Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr2
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 61750188
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 1877335 characters in sequence are not A, C, G, or T
File 79 of 186
Found at i:25437258 original size:101 final size:101
Alignment explanation
Indices: 25437078--25437260 Score: 294
Period size: 101 Copynumber: 1.8 Consensus size: 101
25437068 TCGTTGTGAG
* * *
25437078 TCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATTGATAGGTCGCATGTGTAGTAC
1 TCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATGGATAAGTCACATGTGTAGTAC
25437143 TAAGTGCAGGCTACTATACGTACCCGTTAACTTCGA
66 TAAGTGCAGGCTACTATACGTACCCGTTAACTTCGA
* * ** *
25437179 TCACGTGTGTAGTACTAAGTGCAGGGTACTACGTGTATTAGATGGTTAAGTCACATGTGTAGTAC
1 TCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATGGATAAGTCACATGTGTAGTAC
25437244 TAAGTGCAGGCTACTAT
66 TAAGTGCAGGCTACTAT
25437261 GTGTACTAGA
Statistics
Matches: 74, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
101 74 1.00
ACGTcount: A:0.27, C:0.18, G:0.25, T:0.30
Consensus pattern (101 bp):
TCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATGGATAAGTCACATGTGTAGTAC
TAAGTGCAGGCTACTATACGTACCCGTTAACTTCGA
Found at i:25442684 original size:39 final size:39
Alignment explanation
Indices: 25442630--25442862 Score: 385
Period size: 39 Copynumber: 6.0 Consensus size: 39
25442620 AAGACACTGA
*
25442630 AAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTGCTGG
1 AAATGTATCCGGGCCAAAGTCCCGCAGGCTTCGTGCTGG
* *
25442669 AAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTGTTGG
1 AAATGTATCCGGGCCAAAGTCCCGCAGGCTTCGTGCTGG
*
25442708 AAATATATCCGGGCCAAAGTCCCGCAGGCTTCGTGCTGG
1 AAATGTATCCGGGCCAAAGTCCCGCAGGCTTCGTGCTGG
* *
25442747 AAATGTATCCGGGCCAAAGTCCCGCAGGCTTTGTGCTAG
1 AAATGTATCCGGGCCAAAGTCCCGCAGGCTTCGTGCTGG
25442786 AAATGTATCCGGGCCAAAGTCCCGCAGGCTTCGTGCTGG
1 AAATGTATCCGGGCCAAAGTCCCGCAGGCTTCGTGCTGG
** *
25442825 AAATGTATCCGGGTTAAAGTCCCGCAGGCTTTGTGCTG
1 AAATGTATCCGGGCCAAAGTCCCGCAGGCTTCGTGCTG
25442863 ATAATATAAT
Statistics
Matches: 182, Mismatches: 12, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
39 182 1.00
ACGTcount: A:0.21, C:0.25, G:0.30, T:0.24
Consensus pattern (39 bp):
AAATGTATCCGGGCCAAAGTCCCGCAGGCTTCGTGCTGG
Found at i:25448053 original size:40 final size:39
Alignment explanation
Indices: 25447999--25448132 Score: 115
Period size: 39 Copynumber: 3.4 Consensus size: 39
25447989 TGAATTCAAT
* * *
25447999 CACCAACACAAAGCCTACGGGACGTTAACCCCGGATATAG
1 CACCAGCACGAAGCCTAC-GGACCTTAACCCCGGATATAG
* * **
25448039 CACCAGTACGAAGCCTGCGGACCTTAAGTCCGGATATAG
1 CACCAGCACGAAGCCTACGGACCTTAACCCCGGATATAG
* * * ** * *
25448078 TACCAGCACGAAGCCTGCGGATCTTAAGTCCGGATACAA
1 CACCAGCACGAAGCCTACGGACCTTAACCCCGGATATAG
**
25448117 TTCCAGCACGAAGCCT
1 CACCAGCACGAAGCCT
25448133 GCGGGTCTTT
Statistics
Matches: 81, Mismatches: 13, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
39 67 0.83
40 14 0.17
ACGTcount: A:0.31, C:0.31, G:0.22, T:0.16
Consensus pattern (39 bp):
CACCAGCACGAAGCCTACGGACCTTAACCCCGGATATAG
Found at i:25448156 original size:40 final size:40
Alignment explanation
Indices: 25448041--25448313 Score: 286
Period size: 40 Copynumber: 6.9 Consensus size: 40
25448031 GGATATAGCA
* * * * * * *
25448041 CCAGTACGAAGCCTGC-GGACCTTAAGTCCGGATATAGTA
1 CCAGCACGAAGCCTGCGGGTCTTTAAGCCCGGATACAATT
* *
25448080 CCAGCACGAAGCCTGCGGATC-TTAAGTCCGGATACAATT
1 CCAGCACGAAGCCTGCGGGTCTTTAAGCCCGGATACAATT
25448119 CCAGCACGAAGCCTGCGGGTCTTTAAGCCCGGATACAATT
1 CCAGCACGAAGCCTGCGGGTCTTTAAGCCCGGATACAATT
* *
25448159 CCAGCA-TATAGCCTGCTGGTCTTTAAGCCCGGATACAATT
1 CCAGCACGA-AGCCTGCGGGTCTTTAAGCCCGGATACAATT
* * * * *
25448199 CCAGCACGAAACCTGCGGATCTTTAAGCCTGAATATAATT
1 CCAGCACGAAGCCTGCGGGTCTTTAAGCCCGGATACAATT
* * *
25448239 CCAGCA-TATAGCCTGCGGGTCTTTAAGCCCGAATATAATT
1 CCAGCACGA-AGCCTGCGGGTCTTTAAGCCCGGATACAATT
* * *
25448279 CCAGCA-TATAGCCTGTGGGTCTTTAGGCCCGGATA
1 CCAGCACGA-AGCCTGCGGGTCTTTAAGCCCGGATA
25448314 TACATCAAAT
Statistics
Matches: 205, Mismatches: 24, Indels: 9
0.86 0.10 0.04
Matches are distributed among these distances:
39 52 0.25
40 152 0.74
41 1 0.00
ACGTcount: A:0.27, C:0.27, G:0.23, T:0.24
Consensus pattern (40 bp):
CCAGCACGAAGCCTGCGGGTCTTTAAGCCCGGATACAATT
Found at i:25448206 original size:80 final size:79
Alignment explanation
Indices: 25448041--25448315 Score: 315
Period size: 80 Copynumber: 3.5 Consensus size: 79
25448031 GGATATAGCA
* * * * * * *
25448041 CCAGTACGAAGCCTGC-GGACCTTAAGTCCGGATATAGTACCAGCACGA-AGCCTGCGGATC-TT
1 CCAGCACGAAGCCTGCGGGTCTTTAAGCCCGGATATAATTCCAGCA-TATAGCCTGCGG-TCTTT
*
25448103 AAGTCCGGATACAATT
64 AAGCCCGGATACAATT
*
25448119 CCAGCACGAAGCCTGCGGGTCTTTAAGCCCGGATACAATTCCAGCATATAGCCTGCTGGTCTTTA
1 CCAGCACGAAGCCTGCGGGTCTTTAAGCCCGGATATAATTCCAGCATATAGCCTGC-GGTCTTTA
25448184 AGCCCGGATACAATT
65 AGCCCGGATACAATT
* * * *
25448199 CCAGCACGAAACCTGCGGATCTTTAAGCCTGAATATAATTCCAGCATATAGCCTGCGGGTCTTTA
1 CCAGCACGAAGCCTGCGGGTCTTTAAGCCCGGATATAATTCCAGCATATAGCCTGC-GGTCTTTA
* *
25448264 AGCCCGAATATAATT
65 AGCCCGGATACAATT
* * *
25448279 CCAGCA-TATAGCCTGTGGGTCTTTAGGCCCGGATATA
1 CCAGCACGA-AGCCTGCGGGTCTTTAAGCCCGGATATA
25448316 CATCAAATAT
Statistics
Matches: 168, Mismatches: 24, Indels: 8
0.84 0.12 0.04
Matches are distributed among these distances:
78 16 0.10
79 33 0.20
80 119 0.71
ACGTcount: A:0.27, C:0.27, G:0.23, T:0.24
Consensus pattern (79 bp):
CCAGCACGAAGCCTGCGGGTCTTTAAGCCCGGATATAATTCCAGCATATAGCCTGCGGTCTTTAA
GCCCGGATACAATT
Found at i:25448266 original size:120 final size:119
Alignment explanation
Indices: 25448062--25448313 Score: 348
Period size: 120 Copynumber: 2.1 Consensus size: 119
25448052 CCTGCGGACC
* * * * *
25448062 TTAAGTCCGGATATAGTACCAGCACGAAGCCTGCGGATCTTAAGTCCGGATACAATTCCAGCACG
1 TTAAGCCCGGATACAATACCAGCACGAAACCTGCGGATCTTAAGTCCGAATACAATTCCAGCACG
*
25448127 AAGCCTGCGGGTCTTTAAGCCCGGATACAATTCCAGCATATAGCCTGCT-GGTCT
66 AAGCCTGCGGGTCTTTAAGCCCGAATACAATTCCAGCATATAGCCTG-TGGGTCT
* *
25448181 TTAAGCCCGGATACAATTCCAGCACGAAACCTGCGGATCTTTAAG-CCTGAATATAATTCCAGCA
1 TTAAGCCCGGATACAATACCAGCACGAAACCTGCGGATC-TTAAGTCC-GAATACAATTCCAGCA
* *
25448245 -TATAGCCTGCGGGTCTTTAAGCCCGAATATAATTCCAGCATATAGCCTGTGGGTCT
64 CGA-AGCCTGCGGGTCTTTAAGCCCGAATACAATTCCAGCATATAGCCTGTGGGTCT
*
25448301 TTAGGCCCGGATA
1 TTAAGCCCGGATA
25448314 TACATCAAAT
Statistics
Matches: 118, Mismatches: 11, Indels: 7
0.87 0.08 0.05
Matches are distributed among these distances:
119 38 0.32
120 80 0.68
ACGTcount: A:0.27, C:0.26, G:0.22, T:0.25
Consensus pattern (119 bp):
TTAAGCCCGGATACAATACCAGCACGAAACCTGCGGATCTTAAGTCCGAATACAATTCCAGCACG
AAGCCTGCGGGTCTTTAAGCCCGAATACAATTCCAGCATATAGCCTGTGGGTCT
Found at i:25465790 original size:46 final size:47
Alignment explanation
Indices: 25465684--25465805 Score: 138
Period size: 46 Copynumber: 2.6 Consensus size: 47
25465674 TGTCTTCGAC
** * *
25465684 ATGGACTTACATGAATTATTCCTGTCTCCAATGCCATATATATATATAAT
1 ATGGACTTACATGGCTCATTCCTGTCTCCAAAGCC--A-ATATATATAAT
* * *
25465734 ATGGGCTTACATGGCTCATTCCTGTCTCCAAAGCC-ATATATCTGAT
1 ATGGACTTACATGGCTCATTCCTGTCTCCAAAGCCAATATATATAAT
*
25465780 ATGGACTTACATGGCTCATTTCTGTC
1 ATGGACTTACATGGCTCATTCCTGTC
25465806 CTGTCCTGTC
Statistics
Matches: 63, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
46 33 0.52
50 30 0.48
ACGTcount: A:0.27, C:0.22, G:0.15, T:0.36
Consensus pattern (47 bp):
ATGGACTTACATGGCTCATTCCTGTCTCCAAAGCCAATATATATAAT
Found at i:25474960 original size:25 final size:25
Alignment explanation
Indices: 25474932--25474999 Score: 100
Period size: 25 Copynumber: 2.7 Consensus size: 25
25474922 GTACATGTAC
*
25474932 GCTCACATGAGCTGTGAATCAAAAT
1 GCTCACACGAGCTGTGAATCAAAAT
* *
25474957 GCTCACACAAGCTGTGAATCAGAAT
1 GCTCACACGAGCTGTGAATCAAAAT
*
25474982 GCTCACACGAGTTGTGAA
1 GCTCACACGAGCTGTGAA
25475000 AATGGGCCTG
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 38 1.00
ACGTcount: A:0.34, C:0.22, G:0.22, T:0.22
Consensus pattern (25 bp):
GCTCACACGAGCTGTGAATCAAAAT
Found at i:25475741 original size:21 final size:20
Alignment explanation
Indices: 25475716--25475759 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
25475706 TACTTTTAAA
*
25475716 TATCAATCAACATTCTAAATT
1 TATCAATCAACA-TCTAAAAT
* *
25475737 TATCAGTTAACATCTAAAAT
1 TATCAATCAACATCTAAAAT
25475757 TAT
1 TAT
25475760 AAGTTTCATC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 10 0.50
21 10 0.50
ACGTcount: A:0.43, C:0.16, G:0.02, T:0.39
Consensus pattern (20 bp):
TATCAATCAACATCTAAAAT
Found at i:25475754 original size:20 final size:21
Alignment explanation
Indices: 25475724--25475764 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
25475714 AATATCAATC
* *
25475724 AACATTCTAAATTTATCAGTT
1 AACATTCTAAAATTATAAGTT
25475745 AACA-TCTAAAATTATAAGTT
1 AACATTCTAAAATTATAAGTT
25475765 TCATCAATAG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.44, C:0.12, G:0.05, T:0.39
Consensus pattern (21 bp):
AACATTCTAAAATTATAAGTT
Found at i:25477051 original size:30 final size:30
Alignment explanation
Indices: 25477015--25477077 Score: 101
Period size: 30 Copynumber: 2.1 Consensus size: 30
25477005 ACTTAACAAG
*
25477015 CAAATGT-TTCTAAAATAATAACAAAATTAA
1 CAAATGTCTT-TAAAATAATAAAAAAATTAA
25477045 CAAATGTCTTTAAAATAATAAAAAAATTAA
1 CAAATGTCTTTAAAATAATAAAAAAATTAA
25477075 CAA
1 CAA
25477078 TAAAATAAGT
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
30 29 0.94
31 2 0.06
ACGTcount: A:0.59, C:0.10, G:0.03, T:0.29
Consensus pattern (30 bp):
CAAATGTCTTTAAAATAATAAAAAAATTAA
Found at i:25477132 original size:22 final size:22
Alignment explanation
Indices: 25477106--25477154 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
25477096 ATATCCAAAC
25477106 AATAACAACAAAATAGTAGCAA
1 AATAACAACAAAATAGTAGCAA
* * **
25477128 CATAATAGTAAAATAGTAGCAA
1 AATAACAACAAAATAGTAGCAA
25477150 AATAA
1 AATAA
25477155 AGAGAAAGTA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.61, C:0.10, G:0.10, T:0.18
Consensus pattern (22 bp):
AATAACAACAAAATAGTAGCAA
Found at i:25477153 original size:11 final size:11
Alignment explanation
Indices: 25477114--25477153 Score: 53
Period size: 11 Copynumber: 3.6 Consensus size: 11
25477104 ACAATAACAA
25477114 CAAAATAGTAG
1 CAAAATAGTAG
* *
25477125 CAACATAATAG
1 CAAAATAGTAG
*
25477136 TAAAATAGTAG
1 CAAAATAGTAG
25477147 CAAAATA
1 CAAAATA
25477154 AAGAGAAAGT
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
11 23 1.00
ACGTcount: A:0.57, C:0.10, G:0.12, T:0.20
Consensus pattern (11 bp):
CAAAATAGTAG
Found at i:25490394 original size:51 final size:49
Alignment explanation
Indices: 25490266--25490404 Score: 188
Period size: 51 Copynumber: 2.8 Consensus size: 49
