Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr09 85040211
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: 85040211
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 160 characters in sequence are not A, C, G, or T
File 35 of 292
Found at i:9361521 original size:20 final size:20
Alignment explanation
Indices: 9361492--9361550 Score: 61
Period size: 20 Copynumber: 3.0 Consensus size: 20
9361482 TAAAAAATAT
9361492 AAAA-ATATAAAAAATTCTA
1 AAAATATATAAAAAATTCTA
*
9361511 AAAATATATAAAGAAAGT-TA
1 AAAATATATAAA-AAATTCTA
*
9361531 AAAAT-TTTAAAAAAATTCTA
1 AAAATATAT-AAAAAATTCTA
9361551 GAATGCTAAC
Statistics
Matches: 33, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
19 10 0.30
20 19 0.58
21 4 0.12
ACGTcount: A:0.64, C:0.03, G:0.03, T:0.29
Consensus pattern (20 bp):
AAAATATATAAAAAATTCTA
Found at i:9361657 original size:16 final size:16
Alignment explanation
Indices: 9361638--9361668 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
9361628 TTGAAAAAGT
9361638 TTTCAAATATATATGG
1 TTTCAAATATATATGG
*
9361654 TTTCAAATTTATATG
1 TTTCAAATATATATG
9361669 CTCTAACATG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.35, C:0.06, G:0.10, T:0.48
Consensus pattern (16 bp):
TTTCAAATATATATGG
Found at i:9362217 original size:29 final size:29
Alignment explanation
Indices: 9362143--9362210 Score: 86
Period size: 29 Copynumber: 2.3 Consensus size: 29
9362133 TATTTAACCT
*
9362143 TAATATTT-ATAAGCTAT-TATAATTTTTAA
1 TAAT-TTTAATAAG-TATATATAAATTTTAA
9362172 TAATTTTAATAAGTATATATAAATTTTAA
1 TAATTTTAATAAGTATATATAAATTTTAA
*
9362201 TATTTTTAAT
1 TAATTTTAAT
9362211 TTTTATAATT
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
28 6 0.17
29 29 0.83
ACGTcount: A:0.43, C:0.01, G:0.03, T:0.53
Consensus pattern (29 bp):
TAATTTTAATAAGTATATATAAATTTTAA
Found at i:9362233 original size:19 final size:19
Alignment explanation
Indices: 9362198--9362248 Score: 54
Period size: 19 Copynumber: 2.7 Consensus size: 19
9362188 ATATAAATTT
9362198 TAATATTTTTA--ATTTTTA
1 TAATATTTTTATGA-TTTTA
*
9362216 TAAT-TCTTTTATGATTTTT
1 TAATAT-TTTTATGATTTTA
9362235 TAATATTTTTATGA
1 TAATATTTTTATGA
9362249 AACAATATTA
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
17 1 0.04
18 9 0.32
19 16 0.57
20 2 0.07
ACGTcount: A:0.29, C:0.02, G:0.04, T:0.65
Consensus pattern (19 bp):
TAATATTTTTATGATTTTA
Found at i:9365604 original size:45 final size:45
Alignment explanation
Indices: 9365553--9365641 Score: 169
Period size: 45 Copynumber: 2.0 Consensus size: 45
9365543 ATCAAAGTTA
9365553 ATTATATACTATATTTGACCCATATAAATAAAATAATAAGATTTC
1 ATTATATACTATATTTGACCCATATAAATAAAATAATAAGATTTC
*
9365598 ATTATATACTATATTTGACCCATATAAATAGAATAATAAGATTT
1 ATTATATACTATATTTGACCCATATAAATAAAATAATAAGATTT
9365642 GTAGACTAAT
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 43 1.00
ACGTcount: A:0.46, C:0.10, G:0.06, T:0.38
Consensus pattern (45 bp):
ATTATATACTATATTTGACCCATATAAATAAAATAATAAGATTTC
Found at i:9373009 original size:22 final size:21
Alignment explanation
Indices: 9372977--9373043 Score: 59
Period size: 22 Copynumber: 3.1 Consensus size: 21
9372967 TTTTCTTTTC
*
9372977 TTTATTATTATTTGTTATATTA
1 TTTATTTTTATTT-TTATATTA
9372999 TTTATTTTTATTTTCCTA-ATTTA
1 TTTATTTTTATTTT--TATA-TTA
9373022 TTTA-TTTTATTTATT-TATTA
1 TTTATTTTTATTT-TTATATTA
9373042 TT
1 TT
9373044 CTTATACTTA
Statistics
Matches: 39, Mismatches: 1, Indels: 12
0.75 0.02 0.23
Matches are distributed among these distances:
20 5 0.13
21 3 0.08
22 21 0.54
23 10 0.26
ACGTcount: A:0.24, C:0.03, G:0.01, T:0.72
Consensus pattern (21 bp):
TTTATTTTTATTTTTATATTA
Found at i:9373093 original size:9 final size:9
Alignment explanation
Indices: 9373081--9373120 Score: 71
Period size: 9 Copynumber: 4.3 Consensus size: 9
9373071 AGTTTTTTGC
9373081 TATTTTTAT
1 TATTTTTAT
9373090 TATTTTTAT
1 TATTTTTAT
9373099 TATTTTTAT
1 TATTTTTAT
9373108 TATTTTTTAT
1 TA-TTTTTAT
9373118 TAT
1 TAT
9373121 AATTATTACA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
9 21 0.70
10 9 0.30
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.78
Consensus pattern (9 bp):
TATTTTTAT
Found at i:9373095 original size:18 final size:18
Alignment explanation
Indices: 9373074--9373114 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
9373064 TTATCTAAGT
*
9373074 TTTTTGCTATTTTTATTA
1 TTTTTACTATTTTTATTA
*
9373092 TTTTTATTATTTTTATTA
1 TTTTTACTATTTTTATTA
9373110 TTTTT
1 TTTTT
9373115 TATTATAATT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.17, C:0.02, G:0.02, T:0.78
Consensus pattern (18 bp):
TTTTTACTATTTTTATTA
Found at i:9373188 original size:18 final size:18
Alignment explanation
Indices: 9373165--9373200 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
9373155 ATTGAGTTTA
9373165 TTATTTT-TTGTTTTATTT
1 TTATTTTATT-TTTTATTT
9373183 TTATTTTATTTTTTATTT
1 TTATTTTATTTTTTATTT
9373201 ATCTTTCTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 15 0.88
19 2 0.12
ACGTcount: A:0.14, C:0.00, G:0.03, T:0.83
Consensus pattern (18 bp):
TTATTTTATTTTTTATTT
Found at i:9373189 original size:11 final size:12
Alignment explanation
Indices: 9373165--9373200 Score: 56
Period size: 12 Copynumber: 3.1 Consensus size: 12
9373155 ATTGAGTTTA
*
9373165 TTATTTTTTGTT
1 TTATTTTTTATT
9373177 TTA-TTTTTATT
1 TTATTTTTTATT
9373188 TTATTTTTTATT
1 TTATTTTTTATT
9373200 T
1 T
9373201 ATCTTTCTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
11 10 0.45
12 12 0.55
ACGTcount: A:0.14, C:0.00, G:0.03, T:0.83
Consensus pattern (12 bp):
TTATTTTTTATT
Found at i:9373213 original size:23 final size:23
Alignment explanation
Indices: 9373165--9373211 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 23
9373155 ATTGAGTTTA
*
9373165 TTATTTTTTGTTTTATTTTTATT
1 TTATTTTTTGATTTATTTTTATT
* *
9373188 TTATTTTTT-ATTTATCTTTCTT
1 TTATTTTTTGATTTATTTTTATT
9373210 TT
1 TT
9373212 TAATTTTGTT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
22 12 0.57
23 9 0.43
ACGTcount: A:0.13, C:0.04, G:0.02, T:0.81
Consensus pattern (23 bp):
TTATTTTTTGATTTATTTTTATT
Found at i:9379001 original size:2 final size:2
Alignment explanation
Indices: 9378994--9379039 Score: 85
Period size: 2 Copynumber: 23.5 Consensus size: 2
9378984 TTATTGTAAA
9378994 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A- AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
9379035 AG AG A
1 AG AG A
9379040 AGAAAGAAAT
Statistics
Matches: 43, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 42 0.98
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:9380055 original size:44 final size:44
Alignment explanation
Indices: 9379988--9380190 Score: 233
Period size: 44 Copynumber: 4.7 Consensus size: 44
9379978 TATGTGTTAT
* *
9379988 CGTGTAAGACCACGTCTGTGACGTTGGTATCAACTTATGATTTA
1 CGTGTAAGACCACGTCTGGGACGTTGGCATCAACTTATGATTTA
* *
9380032 CGTGTAAGACCACGTCTGGGACGTTGGTATCGACTTATGATTTA
1 CGTGTAAGACCACGTCTGGGACGTTGGCATCAACTTATGATTTA
** *
9380076 CGTGTAAGACCACGTCTGGGACGTTGGCATC-GTTTTTGAGTTT-
1 CGTGTAAGACCACGTCTGGGACGTTGGCATCAACTTATGA-TTTA
9380119 -GTGTAAGACC-CTGTCTGGGACAG-TGGCATCAA--TATTCGA-TTA
1 CGTGTAAGACCAC-GTCTGGGAC-GTTGGCATCAACTTA-T-GATTTA
*
9380161 CATGTAAGACCACGTCTGGGACGTTGGCAT
1 CGTGTAAGACCACGTCTGGGACGTTGGCAT
9380191 TGTACGAGCT
Statistics
Matches: 140, Mismatches: 9, Indels: 21
0.82 0.05 0.12
Matches are distributed among these distances:
41 4 0.03
42 28 0.20
43 32 0.23
44 76 0.54
ACGTcount: A:0.23, C:0.19, G:0.27, T:0.31
Consensus pattern (44 bp):
CGTGTAAGACCACGTCTGGGACGTTGGCATCAACTTATGATTTA
Found at i:9383863 original size:20 final size:20
Alignment explanation
Indices: 9383840--9383887 Score: 78
Period size: 20 Copynumber: 2.4 Consensus size: 20
9383830 AGAGGCATCC
* *
9383840 AAGTGCAAACAGAGTCACCG
1 AAGTGCAAACAAAGTCACCA
9383860 AAGTGCAAACAAAGTCACCA
1 AAGTGCAAACAAAGTCACCA
9383880 AAGTGCAA
1 AAGTGCAA
9383888 TCTTGTACAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.46, C:0.23, G:0.21, T:0.10
Consensus pattern (20 bp):
AAGTGCAAACAAAGTCACCA
Found at i:9385906 original size:22 final size:22
Alignment explanation
Indices: 9385881--9385924 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
9385871 CCAAGAACTC
*
9385881 AAAGAATGAAAAGAAGATTACT
1 AAAGAATCAAAAGAAGATTACT
*
9385903 AAAGAATCAAAGGAAGATTACT
1 AAAGAATCAAAAGAAGATTACT
9385925 TAACTCATTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.57, C:0.07, G:0.18, T:0.18
Consensus pattern (22 bp):
AAAGAATCAAAAGAAGATTACT
Found at i:9397480 original size:25 final size:25
Alignment explanation
Indices: 9397450--9397531 Score: 103
Period size: 25 Copynumber: 3.3 Consensus size: 25
9397440 TATCTTGTGT
*
9397450 GAGCATATTGATTTATAGCTCGTGA
1 GAGCATACTGATTTATAGCTCGTGA
*
9397475 GAGCATACTGA-TTACAGCTCGTGA
1 GAGCATACTGATTTATAGCTCGTGA
* * * *
9397499 GAGCATACCGATCTATAGCTCGAGC
1 GAGCATACTGATTTATAGCTCGTGA
9397524 GAGCATAC
1 GAGCATAC
9397532 CAATTCATAG
Statistics
Matches: 49, Mismatches: 7, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
24 22 0.45
25 27 0.55
ACGTcount: A:0.29, C:0.21, G:0.24, T:0.26
Consensus pattern (25 bp):
GAGCATACTGATTTATAGCTCGTGA
Found at i:9397532 original size:25 final size:24
Alignment explanation
