Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010017.1 Corchorus capsularis cultivar CVL-1 contig10038, 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: 25121
ACGTcount: A:0.33, C:0.17, G:0.15, T:0.34
Found at i:6399 original size:18 final size:17
Alignment explanation
Indices: 6369--6409 Score: 55
Period size: 18 Copynumber: 2.4 Consensus size: 17
6359 AAAGGTTTTC
* *
6369 CAAAAATCCAAAAAATT
1 CAAAAATCAAAAAAAAT
6386 CAAAAATTCAAAAAAAAT
1 CAAAAA-TCAAAAAAAAT
6404 CAAAAA
1 CAAAAA
6410 AGGAATTTCA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 6 0.29
18 15 0.71
ACGTcount: A:0.71, C:0.15, G:0.00, T:0.15
Consensus pattern (17 bp):
CAAAAATCAAAAAAAAT
Found at i:7991 original size:439 final size:439
Alignment explanation
Indices: 7301--8233 Score: 1490
Period size: 439 Copynumber: 2.1 Consensus size: 439
7291 AGGACTAAGT
* * * *
7301 AATATGAGGGTCATTTGATAAATAATCCAAATAAAAAAATGTTTGTTAATGGAAATTTTGAACAT
1 AATATGAGGATCATTAGATAAATAATCC-AATAAAAAAATATTTGTTAATGGAGATTTTGAACAT
* * *
7366 AAAAATTCCCTTTTGAACCCTTCATGAAACTCGTAGATTAAATTTAGCTTTCGAGTCCTGCATGA
65 AAAAACTCCCTATTGAACCCTTCATGAAACTCGTAGATCAAATTTAGCTTTCGAGTCCTGCATGA
* * * * * *
7431 AAGTTGTAAATCATGCAATAACCTTTTGACCGACACTTCAATAACTTCAATTGGATATGTGAACA
130 AAATCGTAAATCATGCAATAACCTTCTAACCGACACTTCAATAACTTCAATTGGACATATGAACA
*
7496 AAAAGTTATACGATATTAAATTGACCGGCAATCAAAACCACAAAATTTCAGAAGCATTTTTTAGA
195 AAAAATTATACGATATTAAATTGACCGGCAATCAAAACCACAAAATTTCAGAAGCATTTTTTAGA
7561 ATCAAAACATCAAAATTGGCTTCTGAGTTCTTCAT-AAAAATTGTAGATCATGAAATTACCTCTT
260 ATCAAAACATCAAAATTGGCTTCTGAGTTCTTCATGAAAAA-TGTAGATCATGAAATTACCTCTT
*
7625 AATAGACACTTGAATCACCTTAATCGGATAAATAGGAAAAAAATACAAAAATAAATGCGAACGCG
324 AATAGACACTTGAATCACCTTAATCGGACAAATAGGAAAAAAATACAAAAATAAATGCGAACGCG
* **
7690 TCAAATCGTCCAACCTATAATCGTAAAGAACTAAATAGCATAAAGTATAAA
389 TCAAATCATCCAACCTATAATCGTAAAGAACTAAATAGCATAAAACATAAA
*
7741 AGTATGAGGATCATTAGATAAATAATCCAATAAAAAAATATTTGTTAATGGAGATTTTGAACATA
1 AATATGAGGATCATTAGATAAATAATCCAATAAAAAAATATTTGTTAATGGAGATTTTGAACATA
* * *
7806 AAAACTCCCTATTGAGCCCTTCATGAAACTCGTAGATCAAATTTAGCTTTCGGGTCCTTCATGAA
66 AAAACTCCCTATTGAACCCTTCATGAAACTCGTAGATCAAATTTAGCTTTCGAGTCCTGCATGAA
* * * *
7871 AATCGTAAATCATTCAATAACCTTCTAACCGATACTTTAATAACTTCAATTGGACATATGGACAA
131 AATCGTAAATCATGCAATAACCTTCTAACCGACACTTCAATAACTTCAATTGGACATATGAACAA
* *
7936 AAAATTATACGATATTAAATTGACTGGCAATCAAAACCACAAAATTTCGGAAGCATTTTTTAGAA
196 AAAATTATACGATATTAAATTGACCGGCAATCAAAACCACAAAATTTCAGAAGCATTTTTTAGAA
* * *
8001 TCAAAACATTAAAATTGGCTTTTGAGTTCTTCATGAAAAATGTAGATCATGAAATTACCTTTTAA
261 TCAAAACATCAAAATTGGCTTCTGAGTTCTTCATGAAAAATGTAGATCATGAAATTACCTCTTAA
* * *
8066 TAGACACTTGAATTACCTTAATCGGACAAATAGGAAAAAAATACAATAATAAATGCGAACGCGTT
326 TAGACACTTGAATCACCTTAATCGGACAAATAGGAAAAAAATACAAAAATAAATGCGAACGCGTC
* *
8131 AAATCATCCAACCTATAATTGTAAAGGACTAAATAGCATAAAACATAAA
391 AAATCATCCAACCTATAATCGTAAAGAACTAAATAGCATAAAACATAAA
* * *
8180 AATATGAGGATCATTAGATAAATAATCCAACAAAAAAATATTAGTTTATGGAGA
1 AATATGAGGATCATTAGATAAATAATCCAATAAAAAAATATTTGTTAATGGAGA
8234 ATGGGACCCA
Statistics
Matches: 452, Mismatches: 40, Indels: 3
0.91 0.08 0.01
Matches are distributed among these distances:
439 422 0.93
440 30 0.07
