Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D07
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: 56457815
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1765025 characters in sequence are not A, C, G, or T
File 179 of 189
Found at i:53157358 original size:18 final size:19
Alignment explanation
Indices: 53157324--53157374 Score: 63
Period size: 19 Copynumber: 2.8 Consensus size: 19
53157314 CTTAATATTC
*
53157324 TTTAATA-TTTAATGA-TT
1 TTTAATATTTTTATGATTT
53157341 TTT-ATGATTTTTATGATTT
1 TTTAAT-ATTTTTATGATTT
53157360 TTTAATATTTTTATG
1 TTTAATATTTTTATG
53157375 GGAAAATATT
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
16 2 0.07
17 4 0.14
18 7 0.24
19 14 0.48
20 2 0.07
ACGTcount: A:0.27, C:0.00, G:0.08, T:0.65
Consensus pattern (19 bp):
TTTAATATTTTTATGATTT
Found at i:53158840 original size:18 final size:18
Alignment explanation
Indices: 53158817--53158854 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
53158807 ATTATATAAT
53158817 ACTCTAATAATACAAAGC
1 ACTCTAATAATACAAAGC
53158835 ACTCTAATAATACAAAGC
1 ACTCTAATAATACAAAGC
53158853 AC
1 AC
53158855 AATGATTAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.50, C:0.24, G:0.05, T:0.21
Consensus pattern (18 bp):
ACTCTAATAATACAAAGC
Found at i:53160331 original size:30 final size:30
Alignment explanation
Indices: 53160288--53160345 Score: 73
Period size: 30 Copynumber: 1.9 Consensus size: 30
53160278 TTTTATATAC
*
53160288 TATATAATTTATAACAC-ATAATCTAAATT
1 TATATAATATATAACACTATAATCTAAATT
* *
53160317 TATAGTAATATATAATACTATAATGTAAA
1 TATA-TAATATATAACACTATAATCTAAA
53160346 CATTAAAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 4 0.17
30 11 0.46
31 9 0.38
ACGTcount: A:0.50, C:0.07, G:0.03, T:0.40
Consensus pattern (30 bp):
TATATAATATATAACACTATAATCTAAATT
Found at i:53162619 original size:27 final size:28
Alignment explanation
Indices: 53162569--53162626 Score: 82
Period size: 27 Copynumber: 2.1 Consensus size: 28
53162559 ATTATGGTCA
*
53162569 AAGTTGTTACTAAAGTCAGTTAGCAGTT
1 AAGTGGTTACTAAAGTCAGTTAGCAGTT
**
53162597 AAGTGGTTACT-AAGTTGGTTAGCAGTT
1 AAGTGGTTACTAAAGTCAGTTAGCAGTT
53162624 AAG
1 AAG
53162627 AAGTTAGCTA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
27 17 0.63
28 10 0.37
ACGTcount: A:0.31, C:0.09, G:0.26, T:0.34
Consensus pattern (28 bp):
AAGTGGTTACTAAAGTCAGTTAGCAGTT
Found at i:53167215 original size:27 final size:28
Alignment explanation
Indices: 53167165--53167222 Score: 82
Period size: 27 Copynumber: 2.1 Consensus size: 28
53167155 ATTATGGTCA
*
53167165 AAGTTGTTACTAAAGTCAGTTAGCAGTT
1 AAGTGGTTACTAAAGTCAGTTAGCAGTT
**
53167193 AAGTGGTTACT-AAGTTGGTTAGCAGTT
1 AAGTGGTTACTAAAGTCAGTTAGCAGTT
53167220 AAG
1 AAG
53167223 AAGTTAGCTA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
27 17 0.63
28 10 0.37
ACGTcount: A:0.31, C:0.09, G:0.26, T:0.34
Consensus pattern (28 bp):
AAGTGGTTACTAAAGTCAGTTAGCAGTT
Found at i:53168196 original size:18 final size:19
Alignment explanation
Indices: 53168159--53168196 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
53168149 AAGTTCGTAA
**
53168159 TTTATTATATTATGTTATT
1 TTTATTATATTATGCAATT
53168178 TTTA-TATATTATGCAATT
1 TTTATTATATTATGCAATT
53168196 T
1 T
53168197 ATAACATATA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 13 0.76
19 4 0.24
ACGTcount: A:0.29, C:0.03, G:0.05, T:0.63
Consensus pattern (19 bp):
TTTATTATATTATGCAATT
Found at i:53170134 original size:31 final size:31
Alignment explanation
Indices: 53170099--53170178 Score: 133
Period size: 31 Copynumber: 2.6 Consensus size: 31
53170089 CGCCCGTATG
*
53170099 TATACAATTGAATCAAAATCAAAATTTTATA
1 TATACAATTGAATCAAAATCAAAATTTAATA
*
53170130 TATACATTTGAATCAAAATCAAAATTTAATA
1 TATACAATTGAATCAAAATCAAAATTTAATA
*
53170161 TATATAATTGAATCAAAA
1 TATACAATTGAATCAAAA
53170179 ATAAAGATCA
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 45 1.00
ACGTcount: A:0.53, C:0.09, G:0.04, T:0.35
Consensus pattern (31 bp):
TATACAATTGAATCAAAATCAAAATTTAATA
Found at i:53179047 original size:5 final size:5
Alignment explanation
Indices: 53179037--53179092 Score: 53
Period size: 5 Copynumber: 11.4 Consensus size: 5
53179027 AGAATAGGAC
* * *
53179037 ATGAT ATGAT ATGTT TTGAT -TCGAT ATGAT ATGAT ACG-T ATGAT ATGAT
1 ATGAT ATGAT ATGAT ATGAT AT-GAT ATGAT ATGAT ATGAT ATGAT ATGAT
*
53179086 AAGAT AT
1 ATGAT AT
53179093 AAGTTAGCTT
Statistics
Matches: 41, Mismatches: 7, Indels: 6
0.76 0.13 0.11
Matches are distributed among these distances:
4 4 0.10
5 36 0.88
6 1 0.02
ACGTcount: A:0.36, C:0.04, G:0.20, T:0.41
Consensus pattern (5 bp):
ATGAT
Found at i:53180171 original size:17 final size:17
Alignment explanation
Indices: 53180149--53180182 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
53180139 TATAAACATG
*
53180149 TTAATTTAATTTATTTT
1 TTAATTTAATGTATTTT
*
53180166 TTAATTTGATGTATTTT
1 TTAATTTAATGTATTTT
53180183 GTAGTTTTTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.26, C:0.00, G:0.06, T:0.68
Consensus pattern (17 bp):
TTAATTTAATGTATTTT
Found at i:53187650 original size:8 final size:8
Alignment explanation
Indices: 53187637--53187663 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
53187627 TTTTACTTTA
53187637 AAAAATTT
1 AAAAATTT
53187645 AAAAATTT
1 AAAAATTT
53187653 AAAAATTT
1 AAAAATTT
53187661 AAA
1 AAA
53187664 CATAAGTGGC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (8 bp):
AAAAATTT
Found at i:53189906 original size:106 final size:106
Alignment explanation
Indices: 53189602--53190023 Score: 711
Period size: 106 Copynumber: 4.0 Consensus size: 106
53189592 TGGATTTAGA
* * *
53189602 TTTAATAGGATATTTGGCTATTTGGTCGAACGAGAAATCGAAACCCAGCACGTTAGGGCACATTC
1 TTTAAAAGGATATTTGGCTATTTGGTCGAACGAGAAATCGAAACCCAGCACGTTAGGGCACGTTT
*
53189667 TCTTGAATTTCCAAACGCAAAATATTGCCTTACTTTGAAAG
66 TCTCGAATTTCCAAACGCAAAATATTGCCTTACTTTGAAAG
*
53189708 TTTAAAAGGGATATTTGGCTATTTGGTCGAACGAGAAATCAAAACCCAGCACGTTAGGGCACGTT
1 TTTAAAA-GGATATTTGGCTATTTGGTCGAACGAGAAATCGAAACCCAGCACGTTAGGGCACGTT
*
53189773 TTCTCGAATTTTCAAAC-CAAAATATTGCCTTACTTTGAAAG
65 TTCTCGAATTTCCAAACGCAAAATATTGCCTTACTTTGAAAG
53189814 TTTAAAAGGATATTTGGCTATTTGGTCGAACGAGAAATCGAAACCCAGCACGTTAGGGCACGTTT
1 TTTAAAAGGATATTTGGCTATTTGGTCGAACGAGAAATCGAAACCCAGCACGTTAGGGCACGTTT
* *
53189879 TCTCGAATTTCCAAACGCGAAATATTGCCTTACTTTGAAAT
66 TCTCGAATTTCCAAACGCAAAATATTGCCTTACTTTGAAAG
* * * *
53189920 TTTGAAAGAATATTCGGCTATTTGGTCGAACGAGAAATCGAAACCCAACACGTTAGGGCACGTTT
1 TTTAAAAGGATATTTGGCTATTTGGTCGAACGAGAAATCGAAACCCAGCACGTTAGGGCACGTTT
*
53189985 TCTCGAATTTCCAAACGCAAAATATTGTCTTACTTTGAA
66 TCTCGAATTTCCAAACGCAAAATATTGCCTTACTTTGAA
53190024 TTTTTTTTGA
Statistics
Matches: 298, Mismatches: 16, Indels: 4
0.94 0.05 0.01
Matches are distributed among these distances:
105 72 0.24
106 157 0.53
107 69 0.23
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.30
Consensus pattern (106 bp):
TTTAAAAGGATATTTGGCTATTTGGTCGAACGAGAAATCGAAACCCAGCACGTTAGGGCACGTTT
TCTCGAATTTCCAAACGCAAAATATTGCCTTACTTTGAAAG
Found at i:53198377 original size:26 final size:24
Alignment explanation
Indices: 53198322--53198379 Score: 62
Period size: 24 Copynumber: 2.3 Consensus size: 24
53198312 AATAGAATTT
* * * *
53198322 TTTTTAAATTATAAAAAATTATAA
1 TTTTAAAAATATAAAAAATAAAAA
53198346 TTTTAAAAATATATAAAAATAAAAA
1 TTTTAAAAATATA-AAAAATAAAAA
53198371 TTATTAAAA
1 TT-TTAAAA
53198380 TTCATTTAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
24 11 0.39
25 11 0.39
26 6 0.21
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (24 bp):
TTTTAAAAATATAAAAAATAAAAA
Found at i:53198380 original size:25 final size:23
Alignment explanation
Indices: 53198323--53198380 Score: 62
Period size: 25 Copynumber: 2.4 Consensus size: 23
53198313 ATAGAATTTT
* * *
53198323 TTTTAAATTATAAAAAATTATAA
1 TTTTAAAATATAAAAAATAAAAA
53198346 TTTTAAAAATATATAAAAATAAAAA
1 TTTT-AAAATATA-AAAAATAAAAA
53198371 TTATTAAAAT
1 TT-TTAAAAT
53198381 TCATTTAAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
23 4 0.14
24 7 0.24
25 16 0.55
26 2 0.07
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (23 bp):
TTTTAAAATATAAAAAATAAAAA
Found at i:53198417 original size:17 final size:18
Alignment explanation
Indices: 53198395--53198429 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
53198385 TTAAAATAGT
*
53198395 ATAAAA-TTGCAAAAAAA
1 ATAAAATTTACAAAAAAA
53198412 ATAAAATTTACAAAAAAA
1 ATAAAATTTACAAAAAAA
53198430 TATATATTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.71, C:0.06, G:0.03, T:0.20
Consensus pattern (18 bp):
ATAAAATTTACAAAAAAA
Found at i:53198483 original size:33 final size:34
Alignment explanation
Indices: 53198412--53198484 Score: 89
Period size: 31 Copynumber: 2.2 Consensus size: 34
53198402 TGCAAAAAAA
* * *
53198412 ATAAAATTTACAAAAAAATATATATTAAAATTAT
1 ATAAAATTTACAAAAAAATAAAAATAAAAATTAT
53198446 -TAAAATTT-C-AAAAAATAAAAATAAAAAGTTAT
1 ATAAAATTTACAAAAAAATAAAAATAAAAA-TTAT
53198478 ATAAAAT
1 ATAAAAT
53198485 CATGAAAAAG
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
31 15 0.44
32 5 0.15
33 14 0.41
ACGTcount: A:0.64, C:0.03, G:0.01, T:0.32
Consensus pattern (34 bp):
ATAAAATTTACAAAAAAATAAAAATAAAAATTAT
Found at i:53198835 original size:32 final size:33
Alignment explanation
Indices: 53198789--53198869 Score: 94
Period size: 32 Copynumber: 2.5 Consensus size: 33
53198779 AAATCAGGTG
* * *
53198789 AAAATTTTTATAATTTTTTATAAATTTAT-TTTT
1 AAAA-TTTTATAATTTTTGAAAAATTCATATTTT
**
53198822 CTAATTTTATAATTTTTGAAAAATTCATATTTT
1 AAAATTTTATAATTTTTGAAAAATTCATATTTT
53198855 AAAATTTTA-AATTTT
1 AAAATTTTATAATTTT
53198870 CTATTCTTTT
Statistics
Matches: 40, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
32 27 0.68
33 13 0.32
ACGTcount: A:0.38, C:0.02, G:0.01, T:0.58
Consensus pattern (33 bp):
AAAATTTTATAATTTTTGAAAAATTCATATTTT
Found at i:53199770 original size:52 final size:52
Alignment explanation
Indices: 53199692--53199795 Score: 181
Period size: 52 Copynumber: 2.0 Consensus size: 52
53199682 CCGAGAAAAT
*
53199692 TTTAGTGCTTTCCATTGCCCTAAATTTTTCTTTGAGCCATTTACCCCTTTCC
1 TTTAGTGCTTTCCATTGCCATAAATTTTTCTTTGAGCCATTTACCCCTTTCC
* *