Indices: 9397462--9397544 Score: 103
Period size: 25 Copynumber: 3.4 Consensus size: 24
9397452 GCATATTGAT
*
9397462 TTATAGCTCGTGAGAGCATACTGA
1 TTATAGCTCGTGAGAGCATACCGA
*
9397486 TTACAGCTCGTGAGAGCATACCGA
1 TTATAGCTCGTGAGAGCATACCGA
* * *
9397510 TCTATAGCTCGAGCGAGCATACCAA
1 T-TATAGCTCGTGAGAGCATACCGA
9397535 TTCATAGCTC
1 TT-ATAGCTC
9397545 TTATGAGCAT
Statistics
Matches: 51, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
24 24 0.47
25 27 0.53
ACGTcount: A:0.29, C:0.24, G:0.22, T:0.25
Consensus pattern (24 bp):
TTATAGCTCGTGAGAGCATACCGA
Found at i:9406512 original size:35 final size:35
Alignment explanation
Indices: 9406473--9406543 Score: 124
Period size: 35 Copynumber: 2.0 Consensus size: 35
9406463 GTTTTAGTTG
*
9406473 ATAGAGCACACAAGGCTGAAGAACTCAGCAAAGAA
1 ATAGAGCACACAAGGCTGAAAAACTCAGCAAAGAA
*
9406508 ATAGAGCACACAAGGCTGAAAAACTTAGCAAAGAA
1 ATAGAGCACACAAGGCTGAAAAACTCAGCAAAGAA
9406543 A
1 A
9406544 AAAGAAAAGC
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.51, C:0.18, G:0.21, T:0.10
Consensus pattern (35 bp):
ATAGAGCACACAAGGCTGAAAAACTCAGCAAAGAA
Found at i:9414958 original size:40 final size:40
Alignment explanation
Indices: 9414914--9415004 Score: 128
Period size: 40 Copynumber: 2.3 Consensus size: 40
9414904 GTGCTAAGTG
* * * *
9414914 ACTAAATCCGGACTAAGATCCGACGGCATACGTGCGAGTT
1 ACTAAATCCGGACTAAGATCCGAAGGCATACGAGCAAGCT
* *
9414954 ACTAAATCCGGACTAAGATCCGAAGGCTTTCGAGCAAGCT
1 ACTAAATCCGGACTAAGATCCGAAGGCATACGAGCAAGCT
9414994 ACTAAATCCGG
1 ACTAAATCCGG
9415005 GTTGAGTCCC
Statistics
Matches: 45, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
40 45 1.00
ACGTcount: A:0.32, C:0.25, G:0.23, T:0.20
Consensus pattern (40 bp):
ACTAAATCCGGACTAAGATCCGAAGGCATACGAGCAAGCT
Found at i:9428003 original size:14 final size:14
Alignment explanation
Indices: 9427984--9428013 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
9427974 TGGCTCAAAG
*
9427984 AAAATAAATTATTA
1 AAAATAAAATATTA
9427998 AAAATAAAATATTA
1 AAAATAAAATATTA
9428012 AA
1 AA
9428014 CATTATAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (14 bp):
AAAATAAAATATTA
Found at i:9428889 original size:12 final size:12
Alignment explanation
Indices: 9428872--9428896 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
9428862 TTTAATCCTA
9428872 AACAATATTTTT
1 AACAATATTTTT
9428884 AACAATATTTTT
1 AACAATATTTTT
9428896 A
1 A
9428897 TTATTATATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.44, C:0.08, G:0.00, T:0.48
Consensus pattern (12 bp):
AACAATATTTTT
Found at i:9429166 original size:17 final size:17
Alignment explanation
Indices: 9429144--9429176 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
9429134 ACTGAGCTTA
9429144 ATATATTATGTCAAAAT
1 ATATATTATGTCAAAAT
9429161 ATATATTATGTCAAAA
1 ATATATTATGTCAAAA
9429177 GTATGATTGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.48, C:0.06, G:0.06, T:0.39
Consensus pattern (17 bp):
ATATATTATGTCAAAAT
Found at i:9435298 original size:29 final size:29
Alignment explanation
Indices: 9435255--9435319 Score: 78
Period size: 29 Copynumber: 2.2 Consensus size: 29
9435245 TTTAATTAGT
** * *
9435255 TTTTTAAAATTTTAAAAA-TTTAAAATTTA
1 TTTTTAAAAAATTAAAAAGTATAAAA-ATA
9435284 TTTTTAAAAAATTAAAAAGTATAAAAATA
1 TTTTTAAAAAATTAAAAAGTATAAAAATA
9435313 TTTTTAA
1 TTTTTAA
9435320 GTTTTAGAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
29 25 0.81
30 6 0.19
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (29 bp):
TTTTTAAAAAATTAAAAAGTATAAAAATA
Found at i:9436312 original size:31 final size:32
Alignment explanation
Indices: 9436285--9436363 Score: 97
Period size: 33 Copynumber: 2.4 Consensus size: 32
9436275 TGTTTTATAT
9436285 TTTAAATAAAAATATTATAATTTTTTTAAAAA
1 TTTAAATAAAAATATTATAATTTTTTTAAAAA
* *
9436317 TTTAAA-AATAATATTTTAAATTTTTTTTAAAAA
1 TTTAAATAAAAATATTAT-AA-TTTTTTTAAAAA
**
9436350 TGAAAATAAAAATA
1 TTTAAATAAAAATA
9436364 AAAAGTCTTT
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
31 9 0.23
32 8 0.21
33 16 0.41
34 6 0.15
ACGTcount: A:0.54, C:0.00, G:0.01, T:0.44
Consensus pattern (32 bp):
TTTAAATAAAAATATTATAATTTTTTTAAAAA
Found at i:9436398 original size:19 final size:19
Alignment explanation
Indices: 9436374--9436417 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
9436364 AAAAGTCTTT
9436374 AAAATTAAAGAAAATAAA-A
1 AAAATTAAA-AAAATAAACA
* *
9436393 AAAATTACAAATATAAACA
1 AAAATTAAAAAAATAAACA
9436412 AAAATT
1 AAAATT
9436418 TCAAAATTCA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 7 0.32
19 15 0.68
ACGTcount: A:0.73, C:0.05, G:0.02, T:0.20
Consensus pattern (19 bp):
AAAATTAAAAAAATAAACA
Found at i:9436408 original size:18 final size:19
Alignment explanation
Indices: 9436387--9436422 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
9436377 ATTAAAGAAA
9436387 ATAAA-AAAAATTACAAAT
1 ATAAACAAAAATTACAAAT
*
9436405 ATAAACAAAAATTTCAAA
1 ATAAACAAAAATTACAAA
9436423 ATTCAATGTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.69, C:0.08, G:0.00, T:0.22
Consensus pattern (19 bp):
ATAAACAAAAATTACAAAT
Found at i:9436800 original size:6 final size:7
Alignment explanation
Indices: 9436772--9436798 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
9436762 ATAAAGACTG
9436772 AATTTTT
1 AATTTTT
9436779 AATTTTT
1 AATTTTT
9436786 AATTTTT
1 AATTTTT
9436793 AATTTT
1 AATTTT
9436799 AAAAGAGTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (7 bp):
AATTTTT
Found at i:9442869 original size:9 final size:9
Alignment explanation
Indices: 9442855--9442888 Score: 59
Period size: 9 Copynumber: 3.8 Consensus size: 9
9442845 ATAAGTATAA
9442855 AATTAACCG
1 AATTAACCG
*
9442864 AATTAATCG
1 AATTAACCG
9442873 AATTAACCG
1 AATTAACCG
9442882 AATTAAC
1 AATTAAC
9442889 TAAATTATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
9 23 1.00
ACGTcount: A:0.47, C:0.18, G:0.09, T:0.26
Consensus pattern (9 bp):
AATTAACCG
Found at i:9442930 original size:5 final size:6
Alignment explanation
Indices: 9442915--9442955 Score: 55
Period size: 6 Copynumber: 6.5 Consensus size: 6
9442905 AATTATATGT
*
9442915 TTTTTA TTTTTA TTTTTA GTTTTAGA TTTTTA TTTTTA TTT
1 TTTTTA TTTTTA TTTTTA -TTTT-TA TTTTTA TTTTTA TTT
9442956 ATTAAATTAT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
6 22 0.71
7 8 0.26
8 1 0.03
ACGTcount: A:0.17, C:0.00, G:0.05, T:0.78
Consensus pattern (6 bp):
TTTTTA
Found at i:9443114 original size:18 final size:18
Alignment explanation
Indices: 9443091--9443127 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
9443081 ATTTTTTATT
9443091 AATTTTTTCGGTTAACCG
1 AATTTTTTCGGTTAACCG
9443109 AATTTTTTCGGTTAACCG
1 AATTTTTTCGGTTAACCG
9443127 A
1 A
9443128 TCGGTTTCGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.24, C:0.16, G:0.16, T:0.43
Consensus pattern (18 bp):
AATTTTTTCGGTTAACCG
Found at i:9447754 original size:13 final size:13
Alignment explanation
Indices: 9447736--9447763 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
9447726 AAACAACAGT
9447736 ACATATCTACATA
1 ACATATCTACATA
9447749 ACATATCTACATA
1 ACATATCTACATA
9447762 AC
1 AC
9447764 TTTAGTTTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.46, C:0.25, G:0.00, T:0.29
Consensus pattern (13 bp):
ACATATCTACATA
Found at i:9448307 original size:21 final size:21
Alignment explanation
Indices: 9448279--9448321 Score: 79
Period size: 20 Copynumber: 2.1 Consensus size: 21
9448269 AGTCTTTAAT
9448279 TTAATTTTTTGTTG-TTTTAG
1 TTAATTTTTTGTTGTTTTTAG
9448299 TTAATTTTTTGTTGTTTTTAG
1 TTAATTTTTTGTTGTTTTTAG
9448320 TT
1 TT
9448322 CTTAAACCCT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
20 14 0.64
21 8 0.36
ACGTcount: A:0.14, C:0.00, G:0.14, T:0.72
Consensus pattern (21 bp):
TTAATTTTTTGTTGTTTTTAG
Found at i:9448487 original size:29 final size:31
Alignment explanation
Indices: 9448435--9448506 Score: 98
Period size: 30 Copynumber: 2.4 Consensus size: 31
9448425 ATAAATATTT
*
9448435 AATTAATTTTTAAAAATTATAAAA-ATAAAA
1 AATTTATTTTTAAAAATTATAAAAGATAAAA
9448465 AATTTATTTTTAAAAATTA-AAAAGTATAAAA
1 AATTTATTTTTAAAAATTATAAAAG-ATAAAA
9448496 AA--TATTTTTAA
1 AATTTATTTTTAA
9448507 GTTTTAGAAA
Statistics
Matches: 39, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
29 13 0.33
30 18 0.46
31 8 0.21
ACGTcount: A:0.58, C:0.00, G:0.01, T:0.40
Consensus pattern (31 bp):
AATTTATTTTTAAAAATTATAAAAGATAAAA
Found at i:9448989 original size:29 final size:27
Alignment explanation
Indices: 9448930--9448990 Score: 68
Period size: 29 Copynumber: 2.2 Consensus size: 27
9448920 TTACCTTATT
* * * *
9448930 ATAATTTAGACTTATTTAATTTTTTTG
1 ATAATTTAGACTAATTTAATCTATTTA
9448957 ATAATTTAGGGACTAATTTAATCTATTTA
1 ATAATTTA--GACTAATTTAATCTATTTA
9448986 ATAAT
1 ATAAT
9448991 AGATAGATAA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
27 8 0.29
29 20 0.71
ACGTcount: A:0.36, C:0.05, G:0.08, T:0.51
Consensus pattern (27 bp):
ATAATTTAGACTAATTTAATCTATTTA
Found at i:9449374 original size:16 final size:18
Alignment explanation
Indices: 9449335--9449376 Score: 54
Period size: 17 Copynumber: 2.5 Consensus size: 18
9449325 TAAATTTATA
9449335 ATATTT-TATATTATGTT
1 ATATTTATATATTATGTT
*
9449352 ATTTTTATATATTAT-TT
1 ATATTTATATATTATGTT
9449369 A-ATTTATA
