Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011575.1 Corchorus capsularis cultivar CVL-1 contig11596, 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: 39696
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.32
Found at i:6963 original size:19 final size:19
Alignment explanation
Indices: 6905--6965 Score: 68
Period size: 19 Copynumber: 3.2 Consensus size: 19
6895 CTTTTTCTAC
*
6905 TTTTATTTTATTTATTTAT
1 TTTTATTTTATTTATTCAT
* * * **
6924 ATTTATATTATTAATGGAT
1 TTTTATTTTATTTATTCAT
6943 TTTTATTTTATTTATTCAT
1 TTTTATTTTATTTATTCAT
6962 TTTT
1 TTTT
6966 TTACTTGTGT
Statistics
Matches: 32, Mismatches: 10, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
19 32 1.00
ACGTcount: A:0.25, C:0.02, G:0.03, T:0.70
Consensus pattern (19 bp):
TTTTATTTTATTTATTCAT
Found at i:8182 original size:24 final size:24
Alignment explanation
Indices: 8137--8186 Score: 59
Period size: 25 Copynumber: 2.1 Consensus size: 24
8127 TTTGGTAAAA
8137 GTTCTCTTTTTAGGACACTTTGCAG
1 GTTCTCTTTTTAGGACACTTTG-AG
*
8162 GTTCTGTTTTT-GGA-ACATTTGAG
1 GTTCTCTTTTTAGGACAC-TTTGAG
8185 GT
1 GT
8187 AGTAAACGAT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
23 6 0.26
24 7 0.30
25 10 0.43
ACGTcount: A:0.16, C:0.14, G:0.24, T:0.46
Consensus pattern (24 bp):
GTTCTCTTTTTAGGACACTTTGAG
Found at i:13257 original size:194 final size:194
Alignment explanation
Indices: 12921--13295 Score: 723
Period size: 194 Copynumber: 1.9 Consensus size: 194
12911 TTGACTTTGG
12921 CCTATGGTGGACTAAATCCAACCATCCATAGGACTTTTGGGAGTAAATCTCAGCCATTGATCTTG
1 CCTATGGTGGACTAAATCCAACCATCCATAGGACTTTTGGGAGTAAATCTCAGCCATTGATCTTG
* *
12986 TACCAGCATGTACATTTACAATTTTACCCTAATTGTAAATTGTGGTATAAACAGGACCAATTTAT
66 TACCACCATGTACATTTACAATTTGACCCTAATTGTAAATTGTGGTATAAACAGGACCAATTTAT
13051 ATATACAGTCTTTTAATCTGGTACGTCCATCAAATAACTAGTTGAACGGTAGAGACAGTTTTAC
131 ATATACAGTCTTTTAATCTGGTACGTCCATCAAATAACTAGTTGAACGGTAGAGACAGTTTTAC
13115 CCTATGGTGGACTAAATCCAACCATCCATAGGACTTTTGGGAGTAAATCTCAGCCATTGATCTTG
1 CCTATGGTGGACTAAATCCAACCATCCATAGGACTTTTGGGAGTAAATCTCAGCCATTGATCTTG
13180 TACCACCATGTACATTTACAATTTGACCCTAATTGTAAATTGTGGTATAAACAGGACCAATTTAT
66 TACCACCATGTACATTTACAATTTGACCCTAATTGTAAATTGTGGTATAAACAGGACCAATTTAT
*
13245 ATATATAGTCTTTTAATCTGGTACGTCCATCAAATAACTAGTTGAACGGTA
131 ATATACAGTCTTTTAATCTGGTACGTCCATCAAATAACTAGTTGAACGGTA
13296 TAGATTTACT
Statistics
Matches: 178, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
194 178 1.00
ACGTcount: A:0.32, C:0.19, G:0.16, T:0.33
Consensus pattern (194 bp):
CCTATGGTGGACTAAATCCAACCATCCATAGGACTTTTGGGAGTAAATCTCAGCCATTGATCTTG
