Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01000346.1 Corchorus capsularis cultivar CVL-1 contig00346, 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: 7298
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.35
Found at i:2373 original size:11 final size:11
Alignment explanation
Indices: 2340--2374 Score: 54
Period size: 11 Copynumber: 3.3 Consensus size: 11
2330 AACCAACTTT
2340 TTAG-TTTTTA
1 TTAGTTTTTTA
*
2350 TCAGTTTTTTA
1 TTAGTTTTTTA
2361 TTAGTTTTTTA
1 TTAGTTTTTTA
2372 TTA
1 TTA
2375 ATATAACTTG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
10 3 0.14
11 19 0.86
ACGTcount: A:0.20, C:0.03, G:0.09, T:0.69
Consensus pattern (11 bp):
TTAGTTTTTTA
Found at i:2600 original size:60 final size:60
Alignment explanation
Indices: 2532--2694 Score: 238
Period size: 60 Copynumber: 2.7 Consensus size: 60
2522 GCTAATTGTT
* * * *
2532 CAAATAAGGGCCTAACGTTTGTC-AAAATACTCAAATAAGGGTCCGATCTTTTAATTTGGC
1 CAAATAAGGGCCTAACG-TTATCGAAAATGCTCAAATAAGGGCCCGATCTTTTAATTTGAC
* **
2592 CAAATAAGGGCCTAACATTATCGAAAATGCTCAAATAAGAACCCGATCTTTTAATTTGAC
1 CAAATAAGGGCCTAACGTTATCGAAAATGCTCAAATAAGGGCCCGATCTTTTAATTTGAC
*
2652 CAAATAAGGGTCTAACGTTATCGAAAATGCTCAAATAAGGGCC
1 CAAATAAGGGCCTAACGTTATCGAAAATGCTCAAATAAGGGCC
2695 TGGTGTCAGT
Statistics
Matches: 91, Mismatches: 11, Indels: 2
0.88 0.11 0.02
Matches are distributed among these distances:
59 4 0.04
60 87 0.96
ACGTcount: A:0.37, C:0.19, G:0.17, T:0.26
Consensus pattern (60 bp):
CAAATAAGGGCCTAACGTTATCGAAAATGCTCAAATAAGGGCCCGATCTTTTAATTTGAC
Found at i:2630 original size:31 final size:30
Alignment explanation
Indices: 2592--2695 Score: 79
Period size: 31 Copynumber: 3.4 Consensus size: 30
2582 TTAATTTGGC
2592 CAAATAAGGGCCTAACATTATCGAAAATGCT
1 CAAATAAGGGCCTAAC-TTATCGAAAATGCT
** * * * **
2623 CAAATAAGAACCCGATCTT-T-TAATTTGAC-
1 CAAATAAG-GGCCTAACTTATCGAAAATG-CT
*
2652 CAAATAAGGGTCTAACGTTATCGAAAATGCT
1 CAAATAAGGGCCTAAC-TTATCGAAAATGCT
2683 CAAATAAGGGCCT
1 CAAATAAGGGCCT
2696 GGTGTCAGTT
Statistics
Matches: 51, Mismatches: 16, Indels: 12
0.65 0.20 0.15
Matches are distributed among these distances:
28 3 0.06
29 14 0.27
30 4 0.08
31 26 0.51
32 4 0.08
ACGTcount: A:0.39, C:0.19, G:0.16, T:0.25
Consensus pattern (30 bp):
CAAATAAGGGCCTAACTTATCGAAAATGCT
Found at i:2762 original size:31 final size:31
Alignment explanation
Indices: 2727--2888 Score: 142
Period size: 31 Copynumber: 5.4 Consensus size: 31
2717 TGAGACAGGT
2727 CCTTATTTGAGCATTTTGGCAAACGTTAGGC
1 CCTTATTTGAGCATTTTGGCAAACGTTAGGC
** * *
2758 CCTTATTTG-GCAAAATT--CAAA-GATAGGGT
1 CCTTATTTGAGC-ATTTTGGCAAACGTTA-GGC
*
2787 CCTTATTTGAGCATTTTGGCAAACGTTAGGT
1 CCTTATTTGAGCATTTTGGCAAACGTTAGGC
** * *
2818 CCTTATTTG-GCCAAATTAG--AA-GATCAGGC
1 CCTTATTTGAG-CATTTTGGCAAACG-TTAGGC
*
2847 CCTTATTTGAGCATTTTGGCAAACGTTAAGC
1 CCTTATTTGAGCATTTTGGCAAACGTTAGGC
2878 CCTTATTTGAG
1 CCTTATTTGAG
2889 TAATTAGCCT
Statistics
Matches: 102, Mismatches: 17, Indels: 24
0.71 0.12 0.17
Matches are distributed among these distances:
28 4 0.04
29 38 0.37
30 6 0.06
31 50 0.49
32 4 0.04
ACGTcount: A:0.27, C:0.18, G:0.21, T:0.35
Consensus pattern (31 bp):
CCTTATTTGAGCATTTTGGCAAACGTTAGGC
Found at i:2797 original size:60 final size:60
Alignment explanation
Indices: 2722--2886 Score: 262
Period size: 60 Copynumber: 2.8 Consensus size: 60
2712 ACGAGTGAGA
2722 CAGGTCCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTGGCAAAATTCA-AAGAT
1 CAGGTCCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTGGCAAAATT-AGAAGAT
* *
2782 -AGGGTCCTTATTTGAGCATTTTGGCAAACGTTAGGTCCTTATTTGGCCAAATTAGAAGAT
1 CA-GGTCCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTGGCAAAATTAGAAGAT
* *
2842 CAGGCCCTTATTTGAGCATTTTGGCAAACGTTAAGCCCTTATTTG
1 CAGGTCCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTG
2887 AGTAATTAGC
Statistics
Matches: 97, Mismatches: 5, Indels: 6
0.90 0.05 0.06
Matches are distributed among these distances:
59 2 0.02
60 94 0.97
61 1 0.01
ACGTcount: A:0.26, C:0.18, G:0.21, T:0.35
Consensus pattern (60 bp):
CAGGTCCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTGGCAAAATTAGAAGAT
Found at i:4038 original size:38 final size:37
Alignment explanation
Indices: 3967--4046 Score: 117
Period size: 38 Copynumber: 2.1 Consensus size: 37
3957 TACATTTAAA
3967 TAAAAAAAAAACTACTCCCTATTAAATTAGTTACCCAT
1 TAAAAAAAAAACTACTCCCTATT-AATTAGTTACCCAT
*
4005 TAAAATAAAATAACTACTCCCTATT-ATTGGTTACCCAT
1 TAAAA-AAAA-AACTACTCCCTATTAATTAGTTACCCAT
4043 TAAA
1 TAAA
4047 CTTCTTCATG
Statistics
Matches: 39, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
38 21 0.54
39 4 0.10
40 14 0.36
ACGTcount: A:0.45, C:0.20, G:0.04, T:0.31
Consensus pattern (37 bp):
TAAAAAAAAAACTACTCCCTATTAATTAGTTACCCAT
Found at i:4477 original size:16 final size:15
Alignment explanation
Indices: 4452--4482 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
4442 GCAATTGAGA
4452 TTTTTGTTTTTTTAT
1 TTTTTGTTTTTTTAT
4467 TTTTTGCTTTTTTTAT
1 TTTTTG-TTTTTTTAT
4483 AACAGTCAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.40
16 9 0.60
ACGTcount: A:0.06, C:0.03, G:0.06, T:0.84
Consensus pattern (15 bp):
TTTTTGTTTTTTTAT
Done.