Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023227.1 Corchorus olitorius cultivar O-4 contig23260, 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: 57369
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32
Found at i:1000 original size:21 final size:21
Alignment explanation
Indices: 976--1025 Score: 82
Period size: 21 Copynumber: 2.4 Consensus size: 21
966 CGCCCATTCA
**
976 CCGTGCCACCACCGGTTAAGC
1 CCGTGCCACCACCGGCCAAGC
997 CCGTGCCACCACCGGCCAAGC
1 CCGTGCCACCACCGGCCAAGC
1018 CCGTGCCA
1 CCGTGCCA
1026 TCGCCATTCC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.18, C:0.48, G:0.24, T:0.10
Consensus pattern (21 bp):
CCGTGCCACCACCGGCCAAGC
Found at i:4315 original size:15 final size:15
Alignment explanation
Indices: 4285--4326 Score: 75
Period size: 15 Copynumber: 2.7 Consensus size: 15
4275 TTACTCTGCT
4285 TTGTTTTCTAGTTTAA
1 TTGTTTTCT-GTTTAA
4301 TTGTTTTCTGTTTAA
1 TTGTTTTCTGTTTAA
4316 TTGTTTTCTGT
1 TTGTTTTCTGT
4327 CAACCTCTGT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
15 17 0.65
16 9 0.35
ACGTcount: A:0.12, C:0.07, G:0.14, T:0.67
Consensus pattern (15 bp):
TTGTTTTCTGTTTAA
Found at i:17722 original size:30 final size:30
Alignment explanation
Indices: 17683--17749 Score: 107
Period size: 30 Copynumber: 2.2 Consensus size: 30
17673 GAGTATGACG
*
17683 AGGAGGAAGATTCCGATCTCTTTGTTTGTGA
1 AGGA-GAAGATTACGATCTCTTTGTTTGTGA
*
17714 AGGAGAAGATTATGATCTCTTTGTTTGTGA
1 AGGAGAAGATTACGATCTCTTTGTTTGTGA
17744 AGGAGA
1 AGGAGA
17750 GAATTCTGAT
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
30 30 0.88
31 4 0.12
ACGTcount: A:0.27, C:0.09, G:0.30, T:0.34
Consensus pattern (30 bp):
AGGAGAAGATTACGATCTCTTTGTTTGTGA
Found at i:21599 original size:23 final size:23
Alignment explanation
Indices: 21573--21621 Score: 73
Period size: 23 Copynumber: 2.1 Consensus size: 23
21563 AGCCCAAGGA
*
21573 TTCAAAC-CTCTAAATCCCCAGAT
1 TTCAAACACT-TAAATCCCCAAAT
21596 TTCAAACACTTAAATCCCCAAAT
1 TTCAAACACTTAAATCCCCAAAT
21619 TTC
1 TTC
21622 CCAACAATAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
23 22 0.92
24 2 0.08
ACGTcount: A:0.37, C:0.33, G:0.02, T:0.29
Consensus pattern (23 bp):
TTCAAACACTTAAATCCCCAAAT
Found at i:30619 original size:75 final size:75
Alignment explanation
Indices: 30475--30699 Score: 324
Period size: 75 Copynumber: 3.0 Consensus size: 75
30465 TTTGAATACC
* * ** *
30475 CTCTGGAAATTACTGATAGCTCCAATCAACTTTTAACGTGGGAGAACCTTTTCATCCTGTTTTGG
1 CTCTGGAAATTACTAATAGCTCCCATCAACTTTTAACGTGGGAGAACCTTTTCGCCCCGTTTTGG
30540 TCTTTTCTCA
66 TCTTTTCTCA
* * * * * *
30550 TTCTGAAAATTACCAATAGCTCCCATCAACTTTTAACGTGGGAGAACCTTTTCGCCCCGCTTCGA
1 CTCTGGAAATTACTAATAGCTCCCATCAACTTTTAACGTGGGAGAACCTTTTCGCCCCGTTTTGG
30615 TCTTTTCTCA
66 TCTTTTCTCA
* * *
30625 CTATGGAATTTACTAATAGCTCCCATCAAATTTTAACGTGGGAGAACCTTTTCGCCCCGTTTTGG
1 CTCTGGAAATTACTAATAGCTCCCATCAACTTTTAACGTGGGAGAACCTTTTCGCCCCGTTTTGG
30690 TCTTTTCTCA
66 TCTTTTCTCA
30700 ATCTAGTTAA
Statistics
Matches: 130, Mismatches: 20, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
75 130 1.00
ACGTcount: A:0.23, C:0.25, G:0.15, T:0.36
Consensus pattern (75 bp):
CTCTGGAAATTACTAATAGCTCCCATCAACTTTTAACGTGGGAGAACCTTTTCGCCCCGTTTTGG
TCTTTTCTCA
Found at i:33984 original size:40 final size:40
Alignment explanation
