Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007261.1 Corchorus capsularis cultivar CVL-1 contig07282, 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: 22656
ACGTcount: A:0.34, C:0.18, G:0.19, T:0.29
Found at i:5659 original size:27 final size:26
Alignment explanation
Indices: 5610--5657 Score: 82
Period size: 26 Copynumber: 1.9 Consensus size: 26
5600 CACTTGTTTG
5610 AGCTTGGGGAAAGCTCTGTGTTGTCA
1 AGCTTGGGGAAAGCTCTGTGTTGTCA
5636 AGCTTGGGGAAAGCT-TG-GTTGT
1 AGCTTGGGGAAAGCTCTGTGTTGT
5658 TGTAACGGTT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
24 5 0.23
25 2 0.09
26 15 0.68
ACGTcount: A:0.19, C:0.12, G:0.38, T:0.31
Consensus pattern (26 bp):
AGCTTGGGGAAAGCTCTGTGTTGTCA
Found at i:11558 original size:71 final size:71
Alignment explanation
Indices: 11442--11580 Score: 190
Period size: 71 Copynumber: 2.0 Consensus size: 71
11432 GTTAAGAAAG
* * * *
11442 TAATTAAGAAAAGAGAGTACAATCAAGCTCCTAAGTTGGGCAATTAAGAAGAATAATGTCTTATT
1 TAATTAAGAAAAGAAAGTACAATCAAGCTCCTAAGTTGGACAATTAAGAAGAATAAAGTCTTAAT
11507 TCAGGA
66 TCAGGA
* * * *
11513 TAATTAGGAGAAGAAAGTACAGTCGAAG-TCCTAAGTTGGACAATTAAGAAGAGTAAAGTCTTAA
1 TAATTAAGAAAAGAAAGTACAATC-AAGCTCCTAAGTTGGACAATTAAGAAGAATAAAGTCTTAA
11577 TTCA
65 TTCA
11581 AGGTTATTAA
Statistics
Matches: 59, Mismatches: 8, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
71 56 0.95
72 3 0.05
ACGTcount: A:0.42, C:0.11, G:0.21, T:0.26
Consensus pattern (71 bp):
TAATTAAGAAAAGAAAGTACAATCAAGCTCCTAAGTTGGACAATTAAGAAGAATAAAGTCTTAAT
TCAGGA
Found at i:11692 original size:42 final size:42
Alignment explanation
Indices: 11628--12290 Score: 1061
Period size: 42 Copynumber: 15.9 Consensus size: 42
11618 AATTTGGATA
* *
11628 AATCCAGGGTGATTAAGGAAAGTCAAACATGGTAAGAGTCCT
1 AATCCAGGGTGATTAAGAAAAGTCAAACATGGTTAGAGTCCT
*
11670 AATCCAGGGTGATTAAGAAAAGTCAAACATGGTTAGAATCCT
1 AATCCAGGGTGATTAAGAAAAGTCAAACATGGTTAGAGTCCT
* *
11712 AATCCAAGGTGATTAAGAAAAGTCGAACATGGTTAGAGTCCT
1 AATCCAGGGTGATTAAGAAAAGTCAAACATGGTTAGAGTCCT
*
11754 AATCCGGGGTGATTAAGAAAAGTCAAACATGGTTAGAGTCCT
1 AATCCAGGGTGATTAAGAAAAGTCAAACATGGTTAGAGTCCT
*
11796 AATCCGGGGTGATTAAGAAAAGTCAAACATGGTTAGAGTCCT
1 AATCCAGGGTGATTAAGAAAAGTCAAACATGGTTAGAGTCCT
* *
11838 ACTCCAGGGTGATTAAGAAAAGTCAAACATGGTTAGAATCCT
1 AATCCAGGGTGATTAAGAAAAGTCAAACATGGTTAGAGTCCT
* *
11880 AATCCAGGGTGATTAAGAAAAGTCGAACATGGTTAAAG-CCT
1 AATCCAGGGTGATTAAGAAAAGTCAAACATGGTTAGAGTCCT
*
