Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012428.1 Corchorus capsularis cultivar CVL-1 contig12449, 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: 42576
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:4039 original size:12 final size:12
Alignment explanation
Indices: 4024--4049 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
4014 CAAATTTACC
4024 TTTTTTCTTTTT
1 TTTTTTCTTTTT
4036 TTTTTTCTTTTT
1 TTTTTTCTTTTT
4048 TT
1 TT
4050 CTCTCTGGGT
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:0.00, C:0.08, G:0.00, T:0.92
Consensus pattern (12 bp):
TTTTTTCTTTTT
Found at i:9321 original size:56 final size:57
Alignment explanation
Indices: 9254--9367 Score: 221
Period size: 57 Copynumber: 2.0 Consensus size: 57
9244 AATAAAGTAA
9254 GAAACAGAGTGATGATCAG-AACAGAGCACACTCTGTTTTGCCAAAGGCCAAATATT
1 GAAACAGAGTGATGATCAGAAACAGAGCACACTCTGTTTTGCCAAAGGCCAAATATT
9310 GAAACAGAGTGATGATCAGAAACAGAGCACACTCTGTTTTGCCAAAGGCCAAATATT
1 GAAACAGAGTGATGATCAGAAACAGAGCACACTCTGTTTTGCCAAAGGCCAAATATT
9367 G
1 G
9368 GTGTGAAGTG
Statistics
Matches: 57, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
56 19 0.33
57 38 0.67
ACGTcount: A:0.38, C:0.19, G:0.22, T:0.21
Consensus pattern (57 bp):
GAAACAGAGTGATGATCAGAAACAGAGCACACTCTGTTTTGCCAAAGGCCAAATATT
Found at i:20014 original size:32 final size:32
Alignment explanation
Indices: 19971--20034 Score: 110
Period size: 32 Copynumber: 2.0 Consensus size: 32
19961 CTCAAATATA
*
19971 GGTAAGGTTTGGGCTCAATGGCCCAAAAGAAG
1 GGTAAGATTTGGGCTCAATGGCCCAAAAGAAG
*
20003 GGTAAGATTTGGGCTGAATGGCCCAAAAGAAG
1 GGTAAGATTTGGGCTCAATGGCCCAAAAGAAG
20035 AAATGGGTGA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.33, C:0.14, G:0.34, T:0.19
Consensus pattern (32 bp):
GGTAAGATTTGGGCTCAATGGCCCAAAAGAAG
Found at i:27495 original size:60 final size:60
Alignment explanation
Indices: 27402--27560 Score: 219
Period size: 60 Copynumber: 2.6 Consensus size: 60
27392 GCTAATTGTT
* * * * * * * *
27402 CAAATAAGGGCTTAACGTTTGACAAAATACTCAAATAAGGGTCTGATCTTTTAATTTGGC
1 CAAATAAGGGCATAAAGTTTGCCAAAATGCTCAAATAAGGGCCCGATCTTTGAATTTGAC
* *
27462 CAAATAAGGGCCTAAAGTTTGCCAAAATGCTCAAAAAAGGGCCCGATCTTTGAATTTGAC
1 CAAATAAGGGCATAAAGTTTGCCAAAATGCTCAAATAAGGGCCCGATCTTTGAATTTGAC
*
27522 CAAATAAGGGCATAATGTTTGCCAAAATGCTCAAATAAG
1 CAAATAAGGGCATAAAGTTTGCCAAAATGCTCAAATAAG
27561 AGCCTATCTC
Statistics
Matches: 87, Mismatches: 12, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
60 87 1.00
ACGTcount: A:0.38, C:0.17, G:0.19, T:0.26
Consensus pattern (60 bp):
CAAATAAGGGCATAAAGTTTGCCAAAATGCTCAAATAAGGGCCCGATCTTTGAATTTGAC
Found at i:27560 original size:31 final size:31
Alignment explanation
Indices: 27401--27566 Score: 101
Period size: 31 Copynumber: 5.5 Consensus size: 31
27391 GGCTAATTGT
* * * *
