Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006350.1 Corchorus capsularis cultivar CVL-1 contig06371, 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: 29848
ACGTcount: A:0.32, C:0.20, G:0.19, T:0.29
Found at i:10414 original size:9 final size:9
Alignment explanation
Indices: 10400--10429 Score: 60
Period size: 9 Copynumber: 3.3 Consensus size: 9
10390 AACACATATG
10400 TGCGCCAAA
1 TGCGCCAAA
10409 TGCGCCAAA
1 TGCGCCAAA
10418 TGCGCCAAA
1 TGCGCCAAA
10427 TGC
1 TGC
10430 AGCCTTAACA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.30, C:0.33, G:0.23, T:0.13
Consensus pattern (9 bp):
TGCGCCAAA
Found at i:10631 original size:246 final size:246
Alignment explanation
Indices: 10195--10657 Score: 890
Period size: 246 Copynumber: 1.9 Consensus size: 246
10185 AGATTACCCT
*
10195 AGAAAGATAATTGAAGAATCTACTCAGCAACTGTGGAACTGAATGGAAGAAAAGCTCAAAGGATT
1 AGAAAGATAATTGAAGAATCTACTCAGCAACTGTGGAACCGAATGGAAGAAAAGCTCAAAGGATT
*
10260 AAGCGGCAACCAAGCATATTTCAAGGGAGTGGATAAGGTGTCCCTAGTTACGGATTTAGTGTTGC
66 AAGCAGCAACCAAGCATATTTCAAGGGAGTGGATAAGGTGTCCCTAGTTACGGATTTAGTGTTGC
10325 CGCATAAGTTCAAAGTCCCAGATTTTGAAAAATTTGATGGTACTAGATCCCCTGAAGACCATGTT
131 CGCATAAGTTCAAAGTCCCAGATTTTGAAAAATTTGATGGTACTAGATCCCCTGAAGACCATGTT
10390 AACACATATGTGCGCCAAATGCGCCAAATGCGCCAAATGCAGCCTTAACAC
196 AACACATATGTGCGCCAAATGCGCCAAATGCGCCAAATGCAGCCTTAACAC
10441 AGAAAGATAATTGAAGAATCTACTCAGCAACTGTGGAACCGAATGGAAGAAAAGCTCAAAGGATT
1 AGAAAGATAATTGAAGAATCTACTCAGCAACTGTGGAACCGAATGGAAGAAAAGCTCAAAGGATT
10506 AAGCAGCAACCAAGCATATTTCAAGGGAGTGGATAAGGTGTCCCTAGTTACGGATTTAGTGTTGC
66 AAGCAGCAACCAAGCATATTTCAAGGGAGTGGATAAGGTGTCCCTAGTTACGGATTTAGTGTTGC
* *
10571 CGCATAAGTTCAAAGTCCCGGATTTTGAAAAATTTGATGGTACTAGATCCCCTTAAGACCATGTT
131 CGCATAAGTTCAAAGTCCCAGATTTTGAAAAATTTGATGGTACTAGATCCCCTGAAGACCATGTT
10636 AACACATATGTGCGCCAAATGC
196 AACACATATGTGCGCCAAATGC
10658 AGCCTTACAG
Statistics
Matches: 213, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
246 213 1.00
ACGTcount: A:0.35, C:0.19, G:0.22, T:0.24
Consensus pattern (246 bp):
AGAAAGATAATTGAAGAATCTACTCAGCAACTGTGGAACCGAATGGAAGAAAAGCTCAAAGGATT
AAGCAGCAACCAAGCATATTTCAAGGGAGTGGATAAGGTGTCCCTAGTTACGGATTTAGTGTTGC
CGCATAAGTTCAAAGTCCCAGATTTTGAAAAATTTGATGGTACTAGATCCCCTGAAGACCATGTT
AACACATATGTGCGCCAAATGCGCCAAATGCGCCAAATGCAGCCTTAACAC
Found at i:20511 original size:18 final size:17
Alignment explanation
Indices: 20484--20519 Score: 63
Period size: 18 Copynumber: 2.1 Consensus size: 17
20474 TTTCTCTTCA
20484 TCTATTTTTCTTCTAGT
1 TCTATTTTTCTTCTAGT
