Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D02
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: 67659327
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 461372 characters in sequence are not A, C, G, or T
File 179 of 216
Found at i:55918312 original size:33 final size:32
Alignment explanation
Indices: 55918269--55918358 Score: 82
Period size: 28 Copynumber: 2.8 Consensus size: 32
55918259 AATCAGTCTA
*
55918269 GGCCTGAGCCCTATACAGTATCAGTACAGTGTG
1 GGCCTTAGCCC-ATACAGTATCAGTACAGTGTG
55918302 GGCCTTAGCCCAT----TA-CAGTAACAGTGTG
1 GGCCTTAGCCCATACAGTATCAGT-ACAGTGTG
* *
55918330 GGCCTTATCCCAATACAGAAATCAGTACA
1 GGCCTTAGCCC-ATACAG-TATCAGTACA
55918359 ATGCAGTGAT
Statistics
Matches: 46, Mismatches: 3, Indels: 15
0.72 0.05 0.23
Matches are distributed among these distances:
27 4 0.09
28 20 0.43
29 2 0.04
32 2 0.04
33 10 0.22
34 4 0.09
35 4 0.09
ACGTcount: A:0.29, C:0.26, G:0.22, T:0.23
Consensus pattern (32 bp):
GGCCTTAGCCCATACAGTATCAGTACAGTGTG
Found at i:55918329 original size:28 final size:27
Alignment explanation
Indices: 55918290--55918347 Score: 89
Period size: 28 Copynumber: 2.1 Consensus size: 27
55918280 TATACAGTAT
*
55918290 CAGTACAGTGTGGGCCTTAGCCCATTA
1 CAGTACAGTGTGGGCCTTAGCCCAATA
*
55918317 CAGTAACAGTGTGGGCCTTATCCCAATA
1 CAGT-ACAGTGTGGGCCTTAGCCCAATA
55918345 CAG
1 CAG
55918348 AAATCAGTAC
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
27 4 0.14
28 24 0.86
ACGTcount: A:0.26, C:0.26, G:0.24, T:0.24
Consensus pattern (27 bp):
CAGTACAGTGTGGGCCTTAGCCCAATA
Found at i:55918740 original size:27 final size:27
Alignment explanation
Indices: 55918683--55918902 Score: 228
Period size: 27 Copynumber: 8.2 Consensus size: 27
55918673 TATAACAGTC
* * * * *
55918683 ATTTTAACCTACGAAGGTATTTTGGTC
1 ATTTTACCCTTCGAGGGTATTTCGGTA
* *
55918710 ATTTTACCCTTTG-GGGTATTTAGGGTA
1 ATTTTACCCTTCGAGGGTATTT-CGGTA
* * *
55918737 ATTTTACCTTTTGAGGGTTTTTCGGTA
1 ATTTTACCCTTCGAGGGTATTTCGGTA
* * *
55918764 ATTTTACCCTTCAAGAG-ATTTCGATA
1 ATTTTACCCTTCGAGGGTATTTCGGTA
**
55918790 ATTTTACCCTTCGAGGGTATTTCAATA
1 ATTTTACCCTTCGAGGGTATTTCGGTA
* *
55918817 ATTTTACCATTCGAGGGTATTTTGGTA
1 ATTTTACCCTTCGAGGGTATTTCGGTA
* *
55918844 ATTTAACCCTTCGTGGGTATTTCGGTA
1 ATTTTACCCTTCGAGGGTATTTCGGTA
* *
55918871 ATTTTACCTTTCGAGGGTATTTCGATA
1 ATTTTACCCTTCGAGGGTATTTCGGTA
55918898 ATTTT
1 ATTTT
55918903 CCTACCCAAG
Statistics
Matches: 160, Mismatches: 30, Indels: 6
0.82 0.15 0.03
Matches are distributed among these distances:
26 29 0.18
27 124 0.77
28 7 0.04
ACGTcount: A:0.22, C:0.15, G:0.19, T:0.44
Consensus pattern (27 bp):
ATTTTACCCTTCGAGGGTATTTCGGTA
Found at i:55920762 original size:46 final size:46
Alignment explanation
Indices: 55920706--55920852 Score: 186
Period size: 46 Copynumber: 3.2 Consensus size: 46
55920696 TTACCCGTTT
* **
55920706 GGGTTAAACCTACACGAATTGGATAATTGTGCATGGTCACCCATTA
1 GGGTTGAACCTACACGAATTGGATAATTGTGCATGGTCACCTGTTA
* *
55920752 GGGTTGAACCTACACGAATTGGGTAATTGTGCTTGGTCACCTGTTA
1 GGGTTGAACCTACACGAATTGGATAATTGTGCATGGTCACCTGTTA
* * * * * *
55920798 GGGTTGAACCTACATGAATCGAATAATAGTACATTGTCACCTGTTA
1 GGGTTGAACCTACACGAATTGGATAATTGTGCATGGTCACCTGTTA
*
55920844 GGATTGAAC
1 GGGTTGAAC
55920853 GTGCACAGGA
Statistics
Matches: 87, Mismatches: 14, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
46 87 1.00
ACGTcount: A:0.29, C:0.18, G:0.24, T:0.30
Consensus pattern (46 bp):
GGGTTGAACCTACACGAATTGGATAATTGTGCATGGTCACCTGTTA
Found at i:55921582 original size:20 final size:20
Alignment explanation
Indices: 55921557--55921594 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
55921547 TCCATCAAAG
* *
55921557 ATTCAAAATCTACCATAAAC
1 ATTCAAAAACTACAATAAAC
55921577 ATTCAAAAACTACAATAA
1 ATTCAAAAACTACAATAA
55921595 TATCAATGGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.55, C:0.21, G:0.00, T:0.24
Consensus pattern (20 bp):
ATTCAAAAACTACAATAAAC
Found at i:55924050 original size:10 final size:11
Alignment explanation
Indices: 55924032--55924063 Score: 57
Period size: 10 Copynumber: 3.0 Consensus size: 11
55924022 TTTGCATAAG
55924032 ATATGAATTGA
1 ATATGAATTGA
55924043 AT-TGAATTGA
1 ATATGAATTGA
55924053 ATATGAATTGA
1 ATATGAATTGA
55924064 TGTTAAATTC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
10 10 0.50
11 10 0.50
ACGTcount: A:0.44, C:0.00, G:0.19, T:0.38
Consensus pattern (11 bp):
ATATGAATTGA
Found at i:55924602 original size:24 final size:24
Alignment explanation
Indices: 55924575--55924666 Score: 78
Period size: 24 Copynumber: 3.8 Consensus size: 24
55924565 ATCCCAATTA
55924575 ATTGGCTCTCCGGAGCTTCTCGAT
1 ATTGGCTCTCCGGAGCTTCTCGAT
* * * *
55924599 ATTGGCTCGCTTGAACCTTCAT-GAT
1 ATTGGCTCTC-CGGAGCTTC-TCGAT
*** *
55924624 ATTGGCTCTTATGAGCTTCTCGTT
1 ATTGGCTCTCCGGAGCTTCTCGAT
*
55924648 AATGGCTCTCCGGAGCTTC
1 ATTGGCTCTCCGGAGCTTC
55924667 CTATTACATA
Statistics
Matches: 50, Mismatches: 15, Indels: 6
0.70 0.21 0.08
Matches are distributed among these distances:
23 1 0.02
24 31 0.62
25 17 0.34
26 1 0.02
ACGTcount: A:0.15, C:0.26, G:0.23, T:0.36
Consensus pattern (24 bp):
ATTGGCTCTCCGGAGCTTCTCGAT
Found at i:55948086 original size:33 final size:34
Alignment explanation
Indices: 55948035--55948243 Score: 140
Period size: 33 Copynumber: 5.7 Consensus size: 34
55948025 TTATCCGTTA
* *
55948035 TCGGTGGATTCAGCACTTAGCAACCACCAGTGAT
1 TCGGTGGAATCAGCACTTAGCAACCACCAATGAT
55948069 TCGG-GGAATCAGCACTTAGCAACCCCTTTCACATTCAATGAT
1 TCGGTGGAATCAGCACTTAGCAA---C---CAC---CAATGAT
* *
55948111 ACGGTGGAATCAGCACTTAGCAACCACCAATGAA
1 TCGGTGGAATCAGCACTTAGCAACCACCAATGAT
*
55948145 TCGG-GGAATCAGCACTTAGCAACCCCTTTCACATTTAAGAT
1 TCGGTGGAATCAGCACTTAGCAACCAC---CA-A--T--GAT
*
55948186 AT-GGTGGGATCAGCACTTAGCAACCACCAATGAAT
1 -TCGGTGGAATCAGCACTTAGCAACCACCAATG-AT
* *
55948221 T-GG-GGAATTAACACTTAGCAACC
1 TCGGTGGAATCAGCACTTAGCAACC
55948244 CTTGGGGGAA
Statistics
Matches: 142, Mismatches: 12, Indels: 43
0.72 0.06 0.22
Matches are distributed among these distances:
33 55 0.39
34 17 0.12
35 2 0.01
36 4 0.03
37 4 0.03
38 1 0.01
39 6 0.04
40 1 0.01
41 4 0.03
42 30 0.21
43 18 0.13
ACGTcount: A:0.32, C:0.26, G:0.20, T:0.22
Consensus pattern (34 bp):
TCGGTGGAATCAGCACTTAGCAACCACCAATGAT
Found at i:55948162 original size:76 final size:75
Alignment explanation
Indices: 55948036--55948244 Score: 328
Period size: 76 Copynumber: 2.8 Consensus size: 75
55948026 TATCCGTTAT
* * *
55948036 CGGTGGATTCAGCACTTAGCAACCACCAGTGATTCGGGGAATCAGCACTTAGCAACCCCTTTCAC
1 CGGTGGAATCAGCACTTAGCAACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTTTCAC
55948101 ATTCAATGATA
66 ATTCAA-GATA
55948112 CGGTGGAATCAGCACTTAGCAACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTTTCAC
1 CGGTGGAATCAGCACTTAGCAACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTTTCAC
*
55948177 ATTTAAGATA
66 ATTCAAGATA
* * * * *
55948187 TGGTGGGATCAGCACTTAGCAACCACCAATGAATTGGGGAATTAACACTTAGCAACCC
1 CGGTGGAATCAGCACTTAGCAACCACCAATGAATCGGGGAATCAGCACTTAGCAACCC
55948245 TTGGGGGAAT
Statistics
Matches: 124, Mismatches: 9, Indels: 1
0.93 0.07 0.01
Matches are distributed among these distances:
75 57 0.46
76 67 0.54
ACGTcount: A:0.32, C:0.26, G:0.20, T:0.22
Consensus pattern (75 bp):
CGGTGGAATCAGCACTTAGCAACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTTTCAC
ATTCAAGATA
Found at i:55948299 original size:101 final size:101
Alignment explanation
Indices: 55948147--55948345 Score: 310
Period size: 101 Copynumber: 2.0 Consensus size: 101
55948137 CCAATGAATC
* * * *
55948147 GGGGAATCAGCACTTAGCAACCCCTTTCACATTTAAGATATGGTGGGATCAGCACTTAGCAACCA
1 GGGGAATCAGCACTTAGCAACCCCCTTCACATTTAAAATACGGTGGAATCAGCACTTAGCAACCA
* *
55948212 CCAATGAATTGGGGAATTAACACTTAGCAACCCTTG
66 CCAATGAATCGGGGAATCAACACTTAGCAACCCTTG
*
55948248 GGGGAATC-GACACTTAGCAACCCCCTTCACATTTAAAATACGGTGGAATCAGCACTTAGCAATC
1 GGGGAATCAG-CACTTAGCAACCCCCTTCACATTTAAAATACGGTGGAATCAGCACTTAGCAACC
*
55948312 ACCAATGAATCGGGGAATCAGCACTTAGCAACCC
65 ACCAATGAATCGGGGAATCAACACTTAGCAACCC
55948346 CCTTTATATT
Statistics
Matches: 89, Mismatches: 8, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
100 1 0.01
101 88 0.99
ACGTcount: A:0.33, C:0.26, G:0.20, T:0.22
Consensus pattern (101 bp):
GGGGAATCAGCACTTAGCAACCCCCTTCACATTTAAAATACGGTGGAATCAGCACTTAGCAACCA
CCAATGAATCGGGGAATCAACACTTAGCAACCCTTG
Found at i:55950104 original size:24 final size:24
Alignment explanation
Indices: 55950059--55950106 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
55950049 TATATGTCTA
* * *
55950059 TTCGGAGCTTCCCGTTAATGGCTC
1 TTCGGAGCTACCCATCAATGGCTC
*
55950083 TTCGGAGCTACCCATCATTGGCTC
1 TTCGGAGCTACCCATCAATGGCTC
55950107 GCATGAGCTT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.15, C:0.31, G:0.23, T:0.31
Consensus pattern (24 bp):
TTCGGAGCTACCCATCAATGGCTC
Found at i:55951775 original size:26 final size:26
Alignment explanation
Indices: 55951746--55951818 Score: 87
Period size: 26 Copynumber: 2.8 Consensus size: 26
55951736 CCCGTTATTT
55951746 GGCTCTTCGTGAGCTTTCCGATTAAA
1 GGCTCTTCGTGAGCTTTCCGATTAAA
* *
55951772 GGCTCTTTGTGAGC-TTCCTGATTAAT
1 GGCTCTTCGTGAGCTTTCC-GATTAAA
* *
55951798 GGCTCTTC-AGAGTTTTCCGAT
1 GGCTCTTCGTGAGCTTTCCGAT
55951819 ATGGCTCTCT
Statistics
Matches: 40, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
25 10 0.25
26 30 0.75
ACGTcount: A:0.16, C:0.22, G:0.23, T:0.38
Consensus pattern (26 bp):
GGCTCTTCGTGAGCTTTCCGATTAAA
Found at i:55954026 original size:14 final size:14
Alignment explanation
Indices: 55954009--55954037 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
55953999 TATACATCAA
55954009 AACATACCATCACT
1 AACATACCATCACT
55954023 AACATACCATCACT
1 AACATACCATCACT
55954037 A
1 A
55954038 GCCATTCCAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.45, C:0.34, G:0.00, T:0.21
Consensus pattern (14 bp):
AACATACCATCACT
Found at i:55955801 original size:27 final size:27
