Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010348.1 Corchorus capsularis cultivar CVL-1 contig10369, 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: 63724
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Found at i:1389 original size:4 final size:4
Alignment explanation
Indices: 1380--1405 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
1370 GAATAATTTC
1380 ATTA ATTA ATTA ATTA ATTA ATTA AT
1 ATTA ATTA ATTA ATTA ATTA ATTA AT
1406 CATCAAAACC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (4 bp):
ATTA
Found at i:3409 original size:30 final size:31
Alignment explanation
Indices: 3373--3450 Score: 113
Period size: 31 Copynumber: 2.5 Consensus size: 31
3363 TCCTTTTGTG
3373 CACGTGGCATGCCACGTGCCAC-TTCTGGTA
1 CACGTGGCATGCCACGTGCCACTTTCTGGTA
* * * *
3403 CACGTGGCATGTCATGTGTCACTTTTTGGTA
1 CACGTGGCATGCCACGTGCCACTTTCTGGTA
3434 CACGTGGCATGCCACGT
1 CACGTGGCATGCCACGT
3451 CAGACACCGT
Statistics
Matches: 41, Mismatches: 6, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
30 19 0.46
31 22 0.54
ACGTcount: A:0.17, C:0.28, G:0.27, T:0.28
Consensus pattern (31 bp):
CACGTGGCATGCCACGTGCCACTTTCTGGTA
Found at i:6495 original size:2 final size:2
Alignment explanation
Indices: 6488--6520 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
6478 TTATGTCTAA
6488 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
6521 AGCTCATCAA
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:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:11066 original size:31 final size:29
Alignment explanation
Indices: 11016--11100 Score: 84
Period size: 29 Copynumber: 2.9 Consensus size: 29
11006 AGGTTCTTCC
* *
11016 CCAAATTGACA-G-TTTGCCCCTAATTGA
1 CCAAATTGAAACGTTTTGCCCCAAATTGA
* * *
11043 CGCGAATCTGAAATGTTTTGCCCCAAATAGA
1 C-CAAAT-TGAAACGTTTTGCCCCAAATTGA
*
11074 CCAAATTGAAACGTTGTGCCCCAAATT
1 CCAAATTGAAACGTTTTGCCCCAAATT
11101 AATATGCGTG
Statistics
Matches: 46, Mismatches: 8, Indels: 6
0.77 0.13 0.10
Matches are distributed among these distances:
27 1 0.02
28 4 0.09
29 22 0.48
30 5 0.11
31 14 0.30
ACGTcount: A:0.32, C:0.25, G:0.16, T:0.27
Consensus pattern (29 bp):
CCAAATTGAAACGTTTTGCCCCAAATTGA
Found at i:12669 original size:30 final size:31
Alignment explanation
Indices: 12583--12679 Score: 142
Period size: 31 Copynumber: 3.2 Consensus size: 31
12573 GTGTCCGACG
**
12583 TGGCACGTCACGTGTACCAAAAAGTGACATG
1 TGGCACGTCACGTGTACCAAAAAGTGACACA
* *
12614 TGGCACGCCACATGTACCAAAAAGTGACACA
1 TGGCACGTCACGTGTACCAAAAAGTGACACA
*
12645 TGTCACGTCACGTGTACC-AAAAGTGACACA
1 TGGCACGTCACGTGTACCAAAAAGTGACACA
12675 TGGCA
1 TGGCA
12680 TGCCACATGT
Statistics
Matches: 58, Mismatches: 8, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
30 16 0.28
31 42 0.72
ACGTcount: A:0.34, C:0.26, G:0.23, T:0.18
Consensus pattern (31 bp):
TGGCACGTCACGTGTACCAAAAAGTGACACA