25490256 TATTGTGAGG
* * * * * *
25490266 TCACGTGTATAGTACTAAGTGCAGGCTACTACGTGTACCGAATAATTGG
1 TCACGTGTGTAGTACTAAGTGCAGGCTACTATGCGTACCCAAAAATTGA
* *
25490315 TCGCATGTGTAGTACTAAGTGCAGGCTACTATGCGTACCCAAAAACTGTGA
1 TCACGTGTGTAGTACTAAGTGCAGGCTACTATGCGTACCCAAAAA-T-TGA
25490366 TCACGTGTGTAGTACTAAGTGCAGGCTACTATGCGTACC
1 TCACGTGTGTAGTACTAAGTGCAGGCTACTATGCGTACC
25490405 AGATAGCTTC
Statistics
Matches: 78, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
49 38 0.49
50 1 0.01
51 39 0.50
ACGTcount: A:0.27, C:0.21, G:0.24, T:0.27
Consensus pattern (49 bp):
TCACGTGTGTAGTACTAAGTGCAGGCTACTATGCGTACCCAAAAATTGA
Found at i:25496442 original size:30 final size:26
Alignment explanation
Indices: 25496374--25496428 Score: 101
Period size: 26 Copynumber: 2.1 Consensus size: 26
25496364 TAATCTCATG
*
25496374 ACCATAATTCCTTCCATCACAAACTT
1 ACCATAATTCATTCCATCACAAACTT
25496400 ACCATAATTCATTCCATCACAAACTT
1 ACCATAATTCATTCCATCACAAACTT
25496426 ACC
1 ACC
25496429 TTGAAATCAT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.36, C:0.35, G:0.00, T:0.29
Consensus pattern (26 bp):
ACCATAATTCATTCCATCACAAACTT
Found at i:25498637 original size:18 final size:17
Alignment explanation
Indices: 25498601--25498639 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 17
25498591 ATCAAAGGAT
25498601 ATAAACTTACTATTAAC
1 ATAAACTTACTATTAAC
25498618 ATAAACTTA-TATGCTAAC
1 ATAAACTTACTAT--TAAC
25498636 ATAA
1 ATAA
25498640 TCCCATCAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
16 3 0.15
17 9 0.45
18 8 0.40
ACGTcount: A:0.49, C:0.15, G:0.03, T:0.33
Consensus pattern (17 bp):
ATAAACTTACTATTAAC
Found at i:25500994 original size:50 final size:50
Alignment explanation
Indices: 25500940--25501040 Score: 193
Period size: 50 Copynumber: 2.0 Consensus size: 50
25500930 ACGGGAATTT
*
25500940 TTTAAATTTTTAGCTAAATGTTAAATATGTCTGTAGGTAAAAGTAGAGCA
1 TTTAAATTTTTAGCTAAATATTAAATATGTCTGTAGGTAAAAGTAGAGCA
25500990 TTTAAATTTTTAGCTAAATATTAAATATGTCTGTAGGTAAAAGTAGAGCA
1 TTTAAATTTTTAGCTAAATATTAAATATGTCTGTAGGTAAAAGTAGAGCA
25501040 T
1 T
25501041 CAGGTATCGT
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
50 50 1.00
ACGTcount: A:0.39, C:0.06, G:0.17, T:0.39
Consensus pattern (50 bp):
TTTAAATTTTTAGCTAAATATTAAATATGTCTGTAGGTAAAAGTAGAGCA
Found at i:25503669 original size:23 final size:23
Alignment explanation
Indices: 25503639--25503688 Score: 82
Period size: 23 Copynumber: 2.2 Consensus size: 23
25503629 AATTGTTGTA
*
25503639 TTTATTTCATTAAGATTTTTGGT
1 TTTATTTCAGTAAGATTTTTGGT
*
25503662 TTTATTTCAGTAAGATTTTTTGT
1 TTTATTTCAGTAAGATTTTTGGT
25503685 TTTA
1 TTTA
25503689 ATACGTCAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.22, C:0.04, G:0.12, T:0.62
Consensus pattern (23 bp):
TTTATTTCAGTAAGATTTTTGGT
Found at i:25514806 original size:17 final size:19
Alignment explanation
Indices: 25514770--25514806 Score: 51
Period size: 17 Copynumber: 2.1 Consensus size: 19
25514760 TAAAGAGCAA
*
25514770 AAATGTTGTTCTATTAGCT
1 AAATGTTGTTCTAATAGCT
25514789 AAATG-TGTTC-AATAGCT
1 AAATGTTGTTCTAATAGCT
25514806 A
1 A
25514807 TAGAACCATA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
17 7 0.41
18 5 0.29
19 5 0.29
ACGTcount: A:0.32, C:0.11, G:0.16, T:0.41
Consensus pattern (19 bp):
AAATGTTGTTCTAATAGCT
Found at i:25521719 original size:40 final size:40
Alignment explanation
Indices: 25521664--25521799 Score: 163
Period size: 40 Copynumber: 3.4 Consensus size: 40
25521654 GATGATAACG
* *
25521664 GGGCTAAGTCCCGAAGGCATTTGTGC-TAGTGACTA-ATTCC
1 GGGCTAAGTCCCGAAGGCATTTGTGCGAACT-ACTATA-TCC
25521704 GGGCTAAGTCCCGAAGGCATTTGTGCGAACTACTATATCC
1 GGGCTAAGTCCCGAAGGCATTTGTGCGAACTACTATATCC
* *
25521744 GGGCTAAGTCCCGAAGGCATTTGAGCG-AGTAGCTATATCC
1 GGGCTAAGTCCCGAAGGCATTTGTGCGAACTA-CTATATCC
* *
25521784 -GGTTAAATCCCGAAGG
1 GGGCTAAGTCCCGAAGG
25521800 TACTTGGTTT
Statistics
Matches: 87, Mismatches: 6, Indels: 7
0.87 0.06 0.07
Matches are distributed among these distances:
39 17 0.20
40 67 0.77
41 3 0.03
ACGTcount: A:0.25, C:0.23, G:0.28, T:0.24
Consensus pattern (40 bp):
GGGCTAAGTCCCGAAGGCATTTGTGCGAACTACTATATCC
Found at i:25524562 original size:8 final size:8
Alignment explanation
Indices: 25524541--25524573 Score: 57
Period size: 8 Copynumber: 4.0 Consensus size: 8
25524531 AAAAATTTTG
25524541 AAAGAATAA
1 AAAGAAT-A
25524550 AAAGAATA
1 AAAGAATA
25524558 AAAGAATA
1 AAAGAATA
25524566 AAAGAATA
1 AAAGAATA
25524574 GGAAAACTCT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 17 0.71
9 7 0.29
ACGTcount: A:0.76, C:0.00, G:0.12, T:0.12
Consensus pattern (8 bp):
AAAGAATA
Found at i:25525610 original size:21 final size:21
Alignment explanation
Indices: 25525586--25525655 Score: 61
Period size: 21 Copynumber: 3.2 Consensus size: 21
25525576 ACTATGTGAG
25525586 CTGAACTCATTGAGTTGTGGT
1 CTGAACTCATTGAGTTGTGGT
** *
25525607 CTGAGTTCA-TGATATATGTGGCAT
1 CTGAACTCATTGA-GT-TGTGG--T
*
25525631 CTGAACTCATTGAGTTATGGT
1 CTGAACTCATTGAGTTGTGGT
25525652 CTGA
1 CTGA
25525656 GTTCATGATG
Statistics
Matches: 37, Mismatches: 7, Indels: 10
0.69 0.13 0.19
Matches are distributed among these distances:
20 3 0.08
21 13 0.35
22 5 0.14
23 4 0.11
24 9 0.24
25 3 0.08
ACGTcount: A:0.23, C:0.14, G:0.26, T:0.37
Consensus pattern (21 bp):
CTGAACTCATTGAGTTGTGGT
Found at i:25525640 original size:45 final size:45
Alignment explanation
Indices: 25525586--25525671 Score: 154
Period size: 45 Copynumber: 1.9 Consensus size: 45
25525576 ACTATGTGAG
*
25525586 CTGAACTCATTGAGTTGTGGTCTGAGTTCATGATATATGTGGCAT
1 CTGAACTCATTGAGTTATGGTCTGAGTTCATGATATATGTGGCAT
*
25525631 CTGAACTCATTGAGTTATGGTCTGAGTTCATGATGTATGTG
1 CTGAACTCATTGAGTTATGGTCTGAGTTCATGATATATGTG
25525672 ACACAAGTTT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
45 39 1.00
ACGTcount: A:0.22, C:0.13, G:0.27, T:0.38
Consensus pattern (45 bp):
CTGAACTCATTGAGTTATGGTCTGAGTTCATGATATATGTGGCAT
Found at i:25537265 original size:82 final size:83
Alignment explanation
Indices: 25537079--25537265 Score: 218
Period size: 83 Copynumber: 2.3 Consensus size: 83
25537069 TAGTAACATG
** * *
25537079 GGCATGTGGTTAGGTCGTGTGTCACCTGTACCTTAATATTGAGAAACAGAATGCTCATAATTGGT
1 GGCATGTGGTTAGACCGTGTGTCACCTGCACCTTAATATTGAGAAACAGAATGCTCAGAATTGGT
* **
25537144 CACACGGGCAGAGACATG
66 CACACGAGCAGAGACACA
* * * *
25537162 GGCATGTGGTTAGGCCATGTGTCTCCTGCACCTTAATTTTGAGAAACA-AATGCTCAGAATTGGG
1 GGCATGTGGTTAGACCGTGTGTCACCTGCACCTTAATATTGAGAAACAGAATGCTCAGAATT-GG
*
25537226 T-ACACGAGTAGAGACACA
65 TCACACGAGCAGAGACACA
*
25537244 GGCATGT-GTCTCGACCGTGTGT
1 GGCATGTGGT-TAGACCGTGTGT
25537266 GCTACATAGC
Statistics
Matches: 89, Mismatches: 13, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
81 2 0.02
82 41 0.46
83 46 0.52
ACGTcount: A:0.26, C:0.19, G:0.28, T:0.27
Consensus pattern (83 bp):
GGCATGTGGTTAGACCGTGTGTCACCTGCACCTTAATATTGAGAAACAGAATGCTCAGAATTGGT
CACACGAGCAGAGACACA
Found at i:25545816 original size:50 final size:51
Alignment explanation
Indices: 25545760--25545896 Score: 177
Period size: 51 Copynumber: 2.7 Consensus size: 51
25545750 ATCTAGTACG
*
25545760 CATAGTAGCCTGCACTTAGTACTACACACGTGACCTAA-CCATCTAATACA
1 CATAGTAGCCTGCACTTAGTACTACACACGTGACCTAAGCCATCGAATACA
* * * * ** ** *
25545810 CGTAGTAGCCTGCACTTAGTACTACACATGTGATCGAAGTTATCGGGTACG
1 CATAGTAGCCTGCACTTAGTACTACACACGTGACCTAAGCCATCGAATACA
25545861 CATAGTAGCCTGCACTTAGTACTACACACGTGACCT
1 CATAGTAGCCTGCACTTAGTACTACACACGTGACCT
25545897 CACAATAGAT
Statistics
Matches: 72, Mismatches: 14, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
50 34 0.47
51 38 0.53
ACGTcount: A:0.29, C:0.27, G:0.18, T:0.26
Consensus pattern (51 bp):
CATAGTAGCCTGCACTTAGTACTACACACGTGACCTAAGCCATCGAATACA
Found at i:25545888 original size:51 final size:50
Alignment explanation
Indices: 25545754--25545895 Score: 185
Period size: 50 Copynumber: 2.8 Consensus size: 50
25545744 AAGGCAATCT
* *
25545754 AGTACGCATAGTAGCCTGCACTTAGTACTACACACGTGACCTAACCATCT
1 AGTACGCATAGTAGCCTGCACTTAGTACTACACACGTGACCGAACCATCG
* * * * * **
25545804 AATACACGTAGTAGCCTGCACTTAGTACTACACATGTGATCGAAGTTATCG
1 AGTACGCATAGTAGCCTGCACTTAGTACTACACACGTGACCGAA-CCATCG
*
25545855 GGTACGCATAGTAGCCTGCACTTAGTACTACACACGTGACC
1 AGTACGCATAGTAGCCTGCACTTAGTACTACACACGTGACC
25545896 TCACAATAGA
Statistics
Matches: 76, Mismatches: 15, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
50 38 0.50
51 38 0.50
ACGTcount: A:0.30, C:0.27, G:0.19, T:0.25
Consensus pattern (50 bp):
AGTACGCATAGTAGCCTGCACTTAGTACTACACACGTGACCGAACCATCG
Found at i:25557434 original size:17 final size:17
Alignment explanation
Indices: 25557412--25557445 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
25557402 ATCCACTAAT
*
25557412 CCACTACCACCAACAAC
1 CCACTACCAACAACAAC
25557429 CCACTACCAACAACAAC
1 CCACTACCAACAACAAC
25557446 AATCCACTAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.50, G:0.00, T:0.06
Consensus pattern (17 bp):
CCACTACCAACAACAAC
Found at i:25562073 original size:17 final size:17
Alignment explanation
Indices: 25562051--25562084 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
25562041 ATCCACTAAT
*
25562051 CCACTACCACCAACAAC
1 CCACTACCAACAACAAC
25562068 CCACTACCAACAACAAC
1 CCACTACCAACAACAAC
25562085 AATCCACTAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.50, G:0.00, T:0.06
Consensus pattern (17 bp):
CCACTACCAACAACAAC
Found at i:25569364 original size:7 final size:7
Alignment explanation
Indices: 25569352--25569376 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
25569342 TTAGCTTCCA
25569352 TTTTCTT
1 TTTTCTT
25569359 TTTTCTT
1 TTTTCTT
25569366 TTTTCTT
1 TTTTCTT
25569373 TTTT
1 TTTT
25569377 ATTACTAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (7 bp):
TTTTCTT
Found at i:25569778 original size:17 final size:18
Alignment explanation
Indices: 25569756--25569796 Score: 66
Period size: 17 Copynumber: 2.3 Consensus size: 18
25569746 AAAAAACCTA
25569756 TAAAAATTATTAAA-AAT
1 TAAAAATTATTAAATAAT
*
25569773 TAAAAATTATTAAATTAT
1 TAAAAATTATTAAATAAT
25569791 TAAAAA
1 TAAAAA
25569797 AGTATAAATT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 14 0.64
18 8 0.36
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (18 bp):
TAAAAATTATTAAATAAT
Found at i:25580576 original size:35 final size:36
Alignment explanation
Indices: 25580536--25580611 Score: 86
Period size: 35 Copynumber: 2.2 Consensus size: 36
25580526 CACTAGTCAG
**
25580536 ACAGATTTACA-A-TAGGGCCTGCGCCCATGTCAGAT
1 ACAGA-TTACAGATTAGGGCCTGAACCCATGTCAGAT
* *
25580571 ACAGA-TACAGATTCGGGCCTGAACCCATTTCAGAT
1 ACAGATTACAGATTAGGGCCTGAACCCATGTCAGAT
25580606 ACAGAT
1 ACAGAT
25580612 ATAGTTACAG
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
33 4 0.12
34 1 0.03
