Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013881.1 Corchorus olitorius cultivar O-4 contig13914, 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: 23410
ACGTcount: A:0.33, C:0.19, G:0.16, T:0.33
Found at i:945 original size:178 final size:178
Alignment explanation
Indices: 671--994 Score: 481
Period size: 178 Copynumber: 1.8 Consensus size: 178
661 CTAATTAAGG
* * * *
671 TGATTTAAGTGTCTATTAAAAGATTGTTCGATGATCTACAACTTTCATGAAGGACTCGAACACTA
1 TGATTCAAGTGTCTATTAAAAGATTGTTCCATGATCTACAACTTCCATGAAGGACTCGAAAACTA
* * *
736 AATTTAATGTTTCAAGTATCAAAATTGCTTCCAAAAAATTTGTTATTTCGGTTAAC-GAGAATAA
66 AATTTAATGTTTCAAGTATAAAAAATGCTTCCAAAAAATTAGTTATTTCGGTTAACGGA-AATAA
800 ACGGTCCACTTAATATTATATAACTTTTGCTCTAGATGTCTGATTGAAA
130 ACGGTCCACTTAATATTATATAACTTTTGCTCTAGATGTCTGATTGAAA
* * * *
849 TGATTCAAGTGTCTCTTGAAAGGTTGTTCCATGATCTACAACTTCCATGAAGGACTTGAAAACTA
1 TGATTCAAGTGTCTATTAAAAGATTGTTCCATGATCTACAACTTCCATGAAGGACTCGAAAACTA
* * *
914 AATTTAATG-TTCAAGATATAAAAAATGCTTCCAAAGAATTAGTTGTTTCGGTTAACGGAAATAG
66 AATTTAATGTTTCAAG-TATAAAAAATGCTTCCAAAAAATTAGTTATTTCGGTTAACGGAAATAA
*
978 ACGGTCTACTTAATATT
130 ACGGTCCACTTAATATT
995 TCACCTACTT
Statistics
Matches: 129, Mismatches: 15, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
177 6 0.05
178 121 0.94
179 2 0.02
ACGTcount: A:0.35, C:0.14, G:0.16, T:0.35
Consensus pattern (178 bp):
TGATTCAAGTGTCTATTAAAAGATTGTTCCATGATCTACAACTTCCATGAAGGACTCGAAAACTA
AATTTAATGTTTCAAGTATAAAAAATGCTTCCAAAAAATTAGTTATTTCGGTTAACGGAAATAAA
CGGTCCACTTAATATTATATAACTTTTGCTCTAGATGTCTGATTGAAA
Found at i:1492 original size:31 final size:31
Alignment explanation
Indices: 1430--1493 Score: 92
Period size: 31 Copynumber: 2.1 Consensus size: 31
1420 AAACCTGCCA
* *
1430 TTTAGAAATGAATAGATTTTTGTTAATTGCT
1 TTTAGAAATAAATAGATTTTTGTTAAGTGCT
* *
1461 TTTAGAGATAAATAGATTTTTGTTAGGTGCT
1 TTTAGAAATAAATAGATTTTTGTTAAGTGCT
1492 TT
1 TT
1494 CATTAAGCCA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.30, C:0.03, G:0.19, T:0.48
Consensus pattern (31 bp):
TTTAGAAATAAATAGATTTTTGTTAAGTGCT
Found at i:3270 original size:43 final size:43
Alignment explanation
Indices: 3221--3311 Score: 182
Period size: 43 Copynumber: 2.1 Consensus size: 43
3211 ATTTGATCAA
3221 AAAATGAAAACTAGATAATAATGAATTGAATTACATAACCCAT
1 AAAATGAAAACTAGATAATAATGAATTGAATTACATAACCCAT
3264 AAAATGAAAACTAGATAATAATGAATTGAATTACATAACCCAT
1 AAAATGAAAACTAGATAATAATGAATTGAATTACATAACCCAT
3307 AAAAT
1 AAAAT
3312 AAAGACAAAT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 48 1.00
ACGTcount: A:0.55, C:0.11, G:0.09, T:0.25
Consensus pattern (43 bp):
AAAATGAAAACTAGATAATAATGAATTGAATTACATAACCCAT
Found at i:3549 original size:3 final size:3
Alignment explanation
Indices: 3442--3538 Score: 155
Period size: 3 Copynumber: 33.0 Consensus size: 3
3432 GAGAAACTAT
*
3442 TAA TAA TTAA T-A TAA CAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA -TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
3487 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-A TAA T-A
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
3533 TAA TAA
1 TAA TAA
3539 ATGTTAATAA
Statistics
Matches: 88, Mismatches: 2, Indels: 8
0.90 0.02 0.08
Matches are distributed among these distances:
2 6 0.07
3 79 0.90
4 3 0.03
ACGTcount: A:0.65, C:0.01, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:7284 original size:12 final size:12
Alignment explanation
Indices: 7263--7295 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
7253 TTTCTCTTCA
7263 TCTA-TTTTTCT
1 TCTAGTTTTTCT
*
7274 TGTAGTTTTTCT
1 TCTAGTTTTTCT
7286 TCTAGTTTTT
1 TCTAGTTTTT
7296 AGGTAAGGGT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
11 3 0.16
12 16 0.84
ACGTcount: A:0.09, C:0.12, G:0.09, T:0.70
Consensus pattern (12 bp):
TCTAGTTTTTCT
Found at i:14595 original size:33 final size:32
Alignment explanation
Indices: 14526--14597 Score: 101
Period size: 32 Copynumber: 2.2 Consensus size: 32
14516 CTACTCACAC
*
14526 TTAACTTGTCCAATTTACCCTTATATATTTTA
1 TTAACTTCTCCAATTTACCCTTATATATTTTA
*
14558 TTAACTTCTCCAATTTACCCTTCCAT-TTTTTTA
1 TTAACTTCTCCAATTTACCCTT--ATATATTTTA
14591 TTAACTT
1 TTAACTT
14598 TACATCAATT
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
32 21 0.58
33 13 0.36
34 2 0.06
ACGTcount: A:0.25, C:0.22, G:0.01, T:0.51
Consensus pattern (32 bp):
TTAACTTCTCCAATTTACCCTTATATATTTTA
Done.