Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008053.1 Corchorus capsularis cultivar CVL-1 contig08074, 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: 21869
ACGTcount: A:0.29, C:0.21, G:0.18, T:0.32
Found at i:1675 original size:21 final size:21
Alignment explanation
Indices: 1649--1689 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
1639 CACAAGTGAC
*
1649 CGGCCATGCGACTTGGAGATT
1 CGGCCACGCGACTTGGAGATT
1670 CGGCCACGCGACTTGGAGAT
1 CGGCCACGCGACTTGGAGAT
1690 GCCCGCGCAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.20, C:0.27, G:0.34, T:0.20
Consensus pattern (21 bp):
CGGCCACGCGACTTGGAGATT
Found at i:1740 original size:33 final size:33
Alignment explanation
Indices: 1670--1775 Score: 117
Period size: 33 Copynumber: 3.2 Consensus size: 33
1660 CTTGGAGATT
* *
1670 CGGCCACGCGACTTGGAGATGCCC-GCGCAACAT
1 CGGCCACGCGACATGGAGATGCCCGGC-CAACAC
* **
1703 CGGCCATGCGACATGGAGATGCCCGGCCTTCAC
1 CGGCCACGCGACATGGAGATGCCCGGCCAACAC
**
1736 CGGCCACGCGACATGGCCATGCCCGGCCAA-ACC
1 CGGCCACGCGACATGGAGATGCCCGGCCAACA-C
1769 CGGCCAC
1 CGGCCAC
1776 ATGACTCGGC
Statistics
Matches: 61, Mismatches: 10, Indels: 4
0.81 0.13 0.05
Matches are distributed among these distances:
32 1 0.02
33 58 0.95
34 2 0.03
ACGTcount: A:0.20, C:0.41, G:0.29, T:0.10
Consensus pattern (33 bp):
CGGCCACGCGACATGGAGATGCCCGGCCAACAC
Found at i:1787 original size:33 final size:33
Alignment explanation
Indices: 1750--1812 Score: 101
Period size: 33 Copynumber: 1.9 Consensus size: 33
1740 CACGCGACAT
1750 GGCCATGCCCGGCCA-AACCCGGCCACATGACTC
1 GGCCATGCCCGGCCACAA-CCGGCCACATGACTC
*
1783 GGCCATGCCCGGCCACAACCGGCCATATGA
1 GGCCATGCCCGGCCACAACCGGCCACATGA
1813 TCCTTTAGCT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
33 26 0.93
34 2 0.07
ACGTcount: A:0.22, C:0.43, G:0.25, T:0.10
Consensus pattern (33 bp):
GGCCATGCCCGGCCACAACCGGCCACATGACTC
Found at i:4447 original size:13 final size:12
Alignment explanation
Indices: 4424--4466 Score: 77
Period size: 12 Copynumber: 3.5 Consensus size: 12
4414 TTAATACAGG
4424 TATCGACGGATA
1 TATCGACGGATA
4436 TATCGAACGGATA
1 TATCG-ACGGATA
4449 TATCGACGGATA
1 TATCGACGGATA
4461 TATCGA
1 TATCGA
4467 GGTATCGATG
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
12 18 0.60
13 12 0.40
ACGTcount: A:0.35, C:0.16, G:0.23, T:0.26
Consensus pattern (12 bp):
TATCGACGGATA
Found at i:5544 original size:3 final size:3
Alignment explanation
Indices: 5536--5571 Score: 65
Period size: 3 Copynumber: 12.3 Consensus size: 3
5526 TCATTTCCCC
5536 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
5572 TTCCGTGAGC
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:6175 original size:10 final size:10
Alignment explanation
Indices: 6163--6198 Score: 63
Period size: 10 Copynumber: 3.6 Consensus size: 10
6153 AATTTAATAT
