Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr01 113035596
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: 113035596
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Warning! 271 characters in sequence are not A, C, G, or T
File 7 of 378
Found at i:2124220 original size:54 final size:54
Alignment explanation
Indices: 2124154--2124258 Score: 192
Period size: 54 Copynumber: 1.9 Consensus size: 54
2124144 AAAACGCCGC
*
2124154 TAAAGGTCAAGGCTTTTAGCGGCGTTTGTGGGAAAAACGCCGCTAAAGGTCCGT
1 TAAAGGTCAAGGCTTTTAGCGGCGTTTGTGGAAAAAACGCCGCTAAAGGTCCGT
*
2124208 TAAAGGTTAAGGCTTTTAGCGGCGTTTGTGGAAAAAACGCCGCTAAAGGTC
1 TAAAGGTCAAGGCTTTTAGCGGCGTTTGTGGAAAAAACGCCGCTAAAGGTC
2124259 AAGGCTTTTA
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
54 49 1.00
ACGTcount: A:0.28, C:0.17, G:0.30, T:0.25
Consensus pattern (54 bp):
TAAAGGTCAAGGCTTTTAGCGGCGTTTGTGGAAAAAACGCCGCTAAAGGTCCGT
Found at i:2124426 original size:31 final size:32
Alignment explanation
Indices: 2124391--2124473 Score: 96
Period size: 31 Copynumber: 2.6 Consensus size: 32
2124381 CTTCCTGCAT
* *
2124391 TAAAATCCAACCAAATACAACAAATATAA-TA
1 TAAAATACAACCAAAAACAACAAATATAACTA
* * *
2124422 TAAAATGCAGCCAAAAACAACAAATTTAACGTA
1 TAAAATACAACCAAAAACAACAAATATAAC-TA
*
2124455 AAAAATACAACCAAAAACA
1 TAAAATACAACCAAAAACA
2124474 TCAATTCTAA
Statistics
Matches: 43, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
31 25 0.58
33 18 0.42
ACGTcount: A:0.61, C:0.19, G:0.04, T:0.16
Consensus pattern (32 bp):
TAAAATACAACCAAAAACAACAAATATAACTA
Found at i:2132568 original size:24 final size:24
Alignment explanation
Indices: 2132518--2132564 Score: 78
Period size: 23 Copynumber: 2.0 Consensus size: 24
2132508 AGGTTTCGTC
2132518 TTTCGTAGAAATGGGGGGTAAGGG
1 TTTCGTAGAAATGGGGGGTAAGGG
*
2132542 TTTCGTTGAAAT-GGGGGTAAGGG
1 TTTCGTAGAAATGGGGGGTAAGGG
2132565 GTTTGAATAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 11 0.50
24 11 0.50
ACGTcount: A:0.23, C:0.04, G:0.45, T:0.28
Consensus pattern (24 bp):
TTTCGTAGAAATGGGGGGTAAGGG
Found at i:2132952 original size:9 final size:9
Alignment explanation
Indices: 2132927--2132972 Score: 56
Period size: 9 Copynumber: 5.0 Consensus size: 9
2132917 TCGAAAAAAA
2132927 AATTCGAGTT
1 AATTCGA-TT
*
2132937 GATTCGATT
1 AATTCGATT
2132946 AATTCGATT
1 AATTCGATT
*
2132955 AACTCGATT
1 AATTCGATT
*
2132964 AACTCGATT
1 AATTCGATT
2132973 CGAATAATTC
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
9 27 0.82
10 6 0.18
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.39
Consensus pattern (9 bp):
AATTCGATT
Found at i:2133700 original size:14 final size:15
Alignment explanation
Indices: 2133676--2133705 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
2133666 CACAAACTTC
2133676 AGAATTTATGTATTT
1 AGAATTTATGTATTT
2133691 AGAA-TTATGTATTT
1 AGAATTTATGTATTT
2133705 A
1 A
2133706 TATAAACACA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 11 0.73
15 4 0.27
ACGTcount: A:0.37, C:0.00, G:0.13, T:0.50
Consensus pattern (15 bp):
AGAATTTATGTATTT
Found at i:2135885 original size:41 final size:43
Alignment explanation
Indices: 2135803--2135888 Score: 113
Period size: 43 Copynumber: 2.0 Consensus size: 43
2135793 GATAACAAAC
* *
2135803 CCGGCCCATACCATTAACTTAATATATATACTATACCATTGAA
1 CCGGCCCAAACCATAAACTTAATATATATACTATACCATTGAA
* * *
2135846 CCGGCCTAAACCATAAACTTAA-A-ATATATTCTACCATTGAA
1 CCGGCCCAAACCATAAACTTAATATATATACTATACCATTGAA
2135887 CC
1 CC
2135889 CTAAACCATA
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
41 18 0.47
42 1 0.03
43 19 0.50
ACGTcount: A:0.38, C:0.27, G:0.07, T:0.28
Consensus pattern (43 bp):
CCGGCCCAAACCATAAACTTAATATATATACTATACCATTGAA
Found at i:2137097 original size:16 final size:16
Alignment explanation
Indices: 2137078--2137113 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
2137068 CTTTATATGC
2137078 TTTATGTATTATTTAT
1 TTTATGTATTATTTAT
* *
2137094 TTTATTTTTTATTTAT
1 TTTATGTATTATTTAT
2137110 TTTA
1 TTTA
2137114 CAATCTATTG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.22, C:0.00, G:0.03, T:0.75
Consensus pattern (16 bp):
TTTATGTATTATTTAT
Found at i:2137847 original size:78 final size:77
Alignment explanation
Indices: 2137747--2138114 Score: 319
Period size: 78 Copynumber: 4.5 Consensus size: 77
2137737 AATTTCTGCC
*
2137747 TTTCAAAAAAATCAACTCATATTGCGAGAGGTAAGTTGAGCCTTGGCTCACGCACTGAGCTATTT
1 TTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGCTCACGCACTGAGCTATTT
*
2137812 TCAATTTCTATC
66 TCAATTTCTATT
* * * *
2137824 TTTCAGAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAG-CTTCAGATCACACACTGAGGTAT
1 TTTCA-AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTT-GGCTCACGCACTGAGCTA-
*
2137888 TTTTTCAATTTATATT
63 -TTTTCAATTTCTATT
* * * * * * *
2137904 TTTCAAAAAAATCAACTCACATTGTGAGATGTGAGTTGAGCCTCGGGTCA--CATGTCGAGGTAT
1 TTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGCTCACGCA-CT-GAGCTAT
** *
2137967 TTTCAAAATCTGTT
64 TTTCAATTTCTATT
* *
2137981 TTTCAAATTTTGTTTTCAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTTGGCTCACGTA
1 TTTC-AA----------AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGCTCACGCA
* *
2138046 CTGAGCTATTTTCAATTCTTGTTTTTT
55 CTGAGCTATTTTCAA---TT-TCTATT
*
2138073 TTTCAAAAAAATTCAACTCATATTGCGAGATGTGAGTTGAGC
1 TTTCAAAAAAA-TCAACTCATATTGCGAGAGGTGAGTTGAGC
2138115 TTTTTAATTT
Statistics
Matches: 235, Mismatches: 31, Indels: 45
0.76 0.10 0.14
Matches are distributed among these distances:
77 25 0.11
78 51 0.22
79 42 0.18
80 20 0.09
81 5 0.02
82 29 0.12
88 51 0.22
89 1 0.00
90 1 0.00
91 2 0.01
92 8 0.03
ACGTcount: A:0.30, C:0.17, G:0.18, T:0.35
Consensus pattern (77 bp):
TTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGCTCACGCACTGAGCTATTT
TCAATTTCTATT
Found at i:2137955 original size:79 final size:77
Alignment explanation
Indices: 2137746--2138114 Score: 281
Period size: 88 Copynumber: 4.5 Consensus size: 77
2137736 TAATTTCTGC
* * * *
2137746 CTTTCAAAAAAATCAACTCATATTGCGAGAGGTAAGTTGAGCCTTGGCTCACGCACTGAGCTATT
1 CTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGATCACACACTGAGCTATT
*
2137811 TTCAATTTCTAT
66 TTCAATTTATAT
* * *
2137823 CTTTCAGAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCTTCAGATCACACACTGAGGTAT
1 CTTTCA-AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGATCACACACTGAGCTA-
2137888 TTTTTCAATTTATAT
64 -TTTTCAATTTATAT
* * * * * ** *
2137903 TTTTCAAAAAAATCAACTCACATTGTGAGATGTGAGTTGAGCCTCGGGTCACA-TGTCGAGGTAT
1 CTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGATCACACACT-GAGCTAT
*
2137967 TTTCAAAATCTGTTTTTCAAATT
65 TTTC--AA------TTT-ATA-T
* *** * * * **
2137990 TTGTTTTCAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTTGGCTCACGTACTGAGCTAT
1 CT-TTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGATCACACACTGAGCTAT
* *
2138055 TTTCAATTCTTGTTTTT
65 TTTCAA---TT-TATAT
* *
2138072 TTTTCAAAAAAATTCAACTCATATTGCGAGATGTGAGTTGAGC
1 CTTTCAAAAAAA-TCAACTCATATTGCGAGAGGTGAGTTGAGC
2138115 TTTTTAATTT
Statistics
Matches: 235, Mismatches: 39, Indels: 31
0.77 0.13 0.10
Matches are distributed among these distances:
77 11 0.05
78 51 0.22
79 49 0.21
80 18 0.08
81 7 0.03
82 32 0.14
83 3 0.01
84 1 0.00
85 3 0.01
86 4 0.02
87 3 0.01
88 52 0.22
89 1 0.00
ACGTcount: A:0.30, C:0.17, G:0.18, T:0.35
Consensus pattern (77 bp):
CTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGATCACACACTGAGCTATT
TTCAATTTATAT
Found at i:2138139 original size:30 final size:30
Alignment explanation
Indices: 2138105--2138186 Score: 139
Period size: 30 Copynumber: 2.7 Consensus size: 30
2138095 TTGCGAGATG
*
2138105 TGAGTTGAG-CTTTTTAATTTCTACGAGAGT
1 TGAGTTGAGTC-TTTTAATTTCTACAAGAGT
2138135 TGAGTTGAGTCTTTTAATTTCTACAAGAGT
1 TGAGTTGAGTCTTTTAATTTCTACAAGAGT
2138165 TGAGTTGAGTCTTTTAATTTCT
1 TGAGTTGAGTCTTTTAATTTCT
2138187 GTTTTTCAAA
Statistics
Matches: 50, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
30 49 0.98
31 1 0.02
ACGTcount: A:0.23, C:0.10, G:0.21, T:0.46
Consensus pattern (30 bp):
TGAGTTGAGTCTTTTAATTTCTACAAGAGT
Found at i:2139064 original size:26 final size:25
Alignment explanation
Indices: 2139003--2139075 Score: 105
Period size: 26 Copynumber: 3.0 Consensus size: 25
2138993 CTCCCCCAAA
2139003 AAAAAACCTAA--CAAAAAAAAAAG
1 AAAAAACCTAACCCAAAAAAAAAAG
2139026 AAAAAACCTAACCCAAAAAAAAAAAG
1 AAAAAACCTAACCC-AAAAAAAAAAG
**
2139052 AAAAAACCTAACCCCCAAAAAAAA
1 AAAAAACCTAACCCAAAAAAAAAA
2139076 CCAAGAAACC
Statistics
Matches: 45, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
23 11 0.24
25 9 0.20
26 25 0.56
ACGTcount: A:0.73, C:0.21, G:0.03, T:0.04
Consensus pattern (25 bp):
AAAAAACCTAACCCAAAAAAAAAAG
Found at i:2139088 original size:27 final size:26
Alignment explanation
Indices: 2139003--2139085 Score: 91
Period size: 26 Copynumber: 3.3 Consensus size: 26
2138993 CTCCCCCAAA
*
2139003 AAAAAACCTAA--C-AAAAAAAAAAG
1 AAAAAACCTAACCCAAAAAAAAAAAC
*
2139026 AAAAAACCTAACCCAAAAAAAAAAAG
1 AAAAAACCTAACCCAAAAAAAAAAAC
** *
2139052 AAAAAACCTAACCCCCAAAAAAAACC
1 AAAAAACCTAACCCAAAAAAAAAAAC
*
2139078 AAGAAACC
1 AAAAAACC
2139086 CTAGCCACCT
Statistics
Matches: 52, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
23 11 0.21
25 1 0.02
26 40 0.77
ACGTcount: A:0.70, C:0.23, G:0.04, T:0.04
Consensus pattern (26 bp):
AAAAAACCTAACCCAAAAAAAAAAAC
Found at i:2139607 original size:39 final size:39
Alignment explanation
Indices: 2139535--2139609 Score: 98
Period size: 39 Copynumber: 1.9 Consensus size: 39
2139525 TTTATATATA
* * *
2139535 TTATGTATATATTTTTTAATGCCATTAGTTATATATTTC
1 TTATGTATATATTCTTAAATACCATTAGTTATATATTTC
*
2139574 TTATGTATATATTCTTAAATACTATTA-TATATATAT
1 TTATGTATATATTCTTAAATACCATTAGT-TATATAT
2139610 ATATATATTT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
38 1 0.03
39 30 0.97
ACGTcount: A:0.33, C:0.07, G:0.05, T:0.55
Consensus pattern (39 bp):
TTATGTATATATTCTTAAATACCATTAGTTATATATTTC
Found at i:2139727 original size:2 final size:2
