Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014935.1 Corchorus olitorius cultivar O-4 contig14968, 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: 5931
ACGTcount: A:0.27, C:0.15, G:0.19, T:0.39
Found at i:2777 original size:122 final size:122
Alignment explanation
Indices: 2580--2799 Score: 361
Period size: 122 Copynumber: 1.8 Consensus size: 122
2570 CTGATTTTGC
* ** *
2580 TTTTTCTGCTCTGATGGTTTCTTGATAGTGTTTCTTCTCTTCTGCAGTTGTCTCCCCATTGGATC
1 TTTTTCTGCTCTGATGGTTTCTGGATAACGTTTCTTCTCTTCTGCAGTTGTCTCCCCATTGGAGC
* * *
2645 TGAGCGTATCCTTGTGGCAGCTAGGATTGCCTTCAGATTTTTTTGTTGTAAGTTTCT
66 TGAGCATATCCTTGTAGCAGCAAGGATTGCCTTCAGATTTTTTTGTTGTAAGTTTCT
2702 TTTTTCTGCTCTGATGGTTTCTGGATAACGTTTCTTCTCCTT-TGCAGTTGTCTCCCCATTGGAG
1 TTTTTCTGCTCTGATGGTTTCTGGATAACGTTTCTTCT-CTTCTGCAGTTGTCTCCCCATTGGAG
2766 CTGAGCATATCCTTGTAGCAGCAAGGATTGCCTT
65 CTGAGCATATCCTTGTAGCAGCAAGGATTGCCTT
2800 ATTGTCATGA
Statistics
Matches: 90, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
122 87 0.97
123 3 0.03
ACGTcount: A:0.14, C:0.21, G:0.21, T:0.44
Consensus pattern (122 bp):
TTTTTCTGCTCTGATGGTTTCTGGATAACGTTTCTTCTCTTCTGCAGTTGTCTCCCCATTGGAGC
TGAGCATATCCTTGTAGCAGCAAGGATTGCCTTCAGATTTTTTTGTTGTAAGTTTCT
Found at i:2923 original size:20 final size:20
Alignment explanation
Indices: 2864--2930 Score: 71
Period size: 20 Copynumber: 3.3 Consensus size: 20
2854 CATTGAGGGC
2864 CAATGTGAATTAAGGCAAGTT
1 CAATGTG-ATTAAGGCAAGTT
* ** *
2885 CAATGTCATTTGGGAAAGTT
1 CAATGTGATTAAGGCAAGTT
**
2905 GGATGTGATTAAGGCAAGTT
1 CAATGTGATTAAGGCAAGTT
2925 CAATGT
1 CAATGT
2931 CATTTGGATG
Statistics
Matches: 34, Mismatches: 12, Indels: 1
0.72 0.26 0.02
Matches are distributed among these distances:
20 28 0.82
21 6 0.18
ACGTcount: A:0.33, C:0.09, G:0.27, T:0.31
Consensus pattern (20 bp):
CAATGTGATTAAGGCAAGTT
Found at i:2953 original size:32 final size:32
Alignment explanation
Indices: 2903--3264 Score: 559
Period size: 32 Copynumber: 11.1 Consensus size: 32
2893 TTTGGGAAAG
2903 TTGGATGTG-ATTAAGGCAAGTTCAATGTCAT
1 TTGGATGTGAATTAAGGCAAGTTCAATGTCAT
*
2934 TTGGATGTGAATTAAGGCAAGTTCAATGTTAT
1 TTGGATGTGAATTAAGGCAAGTTCAATGTCAT
*
2966 TTGGATGTGAATTAAGGCAAGTTCAATGTTAT
1 TTGGATGTGAATTAAGGCAAGTTCAATGTCAT
*
2998 TTGGATGTGAATTAAGGCAAGTTCAATGTTAT
1 TTGGATGTGAATTAAGGCAAGTTCAATGTCAT
3030 TTGGATGTGAATTAAGGCAAGTTCAATGTCAT
1 TTGGATGTGAATTAAGGCAAGTTCAATGTCAT
*
3062 TTGGGAAAGTTGGATGTGATTAAGGCAAGTTCAATGTCAT
1 TT-GG--A--T-G-TG-AATTAAGGCAAGTTCAATGTCAT
*
3102 TTGGATGTGAATTAAGGCAAGTTCAATGTTAT
1 TTGGATGTGAATTAAGGCAAGTTCAATGTCAT
*
3134 TTGGATGTGAATTAAGGCAAGTTCAATGTCAC
1 TTGGATGTGAATTAAGGCAAGTTCAATGTCAT
3166 TTGGATGTGAATTAAGGCAAGTTCAATGTCAT
1 TTGGATGTGAATTAAGGCAAGTTCAATGTCAT
3198 TTGGATGTGAATTAAGGCAAGTTCAATGTCAT
1 TTGGATGTGAATTAAGGCAAGTTCAATGTCAT
*
3230 TTGGATGTGAA-TAAGGCAA-TTCCAATGTCAA
1 TTGGATGTGAATTAAGGCAAGTT-CAATGTCAT
3261 TTGG
1 TTGG
3265 GAGAGTTAAA
Statistics
Matches: 312, Mismatches: 9, Indels: 20
0.91 0.03 0.06
