Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016856.1 Corchorus olitorius cultivar O-4 contig16889, 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: 27162
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Found at i:497 original size:39 final size:40
Alignment explanation
Indices: 443--523 Score: 137
Period size: 39 Copynumber: 2.0 Consensus size: 40
433 ATACCTAAGA
*
443 ATTTAATTAATGTAAGTATTTCAGTTATTATA-GTATTAC
1 ATTTAATTAATGTAAGTATTTCAGTTATTATATATATTAC
*
482 ATTTAATTAATGTAAGTATTTTAGTTATTATATATATTAC
1 ATTTAATTAATGTAAGTATTTCAGTTATTATATATATTAC
522 AT
1 AT
524 AGAAATTAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
39 31 0.79
40 8 0.21
ACGTcount: A:0.37, C:0.04, G:0.09, T:0.51
Consensus pattern (40 bp):
ATTTAATTAATGTAAGTATTTCAGTTATTATATATATTAC
Found at i:2235 original size:2 final size:2
Alignment explanation
Indices: 2228--2266 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
2218 GCACAGCTTT
2228 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
2267 TCCCTTCTGT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:6705 original size:7 final size:7
Alignment explanation
Indices: 6680--6729 Score: 75
Period size: 7 Copynumber: 7.3 Consensus size: 7
6670 CATTACCAAA
6680 AAAAAAG
1 AAAAAAG
*
6687 ACAAAA-
1 AAAAAAG
6693 AAAAAAG
1 AAAAAAG
*
6700 AGAAAAG
1 AAAAAAG
6707 AAAAAAG
1 AAAAAAG
6714 AAAAAAG
1 AAAAAAG
6721 AAAAAAG
1 AAAAAAG
6728 AA
1 AA
6730 GCAGTCAATG
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
6 5 0.13
7 33 0.87
ACGTcount: A:0.84, C:0.02, G:0.14, T:0.00
Consensus pattern (7 bp):
AAAAAAG
Found at i:13563 original size:15 final size:15
Alignment explanation
Indices: 13543--13572 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
13533 GCTTGTCTTT
13543 TCCTTTCTTATTTAA
1 TCCTTTCTTATTTAA
13558 TCCTTTCTTATTTAA
1 TCCTTTCTTATTTAA
13573 GGGGGAAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.20, C:0.20, G:0.00, T:0.60
Consensus pattern (15 bp):
TCCTTTCTTATTTAA
Found at i:17317 original size:6 final size:6
Alignment explanation
Indices: 17306--17334 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
17296 GCAATCTGAC
17306 TCTCTG TCTCTG TCTCTG TCTCTG TCTCT
1 TCTCTG TCTCTG TCTCTG TCTCTG TCTCT
17335 CTATATATGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.00, C:0.34, G:0.14, T:0.52
Consensus pattern (6 bp):
TCTCTG
Found at i:21293 original size:21 final size:22
Alignment explanation
Indices: 21269--21309 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
21259 GTGTATAATA
*
21269 TTCTTGGGTCATT-GGGTTATC
1 TTCTCGGGTCATTCGGGTTATC
*
21290 TTCTCGGGTTATTCGGGTTA
1 TTCTCGGGTCATTCGGGTTA
21310 CAAGTTTGTC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 11 0.65
22 6 0.35
ACGTcount: A:0.10, C:0.15, G:0.29, T:0.46
Consensus pattern (22 bp):
TTCTCGGGTCATTCGGGTTATC
Found at i:23089 original size:22 final size:22
Alignment explanation
Indices: 23064--23110 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
23054 TTTTTAGTTG
*
23064 AGTAAAACT-ATAAAAGTAAAAT
1 AGTAAAA-TGATAAAAATAAAAT
*
23086 AGTAAAATGGTAAAAATAAAAT
1 AGTAAAATGATAAAAATAAAAT
23108 AGT
1 AGT
23111 TATAAGTATA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 1 0.05
22 21 0.95
ACGTcount: A:0.62, C:0.02, G:0.13, T:0.23
Consensus pattern (22 bp):
AGTAAAATGATAAAAATAAAAT
Found at i:23772 original size:12 final size:12
Alignment explanation
Indices: 23755--23785 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
23745 TTGGGTTATT
23755 TGAGTTTTTGAG
1 TGAGTTTTTGAG
23767 TGAGTTTTTGAG
1 TGAGTTTTTGAG
*
23779 TCAGTTT
1 TGAGTTT
23786 GTTAGTCATA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.16, C:0.03, G:0.29, T:0.52
Consensus pattern (12 bp):
TGAGTTTTTGAG
Found at i:26410 original size:3 final size:3
Alignment explanation
Indices: 26402--26426 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
26392 GTTTCTATAA
26402 ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT A
26427 ATCATAAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:26527 original size:23 final size:22
Alignment explanation
Indices: 26500--26549 Score: 82
Period size: 23 Copynumber: 2.2 Consensus size: 22
26490 AATACCAGAA
26500 AAAAAAAAAGTTTGTTCACACC
1 AAAAAAAAAGTTTGTTCACACC
*
26522 ATAAAAATAAGTTTGTTCACACC
1 A-AAAAAAAAGTTTGTTCACACC
26545 AAAAA
1 AAAAA
26550 GCCCTCTCCC
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
22 5 0.19
23 21 0.81
ACGTcount: A:0.52, C:0.16, G:0.08, T:0.24
Consensus pattern (22 bp):
AAAAAAAAAGTTTGTTCACACC
Done.