Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013452.1 Corchorus olitorius cultivar O-4 contig13485, 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: 36907
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.33
Found at i:2587 original size:15 final size:15
Alignment explanation
Indices: 2542--2591 Score: 73
Period size: 15 Copynumber: 3.3 Consensus size: 15
2532 TGCACCATTT
* *
2542 CCATTATTGTTCACA
1 CCATTGTTGTTCGCA
2557 CCATTGTTGTTCGCA
1 CCATTGTTGTTCGCA
*
2572 CCATTGTTGTTTGCA
1 CCATTGTTGTTCGCA
2587 CCATT
1 CCATT
2592 CACCCTAGCA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 32 1.00
ACGTcount: A:0.18, C:0.26, G:0.14, T:0.42
Consensus pattern (15 bp):
CCATTGTTGTTCGCA
Found at i:3514 original size:49 final size:47
Alignment explanation
Indices: 3413--3554 Score: 169
Period size: 49 Copynumber: 3.0 Consensus size: 47
3403 GAGCGTGCCA
* * * *
3413 ATCAATTTTGTCAAAAAATTGATAAAAAGTGCGATGAAAATTAAAAG
1 ATCAATTTTGTCTAAAAATTGAGAAAAAGTGCAATGAAAAATAAAAG
3460 ATCAATTTTGTCTTAAAAATTGAGAAAAAGATGCAA-GTAAAAATAAAAG
1 ATCAATTTTGTC-TAAAAATTGAGAAAAAG-TGCAATG-AAAAATAAAAG
* * * *
3509 TTCAATTTTGTAGTAAAAATTGAGAAAAAGTGCAGTGAAAAGTAAA
1 ATCAATTTTGT-CTAAAAATTGAGAAAAAGTGCAATGAAAAATAAA
3555 GGATTGCTTG
Statistics
Matches: 82, Mismatches: 8, Indels: 9
0.83 0.08 0.09
Matches are distributed among these distances:
47 12 0.15
48 28 0.34
49 42 0.51
ACGTcount: A:0.51, C:0.06, G:0.16, T:0.27
Consensus pattern (47 bp):
ATCAATTTTGTCTAAAAATTGAGAAAAAGTGCAATGAAAAATAAAAG
Found at i:7737 original size:36 final size:36
Alignment explanation
Indices: 7656--7793 Score: 158
Period size: 34 Copynumber: 3.8 Consensus size: 36
7646 AACTAGGACC
*
7656 TGATGGGAACTCTCCCAA-TTTAAAACTTTGAAAAAAAC-
1 TGATGGGAACTTTCCCAATTTTAAAAC-TT---AAAAACT
*
7694 CGAATGGGAACTTTCCCAATTTTAAAACTTAAAAACT
1 TG-ATGGGAACTTTCCCAATTTTAAAACTTAAAAACT
*
7731 TGATGGGAACTTTCCCAATTTAAAAAC-T-AAAACT
1 TGATGGGAACTTTCCCAATTTTAAAACTTAAAAACT
* *
7765 TGGTGGGAACTTTCCCAATTTGAAAACTT
1 TGATGGGAACTTTCCCAATTTTAAAACTT
7794 CGAAGACCTA
Statistics
Matches: 90, Mismatches: 6, Indels: 11
0.84 0.06 0.10
Matches are distributed among these distances:
34 31 0.34
35 2 0.02
36 30 0.33
37 1 0.01
38 1 0.01
39 17 0.19
40 8 0.09
ACGTcount: A:0.38, C:0.18, G:0.14, T:0.30
Consensus pattern (36 bp):
TGATGGGAACTTTCCCAATTTTAAAACTTAAAAACT
Found at i:9027 original size:15 final size:15
Alignment explanation
Indices: 9016--9045 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
9006 CCCAAATCTC
9016 AACCTCCAAAATTCG
1 AACCTCCAAAATTCG
9031 AACCTCCCAAAATTC
1 AACCT-CCAAAATTC
9046 TCTATTAGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.40, C:0.37, G:0.03, T:0.20
Consensus pattern (15 bp):
AACCTCCAAAATTCG
Found at i:9042 original size:16 final size:15
Alignment explanation
Indices: 9004--9045 Score: 52
Period size: 15 Copynumber: 2.8 Consensus size: 15
8994 AAACTTCCCT
9004 CTCCC-AAATCTCAAC
1 CTCCCAAAAT-TCAAC
9019 CT-CCAAAATTCGAAC
1 CTCCCAAAATTC-AAC
9034 CTCCCAAAATTC
1 CTCCCAAAATTC
9046 TCTATTAGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
14 4 0.17
15 11 0.46
16 9 0.38
