Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012731.1 Corchorus olitorius cultivar O-4 contig12764, 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: 10048
ACGTcount: A:0.30, C:0.17, G:0.20, T:0.33
Found at i:734 original size:26 final size:26
Alignment explanation
Indices: 703--793 Score: 69
Period size: 26 Copynumber: 3.3 Consensus size: 26
693 TATTGTAGAG
703 GCTAGAGAAAAGCATGTTATTTCAAT
1 GCTAGAGAAAAGCATGTTATTTCAAT
* *
729 GCTAGAGGACATTAG-ATGGAGTTATTGT-AGAG
1 GCTAGA-GA-A-AAGCAT---GTTATT-TCA-AT
*
761 GTTAGAGAAAAGCATGTTATTTCAAT
1 GCTAGAGAAAAGCATGTTATTTCAAT
787 GCTAGAG
1 GCTAGAG
794 GACATTAGGG
Statistics
Matches: 49, Mismatches: 6, Indels: 20
0.65 0.08 0.27
Matches are distributed among these distances:
26 14 0.29
27 9 0.18
28 3 0.06
29 4 0.08
30 3 0.06
31 9 0.18
32 7 0.14
ACGTcount: A:0.35, C:0.09, G:0.26, T:0.30
Consensus pattern (26 bp):
GCTAGAGAAAAGCATGTTATTTCAAT
Found at i:780 original size:58 final size:58
Alignment explanation
Indices: 690--801 Score: 215
Period size: 58 Copynumber: 1.9 Consensus size: 58
680 CTTTTAATGA
690 AGTTATTGTAGAGGCTAGAGAAAAGCATGTTATTTCAATGCTAGAGGACATTAGATGG
1 AGTTATTGTAGAGGCTAGAGAAAAGCATGTTATTTCAATGCTAGAGGACATTAGATGG
*
748 AGTTATTGTAGAGGTTAGAGAAAAGCATGTTATTTCAATGCTAGAGGACATTAG
1 AGTTATTGTAGAGGCTAGAGAAAAGCATGTTATTTCAATGCTAGAGGACATTAG
802 GGTGTATGTG
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
58 53 1.00
ACGTcount: A:0.35, C:0.08, G:0.27, T:0.30
Consensus pattern (58 bp):
AGTTATTGTAGAGGCTAGAGAAAAGCATGTTATTTCAATGCTAGAGGACATTAGATGG
Found at i:5074 original size:96 final size:96
Alignment explanation
Indices: 4910--5085 Score: 334
Period size: 96 Copynumber: 1.8 Consensus size: 96
4900 TTTTAAACTT
4910 TGTGGGAGCCTTTTTGTGGGAATGTGAGAAAGGCCTGGTTTGACTCACTATGGGCTCAAGCCTAG
1 TGTGGGAGCCTTTTTGTGGGAATGTGAGAAAGGCCTGGTTTGACTCACTATGGGCTCAAGCCTAG
4975 CCCAAATCTCCCCAGCGGAGTCGCTAGAAAA
66 CCCAAATCTCCCCAGCGGAGTCGCTAGAAAA
* *
5006 TGTGGGAGCCTTTTTGTGGGAATGTGAGAAAGGCCTGGTTTGCCTCACTATGGGCTCAAGTCTAG
1 TGTGGGAGCCTTTTTGTGGGAATGTGAGAAAGGCCTGGTTTGACTCACTATGGGCTCAAGCCTAG
5071 CCCAAATCTCCCCAG
66 CCCAAATCTCCCCAG
5086 AAGAGGAGCT
Statistics
Matches: 78, Mismatches: 2, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
96 78 1.00
ACGTcount: A:0.22, C:0.23, G:0.29, T:0.26
Consensus pattern (96 bp):
TGTGGGAGCCTTTTTGTGGGAATGTGAGAAAGGCCTGGTTTGACTCACTATGGGCTCAAGCCTAG
CCCAAATCTCCCCAGCGGAGTCGCTAGAAAA
Found at i:7964 original size:11 final size:11
Alignment explanation
Indices: 7948--7995 Score: 50
Period size: 11 Copynumber: 4.7 Consensus size: 11
7938 GAAGTTCGTG
7948 TTTGAAGACCA
1 TTTGAAGACCA
**
7959 TTTGAAGATAA
1 TTTGAAGACCA
7970 TTTGAAGA-C-