*
6163 GGATATTTAT
1 GGATATTTAC
6173 GGATATTTAC
1 GGATATTTAC
6183 GGATATTTAC
1 GGATATTTAC
6193 GGATAT
1 GGATAT
6199 ATCGAGATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
10 25 1.00
ACGTcount: A:0.31, C:0.06, G:0.22, T:0.42
Consensus pattern (10 bp):
GGATATTTAC
Found at i:6326 original size:12 final size:12
Alignment explanation
Indices: 6309--6347 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
6299 GTACAGATAT
6309 CGGATATATCGA
1 CGGATATATCGA
6321 CGGATATATCGA
1 CGGATATATCGA
6333 -GG---TATCGA
1 CGGATATATCGA
6341 CGGATAT
1 CGGATAT
6348 TTAATTCCAT
Statistics
Matches: 23, Mismatches: 0, Indels: 8
0.74 0.00 0.26
Matches are distributed among these distances:
8 6 0.26
9 2 0.09
11 2 0.09
12 13 0.57
ACGTcount: A:0.31, C:0.15, G:0.28, T:0.26
Consensus pattern (12 bp):
CGGATATATCGA
Found at i:12532 original size:13 final size:13
Alignment explanation
Indices: 12514--12538 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
12504 TGAGTCTCAG
12514 CTTCAACTTTCTC
1 CTTCAACTTTCTC
12527 CTTCAACTTTCT
1 CTTCAACTTTCT
12539 TGTATCCTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.16, C:0.36, G:0.00, T:0.48
Consensus pattern (13 bp):
CTTCAACTTTCTC
Found at i:14118 original size:17 final size:19
Alignment explanation
Indices: 14086--14123 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
14076 TGCAAAATGC
*
14086 AAAGCGAAAGAAC-AAAGA
1 AAAGCGAAACAACAAAAGA
14104 AAAGC-AAACAACAAAAGA
1 AAAGCGAAACAACAAAAGA
14122 AA
1 AA
14124 TTAGTTAGTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 6 0.33
18 12 0.67
ACGTcount: A:0.71, C:0.13, G:0.16, T:0.00
Consensus pattern (19 bp):
AAAGCGAAACAACAAAAGA
Found at i:15410 original size:32 final size:30
Alignment explanation
Indices: 15371--15443 Score: 96
Period size: 30 Copynumber: 2.4 Consensus size: 30
15361 ACTGCTCTTA
15371 ATTACTTCTT-TTCCTTTAGCTCTTTTCTACTG
1 ATTACTTCTTCTTCCTTTA-CTC--TTCTACTG
*
15403 ATTACTTCTTCTTCTTTTACTCTTCTACTG
1 ATTACTTCTTCTTCCTTTACTCTTCTACTG
15433 ATTACTT-TTCT
1 ATTACTTCTTCT
15444 ACTTTTACCC
Statistics
Matches: 39, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
29 4 0.10
30 15 0.38
32 13 0.33
33 7 0.18
ACGTcount: A:0.14, C:0.25, G:0.04, T:0.58
Consensus pattern (30 bp):
ATTACTTCTTCTTCCTTTACTCTTCTACTG
Found at i:15428 original size:14 final size:14
Alignment explanation
Indices: 15404--15466 Score: 63
Period size: 14 Copynumber: 4.4 Consensus size: 14
15394 TTTCTACTGA
*
15404 TTACTTCTTCTTCTT
1 TTAC-TCTTCTACTT
*
15419 TTACTCTTCTACTGA
1 TTACTCTTCTACT-T
*
15434 TTACTTTTCTACTT
1 TTACTCTTCTACTT
* *
15448 TTACCCTTTTACTT
1 TTACTCTTCTACTT
15462 TTACT
1 TTACT
15467 GATTGCCTCT
Statistics
Matches: 39, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
14 23 0.59
15 16 0.41
ACGTcount: A:0.14, C:0.25, G:0.02, T:0.59