Alignment explanation
Indices: 55955166--55955803 Score: 742
Period size: 27 Copynumber: 23.6 Consensus size: 27
55955156 AATCGGCCTC
*
55955166 TAAAATGA-CTGAAATACCCTCGATGGG
1 TAAAATGATC-GAAATACCCTCGAAGGG
* *
55955193 TAAAATTATCGAAATACCCTCGATGGG
1 TAAAATGATCGAAATACCCTCGAAGGG
* *
55955220 TAAAATGATCGAAATACCATCAAAGGG
1 TAAAATGATCGAAATACCCTCGAAGGG
55955247 TAAAATGA-CTGAAATACCCTCGAAGGG
1 TAAAATGATC-GAAATACCCTCGAAGGG
*
55955274 TAAAATGATCGAAATACCCTTGAAGGG
1 TAAAATGATCGAAATACCCTCGAAGGG
*
55955301 TAAAATGATCGAAATACCC-CTGTAGGG
1 TAAAATGATCGAAATACCCTC-GAAGGG
* *
55955328 TAAAATGATCGAAAGACCCTCGAAGGA
1 TAAAATGATCGAAATACCCTCGAAGGG
*
55955355 TAGAATGA-CGGAAATACCCTCGAAGGG
1 TAAAATGATC-GAAATACCCTCGAAGGG
* * *
55955382 TAAAATGACCGAAATACCCCCAAAGGG
1 TAAAATGATCGAAATACCCTCGAAGGG
*
55955409 TAAAATGATCGAAATACCCTTGAAGGG
1 TAAAATGATCGAAATACCCTCGAAGGG
* **
55955436 TAAAATGATCGAAATACTCTCGAAATG
1 TAAAATGATCGAAATACCCTCGAAGGG
*
55955463 TAAAATGACCGAAATACCCTCGAAGGG
1 TAAAATGATCGAAATACCCTCGAAGGG
* *
55955490 TAAAAT-AACTGAAATACTCAT-GAAGGG
1 TAAAATGATC-GAAATAC-CCTCGAAGGG
55955517 TAAAATGA-CTGAAATACCCTCGAAGGG
1 TAAAATGATC-GAAATACCCTCGAAGGG
55955544 TAAAATGATCGAAATACCCTCGAAGGG
1 TAAAATGATCGAAATACCCTCGAAGGG
*
55955571 TAAAATGACCGAAATACCC-CTGAAGGG
1 TAAAATGATCGAAATACCCTC-GAAGGG
* *
55955598 TAAAATGACCGAAATACCCTTGAAGGG
1 TAAAATGATCGAAATACCCTCGAAGGG
* *
55955625 TAAAATGATAGAAATACCCCCGAAGGG
1 TAAAATGATCGAAATACCCTCGAAGGG
55955652 TAAAATGA-CTGAAATACCCTCGATA-GG
1 TAAAATGATC-GAAATACCCTCGA-AGGG
**
55955679 TAAAATGATCGAAATACCCTTTAATGGG
1 TAAAATGATCGAAATACCCTCGAA-GGG
* * * *
55955707 TAAATTTA-CTAAAATACCCTCGATGGG
1 TAAAATGATC-GAAATACCCTCGAAGGG
* ** *
55955734 TAAAATTATTAAAATACCCCCGAAGGG
1 TAAAATGATCGAAATACCCTCGAAGGG
*
55955761 TAAAATGA-CTGAAATACCCTCGATGGG
1 TAAAATGATC-GAAATACCCTCGAAGGG
*
55955788 TAAAATTATCGAAATA
1 TAAAATGATCGAAATA
55955804 TCCTTATATG
Statistics
Matches: 528, Mismatches: 60, Indels: 46
0.83 0.09 0.07
Matches are distributed among these distances:
26 8 0.02
27 491 0.93
28 29 0.05
ACGTcount: A:0.42, C:0.18, G:0.20, T:0.21
Consensus pattern (27 bp):
TAAAATGATCGAAATACCCTCGAAGGG
Found at i:55956118 original size:26 final size:27
Alignment explanation
Indices: 55956021--55956116 Score: 108
Period size: 26 Copynumber: 3.7 Consensus size: 27
55956011 ACAAATATTG
55956021 TTACTGGCAGCTTTGCTGCGTTACTGA
1 TTACTGGCAGCTTTGCTGCGTTACTGA
* * ** *
55956048 -TACTGGCAACTCTATTGCATTACTG-
1 TTACTGGCAGCTTTGCTGCGTTACTGA
* *
55956073 TTATTGGCAGCTTTGCTGTGTTAC-GA
1 TTACTGGCAGCTTTGCTGCGTTACTGA
55956099 TTACTGGCAGCTTTGCTG
1 TTACTGGCAGCTTTGCTG
55956117 TGATATTGGT
Statistics
Matches: 54, Mismatches: 13, Indels: 5
0.75 0.18 0.07
Matches are distributed among these distances:
25 1 0.02
26 53 0.98
ACGTcount: A:0.17, C:0.21, G:0.24, T:0.39
Consensus pattern (27 bp):
TTACTGGCAGCTTTGCTGCGTTACTGA
Found at i:55956263 original size:30 final size:30
Alignment explanation
Indices: 55956224--55956311 Score: 113
Period size: 30 Copynumber: 2.9 Consensus size: 30
55956214 ACTGCATTTG
*
55956224 CACTATTACTGTATTGGGCTAAGGCCCACA
1 CACTGTTACTGTATTGGGCTAAGGCCCACA
* *
55956254 CTCTGTTACTGTATTGGGCTATGGCCCACA
1 CACTGTTACTGTATTGGGCTAAGGCCCACA
* * * *
55956284 CAGTGCTACTGTATAGGGCTCAGGCCCA
1 CACTGTTACTGTATTGGGCTAAGGCCCA
55956312 AATTGATTCT
Statistics
Matches: 49, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 49 1.00
ACGTcount: A:0.22, C:0.27, G:0.24, T:0.27
Consensus pattern (30 bp):
CACTGTTACTGTATTGGGCTAAGGCCCACA
Found at i:55957454 original size:25 final size:25
Alignment explanation
Indices: 55957423--55957470 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
55957413 CAAGCGAACC
55957423 ATATCAGGA-AGCTCACAAAGAGCCT
1 ATATCAGGATA-CTCACAAAGAGCCT
*
55957448 ATATCAGGATACTCATAAAGAGC
1 ATATCAGGATACTCACAAAGAGC
55957471 TGTGGTATGT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 20 0.95
26 1 0.05
ACGTcount: A:0.42, C:0.21, G:0.19, T:0.19
Consensus pattern (25 bp):
ATATCAGGATACTCACAAAGAGCCT
Found at i:55964482 original size:25 final size:24
Alignment explanation
Indices: 55964449--55964500 Score: 70
Period size: 25 Copynumber: 2.1 Consensus size: 24
55964439 TGTTCAAGCT
55964449 AGCCATATCAGGA-AGCTCACAAAG
1 AGCCATATCAGGACA-CTCACAAAG
*
55964473 AGCCTATATCAGGACACTCATAAAG
1 AGCC-ATATCAGGACACTCACAAAG
55964498 AGC
1 AGC
55964501 TGTAGTATGT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
24 4 0.16
25 20 0.80
26 1 0.04
ACGTcount: A:0.40, C:0.25, G:0.19, T:0.15
Consensus pattern (24 bp):
AGCCATATCAGGACACTCACAAAG
Found at i:55965315 original size:25 final size:25
Alignment explanation
Indices: 55965286--55965338 Score: 106
Period size: 25 Copynumber: 2.1 Consensus size: 25
55965276 TTTCATTTTC
55965286 TACCATAAATTTCAAAATTTCAACA
1 TACCATAAATTTCAAAATTTCAACA
55965311 TACCATAAATTTCAAAATTTCAACA
1 TACCATAAATTTCAAAATTTCAACA
55965336 TAC
1 TAC
55965339 TCATCCATGG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.47, C:0.21, G:0.00, T:0.32
Consensus pattern (25 bp):
TACCATAAATTTCAAAATTTCAACA
Found at i:55978622 original size:27 final size:27
Alignment explanation
Indices: 55978584--55978663 Score: 106
Period size: 27 Copynumber: 3.0 Consensus size: 27
55978574 TTGCAGTTCA
*
55978584 TCTCACAGCTTGCCACTTGTGGAGACT
1 TCTCGCAGCTTGCCACTTGTGGAGACT
* *
55978611 TCTCGTAGCTTGCCACTTGTGAAGACT
1 TCTCGCAGCTTGCCACTTGTGGAGACT
* * *
55978638 TCTCGCAGCTCGTCACTTGTAGAGAC
1 TCTCGCAGCTTGCCACTTGTGGAGAC
55978664 ATCTTGCAAT
Statistics
Matches: 45, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 45 1.00
ACGTcount: A:0.19, C:0.29, G:0.23, T:0.30
Consensus pattern (27 bp):
TCTCGCAGCTTGCCACTTGTGGAGACT
Found at i:55988939 original size:19 final size:19
Alignment explanation
Indices: 55988917--55988979 Score: 58
Period size: 19 Copynumber: 3.3 Consensus size: 19
55988907 AAAATTCAAA
*
55988917 AAAATAAAAAATTATTTTT
1 AAAATAAAAAATCATTTTT
* *
55988936 AAAAATTAAAAATCA--TTA
1 -AAAATAAAAAATCATTTTT
55988954 AAATTATAAAAAATCATTTTT
1 AAA--ATAAAAAATCATTTTT
55988975 AAAAT
1 AAAAT
55988980 TTAAAAAATT
Statistics
Matches: 34, Mismatches: 5, Indels: 9
0.71 0.10 0.19
Matches are distributed among these distances:
17 3 0.09
18 2 0.06
19 12 0.35
20 12 0.35
21 5 0.15
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.37
Consensus pattern (19 bp):
AAAATAAAAAATCATTTTT
Found at i:55988941 original size:39 final size:41
Alignment explanation
Indices: 55988886--55988998 Score: 121
Period size: 39 Copynumber: 2.9 Consensus size: 41
55988876 ATCAACATTT
55988886 AATTAATTTTTAAAAATTTTAAAAATTCA-AAAA-AATAAAA
1 AATT-ATTTTTAAAAATTTTAAAAATTCATAAAATAATAAAA
*
55988926 AATTATTTTTAAAAA--TTAAAAA-TCATTAAAATTATAAAA
1 AATTATTTTTAAAAATTTTAAAAATTCA-TAAAATAATAAAA
* * * *
55988965 AATCATTTTT-AAAATTTAAAAAATTAATTAAATA
1 AATTATTTTTAAAAATTTTAAAAATTCATAAAATA
55988999 TTAACATCTC
Statistics
Matches: 61, Mismatches: 6, Indels: 12
0.77 0.08 0.15
Matches are distributed among these distances:
36 3 0.05
37 7 0.11
38 8 0.13
39 26 0.43
40 15 0.25
41 2 0.03
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (41 bp):
AATTATTTTTAAAAATTTTAAAAATTCATAAAATAATAAAA
Found at i:55995496 original size:18 final size:18
Alignment explanation
Indices: 55995452--55995496 Score: 65
Period size: 18 Copynumber: 2.5 Consensus size: 18
55995442 TAACCTTTAA
55995452 CCTTTAACCTTTCATCTT
1 CCTTTAACCTTTCATCTT
*
55995470 CCTTAAACCTTTCATC-T
1 CCTTTAACCTTTCATCTT
55995487 CCTTGTAACC
1 CCTT-TAACC
55995497 CTTTTTTTCT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
17 5 0.21
18 19 0.79
ACGTcount: A:0.20, C:0.36, G:0.02, T:0.42
Consensus pattern (18 bp):
CCTTTAACCTTTCATCTT
Found at i:55996648 original size:18 final size:18
Alignment explanation
Indices: 55996625--55996660 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
55996615 AAAAAAAGTG
55996625 CGATTGATAGTGTGATTT
1 CGATTGATAGTGTGATTT
55996643 CGATTGATAGTGTGATTT
1 CGATTGATAGTGTGATTT
55996661 GGCTCCGACC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.22, C:0.06, G:0.28, T:0.44
Consensus pattern (18 bp):
CGATTGATAGTGTGATTT
Found at i:56005257 original size:22 final size:21
Alignment explanation
Indices: 56005217--56005258 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
56005207 CAATTATCAT
*
56005217 TCAACCAAAAACTCACCTAAA
1 TCAACCAAAAACTAACCTAAA
56005238 TCAACCAAAAACTAAGCCTAA
1 TCAACCAAAAACTAA-CCTAA
56005259 GCTATATTCT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 14 0.74
22 5 0.26
ACGTcount: A:0.52, C:0.31, G:0.02, T:0.14
Consensus pattern (21 bp):
TCAACCAAAAACTAACCTAAA
Found at i:56006486 original size:28 final size:28
Alignment explanation
Indices: 56006450--56006726 Score: 86
Period size: 29 Copynumber: 9.9 Consensus size: 28
56006440 GTCTGCCTAT
*
56006450 GGCATTCCTTTAACAGAGATGGCCACAAA
1 GGCA-TCCTTTAACAGAGATAGCCACAAA
* *
56006479 GGCATCCTTTTGACAGAGATAGCCATAAA
1 GGCATCC-TTTAACAGAGATAGCCACAAA
* * * *
56006508 GACATCCTTTTGACAGAGGTTGCC-CTAAAA
1 GGCATCC-TTTAACAGAGATAGCCAC--AAA
* * * *
56006538 TG-ATTCATTTAACTGAGAAAGCCACAAA
1 GGCA-TCCTTTAACAGAGATAGCCACAAA
** * * * *
56006566 GATATTCGTTTAAAAAAGATAGCCATAAA
1 GGCA-TCCTTTAACAGAGATAGCCACAAA
* * * * * *
56006595 TGCAGCCTTTTAACAAAGATGGCTATAAA
1 GGCATCC-TTTAACAGAGATAGCCACAAA
* * * *
56006624 GGCTTTCTTATAACAGAGATTGACACAAA
1 GGCATCCTT-TAACAGAGATAGCCACAAA
* * * * *
56006653 GGCTTCCATT--CAAAGATAACTACAAA
1 GGCATCCTTTAACAGAGATAGCCACAAA
*
56006679 GGCTTCCATTT---AGAGATAGCCACAAA
1 GGCATCC-TTTAACAGAGATAGCCACAAA
* *
56006705 GGCTTCCTTT--TAGAGATAGCCA
1 GGCATCCTTTAACAGAGATAGCCA
56006727 TAAAAGTGTC
Statistics
Matches: 187, Mismatches: 51, Indels: 23
0.72 0.20 0.09
Matches are distributed among these distances:
25 3 0.02
26 48 0.26
27 2 0.01
28 10 0.05
29 118 0.63
30 6 0.03
ACGTcount: A:0.37, C:0.20, G:0.18, T:0.26
