Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr13 124041150
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: 124041150
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 335 characters in sequence are not A, C, G, or T
File 174 of 410
Found at i:53498481 original size:31 final size:31
Alignment explanation
Indices: 53498443--53498519 Score: 127
Period size: 31 Copynumber: 2.5 Consensus size: 31
53498433 TAACGGTTAT
53498443 TAGGCCGAAGCCTTTTCATAAATCATATCAC
1 TAGGCCGAAGCCTTTTCATAAATCATATCAC
* *
53498474 TAGGCCGAAGCCTTTTCATAAATCATATTAT
1 TAGGCCGAAGCCTTTTCATAAATCATATCAC
*
53498505 TAGGCCAAAGCCTTT
1 TAGGCCGAAGCCTTT
53498520 ACTGTAAACG
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 43 1.00
ACGTcount: A:0.31, C:0.23, G:0.14, T:0.31
Consensus pattern (31 bp):
TAGGCCGAAGCCTTTTCATAAATCATATCAC
Found at i:53498590 original size:42 final size:42
Alignment explanation
Indices: 53498543--53498634 Score: 139
Period size: 42 Copynumber: 2.2 Consensus size: 42
53498533 TGGCCCTTAG
* ** *
53498543 GCCCATTTCAATATCACATGTAATGTCAATGGATGCATGCAA
1 GCCCATTTCAATATCACATGAAATACCAATGAATGCATGCAA
*
53498585 GCCCATTTCAATATCACATGAAATACCAATGAATGTATGCAA
1 GCCCATTTCAATATCACATGAAATACCAATGAATGCATGCAA
53498627 GCCCATTT
1 GCCCATTT
53498635 GGGGAGACTA
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 45 1.00
ACGTcount: A:0.35, C:0.23, G:0.14, T:0.28
Consensus pattern (42 bp):
GCCCATTTCAATATCACATGAAATACCAATGAATGCATGCAA
Found at i:53498848 original size:26 final size:26
Alignment explanation
Indices: 53498779--53498875 Score: 162
Period size: 26 Copynumber: 3.8 Consensus size: 26
53498769 CCTCTTTAAT
53498779 AACTGGGGCA-AAGCCCTTTTCGGTA
1 AACTGGGGCATAAGCCCTTTTCGGTA
**
53498804 AACTGGGG-ATAAGCCCTTTTCAATA
1 AACTGGGGCATAAGCCCTTTTCGGTA
53498829 AACTGGGGCATAAGCCCTTTTCGGTA
1 AACTGGGGCATAAGCCCTTTTCGGTA
53498855 AACTGGGGCATAAGCCCTTTT
1 AACTGGGGCATAAGCCCTTTT
53498876 GCACTTCCTC
Statistics
Matches: 66, Mismatches: 4, Indels: 3
0.90 0.05 0.04
Matches are distributed among these distances:
24 1 0.02
25 29 0.44
26 36 0.55
ACGTcount: A:0.26, C:0.23, G:0.25, T:0.27
Consensus pattern (26 bp):
AACTGGGGCATAAGCCCTTTTCGGTA
Found at i:53498850 original size:51 final size:51
Alignment explanation
Indices: 53498779--53498875 Score: 178
Period size: 51 Copynumber: 1.9 Consensus size: 51
53498769 CCTCTTTAAT
53498779 AACTGGGGCAAAGCCCTTTTCGGTAAACTGGGG-ATAAGCCCTTTTCAATA
1 AACTGGGGCAAAGCCCTTTTCGGTAAACTGGGGCATAAGCCCTTTTCAATA
53498829 AACTGGGGCATAAGCCCTTTTCGGTAAACTGGGGCATAAGCCCTTTT
1 AACTGGGGCA-AAGCCCTTTTCGGTAAACTGGGGCATAAGCCCTTTT
53498876 GCACTTCCTC
Statistics
Matches: 45, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
50 10 0.22
51 23 0.51
52 12 0.27
ACGTcount: A:0.26, C:0.23, G:0.25, T:0.27
Consensus pattern (51 bp):
AACTGGGGCAAAGCCCTTTTCGGTAAACTGGGGCATAAGCCCTTTTCAATA
Found at i:53499774 original size:27 final size:27
Alignment explanation
Indices: 53499679--53499757 Score: 133
Period size: 27 Copynumber: 2.9 Consensus size: 27
53499669 TATTCATCAT
*
53499679 TTTACCATACAGGGG-TATTACGGTCAC
1 TTTACCCTACAGGGGCT-TTACGGTCAC
53499706 TTTACCCTACAGGGGCTTTACGGTCAC
1 TTTACCCTACAGGGGCTTTACGGTCAC
53499733 TTTACCCTACAGGGGCTTTACGGTC
1 TTTACCCTACAGGGGCTTTACGGTC
53499758 TTTTTACCTA
Statistics
Matches: 50, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
27 49 0.98
28 1 0.02
ACGTcount: A:0.20, C:0.27, G:0.23, T:0.30
Consensus pattern (27 bp):
TTTACCCTACAGGGGCTTTACGGTCAC
Found at i:53499848 original size:27 final size:27
Alignment explanation
Indices: 53499818--53499869 Score: 79
Period size: 27 Copynumber: 1.9 Consensus size: 27
53499808 GTAAATCTAC
*
53499818 AAACCACTGGTATTT-CAGTAATTTTGT
1 AAACCAATGGTATTTCCA-TAATTTTGT
53499845 AAACCAATGGTATTTCCATAATTTT
1 AAACCAATGGTATTTCCATAATTTT
53499870 TAGAAAGTCG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
27 21 0.91
28 2 0.09
ACGTcount: A:0.33, C:0.15, G:0.12, T:0.40
Consensus pattern (27 bp):
AAACCAATGGTATTTCCATAATTTTGT
Found at i:53499923 original size:56 final size:54
Alignment explanation
Indices: 53499826--53500154 Score: 161
Period size: 54 Copynumber: 6.1 Consensus size: 54
53499816 ACAAACCACT
* * *
53499826 GGTATTTCAGTAATTTTGTAAACCAATGGTATTTCCATAATTTTTAGAAAGTCGAG
1 GGTATTTCAGTAACTTTGTAAACCAAGGGTATTTCCATAA-TTTTACAAA-TCGAG
* * * *** *
53499882 GGTATTTCTGTAACTTTGTAAATCAGGGGTATTTTGGTAATTTTACAAATTGAG
1 GGTATTTCAGTAACTTTGTAAACCAAGGGTATTTCCATAATTTTACAAATCGAG
** * *** *
53499936 GGTATTTC-GATAA-TTTCAAAAACCAATGGTATTTTGGTAATTTTACAAA-CTAGG
1 GGTATTTCAG-TAACTTT-GTAAACCAAGGGTATTTCCATAATTTTACAAATCGA-G
** * ** ** ** *
53499990 GGTATTTTGGTAATTTTACAAATTAAGGGTATTTCGGTAATTTTACAAA-CCAGG
1 GGTATTTCAGTAACTTTGTAAACCAAGGGTATTTCCATAATTTTACAAATCGA-G
* * * *** *
53500044 GGTATTTTAGCAA-TTT-TACAGA-CTAGGGTATTTTGGTAATTTTACTAATCGAG
1 GGTATTTCAGTAACTTTGTA-A-ACCAAGGGTATTTCCATAATTTTACAAATCGAG
** * * **
53500097 GGTATTTTGGTAATTTTGTAAACCAAGGGTATTT-TAGTAATTTTTTAAATCGAG
1 GGTATTTCAGTAACTTTGTAAACCAAGGGTATTTCCA-TAATTTTACAAATCGAG
53500151 GGTA
1 GGTA
53500155 AAACAGTAAT
Statistics
Matches: 221, Mismatches: 40, Indels: 26
0.77 0.14 0.09
Matches are distributed among these distances:
52 1 0.00
53 44 0.20
54 130 0.59
55 14 0.06
56 32 0.14
ACGTcount: A:0.31, C:0.09, G:0.20, T:0.40
Consensus pattern (54 bp):
GGTATTTCAGTAACTTTGTAAACCAAGGGTATTTCCATAATTTTACAAATCGAG
Found at i:53499967 original size:54 final size:54
Alignment explanation
Indices: 53499867--53500154 Score: 253
Period size: 54 Copynumber: 5.3 Consensus size: 54
53499857 TTTCCATAAT
* * ** * *
53499867 TTTTAGAAAGTCGAGGGTATTTCTG-TAACTTTGTAAATCAGGGGTATTTTGGTAA
1 TTTTACAAA-TCGAGGGTATTT-TGATAATTTTACAAACCAAGGGTATTTTGGTAA
* * * * *
53499922 TTTTACAAATTGAGGGTATTTCGATAATTTCAAAAACCAATGGTATTTTGGTAA
1 TTTTACAAATCGAGGGTATTTTGATAATTTTACAAACCAAGGGTATTTTGGTAA
* * ** *
53499976 TTTTACAAA-CTAGGGGTATTTTGGTAATTTTACAAATTAAGGGTATTTCGGTAA
1 TTTTACAAATCGA-GGGTATTTTGATAATTTTACAAACCAAGGGTATTTTGGTAA
* * * *
53500030 TTTTACAAA-CCAGGGGTATTTT-AGCAATTTTACAGA-CTAGGGTATTTTGGTAA
1 TTTTACAAATCGA-GGGTATTTTGA-TAATTTTACAAACCAAGGGTATTTTGGTAA
* * ** *
53500083 TTTTACTAATCGAGGGTATTTTGGTAATTTTGTAAACCAAGGGTATTTTAGTAA
1 TTTTACAAATCGAGGGTATTTTGATAATTTTACAAACCAAGGGTATTTTGGTAA
**
53500137 TTTTTTAAATCGAGGGTA
1 TTTTACAAATCGAGGGTA
53500155 AAACAGTAAT
Statistics
Matches: 188, Mismatches: 39, Indels: 13
0.78 0.16 0.05
Matches are distributed among these distances:
53 41 0.22
54 139 0.74
55 8 0.04
ACGTcount: A:0.31, C:0.08, G:0.21, T:0.40
Consensus pattern (54 bp):
TTTTACAAATCGAGGGTATTTTGATAATTTTACAAACCAAGGGTATTTTGGTAA
Found at i:53500002 original size:81 final size:81
Alignment explanation
Indices: 53499906--53500140 Score: 337
Period size: 81 Copynumber: 2.9 Consensus size: 81
53499896 TTTGTAAATC
* * *
53499906 AGGGGTATTTTGGTAATTTTACAAATTGAGGGTATTTCGATAATTTCAAAAACCAATGGTATTTT
1 AGGGGTATTTTGGTAATTTTACAAATTGAGGGTATTTCGGTAATTTTAAAAACCAAGGGTATTTT
*
53499971 GGTAATTTTACAAACT
66 AGTAATTTTACAAACT
* * *
53499987 AGGGGTATTTTGGTAATTTTACAAATTAAGGGTATTTCGGTAATTTTACAAACCAGGGGTATTTT
1 AGGGGTATTTTGGTAATTTTACAAATTGAGGGTATTTCGGTAATTTTAAAAACCAAGGGTATTTT
* *
53500052 AGCAATTTTACAGACT
66 AGTAATTTTACAAACT
* * * **
53500068 A-GGGTATTTTGGTAATTTTACTAATCGAGGGTATTTTGGTAATTTTGTAAACCAAGGGTATTTT
1 AGGGGTATTTTGGTAATTTTACAAATTGAGGGTATTTCGGTAATTTTAAAAACCAAGGGTATTTT
53500132 AGTAATTTT
66 AGTAATTTT
53500141 TTAAATCGAG
Statistics
Matches: 137, Mismatches: 17, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
80 64 0.47
81 73 0.53
ACGTcount: A:0.31, C:0.08, G:0.20, T:0.41
Consensus pattern (81 bp):
AGGGGTATTTTGGTAATTTTACAAATTGAGGGTATTTCGGTAATTTTAAAAACCAAGGGTATTTT
AGTAATTTTACAAACT
Found at i:53500153 original size:27 final size:27
Alignment explanation
Indices: 53499901--53500154 Score: 242
Period size: 27 Copynumber: 9.4 Consensus size: 27
53499891 GTAACTTTGT
*
53499901 AAATCAGGGGTATTTTGGTAATTTTAC
1 AAATCAAGGGTATTTTGGTAATTTTAC
** * * * *
53499928 AAATTGAGGGTATTTCGATAATTTCAA
1 AAATCAAGGGTATTTTGGTAATTTTAC
* *
53499955 AAACCAATGGTATTTTGGTAATTTTAC
1 AAATCAAGGGTATTTTGGTAATTTTAC
*
53499982 AAA-CTAGGGGTATTTTGGTAATTTTAC
1 AAATC-AAGGGTATTTTGGTAATTTTAC
* *
53500009 AAATTAAGGGTATTTCGGTAATTTTAC
1 AAATCAAGGGTATTTTGGTAATTTTAC
* * * *
53500036 AAACCAGGGGTATTTTAGCAATTTTAC
1 AAATCAAGGGTATTTTGGTAATTTTAC
* *
53500063 AGA-CTAGGGTATTTTGGTAATTTTAC
1 AAATCAAGGGTATTTTGGTAATTTTAC
* * **
53500089 TAATCGAGGGTATTTTGGTAATTTTGT
1 AAATCAAGGGTATTTTGGTAATTTTAC
* * **
53500116 AAACCAAGGGTATTTTAGTAATTTTTT
1 AAATCAAGGGTATTTTGGTAATTTTAC
*
53500143 AAATCGAGGGTA
1 AAATCAAGGGTA
53500155 AAACAGTAAT
Statistics
Matches: 181, Mismatches: 43, Indels: 6
0.79 0.19 0.03
Matches are distributed among these distances:
26 21 0.12
27 160 0.88
ACGTcount: A:0.31, C:0.08, G:0.20, T:0.40
Consensus pattern (27 bp):
AAATCAAGGGTATTTTGGTAATTTTAC
Found at i:53500162 original size:27 final size:27
Alignment explanation
Indices: 53500132--53500262 Score: 183
Period size: 27 Copynumber: 4.9 Consensus size: 27
53500122 AGGGTATTTT
* *
53500132 AGTAATTTTTTAAATCGAGGGTAAAAC
1 AGTAATTCTATAAATCGAGGGTAAAAC
* *
53500159 AGTAATTCTATAAATCAAGGGTAAGAC
1 AGTAATTCTATAAATCGAGGGTAAAAC
53500186 AGTAATTCTATAAATCGAGGGTAAAAC
1 AGTAATTCTATAAATCGAGGGTAAAAC
* *
53500213 GGTAATTCTGTAAATCGAGGGTAAAAC
1 AGTAATTCTATAAATCGAGGGTAAAAC
*
53500240 -GATAATTCTATAAATCAAGGGTA
1 AG-TAATTCTATAAATCGAGGGTA
53500263 CTTTGGTAAT
Statistics
Matches: 93, Mismatches: 10, Indels: 2
0.89 0.10 0.02
Matches are distributed among these distances:
26 1 0.01
27 92 0.99
ACGTcount: A:0.42, C:0.10, G:0.20, T:0.28
Consensus pattern (27 bp):
AGTAATTCTATAAATCGAGGGTAAAAC
Found at i:53500307 original size:81 final size:80
Alignment explanation
Indices: 53500122--53500307 Score: 185
Period size: 81 Copynumber: 2.3 Consensus size: 80
53500112 TTGTAAACCA
* *
53500122 AGGGTATTTTAGTAATTTTTTAAATCGAGGGTAAAACAGTAATTCTATAAATCAAGGGTAAGACA
1 AGGGTATTTCAGTAA-TTTGTAAATCGAGGGTAAAACAGTAATTCTATAAATCAAGGGTAAGACA
*
53500187 GTAATTCTATAAATCG
65 GTAATTCTACAAATCG
*** * ****
53500203 AGGGTAAAACGGTAATTCTGTAAATCGAGGGTAAAAC-GATAATTCTATAAATCAAGGGTACTTT
1 AGGGTATTTCAGTAATT-TGTAAATCGAGGGTAAAACAG-TAATTCTATAAATCAAGGGTAAGAC
* * * *
53500267 GGTAATTTTACAATTTG
64 AGTAATTCTACAAATCG
*
53500284 AGGGCATTTCAGTAATTTGGTAAA
1 AGGGTATTTCAGTAATTT-GTAAA
53500308 CTAAAGTATT
Statistics
Matches: 82, Mismatches: 20, Indels: 6
0.76 0.19 0.06
Matches are distributed among these distances:
80 4 0.05
81 78 0.95
ACGTcount: A:0.38, C:0.09, G:0.20, T:0.33
