Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014167.1 Corchorus capsularis cultivar CVL-1 contig14188, 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: 20918
ACGTcount: A:0.33, C:0.19, G:0.16, T:0.32
Found at i:1453 original size:9 final size:8
Alignment explanation
Indices: 1435--1468 Score: 59
Period size: 8 Copynumber: 4.1 Consensus size: 8
1425 GAATCGGCTA
1435 TGAATTTT
1 TGAATTTT
1443 TGAAGTTTT
1 TGAA-TTTT
1452 TGAATTTT
1 TGAATTTT
1460 TGAATTTT
1 TGAATTTT
1468 T
1 T
1469 CAAGCAGGTG
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
8 17 0.68
9 8 0.32
ACGTcount: A:0.24, C:0.00, G:0.15, T:0.62
Consensus pattern (8 bp):
TGAATTTT
Found at i:1457 original size:17 final size:16
Alignment explanation
Indices: 1435--1468 Score: 59
Period size: 17 Copynumber: 2.1 Consensus size: 16
1425 GAATCGGCTA
1435 TGAATTTTTGAAGTTTT
1 TGAATTTTTGAA-TTTT
1452 TGAATTTTTGAATTTT
1 TGAATTTTTGAATTTT
1468 T
1 T
1469 CAAGCAGGTG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.29
17 12 0.71
ACGTcount: A:0.24, C:0.00, G:0.15, T:0.62
Consensus pattern (16 bp):
TGAATTTTTGAATTTT
Found at i:2448 original size:33 final size:33
Alignment explanation
Indices: 2376--2481 Score: 135
Period size: 33 Copynumber: 3.2 Consensus size: 33
2366 CAAAGGGTCA
* *
2376 CGTGGCCGGTTGTGGCCGGGCATGGCCGA-GTCG
1 CGTGGCCGGTTGTGGCCGGACATGTCC-ATGTCG
** *
2409 TTTGGCCGGTTGTAGCCGGACATGTCCATGTCG
1 CGTGGCCGGTTGTGGCCGGACATGTCCATGTCG
2442 CGTGGCCGG-TGATGGCCGGACATGTCCATGTCG
1 CGTGGCCGGTTG-TGGCCGGACATGTCCATGTCG
2475 CGTGGCC
1 CGTGGCC
2482 AGTCTTGTGG
Statistics
Matches: 63, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
32 3 0.05
33 60 0.95
ACGTcount: A:0.09, C:0.27, G:0.41, T:0.23
Consensus pattern (33 bp):
CGTGGCCGGTTGTGGCCGGACATGTCCATGTCG
Found at i:6519 original size:29 final size:29
Alignment explanation
Indices: 6454--6534 Score: 108
Period size: 29 Copynumber: 2.7 Consensus size: 29
6444 GCTTAATACC
* **
6454 CAAATTAGCCCCTTAACTATCCATTTTGGGA
1 CAAATTGGCCCCTTAACT-T-TTTTTTGGGA
*
6485 TAAATTGGCCCCTTAACTTTTTTTTGGGA
1 CAAATTGGCCCCTTAACTTTTTTTTGGGA
6514 CAAATTGGCCCCTTAACTTTT
1 CAAATTGGCCCCTTAACTTTT
6535 AAAAACGAGA
Statistics
Matches: 45, Mismatches: 5, Indels: 2
0.87 0.10 0.04
Matches are distributed among these distances:
29 28 0.62
30 1 0.02
31 16 0.36
ACGTcount: A:0.25, C:0.23, G:0.14, T:0.38
Consensus pattern (29 bp):
CAAATTGGCCCCTTAACTTTTTTTTGGGA
Found at i:7263 original size:29 final size:28
Alignment explanation
Indices: 7226--7282 Score: 105
Period size: 29 Copynumber: 2.0 Consensus size: 28
7216 TCTCGTTTTT
7226 AAAAATTAAGGGGCCAATTTGTCCCAAA
1 AAAAATTAAGGGGCCAATTTGTCCCAAA
7254 AAAAATTTAAGGGGCCAATTTGTCCCAAA
1 AAAAA-TTAAGGGGCCAATTTGTCCCAAA
7283 TAGATGGGAA
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
28 5 0.18
29 23 0.82
ACGTcount: A:0.42, C:0.18, G:0.18, T:0.23
Consensus pattern (28 bp):
AAAAATTAAGGGGCCAATTTGTCCCAAA
Found at i:10852 original size:16 final size:17
Alignment explanation
Indices: 10827--10858 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
10817 CACGTCATAT
10827 TTTTTATTAAAAAATAA
1 TTTTTATTAAAAAATAA
10844 TTTTT-TTAAAAAATA
1 TTTTTATTAAAAAATA
10859 TATAATTTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
TTTTTATTAAAAAATAA
Found at i:11584 original size:16 final size:17