Consensus pattern (28 bp):
GGCATCCTTTAACAGAGATAGCCACAAA
Found at i:56006536 original size:29 final size:29
Alignment explanation
Indices: 56006462--56006525 Score: 101
Period size: 29 Copynumber: 2.2 Consensus size: 29
56006452 CATTCCTTTA
* * *
56006462 ACAGAGATGGCCACAAAGGCATCCTTTTG
1 ACAGAGATAGCCATAAAGACATCCTTTTG
56006491 ACAGAGATAGCCATAAAGACATCCTTTTG
1 ACAGAGATAGCCATAAAGACATCCTTTTG
56006520 ACAGAG
1 ACAGAG
56006526 GTTGCCCTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.36, C:0.22, G:0.22, T:0.20
Consensus pattern (29 bp):
ACAGAGATAGCCATAAAGACATCCTTTTG
Found at i:56006716 original size:26 final size:26
Alignment explanation
Indices: 56006638--56006726 Score: 115
Period size: 26 Copynumber: 3.4 Consensus size: 26
56006628 TTCTTATAAC
* * *
56006638 AGAGATTGACACAAAGGCTTCCATTC
1 AGAGATAGCCACAAAGGCTTCCATTT
* * *
56006664 AAAGATAACTACAAAGGCTTCCATTT
1 AGAGATAGCCACAAAGGCTTCCATTT
*
56006690 AGAGATAGCCACAAAGGCTTCCTTTT
1 AGAGATAGCCACAAAGGCTTCCATTT
56006716 AGAGATAGCCA
1 AGAGATAGCCA
56006727 TAAAAGTGTC
Statistics
Matches: 53, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 53 1.00
ACGTcount: A:0.37, C:0.21, G:0.18, T:0.24
Consensus pattern (26 bp):
AGAGATAGCCACAAAGGCTTCCATTT
Found at i:56017350 original size:14 final size:14
Alignment explanation
Indices: 56017315--56017353 Score: 53
Period size: 14 Copynumber: 2.8 Consensus size: 14
56017305 CTCCAAACTG
*
56017315 AGGACTTAACACTA
1 AGGACTTAACTCTA
56017329 AGGACTTAACTCTA
1 AGGACTTAACTCTA
56017343 A-GAGCTTAACT
1 AGGA-CTTAACT
56017354 TTAAAGATTC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 2 0.09
14 21 0.91
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (14 bp):
AGGACTTAACTCTA
Found at i:56017811 original size:16 final size:17
Alignment explanation
Indices: 56017790--56017827 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
56017780 GTTTCTTACG
* *
56017790 ATATAAATTACATAAT-
1 ATATAAAATAAATAATA
56017806 ATATAAAATAAATAATA
1 ATATAAAATAAATAATA
56017823 ATATA
1 ATATA
56017828 TTAAAAATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 14 0.74
17 5 0.26
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.34
Consensus pattern (17 bp):
ATATAAAATAAATAATA
Found at i:56017835 original size:21 final size:21
Alignment explanation
Indices: 56017792--56017833 Score: 61
Period size: 19 Copynumber: 2.0 Consensus size: 21
56017782 TTCTTACGAT
56017792 ATAAATTACATAATATATAAA
1 ATAAATTACATAATATATAAA
56017813 ATAAA-TA-ATAATATATTAAA
1 ATAAATTACATAATATA-TAAA
56017833 A
1 A
56017834 ATTTGAAAAC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
19 8 0.40
20 7 0.35
21 5 0.25
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.33
Consensus pattern (21 bp):
ATAAATTACATAATATATAAA
Found at i:56021488 original size:14 final size:14
Alignment explanation
Indices: 56021466--56021495 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
56021456 AAGATTAGGC
56021466 TTTTCTTTCTCTTT
1 TTTTCTTTCTCTTT
*
56021480 TTTTTTTTCTCTTT
1 TTTTCTTTCTCTTT
56021494 TT
1 TT
56021496 GCGGAGAGAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (14 bp):
TTTTCTTTCTCTTT
Found at i:56024938 original size:9 final size:9
Alignment explanation
Indices: 56024917--56024946 Score: 51
Period size: 9 Copynumber: 3.2 Consensus size: 9
56024907 TAAAAATTAG
56024917 TTATAAGAAA
1 TTATAA-AAA
56024927 TTATAAAAA
1 TTATAAAAA
56024936 TTATAAAAA
1 TTATAAAAA
56024945 TT
1 TT
56024947 GGGTAAAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 14 0.70
10 6 0.30
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.37
Consensus pattern (9 bp):
TTATAAAAA
Found at i:56026251 original size:9 final size:9
Alignment explanation
Indices: 56026194--56026358 Score: 72
Period size: 9 Copynumber: 17.3 Consensus size: 9
56026184 CTTTACCAAA
*
56026194 GTATGTTAT
1 GTATATTAT
56026203 GTATATTACT
1 GTATATTA-T
56026213 GT-TATGTAT
1 GTATAT-TAT
*
56026222 GTCTATTAT
1 GTATATTAT
*
56026231 GTTTAATGTAT
1 GTAT-AT-TAT
*
56026242 GTCTATTAT
1 GTATATTAT
*
56026251 GTATGTTAT
1 GTATATTAT
56026260 GTATATTATT
1 GTATATTA-T
56026270 GT-TATGTAT
1 GTATAT-TAT
*
56026279 GAGATTATTAT
1 G-TA-TATTAT
*
56026290 GTGGTA-TAT
1 GT-ATATTAT
*
56026299 -TACTTTTAT
1 GTA-TATTAT
56026308 GCT-TCATGTAT
1 G-TAT-AT-TAT
56026319 GTATATTAT
1 GTATATTAT
*
56026328 GTATGTTAT
1 GTATATTAT
56026337 GTATATTACT
1 GTATATTA-T
56026347 GT-TATGTAT
1 GTATAT-TAT
56026356 GTA
1 GTA
56026359 AGTTATGTGG
Statistics
Matches: 121, Mismatches: 14, Indels: 41
0.69 0.08 0.23
Matches are distributed among these distances:
8 2 0.02
9 72 0.60
10 28 0.23
11 16 0.13
12 3 0.02
ACGTcount: A:0.25, C:0.04, G:0.17, T:0.53
Consensus pattern (9 bp):
GTATATTAT
Found at i:56026985 original size:19 final size:20
Alignment explanation
Indices: 56026953--56026996 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
56026943 CATTATTGAA
* *
56026953 TTTATGAGA-TTTTTTAAGT
1 TTTATGAGAGTTTTGTAAGC
*
56026972 TTTATGATAGTTTTGTAAGC
1 TTTATGAGAGTTTTGTAAGC
56026992 TTTAT
1 TTTAT
56026997 AGTTAAATAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 8 0.38
20 13 0.62
ACGTcount: A:0.25, C:0.02, G:0.16, T:0.57
Consensus pattern (20 bp):
TTTATGAGAGTTTTGTAAGC
Found at i:56028865 original size:29 final size:29
Alignment explanation
Indices: 56028831--56028890 Score: 102
Period size: 29 Copynumber: 2.1 Consensus size: 29
56028821 GTTTATGTAA
*
56028831 GTATATTATGTATGTTATGTTTAATGCAT
1 GTATATTATGTATGTTATATTTAATGCAT
*
56028860 GTATATTATGTATGTTATATTTAATGTAT
1 GTATATTATGTATGTTATATTTAATGCAT
56028889 GT
1 GT
56028891 TATGTTTAGC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.28, C:0.02, G:0.17, T:0.53
Consensus pattern (29 bp):
GTATATTATGTATGTTATATTTAATGCAT
Found at i:56028888 original size:16 final size:16
Alignment explanation
Indices: 56028838--56028898 Score: 74
Period size: 16 Copynumber: 4.0 Consensus size: 16
56028828 TAAGTATATT
*
56028838 ATGTATGTTATGTTTA
1 ATGTATGTTATATTTA
*
56028854 ATGCATG-TATA-TT-
1 ATGTATGTTATATTTA
56028867 ATGTATGTTATATTTA
1 ATGTATGTTATATTTA
*
56028883 ATGTATGTTATGTTTA
1 ATGTATGTTATATTTA
56028899 GCACTGTTTA
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
13 6 0.16
14 6 0.16
15 5 0.13
16 21 0.55
ACGTcount: A:0.28, C:0.02, G:0.16, T:0.54
Consensus pattern (16 bp):
ATGTATGTTATATTTA
Found at i:56031076 original size:25 final size:25
Alignment explanation
Indices: 56031048--56031095 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
56031038 ATTGGCTTGT
* *
56031048 ATGAGCTTTCTGTTACATGGCTCAC
1 ATGAACTTCCTGTTACATGGCTCAC
*
56031073 ATGAACTTCCTGTTATATGGCTC
1 ATGAACTTCCTGTTACATGGCTC
56031096 GAAAGAGCTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.21, C:0.23, G:0.19, T:0.38
Consensus pattern (25 bp):
ATGAACTTCCTGTTACATGGCTCAC
Found at i:56031106 original size:25 final size:25
Alignment explanation
Indices: 56031050--56031117 Score: 66
Period size: 25 Copynumber: 2.7 Consensus size: 25
56031040 TGGCTTGTAT
* *
56031050 GAGCTTTCTGTTACATGGCTCACAT
1 GAGCTTCCTGTTACATGGCTCACAA
* *
56031075 GAACTTCCTGTTATATGGCTCGA-AA
1 GAGCTTCCTGTTACATGGCTC-ACAA
*
56031100 GAGCTTCCCGTTTACATG
1 GAGCTTCCTG-TTACATG
56031118 TTTGCATAAG
Statistics
Matches: 34, Mismatches: 7, Indels: 3
0.77 0.16 0.07
Matches are distributed among these distances:
25 27 0.79
26 7 0.21
ACGTcount: A:0.22, C:0.24, G:0.21, T:0.34
Consensus pattern (25 bp):
GAGCTTCCTGTTACATGGCTCACAA
Found at i:56034802 original size:24 final size:24
Alignment explanation
Indices: 56034755--56034810 Score: 67
Period size: 24 Copynumber: 2.3 Consensus size: 24
56034745 CAATTGGAAT
** *
56034755 AGCTCCAATAGCTCCTTTTTCACC
1 AGCTCCAATAGCTCCTACTCCACC
*
56034779 AGCTCCAGTAGCTCCTACTCCACC
1 AGCTCCAATAGCTCCTACTCCACC
*
56034803 AGCCCCAA
1 AGCTCCAA
56034811 CAACTCCTTC
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.23, C:0.43, G:0.11, T:0.23
Consensus pattern (24 bp):
AGCTCCAATAGCTCCTACTCCACC
Found at i:56038966 original size:21 final size:21
Alignment explanation
Indices: 56038922--56038971 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
56038912 TAGTTCTCAC
56038922 GAGCTTCTGTTAAACTCATAT
1 GAGCTTCTGTTAAACTCATAT
* * * *
56038943 GAGTTTCTGTTAAGCTCTTTT
1 GAGCTTCTGTTAAACTCATAT
56038964 GAGCTTCT
1 GAGCTTCT
56038972 ATTTAACCCT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.20, C:0.18, G:0.18, T:0.44
Consensus pattern (21 bp):
GAGCTTCTGTTAAACTCATAT
Found at i:56039016 original size:21 final size:21
Alignment explanation
Indices: 56038952--56039027 Score: 57
Period size: 21 Copynumber: 3.6 Consensus size: 21
56038942 TGAGTTTCTG
* * *
56038952 TTAAGCTCTTTTGAGCTTCTA
1 TTAAGCCCTTATGAGCTTCCA
* *
56038973 TTTAA-CCCTTAT-AGGTTTTCA
1 -TTAAGCCCTTATGA-GCTTCCA
*
56038994 TTAAGCTCTTATGAGCTTCCA
1 TTAAGCCCTTATGAGCTTCCA
*
56039015 TTAACCCCTTATG
1 TTAAGCCCTTATG
56039028 GGTTTCTGTT
Statistics
Matches: 41, Mismatches: 10, Indels: 7
0.71 0.17 0.12
Matches are distributed among these distances:
20 5 0.12
21 31 0.76
22 5 0.12
ACGTcount: A:0.22, C:0.22, G:0.12, T:0.43
Consensus pattern (21 bp):
TTAAGCCCTTATGAGCTTCCA
Found at i:56039047 original size:42 final size:42
Alignment explanation
Indices: 56038940--56039055 Score: 128
Period size: 42 Copynumber: 2.8 Consensus size: 42
56038930 GTTAAACTCA
* * *
56038940 TATGAGTTTCTGTTAAGCTCTTTTGAGCTTCTATTTAACCCT
1 TATGGGTTTCTGTTAAGCTCTTATGAGCTTCCATTTAACCCT
* *
56038982 TATAGGTTT-TCATTAAGCTCTTATGAGCTTCCA-TTAACCCCT
1 TATGGGTTTCT-GTTAAGCTCTTATGAGCTTCCATTTAA-CCCT
* * *
56039024 TATGGGTTTCTGTTTAGCACTTATGTGCTTCC
1 TATGGGTTTCTGTTAAGCTCTTATGAGCTTCC
56039056 GTTCAGCCTT
Statistics
Matches: 61, Mismatches: 10, Indels: 6
0.79 0.13 0.08
Matches are distributed among these distances:
41 5 0.08
42 55 0.90
43 1 0.02
ACGTcount: A:0.19, C:0.21, G:0.16, T:0.45
Consensus pattern (42 bp):
