Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010215.1 Corchorus capsularis cultivar CVL-1 contig10236, 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: 15519
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Found at i:340 original size:31 final size:31
Alignment explanation
Indices: 302--408 Score: 114
Period size: 31 Copynumber: 3.5 Consensus size: 31
292 TTTGGCTAAT
302 TGCTCAAATAAGGGCCTAACGTTTGTCAAAA
1 TGCTCAAATAAGGGCCTAACGTTTGTCAAAA
* * **
333 TGCTCAAATAAGGGTCCGATC-TTT-T-AATT
1 TGCTCAAATAAGGG-CCTAACGTTTGTCAAAA
* *
362 TGGC-CAAATAAGGACCTAACGTTTGCCAAAA
1 T-GCTCAAATAAGGGCCTAACGTTTGTCAAAA
393 TGCTCAAATAAGGGCC
1 TGCTCAAATAAGGGCC
409 CCATCTTTGA
Statistics
Matches: 59, Mismatches: 11, Indels: 12
0.72 0.13 0.15
Matches are distributed among these distances:
28 4 0.07
29 15 0.25
30 5 0.08
31 31 0.53
32 4 0.07
ACGTcount: A:0.34, C:0.21, G:0.20, T:0.26
Consensus pattern (31 bp):
TGCTCAAATAAGGGCCTAACGTTTGTCAAAA
Found at i:380 original size:60 final size:60
Alignment explanation
Indices: 306--465 Score: 248
Period size: 60 Copynumber: 2.7 Consensus size: 60
296 GCTAATTGCT
* * * * *
306 CAAATAAGGGCCTAACGTTTGTCAAAATGCTCAAATAAGGGTCCGATCTTTTAATTTGGC
1 CAAATAAGGACCTAACGTTTGCCAAAATGCTCAAATAAGGGCCCCATCTTTGAATTTGGC
366 CAAATAAGGACCTAACGTTTGCCAAAATGCTCAAATAAGGGCCCCATCTTTGAATTTGGC
1 CAAATAAGGACCTAACGTTTGCCAAAATGCTCAAATAAGGGCCCCATCTTTGAATTTGGC
* * *
426 CAAATAAGGCCCTGATGTTTGCCAAAATGCTCAAATAAGG
1 CAAATAAGGACCTAACGTTTGCCAAAATGCTCAAATAAGG
466 ATCTGTCTCA
Statistics
Matches: 92, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
60 92 1.00
ACGTcount: A:0.34, C:0.21, G:0.19, T:0.26
Consensus pattern (60 bp):
CAAATAAGGACCTAACGTTTGCCAAAATGCTCAAATAAGGGCCCCATCTTTGAATTTGGC
Found at i:463 original size:31 final size:30
Alignment explanation
Indices: 302--465 Score: 88
Period size: 31 Copynumber: 5.4 Consensus size: 30
292 TTTGGCTAAT
* *
302 TGCTCAAATAAGGGCCTAACGTTTGTCAAAA
1 TGCTCAAATAAGGCCCTAATGTTTG-CAAAA
* * * * **
333 TGCTCAAATAAGGGTCC-GATCTTT-TAATT
1 TGCTCAAATAA-GGCCCTAATGTTTGCAAAA
* *
362 TGGC-CAAATAAGGACCTAACGTTTGCCAAAA
1 T-GCTCAAATAAGGCCCTAATGTTTG-CAAAA
* * **
393 TGCTCAAATAAGGGCCC-CATCTTTG-AATT
1 TGCTCAAATAA-GGCCCTAATGTTTGCAAAA
*
422 TGGC-CAAATAAGGCCCTGATGTTTGCCAAAA
1 T-GCTCAAATAAGGCCCTAATGTTTG-CAAAA
453 TGCTCAAATAAGG
1 TGCTCAAATAAGG
466 ATCTGTCTCA
Statistics
Matches: 97, Mismatches: 24, Indels: 24
0.67 0.17 0.17
Matches are distributed among these distances:
28 9 0.09
29 30 0.31
30 8 0.08
31 42 0.43
32 8 0.08
ACGTcount: A:0.33, C:0.21, G:0.20, T:0.27
Consensus pattern (30 bp):
TGCTCAAATAAGGCCCTAATGTTTGCAAAA
Found at i:577 original size:60 final size:60
Alignment explanation
Indices: 500--660 Score: 243
Period size: 60 Copynumber: 2.7 Consensus size: 60
490 TGACACCGGG
* * *
500 CCCTTATTTGAGCATTTTCGAAAACGTTAGGCTCTTATTTGGCCAAATTAAAAGATCGGG
1 CCCTTATTTGAACATTTTCGAAAACGTTAGGCCCTTATTTGGCCAAATTAAAAGATCGGA
