Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr10
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: 57797951
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Warning! 1092422 characters in sequence are not A, C, G, or T
File 178 of 187
Found at i:54455806 original size:24 final size:24
Alignment explanation
Indices: 54455728--54455951 Score: 68
Period size: 24 Copynumber: 9.1 Consensus size: 24
54455718 CTGTATAATA
54455728 GGAAGCTCAT-AAGAGCCATAATCG
1 GGAAGCTCATGAAGAGCCATAA-CG
* * * *
54455752 AGAAGCTCATG-CGAGCTAATAACA
1 GGAAGCTCATGAAGAGC-CATAACG
*
54455776 GGTAGCTC-TGAAGAGCCATTAACG
1 GGAAGCTCATGAAGAGCCA-TAACG
* *
54455800 GGAAGCTTCA-G-ATAGCCATATAGTG
1 GGAAGC-TCATGAAGAGCCATA-A-CG
* * * *
54455825 GGAAGTTCAAG-TGAGCCATATCG
1 GGAAGCTCATGAAGAGCCATAACG
* *
54455848 GGAAGCTC-CGAAGAGCCATTAATCA
1 GGAAGCTCATGAAGAGCCA-TAA-CG
* ** *
54455873 AGAAGCTCACAAAGAGCCTTTAATCG
1 GGAAGCTCATGAAGAGCC-ATAA-CG
** *
54455899 AAAAACTCATGAAGAGCCATATATCG
1 GGAAGCTCATGAAGAGCCATA-A-CG
* * *
54455925 GGATGCTCAT-AATAGCTATTAACG
1 GGAAGCTCATGAAGAGCCA-TAACG
54455949 GGA
1 GGA
54455952 TCGAGATGCT
Statistics
Matches: 147, Mismatches: 37, Indels: 32
0.68 0.17 0.15
Matches are distributed among these distances:
22 1 0.01
23 19 0.13
24 50 0.34
25 38 0.26
26 39 0.27
ACGTcount: A:0.36, C:0.20, G:0.24, T:0.20
Consensus pattern (24 bp):
GGAAGCTCATGAAGAGCCATAACG
Found at i:54455907 original size:26 final size:26
Alignment explanation
Indices: 54455858--54455918 Score: 70
Period size: 26 Copynumber: 2.3 Consensus size: 26
54455848 GGAAGCTCCG
*
54455858 AAGAGCCATTAATCAAGAAGCTCACA
1 AAGAGCCATTAATCAAGAAACTCACA
* **
54455884 AAGAGCCTTTAATCGAA-AAACTCATG
1 AAGAGCCATTAATC-AAGAAACTCACA
54455910 AAGAGCCAT
1 AAGAGCCAT
54455919 ATATCGGGAT
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
26 27 0.93
27 2 0.07
ACGTcount: A:0.44, C:0.21, G:0.16, T:0.18
Consensus pattern (26 bp):
AAGAGCCATTAATCAAGAAACTCACA
Found at i:54455969 original size:30 final size:30
Alignment explanation
Indices: 54455921--54455981 Score: 97
Period size: 30 Copynumber: 2.0 Consensus size: 30
54455911 AGAGCCATAT
*
54455921 ATCGGGATGCTCATAATAGCTATTAACGGG
1 ATCGAGATGCTCATAATAGCTATTAACGGG
54455951 ATCGAGATGCTTCA-AATAGCTATTAACGGG
1 ATCGAGATGC-TCATAATAGCTATTAACGGG
54455981 A
1 A
54455982 AGCTCGCAAG
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
30 26 0.90
31 3 0.10
ACGTcount: A:0.33, C:0.16, G:0.25, T:0.26
Consensus pattern (30 bp):
ATCGAGATGCTCATAATAGCTATTAACGGG
Found at i:54460025 original size:40 final size:40
Alignment explanation
Indices: 54459981--54460115 Score: 152
Period size: 40 Copynumber: 3.4 Consensus size: 40
54459971 CGTTTGGACA
*
54459981 AAAAACGCCACTAAAAATCAAGCATTAGCCGCGCTTTTCT-
1 AAAAACGCCGCTAAAAATCAAGCATTAGCCGCGCTTTT-TG
** *
54460021 AAAAACGCCGCTAAAGGTCAAGCATTAGCGGCGCTTTTTG
1 AAAAACGCCGCTAAAAATCAAGCATTAGCCGCGCTTTTTG
* **
54460061 GAAAACGCCGCTAAAAAT-AAGCATTAG-CGACATTTTTTG
1 AAAAACGCCGCTAAAAATCAAGCATTAGCCG-CGCTTTTTG
*
54460100 ACAAACGCCG-TAAAAA
1 AAAAACGCCGCTAAAAA
54460116 GCCTAAGCCC
Statistics
Matches: 81, Mismatches: 12, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
38 7 0.09
39 25 0.31
40 49 0.60
ACGTcount: A:0.38, C:0.23, G:0.18, T:0.21
Consensus pattern (40 bp):
AAAAACGCCGCTAAAAATCAAGCATTAGCCGCGCTTTTTG
Found at i:54460265 original size:41 final size:41
Alignment explanation
Indices: 54460151--54460432 Score: 424
Period size: 41 Copynumber: 6.9 Consensus size: 41
54460141 TGAGTTTTTA
* * *
54460151 GGGCCTTTAGCGGCGTTTTTCAAGAAGTGTCGCTAATGCTC
1 GGGCCTTTAGCGGCGTTTTTGAAGAAGCGCCGCTAATGCTC
* * * *
54460192 GGGCTTTTAAC-G-GTTTTTTAAGAAGCGTCGCTAATGCTC
1 GGGCCTTTAGCGGCGTTTTTGAAGAAGCGCCGCTAATGCTC
*
54460231 GGGCCTTTAGCGGCGTTTTTGAAGAAGCGCCGCTAATGTTC
1 GGGCCTTTAGCGGCGTTTTTGAAGAAGCGCCGCTAATGCTC
54460272 GGGCCTTTAGCGGCGTTTTTGAAGAAGCGCCGCTAATGCTC
1 GGGCCTTTAGCGGCGTTTTTGAAGAAGCGCCGCTAATGCTC
* *
54460313 GGTCCTTTAGCGGCGTTTTTGAGGAAGCGCCGCTAATGCTC
1 GGGCCTTTAGCGGCGTTTTTGAAGAAGCGCCGCTAATGCTC
* *
54460354 GGGCCTTTAGCGGCTTTTTTGAAGAAGCGCTGCTAATGCTC
1 GGGCCTTTAGCGGCGTTTTTGAAGAAGCGCCGCTAATGCTC
* *
54460395 GGGCCTTTAGCGGTGTTTTTGAAAAAGCGCCGCTAATG
1 GGGCCTTTAGCGGCGTTTTTGAAGAAGCGCCGCTAATG
54460433 TCCGTTTTTG
Statistics
Matches: 219, Mismatches: 20, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
39 34 0.16
40 2 0.01
41 183 0.84
ACGTcount: A:0.18, C:0.22, G:0.30, T:0.30
Consensus pattern (41 bp):
GGGCCTTTAGCGGCGTTTTTGAAGAAGCGCCGCTAATGCTC
Found at i:54460816 original size:14 final size:14
Alignment explanation
Indices: 54460799--54460835 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
54460789 GGGTTTAATA
54460799 TATATGGTTTAGGG
1 TATATGGTTTAGGG
*
54460813 TATATGATTTAGGG
1 TATATGGTTTAGGG
54460827 TATATGGTT
1 TATATGGTT
54460836 AATTTAGATT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.30, T:0.46
Consensus pattern (14 bp):
TATATGGTTTAGGG
Found at i:54461082 original size:14 final size:13
Alignment explanation
Indices: 54461037--54461087 Score: 50
Period size: 14 Copynumber: 3.8 Consensus size: 13
54461027 GAACAATGTG
*
54461037 TAGGGGTTAGGGGT
1 TAGGGTTTA-GGGT
*
54461051 TAGAGATTT-GGGT
1 TAG-GGTTTAGGGT
54461064 TAGGGTTTAGGGTT
1 TAGGGTTTAGGG-T
54461078 TAGGGTTTAG
1 TAGGGTTTAG
54461088 TGTCTAGATT
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
12 4 0.13
13 10 0.32
14 14 0.45
15 3 0.10
ACGTcount: A:0.18, C:0.00, G:0.45, T:0.37
Consensus pattern (13 bp):
TAGGGTTTAGGGT
Found at i:54461156 original size:7 final size:7
Alignment explanation
Indices: 54461133--54461177 Score: 54
Period size: 7 Copynumber: 6.4 Consensus size: 7
54461123 TAAATAAGAT
54461133 TTAGGGG
1 TTAGGGG
**
54461140 TTAGTAG
1 TTAGGGG
54461147 TTAGGGG
1 TTAGGGG
*
54461154 TTAGGGA
1 TTAGGGG
*
54461161 TTAGGGA
1 TTAGGGG
54461168 TTAGGGG
1 TTAGGGG
54461175 TTA
1 TTA
54461178 AAGGTTAAGA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
7 32 1.00
ACGTcount: A:0.22, C:0.00, G:0.44, T:0.33
Consensus pattern (7 bp):
TTAGGGG
Found at i:54465774 original size:43 final size:43
Alignment explanation
Indices: 54465714--54465804 Score: 130
Period size: 43 Copynumber: 2.1 Consensus size: 43
54465704 CTTTGAGTTC
* * * *
54465714 ATTA-CAAGATTTCCTTGATTAAGTAAATGTATTATATCTTTT
1 ATTACCAAGATTTACTTGATTAAGAAAATGCATTATATATTTT
*
54465756 ATTACCAAGATTTACTTGATTAAGAAAATGCATTGTATATTTT
1 ATTACCAAGATTTACTTGATTAAGAAAATGCATTATATATTTT
54465799 ATTACC
1 ATTACC
54465805 TTGCATATGT
Statistics
Matches: 43, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
42 4 0.09
43 39 0.91
ACGTcount: A:0.35, C:0.11, G:0.10, T:0.44
Consensus pattern (43 bp):
ATTACCAAGATTTACTTGATTAAGAAAATGCATTATATATTTT
Found at i:54466154 original size:43 final size:43
Alignment explanation
Indices: 54466080--54466391 Score: 325
Period size: 43 Copynumber: 7.3 Consensus size: 43
54466070 AAGATATATT
* * **
54466080 TTTAGCGGCTTTTGTGTGAAAAGCATCGCTAAAGGTCTAT-TC
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTATGTC
* * * * *
54466122 TATAGCGGCGTTTGCGGGAAAAAGCGCCGCTAAAGCTCAATATC
1 TTTAGCGGCGTTTGTGGG-AAAAGCGCCGCTAAAGGTCTATGTC
54466166 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCT-TGGTC
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTAT-GTC
* * * * *
54466209 TTTAGCGGTGTTTATAGAAAAAGCGCCGCTAAAAGTC-ATGGTC
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTAT-GTC
54466252 TTTAGCGGCGTTTGTGGG-AAAGCGCC-CTAAAGGTC-ATGGTC
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTAT-GTC
* *
54466293 TTTAGTGGCGTTTGTGGGAAAAGTGCCGCTAAAGG-CTATGGTC
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTAT-GTC
* * * *
54466336 TTTAGCGGCGTTTGTTGAAAAAGTGCCGCTAAATGTC-ATGGTC
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTAT-GTC
*
54466379 TTTAGTGGCGTTT
1 TTTAGCGGCGTTT
54466392 ATTTATAAAA
Statistics
Matches: 232, Mismatches: 30, Indels: 15
0.84 0.11 0.05
Matches are distributed among these distances:
41 31 0.13
42 31 0.13
43 151 0.65
44 19 0.08
ACGTcount: A:0.23, C:0.17, G:0.30, T:0.30
Consensus pattern (43 bp):
TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTATGTC
Found at i:54466308 original size:127 final size:129
Alignment explanation
Indices: 54466124--54466391 Score: 382
Period size: 127 Copynumber: 2.1 Consensus size: 129
54466114 GTCTATTCTA
54466124 TAGCGGCGTTTGCGGGAAAAAGCGCCGCTAAAGCTCAATATCTTTAGCGGCGTTTGTGGGAAAAG
1 TAGCGGCGTTTGCGGG-AAAAGCGCCGCTAAAGCTCAATATCTTTAGCGGCGTTTGTGGGAAAAG
*
54466189 CGCCGCTAAAGGTCT-TGGTCTTTAGCGGTGTTTATAGAAAAAGCGCCGCTAAAAGTCATGGTCT
65 CGCCGCTAAAGG-CTATGGTCTTTAGCGGCGTTTATAGAAAAAGCGCCGCTAAAAGTCATGGTCT
54466253 T
129 T
* * * *
54466254 TAGCGGCGTTTGTGGG-AAAGCGCC-CTAAAGGTC-ATGGTCTTTAGTGGCGTTTGTGGGAAAAG
1 TAGCGGCGTTTGCGGGAAAAGCGCCGCTAAAGCTCAAT-ATCTTTAGCGGCGTTTGTGGGAAAAG
* * * * *
54466316 TGCCGCTAAAGGCTATGGTCTTTAGCGGCGTTTGTTGAAAAAGTGCCGCTAAATGTCATGGTCTT
65 CGCCGCTAAAGGCTATGGTCTTTAGCGGCGTTTATAGAAAAAGCGCCGCTAAAAGTCATGGTCTT
*
54466381 TAGTGGCGTTT
1 TAGCGGCGTTT
54466392 ATTTATAAAA
Statistics
Matches: 125, Mismatches: 11, Indels: 7
0.87 0.08 0.05
Matches are distributed among these distances:
126 4 0.03
127 98 0.78
128 8 0.06
130 15 0.12
ACGTcount: A:0.23, C:0.18, G:0.31, T:0.29
Consensus pattern (129 bp):
TAGCGGCGTTTGCGGGAAAAGCGCCGCTAAAGCTCAATATCTTTAGCGGCGTTTGTGGGAAAAGC
GCCGCTAAAGGCTATGGTCTTTAGCGGCGTTTATAGAAAAAGCGCCGCTAAAAGTCATGGTCTT
Found at i:54466880 original size:20 final size:19
Alignment explanation
Indices: 54466857--54466899 Score: 59
Period size: 20 Copynumber: 2.2 Consensus size: 19
54466847 TCAATTTGGG
* *
54466857 AAAAATTTGGAAAATTTAGT
1 AAAAATATGCAAAATTT-GT
54466877 AAAAATATGCAAAATTTGT
1 AAAAATATGCAAAATTTGT
54466896 AAAA
1 AAAA
54466900 CAGGGGTCAC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 6 0.29
20 15 0.71
ACGTcount: A:0.56, C:0.02, G:0.12, T:0.30
Consensus pattern (19 bp):
AAAAATATGCAAAATTTGT
Found at i:54467675 original size:18 final size:18
Alignment explanation
Indices: 54467648--54467683 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
54467638 GAAGCTTAGT
54467648 AAGTTCAACGTGCTAAAA
1 AAGTTCAACGTGCTAAAA
*
54467666 AAGTTTAACGTGCTAAAA
1 AAGTTCAACGTGCTAAAA
54467684 TGATAAATCT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.44, C:0.14, G:0.17, T:0.25
Consensus pattern (18 bp):
AAGTTCAACGTGCTAAAA
Found at i:54469348 original size:20 final size:19
Alignment explanation
Indices: 54469322--54469381 Score: 77
Period size: 19 Copynumber: 3.2 Consensus size: 19
54469312 ATCTCTCTAA
*
54469322 ATAAAAATTTAAAATAATTT
1 ATAAAAATTCAAAAT-ATTT
*
54469342 TTAAAAATTCAAAATATTT
1 ATAAAAATTCAAAATATTT
*
54469361 ATAAAAATTCCAAA-ATTT
1 ATAAAAATTCAAAATATTT
54469379 ATA
1 ATA
54469382 TTTTAAAAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
18 7 0.19
19 16 0.44
20 13 0.36
ACGTcount: A:0.57, C:0.05, G:0.00, T:0.38
Consensus pattern (19 bp):
ATAAAAATTCAAAATATTT
Found at i:54469413 original size:25 final size:26
Alignment explanation
Indices: 54469372--54469424 Score: 65
Period size: 25 Copynumber: 2.1 Consensus size: 26
54469362 TAAAAATTCC
* *
54469372 AAAATTTATATTTTAAA-AAA-TATA
1 AAAATTTAAATTCTAAATAAATTATA
54469396 AAAATTCTAAATTCTAAATAAATTATA
1 AAAATT-TAAATTCTAAATAAATTATA
54469423 AA
1 AA
54469425 GAATATATAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
24 6 0.25
25 9 0.38
26 3 0.12
27 6 0.25
ACGTcount: A:0.58, C:0.04, G:0.00, T:0.38
Consensus pattern (26 bp):
AAAATTTAAATTCTAAATAAATTATA
Found at i:54470901 original size:21 final size:22
Alignment explanation
Indices: 54470871--54470912 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
54470861 ACAAAGACAT
*
54470871 TTATGTAT-AATGAGTTTTCAA
1 TTATGGATAAATGAGTTTTCAA
54470892 TTATGGATAAATGAGTTTTCA
1 TTATGGATAAATGAGTTTTCA
54470913 TGATTAATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 7 0.37
22 12 0.63
ACGTcount: A:0.33, C:0.05, G:0.17, T:0.45
Consensus pattern (22 bp):
TTATGGATAAATGAGTTTTCAA
Found at i:54471402 original size:6 final size:6
Alignment explanation
Indices: 54471391--54471428 Score: 76
Period size: 6 Copynumber: 6.3 Consensus size: 6
54471381 TTATTTATGA
54471391 ACCACT ACCACT ACCACT ACCACT ACCACT ACCACT AC
1 ACCACT ACCACT ACCACT ACCACT ACCACT ACCACT AC
54471429 TATATATATA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 32 1.00
ACGTcount: A:0.34, C:0.50, G:0.00, T:0.16
Consensus pattern (6 bp):
ACCACT
Found at i:54473130 original size:31 final size:29
Alignment explanation
Indices: 54473087--54473148 Score: 72
Period size: 30 Copynumber: 2.1 Consensus size: 29
54473077 TTTTATAAAT
*
54473087 AATTAATATTTAT-TAATTAAAAATATTTAC
1 AATTAATATTTATAT-ATT-AAAATATTAAC
*
54473117 AATTTATATTTTATATATTAAAATATTAAC
1 AATTAATA-TTTATATATTAAAATATTAAC
54473147 AA
1 AA
54473149 CAAGTTATAA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