TATGGGTTTCTGTTAAGCTCTTATGAGCTTCCATTTAACCCT
Found at i:56046690 original size:42 final size:42
Alignment explanation
Indices: 56046640--56046772 Score: 158
Period size: 42 Copynumber: 3.2 Consensus size: 42
56046630 TAGCTCGCAC
* * * * *
56046640 GAGCTTCTGTTAAACTCATATGAGTTTTTGTTCAGCTCTTTT
1 GAGCTTCTGTTAAACCCTTATGGGTTTTTGTTAAGCTCTTAT
* **
56046682 GAGCTTCTGTTTAACCCTTATGGGTTTTCATTAAGCTCTTAT
1 GAGCTTCTGTTAAACCCTTATGGGTTTTTGTTAAGCTCTTAT
* * *
56046724 GAGCTTCTATTAAACCCTTATGGGTTTTTGTTTAGCACTTAT
1 GAGCTTCTGTTAAACCCTTATGGGTTTTTGTTAAGCTCTTAT
*
56046766 GTGCTTC
1 GAGCTTC
56046773 CGTTCAGCCT
Statistics
Matches: 76, Mismatches: 15, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
42 76 1.00
ACGTcount: A:0.19, C:0.18, G:0.17, T:0.46
Consensus pattern (42 bp):
GAGCTTCTGTTAAACCCTTATGGGTTTTTGTTAAGCTCTTAT
Found at i:56046692 original size:21 final size:21
Alignment explanation
Indices: 56046640--56046692 Score: 52
Period size: 21 Copynumber: 2.5 Consensus size: 21
56046630 TAGCTCGCAC
56046640 GAGCTTCTGTTAAACTCATAT
1 GAGCTTCTGTTAAACTCATAT
* * * * * *
56046661 GAGTTTTTGTTCAGCTCTTTT
1 GAGCTTCTGTTAAACTCATAT
56046682 GAGCTTCTGTT
1 GAGCTTCTGTT
56046693 TAACCCTTAT
Statistics
Matches: 24, Mismatches: 8, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.17, C:0.17, G:0.19, T:0.47
Consensus pattern (21 bp):
GAGCTTCTGTTAAACTCATAT
Found at i:56046722 original size:21 final size:22
Alignment explanation
Indices: 56046694--56046751 Score: 66
Period size: 21 Copynumber: 2.7 Consensus size: 22
56046684 GCTTCTGTTT
56046694 AACCCTTATGGGTTTTC-ATTA
1 AACCCTTATGGGTTTTCTATTA
* * * *
56046715 AGCTCTTATGAG-CTTCTATTA
1 AACCCTTATGGGTTTTCTATTA
56046736 AACCCTTATGGGTTTT
1 AACCCTTATGGGTTTT
56046752 TGTTTAGCAC
Statistics
Matches: 27, Mismatches: 8, Indels: 3
0.71 0.21 0.08
Matches are distributed among these distances:
20 3 0.11
21 22 0.81
22 2 0.07
ACGTcount: A:0.22, C:0.19, G:0.16, T:0.43
Consensus pattern (22 bp):
AACCCTTATGGGTTTTCTATTA
Found at i:56048290 original size:9 final size:9
Alignment explanation
Indices: 56048276--56048303 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
56048266 TGTTTTTTAT
56048276 TATTAAAAA
1 TATTAAAAA
56048285 TATTAAAAA
1 TATTAAAAA
56048294 TATTAAAAA
1 TATTAAAAA
56048303 T
1 T
56048304 TTTCCTAGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (9 bp):
TATTAAAAA
Found at i:56049510 original size:31 final size:31
Alignment explanation
Indices: 56049449--56049525 Score: 86
Period size: 31 Copynumber: 2.5 Consensus size: 31
56049439 AAAAATATTT
* *
56049449 TTTAAATGACTAAAATAAGAACTACCTAAAA
1 TTTAAATAACTAAAATAAGAAATACCTAAAA
*
56049480 TTTAAATAACTAAAATAA-AAATACATTAAAA
1 TTTAAATAACTAAAATAAGAAATAC-CTAAAA
* *
56049511 GTTAAATTAC-AAAAT
1 TTTAAATAACTAAAAT
56049526 TACAAAGATT
Statistics
Matches: 40, Mismatches: 5, Indels: 3
0.83 0.10 0.06
Matches are distributed among these distances:
30 10 0.25
31 30 0.75
ACGTcount: A:0.58, C:0.09, G:0.04, T:0.29
Consensus pattern (31 bp):
TTTAAATAACTAAAATAAGAAATACCTAAAA
Found at i:56058126 original size:15 final size:16
Alignment explanation
Indices: 56058096--56058126 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
56058086 TTTATTTCCA
56058096 ATTCCCTTTTTGTTTT
1 ATTCCCTTTTTGTTTT
56058112 ATTCCCTTTTT-TTTT
1 ATTCCCTTTTTGTTTT
56058127 CTTTTTGCAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 4 0.27
16 11 0.73
ACGTcount: A:0.06, C:0.19, G:0.03, T:0.71
Consensus pattern (16 bp):
ATTCCCTTTTTGTTTT
Found at i:56062988 original size:7 final size:7
Alignment explanation
Indices: 56062978--56063014 Score: 56
Period size: 7 Copynumber: 5.1 Consensus size: 7
56062968 GCTCATTTCT
56062978 CATCATC
1 CATCATC
56062985 CATCATC
1 CATCATC
56062992 CATCATC
1 CATCATC
*
56062999 CCTCATC
1 CATCATC
56063006 TCATCATC
1 -CATCATC
56063014 C
1 C
56063015 CTCTCATCTC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
7 21 0.78
8 6 0.22
ACGTcount: A:0.24, C:0.46, G:0.00, T:0.30
Consensus pattern (7 bp):
CATCATC
Found at i:56063032 original size:15 final size:16
Alignment explanation
Indices: 56062975--56063033 Score: 72
Period size: 14 Copynumber: 3.9 Consensus size: 16
56062965 AGAGCTCATT
*
56062975 TCTCATCATCC-ATCA
1 TCTCATCATCCTCTCA
56062990 TC-CATCATCC-CTCA
1 TCTCATCATCCTCTCA
56063004 TCTCATCATCCCTCTCA
1 TCTCATCAT-CCTCTCA
56063021 TCTC-TCATCCTCT
1 TCTCATCATCCTCT
56063034 TTCTCAACTC
Statistics
Matches: 40, Mismatches: 1, Indels: 6
0.85 0.02 0.13
Matches are distributed among these distances:
14 13 0.32
15 13 0.32
16 6 0.15
17 8 0.20
ACGTcount: A:0.19, C:0.46, G:0.00, T:0.36
Consensus pattern (16 bp):
TCTCATCATCCTCTCA
Found at i:56069699 original size:20 final size:20
Alignment explanation
Indices: 56069674--56069711 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
56069664 ATTTTTCTAG
56069674 TTTAAATTATTT-TGTTAAAT
1 TTTAAATT-TTTATGTTAAAT
56069694 TTTAAATTTTTATGTTAA
1 TTTAAATTTTTATGTTAA
56069712 TAAAGGGCGT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 3 0.18
20 14 0.82
ACGTcount: A:0.34, C:0.00, G:0.05, T:0.61
Consensus pattern (20 bp):
TTTAAATTTTTATGTTAAAT
Found at i:56073607 original size:17 final size:17
Alignment explanation
Indices: 56073587--56073627 Score: 61
Period size: 15 Copynumber: 2.6 Consensus size: 17
56073577 GAGTTCATTT
56073587 CTCATCATCTATCATCC
1 CTCATCATCTATCATCC
56073604 CTCATC-TC-ATCATCC
1 CTCATCATCTATCATCC
56073619 CTC-TCATCT
1 CTCATCATCT
56073628 CTTATCCTCT
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
14 2 0.09
15 12 0.55
16 2 0.09
17 6 0.27
ACGTcount: A:0.20, C:0.44, G:0.00, T:0.37
Consensus pattern (17 bp):
CTCATCATCTATCATCC
Found at i:56073639 original size:17 final size:17
Alignment explanation
Indices: 56073586--56073640 Score: 51
Period size: 17 Copynumber: 3.2 Consensus size: 17
56073576 AGAGTTCATT
*
56073586 TCTCATCATC-TATCATC
1 TCTCATC-TCTTATCCTC
* *
56073603 CCTCATCTCATCATCC-C
1 TCTCATCTC-TTATCCTC
56073620 TCTCATCTCTTATCCTC
1 TCTCATCTCTTATCCTC
56073637 TCTC
1 TCTC
56073641 TCAAATCTCT
Statistics
Matches: 30, Mismatches: 5, Indels: 6
0.73 0.12 0.15
Matches are distributed among these distances:
16 7 0.23
17 20 0.67
18 3 0.10
ACGTcount: A:0.16, C:0.44, G:0.00, T:0.40
Consensus pattern (17 bp):
TCTCATCTCTTATCCTC
Found at i:56091665 original size:16 final size:16
Alignment explanation
Indices: 56091644--56091677 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
56091634 CTTCAACCTC
*
56091644 TCATTTCCTTCTCATT
1 TCATTTCCTCCTCATT
56091660 TCATTTCCTCCTCATT
1 TCATTTCCTCCTCATT
56091676 TC
1 TC
56091678 CTCTCCGTCC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.12, C:0.35, G:0.00, T:0.53
Consensus pattern (16 bp):
TCATTTCCTCCTCATT
Found at i:56092301 original size:18 final size:18
Alignment explanation
Indices: 56092275--56092314 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
56092265 ATCTATCTGT
*
56092275 ATTTTTTTAAAGTTGTGC
1 ATTTGTTTAAAGTTGTGC
*
56092293 ATTTGTTTAAAGTTGTTC
1 ATTTGTTTAAAGTTGTGC
56092311 ATTT
1 ATTT
56092315 TTTCAATTGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.23, C:0.05, G:0.15, T:0.57
Consensus pattern (18 bp):
ATTTGTTTAAAGTTGTGC
Found at i:56092586 original size:11 final size:11
Alignment explanation
Indices: 56092570--56092602 Score: 57
Period size: 11 Copynumber: 3.0 Consensus size: 11
56092560 TTTTTTCTCA
56092570 TATATTGTACT
1 TATATTGTACT
*
56092581 TATATTGTACA
1 TATATTGTACT
56092592 TATATTGTACT
1 TATATTGTACT
56092603 AATTCCTGCA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.30, C:0.09, G:0.09, T:0.52
Consensus pattern (11 bp):
TATATTGTACT
Found at i:56093836 original size:34 final size:35
Alignment explanation
Indices: 56093782--56093848 Score: 100
Period size: 34 Copynumber: 1.9 Consensus size: 35
56093772 CAAACACCAG
*
56093782 AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
* *
56093817 AAAACATTTTCTAG-AAATCATTTTACGGAAAA
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAA
56093849 CATTGAATTA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 17 0.59
35 12 0.41
ACGTcount: A:0.46, C:0.12, G:0.09, T:0.33
Consensus pattern (35 bp):
AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
Found at i:56099721 original size:49 final size:49
Alignment explanation
Indices: 56099664--56099762 Score: 198
Period size: 49 Copynumber: 2.0 Consensus size: 49
56099654 CCAAGTGAAC
56099664 TCTTCAAGTATCTCAGAATTTGAAACACTGCTTCTTCATGTTCCTCCAT
1 TCTTCAAGTATCTCAGAATTTGAAACACTGCTTCTTCATGTTCCTCCAT
56099713 TCTTCAAGTATCTCAGAATTTGAAACACTGCTTCTTCATGTTCCTCCAT
1 TCTTCAAGTATCTCAGAATTTGAAACACTGCTTCTTCATGTTCCTCCAT
56099762 T
1 T
56099763 GGGGAGTGCA
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 50 1.00
ACGTcount: A:0.24, C:0.26, G:0.10, T:0.39
Consensus pattern (49 bp):
TCTTCAAGTATCTCAGAATTTGAAACACTGCTTCTTCATGTTCCTCCAT
Found at i:56103360 original size:42 final size:42
Alignment explanation
Indices: 56103301--56103387 Score: 156
Period size: 42 Copynumber: 2.1 Consensus size: 42
56103291 AATCATAATT
*
56103301 TAATTCAATCATAAATTCCAAACATCATTTAAAAACATATTC
1 TAATTCAATCATAAATTCCAAAAATCATTTAAAAACATATTC
*
56103343 TAATTCAATCATCAATTCCAAAAATCATTTAAAAACATATTC
1 TAATTCAATCATAAATTCCAAAAATCATTTAAAAACATATTC
56103385 TAA
1 TAA
56103388 CTATATATCA
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
42 43 1.00
ACGTcount: A:0.48, C:0.18, G:0.00, T:0.33
Consensus pattern (42 bp):
TAATTCAATCATAAATTCCAAAAATCATTTAAAAACATATTC
Found at i:56104516 original size:20 final size:21
Alignment explanation
Indices: 56104487--56104529 Score: 70
Period size: 20 Copynumber: 2.1 Consensus size: 21
56104477 ATTGACTTAA
*
56104487 TTTAATATATATTT-TAATTT
1 TTTAAAATATATTTATAATTT
56104507 TTTAAAATATATTTATAATTT
1 TTTAAAATATATTTATAATTT
56104528 TT
1 TT