ACGTcount: A:0.42, C:0.15, G:0.13, T:0.29
Consensus pattern (439 bp):
AATATGAGGATCATTAGATAAATAATCCAATAAAAAAATATTTGTTAATGGAGATTTTGAACATA
AAAACTCCCTATTGAACCCTTCATGAAACTCGTAGATCAAATTTAGCTTTCGAGTCCTGCATGAA
AATCGTAAATCATGCAATAACCTTCTAACCGACACTTCAATAACTTCAATTGGACATATGAACAA
AAAATTATACGATATTAAATTGACCGGCAATCAAAACCACAAAATTTCAGAAGCATTTTTTAGAA
TCAAAACATCAAAATTGGCTTCTGAGTTCTTCATGAAAAATGTAGATCATGAAATTACCTCTTAA
TAGACACTTGAATCACCTTAATCGGACAAATAGGAAAAAAATACAAAAATAAATGCGAACGCGTC
AAATCATCCAACCTATAATCGTAAAGAACTAAATAGCATAAAACATAAA
Found at i:12001 original size:67 final size:70
Alignment explanation
Indices: 11886--12023 Score: 183
Period size: 67 Copynumber: 2.0 Consensus size: 70
11876 TTCCAAATTT
* **
11886 CATTTTTATCTTTTACAAATCATAACTATCTCCACACTCCTTTTCACAC-CCT-TA-TATGCCTT
1 CATTTTTATCTTTTACAAATCATAACTAACTCCACACTCCTTCCCACACTCCTATATTATGCCTT
11948 TTATA
66 TTATA
* ** * *
11953 CATTTTTATCTTTTACAAGTCATAGGTAACTCCACACTTCTTCCCACACTCTTATATTATGCCTT
1 CATTTTTATCTTTTACAAATCATAACTAACTCCACACTCCTTCCCACACTCCTATATTATGCCTT
12018 TTATA
66 TTATA
12023 C
1 C
12024 CCTTTATTAT
Statistics
Matches: 60, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
67 42 0.70
68 2 0.03
69 2 0.03
70 14 0.23
ACGTcount: A:0.26, C:0.28, G:0.04, T:0.43
Consensus pattern (70 bp):
CATTTTTATCTTTTACAAATCATAACTAACTCCACACTCCTTCCCACACTCCTATATTATGCCTT
TTATA
Found at i:12701 original size:16 final size:17
Alignment explanation
Indices: 12673--12709 Score: 58
Period size: 16 Copynumber: 2.2 Consensus size: 17
12663 GATTTTTTTA
12673 TTATCTTTATTATCTAT
1 TTATCTTTATTATCTAT
*
12690 TTATCTTT-TTATTTAT
1 TTATCTTTATTATCTAT
12706 TTAT
1 TTAT
12710 TTAGCTATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 11 0.58
17 8 0.42
ACGTcount: A:0.22, C:0.08, G:0.00, T:0.70
Consensus pattern (17 bp):
TTATCTTTATTATCTAT
Found at i:12702 original size:19 final size:20
Alignment explanation
Indices: 12683--12757 Score: 57
Period size: 19 Copynumber: 3.9 Consensus size: 20
12673 TTATCTTTAT
**
12683 TATCTATTTATCTTTTTATT
1 TATCTATTTATCTTTTTACC
* * *
12703 TATTTATTTAGC-TATTACC
1 TATCTATTTATCTTTTTACC
12722 TATCTATTTATCTATTTT--C
1 TATCTATTTATCT-TTTTACC
* *
12741 TATTTATGTATCTTTTT
1 TATCTATTTATCTTTTT
12758 GTTTACATAA
Statistics
Matches: 43, Mismatches: 10, Indels: 6
0.73 0.17 0.10
Matches are distributed among these distances:
18 4 0.09
19 26 0.60
20 10 0.23
21 3 0.07
ACGTcount: A:0.21, C:0.12, G:0.03, T:0.64
Consensus pattern (20 bp):
TATCTATTTATCTTTTTACC
Found at i:12742 original size:7 final size:8
Alignment explanation
Indices: 12682--12747 Score: 55
Period size: 8 Copynumber: 8.5 Consensus size: 8
12672 ATTATCTTTA
12682 TTATCTAT
1 TTATCTAT
*
12690 TTATCTTT
1 TTATCTAT
*
12698 TTATTTAT
1 TTATCTAT
* *
12706 TTATTTAG
1 TTATCTAT
* *
12714 CTAT-TAC
1 TTATCTAT
*
12721 CTATCTAT
1 TTATCTAT
12729 TTATCTAT
1 TTATCTAT
12737 TT-TCTAT
1 TTATCTAT
12744 TTAT
1 TTAT
12748 GTATCTTTTT
Statistics
Matches: 48, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
7 13 0.27
8 35 0.73
ACGTcount: A:0.23, C:0.12, G:0.02, T:0.64
Consensus pattern (8 bp):
TTATCTAT
Found at i:16197 original size:25 final size:27
Alignment explanation
Indices: 16145--16197 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