1 ATATTTATA
9449377 ACACATAATA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
16 6 0.27
17 8 0.36
18 8 0.36
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.64
Consensus pattern (18 bp):
ATATTTATATATTATGTT
Found at i:9450072 original size:21 final size:21
Alignment explanation
Indices: 9450042--9450082 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
9450032 TTTAAAATTA
9450042 AAAAAAATAAA-AAATAATTTT
1 AAAAAAATAAACAAA-AATTTT
*
9450063 AAAAATATAAACAAAAATTT
1 AAAAAAATAAACAAAAATTT
9450083 CCAAAATTCA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 15 0.83
22 3 0.17
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.27
Consensus pattern (21 bp):
AAAAAAATAAACAAAAATTTT
Found at i:9450326 original size:7 final size:7
Alignment explanation
Indices: 9450314--9450338 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
9450304 AAATTTATTT
9450314 AAAAATA
1 AAAAATA
9450321 AAAAATA
1 AAAAATA
9450328 AAAAATA
1 AAAAATA
9450335 AAAA
1 AAAA
9450339 TATTTTTAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (7 bp):
AAAAATA
Found at i:9455245 original size:62 final size:62
Alignment explanation
Indices: 9455165--9455290 Score: 252
Period size: 62 Copynumber: 2.0 Consensus size: 62
9455155 TATTAGTGGT
9455165 TAGAAAATGGGAGTTTTCTTTCACTACTTAGTGACGACCTTATGTAAAAAGGCAAGTGTACC
1 TAGAAAATGGGAGTTTTCTTTCACTACTTAGTGACGACCTTATGTAAAAAGGCAAGTGTACC
9455227 TAGAAAATGGGAGTTTTCTTTCACTACTTAGTGACGACCTTATGTAAAAAGGCAAGTGTACC
1 TAGAAAATGGGAGTTTTCTTTCACTACTTAGTGACGACCTTATGTAAAAAGGCAAGTGTACC
9455289 TA
1 TA
9455291 TGACATCCAC
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
62 64 1.00
ACGTcount: A:0.33, C:0.16, G:0.21, T:0.31
Consensus pattern (62 bp):
TAGAAAATGGGAGTTTTCTTTCACTACTTAGTGACGACCTTATGTAAAAAGGCAAGTGTACC
Found at i:9461547 original size:18 final size:18
Alignment explanation
Indices: 9461524--9461565 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 18
9461514 GTCATGTTAA
9461524 TTAAT-ATTTATATACTTT
1 TTAATAATTTATATA-TTT
*
9461542 TTAATAAATTTATTTATTT
1 TTAAT-AATTTATATATTT
9461561 TTAAT
1 TTAAT
9461566 TTAAGAATTA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
18 5 0.24
19 8 0.38
20 8 0.38
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (18 bp):
TTAATAATTTATATATTT
Found at i:9462098 original size:2 final size:2
Alignment explanation
Indices: 9462091--9462121 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
9462081 TAATGTAATA
9462091 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
9462122 ATATATATAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:9463250 original size:50 final size:50
Alignment explanation
Indices: 9463191--9463294 Score: 199
Period size: 50 Copynumber: 2.1 Consensus size: 50
9463181 TTATTATACT
*
9463191 TATTATTAAATTTTTAAAAATCATTATAAATATTGTAATGTTATATGCAA
1 TATTATTAAATTTTTAAAAATCATTATAAATATTGCAATGTTATATGCAA
9463241 TATTATTAAATTTTTAAAAATCATTATAAATATTGCAATGTTATATGCAA
1 TATTATTAAATTTTTAAAAATCATTATAAATATTGCAATGTTATATGCAA
9463291 TATT
1 TATT
9463295 CATTTTCTCA
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
50 53 1.00
ACGTcount: A:0.43, C:0.05, G:0.06, T:0.46
Consensus pattern (50 bp):
TATTATTAAATTTTTAAAAATCATTATAAATATTGCAATGTTATATGCAA
Found at i:9463610 original size:32 final size:32
Alignment explanation
Indices: 9463550--9463611 Score: 81
Period size: 32 Copynumber: 1.9 Consensus size: 32
9463540 TAAAATGAGG
* *
9463550 TTTTAAGTTCCTTAAAAGTTGGAGAAAAATTT
1 TTTTAAGTCCCTTAAAAGGTGGAGAAAAATTT
*
9463582 TTTTAGGTCCCTTAAAAGGTGGTA-AAAAAT
1 TTTTAAGTCCCTTAAAAGGTGG-AGAAAAAT
9463612 ATTTGGGCCC
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
32 25 0.96
33 1 0.04
ACGTcount: A:0.37, C:0.08, G:0.18, T:0.37
Consensus pattern (32 bp):
TTTTAAGTCCCTTAAAAGGTGGAGAAAAATTT
Found at i:9467502 original size:50 final size:50
Alignment explanation
Indices: 9467427--9467522 Score: 183
Period size: 50 Copynumber: 1.9 Consensus size: 50
9467417 GGACAGCTGC
9467427 CATGCATTTACTCCTAGCCAGCATATTTCATTTTCATTTTCCTTTAATCT
1 CATGCATTTACTCCTAGCCAGCATATTTCATTTTCATTTTCCTTTAATCT
*
9467477 CATGCATTTACTCCTAGCCAGCATATTTCATTTTTATTTTCCTTTA
1 CATGCATTTACTCCTAGCCAGCATATTTCATTTTCATTTTCCTTTA
9467523 CAGGTAGTAG
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
50 45 1.00
ACGTcount: A:0.22, C:0.25, G:0.06, T:0.47
Consensus pattern (50 bp):
CATGCATTTACTCCTAGCCAGCATATTTCATTTTCATTTTCCTTTAATCT
Found at i:9468707 original size:7 final size:7
Alignment explanation
Indices: 9468697--9468766 Score: 54
Period size: 7 Copynumber: 9.7 Consensus size: 7
9468687 TATAATGATA
9468697 ATTATTT
1 ATTATTT
9468704 ATTATTT
1 ATTATTT
9468711 ATT-TTT
1 ATTATTT
9468717 ATTACTTT
1 ATTA-TTT
**
9468725 AAAATTT
1 ATTATTT
*
9468732 CATAACTTT
1 -ATTA-TTT
*
9468741 CATAATTT
1 -ATTATTT
9468749 ATTATTT
1 ATTATTT
9468756 ATTA-TT
1 ATTATTT
9468762 ATTAT
1 ATTAT
9468767 GTATGGATTA
Statistics
Matches: 54, Mismatches: 4, Indels: 10
0.79 0.06 0.15
Matches are distributed among these distances:
6 12 0.22
7 23 0.43
8 11 0.20
9 8 0.15
ACGTcount: A:0.33, C:0.06, G:0.00, T:0.61
Consensus pattern (7 bp):
ATTATTT
Found at i:9476988 original size:14 final size:14
Alignment explanation
Indices: 9476969--9476996 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
9476959 GAAATCAAAT
9476969 CAATCAACGTACGG
1 CAATCAACGTACGG
9476983 CAATCAACGTACGG
1 CAATCAACGTACGG
9476997 TTTTAACGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.29, G:0.21, T:0.14
Consensus pattern (14 bp):
CAATCAACGTACGG
Found at i:9477529 original size:27 final size:29
Alignment explanation
Indices: 9477489--9477544 Score: 73
Period size: 27 Copynumber: 2.0 Consensus size: 29
9477479 ATAATTATGT
*
9477489 TAAAATATGATTAA-AAT-ATTTTTTTAA
1 TAAAATATGATTAACAATAATTTTATTAA
9477516 TAAAATAT-ATTTAACAATAATTTTATTAA
1 TAAAATATGA-TTAACAATAATTTTATTAA
9477545 AATTTAATAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
26 1 0.04
27 12 0.48
28 3 0.12
29 9 0.36
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.46
Consensus pattern (29 bp):
TAAAATATGATTAACAATAATTTTATTAA
Found at i:9477737 original size:16 final size:16
Alignment explanation
Indices: 9477716--9477788 Score: 110
Period size: 16 Copynumber: 4.6 Consensus size: 16
9477706 TTGAATTACT
9477716 TATTACAGCTCTATTC
1 TATTACAGCTCTATTC
9477732 TATTACAGCTCTATTC
1 TATTACAGCTCTATTC
*
9477748 CATTACAGCTCTATTC
1 TATTACAGCTCTATTC
* * *
9477764 AATTACAACCCTATTC
1 TATTACAGCTCTATTC
9477780 TATTACAGC
1 TATTACAGC
9477789 CAACCAAACG
Statistics
Matches: 51, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 51 1.00
ACGTcount: A:0.29, C:0.27, G:0.05, T:0.38
Consensus pattern (16 bp):
TATTACAGCTCTATTC
Found at i:9478734 original size:78 final size:78
Alignment explanation
Indices: 9478642--9478794 Score: 297
Period size: 78 Copynumber: 2.0 Consensus size: 78
9478632 ATATGAAAAA
9478642 ACCAAAATCAAATCGAATTCACTCCTAATATAGAGAAGGCCGATGCCTATGATGTTCTTTTTGTA
1 ACCAAAATCAAATCGAATTCACTCCTAATATAGAGAAGGCCGATGCCTATGATGTTCTTTTTGTA
9478707 TTTCACTATGATT
66 TTTCACTATGATT
*
9478720 ACCAAAATCAAATCGAATTCACTCCTAATATAGAGAAGGCCGATGCCTGTGATGTTCTTTTTGTA
1 ACCAAAATCAAATCGAATTCACTCCTAATATAGAGAAGGCCGATGCCTATGATGTTCTTTTTGTA
9478785 TTTCACTATG
66 TTTCACTATG
9478795 GTTAAGTTAA
Statistics
Matches: 74, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
78 74 1.00
ACGTcount: A:0.31, C:0.20, G:0.15, T:0.34
Consensus pattern (78 bp):
ACCAAAATCAAATCGAATTCACTCCTAATATAGAGAAGGCCGATGCCTATGATGTTCTTTTTGTA
TTTCACTATGATT
Found at i:9482573 original size:13 final size:14
Alignment explanation
Indices: 9482555--9482588 Score: 52
Period size: 13 Copynumber: 2.5 Consensus size: 14
9482545 TCTTTTTGTC
9482555 TTTATTTATT-TTA
1 TTTATTTATTATTA
9482568 TTTATTTATTATTA
1 TTTATTTATTATTA
*
9482582 TTAATTT
1 TTTATTT
9482589 TAAAATTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 10 0.53
14 9 0.47
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (14 bp):
TTTATTTATTATTA
Found at i:9482620 original size:24 final size:22
Alignment explanation
Indices: 9482585--9482661 Score: 75
Period size: 24 Copynumber: 3.4 Consensus size: 22
9482575 ATTATTATTA
*
9482585 ATTTTAAAATTTTTGAAATATAT
1 ATTTGAAAATTTTT-AAATATAT
*
9482608 ATTTGAAATATTTTATTAATATAT
1 ATTTGAAA-ATTTT-TAAATATAT
**
9482632 ATTTTTAAA-TTTTAAATATAT
1 ATTTGAAAATTTTTAAATATAT
9482653 ATTTTGAAA
1 A-TTTGAAA
9482662 TTATTTTTTA
Statistics
Matches: 44, Mismatches: 7, Indels: 7
0.76 0.12 0.12
Matches are distributed among these distances:
21 9 0.20
22 8 0.18
23 8 0.18
24 18 0.41
25 1 0.02
ACGTcount: A:0.43, C:0.00, G:0.04, T:0.53
Consensus pattern (22 bp):
ATTTGAAAATTTTTAAATATAT
Found at i:9482623 original size:47 final size:47
Alignment explanation
Indices: 9482572--9482672 Score: 129
Period size: 47 Copynumber: 2.2 Consensus size: 47
9482562 ATTTTATTTA
*
9482572 TTTATTATTAT-TAATTTTAAAATTTTTGAAATATATA-TTTGAAA-TAT
1 TTTATTAATATAT-ATTTTAAAA-TTTT-AAATATATATTTTGAAATTAT
*
9482619 TTTATTAATATATATTTTTAAATTTTAAATATATATTTTGAAATTAT
1 TTTATTAATATATATTTTAAAATTTTAAATATATATTTTGAAATTAT
9482666 TTT-TTAA
1 TTTATTAA
9482673 AATTTTAAAT
Statistics
Matches: 49, Mismatches: 2, Indels: 7
0.84 0.03 0.12
