Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr5
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: 39371879
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 2227820 characters in sequence are not A, C, G, or T
File 19 of 103
Found at i:6925043 original size:28 final size:27
Alignment explanation
Indices: 6925007--6925059 Score: 79
Period size: 28 Copynumber: 1.9 Consensus size: 27
6924997 ATATCCTGGT
*
6925007 GGTGGAAAATTACAATTTTGCCCCTGA
1 GGTGGAAAATTACAATTTTACCCCTGA
*
6925034 GGTGGCAAAATTACCATTTTACCCCT
1 GGTGG-AAAATTACAATTTTACCCCT
6925060 ATAGTCCAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
27 5 0.22
28 18 0.78
ACGTcount: A:0.28, C:0.23, G:0.19, T:0.30
Consensus pattern (27 bp):
GGTGGAAAATTACAATTTTACCCCTGA
Found at i:6925129 original size:20 final size:20
Alignment explanation
Indices: 6925104--6925149 Score: 83
Period size: 20 Copynumber: 2.3 Consensus size: 20
6925094 CTTTTAAACC
6925104 TCAAATCATACTCCAATAAG
1 TCAAATCATACTCCAATAAG
*
6925124 TCAAATTATACTCCAATAAG
1 TCAAATCATACTCCAATAAG
6925144 TCAAAT
1 TCAAAT
6925150 GGGGCCAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.46, C:0.22, G:0.04, T:0.28
Consensus pattern (20 bp):
TCAAATCATACTCCAATAAG
Found at i:6926911 original size:20 final size:20
Alignment explanation
Indices: 6926886--6926929 Score: 88
Period size: 20 Copynumber: 2.2 Consensus size: 20
6926876 AATAAGATAC
6926886 ATTGAAAATGTATTATTCAT
1 ATTGAAAATGTATTATTCAT
6926906 ATTGAAAATGTATTATTCAT
1 ATTGAAAATGTATTATTCAT
6926926 ATTG
1 ATTG
6926930 GATGAATCTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.39, C:0.05, G:0.11, T:0.45
Consensus pattern (20 bp):
ATTGAAAATGTATTATTCAT
Found at i:6929963 original size:3 final size:3
Alignment explanation
Indices: 6929949--6929981 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
6929939 TAGAATTATA
*
6929949 AAT AAC AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
6929982 TCAAAGGTAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:6934817 original size:42 final size:42
Alignment explanation
Indices: 6934758--6934880 Score: 210
Period size: 42 Copynumber: 2.9 Consensus size: 42
6934748 GTTGATTTGA
6934758 ACCCGGCTATGTGCGAGTAGGAGTGCACATAAGCCGTTGCTG
1 ACCCGGCTATGTGCGAGTAGGAGTGCACATAAGCCGTTGCTG
* *
6934800 ACCCGACTATGTGCGAGTAGGAGTGCATATAAGCCGTTGCTG
1 ACCCGGCTATGTGCGAGTAGGAGTGCACATAAGCCGTTGCTG
* *
6934842 ACCCGGCTATGTGTGAGTGGGAGTGCACATAAGCCGTTG
1 ACCCGGCTATGTGCGAGTAGGAGTGCACATAAGCCGTTG
6934881 TTGCCCCCAT
Statistics
Matches: 75, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 75 1.00
ACGTcount: A:0.22, C:0.22, G:0.33, T:0.23
Consensus pattern (42 bp):
ACCCGGCTATGTGCGAGTAGGAGTGCACATAAGCCGTTGCTG
Found at i:6935151 original size:26 final size:26
Alignment explanation
Indices: 6935115--6935176 Score: 106
Period size: 26 Copynumber: 2.4 Consensus size: 26
6935105 TTGCATATGA
6935115 GATGATGATGATGGGATGATGTGCAT
1 GATGATGATGATGGGATGATGTGCAT
*
6935141 GATGATGATGATGGGATGGTGTGCAT
1 GATGATGATGATGGGATGATGTGCAT
*
6935167 GTTGATGATG
1 GATGATGATG
6935177 GGTATATGGT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 34 1.00
ACGTcount: A:0.24, C:0.03, G:0.40, T:0.32
Consensus pattern (26 bp):
GATGATGATGATGGGATGATGTGCAT
Found at i:6940156 original size:13 final size:13
Alignment explanation
Indices: 6940138--6940162 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
6940128 NNNNAGAAAA
6940138 TTTATAAAATCAT
1 TTTATAAAATCAT
6940151 TTTATAAAATCA
1 TTTATAAAATCA
6940163 CAATTTCTCT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.08, G:0.00, T:0.44
Consensus pattern (13 bp):
TTTATAAAATCAT
Found at i:6941287 original size:28 final size:27
Alignment explanation
Indices: 6941241--6941294 Score: 72
Period size: 28 Copynumber: 2.0 Consensus size: 27
6941231 CAGTCCTGGT
** *
6941241 GGTGGAAAATTACTGTTTTGCCCCTAG
1 GGTGGAAAATTACCATTTTACCCCTAG
6941268 GGTGGTAAAATTACCATTTTACCCCTA
1 GGTGG-AAAATTACCATTTTACCCCTA
6941295 TACTCTAAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
27 5 0.22
28 18 0.78
ACGTcount: A:0.26, C:0.20, G:0.20, T:0.33
Consensus pattern (27 bp):
GGTGGAAAATTACCATTTTACCCCTAG
Found at i:6945388 original size:35 final size:35
Alignment explanation
Indices: 6945260--6945449 Score: 179
Period size: 35 Copynumber: 5.4 Consensus size: 35
6945250 GCAAGGGCTG
*
6945260 GTGCTGTCGGGTTTGTGAGGGAGAAA--ACAGGAGTT
1 GTGCTGCCGGGTTTGTGAGGGAGAAAGGA-AGG-GTT
* * * * *
6945295 GTTGCTG-CTGGTTTGAGAGAGAGAAATGAGGGGTT
1 G-TGCTGCCGGGTTTGTGAGGGAGAAAGGAAGGGTT
* * * *
6945330 GTGCTACTGGGTTTATGAAGGAGAAAGGAAGGGTT
1 GTGCTGCCGGGTTTGTGAGGGAGAAAGGAAGGGTT
**
6945365 GTGCTGCCAAGTTTGTGAGGGAGAAAGGAAGGGTT
1 GTGCTGCCGGGTTTGTGAGGGAGAAAGGAAGGGTT
* * * *
6945400 GTGTTGTCGGGTTTGTGAGGGAGAAAAGAAAGGTT
1 GTGCTGCCGGGTTTGTGAGGGAGAAAGGAAGGGTT
*
6945435 GTGCTGCCGGTTTTG
1 GTGCTGCCGGGTTTG
6945450 AGAGTGAAGG
Statistics
Matches: 123, Mismatches: 28, Indels: 8
0.77 0.18 0.05
Matches are distributed among these distances:
34 4 0.03
35 111 0.90
36 7 0.06
37 1 0.01
ACGTcount: A:0.23, C:0.07, G:0.42, T:0.27
Consensus pattern (35 bp):
GTGCTGCCGGGTTTGTGAGGGAGAAAGGAAGGGTT
Found at i:6945464 original size:70 final size:69
Alignment explanation
Indices: 6945260--6945466 Score: 197
Period size: 70 Copynumber: 3.0 Consensus size: 69
6945250 GCAAGGGCTG
* * * *
6945260 GTGCTGTCGGGTTTGTGAGGGAGAAAA-CAGGAGTTGTTGCTGCTGG-TTTGAGAGAGAGAAATG
1 GTGCTGTCGGGTTTGTGAGGGAGAAAAGAAGG-GTTG-TGCTGCCGGTTTTGAGAGAGA-AGAGG
*
6945323 AGGGGTT
63 AAGGGTT
* * * * * *
6945330 GTGCT-ACTGGGTTTATGAAGGAGAAAGGAAGGGTTGTGCTGCCAAGTTTGTGAGGGAGAA-AGG
1 GTGCTGTC-GGGTTTGTGAGGGAGAAAAGAAGGGTTGTGCTGCC-GGTTT-TGAGAGAGAAGAGG
6945393 AAGGGTT
63 AAGGGTT
* * *
6945400 GTGTTGTCGGGTTTGTGAGGGAGAAAAGAAAGGTTGTGCTGCCGGTTTTGAGAGTGAAGGAGGAA
1 GTGCTGTCGGGTTTGTGAGGGAGAAAAGAAGGGTTGTGCTGCCGGTTTTGAGAGAGAA-GAGGAA
6945465 GG
65 GG
6945467 ATGGGGGTTG
Statistics
Matches: 110, Mismatches: 19, Indels: 16
0.76 0.13 0.11
Matches are distributed among these distances:
68 8 0.07
69 11 0.10
70 76 0.69
71 7 0.06
72 8 0.07
ACGTcount: A:0.25, C:0.07, G:0.43, T:0.26
Consensus pattern (69 bp):
GTGCTGTCGGGTTTGTGAGGGAGAAAAGAAGGGTTGTGCTGCCGGTTTTGAGAGAGAAGAGGAAG
GGTT
Found at i:6950246 original size:20 final size:20
Alignment explanation
Indices: 6950221--6950258 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
6950211 TTCAAATTCA
*
6950221 TGCCCATTTATCAATAGACG
1 TGCCCATCTATCAATAGACG
*
6950241 TGCCCATCTATCGATAGA
1 TGCCCATCTATCAATAGA
6950259 TGCAAGTCAA
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:0.29, C:0.26, G:0.16, T:0.29
Consensus pattern (20 bp):
TGCCCATCTATCAATAGACG
Found at i:6960919 original size:45 final size:45
Alignment explanation
Indices: 6960846--6960947 Score: 120
Period size: 45 Copynumber: 2.3 Consensus size: 45
6960836 GAAATGAAAA
* * *
6960846 TATTTAA-A-TATTATTTAACTATAATAAATATTATAAAGAATAT
1 TATTTAATATTATTATTTAACTATAATAAATATAATAAAAAACAT
* *
6960889 TATTTAATATTATTATTTGAA-TATATTAAATGTAATAAAAAACAT
1 TATTTAATATTATTATTT-AACTATAATAAATATAATAAAAAACAT
*
6960934 TATTTAGTATTATT
1 TATTTAATATTATT
6960948 TAAATTTAAT
Statistics
Matches: 50, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
43 7 0.14
44 1 0.02
45 40 0.80
46 2 0.04
ACGTcount: A:0.47, C:0.02, G:0.04, T:0.47
Consensus pattern (45 bp):
TATTTAATATTATTATTTAACTATAATAAATATAATAAAAAACAT
Found at i:6961054 original size:22 final size:22
Alignment explanation
Indices: 6960985--6961091 Score: 65
Period size: 22 Copynumber: 4.8 Consensus size: 22
6960975 TTTTAATATT
*
6960985 AAATATTATTTAATTATAATAA
1 AAATATTATTAAATTATAATAA
* * ** * *
6961007 AAGGT-TTAATATCTTTTAGTACA
1 AA-ATATTATTAAATTATAATA-A
6961030 AAATATTATTAAATTATAATAA
1 AAATATTATTAAATTATAATAA
* * * *
6961052 AAATATGT-TTACATTTTGATGA
1 AAATAT-TATTAAATTATAATAA
*
6961074 AAATATTATTTAATTATA
1 AAATATTATTAAATTATA
6961092 GAAAAAGGTA
Statistics
Matches: 59, Mismatches: 21, Indels: 10
0.66 0.23 0.11
Matches are distributed among these distances:
21 1 0.02
22 42 0.71
23 16 0.27
ACGTcount: A:0.47, C:0.03, G:0.06, T:0.45
Consensus pattern (22 bp):
AAATATTATTAAATTATAATAA
Found at i:6961407 original size:23 final size:23
Alignment explanation
Indices: 6961342--6961408 Score: 57
Period size: 23 Copynumber: 2.9 Consensus size: 23
6961332 TTGTAATATT
*
6961342 AAATATTATTTAATTAT-A-ACA
1 AAATATTATTAAATTATAATACA
* ** *
6961363 AAAGATTTAATTATCTTCTAATACA
1 AAATA-TT-ATTAAATTATAATACA
6961388 AAATATTATTAAATTATAATA
1 AAATATTATTAAATTATAATA
6961409 AAATATGTTT
Statistics
Matches: 33, Mismatches: 9, Indels: 6
0.69 0.19 0.12
Matches are distributed among these distances:
21 4 0.12
22 2 0.06
23 17 0.52
24 3 0.09
25 7 0.21
ACGTcount: A:0.51, C:0.06, G:0.01, T:0.42
Consensus pattern (23 bp):
AAATATTATTAAATTATAATACA
Found at i:6966281 original size:13 final size:13
Alignment explanation
Indices: 6966263--6966287 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
6966253 TTCCAGAAAA
6966263 TTTATAAAATCAT
1 TTTATAAAATCAT
6966276 TTTATAAAATCA
1 TTTATAAAATCA
6966288 CAATTTCTCC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.08, G:0.00, T:0.44
Consensus pattern (13 bp):
TTTATAAAATCAT
Found at i:6967462 original size:19 final size:19
Alignment explanation
Indices: 6967438--6967475 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
6967428 ACTTCTAAAC
6967438 CTCAAATCATACTCCAATA
1 CTCAAATCATACTCCAATA
6967457 CTCAAATCATACTCCAATA
1 CTCAAATCATACTCCAATA
6967476 AGTCAAATGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.42, C:0.32, G:0.00, T:0.26
Consensus pattern (19 bp):
CTCAAATCATACTCCAATA
Found at i:6972591 original size:22 final size:21
Alignment explanation
Indices: 6972562--6972605 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 21
6972552 ATAGATTTTT
6972562 TTTACTTAATT-TTGATAATAA
1 TTTACTTAATTCTTG-TAATAA
*
6972583 TTTAGCTTAGTTCTTGTAATAA
1 TTTA-CTTAATTCTTGTAATAA
6972605 T
1 T
6972606 GTATAGAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
21 4 0.20
22 13 0.65
23 3 0.15
ACGTcount: A:0.32, C:0.07, G:0.09, T:0.52
Consensus pattern (21 bp):
TTTACTTAATTCTTGTAATAA
Found at i:6974582 original size:37 final size:37
Alignment explanation
Indices: 6974424--6974584 Score: 115
Period size: 37 Copynumber: 4.4 Consensus size: 37
6974414 TTGATTTATG
* * * * *
6974424 CACTGTGCGTGATTTGACTTTTCGTCTGTTGCTTCGA
1 CACTGAGCATGATTTGACTCTCCGTCAGTTGCTTCGA
* * * * * * * *
6974461 CAGTAATCGTGATTTGATTCTCCGCCCGTTGCTTCAA
1 CACTGAGCATGATTTGACTCTCCGTCAGTTGCTTCGA
* * * ** * *
6974498 CACTGACCATGATTTGATTCTCCATTGGTTGCTTGGG
1 CACTGAGCATGATTTGACTCTCCGTCAGTTGCTTCGA
* * *
6974535 CATTGTGCATGATTTGACTCTCCGTCAATTGCTTCGA
1 CACTGAGCATGATTTGACTCTCCGTCAGTTGCTTCGA
