCGTTTATGATAAAAGCACCGCTAAAGAGCATATTCTTTAGCGGCATTTATGATAAAA
ACGCTGCTAAAGAACATGTTCTTTAGCGGCATTTTGATAAAAACACTGCTAAAGATCATGTTC
Found at i:31540217 original size:86 final size:86
Alignment explanation
Indices: 31539971--31540243 Score: 325
Period size: 86 Copynumber: 3.2 Consensus size: 86
31539961 GAATTGTACT
* * * * *
31539971 TTTAGCGGCGTTTATGATAAAAGCGCCGCTAAAGAGCATATTTTTTAGCGGCATTTGTGATAAAA
1 TTTAGCGGCGTTTATGATAAAAGCACCGCTAAAGAACATGTTCTTTAGCGGCGTTTGTGATAAAA
*
31540036 ACGCTGCTAAAGATCATGTTC
66 GCGCTGCTAAAGATCATGTTC
* * * * * *
31540057 TTTAGCGGCATTTGTGATAAAAACACTGCTAAAGATCATGTTCTTTAGTGGCGTTTGTGATAAAA
1 TTTAGCGGCGTTTATGATAAAAGCACCGCTAAAGAACATGTTCTTTAGCGGCGTTTGTGATAAAA
*
31540122 GCACTGCTAAAGATCATGTTC
66 GCGCTGCTAAAGATCATGTTC
* **
31540143 TTTAGCGGCGTTTATAGGT-AAAGCACCGCTAAAGAACATGTTCTTTAGCGGCGTTT-TGATTTT
1 TTTAGCGGCGTTTAT-GATAAAAGCACCGCTAAAGAACATGTTCTTTAGCGGCGTTTGTGA-TAA
* * **
31540206 AAGCGCCGCTAAAGAACATGACC
64 AAGCGCTGCTAAAGATCATGTTC
*
31540229 TTTAGCGGAGTTTAT
1 TTTAGCGGCGTTTAT
31540244 TTCTGTAAAC
Statistics
Matches: 158, Mismatches: 27, Indels: 4
0.84 0.14 0.02
Matches are distributed among these distances:
85 3 0.02
86 153 0.97
87 2 0.01
ACGTcount: A:0.29, C:0.16, G:0.22, T:0.32
Consensus pattern (86 bp):
TTTAGCGGCGTTTATGATAAAAGCACCGCTAAAGAACATGTTCTTTAGCGGCGTTTGTGATAAAA
GCGCTGCTAAAGATCATGTTC
Found at i:31540217 original size:129 final size:129
Alignment explanation
Indices: 31539954--31540243 Score: 300
Period size: 129 Copynumber: 2.2 Consensus size: 129
31539944 CCATAAATGA
* * * *
31539954 CGCTAAAGAA-TTGTACTTTTAGCGGCGTTTATGATAAAAGCGCCGCTAAAGAGCATATTTTTTA
1 CGCTAAAGAACATGTTC-TTTAGCGGCGTTTATGATAAAAGCACCGCTAAAGAGCATATTCTTTA
* *
31540018 GCGGCATTTGTGATAAAAACGCTGCTAAAGATCATGTTCTTTAGCGGCATTTGTGATAAAAACAC
65 GCGGCATTTATGATAAAAACGCTGCTAAAGAACATGTTCTTTAGCGGCATTTGTGATAAAAACAC
* * * * * * *
31540083 TGCTAAAGATCATGTTCTTTAGTGGCGTTTGTGATAAAAGCACTGCTAAAGATCATGTTCTTTAG
1 CGCTAAAGAACATGTTCTTTAGCGGCGTTTATGATAAAAGCACCGCTAAAGAGCATATTCTTTAG
* * * * ** *
31540148 CGGCGTTTATAGGTAAAGCAC-C-GCTAAAGAACATGTTCTTTAGCGGCGTTT-TGATTTTAAGC
66 CGGCATTTAT-GATAAA-AACGCTGCTAAAGAACATGTTCTTTAGCGGCATTTGTGA-TAAAAAC
*
31540210 GC
128 AC
** *
31540212 CGCTAAAGAACATGACCTTTAGCGGAGTTTAT
1 CGCTAAAGAACATGTTCTTTAGCGGCGTTTAT
31540244 TTCTGTAAAC
Statistics
Matches: 129, Mismatches: 28, Indels: 8
0.78 0.17 0.05
Matches are distributed among these distances:
128 3 0.02
129 114 0.88
130 10 0.08
131 2 0.02
ACGTcount: A:0.29, C:0.17, G:0.22, T:0.32
Consensus pattern (129 bp):
CGCTAAAGAACATGTTCTTTAGCGGCGTTTATGATAAAAGCACCGCTAAAGAGCATATTCTTTAG
CGGCATTTATGATAAAAACGCTGCTAAAGAACATGTTCTTTAGCGGCATTTGTGATAAAAACAC
Found at i:31540374 original size:22 final size:22
Alignment explanation
Indices: 31540331--31540374 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
31540321 TAGTGGCGCT
* **
31540331 AAAAAGCGCCGCTAAAGGCCTA
1 AAAAAACGCCGCTAAAAACCTA
*
31540353 AAAAAACGCCGTTAAAAACCTA
1 AAAAAACGCCGCTAAAAACCTA
