Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032254.1 Gossypioides kirkii chromosome KI_12
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: 43711324
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 1700 characters in sequence are not A, C, G, or T
File 30 of 135
Found at i:11844251 original size:12 final size:12
Alignment explanation
Indices: 11844236--11844260 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
11844226 CCCTCCCCTT
11844236 CCTCCTCCTCCA
1 CCTCCTCCTCCA
11844248 CCTCCTCCTCCA
1 CCTCCTCCTCCA
11844260 C
1 C
11844261 TGCCCGCCAA
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:0.08, C:0.68, G:0.00, T:0.24
Consensus pattern (12 bp):
CCTCCTCCTCCA
Found at i:11853403 original size:30 final size:30
Alignment explanation
Indices: 11853367--11853424 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
11853357 AGTGAACTGA
*
11853367 GTTGCTCACACAAGTTGAAATTACATCAAG
1 GTTGCTCACACAAGCTGAAATTACATCAAG
* *
11853397 GTTGCTCATACAAGCTGAAATTATATCA
1 GTTGCTCACACAAGCTGAAATTACATCA
11853425 GGATACCTCT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.36, C:0.19, G:0.16, T:0.29
Consensus pattern (30 bp):
GTTGCTCACACAAGCTGAAATTACATCAAG
Found at i:11853823 original size:26 final size:26
Alignment explanation
Indices: 11853794--11853844 Score: 93
Period size: 26 Copynumber: 2.0 Consensus size: 26
11853784 CCCTGCCAGT
11853794 CCTCTCTTGAATTCGCCTCTGCCTCC
1 CCTCTCTTGAATTCGCCTCTGCCTCC
*
11853820 CCTCTCTTGAATTCGCCTCTTCCTC
1 CCTCTCTTGAATTCGCCTCTGCCTC
11853845 TCTCATTCTC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.08, C:0.45, G:0.10, T:0.37
Consensus pattern (26 bp):
CCTCTCTTGAATTCGCCTCTGCCTCC
Found at i:11865641 original size:6 final size:6
Alignment explanation
Indices: 11865630--11865655 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
11865620 GACCATTAAG
11865630 AAAGAA AAAGAA AAAGAA AAAGAA AA
1 AAAGAA AAAGAA AAAGAA AAAGAA AA
11865656 GCCCAAGAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (6 bp):
AAAGAA
Found at i:11871352 original size:30 final size:31
Alignment explanation
Indices: 11871318--11871390 Score: 94
Period size: 30 Copynumber: 2.3 Consensus size: 31
11871308 CGGGAGGGCG
*
11871318 AACTGCAGGTATTGGAGCAATA-GGTGGCAC
1 AACTGCAGGTAGTGGAGCAATATGGTGGCAC
* *
11871348 AACTGCTGGTAGTGGAGCAATAGTTGGTGGTAC
1 AACTGCAGGTAGTGGAGCAATA--TGGTGGCAC
11871381 AACTGCAGGT
1 AACTGCAGGT
11871391 GGGACCACTG
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
30 20 0.56
33 16 0.44
ACGTcount: A:0.27, C:0.15, G:0.34, T:0.23
Consensus pattern (31 bp):
AACTGCAGGTAGTGGAGCAATATGGTGGCAC
Found at i:11875184 original size:22 final size:21
Alignment explanation
Indices: 11875142--11875184 Score: 50
Period size: 22 Copynumber: 2.0 Consensus size: 21
11875132 TTTTATTAAA
*
11875142 TTTATTCCATGTACATTTGTT
1 TTTATTCCATGTACATATGTT
**
11875163 TTTATTCTCATGTTTATATGTT
1 TTTATTC-CATGTACATATGTT
11875185 CCCTTAATTT
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.19, C:0.12, G:0.09, T:0.60
Consensus pattern (21 bp):
TTTATTCCATGTACATATGTT
Found at i:11881053 original size:3 final size:3
Alignment explanation
Indices: 11881045--11881106 Score: 79
Period size: 3 Copynumber: 20.7 Consensus size: 3
11881035 TTGAATACTT
* * * * *
11881045 TTA TTA TTA TTA TTA TTA TTA CTA CTA CTA CTA CTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
11881093 TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TT
11881107 GTGATTTTAG
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
3 57 1.00
ACGTcount: A:0.32, C:0.08, G:0.00, T:0.60
Consensus pattern (3 bp):
TTA
Found at i:11883712 original size:6 final size:6
Alignment explanation
Indices: 11883701--11883735 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
11883691 AAAATATCTC
* *
11883701 TCCCTG TTCCTG TTCCTG TCCCTG TCCCTG TCCCT
1 TCCCTG TCCCTG TCCCTG TCCCTG TCCCTG TCCCT
11883736 CTACCCCTCT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.00, C:0.46, G:0.14, T:0.40
Consensus pattern (6 bp):
TCCCTG
Found at i:11885524 original size:15 final size:15
Alignment explanation
Indices: 11885504--11885534 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
11885494 GAAAACTTTC
11885504 TGTTGGTGTTTTGTA
1 TGTTGGTGTTTTGTA
11885519 TGTTGGTGTTTTGTA
1 TGTTGGTGTTTTGTA
11885534 T
1 T
11885535 CGAGAGAGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.06, C:0.00, G:0.32, T:0.61
Consensus pattern (15 bp):
TGTTGGTGTTTTGTA
Found at i:11892286 original size:25 final size:24
Alignment explanation
Indices: 11892252--11892313 Score: 63
Period size: 25 Copynumber: 2.6 Consensus size: 24
11892242 TATTTTATAT
* *
11892252 AATTAATTAATATTATTATATTTGA
1 AATTATTTAATATTATT-CATTTGA
* *
11892277 AATTATTTAATCTAATTCATTTGA
1 AATTATTTAATATTATTCATTTGA
*
11892301 TA-TATTTAATATT
1 AATTATTTAATATT
11892314 TAAATATATT
Statistics
Matches: 30, Mismatches: 7, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
23 9 0.30
24 7 0.23
25 14 0.47
ACGTcount: A:0.40, C:0.03, G:0.03, T:0.53
Consensus pattern (24 bp):
AATTATTTAATATTATTCATTTGA
Found at i:11897946 original size:17 final size:18
Alignment explanation
Indices: 11897914--11897947 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
11897904 AATATAGGTC
11897914 AGCTTAGATAAAATTTGA
1 AGCTTAGATAAAATTTGA
*
11897932 AGCTTA-ATCAAATTTG
1 AGCTTAGATAAAATTTG
11897948 GCTTGAACAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.41, C:0.09, G:0.15, T:0.35
Consensus pattern (18 bp):
AGCTTAGATAAAATTTGA
Found at i:11902396 original size:18 final size:18
Alignment explanation
Indices: 11902373--11902410 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
11902363 ACACTAATTT
11902373 TTATTTGAATTATTCAAA
1 TTATTTGAATTATTCAAA
*
11902391 TTATTTGAGTTATTCAAA
1 TTATTTGAATTATTCAAA
11902409 TT
1 TT
11902411 GTAAAGTTCA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.34, C:0.05, G:0.08, T:0.53
Consensus pattern (18 bp):
TTATTTGAATTATTCAAA
Found at i:11904009 original size:16 final size:15
Alignment explanation
Indices: 11903989--11904029 Score: 64
Period size: 16 Copynumber: 2.6 Consensus size: 15
11903979 TAATTTTTTA
11903989 AAAATTATAAAAAAT
1 AAAATTATAAAAAAT
11904004 ATAAATTATTAAAAAAT
1 A-AAATTA-TAAAAAAT
11904021 AAAATTATA
1 AAAATTATA
11904030 TTTTTTATCA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
15 3 0.12
16 12 0.50
17 9 0.38
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (15 bp):
AAAATTATAAAAAAT
Found at i:11910761 original size:16 final size:16
Alignment explanation
Indices: 11910740--11910773 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
11910730 GTCATTCAGA
*
11910740 GGATAAAGTGAAGGAT
1 GGATAAAGTAAAGGAT
11910756 GGATAAAGTAAAGGAT
1 GGATAAAGTAAAGGAT
11910772 GG
1 GG
11910774 CTATTCAAGG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.44, C:0.00, G:0.38, T:0.18
Consensus pattern (16 bp):
GGATAAAGTAAAGGAT
Found at i:11914569 original size:7 final size:7
Alignment explanation
Indices: 11914557--11914583 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
11914547 CATTGTTCTC
11914557 GAATTTG
1 GAATTTG
11914564 GAATTTG
1 GAATTTG
11914571 GAATTTG
1 GAATTTG
11914578 GAATTT
1 GAATTT
11914584 TATTATTTAT
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:0.26, T:0.44
Consensus pattern (7 bp):
GAATTTG
Found at i:11934549 original size:76 final size:71
Alignment explanation
Indices: 11934436--11934619 Score: 208
Period size: 76 Copynumber: 2.5 Consensus size: 71
11934426 AATTCAAGAG
* * * *
11934436 AATAAAATTAAGATAAATAAGTGGTTTAGATTTTCATAAGTAGAAAAC-ACCAACTTTGACCATA
1 AATAAAATTAAGATAAAAAAATGGTTAAGATTTTCATAAGTAGAAAACTACAAAC-TTGACC--A
11934500 AGGTTTAGAA
63 A-GTTTAGAA
* *
11934510 AATAAAATTAAGATAAGAAAACATGGTTAAGATTTTCATAAGTAGAAAACTGCAAACTTGATCAA
1 AATAAAATTAAGATAA-AAAA-ATGGTTAAGATTTTCATAAGTAGAAAACTACAAACTTGACCAA
*
11934575 GTTTTGAA
64 GTTTAGAA
* * *
11934583 AATAAAATTAAGATAAATATATGGTTTAGATATTTCA
1 AATAAAATTAAGATAAAAAAATGGTTAAGAT-TTTCA
11934620 ACTGATGAAC
Statistics
Matches: 96, Mismatches: 10, Indels: 10
0.83 0.09 0.09
Matches are distributed among these distances:
71 10 0.10
72 7 0.07
73 23 0.24
74 18 0.19
75 3 0.03
76 31 0.32
77 4 0.04
ACGTcount: A:0.47, C:0.08, G:0.14, T:0.31
Consensus pattern (71 bp):
AATAAAATTAAGATAAAAAAATGGTTAAGATTTTCATAAGTAGAAAACTACAAACTTGACCAAGT
TTAGAA
Found at i:11935958 original size:24 final size:24
Alignment explanation
Indices: 11935931--11935985 Score: 76
Period size: 24 Copynumber: 2.3 Consensus size: 24
11935921 GTTTGGTTAC
* *
11935931 ATTGTTTGGGT-ATATTTCATAGGT
1 ATTGTTTGGGTAATA-TTCACAAGT
11935955 ATTGTTTGGGTAATATTCACAAGT
1 ATTGTTTGGGTAATATTCACAAGT
11935979 ATTGTTT
1 ATTGTTT
11935986 TTGGGCTACC
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
24 25 0.89
25 3 0.11
ACGTcount: A:0.24, C:0.05, G:0.22, T:0.49
Consensus pattern (24 bp):
ATTGTTTGGGTAATATTCACAAGT
Found at i:11953371 original size:28 final size:28
Alignment explanation
Indices: 11953325--11953391 Score: 73
Period size: 28 Copynumber: 2.4 Consensus size: 28
11953315 AATTAAATAA
* *
11953325 TAAATATTAAAACTCTAAACTCTTAACCT
1 TAAAT-TTAAAACTCTAAACCCTAAACCT
