Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006721.1 Corchorus capsularis cultivar CVL-1 contig06742, 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: 15622
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.31
Found at i:99 original size:38 final size:38
Alignment explanation
Indices: 2--182 Score: 292
Period size: 38 Copynumber: 4.8 Consensus size: 38
1 T
*
2 CAGTTTAACCCCCTGAGGCGCGGGTCCACTCTTACCAA
1 CAGTTTAACCCCCTGAGGCACGGGTCCACTCTTACCAA
40 CAGTTTAA-CCCCTGAGGCACGGGTCCACTCTTACCAA
1 CAGTTTAACCCCCTGAGGCACGGGTCCACTCTTACCAA
* * * *
77 CAGTTTAATCCCCTAAGGCACGGGTCAACTCTTACCAT
1 CAGTTTAACCCCCTGAGGCACGGGTCCACTCTTACCAA
*
115 CAGTTTAACCCCCTGAGGCACGGGTCCACTCTTACCAT
1 CAGTTTAACCCCCTGAGGCACGGGTCCACTCTTACCAA
*
153 CAGTTTAACCCCCTGAGGCGCGGGTCCACT
1 CAGTTTAACCCCCTGAGGCACGGGTCCACT
183 ATGCACAGCC
Statistics
Matches: 134, Mismatches: 8, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
37 36 0.27
38 98 0.73
ACGTcount: A:0.22, C:0.35, G:0.20, T:0.23
Consensus pattern (38 bp):
CAGTTTAACCCCCTGAGGCACGGGTCCACTCTTACCAA
Found at i:328 original size:20 final size:20
Alignment explanation
Indices: 291--331 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
281 CGATTTTACG
* * *
291 AAAACAACGATACTCTTTCA
1 AAAACAACAAAACACTTTCA
311 AAAACAACAAAACACTTTCA
1 AAAACAACAAAACACTTTCA
331 A
1 A
332 TCATTTATAG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.54, C:0.24, G:0.02, T:0.20
Consensus pattern (20 bp):
AAAACAACAAAACACTTTCA
Found at i:2492 original size:91 final size:91
Alignment explanation
Indices: 2382--2556 Score: 350
Period size: 91 Copynumber: 1.9 Consensus size: 91
2372 TGAATTAAAG
2382 AAATCAAGGACATTAAACCCTTCTCCATTGTCTATTCTAACACACTTAACAGAAATATTAAATTG
1 AAATCAAGGACATTAAACCCTTCTCCATTGTCTATTCTAACACACTTAACAGAAATATTAAATTG
2447 AGTATAAACATATGTAATGCAAAATC
66 AGTATAAACATATGTAATGCAAAATC
2473 AAATCAAGGACATTAAACCCTTCTCCATTGTCTATTCTAACACACTTAACAGAAATATTAAATTG
1 AAATCAAGGACATTAAACCCTTCTCCATTGTCTATTCTAACACACTTAACAGAAATATTAAATTG
2538 AGTATAAACATATGTAATG
66 AGTATAAACATATGTAATG
2557 AAATTTTGCA
Statistics
Matches: 84, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
91 84 1.00
ACGTcount: A:0.42, C:0.18, G:0.09, T:0.30
Consensus pattern (91 bp):
AAATCAAGGACATTAAACCCTTCTCCATTGTCTATTCTAACACACTTAACAGAAATATTAAATTG
AGTATAAACATATGTAATGCAAAATC
Found at i:5722 original size:42 final size:44
Alignment explanation
Indices: 5671--5764 Score: 140
Period size: 45 Copynumber: 2.2 Consensus size: 44
5661 AATGCATTAT
*
5671 CTAA-ATTCTACT-CT-ATCTCTAGGTAATTCATCAAAATAAAG