Alignment explanation
Indices: 2139715--2139756 Score: 57
Period size: 2 Copynumber: 21.0 Consensus size: 2
2139705 TTTTATGTAC
* * *
2139715 AT AT GT AT AT AT AT AT AT AC AT AC 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
2139757 TTGTACATAT
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.48, C:0.05, G:0.02, T:0.45
Consensus pattern (2 bp):
AT
Found at i:2139808 original size:15 final size:15
Alignment explanation
Indices: 2139788--2139817 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
2139778 ATTATTGTTG
2139788 TATATTTTTTATGTA
1 TATATTTTTTATGTA
2139803 TATATTTTTTATGTA
1 TATATTTTTTATGTA
2139818 CGTTTCCTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.27, C:0.00, G:0.07, T:0.67
Consensus pattern (15 bp):
TATATTTTTTATGTA
Found at i:2139876 original size:37 final size:37
Alignment explanation
Indices: 2139834--2139935 Score: 93
Period size: 37 Copynumber: 2.6 Consensus size: 37
2139824 CTAATATTTT
2139834 CTTTTATTGTAGATATTATTATTATTATTAT-TACATA
1 CTTTTATT-TAGATATTATTATTATTATTATGTACATA
*
2139871 CTTTTATTATATGCATATATATATATGTATTTTTATGTACATA
1 CTTTTATT-TA-G-ATAT-TAT-TAT-TATTATTATGTACATA
*
2139914 -TTATTATTT-TATATTATTATTA
1 CTT-TTATTTAGATATTATTATTA
2139936 CCAAATATAT
Statistics
Matches: 55, Mismatches: 3, Indels: 15
0.75 0.04 0.21
Matches are distributed among these distances:
36 2 0.04
37 13 0.24
38 4 0.07
39 8 0.15
40 3 0.05
41 3 0.05
42 11 0.20
43 11 0.20
ACGTcount: A:0.32, C:0.05, G:0.05, T:0.58
Consensus pattern (37 bp):
CTTTTATTTAGATATTATTATTATTATTATGTACATA
Found at i:2140571 original size:19 final size:19
Alignment explanation
Indices: 2140547--2140584 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
2140537 TTGAGATTGC
2140547 CAACCTATTTGCATGAAAT
1 CAACCTATTTGCATGAAAT
*
2140566 CAACCTATTTGCCTGAAAT
1 CAACCTATTTGCATGAAAT
2140585 TATTAATTTC
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:0.34, C:0.24, G:0.11, T:0.32
Consensus pattern (19 bp):
CAACCTATTTGCATGAAAT
Found at i:2142034 original size:41 final size:41
Alignment explanation
Indices: 2141989--2142203 Score: 222
Period size: 41 Copynumber: 5.3 Consensus size: 41
2141979 CGTTTAGACC
* * *
2141989 AAAAACGCGGCTATTAATCAGTTTTTAGTGGTGTTTTGGAT
1 AAAAACGCCGCTATTGATCAGTTTTTAGTGGCGTTTTGGAT
* * *
2142030 AAAAACGCCACAATTGATCAGTTTTTAGTGGCGTTTGGGAT
1 AAAAACGCCGCTATTGATCAGTTTTTAGTGGCGTTTTGGAT
* *
2142071 AAAAACGCCGCTATTGATCAGCTTTTAATGGCGTTTTGCG--
1 AAAAACGCCGCTATTGATCAGTTTTTAGTGGCGTTTTG-GAT
* * **
2142111 AAAAACGCCGCTATTGACCAGTTTTTAGTGGCGTTTTTGCC
1 AAAAACGCCGCTATTGATCAGTTTTTAGTGGCGTTTTGGAT
* * * * * *
2142152 AAAAACGCCGTTATAGTTTAGCTTTTAGTGGCGTTTCGG--
1 AAAAACGCCGCTATTGATCAGTTTTTAGTGGCGTTTTGGAT
*
2142191 ACAAACGCCGCTA
1 AAAAACGCCGCTA
2142204 ATGTTTATTA
Statistics
Matches: 146, Mismatches: 25, Indels: 8
0.82 0.14 0.04
Matches are distributed among these distances:
39 12 0.08
40 34 0.23
41 99 0.68
42 1 0.01
ACGTcount: A:0.26, C:0.18, G:0.23, T:0.33
Consensus pattern (41 bp):
AAAAACGCCGCTATTGATCAGTTTTTAGTGGCGTTTTGGAT
Found at i:2142156 original size:81 final size:80
Alignment explanation
Indices: 2141977--2142203 Score: 247
Period size: 81 Copynumber: 2.8 Consensus size: 80
2141967 AACTTTTTGC
* * * * * * * *
2141977 GGCGTTTAGACCAAAAACGCGGCTATTAATCAGTTTTTAGTGGTGTTTTGGATAAAAACGCCACA
1 GGCGTTTGGGCCAAAAACGCCGCTATTGATCAGCTTTTAGTGGCGTTTTGG--AAAAACGCCGCT
*
2142042 ATTGATCAGTTTTTAGT
64 ATTGACCAGTTTTTAGT
** *
2142059 GGCGTTTGGGATAAAAACGCCGCTATTGATCAGCTTTTAATGGCGTTTTGCGAAAAACGCCGCTA
1 GGCGTTTGGGCCAAAAACGCCGCTATTGATCAGCTTTTAGTGGCGTTTTG-GAAAAACGCCGCTA
2142124 TTGACCAGTTTTTAGT
65 TTGACCAGTTTTTAGT
** * * * * * *
2142140 GGCGTTTTTGCCAAAAACGCCGTTATAGTTTAGCTTTTAGTGGCGTTTCGGACAAACGCCGCTA
1 GGCGTTTGGGCCAAAAACGCCGCTATTGATCAGCTTTTAGTGGCGTTTTGGAAAAACGCCGCTA
2142204 ATGTTTATTA
Statistics
Matches: 121, Mismatches: 23, Indels: 4
0.82 0.16 0.03
Matches are distributed among these distances:
80 13 0.11
81 66 0.55
82 41 0.34
83 1 0.01
ACGTcount: A:0.26, C:0.18, G:0.24, T:0.33
Consensus pattern (80 bp):
GGCGTTTGGGCCAAAAACGCCGCTATTGATCAGCTTTTAGTGGCGTTTTGGAAAAACGCCGCTAT
TGACCAGTTTTTAGT
Found at i:2147269 original size:29 final size:30
Alignment explanation
Indices: 2147226--2147282 Score: 73
Period size: 29 Copynumber: 1.9 Consensus size: 30
2147216 CCCCCCCCAA
*
2147226 AAAAAAAGAAGAAAA-AATGAAAAACCTAAC
1 AAAAAAAGAAGAAAATAA-AAAAAACCTAAC
*
2147256 AAAAAAATAA-AAAATAAAAAAAACCTA
1 AAAAAAAGAAGAAAATAAAAAAAACCTA
2147283 GCCACCTAAC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 13 0.54
30 11 0.46
ACGTcount: A:0.77, C:0.09, G:0.05, T:0.09
Consensus pattern (30 bp):
AAAAAAAGAAGAAAATAAAAAAAACCTAAC
Found at i:2147511 original size:18 final size:17
Alignment explanation
Indices: 2147472--2147510 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
2147462 CCTAAAGGTG
*
2147472 ATTTTATCTTCTTTATT
1 ATTTTATCTTATTTATT
2147489 ATTTTACTCTTATTT-TT
1 ATTTTA-TCTTATTTATT
2147506 ATTTT
1 ATTTT
2147511 TTATTTTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 13 0.65
18 7 0.35
ACGTcount: A:0.18, C:0.10, G:0.00, T:0.72
Consensus pattern (17 bp):
ATTTTATCTTATTTATT
Found at i:2147792 original size:29 final size:29
Alignment explanation
Indices: 2147736--2147792 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 29
2147726 TCTCTTCTTT
* *
2147736 TTTCATTTATTTTTCGTATTTACCTTAGA
1 TTTCATTTATTTTGCGTATTTAACTTAGA
*
2147765 TTTCATATTATTTTGC-TATTTAATTTAG
1 TTTCAT-TTATTTTGCGTATTTAACTTAG
2147793 CTTTAAATAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 16 0.67
30 8 0.33
ACGTcount: A:0.23, C:0.11, G:0.07, T:0.60
Consensus pattern (29 bp):
TTTCATTTATTTTGCGTATTTAACTTAGA
Found at i:2148053 original size:11 final size:11
Alignment explanation
Indices: 2148035--2148064 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
2148025 GTGTATATTG
2148035 TATATATTATA
1 TATATATTATA
*
2148046 TTTATATTATA
1 TATATATTATA
2148057 TATATATT
1 TATATATT
2148065 CTTAATGTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (11 bp):
TATATATTATA
Found at i:2152304 original size:12 final size:12
Alignment explanation
Indices: 2152287--2152322 Score: 63
Period size: 12 Copynumber: 3.0 Consensus size: 12
2152277 AACATTTTGA
2152287 CATTCATGCATT
1 CATTCATGCATT
2152299 CATTCATGCATT
1 CATTCATGCATT
*
2152311 CATTCATACATT
1 CATTCATGCATT
2152323 GCATATCCCA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.28, C:0.25, G:0.06, T:0.42
Consensus pattern (12 bp):
CATTCATGCATT
Found at i:2160907 original size:72 final size:72
Alignment explanation
Indices: 2160785--2161303 Score: 531
Period size: 72 Copynumber: 7.2 Consensus size: 72
2160775 AAGCCTTTTT
* * * * * *
2160785 ATTTTTGTTTTTCAAAATCAACTCATATTGCTAGAGGTGAGTCGAACCTCAGGTCACGCTGAGGT
1 ATTTTTGTGTTTAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGT
2160850 ATTTTCA
66 ATTTTCA
* **
2160857 ATTTTTGTGTTTTAATTTCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGT
1 ATTTTTGTGTTTAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGT
*
2160922 AATTTCA
66 ATTTTCA
* ** * * * * *
2160929 ATTTCTGTTGTCAAAAAAATCAACTCGTATTGCAAGCGGCGAGTTGAGCCTCAGGTCACACGCCG
1 ATTTTTG-TGT-TTAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGG--ACACGCTG
2160994 AGGTATTTTCA
62 AGGTATTTTCA
*
2161005 A-TTTT-TG---AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGCTGAGGT
1 ATTTTTGTGTTTAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGT
*
2161065 AATTTCA
66 ATTTTCA
* ** * * * * *
2161072 ATTTCTGTTGTCAAAAAAATCAACTCGTATTGCAAGCGGCGAGTTGAGCCTCAGGTCACACGCCG
1 ATTTTTG-TGT-TTAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGG--ACACGCTG
2161137 AGGTATTTTCA
62 AGGTATTTTCA
*
2161148 A-TTTT-TG---AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGCTGAGGT
1 ATTTTTGTGTTTAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGT
*
2161208 AATTTCA
66 ATTTTCA
* * ** * *
2161215 ATTTCTGT-TTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGG
1 ATTTTTGTGTTT-AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGG
2161279 TATTTTCA
65 TATTTTCA
*
2161287 ATTTCTGT-TTTCAAAAA
1 ATTTTTGTGTTT-AAAAA
2161304 AAAAAAAAAT
Statistics
Matches: 374, Mismatches: 54, Indels: 38
0.80 0.12 0.08
Matches are distributed among these distances:
67 36 0.10
68 6 0.02
69 73 0.20
70 2 0.01
72 138 0.37
73 7 0.02
74 70 0.19
75 6 0.02
76 36 0.10
ACGTcount: A:0.28, C:0.18, G:0.22, T:0.32
Consensus pattern (72 bp):
ATTTTTGTGTTTAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGT
ATTTTCA
Found at i:2161055 original size:143 final size:142
Alignment explanation
Indices: 2160798--2161290 Score: 697
Period size: 143 Copynumber: 3.5 Consensus size: 142
2160788 TTTGTTTTTC
* * * * *
2160798 AAAATCAACTCATATTGCTAGAGGTGAGTCGAACCTCAGGT-CACGCTGAGGTATTTTCAATTTT
1 AAAATCAACTCATATTGCAAGAGGCGAGTTGAGCCTCAGGTACACGCCGAGGTATTTTCAA-TTT
* ** *
2160862 TGTGTTTTAATTTCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTT
65 T-TG---AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGCTGAGGTAATTT
2160927 CAATTTCTGTTGTCAAA
126 CAATTTCTGTTGTCAAA
* *
2160944 AAAATCAACTCGTATTGCAAGCGGCGAGTTGAGCCTCAGGTCACACGCCGAGGTATTTTCAATTT
1 AAAATCAACTCATATTGCAAGAGGCGAGTTGAGCCTCAGGT-ACACGCCGAGGTATTTTCAATTT
2161009 TTGAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGCTGAGGTAATTTCAAT
65 TTGAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGCTGAGGTAATTTCAAT
2161074 TTCTGTTGTCAAA
130 TTCTGTTGTCAAA
* *
2161087 AAAATCAACTCGTATTGCAAGCGGCGAGTTGAGCCTCAGGTCACACGCCGAGGTATTTTCAATTT
1 AAAATCAACTCATATTGCAAGAGGCGAGTTGAGCCTCAGGT-ACACGCCGAGGTATTTTCAATTT
2161152 TTGAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGCTGAGGTAATTTCAAT
65 TTGAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGCTGAGGTAATTTCAAT
*
2161217 TTCTGTTTTC--A
130 TTCTGTTGTCAAA
* * *** * **
2161228 AAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAG-ACACGTTGAGGTATTTTCAATTT
1 AAAATCAACTCATATTGCAAGAGGCGAGTTGAGCCTCAGGTACACGCCGAGGTATTTTCAATTT