Matches are distributed among these distances:
30 2 0.01
31 29 0.09
32 243 0.78
33 4 0.01
34 1 0.00
35 2 0.01
37 2 0.01
38 1 0.00
39 4 0.01
40 24 0.08
ACGTcount: A:0.31, C:0.09, G:0.26, T:0.35
Consensus pattern (32 bp):
TTGGATGTGAATTAAGGCAAGTTCAATGTCAT
Found at i:3098 original size:20 final size:20
Alignment explanation
Indices: 3034--3098 Score: 67
Period size: 20 Copynumber: 3.2 Consensus size: 20
3024 TGTTATTTGG
3034 ATGTGAATTAAGGCAAGTTCA
1 ATGTG-ATTAAGGCAAGTTCA
* ** * **
3055 ATGTCATTTGGGAAAGTTGG
1 ATGTGATTAAGGCAAGTTCA
3075 ATGTGATTAAGGCAAGTTCA
1 ATGTGATTAAGGCAAGTTCA
3095 ATGT
1 ATGT
3099 CATTTGGATG
Statistics
Matches: 32, Mismatches: 12, Indels: 1
0.71 0.27 0.02
Matches are distributed among these distances:
20 28 0.88
21 4 0.12
ACGTcount: A:0.32, C:0.08, G:0.28, T:0.32
Consensus pattern (20 bp):
ATGTGATTAAGGCAAGTTCA
Found at i:3144 original size:168 final size:168
Alignment explanation
Indices: 2866--3233 Score: 709
Period size: 168 Copynumber: 2.2 Consensus size: 168
2856 TTGAGGGCCA
2866 ATGTGAATTAAGGCAAGTTCAATGTCATTTGGGAAAGTTGGATGTGATTAAGGCAAGTTCAATGT
1 ATGTGAATTAAGGCAAGTTCAATGTCATTTGGGAAAGTTGGATGTGATTAAGGCAAGTTCAATGT
*
2931 CATTTGGATGTGAATTAAGGCAAGTTCAATGTTATTTGGATGTGAATTAAGGCAAGTTCAATGTT
66 CATTTGGATGTGAATTAAGGCAAGTTCAATGTTATTTGGATGTGAATTAAGGCAAGTTCAATGTC
* *
2996 ATTTGGATGTGAATTAAGGCAAGTTCAATGTTATTTGG
131 ACTTGGATGTGAATTAAGGCAAGTTCAATGTCATTTGG
3034 ATGTGAATTAAGGCAAGTTCAATGTCATTTGGGAAAGTTGGATGTGATTAAGGCAAGTTCAATGT
1 ATGTGAATTAAGGCAAGTTCAATGTCATTTGGGAAAGTTGGATGTGATTAAGGCAAGTTCAATGT
3099 CATTTGGATGTGAATTAAGGCAAGTTCAATGTTATTTGGATGTGAATTAAGGCAAGTTCAATGTC
66 CATTTGGATGTGAATTAAGGCAAGTTCAATGTTATTTGGATGTGAATTAAGGCAAGTTCAATGTC
3164 ACTTGGATGTGAATTAAGGCAAGTTCAATGTCATTTGG
131 ACTTGGATGTGAATTAAGGCAAGTTCAATGTCATTTGG
3202 ATGTGAATTAAGGCAAGTTCAATGTCATTTGG
1 ATGTGAATTAAGGCAAGTTCAATGTCATTTGG
3234 ATGTGAATAA
Statistics
Matches: 197, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
168 197 1.00
ACGTcount: A:0.31, C:0.08, G:0.26, T:0.35
Consensus pattern (168 bp):
ATGTGAATTAAGGCAAGTTCAATGTCATTTGGGAAAGTTGGATGTGATTAAGGCAAGTTCAATGT
CATTTGGATGTGAATTAAGGCAAGTTCAATGTTATTTGGATGTGAATTAAGGCAAGTTCAATGTC
ACTTGGATGTGAATTAAGGCAAGTTCAATGTCATTTGG
Found at i:3721 original size:17 final size:17
Alignment explanation
Indices: 3699--3736 Score: 76
Period size: 17 Copynumber: 2.2 Consensus size: 17
3689 AATTTGCCAA
3699 ATTGTTTGCTGTTTGTG
1 ATTGTTTGCTGTTTGTG
3716 ATTGTTTGCTGTTTGTG
1 ATTGTTTGCTGTTTGTG
3733 ATTG
1 ATTG
3737 GATGGGGATG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.08, C:0.05, G:0.29, T:0.58
Consensus pattern (17 bp):
ATTGTTTGCTGTTTGTG
Found at i:5883 original size:2 final size:2
Alignment explanation
Indices: 5876--5904 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
5866 GGTGTTTAAT
5876 TA TA 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 TA TA T
5905 TTTATGAGAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Done.