6974572 CACTGAGCATGAT
1 CACTGAGCATGAT
6974585 CCATTGATTG
Statistics
Matches: 91, Mismatches: 33, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
37 91 1.00
ACGTcount: A:0.17, C:0.24, G:0.22, T:0.37
Consensus pattern (37 bp):
CACTGAGCATGATTTGACTCTCCGTCAGTTGCTTCGA
Found at i:6975297 original size:14 final size:14
Alignment explanation
Indices: 6975278--6975311 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
6975268 GTGTAAGTAC
6975278 TATGTTGCCGTTAT
1 TATGTTGCCGTTAT
6975292 TATGTTGCCGTTAT
1 TATGTTGCCGTTAT
*
6975306 TTTGTT
1 TATGTT
6975312 TAAGGATTGT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.12, C:0.12, G:0.21, T:0.56
Consensus pattern (14 bp):
TATGTTGCCGTTAT
Found at i:6977829 original size:2 final size:2
Alignment explanation
Indices: 6977822--6977847 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
6977812 CCAAGTCAAG
6977822 CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT
6977848 NTTGGTTTTT
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:6977879 original size:54 final size:52
Alignment explanation
Indices: 6977797--6977901 Score: 192
Period size: 54 Copynumber: 2.0 Consensus size: 52
6977787 AACTTCCCTA
6977797 TGGTTTTTTCTTTTTCCAAGTCAAGCTCTCTCTCTCTCTCTCTCTCTCTCTNT
1 TGGTTTTTTCTTTTTCCAAGTCAAGCTCTCTCTCTCTCTCTCTCTCTCTCT-T
6977850 TGGTTTTTTCTTTTTCCTAAGTCAAGCTCTCTCTCTCTCTCTCTCTCTCTCT
1 TGGTTTTTTCTTTTTCC-AAGTCAAGCTCTCTCTCTCTCTCTCTCTCTCTCT
6977902 AGAGCCTGTA
Statistics
Matches: 51, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
53 17 0.33
54 34 0.67
ACGTcount: A:0.08, C:0.32, G:0.08, T:0.51
Consensus pattern (52 bp):
TGGTTTTTTCTTTTTCCAAGTCAAGCTCTCTCTCTCTCTCTCTCTCTCTCTT
Found at i:6977883 original size:2 final size:2
Alignment explanation
Indices: 6977876--6977901 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
6977866 CTAAGTCAAG
6977876 CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT
6977902 AGAGCCTGTA
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:6982631 original size:26 final size:26
Alignment explanation
Indices: 6982595--6982648 Score: 108
Period size: 26 Copynumber: 2.1 Consensus size: 26
6982585 GATGTGAAAC
6982595 TCAAACTAGGGGAAGAAAAGAAGGGG
1 TCAAACTAGGGGAAGAAAAGAAGGGG
6982621 TCAAACTAGGGGAAGAAAAGAAGGGG
1 TCAAACTAGGGGAAGAAAAGAAGGGG
6982647 TC
1 TC
6982649 TGATCAGAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.44, C:0.09, G:0.37, T:0.09
Consensus pattern (26 bp):
TCAAACTAGGGGAAGAAAAGAAGGGG
Found at i:6986381 original size:2 final size:2
Alignment explanation
Indices: 6986374--6986405 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
6986364 ATATGACAAT
*
6986374 GA GA GA GA GA GA GC GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
6986406 AGGAGGTAAG
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:0.47, C:0.03, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:6996578 original size:18 final size:19
Alignment explanation
Indices: 6996555--6996591 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
6996545 TCTGTCAGTC
6996555 GATTTTTTT-GTTTTATTT
1 GATTTTTTTAGTTTTATTT
*
6996573 GATTTTTTTATTTTTATTT
1 GATTTTTTTAGTTTTATTT
6996592 TTTAAAAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 9 0.53
19 8 0.47
ACGTcount: A:0.14, C:0.00, G:0.08, T:0.78
Consensus pattern (19 bp):
GATTTTTTTAGTTTTATTT
Found at i:7006258 original size:2 final size:2
Alignment explanation
Indices: 7006251--7006292 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
7006241 CATTAATGAC
7006251 AT AT AT AT AT AT AT AT 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 AT AT AT AT AT AT AT AT
7006293 NNNNNNNNNN
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:7006347 original size:2 final size:2
Alignment explanation
Indices: 7006340--7006390 Score: 93
Period size: 2 Copynumber: 25.5 Consensus size: 2
7006330 NNNNNNNNNN
7006340 AT AT AT AT AT AT AT AT 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 AT AT AT AT AT AT AT AT
*
7006382 AT AT GT AT A
1 AT AT AT AT A
7006391 GATAGATAGA
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
AT
Found at i:7009739 original size:2 final size:2
Alignment explanation
Indices: 7009732--7009772 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
7009722 TAATACTGTT
7009732 TA TA TA TA TA TA TA TA 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 TA TA TA TA TA TA TA TA T
7009773 GNNNNNNNNN
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:7011265 original size:29 final size:30
Alignment explanation
Indices: 7011208--7011265 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 30
7011198 GTGTAAGGGG
* *
7011208 TTTATTTAAATCAAAATAAAAATTTAAGAA
1 TTTATTTAAATCAAAATAAAAAATAAAGAA
* *
7011238 TTTATTTGAAT-ATAATAAAAAATAAAGA
1 TTTATTTAAATCAAAATAAAAAATAAAGA
7011266 CTGAATTGAT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
29 14 0.58
30 10 0.42
ACGTcount: A:0.57, C:0.02, G:0.05, T:0.36
Consensus pattern (30 bp):
TTTATTTAAATCAAAATAAAAAATAAAGAA
Found at i:7013537 original size:114 final size:114
Alignment explanation
Indices: 7013337--7013564 Score: 266
Period size: 114 Copynumber: 2.0 Consensus size: 114
7013327 TAGTCTAATC
* * * *
7013337 CGTCATATTTAAGAGTCAAATAGATTAAACATTTTTAAAAAATCAATCAAAATTGACCAAATATG
1 CGTCATATGTAAGAATCAAATAGATCAAACATTTTTAAAAAATCAATCAAAATTGACCAAATATA
* * *
7013402 AAGTAGAATTGAATTGATCAAACATCGAATTGATTTGATC-AGTTCGATT
66 AAGTAGAATCGAACTGATCAAACATCGAATCGATTTGATCGA-TTCGATT
* ** * *
7013451 CGTCATATGTAAGAATCAAATGAGA-CAAATATTTTTAAAAAATTGA-CGAGAATTGATCAAATA
1 CGTCATATGTAAGAATCAAAT-AGATCAAACATTTTTAAAAAATCAATC-AAAATTGACCAAATA
* *
7013514 TAAAAG-AGAATCGAACTGATCAAATATCGAATCGGTTTGATCGATTCGATT
64 T-AAAGTAGAATCGAACTGATCAAACATCGAATCGATTTGATCGATTCGATT
7013565 TTGGATTAAA
Statistics
Matches: 96, Mismatches: 14, Indels: 8
0.81 0.12 0.07
Matches are distributed among these distances:
113 1 0.01
114 88 0.92
115 7 0.07
ACGTcount: A:0.43, C:0.11, G:0.15, T:0.31
Consensus pattern (114 bp):
CGTCATATGTAAGAATCAAATAGATCAAACATTTTTAAAAAATCAATCAAAATTGACCAAATATA
AAGTAGAATCGAACTGATCAAACATCGAATCGATTTGATCGATTCGATT
Found at i:7020223 original size:20 final size:19
Alignment explanation
Indices: 7020200--7020253 Score: 56
Period size: 20 Copynumber: 2.8 Consensus size: 19
7020190 TAAATATAAA
7020200 TAACATAAAACT-AACATTAT
1 TAACATAAAA-TAAACATT-T
*
7020220 TAACTTAAAATAAACATTT
1 TAACATAAAATAAACATTT
* *
7020239 AAACATAAATTAAAC
1 TAACATAAAATAAAC
7020254 TAAACTAATA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
19 14 0.48
20 15 0.52
ACGTcount: A:0.57, C:0.13, G:0.00, T:0.30
Consensus pattern (19 bp):
TAACATAAAATAAACATTT
Found at i:7036905 original size:5 final size:5
Alignment explanation
Indices: 7036895--7036926 Score: 64
Period size: 5 Copynumber: 6.4 Consensus size: 5
7036885 TACAATTCAG
7036895 GGAAA GGAAA GGAAA GGAAA GGAAA GGAAA GG
1 GGAAA GGAAA GGAAA GGAAA GGAAA GGAAA GG
7036927 CATACGTGAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 27 1.00
ACGTcount: A:0.56, C:0.00, G:0.44, T:0.00
Consensus pattern (5 bp):
GGAAA
Found at i:7040566 original size:23 final size:23
Alignment explanation
Indices: 7040540--7040584 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
7040530 TTGTGAAATG
*
7040540 TCATGGTTG-GAATGTGTGACACA
1 TCATGG-TGAGAATATGTGACACA
7040563 TCATGGTGAGAATATGTGACAC
1 TCATGGTGAGAATATGTGACAC
7040585 GGTTGTGACA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 2 0.10
23 18 0.90
ACGTcount: A:0.29, C:0.13, G:0.29, T:0.29
Consensus pattern (23 bp):
TCATGGTGAGAATATGTGACACA
Found at i:7040633 original size:81 final size:81
Alignment explanation
Indices: 7040493--7040642 Score: 203
Period size: 81 Copynumber: 1.9 Consensus size: 81
7040483 GTAGTAAACC
* * *** * *
7040493 ATATGTGACATGGTTGTGTCACGGTAAGGTTTAGAGTTTGTGAAATGTCATGGTTGGAATGTGTG
1 ATATGTGACACGGTTGTGACACGGTAAGGTTTAGAGTTTGTGAAACACCATGGTGGGAATATGTG
7040558 ACACATCATGGTGAGA
66 ACACATCATGGTGAGA
* *
7040574 ATATGTGACACGGTTGTGACACGGTAGGGTTTAGAGTTTGTGACACACCAT-GTAGGGAATATGT
1 ATATGTGACACGGTTGTGACACGGTAAGGTTTAGAGTTTGTGAAACACCATGGT-GGGAATATGT
7040638 GACAC
65 GACAC
7040643 GACAAGGCAA
Statistics
Matches: 59, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
80 2 0.03
81 57 0.97
ACGTcount: A:0.27, C:0.11, G:0.31, T:0.31
Consensus pattern (81 bp):
ATATGTGACACGGTTGTGACACGGTAAGGTTTAGAGTTTGTGAAACACCATGGTGGGAATATGTG
ACACATCATGGTGAGA
Found at i:7040656 original size:81 final size:81
Alignment explanation
Indices: 7040493--7040666 Score: 199
Period size: 81 Copynumber: 2.1 Consensus size: 81
7040483 GTAGTAAACC
* * *** * *
7040493 ATATGTGACATGGTTGTGTCACGGTAAGGTTTAGAGTTTGTGAAATGTCATGGTTGGAATGTGTG
1 ATATGTGACACGGTTGTGACACGGTAAGGTTTAGAGTTTGTGAAACACCATGGTGGGAATATGTG
* **
7040558 ACACATCATGGTGAGA
66 ACACATCAAGGCAAGA
* *
7040574 ATATGTGACACGGTTGTGACACGGTAGGGTTTAGAGTTTGTGACACACCAT-GTAGGGAATATGT
1 ATATGTGACACGGTTGTGACACGGTAAGGTTTAGAGTTTGTGAAACACCATGGT-GGGAATATGT
7040638 GACACGA-CAAGGCAAGA
65 GACAC-ATCAAGGCAAGA
*
7040655 ATATGTAACACG
1 ATATGTGACACG
7040667 ACTTGGAGGG
Statistics
Matches: 78, Mismatches: 13, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
80 2 0.03
81 75 0.96
82 1 0.01
ACGTcount: A:0.29, C:0.12, G:0.30, T:0.28
Consensus pattern (81 bp):
ATATGTGACACGGTTGTGACACGGTAAGGTTTAGAGTTTGTGAAACACCATGGTGGGAATATGTG
ACACATCAAGGCAAGA
Found at i:7040742 original size:21 final size:23
Alignment explanation
Indices: 7040676--7041043 Score: 112
Period size: 23 Copynumber: 15.9 Consensus size: 23
7040666 GACTTGGAGG
* * *
7040676 GAATATGTGAGACGACATGGTGA
1 GAATATGTGACATGCCATGGTGA
* **
7040699 GAATATGTGACACGTTA-GTGTGA
1 GAATATGTGACATGCCATG-GTGA
7040722 G-A-ATGTGACATGCCATGGTGA
1 GAATATGTGACATGCCATGGTGA
* * *
7040743 GAATATGTGAGACGGCATGGTGA
1 GAATATGTGACATGCCATGGTGA
* *
7040766 GCATATGTGACATG--ATAGGATTTA
1 GAATATGTGACATGCCAT-GG--TGA
* * * *
7040790 GAGTTTGTGACATGCCATGGAGG
1 GAATATGTGACATGCCATGGTGA
* * *
7040813 GAATCTATGACATAG-CAAGGTGA
1 GAATATGTGACAT-GCCATGGTGA
* * *
7040836 GAATGTGT-ACGATGACATGGTAA
1 GAATATGTGAC-ATGCCATGGTGA
** ** * *
7040859 GAATATGTGACGGGGTAAGGTTCA
1 GAATATGTGACATGCCATGG-TGA
* *
7040883 -AAGTTTGTGACATGCCATAGTG-
1 GAA-TATGTGACATGCCATGGTGA
* *
7040905 GAAATGTGTGACATGGCATGGTGA
1 G-AATATGTGACATGCCATGGTGA
* * *
7040929 GAATTTGTGACACAG-CATGTTGA
1 GAATATGTGACA-TGCCATGGTGA
* * * *
7040952 -AATCGTGTGAGACGGCATGGTGA
1 GAAT-ATGTGACATGCCATGGTGA
* *
7040975 GAATCTGTGACACGCCATGGTGA
1 GAATATGTGACATGCCATGGTGA
* * ** *
7040998 GCATATATGAGATAAACCATGGCT-T
1 G-A-ATATGTGACATGCCATGG-TGA
*
7041023 GAATATGTGGCATGCCATGGT
1 GAATATGTGACATGCCATGGT
7041044 TTGAAATAGA
Statistics
Matches: 252, Mismatches: 68, Indels: 51