35 29 0.85
ACGTcount: A:0.32, C:0.25, G:0.21, T:0.22
Consensus pattern (36 bp):
ACAGATTACAGATTAGGGCCTGAACCCATGTCAGAT
Found at i:25582275 original size:21 final size:21
Alignment explanation
Indices: 25582233--25582275 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
25582223 TTAATTTTAG
***
25582233 TCTTAGTTTTTCTAGGTTTTC
1 TCTTAGTTTTTCTAGAACTTC
*
25582254 TCTTAGTTTTTCTATAACTTC
1 TCTTAGTTTTTCTAGAACTTC
25582275 T
1 T
25582276 TCTACGGTTT
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:0.14, C:0.16, G:0.09, T:0.60
Consensus pattern (21 bp):
TCTTAGTTTTTCTAGAACTTC
Found at i:25583652 original size:24 final size:23
Alignment explanation
Indices: 25583616--25583701 Score: 84
Period size: 23 Copynumber: 3.7 Consensus size: 23
25583606 CCGATATATT
*
25583616 AGCTCATAAGAGCTTACTATTTTC
1 AGCTCATTAGAGCTTAC-ATTTTC
* **
25583640 AGCTCATTGGAGCTTACCGTTTC
1 AGCTCATTAGAGCTTACATTTTC
*
25583663 AGCTCAATAGAGCTTACCATTTT-
1 AGCTCATTAGAGCTTA-CATTTTC
* *
25583686 TGCTCAATAGAGCTTA
1 AGCTCATTAGAGCTTA
25583702 TTGTTCATCA
Statistics
Matches: 52, Mismatches: 9, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
23 33 0.63
24 19 0.37
ACGTcount: A:0.27, C:0.22, G:0.16, T:0.35
Consensus pattern (23 bp):
AGCTCATTAGAGCTTACATTTTC
Found at i:25583666 original size:23 final size:23
Alignment explanation
Indices: 25583636--25583701 Score: 87
Period size: 23 Copynumber: 2.9 Consensus size: 23
25583626 AGCTTACTAT
* *
25583636 TTTCAGCTCATTGGAGCTTACCG
1 TTTCAGCTCAATAGAGCTTACCG
*
25583659 TTTCAGCTCAATAGAGCTTACCA
1 TTTCAGCTCAATAGAGCTTACCG
**
25583682 TTTTTGCTCAATAGAGCTTA
1 TTTCAGCTCAATAGAGCTTA
25583702 TTGTTCATCA
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.24, C:0.23, G:0.17, T:0.36
Consensus pattern (23 bp):
TTTCAGCTCAATAGAGCTTACCG
Found at i:25585538 original size:13 final size:13
Alignment explanation
Indices: 25585520--25585546 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
25585510 TTTTGCAAAA
25585520 GTTGTAAAAATGT
1 GTTGTAAAAATGT
25585533 GTTGTAAAAATGT
1 GTTGTAAAAATGT
25585546 G
1 G
25585547 AAAATAATGG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.37, C:0.00, G:0.26, T:0.37
Consensus pattern (13 bp):
GTTGTAAAAATGT
Found at i:25587859 original size:46 final size:46
Alignment explanation
Indices: 25587792--25587969 Score: 214
Period size: 46 Copynumber: 3.8 Consensus size: 46
25587782 TGTAACCCGC
*
25587792 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGTGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGATGTTCGCAT
* * * *
25587838 CCATAAGTAAACTCGGACTCAACTCAACGAGCTCGGATGCCTAG-TT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGATG-TTCGCAT
* *** * * **
25587884 ACATCTCTCGAACTCGGACTCAACTCAATGAGTTCGGACATTCGCAT
1 CCATAAGT-GAACTCGGACTCAACTCAACGAGCTCGGATGTTCGCAT
25587931 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGATG
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGATG
25587970 CTCAACCATC
Statistics
Matches: 104, Mismatches: 25, Indels: 6
0.77 0.19 0.04
Matches are distributed among these distances:
46 71 0.68
47 33 0.32
ACGTcount: A:0.29, C:0.29, G:0.21, T:0.22
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGATGTTCGCAT
Found at i:25587928 original size:93 final size:93
Alignment explanation
Indices: 25587800--25587970 Score: 288
Period size: 93 Copynumber: 1.8 Consensus size: 93
25587790 GCCCATAAGT
***
25587800 GAACTCGGACTCAACTCAACGAGCTCGGGTGTTCGCATCCATAAGTAAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTAAACTCGGACTCAACTCAA
25587865 CGAGCTCGGATGCCTAGTTACATCTCTC
66 CGAGCTCGGATGCCTAGTTACATCTCTC
* * *
25587893 GAACTCGGACTCAACTCAATGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTAAACTCGGACTCAACTCAA
25587958 CGAGCTCGGATGC
66 CGAGCTCGGATGC
25587971 TCAACCATCC
Statistics
Matches: 72, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
93 72 1.00
ACGTcount: A:0.28, C:0.29, G:0.21, T:0.22
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTAAACTCGGACTCAACTCAA
CGAGCTCGGATGCCTAGTTACATCTCTC
Found at i:25589044 original size:207 final size:207
Alignment explanation
Indices: 25588689--25589109 Score: 779
Period size: 207 Copynumber: 2.0 Consensus size: 207
25588679 CACCTATGGG
* * * *
25588689 TATTTTTCCAAATATGAACCCTAGGTTGAATTATTGCTAGCATAAGCTTAATTGAGCTACCGGGA
1 TATTTTTCCAAATATAAACCCTAGGTTAAATTATTGCTAACATAAGCTTAATCGAGCTACCGGGA
25588754 CTCCAAAAACGTAAAAATCATTAAAAACGGGGCTTGGAATCACTTACTATGGAGCTTGGAAGCTT
66 CTCCAAAAACGTAAAAATCATTAAAAACGGGGCTTGGAATCACTTACTATGGAGCTTGGAAGCTT
25588819 GAAACAAACCCTAGCTATGGAGAACCCTTGAAATTTCGGCCTAATGAAGAAGATGGACAAAAATT
131 GAAACAAACCCTAGCTATGGAGAACCCTTGAAATTTCGGCCTAATGAAGAAGATGGACAAAAATT
25588884 GGCTTTTAATTT
196 GGCTTTTAATTT
25588896 TATTTTTCCAAATATAAACCCTAGGTTAAATTATTGCTAACATAAGCTTAATCGAGCTACCGGGA
1 TATTTTTCCAAATATAAACCCTAGGTTAAATTATTGCTAACATAAGCTTAATCGAGCTACCGGGA
* *
25588961 TTCCAAAAACGTAAAGATCATTAAAAACGGGGCTTGGAATCACTTACTATGGAGCTTGGAAGCTT
66 CTCCAAAAACGTAAAAATCATTAAAAACGGGGCTTGGAATCACTTACTATGGAGCTTGGAAGCTT
25589026 GAAACAAACCCTAGCTATGGAGAACCCTTGAAATTTCGGCCTAATGAAGAAGATGGACAAAAATT
131 GAAACAAACCCTAGCTATGGAGAACCCTTGAAATTTCGGCCTAATGAAGAAGATGGACAAAAATT
25589091 GGCTTTTAATTT
196 GGCTTTTAATTT
*
25589103 TGTTTTT
1 TATTTTT
25589110 AATTCATTTT
Statistics
Matches: 207, Mismatches: 7, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
207 207 1.00
ACGTcount: A:0.35, C:0.17, G:0.19, T:0.29
Consensus pattern (207 bp):
TATTTTTCCAAATATAAACCCTAGGTTAAATTATTGCTAACATAAGCTTAATCGAGCTACCGGGA
CTCCAAAAACGTAAAAATCATTAAAAACGGGGCTTGGAATCACTTACTATGGAGCTTGGAAGCTT
GAAACAAACCCTAGCTATGGAGAACCCTTGAAATTTCGGCCTAATGAAGAAGATGGACAAAAATT
GGCTTTTAATTT
Found at i:25589171 original size:35 final size:35
Alignment explanation
Indices: 25589125--25589193 Score: 129
Period size: 35 Copynumber: 2.0 Consensus size: 35
25589115 ATTTTAATAA
25589125 CTAAATGACCAAAATACCCTTACTACTAAACTTTG
1 CTAAATGACCAAAATACCCTTACTACTAAACTTTG
*
25589160 CTAAATGACCAAAATACCCTTACTGCTAAACTTT
1 CTAAATGACCAAAATACCCTTACTACTAAACTTT
25589194 CCAAAAATTC
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.39, C:0.26, G:0.06, T:0.29
Consensus pattern (35 bp):
CTAAATGACCAAAATACCCTTACTACTAAACTTTG
Found at i:25591380 original size:19 final size:19
Alignment explanation
Indices: 25591356--25591415 Score: 120
Period size: 19 Copynumber: 3.2 Consensus size: 19
25591346 TTAGAATACT
25591356 CTAGTGTTTTATTGTAACA
1 CTAGTGTTTTATTGTAACA
25591375 CTAGTGTTTTATTGTAACA
1 CTAGTGTTTTATTGTAACA
25591394 CTAGTGTTTTATTGTAACA
1 CTAGTGTTTTATTGTAACA
25591413 CTA
1 CTA
25591416 AAAATATTAT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 41 1.00
ACGTcount: A:0.27, C:0.12, G:0.15, T:0.47
Consensus pattern (19 bp):
CTAGTGTTTTATTGTAACA
Found at i:25600145 original size:40 final size:40
Alignment explanation
Indices: 25600090--25600391 Score: 511
Period size: 40 Copynumber: 7.6 Consensus size: 40
25600080 TATTCGGATG
*
25600090 ATAACCAGACTAAGATCCGAAGGCATTTGTGCTAGTTACT
1 ATAACCGGACTAAGATCCGAAGGCATTTGTGCTAGTTACT
25600130 ATAACCGGACTAAGATCCGAAGGCATTTGTGCTAGTTACT
1 ATAACCGGACTAAGATCCGAAGGCATTTGTGCTAGTTACT
25600170 ATAACCGGACTAAGATCCGAAGGCATTTGTGCTAGTTACT
1 ATAACCGGACTAAGATCCGAAGGCATTTGTGCTAGTTACT
25600210 ATAACCGGACTAAGATCCGAAGGCATTTGTGCTAGTTACT
1 ATAACCGGACTAAGATCCGAAGGCATTTGTGCTAGTTACT
25600250 ATAACCGGACTAAGATCCGAAGGCATTTGTGCTAGTTACT
1 ATAACCGGACTAAGATCCGAAGGCATTTGTGCTAGTTACT
25600290 ATAACCGGACTAAGATCCGAAGGCATTTGTGCTAGTTACT
1 ATAACCGGACTAAGATCCGAAGGCATTTGTGCTAGTTACT
* * * *
25600330 ATATCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTGCT
1 ATAACCGGACTAAGAT-CCGAAGGCATTTGTGCTAGTTACT
*
25600370 ATATCCGG-CTAA-ATCCCGAAGG
1 ATAACCGGACTAAGAT-CCGAAGG
25600392 TACTTGGGTT
Statistics
Matches: 255, Mismatches: 5, Indels: 5
0.96 0.02 0.02
Matches are distributed among these distances:
39 14 0.05
40 241 0.95
ACGTcount: A:0.29, C:0.21, G:0.23, T:0.27
Consensus pattern (40 bp):
ATAACCGGACTAAGATCCGAAGGCATTTGTGCTAGTTACT
Found at i:25605327 original size:34 final size:34
Alignment explanation
Indices: 25605262--25605335 Score: 93
Period size: 34 Copynumber: 2.2 Consensus size: 34
25605252 GAAGGAAGTG
25605262 TACTGAAA--GGCTAAGGCCCAGATTGTCACTGT
1 TACTGAAATGGGCTAAGGCCCAGATTGTCACTGT
*
25605294 TATTGAAATGGGCTAAGGCCCAG-TCTG-CTACTGT
1 TACTGAAATGGGCTAAGGCCCAGAT-TGTC-ACTGT
25605328 TACTGAAA
1 TACTGAAA
25605336 AAGGGGCATA
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
32 7 0.19
33 2 0.06
34 27 0.75
ACGTcount: A:0.28, C:0.20, G:0.24, T:0.27
Consensus pattern (34 bp):
TACTGAAATGGGCTAAGGCCCAGATTGTCACTGT
Found at i:25613113 original size:34 final size:34
Alignment explanation
Indices: 25613036--25613121 Score: 104
Period size: 34 Copynumber: 2.5 Consensus size: 34
25613026 GACTCTTTGC
25613036 TTGCATACTG-TACTGAAATGGGCTAAGGCCCAGA
1 TTGC-TACTGTTACTGAAATGGGCTAAGGCCCAGA
* * * *
25613070 CTG-TCACTGTTATTGAAATGGGCTGAGGCCCAGT
1 TTGCT-ACTGTTACTGAAATGGGCTAAGGCCCAGA
25613104 TTGCTACTGTTACTGAAA
1 TTGCTACTGTTACTGAAA
25613122 AAGGGGCTAA
Statistics
Matches: 43, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
32 1 0.02
33 4 0.09
34 37 0.86
35 1 0.02
ACGTcount: A:0.26, C:0.20, G:0.26, T:0.29
Consensus pattern (34 bp):
TTGCTACTGTTACTGAAATGGGCTAAGGCCCAGA
Found at i:25621273 original size:20 final size:20
Alignment explanation
Indices: 25621248--25621287 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
25621238 AAATAACAAG
*
25621248 GGCGTGTACCTGTATACACA
1 GGCGTGTACCGGTATACACA
25621268 GGCGTGTACCGGTATACACA
1 GGCGTGTACCGGTATACACA
25621288 AGTGTGGGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.25, C:0.25, G:0.28, T:0.23
Consensus pattern (20 bp):
GGCGTGTACCGGTATACACA
Found at i:25623448 original size:13 final size:13
Alignment explanation
Indices: 25623430--25623456 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
25623420 GGAGTAATCG
25623430 CACACGGGCGTGT
1 CACACGGGCGTGT
25623443 CACACGGGCGTGT
1 CACACGGGCGTGT
25623456 C
1 C
25623457 CCTGCCGAGC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.15, C:0.33, G:0.37, T:0.15
Consensus pattern (13 bp):
CACACGGGCGTGT
Found at i:25647746 original size:221 final size:221
Alignment explanation
Indices: 25647363--25647807 Score: 890
Period size: 221 Copynumber: 2.0 Consensus size: 221
25647353 TCTCAAAAAT
25647363 AGATTTGAGATCGGGCTATTATCAGTTGCGAATCCGAGATTCAGATATTCCCAAAACTGCCTTCA
1 AGATTTGAGATCGGGCTATTATCAGTTGCGAATCCGAGATTCAGATATTCCCAAAACTGCCTTCA
25647428 GAACGAGATATGGTCACTACGAATTCTTAGTGATGCCGTTTGGGCTCACTAATGCCCCTGCAGTA
66 GAACGAGATATGGTCACTACGAATTCTTAGTGATGCCGTTTGGGCTCACTAATGCCCCTGCAGTA
25647493 TTTATGGATTTGATGAATCGGATCTTCAGACCGTATTTGGATCGGTTCGTAGTGGTGTTCATTGA