2161291 CTGTTTTCAA
Statistics
Matches: 323, Mismatches: 22, Indels: 11
0.91 0.06 0.03
Matches are distributed among these distances:
139 21 0.07
141 33 0.10
143 210 0.65
146 37 0.11
147 4 0.01
148 18 0.06
ACGTcount: A:0.29, C:0.18, G:0.23, T:0.30
Consensus pattern (142 bp):
AAAATCAACTCATATTGCAAGAGGCGAGTTGAGCCTCAGGTACACGCCGAGGTATTTTCAATTTT
TGAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGCTGAGGTAATTTCAATT
TCTGTTGTCAAA
Found at i:2161238 original size:215 final size:213
Alignment explanation
Indices: 2160792--2161305 Score: 585
Period size: 215 Copynumber: 2.4 Consensus size: 213
2160782 TTTATTTTTG
* * * *
2160792 TTTTTCAAAATCAACTCATATTGCTAGAGGTGAGTCGAACCTCAGGTCACGCTGAGGTATTTTCA
1 TTTTTCAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCA
* *** ** * * *
2160857 ATTTTTG-TGT-TTTAATTTCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAG
66 ATTTCTGTTGTCAAAAAAATCAACTCATATTGCAAGAGGCGAGTTGAGCCTCAGGACACGCCGAG
* *
2160920 GTAATTTCAATTTCTGTTGTCAAAAAAATCAACTCGTATTGCAAGCGGCGAGTTGAGCCTCAGGT
131 GTAATTTCAATTTCTGTTG---AAAAAATCAACTCATATTGCAAGAGGCGAGTTGAGCCTCAGGT
*
2160985 CACACGCCGAGGTATTTTCAA
193 CACACGCCGAGGTAATTTCAA
* * *
2161006 TTTTTGAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGCTGAGGTAATTTC
1 TTTTT-CAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTC
* *
2161071 AATTTCTGTTGTCAAAAAAATCAACTCGTATTGCAAGCGGCGAGTTGAGCCTCAGGTCACACGCC
65 AATTTCTGTTGTCAAAAAAATCAACTCATATTGCAAGAGGCGAGTTGAGCCTCAGG--ACACGCC
* * *
2161136 GAGGTATTTTCAA-TT-T-TTG-AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC-GG-
128 GAGGTAATTTCAATTTCTGTTGAAAAAATCAACTCATATTGCAAGAGGCGAGTTGAGCCTCAGGT
* *
2161195 GACACGCTGAGGTAATTTCAA
193 CACACGCCGAGGTAATTTCAA
** * *
2161216 TTTCTGTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTA
1 ----T-TTTTCAAAA-TCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTA
*
2161281 TTTTCAATTTCTGTTTTCAAAAAAA
60 TTTTCAATTTCTGTTGTCAAAAAAA
2161306 AAAAAAATCA
Statistics
Matches: 255, Mismatches: 34, Indels: 21
0.82 0.11 0.07
Matches are distributed among these distances:
210 18 0.07
211 2 0.01
212 34 0.13
214 10 0.04
215 130 0.51
216 6 0.02
217 35 0.14
218 2 0.01
219 18 0.07
ACGTcount: A:0.29, C:0.18, G:0.22, T:0.31
Consensus pattern (213 bp):
TTTTTCAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCA
ATTTCTGTTGTCAAAAAAATCAACTCATATTGCAAGAGGCGAGTTGAGCCTCAGGACACGCCGAG
GTAATTTCAATTTCTGTTGAAAAAATCAACTCATATTGCAAGAGGCGAGTTGAGCCTCAGGTCAC
ACGCCGAGGTAATTTCAA
Found at i:2162173 original size:29 final size:30
Alignment explanation
Indices: 2162130--2162186 Score: 73
Period size: 29 Copynumber: 1.9 Consensus size: 30
2162120 CCCCCCCCAA
*
2162130 AAAAAAAGAAGAAAA-AATGAAAAACCTAAC
1 AAAAAAAGAAGAAAATAA-AAAAAACCTAAC
*
2162160 AAAAAAATAA-AAAATAAAAAAAACCTA
1 AAAAAAAGAAGAAAATAAAAAAAACCTA
2162187 GCCACCTAAC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 13 0.54
30 11 0.46
ACGTcount: A:0.77, C:0.09, G:0.05, T:0.09
Consensus pattern (30 bp):
AAAAAAAGAAGAAAATAAAAAAAACCTAAC
Found at i:2162414 original size:18 final size:17
Alignment explanation
Indices: 2162375--2162413 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
2162365 CCTAAAGGTG
*
2162375 ATTTTATCTTCTTTATT
1 ATTTTATCTTATTTATT
2162392 ATTTTACTCTTATTT-TT
1 ATTTTA-TCTTATTTATT
2162409 ATTTT
1 ATTTT
2162414 TTATTTTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 13 0.65
18 7 0.35
ACGTcount: A:0.18, C:0.10, G:0.00, T:0.72
Consensus pattern (17 bp):
ATTTTATCTTATTTATT
Found at i:2162952 original size:11 final size:11
Alignment explanation
Indices: 2162934--2162963 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
2162924 GTGTATATTG
2162934 TATATATTATA
1 TATATATTATA
*
2162945 TTTATATTATA
1 TATATATTATA
2162956 TATATATT
1 TATATATT
2162964 CTTAATGTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (11 bp):
TATATATTATA
Found at i:2164916 original size:18 final size:17
Alignment explanation
Indices: 2164888--2164929 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 17
2164878 TATTTATATA
2164888 TTTTTTATT-AATTTGAT
1 TTTTTTATTAAATTT-AT
2164905 TTTTTTAGTTAAATTTAT
1 TTTTTTA-TTAAATTTAT
*
2164923 GTTTTTA
1 TTTTTTA
2164930 AAATATTAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
17 7 0.32
18 10 0.45
19 5 0.23
ACGTcount: A:0.24, C:0.00, G:0.07, T:0.69
Consensus pattern (17 bp):
TTTTTTATTAAATTTAT
Found at i:2167993 original size:46 final size:44
Alignment explanation
Indices: 2167889--2167996 Score: 144
Period size: 44 Copynumber: 2.4 Consensus size: 44
2167879 TGTCTTTGAC
** * * *
2167889 ATGGACTTACATGAATTATTCCTGTCTCCAATGCCATATATAAT
1 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATATAAT
*
2167933 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATTTCTAAT
1 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATA--TATAAT
2167979 ATGGACTTACATGGCTCA
1 ATGGACTTACATGGCTCA
2167997 TTTCTGTTCT
Statistics
Matches: 56, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
44 33 0.59
46 23 0.41
ACGTcount: A:0.30, C:0.23, G:0.14, T:0.33
Consensus pattern (44 bp):
ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATATAAT
Found at i:2169842 original size:30 final size:30
Alignment explanation
Indices: 2169773--2169842 Score: 79
Period size: 30 Copynumber: 2.4 Consensus size: 30
2169763 AATATACGGG
* *
2169773 AATA-AGTTGCTTACACGAGCTGACAGTAT
1 AATAGAGTTGCTCACACAAGCTGACAGTAT
** * *
2169802 ACCAGGGTTGCTCACACAAGCTGACATTAT
1 AATAGAGTTGCTCACACAAGCTGACAGTAT
2169832 AATAGAGTTGC
1 AATAGAGTTGC
2169843 CCAAAAAAGC
Statistics
Matches: 31, Mismatches: 9, Indels: 1
0.76 0.22 0.02
Matches are distributed among these distances:
29 2 0.06
30 29 0.94
ACGTcount: A:0.33, C:0.20, G:0.21, T:0.26
Consensus pattern (30 bp):
AATAGAGTTGCTCACACAAGCTGACAGTAT
Found at i:2173882 original size:131 final size:132
Alignment explanation
Indices: 2173583--2173980 Score: 446
Period size: 131 Copynumber: 3.0 Consensus size: 132
2173573 TTGCCTCGCC
* * * * *
2173583 TTAGAAAACACGAGTGAAATTCTGAATGG-ATAC-TCGATTATTTTGAACAAACGGGAGATTGCA
1 TTAGAAAACATGAGTGAAATTC-CAAAGGAAT-CTTCGATTATTTTGAACAAACGAGAAATTGCA
* * * *
2173646 ACCCAGCACGATAGGGCACTATTCCCCGAATTGCCAAACATCAAACATTTCTTTCGTTTTAAATA
64 ACCCAGCACGATAGGGCACTATTCCCCGAATTGCCAAACATCGAACATTTCCTTCGTTTCAAAGA
2173711 GTTT
129 GTTT
* * * * **
2173715 TTAGAAAACGTGAGTGAAATTCCGAAGGAATCTTCGATTGTTTTGAACAAACGAAAAAGCGCAAC
1 TTAGAAAACATGAGTGAAATTCCAAAGGAATCTTCGATTATTTTGAACAAACGAGAAATTGCAAC
* * * * *
2173780 CCAGCACGATAGGGCACGATT-CTCAAATCGCCAAACATCGAACATTTCCTTCGTTTCAAAGATT
66 CCAGCACGATAGGGCACTATTCCCCGAATTGCCAAACATCGAACATTTCCTTCGTTTCAAAGAGT
2173844 TT
131 TT
* * * * *
2173846 TTAGGAACCATGAGTGAAATTCTAAAGGGA-CGTTCGATTATTTTGAGCAAACGAGAAATTGCAA
1 TTAGAAAACATGAGTGAAATTCCAAAGGAATC-TTCGATTATTTTGAACAAACGAGAAATTGCAA
* * * ** *
2173910 TCCAGCACGATAGGGCACTATTCCGCGGATTGCCAAACATCGAACATCGCCTTCGTTTTGAAAG-
65 CCCAGCACGATAGGGCACTATTCCCCGAATTGCCAAACATCGAACATTTCCTTCG-TTTCAAAGA
2173974 GTTT
129 GTTT
2173978 TTA
1 TTA
2173981 AATGAATAAT
Statistics
Matches: 220, Mismatches: 41, Indels: 10
0.81 0.15 0.04
Matches are distributed among these distances:
130 1 0.00
131 112 0.51
132 100 0.45
133 7 0.03
ACGTcount: A:0.33, C:0.20, G:0.19, T:0.27
Consensus pattern (132 bp):
TTAGAAAACATGAGTGAAATTCCAAAGGAATCTTCGATTATTTTGAACAAACGAGAAATTGCAAC
CCAGCACGATAGGGCACTATTCCCCGAATTGCCAAACATCGAACATTTCCTTCGTTTCAAAGAGT
TT
Found at i:2181925 original size:13 final size:13
Alignment explanation
Indices: 2181907--2181931 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2181897 CCGTGTAGAG
2181907 ATACAAAAATGGT
1 ATACAAAAATGGT
2181920 ATACAAAAATGG
1 ATACAAAAATGG
2181932 CAATTTATAA
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:0.56, C:0.08, G:0.16, T:0.20
Consensus pattern (13 bp):
ATACAAAAATGGT
Found at i:2182055 original size:34 final size:33
Alignment explanation
Indices: 2182017--2182115 Score: 88
Period size: 34 Copynumber: 3.2 Consensus size: 33
2182007 TGAACACAAC
*
2182017 AATTTATAACATTATCCTAAATTACTAATAAATT
1 AATTTATAACA-TATCCTAAATTACTAACAAATT
* *
2182051 AATTT-TAA-A-A---T-AATTACAAACACAA-C
1 AATTTATAACATATCCTAAATTACTAACA-AATT
2182077 AATTTATAACATAATCCTAAATTACTAACAAATT
1 AATTTATAACAT-ATCCTAAATTACTAACAAATT
2182111 AATTT
1 AATTT
2182116 TAAAATAATT
Statistics
Matches: 50, Mismatches: 5, Indels: 20
0.67 0.07 0.27
Matches are distributed among these distances:
26 14 0.28
27 6 0.12
28 1 0.02
30 2 0.04
32 1 0.02
33 6 0.12
34 20 0.40
ACGTcount: A:0.51, C:0.13, G:0.00, T:0.36
Consensus pattern (33 bp):
AATTTATAACATATCCTAAATTACTAACAAATT
Found at i:2182076 original size:60 final size:60
Alignment explanation
Indices: 2182009--2182126 Score: 218
Period size: 60 Copynumber: 2.0 Consensus size: 60
2181999 TACTAAAATG
* *
2182009 AACACAACAATTTATAACATTATCCTAAATTACTAATAAATTAATTTTAAAATAATTACA
1 AACACAACAATTTATAACATAATCCTAAATTACTAACAAATTAATTTTAAAATAATTACA
2182069 AACACAACAATTTATAACATAATCCTAAATTACTAACAAATTAATTTTAAAATAATTA
1 AACACAACAATTTATAACATAATCCTAAATTACTAACAAATTAATTTTAAAATAATTA
2182127 TAAAAAAATT
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
60 56 1.00
ACGTcount: A:0.53, C:0.14, G:0.00, T:0.34
Consensus pattern (60 bp):
AACACAACAATTTATAACATAATCCTAAATTACTAACAAATTAATTTTAAAATAATTACA
Found at i:2182762 original size:37 final size:37
Alignment explanation
Indices: 2182721--2182793 Score: 137
Period size: 37 Copynumber: 2.0 Consensus size: 37
2182711 AGGCTATTAA
*
2182721 ATGTGTTTTTACTTAAAATGTATTTAAGTTTAAAATT
1 ATGTGTTTTTACTTAAAATATATTTAAGTTTAAAATT
2182758 ATGTGTTTTTACTTAAAATATATTTAAGTTTAAAAT
1 ATGTGTTTTTACTTAAAATATATTTAAGTTTAAAAT
2182794 AATTTTAATA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 35 1.00
ACGTcount: A:0.37, C:0.03, G:0.10, T:0.51
Consensus pattern (37 bp):
ATGTGTTTTTACTTAAAATATATTTAAGTTTAAAATT
Found at i:2196653 original size:16 final size:16
Alignment explanation
