Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020501.1 Corchorus olitorius cultivar O-4 contig20534, 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: 20998
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32
Found at i:1550 original size:16 final size:16
Alignment explanation
Indices: 1529--1564 Score: 72
Period size: 16 Copynumber: 2.2 Consensus size: 16
1519 ATTCTTATTT
1529 AGATGTTTGGGTATAA
1 AGATGTTTGGGTATAA
1545 AGATGTTTGGGTATAA
1 AGATGTTTGGGTATAA
1561 AGAT
1 AGAT
1565 TTATTTGAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.33, C:0.00, G:0.31, T:0.36
Consensus pattern (16 bp):
AGATGTTTGGGTATAA
Found at i:2121 original size:28 final size:30
Alignment explanation
Indices: 2051--2123 Score: 80
Period size: 31 Copynumber: 2.5 Consensus size: 30
2041 CTAAATAATC
* *
2051 AATTCAGGATATAACGTTTGCCCAAAAAATT
1 AATTCAGGATATAACGTTT-CCAAAAAAACT
*
2082 AATT-TGGAATATAACGTTT-CAAAAAAACT
1 AATTCAGG-ATATAACGTTTCCAAAAAAACT
2111 -ATTCAGGATATAA
1 AATTCAGGATATAA
2124 TGTTAAGAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 7
0.77 0.09 0.15
Matches are distributed among these distances:
28 9 0.25
29 10 0.28
30 2 0.06
31 15 0.42
ACGTcount: A:0.45, C:0.12, G:0.12, T:0.30
Consensus pattern (30 bp):
AATTCAGGATATAACGTTTCCAAAAAAACT
Found at i:3739 original size:31 final size:29
Alignment explanation
Indices: 3664--3739 Score: 80
Period size: 31 Copynumber: 2.6 Consensus size: 29
3654 ATTTCCTAAT
* ***
3664 GTTATATCCTGAATAGTTTTTTTTGAAAC
1 GTTATATCCTGAATTGTTTTTCGGGAAAC
**
3693 GTTATATCCCAAATTGATTTTTCGGGCAAAC
1 GTTATATCCTGAATTG-TTTTTCGGG-AAAC
3724 GTTATATCCTGAATTG
1 GTTATATCCTGAATTG
3740 GTTATTTAGC
Statistics
Matches: 37, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
29 13 0.35
30 6 0.16
31 18 0.49
ACGTcount: A:0.28, C:0.14, G:0.16, T:0.42
Consensus pattern (29 bp):
GTTATATCCTGAATTGTTTTTCGGGAAAC
Found at i:7115 original size:1 final size:1
Alignment explanation
Indices: 7109--7141 Score: 66
Period size: 1 Copynumber: 33.0 Consensus size: 1
7099 CTTCTGCTTC
7109 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
7142 AATATTCCTC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 32 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:17739 original size:22 final size:22
Alignment explanation
Indices: 17709--17751 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
17699 AAAATTCAGA
*
17709 ACAAGTCCTGCCCAAGACTTGG
1 ACAACTCCTGCCCAAGACTTGG
*
17731 ACAACTCCTGCCCAGGACTTG
1 ACAACTCCTGCCCAAGACTTG
17752 TTGCGGGAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.26, C:0.35, G:0.21, T:0.19
Consensus pattern (22 bp):
ACAACTCCTGCCCAAGACTTGG
Found at i:18804 original size:21 final size:21
Alignment explanation
Indices: 18780--18843 Score: 112
Period size: 21 Copynumber: 3.1 Consensus size: 21
18770 CCTTAGGCAA
18780 CTCCAATGAGCTTGAAACCTT
1 CTCCAATGAGCTTGAAACCTT
*
18801 CTCCAATGAGCTTGAAACTTT
1 CTCCAATGAGCTTGAAACCTT
18822 CTCCAATGAGCTTGAAA-CTT
1 CTCCAATGAGCTTGAAACCTT
18842 CT
1 CT
18844 TTGTGTGAAT
Statistics
Matches: 41, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
20 4 0.10
21 37 0.90
ACGTcount: A:0.28, C:0.27, G:0.14, T:0.31
Consensus pattern (21 bp):
CTCCAATGAGCTTGAAACCTT
Found at i:19838 original size:22 final size:22
Alignment explanation
Indices: 19807--19850 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
19797 TTCTTTCCGC
*
19807 AACAACTTCTGTCCCGAAGTTG
1 AACAACTTCTGGCCCGAAGTTG
* *
19829 AACAAGTTCTGGGCCGAAGTTG
1 AACAACTTCTGGCCCGAAGTTG
19851 TCTTGCGCAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.27, C:0.23, G:0.25, T:0.25
Consensus pattern (22 bp):
AACAACTTCTGGCCCGAAGTTG
Found at i:19861 original size:52 final size:52
Alignment explanation
Indices: 19804--19904 Score: 193
Period size: 52 Copynumber: 1.9 Consensus size: 52
19794 TTTTTCTTTC
19804 CGCAACAACTTCTGTCCCGAAGTTGAACAAGTTCTGGGCCGAAGTTGTCTTG
1 CGCAACAACTTCTGTCCCGAAGTTGAACAAGTTCTGGGCCGAAGTTGTCTTG
*
19856 CGCAACAACTTCTGTCCGGAAGTTGAACAAGTTCTGGGCCGAAGTTGTC
1 CGCAACAACTTCTGTCCCGAAGTTGAACAAGTTCTGGGCCGAAGTTGTC
19905 CTGCAATTCT
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
52 48 1.00
ACGTcount: A:0.24, C:0.25, G:0.26, T:0.26
Consensus pattern (52 bp):
CGCAACAACTTCTGTCCCGAAGTTGAACAAGTTCTGGGCCGAAGTTGTCTTG
Found at i:19958 original size:21 final size:21
Alignment explanation
Indices: 19934--19987 Score: 90
Period size: 21 Copynumber: 2.6 Consensus size: 21
19924 TTCAACAGGC
*
19934 CAACTTCTGGGCAGAAGTTGA
1 CAACATCTGGGCAGAAGTTGA
*
19955 CAACATCTCGGCAGAAGTTGA
1 CAACATCTGGGCAGAAGTTGA
19976 CAACATCTGGGC
1 CAACATCTGGGC
19988 CGATATTGTA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.30, C:0.24, G:0.26, T:0.20
Consensus pattern (21 bp):
CAACATCTGGGCAGAAGTTGA
Found at i:20518 original size:16 final size:15
Alignment explanation
Indices: 20480--20521 Score: 75
Period size: 15 Copynumber: 2.7 Consensus size: 15
20470 ACAGAGATTG
20480 ACAGAAAACAATTAA
1 ACAGAAAACAATTAA
20495 ACAGAAAACAATTAA
1 ACAGAAAACAATTAA
20510 ACTAGAAAACAA
1 AC-AGAAAACAA
20522 AGCAAAGTTA
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:0.67, C:0.14, G:0.07, T:0.12
Consensus pattern (15 bp):
ACAGAAAACAATTAA
Done.