Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021417.1 Corchorus olitorius cultivar O-4 contig21450, 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: 10130
ACGTcount: A:0.33, C:0.15, G:0.18, T:0.34
Found at i:2344 original size:123 final size:121
Alignment explanation
Indices: 2101--2345 Score: 264
Period size: 124 Copynumber: 2.0 Consensus size: 121
2091 TTTTTTAAAT
2101 TAAAATGGTAAAAATAAAATAATTATAAAATATTAAATTTAATTAAATAAAAATAGAGTTTCTAA
1 TAAAATGGTAAAAATAAAATAATTATAAAATATTAAATTTAATTAAATAAAAATAGAGTTTCTAA
* ** ** * *
2166 TATAATAAAACTGTATATTAAAAGATTTTAATATATCCAAATTTTTATTGAAAAATAG
66 TAGAATAAAACTCAATATTAAAAGACATT-ATATA-CCAAATATGTATTGAAAAATAG
* * * *
2224 TAAAATGGTAAAAATAAAGTAATTATAAAGATATTAGATTTAATTGAATAAAAATAGAGTTTTTA
1 TAAAATGGTAAAAATAAAATAATTATAAA-ATATTAAATTTAATTAAATAAAAATAGAGTTTCTA
* * *
2289 GTAGAATAAAATTACAATAGTTAAGTAATGACATT-TA-A-GAAATATGT-TTGAAAAATA
65 ATAGAATAAAACT-CAATA-TTAA--AA-GACATTATATACCAAATATGTATTGAAAAATA
2346 AGGGTATAAT
Statistics
Matches: 102, Mismatches: 14, Indels: 12
0.80 0.11 0.09
Matches are distributed among these distances:
123 38 0.37
124 48 0.47
125 3 0.03
126 5 0.05
127 2 0.02
128 2 0.02
129 4 0.04
ACGTcount: A:0.53, C:0.02, G:0.10, T:0.35
Consensus pattern (121 bp):
TAAAATGGTAAAAATAAAATAATTATAAAATATTAAATTTAATTAAATAAAAATAGAGTTTCTAA
TAGAATAAAACTCAATATTAAAAGACATTATATACCAAATATGTATTGAAAAATAG
Found at i:6282 original size:16 final size:16
Alignment explanation
Indices: 6261--6292 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
6251 GAGCCTCTGA
6261 TTTTCAGATTCAGGTC
1 TTTTCAGATTCAGGTC
6277 TTTTCAGATTCAGGTC
1 TTTTCAGATTCAGGTC
6293 ATTTAAATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.19, C:0.19, G:0.19, T:0.44
Consensus pattern (16 bp):
TTTTCAGATTCAGGTC
Found at i:6878 original size:265 final size:265
Alignment explanation
Indices: 6405--6938 Score: 1023
Period size: 265 Copynumber: 2.0 Consensus size: 265
6395 CCGGTGAACC
*
6405 TTCACATGCTGGCTTCTGCTAGTGATGACCGAAAAATTCGAATTTGGGGTTTAGATAACTTAAAC
1 TTCACATGCTGGCTTCTGCTAGTGATGACCGAAAAATTCGAATTTGAGGTTTAGATAACTTAAAC
6470 CTGAAAACTCGAGACCATTGCAATGGTGCCATCCACCACTGTAATGGGAGTAGCTGAAACAATTT
66 CTGAAAACTCGAGACCATTGCAATGGTGCCATCCACCACTGTAATGGGAGTAGCTGAAACAATTT
*
6535 GTATCCTCCTGTCAAATAATTCCTCAAGTTGTAACACCTTCATTAACATTTGGGTAAATTCTACA
131 GTATCCTCCTGTCAAATAATTCCTCAAGTTGTAACACCTTCATTAACATTTGGGTAAATTCTAAA
*
6600 ATCATTTTGCATCTGTTCTTTGGCATTAAAAAGCAGGCAAAAAAAGCCAAATGCTATCTGCTATG
196 ATCATTTTGCATCTGTTCTTTGGCATTAAAAAGCAGGCAAAAAAAGCCAAATGCTATCTACTATG
6665 ACACA
261 ACACA
*
6670 TTCACATGCTGGCTTCTGCTAGTGATGACCGAACAATTCGAATTTGAGGTTTAGATAACTTAAAC
1 TTCACATGCTGGCTTCTGCTAGTGATGACCGAAAAATTCGAATTTGAGGTTTAGATAACTTAAAC
6735 CTGAAAACTCGAGACCATTGCAATGGTGCCATCCACCACTGTAATGGGAGTAGCTGAAACAATTT
66 CTGAAAACTCGAGACCATTGCAATGGTGCCATCCACCACTGTAATGGGAGTAGCTGAAACAATTT
*
6800 GTATCCTCCTGTCAAATAATTCCTCAAGTTGTAACACCTTCATTAACATTTGTGTAAATTCTAAA
131 GTATCCTCCTGTCAAATAATTCCTCAAGTTGTAACACCTTCATTAACATTTGGGTAAATTCTAAA
6865 ATCATTTTGCATCTGTTCTTTGGCATTAAAAAGCAGGCAAAAAAAGCCAAATGCTATCTACTATG
196 ATCATTTTGCATCTGTTCTTTGGCATTAAAAAGCAGGCAAAAAAAGCCAAATGCTATCTACTATG
6930 ACACA
261 ACACA
6935 TTCA
1 TTCA
6939 ACTTTGACCT
Statistics
Matches: 264, Mismatches: 5, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
265 264 1.00
ACGTcount: A:0.32, C:0.21, G:0.17, T:0.30
Consensus pattern (265 bp):
TTCACATGCTGGCTTCTGCTAGTGATGACCGAAAAATTCGAATTTGAGGTTTAGATAACTTAAAC
CTGAAAACTCGAGACCATTGCAATGGTGCCATCCACCACTGTAATGGGAGTAGCTGAAACAATTT
GTATCCTCCTGTCAAATAATTCCTCAAGTTGTAACACCTTCATTAACATTTGGGTAAATTCTAAA
ATCATTTTGCATCTGTTCTTTGGCATTAAAAAGCAGGCAAAAAAAGCCAAATGCTATCTACTATG
ACACA
Found at i:8180 original size:24 final size:24
Alignment explanation
Indices: 8143--8240 Score: 142
Period size: 24 Copynumber: 4.1 Consensus size: 24
8133 TGTCGATGAC
* *
8143 TCTGATTTTGACGACCGTGATTTT
1 TCTGGTTTTGACGACTGTGATTTT
* *
8167 TTTGGTTTTGACGATTGTGATTTT
1 TCTGGTTTTGACGACTGTGATTTT
* *
8191 TCTGCTTTTGACAACTGTGATTTT
1 TCTGGTTTTGACGACTGTGATTTT
8215 TCTGGTTTTGACGACTGTGATTTT
1 TCTGGTTTTGACGACTGTGATTTT
8239 TC
1 TC
8241 GGATTTTTCG
Statistics
Matches: 64, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 64 1.00
ACGTcount: A:0.14, C:0.13, G:0.21, T:0.51
Consensus pattern (24 bp):
TCTGGTTTTGACGACTGTGATTTT
Done.