1 CTAATATTCTACTCCTCATCTCTAGATAATTCATCAAAATAAAG
*
5712 CTAATATTCTACTCCTCCATCTCTAGATAATTTATCAAAATAAAG
1 CTAATATTCTACTCCT-CATCTCTAGATAATTCATCAAAATAAAG
5757 CTAATATT
1 CTAATATT
5765 AATTGTTGTT
Statistics
Matches: 47, Mismatches: 2, Indels: 4
0.89 0.04 0.08
Matches are distributed among these distances:
41 4 0.09
42 8 0.17
43 2 0.04
45 33 0.70
ACGTcount: A:0.38, C:0.20, G:0.05, T:0.36
Consensus pattern (44 bp):
CTAATATTCTACTCCTCATCTCTAGATAATTCATCAAAATAAAG
Found at i:6973 original size:14 final size:14
Alignment explanation
Indices: 6954--6980 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
6944 TTCTTGCTAA
6954 ACTTAATTACCCTT
1 ACTTAATTACCCTT
6968 ACTTAATTACCCT
1 ACTTAATTACCCT
6981 GAATTAAGTT
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:0.30, C:0.30, G:0.00, T:0.41
Consensus pattern (14 bp):
ACTTAATTACCCTT
Found at i:7017 original size:35 final size:35
Alignment explanation
Indices: 6968--7609 Score: 831
Period size: 35 Copynumber: 18.1 Consensus size: 35
6958 AATTACCCTT
* * *
6968 ACTTAATTACCCTGAATTAAGTTAACTATTGACTC
1 ACTTAATTACCCTGAATTAAGTTGATTACTGACTC
* * *
7003 ACTTAATTATCCTGAATTAAGTTGATTAATGACTT
1 ACTTAATTACCCTGAATTAAGTTGATTACTGACTC
* * *
7038 ACTTAATTATCCTGAATTAAGTTTATTACTGACTT
1 ACTTAATTACCCTGAATTAAGTTGATTACTGACTC
* *
7073 ACTTAATCACCCTGAATTAAGTTGATTACTGACTT
1 ACTTAATTACCCTGAATTAAGTTGATTACTGACTC
* *
7108 ACTTAATTACCCTGAATTAAGTTGACTACTGATTC
1 ACTTAATTACCCTGAATTAAGTTGATTACTGACTC
* * * *
7143 ACTTAATTACCCTGAATTAAGTTAATTACCGAATT
1 ACTTAATTACCCTGAATTAAGTTGATTACTGACTC
* *
7178 ACTTAATTACTCTGAATTAAGTTGATTACTGACCC
1 ACTTAATTACCCTGAATTAAGTTGATTACTGACTC
* * * *
7213 ACTTAATTACCCTGAATTAAGTTAATTACCGAATT
1 ACTTAATTACCCTGAATTAAGTTGATTACTGACTC
7248 ACTTAATTACCCTGAATTAAGTTGATTACTGACTC
1 ACTTAATTACCCTGAATTAAGTTGATTACTGACTC
* *
7283 ACTTAATTACCCTGAATTAAGTTGATTACTGAATT
1 ACTTAATTACCCTGAATTAAGTTGATTACTGACTC
*
7318 ACTTAATTACCCTGAACTAAGTTGATTACTGACTC
1 ACTTAATTACCCTGAATTAAGTTGATTACTGACTC
* *
7353 TCTTAATTACCCTGAATTAAGTTGATTACTGAATTACTGAATT
1 ACTTAATTACCCTGAATTAAGTTGATTACTG----AC----TC
*
7396 ACTTAATTATCCTGAATTAAGTT-ACTTACTGACTC
1 ACTTAATTACCCTGAATTAAGTTGA-TTACTGACTC
* *
7431 ACTTAATTACCCTGAATTAAGTTGATTACTGAATT
1 ACTTAATTACCCTGAATTAAGTTGATTACTGACTC
7466 ACTTAATTACCCTGAATTAAGTT-ACTTACTGACTC
1 ACTTAATTACCCTGAATTAAGTTGA-TTACTGACTC
* *
7501 ACTCAATTACCCTGAATTAAGTT-ACTTATTGACTC
1 ACTTAATTACCCTGAATTAAGTTGA-TTACTGACTC
* *
7536 ACTTAATTACCCTGAATTAAGTTGATTACTGAATT
1 ACTTAATTACCCTGAATTAAGTTGATTACTGACTC
* *
7571 ACTTAAGTACCTTGAATTAAGTTGATTACTGACTC
1 ACTTAATTACCCTGAATTAAGTTGATTACTGACTC
