Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015787.1 Corchorus capsularis cultivar CVL-1 contig15808, 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: 21908
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Found at i:4133 original size:27 final size:27
Alignment explanation
Indices: 4095--4157 Score: 108
Period size: 27 Copynumber: 2.3 Consensus size: 27
4085 TACGGCTCTC
4095 CCCACTTCGACCCCAGCAGTGGATCCT
1 CCCACTTCGACCCCAGCAGTGGATCCT
* *
4122 CCCACTTTGACCCCATCAGTGGATCCT
1 CCCACTTCGACCCCAGCAGTGGATCCT
4149 CCCACTTCG
1 CCCACTTCG
4158 CCTCGGGTCG
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 33 1.00
ACGTcount: A:0.17, C:0.44, G:0.16, T:0.22
Consensus pattern (27 bp):
CCCACTTCGACCCCAGCAGTGGATCCT
Found at i:4982 original size:17 final size:17
Alignment explanation
Indices: 4960--4994 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
4950 GAAAAAGTGC
4960 ATTCTTGGTGGCACATT
1 ATTCTTGGTGGCACATT
* *
4977 ATTCTTGTTGGCATATT
1 ATTCTTGGTGGCACATT
4994 A
1 A
4995 ACATTATGCA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.20, C:0.14, G:0.20, T:0.46
Consensus pattern (17 bp):
ATTCTTGGTGGCACATT
Found at i:7733 original size:392 final size:392
Alignment explanation
Indices: 7009--7734 Score: 1094
Period size: 392 Copynumber: 1.9 Consensus size: 392
6999 CTCCATGAAG
* * ** *
7009 TTTAAATTGTGCCACTTTGCCCCCTGAATTTGTAAAATCAGGCCAATCCCTTTCTTCACGTGATG
1 TTTAAATTGTGCCACTTTACCCCCTGAATTTGCAAAATCAGGCCAATCCCCCTCTTCACGTGACG
* * * *
7074 GATTCCGTTAAGTGCCATCAGATTTGCTGACGTGGCAAATTTATCCTAACATGGTATTTCCATGT
66 GATTCCATTAAATCCCATCAGATTTGCTGACGTGGCAAATTCATCCTAACATGGTATTTCCATGT
*
7139 CAACGCTTATGTGGGCCTCACATGACCCAAAATGTTATGGTGGGGCCCACATGAGCGTTGACATG
131 CAACGCTTATGTGGGCCCCACATGACCCAAAATGTTATGGTGGGGCCCACATGAGCGTTGACATG
* * * * * *
7204 GAAATGCCACGTCAGCGTAATTAAGTTTGCCACGTCAGTAAATTTAGTGGGACTTAACGGCCACG
196 AAAATACCACGTCAACATAATTAAGTTTGCCACGTCAGCAAATTTAGTGGGACTTAACGGACACG
* * ** **
7269 TTAGTCAAGCGTCAAGTCAAGGGGTAAATTGGCCTGATTATACAAATCTAGGGGGTAAAGTGGCA
261 TTAGTCAACCGTCAAATCAAGGGACAAATTGGCCTGATTATACAAATCTAGGGGACAAAGTGGCA
*
7334 CAATTTAAAGTTCAAGCTTAATAGCCACTTTGCAAATTTAGGATAGCTTGCTCTATGAACTTTAA
326 AAATTTAAAGTTCAAGCTTAATAGCCACTTTGCAAATTTAGGATAGCTTGCTCTATGAACTTTAA
7399 AA
391 AA
* * *
7401 TTTAAATTGTGCCACTTTATCCCTTGAATTTGCAAAATCAGGCCAATCCCCCTCTTTACGTGACG
1 TTTAAATTGTGCCACTTTACCCCCTGAATTTGCAAAATCAGGCCAATCCCCCTCTTCACGTGACG
* * * * *
7466 GATTTCATTAAATCCCATCAGATTTGCTGATGTGGCAAATTCATGCTGACATGGTATTTCCCTGT
66 GATTCCATTAAATCCCATCAGATTTGCTGACGTGGCAAATTCATCCTAACATGGTATTTCCATGT
* *
7531 CAACGCTTATGTGGGCCCCACATGATCTAAAATGTTATGGTGGGGCCCACATGAGCGTTGACATG
131 CAACGCTTATGTGGGCCCCACATGACCCAAAATGTTATGGTGGGGCCCACATGAGCGTTGACATG
* *
7596 AAAATATCACGTCAACATAATTAAGTTTGCCACGTCAGCAAATTTAGTGGGACTTAACGGATACG
196 AAAATACCACGTCAACATAATTAAGTTTGCCACGTCAGCAAATTTAGTGGGACTTAACGGACACG
* * *
7661 TTAGTCAACCGTCAAATCAAGGGACAAATTGGCCTGATTTTTCAAAT-TCATGGGACAAAGTGGC