Found at i:12696 original size:30 final size:31
Alignment explanation
Indices: 12583--12716 Score: 135
Period size: 31 Copynumber: 4.4 Consensus size: 31
12573 GTGTCCGACG
* * **
12583 TGGCACGTCACGTGTACCAAAAAGTGACATG
1 TGGCACGCCACATGTACCAAAAAGTGACACA
12614 TGGCACGCCACATGTACCAAAAAGTGACACA
1 TGGCACGCCACATGTACCAAAAAGTGACACA
* * *
12645 TGTCACGTCACGTGTACC-AAAAGTGACACA
1 TGGCACGCCACATGTACCAAAAAGTGACACA
* ** * * *
12675 TGGCATGCCACATGTTTCAAAAAATGGCACG
1 TGGCACGCCACATGTACCAAAAAGTGACACA
*
12706 TGGCATGCCAC
1 TGGCACGCCAC
12717 GTGCACAAAA
Statistics
Matches: 86, Mismatches: 16, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
30 24 0.28
31 62 0.72
ACGTcount: A:0.33, C:0.26, G:0.22, T:0.19
Consensus pattern (31 bp):
TGGCACGCCACATGTACCAAAAAGTGACACA
Found at i:12718 original size:61 final size:61
Alignment explanation
Indices: 12580--12740 Score: 173
Period size: 61 Copynumber: 2.7 Consensus size: 61
12570 ACGGTGTCCG
** *
12580 ACGTGGCACGTCACGTGTACCAAAAAGTGACATGTGGCACGCCACATGTACCAAAAAGTGAC
1 ACGTGGCACGTCACGTGTACC-AAAAGTGACACATGGCACGCCACATGTACCAAAAAATGAC
* * * ** *
12642 ACATGTCACGTCACGTGTACCAAAAGTGACACATGGCATGCCACATGTTTCAAAAAATGGC
1 ACGTGGCACGTCACGTGTACCAAAAGTGACACATGGCACGCCACATGTACCAAAAAATGAC
* * * * *
12703 ACGTGGCATGCCACGTGCA-CAAAAG-GATACATGTCACG
1 ACGTGGCACGTCACGTGTACCAAAAGTGACACATGGCACG
12741 TGTCATTTTT
Statistics
Matches: 82, Mismatches: 17, Indels: 3
0.80 0.17 0.03
Matches are distributed among these distances:
59 10 0.12
60 6 0.07
61 47 0.57
62 19 0.23
ACGTcount: A:0.34, C:0.25, G:0.23, T:0.18
Consensus pattern (61 bp):
ACGTGGCACGTCACGTGTACCAAAAGTGACACATGGCACGCCACATGTACCAAAAAATGAC
Found at i:14249 original size:2 final size:2
Alignment explanation
Indices: 14197--14230 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
14187 ATTCAAGAGC
14197 TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
14231 TCTTTGCTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:31166 original size:3 final size:3
Alignment explanation
Indices: 31158--31187 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
31148 AAAAAGAAAA
31158 AAG AAG AAG AAG AAG AAG AAG AAG AA- AAG A
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG A
31188 TGAAAGGAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.08
3 24 0.92
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:32297 original size:12 final size:12
Alignment explanation
Indices: 32274--32330 Score: 53
Period size: 12 Copynumber: 4.8 Consensus size: 12
32264 TATGAATGAA
32274 CTTTTTTC-TTT
1 CTTTTTTCTTTT
32285 CTTTTTTCTTTT
1 CTTTTTTCTTTT
* ** *
32297 CCTTTTTCCCCTG
1 -CTTTTTTCTTTT
32310 CTTTTTTCTTTT
1 CTTTTTTCTTTT
*
32322 CTTTATTCT
1 CTTTTTTCT
32331 AATGGGGGGT
Statistics
Matches: 35, Mismatches: 9, Indels: 3
0.74 0.19 0.06
Matches are distributed among these distances:
11 8 0.23
12 19 0.54
13 8 0.23
ACGTcount: A:0.02, C:0.25, G:0.02, T:0.72
