Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013107.1 Corchorus olitorius cultivar O-4 contig13140, 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: 41245
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:749 original size:26 final size:25
Alignment explanation
Indices: 711--762 Score: 59
Period size: 26 Copynumber: 2.0 Consensus size: 25
701 TCATTACTAA
711 AAATAATAGAAATAAACATTAGATAT
1 AAATAATAGAAATAAAC-TTAGATAT
* * * *
737 AAATCATATAAATGAACTTATATAT
1 AAATAATAGAAATAAACTTAGATAT
762 A
1 A
763 TCTCATTGAC
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
25 8 0.36
26 14 0.64
ACGTcount: A:0.58, C:0.06, G:0.06, T:0.31
Consensus pattern (25 bp):
AAATAATAGAAATAAACTTAGATAT
Found at i:1442 original size:37 final size:37
Alignment explanation
Indices: 1398--1468 Score: 133
Period size: 37 Copynumber: 1.9 Consensus size: 37
1388 CTTGATCAAC
*
1398 ATACATGTCTTTTCATATAGACATAACTTTATGATCA
1 ATACATGTCTTTTCAAATAGACATAACTTTATGATCA
1435 ATACATGTCTTTTCAAATAGACATAACTTTATGA
1 ATACATGTCTTTTCAAATAGACATAACTTTATGA
1469 ATAATTATGT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 33 1.00
ACGTcount: A:0.37, C:0.15, G:0.08, T:0.39
Consensus pattern (37 bp):
ATACATGTCTTTTCAAATAGACATAACTTTATGATCA
Found at i:12999 original size:25 final size:24
Alignment explanation
Indices: 12965--13016 Score: 77
Period size: 25 Copynumber: 2.1 Consensus size: 24
12955 ATTAGGCGAG
12965 ACTCGTAAGGGCCATAGTTACCATC
1 ACTCGTAAGGGCCATAG-TACCATC
* *
12990 ACTCGTAAGGGTCATAGTGCCATC
1 ACTCGTAAGGGCCATAGTACCATC
13014 ACT
1 ACT
13017 AGGTGATTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
24 9 0.36
25 16 0.64
ACGTcount: A:0.27, C:0.27, G:0.21, T:0.25
Consensus pattern (24 bp):
ACTCGTAAGGGCCATAGTACCATC
Found at i:16634 original size:42 final size:44
Alignment explanation
Indices: 16587--16673 Score: 133
Period size: 45 Copynumber: 2.0 Consensus size: 44
16577 TATCTAAATG
* *
16587 CTACT-CT-ATCTCTAGGTAATTCATCAAAATAAAGCTGATATT
1 CTACTCCTCATCTCTAGATAATTCATCAAAATAAAGCTAATATT
16629 CTACTCCTCCATCTCTAGATAATTCATCAAAATAAAGCTAATATT
1 CTACTCCT-CATCTCTAGATAATTCATCAAAATAAAGCTAATATT
16674 AATTGTTGTT
Statistics
Matches: 40, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
42 5 0.12
43 2 0.05
45 33 0.82
ACGTcount: A:0.37, C:0.22, G:0.07, T:0.34
Consensus pattern (44 bp):
CTACTCCTCATCTCTAGATAATTCATCAAAATAAAGCTAATATT
Found at i:20324 original size:2 final size:2
Alignment explanation
Indices: 20317--20342 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
20307 GATAAAAATA
20317 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
20343 CTTTCAAAAG
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:27385 original size:216 final size:216
Alignment explanation
Indices: 27011--27441 Score: 835
Period size: 216 Copynumber: 2.0 Consensus size: 216
27001 TAGATGGCAA
27011 GTTTACGTGACTGGTCATAGTTTGGGTGGTGCACTAGCTACCCTGCTTGCTCTTGAGCTTTCATC
1 GTTTACGTGACTGGTCATAGTTTGGGTGGTGCACTAGCTACCCTGCTTGCTCTTGAGCTTTCATC
27076 AAGTCAATTAGCAAAGTAAGTTTCTCTCTCTCGTCACTTAAGAACGAAGTTCTTTACTTGTTCTT
66 AAGTCAATTAGCAAAGTAAGTTTCTCTCTCTCGTCACTTAAGAACGAAGTTCTTTACTTGTTCTT
* *
27141 AATGTGGTACATCCTATTCAAATAGAACCAAGTAACACACACACATTATGCTTGAAACTATTTAA
