Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023628.1 Corchorus olitorius cultivar O-4 contig23661, 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: 9057
ACGTcount: A:0.32, C:0.17, G:0.20, T:0.31
Found at i:3513 original size:27 final size:27
Alignment explanation
Indices: 3386--3512 Score: 191
Period size: 27 Copynumber: 4.7 Consensus size: 27
3376 TATGAACTTA
* *
3386 AAATGACCAAAATGTCCCTGAATGTGC
1 AAATGACTAAAATGCCCCTGAATGTGC
* * *
3413 AAATGACTAAATTGCCCCTGCATATGC
1 AAATGACTAAAATGCCCCTGAATGTGC
*
3440 AAATGACTAAAATGTCCCTGAATGTGC
1 AAATGACTAAAATGCCCCTGAATGTGC
*
3467 AAATGACTAAAATGCCCCTAAATGTGC
1 AAATGACTAAAATGCCCCTGAATGTGC
3494 AAATGACTAAAATGCCCCT
1 AAATGACTAAAATGCCCCT
3513 AGATTTTTGA
Statistics
Matches: 89, Mismatches: 11, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 89 1.00
ACGTcount: A:0.38, C:0.23, G:0.16, T:0.24
Consensus pattern (27 bp):
AAATGACTAAAATGCCCCTGAATGTGC
Found at i:3835 original size:48 final size:48
Alignment explanation
Indices: 3759--3859 Score: 157
Period size: 48 Copynumber: 2.1 Consensus size: 48
3749 CGAATCAATC
* *
3759 TGATCTATTTGAAGATTTGTTGCACCGAGCCCACTGAGTCCATATTGA
1 TGATGTATTTGAAGATTTGATGCACCGAGCCCACTGAGTCCATATTGA
* *
3807 TGATGTATTTGAAGATTTGATGCACCGAGCCTACTGAGTCCATGTTGA
1 TGATGTATTTGAAGATTTGATGCACCGAGCCCACTGAGTCCATATTGA
*
3855 AGATG
1 TGATG
3860 CTACATCGAG
Statistics
Matches: 48, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
48 48 1.00
ACGTcount: A:0.26, C:0.18, G:0.24, T:0.33
Consensus pattern (48 bp):
TGATGTATTTGAAGATTTGATGCACCGAGCCCACTGAGTCCATATTGA
Found at i:3893 original size:35 final size:36
Alignment explanation
Indices: 3851--4017 Score: 243
Period size: 35 Copynumber: 4.8 Consensus size: 36
3841 TGAGTCCATG
* *
3851 TTGAAGATGCTACATCGAGTCATCTGAATTAT-TCT
1 TTGAAGATGCTACACCGAGTCATCTGAATTATAACT
* *
3886 TTGAAGATGCTACACCTAGTCATTTGAA-TATAACT
1 TTGAAGATGCTACACCGAGTCATCTGAATTATAACT
*
3921 TTGAAGATGCTACACCGAGTCATCT-AAATATAACT
1 TTGAAGATGCTACACCGAGTCATCTGAATTATAACT
*
3956 TTGAAGATGCTACACCGAGTCATCTGAATT-CAACT
1 TTGAAGATGCTACACCGAGTCATCTGAATTATAACT
*
3991 TTGAAGATGCTACATCGAGTCATCTGA
1 TTGAAGATGCTACACCGAGTCATCTGA
4018 GAAGATGGTA
Statistics
Matches: 120, Mismatches: 9, Indels: 6
0.89 0.07 0.04
Matches are distributed among these distances:
34 5 0.04
35 112 0.93
36 3 0.03
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32
Consensus pattern (36 bp):
TTGAAGATGCTACACCGAGTCATCTGAATTATAACT
Found at i:4773 original size:50 final size:50
Alignment explanation
Indices: 4719--4867 Score: 192
Period size: 50 Copynumber: 3.0 Consensus size: 50
4709 CTTAAATGCC
* *
4719 CTTTGAAAAGTGAATTTTGATCTTGGACTCACAACTGGAATGCAATCTTA
1 CTTTGAAAAGTGAATTTTGATCTTGAACTCACAACTGGAAAGCAATCTTA
* * *
4769 CTTTGAAAAGCGAATTTTAATCTTGAACTCACAAAC-GGAAAGCAATTTTA
1 CTTTGAAAAGTGAATTTTGATCTTGAACTCAC-AACTGGAAAGCAATCTTA
* * * * *
4819 TTTTGAAAAGTGAATTTTGATCATGAACTCATAAATGGAAAGAAATCTT
1 CTTTGAAAAGTGAATTTTGATCTTGAACTCACAACTGGAAAGCAATCTT
4868 GTTATAAAAC
Statistics
Matches: 84, Mismatches: 13, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