1 TTTGAAGACCA
7979 -TTGAAGACCA
1 TTTGAAGACCA
7989 -TTGAAGA
1 TTTGAAGA
7996 TTTATTTCAA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
8 7 0.22
9 1 0.03
10 7 0.22
11 17 0.53
ACGTcount: A:0.40, C:0.10, G:0.21, T:0.29
Consensus pattern (11 bp):
TTTGAAGACCA
Found at i:8611 original size:11 final size:11
Alignment explanation
Indices: 8595--8620 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
8585 AGATATTTTC
8595 TTTTCTTCTAG
1 TTTTCTTCTAG
8606 TTTTCTTCTAG
1 TTTTCTTCTAG
8617 TTTT
1 TTTT
8621 TAGGCAAAGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.08, C:0.15, G:0.08, T:0.69
Consensus pattern (11 bp):
TTTTCTTCTAG
Found at i:9395 original size:15 final size:15
Alignment explanation
Indices: 9365--9406 Score: 66
Period size: 15 Copynumber: 2.7 Consensus size: 15
9355 TTACTTTGTT
9365 TTGTTTTCTAGTTTAA
1 TTGTTTTCT-GTTTAA
9381 TTGTTTTCTGTTTAA
1 TTGTTTTCTGTTTAA
*
9396 TTGCTTTCTGT
1 TTGTTTTCTGT
9407 CAACCTCTGT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
15 16 0.64
16 9 0.36
ACGTcount: A:0.12, C:0.10, G:0.14, T:0.64
Consensus pattern (15 bp):
TTGTTTTCTGTTTAA
Found at i:9745 original size:22 final size:23
Alignment explanation
Indices: 9701--9745 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 23
9691 AAAAAATACA
* **
9701 ATTTGTTGTTTTTGCGTTTTTTT
1 ATTTGTTGTGTTTGCGTCGTTTT
9724 ATTT-TTGTGTTTGCGTCGTTTT
1 ATTTGTTGTGTTTGCGTCGTTTT
9746 GAAAAAGAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.04, C:0.07, G:0.20, T:0.69
Consensus pattern (23 bp):
ATTTGTTGTGTTTGCGTCGTTTT
Found at i:9816 original size:20 final size:19
Alignment explanation
Indices: 9774--9815 Score: 68
Period size: 19 Copynumber: 2.2 Consensus size: 19
9764 TTGTTTTGTG
9774 TTTTGCGTCGAAAAAAAAA
1 TTTTGCGTCGAAAAAAAAA
9793 TTTTGCGTC-ATAAAAAAAA
1 TTTTGCGTCGA-AAAAAAAA
9812 TTTT
1 TTTT
9816 TTGTTTTTGC
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
18 1 0.05
19 21 0.95
ACGTcount: A:0.43, C:0.10, G:0.12, T:0.36
Consensus pattern (19 bp):
TTTTGCGTCGAAAAAAAAA
Found at i:9846 original size:25 final size:24
Alignment explanation
Indices: 9818--9893 Score: 73
Period size: 25 Copynumber: 3.0 Consensus size: 24
9808 AAAATTTTTT
9818 GTTTTTGCGTCATAAAAAAAAAAGG
1 GTTTTTGCGTCATAAAAAAAAAA-G
*
9843 GTTTTTGCGTTTTTC-TAAAAAAAAAAT
1 GTTTTTGCG----TCATAAAAAAAAAAG
*
9870 GATTTTGCGTCATAAAAAGAAAAA
1 GTTTTTGCGTCATAAAAA-AAAAA
9894 AAATTTTGTC
Statistics
Matches: 43, Mismatches: 2, Indels: 12
0.75 0.04 0.21
Matches are distributed among these distances:
23 2 0.05
24 6 0.14
25 14 0.33
27 8 0.19
28 11 0.26
29 2 0.05
ACGTcount: A:0.43, C:0.08, G:0.16, T:0.33
Consensus pattern (24 bp):
GTTTTTGCGTCATAAAAAAAAAAG
Done.