30 19 0.68
31 8 0.29
32 1 0.04
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (29 bp):
AATTAATATTTATATATTAAAATATTAAC
Found at i:54485998 original size:21 final size:21
Alignment explanation
Indices: 54485956--54485999 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
54485946 CGATTTCTAC
*
54485956 AATTTATAATTATTTTTTAAA
1 AATTTATAATTATTTTTCAAA
54485977 AATTGTATAATTA-TTTTCAAA
1 AATT-TATAATTATTTTTCAAA
54485998 AA
1 AA
54486000 AAATTTAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 13 0.62
22 8 0.38
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.50
Consensus pattern (21 bp):
AATTTATAATTATTTTTCAAA
Found at i:54485999 original size:22 final size:21
Alignment explanation
Indices: 54485956--54486014 Score: 66
Period size: 22 Copynumber: 2.7 Consensus size: 21
54485946 CGATTTCTAC
**
54485956 AATTTATAATTATTTTTTAAA
1 AATTTATAATTATTTTCAAAA
54485977 AATTGTATAATTATTTTCAAAAAA
1 AATT-TATAATTATTTTC--AAAA
54486001 AATTTA-AATTATTT
1 AATTTATAATTATTT
54486015 AATATTTTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
21 4 0.12
22 20 0.61
23 2 0.06
24 7 0.21
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.51
Consensus pattern (21 bp):
AATTTATAATTATTTTCAAAA
Found at i:54486097 original size:10 final size:10
Alignment explanation
Indices: 54486084--54486183 Score: 57
Period size: 10 Copynumber: 9.8 Consensus size: 10
54486074 CTTTTACAAC
54486084 TTTTT-AATA
1 TTTTTAAATA
54486093 TTTTTAAATTA
1 TTTTTAAA-TA
*
54486104 TTTTTATATA
1 TTTTTAAATA
54486114 TTTTTAAATAA
1 TTTTTAAAT-A
**
54486125 AGTTTAAA-A
1 TTTTTAAATA
*
54486134 TTTTATATATGA
1 TTTT-TAAAT-A
54486146 TTTTTACTAAT-
1 TTTTTA--AATA
*
54486157 TTTATAAA-A
1 TTTTTAAATA
54486166 TTTTATAAA-A
1 TTTT-TAAATA
54486176 TTTTTAAA
1 TTTTTAAA
54486184 GTTGTTTCGT
Statistics
Matches: 71, Mismatches: 10, Indels: 20
0.70 0.10 0.20
Matches are distributed among these distances:
9 17 0.24
10 24 0.34
11 23 0.32
12 5 0.07
13 2 0.03
ACGTcount: A:0.40, C:0.01, G:0.02, T:0.57
Consensus pattern (10 bp):
TTTTTAAATA
Found at i:54486130 original size:21 final size:20
Alignment explanation
Indices: 54486086--54486137 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 20
54486076 TTTACAACTT
* **
54486086 TTTAATATTTTTAAATTATT
1 TTTAATATTTTTAAATAAAG
54486106 TTTATATATTTTTAAATAAAG
1 TTTA-ATATTTTTAAATAAAG
*
54486127 TTTAAAATTTT
1 TTTAATATTTT
54486138 ATATATGATT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
20 10 0.37
21 17 0.63
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (20 bp):
TTTAATATTTTTAAATAAAG
Found at i:54488107 original size:26 final size:27
Alignment explanation
Indices: 54488076--54488138 Score: 69
Period size: 26 Copynumber: 2.4 Consensus size: 27
54488066 ATAAATTATG
*
54488076 TTATATATTC-AATTTAAATTTAATTT-
1 TTATATATTCAAACTTAAA-TTAATTTA
*
54488102 TTATAT-TTCAAACTTAAATTATTTTA
1 TTATATATTCAAACTTAAATTAATTTA
54488128 TTATATTATTC
1 TTATA-TATTC
54488139 TATAATTTAA
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
25 9 0.29
26 18 0.58
27 1 0.03
28 3 0.10
ACGTcount: A:0.37, C:0.06, G:0.00, T:0.57
Consensus pattern (27 bp):
TTATATATTCAAACTTAAATTAATTTA
Found at i:54488479 original size:30 final size:30
Alignment explanation
Indices: 54488438--54488623 Score: 134
Period size: 30 Copynumber: 6.2 Consensus size: 30
54488428 ATTTTTTTTG
* **
54488438 CATTTTTACCCCTGTACTTTTC-AAAATTTA
1 CATTTTGACCCCTAAACTTTTCTAAAA-TTA
54488468 CATTTTGACCCC-AAACTTTTCTAAAATTTA
1 CATTTTGACCCCTAAACTTTTCTAAAA-TTA
* **
54488498 CATTTTAACCCC-AAAAATTTCTAAAATTA
1 CATTTTGACCCCTAAACTTTTCTAAAATTA
* * *
54488527 CATTTTGACCCTTAGAC-TTTCTCAAAATTG
1 CATTTTGACCCCTAAACTTTTCT-AAAATTA
* * *
54488557 CACTTTGACCCCTAAAC-TCTCAAGAAATTA
1 CATTTTGACCCCTAAACTTTTCTA-AAATTA
* * *
54488587 CATTTTG-GCCC-ATATTTTTGCTAAAATTA
1 CATTTTGACCCCTAAACTTTT-CTAAAATTA
54488616 CACTTTTG
1 CA-TTTTG
54488624 CCTCAGAAGC
Statistics
Matches: 126, Mismatches: 23, Indels: 14
0.77 0.14 0.09
Matches are distributed among these distances:
28 2 0.02
29 39 0.31
30 85 0.67
ACGTcount: A:0.32, C:0.23, G:0.06, T:0.39
Consensus pattern (30 bp):
CATTTTGACCCCTAAACTTTTCTAAAATTA
Found at i:54488568 original size:59 final size:58
Alignment explanation
Indices: 54488456--54488621 Score: 142
Period size: 59 Copynumber: 2.8 Consensus size: 58
54488446 CCCCTGTACT
*
54488456 TTTCAAAATTTACATTTTGACCCCAAACTTTTCTAAAATTTACATTTTAACCCCAAAAA
1 TTTCAAAA-TTACATTTTGACCCCAAACTTTTCTAAAATTTACACTTTAACCCCAAAAA
* * * * * *
54488515 TTTCTAAAATTACATTTTGACCCTTAGAC-TTTCTCAAAA-TTGCACTTTGACCCCTAAAC
1 TTTC-AAAATTACATTTTGACCC-CAAACTTTTCT-AAAATTTACACTTTAACCCCAAAAA
* * * *
54488574 TCTCAAGAAATTACATTTTG-GCCCATATTTTTGCTAAAA-TTACACTTT
1 TTTC-A-AAATTACATTTTGACCCCAAACTTTT-CTAAAATTTACACTTT
54488622 TGCCTCAGAA
Statistics
Matches: 87, Mismatches: 14, Indels: 12
0.77 0.12 0.11
Matches are distributed among these distances:
58 2 0.02
59 59 0.68
60 26 0.30
ACGTcount: A:0.34, C:0.22, G:0.05, T:0.39
Consensus pattern (58 bp):
TTTCAAAATTACATTTTGACCCCAAACTTTTCTAAAATTTACACTTTAACCCCAAAAA
Found at i:54489171 original size:4 final size:4
Alignment explanation
Indices: 54489164--54489212 Score: 50
Period size: 4 Copynumber: 12.5 Consensus size: 4
54489154 AAGGAAGAAG
*
54489164 AAGA AAGA AAGA AA-A AAGA GAA-A AA-A AAGA AAGA AAAA AGAGA AAGA
1 AAGA AAGA AAGA AAGA AAGA -AAGA AAGA AAGA AAGA AAGA A-AGA AAGA
54489211 AA
1 AA
54489213 AAAATAAAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
3 8 0.21
4 26 0.67
5 5 0.13
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (4 bp):
AAGA
Found at i:54489181 original size:11 final size:11
Alignment explanation
Indices: 54489161--54489240 Score: 69
Period size: 11 Copynumber: 7.2 Consensus size: 11
54489151 GGGAAGGAAG
*
54489161 AAGAAGAAAGA
1 AAGAAAAAAGA
54489172 AAGAAAAAAGA
1 AAGAAAAAAGA
54489183 GAA-AAAAAAGA
1 -AAGAAAAAAGA
54489194 AAGAAAAAAGAGA
1 AAG-AAAAA-AGA
54489207 AAGAAAAAA-A
1 AAGAAAAAAGA
*
54489217 TAA-AAAAAATA
1 -AAGAAAAAAGA
54489228 AA-AGAAAAAGA
1 AAGA-AAAAAGA
54489239 AA
1 AA
54489241 TACATCACAG
Statistics
Matches: 60, Mismatches: 2, Indels: 14
0.79 0.03 0.18
Matches are distributed among these distances:
10 12 0.20
11 30 0.50
12 12 0.20
13 6 0.10
ACGTcount: A:0.81, C:0.00, G:0.16, T:0.03
Consensus pattern (11 bp):
AAGAAAAAAGA
Found at i:54489187 original size:9 final size:9
Alignment explanation
Indices: 54489161--54489240 Score: 58
Period size: 9 Copynumber: 8.7 Consensus size: 9
54489151 GGGAAGGAAG
54489161 AAGAAGAAAGA
1 AAGAA-AAA-A
54489172 AAGAAAAAA
1 AAGAAAAAA
*
54489181 GAGAAAAAA
1 AAGAAAAAA
*
54489190 AAGAAAGAA
1 AAGAAAAAA
* *
54489199 AA-AAGAGA
1 AAGAAAAAA
54489207 AAGAAAAAA
1 AAGAAAAAA
54489216 ATA-AAAAAA
1 A-AGAAAAAA
54489225 ATA-AAAGAAA
1 A-AGAAA-AAA
54489235 AAGAAA
1 AAGAAA
54489241 TACATCACAG
Statistics
Matches: 57, Mismatches: 8, Indels: 9
0.77 0.11 0.12
Matches are distributed among these distances:
8 5 0.09
9 36 0.63
10 11 0.19
11 5 0.09
ACGTcount: A:0.81, C:0.00, G:0.16, T:0.03
Consensus pattern (9 bp):
AAGAAAAAA
Found at i:54489191 original size:13 final size:12
Alignment explanation
Indices: 54489167--54489236 Score: 63
Period size: 13 Copynumber: 5.8 Consensus size: 12
54489157 GAAGAAGAAG
54489167 AAAGAAAGAAAAA
1 AAAGAAA-AAAAA
*
54489180 AGAGAAAAAAAA
1 AAAGAAAAAAAA
*
54489192 GAAAGAAAAAAGAG
1 -AAAGAAAAAA-AA
54489206 AAAG-AAAAAAA
1 AAAGAAAAAAAA
* *
54489217 TAA-AAAAAATA
1 AAAGAAAAAAAA
54489228 AAAGAAAAA
1 AAAGAAAAA
54489237 GAAATACATC
Statistics
Matches: 46, Mismatches: 7, Indels: 9
0.74 0.11 0.15
Matches are distributed among these distances:
11 11 0.24
12 15 0.33
13 19 0.41
14 1 0.02
ACGTcount: A:0.83, C:0.00, G:0.14, T:0.03
Consensus pattern (12 bp):
AAAGAAAAAAAA
Found at i:54489192 original size:22 final size:23
Alignment explanation
Indices: 54489161--54489240 Score: 103
Period size: 22 Copynumber: 3.5 Consensus size: 23
54489151 GGGAAGGAAG
54489161 AAGAAGAAAGAAAGAAAAAAGAGA
1 AAGAA-AAAGAAAGAAAAAAGAGA
54489185 AA-AAAAAGAAAGAAAAAAGAGA
1 AAGAAAAAGAAAGAAAAAAGAGA
* *
54489207 AAGAAAAA-AATAAAAAAAATA-A
1 AAGAAAAAGAA-AGAAAAAAGAGA
54489229 AAGAAAAAGAAA
1 AAGAAAAAGAAA
54489241 TACATCACAG
Statistics
Matches: 51, Mismatches: 2, Indels: 8
0.84 0.03 0.13
Matches are distributed among these distances:
22 32 0.63
23 17 0.33
24 2 0.04
ACGTcount: A:0.81, C:0.00, G:0.16, T:0.03
Consensus pattern (23 bp):
AAGAAAAAGAAAGAAAAAAGAGA
Found at i:54489198 original size:26 final size:26
Alignment explanation
Indices: 54489158--54489240 Score: 75
Period size: 28 Copynumber: 3.2 Consensus size: 26
54489148 GAAGGGAAGG
*
54489158 AAGAAGAAGAAAGAAAG-AAAAA-AG-
1 AAGAA-AAAAAAGAAAGAAAAAAGAGA
54489182 -AGAAAAAAAAGAAAGAAAAAAGAGA
1 AAGAAAAAAAAGAAAGAAAAAAGAGA
* * *
54489207 AAGAAAAAAATAAAAAAAATAAAAGAAA
1 AAGAAAAAAA-AGAAAGAA-AAAAGAGA
54489235 AAGAAA
1 AAGAAA
54489241 TACATCACAG
Statistics
Matches: 49, Mismatches: 4, Indels: 8
0.80 0.07 0.13
Matches are distributed among these distances:
22 10 0.20
23 9 0.18
24 2 0.04
26 9 0.18
27 6 0.12
28 13 0.27
ACGTcount: A:0.81, C:0.00, G:0.17, T:0.02
Consensus pattern (26 bp):
AAGAAAAAAAAGAAAGAAAAAAGAGA
Found at i:54489213 original size:35 final size:35
Alignment explanation
Indices: 54489169--54489236 Score: 102
Period size: 35 Copynumber: 1.9 Consensus size: 35
54489159 AGAAGAAGAA
*
54489169 AGAAAGAAAAAAGAGAAAAAAAA-GAAAGAAAAAAG
1 AGAAAGAAAAAA-AGAAAAAAAATAAAAGAAAAAAG
*
54489204 AGAAAGAAAAAAATAAAAAAAATAAAAGAAAAA
1 AGAAAGAAAAAAAGAAAAAAAATAAAAGAAAAA
54489237 GAAATACATC
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
34 9 0.30
35 21 0.70
ACGTcount: A:0.82, C:0.00, G:0.15, T:0.03
Consensus pattern (35 bp):
AGAAAGAAAAAAAGAAAAAAAATAAAAGAAAAAAG
Found at i:54489362 original size:20 final size:20
Alignment explanation
Indices: 54489336--54489375 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
54489326 CAAAAAAAGA
*
54489336 AAAAAAAGAAATAGCAGCAGC
1 AAAAAAA-AAACAGCAGCAGC
54489357 AAAAAAAAAACAGCAGCAG
1 AAAAAAAAAACAGCAGCAG
54489376 GCCAGGCCCA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 11 0.61
21 7 0.39
ACGTcount: A:0.65, C:0.15, G:0.17, T:0.03
Consensus pattern (20 bp):
AAAAAAAAAACAGCAGCAGC
Found at i:54490745 original size:79 final size:78
Alignment explanation
Indices: 54490313--54490977 Score: 687
Period size: 80 Copynumber: 8.5 Consensus size: 78
54490303 TTTTTTTTTT
* * ** *
54490313 AAAAATCAACTCATAATAC-AGAGGTGAGTTGAGCCTC-GAGTCACGTTGAGGTATTTTTTAATT
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGA-TCACGCCGAGGTATTTCTT--TT
* *
54490376 TAATTTCTGTTTTTTCA
63 AAATTTATG-TTTTTCA
* * ** *
54490393 AAAAATCAACTCATAATAC-AGAGGTGAGTTGAGCCTC-GAGTCACGTTGAGGTATTTTTTAATT
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGA-TCACGCCGAGGTATTTCTT--TT
* *
54490456 TAATTTCTGTTTTTTCA
63 AAATTTATG-TTTTTCA
* * * *
54490473 AAAAATCAACTCATAATAC-AGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTA--T-TTTT-AA
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGATCACGCCGAGGTATTTCTTTTAAA
*
54490533 TTTATGTATTTT-T
66 TTTATGT-TTTTCA
** * ** * *
54490546 TTAAATCAACTCATAATATGAGAGGTGAGTTGTGCCTCAGG-TCACGCTGAGGTATTTCTTTTAA
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC-GGATCACGCCGAGGTATTTCTTTTAA
*
54490610 ATTTCTGTTTTTTTTTTCAA
65 ATTTATG-----TTTTTC-A
* * *
54490630 AAAAATCAACTCATATTGCGAGAGGTGAGTTAAGCCTCGGACCATGCCGAGGTATTTCTTTTAAA
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGATCACGCCGAGGTATTTCTTTTAAA
54490695 TTTATGTTTTTCAA
66 TTTATGTTTTTC-A
* * *
54490709 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGACCATGCCGAGGTATTTCTTTTAAA
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGATCACGCCGAGGTATTTCTTTTAAA
54490774 TTTATGTTTTTCA
66 TTTATGTTTTTCA
* * * *
54490787 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGACCATGCCGAGGTGTTTCTTTTAAA
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGATCACGCCGAGGTATTTCTTTTAAA
*
54490852 TTTCTGTTTTTC-
66 TTTATGTTTTTCA
* *
54490864 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACGCCGAGGTA--T-TTTTCAA
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGATCACGCCGAGGTATTTCTTTTAAA
*
54490926 TTCATGTTTTTC-
66 TTTATGTTTTTCA
*
54490938 AAAAATCAACTCATTTTGCGAGAGGTGAGTTGAGCCTCGG
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGG
54490978 GGCACATGTC
Statistics
Matches: 535, Mismatches: 34, Indels: 38
0.88 0.06 0.06
Matches are distributed among these distances:
73 17 0.03
74 96 0.18
75 5 0.01
76 1 0.00
77 55 0.10
78 84 0.16
79 83 0.16
80 129 0.24
81 1 0.00
82 4 0.01
83 3 0.01
84 57 0.11
ACGTcount: A:0.28, C:0.15, G:0.20, T:0.36
Consensus pattern (78 bp):
AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGATCACGCCGAGGTATTTCTTTTAAA
TTTATGTTTTTCA
Found at i:54490845 original size:157 final size:157