53199744 TTTAGTGGTTTCCATTGCCATAAATTTTTCTTTGAGCCATTTACGCCTTTCC
1 TTTAGTGCTTTCCATTGCCATAAATTTTTCTTTGAGCCATTTACCCCTTTCC
53199796 CCTAGCCATT
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 49 1.00
ACGTcount: A:0.16, C:0.26, G:0.12, T:0.46
Consensus pattern (52 bp):
TTTAGTGCTTTCCATTGCCATAAATTTTTCTTTGAGCCATTTACCCCTTTCC
Found at i:53201034 original size:11 final size:12
Alignment explanation
Indices: 53201002--53201034 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
53200992 ATTCCCCTCT
53201002 CTTCTCT-TTCC
1 CTTCTCTCTTCC
53201013 CTTCTCTCTTCC
1 CTTCTCTCTTCC
53201025 C-TCTCTCTTC
1 CTTCTCTCTTC
53201035 TTTTTTTTCT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 16 0.76
12 5 0.24
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (12 bp):
CTTCTCTCTTCC
Found at i:53201534 original size:3 final size:3
Alignment explanation
Indices: 53201500--53201565 Score: 60
Period size: 3 Copynumber: 21.3 Consensus size: 3
53201490 AATATCCTTG
* * * *
53201500 TTA TTT TTA TTA GTA TTA TTA GTA TTA CTA TTA TTA TTA TTA TGTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA
* *
53201546 TTA GTA TATA TTT TTA TTA T
1 TTA TTA T-TA TTA TTA TTA T
53201566 GTACGTGTAT
Statistics
Matches: 49, Mismatches: 12, Indels: 4
0.75 0.18 0.06
Matches are distributed among these distances:
3 43 0.88
4 6 0.12
ACGTcount: A:0.30, C:0.02, G:0.06, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:53201562 original size:23 final size:22
Alignment explanation
Indices: 53201507--53201568 Score: 81
Period size: 23 Copynumber: 2.8 Consensus size: 22
53201497 TTGTTATTTT
*
53201507 TATTAGTATTATTA-GTATTAC
1 TATTATTATTATTATGTATTAC
*
53201528 TATTATTATTATTATGTATTAG
1 TATTATTATTATTATGTATTAC
*
53201550 TATATATTTTTATTATGTA
1 TAT-TATTATTATTATGTA
53201569 CGTGTATACA
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
21 13 0.36
22 9 0.25
23 14 0.39
ACGTcount: A:0.32, C:0.02, G:0.08, T:0.58
Consensus pattern (22 bp):
TATTATTATTATTATGTATTAC
Found at i:53201575 original size:23 final size:23
Alignment explanation
Indices: 53201507--53201576 Score: 63
Period size: 23 Copynumber: 3.0 Consensus size: 23
53201497 TTGTTATTTT
* *
53201507 TATTAGTATTAT-TAGTATTACTA
1 TATTATTATTATGTAGTAGTA-TA
*
53201530 TTATTATTATTATGTATTAGTATA
1 -TATTATTATTATGTAGTAGTATA
*
53201554 TATTTTTATTATGTACGT-GTATA
1 TATTATTATTATGTA-GTAGTATA
53201577 CATATATATA
Statistics
Matches: 39, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
23 19 0.49
24 14 0.36
25 6 0.15
ACGTcount: A:0.31, C:0.03, G:0.10, T:0.56
Consensus pattern (23 bp):
TATTATTATTATGTAGTAGTATA
Found at i:53205906 original size:13 final size:12
Alignment explanation
Indices: 53205879--53205915 Score: 56
Period size: 13 Copynumber: 2.9 Consensus size: 12
53205869 ATTCATTTGA
53205879 CATTCATGCATT
1 CATTCATGCATT
53205891 CATTCATGCAATT
1 CATTCATGC-ATT
53205904 CATTCATTGCAT
1 CATTCA-TGCAT
53205916 ATCCCATACT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 9 0.39
13 11 0.48
14 3 0.13
ACGTcount: A:0.27, C:0.24, G:0.08, T:0.41
Consensus pattern (12 bp):
CATTCATGCATT
Found at i:53214243 original size:56 final size:56
Alignment explanation
Indices: 53214138--53214250 Score: 165
Period size: 56 Copynumber: 2.0 Consensus size: 56
53214128 TTCCAAGGAA
**
53214138 AATCAACTCATATTGCGAGAGATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTT
1 AATCAACTCATATTGCGAGAGATGAGTTGAGCCTCAAGACACGCCGAGGTATTTTT
** *
53214194 AATCAACTCATATTGCGAGA-AGTGAGTTGAGCCTCGGGGCACGCCGAGGTATTTTT
1 AATCAACTCATATTGCGAGAGA-TGAGTTGAGCCTCAAGACACGCCGAGGTATTTTT
53214250 A
1 A
53214251 GTTTATGTTT
Statistics
Matches: 51, Mismatches: 5, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
55 1 0.02
56 50 0.98
ACGTcount: A:0.28, C:0.18, G:0.26, T:0.28
Consensus pattern (56 bp):
AATCAACTCATATTGCGAGAGATGAGTTGAGCCTCAAGACACGCCGAGGTATTTTT
Found at i:53214520 original size:72 final size:72
Alignment explanation
Indices: 53214194--53214867 Score: 641
Period size: 71 Copynumber: 9.4 Consensus size: 72
53214184 AGGTATTTTT
* * * * * *
53214194 AATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACGCCGAGGT-ATTTTTAGTTTATG
1 AATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC-AGGCACGCTGAGGTAATTTTCAATTTTTG
53214258 -TTTT--A
65 TTTTTCAA
** *
53214263 AATTGACTCATATTGCGAGA--T-AGTTGAGCCTC-GGATACGCTGAGGTAA-TTTCAA--TTTG
1 AATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGG-CACGCTGAGGTAATTTTCAATTTTTG
53214321 TTTTTC-A
65 TTTTTCAA
* *
53214328 AATCAACTCATATTGCTAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAA-TTTCAATTTCTG
1 AATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGG-CACGCTGAGGTAATTTTCAATTTTTG
53214392 --TTTCAA
65 TTTTTCAA
* **
53214398 AA-AAACTATCATATTGCGAGAAATGAGTTGAGCCTCAGGACACGCTGAGGTAATTTTCAATTTT
1 AATCAAC--TCATATTGCGAGAGGTGAGTTGAGCCTCAGG-CACGCTGAGGTAATTTTCAATTTT
53214462 TGTTTTTCAA
63 TGTTTTTCAA
*
53214472 AATCAACTCATATTGCTAGAGGTGAGTTGAGCCTCAGGCACGCTGAGGTAA-TTTCAATTTCTTT
1 AATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGCACGCTGAGGTAATTTTCAA-TT-TTT
*****
53214536 GTCAAAAAA
64 GTTTTTCAA
* ** *
53214545 AATCAACTCATATTGCGAGAGGT--G-TGAGCCTCAAGACACATTGAGGT-ATTTTCAATTTCTG
1 AATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC-AGGCACGCTGAGGTAATTTTCAATTTTTG
53214606 -TTTTCAAGAA
65 TTTTTC---AA
* *
53214616 AATCAACTCATATT--GAGAGGTGAGTTGAGCCTCAAGACACGTTGAGGTATTTTCAATCCTGTT
1 AATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC-AGGCACGCTGAGG-----T-AAT--T-TT
*
53214679 CAATTTATGTTTTTCAA
56 CAATTTTTGTTTTTCAA
*
53214696 AATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAA-TTTCAATTTCTG
1 AATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGG-CACGCTGAGGTAATTTTCAATTTTTG
53214760 TTTTTCAA
65 TTTTTCAA
* **
53214768 AATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGGCACGC-GAGGT-ATTTTCAA-TTTAC
1 AATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC-AGGCACGCTGAGGTAATTTTCAATTTTTG
53214830 TTTTTCAAA
65 TTTTTC-AA
53214839 AATCAACTCATATTGCGAGAGGTG-GTTGA
1 AATCAACTCATATTGCGAGAGGTGAGTTGA
53214868 ACTTTTAATT
Statistics
Matches: 516, Mismatches: 45, Indels: 87
0.80 0.07 0.13
Matches are distributed among these distances:
63 3 0.01
64 6 0.01
65 31 0.06
66 12 0.02
67 2 0.00
68 11 0.02
69 56 0.11
70 28 0.05
71 123 0.24
72 105 0.20
73 60 0.12
74 8 0.02
75 3 0.01
76 2 0.00
77 2 0.00
79 2 0.00
80 16 0.03
81 3 0.01
82 38 0.07
83 5 0.01
ACGTcount: A:0.29, C:0.17, G:0.22, T:0.33
Consensus pattern (72 bp):
AATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGCACGCTGAGGTAATTTTCAATTTTTGT
TTTTCAA
Found at i:53214575 original size:143 final size:142
Alignment explanation
Indices: 53214268--53214862 Score: 666
Period size: 143 Copynumber: 4.1 Consensus size: 142
53214258 TTTTAAATTG
* *
53214268 ACTCATATTGCGAGATAGT-TGAGCCTC-GGATACGCTGAGGTAATTTCAA-TT-TGTTTTTC-A
1 ACTCATATTGCGAGA-GGTGTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTCTGTTTTTCAA
53214328 AATCAACTCATATTGCTAGAGGTGAGTTGAGCCTC-AGGACACGCTGAGGTAATTTCAATTTCTG
65 AATCAACTCATATTGCTAGAGGTGAGTTGAGCCTCAAGG-CACGCTGAGGTAATTTCAATTTCT-
*
53214392 TT-TCAAAAAAA-CT
128 TTGTCAAAAAAATCA
*
53214405 A-TCATATTGCGAGAAATGAGT-TGAGCCTCAGGACACGCTGAGGTAATTTTCAATTTTTGTTTT
1 ACTCATATTGCGAG--A-G-GTGTGAGCCTCAGGACACGCTGAGGTAA-TTTCAATTTCTGTTTT
53214468 TCAAAATCAACTCATATTGCTAGAGGTGAGTTGAGCCTC-AGGCACGCTGAGGTAATTTCAATTT
61 TCAAAATCAACTCATATTGCTAGAGGTGAGTTGAGCCTCAAGGCACGCTGAGGTAATTTCAATTT
53214532 CTTTGTCAAAAAAAATCA
126 CTTTGTC-AAAAAAATCA
* ** *
53214550 ACTCATATTGCGAGAGGTGTGAGCCTCAAGACACATTGAGGTATTTTCAATTTCTG-TTTTCAAG
1 ACTCATATTGCGAGAGGTGTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTCTGTTTTTC---
* * *
53214614 AAAATCAACTCATATTG--AGAGGTGAGTTGAGCCTCAAGACACGTTGAGGTATTTTCAATCCTG
63 AAAATCAACTCATATTGCTAGAGGTGAGTTGAGCCTCAAGGCACGCTGAGGTAATTTCAA---T-
****
53214677 TTCAATTTATGTTTTTCAAAATCA
124 TTC---TT-TG-TCAAAAAAATCA
53214701 ACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTCTGTTTTTC
1 ACTCATATTGCGAGAGGT--G-TGAGCCTCAGGACACGCTGAGGTAATTTCAATTTCTGTTTTTC
* ** *
53214766 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGGCACGC-GAGGTATTTTCAATTTAC
63 AAAATCAACTCATATTGCTAGAGGTGAGTTGAGCCTCAAGGCACGCTGAGGTAATTTCAATTT-C
*
53214830 TTTTTC--AAAAATCA
127 TTTGTCAAAAAAATCA
53214844 ACTCATATTGCGAGAGGTG
1 ACTCATATTGCGAGAGGTG
53214863 GTTGAACTTT
Statistics
Matches: 399, Mismatches: 26, Indels: 62
0.82 0.05 0.13
Matches are distributed among these distances:
136 12 0.03
137 1 0.00
138 2 0.01
139 10 0.03
140 15 0.04
141 12 0.03
142 35 0.09
143 100 0.25
144 64 0.16
145 3 0.01
146 14 0.04
147 5 0.01
149 2 0.01
150 4 0.01
151 27 0.07
152 18 0.05
153 14 0.04
154 56 0.14
155 5 0.01
ACGTcount: A:0.29, C:0.17, G:0.21, T:0.33
Consensus pattern (142 bp):
ACTCATATTGCGAGAGGTGTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTCTGTTTTTCAAA
ATCAACTCATATTGCTAGAGGTGAGTTGAGCCTCAAGGCACGCTGAGGTAATTTCAATTTCTTTG
TCAAAAAAATCA
Found at i:53214737 original size:82 final size:78
Alignment explanation
Indices: 53214592--53214827 Score: 276
Period size: 72 Copynumber: 3.1 Consensus size: 78
53214582 ACATTGAGGT
* *
53214592 ATTTTCAATTTCTG-TTTTCAAGAAAATCAACTCATATT--GAGAGGTGAGTTGAGCCTCAAGAC
1 ATTTTCAATTTATGTTTTTC---AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGAC
53214654 ACGTTGAGGTATTTTCA
63 ACG-TGAGGTATTTTCA
53214671 ATCCTGTTCAATTTATGTTTTTCAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGAC
1 AT--T-TTCAATTTATGTTTTTCAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGAC
53214736 ACGCTGAGG-----T-A
63 ACG-TGAGGTATTTTCA
* * *
53214747 A-TTTCAATTTCTGTTTTTCAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGGCACG
1 ATTTTCAATTTATGTTTTTCAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACG
*
53214811 CGAGGTATTTTCA
66 TGAGGTATTTTCA
53214824 ATTT
1 ATTT
53214828 ACTTTTTCAA
Statistics
Matches: 137, Mismatches: 7, Indels: 27
0.80 0.04 0.16
Matches are distributed among these distances:
71 4 0.03
72 59 0.43
73 1 0.01
76 3 0.02
77 3 0.02
78 2 0.01
79 2 0.01
80 16 0.12
81 1 0.01
82 41 0.30
83 5 0.04
ACGTcount: A:0.28, C:0.17, G:0.21, T:0.34