Matches are distributed among these distances:
45 9 0.18
46 15 0.31
47 24 0.49
48 1 0.02
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (47 bp):
TTTATTAATATATATTTTAAAATTTTAAATATATATTTTGAAATTAT
Found at i:9482651 original size:21 final size:21
Alignment explanation
Indices: 9482585--9482663 Score: 86
Period size: 21 Copynumber: 3.5 Consensus size: 21
9482575 ATTATTATTA
9482585 ATTTTAAAATTTTTGAAATATAT
1 ATTTTAAAA-TTTT-AAATATAT
*
9482608 ATTTGAAATATTTTATTAATATAT
1 ATTTTAAA-ATTTTA--AATATAT
*
9482632 ATTTTTAAATTTTAAATATAT
1 ATTTTAAAATTTTAAATATAT
*
9482653 ATTTTGAAATT
1 ATTTTAAAATT
9482664 ATTTTTTAAA
Statistics
Matches: 49, Mismatches: 4, Indels: 8
0.80 0.07 0.13
Matches are distributed among these distances:
21 17 0.35
22 1 0.02
23 17 0.35
24 14 0.29
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.54
Consensus pattern (21 bp):
ATTTTAAAATTTTAAATATAT
Found at i:9482656 original size:13 final size:13
Alignment explanation
Indices: 9482595--9482673 Score: 50
Period size: 13 Copynumber: 6.5 Consensus size: 13
9482585 ATTTTAAAAT
9482595 TTTTGAAATATATA
1 TTTT-AAATATATA
*
9482609 TTTGAAATAT-T-
1 TTTTAAATATATA
9482620 TTATT-AATATATA
1 TT-TTAAATATATA
9482633 TTTT---TA-A-A
1 TTTTAAATATATA
9482641 TTTTAAATATATA
1 TTTTAAATATATA
*
9482654 TTTTGAAAT-TATT
1 TTTT-AAATATATA
9482667 TTTTAAA
1 TTTTAAA
9482674 ATTTTAAATA
Statistics
Matches: 53, Mismatches: 3, Indels: 20
0.70 0.04 0.26
Matches are distributed among these distances:
8 5 0.09
9 1 0.02
10 2 0.04
11 9 0.17
12 9 0.17
13 20 0.38
14 7 0.13
ACGTcount: A:0.41, C:0.00, G:0.04, T:0.56
Consensus pattern (13 bp):
TTTTAAATATATA
Found at i:9482687 original size:22 final size:21
Alignment explanation
Indices: 9482653--9482707 Score: 67
Period size: 22 Copynumber: 2.6 Consensus size: 21
9482643 TTAAATATAT
*
9482653 ATTTTGAA-ATTATTTTTTAAA
1 ATTTTAAATATTATTTTTT-AA
*
9482674 ATTTTAAATATTATTTTTTTA
1 ATTTTAAATATTATTTTTTAA
9482695 ATATTTAAATATT
1 AT-TTTAAATATT
9482708 TTAAACTTTC
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
21 10 0.33
22 20 0.67
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (21 bp):
ATTTTAAATATTATTTTTTAA
Found at i:9483001 original size:19 final size:20
Alignment explanation
Indices: 9482979--9483019 Score: 66
Period size: 19 Copynumber: 2.1 Consensus size: 20
9482969 TAAAAAATAC
*
9482979 TTGTTAAAAAA-AGATTTAT
1 TTGTTAAAAAATAAATTTAT
9482998 TTGTTAAAAAATAAATTTAT
1 TTGTTAAAAAATAAATTTAT
9483018 TT
1 TT
9483020 AAAAATATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
19 11 0.55
20 9 0.45
ACGTcount: A:0.46, C:0.00, G:0.07, T:0.46
Consensus pattern (20 bp):
TTGTTAAAAAATAAATTTAT
Found at i:9483007 original size:20 final size:19
Alignment explanation
Indices: 9482979--9483019 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 19
9482969 TAAAAAATAC
9482979 TTGTTAAAAA-AAGATTTAT
1 TTGTTAAAAATAA-ATTTAT
9482998 TTGTTAAAAAATAAATTTAT
1 TTGTT-AAAAATAAATTTAT
9483018 TT
1 TT
9483020 AAAAATATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
19 5 0.25
20 13 0.65
21 2 0.10
ACGTcount: A:0.46, C:0.00, G:0.07, T:0.46
Consensus pattern (19 bp):
TTGTTAAAAATAAATTTAT
Found at i:9483015 original size:16 final size:16
Alignment explanation
Indices: 9482996--9483044 Score: 53
Period size: 16 Copynumber: 3.1 Consensus size: 16
9482986 AAAAAGATTT
*
9482996 ATTTGTTAAAAAATAA
1 ATTTATTAAAAAATAA
* *
9483012 ATTTATTTAAAAATAT
1 ATTTATTAAAAAATAA
* *
9483028 ATATATTAAAAAGTAA
1 ATTTATTAAAAAATAA
9483044 A
1 A
9483045 AATTAAAATT
Statistics
Matches: 26, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
16 26 1.00
ACGTcount: A:0.57, C:0.00, G:0.04, T:0.39
Consensus pattern (16 bp):
ATTTATTAAAAAATAA
Found at i:9483046 original size:7 final size:7
Alignment explanation
Indices: 9483018--9483065 Score: 53
Period size: 7 Copynumber: 6.9 Consensus size: 7
9483008 ATAAATTTAT
9483018 TTAAAAA
1 TTAAAAA
* *
9483025 TATATATA
1 T-TAAAAA
9483033 TTAAAAA
1 TTAAAAA
*
9483040 GTAAAAA
1 TTAAAAA
9483047 TT-AAAA
1 TTAAAAA
9483053 TTAAAAA
1 TTAAAAA
9483060 TTAAAA
1 TTAAAA
9483066 TTATATATTA
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
6 6 0.18
7 22 0.67
8 5 0.15
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (7 bp):
TTAAAAA
Found at i:9483075 original size:13 final size:13
Alignment explanation
Indices: 9483036--9483068 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
9483026 ATATATATTA
*
9483036 AAAAGTAAAAATT
1 AAAATTAAAAATT
9483049 AAAATTAAAAATT
1 AAAATTAAAAATT
9483062 AAAATTA
1 AAAATTA
9483069 TATATTATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.70, C:0.00, G:0.03, T:0.27
Consensus pattern (13 bp):
AAAATTAAAAATT
Found at i:9483541 original size:216 final size:215
Alignment explanation
Indices: 9483121--9483743 Score: 964
Period size: 216 Copynumber: 2.8 Consensus size: 215
9483111 AACATCAAAT
9483121 AATATGTTATTTGAAAAATAACTATTATTGTAATGAGATACATGTTCTATTAGGTATAAGTATTT
1 AATATGTTATTTG-AAAATAACTATTATTGTAATGAGATACATGTTCTATTAGGTATAAGTATTT
**
9483186 AAATTTTTGTTTTTGTAATGTGATACATGCGTAAATATATATATATATA-G-AATCATATTAGTG
65 AAATTTTTGTTTTTGTAATGTGATACATGAATAAATATATATATATATATGTAATCATATTAGTG
*
9483249 AATCTGCTAATACATACTTCATCCGGATAAAGTATGCATTATTAAAATTAAATTAAAATATTAAA
130 AATCTGCTAATACATACTTCATCCGGATAAAGTATGCATTATTAAAATTAAACTAAAATATTAAA
*
9483314 TAAGAAATAAAATTATAAAAC
195 TAAAAAATAAAATTATAAAAC
9483335 AATATGTTATTTAGAAAATAACTATTATTGTAATGAGATACATGTTCTATTAGGTATAAGTATTT
1 AATATGTTATTT-GAAAATAACTATTATTGTAATGAGATACATGTTCTATTAGGTATAAGTATTT
*
9483400 AAATTTTTGTTTTTGTAATGTGATGA-ATGAATAAATCTATATATATATATGTAATCATATTAGT
65 AAATTTTTGTTTTTGTAATGTGAT-ACATGAATAAATATATATATATATATGTAATCATATTAGT
* *
9483464 GAATCTACTAATACATACTTCATCCAGATAAAGTATGCATTATTAAAATTAAACTAAAATATTAA
129 GAATCTGCTAATACATACTTCATCCGGATAAAGTATGCATTATTAAAATTAAACTAAAATATTAA
9483529 ATAAAAAATAAAATTATAAAAC
194 ATAAAAAATAAAATTATAAAAC
*
9483551 AATATGTTATTTGGAAAATAACTATTATTGTAATGAGATACATGTTTTATTAGGTATAAGTATTT
1 AATATGTTATTT-GAAAATAACTATTATTGTAATGAGATACATGTTCTATTAGGTATAAGTATTT
* * *
9483616 AAATTTTAGTTTTTGTAATATGATACATACGTAAATATTTATATATATATATATATATATATATA
65 AAATTTTTGTTTTTGTAATGTGATACAT--G-----A---ATA-A-ATATATATATATATATGTA
* *
9483681 ATCATATTAGTGAATTTGTTAATACATACTTCATCCGGATAAAGTATGCATTATTAAAATTAA
118 ATCATATTAGTGAATCTGCTAATACATACTTCATCCGGATAAAGTATGCATTATTAAAATTAA
9483744 TGGTTTGTTT
Statistics
Matches: 375, Mismatches: 17, Indels: 20
0.91 0.04 0.05
Matches are distributed among these distances:
214 107 0.29
215 4 0.01
216 182 0.49
218 1 0.00
223 1 0.00
226 3 0.01
227 1 0.00
228 76 0.20
ACGTcount: A:0.43, C:0.07, G:0.11, T:0.40
Consensus pattern (215 bp):
AATATGTTATTTGAAAATAACTATTATTGTAATGAGATACATGTTCTATTAGGTATAAGTATTTA
AATTTTTGTTTTTGTAATGTGATACATGAATAAATATATATATATATATGTAATCATATTAGTGA
ATCTGCTAATACATACTTCATCCGGATAAAGTATGCATTATTAAAATTAAACTAAAATATTAAAT
AAAAAATAAAATTATAAAAC
Found at i:9483662 original size:2 final size:2
Alignment explanation
Indices: 9483650--9483680 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
9483640 ACATACGTAA
*
9483650 AT AT TT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
9483681 ATCATATTAG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:9488864 original size:3 final size:3
Alignment explanation
Indices: 9488858--9488899 Score: 66
Period size: 3 Copynumber: 14.0 Consensus size: 3
9488848 TGCTACTGCC
* *
9488858 TCT TCT TCT TCT TCT TTT TCT TCT TCT TCT TCT TTT TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
9488900 CTGTTAAAGG
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (3 bp):
TCT
Found at i:9491640 original size:46 final size:46
Alignment explanation
Indices: 9491590--9491761 Score: 208
Period size: 46 Copynumber: 3.7 Consensus size: 46
9491580 TGGTTGAGCA
*
9491590 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
* * * *
9491636 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATGTAACTAGGCA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAA--A--CG
*
9491683 TCCGAACTCGTTGAGTTGAGT-CGAGTTCACTTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
* *
9491728 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTA
9491762 GGGGCGGGTT
Statistics
Matches: 106, Mismatches: 12, Indels: 16
0.79 0.09 0.12
Matches are distributed among these distances:
43 6 0.06
45 23 0.22
46 48 0.45
47 24 0.23
49 5 0.05
ACGTcount: A:0.22, C:0.21, G:0.28, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
Found at i:9491745 original size:92 final size:93
Alignment explanation
Indices: 9491587--9491756 Score: 297
Period size: 92 Copynumber: 1.8 Consensus size: 93
9491577 GGATGGTTGA
* *
9491587 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGCCCGAACTCGTTGAGT
9491652 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
* *
9491680 GCATCCGAACTCGTTGAGTTGAGT-CGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGCCCGAACTCGTTGAGT
9491744 TGAGTCCGAGTTC
66 TGAGTCCGAGTTC
9491757 ACTTAGGGGC
Statistics
Matches: 73, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
92 49 0.67
93 24 0.33
ACGTcount: A:0.22, C:0.21, G:0.29, T:0.28
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:9498472 original size:46 final size:46