131 TTTATGGATTTGATGAATCGGATCTTCAGACCGTATTTGGATCGGTTCGTAGTGGTGTTCATTGA
25647558 TGACATTTTGGTCTATTCAAGAGACG
196 TGACATTTTGGTCTATTCAAGAGACG
25647584 AGATTTGAGATCGGGCTATTATCAGTTGCGAATCCGAGATTCAGATATTCCCAAAACTGCCTTCA
1 AGATTTGAGATCGGGCTATTATCAGTTGCGAATCCGAGATTCAGATATTCCCAAAACTGCCTTCA
25647649 GAACGAGATATGGTCACTACGAATTCTTAGTGATGCCGTTTGGGCTCACTAATGCCCCTGCAGTA
66 GAACGAGATATGGTCACTACGAATTCTTAGTGATGCCGTTTGGGCTCACTAATGCCCCTGCAGTA
25647714 TTTATGGATTTGATGAATCGGATCTTCAGACCGTATTTGGATCGGTTCGTAGTGGTGTTCATTGA
131 TTTATGGATTTGATGAATCGGATCTTCAGACCGTATTTGGATCGGTTCGTAGTGGTGTTCATTGA
25647779 TGACATTTTGGTCTATTCAAGAGACG
196 TGACATTTTGGTCTATTCAAGAGACG
25647805 AGA
1 AGA
25647808 CCGAACATGC
Statistics
Matches: 224, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
221 224 1.00
ACGTcount: A:0.25, C:0.18, G:0.24, T:0.32
Consensus pattern (221 bp):
AGATTTGAGATCGGGCTATTATCAGTTGCGAATCCGAGATTCAGATATTCCCAAAACTGCCTTCA
GAACGAGATATGGTCACTACGAATTCTTAGTGATGCCGTTTGGGCTCACTAATGCCCCTGCAGTA
TTTATGGATTTGATGAATCGGATCTTCAGACCGTATTTGGATCGGTTCGTAGTGGTGTTCATTGA
TGACATTTTGGTCTATTCAAGAGACG
Found at i:25650629 original size:19 final size:20
Alignment explanation
Indices: 25650605--25650642 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
25650595 GGTACCACCA
25650605 AAACAT-ATATCA-CATCTTT
1 AAACATCAT-TCATCATCTTT
25650624 AAACATCATTCATCATCTT
1 AAACATCATTCATCATCTT
25650643 ACCACCTTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.39, C:0.24, G:0.00, T:0.37
Consensus pattern (20 bp):
AAACATCATTCATCATCTTT
Found at i:25657918 original size:30 final size:30
Alignment explanation
Indices: 25657883--25657951 Score: 111
Period size: 30 Copynumber: 2.3 Consensus size: 30
25657873 ATGGGACAGA
*
25657883 CCATGTGTCACACACGGCCTAGCCACATGC
1 CCATGTGTCACACACGACCTAGCCACATGC
*
25657913 CCATGTGTCACACACGACCTAGTCACATGC
1 CCATGTGTCACACACGACCTAGCCACATGC
*
25657943 CCGTGTGTC
1 CCATGTGTC
25657952 TACCTGTGTG
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
30 36 1.00
ACGTcount: A:0.22, C:0.38, G:0.20, T:0.20
Consensus pattern (30 bp):
CCATGTGTCACACACGACCTAGCCACATGC
Found at i:25661317 original size:14 final size:14
Alignment explanation
Indices: 25661298--25661329 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
25661288 AGGTCATTTA
25661298 GCCCAACCAAACTG
1 GCCCAACCAAACTG
*
25661312 GCCCAACCAAACTT
1 GCCCAACCAAACTG
25661326 GCCC
1 GCCC
25661330 GGTGATTGGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.31, C:0.47, G:0.12, T:0.09
Consensus pattern (14 bp):
GCCCAACCAAACTG
Found at i:25666442 original size:14 final size:14
Alignment explanation
Indices: 25666423--25666454 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
25666413 AGGTCATTTA
25666423 GCCCAACCAAACTG
1 GCCCAACCAAACTG
25666437 GCCCAACCAAACTG
1 GCCCAACCAAACTG
25666451 GCCC
1 GCCC
25666455 GGTGATTGGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.31, C:0.47, G:0.16, T:0.06
Consensus pattern (14 bp):
GCCCAACCAAACTG
Found at i:25667057 original size:19 final size:19
Alignment explanation
Indices: 25667016--25667054 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
25667006 CAACAGAATC
*
25667016 TCTTAAAAATTATTAAATT
1 TCTTAAAAATTACTAAATT
*
25667035 TCTTAAAAAGTTGCTAAATT
1 TCTTAAAAA-TTACTAAATT
25667055 CTTTATGGTT
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:0.44, C:0.08, G:0.05, T:0.44
Consensus pattern (19 bp):
TCTTAAAAATTACTAAATT
Found at i:25668021 original size:28 final size:27
Alignment explanation
Indices: 25667965--25668027 Score: 65
Period size: 28 Copynumber: 2.3 Consensus size: 27
25667955 ATATCTCAAA
*
25667965 AATTATATATAACTTTAATTTTATGTGC
1 AATTATATATAACTTTAATTTGA-GTGC
*
25667993 AATTATATACATAATTTTAATTTGA-TGC
1 AATTATAT--ATAACTTTAATTTGAGTGC
*
25668021 AGTTATA
1 AATTATA
25668028 AACGTAAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
28 17 0.57
30 13 0.43
ACGTcount: A:0.38, C:0.06, G:0.08, T:0.48
Consensus pattern (27 bp):
AATTATATATAACTTTAATTTGAGTGC
Found at i:25668290 original size:33 final size:29
Alignment explanation
Indices: 25668209--25668300 Score: 96
Period size: 30 Copynumber: 3.0 Consensus size: 29
25668199 TAATTTCGAG
*
25668209 AATTAAATAAAATTAAAATTTTATGTATAA
1 AATTACATAAAATTAAAA-TTTATGTATAA
*
25668239 AATTACATAAAATCAAAATTTATGTATATA
1 AATTACATAAAATTAAAATTTATGTATA-A
*
25668269 TAATTACACTTTAAATTAAAATTCT-TGTATAA
1 -AATTACA--TAAAATTAAAATT-TATGTATAA
25668301 TTTTAAAATT
Statistics
Matches: 53, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
29 10 0.19
30 17 0.32
31 7 0.13
32 1 0.02
33 17 0.32
34 1 0.02
ACGTcount: A:0.51, C:0.05, G:0.03, T:0.40
Consensus pattern (29 bp):
AATTACATAAAATTAAAATTTATGTATAA
Found at i:25675813 original size:23 final size:23
Alignment explanation
Indices: 25675786--25675832 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 23
25675776 GATTTTCGGT
*
25675786 AAGAAAGTGCATATATGAAATTA
1 AAGAAAGTCCATATATGAAATTA
25675809 AAGAAAGTCCATATATGAAATTA
1 AAGAAAGTCCATATATGAAATTA
25675832 A
1 A
25675833 CTAGTTAAGT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.53, C:0.06, G:0.15, T:0.26
Consensus pattern (23 bp):
AAGAAAGTCCATATATGAAATTA
Found at i:25676249 original size:12 final size:12
Alignment explanation
Indices: 25676229--25676267 Score: 60
Period size: 12 Copynumber: 3.2 Consensus size: 12
25676219 GTTTGGCACA
*
25676229 GCCTAGCACACG
1 GCCTGGCACACG
25676241 GCCTGGCACACG
1 GCCTGGCACACG
*
25676253 GCCTGGCACATG
1 GCCTGGCACACG
25676265 GCC
1 GCC
25676268 GTATGTGGCC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.18, C:0.41, G:0.31, T:0.10
Consensus pattern (12 bp):
GCCTGGCACACG
Found at i:25682020 original size:47 final size:47
Alignment explanation
Indices: 25681951--25682044 Score: 188
Period size: 47 Copynumber: 2.0 Consensus size: 47
25681941 AAGTTAGATT
25681951 TTTGGGACATATTATTTTAGCAGAAGGCATCCGAGTTGATCCAAATA
1 TTTGGGACATATTATTTTAGCAGAAGGCATCCGAGTTGATCCAAATA
25681998 TTTGGGACATATTATTTTAGCAGAAGGCATCCGAGTTGATCCAAATA
1 TTTGGGACATATTATTTTAGCAGAAGGCATCCGAGTTGATCCAAATA
25682045 AAATTTCAGC
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 47 1.00
ACGTcount: A:0.32, C:0.15, G:0.21, T:0.32
Consensus pattern (47 bp):
TTTGGGACATATTATTTTAGCAGAAGGCATCCGAGTTGATCCAAATA
Found at i:25690012 original size:107 final size:107
Alignment explanation
Indices: 25689826--25690040 Score: 394
Period size: 107 Copynumber: 2.0 Consensus size: 107
25689816 ATAACCTTAC
*
25689826 CACATCCCGGTCACTTAATGTACACATCATTCACATAACCAAGTTCCTACACTTATTCATCACAA
1 CACATCCCGGTCACTTAATGAACACATCATTCACATAACCAAGTTCCTACACTTATTCATCACAA
25689891 AACTCACAAAGCAATACATAGAGAGTCTCCCATTGAACACTT
66 AACTCACAAAGCAATACATAGAGAGTCTCCCATTGAACACTT
* *
25689933 CACATCCTGGTCACTTAATGAACACATCATTCACATAACCAAGTTCCTGCACTTATTCATCACAA
1 CACATCCCGGTCACTTAATGAACACATCATTCACATAACCAAGTTCCTACACTTATTCATCACAA
*
25689998 AACTCACAAAGCAATACATAGAGAGTCTCCCGTTGAACACTT
66 AACTCACAAAGCAATACATAGAGAGTCTCCCATTGAACACTT
25690040 C
1 C
25690041 GGATCAATCC
Statistics
Matches: 104, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
107 104 1.00
ACGTcount: A:0.36, C:0.30, G:0.09, T:0.25
Consensus pattern (107 bp):
CACATCCCGGTCACTTAATGAACACATCATTCACATAACCAAGTTCCTACACTTATTCATCACAA
AACTCACAAAGCAATACATAGAGAGTCTCCCATTGAACACTT
Found at i:25691051 original size:30 final size:30
Alignment explanation
Indices: 25691017--25691077 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
25691007 TCCTTAACTC
25691017 AAACTTTGGAAAAATTACAATTTTGCCCCT
1 AAACTTTGGAAAAATTACAATTTTGCCCCT
* * * * *
25691047 AAACTTTTGCATATTTACACTTTTGCCCCT
1 AAACTTTGGAAAAATTACAATTTTGCCCCT
25691077 A
1 A
25691078 GGCTCGGGAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.31, C:0.23, G:0.08, T:0.38
Consensus pattern (30 bp):
AAACTTTGGAAAAATTACAATTTTGCCCCT
Found at i:25694086 original size:13 final size:13
Alignment explanation
Indices: 25694068--25694094 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
25694058 GCTCGGCAGG
25694068 GACACGCCCATGT
1 GACACGCCCATGT
25694081 GACACGCCCATGT
1 GACACGCCCATGT
25694094 G
1 G
25694095 CGATTACTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.22, C:0.37, G:0.26, T:0.15
Consensus pattern (13 bp):
GACACGCCCATGT
Found at i:25696359 original size:31 final size:31
Alignment explanation
Indices: 25696321--25696384 Score: 110
Period size: 31 Copynumber: 2.1 Consensus size: 31
25696311 GCTGGCTCAA
* *
25696321 GGACTAATTTTCAAAACTGTTAAAGGTTTAG
1 GGACTAATTTACAAAACTGTTAAAAGTTTAG
25696352 GGACTAATTTACAAAACTGTTAAAAGTTTAG
1 GGACTAATTTACAAAACTGTTAAAAGTTTAG
25696383 GG
1 GG
25696385 TTTTTCTATT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.38, C:0.09, G:0.20, T:0.33
Consensus pattern (31 bp):
GGACTAATTTACAAAACTGTTAAAAGTTTAG
Found at i:25701763 original size:85 final size:84
Alignment explanation
Indices: 25701615--25701775 Score: 200
Period size: 85 Copynumber: 1.9 Consensus size: 84
25701605 CGATATGTGT
* * * *
25701615 TTTTGTGTAAGACCATGTCTGGGACATTAGCATCGACTTTTGATTTTACGTGTAAGCATGTCTGG
1 TTTTGTGTAAGACCATCTCTGGGACAGTAGCATCGACTTTT-ATTTTACATGTAAGCACGTCTGG
25701680 AACATCGGCATCGTATTTGA
65 AACATCGGCATCGTATTTGA
* *
25701700 TTTTGTGTAAGACCTTCTCTGGGACAGTGGCATCGA-TATTT-TTTTACATGTAAGACCACGTCT
1 TTTTGTGTAAGACCATCTCTGGGACAGTAGCATCGACT-TTTATTTTACATGTAAG--CACGTCT
* *
25701763 GGGACGTCGGCAT
63 GGAACATCGGCAT
25701776 TGTACGAGCT
Statistics
Matches: 65, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
83 12 0.18
84 1 0.02
85 52 0.80
ACGTcount: A:0.22, C:0.18, G:0.24, T:0.35
Consensus pattern (84 bp):
TTTTGTGTAAGACCATCTCTGGGACAGTAGCATCGACTTTTATTTTACATGTAAGCACGTCTGGA
ACATCGGCATCGTATTTGA
Found at i:25701764 original size:43 final size:45
Alignment explanation
Indices: 25701619--25701775 Score: 131
Period size: 43 Copynumber: 3.7 Consensus size: 45
25701609 ATGTGTTTTT
* **
25701619 GTGTAAGACCATGTCTGGGACA-TTAGCATCGACT-TTTGATTTTAC
1 GTGTAAGACCACGTCTGGGACAGTCGGCATCGA-TATTT-ATTTTAC
* *
25701664 GTGTAAG--CATGTCTGGAACA-TCGGCATCG-TATTTGATTTT--
1 GTGTAAGACCACGTCTGGGACAGTCGGCATCGATATTT-ATTTTAC
*
25701704 GTGTAAGACCTTC-TCTGGGACAGT-GGCATCGATATTT-TTTTAC
1 GTGTAAGACC-ACGTCTGGGACAGTCGGCATCGATATTTATTTTAC
*
25701747 ATGTAAGACCACGTCTGGGAC-GTCGGCAT
1 GTGTAAGACCACGTCTGGGACAGTCGGCAT
25701776 TGTACGAGCT
Statistics
Matches: 94, Mismatches: 8, Indels: 22
0.76 0.06 0.18
Matches are distributed among these distances:
40 7 0.07
41 5 0.05
42 28 0.30
43 47 0.50
45 7 0.07
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.34
Consensus pattern (45 bp):
GTGTAAGACCACGTCTGGGACAGTCGGCATCGATATTTATTTTAC
Found at i:25704081 original size:30 final size:30
Alignment explanation
