Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01005063.1 Kokia drynarioides strain JFW-HI SEQ_118859, 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: 44189
ACGTcount: A:0.34, C:0.16, G:0.19, T:0.31
Found at i:943 original size:24 final size:25
Alignment explanation
Indices: 916--963 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 25
906 TTTTTGAATG
**
916 ATATTTTTGTTAAAA-AATAATATA
1 ATATTTTAATTAAAATAATAATATA
940 ATATTTTAATTAAAATAATAATAT
1 ATATTTTAATTAAAATAATAATAT
964 TTTATAAGTA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 13 0.62
25 8 0.38
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (25 bp):
ATATTTTAATTAAAATAATAATATA
Found at i:976 original size:20 final size:20
Alignment explanation
Indices: 931--980 Score: 61
Period size: 20 Copynumber: 2.5 Consensus size: 20
921 TTTGTTAAAA
931 AATAATATAATATTTTAATT
1 AATAATATAATATTTTAATT
951 AA-AATAATAATATTTT-A-T
1 AATAAT-ATAATATTTTAATT
969 AAGTAATATAAT
1 AA-TAATATAAT
981 TATATATAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
18 3 0.11
19 9 0.33
20 15 0.56
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (20 bp):
AATAATATAATATTTTAATT
Found at i:979 original size:22 final size:21
Alignment explanation
Indices: 937--985 Score: 55
Period size: 22 Copynumber: 2.3 Consensus size: 21
927 AAAAAATAAT
*
937 ATAATA-TTTTAATTAAAATA
1 ATAATATTTTTAAGTAAAATA
*
957 ATAATATTTTATAAGTAATATA
1 ATAATATTTT-TAAGTAAAATA
*
979 ATTATAT
1 ATAATAT
986 ATAAAGAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 6 0.25
21 3 0.12
22 15 0.62
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (21 bp):
ATAATATTTTTAAGTAAAATA
Found at i:1627 original size:55 final size:55
Alignment explanation
Indices: 1543--1676 Score: 180
Period size: 55 Copynumber: 2.4 Consensus size: 55
1533 ATTTGGATTG
* * * * *
1543 AATCGATTGTTATGCTGGAATATTGCTTCTTTTGAATCGATTGTTCT-TATGCTTA
1 AATCGATTGTCATGTTGAAATACTGCTTCTTTTGAATCGATTGTT-TATATACTTA
* *
1598 AATCGGTTGTCATGTTGAAATACTGCTTCTTTTGAATCGATTGTTTATATATTTA
1 AATCGATTGTCATGTTGAAATACTGCTTCTTTTGAATCGATTGTTTATATACTTA
*
1653 AATCAATTGTCATGTTGAAATACT
1 AATCGATTGTCATGTTGAAATACT
1677 TTTATGCAGG
Statistics
Matches: 69, Mismatches: 9, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
54 1 0.01
55 68 0.99
ACGTcount: A:0.26, C:0.12, G:0.16, T:0.46
Consensus pattern (55 bp):
AATCGATTGTCATGTTGAAATACTGCTTCTTTTGAATCGATTGTTTATATACTTA
Found at i:3051 original size:56 final size:54
Alignment explanation
Indices: 2948--3055 Score: 162
Period size: 56 Copynumber: 2.0 Consensus size: 54
2938 ATTTCAACAA
* * *
2948 GACAATTGATTTAAATATATAAAAATAGATTCAAAAGAAGCAGTATTCCAACTT
1 GACAATTGATTTAAACATAAAAAAATAGATTCAAAAGAAGCAATATTCCAACTT
*
3002 GACAATTGATTTAAACATAAAAAACAATCGATTCAAAAGAAGCAATATTCCAAC
1 GACAATTGATTTAAACAT-AAAAA-AATAGATTCAAAAGAAGCAATATTCCAAC
3056 ATAACAATCG
Statistics
