Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007212.1 Corchorus capsularis cultivar CVL-1 contig07233, whole genome shotgun sequence
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: 121830
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.32
Found at i:481 original size:18 final size:18
Alignment explanation
Indices: 458--548 Score: 110
Period size: 18 Copynumber: 5.1 Consensus size: 18
448 GCACCAGGCG
*
458 CCACACCCAGTGGTCGCA
1 CCACACCAAGTGGTCGCA
476 CCACACCAAGTGGTCGCA
1 CCACACCAAGTGGTCGCA
* *
494 CCACACCAAGTGATTGCA
1 CCACACCAAGTGGTCGCA
* *
512 CCGCACCAAGTGGCCGCA
1 CCACACCAAGTGGTCGCA
* * *
530 CCGCACCAATTGGCCGCA
1 CCACACCAAGTGGTCGCA
548 C
1 C
549 TTGTTCAACA
Statistics
Matches: 65, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 65 1.00
ACGTcount: A:0.25, C:0.42, G:0.22, T:0.11
Consensus pattern (18 bp):
CCACACCAAGTGGTCGCA
Found at i:2852 original size:66 final size:66
Alignment explanation
Indices: 2770--2901 Score: 255
Period size: 66 Copynumber: 2.0 Consensus size: 66
2760 AATACTCGTA
*
2770 GCGCTAGCGCGGTCTAATATGACTTGCTTTTTTTTTTTAATTTAAATTCAAATTCAAGTTCGAGT
1 GCGCTAACGCGGTCTAATATGACTTGCTTTTTTTTTTTAATTTAAATTCAAATTCAAGTTCGAGT
2835 G
66 G
2836 GCGCTAACGCGGTCTAATATGACTTGCTTTTTTTTTTTAATTTAAATTCAAATTCAAGTTCGAGT
1 GCGCTAACGCGGTCTAATATGACTTGCTTTTTTTTTTTAATTTAAATTCAAATTCAAGTTCGAGT
2901 G
66 G
2902 ACGCATATGT
Statistics
Matches: 65, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
66 65 1.00
ACGTcount: A:0.25, C:0.15, G:0.17, T:0.42
Consensus pattern (66 bp):
GCGCTAACGCGGTCTAATATGACTTGCTTTTTTTTTTTAATTTAAATTCAAATTCAAGTTCGAGT
G
Found at i:12486 original size:6 final size:6
Alignment explanation
Indices: 12475--12499 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
12465 TGAACCTTTG
12475 GAAGGT GAAGGT GAAGGT GAAGGT G
1 GAAGGT GAAGGT GAAGGT GAAGGT G
12500 GCAACAAACT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.52, T:0.16
Consensus pattern (6 bp):
GAAGGT
Found at i:12960 original size:17 final size:17
Alignment explanation
Indices: 12938--12970 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
12928 GTGGGTATAA
*
12938 AATTTCATCTATATTAG
1 AATTTCATCCATATTAG
12955 AATTTCATCCATATTA
1 AATTTCATCCATATTA
12971 ATGTATAGTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.36, C:0.15, G:0.03, T:0.45
Consensus pattern (17 bp):
AATTTCATCCATATTAG
Found at i:14287 original size:269 final size:269
Alignment explanation
Indices: 13797--14323 Score: 930
Period size: 269 Copynumber: 2.0 Consensus size: 269
13787 GTGCAGAGTC
13797 ATATTCTTATCAATTGACAACCCCAACACAAAGAAAATAAATACCGAAATATAAGTAATTTGTTT
1 ATATTCTTATCAATTGACAACCCCAACACAAAGAAAATAAATACCGAAATATAAGTAATTTGTTT
*
13862 AATGAAAAACTATATATTTTGTAGATTTAATTAAATGCAAATTAATAAAATTAAAAATTAATTGT
66 AATGAAAAACTATATATTTTGTAGATTTAATTAAATGCAAATTAACAAAATTAAAAATTAATTGT
* * *
13927 ATAATGACAATTTTTAGAAATATGTTAGATAAGTAAGGATATGATAGATATTTTAAAAGTTAAAC
131 ATAATGACAATTTTTAGAAATATGTTAGACAAGTAAGGATATAATAGATATTTTAAAAATTAAAC
*
13992 AAGGGTACAATAGGCATTTCAAAAGTTTCTCAAAACTCATACTTTATATATAGTATAGATATAGA
196 AAGGGTACAATAAGCATTTCAAAAGTTTCTCAAAACTCATACTTTATATATAGTATAGATATAGA
14057 TATAAAATT
261 TATAAAATT
* * *
14066 ATATTCTTATCAATTGTCAACCCCAACGCAAAGAAAATAAATACCGAGATATAAGTAATTTGTTT
1 ATATTCTTATCAATTGACAACCCCAACACAAAGAAAATAAATACCGAAATATAAGTAATTTGTTT
*
14131 AATGAAAAATTATATATTTTGTAGATTTAATTAAATGCAAATTAACAAAATTAAAAATTAATTGT
66 AATGAAAAACTATATATTTTGTAGATTTAATTAAATGCAAATTAACAAAATTAAAAATTAATTGT
*
14196 ATAATGGCAATTTTTAGAAATATGTTAGACAAGTAAGGATATAATA-AGTATTTTAAAAATTAAA
131 ATAATGACAATTTTTAGAAATATGTTAGACAAGTAAGGATATAATAGA-TATTTTAAAAATTAAA
* *
14260 CAAGGGTACAATAAGCATTTTAAAAGTTTCTCAAAACTCGTACTTTATATATAGTATAGATATA
195 CAAGGGTACAATAAGCATTTCAAAAGTTTCTCAAAACTCATACTTTATATATAGTATAGATATA
14324 TTTTAGCTGT
Statistics
Matches: 245, Mismatches: 12, Indels: 2
0.95 0.05 0.01
Matches are distributed among these distances:
268 1 0.00
269 244 1.00
ACGTcount: A:0.46, C:0.09, G:0.11, T:0.34
Consensus pattern (269 bp):
ATATTCTTATCAATTGACAACCCCAACACAAAGAAAATAAATACCGAAATATAAGTAATTTGTTT
AATGAAAAACTATATATTTTGTAGATTTAATTAAATGCAAATTAACAAAATTAAAAATTAATTGT
ATAATGACAATTTTTAGAAATATGTTAGACAAGTAAGGATATAATAGATATTTTAAAAATTAAAC
AAGGGTACAATAAGCATTTCAAAAGTTTCTCAAAACTCATACTTTATATATAGTATAGATATAGA
TATAAAATT
Found at i:21739 original size:20 final size:20
Alignment explanation
Indices: 21716--21755 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
21706 AACAAGGGTC
21716 CACCCCTCCAAAACCCTCCA
1 CACCCCTCCAAAACCCTCCA
*
21736 CACCCCTCCAAAACCTTCCA
1 CACCCCTCCAAAACCCTCCA
21756 ACCAAACAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.30, C:0.57, G:0.00, T:0.12
Consensus pattern (20 bp):
CACCCCTCCAAAACCCTCCA
Found at i:22536 original size:15 final size:15
Alignment explanation
Indices: 22513--22577 Score: 67
Period size: 16 Copynumber: 4.1 Consensus size: 15
22503 CTGAACCCGA
* *
22513 ACCCGAATTAACTTG
1 ACCCAAATTAACCTG
*
22528 ACCCAAATTCAACCCG
1 ACCCAAATT-AACCTG
*
22544 AACCCGAATTAACCTG
1 -ACCCAAATTAACCTG
22560 ACCCAAATTTAACCTG
1 ACCCAAA-TTAACCTG
22576 AC
1 AC
22578 TTGACTTAAG
Statistics
Matches: 41, Mismatches: 6, Indels: 5
0.79 0.12 0.10
Matches are distributed among these distances:
15 14 0.34
16 19 0.46
17 8 0.20
ACGTcount: A:0.37, C:0.34, G:0.09, T:0.20
Consensus pattern (15 bp):
ACCCAAATTAACCTG
Found at i:22542 original size:32 final size:32
Alignment explanation
Indices: 22496--22573 Score: 120
Period size: 32 Copynumber: 2.4 Consensus size: 32
22486 TCTGGTCAAA
* * *
22496 ACCCAAACTGAACCCGAACCCGAATTAACTTG
1 ACCCAAATTCAACCCGAACCCGAATTAACCTG
22528 ACCCAAATTCAACCCGAACCCGAATTAACCTG
1 ACCCAAATTCAACCCGAACCCGAATTAACCTG
*
22560 ACCCAAATTTAACC
1 ACCCAAATTCAACC
22574 TGACTTGACT
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 42 1.00
ACGTcount: A:0.38, C:0.36, G:0.09, T:0.17
Consensus pattern (32 bp):
ACCCAAATTCAACCCGAACCCGAATTAACCTG
Found at i:22680 original size:32 final size:32
Alignment explanation
Indices: 22639--22706 Score: 118
Period size: 32 Copynumber: 2.1 Consensus size: 32
22629 CATGCTTTTG
22639 AACCTAGAAACTAGAAACTATAACTACCTACA
1 AACCTAGAAACTAGAAACTATAACTACCTACA
* *
22671 AACCTAGAAACTAGAAACTATAACTGCCTTCA
1 AACCTAGAAACTAGAAACTATAACTACCTACA
22703 AACC
1 AACC
22707 AAATAAACAA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.47, C:0.26, G:0.07, T:0.19
Consensus pattern (32 bp):
AACCTAGAAACTAGAAACTATAACTACCTACA
Found at i:23278 original size:39 final size:39
Alignment explanation
Indices: 23220--23314 Score: 156
Period size: 39 Copynumber: 2.5 Consensus size: 39
23210 CGATACTCGG
* *
23220 CTCGAGCTCAATTGAGTATCGATTATGGGGATCGAGCTA
1 CTCGAGCTCGATCGAGTATCGATTATGGGGATCGAGCTA
*
23259 CTCGAGCTCGATCGTGTATCGATTATGGGGATCGAGCTA
1 CTCGAGCTCGATCGAGTATCGATTATGGGGATCGAGCTA
23298 CTCGAGCTCGATC-AGTA
1 CTCGAGCTCGATCGAGTA
23315 AGCTCAACCT
Statistics
Matches: 52, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
38 3 0.06
39 49 0.94
ACGTcount: A:0.23, C:0.21, G:0.28, T:0.27
Consensus pattern (39 bp):
CTCGAGCTCGATCGAGTATCGATTATGGGGATCGAGCTA
Found at i:23688 original size:5 final size:5
Alignment explanation
Indices: 23678--23712 Score: 70
Period size: 5 Copynumber: 7.0 Consensus size: 5
23668 TCAACAAGTT
23678 AGAAA AGAAA AGAAA AGAAA AGAAA AGAAA AGAAA
1 AGAAA AGAAA AGAAA AGAAA AGAAA AGAAA AGAAA
23713 CGAATACTTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 30 1.00
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (5 bp):
AGAAA
Found at i:25259 original size:2 final size:2
Alignment explanation
Indices: 25252--25278 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
25242 ATAATTTTCC
25252 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
25279 TACTAAACGG
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:26320 original size:19 final size:19
Alignment explanation
Indices: 26296--26337 Score: 75
