Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014889.1 Corchorus capsularis cultivar CVL-1 contig14910, 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: 25564
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:8 original size:2 final size:2
Alignment explanation
Indices: 2--34 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1 T
2 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
35 TATGAGTATT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:761 original size:329 final size:327
Alignment explanation
Indices: 24--937 Score: 1136
Period size: 329 Copynumber: 2.8 Consensus size: 327
14 TATATATATA
* * * *
24 TATATATATATTATGAGTATTTTATCCAAAAATTTATGGAAAAAATCTTTCGGGTCAATTTTTGC
1 TATATAT-TTTTATGAGTATTTTAACCAAAAA-TTAAGG-AAAAATCTTTCGGATCAATTTTTGC
* * *
89 AAATTTTTAGCTGAAATCGTGTACTAACCACCATCACGGTTTTCGGCTAAAAATGCATTCTGGGG
63 AAATTTTTAGCCGAAATCGTGTACT-A--ACCATCACGGTTTTCGGCT-AAAACGCATTCCGGGG
* * *
154 CCCGACTCAGTTATTT-ATGATTTTTGGTGCCAAGACTCCTTGAAAAATCTATATTCATCTAATC
124 CACGACTCAGTT-TTTCATGA-TTTTGGTGCCAAGACTACTTGAAATATCTATATTCATCTAATC
* *
218 AAATCTCAGCCACATTGAATTTAATGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAA
187 AAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAA
* * * **
283 TTAGAAATTAATTCAGAAAAATATGAAAAACGATATTAAAAGCGTGAAAAAGGATTTCAATTTTT
252 TTAGAAATTAATTCAGAAAAACAGGAAAAACAATATTAAAAGCGTGAAAAACCATTTCAATTTTT
*
348 TGTTATTGAAT
317 TGATATTGAAT
** * * *
359 TATATATTTTTCATGAGTATTTTCGCTAGAAATCAAGGAAAAATCTTTC-GAGTCAATTTTTGCA
1 TATATATTTTT-ATGAGTATTTTAACCAAAAATTAAGGAAAAATCTTTCGGA-TCAATTTTTGCA
* **
423 AATTTTTAGCCGAAATCATGTACTAACCATCACGGTTTTCGGCTAAAACCGCATTCCGGGGTTCG
64 AATTTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTCGGCTAAAA-CGCATTCCGGGGCACG
* *
488 ACTCAGTTTTTCATGATTTTGGTGCCAAGACTACTTGAAATAGCTATATTCATCTAA-CTGAATC
128 ACTCAGTTTTTCATGATTTTGGTGCCAAGACTACTTGAAATATCTATATTCATCTAATC-AAATC
*
552 TCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCGTGTTTCGATTTAATTAGA
192 TCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGA
* * * *
617 AATTAATTTA-AAAAACAGGAAAAACAATATTAGAAGCGTTAAAATCCA-TTCAATATTTTTGAT
257 AATTAATTCAGAAAAACAGGAAAAACAATATTAAAAGCGTGAAAAACCATTTCAAT-TTTTTGAT
*
680 GTTGAAT
321 ATTGAAT
* * *
687 TATATATTTTCTATGAGGATTTTAACCAAAAATTGAGGAAATATCTTTCGGATCAATTTTTGCAA
1 TATATATTTT-TATGAGTATTTTAACCAAAAATTAAGGAAAAATCTTTCGGATCAATTTTTGC-A
* * * *
752 AAATTTTAGCCGAAATCGTGTACTAACCATTACGGTTTTTGGCTAGAAACGCGTTCCGGGGCCAC
64 AATTTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTCGGCTA-AAACGCATTCCGGGG-CAC
* * * * * * *
817 GGCTCTGTTTTGCATGATTCTTGGCGCCGAGACTTCTTGAAATATCTTTATTCATCTAATCAAAT
127 GACTCAGTTTTTCATGATT-TTGGTGCCAAGACTACTTGAAATATCTATATTCATCTAATCAAAT
* * * * * *
882 CTCAGGCACATTAGATTTAAGGATTTGTTTTTATGTGAATTTGAATCTTGTTTCGA
191 CTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGA
938 ATGCTCGGGT
Statistics
Matches: 503, Mismatches: 63, Indels: 30
0.84 0.11 0.05
Matches are distributed among these distances:
327 6 0.01
328 94 0.19
329 176 0.35
330 63 0.13
331 86 0.17