Alignment explanation
Indices: 9498422--9498594 Score: 208
Period size: 46 Copynumber: 3.7 Consensus size: 46
9498412 TGGTTGAGCA
*
9498422 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
* * * *
9498468 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATGTAACTAGGCA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAA--A--CG
* *
9498515 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
* *
9498561 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTA
9498595 GGGGCGGGTT
Statistics
Matches: 109, Mismatches: 11, Indels: 14
0.81 0.08 0.10
Matches are distributed among these distances:
43 6 0.06
45 3 0.03
46 63 0.58
47 29 0.27
48 3 0.03
50 5 0.05
ACGTcount: A:0.23, C:0.21, G:0.27, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
Found at i:9498578 original size:93 final size:93
Alignment explanation
Indices: 9498419--9498589 Score: 297
Period size: 93 Copynumber: 1.8 Consensus size: 93
9498409 GGATGGTTGA
***
9498419 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACACCCGAACTCGTTGAGT
9498484 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
* *
9498512 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACACCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACACCCGAACTCGTTGAGT
9498577 TGAGTCCGAGTTC
66 TGAGTCCGAGTTC
9498590 ACTTAGGGGC
Statistics
Matches: 73, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
93 73 1.00
ACGTcount: A:0.22, C:0.22, G:0.28, T:0.28
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACACCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:9499978 original size:47 final size:45
Alignment explanation
Indices: 9499925--9500190 Score: 209
Period size: 47 Copynumber: 5.7 Consensus size: 45
9499915 ACAAATCTTA
*
9499925 GCCGATGCGTGTCCCAGACATGTCTTACACTGGCTATCTCTGTCGAG
1 GCCGATGCATGTCCCAGACATGTCTTACACTGGCTATCTCTGT--AG
*
9499972 GCCGATGCATGTCCCAGACATGTCTTAAACTGGCACTTATCTCTGT--
1 GCCGATGCATGTCCCAGACATGTCTTACACTGG--C-TATCTCTGTAG
* *
9500018 GCCGATGTCATGTGCCAGACATGGTCTTACACTGGCTATCAT-AGTATG
1 GCCGATG-CATGTCCCAGACAT-GTCTTACACTGGCTATC-TCTGTA-G
* * * * * * * *
9500066 GCTGATGCATATCCCAAACATGTCTTACACTAGCCCT-TGTTTGGAT
1 GCCGATGCATGTCCCAGACATGTCTTACACT-G-GCTATCTCTGTAG
* *
9500112 GCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATAATGT-G
1 GCCGATG-CATGTCCCAGACAT-GTCTTACACTGGCTATC-T-CTGTAG
* * *
9500160 GCTGAAGCATGTCTCAGACATGTCTTACACT
1 GCCGATGCATGTCCCAGACATGTCTTACACT
9500191 AGCGCACAAA
Statistics
Matches: 177, Mismatches: 25, Indels: 35
0.75 0.11 0.15
Matches are distributed among these distances:
45 6 0.03
46 38 0.21
47 86 0.49
48 35 0.20
49 3 0.02
50 9 0.05
ACGTcount: A:0.22, C:0.27, G:0.22, T:0.29
Consensus pattern (45 bp):
GCCGATGCATGTCCCAGACATGTCTTACACTGGCTATCTCTGTAG
Found at i:9500115 original size:94 final size:93
Alignment explanation
Indices: 9499925--9500193 Score: 305
Period size: 94 Copynumber: 2.9 Consensus size: 93
9499915 ACAAATCTTA
* * *
9499925 GCCGATGCGTGTCCCAGACAT-GTCTTACACTGGCTATC-TCTGTCGA-GGCCGATGCATGTCCC
1 GCCGATGCATGTCCCAGACATGGTCTTACACTGGCTATCAT-AGT--ATGGCTGATGCATGTCCC
* *
9499987 AGACATGTCTTAAACTGGCACTTATCTCTGT
63 AGACATGTCTTACACTAGCACTTATCTCTGT
* * *
9500018 GCCGATGTCATGTGCCAGACATGGTCTTACACTGGCTATCATAGTATGGCTGATGCATATCCCAA
1 GCCGATG-CATGTCCCAGACATGGTCTTACACTGGCTATCATAGTATGGCTGATGCATGTCCCAG
* *
9500083 ACATGTCTTACACTAGCCCTTGT-T-TGGAT
65 ACATGTCTTACACTAGCACTTATCTCT-G-T
* * * * *
9500112 GCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATAATGTGGCTGAAGCATGTCTCAG
1 GCCGATG-CATGTCCCAGACATGGTCTTACACTGGCTATCATAGTATGGCTGATGCATGTCCCAG
9500177 ACATGTCTTACACTAGC
65 ACATGTCTTACACTAGC
9500194 GCACAAATCA
Statistics
Matches: 151, Mismatches: 19, Indels: 11
0.83 0.10 0.06
Matches are distributed among these distances:
92 1 0.01
93 10 0.07
94 120 0.79
95 19 0.13
96 1 0.01
ACGTcount: A:0.22, C:0.27, G:0.22, T:0.29
Consensus pattern (93 bp):
GCCGATGCATGTCCCAGACATGGTCTTACACTGGCTATCATAGTATGGCTGATGCATGTCCCAGA
CATGTCTTACACTAGCACTTATCTCTGT
Found at i:9505163 original size:22 final size:23
Alignment explanation
Indices: 9505138--9505182 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 23
9505128 CCATTAAACA
9505138 TTCAACTAAACA-TCATTATAAG
1 TTCAACTAAACAGTCATTATAAG
* *
9505160 TTCATCTATACATGTCATTATAA
1 TTCAACTAAACA-GTCATTATAA
9505183 CATTGGCCAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 10 0.53
24 9 0.47
ACGTcount: A:0.40, C:0.18, G:0.04, T:0.38
Consensus pattern (23 bp):
TTCAACTAAACAGTCATTATAAG
Found at i:9509806 original size:21 final size:22
Alignment explanation
Indices: 9509780--9509836 Score: 57
Period size: 21 Copynumber: 2.7 Consensus size: 22
9509770 GTAAGGAGTA
9509780 GCACACGGCCGTGTG-GCAGAG
1 GCACACGGCCGTGTGTGCAGAG
** *
9509801 GCACACACCCATGTGGTGCAGAG
1 GCACACGGCCGTGT-GTGCAGAG
9509824 G--CACGGCCGTGTG
1 GCACACGGCCGTGTG
9509837 ATCAGGCCGT
Statistics
Matches: 28, Mismatches: 6, Indels: 5
0.72 0.15 0.13
Matches are distributed among these distances:
20 1 0.04
21 19 0.68
22 1 0.04
23 7 0.25
ACGTcount: A:0.19, C:0.30, G:0.39, T:0.12
Consensus pattern (22 bp):
GCACACGGCCGTGTGTGCAGAG
Found at i:9515501 original size:93 final size:93
Alignment explanation
Indices: 9515389--9515560 Score: 317
Period size: 93 Copynumber: 1.8 Consensus size: 93
9515379 GCCCATAAGT
* *
9515389 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACGCTCGCATCCATAAGTGAACTCGGACTCAACTCAA
9515454 CGAGTTCGGATGCCTAGTTACATCTCAC
66 CGAGTTCGGATGCCTAGTTACATCTCAC
*
9515482 GAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACGCTCGCATCCATAAGTGAACTCGGACTCAACTCAA
9515547 CGAGTTCGGATGCC
66 CGAGTTCGGATGCC
9515561 CAAATATCCC
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 76 1.00
ACGTcount: A:0.27, C:0.30, G:0.22, T:0.20
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACGCTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATCTCAC
Found at i:9515556 original size:46 final size:46
Alignment explanation
Indices: 9515381--9515556 Score: 232
Period size: 46 Copynumber: 3.8 Consensus size: 46
9515371 TGTAACCCGC
* * *
9515381 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCAT
* *
9515427 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACG-CTCG---CAT
* *
9515477 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCAT
9515520 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
9515557 TGCCCAAATA
Statistics
Matches: 112, Mismatches: 11, Indels: 14
0.82 0.08 0.10
Matches are distributed among these distances:
43 3 0.03
44 1 0.01
45 2 0.02
46 68 0.61
47 32 0.29
48 2 0.02
49 1 0.01
50 3 0.03
ACGTcount: A:0.28, C:0.30, G:0.22, T:0.20
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCAT
Found at i:9517969 original size:30 final size:30
Alignment explanation
Indices: 9517925--9518013 Score: 101
Period size: 30 Copynumber: 3.0 Consensus size: 30
9517915 CAAAGATAAC
9517925 AAGAAAACC-GAATAAAGAAATCCAAGATA
1 AAGAAAACCAGAATAAAGAAATCCAAGATA
* *
9517954 GAGAAACCCAGAATAAAGAAATCC-AGAATA
1 AAGAAAACCAGAATAAAGAAATCCAAG-ATA
* * * *
9517984 AAGAGATCCAGGATAAAGAAACCCAAGATA
1 AAGAAAACCAGAATAAAGAAATCCAAGATA
9518014 CGATACTATG
Statistics
Matches: 50, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
29 9 0.18
30 39 0.78
31 2 0.04
ACGTcount: A:0.57, C:0.16, G:0.17, T:0.10
Consensus pattern (30 bp):
AAGAAAACCAGAATAAAGAAATCCAAGATA
Found at i:9517973 original size:15 final size:15
Alignment explanation
Indices: 9517925--9518004 Score: 92
Period size: 15 Copynumber: 5.4 Consensus size: 15
9517915 CAAAGATAAC
*
9517925 AAGAAAACC-GAATA
1 AAGAAATCCAGAATA
9517939 AAGAAATCCA-AGATA
1 AAGAAATCCAGA-ATA
* *
9517954 GAGAAACCCAGAATA
1 AAGAAATCCAGAATA
9517969 AAGAAATCCAGAATA
1 AAGAAATCCAGAATA
* *
9517984 AAGAGATCCAGGATA
1 AAGAAATCCAGAATA
9517999 AAGAAA
1 AAGAAA
9518005 CCCAAGATAC
Statistics
Matches: 55, Mismatches: 8, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
14 9 0.16
15 45 0.82
16 1 0.02
ACGTcount: A:0.59, C:0.14, G:0.17, T:0.10
Consensus pattern (15 bp):
AAGAAATCCAGAATA
Found at i:9518013 original size:15 final size:15
Alignment explanation
Indices: 9517936--9518013 Score: 79
Period size: 15 Copynumber: 5.2 Consensus size: 15
9517926 AGAAAACCGA
9517936 ATAAAGAAATCCAAG
1 ATAAAGAAATCCAAG
* *
9517951 ATAGAGAAA-CCCAG
1 ATAAAGAAATCCAAG
9517965 AATAAAGAAATCC-AG
1 -ATAAAGAAATCCAAG
* *
9517980 AATAAAGAGATCCAGG
1 -ATAAAGAAATCCAAG
*
9517996 ATAAAGAAACCCAAG
1 ATAAAGAAATCCAAG
9518011 ATA
1 ATA
9518014 CGATACTATG
Statistics
Matches: 52, Mismatches: 8, Indels: 6
0.79 0.12 0.09
Matches are distributed among these distances:
14 4 0.08
15 45 0.87
16 3 0.06
ACGTcount: A:0.56, C:0.15, G:0.17, T:0.12
Consensus pattern (15 bp):
ATAAAGAAATCCAAG
Found at i:9521078 original size:93 final size:93
Alignment explanation
Indices: 9520966--9521137 Score: 317
Period size: 93 Copynumber: 1.8 Consensus size: 93
9520956 GCCCATAAGT
* *
9520966 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACGCTCGCATCCATAAGTGAACTCGGACTCAACTCAA
9521031 CGAGTTCGGATGCCTAGTTACATCTCAC
66 CGAGTTCGGATGCCTAGTTACATCTCAC
*
9521059 GAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACGCTCGCATCCATAAGTGAACTCGGACTCAACTCAA