*
11953354 TAAATTTAAAA-TCTTAAACCCTAAATCT
1 TAAATTTAAAACTC-TAAACCCTAAACCT
*
11953382 AAAATTTAAA
1 TAAATTTAAA
11953392 TTCTAAATCT
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
27 2 0.06
28 26 0.79
29 5 0.15
ACGTcount: A:0.49, C:0.16, G:0.00, T:0.34
Consensus pattern (28 bp):
TAAATTTAAAACTCTAAACCCTAAACCT
Found at i:11953397 original size:20 final size:21
Alignment explanation
Indices: 11953338--11953402 Score: 71
Period size: 20 Copynumber: 3.2 Consensus size: 21
11953328 ATATTAAAAC
* *
11953338 TCTAAACTCTT-AACCTTAAA
1 TCTAAAATCTTAAACCCTAAA
*
11953358 TTTAAAATCTTAAACCCTAAA
1 TCTAAAATCTTAAACCCTAAA
**
11953379 TCTAAAAT-TTAAATTCTAAA
1 TCTAAAATCTTAAACCCTAAA
11953399 TCTA
1 TCTA
11953403 GGAATTATTA
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
20 23 0.61
21 15 0.39
ACGTcount: A:0.45, C:0.18, G:0.00, T:0.37
Consensus pattern (21 bp):
TCTAAAATCTTAAACCCTAAA
Found at i:11954654 original size:5 final size:5
Alignment explanation
Indices: 11954635--11954674 Score: 71
Period size: 5 Copynumber: 7.8 Consensus size: 5
11954625 TCGCTCACGC
11954635 TTCTT TTCTT CTTCTT TTCTT TTCTT TTCTT TTCTT TTCT
1 TTCTT TTCTT -TTCTT TTCTT TTCTT TTCTT TTCTT TTCT
11954675 CTGACACTAA
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
5 29 0.85
6 5 0.15
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.78
Consensus pattern (5 bp):
TTCTT
Found at i:11958966 original size:27 final size:28
Alignment explanation
Indices: 11958907--11958967 Score: 81
Period size: 27 Copynumber: 2.2 Consensus size: 28
11958897 AGTTAAAAGA
* *
11958907 AAATAT-ATAAAAATTATATAATTTTTT
1 AAATATAATAAAAATTATATAATTATAT
11958934 AAATATAATAAAAATTATA-AATTATAT
1 AAATATAATAAAAATTATATAATTATAT
*
11958961 ATATATA
1 AAATATA
11958968 TATCTAAAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
27 18 0.60
28 12 0.40
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (28 bp):
AAATATAATAAAAATTATATAATTATAT
Found at i:11961987 original size:24 final size:24
Alignment explanation
Indices: 11961955--11962026 Score: 117
Period size: 24 Copynumber: 3.0 Consensus size: 24
11961945 AATGTCCCTC
*
11961955 CTTCAGCACCTGGTTTTCCTGGCT
1 CTTCAGCACCTGGCTTTCCTGGCT
11961979 CTTCAGCACCTGGCTTTCCTGGCT
1 CTTCAGCACCTGGCTTTCCTGGCT
* *
11962003 CTTCAGCTCCAGGCTTTCCTGGCT
1 CTTCAGCACCTGGCTTTCCTGGCT
11962027 TTCCTGGCTC
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 45 1.00
ACGTcount: A:0.08, C:0.36, G:0.21, T:0.35
Consensus pattern (24 bp):
CTTCAGCACCTGGCTTTCCTGGCT
Found at i:11962316 original size:2 final size:2
Alignment explanation
Indices: 11962309--11962335 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
11962299 CTTGCTTGTA
11962309 CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT C
11962336 GCATTGTAGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:11963276 original size:24 final size:24
Alignment explanation
Indices: 11963248--11963295 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
11963238 GGTTGAGTCG
*
11963248 TTGGCA-ATGTTGGTATAGTTGGCA
1 TTGGCAGAT-TTGGAATAGTTGGCA
*
11963272 TTGGCAGATTTGGAATCGTTGGCA
1 TTGGCAGATTTGGAATAGTTGGCA
11963296 AGGGAGGTAC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 19 0.90
25 2 0.10
ACGTcount: A:0.21, C:0.10, G:0.33, T:0.35
Consensus pattern (24 bp):
TTGGCAGATTTGGAATAGTTGGCA
Found at i:11967675 original size:29 final size:29
Alignment explanation
Indices: 11967619--11967675 Score: 69
Period size: 29 Copynumber: 2.0 Consensus size: 29
11967609 TAATATAAAA
* *
11967619 AGATTAATTAATTACAAAAATTGATTGAG
1 AGATAAATTAATTACAAAAATGGATTGAG
* * *
11967648 AGATAAATTATTTACGAAAATGGGTTGA
1 AGATAAATTAATTACAAAAATGGATTGA
11967676 TTGTTACATT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.46, C:0.04, G:0.18, T:0.33
Consensus pattern (29 bp):
AGATAAATTAATTACAAAAATGGATTGAG
Found at i:11970878 original size:24 final size:24
Alignment explanation
Indices: 11970846--11971009 Score: 238
Period size: 24 Copynumber: 6.8 Consensus size: 24
11970836 TTAAACTCTG
*
11970846 TCTGGGCTCGTAAAAGCTAACCAT
1 TCTGGGCTCGTAAGAGCTAACCAT
*
11970870 TCTGGGCTCGTAAGAACTAACCAT
1 TCTGGGCTCGTAAGAGCTAACCAT
*
11970894 TCTGGGCTCGTGAGAGCTAACCAT
1 TCTGGGCTCGTAAGAGCTAACCAT
* *
11970918 TCTGGGCTTGTAAGAGTTAACCAT
1 TCTGGGCTCGTAAGAGCTAACCAT
*
11970942 TCTGGGCTCGTGAGAGCTAACCAT
1 TCTGGGCTCGTAAGAGCTAACCAT
**
11970966 TCTAAGCTCGTAAGAGCTAACCAT
1 TCTGGGCTCGTAAGAGCTAACCAT
**
11970990 TCTGGGCTCGTGTGAGCTAA
1 TCTGGGCTCGTAAGAGCTAA
11971010 ATTTTTGAAA
Statistics
Matches: 123, Mismatches: 17, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 123 1.00
ACGTcount: A:0.25, C:0.23, G:0.25, T:0.27
Consensus pattern (24 bp):
TCTGGGCTCGTAAGAGCTAACCAT
Found at i:11971568 original size:21 final size:21
Alignment explanation
Indices: 11971539--11971578 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
11971529 TTGACATCTG
*
11971539 CATACTTGTTTCGGTAGAACC
1 CATACTTGTATCGGTAGAACC
*
11971560 CATAGTTGTATCGGTAGAA
1 CATACTTGTATCGGTAGAA
11971579 GTATAGAGTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.28, C:0.17, G:0.23, T:0.33
Consensus pattern (21 bp):
CATACTTGTATCGGTAGAACC
Found at i:11978117 original size:3 final size:3
Alignment explanation
Indices: 11978109--11978145 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
11978099 TCCAACATCT
11978109 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
11978146 AAAATGGAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:11994217 original size:21 final size:21
Alignment explanation
Indices: 11994167--11994235 Score: 68
Period size: 21 Copynumber: 3.1 Consensus size: 21
11994157 TATATTGTTG
* *
11994167 TTTTGGTGCTTTTTTTACTGTT
1 TTTTGATGTTTTTTTTACTG-T
11994189 TTAGTTGATGTTTTTTTTACTGT
1 TT--TTGATGTTTTTTTTACTGT
*
11994212 TTTTGA-GTTGTTTTTTATTGT
1 TTTTGATGTT-TTTTTTACTGT
11994233 TTT
1 TTT
11994236 GATTGCTATT
Statistics
Matches: 41, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
20 3 0.07
21 17 0.41
22 2 0.05
23 3 0.07
24 16 0.39
ACGTcount: A:0.09, C:0.04, G:0.17, T:0.70
Consensus pattern (21 bp):
TTTTGATGTTTTTTTTACTGT
Found at i:11994223 original size:23 final size:24
Alignment explanation
Indices: 11994176--11994227 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
11994166 GTTTTGGTGC
*
11994176 TTTTTTTACTGTTTTAGTTGATGT
1 TTTTTTTACTGTTTTAGTAGATGT
* *
11994200 TTTTTTTACTGTTTTTG-AGTTGT
1 TTTTTTTACTGTTTTAGTAGATGT
11994223 TTTTT
1 TTTTT
11994228 ATTGTTTTGA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
23 9 0.36
24 16 0.64
ACGTcount: A:0.10, C:0.04, G:0.15, T:0.71
Consensus pattern (24 bp):
TTTTTTTACTGTTTTAGTAGATGT
Found at i:11994259 original size:12 final size:12
Alignment explanation
Indices: 11994250--11994351 Score: 59
Period size: 12 Copynumber: 8.8 Consensus size: 12
11994240 GCTATTTTCG
11994250 TGTTATTTTTGC
1 TGTTATTTTTGC
*
11994262 TGTTATTTTTGT
1 TGTTATTTTTGC
* * **
11994274 TGCTGTTTTTAT
1 TGTTATTTTTGC
* *
11994286 TGCTATTTTTGT
1 TGTTATTTTTGC
*
11994298 TGTT-TTTAT--
1 TGTTATTTTTGC
* *
11994307 TGTT-GTTTTAC
1 TGTTATTTTTGC
11994318 TGTTATTTTTGC
1 TGTTATTTTTGC
* **
11994330 TGCTATTTTTTT
1 TGTTATTTTTGC
11994342 TGTTATTTTT
1 TGTTATTTTT
11994352 ATTTTTTGGA
Statistics
Matches: 71, Mismatches: 16, Indels: 6
0.76 0.17 0.06
Matches are distributed among these distances:
9 7 0.10
11 8 0.11
12 56 0.79
ACGTcount: A:0.09, C:0.06, G:0.15, T:0.71
Consensus pattern (12 bp):
TGTTATTTTTGC
Found at i:11994280 original size:68 final size:68
Alignment explanation
Indices: 11994199--11994339 Score: 171
Period size: 68 Copynumber: 2.1 Consensus size: 68
11994189 TTAGTTGATG
*
11994199 TTTTTTTTACTGTTTTTGAGTTG-T-TTTTTATTGTTTTGATTGCTATTTT-CGTGTTATTTTTG
1 TTTTTGTTACTGTTTTT-A-TTGCTATTTTTATTGTTTTGATTGCTATTTTAC-TGTTATTTTTG
*
11994261 CTGTTA
63 CTGCTA
* * * * *
11994267 TTTTTGTTGCTGTTTTTATTGCTATTTTTGTTGTTTTTATTGTTGTTTTACTGTTATTTTTGCTG
1 TTTTTGTTACTGTTTTTATTGCTATTTTTATTGTTTTGATTGCTATTTTACTGTTATTTTTGCTG
11994332 CTA
66 CTA
11994335 TTTTT
1 TTTTT
11994340 TTTGTTATTT
Statistics
Matches: 63, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
66 3 0.05
67 2 0.03
68 57 0.90
69 1 0.02
ACGTcount: A:0.09, C:0.06, G:0.16, T:0.69
Consensus pattern (68 bp):
TTTTTGTTACTGTTTTTATTGCTATTTTTATTGTTTTGATTGCTATTTTACTGTTATTTTTGCTG
CTA
Found at i:11994314 original size:33 final size:32
Alignment explanation
Indices: 11994262--11994328 Score: 80
Period size: 32 Copynumber: 2.1 Consensus size: 32
11994252 TTATTTTTGC
* *
11994262 TGTTATTTTTGTTGCTGTTTTTATTGCTATTTT
1 TGTTATTTTTATTGCTG-TTTTACTGCTATTTT
* * *
11994295 TGTTGTTTTTATTGTTGTTTTACTGTTATTTT
1 TGTTATTTTTATTGCTGTTTTACTGCTATTTT
11994327 TG
1 TG
11994329 CTGCTATTTT
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
32 15 0.52
33 14 0.48
ACGTcount: A:0.09, C:0.04, G:0.16, T:0.70
Consensus pattern (32 bp):
TGTTATTTTTATTGCTGTTTTACTGCTATTTT
Found at i:11994351 original size:68 final size:68
Alignment explanation
Indices: 11994223--11994354 Score: 176
Period size: 68 Copynumber: 1.9 Consensus size: 68
11994213 TTTGAGTTGT
* *
11994223 TTTTTATTGTTTTGATTGCTATTTTCGTGTTATTTTTGCTGTTATTTTTGTTGCTGTTTTTATTG