Period size: 19 Copynumber: 2.2 Consensus size: 19
26286 AGATGATGAT
26296 AAAAGAGAAAAATTAAATA
1 AAAAGAGAAAAATTAAATA
*
26315 AAAAGATAAAAATTAAATA
1 AAAAGAGAAAAATTAAATA
26334 AAAA
1 AAAA
26338 ATTATTTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.76, C:0.00, G:0.07, T:0.17
Consensus pattern (19 bp):
AAAAGAGAAAAATTAAATA
Found at i:33446 original size:18 final size:19
Alignment explanation
Indices: 33411--33446 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
33401 GATTATCAAT
*
33411 ATCTTCATTCTCTCCATGC
1 ATCTTCATACTCTCCATGC
33430 ATCTTCATACT-TCCATG
1 ATCTTCATACTCTCCATG
33447 AAGCTCTTGC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 6 0.38
19 10 0.62
ACGTcount: A:0.19, C:0.33, G:0.06, T:0.42
Consensus pattern (19 bp):
ATCTTCATACTCTCCATGC
Found at i:42984 original size:6 final size:6
Alignment explanation
Indices: 42968--42998 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
42958 CTAAGCAAAG
42968 TAAAT- TAAATC TAAATC TAAATC TAAATC TA
1 TAAATC TAAATC TAAATC TAAATC TAAATC TA
42999 TAGCAATTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 5 0.20
6 20 0.80
ACGTcount: A:0.52, C:0.13, G:0.00, T:0.35
Consensus pattern (6 bp):
TAAATC
Found at i:44364 original size:18 final size:19
Alignment explanation
Indices: 44341--44379 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
44331 TTCTTGAAAT
*
44341 AATTCTTC-AATTGTCTTC
1 AATTCTTCAAATTATCTTC
44359 AATTCTTCAAATTATCTTC
1 AATTCTTCAAATTATCTTC
44378 AA
1 AA
44380 ATAATCTTCA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 8 0.42
19 11 0.58
ACGTcount: A:0.31, C:0.21, G:0.03, T:0.46
Consensus pattern (19 bp):
AATTCTTCAAATTATCTTC
Found at i:44378 original size:11 final size:11
Alignment explanation
Indices: 44362--44391 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
44352 TGTCTTCAAT
*
44362 TCTTCAAATTA
1 TCTTCAAATAA
44373 TCTTCAAATAA
1 TCTTCAAATAA
44384 TCTTCAAA
1 TCTTCAAA
44392 CACGAACTTC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.40, C:0.20, G:0.00, T:0.40
Consensus pattern (11 bp):
TCTTCAAATAA
Found at i:44390 original size:22 final size:22
Alignment explanation
Indices: 44332--44391 Score: 65
Period size: 22 Copynumber: 2.9 Consensus size: 22
44322 AATTCTTACT
* *
44332 TCTTGAAATAATTCTTC-AATTG
1 TCTTCAAATAA-TCTTCAAATTA
44354 TCTTC-AAT--TCTTCAAATTA
1 TCTTCAAATAATCTTCAAATTA
44373 TCTTCAAATAATCTTCAAA
1 TCTTCAAATAATCTTCAAA
44392 CACGAACTTC
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
18 5 0.16
19 9 0.28
20 3 0.09
21 3 0.09
22 12 0.38
ACGTcount: A:0.35, C:0.18, G:0.03, T:0.43
Consensus pattern (22 bp):
TCTTCAAATAATCTTCAAATTA
Found at i:45708 original size:19 final size:18
Alignment explanation
Indices: 45675--45712 Score: 58
Period size: 19 Copynumber: 2.1 Consensus size: 18
45665 TTAAAATAAT
*
45675 TCTTCAATAATCTTCAAA
1 TCTTCAAAAATCTTCAAA
45693 TCTTCAAAATATCTTCAAA
1 TCTTCAAAA-ATCTTCAAA
45712 T
1 T
45713 ACGAACTTCG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 8 0.44
19 10 0.56
ACGTcount: A:0.39, C:0.21, G:0.00, T:0.39
Consensus pattern (18 bp):
TCTTCAAAAATCTTCAAA
Found at i:56004 original size:30 final size:31
Alignment explanation
Indices: 55955--56027 Score: 76
Period size: 31 Copynumber: 2.4 Consensus size: 31
55945 GGCGAAAATG
* * *
55955 CAATCCAGGATACACCGTTA-CGACTTGTTT
1 CAATTCAGGATACAACGTTATCGACTTGTGT
* * **
55985 CAATTTAGGATATAACGTTATCGGGTTGTGT
1 CAATTCAGGATACAACGTTATCGACTTGTGT
56016 CAATTCAGGATA
1 CAATTCAGGATA
56028 AAATCAGAAT
Statistics
Matches: 34, Mismatches: 8, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
30 16 0.47
31 18 0.53
ACGTcount: A:0.29, C:0.18, G:0.21, T:0.33
Consensus pattern (31 bp):
CAATTCAGGATACAACGTTATCGACTTGTGT
Found at i:57292 original size:25 final size:23
Alignment explanation
Indices: 57251--57304 Score: 76
Period size: 23 Copynumber: 2.3 Consensus size: 23
57241 CTTTTCAAAG
57251 AAATTTAT--TTTTATTTATTTTT
1 AAATTTATCATTTTATTTA-TTTT
57273 AATATTTATCATTTTATTTATTTT
1 AA-ATTTATCATTTTATTTATTTT
57297 AAATTTAT
1 AAATTTAT
57305 TTAATGATAA
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
22 2 0.07
23 12 0.41
24 6 0.21
25 9 0.31
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (23 bp):
AAATTTATCATTTTATTTATTTT
Found at i:58356 original size:35 final size:34
Alignment explanation
Indices: 58305--58988 Score: 623
Period size: 35 Copynumber: 19.8 Consensus size: 34
58295 TTCTTACTAA
* *
58305 ACTTAATTACCTTGAATTAAGTTACTTATTGAACT
1 ACTTAATTACCCTGAATTAAGTTACTTACTG-ACT
* * *
58340 ACTTAATTACCCTGAATTAAGTTACTCATTAACT
1 ACTTAATTACCCTGAATTAAGTTACTTACTGACT
* *
58374 CACTTAATTACCCTGAATTAAAGTTGA-TTATTGATT
1 -ACTTAATTACCCTGAATT-AAGTT-ACTTACTGACT
*
58410 CACTTAATTACCCTGAATTAAGTTTGA-TTACCGACT
1 -ACTTAATTACCCTGAATTAAG-TT-ACTTACTGACT
* *
58446 CACTTAACTACCCTGAATTAAGTTGA-TTACCGACT
1 -ACTTAATTACCCTGAATTAAGTT-ACTTACTGACT
*
58481 CACTTAATTACCCTGAATTAAGTTACTTATTGAACT
1 -ACTTAATTACCCTGAATTAAGTTACTTACTG-ACT
*
58517 ACTTAATTACCCTGAATTAAGTTGA-TTACCGACT
1 ACTTAATTACCCTGAATTAAGTT-ACTTACTGACT
*
58551 CACTTAATTACCCTGAATTAAGTTGA-TTACCGACT
1 -ACTTAATTACCCTGAATTAAGTT-ACTTACTGACT
* *
58586 CACTTAATTACCCTGAATTAAGTTACTCATTGAACT
1 -ACTTAATTACCCTGAATTAAGTTACTTACTG-ACT
* * *
58622 ACTTAATTACCCTGAGTTAAGTTACTTATTAACT
1 ACTTAATTACCCTGAATTAAGTTACTTACTGACT
*
58656 CACTTAATTACCCTGAATTAAATTTTA-TTACTGACT
1 -ACTTAATTACCCTGAATT-AA-GTTACTTACTGACT
* *
58692 CACTTAATTACCCTAAATTAAGTCGA-TTACTGACTT
1 -ACTTAATTACCCTGAATTAAGT-TACTTACTGAC-T
* * * *
58728 GCTTAATTATCCAGAATTAAGTTGA-TTACTGAATT
1 ACTTAATTACCCTGAATTAAGTT-ACTTACTG-ACT
**
58763 ACTTAATTACCCTGAATTAAGTTACTGCCT---T
1 ACTTAATTACCCTGAATTAAGTTACTTACTGACT
* * *
58794 ACTTAATTTCCCTGAACTAAGTTACTAACTGACTTT
1 ACTTAATTACCCTGAATTAAGTTACTTACTGAC--T
* *
58830 ACTTAGTTACCCTGAATTAAGCTACTTACTG---
1 ACTTAATTACCCTGAATTAAGTTACTTACTGACT
* *
58861 ACTTAATTACCCTGAATTAAGTTACCTA-TTACTT
1 ACTTAATTACCCTGAATTAAGTTACTTACTGAC-T
* * *
58895 ATTTAATTACCCTGAATTAAGTTGCTGACT---T
1 ACTTAATTACCCTGAATTAAGTTACTTACTGACT
*
58926 ACTTAATTACCCTGAATTAAGCTA-TTCACTGACTT
1 ACTTAATTACCCTGAATTAAGTTACTT-ACTGAC-T
*
58961 ACTTAATTGCCCTGAATTAAGTTACTTA
1 ACTTAATTACCCTGAATTAAGTTACTTA
58989 TTACTGATTC
Statistics
Matches: 553, Mismatches: 62, Indels: 68
0.81 0.09 0.10
Matches are distributed among these distances:
30 2 0.00
31 77 0.14
34 37 0.07
35 307 0.56
36 126 0.23
37 4 0.01
ACGTcount: A:0.32, C:0.20, G:0.10, T:0.38
Consensus pattern (34 bp):
ACTTAATTACCCTGAATTAAGTTACTTACTGACT
Found at i:58562 original size:16 final size:16
Alignment explanation
Indices: 58541--58597 Score: 51
Period size: 16 Copynumber: 3.4 Consensus size: 16
58531 AATTAAGTTG
58541 ATTACCGACTCACTTA
1 ATTACCGACTCACTTA
* * * *
58557 ATTACCCTGAATTAAGTTG
1 ATTA-CC-G-ACTCACTTA
58576 ATTACCGACTCACTTA
1 ATTACCGACTCACTTA
58592 ATTACC
1 ATTACC
58598 CTGAATTAAG
Statistics
Matches: 30, Mismatches: 8, Indels: 6
0.68 0.18 0.14
Matches are distributed among these distances:
16 15 0.50
17 3 0.10
18 3 0.10
19 9 0.30
ACGTcount: A:0.32, C:0.26, G:0.09, T:0.33
Consensus pattern (16 bp):
ATTACCGACTCACTTA
Found at i:58576 original size:105 final size:104
Alignment explanation
Indices: 58305--58983 Score: 680
Period size: 106 Copynumber: 6.5 Consensus size: 104
58295 TTCTTACTAA
* * *
58305 ACTTAATTACCTTGAATTAAGTTACTTATTGAACT-ACTTAATTACCCTGAATTAAGTT-ACTCA
1 ACTTAATTACCCTGAATTAAGTTA-TTACTG-ACTCACTTAATTACCCTGAATTAAGTTGA-TTA
* *
58368 TTAACTCACTTAATTACCCTGAATTAAAGTTGA-TTATTGA-TT
63 CTGACTCACTTAATTACCCTGAATT-AAGTT-ACTTATTGACTT
* *
58410 CACTTAATTACCCTGAATTAAGTTTGATTACCGACTCACTTAACTACCCTGAATTAAGTTGATTA
1 -ACTTAATTACCCTGAATTAAG-TT-ATTACTGACTCACTTAATTACCCTGAATTAAGTTGATTA
*
58475 CCGACTCACTTAATTACCCTGAATTAAGTTACTTATTGAAC-T
63 CTGACTCACTTAATTACCCTGAATTAAGTTACTTATTG-ACTT
* *
58517 ACTTAATTACCCTGAATTAAGTTGATTACCGACTCACTTAATTACCCTGAATTAAGTTGATTACC
