Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013752.1 Corchorus capsularis cultivar CVL-1 contig13773, 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: 48677
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33
Found at i:750 original size:12 final size:13
Alignment explanation
Indices: 720--756 Score: 58
Period size: 12 Copynumber: 2.8 Consensus size: 13
710 CTCTCTTTAA
720 TTTCCTTATTTCTT
1 TTTCCTT-TTTCTT
734 TTTCCTTTTTC-T
1 TTTCCTTTTTCTT
746 TTTCCTTTTTC
1 TTTCCTTTTTC
757 CTCTTATTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
12 12 0.52
13 4 0.17
14 7 0.30
ACGTcount: A:0.03, C:0.24, G:0.00, T:0.73
Consensus pattern (13 bp):
TTTCCTTTTTCTT
Found at i:2287 original size:13 final size:13
Alignment explanation
Indices: 2271--2332 Score: 56
Period size: 13 Copynumber: 4.6 Consensus size: 13
2261 GTTATTATTG
*
2271 ATTATTTATATAT
1 ATTATATATATAT
2284 ATTA-ATAATTAATAAT
1 ATTATAT-A-T-AT-AT
2300 ATTATATATATAT
1 ATTATATATATAT
*
2313 ATTATATAAATAT
1 ATTATATATATAT
2326 A-TATATA
1 ATTATATA
2333 ATAAAATCTA
Statistics
Matches: 42, Mismatches: 2, Indels: 11
0.76 0.04 0.20
Matches are distributed among these distances:
12 7 0.17
13 20 0.48
14 3 0.07
15 3 0.07
16 7 0.17
17 2 0.05
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (13 bp):
ATTATATATATAT
Found at i:2305 original size:23 final size:22
Alignment explanation
Indices: 2278--2336 Score: 61
Period size: 24 Copynumber: 2.6 Consensus size: 22
2268 TTGATTATTT
2278 ATATATATTAATAATTA-AT-A
1 ATATATATTAATAATTATATAA
2298 ATAT-TATATATATATATTATATAA
1 ATATATAT-TA-ATA-ATTATATAA
2322 ATATATATATAATAA
1 ATATATAT-TAATAA
2337 AATCTAAAGT
Statistics
Matches: 33, Mismatches: 0, Indels: 9
0.79 0.00 0.21
Matches are distributed among these distances:
19 3 0.09
20 6 0.18
21 3 0.09
22 4 0.12
23 3 0.09
24 8 0.24
25 6 0.18
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (22 bp):
ATATATATTAATAATTATATAA
Found at i:9573 original size:2 final size:2
Alignment explanation
Indices: 9566--9592 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
9556 CTTGTTTGTA
9566 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
9593 GGGTTATAAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:11533 original size:15 final size:15
Alignment explanation
Indices: 11515--11569 Score: 51
Period size: 15 Copynumber: 3.5 Consensus size: 15
11505 TCATTGTCAT
11515 CATCTTCATTAAGCA
1 CATCTTCATTAAGCA
11530 CATCTTCCAAATTCAA--A
1 CATCTT-C--ATT-AAGCA
11547 TCATCTTCATTAAGCA
1 -CATCTTCATTAAGCA
11563 CATCTTC
1 CATCTTC
11570 CAAATTCAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 14
0.70 0.00 0.30
Matches are distributed among these distances:
14 2 0.06
15 16 0.48
16 2 0.06
17 2 0.06
18 9 0.27
19 2 0.06
ACGTcount: A:0.33, C:0.29, G:0.04, T:0.35
Consensus pattern (15 bp):
CATCTTCATTAAGCA
Found at i:11550 original size:33 final size:33
Alignment explanation
Indices: 11513--11585 Score: 146
Period size: 33 Copynumber: 2.2 Consensus size: 33
11503 ACTCATTGTC
11513 ATCATCTTCATTAAGCACATCTTCCAAATTCAA
1 ATCATCTTCATTAAGCACATCTTCCAAATTCAA
11546 ATCATCTTCATTAAGCACATCTTCCAAATTCAA
1 ATCATCTTCATTAAGCACATCTTCCAAATTCAA
11579 ATCATCT
1 ATCATCT
11586 ATATAATATG
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 40 1.00
ACGTcount: A:0.36, C:0.27, G:0.03, T:0.34
Consensus pattern (33 bp):
ATCATCTTCATTAAGCACATCTTCCAAATTCAA
