Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009496.1 Corchorus capsularis cultivar CVL-1 contig09517, 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: 34603
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32
Found at i:14302 original size:18 final size:18
Alignment explanation
Indices: 14252--14291 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
14242 TATCTCACAT
* *
14252 TTCTGCTGCACCAGAAGC
1 TTCTCCTGCACCTGAAGC
14270 TTCTCCTGCACCTGAAGC
1 TTCTCCTGCACCTGAAGC
14288 TTCT
1 TTCT
14292 GCTTCCCCTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.17, C:0.35, G:0.17, T:0.30
Consensus pattern (18 bp):
TTCTCCTGCACCTGAAGC
Found at i:29521 original size:13 final size:13
Alignment explanation
Indices: 29503--29528 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
29493 TGCTTCCTAA
29503 GAAAAAGGAATAT
1 GAAAAAGGAATAT
29516 GAAAAAGGAATAT
1 GAAAAAGGAATAT
29529 AAGATACACT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.62, C:0.00, G:0.23, T:0.15
Consensus pattern (13 bp):
GAAAAAGGAATAT
Found at i:32962 original size:332 final size:332
Alignment explanation
Indices: 32263--34600 Score: 3279
Period size: 332 Copynumber: 7.0 Consensus size: 332
32253 TTTAATTTTA
*
32263 CCTTCAAACTTTTTGGCGTTGAATTATACTTTATATATTTTTATGAGTATTTTGGCCAAAAATTG
1 CCTTCAAACTTTTTGGCATTGAA-T-TA---TATAT-TTTTTATGAGTATTTTGGCCAAAAATTG
* ** * * * * * * *
32328 AGGAAAAATATTTCAGGTCAATTTTTATAAACTTTTAGGCAAAATAGTATACTAACCAACACGTT
60 AGGAAAAATATTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCACGGT
* * * * * * * * * * * *
32393 TTTTGGCTAAAACCGCATTCCGGGGTACCAACACAGTTTTGCATTAATTTTGGCGCCGAGAGTCG
125 TTTTGACTAAAAACGCGTTCCGGGGCACCAACTCATTTTTGTATGATTTTTGGTGACGAGAGCCG
* * * *
32458 TTAAAATATCAATATTCATCTAACCAAATCTTAGCCACATTGGATTTGAGGATTGT-TTTTTACG
190 TTAAAATATCTATATTCATCTAACCAAATCTCAGCCACACTAGATTTGAGGATT-TATTTTTACG
* ** * * *
32522 AGTATCTAAATCTTGTTTCAATTTAATCTGAAATTAGTTTAGAAAAAAATTGGAAAATGATATTA
254 AGCATCTAAATCTTGTTTTGATTTAATCAGAAATTAATTTAGAAAAAAATTGGAAAACGATATTA
*
32587 GAAACGTCAAAAGC
319 GAAACGTTAAAAGC
* * * * * *
32601 CCTTCTAACTTTTTGACGTTGAATTATATATTTTTTATGTGTATTATGGCCAAAAATTAAGGAAA
1 CCTTCAAACTTTTTGGCATTGAATTATATATTTTTTATGAGTATTTTGGCCAAAAATTGAGGAAA
* *
32666 AATATTTCGGGTCAATTTTTGCAAAGTTTTAGCCGAAATCGTGTACTAACCATCACAGTGTTTTG
66 AATATTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCACGGT-TTTTG
* **** * * * * *
32731 -CTAAAAACGCGTTCCGGGACATTGGCTCAATTTTGCA-GAATTTTTGGTGCCGAGAGTCGTAAA
130 ACTAAAAACGCGTTCCGGGGCACCAACTCATTTTTGTATG-ATTTTTGGTGACGAGAGCCGTTAA
