Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008664.1 Corchorus capsularis cultivar CVL-1 contig08685, 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: 18429
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.32
Found at i:1785 original size:89 final size:89
Alignment explanation
Indices: 1675--1837 Score: 256
Period size: 89 Copynumber: 1.8 Consensus size: 89
1665 ATGTTAGGAT
* * ** *
1675 TCACATGTGAGGGAAACATCCCACATCATAATGAGAT-GAGTTGTTTGAGTGACATATATACATG
1 TCACATGTAAGGAAAACATCCCACATCATAAAAAAATGGA-TTGTTTGAGTGACATATATACATG
1739 AAGGACCCAAGAAAGTGATTCACAA
65 AAGGACCCAAGAAAGTGATTCACAA
*
1764 TCACATGTAAGGAAAACATCCCACATCATAAAAAAATGGATTGTTTGAGTGGCATATATACATGA
1 TCACATGTAAGGAAAACATCCCACATCATAAAAAAATGGATTGTTTGAGTGACATATATACATGA
1829 AGGACCCAA
66 AGGACCCAA
1838 AAATTTATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
89 65 0.97
90 2 0.03
ACGTcount: A:0.40, C:0.17, G:0.20, T:0.23
Consensus pattern (89 bp):
TCACATGTAAGGAAAACATCCCACATCATAAAAAAATGGATTGTTTGAGTGACATATATACATGA
AGGACCCAAGAAAGTGATTCACAA
Found at i:2280 original size:31 final size:31
Alignment explanation
Indices: 2242--2409 Score: 152
Period size: 31 Copynumber: 5.5 Consensus size: 31
2232 AAAGGCTAAT
2242 TGCTCAAATAAGGGCCTAACGTTTGCCAAAA
1 TGCTCAAATAAGGGCCTAACGTTTGCCAAAA
* * * **
2273 TGCTCAAATAAGGGCCCGATC-TTT--TAATT
1 TGCTCAAATAAGGG-CCTAACGTTTGCCAAAA
*
2302 TGGC-CAAATAAGGGTCTAACGTTTGCCAAAA
1 T-GCTCAAATAAGGGCCTAACGTTTGCCAAAA
* * * **
2333 TACTCAAATAAGGGCCCCATC-TTTG--AATT
1 TGCTCAAATAAGGG-CCTAACGTTTGCCAAAA
*
2362 TGCCCAAATAAGGGCCTAACGTTTGCCAAAA
1 TGCTCAAATAAGGGCCTAACGTTTGCCAAAA
2393 TGCTCAAATAAGGGCCT
1 TGCTCAAATAAGGGCCT
2410 GTCTCACGCG
Statistics
Matches: 103, Mismatches: 24, Indels: 20
0.70 0.16 0.14
Matches are distributed among these distances:
28 7 0.07
29 34 0.33
30 3 0.03
31 52 0.50
32 7 0.07
ACGTcount: A:0.33, C:0.23, G:0.19, T:0.26
Consensus pattern (31 bp):
TGCTCAAATAAGGGCCTAACGTTTGCCAAAA
Found at i:2314 original size:60 final size:60
Alignment explanation
Indices: 2241--2408 Score: 282
Period size: 60 Copynumber: 2.8 Consensus size: 60
2231 TAAAGGCTAA
* * *
2241 TTGCTCAAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGGCCCGATCTTTTAAT
1 TTGCCCAAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGGCCCCATCTTTGAAT
* * *
2301 TTGGCCAAATAAGGGTCTAACGTTTGCCAAAATACTCAAATAAGGGCCCCATCTTTGAAT
1 TTGCCCAAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGGCCCCATCTTTGAAT
2361 TTGCCCAAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGGCC
1 TTGCCCAAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGGCC
2409 TGTCTCACGC
Statistics
Matches: 99, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
60 99 1.00
ACGTcount: A:0.33, C:0.23, G:0.19, T:0.26
Consensus pattern (60 bp):
TTGCCCAAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGGCCCCATCTTTGAAT
Found at i:2476 original size:31 final size:31
Alignment explanation