Alignment explanation
Indices: 54490313--54490977 Score: 655
Period size: 157 Copynumber: 4.3 Consensus size: 157
54490303 TTTTTTTTTT
* * * * ** * *
54490313 AAAAATCAACTCATAATAC-AGAGGTGAGTTGAGCCTC-GAGTCACGTTGAGGTATTTTTTAATT
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGA-CCATGCCGAGGTGTTTCTT--TT
* * * *
54490376 TAATTTCTGTTTTTTCAAAAAATCAACTCATAATAC-AGAGGTGAGTTGAGCC-TCGAGTCACGT
63 AAATTTATG-TTTTTCAAAAAATCAACTCATAATACGAGAGGTGAGTTGAGCCTTGGA-TCACGC
* * * *
54490439 TGAGGTATTTTTTAATTTAATTTCTGTTTTTTCA
126 CGAGGTATTTCTT--TTAAATTTATGTTTTTTCA
* * ** * * *
54490473 AAAAATCAACTCATAATAC-AGAGGTGAGTTGAGCCTCGGGTCACGCTGA-G-GTAT-TTTT-AA
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGACCATGCCGAGGTGTTTCTTTTAAA
*** * * * *
54490533 TTTATGTATTTT-TTTAAATCAACTCATAATATGAGAGGTGAGTTGTGCCTCAGG-TCACGCTGA
66 TTTATGT-TTTTCAAAAAATCAACTCATAATACGAGAGGTGAGTTGAGCCT-TGGATCACGCCGA
*
54490596 GGTATTTCTTTTAAATTTCTGTTTTTTTTTTCAA
129 GGTATTTCTTTTAAATTTATG----TTTTTTC-A
* *
54490630 AAAAATCAACTCATATTGCGAGAGGTGAGTTAAGCCTCGGACCATGCCGAGGTATTTCTTTTAAA
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGACCATGCCGAGGTGTTTCTTTTAAA
* * * *
54490695 TTTATGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGACCATGCCGAG
66 TTTATGTTTTTC-AAAAAATCAACTCATAATACGAGAGGTGAGTTGAGCCTTGGATCACGCCGAG
54490760 GTATTTCTTTTAAATTTATG-TTTTTCA
130 GTATTTCTTTTAAATTTATGTTTTTTCA
*
54490787 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGACCATGCCGAGGTGTTTCTTTTAAA
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGACCATGCCGAGGTGTTTCTTTTAAA
* * * * *
54490852 TTTCTGTTTTTC-AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACGCCGAGG
66 TTTATGTTTTTCAAAAAATCAACTCATAATACGAGAGGTGAGTTGAGCCTTGGATCACGCCGAGG
* *
54490916 TA--T-TTTTCAATTCATG-TTTTTC-
131 TATTTCTTTTAAATTTATGTTTTTTCA
*
54490938 AAAAATCAACTCATTTTGCGAGAGGTGAGTTGAGCCTCGG
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGG
54490978 GGCACATGTC
Statistics
Matches: 439, Mismatches: 48, Indels: 45
0.83 0.09 0.08
Matches are distributed among these distances:
151 38 0.09
152 27 0.06
153 18 0.04
154 43 0.10
155 52 0.12
156 8 0.02
157 94 0.21
158 33 0.08
159 2 0.00
160 47 0.11
161 9 0.02
162 11 0.03
163 57 0.13
ACGTcount: A:0.28, C:0.15, G:0.20, T:0.36
Consensus pattern (157 bp):
AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGACCATGCCGAGGTGTTTCTTTTAAA
TTTATGTTTTTCAAAAAATCAACTCATAATACGAGAGGTGAGTTGAGCCTTGGATCACGCCGAGG
TATTTCTTTTAAATTTATGTTTTTTCA
Found at i:54491087 original size:75 final size:74
Alignment explanation
Indices: 54490630--54491090 Score: 394
Period size: 79 Copynumber: 6.0 Consensus size: 74
54490620 TTTTTTTCAA
* * * **
54490630 AAAAATCAACTCATATTGCGAGAGGTGAGTTAAGCCTC-GGACCATGCCGAGGTATTTCTTTTAA
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCCACGCCGAGGTA----TTTTCG
*
54490694 ATTTATGTTTTTC
62 ATTTCTGTTTTTC
* * *
54490707 AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCT-TGGACCATGCCGAGGTATTTCTTTT
1 --AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCCACGCCGAGGTA----TTTT
** *
54490771 AAATTTATGTTTTTC
60 CGATTTCTGTTTTTC
* * * * *
54490786 AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCT-TGGACCATGCCGAGGTGTTTCTTTTA
1 -AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCCACGCCGA-G-G--TATTTTC
*
54490850 AATTTCTGTTTTTC
61 GATTTCTGTTTTTC
*
54490864 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGT-CACGCCGAGGTATTTTTC-AAT
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCCACGCCGAGGTA-TTTTCGATT
54490927 TCATGTTTTTC
65 TC-TGTTTTTC
* * * * *
54490938 AAAAATCAACTCATTTTGCGAGAGGTGAGTTGAGCCTCGGGGCACATGTCGAGGTATTTTTGATA
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTC-CACGCCGAGGTATTTTCGAT-
54491003 TT-TGTTTTTC
64 TTCTGTTTTTC
* * * * * * * * *
54491013 GAAGATCAACTCATAATCCAAGAGGTGAATTGAGTCTCGGGTCGCACGCCGAGCTATTCTCGATT
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTC-CACGCCGAGGTATTTTCGATT
*
54491078 TCTGCTTTTC
65 TCTGTTTTTC
54491088 AAA
1 AAA
54491091 TAAAGAGGAA
Statistics
Matches: 337, Mismatches: 32, Indels: 30
0.84 0.08 0.08
Matches are distributed among these distances:
73 5 0.01
74 54 0.16
75 71 0.21
76 12 0.04
77 46 0.14
78 71 0.21
79 76 0.23
80 1 0.00
82 1 0.00
ACGTcount: A:0.27, C:0.18, G:0.22, T:0.34
Consensus pattern (74 bp):
AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCCACGCCGAGGTATTTTCGATTT
CTGTTTTTC
Found at i:54491287 original size:30 final size:29
Alignment explanation
Indices: 54491246--54491401 Score: 120
Period size: 30 Copynumber: 5.2 Consensus size: 29
54491236 TATTTTTTTG
* *
54491246 CATTTTTACCCCTATACTTTTCAAAATTTA
1 CATTTTGACCCCTAAACTTTTCAAAA-TTA
54491276 CATTTTGACCCC-AAACTTTTCTAAAATTTA
1 CATTTTGACCCCTAAACTTTTC-AAAA-TTA
* **
54491306 CATTTTAACCCC-AAAAATTTCTAAAATTA
1 CATTTTGACCCCTAAACTTTTC-AAAATTA
* * * * *
54491335 TATTTCGACCCTTAGACTTTCTCAAAATTG
1 CATTTTGACCCCTAAACTTT-TCAAAATTA
* *
54491365 CACTTTGACCCCTAAAC-TCTCAAGAAATTA
1 CATTTTGACCCCTAAACTTTTC-A-AAATTA
54491395 CATTTTG
1 CATTTTG
54491402 GCCCATATTT
Statistics
Matches: 100, Mismatches: 21, Indels: 10
0.76 0.16 0.08
Matches are distributed among these distances:
28 2 0.02
29 21 0.21
30 75 0.75
31 2 0.02
ACGTcount: A:0.33, C:0.24, G:0.04, T:0.38
Consensus pattern (29 bp):
CATTTTGACCCCTAAACTTTTCAAAATTA
Found at i:54491979 original size:4 final size:4
Alignment explanation
Indices: 54491972--54492031 Score: 65
Period size: 4 Copynumber: 15.5 Consensus size: 4
54491962 AAGGAAGAAG
*
54491972 AAGA AAGA AAGA AA-A AAGA GAA-A AAGA AAGA AAG- AA-A AAGA AGAAA
1 AAGA AAGA AAGA AAGA AAGA -AAGA AAGA AAGA AAGA AAGA AAGA A-AGA
54492018 AAGA AAGA AAGA AA
1 AAGA AAGA AAGA AA
54492032 AAGAAGAAAA
Statistics
Matches: 48, Mismatches: 2, Indels: 12
0.77 0.03 0.19
Matches are distributed among these distances:
3 9 0.19
4 34 0.71
5 5 0.10
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (4 bp):
AAGA
Found at i:54491998 original size:23 final size:23
Alignment explanation
Indices: 54491965--54492066 Score: 133
Period size: 23 Copynumber: 4.6 Consensus size: 23
54491955 CGAAGGGAAG
*
54491965 GAAGAAGAAGAAAGAAAGAAAAA
1 GAAGAAAAAGAAAGAAAGAAAAA
54491988 -AGAGAAAAAGAAAGAAAGAAAAA
1 GA-AGAAAAAGAAAGAAAGAAAAA
54492011 GAAGAAAAAGAAAGAAAGAAAAA
1 GAAGAAAAAGAAAGAAAGAAAAA
*
54492034 GAAGAAAAA-ATAA-AAA-AATAA
1 GAAGAAAAAGA-AAGAAAGAAAAA
54492055 -AAGAAAAAGAAA
1 GAAGAAAAAGAAA
54492067 TACATCACAG
Statistics
Matches: 73, Mismatches: 2, Indels: 11
0.85 0.02 0.13
Matches are distributed among these distances:
20 10 0.14
21 5 0.07
22 5 0.07
23 52 0.71
24 1 0.01
ACGTcount: A:0.78, C:0.00, G:0.20, T:0.02
Consensus pattern (23 bp):
GAAGAAAAAGAAAGAAAGAAAAA
Found at i:54492190 original size:20 final size:20
Alignment explanation
Indices: 54492164--54492203 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
54492154 AAAAAAAGAA
*
54492164 AAAAAAAGAAATAGCAGCAGC
1 AAAAAAA-AAACAGCAGCAGC
54492185 AAAAAAAAAACAGCAGCAG
1 AAAAAAAAAACAGCAGCAG
54492204 GCCAGGCCCA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 11 0.61
21 7 0.39
ACGTcount: A:0.65, C:0.15, G:0.17, T:0.03
Consensus pattern (20 bp):
AAAAAAAAAACAGCAGCAGC
Found at i:54492969 original size:15 final size:16
Alignment explanation
Indices: 54492949--54492981 Score: 59
Period size: 15 Copynumber: 2.1 Consensus size: 16
54492939 TTTTAAAAAT
54492949 AATTTCCGTA-TTTCA
1 AATTTCCGTATTTTCA
54492964 AATTTCCGTATTTTCA
1 AATTTCCGTATTTTCA
54492980 AA
1 AA
54492982 AATTTTCGTG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 10 0.59
16 7 0.41
ACGTcount: A:0.30, C:0.18, G:0.06, T:0.45
Consensus pattern (16 bp):
AATTTCCGTATTTTCA
Found at i:54492984 original size:18 final size:18
Alignment explanation
Indices: 54492963--54493178 Score: 142
Period size: 18 Copynumber: 12.2 Consensus size: 18
54492953 TCCGTATTTC
*
54492963 AAATTTCCGTATTTTCAA
1 AAATTTCCGTGTTTTCAA
* *
54492981 AAATTTTCGTGTTTTAAA
1 AAATTTCCGTGTTTTCAA
54492999 AAATCTT-CGTGTTTTCAA
1 AAAT-TTCCGTGTTTTCAA
* * *
54493017 GAA-TCCTCGTATTTTCAA
1 AAATTTC-CGTGTTTTCAA
* *
54493035 AAA-TTCCG-GTGTCTCGA
1 AAATTTCCGTGT-TTTCAA
* * *
54493052 AATTTTTCATGTTTTCAA
1 AAATTTCCGTGTTTTCAA
*
54493070 AAATTCCCGTGTTTT-AA
1 AAATTTCCGTGTTTTCAA
54493087 AAATTTCCGTGTTTTCAA
1 AAATTTCCGTGTTTTCAA
* * *
54493105 AAATTTTCGTATTTTTAA
1 AAATTTCCGTGTTTTCAA
* * * *
54493123 GAATTTTCGTG-TCTCTA
1 AAATTTCCGTGTTTTCAA
54493140 AAA-TTCTCGTGTTTT-AA
1 AAATTTC-CGTGTTTTCAA
* *
54493157 AATTTTTTCGTGTTTTCAA
1 AA-ATTTCCGTGTTTTCAA
54493176 AAA
1 AAA
54493179 AATAAATGTT
Statistics
Matches: 149, Mismatches: 37, Indels: 24
0.71 0.18 0.11
Matches are distributed among these distances:
16 4 0.03
17 36 0.24
18 99 0.66
19 10 0.07
ACGTcount: A:0.29, C:0.14, G:0.11, T:0.46
Consensus pattern (18 bp):
AAATTTCCGTGTTTTCAA
Found at i:54493068 original size:35 final size:35
Alignment explanation
Indices: 54493028--54493109 Score: 101
Period size: 35 Copynumber: 2.3 Consensus size: 35
54493018 AATCCTCGTA
* * * *
54493028 TTTTCAAAAATTCCGGTGTCTCGAAATTTTTCATG
1 TTTTCAAAAATTCCCGTGTCTCAAAAATTTCCATG
* * *
54493063 TTTTCAAAAATTCCCGTGTTTTAAAAATTTCCGTG
1 TTTTCAAAAATTCCCGTGTCTCAAAAATTTCCATG
54493098 TTTTCAAAAATT
1 TTTTCAAAAATT
54493110 TTCGTATTTT
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
35 40 1.00
ACGTcount: A:0.29, C:0.16, G:0.11, T:0.44
Consensus pattern (35 bp):
TTTTCAAAAATTCCCGTGTCTCAAAAATTTCCATG
Found at i:54493090 original size:17 final size:17
Alignment explanation
Indices: 54492963--54493215 Score: 132
Period size: 18 Copynumber: 14.3 Consensus size: 17
54492953 TCCGTATTTC
* *
54492963 AAATTTCCGTATTTTCAA
1 AAATTTTCGTGTTTT-AA
54492981 AAATTTTCGTGTTTTAAA
1 AAATTTTCGTGTTTT-AA
*
54492999 AAATCTTCGTGTTTTCAA
1 AAATTTTCGTGTTTT-AA
* ** *
54493017 GAATCCTCGTATTTTCAA
1 AAATTTTCGTGTTTT-AA
* * **
54493035 AAA-TTCCGGTGTCTCGA
1 AAATTTTC-GTGTTTTAA
* *
54493052 AATTTTTCATGTTTTCAA
1 AAATTTTCGTGTTTT-AA
**
54493070 AAATTCCCGTGTTTTAA
1 AAATTTTCGTGTTTTAA
*
54493087 AAATTTCCGTGTTTTCAA
1 AAATTTTCGTGTTTT-AA
*
54493105 AAATTTTCGTATTTTTAA
1 AAATTTTCGT-GTTTTAA
* *
54493123 GAATTTTCGTGTCTCT-A
1 AAATTTTCGTGT-TTTAA
*
54493140 AAATTCTCGTGTTTTAA
1 AAATTTTCGTGTTTTAA
*
54493157 AATTTTTTCGTGTTTTCAA
1 AA-ATTTTCGTGTTTT-AA
** *** *
54493176 AAAAATAAATGTTTCAA
1 AAATTTTCGTGTTTTAA
*
54493193 AAATCTTCGTGTTTTTAA
1 AAATTTTCGTG-TTTTAA
54493211 AAATT
1 AAATT
54493216 CTCATATTTT
Statistics
Matches: 174, Mismatches: 51, Indels: 20
0.71 0.21 0.08
Matches are distributed among these distances:
16 2 0.01
17 47 0.27
18 117 0.67
19 8 0.05
ACGTcount: A:0.30, C:0.13, G:0.11, T:0.45
Consensus pattern (17 bp):
AAATTTTCGTGTTTTAA
Found at i:54493112 original size:53 final size:53
Alignment explanation
Indices: 54492963--54493178 Score: 172
Period size: 53 Copynumber: 4.1 Consensus size: 53
54492953 TCCGTATTTC
* * * *
54492963 AAATTTCCGTATTTTCAAAAATTTTCGTGTTTTAAAAAATCTTCGTGTTTTCAA
1 AAATTCCCGTATTTTCAAAAA-TTCCGTGTTTTCAAAAATTTTCGTGTTTTCAA
* * * * *
54493017 GAA-TCCTCGTATTTTCAAAAATTCCG-GTGTCTCGAAATTTTTCATGTTTTCAA
1 AAATTCC-CGTATTTTCAAAAATTCCGTGT-TTTCAAAAATTTTCGTGTTTTCAA
* * *
54493070 AAATTCCCGTGTTTT-AAAAATTTCCGTGTTTTCAAAAATTTTCGTATTTTTAA
1 AAATTCCCGTATTTTCAAAAA-TTCCGTGTTTTCAAAAATTTTCGTGTTTTCAA
* ** * * * *
54493123 GAATTTTCGT-GTCTCTAAAATTCTCGTGTTTT-AAAATTTTTTCGTGTTTTCAA
1 AAATTCCCGTATTTTCAAAAATTC-CGTGTTTTCAAAA-ATTTTCGTGTTTTCAA
54493176 AAA
1 AAA
54493179 AATAAATGTT
Statistics
Matches: 127, Mismatches: 27, Indels: 17
0.74 0.16 0.10
Matches are distributed among these distances:
52 16 0.13
53 90 0.71
54 21 0.17
ACGTcount: A:0.29, C:0.14, G:0.11, T:0.46
Consensus pattern (53 bp):
AAATTCCCGTATTTTCAAAAATTCCGTGTTTTCAAAAATTTTCGTGTTTTCAA
Found at i:54493169 original size:35 final size:33
Alignment explanation
Indices: 54493066--54493162 Score: 104
Period size: 35 Copynumber: 2.8 Consensus size: 33
54493056 TTTCATGTTT
* * *
54493066 TCAAAAATTCCCGTGTTTTAAAAATTTCCGTGTTT
1 TCAAAAATTCTCGTGTTTT-AAAATTTTCGTG-TC
* *
54493101 TCAAAAATTTTCGTATTTTTAAGAATTTTCGTGTC
1 TCAAAAATTCTCGT-GTTTTAA-AATTTTCGTGTC
*
54493136 TCTAAAATTCTCGTGTTTTAAAATTTT
1 TCAAAAATTCTCGTGTTTTAAAATTTT
54493163 TTCGTGTTTT
Statistics
Matches: 52, Mismatches: 8, Indels: 6
0.79 0.12 0.09
Matches are distributed among these distances:
33 6 0.12
34 6 0.12
35 27 0.52
36 13 0.25
ACGTcount: A:0.29, C:0.13, G:0.10, T:0.47
Consensus pattern (33 bp):
TCAAAAATTCTCGTGTTTTAAAATTTTCGTGTC
Found at i:54498757 original size:9 final size:9
Alignment explanation
Indices: 54498743--54498802 Score: 52
Period size: 9 Copynumber: 6.7 Consensus size: 9
54498733 TATTATGCTT
54498743 AAAAAAACA
1 AAAAAAACA
*
54498752 AAAAAAATA
1 AAAAAAACA
54498761 GAGAAAAAACA
1 -A-AAAAAACA
*
54498772 GAAAAAACA
1 AAAAAAACA
* *
54498781 GACAAAAC-
1 AAAAAAACA
