Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008393.1 Corchorus capsularis cultivar CVL-1 contig08414, 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: 55979
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.32
Found at i:2916 original size:15 final size:15
Alignment explanation
Indices: 2896--2926 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
2886 AGTTGCTCTT
*
2896 GTGGCTCATCTTCTG
1 GTGGCTCAACTTCTG
2911 GTGGCTCAACTTCTG
1 GTGGCTCAACTTCTG
2926 G
1 G
2927 CTTGGCAAGG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.10, C:0.26, G:0.29, T:0.35
Consensus pattern (15 bp):
GTGGCTCAACTTCTG
Found at i:4023 original size:22 final size:25
Alignment explanation
Indices: 3979--4037 Score: 72
Period size: 22 Copynumber: 2.5 Consensus size: 25
3969 CTTTTTTTTC
3979 GCAATTTTTTTTTAATCGCAAAA-A
1 GCAATTTTTTTTTAATCGCAAAACA
* *
4003 GCAATTTTTTTTT-A-GGGAAAACA
1 GCAATTTTTTTTTAATCGCAAAACA
4026 -CAATTTTTTTTT
1 GCAATTTTTTTTT
4038 TAGAAAAAAC
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
22 17 0.53
23 2 0.06
24 13 0.41
ACGTcount: A:0.32, C:0.10, G:0.10, T:0.47
Consensus pattern (25 bp):
GCAATTTTTTTTTAATCGCAAAACA
Found at i:4333 original size:21 final size:20
Alignment explanation
Indices: 4294--4338 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
4284 AATTATCAAT
* *
4294 TAAAAATAAAGCAATTAAAC
1 TAAAAACAAAGCAAGTAAAC
*
4314 TAAAAACAAAGCAAAGTAAAT
1 TAAAAACAAAGC-AAGTAAAC
4335 TAAA
1 TAAA
4339 TCTAAATCTA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 11 0.52
21 10 0.48
ACGTcount: A:0.67, C:0.09, G:0.07, T:0.18
Consensus pattern (20 bp):
TAAAAACAAAGCAAGTAAAC
Found at i:11545 original size:14 final size:16
Alignment explanation
Indices: 11528--11570 Score: 56
Period size: 14 Copynumber: 2.8 Consensus size: 16
11518 AAAAAGAAAG
11528 TATAAAATTTCAG-A-
1 TATAAAATTTCAGAAC
11542 TATAGAAA-TTCAGAAC
1 TATA-AAATTTCAGAAC
11558 TATAAAATTTCAG
1 TATAAAATTTCAG
11571 TAAAAAAAGA
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
14 9 0.36
15 7 0.28
16 9 0.36
ACGTcount: A:0.49, C:0.09, G:0.09, T:0.33
Consensus pattern (16 bp):
TATAAAATTTCAGAAC
Found at i:14659 original size:258 final size:251
Alignment explanation
Indices: 14084--14729 Score: 886
Period size: 258 Copynumber: 2.5 Consensus size: 251
14074 TCCCATTTTT
*
14084 CTAATTTAGCGGCGTTTTA-GGTCAAGACGCCGCTATTTTTTAGTCTTCATGTTTACTCAAAAGC
1 CTAATTTAGCGGCG-TTCAGGGTCAAGACGCCGCTATTTTTTAGTCTTCATGTTTACTCAAAAGC
14148 CAATTTCTCCGAAAAAATTAAATATGGCGGCGTTTGAACATCAGACGCCACCATTTAGCGGCGTC
