Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023646.1 Corchorus olitorius cultivar O-4 contig23679, 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: 17367
ACGTcount: A:0.30, C:0.19, G:0.18, T:0.33
Found at i:4880 original size:15 final size:15
Alignment explanation
Indices: 4850--4891 Score: 75
Period size: 15 Copynumber: 2.7 Consensus size: 15
4840 TTACTTTGTT
4850 TTGTTTTCTAGTTTAA
1 TTGTTTTCT-GTTTAA
4866 TTGTTTTCTGTTTAA
1 TTGTTTTCTGTTTAA
4881 TTGTTTTCTGT
1 TTGTTTTCTGT
4892 CAACCTCTGT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
15 17 0.65
16 9 0.35
ACGTcount: A:0.12, C:0.07, G:0.14, T:0.67
Consensus pattern (15 bp):
TTGTTTTCTGTTTAA
Found at i:5318 original size:145 final size:145
Alignment explanation
Indices: 5050--5401 Score: 641
Period size: 145 Copynumber: 2.4 Consensus size: 145
5040 CGACCGATCA
5050 GGAGGTTTCTGAAATGGTGCCCGGAGGTCTTACAAATGCAAACTCAACCTTGAGCAAGGTTTTGA
1 GGAGGTTTCTGAAATGGTGCCCGGAGGTCTTACAAATGCAAACTCAACCTTGAGCAAGGTTTTGA
5115 TTTTGAAATTTAAATGCAACTTTGATTAAAAACTTGATGAAATGAAATGATACCCGGAGGATTTA
66 TTTTGAAATTTAAATGCAACTTTGATTAAAAACTTGATGAAATGAAATGATACCCGGAGGATTTA
5180 TCAGAATTAATACCC
131 TCAGAATTAATACCC
* * *
5195 GGAGGTTTCTGAGATGGTGCCCGGAGGTTTTATAAATGCAAACTCAACCTTGAGCAAGGTTTTGA
1 GGAGGTTTCTGAAATGGTGCCCGGAGGTCTTACAAATGCAAACTCAACCTTGAGCAAGGTTTTGA
* *
5260 TTTTGAAATTTAAATGCAACTTTGATTAAAAATTTGATGAAATGAAATGATACTCGGAGGATTTA
66 TTTTGAAATTTAAATGCAACTTTGATTAAAAACTTGATGAAATGAAATGATACCCGGAGGATTTA
5325 TCAGAATTAATACCC
131 TCAGAATTAATACCC
* *
5340 GAAGGTTTCTGAAATGGTGCCCGGAGGTCTTACAAATGCAAACTCGACCTTGAGCAAGGTTT
1 GGAGGTTTCTGAAATGGTGCCCGGAGGTCTTACAAATGCAAACTCAACCTTGAGCAAGGTTT
5402 ATTAAAATTT
Statistics
Matches: 197, Mismatches: 10, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
145 197 1.00
ACGTcount: A:0.33, C:0.15, G:0.22, T:0.30
Consensus pattern (145 bp):
GGAGGTTTCTGAAATGGTGCCCGGAGGTCTTACAAATGCAAACTCAACCTTGAGCAAGGTTTTGA
TTTTGAAATTTAAATGCAACTTTGATTAAAAACTTGATGAAATGAAATGATACCCGGAGGATTTA
TCAGAATTAATACCC
Found at i:6649 original size:7 final size:7
Alignment explanation
Indices: 6624--6669 Score: 51
Period size: 7 Copynumber: 6.9 Consensus size: 7
6614 ATCTTATACT
6624 TTTTCAA
1 TTTTCAA
*
6631 TTTTTAA
1 TTTTCAA
6638 TTTTCAA
1 TTTTCAA
6645 TTTTC-A
1 TTTTCAA
*
6651 CTTTC-A
1 TTTTCAA
*
6657 CTTTCAA
1 TTTTCAA
6664 TTTTCA
1 TTTTCA
6670 CTTCTTTTTT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
6 11 0.32
7 23 0.68
ACGTcount: A:0.24, C:0.17, G:0.00, T:0.59
Consensus pattern (7 bp):
TTTTCAA
Found at i:6694 original size:15 final size:14
Alignment explanation
Indices: 6674--6713 Score: 53
Period size: 14 Copynumber: 2.8 Consensus size: 14
6664 TTTTCACTTC
*
6674 TTTTTTCGTTTTCT
1 TTTTTTTGTTTTCT
*
6688 TTTTTTTGTTTTGT
1 TTTTTTTGTTTTCT
6702 TTTGTTTTGTTT
1 TTT-TTTTGTTT
6714 GTTTGTTTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 15 0.65
15 8 0.35
ACGTcount: A:0.00, C:0.05, G:0.12, T:0.82
Consensus pattern (14 bp):
TTTTTTTGTTTTCT
Found at i:6716 original size:4 final size:5
Alignment explanation
Indices: 6676--6733 Score: 59
Period size: 5 Copynumber: 12.0 Consensus size: 5
6666 TTCACTTCTT
* *
6676 TTTTCG TTTTC TTTT- TTTTG TTTTG TTTTG TTTTG -TTTG -TTTG TTTTT
1 TTTT-G TTTTG TTTTG TTTTG TTTTG TTTTG TTTTG TTTTG TTTTG TTTTG
*
6724 TTTTT TTTTG
1 TTTTG TTTTG
6734 CATATTCATT
Statistics
Matches: 47, Mismatches: 3, Indels: 5
0.85 0.05 0.09
Matches are distributed among these distances:
4 12 0.26
5 31 0.66
6 4 0.09
ACGTcount: A:0.00, C:0.03, G:0.14, T:0.83
Consensus pattern (5 bp):
TTTTG
Found at i:6733 original size:19 final size:19
Alignment explanation
Indices: 6676--6730 Score: 69
Period size: 19 Copynumber: 2.9 Consensus size: 19
6666 TTCACTTCTT
6676 TTTTCGTTTTCTTTTTTTTG
1 TTTT-GTTTTCTTTTTTTTG
* *
6696 TTTTGTTTTGTTTTGTTTG
1 TTTTGTTTTCTTTTTTTTG
6715 -TTTGTTTT-TTTTTTTT
1 TTTTGTTTTCTTTTTTTT
6731 TTGCATATTC
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
17 7 0.22
18 8 0.25
19 13 0.41
20 4 0.12
ACGTcount: A:0.00, C:0.04, G:0.13, T:0.84
Consensus pattern (19 bp):
TTTTGTTTTCTTTTTTTTG
Found at i:14716 original size:12 final size:12
Alignment explanation
Indices: 14692--14726 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
14682 CTGTTTTGTT
*
14692 TTATTGTTATGG
1 TTATTGCTATGG
*
14704 TTGTTGCTATGG
1 TTATTGCTATGG
14716 TTATTGCTATG
1 TTATTGCTATG
14727 TCAGTGGGTA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.14, C:0.06, G:0.26, T:0.54
Consensus pattern (12 bp):
TTATTGCTATGG
Found at i:16936 original size:12 final size:13
Alignment explanation
Indices: 16914--16943 Score: 53
Period size: 12 Copynumber: 2.4 Consensus size: 13
16904 ACTAACAATT
16914 AAAATCAATCAAG
1 AAAATCAATCAAG
16927 AAAA-CAATCAAG
1 AAAATCAATCAAG
16939 AAAAT
1 AAAAT
16944 TAAAGAAAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
12 12 0.75
13 4 0.25
ACGTcount: A:0.67, C:0.13, G:0.07, T:0.13
Consensus pattern (13 bp):
AAAATCAATCAAG
Done.