Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019548.1 Corchorus olitorius cultivar O-4 contig19581, 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: 4585
ACGTcount: A:0.37, C:0.13, G:0.13, T:0.37
Found at i:3031 original size:19 final size:19
Alignment explanation
Indices: 2992--3031 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
2982 CTATTTAGTA
* * *
2992 TATATTTTTATTTATATAT
1 TATATTTTTACTTAAAAAT
3011 TATATTTTTACTTAAAAAT
1 TATATTTTTACTTAAAAAT
3030 TA
1 TA
3032 CTCCTAATTA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.60
Consensus pattern (19 bp):
TATATTTTTACTTAAAAAT
Found at i:3536 original size:2 final size:2
Alignment explanation
Indices: 3529--3578 Score: 66
Period size: 2 Copynumber: 24.0 Consensus size: 2
3519 TTTCACCGTT
3529 TA TA TA TA TA TA TA TA TA CTA TA TA -A GTA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA -TA TA TA TA -TA TA TA TA TA TA TA TA
3572 CTA TA TA
1 -TA TA TA
3579 AGTCTAAACT
Statistics
Matches: 44, Mismatches: 0, Indels: 8
0.85 0.00 0.15
Matches are distributed among these distances:
1 1 0.02
2 38 0.86
3 5 0.11
ACGTcount: A:0.48, C:0.04, G:0.02, T:0.46
Consensus pattern (2 bp):
TA
Found at i:3559 original size:25 final size:25
Alignment explanation
Indices: 3531--3581 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
3521 TCACCGTTTA
3531 TATATATATATATATACTATATAAG
1 TATATATATATATATACTATATAAG
3556 TATATATATATATATACTATATAAG
1 TATATATATATATATACTATATAAG
3581 T
1 T
3582 CTAAACTTCA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.47, C:0.04, G:0.04, T:0.45
Consensus pattern (25 bp):
TATATATATATATATACTATATAAG
Found at i:3893 original size:15 final size:14
Alignment explanation
Indices: 3858--3941 Score: 57
Period size: 15 Copynumber: 5.9 Consensus size: 14
3848 TAATTTAGAC
3858 TTATTATTATTATAA
1 TTATTATTATTA-AA
3873 -TA--ATTATTAAA
1 TTATTATTATTAAA
***
3884 CTTATTATTAGTGGTA
1 -TTATTATTA-TTAAA
*
3900 TTATAATTATTAAA
1 TTATTATTATTAAA
3914 CTTATTATTATTATAA
1 -TTATTATTATTA-AA
*
3930 TAATTATTATTA
1 TTATTATTATTA
3942 GTGGTATGTA
Statistics
Matches: 53, Mismatches: 9, Indels: 14
0.70 0.12 0.18
Matches are distributed among these distances:
11 2 0.04
12 7 0.13
13 2 0.04
14 4 0.08
15 34 0.64
16 4 0.08
ACGTcount: A:0.40, C:0.02, G:0.04, T:0.54
Consensus pattern (14 bp):
TTATTATTATTAAA
Found at i:3906 original size:30 final size:27
Alignment explanation
Indices: 3856--3938 Score: 130
Period size: 30 Copynumber: 3.0 Consensus size: 27
3846 GTTAATTTAG
3856 ACTTATTATTATTATAATAATTATTAA
1 ACTTATTATTATTATAATAATTATTAA
*
3883 ACTTATTATTAGTGGTATTATAATTATTAA
1 ACTTATTATTA-T--TATAATAATTATTAA
3913 ACTTATTATTATTATAATAATTATTA
1 ACTTATTATTATTATAATAATTATTA
3939 TTAGTGGTAT
Statistics
Matches: 51, Mismatches: 2, Indels: 6
0.86 0.03 0.10
Matches are distributed among these distances:
27 24 0.47
28 1 0.02
29 1 0.02
30 25 0.49
ACGTcount: A:0.41, C:0.04, G:0.04, T:0.52
Consensus pattern (27 bp):
ACTTATTATTATTATAATAATTATTAA
Found at i:3910 original size:9 final size:9
Alignment explanation
Indices: 3858--3939 Score: 60
Period size: 9 Copynumber: 8.8 Consensus size: 9
3848 TAATTTAGAC
*
3858 TTATTATTA
1 TTATTATAA
*
3867 TTATAATAA
1 TTATTATAA
3876 TTATTA-AA
1 TTATTATAA
*
3884 CTTATTATTAG
1 -TTATTA-TAA
3895 TGGTATTATAA
1 T--TATTATAA
3906 TTATTA-AA
1 TTATTATAA
*
3914 CTTATTATTA
1 -TTATTATAA
*
3924 TTATAATAA
1 TTATTATAA
3933 TTATTAT
1 TTATTAT
3940 TAGTGGTATG
Statistics
Matches: 57, Mismatches: 9, Indels: 14
0.71 0.11 0.17
Matches are distributed among these distances:
8 4 0.07
9 42 0.74
10 2 0.04
11 4 0.07
12 5 0.09
ACGTcount: A:0.40, C:0.02, G:0.04, T:0.54
Consensus pattern (9 bp):
TTATTATAA
Done.