65 CAATTTCTCCG-AAAAATTAAATATGGCGGCG-TTGAACATCAGACGCCACCATTTAGCGGCGTC
* *
14213 TTGGACCTCAAGCGCCACTATTTAGCGGCGTTTAGGGCAAGAAGCCACTATTTCTAGGCTTCATT
128 TTGGACCTCAAACGCCACTATTTAGCGACGTTTAGGGCAAGAAGCCACTATTTCTAGGCTTCATT
* *
14278 TTTAGATTTCATTGCATTTCTCCGAAAAGATTAAATATGGCGGGGACAATTTCTCCCATTTTT
193 TTTAGATTTCATTGCATTTCTCCGAAAAGATTAAATATGGCGGGGACAATATCTCCC----TG
**
14341 CTAATTTAGCGGCGTTTTGGGTCAAGACGCCGCTATTTTTTAGTCTTCATGTTTACTCAAAAGCC
1 CTAATTTAGCGGCGTTCAGGGTCAAGACGCCGCTATTTTTTAGTCTTCATGTTTACTCAAAAGCC
14406 AATTTCTCCGAAAAATTAAATATGGCGGCAGTTGAACATCAGACGCCACCATTTAGCGGCGTCTT
66 AATTTCTCCGAAAAATTAAATATGGCGGC-GTTGAACATCAGACGCCACCATTTAGCGGCGTCTT
* * *
14471 GGACCTCAAACGCCACTATTTAGCGACGTTTAGGGTGAAGACGCCGCTATTTTCTAGGCTTCATT
130 GGACCTCAAACGCCACTATTTAGCGACGTTTAGGG-CAAGAAGCCACTA-TTTCTAGGCTTCATT
**
14536 TTTAGATTTCATTGCATTTCTCCGAAAAGATTAAATATGGCGGCGTTTCGAATATCATACGCC-G
193 TTTAGATTTCATTGCATTTCTCCGAAAAGATTAAATATGGCGG-G-GAC-AATATC-T-C-CCTG
* * * * * ***
14600 C-CATTTAGTGGCGTTCAGGGTCAAGACGCCGCTATGTTTTAGGCTTCATTTTTACTCAAATTAC
1 CTAATTTAGCGGCGTTCAGGGTCAAGACGCCGCTATTTTTTAGTCTTCATGTTTACTCAAAAGCC
* * *
14664 -ATTTCTCCGAAAAGATTAAATATGGCGGCGTCTCGTACTTCAGACGCCACCATTTAACGGCGTC
66 AATTTCTCCGAAAA-ATTAAATATGGCGGCGT-T-GAACATCAGACGCCACCATTTAGCGGCGTC
14728 TT
128 TT
14730 TTGCCAAGAC
Statistics
Matches: 353, Mismatches: 23, Indels: 24
0.88 0.06 0.06
Matches are distributed among these distances:
256 89 0.25
257 96 0.27
258 127 0.36
259 31 0.09
260 1 0.00
261 5 0.01
262 1 0.00
263 1 0.00
264 2 0.01
ACGTcount: A:0.26, C:0.22, G:0.20, T:0.32
Consensus pattern (251 bp):
CTAATTTAGCGGCGTTCAGGGTCAAGACGCCGCTATTTTTTAGTCTTCATGTTTACTCAAAAGCC
AATTTCTCCGAAAAATTAAATATGGCGGCGTTGAACATCAGACGCCACCATTTAGCGGCGTCTTG
GACCTCAAACGCCACTATTTAGCGACGTTTAGGGCAAGAAGCCACTATTTCTAGGCTTCATTTTT
AGATTTCATTGCATTTCTCCGAAAAGATTAAATATGGCGGGGACAATATCTCCCTG
Found at i:14717 original size:113 final size:113
Alignment explanation
Indices: 14461--14719 Score: 315
Period size: 114 Copynumber: 2.3 Consensus size: 113
14451 CCACCATTTA
* * * * *
14461 GCGGCGTCTTGGACCTCAAACGCCACTATTTAGCGACGTTTAGGGTGAAGACGCCGCTATTTTCT
1 GCGGCGTC-TCGACTTCAAACGCCACCATTTAGCGACGTTCAGGGTCAAGACGCCGCTATTTTCT
*** *
14526 AGGCTTCATTTTTAGATTTCATTGCATTTCTCCGAAAAGATTAAATATG
65 AGGCTTCATTTTTAGATCAAATTACATTTCTCCGAAAAGATTAAATATG
* * * * * *
14575 GCGGCGTTTCGAATATCATACGCCGCCATTTAGTGGCGTTCAGGGTCAAGACGCCGCTATGTTT-
1 GCGGCGTCTCGACT-TCAAACGCCACCATTTAGCGACGTTCAGGGTCAAGACGCCGCTAT-TTTC
*