9521124 CGAGTTCGGATGCC
66 CGAGTTCGGATGCC
9521138 CAAATATCCA
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 76 1.00
ACGTcount: A:0.27, C:0.30, G:0.22, T:0.20
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACGCTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATCTCAC
Found at i:9521133 original size:46 final size:46
Alignment explanation
Indices: 9520958--9521133 Score: 232
Period size: 46 Copynumber: 3.8 Consensus size: 46
9520948 TGTAACCCGC
* * *
9520958 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCAT
* *
9521004 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACG-CTCG---CAT
* *
9521054 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCAT
9521097 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
9521134 TGCCCAAATA
Statistics
Matches: 112, Mismatches: 11, Indels: 14
0.82 0.08 0.10
Matches are distributed among these distances:
43 3 0.03
44 1 0.01
45 2 0.02
46 68 0.61
47 32 0.29
48 2 0.02
49 1 0.01
50 3 0.03
ACGTcount: A:0.28, C:0.30, G:0.22, T:0.20
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCAT
Found at i:9523528 original size:19 final size:21
Alignment explanation
Indices: 9523469--9523530 Score: 74
Period size: 21 Copynumber: 3.0 Consensus size: 21
9523459 ATTGGGTGGA
*
9523469 TCAACTCTTATGAGCTTCTGT
1 TCAACTCTTACGAGCTTCTGT
*
9523490 TCAACTCTTACGAACTTCTGT
1 TCAACTCTTACGAGCTTCTGT
* *
9523511 TTAGCT-TT-CGAGCTTCTGT
1 TCAACTCTTACGAGCTTCTGT
9523530 T
1 T
9523531 AACGATGTAC
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
19 11 0.31
20 2 0.06
21 23 0.64
ACGTcount: A:0.18, C:0.24, G:0.15, T:0.44
Consensus pattern (21 bp):
TCAACTCTTACGAGCTTCTGT
Found at i:9524662 original size:5 final size:5
Alignment explanation
Indices: 9524647--9524676 Score: 51
Period size: 5 Copynumber: 5.8 Consensus size: 5
9524637 GTTAATCCAA
9524647 ATTTGT ATTTT ATTTT ATTTT ATTTT ATTT
1 ATTT-T ATTTT ATTTT ATTTT ATTTT ATTT
9524677 CCTATTCTCT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 20 0.83
6 4 0.17
ACGTcount: A:0.20, C:0.00, G:0.03, T:0.77
Consensus pattern (5 bp):
ATTTT
Found at i:9533862 original size:8 final size:8
Alignment explanation
Indices: 9533849--9533874 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
9533839 GCCAAATATC
9533849 TTTTATTA
1 TTTTATTA
9533857 TTTTATTA
1 TTTTATTA
9533865 TTTTATTA
1 TTTTATTA
9533873 TT
1 TT
9533875 CTGAATTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (8 bp):
TTTTATTA
Found at i:9539206 original size:13 final size:12
Alignment explanation
Indices: 9539178--9539202 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
9539168 ATATAATATG
9539178 TAAAAAACTAAA
1 TAAAAAACTAAA
9539190 TAAAAAACTAAA
1 TAAAAAACTAAA
9539202 T
1 T
9539203 TAAATTAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.72, C:0.08, G:0.00, T:0.20
Consensus pattern (12 bp):
TAAAAAACTAAA
Found at i:9539457 original size:10 final size:10
Alignment explanation
Indices: 9539415--9539457 Score: 54
Period size: 10 Copynumber: 4.4 Consensus size: 10
9539405 GTTATTTGTT
9539415 TTTTAGTTTAA
1 TTTTA-TTTAA
*
9539426 TTTAATTTAA
1 TTTTATTTAA
9539436 TTTT-TTT-A
1 TTTTATTTAA
9539444 TTTTATTTAA
1 TTTTATTTAA
9539454 TTTT
1 TTTT
9539458 TCACATAATG
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
8 5 0.18
9 6 0.21
10 13 0.46
11 4 0.14
ACGTcount: A:0.26, C:0.00, G:0.02, T:0.72
Consensus pattern (10 bp):
TTTTATTTAA
Found at i:9543346 original size:21 final size:23
Alignment explanation
Indices: 9543300--9543350 Score: 70
Period size: 23 Copynumber: 2.3 Consensus size: 23
9543290 AAGTTTTTTA
9543300 ATTTTAAAAATTTGTAAGTAATT
1 ATTTTAAAAATTTGTAAGTAATT
* *
9543323 ATTTTAAAATTTTGTTA-T-ATT
1 ATTTTAAAAATTTGTAAGTAATT
9543344 ATTTTAA
1 ATTTTAA
9543351 CTTATTTTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
21 10 0.38
22 1 0.04
23 15 0.58
ACGTcount: A:0.39, C:0.00, G:0.06, T:0.55
Consensus pattern (23 bp):
ATTTTAAAAATTTGTAAGTAATT
Found at i:9548481 original size:25 final size:25
Alignment explanation
Indices: 9548453--9548504 Score: 95
Period size: 25 Copynumber: 2.1 Consensus size: 25
9548443 ATATAGGTTC
9548453 AAAAAATGAGGTTGAACAAAAAAAT
1 AAAAAATGAGGTTGAACAAAAAAAT
*
9548478 AAAAAATGAGGTTGAATAAAAAAAT
1 AAAAAATGAGGTTGAACAAAAAAAT
9548503 AA
1 AA
9548505 GACCTGTTTA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.65, C:0.02, G:0.15, T:0.17
Consensus pattern (25 bp):
AAAAAATGAGGTTGAACAAAAAAAT
Found at i:9549390 original size:29 final size:29
Alignment explanation
Indices: 9549351--9549428 Score: 102
Period size: 29 Copynumber: 2.7 Consensus size: 29
9549341 GCAATCACTA
**
9549351 TTCTCTCATTTTCTGTCAAAAAATTTTTC
1 TTCTCTCATTTTCTCCCAAAAAATTTTTC
* *
9549380 TTCTCTCATTTTCTCCCAACATATTTTTC
1 TTCTCTCATTTTCTCCCAAAAAATTTTTC
*
9549409 TTCTTTCATTTTCTCTCCAA
1 TTCTCTCATTTTCTC-CCAA
9549429 CATAACATAT
Statistics
Matches: 43, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
29 39 0.91
30 4 0.09
ACGTcount: A:0.19, C:0.27, G:0.01, T:0.53
Consensus pattern (29 bp):
TTCTCTCATTTTCTCCCAAAAAATTTTTC
Found at i:9558333 original size:62 final size:58
Alignment explanation
Indices: 9558215--9558348 Score: 164
Period size: 62 Copynumber: 2.2 Consensus size: 58
9558205 ACCACTTTAA
* * *
9558215 TATTAAATTAATATAATATTTATCAAGATAAATATTATATTAACTTTAATATTAAATC
1 TATTAAATTAATATAATATTTATCAAGATAAACATTATATCAAATTTAATATTAAATC
9558273 TTATTAAATTAATAGT-ATATTTATCTACAAGATAAACATTA-AGTCAAATTTAATATTAAATC
1 -TATTAAATTAATA-TAATATTTA--T-CAAGATAAACATTATA-TCAAATTTAATATTAAATC
*
9558335 TATTAAAATAATAT
1 TATTAAATTAATAT
9558349 TATTTTTGGA
Statistics
Matches: 66, Mismatches: 4, Indels: 9
0.84 0.05 0.11
Matches are distributed among these distances:
59 20 0.30
60 2 0.03
61 14 0.21
62 30 0.45
ACGTcount: A:0.49, C:0.06, G:0.03, T:0.43
Consensus pattern (58 bp):
TATTAAATTAATATAATATTTATCAAGATAAACATTATATCAAATTTAATATTAAATC
Found at i:9563469 original size:16 final size:16
Alignment explanation
Indices: 9563458--9563517 Score: 50
Period size: 16 Copynumber: 3.7 Consensus size: 16
9563448 TTAATTACTT
9563458 TAATATTAAATTAATA
1 TAATATTAAATTAATA
* * *
9563474 TAATATT-TATCAAGA
1 TAATATTAAATTAATA
* *
9563489 TAAATATTAGATTAAATT
1 T-AATATTAAATT-AATA
9563507 TAATATTAAAT
1 TAATATTAAAT
9563518 CTTATTAAAT
Statistics
Matches: 33, Mismatches: 8, Indels: 5
0.72 0.17 0.11
Matches are distributed among these distances:
15 6 0.18
16 13 0.39
17 11 0.33
18 3 0.09
ACGTcount: A:0.52, C:0.02, G:0.03, T:0.43
Consensus pattern (16 bp):
TAATATTAAATTAATA
Found at i:9563530 original size:59 final size:59
Alignment explanation
Indices: 9563461--9563575 Score: 162
Period size: 59 Copynumber: 1.9 Consensus size: 59
9563451 ATTACTTTAA
* * *
9563461 TATTAAATTAATATAATATTTATC-A-AGATAAATATTAGATTAAATTTAATATTAAATCT
1 TATTAAATTAATAGAATATTTATCAAGAGATAAA-ATTAAATTAAATTAAAT-TTAAATCT
9563520 TATTAAATTAATAGAATATTTATCTAAGAGATAAAATTAAATTAAATTAAATTTAA
1 TATTAAATTAATAGAATATTTATC-AAGAGATAAAATTAAATTAAATTAAATTTAA
9563576 GATTAAAATA
Statistics
Matches: 50, Mismatches: 3, Indels: 5
0.86 0.05 0.09
Matches are distributed among these distances:
59 23 0.46
60 4 0.08
61 16 0.32
62 7 0.14
ACGTcount: A:0.51, C:0.03, G:0.04, T:0.42
Consensus pattern (59 bp):
TATTAAATTAATAGAATATTTATCAAGAGATAAAATTAAATTAAATTAAATTTAAATCT
Found at i:9565201 original size:15 final size:14
Alignment explanation
Indices: 9565181--9565219 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 14
9565171 ATGCATGCAC
9565181 AATATGAAAGATAGA
1 AATATGAAAGATA-A
*
9565196 AATATGAAAGGTAA
1 AATATGAAAGATAA
9565210 AATAGTGAAA
1 AATA-TGAAA
9565220 TGTGAAATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 5 0.23
15 17 0.77
ACGTcount: A:0.59, C:0.00, G:0.21, T:0.21
Consensus pattern (14 bp):
AATATGAAAGATAA
Found at i:9572894 original size:45 final size:43
Alignment explanation
Indices: 9572829--9572975 Score: 120
Period size: 45 Copynumber: 3.3 Consensus size: 43
9572819 AAAACCATGA
*
9572829 TTGAAAGATATCGT-GACATTATACCTGAAATGAAAAAGACCATAG
1 TTGAAAGATA-C-TAGACATTATATC-GAAATGAAAAAGACCATAG
* * * * **
9572874 TTGAAAGATATTATAGCATTAAATCGAAA-CAGGTAAGACTC-TAG
1 TTGAAAGATACTAGA-CATTATATCGAAATGA-AAAAGAC-CATAG
* *
9572918 TTGAAAGATACTAGACACTATATCGGAAAATGAACAAGACCATAG
1 TTGAAAGATACTAGACATTATATC-G-AAATGAAAAAGACCATAG
9572963 TTGAAAGATACTA
1 TTGAAAGATACTA
9572976 TGGCACCACT
Statistics
Matches: 80, Mismatches: 14, Indels: 16
0.73 0.13 0.15
Matches are distributed among these distances:
43 9 0.11
44 28 0.35
45 42 0.52
46 1 0.01
ACGTcount: A:0.45, C:0.13, G:0.18, T:0.24
Consensus pattern (43 bp):
TTGAAAGATACTAGACATTATATCGAAATGAAAAAGACCATAG
Found at i:9578584 original size:21 final size:21
Alignment explanation
Indices: 9578558--9578598 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
9578548 AGACAAGCGA
* *
9578558 TACTCCACAGCAGGTGGAGTG
1 TACTCCAAAACAGGTGGAGTG
9578579 TACTCCAAAACAGGTGGAGT
1 TACTCCAAAACAGGTGGAGT
9578599 TTGAGCAGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.22, G:0.29, T:0.20
Consensus pattern (21 bp):
TACTCCAAAACAGGTGGAGTG
Found at i:9595781 original size:1 final size:1
Alignment explanation
Indices: 9595775--9595803 Score: 58
Period size: 1 Copynumber: 29.0 Consensus size: 1
