Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022536.1 Corchorus olitorius cultivar O-4 contig22569, 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: 43677
ACGTcount: A:0.29, C:0.18, G:0.19, T:0.33
Found at i:7928 original size:6 final size:6
Alignment explanation
Indices: 7917--7945 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
7907 ATTTCTTGCG
7917 CCATTA CCATTA CCATTA CCATTA CCATT
1 CCATTA CCATTA CCATTA CCATTA CCATT
7946 CCTCACGTGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.31, C:0.34, G:0.00, T:0.34
Consensus pattern (6 bp):
CCATTA
Found at i:10647 original size:20 final size:19
Alignment explanation
Indices: 10592--10647 Score: 62
Period size: 17 Copynumber: 2.9 Consensus size: 19
10582 CATGGGATTT
10592 TTAATAATAATT-ATTTAA
1 TTAATAATAATTAATTTAA
*
10610 -TAAAAATAATTATTATTTAA
1 TTAATAATAATTA--ATTTAA
10630 TTAATAATTAATTAATTT
1 TTAATAA-TAATTAATTT
10648 CAGCCCTTGC
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
17 10 0.32
20 10 0.32
21 5 0.16
22 6 0.19
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (19 bp):
TTAATAATAATTAATTTAA
Found at i:10857 original size:22 final size:22
Alignment explanation
Indices: 10794--10855 Score: 115
Period size: 22 Copynumber: 2.8 Consensus size: 22
10784 CTCAATTGTA
10794 AATTGAGGTATAAACAAATACT
1 AATTGAGGTATAAACAAATACT
10816 AATTGAGGTATAAACAAATACT
1 AATTGAGGTATAAACAAATACT
10838 AATTGAGGTATAATACAA
1 AATTGAGGTATAA-ACAA
10856 TATATTTATT
Statistics
Matches: 39, Mismatches: 0, Indels: 1
0.98 0.00 0.03
Matches are distributed among these distances:
22 35 0.90
23 4 0.10
ACGTcount: A:0.50, C:0.08, G:0.15, T:0.27
Consensus pattern (22 bp):
AATTGAGGTATAAACAAATACT
Found at i:11248 original size:43 final size:45
Alignment explanation
Indices: 11172--11262 Score: 130
Period size: 47 Copynumber: 1.9 Consensus size: 45
11162 TCATGCTATA
11172 TGTATCGGTACGGTTTAATGCTTATATAATATAATTAATTAATTTTG
1 TGTATCGGTACGGTTTAATGC-T-TATAATATAATTAATTAATTTTG
11219 TGTATCCGGTACGGTTTAATGCTTAT-ATAATTAATTAATTAATT
1 TGTAT-CGGTACGGTTTAATGCTTATAAT-A-TAATTAATTAATT
11263 AATTTTTGTA
Statistics
Matches: 41, Mismatches: 0, Indels: 6
0.87 0.00 0.13
Matches are distributed among these distances:
45 2 0.05
46 4 0.10
47 19 0.46
48 16 0.39
ACGTcount: A:0.32, C:0.08, G:0.14, T:0.46
Consensus pattern (45 bp):
TGTATCGGTACGGTTTAATGCTTATAATATAATTAATTAATTTTG
Found at i:11256 original size:47 final size:47
Alignment explanation
Indices: 11172--11262 Score: 166
Period size: 48 Copynumber: 1.9 Consensus size: 47
11162 TCATGCTATA
11172 TGTATCGGTACGGTTTAATGCTTATATAATATAATTAATTAATTTTG
1 TGTATCGGTACGGTTTAATGCTTATATAATATAATTAATTAATTTTG
11219 TGTATCCGGTACGGTTTAATGCTTATATAAT-TAATTAATTAATT
1 TGTAT-CGGTACGGTTTAATGCTTATATAATATAATTAATTAATT
11263 AATTTTTGTA
Statistics
Matches: 43, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
47 18 0.42
48 25 0.58
ACGTcount: A:0.32, C:0.08, G:0.14, T:0.46
Consensus pattern (47 bp):
TGTATCGGTACGGTTTAATGCTTATATAATATAATTAATTAATTTTG
Found at i:19483 original size:15 final size:15
Alignment explanation
Indices: 19460--19489 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
19450 GAATGCATTC
19460 TTTTCTTTCCATTTT
1 TTTTCTTTCCATTTT
*
19475 TTTTTTTTCCATTTT
1 TTTTCTTTCCATTTT
19490 ATACTTAATC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.07, C:0.17, G:0.00, T:0.77
Consensus pattern (15 bp):
TTTTCTTTCCATTTT
Found at i:42594 original size:21 final size:21
Alignment explanation
Indices: 42570--42616 Score: 85
Period size: 21 Copynumber: 2.2 Consensus size: 21
42560 ACCTTTTACC
*
42570 TTTGCAAAAGCTTTGAACAAT
1 TTTGAAAAAGCTTTGAACAAT
42591 TTTGAAAAAGCTTTGAACAAT
1 TTTGAAAAAGCTTTGAACAAT
42612 TTTGA
1 TTTGA
42617 CGTCCAGATT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.38, C:0.11, G:0.15, T:0.36
Consensus pattern (21 bp):
TTTGAAAAAGCTTTGAACAAT
Found at i:43496 original size:15 final size:15
Alignment explanation
Indices: 43476--43506 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
43466 ACAATACATT
43476 AACTATCAAATAGAA
1 AACTATCAAATAGAA
43491 AACTATCAAATAGAA
1 AACTATCAAATAGAA
43506 A
1 A
43507 CAGGTTAATC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.61, C:0.13, G:0.06, T:0.19
Consensus pattern (15 bp):
AACTATCAAATAGAA
Found at i:43549 original size:14 final size:14
Alignment explanation
Indices: 43530--43567 Score: 67
Period size: 14 Copynumber: 2.7 Consensus size: 14
43520 ATAACCTTTT
43530 AAATAAAATAGTAA
1 AAATAAAATAGTAA
*
43544 AAATAAAATGGTAA
1 AAATAAAATAGTAA
43558 AAATAAAATA
1 AAATAAAATA
43568 ATTATAAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.71, C:0.00, G:0.08, T:0.21
Consensus pattern (14 bp):
AAATAAAATAGTAA
Done.