14639 TAGGCTTCATTTTTA-CTCAAATTACATTTCTCCGAAAAGATTAAATATG
64 TAGGCTTCATTTTTAGATCAAATTACATTTCTCCGAAAAGATTAAATATG
*
14688 GCGGCGTCTCGTACTTCAGACGCCACCATTTA
1 GCGGCGTCTCG-ACTTCAAACGCCACCATTTA
14720 ACGGCGTCTT
Statistics
Matches: 122, Mismatches: 20, Indels: 7
0.82 0.13 0.05
Matches are distributed among these distances:
113 57 0.47
114 62 0.51
115 3 0.02
ACGTcount: A:0.24, C:0.23, G:0.21, T:0.32
Consensus pattern (113 bp):
GCGGCGTCTCGACTTCAAACGCCACCATTTAGCGACGTTCAGGGTCAAGACGCCGCTATTTTCTA
GGCTTCATTTTTAGATCAAATTACATTTCTCCGAAAAGATTAAATATG
Found at i:14726 original size:113 final size:113
Alignment explanation
Indices: 14461--14726 Score: 320
Period size: 113 Copynumber: 2.3 Consensus size: 113
14451 CCACCATTTA
* * * * * *
14461 GCGGCGTCTTGGACCTCAAACGCCACTATTTAGCGACGTTTAGGGTGAAGACGCCGCTATTTTCT
1 GCGGCGTC-TCGACTTCAAACGCCACCATTTAGCGGCGTTCAGGGTCAAGACGCCGCTATTTTCT
*** *
14526 AGGCTTCATTTTTAGATTTCATTGCATTTCTCCGAAAAGATTAAATATG
65 AGGCTTCATTTTTAGATCAAATTACATTTCTCCGAAAAGATTAAATATG
* * * * *
14575 GCGGCGTTTCGAATATCATACGCCGCCATTTAGTGGCGTTCAGGGTCAAGACGCCGCTATGTTT-
1 GCGGCGTCTCGACT-TCAAACGCCACCATTTAGCGGCGTTCAGGGTCAAGACGCCGCTAT-TTTC
*
14639 TAGGCTTCATTTTTA-CTCAAATTACATTTCTCCGAAAAGATTAAATATG
64 TAGGCTTCATTTTTAGATCAAATTACATTTCTCCGAAAAGATTAAATATG
* *
14688 GCGGCGTCTCGTACTTCAGACGCCACCATTTAACGGCGT
1 GCGGCGTCTCG-ACTTCAAACGCCACCATTTAGCGGCGT
14727 CTTTTGCCAA
Statistics
Matches: 127, Mismatches: 22, Indels: 7
0.81 0.14 0.04
Matches are distributed among these distances:
113 62 0.49
114 62 0.49
115 3 0.02
ACGTcount: A:0.24, C:0.23, G:0.21, T:0.32
Consensus pattern (113 bp):
GCGGCGTCTCGACTTCAAACGCCACCATTTAGCGGCGTTCAGGGTCAAGACGCCGCTATTTTCTA
GGCTTCATTTTTAGATCAAATTACATTTCTCCGAAAAGATTAAATATG
Found at i:18642 original size:21 final size:21
Alignment explanation
Indices: 18600--18648 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 21
18590 GCACTGGAGG
* * *
18600 ACATGGGTCGCGAGGCAAACC
1 ACATGGGGCGCCAAGCAAACC
*
18621 ACATGGGGCGCCAAGCATACC
1 ACATGGGGCGCCAAGCAAACC
*
18642 ACTTGGG
1 ACATGGG
18649 CCCCCAGCTA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.27, C:0.29, G:0.33, T:0.12
Consensus pattern (21 bp):
ACATGGGGCGCCAAGCAAACC
Found at i:18755 original size:21 final size:21
Alignment explanation
Indices: 18699--18747 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 21
18689 GGCGCTGGTG
** * *
18699 ACATGGGCGCTGAGGCCAACT
1 ACATGGGCGCACAAGCCAACC
*
18720 ACCTGGGCGCACAAGCCAACC
1 ACATGGGCGCACAAGCCAACC
18741 ACATGGG
1 ACATGGG
18748 TGCCCAAGGG