Indices: 33929--34005 Score: 118
Period size: 40 Copynumber: 1.9 Consensus size: 40
33919 TTAATCAAAT
*
33929 TTTCAAAATCAGTTTTAATCAAAGCTATGATTTCGAGATC
1 TTTCAAAATCAGTTTTAATCAAAGCAATGATTTCGAGATC
* **
33969 TTTCAAAATTAGTTTTGGTCAAAGCAATGATTTCGAG
1 TTTCAAAATCAGTTTTAATCAAAGCAATGATTTCGAG
34006 GTGACTGAAT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
40 33 1.00
ACGTcount: A:0.34, C:0.13, G:0.16, T:0.38
Consensus pattern (40 bp):
TTTCAAAATCAGTTTTAATCAAAGCAATGATTTCGAGATC
Found at i:41996 original size:34 final size:37
Alignment explanation
Indices: 41958--42027 Score: 92
Period size: 37 Copynumber: 1.9 Consensus size: 37
41948 TCCACGCCAA
*
41958 GCAGCA-A-GCCGCTGCTGCTGCCT-AGCCCGCGCGC
1 GCAGCACAGGCCGATGCTGCTGCCTCAGCCCGCGCGC
*
41992 GCAGCAGCAGGTCGATGCTGCTGCCTCAGCCCGCGC
1 GCAGCA-CAGGCCGATGCTGCTGCCTCAGCCCGCGC
42028 ACAAGGCAGC
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
34 6 0.20
36 1 0.03
37 14 0.47
38 9 0.30
ACGTcount: A:0.13, C:0.41, G:0.33, T:0.13
Consensus pattern (37 bp):
GCAGCACAGGCCGATGCTGCTGCCTCAGCCCGCGCGC
Found at i:46627 original size:9 final size:9
Alignment explanation
Indices: 46613--46681 Score: 72
Period size: 9 Copynumber: 7.7 Consensus size: 9
46603 TGAGAAACTA
46613 AAAAAAATC
1 AAAAAAATC
46622 AAAAAAATC
1 AAAAAAATC
46631 -AAAAAATC
1 AAAAAAATC
46639 AAAAAAATC
1 AAAAAAATC
46648 AATAAAAA--
1 AA-AAAAATC
**
46656 AATCAAATC
1 AAAAAAATC
46665 AAATCAAAATC
1 AAA--AAAATC
46676 AAAAAA
1 AAAAAA
46682 GAATTGATTG
Statistics
Matches: 50, Mismatches: 4, Indels: 12
0.76 0.06 0.18
Matches are distributed among these distances:
7 3 0.06
8 10 0.20
9 24 0.48
10 5 0.10
11 8 0.16
ACGTcount: A:0.75, C:0.12, G:0.00, T:0.13
Consensus pattern (9 bp):
AAAAAAATC
Found at i:46636 original size:17 final size:17
Alignment explanation
Indices: 46614--46654 Score: 73
Period size: 17 Copynumber: 2.4 Consensus size: 17
46604 GAGAAACTAA
46614 AAAAAATCAAAAAAATC
1 AAAAAATCAAAAAAATC
46631 AAAAAATCAAAAAAATC
1 AAAAAATCAAAAAAATC
46648 AATAAAA
1 AA-AAAA
46655 AAATCAAATC
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
17 19 0.83
18 4 0.17
ACGTcount: A:0.78, C:0.10, G:0.00, T:0.12
Consensus pattern (17 bp):
AAAAAATCAAAAAAATC
Found at i:46649 original size:26 final size:25
Alignment explanation
Indices: 46613--46681 Score: 77
Period size: 26 Copynumber: 2.6 Consensus size: 25
46603 TGAGAAACTA
46613 AAAAAAATCAAAAAAATCAA-AAAATC
1 AAAAAAATCAAAAAAA--AATAAAATC
*
46639 AAAAAAATCAATAAAAAAATCAAATC
1 AAAAAAATCAA-AAAAAAATAAAATC
46665 AAATCAAAATCAAAAAA
1 AAA--AAAATCAAAAAA
46682 GAATTGATTG
Statistics
Matches: 38, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
25 2 0.05
26 19 0.50
27 9 0.24
28 8 0.21
ACGTcount: A:0.75, C:0.12, G:0.00, T:0.13
Consensus pattern (25 bp):
AAAAAAATCAAAAAAAAATAAAATC
Found at i:47343 original size:50 final size:50
Alignment explanation
Indices: 47268--47413 Score: 186
Period size: 50 Copynumber: 2.9 Consensus size: 50
47258 TTACAGTAAG
* * * * *
47268 ATTGCATTCCATTTGTGAGCCCAAGATTAAAATTCGCTTTTCAAAGTAAA
1 ATTGCATTCCAATTGTAAGTCCAAGATCAAAATTCGCTTTTCAAAGCAAA
* **
47318 ATTGC-TTCCCAATTGTAAGTTCAAGATCAAAATTCGCTTTTCAAAGCAGG
1 ATTGCATT-CCAATTGTAAGTCCAAGATCAAAATTCGCTTTTCAAAGCAAA
* *
47368 ATTGCATTCCATTTGTGAGTCCAAGATCAAAATTCGCTTTTCAAAG
