Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013949.1 Corchorus capsularis cultivar CVL-1 contig13970, 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: 17211
ACGTcount: A:0.34, C:0.17, G:0.18, T:0.31
Found at i:428 original size:17 final size:17
Alignment explanation
Indices: 372--428 Score: 53
Period size: 17 Copynumber: 3.4 Consensus size: 17
362 TAAAATTTGA
* *
372 AGAAAAATGAAAAAAGAC
1 AGAAAAATGGAAAAA-TC
* *
390 AGGAAAA-GGAAAAATG
1 AGAAAAATGGAAAAATC
*
406 AAAAAAATGGAAAAATC
1 AGAAAAATGGAAAAATC
423 AGAAAA
1 AGAAAA
429 TTAAAAGATG
Statistics
Matches: 30, Mismatches: 8, Indels: 3
0.73 0.20 0.07
Matches are distributed among these distances:
16 5 0.17
17 19 0.63
18 6 0.20
ACGTcount: A:0.70, C:0.04, G:0.19, T:0.07
Consensus pattern (17 bp):
AGAAAAATGGAAAAATC
Found at i:2149 original size:27 final size:26
Alignment explanation
Indices: 2100--2158 Score: 75
Period size: 27 Copynumber: 2.3 Consensus size: 26
2090 ATTTTCTGAT
* *
2100 TTTTCC-ATTTTTTTTCATGTTTTCC
1 TTTTCCTATCTTTTTTCATGTTTTCA
*
2125 TTTTCCTATCTTTTTTCATTTTTTTCA
1 TTTTCCTATCTTTTTTCA-TGTTTTCA
2152 TTTTCCT
1 TTTTCCT
2159 TCAAATTTTG
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
25 6 0.21
26 10 0.34
27 13 0.45
ACGTcount: A:0.08, C:0.20, G:0.02, T:0.69
Consensus pattern (26 bp):
TTTTCCTATCTTTTTTCATGTTTTCA
Found at i:5861 original size:27 final size:27
Alignment explanation
Indices: 5839--5960 Score: 174
Period size: 27 Copynumber: 4.5 Consensus size: 27
5829 TCAAAATAAT
5839 CAAAATGCCCCTGAATGCAAAAATGA-
1 CAAAATGCCCCTGAATGCAAAAATGAC
*
5865 CAAGAATGCCCCTGAATGTAAAAATGAC
1 CAA-AATGCCCCTGAATGCAAAAATGAC
*
5893 CAAAATACCCCCTGAATGCAAAAATGAC
1 CAAAAT-GCCCCTGAATGCAAAAATGAC
* **
5921 CAAAATACCCCTGAATGTGAAAATGAC
1 CAAAATGCCCCTGAATGCAAAAATGAC
5948 CAAAATGCCCCTG
1 CAAAATGCCCCTG
5961 GGTGACCCTA
Statistics
Matches: 86, Mismatches: 7, Indels: 5
0.88 0.07 0.05
Matches are distributed among these distances:
26 3 0.03
27 55 0.64
28 28 0.33
ACGTcount: A:0.43, C:0.25, G:0.15, T:0.16
Consensus pattern (27 bp):
CAAAATGCCCCTGAATGCAAAAATGAC
Found at i:5914 original size:55 final size:55
Alignment explanation
Indices: 5846--5958 Score: 183
Period size: 55 Copynumber: 2.1 Consensus size: 55
5836 AATCAAAATG
*
5846 CCCCTGAATGCAAAAATGA-CAAGAATGCCCCTGAATGTAAAAATGACCAAAATAC
1 CCCCTGAATGCAAAAATGACCAA-AATACCCCTGAATGTAAAAATGACCAAAATAC
* *
5901 CCCCTGAATGCAAAAATGACCAAAATACCCCTGAATGTGAAAATGACCAAAATGC
1 CCCCTGAATGCAAAAATGACCAAAATACCCCTGAATGTAAAAATGACCAAAATAC
5956 CCC
1 CCC
5959 TGGGTGACCC
Statistics
Matches: 54, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
55 51 0.94
56 3 0.06
ACGTcount: A:0.43, C:0.27, G:0.14, T:0.16
Consensus pattern (55 bp):
CCCCTGAATGCAAAAATGACCAAAATACCCCTGAATGTAAAAATGACCAAAATAC
Found at i:6262 original size:22 final size:22
Alignment explanation
Indices: 6234--6414 Score: 131
Period size: 22 Copynumber: 8.4 Consensus size: 22
6224 AGAAAGATGC
