Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014663.1 Corchorus olitorius cultivar O-4 contig14696, 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: 42332
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.32
Found at i:8925 original size:6 final size:6
Alignment explanation
Indices: 8914--8978 Score: 58
Period size: 6 Copynumber: 10.8 Consensus size: 6
8904 TGATAAAGAG
* * * * *
8914 CGTGAT CGTGAT AGGGAT CGTGAA CGTGAT CGGGAG CGTGAT CGTGAT
1 CGTGAT CGTGAT CGTGAT CGTGAT CGTGAT CGTGAT CGTGAT CGTGAT
* * *
8962 CGAGAG CGGGAT CGTGA
1 CGTGAT CGTGAT CGTGA
8979 CTTGGATTTG
Statistics
Matches: 44, Mismatches: 15, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
6 44 1.00
ACGTcount: A:0.22, C:0.15, G:0.42, T:0.22
Consensus pattern (6 bp):
CGTGAT
Found at i:8935 original size:18 final size:18
Alignment explanation
Indices: 8911--8978 Score: 82
Period size: 18 Copynumber: 3.8 Consensus size: 18
8901 CCATGATAAA
8911 GAGCGTGATCGTGATAGG
1 GAGCGTGATCGTGATAGG
* * *
8929 GATCGTGAACGTGATCGG
1 GAGCGTGATCGTGATAGG
* *
8947 GAGCGTGATCGTGATCGA
1 GAGCGTGATCGTGATAGG
*
8965 GAGCGGGATCGTGA
1 GAGCGTGATCGTGA
8979 CTTGGATTTG
Statistics
Matches: 43, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 43 1.00
ACGTcount: A:0.22, C:0.15, G:0.43, T:0.21
Consensus pattern (18 bp):
GAGCGTGATCGTGATAGG
Found at i:9043 original size:18 final size:18
Alignment explanation
Indices: 8996--9044 Score: 53
Period size: 18 Copynumber: 2.7 Consensus size: 18
8986 TTGGGACATG
* * *
8996 ATCGAGAGCGTGAGCGTT
1 ATCGAGAACGTGACCATT
* *
9014 ATCGTGATCGTGACCATT
1 ATCGAGAACGTGACCATT
9032 ATCGAGAACGTGA
1 ATCGAGAACGTGA
9045 TCGCCATCGT
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.27, C:0.18, G:0.31, T:0.24
Consensus pattern (18 bp):
ATCGAGAACGTGACCATT
Found at i:16682 original size:13 final size:14
Alignment explanation
Indices: 16656--16687 Score: 57
Period size: 13 Copynumber: 2.4 Consensus size: 14
16646 ATATTTATTT
16656 ATAAAATAAATCAA
1 ATAAAATAAATCAA
16670 ATAAAAT-AATCAA
1 ATAAAATAAATCAA
16683 ATAAA
1 ATAAA
16688 TTTAAGTATT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 11 0.61
14 7 0.39
ACGTcount: A:0.72, C:0.06, G:0.00, T:0.22
Consensus pattern (14 bp):
ATAAAATAAATCAA
Found at i:19621 original size:1 final size:1
Alignment explanation
Indices: 19615--19639 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
19605 AATTCAAAGA
19615 GGGGGGGGGGGGGGGGGGGGGGGGG
1 GGGGGGGGGGGGGGGGGGGGGGGGG
19640 AGTGTAAACA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:0.00, C:0.00, G:1.00, T:0.00
Consensus pattern (1 bp):
G
Found at i:21565 original size:22 final size:25
Alignment explanation
Indices: 21518--21566 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 25
21508 AATTGAATAC
21518 AAAATGCAATGTGGAAACTAACTCCT
1 AAAATGCAATGT-GAAACTAACTCCT
21544 AAAATGCAAT-T-AAACT-ACTCCT
1 AAAATGCAATGTGAAACTAACTCCT
21566 A
1 A
21567 GAACTAAAGC
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
22 7 0.30
23 5 0.22
25 1 0.04
26 10 0.43
ACGTcount: A:0.45, C:0.20, G:0.10, T:0.24