Consensus pattern (80 bp):
AGGGTATTTCAGTAATTTGTAAATCGAGGGTAAAACAGTAATTCTATAAATCAAGGGTAAGACAG
TAATTCTACAAATCG
Found at i:53505747 original size:25 final size:25
Alignment explanation
Indices: 53505718--53505767 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
53505708 CATTGTTTGG
53505718 TATACACCTAGAGCCAAAAAAATAA
1 TATACACCTAGAGCCAAAAAAATAA
53505743 TATACACCTAGAGCCAAAAAAATAA
1 TATACACCTAGAGCCAAAAAAATAA
53505768 CCCTATTATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.56, C:0.20, G:0.08, T:0.16
Consensus pattern (25 bp):
TATACACCTAGAGCCAAAAAAATAA
Found at i:53509630 original size:40 final size:39
Alignment explanation
Indices: 53509586--53509714 Score: 111
Period size: 40 Copynumber: 3.3 Consensus size: 39
53509576 GACTCGCTCA
*
53509586 AATGCCTTCGGGAC-GAAGCCC-GGTTATAGCGACTTGCAC
1 AATGCCTTCGGGACTGAA-CCCGGGTT-TAGCAACTTGCAC
* *
53509625 GAATGCCTTCGGGACTTAACCCGGGTTTAGTAACTTGCAC
1 -AATGCCTTCGGGACTGAACCCGGGTTTAGCAACTTGCAC
* * * * ** *
53509665 AAAGCCTTCGGGA-TTAGCCCGGATTTATTAACTCGCAC
1 AATGCCTTCGGGACTGAACCCGGGTTTAGCAACTTGCAC
53509703 GAATGCCTTCGG
1 -AATGCCTTCGG
53509715 ATCCTAGTCC
Statistics
Matches: 77, Mismatches: 9, Indels: 7
0.83 0.10 0.08
Matches are distributed among these distances:
38 21 0.27
39 22 0.29
40 28 0.36
41 6 0.08
ACGTcount: A:0.23, C:0.26, G:0.26, T:0.25
Consensus pattern (39 bp):
AATGCCTTCGGGACTGAACCCGGGTTTAGCAACTTGCAC
Found at i:53509714 original size:78 final size:80
Alignment explanation
Indices: 53509621--53509767 Score: 210
Period size: 78 Copynumber: 1.9 Consensus size: 80
53509611 ATAGCGACTT
* * *
53509621 GCACGAATGCCTTCGGGA-CTTAACCCGGGTTTAGTAACTT-GCACAAAGCCTTCGGGA-TTAGC
1 GCACGAATGCCTTC-GGATCCTAACCCGGATATAGTAACTTAGCACAAAGCCTTCGGGACTTAGC
53509683 CCGGATTTATTAACTC
65 CCGGATTTATTAACTC
** *
53509699 GCACGAATGCCTTCGGATCCTAGTCCGGATATAGTCACTTAGCACAAAGCCTTCGGGACTTAGCC
1 GCACGAATGCCTTCGGATCCTAACCCGGATATAGTAACTTAGCACAAAGCCTTCGGGACTTAGCC
53509764 CGGA
66 CGGA
53509768 CATCATTCGA
Statistics
Matches: 60, Mismatches: 6, Indels: 4
0.86 0.09 0.06
Matches are distributed among these distances:
77 3 0.05
78 30 0.50
79 17 0.28
80 10 0.17
ACGTcount: A:0.24, C:0.27, G:0.24, T:0.24
Consensus pattern (80 bp):
GCACGAATGCCTTCGGATCCTAACCCGGATATAGTAACTTAGCACAAAGCCTTCGGGACTTAGCC
CGGATTTATTAACTC
Found at i:53509751 original size:40 final size:37
Alignment explanation
Indices: 53509602--53509767 Score: 125
Period size: 40 Copynumber: 4.2 Consensus size: 37
53509592 TTCGGGACGA
* ** *
53509602 AGCCCGGTTATAGCGACTTGCACGAATGCCTTCGGGACTT
1 AGCCCGGATATAGTAACTTGCAC-AAAGCCTTC-GGA-TT
* * *
53509642 AACCCGGGTTTAGTAACTTGCACAAAGCCTTCGGGATT
1 AGCCCGGATATAGTAACTTGCACAAAGCCTTC-GGATT
* * * *
53509680 AGCCCGGATTTATTAACTCGCACGAATGCCTTCGGATCCT
1 AGCCCGGATATAGTAACTTGCAC-AAAGCCTTCGGAT--T
* *
53509720 AGTCCGGATATAGTCACTTAGCACAAAGCCTTCGGGACTT
1 AGCCCGGATATAGTAACTT-GCACAAAGCCTTC-GGA-TT
53509760 AGCCCGGA
1 AGCCCGGA
53509768 CATCATTCGA
Statistics
Matches: 102, Mismatches: 18, Indels: 12
0.77 0.14 0.09
Matches are distributed among these distances:
38 25 0.25
39 20 0.20
40 49 0.48
41 7 0.07
42 1 0.01
ACGTcount: A:0.24, C:0.27, G:0.24, T:0.25
Consensus pattern (37 bp):
AGCCCGGATATAGTAACTTGCACAAAGCCTTCGGATT
Found at i:53517712 original size:40 final size:39
Alignment explanation
Indices: 53517668--53517796 Score: 111
Period size: 40 Copynumber: 3.3 Consensus size: 39
53517658 GACTCGCTCA
*
53517668 AATGCCTTCGGGAC-GAAGCCC-GGTTATAGCGACTTGCAC
1 AATGCCTTCGGGACTGAA-CCCGGGTT-TAGCAACTTGCAC
* *
53517707 GAATGCCTTCGGGACTTAACCCGGGTTTAGTAACTTGCAC
1 -AATGCCTTCGGGACTGAACCCGGGTTTAGCAACTTGCAC
* * * * ** *
53517747 AAAGCCTTCGGGA-TTAGCCCGGATTTATTAACTCGCAC
1 AATGCCTTCGGGACTGAACCCGGGTTTAGCAACTTGCAC
53517785 GAATGCCTTCGG
1 -AATGCCTTCGG
53517797 ATCCTAGTCC
Statistics
Matches: 77, Mismatches: 9, Indels: 7
0.83 0.10 0.08
Matches are distributed among these distances:
38 21 0.27
39 22 0.29
40 28 0.36
41 6 0.08
ACGTcount: A:0.23, C:0.26, G:0.26, T:0.25
Consensus pattern (39 bp):
AATGCCTTCGGGACTGAACCCGGGTTTAGCAACTTGCAC
Found at i:53517796 original size:78 final size:80
Alignment explanation
Indices: 53517703--53517849 Score: 210
Period size: 78 Copynumber: 1.9 Consensus size: 80
53517693 ATAGCGACTT
* * *
53517703 GCACGAATGCCTTCGGGA-CTTAACCCGGGTTTAGTAACTT-GCACAAAGCCTTCGGGA-TTAGC
1 GCACGAATGCCTTC-GGATCCTAACCCGGATATAGTAACTTAGCACAAAGCCTTCGGGACTTAGC
53517765 CCGGATTTATTAACTC
65 CCGGATTTATTAACTC
** *
53517781 GCACGAATGCCTTCGGATCCTAGTCCGGATATAGTCACTTAGCACAAAGCCTTCGGGACTTAGCC
1 GCACGAATGCCTTCGGATCCTAACCCGGATATAGTAACTTAGCACAAAGCCTTCGGGACTTAGCC
53517846 CGGA
66 CGGA
53517850 CATCATTCGA
Statistics
Matches: 60, Mismatches: 6, Indels: 4
0.86 0.09 0.06
Matches are distributed among these distances:
77 3 0.05
78 30 0.50
79 17 0.28
80 10 0.17
ACGTcount: A:0.24, C:0.27, G:0.24, T:0.24
Consensus pattern (80 bp):
GCACGAATGCCTTCGGATCCTAACCCGGATATAGTAACTTAGCACAAAGCCTTCGGGACTTAGCC
CGGATTTATTAACTC
Found at i:53517833 original size:40 final size:37
Alignment explanation
Indices: 53517684--53517849 Score: 125
Period size: 40 Copynumber: 4.2 Consensus size: 37
53517674 TTCGGGACGA
* ** *
53517684 AGCCCGGTTATAGCGACTTGCACGAATGCCTTCGGGACTT
1 AGCCCGGATATAGTAACTTGCAC-AAAGCCTTC-GGA-TT
* * *
53517724 AACCCGGGTTTAGTAACTTGCACAAAGCCTTCGGGATT
1 AGCCCGGATATAGTAACTTGCACAAAGCCTTC-GGATT
* * * *
53517762 AGCCCGGATTTATTAACTCGCACGAATGCCTTCGGATCCT
1 AGCCCGGATATAGTAACTTGCAC-AAAGCCTTCGGAT--T
* *
53517802 AGTCCGGATATAGTCACTTAGCACAAAGCCTTCGGGACTT
1 AGCCCGGATATAGTAACTT-GCACAAAGCCTTC-GGA-TT
53517842 AGCCCGGA
1 AGCCCGGA
53517850 CATCATTCGA
Statistics
Matches: 102, Mismatches: 18, Indels: 12
0.77 0.14 0.09
Matches are distributed among these distances:
38 25 0.25
39 20 0.20
40 49 0.48
41 7 0.07
42 1 0.01
ACGTcount: A:0.24, C:0.27, G:0.24, T:0.25
Consensus pattern (37 bp):
AGCCCGGATATAGTAACTTGCACAAAGCCTTCGGATT
Found at i:53520950 original size:28 final size:29
Alignment explanation
Indices: 53520918--53521001 Score: 111
Period size: 28 Copynumber: 3.0 Consensus size: 29
53520908 ACATACATGT
*
53520918 ATATGGCCCACTAGGCCC-AATCTCATTC
1 ATATGGCCCACTAGGCCCAAATCACATTC
*
53520946 ATATGGCCCATTAGGCCCAAATCACATTC
1 ATATGGCCCACTAGGCCCAAATCACATTC
* *
53520975 ATATGGCCCA-TCGGCCCGAATCA-ATTC
1 ATATGGCCCACTAGGCCCAAATCACATTC
53521002 CAAGCCATGT
Statistics
Matches: 51, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
27 4 0.08
28 28 0.55
29 19 0.37
ACGTcount: A:0.27, C:0.33, G:0.15, T:0.24
Consensus pattern (29 bp):
ATATGGCCCACTAGGCCCAAATCACATTC
Found at i:53524907 original size:26 final size:26
Alignment explanation
Indices: 53524878--53524935 Score: 64
Period size: 26 Copynumber: 2.2 Consensus size: 26
53524868 AGTGTGTTTG
* *
53524878 GTGAGCCGGTGTTTGCCATGT-AAGTT
1 GTGAACCGGGGTTTGCCA-GTCAAGTT
* *
53524904 GTGAACTGGGGTTTGCTAGTCAAGTT
1 GTGAACCGGGGTTTGCCAGTCAAGTT
53524930 GTGAAC
1 GTGAAC
53524936 TAGGTTCGCT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
25 2 0.07
26 25 0.93
ACGTcount: A:0.19, C:0.14, G:0.34, T:0.33
Consensus pattern (26 bp):
GTGAACCGGGGTTTGCCAGTCAAGTT
Found at i:53524947 original size:25 final size:26
Alignment explanation
Indices: 53524899--53524951 Score: 81
Period size: 25 Copynumber: 2.1 Consensus size: 26
53524889 TTTGCCATGT
* *
53524899 AAGTTGTGAACTGGGGTTTGCTAGTC
1 AAGTTGTGAACTGAGGTTCGCTAGTC
53524925 AAGTTGTGAACT-AGGTTCGCTAGTC
1 AAGTTGTGAACTGAGGTTCGCTAGTC
53524950 AA
1 AA
53524952 AGATATAGGT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
25 13 0.52
26 12 0.48
ACGTcount: A:0.25, C:0.13, G:0.30, T:0.32
Consensus pattern (26 bp):
AAGTTGTGAACTGAGGTTCGCTAGTC
Found at i:53525759 original size:14 final size:14
Alignment explanation
Indices: 53525740--53525794 Score: 83
Period size: 14 Copynumber: 3.9 Consensus size: 14
53525730 ATGGTAAGAG
53525740 TGGTATGAACGAAA
1 TGGTATGAACGAAA
*
53525754 TGGTATGAATGAAA
1 TGGTATGAACGAAA
*
53525768 TGGTATGAACGAAG
1 TGGTATGAACGAAA
*
53525782 GGGTATGAACGAA
1 TGGTATGAACGAA
53525795 TTAGTCGGTT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 37 1.00
ACGTcount: A:0.40, C:0.05, G:0.33, T:0.22
Consensus pattern (14 bp):
TGGTATGAACGAAA
Found at i:53528722 original size:94 final size:92
Alignment explanation
Indices: 53528526--53528738 Score: 248
Period size: 94 Copynumber: 2.3 Consensus size: 92
53528516 AAGCTGACGC
* * * * *
53528526 TATGTCCCAGATAGGTCTTACACTAGCTTGTATATCTCGAGGCCGTGCATGTCCCAGACATGTCT
1 TATGTCCCAGACATGTCTTACACTAGCTAGTATAGCTCGAGGCCGTGAATGTCCCAGACATGTCT
** *
53528591 TACACTAGCTCTTGTCTCAATGCTGATA
66 TACACTAGCTCTAATAT-AATGCTGATA
*
53528619 CATGTCCCAGACATGTCTTACACTAGCTAGTATAGCTCGAGGCCGATGAATGTCCCAGACATGTC
1 TATGTCCCAGACATGTCTTACACTAGCTAGTATAGCTCGAGGCCG-TGAATGTCCCAGACATGTC
* * * * *
53528684 TTACATTGGCTCTCAATAT-GTGGTCGATG
65 TTACACTAGCTCT-AATATAATGCT-GATA
*
53528713 TATGTCCCAGACATGTATTACACTAG
1 TATGTCCCAGACATGTCTTACACTAG
53528739 TACACATATC
Statistics
Matches: 101, Mismatches: 16, Indels: 5
0.83 0.13 0.04
Matches are distributed among these distances:
93 43 0.43
94 56 0.55
95 2 0.02
ACGTcount: A:0.24, C:0.25, G:0.20, T:0.31
Consensus pattern (92 bp):
TATGTCCCAGACATGTCTTACACTAGCTAGTATAGCTCGAGGCCGTGAATGTCCCAGACATGTCT
TACACTAGCTCTAATATAATGCTGATA
Found at i:53530545 original size:46 final size:46
Alignment explanation
Indices: 53530478--53530570 Score: 141
Period size: 46 Copynumber: 2.0 Consensus size: 46
53530468 ACAGTTTTAC
* * *
53530478 AAGTTGTGTATCAGCCAAGCTCCCTACGTGAGCTCTCTATGATAAG
1 AAGTTGTGTATCAACCAAGCTCCCCACGTGAACTCTCTATGATAAG
* *
53530524 AAGTTGTGTATCAACCAAGCTCCCCATGTGAACTCTCTGTGATAAG
1 AAGTTGTGTATCAACCAAGCTCCCCACGTGAACTCTCTATGATAAG
53530570 A
1 A
53530571 TTTTATTCCT
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
46 42 1.00
ACGTcount: A:0.28, C:0.24, G:0.20, T:0.28
Consensus pattern (46 bp):
AAGTTGTGTATCAACCAAGCTCCCCACGTGAACTCTCTATGATAAG
Found at i:53542548 original size:15 final size:15
Alignment explanation
Indices: 53542515--53542548 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
53542505 TAATTAAAAG
*
53542515 AATAATAATGAGAAT
1 AATAATAATGAGAAC
*
53542530 AATAATAATGATAAC
1 AATAATAATGAGAAC
53542545 AATA
1 AATA
53542549 TCTCAAAGTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.62, C:0.03, G:0.09, T:0.26
Consensus pattern (15 bp):
AATAATAATGAGAAC
Found at i:53542885 original size:16 final size:16
Alignment explanation
Indices: 53542864--53542894 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
53542854 TTATTAAAAT