56104530 ATATAAAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
20 13 0.62
21 8 0.38
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (21 bp):
TTTAAAATATATTTATAATTT
Found at i:56108075 original size:24 final size:24
Alignment explanation
Indices: 56108040--56108091 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
56108030 AATATTAAAG
56108040 ATATTTTAGTTAATATA-TATTATT
1 ATATTTTAGTTAATATATTA-TATT
56108064 ATATTATT-GTTAATATATTATATT
1 ATATT-TTAGTTAATATATTATATT
56108088 ATAT
1 ATAT
56108092 ATATAAAACA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
24 22 0.85
25 4 0.15
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (24 bp):
ATATTTTAGTTAATATATTATATT
Found at i:56108093 original size:14 final size:14
Alignment explanation
Indices: 56108055--56108095 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 14
56108045 TTAGTTAATA
56108055 TATATTAT-TATAT
1 TATATTATATATAT
*
56108068 TATTGTTA-ATATAT
1 TA-TATTATATATAT
56108082 TATATTATATATAT
1 TATATTATATATAT
56108096 AAAACAAAAG
Statistics
Matches: 23, Mismatches: 2, Indels: 5
0.77 0.07 0.17
Matches are distributed among these distances:
13 6 0.26
14 17 0.74
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (14 bp):
TATATTATATATAT
Found at i:56112201 original size:21 final size:19
Alignment explanation
Indices: 56112156--56112208 Score: 61
Period size: 21 Copynumber: 2.7 Consensus size: 19
56112146 ACCATTATTT
* *
56112156 CTAATCTCACTGCTAGTAC
1 CTAATCTCACCGCTAGTAA
*
56112175 CCAATCTCACCGCTACAGTAA
1 CTAATCTCACCGCT--AGTAA
56112196 CTAATCTCACCGC
1 CTAATCTCACCGC
56112209 CACCGCTGTT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
19 12 0.43
21 16 0.57
ACGTcount: A:0.28, C:0.38, G:0.09, T:0.25
Consensus pattern (19 bp):
CTAATCTCACCGCTAGTAA
Found at i:56114350 original size:21 final size:21
Alignment explanation
Indices: 56114321--56114521 Score: 181
Period size: 21 Copynumber: 9.6 Consensus size: 21
56114311 GAAGATCGAA
*
56114321 AGCTGAACAGAAGCTCATGAG
1 AGCTGAACAGAAGCTCATAAG
* * * *
56114342 AGCTAAACAAAAACCCATAAG
1 AGCTGAACAGAAGCTCATAAG
* * *
56114363 GGTTTAACAGAAGCTCGA-AAG
1 AGCTGAACAGAAGCTC-ATAAG
* *
56114384 AGCTGAACAAAAACTCATAAG
1 AGCTGAACAGAAGCTCATAAG
* *
56114405 AGTTGAACGGAAGCTCATAAG
1 AGCTGAACAGAAGCTCATAAG
* *
56114426 AGCTGAA-TGAAAACTCATAAG
1 AGCTGAACAG-AAGCTCATAAG
* *
56114447 AGTTGAACAGAAGCTCAAAAG
1 AGCTGAACAGAAGCTCATAAG
* *
56114468 AGCTGAACAGAAACTCATATG
1 AGCTGAACAGAAGCTCATAAG
* * *
56114489 AGTTAAACAAAAGCTCATAAG
1 AGCTGAACAGAAGCTCATAAG
56114510 AGCTGAACAGAA
1 AGCTGAACAGAA
56114522 AGTAAAACAC
Statistics
Matches: 137, Mismatches: 39, Indels: 8
0.74 0.21 0.04
Matches are distributed among these distances:
20 2 0.01
21 133 0.97
22 2 0.01
ACGTcount: A:0.46, C:0.17, G:0.21, T:0.16
Consensus pattern (21 bp):
AGCTGAACAGAAGCTCATAAG
Found at i:56114386 original size:42 final size:42
Alignment explanation
Indices: 56114324--56114518 Score: 257
Period size: 42 Copynumber: 4.6 Consensus size: 42
56114314 GATCGAAAGC
* * * *
56114324 TGAACAGAAGCTCATGAGAGCTAAACAAAAACCCATAAGGGT
1 TGAACAGAAGCTCATAAGAGCTGAACAAAAACTCATAAGAGT
*
56114366 TTAACAGAAGCTCGA-AAGAGCTGAACAAAAACTCATAAGAGT
1 TGAACAGAAGCTC-ATAAGAGCTGAACAAAAACTCATAAGAGT
* **
56114408 TGAACGGAAGCTCATAAGAGCTGAATGAAAACTCATAAGAGT
1 TGAACAGAAGCTCATAAGAGCTGAACAAAAACTCATAAGAGT
* * *
56114450 TGAACAGAAGCTCAAAAGAGCTGAACAGAAACTCATATGAGT
1 TGAACAGAAGCTCATAAGAGCTGAACAAAAACTCATAAGAGT
* *
56114492 TAAACAAAAGCTCATAAGAGCTGAACA
1 TGAACAGAAGCTCATAAGAGCTGAACA
56114519 GAAAGTAAAA
Statistics
Matches: 133, Mismatches: 18, Indels: 4
0.86 0.12 0.03
Matches are distributed among these distances:
41 1 0.01
42 131 0.98
43 1 0.01
ACGTcount: A:0.46, C:0.17, G:0.21, T:0.16
Consensus pattern (42 bp):
TGAACAGAAGCTCATAAGAGCTGAACAAAAACTCATAAGAGT
Found at i:56118096 original size:147 final size:147
Alignment explanation
Indices: 56117829--56118111 Score: 476
Period size: 147 Copynumber: 1.9 Consensus size: 147
56117819 TATTTTGATA
*
56117829 ATCAATTGAAACGGTGTAAAAGCATGATATTTGAGTATTGAATATGCAAAGTGATCTGGTTGAAT
1 ATCAATTGAAACGGAGTAAAAGCATGATATTTGAGTATTGAATATGCAAAGTGATCTGGTTGAAT
*
56117894 TGTGGCATATATTGATTGAATTTCTATATTAAGTATGCTTATTTGTGACTTGAATCATAAAAGTA
66 TGTGACATATATTGATTGAATTTCTATATTAAGTATGCTTATTTGTGACTTGAATCATAAAAGTA
56117959 CCACTGCTAGTTTAATC
131 CCACTGCTAGTTTAATC
* * * * *
56117976 ATCAATTGAAATGGAGTAAAAGTATGATATTTGAGTATTGAATATGCAAATTTATTTGGTTGAAT
1 ATCAATTGAAACGGAGTAAAAGCATGATATTTGAGTATTGAATATGCAAAGTGATCTGGTTGAAT
* * *
56118041 TGTGACATATATTGATTGAATTTCTATATTGAGTATGCTTATTTGTTACTTGAATCATGAAAGTA
66 TGTGACATATATTGATTGAATTTCTATATTAAGTATGCTTATTTGTGACTTGAATCATAAAAGTA
56118106 CCACTG
131 CCACTG
56118112 AGCTTTATTG
Statistics
Matches: 126, Mismatches: 10, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
147 126 1.00
ACGTcount: A:0.34, C:0.09, G:0.19, T:0.39
Consensus pattern (147 bp):
ATCAATTGAAACGGAGTAAAAGCATGATATTTGAGTATTGAATATGCAAAGTGATCTGGTTGAAT
TGTGACATATATTGATTGAATTTCTATATTAAGTATGCTTATTTGTGACTTGAATCATAAAAGTA
CCACTGCTAGTTTAATC
Found at i:56127864 original size:2 final size:2
Alignment explanation
Indices: 56127857--56127882 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
56127847 ATTTCATTTC
56127857 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
56127883 TGGATGATGC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:56137344 original size:2 final size:2
Alignment explanation
Indices: 56137337--56137386 Score: 91
Period size: 2 Copynumber: 25.0 Consensus size: 2
56137327 CATCTCAAAT
*
56137337 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA TA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
56137379 CA CA CA CA
1 CA CA CA CA
56137387 TTTACAAACC
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.48, G:0.00, T:0.02
Consensus pattern (2 bp):
CA
Found at i:56138048 original size:20 final size:20
Alignment explanation
Indices: 56138025--56138096 Score: 56
Period size: 20 Copynumber: 3.6 Consensus size: 20
56138015 AGCATGAATA
*
56138025 TGCTATCAGGAGCAAAGTAG
1 TGCTAACAGGAGCAAAGTAG
* *
56138045 TGCTAAAAGGAGCACAAAT-G
1 TGCTAACAGGAGCA-AAGTAG
** * **
56138065 TGCTATTAAGAGCACCGTAG
1 TGCTAACAGGAGCAAAGTAG
56138085 TGCTAACAGGAG
1 TGCTAACAGGAG
56138097 GACGAAAGTA
Statistics
Matches: 38, Mismatches: 12, Indels: 4
0.70 0.22 0.07
Matches are distributed among these distances:
19 1 0.03
20 34 0.89
21 3 0.08
ACGTcount: A:0.36, C:0.17, G:0.28, T:0.19
Consensus pattern (20 bp):
TGCTAACAGGAGCAAAGTAG
Found at i:56138056 original size:40 final size:40
Alignment explanation
Indices: 56138012--56138118 Score: 108
Period size: 40 Copynumber: 2.7 Consensus size: 40
56138002 TAATGCAAAC
*
56138012 AGGAGCATGAATATGCTATCAGGAGCAAAGTAGTGCTAAA
1 AGGAGCACGAATATGCTATCAGGAGCAAAGTAGTGCTAAA
* * * * ** *
56138052 AGGAGCACAAATGTGCTATTAAGAGCACCGTAGTGCTAAC
1 AGGAGCACGAATATGCTATCAGGAGCAAAGTAGTGCTAAA
* *
56138092 AGGAGGACGAA-AGTACTATCAGGAGCA
1 AGGAGCACGAATA-TGCTATCAGGAGCA
56138119 CTTATTCAAG
Statistics
Matches: 52, Mismatches: 14, Indels: 2
0.76 0.21 0.03
Matches are distributed among these distances:
40 52 1.00
ACGTcount: A:0.38, C:0.16, G:0.28, T:0.18
Consensus pattern (40 bp):
AGGAGCACGAATATGCTATCAGGAGCAAAGTAGTGCTAAA
Found at i:56144097 original size:45 final size:45
Alignment explanation
Indices: 56144004--56144089 Score: 111
Period size: 45 Copynumber: 1.9 Consensus size: 45
56143994 GTCATAGCGC
* * * *
56144004 CTTTCAGCTATGGTCTTACTCATTTCTATCACGATGCTATAACAT
1 CTTTCAACTATGGTCTTACTCATTTCAATCACGATACCATAACAT
*
56144049 CTTTCAACTATGGTCTTACTCATCTT-AATCATGATACCATA
1 CTTTCAACTATGGTCTTACTCAT-TTCAATCACGATACCATA
56144090 GTGTCTTTTA
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
45 33 0.94
46 2 0.06
ACGTcount: A:0.27, C:0.24, G:0.09, T:0.40
Consensus pattern (45 bp):
CTTTCAACTATGGTCTTACTCATTTCAATCACGATACCATAACAT
Found at i:56154955 original size:72 final size:72
Alignment explanation
Indices: 56154819--56154955 Score: 193
Period size: 72 Copynumber: 1.9 Consensus size: 72
56154809 GGCATCATGA
* * **
56154819 TAAAATATGTAAGACCATAGCTAAAAGATGTTATGGCATCATAGATAGTCCGTCGATATGATAAA
1 TAAAATATGTAAGACCATAGCTAAAAGATGTTATGGCATCATAGATAGTCCATCGAGACAATAAA
56154884 CACGAGT
66 CACGAGT
* * * * *
56154891 TAAACTATGTAAGACCGTAGCTGAAAGATGTTATGGTATCATAGATAGTCTATCGAGACAATAAA
1 TAAAATATGTAAGACCATAGCTAAAAGATGTTATGGCATCATAGATAGTCCATCGAGACAATAAA
56154956 TATGGGATAG
Statistics
Matches: 56, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
72 56 1.00
ACGTcount: A:0.40, C:0.13, G:0.20, T:0.27
Consensus pattern (72 bp):
TAAAATATGTAAGACCATAGCTAAAAGATGTTATGGCATCATAGATAGTCCATCGAGACAATAAA
CACGAGT
Found at i:56156346 original size:144 final size:144
Alignment explanation
Indices: 56156081--56156369 Score: 551
Period size: 144 Copynumber: 2.0 Consensus size: 144
56156071 AGAACACATG
*
56156081 AGCCAGGGACACTGGCATGTGTCCAGGCTGTGTGGGGATTATTTTGAGGCTTGGGTCGCACGGGC
1 AGCCAGGGACACTGGCATGTGTCCAGGCTATGTGGGGATTATTTTGAGGCTTGGGTCGCACGGGC
* *
56156146 TTGTGTTTGACCGTATGCTAGACCATGTAACTCACTGTTTTAAGCTACACAGCCTTGTGCTAGGC
66 TTGTGTTTGACCGTATGCTAGACCATGTAACTCACTATTTTAAGCTACACAACCTTGTGCTAGGC
56156211 CGTGTATGCCATAT
131 CGTGTATGCCATAT
56156225 AGCCAGGGACACTGGCATGTGTCCAGGCTATGTGGGGATTATTTTGAGGCTTGGGTCGCACGGGC
1 AGCCAGGGACACTGGCATGTGTCCAGGCTATGTGGGGATTATTTTGAGGCTTGGGTCGCACGGGC
56156290 TTGTGTTTGACCGTATGCTAGACCATGTAACTCACTATTTTAAGCTACACAACCTTGTGCTAGGC
66 TTGTGTTTGACCGTATGCTAGACCATGTAACTCACTATTTTAAGCTACACAACCTTGTGCTAGGC
56156355 CGTGTATGCCATAT
131 CGTGTATGCCATAT
56156369 A
1 A
56156370 AAAGGGCCAC
Statistics
Matches: 142, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
144 142 1.00
ACGTcount: A:0.20, C:0.21, G:0.29, T:0.30
Consensus pattern (144 bp):
AGCCAGGGACACTGGCATGTGTCCAGGCTATGTGGGGATTATTTTGAGGCTTGGGTCGCACGGGC
TTGTGTTTGACCGTATGCTAGACCATGTAACTCACTATTTTAAGCTACACAACCTTGTGCTAGGC