54498789 -AAAAAACA
1 AAAAAAACA
54498797 AAAAAA
1 AAAAAA
54498803 GGGAAAAAAA
Statistics
Matches: 42, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
7 6 0.14
9 28 0.67
10 1 0.02
11 7 0.17
ACGTcount: A:0.82, C:0.10, G:0.07, T:0.02
Consensus pattern (9 bp):
AAAAAAACA
Found at i:54498769 original size:20 final size:20
Alignment explanation
Indices: 54498744--54498821 Score: 68
Period size: 20 Copynumber: 3.8 Consensus size: 20
54498734 ATTATGCTTA
54498744 AAAAAACAAAAAAAATAGAG
1 AAAAAACAAAAAAAATAGAG
* * *
54498764 AAAAAACAGAAAAAACAGAC
1 AAAAAACAAAAAAAATAGAG
* * *
54498784 AAAACAAAAAACAAAAAAAGGG
1 AAAA-AACAAA-AAAAATAGAG
54498806 AAAAAA-AGAAAAAAAT
1 AAAAAACA-AAAAAAAT
54498822 CACGATGAAA
Statistics
Matches: 46, Mismatches: 9, Indels: 6
0.75 0.15 0.10
Matches are distributed among these distances:
20 27 0.59
21 8 0.17
22 11 0.24
ACGTcount: A:0.79, C:0.08, G:0.10, T:0.03
Consensus pattern (20 bp):
AAAAAACAAAAAAAATAGAG
Found at i:54499914 original size:77 final size:76
Alignment explanation
Indices: 54499687--54500097 Score: 616
Period size: 74 Copynumber: 5.4 Consensus size: 76
54499677 TTTCAAGAAA
* *
54499687 TATTTTTAAAATTCTGTTTTTTTTTCAAAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTC
1 TATTTTT-AATTTCTGTCTTTTTTT--AAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTC
54499752 GGGTCACGCTGAGG
63 GGGTCACGCTGAGG
* *
54499766 TATTTTTTAATTTAATTTCTATTTTTTCAAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCT
1 TA-TTTTTAATTT-CTGTCT-TTTTTT-AAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCT
54499831 CGGGTCACGCTGAGG
62 CGGGTCACGCTGAGG
*
54499846 TATTTTTTAAATTTCTG-CTTTTTTTAAAAAAGCAACTCATAATACAGAGGTGAGTTGAGCCTCG
1 TA-TTTTT-AATTTCTGTCTTTTTTTAAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCG
54499910 GGTCACGCTGAGG
64 GGTCACGCTGAGG
* *
54499923 TATTTTTAATTTCGGTCTTTTTTT--AAAATCAACTCATAATACAGAGGTGAGTTGAGCATCGGG
1 TATTTTTAATTTCTGTCTTTTTTTAAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGG
54499986 TCACGCTGAGG
66 TCACGCTGAGG
* *
54499997 TATTTTTAATTTATGTCTTTTTTT--TAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGG
1 TATTTTTAATTTCTGTCTTTTTTTAAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGG
54500060 TCACGCTGAGG
66 TCACGCTGAGG
*
54500071 TATTTTTAATTTATGTCTTTTTTTAAA
1 TATTTTTAATTTCTGTCTTTTTTTAAA
54500098 NNNNNNNNNN
Statistics
Matches: 309, Mismatches: 16, Indels: 17
0.90 0.05 0.05
Matches are distributed among these distances:
74 142 0.46
75 7 0.02
76 13 0.04
77 53 0.17
78 6 0.02
79 8 0.03
80 69 0.22
81 11 0.04
ACGTcount: A:0.28, C:0.14, G:0.19, T:0.39
Consensus pattern (76 bp):
TATTTTTAATTTCTGTCTTTTTTTAAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGG
TCACGCTGAGG
Found at i:54504959 original size:9 final size:9
Alignment explanation
Indices: 54504945--54505004 Score: 52
Period size: 9 Copynumber: 6.7 Consensus size: 9
54504935 TATTATGCTT
54504945 AAAAAAACA
1 AAAAAAACA
*
54504954 AAAAAAATA
1 AAAAAAACA
54504963 GAGAAAAAACA
1 -A-AAAAAACA
*
54504974 GAAAAAACA
1 AAAAAAACA
* *
54504983 GACAAAAC-
1 AAAAAAACA
54504991 -AAAAAACA
1 AAAAAAACA
54504999 AAAAAA
1 AAAAAA
54505005 GGGAAAAAAA
Statistics
Matches: 42, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
7 6 0.14
9 28 0.67
10 1 0.02
11 7 0.17
ACGTcount: A:0.82, C:0.10, G:0.07, T:0.02
Consensus pattern (9 bp):
AAAAAAACA
Found at i:54504971 original size:20 final size:20
Alignment explanation
Indices: 54504946--54505023 Score: 68
Period size: 20 Copynumber: 3.8 Consensus size: 20
54504936 ATTATGCTTA
54504946 AAAAAACAAAAAAAATAGAG
1 AAAAAACAAAAAAAATAGAG
* * *
54504966 AAAAAACAGAAAAAACAGAC
1 AAAAAACAAAAAAAATAGAG
* * *
54504986 AAAACAAAAAACAAAAAAAGGG
1 AAAA-AACAAA-AAAAATAGAG
54505008 AAAAAA-AGAAAAAAAT
1 AAAAAACA-AAAAAAAT
54505024 CACGATGAAA
Statistics
Matches: 46, Mismatches: 9, Indels: 6
0.75 0.15 0.10
Matches are distributed among these distances:
20 27 0.59
21 8 0.17
22 11 0.24
ACGTcount: A:0.79, C:0.08, G:0.10, T:0.03
Consensus pattern (20 bp):
AAAAAACAAAAAAAATAGAG
Found at i:54506288 original size:151 final size:145
Alignment explanation
Indices: 54505999--54506283 Score: 336
Period size: 151 Copynumber: 1.9 Consensus size: 145
54505989 TTTTTTCAAA
* *
54505999 AAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTATTTTTTAAATTTCT
1 AAATCAACTCATAATACAGAGGTGAATTGAGCCTCAGGTCACGCTGAGGTATTTTTTAAATTTCT
* ** *
54506064 GCTTTTTTTAAAAAAGCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTATT
66 GCTTTTTTTAAAAAAGCAACTCATAATACAGAGGTGAGTTAAGCCTCGGACCACGCCGAGG----
54506129 TTTAATTTCGGTCTTTTTTT
127 -TTAATTTCGGTCTTTTTTT
* *
54506149 AAATCAACTCATAATATGAGAGGTGAATTGTGCCTCAGGTCACGCTGAGGTATTTCTTTTAAATT
1 AAATCAACTCATAATA-CAGAGGTGAATTGAGCCTCAGGTCACGCTGAGGTA-TT-TTTTAAATT
* * * * *
54506214 TCTGTTTTTTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTAAGCCTCGGACCATGCC
63 TCTG--CTTTTTTT--AAAAAAGCAACTCATAATAC-AGAGGTGAGTTAAGCCTCGGACCACGCC
54506279 GAGGT
123 GAGGT
54506284 ATTTCTTTTA
Statistics
Matches: 114, Mismatches: 13, Indels: 13
0.81 0.09 0.09
Matches are distributed among these distances:
150 16 0.14
151 31 0.27
152 2 0.02
153 14 0.12
155 7 0.06
157 17 0.15
158 27 0.24
ACGTcount: A:0.28, C:0.16, G:0.21, T:0.35
Consensus pattern (145 bp):
AAATCAACTCATAATACAGAGGTGAATTGAGCCTCAGGTCACGCTGAGGTATTTTTTAAATTTCT
GCTTTTTTTAAAAAAGCAACTCATAATACAGAGGTGAGTTAAGCCTCGGACCACGCCGAGGTTAA
TTTCGGTCTTTTTTT
Found at i:54506346 original size:79 final size:77
Alignment explanation
Indices: 54505909--54506401 Score: 516
Period size: 79 Copynumber: 6.3 Consensus size: 77
54505899 ATTCTGTTTT
*
54505909 TTTTTCAAAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTATTTT
1 TTTTTC-AAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTATTTC
* *
54505974 TTAATTTAATTTCTAT
65 TT--TTAAATTTCT-G
54505990 TTTTTCAAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTA-TT-T
1 TTTTTCAAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTATTTCT
54506053 TTTAAATTTCTG
66 TTTAAATTTCTG
* *
54506065 CTTTTTTTAAAAAAGCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTA--T
1 --TTTTTCAAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTATTT
*
54506128 -TTTT-AATTTCGG
64 CTTTTAAATTTCTG
*** * * * *
54506140 TCTTTT-TTTAAATCAACTCATAATATGAGAGGTGAATTGTGCCTCAGGTCACGCTGAGGTATTT
1 T-TTTTCAAAAAATCAACTCATAATA-CAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTATTT
54506204 CTTTTAAATTTCTG
64 CTTTTAAATTTCTG
* * * ** * *
54506218 TTTTTTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTAAGCCTCGGACCATGCCGAGG
1 -----TTTTTC-AAAAAATCAACTCATAATAC-AGAGGTGAGTTGAGCCTCGGGTCACGCTGAGG
*
54506283 TATTTCTTTTAAATTTATG
59 TATTTCTTTTAAATTTCTG
* * * ** * * *
54506302 TTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGACCATGCCGAGGTGTTT
1 TTTTTC-AAAAAATCAACTCATAATAC-AGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTATTT
54506367 CTTTTAAATTTCTG
64 CTTTTAAATTTCTG
54506381 TTTTTC-AAAAATCAACTCATA
1 TTTTTCAAAAAATCAACTCATA
54506402 TTGCNTATAA
Statistics
Matches: 363, Mismatches: 33, Indels: 36
0.84 0.08 0.08
Matches are distributed among these distances:
73 16 0.04
74 35 0.10
75 7 0.02
76 15 0.04
77 77 0.21
78 9 0.02
79 83 0.23
80 54 0.15
81 6 0.02
82 4 0.01
83 1 0.00
84 56 0.15
ACGTcount: A:0.29, C:0.16, G:0.19, T:0.37
Consensus pattern (77 bp):
TTTTTCAAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTATTTCT
TTTAAATTTCTG
Found at i:54506567 original size:30 final size:30
Alignment explanation
Indices: 54506510--54506695 Score: 125
Period size: 30 Copynumber: 6.2 Consensus size: 30
54506500 TATTTTTTTG
** *
54506510 CATTTTAACCCTTTTACTTTT-TGAAATTCA
1 CATTTTAACCCTTAAACTTTTCTAAAATT-A
54506540 CATTTTAACCC-TAAACTTTTCTAAAATTTA
1 CATTTTAACCCTTAAACTTTTCTAAAA-TTA
* **
54506570 CATTTTGACCCCAAAAC-TTTCTAAAATTA
1 CATTTTAACCCTTAAACTTTTCTAAAATTA
* * *
54506599 CATTTCAACCCTTAGA-TTTTCTCAAAATTT
1 CATTTTAACCCTTAAACTTTTCT-AAAATTA
* * * *
54506629 CACTTTGACCCTTAAAC-TCTCAAGAAATTA
1 CATTTTAACCCTTAAACTTTTCTA-AAATTA
* * *
54506659 CATTTTGACCC--ATATTTTTGCTAAAATTA
1 CATTTTAACCCTTAAACTTTT-CTAAAATTA
54506688 CACTTTTA
1 CA-TTTTA
54506696 CCCCAGAAGC
Statistics
Matches: 122, Mismatches: 24, Indels: 20
0.73 0.14 0.12
Matches are distributed among these distances:
28 2 0.02
29 37 0.30
30 77 0.63
31 6 0.05
ACGTcount: A:0.33, C:0.22, G:0.04, T:0.41
Consensus pattern (30 bp):
CATTTTAACCCTTAAACTTTTCTAAAATTA
Found at i:54506685 original size:59 final size:58
Alignment explanation
Indices: 54506532--54506700 Score: 162
Period size: 59 Copynumber: 2.8 Consensus size: 58
54506522 TTTACTTTTT
* * *
54506532 GAAATTCACATTTTAACCC-TAAACTTTTCTAAAATTTACATTTTGACCCCAAAACTTTCTA
1 GAAATT-ACATTTTAACCCAT-AA-TTTTCTAAAATTT-CACTTTGACCCCAAAACTCTCAA
* * **
54506593 -AAATTACATTTCAACCCTTAGATTTTCTCAAAATTTCACTTTGACCCTTAAACTCTCAA
1 GAAATTACATTTTAACCCATA-ATTTTCT-AAAATTTCACTTTGACCCCAAAACTCTCAA
* * * *
54506652 GAAATTACATTTTGACCCATATTTTTGCTAAAATTACACTTTTACCCCA
1 GAAATTACATTTTAACCCATAATTTT-CTAAAATTTCACTTTGACCCCA
54506701 GAAGCTTTTC
Statistics
Matches: 89, Mismatches: 14, Indels: 12
0.77 0.12 0.10
Matches are distributed among these distances:
59 56 0.63
60 33 0.37
ACGTcount: A:0.34, C:0.24, G:0.04, T:0.38
Consensus pattern (58 bp):
GAAATTACATTTTAACCCATAATTTTCTAAAATTTCACTTTGACCCCAAAACTCTCAA
Found at i:54507252 original size:21 final size:19
Alignment explanation
Indices: 54507227--54507303 Score: 73
Period size: 21 Copynumber: 3.8 Consensus size: 19
54507217 GAAGGGAAGG
54507227 AAGAAGAAGAAAGAAAAAAA
1 AAGAAGAA-AAAGAAAAAAA
* *
54507247 AGAGAAAAAGAAAGAAAGAAA
1 A-AGAAGAA-AAAGAAAAAAA
*
54507268 AAGAAGAAAAAAATAAAAAA
1 AAGAAGAAAAAGA-AAAAAA
*
54507288 ATAAAAGAAAAAGAAA
1 A-AGAAGAAAAAGAAA
54507304 TACATCACAG
Statistics
Matches: 47, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
19 4 0.09
20 15 0.32
21 28 0.60
ACGTcount: A:0.81, C:0.00, G:0.17, T:0.03
Consensus pattern (19 bp):
AAGAAGAAAAAGAAAAAAA
Found at i:54507261 original size:25 final size:25
Alignment explanation
Indices: 54507233--54507303 Score: 81
Period size: 25 Copynumber: 2.8 Consensus size: 25
54507223 AAGGAAGAAG
54507233 AAGAAAGAAAAAAAAGAGAAAAAGA
1 AAGAAAGAAAAAAAAGAGAAAAAGA
* * *
54507258 AAGAAAGAAAAAGAAGAAAAAAATA
1 AAGAAAGAAAAAAAAGAGAAAAAGA
* *
54507283 AAAAAATAAAAGAAAA-AGAAA
1 AAGAAAGAAAA-AAAAGAGAAA
54507304 TACATCACAG
Statistics
Matches: 38, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
25 35 0.92
26 3 0.08
ACGTcount: A:0.82, C:0.00, G:0.15, T:0.03
Consensus pattern (25 bp):
AAGAAAGAAAAAAAAGAGAAAAAGA
Found at i:54507278 original size:10 final size:9
Alignment explanation
Indices: 54507236--54507303 Score: 54
Period size: 9 Copynumber: 7.8 Consensus size: 9
54507226 GAAGAAGAAG
54507236 AAAGAAAAA
1 AAAGAAAAA
*
54507245 AAAG-AGAA
1 AAAGAAAAA
*
54507253 AAAG-AAAG
1 AAAGAAAAA
54507261 AAAGAAAAA
1 AAAGAAAAA
*
54507270 GAAGAAAAA
1 AAAGAAAAA
54507279 AATA-AAAAA
1 AA-AGAAAAA
*
54507288 ATAA-AAGAA
1 A-AAGAAAAA
54507297 AAAGAAA
1 AAAGAAA
54507304 TACATCACAG
Statistics
Matches: 47, Mismatches: 8, Indels: 8
0.75 0.13 0.13
Matches are distributed among these distances:
8 15 0.32
9 30 0.64
10 2 0.04
ACGTcount: A:0.82, C:0.00, G:0.15, T:0.03
Consensus pattern (9 bp):
AAAGAAAAA
Found at i:54507285 original size:8 final size:8
Alignment explanation
Indices: 54507236--54507293 Score: 62
Period size: 8 Copynumber: 7.0 Consensus size: 8
54507226 GAAGAAGAAG
54507236 AAAGAAAAA
1 AAAG-AAAA
*
54507245 AAAGAGAA
1 AAAGAAAA
*
54507253 AAAGAAAG
1 AAAGAAAA
54507261 AAAGAAAA
1 AAAGAAAA
54507269 AGAAGAAAA
1 A-AAGAAAA
*
54507278 AAATAAAA
1 AAAGAAAA
*
54507286 AAATAAAA
1 AAAGAAAA
54507294 GAAAAAGAAA
Statistics
Matches: 43, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
8 31 0.72
9 12 0.28
ACGTcount: A:0.83, C:0.00, G:0.14, T:0.03
Consensus pattern (8 bp):
AAAGAAAA
Found at i:54507285 original size:17 final size:15
Alignment explanation
Indices: 54507236--54507299 Score: 56
Period size: 17 Copynumber: 3.9 Consensus size: 15
54507226 GAAGAAGAAG
54507236 AAAGAAAAAAAAGAGAA
1 AAAGAAAAAAAA-A-AA
54507253 AAAGAAAGAAAGAAAAA
1 AAAGAAA-AAA-AAAAA
*
54507270 GAAGAAAAAAATAAAA
1 AAAGAAAAAAA-AAAA
*
54507286 AAATAAAAGAAAAA
1 AAAGAAAA-AAAAA
54507300 GAAATACATC
Statistics
Matches: 40, Mismatches: 3, Indels: 9
0.77 0.06 0.17
Matches are distributed among these distances:
15 1 0.03
16 15 0.38
17 18 0.45
18 4 0.10
19 2 0.05
ACGTcount: A:0.83, C:0.00, G:0.14, T:0.03
Consensus pattern (15 bp):
AAAGAAAAAAAAAAA
Found at i:54507431 original size:18 final size:19
Alignment explanation
Indices: 54507404--54507439 Score: 65
Period size: 18 Copynumber: 1.9 Consensus size: 19
54507394 AAAAGAAAAA
54507404 AAAAAGAAATAGCAGCAGC
1 AAAAAGAAATAGCAGCAGC
54507423 AAAAA-AAATAGCAGCAG
1 AAAAAGAAATAGCAGCAG
