Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01005737.1 Corchorus capsularis cultivar CVL-1 contig05755, 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: 4784
ACGTcount: A:0.29, C:0.16, G:0.21, T:0.34
Found at i:2294 original size:37 final size:37
Alignment explanation
Indices: 2247--2378 Score: 201
Period size: 37 Copynumber: 3.6 Consensus size: 37
2237 TGGTATTTCG
*
2247 TTGGATTTGAGCCCGAGGCTCTCTTATTGATATTTGT
1 TTGGACTTGAGCCCGAGGCTCTCTTATTGATATTTGT
** ** *
2284 TTGGACTTGAGCCCGAGGCTCAGTGGTTGATTTTTGT
1 TTGGACTTGAGCCCGAGGCTCTCTTATTGATATTTGT
*
2321 TTGGACTTGAGCCCGAGGCTCTCTTATTGATATTGGT
1 TTGGACTTGAGCCCGAGGCTCTCTTATTGATATTTGT
2358 TTGGACTTGAGCCCGAGGCTC
1 TTGGACTTGAGCCCGAGGCTC
2379 AGTGGTTGAT
Statistics
Matches: 83, Mismatches: 12, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
37 83 1.00
ACGTcount: A:0.15, C:0.19, G:0.29, T:0.37
Consensus pattern (37 bp):
TTGGACTTGAGCCCGAGGCTCTCTTATTGATATTTGT
Found at i:2340 original size:74 final size:74
Alignment explanation
Indices: 2247--2416 Score: 286
Period size: 74 Copynumber: 2.3 Consensus size: 74
2237 TGGTATTTCG
*
2247 TTGGATTTGAGCCCGAGGCTCTCTTATTGATATTTGTTTGGACTTGAGCCCGAGGCTCAGTGGTT
1 TTGGATTTGAGCCCGAGGCTCTCTTATTGATATTGGTTTGGACTTGAGCCCGAGGCTCAGTGGTT
** *
2312 GATTTTTGT
66 GATGATTGC
*
2321 TTGGACTTGAGCCCGAGGCTCTCTTATTGATATTGGTTTGGACTTGAGCCCGAGGCTCAGTGGTT
1 TTGGATTTGAGCCCGAGGCTCTCTTATTGATATTGGTTTGGACTTGAGCCCGAGGCTCAGTGGTT
2386 GATGATTGC
66 GATGATTGC
*
2395 TTGGATTTGAGCCTGAGGCTCT
1 TTGGATTTGAGCCCGAGGCTCT
2417 TTTTGCTGTT
Statistics
Matches: 89, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
74 89 1.00
ACGTcount: A:0.15, C:0.18, G:0.30, T:0.37
Consensus pattern (74 bp):
TTGGATTTGAGCCCGAGGCTCTCTTATTGATATTGGTTTGGACTTGAGCCCGAGGCTCAGTGGTT
GATGATTGC
Found at i:2388 original size:37 final size:37
Alignment explanation
Indices: 2247--2415 Score: 196
Period size: 37 Copynumber: 4.6 Consensus size: 37
2237 TGGTATTTCG
* * *
2247 TTGGATTTGAGCCCGAGGCTCTCTTATTGATATTTGT
1 TTGGACTTGAGCCCGAGGCTCACTGATTGATATTTGT
* * *
2284 TTGGACTTGAGCCCGAGGCTCAGTGGTTGATTTTTGT
1 TTGGACTTGAGCCCGAGGCTCACTGATTGATATTTGT
* * *
2321 TTGGACTTGAGCCCGAGGCTCTCTTATTGATATTGGT
1 TTGGACTTGAGCCCGAGGCTCACTGATTGATATTTGT
* * *
2358 TTGGACTTGAGCCCGAGGCTCAGTGGTTGATGA-TTGC
1 TTGGACTTGAGCCCGAGGCTCACTGATTGAT-ATTTGT
* *
2395 TTGGATTTGAGCCTGAGGCTC
1 TTGGACTTGAGCCCGAGGCTC
2416 TTTTTGCTGT
Statistics