Consensus pattern (78 bp):
ATTTTCAATTTATGTTTTTCAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACG
TGAGGTATTTTCA
Found at i:53214752 original size:154 final size:149
Alignment explanation
Indices: 53214543--53214825 Score: 408
Period size: 154 Copynumber: 1.9 Consensus size: 149
53214533 TTTGTCAAAA
* *
53214543 AAAATCAACTCATATTGCGAGAGGTGTGAGCCTCAAGACACATTGAGGTATTTTCAATTTCTG-T
1 AAAATCAACTCATATTGCGAGAGGTGTGAGCCTCAAGACACACTGAGGTAATTTCAATTTCTGTT
*
53214607 TTTCAAGAAAATCAACTCATATT-GAGAGGTGAGTTGAGCCTCAAGACACGTTGAGGTATTTTCA
66 TTTC---AAAATCAACTCATATTCGAGAGGTGAGTTGAGCCTCAAGACACG-CGAGGTATTTTCA
53214671 ATCCTGTTCAATTTATGTTTTTC
127 ATCCTGTTCAATTTATGTTTTTC
* *
53214694 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTCT
1 AAAATCAACTCATATTGCGAGAGGT--G-TGAGCCTCAAGACACACTGAGGTAATTTCAATTTCT
** *
53214759 GTTTTTCAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGGCACGCGAGGTATTTTCA
63 GTTTTTCAAAATCAACTCATATT-CGAGAGGTGAGTTGAGCCTCAAGACACGCGAGGTATTTTCA
53214824 AT
127 AT
53214826 TTACTTTTTC
Statistics
Matches: 118, Mismatches: 8, Indels: 10
0.87 0.06 0.07
Matches are distributed among these distances:
151 25 0.21
152 16 0.14
153 15 0.13
154 57 0.48
155 5 0.04
ACGTcount: A:0.29, C:0.17, G:0.22, T:0.32
Consensus pattern (149 bp):
AAAATCAACTCATATTGCGAGAGGTGTGAGCCTCAAGACACACTGAGGTAATTTCAATTTCTGTT
TTTCAAAATCAACTCATATTCGAGAGGTGAGTTGAGCCTCAAGACACGCGAGGTATTTTCAATCC
TGTTCAATTTATGTTTTTC
Found at i:53279209 original size:3 final size:3
Alignment explanation
Indices: 53279194--53279242 Score: 71
Period size: 3 Copynumber: 16.3 Consensus size: 3
53279184 TGTTTATTGT
* * *
53279194 TTG TTG TTA TTG TTG TTG TTG TTG TTG TTG TTG TTG CTG CTG TTG TTG
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG
53279242 T
1 T
53279243 GTGTGTGTTT
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.02, C:0.04, G:0.31, T:0.63
Consensus pattern (3 bp):
TTG
Found at i:53280351 original size:24 final size:24
Alignment explanation
Indices: 53280324--53280373 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
53280314 AAATATAAAG
53280324 AAAACTAACAATTTAATGGTTACC
1 AAAACTAACAATTTAATGGTTACC
53280348 AAAACTAACAATTTAATGGTTACC
1 AAAACTAACAATTTAATGGTTACC
53280372 AA
1 AA
53280374 CCATGGATGC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.48, C:0.16, G:0.08, T:0.28
Consensus pattern (24 bp):
AAAACTAACAATTTAATGGTTACC
Found at i:53293586 original size:85 final size:85
Alignment explanation
Indices: 53293443--53293605 Score: 308
Period size: 85 Copynumber: 1.9 Consensus size: 85
53293433 TAAACCATAT
*
53293443 AAGAGAAGCAACATAATACCAAAGAGAAAAGCACAATTGCCATCATAAATAACCTTTTGAATCTC
1 AAGAGAAGCAACATAATACCAAAGAGAAAAACACAATTGCCATCATAAATAACCTTTTGAATCTC
53293508 AGGAGTTATATGTACAGTAC
66 AGGAGTTATATGTACAGTAC
*
53293528 AAGAGAAGCAACATAATACCAAAGAGAAAAACACAATTGCCATCATAAATCACCTTTTGAATCTC
1 AAGAGAAGCAACATAATACCAAAGAGAAAAACACAATTGCCATCATAAATAACCTTTTGAATCTC
53293593 AGGAGTTATATGT
66 AGGAGTTATATGT
53293606 CCAATCCTAT
Statistics
Matches: 76, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
85 76 1.00
ACGTcount: A:0.45, C:0.18, G:0.15, T:0.23
Consensus pattern (85 bp):
AAGAGAAGCAACATAATACCAAAGAGAAAAACACAATTGCCATCATAAATAACCTTTTGAATCTC
AGGAGTTATATGTACAGTAC
Found at i:53303834 original size:24 final size:24
Alignment explanation
Indices: 53303807--53303870 Score: 65
Period size: 24 Copynumber: 2.7 Consensus size: 24
53303797 ATCTTATTTG
* * *
53303807 TCTTCGCCTCGACCCTTGTATTCA
1 TCTTCACCTCCACCATTGTATTCA
* *
53303831 TCTTCATCTCCACCATTGTCTTCA
1 TCTTCACCTCCACCATTGTATTCA
* *
53303855 TCTTCATCACCACCAT
1 TCTTCACCTCCACCAT
53303871 CGGTTTTTTC
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 34 1.00
ACGTcount: A:0.17, C:0.39, G:0.06, T:0.38
Consensus pattern (24 bp):
TCTTCACCTCCACCATTGTATTCA
Found at i:53307822 original size:7 final size:7
Alignment explanation
Indices: 53307810--53307855 Score: 53
Period size: 7 Copynumber: 6.9 Consensus size: 7
53307800 AAAGAAAGGG
53307810 AGAAAAT
1 AGAAAAT
53307817 AGAAAAT
1 AGAAAAT
53307824 AGAAAA-
1 AGAAAAT
*
53307830 GGAAAA-
1 AGAAAAT
53307836 AGAAAAT
1 AGAAAAT
53307843 AGAGAAAT
1 AGA-AAAT
53307851 A-AAAA
1 AGAAAA
53307856 GGAAAAATCT
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
6 13 0.37
7 17 0.49
8 5 0.14
ACGTcount: A:0.74, C:0.00, G:0.17, T:0.09
Consensus pattern (7 bp):
AGAAAAT
Found at i:53307839 original size:26 final size:26
Alignment explanation
Indices: 53307810--53307862 Score: 90
Period size: 26 Copynumber: 2.0 Consensus size: 26
53307800 AAAGAAAGGG
53307810 AGAAAATAGA-AAATAGAAAAGGAAAA
1 AGAAAATAGAGAAATA-AAAAGGAAAA
53307836 AGAAAATAGAGAAATAAAAAGGAAAA
1 AGAAAATAGAGAAATAAAAAGGAAAA
53307862 A
1 A
53307863 TCTCCCAAGC
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
26 21 0.81
27 5 0.19
ACGTcount: A:0.74, C:0.00, G:0.19, T:0.08
Consensus pattern (26 bp):
AGAAAATAGAGAAATAAAAAGGAAAA
Found at i:53330168 original size:36 final size:38
Alignment explanation
Indices: 53330125--53330207 Score: 109
Period size: 38 Copynumber: 2.2 Consensus size: 38
53330115 TATAAAAGAA
* *
53330125 TCCCTAAAAT-TCAAATTTTACA-A-TTTTACAATTTAG
1 TCCCTAAAATCCCAAA-TTTACACACTTTTACAATTCAG
*
53330161 TCTCTAAAATCCCAAATTTACACACTTTTACAATTCAG
1 TCCCTAAAATCCCAAATTTACACACTTTTACAATTCAG
53330199 TCCCTAAAA
1 TCCCTAAAA
53330208 ATAAGATATT
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
36 15 0.38
37 5 0.12
38 20 0.50
ACGTcount: A:0.39, C:0.23, G:0.02, T:0.36
Consensus pattern (38 bp):
TCCCTAAAATCCCAAATTTACACACTTTTACAATTCAG
Found at i:53332270 original size:23 final size:23
Alignment explanation
Indices: 53332244--53332319 Score: 143
Period size: 23 Copynumber: 3.3 Consensus size: 23
53332234 ATAAGTGCCA
53332244 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
53332267 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
*
53332290 CACTGAAATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
53332313 CACTGAT
1 CACTGAT
53332320 CAATAACACT
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 51 1.00
ACGTcount: A:0.32, C:0.26, G:0.21, T:0.21
Consensus pattern (23 bp):
CACTGATATGTAGCCGAAGCTAC
Found at i:53332419 original size:8 final size:8
Alignment explanation
Indices: 53332406--53332434 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
53332396 ACCCGGGACT
53332406 CACTGTAA
1 CACTGTAA
53332414 CACTGTAA
1 CACTGTAA
53332422 CACTGTAA
1 CACTGTAA
53332430 CACTG
1 CACTG
53332435 GTCTCTAGTG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.34, C:0.28, G:0.14, T:0.24
Consensus pattern (8 bp):
CACTGTAA
Found at i:53332565 original size:18 final size:17
Alignment explanation
Indices: 53332539--53332577 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
53332529 ATTTTCCTTC
53332539 CACATTC-AATATTAATT
1 CACATTCAAATA-TAATT
53332556 CACATATCAAATATAATT
1 CACAT-TCAAATATAATT
53332574 CACA
1 CACA
53332578 ATTTATACAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 5 0.25
18 11 0.55
19 4 0.20
ACGTcount: A:0.46, C:0.21, G:0.00, T:0.33
Consensus pattern (17 bp):
CACATTCAAATATAATT
Found at i:53339586 original size:23 final size:23
Alignment explanation
Indices: 53339560--53339635 Score: 143
Period size: 23 Copynumber: 3.3 Consensus size: 23
53339550 ATAAGTGCCA
53339560 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
53339583 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
*
53339606 CACTGAAATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
53339629 CACTGAT
1 CACTGAT
53339636 CAATAACACT
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 51 1.00
ACGTcount: A:0.32, C:0.26, G:0.21, T:0.21
Consensus pattern (23 bp):
CACTGATATGTAGCCGAAGCTAC
Found at i:53339735 original size:8 final size:8
Alignment explanation
Indices: 53339722--53339750 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
53339712 ACCCGGGACT
53339722 CACTGTAA
1 CACTGTAA
53339730 CACTGTAA
1 CACTGTAA
53339738 CACTGTAA
1 CACTGTAA
53339746 CACTG
1 CACTG
53339751 GTCTCTAGTG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.34, C:0.28, G:0.14, T:0.24
Consensus pattern (8 bp):
CACTGTAA
Found at i:53349349 original size:4 final size:4
Alignment explanation
Indices: 53349340--53349383 Score: 88
Period size: 4 Copynumber: 11.0 Consensus size: 4
53349330 TCTATGCATA
53349340 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
53349384 CTATCTAATA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 40 1.00
ACGTcount: A:0.25, C:0.00, G:0.25, T:0.50
Consensus pattern (4 bp):
TATG
Found at i:53351117 original size:26 final size:24
Alignment explanation
Indices: 53351080--53351127 Score: 69
Period size: 26 Copynumber: 1.9 Consensus size: 24
53351070 GAAAATCAAA
53351080 ATATTTATAAAAATTCTAAAATTT
1 ATATTTATAAAAATTCTAAAATTT
*
53351104 ATATTTATTAAAAAATTTTAAAAT
1 ATATTTA-T-AAAAATTCTAAAAT
53351128 CTTTTAAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 7 0.33
25 1 0.05
26 13 0.62
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (24 bp):
ATATTTATAAAAATTCTAAAATTT
Found at i:53361391 original size:4 final size:4
Alignment explanation
Indices: 53361382--53361411 Score: 60
Period size: 4 Copynumber: 7.5 Consensus size: 4
53361372 CCACCGGGGG
53361382 TAGC TAGC TAGC TAGC TAGC TAGC TAGC TA
1 TAGC TAGC TAGC TAGC TAGC TAGC TAGC TA
53361412 ATTATGCTGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.27, C:0.23, G:0.23, T:0.27
Consensus pattern (4 bp):
TAGC
Found at i:53369823 original size:15 final size:16
Alignment explanation
Indices: 53369803--53369832 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
53369793 TTTAACTTTA
53369803 ATAAAT-TTTTTATTT
1 ATAAATATTTTTATTT
53369818 ATAAATATTTTTATT
1 ATAAATATTTTTATT
53369833 AAATGTGTTC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (16 bp):
ATAAATATTTTTATTT
Found at i:53370701 original size:20 final size:19
Alignment explanation
Indices: 53370643--53370708 Score: 75
Period size: 20 Copynumber: 3.5 Consensus size: 19
53370633 TTTATCAAAT
53370643 ATATTTAAATTATTTATT-
1 ATATTTAAATTATTTATTA
*
53370661 ATATTT-AA-TACTTAATTA
1 ATATTTAAATTA-TTTATTA
