Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015506.1 Corchorus olitorius cultivar O-4 contig15539, 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: 15674
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:3432 original size:28 final size:30
Alignment explanation
Indices: 3400--3475 Score: 95
Period size: 29 Copynumber: 2.6 Consensus size: 30
3390 TATGACGCAA
3400 AAAACTCTTTTTTTTTTCGACGCAAAA-AC
1 AAAACTCTTTTTTTTTTCGACGCAAAACAC
* *
3429 -AAACATATTTTTTTCTT-GACGCAAAACAC
1 AAAAC-TCTTTTTTTTTTCGACGCAAAACAC
*
3458 AAAACCCTTTTTTTTTTC
1 AAAACTCTTTTTTTTTTC
3476 AAAAACGCAA
Statistics
Matches: 38, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
28 13 0.34
29 21 0.55
30 4 0.11
ACGTcount: A:0.33, C:0.21, G:0.05, T:0.41
Consensus pattern (30 bp):
AAAACTCTTTTTTTTTTCGACGCAAAACAC
Found at i:3926 original size:15 final size:16
Alignment explanation
Indices: 3906--3948 Score: 61
Period size: 15 Copynumber: 2.7 Consensus size: 16
3896 ACAGAGGTTG
3906 ACAGAAAACAA-TAAA
1 ACAGAAAACAATTAAA
*
3921 ACAGAAAACAATTTAA
1 ACAGAAAACAATTAAA
3937 ACTAGAAAACAA
1 AC-AGAAAACAA
3949 AGCAAAGTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
15 11 0.44
16 5 0.20
17 9 0.36
ACGTcount: A:0.67, C:0.14, G:0.07, T:0.12
Consensus pattern (16 bp):
ACAGAAAACAATTAAA
Found at i:5545 original size:28 final size:30
Alignment explanation
Indices: 5476--5545 Score: 83
Period size: 28 Copynumber: 2.4 Consensus size: 30
5466 CCCTTTTTAC
*
5476 CCCCCTGAACTTCTATGATTTTGACGTTTTG
1 CCCCCTGAACTTCTA-GATTTGGACGTTTTG
*
5507 CCCCCTAAACTT-TA-ATTGTGGACG-TTTG
1 CCCCCTGAACTTCTAGATT-TGGACGTTTTG
5535 CCCCCTGAACT
1 CCCCCTGAACT
5546 CACAATTTGG
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
28 17 0.49
29 5 0.14
30 2 0.06
31 11 0.31
ACGTcount: A:0.19, C:0.30, G:0.16, T:0.36
Consensus pattern (30 bp):
CCCCCTGAACTTCTAGATTTGGACGTTTTG
Found at i:5556 original size:28 final size:28
Alignment explanation
Indices: 5493--5556 Score: 67
Period size: 28 Copynumber: 2.2 Consensus size: 28
5483 AACTTCTATG
* **
5493 ATTTTGACGTTTTGCCCCCTAAACTTTA
1 ATTTGGACGTTTTGCCCCCTAAACTACA
*
5521 ATTGTGGACG-TTTGCCCCCTGAACTCACA
1 ATT-TGGACGTTTTGCCCCCTAAACT-ACA
5550 ATTTGGA
1 ATTTGGA
5557 TCCAATTTAG
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
28 21 0.70
29 9 0.30
ACGTcount: A:0.22, C:0.25, G:0.17, T:0.36
Consensus pattern (28 bp):
ATTTGGACGTTTTGCCCCCTAAACTACA
Found at i:8585 original size:21 final size:21
Alignment explanation
Indices: 8561--8669 Score: 64
Period size: 21 Copynumber: 5.2 Consensus size: 21
8551 AATTCGCTGT
8561 AAATTAAGAAATACTCAACTC
1 AAATTAAGAAATACTCAACTC
* * ** *
8582 AAATCATAGAAA-ATTC-TTTGT
1 AAATTA-AGAAATACTCAACT-C
8603 AAATTAAGAAATACTCAACTC
1 AAATTAAGAAATACTCAACTC
* * ** *
8624 AAATCATAGAAA-ATTC-TTTGT
1 AAATTA-AGAAATACTCAACT-C
8645 AAATTAAGAAATACTCAACTC
1 AAATTAAGAAATACTCAACTC
8666 AAAT
1 AAAT
8670 CCTAAGCCTT
Statistics
Matches: 60, Mismatches: 20, Indels: 16
0.62 0.21 0.17
Matches are distributed among these distances:
20 12 0.20
21 36 0.60
22 12 0.20
ACGTcount: A:0.50, C:0.15, G:0.06, T:0.29
Consensus pattern (21 bp):
AAATTAAGAAATACTCAACTC
Found at i:8607 original size:42 final size:42
Alignment explanation
Indices: 8548--8670 Score: 228
Period size: 42 Copynumber: 2.9 Consensus size: 42
8538 GCTAAGTCTT
**
8548 GAAAATTCGCTGTAAATTAAGAAATACTCAACTCAAATCATA
1 GAAAATTCTTTGTAAATTAAGAAATACTCAACTCAAATCATA
8590 GAAAATTCTTTGTAAATTAAGAAATACTCAACTCAAATCATA
1 GAAAATTCTTTGTAAATTAAGAAATACTCAACTCAAATCATA
8632 GAAAATTCTTTGTAAATTAAGAAATACTCAACTCAAATC
1 GAAAATTCTTTGTAAATTAAGAAATACTCAACTCAAATC
8671 CTAAGCCTTA
Statistics
Matches: 79, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 79 1.00
ACGTcount: A:0.47, C:0.15, G:0.08, T:0.29
Consensus pattern (42 bp):
GAAAATTCTTTGTAAATTAAGAAATACTCAACTCAAATCATA
Found at i:8812 original size:57 final size:57
Alignment explanation
Indices: 8736--8851 Score: 196
Period size: 57 Copynumber: 2.0 Consensus size: 57
8726 TTTATTTTGT
* * *
8736 AGAATAATTAAGTAGAGATAGAGGGGATATGATTTATTATAACATTTATTGTGTGAA
1 AGAATAATTAAGTAAAGATAGAGGAGATAAGATTTATTATAACATTTATTGTGTGAA
*
8793 AGAATAATTAAGTAAAGATAGAGGATATAAGATTTATTATAACATTTATTGTGTGAA
1 AGAATAATTAAGTAAAGATAGAGGAGATAAGATTTATTATAACATTTATTGTGTGAA
8850 AG
1 AG
8852 GAAACAGATA
Statistics
Matches: 55, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
57 55 1.00
ACGTcount: A:0.43, C:0.02, G:0.21, T:0.34
Consensus pattern (57 bp):
AGAATAATTAAGTAAAGATAGAGGAGATAAGATTTATTATAACATTTATTGTGTGAA
Found at i:9176 original size:17 final size:18
Alignment explanation
Indices: 9154--9192 Score: 62
Period size: 17 Copynumber: 2.2 Consensus size: 18
9144 CTCTTGAAAT
9154 AAATCTTCAAA-GTCTTC
1 AAATCTTCAAAGGTCTTC
9171 AAATCTTCAAATGGTCTTC
1 AAATCTTCAAA-GGTCTTC
9190 AAA
1 AAA
9193 CACGAACTTC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
17 11 0.55
19 9 0.45
ACGTcount: A:0.38, C:0.21, G:0.08, T:0.33
Consensus pattern (18 bp):
AAATCTTCAAAGGTCTTC
Done.