7606 ACTT
1 ACTT
7610 TTTCTTACTT
Statistics
Matches: 534, Mismatches: 61, Indels: 24
0.86 0.10 0.04
Matches are distributed among these distances:
34 1 0.00
35 498 0.93
36 2 0.00
39 4 0.01
42 1 0.00
43 28 0.05
ACGTcount: A:0.33, C:0.18, G:0.10, T:0.39
Consensus pattern (35 bp):
ACTTAATTACCCTGAATTAAGTTGATTACTGACTC
Found at i:7398 original size:16 final size:17
Alignment explanation
Indices: 7377--7484 Score: 53
Period size: 16 Copynumber: 6.2 Consensus size: 17
7367 AATTAAGTTG
7377 ATTACTGAATTA-CTGA
1 ATTACTGAATTACCTGA
*
7393 ATTACTTAATTATCCTGA
1 ATTACTGAATTA-CCTGA
* * *
7411 ATTAAGTTACTTA-CTGA
1 ATT-ACTGAATTACCTGA
* * *
7428 CTCACTTAATTACCCTGA
1 ATTACTGAATTA-CCTGA
*
7446 ATTAAGTTG-ATTA-CTGA
1 ATT-A-CTGAATTACCTGA
*
7463 ATTACTTAATTACCCTGA
1 ATTACTGAATTA-CCTGA
7481 ATTA
1 ATTA
7485 AGTTACTTAC
Statistics
Matches: 69, Mismatches: 13, Indels: 18
0.69 0.13 0.18
Matches are distributed among these distances:
15 1 0.01
16 23 0.33
17 12 0.17
18 20 0.29
19 12 0.17
20 1 0.01
ACGTcount: A:0.34, C:0.17, G:0.09, T:0.40
Consensus pattern (17 bp):
ATTACTGAATTACCTGA
Found at i:7464 original size:17 final size:16
Alignment explanation
Indices: 7385--7497 Score: 52
Period size: 19 Copynumber: 6.5 Consensus size: 16
7375 TGATTACTGA
*
7385 ATTACTGAATT-ACTT
1 ATTACTGAATTAAGTT
7400 AATTATCCTGAATTAAGTT
1 -ATTA--CTGAATTAAGTT
* * *
7419 ACTTACTG-ACTCACTT
1 A-TTACTGAATTAAGTT
7435 AATTACCCTGAATTAAGTT
1 -ATTA--CTGAATTAAGTT
*
7454 GATTACTGAATT-ACTT
1 -ATTACTGAATTAAGTT
7470 AATTACCCTGAATTAAGTT
1 -ATTA--CTGAATTAAGTT
7489 ACTTACTGA
1 A-TTACTGA
7498 CTCACTCAAT
Statistics
Matches: 74, Mismatches: 11, Indels: 23
0.69 0.10 0.21
Matches are distributed among these distances:
16 19 0.26
17 15 0.20
18 19 0.26
19 21 0.28
ACGTcount: A:0.34, C:0.17, G:0.10, T:0.40
Consensus pattern (16 bp):
ATTACTGAATTAAGTT
Found at i:7569 original size:17 final size:17
Alignment explanation
Indices: 7547--7602 Score: 60
Period size: 17 Copynumber: 3.2 Consensus size: 17
7537 CTTAATTACC
7547 CTGAATTAAGTTGATTA
1 CTGAATTAAGTTGATTA
* * *
7564 CTGAATT-ACTTAAGTA
1 CTGAATTAAGTTGATTA
7580 CCTTGAATTAAGTTGATTA
1 -C-TGAATTAAGTTGATTA
7599 CTGA
1 CTGA
7603 CTCACTTTTT
Statistics
Matches: 30, Mismatches: 6, Indels: 6
0.71 0.14 0.14
Matches are distributed among these distances:
16 6 0.20
17 11 0.37
18 7 0.23
19 6 0.20
ACGTcount: A:0.34, C:0.11, G:0.16, T:0.39
Consensus pattern (17 bp):
CTGAATTAAGTTGATTA
Found at i:10906 original size:22 final size:22
Alignment explanation