*
53542864 TAATTAATTAATTTTA
1 TAATTAAATAATTTTA
53542880 TAATTAAATAATTTT
1 TAATTAAATAATTTT
53542895 CTAAACTTAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (16 bp):
TAATTAAATAATTTTA
Found at i:53547732 original size:96 final size:96
Alignment explanation
Indices: 53547562--53547739 Score: 261
Period size: 96 Copynumber: 1.9 Consensus size: 96
53547552 TTATTTTTGC
* *
53547562 TCCTTTTTGCTCTATTGGTTTCGGCTTTTCCCTTTCTCGAACTAAGCTTCTTGGGCTCATTGTCT
1 TCCTCTTTGCTCTATTGGTTTCGGCTTTTCCCTTACTCGAACTAAGCTTCTTGGGCTCATTGTCT
*
53547627 GTTCCATCGTTCCCTTCGATGACAGACTTGT
66 GCTCCATCGTTCCCTTCGATGACAGACTTGT
*
53547658 TCCTCTTTGCTCTCTTGGTTTCGGCTTTTCCCTTACTCGAA-TCAAGCTTCTTGGGCCTC-TTGT
1 TCCTCTTTGCTCTATTGGTTTCGGCTTTTCCCTTACTCGAACT-AAGCTTCTTGGG-CTCATTGT
* * *
53547721 TTGCTCTATCGTTCTCTTC
64 CTGCTCCATCGTTCCCTTC
53547740 AATAAAAACT
Statistics
Matches: 73, Mismatches: 7, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
95 1 0.01
96 69 0.95
97 3 0.04
ACGTcount: A:0.10, C:0.29, G:0.17, T:0.45
Consensus pattern (96 bp):
TCCTCTTTGCTCTATTGGTTTCGGCTTTTCCCTTACTCGAACTAAGCTTCTTGGGCTCATTGTCT
GCTCCATCGTTCCCTTCGATGACAGACTTGT
Found at i:53567737 original size:24 final size:22
Alignment explanation
Indices: 53567680--53567739 Score: 57
Period size: 24 Copynumber: 2.5 Consensus size: 22
53567670 TTAGATTAAT
* *
53567680 TTATATTTTAGATATTATTATA
1 TTATATTTTAAATATCATTATA
*
53567702 TTAAATTATTTAAATATCATTTATTA
1 TTATA-T-TTTAAATATCA-TTA-TA
53567728 TTATATTTTAAA
1 TTATATTTTAAA
53567740 ATTTTAAAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 6
0.75 0.10 0.15
Matches are distributed among these distances:
22 4 0.13
23 1 0.03
24 15 0.50
25 4 0.13
26 6 0.20
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.57
Consensus pattern (22 bp):
TTATATTTTAAATATCATTATA
Found at i:53568155 original size:20 final size:20
Alignment explanation
Indices: 53568113--53568165 Score: 54
Period size: 20 Copynumber: 2.7 Consensus size: 20
53568103 ATTCAATTGT
* * *
53568113 TTTTTAGTCGGTTCAATCGA
1 TTTTTAGTTGGTTCAACCAA
*
53568133 TTTTTAGTTGGTTTAACCAA
1 TTTTTAGTTGGTTCAACCAA
*
53568153 TTTGTA-TTGGTTC
1 TTTTTAGTTGGTTC
53568166 TCAATCCAAC
Statistics
Matches: 27, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
19 6 0.22
20 21 0.78
ACGTcount: A:0.19, C:0.11, G:0.19, T:0.51
Consensus pattern (20 bp):
TTTTTAGTTGGTTCAACCAA
Found at i:53569247 original size:50 final size:52
Alignment explanation
Indices: 53569188--53569286 Score: 130
Period size: 50 Copynumber: 1.9 Consensus size: 52
53569178 TTAATAAAAT
* *** *
53569188 CATGCATTATGTAAATCTTGTGTTAGTT-AAGTTTGCATCA-TAAATTATGA
1 CATGAATTATGTAAATCCCATGTTAGTTAAAATTTGCATCATTAAATTATGA
*
53569238 CATGAATTATGTAACTCCCATGTTAGTTAAAATTTGCATCATTAAATTA
1 CATGAATTATGTAAATCCCATGTTAGTTAAAATTTGCATCATTAAATTA
53569287 ATTCATGCAT
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
50 23 0.56
51 11 0.27
52 7 0.17
ACGTcount: A:0.34, C:0.12, G:0.13, T:0.40
Consensus pattern (52 bp):
CATGAATTATGTAAATCCCATGTTAGTTAAAATTTGCATCATTAAATTATGA
Found at i:53572486 original size:46 final size:46
Alignment explanation
Indices: 53572431--53572611 Score: 233
Period size: 46 Copynumber: 3.9 Consensus size: 46
53572421 TAGGATGGTT
53572431 GAGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGC
1 GAGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGC
* * *
53572477 GAGCGTCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATGTAAC
1 GAGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATG---C
*
53572523 TAGGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGC
1 GA-GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGC
* ** *
53572570 GAACGCCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 GAGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
53572612 GCGGGTTACA
Statistics
Matches: 116, Mismatches: 12, Indels: 14
0.82 0.08 0.10
Matches are distributed among these distances:
43 4 0.03
45 2 0.02
46 71 0.61
47 33 0.28
48 2 0.02
50 4 0.03
ACGTcount: A:0.21, C:0.22, G:0.30, T:0.28
Consensus pattern (46 bp):
GAGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGC
Found at i:53572592 original size:93 final size:93
Alignment explanation
Indices: 53572433--53572603 Score: 315
Period size: 93 Copynumber: 1.8 Consensus size: 93
53572423 GGATGGTTGA
* *
53572433 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
53572498 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
*
53572526 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
53572591 TGAGTCCGAGTTC
66 TGAGTCCGAGTTC
53572604 ACTTATGGGC
Statistics
Matches: 75, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 75 1.00
ACGTcount: A:0.20, C:0.22, G:0.30, T:0.27
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:53578577 original size:10 final size:10
Alignment explanation
Indices: 53578562--53578611 Score: 59
Period size: 10 Copynumber: 5.0 Consensus size: 10
53578552 TAATTTTAGG
53578562 ATTTAT-TTT
1 ATTTATCTTT
53578571 CATTTATCTTT
1 -ATTTATCTTT
*
53578582 AATTATCTTT
1 ATTTATCTTT
53578592 ATTTAT-TTGT
1 ATTTATCTT-T
53578602 ATTTATCTTT
1 ATTTATCTTT
53578612 TAGAATTTAA
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
9 2 0.06
10 28 0.80
11 5 0.14
ACGTcount: A:0.22, C:0.08, G:0.02, T:0.68
Consensus pattern (10 bp):
ATTTATCTTT
Found at i:53579345 original size:17 final size:18
Alignment explanation
Indices: 53579313--53579346 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
53579303 TATTCTTCAT
53579313 TTTAATTTCTGTAATTTA
1 TTTAATTTCTGTAATTTA
53579331 TTTAATTTC-GTAATTT
1 TTTAATTTCTGTAATTT
53579347 CAATTCACTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.26, C:0.06, G:0.06, T:0.62
Consensus pattern (18 bp):
TTTAATTTCTGTAATTTA
Found at i:53584312 original size:29 final size:29
Alignment explanation
Indices: 53584279--53584467 Score: 238
Period size: 29 Copynumber: 6.5 Consensus size: 29
53584269 GTGACGAGAT
53584279 TGGCACTAAGTGTGCATGCTGGAAATATA
1 TGGCACTAAGTGTGCATGCTGGAAATATA
53584308 TGGCACTAAGTGTGCATGCTGGAAATATA
1 TGGCACTAAGTGTGCATGCTGGAAATATA
53584337 TGGCACTAAGTGTGCATGCTGGAAATATA
1 TGGCACTAAGTGTGCATGCTGGAAATATA
53584366 TGGCACTAAGTGTGCATGCTGGAAATATA
1 TGGCACTAAGTGTGCATGCTGGAAATATA
* ** * ***
53584395 CGGCACTGGGTGTGCGA-GCTCGAAGGGTA
1 TGGCACTAAGTGTGC-ATGCTGGAAATATA
* ** * *
53584424 TGGCACTATGTGTGCGGGCT-TAAATCACA
1 TGGCACTAAGTGTGCATGCTGGAAAT-ATA
53584453 TGGCACTAAGTGTGC
1 TGGCACTAAGTGTGC
53584468 GAAATCGAGT
Statistics
Matches: 140, Mismatches: 17, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
28 2 0.01
29 137 0.98
30 1 0.01
ACGTcount: A:0.27, C:0.16, G:0.31, T:0.26
Consensus pattern (29 bp):
TGGCACTAAGTGTGCATGCTGGAAATATA
Found at i:53592295 original size:29 final size:29
Alignment explanation
Indices: 53592262--53592346 Score: 170
Period size: 29 Copynumber: 2.9 Consensus size: 29
53592252 GTGACGAGAT
53592262 TGGCACTAAGTGTGCATGCTGGAAATATA
1 TGGCACTAAGTGTGCATGCTGGAAATATA
53592291 TGGCACTAAGTGTGCATGCTGGAAATATA
1 TGGCACTAAGTGTGCATGCTGGAAATATA
53592320 TGGCACTAAGTGTGCATGCTGGAAATA
1 TGGCACTAAGTGTGCATGCTGGAAATA
53592347 GGCACTGGGT
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 56 1.00
ACGTcount: A:0.31, C:0.14, G:0.28, T:0.27
Consensus pattern (29 bp):
TGGCACTAAGTGTGCATGCTGGAAATATA
Found at i:53598641 original size:40 final size:40
Alignment explanation
Indices: 53598582--53598789 Score: 197
Period size: 40 Copynumber: 5.2 Consensus size: 40
53598572 CAATTGAATG
* * * * *
53598582 ATATCCGGGCTAAGTCCCGAAGACATTTATGCTAGTAATC
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTGATC
* * * *
53598622 ATATCCGGGTTAAGACCCGAAGGCCA-TTGTGCTAGCGACC
1 ATATCCGGGCTAAGACCCGAAGG-CATTTGTGCAAGTGATC
* * *
53598662 ACATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTTG-TT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAG-TGATC
* * *
53598702 AAATCCGGGCTAATACCCGAAGGCATTTGTGCAAGTCGTTC
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGT-GATC
* * * *
53598743 -TATCCGGGCTAAGACCCGAAGGCATTCGTGCATGTGGTT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTGATC
53598782 ATATCCGG
1 ATATCCGG
53598790 TTGTATTCCG
Statistics
Matches: 138, Mismatches: 24, Indels: 12
0.79 0.14 0.07
Matches are distributed among these distances:
39 5 0.04
40 129 0.93
41 4 0.03
ACGTcount: A:0.25, C:0.25, G:0.26, T:0.24
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTGATC
Found at i:53598720 original size:80 final size:80
Alignment explanation
Indices: 53598624--53598789 Score: 219
Period size: 80 Copynumber: 2.1 Consensus size: 80
53598614 TAGTAATCAT
* *
53598624 ATCCGGGTTAAGACCCGAAGGCCA-TTGTGCTAG-CGACCACATCCGGGCTAAGACCCGAAGGCA
1 ATCCGGGCTAAGACCCGAAGG-CATTTGTGCAAGTCGACC-CATCCGGGCTAAGACCCGAAGGCA
*
53598687 TTCGTGCAAGTTGTTAA
64 TTCGTGCAAGTGGTTAA
* ** *
53598704 ATCCGGGCTAATACCCGAAGGCATTTGTGCAAGTCGTTCTATCCGGGCTAAGACCCGAAGGCATT
1 ATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTCGACCCATCCGGGCTAAGACCCGAAGGCATT
* *
53598769 CGTGCATGTGGTTAT
66 CGTGCAAGTGGTTAA
53598784 ATCCGG
1 ATCCGG
53598790 TTGTATTCCG
Statistics
Matches: 75, Mismatches: 9, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
79 2 0.03
80 70 0.93
81 3 0.04
ACGTcount: A:0.24, C:0.25, G:0.28, T:0.23
Consensus pattern (80 bp):
ATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTCGACCCATCCGGGCTAAGACCCGAAGGCATT
CGTGCAAGTGGTTAA
Found at i:53602531 original size:50 final size:49
Alignment explanation
Indices: 53602408--53602637 Score: 189
Period size: 50 Copynumber: 4.6 Consensus size: 49
53602398 CTGATACGCA
* * *
53602408 TAGTAGCCTGCACTTAGTACTACACATGCGACCAACAATCCAGTACATG
1 TAGTAGCCTGCACTTAGTACTACACACGTGACCAACAATCCAGTACAGG
* * *
53602457 TAGTAGCCTGCACTTAGTACTACACACGTGACCTCACCAT-CTGATACAGG
1 TAGTAGCCTGCACTTAGTACTACACACGTGACC-AACAATCCAG-TACAGG
** * * **
53602507 TAGTAGCCTGCACTTCCTACTACACACGTTATCGAAGTC-ATTGAGTATGCA--
1 TAGTAGCCTGCACTTAGTACTACACACGTGA-CCAA--CAATCCAGTA--CAGG
* * * *** *
53602558 TAGTAGCCTGCACTTAGTACTACACATGTGACTTAACAGTATGGTACACG
1 TAGTAGCCTGCACTTAGTACTACACACGTGAC-CAACAATCCAGTACAGG
53602608 TAGTAGCCTGCACTTAGTACTACACACGTG
1 TAGTAGCCTGCACTTAGTACTACACACGTG
53602638 TATTCACAAT
Statistics
Matches: 146, Mismatches: 23, Indels: 23
0.76 0.12 0.12
Matches are distributed among these distances:
48 2 0.01
49 34 0.23
50 72 0.49
51 34 0.23
52 2 0.01
53 2 0.01
ACGTcount: A:0.29, C:0.27, G:0.18, T:0.26
Consensus pattern (49 bp):
TAGTAGCCTGCACTTAGTACTACACACGTGACCAACAATCCAGTACAGG
Found at i:53606389 original size:20 final size:21