1 ACTTAATTACCCTGAATTAAGTT-ATTACTGACTCACTTAATTACCCTGAATTAAGTTGATTACT
*
58582 GACTCACTTAATTACCCTGAATTAAGTTACTCATTGAAC-T
65 GACTCACTTAATTACCCTGAATTAAGTTACTTATTG-ACTT
* * * * *
58622 ACTTAATTACCCTGAGTTAAGTTACTTATTAACTCACTTAATTACCCTGAATTAAATTTTATTAC
1 ACTTAATTACCCTGAATTAAGTTA-TTACTGACTCACTTAATTACCCTGAATT-AAGTTGATTAC
* * *
58687 TGACTCACTTAATTACCCTAAATTAAGTCGA-TTACTGACTT
64 TGACTCACTTAATTACCCTGAATTAAGT-TACTTATTGACTT
* * * * *
58728 GCTTAATTATCCAGAATTAAGTTGATTACTGAATTACTTAATTACCCTGAATTAA---G-TTACT
1 ACTTAATTACCCTGAATTAAGTT-ATTACTGACTCACTTAATTACCCTGAATTAAGTTGATTACT
* * * * * *
58789 GCCTTACTTAATTTCCCTGAACTAAGTTACTAACTGACTTT
65 GACTCACTTAATTACCCTGAATTAAGTTACTTATTGAC-TT
* * *
58830 ACTTAGTTACCCTGAATTAAGCTACTTACTG----ACTTAATTACCCTGAATTAAGTT-ACCTA-
1 ACTTAATTACCCTGAATTAAGTTA-TTACTGACTCACTTAATTACCCTGAATTAAGTTGA-TTAC
* * * *
58889 TTACTTATTTAATTACCCTGAATTAAGTTGC----TGACTT
64 TGACTCACTTAATTACCCTGAATTAAGTTACTTATTGACTT
* * *
58926 ACTTAATTACCCTGAATTAAGCTATTCACTGACTTACTTAATTGCCCTGAATTAAGTT
1 ACTTAATTACCCTGAATTAAGTTATT-ACTGACTCACTTAATTACCCTGAATTAAGTT
58984 ACTTATTACT
Statistics
Matches: 497, Mismatches: 51, Indels: 56
0.82 0.08 0.09
Matches are distributed among these distances:
95 2 0.00
96 29 0.06
97 4 0.01
98 20 0.04
100 23 0.05
101 60 0.12
102 28 0.06
104 1 0.00
105 134 0.27
106 138 0.28
107 56 0.11
108 2 0.00
ACGTcount: A:0.32, C:0.20, G:0.10, T:0.38
Consensus pattern (104 bp):
ACTTAATTACCCTGAATTAAGTTATTACTGACTCACTTAATTACCCTGAATTAAGTTGATTACTG
ACTCACTTAATTACCCTGAATTAAGTTACTTATTGACTT
Found at i:58880 original size:14 final size:15
Alignment explanation
Indices: 58834--58886 Score: 54
Period size: 15 Copynumber: 3.5 Consensus size: 15
58824 GACTTTACTT
58834 AGTTACCCTGAATTA
1 AGTTACCCTGAATTA
* * *
58849 AGCTACTTACTGACTTA
1 AGTTAC--CCTGAATTA
58866 A-TTACCCTGAATTA
1 AGTTACCCTGAATTA
58880 AGTTACC
1 AGTTACC
58887 TATTACTTAT
Statistics
Matches: 29, Mismatches: 6, Indels: 6
0.71 0.15 0.15
Matches are distributed among these distances:
14 8 0.28
15 10 0.34
16 3 0.10
17 8 0.28
ACGTcount: A:0.32, C:0.23, G:0.11, T:0.34
Consensus pattern (15 bp):
AGTTACCCTGAATTA
Found at i:59550 original size:33 final size:33
Alignment explanation
Indices: 59508--59573 Score: 89
Period size: 33 Copynumber: 2.0 Consensus size: 33
59498 ATTTCATCTT
* * *
59508 TTACTTAAAAGATTTAAT-TTTTATTTACAAAAA
1 TTACTTAAAAG-TTCAATCTTTTAATTAAAAAAA
59541 TTACTTAAAAGTTCAATCTTTTAATTAAAAAAA
1 TTACTTAAAAGTTCAATCTTTTAATTAAAAAAA
59574 GATTCAATCT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
32 5 0.17
33 24 0.83
ACGTcount: A:0.47, C:0.08, G:0.03, T:0.42
Consensus pattern (33 bp):
TTACTTAAAAGTTCAATCTTTTAATTAAAAAAA
Found at i:59588 original size:56 final size:55
Alignment explanation
Indices: 59514--59671 Score: 155
Period size: 51 Copynumber: 2.9 Consensus size: 55
59504 TCTTTTACTT
* * * *
59514 AAAAGATTTAATTTTTATTTACAAAAATTACTTAAAAG-TTCAATCTTTTAATTAAA
1 AAAAGATTCAATCTTTA-TT-CAAAAATTACTTAAAAGATTCAATCTTTCAACTAAA
* * *
59570 AAAAGATTCAATCTTTATTCACAAATTACTTTAAAGATTTAATCTTTCAACT---
1 AAAAGATTCAATCTTTATTCAAAAATTACTTAAAAGATTCAATCTTTCAACTAAA
* * ** *
59622 AAAA-ACTCAATCTTTATTCACAAATTACTCCAAAGATTTAATCTTTCAAC
1 AAAAGATTCAATCTTTATTCAAAAATTACTTAAAAGATTCAATCTTTCAAC
59672 ACAAATATTA
Statistics
Matches: 91, Mismatches: 10, Indels: 7
0.84 0.09 0.06
Matches are distributed among these distances:
51 43 0.47
52 4 0.04
54 15 0.16
55 14 0.15
56 15 0.16
ACGTcount: A:0.43, C:0.15, G:0.03, T:0.39
Consensus pattern (55 bp):
AAAAGATTCAATCTTTATTCAAAAATTACTTAAAAGATTCAATCTTTCAACTAAA
Found at i:62743 original size:9 final size:9
Alignment explanation
Indices: 62709--62743 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
62699 TTTTTTTATT
62709 TTATTTTTA
1 TTATTTTTA
*
62718 TTATTATTA
1 TTATTTTTA
*
62727 TTAATTTTA
1 TTATTTTTA
62736 TTATTTTT
1 TTATTTTT
62744 TTAGCTTTGA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (9 bp):
TTATTTTTA
Found at i:70773 original size:43 final size:43
Alignment explanation
Indices: 70696--70777 Score: 105
Period size: 43 Copynumber: 1.9 Consensus size: 43
70686 TTGATTATTT
*
70696 ACTTAATTACACCGAATTAATCTTATTACTGATTTACTTAATC
1 ACTTAATTACACCGAATTAATCTGATTACTGATTTACTTAATC
* *
70739 ACTTAATTTCACCGAGTTAAAT-TGATTAAC-GATTTACTT
1 ACTTAATTACACCGAATT-AATCTGATT-ACTGATTTACTT
70778 TATTTAATTA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
43 29 0.85
44 5 0.15
ACGTcount: A:0.34, C:0.17, G:0.07, T:0.41
Consensus pattern (43 bp):
ACTTAATTACACCGAATTAATCTGATTACTGATTTACTTAATC
Found at i:70924 original size:35 final size:35
Alignment explanation
Indices: 70875--70952 Score: 95
Period size: 35 Copynumber: 2.2 Consensus size: 35
70865 GAATTGCTGT
* * * *
70875 TTTATTTAATTACACCGAATTAAGTT-AGTTACCAA
1 TTTACTTAACTACACCGAACTAAATTGA-TTACCAA
70910 TTTACTTAACTACACCGAACTAAATTGATTACCAA
1 TTTACTTAACTACACCGAACTAAATTGATTACCAA
*
70945 ATTACTTA
1 TTTACTTA
70953 GTCTAATCTC
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
35 36 0.97
36 1 0.03
ACGTcount: A:0.38, C:0.18, G:0.06, T:0.37
Consensus pattern (35 bp):
TTTACTTAACTACACCGAACTAAATTGATTACCAA
Found at i:70966 original size:56 final size:56
Alignment explanation
Indices: 70905--71282 Score: 576
Period size: 56 Copynumber: 6.9 Consensus size: 56
70895 TAAGTTAGTT
* * * * *
70905 ACCAATTTACTTAACTACACCGAACTAAATTGATTACCAAATTACTTAGTCTAATC
1 ACCAATTTACTTAATTACACCGAATTAAGTTGATTACCAAATTACTTAATTTAATC
* * * *
70961 TCCAATTTTCTTAATTACACCGAATTAAGTTGATTACCAAATTACTTAACTTAATT
1 ACCAATTTACTTAATTACACCGAATTAAGTTGATTACCAAATTACTTAATTTAATC
* * *
71017 TCCAA-TTACTTAATTACGCCGAATTAAGTTGATTACCAAATTACTTAATTTAATT
1 ACCAATTTACTTAATTACACCGAATTAAGTTGATTACCAAATTACTTAATTTAATC
*
71072 ACCAATTTACTTAATTACACCGAATTAAGTTGATTACCAATTTACTTAATTTAATC
1 ACCAATTTACTTAATTACACCGAATTAAGTTGATTACCAAATTACTTAATTTAATC
71128 ACCAATTTACTTAATTACACCGAATTAAGTTGATTACCAAATTACTTAATTTAATC
1 ACCAATTTACTTAATTACACCGAATTAAGTTGATTACCAAATTACTTAATTTAATC
71184 ACCAATTTACTTAATTACACCGAATTAAGTTGATTACCAAATTACTTAATTTAATC
1 ACCAATTTACTTAATTACACCGAATTAAGTTGATTACCAAATTACTTAATTTAATC
71240 ACC-----A---AATTACACCGAATTAAGTTGATTACCAAATTACTTAATT
1 ACCAATTTACTTAATTACACCGAATTAAGTTGATTACCAAATTACTTAATT
71283 ACCAATTTAC
Statistics
Matches: 304, Mismatches: 17, Indels: 10
0.92 0.05 0.03
Matches are distributed among these distances:
48 39 0.13
51 1 0.00
55 51 0.17
56 213 0.70
ACGTcount: A:0.38, C:0.19, G:0.06, T:0.37
Consensus pattern (56 bp):
ACCAATTTACTTAATTACACCGAATTAAGTTGATTACCAAATTACTTAATTTAATC
Found at i:71005 original size:27 final size:27
Alignment explanation
Indices: 70973--71060 Score: 72
Period size: 27 Copynumber: 3.2 Consensus size: 27
70963 CAATTTTCTT
70973 AATTACACCGAATTAAGTTGATTACCA
1 AATTACACCGAATTAAGTTGATTACCA
** * * **
71000 AATT--ACTTAACTTAATTTCCAATTACTT
1 AATTACACCGAA-TTAAGTT--GATTACCA
*
71028 AATTACGCCGAATTAAGTTGATTACCA
1 AATTACACCGAATTAAGTTGATTACCA
71055 AATTAC
1 AATTAC
71061 TTAATTTAAT
Statistics
Matches: 43, Mismatches: 13, Indels: 10
0.65 0.20 0.15
Matches are distributed among these distances:
25 4 0.09
26 6 0.14
27 15 0.35
28 9 0.21
29 6 0.14
30 3 0.07
ACGTcount: A:0.39, C:0.18, G:0.08, T:0.35
Consensus pattern (27 bp):
AATTACACCGAATTAAGTTGATTACCA
Found at i:71072 original size:21 final size:21
Alignment explanation
Indices: 71051--71249 Score: 98
Period size: 21 Copynumber: 10.5 Consensus size: 21
71041 TAAGTTGATT
*
71051 ACCAAATTACTTAATTTAATT
1 ACCAAATTACTTAATTTAATC
*
71072 ACCAATTTACTTAA-TT-A-C
1 ACCAAATTACTTAATTTAATC
* * * *
71090 ACC-GA--A-TTAAGTTGATT
1 ACCAAATTACTTAATTTAATC
*
71107 ACCAATTTACTTAATTTAATC
1 ACCAAATTACTTAATTTAATC
*
71128 ACCAATTTACTTAA-TT-A-C
1 ACCAAATTACTTAATTTAATC
* * * *
71146 ACC-GA--A-TTAAGTTGATT
1 ACCAAATTACTTAATTTAATC
71163 ACCAAATTACTTAATTTAATC
1 ACCAAATTACTTAATTTAATC
*
71184 ACCAATTTACTTAA-TT-A-C
1 ACCAAATTACTTAATTTAATC
* * * *