TACCACCATGTACATTTACAATTTGACCCTAATTGTAAATTGTGGTATAAACAGGACCAATTTAT
ATATACAGTCTTTTAATCTGGTACGTCCATCAAATAACTAGTTGAACGGTAGAGACAGTTTTAC
Found at i:13525 original size:51 final size:51
Alignment explanation
Indices: 13449--13546 Score: 196
Period size: 51 Copynumber: 1.9 Consensus size: 51
13439 CTATGCCGCA
13449 CATAAGGAAAACTTGTAATGATAAAGTTAAGAAGGCATAGAACTTAACGCG
1 CATAAGGAAAACTTGTAATGATAAAGTTAAGAAGGCATAGAACTTAACGCG
13500 CATAAGGAAAACTTGTAATGATAAAGTTAAGAAGGCATAGAACTTAA
1 CATAAGGAAAACTTGTAATGATAAAGTTAAGAAGGCATAGAACTTAA
13547 TTTGATTGAT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
51 47 1.00
ACGTcount: A:0.47, C:0.10, G:0.20, T:0.22
Consensus pattern (51 bp):
CATAAGGAAAACTTGTAATGATAAAGTTAAGAAGGCATAGAACTTAACGCG
Found at i:13620 original size:56 final size:60
Alignment explanation
Indices: 13534--13647 Score: 182
Period size: 56 Copynumber: 1.9 Consensus size: 60
13524 AGTTAAGAAG
13534 GCATAGAACTTAATTTGATTGATGAACATGAAG-T-G-G-AGTAGACCCATACGTGCTAC
1 GCATAGAACTTAATTTGATTGATGAACATGAAGTTAGTGTAGTAGACCCATACGTGCTAC
*
13590 GCATATAACTTAATTTGATTGATGAACATGAAGTTAAGTGTAGTAGACCCATACGTGC
1 GCATAGAACTTAATTTGATTGATGAACATGAAGTT-AGTGTAGTAGACCCATACGTGC
13648 AAAGCCGACT
Statistics
Matches: 52, Mismatches: 1, Indels: 5
0.90 0.02 0.09
Matches are distributed among these distances:
56 32 0.62
57 1 0.02
59 1 0.02
60 1 0.02
61 17 0.33
ACGTcount: A:0.34, C:0.15, G:0.22, T:0.29
Consensus pattern (60 bp):
GCATAGAACTTAATTTGATTGATGAACATGAAGTTAGTGTAGTAGACCCATACGTGCTAC
Found at i:15529 original size:127 final size:127
Alignment explanation
Indices: 15303--15558 Score: 449
Period size: 127 Copynumber: 2.0 Consensus size: 127
15293 TCTGTCCATT
15303 TATCCAAATCGAGCACTGAAAGTTGTCTGCAACATTAAAGAAGAAATTGATGAAAAGAGAATCAT
1 TATCCAAATCGAGCACTGAAAGTTGTCTGCAACATTAAAGAAGAAATTGATGAAAAGAGAATCAT
*
15368 AAGCTAAAAATATGATGGTAATCCTATGCAAACTTCTGACCAAGCAAAGATTACACTACTAC
66 AAGCTAAAAATACGATGGTAATCCTATGCAAACTTCTGACCAAGCAAAGATTACACTACTAC
* *
15430 TATCCAAATCGAGCATTGAAAGTTGTCTGCAACATTAAAGAAGTAATTGATGAAAAGAGAATCAT
1 TATCCAAATCGAGCACTGAAAGTTGTCTGCAACATTAAAGAAGAAATTGATGAAAAGAGAATCAT
* * * *
15495 AAGCTAAGAATACGATGGTAATCCTGTTCAAACTTCTGACCAAGCAAAGATTATACTACTAC
66 AAGCTAAAAATACGATGGTAATCCTATGCAAACTTCTGACCAAGCAAAGATTACACTACTAC
15557 TA
1 TA
15559 CTGTTGCTGC
Statistics
Matches: 122, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
127 122 1.00
ACGTcount: A:0.42, C:0.17, G:0.16, T:0.25
Consensus pattern (127 bp):
TATCCAAATCGAGCACTGAAAGTTGTCTGCAACATTAAAGAAGAAATTGATGAAAAGAGAATCAT
