Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016037.1 Corchorus olitorius cultivar O-4 contig16070, 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: 10897
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.31
Found at i:4660 original size:77 final size:74
Alignment explanation
Indices: 4531--4681 Score: 196
Period size: 77 Copynumber: 2.0 Consensus size: 74
4521 TTTATCTGGA
* * *
4531 CTGTGAGCAAAGGAATGATGAGTTTTAATCAAAATTTTTTCAAAATCAGTTTTAATCAAAACTAT
1 CTGTGAGCAAAGGAATGACGAGTTTTAATCAAAATGTTTTCAAAATCAGTTTTAATCAAAACAAT
4596 GATTTCGAG
66 GATTTCGAG
* ** *
4605 CTGTGAGCGAAGGAATGACG-GTATGTTAATCAAAAGATGTTTTCAAAATCAGTTTTGGTCAAAG
1 CTGTGAGCAAAGGAATGACGAGT-T-TTAATC-AAA-ATGTTTTCAAAATCAGTTTTAATCAAAA
4669 CAATGATTTCGAG
62 CAATGATTTCGAG
4682 GTGACTGAAT
Statistics
Matches: 66, Mismatches: 7, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
73 2 0.03
74 19 0.29
75 6 0.09
76 3 0.05
77 36 0.55
ACGTcount: A:0.36, C:0.11, G:0.21, T:0.32
Consensus pattern (74 bp):
CTGTGAGCAAAGGAATGACGAGTTTTAATCAAAATGTTTTCAAAATCAGTTTTAATCAAAACAAT
GATTTCGAG
Found at i:5501 original size:10 final size:10
Alignment explanation
Indices: 5485--5522 Score: 51
Period size: 10 Copynumber: 3.9 Consensus size: 10
5475 TTCAAGAAAT
5485 AAAAAAAA-A
1 AAAAAAAACA
*
5494 ACAAAAAACA
1 AAAAAAAACA
*
5504 AAACAAAACA
1 AAAAAAAACA
5514 AAAAAAAAC
1 AAAAAAAAC
5523 CGAAATTTGA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
9 7 0.29
10 17 0.71
ACGTcount: A:0.87, C:0.13, G:0.00, T:0.00
Consensus pattern (10 bp):
AAAAAAAACA
Found at i:5506 original size:12 final size:11
Alignment explanation
Indices: 5485--5518 Score: 50
Period size: 12 Copynumber: 2.9 Consensus size: 11
5475 TTCAAGAAAT
5485 AAAAAAAAAAC
1 AAAAAAAAAAC
5496 AAAAAACAAAAC
1 AAAAAA-AAAAC
5508 AAAACAAAAAA
1 AAAA-AAAAAA
5519 AAACCGAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
11 6 0.29
12 13 0.62
13 2 0.10
ACGTcount: A:0.88, C:0.12, G:0.00, T:0.00
Consensus pattern (11 bp):
AAAAAAAAAAC
Found at i:5511 original size:17 final size:17
Alignment explanation
Indices: 5486--5518 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
5476 TCAAGAAATA
5486 AAAAAAAAACAAAAAAC
1 AAAAAAAAACAAAAAAC
*
5503 AAAACAAAACAAAAAA
1 AAAAAAAAACAAAAAA
5519 AAACCGAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.88, C:0.12, G:0.00, T:0.00
Consensus pattern (17 bp):
AAAAAAAAACAAAAAAC
Found at i:6179 original size:50 final size:50
Alignment explanation
Indices: 6115--6268 Score: 193
Period size: 50 Copynumber: 3.1 Consensus size: 50
6105 AAAACAAGAA
* * *
6115 TTTTTGTAATAAGATTGCATTCCATTTGTGAGTCCAAGGTCAAAATTCGC
1 TTTTTATAATAAGATTGCATTCCATTTGTGACTCCAAGATCAAAATTCGC
* * *
6165 TTTTTATAATAAGATTGCTTTCCATCTT-TGATTCCGAGATCAAAATTCGC
1 TTTTTATAATAAGATTGCATTCCAT-TTGTGACTCCAAGATCAAAATTCGC
* * * * *
6215 TTTTCAAAATAAGATTGCATTCCATTTGTGACTACAAGACCAAAGTTCGC
1 TTTTTATAATAAGATTGCATTCCATTTGTGACTCCAAGATCAAAATTCGC
6265 TTTT
1 TTTT
6269 CGAAGGGCAT
Statistics
Matches: 89, Mismatches: 13, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
49 2 0.02
50 85 0.96
51 2 0.02
ACGTcount: A:0.29, C:0.18, G:0.14, T:0.39
Consensus pattern (50 bp):