1 TTTTTATTGTTTTGATTGCTATTTTCGTGTTATTTTTGCTGCTATTTTTGTTGCTATTTTTATTG
11994288 CTA
66 CTA
* * * * * *
11994291 TTTTTGTTGTTTTTATTGTTGTTTTAC-TGTTATTTTTGCTGCTATTTTTTTTGTTATTTTTATT
1 TTTTTATTGTTTTGATTGCTATTTT-CGTGTTATTTTTGCTGCTATTTTTGTTGCTATTTTTATT
11994355 TTTTGGATGT
Statistics
Matches: 55, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
68 54 0.98
69 1 0.02
ACGTcount: A:0.10, C:0.06, G:0.14, T:0.70
Consensus pattern (68 bp):
TTTTTATTGTTTTGATTGCTATTTTCGTGTTATTTTTGCTGCTATTTTTGTTGCTATTTTTATTG
CTA
Found at i:11994575 original size:49 final size:47
Alignment explanation
Indices: 11994482--11994576 Score: 111
Period size: 49 Copynumber: 2.0 Consensus size: 47
11994472 TATCTTAATA
* * * *
11994482 TAATTTTTTAATGTATTTTAAATTTATTTATTTTTTAATGTTTGTTT
1 TAATTTTTTAATGTATTTGAAATTTATATATATTTTAATATTTGTTT
*
11994529 TAATGTTTTTAAGTGTATTTGATATATTATATATATTTTAA-ATTTGTT
1 TAAT-TTTTTAA-TGTATTTGAAAT-TTATATATATTTTAATATTTGTT
11994577 GTATGTAATA
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
47 4 0.10
48 7 0.17
49 16 0.40
50 13 0.32
ACGTcount: A:0.28, C:0.00, G:0.08, T:0.63
Consensus pattern (47 bp):
TAATTTTTTAATGTATTTGAAATTTATATATATTTTAATATTTGTTT
Found at i:12000623 original size:2 final size:2
Alignment explanation
Indices: 12000610--12000641 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
12000600 TGAGAAGTAA
*
12000610 AT AT AT AA AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
12000642 GTAGATACCT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:12015520 original size:3 final size:3
Alignment explanation
Indices: 12015512--12015541 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
12015502 TACATCCCAA
12015512 AAT AAT AAT AAT AAT AAT AAT AAT AA- AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
12015542 GAATAGAATA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.08
3 24 0.92
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:12016611 original size:20 final size:20
Alignment explanation
Indices: 12016586--12016627 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
12016576 GTTTTTCGAA
*
12016586 AAAGTCAACGGTCAACGATC
1 AAAGTCAACGATCAACGATC
*
12016606 AAAGTCAACGATCAACGGTC
1 AAAGTCAACGATCAACGATC
12016626 AA
1 AA
12016628 CGATCAATCA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.43, C:0.24, G:0.19, T:0.14
Consensus pattern (20 bp):
AAAGTCAACGATCAACGATC
Found at i:12016626 original size:14 final size:14
Alignment explanation
Indices: 12016590--12016634 Score: 74
Period size: 14 Copynumber: 3.3 Consensus size: 14
12016580 TTCGAAAAAG
12016590 TCAACGGTCAACGA
1 TCAACGGTCAACGA
*
12016604 TCAA-AGTCAACGA
1 TCAACGGTCAACGA
12016617 TCAACGGTCAACGA
1 TCAACGGTCAACGA
12016631 TCAA
1 TCAA
12016635 TCAACACCGG
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
13 12 0.43
14 16 0.57
ACGTcount: A:0.40, C:0.27, G:0.18, T:0.16
Consensus pattern (14 bp):
TCAACGGTCAACGA
Found at i:12016660 original size:21 final size:21
Alignment explanation
Indices: 12016594--12016650 Score: 60
Period size: 27 Copynumber: 2.4 Consensus size: 21
12016584 AAAAAGTCAA
12016594 CGGTCAACGATCAAAGTCAACGATC
1 CGGTCAACGATC-AA-TCAAC-A-C
12016619 AACGGTCAACGATCAATCAACAC
1 --CGGTCAACGATCAATCAACAC
12016642 CGGTCAACG
1 CGGTCAACG
12016651 GTCGGTCAAC
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
21 9 0.30
23 1 0.03
24 1 0.03
25 5 0.17
26 2 0.07
27 12 0.40
ACGTcount: A:0.37, C:0.30, G:0.19, T:0.14
Consensus pattern (21 bp):
CGGTCAACGATCAATCAACAC
Found at i:12016664 original size:10 final size:10
Alignment explanation
Indices: 12016642--12016689 Score: 51
Period size: 10 Copynumber: 4.7 Consensus size: 10
12016632 CAATCAACAC
12016642 CGGTCAACGGT
1 CGGTCAAC-GT
12016653 CGGTCAACGT
1 CGGTCAACGT
* *
12016663 CGATCAACGC
1 CGGTCAACGT
* *
12016673 CAGTCAACAT
1 CGGTCAACGT
12016683 CGGTCAA
1 CGGTCAA
12016690 TGGTTTGACT
Statistics
Matches: 30, Mismatches: 7, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
10 22 0.73
11 8 0.27
ACGTcount: A:0.27, C:0.31, G:0.25, T:0.17
Consensus pattern (10 bp):
CGGTCAACGT
Found at i:12016746 original size:15 final size:15
Alignment explanation
Indices: 12016726--12016755 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
12016716 TGGTTCATTT
12016726 GGTTTGGTTCAAATG
1 GGTTTGGTTCAAATG
*
12016741 GGTTTGGTTTAAATG
1 GGTTTGGTTCAAATG
12016756 CATGTGGGTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.20, C:0.03, G:0.33, T:0.43
Consensus pattern (15 bp):
GGTTTGGTTCAAATG
Found at i:12017181 original size:23 final size:23
Alignment explanation
Indices: 12017155--12017227 Score: 74
Period size: 23 Copynumber: 3.1 Consensus size: 23
12017145 AAGTGTGATT
* *
12017155 AAAAGAGGAAGAAAATAGAAAAG
1 AAAAGAGAAAGAAAAAAGAAAAG
*
12017178 AAAAGAGAAAGAAAAAAGAAATG
1 AAAAGAGAAAGAAAAAAGAAAAG
* * * *
12017201 AATGAGAAAAAGAAAAGAGAAAGG
1 AA-AAGAGAAAGAAAAAAGAAAAG
12017225 AAA
1 AAA
12017228 GATAAGAGGC
Statistics
Matches: 41, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
23 22 0.54
24 19 0.46
ACGTcount: A:0.71, C:0.00, G:0.25, T:0.04
Consensus pattern (23 bp):
AAAAGAGAAAGAAAAAAGAAAAG
Found at i:12017188 original size:11 final size:11
Alignment explanation
Indices: 12017155--12017229 Score: 69
Period size: 11 Copynumber: 6.5 Consensus size: 11
12017145 AAGTGTGATT
*
12017155 AAAAGAGGAAG
1 AAAAGAGAAAG
*
12017166 AAAATAGAAAAG
1 AAAAGAG-AAAG
12017178 AAAAGAGAAAG
1 AAAAGAGAAAG
*
12017189 AAAAAAGAAATG
1 AAAAGAGAAA-G
* *
12017201 AATGAGAAAAAG
1 AA-AAGAGAAAG
12017213 AAAAGAGAAAG
1 AAAAGAGAAAG
*
12017224 GAAAGA
1 AAAAGA
12017230 TAAGAGGCTT
Statistics
Matches: 51, Mismatches: 10, Indels: 6
0.76 0.15 0.09
Matches are distributed among these distances:
11 31 0.61
12 15 0.29
13 5 0.10
ACGTcount: A:0.71, C:0.00, G:0.25, T:0.04
Consensus pattern (11 bp):
AAAAGAGAAAG
Found at i:12017227 original size:18 final size:18
Alignment explanation
Indices: 12017173--12017227 Score: 60
Period size: 18 Copynumber: 3.1 Consensus size: 18
12017163 AAGAAAATAG
*
12017173 AAAAGAAAAGAGAAAGAA
1 AAAAGAAAAGAGAAAGGA
* *
12017191 AAAAG-AAA-TGAATGAGA
1 AAAAGAAAAGAGAAAG-GA
12017208 AAAAGAAAAGAGAAAGGA
1 AAAAGAAAAGAGAAAGGA
12017226 AA
1 AA
12017228 GATAAGAGGC
Statistics
Matches: 29, Mismatches: 5, Indels: 6
0.73 0.12 0.15
Matches are distributed among these distances:
16 4 0.14
17 9 0.31
18 12 0.41
19 4 0.14
ACGTcount: A:0.73, C:0.00, G:0.24, T:0.04
Consensus pattern (18 bp):
AAAAGAAAAGAGAAAGGA
Found at i:12022617 original size:3 final size:3
Alignment explanation
Indices: 12022609--12022659 Score: 95
Period size: 3 Copynumber: 17.3 Consensus size: 3
12022599 TACATCCCAA
12022609 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA-
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
12022656 AAT A
1 AAT A
12022660 GAATAGAATA
Statistics
Matches: 47, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 2 0.04
3 45 0.96
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:12023734 original size:20 final size:20
Alignment explanation
Indices: 12023705--12023746 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
12023695 GTTTTTCGAA
*
12023705 AAAGTTAACGATCAACGATC
1 AAAGTCAACGATCAACGATC
* *
12023725 AAAGTCAACGGTCAACGGTC
1 AAAGTCAACGATCAACGATC
12023745 AA
1 AA
12023747 TCGATACCGG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.43, C:0.21, G:0.19, T:0.17
Consensus pattern (20 bp):
AAAGTCAACGATCAACGATC
Found at i:12023873 original size:15 final size:15
Alignment explanation
Indices: 12023839--12023874 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
12023829 GGTTCATTTG
*
12023839 ATTTGGTTCAAATGG
1 ATTTGGTTCAAATGA
*
12023854 GTTTGGTTCAAATGA
1 ATTTGGTTCAAATGA
12023869 ATTTGG
1 ATTTGG
12023875 GTTTGGTTCA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.25, C:0.06, G:0.28, T:0.42
Consensus pattern (15 bp):
ATTTGGTTCAAATGA
Found at i:12023875 original size:21 final size:21
Alignment explanation
Indices: 12023851--12023918 Score: 100
Period size: 21 Copynumber: 3.2 Consensus size: 21
12023841 TTGGTTCAAA
12023851 TGGGTTTGGTTCAAATGAATT
1 TGGGTTTGGTTCAAATGAATT
12023872 TGGGTTTGGTTCAAATGAATT
1 TGGGTTTGGTTCAAATGAATT
* * *
12023893 TGAGTTTGGTTTAAATAGGATT
1 TGGGTTTGGTTCAAAT-GAATT
12023915 TGGG
1 TGGG
12023919 CTTAATGGGT
Statistics
Matches: 42, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
21 35 0.83
22 7 0.17
ACGTcount: A:0.24, C:0.03, G:0.31, T:0.43
Consensus pattern (21 bp):
TGGGTTTGGTTCAAATGAATT
Found at i:12024322 original size:11 final size:11
Alignment explanation
Indices: 12024289--12024363 Score: 62
Period size: 11 Copynumber: 6.5 Consensus size: 11
12024279 AAGTGTGATT
*
12024289 AAAAGAGGAAG
1 AAAAGAGAAAG
*
12024300 AAAATAGAAAAG
1 AAAAGAG-AAAG
12024312 AAAAGAGAAAG
1 AAAAGAGAAAG
12024323 AAATA-AGAAATG
1 AAA-AGAGAAA-G
* *
12024335 AATGAGAAAAAG
1 AA-AAGAGAAAG
12024347 AAAAGAGAAAG
1 AAAAGAGAAAG
*
12024358 GAAAGA
1 AAAAGA
12024364 TGAGAGGCTT
Statistics
Matches: 51, Mismatches: 8, Indels: 10
0.74 0.12 0.14
Matches are distributed among these distances:
11 30 0.59
12 17 0.33
13 4 0.08
ACGTcount: A:0.69, C:0.00, G:0.25, T:0.05