Indices: 2196632--2196682 Score: 59
Period size: 16 Copynumber: 3.2 Consensus size: 16
2196622 TTTAGTTCGA
*
2196632 TGTAATATAATAGAAC
1 TGTAATATAATAGAGC
*
2196648 TGTAATGA-AATAGAGT
1 TGTAAT-ATAATAGAGC
*
2196664 TGTAATGTAATAGAGC
1 TGTAATATAATAGAGC
2196680 TGT
1 TGT
2196683 GATCAGTAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
16 28 0.97
17 1 0.03
ACGTcount: A:0.41, C:0.04, G:0.22, T:0.33
Consensus pattern (16 bp):
TGTAATATAATAGAGC
Found at i:2198519 original size:39 final size:38
Alignment explanation
Indices: 2198438--2198587 Score: 185
Period size: 39 Copynumber: 3.9 Consensus size: 38
2198428 ATTCCACTCC
* * * *
2198438 CCCCATGCTACTTTGTTTTATTATTAATAAAAAAC-ACT
1 CCCCATACTATTTTGTTTTATTATTAAT-TAAAACTATT
* *
2198476 CCCCATGCTATTTTGTTTTATTGTTAATTAAAACTATTT
1 CCCCATACTATTTTGTTTTATTATTAATTAAAACTA-TT
* *
2198515 CCCCATACTAGTTTGTTTTATTGTTAATTAAAACTACTT
1 CCCCATACTATTTTGTTTTATTATTAATTAAAACTA-TT
*
2198554 CCTCATACTATTTTGTTTTATTATTAATTAAAAC
1 CCCCATACTATTTTGTTTTATTATTAATTAAAAC
2198588 CATACTTTAT
Statistics
Matches: 100, Mismatches: 10, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
37 5 0.05
38 27 0.27
39 68 0.68
ACGTcount: A:0.30, C:0.17, G:0.06, T:0.47
Consensus pattern (38 bp):
CCCCATACTATTTTGTTTTATTATTAATTAAAACTATT
Found at i:2198581 original size:78 final size:77
Alignment explanation
Indices: 2198438--2198587 Score: 212
Period size: 78 Copynumber: 1.9 Consensus size: 77
2198428 ATTCCACTCC
* * *
2198438 CCCCATGCTACTTTGTTTTATTATTAATAAAAAACACTCCCCATGCTATTTTGTTTTATTGTTAA
1 CCCCATACTACTTTGTTTTATTATTAATAAAAAACACTCCCCATACTATTTTGTTTTATTATTAA
2198503 TTAAAACTATTT
66 TTAAAACTATTT
* * * *
2198515 CCCCATACTAGTTTGTTTTATTGTTAAT-TAAAACTACTTCCTCATACTATTTTGTTTTATTATT
1 CCCCATACTACTTTGTTTTATTATTAATAAAAAAC-AC-TCCCCATACTATTTTGTTTTATTATT
2198579 AATTAAAAC
64 AATTAAAAC
2198588 CATACTTTAT
Statistics
Matches: 64, Mismatches: 7, Indels: 3
0.86 0.09 0.04
Matches are distributed among these distances:
76 5 0.08
77 27 0.42
78 32 0.50
ACGTcount: A:0.30, C:0.17, G:0.06, T:0.47
Consensus pattern (77 bp):
CCCCATACTACTTTGTTTTATTATTAATAAAAAACACTCCCCATACTATTTTGTTTTATTATTAA
TTAAAACTATTT
Found at i:2199238 original size:21 final size:21
Alignment explanation
Indices: 2199199--2199238 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
2199189 CAACCCCTCT
** *
2199199 AATACAATCTCTTCTCTCCAA
1 AATACAATCAATTCCCTCCAA
2199220 AATACAATCAATTCCCTCC
1 AATACAATCAATTCCCTCC
2199239 TCTCCCCTGG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.35, C:0.35, G:0.00, T:0.30
Consensus pattern (21 bp):
AATACAATCAATTCCCTCCAA
Found at i:2199824 original size:20 final size:20
Alignment explanation
Indices: 2199775--2199830 Score: 71
Period size: 20 Copynumber: 2.9 Consensus size: 20
2199765 TTTTTAATAT
*
2199775 TATAATTTAATA--ATAAAA
1 TATAATTTAATATTATTAAA
*
2199793 TCATATTTTAATATTATTAAA
1 T-ATAATTTAATATTATTAAA
2199814 TATAATTTAATATTATT
1 TATAATTTAATATTATT
2199831 TTTAATATAA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
18 1 0.03
19 10 0.31
20 15 0.47
21 6 0.19
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (20 bp):
TATAATTTAATATTATTAAA
Found at i:2199834 original size:32 final size:30
Alignment explanation
Indices: 2199755--2199838 Score: 96
Period size: 32 Copynumber: 2.7 Consensus size: 30
2199745 GAGATGATAT
*
2199755 TTTAATATTATTTTTAATATTATAATTTAA
1 TTTAATATTATTTTTAATATTATAATATAA
* * *
2199785 TAATAAAATCATATTTTAATATTATTAAATATAA
1 T-TTAATATTAT-TTTTAATATTA-T-AATATAA
2199819 TTTAATATTATTTTTAATAT
1 TTTAATATTATTTTTAATAT
2199839 AATATTTTTA
Statistics
Matches: 43, Mismatches: 7, Indels: 6
0.77 0.12 0.11
Matches are distributed among these distances:
30 1 0.02
31 7 0.16
32 20 0.47
33 8 0.19
34 7 0.16
ACGTcount: A:0.44, C:0.01, G:0.00, T:0.55
Consensus pattern (30 bp):
TTTAATATTATTTTTAATATTATAATATAA
Found at i:2206727 original size:25 final size:25
Alignment explanation
Indices: 2206672--2206760 Score: 106
Period size: 27 Copynumber: 3.4 Consensus size: 25
2206662 TTTTAGGGGT
*
2206672 TTTTTTGTTTTTTAGAAGAGGTGTTTT
1 TTTTTTGTTTTTTAGAAGAGG-G-TTG
* *
2206699 TTTTTTGTTTTTTGGAGGAGGGTTG
1 TTTTTTGTTTTTTAGAAGAGGGTTG
* *
2206724 TTTTTTGTTTTTTTGAATAGGGGTTG
1 TTTTTTGTTTTTTAGAAGA-GGGTTG
2206750 TTTTTTGTTTT
1 TTTTTTGTTTT
2206761 GGAAAGGTTA
Statistics
Matches: 55, Mismatches: 6, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
25 18 0.33
26 18 0.33
27 19 0.35
ACGTcount: A:0.10, C:0.00, G:0.26, T:0.64
Consensus pattern (25 bp):
TTTTTTGTTTTTTAGAAGAGGGTTG
Found at i:2207093 original size:3 final size:3
Alignment explanation
Indices: 2207082--2207161 Score: 53
Period size: 3 Copynumber: 26.3 Consensus size: 3
2207072 TTTATTTTTT
* *
2207082 TTA TT- TTA TTA TTT TTA CTA TTA TT- TATA TTA TTA TTA TTA TT-
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA TTA TTA
2207125 TCTCA TGTA TATA TTA TTA TT- TATA TTA TTA -TA TTA T
1 T-T-A T-TA T-TA TTA TTA TTA T-TA TTA TTA TTA TTA T
2207162 ATATGCCTTC
Statistics
Matches: 62, Mismatches: 6, Indels: 18
0.72 0.07 0.21
Matches are distributed among these distances:
2 7 0.11
3 46 0.74
4 7 0.11
5 2 0.03
ACGTcount: A:0.30, C:0.04, G:0.01, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:2207139 original size:21 final size:18
Alignment explanation
Indices: 2207086--2207161 Score: 82
Period size: 18 Copynumber: 4.1 Consensus size: 18
2207076 TTTTTTTTAT
* *
2207086 TTTATTATTTTTACTATTA
1 TTTA-TATTATTATTATTA
2207105 TTTATATTATTATTATTA
1 TTTATATTATTATTATTA
*
2207123 TTTCTCATGTATATATTATTA
1 TTTAT-AT-TAT-TATTATTA
2207144 TTTATATTATTA-TATTA
1 TTTATATTATTATTATTA
2207161 T
1 T
2207162 ATATGCCTTC
Statistics
Matches: 50, Mismatches: 4, Indels: 8
0.81 0.06 0.13
Matches are distributed among these distances:
17 6 0.12
18 18 0.36
19 9 0.18
20 5 0.10
21 12 0.24
ACGTcount: A:0.30, C:0.04, G:0.01, T:0.64
Consensus pattern (18 bp):
TTTATATTATTATTATTA
Found at i:2207162 original size:27 final size:26
Alignment explanation
Indices: 2207073--2207165 Score: 82
Period size: 26 Copynumber: 3.6 Consensus size: 26
2207063 GAGCTTTGTT
* * * *
2207073 TTATTTTTTTTATTTTATTATTTTTA
1 TTATTATTTATATATTATTATTTATA
*
2207099 CTATTATTTATATTATTATTA-TTAT-
1 TTATTATTTATA-TATTATTATTTATA
* * *
2207124 TTCTCATGTATATATTATTATTTATA
1 TTATTATTTATATATTATTATTTATA
2207150 TTATTATATTATATAT
1 TTATTAT-TTATATAT
2207166 GCCTTCTCCA
Statistics
Matches: 51, Mismatches: 12, Indels: 7
0.73 0.17 0.10
Matches are distributed among these distances:
24 8 0.16
25 12 0.24
26 17 0.33
27 14 0.27
ACGTcount: A:0.29, C:0.03, G:0.01, T:0.67
Consensus pattern (26 bp):
TTATTATTTATATATTATTATTTATA
Found at i:2207488 original size:3 final size:3
Alignment explanation
Indices: 2207480--2207527 Score: 78
Period size: 3 Copynumber: 16.0 Consensus size: 3
2207470 TGTATTTCTA
* *
2207480 TAT TAT TAT TAT TAT TAT TAT TAT TAT TGT TAT TAT TAT TAT TTT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
2207528 CATTGTTTGT
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (3 bp):
TAT
Found at i:2208054 original size:132 final size:132
Alignment explanation
Indices: 2207829--2208068 Score: 340
Period size: 132 Copynumber: 1.8 Consensus size: 132
2207819 AACGGAGACG
* * * * * *
2207829 ATGTTCGATGTTTAGCAATTCGGGGAATCGTGCCCTATCGTGTTGGGTTGTAATTTTTTGTTTGC
1 ATGTTCGACGTTCAGCAATTCGGGGAATCGTGCCCTATCATGCTGGGTTGTAATTTCTCGTTTGC
* * *
2207894 TCAAAATAATCGGATGTCTCTTTAGAATTTCGTTCATGTTTTCTAAAAACTTTTTAAAACGAAGG
66 TCAAAATAATCGAATGTCTCTTTAGAATTTCATTCACGTTTTCTAAAAACTTTTTAAAACGAAGG
2207959 AA
131 AA
*
2207961 ATGTTCGACGTTCGGCAATTCGGGGAATCGTGCCCTATCATGCTGGGTTGTAATTTCTCGTTTG-
1 ATGTTCGACGTTCAGCAATTCGGGGAATCGTGCCCTATCATGCTGGGTTGTAATTTCTCGTTTGC
* *
2208025 TGCAAAATAATCGAATAT-TCCTTTGGAATTTCATTCACGTTTTC
66 T-CAAAATAATCGAATGTCT-CTTTAGAATTTCATTCACGTTTTC
2208069 CAAAGCGAGA
Statistics
Matches: 94, Mismatches: 12, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
131 2 0.02
132 92 0.98
ACGTcount: A:0.24, C:0.16, G:0.21, T:0.39
Consensus pattern (132 bp):
ATGTTCGACGTTCAGCAATTCGGGGAATCGTGCCCTATCATGCTGGGTTGTAATTTCTCGTTTGC
TCAAAATAATCGAATGTCTCTTTAGAATTTCATTCACGTTTTCTAAAAACTTTTTAAAACGAAGG
AA
Found at i:2210557 original size:23 final size:22
Alignment explanation
Indices: 2210529--2210585 Score: 75
Period size: 21 Copynumber: 2.6 Consensus size: 22
2210519 AATTTTTTTA
2210529 TTTCTTTATTTTTCTTCTCTTCT
1 TTTCTTTATTTTTCTTCTC-TCT
2210552 TTTCTTT-TTTTT-TTCTCTCT
1 TTTCTTTATTTTTCTTCTCTCT
2210572 TTATC-TTATTTTTC
1 TT-TCTTTATTTTTC
2210586 ACTACAGAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
20 7 0.23
21 12 0.39
22 5 0.16
23 7 0.23
ACGTcount: A:0.05, C:0.19, G:0.00, T:0.75
Consensus pattern (22 bp):
TTTCTTTATTTTTCTTCTCTCT
Found at i:2217968 original size:32 final size:32
Alignment explanation
Indices: 2217927--2217991 Score: 114
Period size: 32 Copynumber: 2.0 Consensus size: 32
2217917 ACATGGATCC
2217927 TTTGTTCAATCATTG-CAAATGTAAATTCTCTT
1 TTTGTTCAATCATTGTC-AATGTAAATTCTCTT
2217959 TTTGTTCAATCATTGTCAATGTAAATTCTCTT
1 TTTGTTCAATCATTGTCAATGTAAATTCTCTT
2217991 T
1 T
2217992 CTCTTGCTGG
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
32 31 0.97
33 1 0.03
ACGTcount: A:0.26, C:0.15, G:0.09, T:0.49
Consensus pattern (32 bp):
TTTGTTCAATCATTGTCAATGTAAATTCTCTT
Found at i:2221477 original size:26 final size:26
Alignment explanation
Indices: 2221448--2221498 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 26
2221438 ATTGCTCCGA
*
2221448 TCAATTTTTAAAA-AAAATTAATTTAC
1 TCAA-TTTCAAAATAAAATTAATTTAC
2221474 TCAATTTCAAAATTAAAATTAATTT
1 TCAATTTCAAAA-TAAAATTAATTT
2221499 TATTTTCAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
25 7 0.32
26 4 0.18
27 11 0.50
ACGTcount: A:0.49, C:0.08, G:0.00, T:0.43
Consensus pattern (26 bp):
TCAATTTCAAAATAAAATTAATTTAC
Found at i:2237620 original size:20 final size:20
Alignment explanation
Indices: 2237595--2237632 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
