Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01005679.1 Corchorus capsularis cultivar CVL-1 contig05697, 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: 3447
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.33
Found at i:1320 original size:24 final size:24
Alignment explanation
Indices: 1288--1335 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
1278 CAACAACAAA
1288 GTAGTTCCAACTCAAAGAGTTCAG
1 GTAGTTCCAACTCAAAGAGTTCAG
1312 GTAGTTCCAACTCAAAGAGTTCAG
1 GTAGTTCCAACTCAAAGAGTTCAG
1336 CCACTCCTAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.33, C:0.21, G:0.21, T:0.25
Consensus pattern (24 bp):
GTAGTTCCAACTCAAAGAGTTCAG
Found at i:2352 original size:31 final size:31
Alignment explanation
Indices: 2311--2571 Score: 243
Period size: 31 Copynumber: 8.5 Consensus size: 31
2301 AAAGGCTAAT
2311 TGCTCAAATAAGGGCCTAACGTTTGTC-AAAA
1 TGCTCAAATAAGGGCCTAACGTTT-TCGAAAA
* * **
2342 TGGTCAAATAAGGGCCTCATC-TTTT--AATT
1 TGCTCAAATAAGGGCCT-AACGTTTTCGAAAA
*
2371 TGGC-CAAATAAGGGCCTAACGTTATCGAAAA
1 T-GCTCAAATAAGGGCCTAACGTTTTCGAAAA
* * * **
2402 TGCTCAAATAAGGACCCGATC-TTTT--AATT
1 TGCTCAAATAAGG-GCCTAACGTTTTCGAAAA
* * * **
2431 TGGTCAAATAAGGGCCAAACATTACCGAAAA
1 TGCTCAAATAAGGGCCTAACGTTTTCGAAAA
* **
2462 TGCTCAAATAAGGGCCAAACGTTGCCGAAAA
1 TGCTCAAATAAGGGCCTAACGTTTTCGAAAA
*
2493 TGCTCAAATAAGGGCCTAACGTTATCGAAAA
1 TGCTCAAATAAGGGCCTAACGTTTTCGAAAA
2524 TGCTCAAATAAGGGCCTAACGTTATT-GAAAA
1 TGCTCAAATAAGGGCCTAACGTT-TTCGAAAA
2555 TGCTCAAATAAGGGCCT
1 TGCTCAAATAAGGGCCT
2572 GGTGTCAGTT
Statistics
Matches: 189, Mismatches: 30, Indels: 22
0.78 0.12 0.09
Matches are distributed among these distances:
28 6 0.03
29 35 0.19
30 4 0.02
31 137 0.72
32 7 0.04
ACGTcount: A:0.36, C:0.20, G:0.20, T:0.25
Consensus pattern (31 bp):
TGCTCAAATAAGGGCCTAACGTTTTCGAAAA
Found at i:2409 original size:60 final size:59
Alignment explanation
Indices: 2315--2539 Score: 256
Period size: 60 Copynumber: 3.7 Consensus size: 59
2305 GCTAATTGCT
* *
2315 CAAATAAGGGCCTAACGTTTGTC-AAAATGGTCAAATAAGGGCCTCATCTTTTAATTTGGC
1 CAAATAAGGGCCTAACG-TTATCGAAAATGCTCAAATAAGGGCC-CATCTTTTAATTTGGC
* *
2375 CAAATAAGGGCCTAACGTTATCGAAAATGCTCAAATAAGGACCCGATCTTTTAATTTGGT
1 CAAATAAGGGCCTAACGTTATCGAAAATGCTCAAATAAGGGCCC-ATCTTTTAATTTGGC
* * * * * ** **
2435 CAAATAAGGGCCAAACATTACCGAAAATGCTCAAATAAGGGCCAAACGTTGCCGAAAAT-GC
1 CAAATAAGGGCCTAACGTTATCGAAAATGCTCAAATAAGGGCCCATC-TT--TTAATTTGGC
2496 TCAAATAAGGGCCTAACGTTATCGAAAATGCTCAAATAAGGGCC
1 -CAAATAAGGGCCTAACGTTATCGAAAATGCTCAAATAAGGGCC
2540 TAACGTTATT
Statistics
Matches: 141, Mismatches: 18, Indels: 10
0.83 0.11 0.06
Matches are distributed among these distances:
59 7 0.05
60 90 0.64
61 1 0.01
62 43 0.30
ACGTcount: A:0.37, C:0.20, G:0.20, T:0.24
Consensus pattern (59 bp):
CAAATAAGGGCCTAACGTTATCGAAAATGCTCAAATAAGGGCCCATCTTTTAATTTGGC
Found at i:2523 original size:62 final size:60
Alignment explanation
Indices: 2311--2571 Score: 251
Period size: 60 Copynumber: 4.3 Consensus size: 60
2301 AAAGGCTAAT
