Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019662.1 Corchorus olitorius cultivar O-4 contig19695, 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: 38292
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Found at i:217 original size:71 final size:71
Alignment explanation
Indices: 101--245 Score: 272
Period size: 71 Copynumber: 2.0 Consensus size: 71
91 GTTGGAAATT
*
101 CTAATACGAGTATATGACCAATTTAGGACATCCTATATTGGGGATGTGTGGTCTATTGGGCCAGG
1 CTAATACGAGTATATGACCAATTTAGGACATCCTATATTGGGGATGTGTAGTCTATTGGGCCAGG
166 CCTGAG
66 CCTGAG
*
172 CTAATACGAGTATATGACCAATTTAGGACATCCTATATTGGGGATGTGTATTCTATTGGGCCAGG
1 CTAATACGAGTATATGACCAATTTAGGACATCCTATATTGGGGATGTGTAGTCTATTGGGCCAGG
237 CCTGAG
66 CCTGAG
243 CTA
1 CTA
246 TCATGTGAAA
Statistics
Matches: 72, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
71 72 1.00
ACGTcount: A:0.26, C:0.17, G:0.26, T:0.30
Consensus pattern (71 bp):
CTAATACGAGTATATGACCAATTTAGGACATCCTATATTGGGGATGTGTAGTCTATTGGGCCAGG
CCTGAG
Found at i:4084 original size:87 final size:87
Alignment explanation
Indices: 3938--4108 Score: 290
Period size: 87 Copynumber: 2.0 Consensus size: 87
3928 GTGGTTCGGG
* *
3938 TTCGAATTCGAGTCTTCTGAATATAAAAATTTCGTTGTCGGAAGAGTTTTACGTCATAATAGTGA
1 TTCGAATTCGAGTCTTCTGAATAAAAAAATTTCATTGTCGGAAGAGTTTTACGTCATAATAGTGA
4003 ATTAACCAGACTCGAATAAAGT
66 ATTAACCAGACTCGAATAAAGT
* *
4025 TTCGAGTTCGAGTCTTTTGAATACAAAAAATTT-ATTGTCGGAAGAGTTTTACGTCATAATAGTG
1 TTCGAATTCGAGTCTTCTGAATA-AAAAAATTTCATTGTCGGAAGAGTTTTACGTCATAATAGTG
4089 AATTAACCAGACTCGAATAA
65 AATTAACCAGACTCGAATAA
4109 GGTTAACTTA
Statistics
Matches: 79, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
87 71 0.90
88 8 0.10
ACGTcount: A:0.35, C:0.13, G:0.18, T:0.33
Consensus pattern (87 bp):
TTCGAATTCGAGTCTTCTGAATAAAAAAATTTCATTGTCGGAAGAGTTTTACGTCATAATAGTGA
ATTAACCAGACTCGAATAAAGT
Found at i:4140 original size:87 final size:88
Alignment explanation
Indices: 3962--4140 Score: 202
Period size: 87 Copynumber: 2.0 Consensus size: 88
3952 TTCTGAATAT
* *
3962 AAAAATTTCGTTGTCGGAAGAGTTTTACGTCATAATAGTGAATTAACCAGACTCGAATAAAGTTT
1 AAAAATTTCATTGTCGGAAGAGTTTTACGTCATAATAGTGAATTAACCAGACTCGAATAAAGGTT
* * ** * * **** *
4027 CGAGTTCGAGTCTTTTGAATACA
66 CAACTTAAAATATCAAAAATAAA
4050 AAAAATTT-ATTGTCGGAAGAGTTTTACGTCATAATAGTGAATTAACCAGACTCGAAT-AAGGTT
1 AAAAATTTCATTGTCGGAAGAGTTTTACGTCATAATAGTGAATTAACCAGACTCGAATAAAGGTT
4113 -AACTTAAAAATATACAAAAATAAA
66 CAACTT-AAAATAT-CAAAAATAAA
4137 AAAA
1 AAAA
4141 CTGACCAACT
Statistics
Matches: 76, Mismatches: 13, Indels: 5
0.81 0.14 0.05
Matches are distributed among these distances:
85 3 0.04
86 8 0.11
87 57 0.75
88 8 0.11
ACGTcount: A:0.42, C:0.12, G:0.16, T:0.30
Consensus pattern (88 bp):
AAAAATTTCATTGTCGGAAGAGTTTTACGTCATAATAGTGAATTAACCAGACTCGAATAAAGGTT
CAACTTAAAATATCAAAAATAAA
Found at i:5120 original size:2 final size:2
Alignment explanation
Indices: 5113--5142 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
5103 ATTTTGAAGC
*
5113 AT AT AT AT AT AT AT AT AT AT AT AT AC AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5143 TATTTGAAAC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:11364 original size:2 final size:2
Alignment explanation
Indices: 11357--11389 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
11347 GCTTTAATTC
11357 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
11390 AGAACTACGT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:11757 original size:2 final size:2
Alignment explanation
Indices: 11750--11790 Score: 57
Period size: 2 Copynumber: 21.0 Consensus size: 2
11740 ATATTTTCTT
* *
11750 TA TA TA TA TA TA TA TA TA TA TA TA T- TA AA AA 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
11791 CCTTGCCTAG
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (2 bp):
TA
Found at i:26051 original size:2 final size:2
Alignment explanation
Indices: 26044--26077 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
26034 CTGATCATTC
26044 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
26078 TGATATCTAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:26606 original size:2 final size:2
Alignment explanation
Indices: 26599--26629 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
26589 GAAGATACAA
26599 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
26630 AACTAAGTCT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:35756 original size:6 final size:6
Alignment explanation
Indices: 35745--35769 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
35735 GTCTTGTAGA
35745 ATTAGG ATTAGG ATTAGG ATTAGG A
1 ATTAGG ATTAGG ATTAGG ATTAGG A
35770 AATTAGTATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.36, C:0.00, G:0.32, T:0.32
Consensus pattern (6 bp):
ATTAGG
Found at i:36920 original size:6 final size:7
Alignment explanation
Indices: 36903--36927 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
36893 CTTTTGATTA
36903 AAAAAAG
1 AAAAAAG
36910 AAAAAAG
1 AAAAAAG
36917 AAAAAAG
1 AAAAAAG
36924 AAAA
1 AAAA
36928 CCGTTATGTC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (7 bp):
AAAAAAG
Done.