*
53370679 ATATTAAAATTATTTATTTA
1 ATATTTAAATTATTTA-TTA
53370699 ATATTTAAAT
1 ATATTTAAAT
53370709 CCGTTTCAAT
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
16 2 0.05
17 7 0.18
18 11 0.28
19 5 0.13
20 14 0.36
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.55
Consensus pattern (19 bp):
ATATTTAAATTATTTATTA
Found at i:53371932 original size:96 final size:97
Alignment explanation
Indices: 53371767--53372050 Score: 385
Period size: 96 Copynumber: 2.9 Consensus size: 97
53371757 CCAGAATTAT
* * *
53371767 GTATGAATGACATG-GAAAAAAATTACTGAAATGTCGTTCAATAATTAGAAAGGGATCATGGATG
1 GTATGAATGACATGAG-AAAAAATTATTGAAATGTCATTAAATAATTAGAAAGGGATCATGGATG
* *
53371831 ATGTGGTGGGAAGGGTTCATAAAATAATTTCTC
65 ATGTGGTGGGAAGGGTCCATAAAATAATATCTC
* *
53371864 GTATGAATGACA-GAGAAAAAATTGTTGAAATGTCATTAAATGATTAGAAAGGGATCATGGATGA
1 GTATGAATGACATGAGAAAAAATTATTGAAATGTCATTAAATAATTAGAAAGGGATCATGGATGA
*
53371928 TGTGGTGGGAATGGTCCATAAAATAATATCTC
66 TGTGGTGGGAAGGGTCCATAAAATAATATCTC
* * * * * *
53371960 GTATAAAAGACATGA-AAAAAATTATTGAAATGTTATTAAATAATTGGAAAGAGAACATGGATGA
1 GTATGAATGACATGAGAAAAAATTATTGAAATGTCATTAAATAATTAGAAAGGGATCATGGATGA
* * *
53372024 TGTGGTGGGAAAGATCCAAAAAATAAT
66 TGTGGTGGGAAGGGTCCATAAAATAAT
53372051 TCCTCCCTGT
Statistics
Matches: 166, Mismatches: 19, Indels: 5
0.87 0.10 0.03
Matches are distributed among these distances:
96 151 0.91
97 15 0.09
ACGTcount: A:0.42, C:0.07, G:0.24, T:0.27
Consensus pattern (97 bp):
GTATGAATGACATGAGAAAAAATTATTGAAATGTCATTAAATAATTAGAAAGGGATCATGGATGA
TGTGGTGGGAAGGGTCCATAAAATAATATCTC
Found at i:53372389 original size:5 final size:5
Alignment explanation
Indices: 53372379--53372404 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
53372369 AAGACAACTC
53372379 AATAA AATAA AATAA AATAA AATAA A
1 AATAA AATAA AATAA AATAA AATAA A
53372405 TCATTAAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
AATAA
Found at i:53384260 original size:20 final size:19
Alignment explanation
Indices: 53384232--53384272 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
53384222 AGATTAATTG
* *
53384232 TTATTCCTATAAAATAGAAT
1 TTATACCTAGAAAATA-AAT
53384252 TTATACCTAGAAAATAAAT
1 TTATACCTAGAAAATAAAT
53384271 TT
1 TT
53384273 CCCATTAATT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 5 0.26
20 14 0.74
ACGTcount: A:0.46, C:0.10, G:0.05, T:0.39
Consensus pattern (19 bp):
TTATACCTAGAAAATAAAT
Found at i:53387846 original size:21 final size:21
Alignment explanation
Indices: 53387807--53387846 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
53387797 AAAACAAAAC
*
53387807 AAAAAAAAAACATATAAGTCT
1 AAAAAAAAAACATAAAAGTCT
53387828 AAAAAAATAAA-ATAAAAGT
1 AAAAAAA-AAACATAAAAGT
53387847 ACAAATAGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 14 0.82
22 3 0.18
ACGTcount: A:0.72, C:0.05, G:0.05, T:0.17
Consensus pattern (21 bp):
AAAAAAAAAACATAAAAGTCT
Found at i:53388571 original size:16 final size:16
Alignment explanation
Indices: 53388552--53388582 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
53388542 TTATTTTAAA
*
53388552 TTAATTAATTTTTCAT
1 TTAAATAATTTTTCAT
53388568 TTAAATAATTTTTCA
1 TTAAATAATTTTTCA
53388583 CAACCCAATT
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:0.00, T:0.58
Consensus pattern (16 bp):
TTAAATAATTTTTCAT
Found at i:53394275 original size:50 final size:50
Alignment explanation
Indices: 53394200--53394301 Score: 204
Period size: 50 Copynumber: 2.0 Consensus size: 50
53394190 GGGCACCAGA
53394200 TCCAAAGTCTCCCACTTGCCCTAGTGAAATAGATGAGTCATATTTTGCAT
1 TCCAAAGTCTCCCACTTGCCCTAGTGAAATAGATGAGTCATATTTTGCAT
53394250 TCCAAAGTCTCCCACTTGCCCTAGTGAAATAGATGAGTCATATTTTGCAT
1 TCCAAAGTCTCCCACTTGCCCTAGTGAAATAGATGAGTCATATTTTGCAT
53394300 TC
1 TC
53394302 TCATGCTCTC
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 52 1.00
ACGTcount: A:0.27, C:0.25, G:0.16, T:0.32
Consensus pattern (50 bp):
TCCAAAGTCTCCCACTTGCCCTAGTGAAATAGATGAGTCATATTTTGCAT
Found at i:53396077 original size:73 final size:74
Alignment explanation
Indices: 53395931--53396080 Score: 230
Period size: 73 Copynumber: 2.0 Consensus size: 74
53395921 CTTAGACATG
* * * *
53395931 TCATTAGCTCATTAAGTTTCATCGGATCAACAACTTAGGCCTCTTCAATTATTGTCACCTTTATT
1 TCATTAGCTCATTAAGATTCATCGCATCAACAACTTAAGCCTCTTCAATTATTGTCACCTTGATT
53395996 GCAAACCTT
66 GCAAACCTT
* * *
53396005 TCATTAGCTCATTAAGATTCATTGCATCAACAA-TTAAGCCTCTTGAATTGTTGTCACCTTGATT
1 TCATTAGCTCATTAAGATTCATCGCATCAACAACTTAAGCCTCTTCAATTATTGTCACCTTGATT
53396069 GCAAACCTT
66 GCAAACCTT
53396078 TCA
1 TCA
53396081 AGTAGGAACA
Statistics
Matches: 69, Mismatches: 7, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
73 39 0.57
74 30 0.43
ACGTcount: A:0.28, C:0.23, G:0.11, T:0.37
Consensus pattern (74 bp):
TCATTAGCTCATTAAGATTCATCGCATCAACAACTTAAGCCTCTTCAATTATTGTCACCTTGATT
GCAAACCTT
Found at i:53400127 original size:30 final size:28
Alignment explanation
Indices: 53400091--53400150 Score: 102
Period size: 30 Copynumber: 2.1 Consensus size: 28
53400081 GGAACATAAC
53400091 GAAATAATAGAACCGATACAGGCCAATGGG
1 GAAATAATAGAACCGATACAGG--AATGGG
53400121 GAAATAATAGAACCGATACAGGAATGGG
1 GAAATAATAGAACCGATACAGGAATGGG
53400149 GA
1 GA
53400151 GCAATAGGGA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
28 8 0.27
30 22 0.73
ACGTcount: A:0.45, C:0.13, G:0.28, T:0.13
Consensus pattern (28 bp):
GAAATAATAGAACCGATACAGGAATGGG
Found at i:53401540 original size:16 final size:16
Alignment explanation
Indices: 53401519--53401550 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
53401509 TTACAGTGGA
53401519 GTTTCAGGTTTATTAT
1 GTTTCAGGTTTATTAT
53401535 GTTTCAGGTTTATTAT
1 GTTTCAGGTTTATTAT
53401551 CAATTCAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.19, C:0.06, G:0.19, T:0.56
Consensus pattern (16 bp):
GTTTCAGGTTTATTAT
Found at i:53402750 original size:26 final size:26
Alignment explanation
Indices: 53402715--53402770 Score: 80
Period size: 26 Copynumber: 2.2 Consensus size: 26
53402705 GTGGTTATTG
53402715 AACTCTTAAG-GCAGTTGCCTACCTTGA
1 AACTCTTAAGCG-AGTTGCCTACCTT-A
53402742 AACTC-TAAGCGAGTTGCCTACCTTA
1 AACTCTTAAGCGAGTTGCCTACCTTA
53402767 AACT
1 AACT
53402771 TACTGAAACT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
25 5 0.18
26 17 0.61
27 6 0.21
ACGTcount: A:0.29, C:0.27, G:0.16, T:0.29
Consensus pattern (26 bp):
AACTCTTAAGCGAGTTGCCTACCTTA
Found at i:53405046 original size:23 final size:22
Alignment explanation
Indices: 53405020--53405104 Score: 64
Period size: 22 Copynumber: 3.6 Consensus size: 22
53405010 TATTGAATTT
*
53405020 TATTTTAAATATAAAATATTATG
1 TATTTTAAAT-TAAAATATTATA
* * *
53405043 TA-TTTAAATTTAAATGTTTTA
1 TATTTTAAATTAAAATATTATA
*
53405064 TATTTTAATATTTAAAATATAGTTTA
1 TATTTTAA-A-TTAAAATAT--TATA
53405090 TATATTTAAATTAAA
1 TAT-TTTAAATTAAA
53405105 TTTTATAAAT
Statistics
Matches: 50, Mismatches: 6, Indels: 10
0.76 0.09 0.15
Matches are distributed among these distances:
21 10 0.20
22 12 0.24
23 3 0.06
24 7 0.14
25 5 0.10
26 8 0.16
27 5 0.10
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.52
Consensus pattern (22 bp):
TATTTTAAATTAAAATATTATA
Found at i:53405109 original size:20 final size:20
Alignment explanation
Indices: 53405065--53405111 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
53405055 AATGTTTTAT
*
53405065 ATTTTA-ATATTTAAAATAT
1 ATTTTATATATTTAAAATAA
* *
53405084 AGTTTATATATTTAAATTAA
1 ATTTTATATATTTAAAATAA
53405104 ATTTTATA
1 ATTTTATA
53405112 AATAATTAAT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
19 5 0.22
20 18 0.78
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (20 bp):
ATTTTATATATTTAAAATAA
Found at i:53422907 original size:21 final size:22
Alignment explanation
Indices: 53422875--53422919 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 22
53422865 TAAAAAATTC
*
53422875 AAATATTAAAAATTAGAAAAAA
1 AAATATTAAAAATCAGAAAAAA
*
53422897 AAATA-TAAAAATCATAAAAAA
1 AAATATTAAAAATCAGAAAAAA
53422918 AA
1 AA
53422920 TAAAAATTGT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 16 0.76
22 5 0.24
ACGTcount: A:0.76, C:0.02, G:0.02, T:0.20
Consensus pattern (22 bp):
AAATATTAAAAATCAGAAAAAA
Found at i:53422978 original size:20 final size:20
Alignment explanation
Indices: 53422938--53422984 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
53422928 GTAAAATTTT
*
53422938 ATAAAATATTTAAAAAAATA
1 ATAAAATATGTAAAAAAATA
* *
53422958 ATAAAATATGTAGAAATATA
1 ATAAAATATGTAAAAAAATA
*
53422978 AAAAAAT
1 ATAAAAT
53422985 TATAAAATTT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.68, C:0.00, G:0.04, T:0.28
Consensus pattern (20 bp):
ATAAAATATGTAAAAAAATA
Found at i:53423564 original size:87 final size:88
Alignment explanation
Indices: 53423361--53423640 Score: 352
Period size: 87 Copynumber: 3.2 Consensus size: 88
53423351 TAATAAGAGC
**
53423361 AGGGGCTTAATTG-TTTTTTTGAAAAAAAATTAAGGGTCTTTTTTATACATTTTTAAAGTTCAAG
1 AGGGGCTTAATTGCTTTTTTTGAAAAAATTTTAAGGGTCTTTTTTATACATTTTTAAAGTTCAAG
53423425 TATCCAATTGAGTGAAAAAAATT
66 TATCCAATTGAGTGAAAAAAATT
* * *
53423448 AGGCGCTTAATT-TTTTTTTTGAAAAAATTTTAAAGGTCTTTTTTATACATTTTTAAAGTTCAAG
1 AGGGGCTTAATTGCTTTTTTTGAAAAAATTTTAAGGGTCTTTTTTATACATTTTTAAAGTTCAAG
*
53423512 TATCCAATTGAATGAAAAAAATT
66 TATCCAATTGAGTGAAAAAAATT
* * * * ** *
53423535 AGGGGCTTAATTGCTTTTTTTG-AAGAATTTTGAGGGCCTTTTTAATGTATTTTGAAAGTTCAAG
1 AGGGGCTTAATTGCTTTTTTTGAAAAAATTTTAAGGGTCTTTTTTATACATTTTTAAAGTTCAAG
* * *
53423599 T-GCTCAATTGGGTGCAAAAAAAAATG
66 TATC-CAATTGAGTG---AAAAAAATT
53423625 AGGGGCTTAATTGCTT
1 AGGGGCTTAATTGCTT
53423641 CTTCTTCTTT
Statistics
Matches: 168, Mismatches: 19, Indels: 9
0.86 0.10 0.05
Matches are distributed among these distances:
86 1 0.01
87 135 0.80
88 8 0.05
90 24 0.14
ACGTcount: A:0.34, C:0.08, G:0.18, T:0.40
Consensus pattern (88 bp):
AGGGGCTTAATTGCTTTTTTTGAAAAAATTTTAAGGGTCTTTTTTATACATTTTTAAAGTTCAAG
TATCCAATTGAGTGAAAAAAATT
Found at i:53423753 original size:22 final size:20
Alignment explanation
Indices: 53423714--53423752 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
53423704 AATCTTCAAA
*
53423714 TATATAAATTATTAAAAAAT
1 TATATAAATTAATAAAAAAT
53423734 TATATAAA-TAATAATAAAA