* * * * * **
2311 TGCTCAAATAAGGGCCTAACGTTTGTC-AAAATGGTCAAATAAGGGCCTCATC-TTTTAATT
1 TGCTCAAATAAGGGCCTAACG-TTATCGAAAATGCTCAAATAAGGGCC-AAACGTTTGAAAA
* * * * **
2371 TGGC-CAAATAAGGGCCTAACGTTATCGAAAATGCTCAAATAAGGACCCGATC-TTTTAATT
1 T-GCTCAAATAAGGGCCTAACGTTATCGAAAATGCTCAAATAAGG-GCCAAACGTTTGAAAA
* * * * *
2431 TGGTCAAATAAGGGCCAAACATTACCGAAAATGCTCAAATAAGGGCCAAACGTTGCCGAAAA
1 TGCTCAAATAAGGGCCTAACGTTATCGAAAATGCTCAAATAAGGGCCAAACGTT--TGAAAA
*
2493 TGCTCAAATAAGGGCCTAACGTTATCGAAAATGCTCAAATAAGGGCCTAACGTTATTGAAAA
1 TGCTCAAATAAGGGCCTAACGTTATCGAAAATGCTCAAATAAGGGCCAAACG-T-TTGAAAA
2555 TGCTCAAATAAGGGCCT
1 TGCTCAAATAAGGGCCT
2572 GGTGTCAGTT
Statistics
Matches: 171, Mismatches: 21, Indels: 16
0.82 0.10 0.08
Matches are distributed among these distances:
59 9 0.05
60 85 0.50
61 4 0.02
62 71 0.42
63 1 0.01
64 1 0.01
ACGTcount: A:0.36, C:0.20, G:0.20, T:0.25
Consensus pattern (60 bp):
TGCTCAAATAAGGGCCTAACGTTATCGAAAATGCTCAAATAAGGGCCAAACGTTTGAAAA
Found at i:2696 original size:60 final size:59
Alignment explanation
Indices: 2603--2762 Score: 196
Period size: 60 Copynumber: 2.7 Consensus size: 59
2593 TGAGGCAGGC
* * * * * *
2603 CCTTATTTAAGTATTTTAGCAAACGTTAAGCCCTTATTTGGCCTAATTCAAGGATGGGG
1 CCTTATTTGAGCATTTTAGCAAACGTTAGGCCCTTATTTGGCCAAATTCAAAGATGAGG
* * *
2662 ACCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTGGCCAAATTGAAAGATTAGG
1 -CCTTATTTGAGCATTTTAGCAAACGTTAGGCCCTTATTTGGCCAAATTCAAAGATGAGG
*
2722 CACTTATTTGAGCATTTTCG-ATAACGTTAGGCCCTTATTTG
1 C-CTTATTTGAGCATTTTAGCA-AACGTTAGGCCCTTATTTG
2763 AGCAATTAGC
Statistics
Matches: 88, Mismatches: 10, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
59 2 0.02
60 86 0.98
ACGTcount: A:0.26, C:0.17, G:0.20, T:0.36
Consensus pattern (59 bp):
CCTTATTTGAGCATTTTAGCAAACGTTAGGCCCTTATTTGGCCAAATTCAAAGATGAGG
Found at i:2701 original size:31 final size:29
Alignment explanation
Indices: 2663--2766 Score: 113
Period size: 31 Copynumber: 3.4 Consensus size: 29
2653 AGGATGGGGA
2663 CCTTATTTGAGCATTTTGGCAAACGTTAGGC
1 CCTTATTTGAGCATTTT-G-AAACGTTAGGC
**
2694 CCTTATTTG-GCCAAATTGAAA-GATTAGGC
1 CCTTATTTGAG-CATTTTGAAACG-TTAGGC
*
2723 ACTTATTTGAGCATTTTCGATAACGTTAGGC
1 CCTTATTTGAGCATTTT-GA-AACGTTAGGC
2754 CCTTATTTGAGCA
1 CCTTATTTGAGCA
2767 ATTAGCCTAA
Statistics
Matches: 61, Mismatches: 6, Indels: 12
0.77 0.08 0.15
Matches are distributed among these distances:
28 1 0.02
29 21 0.34
30 5 0.08
31 33 0.54
32 1 0.02
ACGTcount: A:0.26, C:0.18, G:0.20, T:0.36
Consensus pattern (29 bp):
CCTTATTTGAGCATTTTGAAACGTTAGGC
Found at i:2928 original size:19 final size:19
Alignment explanation
Indices: 2901--2951 Score: 84
Period size: 19 Copynumber: 2.7 Consensus size: 19
2891 TTTACTCATT
* *
2901 TCTACATGGTCATGTAAAC
1 TCTAAATGGTAATGTAAAC
2920 TCTAAATGGTAATGTAAAC
1 TCTAAATGGTAATGTAAAC
2939 TCTAAATGGTAAT
1 TCTAAATGGTAAT
2952 TATGTATATG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 30 1.00
ACGTcount: A:0.37, C:0.14, G:0.16, T:0.33
Consensus pattern (19 bp):
TCTAAATGGTAATGTAAAC
Done.