Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014279.1 Corchorus olitorius cultivar O-4 contig14312, 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: 4182
ACGTcount: A:0.35, C:0.16, G:0.17, T:0.33
Found at i:136 original size:18 final size:18
Alignment explanation
Indices: 113--147 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
103 TACACTTTAA
113 ATCATTAGGAAA-AATTAT
1 ATCATTA-GAAAGAATTAT
131 ATCATTAGAAAGAATTA
1 ATCATTAGAAAGAATTA
148 ATTGAGACCT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.51, C:0.06, G:0.11, T:0.31
Consensus pattern (18 bp):
ATCATTAGAAAGAATTAT
Found at i:425 original size:36 final size:35
Alignment explanation
Indices: 356--447 Score: 139
Period size: 36 Copynumber: 2.6 Consensus size: 35
346 ATAAACTATA
* *
356 AAAACAACTAAACATGACAATAGTATTACACAATT
1 AAAACAACTAAACATGAGAATAGTAATACACAATT
*
391 AAAACAACTAAACATGAGAATACGTAATAGACAATT
1 AAAACAACTAAACATGAGAATA-GTAATACACAATT
*
427 AAAATAACTAAACATGAGAAT
1 AAAACAACTAAACATGAGAAT
448 GCTAGTTTTA
Statistics
Matches: 52, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
35 21 0.40
36 31 0.60
ACGTcount: A:0.57, C:0.14, G:0.09, T:0.21
Consensus pattern (35 bp):
AAAACAACTAAACATGAGAATAGTAATACACAATT
Found at i:465 original size:25 final size:25
Alignment explanation
Indices: 431--478 Score: 87
Period size: 25 Copynumber: 1.9 Consensus size: 25
421 ACAATTAAAA
*
431 TAACTAAACATGAGAATGCTAGTTT
1 TAACTAAACATGAGAATACTAGTTT
456 TAACTAAACATGAGAATACTAGT
1 TAACTAAACATGAGAATACTAGT
479 AGACAATTAC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.44, C:0.12, G:0.15, T:0.29
Consensus pattern (25 bp):
TAACTAAACATGAGAATACTAGTTT
Found at i:2090 original size:51 final size:52
Alignment explanation
Indices: 2002--2114 Score: 167
Period size: 51 Copynumber: 2.2 Consensus size: 52
1992 ATTGAATGAC
*
2002 ATTATATTCTTCTGCTTTTTTTTTTGTCATACAATGACAAT-ATATTCAAACG
1 ATTATATTCTTCTGCTTCTTTTTTTGTCATACAATGACAATGA-ATTCAAACG
* *
2054 ATTATATTCTTCTTC-TCTTTTTTTGTCATACAATGACATTGAATTCAAACG
1 ATTATATTCTTCTGCTTCTTTTTTTGTCATACAATGACAATGAATTCAAACG
*
2105 AATATATTCT
1 ATTATATTCT
2115 AAAGGAAAGG
Statistics
Matches: 56, Mismatches: 4, Indels: 3
0.89 0.06 0.05
Matches are distributed among these distances:
51 41 0.73
52 15 0.27
ACGTcount: A:0.29, C:0.16, G:0.07, T:0.48
Consensus pattern (52 bp):
ATTATATTCTTCTGCTTCTTTTTTTGTCATACAATGACAATGAATTCAAACG
Found at i:2129 original size:20 final size:20
Alignment explanation
Indices: 2104--2159 Score: 67
Period size: 24 Copynumber: 2.6 Consensus size: 20
2094 GAATTCAAAC
*
2104 GAATATATTCTAAAGGAAAG
1 GAATATATTCTAAAAGAAAG
2124 GAATATATTCTATTGAAAAGAAAG
1 GAATATATTC---T-AAAAGAAAG
2148 GAATATATTCTA
1 GAATATATTCTA
2160 CTGGAAAAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 8
0.77 0.03 0.20
Matches are distributed among these distances:
20 11 0.35
21 1 0.03
23 1 0.03
24 18 0.58
ACGTcount: A:0.48, C:0.05, G:0.16, T:0.30
Consensus pattern (20 bp):
GAATATATTCTAAAAGAAAG
Found at i:2171 original size:24 final size:24
Alignment explanation
Indices: 2119--2171 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
2109 TATTCTAAAG
*
2119 GAAAGGAATATATTCTATTGAAAA
1 GAAAGGAATATATTCTATGGAAAA
2143 GAAAGGAATATATTCTACTGGAAAA
1 GAAAGGAATATATTCTA-TGGAAAA
2168 -AAAG
1 GAAAG
2172 AGACTTTATA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
24 21 0.78
25 6 0.22
ACGTcount: A:0.51, C:0.06, G:0.19, T:0.25
Consensus pattern (24 bp):
GAAAGGAATATATTCTATGGAAAA
Found at i:2540 original size:42 final size:43
Alignment explanation
Indices: 2489--2582 Score: 138
Period size: 45 Copynumber: 2.2 Consensus size: 43
2479 AGTGCATTAT
**
2489 CTAA-ATTCTA-CTCCATCTCTAGGTAATTCATCAAAATAAAG
1 CTAATATTCTACCTCCATCTCTAGACAATTCATCAAAATAAAG
2530 CTAATATTCTACTCCTCCATCTCTAGACAATTCATCAAAATAAAG
1 CTAATATTCTA--CCTCCATCTCTAGACAATTCATCAAAATAAAG
2575 CTAATATT
1 CTAATATT
2583 AATTGTTGCT
Statistics
Matches: 47, Mismatches: 2, Indels: 4
0.89 0.04 0.08
Matches are distributed among these distances:
41 4 0.09
42 6 0.13
45 37 0.79
ACGTcount: A:0.38, C:0.23, G:0.05, T:0.33
Consensus pattern (43 bp):
CTAATATTCTACCTCCATCTCTAGACAATTCATCAAAATAAAG
Found at i:3520 original size:6 final size:6
Alignment explanation
Indices: 3509--3539 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
3499 CATATTTTCT
*
3509 ATCTTC ATCTTC ATCCTC ATCTTC ATCTTC A
1 ATCTTC ATCTTC ATCTTC ATCTTC ATCTTC A
3540 GAGGATGATA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.19, C:0.35, G:0.00, T:0.45
Consensus pattern (6 bp):
ATCTTC
Done.