261 TTAGTCAACCGTCAAATCAAGGGACAAATTGGCCTGATTATACAAATCT-AGGGGACAAAGTGGC
7725 AAAATTTAAA
325 AAAATTTAAA
7735 ATTTAAGAGG
Statistics
Matches: 295, Mismatches: 38, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
391 1 0.00
392 294 1.00
ACGTcount: A:0.29, C:0.21, G:0.21, T:0.30
Consensus pattern (392 bp):
TTTAAATTGTGCCACTTTACCCCCTGAATTTGCAAAATCAGGCCAATCCCCCTCTTCACGTGACG
GATTCCATTAAATCCCATCAGATTTGCTGACGTGGCAAATTCATCCTAACATGGTATTTCCATGT
CAACGCTTATGTGGGCCCCACATGACCCAAAATGTTATGGTGGGGCCCACATGAGCGTTGACATG
AAAATACCACGTCAACATAATTAAGTTTGCCACGTCAGCAAATTTAGTGGGACTTAACGGACACG
TTAGTCAACCGTCAAATCAAGGGACAAATTGGCCTGATTATACAAATCTAGGGGACAAAGTGGCA
AAATTTAAAGTTCAAGCTTAATAGCCACTTTGCAAATTTAGGATAGCTTGCTCTATGAACTTTAA
AA
Found at i:10139 original size:13 final size:15
Alignment explanation
Indices: 10114--10150 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
10104 TCATTACTTG
*
10114 AATTT-ATTTTTTAT
1 AATTTAATTTTTAAT
10128 AA-TTAATTTTTAAT
1 AATTTAATTTTTAAT
10142 AATTTAATT
1 AATTTAATT
10151 AATTCAACGC
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
13 2 0.10
14 12 0.60
15 6 0.30
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (15 bp):
AATTTAATTTTTAAT
Found at i:17727 original size:71 final size:71
Alignment explanation
Indices: 17652--17791 Score: 280
Period size: 71 Copynumber: 2.0 Consensus size: 71
17642 AGATCATAGC
17652 AAAAAAAAATAAGAATCTCATTAAAAATTCACATTGATTGATCAACTTTTTGACTTAATGATTTG
1 AAAAAAAAATAAGAATCTCATTAAAAATTCACATTGATTGATCAACTTTTTGACTTAATGATTTG
17717 CATAAT
66 CATAAT
17723 AAAAAAAAATAAGAATCTCATTAAAAATTCACATTGATTGATCAACTTTTTGACTTAATGATTTG
1 AAAAAAAAATAAGAATCTCATTAAAAATTCACATTGATTGATCAACTTTTTGACTTAATGATTTG
17788 CATA
66 CATA
17792 TACATAGCTG
Statistics
Matches: 69, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
71 69 1.00
ACGTcount: A:0.45, C:0.11, G:0.09, T:0.35
Consensus pattern (71 bp):
AAAAAAAAATAAGAATCTCATTAAAAATTCACATTGATTGATCAACTTTTTGACTTAATGATTTG
CATAAT
Found at i:20946 original size:14 final size:13
Alignment explanation
Indices: 20927--20961 Score: 52
Period size: 13 Copynumber: 2.6 Consensus size: 13
20917 AATTGCCAGA
20927 GTTGTTTGGCTTTT
1 GTTGTTTGG-TTTT
20941 GTTGTTTGGTTTT
1 GTTGTTTGGTTTT
*
20954 GGTGTTTG
1 GTTGTTTG
20962 ATCATTACTG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 11 0.55
14 9 0.45
ACGTcount: A:0.00, C:0.03, G:0.34, T:0.63
Consensus pattern (13 bp):
GTTGTTTGGTTTT
Found at i:21271 original size:29 final size:29
Alignment explanation
Indices: 21239--21299 Score: 86
Period size: 29 Copynumber: 2.1 Consensus size: 29
21229 ATCTTTGAAT
21239 AAAAACTTATTATGATCTAATTGGTTATG
1 AAAAACTTATTATGATCTAATTGGTTATG
* * * *
21268 AAAAACTTCTTTTGATTTAGTTGGTTATG
1 AAAAACTTATTATGATCTAATTGGTTATG
21297 AAA
1 AAA
21300 TTGATTTATT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.36, C:0.07, G:0.15, T:0.43
Consensus pattern (29 bp):
AAAAACTTATTATGATCTAATTGGTTATG
Done.