Indices: 10878--10922 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
10868 CAAAACTAAA
*
10878 TTGCATTGT-GTCTTCTTTACTT
1 TTGCATTGTGGTCTCCTTT-CTT
10900 TTGCATTGTGGTCTCCTTTCTT
1 TTGCATTGTGGTCTCCTTTCTT
10922 T
1 T
10923 ACTTATGGTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 13 0.62
23 8 0.38
ACGTcount: A:0.07, C:0.20, G:0.16, T:0.58
Consensus pattern (22 bp):
TTGCATTGTGGTCTCCTTTCTT
Found at i:14624 original size:40 final size:39
Alignment explanation
Indices: 14538--14613 Score: 120
Period size: 40 Copynumber: 2.0 Consensus size: 39
14528 AAGGGACAAA
14538 AGTAAAAGAAGTAATCAGTAAAATGGTAATTATGAGTAAG
1 AGTAAAAGAAGTAATCAGTAAAATGGTAA-TATGAGTAAG
*
14578 AGTAAAAGAAGTAATCAGTAAATTGGTAA-A-GAGTAA
1 AGTAAAAGAAGTAATCAGTAAAATGGTAATATGAGTAA
14614 AGATGATAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
37 6 0.17
38 1 0.03
40 28 0.80
ACGTcount: A:0.51, C:0.03, G:0.22, T:0.24
Consensus pattern (39 bp):
AGTAAAAGAAGTAATCAGTAAAATGGTAATATGAGTAAG
Found at i:14871 original size:35 final size:34
Alignment explanation
Indices: 14827--14939 Score: 129
Period size: 35 Copynumber: 3.2 Consensus size: 34
14817 GTAATTGGAT
14827 AATAGTAATCAGTAAAAAGTAATCGGTAAGAGTAA
1 AATAGTAATCAGTAAAAAGTAAT-GGTAAGAGTAA
* * * *
14862 AATAATAATCAGT-AAGAGCAAAGTGGTAATAGTAA
1 AATAGTAATCAGTAAAAAG-TAA-TGGTAAGAGTAA
* *
14897 AATAGTAATCAGTAAAAGGTAATTAGTAAGAGTAA
1 AATAGTAATCAGTAAAAAGTAA-TGGTAAGAGTAA
14932 AATAGTAA
1 AATAGTAA
14940 AGAGTAAGAT
Statistics
Matches: 64, Mismatches: 11, Indels: 6
0.79 0.14 0.07
Matches are distributed among these distances:
34 4 0.06
35 56 0.88
36 4 0.06
ACGTcount: A:0.52, C:0.04, G:0.19, T:0.24
Consensus pattern (34 bp):
AATAGTAATCAGTAAAAAGTAATGGTAAGAGTAA
Found at i:14946 original size:35 final size:35
Alignment explanation
Indices: 14827--15041 Score: 123
Period size: 35 Copynumber: 6.0 Consensus size: 35
14817 GTAATTGGAT
* * ***
14827 AATAGTAATCAGTAAAAAGTAATCGGTAAGAGTAA
1 AATAGTAAACAGTAAAAGGTAAAAAGTAAGAGTAA
* * * * ** *
14862 AATAATAATCAGTAAGA-GCAAAGTGGTAATAGTAA
1 AATAGTAAACAGTAAAAGGTAAA-AAGTAAGAGTAA
* **
14897 AATAGTAATCAGTAAAAGGTAATTAGTAAGAGTAA
1 AATAGTAAACAGTAAAAGGTAAAAAGTAAGAGTAA
* * *
14932 AATAGTAAAGAGTAAGATGATAAAAAGTAAAGAGTAA
1 AATAGTAAACAGTAA-AAGGTAAAAAGT-AAGAGTAA
* *
14969 TA-AGTAAAGAGTAAAATGGTAAAAAGTAAAGAGT--
1 AATAGTAAACAGTAAAA-GGTAAAAAGT-AAGAGTAA
* *
15003 AATCAGTAAAAGAGTAAAATGGTAAAAGGTAAAGAGTAA
1 AAT-AGT-AAACAGTAAAA-GGTAAAAAGT-AAGAGTAA
15042 TCAGTAAAGA
Statistics
Matches: 147, Mismatches: 23, Indels: 16
0.79 0.12 0.09
Matches are distributed among these distances:
34 4 0.03
