Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009571.1 Corchorus capsularis cultivar CVL-1 contig09592, 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: 18260
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.33
Found at i:431 original size:26 final size:26
Alignment explanation
Indices: 402--452 Score: 86
Period size: 26 Copynumber: 2.0 Consensus size: 26
392 GCACAAATGA
402 ATTTAATTAGTGCAA-GATTTTGTAGC
1 ATTTAATTAGTG-AAGGATTTTGTAGC
428 ATTTAATTAGTGAAGGATTTTGTAG
1 ATTTAATTAGTGAAGGATTTTGTAG
453 TAATGACAGC
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
25 2 0.08
26 22 0.92
ACGTcount: A:0.31, C:0.04, G:0.22, T:0.43
Consensus pattern (26 bp):
ATTTAATTAGTGAAGGATTTTGTAGC
Found at i:3274 original size:27 final size:29
Alignment explanation
Indices: 3243--3299 Score: 100
Period size: 27 Copynumber: 2.0 Consensus size: 29
3233 CTAAGTTTCC
3243 AAGAAATTATAAGG-TA-ACTAGGGAACT
1 AAGAAATTATAAGGTTATACTAGGGAACT
3270 AAGAAATTATAAGGTTATACTAGGGAACT
1 AAGAAATTATAAGGTTATACTAGGGAACT
3299 A
1 A
3300 CGTACGTATA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
27 14 0.50
28 2 0.07
29 12 0.43
ACGTcount: A:0.47, C:0.07, G:0.21, T:0.25
Consensus pattern (29 bp):
AAGAAATTATAAGGTTATACTAGGGAACT
Found at i:4306 original size:20 final size:20
Alignment explanation
Indices: 4261--4307 Score: 87
Period size: 19 Copynumber: 2.4 Consensus size: 20
4251 TTGCTATCGA
4261 TTTTGGGATTGATTTTGGCC
1 TTTTGGGATTGATTTTGGCC
4281 -TTTGGGATTGATTTTGGCC
1 TTTTGGGATTGATTTTGGCC
4300 TTTTGGGA
1 TTTTGGGA
4308 AGATCCTGTG
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
19 19 0.73
20 7 0.27
ACGTcount: A:0.11, C:0.09, G:0.32, T:0.49
Consensus pattern (20 bp):
TTTTGGGATTGATTTTGGCC
Found at i:6441 original size:27 final size:27
Alignment explanation
Indices: 6410--6464 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
6400 CTAAGTTTCC
*
6410 AAGAAATTATAAGGTAACTAGGGAACT
1 AAGAAAATATAAGGTAACTAGGGAACT
** *
6437 AAGAAAATATAATTTTACTAGGGAACT
1 AAGAAAATATAAGGTAACTAGGGAACT
6464 A
1 A
6465 CGCACGTATA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.49, C:0.07, G:0.18, T:0.25
Consensus pattern (27 bp):
AAGAAAATATAAGGTAACTAGGGAACT
Found at i:11812 original size:29 final size:29
Alignment explanation
Indices: 11770--11830 Score: 104
Period size: 29 Copynumber: 2.1 Consensus size: 29
11760 TCATCATTAA
*
11770 TATGACAACTTCGGGTGTCAAAATGATAC
1 TATGACAACTTCGGATGTCAAAATGATAC
*
11799 TATGACAACTTCGGATGTCAAAGTGATAC
1 TATGACAACTTCGGATGTCAAAATGATAC
11828 TAT
1 TAT
11831 ATTTTTGATG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.34, C:0.16, G:0.20, T:0.30
Consensus pattern (29 bp):
TATGACAACTTCGGATGTCAAAATGATAC
Found at i:11877 original size:33 final size:33
Alignment explanation
Indices: 11835--11964 Score: 197
Period size: 33 Copynumber: 3.9 Consensus size: 33
11825 TACTATATTT
*
11835 TTGATGTGACAACTTCAGGTGCCACTAACATGC
1 TTGATGTGACAACTTCAGGTGCCACTAATATGC
* *
11868 TTGATGTGACAACTTCAAGTGCCACTGATATGC
1 TTGATGTGACAACTTCAGGTGCCACTAATATGC
* * *
11901 TTGATGTGACAACTTCAGATGCCACTGATATTC
1 TTGATGTGACAACTTCAGGTGCCACTAATATGC
*
11934 TTGATGTGATAACTTCAGGTGCCACTAATAT
1 TTGATGTGACAACTTCAGGTGCCACTAATAT
11965 TCAAGGATAG
Statistics
Matches: 88, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 88 1.00
ACGTcount: A:0.28, C:0.21, G:0.20, T:0.32
Consensus pattern (33 bp):
TTGATGTGACAACTTCAGGTGCCACTAATATGC
Found at i:12307 original size:19 final size:19
Alignment explanation
Indices: 12264--12308 Score: 67
Period size: 17 Copynumber: 2.5 Consensus size: 19
12254 AGAATTGAAG
*
12264 TATGGAAAAAACAAGAGAA
1 TATGGAGAAAACAAGAGAA
12283 T-T-GAGAAAACAAGAGAA
1 TATGGAGAAAACAAGAGAA
12300 TATGGAGAA
1 TATGGAGAA
12309 TGTGAGAGAT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
17 15 0.65
18 2 0.09
19 6 0.26
ACGTcount: A:0.58, C:0.04, G:0.24, T:0.13
Consensus pattern (19 bp):
TATGGAGAAAACAAGAGAA
Found at i:12935 original size:15 final size:15
Alignment explanation
Indices: 12915--12945 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
12905 TAACTACTTT
12915 TCTTAAACTTTGTGA
1 TCTTAAACTTTGTGA
12930 TCTTAAACTTTGTGA
1 TCTTAAACTTTGTGA
12945 T
1 T
12946 ACGGTTAAAA
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:0.26, C:0.13, G:0.13, T:0.48
Consensus pattern (15 bp):
TCTTAAACTTTGTGA
Found at i:15668 original size:2 final size:2
Alignment explanation
Indices: 15661--15686 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
15651 GTGCTACATT
15661 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
15687 ATCTAGAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Done.