1 TATATAAATTAATAA-AAAA
53423753 ATTCAAGAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (20 bp):
TATATAAATTAATAAAAAAT
Found at i:53428395 original size:16 final size:16
Alignment explanation
Indices: 53428374--53428406 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
53428364 TTAAAAAATT
*
53428374 ATTAAAAATTTTAAAA
1 ATTAAAAATATTAAAA
53428390 ATTAAAAATATTAAAA
1 ATTAAAAATATTAAAA
53428406 A
1 A
53428407 AGTCAATTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (16 bp):
ATTAAAAATATTAAAA
Found at i:53441742 original size:32 final size:32
Alignment explanation
Indices: 53441706--53441767 Score: 124
Period size: 32 Copynumber: 1.9 Consensus size: 32
53441696 TACAAAGTTT
53441706 AAAAAAATCAAACAAATAACCTAGATAAACTA
1 AAAAAAATCAAACAAATAACCTAGATAAACTA
53441738 AAAAAAATCAAACAAATAACCTAGATAAAC
1 AAAAAAATCAAACAAATAACCTAGATAAAC
53441768 CAACATGAGA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.66, C:0.16, G:0.03, T:0.15
Consensus pattern (32 bp):
AAAAAAATCAAACAAATAACCTAGATAAACTA
Found at i:53449385 original size:21 final size:19
Alignment explanation
Indices: 53449354--53449396 Score: 50
Period size: 21 Copynumber: 2.2 Consensus size: 19
53449344 TTTATTTTTC
* *
53449354 ATATAATATAAATTATAAA
1 ATATAATATAAAATAAAAA
53449373 ATATACATAATAAAATAAAAA
1 ATATA-AT-ATAAAATAAAAA
53449394 ATA
1 ATA
53449397 CTAAAATCTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 5 0.25
20 2 0.10
21 13 0.65
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.30
Consensus pattern (19 bp):
ATATAATATAAAATAAAAA
Found at i:53450044 original size:17 final size:18
Alignment explanation
Indices: 53450003--53450042 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
53449993 TATATTTTAA
53450003 AAAAATATATAATACATC
1 AAAAATATATAATACATC
*
53450021 AAAAATACTATAA-ACATT
1 AAAAATA-TATAATACATC
53450039 AAAA
1 AAAA
53450043 TAAATGTTTC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 15 0.75
19 5 0.25
ACGTcount: A:0.65, C:0.10, G:0.00, T:0.25
Consensus pattern (18 bp):
AAAAATATATAATACATC
Found at i:53450212 original size:22 final size:22
Alignment explanation
Indices: 53450187--53450229 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
53450177 TATCCAAACA
53450187 ATAACAACAAAAT-AGTAGCAAT
1 ATAACAACAAAATGA-TAGCAAT
* *
53450209 ATAATAACGAAATGATAGCAA
1 ATAACAACAAAATGATAGCAA
53450230 AATAGTGAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 17 0.94
23 1 0.06
ACGTcount: A:0.58, C:0.12, G:0.12, T:0.19
Consensus pattern (22 bp):
ATAACAACAAAATGATAGCAAT
Found at i:53450514 original size:18 final size:18
Alignment explanation
Indices: 53450487--53450525 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
53450477 CTATGCTCAA
* * *
53450487 TTATTTATTTTTAAATTC
1 TTATTAATTTTAAAAATC
53450505 TTATTAATTTTAAAAATC
1 TTATTAATTTTAAAAATC
53450523 TTA
1 TTA
53450526 AATGAAATGT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.36, C:0.05, G:0.00, T:0.59
Consensus pattern (18 bp):
TTATTAATTTTAAAAATC
Found at i:53460155 original size:27 final size:27
Alignment explanation
Indices: 53460117--53460172 Score: 112
Period size: 27 Copynumber: 2.1 Consensus size: 27
53460107 AAGATAACAA
53460117 TGTGCATGGTGCAACTGAAAATTCTTT
1 TGTGCATGGTGCAACTGAAAATTCTTT
53460144 TGTGCATGGTGCAACTGAAAATTCTTT
1 TGTGCATGGTGCAACTGAAAATTCTTT
53460171 TG
1 TG
53460173 GTGCTTTAAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.25, C:0.14, G:0.23, T:0.38
Consensus pattern (27 bp):
TGTGCATGGTGCAACTGAAAATTCTTT
Found at i:53462039 original size:33 final size:33
Alignment explanation
Indices: 53461997--53462086 Score: 87
Period size: 31 Copynumber: 2.7 Consensus size: 33
53461987 CAGGCTTACC
* *
53461997 ATATTATTTTTAAATTTTTAA-AAAAATTATATT
1 ATATTATTTTTAAATATTTAATAAAAAATA-ATT
53462030 ATATTA-TTTT-AATATTTAATAAAAAATAATT
1 ATATTATTTTTAAATATTTAATAAAAAATAATT
* *
53462061 AAATTTTTTTATATAATATCTTAATA
1 ATATTATTTT-TA-AATAT-TTAATA
53462087 TTATTTTAAT
Statistics
Matches: 47, Mismatches: 4, Indels: 9
0.78 0.07 0.15
Matches are distributed among these distances:
31 15 0.32
32 14 0.30
33 7 0.15
35 5 0.11
36 6 0.13
ACGTcount: A:0.47, C:0.01, G:0.00, T:0.52
Consensus pattern (33 bp):
ATATTATTTTTAAATATTTAATAAAAAATAATT
Found at i:53462126 original size:17 final size:19
Alignment explanation
Indices: 53462104--53462139 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
53462094 AATGTGTTTT
53462104 AAATT-ACATA-ATATATA
1 AAATTAACATATATATATA
53462121 AAATTAACATATATATATA
1 AAATTAACATATATATATA
53462140 TAAACTTAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 5 0.29
18 5 0.29
19 7 0.41
ACGTcount: A:0.58, C:0.06, G:0.00, T:0.36
Consensus pattern (19 bp):
AAATTAACATATATATATA
Found at i:53466887 original size:16 final size:16
Alignment explanation
Indices: 53466866--53466896 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
53466856 GTGTCATGAA
*
53466866 TCAATTGAATATTAAT
1 TCAATTGAAAATTAAT
53466882 TCAATTGAAAATTAA
1 TCAATTGAAAATTAA
53466897 CTAAAAATAT
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:0.48, C:0.06, G:0.06, T:0.39
Consensus pattern (16 bp):
TCAATTGAAAATTAAT
Found at i:53467833 original size:19 final size:19
Alignment explanation
Indices: 53467809--53467845 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
53467799 TCTCATGAAA
* *
53467809 ATATATATATTTATATAAT
1 ATATATACATGTATATAAT
53467828 ATATATACATGTATATAA
1 ATATATACATGTATATAA
53467846 AGGACTTCAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.49, C:0.03, G:0.03, T:0.46
Consensus pattern (19 bp):
ATATATACATGTATATAAT
Found at i:53474058 original size:18 final size:18
Alignment explanation
Indices: 53474020--53474058 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
53474010 ATTGCTCCTC
*
53474020 AAAAGCACTTTTGGGACA
1 AAAAGCACTTTTGAGACA
* *
53474038 AAAAGTACTTTTGAGATA
1 AAAAGCACTTTTGAGACA
53474056 AAA
1 AAA
53474059 GCATTACTAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.46, C:0.10, G:0.18, T:0.26
Consensus pattern (18 bp):
AAAAGCACTTTTGAGACA
Found at i:53476390 original size:15 final size:16
Alignment explanation
Indices: 53476361--53476393 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
53476351 TTTTTATAAC
*
53476361 TTTTTAATATTTTTAT
1 TTTTTAATATATTTAT
53476377 TTTTTAATA-ATTTAT
1 TTTTTAATATATTTAT
53476392 TT
1 TT
53476394 GTTTTGAACT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 7 0.44
16 9 0.56
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (16 bp):
TTTTTAATATATTTAT
Found at i:53476659 original size:26 final size:26
Alignment explanation
Indices: 53476607--53476659 Score: 72
Period size: 26 Copynumber: 2.1 Consensus size: 26
53476597 AAATTTGTTG
*
53476607 TTTATGTTTTTAAAATTATTTTATTT
1 TTTATGTTTTTAAAATTATTATATTT
* *
53476633 TTTATTTTTTTAAAATTA-TATACTT
1 TTTATGTTTTTAAAATTATTATATTT
53476658 TT
1 TT
53476660 AAAGGGTGAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
25 7 0.29
26 17 0.71
ACGTcount: A:0.28, C:0.02, G:0.02, T:0.68
Consensus pattern (26 bp):
TTTATGTTTTTAAAATTATTATATTT
Found at i:53487523 original size:43 final size:42
Alignment explanation
Indices: 53487435--53487527 Score: 105
Period size: 42 Copynumber: 2.2 Consensus size: 42
53487425 GAATGGTACT
* ** **
53487435 TTTAGCGGCGTTTGTGAAAAAAGTACCCTAAAGGTCATGTTC
1 TTTAGCGGCGTTTGTGAAAAAAGCACCCTAAAGAACATGGCC
* * *
53487477 TTTAGCGGCGTTTGTGATAAGAGCCCCGCTAAAGAACATGGCC
1 TTTAGCGGCGTTTGTGAAAAAAGCACC-CTAAAGAACATGGCC
53487520 TTTAGCGG
1 TTTAGCGG
53487528 TGCTTCTCTT
Statistics
Matches: 42, Mismatches: 8, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
42 23 0.55
43 19 0.45
ACGTcount: A:0.26, C:0.19, G:0.27, T:0.28
Consensus pattern (42 bp):
TTTAGCGGCGTTTGTGAAAAAAGCACCCTAAAGAACATGGCC
Found at i:53487594 original size:43 final size:43
Alignment explanation
Indices: 53487435--53487635 Score: 160
Period size: 43 Copynumber: 4.7 Consensus size: 43
53487425 GAATGGTACT
53487435 TTTAGCGGCGTTTGTGA-AAAAA-GTACC-CTAAAGGTCATGTTC
1 TTTAGCGGCGTTTGTGATAAAAACG--CCGCTAAAGGTCATGTTC
* * * ** **
53487477 TTTAGCGGCGTTTGTGATAAGAGCCCCGCTAAAGAACATGGCC
1 TTTAGCGGCGTTTGTGATAAAAACGCCGCTAAAGGTCATGTTC
* * * * *** *
53487520 TTTAGCGGTGCTTCT-CTTTGAACGCCGCTAAAGGTCATGATC
1 TTTAGCGGCGTTTGTGATAAAAACGCCGCTAAAGGTCATGTTC
* * *
53487562 TTTAGCGGCGATTGTGATAAAAATGCCGCTAAATGTCATGTTC
1 TTTAGCGGCGTTTGTGATAAAAACGCCGCTAAAGGTCATGTTC
53487605 TTTAGCGGCGTTTATGTGA-AAGAAACGCCGC
1 TTTAGCGGCG-TT-TGTGATAA-AAACGCCGC
53487636 CAAAATTAGC
Statistics
Matches: 121, Mismatches: 31, Indels: 11
0.74 0.19 0.07
Matches are distributed among these distances:
42 49 0.40
43 56 0.46
44 3 0.02
45 13 0.11
ACGTcount: A:0.25, C:0.20, G:0.25, T:0.29
Consensus pattern (43 bp):
TTTAGCGGCGTTTGTGATAAAAACGCCGCTAAAGGTCATGTTC
Found at i:53488143 original size:20 final size:21
Alignment explanation
Indices: 53488118--53488159 Score: 68
Period size: 20 Copynumber: 2.0 Consensus size: 21
53488108 GTTAAAAATG
53488118 TTTTAATTAT-TATTTGAATT
1 TTTTAATTATATATTTGAATT
53488138 TTTTAATTATAATATTTGAATT
1 TTTTAATTAT-ATATTTGAATT
53488160 AACAAGTCAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 10 0.50
22 10 0.50
ACGTcount: A:0.33, C:0.00, G:0.05, T:0.62
Consensus pattern (21 bp):
TTTTAATTATATATTTGAATT
Found at i:53488531 original size:18 final size:18
Alignment explanation
Indices: 53488508--53488545 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 18
53488498 AAAAATTGTG
53488508 ATAATTATAA-TTATAGTT
1 ATAATT-TAATTTATAGTT
53488526 ATAATTTAATTTATAGTT
1 ATAATTTAATTTATAGTT
53488544 AT
1 AT
53488546 TAGTTAAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 3 0.16
18 16 0.84
ACGTcount: A:0.42, C:0.00, G:0.05, T:0.53
Consensus pattern (18 bp):
ATAATTTAATTTATAGTT
Found at i:53488552 original size:18 final size:18
Alignment explanation
Indices: 53488518--53488552 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
53488508 ATAATTATAA
*
53488518 TTATAGTTATAATTTAAT
1 TTATAGTTATAAGTTAAT
*
53488536 TTATAGTTATTAGTTAA
1 TTATAGTTATAAGTTAA
53488553 AATTTTGACA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.37, C:0.00, G:0.09, T:0.54
