Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019407.1 Corchorus olitorius cultivar O-4 contig19440, 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: 5259
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Found at i:1356 original size:330 final size:329
Alignment explanation
Indices: 19--1654 Score: 1394
Period size: 330 Copynumber: 5.0 Consensus size: 329
9 CTTTTGTGAA
* * * * **
19 ATTTGATTAGATAAATATGGGTATCTCAAGGAGTCTTAGCGCCAAAAATCATGCAAAACTG-ACT
1 ATTTGATTAGATGAATATAGATATTTCAAGGAGTCTCGGCGCCAAAAATCATGCAAAACTGAAC-
* ** * * *
83 CGGGGCCCTGGAGCGCGTTTTTAGCCAAAGA-CTGTGATGATTATTACACGATTTCGGCTAAAAC
65 CGGGGCCC-GAAATGCGTTTTTAGCCAAAAATC-GTGATGGTTATTACACGATTTCGGCTAAAAT
* *
147 TTTGCAAAAATTGACCGGAAAGATATTTCCTCAAGTTTTTGGCTAAAATACTCATAAAAAATATA
128 TTTGCAAAAATTGACCCGAAAGATATTTCCTCAA-TTTTTGGATAAAATACTCATAAAAAATATA
* * * * * * * * * *
212 TAATTCAACGCAAAAAATATTGAAGGATTTTTTATGATTCTAATATCGTTTTTCCTA-CTTTTCC
192 TAATTCAACGCCAAAAATATTGGAGGACTTTTCACGCTTTTAATATCGTTTTTCATATTTTTTCT
* * * * *
276 GAATTAATTTCTAATTAAATCGAAACAAGATTTAGATGCTTGT------AAATCCTTAAATCCAA
257 AAATTAATTTCTAAATAAATCAAAACAAGATTCAGAT-C-TGTAAAAACAAATTCTTAAATCCAA
335 TGTGGCTGAG
320 TGTGGCTGAG
* * *
345 ATTTGATTAGATGAATATAGATATTTCAAGGAGTCTAGGCGCCAAAAATCATGTAAAACTGACCC
1 ATTTGATTAGATGAATATAGATATTTCAAGGAGTCTCGGCGCCAAAAATCATGCAAAACTGAACC
** * *** *** * * *
410 GAAGCTCCGGAACAAGTTTTTAG-CAAAAA--AAAAAGGTGA-T-----ATTT---C--AATTTA
66 GGGGC-CCGAAATGCGTTTTTAGCCAAAAATCGTGATGGTTATTACACGATTTCGGCTAAAATT-
* * * * * * ** * * *
461 TTGCAAAAACTGACCCAAAATATTTTTTTCTCAATTTTTAGCCACAGTCCTCATAAAAAATATAT
129 TTGCAAAAATTGACCCGAAAGA-TATTTCCTCAATTTTTGGATAAAATACTCATAAAAAATATAT
* * * ** **
526 ACTTCAACGCCAAAAAGATTGAAGGGTTTTTTCACGCTTCGAATATCGTTTTTCATATTTTTTTC
193 AATTCAACGCCAAAAATATTGGA-GGACTTTTCACGCTTTTAATATCGTTTTTCATA-TTTTTT-
** * * * * * * * **
591 CCGAAGTAA-TTCTTAATTAAAACGAAACATGATT--GAGCTG------C---TT-GTAAAAACA
255 CTAAATTAATTTC-TAAATAAATCAAAACAAGATTCAGATCTGTAAAAACAAATTCTTAAATCCA
643 A--TGGCTCG-G
319 ATGTGGCT-GAG
* * *
652 ATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTCGGCGCAAAAAATCATTCAAAACTGAACC
1 ATTTGATTAGATGAATATAGATATTTCAAGGAGTCTCGGCGCCAAAAATCATGCAAAACTGAACC
* * * * * * *
717 -GAGCCTTGGAACGCGTTTTTAGCCAAAAATCGTGATGATTATTACATGATTTCAGCTAAAATTT
66 GGGGCC-CGAAATGCGTTTTTAGCCAAAAATCGTGATGGTTATTACACGATTTCGGCTAAAATTT
* * *
781 TGCAGAAATTGACCCGAATGATATTTCCTCAATTTTT--ATCCATAATACTCATAAAAAATATAT
130 TGCAAAAATTGACCCGAAAGATATTTCCTCAATTTTTGGAT--AAAATACTCATAAAAAATATAT
* *
844 AATTCAACGCCAGAAAA-ATTGAAGGGCTTTTCACGCTTTTAATATCGTTTTTCATATTTTTTCT
193 AATTCAACGCCA-AAAATATTGGAGGACTTTTCACGCTTTTAATATCGTTTTTCATATTTTTTCT
* * * * * * *
