Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012838.1 Corchorus olitorius cultivar O-4 contig12871, 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: 25477
ACGTcount: A:0.33, C:0.20, G:0.18, T:0.30
Found at i:11579 original size:11 final size:11
Alignment explanation
Indices: 11555--11589 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
11545 TTGACAGCGC
11555 AACAAAAACAA
1 AACAAAAACAA
* *
11566 AACGAAAACGA
1 AACAAAAACAA
11577 AACAAAAACAA
1 AACAAAAACAA
11588 AA
1 AA
11590 AACAGAAAAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.77, C:0.17, G:0.06, T:0.00
Consensus pattern (11 bp):
AACAAAAACAA
Found at i:11581 original size:16 final size:16
Alignment explanation
Indices: 11560--11618 Score: 50
Period size: 16 Copynumber: 3.7 Consensus size: 16
11550 AGCGCAACAA
11560 AAACAAAACGAAAACG
1 AAACAAAACGAAAACG
*
11576 AAACAAAAACAAAAAAC-
1 AAAC-AAAAC-GAAAACG
*
11593 AGA-AAAACGAAAACG
1 AAACAAAACGAAAACG
* *
11608 ATACCAAACGA
1 AAACAAAACGA
11619 CCCCTTAACA
Statistics
Matches: 34, Mismatches: 5, Indels: 8
0.72 0.11 0.17
Matches are distributed among these distances:
14 5 0.15
15 7 0.21
16 10 0.29
17 7 0.21
18 5 0.15
ACGTcount: A:0.69, C:0.19, G:0.10, T:0.02
Consensus pattern (16 bp):
AAACAAAACGAAAACG
Found at i:14388 original size:8 final size:7
Alignment explanation
Indices: 14360--14386 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
14350 GAAGGACTCT
14360 TTTTTTC
1 TTTTTTC
14367 TTTTTTC
1 TTTTTTC
14374 TTTTTTC
1 TTTTTTC
14381 TTTTTT
1 TTTTTT
14387 TCAGAGGGAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.00, C:0.11, G:0.00, T:0.89
Consensus pattern (7 bp):
TTTTTTC
Found at i:14918 original size:13 final size:12
Alignment explanation
Indices: 14888--14933 Score: 74
Period size: 12 Copynumber: 3.8 Consensus size: 12
14878 TCTATGCATG
14888 TAGACTCTCCAT
1 TAGACTCTCCAT
*
14900 TAGACTCTCTAT
1 TAGACTCTCCAT
14912 GTAGACTCTCCAT
1 -TAGACTCTCCAT
14925 TAGACTCTC
1 TAGACTCTC
14934 TCCCCCACAC
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
12 20 0.65
13 11 0.35
ACGTcount: A:0.24, C:0.30, G:0.11, T:0.35
Consensus pattern (12 bp):
TAGACTCTCCAT
Found at i:14919 original size:25 final size:25
Alignment explanation
Indices: 14885--14934 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
14875 ATTTCTATGC
14885 ATGTAGACTCTCCATTAGACTCTCT
1 ATGTAGACTCTCCATTAGACTCTCT
14910 ATGTAGACTCTCCATTAGACTCTCT
1 ATGTAGACTCTCCATTAGACTCTCT
14935 CCCCCACACT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.24, C:0.28, G:0.12, T:0.36
Consensus pattern (25 bp):
ATGTAGACTCTCCATTAGACTCTCT
Found at i:18529 original size:18 final size:18
Alignment explanation
Indices: 18492--18529 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
18482 CTAACCCTAA
*
18492 AACTAGAAGAAAAACTAG
1 AACTAGAAGAAAAACAAG
18510 AACTAGAAGAGAAAA-AAG
1 AACTAGAAGA-AAAACAAG
18528 AA
1 AA
18530 GGGAAAATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 14 0.78
19 4 0.22
ACGTcount: A:0.66, C:0.08, G:0.18, T:0.08
Consensus pattern (18 bp):
AACTAGAAGAAAAACAAG
Done.