Alignment explanation
Indices: 53606364--53606402 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
53606354 AGTCATCTAC
*
53606364 TTTTATT-TTTTTTCTTTTAT
1 TTTTATTGTTTCTTCTTTTAT
53606384 TTTTATTGTTTCTTCTTTT
1 TTTTATTGTTTCTTCTTTT
53606403 TTACTTATCT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.08, C:0.08, G:0.03, T:0.82
Consensus pattern (21 bp):
TTTTATTGTTTCTTCTTTTAT
Found at i:53610104 original size:2 final size:2
Alignment explanation
Indices: 53610097--53610121 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
53610087 TCATGACATG
53610097 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
53610122 GACTAGTCTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:53613307 original size:40 final size:40
Alignment explanation
Indices: 53613251--53613432 Score: 199
Period size: 40 Copynumber: 4.5 Consensus size: 40
53613241 GGATATGGCG
* * * **
53613251 ACTCGCTCAAAAGCCTTCGGGACATAGCCCGG-TTATAATA
1 ACTCGCACAAATGCCTTCGGGACATAACCCGGATT-TGGTA
* *
53613291 GCTCGCACAAATGCCTTCGGGACTTAACCCGGATTTGGTA
1 ACTCGCACAAATGCCTTCGGGACATAACCCGGATTTGGTA
*
53613331 ACTCGCACAATTGCCTTCGGGA-ATTAACCCGGATTTGGTA
1 ACTCGCACAAATGCCTTCGGGACA-TAACCCGGATTTGGTA
* *
53613371 ACTCGCACAAATGCCTTCGGGA-ATTAACCCGGATTTAGTC
1 ACTCGCACAAATGCCTTCGGGACA-TAACCCGGATTTGGTA
* *
53613411 ACTTAGCACAAAAGCCTTCGGG
1 AC-TCGCACAAATGCCTTCGGG
53613433 GCTTAGCCCG
Statistics
Matches: 124, Mismatches: 15, Indels: 5
0.86 0.10 0.03
Matches are distributed among these distances:
40 105 0.85
41 19 0.15
ACGTcount: A:0.27, C:0.27, G:0.22, T:0.24
Consensus pattern (40 bp):
ACTCGCACAAATGCCTTCGGGACATAACCCGGATTTGGTA
Found at i:53613443 original size:41 final size:40
Alignment explanation
Indices: 53613292--53613432 Score: 219
Period size: 40 Copynumber: 3.5 Consensus size: 40
53613282 GTTATAATAG
*
53613292 CTCGCACAAATGCCTTCGGGACTTAACCCGGATTTGGTAA
1 CTCGCACAAATGCCTTCGGGAATTAACCCGGATTTGGTAA
*
53613332 CTCGCACAATTGCCTTCGGGAATTAACCCGGATTTGGTAA
1 CTCGCACAAATGCCTTCGGGAATTAACCCGGATTTGGTAA
* *
53613372 CTCGCACAAATGCCTTCGGGAATTAACCCGGATTTAGTCA
1 CTCGCACAAATGCCTTCGGGAATTAACCCGGATTTGGTAA
* *
53613412 CTTAGCACAAAAGCCTTCGGG
1 C-TCGCACAAATGCCTTCGGG
53613433 GCTTAGCCCG
Statistics
Matches: 93, Mismatches: 7, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
40 76 0.82
41 17 0.18
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.25
Consensus pattern (40 bp):
CTCGCACAAATGCCTTCGGGAATTAACCCGGATTTGGTAA
Found at i:53618589 original size:46 final size:46
Alignment explanation
Indices: 53618522--53618649 Score: 193
Period size: 46 Copynumber: 2.8 Consensus size: 46
53618512 GTAACCCGCA
* * *
53618522 CATAAGTGAACTCAGACTCAACTCAACGAGCTCGGGCGTTCGCATC
1 CATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATC
* * *
53618568 CATAAGTGAACTCGGACTCAACTCAACGAGTTTGAACATTCGCATC
1 CATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATC
*
53618614 CATAAGTGAACTCGGACTCAACTCAACGAACTCGGA
1 CATAAGTGAACTCGGACTCAACTCAACGAGCTCGGA
53618650 TGCCCAAATA
Statistics
Matches: 72, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
46 72 1.00
ACGTcount: A:0.32, C:0.28, G:0.20, T:0.20
Consensus pattern (46 bp):
CATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATC
Found at i:53622369 original size:29 final size:29
Alignment explanation
Indices: 53622336--53622393 Score: 107
Period size: 29 Copynumber: 2.0 Consensus size: 29
53622326 GATGGCACTA
53622336 AAAGAGAAAAAAGGATGATGTTTTGTTTT
1 AAAGAGAAAAAAGGATGATGTTTTGTTTT
*
53622365 AAAGAGAAAGAAGGATGATGTTTTGTTTT
1 AAAGAGAAAAAAGGATGATGTTTTGTTTT
53622394 TCTTCCCACT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.40, C:0.00, G:0.26, T:0.34
Consensus pattern (29 bp):
AAAGAGAAAAAAGGATGATGTTTTGTTTT
Found at i:53629960 original size:20 final size:19
Alignment explanation
Indices: 53629920--53629961 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
53629910 CAAACATCAT
*
53629920 AAAAGTAAATCATTTCTAA
1 AAAAGTAAATCATTTCAAA
53629939 AAAAGTAAATCATTTTCAAA
1 AAAAGTAAATCA-TTTCAAA
53629959 AAA
1 AAA
53629962 TTATTTTCCG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
19 12 0.57
20 9 0.43
ACGTcount: A:0.57, C:0.10, G:0.05, T:0.29
Consensus pattern (19 bp):
AAAAGTAAATCATTTCAAA
Found at i:53630128 original size:17 final size:17
Alignment explanation
Indices: 53630108--53630140 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
53630098 ATAATGAATG
53630108 TTATTAAATTATATTTT
1 TTATTAAATTATATTTT
53630125 TTATTAAATTATATTT
1 TTATTAAATTATATTT
53630141 AATAATTATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (17 bp):
TTATTAAATTATATTTT
Found at i:53630408 original size:16 final size:16
Alignment explanation
Indices: 53630387--53630441 Score: 83
Period size: 16 Copynumber: 3.4 Consensus size: 16
53630377 TGAATTACTT
*
53630387 ATTACAGCCCTATTCC
1 ATTACAGCTCTATTCC
*
53630403 ATTACAGTTCTATTCC
1 ATTACAGCTCTATTCC
53630419 ATTACAGCTCTATTCC
1 ATTACAGCTCTATTCC
*
53630435 ATCACAG
1 ATTACAG
53630442 TGAACCAAAC
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 35 1.00
ACGTcount: A:0.27, C:0.31, G:0.07, T:0.35
Consensus pattern (16 bp):
ATTACAGCTCTATTCC
Found at i:53638356 original size:41 final size:41
Alignment explanation
Indices: 53638311--53638391 Score: 144
Period size: 41 Copynumber: 2.0 Consensus size: 41
53638301 ATCTAATTGA
*
53638311 GAAAATAATTTCCTTATTCTAATAAACTACTAAAAGATTAG
1 GAAAATAATTCCCTTATTCTAATAAACTACTAAAAGATTAG
*
53638352 GAAAATAATTCCCTTTTTCTAATAAACTACTAAAAGATTA
1 GAAAATAATTCCCTTATTCTAATAAACTACTAAAAGATTA
53638392 AAAAAATATT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 38 1.00
ACGTcount: A:0.46, C:0.14, G:0.06, T:0.35
Consensus pattern (41 bp):
GAAAATAATTCCCTTATTCTAATAAACTACTAAAAGATTAG
Found at i:53638450 original size:19 final size:19
Alignment explanation
Indices: 53638426--53638466 Score: 73
Period size: 19 Copynumber: 2.2 Consensus size: 19
53638416 ATATTTTTTC
*
53638426 TAAGATTTATCTACTTAAA
1 TAAGATTTATCTACCTAAA
53638445 TAAGATTTATCTACCTAAA
1 TAAGATTTATCTACCTAAA
53638464 TAA
1 TAA
53638467 CTTTAAAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.44, C:0.12, G:0.05, T:0.39
Consensus pattern (19 bp):
TAAGATTTATCTACCTAAA
Found at i:53643533 original size:27 final size:28
Alignment explanation
Indices: 53643477--53643546 Score: 124
Period size: 27 Copynumber: 2.5 Consensus size: 28
53643467 AAACTTGTAC
53643477 AGCACTAAGTGTGCGAGTTTGATCATAT
1 AGCACTAAGTGTGCGAGTTTGATCATAT
*
53643505 AGCACTAAGTGTGCGAG-TTGATTATAT
1 AGCACTAAGTGTGCGAGTTTGATCATAT
53643532 AGCACTAAGTGTGCG
1 AGCACTAAGTGTGCG
53643547 GACTCACTAT
Statistics
Matches: 41, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
27 24 0.59
28 17 0.41
ACGTcount: A:0.29, C:0.14, G:0.27, T:0.30
Consensus pattern (28 bp):
AGCACTAAGTGTGCGAGTTTGATCATAT
Found at i:53643557 original size:27 final size:27
Alignment explanation
Indices: 53643477--53643558 Score: 78
Period size: 27 Copynumber: 3.0 Consensus size: 27
53643467 AAACTTGTAC
* *
53643477 AGCACTAAGTGTGCGAGTTTGA-TCATAT
1 AGCACTAAGTGTGCGAG-CTCACT-ATAT
* * *
53643505 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGAGCTCACTATAT
53643532 AGCACTAAGTGTGCG-GACTCACTATAT
1 AGCACTAAGTGTGCGAG-CTCACTATAT
53643559 GCTTTTGAAT
Statistics
Matches: 49, Mismatches: 3, Indels: 5
0.86 0.05 0.09
Matches are distributed among these distances:
26 1 0.02
27 30 0.61
28 18 0.37
ACGTcount: A:0.29, C:0.16, G:0.24, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGAGCTCACTATAT
Found at i:53646341 original size:42 final size:41
Alignment explanation
Indices: 53646245--53646341 Score: 115
Period size: 42 Copynumber: 2.3 Consensus size: 41
53646235 TCCTAATTGG
*
53646245 AAAAATAGTTCCCTTATTCTAATAAACTACCAAAACATAAA
1 AAAAATAGTTCCTTTATTCTAATAAACTACCAAAACATAAA
* * * *
53646286 AGAAATTAGTTCCTTTATTTTAATAAACTACTAAAAGATATAA
1 A-AAAATAGTTCCTTTATTCTAATAAACTACCAAAACATA-AA
53646329 TAAAAATA-TTCCT
1 -AAAAATAGTTCCT
53646342 AGAATGTGAA
Statistics
Matches: 47, Mismatches: 6, Indels: 5
0.81 0.10 0.09
Matches are distributed among these distances:
41 1 0.02
42 38 0.81
43 7 0.15
44 1 0.02
ACGTcount: A:0.48, C:0.14, G:0.04, T:0.33
Consensus pattern (41 bp):
AAAAATAGTTCCTTTATTCTAATAAACTACCAAAACATAAA
Found at i:53646380 original size:19 final size:18
Alignment explanation
Indices: 53646358--53646397 Score: 62
Period size: 19 Copynumber: 2.2 Consensus size: 18
53646348 TGAATAAAAC
53646358 TTATCTACCAAAATAAGAT
1 TTATCTACCAAAATAA-AT
*
53646377 TTATCTACCTAAATAAAT
1 TTATCTACCAAAATAAAT
53646395 TTA
1 TTA
53646398 AAATATATAC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 5 0.25
19 15 0.75
ACGTcount: A:0.45, C:0.15, G:0.03, T:0.38
Consensus pattern (18 bp):
TTATCTACCAAAATAAAT
Found at i:53653451 original size:24 final size:25
Alignment explanation
Indices: 53653419--53653471 Score: 72
Period size: 25 Copynumber: 2.2 Consensus size: 25
53653409 AAAGGTTCCA
* *
53653419 GTATATGAGTG-CCCTTTATGGGAC
1 GTATATGAGAGCCCCTTTATAGGAC
*
53653443 GTATATGAGAGCCCCTTTATAGGAT
1 GTATATGAGAGCCCCTTTATAGGAC
53653468 GTAT
1 GTAT
53653472 GAATGTAACA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
24 10 0.40
25 15 0.60
ACGTcount: A:0.25, C:0.15, G:0.26, T:0.34
Consensus pattern (25 bp):
GTATATGAGAGCCCCTTTATAGGAC
Found at i:53654775 original size:42 final size:42
Alignment explanation
Indices: 53654724--53654846 Score: 156
Period size: 43 Copynumber: 2.9 Consensus size: 42
53654714 GACTTATGAT
* *
53654724 TTACGTGTAAGACCATGTCTAGGACATTGGCATCGTATTTGA
1 TTACGTGTAAGACCATGTCTGGGACATTGGCATTGTATTTGA
** * * *
53654766 TTTTGTGTAAGACCCTGTCTGGGACAGTGGGATTGATATTTGA
1 TTACGTGTAAGACCATGTCTGGGACATTGGCATTG-TATTTGA
* *
53654809 TTACATGTAAGACCACGTCTGGGACATTGGCATTGTAT
1 TTACGTGTAAGACCATGTCTGGGACATTGGCATTGTAT
53654847 GAGCTTTTCG
Statistics
Matches: 66, Mismatches: 14, Indels: 2
0.80 0.17 0.02
Matches are distributed among these distances:
42 31 0.47
43 35 0.53
ACGTcount: A:0.24, C:0.15, G:0.26, T:0.34
Consensus pattern (42 bp):
TTACGTGTAAGACCATGTCTGGGACATTGGCATTGTATTTGA
Found at i:53659102 original size:30 final size:28
Alignment explanation
Indices: 53659048--53659104 Score: 78
Period size: 30 Copynumber: 2.0 Consensus size: 28
53659038 TTTCTTCCAC
* *
53659048 ACTTTCTTTTTGCTCACTCTCTTTTTCA
1 ACTTTCTTTTTGCACACACTCTTTTTCA
53659076 ACTTTACTTTCTTGCACACACTCTTTTTC
1 ACTTT-CTTT-TTGCACACACTCTTTTTC
53659105 TTTTTCGACT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 5 0.20
29 4 0.16
30 16 0.64
ACGTcount: A:0.14, C:0.30, G:0.04, T:0.53