Consensus pattern (14 bp):
TTACTCTTCTACTT
Found at i:15437 original size:15 final size:15
Alignment explanation
Indices: 15395--15446 Score: 61
Period size: 15 Copynumber: 3.5 Consensus size: 15
15385 TTTAGCTCTT
15395 TTCTACTGATTACTTC
1 TTCTACTGATTAC-TC
* *
15411 TTCTTCT-TTTACTC
1 TTCTACTGATTACTC
*
15425 TTCTACTGATTACTT
1 TTCTACTGATTACTC
15440 TTCTACT
1 TTCTACT
15447 TTTACCCTTT
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
14 8 0.27
15 16 0.53
16 6 0.20
ACGTcount: A:0.15, C:0.25, G:0.04, T:0.56
Consensus pattern (15 bp):
TTCTACTGATTACTC
Found at i:15460 original size:29 final size:30
Alignment explanation
Indices: 15395--15460 Score: 98
Period size: 29 Copynumber: 2.2 Consensus size: 30
15385 TTTAGCTCTT
* *
15395 TTCTACTGATTACTTCTTCTTCTTTTACTC
1 TTCTACTGATTACTTCTTCTACTTTTACCC
15425 TTCTACTGATTACTT-TTCTACTTTTACCC
1 TTCTACTGATTACTTCTTCTACTTTTACCC
*
15454 TTTTACT
1 TTCTACT
15461 TTTACTGATT
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
29 18 0.55
30 15 0.45
ACGTcount: A:0.15, C:0.26, G:0.03, T:0.56
Consensus pattern (30 bp):
TTCTACTGATTACTTCTTCTACTTTTACCC
Found at i:15543 original size:36 final size:36
Alignment explanation
Indices: 15415--15565 Score: 177
Period size: 36 Copynumber: 4.3 Consensus size: 36
15405 TACTTCTTCT
*
15415 TCTTTTACTCTTCTACTGATTACTT-TTCTACTTTTAC
1 TCTTTTA--CTTCTACTGATTACTTCTTTTACTTTTAC
* * * *
15452 CCTTTTACTTTTACTGATTGCCTCTTTTAC-TTT-C
1 TCTTTTACTTCTACTGATTACTTCTTTTACTTTTAC
* *
15486 AC-TTTAC-TCTGCTGATTACTTCTTTTACTTTTAC
1 TCTTTTACTTCTACTGATTACTTCTTTTACTTTTAC
*
15520 TCTTTCACTTCTACTGATTACTTCTTTTACTTTTAC
1 TCTTTTACTTCTACTGATTACTTCTTTTACTTTTAC
15556 TCTTTTACTT
1 TCTTTTACTT
15566 TTATTGATAA
Statistics
Matches: 95, Mismatches: 14, Indels: 11
0.79 0.12 0.09
Matches are distributed among these distances:
32 17 0.18
33 8 0.08
34 4 0.04
35 20 0.21
36 40 0.42
37 6 0.06
ACGTcount: A:0.15, C:0.25, G:0.04, T:0.56
Consensus pattern (36 bp):
TCTTTTACTTCTACTGATTACTTCTTTTACTTTTAC
Found at i:15551 original size:22 final size:21
Alignment explanation
Indices: 15516--15556 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
15506 TCTTTTACTT
15516 TTACTCTTTCACTTCTACTGA
1 TTACTCTTTCACTTCTACTGA
* *
15537 TTACTTCTTTTACTTTTACT
1 TTAC-TCTTTCACTTCTACT
15557 CTTTTACTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 4 0.24
22 13 0.76
ACGTcount: A:0.17, C:0.24, G:0.02, T:0.56
Consensus pattern (21 bp):
TTACTCTTTCACTTCTACTGA
Found at i:15561 original size:14 final size:15
Alignment explanation
Indices: 15537--15568 Score: 57
Period size: 14 Copynumber: 2.2 Consensus size: 15
15527 CTTCTACTGA
15537 TTACTTCTTTTACTT
1 TTACTTCTTTTACTT
15552 TTAC-TCTTTTACTT
1 TTACTTCTTTTACTT
15566 TTA
1 TTA
15569 TTGATAACTA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 13 0.76
15 4 0.24