332 3 0.01
333 45 0.09
334 7 0.01
335 23 0.05
ACGTcount: A:0.32, C:0.15, G:0.16, T:0.37
Consensus pattern (327 bp):
TATATATTTTTATGAGTATTTTAACCAAAAATTAAGGAAAAATCTTTCGGATCAATTTTTGCAAA
TTTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTCGGCTAAAACGCATTCCGGGGCACGACT
CAGTTTTTCATGATTTTGGTGCCAAGACTACTTGAAATATCTATATTCATCTAATCAAATCTCAG
CCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATT
AATTCAGAAAAACAGGAAAAACAATATTAAAAGCGTGAAAAACCATTTCAATTTTTTGATATTGA
AT
Found at i:9648 original size:15 final size:16
Alignment explanation
Indices: 9615--9647 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
9605 ATCACCTACT
9615 AATTACACAAAAATAA
1 AATTACACAAAAATAA
9631 AATTACACAAAAATAA
1 AATTACACAAAAATAA
9647 A
1 A
9648 TAGGAATGCC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.70, C:0.12, G:0.00, T:0.18
Consensus pattern (16 bp):
AATTACACAAAAATAA
Found at i:16621 original size:29 final size:30
Alignment explanation
Indices: 16579--16650 Score: 85
Period size: 29 Copynumber: 2.4 Consensus size: 30
16569 ACTTTGCCAT
* *
16579 AAATCTCAAATAAGGG-TCTGAAC-TTTAGA
1 AAATGTCAAATAAGGGCTC-CAACTTTTAGA
16608 AAATGTCAAATAAGGGCTCCAACTTTTAGA
1 AAATGTCAAATAAGGGCTCCAACTTTTAGA
*
16638 AAAGGCTCAAATA
1 AAATG-TCAAATA
16651 GGTCCAATCC
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
29 18 0.49
30 12 0.32
31 7 0.19
ACGTcount: A:0.43, C:0.15, G:0.17, T:0.25
Consensus pattern (30 bp):
AAATGTCAAATAAGGGCTCCAACTTTTAGA
Found at i:18383 original size:18 final size:17
Alignment explanation
Indices: 18351--18389 Score: 62
Period size: 18 Copynumber: 2.3 Consensus size: 17
18341 CAAATAAGAA
18351 AAAT-GAAAAAGAAATT
1 AAATAGAAAAAGAAATT
18367 AAATAGAAAATAGAAATT
1 AAATAGAAAA-AGAAATT
18385 AAATA
1 AAATA
18390 AAATGAAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 4 0.19
17 5 0.24
18 12 0.57
ACGTcount: A:0.69, C:0.00, G:0.10, T:0.21
Consensus pattern (17 bp):
AAATAGAAAAAGAAATT
Found at i:20089 original size:7 final size:6
Alignment explanation
Indices: 20060--20088 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
20050 GGGCTTATCT
20060 TTTTTC TTTTTC TTTTTC TTTTTC TTTTT
1 TTTTTC TTTTTC TTTTTC TTTTTC TTTTT
20089 TTGTGAGGCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (6 bp):
TTTTTC
Found at i:20994 original size:3 final size:3
Alignment explanation
Indices: 20986--21024 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
20976 AAGTTATTTA
20986 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
21025 CACTTCTTGA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:24522 original size:23 final size:24
Alignment explanation
Indices: 24471--24522 Score: 88
Period size: 24 Copynumber: 2.2 Consensus size: 24
24461 GCATTAATAA
24471 AGGAAAAAAAGTGAAAGAAGGGAT
1 AGGAAAAAAAGTGAAAGAAGGGAT
*
24495 AGGAAAAAAGGTGAAAGAAGGGAT
1 AGGAAAAAAAGTGAAAGAAGGGAT
24519 -GGAA
1 AGGAA
24523 TAGCTTTTGG
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
23 4 0.15
24 23 0.85
ACGTcount: A:0.56, C:0.00, G:0.37, T:0.08
Consensus pattern (24 bp):
AGGAAAAAAAGTGAAAGAAGGGAT
Done.