Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012918.1 Corchorus olitorius cultivar O-4 contig12951, 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: 24673
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:1387 original size:27 final size:26
Alignment explanation
Indices: 1331--1387 Score: 64
Period size: 27 Copynumber: 2.2 Consensus size: 26
1321 TTAAGGATTA
*
1331 ATTATTTATTTATTGTATTTTCTCTT
1 ATTATTTATTTATTGTATTTTCTCTC
1357 ATTATTTTATTTATAT-TATTATTC-CTC
1 ATTA-TTTATTTAT-TGTATT-TTCTCTC
1384 ATTA
1 ATTA
1388 AGTTGGTGAC
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
26 4 0.15
27 19 0.70
28 4 0.15
ACGTcount: A:0.25, C:0.09, G:0.02, T:0.65
Consensus pattern (26 bp):
ATTATTTATTTATTGTATTTTCTCTC
Found at i:3558 original size:21 final size:21
Alignment explanation
Indices: 3532--3574 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
3522 CGGCCTTTTT
*
3532 AGGCCCTAAAGGAAACGTTGA
1 AGGCCCTAAACGAAACGTTGA
3553 AGGCCCTAAACGAAACGTTGA
1 AGGCCCTAAACGAAACGTTGA
3574 A
1 A
3575 CTATGAGGTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.40, C:0.21, G:0.26, T:0.14
Consensus pattern (21 bp):
AGGCCCTAAACGAAACGTTGA
Found at i:3946 original size:19 final size:17
Alignment explanation
Indices: 3922--3960 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
3912 CAATCCAGTA
3922 TTTCTTACTCTCTTTTTCT
1 TTTCTT-CTCTCTTTTT-T
*
3941 TTTCTTTTCTCTTTTTT
1 TTTCTTCTCTCTTTTTT
3958 TTT
1 TTT
3961 AGTTTCCAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 4 0.21
18 9 0.47
19 6 0.32
ACGTcount: A:0.03, C:0.21, G:0.00, T:0.77
Consensus pattern (17 bp):
TTTCTTCTCTCTTTTTT
Found at i:7121 original size:21 final size:21
Alignment explanation
Indices: 7097--7143 Score: 85
Period size: 21 Copynumber: 2.2 Consensus size: 21
7087 TACTACCATG
7097 TATAATGTTCCACTTCTACTA
1 TATAATGTTCCACTTCTACTA
7118 TATAATGTTCCACTTCTACTA
1 TATAATGTTCCACTTCTACTA
*
7139 AATAA
1 TATAA
7144 ATAAAATATC
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:0.34, C:0.21, G:0.04, T:0.40
Consensus pattern (21 bp):
TATAATGTTCCACTTCTACTA
Found at i:11636 original size:34 final size:34
Alignment explanation
Indices: 11593--11661 Score: 129
Period size: 34 Copynumber: 2.0 Consensus size: 34
11583 TATACACTAC
11593 TAAATCCAAATATAAAAGTATTTTACTTTTTAAT
1 TAAATCCAAATATAAAAGTATTTTACTTTTTAAT
*
11627 TAAATCCAAATATAAAAGTATTTTGCTTTTTAAT
1 TAAATCCAAATATAAAAGTATTTTACTTTTTAAT
11661 T
1 T
11662 TAATTATTTA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.42, C:0.09, G:0.04, T:0.45
Consensus pattern (34 bp):
TAAATCCAAATATAAAAGTATTTTACTTTTTAAT
Found at i:13369 original size:23 final size:21
Alignment explanation
Indices: 13326--13367 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
13316 GTTGAATTCA
* *
13326 GGACGGCAATTTTTGCTATAT
1 GGACGGCAATATTTCCTATAT
13347 GGACGGCAATATTTCCTATAT
1 GGACGGCAATATTTCCTATAT
13368 ATATAAGTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.26, C:0.17, G:0.21, T:0.36
Consensus pattern (21 bp):
GGACGGCAATATTTCCTATAT
Found at i:19522 original size:21 final size:22
Alignment explanation
Indices: 19493--19533 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
19483 TGTGGCTTAT
19493 AAATAGAAATAGAGAGAGTAAA
1 AAATAGAAATAGAGAGAGTAAA
*
19515 AAAT-GAAATAGAGCGAGTA
1 AAATAGAAATAGAGAGAGTA
19534 CTTATGTATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.59, C:0.02, G:0.24, T:0.15
Consensus pattern (22 bp):
AAATAGAAATAGAGAGAGTAAA
Found at i:19732 original size:1 final size:1
Alignment explanation
Indices: 19726--19767 Score: 75
Period size: 1 Copynumber: 42.0 Consensus size: 1
19716 ACCCATTAGG
*
19726 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTCTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
19768 CTTTCTCTAT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
1 39 1.00
ACGTcount: A:0.00, C:0.02, G:0.00, T:0.98
Consensus pattern (1 bp):
T
Found at i:19772 original size:10 final size:9
Alignment explanation
Indices: 19726--19773 Score: 59
Period size: 8 Copynumber: 5.7 Consensus size: 9
19716 ACCCATTAGG
19726 TTTT-TTTT
1 TTTTCTTTT
19734 TTTT-TTTT
1 TTTTCTTTT
19742 TTTT-TTTT
1 TTTTCTTTT
19750 TTTT-TTTT
1 TTTTCTTTT
19758 TTTTCTTTT
1 TTTTCTTTT
19767 TCTTTCT
1 T-TTTCT
19774 CTATTTTAAA
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
8 28 0.74
9 5 0.13
10 5 0.13
ACGTcount: A:0.00, C:0.06, G:0.00, T:0.94
Consensus pattern (9 bp):
TTTTCTTTT
Found at i:24233 original size:2 final size:2
Alignment explanation
Indices: 24226--24255 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
24216 TATACCAAAG
24226 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
24256 TCATCTAACC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:24429 original size:22 final size:20
Alignment explanation
Indices: 24387--24427 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
24377 GCTTAAATTA
24387 TGGCGTTAAATTATATATTT
1 TGGCGTTAAATTATATATTT
24407 TGGCGTTAAATTATATATTT
1 TGGCGTTAAATTATATATTT
24427 T
1 T
24428 TTATGATTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.29, C:0.05, G:0.15, T:0.51
Consensus pattern (20 bp):
TGGCGTTAAATTATATATTT
Done.