Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01010842.1 Corchorus olitorius cultivar O-4 contig10874, 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: 7279
ACGTcount: A:0.35, C:0.17, G:0.18, T:0.31
Found at i:564 original size:26 final size:26
Alignment explanation
Indices: 524--682 Score: 90
Period size: 27 Copynumber: 5.9 Consensus size: 26
514 TTAAGAGTGG
**
524 ACTTAAAATGACCAATGTGCCCCTGA
1 ACTTAAAATGACCAAAATGCCCCTGA
*
550 ACTTAAAATGGCCAAAATGCCCCTGA
1 ACTTAAAATGACCAAAATGCCCCTGA
* * *
576 A-TGTGCAAATGACTAAAATGCCCCTGG
1 ACT-T-AAAATGACCAAAATGCCCCTGA
* * *
603 A-TGTGCAAATAACTAAAATGCCCCTGA
1 ACT-T-AAAATGACCAAAATGCCCCTGA
* **
630 A-TGTGCAAATGATTAAAATGCCCCTAGA
1 ACT-T-AAAATGACCAAAATGCCCCT-GA
** *
658 TTTTGAAAATGACCGAAATGCCCCT
1 ACTT-AAAATGACCAAAATGCCCCT
683 AGTTGATCCT
Statistics
Matches: 113, Mismatches: 16, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
25 1 0.01
26 25 0.22
27 66 0.58
28 20 0.18
29 1 0.01
ACGTcount: A:0.36, C:0.23, G:0.17, T:0.23
Consensus pattern (26 bp):
ACTTAAAATGACCAAAATGCCCCTGA
Found at i:593 original size:27 final size:27
Alignment explanation
Indices: 563--682 Score: 159
Period size: 27 Copynumber: 4.4 Consensus size: 27
553 TAAAATGGCC
563 AAAATGCCCCTGAATGTGCAAATGACT
1 AAAATGCCCCTGAATGTGCAAATGACT
* *
590 AAAATGCCCCTGGATGTGCAAATAACT
1 AAAATGCCCCTGAATGTGCAAATGACT
*
617 AAAATGCCCCTGAATGTGCAAATGATT
1 AAAATGCCCCTGAATGTGCAAATGACT
* * * *
644 AAAATGCCCCTAGATTTTGAAAATGACC
1 AAAATGCCCCT-GAATGTGCAAATGACT
*
672 GAAATGCCCCT
1 AAAATGCCCCT
683 AGTTGATCCT
Statistics
Matches: 81, Mismatches: 11, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
27 60 0.74
28 21 0.26
ACGTcount: A:0.37, C:0.23, G:0.17, T:0.23
Consensus pattern (27 bp):
AAAATGCCCCTGAATGTGCAAATGACT
Found at i:1420 original size:16 final size:15
Alignment explanation
Indices: 1400--1470 Score: 63
Period size: 16 Copynumber: 4.5 Consensus size: 15
1390 GGTTCAGGCT
1400 TTTTCGGGTTCGGGA
1 TTTTCGGGTTCGGGA
*
1415 TCTTTCGGGTTCAGGTA
1 T-TTTCGGGTTC-GGGA
* *
1432 TTTTTGGGCTCGGG-
1 TTTTCGGGTTCGGGA
1446 TTATATCGGGTTCGGGTA
1 TT-T-TCGGGTTCGGG-A
1464 TTTTCGG
1 TTTTCGG
1471 TCTCGAGTCG
Statistics
Matches: 44, Mismatches: 6, Indels: 11
0.72 0.10 0.18
Matches are distributed among these distances:
14 2 0.05
15 4 0.09
16 31 0.70
17 5 0.11
18 2 0.05
ACGTcount: A:0.08, C:0.14, G:0.35, T:0.42
Consensus pattern (15 bp):
TTTTCGGGTTCGGGA
Found at i:1445 original size:32 final size:32
Alignment explanation
Indices: 1390--1475 Score: 93
Period size: 32 Copynumber: 2.7 Consensus size: 32
1380 GGGTACTGCT
* * *
1390 GGTTCAGGCT-TTTTCGGGTTCGGGATCTTTCG
1 GGTTCAGG-TATTTTCGGGCTCGGGATATATCG
* *
1422 GGTTCAGGTATTTTTGGGCTCGGGTTATATCG
1 GGTTCAGGTATTTTCGGGCTCGGGATATATCG
* *
1454 GGTTCGGGTATTTTCGGTCTCG
1 GGTTCAGGTATTTTCGGGCTCG
1476 AGTCGGGTTC
Statistics
Matches: 45, Mismatches: 8, Indels: 2
0.82 0.15 0.04
Matches are distributed among these distances:
31 1 0.02
32 44 0.98
ACGTcount: A:0.08, C:0.16, G:0.35, T:0.41
Consensus pattern (32 bp):
GGTTCAGGTATTTTCGGGCTCGGGATATATCG
Found at i:1950 original size:31 final size:31
Alignment explanation
Indices: 1915--1986 Score: 76
Period size: 31 Copynumber: 2.3 Consensus size: 31
1905 TAAATTATTG
* *
1915 CAAATTAAAACAAAT-TAAGTATTAAATTAAA
1 CAAATTAAAA-AAATGAAAGCATTAAATTAAA
* *
1946 CAAA-TAATTAAAATGAAAGCCTTAAATTAAA
1 CAAATTAA-AAAAATGAAAGCATTAAATTAAA
1977 CAAATTAAAA
1 CAAATTAAAA
1987 GCTGATAGAC
Statistics
Matches: 33, Mismatches: 5, Indels: 6
0.75 0.11 0.14
Matches are distributed among these distances:
30 7 0.21
31 23 0.70
32 3 0.09
ACGTcount: A:0.61, C:0.08, G:0.04, T:0.26
Consensus pattern (31 bp):
CAAATTAAAAAAATGAAAGCATTAAATTAAA
Found at i:2231 original size:14 final size:14
Alignment explanation
Indices: 2212--2242 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
2202 TTTTGCTTTA
2212 AGTTATATATATAT
1 AGTTATATATATAT
2226 AGTTATATATATAT
1 AGTTATATATATAT
2240 AGT
1 AGT
2243 AGTTTAGCAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.42, C:0.00, G:0.10, T:0.48
Consensus pattern (14 bp):
AGTTATATATATAT
Found at i:2455 original size:22 final size:22
Alignment explanation
Indices: 2414--2455 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
2404 GATAAACATG
*
2414 TAACCCAAATGACCCGAGAAGT
1 TAACCCAAATGACCCAAGAAGT
* *
2436 TAACCCGAATGATCCAAGAA
1 TAACCCAAATGACCCAAGAA
2456 TATTATAAAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.43, C:0.26, G:0.17, T:0.14
Consensus pattern (22 bp):
TAACCCAAATGACCCAAGAAGT
Done.