Consensus pattern (18 bp):
TTATAGTTATAAGTTAAT
Found at i:53489713 original size:5 final size:5
Alignment explanation
Indices: 53489703--53489759 Score: 73
Period size: 5 Copynumber: 11.2 Consensus size: 5
53489693 AATTATGTTT
53489703 TTATA TTATA TTATTA TTA-A -TATA TTATA TTATA TTATA TTATTA TTATA
1 TTATA TTATA TTA-TA TTATA TTATA TTATA TTATA TTATA TTA-TA TTATA
53489753 TATATA T
1 T-TATA T
53489760 GACAAAGAAA
Statistics
Matches: 47, Mismatches: 0, Indels: 9
0.84 0.00 0.16
Matches are distributed among these distances:
3 2 0.04
4 2 0.04
5 28 0.60
6 15 0.32
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (5 bp):
TTATA
Found at i:53489829 original size:40 final size:40
Alignment explanation
Indices: 53489772--53489867 Score: 147
Period size: 40 Copynumber: 2.4 Consensus size: 40
53489762 CAAAGAAAGA
53489772 AAGAAAGAAAAGAAACAGAGAGCAAAACAAAACAGAGAAGG
1 AAGAAAG-AAAGAAACAGAGAGCAAAACAAAACAGAGAAGG
* *
53489813 GAGAAAGAAAGAAACAGAGAGCAAAACGAAACAGAGAAGG
1 AAGAAAGAAAGAAACAGAGAGCAAAACAAAACAGAGAAGG
*
53489853 AAGGAAGGAAAGAAA
1 AA-GAAAGAAAGAAA
53489868 GAAAGAAAAG
Statistics
Matches: 50, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
40 33 0.66
41 17 0.34
ACGTcount: A:0.64, C:0.08, G:0.28, T:0.00
Consensus pattern (40 bp):
AAGAAAGAAAGAAACAGAGAGCAAAACAAAACAGAGAAGG
Found at i:53491157 original size:24 final size:24
Alignment explanation
Indices: 53491119--53491223 Score: 126
Period size: 24 Copynumber: 4.4 Consensus size: 24
53491109 CTTTAGCGCG
53491119 CTCTGATTATTAGCACGTTGGTGCT
1 CTCTGA-TATTAGCACGTTGGTGCT
53491144 CTCTGATATTAGCACGTTGGTGCT
1 CTCTGATATTAGCACGTTGGTGCT
** *
53491168 CTCTGATATTTAGCACGTCAGTGTT
1 CTCTGATA-TTAGCACGTTGGTGCT
* *
53491193 CTCTG-T-TTAGCACATTTGTGCT
1 CTCTGATATTAGCACGTTGGTGCT
53491215 CTCTG-TATT
1 CTCTGATATT
53491224 TGTTCCGTAT
Statistics
Matches: 71, Mismatches: 7, Indels: 6
0.85 0.08 0.07
Matches are distributed among these distances:
22 18 0.25
23 2 0.03
24 27 0.38
25 24 0.34
ACGTcount: A:0.16, C:0.21, G:0.21, T:0.42
Consensus pattern (24 bp):
CTCTGATATTAGCACGTTGGTGCT
Found at i:53491214 original size:47 final size:49
Alignment explanation
Indices: 53491119--53491224 Score: 130
Period size: 49 Copynumber: 2.2 Consensus size: 49
53491109 CTTTAGCGCG
** *
53491119 CTCTGAT-TATTAGCACGTTGGTGCTCTCTGATATTAGCACGTTGGTGCT
1 CTCTGATAT-TTAGCACGTCAGTGCTCTCTGATATTAGCACATTGGTGCT
* *
53491168 CTCTGATATTTAGCACGTCAGTGTTCTCTG-T-TTAGCACATTTGTGCT
1 CTCTGATATTTAGCACGTCAGTGCTCTCTGATATTAGCACATTGGTGCT
53491215 CTCTG-TATTT
1 CTCTGATATTT
53491225 GTTCCGTATA
Statistics
Matches: 51, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
46 5 0.10
47 19 0.37
48 1 0.02
49 25 0.49
50 1 0.02
ACGTcount: A:0.16, C:0.21, G:0.21, T:0.42
Consensus pattern (49 bp):
CTCTGATATTTAGCACGTCAGTGCTCTCTGATATTAGCACATTGGTGCT
Found at i:53493349 original size:116 final size:117
Alignment explanation
Indices: 53493147--53493359 Score: 367
Period size: 116 Copynumber: 1.8 Consensus size: 117
53493137 GACTGTAACA
53493147 CCCTAAAACATAAGTTCGGTTAAGCGACAAAATTAAGTAAGAAATAGGCAACAACCTAACGATTA
1 CCCTAAAACATAAGTTCGGTTAAGCGACAAAATTAAGTAAGAAATAGGCAACAACCTAACGATTA
53493212 AGCTTTAGTCTCTCCCCCTTGCTTACCCAAGTGCCTTCCTCCATTGTGACAC
66 AGCTTTAGTCTCTCCCCCTTGCTTACCCAAGTGCCTTCCTCCATTGTGACAC
* * *
53493264 CCCT-AAACATAAGTTCGGTTAAGCGACGAAATTAAGTAAGAAATGGGCAACAACCTAATGATTA
1 CCCTAAAACATAAGTTCGGTTAAGCGACAAAATTAAGTAAGAAATAGGCAACAACCTAACGATTA
*
53493328 AG-TGTTAGTCTCTCCCTCTTGCTTACCCAAGT
66 AGCT-TTAGTCTCTCCCCCTTGCTTACCCAAGT
53493360 TCGAGCCCCC
Statistics
Matches: 91, Mismatches: 4, Indels: 3
0.93 0.04 0.03
Matches are distributed among these distances:
115 1 0.01
116 86 0.95
117 4 0.04
ACGTcount: A:0.33, C:0.25, G:0.16, T:0.26
Consensus pattern (117 bp):
CCCTAAAACATAAGTTCGGTTAAGCGACAAAATTAAGTAAGAAATAGGCAACAACCTAACGATTA
AGCTTTAGTCTCTCCCCCTTGCTTACCCAAGTGCCTTCCTCCATTGTGACAC
Found at i:53493789 original size:116 final size:117
Alignment explanation
Indices: 53493587--53493799 Score: 367
Period size: 116 Copynumber: 1.8 Consensus size: 117
53493577 GACTGTAACA
53493587 CCCTAAAACATAAGTTCGGTTAAGCGACAAAATTAAGTAAGAAATAGGCAACAACCTAACGATTA
1 CCCTAAAACATAAGTTCGGTTAAGCGACAAAATTAAGTAAGAAATAGGCAACAACCTAACGATTA
53493652 AGCTTTAGTCTCTCCCCCTTGCTTACCCAAGTGCCTTCCTCCATTGTGACAC
66 AGCTTTAGTCTCTCCCCCTTGCTTACCCAAGTGCCTTCCTCCATTGTGACAC
* * *
53493704 CCCT-AAACATAAGTTCGGTTAAGCGACGAAATTAAGTAAGAAATGGGCAACAACCTAATGATTA
1 CCCTAAAACATAAGTTCGGTTAAGCGACAAAATTAAGTAAGAAATAGGCAACAACCTAACGATTA
*
53493768 AG-TGTTAGTCTCTCCCTCTTGCTTACCCAAGT
66 AGCT-TTAGTCTCTCCCCCTTGCTTACCCAAGT
53493800 TCGAGCCCCC
Statistics
Matches: 91, Mismatches: 4, Indels: 3
0.93 0.04 0.03
Matches are distributed among these distances:
115 1 0.01
116 86 0.95
117 4 0.04
ACGTcount: A:0.33, C:0.25, G:0.16, T:0.26
Consensus pattern (117 bp):
CCCTAAAACATAAGTTCGGTTAAGCGACAAAATTAAGTAAGAAATAGGCAACAACCTAACGATTA
AGCTTTAGTCTCTCCCCCTTGCTTACCCAAGTGCCTTCCTCCATTGTGACAC
Found at i:53493944 original size:440 final size:440
Alignment explanation
Indices: 53493123--53494003 Score: 1762
Period size: 440 Copynumber: 2.0 Consensus size: 440
53493113 CCTCTTTTGT
53493123 TTTTATTTAATTTCGACTGTAACACCCTAAAACATAAGTTCGGTTAAGCGACAAAATTAAGTAAG
1 TTTTATTTAATTTCGACTGTAACACCCTAAAACATAAGTTCGGTTAAGCGACAAAATTAAGTAAG
53493188 AAATAGGCAACAACCTAACGATTAAGCTTTAGTCTCTCCCCCTTGCTTACCCAAGTGCCTTCCTC
66 AAATAGGCAACAACCTAACGATTAAGCTTTAGTCTCTCCCCCTTGCTTACCCAAGTGCCTTCCTC
53493253 CATTGTGACACCCCTAAACATAAGTTCGGTTAAGCGACGAAATTAAGTAAGAAATGGGCAACAAC
131 CATTGTGACACCCCTAAACATAAGTTCGGTTAAGCGACGAAATTAAGTAAGAAATGGGCAACAAC
53493318 CTAATGATTAAGTGTTAGTCTCTCCCTCTTGCTTACCCAAGTTCGAGCCCCCTCATTCCCCTTTT
196 CTAATGATTAAGTGTTAGTCTCTCCCTCTTGCTTACCCAAGTTCGAGCCCCCTCATTCCCCTTTT
53493383 AATTTTGAGATTTCGGCAAACACAAAATGTATATTGTTAGTAATAAAAATTAGAGAAGAAATGGG
261 AATTTTGAGATTTCGGCAAACACAAAATGTATATTGTTAGTAATAAAAATTAGAGAAGAAATGGG
53493448 CAATAGCCCAATGGTTAAGAGATAGCCTTCCTCTATTGTGTTCCTAAGTTTAAATCACGCCCTTC
326 CAATAGCCCAATGGTTAAGAGATAGCCTTCCTCTATTGTGTTCCTAAGTTTAAATCACGCCCTTC
53493513 CTTTCCATATTTTTTTGAAATTTTGTCAGCTTTAGGAAAATTACAAGTGA
391 CTTTCCATATTTTTTTGAAATTTTGTCAGCTTTAGGAAAATTACAAGTGA
53493563 TTTTATTTAATTTCGACTGTAACACCCTAAAACATAAGTTCGGTTAAGCGACAAAATTAAGTAAG
1 TTTTATTTAATTTCGACTGTAACACCCTAAAACATAAGTTCGGTTAAGCGACAAAATTAAGTAAG
53493628 AAATAGGCAACAACCTAACGATTAAGCTTTAGTCTCTCCCCCTTGCTTACCCAAGTGCCTTCCTC
66 AAATAGGCAACAACCTAACGATTAAGCTTTAGTCTCTCCCCCTTGCTTACCCAAGTGCCTTCCTC
53493693 CATTGTGACACCCCTAAACATAAGTTCGGTTAAGCGACGAAATTAAGTAAGAAATGGGCAACAAC
131 CATTGTGACACCCCTAAACATAAGTTCGGTTAAGCGACGAAATTAAGTAAGAAATGGGCAACAAC
53493758 CTAATGATTAAGTGTTAGTCTCTCCCTCTTGCTTACCCAAGTTCGAGCCCCCTCATTCCCCTTTT
196 CTAATGATTAAGTGTTAGTCTCTCCCTCTTGCTTACCCAAGTTCGAGCCCCCTCATTCCCCTTTT
53493823 AATTTTGAGATTTCGGCAAACACAAAATGTATATTGTTAGTAATAAAAATTAGAGAAGAAATGGG
261 AATTTTGAGATTTCGGCAAACACAAAATGTATATTGTTAGTAATAAAAATTAGAGAAGAAATGGG
53493888 CAATAGCCCAATGGTTAAGAGATAGCCTTCCTCTATTGTGTTCCTAAGTTTAAATCACGCCCTTC
326 CAATAGCCCAATGGTTAAGAGATAGCCTTCCTCTATTGTGTTCCTAAGTTTAAATCACGCCCTTC
53493953 CTTTCCATATTTTTTTGAAATTTTGTCAGCTTTAGGAAAATTACAAGTGA
391 CTTTCCATATTTTTTTGAAATTTTGTCAGCTTTAGGAAAATTACAAGTGA
53494003 T
1 T
53494004 GCCCCTAAGG
Statistics
Matches: 441, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
440 441 1.00
ACGTcount: A:0.32, C:0.21, G:0.15, T:0.31
Consensus pattern (440 bp):
TTTTATTTAATTTCGACTGTAACACCCTAAAACATAAGTTCGGTTAAGCGACAAAATTAAGTAAG
AAATAGGCAACAACCTAACGATTAAGCTTTAGTCTCTCCCCCTTGCTTACCCAAGTGCCTTCCTC
CATTGTGACACCCCTAAACATAAGTTCGGTTAAGCGACGAAATTAAGTAAGAAATGGGCAACAAC
CTAATGATTAAGTGTTAGTCTCTCCCTCTTGCTTACCCAAGTTCGAGCCCCCTCATTCCCCTTTT
AATTTTGAGATTTCGGCAAACACAAAATGTATATTGTTAGTAATAAAAATTAGAGAAGAAATGGG
CAATAGCCCAATGGTTAAGAGATAGCCTTCCTCTATTGTGTTCCTAAGTTTAAATCACGCCCTTC
CTTTCCATATTTTTTTGAAATTTTGTCAGCTTTAGGAAAATTACAAGTGA
Found at i:53494697 original size:33 final size:35
Alignment explanation
Indices: 53494601--53494698 Score: 91
Period size: 33 Copynumber: 2.9 Consensus size: 35
53494591 GTCAATATTT
*
53494601 TAATATATGAAATATAAATTTTAAATATTT--TTAAG
1 TAATATAT-AAAT-TATATTTTAAATATTTAATTAAG
* *
53494636 TAATAAATATTAATTAT-TTATAAA-ATTTAATT-AG
1 TAAT--ATATAAATTATATTTTAAATATTTAATTAAG
53494670 -AATATATAAATTATATTTTAAATATTTAA
1 TAATATATAAATTATATTTTAAATATTTAA
53494699 ATATAACCAT
Statistics
Matches: 52, Mismatches: 5, Indels: 14
0.73 0.07 0.20
Matches are distributed among these distances:
31 10 0.19
32 6 0.12
33 13 0.25
34 8 0.15
35 8 0.15
36 3 0.06
37 4 0.08
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (35 bp):
TAATATATAAATTATATTTTAAATATTTAATTAAG
Found at i:53499874 original size:14 final size:14
Alignment explanation
Indices: 53499855--53499903 Score: 66
Period size: 14 Copynumber: 3.6 Consensus size: 14
53499845 AATTATGATT
53499855 TTAATATATTAAAA
1 TTAATATATTAAAA
*
53499869 TTAATAAATTAAATA
1 TTAATATATTAAA-A
53499884 TTAATAT-TTAAAA
1 TTAATATATTAAAA
53499897 TT-ATATA
1 TTAATATA
53499904 GAAGCTTCAT
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
12 4 0.13
13 3 0.10
14 17 0.55
15 7 0.23
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (14 bp):
TTAATATATTAAAA
Found at i:53500261 original size:25 final size:25
Alignment explanation
Indices: 53500211--53500263 Score: 63
Period size: 24 Copynumber: 2.1 Consensus size: 25
53500201 AGCAATTATC
*
53500211 ATTATAAATTACAACTTTTTATAAA
1 ATTATAAATTACAACTTATTATAAA
*
53500236 ATTAT-AATTACAACATTAATTAAAAA
1 ATTATAAATTACAAC-TT-ATTATAAA
53500262 AT
1 AT
53500264 AATATAAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
24 9 0.38
25 7 0.29
26 8 0.33
ACGTcount: A:0.53, C:0.08, G:0.00, T:0.40
Consensus pattern (25 bp):
ATTATAAATTACAACTTATTATAAA
Found at i:53501682 original size:22 final size:23
Alignment explanation
Indices: 53501657--53501722 Score: 68
Period size: 22 Copynumber: 3.0 Consensus size: 23
53501647 ACATTAATCG
53501657 AATAATTTTATATATTATTAA-A
1 AATAATTTTATATATTATTAATA
*
53501679 AAT-ATTTTTTGAATATT-TTAATA
1 AATAATTTTAT--ATATTATTAATA
*
53501702 ATTAA-TTTATATATTATTAAT
1 AATAATTTTATATATTATTAAT
53501723 TGATATTTAA
Statistics