54507440 GCCAGGCCCA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 12 0.71
19 5 0.29
ACGTcount: A:0.61, C:0.14, G:0.19, T:0.06
Consensus pattern (19 bp):
AAAAAGAAATAGCAGCAGC
Found at i:54507755 original size:8 final size:8
Alignment explanation
Indices: 54507712--54507763 Score: 59
Period size: 8 Copynumber: 6.4 Consensus size: 8
54507702 TTGTTTCATT
54507712 AAAAAAGA
1 AAAAAAGA
*
54507720 GAAAAAGA
1 AAAAAAGA
*
54507728 AAGAAAGA
1 AAAAAAGA
54507736 AAAAGAAGA
1 AAAA-AAGA
*
54507745 AAAAAATA
1 AAAAAAGA
*
54507753 AAAAAATA
1 AAAAAAGA
54507761 AAA
1 AAA
54507764 GAAAAAGAAA
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
8 30 0.79
9 8 0.21
ACGTcount: A:0.83, C:0.00, G:0.13, T:0.04
Consensus pattern (8 bp):
AAAAAAGA
Found at i:54507901 original size:18 final size:19
Alignment explanation
Indices: 54507874--54507909 Score: 65
Period size: 18 Copynumber: 1.9 Consensus size: 19
54507864 AAAAGAAAAA
54507874 AAAAAGAAATAGCAGCAGC
1 AAAAAGAAATAGCAGCAGC
54507893 AAAAA-AAATAGCAGCAG
1 AAAAAGAAATAGCAGCAG
54507910 GCCAGGCCCA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 12 0.71
19 5 0.29
ACGTcount: A:0.61, C:0.14, G:0.19, T:0.06
Consensus pattern (19 bp):
AAAAAGAAATAGCAGCAGC
Found at i:54511530 original size:74 final size:73
Alignment explanation
Indices: 54511340--54511697 Score: 457
Period size: 74 Copynumber: 4.8 Consensus size: 73
54511330 NNNNNNNNNA
* ** * *
54511340 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGACCATGCCGAGGTATTTCTTTTAAA
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACGCCGAGGTA--T-TTTTCAA
54511405 TTTCTGTTTTTC
63 -TTCTGTTTTTC
54511417 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACGCCGAGGTATTTTTCAATTC
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACGCCGAGGTATTTTTCAATTC
54511482 ATGTTTTTC
66 -TGTTTTTC
*
54511491 AAAAATCAACTCATTTTGCGAGAGGTGAGTTGAGCCTCGGGTCACGCCGAGGTATTTTTCAATTC
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACGCCGAGGTATTTTTCAATTC
54511556 ATGTTTTTC
66 -TGTTTTTC
* * * *
54511565 AAAAATCAACTCATTTTGCGAGAGGTGAGTTGAGCCTCGGGGCACATGTCGAGGTATTTTTGATA
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCAC--GCCGAGGTATTTTTCA-A
54511630 TT-TGTTTTTC
63 TTCTGTTTTTC
* * * * * * *
54511640 GAAGATCAACTCATAATCCAAGAGGTGAGTTGAGTCTCGGGTCGCACGCCGAGCTATT
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGT--CACGCCGAGGTATT
54511698 CTCGATTTCT
Statistics
Matches: 256, Mismatches: 19, Indels: 14
0.89 0.07 0.05
Matches are distributed among these distances:
73 3 0.01
74 131 0.51
75 52 0.20
76 14 0.05
77 56 0.22
ACGTcount: A:0.25, C:0.18, G:0.24, T:0.33
Consensus pattern (73 bp):
AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACGCCGAGGTATTTTTCAATTC
TGTTTTTC
Found at i:54511915 original size:30 final size:30
Alignment explanation
Indices: 54511881--54511979 Score: 132
Period size: 30 Copynumber: 3.4 Consensus size: 30
54511871 TTTTTTTTTG
* *
54511881 CATTTTTACCCCTATACTTTTC-AAAATTTA
1 CATTTTGACCCC-AAACTTTTCTAAAATTTA
54511911 CATTTTGACCCCAAACTTTTCTAAAATTTA
1 CATTTTGACCCCAAACTTTTCTAAAATTTA
*
54511941 CATTTTGACCCCAAA-ATTTCTAAAA-TTA
1 CATTTTGACCCCAAACTTTTCTAAAATTTA
*
54511969 CATTTCGACCC
1 CATTTTGACCC
54511980 TTAGACTTTC
Statistics
Matches: 64, Mismatches: 4, Indels: 4
0.89 0.06 0.06
Matches are distributed among these distances:
28 13 0.20
29 17 0.27
30 34 0.53
ACGTcount: A:0.32, C:0.25, G:0.03, T:0.39
Consensus pattern (30 bp):
CATTTTGACCCCAAACTTTTCTAAAATTTA
Found at i:54512708 original size:15 final size:16
Alignment explanation
Indices: 54512688--54512720 Score: 59
Period size: 15 Copynumber: 2.1 Consensus size: 16
54512678 TTTTAAAAAT
54512688 AATTTCCGTA-TTTCA
1 AATTTCCGTATTTTCA
54512703 AATTTCCGTATTTTCA
1 AATTTCCGTATTTTCA
54512719 AA
1 AA
54512721 AATTTTCGTG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 10 0.59
16 7 0.41
ACGTcount: A:0.30, C:0.18, G:0.06, T:0.45
Consensus pattern (16 bp):
AATTTCCGTATTTTCA
Found at i:54512723 original size:18 final size:18
Alignment explanation
Indices: 54512702--54512916 Score: 169
Period size: 18 Copynumber: 12.2 Consensus size: 18
54512692 TCCGTATTTC
*
54512702 AAATTTCCGTATTTTCAA
1 AAATTTCCGTGTTTTCAA
* *
54512720 AAATTTTCGTGTTTTAAA
1 AAATTTCCGTGTTTTCAA
54512738 AAATCTT-CGTGTTTTCAA
1 AAAT-TTCCGTGTTTTCAA
* *
54512756 GAA-TCCTCGTGTTTTC-A
1 AAATTTC-CGTGTTTTCAA
54512773 AAA-TTCCG-GTGTTTCAA
1 AAATTTCCGTGT-TTTCAA
* *
54512790 AAATTTTCATGTTTTCAA
1 AAATTTCCGTGTTTTCAA
*
54512808 AAATTCCCGTGTTTT-AA
1 AAATTTCCGTGTTTTCAA
54512825 AAATTTCCGTGTTTTCAA
1 AAATTTCCGTGTTTTCAA
* * * *
54512843 AAATTTTCATATTTTTAA
1 AAATTTCCGTGTTTTCAA
* * * *
54512861 GAATTTTCGTG-TCTCTA
1 AAATTTCCGTGTTTTCAA
54512878 AAA-TTCTCGTGTTTT-AA
1 AAATTTC-CGTGTTTTCAA
*
54512895 AAATTTTTCGTGTTTTCAA
1 AAA-TTTCCGTGTTTTCAA
54512914 AAA
1 AAA
54512917 AATAAATGTT
Statistics
Matches: 155, Mismatches: 29, Indels: 25
0.74 0.14 0.12
Matches are distributed among these distances:
15 2 0.01
16 9 0.06
17 38 0.25
18 95 0.61
19 11 0.07
ACGTcount: A:0.30, C:0.14, G:0.11, T:0.46
Consensus pattern (18 bp):
AAATTTCCGTGTTTTCAA
Found at i:54512777 original size:53 final size:54
Alignment explanation
Indices: 54512713--54512913 Score: 200
Period size: 53 Copynumber: 3.8 Consensus size: 54
54512703 AATTTCCGTA
* * *
54512713 TTTTCAAAAATTTTCGTGTTTTAAAAAATCTTCGTGTTTTCAAGAATCCTCGTG
1 TTTTCAAAAATTTCCGTGTTTTAAAAAATTTTCATGTTTTCAAGAATCCTCGTG
* *
54512767 TTTTC-AAAA-TTCCG-GTGTTTCAAAAATTTTCATGTTTTCAAAAATTCC-CGTG
1 TTTTCAAAAATTTCCGTGT-TTTAAAAAATTTTCATGTTTTCAAGAA-TCCTCGTG
* * * **
54512819 TTTT-AAAAATTTCCGTGTTTTCAAAAATTTTCATATTTTTAAGAATTTTCGTG
1 TTTTCAAAAATTTCCGTGTTTTAAAAAATTTTCATGTTTTCAAGAATCCTCGTG
* * * *
54512872 -TCTCTAAAA-TTCTCGTGTTTTAAAAATTTTTCGTGTTTTCAA
1 TTTTCAAAAATTTC-CGTGTTTTAAAAAATTTTCATGTTTTCAA
54512914 AAAAATAAAT
Statistics
Matches: 122, Mismatches: 17, Indels: 17
0.78 0.11 0.11
Matches are distributed among these distances:
51 2 0.02
52 45 0.37
53 68 0.56
54 7 0.06
ACGTcount: A:0.28, C:0.14, G:0.11, T:0.47
Consensus pattern (54 bp):
TTTTCAAAAATTTCCGTGTTTTAAAAAATTTTCATGTTTTCAAGAATCCTCGTG
Found at i:54514617 original size:15 final size:16
Alignment explanation
Indices: 54514597--54514629 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
54514587 ATCCAAAACT
*
54514597 AACTCG-AATGATCCA
1 AACTCGAAATGACCCA
54514612 AACTCGAAATGACCCA
1 AACTCGAAATGACCCA
54514628 AA
1 AA
54514630 TAAGTAACTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 6 0.38
16 10 0.62
ACGTcount: A:0.45, C:0.27, G:0.12, T:0.15
Consensus pattern (16 bp):
AACTCGAAATGACCCA
Found at i:54518725 original size:13 final size:13
Alignment explanation
Indices: 54518707--54518736 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
54518697 TATGTAACTG
54518707 TGTAATTACAATT
1 TGTAATTACAATT
54518720 TGTAATTACAATT
1 TGTAATTACAATT
54518733 TGTA
1 TGTA
54518737 CTACCAAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.37, C:0.07, G:0.10, T:0.47
Consensus pattern (13 bp):
TGTAATTACAATT
Found at i:54523321 original size:21 final size:21
Alignment explanation
Indices: 54523275--54523322 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
54523265 TCACGTGGTT
*
54523275 GGTCAACGCGTAGTCAATGAC
1 GGTCAACACGTAGTCAATGAC
*
54523296 AGTCAACAC-TAGTCAATGATC
1 GGTCAACACGTAGTCAATGA-C
54523317 GGTCAA
1 GGTCAA
54523323 AGTAAAAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
20 10 0.43
21 13 0.57
ACGTcount: A:0.33, C:0.23, G:0.23, T:0.21
Consensus pattern (21 bp):
GGTCAACACGTAGTCAATGAC
Found at i:54530071 original size:12 final size:11
Alignment explanation
Indices: 54530054--54530087 Score: 50
Period size: 12 Copynumber: 2.9 Consensus size: 11
54530044 TGATTTATGC
54530054 CAAAAGAAGCAA
1 CAAAAGAA-CAA
54530066 CAAAAGAACAA
1 CAAAAGAACAA
54530077 CAGAAAGAACA
1 CA-AAAGAACA
54530088 CACACAAGGT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 5 0.24
12 16 0.76
ACGTcount: A:0.68, C:0.18, G:0.15, T:0.00
Consensus pattern (11 bp):
CAAAAGAACAA
Found at i:54534899 original size:12 final size:13
Alignment explanation
Indices: 54534872--54534905 Score: 52
Period size: 12 Copynumber: 2.7 Consensus size: 13
54534862 AGTCACTTAG
54534872 TTTATTTTAGGGT
1 TTTATTTTAGGGT
*
54534885 TTTATTTTA-GTT
1 TTTATTTTAGGGT
54534897 TTTATTTTA
1 TTTATTTTA
54534906 TTTCAATTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
12 11 0.55
13 9 0.45
ACGTcount: A:0.18, C:0.00, G:0.12, T:0.71
Consensus pattern (13 bp):
TTTATTTTAGGGT
Found at i:54547219 original size:27 final size:25
Alignment explanation
Indices: 54547172--54547224 Score: 61
Period size: 27 Copynumber: 2.0 Consensus size: 25
54547162 CCTGAATTTG
*
54547172 ATTTTTTTTACTAATTTGATACTTA
1 ATTTTTTTTACTAATTAGATACTTA
* *
54547197 ATTTTTTTTAATTAGATTAGATATTTA
1 ATTTTTTTT-ACTA-ATTAGATACTTA
54547224 A
1 A
54547225 ATTTGACACT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
25 9 0.39
26 3 0.13
27 11 0.48
ACGTcount: A:0.32, C:0.04, G:0.06, T:0.58
Consensus pattern (25 bp):
ATTTTTTTTACTAATTAGATACTTA
Found at i:54550079 original size:21 final size:21
Alignment explanation
Indices: 54550054--54550093 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
54550044 AAAATCGCAT
*
54550054 GATTTACCAAACTAAAAATTC
1 GATTTACAAAACTAAAAATTC
* *
54550075 GATTTTCAAAATTAAAAAT
1 GATTTACAAAACTAAAAAT
54550094 CTAGAAATTT
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:0.50, C:0.12, G:0.05, T:0.33
Consensus pattern (21 bp):
GATTTACAAAACTAAAAATTC
Found at i:54550563 original size:31 final size:31
Alignment explanation
Indices: 54550522--54550588 Score: 107
Period size: 31 Copynumber: 2.2 Consensus size: 31
54550512 AAGATCACTA
*
54550522 AACTATTCGAAAGTTTTCATTTAAGTCATTG
1 AACTAGTCGAAAGTTTTCATTTAAGTCATTG
*
54550553 AACTAGTCGAAAGTTTTTATTTAAGTCATTG
1 AACTAGTCGAAAGTTTTCATTTAAGTCATTG
*
54550584 GACTA
1 AACTA
54550589 CTTAAGTTTT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.33, C:0.12, G:0.15, T:0.40
Consensus pattern (31 bp):
AACTAGTCGAAAGTTTTCATTTAAGTCATTG
Found at i:54552290 original size:243 final size:243
Alignment explanation
Indices: 54551858--54552349 Score: 885
Period size: 243 Copynumber: 2.0 Consensus size: 243
54551848 TTCCTCATCC
54551858 GGAATGTCCAAATCCCATACCCTGAAGATATCCACTGTTGATGAATTCATCTCTTCTGCAGATAA
1 GGAATGTCCAAATCCCATACCCTGAAGATATCCACTGTTGATGAATTCATCTCTTCTGCAGATAA
*
54551923 GCTTGATTTAACTCCTGAATCAGCAGCACTATCCTTTCTTTCATTCTCCTTGTAGGTGGGTCGGA
66 GCTTGATTTAACTCCTGAATCAACAGCACTATCCTTTCTTTCATTCTCCTTGTAGGTGGGTCGGA
* *
54551988 AAGGATCTCCCCGAAACACTTCAGTGGAATCTTCCTGAAGAAATTGCAGCTCAGTACCAGTCCTC
131 AAGGATCTCCCCAAAACACTTCAGCGGAATCTTCCTGAAGAAATTGCAGCTCAGTACCAGTCCTC
*
54552053 TTTTTGATAGGAATGTTGTTGGTGTTTATTCCATTGTCCCCATCTACT
196 TTTTTGATAGGAATGTTGTTGGTGTTTATTCCATTGTCCCCATCCACT
*
54552101 GGAATGTCCAAATCCCATACCCTGAAGATATCCGCTGTTGATGAATTCATCTCTTCTGCAGATAA
1 GGAATGTCCAAATCCCATACCCTGAAGATATCCACTGTTGATGAATTCATCTCTTCTGCAGATAA
*
54552166 GCTTGATTTAACTCCTGAATCAACAGCACTATCCTTTCTTTCATTCTCCTTGTAGGTGGGTTGGA
66 GCTTGATTTAACTCCTGAATCAACAGCACTATCCTTTCTTTCATTCTCCTTGTAGGTGGGTCGGA
* * **
54552231 AAGGATCTCCCCAAAACATTTCAGCGGAGTCTTCCTGAAGAAATTGCAGCTGGGTACCAGTCCTC
131 AAGGATCTCCCCAAAACACTTCAGCGGAATCTTCCTGAAGAAATTGCAGCTCAGTACCAGTCCTC
*
54552296 TTTTTGATAGGAATGTTGTTGGTGTTTATTCCATTGTCTCCATCCACT
196 TTTTTGATAGGAATGTTGTTGGTGTTTATTCCATTGTCCCCATCCACT
54552344 GGAATG
1 GGAATG
54552350 ACAAGAAGAT
Statistics
Matches: 238, Mismatches: 11, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
243 238 1.00
ACGTcount: A:0.24, C:0.24, G:0.19, T:0.33
Consensus pattern (243 bp):
GGAATGTCCAAATCCCATACCCTGAAGATATCCACTGTTGATGAATTCATCTCTTCTGCAGATAA
GCTTGATTTAACTCCTGAATCAACAGCACTATCCTTTCTTTCATTCTCCTTGTAGGTGGGTCGGA
AAGGATCTCCCCAAAACACTTCAGCGGAATCTTCCTGAAGAAATTGCAGCTCAGTACCAGTCCTC
TTTTTGATAGGAATGTTGTTGGTGTTTATTCCATTGTCCCCATCCACT
Found at i:54561560 original size:11 final size:9
Alignment explanation
Indices: 54561536--54561597 Score: 51
Period size: 9 Copynumber: 7.1 Consensus size: 9
54561526 TATTTTCTCA
54561536 TAAAAATAT
1 TAAAAATAT
54561545 TAAAAATAT
1 TAAAAATAT
*
54561554 ATAAAAA-AA
1 -TAAAAATAT
* *
54561563 GAAAAGTA-
1 TAAAAATAT
54561571 TAAAAAT-T
1 TAAAAATAT
54561579 ATAAAAA-AT
1 -TAAAAATAT
54561588 TAAAAATAT
1 TAAAAATAT
54561597 T
1 T
54561598 TTTTAAAAAT
Statistics
Matches: 42, Mismatches: 5, Indels: 12
0.71 0.08 0.20
Matches are distributed among these distances:
8 15 0.36
9 21 0.50
10 6 0.14
ACGTcount: A:0.69, C:0.00, G:0.03, T:0.27
Consensus pattern (9 bp):
TAAAAATAT
Found at i:54561592 original size:25 final size:27
Alignment explanation
Indices: 54561535--54561597 Score: 85
Period size: 25 Copynumber: 2.4 Consensus size: 27
54561525 ATATTTTCTC
54561535 ATAAAAATATTAAAAATATATAAAAAA
1 ATAAAAATATTAAAAATATATAAAAAA
* *