0.68 0.18 0.14
Matches are distributed among these distances:
21 17 0.07
22 14 0.06
23 165 0.65
24 37 0.15
25 16 0.06
26 3 0.01
ACGTcount: A:0.30, C:0.12, G:0.32, T:0.26
Consensus pattern (23 bp):
GAATATGTGACATGCCATGGTGA
Found at i:7040761 original size:23 final size:23
Alignment explanation
Indices: 7040630--7040777 Score: 131
Period size: 23 Copynumber: 6.5 Consensus size: 23
7040620 ACCATGTAGG
* **
7040630 GAATATGTGACACGACAAGGCAA
1 GAATATGTGACACGACATGGTGA
* * * *
7040653 GAATATGTAACACGACTTGGAGG
1 GAATATGTGACACGACATGGTGA
*
7040676 GAATATGTGAGACGACATGGTGA
1 GAATATGTGACACGACATGGTGA
**
7040699 GAATATGTGACACGTTA-GTGTGA
1 GAATATGTGACACGACATG-GTGA
* *
7040722 G-A-ATGTGACATGCCATGGTGA
1 GAATATGTGACACGACATGGTGA
* *
7040743 GAATATGTGAGACGGCATGGTGA
1 GAATATGTGACACGACATGGTGA
*
7040766 GCATATGTGACA
1 GAATATGTGACA
7040778 TGATAGGATT
Statistics
Matches: 99, Mismatches: 22, Indels: 8
0.77 0.17 0.06
Matches are distributed among these distances:
21 15 0.15
22 4 0.04
23 80 0.81
ACGTcount: A:0.34, C:0.12, G:0.32, T:0.22
Consensus pattern (23 bp):
GAATATGTGACACGACATGGTGA
Found at i:7040766 original size:44 final size:46
Alignment explanation
Indices: 7040691--7040779 Score: 121
Period size: 44 Copynumber: 2.0 Consensus size: 46
7040681 TGTGAGACGA
**
7040691 CATGGTGAGAATATGTGACACGTTAGTGTGAG-A-ATGTGACATGC
1 CATGGTGAGAATATGTGACACGGCAGTGTGAGCATATGTGACATGC
*
7040735 CATGGTGAGAATATGTGAGACGGCA-TGGTGAGCATATGTGACATG
1 CATGGTGAGAATATGTGACACGGCAGT-GTGAGCATATGTGACATG
7040780 ATAGGATTTA
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
43 1 0.03
44 27 0.69
45 1 0.03
46 10 0.26
ACGTcount: A:0.29, C:0.11, G:0.34, T:0.26
Consensus pattern (46 bp):
CATGGTGAGAATATGTGACACGGCAGTGTGAGCATATGTGACATGC
Found at i:7040855 original size:93 final size:93
Alignment explanation
Indices: 7040758--7040932 Score: 208
Period size: 93 Copynumber: 1.9 Consensus size: 93
7040748 TGTGAGACGG
* * * * * * *
7040758 CATGGTGAGCATATGTGACATGAT-AGGATTTAGAGTTTGTGACATGCCATGGAGGGAATCTATG
1 CATGGTAAGAATATGTGACAGGATAAGG-TTCAAAGTTTGTGACATGCCATAGAGGAAATCTATG
7040822 ACATAGCAAGGTGAGAATGTGTACGATGA
65 ACATAGCAAGGTGAGAATGTGTACGATGA
* * * * *
7040851 CATGGTAAGAATATGTGACGGGGTAAGGTTCAAAGTTTGTGACATGCCATAGTGGAAATGTGTGA
1 CATGGTAAGAATATGTGACAGGATAAGGTTCAAAGTTTGTGACATGCCATAGAGGAAATCTATGA
* *
7040916 CATGGCATGGTGAGAAT
66 CATAGCAAGGTGAGAAT
7040933 TTGTGACACA
Statistics
Matches: 67, Mismatches: 14, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
93 64 0.96
94 3 0.04
ACGTcount: A:0.31, C:0.10, G:0.32, T:0.27
Consensus pattern (93 bp):
CATGGTAAGAATATGTGACAGGATAAGGTTCAAAGTTTGTGACATGCCATAGAGGAAATCTATGA
CATAGCAAGGTGAGAATGTGTACGATGA
Found at i:7040937 original size:23 final size:23
Alignment explanation
Indices: 7040676--7041003 Score: 125
Period size: 23 Copynumber: 14.3 Consensus size: 23
7040666 GACTTGGAGG
* * *
7040676 GAATATGTGAGACGACATGGTGA
1 GAATATGTGACATGGCATGGTGA
* **
7040699 GAATATGTGACACGTTA-GTGTGA
1 GAATATGTGACATGGCATG-GTGA
*
7040722 G-A-ATGTGACATGCCATGGTGA
1 GAATATGTGACATGGCATGGTGA
* *
7040743 GAATATGTGAGACGGCATGGTGA
1 GAATATGTGACATGGCATGGTGA
* *
7040766 GCATATGTGACAT-G-ATAGGATTTA
1 GAATATGTGACATGGCAT-GG--TGA
* * * * *
7040790 GAGTTTGTGACATGCCATGGAGG
1 GAATATGTGACATGGCATGGTGA
* * * *
7040813 GAATCTATGACATAGCAAGGTGA
1 GAATATGTGACATGGCATGGTGA
* * *
7040836 GAATGTGT-ACGATGACATGGTAA
1 GAATATGTGAC-ATGGCATGGTGA
** * * *
7040859 GAATATGTGACGGGGTAAGGTTCA
1 GAATATGTGACATGGCATGG-TGA
* * *
7040883 -AAGTTTGTGACATGCCATAGTG-
1 GAA-TATGTGACATGGCATGGTGA
*
7040905 GAAATGTGTGACATGGCATGGTGA
1 G-AATATGTGACATGGCATGGTGA
* ** *
7040929 GAATTTGTGACACAGCATGTTGA
1 GAATATGTGACATGGCATGGTGA
* * *
7040952 -AATCGTGTGAGACGGCATGGTGA
1 GAAT-ATGTGACATGGCATGGTGA
* * *
7040975 GAATCTGTGACACGCCATGGTGA
1 GAATATGTGACATGGCATGGTGA
*
7040998 GCATAT
1 GAATAT
7041004 ATGAGATAAA
Statistics
Matches: 222, Mismatches: 65, Indels: 36
0.69 0.20 0.11
Matches are distributed among these distances:
21 17 0.08
22 12 0.05
23 157 0.71
24 32 0.14
25 2 0.01
26 2 0.01
ACGTcount: A:0.30, C:0.12, G:0.32, T:0.26
Consensus pattern (23 bp):
GAATATGTGACATGGCATGGTGA
Found at i:7041703 original size:87 final size:87
Alignment explanation
Indices: 7041548--7041709 Score: 234
Period size: 87 Copynumber: 1.9 Consensus size: 87
7041538 GGTTTTTAGC
* ** * * * *
7041548 GTGTCACCACATTGGGTATTTTAGGGTAGTTTATGTAACGAGTTAGTAATTATAGTGATTGGCAT
1 GTGTCACCACATTGGGAATTTTAGGACAATTCATGTAACGAGTCAGTAATTATAGTGATCGGCAT
*
7041613 GTCATGACACGACATAGTTGAT
66 GTCAAGACACGACATAGTTGAT
* *
7041635 GTGTCACCACATTGGGAATTTTAGGACAATTCATGTAATGAGTCAGTAATTATAGTGATCGGCGT
1 GTGTCACCACATTGGGAATTTTAGGACAATTCATGTAACGAGTCAGTAATTATAGTGATCGGCAT
7041700 GTCAAGACAC
66 GTCAAGACAC
7041710 AGCATGGTTG
Statistics
Matches: 65, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
87 65 1.00
ACGTcount: A:0.29, C:0.14, G:0.25, T:0.33
Consensus pattern (87 bp):
GTGTCACCACATTGGGAATTTTAGGACAATTCATGTAACGAGTCAGTAATTATAGTGATCGGCAT
GTCAAGACACGACATAGTTGAT
Found at i:7041727 original size:87 final size:87
Alignment explanation
Indices: 7041549--7041733 Score: 219
Period size: 87 Copynumber: 2.1 Consensus size: 87
7041539 GTTTTTAGCG
* ** * * * *
7041549 TGTCACCACATTGGGTATTTTAGGGTAGTTTATGTAACGAGTTAGTAATTATAGTGATTGGCATG
1 TGTCACCACATTGGGAATTTTAGGACAATTCATGTAACGAGTCAGTAATTATAGTGATCGGCATG
* **
7041614 TCATGACACGACATAGTTGATG
66 TCAAGACACGACATAGTTGACA
* *
7041636 TGTCACCACATTGGGAATTTTAGGACAATTCATGTAATGAGTCAGTAATTATAGTGATCGGCGTG
1 TGTCACCACATTGGGAATTTTAGGACAATTCATGTAACGAGTCAGTAATTATAGTGATCGGCATG
* *
7041701 TCAAGACAC-AGCATGGTTGGCA
66 TCAAGACACGA-CATAGTTGACA
*
7041723 TGTCACAACAT
1 TGTCACCACAT
7041734 GGCTCAGCGT
Statistics
Matches: 82, Mismatches: 15, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
86 1 0.01
87 81 0.99
ACGTcount: A:0.29, C:0.15, G:0.24, T:0.32
Consensus pattern (87 bp):
TGTCACCACATTGGGAATTTTAGGACAATTCATGTAACGAGTCAGTAATTATAGTGATCGGCATG
TCAAGACACGACATAGTTGACA
Found at i:7041788 original size:31 final size:31
Alignment explanation
Indices: 7041750--7041854 Score: 147
Period size: 31 Copynumber: 3.4 Consensus size: 31
7041740 GCGTTGGCGC
* *
7041750 GTAACAATATTTGACTTGGTGTGCTTAGTGT
1 GTAACAACATTTGACTTGGTATGCTTAGTGT
* *
7041781 GTAACAATATTTGACTTGGTATGCTTAGTAT
1 GTAACAACATTTGACTTGGTATGCTTAGTGT
* * *
7041812 GTAACAACATTTTACTTGGTATGCATAGCGT
1 GTAACAACATTTGACTTGGTATGCTTAGTGT
7041843 GTAACAACATTT
1 GTAACAACATTT
7041855 ATTTCTTTCT
Statistics
Matches: 67, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 67 1.00
ACGTcount: A:0.29, C:0.12, G:0.20, T:0.39
Consensus pattern (31 bp):
GTAACAACATTTGACTTGGTATGCTTAGTGT
Found at i:7043681 original size:151 final size:150
Alignment explanation
Indices: 7043375--7043764 Score: 379
Period size: 151 Copynumber: 2.6 Consensus size: 150
7043365 CGAGCTGTCG
* * *
7043375 GTAAGAACGGTTCTAATGATTTGTGTTCAATATTTCCACATATGTTTATTGAATAACACAATAAT
1 GTAAGAACAGTTCTAATGATTTGTGTTCAATATTTTCACATATGTTTATTGAATAACACAGTAA-
* ** ** * *
7043440 TTTTGTTATTGCAGTTGACGGAGGTGACGACAGCTTTTCAACCACCAATCGATTCTGCCTAGCTG
65 TTTTGTTATTGTAGTTGACGGAGGCAACGACAGCTCCTCAACCACCAATCGATCCTACCTAGCTG
* * * * *
7043505 CACAGTGCTAATTAACCTCCG
130 CACAATACTAATCAACCGCCC
* * *
7043526 GTAAGAACAGTTCTAACGATTTGTGTTCAATATTTTCACATATGTTTATCGAATAACATAGTAAT
1 GTAAGAACAGTTCTAATGATTTGTGTTCAATATTTTCACATATGTTTATTGAATAACACAGTAAT
* * *** *
7043591 TTCTGTTATTGTAGTTGATGGAGGCAACTACAGCTCCTCAACCATTGATCGATCCTACTTAGCCT
66 TT-TGTTATTGTAGTTGACGGAGGCAACGACAGCTCCTCAACCACCAATCGATCCTACCTAG-CT
*
7043656 -CACAATACTAA-CAAGTCGCCC
129 GCACAATACTAATCAA-CCGCCC
* * * * * * * *
7043677 GTAAGGATATTAAAGTTCTAATGGTTTATATTCAACAATTTCATATATGATTATTGAATAACACA
1 GTAA-G--A--ACAGTTCTAATGATTTGTGTTCAATATTTTCACATATGTTTATTGAATAACACA
*
7043742 GTAATATTGTTATTGTAGTTGAC
61 GTAATTTTGTTATTGTAGTTGAC
7043765 CCTTTCTACG
Statistics
Matches: 193, Mismatches: 38, Indels: 12
0.79 0.16 0.05
Matches are distributed among these distances:
150 5 0.03
151 120 0.62
152 3 0.02
154 1 0.01
155 15 0.08
156 49 0.25
ACGTcount: A:0.31, C:0.18, G:0.16, T:0.35
Consensus pattern (150 bp):
GTAAGAACAGTTCTAATGATTTGTGTTCAATATTTTCACATATGTTTATTGAATAACACAGTAAT
TTTGTTATTGTAGTTGACGGAGGCAACGACAGCTCCTCAACCACCAATCGATCCTACCTAGCTGC
ACAATACTAATCAACCGCCC
Found at i:7044443 original size:81 final size:81
Alignment explanation
Indices: 7044308--7044475 Score: 194
Period size: 81 Copynumber: 2.1 Consensus size: 81
7044298 GGACTTTCAC
* * ** *
7044308 TCAGTTGAGGTTAAAGGAGACCATGTTTTTAAGGCCGATGCGATTGTCAAGGCAGTTGCTAGAAG
1 TCAGTTGAGGTTAAAGGAAACCATGTTTCTAAGGCCGATGCGATAATCAAGGCAGTTGCGAGAAG
*
7044373 AGATGGGA-ACCTTACA
66 AGAT-AGACACCTTACA
* * * * * *
7044389 TCAGTTGAGGTTAAATGAAACCATGTTTCTCAGGTCGATGTGGTAATCGAGGCAGTTGCGAGAAG
1 TCAGTTGAGGTTAAAGGAAACCATGTTTCTAAGGCCGATGCGATAATCAAGGCAGTTGCGAGAAG
* *
7044454 GGATAGACACCTTGCA
66 AGATAGACACCTTACA
7044470 TCAGTT
1 TCAGTT
7044476 CAGGCTGAAA
Statistics
Matches: 72, Mismatches: 14, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
80 2 0.03
81 70 0.97
ACGTcount: A:0.29, C:0.15, G:0.29, T:0.27
Consensus pattern (81 bp):
TCAGTTGAGGTTAAAGGAAACCATGTTTCTAAGGCCGATGCGATAATCAAGGCAGTTGCGAGAAG
AGATAGACACCTTACA
Found at i:7045950 original size:76 final size:74
Alignment explanation
Indices: 7045839--7047531 Score: 1608
Period size: 76 Copynumber: 22.3 Consensus size: 74
7045829 ACATCTAACA
* * * *
7045839 AGCGTGGCGTGTCA-CCATAGTACTGCAACGACTCAGCGTGTCACCATAAGATGTCAATGACATA
1 AGCGTGGCGTGTCACCCATAATACTGCAAC-ACTCAGCGTGTCACCACAAGATGTCAACGACATC
* *
7045903 TAATAATTAG
65 TAACAATTGG
* * * *
7045913 AGCGTAGCGTGTCATCCCATAATATTGCAATCACTCAGCGTGTCACCACAAAATGTCAATGACAT
1 AGCGTGGCGTGTCA-CCCATAATACTGCAA-CACTCAGCGTGTCACCACAAGATGTCAACGACAT
* * *
7045978 ATAATAATTGA
64 CTAACAATTGG
* * * * * *
7045989 AGCGTGGCGTGTCTCCCCATAATACTACAATGACTTAGC-TCGTCACTAGAAGATGTCAACGACA
1 AGCGTGGCGTGTC-ACCCATAATACTGCAA-CACTCAGCGT-GTCACCACAAGATGTCAACGACA
*
7046053 TCTAACAATTGT
63 TCTAACAATTGG
* * * * *
7046065 AGCTTGGCATGTCACCCTATAATACTGCAACCATTCAGTGCGTCACCACAAGATGTCAACGACAT
1 AGCGTGGCGTGTCACCC-ATAATACTGCAA-CACTCAGCGTGTCACCACAAGATGTCAACGACAT
* *
7046130 CTAATAATCGG
64 CTAACAATTGG
* ** * * * *
7046141 AGCATGGAATGTCACCCCATAATACTGCAATAACTTAGCGTGTTACCACAAGATGTCAACGACAA
1 AGCGTGGCGTGTCA-CCCATAATACTGCAA-CACTCAGCGTGTCACCACAAGATGTCAACGACAT
* * *
7046206 CGAACAAATGT
64 CTAACAATTGG
* * * * * *
7046217 AGCATGGCGTGTCACCCCATAATATTGTAACAACTCAGTGTGTCACCACAAGATGTCAATGATAT
1 AGCGTGGCGTGTCA-CCCATAATACTGCAAC-ACTCAGCGTGTCACCACAAGATGTCAACGACAT
*
7046282 CTAATAATTGG
64 CTAACAATTGG
* * * *
7046293 AGCTTGGCGTGTCACCCTATAATATTGCAACGACTCAGCGTGTCACCAAAAGATGTCAACAACAT
1 AGCGTGGCGTGTCACCC-ATAATACTGCAAC-ACTCAGCGTGTCACCACAAGATGTCAACGACAT