Matches: 36, Mismatches: 3, Indels: 10
0.73 0.06 0.20
Matches are distributed among these distances:
21 11 0.31
22 12 0.33
23 12 0.33
24 1 0.03
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.55
Consensus pattern (23 bp):
AATAATTTTATATATTATTAATA
Found at i:53501713 original size:19 final size:21
Alignment explanation
Indices: 53501691--53501736 Score: 53
Period size: 19 Copynumber: 2.3 Consensus size: 21
53501681 TATTTTTTGA
53501691 ATATTTTAATAATT-A-ATTT
1 ATATTTTAATAATTGATATTT
* *
53501710 ATATATTATTAATTGATATTT
1 ATATTTTAATAATTGATATTT
53501731 A-ATTTT
1 ATATTTT
53501737 TTTAAGAGTA
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
19 12 0.55
20 5 0.23
21 5 0.23
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (21 bp):
ATATTTTAATAATTGATATTT
Found at i:53502961 original size:30 final size:31
Alignment explanation
Indices: 53502897--53502961 Score: 80
Period size: 31 Copynumber: 2.1 Consensus size: 31
53502887 ATATTAGTGG
*
53502897 GTGATTGATTTGTCACTTTTCAATAATGTTA
1 GTGATTGATTTGTCACTTTTCAATAAAGTTA
* *
53502928 GTGATTGATTTGTTA-TTTTC-CTAAAGTTGA
1 GTGATTGATTTGTCACTTTTCAATAAAGTT-A
53502958 GTGA
1 GTGA
53502962 CTACTAATGT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
29 6 0.20
30 10 0.33
31 14 0.47
ACGTcount: A:0.25, C:0.08, G:0.20, T:0.48
Consensus pattern (31 bp):
GTGATTGATTTGTCACTTTTCAATAAAGTTA
Found at i:53506655 original size:17 final size:19
Alignment explanation
Indices: 53506624--53506679 Score: 55
Period size: 17 Copynumber: 3.1 Consensus size: 19
53506614 TAAATTTATT
*
53506624 ATTTTAA-AATATTTTAAA
1 ATTTTAAGAATTTTTTAAA
* *
53506642 ATTTT-A-ACTTTTTTATA
1 ATTTTAAGAATTTTTTAAA
*
53506659 TTTTTAAGAATTTTTTAAA
1 ATTTTAAGAATTTTTTAAA
53506678 AT
1 AT
53506680 AATTTTTGAA
Statistics
Matches: 29, Mismatches: 7, Indels: 3
0.74 0.18 0.08
Matches are distributed among these distances:
17 13 0.45
18 6 0.21
19 10 0.34
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.57
Consensus pattern (19 bp):
ATTTTAAGAATTTTTTAAA
Found at i:53507380 original size:106 final size:103
Alignment explanation
Indices: 53507196--53507407 Score: 388
Period size: 106 Copynumber: 2.0 Consensus size: 103
53507186 AATTTTTTCA
53507196 ATTTCAAGCACACTTTCAATTAGTCTAGTTTCTTATTACGAGTAAAGATCAAACTCCTAATCTTA
1 ATTTCAAGCACACTTTCAATTAGTCTAGTTTCTTATTACGAGTAAAGATCAAACTCCTAATCTTA
53507261 TTTCTATAAGCAATCACCCCACCACACATACTTTCCTG
66 TTTCTATAAGCAATCACCCCACCACACATACTTTCCTG
*
53507299 ATTTCAAGCACACTTTCAATTAGTCTAGTTTCTTATTGCTACGAGTAAAGATCAAACTTCTAATC
1 ATTTCAAGCACACTTTCAATTAGTCTAGTTTCTTA-T--TACGAGTAAAGATCAAACTCCTAATC
53507364 TTATTTCTATAAGCAATCACCCCACCACACATACTTTCCTG
63 TTATTTCTATAAGCAATCACCCCACCACACATACTTTCCTG
53507405 ATT
1 ATT
53507408 CATACTTTTT
Statistics
Matches: 105, Mismatches: 1, Indels: 3
0.96 0.01 0.03
Matches are distributed among these distances:
103 35 0.33
104 1 0.01
106 69 0.66
ACGTcount: A:0.32, C:0.25, G:0.08, T:0.35
Consensus pattern (103 bp):
ATTTCAAGCACACTTTCAATTAGTCTAGTTTCTTATTACGAGTAAAGATCAAACTCCTAATCTTA
TTTCTATAAGCAATCACCCCACCACACATACTTTCCTG
Found at i:53509891 original size:18 final size:19
Alignment explanation
Indices: 53509868--53509910 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 19
53509858 AATTTAAGTG
*
53509868 TAATTAATTTAAAATT-TT
1 TAATTAAGTTAAAATTATT
*
53509886 TAATT-AGTTAAATTTATT
1 TAATTAAGTTAAAATTATT
53509904 TAATTAA
1 TAATTAA
53509911 AAATCTATTC
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
17 8 0.38
18 12 0.57
19 1 0.05
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.53
Consensus pattern (19 bp):
TAATTAAGTTAAAATTATT
Found at i:53517396 original size:35 final size:34
Alignment explanation
Indices: 53517343--53517440 Score: 105
Period size: 35 Copynumber: 2.9 Consensus size: 34
53517333 TTTGTCTAAG
53517343 TATA-TATATAATTAATGAT-ATTAAAATATAATT
1 TATATTATATAATTAATGATAATTAAAATATAA-T
* *
53517376 TATATTATATGAATTTATGATAATTAAATTATAAT
1 TATATTATAT-AATTAATGATAATTAAAATATAAT
* *
53517411 GATATTATATTATTAA--ATAAATTAAAATAT
1 TATATTATATAATTAATGAT-AATTAAAATAT
53517441 GCCAATTGTA
Statistics
Matches: 55, Mismatches: 6, Indels: 8
0.80 0.09 0.12
Matches are distributed among these distances:
32 2 0.04
33 14 0.25
34 9 0.16
35 19 0.35
36 11 0.20
ACGTcount: A:0.50, C:0.00, G:0.04, T:0.46
Consensus pattern (34 bp):
TATATTATATAATTAATGATAATTAAAATATAAT
Found at i:53517412 original size:25 final size:23
Alignment explanation
Indices: 53517368--53517428 Score: 61
Period size: 24 Copynumber: 2.5 Consensus size: 23
53517358 TGATATTAAA
*
53517368 ATATAATTTATATTATATGA-ATTT
1 ATATAA-TTAAATTATATGATA-TT
53517392 ATGATAATTAAATTATAATGATATT
1 AT-ATAATTAAATTAT-ATGATATT
*
53517417 ATATTATTAAAT
1 ATATAATTAAAT
53517429 AAATTAAAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
24 19 0.59
25 12 0.38
26 1 0.03
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.49
Consensus pattern (23 bp):
ATATAATTAAATTATATGATATT
Found at i:53517871 original size:12 final size:12
Alignment explanation
Indices: 53517839--53517879 Score: 50
Period size: 12 Copynumber: 3.5 Consensus size: 12
53517829 AAAGTAAAAT
53517839 AAAAGAAACA-A
1 AAAAGAAACAGA
53517850 AAGAAG-AACAGA
1 AA-AAGAAACAGA
53517862 AAAAGAAACAGA
1 AAAAGAAACAGA
*
53517874 GAAAGA
1 AAAAGA
53517880 GACGAAACAG
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
11 9 0.35
12 17 0.65
ACGTcount: A:0.73, C:0.07, G:0.20, T:0.00
Consensus pattern (12 bp):
AAAAGAAACAGA
Found at i:53518954 original size:39 final size:38
Alignment explanation
Indices: 53518875--53518960 Score: 102
Period size: 39 Copynumber: 2.3 Consensus size: 38
53518865 ATTTGCCGGC
*
53518875 TTACTGATTAGGCACTTATGTGCCGACTACTATTACTG
1 TTACTGATTAGGCACTTATGTGCCGAATACTATTACTG
* * * * *
53518913 TTACTGATTCGGTACTTTGTGTGTCGAATACTGTTACTG
1 TTACTGATTAGGCAC-TTATGTGCCGAATACTATTACTG
53518952 TTACT-ATTA
1 TTACTGATTA
53518961 CCAATTCGGC
Statistics
Matches: 40, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
38 16 0.40
39 24 0.60
ACGTcount: A:0.22, C:0.17, G:0.19, T:0.42
Consensus pattern (38 bp):
TTACTGATTAGGCACTTATGTGCCGAATACTATTACTG
Found at i:53518977 original size:45 final size:46
Alignment explanation
Indices: 53518918--53519051 Score: 173
Period size: 45 Copynumber: 3.0 Consensus size: 46
53518908 TACTGTTACT
*
53518918 GATTCGGTACTTTGTGTGTCGAATACTGTTACTGTTACTATTACCA
1 GATTCGGCACTTTGTGTGTCGAATACTGTTACTGTTACTATTACCA
* **
53518964 -ATTCGGCATTTTGTGTGTCGAATACTGTTACCATTACTATTA-CA
1 GATTCGGCACTTTGTGTGTCGAATACTGTTACTGTTACTATTACCA
** * * *
53519008 GATTCAACACTTTGTGTGTTGAATATTGTTACTGTTACTGTTAC
1 GATTCGGCACTTTGTGTGTCGAATACTGTTACTGTTACTATTAC
53519052 TGCTACCGTT
Statistics
Matches: 74, Mismatches: 12, Indels: 4
0.82 0.13 0.04
Matches are distributed among these distances:
44 2 0.03
45 72 0.97
ACGTcount: A:0.23, C:0.16, G:0.18, T:0.43
Consensus pattern (46 bp):
GATTCGGCACTTTGTGTGTCGAATACTGTTACTGTTACTATTACCA
Found at i:53519078 original size:7 final size:6
Alignment explanation
Indices: 53519034--53519074 Score: 55
Period size: 6 Copynumber: 6.7 Consensus size: 6
53519024 TGTTGAATAT
* *
53519034 TGTTAC TGTTAC TGTTAC TGCTAC CGTTAC TGATTAC TGTT
1 TGTTAC TGTTAC TGTTAC TGTTAC TGTTAC TG-TTAC TGTT
53519075 TACTAGTGTG
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
6 24 0.80
7 6 0.20
ACGTcount: A:0.17, C:0.20, G:0.17, T:0.46
Consensus pattern (6 bp):
TGTTAC
Found at i:53527206 original size:15 final size:15
Alignment explanation
Indices: 53527186--53527214 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
53527176 GGTTCCCAGG
53527186 ATTGAAAATTTGAAA
1 ATTGAAAATTTGAAA
53527201 ATTGAAAATTTGAA
1 ATTGAAAATTTGAA
53527215 TAGGATTATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.52, C:0.00, G:0.14, T:0.34
Consensus pattern (15 bp):
ATTGAAAATTTGAAA
Found at i:53532597 original size:18 final size:17
Alignment explanation
Indices: 53532564--53532602 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
53532554 TTTTATAAAT
53532564 TGTGAATTATATTTGATA
1 TGTGAATTATATTTGA-A
53532582 TGTGAATTA-ATATTGAA
1 TGTGAATTATAT-TTGAA
53532599 TGTG
1 TGTG
53532603 GAAGGAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.33, C:0.00, G:0.21, T:0.46
Consensus pattern (17 bp):
TGTGAATTATATTTGAA
Found at i:53541467 original size:13 final size:13
Alignment explanation
Indices: 53541418--53541461 Score: 52
Period size: 13 Copynumber: 3.2 Consensus size: 13
53541408 TTCGAAGATC
*
53541418 TTCAATTCAAATA
1 TTCAATTCAAATT
53541431 TTCGAAGTTTCAAATT
1 TTC-AA--TTCAAATT
53541447 TTCAATTCAAATT
1 TTCAATTCAAATT
53541460 TT
1 TT
53541462 ATATTCGTTC
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
13 13 0.48
14 2 0.07
15 2 0.07
16 10 0.37
ACGTcount: A:0.36, C:0.14, G:0.05, T:0.45
Consensus pattern (13 bp):
TTCAATTCAAATT
Found at i:53549325 original size:12 final size:12
Alignment explanation
Indices: 53549293--53549327 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
53549283 GCACATTTTG
53549293 TTCTTATTATTA
1 TTCTTATTATTA
*
53549305 TTCTCATTATTA
1 TTCTTATTATTA
*
53549317 TTGTTATTATT
1 TTCTTATTATT
53549328 TATTTTTCAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.23, C:0.09, G:0.03, T:0.66
Consensus pattern (12 bp):
TTCTTATTATTA
Found at i:53549347 original size:8 final size:8
Alignment explanation
Indices: 53549326--53549363 Score: 51
Period size: 8 Copynumber: 4.8 Consensus size: 8
53549316 ATTGTTATTA
53549326 TTTA-TTT
1 TTTATTTT
*
53549333 TTCATTTT
1 TTTATTTT
53549341 TTTATTTT
1 TTTATTTT
53549349 TTTATTTT
1 TTTATTTT
53549357 TTATATT
1 TT-TATT
53549364 AATATTTAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
7 3 0.11
8 20 0.74
9 4 0.15
ACGTcount: A:0.16, C:0.03, G:0.00, T:0.82
Consensus pattern (8 bp):
TTTATTTT
Found at i:53556163 original size:26 final size:26
Alignment explanation
Indices: 53556126--53556176 Score: 84
Period size: 26 Copynumber: 2.0 Consensus size: 26
53556116 GGTGAGCTCA
*
53556126 TAGTTCGCAGGTGAGCTTGCAGTTCG
1 TAGTTCGCAGGTGAGCTCGCAGTTCG
*
53556152 TAGTTCGTAGGTGAGCTCGCAGTTC
1 TAGTTCGCAGGTGAGCTCGCAGTTC