Consensus pattern (28 bp):
ACTTTCTTTTTGCACACACTCTTTTTCA
Found at i:53660189 original size:12 final size:12
Alignment explanation
Indices: 53660172--53660211 Score: 59
Period size: 12 Copynumber: 3.6 Consensus size: 12
53660162 AAAAAAAATC
53660172 GAATTTTTTTCT
1 GAATTTTTTTCT
53660184 GAATTTTTTTCT
1 GAATTTTTTTCT
53660196 -AA-TTTTTTC-
1 GAATTTTTTTCT
53660205 GAATTTT
1 GAATTTT
53660212 GAACTTTTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
10 9 0.35
11 5 0.19
12 12 0.46
ACGTcount: A:0.20, C:0.07, G:0.07, T:0.65
Consensus pattern (12 bp):
GAATTTTTTTCT
Found at i:53664574 original size:99 final size:100
Alignment explanation
Indices: 53664461--53664647 Score: 313
Period size: 99 Copynumber: 1.9 Consensus size: 100
53664451 GAAGCTATCT
* * * *
53664461 GGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCAATAATCTGGTACACGTAGTA-AT
1 GGTACGCATAGTAGCCTACACTTAGTACTACACATGCGACCAATAATCCGGTACACGTAATAGAC
53664525 TGCACTTAGTACTACACACGTGATCACAGTTTTTG
66 TGCACTTAGTACTACACACGTGATCACAGTTTTTG
* *
53664560 GGTACGCATAGTAGCCTACACTTAGTACTACACATGCGACCAATTATCCGGTACACGTAATAGCC
1 GGTACGCATAGTAGCCTACACTTAGTACTACACATGCGACCAATAATCCGGTACACGTAATAGAC
53664625 TGCACTTAGTACTACACACGTGA
66 TGCACTTAGTACTACACACGTGA
53664648 CCTCACAATA
Statistics
Matches: 81, Mismatches: 6, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
99 58 0.72
100 23 0.28
ACGTcount: A:0.30, C:0.25, G:0.19, T:0.26
Consensus pattern (100 bp):
GGTACGCATAGTAGCCTACACTTAGTACTACACATGCGACCAATAATCCGGTACACGTAATAGAC
TGCACTTAGTACTACACACGTGATCACAGTTTTTG
Found at i:53664590 original size:51 final size:49
Alignment explanation
Indices: 53664456--53664649 Score: 156
Period size: 49 Copynumber: 3.9 Consensus size: 49
53664446 TAGCCGAAGC
* * * * * *
53664456 TATCTGGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCAAT
1 TATCCGGTACACATAATAGCCTACACTTAGTACTACACACGTGACCAAT
* * * * ** * *
53664505 AATCTGGTACACGTAGTA-ATTGCACTTAGTACTACACACGTGATCACAGT
1 TATCCGGTACACATAATAGCCTACACTTAGTACTACACACGTGA-C-CAAT
* ** * * * *
53664555 TTTTGGGTACGCATAGTAGCCTACACTTAGTACTACACATGCGACCAAT
1 TATCCGGTACACATAATAGCCTACACTTAGTACTACACACGTGACCAAT
* *
53664604 TATCCGGTACACGTAATAGCCTGCACTTAGTACTACACACGTGACC
1 TATCCGGTACACATAATAGCCTACACTTAGTACTACACACGTGACC
53664650 TCACAATAGT
Statistics
Matches: 113, Mismatches: 29, Indels: 6
0.76 0.20 0.04
Matches are distributed among these distances:
48 21 0.19
49 56 0.50
50 16 0.14
51 20 0.18
ACGTcount: A:0.29, C:0.26, G:0.18, T:0.27
Consensus pattern (49 bp):
TATCCGGTACACATAATAGCCTACACTTAGTACTACACACGTGACCAAT
Found at i:53664631 original size:49 final size:49
Alignment explanation
Indices: 53664469--53664642 Score: 197
Period size: 49 Copynumber: 3.5 Consensus size: 49
53664459 CTGGTACGCA
* *
53664469 TAGTAGCCTGCACTTAGTACTACACATGCGACCAATAATCTGGTACACG
1 TAGTAGCCTGCACTTAGTACTACACATGCGACCAATTATCCGGTACACG
** * * * * ** * *
53664518 TAGTA-ATTGCACTTAGTACTACACACGTGATCACAGTTTTTGGGTACGCA
1 TAGTAGCCTGCACTTAGTACTACACATGCGA-C-CAATTATCCGGTACACG
*
53664568 TAGTAGCCTACACTTAGTACTACACATGCGACCAATTATCCGGTACACG
1 TAGTAGCCTGCACTTAGTACTACACATGCGACCAATTATCCGGTACACG
*
53664617 TAATAGCCTGCACTTAGTACTACACA
1 TAGTAGCCTGCACTTAGTACTACACA
53664643 CGTGACCTCA
Statistics
Matches: 98, Mismatches: 24, Indels: 6
0.77 0.19 0.05
Matches are distributed among these distances:
48 21 0.21
49 41 0.42
50 16 0.16
51 20 0.20
ACGTcount: A:0.30, C:0.25, G:0.17, T:0.27
Consensus pattern (49 bp):
TAGTAGCCTGCACTTAGTACTACACATGCGACCAATTATCCGGTACACG
Found at i:53666199 original size:21 final size:22
Alignment explanation
Indices: 53666173--53666213 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
53666163 CATTTAACAC
53666173 AGGGGC-ACACGCCCGTGTGGG
1 AGGGGCAACACGCCCGTGTGGG
53666194 AGGGGCAACACGCCCGTGTG
1 AGGGGCAACACGCCCGTGTG
53666214 ACAATTCAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 6 0.32
22 13 0.68
ACGTcount: A:0.17, C:0.29, G:0.44, T:0.10
Consensus pattern (22 bp):
AGGGGCAACACGCCCGTGTGGG
Found at i:53669297 original size:42 final size:43
Alignment explanation
Indices: 53669147--53669339 Score: 264
Period size: 43 Copynumber: 4.5 Consensus size: 43
53669137 GGGCTTAAAA
* * *
53669147 CTAGCAGGCTATAATGCCGGTTAGTTAATATCGAGCTTCGAGC
1 CTAGCAGGCTATAATGCCGGTGAGTTAATATCGGGCTTCGATC
* *
53669190 CTAGCAAGCTATAATGCCGGTGAGTTAATATTGGGCTTCGATC
1 CTAGCAGGCTATAATGCCGGTGAGTTAATATCGGGCTTCGATC
*
53669233 CTAGAAGGCTATAATGCCGGTGAGTTAATATCGGGCTTCG-TC
1 CTAGCAGGCTATAATGCCGGTGAGTTAATATCGGGCTTCGATC
* * ** *
53669275 CTGGCAGGCTATAATGCTGGTGAGTTAATATTAGGCTTCGAGC
1 CTAGCAGGCTATAATGCCGGTGAGTTAATATCGGGCTTCGATC
*
53669318 CTAGCAGGC-GTAATGCCGGTGA
1 CTAGCAGGCTATAATGCCGGTGA
53669340 ATGAGTTCAG
Statistics
Matches: 132, Mismatches: 17, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
42 48 0.36
43 84 0.64
ACGTcount: A:0.24, C:0.19, G:0.28, T:0.28
Consensus pattern (43 bp):
CTAGCAGGCTATAATGCCGGTGAGTTAATATCGGGCTTCGATC
Found at i:53676306 original size:20 final size:21
Alignment explanation
Indices: 53676281--53676321 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 21
53676271 CTATTCTGAC
*
53676281 TTTAAAAAATCATTAA-AAAT
1 TTTAAAAAATAATTAATAAAT
53676301 TTTAAAAAATAATTAATAAAT
1 TTTAAAAAATAATTAATAAAT
53676322 ATATTTTATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 15 0.79
21 4 0.21
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (21 bp):
TTTAAAAAATAATTAATAAAT
Found at i:53682395 original size:41 final size:40
Alignment explanation
Indices: 53682268--53682412 Score: 184
Period size: 40 Copynumber: 3.6 Consensus size: 40
53682258 CTCGCCCAAG
* * * *
53682268 GCCTTCGGGTCTTAGCCCAGATATGGTCACTAGCATAAAT
1 GCCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAAT
*
53682308 GCCTTCGGGACTTAGCCCGGATATAGTTACTAGCACAAAT
1 GCCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAAT
* * * *
53682348 GCCTTC-GGATCTTAGTCCGGATGTAGTCGCTTAGCACAAAA
1 GCCTTCGGGA-CTTAGCCCGGATATAGTCAC-TAGCACAAAT
53682389 GCCTTCGGGACTTAGCCCGGATAT
1 GCCTTCGGGACTTAGCCCGGATAT
53682413 CATTCGAGTA
Statistics
Matches: 90, Mismatches: 12, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
39 3 0.03
40 57 0.63
41 27 0.30
42 3 0.03
ACGTcount: A:0.24, C:0.26, G:0.24, T:0.26
Consensus pattern (40 bp):
GCCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAAT
Found at i:53683128 original size:2 final size:2
Alignment explanation
Indices: 53683121--53683152 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
53683111 ATGTGCAAAC
*
53683121 AT AT AT AT AT AT AT AT AT AT AC AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
53683153 GTGCAAGAGC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:53690214 original size:43 final size:43
Alignment explanation
Indices: 53690153--53690409 Score: 327
Period size: 43 Copynumber: 5.8 Consensus size: 43
53690143 ACGTTACTAT
* *
53690153 TCGGGCTTCGAGCCTAGCAAGCTATAATGCTGGTGAGTTAATA
1 TCGGGCTTCGAGCCTAGCAGGCTATAATGCCGGTGAGTTAATA
53690196 TCGGGCTTCGAGCCTAGCAGGCTATAATGCCGGTGAGTTAATA
1 TCGGGCTTCGAGCCTAGCAGGCTATAATGCCGGTGAGTTAATA
*
53690239 TCGGGCTTCGAGCTTCGAGCCTAGTAGGCTATAATGCCGGTGAGTTAATA
1 TC--G----G-GCTTCGAGCCTAGCAGGCTATAATGCCGGTGAGTTAATA
* * * ***
53690289 TCGGGCTTCAAGACTAGTAGGCTATAATATAGGTGAGTTAATA
1 TCGGGCTTCGAGCCTAGCAGGCTATAATGCCGGTGAGTTAATA
* *
53690332 TTGGGCTTCGAGCCTAGCAGGCTATAATACCGGTGAGTTAATA
1 TCGGGCTTCGAGCCTAGCAGGCTATAATGCCGGTGAGTTAATA
* *
53690375 TCAGGCTTCGAGCCTAGCAGGC-GTAATGCCGGTGA
1 TCGGGCTTCGAGCCTAGCAGGCTATAATGCCGGTGA
53690410 ATGAGTTCAG
Statistics
Matches: 189, Mismatches: 18, Indels: 15
0.85 0.08 0.07
Matches are distributed among these distances:
42 11 0.06
43 134 0.71
44 1 0.01
45 1 0.01
48 1 0.01
49 1 0.01
50 40 0.21
ACGTcount: A:0.25, C:0.19, G:0.29, T:0.27
Consensus pattern (43 bp):
TCGGGCTTCGAGCCTAGCAGGCTATAATGCCGGTGAGTTAATA
Found at i:53690311 original size:93 final size:87
Alignment explanation
Indices: 53690145--53690409 Score: 336
Period size: 93 Copynumber: 3.0 Consensus size: 87
53690135 ATTATCGTAC
* * *
53690145 GTTACTATTCGGGCTTCGAGCCTAGCAAGCTATAATGCTGGTGAGTTAATATCGGGCTTCGAGCC
1 GTTAATATTCGGGCTTCGAGCCTAGCAGGCTATAATGCCGGTGAGTTAATATCGGGCTTCGAGCC
53690210 TAGCAGGCTATAATGCCGGTGA
66 TAGCAGGCTATAATGCCGGTGA
* *
53690232 GTTAATATCGGGCTTCGAGCTTCGAGCCTAGTAGGCTATAATGCCGGTGAGTTAATATCGGGCTT
1 GTTAATA------TTCGGGCTTCGAGCCTAGCAGGCTATAATGCCGGTGAGTTAATATCGGGCTT
* * * ***
53690297 CAAGACTAGTAGGCTATAATATAGGTGA
60 CGAGCCTAGCAGGCTATAATGCCGGTGA
* *
53690325 GTTAATATT-GGGCTTCGAGCCTAGCAGGCTATAATACCGGTGAGTTAATATCAGGCTTCGAGCC
1 GTTAATATTCGGGCTTCGAGCCTAGCAGGCTATAATGCCGGTGAGTTAATATCGGGCTTCGAGCC
*
53690389 TAGCAGGC-GTAATGCCGGTGA
66 TAGCAGGCTATAATGCCGGTGA
53690410 ATGAGTTCAG
Statistics
Matches: 150, Mismatches: 22, Indels: 14
0.81 0.12 0.08
Matches are distributed among these distances:
85 9 0.06
86 56 0.37
87 8 0.05
93 77 0.51
ACGTcount: A:0.25, C:0.19, G:0.29, T:0.28
Consensus pattern (87 bp):
GTTAATATTCGGGCTTCGAGCCTAGCAGGCTATAATGCCGGTGAGTTAATATCGGGCTTCGAGCC
TAGCAGGCTATAATGCCGGTGA
Found at i:53691005 original size:16 final size:18
Alignment explanation
Indices: 53690974--53691006 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
53690964 AACTCCTCAC
53690974 ACTATCTATCGTTTTGGT
1 ACTATCTATCGTTTTGGT
53690992 ACTAT-TAT-GTTTTGG
1 ACTATCTATCGTTTTGG
53691007 AATTCGTATG
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:53695558 original size:26 final size:26
Alignment explanation
Indices: 53695528--53695590 Score: 126
Period size: 26 Copynumber: 2.4 Consensus size: 26
53695518 AAGCTCTTCC
53695528 TTGTGCCATCCCTAAGCAGCCCCTCT
1 TTGTGCCATCCCTAAGCAGCCCCTCT
53695554 TTGTGCCATCCCTAAGCAGCCCCTCT
1 TTGTGCCATCCCTAAGCAGCCCCTCT
53695580 TTGTGCCATCC
1 TTGTGCCATCC
53695591 ATGGTTGTGT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 37 1.00
ACGTcount: A:0.14, C:0.41, G:0.16, T:0.29
Consensus pattern (26 bp):
TTGTGCCATCCCTAAGCAGCCCCTCT
Found at i:53696570 original size:40 final size:41
Alignment explanation
Indices: 53696515--53696612 Score: 126
Period size: 41 Copynumber: 2.4 Consensus size: 41
53696505 TTACTAAAAC
53696515 TGTTACCATAAGCATG-TTAAGCACACCACTAAATTGAATA
1 TGTTACCATAAGCATGTTTAAGCACACCACTAAATTGAATA
* * ** * *
53696555 TGTTACTATGAGCATGTTTAAGCATTCCATTGAATTGAATA
1 TGTTACCATAAGCATGTTTAAGCACACCACTAAATTGAATA
*
53696596 TGTTACCGTAAGCATGT
1 TGTTACCATAAGCATGT
53696613 AAAACATGCC
Statistics
Matches: 48, Mismatches: 9, Indels: 1
0.83 0.16 0.02
Matches are distributed among these distances:
40 14 0.29
41 34 0.71
