Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009689.1 Corchorus capsularis cultivar CVL-1 contig09710, 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: 18338
ACGTcount: A:0.31, C:0.22, G:0.21, T:0.26
Found at i:3703 original size:9 final size:9
Alignment explanation
Indices: 3689--3713 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
3679 AACCTAACAT
3689 TAACGTTTC
1 TAACGTTTC
3698 TAACGTTTC
1 TAACGTTTC
3707 TAACGTT
1 TAACGTT
3714 AACGCTATGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.24, C:0.20, G:0.12, T:0.44
Consensus pattern (9 bp):
TAACGTTTC
Found at i:3927 original size:72 final size:71
Alignment explanation
Indices: 3850--4005 Score: 240
Period size: 71 Copynumber: 2.2 Consensus size: 71
3840 AATCAAAGAA
* * *
3850 ATTTTTTTTTGCCAATCAAAGTTAAAGTTTAAAAGTTGAATTTAAATAAAAGTTTAAGAAGATAT
1 ATTTTTTTTT-ACAATCAAAGTTAAAGTTTAAAAGTTGAATTTAAATAAAAGTTTAAAAAGATAC
3915 ATTTTAG
65 ATTTTAG
* *
3922 ATTTTTTTTTATAATCAAAGTTAAAGTTTAAAAGTTGAATTTAAATAAATGTTTAAAAAGATACA
1 ATTTTTTTTTACAATCAAAGTTAAAGTTTAAAAGTTGAATTTAAATAAAAGTTTAAAAAGATACA
3987 TTTTAG
66 TTTTAG
3993 ATATTTCTTTTTA
1 AT-TTT-TTTTTA
4006 TATTAAATAA
Statistics
Matches: 77, Mismatches: 5, Indels: 3
0.91 0.06 0.04
Matches are distributed among these distances:
71 58 0.75
72 13 0.17
73 6 0.08
ACGTcount: A:0.41, C:0.04, G:0.10, T:0.45
Consensus pattern (71 bp):
ATTTTTTTTTACAATCAAAGTTAAAGTTTAAAAGTTGAATTTAAATAAAAGTTTAAAAAGATACA
TTTTAG
Found at i:4171 original size:6 final size:6
Alignment explanation
Indices: 4160--4212 Score: 61
Period size: 6 Copynumber: 8.5 Consensus size: 6
4150 ATTATAGAAT
* * *
4160 ATAAAG ATAAAG ATAAAG ATAAAG ATGAAAAA AAAAAG ATAAAG AGAAAG
1 ATAAAG ATAAAG ATAAAG ATAAAG AT--AAAG ATAAAG ATAAAG ATAAAG
4210 ATA
1 ATA
4213 TGATGAAAAA
Statistics
Matches: 39, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
6 35 0.90
8 4 0.10
ACGTcount: A:0.70, C:0.00, G:0.17, T:0.13
Consensus pattern (6 bp):
ATAAAG
Found at i:8341 original size:26 final size:26
Alignment explanation
Indices: 8312--8363 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
8302 TAGTTACATT
8312 TCCCCATTTGGTTGCATCTAAAAGGC
1 TCCCCATTTGGTTGCATCTAAAAGGC
8338 TCCCCATTTGGTTGCATCTAAAAGGC
1 TCCCCATTTGGTTGCATCTAAAAGGC
8364 CAAAGTAAAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.23, C:0.27, G:0.19, T:0.31
Consensus pattern (26 bp):
TCCCCATTTGGTTGCATCTAAAAGGC
Found at i:10700 original size:11 final size:11
Alignment explanation
Indices: 10673--10701 Score: 51
Period size: 10 Copynumber: 2.7 Consensus size: 11
10663 CCTCACCTGT
10673 TTTATTTTCTG
1 TTTATTTTCTG
10684 -TTATTTTCTG
1 TTTATTTTCTG
10694 TTTATTTT
1 TTTATTTT
10702 TAATGCTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
10 10 0.59
11 7 0.41
ACGTcount: A:0.10, C:0.07, G:0.07, T:0.76
