Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010458.1 Corchorus capsularis cultivar CVL-1 contig10479, 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: 12566
ACGTcount: A:0.37, C:0.15, G:0.15, T:0.34
Found at i:1412 original size:103 final size:103
Alignment explanation
Indices: 1233--1433 Score: 341
Period size: 103 Copynumber: 2.0 Consensus size: 103
1223 ACAAGGAATG
* *
1233 TATTATTGTTCATCCTGATAAGAACAAATTTGATGTTTACTCTGATGGTGATTATATGGTTATGG
1 TATTATTGTTCATCCCGATAAGAACAAATTTGAGGTTTACTCTGATGGTGATTATATGGTTATGG
*
1298 GAATTGTTAGAGTGGTAATATCCTACATTGGTTGAGTA
66 GAATTGTTAGAGTGGTAATATCCCACATTGGTTGAGTA
* *
1336 TATTATTGTTCATCCCGATAAGAACAAGTTTGAGGTTTACTCTTATGGTGATTATA-GGCTTATG
1 TATTATTGTTCATCCCGATAAGAACAAATTTGAGGTTTACTCTGATGGTGATTATATGG-TTATG
1400 GGAATTGTTAGAGTGGTAATATCCCACATTGGTT
65 GGAATTGTTAGAGTGGTAATATCCCACATTGGTT
1434 ATGTTTGATA
Statistics
Matches: 92, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
102 2 0.02
103 90 0.98
ACGTcount: A:0.27, C:0.10, G:0.22, T:0.40
Consensus pattern (103 bp):
TATTATTGTTCATCCCGATAAGAACAAATTTGAGGTTTACTCTGATGGTGATTATATGGTTATGG
GAATTGTTAGAGTGGTAATATCCCACATTGGTTGAGTA
Found at i:3296 original size:439 final size:440
Alignment explanation
Indices: 2401--3408 Score: 1272
Period size: 440 Copynumber: 2.3 Consensus size: 440
2391 CAAATAGAAC
* * * * * *
2401 ACAAAAAGAAAAGTCAAAACGTTAAATCGTCCAACCTATAATTGTAAAGGATTCAATAGCATGAA
1 ACAAAAATAAAAGCCGAAACGTTAAATCGTCCAACCCATAATTGTAAAGGATTAAATAGCATAAA
* * * * *
2466 ACATAAAAGTATGAGGGTCATTAGATAAATAATTCAGCAAAAAAAAATATTAGTTTATGGAGACA
66 ACATAAAAGTATAAGGATCATTTGATAAATAATTCAGC-AAAAAATATATTTGTTTATGGAGACA
* * *
2531 AAACATAAAAATTGCCTCTTGAATCCTCCACGAAACTCATTAATCAAATTCAACTTTCATGCCCT
130 AAACATAAAAATTGCCTCTCGAACCCTCCACGAAACTCATTAATCAAATTCAACTTTCAGGCCCT
** * * ** *
2596 TAATGAAAGTCGTAGATCACACAATAATCTTTTAACCGACAATTGAACAACTTCAATCAGACAAG
195 TAACAAAAGTCATAGATCACACAATAACCTTTTAAAAGACAATTGAACAACCTCAATCAGACAAG
* *
2661 TGGACCAAAAATTATACGATATAAAATAGACCGGCAATCAAAACCAAAAAAATTTAAGAAACATT
260 TGGACCAAAAATTATACAATATAAAATAGACCGACAATCAAAACCAAAAAAATTTAAGAAACATT
* ** *
2726 TTTTAGAATCAAAACATTAAAATTGACTTCTAAGTTTTTCATTAAAGTTGTAGATCATGAAATTA
325 TTTTAGAATCAAAACATGAAAATTGACTTCTAAGTCATTCATGAAAGTTGTAGATCATGAAATTA
* *
2791 CCTTTTAATAGACACTTCAATCACCTTGATTGGACAAATAGAACAGAAAAT
390 CCTTTTAATAGACACTTCAATCACCTTGATTGGACAAATAAAACAAAAAAT
** * *
2842 ACAAAAATAAAAGCCGACGCGTTAAATCGTCCAACCCATAATTGCAAATGATTAAATAGCATAAA
1 ACAAAAATAAAAGCCGAAACGTTAAATCGTCCAACCCATAATTGTAAAGGATTAAATAGCATAAA
* * *
2907 ACATAAAAGTATAAGGATCATTTGATAAATAATCCAACAAAAAATATATTTGTTTATGGAGACCA
66 ACATAAAAGTATAAGGATCATTTGATAAATAATTCAGCAAAAAATATATTTGTTTATGGAGACAA
* * * * *
2972 AACATAAAAGTT-CCATCTCGAACCCTCCATGAAACTCATTGATCAAATTCAGCTTTCAGGTCCT
131 AACATAAAAATTGCC-TCTCGAACCCTCCACGAAACTCATTAATCAAATTCAACTTTCAGGCCCT
* * * *
3036 TGACAAAAGTCATAGATCACACAATAACCTTTTAAAAGACACTTGAACAACCTCAATCGGACAAT
195 TAACAAAAGTCATAGATCACACAATAACCTTTTAAAAGACAATTGAACAACCTCAATCAGACAAG
* * * * * * *
3101 TGGATCGAAAATTATACAATATTAGATAGACCGACAATCGAGACC-ACAAAATTTAAGAAGA-AT
260 TGGACCAAAAATTATACAATATAAAATAGACCGACAATCAAAACCAAAAAAATTTAAGAA-ACAT
** ** * *
3164 TTTTTAG-ATACGTAACATGAAAATTGGTTTTTCAGTCATTCATGAAAGTTGTAGATCATGAAAT
324 TTTTTAGAAT-CAAAACATGAAAATTGACTTCTAAGTCATTCATGAAAGTTGTAGATCATGAAAT
* * *