2237585 TTGTCTAAAT
2237595 TTTCTTTCACTTTCTCTCAC
1 TTTCTTTCACTTTCTCTCAC
*
2237615 TTTCTTTCATTTTCTCTC
1 TTTCTTTCACTTTCTCTC
2237633 TCTGCTTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.08, C:0.32, G:0.00, T:0.61
Consensus pattern (20 bp):
TTTCTTTCACTTTCTCTCAC
Found at i:2252587 original size:38 final size:38
Alignment explanation
Indices: 2252531--2252622 Score: 116
Period size: 38 Copynumber: 2.4 Consensus size: 38
2252521 ACGTAAAACT
*
2252531 TAAATGATTTT-AC-ATCATTTCATAACTCTATATACAA
1 TAAAT-ATTTTAACAATCATTTCACAACTCTATATACAA
* * * *
2252568 TGAATATTTTAACAATCATTTCACAGCTTTATATACAC
1 TAAATATTTTAACAATCATTTCACAACTCTATATACAA
2252606 TAAATATTTTAACAATC
1 TAAATATTTTAACAATC
2252623 CAACATCATA
Statistics
Matches: 47, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
36 5 0.11
37 6 0.13
38 36 0.77
ACGTcount: A:0.40, C:0.16, G:0.03, T:0.40
Consensus pattern (38 bp):
TAAATATTTTAACAATCATTTCACAACTCTATATACAA
Found at i:2255614 original size:19 final size:19
Alignment explanation
Indices: 2255590--2255646 Score: 64
Period size: 19 Copynumber: 3.1 Consensus size: 19
2255580 AATCACTTTT
2255590 TTAAAAATAATAAAAATTA
1 TTAAAAATAATAAAAATTA
*
2255609 TTAAAAATTAT-AAAATT-
1 TTAAAAATAATAAAAATTA
**
2255626 TTATTTAATAATAAAAATTA
1 TTA-AAAATAATAAAAATTA
2255646 T
1 T
2255647 AATAATATTT
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
17 3 0.10
18 11 0.35
19 16 0.52
20 1 0.03
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (19 bp):
TTAAAAATAATAAAAATTA
Found at i:2255661 original size:25 final size:25
Alignment explanation
Indices: 2255610--2255661 Score: 61
Period size: 27 Copynumber: 2.0 Consensus size: 25
2255600 TAAAAATTAT
2255610 TAAAAATTATAAAATTTTATTTAATAA
1 TAAAAATTATAAAA--TTATTTAATAA
*
2255637 TAAAAATTATAATAA-TATTTTATAA
1 TAAAAATTATAA-AATTATTTAATAA
2255662 CTTGCAGAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
25 9 0.39
27 12 0.52
28 2 0.09
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (25 bp):
TAAAAATTATAAAATTATTTAATAA
Found at i:2263690 original size:21 final size:20
Alignment explanation
Indices: 2263658--2263696 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
2263648 TTGAGAGTGA
2263658 GCAAATGTTAATATTATTAG
1 GCAAATGTTAATATTATTAG
* *
2263678 GCAATTGTATAATTTTATT
1 GCAAATGT-TAATATTATT
2263697 GGTATAATAA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 7 0.44
21 9 0.56
ACGTcount: A:0.36, C:0.05, G:0.13, T:0.46
Consensus pattern (20 bp):
GCAAATGTTAATATTATTAG
Found at i:2263840 original size:52 final size:52
Alignment explanation
Indices: 2263739--2263839 Score: 145
Period size: 52 Copynumber: 2.0 Consensus size: 52
2263729 CAAATTTTAA
* *
2263739 CAATTTGATCTTGATTTAATAAATTTAGCCAGCAACAGTTACACATTTTTGT
1 CAATTTGATCTTAATTTAATAAATTTAGCCAGCAACAATTACACATTTTTGT
2263791 CAATTTGGATC-TAATTTAATAAATTTAGCTC-GCAACAATT-CACATTTTT
1 CAATTT-GATCTTAATTTAATAAATTTAGC-CAGCAACAATTACACATTTTT
2263840 TCTACATTTA
Statistics
Matches: 45, Mismatches: 2, Indels: 5
0.87 0.04 0.10
Matches are distributed among these distances:
51 9 0.20
52 31 0.69
53 5 0.11
ACGTcount: A:0.34, C:0.16, G:0.10, T:0.41
Consensus pattern (52 bp):
CAATTTGATCTTAATTTAATAAATTTAGCCAGCAACAATTACACATTTTTGT
Found at i:2273609 original size:39 final size:39
Alignment explanation
Indices: 2273536--2273612 Score: 102
Period size: 39 Copynumber: 1.9 Consensus size: 39
2273526 TAAAAACTAT
2273536 TTATATTAAAAACACTACCATAAATATAACAAATATTTTA
1 TTATATTAAAAACACTA-CATAAATATAACAAATATTTTA
* * *
2273576 TTATATTAAAAAACATTA-ATAAATATGATAAATATTT
1 TTATATT-AAAAACACTACATAAATATAACAAATATTT
2273613 ATTGCATTAA
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
39 17 0.52
40 7 0.21
41 9 0.27
ACGTcount: A:0.53, C:0.08, G:0.01, T:0.38
Consensus pattern (39 bp):
TTATATTAAAAACACTACATAAATATAACAAATATTTTA
Found at i:2274655 original size:29 final size:28
Alignment explanation
Indices: 2274613--2274685 Score: 76
Period size: 29 Copynumber: 2.5 Consensus size: 28
2274603 TTCATCCCAT
2274613 TTAAATTCAAAATAATTCGAA-AAAATTAA
1 TTAAATT-AAAATAATTCGAATAAAA-TAA
*
2274642 TTAAATCTAAAATAATTCTAATAAAATAA
1 TTAAAT-TAAAATAATTCGAATAAAATAA
* *
2274671 CTAAAAATAAAATAA
1 -TTAAATTAAAATAA
2274686 AATTCACCTA
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
29 29 0.76
30 9 0.24
ACGTcount: A:0.62, C:0.07, G:0.01, T:0.30
Consensus pattern (28 bp):
TTAAATTAAAATAATTCGAATAAAATAA
Found at i:2280802 original size:28 final size:30
Alignment explanation
Indices: 2280755--2280812 Score: 75
Period size: 28 Copynumber: 2.0 Consensus size: 30
2280745 GACTCAATCG
* **
2280755 ACATTTTTATTAAAGCTAATA-A-TATATT
1 ACATTTTTATAAAAAATAATATATTATATT
2280783 ACATTTTTATAAAAAATAATATATTATATT
1 ACATTTTTATAAAAAATAATATATTATATT
2280813 GCATCATATT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 18 0.72
29 1 0.04
30 6 0.24
ACGTcount: A:0.47, C:0.05, G:0.02, T:0.47
Consensus pattern (30 bp):
ACATTTTTATAAAAAATAATATATTATATT
Found at i:2280886 original size:12 final size:12
Alignment explanation
Indices: 2280869--2280901 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
2280859 ATGTAGCATT
2280869 ATATATATAAAA
1 ATATATATAAAA
*
2280881 ATATATATAAAT
1 ATATATATAAAA
2280893 ATATATATA
1 ATATATATA
2280902 TATAACTTGA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (12 bp):
ATATATATAAAA
Found at i:2280898 original size:10 final size:10
Alignment explanation
Indices: 2280871--2280905 Score: 52
Period size: 10 Copynumber: 3.5 Consensus size: 10
2280861 GTAGCATTAT
*
2280871 ATATATAAAA
1 ATATATATAA
2280881 ATATATATAA
1 ATATATATAA
*
2280891 ATATATATAT
1 ATATATATAA
2280901 ATATA
1 ATATA
2280906 ACTTGAATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
10 23 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (10 bp):
ATATATATAA
Found at i:2282558 original size:15 final size:15
Alignment explanation
Indices: 2282538--2282568 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
2282528 AATTAACATG
2282538 TATTTTTGTAATATT
1 TATTTTTGTAATATT
*
2282553 TATTTTTTTAATATT
1 TATTTTTGTAATATT
2282568 T
1 T
2282569 TAATATACCC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.26, C:0.00, G:0.03, T:0.71
Consensus pattern (15 bp):
TATTTTTGTAATATT
Found at i:2283655 original size:23 final size:23
Alignment explanation
Indices: 2283629--2283694 Score: 62
Period size: 23 Copynumber: 2.8 Consensus size: 23
2283619 GTGAATTTTG
2283629 AATTTAAATTTGATTTAAAATTT
1 AATTTAAATTTGATTTAAAATTT
* * *
2283652 AATTTAAGTTCGA-TTAAACTTT
1 AATTTAAATTTGATTTAAAATTT
*
2283674 ACTTTTAAAGTTTGAATTTAA
1 A-ATTTAAA-TTTG-ATTTAA
2283695 TTCGAGAATT
Statistics
Matches: 33, Mismatches: 6, Indels: 5
0.75 0.14 0.11
Matches are distributed among these distances:
22 9 0.27
23 16 0.48
24 3 0.09
25 1 0.03
26 4 0.12
ACGTcount: A:0.39, C:0.05, G:0.08, T:0.48
Consensus pattern (23 bp):
AATTTAAATTTGATTTAAAATTT
Found at i:2293292 original size:18 final size:17
Alignment explanation
Indices: 2293263--2293297 Score: 61
Period size: 18 Copynumber: 2.0 Consensus size: 17
2293253 GTTCCAATTT
2293263 TATAAAAATATATATTA
1 TATAAAAATATATATTA
2293280 TATAAATAATATATATTA
1 TATAAA-AATATATATTA
2293298 AATGTTCAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 6 0.35
18 11 0.65
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (17 bp):
TATAAAAATATATATTA
Found at i:2297091 original size:17 final size:17
Alignment explanation
Indices: 2297061--2297094 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
2297051 TTGGGTGAAC
*
2297061 TTATATTATAATTTTAT
1 TTATAATATAATTTTAT
*
2297078 TTATAATATTATTTTAT
1 TTATAATATAATTTTAT
2297095 ATCTTGCATT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (17 bp):
TTATAATATAATTTTAT
Found at i:2297623 original size:20 final size:20
Alignment explanation
Indices: 2297576--2297613 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
2297566 CTAATAATGT
2297576 TAAAATT-TTAATTTTAACC
1 TAAAATTCTTAATTTTAACC
2297595 TAAAATTCTTAATTTTAAC
1 TAAAATTCTTAATTTTAAC
2297614 TTAATTTTCT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 7 0.39
20 11 0.61
ACGTcount: A:0.42, C:0.11, G:0.00, T:0.47
Consensus pattern (20 bp):
TAAAATTCTTAATTTTAACC
Found at i:2298049 original size:32 final size:33
Alignment explanation
Indices: 2298005--2298085 Score: 96
Period size: 33 Copynumber: 2.5 Consensus size: 33
2297995 TTATTTTATA
*
2298005 TAAAAAATTTAAAATATAATACAT-TAA-AATAT
1 TAAAAAAATTAAAATATAATACATCTAATAA-AT
**
2298037 TAAAAAAATTAAAAT-TAATATTTCCTAATAAAT
1 TAAAAAAATTAAAATATAATACAT-CTAATAAAT
2298070 TAAAAAAATTAAAATA
1 TAAAAAAATTAAAATA
2298086 ATTATTTATA
Statistics
Matches: 42, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
31 6 0.14
32 14 0.33
33 20 0.48
34 2 0.05
ACGTcount: A:0.63, C:0.04, G:0.00, T:0.33
Consensus pattern (33 bp):
TAAAAAAATTAAAATATAATACATCTAATAAAT
Found at i:2303322 original size:76 final size:76
Alignment explanation
Indices: 2303240--2303385 Score: 238
Period size: 76 Copynumber: 1.9 Consensus size: 76
2303230 AACCGAATTA
* * *
2303240 AAATATTTCAATTAAATCAGTCAGTTAATTGAATTAATTGAAATTTAAATGTTTTTATCTTTTGG
1 AAATATTTCAATTAAATCAGTCAGTTAAGTGAATTAATCGAAATTTAAATATTTTTATCTTTTGG
2303305 TTTTTGAACCG
66 TTTTTGAACCG
* * *
2303316 AAATATTTTAATTAAATTAGTCAGTTAAGTGAATTAATCGAAATTTATATATTTTTATCTTTTGG
1 AAATATTTCAATTAAATCAGTCAGTTAAGTGAATTAATCGAAATTTAAATATTTTTATCTTTTGG
2303381 TTTTT
66 TTTTT
2303386 AAATAAGAAC
Statistics
Matches: 64, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
76 64 1.00
ACGTcount: A:0.34, C:0.06, G:0.11, T:0.49
Consensus pattern (76 bp):
AAATATTTCAATTAAATCAGTCAGTTAAGTGAATTAATCGAAATTTAAATATTTTTATCTTTTGG
TTTTTGAACCG
Found at i:2304155 original size:19 final size:19
Alignment explanation
Indices: 2304100--2304174 Score: 69
Period size: 19 Copynumber: 3.7 Consensus size: 19
2304090 TTTGATCTTG
*
2304100 AATTAAAAAATTATCTTAAAA
1 AATTAAAAAA-AAT-TTAAAA
* ***
2304121 AATTAATAATTTTTTAAAA
