Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013487.1 Corchorus capsularis cultivar CVL-1 contig13508, 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: 24213
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:7262 original size:14 final size:13
Alignment explanation
Indices: 7232--7289 Score: 62
Period size: 14 Copynumber: 4.3 Consensus size: 13
7222 TGAGACACAT
**
7232 TTTTCAAAAAATA
1 TTTTCAAAAAAGG
7245 TTTTCAAGAAAAGG
1 TTTTCAA-AAAAGG
*
7259 TTTTCAAAAATGAG
1 TTTTCAAAAAAG-G
*
7273 TTTCCAAAAAAGG
1 TTTTCAAAAAAGG
7286 TTTT
1 TTTT
7290 TAGTTTTTTT
Statistics
Matches: 37, Mismatches: 6, Indels: 4
0.79 0.13 0.09
Matches are distributed among these distances:
13 15 0.41
14 22 0.59
ACGTcount: A:0.43, C:0.09, G:0.12, T:0.36
Consensus pattern (13 bp):
TTTTCAAAAAAGG
Found at i:7264 original size:27 final size:27
Alignment explanation
Indices: 7232--7289 Score: 75
Period size: 27 Copynumber: 2.1 Consensus size: 27
7222 TGAGACACAT
*
7232 TTTTCAAAAAAT-A-TTTTCAAGAAAAGG
1 TTTTC-AAAAATGAGTTTCCAA-AAAAGG
7259 TTTTCAAAAATGAGTTTCCAAAAAAGG
1 TTTTCAAAAATGAGTTTCCAAAAAAGG
7286 TTTT
1 TTTT
7290 TAGTTTTTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
26 6 0.21
27 16 0.57
28 6 0.21
ACGTcount: A:0.43, C:0.09, G:0.12, T:0.36
Consensus pattern (27 bp):
TTTTCAAAAATGAGTTTCCAAAAAAGG
Found at i:7591 original size:12 final size:12
Alignment explanation
Indices: 7576--7610 Score: 61
Period size: 12 Copynumber: 2.9 Consensus size: 12
7566 CATCAAATAA
7576 TTCAAATCAAAG
1 TTCAAATCAAAG
*
7588 TTCAAATCAGAG
1 TTCAAATCAAAG
7600 TTCAAATCAAA
1 TTCAAATCAAA
7611 AGTGAATGAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.49, C:0.17, G:0.09, T:0.26
Consensus pattern (12 bp):
TTCAAATCAAAG
Found at i:9619 original size:528 final size:527
Alignment explanation
Indices: 8222--9944 Score: 2900
Period size: 528 Copynumber: 3.3 Consensus size: 527
8212 ACTTCTTTCG
*
8222 ATACGGTGACTTTTTAATAGTTGATAATTTGTTAAGTAGTCATATTGTTAATTTTTTTTCTATCT
1 ATACGGTGACTTTTTAATAG-TGATAATTTGTTAAGTAGACATATTGTTAATTTTTTTTCTATCT
* * *
8287 ATAATTAATATTTGTTTCATTGTTAGCAAGTCACGAAATGACCTTTACTT-AACGTCTACATAAA
65 ATAATTAATATTTGTTTCATTGTTAGCAAGTCACGAAATGACCTCTATTTCAACATCTACATAAA
* ** * *
8351 TGGCTTGACTTCAGCAGCCTAATGCGTGGGTTGGCTACTGCATATTACAAGGATTTTGCGGTGAA
130 TGGATTGACTTGTGCAACCTAATGCATGGGTTGGCTACTGCATATTACAAGG-TTTTGCGGTGAA
* * * * * *
8416 TGCTTCCTTTTCCACCAAAGAGCTAACTGTTCAGATTGGTTCATTGAATCAGGATACCGCTATGA
194 TGCTTCCTTTTCCACCAACGGGCTAACTGTTTAGATTGATCCATTGAATCAGGATACCGCTACGA
* * * **
8481 CTAATGCAATATTGAACTTGTCCAATTGTAT-TTTTTTTTATCACATCAGCTATACACCAAAAGT
259 CTAATGCAGTATTGAACTTGTCCAATTGAATATTATTTTTATTGCATCAGCTATACACCAAAAGT
* *
8545 TCAAAAATAGTCTCATTATCGTGTAAAACACCTCATAAATTTTTTTTAACATATCAATAAATCAA