7046358 CTAACAATTGG
64 CTAACAATTGG
* * * ** * *
7046369 AGTGTGGCATGTCACCCCATAATATTGCAACCACTCAATGTGTCACCATAAGATGTCAATGACAT
1 AGCGTGGCGTGTCA-CCCATAATACTGCAA-CACTCAGCGTGTCACCACAAGATGTCAACGACAT
*
7046434 TTAACAATTGG
64 CTAACAATTGG
* * * * *
7046445 AGTGTGGCGTGTCACTCCATCATATTGCAACAACTCAGCGTGTCACCATAAGATGTCAATGACAT
1 AGCGTGGCGTGTCAC-CCATAATACTGCAAC-ACTCAGCGTGTCACCACAAGATGTCAACGACAT
7046510 CTAACAATTGG
64 CTAACAATTGG
* * * * *
7046521 AGCGTGACGTGTCACCCCATAATACTACAATCACTTAGCGTGCCACCACAAGATGTCAACAACAT
1 AGCGTGGCGTGTCA-CCCATAATACTGCAA-CACTCAGCGTGTCACCACAAGATGTCAACGACAT
* **
7046586 CTAATAATTAA
64 CTAACAATTGG
* * * * * * * * *
7046597 AGTGTGACATGTCACCCTATTATACTGTAACGACTTAGCGTGTCATCATAACATGTCAACGACAT
1 AGCGTGGCGTGTCACCC-ATAATACTGCAAC-ACTCAGCGTGTCACCACAAGATGTCAACGACAT
*
7046662 CTAACAATTGT
64 CTAACAATTGG
* ** * *
7046673 AGCGTGGTGTGTCACTCCATAATACTGCAACACTCAATGTGCCACCACAAGATGTCAACGGCATC
1 AGCGTGGCGTGTCAC-CCATAATACTGCAACACTCAGCGTGTCACCACAAGATGTCAACGACATC
* **
7046738 TAACAGTTAA
65 TAACAATTGG
* * * * * * * *
7046748 AGCGTGGTGTGTCACTTCATAATGCTGCAGCGACTCAACATGTCACCACAAGATGTCAATGGCAT
1 AGCGTGGCGTGTCAC-CCATAATACTGCAAC-ACTCAGCGTGTCACCACAAGATGTCAACGACAT
* *
7046813 ATAAAAATTGG
64 CTAACAATTGG
* * *
7046824 AGCGTGGCGTGTCACCCCATAATACTACAACCAGTCAACGTGTCACCACAAGATGTCAACGACAT
1 AGCGTGGCGTGTCA-CCCATAATACTGCAA-CACTCAGCGTGTCACCACAAGATGTCAACGACAT
*
7046889 TTAACAATTGG
64 CTAACAATTGG
* * * * * *
7046900 AGCATGGCGTGTCACCCCATCATACTGCAACAACTCAGCTTGTCACTACAAAATTTCAACGACAT
1 AGCGTGGCGTGTCA-CCCATAATACTGCAAC-ACTCAGCGTGTCACCACAAGATGTCAACGACAT
*
7046965 TTAACAATTGG
64 CTAACAATTGG
* * * * *
7046976 AGCGTGGTGTGTCACCCCATAATACTGCAATCACTCAACATGTCACCACAAGATATCAACAACAT
1 AGCGTGGCGTGTCA-CCCATAATACTGCAA-CACTCAGCGTGTCACCACAAGATGTCAACGACAT
7047041 CTAACAATTGG
64 CTAACAATTGG
* * * * * * *
7047052 AGCGTGGTGTGTCACCCCATCATATTGCAACGACTCAACATGTCACTACGAGATGTCAACGACAT
1 AGCGTGGCGTGTCA-CCCATAATACTGCAAC-ACTCAGCGTGTCACCACAAGATGTCAACGACAT
7047117 CTAACAATTGG
64 CTAACAATTGG
* * * * *
7047128 AGTGTGGCGCGTCATCCCATAATATTGCAACCACTCAACGTGTCACCACAAGATGTCAACAACAT
1 AGCGTGGCGTGTCA-CCCATAATACTGCAA-CACTCAGCGTGTCACCACAAGATGTCAACGACAT
*
7047193 CTAACAACTGG
64 CTAACAATTGG
* * * *
7047204 AACGTGGCGTGTCACCCTATAATACTGCAACCATTCAACGTGTCACCACAAGATGTCAACAACAT
1 AGCGTGGCGTGTCACCC-ATAATACTGCAA-CACTCAGCGTGTCACCACAAGATGTCAACGACAT
7047269 CTAACAATTGG
64 CTAACAATTGG
* * * * * *
7047280 AGCATGGCGTGTCACCTCATCATACTGCAACGACTTAACGTGCCACCACAAGATGGCAACGACAT
1 AGCGTGGCGTGTCACC-CATAATACTGCAAC-ACTCAGCGTGTCACCACAAGATGTCAACGACAT
*
7047345 TTAACAATTGG
64 CTAACAATTGG
* * * * * * *
7047356 AGTGTGGTGTGTCAACCCATGATATTGCAATGACTCAGCGTGTCAACACAAGATGTCAACGATAT
1 AGCGTGGCGTGTC-ACCCATAATACTGCAA-CACTCAGCGTGTCACCACAAGATGTCAACGACAT
*
7047421 CTAATAATTGG
64 CTAACAATTGG
* * ** * *
7047432 AGTGTGGTGTGTCACCTCATAATACTATAACCACTTAGCGTGTCACCACAAGATGCCAACGACAT
1 AGCGTGGCGTGTCACC-CATAATACTGCAA-CACTCAGCGTGTCACCACAAGATGTCAACGACAT
*
7047497 CTAACAATTAG
64 CTAACAATTGG
7047508 AGCGTGGCGTGTCACCCCATAATA
1 AGCGTGGCGTGTCA-CCCATAATA
7047532 TGACTTCATA
Statistics
Matches: 1354, Mismatches: 232, Indels: 64
0.82 0.14 0.04
Matches are distributed among these distances:
74 13 0.01
75 83 0.06
76 1236 0.91
77 22 0.02
ACGTcount: A:0.33, C:0.25, G:0.18, T:0.24
Consensus pattern (74 bp):
AGCGTGGCGTGTCACCCATAATACTGCAACACTCAGCGTGTCACCACAAGATGTCAACGACATCT
AACAATTGG
Found at i:7050235 original size:19 final size:19
Alignment explanation
Indices: 7050211--7050248 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
7050201 CCATTTAACT
*
7050211 TATTGGAGTATGATTTGAG
1 TATTGGAGTATAATTTGAG
7050230 TATTGGAGTATAATTTGAG
1 TATTGGAGTATAATTTGAG
7050249 GGTTTGGCAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.29, C:0.00, G:0.29, T:0.42
Consensus pattern (19 bp):
TATTGGAGTATAATTTGAG
Found at i:7051566 original size:13 final size:13
Alignment explanation
Indices: 7051548--7051572 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
7051538 AGAGAAATTG
7051548 TGATTTTATAAAA
1 TGATTTTATAAAA
7051561 TGATTTTATAAA
1 TGATTTTATAAA
7051573 TTTTCTAGAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.44, C:0.00, G:0.08, T:0.48
Consensus pattern (13 bp):
TGATTTTATAAAA
Found at i:7053931 original size:23 final size:23
Alignment explanation
Indices: 7053905--7053951 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
7053895 TCAGTCATGT
* * *
7053905 TGTTATACGTCATGTTCAATAAA
1 TGTTACACGCCATGTTCAACAAA
*
7053928 TGTTACATGCCATGTTCAACAAA
1 TGTTACACGCCATGTTCAACAAA
7053951 T
1 T
7053952 ATGTTAGACT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.34, C:0.17, G:0.13, T:0.36
Consensus pattern (23 bp):
TGTTACACGCCATGTTCAACAAA
Found at i:7054790 original size:15 final size:15
Alignment explanation
Indices: 7054756--7054797 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 15
7054746 CTTTACAATA
* *
7054756 CAATGTGATTACAGG
1 CAATGTGATTGCAAG
*
7054771 TAATGTGATTGCAAG
1 CAATGTGATTGCAAG
7054786 CAATGT-ATTGCA
1 CAATGTGATTGCA
7054798 GGAAAAATAA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
14 6 0.26
15 17 0.74
ACGTcount: A:0.33, C:0.12, G:0.24, T:0.31
Consensus pattern (15 bp):
CAATGTGATTGCAAG
Found at i:7055085 original size:34 final size:32
Alignment explanation
Indices: 7055017--7055100 Score: 96
Period size: 34 Copynumber: 2.5 Consensus size: 32
7055007 AATGTCATAA
*
7055017 ATTTTATTTTTATTTTTTATTATAATATTATAT
1 ATTTTA-TTTTATTTTTTAATATAATATTATAT
* *
7055050 ATTTTATTTTCATTTCTTTAATATAATTTTTTAT
1 ATTTTATTTT-ATTT-TTTAATATAATATTATAT
7055084 ATTATATATTTTATTTT
1 ATT-T-TATTTTATTTT
7055101 AATTTCTTTT
Statistics
Matches: 44, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
32 4 0.09
33 10 0.23
34 19 0.43
35 5 0.11
36 6 0.14
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.69
Consensus pattern (32 bp):
ATTTTATTTTATTTTTTAATATAATATTATAT
Found at i:7055119 original size:74 final size:73
Alignment explanation
Indices: 7054986--7055124 Score: 174
Period size: 74 Copynumber: 1.9 Consensus size: 73
7054976 TTATGTAATA
* * *
7054986 TCATTTCTTAAATATATTTTTAATGTCATAAATTTTATTTTTATTTTTTATTATAATATTATATA
1 TCATTTCTTAAATATATTTTTAATATCATAAATTTTATTTTAATTTCTTATTATAATATTATATA
7055051 TTTTATTT
66 TTTTATTT
* * * *
7055059 TCATTTCTTTAATATAATTTTTTATATTATATATTTTATTTTAATTTCTT-TTACCT-ATATTAT
1 TCATTTCTTAAATAT-ATTTTTAATATCATAAATTTTATTTTAATTTCTTATTA--TAATATTAT
7055122 ATA
63 ATA
7055125 AATTTTAATT
Statistics
Matches: 56, Mismatches: 7, Indels: 5
0.82 0.10 0.07
Matches are distributed among these distances:
73 17 0.30
74 38 0.68
75 1 0.02
ACGTcount: A:0.31, C:0.06, G:0.01, T:0.63
Consensus pattern (73 bp):
TCATTTCTTAAATATATTTTTAATATCATAAATTTTATTTTAATTTCTTATTATAATATTATATA
TTTTATTT
Found at i:7055142 original size:19 final size:20
Alignment explanation
Indices: 7055118--7055157 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
7055108 TTTACCTATA
7055118 TTATA-TAAATTTTAATTTT
1 TTATATTAAATTTTAATTTT
**
7055137 TTATATTTTATTTTAATTTT
1 TTATATTAAATTTTAATTTT
7055157 T
1 T
7055158 AATTTTTATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 5 0.28
20 13 0.72
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (20 bp):
TTATATTAAATTTTAATTTT
Found at i:7055176 original size:13 final size:13
Alignment explanation
Indices: 7055048--7055194 Score: 63
Period size: 13 Copynumber: 11.2 Consensus size: 13
7055038 ATAATATTAT
*
7055048 ATATTTTATTTTC
1 ATATTTTATTTTA
* * *
7055061 ATTTCTTTAATATA
1 ATAT-TTTATTTTA
* *
7055075 ATTTTTTATATTA
1 ATATTTTATTTTA
7055088 TATATTTTATTTT-
1 -ATATTTTATTTTA
*
7055101 A-A-TTTCTTTTA
1 ATATTTTATTTTA
* * *
7055112 CCTATATTA-TATA
1 -ATATTTTATTTTA
*
7055125 A-ATTTTAATTTTTT
1 ATATTTT-A-TTTTA
7055139 ATATTTTATTTTA
1 ATATTTTATTTTA
*
7055152 AT-TTTTAATTTTT
1 ATATTTT-ATTTTA
*
7055165 ATATTTTGTTTTA
1 ATATTTTATTTTA
7055178 ATATTTTTTATTTTA
1 ATA--TTTTATTTTA
7055193 AT
1 AT
7055195 TATAATATTA
Statistics
Matches: 97, Mismatches: 23, Indels: 26
0.66 0.16 0.18
Matches are distributed among these distances:
10 7 0.07
11 5 0.05
12 6 0.06
13 33 0.34
14 30 0.31
15 16 0.16
ACGTcount: A:0.29, C:0.03, G:0.01, T:0.67
Consensus pattern (13 bp):
ATATTTTATTTTA
Found at i:7055176 original size:26 final size:28
Alignment explanation
Indices: 7055073--7055184 Score: 101
Period size: 26 Copynumber: 4.0 Consensus size: 28
7055063 TTCTTTAATA
*
7055073 TAATTTTTTATATTATATATTT--TATTT
1 TAATTTTTTATATTTTAT-TTTAATATTT
* *
7055100 TAATTTCTTTTACCTATATTA-TATAA-ATTT
1 TAA-TT-TTTTA--TATTTTATTTTAATATTT
7055130 TAATTTTTTATATTTTATTTTAAT-TTT
1 TAATTTTTTATATTTTATTTTAATATTT
*
7055157 TAA-TTTTTATATTTTGTTTTAATATTT
1 TAATTTTTTATATTTTATTTTAATATTT
7055184 T
1 T
7055185 TTATTTTAAT
Statistics
Matches: 70, Mismatches: 6, Indels: 18
0.74 0.06 0.19
Matches are distributed among these distances:
26 25 0.36
27 17 0.24
28 7 0.10
29 9 0.13
30 7 0.10
31 5 0.07
ACGTcount: A:0.29, C:0.03, G:0.01, T:0.68
Consensus pattern (28 bp):
TAATTTTTTATATTTTATTTTAATATTT
Found at i:7055200 original size:21 final size:21
Alignment explanation
Indices: 7055126--7055203 Score: 81
Period size: 21 Copynumber: 3.8 Consensus size: 21
7055116 TATTATATAA
* *
7055126 ATTTTAATTTT-TTATATTTT
1 ATTTTAATTTTAATATTTTTT
*
7055146 ATTTTAATTTTTAAT-TTTTAT
1 ATTTTAA-TTTTAATATTTTTT
*
7055167 ATTTT-GTTTTAATATTTTTT
1 ATTTTAATTTTAATATTTTTT
*
7055187 ATTTTAATTATAATATT
1 ATTTTAATTTTAATATT
7055204 ATAAAATATT
Statistics
Matches: 47, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
19 7 0.15
20 17 0.36
21 22 0.47
22 1 0.02
ACGTcount: A:0.28, C:0.00, G:0.01, T:0.71
Consensus pattern (21 bp):
ATTTTAATTTTAATATTTTTT
Found at i:7060150 original size:33 final size:34
Alignment explanation
Indices: 7060078--7060176 Score: 146
Period size: 33 Copynumber: 2.9 Consensus size: 34
7060068 TACAATCCTT
* * *
7060078 ACAATGCCTTTTCATGGGAGCAAGTATAACCCAC
1 ACAATGCCTTTTCACGAGAGCAAGCATAACCCAC
* *
7060112 CCAATGCCTTTTCACGAAAGCAA-CATAACCCAC
1 ACAATGCCTTTTCACGAGAGCAAGCATAACCCAC
7060145 ACAATGCCTTTTCACGAGAGCAAGCATAACCC
1 ACAATGCCTTTTCACGAGAGCAAGCATAACCC
7060177 TTTGTCTTTT
Statistics
Matches: 57, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
33 30 0.53
34 27 0.47
ACGTcount: A:0.34, C:0.31, G:0.14, T:0.20
Consensus pattern (34 bp):
ACAATGCCTTTTCACGAGAGCAAGCATAACCCAC
Found at i:7060232 original size:30 final size:30
Alignment explanation
Indices: 7060149--7060239 Score: 87
Period size: 30 Copynumber: 3.0 Consensus size: 30
7060139 ACCCACACAA
* *
7060149 TGCCTTTTCACGAGAGCAAGCATAACC-CTT
1 TGCCTTTTCA-AAGATCAAGCATAACCTCTT
* * * * *
7060179 TGTCTTTTCAAGGGT-TAGACATAACCTTTT
1 TGCCTTTTCAAAGATCAAG-CATAACCTCTT
7060209 TGCCTTTTCAAAGATCAAGCATAACCTCTT