* * * *
560 TCTTTATTTGAACATTTTCGATAATGTTAGGCCCTTATTTGGCCAAATTAAAAGATCGGA
1 CCCTTATTTGAACATTTTCGAAAACGTTAGGCCCTTATTTGGCCAAATTAAAAGATCGGA
620 CCCTTATTTGAACATTTT-GACAAACGTTAGGCCCTTATTTG
1 CCCTTATTTGAACATTTTCGA-AAACGTTAGGCCCTTATTTG
661 AGCAATTAGC
Statistics
Matches: 89, Mismatches: 11, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
59 2 0.02
60 87 0.98
ACGTcount: A:0.28, C:0.18, G:0.17, T:0.37
Consensus pattern (60 bp):
CCCTTATTTGAACATTTTCGAAAACGTTAGGCCCTTATTTGGCCAAATTAAAAGATCGGA
Found at i:3182 original size:19 final size:18
Alignment explanation
Indices: 3144--3180 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
3134 GAAATGTCGA
*
3144 CAACCCCTGGAACAAGCC
1 CAACCCCCGGAACAAGCC
*
3162 CAACCCCCGGAGCAAGCC
1 CAACCCCCGGAACAAGCC
3180 C
1 C
3181 CACCACCCCA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.30, C:0.49, G:0.19, T:0.03
Consensus pattern (18 bp):
CAACCCCCGGAACAAGCC
Found at i:3843 original size:33 final size:33
Alignment explanation
Indices: 3801--3868 Score: 109
Period size: 33 Copynumber: 2.1 Consensus size: 33
3791 TCATCATTAC
*
3801 CTCCTAAATCCTCATTACCATTGTTGTTGTCTA
1 CTCCTAAATCCTCATTACCATTGTTGTTATCTA
* *
3834 CTCCTAAATCCTCATTTCGATTGTTGTTATCTA
1 CTCCTAAATCCTCATTACCATTGTTGTTATCTA
3867 CT
1 CT
3869 TCATCAGCCT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.21, C:0.26, G:0.09, T:0.44
Consensus pattern (33 bp):
CTCCTAAATCCTCATTACCATTGTTGTTATCTA
Found at i:4756 original size:23 final size:23
Alignment explanation
Indices: 4692--4757 Score: 75
Period size: 23 Copynumber: 2.9 Consensus size: 23
4682 GCTTCTTCTG
4692 ACCCTCGAAAA-CCCTCGATTTTA
1 ACCCTC-AAAAGCCCTCGATTTTA
4715 ACCCTCAAAAG-CCTCCGATTTTA
1 ACCCTCAAAAGCCCT-CGATTTTA
*
4738 ACCGT-ATAAAGCCCTCGATT
1 ACCCTCA-AAAGCCCTCGATT
4758 CTAAACCTTA
Statistics
Matches: 38, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
22 8 0.21
23 27 0.71
24 3 0.08
ACGTcount: A:0.30, C:0.33, G:0.11, T:0.26
Consensus pattern (23 bp):
ACCCTCAAAAGCCCTCGATTTTA
Found at i:9174 original size:8 final size:9
Alignment explanation
Indices: 9149--9173 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
9139 GGATCAAGCC
9149 CCACCCCCA
1 CCACCCCCA
9158 CCACCCCCA
1 CCACCCCCA
9167 CCACCCC
1 CCACCCC
9174 ATCTGGCACT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.20, C:0.80, G:0.00, T:0.00
Consensus pattern (9 bp):
CCACCCCCA
Found at i:13480 original size:37 final size:37
Alignment explanation
Indices: 13430--13505 Score: 152
Period size: 37 Copynumber: 2.1 Consensus size: 37
13420 TAGTTACAAA
13430 ATCAGTTGATATCTCTATCTCTATCTAGTGGCTGATG
1 ATCAGTTGATATCTCTATCTCTATCTAGTGGCTGATG
13467 ATCAGTTGATATCTCTATCTCTATCTAGTGGCTGATG
1 ATCAGTTGATATCTCTATCTCTATCTAGTGGCTGATG
13504 AT
1 AT
13506 ACCTGCAGAC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 39 1.00
ACGTcount: A:0.22, C:0.18, G:0.18, T:0.41
Consensus pattern (37 bp):
ATCAGTTGATATCTCTATCTCTATCTAGTGGCTGATG
Done.