CGTGTATGCCATAT
Found at i:56156403 original size:144 final size:144
Alignment explanation
Indices: 56156085--56156403 Score: 534
Period size: 144 Copynumber: 2.2 Consensus size: 144
56156075 CACATGAGCC
56156085 AGGGACACTGGCATGTGTCCAGGCTGTGTGGGGATTATTTTGAGGCTTGGGTCGCACGGGCTTGT
1 AGGGACACTGGCATGTGTCCAGGCTGTGTGGGGATTATTTTGAGGCTTGGGTCGCACGGGCTTGT
* *
56156150 GTTTGACCGTATGCTAGACCATGTAACTCACTGTTTTAAGCTACACAGCCTTGTGCTAGGCCGTG
66 GTTTGACCGTATGCTAGACCATGTAACTCACTATTTTAAGCTACACAACCTTGTGCTAGGCCGTG
**
56156215 TATGCCATATAGCC
131 TATGCCATATAGAA
*
56156229 AGGGACACTGGCATGTGTCCAGGCTATGTGGGGATTATTTTGAGGCTTGGGTCGCACGGGCTTGT
1 AGGGACACTGGCATGTGTCCAGGCTGTGTGGGGATTATTTTGAGGCTTGGGTCGCACGGGCTTGT
56156294 GTTTGACCGTATGCTAGACCATGTAACTCACTATTTTAAGCTACACAACCTTGTGCTAGGCCGTG
66 GTTTGACCGTATGCTAGACCATGTAACTCACTATTTTAAGCTACACAACCTTGTGCTAGGCCGTG
56156359 TATGCCATATA-AA
131 TATGCCATATAGAA
* * *
56156372 AGGGCCACACAGGCACGTG-CCACGCTGTGTGG
1 AGGG--ACACTGGCATGTGTCCAGGCTGTGTGG
56156404 ACCACATGGG
Statistics
Matches: 164, Mismatches: 9, Indels: 4
0.93 0.05 0.02
Matches are distributed among these distances:
143 4 0.02
144 149 0.91
145 11 0.07
ACGTcount: A:0.20, C:0.22, G:0.29, T:0.28
Consensus pattern (144 bp):
AGGGACACTGGCATGTGTCCAGGCTGTGTGGGGATTATTTTGAGGCTTGGGTCGCACGGGCTTGT
GTTTGACCGTATGCTAGACCATGTAACTCACTATTTTAAGCTACACAACCTTGTGCTAGGCCGTG
TATGCCATATAGAA
Found at i:56165316 original size:17 final size:17
Alignment explanation
Indices: 56165259--56165320 Score: 59
Period size: 15 Copynumber: 4.1 Consensus size: 17
56165249 CCCTTTTTAC
56165259 ATTAAAATATTA-TTTT
1 ATTAAAATATTATTTTT
*
56165275 -TTAAAA-ATTATTATT
1 ATTAAAATATTATTTTT
56165290 -TT---AT-TTATTTTT
1 ATTAAAATATTATTTTT
56165302 ATTAAAATATTATTTTT
1 ATTAAAATATTATTTTT
56165319 AT
1 AT
56165321 AACTGGTGTC
Statistics
Matches: 37, Mismatches: 2, Indels: 13
0.71 0.04 0.25
Matches are distributed among these distances:
12 8 0.22
13 2 0.05
14 4 0.11
15 11 0.30
16 2 0.05
17 10 0.27
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (17 bp):
ATTAAAATATTATTTTT
Found at i:56165320 original size:27 final size:26
Alignment explanation
Indices: 56165268--56165317 Score: 75
Period size: 26 Copynumber: 1.9 Consensus size: 26
56165258 CATTAAAATA
56165268 TTATTTTTTAAAAATTATTATTTTAT
1 TTATTTTTTAAAAATTATTATTTTAT
*
56165294 TTATTTTTATTAAAA-TATTATTTT
1 TTATTTTT-TAAAAATTATTATTTT
56165318 TATAACTGGT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
26 17 0.77
27 5 0.23
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (26 bp):
TTATTTTTTAAAAATTATTATTTTAT
Found at i:56168664 original size:45 final size:45
Alignment explanation
Indices: 56168600--56168688 Score: 151
Period size: 45 Copynumber: 2.0 Consensus size: 45
56168590 AATAGATACT
* * *
56168600 CGGTGGATTCAGCACATAGCAACTACCTTATTAATCAATGATGTA
1 CGGTGGAATCAGCACATAGCAACCACCTTACTAATCAATGATGTA
56168645 CGGTGGAATCAGCACATAGCAACCACCTTACTAATCAATGATGT
1 CGGTGGAATCAGCACATAGCAACCACCTTACTAATCAATGATGT
56168689 TCGATTCACA
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 41 1.00
ACGTcount: A:0.34, C:0.22, G:0.18, T:0.26
Consensus pattern (45 bp):
CGGTGGAATCAGCACATAGCAACCACCTTACTAATCAATGATGTA
Found at i:56168757 original size:51 final size:50
Alignment explanation
Indices: 56168690--56168885 Score: 232
Period size: 51 Copynumber: 3.9 Consensus size: 50
56168680 CAATGATGTT
* *
56168690 CGATTCACATAGTAGCCTGCACATAGTACTACACATGTGACCATTACCATC
1 CGATACACATAGTAGCCTGCACATAGTACTACACACGTGACCA-TACCATC
* * * *
56168741 CGATACACGTAGTAGCCTGCACATAGTACTACACACGTGATCGAAACTATC
1 CGATACACATAGTAGCCTGCACATAGTACTACACACGTGA-CCATACCATC
* * * * *
56168792 CGGTACACATAGTAGCCTACACATAGTACTACACATGCGACC-TATCATTC
1 CGATACACATAGTAGCCTGCACATAGTACTACACACGTGACCATACCA-TC
* * *
56168842 CGGTACACGTAGTAGTCTGCACATAGTACTACACACGTGACCAT
1 CGATACACATAGTAGCCTGCACATAGTACTACACACGTGACCAT
56168886 CACTTTCACT
Statistics
Matches: 122, Mismatches: 20, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
49 2 0.02
50 40 0.33
51 78 0.64
52 2 0.02
ACGTcount: A:0.32, C:0.29, G:0.16, T:0.23
Consensus pattern (50 bp):
CGATACACATAGTAGCCTGCACATAGTACTACACACGTGACCATACCATC
Found at i:56168825 original size:12 final size:13
Alignment explanation
Indices: 56168795--56168827 Score: 50
Period size: 14 Copynumber: 2.5 Consensus size: 13
56168785 AACTATCCGG
56168795 TACACATAGTAGCC
1 TACACATAGTA-CC
56168809 TACACATAGTA-C
1 TACACATAGTACC
56168821 TACACAT
1 TACACAT
56168828 GCGACCTATC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 8 0.42
14 11 0.58
ACGTcount: A:0.39, C:0.27, G:0.09, T:0.24
Consensus pattern (13 bp):
TACACATAGTACC
Found at i:56168876 original size:101 final size:101
Alignment explanation
Indices: 56168695--56168881 Score: 304
Period size: 101 Copynumber: 1.8 Consensus size: 101
56168685 ATGTTCGATT
* *
56168695 CACATAGTAGCCTGCACATAGTACTACACATGTGACCATTACCATCCGATACACGTAGTAGCCTG
1 CACATAGTAGCCTACACATAGTACTACACATGCGACCA-TACCATCCGATACACGTAGTAGCCTG
56168760 CACATAGTACTACACACGTGATCGAAACTATCCGGTA
65 CACATAGTACTACACACGTGATCGAAACTATCCGGTA
* * *
56168797 CACATAGTAGCCTACACATAGTACTACACATGCGACC-TATCATTCCGGTACACGTAGTAGTCTG
1 CACATAGTAGCCTACACATAGTACTACACATGCGACCATACCA-TCCGATACACGTAGTAGCCTG
56168861 CACATAGTACTACACACGTGA
65 CACATAGTACTACACACGTGA
56168882 CCATCACTTT
Statistics
Matches: 79, Mismatches: 5, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
100 4 0.05
101 40 0.51
102 35 0.44
ACGTcount: A:0.32, C:0.28, G:0.17, T:0.23
Consensus pattern (101 bp):
CACATAGTAGCCTACACATAGTACTACACATGCGACCATACCATCCGATACACGTAGTAGCCTGC
ACATAGTACTACACACGTGATCGAAACTATCCGGTA
Found at i:56170167 original size:3 final size:3
Alignment explanation
Indices: 56170159--56170185 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
56170149 AATCAAGTAA
56170159 AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT
56170186 TGCTTCGACT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:56171457 original size:23 final size:24
Alignment explanation
Indices: 56171415--56171463 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 24
56171405 AACTAACCTG
*
56171415 ATATGAATGTGTTAAATTATATAA
1 ATATGAATGTATTAAATTATATAA
* *
56171439 ATATGAAT-TATTAACTTATTTAA
1 ATATGAATGTATTAAATTATATAA
56171462 AT
1 AT
56171464 TTATATAAAC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
23 14 0.64
24 8 0.36
ACGTcount: A:0.45, C:0.02, G:0.08, T:0.45
Consensus pattern (24 bp):
ATATGAATGTATTAAATTATATAA
Found at i:56172004 original size:19 final size:19
Alignment explanation
Indices: 56171982--56172030 Score: 55
Period size: 19 Copynumber: 2.5 Consensus size: 19
56171972 ATTACAAAAT
*
56171982 AATTCAAAATCATTT-TTAA
1 AATTCAAAAT-ATTTATAAA
*
56172001 AATTAAAAATATTTATAAA
1 AATTCAAAATATTTATAAA
56172020 AATTTCAAAAT
1 AA-TTCAAAAT
56172031 TTATATTTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
18 4 0.16
19 14 0.56
20 7 0.28
ACGTcount: A:0.55, C:0.06, G:0.00, T:0.39
Consensus pattern (19 bp):
AATTCAAAATATTTATAAA
Found at i:56172014 original size:18 final size:19
Alignment explanation
Indices: 56171982--56172020 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
56171972 ATTACAAAAT
* *
56171982 AATTCAAAATCATTTTTAA
1 AATTAAAAATCATTTATAA
56172001 AATTAAAAAT-ATTTATAA
1 AATTAAAAATCATTTATAA
56172019 AA
1 AA
56172021 ATTTCAAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 9 0.50
19 9 0.50
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.38
Consensus pattern (19 bp):
AATTAAAAATCATTTATAA
Found at i:56181283 original size:204 final size:201
Alignment explanation
Indices: 56180891--56181302 Score: 506
Period size: 204 Copynumber: 2.0 Consensus size: 201
56180881 TCATATGTTT
* * *
56180891 TTTTATTTTTTTAATTTGGTTATGCCAACTTTAACTGTTTTGTCACTCATCTGTTCTTCTCATTC
1 TTTTATTTTTTTAATTCGGTTATGCCAACTGTAACTGTTTTGTCACTCATCTGTTCTTCTCATGC
** * * * * * **
56180956 TGATTGGGATACAAAATTGTAATTTCTTTTCCATAGTCTCCCTCCTGTTTCTTCCTCATGCTATC
66 TGAAAGGGATACAAAAATGAAATTTCTTTTCCACAGACTCCCTCCTGTTTCTTCCACACACTATC
* * * *
56181021 AGTCAAGAACTAGAATTTCTAACTGAATTGGGGAGAACATAACCTGTTTTAACTTCCATTGCTGA
131 AGTCAAGAACTAGAATTTCTAACTGAATTAGGGAGAACACAACCTGTGTTAACTTCCATTGCTAA
56181086 TATTGA
196 TATTGA
* * * *
56181092 TTTTCTTTTTTT-ATTCGGTTATGCCATCTGTAACTGTTTTGTCATTCTTCTGTTCTTCCTCATG
1 TTTTATTTTTTTAATTCGGTTATGCCAACTGTAACTGTTTTGTCACTCATCTGTTCTT-CTCATG
* *
56181156 CTGAAAGGGATACAAAAATGAAATTTCTTTTCCACAGACTTCTTCCT-TTCTCTTCTTCACACAC
65 CTGAAAGGGATACAAAAATGAAATTTCTTTTCCACAGACTCCCTCCTGTT-TCTTC--CACACAC
* * * * *
56181220 TCATCTGTCAAGAACTAGAGTTTCTAACTGATTTAGGGAGAACACAACTTGTGTTAGCTTCCATT
127 T-ATCAGTCAAGAACTAGAATTTCTAACTGAATTAGGGAGAACACAACCTGTGTTAACTTCCATT
*
56181285 GCTAATATTTA
191 GCTAATATTGA
56181296 -TTTATTT
1 TTTTATTT
56181303 ACATACTAAC
Statistics
Matches: 177, Mismatches: 29, Indels: 8
0.83 0.14 0.04
Matches are distributed among these distances:
200 42 0.24
201 60 0.34
203 11 0.06
204 64 0.36
ACGTcount: A:0.24, C:0.20, G:0.13, T:0.43
Consensus pattern (201 bp):
TTTTATTTTTTTAATTCGGTTATGCCAACTGTAACTGTTTTGTCACTCATCTGTTCTTCTCATGC
TGAAAGGGATACAAAAATGAAATTTCTTTTCCACAGACTCCCTCCTGTTTCTTCCACACACTATC
AGTCAAGAACTAGAATTTCTAACTGAATTAGGGAGAACACAACCTGTGTTAACTTCCATTGCTAA
TATTGA
Found at i:56181767 original size:13 final size:12
Alignment explanation
Indices: 56181744--56181787 Score: 52
Period size: 13 Copynumber: 3.5 Consensus size: 12
56181734 AAAAAGCTTG
*
56181744 GTTTGGAAAAGT
1 GTTTTGAAAAGT
56181756 GCTTTTGAAAAGT
1 G-TTTTGAAAAGT
*
56181769 GTTGTGGAAAAGT
1 GTT-TTGAAAAGT
56181782 GTTTTG
1 GTTTTG
56181788 TTAATTTTAA
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
12 5 0.19
13 22 0.81
ACGTcount: A:0.27, C:0.02, G:0.32, T:0.39
Consensus pattern (12 bp):
GTTTTGAAAAGT
Found at i:56189692 original size:24 final size:24
Alignment explanation
