Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017267.1 Corchorus olitorius cultivar O-4 contig17300, 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: 17281
ACGTcount: A:0.27, C:0.20, G:0.19, T:0.33
Found at i:8 original size:2 final size:2
Alignment explanation
Indices: 2--43 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
1 G
*
2 TA TA TA TA TA GA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
44 CATAGAAAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (2 bp):
TA
Found at i:2088 original size:19 final size:18
Alignment explanation
Indices: 2064--2099 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
2054 TGAAGAACAT
2064 TTGAAGATAATTTGAAGAC
1 TTGAAGAT-ATTTGAAGAC
*
2083 TTGAAGATTTTTGAAGA
1 TTGAAGATATTTGAAGA
2100 TTTATTTCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.39, C:0.03, G:0.22, T:0.36
Consensus pattern (18 bp):
TTGAAGATATTTGAAGAC
Found at i:2705 original size:11 final size:11
Alignment explanation
Indices: 2689--2714 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
2679 AGATAATTTC
2689 TTTTCTTCTAG
1 TTTTCTTCTAG
2700 TTTTCTTCTAG
1 TTTTCTTCTAG
2711 TTTT
1 TTTT
2715 TTAGGGCTAG
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:3912 original size:33 final size:33
Alignment explanation
Indices: 3857--3955 Score: 104
Period size: 34 Copynumber: 3.2 Consensus size: 33
3847 TTTAATTTTT
* * *
3857 TTTTTAAAAAAAAAATTGTGTTTTGTGTCTTGCG
1 TTTTTGAAAAAAAAA-TCTGTTTTGTGTTTTGCG
3891 TTTTTGAAAAAAAAATCTGTTTTGT-TTTTGCG
1 TTTTTGAAAAAAAAATCTGTTTTGTGTTTTGCG
*
3923 -TTAT--AAAAAAAA-CT-TTTT-TGTTTTGCG
1 TTTTTGAAAAAAAAATCTGTTTTGTGTTTTGCG
3950 TTTTTG
1 TTTTTG
3956 CGTTTTTCTA
Statistics
Matches: 57, Mismatches: 5, Indels: 11
0.78 0.07 0.15
Matches are distributed among these distances:
26 1 0.02
27 11 0.19
28 5 0.09
29 8 0.14
31 3 0.05
32 6 0.11
33 9 0.16
34 14 0.25
ACGTcount: A:0.28, C:0.06, G:0.15, T:0.51
Consensus pattern (33 bp):
TTTTTGAAAAAAAAATCTGTTTTGTGTTTTGCG
Found at i:3941 original size:28 final size:28
Alignment explanation
Indices: 3898--3951 Score: 83
Period size: 27 Copynumber: 1.9 Consensus size: 28
3888 GCGTTTTTGA
3898 AAAAAAAATCTGTTTTGTTTTTGCGTTAT
1 AAAAAAAATCTGTTTTG-TTTTGCGTTAT
*
3927 AAAAAAAA-CTTTTTTGTTTTGCGTT
1 AAAAAAAATCTGTTTTGTTTTGCGTT
3952 TTTGCGTTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
27 9 0.38
28 7 0.29
29 8 0.33
ACGTcount: A:0.31, C:0.07, G:0.13, T:0.48
Consensus pattern (28 bp):
AAAAAAAATCTGTTTTGTTTTGCGTTAT
Found at i:3987 original size:27 final size:28
Alignment explanation
Indices: 3949--4003 Score: 85
Period size: 27 Copynumber: 2.0 Consensus size: 28
3939 TTTGTTTTGC
3949 GTTTTTGCGTTTTT-CTAAAAAAAAAAA
1 GTTTTTGCGTTTTTACTAAAAAAAAAAA
* *
3976 GTTTTTGCGTTTTTATTTAAAAAAAAAA
1 GTTTTTGCGTTTTTACTAAAAAAAAAAA
4004 TTTCTTTTCT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
27 14 0.56
28 11 0.44
ACGTcount: A:0.40, C:0.05, G:0.11, T:0.44
Consensus pattern (28 bp):
GTTTTTGCGTTTTTACTAAAAAAAAAAA
Found at i:4019 original size:28 final size:28
Alignment explanation
Indices: 3949--4003 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 28
3939 TTTGTTTTGC
*
3949 GTTTTTGCGTT-TT-TCTAAAAAAAAAAA
1 GTTTTTGCGTTGTTAT-TTAAAAAAAAAA
*
3976 GTTTTTGCGTTTTTATTTAAAAAAAAAA
1 GTTTTTGCGTTGTTATTTAAAAAAAAAA
4004 TTTCTTTTCT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
27 11 0.44
28 13 0.52
29 1 0.04
ACGTcount: A:0.40, C:0.05, G:0.11, T:0.44
Consensus pattern (28 bp):
GTTTTTGCGTTGTTATTTAAAAAAAAAA
Found at i:5914 original size:6 final size:6
Alignment explanation
Indices: 5893--5932 Score: 62
Period size: 6 Copynumber: 6.7 Consensus size: 6
5883 AACATGTTAA
**
5893 TTTTCT TTTTAG TTTTCT TTTTCT TTTTCT TTTTCT TTTT
1 TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT TTTT
5933 AGGATTTCAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.03, C:0.12, G:0.03, T:0.82
Consensus pattern (6 bp):
TTTTCT
Found at i:16115 original size:34 final size:33
Alignment explanation
Indices: 16052--16116 Score: 78
Period size: 34 Copynumber: 1.9 Consensus size: 33
16042 TTTATTTAGG
16052 TTTGGAATCTCTTCTTAATTTGGAAAATTTTTGA
1 TTTGGAATCTCTTCTTAATTTGG-AAATTTTTGA
* *
16086 TTTGGATTCTTTTACTTAAGTTTGG-AATTTT
1 TTTGGAATCTCTT-CTTAA-TTTGGAAATTTT
16117 GAATCATCGT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
34 17 0.63
35 5 0.19
36 5 0.19
ACGTcount: A:0.23, C:0.08, G:0.15, T:0.54
Consensus pattern (33 bp):
TTTGGAATCTCTTCTTAATTTGGAAATTTTTGA
Found at i:17035 original size:13 final size:13
Alignment explanation
Indices: 17017--17041 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
17007 TTCACAGGGT
17017 TGCTGAGGTGGAC
1 TGCTGAGGTGGAC
17030 TGCTGAGGTGGA
1 TGCTGAGGTGGA
17042 GTGGGGCCAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.16, C:0.12, G:0.48, T:0.24
Consensus pattern (13 bp):
TGCTGAGGTGGAC
Done.