Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006884.1 Corchorus capsularis cultivar CVL-1 contig06905, 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: 32065
ACGTcount: A:0.31, C:0.18, G:0.17, T:0.33
Found at i:5936 original size:16 final size:16
Alignment explanation
Indices: 5917--5947 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
5907 AAAGTGTAGG
5917 AAAATAAATAAAAATC
1 AAAATAAATAAAAATC
*
5933 AAAATAAGTAAAAAT
1 AAAATAAATAAAAAT
5948 AAACTTGAGA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.74, C:0.03, G:0.03, T:0.19
Consensus pattern (16 bp):
AAAATAAATAAAAATC
Found at i:6377 original size:17 final size:16
Alignment explanation
Indices: 6335--6382 Score: 62
Period size: 15 Copynumber: 3.0 Consensus size: 16
6325 GAGTCTCAAG
6335 TAAGTAGACAAGAGTC
1 TAAGTAGACAAGAGTC
* *
6351 T-TGGAGACAAGAGTC
1 TAAGTAGACAAGAGTC
6366 TCAAGTAGACAAGAGTC
1 T-AAGTAGACAAGAGTC
6383 CAAAAGAAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
15 13 0.50
16 1 0.04
17 12 0.46
ACGTcount: A:0.40, C:0.15, G:0.27, T:0.19
Consensus pattern (16 bp):
TAAGTAGACAAGAGTC
Found at i:6377 original size:32 final size:33
Alignment explanation
Indices: 6316--6382 Score: 100
Period size: 36 Copynumber: 2.0 Consensus size: 33
6306 AGAGGAATGA
6316 TGGAGACAAGAGTCTCAAGTAAGTAGACAAGAGTCT
1 TGGAGACAAGAGTCTC-A--AAGTAGACAAGAGTCT
6352 TGGAGACAAGAGTCTC-AAGTAGACAAGAGTC
1 TGGAGACAAGAGTCTCAAAGTAGACAAGAGTC
6383 CAAAAGAAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
32 15 0.48
36 16 0.52
ACGTcount: A:0.39, C:0.15, G:0.28, T:0.18
Consensus pattern (33 bp):
TGGAGACAAGAGTCTCAAAGTAGACAAGAGTCT
Found at i:7054 original size:22 final size:22
Alignment explanation
Indices: 7014--7076 Score: 74
Period size: 22 Copynumber: 2.9 Consensus size: 22
7004 ACCATCATGT
* * * *
7014 GGCCGAATCTCATGACCACTAT
1 GGCCGAATCTCACGGCCACCAA
7036 GGCC-AGATCTCACGGCCACCAA
1 GGCCGA-ATCTCACGGCCACCAA
7058 GGCCGAATCTCACGGCCAC
1 GGCCGAATCTCACGGCCAC
7077 AGTCTCAAAT
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
21 1 0.03
22 33 0.94
23 1 0.03
ACGTcount: A:0.25, C:0.38, G:0.22, T:0.14
Consensus pattern (22 bp):
GGCCGAATCTCACGGCCACCAA
Found at i:14286 original size:18 final size:18
Alignment explanation
Indices: 14263--14304 Score: 75
Period size: 18 Copynumber: 2.3 Consensus size: 18
14253 AATTCTTGTG
14263 CATTTGTAATCCCAATAT
1 CATTTGTAATCCCAATAT
14281 CATTTGTAATCCCAATAT
1 CATTTGTAATCCCAATAT
*
14299 CTTTTG
1 CATTTG
14305 AGATTTCTCC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.29, C:0.21, G:0.07, T:0.43
Consensus pattern (18 bp):
CATTTGTAATCCCAATAT
Found at i:14409 original size:42 final size:40
Alignment explanation
Indices: 14348--14449 Score: 120
Period size: 38 Copynumber: 2.5 Consensus size: 40
14338 CTAAAGAAAA
* *
14348 AAGATCTTTTCGCAATTTTGCAAAAAAATAAAAAAAAACCTT
1 AAGATCTTTTCCCACTTTTGC-AAAAAA-AAAAAAAAACCTT
* *
14390 AAGATCTTTTCCCACTTTTG--AAAAAAAATACAAACCTT
1 AAGATCTTTTCCCACTTTTGCAAAAAAAAAAAAAAACCTT
14428 AAGATCGTTTT-CCACTTTTGCA
1 AAGATC-TTTTCCCACTTTTGCA
14450 TCACGCCTTC
Statistics
Matches: 53, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
38 26 0.49
39 9 0.17
42 18 0.34
ACGTcount: A:0.41, C:0.19, G:0.08, T:0.32
Consensus pattern (40 bp):
AAGATCTTTTCCCACTTTTGCAAAAAAAAAAAAAAACCTT
Found at i:17657 original size:17 final size:17
Alignment explanation
Indices: 17637--17684 Score: 60
Period size: 17 Copynumber: 2.8 Consensus size: 17
17627 AGAATCTTTG
* **
17637 ATCACCAGTGATCTTGC
1 ATCACTAGTGATCTTAA
*
17654 ATCACTGGTGATCTTAA
1 ATCACTAGTGATCTTAA
17671 ATCACTAGTGATCT
1 ATCACTAGTGATCT
17685 GGGGGGTGCT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
17 26 1.00
ACGTcount: A:0.27, C:0.23, G:0.17, T:0.33
Consensus pattern (17 bp):
ATCACTAGTGATCTTAA
Found at i:23089 original size:15 final size:16
Alignment explanation
Indices: 23058--23094 Score: 58
Period size: 15 Copynumber: 2.3 Consensus size: 16
23048 CAAAGAAAGG
23058 AGAAGGGAGGAAGAAGA
1 AGAA-GGAGGAAGAAGA
23075 AGAAGGAGG-AGAAGA
1 AGAAGGAGGAAGAAGA
23090 AGAAG
1 AGAAG
23095 AAATAAGGGA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
15 11 0.55
16 5 0.25
17 4 0.20
ACGTcount: A:0.54, C:0.00, G:0.46, T:0.00
Consensus pattern (16 bp):
AGAAGGAGGAAGAAGA
Found at i:29492 original size:2 final size:2
Alignment explanation
Indices: 29487--29519 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
29477 TAATTGTGTG
29487 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
29520 CTATCTTGAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:30484 original size:10 final size:11
Alignment explanation
Indices: 30471--30512 Score: 52
Period size: 11 Copynumber: 3.9 Consensus size: 11
30461 TTATCAACAC
30471 TATAA-CAGTA
1 TATAATCAGTA
*
30481 TATAATCAGCA
1 TATAATCAGTA
30492 CTATAA-CAGTA
1 -TATAATCAGTA
30503 TATAATCAGT
1 TATAATCAGT
30513 GAATGTTAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
10 10 0.37
11 12 0.44
12 5 0.19
ACGTcount: A:0.45, C:0.14, G:0.10, T:0.31
Consensus pattern (11 bp):
TATAATCAGTA
Found at i:30493 original size:22 final size:22
Alignment explanation
Indices: 30463--30511 Score: 89
Period size: 22 Copynumber: 2.2 Consensus size: 22
30453 TGCAACTATT
*
30463 ATCAACACTATAACAGTATATA
1 ATCAGCACTATAACAGTATATA
30485 ATCAGCACTATAACAGTATATA
1 ATCAGCACTATAACAGTATATA
30507 ATCAG
1 ATCAG
30512 TGAATGTTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.47, C:0.18, G:0.08, T:0.27
Consensus pattern (22 bp):
ATCAGCACTATAACAGTATATA
Done.