ACGTcount: A:0.36, C:0.40, G:0.02, T:0.21
Consensus pattern (15 bp):
CTCCCAAAATTCAAC
Found at i:14231 original size:19 final size:19
Alignment explanation
Indices: 14207--14244 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
14197 ATAAACAAAC
14207 AAACAAATTACAAATTAAA
1 AAACAAATTACAAATTAAA
14226 AAACAAATTACAAATTAAA
1 AAACAAATTACAAATTAAA
14245 CTCACATTAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.68, C:0.11, G:0.00, T:0.21
Consensus pattern (19 bp):
AAACAAATTACAAATTAAA
Found at i:15434 original size:77 final size:77
Alignment explanation
Indices: 15307--15461 Score: 310
Period size: 77 Copynumber: 2.0 Consensus size: 77
15297 TGTGGGGGCT
15307 ACACAAGGCATTGAAACACAAAATCCCGTGGGTCTCAGTCTATGGACTCAAATTTTGCTAACAAA
1 ACACAAGGCATTGAAACACAAAATCCCGTGGGTCTCAGTCTATGGACTCAAATTTTGCTAACAAA
15372 CTTGGCCTTTTC
66 CTTGGCCTTTTC
15384 ACACAAGGCATTGAAACACAAAATCCCGTGGGTCTCAGTCTATGGACTCAAATTTTGCTAACAAA
1 ACACAAGGCATTGAAACACAAAATCCCGTGGGTCTCAGTCTATGGACTCAAATTTTGCTAACAAA
15449 CTTGGCCTTTTC
66 CTTGGCCTTTTC
15461 A
1 A
15462 TGTGAAATTG
Statistics
Matches: 78, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
77 78 1.00
ACGTcount: A:0.32, C:0.25, G:0.17, T:0.27
Consensus pattern (77 bp):
ACACAAGGCATTGAAACACAAAATCCCGTGGGTCTCAGTCTATGGACTCAAATTTTGCTAACAAA
CTTGGCCTTTTC
Found at i:26496 original size:28 final size:28
Alignment explanation
Indices: 26474--26546 Score: 146
Period size: 28 Copynumber: 2.6 Consensus size: 28
26464 TTTGAATTTT
26474 TAAATTCCACTAATTTTTTTTGACATCA
1 TAAATTCCACTAATTTTTTTTGACATCA
26502 TAAATTCCACTAATTTTTTTTGACATCA
1 TAAATTCCACTAATTTTTTTTGACATCA
26530 TAAATTCCACTAATTTT
1 TAAATTCCACTAATTTT
26547 GCAAGCCATA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 45 1.00
ACGTcount: A:0.33, C:0.18, G:0.03, T:0.47
Consensus pattern (28 bp):
TAAATTCCACTAATTTTTTTTGACATCA
Found at i:31911 original size:12 final size:12
Alignment explanation
Indices: 31894--31929 Score: 65
Period size: 12 Copynumber: 3.1 Consensus size: 12
31884 TAAAATATAA
31894 GGCTCGAAGCTC
1 GGCTCGAAGCTC
31906 GGCTCGAAGCTC
1 GGCTCGAAGCTC
31918 GGCTCGAA-CTC
1 GGCTCGAAGCTC
31929 G
1 G
31930 ATCGAGCCTC
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
11 4 0.17
12 20 0.83
ACGTcount: A:0.17, C:0.33, G:0.33, T:0.17
Consensus pattern (12 bp):
GGCTCGAAGCTC
Found at i:36027 original size:15 final size:16
Alignment explanation
Indices: 36009--36041 Score: 59
Period size: 15 Copynumber: 2.1 Consensus size: 16
35999 GAATAAATAT
36009 TAAAAGAAGTATG-CA
1 TAAAAGAAGTATGACA
36024 TAAAAGAAGTATGACA
1 TAAAAGAAGTATGACA
36040 TA
1 TA
36042 CATCCCACAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 13 0.76
16 4 0.24
ACGTcount: A:0.55, C:0.06, G:0.18, T:0.21
Consensus pattern (16 bp):
TAAAAGAAGTATGACA
Found at i:36410 original size:2 final size:2
Alignment explanation
Indices: 36397--36435 Score: 51
Period size: 2 Copynumber: 19.5 Consensus size: 2
36387 AATTGTTTTG
* * *
36397 AT AT AA AT AT AT AT AT AT AT AT AT AT AT TT AA AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
36436 ACATATACCG
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Done.