*
6234 AATCAGTAAAAGGTAAAATGGT
1 AATCAGTAAAAAGTAAAATGGT
* * *
6256 AATCAGTAAAGAGTAAAGTGAT
1 AATCAGTAAAAAGTAAAATGGT
* *
6278 AATCAGTAAAAAGT--AATAGA
1 AATCAGTAAAAAGTAAAATGGT
* *
6298 AATCAGTAAGAAGT--AATTGT
1 AATCAGTAAAAAGTAAAATGGT
* *
6318 AAACAGTAAAAAAGTAAAAAGGT
1 AATCAGT-AAAAAGTAAAATGGT
*
6341 AATCAGTAAAAAGTAAAAAAGGT
1 AATCAGTAAAAAGT-AAAATGGT
* *
6364 -ATCTG-AAAAGGGTAAAATGGT
1 AATCAGTAAAA-AGTAAAATGGT
* ** * *
6385 AATTAGTAATGAGTAAAGTGAT
1 AATCAGTAAAAAGTAAAATGGT
6407 AATCAGTA
1 AATCAGTA
6415 TAGTAATCAG
Statistics
Matches: 124, Mismatches: 28, Indels: 14
0.75 0.17 0.08
Matches are distributed among these distances:
20 25 0.20
21 17 0.14
22 62 0.50
23 20 0.16
ACGTcount: A:0.52, C:0.04, G:0.20, T:0.23
Consensus pattern (22 bp):
AATCAGTAAAAAGTAAAATGGT
Found at i:6649 original size:10 final size:10
Alignment explanation
Indices: 6636--6660 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
6626 AGTGGTAATC
6636 AGTAAAAAAG
1 AGTAAAAAAG
6646 AGTAAAAAAG
1 AGTAAAAAAG
6656 AGTAA
1 AGTAA
6661 TCAGTAAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.68, C:0.00, G:0.20, T:0.12
Consensus pattern (10 bp):
AGTAAAAAAG
Found at i:6650 original size:17 final size:17
Alignment explanation
Indices: 6646--6714 Score: 59
Period size: 17 Copynumber: 3.9 Consensus size: 17
6636 AGTAAAAAAG
6646 AGTAAAAAAGAGTAATC
1 AGTAAAAAAGAGTAATC
* *
6663 AGTAAAAAGAGTAAGAAATG
1 AGTAAAAA-AG--AGTAATC
*
6683 AGTAAAAAATG-GTCATC
1 AGTAAAAAA-GAGTAATC
*
6700 AGTAAAAAAGGGTAA
1 AGTAAAAAAGAGTAA
6715 AAGAGAGTAA
Statistics
Matches: 41, Mismatches: 6, Indels: 10
0.72 0.11 0.18
Matches are distributed among these distances:
16 1 0.02
17 23 0.56
18 2 0.05
19 1 0.02
20 14 0.34
ACGTcount: A:0.57, C:0.04, G:0.22, T:0.17
Consensus pattern (17 bp):
AGTAAAAAAGAGTAATC
Found at i:6657 original size:37 final size:37
Alignment explanation
Indices: 6578--6660 Score: 98
Period size: 39 Copynumber: 2.2 Consensus size: 37
6568 AATTAAATTC
* *
6578 AAAGAGT-AAAATGGTAGTCAGTAAAAGAGAAAAAGA
1 AAAGAGTAAAAATGGTAATCAGTAAAAAAGAAAAAGA
**
6614 AGAAGAGTAAAAAGTGGTAATCAGTAAAAAAGAGTAA-A
1 A-AAGAGTAAAAA-TGGTAATCAGTAAAAAAGAAAAAGA
6652 AAAGAGTAA
1 AAAGAGTAA
6661 TCAGTAAAAA
Statistics
Matches: 40, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
36 1 0.03
37 14 0.35
38 6 0.15
39 19 0.47
ACGTcount: A:0.59, C:0.02, G:0.24, T:0.14
Consensus pattern (37 bp):
AAAGAGTAAAAATGGTAATCAGTAAAAAAGAAAAAGA
Found at i:6660 original size:27 final size:26
Alignment explanation
Indices: 6616--6687 Score: 92
Period size: 27 Copynumber: 2.7 Consensus size: 26
6606 GAAAAAGAAG
*
6616 AAGAGT-AAAAAGTGGTAATCAGTAAAA
1 AAGAGTAAAAAAG-AGTAATCAGT-AAA
6643 AAGAGTAAAAAAGAGTAATCAGTAAA
1 AAGAGTAAAAAAGAGTAATCAGTAAA
*
6669 AAGAGTAAGAAATGAGTAA
1 AAGAGTAA-AAAAGAGTAA
6688 AAAATGGTCA
Statistics
Matches: 41, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
26 11 0.27
27 24 0.59
28 6 0.15
ACGTcount: A:0.58, C:0.03, G:0.22, T:0.17