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.27, C:0.33, G:0.31, T:0.10
Consensus pattern (21 bp):
ACATGGGCGCACAAGCCAACC
Found at i:20907 original size:12 final size:12
Alignment explanation
Indices: 20890--20925 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
20880 CATGCGATGG
20890 CCGGTCATGTGC
1 CCGGTCATGTGC
*
20902 CCGGTCATGTGG
1 CCGGTCATGTGC
*
20914 CCGGTCTTGTGC
1 CCGGTCATGTGC
20926 GGTCCTTCCA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.06, C:0.31, G:0.36, T:0.28
Consensus pattern (12 bp):
CCGGTCATGTGC
Found at i:25743 original size:20 final size:20
Alignment explanation
Indices: 25715--25752 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
25705 ACCATGGTTC
* *
25715 TGTCTCTGCCGTAACTATAT
1 TGTCCCTGCCGCAACTATAT
25735 TGTCCCTGCCGCAACTAT
1 TGTCCCTGCCGCAACTAT
25753 GACACATCGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.18, C:0.32, G:0.16, T:0.34
Consensus pattern (20 bp):
TGTCCCTGCCGCAACTATAT
Found at i:27012 original size:72 final size:72
Alignment explanation
Indices: 26896--27171 Score: 358
Period size: 72 Copynumber: 3.8 Consensus size: 72
26886 GTAGTAGCAT
* *
26896 GGATTGTGCGAAGGACTGCC-AATGTGGGAACTGCCTCGACTACAATCGCAATGAGGAGGATAAT
1 GGATTGTGCGAAGGACTGCCAAATGTGGGAACTGCCTCGGCTACAATCGCAATGAGGAAGATAAT
26960 CACATAA
66 CACATAA
* * * * * * *
26967 GGATTGTGCGAAGGACTGCTAGATGTGGGAATTGCCTCGGCTACAATCACATTGATGAATATAAT
1 GGATTGTGCGAAGGACTGCCAAATGTGGGAACTGCCTCGGCTACAATCGCAATGAGGAAGATAAT
* *
27032 CGCATGA
66 CACATAA
* * * * *
27039 GGGTTGTGCGAAGGACTACCAAATGTGGGAACTCCCTCGGCTACCATCGCAAT-ATGGAAGATTA
1 GGATTGTGCGAAGGACTGCCAAATGTGGGAACTGCCTCGGCTACAATCGCAATGA-GGAAGATAA
**
27103 TCATGTAA
65 TCACATAA
*
27111 GGATTGTGCGAAGGACTGCCAAATGTGGGAACTGCCTCGGCTACAATCGCAATGAAGAAGA
1 GGATTGTGCGAAGGACTGCCAAATGTGGGAACTGCCTCGGCTACAATCGCAATGAGGAAGA
27172 AGACCATGGG
Statistics
Matches: 170, Mismatches: 32, Indels: 5
0.82 0.15 0.02
Matches are distributed among these distances:
71 20 0.12
72 149 0.88
73 1 0.01
ACGTcount: A:0.30, C:0.19, G:0.28, T:0.22
Consensus pattern (72 bp):
GGATTGTGCGAAGGACTGCCAAATGTGGGAACTGCCTCGGCTACAATCGCAATGAGGAAGATAAT
CACATAA
Found at i:28478 original size:26 final size:26
Alignment explanation
Indices: 28449--28663 Score: 116
Period size: 26 Copynumber: 7.6 Consensus size: 26
28439 TAGATGCCTC
28449 TGTGTTT-AGGGACTTATGAATGCCCT
1 TGTGTTTGA-GGACTTATGAATGCCCT
* *
28475 TGTGTTTGAGGACTTTTTAGAATAGATGCCT
1 TGTGTTTGAGGAC-TTAT-GAAT-G--CCCT
*
28506 CTGTGTTT-AGGGACTTATAAATGCCCT
1 -TGTGTTTGA-GGACTTATGAATGCCCT