20501 TCTAGTTTTTCTTCTAGT
1 TCTA-TTTTTCTTCTAGT
20519 T
1 T
20520 TTAGGTTGAG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 4 0.22
18 14 0.78
ACGTcount: A:0.11, C:0.17, G:0.08, T:0.64
Consensus pattern (17 bp):
TCTATTTTTCTTCTAGT
Found at i:24514 original size:21 final size:21
Alignment explanation
Indices: 24481--24529 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
24471 AAAAATTGTA
**
24481 GCTT-CTTGGAAATGGCTCTT
1 GCTTCCTTGGAAATCCCTCTT
*
24501 GCTTCCTTTGAAATCCCTCTT
1 GCTTCCTTGGAAATCCCTCTT
24522 GCATTCCT
1 GC-TTCCT
24530 AAAGCATTGA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 4 0.17
21 15 0.62
22 5 0.21
ACGTcount: A:0.14, C:0.29, G:0.16, T:0.41
Consensus pattern (21 bp):
GCTTCCTTGGAAATCCCTCTT
Found at i:27897 original size:71 final size:71
Alignment explanation
Indices: 27802--27933 Score: 169
Period size: 71 Copynumber: 1.9 Consensus size: 71
27792 GGACTGGTCT
*
27802 TCTTCAGTTTCAGACCTCAAACAGGTCCCCCTT-AATTTCAAAAGCGACCACAGACTGGTCTCTT
1 TCTTCAATTTCAGACCTCAAACAGGT-CCCCTTCAATTTCAAAAGCGACCACAGACTGGTCTCTT
27866 TCTCATA
65 TCTCATA
* ** * * *
27873 TCTTCAATTCTCA-ACCTCAGACAGGTCTTCTTCGATTTCAACATCGACCACAGACTGGTCT
1 TCTTCAATT-TCAGACCTCAAACAGGTCCCCTTCAATTTCAAAAGCGACCACAGACTGGTCT
27934 TCTCCAAAAT
Statistics
Matches: 52, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
70 4 0.08
71 45 0.87
72 3 0.06
ACGTcount: A:0.26, C:0.31, G:0.13, T:0.30
Consensus pattern (71 bp):
TCTTCAATTTCAGACCTCAAACAGGTCCCCTTCAATTTCAAAAGCGACCACAGACTGGTCTCTTT
CTCATA
Found at i:28001 original size:33 final size:33
Alignment explanation
Indices: 27835--28002 Score: 107
Period size: 33 Copynumber: 5.1 Consensus size: 33
27825 GGTCCCCCTT
* * *
27835 AATTTCAAAAGCGACCACAGACTGGTCTCTTTCTC
1 AATTTCAATATCGACCACAGACTGGTCT-TCT-TC
* * * *
27870 ATATCTTCAATTCTCAACCTCAGACAGGTCTTCTTC
1 A-AT-TTCAA-TATCGACCACAGACTGGTCTTCTTC
* * *
27906 GATTTCAACATCGACCACAGACTGGTCTTCTCC
1 AATTTCAATATCGACCACAGACTGGTCTTCTTC
** **
27939 AA----AAT-T-GACCTTAGAAAGGTCTT-TCTC
1 AATTTCAATATCGACCACAGACTGGTCTTCT-TC
27966 AATTTCAATATCGACCACAGACTGGTCTTCTTC
1 AATTTCAATATCGACCACAGACTGGTCTTCTTC
27999 AATT
1 AATT
28003 CCAGACCTCA
Statistics
Matches: 97, Mismatches: 25, Indels: 24
0.66 0.17 0.16
Matches are distributed among these distances:
26 1 0.01
27 16 0.16
28 1 0.01
29 2 0.02
31 3 0.03
32 1 0.01
33 39 0.40
34 6 0.06
35 3 0.03
36 4 0.04
37 7 0.07
38 14 0.14
ACGTcount: A:0.28, C:0.27, G:0.12, T:0.32
Consensus pattern (33 bp):
AATTTCAATATCGACCACAGACTGGTCTTCTTC
Done.