Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016950.1 Corchorus olitorius cultivar O-4 contig16983, 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: 1749
ACGTcount: A:0.31, C:0.16, G:0.23, T:0.30
Found at i:482 original size:199 final size:201
Alignment explanation
Indices: 1--528 Score: 773
Period size: 201 Copynumber: 2.6 Consensus size: 201
* *
1 AATGA-GTATGTGTCAACTTTTTAACCCGCTTACGGAGTCCAAAATTTACACTGACAGTGTATTG
1 AATGAGGTATGTGTCAACTTCTTAACCCGCTTATGGAGTCCAAAATTTACACTGACAGTGTATTG
** *
65 TATAATAAT-TCTATAAGAAAAATTATACAATACAATGTCAGTGGAGTTTAACATACTGCACGTG
66 TATAATAATCT-TATAAGAAAAATTATACAATACACCGTCAGTGGAGTTTAACAGACTGCACGTG
* *
129 CGGGGTTTAAGAGGCGACATGTGTCCCCTAGAGGAATATGTATTAATATTAAATATATTTAATTA
130 CGGGGTTTAAGAGGCGACACGTGACCCCTAGAGGAATATGTATTAATATTAAATATATTTAATTA
194 ATTATGA
195 ATTATGA
* * *
201 AATGAGGTATGTGTTAATTTCTTAACCCGCTTATGGAGTCCAAAATTTACATTGACAGTGTATTG
1 AATGAGGTATGTGTCAACTTCTTAACCCGCTTATGGAGTCCAAAATTTACACTGACAGTGTATTG
* * * * *
266 TATAACAATCCTATAAGAAAAATTATACAATACACCGTCAATGGAGTTTAATAGACTGTACGTGC
66 TATAATAATCTTATAAGAAAAATTATACAATACACCGTCAGTGGAGTTTAACAGACTGCACGTGC
*
331 GGGGTTTAAG-GGTTGACACGTGACCCCTTAG-GGAATATGTATTAATATT-AA-ATATTTAATT
131 GGGGTTTAAGAGG-CGACACGTGACCCC-TAGAGGAATATGTATTAATATTAAATATATTTAATT
392 AATTATGA
194 AATTATGA
* * *
400 AATTG-GGTATGTGTCAACCTCTTAACCCGCTTATGGAGTCTAAAATTTACACTGACAGTGAATT
1 AA-TGAGGTATGTGTCAACTTCTTAACCCGCTTATGGAGTCCAAAATTTACACTGACAGTGTATT
* * *
464 GTATAATAATCTTATAAGAAAAAGTATACAATACACCGTCAGTGAAGTTTAGCAGACTGCACGTG
65 GTATAATAATCTTATAAGAAAAATTATACAATACACCGTCAGTGGAGTTTAACAGACTGCACGTG
529 TAATACCAAG
Statistics
Matches: 293, Mismatches: 30, Indels: 11
0.88 0.09 0.03
Matches are distributed among these distances:
199 130 0.44
200 11 0.04
201 149 0.51
202 3 0.01
ACGTcount: A:0.35, C:0.14, G:0.18, T:0.32
Consensus pattern (201 bp):
AATGAGGTATGTGTCAACTTCTTAACCCGCTTATGGAGTCCAAAATTTACACTGACAGTGTATTG
TATAATAATCTTATAAGAAAAATTATACAATACACCGTCAGTGGAGTTTAACAGACTGCACGTGC
GGGGTTTAAGAGGCGACACGTGACCCCTAGAGGAATATGTATTAATATTAAATATATTTAATTAA
TTATGA
Found at i:1650 original size:235 final size:241
Alignment explanation
Indices: 1189--1667 Score: 776
Period size: 235 Copynumber: 2.0 Consensus size: 241
1179 TAAAATTGGG
1189 TTTGAATTTGGCTTAAAGAGGGCTGTAATTTATTTTTGAGTCTCACCGGAATCTGGACGGAATCT
1 TTTGAATTTGGCTTAAAGAGGGCTGTAATTTATTTTTGAGTCT--CC-G-A-CT-G-CGGAATCT
1254 GGAATTTTCCAGATTCCGGTGGGTTTTCCGGTTGCCGGAAGAAGAGGGAGAAGAAGGAAAAAAAA
59 GGAATTTTCCAGATTCCGGTGGGTTTTCCGGTTGCCGGAAGAAGAGGGAGAAGAAGGAAAAAAAA
* *
1319 AAGAAGAAAAAGGGCCACTTGGGCCAGCAAGGCACGGCCCAAGCGCTTGGCCCAGGCGTGCGGGC
124 AAGAAAAAAAAGGGCCACTTGGGCCAGCAAGGCACGGCCCAAGCGCTTGGCCCAGGCGCGCGGGC
1384 CAGCGCTTGGCCCAGAGCCAGGCCAGGCGCGCGGGCCAGCG-TTGGCCCGCGC
189 CAGCGCTTGGCCCAGAGCCAGGCCAGGCGCGCGGGCCAGCGCTTGGCCCGCGC
1436 TTTGAATTTGGCTTAAAGAGGGCTGTAATTTA-TTTTGAGTCT-C-A-T-CGGAATCTGGAATTT
1 TTTGAATTTGGCTTAAAGAGGGCTGTAATTTATTTTTGAGTCTCCGACTGCGGAATCTGGAATTT
*
1496 TCCAGATTCCGGTGGGTTTTCCGGTTGCCGGAAGAAGAGGGAGAAGAA-GAAAAAAAAATGAAAA
66 TCCAGATTCCGGTGGGTTTTCCGGTTGCCGGAAGAAGAGGGAGAAGAAGGAAAAAAAAAAG-AAA
*
1560 AAAAAGGGCCACTTGGGCCAGCAAGGCACGGCCCAAGCGCTTGGCCCAGGCGCGCGGGCCAGCGT
130 AAAAAGGGCCACTTGGGCCAGCAAGGCACGGCCCAAGCGCTTGGCCCAGGCGCGCGGGCCAGCGC
*
1625 TTGGCCCAGCGCCAGG-CATGGCGCGCGGGCCAGCGCTTGGCCC
195 TTGGCCCAGAGCCAGGCCA-GGCGCGCGGGCCAGCGCTTGGCCC
1668 AACGCCTGGG
Statistics
Matches: 224, Mismatches: 5, Indels: 17
0.91 0.02 0.07
Matches are distributed among these distances:
234 13 0.06
235 159 0.71
236 7 0.03
238 1 0.00
240 1 0.00
243 1 0.00
246 10 0.04
247 32 0.14
ACGTcount: A:0.25, C:0.23, G:0.33, T:0.19
Consensus pattern (241 bp):
TTTGAATTTGGCTTAAAGAGGGCTGTAATTTATTTTTGAGTCTCCGACTGCGGAATCTGGAATTT
TCCAGATTCCGGTGGGTTTTCCGGTTGCCGGAAGAAGAGGGAGAAGAAGGAAAAAAAAAAGAAAA
AAAAGGGCCACTTGGGCCAGCAAGGCACGGCCCAAGCGCTTGGCCCAGGCGCGCGGGCCAGCGCT
TGGCCCAGAGCCAGGCCAGGCGCGCGGGCCAGCGCTTGGCCCGCGC
Done.