Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01010060.1 Corchorus olitorius cultivar O-4 contig10092, 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: 11157
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.36
Found at i:420 original size:16 final size:16
Alignment explanation
Indices: 369--427 Score: 75
Period size: 16 Copynumber: 3.7 Consensus size: 16
359 TGTGACTTCC
* *
369 TTTCCCTTCCTCCCTA
1 TTTCCTTTCCTTCCTA
*
385 TTTCCTTTCTCTTGCTA
1 TTTCCTTTC-CTTCCTA
402 TTTCCTTTCCTTCCTA
1 TTTCCTTTCCTTCCTA
418 TTT-CTTTCCT
1 TTTCCTTTCCT
428 CCCAACCAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
15 7 0.18
16 17 0.45
17 14 0.37
ACGTcount: A:0.05, C:0.37, G:0.02, T:0.56
Consensus pattern (16 bp):
TTTCCTTTCCTTCCTA
Found at i:1648 original size:2 final size:2
Alignment explanation
Indices: 1641--1677 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
1631 GTCCAATTTG
1641 AT AT AT AT AT 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 AT AT AT AT AT A
1678 CTAAATGTTA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3070 original size:12 final size:12
Alignment explanation
Indices: 3053--3078 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
3043 CAGAAGAATT
3053 TTAGGCTACATC
1 TTAGGCTACATC
3065 TTAGGCTACATC
1 TTAGGCTACATC
3077 TT
1 TT
3079 TTCTCCAAGC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.23, C:0.23, G:0.15, T:0.38
Consensus pattern (12 bp):
TTAGGCTACATC
Found at i:3106 original size:2 final size:2
Alignment explanation
Indices: 3099--3136 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
3089 ATACAAAACT
3099 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
3137 AACCTTAGGC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:3698 original size:185 final size:188
Alignment explanation
Indices: 3384--3758 Score: 623
Period size: 185 Copynumber: 2.0 Consensus size: 188
3374 TGAGTTTGAT
3384 GACACGTCACCTTGTAATTAAGTAAGAAGACGTCTCATGGGCCGAGATTAGTAAGCATAAGCCGC
1 GACACGTCACCTTGTAATTAAGTAAGAAGACGTCTCATGGGCCGAGATTAGTAAGCATAAGCCGC
*
3449 CTTCTGCAGTCCAGGAGACGCCTCCCTGTTTCCAGGAGCTGTCTCCTTATCTTTTGTATTTAAGG
66 CTCCTGCAGTCCAGGAGACGCCTCCCTGTTTCCAGGAGCTGTCTCCTTATCTTTTGTATTTAAGG
* *
3514 GGTTGGCGAGTTAATATTTGTC-GCGAGCATTTATCTATCTACATAAGAGAGGCATGA
131 AGTTGGCAAGTTAATATTTGTCGGCGAGCATTTATCTATCTACATAAGAGAGGCATGA
*
3571 GACACGTCACCTTGTAATTAAGTAAG-AGCCGTCTCAT-GGCCGAGATTAGTAAGCATAAGCCGC
1 GACACGTCACCTTGTAATTAAGTAAGAAGACGTCTCATGGGCCGAGATTAGTAAGCATAAGCCGC
* ** *
3634 CTCCTGCAG-CCGAGGAGGCGCCTCCCTGTTTTTAGGAGTTGTCTCCTTATCTTTTGTATTTAAG
66 CTCCTGCAGTCC-AGGAGACGCCTCCCTGTTTCCAGGAGCTGTCTCCTTATCTTTTGTATTTAAG
* *
3698 GAGTTTGCAAGTTAATATTTGTCGGCGAGCATTTATCTATCTACATAAGAGAGGCGTGA
130 GAGTTGGCAAGTTAATATTTGTCGGCGAGCATTTATCTATCTACATAAGAGAGGCATGA
3757 GA
1 GA
3759 TGTTAAGGCT
Statistics
Matches: 176, Mismatches: 10, Indels: 5
0.92 0.05 0.03
Matches are distributed among these distances:
184 2 0.01
185 102 0.58
186 46 0.26
187 26 0.15
ACGTcount: A:0.25, C:0.21, G:0.24, T:0.30
Consensus pattern (188 bp):
GACACGTCACCTTGTAATTAAGTAAGAAGACGTCTCATGGGCCGAGATTAGTAAGCATAAGCCGC
