Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015166.1 Corchorus olitorius cultivar O-4 contig15199, 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: 8930
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.32
Found at i:870 original size:327 final size:325
Alignment explanation
Indices: 2--927 Score: 922
Period size: 337 Copynumber: 2.8 Consensus size: 325
1 T
* *
2 ATACACGATTGCGACTAAAATTTTGCAAAAATTGACCCGAAAGTTTTTTCCTCAATTTTTAGCCA
1 ATACACGATTTCGACTAAAATTTTGCAAAAATTGACCCGAAAGTTTTTTCCTCAA-TTTTGGCCA
** * * *
67 CTATAATCAT-AGAAAATATGTAATTCAACGCCAAAAAAATTGAAGGATTTTTCACGCTTCTAAT
65 AAATACTCATCA-AAAATATATAATTCAACGCC-AAAAAATTGAAGG--CTTTCACGCTTCTAAT
* * * *
131 ATCGTTTTTCATATTTTTTTCCAAATTAATTTCTGATTAAATC-ATAACTGGTTTCATATGCTCG
126 ATTGTTTTTCATATTTTTTTCTAAATTAATTTCTAATTAAATCGA-AAC-AGTTTCATATGCTCG
* *
195 AAAAAACAAATCCTTATATCCAATGTGGCTGAGATTTTGTTAGATGAATATAGATATTTCGATTA
189 AAAAAACAAATCCTTATATCCAATGTGGCTGAGA-TTTGTTAGATGAATATAGATATTTCAATGA
* * * * * * * *
260 GTCTCAACGCCAAAATTCATGTAGAACTGAACAGGGCCTCGTAACGCGTTTTTAGCCAAATATTG
253 GTCTCAACGCCAAAAATCATGCAAAAATGAACAGGGCCCCGGAACGCATTTTTAACCAAATA-T-
** *
325 TGATTTAACG
316 ACATATAACG
* * ** *
335 -TACACGATTTCAGGTAATATTTTTAATTTTGCAAAAATTGATTCGAAA-TATTTTTACTCAATA
1 ATACACGATTTC--G-ACTA----AAATTTTGCAAAAATTGACCCGAAAGT-TTTTTCCTCAAT-
* * * *
398 TTTGGCCAAAATACTCCTCAAAAATATATAATTTAAAGCCAAAAAATTGGAGGCTTTTCACGCTT
57 TTTGGCCAAAATACTCATCAAAAATATATAATTCAACGCCAAAAAATTGAAGGC-TTTCACGCTT
* * * ** * *
463 CTAAATATTGTTTTCCCTA-TTTTTTCTCAATTAATTTGAAATAAAATCGAAACAGCTTTCTTAT
121 CT-AATATTGTTTTTCATATTTTTTTCTAAATTAATTTCTAATTAAATCGAAACAG-TTTCATAT
*
527 GCTCGGAAAAACAAATCCTTATATCCAATGTGGCTGAGATTTGATTAGATGAATATAGATATTTC
184 GCTCGAAAAAACAAATCCTTATATCCAATGTGGCTGAGATTTG-TTAGATGAATATAGATATTTC
* * **
592 AATGGGTCT--TCGCCCGAAAAATCATGCAAAAATGTGTC-GGGACCCCGGAACGCATTTTTAAC
248 AATGAGTCTCAACG-CC-AAAAATCATGCAAAAATG-AACAGGG-CCCCGGAACGCATTTTTAAC
654 CAAA-A-ACA-ATAA-G
309 CAAATATACATATAACG
* * * *
667 ATACACGATTTCGACTACAATTTTGTAAGAATTAACCCGAAAGTTTTTTCCTCAATTTCTGGCCA
1 ATACACGATTTCGACTAAAATTTTGCAAAAATTGACCCGAAAGTTTTTTCCTCAATTT-TGGCCA
*
732 AAATACGCATCAAAAATATATAATTCAACGCCAAAAAGATTGAAAGGCTTTCACGCTTCTAATAT
65 AAATACTCATCAAAAATATATAATTCAACGCCAAAAA-ATTG-AAGGCTTTCACGCTTCTAATAT
* * * * * * *
797 TATTTTTCTTATTTTTTTCTGAATTAATTTCTAATTAAATCGAATCAAGATTCAAATGCTCGTAA
128 TGTTTTTCATATTTTTTTCTAAATTAATTTCTAATTAAATCGAAAC-AGTTTCATATGCTCGAAA
* * * * *
862 AAACAAATCTTTAAATCCAATGTGGCTGAGATTTGGTTAAATGAATATAGGTATTTCAAGGAGTC
192 AAACAAATCCTTATATCCAATGTGGCTGAGATTT-GTTAGATGAATATAGATATTTCAATGAGTC
927 T
256 T
928 GGGCACCAAA
Statistics
Matches: 490, Mismatches: 76, Indels: 60
0.78 0.12 0.10
Matches are distributed among these distances:
325 2 0.00
326 82 0.17
327 116 0.24
328 7 0.01
330 3 0.01
331 1 0.00