324 TCAAAAATAGTCTCATTATCGCGTAAAACACCTCATAAAATTTTTTTAACATATCAATAAATCAA
*
8610 TAAAAAATTTGTTATAAATATCTAAGGGTCCGCAACCACTATTTTTTTGTTTATCTTATATGATA
389 TAAAAAATTTGTTATAAATATCTAAGGGCCCGCAACCACTATTTTTTTGTTTATCTTATATGATA
*
8675 TCAGAGTCAACATATTTATTTTAAACCATGTATGCTTAGTATATTGATGATCAACTCGGTAAATA
454 TCAGAGTCAACATATTTATTTTAAGCCATGTATGCTTAGTATATTGATGATCAACTCGGTAAATA
8740 TTCCTTATA
519 TTCCTTATA
*
8749 ATACGGTGACTTTTTAATAGGTGATAATTTGTTAAGTAGAGATATTGTTAATTTTTTTTCTATCT
1 ATACGGTGACTTTTTAATA-GTGATAATTTGTTAAGTAGACATATTGTTAATTTTTTTTCTATCT
* * **
8814 ATAATT-ATATTTGTTTCATTATTAGCAAGTCACGAAATGACCTCTATTTTAACATAAACATAAA
65 ATAATTAATATTTGTTTCATTGTTAGCAAGTCACGAAATGACCTCTATTTCAACATCTACATAAA
* * * *
8878 TGGAATGACTTGTGCAATCTAATGCATGGGTTGGCTACTGCATATTACAACGTATTGCGGTGAAT
130 TGGATTGACTTGTGCAACCTAATGCATGGGTTGGCTACTGCATATTACAAGGTTTTGCGGTGAAT
* * *
8943 TCTTCCTTTTCCTCCAACGGCCTAACTGTTTAGATTGATCCATTGAATCAGGATACCGCTACGAC
195 GCTTCCTTTTCCACCAACGGGCTAACTGTTTAGATTGATCCATTGAATCAGGATACCGCTACGAC
9008 TAATGCAGTATTGAACTTGTCCAATTGAATATTATTTTTATTGCATCAGCTATACACCAAAAGTT
260 TAATGCAGTATTGAACTTGTCCAATTGAATATTATTTTTATTGCATCAGCTATACACCAAAAGTT
* * *
9073 TAAAAATAGTCTCATTATCGCGTAAAACACATCATAAAATTTCTTTAACATATCAATAAATCAAT
325 CAAAAATAGTCTCATTATCGCGTAAAACACCTCATAAAATTTTTTTAACATATCAATAAATCAAT
*
9138 AAAAAATTTGTTATAAATATCTAAGGCCCCGCAACCACTATTTTTTTGTTTATCTTATATGATAT
390 AAAAAATTTGTTATAAATATCTAAGGGCCCGCAACCACTATTTTTTTGTTTATCTTATATGATAT
*
9203 CAGAGTCAACATATTTATTTTAAGTCATGTATGCTTAGTATATTGATGATCAACTCGGTAAATAT
455 CAGAGTCAACATATTTATTTTAAGCCATGTATGCTTAGTATATTGATGATCAACTCGGTAAATAT
* * *
9268 ACCATATT
520 TCCTTATA
*
9276 ATACGGTGACTTTTTAATATGTAATAATTTGTTAAGTAGACATATTGTTAATTTTTTTTCTATCT
1 ATACGGTGACTTTTTAATA-GTGATAATTTGTTAAGTAGACATATTGTTAATTTTTTTTCTATCT
*
9341 ATAATTAGTATTTGTTTCATTGTTAGCAAGTCACGAAATGACCTCTATTTCAACATCTACATAAA
65 ATAATTAATATTTGTTTCATTGTTAGCAAGTCACGAAATGACCTCTATTTCAACATCTACATAAA
*
9406 TGGATTGACTTGTGCAACCTAATGCATAGGTTGGCTACTGCATATTACAAGGTTTTGCGGTGAAT
130 TGGATTGACTTGTGCAACCTAATGCATGGGTTGGCTACTGCATATTACAAGGTTTTGCGGTGAAT
* * *
9471 GCTTCCTTTTCCACCAACGGGCTAACTATTTAGATTGATCCATTGAATCATGATACTGCTACGAC
195 GCTTCCTTTTCCACCAACGGGCTAACTGTTTAGATTGATCCATTGAATCAGGATACCGCTACGAC
9536 TAATGCAGTATTGAACTTGTCCAATTGAATATTATTTTTATTGCATCAGCTATACACCAAAAGTT
260 TAATGCAGTATTGAACTTGTCCAATTGAATATTATTTTTATTGCATCAGCTATACACCAAAAGTT
9601 CAAAAATAGTCTCATTATCGCGTAAAACACCTCAT-AAATTTTTTTAAACATATCAATAAATCAA
325 CAAAAATAGTCTCATTATCGCGTAAAACACCTCATAAAATTTTTTT-AACATATCAATAAATCAA
9665 TAAAAAATTTGTTATAAATATCTAAGGGCCCGCAACCACTATTTTTTTGTTTATCTTATATGATA
389 TAAAAAATTTGTTATAAATATCTAAGGGCCCGCAACCACTATTTTTTTGTTTATCTTATATGATA
9730 TCAGAGTCAACATATTTATTTTAAGCCATGTATGCTTAGTATATTGATGATCAACTCGGTAAATA
454 TCAGAGTCAACATATTTATTTTAAGCCATGTATGCTTAGTATATTGATGATCAACTCGGTAAATA
9795 TTCCTTATA