Indices: 2441--2511 Score: 124
Period size: 31 Copynumber: 2.3 Consensus size: 31
2431 GACACCAGAC
2441 CCTTATTTGAGCATTTTCGATAACGTTAAGA
1 CCTTATTTGAGCATTTTCGATAACGTTAAGA
* *
2472 CCTTATTTGAGCATTTTCGATAACGTTAGGC
1 CCTTATTTGAGCATTTTCGATAACGTTAAGA
2503 CCTTATTTG
1 CCTTATTTG
2512 GCCAAATTAA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
31 38 1.00
ACGTcount: A:0.24, C:0.18, G:0.17, T:0.41
Consensus pattern (31 bp):
CCTTATTTGAGCATTTTCGATAACGTTAAGA
Found at i:2638 original size:59 final size:60
Alignment explanation
Indices: 2472--2630 Score: 232
Period size: 59 Copynumber: 2.7 Consensus size: 60
2462 AACGTTAAGA
* *
2472 CCTTATTTGAGCATTTTCGATAACGTTAGGCCCTTATTTGGCCAAATTAAAAGACCGGGC
1 CCTTATTTGAGCATTTTCGATAACGTTAGGCCCTTATTTGGCCAAATTAAAAGACCAGAC
* * *
2532 CCTTATTTGA-CATTTTCGATAACGTTAGACCCTTATTTGGTCAAATTAAAAGATCAGAC
1 CCTTATTTGAGCATTTTCGATAACGTTAGGCCCTTATTTGGCCAAATTAAAAGACCAGAC
* *
2591 CCTTATTTGAGCATTTTGCCA-AACGTTAGGCTCTTATTTG
1 CCTTATTTGAGCATTTT-CGATAACGTTAGGCCCTTATTTG
2631 AGCAATTAGC
Statistics
Matches: 89, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
59 54 0.61
60 33 0.37
61 2 0.02
ACGTcount: A:0.27, C:0.20, G:0.17, T:0.36
Consensus pattern (60 bp):
CCTTATTTGAGCATTTTCGATAACGTTAGGCCCTTATTTGGCCAAATTAAAAGACCAGAC
Found at i:3744 original size:20 final size:20
Alignment explanation
Indices: 3705--3744 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
3695 TTTGCTATCC
*
3705 TCTTCTAATAAATCTAATTT
1 TCTTCTAATAAATATAATTT
3725 TCTT-TAATAAATATACATTT
1 TCTTCTAATAAATATA-ATTT
3745 ATTTTTCAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 10 0.56
20 8 0.44
ACGTcount: A:0.38, C:0.12, G:0.00, T:0.50
Consensus pattern (20 bp):
TCTTCTAATAAATATAATTT
Found at i:8363 original size:27 final size:29
Alignment explanation
Indices: 8333--8395 Score: 85
Period size: 27 Copynumber: 2.2 Consensus size: 29
8323 TAAAAATTTG
* *
8333 AAAAGAACAATGAAAG-AAAA-AATGAGA
1 AAAAGAACAAAGAAAGAAAAAGAATAAGA
*
8360 AAAAAAACAAAGAAAGAAAAAGAATAAGA
1 AAAAGAACAAAGAAAGAAAAAGAATAAGA
8389 AAAAGAA
1 AAAAGAA
8396 AGGGAACAGA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
27 14 0.47
28 4 0.13
29 12 0.40
ACGTcount: A:0.76, C:0.03, G:0.16, T:0.05
Consensus pattern (29 bp):
AAAAGAACAAAGAAAGAAAAAGAATAAGA
Found at i:8589 original size:20 final size:20
Alignment explanation
Indices: 8550--8589 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
8540 TATGAAAAGG
*
8550 GAAGACACGTGTATTATTGT
1 GAAGACACGTGCATTATTGT
*
8570 GAAGACACGTGCATTGTTGT
1 GAAGACACGTGCATTATTGT
8590 TGAGAGTTGA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.28, C:0.12, G:0.28, T:0.33
Consensus pattern (20 bp):
GAAGACACGTGCATTATTGT
Found at i:11385 original size:6 final size:6
Alignment explanation
Indices: 11374--11404 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
11364 TATCCATTTA
*
11374 GAATCC GAATCC GAATCC GAATCC GTATCC G
1 GAATCC GAATCC GAATCC GAATCC GAATCC G