908 GAATAAATTTCTAATTAAATCAAAACAAGATTTAGATTCTCGTAAAAAGAAATCCTTAAATGCAA
257 AAATTAATTTCTAAATAAATCAAAACAAGATTCAGA-TCT-GTAAAAACAAATTCTTAAATCCAA
*
973 TGTGGCTAAG
320 TGTGGCTGAG
* * * *
983 ATTTTATTAGATGAATATAGATATTTCAAGGAGTGTCGGCGCCAAAAATCATGCAAAATTGATCC
1 ATTTGATTAGATGAATATAGATATTTCAAGGAGTCTCGGCGCCAAAAATCATGCAAAACTGAACC
* * *
1048 GGGGCACCGAAATGCGTTTTTAGCCAAAAATCGTGATGGTTAGTACACGCTTTTGGCTAAAATTT
66 GGGGC-CCGAAATGCGTTTTTAGCCAAAAATCGTGATGGTTATTACACGATTTCGGCTAAAATTT
* * *
1113 TGCAAAAAATGACCCGAAAAATTTTTCCTCAATTTTTGGATAAAATACTCAT-AAAAATATATAA
130 TGCAAAAATTGACCCGAAAGATATTTCCTCAATTTTTGGATAAAATACTCATAAAAAATATATAA
* *
1177 TTTAACACCAAAAATATTGGAGGACTTTTCACGCTTTTAATATCGTTTTTCATA-TTTTTCTAAA
195 TTCAACGCCAAAAATATTGGAGGACTTTTCACGCTTTTAATATCGTTTTTCATATTTTTTCTAAA
*
1241 TTAATTTCTAACTAAATCAAAACAAGATTCAGATGCTTGTAAAAACAAATTCTTAAATCCAATGT
260 TTAATTTCTAAATAAATCAAAACAAGATTCAGAT-C-TGTAAAAACAAATTCTTAAATCCAATGT
1306 GGCTGAG
323 GGCTGAG
* * * * * * *
1313 ATTTGACTAGATGAATATGGATATCTCAAGGAGTCTTGGCGCCAAAAAACATGTAAAACTGAGCC
1 ATTTGATTAGATGAATATAGATATTTCAAGGAGTCTCGGCGCCAAAAATCATGCAAAACTGAACC
* * ** * * *
1378 GGGTCCCCAGAATGTTTTTTTATCCGAAAA-CTGTGATGGTTATTACACGGTTTCGGCTAAAATT
66 GGGGCCCGA-AATGCGTTTTTAGCCAAAAATC-GTGATGGTTATTACACGATTTCGGCTAAAATT
* * *
1442 TTGTAAAAATTGATCCGAAAGATATTTCCTCAATTTTTGGCTAAAATACTCATAAAAAATATATA
129 TTGCAAAAATTGACCCGAAAGATATTTCCTCAATTTTTGGATAAAATACTCATAAAAAATATATA
** * * * * * *
1507 ATTCAACGCCAAAAATATT-GAAAAGCTTTTGAC-ATTTCTAATATCATTTTCCCTATTTTTTCC
194 ATTCAACGCCAAAAATATTGGAGGA-CTTTTCACGCTTT-TAATATCGTTTTTCATATTTTTTCT
* * * *
1570 AAATTAATTTCTAATATAAATCGAAATAAGATTCAGA---GTAAAAATAAAATCTTAAATCCAAT
257 AAATTAATTTCTAA-ATAAATCAAAACAAGATTCAGATCTGTAAAAACAAATTCTTAAATCCAAT
**
1632 GTTACTGAG
321 GTGGCTGAG
*
1641 ATTTGGTTAGATGA
1 ATTTGATTAGATGA
1655 TGTAAAGTAT
Statistics
Matches: 1072, Mismatches: 177, Indels: 120
0.78 0.13 0.09
Matches are distributed among these distances:
305 1 0.00
306 16 0.01
307 71 0.07
308 1 0.00
309 11 0.01
310 2 0.00
312 3 0.00
313 66 0.06
314 38 0.04
315 30 0.03
316 16 0.01
317 62 0.06
318 53 0.05
319 22 0.02
320 4 0.00
322 1 0.00
323 4 0.00
325 5 0.00
326 70 0.07
327 3 0.00
328 43 0.04
329 12 0.01
330 231 0.22
331 171 0.16
332 114 0.11
333 20 0.02
334 2 0.00
ACGTcount: A:0.36, C:0.16, G:0.15, T:0.33
Consensus pattern (329 bp):
ATTTGATTAGATGAATATAGATATTTCAAGGAGTCTCGGCGCCAAAAATCATGCAAAACTGAACC
GGGGCCCGAAATGCGTTTTTAGCCAAAAATCGTGATGGTTATTACACGATTTCGGCTAAAATTTT
GCAAAAATTGACCCGAAAGATATTTCCTCAATTTTTGGATAAAATACTCATAAAAAATATATAAT
TCAACGCCAAAAATATTGGAGGACTTTTCACGCTTTTAATATCGTTTTTCATATTTTTTCTAAAT
TAATTTCTAAATAAATCAAAACAAGATTCAGATCTGTAAAAACAAATTCTTAAATCCAATGTGGC
TGAG
Done.