Consensus pattern (12 bp):
CTTTTTTCTTTT
Found at i:35133 original size:33 final size:33
Alignment explanation
Indices: 35088--35204 Score: 146
Period size: 33 Copynumber: 3.5 Consensus size: 33
35078 TAATCCGTGT
*
35088 CGCCCCAGGAGGGCGGCTTACCATGGCTCAAGC
1 CGCCCCACGAGGGCGGCTTACCATGGCTCAAGC
* * *
35121 CGCCCCAAGAGGGTGGCTTACCATGGCTCGAGC
1 CGCCCCACGAGGGCGGCTTACCATGGCTCAAGC
* * *
35154 CGCCCCACTAGGGCGGCTTCACCATGG-GCAGGC
1 CGCCCCACGAGGGCGGCTT-ACCATGGCTCAAGC
*
35187 CGCCCCACTAGGGCGGCT
1 CGCCCCACGAGGGCGGCT
35205 AGGCTATTTT
Statistics
Matches: 74, Mismatches: 9, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
33 67 0.91
34 7 0.09
ACGTcount: A:0.16, C:0.38, G:0.33, T:0.13
Consensus pattern (33 bp):
CGCCCCACGAGGGCGGCTTACCATGGCTCAAGC
Found at i:51061 original size:28 final size:28
Alignment explanation
Indices: 51009--51062 Score: 72
Period size: 28 Copynumber: 1.9 Consensus size: 28
50999 TCCAAATTGC
* ** *
51009 AAGTTTAGGGGACAAAATGTTAAAATTA
1 AAGTTTAGGGAACAAAACATCAAAATTA
51037 AAGTTTAGGGAACAAAACATCAAAAT
1 AAGTTTAGGGAACAAAACATCAAAAT
51063 CGTATAAGTT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 22 1.00
ACGTcount: A:0.50, C:0.07, G:0.19, T:0.24
Consensus pattern (28 bp):
AAGTTTAGGGAACAAAACATCAAAATTA
Found at i:54384 original size:107 final size:105
Alignment explanation
Indices: 54162--54424 Score: 395
Period size: 107 Copynumber: 2.5 Consensus size: 105
54152 AATTTTTCTA
* * **
54162 ACCCTCAAAATAAAATTTTAATTTTAATTT-GGGCTAAACTTAGTG-AATTAATTATATATTTTA
1 ACCCTTAAAATAAAAATAAAATTTTAATTTGGGGCTAAACTTAGTGAAATTAATTATATATTTTA
*
54225 TTTCTAAAACCCTATAACAATATTATTAATTATGGAATTT
66 TTTCTAAAACCCTATAACAATATTATTAATTATGAAATTT
* * *
54265 ACCCTTAAAATAAAAATAAAATTTTAATTTGGGGCTAAACTTAGTGAAATTAGTTTTGTATTTTA
1 ACCCTTAAAATAAAAATAAAATTTTAATTTGGGGCTAAACTTAGTGAAATTAATTATATATTTTA
* * *
54330 TTTCTAAAATCCTATAATAATAAATTATTAATTTTGAAATTT
66 TTTCTAAAACCCTATAACAAT--ATTATTAATTATGAAATTT
54372 ACCCTTAAAATAAAAATAAAATTTTAATTTGGGGCTAAACTTAGTGAAATTAA
1 ACCCTTAAAATAAAAATAAAATTTTAATTTGGGGCTAAACTTAGTGAAATTAA
54425 GGCTAAACTT
Statistics
Matches: 144, Mismatches: 12, Indels: 4
0.90 0.08 0.03
Matches are distributed among these distances:
103 26 0.18
104 15 0.10
105 34 0.24
107 69 0.48
ACGTcount: A:0.42, C:0.09, G:0.08, T:0.41
Consensus pattern (105 bp):
ACCCTTAAAATAAAAATAAAATTTTAATTTGGGGCTAAACTTAGTGAAATTAATTATATATTTTA
TTTCTAAAACCCTATAACAATATTATTAATTATGAAATTT
Found at i:57660 original size:19 final size:19
Alignment explanation
Indices: 57636--57676 Score: 82
Period size: 19 Copynumber: 2.2 Consensus size: 19
57626 ATGACTGTGG
57636 TGGGATTTGGGATAAAAGA
1 TGGGATTTGGGATAAAAGA
57655 TGGGATTTGGGATAAAAGA
1 TGGGATTTGGGATAAAAGA
57674 TGG
1 TGG
57677 TTAACATTAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.34, C:0.00, G:0.39, T:0.27
Consensus pattern (19 bp):
TGGGATTTGGGATAAAAGA
Done.