Found at i:11551 original size:18 final size:18
Alignment explanation
Indices: 11530--11585 Score: 59
Period size: 18 Copynumber: 3.3 Consensus size: 18
11520 TCATTAAGCA
11530 CATCTTCCAAATTCAAAT
1 CATCTTCCAAATTCAAAT
11548 CATCTT-C--ATT-AAGCA-
1 CATCTTCCAAATTCAA--AT
11563 CATCTTCCAAATTCAAAT
1 CATCTTCCAAATTCAAAT
11581 CATCT
1 CATCT
11586 ATATAATATG
Statistics
Matches: 31, Mismatches: 0, Indels: 14
0.69 0.00 0.31
Matches are distributed among these distances:
14 2 0.06
15 9 0.29
16 2 0.06
17 2 0.06
18 14 0.45
19 2 0.06
ACGTcount: A:0.36, C:0.29, G:0.02, T:0.34
Consensus pattern (18 bp):
CATCTTCCAAATTCAAAT
Found at i:15471 original size:54 final size:54
Alignment explanation
Indices: 15413--15518 Score: 151
Period size: 54 Copynumber: 2.0 Consensus size: 54
15403 AAAAAACATT
*
15413 TCATTATACATACATGATCAAACCCCAAAGTTTGG-TAGTCAAACCACAAAAAAA
1 TCATTATACATACATGATCAAACCCCAAAG-TTGGATAATCAAACCACAAAAAAA
* * * *
15467 TCATTGTACATGCATGGTCAAACCCTAAAGTTGGATAATCAAACCACAAAAA
1 TCATTATACATACATGATCAAACCCCAAAGTTGGATAATCAAACCACAAAAA
15519 GCATTTTTAT
Statistics
Matches: 46, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
53 4 0.09
54 42 0.91
ACGTcount: A:0.44, C:0.22, G:0.11, T:0.23
Consensus pattern (54 bp):
TCATTATACATACATGATCAAACCCCAAAGTTGGATAATCAAACCACAAAAAAA
Found at i:15606 original size:20 final size:19
Alignment explanation
Indices: 15562--15606 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
15552 AATTTGGGTC
*
15562 AAACTCCAAATTTTGATAGT
1 AAAC-CCAAAATTTGATAGT
*
15582 CAACCCAAAATTTGATAGTT
1 AAACCCAAAATTTGATAG-T
15602 AAACC
1 AAACC
15607 ACGTTAAACC
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
19 13 0.62
20 8 0.38
ACGTcount: A:0.42, C:0.20, G:0.09, T:0.29
Consensus pattern (19 bp):
AAACCCAAAATTTGATAGT
Found at i:19584 original size:41 final size:41
Alignment explanation
Indices: 19534--19614 Score: 119
Period size: 41 Copynumber: 2.0 Consensus size: 41
19524 ATATCATAAT
*
19534 AATATATCCTTT-AAAAAATACATTCTTAAATATCCTTCAAA
1 AATAAATCCTTTAAAAAAATA-ATTCTTAAATATCCTTCAAA
* *
19575 AATAAATCCTTTAAAAAAATATTTTTTAAATATCCTTCAA
1 AATAAATCCTTTAAAAAAATAATTCTTAAATATCCTTCAA
19615 CAATGGAGGA
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
41 28 0.78
42 8 0.22
ACGTcount: A:0.47, C:0.15, G:0.00, T:0.38
Consensus pattern (41 bp):
AATAAATCCTTTAAAAAAATAATTCTTAAATATCCTTCAAA
Found at i:19589 original size:26 final size:26
Alignment explanation
Indices: 19537--19585 Score: 64
Period size: 25 Copynumber: 1.9 Consensus size: 26
19527 TCATAATAAT
* *
19537 ATATCCTTTAAAAAATACATTCTTAA
1 ATATCCTTTAAAAAATAAATCCTTAA
*
19563 ATATCC-TTCAAAAATAAATCCTT
1 ATATCCTTTAAAAAATAAATCCTT
19586 TAAAAAAATA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
25 14 0.70
26 6 0.30
ACGTcount: A:0.45, C:0.18, G:0.00, T:0.37
Consensus pattern (26 bp):
ATATCCTTTAAAAAATAAATCCTTAA
Found at i:19939 original size:14 final size:14
Alignment explanation
Indices: 19920--19946 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
19910 TCTAATTACA
19920 AAAAAAATAAAAAT
1 AAAAAAATAAAAAT
19934 AAAAAAATAAAAA
1 AAAAAAATAAAAA
19947 ACAAACCCCC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.89, C:0.00, G:0.00, T:0.11
Consensus pattern (14 bp):
AAAAAAATAAAAAT
Found at i:22483 original size:32 final size:32
Alignment explanation
Indices: 22447--22538 Score: 157