Consensus pattern (11 bp):
AAAAGAGAAAG
Found at i:12024331 original size:23 final size:23
Alignment explanation
Indices: 12024289--12024361 Score: 67
Period size: 23 Copynumber: 3.1 Consensus size: 23
12024279 AAGTGTGATT
*
12024289 AAAAGAGGAAGAAAATAGAAAAG
1 AAAAGAGAAAGAAAATAGAAAAG
*
12024312 AAAAGAGAAAG-AAATAAGAAATG
1 AAAAGAGAAAGAAAAT-AGAAAAG
* * * *
12024335 AATGAGAAAAAGAAAAGAGAAAGG
1 AA-AAGAGAAAGAAAATAGAAAAG
12024359 AAA
1 AAA
12024362 GATGAGAGGC
Statistics
Matches: 40, Mismatches: 7, Indels: 6
0.75 0.13 0.11
Matches are distributed among these distances:
22 4 0.10
23 18 0.45
24 15 0.38
25 3 0.08
ACGTcount: A:0.70, C:0.00, G:0.25, T:0.05
Consensus pattern (23 bp):
AAAAGAGAAAGAAAATAGAAAAG
Found at i:12036439 original size:23 final size:23
Alignment explanation
Indices: 12036290--12036427 Score: 129
Period size: 23 Copynumber: 5.9 Consensus size: 23
12036280 CGAAGTACTT
12036290 AACAGTAAGCACAC-AAGTGCTAGAGA
1 AACAGTAAGCACACAAAGTGC----GA
*
12036316 AACAGTAAGCACACATAGTGC-A
1 AACAGTAAGCACACAAAGTGCGA
* * * * *
12036338 ATCAGTAGGCGCACATAGCGC-A
1 AACAGTAAGCACACAAAGTGCGA
*
12036360 AATCAGTAGGCACACAAAGTGCGA
1 AA-CAGTAAGCACACAAAGTGCGA
*
12036384 AACAGTAGGCACACAAAGTGCGA
1 AACAGTAAGCACACAAAGTGCGA
*
12036407 AACAGTAAGCACACACAGTGC
1 AACAGTAAGCACACAAAGTGC
12036428 TGAACGGTAA
Statistics
Matches: 98, Mismatches: 11, Indels: 9
0.83 0.09 0.08
Matches are distributed among these distances:
22 20 0.20
23 56 0.57
24 3 0.03
26 14 0.14
27 5 0.05
ACGTcount: A:0.42, C:0.23, G:0.23, T:0.12
Consensus pattern (23 bp):
AACAGTAAGCACACAAAGTGCGA
Found at i:12043291 original size:30 final size:29
Alignment explanation
Indices: 12043257--12043424 Score: 108
Period size: 30 Copynumber: 5.7 Consensus size: 29
12043247 TATGGATACC
12043257 CGGGGGTAAAATGGTAATTTTCGGTGAAAT
1 CGGGGGTAAAATGG-AATTTTCGGTGAAAT
* * **
12043287 CGGGGTTAAAAATGGAATTTTAGAG-G-CTT
1 CGGGGGT-AAAATGGAATTTTCG-GTGAAAT
* *
12043316 CGGGGGCAAAATGGTAATTTTCGGTGAAAA
1 CGGGGGTAAAATGG-AATTTTCGGTGAAAT
* * * ** **
12043346 CGGGGTTGAAAACGGAATTTTAGAAGCTA-
1 CGGGGGT-AAAATGGAATTTTCGGTGAAAT
* *
12043375 CGGGGGTAAAATGGTAAATTTCGGTGAAGT
1 CGGGGGTAAAATGG-AATTTTCGGTGAAAT
* *
12043405 AGGGGTTAAAATGGAATTTT
1 CGGGGGTAAAATGGAATTTT
12043425 AGAAGATTCG
Statistics
Matches: 100, Mismatches: 30, Indels: 17
0.68 0.20 0.12
Matches are distributed among these distances:
28 14 0.14
29 32 0.32
30 40 0.40
31 14 0.14
ACGTcount: A:0.32, C:0.07, G:0.33, T:0.28
Consensus pattern (29 bp):
CGGGGGTAAAATGGAATTTTCGGTGAAAT
Found at i:12043320 original size:59 final size:58
Alignment explanation
Indices: 12043257--12043454 Score: 270
Period size: 59 Copynumber: 3.4 Consensus size: 58
12043247 TATGGATACC
*
12043257 CGGGGGTAAAATGGTAATTTTCGGTGAAATCGGGGTTAAAAATGGAATTTTAGAGGCTT
1 CGGGGGTAAAATGGTAATTTTCGGTGAAATCGGGGTT-AAAATGGAATTTTAGAAGCTT
* * * *
12043316 CGGGGGCAAAATGGTAATTTTCGGTGAAAACGGGGTTGAAAACGGAATTTTAGAAGCTA
1 CGGGGGTAAAATGGTAATTTTCGGTGAAATCGGGGTT-AAAATGGAATTTTAGAAGCTT
* * * *
12043375 CGGGGGTAAAATGGTAAATTTCGGTGAAGTAGGGGTTAAAATGGAATTTTAGAAGATT
1 CGGGGGTAAAATGGTAATTTTCGGTGAAATCGGGGTTAAAATGGAATTTTAGAAGCTT
* *
12043433 CGGGGGGGAAAATGATAATTTT
1 C-GGGGGTAAAATGGTAATTTT
12043455 TGAAAGTTTT
Statistics
Matches: 121, Mismatches: 17, Indels: 2
0.86 0.12 0.01
Matches are distributed among these distances:
58 19 0.16
59 102 0.84
ACGTcount: A:0.33, C:0.07, G:0.33, T:0.28
Consensus pattern (58 bp):
CGGGGGTAAAATGGTAATTTTCGGTGAAATCGGGGTTAAAATGGAATTTTAGAAGCTT
Found at i:12043438 original size:29 final size:29
Alignment explanation
Indices: 12043288--12043438 Score: 67
Period size: 29 Copynumber: 5.1 Consensus size: 29
12043278 CGGTGAAATC
* *
12043288 GGGGTTAAAAATGGAATTTTAGAGGCTTCG
1 GGGGTT-AAAATGGAATTTTAGAAGATTCG
* * ** **
12043318 GGGG-CAAAATGGTAATTTTCGGTGAAAAC-
1 GGGGTTAAAATGG-AATTTTAGAAG-ATTCG
* * *
12043347 GGGGTTGAAAACGGAATTTTAGAAGCTACG
1 GGGGTT-AAAATGGAATTTTAGAAGATTCG
* * ** * *
12043377 GGGG-TAAAATGGTAAATTTCGGTGAAGT-A
1 GGGGTTAAAATGG-AATTTTAGAAG-ATTCG
12043406 GGGGTTAAAATGGAATTTTAGAAGATTCG
1 GGGGTTAAAATGGAATTTTAGAAGATTCG
12043435 GGGG
1 GGGG
12043439 GGAAAATGAT
Statistics
Matches: 83, Mismatches: 29, Indels: 19
0.63 0.22 0.15
Matches are distributed among these distances:
28 15 0.18
29 37 0.45
30 25 0.30
31 6 0.07
ACGTcount: A:0.32, C:0.07, G:0.34, T:0.26
Consensus pattern (29 bp):
GGGGTTAAAATGGAATTTTAGAAGATTCG
Found at i:12043475 original size:30 final size:30
Alignment explanation
Indices: 12043441--12043547 Score: 162
Period size: 30 Copynumber: 3.5 Consensus size: 30
12043431 TTCGGGGGGG
*
12043441 AAAATGATAATTTTTG-AAAGTTTTGGGGTC
1 AAAATG-TAATTTTGGAAAAGTTTTGGGGTC
*
12043471 AAAATATAATTTTGGAAAAGTTTTGGGGTC
1 AAAATGTAATTTTGGAAAAGTTTTGGGGTC
*
12043501 AAAATGTAATTTTGGAAAAGTTTTAGGGTC
1 AAAATGTAATTTTGGAAAAGTTTTGGGGTC
12043531 AAAATGTAATTTCTGGA
1 AAAATGTAATTT-TGGA
12043548 CAATTTAGGA
Statistics
Matches: 71, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
29 8 0.11
30 59 0.83
31 4 0.06
ACGTcount: A:0.36, C:0.04, G:0.22, T:0.37
Consensus pattern (30 bp):
AAAATGTAATTTTGGAAAAGTTTTGGGGTC
Found at i:12043819 original size:161 final size:161
Alignment explanation
Indices: 12043635--12043951 Score: 492
Period size: 161 Copynumber: 2.0 Consensus size: 161
12043625 GATTAAGTTG
* * *
12043635 TAAATCTTGAAAAATTCTTGGGCCAATTTCATAATT-AAATAAAAGTTGATTTGGGATTAAATTA
1 TAAACCTTGAAAAATTATTGGGCCAATTTCATAATTAAAAT-AAAGTTGATTGGGGATTAAATTA
* * *
12043699 AAACAAATTAAAAATAAAAAGGACTAAATGCATAAATAATCCAAAAAGTGACACGTGGCAGCCTC
65 AAACAAATTAAAAATAAAAAGGACTAAATGCAGAAATAATCCAAAAAATGACACGTGGCAGACTC
*
12043764 TGGTACAGTCAAACAGTCAAAGGACTAGTTTA
130 TGATACAGTCAAACAGTCAAAGGACTAGTTTA
*
12043796 TAAACCTTGAAAAATTATTGGGCCAATTTCGTAATTAAAATAAAGTTGATTGGGGATTAAATTAA
1 TAAACCTTGAAAAATTATTGGGCCAATTTCATAATTAAAATAAAGTTGATTGGGGATTAAATTAA
* *** * *
12043861 AACAAATTAGAAATGTCAGGGACTAAATGCAGAAATGATCCAAAAAATGACACGTGGCAGACTCT
66 AACAAATTAAAAATAAAAAGGACTAAATGCAGAAATAATCCAAAAAATGACACGTGGCAGACTCT
12043926 GATACAGTCAAACAGTCAAAGGACTA
131 GATACAGTCAAACAGTCAAAGGACTA
12043952 AATTGAAAGT
Statistics
Matches: 141, Mismatches: 14, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
161 137 0.97
162 4 0.03
ACGTcount: A:0.44, C:0.13, G:0.17, T:0.26
Consensus pattern (161 bp):
TAAACCTTGAAAAATTATTGGGCCAATTTCATAATTAAAATAAAGTTGATTGGGGATTAAATTAA
AACAAATTAAAAATAAAAAGGACTAAATGCAGAAATAATCCAAAAAATGACACGTGGCAGACTCT
GATACAGTCAAACAGTCAAAGGACTAGTTTA
Found at i:12045377 original size:20 final size:21
Alignment explanation
Indices: 12045345--12045384 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
12045335 CAGGGCATGG
*
12045345 TGGAGCTTGGTGGTCAGCAGA
1 TGGAGCTTGGTGGCCAGCAGA
12045366 TGGAGC-TGGTGGCCAGCAG
1 TGGAGCTTGGTGGCCAGCAG
12045385 CAGTAGGCAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.17, C:0.17, G:0.45, T:0.20
Consensus pattern (21 bp):
TGGAGCTTGGTGGCCAGCAGA
Found at i:12045446 original size:14 final size:14
Alignment explanation
Indices: 12045429--12045455 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
12045419 ATTTGGACTA
12045429 TTGTAATTGGGCCT
1 TTGTAATTGGGCCT
12045443 TTGTAATTGGGCC
1 TTGTAATTGGGCC
12045456 CTGGGCCATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.15, C:0.15, G:0.30, T:0.41
Consensus pattern (14 bp):
TTGTAATTGGGCCT
Found at i:12045552 original size:48 final size:48
Alignment explanation
Indices: 12045492--12045598 Score: 119
Period size: 48 Copynumber: 2.2 Consensus size: 48
12045482 ATTTGGACTT
* * ** *
12045492 TTAAATGTTAAAT-TTAATATTTTAATTTTTATTTAAATTTAAATTCAAA
1 TTAAAT-TTAAATATTAA-ATTTTAAATTTAAAATAAATCTAAATTCAAA
* *
12045541 TTAAATTTAAATATTTAATTTTAAATTTAAAATAAATCTAAATTTAAA
1 TTAAATTTAAATATTAAATTTTAAATTTAAAATAAATCTAAATTCAAA
12045589 -TAAATTTAAA
1 TTAAATTTAAA
12045599 ATCAATTTAA
Statistics
Matches: 50, Mismatches: 7, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
47 10 0.20
48 31 0.62
49 9 0.18
ACGTcount: A:0.49, C:0.02, G:0.01, T:0.49
Consensus pattern (48 bp):
TTAAATTTAAATATTAAATTTTAAATTTAAAATAAATCTAAATTCAAA
Found at i:12045556 original size:31 final size:31
Alignment explanation
Indices: 12045521--12045583 Score: 90
Period size: 31 Copynumber: 2.0 Consensus size: 31
12045511 TTTTAATTTT
* *
12045521 TATTTAAATTTAAATTCAAATTAAATTTAAA
1 TATTTAAATTTAAATTCAAAATAAATCTAAA
* *
12045552 TATTTAATTTTAAATTTAAAATAAATCTAAA
1 TATTTAAATTTAAATTCAAAATAAATCTAAA
12045583 T
1 T
12045584 TTAAATAAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (31 bp):
TATTTAAATTTAAATTCAAAATAAATCTAAA
Found at i:12045571 original size:6 final size:6
Alignment explanation
Indices: 12045491--12045598 Score: 89
Period size: 6 Copynumber: 18.0 Consensus size: 6
12045481 CATTTGGACT
* ** *
12045491 TTTAAA TGTTAAA TTTAATA TTTTAA TTTTTA TTTAAA TTTAAA TTCAAA
1 TTTAAA T-TTAAA TTTAA-A TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
* * *
12045541 -TTAAA TTTAAATA TTTAAT TTTAAA TTTAAA -ATAAA TCTAAA TTTAAA
1 TTTAAA TTT-AA-A TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
12045589 --TAAA TTTAAA
1 TTTAAA TTTAAA
12045599 ATCAATTTAA
Statistics
Matches: 83, Mismatches: 11, Indels: 16