CTCCTGCAGTCCAGGAGACGCCTCCCTGTTTCCAGGAGCTGTCTCCTTATCTTTTGTATTTAAGG
AGTTGGCAAGTTAATATTTGTCGGCGAGCATTTATCTATCTACATAAGAGAGGCATGA
Found at i:3978 original size:15 final size:15
Alignment explanation
Indices: 3958--3988 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
3948 CTTGAGCTCC
3958 ATCCGACGTAGTTGG
1 ATCCGACGTAGTTGG
3973 ATCCGACGTAGTTGG
1 ATCCGACGTAGTTGG
3988 A
1 A
3989 AAAACTTTGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.23, C:0.19, G:0.32, T:0.26
Consensus pattern (15 bp):
ATCCGACGTAGTTGG
Found at i:5681 original size:15 final size:15
Alignment explanation
Indices: 5661--5690 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
5651 TATAATTCAT
5661 TCTCTCATTTCTCAA
1 TCTCTCATTTCTCAA
5676 TCTCTCATTTCTCAA
1 TCTCTCATTTCTCAA
5691 GATCGCGTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.20, C:0.33, G:0.00, T:0.47
Consensus pattern (15 bp):
TCTCTCATTTCTCAA
Found at i:7281 original size:434 final size:429
Alignment explanation
Indices: 6298--7284 Score: 1254
Period size: 434 Copynumber: 2.3 Consensus size: 429
6288 AGTCATTTAA
*
6298 GTGTCTATTAAAAGGTAATTTCATGATCTACAATTTTCATG-AAGAACTCAAAAGCCAATTTTAA
1 GTGTCTATTAAAAGGTAATTTCATGATCTACAACTTTCATGAAAG-ACTCAAAAG-CAATTTTAA
* * ** * * * *
6362 TGTTTTGATTCTAAAAGTGC--TT--CCTTTGTGGTTTTGATTGCCAGTCAATTTAATATCATAT
64 TGTTTTAATTCTAAAAATGCTTTTAAATTTTGT-GTTTCGATTGACAGTCTATTTAATACCATAT
* * * * * * *
6423 AATTTTTTGTCCACATGTCCGATTGAAGTTATTGAAGTGTCGGTTAAAAGGTTATTGCATGATTT
128 AACTTTTCGTCCACATGTCCGATTAAAGTTATTCAAGTGTCAGTTAAAAGGTTATCGCATGATCT
* *
6488 ACGACTTTCATGAAGGACCCGAAAGCTAAATTTGATCTACGAGTTTCATGAAGGGTTGAAAAGGG
193 ACGACTTTCATGAAGAACCCGAAAGCTAAATTTGATCTACGAGTTTCATGAAGGGTTCAAAAGGG
* * * *
6553 AATTTTTATGTTTCAAGATCTCCATTAACAAACATTTTTTTATTTGGATTATTTATCAAATGATC
258 AATTTTTATGTTTCAAGATCTCCATTAACAAACATTTTCTTATTTGAATTAGTTATCAAATGACC
*
6618 CTCATACTTTTCTACTTTATACTACTTAGTCCTTTCCAAATTCTATCTTAATTTAACGTTTAAGA
323 CTCATACTTTTCTACTTTATACTACTTAGTCCTTTACAAATTCTATCTTAATTTAACGTTT---A
* * * * *
6683 TTTTTTTTTATTCTTTGTTCTATTTGTCTGATTAAGTTGATTCAT
385 CTTTTTTTTATTCTTTGTTCTATTTATCTAATTAAGGTAATTCAT
* * *
6728 GTGTCTATTAAAAGGTAATTTCATGATCTACAACTTTCATGAAGGAATCAAAAGCAATTTTTATG
1 GTGTCTATTAAAAGGTAATTTCATGATCTACAACTTTCATGAAAGACTCAAAAGCAATTTTAATG
* * * ***
6793 TTTTAATTCAAAAAAATGCTTCCTAAATTTGGTCGTTTCGATTGGTGGTCTATTTAATACCATAT
66 TTTTAATTC-TAAAAATGCTT-TTAAATTTTGT-GTTTCGATTGACAGTCTATTTAATACCATAT
* *
6858 -ACTTTTCGATTCACATGTCCGATTAAAGTTATTCAAGTGTCAGTTAAAAGGTTATCGTATGATC
128 AACTTTTCG-TCCACATGTCCGATTAAAGTTATTCAAGTGTCAGTTAAAAGGTTATCGCATGATC
* *
6922 TACGACTTTCATGAAGAACCCGAAAG-TTAATTTGATTTACGAGTTTCATGAAGGGTTCAAAAGG
192 TACGACTTTCATGAAGAACCCGAAAGCTAAATTTGATCTACGAGTTTCATGAAGGGTTCAAAAGG
* *
6986 GAATTTTTATGTTTCAAGATCTCCATTAAGAAATATTTTCTTATTTGAATTAGTTATCAAATGAC
257 GAATTTTTATGTTTCAAGATCTCCATTAACAAACATTTTCTTATTTGAATTAGTTATCAAATGAC
* * *
7051 CCTCATACTTTTCTATTTTATGCTACTTAGTCCTTTACAAATTCTGTCTTACTCGATTTAACGTT
322 CCTCATACTTTTCTACTTTATACTACTTAGTCCTTTACAAATTCTATCTTA----ATTTAACGTT
*
7116 T-CTTTTTTTT-TTCTTTGTTCTTTTTATCTAATTAAGGTAATTCAT