AAGCTAAAAATACGATGGTAATCCTATGCAAACTTCTGACCAAGCAAAGATTACACTACTAC
Found at i:18379 original size:29 final size:29
Alignment explanation
Indices: 18346--18406 Score: 122
Period size: 29 Copynumber: 2.1 Consensus size: 29
18336 GAGAGAAAAG
18346 AGAGATGAGTAAAAAGGGAGGGGAAAATC
1 AGAGATGAGTAAAAAGGGAGGGGAAAATC
18375 AGAGATGAGTAAAAAGGGAGGGGAAAATC
1 AGAGATGAGTAAAAAGGGAGGGGAAAATC
18404 AGA
1 AGA
18407 AGGAAAGGTC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.49, C:0.03, G:0.38, T:0.10
Consensus pattern (29 bp):
AGAGATGAGTAAAAAGGGAGGGGAAAATC
Found at i:19871 original size:31 final size:31
Alignment explanation
Indices: 19768--19905 Score: 152
Period size: 31 Copynumber: 4.5 Consensus size: 31
19758 ACCGTGTCCG
*
19768 ACGTGGCATGCCACGTGTACCAAAAAGTGAC
1 ACGTGGCATGCCACATGTACCAAAAAGTGAC
* * ** *
19799 ATGTGACACACCACGTGTACCAAAAAGTGAC
1 ACGTGGCATGCCACATGTACCAAAAAGTGAC
* *
19830 ACATGTCATGCCACATGTACCAAAAAGTGAC
1 ACGTGGCATGCCACATGTACCAAAAAGTGAC
**
19861 ACGTGGCATGCCACATGTTTCAAAATA-TGAC
1 ACGTGGCATGCCACATGTACCAAAA-AGTGAC
* *
19892 ATGTAGCATGCCAC
1 ACGTGGCATGCCAC
19906 GTGTCATTTT
Statistics
Matches: 90, Mismatches: 16, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
31 89 0.99
32 1 0.01
ACGTcount: A:0.35, C:0.25, G:0.20, T:0.20
Consensus pattern (31 bp):
ACGTGGCATGCCACATGTACCAAAAAGTGAC
Found at i:20440 original size:4 final size:4
Alignment explanation
Indices: 20433--20457 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
20423 TATTTAAAAA
20433 AAAG AAAG AAAG AAAG AAAG AAAG A
1 AAAG AAAG AAAG AAAG AAAG AAAG A
20458 CATGGCGGGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (4 bp):
AAAG
Found at i:26601 original size:18 final size:18
Alignment explanation
Indices: 26578--26612 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
26568 GATGCCTTAC
26578 AAAAAAAAAGAAAAGGAA
1 AAAAAAAAAGAAAAGGAA
*
26596 AAAAAAAACGAAAAGGA
1 AAAAAAAAAGAAAAGGA
26613 GCTGGAATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.80, C:0.03, G:0.17, T:0.00
Consensus pattern (18 bp):
AAAAAAAAAGAAAAGGAA
Found at i:32969 original size:33 final size:33
Alignment explanation
Indices: 32927--32992 Score: 132
Period size: 33 Copynumber: 2.0 Consensus size: 33
32917 GAGCTTCTTT
32927 TCGCAATAATCTTGTTAACTACTGTCATCAAAG
1 TCGCAATAATCTTGTTAACTACTGTCATCAAAG
32960 TCGCAATAATCTTGTTAACTACTGTCATCAAAG
1 TCGCAATAATCTTGTTAACTACTGTCATCAAAG
32993 CATTAACCCT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.33, C:0.21, G:0.12, T:0.33
Consensus pattern (33 bp):
TCGCAATAATCTTGTTAACTACTGTCATCAAAG
Done.