Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011495.1 Corchorus capsularis cultivar CVL-1 contig11516, 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: 22106
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:855 original size:109 final size:110
Alignment explanation
Indices: 577--850 Score: 421
Period size: 108 Copynumber: 2.5 Consensus size: 110
567 ACTATTATAG
* * *
577 TTTTATTCTACTAGAAACTCTATTTTTATTCAATTAAATTAAATCTAATATCTTTATAATTACTT
1 TTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAA-T---TCTAATATCTTTATAATTACTT
**
642 TATTTTTACCAAAAATTTTGGATATACTAAAATTTTTTCTAATATACAA
62 TATTTTTACCAAAAAAATTGGATATACTAAAATTTTTTCTAATATACAA
*
691 TTTTATTCTACTAAAAACTCAATTTTCATTTAATTAAA-TCTAATATCTTTATAATTACTTTA-T
1 TTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAATTCTAATATCTTTATAATTACTTTATT
*
754 TTTACCAAAAAAATTGGATATATTAAAATTTTTTCTAATATACAA
66 TTTACCAAAAAAATTGGATATACTAAAATTTTTTCTAATATACAA
799 TTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAATTC-AATAT-TTTATA
1 TTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAATTCTAATATCTTTATA
851 TAATTTTTTT
Statistics
Matches: 151, Mismatches: 8, Indels: 9
0.90 0.05 0.05
Matches are distributed among these distances:
107 6 0.04
108 85 0.56
109 26 0.17
114 34 0.23
ACGTcount: A:0.39, C:0.11, G:0.02, T:0.48
Consensus pattern (110 bp):
TTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAATTCTAATATCTTTATAATTACTTTATT
TTTACCAAAAAAATTGGATATACTAAAATTTTTTCTAATATACAA
Found at i:1736 original size:31 final size:29
Alignment explanation
Indices: 1678--1741 Score: 92
Period size: 29 Copynumber: 2.1 Consensus size: 29
1668 TATTTTATGT
* *
1678 TTTCCGATTGTACTCCTTTTAAAAATATA
1 TTTCCGATTATACCCCTTTTAAAAATATA
1707 TTTCCGATTATACCCCTGTTTAAAAAATATA
1 TTTCCGATTATACCCCT-TTT-AAAAATATA
1738 TTTC
1 TTTC
1742 TAAATTGACA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
29 15 0.48
30 3 0.10
31 13 0.42
ACGTcount: A:0.31, C:0.19, G:0.06, T:0.44
Consensus pattern (29 bp):
TTTCCGATTATACCCCTTTTAAAAATATA
Found at i:5342 original size:37 final size:37
Alignment explanation
Indices: 5285--5356 Score: 101
Period size: 37 Copynumber: 1.9 Consensus size: 37
5275 ATAACATGTT
* *
5285 GTATATACTACCGAGTGGAGGAGCTCAATTTGAATAC
1 GTATATACTACCAAGTGGAGGAGCTCAATATGAATAC
*
5322 GTATATACTACCAAAG-GGAGGAGTTCAATATGAAT
1 GTATATACTACC-AAGTGGAGGAGCTCAATATGAAT
5357 GATATATGTT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
37 29 0.94
38 2 0.06
ACGTcount: A:0.36, C:0.14, G:0.24, T:0.26
Consensus pattern (37 bp):
GTATATACTACCAAGTGGAGGAGCTCAATATGAATAC
Found at i:12857 original size:3 final size:3
Alignment explanation
Indices: 12824--12900 Score: 50
Period size: 3 Copynumber: 25.7 Consensus size: 3
12814 TCTAAGGGAT
* * * * * * *
12824 ATA ATA TATG ATA AGA ATA ATT ATG ATA ATA ATA ATT ATA TTA ATT
1 ATA ATA -ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
*
12870 ATA ATT ATA AT- ATA TATA AT- ATA ATA ATA AT
1 ATA ATA ATA ATA ATA -ATA ATA ATA ATA ATA AT
12901 GCAACACGAT
Statistics
Matches: 55, Mismatches: 15, Indels: 8
0.71 0.19 0.10
Matches are distributed among these distances:
2 4 0.07
3 46 0.84
4 5 0.09
ACGTcount: A:0.55, C:0.00, G:0.04, T:0.42
Consensus pattern (3 bp):
ATA
Found at i:12868 original size:15 final size:15
Alignment explanation
Indices: 12824--12900 Score: 77
Period size: 15 Copynumber: 5.1 Consensus size: 15
12814 TCTAAGGGAT
* *
12824 ATAATATATGATAAGA
1 ATAAT-TATAATAATA
*
12840 ATAATTATGATAATA
1 ATAATTATAATAATA
* *
12855 ATAATTATATTAATT
1 ATAATTATAATAATA
12870 ATAATTATAAT-ATA
1 ATAATTATAATAATA
12884 TATAA-TATAATAATA
1 -ATAATTATAATAATA
12899 AT
1 AT
12901 GCAACACGAT
Statistics
Matches: 53, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
14 10 0.19
15 38 0.72
16 5 0.09
ACGTcount: A:0.55, C:0.00, G:0.04, T:0.42
Consensus pattern (15 bp):
ATAATTATAATAATA
Found at i:13834 original size:74 final size:74
Alignment explanation
Indices: 13756--13912 Score: 262
Period size: 74 Copynumber: 2.1 Consensus size: 74
13746 TGGTCTTTTC
* * *
13756 ACACTTTTCAGG-TGACTAAAAAGTCCCTCTATGAGTTTCCCCTATTTCTTTTCCTTCTACCCTT
1 ACACTTTTC-GGATGACTAAAAAGCCCCTCTATGAGTTTCCCCCATTCCTTTTCCTTCTACCCTT
13820 TTTCGTAATT
65 TTTCGTAATT
13830 ACACTTTTCGGATGACTAAAAAGCCCCTCTATGAGTTTCCCCCATTCCTTTTCCTTCTACCCTTT
1 ACACTTTTCGGATGACTAAAAAGCCCCTCTATGAGTTTCCCCCATTCCTTTTCCTTCTACCCTTT
13895 TTCGTAATT
66 TTCGTAATT
*
13904 ACACATTTC
1 ACACTTTTC
13913 CCTTCCTTAA
Statistics
Matches: 78, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
73 2 0.03
74 76 0.97
ACGTcount: A:0.21, C:0.29, G:0.09, T:0.41
Consensus pattern (74 bp):
ACACTTTTCGGATGACTAAAAAGCCCCTCTATGAGTTTCCCCCATTCCTTTTCCTTCTACCCTTT
TTCGTAATT
Found at i:21512 original size:21 final size:21
Alignment explanation
Indices: 21488--21536 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
21478 CAGCTGGGGG
* * *
21488 CCCATGTGGTATGCTTGGCGC
1 CCCATGTGGTATGCCTCGCGA
*
21509 CCCATGTGGTTTGCCTCGCGA
1 CCCATGTGGTATGCCTCGCGA
21530 CCCATGT
1 CCCATGT
21537 CCTCCAGTGC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.10, C:0.33, G:0.29, T:0.29
Consensus pattern (21 bp):
CCCATGTGGTATGCCTCGCGA
Done.