Indices: 25704047--25704103 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 30
25704037 TTTACAAGCA
* *
25704047 TAAGGGCAAAATCGTAATTTTTGTAAAGTC
1 TAAGGGCAAAATAGTAATTTTTCTAAAGTC
* *
25704077 TAAGGGTAAAATAGTCATTTTTCTAAA
1 TAAGGGCAAAATAGTAATTTTTCTAAA
25704104 TTGTGAATTA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 23 1.00
ACGTcount: A:0.39, C:0.09, G:0.18, T:0.35
Consensus pattern (30 bp):
TAAGGGCAAAATAGTAATTTTTCTAAAGTC
Found at i:25711544 original size:41 final size:39
Alignment explanation
Indices: 25711499--25711636 Score: 143
Period size: 40 Copynumber: 3.4 Consensus size: 39
25711489 CTATTATAAT
* * *
25711499 CTCGCACAATAAGTGCCTTTCATAGCCAAAGCTATCTCGAC
1 CTCGCACACTAAGTGCCTAT-ATAGCCAAAGCTATCTC-AA
*
25711540 CTCGCACACTAAGTGTCATATATAGCCAAAGCTAATC-CAA
1 CTCGCACACTAAGTG-CCTATATAGCCAAAGCT-ATCTCAA
* *
25711580 TTCGCACACTAAGTGCTCTATATAGCCAAAGATATCTCAA
1 CTCGCACACTAAGTGC-CTATATAGCCAAAGCTATCTCAA
** *
25711620 AACGCACACAAAGTGCC
1 CTCGCACACTAAGTGCC
25711637 AAAATTAGTC
Statistics
Matches: 83, Mismatches: 10, Indels: 10
0.81 0.10 0.10
Matches are distributed among these distances:
39 5 0.06
40 45 0.54
41 27 0.33
42 6 0.07
ACGTcount: A:0.35, C:0.29, G:0.14, T:0.22
Consensus pattern (39 bp):
CTCGCACACTAAGTGCCTATATAGCCAAAGCTATCTCAA
Found at i:25718922 original size:41 final size:41
Alignment explanation
Indices: 25718868--25718946 Score: 124
Period size: 41 Copynumber: 1.9 Consensus size: 41
25718858 AATGCTAACG
*
25718868 CATAGCCGAAGCTAT-TATAATCTCACACACTAAGTGCCTTC
1 CATAGCCGAAGCTATCT-TAACCTCACACACTAAGTGCCTTC
*
25718909 CATAGCTGAAGCTATCTTAACCTCACACACTAAGTGCC
1 CATAGCCGAAGCTATCTTAACCTCACACACTAAGTGCC
25718947 ATATATAGCC
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
41 34 0.97
42 1 0.03
ACGTcount: A:0.32, C:0.30, G:0.13, T:0.25
Consensus pattern (41 bp):
CATAGCCGAAGCTATCTTAACCTCACACACTAAGTGCCTTC
Found at i:25718955 original size:41 final size:41
Alignment explanation
Indices: 25718868--25718956 Score: 117
Period size: 41 Copynumber: 2.2 Consensus size: 41
25718858 AATGCTAACG
* * *
25718868 CATAGCCGAAGCTATTATAATCTCACACACTAAGTGCCTTC
1 CATAGCCGAAGCTATTATAACCTCACACACTAAGTGCCATA
*
25718909 CATAGCTGAAGCTATCT-TAACCTCACACACTAAGTGCCATA
1 CATAGCCGAAGCTAT-TATAACCTCACACACTAAGTGCCATA
*
25718950 TATAGCC
1 CATAGCC
25718957 AAAACTAATC
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
41 40 0.98
42 1 0.02
ACGTcount: A:0.33, C:0.29, G:0.12, T:0.26
Consensus pattern (41 bp):
CATAGCCGAAGCTATTATAACCTCACACACTAAGTGCCATA
Found at i:25722218 original size:43 final size:43
Alignment explanation
Indices: 25722162--25722300 Score: 224
Period size: 43 Copynumber: 3.2 Consensus size: 43
25722152 TCGGGCCTTT
*
25722162 GAGCCTAGCAGGCTATAATGTCGGTGAGTTAATATCGGGCTTC
1 GAGCCTAGCAGGCTATAATGTCGGTGAGTTAATATCAGGCTTC
*
25722205 GAGCCTAGTAGGCTATAATGTCGGTGAGTTAATATCAGGCTTC
1 GAGCCTAGCAGGCTATAATGTCGGTGAGTTAATATCAGGCTTC
* ** *
25722248 GAACCTAGCAGGCTATAATACCGATGAGTTAATATCAGGCTTC
1 GAGCCTAGCAGGCTATAATGTCGGTGAGTTAATATCAGGCTTC
25722291 GAGCCTAGCA
1 GAGCCTAGCA
25722301 AGCGTAATGC
Statistics
Matches: 88, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
43 88 1.00
ACGTcount: A:0.27, C:0.19, G:0.27, T:0.27
Consensus pattern (43 bp):
GAGCCTAGCAGGCTATAATGTCGGTGAGTTAATATCAGGCTTC
Found at i:25722896 original size:16 final size:18
Alignment explanation
Indices: 25722865--25722897 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
25722855 AACTTGTCAC
25722865 ACTATCTATCGTTTTGGT
1 ACTATCTATCGTTTTGGT
25722883 ACTAT-TAT-GTTTTGG
1 ACTATCTATCGTTTTGG
25722898 AATTCATATG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
17 3 0.20
18 5 0.33
ACGTcount: A:0.18, C:0.12, G:0.18, T:0.52
Consensus pattern (18 bp):
ACTATCTATCGTTTTGGT
Found at i:25724051 original size:21 final size:21
Alignment explanation
Indices: 25724027--25724075 Score: 89
Period size: 21 Copynumber: 2.3 Consensus size: 21
25724017 ACAATGAATC
25724027 CGGCTTCTGAGATGGATCAAT
1 CGGCTTCTGAGATGGATCAAT
25724048 CGGCTTCTGAGATGGATCAAT
1 CGGCTTCTGAGATGGATCAAT
*
25724069 CGACTTC
1 CGGCTTC
25724076 CCTTGAGTAA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.22, C:0.22, G:0.27, T:0.29
Consensus pattern (21 bp):
CGGCTTCTGAGATGGATCAAT
Found at i:25736564 original size:36 final size:36
Alignment explanation
Indices: 25736524--25736596 Score: 146
Period size: 36 Copynumber: 2.0 Consensus size: 36
25736514 ATAGCTAATC
25736524 CACTAGAAAACCCTGCACAATAATCAATTAATCATA
1 CACTAGAAAACCCTGCACAATAATCAATTAATCATA
25736560 CACTAGAAAACCCTGCACAATAATCAATTAATCATA
1 CACTAGAAAACCCTGCACAATAATCAATTAATCATA
25736596 C
1 C
25736597 CTTCACTCCC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.47, C:0.26, G:0.05, T:0.22
Consensus pattern (36 bp):
CACTAGAAAACCCTGCACAATAATCAATTAATCATA
Found at i:25742351 original size:14 final size:14
Alignment explanation
Indices: 25742334--25742367 Score: 54
Period size: 12 Copynumber: 2.6 Consensus size: 14
25742324 TATTGAATTA
25742334 ATGATTATTTTTGT
1 ATGATTATTTTTGT
25742348 ATGA--ATTTTTGT
1 ATGATTATTTTTGT
25742360 ATGATTAT
1 ATGATTAT
25742368 ATTGATATAG
Statistics
Matches: 18, Mismatches: 0, Indels: 4
0.82 0.00 0.18
Matches are distributed among these distances:
12 12 0.67
14 6 0.33
ACGTcount: A:0.26, C:0.00, G:0.15, T:0.59
Consensus pattern (14 bp):
ATGATTATTTTTGT
Found at i:25763665 original size:27 final size:27
Alignment explanation
Indices: 25763597--25763655 Score: 91
Period size: 27 Copynumber: 2.2 Consensus size: 27
25763587 CTAGTTTAGT
*
25763597 AAATGACCATAATGCCCCTGTAAGGTA
1 AAATGACCGTAATGCCCCTGTAAGGTA
*
25763624 AAATGACCGTAATGCCCCTGTATGGTA
1 AAATGACCGTAATGCCCCTGTAAGGTA
*
25763651 GAATG
1 AAATG
25763656 GCGATTATGC
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.34, C:0.20, G:0.22, T:0.24
Consensus pattern (27 bp):
AAATGACCGTAATGCCCCTGTAAGGTA
Found at i:25764122 original size:27 final size:27
Alignment explanation
Indices: 25764074--25764125 Score: 79
Period size: 27 Copynumber: 1.9 Consensus size: 27
25764064 GCATCTGATA
*
25764074 CTGATTTTGTATTGGGCTTAGGCCCGC
1 CTGATTTTGTAATGGGCTTAGGCCCGC
25764101 CTGATTTTGTTAATGGGC-TAGGCCC
1 CTGATTTTG-TAATGGGCTTAGGCCC
25764126 AACTGTTACT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
27 16 0.70
28 7 0.30
ACGTcount: A:0.13, C:0.21, G:0.29, T:0.37
Consensus pattern (27 bp):
CTGATTTTGTAATGGGCTTAGGCCCGC
Found at i:25768055 original size:34 final size:34
Alignment explanation
Indices: 25768007--25768073 Score: 125
Period size: 34 Copynumber: 2.0 Consensus size: 34
25767997 CTTGAGTATG
25768007 GGTCCGTAAGGAGGTTGTATATAAGTATTTAATA
1 GGTCCGTAAGGAGGTTGTATATAAGTATTTAATA
*
25768041 GGTCTGTAAGGAGGTTGTATATAAGTATTTAAT
1 GGTCCGTAAGGAGGTTGTATATAAGTATTTAAT
25768074 CATGCAAGGA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 32 1.00
ACGTcount: A:0.31, C:0.04, G:0.27, T:0.37
Consensus pattern (34 bp):
GGTCCGTAAGGAGGTTGTATATAAGTATTTAATA
Found at i:25772565 original size:27 final size:27
Alignment explanation
Indices: 25772534--25772689 Score: 131
Period size: 27 Copynumber: 5.8 Consensus size: 27
25772524 TTAGTTTACC
* * *
25772534 AAATTACTGAAATACCCTCAACTTGTA
1 AAATTACTCAAATACCCTCGATTTGTA
* *
25772561 AAATTAC-CAAAGTACCCCCGATTTATA
1 AAATTACTCAAA-TACCCTCGATTTGTA
* *
25772588 AAATTACCCAAATATCCTCGATTTGTA
1 AAATTACTCAAATACCCTCGATTTGTA
* *
25772615 AAATTA-TAGAAATACCCTC-AGTTTGCA
1 AAATTACT-CAAATACCCTCGA-TTTGTA
* * **
25772642 AAATTATTGAAATACCCTCGACATGTA
1 AAATTACTCAAATACCCTCGATTTGTA
25772669 AAATTA-TCAAAGTACCCTCGA
1 AAATTACTCAAA-TACCCTCGA
25772690 ATTACAAAAT
Statistics
Matches: 106, Mismatches: 16, Indels: 14
0.78 0.12 0.10
Matches are distributed among these distances:
26 8 0.08
27 92 0.87
28 6 0.06
ACGTcount: A:0.40, C:0.22, G:0.09, T:0.29
Consensus pattern (27 bp):
AAATTACTCAAATACCCTCGATTTGTA
Found at i:25772685 original size:54 final size:55
Alignment explanation
Indices: 25772528--25772702 Score: 187
Period size: 54 Copynumber: 3.2 Consensus size: 55
25772518 AATACTTTAG
* * * *
25772528 TTTACCAAATTACTGAAATACCCTCAACTTGTAAAATTACCAAAGTACCC-CCGA
1 TTTACAAAATTACTGAAATACCCTCGACTTGTAAAATTATCAAAGTACCCTCAGA
* ** * * *
25772582 TTTATAAAATTACCCAAATATCCTCGATTTGTAAAATTAT-AGAAATACCCTCAG-
1 TTTACAAAATTACTGAAATACCCTCGACTTGTAAAATTATCA-AAGTACCCTCAGA
* * *
25772636 TTTGCAAAATTATTGAAATACCCTCGACATGTAAAATTATCAAAGTACCCTC-GA
1 TTTACAAAATTACTGAAATACCCTCGACTTGTAAAATTATCAAAGTACCCTCAGA
*
25772690 ATTACAAAATTAC
1 TTTACAAAATTAC
25772703 CATTTTACCC
Statistics
Matches: 95, Mismatches: 22, Indels: 8
0.76 0.18 0.06
Matches are distributed among these distances:
53 2 0.02
54 90 0.95
55 3 0.03
ACGTcount: A:0.41, C:0.22, G:0.08, T:0.30
Consensus pattern (55 bp):
TTTACAAAATTACTGAAATACCCTCGACTTGTAAAATTATCAAAGTACCCTCAGA
Found at i:25772739 original size:81 final size:81
Alignment explanation
Indices: 25772654--25772824 Score: 202
Period size: 81 Copynumber: 2.1 Consensus size: 81
25772644 ATTATTGAAA
**
25772654 TACCCTCGACATGTAAAATTA-TCAAAGTACCCTCGAA-TTACAAAATTACCATTTTACCCTCGA
1 TACCCTCGACATACAAAATTACT-AAAGTACCCTC-AATTTACAAAATTACCATTTTACCCTCGA
* *
25772717 TTTACAGAATTACTGTTT
64 TTTACAAAATTACTATTT
** *** * **
25772735 TACCCTCGATTTACAAAATTACTATTTTACCCTCAATTTACAGAATTACTGTTTTACCCTCGATT
1 TACCCTCGACATACAAAATTACTAAAGTACCCTCAATTTACAAAATTACCATTTTACCCTCGATT
25772800 TACAAAATTACTATTT
66 TACAAAATTACTATTT
25772816 TACCCTCGA
1 TACCCTCGA
25772825 TTTACAGAAT
Statistics
Matches: 76, Mismatches: 12, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
80 2 0.03
81 73 0.96
82 1 0.01
ACGTcount: A:0.33, C:0.24, G:0.07, T:0.36
Consensus pattern (81 bp):
TACCCTCGACATACAAAATTACTAAAGTACCCTCAATTTACAAAATTACCATTTTACCCTCGATT
TACAAAATTACTATTT
Found at i:25772866 original size:27 final size:27
Alignment explanation
Indices: 25772681--25772864 Score: 260
Period size: 27 Copynumber: 6.8 Consensus size: 27
25772671 ATTATCAAAG
* **
25772681 TACCCTCGAATTACAAAATTACCATTT
1 TACCCTCGATTTACAAAATTACTGTTT
*
25772708 TACCCTCGATTTACAGAATTACTGTTT
1 TACCCTCGATTTACAAAATTACTGTTT
*
25772735 TACCCTCGATTTACAAAATTACTATTT
1 TACCCTCGATTTACAAAATTACTGTTT
* *
25772762 TACCCTCAATTTACAGAATTACTGTTT
1 TACCCTCGATTTACAAAATTACTGTTT
*
25772789 TACCCTCGATTTACAAAATTACTATTT
1 TACCCTCGATTTACAAAATTACTGTTT
* *
25772816 TACCCTCGATTTACAGAATTACCGTTT
1 TACCCTCGATTTACAAAATTACTGTTT
* *
25772843 TACCCTAGATTTATAAAATTAC
1 TACCCTCGATTTACAAAATTAC
25772865 CGAAATACCC
Statistics
Matches: 139, Mismatches: 18, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 139 1.00
ACGTcount: A:0.32, C:0.23, G:0.07, T:0.39
Consensus pattern (27 bp):
TACCCTCGATTTACAAAATTACTGTTT
Found at i:25772873 original size:27 final size:27
Alignment explanation