Consensus pattern (26 bp):
AAGAGTAAAAAAGAGTAATCAGTAAA
Found at i:6686 original size:37 final size:36
Alignment explanation
Indices: 6636--6724 Score: 108
Period size: 37 Copynumber: 2.4 Consensus size: 36
6626 AGTGGTAATC
6636 AGTAAAAAAGAGTAAAAAA-GAGTAATCAGTAAAAAG
1 AGTAAAAAAGAGTAAAAAATG-GTAATCAGTAAAAAG
* *
6672 AGTAAGAAATGAGTAAAAAATGGTCATCAGTAAAAAAG
1 AGTAA-AAAAGAGTAAAAAATGGTAATCAGT-AAAAAG
* *
6710 GGTAAAAGAGAGTAA
1 AGTAAAAAAGAGTAA
6725 TTAGTATAAA
Statistics
Matches: 45, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
36 5 0.11
37 29 0.64
38 11 0.24
ACGTcount: A:0.58, C:0.03, G:0.22, T:0.16
Consensus pattern (36 bp):
AGTAAAAAAGAGTAAAAAATGGTAATCAGTAAAAAG
Found at i:6715 original size:27 final size:27
Alignment explanation
Indices: 6672--6769 Score: 83
Period size: 27 Copynumber: 3.6 Consensus size: 27
6662 CAGTAAAAAG
* *
6672 AGTAAGAAATGAGTAAAAAATGGTCATC
1 AGTAA-AAAAGAGTAAAAAATGGTAATC
* * *
6700 AGTAAAAAAGGGTAAAAGA-GAGTAATT
1 AGTAAAAAAGAGTAAAAAATG-GTAATC
* * * *
6727 AGT-ATAAAGTGTAAGAAATGGTGATC
1 AGTAAAAAAGAGTAAAAAATGGTAATC
6753 AGTAAAAAAGAGTAAAA
1 AGTAAAAAAGAGTAAAA
6770 TGTGGTATTT
Statistics
Matches: 53, Mismatches: 14, Indels: 7
0.72 0.19 0.09
Matches are distributed among these distances:
26 19 0.36
27 29 0.55
28 5 0.09
ACGTcount: A:0.53, C:0.03, G:0.23, T:0.20
Consensus pattern (27 bp):
AGTAAAAAAGAGTAAAAAATGGTAATC
Found at i:6741 original size:64 final size:64
Alignment explanation
Indices: 6578--6746 Score: 198
Period size: 64 Copynumber: 2.6 Consensus size: 64
6568 AATTAAATTC
* * ** * *
6578 AAAGAGT-AAAATG-GTAGTCAGTAAAAGAGAAAAAGAAGAAGAGTAAAAAGTGGTAATCAGTAA
1 AAAGAGTAAAAAAGAGTAATCAGTAAAA-AGAGTAAGAA-ATGAGTAAAAAATGGTAATCAGTAA
6641 A
64 A
*
6642 AAAGAGTAAAAAAGAGTAATCAGTAAAAAGAGTAAGAAATGAGTAAAAAATGGTCATCAGTAAA
1 AAAGAGTAAAAAAGAGTAATCAGTAAAAAGAGTAAGAAATGAGTAAAAAATGGTAATCAGTAAA
* * * * *
6706 AAAGGGTAAAAGAGAGTAATTAGTATAAAGTGTAAGAAATG
1 AAAGAGTAAAAAAGAGTAATCAGTAAAAAGAGTAAGAAATG
6747 GTGATCAGTA
Statistics
Matches: 91, Mismatches: 12, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
64 66 0.73
65 13 0.14
66 12 0.13
ACGTcount: A:0.56, C:0.03, G:0.24, T:0.18
Consensus pattern (64 bp):
AAAGAGTAAAAAAGAGTAATCAGTAAAAAGAGTAAGAAATGAGTAAAAAATGGTAATCAGTAAA
Found at i:6849 original size:26 final size:27
Alignment explanation
Indices: 6792--6857 Score: 98
Period size: 27 Copynumber: 2.4 Consensus size: 27
6782 TAAGAAAAGG
6792 GGTAATCAGTAAAAAAGAGTAAAAATAT
1 GGTAATCAGT-AAAAAGAGTAAAAATAT
*
6820 GGTAATCAGTACAAAGAGTAAAAA-AT
1 GGTAATCAGTAAAAAGAGTAAAAATAT
*
6846 GGTAATTAGTAA
1 GGTAATCAGTAA
6858 TCAAGAAATA
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
26 12 0.34
27 13 0.37
28 10 0.29
ACGTcount: A:0.53, C:0.05, G:0.20, T:0.23
Consensus pattern (27 bp):
GGTAATCAGTAAAAAGAGTAAAAATAT
Found at i:8159 original size:25 final size:24
Alignment explanation
Indices: 8093--8159 Score: 66
