Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017968.1 Corchorus olitorius cultivar O-4 contig18001, 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: 2159
ACGTcount: A:0.33, C:0.18, G:0.15, T:0.34
Found at i:807 original size:326 final size:327
Alignment explanation
Indices: 42--1864 Score: 1815
Period size: 334 Copynumber: 5.5 Consensus size: 327
32 GTGATGGTCA
* * * *
42 GTACAAGATTTCGGCTTAAATTTTGCAAAAATT-AACGGAAAGTTTTTCCCTCAATTTTTGGTAA
1 GTACACGATTTCGGCTTAAATTTTCCAAAAATTGAACCGAAAGTTTTTCCCTCAATTTTTGGTCA
* * * * *
106 CAATACTCATAAAAAGTATATAATTCACCACC-AAGAAGATCGAAGGGCTTTTGAC-ATTGCTTA
66 CAATACTCATAAAAAGTATATAATTCATCGCCGAAGAAGATCGAAGGGCTTTTCACGCTT-CTAA
* * * * * *
169 TATCGTTTTTTCT-ATATTTTTCCGAAATAATTTCTAATTAAATTGAAACCGGTTTCTGATGCTC
130 TATCATTTTTCCTGTTTTTTTTCCGAATTAATTTCTAATTAAATTGAAACCGGTTTATGATGCTC
* *
233 GTAAAATCAAATCCTTAAATCTGACATGCGTGAGATTTGGTTAGATGAATATAGATATTACAAGG
195 GTAAAAACAAATCCTTAAATCTGACATGCCTGAGATTTGGTTAGATGAATATAGATATTACAAGG
* *
298 AGTCTTGGCATCCAAAAATAATGCAAAACTGAGCCGGGGCTCCGGAGCGCGTTTTTTGCT-AAAA
260 AGTCTTGGCAGCCAAAAATAATGCAAAACTGAGCCGGGGCCCCGGAGCGCGTTTTTTGCTAAAAA
362 ACTTT
325 AC--T
*
367 GATACACGATTTCGGCTTAAATTTTCCAAAAATTGAACCGAAAGGTTTTCCCTCAATTTTTGGTC
1 G-TACACGATTTCGGCTTAAATTTTCCAAAAATTGAACCGAAAGTTTTTCCCTCAATTTTTGGTC
* *
432 ACAATACTCATAAAATGTATATAATTCATCG-CGAAAGAAGATTGAAGGGCTTTTCACGCTTCTA
65 ACAATACTCATAAAAAGTATATAATTCATCGCCG-AAGAAGATCGAAGGGCTTTTCACGCTTCTA
* * *
496 ATTTCATTTTTCCTGTTTTTTTTTCAGAATTAATTTCTAATTAAATTGAAACCGGTTTCTGATGC
129 ATATCATTTTTCCTG-TTTTTTTTCCGAATTAATTTCTAATTAAATTGAAACCGGTTTATGATGC
* *
561 TCGTAAAAACAAATCCTTTAATCTGACATGCCTGAGATTTGGTTAGATGAATATAGATATTAGAA
193 TCGTAAAAACAAATCCTTAAATCTGACATGCCTGAGATTTGGTTAGATGAATATAGATATTACAA
** * *
626 GGAGTCTTGGC-GCCAAAAATAATGCACTACTGAGTCAGGGCCCCGGAGCGCGTTTTTTGCTAAA
258 GGAGTCTTGGCAGCCAAAAATAATGCAAAACTGAGCCGGGGCCCCGGAGCGCGTTTTTTGCTAAA
690 AAAC-
323 AAACT
694 GTACACGATTTCGGCTTAAATTTTCCAAAAATTGAACCGAAAGTTTTTCCCTCAATTTTTGGTCA
1 GTACACGATTTCGGCTTAAATTTTCCAAAAATTGAACCGAAAGTTTTTCCCTCAATTTTTGGTCA
759 CAATACTCATAAAAAGTATATAATTCATCGCCGAAGAAGATCGAAGGGCTTTTCACGCTTCTAAT
66 CAATACTCATAAAAAGTATATAATTCATCGCCGAAGAAGATCGAAGGGCTTTTCACGCTTCTAAT
