Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020238.1 Corchorus olitorius cultivar O-4 contig20271, 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: 58677
ACGTcount: A:0.29, C:0.17, G:0.18, T:0.35
Found at i:5543 original size:13 final size:13
Alignment explanation
Indices: 5500--5547 Score: 60
Period size: 13 Copynumber: 3.7 Consensus size: 13
5490 TCAAAAAAAA
5500 ATGACGTGGCCTG
1 ATGACGTGGCCTG
* * *
5513 ATGACTTAGCCCG
1 ATGACGTGGCCTG
*
5526 GTGACGTGGCCTG
1 ATGACGTGGCCTG
5539 ATGACGTGG
1 ATGACGTGG
5548 TCAAAATAGA
Statistics
Matches: 27, Mismatches: 8, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
13 27 1.00
ACGTcount: A:0.17, C:0.23, G:0.38, T:0.23
Consensus pattern (13 bp):
ATGACGTGGCCTG
Found at i:9410 original size:24 final size:24
Alignment explanation
Indices: 9374--9428 Score: 60
Period size: 24 Copynumber: 2.3 Consensus size: 24
9364 CATTGGATGC
9374 TTCTGTT-TCTTGTACA-AATGTTGA
1 TTCTGTTGT-TTGTA-ATAATGTTGA
* *
9398 TTTTGTTGTTTGTAATGATGTTGA
1 TTCTGTTGTTTGTAATAATGTTGA
9422 TTCTGTT
1 TTCTGTT
9429 CTATGGCATA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
23 1 0.04
24 24 0.92
25 1 0.04
ACGTcount: A:0.16, C:0.07, G:0.20, T:0.56
Consensus pattern (24 bp):
TTCTGTTGTTTGTAATAATGTTGA
Found at i:12819 original size:2 final size:2
Alignment explanation
Indices: 12814--12855 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
12804 AGATCTAGTA
*
12814 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
12856 TAAGACTTGA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
AT
Found at i:12838 original size:114 final size:114
Alignment explanation
Indices: 12622--12840 Score: 343
Period size: 114 Copynumber: 1.9 Consensus size: 114
12612 CTATAGTATT
12622 ATACTGTAATATGAAGACATGGATAATTGACAGTTGGATTGATTAAAGTTTCTAGGTAAATTGGG
1 ATACTGTAATATGAAGACATGG--AATTGACAGTTGGATTGATTAAAGTTTCTAGGTAAATTGGG
*
12687 GAGATCTAGTACCATATAATATATATGTATATAATATAATAAATTAATAATA
64 GAGATCTAGTA-CATATAATATATATATATATAATATAATAAATTAATAATA
*
12739 ATACTGTAATATGAAGACATGG-ATTGACAGTTGGATTGGTTAAAGTTTCTAGGTAAATTGGTGA
1 ATACTGTAATATGAAGACATGGAATTGACAGTTGGATTGATTAAAGTTTCTAGGTAAATTGG-G-
12803 GAGATCTAGTA-ATATATATATATATATATATATATATA
64 GAGATCTAGTACATATA-ATATATATATATATA-ATATA
12841 TATATATATG
Statistics
Matches: 96, Mismatches: 2, Indels: 9
0.90 0.02 0.08
Matches are distributed among these distances:
114 43 0.45
115 15 0.16
116 16 0.17
117 22 0.23
ACGTcount: A:0.40, C:0.05, G:0.18, T:0.36
Consensus pattern (114 bp):
ATACTGTAATATGAAGACATGGAATTGACAGTTGGATTGATTAAAGTTTCTAGGTAAATTGGGGA
GATCTAGTACATATAATATATATATATATAATATAATAAATTAATAATA
Found at i:14748 original size:42 final size:42
Alignment explanation
Indices: 14689--14813 Score: 232
Period size: 42 Copynumber: 3.0 Consensus size: 42
14679 TAAGGATTAG
*
14689 GATTTGAGTTGAGTATTTCTAAATTTACAAAGAATTTTCAAT
1 GATTTGAGTTGAGTATTTCTTAATTTACAAAGAATTTTCAAT
14731 GATTTGAGTTGAGTATTTCTTAATTTACAAAGAATTTTCAAT
1 GATTTGAGTTGAGTATTTCTTAATTTACAAAGAATTTTCAAT
*
14773 GATTTGAGTTGAATATTTCTTAATTTACAAAGAATTTTCAA
1 GATTTGAGTTGAGTATTTCTTAATTTACAAAGAATTTTCAA
14814 GACTTAGTTA
Statistics
Matches: 81, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 81 1.00
ACGTcount: A:0.35, C:0.07, G:0.14, T:0.44
Consensus pattern (42 bp):
GATTTGAGTTGAGTATTTCTTAATTTACAAAGAATTTTCAAT
Found at i:26185 original size:16 final size:16
Alignment explanation
Indices: 26164--26199 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
26154 AAGAACATTT
26164 AAATTTTAATATAAAA
1 AAATTTTAATATAAAA
* *
26180 AAATTTTAATTTACAA
1 AAATTTTAATATAAAA
26196 AAAT
1 AAAT
26200 CAATCAGTCA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (16 bp):
AAATTTTAATATAAAA
Found at i:39022 original size:22 final size:22
Alignment explanation
Indices: 38996--39037 Score: 84
Period size: 22 Copynumber: 1.9 Consensus size: 22
38986 CAATTTACCT
38996 CAAGTAATATCATTTAATCATG
1 CAAGTAATATCATTTAATCATG
39018 CAAGTAATATCATTTAATCA
1 CAAGTAATATCATTTAATCA
39038 CATGCTTCTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.43, C:0.14, G:0.07, T:0.36
Consensus pattern (22 bp):
CAAGTAATATCATTTAATCATG
Done.