Indices: 25772528--25772875 Score: 91
Period size: 27 Copynumber: 12.9 Consensus size: 27
25772518 AATACTTTAG
* *
25772528 TTTACCAAATTACTGAAATACCCTCA-A
1 TTTACAAAATTACCGAAATACCCT-AGA
* ** **
25772555 CTTGTAAAATTACC-AAAGTACCCCCGA
1 TTTACAAAATTACCGAAA-TACCCTAGA
* * * *
25772582 TTTATAAAATTACCCAAATATCCTCGA
1 TTTACAAAATTACCGAAATACCCTAGA
** **
25772609 TTTGTAAAATTATAGAAATACCCTCAG-
1 TTTACAAAATTACCGAAATACCCT-AGA
* ** *
25772636 TTTGCAAAATTATTGAAATACCCTCGA
1 TTTACAAAATTACCGAAATACCCTAGA
** ** * *
25772663 CATGTAAAATTATC-AAAGTACCCTCGA
1 TTTACAAAATTACCGAAA-TACCCTAGA
* ** *
25772690 ATTACAAAATTACC-ATTTTACCCTCGA
1 TTTACAAAATTACCGA-AATACCCTAGA
* * *** *
25772717 TTTACAGAATTACTGTTTTACCCTCGA
1 TTTACAAAATTACCGAAATACCCTAGA
* **
25772744 TTTACAAAATTA-CTATTTTACCCTCA-A
1 TTTACAAAATTACCGA-AATACCCT-AGA
* * *** *
25772771 TTTACAGAATTACTGTTTTACCCTCGA
1 TTTACAAAATTACCGAAATACCCTAGA
* ** *
25772798 TTTACAAAATTA-CTATTTTACCCTCGA
1 TTTACAAAATTACCGA-AATACCCTAGA
* ***
25772825 TTTACAGAATTACCGTTTTACCCTAGA
1 TTTACAAAATTACCGAAATACCCTAGA
*
25772852 TTTATAAAATTACCGAAATACCCT
1 TTTACAAAATTACCGAAATACCCT
25772876 TGTAAGGTAG
Statistics
Matches: 249, Mismatches: 58, Indels: 28
0.74 0.17 0.08
Matches are distributed among these distances:
26 7 0.03
27 237 0.95
28 5 0.02
ACGTcount: A:0.36, C:0.22, G:0.07, T:0.34
Consensus pattern (27 bp):
TTTACAAAATTACCGAAATACCCTAGA
Found at i:25772875 original size:54 final size:54
Alignment explanation
Indices: 25772681--25772864 Score: 314
Period size: 54 Copynumber: 3.4 Consensus size: 54
25772671 ATTATCAAAG
* *
25772681 TACCCTCGAATTACAAAATTACCATTTTACCCTCGATTTACAGAATTACTGTTT
1 TACCCTCGATTTACAAAATTACTATTTTACCCTCGATTTACAGAATTACTGTTT
*
25772735 TACCCTCGATTTACAAAATTACTATTTTACCCTCAATTTACAGAATTACTGTTT
1 TACCCTCGATTTACAAAATTACTATTTTACCCTCGATTTACAGAATTACTGTTT
*
25772789 TACCCTCGATTTACAAAATTACTATTTTACCCTCGATTTACAGAATTACCGTTT
1 TACCCTCGATTTACAAAATTACTATTTTACCCTCGATTTACAGAATTACTGTTT
* *
25772843 TACCCTAGATTTATAAAATTAC
1 TACCCTCGATTTACAAAATTAC
25772865 CGAAATACCC
Statistics
Matches: 123, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
54 123 1.00
ACGTcount: A:0.32, C:0.23, G:0.07, T:0.39
Consensus pattern (54 bp):
TACCCTCGATTTACAAAATTACTATTTTACCCTCGATTTACAGAATTACTGTTT
Found at i:25772892 original size:27 final size:27
Alignment explanation
Indices: 25772862--25772941 Score: 142
Period size: 27 Copynumber: 3.0 Consensus size: 27
25772852 TTTATAAAAT
*
25772862 TACCGAAATACCCTTGTAAGGTAGAAA
1 TACCGAAATACCCTTGTAGGGTAGAAA
25772889 TACCGAAATACCCTTGTAGGGTAGAAA
1 TACCGAAATACCCTTGTAGGGTAGAAA
*
25772916 TACCGAAATACCCCTGTAGGGTAGAA
1 TACCGAAATACCCTTGTAGGGTAGAA
25772942 TNNNNNNNNN
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 51 1.00
ACGTcount: A:0.38, C:0.20, G:0.21, T:0.21
Consensus pattern (27 bp):
TACCGAAATACCCTTGTAGGGTAGAAA
Found at i:25773347 original size:6 final size:6
Alignment explanation
Indices: 25773336--25773380 Score: 56
Period size: 6 Copynumber: 7.3 Consensus size: 6
25773326 NNNNNNNNNN
*
25773336 CTGATT CTGATT CTGATT CTG-TCAC CTGATT CTGATT CTGATT CT
1 CTGATT CTGATT CTGATT CTGAT--T CTGATT CTGATT CTGATT CT
25773381 CATTTTGGTT
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
5 1 0.03
6 29 0.85
7 3 0.09
8 1 0.03
ACGTcount: A:0.16, C:0.22, G:0.16, T:0.47
Consensus pattern (6 bp):
CTGATT
Found at i:25777206 original size:34 final size:34
Alignment explanation
Indices: 25777163--25777239 Score: 111
Period size: 34 Copynumber: 2.3 Consensus size: 34
25777153 TGATTGCCTT
* *
25777163 ACTGATACTGTTACTGTGATGGGCTAAGGCCC-A
1 ACTGATACTGATACTGTAATGGGCTAAGGCCCTA
*
25777196 CACTGATACTGATACTGTAATGGGCTATGGCCCTA
1 -ACTGATACTGATACTGTAATGGGCTAAGGCCCTA
25777231 ACTGATACT
1 ACTGATACT
25777240 AGACTGTCAC
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
34 38 0.97
35 1 0.03
ACGTcount: A:0.26, C:0.22, G:0.23, T:0.29
Consensus pattern (34 bp):
ACTGATACTGATACTGTAATGGGCTAAGGCCCTA
Found at i:25782212 original size:39 final size:40
Alignment explanation
Indices: 25782167--25782351 Score: 178
Period size: 40 Copynumber: 4.7 Consensus size: 40
25782157 GCTCCTCGTT
* * *
25782167 CAAATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACA
1 CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
**
25782207 C-AATGCCTTCGGGACATAACCCGGATTTAACAACTCGCA
1 CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
* * *
25782246 CGAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCA
1 CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
* * * * * * *
25782286 CAAAGGCCTTC-GGATCTTAATCCGGATATATTCACTTAGCA
1 CAAATGCCTTCGGGA-CATAACCCGGATTTAGTAAC-TCGCA
* *
25782327 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACATAACCCGGA
25782352 CAGCATTCAA
Statistics
Matches: 122, Mismatches: 19, Indels: 8
0.82 0.13 0.05
Matches are distributed among these distances:
39 37 0.30
40 74 0.61
41 11 0.09
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24
Consensus pattern (40 bp):
CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
Found at i:25782267 original size:40 final size:39
Alignment explanation
Indices: 25782134--25782351 Score: 165
Period size: 40 Copynumber: 5.5 Consensus size: 39
25782124 AAATCACGTA
* * **
25782134 CCTTCGGGATTTAA-CCGGATATAGCTCCTCGTTCA-AATG
1 CCTTCGGGACTTAACCCGGATTTAGCAACTCG--CACAATG
* * * * *
25782173 CCTTCGGGACATAGCCCGGTTTTAGTAACTCACACAATG
1 CCTTCGGGACTTAACCCGGATTTAGCAACTCGCACAATG
* *
25782212 CCTTCGGGACATAACCCGGATTTAACAACTCGCACGAATG
1 CCTTCGGGACTTAACCCGGATTTAGCAACTCGCAC-AATG
* * *
25782252 CCTTCGGGACTTAACCCGGATTTAGTATCTCGCACAAAGG
1 CCTTCGGGACTTAACCCGGATTTAGCAACTCGCAC-AATG
* * * * *
25782292 CCTTC-GGATCTTAATCCGGATATATTC-ACTTAGCACAAAG
1 CCTTCGGGA-CTTAACCCGGATTTA-GCAAC-TCGCACAATG
*
25782332 CCTTCGGGACTTAGCCCGGA
1 CCTTCGGGACTTAACCCGGA
25782352 CAGCATTCAA
Statistics
Matches: 143, Mismatches: 29, Indels: 13
0.77 0.16 0.07
Matches are distributed among these distances:
38 2 0.01
39 48 0.34
40 85 0.59
41 8 0.06
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.26
Consensus pattern (39 bp):
CCTTCGGGACTTAACCCGGATTTAGCAACTCGCACAATG
Found at i:25792083 original size:40 final size:39
Alignment explanation
Indices: 25791992--25792254 Score: 287
Period size: 40 Copynumber: 6.6 Consensus size: 39
25791982 TCCTCGTTCA
* * * *
25791992 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC
1 AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC
*
25792031 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCAC
1 AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC
*
25792070 GAATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCAC
1 -AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC
*
25792110 GAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCAC
1 -AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC
* * *
25792150 AAAGGCCTTCGGGGCTTAACCCGGAATTT-GTATCTCGCAC
1 -AATGCCTTCGGGACTTAACCCGG-ATTTAGTAACTCGCAC
** * * * *
25792190 AAATGCCTTC-GGATCTTAGTCCGGATATATTCACTTAGCAC
1 -AATGCCTTCGGGA-CTTAACCCGGATTTAGTAAC-TCGCAC
* *
25792231 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
25792255 CAGCATTCAA
Statistics
Matches: 197, Mismatches: 21, Indels: 11
0.86 0.09 0.05
Matches are distributed among these distances:
39 39 0.20
40 146 0.74
41 12 0.06
ACGTcount: A:0.25, C:0.27, G:0.21, T:0.26
Consensus pattern (39 bp):
AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC
Found at i:25792200 original size:120 final size:119
Alignment explanation
Indices: 25791992--25792254 Score: 316
Period size: 120 Copynumber: 2.2 Consensus size: 119
25791982 TCCTCGTTCA
* * *
25791992 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACACAATGCCTTCGGGACTTAACCCGGATT
1 AATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCACACAAGGCCTTCGGGACTTAACCCGGATT
* * *
25792057 TAATAACTCGCACGAATGCCTTCGGGA-CTTAACCCGGATTTAATAAC-TCGCAC
66 TAATAACTCGCACAAATGCCTTC-GGATCTTAACCCGGATATAATAACTTAGCAC
* * * *
25792110 GAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACAAAGGCCTTCGGGGCTTAACCCGGA
1 -AATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCACAC-AAGGCCTTCGGGACTTAACCCGG-
* * ** * *
25792175 ATTT-GTATCTCGCACAAATGCCTTCGGATCTTAGTCCGGATATATTCACTTAGCAC
63 ATTTAATAACTCGCACAAATGCCTTCGGATCTTAACCCGGATATAATAACTTAGCAC
*
25792231 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAGCCCGGA
25792255 CAGCATTCAA
Statistics
Matches: 122, Mismatches: 18, Indels: 7
0.83 0.12 0.05
Matches are distributed among these distances:
119 37 0.30
120 76 0.62
121 9 0.07
ACGTcount: A:0.25, C:0.27, G:0.21, T:0.26
Consensus pattern (119 bp):
AATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCACACAAGGCCTTCGGGACTTAACCCGGATT
TAATAACTCGCACAAATGCCTTCGGATCTTAACCCGGATATAATAACTTAGCAC
Found at i:25792263 original size:41 final size:41
Alignment explanation
Indices: 25792186--25792263 Score: 97
Period size: 40 Copynumber: 1.9 Consensus size: 41
25792176 TTTGTATCTC
* * *
25792186 GCACAAATGCCTTCGGATCTTAGTCCGGATATATTCACTTA
1 GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
25792227 GCACAAA-GCCTTCGGGA-CTTAGCCCGGACAGCATTCA
1 GCACAAATGCCTTC-GGATCTTAGCCCGGACA-CATTCA
25792264 ATTAATCATG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
40 17 0.53
41 15 0.47
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24
Consensus pattern (41 bp):
GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
Found at i:25798552 original size:42 final size:43
Alignment explanation
Indices: 25798496--25798609 Score: 137
Period size: 42 Copynumber: 2.7 Consensus size: 43
25798486 ATGTGATTCA
*
25798496 TGTAAGACCATAGCTAGGCTATGGCATCGA-TATATGAATATG
1 TGTAAGACCATAGCTAGGCTATGGCATCGATTATATGAAGATG
* *
25798538 TGTAAGACCATAGCTGGGCGTA-GGCATC-ATTATGTGAAGATG
1 TGTAAGACCATAGCTAGGC-TATGGCATCGATTATATGAAGATG
* *
25798580 TGTAAGACCATAG-TTGAACTATGGCATCGA
1 TGTAAGACCATAGCTAG-GCTATGGCATCGA
25798610 GAAAATGAAG
Statistics
Matches: 62, Mismatches: 5, Indels: 9
0.82 0.07 0.12
Matches are distributed among these distances:
41 5 0.08
42 54 0.87
43 3 0.05
ACGTcount: A:0.32, C:0.15, G:0.26, T:0.27
Consensus pattern (43 bp):
TGTAAGACCATAGCTAGGCTATGGCATCGATTATATGAAGATG
Found at i:25800523 original size:34 final size:34
Alignment explanation
Indices: 25800446--25800511 Score: 96
Period size: 34 Copynumber: 1.9 Consensus size: 34
25800436 TGATTGCATT
* * *
25800446 ACTGATGCTGTTACTGTGATGGGCTAAGGCCCAC
1 ACTGATACTGATACTGTAATGGGCTAAGGCCCAC
*
25800480 ACTGATACTGATACTGTAATGGGCTATGGCCC
1 ACTGATACTGATACTGTAATGGGCTAAGGCCC
25800512 TAATTGATAC
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
34 28 1.00
ACGTcount: A:0.23, C:0.23, G:0.27, T:0.27
Consensus pattern (34 bp):