ACGTcount: A:0.16, C:0.19, G:0.00, T:0.66
Consensus pattern (15 bp):
TTACTTCTTTTACTT
Found at i:15781 original size:37 final size:37
Alignment explanation
Indices: 15740--15855 Score: 112
Period size: 37 Copynumber: 3.2 Consensus size: 37
15730 TTAATTACTG
15740 ATTTACTGAATACTATCACCTTGACTCTTAATTATCA
1 ATTTACTGAATACTATCACCTTGACTCTTAATTATCA
* * * ** * * *
15777 ATTTACTGACTA--ATCTCTTTTTCACTTAGTTA-CTG
1 ATTTACTGAATACTATCACCTTGACTCTTAATTATC-A
* *
15812 ATTTACTGATTGCTATCACCTTGACTCTTAATTATCA
1 ATTTACTGAATACTATCACCTTGACTCTTAATTATCA
15849 ATTTACT
1 ATTTACT
15856 AATTAATCCC
Statistics
Matches: 58, Mismatches: 17, Indels: 8
0.70 0.20 0.10
Matches are distributed among these distances:
34 1 0.02
35 24 0.41
37 32 0.55
38 1 0.02
ACGTcount: A:0.28, C:0.21, G:0.07, T:0.45
Consensus pattern (37 bp):
ATTTACTGAATACTATCACCTTGACTCTTAATTATCA
Found at i:15920 original size:71 final size:71
Alignment explanation
Indices: 15687--15923 Score: 341
Period size: 72 Copynumber: 3.3 Consensus size: 71
15677 CCTTTTTACT
* * *
15687 TTGACTCTTAGTTATCAATTTACTGATTAATCTCTTTTTTTACTTAATTACTGATTTACTGAATA
1 TTGACTCTTAATTATCAATTTACTGATTAATC-C-CTTTTTACTTAATTACTGATTTACTGATTA
15752 CTATCACC
64 CTATCACC
* * * *
15760 TTGACTCTTAATTATCAATTTACTGACTAATCTCTTTTTCACTTAGTTACTGATTTACTGATTGC
1 TTGACTCTTAATTATCAATTTACTGATTAATCCCTTTTT-ACTTAATTACTGATTTACTGATTAC
15825 TATCACC
65 TATCACC
*
15832 TTGACTCTTAATTATCAATTTACTAATTAATCCCTTTTTACTTAATTACTGATTTACTGATTACT
1 TTGACTCTTAATTATCAATTTACTGATTAATCCCTTTTTACTTAATTACTGATTTACTGATTACT
*
15897 ATTACC
66 ATCACC
*
15903 TTGACTC-TGATTAATCAATTT
1 TTGACTCTTAATT-ATCAATTT
15924 TCACTTAATT
Statistics
Matches: 148, Mismatches: 14, Indels: 6
0.88 0.08 0.04
Matches are distributed among these distances:
70 4 0.03
71 49 0.33
72 65 0.44
73 30 0.20
ACGTcount: A:0.27, C:0.19, G:0.07, T:0.47
Consensus pattern (71 bp):
TTGACTCTTAATTATCAATTTACTGATTAATCCCTTTTTACTTAATTACTGATTTACTGATTACT
ATCACC
Found at i:15925 original size:126 final size:126
Alignment explanation
Indices: 15795--16105 Score: 523
Period size: 126 Copynumber: 2.5 Consensus size: 126
15785 ACTAATCTCT
* * * *
15795 TTTTCACTTAGTTACTGATTTACTGATTGCTATCACCTTGACTCTTAATTATCAATTTACTAATT
1 TTTTCACTTAATTACTGATTTACTGATTACTATTACCTTGACTCTGAATTATCAATTTACTAATT
*
15860 AATCCCTTTTTACTTAATTACTGATTTACTGATTACTATTACCTTGACTCTGATTAATCAA
66 AATCCCTTTTTACTTAATTACTGATTTACTGATTACTATTACCTTGACTATGATTAATCAA
* * *
15921 TTTTCACTTAATTACTGATTTACTGATTACTATTACCTTGACTCTGAATTATTAACTTACTGATT
1 TTTTCACTTAATTACTGATTTACTGATTACTATTACCTTGACTCTGAATTATCAATTTACTAATT
15986 AATCCCTTTTTACTTAATTACTGATTTACTGATTACTATTACCTTGACTATGATTAATCAA
66 AATCCCTTTTTACTTAATTACTGATTTACTGATTACTATTACCTTGACTATGATTAATCAA
* *
16047 TTTTCACTTAATTACTGATTTTCTGATTTCTATTACCTTGACTCTGAATTAATCAATTT
1 TTTTCACTTAATTACTGATTTACTGATTACTATTACCTTGACTCTGAATT-ATCAATTT