71202 ACC-GA--A-TTAAGTTGATT
1 ACCAAATTACTTAATTTAATC
71219 ACCAAATTACTTAATTTAATC
1 ACCAAATTACTTAATTTAATC
71240 ACCAAATTAC
1 ACCAAATTAC
71250 ACCGAATTAA
Statistics
Matches: 132, Mismatches: 25, Indels: 42
0.66 0.13 0.21
Matches are distributed among these distances:
14 12 0.09
15 9 0.07
16 3 0.02
17 9 0.07
18 13 0.10
19 3 0.02
20 9 0.07
21 74 0.56
ACGTcount: A:0.40, C:0.18, G:0.05, T:0.38
Consensus pattern (21 bp):
ACCAAATTACTTAATTTAATC
Found at i:71108 original size:35 final size:35
Alignment explanation
Indices: 71061--71234 Score: 136
Period size: 35 Copynumber: 4.8 Consensus size: 35
71051 ACCAAATTAC
*
71061 TTAATTTAATTACCAATTTACTTAATTACACCGAA
1 TTAAGTTAATTACCAATTTACTTAATTACACCGAA
*
71096 TTAAGTTGATTACCAATTTACTTAATTTAATCACC-AA
1 TTAAGTTAATTACCAATTTACTTAA-TT-A-CACCGAA
* * * * * **
71133 TTTACTTAATTACACCGAATTAAGTTGATTAC-CAAATTA
1 TTAAGTTAATT--ACC-AATTTACTTAATTACACCGA--A
* *
71172 CTTAATTTAATCACCAATTTACTTAATTACACCGAA
1 -TTAAGTTAATTACCAATTTACTTAATTACACCGAA
* *
71208 TTAAGTTGATTACCAAATTACTTAATT
1 TTAAGTTAATTACCAATTTACTTAATT
71235 TAATCACCAA
Statistics
Matches: 107, Mismatches: 21, Indels: 22
0.71 0.14 0.15
Matches are distributed among these distances:
35 46 0.43
36 4 0.04
37 25 0.23
38 10 0.09
39 6 0.06
40 16 0.15
ACGTcount: A:0.39, C:0.17, G:0.05, T:0.40
Consensus pattern (35 bp):
TTAAGTTAATTACCAATTTACTTAATTACACCGAA
Found at i:71226 original size:27 final size:27
Alignment explanation
Indices: 71196--71276 Score: 93
Period size: 27 Copynumber: 3.2 Consensus size: 27
71186 CAATTTACTT
71196 AATTACACCGAATTAAGTTGATTACCA
1 AATTACACCGAATTAAGTTGATTACCA
* * *
71223 AATT--A-C---TTAATTTAATCACCA
1 AATTACACCGAATTAAGTTGATTACCA
71244 AATTACACCGAATTAAGTTGATTACCA
1 AATTACACCGAATTAAGTTGATTACCA
71271 AATTAC
1 AATTAC
71277 TTAATTACCA
Statistics
Matches: 42, Mismatches: 6, Indels: 12
0.70 0.10 0.20
Matches are distributed among these distances:
21 16 0.38
23 1 0.02
24 2 0.05
25 1 0.02
27 22 0.52
ACGTcount: A:0.42, C:0.19, G:0.07, T:0.32
Consensus pattern (27 bp):
AATTACACCGAATTAAGTTGATTACCA
Found at i:71296 original size:15 final size:16
Alignment explanation
Indices: 71264--71298 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
71254 AATTAAGTTG
71264 ATTACCAAATTACTTA
1 ATTACCAAATTACTTA
*
71280 ATTACCAATTTAC-TA
1 ATTACCAAATTACTTA
71295 ATTA
1 ATTA
71299 ATTCCTTTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 6 0.33
16 12 0.67
ACGTcount: A:0.43, C:0.17, G:0.00, T:0.40
Consensus pattern (16 bp):
ATTACCAAATTACTTA
Found at i:71311 original size:29 final size:28
Alignment explanation
Indices: 71277--71336 Score: 84
Period size: 29 Copynumber: 2.1 Consensus size: 28
71267 ACCAAATTAC
*
71277 TTAATTACCAATTTACTAATTAATTCCTT
1 TTAATTACCAATTTACTAATT-ATTACTT
* *
71306 TTAATTACCGATTTACTGATTATTACTT
1 TTAATTACCAATTTACTAATTATTACTT
71334 TTA
1 TTA
71337 CCTTGACTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
28 9 0.32
29 19 0.68
ACGTcount: A:0.32, C:0.15, G:0.03, T:0.50
Consensus pattern (28 bp):
TTAATTACCAATTTACTAATTATTACTT
Found at i:71398 original size:19 final size:19
Alignment explanation
Indices: 71374--71437 Score: 67
Period size: 19 Copynumber: 3.4 Consensus size: 19
71364 ATTACTATTT
71374 TTTTACTCTTAATTATCAA
1 TTTTACTCTTAATTATCAA
* * *
71393 TTTTACTGATT-ATTATTAC
1 TTTTACT-CTTAATTATCAA
* *
71412 TTTGATTCTTAATTATCAA
1 TTTTACTCTTAATTATCAA
71431 TTTTACT
1 TTTTACT
71438 GATTACTATT
Statistics
Matches: 33, Mismatches: 10, Indels: 4
0.70 0.21 0.09
Matches are distributed among these distances:
18 2 0.06
19 29 0.88
20 2 0.06
ACGTcount: A:0.28, C:0.12, G:0.03, T:0.56
Consensus pattern (19 bp):
TTTTACTCTTAATTATCAA
Found at i:71428 original size:38 final size:38
Alignment explanation
Indices: 71327--71473 Score: 192
Period size: 38 Copynumber: 3.9 Consensus size: 38
71317 TTTACTGATT
* * *
71327 ATTACTTTTACCTTGACTT-TTAATTATCGA-TTTACTG
1 ATTACTATTACTTTGA-TTCTTAATTATCAATTTTACTG
* * *
71364 ATTACTATT-TTTTTACTCTTAATTATCAATTTTACTG
1 ATTACTATTACTTTGATTCTTAATTATCAATTTTACTG
*
71401 ATTATTATTACTTTGATTCTTAATTATCAATTTTACTG
1 ATTACTATTACTTTGATTCTTAATTATCAATTTTACTG
*
71439 ATTACTATTGCTTTGATTCTTAATTATCAATTTTA
1 ATTACTATTACTTTGATTCTTAATTATCAATTTTA
71474 TTGGGGTACT
Statistics
Matches: 95, Mismatches: 12, Indels: 5
0.85 0.11 0.04
Matches are distributed among these distances:
35 1 0.01
36 13 0.14
37 23 0.24
38 58 0.61
ACGTcount: A:0.27, C:0.13, G:0.05, T:0.54
Consensus pattern (38 bp):
ATTACTATTACTTTGATTCTTAATTATCAATTTTACTG
Found at i:71490 original size:76 final size:74
Alignment explanation
Indices: 71346--71490 Score: 166
Period size: 76 Copynumber: 1.9 Consensus size: 74
71336 ACCTTGACTT
* * * * * **
71346 TTAATTATCGATTTACTGATTACTATTTTTTTACTCTTAATTATCAATTTTACTGATTATTATTA
1 TTAATTATCAATTTACTGATTACTATTCTTTGACTCTTAATTATCAATTTTACTGAGTACTAGGA
71411 CTTTGATTC
66 CTTTGATTC
* * *
71420 TTAATTATCAATTTTACTGATTACTATTGCTTTGATTCTTAATTATCAATTTTATTGGGGTACT-
1 TTAATTATCAA-TTTACTGATTACTATT-CTTTGACTCTTAATTATCAATTTTACT-GAGTACTA
71484 GGACTTT
63 GGACTTT
71491 AAGTGCATGG
Statistics
Matches: 58, Mismatches: 10, Indels: 4
0.81 0.14 0.06
Matches are distributed among these distances:
74 10 0.17
75 16 0.28
76 28 0.48
77 4 0.07
ACGTcount: A:0.26, C:0.12, G:0.09, T:0.53
Consensus pattern (74 bp):
TTAATTATCAATTTACTGATTACTATTCTTTGACTCTTAATTATCAATTTTACTGAGTACTAGGA
CTTTGATTC
Found at i:72102 original size:14 final size:14
Alignment explanation
Indices: 72083--72114 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
72073 TAACTTTGAC
72083 TTATCATGAATCTA
1 TTATCATGAATCTA
72097 TTATCATGAATCTA
1 TTATCATGAATCTA
72111 TTAT
1 TTAT
72115 TATATTATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.34, C:0.12, G:0.06, T:0.47
Consensus pattern (14 bp):
TTATCATGAATCTA
Found at i:72653 original size:33 final size:33
Alignment explanation
Indices: 72575--72679 Score: 106
Period size: 33 Copynumber: 3.2 Consensus size: 33
72565 TTGCAAAGAG
* * * *
72575 TGTTTTAGATGTTGTTTGCGATGATACTAAAGC
1 TGTTTTAGGTGTTGTTTTCGATGAAACTAAATC
** * *
72608 TAATTT-GAGTGTTGTTTTCAATGACACTAAATC
1 TGTTTTAG-GTGTTGTTTTCGATGAAACTAAATC
72641 TGTTTTAGGTGTTGTTTGT-GATGAAACTAAATC
1 TGTTTTAGGTGTTGTTT-TCGATGAAACTAAATC
72674 TGTTTT
1 TGTTTT
72680 GGATGCTAAT
Statistics
Matches: 58, Mismatches: 11, Indels: 6
0.77 0.15 0.08
Matches are distributed among these distances:
32 1 0.02
33 55 0.95
34 2 0.03
ACGTcount: A:0.25, C:0.09, G:0.21, T:0.46
Consensus pattern (33 bp):
TGTTTTAGGTGTTGTTTTCGATGAAACTAAATC
Found at i:72693 original size:33 final size:32
Alignment explanation
Indices: 72628--72713 Score: 93
Period size: 33 Copynumber: 2.6 Consensus size: 32
72618 GTTGTTTTCA
* * **
72628 ATGACACTAAATCTGTTTTAGGTGTTGTTTGTG
1 ATGAAACTAAATCTGTTTT-GGTGCTAATTGTG
72661 ATGAAACTAAATCTGTTTTGGATGCTAATTGTG
1 ATGAAACTAAATCTGTTTTGG-TGCTAATTGTG
*
72694 ATGTAAAC-AAATCTATTTTG
1 ATG-AAACTAAATCTGTTTTG
72714 ATTGATCATA
Statistics
Matches: 46, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
32 2 0.04
33 40 0.87
34 4 0.09
ACGTcount: A:0.29, C:0.09, G:0.20, T:0.42
Consensus pattern (32 bp):
ATGAAACTAAATCTGTTTTGGTGCTAATTGTG
Found at i:72746 original size:33 final size:33
Alignment explanation
Indices: 72709--72813 Score: 156
Period size: 33 Copynumber: 3.2 Consensus size: 33
72699 AACAAATCTA
* *
72709 TTTTGATTGATCATAGCATTGCAAATAATTCTG
1 TTTTGGTTGATCATAACATTGCAAATAATTCTG
*
72742 TTTTGGTTGATCATAACATTGCAAATAATTCTA
1 TTTTGGTTGATCATAACATTGCAAATAATTCTG
* * *
72775 TTTTGGTTGATCATAATATTGAAAATAATTCCG
1 TTTTGGTTGATCATAACATTGCAAATAATTCTG
72808 TTTTGG
1 TTTTGG
72814 GTGAAAAGAA
Statistics
Matches: 65, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 65 1.00
ACGTcount: A:0.30, C:0.10, G:0.15, T:0.44
Consensus pattern (33 bp):
TTTTGGTTGATCATAACATTGCAAATAATTCTG
Found at i:73518 original size:6 final size:6
Alignment explanation