16135 TTACTCAACT
**
16145 AAAAACTCTATTTTTATTTTTCTGTAA
1 AAAAACTCTATTTTTATTTTAATGTAA
16172 AAAAACTCTATTTTTA-TTTAAT-TAA
1 AAAAACTCTATTTTTATTTTAATGTAA
16197 A
1 A
16198 TCTAATATTC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 4 0.17
26 4 0.17
27 16 0.67
ACGTcount: A:0.40, C:0.09, G:0.02, T:0.49
Consensus pattern (27 bp):
AAAAACTCTATTTTTATTTTAATGTAA
Found at i:17201 original size:2 final size:2
Alignment explanation
Indices: 17194--17236 Score: 70
Period size: 2 Copynumber: 22.0 Consensus size: 2
17184 ACTACTCCTA
*
17194 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T CT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
17235 AT
1 AT
17237 TATTTTTAAT
Statistics
Matches: 39, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
1 1 0.03
2 38 0.97
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:19604 original size:14 final size:14
Alignment explanation
Indices: 19587--19635 Score: 56
Period size: 14 Copynumber: 3.9 Consensus size: 14
19577 TTATTGGAAA
19587 ATAATTATTATTTT
1 ATAATTATTATTTT
19601 ATAATTATTA--TT
1 ATAATTATTATTTT
19613 -T-A--ATTATTTT
1 ATAATTATTATTTT
19623 ATAATTATTATTT
1 ATAATTATTATTT
19636 AATTCAATAA
Statistics
Matches: 29, Mismatches: 0, Indels: 12
0.71 0.00 0.29
Matches are distributed among these distances:
8 4 0.14
10 3 0.10
11 2 0.07
12 3 0.10
14 17 0.59
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (14 bp):
ATAATTATTATTTT
Found at i:19618 original size:22 final size:22
Alignment explanation
Indices: 19593--19639 Score: 94
Period size: 22 Copynumber: 2.1 Consensus size: 22
19583 GAAAATAATT
19593 ATTATTTTATAATTATTATTTA
1 ATTATTTTATAATTATTATTTA
19615 ATTATTTTATAATTATTATTTA
1 ATTATTTTATAATTATTATTTA
19637 ATT
1 ATT
19640 CAATAATGAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (22 bp):
ATTATTTTATAATTATTATTTA
Found at i:19639 original size:11 final size:11
Alignment explanation
Indices: 19593--19631 Score: 62
Period size: 11 Copynumber: 3.5 Consensus size: 11
19583 GAAAATAATT
19593 ATTATTTTATA
1 ATTATTTTATA
19604 ATTATTATT-TA
1 ATTATT-TTATA
19615 ATTATTTTATA
1 ATTATTTTATA
19626 ATTATT
1 ATTATT
19632 ATTTAATTCA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
10 2 0.08
11 22 0.85
12 2 0.08
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (11 bp):
ATTATTTTATA
Found at i:24395 original size:12 final size:13
Alignment explanation
Indices: 24363--24397 Score: 54
Period size: 12 Copynumber: 2.8 Consensus size: 13
24353 GTATTGCTAC
24363 TTGACCCTCCAAT
1 TTGACCCTCCAAT
*
24376 TTGTCCCTCC-AT
1 TTGACCCTCCAAT
24388 TTGACCCTCC
1 TTGACCCTCC
24398 TAACGTGTCA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
12 11 0.55
13 9 0.45
ACGTcount: A:0.14, C:0.43, G:0.09, T:0.34
Consensus pattern (13 bp):
TTGACCCTCCAAT
Found at i:24752 original size:20 final size:20
Alignment explanation
Indices: 24727--24764 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
24717 ATTTTGTGAA
24727 TTACTAAATACCGCCCCCTT
1 TTACTAAATACCGCCCCCTT
**
24747 TTACTAGCTACCGCCCCC
1 TTACTAAATACCGCCCCC
24765 CTCTTGGACT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.21, C:0.45, G:0.08, T:0.26
Consensus pattern (20 bp):
TTACTAAATACCGCCCCCTT
Done.