1 AATTAAAAAAAATTTAAAA
2304140 AATTAAAAAAAATTTAAAA
1 AATTAAAAAAAATTTAAAA
2304159 AATATATAAAAAAATT
1 AAT-TA-AAAAAAATT
2304175 AGCTTCGAAT
Statistics
Matches: 45, Mismatches: 7, Indels: 4
0.80 0.12 0.07
Matches are distributed among these distances:
19 24 0.53
20 4 0.09
21 17 0.38
ACGTcount: A:0.64, C:0.01, G:0.00, T:0.35
Consensus pattern (19 bp):
AATTAAAAAAAATTTAAAA
Found at i:2313094 original size:14 final size:14
Alignment explanation
Indices: 2313077--2313111 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
2313067 ATACATAAAT
2313077 TATAATTTTATTAA
1 TATAATTTTATTAA
2313091 TATAATTTTATTAA
1 TATAATTTTATTAA
2313105 TA-AATTT
1 TATAATTT
2313112 AACAGTTGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 5 0.24
14 16 0.76
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (14 bp):
TATAATTTTATTAA
Found at i:2314339 original size:25 final size:23
Alignment explanation
Indices: 2314309--2314378 Score: 61
Period size: 25 Copynumber: 2.9 Consensus size: 23
2314299 AGGCCCGCCC
2314309 ATTTTATTTTTAATTTTTTTAAAA
1 ATTTTATTTTTAATTTTTTT-AAA
* * *
2314333 ATATTTA-TATTATATTATTTTAAT
1 AT-TTTATTTTTA-ATTTTTTTAAA
2314357 ATTTTATATTTTAATATTTTTT
1 ATTTTAT-TTTTAAT-TTTTTT
2314379 TATTTATTGA
Statistics
Matches: 36, Mismatches: 5, Indels: 9
0.72 0.10 0.18
Matches are distributed among these distances:
23 4 0.11
24 12 0.33
25 20 0.56
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (23 bp):
ATTTTATTTTTAATTTTTTTAAA
Found at i:2314359 original size:8 final size:8
Alignment explanation
Indices: 2314348--2314376 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
2314338 TATATTATAT
2314348 TATTTTAA
1 TATTTTAA
2314356 TATTTT-A
1 TATTTTAA
2314363 TATTTTAA
1 TATTTTAA
2314371 TATTTT
1 TATTTT
2314377 TTTATTTATT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
7 7 0.35
8 13 0.65
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (8 bp):
TATTTTAA
Found at i:2314365 original size:23 final size:22
Alignment explanation
Indices: 2314332--2314385 Score: 63
Period size: 23 Copynumber: 2.4 Consensus size: 22
2314322 TTTTTTTAAA
*
2314332 AATATTTATATTATATTATTTT
1 AATATTTATATTATAATATTTT
*
2314354 AATATTTTATATTTTAATATTTT
1 AATA-TTTATATTATAATATTTT
**
2314377 TTTATTTAT
1 AATATTTAT
2314386 TGAATTTTTG
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
22 9 0.33
23 18 0.67
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (22 bp):
AATATTTATATTATAATATTTT
Found at i:2314384 original size:15 final size:15
Alignment explanation
Indices: 2314348--2314376 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
2314338 TATATTATAT
2314348 TATTTTAATATTTTA
1 TATTTTAATATTTTA
2314363 TATTTTAATATTTT
1 TATTTTAATATTTT
2314377 TTTATTTATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (15 bp):
TATTTTAATATTTTA
Found at i:2321561 original size:21 final size:21
Alignment explanation
Indices: 2321536--2321577 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
2321526 ATATTTGATG
*
2321536 ATATTATATATTA-TTATTATT
1 ATATTA-ATAATATTTATTATT
2321557 ATATTAATAATATTTATTATT
1 ATATTAATAATATTTATTATT
2321578 GTTAGTTGAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 5 0.26
21 14 0.74
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (21 bp):
ATATTAATAATATTTATTATT
Found at i:2322652 original size:9 final size:9
Alignment explanation
Indices: 2322634--2322673 Score: 55
Period size: 9 Copynumber: 4.6 Consensus size: 9
2322624 ACCAATTTAA
2322634 TAATTAATT
1 TAATTAATT
*
2322643 TAAATAATT
1 TAATTAATT
*
2322652 T-TTTAATT
1 TAATTAATT
2322660 TAATTAATT
1 TAATTAATT
2322669 TAATT
1 TAATT
2322674 TATACTTTAT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
8 6 0.23
9 20 0.77
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.57
Consensus pattern (9 bp):
TAATTAATT
Found at i:2322659 original size:17 final size:17
Alignment explanation
Indices: 2322637--2322669 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
2322627 AATTTAATAA
2322637 TTAATTTAAATAATTTT
1 TTAATTTAAATAATTTT
*
2322654 TTAATTTAATTAATTT
1 TTAATTTAAATAATTT
2322670 AATTTATACT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (17 bp):
TTAATTTAAATAATTTT
Found at i:2329219 original size:108 final size:109
Alignment explanation
Indices: 2329053--2329263 Score: 320
Period size: 108 Copynumber: 1.9 Consensus size: 109
2329043 TGCACAAAAA
* * *
2329053 TCCACCCAACATGTTTCCCACATCTTTTTTTCATTAATTTATTTTGTTTTTATTTTATTAATTAA
1 TCCACCCAACATGTCTACCACATCTTTTTTTCATTAATTTATTTTGTTTTTATCTTATTAATTAA
* *
2329118 T-AATGTTAAATTTTA-TAAAAATAATTCATTTACCACTAGATGTG
66 TAAAAGTTAAATTTTATTAAAAA-AAATCATTTA-CACTAGATGTG
* *
2329162 TCCACCCAACATGTCTATCACAT-TTTTTTTCATTCATTTATTTTGTTTTTATCTTATTAATTAA
1 TCCACCCAACATGTCTACCACATCTTTTTTTCATTAATTTATTTTGTTTTTATCTTATTAATTAA
2329226 TAAAAGTTAAATTTTATTAAAAAAAATCATTTACACTA
66 TAAAAGTTAAATTTTATTAAAAAAAATCATTTACACTA
2329264 AAGGAGTCAA
Statistics
Matches: 93, Mismatches: 7, Indels: 5
0.89 0.07 0.05
Matches are distributed among these distances:
108 45 0.48
109 42 0.45
110 6 0.06
ACGTcount: A:0.33, C:0.15, G:0.04, T:0.48
Consensus pattern (109 bp):
TCCACCCAACATGTCTACCACATCTTTTTTTCATTAATTTATTTTGTTTTTATCTTATTAATTAA
TAAAAGTTAAATTTTATTAAAAAAAATCATTTACACTAGATGTG
Found at i:2331187 original size:20 final size:20
Alignment explanation
Indices: 2331162--2331202 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
2331152 TACAAACAAG
*
2331162 TTAGTTTTTAGCTTTATTAT
1 TTAGTTTTTAGCTTCATTAT
2331182 TTAGTTTTTAGCTTCATTAT
1 TTAGTTTTTAGCTTCATTAT
2331202 T
1 T
2331203 CAATTAGAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.20, C:0.07, G:0.10, T:0.63
Consensus pattern (20 bp):
TTAGTTTTTAGCTTCATTAT
Found at i:2334791 original size:3 final size:3
Alignment explanation
Indices: 2334783--2334826 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
2334773 TACGTTTTCA
2334783 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
2334827 TTTATAAAGA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:2340278 original size:15 final size:17
Alignment explanation
Indices: 2340246--2340279 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
2340236 AAACCTCCTA
2340246 AAAATATAATTTTATTT
1 AAAATATAATTTTATTT
2340263 AAAATA-AATTTT-TTT
1 AAAATATAATTTTATTT
2340278 AA
1 AA
2340280 TAAAATTATA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 5 0.29
16 6 0.35
17 6 0.35
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
AAAATATAATTTTATTT
Found at i:2340338 original size:30 final size:31
Alignment explanation
Indices: 2340277--2340352 Score: 77
Period size: 30 Copynumber: 2.5 Consensus size: 31
2340267 TAAATTTTTT
* *
2340277 TAATAAAATTATATTTTTAATTTCTTTAAAA
1 TAATAAAATTATATATTTAATTTCTTAAAAA
*
2340308 TAATAAAATTTTA-ATTTAATCTT-TTAAAAA
1 TAATAAAATTATATATTTAAT-TTCTTAAAAA
*
2340338 TTAT-AAATATATATA
1 TAATAAAAT-TATATA
2340353 CTATTAAAAT
Statistics
Matches: 37, Mismatches: 5, Indels: 6
0.77 0.10 0.12
Matches are distributed among these distances:
29 4 0.11
30 18 0.49
31 15 0.41
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (31 bp):
TAATAAAATTATATATTTAATTTCTTAAAAA
Found at i:2352414 original size:31 final size:31
Alignment explanation
Indices: 2352379--2352453 Score: 114
Period size: 31 Copynumber: 2.4 Consensus size: 31
2352369 TTAATATAAT
*
2352379 ATTTGGTATTTAAACTTAACACTTTTTCTTA
1 ATTTGGTACTTAAACTTAACACTTTTTCTTA
* *
2352410 ATTTGGTACCTAAACTTGACACTTTTTCTTA
1 ATTTGGTACTTAAACTTAACACTTTTTCTTA
*
2352441 AGTTGGTACTTAA
1 ATTTGGTACTTAA
2352454 TCTTTTTTGC
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 39 1.00
ACGTcount: A:0.28, C:0.15, G:0.11, T:0.47
Consensus pattern (31 bp):
ATTTGGTACTTAAACTTAACACTTTTTCTTA
Found at i:2361331 original size:17 final size:17
Alignment explanation
Indices: 2361306--2361339 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
2361296 CTGAATATTG
2361306 TTTTAAAATTATAAGTA
1 TTTTAAAATTATAAGTA
*
2361323 TTTTTAAATTATAAGTA
1 TTTTAAAATTATAAGTA
2361340 ATATATAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (17 bp):
TTTTAAAATTATAAGTA
Found at i:2362581 original size:15 final size:15
Alignment explanation
Indices: 2362541--2362584 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 15
2362531 TTAATTGTTT
*
2362541 ATTTTTATATA-TAA
1 ATTTTTATAAATTAA
*
2362555 ATTTTTATTAAATTTA
1 ATTTTTA-TAAATTAA
2362571 ATTTTTATAAATTA
1 ATTTTTATAAATTA
2362585 TTAATATAGT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
14 7 0.28
15 9 0.36
16 9 0.36
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (15 bp):
ATTTTTATAAATTAA
Found at i:2369195 original size:31 final size:31
Alignment explanation
Indices: 2369123--2369266 Score: 89
Period size: 31 Copynumber: 4.6 Consensus size: 31
2369113 ATTATCTTAA
* * ** *
2369123 TAATAAATTTAATTTTTTAATATTTAAGCATT
1 TAATAAATTTAA-TTTTAAATATTAAAAAAAT
* *
2369155 TTATTAATTTAATTTTAAATATTAAAAAAAT
1 TAATAAATTTAATTTTAAATATTAAAAAAAT
* *
2369186 TAATAAATTTAA-TTTATAATATTTACAAAAT
1 TAATAAATTTAATTTTA-AATATTAAAAAAAT
* ** *
2369217 TTATTTATTTAA-TTTAAAT-TCTAAAAAATT
1 TAATAAATTTAATTTTAAATAT-TAAAAAAAT
*
2369247 TAAAAAAATATT-ATTTTAAA
1 T-AATAAAT-TTAATTTTAAA
2369267 AATAATTTTT
Statistics
Matches: 86, Mismatches: 21, Indels: 10
0.74 0.18 0.09
Matches are distributed among these distances:
29 1 0.01
30 14 0.16
31 53 0.62
32 18 0.21
ACGTcount: A:0.49, C:0.02, G:0.01, T:0.49
Consensus pattern (31 bp):
TAATAAATTTAATTTTAAATATTAAAAAAAT
Found at i:2369220 original size:62 final size:62
Alignment explanation
Indices: 2369123--2369249 Score: 161
Period size: 62 Copynumber: 2.0 Consensus size: 62
2369113 ATTATCTTAA
* * *
2369123 TAATAAATTTAATTTTTTAATATTTAAGCATTTTATTAATTTAATTTTAAATAT-TAAAAAAAT
1 TAATAAATTTAATTTTATAATATTTAAGAAATTTATTAATTTAA-TTTAAAT-TCTAAAAAAAT
* *
2369186 TAATAAATTTAA-TTTATAATATTTACA-AAATTTATTTATTTAATTTAAATTCTAAAAAATT
1 TAATAAATTTAATTTTATAATATTTA-AGAAATTTATTAATTTAATTTAAATTCTAAAAAAAT
2369247 TAA
1 TAA