3228 TACTTTTTAATAGACACTTGAATCACCTTGATTGGACAAGTAAAACAAAAAAT
388 TACCTTTTAATAGACACTTCAATCACCTTGATTGGACAAATAAAACAAAAAAT
* * * * * * * *
3281 A-AAAGAATTAAAGCCGAAACGTTCAATCGTCCAACCCAGAATTTGTGAGGGACTGAATAACATA
1 ACAAA-AATAAAAGCCGAAACGTTAAATCGTCCAACCCATAA-TTGTAAAGGATTAAATAGCATA
* *
3345 AAGCATAAAAGTATAAGGATCATTTGATAAATAATTCAGC-AAAAATATGATTTGTTTATTGAGA
64 AAACATAAAAGTATAAGGATCATTTGATAAATAATTCAGCAAAAAATAT-ATTTGTTTATGGAGA
3409 GCGGGGTCCA
Statistics
Matches: 484, Mismatches: 77, Indels: 13
0.84 0.13 0.02
Matches are distributed among these distances:
438 5 0.01
439 156 0.32
440 235 0.49
441 88 0.18
ACGTcount: A:0.44, C:0.16, G:0.13, T:0.27
Consensus pattern (440 bp):
ACAAAAATAAAAGCCGAAACGTTAAATCGTCCAACCCATAATTGTAAAGGATTAAATAGCATAAA
ACATAAAAGTATAAGGATCATTTGATAAATAATTCAGCAAAAAATATATTTGTTTATGGAGACAA
AACATAAAAATTGCCTCTCGAACCCTCCACGAAACTCATTAATCAAATTCAACTTTCAGGCCCTT
AACAAAAGTCATAGATCACACAATAACCTTTTAAAAGACAATTGAACAACCTCAATCAGACAAGT
GGACCAAAAATTATACAATATAAAATAGACCGACAATCAAAACCAAAAAAATTTAAGAAACATTT
TTTAGAATCAAAACATGAAAATTGACTTCTAAGTCATTCATGAAAGTTGTAGATCATGAAATTAC
CTTTTAATAGACACTTCAATCACCTTGATTGGACAAATAAAACAAAAAAT
Found at i:4782 original size:131 final size:131
Alignment explanation
Indices: 4646--4904 Score: 403
Period size: 132 Copynumber: 2.0 Consensus size: 131
4636 ATTTAAGAAA
* * *
4646 TATATTTTAAAAATTCTAATATATCTAAGTTTTTT-AATTAAATTAGTAAAATGATAAAAATAAA
1 TATATTTAAAAAATTCTAATATATATAAGTTTTTTAAATTAAAATAGTAAAATGATAAAAATAAA
* *
4710 ATAGGTATAAAGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTATAAA
66 ATAGGTATAAAGATATTAGATTTAATTAAATAAAAATAGAGTTTTTA-ATAAGTAAAACTATAAA
4775 AG
130 AG
* * *
4777 TATATTTAAAAAATTCTAATATATATAATTTTTTTAAATTAAAATAGTAAAATGGTAAAAATTAA
1 TATATTTAAAAAATTCTAATATATATAAGTTTTTTAAATTAAAATAGTAAAATGATAAAAATAAA
* * *
4842 ATAGTTATAAGGATATTAGATTTAATTTAATAAAAATAGAGTTTTTAATAAGTAAAACTATAA
66 ATAGGTATAAAGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAATAAGTAAAACTATAA
4905 CAGTTTAAAC
Statistics
Matches: 116, Mismatches: 11, Indels: 2
0.90 0.09 0.02
Matches are distributed among these distances:
131 46 0.40
132 70 0.60
ACGTcount: A:0.50, C:0.02, G:0.09, T:0.39
Consensus pattern (131 bp):
TATATTTAAAAAATTCTAATATATATAAGTTTTTTAAATTAAAATAGTAAAATGATAAAAATAAA
ATAGGTATAAAGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAATAAGTAAAACTATAAAA
G
Found at i:7613 original size:13 final size:13
Alignment explanation
Indices: 7595--7622 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
7585 TTTGAAATCC
7595 AAATAATATTTAT
1 AAATAATATTTAT
7608 AAATAATATTTAT
1 AAATAATATTTAT
7621 AA
1 AA
7623 TATTGAATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (13 bp):
AAATAATATTTAT
Found at i:12239 original size:27 final size:27
Alignment explanation
Indices: 12201--12254 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
12191 AAGAACCTGT
12201 TGGCATCGTCCTCAACAATCAAGTCTC
1 TGGCATCGTCCTCAACAATCAAGTCTC
12228 TGGCATCGTCCTCAACAATCAAGTCTC
1 TGGCATCGTCCTCAACAATCAAGTCTC
12255 CAACAAACGC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.26, C:0.33, G:0.15, T:0.26
Consensus pattern (27 bp):
TGGCATCGTCCTCAACAATCAAGTCTC
Found at i:12547 original size:2 final size:2
Alignment explanation
Indices: 12540--12566 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
12530 AATAACTTAC
12540 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Done.