* * *
28533 TGTGTTTGAGGACTTTTTAGTATAGAGGCCT
1 TGTGTTTGAGGAC-TTAT-G-A-A-TGCCCT
28564 CTGTGTTT-AGGGACTTATGAATGCCCT
1 -TGTGTTTGA-GGACTTATGAATGCCCT
*
28591 TGTGTTTGAGGACTTTTTAGTATAGATG-CCT
1 TGTGTTTGAGGAC---TTA-T-GA-ATGCCCT
28622 CTGTGTTT-AGGGACTTATGAATGCCCT
1 -TGTGTTTGA-GGACTTATGAATGCCCT
*
28649 GGTGTTTGAGGACTT
1 TGTGTTTGAGGACTT
28664 TTTGATAGAG
Statistics
Matches: 147, Mismatches: 15, Indels: 54
0.68 0.07 0.25
Matches are distributed among these distances:
26 48 0.33
27 21 0.14
28 6 0.04
29 10 0.07
30 6 0.04
31 20 0.14
32 36 0.24
ACGTcount: A:0.20, C:0.13, G:0.27, T:0.40
Consensus pattern (26 bp):
TGTGTTTGAGGACTTATGAATGCCCT
Found at i:28504 original size:32 final size:32
Alignment explanation
Indices: 28419--28637 Score: 139
Period size: 32 Copynumber: 7.5 Consensus size: 32
28409 AGATTGCCCA
* * *
28419 TGTGCTTAGGGAC-TTTGATATAGATG-CCTC
1 TGTGTTTAGGGACTTTTTAGATAGATGCCCTC
*
28449 TGTGTTTAGGGAC-TTAT-G--A-ATGCCCT-
1 TGTGTTTAGGGACTTTTTAGATAGATGCCCTC
28475 TGTGTTT-GAGGACTTTTTAGAATAGATG-CCTC
1 TGTGTTTAG-GGACTTTTTAG-ATAGATGCCCTC
*
28507 TGTGTTTAGGGAC---TT--ATAAATGCCCT-
1 TGTGTTTAGGGACTTTTTAGATAGATGCCCTC
*
28533 TGTGTTT-GAGGACTTTTTAGTATAGA-GGCCTC
1 TGTGTTTAG-GGACTTTTTAG-ATAGATGCCCTC
*
28565 TGTGTTTAGGGAC-TTAT-G--A-ATGCCCT-
1 TGTGTTTAGGGACTTTTTAGATAGATGCCCTC
28591 TGTGTTT-GAGGACTTTTTAGTATAGATG-CCTC
1 TGTGTTTAG-GGACTTTTTAG-ATAGATGCCCTC
28623 TGTGTTTAGGGACTT
1 TGTGTTTAGGGACTT
28638 ATGAATGCCC
Statistics
Matches: 148, Mismatches: 11, Indels: 58
0.68 0.05 0.27
Matches are distributed among these distances:
25 3 0.02
26 43 0.29
27 18 0.12
28 2 0.01
29 4 0.03
30 15 0.10
31 15 0.10
32 45 0.30
33 3 0.02
ACGTcount: A:0.20, C:0.14, G:0.26, T:0.40
Consensus pattern (32 bp):
TGTGTTTAGGGACTTTTTAGATAGATGCCCTC
Found at i:28507 original size:58 final size:58
Alignment explanation
Indices: 28437--28666 Score: 424
Period size: 58 Copynumber: 4.0 Consensus size: 58
28427 GGGACTTTGA
28437 TATAGATGCCTCTGTGTTTAGGGACTTATGAATGCCCTTGTGTTTGAGGACTTTTTAG
1 TATAGATGCCTCTGTGTTTAGGGACTTATGAATGCCCTTGTGTTTGAGGACTTTTTAG
* *
28495 AATAGATGCCTCTGTGTTTAGGGACTTATAAATGCCCTTGTGTTTGAGGACTTTTTAG
1 TATAGATGCCTCTGTGTTTAGGGACTTATGAATGCCCTTGTGTTTGAGGACTTTTTAG
*
28553 TATAGAGGCCTCTGTGTTTAGGGACTTATGAATGCCCTTGTGTTTGAGGACTTTTTAG
1 TATAGATGCCTCTGTGTTTAGGGACTTATGAATGCCCTTGTGTTTGAGGACTTTTTAG
*
28611 TATAGATGCCTCTGTGTTTAGGGACTTATGAATGCCCTGGTGTTTGAGGACTTTTT
1 TATAGATGCCTCTGTGTTTAGGGACTTATGAATGCCCTTGTGTTTGAGGACTTTTT
28667 GATAGAGGAT
Statistics