Indices: 56189665--56189716 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
56189655 ATTTGAGAAG
*
56189665 ATTTAGTATTTATT-AGTATAATAT
1 ATTTAGCATTTATTGA-TATAATAT
*
56189689 ATTTAGCATTTATTGATATAATTT
1 ATTTAGCATTTATTGATATAATAT
56189713 ATTT
1 ATTT
56189717 GACCTACGAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 24 0.96
25 1 0.04
ACGTcount: A:0.35, C:0.02, G:0.08, T:0.56
Consensus pattern (24 bp):
ATTTAGCATTTATTGATATAATAT
Found at i:56191730 original size:1 final size:1
Alignment explanation
Indices: 56191724--56191767 Score: 52
Period size: 1 Copynumber: 44.0 Consensus size: 1
56191714 AACATTTCGC
* * * *
56191724 AAAAAAAAAAAAAAAAAAACAAAAACAAAAACAAAAACAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
56191768 CTTCCATCTT
Statistics
Matches: 35, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
1 35 1.00
ACGTcount: A:0.91, C:0.09, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:56191747 original size:18 final size:18
Alignment explanation
Indices: 56191726--56191767 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
56191716 CATTTCGCAA
56191726 AAAAAAAAAAAAAAAAAC
1 AAAAAAAAAAAAAAAAAC
* *
56191744 AAAAACAAAAACAAAAAC
1 AAAAAAAAAAAAAAAAAC
56191762 AAAAAA
1 AAAAAA
56191768 CTTCCATCTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.90, C:0.10, G:0.00, T:0.00
Consensus pattern (18 bp):
AAAAAAAAAAAAAAAAAC
Found at i:56197941 original size:18 final size:17
Alignment explanation
Indices: 56197918--56197978 Score: 68
Period size: 18 Copynumber: 3.4 Consensus size: 17
56197908 CTACATTTGT
*
56197918 GAGCTCACCAAAAGTTGC
1 GAGCTCACAAAAAG-TGC
*
56197936 GAGCTCAACTAAAAGTGC
1 GAGCTC-ACAAAAAGTGC
*
56197954 GAGCTCATAAAAAGATGC
1 GAGCTCACAAAAAG-TGC
56197972 GAGCTCA
1 GAGCTCA
56197979 ACTTAAATTG
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
17 6 0.16
18 25 0.66
19 7 0.18
ACGTcount: A:0.38, C:0.23, G:0.23, T:0.16
Consensus pattern (17 bp):
GAGCTCACAAAAAGTGC
Found at i:56204200 original size:18 final size:20
Alignment explanation
Indices: 56204174--56204221 Score: 59
Period size: 18 Copynumber: 2.6 Consensus size: 20
56204164 GCTCTACATT
*
56204174 TGCGTGCTCAACT-AAAAG-
1 TGCGAGCTCAACTAAAAAGA
56204192 TGCGAGCTC-A-TAAAAAGA
1 TGCGAGCTCAACTAAAAAGA
56204210 TGCGAGCTCAAC
1 TGCGAGCTCAAC
56204222 CTGAATTGCT
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
16 1 0.04
17 6 0.24
18 17 0.68
19 1 0.04
ACGTcount: A:0.35, C:0.23, G:0.23, T:0.19
Consensus pattern (20 bp):
TGCGAGCTCAACTAAAAAGA
Found at i:56205201 original size:29 final size:29
Alignment explanation
Indices: 56205165--56205222 Score: 107
Period size: 29 Copynumber: 2.0 Consensus size: 29
56205155 TTCTGAATTA
56205165 ACTAAAATTGTGATTTCGATAGAAATTCG
1 ACTAAAATTGTGATTTCGATAGAAATTCG
*
56205194 ACTAAAATTGTGATTTTGATAGAAATTCG
1 ACTAAAATTGTGATTTCGATAGAAATTCG
56205223 TTAGGGAATA
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:0.38, C:0.09, G:0.17, T:0.36
Consensus pattern (29 bp):
ACTAAAATTGTGATTTCGATAGAAATTCG
Found at i:56206296 original size:29 final size:29
Alignment explanation
Indices: 56206252--56206332 Score: 101
Period size: 31 Copynumber: 2.7 Consensus size: 29
56206242 GATTTAATCA
* *
56206252 AAATTAAAGTTTCATGTATATAATTG-CATT
1 AAATCAAAG-TTCATGTATA-AAATGACATT
56206282 AAATCAAAGTTCATGTATCAAAATGCACATT
1 AAATCAAAGTTCATGTAT-AAAATG-ACATT
56206313 AAATCAAAGTTCATGTATAA
1 AAATCAAAGTTCATGTATAA
56206333 TTTTGAGATT
Statistics
Matches: 46, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
29 13 0.28
30 11 0.24
31 22 0.48
ACGTcount: A:0.44, C:0.11, G:0.10, T:0.35
Consensus pattern (29 bp):
AAATCAAAGTTCATGTATAAAATGACATT
Found at i:56211565 original size:53 final size:50
Alignment explanation
Indices: 56211483--56211642 Score: 151
Period size: 50 Copynumber: 3.1 Consensus size: 50
56211473 TAAGCAACTC
* ** * *
56211483 TTTTTTTTAGCAAATGCCGACTTTCATAATGAAATGGATTTGAAAGATGACCA
1 TTTTTTTTAGCAAATACAAATTTTCATAATGAAATGAATTTGAAAGAT-A--A
* *
56211536 TTTTTTTTAGCAAATACAAATTTTTATAATTAAATGAATTTGAAAGATAA
1 TTTTTTTTAGCAAATACAAATTTTCATAATGAAATGAATTTGAAAGATAA
* * * * * *
56211586 TTATTTTTAGAAAATACTAATTTTCATAACT-AAAAGAATCTGAAAAATAA
1 TTTTTTTTAGCAAATACAAATTTTCATAA-TGAAATGAATTTGAAAGATAA
*
56211636 CTTTTTT
1 TTTTTTT
56211643 AACAATTACT
Statistics
Matches: 90, Mismatches: 16, Indels: 5
0.81 0.14 0.05
Matches are distributed among these distances:
50 47 0.52
51 1 0.01
52 1 0.01
53 41 0.46
ACGTcount: A:0.41, C:0.09, G:0.10, T:0.41
Consensus pattern (50 bp):
TTTTTTTTAGCAAATACAAATTTTCATAATGAAATGAATTTGAAAGATAA
Found at i:56211658 original size:49 final size:50
Alignment explanation
Indices: 56211539--56211663 Score: 137
Period size: 50 Copynumber: 2.5 Consensus size: 50
56211529 ATGACCATTT
* * * * * * * *
56211539 TTTTTAGCAAATACAAATTTTTATAATTAAATGAATTTGAAAGATAATTA
1 TTTTTAGAAAATACTAATTTTCATAACTAAAAGAATCTGAAAAATAACTA
56211589 TTTTTAGAAAATACTAATTTTCATAACTAAAAGAATCTGAAAAATAACT-
1 TTTTTAGAAAATACTAATTTTCATAACTAAAAGAATCTGAAAAATAACTA
* *
56211638 TTTTTA-ACAATTACTTATTTTCATAA
1 TTTTTAGA-AAATACTAATTTTCATAA
56211664 GTAGTGTTTG
Statistics
Matches: 64, Mismatches: 10, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
48 1 0.02
49 22 0.34
50 41 0.64
ACGTcount: A:0.45, C:0.08, G:0.06, T:0.42
Consensus pattern (50 bp):
TTTTTAGAAAATACTAATTTTCATAACTAAAAGAATCTGAAAAATAACTA
Found at i:56211757 original size:14 final size:14
Alignment explanation
Indices: 56211738--56211767 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
56211728 TAATTTTAAA
*
56211738 AAAAATTATTTTAT
1 AAAAATTATATTAT
56211752 AAAAATTATATTAT
1 AAAAATTATATTAT
56211766 AA
1 AA
56211768 GCATAAACAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (14 bp):
AAAAATTATATTAT
Found at i:56212220 original size:14 final size:14
Alignment explanation
Indices: 56212174--56212221 Score: 53
Period size: 14 Copynumber: 3.3 Consensus size: 14
56212164 TTTGGATAAC
56212174 TTATAAAATATTAT-
1 TTAT-AAATATTATA
*
56212188 TTATAAATGTTAAATA
1 TTATAAATATT--ATA
56212204 TTATAAATATTATA
1 TTATAAATATTATA
56212218 TTAT
1 TTAT
56212222 TTTTTTTGCT
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
13 6 0.21
14 11 0.38
15 2 0.07
16 10 0.34
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (14 bp):
TTATAAATATTATA
Found at i:56214975 original size:27 final size:27
Alignment explanation
Indices: 56214945--56215072 Score: 78
Period size: 27 Copynumber: 4.7 Consensus size: 27
56214935 TTCATGATTT
*
56214945 GCCACAAAAGCGTTCCTTTTATATTGC
1 GCCACAAAAGCGTTCCTTTCATATTGC
* * * *
56214972 GCCATAAAGGCTTTCCTTTCATATTGT
1 GCCACAAAAGCGTTCCTTTCATATTGC
* * * * **
56214999 GCTAGAAAGGCATTATTTTCATAATT-C
1 GCCACAAAAGCGTTCCTTTCAT-ATTGC
* * * * *
56215026 ACCACAAATGCTTTACTTTCATATTGT
1 GCCACAAAAGCGTTCCTTTCATATTGC
* *
56215053 GCCACAAAGGCTTTCCTTTC
1 GCCACAAAAGCGTTCCTTTC
56215073 TTGACATGTT
Statistics
Matches: 78, Mismatches: 21, Indels: 4
0.76 0.20 0.04
Matches are distributed among these distances:
26 3 0.04
27 72 0.92
28 3 0.04
ACGTcount: A:0.27, C:0.23, G:0.13, T:0.37
Consensus pattern (27 bp):
GCCACAAAAGCGTTCCTTTCATATTGC
Found at i:56218822 original size:6 final size:6
Alignment explanation
Indices: 56218811--56218838 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
56218801 TTCATCTTCT
56218811 TTCTTG TTCTTG TTCTTG TTCTTG TTCT
1 TTCTTG TTCTTG TTCTTG TTCTTG TTCT
56218839 CTCTTTCTCT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.00, C:0.18, G:0.14, T:0.68
Consensus pattern (6 bp):
TTCTTG
Found at i:56219210 original size:30 final size:28
Alignment explanation
Indices: 56219174--56219235 Score: 79
Period size: 29 Copynumber: 2.1 Consensus size: 28
56219164 AAAGCCGTTT
56219174 TTTTTTTCAAAATTTACCGAAATGGGCCGA
1 TTTTTTT-AAAATTTACCGAAATGGGCC-A
** *
56219204 TTTTTTTATTATTTACCGGAATGGGCCA
1 TTTTTTTAAAATTTACCGAAATGGGCCA
56219232 TTTT
1 TTTT
56219236 CCGCAAAATC
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
28 5 0.17
29 17 0.59
30 7 0.24
ACGTcount: A:0.24, C:0.15, G:0.16, T:0.45
Consensus pattern (28 bp):
TTTTTTTAAAATTTACCGAAATGGGCCA
Found at i:56220754 original size:64 final size:63
Alignment explanation
Indices: 56220675--56220800 Score: 171
Period size: 63 Copynumber: 2.0 Consensus size: 63
56220665 CTACAATCCA
* * * *
56220675 GACATTCAAACAAAACTTAGTTTCATCAATTGAAACATAAAAATCTTTGTCATTAGATGAACCG
1 GACATTCAAACAAAACTTAGTTTCAT-AATAGAAACATAAAAACCTTTATCATCAGATGAACCG
* * * *
56220739 GACATTCAAACAAAACTTGGTTTCATTATAGAAATATACAAACCTTTATCATCAGATGAACC
1 GACATTCAAACAAAACTTAGTTTCATAATAGAAACATAAAAACCTTTATCATCAGATGAACC
56220801 AGACTAAACA
Statistics
Matches: 54, Mismatches: 8, Indels: 1
0.86 0.13 0.02
Matches are distributed among these distances:
63 29 0.54
64 25 0.46
ACGTcount: A:0.42, C:0.18, G:0.10, T:0.29
Consensus pattern (63 bp):
GACATTCAAACAAAACTTAGTTTCATAATAGAAACATAAAAACCTTTATCATCAGATGAACCG
Found at i:56222393 original size:5 final size:5
Alignment explanation
Indices: 56222383--56222407 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
56222373 TATCTTGTGA
56222383 AAATT AAATT AAATT AAATT AAATT
1 AAATT AAATT AAATT AAATT AAATT
56222408 TTTATATATG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
AAATT
Found at i:56227304 original size:14 final size:14
Alignment explanation
Indices: 56227265--56227305 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 14
56227255 ATCCATGAGC
56227265 ATCTCTTTTCTTT-T
1 ATCTC-TTTCTTTAT
56227279 AT-TCTATTCTTTAT
1 ATCTCT-TTCTTTAT
56227293 ATCTCTTTCTTTA
1 ATCTCTTTCTTTA
56227306 ACATTATTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
12 1 0.04
13 8 0.33
14 12 0.50
15 3 0.12
ACGTcount: A:0.15, C:0.20, G:0.00, T:0.66
Consensus pattern (14 bp):
ATCTCTTTCTTTAT
Found at i:56229189 original size:19 final size:19
Alignment explanation
Indices: 56229167--56229208 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