519 TTCCTTATA
9804 ATACGGTGACTTTTTAATAAGTGATAATTTGTTAAGTAGACATATTGTTAA-TTTTTTT-TATCT
1 ATACGGTGACTTTTTAAT-AGTGATAATTTGTTAAGTAGACATATTGTTAATTTTTTTTCTATCT
9867 ATAATTAATATTTGTTTCATTGTTAGCAAGTCACGAAATGACCTCTATTTCAACATCTACATAAA
65 ATAATTAATATTTGTTTCATTGTTAGCAAGTCACGAAATGACCTCTATTTCAACATCTACATAAA
9932 TGGATTGACTTGT
130 TGGATTGACTTGT
9945 TGGTCCTGAA
Statistics
Matches: 1118, Mismatches: 72, Indels: 13
0.93 0.06 0.01
Matches are distributed among these distances:
526 218 0.19
527 428 0.38
528 471 0.42
529 1 0.00
ACGTcount: A:0.32, C:0.16, G:0.13, T:0.39
Consensus pattern (527 bp):
ATACGGTGACTTTTTAATAGTGATAATTTGTTAAGTAGACATATTGTTAATTTTTTTTCTATCTA
TAATTAATATTTGTTTCATTGTTAGCAAGTCACGAAATGACCTCTATTTCAACATCTACATAAAT
GGATTGACTTGTGCAACCTAATGCATGGGTTGGCTACTGCATATTACAAGGTTTTGCGGTGAATG
CTTCCTTTTCCACCAACGGGCTAACTGTTTAGATTGATCCATTGAATCAGGATACCGCTACGACT
AATGCAGTATTGAACTTGTCCAATTGAATATTATTTTTATTGCATCAGCTATACACCAAAAGTTC
AAAAATAGTCTCATTATCGCGTAAAACACCTCATAAAATTTTTTTAACATATCAATAAATCAATA
AAAAATTTGTTATAAATATCTAAGGGCCCGCAACCACTATTTTTTTGTTTATCTTATATGATATC
AGAGTCAACATATTTATTTTAAGCCATGTATGCTTAGTATATTGATGATCAACTCGGTAAATATT
CCTTATA
Found at i:13055 original size:42 final size:42
Alignment explanation
Indices: 12979--13090 Score: 147
Period size: 42 Copynumber: 2.7 Consensus size: 42
12969 GTCAAATGGT
* * *
12979 CGGTTGTGGCCGGATGGC-CCGTGAGATGTCCCATGCGTTGGC
1 CGGTTGTGGCCGG-TTGCTCCATGCGATGTCCCATGCGTTGGC
13021 CGGTTGTGGCCGGTTGCTCCATGCGATG-CTCCATGCGTTGGC
1 CGGTTGTGGCCGGTTGCTCCATGCGATGTC-CCATGCGTTGGC
**
13063 CGGTCATGGCCGGTTGCTCCATGCGATG
1 CGGTTGTGGCCGGTTGCTCCATGCGATG
13091 GTAGTCGGTC
Statistics
Matches: 63, Mismatches: 5, Indels: 4
0.88 0.07 0.06
Matches are distributed among these distances:
41 4 0.06
42 59 0.94
ACGTcount: A:0.09, C:0.28, G:0.38, T:0.26
Consensus pattern (42 bp):
CGGTTGTGGCCGGTTGCTCCATGCGATGTCCCATGCGTTGGC
Found at i:19918 original size:23 final size:23
Alignment explanation
Indices: 19890--19934 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
19880 TAAACCACCA
*
19890 AAAGAGTATTAACTTGTTTTCCC
1 AAAGAGTATGAACTTGTTTTCCC
19913 AAAGAGTATGAACTTGTTTTCC
1 AAAGAGTATGAACTTGTTTTCC
19935 ACAGGACCAC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.38
Consensus pattern (23 bp):
AAAGAGTATGAACTTGTTTTCCC
Found at i:23402 original size:25 final size:25
Alignment explanation
Indices: 23353--23403 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 25
23343 TTAGTAGAAT
*
23353 AATTGTAAAAGTTTATTTCTAAAAA
1 AATTGTAAAAGTATATTTCTAAAAA
23378 AATTGTAAAAGAATATATTT-TAAAAA
1 AATTGTAAAAG--TATATTTCTAAAAA
23404 TTCTAATATG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
25 11 0.48
26 6 0.26
27 6 0.26
ACGTcount: A:0.53, C:0.02, G:0.08, T:0.37
Consensus pattern (25 bp):
AATTGTAAAAGTATATTTCTAAAAA
Done.