54561562 AGAAAAGTA-TAAAAAT-TATAAAAAA
1 ATAAAAATATTAAAAATATATAAAAAA
*
54561587 TTAAAAATATT
1 ATAAAAATATT
54561598 TTTTAAAAAT
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
25 15 0.50
26 8 0.27
27 7 0.23
ACGTcount: A:0.70, C:0.00, G:0.03, T:0.27
Consensus pattern (27 bp):
ATAAAAATATTAAAAATATATAAAAAA
Found at i:54561789 original size:9 final size:9
Alignment explanation
Indices: 54561535--54561791 Score: 54
Period size: 10 Copynumber: 26.8 Consensus size: 9
54561525 ATATTTTCTC
54561535 ATAAAAA-T
1 ATAAAAATT
54561543 ATTAAAAATAT
1 A-TAAAAAT-T
54561554 ATAAAAA--
1 ATAAAAATT
*
54561561 A-AGAAAAGT
1 ATA-AAAATT
54561570 ATAAAAATT
1 ATAAAAATT
54561579 ATAAAAAATT
1 AT-AAAAATT
54561589 A-AAAATATTTT
1 ATAAAA-A--TT
*
54561600 TTAAAAATACT
1 ATAAAAAT--T
*
54561611 ATTAAAATT
1 ATAAAAATT
*
54561620 A-ACATATACTT
1 ATA-A-A-AATT
*
54561631 ATAAATATT
1 ATAAAAATT
54561640 ATTAAAAATCT
1 A-TAAAAAT-T
*
54561651 AGT-AAACTT
1 A-TAAAAATT
54561660 -TAATAAATT
1 ATAA-AAATT
54561669 ATAAAAAATT
1 AT-AAAAATT
54561679 AATAAAAAATT
1 -AT-AAAAATT
*
54561690 -TAAAATTT
1 ATAAAAATT
54561698 CATAAAAACGTT
1 -ATAAAAA--TT
54561710 -T-AAAATT
1 ATAAAAATT
*
54561717 CTTAAAACAATT
1 -AT-AAA-AATT
*
54561729 ATAATAAATC
1 ATAA-AAATT
54561739 ATAAAAA-T
1 ATAAAAATT
*
54561747 ATTTAAAA-T
1 A-TAAAAATT
*
54561756 ATTAAAATT
1 ATAAAAATT
*
54561765 GATATAAATGT
1 -ATAAAAAT-T
54561776 ATAAAAATT
1 ATAAAAATT
54561785 ATAAAAA
1 ATAAAAA
54561792 AAATCATAAA
Statistics
Matches: 189, Mismatches: 21, Indels: 77
0.66 0.07 0.27
Matches are distributed among these distances:
6 1 0.01
7 8 0.04
8 19 0.10
9 52 0.28
10 61 0.32
11 37 0.20
12 11 0.06
ACGTcount: A:0.60, C:0.04, G:0.02, T:0.34
Consensus pattern (9 bp):
ATAAAAATT
Found at i:54562466 original size:9 final size:10
Alignment explanation
Indices: 54562448--54562561 Score: 50
Period size: 10 Copynumber: 11.9 Consensus size: 10
54562438 TTTATACGTT
54562448 TTTTATAATA
1 TTTTATAATA
54562458 TTTTA-AATA
1 TTTTATAATA
*
54562467 TGTTT-TATTAA
1 T-TTTATAAT-A
*
54562478 TTTTATAAAA
1 TTTTATAATA
54562488 TTTTATAACTA
1 TTTTATAA-TA
54562499 --TTA-ACAT-
1 TTTTATA-ATA
*
54562506 TTTTATAATC
1 TTTTATAATA
*
54562516 TTATATTAAT-
1 TTTTA-TAATA
* *
54562526 TATAATAATA
1 TTTTATAATA
54562536 -TTT-TAATA
1 TTTTATAATA
*
54562544 TTTAATAAT-
1 TTTTATAATA
54562553 TTTTATAAT
1 TTTTATAAT
54562562 TTTGTCCTGA
Statistics
Matches: 78, Mismatches: 12, Indels: 29
0.66 0.10 0.24
Matches are distributed among these distances:
8 7 0.09
9 29 0.37
10 33 0.42
11 9 0.12
ACGTcount: A:0.40, C:0.03, G:0.01, T:0.56
Consensus pattern (10 bp):
TTTTATAATA
Found at i:54562562 original size:9 final size:9
Alignment explanation
Indices: 54562416--54562564 Score: 61
Period size: 9 Copynumber: 15.4 Consensus size: 9
54562406 TTTTTTTTAT
54562416 TTTTTATAA
1 TTTTTATAA
*
54562425 GTTTTTAAGAA
1 -TTTTT-ATAA
*
54562436 TTTTTATACGT
1 TTTTTATA--A
54562447 TTTTTATAA
1 TTTTTATAA
*
54562456 TATTTTAAATA
1 T-TTTTATA-A
54562467 TGTTTTATTAA
1 T-TTTTA-TAA
54562478 -TTTTATAAA
1 TTTTTAT-AA
*
54562487 ATTTTATAA
1 TTTTTATAA
* *
54562496 CTATTA-ACA
1 TTTTTATA-A
54562505 TTTTTATAA
1 TTTTTATAA
*
54562514 TCTTATATTAA
1 T-TTTTA-TAA
* *
54562525 TTATAATAA
1 TTTTTATAA
*
54562534 TATTT-TAA
1 TTTTTATAA
*
54562542 TATTTAATAA
1 T-TTTTATAA
54562552 TTTTTATAA
1 TTTTTATAA
54562561 TTTT
1 TTTT
54562565 GTCCTGATAT
Statistics
Matches: 104, Mismatches: 21, Indels: 29
0.68 0.14 0.19
Matches are distributed among these distances:
8 6 0.06
9 41 0.39
10 33 0.32
11 23 0.22
12 1 0.01
ACGTcount: A:0.37, C:0.03, G:0.03, T:0.58
Consensus pattern (9 bp):
TTTTTATAA
Found at i:54563574 original size:20 final size:21
Alignment explanation
Indices: 54563541--54563587 Score: 62
Period size: 19 Copynumber: 2.3 Consensus size: 21
54563531 AAAAATTACT
*
54563541 ATAAAATTATTAAAATATTTC
1 ATAAAAATATTAAAATATTTC
54563562 ATAAAAATA-TAAAATA-TTC
1 ATAAAAATATTAAAATATTTC
*
54563581 TTAAAAA
1 ATAAAAA
54563588 ACCTAAAATT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 9 0.38
20 7 0.29
21 8 0.33
ACGTcount: A:0.60, C:0.04, G:0.00, T:0.36
Consensus pattern (21 bp):
ATAAAAATATTAAAATATTTC
Found at i:54563588 original size:20 final size:20
Alignment explanation
Indices: 54563541--54563579 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
54563531 AAAAATTACT
*
54563541 ATAAAATTATTAAAATATTTC
1 ATAAAAATA-TAAAATATTTC
54563562 ATAAAAATATAAAATATT
1 ATAAAAATATAAAATATT
54563580 CTTAAAAAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (20 bp):
ATAAAAATATAAAATATTTC
Found at i:54566221 original size:18 final size:18
Alignment explanation
Indices: 54566200--54566242 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
54566190 TATTCATCTA
**
54566200 AACCCAAGTATTCAACCC
1 AACCCAAGTACCCAACCC
*
54566218 AACCCAATTACCCAACCC
1 AACCCAAGTACCCAACCC
54566236 AACCCAA
1 AACCCAA
54566243 TCATAAAATT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.42, C:0.44, G:0.02, T:0.12
Consensus pattern (18 bp):
AACCCAAGTACCCAACCC
Found at i:54566367 original size:9 final size:9
Alignment explanation
Indices: 54566350--54566425 Score: 93
Period size: 9 Copynumber: 8.4 Consensus size: 9
54566340 GTAGTGATTC
*
54566350 AATTTGGTT
1 AATTCGGTT
54566359 AATTCGGTT
1 AATTCGGTT
*
54566368 AATTCGGGT
1 AATTCGGTT
54566377 AATTCGAG-T
1 AATTCG-GTT
54566386 AATTCGGTT
1 AATTCGGTT
54566395 AATTCAGG-T
1 AATTC-GGTT
*
54566404 AATTCGGTC
1 AATTCGGTT
54566413 AATTCGGTT
1 AATTCGGTT
54566422 AATT
1 AATT
54566426 TTTAACCAAA
Statistics
Matches: 59, Mismatches: 4, Indels: 8
0.83 0.06 0.11
Matches are distributed among these distances:
8 3 0.05
9 53 0.90
10 3 0.05
ACGTcount: A:0.26, C:0.11, G:0.22, T:0.41
Consensus pattern (9 bp):
AATTCGGTT
Found at i:54566388 original size:27 final size:26
Alignment explanation
Indices: 54566358--54566425 Score: 109
Period size: 27 Copynumber: 2.5 Consensus size: 26
54566348 TCAATTTGGT
*
54566358 TAATTCGGTTAATTCGGGTAATTCGAG
1 TAATTCGGTTAATTCAGGTAATTCG-G
54566385 TAATTCGGTTAATTCAGGTAATTCGG
1 TAATTCGGTTAATTCAGGTAATTCGG
54566411 TCAATTCGGTTAATT
1 T-AATTCGGTTAATT
54566426 TTTAACCAAA
Statistics
Matches: 39, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
26 2 0.05
27 37 0.95
ACGTcount: A:0.26, C:0.12, G:0.22, T:0.40
Consensus pattern (26 bp):
TAATTCGGTTAATTCAGGTAATTCGG
Found at i:54578877 original size:46 final size:46
Alignment explanation
Indices: 54578779--54579030 Score: 393
Period size: 46 Copynumber: 5.5 Consensus size: 46
54578769 TACGTATGAT
* *
54578779 CACTTATCAC-TTGTC-CCTAATCAGATAAGTGTAGCT-AGGCTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGGCTAC
*
54578822 CACTTATCACTTTGTCACTTGATCAGGTAAGTGTAGCTAAGGCTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGGCTAC
* *
54578868 CACTTATCACTTTGTCACTTGATCAAATAAGTGTAGCTAAGGCTAA
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGGCTAC
54578914 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGGCTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGGCTAC
* **
54578960 CACTTATCACTTTCTCACTTGATCAGATAAGTGTAGCTAAAACTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGGCTAC
* *
54579006 CACTTATCACTTTATCTCTTGATCA
1 CACTTATCACTTTGTCACTTGATCA
54579031 AAAGTACTTA
Statistics
Matches: 193, Mismatches: 13, Indels: 3
0.92 0.06 0.01
Matches are distributed among these distances:
43 10 0.05
44 5 0.03
45 18 0.09
46 160 0.83
ACGTcount: A:0.29, C:0.23, G:0.15, T:0.33
Consensus pattern (46 bp):
CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGGCTAC
Found at i:54581698 original size:23 final size:23
Alignment explanation
Indices: 54581672--54581793 Score: 172
Period size: 23 Copynumber: 5.3 Consensus size: 23
54581662 ATAAGTGCAA
54581672 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
*
54581695 CACTGTTATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
* * *
54581718 CACTAAAATGTAGCTGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
*
54581741 CACTGTTATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
* * *
54581764 CACTAAAACGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
54581787 CACTGAT
1 CACTGAT
54581794 CAATAACACT
Statistics
Matches: 84, Mismatches: 15, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 84 1.00
ACGTcount: A:0.32, C:0.26, G:0.20, T:0.22
Consensus pattern (23 bp):
CACTGATATGTAGCCGAAGCTAC
Found at i:54581746 original size:46 final size:46
Alignment explanation
Indices: 54581679--54581791 Score: 208
Period size: 46 Copynumber: 2.5 Consensus size: 46
54581669 CAACACTGAT
54581679 ATGTAGCCGAAGCTACCACTGTTATGTAGCCGAAGCTACCACTAAA
1 ATGTAGCCGAAGCTACCACTGTTATGTAGCCGAAGCTACCACTAAA
*
54581725 ATGTAGCTGAAGCTACCACTGTTATGTAGCCGAAGCTACCACTAAA
1 ATGTAGCCGAAGCTACCACTGTTATGTAGCCGAAGCTACCACTAAA
*
54581771 ACGTAGCCGAAGCTACCACTG
1 ATGTAGCCGAAGCTACCACTG
54581792 ATCAATAACA
Statistics
Matches: 64, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
46 64 1.00
ACGTcount: A:0.32, C:0.27, G:0.20, T:0.21
Consensus pattern (46 bp):
ATGTAGCCGAAGCTACCACTGTTATGTAGCCGAAGCTACCACTAAA
Found at i:54591681 original size:78 final size:78
Alignment explanation
Indices: 54591552--54591703 Score: 277
Period size: 78 Copynumber: 1.9 Consensus size: 78
54591542 AATCCAAATC
*
54591552 TGATAAGTTTGAGGCGAAGTGTGCGGTGCAAAACGGCACATGTTCATGGAAAATCTACGCCTCGT
1 TGATAAGTTTGAGGCGAAGTGTGCGGTGCAAAACGACACATGTTCATGGAAAATCTACGCCTCGT
54591617 TAAGGAAAAAGAT
66 TAAGGAAAAAGAT
* *
54591630 TGATAAGTTTGAGGCGAAGTGTGCGGTGGAAGACGACACATGTTCATGGAAAATCTACGCCTCGT
1 TGATAAGTTTGAGGCGAAGTGTGCGGTGCAAAACGACACATGTTCATGGAAAATCTACGCCTCGT
54591695 TAAGGAAAA
66 TAAGGAAAA
54591704 GGACAGGGTT
Statistics
Matches: 71, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
78 71 1.00
ACGTcount: A:0.33, C:0.15, G:0.29, T:0.23
Consensus pattern (78 bp):
TGATAAGTTTGAGGCGAAGTGTGCGGTGCAAAACGACACATGTTCATGGAAAATCTACGCCTCGT
TAAGGAAAAAGAT
Found at i:54591950 original size:99 final size:99
Alignment explanation
Indices: 54591774--54591971 Score: 378
Period size: 99 Copynumber: 2.0 Consensus size: 99
54591764 TATTGACGGT
*
54591774 TTCTAAATAATACTTTTATTATGTGATGTTGCATTATTTAATGTACTCCGTTTATAGGTGTTTCA
1 TTCTAAATAATACTTTTATTATGTAATGTTGCATTATTTAATGTACTCCGTTTATAGGTGTTTCA
54591839 CAAGATCATCCCAAGATGGATTCAGCTATGTTAG
66 CAAGATCATCCCAAGATGGATTCAGCTATGTTAG
*
54591873 TTCTGAATAATACTTTTATTATGTAATGTTGCATTATTTAATGTACTCCGTTTATAGGTGTTTCA
1 TTCTAAATAATACTTTTATTATGTAATGTTGCATTATTTAATGTACTCCGTTTATAGGTGTTTCA
54591938 CAAGATCATCCCAAGATGGATTCAGCTATGTTAG
66 CAAGATCATCCCAAGATGGATTCAGCTATGTTAG
54591972 CTAGCTTGAT
Statistics
Matches: 97, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
99 97 1.00
ACGTcount: A:0.28, C:0.14, G:0.16, T:0.41
Consensus pattern (99 bp):
TTCTAAATAATACTTTTATTATGTAATGTTGCATTATTTAATGTACTCCGTTTATAGGTGTTTCA
CAAGATCATCCCAAGATGGATTCAGCTATGTTAG
Found at i:54593787 original size:15 final size:15
Alignment explanation
Indices: 54593745--54593845 Score: 52
Period size: 14 Copynumber: 6.9 Consensus size: 15
54593735 ATTTAACTTA
54593745 AGGG-TTAGGGTTTT
1 AGGGTTTAGGGTTTT
** *
54593759 AAAG-TTAAGGTTTT
1 AGGGTTTAGGGTTTT
54593773 AGGGTTTAGGGTTTTT
1 AGGGTTTAGGG-TTTT
** *
54593789 A-AATTTAGGGTTTA
1 AGGGTTTAGGGTTTT
*
54593803 AGGTTTTTA-GG-TTT
1 AGG-GTTTAGGGTTTT
* *
54593817 ATGGTTTATGGTTTTT
1 AGGGTTTA-GGGTTTT
54593833 A-GGTTTAGGGTTT
1 AGGGTTTAGGGTTT
54593846 ATGTTTTGTG
Statistics
Matches: 64, Mismatches: 16, Indels: 14
0.68 0.17 0.15
Matches are distributed among these distances:
13 4 0.06
14 26 0.41
15 21 0.33
16 13 0.20
ACGTcount: A:0.20, C:0.00, G:0.31, T:0.50
Consensus pattern (15 bp):
AGGGTTTAGGGTTTT
Found at i:54593795 original size:22 final size:22
Alignment explanation
Indices: 54593770--54594018 Score: 144
Period size: 22 Copynumber: 10.8 Consensus size: 22
54593760 AAGTTAAGGT
*
54593770 TTTAGGGTTTAGGGTTTTTAAA
1 TTTAGGGTTTAGGGTTTTTAAG
* *
54593792 TTTAGGGTTTAAGGTTTTTAGG
1 TTTAGGGTTTAGGGTTTTTAAG
* * *
54593814 TTTATGGTTTATGGTTTTTAGG
1 TTTAGGGTTTAGGGTTTTTAAG
* * *
54593836 TTTAGGGTTTATGTTTTGTGGTTTTTAA
1 TTTAGGGTTTA-G----G-GTTTTTAAG
* * *
54593864 GTTAAGGGTTAGGGTTTTTAAG
1 TTTAGGGTTTAGGGTTTTTAAG
*
54593886 TTTAAGGG-TTGGGGTTTTTAAG
1 TTT-AGGGTTTAGGGTTTTTAAG
*
54593908 TTTAGGGTTTAGGG-TTTAAAG
1 TTTAGGGTTTAGGGTTTTTAAG
* * *
54593929 TTTTTAAGTTTAAGGTTT-GGGGTTTTTAA
1 --TTT-AG-----GGTTTAGGGTTTTTAAG
* ** *
54593958 GTTAGGGTTTAATGTTTTTATG
1 TTTAGGGTTTAGGGTTTTTAAG
*
54593980 TTTAAGGTTTAGGGTTTTTAAG
1 TTTAGGGTTTAGGGTTTTTAAG
54594002 TTTAGGGTTTAGGGTTT
1 TTTAGGGTTTAGGGTTT
54594019 AAGGTTTTTA
Statistics
Matches: 171, Mismatches: 38, Indels: 36
0.70 0.16 0.15
Matches are distributed among these distances:
21 15 0.09
22 116 0.68
23 7 0.04
24 2 0.01
26 2 0.01
27 4 0.02
28 16 0.09
29 9 0.05
ACGTcount: A:0.19, C:0.00, G:0.30, T:0.51
