Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014697.1 Corchorus olitorius cultivar O-4 contig14730, 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: 26164
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:940 original size:31 final size:28
Alignment explanation
Indices: 867--942 Score: 73
Period size: 31 Copynumber: 2.6 Consensus size: 28
857 CCAAATTGTG
* *
867 AGTTCAGGGGGCAAACA-TCCAAATTAA
1 AGTTCAGGGGGCAAAAAGTCAAAATTAA
* * *
894 AGTTTAGAGGACAAAAAGTCAAAATCGTAAA
1 AGTTCAGGGGGCAAAAAGTCAAAAT--T-AA
925 AGTTCAGGGGGCAAAAAG
1 AGTTCAGGGGGCAAAAAG
943 GGCATTAAGC
Statistics
Matches: 37, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
27 13 0.35
28 6 0.16
30 1 0.03
31 17 0.46
ACGTcount: A:0.45, C:0.13, G:0.25, T:0.17
Consensus pattern (28 bp):
AGTTCAGGGGGCAAAAAGTCAAAATTAA
Found at i:5159 original size:12 final size:12
Alignment explanation
Indices: 5142--5166 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
5132 GAAAGCTCGG
5142 CCGAGCTCGAGC
1 CCGAGCTCGAGC
5154 CCGAGCTCGAGC
1 CCGAGCTCGAGC
5166 C
1 C
5167 TTGAATTTTC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.44, G:0.32, T:0.08
Consensus pattern (12 bp):
CCGAGCTCGAGC
Found at i:5190 original size:31 final size:31
Alignment explanation
Indices: 5148--5226 Score: 149
Period size: 31 Copynumber: 2.5 Consensus size: 31
5138 TCGGCCGAGC
*
5148 TCGAGCCCGAGCTCGAGCCTTGAATTTTCAG
1 TCGAGCTCGAGCTCGAGCCTTGAATTTTCAG
5179 TCGAGCTCGAGCTCGAGCCTTGAATTTTCAG
1 TCGAGCTCGAGCTCGAGCCTTGAATTTTCAG
5210 TCGAGCTCGAGCTCGAG
1 TCGAGCTCGAGCTCGAG
5227 TATTGAGATA
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
31 47 1.00
ACGTcount: A:0.19, C:0.28, G:0.28, T:0.25
Consensus pattern (31 bp):
TCGAGCTCGAGCTCGAGCCTTGAATTTTCAG
Found at i:5303 original size:23 final size:24
Alignment explanation
Indices: 5273--5321 Score: 82
Period size: 23 Copynumber: 2.1 Consensus size: 24
5263 CCCTAGTGTC
*
5273 AACTGTCATGAAA-TAAAAAAAAA
1 AACTGTCATGAAACGAAAAAAAAA
5296 AACTGTCATGAAACGAAAAAAAAA
1 AACTGTCATGAAACGAAAAAAAAA
5320 AA
1 AA
5322 AAGTGATTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 13 0.54
24 11 0.46
ACGTcount: A:0.65, C:0.10, G:0.10, T:0.14
Consensus pattern (24 bp):
AACTGTCATGAAACGAAAAAAAAA
Found at i:6167 original size:26 final size:26
Alignment explanation
Indices: 6138--6191 Score: 99
Period size: 26 Copynumber: 2.1 Consensus size: 26
6128 TAAGTCAACC
6138 TAATAGATTTTATAAACCTTAACTGA
1 TAATAGATTTTATAAACCTTAACTGA
*
6164 TAATAGATTTTCTAAACCTTAACTGA
1 TAATAGATTTTATAAACCTTAACTGA
6190 TA
1 TA
6192 TTGAAAAAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.41, C:0.13, G:0.07, T:0.39
Consensus pattern (26 bp):
TAATAGATTTTATAAACCTTAACTGA
Found at i:6274 original size:28 final size:28
Alignment explanation
Indices: 6227--6280 Score: 92
Period size: 27 Copynumber: 2.0 Consensus size: 28
6217 AGGCTTTTTC
6227 TTGAATCTTTTATAATAAAAAATTTACT
1 TTGAATCTTTTATAATAAAAAATTTACT
*
6255 TTGAA-CTTTTTTAATAAAAAATTTAC
1 TTGAATCTTTTATAATAAAAAATTTAC
6281 CTAATTTCTT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
27 20 0.80
28 5 0.20
ACGTcount: A:0.43, C:0.07, G:0.04, T:0.46
Consensus pattern (28 bp):
TTGAATCTTTTATAATAAAAAATTTACT
Done.