Matches: 48, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
54 17 0.35
55 4 0.08
56 27 0.56
ACGTcount: A:0.50, C:0.14, G:0.10, T:0.26
Consensus pattern (54 bp):
GACAATTGATTTAAACATAAAAAAATAGATTCAAAAGAAGCAATATTCCAACTT
Found at i:3063 original size:56 final size:54
Alignment explanation
Indices: 2949--3068 Score: 159
Period size: 56 Copynumber: 2.2 Consensus size: 54
2939 TTTCAACAAG
* * * * *
2949 ACAATTGATTTAAATATATAAAAATAGATTCAAAAGAAGCAGTATTCCAACTTG
1 ACAATTGATTTAAACATAAAAAAATAGATTCAAAAGAAGCAATATTCCAACATA
*
3003 ACAATTGATTTAAACATAAAAAACAATCGATTCAAAAGAAGCAATATTCCAACATA
1 ACAATTGATTTAAACAT-AAAAA-AATAGATTCAAAAGAAGCAATATTCCAACATA
*
3059 ACAATCGATT
1 ACAATTGATT
3069 CAATCCAAAT
Statistics
Matches: 57, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
54 16 0.28
55 4 0.07
56 37 0.65
ACGTcount: A:0.50, C:0.14, G:0.09, T:0.27
Consensus pattern (54 bp):
ACAATTGATTTAAACATAAAAAAATAGATTCAAAAGAAGCAATATTCCAACATA
Found at i:4742 original size:55 final size:55
Alignment explanation
Indices: 4649--4782 Score: 180
Period size: 55 Copynumber: 2.4 Consensus size: 55
4639 CCTGCATAAA
* *
4649 AGTATTTCAACATGACAATTGATTTAAATATATAAACAATCGATTCAAAAGAAGC
1 AGTATTTCAACATGACAATCGATTTAAACATATAAACAATCGATTCAAAAGAAGC
* *
4704 AGTATTTCAACATGACAACCGATTTAAGCATA-AGAACAATCGATTCAAAAGAAGC
1 AGTATTTCAACATGACAATCGATTTAAACATATA-AACAATCGATTCAAAAGAAGC
* * * *
4759 AATATTCCAGCATAACAATCGATT
1 AGTATTTCAACATGACAATCGATT
4783 CAATCCAAAT
Statistics
Matches: 69, Mismatches: 9, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
54 1 0.01
55 68 0.99
ACGTcount: A:0.46, C:0.16, G:0.12, T:0.26
Consensus pattern (55 bp):
AGTATTTCAACATGACAATCGATTTAAACATATAAACAATCGATTCAAAAGAAGC
Found at i:7566 original size:30 final size:29
Alignment explanation
Indices: 7532--7596 Score: 78
Period size: 30 Copynumber: 2.2 Consensus size: 29
7522 ATAAAAGACT
* *
7532 AAATT-GAAAACACAAATAAATTAAATATAC
1 AAATTAGAAAA-ACAAATAAAATAAA-ATAA
*
7562 AAATTAGAAAAAGAAATAAAATAAAATAA
1 AAATTAGAAAAACAAATAAAATAAAATAA
7591 AAATTA
1 AAATTA
7597 CAGGGACCAA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
29 9 0.29
30 17 0.55
31 5 0.16
ACGTcount: A:0.69, C:0.05, G:0.05, T:0.22
Consensus pattern (29 bp):
AAATTAGAAAAACAAATAAAATAAAATAA
Found at i:14153 original size:24 final size:24
Alignment explanation
Indices: 14126--14179 Score: 74
Period size: 24 Copynumber: 2.2 Consensus size: 24
14116 GGCTTGAATA
*
14126 AGCTAA-CTAATTTGGGCTCGTAAG
1 AGCTAACCT-ATTTGGGCTCATAAG
*
14150 AGCTAACCTATTTGGGCTCATATG
1 AGCTAACCTATTTGGGCTCATAAG
14174 AGCTAA
1 AGCTAA
14180 ATTTTTGGAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
24 25 0.93
25 2 0.07
ACGTcount: A:0.30, C:0.19, G:0.22, T:0.30
Consensus pattern (24 bp):
AGCTAACCTATTTGGGCTCATAAG
Found at i:15833 original size:21 final size:21
Alignment explanation
Indices: 15807--15848 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