Consensus pattern (22 bp):
TTTAGGGTTTAGGGTTTTTAAG
Found at i:54593802 original size:29 final size:29
Alignment explanation
Indices: 54593745--54593808 Score: 78
Period size: 29 Copynumber: 2.2 Consensus size: 29
54593735 ATTTAACTTA
*
54593745 AGGG-TTAGGGTTTTAAAGTTAAGGTTTT
1 AGGGTTTAGGGTTTTAAAGTTAAGGGTTT
*
54593773 AGGGTTTAGGGTTTTTAAA-TTTAGGGTTT
1 AGGGTTTAGGG-TTTTAAAGTTAAGGGTTT
*
54593802 AAGGTTT
1 AGGGTTT
54593809 TTAGGTTTAT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
28 4 0.13
29 20 0.65
30 7 0.23
ACGTcount: A:0.23, C:0.00, G:0.31, T:0.45
Consensus pattern (29 bp):
AGGGTTTAGGGTTTTAAAGTTAAGGGTTT
Found at i:54593841 original size:6 final size:7
Alignment explanation
Indices: 54593792--54593859 Score: 55
Period size: 7 Copynumber: 9.4 Consensus size: 7
54593782 GGTTTTTAAA
*
54593792 TTTAGGG
1 TTTATGG
*
54593799 TTTAAGG
1 TTTATGG
*
54593806 TTTTTAGG
1 TTTAT-GG
54593814 TTTATGG
1 TTTATGG
54593821 TTTATGG
1 TTTATGG
*
54593828 TTTTTAGG
1 TTTAT-GG
*
54593836 TTTAGGG
1 TTTATGG
*
54593843 TTTATGT
1 TTTATGG
*
54593850 TTTGTGG
1 TTTATGG
54593857 TTT
1 TTT
54593860 TTAAGTTAAG
Statistics
Matches: 48, Mismatches: 11, Indels: 4
0.76 0.17 0.06
Matches are distributed among these distances:
7 37 0.77
8 11 0.23
ACGTcount: A:0.13, C:0.00, G:0.29, T:0.57
Consensus pattern (7 bp):
TTTATGG
Found at i:54593844 original size:29 final size:29
Alignment explanation
Indices: 54593808--54593873 Score: 89
Period size: 29 Copynumber: 2.3 Consensus size: 29
54593798 GTTTAAGGTT
*
54593808 TTTA-GGTTTATGGTTTATGGTTTTTAGG
1 TTTAGGGTTTATGGTTTATGGTTTTTAAG
* *
54593836 TTTAGGGTTTATGTTTTGTGGTTTTTAAG
1 TTTAGGGTTTATGGTTTATGGTTTTTAAG
*
54593865 TTAAGGGTT
1 TTTAGGGTT
54593874 AGGGTTTTTA
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
28 4 0.12
29 29 0.88
ACGTcount: A:0.15, C:0.00, G:0.29, T:0.56
Consensus pattern (29 bp):
TTTAGGGTTTATGGTTTATGGTTTTTAAG
Found at i:54593880 original size:29 final size:29
Alignment explanation
Indices: 54593812--54593881 Score: 72
Period size: 29 Copynumber: 2.4 Consensus size: 29
54593802 AAGGTTTTTA
* * *
54593812 GGTTTATGG-TTTATGGTTTTTAGGTTTAG
1 GGTTTA-GGTTTTGTGGTTTTTAAGTTAAG
*
54593841 GGTTTATGTTTTGTGGTTTTTAAGTTAAG
1 GGTTTAGGTTTTGTGGTTTTTAAGTTAAG
54593870 GG-TTAGGGTTTT
1 GGTTTA-GGTTTT
54593882 TAAGTTTAAG
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
28 4 0.12
29 30 0.88
ACGTcount: A:0.14, C:0.00, G:0.31, T:0.54
Consensus pattern (29 bp):
GGTTTAGGTTTTGTGGTTTTTAAGTTAAG
Found at i:54593903 original size:51 final size:51
Alignment explanation
Indices: 54593859--54594101 Score: 232
Period size: 51 Copynumber: 5.1 Consensus size: 51
54593849 TTTTGTGGTT
*
54593859 TTTA-AGTTAAGGG-TTAGGGTTTTTAAGTTTAAGGGTTGGGGTTTTTAAG
1 TTTAGAGTTAAGGGTTTAAGGTTTTTAAGTTTAAGGGTTGGGGTTTTTAAG
* * * *
54593908 TTTAGGGTTTAGGGTTTAAAGTTTTTAAGTTTAAGGTTTGGGG---TT---
1 TTTAGAGTTAAGGGTTTAAGGTTTTTAAGTTTAAGGGTTGGGGTTTTTAAG
* * * *
54593953 TTTA-AGTT-AGGGTTTAATGTTTTTATGTTTAAGGTTTAGGGTTTTTAAG
1 TTTAGAGTTAAGGGTTTAAGGTTTTTAAGTTTAAGGGTTGGGGTTTTTAAG
* * *
54594002 TTTAGGGTTTAGGGTTTAAGGTTTTTAAGTTTAAGGTTTGGGGTTTTTAAG
1 TTTAGAGTTAAGGGTTTAAGGTTTTTAAGTTTAAGGGTTGGGGTTTTTAAG
* * *
54594053 --T----TT-AGGGTTTAAGGTTTTTATGTTTAAGGTTTAGGGTTTTTAAG
1 TTTAGAGTTAAGGGTTTAAGGTTTTTAAGTTTAAGGGTTGGGGTTTTTAAG
54594097 TTTAG
1 TTTAG
54594102 GGCTTATGGT
Statistics
Matches: 165, Mismatches: 15, Indels: 29
0.79 0.07 0.14
Matches are distributed among these distances:
43 30 0.18
44 42 0.25
45 6 0.04
46 3 0.02
48 2 0.01
49 9 0.05
50 10 0.06
51 63 0.38
ACGTcount: A:0.21, C:0.00, G:0.29, T:0.50
Consensus pattern (51 bp):
TTTAGAGTTAAGGGTTTAAGGTTTTTAAGTTTAAGGGTTGGGGTTTTTAAG
Found at i:54593904 original size:94 final size:93
Alignment explanation
Indices: 54593771--54594191 Score: 414
Period size: 94 Copynumber: 4.6 Consensus size: 93
54593761 AGTTAAGGTT
* * * * * *
54593771 TTAGGGTTTAGGGTTTTTAAATTT-AGGGTTTAAGGTTTTTAGGTTTATGGTTTATGGTTTTTAG
1 TTAGGGTTTAAGGTTTTTAAGTTTAAGGG-TTAGGGTTTTTAAGTTTAGGGTTTATGGTTTTAAG
* * * *
54593835 GTTTAGGGTTTATGTTTTGTGGTTTTTAAG
65 GTTTA-AGTTTAAGGTTTGGGGTTTTTAAG
* * * *
54593865 TTAAGGG-TTAGGGTTTTTAAGTTTAAGGGTTGGGGTTTTTAAGTTTAGGGTTTAGGGTTTAAAG
1 TT-AGGGTTTAAGGTTTTTAAGTTTAAGGGTTAGGGTTTTTAAGTTTAGGGTTTATGGTTTTAAG
*
54593929 TTTTTAAGTTTAAGGTTTGGGGTTTTTAAG
65 -GTTTAAGTTTAAGGTTTGGGGTTTTTAAG
* * * *
54593959 TTAGGGTTTAATGTTTTTATGTTTAAGGTTTAGGGTTTTTAAGTTTAGGGTTTA-GGGTTTAAGG
1 TTAGGGTTTAAGGTTTTTAAGTTTAAGGGTTAGGGTTTTTAAGTTTAGGGTTTATGGTTTTAAGG
54594023 TTTTTAAGTTTAAGGTTTGGGGTTTTTAAG
66 --TTTAAGTTTAAGGTTTGGGGTTTTTAAG
* * * *
54594053 TTTAGGGTTTAAGGTTTTTATGTTTAAGGTTTAGGGTTTTTAAGTTTAGGGCTTATGGTTTTTAG
1 -TTAGGGTTTAAGGTTTTTAAGTTTAAGGGTTAGGGTTTTTAAGTTTAGGGTTTATGGTTTTAAG
54594118 GTTT-AG-----GGTTTGGGGTTTTTAAGG
65 GTTTAAGTTTAAGGTTTGGGGTTTTTAA-G
* * *** * * *
54594142 TAAAGG-TTACCCTTTTTTA-TTTAAGGGTTAAGGTTTTTAAGTTAAGGGTT
1 TTAGGGTTTAAGGTTTTTAAGTTTAAGGGTTAGGGTTTTTAAGTTTAGGGTT
54594192 CGGGTTAGGG
Statistics
Matches: 282, Mismatches: 36, Indels: 26
0.82 0.10 0.08
Matches are distributed among these distances:
86 27 0.10
87 8 0.03
88 20 0.07
89 1 0.00
93 13 0.05
94 141 0.50
95 64 0.23
96 8 0.03
ACGTcount: A:0.20, C:0.01, G:0.29, T:0.50
Consensus pattern (93 bp):
TTAGGGTTTAAGGTTTTTAAGTTTAAGGGTTAGGGTTTTTAAGTTTAGGGTTTATGGTTTTAAGG
TTTAAGTTTAAGGTTTGGGGTTTTTAAG
Found at i:54593989 original size:7 final size:7
Alignment explanation
Indices: 54593979--54594091 Score: 61
Period size: 7 Copynumber: 15.6 Consensus size: 7
54593969 ATGTTTTTAT
54593979 GTTTAAG
1 GTTTAAG
*
54593986 GTTTAGG
1 GTTTAAG
54593993 GTTTTTAA-
1 G--TTTAAG
*
54594001 GTTTAGG
1 GTTTAAG
*
54594008 GTTTAGG
1 GTTTAAG
54594015 GTTTAAG
1 GTTTAAG
54594022 GTTTTTAA-
1 G--TTTAAG
54594030 GTTTAAG
1 GTTTAAG
**
54594037 GTTTGGG
1 GTTTAAG
54594044 GTTTTTAA-
1 G--TTTAAG
*
54594052 GTTTAGG
1 GTTTAAG
54594059 GTTTAAG
1 GTTTAAG
* *
54594066 GTTTTTAT
1 G-TTTAAG
54594074 GTTTAAG
1 GTTTAAG
*
54594081 GTTTAGG
1 GTTTAAG
54594088 GTTT
1 GTTT
54594092 TTAAGTTTAG
Statistics
Matches: 81, Mismatches: 15, Indels: 20
0.70 0.13 0.17
Matches are distributed among these distances:
6 13 0.16
7 48 0.59
8 8 0.10
9 12 0.15
ACGTcount: A:0.19, C:0.00, G:0.30, T:0.50
Consensus pattern (7 bp):
GTTTAAG
Found at i:54593992 original size:29 final size:28
Alignment explanation
Indices: 54593959--54594047 Score: 91
Period size: 29 Copynumber: 3.3 Consensus size: 28
54593949 GGTTTTTAAG
*
54593959 TTAGGGTTTAATGTTTTTATGTTTAAGGT
1 TTAGGGTTTAA-GTTTTTAAGTTTAAGGT
*
54593988 TTA-GG-----GTTTTTAAGTTTAGGGT
1 TTAGGGTTTAAGTTTTTAAGTTTAAGGT
54594010 TTAGGGTTTAAGGTTTTTAAGTTTAAGGT
1 TTAGGGTTTAA-GTTTTTAAGTTTAAGGT
*
54594039 TTGGGGTTT
1 TTAGGGTTT
54594048 TTAAGTTTAG
Statistics
Matches: 49, Mismatches: 4, Indels: 14
0.73 0.06 0.21
Matches are distributed among these distances:
22 18 0.37
23 2 0.04
28 2 0.04
29 27 0.55
ACGTcount: A:0.19, C:0.00, G:0.29, T:0.52
Consensus pattern (28 bp):
TTAGGGTTTAAGTTTTTAAGTTTAAGGT
Found at i:54594033 original size:22 final size:22
Alignment explanation
Indices: 54594008--54594191 Score: 167
Period size: 22 Copynumber: 8.5 Consensus size: 22
54593998 TAAGTTTAGG
54594008 GTTTAGGGTTTAAGGTTTTTAA
1 GTTTAGGGTTTAAGGTTTTTAA
* **
54594030 GTTTAAGGTTTGGGGTTTTTAA
1 GTTTAGGGTTTAAGGTTTTTAA
*
54594052 GTTTAGGGTTTAAGGTTTTTAT
1 GTTTAGGGTTTAAGGTTTTTAA
* *
54594074 GTTTAAGGTTTAGGGTTTTTAA
1 GTTTAGGGTTTAAGGTTTTTAA
* * *
54594096 GTTTAGGGCTTATGGTTTTTAG
1 GTTTAGGGTTTAAGGTTTTTAA
**
54594118 GTTTAGGGTTTGGGGTTTTTAA
1 GTTTAGGGTTTAAGGTTTTTAA
* * * *** *
54594140 GGTAAAGG-TTACCCTTTTTTA
1 GTTTAGGGTTTAAGGTTTTTAA
54594161 -TTTAAGGG-TTAAGGTTTTTAA
1 GTTT-AGGGTTTAAGGTTTTTAA
*
54594182 GTTAAGGGTT
1 GTTTAGGGTT
54594192 CGGGTTAGGG
Statistics
Matches: 125, Mismatches: 34, Indels: 6
0.76 0.21 0.04
Matches are distributed among these distances:
20 1 0.01
21 24 0.19
22 100 0.80
ACGTcount: A:0.20, C:0.02, G:0.29, T:0.49
Consensus pattern (22 bp):
GTTTAGGGTTTAAGGTTTTTAA
Found at i:54594055 original size:15 final size:16
Alignment explanation
Indices: 54593980--54594103 Score: 75
Period size: 15 Copynumber: 7.9 Consensus size: 16
54593970 TGTTTTTATG
54593980 TTTAAGGTTTAGGGTT
1 TTTAAGGTTTAGGGTT
54593996 TTTAA-GTTTAGGG--
1 TTTAAGGTTTAGGGTT
* *
54594009 TTTAGGGTTTAAGGTTTTT
1 TTTAAGGTTT-AGG--GTT
*
54594028 AAGTTTAAGGTTTGGGGTT
1 ---TTTAAGGTTTAGGGTT
54594047 TTTAA-GTTTAGGG--
1 TTTAAGGTTTAGGGTT
*** *
54594060 TTTAAGGTTT-TTATG
1 TTTAAGGTTTAGGGTT
54594075 TTTAAGGTTTAGGGTT
1 TTTAAGGTTTAGGGTT
54594091 TTTAA-GTTTAGGG
1 TTTAAGGTTTAGGG
54594104 CTTATGGTTT
Statistics
Matches: 82, Mismatches: 13, Indels: 27
0.67 0.11 0.22
Matches are distributed among these distances:
13 9 0.11
14 8 0.10
15 36 0.44
16 16 0.20
19 2 0.02
21 2 0.02
22 9 0.11
ACGTcount: A:0.20, C:0.00, G:0.30, T:0.50
Consensus pattern (16 bp):
TTTAAGGTTTAGGGTT
Found at i:54594113 original size:51 final size:49
Alignment explanation
Indices: 54593876--54594140 Score: 285
Period size: 44 Copynumber: 5.7 Consensus size: 49
54593866 TAAGGGTTAG
*
54593876 GGTTTTTAAGTTTAAGGGTTGGGGTTTTTAAGTTTAGGGTTTAGGGTTTAA
1 GGTTTTTAAGTTTAAGGTTTGGGGTTTTTAAGTTTAGGG-TTA-GGTTTAA
*
54593927 AGTTTTTAAGTTTAAGGTTTGGGGTTTTTAAG-TTA--G---GGTTTAA
1 GGTTTTTAAGTTTAAGGTTTGGGGTTTTTAAGTTTAGGGTTAGGTTTAA
* * *
54593970 TGTTTTTATGTTTAAGGTTTAGGGTTTTTAAGTTTAGGGTTTAGGGTTTAA
1 GGTTTTTAAGTTTAAGGTTTGGGGTTTTTAAGTTTAGGG-TTA-GGTTTAA
54594021 GGTTTTTAAGTTTAAGGTTTGGGGTTTTTAAGTTTA--G---GGTTTAA
1 GGTTTTTAAGTTTAAGGTTTGGGGTTTTTAAGTTTAGGGTTAGGTTTAA
* *
54594065 GGTTTTTATGTTTAAGGTTTAGGGTTTTTAAGTTTAGGGCTTA----T--
1 GGTTTTTAAGTTTAAGGTTTGGGGTTTTTAAGTTTAGGG-TTAGGTTTAA
* *
54594109 GGTTTTTAGGTTTAGGGTTTGGGGTTTTTAAG
1 GGTTTTTAAGTTTAAGGTTTGGGGTTTTTAAG
54594141 GTAAAGGTTA
Statistics
Matches: 187, Mismatches: 13, Indels: 35
0.80 0.06 0.15
Matches are distributed among these distances:
43 36 0.19
44 73 0.39
46 3 0.02
48 1 0.01
49 1 0.01
50 3 0.02
51 70 0.37
ACGTcount: A:0.19, C:0.00, G:0.30, T:0.50
Consensus pattern (49 bp):
GGTTTTTAAGTTTAAGGTTTGGGGTTTTTAAGTTTAGGGTTAGGTTTAA
Found at i:54594800 original size:18 final size:18
Alignment explanation
Indices: 54594777--54594814 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
54594767 CTGGGAAAAA
* *
54594777 GATACATATAAGGGTTAG
1 GATACATAAAAGGGCTAG
54594795 GATACATAAAAGGGCTAG
1 GATACATAAAAGGGCTAG
54594813 GA
1 GA
54594815 AACGCACCTG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.42, C:0.08, G:0.29, T:0.21
Consensus pattern (18 bp):
GATACATAAAAGGGCTAG
Found at i:54597076 original size:602 final size:602
Alignment explanation
Indices: 54595932--54597135 Score: 2408
Period size: 602 Copynumber: 2.0 Consensus size: 602
54595922 TGTACCGGCT
54595932 CCGTGACAAGTCCGGCATCAGATAACCTCCAATTAACTGAAGAATGTATGTCCGAACATATCGGA
1 CCGTGACAAGTCCGGCATCAGATAACCTCCAATTAACTGAAGAATGTATGTCCGAACATATCGGA
54595997 TTCTTTCTATTTAGGTTGAATCTTCATCCGGATCTGGGAATGTGTCTCGTAACCAGCCCATCTTG
66 TTCTTTCTATTTAGGTTGAATCTTCATCCGGATCTGGGAATGTGTCTCGTAACCAGCCCATCTTG
54596062 ATCTTACCTCCGTCCATTTTCTCCGGAATAGCGCCCAGAACCTTGTAGCCCACCGCTGGCCAATC
131 ATCTTACCTCCGTCCATTTTCTCCGGAATAGCGCCCAGAACCTTGTAGCCCACCGCTGGCCAATC
54596127 GCTAGATTGGGCAGACCCCGTGACTGGGTACTCGTCCACCGGCAATCCCAATTGCAGGTTGACGT
196 GCTAGATTGGGCAGACCCCGTGACTGGGTACTCGTCCACCGGCAATCCCAATTGCAGGTTGACGT
54596192 CTTCCAAAGTGACAGTGCACTCTCTAAATGGAAGATGGAATGTGTGCGTCTCGAGTCTCCACCTC
261 CTTCCAAAGTGACAGTGCACTCTCTAAATGGAAGATGGAATGTGTGCGTCTCGAGTCTCCACCTC
54596257 TCGATCAACGCACTGATTAGTTTCAGGTCCACCTTGCATCCCCGGCCTACCGTCGCCACGTACCA
326 TCGATCAACGCACTGATTAGTTTCAGGTCCACCTTGCATCCCCGGCCTACCGTCGCCACGTACCA
54596322 AAAACCCGCTTCCCGCAGGTAGTTCTCTACCAACGGTGATGGAGGAGCATGCATAGTCTGGATTT
391 AAAACCCGCTTCCCGCAGGTAGTTCTCTACCAACGGTGATGGAGGAGCATGCATAGTCTGGATTT
54596387 TGCATTCCAATACCCGATCTATAGACTTTTATAACAAATAATAAATTAATAATTATCTAAAAATG
456 TGCATTCCAATACCCGATCTATAGACTTTTATAACAAATAATAAATTAATAATTATCTAAAAATG
54596452 CATAAATAAAAAAATCTTAAATAATATTTAAAAATTAAATTTAACACTTACCATCTTCATTTGTT
521 CATAAATAAAAAAATCTTAAATAATATTTAAAAATTAAATTTAACACTTACCATCTTCATTTGTT
54596517 CTACGGATATGTGGTGA
586 CTACGGATATGTGGTGA
54596534 CCGTGACAAGTCCGGCATCAGATAACCTCCAATTAACTGAAGAATGTATGTCCGAACATATCGGA
1 CCGTGACAAGTCCGGCATCAGATAACCTCCAATTAACTGAAGAATGTATGTCCGAACATATCGGA
54596599 TTCTTTCTATTTAGGTTGAATCTTCATCCGGATCTGGGAATGTGTCTCGTAACCAGCCCATCTTG
66 TTCTTTCTATTTAGGTTGAATCTTCATCCGGATCTGGGAATGTGTCTCGTAACCAGCCCATCTTG
54596664 ATCTTACCTCCGTCCATTTTCTCCGGAATAGCGCCCAGAACCTTGTAGCCCACCGCTGGCCAATC
131 ATCTTACCTCCGTCCATTTTCTCCGGAATAGCGCCCAGAACCTTGTAGCCCACCGCTGGCCAATC
54596729 GCTAGATTGGGCAGACCCCGTGACTGGGTACTCGTCCACCGGCAATCCCAATTGCAGGTTGACGT
196 GCTAGATTGGGCAGACCCCGTGACTGGGTACTCGTCCACCGGCAATCCCAATTGCAGGTTGACGT
54596794 CTTCCAAAGTGACAGTGCACTCTCTAAATGGAAGATGGAATGTGTGCGTCTCGAGTCTCCACCTC