Consensus pattern (11 bp):
TTTATTTTCTG
Found at i:14557 original size:75 final size:76
Alignment explanation
Indices: 14402--14747 Score: 565
Period size: 75 Copynumber: 4.6 Consensus size: 76
14392 CAAATTCTCA
* *
14402 TATAAATCATAAGCGAGGTCGAACGTCCAAGTAGACGTCACCCGCAGACGGCTGAGCGCCTAGGC
1 TATAAATCATAAGCGAGGTCGAACGTCCAAGCAGACGTCACCCGCAGACGGCTGAGCGCCTAGAC
14467 TGGTGCCCCCG
66 TGGTGCCCCCG
14478 TATAAATCATAAGCGAGGTCGAACGTCCTAA-CAGACGTCA-CCGCAGACGGCTGAGCGCCTAGA
1 TATAAATCATAAGCGAGGTCGAACGTCC-AAGCAGACGTCACCCGCAGACGGCTGAGCGCCTAGA
*
14541 CTGGTGCCCACG
65 CTGGTGCCCCCG
*
14553 TATAAATCATAAGCGAGGTCGAACGTCCAAGCAGACATCACCCGCAGACGGCTGAGCGCCTAGAC
1 TATAAATCATAAGCGAGGTCGAACGTCCAAGCAGACGTCACCCGCAGACGGCTGAGCGCCTAGAC
14618 TGGTG-CCCCG
66 TGGTGCCCCCG
14628 TATAAATCATAAGCGAGGTCGAACGTCCAAGCAGACGTCACCCGCAGACGGCTGAGCGCCTAGAC
1 TATAAATCATAAGCGAGGTCGAACGTCCAAGCAGACGTCACCCGCAGACGGCTGAGCGCCTAGAC
*
14693 TAGTGCCCCCG
66 TGGTGCCCCCG
* * * * *
14704 TAT-AATCTTAAACGAGGTTGAACGTCTAAGTAGACGTCACCCGC
1 TATAAATCATAAGCGAGGTCGAACGTCCAAGCAGACGTCACCCGC
14748 GAGAGTCTCC
Statistics
Matches: 254, Mismatches: 12, Indels: 9
0.92 0.04 0.03
Matches are distributed among these distances:
74 2 0.01
75 177 0.70
76 73 0.29
77 2 0.01
ACGTcount: A:0.28, C:0.29, G:0.26, T:0.16
Consensus pattern (76 bp):
TATAAATCATAAGCGAGGTCGAACGTCCAAGCAGACGTCACCCGCAGACGGCTGAGCGCCTAGAC
TGGTGCCCCCG
Found at i:14676 original size:151 final size:151
Alignment explanation
Indices: 14402--14747 Score: 572
Period size: 151 Copynumber: 2.3 Consensus size: 151
14392 CAAATTCTCA
*
14402 TATAAATCATAAGCGAGGTCGAACGTCCAAGTAGACGTCACCCGCAGACGGCTGAGCGCCTAGGC
1 TATAAATCATAAGCGAGGTCGAACGTCCAAGTAGACGTCACCCGCAGACGGCTGAGCGCCTAGAC
14467 TGGTGCCCCCGTATAAATCATAAGCGAGGTCGAACGTCCTAACAGACGTCACCGCAGACGGCTGA
66 TGGTGCCCCCGTATAAATCATAAGCGAGGTCGAACGTCCTAACAGACGTCACCGCAGACGGCTGA
*
14532 GCGCCTAGACTGGTGCCCACG
131 GCGCCTAGACTAGTGCCCACG
* *
14553 TATAAATCATAAGCGAGGTCGAACGTCCAAGCAGACATCACCCGCAGACGGCTGAGCGCCTAGAC
1 TATAAATCATAAGCGAGGTCGAACGTCCAAGTAGACGTCACCCGCAGACGGCTGAGCGCCTAGAC
14618 TGGTG-CCCCGTATAAATCATAAGCGAGGTCGAACGTCC-AAGCAGACGTCACCCGCAGACGGCT
66 TGGTGCCCCCGTATAAATCATAAGCGAGGTCGAACGTCCTAA-CAGACGTCA-CCGCAGACGGCT
*
14681 GAGCGCCTAGACTAGTGCCCCCG
129 GAGCGCCTAGACTAGTGCCCACG
* * * *
14704 TAT-AATCTTAAACGAGGTTGAACGTCTAAGTAGACGTCACCCGC
1 TATAAATCATAAGCGAGGTCGAACGTCCAAGTAGACGTCACCCGC
14748 GAGAGTCTCC
Statistics
Matches: 182, Mismatches: 11, Indels: 5
0.92 0.06 0.03
Matches are distributed among these distances:
149 2 0.01
150 77 0.42
151 103 0.57
ACGTcount: A:0.28, C:0.29, G:0.26, T:0.16
Consensus pattern (151 bp):
TATAAATCATAAGCGAGGTCGAACGTCCAAGTAGACGTCACCCGCAGACGGCTGAGCGCCTAGAC
TGGTGCCCCCGTATAAATCATAAGCGAGGTCGAACGTCCTAACAGACGTCACCGCAGACGGCTGA
GCGCCTAGACTAGTGCCCACG
Done.