35 64 0.44
36 42 0.29
37 37 0.25
ACGTcount: A:0.54, C:0.03, G:0.21, T:0.21
Consensus pattern (35 bp):
AATAGTAAACAGTAAAAGGTAAAAAGTAAGAGTAA
Found at i:14962 original size:7 final size:7
Alignment explanation
Indices: 14927--15041 Score: 68
Period size: 7 Copynumber: 15.7 Consensus size: 7
14917 AATTAGTAAG
14927 AGTAAAA
1 AGTAAAA
*
14934 TAGTAAAG
1 -AGTAAAA
*
14942 AGTAAGA
1 AGTAAAA
*
14949 TGATAAAA
1 AG-TAAAA
*
14957 AGTAAAG
1 AGTAAAA
*
14964 AGTAATA
1 AGTAAAA
*
14971 AGTAAAG
1 AGTAAAA
14978 AGTAAAA
1 AGTAAAA
*
14985 TGGTAAAA
1 -AGTAAAA
*
14993 AGTAAAG
1 AGTAAAA
**
15000 AGTAATC
1 AGTAAAA
15007 AGTAAAA
1 AGTAAAA
15014 GAGTAAAA
1 -AGTAAAA
*
15022 TGGTAAAA
1 -AGTAAAA
* *
15030 GGTAAAG
1 AGTAAAA
15037 AGTAA
1 AGTAA
15042 TCAGTAAAGA
Statistics
Matches: 81, Mismatches: 23, Indels: 7
0.73 0.21 0.06
Matches are distributed among these distances:
7 51 0.63
8 30 0.37
ACGTcount: A:0.57, C:0.01, G:0.23, T:0.19
Consensus pattern (7 bp):
AGTAAAA
Found at i:14975 original size:36 final size:36
Alignment explanation
Indices: 14907--15066 Score: 198
Period size: 36 Copynumber: 4.4 Consensus size: 36
14897 AATAGTAATC
** *
14907 AGTAAAA-GGTAATTAGT-AAGAGTAAAATAGTAAAG
1 AGTAAAATGGTAAAAAGTAAAGAGTAATA-AGTAAAG
* *
14942 AGTAAGATGATAAAAAGTAAAGAGTAATAAGTAAAG
1 AGTAAAATGGTAAAAAGTAAAGAGTAATAAGTAAAG
*
14978 AGTAAAATGGTAAAAAGTAAAGAGTAATCAGTAAAAG
1 AGTAAAATGGTAAAAAGTAAAGAGTAATAAGT-AAAG
* *
15015 AGTAAAATGGTAAAAGGTAAAGAGTAATCAGTAAAG
1 AGTAAAATGGTAAAAAGTAAAGAGTAATAAGTAAAG
* *
15051 AGAAAAATGGCAAAAA
1 AGTAAAATGGTAAAAA
15067 AAAAAATAAT
Statistics
Matches: 110, Mismatches: 12, Indels: 5
0.87 0.09 0.04
Matches are distributed among these distances:
35 6 0.05
36 60 0.55
37 44 0.40
ACGTcount: A:0.57, C:0.02, G:0.23, T:0.19
Consensus pattern (36 bp):
AGTAAAATGGTAAAAAGTAAAGAGTAATAAGTAAAG
Found at i:15024 original size:37 final size:36
Alignment explanation
Indices: 14935--15066 Score: 201
Period size: 36 Copynumber: 3.6 Consensus size: 36
14925 AGAGTAAAAT
* * *
14935 AGTAAAGAGTAAGATGATAAAAAGTAAAGAGTAATA
1 AGTAAAGAGTAAAATGGTAAAAAGTAAAGAGTAATC
14971 AGTAAAGAGTAAAATGGTAAAAAGTAAAGAGTAATC
1 AGTAAAGAGTAAAATGGTAAAAAGTAAAGAGTAATC
*
15007 AGTAAAAGAGTAAAATGGTAAAAGGTAAAGAGTAATC
1 AGT-AAAGAGTAAAATGGTAAAAAGTAAAGAGTAATC
* *
15044 AGTAAAGAGAAAAATGGCAAAAA
1 AGTAAAGAGTAAAATGGTAAAAA
15067 AAAAAATAAT
Statistics
Matches: 88, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
36 53 0.60
37 35 0.40
ACGTcount: A:0.58, C:0.02, G:0.23, T:0.17
Consensus pattern (36 bp):
AGTAAAGAGTAAAATGGTAAAAAGTAAAGAGTAATC
Done.