1 TGCCTTTTCAAAGATCAAGCATAACCTCTT
7060239 T
1 T
7060240 ACAACACTAT
Statistics
Matches: 46, Mismatches: 12, Indels: 6
0.72 0.19 0.09
Matches are distributed among these distances:
28 2 0.04
29 8 0.17
30 34 0.74
31 2 0.04
ACGTcount: A:0.26, C:0.24, G:0.14, T:0.35
Consensus pattern (30 bp):
TGCCTTTTCAAAGATCAAGCATAACCTCTT
Found at i:7060823 original size:21 final size:22
Alignment explanation
Indices: 7060767--7060814 Score: 87
Period size: 22 Copynumber: 2.2 Consensus size: 22
7060757 TTTGTGTCTA
7060767 AGAAGTTAGTTCTTTTTGACTG
1 AGAAGTTAGTTCTTTTTGACTG
*
7060789 AGAAGTTAGTTCTTTTTGCCTG
1 AGAAGTTAGTTCTTTTTGACTG
7060811 AGAA
1 AGAA
7060815 TTGATTCTTG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.25, C:0.10, G:0.23, T:0.42
Consensus pattern (22 bp):
AGAAGTTAGTTCTTTTTGACTG
Found at i:7070097 original size:36 final size:36
Alignment explanation
Indices: 7070010--7070089 Score: 133
Period size: 36 Copynumber: 2.2 Consensus size: 36
7070000 CCTCTTGCTT
7070010 CTCTAAACCGACAGCAAATAAACCCCCCAACCTTAC
1 CTCTAAACCGACAGCAAATAAACCCCCCAACCTTAC
* * *
7070046 CTCTATACCGACAGCAAATAAACCCCTCAACCTTTC
1 CTCTAAACCGACAGCAAATAAACCCCCCAACCTTAC
7070082 CTCTAAAC
1 CTCTAAAC
7070090 TGGCAGCAGC
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 40 1.00
ACGTcount: A:0.36, C:0.40, G:0.05, T:0.19
Consensus pattern (36 bp):
CTCTAAACCGACAGCAAATAAACCCCCCAACCTTAC
Found at i:7070412 original size:18 final size:18
Alignment explanation
Indices: 7070390--7070427 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
7070380 TTTTCTTGTT
*
7070390 TTAT-TTTATT-TTATTT
1 TTATATTTATTATTATTA
7070406 TTATATTTATTATTATTA
1 TTATATTTATTATTATTA
7070424 TTAT
1 TTAT
7070428 TTTGTCCTCA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 4 0.21
17 6 0.32
18 9 0.47
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (18 bp):
TTATATTTATTATTATTA
Found at i:7071192 original size:27 final size:29
Alignment explanation
Indices: 7071162--7071237 Score: 111
Period size: 29 Copynumber: 2.7 Consensus size: 29
7071152 AAGTATTAAA
*
7071162 GTGTAACAA-AATATTTTTT-AATATGGC
1 GTGTAACAACAATATTTTTTCAACATGGC
* *
7071189 GTGTAATAACAATATTTTTTCAACATGGT
1 GTGTAACAACAATATTTTTTCAACATGGC
7071218 GTGTAACAACAATATTTTTT
1 GTGTAACAACAATATTTTTT
7071238 TTTCAATATA
Statistics
Matches: 43, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
27 8 0.19
28 10 0.23
29 25 0.58
ACGTcount: A:0.36, C:0.09, G:0.13, T:0.42
Consensus pattern (29 bp):
GTGTAACAACAATATTTTTTCAACATGGC
Found at i:7071254 original size:32 final size:29
Alignment explanation
Indices: 7071162--7071258 Score: 117
Period size: 32 Copynumber: 3.3 Consensus size: 29
7071152 AAGTATTAAA
7071162 GTGTAACAA-AATATTTTTT-AATATGGC
1 GTGTAACAACAATATTTTTTCAATATGGC
* * *
7071189 GTGTAATAACAATATTTTTTCAACATGGT
1 GTGTAACAACAATATTTTTTCAATATGGC
*
7071218 GTGTAACAACAATATTTTTTTTTCAATATAGC
1 GTGTAACAACAATA---TTTTTTCAATATGGC
7071250 GTGTAACAA
1 GTGTAACAA
7071259 TTTAACCATG
Statistics
Matches: 58, Mismatches: 7, Indels: 5
0.83 0.10 0.07
Matches are distributed among these distances:
27 8 0.14
28 10 0.17
29 19 0.33
32 21 0.36
ACGTcount: A:0.36, C:0.10, G:0.13, T:0.40
Consensus pattern (29 bp):
GTGTAACAACAATATTTTTTCAATATGGC
Found at i:7071300 original size:45 final size:45
Alignment explanation
Indices: 7071248--7071482 Score: 281
Period size: 45 Copynumber: 5.2 Consensus size: 45
7071238 TTTCAATATA
**
7071248 GCGTGTAACAATTTAACCATGGCGTGTCACATGTTTTTGTACATG
1 GCGTGTAACAACCTAACCATGGCGTGTCACATGTTTTTGTACATG
* * * *
7071293 ACGTGTAACAACCTAATCATGGCGTGTTACATGTTTTTGTACAAG
1 GCGTGTAACAACCTAACCATGGCGTGTCACATGTTTTTGTACATG
* * **
7071338 ACGTGTAACAACCTAACCGTGATGTGTCACATGTTTTTGTACATG
1 GCGTGTAACAACCTAACCATGGCGTGTCACATGTTTTTGTACATG
* * * *
7071383 GCGTGTAACAACCTAACCATAGTGTGTCATATGTTTTTGTACACG
1 GCGTGTAACAACCTAACCATGGCGTGTCACATGTTTTTGTACATG
* * * * * *
7071428 GTGTGTAACAACCTAACCGTGACATGTAACATGTTTTTATACATG
1 GCGTGTAACAACCTAACCATGGCGTGTCACATGTTTTTGTACATG
*
7071473 GCATGTAACA
1 GCGTGTAACA
7071483 TCATGGTGTG
Statistics
Matches: 160, Mismatches: 30, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
45 160 1.00
ACGTcount: A:0.28, C:0.19, G:0.20, T:0.33
Consensus pattern (45 bp):
GCGTGTAACAACCTAACCATGGCGTGTCACATGTTTTTGTACATG
Found at i:7072760 original size:28 final size:29
Alignment explanation
Indices: 7072719--7072778 Score: 68
Period size: 30 Copynumber: 2.1 Consensus size: 29
7072709 GTCTATGGGC
*
7072719 AATTTTTCAATTTT-TGGGGCAAAAATGT
1 AATTTTTCAATTTTAGGGGGCAAAAATGT
* * *
7072747 AATTTTTGACTTTTACGGGGGCAAAAGTGT
1 AATTTTTCAATTTTA-GGGGGCAAAAATGT
7072777 AA
1 AA
7072779 ATTTCAAAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
28 12 0.46
30 14 0.54
ACGTcount: A:0.32, C:0.08, G:0.22, T:0.38
Consensus pattern (29 bp):
AATTTTTCAATTTTAGGGGGCAAAAATGT
Found at i:7080938 original size:28 final size:29
Alignment explanation
Indices: 7080897--7080956 Score: 68
Period size: 30 Copynumber: 2.1 Consensus size: 29
7080887 GTCTATGGGC
*
7080897 AATTTTTCAATTTT-TGGGGCAAAAATGT
1 AATTTTTCAATTTTAGGGGGCAAAAATGT
* * *
7080925 AATTTTTGACTTTTACGGGGGCAAAAGTGT
1 AATTTTTCAATTTTA-GGGGGCAAAAATGT
7080955 AA
1 AA
7080957 ATTTCAAAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
28 12 0.46
30 14 0.54
ACGTcount: A:0.32, C:0.08, G:0.22, T:0.38
Consensus pattern (29 bp):
AATTTTTCAATTTTAGGGGGCAAAAATGT
Found at i:7096699 original size:21 final size:22
Alignment explanation
Indices: 7096655--7096699 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 22
7096645 AAACTTAATG
* *
7096655 AAATTTAAAGTAATATAACATA
1 AAATTTAAACTAAAATAACATA
*
7096677 AAATTT-AACTAAAATAACTTA
1 AAATTTAAACTAAAATAACATA
7096698 AA
1 AA
7096700 CTAAACTACT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 14 0.70
22 6 0.30
ACGTcount: A:0.60, C:0.07, G:0.02, T:0.31
Consensus pattern (22 bp):
AAATTTAAACTAAAATAACATA
Found at i:7112759 original size:3 final size:3
Alignment explanation
Indices: 7112751--7112779 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
7112741 ATGTTAATGC
7112751 ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
7112780 TTCTCTCTTC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:7117407 original size:41 final size:42
Alignment explanation
Indices: 7117318--7117463 Score: 170
Period size: 42 Copynumber: 3.5 Consensus size: 42
7117308 ATTGACCTGA
* *
7117318 CTATGTGCGAGGGGGAGTGCGCATAAGCCGATGCTGACCCAG
1 CTATGTGCTAGGGGGAGTGCACATAAGCCGATGCTGACCCAG
* * ** *
7117360 CAATGTGCTAGGGGGAGTGC-CATAAGTCGATGCTGATTCGG
1 CTATGTGCTAGGGGGAGTGCACATAAGCCGATGCTGACCCAG
**
7117401 CTATGTG-TGAGTAGGAGTGCACATAAGCCGATGCTGACCCAG
1 CTATGTGCT-AGGGGGAGTGCACATAAGCCGATGCTGACCCAG
* *
7117443 CCATGTGCTAGTGGGAGTGCA
1 CTATGTGCTAGGGGGAGTGCA
7117464 TATGAGTTGA
Statistics
Matches: 86, Mismatches: 15, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
40 1 0.01
41 32 0.37
42 52 0.60
43 1 0.01
ACGTcount: A:0.23, C:0.21, G:0.36, T:0.21
Consensus pattern (42 bp):
CTATGTGCTAGGGGGAGTGCACATAAGCCGATGCTGACCCAG
Found at i:7117517 original size:8 final size:8
Alignment explanation
Indices: 7117504--7117531 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
7117494 TGGTGATGGA
7117504 TATACATG
1 TATACATG
7117512 TATACATG
1 TATACATG
7117520 TATACATG
1 TATACATG
7117528 TATA
1 TATA
7117532 TGTATGTATA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.39, C:0.11, G:0.11, T:0.39
Consensus pattern (8 bp):
TATACATG
Found at i:7117540 original size:18 final size:18
Alignment explanation
Indices: 7117517--7117900 Score: 180
Period size: 18 Copynumber: 21.2 Consensus size: 18
7117507 ACATGTATAC
*
7117517 ATGTATACATGTATATGT
1 ATGTATACATATATATGT
*
7117535 ATGTATACATACATA--T
1 ATGTATACATATATATGT
* *
7117551 A--CAT--ATATATGTGT
1 ATGTATACATATATATGT
*
7117565 ATATATACATATATATGT
1 ATGTATACATATATATGT
**
7117583 ATACATACATATATATGT
1 ATGTATACATATATATGT
**
7117601 ATACATACATATATATGT
1 ATGTATACATATATATGT
**
7117619 ATACATACATATATATGT
1 ATGTATACATATATATGT
**
7117637 ATACATACATATATATGT
1 ATGTATACATATATATGT
**
7117655 ATACATACATATATATGT
1 ATGTATACATATATATGT
** *
7117673 ATACATACATATACATATAT
1 ATGTATACATAT--ATATGT
* * *
7117693 ATGTGTATATATACATATAT
1 A--TGTATACATATATATGT
*
7117713 ATGTATACATACATA--T
1 ATGTATACATATATATGT
** * * *
7117729 ACATATATATGTGTATGT
1 ATGTATACATATATATGT
7117747 ATGTATACATATATATGT
1 ATGTATACATATATATGT
*** **
7117765 A--TATGTGTATATATAC
1 ATGTATACATATATATGT
7117781 ATGTATACATATATATGTAT
1 ATGTATACATATATATG--T
* * *
7117801 ATGTGTATATATACATGTAT
1 ATGTATACATATATATG--T
** *
7117821 ACATGTATATGTGTATATGT
1 --ATGTATACATATATATGT
*
7117841 ACATGTATACATGTATATATAT
1 --ATGTATACA--TATATATGT
* *
7117863 ATGTAT--ATATGTATAT
1 ATGTATACATATATATGT
*
7117879 ATGTATACATATATATAT
1 ATGTATACATATATATGT
7117897 ATGT
1 ATGT
7117901 GTGTGTGTGT
Statistics
Matches: 296, Mismatches: 48, Indels: 44
0.76 0.12 0.11
Matches are distributed among these distances:
12 5 0.02
14 4 0.01
16 39 0.13
18 175 0.59
20 46 0.16
22 27 0.09
ACGTcount: A:0.40, C:0.08, G:0.10, T:0.42
Consensus pattern (18 bp):
ATGTATACATATATATGT
Found at i:7117552 original size:36 final size:36
Alignment explanation
Indices: 7117512--7117685 Score: 213
Period size: 36 Copynumber: 4.6 Consensus size: 36
7117502 GATATACATG
** *
7117512 TATACATGTATACATGTATATGTATGTATACATACA
1 TATACATGTATACATACATATATATGTATACATACA
*
7117548 TATACATATATATGTGTATATATACATATATATGTATACATACA
1 TATAC------A--TGTATACATACATATATATGTATACATACA
*
7117592 TATATATGTATACATACATATATATGTATACATACA
1 TATACATGTATACATACATATATATGTATACATACA
*
7117628 TATATATGTATACATACATATATATGTATACATACA
1 TATACATGTATACATACATATATATGTATACATACA
*
7117664 TATATATGTATACATACATATA
1 TATACATGTATACATACATATA
7117686 CATATATATG
Statistics
Matches: 124, Mismatches: 6, Indels: 16
0.85 0.04 0.11
Matches are distributed among these distances:
36 92 0.74
38 1 0.01
42 1 0.01
44 30 0.24
ACGTcount: A:0.43, C:0.10, G:0.07, T:0.40
Consensus pattern (36 bp):
TATACATGTATACATACATATATATGTATACATACA
Found at i:7117620 original size:54 final size:54
Alignment explanation
Indices: 7117549--7117738 Score: 254
Period size: 54 Copynumber: 3.3 Consensus size: 54
7117539 ATACATACAT
7117549 ATACATATATATGTGTATATATACATATATATGTATACATACATATATATGTATAC
1 ATACATATATA--TGTATATATACATATATATGTATACATACATATATATGTATAC
*
7117605 ATACATATATATGTATACATACATATATATGTATACATACATATATATGTATAC
1 ATACATATATATGTATATATACATATATATGTATACATACATATATATGTATAC
*
7117659 ATACATATATATGTATACATACATATACATATATATGTGTATATATACATATATATGTATAC
1 ATACATATATATG--T--AT--ATATACATATATA--TGTATACATACATATATATGTATAC
* *
7117721 ATACATATACATATATAT
1 ATACATATATATGTATAT
7117739 GTGTATGTAT
Statistics