332 11 0.02
333 14 0.03
334 2 0.00
335 5 0.01
336 7 0.01
337 128 0.26
338 49 0.10
339 62 0.13
340 1 0.00
ACGTcount: A:0.35, C:0.16, G:0.13, T:0.35
Consensus pattern (325 bp):
ATACACGATTTCGACTAAAATTTTGCAAAAATTGACCCGAAAGTTTTTTCCTCAATTTTGGCCAA
AATACTCATCAAAAATATATAATTCAACGCCAAAAAATTGAAGGCTTTCACGCTTCTAATATTGT
TTTTCATATTTTTTTCTAAATTAATTTCTAATTAAATCGAAACAGTTTCATATGCTCGAAAAAAC
AAATCCTTATATCCAATGTGGCTGAGATTTGTTAGATGAATATAGATATTTCAATGAGTCTCAAC
GCCAAAAATCATGCAAAAATGAACAGGGCCCCGGAACGCATTTTTAACCAAATATACATATAACG
Found at i:1074 original size:327 final size:324
Alignment explanation
Indices: 378--986 Score: 719
Period size: 327 Copynumber: 1.9 Consensus size: 324
368 AAAATTGATT
* * *
378 CGAAATATTTTTACTCAATATT-TGGCCAAAATACTCCTCAAAAATATATAATTTAAAGCCAAAA
1 CGAAAGATTTTTCCTCAAT-TTCTGGCCAAAATA--CCTCAAAAATATATAATTCAAAGCCAAAA
* * *
442 AATTGGAGGCTTTTCACGCTTCTAAATATTGTTTTCCCTATTTTTTCTCAATTAATTTGAAATAA
63 AATTGAAGGCTTTTCACGCTTCTAAATATTATTTTCCCTATTTTTTCTCAATTAATTTCAAATAA
* ** *
507 AATCGAAACAGCTTTCTTATGCTCGGAAAAACAAATCCTTATATCCAATGTGGCTGAGATTTGAT
128 AATCGAAACAGCATTCAAATGCTCGGAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGAT
* * * *
572 TAGATGAATATAGATATTTCAATGGGTCTTCGCCCGAAAAATCATGCAAAAATGTGTCGGGACCC
193 TAAATGAATATAGATATTTCAATGGGTCTGCGCCCGAAAAATCATGCAAAAATGAGTCGGAACCC
* * * **
637 CGGAACGCATTTTTAACCAAAAACAATAAGATACACGATTTCGACTACAATTTTGTAAGAATTAA
258 CAGAACGCATTTTTAACAAAAAACAATAAGATACACGATTTCGACTAAAATTTTACAAGAATTAA
702 CC
323 CC
* *
704 CGAAAGTTTTTTCCTCAATTTCTGGCCAAAATACGCATCAAAAATATATAATTCAACGCCAAAAA
1 CGAAAGATTTTTCCTCAATTTCTGGCCAAAATAC-C-TCAAAAATATATAATTCAAAGCCAAAAA
* * * *
769 GATTGAAAGGC-TTTCACGCTTCT-AATATTATTTTTCTTATTTTTTTCTGAATTAATTTCTAAT
64 -ATTG-AAGGCTTTTCACGCTTCTAAATATTATTTTCCCTA-TTTTTTCTCAATTAATTTCAAAT
* * * *
832 TAAATCGAATCAAG-ATTCAAATGCTCGTAAAAACAAATCTTTAAATCCAATGTGGCTGAGATTT
126 AAAATCGAAAC-AGCATTCAAATGCTCGGAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTT
* * * * *
896 GGTTAAATGAATATAGGTATTTCAA-GGAGTCTGGGCACC-AAAAATCTTGCAAAACTGAGTC-G
190 GATTAAATGAATATAGATATTTCAATGG-GTCTGCGC-CCGAAAAATCATGCAAAAATGAGTCGG
** ** *
958 AAGTCCAGAACGTGTTTTTAGCAAAAAAC
253 AACCCCAGAACGCATTTTTAACAAAAAAC
987 CAAAACCCGT
Statistics
Matches: 238, Mismatches: 36, Indels: 18
0.82 0.12 0.06
Matches are distributed among these distances:
324 1 0.00
325 3 0.01
326 90 0.38
327 136 0.57
328 8 0.03
ACGTcount: A:0.36, C:0.17, G:0.14, T:0.33
Consensus pattern (324 bp):
CGAAAGATTTTTCCTCAATTTCTGGCCAAAATACCTCAAAAATATATAATTCAAAGCCAAAAAAT
TGAAGGCTTTTCACGCTTCTAAATATTATTTTCCCTATTTTTTCTCAATTAATTTCAAATAAAAT
CGAAACAGCATTCAAATGCTCGGAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGATTAA
ATGAATATAGATATTTCAATGGGTCTGCGCCCGAAAAATCATGCAAAAATGAGTCGGAACCCCAG
AACGCATTTTTAACAAAAAACAATAAGATACACGATTTCGACTAAAATTTTACAAGAATTAACC
Done.