Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019571.1 Corchorus olitorius cultivar O-4 contig19604, 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: 30386
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Found at i:4658 original size:12 final size:15
Alignment explanation
Indices: 4634--4673 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 15
4624 CTGTCCCTTT
*
4634 TCTCTCTTTCTCT-C
1 TCTCTCCTTCTCTAC
4648 T-TC-CCTTCTCTAC
1 TCTCTCCTTCTCTAC
4661 TCTCTCCTTCTCT
1 TCTCTCCTTCTCT
4674 GTAGTAAACG
Statistics
Matches: 22, Mismatches: 1, Indels: 5
0.79 0.04 0.18
Matches are distributed among these distances:
12 7 0.32
13 4 0.18
14 3 0.14
15 8 0.36
ACGTcount: A:0.03, C:0.45, G:0.00, T:0.53
Consensus pattern (15 bp):
TCTCTCCTTCTCTAC
Found at i:5521 original size:16 final size:18
Alignment explanation
Indices: 5500--5539 Score: 66
Period size: 16 Copynumber: 2.3 Consensus size: 18
5490 ACAATCAAGA
5500 TGTATAGTT-TATATT-C
1 TGTATAGTTATATATTAC
5516 TGTATAGTTATATATTAC
1 TGTATAGTTATATATTAC
5534 TGTATA
1 TGTATA
5540 TCACATGGCC
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
16 9 0.41
17 6 0.27
18 7 0.32
ACGTcount: A:0.30, C:0.05, G:0.12, T:0.53
Consensus pattern (18 bp):
TGTATAGTTATATATTAC
Found at i:6710 original size:31 final size:31
Alignment explanation
Indices: 6666--6737 Score: 76
Period size: 31 Copynumber: 2.3 Consensus size: 31
6656 CCGAACCTAC
*
6666 ATGACCCTAAATCCAGCA-GACCCGAGA-CCCGA
1 ATGA-CCTGAATCCAG-ATGACCCGA-ATCCCGA
*
6698 ATGACCTGAATCCAGATGAGCCGAATCCCGA
1 ATGACCTGAATCCAGATGACCCGAATCCCGA
*
6729 ATGATCTGA
1 ATGACCTGA
6738 GAAAATTACC
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
30 2 0.06
31 29 0.83
32 4 0.11
ACGTcount: A:0.33, C:0.31, G:0.21, T:0.15
Consensus pattern (31 bp):
ATGACCTGAATCCAGATGACCCGAATCCCGA
Found at i:11733 original size:28 final size:28
Alignment explanation
Indices: 11693--11752 Score: 95
Period size: 28 Copynumber: 2.1 Consensus size: 28
11683 CAAGGCCAAG
*
11693 TCACCCATGCCATGATCCAGGGCCA-TT
1 TCACCCATGCCATGATCCAGGACCAGTT
11720 TCACACCATGCCATGATCCAGGACCAGTT
1 TCAC-CCATGCCATGATCCAGGACCAGTT
11749 TCAC
1 TCAC
11753 TCCAAAATGA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
27 4 0.13
28 20 0.67
29 6 0.20
ACGTcount: A:0.25, C:0.37, G:0.17, T:0.22
Consensus pattern (28 bp):
TCACCCATGCCATGATCCAGGACCAGTT
Found at i:14988 original size:4 final size:4
Alignment explanation
Indices: 14979--15003 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
14969 AAAGATTGTT
14979 ACAG ACAG ACAG ACAG ACAG ACAG A
1 ACAG ACAG ACAG ACAG ACAG ACAG A
15004 GAGAGTGCGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.52, C:0.24, G:0.24, T:0.00
Consensus pattern (4 bp):
ACAG
Found at i:22463 original size:40 final size:40
Alignment explanation
Indices: 22419--22497 Score: 95
