Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015065.1 Corchorus capsularis cultivar CVL-1 contig15086, 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: 44689
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.34
Found at i:3164 original size:13 final size:13
Alignment explanation
Indices: 3138--3170 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
3128 TAGTATATAC
3138 ATATTATACATAT
1 ATATTATACATAT
3151 ATATATATAC-TAT
1 ATAT-TATACATAT
3164 ATATTAT
1 ATATTAT
3171 TTTTAGTTAC
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
12 3 0.16
13 11 0.58
14 5 0.26
ACGTcount: A:0.45, C:0.06, G:0.00, T:0.48
Consensus pattern (13 bp):
ATATTATACATAT
Found at i:14695 original size:31 final size:31
Alignment explanation
Indices: 14657--14765 Score: 125
Period size: 31 Copynumber: 3.6 Consensus size: 31
14647 TTACTTTGGC
* *
14657 CAAATAAGGGCTTAATGTTATCGAAAATGCT
1 CAAATAAGGGCCTAACGTTATCGAAAATGCT
* * **
14688 CAAATAAGGGCCTGACCTT-T-GAATTTGGC-
1 CAAATAAGGGCCTAACGTTATCGAAAAT-GCT
14717 CAAATAAGGGCCTAACGTTATCGAAAATGCT
1 CAAATAAGGGCCTAACGTTATCGAAAATGCT
*
14748 CAAATAAGGGCCTGACGT
1 CAAATAAGGGCCTAACGT
14766 CAGTTTGGAT
Statistics
Matches: 63, Mismatches: 11, Indels: 8
0.77 0.13 0.10
Matches are distributed among these distances:
29 21 0.33
30 6 0.10
31 36 0.57
ACGTcount: A:0.35, C:0.18, G:0.22, T:0.25
Consensus pattern (31 bp):
CAAATAAGGGCCTAACGTTATCGAAAATGCT
Found at i:14717 original size:60 final size:60
Alignment explanation
Indices: 14624--14763 Score: 235
Period size: 60 Copynumber: 2.3 Consensus size: 60
14614 ATTGGCTAAT
* * * * *
14624 TGCTCAAATAAGGGCCTGATCTTTTACTTTGGCCAAATAAGGGCTTAATGTTATCGAAAA
1 TGCTCAAATAAGGGCCTGACCTTTGAATTTGGCCAAATAAGGGCCTAACGTTATCGAAAA
14684 TGCTCAAATAAGGGCCTGACCTTTGAATTTGGCCAAATAAGGGCCTAACGTTATCGAAAA
1 TGCTCAAATAAGGGCCTGACCTTTGAATTTGGCCAAATAAGGGCCTAACGTTATCGAAAA
14744 TGCTCAAATAAGGGCCTGAC
1 TGCTCAAATAAGGGCCTGAC
14764 GTCAGTTTGG
Statistics
Matches: 75, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
60 75 1.00
ACGTcount: A:0.32, C:0.19, G:0.21, T:0.27
Consensus pattern (60 bp):
TGCTCAAATAAGGGCCTGACCTTTGAATTTGGCCAAATAAGGGCCTAACGTTATCGAAAA
Found at i:14727 original size:29 final size:29
Alignment explanation
Indices: 14628--14729 Score: 98
Period size: 29 Copynumber: 3.4 Consensus size: 29
14618 GCTAATTGCT
* *
14628 CAAATAAGGGCCTGATCTTTTACTTTGGC
1 CAAATAAGGGCCTGATCTTTGAATTTGGC
* * * **
14657 CAAATAAGGGCTTAATGTTATCGAAAAT-GC
1 CAAATAAGGGCCTGATCTT-T-GAATTTGGC
*
14687 TCAAATAAGGGCCTGACCTTTGAATTTGGC
1 -CAAATAAGGGCCTGATCTTTGAATTTGGC
14717 CAAATAAGGGCCT
1 CAAATAAGGGCCT
14730 AACGTTATCG
Statistics
Matches: 56, Mismatches: 13, Indels: 8
0.73 0.17 0.10
Matches are distributed among these distances:
29 33 0.59
30 6 0.11
31 17 0.30
ACGTcount: A:0.31, C:0.19, G:0.22, T:0.28
Consensus pattern (29 bp):
CAAATAAGGGCCTGATCTTTGAATTTGGC
Found at i:14871 original size:29 final size:29
Alignment explanation
Indices: 14830--14931 Score: 109
Period size: 29 Copynumber: 3.4 Consensus size: 29
14820 GGCAAACGTT
14830 AGGCCCTTATTTGGCCAAATTAAAAGATC
1 AGGCCCTTATTTGGCCAAATTAAAAGATC
** * *
14859 AGGCCCTTATTTGAG-CATTTTGGCAAATG-TT
1 AGGCCCTTATTTG-GCCAAATT---AAAAGATC
14890 AGGCCCTTATTTGGCCAAATTAAAAGATC
1 AGGCCCTTATTTGGCCAAATTAAAAGATC
*
14919 AAGCCCTTATTTG
1 AGGCCCTTATTTG