15797 AATTAAGTAT
*
15807 AAATGGTTTAATCAAGATTAA
1 AAATGGGTTAATCAAGATTAA
* *
15828 AAATGGGTTAATTAAGCTTAA
1 AAATGGGTTAATCAAGATTAA
15849 TGATGAAAGT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.45, C:0.05, G:0.17, T:0.33
Consensus pattern (21 bp):
AAATGGGTTAATCAAGATTAA
Found at i:17684 original size:21 final size:21
Alignment explanation
Indices: 17658--17711 Score: 74
Period size: 21 Copynumber: 2.6 Consensus size: 21
17648 AAAGTTTTTA
17658 GTATCGGTAGAAG-CATGACTT
1 GTATCGGTAGAAGTCAT-ACTT
*
17679 GTATCGGTAGAAGTTATACTT
1 GTATCGGTAGAAGTCATACTT
*
17700 GTATCAGTAGAA
1 GTATCGGTAGAA
17712 CTAGCATAGG
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
21 28 0.93
22 2 0.07
ACGTcount: A:0.31, C:0.11, G:0.26, T:0.31
Consensus pattern (21 bp):
GTATCGGTAGAAGTCATACTT
Found at i:28039 original size:17 final size:18
Alignment explanation
Indices: 28017--28057 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 18
28007 ATAGTTTTCA
28017 TGCATTCTT-ATTGTGC-T
1 TGCATTCTTAATTGT-CTT
28034 TGCATT-TTAATTGTCTT
1 TGCATTCTTAATTGTCTT
28051 TGCATTC
1 TGCATTC
28058 ATTTTATTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
16 3 0.14
17 18 0.86
ACGTcount: A:0.15, C:0.17, G:0.15, T:0.54
Consensus pattern (18 bp):
TGCATTCTTAATTGTCTT
Found at i:28662 original size:19 final size:18
Alignment explanation
Indices: 28638--28674 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
28628 TTAGTCACTT
*
28638 GAAAAATAAAATAAAAAAA
1 GAAAAA-AAAAGAAAAAAA
28657 GAAAAAAAAAGAAAAAAA
1 GAAAAAAAAAGAAAAAAA
28675 AAAGAAATGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 11 0.65
19 6 0.35
ACGTcount: A:0.86, C:0.00, G:0.08, T:0.05
Consensus pattern (18 bp):
GAAAAAAAAAGAAAAAAA
Found at i:28664 original size:9 final size:10
Alignment explanation
Indices: 28650--28681 Score: 55
Period size: 10 Copynumber: 3.1 Consensus size: 10
28640 AAAATAAAAT
28650 AAAAAAAGAA
1 AAAAAAAGAA
28660 AAAAAAAGAAA
1 AAAAAAAG-AA
28671 AAAAAAAGAA
1 AAAAAAAGAA
28681 A
1 A
28682 TGAATAAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
10 11 0.52
11 10 0.48
ACGTcount: A:0.91, C:0.00, G:0.09, T:0.00
Consensus pattern (10 bp):
AAAAAAAGAA
Found at i:28664 original size:11 final size:11
Alignment explanation
Indices: 28650--28681 Score: 57
Period size: 11 Copynumber: 3.0 Consensus size: 11
28640 AAAATAAAAT
28650 AAAAAAAG-AA
1 AAAAAAAGAAA
28660 AAAAAAAGAAA
1 AAAAAAAGAAA
28671 AAAAAAAGAAA
1 AAAAAAAGAAA
28682 TGAATAAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 8 0.38
11 13 0.62
ACGTcount: A:0.91, C:0.00, G:0.09, T:0.00
Consensus pattern (11 bp):
AAAAAAAGAAA
Found at i:30515 original size:6 final size:6
Alignment explanation
Indices: 30494--30572 Score: 56
Period size: 6 Copynumber: 13.3 Consensus size: 6
30484 TTTAAATTGG
** ** **
30494 TTTAAA TTTATT TTTAAA TTTAAA TTTATCTT TTTAAA TTTAAA TTT-GC