ACTGATACTGATACTGTAATGGGCTAAGGCCCAC
Found at i:25801141 original size:20 final size:20
Alignment explanation
Indices: 25801118--25801221 Score: 57
Period size: 20 Copynumber: 5.1 Consensus size: 20
25801108 AAAGTACATC
25801118 CAGGGGTACCGAAGTACAAA
1 CAGGGGTACCGAAGTACAAA
* **** * *
25801138 CAGGGGCACATCTGTGCAATT
1 CAGGGGTACCGAAGTACAA-A
* *
25801159 CAGGGGTACCAAAGTACCAA
1 CAGGGGTACCGAAGTACAAA
* * * *
25801179 CAGGGGCA-CGTATGTGCAATT
1 CAGGGGTACCG-AAGTACAA-A
25801200 CAGGGGTACCGAAGTACAAA
1 CAGGGGTACCGAAGTACAAA
25801220 CA
1 CA
25801222 AGTGTACGTA
Statistics
Matches: 55, Mismatches: 25, Indels: 8
0.62 0.28 0.09
Matches are distributed among these distances:
19 1 0.02
20 27 0.49
21 25 0.45
22 2 0.04
ACGTcount: A:0.34, C:0.22, G:0.29, T:0.15
Consensus pattern (20 bp):
CAGGGGTACCGAAGTACAAA
Found at i:25801175 original size:41 final size:41
Alignment explanation
Indices: 25801118--25801316 Score: 218
Period size: 41 Copynumber: 4.7 Consensus size: 41
25801108 AAAGTACATC
*
25801118 CAGGGGTACCGAAGTACAAACAGGGGCACATCTGTGCAATT
1 CAGGGGTACCGAAGTACAAACAGGGGCACATATGTGCAATT
* * *
25801159 CAGGGGTACCAAAGTACCAACAGGGGCACGTATGTGCAATT
1 CAGGGGTACCGAAGTACAAACAGGGGCACATATGTGCAATT
* * * *
25801200 CAGGGGTACCGAAGTACAAACAAGTGTACGTATGTGCAATTCAAATT
1 CAGGGGTACCGAAGTACAAACAGGGGCACATATGTG-----C-AATT
* ** * *
25801247 CAAGGGTACTAAAGTAAAAACAGGGGCACATATATGCAATT
1 CAGGGGTACCGAAGTACAAACAGGGGCACATATGTGCAATT
*
25801288 CAGGGGTACCGAAGTACAAATAGGGGCAC
1 CAGGGGTACCGAAGTACAAACAGGGGCAC
25801317 CGAAGTACAA
Statistics
Matches: 129, Mismatches: 23, Indels: 12
0.79 0.14 0.07
Matches are distributed among these distances:
41 96 0.74
42 1 0.01
46 1 0.01
47 31 0.24
ACGTcount: A:0.36, C:0.19, G:0.27, T:0.18
Consensus pattern (41 bp):
CAGGGGTACCGAAGTACAAACAGGGGCACATATGTGCAATT
Found at i:25801318 original size:20 final size:20
Alignment explanation
Indices: 25801289--25801336 Score: 87
Period size: 20 Copynumber: 2.4 Consensus size: 20
25801279 TATGCAATTC
*
25801289 AGGGGTACCGAAGTACAAAT
1 AGGGGCACCGAAGTACAAAT
25801309 AGGGGCACCGAAGTACAAAT
1 AGGGGCACCGAAGTACAAAT
25801329 AGGGGCAC
1 AGGGGCAC
25801337 GAATGTGCAA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.38, C:0.19, G:0.33, T:0.10
Consensus pattern (20 bp):
AGGGGCACCGAAGTACAAAT
Found at i:25802792 original size:8 final size:8
Alignment explanation
Indices: 25802779--25802803 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
25802769 TAGTTATGAG
25802779 TTATGTGA
1 TTATGTGA
25802787 TTATGTGA
1 TTATGTGA
25802795 TTATGTGA
1 TTATGTGA
25802803 T
1 T
25802804 CCGGGTGCTG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.24, C:0.00, G:0.24, T:0.52
Consensus pattern (8 bp):
TTATGTGA
Found at i:25815991 original size:9 final size:9
Alignment explanation
Indices: 25815977--25816001 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
25815967 AACCATTCCA
25815977 TCATTCATT
1 TCATTCATT
25815986 TCATTCATT
1 TCATTCATT
25815995 TCATTCA
1 TCATTCA
25816002 AAATAATCCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.24, C:0.24, G:0.00, T:0.52
Consensus pattern (9 bp):
TCATTCATT
Found at i:25820303 original size:20 final size:20
Alignment explanation
Indices: 25820278--25820331 Score: 108
Period size: 20 Copynumber: 2.7 Consensus size: 20
25820268 CATGGCCTGC
25820278 CCACACGGGCGTGTCCCAAA
1 CCACACGGGCGTGTCCCAAA
25820298 CCACACGGGCGTGTCCCAAA
1 CCACACGGGCGTGTCCCAAA
25820318 CCACACGGGCGTGT
1 CCACACGGGCGTGT
25820332 AACCCCTGTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.22, C:0.39, G:0.28, T:0.11
Consensus pattern (20 bp):
CCACACGGGCGTGTCCCAAA
Found at i:25823530 original size:34 final size:34
Alignment explanation
Indices: 25823492--25823564 Score: 101
Period size: 34 Copynumber: 2.1 Consensus size: 34
25823482 CATACTGTAC
* *
25823492 TGAAATGTACTAAGGCCCAGACTACCACTGTTAT
1 TGAAATGGACTAAGGCCCAGACTACCACTGCTAT
* * *
25823526 TGAAATGGGCTCAGGCCCAGACTACTACTGCTAT
1 TGAAATGGACTAAGGCCCAGACTACCACTGCTAT
25823560 TGAAA
1 TGAAA
25823565 GAGGGACTAA
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.32, C:0.23, G:0.21, T:0.25
Consensus pattern (34 bp):
TGAAATGGACTAAGGCCCAGACTACCACTGCTAT
Found at i:25827460 original size:46 final size:45
Alignment explanation
Indices: 25827410--25827585 Score: 212
Period size: 46 Copynumber: 3.8 Consensus size: 45
25827400 TGGTTGAGCA
25827410 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-G
*** * *
25827456 TCCGAACTCGTTGAGTTGAGTCCGAGTTCGAGAGATGTAACTAG-GCA-
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-ACTTATG-GA-T-GCGAAG
*
25827503 TCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-G
* *
25827549 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
25827586 GCGGGTTACA
Statistics
Matches: 111, Mismatches: 12, Indels: 14
0.81 0.09 0.10
Matches are distributed among these distances:
43 1 0.01
44 3 0.03
45 1 0.01
46 69 0.62
47 32 0.29
48 1 0.01
49 3 0.03
50 1 0.01
ACGTcount: A:0.21, C:0.21, G:0.30, T:0.28
Consensus pattern (45 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAAG
Found at i:25827566 original size:93 final size:93
Alignment explanation
Indices: 25827407--25827577 Score: 306
Period size: 93 Copynumber: 1.8 Consensus size: 93
25827397 GGATGGTTGA
* *
25827407 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
25827472 TGAGTCCGAGTTCGAGAGATGTAACTAG
66 TGAGTCCGAGTTCGAGAGATGTAACTAG
* *
25827500 GCATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
25827565 TGAGTCCGAGTTC
66 TGAGTCCGAGTTC
25827578 ACTTATGGGC
Statistics
Matches: 74, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
93 74 1.00
ACGTcount: A:0.21, C:0.22, G:0.30, T:0.27
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGAGAGATGTAACTAG
Found at i:25841495 original size:48 final size:48
Alignment explanation
Indices: 25841380--25841652 Score: 219
Period size: 48 Copynumber: 5.7 Consensus size: 48
25841370 ATAAATTGCT
* * * * *
25841380 GATGCCATATCCCAGACATGGTCTTACACTAGGT-TACATGTCGAGGCC
1 GATGCCATGTCCCAGACATGGTCTTACACTAGCTCT-CATATCAATGCC
* * * * *
25841428 AATACCTTGTCCTAGACATGGTCTTACACTAGCTCTCATCTCAATGCC
1 GATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATATCAATGCC
* * * * *
25841476 GATGCCTTATCCCAAACATGGTCTTACACTGGCTCTCATA--ATGTGGCC
1 GATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATATCA-AT-GCC
* * * * * * *
25841524 GACGCCATGTCCCAGACATTGTCTTACATTAGCACACATATCGATGCT
1 GATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATATCAATGCC
* * * * *
25841572 GATGCCATGCCCCATACATGGTCTTACACTGGCTCTCATAACATTGCC
1 GATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATATCAATGCC
* * * *
25841620 AATGCCATGTACCAAACATGGTATTACACTAGC
1 GATGCCATGTCCCAGACATGGTCTTACACTAGC
25841653 ATACATATCA
Statistics
Matches: 173, Mismatches: 47, Indels: 10
0.75 0.20 0.04
Matches are distributed among these distances:
46 1 0.01
47 1 0.01
48 169 0.98
49 2 0.01
ACGTcount: A:0.26, C:0.29, G:0.17, T:0.27
Consensus pattern (48 bp):
GATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATATCAATGCC
Found at i:25841548 original size:96 final size:96
Alignment explanation
Indices: 25841435--25841662 Score: 267
Period size: 96 Copynumber: 2.4 Consensus size: 96
25841425 GCCAATACCT
* * * * * *
25841435 TGTCCTAGACATGGTCTTACACTAGCTCTCATCTCAATGCCGATGCCTTATCCCAAACATGGTCT
1 TGTCCCAGACATGGTCTTACACTAGCACACATATCAATGCCGATGCCATACCCCAAACATGGTCT
25841500 TACACTGGCTCTCATAATGTGGCCGACGCCA
66 TACACTGGCTCTCATAATGTGGCCGACGCCA
* * * * * *
25841531 TGTCCCAGACATTGTCTTACATTAGCACACATATCGATGCTGATGCCATGCCCCATACATGGTCT
1 TGTCCCAGACATGGTCTTACACTAGCACACATATCAATGCCGATGCCATACCCCAAACATGGTCT
** * * *
25841596 TACACTGGCTCTCATAACATTGCCAATGCCA
66 TACACTGGCTCTCATAATGTGGCCGACGCCA
* * * *
25841627 TGTACCAAACATGGTATTACACTAGCATACATATCA
1 TGTCCCAGACATGGTCTTACACTAGCACACATATCA
25841663 TCCAATGTCA
Statistics
Matches: 108, Mismatches: 24, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
96 108 1.00
ACGTcount: A:0.27, C:0.29, G:0.16, T:0.28
Consensus pattern (96 bp):
TGTCCCAGACATGGTCTTACACTAGCACACATATCAATGCCGATGCCATACCCCAAACATGGTCT
TACACTGGCTCTCATAATGTGGCCGACGCCA
Found at i:25847468 original size:34 final size:35
Alignment explanation
Indices: 25847343--25847503 Score: 227
Period size: 34 Copynumber: 4.6 Consensus size: 35
25847333 AGTACTTTAA
* *
25847343 TAATCCAACCGAAACACACTAGATGCTCATAAGAGC
1 TAATCCATCCGAAACACACCA-ATGCTCATAAGAGC
* * *
25847379 TAATCCATCTGGAACACACCAATGCTCATAAGAGT
1 TAATCCATCCGAAACACACCAATGCTCATAAGAGC
25847414 TAATCCATCCGAAACACACCAATGCTCATAAGAGC
1 TAATCCATCCGAAACACACCAATGCTCATAAGAGC
* * *
25847449 T-ATCCGTCCAAAACACACCAATGTTCATAAGAGC
1 TAATCCATCCGAAACACACCAATGCTCATAAGAGC
25847483 T-ATCCATCCGAAACACACCAA
1 TAATCCATCCGAAACACACCAA
25847504 AACAGAGAGT
Statistics
Matches: 112, Mismatches: 13, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
34 49 0.44
35 46 0.41
36 17 0.15
ACGTcount: A:0.40, C:0.30, G:0.12, T:0.19
Consensus pattern (35 bp):
TAATCCATCCGAAACACACCAATGCTCATAAGAGC
Found at i:25847478 original size:69 final size:70
Alignment explanation
Indices: 25847343--25847503 Score: 227
Period size: 69 Copynumber: 2.3 Consensus size: 70
25847333 AGTACTTTAA
* * ***
25847343 TAATCCAACCGAAACACACTAGATGCTCATAAGAGCTAATCCATCTGGAACACACCAATGCTCAT
1 TAATCCATCCGAAACACACCA-ATGCTCATAAGAGCTAATCCATCCAAAACACACCAATGCTCAT
*
25847408 AAGAGT
65 AAGAGC
* *
25847414 TAATCCATCCGAAACACACCAATGCTCATAAGAGCT-ATCCGTCCAAAACACACCAATGTTCATA
1 TAATCCATCCGAAACACACCAATGCTCATAAGAGCTAATCCATCCAAAACACACCAATGCTCATA
25847478 AGAGC
66 AGAGC
25847483 T-ATCCATCCGAAACACACCAA
1 TAATCCATCCGAAACACACCAA
25847504 AACAGAGAGT
Statistics
Matches: 82, Mismatches: 8, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
68 20 0.24
69 28 0.34
70 15 0.18
71 19 0.23
ACGTcount: A:0.40, C:0.30, G:0.12, T:0.19
Consensus pattern (70 bp):
TAATCCATCCGAAACACACCAATGCTCATAAGAGCTAATCCATCCAAAACACACCAATGCTCATA
AGAGC
Found at i:25852444 original size:43 final size:43
Alignment explanation
Indices: 25852383--25852505 Score: 237
Period size: 43 Copynumber: 2.8 Consensus size: 43
25852373 ACCAAGTTCA
25852383 ATATCTACATGGCAAGAATTAGCAAGAGATTTTTGGTTATTTC
1 ATATCTACATGGCAAGAATTAGCAAGAGATTTTTGGTTATTTC
25852426 ATATCTACATGGCAAGAATTAGCAAGAGATTTTTGGTTATTTC
1 ATATCTACATGGCAAGAATTAGCAAGAGATTTTTGGTTATTTC
25852469 ATATCTACATGGCAAGAATTAGCAAAGAGATTTTTGG
1 ATATCTACATGGCAAGAATTAGC-AAGAGATTTTTGG
25852506 CTAAGTATTT
Statistics
Matches: 79, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
43 66 0.84
44 13 0.16
ACGTcount: A:0.34, C:0.11, G:0.20, T:0.35
Consensus pattern (43 bp):
ATATCTACATGGCAAGAATTAGCAAGAGATTTTTGGTTATTTC
