Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010159.1 Corchorus capsularis cultivar CVL-1 contig10180, 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: 40883
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Found at i:3745 original size:16 final size:16
Alignment explanation
Indices: 3700--3752 Score: 63
Period size: 16 Copynumber: 3.3 Consensus size: 16
3690 CGAAAGAAAC
*
3700 CCGAACCTGAAAAATAT
1 CCGAACCCG-AAAATAT
*
3717 -TGAACCCGAAAATAT
1 CCGAACCCGAAAATAT
*
3732 CCGAACCCGAAAATAC
1 CCGAACCCGAAAATAT
3748 CCGAA
1 CCGAA
3753 TTCAATACTA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
15 7 0.23
16 24 0.77
ACGTcount: A:0.45, C:0.28, G:0.13, T:0.13
Consensus pattern (16 bp):
CCGAACCCGAAAATAT
Found at i:4188 original size:94 final size:94
Alignment explanation
Indices: 4084--4256 Score: 274
Period size: 94 Copynumber: 1.8 Consensus size: 94
4074 CACGAACCTA
* * *
4084 AATTTAACCTGACCTGAAATTGACCCGAATCCGAAAAACCCCGACCCAAATGCGCCCGATCTGAT
1 AATTTAACCTGACCTGAAATTGACCCAAACCCGAAAAACCCCGACCCAAATGCACCCGATCTGAT
4149 GCCATCCCGAACCCGAAATTCCGAACCCG
66 GCCATCCCGAACCCGAAATTCCGAACCCG
* * * *
4178 AATTTAACCTGACCTGAAATTGACCTAAACCCGAAAAACCCTGACCCAAATGCACCTGATTTGAT
1 AATTTAACCTGACCTGAAATTGACCCAAACCCGAAAAACCCCGACCCAAATGCACCCGATCTGAT
*
4243 GCCGTCCCGAACCC
66 GCCATCCCGAACCC
4257 AAAAATCATC
Statistics
Matches: 71, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
94 71 1.00
ACGTcount: A:0.32, C:0.35, G:0.15, T:0.18
Consensus pattern (94 bp):
AATTTAACCTGACCTGAAATTGACCCAAACCCGAAAAACCCCGACCCAAATGCACCCGATCTGAT
GCCATCCCGAACCCGAAATTCCGAACCCG
Found at i:6028 original size:2 final size:2
Alignment explanation
Indices: 6023--6050 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
6013 TTAAATACGA
6023 AT 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 AT
6051 TTTTTTGGTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:8391 original size:33 final size:34
Alignment explanation
Indices: 8337--8435 Score: 114
Period size: 33 Copynumber: 2.9 Consensus size: 34
8327 CATGTTCTAT
* * *
8337 CGGCCCTGGCCAAAGGGTTATAGTA-TCT-GGAAAA
1 CGGCCCT-GCTAACGGGTTATAGTAGT-TAGCAAAA
**
8371 CGGCCCTGCTAACGGGTTATAGTAGTTAGCTTAA
1 CGGCCCTGCTAACGGGTTATAGTAGTTAGCAAAA
8405 -GGCCCTGCTAACGGGTTATAGTAGTTAGCAA
1 CGGCCCTGCTAACGGGTTATAGTAGTTAGCAA
8436 TATGTCGATA
Statistics
Matches: 56, Mismatches: 7, Indels: 5
0.82 0.10 0.07
Matches are distributed among these distances:
33 45 0.80
34 11 0.20
ACGTcount: A:0.26, C:0.20, G:0.28, T:0.25
Consensus pattern (34 bp):
CGGCCCTGCTAACGGGTTATAGTAGTTAGCAAAA
Found at i:9060 original size:2 final size:2
Alignment explanation
Indices: 9053--9082 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
9043 AGATACATAC
9053 AT AT 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 AT AT
9083 TTGATGGAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:31371 original size:31 final size:30
Alignment explanation
Indices: 31326--31397 Score: 85
Period size: 31 Copynumber: 2.4 Consensus size: 30
31316 GCTTATTGCT
31326 CAAA-AAGCCCCCTGAACT-TACACAAAACGGC
1 CAAATAAG-CCCCTGAACTCTACA-AAAA-GGC
**
31357 CAAATAAGCCCCTGAACTCTTTAAAAAGGC
1 CAAATAAGCCCCTGAACTCTACAAAAAGGC
31387 CAAATAAGCCC
1 CAAATAAGCCC
31398 TTTTCTGATG
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
30 14 0.38
31 18 0.49
32 5 0.14
ACGTcount: A:0.42, C:0.32, G:0.12, T:0.14
Consensus pattern (30 bp):
CAAATAAGCCCCTGAACTCTACAAAAAGGC
Found at i:36580 original size:43 final size:43
Alignment explanation
Indices: 36519--36604 Score: 163
Period size: 43 Copynumber: 2.0 Consensus size: 43
36509 CCAGGGTTTT
*
36519 GCCCTGACTAATCCGGATCCGACTCGCGTCGCGCACCTAGTTA
1 GCCCTGACTAATCCGGATCCGACCCGCGTCGCGCACCTAGTTA
36562 GCCCTGACTAATCCGGATCCGACCCGCGTCGCGCACCTAGTTA
1 GCCCTGACTAATCCGGATCCGACCCGCGTCGCGCACCTAGTTA
36605 TGGTGGGTGA
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 42 1.00
ACGTcount: A:0.19, C:0.38, G:0.23, T:0.20
Consensus pattern (43 bp):
GCCCTGACTAATCCGGATCCGACCCGCGTCGCGCACCTAGTTA
Found at i:37723 original size:42 final size:42
Alignment explanation
Indices: 37647--37729 Score: 121
Period size: 42 Copynumber: 2.0 Consensus size: 42
37637 CAAAAATTGT
*** *
37647 ATTTTTCTGAAATCGTCATCAAAATACGGTACGTTATCGTTC
1 ATTTTTCTGAAATCGTCATCAAAATACAACACGTTAACGTTC
*
37689 ATTTTTCTTAAATCGTCATCAAAATACAACACGTTAACGTT
1 ATTTTTCTGAAATCGTCATCAAAATACAACACGTTAACGTT
37730 ATTCTACGTT
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 36 1.00
ACGTcount: A:0.33, C:0.19, G:0.11, T:0.37
Consensus pattern (42 bp):
ATTTTTCTGAAATCGTCATCAAAATACAACACGTTAACGTTC
Done.