Indices: 73492--73533 Score: 54
Period size: 6 Copynumber: 7.5 Consensus size: 6
73482 AGGTTTAGTA
*
73492 TTTTC- TTTTC- TTTTC- TTTTCT TTTTCT GTTTCT TTTTCT TTT
1 TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT TTT
73534 CTTCTTCTCT
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
5 15 0.44
6 19 0.56
ACGTcount: A:0.00, C:0.17, G:0.02, T:0.81
Consensus pattern (6 bp):
TTTTCT
Found at i:73532 original size:23 final size:21
Alignment explanation
Indices: 73492--73541 Score: 73
Period size: 23 Copynumber: 2.3 Consensus size: 21
73482 AGGTTTAGTA
73492 TTTTCTTTTCTTTTCTTTTCT
1 TTTTCTTTTCTTTTCTTTTCT
73513 TTTTCTGTTTCTTTTTCTTTTCT
1 TTTTCT-TTTC-TTTTCTTTTCT
*
73536 TCTTCT
1 TTTTCT
73542 CTCCTCGATA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
21 6 0.23
22 4 0.15
23 16 0.62
ACGTcount: A:0.00, C:0.20, G:0.02, T:0.78
Consensus pattern (21 bp):
TTTTCTTTTCTTTTCTTTTCT
Found at i:73541 original size:6 final size:5
Alignment explanation
Indices: 73492--73541 Score: 64
Period size: 5 Copynumber: 9.2 Consensus size: 5
73482 AGGTTTAGTA
73492 TTTTC TTTTC TTTTC TTTTC TTTTTC TGTTTC TTTTTC TTTTC TTCTTC
1 TTTTC TTTTC TTTTC TTTTC -TTTTC T-TTTC -TTTTC TTTTC TT-TTC
73541 T
1 T
73542 CTCCTCGATA
Statistics
Matches: 41, Mismatches: 0, Indels: 7
0.85 0.00 0.15
Matches are distributed among these distances:
5 23 0.56
6 17 0.41
7 1 0.02
ACGTcount: A:0.00, C:0.20, G:0.02, T:0.78
Consensus pattern (5 bp):
TTTTC
Found at i:76451 original size:46 final size:46
Alignment explanation
Indices: 76384--76490 Score: 151
Period size: 46 Copynumber: 2.3 Consensus size: 46
76374 TGAACAAATC
* * *
76384 TGATTCACCGAATCAAACTTTGAAGAAATACTGCAATGCAGTAACT
1 TGATTCACTGAATCAAACTTTGAAGAAATACTGCAACGCACTAACT
* * *
76430 TGATTCACTGAATCAAACTTTGAAGCAATAGTGCACCGCACTAACT
1 TGATTCACTGAATCAAACTTTGAAGAAATACTGCAACGCACTAACT
*
76476 TGATCCACTGAATCA
1 TGATTCACTGAATCA
76491 CTCTGAACTG
Statistics
Matches: 54, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
46 54 1.00
ACGTcount: A:0.36, C:0.22, G:0.15, T:0.26
Consensus pattern (46 bp):
TGATTCACTGAATCAAACTTTGAAGAAATACTGCAACGCACTAACT
Found at i:76775 original size:90 final size:91
Alignment explanation
Indices: 76434--77200 Score: 848
Period size: 91 Copynumber: 8.6 Consensus size: 91
76424 GTAACTTGAT
* * * * * *
76434 TCACTGAAT-CAAACTTTGAAGCAATAGTGCACCGCAC-TAACTTGATCCACTGAATCA-CTCTG
1 TCACCGAATCCAATCTTTGAAGAAATAATGCACCGC-CTTAACTTGATTCACCGAATCATC-CTG
* **
76496 AACTGTCTGAAAACGTGCTGCACCGAGC
64 AACTGTTTGAAAATATGCTGCACCGAGC
* ** * * *
76524 TCACCGACTTCCAATCTTTGAAG--A-AATGCACTACATCAACTTGATTCACCGAATCATCCCGA
1 TCACCGA-ATCCAATCTTTGAAGAAATAATGCACCGCCTTAACTTGATTCACCGAATCATCCTGA
* *
76586 ACTGTTTGAGAATTTGCTGCACCGAGC
65 ACTGTTTGAAAATATGCTGCACCGAGC
* * *
76613 TCACCGAATTCCAATCTTTGAAG--AT-ATGCACCGCATTAACTTGATTCACCGAACCATCCCGA
1 TCACCGAA-TCCAATCTTTGAAGAAATAATGCACCGCCTTAACTTGATTCACCGAATCATCCTGA
*
76675 ACTGTTTGAAAATTTGCTGCACCGAGC
65 ACTGTTTGAAAATATGCTGCACCGAGC
* * * * * *
76702 TCACTGAATCTAATC-TTGAAGAAATAAGGCATCGCCTCAACTTGATTCACCGAATCATCCTAAA
1 TCACCGAATCCAATCTTTGAAGAAATAATGCACCGCCTTAACTTGATTCACCGAATCATCCTGAA
* * * *
76766 CTGTCTGAAAATCTACTGCATCGAGC
66 CTGTTTGAAAATATGCTGCACCGAGC
* * *
76792 TCACCGAATCCAATC-TTGAAGAAATAAGGCACCGCCTCAACTTGATTCACCGAATCATCCCGAA
1 TCACCGAATCCAATCTTTGAAGAAATAATGCACCGCCTTAACTTGATTCACCGAATCATCCTGAA
*
76856 CTGTTTGAAAATTTGCTGCACC--G-
66 CTGTTTGAAAATATGCTGCACCGAGC
* * *
76879 --A---ATTCCAATCTTTGAAG--A-AATGCACCGCAC-TAACTTGATTCACCGAATCGTCCTAA
1 TCACCGAATCCAATCTTTGAAGAAATAATGCACCGC-CTTAACTTGATTCACCGAATCATCCTGA
*
76935 ACTGTTTGAAAATATGTTGCACCGAGC
65 ACTGTTTGAAAATATGCTGCACCGAGC
* *
76962 TCACCGAATCTAA-CTTTAGAAGAAATAATGCACCGCCTTAACTTGATTCACCGAATCGTCCTGA
1 TCACCGAATCCAATCTTT-GAAGAAATAATGCACCGCCTTAACTTGATTCACCGAATCATCCTGA
*
77026 ATTGTTTGAAAATATGCTGCACCGAGC
65 ACTGTTTGAAAATATGCTGCACCGAGC
* * *
77053 TCACCGAATCCAA-CTTTAGATGAAATAATGCACCGCCTTGACTTGATTCACCGAATCGTCCTGA
1 TCACCGAATCCAATCTTT-GAAGAAATAATGCACCGCCTTAACTTGATTCACCGAATCATCCTGA
*
77117 ATTGTTTGAAAATATGCTGCACCGAGC
65 ACTGTTTGAAAATATGCTGCACCGAGC
* *
77144 TCACCGAATCCAA-CTTTAGAAGAAATAATGCACCGCTTTAACTTGATTCACTGAATC
1 TCACCGAATCCAATCTTT-GAAGAAATAATGCACCGCCTTAACTTGATTCACCGAATC
77201 CAATTTTGGA
Statistics
Matches: 590, Mismatches: 63, Indels: 47
0.84 0.09 0.07
Matches are distributed among these distances:
80 52 0.09
81 2 0.00
82 9 0.02
83 6 0.01
85 2 0.00
87 10 0.02
88 16 0.03
89 140 0.24
90 140 0.24
91 202 0.34
92 11 0.02
ACGTcount: A:0.31, C:0.26, G:0.16, T:0.26
Consensus pattern (91 bp):
TCACCGAATCCAATCTTTGAAGAAATAATGCACCGCCTTAACTTGATTCACCGAATCATCCTGAA
CTGTTTGAAAATATGCTGCACCGAGC
Found at i:77062 original size:44 final size:44
Alignment explanation
Indices: 77009--77153 Score: 113
Period size: 44 Copynumber: 3.2 Consensus size: 44
76999 TTAACTTGAT
77009 TCACCGAATCGTCCTGAATTGTTTGAAAATATGCTGCACCGAGC
1 TCACCGAATCGTCCTGAATTGTTTGAAAATATGCTGCACCGAGC
* * ** * *
77053 TCACCGAA---TCC--AACT-TTAGATGAAATAATGCACCGCCTTGACTTGAT
1 TCACCGAATCGTCCTGAATTGTTTGA--AAAT-ATGCTGCACC--GA---G-C
77100 TCACCGAATCGTCCTGAATTGTTTGAAAATATGCTGCACCGAGC
1 TCACCGAATCGTCCTGAATTGTTTGAAAATATGCTGCACCGAGC
77144 TCACCGAATC
1 TCACCGAATC
77154 CAACTTTAGA
Statistics
Matches: 74, Mismatches: 12, Indels: 30
0.64 0.10 0.26
Matches are distributed among these distances:
38 4 0.05
39 3 0.04
40 4 0.05
41 10 0.14
43 2 0.03
44 18 0.24
45 1 0.01
46 1 0.01
47 8 0.11
48 2 0.03
50 10 0.14
51 4 0.05
52 3 0.04
53 4 0.05
ACGTcount: A:0.29, C:0.26, G:0.18, T:0.27
Consensus pattern (44 bp):
TCACCGAATCGTCCTGAATTGTTTGAAAATATGCTGCACCGAGC
Found at i:77285 original size:85 final size:86
Alignment explanation
Indices: 77187--77369 Score: 210
Period size: 85 Copynumber: 2.1 Consensus size: 86
77177 CGCTTTAACT
* * * * * * * *
77187 TGATTCACTGAATCCAATTTTG-GAGATGCTACGCTGAGTCATCAAATTCACCGAATCCAGCTT-
1 TGATTCACCGAATCCAACTATGAG-GAAGCTACACCGAGTCATCAAATTCACCCAATCCAACTTA
*
77250 GAAGAT-TTTACACCGAGTCATC
65 GAAGATGCTT-CACCGAGTCATC
* * **
77272 TGATTCACCGAATCCACCTATGAGGAAGCTACACCGATTCATCTGATTCACCCAATCCAACTTAG
1 TGATTCACCGAATCCAACTATGAGGAAGCTACACCGAGTCATCAAATTCACCCAATCCAACTTAG
77337 AAGATGCTTCACCGAGTCATC
66 AAGATGCTTCACCGAGTCATC
77358 TGATTCACCGAA
1 TGATTCACCGAA
77370 ACACTTGAGG
Statistics
Matches: 82, Mismatches: 13, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
85 49 0.60
86 31 0.38
87 2 0.02
ACGTcount: A:0.30, C:0.27, G:0.16, T:0.27
Consensus pattern (86 bp):
TGATTCACCGAATCCAACTATGAGGAAGCTACACCGAGTCATCAAATTCACCCAATCCAACTTAG
AAGATGCTTCACCGAGTCATC
Found at i:77315 original size:43 final size:42
Alignment explanation
Indices: 77187--77369 Score: 195
Period size: 43 Copynumber: 4.3 Consensus size: 42
77177 CGCTTTAACT
* * * * *
77187 TGATTCACTGAATCCAATTTTGGAGATGCTACGCTGAGTCATC
1 TGATTCACCGAATCCAA-CTTGAAGATGCTACACCGAGTCATC
** * **
77230 AAATTCACCGAATCCAGCTTGAAGATTTTACACCGAGTCATC
1 TGATTCACCGAATCCAACTTGAAGATGCTACACCGAGTCATC
* * * *
77272 TGATTCACCGAATCCACCTATGAGGAAGCTACACCGATTCATC
1 TGATTCACCGAATCCAACT-TGAAGATGCTACACCGAGTCATC
* *
77315 TGATTCACCCAATCCAACTTAGAAGATGCTTCACCGAGTCATC
1 TGATTCACCGAATCCAACTT-GAAGATGCTACACCGAGTCATC
77358 TGATTCACCGAA
1 TGATTCACCGAA
77370 ACACTTGAGG
Statistics
Matches: 113, Mismatches: 25, Indels: 4
0.80 0.18 0.03
Matches are distributed among these distances:
42 36 0.32
43 77 0.68
ACGTcount: A:0.30, C:0.27, G:0.16, T:0.27
Consensus pattern (42 bp):
TGATTCACCGAATCCAACTTGAAGATGCTACACCGAGTCATC
Found at i:77465 original size:54 final size:54
Alignment explanation
Indices: 77397--78087 Score: 1042
Period size: 54 Copynumber: 12.8 Consensus size: 54
77387 TAATTGACCG
* * * *
77397 CACTGCAAACTTTCTTGACTGACCACACTGGACCACTTGAAGATAAACTTAAAC
1 CACTGGAAACTTTCTTGATTGACCGCACTGGATCACTTGAAGATAAACTTAAAC
77451 CACTGGAAACTTTCTTGATTGACCGCACTGGATCACTTGAAGATAAACTTAAAC
1 CACTGGAAACTTTCTTGATTGACCGCACTGGATCACTTGAAGATAAACTTAAAC