0.75 0.10 0.15
Matches are distributed among these distances:
4 4 0.05
5 8 0.10
6 52 0.63
7 15 0.18
8 4 0.05
ACGTcount: A:0.48, C:0.02, G:0.01, T:0.49
Consensus pattern (6 bp):
TTTAAA
Found at i:12045584 original size:42 final size:43
Alignment explanation
Indices: 12045494--12045589 Score: 110
Period size: 42 Copynumber: 2.2 Consensus size: 43
12045484 TTGGACTTTT
* *
12045494 AAATGTTAAATTTAATATTTTAATTTTTATTTAAATTTAAATTC
1 AAAT-TTAAATTTAATATTTTAATTTTAATTTAAATATAAATTC
12045538 AAA-TTAAATTTAA-ATATTTAATTTTAAATTTAAA-ATAAA-TC
1 AAATTTAAATTTAATAT-TTTAATTTT-AATTTAAATATAAATTC
12045579 TAAATTTAAAT
1 -AAATTTAAAT
12045590 AAATTTAAAA
Statistics
Matches: 46, Mismatches: 2, Indels: 9
0.81 0.04 0.16
Matches are distributed among these distances:
41 4 0.09
42 26 0.57
43 13 0.28
44 3 0.07
ACGTcount: A:0.48, C:0.02, G:0.01, T:0.49
Consensus pattern (43 bp):
AAATTTAAATTTAATATTTTAATTTTAATTTAAATATAAATTC
Found at i:12046034 original size:39 final size:39
Alignment explanation
Indices: 12045971--12046114 Score: 236
Period size: 39 Copynumber: 3.7 Consensus size: 39
12045961 CATTCAACTT
*
12045971 TACTTCAATTTCAAA-GGGACGACGTTGTGTTATCCACTC
1 TACTTCAATTT-AAAGGGGATGACGTTGTGTTATCCACTC
*
12046010 TACGTCAATTTAAAGGGGATGACGTTGTGTTATCCACTC
1 TACTTCAATTTAAAGGGGATGACGTTGTGTTATCCACTC
*
12046049 TACTTCAATTTCAAGGGGATGACGTTGTGTTATCCACTC
1 TACTTCAATTTAAAGGGGATGACGTTGTGTTATCCACTC
*
12046088 TACTTCAATTTCAAGGGGATGACGTTG
1 TACTTCAATTTAAAGGGGATGACGTTG
12046115 CTCTTACTTC
Statistics
Matches: 100, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
38 3 0.03
39 97 0.97
ACGTcount: A:0.25, C:0.19, G:0.22, T:0.34
Consensus pattern (39 bp):
TACTTCAATTTAAAGGGGATGACGTTGTGTTATCCACTC
Found at i:12046165 original size:69 final size:69
Alignment explanation
Indices: 12046079--12046454 Score: 673
Period size: 69 Copynumber: 5.5 Consensus size: 69
12046069 GACGTTGTGT
*
12046079 TATCC-ACTCTACTTCAATTTCAAGGGGATGACGTTGCTCTTACTTCAATTTCAGAGATAAAGAC
1 TATCCAACTCTACTTCAATTTCAAGAGGATGACGTTGCTCTTACTTCAATTTCAGAGATAAAGAC
12046143 TTGA
66 TTGA
* *
12046147 TATCCAACTCTACTTCAATTTCGAGAGGATGACGTTGCTCTTACTTCAATTTCGGAGATAAAGAC
1 TATCCAACTCTACTTCAATTTCAAGAGGATGACGTTGCTCTTACTTCAATTTCAGAGATAAAGAC
12046212 TTGA
66 TTGA
12046216 TATCCAACTCTACTTCAATTTCAAGAGGATGACGTTGCTCTTACTTCAATTTCAGAGATAAAGAC
1 TATCCAACTCTACTTCAATTTCAAGAGGATGACGTTGCTCTTACTTCAATTTCAGAGATAAAGAC
*
12046281 CTGA
66 TTGA
*
12046285 TATCCAAATCTACTTCAATTTCAAGAGGATGACGTTGCTCTTACTTCAATTTCAGAGATAAAGAC
1 TATCCAACTCTACTTCAATTTCAAGAGGATGACGTTGCTCTTACTTCAATTTCAGAGATAAAGAC
*
12046350 CTGA
66 TTGA
* *
12046354 TATCCAACTCTACTTCAATTTCAAGAGGATGACGTTGCTCTTACTTCAATTTCGGAAATAAAGAC
1 TATCCAACTCTACTTCAATTTCAAGAGGATGACGTTGCTCTTACTTCAATTTCAGAGATAAAGAC
12046419 TTGA
66 TTGA
12046423 TATCCAACTCTACTTCAATTTCAAGAGGATGA
1 TATCCAACTCTACTTCAATTTCAAGAGGATGA
12046455 AGACGTGTTA
Statistics
Matches: 296, Mismatches: 11, Indels: 1
0.96 0.04 0.00
Matches are distributed among these distances:
68 5 0.02
69 291 0.98
ACGTcount: A:0.31, C:0.21, G:0.15, T:0.33
Consensus pattern (69 bp):
TATCCAACTCTACTTCAATTTCAAGAGGATGACGTTGCTCTTACTTCAATTTCAGAGATAAAGAC
TTGA
Found at i:12046479 original size:39 final size:40
Alignment explanation
Indices: 12046414--12046493 Score: 126
Period size: 39 Copynumber: 2.0 Consensus size: 40
12046404 TTCGGAAATA
*
12046414 AAGACTTGATATCCAACTCTACTTCAATTTCAAGAGGATG
1 AAGACGTGATATCCAACTCTACTTCAATTTCAAGAGGATG
* *
12046454 AAGACGTGTTATCC-ACTCTACTTCAATTTCAAGGGGATG
1 AAGACGTGATATCCAACTCTACTTCAATTTCAAGAGGATG
12046493 A
1 A
12046494 CGTTGAGACC
Statistics
Matches: 37, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
39 25 0.68
40 12 0.32
ACGTcount: A:0.33, C:0.20, G:0.17, T:0.30
Consensus pattern (40 bp):
AAGACGTGATATCCAACTCTACTTCAATTTCAAGAGGATG
Found at i:12058292 original size:30 final size:29
Alignment explanation
Indices: 12058258--12058425 Score: 108
Period size: 30 Copynumber: 5.7 Consensus size: 29
12058248 TATGGATACC
12058258 CGGGGGTAAAATGGTAATTTTCGGTGAAAT
1 CGGGGGTAAAATGG-AATTTTCGGTGAAAT
* * **
12058288 CGGGGTTAAAAATGGAATTTTAGAG-G-CTT
1 CGGGGGT-AAAATGGAATTTTCG-GTGAAAT
* *
12058317 CGGGGGCAAAATGGTAATTTTCGGTGAAAA
1 CGGGGGTAAAATGG-AATTTTCGGTGAAAT
* * * ** **
12058347 CGGGGTTGAAAACGGAATTTTAGAAGCTA-
1 CGGGGGT-AAAATGGAATTTTCGGTGAAAT
* *
12058376 CGGGGGTAAAATGGTAAATTTCGGTGAAGT
1 CGGGGGTAAAATGG-AATTTTCGGTGAAAT
* *
12058406 AGGGGTTAAAATGGAATTTT
1 CGGGGGTAAAATGGAATTTT
12058426 AGAAGATTCG
Statistics
Matches: 100, Mismatches: 30, Indels: 17
0.68 0.20 0.12
Matches are distributed among these distances:
28 14 0.14
29 32 0.32
30 40 0.40
31 14 0.14
ACGTcount: A:0.32, C:0.07, G:0.33, T:0.28
Consensus pattern (29 bp):
CGGGGGTAAAATGGAATTTTCGGTGAAAT
Found at i:12058321 original size:59 final size:58
Alignment explanation
Indices: 12058258--12058455 Score: 270
Period size: 59 Copynumber: 3.4 Consensus size: 58
12058248 TATGGATACC
*
12058258 CGGGGGTAAAATGGTAATTTTCGGTGAAATCGGGGTTAAAAATGGAATTTTAGAGGCTT
1 CGGGGGTAAAATGGTAATTTTCGGTGAAATCGGGGTT-AAAATGGAATTTTAGAAGCTT
* * * *
12058317 CGGGGGCAAAATGGTAATTTTCGGTGAAAACGGGGTTGAAAACGGAATTTTAGAAGCTA
1 CGGGGGTAAAATGGTAATTTTCGGTGAAATCGGGGTT-AAAATGGAATTTTAGAAGCTT
* * * *
12058376 CGGGGGTAAAATGGTAAATTTCGGTGAAGTAGGGGTTAAAATGGAATTTTAGAAGATT
1 CGGGGGTAAAATGGTAATTTTCGGTGAAATCGGGGTTAAAATGGAATTTTAGAAGCTT
* *
12058434 CGGGGGGGAAAATGATAATTTT
1 C-GGGGGTAAAATGGTAATTTT
12058456 TGAAAGTTTT
Statistics
Matches: 121, Mismatches: 17, Indels: 2
0.86 0.12 0.01
Matches are distributed among these distances:
58 19 0.16
59 102 0.84
ACGTcount: A:0.33, C:0.07, G:0.33, T:0.28
Consensus pattern (58 bp):
CGGGGGTAAAATGGTAATTTTCGGTGAAATCGGGGTTAAAATGGAATTTTAGAAGCTT
Found at i:12058439 original size:29 final size:29
Alignment explanation
Indices: 12058289--12058439 Score: 67
Period size: 29 Copynumber: 5.1 Consensus size: 29
12058279 CGGTGAAATC
* *
12058289 GGGGTTAAAAATGGAATTTTAGAGGCTTCG
1 GGGGTT-AAAATGGAATTTTAGAAGATTCG
* * ** **
12058319 GGGG-CAAAATGGTAATTTTCGGTGAAAAC-
1 GGGGTTAAAATGG-AATTTTAGAAG-ATTCG
* * *
12058348 GGGGTTGAAAACGGAATTTTAGAAGCTACG
1 GGGGTT-AAAATGGAATTTTAGAAGATTCG
* * ** * *
12058378 GGGG-TAAAATGGTAAATTTCGGTGAAGT-A
1 GGGGTTAAAATGG-AATTTTAGAAG-ATTCG
12058407 GGGGTTAAAATGGAATTTTAGAAGATTCG
1 GGGGTTAAAATGGAATTTTAGAAGATTCG
12058436 GGGG
1 GGGG
12058440 GGAAAATGAT
Statistics
Matches: 83, Mismatches: 29, Indels: 19
0.63 0.22 0.15
Matches are distributed among these distances:
28 15 0.18
29 37 0.45
30 25 0.30
31 6 0.07
ACGTcount: A:0.32, C:0.07, G:0.34, T:0.26
Consensus pattern (29 bp):
GGGGTTAAAATGGAATTTTAGAAGATTCG
Found at i:12058476 original size:30 final size:30
Alignment explanation
Indices: 12058442--12058548 Score: 162
Period size: 30 Copynumber: 3.5 Consensus size: 30
12058432 TTCGGGGGGG
*
12058442 AAAATGATAATTTTTG-AAAGTTTTGGGGTC
1 AAAATG-TAATTTTGGAAAAGTTTTGGGGTC
*
12058472 AAAATATAATTTTGGAAAAGTTTTGGGGTC
1 AAAATGTAATTTTGGAAAAGTTTTGGGGTC
*
12058502 AAAATGTAATTTTGGAAAAGTTTTAGGGTC
1 AAAATGTAATTTTGGAAAAGTTTTGGGGTC
12058532 AAAATGTAATTTCTGGA
1 AAAATGTAATTT-TGGA
12058549 CAATTTAGGA
Statistics
Matches: 71, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
29 8 0.11
30 59 0.83
31 4 0.06
ACGTcount: A:0.36, C:0.04, G:0.22, T:0.37
Consensus pattern (30 bp):
AAAATGTAATTTTGGAAAAGTTTTGGGGTC
Found at i:12058820 original size:161 final size:161
Alignment explanation
Indices: 12058636--12058952 Score: 492
Period size: 161 Copynumber: 2.0 Consensus size: 161
12058626 GATTAAGTTG
* * *
12058636 TAAATCTTGAAAAATTCTTGGGCCAATTTCATAATT-AAATAAAAGTTGATTTGGGATTAAATTA
1 TAAACCTTGAAAAATTATTGGGCCAATTTCATAATTAAAAT-AAAGTTGATTGGGGATTAAATTA
* * *
12058700 AAACAAATTAAAAATAAAAAGGACTAAATGCATAAATAATCCAAAAAGTGACACGTGGCAGCCTC
65 AAACAAATTAAAAATAAAAAGGACTAAATGCAGAAATAATCCAAAAAATGACACGTGGCAGACTC
*
12058765 TGGTACAGTCAAACAGTCAAAGGACTAGTTTA
130 TGATACAGTCAAACAGTCAAAGGACTAGTTTA
*
12058797 TAAACCTTGAAAAATTATTGGGCCAATTTCGTAATTAAAATAAAGTTGATTGGGGATTAAATTAA
1 TAAACCTTGAAAAATTATTGGGCCAATTTCATAATTAAAATAAAGTTGATTGGGGATTAAATTAA
* *** * *
12058862 AACAAATTAGAAATGTCAGGGACTAAATGCAGAAATGATCCAAAAAATGACACGTGGCAGACTCT
66 AACAAATTAAAAATAAAAAGGACTAAATGCAGAAATAATCCAAAAAATGACACGTGGCAGACTCT
12058927 GATACAGTCAAACAGTCAAAGGACTA
131 GATACAGTCAAACAGTCAAAGGACTA
12058953 AATTGAAAGT
Statistics
Matches: 141, Mismatches: 14, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
161 137 0.97
162 4 0.03
ACGTcount: A:0.44, C:0.13, G:0.17, T:0.26
Consensus pattern (161 bp):
TAAACCTTGAAAAATTATTGGGCCAATTTCATAATTAAAATAAAGTTGATTGGGGATTAAATTAA
AACAAATTAAAAATAAAAAGGACTAAATGCAGAAATAATCCAAAAAATGACACGTGGCAGACTCT
GATACAGTCAAACAGTCAAAGGACTAGTTTA
Found at i:12060378 original size:20 final size:21
Alignment explanation
Indices: 12060346--12060385 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
12060336 CAGGGCATGG
*
12060346 TGGAGCTTGGTGGTCAGCAGA
1 TGGAGCTTGGTGGCCAGCAGA
12060367 TGGAGC-TGGTGGCCAGCAG
1 TGGAGCTTGGTGGCCAGCAG
12060386 CAGTAGGCGC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.17, C:0.17, G:0.45, T:0.20
Consensus pattern (21 bp):
TGGAGCTTGGTGGCCAGCAGA
Found at i:12060450 original size:12 final size:13