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTA--AA TTTAAA TTTAAA TTTAAA
*
30543 TTTAAA TTTAAA TTT-AA -TTAAA TTTGAA TT
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TT
30573 GATTTAAAAA
Statistics
Matches: 55, Mismatches: 13, Indels: 10
0.71 0.17 0.13
Matches are distributed among these distances:
4 2 0.04
5 7 0.13
6 42 0.76
8 4 0.07
ACGTcount: A:0.38, C:0.03, G:0.03, T:0.57
Consensus pattern (6 bp):
TTTAAA
Found at i:30587 original size:33 final size:34
Alignment explanation
Indices: 30527--30597 Score: 83
Period size: 34 Copynumber: 2.1 Consensus size: 34
30517 ATTTATCTTT
* * *
30527 TTAAATTTAAATTTGCTTT-AAATTTAAATTTAA
1 TTAAATTTAAATTTGATTTAAAATTAAAATTAAA
*
30560 TTAAATTTGAA-TTGATTTAAAAATTAAAATTAAA
1 TTAAATTTAAATTTGATTT-AAAATTAAAATTAAA
30594 TTAA
1 TTAA
30598 GAGCCCAAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
32 6 0.19
33 10 0.31
34 16 0.50
ACGTcount: A:0.48, C:0.01, G:0.04, T:0.46
Consensus pattern (34 bp):
TTAAATTTAAATTTGATTTAAAATTAAAATTAAA
Found at i:31289 original size:17 final size:17
Alignment explanation
Indices: 31256--31289 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
31246 TTAATGCACC
31256 TATCACTTTATTATTAT
1 TATCACTTTATTATTAT
31273 TATCA-TTTATTACTTAT
1 TATCACTTTATTA-TTAT
31290 ATTATCTTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.29, C:0.12, G:0.00, T:0.59
Consensus pattern (17 bp):
TATCACTTTATTATTAT
Found at i:31327 original size:3 final size:3
Alignment explanation
Indices: 31321--31415 Score: 77
Period size: 3 Copynumber: 30.7 Consensus size: 3
31311 ATAATAGCAT
* *
31321 TAA TAA TAA TAG TAA TAA TAA TAA TAA TAA TAA TGAA T-A TAA TAC
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA
* * * *
31366 TAA TGAC T-T TAA TTAA TAA TAA TAA TAT TAA TAA TTAA TAT TAAA TAA
1 TAA T-AA TAA TAA -TAA TAA TAA TAA TAA TAA TAA -TAA TAA T-AA TAA
31414 TA
1 TA
31416 TTTTAAAAAA
Statistics
Matches: 74, Mismatches: 11, Indels: 14
0.75 0.11 0.14
Matches are distributed among these distances:
2 3 0.04
3 58 0.78
4 13 0.18
ACGTcount: A:0.57, C:0.02, G:0.03, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:31327 original size:15 final size:15
Alignment explanation
Indices: 31309--31346 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
31299 ATGCTATCAT
*
31309 TAATAATAGCATTAA
1 TAATAATAGCAATAA
*
31324 TAATAATAGTAATAA
1 TAATAATAGCAATAA
31339 TAATAATA
1 TAATAATA
31347 ATAATAATGA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.58, C:0.03, G:0.05, T:0.34
Consensus pattern (15 bp):
TAATAATAGCAATAA
Found at i:31417 original size:10 final size:12
Alignment explanation
Indices: 31307--31415 Score: 73
Period size: 12 Copynumber: 8.8 Consensus size: 12
31297 TAATGCTATC
**
31307 ATTAATAATAGC
1 ATTAATAATAAT
31319 ATTAATAATAAT
1 ATTAATAATAAT
*
31331 AGTAATAATAAT
1 ATTAATAATAAT
*
31343 AATAATAATAAT