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Consensus pattern (41 bp):
TGTTACCATAAGCATGTTTAAGCACACCACTAAATTGAATA
Found at i:53700836 original size:17 final size:17
Alignment explanation
Indices: 53700814--53700846 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
53700804 TTGGGCCAAA
53700814 ATGGGCCTGTGGGCCCC
1 ATGGGCCTGTGGGCCCC
*
53700831 ATGGGCTTGTGGGCCC
1 ATGGGCCTGTGGGCCC
53700847 ACACGGGTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.06, C:0.30, G:0.42, T:0.21
Consensus pattern (17 bp):
ATGGGCCTGTGGGCCCC
Found at i:53704648 original size:28 final size:29
Alignment explanation
Indices: 53704616--53704674 Score: 84
Period size: 28 Copynumber: 2.1 Consensus size: 29
53704606 ATAACCAAAC
* *
53704616 CTACAAAAACTTTATAT-CATAAATCCAT
1 CTACAAAAACTTCATATCCATAAACCCAT
*
53704644 CTACATAAACTTCATATCCATAAACCCAT
1 CTACAAAAACTTCATATCCATAAACCCAT
53704673 CT
1 CT
53704675 TTGAATCCTT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
28 15 0.56
29 12 0.44
ACGTcount: A:0.42, C:0.27, G:0.00, T:0.31
Consensus pattern (29 bp):
CTACAAAAACTTCATATCCATAAACCCAT
Found at i:53704903 original size:9 final size:9
Alignment explanation
Indices: 53704889--53704922 Score: 59
Period size: 9 Copynumber: 3.8 Consensus size: 9
53704879 AAGTAAGTTT
53704889 AAAAAAACG
1 AAAAAAACG
*
53704898 AAAAAAATG
1 AAAAAAACG
53704907 AAAAAAACG
1 AAAAAAACG
53704916 AAAAAAA
1 AAAAAAA
53704923 TTTCAAACAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
9 23 1.00
ACGTcount: A:0.82, C:0.06, G:0.09, T:0.03
Consensus pattern (9 bp):
AAAAAAACG
Found at i:53704912 original size:18 final size:18
Alignment explanation
Indices: 53704889--53704923 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
53704879 AAGTAAGTTT
53704889 AAAAAAACGAAAAAAATG
1 AAAAAAACGAAAAAAATG
53704907 AAAAAAACGAAAAAAAT
1 AAAAAAACGAAAAAAAT
53704924 TTCAAACAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.80, C:0.06, G:0.09, T:0.06
Consensus pattern (18 bp):
AAAAAAACGAAAAAAATG
Found at i:53706027 original size:30 final size:28
Alignment explanation
Indices: 53705991--53706046 Score: 76
Period size: 30 Copynumber: 1.9 Consensus size: 28
53705981 AAGCGAAAAA
* *
53705991 GAAAAAGAGTGTGTGCAAGAAAGTAAAGTT
1 GAAAAAGAGAGTGAGCAA-AAAG-AAAGTT
53706021 GAAAAAGAGAGTGAGCAAAAAGAAAG
1 GAAAAAGAGAGTGAGCAAAAAGAAAG
53706047 CGTGGAAGAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 4 0.17
29 4 0.17
30 16 0.67
ACGTcount: A:0.54, C:0.04, G:0.30, T:0.12
Consensus pattern (28 bp):
GAAAAAGAGAGTGAGCAAAAAGAAAGTT
Found at i:53709313 original size:29 final size:29
Alignment explanation
Indices: 53709280--53709339 Score: 93
Period size: 29 Copynumber: 2.1 Consensus size: 29
53709270 ATAACCAAAC
* *
53709280 CTACAAAAACTTTATATCCATAAATCCAT
1 CTACAAAAACTTCATATCCATAAACCCAT
*
53709309 CTACATAAACTTCATATCCATAAACCCAT
1 CTACAAAAACTTCATATCCATAAACCCAT
53709338 CT
1 CT
53709340 TTGAATCCTT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.42, C:0.28, G:0.00, T:0.30
Consensus pattern (29 bp):
CTACAAAAACTTCATATCCATAAACCCAT
Found at i:53709332 original size:15 final size:15
Alignment explanation
Indices: 53709286--53709333 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 15
53709276 AAACCTACAA
*
53709286 AAACTTTATATCCAT
1 AAACTTCATATCCAT
* * *
53709301 AAA-TCCATCTACAT
1 AAACTTCATATCCAT
53709315 AAACTTCATATCCAT
1 AAACTTCATATCCAT
53709330 AAAC
1 AAAC
53709334 CCATCTTTGA
Statistics
Matches: 25, Mismatches: 7, Indels: 2
0.74 0.21 0.06
Matches are distributed among these distances:
14 10 0.40
15 15 0.60
ACGTcount: A:0.44, C:0.25, G:0.00, T:0.31
Consensus pattern (15 bp):
AAACTTCATATCCAT
Found at i:53714869 original size:38 final size:38
Alignment explanation
Indices: 53714813--53714892 Score: 115
Period size: 38 Copynumber: 2.1 Consensus size: 38
53714803 GATGTGTATC
* * * *
53714813 CGGGTTAAATCCCGCAGGCTTCGTGCTGGTATTATATT
1 CGGGATAAATCCCGCAGGCCTAGTACTGGTATTATATT
*
53714851 CGGGATAAATCTCGCAGGCCTAGTACTGGTATTATATT
1 CGGGATAAATCCCGCAGGCCTAGTACTGGTATTATATT
53714889 CGGG
1 CGGG
53714893 CCTTCGTGCC
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.21, C:0.20, G:0.28, T:0.31
Consensus pattern (38 bp):
CGGGATAAATCCCGCAGGCCTAGTACTGGTATTATATT
Found at i:53714946 original size:43 final size:43
Alignment explanation
Indices: 53714885--53715008 Score: 196
Period size: 42 Copynumber: 2.9 Consensus size: 43
53714875 ACTGGTATTA
*
53714885 TATTCGGGCCTTCGTGCCTAGCAGCCTTCATGCCGGTGATGTG
1 TATTCGGGCCTTCGTGCCTAGCAGGCTTCATGCCGGTGATGTG
* *
53714928 TATTCGAGCCTTCGTGCCTAGCAGGCTTC-GGCCGGTGATGTG
1 TATTCGGGCCTTCGTGCCTAGCAGGCTTCATGCCGGTGATGTG
* *
53714970 TATTCGGGCCTTCGTGCCTAGCAGGCGTAATGCCGGTGA
1 TATTCGGGCCTTCGTGCCTAGCAGGCTTCATGCCGGTGA
53715009 AATGATATGT
Statistics
Matches: 73, Mismatches: 7, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
42 38 0.52
43 35 0.48
ACGTcount: A:0.13, C:0.27, G:0.32, T:0.28
Consensus pattern (43 bp):
TATTCGGGCCTTCGTGCCTAGCAGGCTTCATGCCGGTGATGTG
Found at i:53715998 original size:17 final size:17
Alignment explanation
Indices: 53715976--53716013 Score: 76
Period size: 17 Copynumber: 2.2 Consensus size: 17
53715966 CAAAGGTGTT
53715976 GCCTAGTGATGTTTTGG
1 GCCTAGTGATGTTTTGG
53715993 GCCTAGTGATGTTTTGG
1 GCCTAGTGATGTTTTGG
53716010 GCCT
1 GCCT
53716014 CGTAAGCCCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.11, C:0.16, G:0.34, T:0.39
Consensus pattern (17 bp):
GCCTAGTGATGTTTTGG
Found at i:53716720 original size:48 final size:48
Alignment explanation
Indices: 53716620--53716722 Score: 111
Period size: 48 Copynumber: 2.1 Consensus size: 48
53716610 GTGCTAAGCG
* * * * *
53716620 TAAGACCTATCCGGGATAGGCATCGGCACAACCTAGTGAGTGTTAGTG
1 TAAGACCTATCCGGGATAGGCATCAGCACAACCTAGAGAGAGCTAGTA
**
53716668 TAAGACCTAT-CGGGAATAGGCATCAGCACATGC-AGAGCAGAGCTAGTA
1 TAAGACCTATCCGGG-ATAGGCATCAGCACAACCTAGAG-AGAGCTAGTA
53716716 TAAGACC
1 TAAGACC
53716723 ATAGTTGGAC
Statistics
Matches: 46, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
47 7 0.15
48 39 0.85
ACGTcount: A:0.32, C:0.21, G:0.27, T:0.19
Consensus pattern (48 bp):
TAAGACCTATCCGGGATAGGCATCAGCACAACCTAGAGAGAGCTAGTA
Found at i:53720394 original size:27 final size:28
Alignment explanation
Indices: 53720329--53720398 Score: 115
Period size: 27 Copynumber: 2.5 Consensus size: 28
53720319 AAATTTGTAC
53720329 AGCACTAAGTGTGCGAGTTGGATCATAT
1 AGCACTAAGTGTGCGAGTTGGATCATAT
*
53720357 AGCACTAAGTGTGCGAGTT-GATTATAT
1 AGCACTAAGTGTGCGAGTTGGATCATAT
*
53720384 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
53720399 GACTCACTAT
Statistics
Matches: 40, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
27 21 0.52
28 19 0.47
ACGTcount: A:0.27, C:0.14, G:0.30, T:0.29
Consensus pattern (28 bp):
AGCACTAAGTGTGCGAGTTGGATCATAT
Found at i:53720409 original size:27 final size:27
Alignment explanation
Indices: 53720329--53720410 Score: 69
Period size: 27 Copynumber: 3.0 Consensus size: 27
53720319 AAATTTGTAC
* *
53720329 AGCACTAAGTGTGCGAGTTGGA-TCATAT
1 AGCACTAAGTGTGCGAGCT-CACT-ATAT
* * *
53720357 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGAGCTCACTATAT
*
53720384 AGCACTGAGTGTGCG-GACTCACTATAT
1 AGCACTAAGTGTGCGAG-CTCACTATAT
53720411 GCTTTTGAAT
Statistics
Matches: 48, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
26 1 0.02
27 27 0.56
28 20 0.42
ACGTcount: A:0.28, C:0.16, G:0.27, T:0.29
Consensus pattern (27 bp):
AGCACTAAGTGTGCGAGCTCACTATAT
Found at i:53727983 original size:40 final size:40
Alignment explanation
Indices: 53727856--53727985 Score: 145
Period size: 40 Copynumber: 3.2 Consensus size: 40
53727846 ATGCTGGAAA
* * * *
53727856 TTATATCCGAGTTAAGACCCGAAGGCAATTGTGCTAGTGG
1 TTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTGG
* * * ***
53727896 CTACATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGACA
1 TTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTGG
*
53727936 TTCTATCCGGGCTAAGACCCGAAGGCATTTGTGC-ACGTGG
1 TTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGA-GTGG
53727976 TTATATCCGG
1 TTATATCCGG
53727986 TTATATTCCG
Statistics
Matches: 71, Mismatches: 18, Indels: 2
0.78 0.20 0.02
Matches are distributed among these distances:
39 1 0.01
40 70 0.99
ACGTcount: A:0.25, C:0.24, G:0.28, T:0.24
Consensus pattern (40 bp):
TTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTGG
Found at i:53727984 original size:80 final size:80
Alignment explanation
Indices: 53727818--53727985 Score: 198
Period size: 80 Copynumber: 2.1 Consensus size: 80
53727808 AAATTGAATG
* *
53727818 ATATCCGGGCTAAGCCCCGAAGACAATTATGCTGGAAATTATATCCGAGTTAAGACCCGAAGGCA
1 ATATCCGGGCTAAGACCCGAAGACAATTATGCTGGAAATTATATCCGAGCTAAGACCCGAAGGCA
53727883 ATTGTGCTAGTGGCT
66 ATTGTGCTAGTGGCT
* * * * * *
53727898 ACATCCGGGCTAAGACCCGAAGGC-ATTCGTGC-GAGACATTCTATCCGGGCTAAGACCCGAAGG
1 ATATCCGGGCTAAGACCCGAAGACAATT-ATGCTG-GAAATTATATCCGAGCTAAGACCCGAAGG
* *
53727961 CATTTGTGC-ACGTGGTT
64 CAATTGTGCTA-GTGGCT
53727978 ATATCCGG
1 ATATCCGG
53727986 TTATATTCCG
Statistics
Matches: 74, Mismatches: 11, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
79 5 0.07
80 69 0.93
ACGTcount: A:0.27, C:0.24, G:0.27, T:0.23
Consensus pattern (80 bp):
ATATCCGGGCTAAGACCCGAAGACAATTATGCTGGAAATTATATCCGAGCTAAGACCCGAAGGCA
ATTGTGCTAGTGGCT
Found at i:53731484 original size:27 final size:27
Alignment explanation
Indices: 53731446--53731514 Score: 120
Period size: 27 Copynumber: 2.6 Consensus size: 27
53731436 AAATTTGTAC
53731446 AGCACTAAGTGTGCGAGTTGATCATAT
1 AGCACTAAGTGTGCGAGTTGATCATAT
*
53731473 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGAGTTGATCATAT
*
53731500 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
53731515 GACTCACTAT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
27 40 1.00
ACGTcount: A:0.28, C:0.14, G:0.29, T:0.29
Consensus pattern (27 bp):
AGCACTAAGTGTGCGAGTTGATCATAT
Found at i:53731525 original size:27 final size:27
Alignment explanation
Indices: 53731446--53731526 Score: 76
Period size: 27 Copynumber: 3.0 Consensus size: 27
53731436 AAATTTGTAC
* *
53731446 AGCACTAAGTGTGCGAGTTGA-TCATAT
1 AGCACTAAGTGTGCGAGCTCACT-ATAT
* * *
53731473 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGAGCTCACTATAT
*
53731500 AGCACTGAGTGTGCG-GACTCACTATAT
1 AGCACTAAGTGTGCGAG-CTCACTATAT
53731527 GCTTTTGAAT
Statistics
Matches: 48, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
26 1 0.02
27 46 0.96
28 1 0.02
ACGTcount: A:0.28, C:0.16, G:0.26, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGAGCTCACTATAT
Found at i:53740576 original size:32 final size:32
Alignment explanation
Indices: 53740540--53740602 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
53740530 GCCCTTCCGT
53740540 CCAAACCAGGGTATCTTCTTCCATGACGAGAC
1 CCAAACCAGGGTATCTTCTTCCATGACGAGAC
*
53740572 CCAAACCAGGGTATCTTTTTCCATGACGAGA
1 CCAAACCAGGGTATCTTCTTCCATGACGAGA
53740603 GCTTGAGAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.29, C:0.29, G:0.19, T:0.24
Consensus pattern (32 bp):
CCAAACCAGGGTATCTTCTTCCATGACGAGAC
Found at i:53742981 original size:10 final size:10
Alignment explanation
Indices: 53742966--53742992 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
53742956 TAAGTTGAAG
53742966 TTGAGCTGAT
1 TTGAGCTGAT
53742976 TTGAGCTGAT
1 TTGAGCTGAT
53742986 TTGAGCT
1 TTGAGCT
53742993 TGAAGGAGTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.19, C:0.11, G:0.30, T:0.41
Consensus pattern (10 bp):
TTGAGCTGAT
Found at i:53748171 original size:12 final size:14
Alignment explanation
Indices: 53748154--53748189 Score: 58
Period size: 14 Copynumber: 2.7 Consensus size: 14
53748144 CATAAATTAC
53748154 TTTTTTTTTC-G-A
1 TTTTTTTTTCGGAA
53748166 TTTTTTTTTCGGAA
1 TTTTTTTTTCGGAA
53748180 TTTTTTTTTC
1 TTTTTTTTTC
53748190 CAAACTTGTA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
12 10 0.45
13 1 0.05
14 11 0.50
ACGTcount: A:0.08, C:0.08, G:0.08, T:0.75
Consensus pattern (14 bp):
TTTTTTTTTCGGAA
Found at i:53755196 original size:30 final size:30
Alignment explanation
Indices: 53755102--53755197 Score: 88
Period size: 30 Copynumber: 3.2 Consensus size: 30
53755092 AGCTCACTCC
53755102 TAGCTCATA-TTCAGCTCACGAGCTAAACCT
1 TAGCTCA-ACTTCAGCTCACGAGCTAAACCT
* * * * * *
53755132 T-GCTCAGCTTCAGCTTAGGAGTTTAATCT
1 TAGCTCAACTTCAGCTCACGAGCTAAACCT
* * *
53755161 CAGCTCAACTTTAGCTCACGAGCTAAAGCT
1 TAGCTCAACTTCAGCTCACGAGCTAAACCT
53755191 TAGCTCA
1 TAGCTCA
53755198 TTTTAGTTTA
Statistics
Matches: 49, Mismatches: 15, Indels: 4
0.72 0.22 0.06
Matches are distributed among these distances:
29 21 0.43
30 28 0.57
ACGTcount: A:0.27, C:0.27, G:0.17, T:0.29
Consensus pattern (30 bp):
TAGCTCAACTTCAGCTCACGAGCTAAACCT
Found at i:53757255 original size:40 final size:39
Alignment explanation
Indices: 53757193--53757269 Score: 100
Period size: 40 Copynumber: 1.9 Consensus size: 39
53757183 CGACTTATCG
* *
53757193 GCTAAAATGGTACTTAGTGTGCAGTTCGAAATAGCTTCA
1 GCTAAAATGGCACTTAGTGTGCAATTCGAAATAGCTTCA
* * *
53757232 GCTAAAAGTGGCACTTGGTGTGCAATTTGAGATAGCTT
1 GCTAAAA-TGGCACTTAGTGTGCAATTCGAAATAGCTT
53757270 TGGCTATATA
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
39 7 0.22
40 25 0.78
ACGTcount: A:0.29, C:0.14, G:0.26, T:0.31
Consensus pattern (39 bp):
GCTAAAATGGCACTTAGTGTGCAATTCGAAATAGCTTCA
Found at i:53761534 original size:2 final size:2
Alignment explanation
Indices: 53761527--53761561 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
53761517 GTACGACAGA
53761527 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
53761562 ACGAATAACT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:53765508 original size:39 final size:39
Alignment explanation
Indices: 53765466--53765636 Score: 288
Period size: 39 Copynumber: 4.4 Consensus size: 39
53765456 CATGGTATTT
*
53765466 GAAATATATCCGGACATGAGGTCCGCAGGCTATATGCTT
1 GAAATATATCCGGACATGAGGTCCGCAGGCTATATGCTG
*
53765505 GAAATATATCTGGACATGAGGTCCGCAGGCTATATGCTG
1 GAAATATATCCGGACATGAGGTCCGCAGGCTATATGCTG
* *
53765544 GAAATATATCCGGACATGAAGTCCGCAGGCTATACGCTG
1 GAAATATATCCGGACATGAGGTCCGCAGGCTATATGCTG
* *
53765583 GGAATATATCCGGACATGAGGTCCACAGGCTATATGCTG
1 GAAATATATCCGGACATGAGGTCCGCAGGCTATATGCTG
53765622 GAAATATATCCGGAC
1 GAAATATATCCGGAC
53765637 TTGAAGTCTG
Statistics
Matches: 122, Mismatches: 10, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 122 1.00
ACGTcount: A:0.30, C:0.20, G:0.26, T:0.23
Consensus pattern (39 bp):
GAAATATATCCGGACATGAGGTCCGCAGGCTATATGCTG
Found at i:53769577 original size:15 final size:15
Alignment explanation
Indices: 53769559--53769589 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
53769549 TAAAAAATTC
53769559 CAATACAAAACATAT
1 CAATACAAAACATAT
*
53769574 CAATCCAAAACATAT
1 CAATACAAAACATAT
53769589 C
1 C
53769590 TTTCATAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.55, C:0.26, G:0.00, T:0.19
Consensus pattern (15 bp):
CAATACAAAACATAT
Found at i:53775701 original size:40 final size:40
Alignment explanation
Indices: 53775639--53775826 Score: 270
Period size: 40 Copynumber: 4.7 Consensus size: 40
53775629 ATAACCACAA
* * *
53775639 GCACAATTGCCTTCGGGTCTTAACCCGGGTATAGCAACTC
1 GCACAAATGCCTTCGGGTCTTAACCCGGATATAGCAACTT
* *
53775679 GGACAAATGCCTTCGGGTCTTAACCCGGATATAACAACTT
1 GCACAAATGCCTTCGGGTCTTAACCCGGATATAGCAACTT
53775719 GCACAAATGCCTTCGGGTCTTAACCCGGATATAGCAACTT
1 GCACAAATGCCTTCGGGTCTTAACCCGGATATAGCAACTT
* *
53775759 GCACAAATGCCTTCGGGTCTTAACCCGGATATAATC-ACTA
1 GCACAAATGCCTTCGGGTCTTAACCCGGATAT-AGCAACTT
* * *
53775799 GCATAAATGCCTTCGGGGCTTAGCCCGG
1 GCACAAATGCCTTCGGGTCTTAACCCGG
53775827 GTATCATTCA
Statistics
Matches: 135, Mismatches: 12, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
40 133 0.99
41 2 0.01
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.24
Consensus pattern (40 bp):
GCACAAATGCCTTCGGGTCTTAACCCGGATATAGCAACTT
Found at i:53775756 original size:80 final size:79
Alignment explanation
Indices: 53775623--53775826 Score: 300
Period size: 80 Copynumber: 2.5 Consensus size: 79
53775613 CAGAATTTAG
* * * *
53775623 CCGGATATAACCACAAGCACAATTGCCTTCGGGTCTTAACCCGGGTATAGCAACTCGGACAAATG
1 CCGGATATAA-CACTAGCACAAATGCCTTCGGGTCTTAACCCGGATATAGCAACTCGCACAAATG
53775688 CCTTCGGGTCTTAAC
65 CCTTCGGGTCTTAAC
* *
53775703 CCGGATATAACAACTTGCACAAATGCCTTCGGGTCTTAACCCGGATATAGCAACTTGCACAAATG
1 CCGGATATAAC-ACTAGCACAAATGCCTTCGGGTCTTAACCCGGATATAGCAACTCGCACAAATG
53775768 CCTTCGGGTCTTAAC
65 CCTTCGGGTCTTAAC
* * *
53775783 CCGGATATAATCACTAGCATAAATGCCTTCGGGGCTTAGCCCGG
1 CCGGATATAA-CACTAGCACAAATGCCTTCGGGTCTTAACCCGG
53775827 GTATCATTCA
Statistics
Matches: 112, Mismatches: 10, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
79 1 0.01
80 110 0.98
81 1 0.01
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24
Consensus pattern (79 bp):
CCGGATATAACACTAGCACAAATGCCTTCGGGTCTTAACCCGGATATAGCAACTCGCACAAATGC
CTTCGGGTCTTAAC
Found at i:53783811 original size:40 final size:39
Alignment explanation
Indices: 53783707--53784068 Score: 440
Period size: 40 Copynumber: 9.1 Consensus size: 39
53783697 TGGAATTTAG
* *
53783707 CCGGATATAACCACAAGCACAATTGCCTTCGGGTCTTAAC
1 CCGGATATAA-CACTAGCACAAATGCCTTCGGGTCTTAAC
* * * *
53783747 CCGG-TATAGCAACTCGCACAAATGCCTTCCGGTCTTAGC
1 CCGGATATAAC-ACTAGCACAAATGCCTTCGGGTCTTAAC
* *
53783786 CCGGATATAACAACTCGCACAAATGCCTTCAGGTCTTAAC
1 CCGGATATAAC-ACTAGCACAAATGCCTTCGGGTCTTAAC
* *
53783826 CCGGATATAATCACTAGCATAAATGCCTTCGGG-CTTAGC
1 CCGGATATAA-CACTAGCACAAATGCCTTCGGGTCTTAAC
* * * *
53783865 CAGGATATAATCACTAGCATAAATGCCTTCGGGGCTTAGC
1 CCGGATATAA-CACTAGCACAAATGCCTTCGGGTCTTAAC
*
53783905 CCGGATATAACAACTCGCACAAATGCCTTCGGGTCTTAAC
1 CCGGATATAAC-ACTAGCACAAATGCCTTCGGGTCTTAAC
* *
53783945 CCGGATATAGCAACTCGCACAAATGCCTTCGGGTCTTAAC
1 CCGGATATAAC-ACTAGCACAAATGCCTTCGGGTCTTAAC
53783985 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAAC
1 CCGGATATAA-CACTAGCACAAATGCCTTCGGGTCTTAAC
* * * *
53784025 CCGGATATAATCACTAGCATAAATGCCTTTGGGGCTTAGC
1 CCGGATATAA-CACTAGCACAAATGCCTTCGGGTCTTAAC
53784065 CCGG
1 CCGG
53784069 GTATCATTCA
Statistics
Matches: 290, Mismatches: 26, Indels: 12
0.88 0.08 0.04
Matches are distributed among these distances:
38 1 0.00
39 69 0.24
40 218 0.75
41 2 0.01
ACGTcount: A:0.28, C:0.28, G:0.20, T:0.24
Consensus pattern (39 bp):
CCGGATATAACACTAGCACAAATGCCTTCGGGTCTTAAC
Found at i:53783918 original size:119 final size:120
Alignment explanation
Indices: 53783707--53784053 Score: 486
Period size: 119 Copynumber: 2.9 Consensus size: 120
53783697 TGGAATTTAG
* * * *
53783707 CCGGATATAACCACAAGCACAATTGCCTTCGGGTCTTAACCCGG-TAT-AGCAACTCGCACAAAT
1 CCGGATATAACCACTAGCACAAATGCCTTCGGGTCTTAACCCGGATATAATC-ACTAGCACAAAT
*
53783770 GCCTTCCGGTCTTAGCCCGGATATAACAACTCGCACAAATGCCTTCAGGTCTTAAC
65 GCCTTCGGGTCTTAGCCCGGATATAACAACTCGCACAAATGCCTTCAGGTCTTAAC
* * * * *
53783826 CCGGATATAATCACTAGCATAAATGCCTTCGGG-CTTAGCCAGGATATAATCACTAGCATAAATG
1 CCGGATATAACCACTAGCACAAATGCCTTCGGGTCTTAACCCGGATATAATCACTAGCACAAATG
* *
53783890 CCTTCGGGGCTTAGCCCGGATATAACAACTCGCACAAATGCCTTCGGGTCTTAAC
66 CCTTCGGGTCTTAGCCCGGATATAACAACTCGCACAAATGCCTTCAGGTCTTAAC
* * *
53783945 CCGGATATAGCAACTCGCACAAATGCCTTCGGGTCTTAACCCGGATATAATCACTAGCACAAATG
1 CCGGATATAACCACTAGCACAAATGCCTTCGGGTCTTAACCCGGATATAATCACTAGCACAAATG
* * *
53784010 CCTTCGGGTCTTAACCCGGATATAATC-ACTAGCATAAATGCCTT
66 CCTTCGGGTCTTAGCCCGGATATAA-CAACTCGCACAAATGCCTT
53784054 TGGGGCTTAG
Statistics
Matches: 200, Mismatches: 24, Indels: 7
0.87 0.10 0.03
Matches are distributed among these distances:
118 8 0.04
119 123 0.62
120 68 0.34
121 1 0.00
ACGTcount: A:0.29, C:0.28, G:0.18, T:0.24
Consensus pattern (120 bp):
CCGGATATAACCACTAGCACAAATGCCTTCGGGTCTTAACCCGGATATAATCACTAGCACAAATG
CCTTCGGGTCTTAGCCCGGATATAACAACTCGCACAAATGCCTTCAGGTCTTAAC
Found at i:53788261 original size:19 final size:20
Alignment explanation
Indices: 53788237--53788275 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
53788227 AAGCTTATAG
*
53788237 TTTCATGTA-TAACATATTC
1 TTTCATATATTAACATATTC
*
53788256 TTTCATATATTAACTTATTC
1 TTTCATATATTAACATATTC
53788276 ATGACTGATT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.31, C:0.15, G:0.03, T:0.51
Consensus pattern (20 bp):
TTTCATATATTAACATATTC
Found at i:53790442 original size:30 final size:30
Alignment explanation
Indices: 53790408--53790504 Score: 99
Period size: 30 Copynumber: 3.2 Consensus size: 30
53790398 TAAACTAAAA
53790408 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
* * * * *
53790438 TGAGCTAAGGC-TAAACTCCTAAGCTGAAGT
1 TGAGCTAA-GCTTTAGCTCGTGAGCTAAAGT
* *
53790468 TGAGCTAAGGTTTAGCTCGTGAGTTGAAAG-
1 TGAGCTAAGCTTTAGCTCGTGAGCT-AAAGT
53790498 TGAGCTA
1 TGAGCTA
53790505 GGAGTGAGCT
Statistics
Matches: 52, Mismatches: 12, Indels: 6
0.74 0.17 0.09
Matches are distributed among these distances:
29 1 0.02
30 46 0.88
31 5 0.10
ACGTcount: A:0.29, C:0.15, G:0.28, T:0.28
Consensus pattern (30 bp):
TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
Found at i:53794869 original size:30 final size:30
Alignment explanation
Indices: 53794798--53794880 Score: 89
Period size: 30 Copynumber: 2.7 Consensus size: 30
53794788 CTTTTGTTTC