31540375 TTTTGGTGTA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.48, C:0.25, G:0.16, T:0.11
Consensus pattern (22 bp):
AAAAAACGCCGCTAAAAACCTA
Found at i:31552176 original size:17 final size:17
Alignment explanation
Indices: 31552156--31552191 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
31552146 AACTCTTAAA
31552156 ATTTTTAACATGCTTTT
1 ATTTTTAACATGCTTTT
31552173 ATTTTTAACATGCTTTT
1 ATTTTTAACATGCTTTT
31552190 AT
1 AT
31552192 AAATCTTCAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.25, C:0.11, G:0.06, T:0.58
Consensus pattern (17 bp):
ATTTTTAACATGCTTTT
Found at i:31553917 original size:45 final size:45
Alignment explanation
Indices: 31553848--31553941 Score: 134
Period size: 45 Copynumber: 2.1 Consensus size: 45
31553838 AAGAGATACT
* * *
31553848 CGGTGGATTCAACACATAGCAACCACCTTATTAATCAATGATGTC
1 CGGTGGAATCAACACATAGAAACCACCTTACTAATCAATGATGTC
* * *
31553893 CGGTGGAATCAGCACATAGAAACCATCTTACTAATCAATGATGTT
1 CGGTGGAATCAACACATAGAAACCACCTTACTAATCAATGATGTC
31553938 CGGT
1 CGGT
31553942 TCACATAGTA
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
45 43 1.00
ACGTcount: A:0.33, C:0.22, G:0.18, T:0.27
Consensus pattern (45 bp):
CGGTGGAATCAACACATAGAAACCACCTTACTAATCAATGATGTC
Found at i:31554005 original size:51 final size:51
Alignment explanation
Indices: 31553943--31554064 Score: 163
Period size: 51 Copynumber: 2.4 Consensus size: 51
31553933 ATGTTCGGTT
* * **
31553943 CACATAGTAGCCTACACATAGTACTACACATGTGACCATTACCATCCGATA
1 CACATAGTAGCCTGCACATAGTACTACACACGTGACCAAAACCATCCGATA
* * * *
31553994 CACGTAGTAGCCTGCACATAGTACTACACACGTGATCAAAACTATCCGGTA
1 CACATAGTAGCCTGCACATAGTACTACACACGTGACCAAAACCATCCGATA
*
31554045 CGCATAGTAGCCTGCACATA
1 CACATAGTAGCCTGCACATA
31554065 ATCCGTGCCA
Statistics
Matches: 61, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
51 61 1.00
ACGTcount: A:0.34, C:0.29, G:0.16, T:0.22
Consensus pattern (51 bp):
CACATAGTAGCCTGCACATAGTACTACACACGTGACCAAAACCATCCGATA
Found at i:31557558 original size:20 final size:20
Alignment explanation
Indices: 31557535--31557578 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
31557525 AACAAAAAAA
* *
31557535 TTAAACGGAAAAACTAAGAC
1 TTAAAAGGAAAAACTAACAC
*
31557555 TTAAAAGGAAAAATTAACAC
1 TTAAAAGGAAAAACTAACAC
31557575 TTAA
1 TTAA
31557579 TCACTGAACC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.57, C:0.11, G:0.11, T:0.20
Consensus pattern (20 bp):
TTAAAAGGAAAAACTAACAC
Found at i:31559784 original size:19 final size:20
Alignment explanation
Indices: 31559746--31559792 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
31559736 AAAAATATAA
* *
31559746 ATTTTGGAATTTTTATAAA-T
1 ATTTT-GAAATTTTAAAAATT
31559766 ATTTTGAAATTTTAAAAATT
1 ATTTTGAAATTTTAAAAATT
31559786 ATTTTGA
1 ATTTTGA
31559793 TTTTTTTAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 11 0.46
20 13 0.54
ACGTcount: A:0.38, C:0.00, G:0.09, T:0.53
Consensus pattern (20 bp):
ATTTTGAAATTTTAAAAATT
Done.