Matches: 121, Mismatches: 5, Indels: 16
0.85 0.04 0.11
Matches are distributed among these distances:
54 55 0.45
56 14 0.12
58 4 0.03
60 13 0.11
62 35 0.29
ACGTcount: A:0.44, C:0.10, G:0.06, T:0.40
Consensus pattern (54 bp):
ATACATATATATGTATATATACATATATATGTATACATACATATATATGTATAC
Found at i:7117703 original size:36 final size:36
Alignment explanation
Indices: 7117554--7117900 Score: 209
Period size: 36 Copynumber: 9.8 Consensus size: 36
7117544 TACATATACA
* * ** *
7117554 TATATATGTGTATATATACATATATATGTATACATA
1 TATATATATGTATACATACATATATATGTATATGTG
* ** *
7117590 CATATATATGTATACATACATATATATGTATACATA
1 TATATATATGTATACATACATATATATGTATATGTG
* ** *
7117626 CATATATATGTATACATACATATATATGTATACATA
1 TATATATATGTATACATACATATATATGTATATGTG
* * *
7117662 CATATATATGTATACATACATATACATATATATGTG
1 TATATATATGTATACATACATATATATGTATATGTG
* * * * * *
7117698 TATATATACATATATATGTATACATACATA--TACATATA
1 TATATAT--ATGTATA--CATACATATATATGTATATGTG
* * **
7117736 TATGTGTATGTATGTATACATATATATGTATATGTG
1 TATATATATGTATACATACATATATATGTATATGTG
* **
7117772 TATATATA--CATGTATACATATATATGTATATGTG
1 TATATATATGTATACATACATATATATGTATATGTG
* *
7117806 ----TATA--TATACAT--GTATACATGTATATGTG
1 TATATATATGTATACATACATATATATGTATATGTG
* * *
7117834 TATATGTACATGTATACATGTATATATATATGTATATATG
1 TATA--TATATGTATACA--TACATATATATGTATATGTG
*
7117874 --TATATATGTATACATATATATATATGT
1 TATATATATGTATACATACATATATATGT
7117901 GTGTGTGTGT
Statistics
Matches: 256, Mismatches: 37, Indels: 38
0.77 0.11 0.11
Matches are distributed among these distances:
28 15 0.06
30 8 0.03
34 52 0.20
36 139 0.54
38 19 0.07
40 23 0.09
ACGTcount: A:0.40, C:0.07, G:0.10, T:0.43
Consensus pattern (36 bp):
TATATATATGTATACATACATATATATGTATATGTG
Found at i:7117767 original size:8 final size:8
Alignment explanation
Indices: 7117734--7117896 Score: 73
Period size: 8 Copynumber: 20.9 Consensus size: 8
7117724 CATATACATA
*
7117734 TATATGTG
1 TATATATG
*
7117742 TATGTATG
1 TATATATG
*
7117750 TATACA--
1 TATATATG
7117756 TATATATG
1 TATATATG
*
7117764 TATATGTG
1 TATATATG
*
7117772 TATATATA
1 TATATATG
* * *
7117780 CATGTATA
1 TATATATG
* *
7117788 CATATATA
1 TATATATG
*
7117796 TGTATATG
1 TATATATG
*
7117804 TGTATA--
1 TATATATG
*
7117810 TATACATG
1 TATATATG
*
7117818 TATACATG
1 TATATATG
*
7117826 TATATGTG
1 TATATATG
* *
7117834 TATATGTA
1 TATATATG
* * *
7117842 CATGTATA
1 TATATATG
* * *
7117850 CATGTATA
1 TATATATG
7117858 TATATATG
1 TATATATG
7117866 TATATATG
1 TATATATG
7117874 TATATATG
1 TATATATG
* *
7117882 TATACATA
1 TATATATG
7117890 TATATAT
1 TATATAT
7117897 ATGTGTGTGT
Statistics
Matches: 123, Mismatches: 28, Indels: 8
0.77 0.18 0.05
Matches are distributed among these distances:
6 9 0.07
8 114 0.93
ACGTcount: A:0.37, C:0.05, G:0.13, T:0.45
Consensus pattern (8 bp):
TATATATG
Found at i:7117769 original size:24 final size:24
Alignment explanation
Indices: 7117520--7117802 Score: 176
Period size: 24 Copynumber: 12.0 Consensus size: 24
7117510 TGTATACATG
*
7117520 TATACATGTATATG--TATGTATA
1 TATACATATATATGTATATGTATA
* * * *
7117542 CATACATATACATATATATGTGTA
1 TATACATATATATGTATATGTATA
*
7117566 TAT--ATACATA--TATATGTATA
1 TATACATATATATGTATATGTATA
* **
7117586 CATACATATATATGTATACATACATA
1 TATACATATATATGTAT--ATGTATA
** * ** * *
7117612 TATATGTATACATACATATATATG
1 TATACATATATATGTATATGTATA
*
7117636 TATACATACATA--TATATGTATA
1 TATACATATATATGTATATGTATA
* ** *
7117658 CATACATATATATGTATACATACA
1 TATACATATATATGTATATGTATA
7117682 TATACATATATATG----TGTATA
1 TATACATATATATGTATATGTATA
** *
7117702 TATACATATATATGTATACATACA
1 TATACATATATATGTATATGTATA
* *
7117726 TATACATATATATGTGTATGTATG
1 TATACATATATATGTATATGTATA
7117750 TATACATATATATGTATATGTGTATA
1 TATACATATATATGTATA--TGTATA
* *
7117776 TATACATGTATACATATATATGTATA
1 TATACA--TATATATGTATATGTATA
7117802 T
1 T
7117803 GTGTATATAT
Statistics
Matches: 194, Mismatches: 49, Indels: 32
0.71 0.18 0.12
Matches are distributed among these distances:
20 28 0.14
22 38 0.20
24 84 0.43
26 34 0.18
28 10 0.05
ACGTcount: A:0.42, C:0.09, G:0.08, T:0.41
Consensus pattern (24 bp):
TATACATATATATGTATATGTATA
Found at i:7117779 original size:44 final size:44
Alignment explanation
Indices: 7117529--7117894 Score: 218
Period size: 44 Copynumber: 8.2 Consensus size: 44
7117519 GTATACATGT
* * * * * *
7117529 ATATGTATGTATACATACATATACATATATATGTGTATATATAC
1 ATATATATGTATATATATATATATATATGTATATGTATATATAC
* * ** ** **
7117573 ATATATATGTATACATACATATATATGTATACATACATATATATGT
1 ATATATATGTAT--ATATATATATATATATGTATATGTATATATAC
* ** * * * * *
7117619 ATACATACATATATATGTATACATACATATATATGTATACATAC
1 ATATATATGTATATATATATATATATATGTATATGTATATATAC
* * * * *
7117663 ATATATATGTATACATACATATACATATATATGTGTATATATAC
1 ATATATATGTATATATATATATATATATGTATATGTATATATAC
* * *
7117707 ATATATATGTATACATACATATACATATATATGTGTATGTATGTATAC
1 ATATATATGTAT--AT--ATATATATATATATGTATATGTATATATAC
* * * * *
7117755 ATATATATGTATATGTGTATATATACATGTATA--CATATATAT
1 ATATATATGTATATATATATATATATATGTATATGTATATATAC
* * * * * *
7117797 GTATATGTGTATATATACATGTATACATGTATATGTGTATATGTAC
1 ATATATATGTATATATATATATATATATGTATA--TGTATATATAC
* * *
7117843 ATGTATACATGTATATATATATGTATATATGTATA--TATGTATAC
1 A--TATATATGTATATATATATATATATATGTATATGTATATATAC
7117887 ATATATAT
1 ATATATAT
7117895 ATATGTGTGT
Statistics
Matches: 240, Mismatches: 70, Indels: 26
0.71 0.21 0.08
Matches are distributed among these distances:
42 39 0.16
44 99 0.41
46 39 0.16
48 63 0.26
ACGTcount: A:0.41, C:0.08, G:0.09, T:0.42
Consensus pattern (44 bp):
ATATATATGTATATATATATATATATATGTATATGTATATATAC
Found at i:7117844 original size:54 final size:54
Alignment explanation
Indices: 7117547--7117897 Score: 171
Period size: 48 Copynumber: 6.7 Consensus size: 54
7117537 GTATACATAC
* * * * *
7117547 ATATACATATATATGTGTATATATACATATATATGTATACATACATATATATGTAT
1 ATATACATATATATGTATATGTGTATATATATATGTATACAT--GTATATATGTAT
* ** * * *
7117603 ACATACATATATATGTATA--CATACATATATATGTATACA--TACATATATAT
1 ATATACATATATATGTATATGTGTATATATATATGTATACATGTATATATGTAT
* * * * * *
7117653 GTATACATACATA--TATA--TGTATACATACA--TATACATATATATGTGTAT
1 ATATACATATATATGTATATGTGTATATATATATGTATACATGTATATATGTAT
* * ** * *
7117701 ATATACATATATATGTATA----CATACATATACATATATATG--TGTATGTAT
1 ATATACATATATATGTATATGTGTATATATATATGTATACATGTATATATGTAT
* *
7117749 GTATACATATATATGTATATGTGTATATATACATGTATACA--TATATATGTAT
1 ATATACATATATATGTATATGTGTATATATATATGTATACATGTATATATGTAT
* * * ** * * * * *
7117801 ATGTGTATATATACATGTATACATGTATATGTGTATATGTACATGTATACATGTAT
1 A--TATACATATATATGTATATGTGTATATATATATGTATACATGTATATATGTAT
* * * *
7117857 ATATATATGTATATATGTATATATGTATACATATATATATA
1 ATATACA--TATATATGTATATGTGTATATATATATGTATA
7117898 TGTGTGTGTG
Statistics
Matches: 226, Mismatches: 51, Indels: 36
0.72 0.16 0.12
Matches are distributed among these distances:
46 6 0.03
48 63 0.28
50 29 0.13
52 20 0.09
54 54 0.24
56 54 0.24
ACGTcount: A:0.41, C:0.08, G:0.09, T:0.42
Consensus pattern (54 bp):
ATATACATATATATGTATATGTGTATATATATATGTATACATGTATATATGTAT
Found at i:7117894 original size:34 final size:34
Alignment explanation
Indices: 7117666--7117902 Score: 170
Period size: 34 Copynumber: 7.0 Consensus size: 34
7117656 TACATACATA
* * * * *
7117666 TATATGTATACATACATATACATATATATGTGTATA
1 TATATGTATACAT--GTATACATATATATATATGTG
** * * * * *
7117702 TATACATATATATGTATACATACATATACATATA
1 TATATGTATACATGTATACATATATATATATGTG
* **
7117736 TATGTGTATGTATGTATACATATATATGTATATGTG
1 TATATGTATACATGTATACATATATA--TATATGTG
7117772 TATA--TATACATGTATACATATATATGTATATGTG
1 TATATGTATACATGTATACATATATA--TATATGTG
*
7117806 TATA--TATACATGTATAC----ATGTATATGTG
1 TATATGTATACATGTATACATATATATATATGTG
*
7117834 TATATG--TACATGTATACATGTATATATATATGTA
1 TATATGTATACATGTATACA--TATATATATATGTG
*
7117868 TATATGTATATATGTATACATATATATATATGTG
1 TATATGTATACATGTATACATATATATATATGTG
7117902 T
1 T
7117903 GTGTGTGTTA
Statistics
Matches: 165, Mismatches: 24, Indels: 26
0.77 0.11 0.12
Matches are distributed among these distances:
28 23 0.14
30 2 0.01
34 111 0.67
36 29 0.18
ACGTcount: A:0.38, C:0.06, G:0.11, T:0.44
Consensus pattern (34 bp):
TATATGTATACATGTATACATATATATATATGTG
Found at i:7122880 original size:31 final size:32
Alignment explanation
Indices: 7122844--7122913 Score: 79
Period size: 34 Copynumber: 2.2 Consensus size: 32
7122834 TTAATGTGGG
7122844 TTGTGC-CTCCTATTAAAAGGCATTGTAAGGC
1 TTGTGCTCTCCTATTAAAAGGCATTGTAAGGC
* * * *
7122875 TTGTGCTTGCTCTTGTTAAAAGGCATTGTGAGGG
1 TTGTGC-T-CTCCTATTAAAAGGCATTGTAAGGC
7122909 TTGTG
1 TTGTG
7122914 TTAAGCTCAG
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
31 6 0.19
34 26 0.81
ACGTcount: A:0.20, C:0.14, G:0.29, T:0.37
Consensus pattern (32 bp):
TTGTGCTCTCCTATTAAAAGGCATTGTAAGGC
Found at i:7122933 original size:33 final size:34
Alignment explanation
Indices: 7122856--7122934 Score: 92
Period size: 34 Copynumber: 2.4 Consensus size: 34
7122846 GTGCCTCCTA
*
7122856 TTAAAAGGCATTGTAAGGCTTGTGCTTGCTCTTG
1 TTAAAAGGCATTGTAAGGCTTGTGCTTGCTCTAG
* *
7122890 TTAAAAGGCATTGTGAGGGTTGTG-TTAAGCTC-AG
1 TTAAAAGGCATTGTAAGGCTTGTGCTT--GCTCTAG
7122924 -TAAAAGGCATT
1 TTAAAAGGCATT
7122935 ATAAAGGTTT
Statistics
Matches: 40, Mismatches: 3, Indels: 5
0.83 0.06 0.10
Matches are distributed among these distances:
33 13 0.32
34 23 0.57
35 4 0.10
ACGTcount: A:0.27, C:0.11, G:0.28, T:0.34
Consensus pattern (34 bp):
TTAAAAGGCATTGTAAGGCTTGTGCTTGCTCTAG
Found at i:7142282 original size:14 final size:14
Alignment explanation
Indices: 7142263--7142295 Score: 66
Period size: 14 Copynumber: 2.4 Consensus size: 14
7142253 CTTTTCTTAA
7142263 ACATGAAAGTATTC
1 ACATGAAAGTATTC
7142277 ACATGAAAGTATTC
1 ACATGAAAGTATTC
7142291 ACATG
1 ACATG
7142296 TTTATATCTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.42, C:0.15, G:0.15, T:0.27
Consensus pattern (14 bp):
ACATGAAAGTATTC
Found at i:7147210 original size:16 final size:16
Alignment explanation
Indices: 7147189--7147220 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
7147179 ATTTGTGCTA
7147189 GAGCTTTTTACATTGG
1 GAGCTTTTTACATTGG
7147205 GAGCTTTTTACATTGG
1 GAGCTTTTTACATTGG
7147221 AAATTTTCAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.19, C:0.12, G:0.25, T:0.44
Consensus pattern (16 bp):
GAGCTTTTTACATTGG
Found at i:7153532 original size:68 final size:68
Alignment explanation
Indices: 7153364--7153630 Score: 255
Period size: 68 Copynumber: 3.9 Consensus size: 68
7153354 CATGTTTGGT
* * * *
7153364 ATGACGAATGCCATAAGATTATGTACATGATGTAAATTCCATATACCGTATGAGATGATTAAGTA
1 ATGATGAATGCCATAAGATTATGTATAAGATGTAAATTCCATATACCATATGAGATGATTAAGTA
7153429 TGC
66 TGC
* * ** * * * * *
7153432 ATGATGTATACTGTAAGATTGTATATATGATGTAAATTTCATATACCATATGAGGTGATTAAGTA