11405 CCTAACCATA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.29, C:0.32, G:0.19, T:0.19
Consensus pattern (6 bp):
GAATCC
Found at i:11985 original size:17 final size:18
Alignment explanation
Indices: 11963--12004 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
11953 ATTTATTAAT
11963 TATTTTAATTA-ATATTA
1 TATTTTAATTAGATATTA
*
11980 TATTTTTATTTAGATATTA
1 TA-TTTTAATTAGATATTA
*
11999 CATTTT
1 TATTTT
12005 TACTTAAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
17 2 0.10
18 12 0.57
19 7 0.33
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.62
Consensus pattern (18 bp):
TATTTTAATTAGATATTA
Found at i:11996 original size:19 final size:18
Alignment explanation
Indices: 11965--12011 Score: 58
Period size: 19 Copynumber: 2.6 Consensus size: 18
11955 TTATTAATTA
*
11965 TTTTAATTAATATTATAT
1 TTTTAATTAATATTACAT
*
11983 TTTTATTTAGATATTACAT
1 TTTTAATTA-ATATTACAT
*
12002 TTTTACTTAA
1 TTTTAATTAA
12012 AAACTACTCA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
18 9 0.36
19 16 0.64
ACGTcount: A:0.34, C:0.04, G:0.02, T:0.60
Consensus pattern (18 bp):
TTTTAATTAATATTACAT
Found at i:13299 original size:167 final size:163
Alignment explanation
Indices: 13010--13495 Score: 542
Period size: 167 Copynumber: 2.9 Consensus size: 163
13000 GAATAAACAT
* ** * * * ** *
13010 GTGGAATTACTAAAAGATCCCCACCCCGAATTAATGAGGAGCAAGAGAATTAATTTTTTTTCGTC
1 GTGGAATTAATAAAAGA-CCCCACCAAGGATTGATGATGAGTTAGAGAACTAA-TTTTTTTCGTC
* * * *
13075 TTTTCCCACTTGGCGGATTACTTAAATGTTCTAACTTTTAATTCTTAAGGGGATTAAATAGCTAG
64 TTTTCCTACTTGGCAGATTACTTAAATGTCCTAACTTTTGATTCTTAA-GGGATTAAATAGCTA-
* *
13140 ACTTTTTGTTCATTTCTCAATTGACTTTAATAGAATA
127 ACTTTTTGGTCATTTCTCAATTGACTTGAATAGAATA
* * * * * * ** * *
13177 GTGGAATTACTAAGAGGTCCCTACCAAGGCTTGCTTTTGGAGTTAGAGAACTTATTTTTTTCGTA
1 GTGGAATTAATAA-AAGACCCCACCAAGGATTGATGAT-GAGTTAGAGAACTAATTTTTTTCGTC
* *
13242 TTTTCTTACTTGGCAGATTACTTAAATGTCCTAACTTTTGATTCTTGAGGAGATTAAATAAG-TA
64 TTTTCCTACTTGGCAGATTACTTAAATGTCCTAACTTTTGATTCTTAAGG-GATTAAAT-AGCTA
* * * * * *
13306 TTCTTTTTGGTCATTTCCCGATGGACTTGACTAGAGTA
127 -ACTTTTTGGTCATTTCTCAATTGACTTGAATAGAATA
* *
13344 GTGGAATTAATAAAAGACCCCATCAAGGATTGATGATGAGTTAGAGAACTAATCTTTTTCGTCTT
1 GTGGAATTAATAAAAGACCCCACCAAGGATTGATGATGAGTTAGAGAACTAATTTTTTTCGTCTT
* *
13409 TACCTACTTGGCAGATTACTTAAATGTCCTAACTTTTGATTCTTAAGGGATTAAATAACTTAACT
66 TTCCTACTTGGCAGATTACTTAAATGTCCTAACTTTTGATTCTTAAGGGATTAAATAGC-TAACT
13474 TTTTGGTCATTTCTCAATTGAC
130 TTTTGGTCATTTCTCAATTGAC
13496 AAATGACTCA
Statistics
Matches: 261, Mismatches: 52, Indels: 15
0.80 0.16 0.05
Matches are distributed among these distances:
163 1 0.00
164 29 0.11
165 72 0.28
166 18 0.07
167 126 0.48
168 15 0.06
ACGTcount: A:0.29, C:0.16, G:0.17, T:0.38
Consensus pattern (163 bp):
GTGGAATTAATAAAAGACCCCACCAAGGATTGATGATGAGTTAGAGAACTAATTTTTTTCGTCTT
TTCCTACTTGGCAGATTACTTAAATGTCCTAACTTTTGATTCTTAAGGGATTAAATAGCTAACTT
TTTGGTCATTTCTCAATTGACTTGAATAGAATA
Done.