Alignment explanation
Indices: 12060431--12060471 Score: 57
Period size: 12 Copynumber: 3.2 Consensus size: 13
12060421 TTTGGACTAT
12060431 TGTAATTGGGCCC
1 TGTAATTGGGCCC
*
12060444 T-TAATTGGGCCTT
1 TGTAATTGGGCC-C
12060457 TGTAATTGGGCCC
1 TGTAATTGGGCCC
12060470 TG
1 TG
12060472 GGCCCTGGGC
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
12 10 0.42
13 4 0.17
14 10 0.42
ACGTcount: A:0.15, C:0.20, G:0.29, T:0.37
Consensus pattern (13 bp):
TGTAATTGGGCCC
Found at i:12060532 original size:6 final size:6
Alignment explanation
Indices: 12060504--12060617 Score: 101
Period size: 6 Copynumber: 19.0 Consensus size: 6
12060494 CATTTGGACT
* **
12060504 TTTAAA TGTTAAA TTTAATA TTTTAA TTTTTA TTTAAA TTTAAA TTTAAA
1 TTTAAA T-TTAAA TTTAA-A TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
* * * *
12060554 TTCAAA -TTAAA TTTAAATA TTTAAT TTTAAA TTTAAA -ATAAA TCTAAA
1 TTTAAA TTTAAA TTT-AA-A TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
12060602 TTTAAA --TAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA
12060618 ATCAATTTAA
Statistics
Matches: 89, Mismatches: 11, Indels: 16
0.77 0.09 0.14
Matches are distributed among these distances:
4 4 0.04
5 8 0.09
6 58 0.65
7 15 0.17
8 4 0.04
ACGTcount: A:0.48, C:0.02, G:0.01, T:0.49
Consensus pattern (6 bp):
TTTAAA
Found at i:12060555 original size:37 final size:36
Alignment explanation
Indices: 12060534--12060617 Score: 104
Period size: 37 Copynumber: 2.4 Consensus size: 36
12060524 TTTTAATTTT
12060534 TATTTAAATTTAAATTTAAATTCAAATTAAATTTAAA
1 TATTTAAATTTAAATTTAAATTCAAATTAAATTT-AA
* *
12060571 TATTTAATTTTAAATTTAAAAT-AAATCTAAATTTAA
1 TATTTAAATTTAAATTTAAATTCAAAT-TAAATTTAA
12060607 -A--TAAATTTAAA
1 TATTTAAATTTAAA
12060618 ATCAATTTAA
Statistics
Matches: 43, Mismatches: 3, Indels: 6
0.83 0.06 0.12
Matches are distributed among these distances:
33 9 0.21
35 1 0.02
36 6 0.14
37 27 0.63
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (36 bp):
TATTTAAATTTAAATTTAAATTCAAATTAAATTTAA
Found at i:12060568 original size:48 final size:48
Alignment explanation
Indices: 12060512--12060617 Score: 137
Period size: 48 Copynumber: 2.2 Consensus size: 48
12060502 CTTTTAAATG
* * *
12060512 TTAAATTT-AATATTTTAATTTT-TATTTAAATTTAAATTTAAATTCAAA
1 TTAAATTTAAATA-TTTAATTTTAAATTTAAA-ATAAATCTAAATTCAAA
*
12060560 TTAAATTTAAATATTTAATTTTAAATTTAAAATAAATCTAAATTTAAA
1 TTAAATTTAAATATTTAATTTTAAATTTAAAATAAATCTAAATTCAAA
12060608 -TAAATTTAAA
1 TTAAATTTAAA
12060618 ATCAATTTAA
Statistics
Matches: 52, Mismatches: 4, Indels: 5
0.85 0.07 0.08
Matches are distributed among these distances:
47 10 0.19
48 31 0.60
49 11 0.21
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (48 bp):
TTAAATTTAAATATTTAATTTTAAATTTAAAATAAATCTAAATTCAAA
Found at i:12060576 original size:31 final size:31
Alignment explanation
Indices: 12060541--12060602 Score: 88
Period size: 31 Copynumber: 2.0 Consensus size: 31
12060531 TTTTATTTAA
* *
12060541 ATTTAAATTTAAATTCAAATTAAATTTAAAT
1 ATTTAAATTTAAATTCAAAATAAATCTAAAT
* *
12060572 ATTTAATTTTAAATTTAAAATAAATCTAAAT
1 ATTTAAATTTAAATTCAAAATAAATCTAAAT
12060603 TTAAATAAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (31 bp):
ATTTAAATTTAAATTCAAAATAAATCTAAAT
Found at i:12060902 original size:19 final size:18
Alignment explanation
Indices: 12060878--12060916 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
12060868 TTTTCTGAAC
*
12060878 TTTTAATCAACCCATATAA
1 TTTTAACCAACCCA-ATAA
*
12060897 TTTTAACCTACCCAATAA
1 TTTTAACCAACCCAATAA
12060915 TT
1 TT
12060917 ATTATTTTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 6 0.33
19 12 0.67
ACGTcount: A:0.38, C:0.23, G:0.00, T:0.38
Consensus pattern (18 bp):
TTTTAACCAACCCAATAA
Found at i:12067076 original size:17 final size:18
Alignment explanation
Indices: 12067034--12067077 Score: 54
Period size: 21 Copynumber: 2.3 Consensus size: 18
12067024 TATTCCTCAG
12067034 CAAATTCAAGATATTTAAGAT
1 CAAATTCAAGATATTT---AT
12067055 CAAATTCAAGATATTT-T
1 CAAATTCAAGATATTTAT
12067072 CAAATT
1 CAAATT
12067078 TCTTTTCTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
17 7 0.30
21 16 0.70
ACGTcount: A:0.45, C:0.11, G:0.07, T:0.36
Consensus pattern (18 bp):
CAAATTCAAGATATTTAT
Found at i:12074691 original size:18 final size:18
Alignment explanation
Indices: 12074668--12074702 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
12074658 ACCATTTCTT
*
12074668 AGTGTGAACACTCTTTTG
1 AGTGTGAAAACTCTTTTG
12074686 AGTGTGAAAACTCTTTT
1 AGTGTGAAAACTCTTTT
12074703 CAGGGACTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.26, C:0.14, G:0.20, T:0.40
Consensus pattern (18 bp):
AGTGTGAAAACTCTTTTG
Found at i:12079766 original size:28 final size:27
Alignment explanation
Indices: 12079705--12079769 Score: 85
Period size: 27 Copynumber: 2.4 Consensus size: 27
12079695 AATATTTTGG
***
12079705 TTCGATTAATAATTAAAAAAATTTCTA
1 TTCGATTAATAATTAAAAAAATTAAAA
12079732 TTCGATTAATAATTAAAAAAATTAAAAA
1 TTCGATTAATAATTAAAAAAATT-AAAA
*
12079760 TTTGATTAAT
1 TTCGATTAAT
12079770 TCAATTAATA
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
27 23 0.70
28 10 0.30
ACGTcount: A:0.51, C:0.05, G:0.05, T:0.40
Consensus pattern (27 bp):
TTCGATTAATAATTAAAAAAATTAAAA
Found at i:12079893 original size:4 final size:4
Alignment explanation
Indices: 12079884--12079918 Score: 70
Period size: 4 Copynumber: 8.8 Consensus size: 4
12079874 GCTACTTCCT
12079884 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA
12079919 TATATATATA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 31 1.00
ACGTcount: A:0.51, C:0.23, G:0.00, T:0.26
Consensus pattern (4 bp):
ATAC
Found at i:12091954 original size:16 final size:16
Alignment explanation
Indices: 12091935--12091969 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
12091925 TTTATTTCCC
12091935 TCAGATTACATTTTAA
1 TCAGATTACATTTTAA
*
12091951 TCAGGTTACATTTTAA
1 TCAGATTACATTTTAA
12091967 TCA
1 TCA
12091970 CTTATATTTG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.34, C:0.14, G:0.09, T:0.43
Consensus pattern (16 bp):
TCAGATTACATTTTAA
Found at i:12100752 original size:33 final size:32
Alignment explanation
Indices: 12100687--12100758 Score: 92
Period size: 33 Copynumber: 2.2 Consensus size: 32
12100677 AACTTTTATG
12100687 AAATATTTTCAAAAAATCTATCAAACAATAGA
1 AAATATTTTCAAAAAATCTATCAAACAATAGA
* * *
12100719 AAATATTTTACACAAATTC-ATCCAAACACTAGA
1 AAATATTTT-CAAAAAATCTAT-CAAACAATAGA
12100752 AAATATT
1 AAATATT
12100759 AACTTTTCAA
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
32 11 0.31
33 24 0.69
ACGTcount: A:0.53, C:0.15, G:0.03, T:0.29
Consensus pattern (32 bp):
AAATATTTTCAAAAAATCTATCAAACAATAGA
Found at i:12106116 original size:24 final size:24
Alignment explanation
Indices: 12106088--12106144 Score: 69
Period size: 24 Copynumber: 2.4 Consensus size: 24
12106078 TAGACTAATA
*
12106088 AGAGTTTGACTCAAACAAATAAAC
1 AGAGTTTAACTCAAACAAATAAAC
* * * *
12106112 AGAGTTTAATTGAAACAATTAAAT
1 AGAGTTTAACTCAAACAAATAAAC
12106136 AGAGTTTAA
1 AGAGTTTAA
12106145 TTGGAAGATT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.49, C:0.09, G:0.14, T:0.28
Consensus pattern (24 bp):
AGAGTTTAACTCAAACAAATAAAC
Found at i:12106145 original size:24 final size:24
Alignment explanation
Indices: 12106100--12106147 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 24
12106090 AGTTTGACTC
12106100 AAACAAATAAACAGAGTTTAATTG
1 AAACAAATAAACAGAGTTTAATTG
* *
12106124 AAACAATTAAATAGAGTTTAATTG
1 AAACAAATAAACAGAGTTTAATTG
12106148 GAAGATTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.52, C:0.06, G:0.12, T:0.29
Consensus pattern (24 bp):
AAACAAATAAACAGAGTTTAATTG
Found at i:12108073 original size:24 final size:24
Alignment explanation
Indices: 12108046--12108096 Score: 93
Period size: 24 Copynumber: 2.1 Consensus size: 24
12108036 AGTTAGACTC
12108046 AAACAAATAAACAGAGTTTAATTG
1 AAACAAATAAACAGAGTTTAATTG
*
12108070 AAACAATTAAACAGAGTTTAATTG
1 AAACAAATAAACAGAGTTTAATTG
12108094 AAA
1 AAA
12108097 GATTATTTCT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.55, C:0.08, G:0.12, T:0.25
Consensus pattern (24 bp):
AAACAAATAAACAGAGTTTAATTG
Found at i:12149265 original size:15 final size:14
Alignment explanation
Indices: 12149219--12149264 Score: 58
Period size: 14 Copynumber: 3.2 Consensus size: 14
12149209 GATGTGTGGA
*
12149219 TTTAATTTCTATAT
1 TTTAATTTTTATAT
12149233 TTTAATTTCATTA-AT
1 TTTAATTT--TTATAT
12149248 TTTAATTTTTATAT
1 TTTAATTTTTATAT
12149262 TTT
1 TTT
12149265 TCGAATTGAA
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
13 3 0.11
14 13 0.46
15 10 0.36
16 2 0.07
ACGTcount: A:0.28, C:0.04, G:0.00, T:0.67
Consensus pattern (14 bp):
TTTAATTTTTATAT
Found at i:12151209 original size:14 final size:14
Alignment explanation
Indices: 12151190--12151220 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
12151180 AGAATAAATC
12151190 TTTAATTAAATAAA
1 TTTAATTAAATAAA
*
12151204 TTTAATTAATTAAA
1 TTTAATTAAATAAA
12151218 TTT
1 TTT
12151221 TTTAAACCCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (14 bp):
TTTAATTAAATAAA
Found at i:12153705 original size:31 final size:31