* * * * *
32794 AAAATCTATATTCATCTAACCAAATCTCAGTCACAATAGATTTGAGGATTTGTTTTTAGGAGCAT
194 AATATCTATATTCATCTAACCAAATCTCAGCCACACTAGATTTGAGGATTTATTTTTACGAGCAT
* * ** * * * *
32859 C-AGAAACTGGTTTCAATTTCAAT-AGAAATTAATTCAGAAAAAAATAGGGAACACCATATTAGA
259 CTA-AATCTTGTTTTGATTT-AATCAGAAATTAATTTAGAAAAAAAT-TGGAAAACGATATTAGA
* *
32922 AGCGTGAAAA-C
321 AACGTTAAAAGC
* * * * ** *
32933 TCTTCAATA-TTTTTTGCGTTGATTTATATA-TTTTTATGAGTATTTTGGTTAAAAATTGAGTAA
1 CCTTCAA-ACTTTTTGGCATTGAATTATATATTTTTTATGAGTATTTTGGCCAAAAATTGAGGAA
* *
32996 AAATATTTCGGGTCAATTTTTGGAAAAATTTTAGCCGAAATCGTGTATTAACCATCACGGTTTTT
65 AAATATTTCGGGTCAATTTTT-GCAAAATTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTT
* * * ** * * *
33061 GACTAAAAACACGTTCCGGGACACCAACACGGTTTTGCT-TGATTTTTGGCGCCGAGAGTCGTTA
129 GACTAAAAACGCGTTCCGGGGCACCAACTCATTTTTG-TATGATTTTTGGTGACGAGAGCCGTTA
* * * * * * * * *
33125 AACTATCTGTATT--TCTAACAAAATCTCAGCCACATTGGATTTTAGAATTTGTTTTTAAGAGCA
193 AAATATCTATATTCATCTAACCAAATCTCAGCCACACTAGATTTGAGGATTTATTTTTACGAGCA
*
33188 TCTAAATCTTGTTTTGATTTAATCAGAAATTAATTTAGAAAAGAATTGGAAAACGATATTAGAAA
258 TCTAAATCTTGTTTTGATTTAATCAGAAATTAATTTAGAAAAAAATTGGAAAACGATATTAGAAA
*
33253 CATTAAAAGC
323 CGTTAAAAGC
33263 CCTTCAAACTTTTTGGCATTGAATTATATATTTTTTATGAGTATTTTGGCCAAAAATTGAGGAAA
1 CCTTCAAACTTTTTGGCATTGAATTATATATTTTTTATGAGTATTTTGGCCAAAAATTGAGGAAA
33328 AATATTTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTG---T-A-CATCACGGTTTTTG
66 AATA-TTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTG
*
33388 ACTAAAAACGCGTTCCGGGGCACCAGCTCATTTTTGTATGATTTTTGGTGACGAGAGCCGTTAAA
130 ACTAAAAACGCGTTCCGGGGCACCAACTCATTTTTGTATGATTTTTGGTGACGAGAGCCGTTAAA
* * *
33453 ATATCTATATTCATGTAACCAAATCTCAGCCACACTAGATTTGAGGATTTA-ATTTACGAGCATT
195 ATATCTATATTCATCTAACCAAATCTCAGCCACACTAGATTTGAGGATTTATTTTTACGAGCATC
**
33517 TAAATCTTGTTTTGATTTAATCAGAAATTAATTTATTAAAAAATTGGAAAACGATATTAGAAACG
260 TAAATCTTGTTTTGATTTAATCAGAAATTAATTTAGAAAAAAATTGGAAAACGATATTAGAAACG
33582 TTAAAAGC
325 TTAAAAGC
33590 CCTTCAAACTTTTTGGCATTGAATTATATATTTTTTATGAGTATTTTGGCCAAAAATTGAGGAAA
1 CCTTCAAACTTTTTGGCATTGAATTATATATTTTTTATGAGTATTTTGGCCAAAAATTGAGGAAA
33655 AATATTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTGA
66 AATATTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTGA
* *
33720 CTAAAAACGCGTTCCGGGACACCATCTCATTTTTGTATGATTTTTGGTGACGAGAGCCGTTAAAA
131 CTAAAAACGCGTTCCGGGGCACCAACTCATTTTTGTATGATTTTTGGTGACGAGAGCCGTTAAAA
33785 TATCTATATTCATCTAACCAAATCTCAGCCACACTAGATTTGAGGATTTATTTTTACGAGCATCT
196 TATCTATATTCATCTAACCAAATCTCAGCCACACTAGATTTGAGGATTTATTTTTACGAGCATCT