9595765 GATTGATTCC
9595775 TTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTT
9595804 AAGGTTGTGG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 28 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:9600174 original size:15 final size:16
Alignment explanation
Indices: 9600154--9600187 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
9600144 GCAGGTATCG
*
9600154 ATACTTTGT-GAAAGT
1 ATACTTTGTAAAAAGT
9600169 ATACTTTGTAAAAAGT
1 ATACTTTGTAAAAAGT
9600185 ATA
1 ATA
9600188 GATACTTGGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 9 0.53
16 8 0.47
ACGTcount: A:0.41, C:0.06, G:0.15, T:0.38
Consensus pattern (16 bp):
ATACTTTGTAAAAAGT
Found at i:9600194 original size:20 final size:20
Alignment explanation
Indices: 9600169--9600217 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 20
9600159 TTGTGAAAGT
9600169 ATACTTTGTAAAAAGTATAG
1 ATACTTTGTAAAAAGTATAG
* **
9600189 ATACTTGGTGCAAAGTATAG
1 ATACTTTGTAAAAAGTATAG
*
9600209 ATATTTTGT
1 ATACTTTGT
9600218 GCAAAGTATC
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.37, C:0.06, G:0.18, T:0.39
Consensus pattern (20 bp):
ATACTTTGTAAAAAGTATAG
Found at i:9600219 original size:20 final size:20
Alignment explanation
Indices: 9600180--9600226 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
9600170 TACTTTGTAA
9600180 AAAGTATAGATACTTGGTGC
1 AAAGTATAGATACTTGGTGC
* *
9600200 AAAGTATAGATATTTTGTGC
1 AAAGTATAGATACTTGGTGC
9600220 AAAGTAT
1 AAAGTAT
9600227 CGGCACCTTG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.38, C:0.06, G:0.21, T:0.34
Consensus pattern (20 bp):
AAAGTATAGATACTTGGTGC
Found at i:9602255 original size:6 final size:6
Alignment explanation
Indices: 9602244--9602270 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
9602234 TTACAAGCAT
9602244 CATTTA CATTTA CATTTA CATTTA CAT
1 CATTTA CATTTA CATTTA CATTTA CAT
9602271 GCCAATATGG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.33, C:0.19, G:0.00, T:0.48
Consensus pattern (6 bp):
CATTTA
Found at i:9604621 original size:49 final size:50
Alignment explanation
Indices: 9604312--9604722 Score: 258
Period size: 49 Copynumber: 8.6 Consensus size: 50
9604302 TATGTGTGCT
* * * *
9604312 AGTGTAAGA-CATGTCTGGGATAT-GCATCGGCCAC-ATTATGA-GAGCC
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCCTCGATGATGATAAGCC
* ** * * * *
9604358 AGTGTAAGACCATGTCTGGGACATGGCATCAGTATTGA-GACGA-GAGCT
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCCTCGATGATGATAAGCC
* * *
9604406 AGTGTAAGA-CATGTTTGGGACAT-GCATCGGTCTCGA-GACG-TAAGCC
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCCTCGATGATGATAAGCC
* * * ** *
9604452 AGTGTAAGA-CATGTCTGGGAGAT-GAATCAG-CT--ATGA-GATGTGTC
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCCTCGATGATGATAAGCC
* * * *
9604496 AATGTAAGACCATGTCTGGGACATGGCATTGGCAC-GGAT-ATG-TAAGAGCT
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGC-CTCGATGATGAT-A-AGCC
* * * *
9604546 AGTGGAAGACCATGTCTGGGATATGGCGTCGGCCTCGATGATGAT-AGTC
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCCTCGATGATGATAAGCC
* * * * * **
9604595 AGTGTAAGACCATGTCTGGGACATGGCGTCGACTTCAATGACGAT-ATTC
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCCTCGATGATGATAAGCC
* * * * *
9604644 AGTGTAAGACCATGTCTGGGACATGACATC-GACT-TAAGAT-ATGAGCC
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCCTCGATGATGATAAGCC
*
9604691 AGTGTAAGACCATGTTTGGGACATGGCATCGG
1 AGTGTAAGACCATGTCTGGGACATGGCATCGG
9604723 TATTCTACCC
Statistics
Matches: 287, Mismatches: 58, Indels: 38
0.75 0.15 0.10
Matches are distributed among these distances:
43 2 0.01
44 13 0.05
45 15 0.05
46 58 0.20
47 59 0.21
48 27 0.09
49 77 0.27
50 32 0.11
51 3 0.01
52 1 0.00
ACGTcount: A:0.28, C:0.18, G:0.30, T:0.25
Consensus pattern (50 bp):
AGTGTAAGACCATGTCTGGGACATGGCATCGGCCTCGATGATGATAAGCC
Found at i:9608577 original size:16 final size:16
Alignment explanation
Indices: 9608556--9608587 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
9608546 CTTTTATAAC
9608556 GTACTTCATGAACCAA
1 GTACTTCATGAACCAA
9608572 GTACTTCATGAACCAA
1 GTACTTCATGAACCAA
9608588 ACATACTATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.38, C:0.25, G:0.12, T:0.25
Consensus pattern (16 bp):
GTACTTCATGAACCAA
Found at i:9619825 original size:13 final size:13
Alignment explanation
Indices: 9619807--9619833 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
9619797 AAAGTAATTG
9619807 CACACGGGCGTGT
1 CACACGGGCGTGT
9619820 CACACGGGCGTGT
1 CACACGGGCGTGT
9619833 C
1 C
9619834 CCTGTCGAGC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.15, C:0.33, G:0.37, T:0.15
Consensus pattern (13 bp):
CACACGGGCGTGT
Found at i:9621252 original size:47 final size:49
Alignment explanation
Indices: 9621146--9621274 Score: 155
Period size: 47 Copynumber: 2.7 Consensus size: 49
9621136 TACGTCCCGA
9621146 GGCTGATGCATGTCCCAGACATGTCTTACACTAGCACTCTTCTCAATGT
1 GGCTGATGCATGTCCCAGACATGTCTTACACTAGCACTCTTCTCAATGT
*
9621195 --C-GATGCCATGTCCCAGACATGGTCTTACACT-G-GCTC-TCAT-AATGT
1 GGCTGATG-CATGTCCCAGACAT-GTCTTACACTAGCACTCTTC-TCAATGT
* *
9621240 GGCTGATGCATGTCTCAGACATGTATTACACTAGC
1 GGCTGATGCATGTCCCAGACATGTCTTACACTAGC
9621275 CCACAATAAC
Statistics
Matches: 69, Mismatches: 3, Indels: 17
0.78 0.03 0.19
Matches are distributed among these distances:
45 7 0.10
46 17 0.25
47 31 0.45
48 14 0.20
ACGTcount: A:0.23, C:0.27, G:0.20, T:0.29
Consensus pattern (49 bp):
GGCTGATGCATGTCCCAGACATGTCTTACACTAGCACTCTTCTCAATGT
Found at i:9621652 original size:30 final size:30
Alignment explanation
Indices: 9621611--9621668 Score: 98
Period size: 30 Copynumber: 1.9 Consensus size: 30
9621601 AAATTTACAT
* *
9621611 CTTTGGTAAAATGACCATTTTGCTCCTAGA
1 CTTTGGCAAAATGACCATTTTGCCCCTAGA
9621641 CTTTGGCAAAATGACCATTTTGCCCCTA
1 CTTTGGCAAAATGACCATTTTGCCCCTA
9621669 TGCCCTAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.26, C:0.24, G:0.16, T:0.34
Consensus pattern (30 bp):
CTTTGGCAAAATGACCATTTTGCCCCTAGA
Found at i:9621905 original size:36 final size:36
Alignment explanation
Indices: 9621865--9621940 Score: 125
Period size: 36 Copynumber: 2.1 Consensus size: 36
9621855 CAAGACTCAT
*
9621865 TTTCTTCAATAAAAACTCAGCAAACAACACAAATCC
1 TTTCTTCAATAAAAACCCAGCAAACAACACAAATCC
* *
9621901 TTTCTTCCATAAAAACCCAGCAAACAACACAAATGC
1 TTTCTTCAATAAAAACCCAGCAAACAACACAAATCC
9621937 TTTC
1 TTTC
9621941 ATGGAAAAAC
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.43, C:0.29, G:0.04, T:0.24
Consensus pattern (36 bp):
TTTCTTCAATAAAAACCCAGCAAACAACACAAATCC
Found at i:9626187 original size:43 final size:42
Alignment explanation
Indices: 9626025--9626185 Score: 173
Period size: 43 Copynumber: 3.8 Consensus size: 42
9626015 TGGCATCGAC
* * * *
9626025 TTACGTGTAAGACCACGTCTTGGATGTTGGCATCGTATTTTA
1 TTACATGTAAGACCACGTCTGGGACGTTGGCATCGTATTTGA
* *
9626067 TTTACCTGTAAGACCACGTCTGGGACATTGGCATCGTATTTGA
1 -TTACATGTAAGACCACGTCTGGGACGTTGGCATCGTATTTGA
** * *
9626110 TTTTATGTAAGACC-CTGTCTGGCACAG-TGGCATTGATATTTGA
1 TTACATGTAAGACCAC-GTCTGGGAC-GTTGGCATCG-TATTTGA
*
9626153 TTACATGTAAGACCACGTTTGGGACGTTGGCAT
1 TTACATGTAAGACCACGTCTGGGACGTTGGCAT
9626186 TGTACAAGCC
Statistics
Matches: 98, Mismatches: 15, Indels: 10
0.80 0.12 0.08
Matches are distributed among these distances:
41 1 0.01
42 27 0.28
43 69 0.70
44 1 0.01
ACGTcount: A:0.23, C:0.18, G:0.24, T:0.35
Consensus pattern (42 bp):
TTACATGTAAGACCACGTCTGGGACGTTGGCATCGTATTTGA
Found at i:9626967 original size:22 final size:22
Alignment explanation
Indices: 9626924--9626967 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
9626914 TATGTCTTGG
* *
9626924 TATGATTTTGGTTTAGATTTGA
1 TATGATTTTGGTTGAGAATTGA
9626946 TATGA-TTTGGTTGATGAATTGA
1 TATGATTTTGGTTGA-GAATTGA
9626968 GACTGAAATT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 8 0.42
22 11 0.58
ACGTcount: A:0.25, C:0.00, G:0.25, T:0.50
Consensus pattern (22 bp):
TATGATTTTGGTTGAGAATTGA
Found at i:9635486 original size:40 final size:40
Alignment explanation
Indices: 9635401--9635551 Score: 134
Period size: 40 Copynumber: 3.8 Consensus size: 40
9635391 AATTGAATGA
* * *
9635401 TATCCGGGCTAA-ATCCCGAAGACAATTATGCTG-GAAATTA-
1 TATCCGGGCTAAGA-CCCGAAGGCAATTGTGC-GAGACA-TAC
* * *
9635441 TATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGC-TAC
1 TATCCGGGCTAAGACCCGAAGGCAATTGTGC--GAGACATAC
*
9635482 -ATCCGGGCTAAGACCCGAAGGC-ATTCGTGCGAGACATTC
1 TATCCGGGCTAAGACCCGAAGGCAATT-GTGCGAGACATAC
*
9635521 TATCCGGGCTAAGACCCGAAGGCATTTGTGC
1 TATCCGGGCTAAGACCCGAAGGCAATTGTGC
9635552 ACGTGATTAT
Statistics
Matches: 92, Mismatches: 11, Indels: 16
0.77 0.09 0.13
Matches are distributed among these distances:
38 3 0.03
39 5 0.05
40 79 0.86
41 4 0.04
42 1 0.01
ACGTcount: A:0.27, C:0.24, G:0.26, T:0.23
Consensus pattern (40 bp):
TATCCGGGCTAAGACCCGAAGGCAATTGTGCGAGACATAC
Found at i:9635565 original size:40 final size:40
Alignment explanation
Indices: 9635437--9635567 Score: 156
Period size: 40 Copynumber: 3.3 Consensus size: 40
9635427 TATGCTGGAA
* * *
9635437 ATTATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTG
1 ATTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTG
** * * **
9635477 GCTACATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGAC
1 ATTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTG
*
9635517 ATTCTATCCGGGCTAAGACCCGAAGGCATTTGTGC-ACGTG
1 ATTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGA-GTG
9635557 ATTATATCCGG
1 ATTATATCCGG
9635568 TTATATTCCG
Statistics
Matches: 73, Mismatches: 17, Indels: 2
0.79 0.18 0.02
Matches are distributed among these distances:
39 1 0.01
40 72 0.99
ACGTcount: A:0.25, C:0.24, G:0.27, T:0.24
Consensus pattern (40 bp):
ATTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTG
Found at i:9642369 original size:137 final size:137
Alignment explanation
Indices: 9642123--9642409 Score: 529
Period size: 137 Copynumber: 2.1 Consensus size: 137
9642113 TATTGGGCCT
**
9642123 AAGCCCATTCAGGTAACAGTGGTACTGGGCCAGAGCCCTTTTCAGATTACAATAAACTGGGCCTT
1 AAGCCCATTTGGGTAACAGTGGTACTGGGCCAGAGCCCTTTTCAGATTACAATAAACTGGGCCTT
* *
9642188 AGCCCCTTATTCAGATAACAGTATGGCCCATAGGCCCATTTCAAAATACATGCAACATCAGTAAA
66 AGCCCCATATTCAGATAACAGTATAGCCCATAGGCCCATTTCAAAATACATGCAACATCAGTAAA
9642253 CATATGC
131 CATATGC
9642260 AAGCCCATTTGGGTAACAGTGGTACTGGGCCAGAGCCCTTTTCAGATTACAATAAACTGGGCCTT
1 AAGCCCATTTGGGTAACAGTGGTACTGGGCCAGAGCCCTTTTCAGATTACAATAAACTGGGCCTT
*
9642325 AGCCCCATATTCAGATAACCGTATAGCCCATAGGCCCATTTCAAAATACATGCAACATCAGTAAA
66 AGCCCCATATTCAGATAACAGTATAGCCCATAGGCCCATTTCAAAATACATGCAACATCAGTAAA
9642390 CATATGC
131 CATATGC
9642397 AAGCCCATTTGGG
1 AAGCCCATTTGGG
9642410 GAGACTACTC
Statistics
Matches: 145, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
137 145 1.00
ACGTcount: A:0.32, C:0.25, G:0.19, T:0.24
Consensus pattern (137 bp):
AAGCCCATTTGGGTAACAGTGGTACTGGGCCAGAGCCCTTTTCAGATTACAATAAACTGGGCCTT
AGCCCCATATTCAGATAACAGTATAGCCCATAGGCCCATTTCAAAATACATGCAACATCAGTAAA
CATATGC
Found at i:9642693 original size:25 final size:27
Alignment explanation
Indices: 9642656--9642708 Score: 74
Period size: 26 Copynumber: 2.0 Consensus size: 27
9642646 TCAAACATGC
9642656 ATTTAGGTCAATTTAAC-CCTAGGGGT
1 ATTTAGGTCAATTTAACTCCTAGGGGT
* *
9642682 ATTTCGGT-AATTTATCTCCTAGGGGT
1 ATTTAGGTCAATTTAACTCCTAGGGGT
9642708 A
1 A
9642709 AAACTGTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 7 0.29
26 17 0.71
ACGTcount: A:0.25, C:0.15, G:0.23, T:0.38
Consensus pattern (27 bp):
ATTTAGGTCAATTTAACTCCTAGGGGT
Found at i:9644230 original size:26 final size:26
Alignment explanation
Indices: 9644194--9644303 Score: 177
Period size: 26 Copynumber: 4.2 Consensus size: 26
9644184 CATGGAATTC
9644194 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
9644220 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
* *
9644246 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCCA
*
9644272 TTATCATTG-AACATTTACCTAACCTA
1 TTATCA-TGAAACATTTACCTAACCCA
9644298 TTATCA
1 TTATCA
9644304 ATTTGTATCA
Statistics
Matches: 81, Mismatches: 2, Indels: 2
0.95 0.02 0.02
Matches are distributed among these distances:
26 79 0.98
27 2 0.02
ACGTcount: A:0.36, C:0.25, G:0.05, T:0.35
Consensus pattern (26 bp):
TTATCATGAAACATTTACCTAACCCA
Found at i:9651316 original size:4 final size:4
Alignment explanation
Indices: 9651307--9651335 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
9651297 GCTTTTTATT
9651307 TTTA TTTA TTTA TTTA TTTA TTTA TTTA T
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA T
9651336 CGTTTCCCAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TTTA
Found at i:9653636 original size:14 final size:14
Alignment explanation
Indices: 9653603--9653636 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
9653593 TTCCAAATAT
9653603 GAAAAA-AAAAAAA
1 GAAAAAGAAAAAAA
9653616 GAAAAAGAAAAAAA
1 GAAAAAGAAAAAAA
9653630 GAAAAAG
1 GAAAAAG
9653637 GATTGAGCGT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 6 0.30
14 14 0.70
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (14 bp):
GAAAAAGAAAAAAA
Found at i:9655996 original size:20 final size:20
Alignment explanation
Indices: 9655964--9656037 Score: 57
Period size: 20 Copynumber: 3.8 Consensus size: 20
9655954 GAAATGCATT
9655964 AAAATCGAT-AAAAATTACTA-
1 AAAATC-ATAAAAAATTA-TAG
* *
9655984 AAAGTCATAAAAAGTTATAG
1 AAAATCATAAAAAATTATAG
9656004 AAAATCATAAAAACA-TATA-
1 AAAATCATAAAAA-ATTATAG
* *
9656023 AATATTATAAAAAAT
1 AAAATCATAAAAAAT
9656038 ATTTTTAAAC
Statistics
Matches: 44, Mismatches: 6, Indels: 9
0.75 0.10 0.15
Matches are distributed among these distances:
18 1 0.02
19 15 0.34
20 28 0.64
ACGTcount: A:0.62, C:0.07, G:0.05, T:0.26
Consensus pattern (20 bp):
AAAATCATAAAAAATTATAG
Found at i:9656015 original size:19 final size:19
Alignment explanation
Indices: 9655964--9656016 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 19
9655954 GAAATGCATT
9655964 AAAATCGATAAAAATTACTA
1 AAAATC-ATAAAAATTACTA
*
9655984 AAAGTCATAAAAAGTTA-TA
1 AAAATCATAAAAA-TTACTA
9656003 GAAAATCATAAAAA
1 -AAAATCATAAAAA
9656017 CATATAAATA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
19 9 0.31
20 20 0.69
ACGTcount: A:0.62, C:0.08, G:0.08, T:0.23
Consensus pattern (19 bp):
AAAATCATAAAAATTACTA
Found at i:9656056 original size:21 final size:22
Alignment explanation
Indices: 9656021--9656061 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
9656011 TAAAAACATA
*
9656021 TAAATATTATAAAAAATATTTT
1 TAAACATTATAAAAAATATTTT
9656043 TAAACATTAT-AAAAATATT
1 TAAACATTATAAAAAATATT
9656062 AAATTAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.41
Consensus pattern (22 bp):
TAAACATTATAAAAAATATTTT
Found at i:9656097 original size:42 final size:41
Alignment explanation
Indices: 9656043--9656177 Score: 172
Period size: 42 Copynumber: 3.3 Consensus size: 41
9656033 AAAATATTTT
*
9656043 TAAACATTATAAAAATATTAAATTAAAAAATGATAAAAATA
1 TAAATATTATAAAAATATTAAATTAAAAAATGATAAAAATA
*
9656084 TAGAATATTATAAAAATATTAAATTGAAAAATGATAAAAATA
1 TA-AATATTATAAAAATATTAAATTAAAAAATGATAAAAATA
*
9656126 TTAAAT-TT-TAAAAATAATTAATATTAAAAAAT-ATTAAAATA
1 -TAAATATTATAAAAAT-ATTAA-ATTAAAAAATGATAAAAATA
9656167 -AAATA-TATAAA
1 TAAATATTATAAA
9656178 TTATGAAAAA
Statistics
Matches: 84, Mismatches: 4, Indels: 13
0.83 0.04 0.13
Matches are distributed among these distances:
39 5 0.06
40 11 0.13
41 17 0.20
42 49 0.58
43 2 0.02
ACGTcount: A:0.64, C:0.01, G:0.03, T:0.33
Consensus pattern (41 bp):
TAAATATTATAAAAATATTAAATTAAAAAATGATAAAAATA
Found at i:9656131 original size:16 final size:16
Alignment explanation
Indices: 9656112--9656187 Score: 70
Period size: 16 Copynumber: 4.8 Consensus size: 16
9656102 TTAAATTGAA
*
9656112 AAATGATAAAAATATT
1 AAATTATAAAAATATT
*
9656128 AAATTTTAAAAATAATT
1 AAATTATAAAAAT-ATT
9656145 AATATTA-AAAAATATT
1 AA-ATTATAAAAATATT
9656161 AAA--AT-AAAATATAT
1 AAATTATAAAAATAT-T
9656175 AAATTATGAAAAA
1 AAATTAT-AAAAA
9656188 ATAAAAAATA
Statistics
Matches: 49, Mismatches: 3, Indels: 14
0.74 0.05 0.21
Matches are distributed among these distances:
13 8 0.16
14 4 0.08
15 1 0.02
16 18 0.37
17 11 0.22
18 7 0.14
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (16 bp):
AAATTATAAAAATATT
Found at i:9656138 original size:24 final size:24
Alignment explanation
Indices: 9656051--9656132 Score: 95
Period size: 24 Copynumber: 3.7 Consensus size: 24
9656041 TTTAAACATT
*
9656051 ATAAAAATATTAAATTAAAAAATG
1 ATAAAAATATTAAATTGAAAAATG
* *
9656075 ATAAAAATA-T--A--G-AATATT
1 ATAAAAATATTAAATTGAAAAATG
9656093 ATAAAAATATTAAATTGAAAAATG
1 ATAAAAATATTAAATTGAAAAATG
9656117 ATAAAAATATTAAATT
1 ATAAAAATATTAAATT
9656133 TTAAAAATAA
Statistics
Matches: 47, Mismatches: 5, Indels: 12
0.73 0.08 0.19
Matches are distributed among these distances:
18 13 0.28
19 1 0.02
21 2 0.04
23 2 0.04
24 29 0.62
ACGTcount: A:0.63, C:0.00, G:0.05, T:0.32
Consensus pattern (24 bp):
ATAAAAATATTAAATTGAAAAATG
Found at i:9656187 original size:23 final size:23
Alignment explanation
Indices: 9656161--9656205 Score: 72
Period size: 24 Copynumber: 1.9 Consensus size: 23
9656151 AAAAAATATT
*
9656161 AAAATAAAATATATAAATTATGAA
1 AAAATAAAAAATA-AAATTATGAA
9656185 AAAATAAAAAATAAAATTATG
1 AAAATAAAAAATAAAATTATG
9656206 GTCTTTTTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 8 0.40
24 12 0.60
ACGTcount: A:0.69, C:0.00, G:0.04, T:0.27
Consensus pattern (23 bp):
AAAATAAAAAATAAAATTATGAA
Found at i:9656273 original size:20 final size:22
Alignment explanation
Indices: 9656250--9656290 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
9656240 TAAAAAATCA
9656250 ATAAAAT-TT-TAAAAAGTATT
1 ATAAAATGTTATAAAAAGTATT
*
9656270 ATAAAATGTTATAAGAAGTAT
1 ATAAAATGTTATAAAAAGTAT
9656291 AAAAGTATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 7 0.39
21 2 0.11
22 9 0.50
ACGTcount: A:0.54, C:0.00, G:0.10, T:0.37
Consensus pattern (22 bp):
ATAAAATGTTATAAAAAGTATT
Found at i:9658242 original size:20 final size:19
Alignment explanation
Indices: 9658217--9658265 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 19
9658207 TATTGATCCA
**
9658217 GTATCGATACTTTTCATTTG
1 GTATCGATAAATTT-ATTTG
9658237 GTATCGATAAAATTTATTTG
1 GTATCGAT-AAATTTATTTG
9658257 GTATCGATA
1 GTATCGATA
9658266 TCTTCATCTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
19 1 0.04
20 21 0.81
21 4 0.15
ACGTcount: A:0.29, C:0.10, G:0.16, T:0.45
Consensus pattern (19 bp):
GTATCGATAAATTTATTTG
Done.