27401 TCAAATAAGGGCTTAACGTTTGACAAAATAC
1 TCAAATAAGGGCCTAATGTTTGCCAAAATGC
* * * * **
27432 TCAAATAAGGGTCTGATCTTT--TAATTTGGC
1 TCAAATAAGGGCCTAATGTTTGCCAAAAT-GC
*
27462 -CAAATAAGGGCCTAAAGTTTGCCAAAATGC
1 TCAAATAAGGGCCTAATGTTTGCCAAAATGC
* ** * **
27492 TCAAAAAAGGGCCCGATCTTTG--AATTTGAC
1 TCAAATAAGGGCCTAATGTTTGCCAAAATG-C
*
27522 -CAAATAAGGGCATAATGTTTGCCAAAATGC
1 TCAAATAAGGGCCTAATGTTTGCCAAAATGC
*
27552 TCAAATAAGAGCCTA
1 TCAAATAAGGGCCTA
27567 TCTCACGCGT
Statistics
Matches: 95, Mismatches: 32, Indels: 16
0.66 0.22 0.11
Matches are distributed among these distances:
29 39 0.41
30 5 0.05
31 51 0.54
ACGTcount: A:0.37, C:0.17, G:0.19, T:0.27
Consensus pattern (31 bp):
TCAAATAAGGGCCTAATGTTTGCCAAAATGC
Found at i:27636 original size:31 final size:30
Alignment explanation
Indices: 27598--27728 Score: 124
Period size: 31 Copynumber: 4.3 Consensus size: 30
27588 ACATCAGGTT
27598 CTTATTTGAGCATTTTCGATAACGTTAGGCC
1 CTTATTTGAGCATTTT-GATAACGTTAGGCC
27629 CTTATTTGAGCATATTTGATAACGTTAGGCC
1 CTTATTTGAGCAT-TTTGATAACGTTAGGCC
* * * * *
27660 CTTATTTG-GCCATATT-A-AAAGATCGAGTC
1 CTTATTTGAG-CATTTTGATAACGTTAG-GCC
* * *
27689 CTTATTTGAGTATTTTCAATAACGTTAAGCC
1 CTTATTTGAGCATTTT-GATAACGTTAGGCC
27720 CTTATTTGA
1 CTTATTTGA
27729 CAAAATTAAA
Statistics
Matches: 81, Mismatches: 12, Indels: 14
0.76 0.11 0.13
Matches are distributed among these distances:
28 5 0.06
29 15 0.19
30 4 0.05
31 50 0.62
32 7 0.09
ACGTcount: A:0.27, C:0.17, G:0.17, T:0.40
Consensus pattern (30 bp):
CTTATTTGAGCATTTTGATAACGTTAGGCC
Found at i:27698 original size:60 final size:58
Alignment explanation
Indices: 27628--27788 Score: 187
Period size: 60 Copynumber: 2.7 Consensus size: 58
27618 AACGTTAGGC
* * * * *
27628 CCTTATTTGAGCATATTTGATAACGTTAGGCCCTTATTTGGCCATATTAAAAGATCGAGT
1 CCTTATTTGAGCAT-TTTGATAACGTTAAGCCCTTATTTGACAAAATTAAAAGATCG-GA
* *
27688 CCTTATTTGAGTATTTTCAATAACGTTAAGCCCTTATTTGACAAAATTAAAAGATCGGA
1 CCTTATTTGAGCATTTT-GATAACGTTAAGCCCTTATTTGACAAAATTAAAAGATCGGA
* * *
27747 CTCTTATTTGAGCATTTTGACAAACGTTAAACCATTATTTGA
1 C-CTTATTTGAGCATTTTGA-TAACGTTAAGCCCTTATTTGA
27789 GCAATTAGCC
Statistics
Matches: 86, Mismatches: 12, Indels: 6
0.83 0.12 0.06
Matches are distributed among these distances:
59 6 0.07
60 80 0.93
ACGTcount: A:0.32, C:0.16, G:0.15, T:0.37
Consensus pattern (58 bp):
CCTTATTTGAGCATTTTGATAACGTTAAGCCCTTATTTGACAAAATTAAAAGATCGGA
Found at i:36317 original size:5 final size:5
Alignment explanation
Indices: 36307--36341 Score: 70
Period size: 5 Copynumber: 7.0 Consensus size: 5
36297 CAAGTTCATC
36307 AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG
1 AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG
36342 TATTCTTAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 30 1.00
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (5 bp):
AAAAG
Done.