Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016765.1 Corchorus olitorius cultivar O-4 contig16798, 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: 22315
ACGTcount: A:0.29, C:0.17, G:0.19, T:0.35
Found at i:6087 original size:213 final size:213
Alignment explanation
Indices: 5720--6151 Score: 756
Period size: 213 Copynumber: 2.0 Consensus size: 213
5710 TGTGGATATG
* * * *
5720 TCAGAAGCTACATCCCATGATGCTGATGCCCAAGGAACTCACACTCAGCAGAATGAATCATTTCG
1 TCAGAAGCTACATCCCATGATGCTGATGCCCAAGGAACTCAAACTCAACAGAATGAACCAGTTCG
*
5785 CAAGCGTCTTGCTTCTACCACTTCTGAGTTGCATGAGGATTCACCAGTTCCGGGTGAGACGAGCG
66 CAAGCGTCTTGCTTCTACCACTTCTGAGTTGCATGAGGATTCACCAGTTCCGGGTGAGACGAGCA
5850 CTGATATCGCTGAGCCACTGCTCAAGAAGTCTAAGGGTTCAGATCCCCCACCAGAGACTTCTGAA
131 CTGATATCGCTGAGCCACTGCTCAAGAAGTCTAAGGGTTCAGATCCCCCACCAGAGACTTCTGAA
* *
5915 GGTCAAGTTGGTGCTGTT
196 GGTCAAGTTGCTGCTATT
* *
5933 TCAGAAGCTACATCCCATGATGCTGATGCTCAAGGAACTCAAACTCAACAGAATGAGCCAGTTCG
1 TCAGAAGCTACATCCCATGATGCTGATGCCCAAGGAACTCAAACTCAACAGAATGAACCAGTTCG
* *
5998 CAAGCGTCTTGCTTCTACGACTTCTGAGTTGCATGAGGATTCACCGGTTCCGGGTGAGACGAGCA
66 CAAGCGTCTTGCTTCTACCACTTCTGAGTTGCATGAGGATTCACCAGTTCCGGGTGAGACGAGCA
*
6063 CTGATGTCGCTGAGCCACTGCTCAAGAAGTCTAAGGGTTCAGATCCCCCACCAGAGACTTCTGAA
131 CTGATATCGCTGAGCCACTGCTCAAGAAGTCTAAGGGTTCAGATCCCCCACCAGAGACTTCTGAA
6128 GGTCAAGTTGCTGCTATT
196 GGTCAAGTTGCTGCTATT
6146 TCAGAA
1 TCAGAA
6152 AATCTTACTG
Statistics
Matches: 207, Mismatches: 12, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
213 207 1.00
ACGTcount: A:0.26, C:0.26, G:0.24, T:0.24
Consensus pattern (213 bp):
TCAGAAGCTACATCCCATGATGCTGATGCCCAAGGAACTCAAACTCAACAGAATGAACCAGTTCG
CAAGCGTCTTGCTTCTACCACTTCTGAGTTGCATGAGGATTCACCAGTTCCGGGTGAGACGAGCA
CTGATATCGCTGAGCCACTGCTCAAGAAGTCTAAGGGTTCAGATCCCCCACCAGAGACTTCTGAA
GGTCAAGTTGCTGCTATT
Found at i:13185 original size:14 final size:14
Alignment explanation
Indices: 13166--13195 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
13156 CTTAGTAATA
13166 TTCTTTCTTTTCTT
1 TTCTTTCTTTTCTT
*
13180 TTCTTTTTTTTCTT
1 TTCTTTCTTTTCTT
13194 TT
1 TT
13196 TCCTTTTTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (14 bp):
TTCTTTCTTTTCTT
Found at i:13206 original size:20 final size:21
Alignment explanation
Indices: 13169--13219 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 21
13159 AGTAATATTC
13169 TTTC-TTTT-CTTTTCTTTTT
1 TTTCTTTTTCCTTTTCTTTTT
13188 TTTCTTTTTCCTTTT-TTTTT
1 TTTCTTTTTCCTTTTCTTTTT
* *
13208 TGTCTTGTTCCT
1 TTTCTTTTTCCT
13220 GGTCACCTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
19 4 0.14
20 19 0.68
21 5 0.18
ACGTcount: A:0.00, C:0.18, G:0.04, T:0.78
Consensus pattern (21 bp):
TTTCTTTTTCCTTTTCTTTTT
Found at i:16882 original size:7 final size:7
Alignment explanation
Indices: 16872--16902 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
16862 ATTCTACCTT
16872 TTTTTTC
1 TTTTTTC
16879 TTTTTTC
1 TTTTTTC
16886 TTTTTTC
1 TTTTTTC
16893 TTTTTT-
1 TTTTTTC
16899 TTTT
1 TTTT
16903 ATCATTGAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 4 0.17
7 20 0.83
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (7 bp):
TTTTTTC
Done.