Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007004.1 Corchorus capsularis cultivar CVL-1 contig07025, 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: 12412
ACGTcount: A:0.32, C:0.20, G:0.17, T:0.32
Found at i:5265 original size:10 final size:10
Alignment explanation
Indices: 5250--5274 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
5240 AAACAAACAC
5250 CAAAATTCCA
1 CAAAATTCCA
5260 CAAAATTCCA
1 CAAAATTCCA
5270 CAAAA
1 CAAAA
5275 ATCAAACAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.56, C:0.28, G:0.00, T:0.16
Consensus pattern (10 bp):
CAAAATTCCA
Found at i:5842 original size:29 final size:30
Alignment explanation
Indices: 5803--5872 Score: 88
Period size: 29 Copynumber: 2.4 Consensus size: 30
5793 ACCGAACCGT
* ***
5803 CAAATAAGCCCCTGAACTATTATTTC-GGC
1 CAAATAAGCCCCCGAACTATTAAAACAGGC
*
5832 CAAATAAGCCCCCGAACTCTTAAAACAGGC
1 CAAATAAGCCCCCGAACTATTAAAACAGGC
5862 CAAATAAGCCC
1 CAAATAAGCCC
5873 TATTGCCAAG
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
29 21 0.60
30 14 0.40
ACGTcount: A:0.37, C:0.31, G:0.13, T:0.19
Consensus pattern (30 bp):
CAAATAAGCCCCCGAACTATTAAAACAGGC
Found at i:6181 original size:32 final size:32
Alignment explanation
Indices: 6145--6208 Score: 128
Period size: 32 Copynumber: 2.0 Consensus size: 32
6135 TGATTTTCAA
6145 TTGAAATAGAAGACGCCGCTATTTCGCGGCGT
1 TTGAAATAGAAGACGCCGCTATTTCGCGGCGT
6177 TTGAAATAGAAGACGCCGCTATTTCGCGGCGT
1 TTGAAATAGAAGACGCCGCTATTTCGCGGCGT
6209 CTGTCACTTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (32 bp):
TTGAAATAGAAGACGCCGCTATTTCGCGGCGT
Found at i:6255 original size:31 final size:31
Alignment explanation
Indices: 6154--6260 Score: 108
Period size: 31 Copynumber: 3.4 Consensus size: 31
6144 ATTGAAATAG
* ** **
6154 AAGACGCCGCTATTTCGCGGCGTTTGAAATAG
1 AAGACGCCGCTATTTCGCGGCGTCTGTCA-CC
*
6186 AAGACGCCGCTATTTCGCGGCGTCTGTCACT
1 AAGACGCCGCTATTTCGCGGCGTCTGTCACC
* * *
6217 TACACGCCGCTATTTTGCGGCGTCTAG-CACC
1 AAGACGCCGCTATTTCGCGGCGTCT-GTCACC
6248 AAGACGCCGCTAT
1 AAGACGCCGCTAT
6261 ATTTTATAGC
Statistics
Matches: 63, Mismatches: 11, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
31 36 0.57
32 27 0.43
ACGTcount: A:0.21, C:0.30, G:0.25, T:0.24
Consensus pattern (31 bp):
AAGACGCCGCTATTTCGCGGCGTCTGTCACC
Found at i:6425 original size:31 final size:31
Alignment explanation
Indices: 6356--6430 Score: 89
Period size: 31 Copynumber: 2.4 Consensus size: 31
6346 TTTGAAAAAG
*
6356 AAGACGCCGCTATTTCACGGCGTCTTACACT
1 AAGACGCCGCTATTTCACGGCGTCTTACACC
* * **
6387 TACACGCCGCTATTTTGCGGCGTC-TAGCACC
1 AAGACGCCGCTATTTCACGGCGTCTTA-CACC
6418 AAGACGCCGCTAT
1 AAGACGCCGCTAT
6431 ATTTTATAGC
Statistics
Matches: 36, Mismatches: 7, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
30 2 0.06
31 34 0.94
ACGTcount: A:0.21, C:0.33, G:0.21, T:0.24
Consensus pattern (31 bp):
AAGACGCCGCTATTTCACGGCGTCTTACACC
Found at i:6454 original size:170 final size:169
Alignment explanation
Indices: 6172--6510 Score: 599
Period size: 170 Copynumber: 2.0 Consensus size: 169
6162 GCTATTTCGC
* *
6172 GGCGTTTGAAATAGAAGACGCCGCTATTTCGCGGCGTCTGTCACTTACACGCCGCTATTTTGCGG
1 GGCGTTTGAAAAAGAAGACGCCGCTATTTCACGGCGTCTGTCACTTACACGCCGCTATTTTGCGG
6237 CGTCTAGCACCAAGACGCCGCTATATTTTATAGCCGTGTAGTTGTAAATTTTTCTTTGTTTTAGG
66 CGTCTAGCACCAAGACGCCGCTATATTTTATAGCCGTGTAGTTGTAAATTTTTCTTTGTTTTAGG
* *
6302 GGAGGGAATTTTTCCCTCCAACAAAAAGGGAAAACAAAAT
131 GGAGGGAATTTTTCCCTCCAA-AAAAAGGAAAAAAAAAAT
6342 GGCGTTTGAAAAAGAAGACGCCGCTATTTCACGGCGTCT-TACACTTACACGCCGCTATTTTGCG
1 GGCGTTTGAAAAAGAAGACGCCGCTATTTCACGGCGTCTGT-CACTTACACGCCGCTATTTTGCG
*
6406 GCGTCTAGCACCAAGACGCCGCTATATTTTATAGCCGTGTTGTTGTAAATTTTTCTTTGTTTTAG
65 GCGTCTAGCACCAAGACGCCGCTATATTTTATAGCCGTGTAGTTGTAAATTTTTCTTTGTTTTAG
*
6471 GGGAGTGAATTTTTCCCTCCAAAAAAAGGAAAAAAAAAAT
130 GGGAGGGAATTTTTCCCTCCAAAAAAAGGAAAAAAAAAAT
6511 CTCTCCCTCC
Statistics
Matches: 162, Mismatches: 6, Indels: 3
0.95 0.04 0.02
Matches are distributed among these distances:
169 17 0.10
170 145 0.90
ACGTcount: A:0.27, C:0.21, G:0.22, T:0.30
Consensus pattern (169 bp):
GGCGTTTGAAAAAGAAGACGCCGCTATTTCACGGCGTCTGTCACTTACACGCCGCTATTTTGCGG
CGTCTAGCACCAAGACGCCGCTATATTTTATAGCCGTGTAGTTGTAAATTTTTCTTTGTTTTAGG
GGAGGGAATTTTTCCCTCCAAAAAAAGGAAAAAAAAAAT
Found at i:12233 original size:13 final size:13
Alignment explanation
Indices: 12215--12239 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
12205 ACATGCATTA
12215 AAAACGGACATGT
1 AAAACGGACATGT
12228 AAAACGGACATG
1 AAAACGGACATG
12240 AATATGATCA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.16, G:0.24, T:0.12
Consensus pattern (13 bp):
AAAACGGACATGT
Done.