49 2 0.02
50 79 0.94
51 3 0.04
ACGTcount: A:0.38, C:0.13, G:0.16, T:0.33
Consensus pattern (50 bp):
CTTTGAAAAGTGAATTTTGATCTTGAACTCACAACTGGAAAGCAATCTTA
Found at i:5474 original size:7 final size:7
Alignment explanation
Indices: 5462--5497 Score: 56
Period size: 7 Copynumber: 5.3 Consensus size: 7
5452 TTTGATTTGA
5462 TTTGATT
1 TTTGATT
5469 TTTGATT
1 TTTGATT
5476 TTTGA-T
1 TTTGATT
5482 TTTGATT
1 TTTGATT
*
5489 TTTTATT
1 TTTGATT
5496 TT
1 TT
5498 GAATTTTTTG
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
6 6 0.22
7 21 0.78
ACGTcount: A:0.14, C:0.00, G:0.11, T:0.75
Consensus pattern (7 bp):
TTTGATT
Found at i:5486 original size:13 final size:13
Alignment explanation
Indices: 5451--5505 Score: 62
Period size: 13 Copynumber: 4.3 Consensus size: 13
5441 ATCAATTCTC
5451 TTTTGA-TTTGA-
1 TTTTGATTTTGAT
5462 -TTTGATTTTTGAT
1 TTTTGA-TTTTGAT
5475 TTTTGATTTTGAT
1 TTTTGATTTTGAT
*
5488 TTTTTATTTTGAAT
1 TTTTGATTTTG-AT
5502 TTTT
1 TTTT
5506 TGATGGAGGG
Statistics
Matches: 38, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
10 5 0.13
12 5 0.13
13 17 0.45
14 11 0.29
ACGTcount: A:0.16, C:0.00, G:0.13, T:0.71
Consensus pattern (13 bp):
TTTTGATTTTGAT
Found at i:5504 original size:20 final size:20
Alignment explanation
Indices: 5457--5497 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
5447 TCTCTTTTGA
5457 TTTGA-TTTGATTTTTGATT
1 TTTGATTTTGATTTTTGATT
*
5476 TTTGATTTTGATTTTTTATT
1 TTTGATTTTGATTTTTGATT
5496 TT
1 TT
5498 GAATTTTTTG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
19 5 0.25
20 15 0.75
ACGTcount: A:0.15, C:0.00, G:0.12, T:0.73
Consensus pattern (20 bp):
TTTGATTTTGATTTTTGATT
Found at i:5923 original size:17 final size:17
Alignment explanation
Indices: 5901--5937 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
5891 TTTTTTTGAA
5901 TTTCATTTTCATTTTTT
1 TTTCATTTTCATTTTTT
**
5918 TTTCATTTTTGTTTTTT
1 TTTCATTTTCATTTTTT
5935 TTT
1 TTT
5938 GGGAAATCAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.08, C:0.08, G:0.03, T:0.81
Consensus pattern (17 bp):
TTTCATTTTCATTTTTT
Found at i:5926 original size:11 final size:11
Alignment explanation
Indices: 5883--5932 Score: 55
Period size: 11 Copynumber: 4.5 Consensus size: 11
5873 TTTATTTTCC
5883 TTTTTCATTTT
1 TTTTTCATTTT
** *
5894 TTTTGAATTTC
1 TTTTTCATTTT
*
5905 ATTTTCATTTT
1 TTTTTCATTTT
5916 TTTTTCATTTT
1 TTTTTCATTTT
5927 TGTTTT
1 T-TTTT
5933 TTTTTGGGAA
Statistics
Matches: 30, Mismatches: 8, Indels: 1
0.77 0.21 0.03
Matches are distributed among these distances:
11 26 0.87
12 4 0.13
ACGTcount: A:0.12, C:0.08, G:0.04, T:0.76
Consensus pattern (11 bp):
TTTTTCATTTT
Found at i:8134 original size:15 final size:14
Alignment explanation
Indices: 8110--8139 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
8100 CAATAACATC
8110 AAACAAACAAAACA
1 AAACAAACAAAACA
8124 AAACGAAACAAAACA
1 AAAC-AAACAAAACA
8139 A
1 A
8140 CGCAACCGAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.27
15 11 0.73
ACGTcount: A:0.77, C:0.20, G:0.03, T:0.00
Consensus pattern (14 bp):
AAACAAACAAAACA
Done.