Alignment explanation
Indices: 12153665--12153828 Score: 142
Period size: 31 Copynumber: 5.4 Consensus size: 31
12153655 AAAAAAAAGC
*
12153665 TTAGGTACCAAATTAAGAAAAAATATCAAGT
1 TTAGGTACCAAATTAGGAAAAAATATCAAGT
* * *
12153696 TCAGGTACCAAATTGGGTCCAAAAA-A--AAGT
1 TTAGGTACCAAATTAGG--AAAAAATATCAAGT
*
12153726 TTAGGTACCAAATTAGGAAAAAATTTCAAGT
1 TTAGGTACCAAATTAGGAAAAAATATCAAGT
* * **
12153757 TTAGGTATCAAATTGGGTCAAAA-A--AAGT
1 TTAGGTACCAAATTAGGAAAAAATATCAAGT
* * *
12153785 TTAGGTACTAAATTAAGAAAAAGTATCAAGT
1 TTAGGTACCAAATTAGGAAAAAATATCAAGT
* *
12153816 TCAAGTACCAAAT
1 TTAGGTACCAAAT
12153829 GTTATATTAA
Statistics
Matches: 102, Mismatches: 23, Indels: 16
0.72 0.16 0.11
Matches are distributed among these distances:
28 25 0.25
29 1 0.01
30 19 0.19
31 51 0.50
32 1 0.01
33 5 0.05
ACGTcount: A:0.46, C:0.11, G:0.16, T:0.26
Consensus pattern (31 bp):
TTAGGTACCAAATTAGGAAAAAATATCAAGT
Found at i:12153814 original size:59 final size:61
Alignment explanation
Indices: 12153655--12153828 Score: 262
Period size: 61 Copynumber: 2.9 Consensus size: 61
12153645 TGAATCTTAA
*
12153655 AAAAAAAAGCTTAGGTACCAAATTAAGAAAAAATATCAAGTTCAGGTACCAAATTGGGTCC
1 AAAAAAAAGTTTAGGTACCAAATTAAGAAAAAATATCAAGTTCAGGTACCAAATTGGGTCC
* * * *
12153716 AAAAAAAAGTTTAGGTACCAAATTAGGAAAAAATTTCAAGTTTAGGTATCAAATTGGGT-C
1 AAAAAAAAGTTTAGGTACCAAATTAAGAAAAAATATCAAGTTCAGGTACCAAATTGGGTCC
* * *
12153776 -AAAAAAAGTTTAGGTACTAAATTAAGAAAAAGTATCAAGTTCAAGTACCAAAT
1 AAAAAAAAGTTTAGGTACCAAATTAAGAAAAAATATCAAGTTCAGGTACCAAAT
12153829 GTTATATTAA
Statistics
Matches: 101, Mismatches: 12, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
59 46 0.46
60 1 0.01
61 54 0.53
ACGTcount: A:0.48, C:0.11, G:0.16, T:0.25
Consensus pattern (61 bp):
AAAAAAAAGTTTAGGTACCAAATTAAGAAAAAATATCAAGTTCAGGTACCAAATTGGGTCC
Found at i:12177411 original size:29 final size:29
Alignment explanation
Indices: 12177376--12177435 Score: 120
Period size: 29 Copynumber: 2.1 Consensus size: 29
12177366 CATTATGCTT
12177376 GTTAGTTGATTATATTTTCAAGTATGCAG
1 GTTAGTTGATTATATTTTCAAGTATGCAG
12177405 GTTAGTTGATTATATTTTCAAGTATGCAG
1 GTTAGTTGATTATATTTTCAAGTATGCAG
12177434 GT
1 GT
12177436 CTGGCAAGTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.27, C:0.07, G:0.22, T:0.45
Consensus pattern (29 bp):
GTTAGTTGATTATATTTTCAAGTATGCAG
Found at i:12186509 original size:21 final size:18
Alignment explanation
Indices: 12186484--12186526 Score: 50
Period size: 21 Copynumber: 2.2 Consensus size: 18
12186474 TTTTGTTATT
12186484 ATTTTCATTTTCATATATATA
1 ATTTTCATTTT--TATA-ATA
*
12186505 ATTTTGATTTTTATAATA
1 ATTTTCATTTTTATAATA
12186523 ATTT
1 ATTT
12186527 AATAAATATA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
18 7 0.33
19 4 0.19
21 10 0.48
ACGTcount: A:0.33, C:0.05, G:0.02, T:0.60
Consensus pattern (18 bp):
ATTTTCATTTTTATAATA
Found at i:12186998 original size:5 final size:5
Alignment explanation
Indices: 12186988--12187015 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
12186978 TGTTTGCTGT
12186988 ACCCA ACCCA ACCCA ACCCA ACCCA ACC
1 ACCCA ACCCA ACCCA ACCCA ACCCA ACC
12187016 ACTCCACTTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.39, C:0.61, G:0.00, T:0.00
Consensus pattern (5 bp):
ACCCA
Found at i:12203444 original size:12 final size:12
Alignment explanation
Indices: 12203427--12203451 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
12203417 AAGATAATAA
12203427 ATTTAAAATTTG
1 ATTTAAAATTTG
12203439 ATTTAAAATTTG
1 ATTTAAAATTTG
12203451 A
1 A
12203452 CTAAAATGGA
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:0.00, G:0.08, T:0.48
Consensus pattern (12 bp):
ATTTAAAATTTG
Found at i:12206232 original size:31 final size:29
Alignment explanation
Indices: 12206165--12206232 Score: 73
Period size: 31 Copynumber: 2.3 Consensus size: 29
12206155 TTAAAATTTC
* * *
12206165 ATATTTAAAATTACATAAAATTAAAATCT
1 ATATATAAAATTACATAAAATCAAAATAT
* *
12206194 ATTTATAACATTACATATTAAATCAAAATAT
1 ATATATAAAATTACATA--AAATCAAAATAT
12206225 ATATATAA
1 ATATATAA
12206233 TTTTAATATT
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
29 14 0.45
31 17 0.55
ACGTcount: A:0.54, C:0.07, G:0.00, T:0.38
Consensus pattern (29 bp):
ATATATAAAATTACATAAAATCAAAATAT
Found at i:12207822 original size:33 final size:33
Alignment explanation
Indices: 12207785--12207847 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 33
12207775 CACTTAATAC
12207785 AATAAAA-TATATTTCCCTTTTTAAT-CTCCACTT
1 AATAAAAGTATA--TCCCTTTTTAATCCTCCACTT
*
12207818 AATAAAAGTATATCTCTTTTTAATCCTCCA
1 AATAAAAGTATATCCCTTTTTAATCCTCCA
12207848 AAATGACTAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
32 11 0.41
33 12 0.44
34 4 0.15
ACGTcount: A:0.35, C:0.21, G:0.02, T:0.43
Consensus pattern (33 bp):
AATAAAAGTATATCCCTTTTTAATCCTCCACTT
Found at i:12214007 original size:31 final size:31
Alignment explanation
Indices: 12213972--12214051 Score: 106
Period size: 31 Copynumber: 2.6 Consensus size: 31
12213962 AGTAAATTTG
*
12213972 CAATTTGATTATTCAATTACTAGTAAGTTGA
1 CAATTTGATCATTCAATTACTAGTAAGTTGA
* * * *
12214003 CAATTTGATCATTTAATTATTGGTAAGTTTA
1 CAATTTGATCATTCAATTACTAGTAAGTTGA
*
12214034 CAATTTGGTCATTCAATT
1 CAATTTGATCATTCAATT
12214052 TTAAAAAGTT
Statistics
Matches: 42, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 42 1.00
ACGTcount: A:0.33, C:0.10, G:0.12, T:0.45
Consensus pattern (31 bp):
CAATTTGATCATTCAATTACTAGTAAGTTGA
Found at i:12220473 original size:3 final size:3
Alignment explanation
Indices: 12220465--12220493 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
12220455 GCTTCTGCTA
12220465 ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
12220494 GATTTTAGGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:12228817 original size:11 final size:11
Alignment explanation
Indices: 12228785--12228822 Score: 60
Period size: 11 Copynumber: 3.5 Consensus size: 11
12228775 ATTCTAGAAA
12228785 TTTTATAATTT
1 TTTTATAATTT
12228796 TCTTTAT-ATTT
1 T-TTTATAATTT
12228807 TTTTATAATTT
1 TTTTATAATTT
12228818 TTTTA
1 TTTTA
12228823 AAATATAAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
10 5 0.20
11 15 0.60
12 5 0.20
ACGTcount: A:0.24, C:0.03, G:0.00, T:0.74
Consensus pattern (11 bp):
TTTTATAATTT
Found at i:12228879 original size:19 final size:19
Alignment explanation
Indices: 12228857--12228897 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
12228847 AAATATTTTA
12228857 AATTTTAAAAATGATATTG
1 AATTTTAAAAATGATATTG
* * *
12228876 AATTTTGAAAATTATTTTG
1 AATTTTAAAAATGATATTG
12228895 AAT
1 AAT
12228898 ATTTTTTTTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.44, C:0.00, G:0.10, T:0.46
Consensus pattern (19 bp):
AATTTTAAAAATGATATTG
Found at i:12239736 original size:72 final size:72
Alignment explanation
Indices: 12239649--12239803 Score: 174
Period size: 72 Copynumber: 2.1 Consensus size: 72
12239639 TCTGGGTCCC
** *
12239649 CCAAAAGTTTTTAATATTATT-AATTTATCCTTGC-ATCATTACTTAAAAATAATGTAAAATT-T
1 CCAAAA-TTTTTAATATT-TTAAACCTATCCTT-CTATCATTACTTAAAAATAATAT-AAATTAT
12239711 GATTTGGCCCTT
62 -ATTTGGCCCTT
* * *
12239723 -CAAATTTTTTAATATTTTAAACCTATCCTTCTATCATTATTTAAAAGTAATATAAATTATATTT
1 CCAAAATTTTTAATATTTTAAACCTATCCTTCTATCATTACTTAAAAATAATATAAATTATATTT
*
12239787 GGTCCTT
66 GGCCCTT
12239794 CCAAAATTTT
1 CCAAAATTTT
12239804 CATTTTAATC
Statistics
Matches: 69, Mismatches: 8, Indels: 10
0.79 0.09 0.11
Matches are distributed among these distances:
71 18 0.26
72 47 0.68
73 4 0.06
ACGTcount: A:0.35, C:0.14, G:0.06, T:0.45
Consensus pattern (72 bp):
CCAAAATTTTTAATATTTTAAACCTATCCTTCTATCATTACTTAAAAATAATATAAATTATATTT
GGCCCTT
Found at i:12240053 original size:17 final size:17
Alignment explanation
Indices: 12240017--12240050 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
12240007 TATAATTAAA
*
12240017 TAATTTTATTCATATTT
1 TAATTATATTCATATTT
12240034 TAATTATATT-ATATTT
1 TAATTATATTCATATTT
12240050 T
1 T
12240051 TAAAAAATTG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (17 bp):
TAATTATATTCATATTT
Found at i:12240086 original size:18 final size:18
Alignment explanation
Indices: 12240046--12240086 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
12240036 ATTATATTAT
12240046 ATTTT-TAAAAAATTGAG
1 ATTTTATAAAAAATTGAG
* *
12240063 ACTTTATAAAAAATTTAG
1 ATTTTATAAAAAATTGAG
12240081 ATTTTA
1 ATTTTA
12240087 ATGAGAAACA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
17 4 0.20
18 16 0.80
ACGTcount: A:0.46, C:0.02, G:0.07, T:0.44
Consensus pattern (18 bp):
ATTTTATAAAAAATTGAG
Found at i:12242921 original size:15 final size:15
Alignment explanation
Indices: 12242855--12242922 Score: 91
Period size: 15 Copynumber: 4.5 Consensus size: 15
12242845 ACCGCCGGGG
*
12242855 TATCCCCCACAAGGA
1 TATCCTCCACAAGGA
12242870 TATCCTCCACAAGGA
1 TATCCTCCACAAGGA
* *
12242885 TATCCTCAACAGGGA
1 TATCCTCCACAAGGA
* *
12242900 TACCCTCCACAGGGA
1 TATCCTCCACAAGGA
12242915 TATCCTCC
1 TATCCTCC
12242923 TCAATATGCT
Statistics
Matches: 47, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 47 1.00
ACGTcount: A:0.29, C:0.37, G:0.15, T:0.19
Consensus pattern (15 bp):
TATCCTCCACAAGGA
Found at i:12245138 original size:3 final size:3