131 AATGTGGTACATCCTATTCAAATAGAACCAAGGAACACACAAACATTATGCTTGAAACTATTTAA
27206 AAGAAAACCAACATCTGTCAT
196 AAGAAAACCAACATCTGTCAT
27227 GTTTACGTGACTGGTCATAGTTTGGGTGGTGCACTAGCTACCCTGCTTGCTCTTGAGCTTTCATC
1 GTTTACGTGACTGGTCATAGTTTGGGTGGTGCACTAGCTACCCTGCTTGCTCTTGAGCTTTCATC
27292 AAGTCAATTAGCAAAGTAAGTTTCTCTCTCTCGTCACTTAAGAACGAAGTTCTTTACTTGTTCTT
66 AAGTCAATTAGCAAAGTAAGTTTCTCTCTCTCGTCACTTAAGAACGAAGTTCTTTACTTGTTCTT
27357 AATGTGGTACATCCTATTCAAATAGAACCAAGGAACACACAAACATTATGCTTGAAACTATTTAA
131 AATGTGGTACATCCTATTCAAATAGAACCAAGGAACACACAAACATTATGCTTGAAACTATTTAA
*
27422 AAGAAAACCAACATGTGTCA
196 AAGAAAACCAACATCTGTCA
27442 GTTAGAAACA
Statistics
Matches: 212, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
216 212 1.00
ACGTcount: A:0.30, C:0.21, G:0.17, T:0.32
Consensus pattern (216 bp):
GTTTACGTGACTGGTCATAGTTTGGGTGGTGCACTAGCTACCCTGCTTGCTCTTGAGCTTTCATC
AAGTCAATTAGCAAAGTAAGTTTCTCTCTCTCGTCACTTAAGAACGAAGTTCTTTACTTGTTCTT
AATGTGGTACATCCTATTCAAATAGAACCAAGGAACACACAAACATTATGCTTGAAACTATTTAA
AAGAAAACCAACATCTGTCAT
Found at i:29742 original size:60 final size:60
Alignment explanation
Indices: 29649--29768 Score: 213
Period size: 60 Copynumber: 2.0 Consensus size: 60
29639 TAGTGATATT
* * *
29649 TAGTTTGACCCTTTCCGACTTGCGCTGATGATTAAGATGTCATTAAGTTATATTTCCTTA
1 TAGTTTGACCCTTCCCGACTTGCACTGATGATTAAGATGTCAATAAGTTATATTTCCTTA
29709 TAGTTTGACCCTTCCCGACTTGCACTGATGATTAAGATGTCAATAAGTTATATTTCCTTA
1 TAGTTTGACCCTTCCCGACTTGCACTGATGATTAAGATGTCAATAAGTTATATTTCCTTA
29769 ATTAAATCCT
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
60 57 1.00
ACGTcount: A:0.25, C:0.19, G:0.16, T:0.40
Consensus pattern (60 bp):
TAGTTTGACCCTTCCCGACTTGCACTGATGATTAAGATGTCAATAAGTTATATTTCCTTA
Found at i:31180 original size:30 final size:30
Alignment explanation
Indices: 31146--31207 Score: 106
Period size: 30 Copynumber: 2.1 Consensus size: 30
31136 GTTAATAAGC
31146 CATTAAAATTTGAAGGTATAAGAGAAAAGT
1 CATTAAAATTTGAAGGTATAAGAGAAAAGT
* *
31176 CATTAAAATTTGAGGGTATAAGAGGAAAGT
1 CATTAAAATTTGAAGGTATAAGAGAAAAGT
31206 CA
1 CA
31208 AGATAAAAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.47, C:0.05, G:0.23, T:0.26
Consensus pattern (30 bp):
CATTAAAATTTGAAGGTATAAGAGAAAAGT
Found at i:32585 original size:14 final size:14
Alignment explanation
Indices: 32566--32606 Score: 57
Period size: 14 Copynumber: 2.9 Consensus size: 14
32556 GAAAGTGTTG
32566 GTTTATCGGGTATC
1 GTTTATCGGGTATC
32580 GTTTATCGGGTA-C
1 GTTTATCGGGTATC
*
32593 TTTTATCGTGGTAT
1 GTTTATCG-GGTAT
32607 GACTGATTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
13 8 0.33
14 16 0.67
ACGTcount: A:0.15, C:0.12, G:0.27, T:0.46
Consensus pattern (14 bp):
GTTTATCGGGTATC
Found at i:32617 original size:32 final size:32
Alignment explanation
Indices: 32581--32643 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
32571 TCGGGTATCG
*
32581 TTTATCGGGTACTTTTATCGTGGTATGACTGA
1 TTTATCGGGTACTTTTACCGTGGTATGACTGA
32613 TTTATCGGGTACTTTTACCGTGGTATGACTG
1 TTTATCGGGTACTTTTACCGTGGTATGACTG
32644 GTTTGAAAGT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.17, C:0.14, G:0.25, T:0.43
Consensus pattern (32 bp):
TTTATCGGGTACTTTTACCGTGGTATGACTGA
Done.