Alignment explanation
Indices: 11565--11596 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
11555 TGAAATTATA
11565 TATTTTTTAA-AAAAAT
1 TATTTTTTAATAAAAAT
11581 TATTTTTTAATAAAAA
1 TATTTTTTAATAAAAA
11597 ATATGACGTG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
TATTTTTTAATAAAAAT
Found at i:14646 original size:42 final size:44
Alignment explanation
Indices: 14596--14691 Score: 126
Period size: 45 Copynumber: 2.2 Consensus size: 44
14586 AGTGCATTCC
* *
14596 CTAA-ATTCTA-CTCCATCTTTAGGTAATTCATCAAAAT-AAAG
1 CTAATATTCTACCTCCATCTCTAGATAATTCATCAAAATAAAAG
14637 CTAATATTCTACTCCTCCATCTCTAGATAATTCATCAAAATAAAAAG
1 CTAATATTCTA--CCTCCATCTCTAGATAATTCATCAAAAT-AAAAG
14684 CTAATATT
1 CTAATATT
14692 AATTGTTGTT
Statistics
Matches: 47, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
41 4 0.09
42 6 0.13
45 25 0.53
47 12 0.26
ACGTcount: A:0.40, C:0.21, G:0.05, T:0.34
Consensus pattern (44 bp):
CTAATATTCTACCTCCATCTCTAGATAATTCATCAAAATAAAAG
Found at i:15552 original size:204 final size:204
Alignment explanation
Indices: 15177--15580 Score: 655
Period size: 204 Copynumber: 2.0 Consensus size: 204
15167 TAGGTTATGT
* *
15177 CATCCTAAGGCACTGCTAAATTAAATTGAATGATCTTATCAACGTCTATCTGGAAATTTTAGGAA
1 CATCCTAAGGCACTGCTAAATTAAATTGAAGGATCTTATCAACGTCCATCTGGAAATTTTAGGAA
* * * *
15242 ACAAAACGGAGTCCATGTAAAACCAATTCAGAGAGATGTTAGGGAAGACAAAACCTATCCAAATA
66 ACAAAACAGAGTCCATGTAAAACCAATTCAGAGAAACGTTAGGGAAGACAAAACCTACCCAAATA
* *
15307 GAAATGAAGACGACAGGAAACAGAACTGAAATGTCAATAGTTTACCCATGAATCAACCATTATTG
131 GAAATGAAGACGAAAGGAAACAGAACTGAAATGTAAATAGTTTACCCATGAATCAACCATTATTG
15372 CAGATCAAC
196 CAGATCAAC
*
15381 CATCCTAAGGCGCTGCTAAATTAAATTGAAGGATCTTATCAACGTCCATCTGGAAATTTTAGGAA
1 CATCCTAAGGCACTGCTAAATTAAATTGAAGGATCTTATCAACGTCCATCTGGAAATTTTAGGAA
* * * *
15446 ACAGAACAGAGTCCATGTGAAACCAATTCAGAGAAACGTTAGGGAAGTCGAAACCTACCCAAATA
66 ACAAAACAGAGTCCATGTAAAACCAATTCAGAGAAACGTTAGGGAAGACAAAACCTACCCAAATA
* * *
15511 GAAATGAAGACGAAAGGAAATAGAATTGGAATGTAAATAGTTTACCCATGAATCAACCATTATTG
131 GAAATGAAGACGAAAGGAAACAGAACTGAAATGTAAATAGTTTACCCATGAATCAACCATTATTG
*
15576 TAGAT
196 CAGAT
15581 ACATTTGTAG
Statistics
Matches: 183, Mismatches: 17, Indels: 0
0.92 0.09 0.00
Matches are distributed among these distances:
204 183 1.00
ACGTcount: A:0.41, C:0.17, G:0.18, T:0.23
Consensus pattern (204 bp):
CATCCTAAGGCACTGCTAAATTAAATTGAAGGATCTTATCAACGTCCATCTGGAAATTTTAGGAA
ACAAAACAGAGTCCATGTAAAACCAATTCAGAGAAACGTTAGGGAAGACAAAACCTACCCAAATA
GAAATGAAGACGAAAGGAAACAGAACTGAAATGTAAATAGTTTACCCATGAATCAACCATTATTG
CAGATCAAC
Found at i:15923 original size:2 final size:2
Alignment explanation
Indices: 15916--15945 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
15906 TTAAGTAGAT
15916 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
15946 GCAATTAGCA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:16166 original size:18 final size:18
Alignment explanation
Indices: 16139--16180 Score: 68
Period size: 19 Copynumber: 2.3 Consensus size: 18
16129 TTTATTTATT
16139 TATCATTT-AAAAAAAAC
1 TATCATTTAAAAAAAAAC
16156 TATCTATTTAAAAAAAAAC
1 TATC-ATTTAAAAAAAAAC
16175 TATCAT
1 TATCAT
16181 AAACTACCTT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 4 0.17
18 6 0.26
19 13 0.57
ACGTcount: A:0.55, C:0.12, G:0.00, T:0.33
Consensus pattern (18 bp):
TATCATTTAAAAAAAAAC
Done.