TTTTTATAATAAGATTGCATTCCATTTGTGACTCCAAGATCAAAATTCGC
Found at i:7331 original size:137 final size:137
Alignment explanation
Indices: 7170--7431 Score: 443
Period size: 137 Copynumber: 1.9 Consensus size: 137
7160 TGCTTTGGCT
* * *
7170 TTTCCATAAGCCAAACTCGTTTCCATACGAGTCAGTTTAAGCATTGGTTCCATCCAAGCCATAGA
1 TTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTTAAGCATTGGTTCCATCCAAGCAACAGA
* *
7235 GGCTTTTCCATAAGCCAAACTCATTTCCATACGAGTCAGTTTAAGCCTTGGTTCCATCCAAGCCA
66 GGCTTTTCCACAAGCCAAACTCATTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATCCAAGCCA
7300 TATAGGC
131 TATAGGC
* *
7307 TTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTTAAGCCTTGGTTCCATCCAAGCAACATA
1 TTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTTAAGCATTGGTTCCATCCAAGCAACAGA
* *
7372 GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCTTTGGTTCCATCCA
66 GGCTTTTCCACAAGCCAAACTCATTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATCCA
7432 TACAGCAGGG
Statistics
Matches: 116, Mismatches: 9, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
137 116 1.00
ACGTcount: A:0.27, C:0.28, G:0.16, T:0.29
Consensus pattern (137 bp):
TTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTTAAGCATTGGTTCCATCCAAGCAACAGA
GGCTTTTCCACAAGCCAAACTCATTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATCCAAGCCA
TATAGGC
Found at i:7348 original size:68 final size:69
Alignment explanation
Indices: 7166--7431 Score: 444
Period size: 69 Copynumber: 3.9 Consensus size: 69
7156 CGAATGCTTT
* *
7166 GGCTTTTCCATAAGCCAAACTCGTTTCCATACGAGTCAGTTTAAGCATTGGTTCCATCCAAGCCA
1 GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTTAAGCCTTGGTTCCATCCAAGCCA
*
7231 TAGA
66 TATA
* *
7235 GGCTTTTCCATAAGCCAAACTCATTTCCATACGAGTCAGTTTAAGCCTTGGTTCCATCCAAGCCA
1 GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTTAAGCCTTGGTTCCATCCAAGCCA
7300 TATA
66 TATA
*
7304 GGC-TTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTTAAGCCTTGGTTCCATCCAAGCAA
1 GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTTAAGCCTTGGTTCCATCCAAGCCA
*
7368 CATA
66 TATA
* *
7372 GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCTTTGGTTCCATCCA
1 GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTTAAGCCTTGGTTCCATCCA
7432 TACAGCAGGG
Statistics
Matches: 187, Mismatches: 9, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
68 64 0.34
69 123 0.66
ACGTcount: A:0.27, C:0.28, G:0.16, T:0.29
Consensus pattern (69 bp):
GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTTAAGCCTTGGTTCCATCCAAGCCA
TATA
Found at i:7853 original size:38 final size:38
Alignment explanation
Indices: 7801--7885 Score: 89
Period size: 38 Copynumber: 2.2 Consensus size: 38
7791 TTTTATTTCG
* *
7801 ATCCTGATTTAGGATCATTGCTTATCAGTTAATTTCAGA
1 ATCCT-ATTCAGGATCATTGCTTATCAGTCAATTTCAGA
* ** * * *
7840 ATCTTATTCAGGATTGTTGTTTATCAGTCGATTTCAGG
1 ATCCTATTCAGGATCATTGCTTATCAGTCAATTTCAGA
7878 ATCCTATT
1 ATCCTATT
7886 TGAAGATCTC
Statistics
Matches: 37, Mismatches: 9, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
38 33 0.89
39 4 0.11
ACGTcount: A:0.25, C:0.15, G:0.16, T:0.44
Consensus pattern (38 bp):
ATCCTATTCAGGATCATTGCTTATCAGTCAATTTCAGA
Done.