Period size: 23 Copynumber: 2.7 Consensus size: 24
8083 TATATAATTC
8093 TATATATCATATAATTAATTTGTATA
1 TATATAT-ATATAA-TAATTTGTATA
* *
8119 TTATATAAATCTTAAT-ATTT-TATA
1 -TATATATAT-ATAATAATTTGTATA
8143 TATATATATATAATAAT
1 TATATATATATAATAAT
8160 CCAAAAAATC
Statistics
Matches: 34, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
22 4 0.12
23 10 0.29
24 4 0.12
25 4 0.12
26 3 0.09
27 9 0.26
ACGTcount: A:0.45, C:0.03, G:0.01, T:0.51
Consensus pattern (24 bp):
TATATATATATAATAATTTGTATA
Found at i:10720 original size:31 final size:31
Alignment explanation
Indices: 10661--10720 Score: 86
Period size: 31 Copynumber: 1.9 Consensus size: 31
10651 ATAGGAGAAA
* *
10661 TTTTCAGATCTGAACAAAAGGGATAAAGAGG
1 TTTTCAGATCTGAACAAAAGGAAGAAAGAGG
10692 TTTTCAGATCTGAACAACAA-GAAGAAAGA
1 TTTTCAGATCTGAACAA-AAGGAAGAAAGA
10721 AGTTCGTGCT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
31 24 0.92
32 2 0.08
ACGTcount: A:0.45, C:0.12, G:0.22, T:0.22
Consensus pattern (31 bp):
TTTTCAGATCTGAACAAAAGGAAGAAAGAGG
Found at i:11660 original size:20 final size:21
Alignment explanation
Indices: 11635--11680 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
11625 TATTTTATTA
*
11635 ACCCGACA-ATGACCCAATTG
1 ACCCGACAGATGAACCAATTG
*
11655 ACCCGACAGTTGAACCAATTG
1 ACCCGACAGATGAACCAATTG
11676 ACCCG
1 ACCCG
11681 TGACCCAGCC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 8 0.35
21 15 0.65
ACGTcount: A:0.33, C:0.35, G:0.17, T:0.15
Consensus pattern (21 bp):
ACCCGACAGATGAACCAATTG
Found at i:14220 original size:48 final size:48
Alignment explanation
Indices: 14166--14576 Score: 592
Period size: 48 Copynumber: 8.6 Consensus size: 48
14156 GACAAATCTA
* * * *
14166 GCACCTTCCGACTGGGATGGGCAAAACTGGAAATAGACACTGAA-AAT
1 GCACCTTCCGACCGGGAAGGGCAAAACTGGAAATAAACACTGAAGACT
* * * * *
14213 AGCACCTTTCGACCGAGAAGGACAACACAGGAAATAAACACTGAAGACT
1 -GCACCTTCCGACCGGGAAGGGCAAAACTGGAAATAAACACTGAAGACT
* * * *
14262 ACACCTTCCGACCGGGAAGGACAAAAATGGAAATAAACACTGAATACT
1 GCACCTTCCGACCGGGAAGGGCAAAACTGGAAATAAACACTGAAGACT
* *
14310 GCACCTTCCAACCGGGAAGGGCAAAACTGGAAATAAACACCGAAGACT
1 GCACCTTCCGACCGGGAAGGGCAAAACTGGAAATAAACACTGAAGACT
* * *
14358 GCACCTTCCGATCGGGAAGGGCAAAACAGGAAATAAACACCGAAGACT
1 GCACCTTCCGACCGGGAAGGGCAAAACTGGAAATAAACACTGAAGACT
* *
14406 GCACCTTCCGACCGGGAAGGGCAAAACTGGAAATAGACACTGAA-AAT
1 GCACCTTCCGACCGGGAAGGGCAAAACTGGAAATAAACACTGAAGACT
14453 AGCACCTTCCGACCGGGAAGGGCAAAACTGGAAATAAACACTGAAGACT
1 -GCACCTTCCGACCGGGAAGGGCAAAACTGGAAATAAACACTGAAGACT
*
14502 GCACCTTCCGACCGGGAAGGGCAAAACTGGAAATAAACACTGAAAACT
1 GCACCTTCCGACCGGGAAGGGCAAAACTGGAAATAAACACTGAAGACT
*
14550 GCAACTTCCGACCGGGAAGGGCAAAAC
1 GCACCTTCCGACCGGGAAGGGCAAAAC
14577 AGGGAATCGA
Statistics
Matches: 326, Mismatches: 34, Indels: 6
0.89 0.09 0.02
Matches are distributed among these distances:
47 2 0.01
48 320 0.98
49 4 0.01
ACGTcount: A:0.39, C:0.25, G:0.24, T:0.12
Consensus pattern (48 bp):
GCACCTTCCGACCGGGAAGGGCAAAACTGGAAATAAACACTGAAGACT
Done.