Found at i:25858708 original size:56 final size:56
Alignment explanation
Indices: 25858634--25858741 Score: 180
Period size: 56 Copynumber: 1.9 Consensus size: 56
25858624 CATATCGGCA
* *
25858634 CCAACGTATTAAACGTGGTCTTACTCGCACACATATATCAGAATCACATATCGATG
1 CCAACATATTAAACGTGGTCTTACTCGCACACATATATCAAAATCACATATCGATG
* *
25858690 CCAACATATTAAATGTGGTCTTACTCGTACACATATATCAAAATCACATATC
1 CCAACATATTAAACGTGGTCTTACTCGCACACATATATCAAAATCACATATC
25858742 AAAATCCTAT
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
56 48 1.00
ACGTcount: A:0.36, C:0.24, G:0.11, T:0.29
Consensus pattern (56 bp):
CCAACATATTAAACGTGGTCTTACTCGCACACATATATCAAAATCACATATCGATG
Found at i:25866912 original size:26 final size:26
Alignment explanation
Indices: 25866878--25866935 Score: 91
Period size: 26 Copynumber: 2.3 Consensus size: 26
25866868 TTCCATACTT
* *
25866878 AGAGAAAGATTTTAAGTTAAGAGAAG
1 AGAGAAAGATTTTAAGTCAAGAAAAG
25866904 AGAGAAAGATTTTAAGTCAAGAAAAG
1 AGAGAAAGATTTTAAGTCAAGAAAAG
25866930 A-AGAAA
1 AGAGAAA
25866936 ACTGCCTTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
25 5 0.17
26 25 0.83
ACGTcount: A:0.55, C:0.02, G:0.24, T:0.19
Consensus pattern (26 bp):
AGAGAAAGATTTTAAGTCAAGAAAAG
Found at i:25872205 original size:27 final size:27
Alignment explanation
Indices: 25872167--25872231 Score: 94
Period size: 27 Copynumber: 2.4 Consensus size: 27
25872157 TGGATAAGTT
25872167 GTAGAATTACCGAAATACCCTTATAGG
1 GTAGAATTACCGAAATACCCTTATAGG
* * *
25872194 GTAGAATTACCGAGATACCCTTGTGGG
1 GTAGAATTACCGAAATACCCTTATAGG
*
25872221 GTAAAATTACC
1 GTAGAATTACC
25872232 ATTTTGCCCC
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 34 1.00
ACGTcount: A:0.34, C:0.18, G:0.22, T:0.26
Consensus pattern (27 bp):
GTAGAATTACCGAAATACCCTTATAGG
Found at i:25873105 original size:26 final size:26
Alignment explanation
Indices: 25873075--25873126 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
25873065 GGTTGGGTGG
25873075 GTCGAGTAGTCTCCCAACATGGTGTA
1 GTCGAGTAGTCTCCCAACATGGTGTA
*
25873101 GTCGAGTAGTCTCCCCACATGGTGTA
1 GTCGAGTAGTCTCCCAACATGGTGTA
25873127 AGGCTGGTAC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.21, C:0.25, G:0.27, T:0.27
Consensus pattern (26 bp):
GTCGAGTAGTCTCCCAACATGGTGTA
Found at i:25884086 original size:12 final size:14
Alignment explanation
Indices: 25884071--25884102 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
25884061 GTGAGAACAC
25884071 ATGTGTA-G-TACT
1 ATGTGTAGGCTACT
25884083 ATGTGTAGGCTACT
1 ATGTGTAGGCTACT
25884097 ATGTGT
1 ATGTGT
25884103 TTAAGATGGT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 7 0.39
13 1 0.06
14 10 0.56
ACGTcount: A:0.22, C:0.09, G:0.28, T:0.41
Consensus pattern (14 bp):
ATGTGTAGGCTACT
Found at i:25884288 original size:49 final size:49
Alignment explanation
Indices: 25884070--25884306 Score: 192
Period size: 49 Copynumber: 4.7 Consensus size: 49
25884060 TGTGAGAACA
* * ** * *
25884070 CATGTGTAGTACTATGTGTAGGCTACTATGTGT-TTAAGATGGTTTTAGGTCA
1 CATGTGTAGTACTAAGTGCAGGCTACTATGTGTACCAA-AT--TATT-GGTCG
* * * * * *
25884122 CGTGTGTAATACTAAGTGCAGGTTACTACGTGTATCAGA-TAGTTAGGTCG
1 CATGTGTAGTACTAAGTGCAGGCTACTATGTGTACCAAATTA-TT-GGTCG
* ** * * *
25884172 CATGTGTAGTACAAAGTGCAGGCTACTATGCATACCCGACAATT-TCGATCA
1 CATGTGTAGTACTAAGTGCAGGCTACTATGTGTA-CC-A-AATTATTGGTCG
* *
25884223 CGTGTGTAGTACTAAGTGCAGGCTACTAGGTGTACCAAATTATTGGTCG
1 CATGTGTAGTACTAAGTGCAGGCTACTATGTGTACCAAATTATTGGTCG
25884272 CATGTGTAGTACTAAGTGCAGGCTACTATGTGTAC
1 CATGTGTAGTACTAAGTGCAGGCTACTATGTGTAC
25884307 TAGATAGCGT
Statistics
Matches: 146, Mismatches: 32, Indels: 17
0.75 0.16 0.09
Matches are distributed among these distances:
48 4 0.03
49 39 0.27
50 36 0.25
51 33 0.23
52 30 0.21
53 3 0.02
54 1 0.01
ACGTcount: A:0.26, C:0.16, G:0.26, T:0.32
Consensus pattern (49 bp):
CATGTGTAGTACTAAGTGCAGGCTACTATGTGTACCAAATTATTGGTCG
Found at i:25884301 original size:100 final size:101
Alignment explanation
Indices: 25884119--25884301 Score: 289
Period size: 101 Copynumber: 1.8 Consensus size: 101
25884109 TGGTTTTAGG
* * *
25884119 TCACGTGTGTAATACTAAGTGCAGGTTACTACGTGTATCAGATAGTTAGGTCGCATGTGTAGTAC
1 TCACGTGTGTAATACTAAGTGCAGGCTACTACGTGTACCAAATAGTTAGGTCGCATGTGTAGTAC
25884184 AAAGTGCAGGCTACTATGCATACCCGACAATTTCGA
66 AAAGTGCAGGCTACTATGCATACCCGACAATTTCGA
* *
25884220 TCACGTGTGTAGTACTAAGTGCAGGCTACTAGGTGTACCAAATTA-TT-GGTCGCATGTGTAGTA
1 TCACGTGTGTAATACTAAGTGCAGGCTACTACGTGTACCAAA-TAGTTAGGTCGCATGTGTAGTA
*
25884283 CTAAGTGCAGGCTACTATG
65 CAAAGTGCAGGCTACTATG
25884302 TGTACTAGAT
Statistics
Matches: 75, Mismatches: 6, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
100 34 0.45
101 39 0.52
102 2 0.03
ACGTcount: A:0.27, C:0.18, G:0.25, T:0.30
Consensus pattern (101 bp):
TCACGTGTGTAATACTAAGTGCAGGCTACTACGTGTACCAAATAGTTAGGTCGCATGTGTAGTAC
AAAGTGCAGGCTACTATGCATACCCGACAATTTCGA
Found at i:25884532 original size:16 final size:15
Alignment explanation
Indices: 25884511--25884540 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
25884501 GAATGGAGTA
25884511 AGTGAAATTATGTAAG
1 AGTGAAATT-TGTAAG
25884527 AGTGAAATTTGTAA
1 AGTGAAATTTGTAA
25884541 TTAAACAGTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.43, C:0.00, G:0.23, T:0.33
Consensus pattern (15 bp):
AGTGAAATTTGTAAG
Found at i:25886751 original size:27 final size:27
Alignment explanation
Indices: 25886721--25886898 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
25886711 ATATTGAGTC
* * * *
25886721 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
25886748 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
25886775 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
25886803 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
25886830 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
25886857 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
25886884 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
25886899 GTACAATTTA
Statistics
Matches: 130, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 24 0.18
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:25886860 original size:82 final size:81
Alignment explanation
Indices: 25886742--25886897 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
25886732 TGCTATATAA
* *
25886742 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
25886807 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
25886824 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
25886888 CACTTAGTGC
65 CACTTAGTGC
25886898 TGTACAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 16 0.24
82 51 0.76
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:25905289 original size:13 final size:13
Alignment explanation
Indices: 25905271--25905301 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
25905261 TAGACTTCCT
25905271 CACACGGGTAAGC
1 CACACGGGTAAGC
25905284 CACACGGGTAAGC
1 CACACGGGTAAGC
25905297 CACAC
1 CACAC
25905302 AGTTGTGTCC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.32, C:0.35, G:0.26, T:0.06
Consensus pattern (13 bp):
CACACGGGTAAGC
Found at i:25911239 original size:51 final size:49
Alignment explanation
Indices: 25911178--25911311 Score: 135
Period size: 49 Copynumber: 2.7 Consensus size: 49
25911168 GTTAGGTCGT
* * *
25911178 ATGTATAGTACTAAGTGCAGGCTACTATGTGTACCCGACAACTTCGATCAT
1 ATGTGTAGTACTAAGTGCAGGCTACTATGTGTACACGA-AACTT-GATCAC
* * * *** * *
25911229 GTGTGTAGTACTAAGTGTAGGCTACTACT-TGTACAGGATTGTTGGTCGC
1 ATGTGTAGTACTAAGTGCAGGCTACTA-TGTGTACACGAAACTTGATCAC
25911278 ATGTGTAGTACTAAGTGCAGGCTACTATGTGTAC
1 ATGTGTAGTACTAAGTGCAGGCTACTATGTGTAC
25911312 TAGATAACTT
Statistics
Matches: 68, Mismatches: 13, Indels: 6
0.78 0.15 0.07
Matches are distributed among these distances:
48 1 0.01
49 33 0.49
50 2 0.03
51 31 0.46
52 1 0.01
ACGTcount: A:0.25, C:0.17, G:0.25, T:0.32
Consensus pattern (49 bp):
ATGTGTAGTACTAAGTGCAGGCTACTATGTGTACACGAAACTTGATCAC
Found at i:25911537 original size:16 final size:15
Alignment explanation
Indices: 25911516--25911545 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
25911506 GAATGGAGTA
25911516 AGTGAAATTATGTAAG
1 AGTGAAATT-TGTAAG
25911532 AGTGAAATTTGTAA
1 AGTGAAATTTGTAA
25911546 TAAAACAGTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.43, C:0.00, G:0.23, T:0.33
Consensus pattern (15 bp):
AGTGAAATTTGTAAG
Found at i:25914566 original size:27 final size:27
Alignment explanation
Indices: 25914518--25914676 Score: 166
Period size: 27 Copynumber: 5.9 Consensus size: 27
25914508 GCGAGGCTGC
* *
25914518 CAGATATTGTGAC-GAAGTCACCAGATA
1 CAGATATTGTGGCAG-AGCCACCAGATA
25914545 CAGATATTGTGGCAGAGCCACCAGA-A
1 CAGATATTGTGGCAGAGCCACCAGATA
25914571 CAGATATATGTGGCAGAGCCACCAGAT-
1 CAGATAT-TGTGGCAGAGCCACCAGATA
* *
25914598 CAGATAATTGTGGCATAGCCACCAG-GA
1 CAGAT-ATTGTGGCAGAGCCACCAGATA
* *
25914625 CAGATATATGTGGTAGAACCACCAGAT-
1 CAGATAT-TGTGGCAGAGCCACCAGATA
* *
25914652 CAGATAATTATGGCATAGCCACCAG
1 CAGAT-ATTGTGGCAGAGCCACCAG
25914677 GATGCTTCCT
Statistics
Matches: 112, Mismatches: 12, Indels: 16
0.80 0.09 0.11
Matches are distributed among these distances:
26 10 0.09
27 97 0.87
28 5 0.04
ACGTcount: A:0.35, C:0.21, G:0.24, T:0.19
Consensus pattern (27 bp):
CAGATATTGTGGCAGAGCCACCAGATA
Found at i:25914677 original size:54 final size:54
Alignment explanation
Indices: 25914536--25914678 Score: 225
Period size: 54 Copynumber: 2.6 Consensus size: 54
25914526 GTGACGAAGT
* * *
25914536 CACCAGATACAGAT-ATTGTGGCAGAGCCACCAGAACAGATATATGTGGCAGAGC
1 CACCAGAT-CAGATAATTGTGGCATAGCCACCAGGACAGATATATGTGGCAGAAC
*
25914590 CACCAGATCAGATAATTGTGGCATAGCCACCAGGACAGATATATGTGGTAGAAC
1 CACCAGATCAGATAATTGTGGCATAGCCACCAGGACAGATATATGTGGCAGAAC
*
25914644 CACCAGATCAGATAATTATGGCATAGCCACCAGGA
1 CACCAGATCAGATAATTGTGGCATAGCCACCAGGA
25914679 TGCTTCCTCC
Statistics
Matches: 83, Mismatches: 5, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
53 5 0.06
54 78 0.94
ACGTcount: A:0.36, C:0.22, G:0.24, T:0.18
Consensus pattern (54 bp):
CACCAGATCAGATAATTGTGGCATAGCCACCAGGACAGATATATGTGGCAGAAC
Found at i:25916024 original size:26 final size:26
Alignment explanation
Indices: 25915993--25916100 Score: 189
Period size: 26 Copynumber: 4.2 Consensus size: 26
25915983 TGAAATGCCC
*
25915993 ATCATGGAACATTTACCTAAACCATT
1 ATCATGGAACATTTACCTAACCCATT
25916019 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
* *
25916045 ATCATGGAATATTTACCTAATCCATT
1 ATCATGGAACATTTACCTAACCCATT
25916071 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
25916097 ATCA
1 ATCA
25916101 ATTTGTACCA
Statistics
Matches: 77, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 77 1.00
ACGTcount: A:0.36, C:0.24, G:0.07, T:0.32
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAACCCATT
Done.