1 ATTAATAATAAT
*
31355 GAATATAATACTAAT
1 --AT-TAATAATAAT
31370 GACTT--TAAT--T
1 -A-TTAATAATAAT
*
31380 AATAATAATAAT
1 ATTAATAATAAT
31392 ATTAATAATTAAT
1 ATTAATAA-TAAT
31405 ATTAAATAATA
1 ATT-AATAATA
31416 TTTTAAAAAA
Statistics
Matches: 77, Mismatches: 10, Indels: 19
0.73 0.09 0.18
Matches are distributed among these distances:
8 1 0.01
9 1 0.01
10 5 0.06
12 43 0.56
13 9 0.12
14 8 0.10
15 10 0.13
ACGTcount: A:0.56, C:0.03, G:0.04, T:0.38
Consensus pattern (12 bp):
ATTAATAATAAT
Found at i:32547 original size:29 final size:29
Alignment explanation
Indices: 32508--32867 Score: 157
Period size: 30 Copynumber: 12.1 Consensus size: 29
32498 AACTATACAA
*
32508 AAAATTACATTTTTACCTCTAAATTTTCC
1 AAAATTCCATTTTTACCTCTAAATTTTCC
* *
32537 AAAATTCCATTTTTAACCTC-AATTTTTCAA
1 AAAATTCCATTTTT-ACCTCTAAATTTTC-C
* * *
32567 AAAATTACATTTTTACC-CATGAACTTTCC
1 AAAATTCCATTTTTACCTC-TAAATTTTCC
* * * **
32596 AAGATTCCATTTTTTACC-CTGATTTCTTTA
1 AAAATTCCA-TTTTTACCTCTAAATT-TTCC
* *
32626 AAAATTACCA-TTTTACCCCTAAACTTTCC
1 AAAATT-CCATTTTTACCTCTAAATTTTCC
* * *
32655 AAAATTCCATTTTCATCCTC-GATTTTTCC
1 AAAATTCCATTTTTA-CCTCTAAATTTTCC
* * *
32684 AAAAATTACATTTTTACACCCT-AACTTTCC
1 -AAAATTCCATTTTTAC-CTCTAAATTTTCC
* *
32714 AAAATTCCATTTTTAACC-CTAATTTTTCTA
1 AAAATTCCATTTTT-ACCTCTAAATTTTC-C
** * * *
32744 AAAATTAAAATTTTACCCCCAAACTTTT-C
1 AAAATTCCATTTTTACCTCTAAA-TTTTCC
* * * **
32773 AAAATTCAAATTTTAACCTTTATTTTTTTCC
1 AAAATTC-CATTTTTACCTCTA-AATTTTCC
* *
32804 AAAAATCACCA-TTTTACC-CTCAAA-CTTCC
1 -AAAAT-TCCATTTTTACCTCT-AAATTTTCC
**
32833 AAAAATTCCATTTTTGACCTCTATTTTTTCC
1 -AAAATTCCATTTTT-ACCTCTAAATTTTCC
32864 AAAA
1 AAAA
32868 ATGACCTTTT
Statistics
Matches: 244, Mismatches: 59, Indels: 55
0.68 0.16 0.15
Matches are distributed among these distances:
28 9 0.04
29 102 0.42
30 105 0.43
31 21 0.09
32 6 0.02
33 1 0.00
ACGTcount: A:0.34, C:0.24, G:0.01, T:0.41
Consensus pattern (29 bp):
AAAATTCCATTTTTACCTCTAAATTTTCC
Found at i:32865 original size:60 final size:60
Alignment explanation
Indices: 32507--32896 Score: 360
Period size: 59 Copynumber: 6.6 Consensus size: 60
32497 AAACTATACA
* * *
32507 AAAAATTA-CATTTTTA-CCTCTAAATTTTCCAAAATTCCATTTTTAACCTC-AATTTTTCA
1 AAAAATTACCA-TTTTACCCTC-AAACTTTCCAAAATTCCATTTTTAACCTCTATTTTTTCC
* * *
32566 AAAAATTA-CATTTTTACCCAT-GAACTTTCCAAGATTCCATTTTTTACC-CTGATTTCTTT--
1 AAAAATTACCA-TTTTACCC-TCAAACTTTCCAAAATTCCATTTTTAACCTCT-ATTT-TTTCC
* * *
32625 AAAAATTACCATTTTACCC-CTAAACTTTCCAAAATTCCATTTTCATCCTCGA-TTTTTCC
1 AAAAATTACCATTTTACCCTC-AAACTTTCCAAAATTCCATTTTTAACCTCTATTTTTTCC
* * *
32684 AAAAATTA-CATTTTTACACC-CTAACTTTCCAAAATTCCATTTTTAACC-CTAATTTTTCT
1 AAAAATTACCA-TTTTAC-CCTCAAACTTTCCAAAATTCCATTTTTAACCTCTATTTTTTCC
** * * * * *
32743 AAAAATTAAAATTTTACCCCCAAACTTTTCAAAATTCAAATTTTAACCTTTATTTTTTTCC
1 AAAAATTACCATTTTACCCTCAAACTTTCCAAAATTCCATTTTTAACCTCTA-TTTTTTCC
* *