* *
53794798 AATTTCTTTTTCATCTTCTTTTTCACTCTCA
1 AATTTCTTTTTCTTC-TCTTTTTCAATCTCA
53794829 AATTTC-TTTTCGTTCTCTTTTTCAATCTC-
1 AATTTCTTTTTC-TTCTCTTTTTCAATCTCA
* *
53794858 ATTTTCTTTTTCATTTTCTTTTT
1 AATTTCTTTTTC-TTCTCTTTTT
53794881 GCTTTTCAAA
Statistics
Matches: 45, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
29 5 0.11
30 32 0.71
31 8 0.18
ACGTcount: A:0.13, C:0.22, G:0.01, T:0.64
Consensus pattern (30 bp):
AATTTCTTTTTCTTCTCTTTTTCAATCTCA
Found at i:53794880 original size:18 final size:18
Alignment explanation
Indices: 53794831--53794886 Score: 51
Period size: 18 Copynumber: 3.1 Consensus size: 18
53794821 CACTCTCAAA
* *
53794831 TTTC-TTTTCGTTCTCTT
1 TTTCATTTTCATTTTCTT
* *
53794848 TTTCAATCTCATTTTCTT
1 TTTCATTTTCATTTTCTT
*
53794866 TTTCATTTTCTTTTTGCTT
1 TTTCATTTTCATTTT-CTT
53794885 TT
1 TT
53794887 CAAAGGCTTT
Statistics
Matches: 30, Mismatches: 7, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
17 4 0.13
18 21 0.70
19 5 0.17
ACGTcount: A:0.07, C:0.20, G:0.04, T:0.70
Consensus pattern (18 bp):
TTTCATTTTCATTTTCTT
Found at i:53794887 original size:12 final size:12
Alignment explanation
Indices: 53794856--53794880 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
53794846 TTTTTCAATC
53794856 TCATTTTCTTTT
1 TCATTTTCTTTT
53794868 TCATTTTCTTTT
1 TCATTTTCTTTT
53794880 T
1 T
53794881 GCTTTTCAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.08, C:0.16, G:0.00, T:0.76
Consensus pattern (12 bp):
TCATTTTCTTTT
Found at i:53794957 original size:5 final size:5
Alignment explanation
Indices: 53794947--53795003 Score: 55
Period size: 5 Copynumber: 11.0 Consensus size: 5
53794937 CTCTTGCCTC
*
53794947 TCTTT TCTTT T-TATT TCATTT TCTTT T-TCT TCTTT TGCTTTT TCTTT
1 TCTTT TCTTT TCT-TT TC-TTT TCTTT TCTTT TCTTT T-C-TTT TCTTT
53794994 TCTTT TCTTT
1 TCTTT TCTTT
53795004 GTTTTCTCTT
Statistics
Matches: 44, Mismatches: 2, Indels: 12
0.76 0.03 0.21
Matches are distributed among these distances:
4 4 0.09
5 29 0.66
6 6 0.14
7 5 0.11
ACGTcount: A:0.04, C:0.18, G:0.02, T:0.77
Consensus pattern (5 bp):
TCTTT
Found at i:53794987 original size:15 final size:14
Alignment explanation
Indices: 53794947--53795003 Score: 60
Period size: 16 Copynumber: 3.7 Consensus size: 14
53794937 CTCTTGCCTC
*
53794947 TCTTTTCTTTTTATT
1 TCTTTTCTTTTT-CT
53794962 TCATTTTCTTTTTCT
1 TC-TTTTCTTTTTCT
53794977 TCTTTTGCTTTTTCTTT
1 TCTTTT-CTTTTTC--T
53794994 TCTTTTCTTT
1 TCTTTTCTTT
53795004 GTTTTCTCTT
Statistics
Matches: 37, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
14 4 0.11
15 12 0.32
16 14 0.38
17 7 0.19
ACGTcount: A:0.04, C:0.18, G:0.02, T:0.77
Consensus pattern (14 bp):
TCTTTTCTTTTTCT
Found at i:53795004 original size:21 final size:21
Alignment explanation
Indices: 53794947--53795014 Score: 61
Period size: 21 Copynumber: 3.2 Consensus size: 21
53794937 CTCTTGCCTC
* *
53794947 TCTTTTCTTTT-TATTTCATTT
1 TCTTTTCTTTTCT-TTGCTTTT
*
53794968 TCTTTT-TCTTCTTTTGCTTTT
1 TCTTTTCTTTTC-TTTGCTTTT
53794989 TCTTTTCTTTTCTTTG-TTTT
1 TCTTTTCTTTTCTTTGCTTTT
53795009 CTCTTT
1 -TCTTT
53795015 ACAAGAATGT
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
20 7 0.18
21 27 0.69
22 5 0.13
ACGTcount: A:0.03, C:0.18, G:0.03, T:0.76
Consensus pattern (21 bp):
TCTTTTCTTTTCTTTGCTTTT
Found at i:53795962 original size:12 final size:12
Alignment explanation
Indices: 53795932--53795973 Score: 52
Period size: 12 Copynumber: 3.6 Consensus size: 12
53795922 TTCAGATTTT
*
53795932 TTTTCTTTTCGAA
1 TTTT-TTTTCAAA
53795945 -TTTTTTT-AAA
1 TTTTTTTTCAAA
53795955 TTTTTTTTCAAA
1 TTTTTTTTCAAA
53795967 TTTTTTT
1 TTTTTTT
53795974 GACTTTATAA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
10 2 0.08
11 11 0.42
12 13 0.50
ACGTcount: A:0.19, C:0.07, G:0.02, T:0.71
Consensus pattern (12 bp):
TTTTTTTTCAAA
Found at i:53795989 original size:39 final size:38
Alignment explanation
Indices: 53795916--53795990 Score: 89
Period size: 39 Copynumber: 1.9 Consensus size: 38
53795906 CATTAAACAC
* * *
53795916 TTTTTTTTCAGATTTTTTTTCTTTTCGAATTTTTTTAAA
1 TTTTTTTTCAAATTTTTTTACTTTTC-AACTTTTTTAAA
53795955 TTTTTTTTCAAATTTTTTTGACTTTAT-AACTTTTTT
1 TTTTTTTTCAAATTTTTTT-ACTTT-TCAACTTTTTT
53795991 TTGTACTATA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
39 26 0.84
40 4 0.13
41 1 0.03
ACGTcount: A:0.19, C:0.08, G:0.04, T:0.69
Consensus pattern (38 bp):
TTTTTTTTCAAATTTTTTTACTTTTCAACTTTTTTAAA
Found at i:53797672 original size:30 final size:30
Alignment explanation
Indices: 53797638--53797734 Score: 88
Period size: 30 Copynumber: 3.2 Consensus size: 30
53797628 TAAACTAAAA
* *
53797638 TGAGCTAAGCTTTAGCTTGTGAGCTAAAGT
1 TGAGCTAAGATTTAGCTCGTGAGCTAAAGT
* * * * * *
53797668 TGAGCTGAGATTAAACTCCTAAGCTGAAGT
1 TGAGCTAAGATTTAGCTCGTGAGCTAAAGT
* *
53797698 TGAGCTAAGGTTTAGCTCGTGAGTTGAAAG-
1 TGAGCTAAGATTTAGCTCGTGAGCT-AAAGT
53797728 TGAGCTA
1 TGAGCTA
53797735 GGAGTGAGCT
Statistics
Matches: 50, Mismatches: 16, Indels: 2
0.74 0.24 0.03
Matches are distributed among these distances:
30 47 0.94
31 3 0.06
ACGTcount: A:0.29, C:0.13, G:0.28, T:0.30
Consensus pattern (30 bp):
TGAGCTAAGATTTAGCTCGTGAGCTAAAGT
Found at i:53798739 original size:27 final size:27
Alignment explanation
Indices: 53798700--53798816 Score: 173
Period size: 27 Copynumber: 4.3 Consensus size: 27
53798690 CCAAATTGAT
* *
53798700 AAATGACTGTTTTACCCTTATGAGGTA
1 AAATGATTGTTTTGCCCTTATGAGGTA
*
53798727 AAATGATTATTTTGCCCTTAT-ATGGTA
1 AAATGATTGTTTTGCCCTTATGA-GGTA
53798754 AAATGATTGTTTTGCCCTTATGAGGTA
1 AAATGATTGTTTTGCCCTTATGAGGTA
* *
53798781 AGATGATTGTTTTGCCCTTATGTGGTA
1 AAATGATTGTTTTGCCCTTATGAGGTA
53798808 AAATGATTG
1 AAATGATTG
53798817 AAATGCCCCT
Statistics
Matches: 81, Mismatches: 7, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
26 1 0.01
27 79 0.98
28 1 0.01
ACGTcount: A:0.27, C:0.11, G:0.21, T:0.41
Consensus pattern (27 bp):
AAATGATTGTTTTGCCCTTATGAGGTA
Found at i:53798824 original size:54 final size:54
Alignment explanation
Indices: 53798714--53798852 Score: 172
Period size: 54 Copynumber: 2.6 Consensus size: 54
53798704 GACTGTTTTA
***
53798714 CCCTTATGAGGTAAAATGATTATTTTGCCCTTATATGGTAAAATGATTGTTTTG
1 CCCTTATGAGGTAAAATGATTATTTTGCCCTTATATGGTAAAATGATTGAAATG
* * *
53798768 CCCTTATGAGGTAAGATGATTGTTTTGCCCTTATGTGGTAAAATGATTGAAATG
1 CCCTTATGAGGTAAAATGATTATTTTGCCCTTATATGGTAAAATGATTGAAATG
* * * *
53798822 CCCCTA-CATGGTAAATTGACTATTTTGCCCT
1 CCCTTATGA-GGTAAAATGATTATTTTGCCCT
53798853 ATGTGAGGTA
Statistics
Matches: 72, Mismatches: 12, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
53 1 0.01
54 71 0.99
ACGTcount: A:0.27, C:0.15, G:0.19, T:0.39
Consensus pattern (54 bp):
CCCTTATGAGGTAAAATGATTATTTTGCCCTTATATGGTAAAATGATTGAAATG
Found at i:53798848 original size:81 final size:82
Alignment explanation
Indices: 53798702--53798862 Score: 200
Period size: 81 Copynumber: 2.0 Consensus size: 82
53798692 AAATTGATAA
** * * * *
53798702 ATGACTGTTTTACCCTTATGAGGTAAAATGATTATTTTGCCCTTATATGGTAAAATGATTGTTTT
1 ATGACTGTTTTACCCTTATGAGGTAAAATGATTATAATGCCCCTACATGGTAAAATGACTATTTT
53798767 GCCCT-TATGAGGTAAG
66 GCCCTATATGAGGTAAG
* * * *
53798783 ATGATTGTTTTGCCCTTATGTGGTAAAATGATTGA-AATGCCCCTACATGGTAAATTGACTATTT
1 ATGACTGTTTTACCCTTATGAGGTAAAATGATT-ATAATGCCCCTACATGGTAAAATGACTATTT
*
53798847 TGCCCTATGTGAGGTA
65 TGCCCTATATGAGGTA
53798863 TTTATATATT
Statistics
Matches: 67, Mismatches: 11, Indels: 3
0.83 0.14 0.04
Matches are distributed among these distances:
81 58 0.87
82 9 0.13
ACGTcount: A:0.27, C:0.14, G:0.20, T:0.39
Consensus pattern (82 bp):
ATGACTGTTTTACCCTTATGAGGTAAAATGATTATAATGCCCCTACATGGTAAAATGACTATTTT
GCCCTATATGAGGTAAG
Found at i:53799206 original size:18 final size:18
Alignment explanation
Indices: 53799160--53799207 Score: 60
Period size: 18 Copynumber: 2.7 Consensus size: 18
53799150 TATTGTTTAA
*
53799160 ACTGTTACTACACTGATT
1 ACTGTTACTGCACTGATT
* * *
53799178 ACTGTTGCTGCTCTGTTT
1 ACTGTTACTGCACTGATT
53799196 ACTGTTACTGCA
1 ACTGTTACTGCA
53799208 ATAGGCCAAG
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.19, C:0.23, G:0.17, T:0.42
Consensus pattern (18 bp):
ACTGTTACTGCACTGATT
Found at i:53807201 original size:30 final size:30
Alignment explanation
Indices: 53807116--53807212 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
53807106 TAAACTAAAA
* *
53807116 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGGTTTAGCTCGTGAGCTGAAGT
* * * * * *
53807146 TGAGCTGAGGCTAAACTCCTAAGCTGAAGT
1 TGAGCTAAGGTTTAGCTCGTGAGCTGAAGT
53807176 TGAGCTAAGGTTTAGCTCGTGAGCTGAA-T
1 TGAGCTAAGGTTTAGCTCGTGAGCTGAAGT
53807205 ATGAGCTA
1 -TGAGCTA
53807213 GGAGTGAGCT
Statistics
Matches: 52, Mismatches: 14, Indels: 2
0.76 0.21 0.03
Matches are distributed among these distances:
29 1 0.02
30 51 0.98
ACGTcount: A:0.28, C:0.16, G:0.28, T:0.28
Consensus pattern (30 bp):
TGAGCTAAGGTTTAGCTCGTGAGCTGAAGT
Found at i:53809080 original size:9 final size:9
Alignment explanation
Indices: 53809066--53809094 Score: 58
Period size: 9 Copynumber: 3.2 Consensus size: 9
53809056 AAACAAAGAA
53809066 TCCTTACCT
1 TCCTTACCT
53809075 TCCTTACCT
1 TCCTTACCT
53809084 TCCTTACCT
1 TCCTTACCT
53809093 TC
1 TC
53809095 GATCGCAAGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.10, C:0.45, G:0.00, T:0.45
Consensus pattern (9 bp):
TCCTTACCT
Found at i:53809394 original size:30 final size:30
Alignment explanation
Indices: 53809323--53809405 Score: 89
Period size: 30 Copynumber: 2.7 Consensus size: 30
53809313 CTTTTGTTTC
* *
53809323 AATTTCTTTTTCATCTTCTTTTTCACTCTCA
1 AATTTCTTTTTCTTC-TCTTTTTCAATCTCA
53809354 AATTTC-TTTTCGTTCTCTTTTTCAATCTC-
1 AATTTCTTTTTC-TTCTCTTTTTCAATCTCA
* *
53809383 ATTTTCTTTTTCATTTTCTTTTT
1 AATTTCTTTTTC-TTCTCTTTTT
53809406 GCTTTTCAAA
Statistics
Matches: 45, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
29 5 0.11
30 32 0.71
31 8 0.18
ACGTcount: A:0.13, C:0.22, G:0.01, T:0.64
Consensus pattern (30 bp):
AATTTCTTTTTCTTCTCTTTTTCAATCTCA
Found at i:53809405 original size:18 final size:18
Alignment explanation
Indices: 53809356--53809411 Score: 51
Period size: 18 Copynumber: 3.1 Consensus size: 18
53809346 CACTCTCAAA
* *
53809356 TTTC-TTTTCGTTCTCTT
1 TTTCATTTTCATTTTCTT
* *
53809373 TTTCAATCTCATTTTCTT
1 TTTCATTTTCATTTTCTT
*
53809391 TTTCATTTTCTTTTTGCTT
1 TTTCATTTTCATTTT-CTT
53809410 TT
1 TT
53809412 CAAAGGCTTT
Statistics
Matches: 30, Mismatches: 7, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
17 4 0.13
18 21 0.70
19 5 0.17
ACGTcount: A:0.07, C:0.20, G:0.04, T:0.70
Consensus pattern (18 bp):
TTTCATTTTCATTTTCTT
Done.