824 ATCATTTTTCCTGTTTTTTTTCCGAATTAATTTCTAATTAAATTGAAACCGGTTTATGATGCTCG
131 ATCATTTTTCCTGTTTTTTTTCCGAATTAATTTCTAATTAAATTGAAACCGGTTTATGATGCTCG
* * *
889 TAAAAACAAATCCTTATATCTGACATGCCTAATATTTGGTTAGATGAATATAGATATTACAAGGA
196 TAAAAACAAATCCTTAAATCTGACATGCCTGAGATTTGGTTAGATGAATATAGATATTACAAGGA
* * *
954 GTCTTGGC-GCAAAAAATAATGCAAAACTGAACCGGGGCCCCAGAGCGCGTTTTTTGCTAAAAAA
261 GTCTTGGCAGCCAAAAATAATGCAAAACTGAGCCGGGGCCCCGGAGCGCGTTTTTTGCTAAAAAA
1018 CT
326 CT
*
1020 GTAACGGTTAGTAAACGATTTCGGCTTAAATTTTCCAAAAATTGAATCGAAAGTTTTTCCCTCAA
1 GT-AC---------ACGATTTCGGCTTAAATTTTCCAAAAATTGAACCGAAAGTTTTTCCCTCAA
* * *
1085 TTTTTGTTCACAATACTCATAAAAAGTATATAATTCATCGCCAAAGAAGATTGAAGGGCTTTTCA
56 TTTTTGGTCACAATACTCATAAAAAGTATATAATTCATCGCCGAAGAAGATCGAAGGGCTTTTCA
*
1150 CGCTTCTAATATCGTTTTTCCTG--TTTTTTCCGAATTAATTTCTAATTAAATTGAAACCGGTTT
121 CGCTTCTAATATCATTTTTCCTGTTTTTTTTCCGAATTAATTTCTAATTAAATTGAAACCGGTTT
* * ** * ** * *
1213 ATGATGCTTGTAAAACCTTATCCTTAAATC-CATTGTGTCTGAGATTTGGTTAGATGAAAATAGA
186 ATGATGCTCGTAAAAACAAATCCTTAAATCTGA-CATGCCTGAGATTTGGTTAGATGAATATAGA
** * * * * * * ** *
1277 TATTTTAAGCAGTCTT-GCTGCCAAAAATCATCCAAAACTGTGACGGGGCCTAGGAACGCGTTTT
250 TATTACAAGGAGTCTTGGCAGCCAAAAATAATGCAAAACTGAGCCGGGGCCCCGGAGCGCGTTTT
* *
1341 TAGC-CAAAAACTGT
315 TTGCTAAAAAAC--T
* * * * ** * * * *
1355 GAGGCGTACACGATCTCGGGC-AAAATTTTGCAAAAACTGTCCCAAAAATTTTTTCCTGAATTTT
1 -----GTACACGATTTC-GGCTTAAATTTTCCAAAAATTGAACCGAAAGTTTTTCCCTCAATTTT
* * * * * * * * ** * **
1419 TAGCCACAATACTCAAAAAAAATATATATAACTCAACGCC-AATAAAATTTAAGAGCTTTTCTGG
60 TGGTCACAATACTC-ATAAAAA-GTATATAATTCATCGCCGAAGAAGATCGAAGGGCTTTTCACG
* * * *** *
1483 CTTCTAATATCCTTTTTCC----TATTTTCCGAATTAATTTCTAATTAAATCGAAACATAATTCA
123 CTTCTAATATCATTTTTCCTGTTTTTTTTCCGAATTAATTTCTAATTAAATTGAAAC-CGGTTTA
* * * * * * *
1544 -GATGCTCGTAAAAA-ATTATTCTTAAATC-CACCGTGGCTGAGATTTGGTTAGATGAGTATAAA
187 TGATGCTCGTAAAAACA-AATCCTTAAATCTGA-CATGCCTGAGATTTGGTTAGATGAATATAGA
* * * * * * * * *
1606 TATTTTC-AGGAGTCTT-GCTGCCAAAAATCATCCAAAGCT-AGGTCAGGGCCCCAGAACGCATG
250 TA-TTACAAGGAGTCTTGGCAGCCAAAAATAATGCAAAACTGA-GCCGGGGCCCCGGAGCGC--G
*
1668 TTTTTAG-TAAAAAACAGTGATGATT
311 TTTTTTGCTAAAAAAC---------T
** * * ** * * * *
1693 AGTACACGATTTCGGCCAAAATTTTGCAAAAACTGTCCCGAAAACTATTT-CCTCAATTTTTTGC