11921 AATCTAGGGTGATTAAGAAAAGTCAAACATGGTTAGAGTCCT
1 AATCCAGGGTGATTAAGAAAAGTCAAACATGGTTAGAGTCCT
11963 AATCCAGGGTGATTAAGAAAAGTCAAACATGGTTAGAGTCCT
1 AATCCAGGGTGATTAAGAAAAGTCAAACATGGTTAGAGTCCT
12005 AATCCAGGGTGATTAAGAAAAGTCAAACATGGTTAGAGTCCT
1 AATCCAGGGTGATTAAGAAAAGTCAAACATGGTTAGAGTCCT
12047 AATCCAGGG-GCATTAAGAAAAGTCAAACATGGTTAGAGTCCT
1 AATCCAGGGTG-ATTAAGAAAAGTCAAACATGGTTAGAGTCCT
*
12089 AATCCAGGGTGATTAAGAAAAGTCAAACATGGTTAGAATCCT
1 AATCCAGGGTGATTAAGAAAAGTCAAACATGGTTAGAGTCCT
* *
12131 AATCCAAGGTGATTAAGAAAAGTCAAACATGG-TAGGGTCCT
1 AATCCAGGGTGATTAAGAAAAGTCAAACATGGTTAGAGTCCT
* *
12172 AATCCAGGGTGATT----AAAGTCAAACGTGGTAAGAGTCCT
1 AATCCAGGGTGATTAAGAAAAGTCAAACATGGTTAGAGTCCT
* *
12210 AATCCAGGGTGATTAAGAAAAGTCGAACATGGTTAGAGTCTT
1 AATCCAGGGTGATTAAGAAAAGTCAAACATGGTTAGAGTCCT
* * *
12252 AATCCAGGGTGATTAGGAAAGGTCAAAACACGGTTAGAG
1 AATCCAGGGTGATTAAGAAAAGTC-AAACATGGTTAGAG
12291 AACTTAATTC
Statistics
Matches: 576, Mismatches: 36, Indels: 17
0.92 0.06 0.03
Matches are distributed among these distances:
37 13 0.02
38 21 0.04
41 59 0.10
42 470 0.82
43 13 0.02
ACGTcount: A:0.38, C:0.14, G:0.25, T:0.23
Consensus pattern (42 bp):
AATCCAGGGTGATTAAGAAAAGTCAAACATGGTTAGAGTCCT
Found at i:12370 original size:37 final size:36
Alignment explanation
Indices: 12284--12471 Score: 261
Period size: 37 Copynumber: 5.1 Consensus size: 36
12274 TCAAAACACG
*
12284 GTTAGAGAACTTAATTCAGGGCAATTAAGTAAAAACA
1 GTTA-AGAACTTAATTCAGGGTAATTAAGTAAAAACA
* *
12321 GTCAA-AATCTTAATTCAGGGTAATTTAGTAAAGAACA
1 GTTAAGAA-CTTAATTCAGGGTAATTAAGTAAA-AACA
* ** *
12358 GTTAAGAACTTAATTCAAGACAATTAAGTAAAAGCA
1 GTTAAGAACTTAATTCAGGGTAATTAAGTAAAAACA
12394 GTTAAGAACTTAATTCAGGGTAATTAAGTAAAAACA
1 GTTAAGAACTTAATTCAGGGTAATTAAGTAAAAACA
*
12430 GTTGAAGGACTTAATTCAGGGTAATTAAGTAAAAACA
1 GTT-AAGAACTTAATTCAGGGTAATTAAGTAAAAACA
12467 GTTAA
1 GTTAA
12472 AAGGTAAGGA
Statistics
Matches: 133, Mismatches: 14, Indels: 9
0.85 0.09 0.06
Matches are distributed among these distances:
35 2 0.02
36 63 0.47
37 66 0.50
38 2 0.02
ACGTcount: A:0.46, C:0.10, G:0.18, T:0.27
Consensus pattern (36 bp):
GTTAAGAACTTAATTCAGGGTAATTAAGTAAAAACA
Found at i:12408 original size:73 final size:72
Alignment explanation
Indices: 12284--12473 Score: 274
Period size: 73 Copynumber: 2.6 Consensus size: 72
12274 TCAAAACACG
* *
12284 GTTAGAGAACTTAATTCAGGGCAATTAAGTAAAAACAGTCAAAATCTTAATTCAGGGTAATTTAG
1 GTTA-AGAACTTAATTCAGGGCAATTAAGTAAAAACAGTTAAAATCTTAATTCAGGGTAATTAAG