383 TACTTTTTTTTATTCTTTGTTCTATTTATCTAATTAAGGTAATTCAT
* * * * *
7161 GTGTATATTAAGAGGTAATTTTATGATCTACAACTTTCATGAAAGACTCAAAAGTTAATTTTCAT
1 GTGTCTATTAAAAGGTAATTTCATGATCTACAACTTTCATGAAAGACTCAAAAG-CAATTTTAAT
* * *
7226 GTTTCAATTCTGAAAAATACTTTTGAAATTTTGTGATTTCGATTGACAATCTATTTAAT
65 GTTTTAATTCT-AAAAATGCTTTT-AAATTTTGTG-TTTCGATTGACAGTCTATTTAAT
7285 TTCATATTTT
Statistics
Matches: 478, Mismatches: 63, Indels: 28
0.84 0.11 0.05
Matches are distributed among these distances:
429 18 0.04
430 55 0.12
431 2 0.00
433 82 0.17
434 208 0.44
435 102 0.21
438 11 0.02
ACGTcount: A:0.30, C:0.14, G:0.14, T:0.42
Consensus pattern (429 bp):
GTGTCTATTAAAAGGTAATTTCATGATCTACAACTTTCATGAAAGACTCAAAAGCAATTTTAATG
TTTTAATTCTAAAAATGCTTTTAAATTTTGTGTTTCGATTGACAGTCTATTTAATACCATATAAC
TTTTCGTCCACATGTCCGATTAAAGTTATTCAAGTGTCAGTTAAAAGGTTATCGCATGATCTACG
ACTTTCATGAAGAACCCGAAAGCTAAATTTGATCTACGAGTTTCATGAAGGGTTCAAAAGGGAAT
TTTTATGTTTCAAGATCTCCATTAACAAACATTTTCTTATTTGAATTAGTTATCAAATGACCCTC
ATACTTTTCTACTTTATACTACTTAGTCCTTTACAAATTCTATCTTAATTTAACGTTTACTTTTT
TTTATTCTTTGTTCTATTTATCTAATTAAGGTAATTCAT
Found at i:9959 original size:85 final size:87
Alignment explanation
Indices: 9812--9979 Score: 268
Period size: 85 Copynumber: 2.0 Consensus size: 87
9802 GGCATTTTCA
* * * *
9812 TTCTATGAATTCTATTTCAATCATTATATGTTTGATTTTGTAACGTTATAGAATATATATGTTTT
1 TTCTATAAATTATATTTAAATCATTATATGTTTGATTTTGTAACGTTATAGAATATAAATGTTTT
9877 TCATTAAATGGAATTAATTTAG
66 TCATTAAATGGAATTAATTTAG
* *
9899 TTCTATAAATTATATTTAAATCA-T-TATGTTTGATTTTTTAACGTTATATAATATAAATGTTTT
1 TTCTATAAATTATATTTAAATCATTATATGTTTGATTTTGTAACGTTATAGAATATAAATGTTTT
9962 TCATTAAATGGAATTAAT
66 TCATTAAATGGAATTAAT
9980 ATACGGTATT
Statistics
Matches: 75, Mismatches: 6, Indels: 2
0.90 0.07 0.02
Matches are distributed among these distances:
85 54 0.72
86 1 0.01
87 20 0.27
ACGTcount: A:0.35, C:0.06, G:0.10, T:0.50
Consensus pattern (87 bp):
TTCTATAAATTATATTTAAATCATTATATGTTTGATTTTGTAACGTTATAGAATATAAATGTTTT
TCATTAAATGGAATTAATTTAG
Found at i:10397 original size:2 final size:2
Alignment explanation
Indices: 10390--10415 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
10380 TTTTTGAATA
10390 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
10416 CTTAAGTTTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:10603 original size:72 final size:72
Alignment explanation
Indices: 10486--10626 Score: 255
Period size: 72 Copynumber: 2.0 Consensus size: 72
10476 GGAACTAAAA
* *
10486 TTGCATTGTCAAGAAAAGAATGATACACATCTATAAGAATTTAGTGTTTGAGAGCAATCTTTAGA
1 TTGCATTGTCAAGAAAAGAAGGATACACATCTATAAGAATTTAGTGTTTGAGAGCAACCTTTAGA
10551 AAAATTT
66 AAAATTT
*
10558 TTGCATTGTCAAGAAAATAAGGATACACATCTATAAGAATTTAGTGTTTGAGAGCAACCTTTAGA
1 TTGCATTGTCAAGAAAAGAAGGATACACATCTATAAGAATTTAGTGTTTGAGAGCAACCTTTAGA
10623 AAAA
66 AAAA
10627 AAAATTTATC
Statistics
Matches: 66, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
72 66 1.00
ACGTcount: A:0.41, C:0.11, G:0.17, T:0.31
Consensus pattern (72 bp):
TTGCATTGTCAAGAAAAGAAGGATACACATCTATAAGAATTTAGTGTTTGAGAGCAACCTTTAGA
AAAATTT
Done.