* *
77505 CACTGGAAACTTTCTTGACTGACCGCACTGGATCACTTGAAGATAAACCTAAAC
1 CACTGGAAACTTTCTTGATTGACCGCACTGGATCACTTGAAGATAAACTTAAAC
* * *
77559 CACTATG-AACTTTCTTAATTGACCGCACTGGATCACTTGAAAATAAACTTAATAC
1 CACT-GGAAACTTTCTTGATTGACCGCACTGGATCACTTGAAGATAAACTTAA-AC
* * *
77614 CACTGGAAACTTTCTTGATTGACTGCACTGGATCACTTAAAGGTAAACTTAAAC
1 CACTGGAAACTTTCTTGATTGACCGCACTGGATCACTTGAAGATAAACTTAAAC
* *
77668 CATTGGAAACTTTCTTGATTGACCGCACTGGATCACTTGAATATAAACTTAAAC
1 CACTGGAAACTTTCTTGATTGACCGCACTGGATCACTTGAAGATAAACTTAAAC
* * ***
77722 CACTAGAAACTTTTTTGACCAACCGCACTGGATCACTTGAAGATAAACTTAAAC
1 CACTGGAAACTTTCTTGATTGACCGCACTGGATCACTTGAAGATAAACTTAAAC
*
77776 CACTGCAAACTTTCTTGATTGACCGCACTGGATCACTTGAAGATAAACTTAAAC
1 CACTGGAAACTTTCTTGATTGACCGCACTGGATCACTTGAAGATAAACTTAAAC
* * *
77830 AATTGGAAACTTTCTTGATTGACCGCACTGGATCACTTGAATATAAACTTAAAC
1 CACTGGAAACTTTCTTGATTGACCGCACTGGATCACTTGAAGATAAACTTAAAC
* * * *
77884 AATTGGAAACTTTCTTGATTAACCGCACTGAATCACTTGAAGATAAACTTAAAC
1 CACTGGAAACTTTCTTGATTGACCGCACTGGATCACTTGAAGATAAACTTAAAC
* * *
77938 CACTGGAGACTTTCTTAATTGACCGCACTGGATCACTTTGAGGATAAACTTAAAC
1 CACTGGAAACTTTCTTGATTGACCGCACTGGATCAC-TTGAAGATAAACTTAAAC
* * *
77993 CACTGGAAACTTTCTTGATTGACCGTACTGAATCACTTAAAGATAAACTTAAAC
1 CACTGGAAACTTTCTTGATTGACCGCACTGGATCACTTGAAGATAAACTTAAAC
*
78047 CATTGGAAACTTTCTTGATTGACCGCACTGGATCACTTGAA
1 CACTGGAAACTTTCTTGATTGACCGCACTGGATCACTTGAA
78088 ACTCGGCTAA
Statistics
Matches: 574, Mismatches: 59, Indels: 8
0.90 0.09 0.01
Matches are distributed among these distances:
54 478 0.83
55 96 0.17
ACGTcount: A:0.34, C:0.22, G:0.15, T:0.29
Consensus pattern (54 bp):
CACTGGAAACTTTCTTGATTGACCGCACTGGATCACTTGAAGATAAACTTAAAC
Found at i:77778 original size:217 final size:215
Alignment explanation
Indices: 77397--78087 Score: 1033
Period size: 217 Copynumber: 3.2 Consensus size: 215
77387 TAATTGACCG
* * * * *
77397 CACTGCAAACTTTCTTGACTGACCACACTGGACCACTTGAAGATAAACTTAAACCACTGGAAACT
1 CACTGGAAACTTTCTTGATTGACCGCACTGGATCACTTGAAGATAAACTTAAACCATTGGAAACT
77462 TTCTTGATTGACCGCACTGGATCACTTGAAGATAAACTTAAACCACTGGAAACTTTCTTGACTGA
66 TTCTTGATTGACCGCACTGGATCACTTGAAGATAAACTTAAACCACTGGAAACTTTCTTGACTGA
* * *
77527 CCGCACTGGATCACTTGAAGATAAACCTAAACCACTATGAACTTTCTTAATTGACCGCACTGGAT
131 CCGCACTGGATCACTTGAAGATAAACTTAAACCACT-CGAACTTTCTTGATTGACCGCACTGGAT
77592 CACTTGAAAATAAACTTAATAC
195 CACTTGAAAATAAACTTAA-AC
* * *
77614 CACTGGAAACTTTCTTGATTGACTGCACTGGATCACTTAAAGGTAAACTTAAACCATTGGAAACT
1 CACTGGAAACTTTCTTGATTGACCGCACTGGATCACTTGAAGATAAACTTAAACCATTGGAAACT
* * * **
77679 TTCTTGATTGACCGCACTGGATCACTTGAATATAAACTTAAACCACTAGAAACTTTTTTGACCAA
66 TTCTTGATTGACCGCACTGGATCACTTGAAGATAAACTTAAACCACTGGAAACTTTCTTGACTGA
*
77744 CCGCACTGGATCACTTGAAGATAAACTTAAACCACTGCAAACTTTCTTGATTGACCGCACTGGAT
131 CCGCACTGGATCACTTGAAGATAAACTTAAACCACT-CGAACTTTCTTGATTGACCGCACTGGAT
*
77809 CACTTGAAGATAAACTTAAAC
195 CACTTGAAAATAAACTTAAAC
* * * *
77830 AATTGGAAACTTTCTTGATTGACCGCACTGGATCACTTGAATATAAACTTAAACAATTGGAAACT
1 CACTGGAAACTTTCTTGATTGACCGCACTGGATCACTTGAAGATAAACTTAAACCATTGGAAACT
* * * * *
77895 TTCTTGATTAACCGCACTGAATCACTTGAAGATAAACTTAAACCACTGGAGACTTTCTTAATTGA
66 TTCTTGATTGACCGCACTGGATCACTTGAAGATAAACTTAAACCACTGGAAACTTTCTTGACTGA
* * * *
77960 CCGCACTGGATCACTTTGAGGATAAACTTAAACCACTGGAAACTTTCTTGATTGACCGTACTGAA
131 CCGCACTGGATCAC-TTGAAGATAAACTTAAACCACTCG-AACTTTCTTGATTGACCGCACTGGA
78025 TCACTT-AAAGATAAACTTAAAC
194 TCACTTGAAA-ATAAACTTAAAC
*
78047 CATTGGAAACTTTCTTGATTGACCGCACTGGATCACTTGAA
1 CACTGGAAACTTTCTTGATTGACCGCACTGGATCACTTGAA
78088 ACTCGGCTAA
Statistics
Matches: 428, Mismatches: 43, Indels: 6
0.90 0.09 0.01
Matches are distributed among these distances:
216 131 0.31
217 297 0.69
ACGTcount: A:0.34, C:0.22, G:0.15, T:0.29
Consensus pattern (215 bp):
CACTGGAAACTTTCTTGATTGACCGCACTGGATCACTTGAAGATAAACTTAAACCATTGGAAACT
TTCTTGATTGACCGCACTGGATCACTTGAAGATAAACTTAAACCACTGGAAACTTTCTTGACTGA
CCGCACTGGATCACTTGAAGATAAACTTAAACCACTCGAACTTTCTTGATTGACCGCACTGGATC
ACTTGAAAATAAACTTAAAC
Found at i:80429 original size:14 final size:13
Alignment explanation
Indices: 80401--80458 Score: 55
Period size: 14 Copynumber: 4.3 Consensus size: 13
80391 TTAAAAACTC
*
80401 AAAATC-TTTTCG
1 AAAATCATTTTTG
80413 AAAACTCATTTTTG
1 AAAA-TCATTTTTG
*
80427 AAAATCTTTTCTTG
1 AAAATCATTT-TTG
*
80441 AAAATAATTTTTTG
1 AAAATCA-TTTTTG
80455 AAAA
1 AAAA
80459 ATGTCTCTTG
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
12 4 0.11
13 7 0.18
14 24 0.63
15 3 0.08
ACGTcount: A:0.40, C:0.10, G:0.07, T:0.43
Consensus pattern (13 bp):
AAAATCATTTTTG
Found at i:80452 original size:28 final size:26
Alignment explanation
Indices: 80401--80458 Score: 73
Period size: 28 Copynumber: 2.2 Consensus size: 26
80391 TTAAAAACTC
*
80401 AAAATCTTTTCGAAAACTCATTTTTG
1 AAAATCTTTTCGAAAACTAATTTTTG
80427 AAAATCTTTTCTTGAAAA-TAATTTTTTG
1 AAAATCTTTTC--GAAAACTAA-TTTTTG
80455 AAAA
1 AAAA
80459 ATGTCTCTTG
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
26 11 0.39
27 2 0.07
28 15 0.54
ACGTcount: A:0.40, C:0.10, G:0.07, T:0.43
Consensus pattern (26 bp):
AAAATCTTTTCGAAAACTAATTTTTG
Found at i:83151 original size:35 final size:35
Alignment explanation
Indices: 83102--83179 Score: 104
Period size: 35 Copynumber: 2.2 Consensus size: 35
83092 GAATTGCTGT
* * *
83102 TTTATTTAATTACACCGAATTAAGTT-AGTTACCAA
1 TTTACTTAACTACACCGAACTAAGTTGA-TTACCAA
83137 TTTACTTAACTACACCGAACTAAGTTGATTACCAA
1 TTTACTTAACTACACCGAACTAAGTTGATTACCAA
*
83172 ATTACTTA
1 TTTACTTA
83180 GTCTAATCTC
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
35 37 0.97
36 1 0.03
ACGTcount: A:0.37, C:0.18, G:0.08, T:0.37
Consensus pattern (35 bp):
TTTACTTAACTACACCGAACTAAGTTGATTACCAA
Found at i:83193 original size:56 final size:55
Alignment explanation
Indices: 83133--83564 Score: 621
Period size: 56 Copynumber: 7.9 Consensus size: 55
83123 AAGTTAGTTA
* * * *
83133 CCAATTTACTTAACTACACCGAACTAAGTTGATTACCAAATTACTTAGTCTAATCT
1 CCAATTTACTTAATTACACCGAATTAAGTTGATTACCAAATTACTTAATTTAAT-T
* *
83189 CCAATTTTCTTAATTACACCGAATTAAGTTGATTACCAAATTACTTAACTTAATTT
1 CCAATTTACTTAATTACACCGAATTAAGTTGATTACCAAATTACTTAATTTAA-TT
83245 CCAA-TTACTTAATTACACCGAATTAAGTTGATTACCAAATTACTTAATTTAATT
1 CCAATTTACTTAATTACACCGAATTAAGTTGATTACCAAATTACTTAATTTAATT
83299 ACCAATTTACTTAATTACACCGAATTAAGTTGATTACCAAATTACTTAATTTAATT
1 -CCAATTTACTTAATTACACCGAATTAAGTTGATTACCAAATTACTTAATTTAATT
* * * *
83355 ACCAATTTTCTTAATTATACCGAATTAAGTTGATTACCAAATTACTT-TTTTAATCA
1 -CCAATTTACTTAATTACACCGAATTAAGTTGATTACCAAATTACTTAATTTAAT-T
83411 CCAATTTACTTAATTACACCGAATTAAGTTGATTACCAAATTACTTAATTTAATT
1 CCAATTTACTTAATTACACCGAATTAAGTTGATTACCAAATTACTTAATTTAATT
*
83466 ACCAATTTACTTAATTACACTGAATTAAGTTGATTACCAAATTACTTAATTTAA-T
1 -CCAATTTACTTAATTACACCGAATTAAGTTGATTACCAAATTACTTAATTTAATT
** *
83521 -C-----ACCAAATTACACCGAATTATGTTGATTACCAAATTACTTAATT
1 CCAATTTACTTAATTACACCGAATTAAGTTGATTACCAAATTACTTAATT
83565 ACCAATTTAC
Statistics
Matches: 349, Mismatches: 21, Indels: 20
0.89 0.05 0.05
Matches are distributed among these distances:
48 39 0.11
53 1 0.00
54 2 0.01
55 101 0.29
56 205 0.59
57 1 0.00
ACGTcount: A:0.38, C:0.18, G:0.06, T:0.39
Consensus pattern (55 bp):
CCAATTTACTTAATTACACCGAATTAAGTTGATTACCAAATTACTTAATTTAATT
Found at i:83262 original size:111 final size:112
Alignment explanation
Indices: 83121--83564 Score: 674
Period size: 111 Copynumber: 4.1 Consensus size: 112
83111 TTACACCGAA
* * * * * *
83121 TTAAGTTAGTTACCAATTTACTTAACTACACCGAACTAAGTTGATTACCAAATTACTTAGTCTAA
1 TTAATTTAATTACCAATTTACTTAATTACACCGAATTAAGTTGATTACCAAATTACTTAATTTAA
* *
83186 TCTCCAATTTTCTTAATTACACCGAATTAAGTTGATTACCAAATTAC
66 TCACCAATTTACTTAATTACACCGAATTAAGTTGATTACCAAATTAC
* *
83233 TTAACTTAATTTCCAA-TTACTTAATTACACCGAATTAAGTTGATTACCAAATTACTTAATTTAA
1 TTAATTTAATTACCAATTTACTTAATTACACCGAATTAAGTTGATTACCAAATTACTTAATTTAA
*
83297 TTACCAATTTACTTAATTACACCGAATTAAGTTGATTACCAAATTAC
66 TCACCAATTTACTTAATTACACCGAATTAAGTTGATTACCAAATTAC