12349 TAAAGAACA
65 TAAA-AACA
* * *
12358 GTTAAGAACTTAATTCAAGACAATTAAGTAAAAGCAGTTAAGAA-CTTAATTCAGGGTAATTAAG
1 GTTAAGAACTTAATTCAGGGCAATTAAGTAAAAACAGTTAA-AATCTTAATTCAGGGTAATTAAG
12422 TAAAAACA
65 TAAAAACA
* *
12430 GTTGAAGGACTTAATTCAGGGTAATTAAGTAAAAACAGTTAAAA
1 GTT-AAGAACTTAATTCAGGGCAATTAAGTAAAAACAGTTAAAA
12474 GGTAAGGATA
Statistics
Matches: 104, Mismatches: 10, Indels: 6
0.87 0.08 0.05
Matches are distributed among these distances:
72 9 0.09
73 89 0.86
74 6 0.06
ACGTcount: A:0.46, C:0.09, G:0.17, T:0.27
Consensus pattern (72 bp):
GTTAAGAACTTAATTCAGGGCAATTAAGTAAAAACAGTTAAAATCTTAATTCAGGGTAATTAAGT
AAAAACA
Found at i:12705 original size:42 final size:37
Alignment explanation
Indices: 12654--12808 Score: 193
Period size: 37 Copynumber: 4.2 Consensus size: 37
12644 ACCTCCGGGG
* * * *
12654 ATTAAGTAAAGAAAAGTATTTGGTTCCAAGGAAGGGA
1 ATTAAGTAGAGTAAAGGACTTGGTTCCAAGGAAGGGA
12691 ATTAAGTAGAGTAAAGGACTTGGTTCCAAGGAAGGGA
1 ATTAAGTAGAGTAAAGGACTTGGTTCCAAGGAAGGGA
* * *
12728 ATTAAGTGGAGTAAAGGACTTAGTTCCAAGGGAGGGA
1 ATTAAGTAGAGTAAAGGACTTGGTTCCAAGGAAGGGA
* * ** * *
12765 ATTAACTAGAGTTAAGGACTTAATTTCAAGGAAGGAA
1 ATTAAGTAGAGTAAAGGACTTGGTTCCAAGGAAGGGA
12802 ATTAAGT
1 ATTAAGT
12809 CAAGAGGCTT
Statistics
Matches: 103, Mismatches: 15, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
37 103 1.00
ACGTcount: A:0.40, C:0.07, G:0.28, T:0.25
Consensus pattern (37 bp):
ATTAAGTAGAGTAAAGGACTTGGTTCCAAGGAAGGGA
Found at i:12714 original size:37 final size:37
Alignment explanation
Indices: 12676--12808 Score: 194
Period size: 37 Copynumber: 3.6 Consensus size: 37
12666 AAAGTATTTG
*
12676 GTTCCAAGGAAGGGAATTAAGTAGAGTAAAGGACTTG
1 GTTCCAAGGAAGGGAATTAAGTAGAGTAAAGGACTTA
*
12713 GTTCCAAGGAAGGGAATTAAGTGGAGTAAAGGACTTA
1 GTTCCAAGGAAGGGAATTAAGTAGAGTAAAGGACTTA
* * *
12750 GTTCCAAGGGAGGGAATTAACTAGAGTTAAGGACTTA
1 GTTCCAAGGAAGGGAATTAAGTAGAGTAAAGGACTTA
* * *
12787 ATTTCAAGGAAGGAAATTAAGT
1 GTTCCAAGGAAGGGAATTAAGT
12809 CAAGAGGCTT
Statistics
Matches: 85, Mismatches: 11, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
37 85 1.00
ACGTcount: A:0.38, C:0.08, G:0.30, T:0.23
Consensus pattern (37 bp):
GTTCCAAGGAAGGGAATTAAGTAGAGTAAAGGACTTA
Found at i:12937 original size:36 final size:36
Alignment explanation
Indices: 12813--13003 Score: 269
Period size: 36 Copynumber: 5.2 Consensus size: 36
12803 TTAAGTCAAG
* *
12813 AGGCTTAATTCAGGGTAATTACGTAGCATCAATAAA