1 -GTACACGATTTCGGCTTAAATTTTCCAAAAATTGAACCG-AAAGTTTTTCCCTCAATTTTTGGT
* * * ** *
1757 CACAATACTCATAACAAA-TATATAATTCAACGAC-AATAA-ATTTTAAGGGCTTTTCAAGCTTC
64 CACAATACTCATAA-AAAGTATATAATTCATCGCCGAAGAAGA-TCGAAGGGCTTTTCACGCTTC
* *
1819 TAATATAATTTTTCC---TATTTTTCCGAATTAATTTCTAATTATAATT
127 TAATATCATTTTTCCTGTTTTTTTTCCGAATTAATTTCTAATTA-AATT
1865 TTTCCTCACT
Statistics
Matches: 1296, Mismatches: 150, Indels: 95
0.84 0.10 0.06
Matches are distributed among these distances:
325 169 0.13
326 168 0.13
327 60 0.05
328 34 0.03
329 174 0.13
330 180 0.14
331 60 0.05
332 64 0.05
333 38 0.03
334 202 0.16
335 8 0.01
336 134 0.10
338 1 0.00
339 2 0.00
340 2 0.00
ACGTcount: A:0.33, C:0.18, G:0.15, T:0.34
Consensus pattern (327 bp):
GTACACGATTTCGGCTTAAATTTTCCAAAAATTGAACCGAAAGTTTTTCCCTCAATTTTTGGTCA
CAATACTCATAAAAAGTATATAATTCATCGCCGAAGAAGATCGAAGGGCTTTTCACGCTTCTAAT
ATCATTTTTCCTGTTTTTTTTCCGAATTAATTTCTAATTAAATTGAAACCGGTTTATGATGCTCG
TAAAAACAAATCCTTAAATCTGACATGCCTGAGATTTGGTTAGATGAATATAGATATTACAAGGA
GTCTTGGCAGCCAAAAATAATGCAAAACTGAGCCGGGGCCCCGGAGCGCGTTTTTTGCTAAAAAA
CT
Found at i:1962 original size:125 final size:123
Alignment explanation
Indices: 1740--1987 Score: 320
Period size: 125 Copynumber: 2.0 Consensus size: 123
1730 CCGAAAACTA
* * * * * * *
1740 TTTCCTCAATTTTTTGCCACAATACTCATAACAAATATATAATTCAACGACAATAAATTTTAAGG
1 TTTCCTCAATTTTTTGCCAAAAAACTCATAAAAAATATATAACTCAACGACAAAAAAATATAAGG
* *
1805 GCTTTTCAAGCTTCTAATATAATTTTTCCTATTTTTCCGAATTAATTTCTAATTATAATT
66 GCTTTTCAAGCTTATAATATAAGTTTTCCTATTTTT-CGAATTAATTTCTAATTA-AATT
* *
1865 TTTCCTCACTTTTTTGCCAAAAAACTCATAAAAAATATATAACTCATCG-CTAAAAAAAATATAA
1 TTTCCTCAATTTTTTGCCAAAAAACTCATAAAAAATATATAACTCAACGAC--AAAAAAATATAA
* * *
1929 GGGCTTTTCATGCTTATAATAT-CGTTTTCCTATTTTTCGAATTAATTTTTAATTAAATT
64 GGGCTTTTCAAGCTTATAATATAAGTTTTCCTATTTTTCGAATTAATTTCTAATTAAATT
1988 GAAACATAAT
Statistics
Matches: 107, Mismatches: 14, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
123 4 0.04
124 18 0.17
125 56 0.52
126 29 0.27
ACGTcount: A:0.35, C:0.16, G:0.06, T:0.42
Consensus pattern (123 bp):
TTTCCTCAATTTTTTGCCAAAAAACTCATAAAAAATATATAACTCAACGACAAAAAAATATAAGG
GCTTTTCAAGCTTATAATATAAGTTTTCCTATTTTTCGAATTAATTTCTAATTAAATT
Done.