* * *
83344 TTAATTTAATTACCAATTTTCTTAATTATACCGAATTAAGTTGATTACCAAATTACTT-TTTTAA
1 TTAATTTAATTACCAATTTACTTAATTACACCGAATTAAGTTGATTACCAAATTACTTAATTTAA
83408 TCACCAATTTACTTAATTACACCGAATTAAGTTGATTACCAAATTAC
66 TCACCAATTTACTTAATTACACCGAATTAAGTTGATTACCAAATTAC
*
83455 TTAATTTAATTACCAATTTACTTAATTACACTGAATTAAGTTGATTACCAAATTACTTAATTTAA
1 TTAATTTAATTACCAATTTACTTAATTACACCGAATTAAGTTGATTACCAAATTACTTAATTTAA
*
83520 TCACC-----A---AATTACACCGAATTATGTTGATTACCAAATTAC
66 TCACCAATTTACTTAATTACACCGAATTAAGTTGATTACCAAATTAC
83559 TTAATT
1 TTAATT
83565 ACCAATTTAC
Statistics
Matches: 309, Mismatches: 21, Indels: 12
0.90 0.06 0.04
Matches are distributed among these distances:
104 38 0.12
107 1 0.00
111 208 0.67
112 62 0.20
ACGTcount: A:0.38, C:0.17, G:0.06, T:0.39
Consensus pattern (112 bp):
TTAATTTAATTACCAATTTACTTAATTACACCGAATTAAGTTGATTACCAAATTACTTAATTTAA
TCACCAATTTACTTAATTACACCGAATTAAGTTGATTACCAAATTAC
Found at i:83330 original size:167 final size:168
Alignment explanation
Indices: 83121--83562 Score: 672
Period size: 167 Copynumber: 2.7 Consensus size: 168
83111 TTACACCGAA
* * * * * *
83121 TTAAGTTAGTTACCAATTTACTTAACTACACCGAACTAAGTTGATTACCAAATTACTTAGTCTAA
1 TTAATTTAATTACCAATTTACTTAATTACACCGAATTAAGTTGATTACCAAATTACTTAATTTAA
**
83186 TCTCCAATTTTCTTAATTACACCGAATTAAGTTGATTACCAAATTACTTAACTTAATTTCCAA-T
66 TCTCCAATTTTCTTAATTACACCGAATTAAGTTGATTACCAAATTACTTAACTTAATCACCAATT
83250 TACTTAATTACACCGAATTAAGTTGATTACCAAATTAC
131 TACTTAATTACACCGAATTAAGTTGATTACCAAATTAC
83288 TTAATTTAATTACCAATTTACTTAATTACACCGAATTAAGTTGATTACCAAATTACTTAATTTAA
1 TTAATTTAATTACCAATTTACTTAATTACACCGAATTAAGTTGATTACCAAATTACTTAATTTAA
* **
83353 T-TACCAATTTTCTTAATTATACCGAATTAAGTTGATTACCAAATTACTT-TTTTAATCACCAAT
66 TCT-CCAATTTTCTTAATTACACCGAATTAAGTTGATTACCAAATTACTTAACTTAATCACCAAT
83416 TTACTTAATTACACCGAATTAAGTTGATTACCAAATTAC
130 TTACTTAATTACACCGAATTAAGTTGATTACCAAATTAC
*
83455 TTAATTTAATTACCAATTTACTTAATTACACTGAATTAAGTTGATTACCAAATTACTTAATTTAA
1 TTAATTTAATTACCAATTTACTTAATTACACCGAATTAAGTTGATTACCAAATTACTTAATTTAA
* *
83520 TCACC-A-------AATTACACCGAATTATGTTGATTACCAAATTACTTAA
66 TCTCCAATTTTCTTAATTACACCGAATTAAGTTGATTACCAAATTACTTAA
83563 TTACCAATTT
Statistics
Matches: 255, Mismatches: 16, Indels: 15
0.89 0.06 0.05
Matches are distributed among these distances:
159 33 0.13
166 11 0.04
167 211 0.83
ACGTcount: A:0.38, C:0.17, G:0.06, T:0.39
Consensus pattern (168 bp):
TTAATTTAATTACCAATTTACTTAATTACACCGAATTAAGTTGATTACCAAATTACTTAATTTAA
TCTCCAATTTTCTTAATTACACCGAATTAAGTTGATTACCAAATTACTTAACTTAATCACCAATT
TACTTAATTACACCGAATTAAGTTGATTACCAAATTAC
Found at i:83578 original size:15 final size:16
Alignment explanation
Indices: 83546--83580 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
83536 AATTATGTTG
83546 ATTACCAAATTACTTA
1 ATTACCAAATTACTTA
*
83562 ATTACCAATTTAC-TA
1 ATTACCAAATTACTTA
83577 ATTA
1 ATTA
83581 ATCCCTTTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 6 0.33
16 12 0.67
ACGTcount: A:0.43, C:0.17, G:0.00, T:0.40
Consensus pattern (16 bp):
ATTACCAAATTACTTA
Found at i:83718 original size:38 final size:39
Alignment explanation
Indices: 83599--83719 Score: 156
Period size: 38 Copynumber: 3.1 Consensus size: 39
83589 TAATTACCGA
* *
83599 TTTACTGATTATTACTTTTACCTTGACTCTTAATTATCGA-
1 TTTACTGATTATTA--TTTACTTTGACTCTTAATTATCAAT
* **
83639 TTTACTGATTACTATTTTTTTTGACTCTTAATTATCAAT
1 TTTACTGATTATTATTTACTTTGACTCTTAATTATCAAT
*
83678 TTTACTGATTATTA-TTACTTTGATTCTTAATTATCAAT
1 TTTACTGATTATTATTTACTTTGACTCTTAATTATCAAT
83716 TTTA
1 TTTA
83720 TTGGGGTACT
Statistics
Matches: 71, Mismatches: 9, Indels: 4
0.85 0.11 0.05
Matches are distributed among these distances:
38 45 0.63
39 13 0.18
40 13 0.18
ACGTcount: A:0.26, C:0.13, G:0.06, T:0.55
Consensus pattern (39 bp):
TTTACTGATTATTATTTACTTTGACTCTTAATTATCAAT
Found at i:84307 original size:12 final size:11
Alignment explanation
Indices: 84287--84318 Score: 55
Period size: 12 Copynumber: 2.8 Consensus size: 11
84277 TATTTTCTTA
84287 TCTTTTCTTTT
1 TCTTTTCTTTT
84298 TCTGTTTCTTTT
1 TCT-TTTCTTTT
84310 TCTTTTCTT
1 TCTTTTCTT
84319 CTACTCTCCT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 9 0.45
12 11 0.55
ACGTcount: A:0.00, C:0.19, G:0.03, T:0.78
Consensus pattern (11 bp):
TCTTTTCTTTT
Found at i:88889 original size:13 final size:12
Alignment explanation
Indices: 88864--88895 Score: 55
Period size: 13 Copynumber: 2.6 Consensus size: 12
88854 GGAGGCAACC
88864 TAATTTTAATTT
1 TAATTTTAATTT
88876 TAATTTTCAATTT
1 TAATTTT-AATTT
88889 TAATTTT
1 TAATTTT
88896 TAGGTTTTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 7 0.37
13 12 0.63
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.66
Consensus pattern (12 bp):
TAATTTTAATTT
Found at i:88897 original size:7 final size:6
Alignment explanation
Indices: 88864--88895 Score: 55
Period size: 6 Copynumber: 5.2 Consensus size: 6
88854 GGAGGCAACC
88864 TAATTT TAATTT TAATTT TCAATTT TAATTT T
1 TAATTT TAATTT TAATTT T-AATTT TAATTT T
88896 TAGGTTTTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
6 19 0.76
7 6 0.24
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.66
Consensus pattern (6 bp):
TAATTT
Found at i:91139 original size:19 final size:18
Alignment explanation
Indices: 91115--91152 Score: 58
Period size: 19 Copynumber: 2.1 Consensus size: 18
91105 TTGAAGACAT
91115 ATTTGAAGATAATTTGAAG
1 ATTTGAAGATAA-TTGAAG
*
91134 ATTTGAAGATCATTGAAG
1 ATTTGAAGATAATTGAAG
91152 A
1 A
91153 ATTATTTCCA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 7 0.39
19 11 0.61
ACGTcount: A:0.42, C:0.03, G:0.21, T:0.34
Consensus pattern (18 bp):
ATTTGAAGATAATTGAAG
Found at i:92670 original size:12 final size:12
Alignment explanation
Indices: 92653--92679 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
92643 CGACCGATCA
92653 CGACGGATATAT
1 CGACGGATATAT
92665 CGACGGATATAT
1 CGACGGATATAT
92677 CGA
1 CGA
92680 GATATCGATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.33, C:0.19, G:0.26, T:0.22
Consensus pattern (12 bp):
CGACGGATATAT
Found at i:93763 original size:3 final size:3
Alignment explanation
Indices: 93755--93790 Score: 65
Period size: 3 Copynumber: 12.3 Consensus size: 3
93745 TCATTTCCCC
93755 CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CA- CAT C
1 CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT C
93791 TTCGGTGAGC
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.06
3 30 0.94
ACGTcount: A:0.33, C:0.36, G:0.00, T:0.31
Consensus pattern (3 bp):
CAT
Found at i:94180 original size:20 final size:21
Alignment explanation
Indices: 94157--94202 Score: 51
Period size: 20 Copynumber: 2.3 Consensus size: 21
94147 GATTTATCGA
* *
94157 GATATCA-ATAAATATCGATG
1 GATATCACAGAAATATCGACG
*
94177 GATA-CACAGATATATCGACG
1 GATATCACAGAAATATCGACG
94197 GATATC
1 GATATC
94203 CCGTGACATT
Statistics
Matches: 21, Mismatches: 3, Indels: 3
0.78 0.11 0.11
Matches are distributed among these distances:
19 2 0.10
20 18 0.86
21 1 0.05
ACGTcount: A:0.41, C:0.15, G:0.17, T:0.26
Consensus pattern (21 bp):
GATATCACAGAAATATCGACG
Found at i:95287 original size:34 final size:34
Alignment explanation
Indices: 95248--95316 Score: 138
Period size: 34 Copynumber: 2.0 Consensus size: 34
95238 GAGAAGAAAT
95248 AAATTTATTTGTTTTTTATCAGAGACAACAATGA
1 AAATTTATTTGTTTTTTATCAGAGACAACAATGA
95282 AAATTTATTTGTTTTTTATCAGAGACAACAATGA
1 AAATTTATTTGTTTTTTATCAGAGACAACAATGA
95316 A
1 A
95317 CTCTTTTCAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.39, C:0.09, G:0.12, T:0.41
Consensus pattern (34 bp):
AAATTTATTTGTTTTTTATCAGAGACAACAATGA
Found at i:96935 original size:43 final size:44
Alignment explanation
Indices: 96877--96968 Score: 177
Period size: 43 Copynumber: 2.1 Consensus size: 44
96867 TTCAACCAAT
96877 ATTTCTAAAAGTGGGAGGAAAATAATCATTTAAGGCAGTGACCA
1 ATTTCTAAAAGTGGGAGGAAAATAATCATTTAAGGCAGTGACCA