1 AGGCTTAATTCAGGGTAATTAAGTAGCGTCAATAAA
* * *
12849 TTGACTTAATTCAGGGTAATTAAGTAGCGTCAA-GAA
1 -AGGCTTAATTCAGGGTAATTAAGTAGCGTCAATAAA
12885 AGTGACTTAATTCAGGGTAATTAAGTAGCGTCAATAAA
1 AG-G-CTTAATTCAGGGTAATTAAGTAGCGTCAATAAA
12923 AGGCTTAATTCAGGGTAATTAAGTAGCGTCAATAAA
1 AGGCTTAATTCAGGGTAATTAAGTAGCGTCAATAAA
* *
12959 AGGCTTAATTCAGGGTAATTAAGTGGAGTCAAT-AA
1 AGGCTTAATTCAGGGTAATTAAGTAGCGTCAATAAA
12994 AGAGCTTAAT
1 AG-GCTTAAT
13004 CAAAGAAGAG
Statistics
Matches: 140, Mismatches: 10, Indels: 9
0.88 0.06 0.06
Matches are distributed among these distances:
35 5 0.04
36 73 0.52
37 58 0.41
38 4 0.03
ACGTcount: A:0.38, C:0.11, G:0.22, T:0.29
Consensus pattern (36 bp):
AGGCTTAATTCAGGGTAATTAAGTAGCGTCAATAAA
Found at i:13038 original size:110 final size:110
Alignment explanation
Indices: 12813--13034 Score: 256
Period size: 109 Copynumber: 2.0 Consensus size: 110
12803 TTAAGTCAAG
* * *
12813 AGGCTTAATTCAGGGTAATTACGTAGCATCAATAAATTGACTTAATTCAGGGTAATTAAGTAGCG
1 AGGCTTAATTCAGGGTAATTAAGTAGCATCAATAAATAGACTTAATTCAGGGTAATTAAGTAGAG
* * * ***
12878 TCAAGAAAGTGACTTAATTCAGGGTAATTAAGTAGCGTCAATAAA
66 TCAAGAAAGAGACTTAATTCAGAGTAATTAAGCAGAAACAATAAA
* * *
12923 AGGCTTAATTCAGGGTAATTAAGTAGCGTCAATAAA-AGGCTTAATTCAGGGTAATTAAGTGGAG
1 AGGCTTAATTCAGGGTAATTAAGTAGCATCAATAAATAGACTTAATTCAGGGTAATTAAGTAGAG
*
12987 TCAATAAAGAG-CTTAA-TCAAAGAAG-AGATTAAGCA-AAACAATAAA
66 TCAAGAAAGAGACTTAATTC--AG-AGTA-ATTAAGCAGAAACAATAAA
13032 AGG
1 AGG
13035 GCTTGATTTA
Statistics
Matches: 95, Mismatches: 13, Indels: 9
0.81 0.11 0.08
Matches are distributed among these distances:
107 2 0.02
108 5 0.05
109 46 0.48
110 42 0.44
ACGTcount: A:0.41, C:0.11, G:0.22, T:0.26
Consensus pattern (110 bp):
AGGCTTAATTCAGGGTAATTAAGTAGCATCAATAAATAGACTTAATTCAGGGTAATTAAGTAGAG
TCAAGAAAGAGACTTAATTCAGAGTAATTAAGCAGAAACAATAAA
Found at i:16838 original size:35 final size:35
Alignment explanation
Indices: 16786--16881 Score: 147
Period size: 35 Copynumber: 2.7 Consensus size: 35
16776 AACAATAGTA
* * *
16786 GCTCTTCCGGAGCCTTCAATTAAATTTGAATACTG
1 GCTCTTCTGGAGCCTTCAATCAAATTTAAATACTG
* *
16821 GCTCTTCTGGAGTCTTCAATCAACTTTAAATACTG
1 GCTCTTCTGGAGCCTTCAATCAAATTTAAATACTG
16856 GCTCTTCTGGAGCCTTCAATCAAATT
1 GCTCTTCTGGAGCCTTCAATCAAATT
16882 CGCACAATCT
Statistics
Matches: 54, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
35 54 1.00
ACGTcount: A:0.25, C:0.24, G:0.16, T:0.35
Consensus pattern (35 bp):
GCTCTTCTGGAGCCTTCAATCAAATTTAAATACTG
Done.