Matches: 165, Mismatches: 7, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
58 165 1.00
ACGTcount: A:0.20, C:0.14, G:0.26, T:0.40
Consensus pattern (58 bp):
TATAGATGCCTCTGTGTTTAGGGACTTATGAATGCCCTTGTGTTTGAGGACTTTTTAG
Found at i:33052 original size:33 final size:33
Alignment explanation
Indices: 33010--33081 Score: 99
Period size: 33 Copynumber: 2.2 Consensus size: 33
33000 GTTAGCATCC
* * *
33010 AAAATAGATTTTGTTTCATCACAAACAACACCT
1 AAAACAGATTTAGTGTCATCACAAACAACACCT
* *
33043 AAAACAGATTTAGTGTCATCGCAAACAACATCT
1 AAAACAGATTTAGTGTCATCACAAACAACACCT
33076 AAAACA
1 AAAACA
33082 CTCTTTGCAA
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.46, C:0.21, G:0.08, T:0.25
Consensus pattern (33 bp):
AAAACAGATTTAGTGTCATCACAAACAACACCT
Found at i:52698 original size:18 final size:17
Alignment explanation
Indices: 52670--52707 Score: 51
Period size: 16 Copynumber: 2.2 Consensus size: 17
52660 GTAAAAATAT
52670 AAAGAAAAAGAATAATTAA
1 AAAGAAAAAG-A-AATTAA
52689 AAAG-AAAAGAAATTAA
1 AAAGAAAAAGAAATTAA
52705 AAA
1 AAA
52708 AACCTCTCCC
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 9 0.47
17 1 0.05
18 5 0.26
19 4 0.21
ACGTcount: A:0.76, C:0.00, G:0.11, T:0.13
Consensus pattern (17 bp):
AAAGAAAAAGAAATTAA
Found at i:53198 original size:14 final size:15
Alignment explanation
Indices: 53179--53207 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
53169 CACATGTTGC
53179 TTCTTTC-TTAATTT
1 TTCTTTCATTAATTT
53193 TTCTTTCATTAATTT
1 TTCTTTCATTAATTT
53208 CTTTTTTCTG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.17, C:0.14, G:0.00, T:0.69
Consensus pattern (15 bp):
TTCTTTCATTAATTT
Found at i:53703 original size:15 final size:15
Alignment explanation
Indices: 53683--53721 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 15
53673 AGAATTAAAC
53683 AAGTTAATTTTCCAG
1 AAGTTAATTTTCCAG
**
53698 AAGTT-ATTTTCTGG
1 AAGTTAATTTTCCAG
53712 AAGTTAATTT
1 AAGTTAATTT
53722 ATGTGAACCA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
14 12 0.57
15 9 0.43
ACGTcount: A:0.31, C:0.08, G:0.15, T:0.46
Consensus pattern (15 bp):
AAGTTAATTTTCCAG
Found at i:53812 original size:21 final size:21
Alignment explanation
Indices: 53799--53839 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
53789 AGAAACTTTC
53799 AAATATAAATAAGAAACCTCT
1 AAATATAAATAAGAAACCTCT
* *
53820 GAATATAAATAAGAGACCTC
1 AAATATAAATAAGAAACCTC
53840 CAACATACGA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.54, C:0.15, G:0.10, T:0.22
Consensus pattern (21 bp):
AAATATAAATAAGAAACCTCT
Done.