33850 AAATCTTGTTTTGATTTAATCAGAAATTAATTTAGAAAAAAATTGGAAAACGATATTAGAAACGT
261 AAATCTTGTTTTGATTTAATCAGAAATTAATTTAGAAAAAAATTGGAAAACGATATTAGAAACGT
*
33915 TAAAAAC
326 TAAAAGC
* *
33922 CCTTCAAACTTTTTGGCAATGAATTATATATTTTTTATGAGTATTTTGGCCAAAAATTGTGGAAA
1 CCTTCAAACTTTTTGGCATTGAATTATATATTTTTTATGAGTATTTTGGCCAAAAATTGAGGAAA
** *
33987 AATATTTCGAATCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCACAGTTTTTGA
66 AATATTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTGA
* * *
34052 CTAAAACCGTGTTCCGGGGCACCAGCTCATTTTTGTATGATTTTTGGTGACGAGAGCCGTTAAAA
131 CTAAAAACGCGTTCCGGGGCACCAACTCATTTTTGTATGATTTTTGGTGACGAGAGCCGTTAAAA
* **
34117 TATCTATATTCATCTAACCAAATCTCACCCACACTAGATTTGAGGAAATATTTTTACGAGCATCT
196 TATCTATATTCATCTAACCAAATCTCAGCCACACTAGATTTGAGGATTTATTTTTACGAGCATCT
*
34182 AAATCTTGTTTTGATTGAATCAGAAATTAATTTAGAAAAAAATTGGAAAACGATATTAGAAACGT
261 AAATCTTGTTTTGATTTAATCAGAAATTAATTTAGAAAAAAATTGGAAAACGATATTAGAAACGT
34247 TAAAAGC
326 TAAAAGC
* *
34254 CCTTCAAAATTTTTGGCATTGAATTATATATTTTTTATGATTATTTTGGCCAAAAATTGAGGAAA
1 CCTTCAAACTTTTTGGCATTGAATTATATATTTTTTATGAGTATTTTGGCCAAAAATTGAGGAAA
*
34319 AATATTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACCAACCATCACGGTTTTTGA
66 AATATTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTGA
* *
34384 CAAAAAAACGCGTTCCGGGGCACCAACTCATTTTTGTATGATTTTTGGTGACGAGAGACGTTAAA
131 C-TAAAAACGCGTTCCGGGGCACCAACTCATTTTTGTATGATTTTTGGTGACGAGAGCCGTTAAA
*
34449 ATATCTATGTTCATCTAACCAAATCTCAGCCACACTAGATTTGAGGATTTATTTTTACGAGCATC
195 ATATCTATATTCATCTAACCAAATCTCAGCCACACTAGATTTGAGGATTTATTTTTACGAGCATC
* *
34514 TAAATCATGTTTTGATTTAATAAGAAATTAATTTAGAAAAAAATTGGAAAACGATATTAGAAACG
260 TAAATCTTGTTTTGATTTAATCAGAAATTAATTTAGAAAAAAATTGGAAAACGATATTAGAAACG
*
34579 TGAAAAGC
325 TTAAAAGC
34587 CCTTCAAACTTTTT
1 CCTTCAAACTTTTT
34601 TGG
Statistics
Matches: 1799, Mismatches: 174, Indels: 59
0.89 0.09 0.03
Matches are distributed among these distances:
325 1 0.00
326 116 0.06
327 149 0.08
328 32 0.02
329 26 0.01
330 103 0.06
331 240 0.13
332 871 0.48
333 237 0.13
336 2 0.00
337 1 0.00
338 21 0.01
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.35
Consensus pattern (332 bp):
CCTTCAAACTTTTTGGCATTGAATTATATATTTTTTATGAGTATTTTGGCCAAAAATTGAGGAAA
AATATTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTGA
CTAAAAACGCGTTCCGGGGCACCAACTCATTTTTGTATGATTTTTGGTGACGAGAGCCGTTAAAA
TATCTATATTCATCTAACCAAATCTCAGCCACACTAGATTTGAGGATTTATTTTTACGAGCATCT
AAATCTTGTTTTGATTTAATCAGAAATTAATTTAGAAAAAAATTGGAAAACGATATTAGAAACGT
TAAAAGC
Done.