2369250 AAAAATATTA
Statistics
Matches: 57, Mismatches: 5, Indels: 6
0.84 0.07 0.09
Matches are distributed among these distances:
60 1 0.02
61 18 0.32
62 25 0.44
63 13 0.23
ACGTcount: A:0.47, C:0.02, G:0.01, T:0.50
Consensus pattern (62 bp):
TAATAAATTTAATTTTATAATATTTAAGAAATTTATTAATTTAATTTAAATTCTAAAAAAAT
Found at i:2374359 original size:20 final size:20
Alignment explanation
Indices: 2374334--2374371 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
2374324 AAAACTAATG
*
2374334 CTTTTTTTATTGTTTTGTCA
1 CTTTTTTTACTGTTTTGTCA
2374354 CTTTTTTTACTGTTTTGT
1 CTTTTTTTACTGTTTTGT
2374372 TATCATTTCG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.08, C:0.11, G:0.11, T:0.71
Consensus pattern (20 bp):
CTTTTTTTACTGTTTTGTCA
Found at i:2374614 original size:15 final size:16
Alignment explanation
Indices: 2374596--2374628 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
2374586 TATATTTTTT
2374596 TTATTTT-ATTTTTAA
1 TTATTTTAATTTTTAA
2374611 TTATTTTAAATTTTTAA
1 TTATTTT-AATTTTTAA
2374628 T
1 T
2374629 ATAACTATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.44
17 9 0.56
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (16 bp):
TTATTTTAATTTTTAA
Found at i:2374701 original size:21 final size:22
Alignment explanation
Indices: 2374686--2374733 Score: 64
Period size: 22 Copynumber: 2.3 Consensus size: 22
2374676 TGTTTTGGTA
2374686 TTATTTTTATTTGTTTTAATAT
1 TTATTTTTATTTGTTTTAATAT
*
2374708 TTATTTTTATGT-TTTTAA-AT
1 TTATTTTTATTTGTTTTAATAT
*
2374728 ATATTT
1 TTATTT
2374734 AATTTATTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 7 0.29
21 6 0.25
22 11 0.46
ACGTcount: A:0.25, C:0.00, G:0.04, T:0.71
Consensus pattern (22 bp):
TTATTTTTATTTGTTTTAATAT
Found at i:2374750 original size:26 final size:24
Alignment explanation
Indices: 2374704--2374763 Score: 75
Period size: 26 Copynumber: 2.4 Consensus size: 24
2374694 ATTTGTTTTA
*
2374704 ATATTTATTTTTATGTTTTTAAAT
1 ATATTTATTTTTATATTTTTAAAT
2374728 ATATTTAATTTATTATATTTTTAAAT
1 ATATTT-ATTT-TTATATTTTTAAAT
* *
2374754 TTTTTTATTT
1 ATATTTATTT
2374764 AATGAAATAA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
24 6 0.19
25 8 0.26
26 17 0.55
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (24 bp):
ATATTTATTTTTATATTTTTAAAT
Found at i:2374763 original size:25 final size:26
Alignment explanation
Indices: 2374707--2374764 Score: 75
Period size: 25 Copynumber: 2.3 Consensus size: 26
2374697 TGTTTTAATA
*
2374707 TTTATTT-TTATGTTTTTAAATATAT
1 TTTATTTATTATATTTTTAAATATAT
* *
2374732 TTAATTTATTATATTTTTAAAT-TTT
1 TTTATTTATTATATTTTTAAATATAT
2374757 TTTATTTA
1 TTTATTTA
2374765 ATGAAATAAG
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
25 15 0.54
26 13 0.46
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (26 bp):
TTTATTTATTATATTTTTAAATATAT
Found at i:2377198 original size:16 final size:17
Alignment explanation
Indices: 2377177--2377210 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
2377167 AATGTCTAGA
2377177 AAAATTA-TTAATTGAG
1 AAAATTACTTAATTGAG
2377193 AAAATTATCTTAATTGAG
1 AAAATTA-CTTAATTGAG
2377211 GGGTTAATTG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
18 9 0.56
ACGTcount: A:0.47, C:0.03, G:0.12, T:0.38
Consensus pattern (17 bp):
AAAATTACTTAATTGAG
Found at i:2382033 original size:17 final size:18
Alignment explanation
Indices: 2382001--2382034 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
2381991 TTTCACTTAT
2382001 ATTATTAAATAAATACAA
1 ATTATTAAATAAATACAA
2382019 ATTATTAAA-AAATACA
1 ATTATTAAATAAATACA
2382035 TGGAAAAGTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.62, C:0.06, G:0.00, T:0.32
Consensus pattern (18 bp):
ATTATTAAATAAATACAA
Found at i:2388223 original size:34 final size:36
Alignment explanation
Indices: 2388168--2388245 Score: 97
Period size: 34 Copynumber: 2.2 Consensus size: 36
2388158 CTTATTATAA
**
2388168 TGGTCTTGGTGCTGGAAATTTAAATGTGAATTTGA-T
1 TGGT-TTGGTGCTGGAAATTTAAATGCAAATTTGACT
*
2388204 TGGTTTGGTG-TGGGAATTTAAATGCAAATTTGACT
1 TGGTTTGGTGCTGGAAATTTAAATGCAAATTTGACT
*
2388239 GGGTTTG
1 TGGTTTG
2388246 CACCTATTAG
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
34 20 0.54
35 13 0.35
36 4 0.11
ACGTcount: A:0.23, C:0.05, G:0.31, T:0.41
Consensus pattern (36 bp):
TGGTTTGGTGCTGGAAATTTAAATGCAAATTTGACT
Found at i:2388650 original size:35 final size:36
Alignment explanation
Indices: 2388595--2388673 Score: 106
Period size: 35 Copynumber: 2.2 Consensus size: 36
2388585 CTTATTATAA
**
2388595 TGGTCTTGGTGCTGGAAATTTAAATGTGAATTTGA-T
1 TGGT-TTGGTGCTGGAAATTTAAATGCAAATTTGACT
*
2388631 TGGTTTGGTGCTGGGAATTTAAATGCAAATTTGACT
1 TGGTTTGGTGCTGGAAATTTAAATGCAAATTTGACT
*
2388667 GGGTTTG
1 TGGTTTG
2388674 CACCTATTAG
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
35 27 0.71
36 11 0.29
ACGTcount: A:0.23, C:0.06, G:0.30, T:0.41
Consensus pattern (36 bp):
TGGTTTGGTGCTGGAAATTTAAATGCAAATTTGACT
Found at i:2388873 original size:428 final size:427
Alignment explanation
Indices: 2388077--2388930 Score: 1600
Period size: 428 Copynumber: 2.0 Consensus size: 427
2388067 CCGAATCATG
*
2388077 TTTTGGATGGGCATTTGCCTAGACCTGGGCCTTGTAGGCTGCATATAGGTGCTCCTCATCCTGGC
1 TTTTGGATGGGCATTTGCCTAGACCTGGGCCTTGTAGGCCGCATATAGGTGCTCCTCATCCTGGC
2388142 CTCTCTCGGCCTTTTGCTTATTATAATGGTCTTGGTGCTGGAAATTTAAATGTGAATTTGATTGG
66 CTCTCTCGGCCTTTTGCTTATTATAATGGTCTTGGTGCTGGAAATTTAAATGTGAATTTGATTGG
*
2388207 TTTGGTGTGGGAATTTAAATGCAAATTTGACTGGGTTTGCACCTATTAGCAATTGTGTGTAGGTT
131 TTTGGTGTGGGAATTTAAATGCAAATTTGACTGGGTTTGCACCTATTAGCAATTGTGTGCAGGTT
*
2388272 GGTTATCCGTTGAGTGGTGATTCGAGAGTTGGCGATGGGCGTGATCCATCGGCACCACCTATTCC
196 GGTTATCCGTTGAGTGGTGATCCGAGAGTTGGCGATGGGCGTGATCCATCGGCACCACCTATTCC
* *
2388337 TTTGTGAACCAAGCCGCGCGTTCGTGTTTATAGTGGCTCAGATCCTTGTATTGGTCTTCCTCGGG
261 TTTGTGAACCAAGCCGCGCGCTCGTGTTTATAGTGGCTCAGATCCGTGTATTGGTCTTCCTCGGG
*
2388402 TTGGTGATTTACATGCATCTAACTATTCAGATTATTCTGGCTCACATTCCAATACTGCTCAGATT
326 TTGGTGATTTACATGCATCTAACTATTCAGATTATTCTGGCTCACATGCCAATACTGCTCAGATT
2388467 GGAGCTAATGGTGATAACACTGGTTCATACATACATA
391 GGAGCTAATGGTGATAACACTGGTTCATACATACATA
*
2388504 TTTTGGATGGGCATTTGCCTAGACCTGGGCCTTGTAGGCCGCATATGGGTGCTCCTCATCCTGGC
1 TTTTGGATGGGCATTTGCCTAGACCTGGGCCTTGTAGGCCGCATATAGGTGCTCCTCATCCTGGC
2388569 CTCTCTCGGCCTTTTGCTTATTATAATGGTCTTGGTGCTGGAAATTTAAATGTGAATTTGATTGG
66 CTCTCTCGGCCTTTTGCTTATTATAATGGTCTTGGTGCTGGAAATTTAAATGTGAATTTGATTGG
2388634 TTTGGTGCTGGGAATTTAAATGCAAATTTGACTGGGTTTGCACCTATTAGCAATTGTGTGCAGGT
131 TTTGGTG-TGGGAATTTAAATGCAAATTTGACTGGGTTTGCACCTATTAGCAATTGTGTGCAGGT
* *
2388699 TGGTTATCCGTTGAGTGGTGATCCGGGAGTTGGCGATGGGCGTGATCCGTCGGCACCACCTATTC
195 TGGTTATCCGTTGAGTGGTGATCCGAGAGTTGGCGATGGGCGTGATCCATCGGCACCACCTATTC
2388764 CTTTGTGAACCAAGCCGCGCGCTCGTGTTTATAGTGGCTCAGATCCGTGTATTGGTCTTCCTCGG
260 CTTTGTGAACCAAGCCGCGCGCTCGTGTTTATAGTGGCTCAGATCCGTGTATTGGTCTTCCTCGG
* *
2388829 GTTGGTGATTTACATGCATCTAATTATTCAGATTATTCTGGCTCATATGCCAATACTGCTCAGAT
325 GTTGGTGATTTACATGCATCTAACTATTCAGATTATTCTGGCTCACATGCCAATACTGCTCAGAT
2388894 TGGAGCTAATGGTGATAACACTGGTTCATACATACAT
390 TGGAGCTAATGGTGATAACACTGGTTCATACATACAT
2388931 GTGCCTGTTG
Statistics
Matches: 415, Mismatches: 11, Indels: 1
0.97 0.03 0.00
Matches are distributed among these distances:
427 135 0.33
428 280 0.67
ACGTcount: A:0.20, C:0.19, G:0.26, T:0.35
Consensus pattern (427 bp):
TTTTGGATGGGCATTTGCCTAGACCTGGGCCTTGTAGGCCGCATATAGGTGCTCCTCATCCTGGC
CTCTCTCGGCCTTTTGCTTATTATAATGGTCTTGGTGCTGGAAATTTAAATGTGAATTTGATTGG
TTTGGTGTGGGAATTTAAATGCAAATTTGACTGGGTTTGCACCTATTAGCAATTGTGTGCAGGTT
GGTTATCCGTTGAGTGGTGATCCGAGAGTTGGCGATGGGCGTGATCCATCGGCACCACCTATTCC
TTTGTGAACCAAGCCGCGCGCTCGTGTTTATAGTGGCTCAGATCCGTGTATTGGTCTTCCTCGGG
TTGGTGATTTACATGCATCTAACTATTCAGATTATTCTGGCTCACATGCCAATACTGCTCAGATT
GGAGCTAATGGTGATAACACTGGTTCATACATACATA
Found at i:2394216 original size:24 final size:21
Alignment explanation
Indices: 2394178--2394229 Score: 59
Period size: 24 Copynumber: 2.3 Consensus size: 21
2394168 AAATTTAATT
*
2394178 TTTTAAAAATTATAAAGATATAAA
1 TTTT-AAAATAATAAA-AT-TAAA
2394202 TTATTAAAATAATAAAATTAAA
1 TT-TTAAAATAATAAAATTAAA
2394224 TTTTAA
1 TTTTAA
2394230 CTATGATAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
21 4 0.15
22 6 0.23
23 2 0.08
24 12 0.46
25 2 0.08
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (21 bp):
TTTTAAAATAATAAAATTAAA
Found at i:2399054 original size:17 final size:18
Alignment explanation
Indices: 2399040--2399128 Score: 77
Period size: 17 Copynumber: 5.3 Consensus size: 18
2399030 TAAATATTAG
2399040 ATTAAATTTAATATTAAT
1 ATTAAATTTAATATTAAT
*
2399058 ATTTAATTTAAT-TTAAT
1 ATTAAATTTAATATTAAT
*
2399075 ATTAAA-TTAATA-AAAT
1 ATTAAATTTAATATTAAT
* *
2399091 ACT--A-TTAAGA-TAATT
1 ATTAAATTTAATATTAA-T
2399106 ATTAAATTTAAT-TTAAT
1 ATTAAATTTAATATTAAT
2399123 ATTAAA
1 ATTAAA
2399129 CTATTATAAA
Statistics
Matches: 57, Mismatches: 8, Indels: 13
0.73 0.10 0.17
Matches are distributed among these distances:
14 8 0.14
15 3 0.05
16 10 0.18
17 18 0.32
18 18 0.32
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.47
Consensus pattern (18 bp):
ATTAAATTTAATATTAAT
Found at i:2399055 original size:12 final size:12
Alignment explanation
Indices: 2399040--2399086 Score: 64
Period size: 11 Copynumber: 4.1 Consensus size: 12
2399030 TAAATATTAG
2399040 ATTAAATTTAAT
1 ATTAAATTTAAT
2399052 ATTAATATTTAAT
1 ATTAA-ATTTAAT
2399065 -TT-AATTTAAT
1 ATTAAATTTAAT
2399075 ATTAAA-TTAAT
1 ATTAAATTTAAT
2399086 A
1 A
2399087 AAATACTATT
Statistics
Matches: 32, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
10 7 0.22
11 9 0.28
12 9 0.28
13 7 0.22
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (12 bp):
ATTAAATTTAAT
Found at i:2399058 original size:23 final size:22
Alignment explanation
Indices: 2399032--2399127 Score: 85
Period size: 23 Copynumber: 4.4 Consensus size: 22
2399022 TATTTTCATA
2399032 AATATTAGATTAAATTTAATATT
1 AATATTA-ATTAAATTTAATATT
*
2399055 AATATTTAATTTAATTTAATATT
