Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018014.1 Corchorus olitorius cultivar O-4 contig18047, 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: 35492
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:20587 original size:31 final size:31
Alignment explanation
Indices: 20552--20630 Score: 108
Period size: 31 Copynumber: 2.5 Consensus size: 31
20542 TAAATCTTTT
20552 ATTTTAG-GAGGATCAATGA-GATAAAACTTCA
1 ATTTTAGTG-GGATCAAT-ATGATAAAACTTCA
*
20583 ATTTTAGTGGGGTCAATATGATAAAACTTCA
1 ATTTTAGTGGGATCAATATGATAAAACTTCA
*
20614 ATTTTAGTGGGGTCAAT
1 ATTTTAGTGGGATCAAT
20631 TGGTAATTTA
Statistics
Matches: 45, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
30 1 0.02
31 43 0.96
32 1 0.02
ACGTcount: A:0.35, C:0.09, G:0.22, T:0.34
Consensus pattern (31 bp):
ATTTTAGTGGGATCAATATGATAAAACTTCA
Found at i:21054 original size:24 final size:25
Alignment explanation
Indices: 21020--21070 Score: 70
Period size: 24 Copynumber: 2.1 Consensus size: 25
21010 ATTAGAGTAT
21020 TTATTTATCTTGTTGT-TTAATTTTA
1 TTATTTATCTTGTT-TATTAATTTTA
*
21045 TTATTT-TCTTGTTTATTTATTTTA
1 TTATTTATCTTGTTTATTAATTTTA
21069 TT
1 TT
21071 GTTCACATAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
23 1 0.04
24 17 0.71
25 6 0.25
ACGTcount: A:0.18, C:0.04, G:0.06, T:0.73
Consensus pattern (25 bp):
TTATTTATCTTGTTTATTAATTTTA
Found at i:21069 original size:21 final size:21
Alignment explanation
Indices: 21017--21070 Score: 58
Period size: 21 Copynumber: 2.6 Consensus size: 21
21007 GTGATTAGAG
* *
21017 TATTTA-TTTATCTTGTTGTT
1 TATTTATTTTATTTTCTTGTT
*
21037 TAATTT-TATTATTTTCTTGTT
1 T-ATTTATTTTATTTTCTTGTT
21058 TATTTATTTTATT
1 TATTTATTTTATT
21071 GTTCACATAA
Statistics
Matches: 27, Mismatches: 4, Indels: 5
0.75 0.11 0.14
Matches are distributed among these distances:
20 5 0.19
21 22 0.81
ACGTcount: A:0.19, C:0.04, G:0.06, T:0.72
Consensus pattern (21 bp):
TATTTATTTTATTTTCTTGTT
Found at i:25470 original size:46 final size:47
Alignment explanation
Indices: 25417--25509 Score: 152
Period size: 49 Copynumber: 2.0 Consensus size: 47
25407 CAGTACCTAA
*
25417 ATTCTA-CTCCATCTCTAGGTAATTCATCAAAATAAAGCTAATATAT
1 ATTCTACCTCCATCTCTAGATAATTCATCAAAATAAAGCTAATATAT
25463 ATTCTACTCCTCCATCTCTAGATAATTCATCAAAATAAAGCTAATAT
1 ATTCTA--CCTCCATCTCTAGATAATTCATCAAAATAAAGCTAATAT
25510 TAATTGTTGC
Statistics
Matches: 43, Mismatches: 1, Indels: 3
0.91 0.02 0.06
Matches are distributed among these distances:
46 6 0.14
49 37 0.86
ACGTcount: A:0.39, C:0.22, G:0.05, T:0.34
Consensus pattern (47 bp):
ATTCTACCTCCATCTCTAGATAATTCATCAAAATAAAGCTAATATAT
Found at i:25847 original size:66 final size:66
Alignment explanation
Indices: 25765--25895 Score: 244
Period size: 66 Copynumber: 2.0 Consensus size: 66
25755 CTTAGCATTG
25765 GCTAACTGTGCTTTTGGAAATGTGAAAATATACTAAATATAAGCAACTAATAGAAACCTCAATAA
1 GCTAACTGTGCTTTTGGAAATGTGAAAATATACTAAATATAAGCAACTAATAGAAACCTCAATAA
25830 T
66 T
* *
25831 GCTAACTGTGCTTTTGGAAATGTGAAAATATACTAAATATACGCAACTAATAGAAACCTTAATAA
1 GCTAACTGTGCTTTTGGAAATGTGAAAATATACTAAATATAAGCAACTAATAGAAACCTCAATAA
25896 AAAGGAAGTC
Statistics
Matches: 63, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
66 63 1.00
ACGTcount: A:0.44, C:0.14, G:0.14, T:0.29
Consensus pattern (66 bp):
GCTAACTGTGCTTTTGGAAATGTGAAAATATACTAAATATAAGCAACTAATAGAAACCTCAATAA
T
Found at i:31458 original size:2 final size:2
Alignment explanation
Indices: 31451--31491 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
31441 CTTATTCGTA
31451 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
31492 ACACGTGTCA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:31680 original size:19 final size:20
Alignment explanation
Indices: 31656--31695 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
31646 TTGTCATTCT
*
31656 TTGTTGG-CTATTTTTTTTA
1 TTGTTGGTCAATTTTTTTTA
31675 TTGTTGGTCAATTTTTTTTA
1 TTGTTGGTCAATTTTTTTTA
31695 T
1 T
31696 ATAAGTAGCT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 7 0.37
20 12 0.63
ACGTcount: A:0.12, C:0.05, G:0.15, T:0.68
Consensus pattern (20 bp):
TTGTTGGTCAATTTTTTTTA
Done.