16106 TTGATTAATC
Statistics
Matches: 172, Mismatches: 12, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
126 166 0.97
127 6 0.03
ACGTcount: A:0.28, C:0.18, G:0.07, T:0.47
Consensus pattern (126 bp):
TTTTCACTTAATTACTGATTTACTGATTACTATTACCTTGACTCTGAATTATCAATTTACTAATT
AATCCCTTTTTACTTAATTACTGATTTACTGATTACTATTACCTTGACTATGATTAATCAA
Found at i:15941 original size:55 final size:55
Alignment explanation
Indices: 15857--15967 Score: 195
Period size: 55 Copynumber: 2.0 Consensus size: 55
15847 CAATTTACTA
** *
15857 ATTAATCCCTTTTTACTTAATTACTGATTTACTGATTACTATTACCTTGACTCTG
1 ATTAATCAATTTTCACTTAATTACTGATTTACTGATTACTATTACCTTGACTCTG
15912 ATTAATCAATTTTCACTTAATTACTGATTTACTGATTACTATTACCTTGACTCTG
1 ATTAATCAATTTTCACTTAATTACTGATTTACTGATTACTATTACCTTGACTCTG
15967 A
1 A
15968 ATTATTAACT
Statistics
Matches: 53, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
55 53 1.00
ACGTcount: A:0.28, C:0.19, G:0.07, T:0.46
Consensus pattern (55 bp):
ATTAATCAATTTTCACTTAATTACTGATTTACTGATTACTATTACCTTGACTCTG
Found at i:15947 original size:34 final size:34
Alignment explanation
Indices: 15909--16020 Score: 93
Period size: 34 Copynumber: 3.2 Consensus size: 34
15899 TACCTTGACT
15909 CTGATTAATCAATTTTCACTTAATTACTGATTTA
1 CTGATTAATCAATTTTCACTTAATTACTGATTTA
* * * * *
15943 CTGATT-A-CTATTACCTTGACTCTGAATTATTAACTTA
1 CTGATTAATCAATT---TTCACT-T-AATTACTGATTTA
** *
15980 CTGATTAATCCCTTTTTACTTAATTACTGATTTA
1 CTGATTAATCAATTTTCACTTAATTACTGATTTA
16014 CTGATTA
1 CTGATTA
16021 CTATTACCTT
Statistics
Matches: 60, Mismatches: 11, Indels: 14
0.71 0.13 0.16
Matches are distributed among these distances:
32 4 0.07
33 1 0.02
34 23 0.38
35 6 0.10
36 6 0.10
37 16 0.27
38 1 0.02
39 3 0.05
ACGTcount: A:0.29, C:0.17, G:0.07, T:0.46
Consensus pattern (34 bp):
CTGATTAATCAATTTTCACTTAATTACTGATTTA
Found at i:16040 original size:55 final size:55
Alignment explanation
Indices: 15981--16106 Score: 189
Period size: 55 Copynumber: 2.3 Consensus size: 55
15971 ATTAACTTAC
** *
15981 TGATTAATCCCTTTTTACTTAATTACTGATTTACTGATTACTATTACCTTGACTA
1 TGATTAATCAATTTTCACTTAATTACTGATTTACTGATTACTATTACCTTGACTA
* * *
16036 TGATTAATCAATTTTCACTTAATTACTGATTTTCTGATTTCTATTACCTTGACTC
1 TGATTAATCAATTTTCACTTAATTACTGATTTACTGATTACTATTACCTTGACTA
16091 TGAATTAATCAATTTT
1 TG-ATTAATCAATTTT
16107 TGATTAATCT
Statistics
Matches: 64, Mismatches: 6, Indels: 1
0.90 0.08 0.01
Matches are distributed among these distances:
55 51 0.80
56 13 0.20
ACGTcount: A:0.28, C:0.17, G:0.07, T:0.48
Consensus pattern (55 bp):
TGATTAATCAATTTTCACTTAATTACTGATTTACTGATTACTATTACCTTGACTA
Found at i:17060 original size:67 final size:69
Alignment explanation
Indices: 16912--17066 Score: 289
Period size: 69 Copynumber: 2.3 Consensus size: 69
16902 ACTAATTCCT