1 ATGATGAATGCCATAAGATTATGTATAAGATGTAAATTCCATATACCATATGAGATGATTAAGTA
7153497 TGC
66 TGC
* * * * * * * * * *
7153500 ATGATAAATGCCATGAGATAATGTATAAGATGTATATTCCGTATACTACATAAGATGATTGAGAA
1 ATGATGAATGCCATAAGATTATGTATAAGATGTAAATTCCATATACCATATGAGATGATTAAGTA
*
7153565 AGC
66 TGC
* * * ** * *
7153568 ATGATGAATGTCATGAGATTATGTATATGATGTATTTTCCATATACCTTATGAGATGAGTAAG
1 ATGATGAATGCCATAAGATTATGTATAAGATGTAAATTCCATATACCATATGAGATGATTAAG
7153631 CTAGTATGTG
Statistics
Matches: 156, Mismatches: 43, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
68 156 1.00
ACGTcount: A:0.37, C:0.10, G:0.19, T:0.34
Consensus pattern (68 bp):
ATGATGAATGCCATAAGATTATGTATAAGATGTAAATTCCATATACCATATGAGATGATTAAGTA
TGC
Found at i:7177550 original size:38 final size:38
Alignment explanation
Indices: 7177458--7177597 Score: 156
Period size: 39 Copynumber: 3.6 Consensus size: 38
7177448 GTGTCAGTAG
* * * *
7177458 TGTGTGGTGTGGGAGAGCACA-CACCGATGATATATGCAA
1 TGTGCGGTGTGGGAGAGCACATGA-TGATGATAT-TGCCA
* *
7177497 TGTGTGGTGTAGGAGAGCACATGATGATGATATTGCCA
1 TGTGCGGTGTGGGAGAGCACATGATGATGATATTGCCA
*
7177535 TGTGCGATGTGGGAGAGCACATGATGATGATATTTGCCA
1 TGTGCGGTGTGGGAGAGCACATGATGATGATA-TTGCCA
* * *
7177574 TCTGCGGTGTGGAAGTGCACATGA
1 TGTGCGGTGTGGGAGAGCACATGA
7177598 GGATATTAGC
Statistics
Matches: 88, Mismatches: 11, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
38 33 0.38
39 54 0.61
40 1 0.01
ACGTcount: A:0.26, C:0.14, G:0.34, T:0.26
Consensus pattern (38 bp):
TGTGCGGTGTGGGAGAGCACATGATGATGATATTGCCA
Found at i:7180384 original size:30 final size:30
Alignment explanation
Indices: 7180348--7180404 Score: 105
Period size: 30 Copynumber: 1.9 Consensus size: 30
7180338 GATGTTGGGC
7180348 TGTTTATGACAATATGTTATTTTAATTTCT
1 TGTTTATGACAATATGTTATTTTAATTTCT
*
7180378 TGTTTATGACAATGTGTTATTTTAATT
1 TGTTTATGACAATATGTTATTTTAATT
7180405 GCTGATGGAT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.26, C:0.05, G:0.12, T:0.56
Consensus pattern (30 bp):
TGTTTATGACAATATGTTATTTTAATTTCT
Found at i:7180970 original size:74 final size:74
Alignment explanation
Indices: 7180833--7181030 Score: 220
Period size: 74 Copynumber: 2.7 Consensus size: 74
7180823 GGCTGGTCCA
* * * * *
7180833 AAAACAGAAAAGACTTAGTTGACCAAAAAGCATGGTTAGTCGACTAAGTGCTCACTACTAGAAAC
1 AAAACAGGAAAGACTTAGTCGACTAAAAAGCATGGTTAGTCGACTAAGAGCTCACTACCAGAAAC
*
7180898 TTCAATAAG
66 TGCAATAAG
* * *
7180907 AAAACAGGGAAGACTTAGTCGACTAAAAAGCATGGTTAGTCGACTAAGAGCTCATTGCCAGAAAC
1 AAAACAGGAAAGACTTAGTCGACTAAAAAGCATGGTTAGTCGACTAAGAGCTCACTACCAGAAAC
** *
7180972 TGGGATCAG
66 TGCAATAAG
* * * * *
7180981 AAGACA-GAAACGACTTAATCGACTAAGAAGTAT-GTTAGTCAACTAAGAGC
1 AAAACAGGAAA-GACTTAGTCGACTAAAAAGCATGGTTAGTCGACTAAGAGC
7181031 ATTCTGTTTG
Statistics
Matches: 105, Mismatches: 18, Indels: 3
0.83 0.14 0.02
Matches are distributed among these distances:
73 19 0.18
74 86 0.82
ACGTcount: A:0.41, C:0.17, G:0.21, T:0.20
Consensus pattern (74 bp):
AAAACAGGAAAGACTTAGTCGACTAAAAAGCATGGTTAGTCGACTAAGAGCTCACTACCAGAAAC
TGCAATAAG
Found at i:7185461 original size:35 final size:35
Alignment explanation
Indices: 7185412--7185482 Score: 115
Period size: 35 Copynumber: 2.0 Consensus size: 35
7185402 GGCAAGTGGG
* * *
7185412 AGATTGTTAGGAATTTGAGAATATGATGCGCTAGA
1 AGATTGTTAAGAATTTGAGAATATAATGCCCTAGA
7185447 AGATTGTTAAGAATTTGAGAATATAATGCCCTAGA
1 AGATTGTTAAGAATTTGAGAATATAATGCCCTAGA
7185482 A
1 A
7185483 AGCAACTATA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.38, C:0.07, G:0.24, T:0.31
Consensus pattern (35 bp):
AGATTGTTAAGAATTTGAGAATATAATGCCCTAGA
Found at i:7189330 original size:29 final size:29
Alignment explanation
Indices: 7189288--7189465 Score: 209
Period size: 29 Copynumber: 6.1 Consensus size: 29
7189278 GTCAACTTTT
* *
7189288 ACATGTTTTGTCTTACTTTAGACAAGAAA
1 ACATGTTATGTCTTAATTTAGACAAGAAA
*
7189317 ACATGTTATGTCTTAATTTAGATAAGAAA
1 ACATGTTATGTCTTAATTTAGACAAGAAA
*
7189346 ACATGTTA-GTCTTAATTTAGACAAGAAC
1 ACATGTTATGTCTTAATTTAGACAAGAAA
* * * *
7189374 ATATGTTTTATCTTAATTTAGACCAGAAA
1 ACATGTTATGTCTTAATTTAGACAAGAAA
7189403 ACATGATTA--TCTTAATTTGAGACAAGAAAA
1 ACATG-TTATGTCTTAATTT-AGACAAG-AAA
* * *
7189433 ACATGTTTTATCTTAATCTAGACAAGAAA
1 ACATGTTATGTCTTAATTTAGACAAGAAA
7189462 ACAT
1 ACAT
7189466 ACAAGATAAC
Statistics
Matches: 128, Mismatches: 15, Indels: 12
0.83 0.10 0.08
Matches are distributed among these distances:
28 33 0.26
29 70 0.55
30 17 0.13
31 8 0.06
ACGTcount: A:0.40, C:0.12, G:0.12, T:0.35
Consensus pattern (29 bp):
ACATGTTATGTCTTAATTTAGACAAGAAA
Found at i:7189367 original size:57 final size:58
Alignment explanation
Indices: 7189288--7189465 Score: 234
Period size: 57 Copynumber: 3.1 Consensus size: 58
7189278 GTCAACTTTT
* * * * * *
7189288 ACATGTTTTGTCTTACTTTAGACAAGAAAACATGTTATGTCTTAATTTAGATAAGAAA
1 ACATGATTAGTCTTAATTTAGACAAGAAAACATGTTTTATCTTAATTTAGACAAGAAA
* * *
7189346 ACATG-TTAGTCTTAATTTAGACAAGAACATATGTTTTATCTTAATTTAGACCAGAAA
1 ACATGATTAGTCTTAATTTAGACAAGAAAACATGTTTTATCTTAATTTAGACAAGAAA
*
7189403 ACATGATTA-TCTTAATTTGAGACAAGAAAAACATGTTTTATCTTAATCTAGACAAGAAA
1 ACATGATTAGTCTTAATTT-AGACAAG-AAAACATGTTTTATCTTAATTTAGACAAGAAA
7189462 ACAT
1 ACAT
7189466 ACAAGATAAC
Statistics
Matches: 105, Mismatches: 12, Indels: 5
0.86 0.10 0.04
Matches are distributed among these distances:
57 58 0.55
58 15 0.14
59 32 0.30
ACGTcount: A:0.40, C:0.12, G:0.12, T:0.35
Consensus pattern (58 bp):
ACATGATTAGTCTTAATTTAGACAAGAAAACATGTTTTATCTTAATTTAGACAAGAAA
Found at i:7194647 original size:9 final size:9
Alignment explanation
Indices: 7194635--7194683 Score: 71
Period size: 9 Copynumber: 5.4 Consensus size: 9
7194625 AATAACACAT
*
7194635 TTAACATGA
1 TTAACACGA
*
7194644 TTAACACGT
1 TTAACACGA
7194653 TTAACACGA
1 TTAACACGA
*
7194662 TTAACACGT
1 TTAACACGA
7194671 TTAACACGA
1 TTAACACGA
7194680 TTAA
1 TTAA
7194684 ATAAAAATAT
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
9 35 1.00
ACGTcount: A:0.41, C:0.18, G:0.10, T:0.31
Consensus pattern (9 bp):
TTAACACGA
Found at i:7194650 original size:18 final size:18
Alignment explanation
Indices: 7194627--7194683 Score: 96
Period size: 18 Copynumber: 3.2 Consensus size: 18
7194617 ATACGATTAA
* *
7194627 TAACACATTTAACATGAT
1 TAACACGTTTAACACGAT
7194645 TAACACGTTTAACACGAT
1 TAACACGTTTAACACGAT
7194663 TAACACGTTTAACACGAT
1 TAACACGTTTAACACGAT
7194681 TAA
1 TAA
7194684 ATAAAAATAT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 37 1.00
ACGTcount: A:0.42, C:0.19, G:0.09, T:0.30
Consensus pattern (18 bp):
TAACACGTTTAACACGAT
Found at i:7194665 original size:27 final size:27
Alignment explanation
Indices: 7194627--7194683 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 27
7194617 ATACGATTAA
* *
7194627 TAACACATTTAACATGATTAACACGTT
1 TAACACATTTAACACGATTAACACGAT
*
7194654 TAACACGA-TTAACACGTTTAACACGAT
1 TAACAC-ATTTAACACGATTAACACGAT
7194681 TAA
1 TAA
7194684 ATAAAAATAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
27 25 0.96
28 1 0.04
ACGTcount: A:0.42, C:0.19, G:0.09, T:0.30
Consensus pattern (27 bp):
TAACACATTTAACACGATTAACACGAT
Found at i:7208089 original size:21 final size:21
Alignment explanation
Indices: 7208047--7208089 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
7208037 CCTGTACCGG
*
7208047 TGGTGGAACTAAAGGAGTAAC
1 TGGTGGAACTAAAGGAGGAAC
* * *
7208068 TGGTGGTACTATAGGTGGAAC
1 TGGTGGAACTAAAGGAGGAAC
7208089 T
1 T
7208090 TGACCAGTCT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.09, G:0.35, T:0.26
Consensus pattern (21 bp):
TGGTGGAACTAAAGGAGGAAC
Found at i:7217742 original size:28 final size:29
Alignment explanation
Indices: 7217688--7217766 Score: 76
Period size: 28 Copynumber: 2.8 Consensus size: 29
7217678 CATAACAAAG
* *
7217688 TGAA-AAAAGAAAGGAAGGAA-AGGAGGA
1 TGAAGAAAAGAAAGAAAGGAAGAGAAGGA
7217715 TGAAGAAAAGAAAGAAAGGAAGA-AAGGA
1 TGAAGAAAAGAAAGAAAGGAAGAGAAGGA
*
7217743 -GAAAGAAGAAAAAGAGAAAGGAAG
1 TG-AAGAA-AAGAA-AGAAAGGAAG
7217767 GTTCGGCTTT
Statistics
Matches: 44, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
27 5 0.11
28 24 0.55
29 5 0.11
30 10 0.23
ACGTcount: A:0.63, C:0.00, G:0.34, T:0.03
Consensus pattern (29 bp):
TGAAGAAAAGAAAGAAAGGAAGAGAAGGA
Found at i:7219143 original size:2 final size:2
Alignment explanation
Indices: 7219138--7219209 Score: 81
Period size: 2 Copynumber: 35.0 Consensus size: 2
7219128 CATATATGTG
* * * *
7219138 TA TA TA TA TA TA TA TA TA TA TA TA TA GA CNA TA TA CCA TA TA TG
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA -TA TA TA TA
*
7219182 TG TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
7219210 GCAATCATCA
Statistics
Matches: 61, Mismatches: 7, Indels: 4
0.85 0.10 0.06
Matches are distributed among these distances:
2 59 0.97
3 2 0.03
ACGTcount: A:0.46, C:0.04, G:0.04, T:0.44
Consensus pattern (2 bp):
TA
Found at i:7219189 original size:46 final size:45
Alignment explanation
Indices: 7219121--7219210 Score: 171
Period size: 46 Copynumber: 2.0 Consensus size: 45
7219111 CATTTACAAC
7219121 CATATACCATATATGTGTATATATATATATATATATATATATAGA
1 CATATACCATATATGTGTATATATATATATATATATATATATAGA
7219166 CNATATACCATATATGTGTATATATATATATATATATATATATAG
1 C-ATATACCATATATGTGTATATATATATATATATATATATATAG
7219211 CAATCATCAT
Statistics
Matches: 44, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
45 1 0.02
46 43 0.98
ACGTcount: A:0.43, C:0.07, G:0.07, T:0.42
Consensus pattern (45 bp):
CATATACCATATATGTGTATATATATATATATATATATATATAGA
Found at i:7219309 original size:42 final size:42
Alignment explanation
Indices: 7219251--7219375 Score: 187
Period size: 42 Copynumber: 3.0 Consensus size: 42
7219241 CATCTCATAT
* * *
7219251 GCAAAGGCTTTTGTGCACTCCCACTCGCACATAGCCGGGTTA
1 GCAACGGCTTATGTGCACTCCCACTCGCACATAGCCGGGTCA
* *
7219293 GCAACGGTTTATGTGCACTCTCACTCGCACATAGCCGGGTCA
1 GCAACGGCTTATGTGCACTCCCACTCGCACATAGCCGGGTCA
* *
7219335 GCAACGGCTTATGTGCACTCCTACTCGCACATAGTCGGGTC
1 GCAACGGCTTATGTGCACTCCCACTCGCACATAGCCGGGTC
7219376 CATATCAACA
Statistics
Matches: 74, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
42 74 1.00
ACGTcount: A:0.21, C:0.31, G:0.24, T:0.24
Consensus pattern (42 bp):
GCAACGGCTTATGTGCACTCCCACTCGCACATAGCCGGGTCA
Found at i:7223742 original size:36 final size:36
Alignment explanation
Indices: 7223702--7223801 Score: 137
Period size: 36 Copynumber: 2.8 Consensus size: 36
7223692 CAGCTGAAGT
*
7223702 CATCGTGTGCACCCCCACATCACGCACAACTAATGC
1 CATCGTGTGCTCCCCCACATCACGCACAACTAATGC
* * *
7223738 CATCGTGTGCTTCCCCACATCGCGCACAGCTAATGC
1 CATCGTGTGCTCCCCCACATCACGCACAACTAATGC
* * *
7223774 CATTGTGAGCTCCCCCACATCATGCACA
1 CATCGTGTGCTCCCCCACATCACGCACA
7223802 TGCACGGTTA
Statistics
Matches: 55, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
36 55 1.00
ACGTcount: A:0.24, C:0.40, G:0.16, T:0.20