Period size: 40 Copynumber: 2.0 Consensus size: 40
22409 ATATATGATC
*
22419 TTTTTTAACACAGAGAGCGGTCAAAGACAACTTTAACCAT
1 TTTTTTAACACAAAGAGCGGTCAAAGACAACTTTAACCAT
* * ** **
22459 TTTTTTTACATAAAGAGTTGTCAAAGACCTCTTTAACCA
1 TTTTTTAACACAAAGAGCGGTCAAAGACAACTTTAACCA
22498 ATAATGACTT
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
40 32 1.00
ACGTcount: A:0.35, C:0.19, G:0.13, T:0.33
Consensus pattern (40 bp):
TTTTTTAACACAAAGAGCGGTCAAAGACAACTTTAACCAT
Found at i:23126 original size:28 final size:28
Alignment explanation
Indices: 23093--23163 Score: 106
Period size: 28 Copynumber: 2.5 Consensus size: 28
23083 ATGTCCGATT
* *
23093 CCGTATTCTGCCCTTGACTTTTTGGGTC
1 CCGTATTCTGCCCTTGACCTTTCGGGTC
*
23121 TCGTATTCTGCCCTTGACCTTTCGGGTC
1 CCGTATTCTGCCCTTGACCTTTCGGGTC
*
23149 CCGTATTTTGCCCTT
1 CCGTATTCTGCCCTT
23164 CTGCCCTTTA
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 38 1.00
ACGTcount: A:0.07, C:0.31, G:0.20, T:0.42
Consensus pattern (28 bp):
CCGTATTCTGCCCTTGACCTTTCGGGTC
Found at i:24495 original size:42 final size:44
Alignment explanation
Indices: 24444--24536 Score: 156
Period size: 44 Copynumber: 2.2 Consensus size: 44
24434 AGTGCATTAC
*
24444 CTAA-ATTCTACT-C-CATCTCTAGGTAATTCATCAAAATAAAG
1 CTAATATTCTACTCCTCATCTCTAGATAATTCATCAAAATAAAG
24485 CTAATATTCTACTCCTCATCTCTAGATAATTCATCAAAATAAAG
1 CTAATATTCTACTCCTCATCTCTAGATAATTCATCAAAATAAAG
24529 CTAATATT
1 CTAATATT
24537 AATTGTTGTT
Statistics
Matches: 48, Mismatches: 1, Indels: 3
0.92 0.02 0.06
Matches are distributed among these distances:
41 4 0.08
42 8 0.17
43 1 0.02
44 35 0.73
ACGTcount: A:0.39, C:0.22, G:0.05, T:0.34
Consensus pattern (44 bp):
CTAATATTCTACTCCTCATCTCTAGATAATTCATCAAAATAAAG
Found at i:27505 original size:27 final size:27
Alignment explanation
Indices: 27472--27526 Score: 94
Period size: 27 Copynumber: 2.0 Consensus size: 27
27462 TTTTAAAAAT
27472 ATTAAAAGAA-AATAAAAAATATTTAAA
1 ATTAAAA-AATAATAAAAAATATTTAAA
27499 ATTAAAAAATAATAAAAAATATTTAAA
1 ATTAAAAAATAATAAAAAATATTTAAA
27526 A
1 A
27527 AAACCACGTA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
26 2 0.07
27 25 0.93
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.27
Consensus pattern (27 bp):
ATTAAAAAATAATAAAAAATATTTAAA
Found at i:29648 original size:3 final size:3
Alignment explanation
Indices: 29640--29728 Score: 153
Period size: 3 Copynumber: 29.3 Consensus size: 3
29630 GCTAATGGAT
29640 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
29688 ATA ATA ATA ATA ATA ATA ATA ATA ATA GCAT- ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA --ATA ATA ATA ATA A
29729 GAAATTTCTA
Statistics
Matches: 83, Mismatches: 0, Indels: 6
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.02
3 79 0.95
5 2 0.02
ACGTcount: A:0.65, C:0.01, G:0.01, T:0.33
Consensus pattern (3 bp):
ATA
Done.