56229157 TTTGTTTTTG
56229167 TTTTTACT-TTTACTTTTAT
1 TTTTTACTATTTA-TTTTAT
**
56229186 TTTTTTTTATTTATTTTAT
1 TTTTTACTATTTATTTTAT
56229205 TTTT
1 TTTT
56229209 ATTAATCTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 16 0.80
20 4 0.20
ACGTcount: A:0.14, C:0.05, G:0.00, T:0.81
Consensus pattern (19 bp):
TTTTTACTATTTATTTTAT
Found at i:56229189 original size:25 final size:25
Alignment explanation
Indices: 56229161--56229211 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 25
56229151 TTAAATTTTG
56229161 TTTTTGTT-TTTACTTTTACTTTTAT
1 TTTTTGTTATTTA-TTTTACTTTTAT
* *
56229186 TTTTTTTTATTTATTTTATTTTTAT
1 TTTTTGTTATTTATTTTACTTTTAT
56229211 T
1 T
56229212 AATCTTTGTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
25 19 0.83
26 4 0.17
ACGTcount: A:0.14, C:0.04, G:0.02, T:0.80
Consensus pattern (25 bp):
TTTTTGTTATTTATTTTACTTTTAT
Found at i:56229198 original size:14 final size:15
Alignment explanation
Indices: 56229181--56229211 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
56229171 TACTTTTACT
56229181 TTTATTTT-TTTTTA
1 TTTATTTTATTTTTA
56229195 TTTATTTTATTTTTA
1 TTTATTTTATTTTTA
56229210 TT
1 TT
56229212 AATCTTTGTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.50
15 8 0.50
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (15 bp):
TTTATTTTATTTTTA
Found at i:56229490 original size:20 final size:20
Alignment explanation
Indices: 56229465--56229506 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
56229455 ATATTTCATA
*
56229465 TTTCTTGTCGTAGTATTTTT
1 TTTCTTGTCATAGTATTTTT
56229485 TTTCTTGTCATAGTATTTTT
1 TTTCTTGTCATAGTATTTTT
56229505 TT
1 TT
56229507 AGGTACTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.12, C:0.10, G:0.12, T:0.67
Consensus pattern (20 bp):
TTTCTTGTCATAGTATTTTT
Found at i:56233771 original size:45 final size:45
Alignment explanation
Indices: 56233745--56233998 Score: 325
Period size: 45 Copynumber: 5.6 Consensus size: 45
56233735 TTTGACATGA
** *
56233745 TGCCATAGTG-CTTTTCAACTATGGTCTTATTCATTTC-CATCATAT
1 TGCCATAGTGTC-TTTCAACTATGGTCTTATTCATTTCTGGT-ATAG
* * * *
56233790 TGCCACAATGTTTTTCAACTGTGGTCTTATTCGA-TTCTGGTATAG
1 TGCCATAGTGTCTTTCAACTATGGTCTTATTC-ATTTCTGGTATAG
* *
56233835 TGCCCTAGTGTCTTTCAACTATGGTCTTATTCATTTCCGGTATAG
1 TGCCATAGTGTCTTTCAACTATGGTCTTATTCATTTCTGGTATAG
* * *
56233880 TGCCATAGTGTCTTTCAATTATGATCTTATTCATTTTTGGTATAG
1 TGCCATAGTGTCTTTCAACTATGGTCTTATTCATTTCTGGTATAG
* *
56233925 TGCCATAGTGTCTTTCAATTATCGTCTTATTCATTTCTGGTATAG
1 TGCCATAGTGTCTTTCAACTATGGTCTTATTCATTTCTGGTATAG
*
56233970 TGCTATAGTGTCTTTCAACTATGGTCTTA
1 TGCCATAGTGTCTTTCAACTATGGTCTTA
56233999 CTCGTATTTC
Statistics
Matches: 181, Mismatches: 24, Indels: 8
0.85 0.11 0.04
Matches are distributed among these distances:
44 1 0.01
45 178 0.98
46 2 0.01
ACGTcount: A:0.20, C:0.19, G:0.16, T:0.45
Consensus pattern (45 bp):
TGCCATAGTGTCTTTCAACTATGGTCTTATTCATTTCTGGTATAG
Found at i:56242210 original size:42 final size:42
Alignment explanation
Indices: 56242164--56242270 Score: 144
Period size: 42 Copynumber: 2.5 Consensus size: 42
56242154 CACAACTGTG
* * *
56242164 TGTATCAAGTTAGTGAGTCACACGGTTTGGCATACGGCCGTC
1 TGTATCAAGTCAGTGAGTCACACGGTCTGGCACACGGCCGTC
* *
56242206 TGTATCAAGTCAGTGAGCCACACGGTCTGGCACACGGCCGTG
1 TGTATCAAGTCAGTGAGTCACACGGTCTGGCACACGGCCGTC
*
56242248 TG-ATCTAAGTCAGTGAGTTACAC
1 TGTATC-AAGTCAGTGAGTCACAC
56242271 AATTTAAGAC
Statistics
Matches: 57, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
41 3 0.05
42 54 0.95
ACGTcount: A:0.23, C:0.23, G:0.28, T:0.25
Consensus pattern (42 bp):
TGTATCAAGTCAGTGAGTCACACGGTCTGGCACACGGCCGTC
Found at i:56244956 original size:27 final size:27
Alignment explanation
Indices: 56244909--56244972 Score: 94
Period size: 27 Copynumber: 2.4 Consensus size: 27
56244899 AAATATTCTT
* *
56244909 TAAATTAAT-AAATATTAATTTATCGA
1 TAAACTAATAAAATATTAATTTAGCGA
*
56244935 TAAACTAATAAAATATTCATTTAGCGA
1 TAAACTAATAAAATATTAATTTAGCGA
56244962 TAAACTAATAA
1 TAAACTAATAA
56244973 CCTCAATAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
26 8 0.24
27 26 0.76
ACGTcount: A:0.52, C:0.08, G:0.05, T:0.36
Consensus pattern (27 bp):
TAAACTAATAAAATATTAATTTAGCGA
Found at i:56247212 original size:45 final size:46
Alignment explanation
Indices: 56247111--56247234 Score: 135
Period size: 45 Copynumber: 2.7 Consensus size: 46
56247101 TCAAAGATGT
* * * * *
56247111 CATAGTGTCTTTCAACTATGATCTTA-TTCATTTTCGTCATATTGT
1 CATAGTGTCTTTCAACTATGGTCTTATTTGATTCTCGTCATAGTGC
* * * *
56247156 CATAATTTCTTTCAACTATGGTATTATTTGATTCTGGT-ATAGTGC
1 CATAGTGTCTTTCAACTATGGTCTTATTTGATTCTCGTCATAGTGC
* *
56247201 CATAGTGTCTTTCATCTATGGTCTTGTTTGATTC
1 CATAGTGTCTTTCAACTATGGTCTTATTTGATTC
56247235 GTGATGCCAT
Statistics
Matches: 64, Mismatches: 14, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
45 56 0.88
46 8 0.12
ACGTcount: A:0.21, C:0.16, G:0.15, T:0.48
Consensus pattern (46 bp):
CATAGTGTCTTTCAACTATGGTCTTATTTGATTCTCGTCATAGTGC
Found at i:56248089 original size:17 final size:17
Alignment explanation
Indices: 56248067--56248101 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
56248057 ATTTAATAAA
56248067 ATTTCATAAAACATATC
1 ATTTCATAAAACATATC
56248084 ATTTCATAAAACATATC
1 ATTTCATAAAACATATC
56248101 A
1 A
56248102 CCTAATCCGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.49, C:0.17, G:0.00, T:0.34
Consensus pattern (17 bp):
ATTTCATAAAACATATC
Found at i:56257041 original size:69 final size:69
Alignment explanation
Indices: 56256925--56257064 Score: 246
Period size: 69 Copynumber: 2.0 Consensus size: 69
56256915 TATCATTGTC
*
56256925 TCAGAAAAGTCACTTTATGATTTTTCTCTCACTGAGAAGAGCAATTGTTATACTAAATTCAACCT
1 TCAGAAAAGTCACTTTATAATTTTTCTCTCACTGAGAAGAGCAATTGTTATACTAAATTCAACCT
56256990 AAAG
66 AAAG
*
56256994 TCAGGAAAGTCACTTTATAATTTTTCTCTCAAC-GAGAAGAGCAATTGTTATACTAAATTCAACC
1 TCAGAAAAGTCACTTTATAATTTTTCTCTC-ACTGAGAAGAGCAATTGTTATACTAAATTCAACC
56257058 TAAAG
65 TAAAG
56257063 TC
1 TC
56257065 TACCAATGTA
Statistics
Matches: 68, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
69 66 0.97
70 2 0.03
ACGTcount: A:0.36, C:0.18, G:0.13, T:0.33
Consensus pattern (69 bp):
TCAGAAAAGTCACTTTATAATTTTTCTCTCACTGAGAAGAGCAATTGTTATACTAAATTCAACCT
AAAG
Found at i:56258572 original size:15 final size:15
Alignment explanation
Indices: 56258552--56258589 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
56258542 ACATTTCATA
56258552 ATTTTTTGAATTTTT-
1 ATTTTTT-AATTTTTC
56258567 ATTTTTATAATTTTTC
1 ATTTTT-TAATTTTTC
56258583 ATTTTTT
1 ATTTTTT
56258590 TATGTGACAA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
15 14 0.67
16 7 0.33
ACGTcount: A:0.21, C:0.03, G:0.03, T:0.74
Consensus pattern (15 bp):
ATTTTTTAATTTTTC
Found at i:56260195 original size:128 final size:129
Alignment explanation
Indices: 56260039--56260300 Score: 490
Period size: 128 Copynumber: 2.0 Consensus size: 129
56260029 TTTTGTAACA
*
56260039 GTTGAACTGAAGAGAAGAAAAGAGAGAAATTGTTGTGTTTAGTAGGAGAGCTCAAAAATTCTGGT
1 GTTGAACTGAAGAGAAGAAAAGAGAGAAATTGTTGTGTTTAGTAGGACAGCTCAAAAATTCTGGT
56260104 GAAGATGAATAACTCAGTGTTTTTAGTGTACATTCTTTTTTATGGTGAAATTGTAAAAGGTG-T
66 GAAGATGAATAACTCAGTGTTTTTAGTGTACATTCTTTTTTATGGTGAAATTGTAAAAGGTGAT
* *
56260167 GTTGAATTGAAGAGAAGAAAAGTGAGAAATTGTTGTGTTTAGTAGGACAGCTCAAAAATTCTGGT
1 GTTGAACTGAAGAGAAGAAAAGAGAGAAATTGTTGTGTTTAGTAGGACAGCTCAAAAATTCTGGT
56260232 GAAGATGAATAACTCAGTGTTTTTAGTGTACATTCTTTTTTATGGTGAAATTGTAAAAGGTGAT
66 GAAGATGAATAACTCAGTGTTTTTAGTGTACATTCTTTTTTATGGTGAAATTGTAAAAGGTGAT
56260296 GTTGA
1 GTTGA
56260301 TTGTGTATTC
Statistics
Matches: 130, Mismatches: 3, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
128 124 0.95
129 6 0.05
ACGTcount: A:0.34, C:0.06, G:0.26, T:0.34
Consensus pattern (129 bp):
GTTGAACTGAAGAGAAGAAAAGAGAGAAATTGTTGTGTTTAGTAGGACAGCTCAAAAATTCTGGT
GAAGATGAATAACTCAGTGTTTTTAGTGTACATTCTTTTTTATGGTGAAATTGTAAAAGGTGAT
Found at i:56263685 original size:14 final size:14
Alignment explanation
Indices: 56263668--56263697 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
56263658 GATAACAAAG
56263668 AAAATATAAAAATA
1 AAAATATAAAAATA
56263682 AAAATATAAAAATA
1 AAAATATAAAAATA
56263696 AA
1 AA
56263698 TAGAAAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (14 bp):
AAAATATAAAAATA
Found at i:56296977 original size:25 final size:25
Alignment explanation
Indices: 56296943--56296996 Score: 81
Period size: 25 Copynumber: 2.2 Consensus size: 25
56296933 TGAGCTACAT
*
56296943 GGCCTGGCACATGGGTGCATGACAC
1 GGCCTGGCACACGGGTGCATGACAC
**
56296968 GGCCTGGCACACGGGTGTGTGACAC
1 GGCCTGGCACACGGGTGCATGACAC
56296993 GGCC
1 GGCC
56296997 GTGTGACCCT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.17, C:0.30, G:0.39, T:0.15
Consensus pattern (25 bp):
GGCCTGGCACACGGGTGCATGACAC
Found at i:56298334 original size:25 final size:22
Alignment explanation
Indices: 56298295--56298339 Score: 63
Period size: 25 Copynumber: 1.9 Consensus size: 22
56298285 CAAATTTGAA
56298295 GCTAAGCACATACCAAGCATTAG
1 GCTAAGCACATACCAA-CATTAG
56298318 GCTAAGCTACCATACCAACATT
1 GCTAAGC-A-CATACCAACATT
56298340 GCCTAAACTA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
23 7 0.35
24 5 0.25
25 8 0.40
ACGTcount: A:0.38, C:0.29, G:0.13, T:0.20
Consensus pattern (22 bp):
GCTAAGCACATACCAACATTAG
Found at i:56298345 original size:23 final size:23
Alignment explanation
Indices: 56298296--56298345 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 23
56298286 AAATTTGAAG
*
56298296 CTAAGCACATACCAAGCATTAGG
1 CTAAGCACATACCAAGCATTAGC
56298319 CTAAGCTACCATACCAA-CATT-GC
1 CTAAGC-A-CATACCAAGCATTAGC
56298342 CTAA
1 CTAA
56298346 ACTATAACCA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
23 11 0.46
24 5 0.21
25 8 0.33
ACGTcount: A:0.38, C:0.30, G:0.12, T:0.20
Consensus pattern (23 bp):
CTAAGCACATACCAAGCATTAGC
Done.