Matches: 111, Mismatches: 20, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
37 110 0.99
38 1 0.01
ACGTcount: A:0.15, C:0.18, G:0.30, T:0.37
Consensus pattern (37 bp):
TTGGACTTGAGCCCGAGGCTCACTGATTGATATTTGT
Found at i:2756 original size:59 final size:58
Alignment explanation
Indices: 2653--2765 Score: 154
Period size: 59 Copynumber: 1.9 Consensus size: 58
2643 GCAACATGCC
* *
2653 TCGGTCCTAAAATGTCTTTTTTAGGCATCTAATAAAAAAACATGTCACTCGATAAGCA
1 TCGGTCATAAAACGTCTTTTTTAGGCATCTAATAAAAAAACATGTCACTCGATAAGCA
* * * * *
2711 TCGGTCATAAAACGTCTTTTATTATGTATCTAATAGAAAAACATGTTACTTGATA
1 TCGGTCATAAAACGTCTTTT-TTAGGCATCTAATAAAAAAACATGTCACTCGATA
2766 TTTGATTAAT
Statistics
Matches: 47, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
58 18 0.38
59 29 0.62
ACGTcount: A:0.36, C:0.16, G:0.13, T:0.35
Consensus pattern (58 bp):
TCGGTCATAAAACGTCTTTTTTAGGCATCTAATAAAAAAACATGTCACTCGATAAGCA
Found at i:4616 original size:201 final size:201
Alignment explanation
Indices: 4270--4668 Score: 710
Period size: 200 Copynumber: 2.0 Consensus size: 201
4260 AGTAACATGC
* *
4270 CCCAGCCAGCAAGGTCAAACCGAACAGGTCTGGTCAAACCGGGCCGGTTCGAGTTTTTCAGATCG
1 CCCAGCCAGCAAGGTCAAACCGAACAGGTCTGGTCAAACCGGGCCGGTTCGAGTTTGTCAGACCG
*
4335 GACCGAACCGGTCCAAAAAATAAAATAATTGAAATTTCGATTTTACCCCCTAAGCTTGTTTCGGA
66 GACCGAACCGGTCCAAAAAATAAAATAATTGAAATTCCGATTTTACCCCCTAAGCTTGTTTCGGA
4400 CCCCGGAATGACTAAATTG-CCCCCAGAAAGTCAGAATTGGTTAAAGAACCGTACTTACGGGACA
131 CCCCGGAATGACTAAATTGCCCCCCAGAAAGTCAGAATTGGTTAAAGAACCGTACTTACGGGACA
4464 ATATGG
196 ATATGG
* * *
4470 CCCAGCCAGCAAGGTCAGACCGGACTGGTCTGGTCAAACCGGGCCGGTTCGAGTTTGTCAGACCG
1 CCCAGCCAGCAAGGTCAAACCGAACAGGTCTGGTCAAACCGGGCCGGTTCGAGTTTGTCAGACCG
*
4535 TACCGAACCGGTCCAAAAAAATAAAATAATTGAAATTCCGATTTTACCCCCTAAGCTTGTTTCGG
66 GACCGAACCGGTCC-AAAAAATAAAATAATTGAAATTCCGATTTTACCCCCTAAGCTTGTTTCGG
*
4600 ACCCCGGAATGACTAAATTGCCCCCCAGAAAGTCAGAATTGGTTAAAGAACCGTACTTACGTGAC
130 ACCCCGGAATGACTAAATTGCCCCCCAGAAAGTCAGAATTGGTTAAAGAACCGTACTTACGGGAC
4665 AATA
195 AATA
4669 CAAGTAAAAA
Statistics
Matches: 189, Mismatches: 8, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
200 73 0.39
201 69 0.37
202 47 0.25
ACGTcount: A:0.31, C:0.25, G:0.22, T:0.22
Consensus pattern (201 bp):
CCCAGCCAGCAAGGTCAAACCGAACAGGTCTGGTCAAACCGGGCCGGTTCGAGTTTGTCAGACCG
GACCGAACCGGTCCAAAAAATAAAATAATTGAAATTCCGATTTTACCCCCTAAGCTTGTTTCGGA
CCCCGGAATGACTAAATTGCCCCCCAGAAAGTCAGAATTGGTTAAAGAACCGTACTTACGGGACA
ATATGG
Done.