Alignment explanation
Indices: 12245130--12245171 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
12245120 AGGAAGGCTC
12245130 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
12245172 GAGATAAGTC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:12246086 original size:32 final size:32
Alignment explanation
Indices: 12246045--12246107 Score: 78
Period size: 32 Copynumber: 2.0 Consensus size: 32
12246035 TTTATTTTTT
12246045 AAATATA-TT-TTATATTAGAATTTAATATTTAAG
1 AAATATATTTATTAT-TTA-AATTTAA-ATTTAAG
12246078 AAAT-TATTTATTATTTAAATTTAAATTTAA
1 AAATATATTTATTATTTAAATTTAAATTTAA
12246108 TTTATGTTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
31 6 0.21
32 9 0.32
33 9 0.32
34 4 0.14
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (32 bp):
AAATATATTTATTATTTAAATTTAAATTTAAG
Found at i:12250267 original size:26 final size:27
Alignment explanation
Indices: 12250238--12250299 Score: 74
Period size: 27 Copynumber: 2.3 Consensus size: 27
12250228 TAATTTTTAT
12250238 TTTAAAAA-TGTAACAAAT-ATTAAAAC
1 TTTAAAAAGTGTAA-AAATAATTAAAAC
* *
12250264 TTTAAAAAGTGTGAAAATAATTAAAAT
1 TTTAAAAAGTGTAAAAATAATTAAAAC
12250291 TTTATAAAA
1 TTTA-AAAA
12250300 ATGACAAATT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
26 12 0.39
27 15 0.48
28 4 0.13
ACGTcount: A:0.56, C:0.03, G:0.06, T:0.34
Consensus pattern (27 bp):
TTTAAAAAGTGTAAAAATAATTAAAAC
Found at i:12250308 original size:27 final size:26
Alignment explanation
Indices: 12250240--12250308 Score: 61
Period size: 27 Copynumber: 2.5 Consensus size: 26
12250230 ATTTTTATTT
12250240 TAAAAATGTAACAAATATTAAAACTTTA
1 TAAAAATG--ACAAATATTAAAACTTTA
* *
12250268 -AAAAGTGTGA-AAATAATTAAAATTTTA
1 TAAAA--ATGACAAAT-ATTAAAACTTTA
12250295 TAAAAATGACAAAT
1 TAAAAATGACAAAT
12250309 TGTAAAAATT
Statistics
Matches: 33, Mismatches: 3, Indels: 11
0.70 0.06 0.23
Matches are distributed among these distances:
26 7 0.21
27 20 0.61
28 4 0.12
29 2 0.06
ACGTcount: A:0.58, C:0.04, G:0.07, T:0.30
Consensus pattern (26 bp):
TAAAAATGACAAATATTAAAACTTTA
Found at i:12256085 original size:14 final size:15
Alignment explanation
Indices: 12256066--12256098 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
12256056 TATTTACCAA
12256066 AAAAATA-ATATTAT
1 AAAAATAGATATTAT
*
12256080 AAAAATAGATATTGT
1 AAAAATAGATATTAT
12256095 AAAA
1 AAAA
12256099 TTCTTGATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 7 0.41
15 10 0.59
ACGTcount: A:0.64, C:0.00, G:0.06, T:0.30
Consensus pattern (15 bp):
AAAAATAGATATTAT
Found at i:12270228 original size:3 final size:3
Alignment explanation
Indices: 12270220--12270250 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
12270210 CAACACACGA
12270220 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
12270251 GAGTTGAATT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:12271482 original size:21 final size:22
Alignment explanation
Indices: 12271436--12271483 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 22
12271426 TATACAGAAT
*
12271436 TTAAAATATATTATTATAATCA
1 TTAAAATATATTATTACAATCA
12271458 -TAAAATAT-TATATTACAAT-A
1 TTAAAATATAT-TATTACAATCA
12271478 TTAAAA
1 TTAAAA
12271484 ATCCACTTGA
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
20 2 0.09
21 21 0.91
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.42
Consensus pattern (22 bp):
TTAAAATATATTATTACAATCA
Found at i:12279246 original size:19 final size:20
Alignment explanation
Indices: 12279196--12279240 Score: 60
Period size: 18 Copynumber: 2.4 Consensus size: 20
12279186 AACCATCTAA
*
12279196 TATTAATAATTTT--AGATT
1 TATTAATACTTTTAAAGATT
12279214 TATTAATACTTTTAAAGATT
1 TATTAATACTTTTAAAGATT
12279234 T-TTAATA
1 TATTAATA
12279241 TATTTATGGT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
18 12 0.50
19 6 0.25
20 6 0.25
ACGTcount: A:0.40, C:0.02, G:0.04, T:0.53
Consensus pattern (20 bp):
TATTAATACTTTTAAAGATT
Found at i:12281157 original size:14 final size:15
Alignment explanation
Indices: 12281133--12281161 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
12281123 TGGGTGGGCA
12281133 TAAAGCCAGCCACCG
1 TAAAGCCAGCCACCG
12281148 TAAA-CCAGCCACCG
1 TAAAGCCAGCCACCG
12281162 CCCAAAACCC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.34, C:0.41, G:0.17, T:0.07
Consensus pattern (15 bp):
TAAAGCCAGCCACCG
Found at i:12297248 original size:41 final size:41
Alignment explanation
Indices: 12297191--12297275 Score: 161
Period size: 41 Copynumber: 2.1 Consensus size: 41
12297181 ACTAAAGAAA
*
12297191 TTTTATACAAATAAATTAAGGATAATCATTTCAACTCAATG
1 TTTTATACAAATAAATTAAGGATAAACATTTCAACTCAATG
12297232 TTTTATACAAATAAATTAAGGATAAACATTTCAACTCAATG
1 TTTTATACAAATAAATTAAGGATAAACATTTCAACTCAATG
12297273 TTT
1 TTT
12297276 CTTGTACAAA
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 43 1.00
ACGTcount: A:0.44, C:0.12, G:0.07, T:0.38
Consensus pattern (41 bp):
TTTTATACAAATAAATTAAGGATAAACATTTCAACTCAATG
Found at i:12297836 original size:192 final size:192
Alignment explanation
Indices: 12297509--12297881 Score: 665
Period size: 192 Copynumber: 1.9 Consensus size: 192
12297499 GATAAATGTG
* *
12297509 GCTTAATGGAGTTTCCTAAGCCTAAGCCTCCCCATGCTTCTTGCAACTCTCTCTCCCTTGCTTCT
1 GCTTAATGGAGTTTCCTAAGCCTAAGCCGCCCCATGCTTCTTGAAACTCTCTCTCCCTTGCTTCT
* *
12297574 CTACGAGATACAGAGAATCTAATCTGCTCACTTGGTTGCTCAGAAGTAGCCATCTTCTCTTTCTC
66 CTACGAGATACAGAGAATCTAATCTGCTCACTTGCTTGCTCAGAACTAGCCATCTTCTCTTTCTC
*
12297639 TAATTTTGATTTGTGTTTAACCAAAATTTGGTCCAGACTACCCTGATCATCTGCCACCTGTT
131 TAATTTTGATTTGTGTTTAACCAAAATTTGATCCAGACTACCCTGATCATCTGCCACCTGTT
*
12297701 GCTTAATGGAGTTTCCTAAGCTTAAGCCGCCCCATGCTTCTTGAAACTCTCTCTCCCTTGCTTCT
1 GCTTAATGGAGTTTCCTAAGCCTAAGCCGCCCCATGCTTCTTGAAACTCTCTCTCCCTTGCTTCT
* * *
12297766 CTACGAGATACAGATAATCTAATCTGCTCACTTGCTTGCTCAGCACTTGCCATCTTCTCTTTCTC
66 CTACGAGATACAGAGAATCTAATCTGCTCACTTGCTTGCTCAGAACTAGCCATCTTCTCTTTCTC
12297831 TAATTTTGATTTGTGTTTAACCAAAATTTGATCCAGACTACCCTGATCATC
131 TAATTTTGATTTGTGTTTAACCAAAATTTGATCCAGACTACCCTGATCATC
12297882 CACTTGTGGC
Statistics
Matches: 172, Mismatches: 9, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
192 172 1.00
ACGTcount: A:0.22, C:0.28, G:0.14, T:0.36
Consensus pattern (192 bp):
GCTTAATGGAGTTTCCTAAGCCTAAGCCGCCCCATGCTTCTTGAAACTCTCTCTCCCTTGCTTCT
CTACGAGATACAGAGAATCTAATCTGCTCACTTGCTTGCTCAGAACTAGCCATCTTCTCTTTCTC
TAATTTTGATTTGTGTTTAACCAAAATTTGATCCAGACTACCCTGATCATCTGCCACCTGTT
Found at i:12300372 original size:125 final size:125
Alignment explanation
Indices: 12300150--12300402 Score: 497
Period size: 125 Copynumber: 2.0 Consensus size: 125
12300140 ATTAAGGCTT
12300150 AGAACACATTCTTCATCTGGTCTACCAGAAAAATCTCAATTAAGAAAAATCCCATATCAGAGCAA
1 AGAACACATTCTTCATCTGGTCTACCAGAAAAATCTCAATTAAGAAAAATCCCATATCAGAGCAA
*
12300215 CTAAAAGACATATTAATATTGCCTTTTTCCTTTGTTTTAAACTCATTAAACTCATTGTAG
66 CTAAAAGACATATTAATATTGCCTTTTTCCTTTGTTTTAAACTCAATAAACTCATTGTAG
12300275 AGAACACATTCTTCATCTGGTCTACCAGAAAAATCTCAATTAAGAAAAATCCCATATCAGAGCAA
1 AGAACACATTCTTCATCTGGTCTACCAGAAAAATCTCAATTAAGAAAAATCCCATATCAGAGCAA
12300340 CTAAAAGACATATTAATATTGCCTTTTTCCTTTGTTTTAAACTCAATAAACTCATTGTAG
66 CTAAAAGACATATTAATATTGCCTTTTTCCTTTGTTTTAAACTCAATAAACTCATTGTAG
12300400 AGA
1 AGA
12300403 CCAATTAACT
Statistics
Matches: 127, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
125 127 1.00
ACGTcount: A:0.38, C:0.20, G:0.10, T:0.32
Consensus pattern (125 bp):
AGAACACATTCTTCATCTGGTCTACCAGAAAAATCTCAATTAAGAAAAATCCCATATCAGAGCAA
CTAAAAGACATATTAATATTGCCTTTTTCCTTTGTTTTAAACTCAATAAACTCATTGTAG
Found at i:12327815 original size:24 final size:22
Alignment explanation
Indices: 12327783--12327832 Score: 64
Period size: 24 Copynumber: 2.2 Consensus size: 22
12327773 TTTGACAATT
12327783 TTTTTTCAATATAAATTTGATAAA
1 TTTTTTCAATATAAATTT-AT-AA
* *
12327807 TTTTTTCAATTTTAATTTATAA
1 TTTTTTCAATATAAATTTATAA
12327829 TTTT
1 TTTT
12327833 GATTCATATA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 6 0.25
23 2 0.08
24 16 0.67
ACGTcount: A:0.34, C:0.04, G:0.02, T:0.60
Consensus pattern (22 bp):
TTTTTTCAATATAAATTTATAA
Found at i:12339205 original size:15 final size:16
Alignment explanation
Indices: 12339185--12339214 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
12339175 TGAGCAGCGA
12339185 AAAAGGA-GGAAAAAG
1 AAAAGGAGGGAAAAAG
12339200 AAAAGGAGGGAAAAA
1 AAAAGGAGGGAAAAA
12339215 AGAGAAGTTG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (16 bp):
AAAAGGAGGGAAAAAG
Found at i:12342421 original size:11 final size:11
Alignment explanation
Indices: 12342405--12342478 Score: 71
Period size: 11 Copynumber: 6.5 Consensus size: 11
12342395 TGTTCGTGCT
12342405 CGTTCGTTTAA
1 CGTTCGTTTAA
*
12342416 CGTTCG-TGAA
1 CGTTCGTTTAA
12342426 CATGTTCGTTTAA
1 C--GTTCGTTTAA
*
12342439 CGTTCG-TGAA
1 CGTTCGTTTAA
12342449 CATGTTCGTTTAA
1 C--GTTCGTTTAA
*
12342462 TGTTCGTTTAA
1 CGTTCGTTTAA
12342473 CGTTCG
1 CGTTCG
12342479 CGAACATGTT
Statistics
Matches: 51, Mismatches: 6, Indels: 12
0.74 0.09 0.17
Matches are distributed among these distances:
10 8 0.16
11 26 0.51
12 10 0.20
13 7 0.14
ACGTcount: A:0.19, C:0.18, G:0.22, T:0.42
Consensus pattern (11 bp):
CGTTCGTTTAA
Done.