1 AATA-TTAATTAAATTTAATATT
* *
2399078 AA-ATTAA-TAAA-ATACTATT
1 AATATTAATTAAATTTAATATT
2399097 AAGATAATT-ATTAAATTTAAT-TT
1 -A-AT-ATTAATTAAATTTAATATT
2399120 AATATTAA
1 AATATTAA
2399128 ACTATTATAA
Statistics
Matches: 59, Mismatches: 6, Indels: 18
0.71 0.07 0.22
Matches are distributed among these distances:
19 6 0.10
20 7 0.12
21 8 0.14
22 3 0.05
23 29 0.49
24 6 0.10
ACGTcount: A:0.50, C:0.01, G:0.02, T:0.47
Consensus pattern (22 bp):
AATATTAATTAAATTTAATATT
Found at i:2400418 original size:29 final size:29
Alignment explanation
Indices: 2400354--2400418 Score: 67
Period size: 29 Copynumber: 2.2 Consensus size: 29
2400344 ATTTGGTCAT
** *
2400354 ATTTAATCTTTTTAATAATAACAAAACTA
1 ATTTAATCCATTTAATAAAAACAAAACTA
** * *
2400383 AAATAATCCATTTAATAAAAATAAGACTA
1 ATTTAATCCATTTAATAAAAACAAAACTA
2400412 ATTTAAT
1 ATTTAAT
2400419 ATGGTTTTTA
Statistics
Matches: 27, Mismatches: 9, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.52, C:0.09, G:0.02, T:0.37
Consensus pattern (29 bp):
ATTTAATCCATTTAATAAAAACAAAACTA
Found at i:2401179 original size:32 final size:32
Alignment explanation
Indices: 2401117--2401186 Score: 81
Period size: 33 Copynumber: 2.2 Consensus size: 32
2401107 ATATTTAAGG
*
2401117 TAAAAAAATTACCAAAATTATATATCAATAAT
1 TAAAAAAATTACCAAAATTATATATAAATAAT
**
2401149 ATAAAAAAATTATTAAAA-TATCAT-TAAATAAT
1 -TAAAAAAATTACCAAAATTAT-ATATAAATAAT
2401181 TAAAAA
1 TAAAAA
2401187 TGAACGATGT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
31 6 0.18
32 10 0.30
33 17 0.52
ACGTcount: A:0.63, C:0.06, G:0.00, T:0.31
Consensus pattern (32 bp):
TAAAAAAATTACCAAAATTATATATAAATAAT
Found at i:2407662 original size:28 final size:30
Alignment explanation
Indices: 2407600--2407663 Score: 71
Period size: 28 Copynumber: 2.2 Consensus size: 30
2407590 ATATGAGGAC
*
2407600 CTAATTAATATACACTCAATAGTTTGGGAT
1 CTAATTAAAATACACTCAATAGTTTGGGAT
* *
2407630 GTAATTAAAATA-ACTTAA-AGTTTAGGGA-
1 CTAATTAAAATACACTCAATAGTTT-GGGAT
2407658 CTAATT
1 CTAATT
2407664 TAGATTGAGG
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
28 10 0.34
29 9 0.31
30 10 0.34
ACGTcount: A:0.41, C:0.09, G:0.14, T:0.36
Consensus pattern (30 bp):
CTAATTAAAATACACTCAATAGTTTGGGAT
Found at i:2412695 original size:15 final size:15
Alignment explanation
Indices: 2412668--2412715 Score: 53
Period size: 15 Copynumber: 3.2 Consensus size: 15
2412658 TGTTTATAAA
2412668 TATTT-AATCATTATT
1 TATTTAAAT-ATTATT
*
2412683 TATTTAAATATTATG
1 TATTTAAATATTATT
* *
2412698 AATTTAAATAATATT
1 TATTTAAATATTATT
2412713 TAT
1 TAT
2412716 ATCAGCGTAT
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
15 24 0.89
16 3 0.11
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.54
Consensus pattern (15 bp):
TATTTAAATATTATT
Found at i:2413398 original size:83 final size:83
Alignment explanation
Indices: 2413254--2413416 Score: 195
Period size: 83 Copynumber: 2.0 Consensus size: 83
2413244 GCTTCTCGCC
* * **
2413254 ACCTCGCGATGTGGAGCACAAAGGAGATGTGTGAGCCGCAGGATGGATTGCCCCATCGTGTCTCA
1 ACCTCGCGAGGTGGAGCACAAAGGAGATATGTGAGCCGCAGGATGGATCACCCCATCGTGTCTCA
* *
2413319 CATCTCATCAACATGATG
66 CACCCCATCAACATGATG
* ** * *
2413337 ACCTCGCTAGGTGGAGCAC-AAGAGAGATATGTGAGTTG-AGAGATGGATCACCTCATTGTGTCT
1 ACCTCGCGAGGTGGAGCACAAAG-GAGATATGTGAGCCGCAG-GATGGATCACCCCATCGTGTCT
2413400 CACACCCCATCAACATG
64 CACACCCCATCAACATG
2413417 GCAACCTCGT
Statistics
Matches: 67, Mismatches: 11, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
82 5 0.07
83 62 0.93
ACGTcount: A:0.27, C:0.25, G:0.26, T:0.22
Consensus pattern (83 bp):
ACCTCGCGAGGTGGAGCACAAAGGAGATATGTGAGCCGCAGGATGGATCACCCCATCGTGTCTCA
CACCCCATCAACATGATG
Found at i:2413424 original size:83 final size:83
Alignment explanation
Indices: 2413254--2413435 Score: 188
Period size: 83 Copynumber: 2.2 Consensus size: 83
2413244 GCTTCTCGCC
* * **
2413254 ACCTCGCGATGTGGAGCACAAAGGAGATGTGTGAGCCGCAGGATGGATTGCCCCATCGTGTCTCA
1 ACCTCGCGAGGTGGAGCACAAAGGAGATATGTGAGCCGCAGGATGGATCACCCCATCGTGTCTCA
* * **
2413319 CATCTCATCAACATGATG
66 CACCCCATCAACATGACA
* ** * *
2413337 ACCTCGCTAGGTGGAGCAC-AAGAGAGATATGTGAGTTG-AGAGATGGATCACCTCATTGTGTCT
1 ACCTCGCGAGGTGGAGCACAAAG-GAGATATGTGAGCCGCAG-GATGGATCACCCCATCGTGTCT
*
2413400 CACACCCCATCAACATGGCA
64 CACACCCCATCAACATGACA
* *
2413420 ACCTCGTGAAGTGGAG
1 ACCTCGCGAGGTGGAG
2413436 AGCAAAGAAC
Statistics
Matches: 80, Mismatches: 17, Indels: 4
0.79 0.17 0.04
Matches are distributed among these distances:
82 5 0.06
83 75 0.94
ACGTcount: A:0.27, C:0.24, G:0.27, T:0.21
Consensus pattern (83 bp):
ACCTCGCGAGGTGGAGCACAAAGGAGATATGTGAGCCGCAGGATGGATCACCCCATCGTGTCTCA
CACCCCATCAACATGACA
Found at i:2414060 original size:30 final size:29
Alignment explanation
Indices: 2413992--2414067 Score: 80
Period size: 30 Copynumber: 2.6 Consensus size: 29
2413982 TATATTAATT
* * ** *
2413992 TTAATTTGATGTAATTATATATACGAAAT
1 TTAATTTAATGTAATTATACATAAAAAAA
2414021 TTAGATTTAATGTAATTATACATAAAAAAA
1 TTA-ATTTAATGTAATTATACATAAAAAAA
*
2414051 TTAATTTTAATTTAATT
1 TTAA-TTTAATGTAATT
2414068 GTATAATTTA
Statistics
Matches: 39, Mismatches: 6, Indels: 3
0.81 0.12 0.06
Matches are distributed among these distances:
29 4 0.10
30 35 0.90
ACGTcount: A:0.45, C:0.03, G:0.07, T:0.46
Consensus pattern (29 bp):
TTAATTTAATGTAATTATACATAAAAAAA
Found at i:2419292 original size:31 final size:31
Alignment explanation
Indices: 2419257--2419323 Score: 91
Period size: 31 Copynumber: 2.2 Consensus size: 31
2419247 TTAATATACT
* *
2419257 ATTTGATATTTGAGTTT-GACTTTAATGTTCA
1 ATTTGATACTCGAGTTTAGA-TTTAATGTTCA
*
2419288 ATTTGATACTCGAGTTTAGATTTATTGTTCA
1 ATTTGATACTCGAGTTTAGATTTAATGTTCA
2419319 ATTTG
1 ATTTG
2419324 GTACCAAATT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
31 30 0.94
32 2 0.06
ACGTcount: A:0.25, C:0.07, G:0.16, T:0.51
Consensus pattern (31 bp):
ATTTGATACTCGAGTTTAGATTTAATGTTCA
Found at i:2420027 original size:2 final size:2
Alignment explanation
Indices: 2420020--2420052 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
2420010 TAATATACAC
2420020 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2420053 CTTATTTATT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2421089 original size:21 final size:22
Alignment explanation
Indices: 2421065--2421105 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
2421055 TCCAAAAATT
*
2421065 AAAT-CATAGAAAAATAAAACA
1 AAATACATAGAAAAAGAAAACA
*
2421086 AAATATATAGAAAAAGAAAA
1 AAATACATAGAAAAAGAAAA
2421106 TTAATGTTGT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 4 0.24
22 13 0.76
ACGTcount: A:0.73, C:0.05, G:0.07, T:0.15
Consensus pattern (22 bp):
AAATACATAGAAAAAGAAAACA
Found at i:2429254 original size:18 final size:19
Alignment explanation
Indices: 2429231--2429269 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
2429221 ATTTAACCAA
*
2429231 ATTTAATATATAT-TATTT
1 ATTTAATATAAATATATTT
*
2429249 ATTTAATTTAAATATATTT
1 ATTTAATATAAATATATTT
2429268 AT
1 AT
2429270 AATATAATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 11 0.61
19 7 0.39
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (19 bp):
ATTTAATATAAATATATTT
Found at i:2429266 original size:22 final size:22
Alignment explanation
Indices: 2429230--2429283 Score: 65
Period size: 22 Copynumber: 2.4 Consensus size: 22
2429220 AATTTAACCA
* *
2429230 AATTT-AATATATATTATTTATTT
1 AATTTAAATATAT-TTA-TAATAT
2429253 AATTTAAATATATTTATAATAT
1 AATTTAAATATATTTATAATAT
2429275 AATTTAAAT
1 AATTTAAAT
2429284 TAATCTAATC
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
22 13 0.46
23 8 0.29
24 7 0.25
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (22 bp):
AATTTAAATATATTTATAATAT
Found at i:2429323 original size:8 final size:8
Alignment explanation
Indices: 2429310--2429339 Score: 53
Period size: 8 Copynumber: 3.9 Consensus size: 8
2429300 GATTATAATA
2429310 TATATTTT
1 TATATTTT
2429318 TATATTTT
1 TATATTTT
2429326 TATATTTT
1 TATATTTT
2429334 TA-ATTT
1 TATATTT
2429340 AAATATATTT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 4 0.18
8 18 0.82
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (8 bp):
TATATTTT
Found at i:2429345 original size:15 final size:16
Alignment explanation
Indices: 2429311--2429352 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 16
2429301 ATTATAATAT
**
2429311 ATATTTTTATATTTTT
1 ATATTTTTATATTTAA
2429327 ATATTTTTA-ATTTAA
1 ATATTTTTATATTTAA
*
2429342 ATATATTTATA
1 ATATTTTTATA
2429353 ATATAATTTA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
15 12 0.55
16 10 0.45
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (16 bp):
ATATTTTTATATTTAA
Found at i:2429345 original size:23 final size:22
Alignment explanation
Indices: 2429302--2429365 Score: 65
Period size: 23 Copynumber: 2.8 Consensus size: 22
2429292 TCTAAATCGA
** *
2429302 TTATAATATATATTTTTATATTT
1 TTATAATATA-ATTTAAATATAT
* *
2429325 TTATATTTTTAATTTAAATATAT
1 TTATA-ATATAATTTAAATATAT
2429348 TTATAATATAATTTAAAT
1 TTATAATATAATTTAAAT
2429366 GAATATTATT
Statistics
Matches: 33, Mismatches: 7, Indels: 3
0.77 0.16 0.07
Matches are distributed among these distances:
22 11 0.33
23 19 0.58
24 3 0.09
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (22 bp):
TTATAATATAATTTAAATATAT
Found at i:2434087 original size:28 final size:27
Alignment explanation
Indices: 2434002--2434087 Score: 66
Period size: 30 Copynumber: 3.0 Consensus size: 27
2433992 TTTCGCTCTA
* * *
2434002 AAAATAATAATATTTATATTTATATTTTT
1 AAAATAATAA-AATTATATTTTTA-TATT
* * *
2434031 AAAATTATTAAAATATAGATTATTA-ATT
1 AAAA-TAATAAAAT-TATATTTTTATATT
2434059 AAAATAATAAAATTATATTTTTACTATT
1 AAAATAATAAAATTATATTTTTA-TATT
2434087 A
1 A
2434088 TATAAATTAT
Statistics
Matches: 44, Mismatches: 9, Indels: 9
0.71 0.15 0.15
Matches are distributed among these distances:
26 8 0.18
27 8 0.18
28 10 0.23
29 6 0.14
30 12 0.27
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.48
Consensus pattern (27 bp):
AAAATAATAAAATTATATTTTTATATT
Done.