Consensus pattern (25 bp):
AAAATGCAATGTGAAACTAACTCCT
Found at i:24410 original size:2 final size:2
Alignment explanation
Indices: 24400--24438 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
24390 TGTATATATG
*
24400 TC TC AC 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
24439 ATATATATAT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.03, C:0.49, G:0.00, T:0.49
Consensus pattern (2 bp):
TC
Found at i:24443 original size:2 final size:2
Alignment explanation
Indices: 24438--24513 Score: 100
Period size: 2 Copynumber: 38.0 Consensus size: 2
24428 TCTCTCTCTC
*
24438 TA TA TA TA TA TA TA TA TA TA -A TA TA GA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * *
24479 TA AA TA TA AA CGA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA
24514 AACGAATTTT
Statistics
Matches: 65, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
1 1 0.02
2 63 0.97
3 1 0.02
ACGTcount: A:0.53, C:0.01, G:0.03, T:0.43
Consensus pattern (2 bp):
TA
Found at i:24512 original size:27 final size:27
Alignment explanation
Indices: 24438--24518 Score: 128
Period size: 27 Copynumber: 3.0 Consensus size: 27
24428 TCTCTCTCTC
*
24438 TATATATATATATATATATAATATA-GA
1 TATATATATATATATATAT-ATAAACGA
*
24465 TATATATATATATATAAATATAAACGA
1 TATATATATATATATATATATAAACGA
24492 TATATATATATATATATATATAAACGA
1 TATATATATATATATATATATAAACGA
24519 ATTTTTGCAT
Statistics
Matches: 50, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
26 4 0.08
27 46 0.92
ACGTcount: A:0.53, C:0.02, G:0.04, T:0.41
Consensus pattern (27 bp):
TATATATATATATATATATATAAACGA
Found at i:26174 original size:3 final size:3
Alignment explanation
Indices: 26166--26194 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
26156 CATAAAGGAA
26166 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
26195 AAAAACTCTC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:30210 original size:31 final size:32
Alignment explanation
Indices: 30150--30226 Score: 102
Period size: 31 Copynumber: 2.4 Consensus size: 32
30140 TCTTTCTATC
* *
30150 GGGGTAAAATGTCTTGAATTTGAGAAGTTCAG
1 GGGGTAAAATGTCCTGAACTTGAGAAGTTCAG
*
30182 GGGGTAAAATGTCCTGAACTT-AGAAGTTCAT
1 GGGGTAAAATGTCCTGAACTTGAGAAGTTCAG
* *
30213 GAGGCAAAATGTCC
1 GGGGTAAAATGTCC
30227 ACATTTGAAG
Statistics
Matches: 40, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
31 21 0.52
32 19 0.47
ACGTcount: A:0.32, C:0.12, G:0.29, T:0.27
Consensus pattern (32 bp):
GGGGTAAAATGTCCTGAACTTGAGAAGTTCAG
Found at i:30247 original size:29 final size:30
Alignment explanation
Indices: 30172--30250 Score: 83
Period size: 31 Copynumber: 2.6 Consensus size: 30
30162 CTTGAATTTG
* *
30172 AGAAGTTCAGGGGGTAAAATGTCCTGAACTT
1 AGAAGTTCAGAGGGCAAAATGTCC-GAACTT
30203 AGAAGTTCATGA-GGCAAAATGTCC--ACATT
1 AGAAGTTCA-GAGGGCAAAATGTCCGAAC-TT
*
30232 TGAAGTTCAGAGGGCAAAA
1 AGAAGTTCAGAGGGCAAAA
30251 AGATTAATAA
Statistics
Matches: 42, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
28 4 0.10
29 17 0.40
31 20 0.48
32 1 0.02
ACGTcount: A:0.37, C:0.14, G:0.27, T:0.23
Consensus pattern (30 bp):
AGAAGTTCAGAGGGCAAAATGTCCGAACTT
Done.