16912 AGATAATTTTTATTCTAAATTTCGAATTAATCTATCTAATATATATATATATATATTTCTTTCTA
1 AGATAATTTTTATTCTAAATTTCGAATTAATCTATCTAATATATATATATATATATTTCTTTCTA
16977 CCAA
66 CCAA
16981 AGATAATTTTTATTCTAAATTTCGAATTAATCTATCTAATATATATATAT-T-TATTTCTTTCTA
1 AGATAATTTTTATTCTAAATTTCGAATTAATCTATCTAATATATATATATATATATTTCTTTCTA
17044 CCAA
66 CCAA
17048 AGATAATTTTTATTC-AAAT
1 AGATAATTTTTATTCTAAAT
17067 CAAATAATAT
Statistics
Matches: 86, Mismatches: 0, Indels: 3
0.97 0.00 0.03
Matches are distributed among these distances:
66 4 0.05
67 31 0.36
68 1 0.01
69 50 0.58
ACGTcount: A:0.37, C:0.11, G:0.03, T:0.48
Consensus pattern (69 bp):
AGATAATTTTTATTCTAAATTTCGAATTAATCTATCTAATATATATATATATATATTTCTTTCTA
CCAA
Found at i:21506 original size:21 final size:21
Alignment explanation
Indices: 21472--21512 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
21462 ATTTATATAT
* * *
21472 AAAGATTGATTTTTTTAAGTA
1 AAAGATTCAATTTTTAAAGTA
21493 AAAGATTCAATTTTTAAAGT
1 AAAGATTCAATTTTTAAAGT
21513 GATTTGTAAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.41, C:0.02, G:0.12, T:0.44
Consensus pattern (21 bp):
AAAGATTCAATTTTTAAAGTA
Found at i:21598 original size:49 final size:49
Alignment explanation
Indices: 21535--21628 Score: 127
Period size: 49 Copynumber: 1.9 Consensus size: 49
21525 AAAGTGGGTT
** *
21535 TTTTAATTAGAAGATGACTCTTTCAAGTAATTTGTAAATAGAGATGAAC
1 TTTTAATTAGAAGATGAAGCTTTCAAGTAATTTGTAAATAAAGATGAAC
* *
21584 TTTTAATT-GAAAGATTAAGCTTTTAAGTAATTTGTAAATAAAGAT
1 TTTTAATTAG-AAGATGAAGCTTTCAAGTAATTTGTAAATAAAGAT
21629 TGAGTTTTTA
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
48 1 0.03
49 38 0.97
ACGTcount: A:0.40, C:0.05, G:0.15, T:0.39
Consensus pattern (49 bp):
TTTTAATTAGAAGATGAAGCTTTCAAGTAATTTGTAAATAAAGATGAAC
Found at i:21659 original size:50 final size:50
Alignment explanation
Indices: 21442--21680 Score: 153
Period size: 51 Copynumber: 4.7 Consensus size: 50
21432 AATCTGGTAC
* * * * * ** * *
21442 AAAGTTTAAGCTTTTAAGTAATTTATATATAAAGATTGATTTTTTTAAGTA
1 AAAGATTAATCTTTAAAGTAATTTGTAAATAAAGATTGA-ACTTTTAATTG
* * * ***
21493 AAAGATTCAATTTTTAAAGTGATTTGTAAATAAA-AGTGGGTTTTTTAATT-
1 AAAGATT-AATCTTTAAAGTAATTTGTAAATAAAGA-TTGAACTTTTAATTG
* * * *
21543 AGAAGATGACTCTTTCAAGTAATTTGTAAATAGAGA-TGAACTTTTAATTG
1 A-AAGATTAATCTTTAAAGTAATTTGTAAATAAAGATTGAACTTTTAATTG
* * ** *
21593 AAAGATTAAGCTTTTAAGTAATTTGTAAATAAAGATTGAGTTTTTAGTTGG
1 AAAGATTAATCTTTAAAGTAATTTGTAAATAAAGATTGAACTTTTAATT-G
* * *
21644 AAA-ATTAAATCTTTAAAGTATTTTGTGAATAAGGATT
1 AAAGATT-AATCTTTAAAGTAATTTGTAAATAAAGATT
21681 AAATGTTTTA
Statistics
Matches: 147, Mismatches: 33, Indels: 16
0.75 0.17 0.08
Matches are distributed among these distances:
49 38 0.26
50 36 0.24
51 51 0.35
52 22 0.15
ACGTcount: A:0.39, C:0.03, G:0.16, T:0.42
Consensus pattern (50 bp):
AAAGATTAATCTTTAAAGTAATTTGTAAATAAAGATTGAACTTTTAATTG
Done.