32804 AAAAATCACCATTTTACCCTCAAAC-TTCCAAAAATTCCATTTTTGACCTCTATTTTTTCC
1 AAAAATTACCATTTTACCCTCAAACTTTCC-AAAATTCCATTTTTAACCTCTATTTTTTCC
* * *
32864 AAAAATGACCTTTTTACCCTCGAAC-TTCCAAAA
1 AAAAATTACCATTTTACCCTCAAACTTTCCAAAA
32897 ATTTATTTTT
Statistics
Matches: 276, Mismatches: 36, Indels: 38
0.79 0.10 0.11
Matches are distributed among these distances:
57 3 0.01
58 9 0.03
59 164 0.59
60 51 0.18
61 49 0.18
ACGTcount: A:0.34, C:0.24, G:0.02, T:0.41
Consensus pattern (60 bp):
AAAAATTACCATTTTACCCTCAAACTTTCCAAAATTCCATTTTTAACCTCTATTTTTTCC
Found at i:32920 original size:29 final size:30
Alignment explanation
Indices: 32828--32925 Score: 78
Period size: 31 Copynumber: 3.3 Consensus size: 30
32818 TACCCTCAAA
* *
32828 CTTCCAAAAATTCCATTTTTGACCTCTATTT
1 CTTCCAAAAATT-CATTTTTGACCTCGAATT
* * *
32859 TTTCCAAAAATGACCTTTTT-ACCCTCGAA--
1 CTTCCAAAAAT-TCATTTTTGA-CCTCGAATT
*
32888 CTTCCAAAAATTTATTTTTGACCTC-AATT
1 CTTCCAAAAATTCATTTTTGACCTCGAATT
*
32917 CTTCTAAAA
1 CTTCCAAAA
32926 GGTGCCATTT
Statistics
Matches: 52, Mismatches: 10, Indels: 12
0.70 0.14 0.16
Matches are distributed among these distances:
27 2 0.04
28 9 0.17
29 19 0.37
30 1 0.02
31 21 0.40
ACGTcount: A:0.31, C:0.24, G:0.04, T:0.41
Consensus pattern (30 bp):
CTTCCAAAAATTCATTTTTGACCTCGAATT
Found at i:32963 original size:59 final size:60
Alignment explanation
Indices: 32533--32969 Score: 224
Period size: 59 Copynumber: 7.4 Consensus size: 60
32523 CCTCTAAATT
* * * * * **
32533 TTCC-AAAATTCCATTTTTAACCTC-AATTTTTCAAAAAATTA-CATTTTTACCCATGAAC
1 TTCCAAAAATTCTATTTTTGACCTCTAATTCTTCCAAAAATGACCA-TTTTACCCCCGAAC
* * * * * * **
32591 TTTCC-AAGATTCCATTTTTTACC-CTGATTTCTT-TAAAAATTACCATTTTACCCCTAAAC
1 -TTCCAAAAATTCTATTTTTGACCTCT-AATTCTTCCAAAAATGACCATTTTACCCCCGAAC
* * * * * * *
32650 TTTCC-AAAATTCCA-TTTTCATCCTC-GATTTTTCCAAAAATTA-CATTTTTACACCCTAAC
1 -TTCCAAAAATTCTATTTTTGA-CCTCTAATTCTTCCAAAAATGACCA-TTTTACCCCCGAAC
* * * * * ** *
32709 TTTCC-AAAATTCCATTTTTAACC-CTAATTTTTCTAAAAATTAAAATTTTACCCCCAAAC
1 -TTCCAAAAATTCTATTTTTGACCTCTAATTCTTCCAAAAATGACCATTTTACCCCCGAAC
* * * * * * * * * *
32768 TTTTC-AAAATTCAAATTTTAACCTTTATTTTTTTCCAAAAATCACCATTTTACCCTCAAAC
1 -TTCCAAAAATTCTATTTTTGACCTCTA-ATTCTTCCAAAAATGACCATTTTACCCCCGAAC
* * * * *
32829 TTCCAAAAATTCCATTTTTGACCTCTATTTTTTCCAAAAATGACCTTTTTACCCTCGAAC
1 TTCCAAAAATTCTATTTTTGACCTCTAATTCTTCCAAAAATGACCATTTTACCCCCGAAC
* *
32889 TTCCAAAAATT-TATTTTTGACCTC-AATTCTTCTAAAAGGTG-CCATTTTACCCCCGAA-
1 TTCCAAAAATTCTATTTTTGACCTCTAATTCTTCCAAAA-ATGACCATTTTACCCCCGAAC
*
32946 TGTCTAAAAATTCTATTTTTGACC
1 T-TCCAAAAATTCTATTTTTGACC
32970 CCCGACTTTC
Statistics
Matches: 314, Mismatches: 48, Indels: 32
0.80 0.12 0.08
Matches are distributed among these distances:
57 1 0.00
58 46 0.15
59 162 0.52
60 60 0.19
61 45 0.14
ACGTcount: A:0.32, C:0.24, G:0.03, T:0.41
Consensus pattern (60 bp):
TTCCAAAAATTCTATTTTTGACCTCTAATTCTTCCAAAAATGACCATTTTACCCCCGAAC
Done.