53556177 ACAATTAGCA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.16, C:0.20, G:0.33, T:0.31
Consensus pattern (26 bp):
TAGTTCGCAGGTGAGCTCGCAGTTCG
Found at i:53559533 original size:13 final size:13
Alignment explanation
Indices: 53559517--53559672 Score: 109
Period size: 13 Copynumber: 11.8 Consensus size: 13
53559507 GTAAGCAATG
*
53559517 TATTTAAGTAACA
1 TATTTAAGTAATA
53559530 TATTTAAGTAATA
1 TATTTAAGTAATA
* **
53559543 AATTTAAACAA-A
1 TATTTAAGTAATA
* *
53559555 TTTTAATAAGTAATG
1 TATT--TAAGTAATA
* *
53559570 TATTTAAGTCACA
1 TATTTAAGTAATA
53559583 TATTTAAGTAATA
1 TATTTAAGTAATA
* **
53559596 AATTTAACCAA-A
1 TATTTAAGTAATA
* * *
53559608 TTTTAGTAAGTAGTG
1 TATT--TAAGTAATA
*
53559623 TATTTAAGTAATT
1 TATTTAAGTAATA
53559636 TATTTAAGTAATA
1 TATTTAAGTAATA
*
53559649 TATTCAAGTAATA
1 TATTTAAGTAATA
*
53559662 TATTAAAGTAA
1 TATTTAAGTAA
53559673 ATTTTAGTAA
Statistics
Matches: 107, Mismatches: 30, Indels: 12
0.72 0.20 0.08
Matches are distributed among these distances:
12 6 0.06
13 86 0.80
14 9 0.08
15 6 0.06
ACGTcount: A:0.46, C:0.04, G:0.09, T:0.41
Consensus pattern (13 bp):
TATTTAAGTAATA
Found at i:53559566 original size:27 final size:26
Alignment explanation
Indices: 53559534--53559619 Score: 84
Period size: 27 Copynumber: 3.2 Consensus size: 26
53559524 GTAACATATT
53559534 TAAGTAATAAATTTAAACAAATTTTAA
1 TAAGTAATAAATTTAAACAAATTTT-A
** * * *
53559561 TAAGTAATGTATTTAAGTCACATATT-
1 TAAGTAATAAATTTAA-ACAAATTTTA
*
53559587 TAAGTAATAAATTTAACCAAATTTTA
1 TAAGTAATAAATTTAAACAAATTTTA
53559613 GTAAGTA
1 -TAAGTA
53559620 GTGTATTTAA
Statistics
Matches: 46, Mismatches: 10, Indels: 6
0.74 0.16 0.10
Matches are distributed among these distances:
25 6 0.13
26 14 0.30
27 20 0.43
28 6 0.13
ACGTcount: A:0.48, C:0.06, G:0.08, T:0.38
Consensus pattern (26 bp):
TAAGTAATAAATTTAAACAAATTTTA
Found at i:53559570 original size:53 final size:53
Alignment explanation
Indices: 53559499--53559648 Score: 237
Period size: 53 Copynumber: 2.8 Consensus size: 53
53559489 ATATATACTT
*
53559499 AAATTTTAGTAAGCAATGTATTTAAGTAACATATTTAAGTAATAAATTTAAAC
1 AAATTTTAGTAAGTAATGTATTTAAGTAACATATTTAAGTAATAAATTTAAAC
* * *
53559552 AAATTTTAATAAGTAATGTATTTAAGTCACATATTTAAGTAATAAATTTAACC
1 AAATTTTAGTAAGTAATGTATTTAAGTAACATATTTAAGTAATAAATTTAAAC
* **
53559605 AAATTTTAGTAAGTAGTGTATTTAAGTAATTTATTTAAGTAATA
1 AAATTTTAGTAAGTAATGTATTTAAGTAACATATTTAAGTAATA
53559649 TATTCAAGTA
Statistics
Matches: 88, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
53 88 1.00
ACGTcount: A:0.45, C:0.05, G:0.10, T:0.41
Consensus pattern (53 bp):
AAATTTTAGTAAGTAATGTATTTAAGTAACATATTTAAGTAATAAATTTAAAC
Found at i:53559699 original size:66 final size:66
Alignment explanation
Indices: 53559561--53559699 Score: 152
Period size: 66 Copynumber: 2.1 Consensus size: 66
53559551 CAAATTTTAA
* * * ** * *
53559561 TAAGTAATGTATTTAAGTCACATATTTAAGTAATAAATTTAACCAAATTTTAGTAAGTAGTGTAT
1 TAAGTAATGTATTTAAGTAACATATTCAAGTAATAAATTAAACCAAATTTTAGTAAAAAATATAT
53559626 T
66 T
* * * ** *
53559627 TAAGTAATTTATTTAAGTAATATATTCAAGTAATATATTAAAGTAAATTTTAGTAAAAAATATGT
1 TAAGTAATGTATTTAAGTAACATATTCAAGTAATAAATTAAACCAAATTTTAGTAAAAAATATAT
53559692 T
66 T
*
53559693 TTAGTAA
1 TAAGTAA
53559700 GTAATGTAAG
Statistics
Matches: 59, Mismatches: 14, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
66 59 1.00
ACGTcount: A:0.44, C:0.04, G:0.11, T:0.42
Consensus pattern (66 bp):
TAAGTAATGTATTTAAGTAACATATTCAAGTAATAAATTAAACCAAATTTTAGTAAAAAATATAT
T
Found at i:53559878 original size:20 final size:19
Alignment explanation
Indices: 53559827--53559881 Score: 69
Period size: 20 Copynumber: 2.9 Consensus size: 19
53559817 TAAAAATATA
*
53559827 TTAAAAATATA-A-TAAAT
1 TTAAAAATATATATTAACT
53559844 ATTAAAAATATATATTAACT
1 -TTAAAAATATATATTAACT
53559864 TTAAAATATATATATTAA
1 TTAAAA-ATATATATTAA
53559882 TAAGTTATTT
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
18 11 0.33
19 7 0.21
20 15 0.45
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (19 bp):
TTAAAAATATATATTAACT
Found at i:53562220 original size:14 final size:15
Alignment explanation
Indices: 53562181--53562222 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
53562171 TTTTAACATA
*
53562181 ATTATTATTAAATAT
1 ATTATAATTAAATAT
53562196 ATTATAATTAAA-AT
1 ATTATAATTAAATAT
*
53562210 A-TATAATTTAATA
1 ATTATAATTAAATA
53562223 AAATTCTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 9 0.38
14 4 0.17
15 11 0.46
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
ATTATAATTAAATAT
Found at i:53562317 original size:120 final size:120
Alignment explanation
Indices: 53562172--53562436 Score: 487
Period size: 120 Copynumber: 2.2 Consensus size: 120
53562162 TTAATCATAT
53562172 TTTAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAAT
1 TTTAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAAT
* *
53562237 CAATATTCTTATATGAATTTACTCACATCATAATATATGATACTATAAAATATAA
66 CAATATTCTTATATGAATTTACTAAAATCATAATATATGATACTATAAAATATAA
*
53562292 TTTAACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAAT
1 TTTAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAAT
53562357 CAATATTCTTATATGAATTTACTAAAATCATAATATATGATACTATAAAATATAA
66 CAATATTCTTATATGAATTTACTAAAATCATAATATATGATACTATAAAATATAA
53562412 TTTGAA-ATAATTATTATTAAATATA
1 TTT-AACATAATTATTATTAAATATA
53562437 ATTTTTCTAA
Statistics
Matches: 141, Mismatches: 3, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
120 139 0.99
121 2 0.01
ACGTcount: A:0.49, C:0.06, G:0.02, T:0.43
Consensus pattern (120 bp):
TTTAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAAT
CAATATTCTTATATGAATTTACTAAAATCATAATATATGATACTATAAAATATAA
Found at i:53562333 original size:18 final size:17
Alignment explanation
Indices: 53562312--53562346 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
53562302 TTATTATTAA
*
53562312 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
53562330 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
53562347 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:53562393 original size:59 final size:59
Alignment explanation
Indices: 53562210--53562393 Score: 157
Period size: 59 Copynumber: 3.1 Consensus size: 59
53562200 TAATTAAAAT
* *
53562210 ATATAATTTAATAAAATTCTTAATAATCAATATTCTTATATGAATTTACTCACATCATA
1 ATATAATTTAATAAAATTCTTAATAATCAATATTCTTATATGAATTTACTAAAATCATA
* * * * * * *
53562269 ATAT-ATGATACTATAAAATATAATTTAA-CAT-AATTATTATTAAATAT-ATTTTAATTAAA--
1 ATATAAT-TTA--ATAAAAT-T--CTTAATAATCAA-TATTCTT--ATATGAATTTACTAAAATC
53562328 AT-
57 ATA
53562330 ATATAATTTAATAAAATTCTTAATAATCAATATTCTTATATGAATTTACTAAAATCATA
1 ATATAATTTAATAAAATTCTTAATAATCAATATTCTTATATGAATTTACTAAAATCATA
53562389 ATATA
1 ATATA
53562394 TGATACTATA
Statistics
Matches: 94, Mismatches: 15, Indels: 32
0.67 0.11 0.23
Matches are distributed among these distances:
55 4 0.04
56 13 0.14
57 8 0.09
58 7 0.07
59 18 0.19
61 13 0.14
62 7 0.07
63 8 0.09
64 12 0.13
65 4 0.04
ACGTcount: A:0.48, C:0.08, G:0.02, T:0.43
Consensus pattern (59 bp):
ATATAATTTAATAAAATTCTTAATAATCAATATTCTTATATGAATTTACTAAAATCATA
Found at i:53562405 original size:61 final size:61
Alignment explanation
Indices: 53562220--53562407 Score: 181
Period size: 61 Copynumber: 3.1 Consensus size: 61
53562210 ATATAATTTA
* *
53562220 ATAAAATTCTTAATAATCAATATTCTTATATGAATTTACTCACATCATAATATATGATACT
1 ATAAAATTCTTAATAATCAATATTCTTATATGAATTTACTAAAATCATAATATATGATACT
* * * * * ** * * * *
53562281 ATAAAA-T-ATAATTTAA-C-ATAATTATTAT-TAAATATATTTTAATTAAAATATATAAT-TT
1 ATAAAATTCTTAA--TAATCAAT-ATTCTTATATGAATTTACTAAAATCATAATATATGATACT
53562339 AATAAAATTCTTAATAATCAATATTCTTATATGAATTTACTAAAATCATAATATATGATACT
1 -ATAAAATTCTTAATAATCAATATTCTTATATGAATTTACTAAAATCATAATATATGATACT
53562401 ATAAAAT
1 ATAAAAT
53562408 ATAATTTGAA
Statistics
Matches: 94, Mismatches: 23, Indels: 20
0.69 0.17 0.15
Matches are distributed among these distances:
58 1 0.01
59 33 0.35
60 18 0.19
61 41 0.44
62 1 0.01
ACGTcount: A:0.48, C:0.08, G:0.02, T:0.42
Consensus pattern (61 bp):
ATAAAATTCTTAATAATCAATATTCTTATATGAATTTACTAAAATCATAATATATGATACT
Found at i:53562598 original size:38 final size:36
Alignment explanation
Indices: 53562543--53562708 Score: 143
Period size: 37 Copynumber: 4.7 Consensus size: 36
53562533 TTAATAAAAA
*
53562543 TATATAATTTAATAAAATTCTTAATATTAAATATTCT
1 TATATAATTTAATAAAA-TCATAATATTAAATATTCT
*
53562580 TATATGAATTTAAGAAAATCATAATA-TATAATA--C-
1 TATAT-AATTTAATAAAATCATAATATTA-AATATTCT
* ** * *
53562614 TATATAATATAATTTAA-CAT-A-ATT-ATTATT-A
1 TATATAATTTAATAAAATCATAATATTAAATATTCT
* *
53562645 AATATAATTTAATAAAATTCTTAATATTAAATATTCT
1 TATATAATTTAATAAAA-TCATAATATTAAATATTCT
53562682 TATATGAATTTAATAAAATCATAATAT
1 TATAT-AATTTAATAAAATCATAATAT
53562709 ATAATACTAT
Statistics
Matches: 100, Mismatches: 16, Indels: 26
0.70 0.11 0.18
Matches are distributed among these distances:
29 3 0.03
30 1 0.01
31 15 0.15
32 3 0.03
33 10 0.10
34 6 0.06
35 4 0.04
36 7 0.07
37 28 0.28
38 23 0.23
ACGTcount: A:0.49, C:0.05, G:0.02, T:0.44
Consensus pattern (36 bp):
TATATAATTTAATAAAATCATAATATTAAATATTCT
Found at i:53571360 original size:16 final size:15
Alignment explanation
Indices: 53571335--53571389 Score: 60
Period size: 16 Copynumber: 3.7 Consensus size: 15
53571325 AAAATTTGAA
53571335 TTGAAGATTTGAAACT
1 TTGAAGATTTG-AACT
*
53571351 TTGAATATTTG-A-T
1 TTGAAGATTTGAACT
53571364 TTGAAGATTTGTAACT
1 TTGAAGATTTG-AACT
*
53571380 TTGAATATTT
1 TTGAAGATTT
53571390 TGGTATGCTT
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
13 11 0.33
14 1 0.03
15 1 0.03
16 20 0.61
ACGTcount: A:0.33, C:0.04, G:0.16, T:0.47
Consensus pattern (15 bp):
TTGAAGATTTGAACT
Found at i:53571370 original size:29 final size:29
Alignment explanation
Indices: 53571328--53571389 Score: 106
Period size: 29 Copynumber: 2.1 Consensus size: 29
53571318 CGAATATAAA
53571328 ATTTGAATTGAAGATTTGAAACTTTGAAT
1 ATTTGAATTGAAGATTTGAAACTTTGAAT
* *
53571357 ATTTGATTTGAAGATTTGTAACTTTGAAT
1 ATTTGAATTGAAGATTTGAAACTTTGAAT
53571386 ATTT
1 ATTT
53571390 TGGTATGCTT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.34, C:0.03, G:0.16, T:0.47
Consensus pattern (29 bp):
ATTTGAATTGAAGATTTGAAACTTTGAAT
Done.