Period size: 32 Copynumber: 2.9 Consensus size: 32
22437 ATAATATCCT
22447 TGTGCATCTCCCGCACACTATAATGATATTTG
1 TGTGCATCTCCCGCACACTATAATGATATTTG
22479 TGTGCATCTCCCGCACACTATAATGATATTTG
1 TGTGCATCTCCCGCACACTATAATGATATTTG
* **
22511 TGTGCATCTCCTGCACAAGATAATGATA
1 TGTGCATCTCCCGCACACTATAATGATA
22539 CCCCATGTAC
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
32 57 1.00
ACGTcount: A:0.27, C:0.24, G:0.16, T:0.33
Consensus pattern (32 bp):
TGTGCATCTCCCGCACACTATAATGATATTTG
Found at i:27963 original size:24 final size:24
Alignment explanation
Indices: 27934--27981 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
27924 TAAGAAACAG
*
27934 TAAAATAAATAAGCAAGAA-AATAA
1 TAAAATAAAGAA-CAAGAAGAATAA
*
27958 TAAAATTAAGAACAAGAAGAATAA
1 TAAAATAAAGAACAAGAAGAATAA
27982 ATACTCTAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 6 0.29
24 15 0.71
ACGTcount: A:0.69, C:0.04, G:0.10, T:0.17
Consensus pattern (24 bp):
TAAAATAAAGAACAAGAAGAATAA
Found at i:30198 original size:72 final size:72
Alignment explanation
Indices: 30093--30243 Score: 191
Period size: 72 Copynumber: 2.1 Consensus size: 72
30083 TGAGGATCTT
** * *
30093 GGTTTGTGGGATTTTAGTTTTGATGCAAAATTTTCTG-TTAAAGTCTTGAGATTGTCAAAAATTG
1 GGTTTGTGGGATCATAGGTTTGATGCAAAATTTTCTGCTGAAAGT-TTGAGATTGTCAAAAATTG
30157 A-CTTTGAC
65 ATC-TTGAC
* *
30165 GGTTTGTGGGATCAT-GGTTTGAATGCGAAATTTTCTGCTGAAAGTTTTAGATTGTCAAAAATTG
1 GGTTTGTGGGATCATAGGTTTG-ATGCAAAATTTTCTGCTGAAAGTTTGAGATTGTCAAAAATTG
*
30229 ATCTTGAT
65 ATCTTGAC
30237 GGTTTGT
1 GGTTTGT
30244 TTGCAAAAAT
Statistics
Matches: 69, Mismatches: 7, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
71 5 0.07
72 57 0.83
73 7 0.10
ACGTcount: A:0.25, C:0.08, G:0.25, T:0.42
Consensus pattern (72 bp):
GGTTTGTGGGATCATAGGTTTGATGCAAAATTTTCTGCTGAAAGTTTGAGATTGTCAAAAATTGA
TCTTGAC
Found at i:33351 original size:29 final size:29
Alignment explanation
Indices: 33309--33369 Score: 95
Period size: 29 Copynumber: 2.1 Consensus size: 29
33299 TACAGGCCCA
* * *
33309 TGCAAGTAAGAGCCGCAAGAACGTATGCT
1 TGCAAGTAAGAGCCACAAAAACGGATGCT
33338 TGCAAGTAAGAGCCACAAAAACGGATGCT
1 TGCAAGTAAGAGCCACAAAAACGGATGCT
33367 TGC
1 TGC
33370 TCTTTGCACA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.36, C:0.21, G:0.26, T:0.16
Consensus pattern (29 bp):
TGCAAGTAAGAGCCACAAAAACGGATGCT
Found at i:36698 original size:2 final size:2
Alignment explanation
Indices: 36664--36688 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
36654 AGGTAATGGT
36664 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 T
36689 GCCCATATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:36752 original size:2 final size:2
Alignment explanation
Indices: 36745--36769 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
36735 TCAATGGATG
36745 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 T
36770 TTTAGGTTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:41225 original size:11 final size:10
Alignment explanation
Indices: 41207--41240 Score: 50
Period size: 11 Copynumber: 3.2 Consensus size: 10
41197 AATTGTTTTC
41207 AAATCTTCAA
1 AAATCTTCAA
41217 AATATCTTCAA
1 AA-ATCTTCAA
41228 GAAATCTTCAA
1 -AAATCTTCAA
41239 AA
1 AA
41241 CACGAACTTC
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
10 4 0.18
11 16 0.73
12 2 0.09
ACGTcount: A:0.50, C:0.18, G:0.03, T:0.29
Consensus pattern (10 bp):
AAATCTTCAA
Done.