14932 AGATTTTGGC
Statistics
Matches: 58, Mismatches: 9, Indels: 12
0.73 0.11 0.15
Matches are distributed among these distances:
28 4 0.07
29 30 0.52
30 2 0.03
31 18 0.31
32 4 0.07
ACGTcount: A:0.29, C:0.20, G:0.19, T:0.32
Consensus pattern (29 bp):
AGGCCCTTATTTGGCCAAATTAAAAGATC
Found at i:14891 original size:60 final size:60
Alignment explanation
Indices: 14798--14961 Score: 287
Period size: 60 Copynumber: 2.8 Consensus size: 60
14788 TTTTCGATGC
*
14798 CAGGCCCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTGGCCAAATTAAAAGAT
1 CAGGCCCTTATTTGAGCATTTTGGCAAATGTTAGGCCCTTATTTGGCCAAATTAAAAGAT
14858 CAGGCCCTTATTTGAGCATTTTGGCAAATGTTAGGCCCTTATTTGGCCAAATTAAAAGAT
1 CAGGCCCTTATTTGAGCATTTTGGCAAATGTTAGGCCCTTATTTGGCCAAATTAAAAGAT
*
14918 CAAGCCCTTATTTGAG-ATTTTGGCAAACT-TTAGGCCCTTATTTG
1 CAGGCCCTTATTTGAGCATTTTGGCAAA-TGTTAGGCCCTTATTTG
14962 AGCAATTAGC
Statistics
Matches: 101, Mismatches: 2, Indels: 3
0.95 0.02 0.03
Matches are distributed among these distances:
59 26 0.26
60 75 0.74
ACGTcount: A:0.27, C:0.20, G:0.20, T:0.34
Consensus pattern (60 bp):
CAGGCCCTTATTTGAGCATTTTGGCAAATGTTAGGCCCTTATTTGGCCAAATTAAAAGAT
Found at i:18084 original size:58 final size:58
Alignment explanation
Indices: 17989--18104 Score: 205
Period size: 58 Copynumber: 2.0 Consensus size: 58
17979 GGGGGGGGGG
* *
17989 GGGATATGAATTCTCCCTTCATTAAGTGAATTAGTATGAATGCCAAAAAAATGCACTT
1 GGGAGATGAATTCTCCCTCCATTAAGTGAATTAGTATGAATGCCAAAAAAATGCACTT
*
18047 GGGAGATGAATTTTCCCTCCATTAAGTGAATTAGTATGAATGCCAAAAAAATGCACTT
1 GGGAGATGAATTCTCCCTCCATTAAGTGAATTAGTATGAATGCCAAAAAAATGCACTT
18105 ATGGCTGCTG
Statistics
Matches: 55, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
58 55 1.00
ACGTcount: A:0.36, C:0.16, G:0.18, T:0.30
Consensus pattern (58 bp):
GGGAGATGAATTCTCCCTCCATTAAGTGAATTAGTATGAATGCCAAAAAAATGCACTT
Found at i:23469 original size:23 final size:23
Alignment explanation
Indices: 23439--23486 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
23429 CTTAAGTGTA
23439 AACTCCTTTTCAATTGCTGTTCT
1 AACTCCTTTTCAATTGCTGTTCT
23462 AACTCCTTTTCAATTGCTGTTCT
1 AACTCCTTTTCAATTGCTGTTCT
23485 AA
1 AA
23487 TAATCTCATC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.21, C:0.25, G:0.08, T:0.46
Consensus pattern (23 bp):
AACTCCTTTTCAATTGCTGTTCT
Found at i:26519 original size:17 final size:17
Alignment explanation
Indices: 26481--26513 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
26471 CTCATAGTAC
26481 CTAGGTAGTATGAGGTA
1 CTAGGTAGTATGAGGTA
26498 CTAGGTAGTATGAGGT
1 CTAGGTAGTATGAGGT
26514 GATAGGCTGC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.27, C:0.06, G:0.36, T:0.30
Consensus pattern (17 bp):
CTAGGTAGTATGAGGTA
Found at i:36025 original size:22 final size:22
Alignment explanation
Indices: 36000--36066 Score: 55
Period size: 22 Copynumber: 3.0 Consensus size: 22
35990 TGATCGAGAG
36000 TAAAGAAAATAATTAAGAAAAC
1 TAAAGAAAATAATTAAGAAAAC
* * *
36022 TAAAGCAAGTAA-TAACAAATAC
1 TAAAGAAAATAATTAAGAAA-AC
* * *
36044 CAAATAAAATAATTTATGAAAAC
1 TAAAGAAAATAA-TTAAGAAAAC
36067 AAATCCTCCA
Statistics
Matches: 33, Mismatches: 9, Indels: 5
0.70 0.19 0.11
Matches are distributed among these distances:
21 6 0.18
22 20 0.61
23 2 0.06
24 5 0.15
ACGTcount: A:0.63, C:0.09, G:0.07, T:0.21
Consensus pattern (22 bp):
TAAAGAAAATAATTAAGAAAAC
Done.