261 CTTCCAAAGTGACAGTGCACTCTCTAAATGGAAGATGGAATGTGTGCGTCTCGAGTCTCCACCTC
54596859 TCGATCAACGCACTGATTAGTTTCAGGTCCACCTTGCATCCCCGGCCTACCGTCGCCACGTACCA
326 TCGATCAACGCACTGATTAGTTTCAGGTCCACCTTGCATCCCCGGCCTACCGTCGCCACGTACCA
54596924 AAAACCCGCTTCCCGCAGGTAGTTCTCTACCAACGGTGATGGAGGAGCATGCATAGTCTGGATTT
391 AAAACCCGCTTCCCGCAGGTAGTTCTCTACCAACGGTGATGGAGGAGCATGCATAGTCTGGATTT
54596989 TGCATTCCAATACCCGATCTATAGACTTTTATAACAAATAATAAATTAATAATTATCTAAAAATG
456 TGCATTCCAATACCCGATCTATAGACTTTTATAACAAATAATAAATTAATAATTATCTAAAAATG
54597054 CATAAATAAAAAAATCTTAAATAATATTTAAAAATTAAATTTAACACTTACCATCTTCATTTGTT
521 CATAAATAAAAAAATCTTAAATAATATTTAAAAATTAAATTTAACACTTACCATCTTCATTTGTT
54597119 CTACGGATATGTGGTGA
586 CTACGGATATGTGGTGA
54597136 TTATCAAGAC
Statistics
Matches: 602, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
602 602 1.00
ACGTcount: A:0.28, C:0.25, G:0.18, T:0.28
Consensus pattern (602 bp):
CCGTGACAAGTCCGGCATCAGATAACCTCCAATTAACTGAAGAATGTATGTCCGAACATATCGGA
TTCTTTCTATTTAGGTTGAATCTTCATCCGGATCTGGGAATGTGTCTCGTAACCAGCCCATCTTG
ATCTTACCTCCGTCCATTTTCTCCGGAATAGCGCCCAGAACCTTGTAGCCCACCGCTGGCCAATC
GCTAGATTGGGCAGACCCCGTGACTGGGTACTCGTCCACCGGCAATCCCAATTGCAGGTTGACGT
CTTCCAAAGTGACAGTGCACTCTCTAAATGGAAGATGGAATGTGTGCGTCTCGAGTCTCCACCTC
TCGATCAACGCACTGATTAGTTTCAGGTCCACCTTGCATCCCCGGCCTACCGTCGCCACGTACCA
AAAACCCGCTTCCCGCAGGTAGTTCTCTACCAACGGTGATGGAGGAGCATGCATAGTCTGGATTT
TGCATTCCAATACCCGATCTATAGACTTTTATAACAAATAATAAATTAATAATTATCTAAAAATG
CATAAATAAAAAAATCTTAAATAATATTTAAAAATTAAATTTAACACTTACCATCTTCATTTGTT
CTACGGATATGTGGTGA
Found at i:54597334 original size:11 final size:12
Alignment explanation
Indices: 54597318--54597369 Score: 67
Period size: 11 Copynumber: 4.6 Consensus size: 12
54597308 ATTAACTATG
54597318 AATTTGAGA-GA
1 AATTTGAGAGGA
54597329 AATTTG-GAAGGA
1 AATTTGAG-AGGA
54597341 AA-TTGAGAGGA
1 AATTTGAGAGGA
54597352 AA-TTGAGAGGA
1 AATTTGAGAGGA
54597363 AATTTGA
1 AATTTGA
54597370 CAGAGGATTT
Statistics
Matches: 37, Mismatches: 0, Indels: 7
0.84 0.00 0.16
Matches are distributed among these distances:
10 1 0.03
11 27 0.73
12 9 0.24
ACGTcount: A:0.44, C:0.00, G:0.31, T:0.25
Consensus pattern (12 bp):
AATTTGAGAGGA
Found at i:54598030 original size:11 final size:11
Alignment explanation
Indices: 54598014--54598069 Score: 53
Period size: 11 Copynumber: 5.0 Consensus size: 11
54598004 ATTAAATATG
54598014 AATTTGAGAGA
1 AATTTGAGAGA
*
54598025 AATTTG-GAAGG
1 AATTTGAG-AGA
54598036 AATTTGAGAGGA
1 AATTTGAGA-GA
*
54598048 AA-TTGAAAGGA
1 AATTTGAGA-GA
54598059 AATTTGAGAGA
1 AATTTGAGAGA
54598070 GGATTTGTTT
Statistics
Matches: 37, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
10 1 0.03
11 27 0.73
12 9 0.24
ACGTcount: A:0.45, C:0.00, G:0.30, T:0.25
Consensus pattern (11 bp):
AATTTGAGAGA
Found at i:54598062 original size:23 final size:23
Alignment explanation
Indices: 54598013--54598068 Score: 80
Period size: 22 Copynumber: 2.5 Consensus size: 23
54598003 GATTAAATAT
*
54598013 GAATTTGAGA-GAAATTTGGAAG
1 GAATTTGAGAGGAAATTTGAAAG
54598035 GAATTTGAGAGGAAA-TTGAAAG
1 GAATTTGAGAGGAAATTTGAAAG
54598057 GAAATTTGAGAG
1 G-AATTTGAGAG
54598069 AGGATTTGTT
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
22 17 0.55
23 14 0.45
ACGTcount: A:0.43, C:0.00, G:0.32, T:0.25
Consensus pattern (23 bp):
GAATTTGAGAGGAAATTTGAAAG
Found at i:54598296 original size:40 final size:40
Alignment explanation
Indices: 54598247--54598324 Score: 93
Period size: 40 Copynumber: 1.9 Consensus size: 40
54598237 GACGTGGCAA
* * * *
54598247 CAAATCGCGCTCTCAAGGCCGCGCTTTGTTGCCACATCAT
1 CAAAGCGCGCTCACAAGGCCGCGCTTTGCTGACACATCAT
* **
54598287 CAAAGCGCGCTGACGTGGCCGCGCTTTGCTGACACATC
1 CAAAGCGCGCTCACAAGGCCGCGCTTTGCTGACACATC
54598325 CCCTGACATC
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
40 31 1.00
ACGTcount: A:0.19, C:0.35, G:0.24, T:0.22
Consensus pattern (40 bp):
CAAAGCGCGCTCACAAGGCCGCGCTTTGCTGACACATCAT
Found at i:54602329 original size:3 final size:3
Alignment explanation
Indices: 54602323--54602360 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
54602313 TTCAAAGCAA
54602323 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
54602361 GATTCTTGAG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:54602542 original size:20 final size:21
Alignment explanation
Indices: 54602484--54602547 Score: 62
Period size: 19 Copynumber: 3.1 Consensus size: 21
54602474 TTTATATATT
54602484 TTTTTAAAAATATAAATTTTGAA
1 TTTTTAAAAAT-T-AATTTTGAA
* * *
54602507 TTTTTTATAATT-ATTTTTAA
1 TTTTTAAAAATTAATTTTGAA
54602527 -TTTTAAAAATTAA-TTTGAA
1 TTTTTAAAAATTAATTTTGAA
54602546 TT
1 TT
54602548 ATTTTGTAAT
Statistics
Matches: 33, Mismatches: 6, Indels: 7
0.72 0.13 0.15
Matches are distributed among these distances:
19 14 0.42
20 9 0.27
22 1 0.03
23 9 0.27
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (21 bp):
TTTTTAAAAATTAATTTTGAA
Found at i:54607043 original size:44 final size:44
Alignment explanation
Indices: 54606905--54607584 Score: 237
Period size: 44 Copynumber: 15.7 Consensus size: 44
54606895 TATTTCTCGG
* * **
54606905 GTCTACTCCACTGCAACTTCAGG-GAGATAAGA-TTATCGGCTTTA
1 GTCTGCTCCACTGCAACTTCAGGAGAGATAAGACTTGT-TAC-TTA
* * * * * ** *
54606949 ATTTGCTCCACTGCAACTTTAAG-GAGATAAGATTTGCCATCTCCA
1 GTCTGCTCCACTGCAACTTCAGGAGAGATAAGACTTGTTA-CT-TA
54606994 GTCTGC-CTCACTGCAACTTCAGGAG-GATAAGACTTGTTTACTTA
1 GTCTGCTC-CACTGCAACTTCAGGAGAGATAAGACTTG-TTACTTA
* * * * *
54607038 GTCTGCTCCATTGCAACTTCAGG-GAGATAAGACTAGATGC-GA
1 GTCTGCTCCACTGCAACTTCAGGAGAGATAAGACTTGTTACTTA
* * **
54607080 -TCTGCT-CTCTGCAAATTCA-GAGAGATAAGATCCAAGGTT--TTA
1 GTCTGCTCCACTGCAACTTCAGGAGAGATAAGA--C-TTGTTACTTA
* * * * **
54607122 ATCCGCTCCACTGCAACTTCAGG-GAGATAGGA-TTATCGGCTTTA
1 GTCTGCTCCACTGCAACTTCAGGAGAGATAAGACTTGT-TAC-TTA
* * * *
54607166 ATCTGCTCCACTGCAACCTCAGG-GAGATAAGATTTGTCATCTTCA
1 GTCTGCTCCACTGCAACTTCAGGAGAGATAAGACTTGTTA-CTT-A
*
54607211 GTCTGC-CTCATTGCAACTTCAGGAG-GATAAGACTTGCTTACTTA
1 GTCTGCTC-CACTGCAACTTCAGGAGAGATAAGACTTG-TTACTTA
* * * * * *
54607255 GTCTGCTCCACTGCAACTCCAAG-GAGATAAGACTAGATGC-GA
1 GTCTGCTCCACTGCAACTTCAGGAGAGATAAGACTTGTTACTTA
* * *
54607297 -TCTGCT-CTCTGCATCTTCA-GAGAGATAAGATCTAAGGTT--TTA
1 GTCTGCTCCACTGCAACTTCAGGAGAGATAAGA-CT--TGTTACTTA
* * * * **
54607339 ATCCGCTCCACTGCAACTTCAGG-GAGATAGGA-TTATCGGCTTTA
1 GTCTGCTCCACTGCAACTTCAGGAGAGATAAGACTTGT-TAC-TTA
* * * **
54607383 ATCTGCTCCACTACAACTTCAGG-GAGATAAGATTTGCCATCTTCA
1 GTCTGCTCCACTGCAACTTCAGGAGAGATAAGACTTGTTA-CTT-A
* * * * *
54607428 ATCTGC-CTCACTGTAGCTTCAGAAG-GATAAGACTAGCTTACTTA
1 GTCTGCTC-CACTGCAACTTCAGGAGAGATAAGACTTG-TTACTTA
* * * * * * *
54607472 GTCTGCTCCACTACAACTCCAAGA-AGATAAGACTAGATGC-GA
1 GTCTGCTCCACTGCAACTTCAGGAGAGATAAGACTTGTTACTTA
* * **
54607514 -TCTGCT-CTCTGCATCTTCA-GAGAGATAAGATCCAAGGTT--TTA
1 GTCTGCTCCACTGCAACTTCAGGAGAGATAAGA--C-TTGTTACTTA
*
54607556 ATCTGCTCCACTGCAACTTCAGG-GAGATA
1 GTCTGCTCCACTGCAACTTCAGGAGAGATA
54607585 GGATTATCGG
Statistics
Matches: 476, Mismatches: 104, Indels: 112
0.69 0.15 0.16
Matches are distributed among these distances:
39 4 0.01
40 57 0.12
41 20 0.04
42 9 0.02
43 30 0.06
44 241 0.51
45 108 0.23
46 7 0.01
ACGTcount: A:0.28, C:0.24, G:0.20, T:0.28
Consensus pattern (44 bp):
GTCTGCTCCACTGCAACTTCAGGAGAGATAAGACTTGTTACTTA
Found at i:54607285 original size:217 final size:217
Alignment explanation
Indices: 54606910--54607595 Score: 1156
Period size: 217 Copynumber: 3.2 Consensus size: 217
54606900 CTCGGGTCTA
* * * *
54606910 CTCCACTGCAACTTCAGGGAGATAAGATTATCGGCTTTAATTTGCTCCACTGCAACTTTAAGGAG
1 CTCCACTGCAACTTCAGGGAGATAGGATTATCGGCTTTAATCTGCTCCACTGCAACTTCAGGGAG
* *
54606975 ATAAGATTTGCCATCTCCAGTCTGCCTCACTGCAACTTCAGGAGGATAAGACTTGTTTACTTAGT
66 ATAAGATTTGCCATCTTCAGTCTGCCTCACTGCAACTTCAGGAGGATAAGACTTGCTTACTTAGT
* * * **
54607040 CTGCTCCATTGCAACTTCAGGGAGATAAGACTAGATGCGATCTGCTCTCTGCAAATTCAGAGAGA
131 CTGCTCCACTGCAACTCCAAGGAGATAAGACTAGATGCGATCTGCTCTCTGCATCTTCAGAGAGA
54607105 TAAGATCCAAGGTTTTAATCCG
196 TAAGATCCAAGGTTTTAATCCG
*
54607127 CTCCACTGCAACTTCAGGGAGATAGGATTATCGGCTTTAATCTGCTCCACTGCAACCTCAGGGAG
1 CTCCACTGCAACTTCAGGGAGATAGGATTATCGGCTTTAATCTGCTCCACTGCAACTTCAGGGAG
* *
54607192 ATAAGATTTGTCATCTTCAGTCTGCCTCATTGCAACTTCAGGAGGATAAGACTTGCTTACTTAGT
66 ATAAGATTTGCCATCTTCAGTCTGCCTCACTGCAACTTCAGGAGGATAAGACTTGCTTACTTAGT
54607257 CTGCTCCACTGCAACTCCAAGGAGATAAGACTAGATGCGATCTGCTCTCTGCATCTTCAGAGAGA
131 CTGCTCCACTGCAACTCCAAGGAGATAAGACTAGATGCGATCTGCTCTCTGCATCTTCAGAGAGA
*
54607322 TAAGATCTAAGGTTTTAATCCG
196 TAAGATCCAAGGTTTTAATCCG
*
54607344 CTCCACTGCAACTTCAGGGAGATAGGATTATCGGCTTTAATCTGCTCCACTACAACTTCAGGGAG
1 CTCCACTGCAACTTCAGGGAGATAGGATTATCGGCTTTAATCTGCTCCACTGCAACTTCAGGGAG
* * * * *
54607409 ATAAGATTTGCCATCTTCAATCTGCCTCACTGTAGCTTCAGAAGGATAAGACTAGCTTACTTAGT
66 ATAAGATTTGCCATCTTCAGTCTGCCTCACTGCAACTTCAGGAGGATAAGACTTGCTTACTTAGT
* *
54607474 CTGCTCCACTACAACTCCAAGAAGATAAGACTAGATGCGATCTGCTCTCTGCATCTTCAGAGAGA
131 CTGCTCCACTGCAACTCCAAGGAGATAAGACTAGATGCGATCTGCTCTCTGCATCTTCAGAGAGA
*
54607539 TAAGATCCAAGGTTTTAATCTG
196 TAAGATCCAAGGTTTTAATCCG
54607561 CTCCACTGCAACTTCAGGGAGATAGGATTATCGGC
1 CTCCACTGCAACTTCAGGGAGATAGGATTATCGGC
54607596 CACCGATCTG
Statistics
Matches: 441, Mismatches: 28, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
217 441 1.00
ACGTcount: A:0.28, C:0.24, G:0.20, T:0.28
Consensus pattern (217 bp):
CTCCACTGCAACTTCAGGGAGATAGGATTATCGGCTTTAATCTGCTCCACTGCAACTTCAGGGAG
ATAAGATTTGCCATCTTCAGTCTGCCTCACTGCAACTTCAGGAGGATAAGACTTGCTTACTTAGT
CTGCTCCACTGCAACTCCAAGGAGATAAGACTAGATGCGATCTGCTCTCTGCATCTTCAGAGAGA
TAAGATCCAAGGTTTTAATCCG
Found at i:54608426 original size:24 final size:28
Alignment explanation
Indices: 54608399--54608453 Score: 82
Period size: 27 Copynumber: 2.1 Consensus size: 28
54608389 AGTGTCTTGA
54608399 AAAGAA-AAAGTA-TT-CAAGAAC-AAC
1 AAAGAATAAAGTATTTACAAGAACAAAC
54608423 AAAGAATAAAGTATTTACAAGAACAAAC
1 AAAGAATAAAGTATTTACAAGAACAAAC
54608451 AAA
1 AAA
54608454 CTCGGTACAA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
24 6 0.22
25 6 0.22
26 2 0.07
27 7 0.26
28 6 0.22
ACGTcount: A:0.64, C:0.11, G:0.11, T:0.15
Consensus pattern (28 bp):
AAAGAATAAAGTATTTACAAGAACAAAC
Found at i:54622736 original size:19 final size:18
Alignment explanation
Indices: 54622701--54622745 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 18
54622691 AAAAATTACT
* * *
54622701 TATAAAAAAATAAATATG
1 TATATAAAAACAAATATA
54622719 TATATAAAAACAACATATA
1 TATATAAAAACAA-ATATA
54622738 TATATAAA
1 TATATAAA
54622746 TCAAAAATAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
18 11 0.48
19 12 0.52
ACGTcount: A:0.64, C:0.04, G:0.02, T:0.29
Consensus pattern (18 bp):
TATATAAAAACAAATATA
Found at i:54624431 original size:21 final size:21
Alignment explanation
Indices: 54624407--54624447 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
54624397 GATAGATAGG
54624407 TAGATAATATAAAATATATAT
1 TAGATAATATAAAATATATAT
** *
54624428 TAGATTTTTTAAAATATATA
1 TAGATAATATAAAATATATA
54624448 ATTTTTTTAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.51, C:0.00, G:0.05, T:0.44
Consensus pattern (21 bp):
TAGATAATATAAAATATATAT
Found at i:54626894 original size:12 final size:12
Alignment explanation
Indices: 54626879--54626908 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
54626869 AAAATATACT
*
54626879 TAACAATTTAAC
1 TAACAATTGAAC
54626891 TAACAATTGAAC
1 TAACAATTGAAC
54626903 TAACAA
1 TAACAA
54626909 AAGTACCAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.53, C:0.17, G:0.03, T:0.27
Consensus pattern (12 bp):
TAACAATTGAAC
Found at i:54641296 original size:151 final size:152
Alignment explanation
Indices: 54641085--54641388 Score: 556
Period size: 151 Copynumber: 2.0 Consensus size: 152
54641075 TGTTTTCATT
54641085 TTTCAAAATCATTTTATAATTTTTAACCAACATATTTTGCTTAGTGTTTTTCATTTTTCAAGAAA
1 TTTCAAAATCATTTTATAATTTTTAACCAAC----TTTGCTTAGTGTTTTTCATTTTTCAAGAAA
54641150 ATGAAAATAAAAATGATATTTGTTTTTTAAACCAAACAAACCCGAATATGAATTATTAATATGAA
62 ATGAAAATAAAAATGATATTTGTTTTTTAAACCAAACAAACCCGAATATGAATTATTAATATGAA
54641215 ATATAAACTCAAATTAAAAAAAAAAC
127 ATATAAACTCAAATTAAAAAAAAAAC
54641241 TTTCAAAATCATTTTATAATTTTTAACCAAC-TTGCTTAGTGTTTTTCATTTTTCAAGAAAATGA
1 TTTCAAAATCATTTTATAATTTTTAACCAACTTTGCTTAGTGTTTTTCATTTTTCAAGAAAATGA
*
54641305 AAATAAAAATGATATTTGTTTTTTAAACCAAACAAACCCGAATATGAATTATTAATATGAATTAT
66 AAATAAAAATGATATTTGTTTTTTAAACCAAACAAACCCGAATATGAATTATTAATATGAAATAT
54641370 AAACTCAAATTAAAAAAAA
131 AAACTCAAATTAAAAAAAA
54641389 CTAGAATTAT
Statistics
Matches: 147, Mismatches: 1, Indels: 5
0.96 0.01 0.03
Matches are distributed among these distances:
151 116 0.79
156 31 0.21
ACGTcount: A:0.45, C:0.11, G:0.07, T:0.38
Consensus pattern (152 bp):
TTTCAAAATCATTTTATAATTTTTAACCAACTTTGCTTAGTGTTTTTCATTTTTCAAGAAAATGA
AAATAAAAATGATATTTGTTTTTTAAACCAAACAAACCCGAATATGAATTATTAATATGAAATAT
AAACTCAAATTAAAAAAAAAAC
Done.