Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023530.1 Corchorus olitorius cultivar O-4 contig23563, 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: 15007
ACGTcount: A:0.30, C:0.19, G:0.17, T:0.34
Found at i:473 original size:18 final size:17
Alignment explanation
Indices: 447--488 Score: 57
Period size: 18 Copynumber: 2.4 Consensus size: 17
437 TTCTTCTCTT
*
447 TTTCTTTTCTCTTTTCC
1 TTTCCTTTCTCTTTTCC
*
464 TCTTCCTTTCTCTTTTTC
1 T-TTCCTTTCTCTTTTCC
482 TTTCCTT
1 TTTCCTT
489 ATGTCTCTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
17 7 0.32
18 15 0.68
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (17 bp):
TTTCCTTTCTCTTTTCC
Found at i:556 original size:12 final size:13
Alignment explanation
Indices: 531--560 Score: 53
Period size: 12 Copynumber: 2.4 Consensus size: 13
521 GCCCACTTTA
531 TTATTATGTTTTT
1 TTATTATGTTTTT
544 TTATTAT-TTTTT
1 TTATTATGTTTTT
556 TTATT
1 TTATT
561 TGGGTCCCAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.59
13 7 0.41
ACGTcount: A:0.17, C:0.00, G:0.03, T:0.80
Consensus pattern (13 bp):
TTATTATGTTTTT
Found at i:644 original size:15 final size:15
Alignment explanation
Indices: 610--691 Score: 83
Period size: 15 Copynumber: 5.3 Consensus size: 15
600 CTGGACCAAG
*
610 GCGCGCCAGGCCCAGC
1 GCGCACCAGG-CCAGC
*
626 GCGCACCAGGCCTGC
1 GCGCACCAGGCCAGC
* *
641 GCGCCAGCTGGCCCAGC
1 GCG-CACCAGG-CCAGC
*
658 GCGCAACAGGCCAGC
1 GCGCACCAGGCCAGC
*
673 GCGCACCAGGCCCGC
1 GCGCACCAGGCCAGC
688 GCGC
1 GCGC
692 CAGGCCTGGC
Statistics
Matches: 55, Mismatches: 9, Indels: 5
0.80 0.13 0.07
Matches are distributed among these distances:
15 29 0.53
16 19 0.35
17 7 0.13
ACGTcount: A:0.15, C:0.48, G:0.35, T:0.02
Consensus pattern (15 bp):
GCGCACCAGGCCAGC
Found at i:658 original size:32 final size:31
Alignment explanation
Indices: 610--699 Score: 105
Period size: 32 Copynumber: 3.0 Consensus size: 31
600 CTGGACCAAG
*
610 GCGCGCCAGGCCCAGCGCGCACCAGGCCTGC
1 GCGCACCAGGCCCAGCGCGCACCAGGCCTGC
* * * *
641 GCGCCAGCTGGCCCAGCGCGCAACAGGCCAGC
1 GCG-CACCAGGCCCAGCGCGCACCAGGCCTGC
673 GCGCACCAGGCCC-GCGCG--CCAGGCCTG
1 GCGCACCAGGCCCAGCGCGCACCAGGCCTG
700 GCCTGCTGCT
Statistics
Matches: 49, Mismatches: 9, Indels: 5
0.78 0.14 0.08
Matches are distributed among these distances:
28 7 0.14
30 5 0.10
31 11 0.22
32 26 0.53
ACGTcount: A:0.14, C:0.47, G:0.36, T:0.03
Consensus pattern (31 bp):
GCGCACCAGGCCCAGCGCGCACCAGGCCTGC
Found at i:1736 original size:18 final size:18
Alignment explanation
Indices: 1709--1749 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
1699 ATGCCAATCC
*
1709 TATT-GGCTTTCACTGGA
1 TATTGGGCTTTCACGGGA
1726 TATTGGGCTTTCACGGGA
1 TATTGGGCTTTCACGGGA
1744 TATTGG
1 TATTGG
1750 AGCCGGACCC
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 4 0.18
18 18 0.82
ACGTcount: A:0.17, C:0.15, G:0.29, T:0.39
Consensus pattern (18 bp):
TATTGGGCTTTCACGGGA
Found at i:2749 original size:53 final size:53
Alignment explanation
Indices: 2682--2897 Score: 396
Period size: 53 Copynumber: 4.1 Consensus size: 53
2672 TGTTTATTCA
2682 ATTGAACCTATTAAATAAGCACACATACCAAATAATACAAAATGCAATGAACT
1 ATTGAACCTATTAAATAAGCACACATACCAAATAATACAAAATGCAATGAACT
* *
2735 ACTAAACCTATTAAATAAGCACACATACCAAATAATACAAAATGCAATGAACT
1 ATTGAACCTATTAAATAAGCACACATACCAAATAATACAAAATGCAATGAACT
* *
2788 ATTGAACTTATTAAATAAGCACACATACCAAATAATACAAAATGCAATGAAAT
1 ATTGAACCTATTAAATAAGCACACATACCAAATAATACAAAATGCAATGAACT
2841 ATTGAACCTATTAAATAAGCACACATACCAAATAATACAAAATGCAATGAACT
1 ATTGAACCTATTAAATAAGCACACATACCAAATAATACAAAATGCAATGAACT
2894 ATTG
1 ATTG
2898 GATTTAAAGA
Statistics
Matches: 155, Mismatches: 8, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
53 155 1.00
ACGTcount: A:0.51, C:0.18, G:0.07, T:0.23
Consensus pattern (53 bp):
ATTGAACCTATTAAATAAGCACACATACCAAATAATACAAAATGCAATGAACT
Found at i:3561 original size:72 final size:71
Alignment explanation
Indices: 3459--3601 Score: 259
Period size: 72 Copynumber: 2.0 Consensus size: 71
3449 TATATATATG
*
3459 TATTCTTGGCTCCCTTTGGGAGTTAATAGGGGTAATTTTGGGATAAAGTTATTTAATAATTAGGT
1 TATTCTTGACTCCCTTTGGGAGTTAATAGGGGTAATTTTGGGATAAAGTTATTTAATAATTAGGT
3524 TTTATA
66 TTTATA
*
3530 TATTCTTGACTCCCTTTGGGGAGTTAATAGGGGTAATTTTGGGATAAAGTTATTTAATTATTAGG
1 TATTCTTGACTCCCTTT-GGGAGTTAATAGGGGTAATTTTGGGATAAAGTTATTTAATAATTAGG
3595 TTTTATA
65 TTTTATA
3602 CTTGGGAATA
Statistics
Matches: 69, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
71 16 0.23
72 53 0.77
ACGTcount: A:0.27, C:0.07, G:0.22, T:0.44
Consensus pattern (71 bp):
TATTCTTGACTCCCTTTGGGAGTTAATAGGGGTAATTTTGGGATAAAGTTATTTAATAATTAGGT
TTTATA
Found at i:5153 original size:13 final size:12
Alignment explanation
Indices: 5132--5166 Score: 61
Period size: 13 Copynumber: 2.8 Consensus size: 12
5122 AATAAAGTAA
5132 TAATACTATTAT
1 TAATACTATTAT
5144 TAATTACTATTAT
1 TAA-TACTATTAT
5157 TAATACTATT
1 TAATACTATT
5167 TCAATGTCTT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
12 10 0.45
13 12 0.55
ACGTcount: A:0.40, C:0.09, G:0.00, T:0.51
Consensus pattern (12 bp):
TAATACTATTAT
Done.