96921 ATTTC-AAAAGTGGGAGGAAAATAATCATTTAAGGCAGTGACCA
1 ATTTCTAAAAGTGGGAGGAAAATAATCATTTAAGGCAGTGACCA
96964 ATTTC
1 ATTTC
96969 GTTAGTAGTT
Statistics
Matches: 48, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
43 43 0.90
44 5 0.10
ACGTcount: A:0.40, C:0.12, G:0.22, T:0.26
Consensus pattern (44 bp):
ATTTCTAAAAGTGGGAGGAAAATAATCATTTAAGGCAGTGACCA
Found at i:97202 original size:1 final size:1
Alignment explanation
Indices: 97196--97230 Score: 70
Period size: 1 Copynumber: 35.0 Consensus size: 1
97186 AGGAGTTATC
97196 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
97231 GTTGTGTGTG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 34 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:102881 original size:30 final size:30
Alignment explanation
Indices: 102847--102919 Score: 112
Period size: 30 Copynumber: 2.4 Consensus size: 30
102837 GTAGTTTACA
* *
102847 GTAGTTTTCTTTTTT-AGTACTTTTAAATTG
1 GTAGTTTTCTTTTTTGA-CACATTTAAATTG
102877 GTAGTTTTCTTTTTTGACACATTTAAATTG
1 GTAGTTTTCTTTTTTGACACATTTAAATTG
102907 GTAGTTTTCTTTT
1 GTAGTTTTCTTTT
102920 AAGTGATATA
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
30 39 0.98
31 1 0.03
ACGTcount: A:0.19, C:0.08, G:0.14, T:0.59
Consensus pattern (30 bp):
GTAGTTTTCTTTTTTGACACATTTAAATTG
Found at i:103078 original size:95 final size:95
Alignment explanation
Indices: 102979--103161 Score: 321
Period size: 95 Copynumber: 1.9 Consensus size: 95
102969 TTTCAAATGG
* * *
102979 GTAGTTTTTTATCTTTTAAAAACTGAGTTTGTATCCGAGTTAACTCGTGACACAAATTCAGGACT
1 GTAGTTTTTAATCTTTTAAAAACTGAGTTTGTATCCGAGTCAACTCGTGACACAAACTCAGGACT
*
103044 TCACATTATAATTAGTATAGATATAGATGA
66 TCACATTATAATTAATATAGATATAGATGA
*
103074 GTAGTTTTTAATCTTTTAAAAACTGAGTTTGTGTCCGAGTCAACTCGTGACACAAACTCAGGACT
1 GTAGTTTTTAATCTTTTAAAAACTGAGTTTGTATCCGAGTCAACTCGTGACACAAACTCAGGACT
103139 TCACATTATAATTAATATAGATA
66 TCACATTATAATTAATATAGATA
103162 AAAACTTTGT
Statistics
Matches: 83, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
95 83 1.00
ACGTcount: A:0.34, C:0.14, G:0.15, T:0.37
Consensus pattern (95 bp):
GTAGTTTTTAATCTTTTAAAAACTGAGTTTGTATCCGAGTCAACTCGTGACACAAACTCAGGACT
TCACATTATAATTAATATAGATATAGATGA
Found at i:104150 original size:19 final size:19
Alignment explanation
Indices: 104126--104170 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 19
104116 TCCAGCTCAA
104126 TTTATTT-GAATTTCGTTCT
1 TTTATTTAG-ATTTCGTTCT
104145 TTTATTTATGATTTCGTTCT
1 TTTATTTA-GATTTCGTTCT
104165 TTTATT
1 TTTATT
104171 CATCCCTTAC
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
19 7 0.29
20 16 0.67
21 1 0.04
ACGTcount: A:0.16, C:0.09, G:0.09, T:0.67
Consensus pattern (19 bp):
TTTATTTAGATTTCGTTCT
Found at i:106238 original size:27 final size:27
Alignment explanation
Indices: 106198--106262 Score: 112
Period size: 27 Copynumber: 2.4 Consensus size: 27
106188 AGAAATCTAC
**
106198 TTGATTTATTTTGGTTATATTTTGTAA
1 TTGATTTAGATTGGTTATATTTTGTAA
106225 TTGATTTAGATTGGTTATATTTTGTAA
1 TTGATTTAGATTGGTTATATTTTGTAA
106252 TTGATTTAGAT
1 TTGATTTAGAT
106263 GACATTTTGT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
27 36 1.00
ACGTcount: A:0.25, C:0.00, G:0.17, T:0.58
Consensus pattern (27 bp):
TTGATTTAGATTGGTTATATTTTGTAA
Found at i:107020 original size:16 final size:16
Alignment explanation
Indices: 107001--107054 Score: 65
Period size: 17 Copynumber: 3.4 Consensus size: 16
106991 TTCCTTTCTC
107001 TTCCTCCCTATTTCCT
1 TTCCTCCCTATTTCCT
**
107017 TTCCCTTGCTATTTCCT
1 TT-CCTCCCTATTTCCT
*
107034 TTCCTTCCTATTT-CT
1 TTCCTCCCTATTTCCT
107049 TTCCTC
1 TTCCTC
107055 TCAACCAAAC
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
15 7 0.21
16 12 0.36
17 14 0.42
ACGTcount: A:0.06, C:0.39, G:0.02, T:0.54
Consensus pattern (16 bp):
TTCCTCCCTATTTCCT
Found at i:107030 original size:17 final size:17
Alignment explanation
Indices: 107007--107052 Score: 69
Period size: 16 Copynumber: 2.8 Consensus size: 17
106997 TCTCTTCCTC
107007 CCTATTTCCTTTCCCTT
1 CCTATTTCCTTTCCCTT
*
107024 GCTATTTCCTTT-CCTT
1 CCTATTTCCTTTCCCTT
107040 CCTATTT-CTTTCC
1 CCTATTTCCTTTCC
107053 TCTCAACCAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
15 4 0.15
16 11 0.42
17 11 0.42
ACGTcount: A:0.07, C:0.37, G:0.02, T:0.54
Consensus pattern (17 bp):
CCTATTTCCTTTCCCTT
Found at i:109064 original size:20 final size:21
Alignment explanation
Indices: 109041--109081 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
109031 TTTTATAGCT
*
109041 ATTTTTCTATG-ATTTTTACC
1 ATTTTTATATGTATTTTTACC
*
109061 ATTTTTATGTGTATTTTTACC
1 ATTTTTATATGTATTTTTACC
109082 CTATTTTACA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 9 0.50
21 9 0.50
ACGTcount: A:0.20, C:0.12, G:0.07, T:0.61
Consensus pattern (21 bp):
ATTTTTATATGTATTTTTACC
Found at i:112998 original size:14 final size:13
Alignment explanation
Indices: 112974--113030 Score: 55
Period size: 14 Copynumber: 4.3 Consensus size: 13
112964 TAATGCACCC
112974 AAAACATTTTAATA
1 AAAACA-TTTAATA
112988 AAAATCATTT-ATA
1 AAAA-CATTTAATA
*
113001 AAAACAATTTATTA
1 AAAAC-ATTTAATA
*
113015 AAAACA-GTAATA
1 AAAACATTTAATA
113027 AAAA
1 AAAA
113031 TAAGTCCCTC
Statistics
Matches: 37, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
12 9 0.24
13 12 0.32
14 14 0.38
15 2 0.05
ACGTcount: A:0.61, C:0.07, G:0.02, T:0.30
Consensus pattern (13 bp):
AAAACATTTAATA
Found at i:113001 original size:13 final size:12
Alignment explanation
Indices: 112974--113030 Score: 51
Period size: 13 Copynumber: 4.3 Consensus size: 12
112964 TAATGCACCC
112974 AAAACATTTTAATA
1 AAAACA-TTT-ATA
112988 AAAATCATTTATA
1 AAAA-CATTTATA
113001 AAAACAATTTATTA
1 AAAAC-ATTTA-TA
* *
113015 AAAACAGTAATA
1 AAAACATTTATA
113027 AAAA
1 AAAA
113031 TAAGTCCCTC
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
12 7 0.18
13 15 0.39
14 14 0.37
15 2 0.05
ACGTcount: A:0.61, C:0.07, G:0.02, T:0.30
Consensus pattern (12 bp):
AAAACATTTATA
Found at i:113030 original size:27 final size:27
Alignment explanation
Indices: 112974--113030 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 27
112964 TAATGCACCC
* * *
112974 AAAACATTTTAATAAAAATCATTTATA
1 AAAACAATTTAATAAAAATCAGTAATA
*
113001 AAAACAATTTATTAAAAA-CAGTAATA
1 AAAACAATTTAATAAAAATCAGTAATA
113027 AAAA
1 AAAA
113031 TAAGTCCCTC
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
26 10 0.38
27 16 0.62
ACGTcount: A:0.61, C:0.07, G:0.02, T:0.30
Consensus pattern (27 bp):
AAAACAATTTAATAAAAATCAGTAATA
Found at i:116089 original size:11 final size:11
Alignment explanation
Indices: 116073--116105 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
116063 AGAGTCTTCA
*
116073 TGCATAGGAAT
1 TGCATAGAAAT
116084 TGCATAGAAAT
1 TGCATAGAAAT
116095 TGCATA-AAAT
1 TGCATAGAAAT
116105 T
1 T
116106 TTTCAAAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
10 5 0.24
11 16 0.76
ACGTcount: A:0.42, C:0.09, G:0.18, T:0.30
Consensus pattern (11 bp):
TGCATAGAAAT
Found at i:117156 original size:20 final size:21
Alignment explanation
Indices: 117133--117173 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
117123 TTTTATAGCT
*
117133 ATTTTTCTATG-ATTTTTACC
1 ATTTTTATATGTATTTTTACC
*
117153 ATTTTTATGTGTATTTTTACC
1 ATTTTTATATGTATTTTTACC
117174 CTATTTTACA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 9 0.50
21 9 0.50
ACGTcount: A:0.20, C:0.12, G:0.07, T:0.61
Consensus pattern (21 bp):
ATTTTTATATGTATTTTTACC
Found at i:120058 original size:17 final size:17
Alignment explanation
Indices: 120036--120086 Score: 75
Period size: 17 Copynumber: 3.0 Consensus size: 17
120026 CCGGTCCTTC
*
120036 CGTGATTCCTGTTGCCG
1 CGTGATTCCTGCTGCCG
*
120053 CGTGATTCCTGCAGCCG
1 CGTGATTCCTGCTGCCG
*
120070 CGCGATTCCTGCTGCCG
1 CGTGATTCCTGCTGCCG
120087 GAATCAACCT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 30 1.00
ACGTcount: A:0.08, C:0.35, G:0.29, T:0.27
Consensus pattern (17 bp):
CGTGATTCCTGCTGCCG
Done.