Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023577.1 Corchorus olitorius cultivar O-4 contig23610, 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: 6523
ACGTcount: A:0.35, C:0.14, G:0.16, T:0.34
Found at i:802 original size:2 final size:2
Alignment explanation
Indices: 795--819 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
785 TGTACCAAGT
795 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
820 GCACACAGAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2758 original size:25 final size:24
Alignment explanation
Indices: 2724--2791 Score: 93
Period size: 25 Copynumber: 2.8 Consensus size: 24
2714 AAGTTGGTAA
2724 TTATAATACTACTATATATATAAAG
1 TTATAATACTACTATATATA-AAAG
***
2749 TTATAATACTACTATATATAACTT
1 TTATAATACTACTATATATAAAAG
2773 TTAT-ATACTACTATATATA
1 TTATAATACTACTATATATA
2792 CTACTATATT
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
23 15 0.38
24 5 0.12
25 20 0.50
ACGTcount: A:0.44, C:0.10, G:0.01, T:0.44
Consensus pattern (24 bp):
TTATAATACTACTATATATAAAAG
Found at i:2768 original size:23 final size:23
Alignment explanation
Indices: 2724--2791 Score: 84
Period size: 23 Copynumber: 2.9 Consensus size: 23
2714 AAGTTGGTAA
*
2724 TTATAATACTACTATATATATAAAG
1 TTATAATACTAC--TATATATAAAC
2749 TTATAATACTACTATATAT-AAC
1 TTATAATACTACTATATATAAAC
*
2771 TTTTATATACTACTATATATA
1 TTATA-ATACTACTATATATA
2792 CTACTATATT
Statistics
Matches: 39, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
22 6 0.15
23 21 0.54
25 12 0.31
ACGTcount: A:0.44, C:0.10, G:0.01, T:0.44
Consensus pattern (23 bp):
TTATAATACTACTATATATAAAC
Found at i:2791 original size:12 final size:12
Alignment explanation
Indices: 2725--2833 Score: 67
Period size: 12 Copynumber: 9.5 Consensus size: 12
2715 AGTTGGTAAT
2725 TATA-ATACTAC
1 TATATATACTAC
2736 TATATATA-TA-
1 TATATATACTAC
*
2746 AAGTTATAATACTAC
1 TA--TAT-ATACTAC
2761 TATATATA--AC
1 TATATATACTAC
*
2771 TTTTATATACTAC
1 -TATATATACTAC
2784 TATATATACTAC
1 TATATATACTAC
*
2796 TATAT-TTCTAAC
1 TATATATACT-AC
*
2808 TTTATATA-TA-
1 TATATATACTAC
2818 TATATATA-TA-
1 TATATATACTAC
2828 TATATA
1 TATATA
2834 AAAATTTTGG
Statistics
Matches: 79, Mismatches: 8, Indels: 23
0.72 0.07 0.21
Matches are distributed among these distances:
10 18 0.23
11 17 0.22
12 32 0.41
13 9 0.11
14 2 0.03
15 1 0.01
ACGTcount: A:0.43, C:0.10, G:0.01, T:0.46
Consensus pattern (12 bp):
TATATATACTAC
Found at i:2826 original size:38 final size:35
Alignment explanation
Indices: 2736--2829 Score: 93
Period size: 38 Copynumber: 2.5 Consensus size: 35
2726 ATAATACTAC
2736 TATATATATAA-AGTTATAATACTACTATATATAACTT
1 TATATATATAATA--TAT-ATACTACTATATATAACTT
* *
2773 T-TATATACTACTATATATACTACTATATTTCTAACTT
1 TATATATA-TAATATATATACTACTATA--TATAACTT
2810 TATATATATATATATATATA
1 TATATATATA-ATATATATA
2830 TATAAAAATT
Statistics
Matches: 48, Mismatches: 3, Indels: 11
0.77 0.05 0.18
Matches are distributed among these distances:
35 11 0.23
36 9 0.19
37 13 0.27
38 15 0.31
ACGTcount: A:0.43, C:0.10, G:0.01, T:0.47
Consensus pattern (35 bp):
TATATATATAATATATATACTACTATATATAACTT
Found at i:4976 original size:21 final size:21
Alignment explanation
Indices: 4952--5018 Score: 57
Period size: 21 Copynumber: 3.2 Consensus size: 21
4942 AATTCCCTGT
4952 AAATTAAGAAATACTCAACTC
1 AAATTAAGAAATACTCAACTC
* * ** *
4973 AAATCATAGAAA-ATTC-TTTGT
1 AAATTA-AGAAATACTCAACT-C
4994 AAATTAAGAAATACTCAACTC
1 AAATTAAGAAATACTCAACTC
5015 AAAT
1 AAAT
5019 CCTGATCCTT
Statistics
Matches: 32, Mismatches: 10, Indels: 8
0.64 0.20 0.16
Matches are distributed among these distances:
20 6 0.19
21 20 0.62
22 6 0.19
ACGTcount: A:0.51, C:0.15, G:0.06, T:0.28
Consensus pattern (21 bp):
AAATTAAGAAATACTCAACTC
Found at i:4999 original size:42 final size:42
Alignment explanation
Indices: 4940--5019 Score: 142
Period size: 42 Copynumber: 1.9 Consensus size: 42
4930 CTAAGTCTTA
4940 AAAATTCCCTGTAAATTAAGAAATACTCAACTCAAATCATAG
1 AAAATTCCCTGTAAATTAAGAAATACTCAACTCAAATCATAG
**
4982 AAAATTCTTTGTAAATTAAGAAATACTCAACTCAAATC
1 AAAATTCCCTGTAAATTAAGAAATACTCAACTCAAATC
5020 CTGATCCTTA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 36 1.00
ACGTcount: A:0.47, C:0.17, G:0.06, T:0.29
Consensus pattern (42 bp):
AAAATTCCCTGTAAATTAAGAAATACTCAACTCAAATCATAG
Found at i:6300 original size:57 final size:58
Alignment explanation
Indices: 6197--6313 Score: 209
Period size: 57 Copynumber: 2.0 Consensus size: 58
6187 TTTATTTTGT
* *
6197 AGAATAATTAAGTAGAGATATGGGGGGATAGGATTTATTATAACATTTATTGTGTGAA
1 AGAATAATTAAGTAGAGATATAGGGGGATAGGATTTATTATAACATTTATTATGTGAA
6255 AGAATAATTAAGTAGAGATA-AGGGGGATAGGATTTATTATAACATTTATTATGTGAA
1 AGAATAATTAAGTAGAGATATAGGGGGATAGGATTTATTATAACATTTATTATGTGAA
6312 AG
1 AG
6314 GAAACGGATA
Statistics
Matches: 57, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
57 37 0.65
58 20 0.35
ACGTcount: A:0.40, C:0.02, G:0.25, T:0.33
Consensus pattern (58 bp):
AGAATAATTAAGTAGAGATATAGGGGGATAGGATTTATTATAACATTTATTATGTGAA
Done.