1 ATTGCATTCCAATTGTAAGTCCAAGATCAAAATTCGCTTTTCAAAG
47414 GGCATTTAAG
Statistics
Matches: 83, Mismatches: 11, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
49 2 0.02
50 79 0.95
51 2 0.02
ACGTcount: A:0.32, C:0.19, G:0.15, T:0.34
Consensus pattern (50 bp):
ATTGCATTCCAATTGTAAGTCCAAGATCAAAATTCGCTTTTCAAAGCAAA
Found at i:47977 original size:79 final size:79
Alignment explanation
Indices: 47868--48020 Score: 270
Period size: 79 Copynumber: 1.9 Consensus size: 79
47858 GTTATCAAAA
*
47868 TTGACCGCAAATTGGTCCTTTTTCATCATCAATCAAGAAGTTTTCAGTTACAACATCAGACTCAG
1 TTGACCGCAAATTGGTCCTCTTTCATCATCAATCAAGAAGTTTTCAGTTACAACATCAGACTCAG
47933 AGTTATTTTTCAAG
66 AGTTATTTTTCAAG
* * *
47947 TTGATCGCAAATTGGTCCTCTTTCATCATCAATCAAGAAGTTTTCAGTTACAACATCATATTCAG
1 TTGACCGCAAATTGGTCCTCTTTCATCATCAATCAAGAAGTTTTCAGTTACAACATCAGACTCAG
48012 AGTTATTTT
66 AGTTATTTT
48021 CCAAAGGTAT
Statistics
Matches: 70, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
79 70 1.00
ACGTcount: A:0.30, C:0.20, G:0.13, T:0.37
Consensus pattern (79 bp):
TTGACCGCAAATTGGTCCTCTTTCATCATCAATCAAGAAGTTTTCAGTTACAACATCAGACTCAG
AGTTATTTTTCAAG
Found at i:48182 original size:50 final size:50
Alignment explanation
Indices: 48107--48242 Score: 236
Period size: 50 Copynumber: 2.7 Consensus size: 50
48097 AATGCTTTGA
* * *
48107 CTTTTCCATAAGTCGAACTCGTTTCCATACGAGTCAATTATCAACGTAGG
1 CTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACGTAGG
48157 CTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACGTAGG
1 CTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACGTAGG
*
48207 CTTTTCCACAAGCCAAACTCATTTCCATACGAGTCA
1 CTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCA
48243 GTTTAAGCCT
Statistics
Matches: 82, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
50 82 1.00
ACGTcount: A:0.29, C:0.28, G:0.13, T:0.29
Consensus pattern (50 bp):
CTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACGTAGG
Found at i:48289 original size:69 final size:69
Alignment explanation
Indices: 48203--48540 Score: 577
Period size: 69 Copynumber: 4.9 Consensus size: 69
48193 ATTATCAACG
*
48203 TAGGCTTTTCCACAAGCCAAACTCATTTCCATACGAGTCAGTTTAAGCCTTGGTTCCATCCAAGC
1 TAGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTTAAGCCTTGGTTCCATCCAAGC
48268 CATA
66 CATA
* *
48272 TAGGCTTTTCCACAAGCCAAACTCGTTTACATACGAGTCAGTTTAAGCATTGGTTCCATCCAAGC
1 TAGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTTAAGCCTTGGTTCCATCCAAGC
48337 CATA
66 CATA
*
48341 TAGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATCCAAGC
1 TAGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTTAAGCCTTGGTTCCATCCAAGC
*
48406 CACA
66 CATA
48410 TAGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTTAAGCCTTGGTTCCATCCAAGC
1 TAGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTTAAGCCTTGGTTCCATCCAAGC
48475 CATA
66 CATA
* * * * * *
48479 TAGACTTTTCCATAAGTCAAACTCGTTTCCATGCGAGTCAGTTTAAACATTGGTTCCATCCA
1 TAGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTTAAGCCTTGGTTCCATCCA
48541 TACGGCAGAG
Statistics
Matches: 254, Mismatches: 15, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
69 254 1.00
ACGTcount: A:0.27, C:0.28, G:0.15, T:0.29
Consensus pattern (69 bp):
TAGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTTAAGCCTTGGTTCCATCCAAGC
CATA
Done.