Consensus pattern (36 bp):
CATCGTGTGCTCCCCCACATCACGCACAACTAATGC
Found at i:7240969 original size:23 final size:24
Alignment explanation
Indices: 7240929--7240974 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 24
7240919 GCCTATAAAA
*
7240929 ACAACCTTTCGGAGGACTTAAGAG
1 ACAACCTTTCGGAGGACTCAAGAG
* *
7240953 ACAACTTTTGGGA-GACTCAAGA
1 ACAACCTTTCGGAGGACTCAAGA
7240975 AGCCAGAAGT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
23 8 0.42
24 11 0.58
ACGTcount: A:0.35, C:0.20, G:0.24, T:0.22
Consensus pattern (24 bp):
ACAACCTTTCGGAGGACTCAAGAG
Found at i:7253026 original size:42 final size:43
Alignment explanation
Indices: 7252965--7253197 Score: 204
Period size: 42 Copynumber: 5.5 Consensus size: 43
7252955 ATATTGAGTC
** *
7252965 GGCTATGTGCGAGTAGGAGTGTGCATAAGCCGATGCTGA-CCA
1 GGCTATGTGCGAGGGGGAGTGCGCATAAGCCGATGCTGACCCA
* * *
7253007 GGCTATGTGCGAGGGGGAGTGCGCATAAGCCAATGCTAACCCC
1 GGCTATGTGCGAGGGGGAGTGCGCATAAGCCGATGCTGACCCA
* * * * * * * * *
7253050 GACTATGTGCAAGGGAGAGTGTGCGTAAGCTGATACTAACTC-
1 GGCTATGTGCGAGGGGGAGTGCGCATAAGCCGATGCTGACCCA
* * *
7253092 GGTTATGTGCGAGGGGGAGTGCACGTAAGCCGATGCTGACCCA
1 GGCTATGTGCGAGGGGGAGTGCGCATAAGCCGATGCTGACCCA
* ** **
7253135 -GCTATGCGCGAGTAGGAGTGCGCATAAGCAAATGCTGACCCA
1 GGCTATGTGCGAGGGGGAGTGCGCATAAGCCGATGCTGACCCA
* * *
7253177 -GCCATGTGCTAGTGGGAGTGC
1 GGCTATGTGCGAGGGGGAGTGC
7253198 ATATGAGCTG
Statistics
Matches: 152, Mismatches: 37, Indels: 4
0.79 0.19 0.02
Matches are distributed among these distances:
42 117 0.77
43 35 0.23
ACGTcount: A:0.24, C:0.21, G:0.35, T:0.20
Consensus pattern (43 bp):
GGCTATGTGCGAGGGGGAGTGCGCATAAGCCGATGCTGACCCA
Found at i:7254405 original size:17 final size:17
Alignment explanation
Indices: 7254379--7254415 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
7254369 AGAAAAATAT
*
7254379 GCATACACTTAGGGGGA
1 GCATACACTTAGGGAGA
*
7254396 GCATATACTTAGGGAGA
1 GCATACACTTAGGGAGA
7254413 GCA
1 GCA
7254416 ATCCTCATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.32, C:0.16, G:0.32, T:0.19
Consensus pattern (17 bp):
GCATACACTTAGGGAGA
Found at i:7255900 original size:14 final size:14
Alignment explanation
Indices: 7255881--7255923 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
7255871 TTGACTCACC
7255881 TAAAATAACTAATT
1 TAAAATAACTAATT
* *
7255895 TAAAATAATTAA-A
1 TAAAATAACTAATT
7255908 TAAAATATACTAATT
1 TAAAATA-ACTAATT
7255923 T
1 T
7255924 TCATGCATTT
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
13 7 0.30
14 15 0.65
15 1 0.04
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.37
Consensus pattern (14 bp):
TAAAATAACTAATT
Found at i:7257637 original size:19 final size:19
Alignment explanation
Indices: 7257613--7257650 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
7257603 CCATTTAACT
*
7257613 TATTGGAGTATTATTTGAG
1 TATTGGAGTATAATTTGAG
7257632 TATTGGAGTATAATTTGAG
1 TATTGGAGTATAATTTGAG
7257651 GGTTTGGCAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.29, C:0.00, G:0.26, T:0.45
Consensus pattern (19 bp):
TATTGGAGTATAATTTGAG
Found at i:7260510 original size:16 final size:17
Alignment explanation
Indices: 7260475--7260510 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
7260465 GTAGAGAAAT
*
7260475 AAAATAACTGATAAGTA
1 AAAATAACTGAAAAGTA
7260492 AAAATAACTGAAAAG-A
1 AAAATAACTGAAAAGTA
7260508 AAA
1 AAA
7260511 TAAACAAAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 4 0.22
17 14 0.78
ACGTcount: A:0.67, C:0.06, G:0.11, T:0.17
Consensus pattern (17 bp):
AAAATAACTGAAAAGTA
Found at i:7264954 original size:2 final size:2
Alignment explanation
Indices: 7264947--7264974 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
7264937 AGGCATAAAA
7264947 AT 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 AT
7264975 GTAATTGAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:7265146 original size:15 final size:15
Alignment explanation
Indices: 7265115--7265155 Score: 59
Period size: 15 Copynumber: 2.9 Consensus size: 15
7265105 ACGGTGGAAG
7265115 AAAG-AAAGAAA-GA
1 AAAGAAAAGAAAGGA
*
7265128 AAAGAAAATAAAGGA
1 AAAGAAAAGAAAGGA
7265143 AAAGAAAAGAAAG
1 AAAGAAAAGAAAG
7265156 TAACAAGGAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
13 4 0.17
14 6 0.25
15 14 0.58
ACGTcount: A:0.76, C:0.00, G:0.22, T:0.02
Consensus pattern (15 bp):
AAAGAAAAGAAAGGA
Found at i:7267272 original size:21 final size:22
Alignment explanation
Indices: 7267238--7267280 Score: 79
Period size: 21 Copynumber: 2.0 Consensus size: 22
7267228 TTTAAGTGGT
7267238 ATCAGAGCTTTTGGTTTTAAAG
1 ATCAGAGCTTTTGGTTTTAAAG
7267260 ATCAGAG-TTTTGGTTTTAAAG
1 ATCAGAGCTTTTGGTTTTAAAG
7267281 TTGTTTTAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 14 0.67
22 7 0.33
ACGTcount: A:0.28, C:0.07, G:0.23, T:0.42
Consensus pattern (22 bp):
ATCAGAGCTTTTGGTTTTAAAG
Found at i:7271380 original size:5 final size:5
Alignment explanation
Indices: 7271361--7271396 Score: 58
Period size: 5 Copynumber: 7.6 Consensus size: 5
7271351 AACGGTGGAA
7271361 AAAAG -AAAG -AAAG AAAAG AAAAG AAAAG AAAAG AAA
1 AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAA
7271397 GTAATAAGGA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
4 8 0.27
5 22 0.73
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:7271438 original size:26 final size:27
Alignment explanation
Indices: 7271399--7271460 Score: 99
Period size: 27 Copynumber: 2.3 Consensus size: 27
7271389 AAAAGAAAGT
* *
7271399 AATAAGGAAGGAAAATGGGCATGGCCC
1 AATAAGAAAGAAAAATGGGCATGGCCC
7271426 AATAAGAAAGAAAAATGGGCATGGCCC
1 AATAAGAAAGAAAAATGGGCATGGCCC
7271453 AAT-AGAAA
1 AATAAGAAA
7271461 TAAGTTGAGG
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
26 5 0.15
27 28 0.85
ACGTcount: A:0.48, C:0.13, G:0.27, T:0.11
Consensus pattern (27 bp):
AATAAGAAAGAAAAATGGGCATGGCCC
Found at i:7278038 original size:40 final size:39
Alignment explanation
Indices: 7277993--7278073 Score: 135
Period size: 40 Copynumber: 2.1 Consensus size: 39
7277983 CTTCATTCCA
* *
7277993 TAGTTTAGTGTTTGATTGAATTTTGTTTTTAATTAATACT
1 TAGTTTAGTGTTTAATTGAATTTAGTTTTTAATTAAT-CT
7278033 TAGTTTAGTGTTTAATTGAATTTAGTTTTTAATTAATCT
1 TAGTTTAGTGTTTAATTGAATTTAGTTTTTAATTAATCT
7278072 TA
1 TA
7278074 CAAAAATTGA
Statistics
Matches: 39, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
39 4 0.10
40 35 0.90
ACGTcount: A:0.27, C:0.02, G:0.14, T:0.57
Consensus pattern (39 bp):
TAGTTTAGTGTTTAATTGAATTTAGTTTTTAATTAATCT
Found at i:7280516 original size:20 final size:20
Alignment explanation
Indices: 7280491--7280542 Score: 68
Period size: 20 Copynumber: 2.6 Consensus size: 20
7280481 ATTCGTTAAG
*
7280491 AATGTATCGATAAATTCCTA
1 AATGTATCGATAAATTCCCA
* *
7280511 AATGTATCAATACATTCCCA
1 AATGTATCGATAAATTCCCA
*
7280531 AATGTATTGATA
1 AATGTATCGATA
7280543 TATTGCTATA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.40, C:0.15, G:0.10, T:0.35
Consensus pattern (20 bp):
AATGTATCGATAAATTCCCA
Found at i:7281188 original size:2 final size:2
Alignment explanation
Indices: 7281181--7281222 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
7281171 AGAGAACTGA
7281181 AT AT AT AT AT AT AT AT 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 AT AT AT AT AT AT AT AT
7281223 GTGTGTGTGT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:7283209 original size:18 final size:18
Alignment explanation
Indices: 7283166--7283212 Score: 69
Period size: 17 Copynumber: 2.6 Consensus size: 18
7283156 TTTATGAGAA
*
7283166 AAATATGAATTTATAAAAT
1 AAAT-TGAAATTATAAAAT
7283185 AAA-TGAAATTATAAAAT
1 AAATTGAAATTATAAAAT
7283202 AAATTGAAATT
1 AAATTGAAATT
7283213 TTTATAAATT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
17 16 0.62
18 7 0.27
19 3 0.12
ACGTcount: A:0.60, C:0.00, G:0.06, T:0.34
Consensus pattern (18 bp):
AAATTGAAATTATAAAAT
Found at i:7285496 original size:2 final size:2
Alignment explanation
Indices: 7285489--7285518 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
7285479 AATCCTAATA
7285489 AT AT 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 AT AT
7285519 CAATATGGAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:7287089 original size:16 final size:16
Alignment explanation
Indices: 7287058--7287110 Score: 63
Period size: 16 Copynumber: 3.2 Consensus size: 16
7287048 TGGTTCTTCT
*
7287058 TTTTAGTTTTTGTTTAA
1 TTTTAG-TTTTCTTTAA
7287075 TTTTAGTTTTCTTTAA
1 TTTTAGTTTTCTTTAA
*
7287091 TTCTTAG-TGTCTTTAA
1 TT-TTAGTTTTCTTTAA
7287107 TTTT
1 TTTT
7287111 GGTTATTTGA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
15 2 0.06
16 21 0.64
17 10 0.30
ACGTcount: A:0.17, C:0.06, G:0.09, T:0.68
Consensus pattern (16 bp):
TTTTAGTTTTCTTTAA
Found at i:7288823 original size:20 final size:20
Alignment explanation
Indices: 7288800--7288851 Score: 54
Period size: 20 Copynumber: 2.6 Consensus size: 20
7288790 TATATGTTGA
7288800 TTAGTTTAAATTAAGTTATT
1 TTAGTTTAAATTAAGTTATT
* *
7288820 TTAG-TTAATTTTATGTTATT
1 TTAGTTTAA-ATTAAGTTATT
*
7288840 TT-TTTTAAATTA
1 TTAGTTTAAATTA
7288852 CTTTAATTAT
Statistics
Matches: 26, Mismatches: 4, Indels: 5
0.74 0.11 0.14
Matches are distributed among these distances:
19 7 0.27
20 19 0.73
ACGTcount: A:0.31, C:0.00, G:0.08, T:0.62
Consensus pattern (20 bp):
TTAGTTTAAATTAAGTTATT
Found at i:7297131 original size:13 final size:15
Alignment explanation
Indices: 7297101--7297143 Score: 56
Period size: 14 Copynumber: 3.1 Consensus size: 15
7297091 TCGGCGGGAG
7297101 AGAGAAGAAAGAAAA
1 AGAGAAGAAAGAAAA
7297116 AGAG-AGAAAG-AAA
1 AGAGAAGAAAGAAAA
*
7297129 AGAAAAGAAA-AAAA
1 AGAGAAGAAAGAAAA
7297143 A
1 A
7297144 AAAATATATA
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
13 6 0.24
14 15 0.60
15 4 0.16
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (15 bp):
AGAGAAGAAAGAAAA
Found at i:7297136 original size:18 final size:19
Alignment explanation
Indices: 7297098--7297134 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
7297088 TGATCGGCGG
7297098 GAGAGAGAAGAAAGAAAAA
1 GAGAGAGAAGAAAGAAAAA
7297117 GAGAGA-AAGAAAAGAAAA
1 GAGAGAGAAG-AAAGAAAA
7297135 GAAAAAAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 3 0.18
19 14 0.82
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (19 bp):
GAGAGAGAAGAAAGAAAAA
Found at i:7306524 original size:18 final size:18
Alignment explanation
Indices: 7306501--7306539 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
7306491 ATTCAAATAA
7306501 AATTTTGAAAGATACCAT
1 AATTTTGAAAGATACCAT
7306519 AATTTTGAAAGATACCAT
1 AATTTTGAAAGATACCAT
7306537 AAT
1 AAT
7306540 CCTAGGTGTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.46, C:0.10, G:0.10, T:0.33
Consensus pattern (18 bp):
AATTTTGAAAGATACCAT
Done.