Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016173.1 Corchorus olitorius cultivar O-4 contig16206, 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: 6890
ACGTcount: A:0.33, C:0.19, G:0.16, T:0.32
Found at i:1777 original size:331 final size:330
Alignment explanation
Indices: 459--1834 Score: 1318
Period size: 333 Copynumber: 4.2 Consensus size: 330
449 TTGAGATTCA
* * * * * **
459 GTTAGCTGAATATAGATATTTCAAAGAGTCTTGACGTCAAAAATCATGCAAAACTAAATC-GGGC
1 GTTAGATGAATATAGATATTTCAAAGAGTCTTGGCGCCAAAAATTATGCAAAACTGAGCCGGGGC
* * * * * * * * *
523 TCCCAAAACACTTTTTTAGCTATAAACTA-TGATGGGCATTTCACGATTT-GACTAAAATTTTAC
66 -CCCGAAACGCGTTTTTAGCCAAAAAC-AGTGATGGGTAATTCACGATTTCGGCTAAAATTTTGC
** * * *
586 AAAAATTGAA-CGAAA-AGTTTTTCCCTCAAAATTTAGCCACAATAATCGTAAAAAAATATAA-T
129 AAAAATTGAACCGAAAGA-TTTTT-CCTCAATTTTTAGCTACAATACTCATAAAAAAATATAATT
* ** * * *
648 TAACGTTAAAAAGATTGAAATACTTTTCAAGCTTCTAATATTGTTTTTTCTATTTTTTTTTGAAT
192 TAACGTCAAAAAGATTGAAGGA-TTTTCACGCTTCTAATATCGTTTTTTCTA-TTTTTTTCGAAT
713 TAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTG
255 TAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTG
*
778 TCTGAAATTTG
320 GCTGAAATTTG
* * * * * * * *
789 ATTAGATTAATAAAAAAATTTGAAAGAGTCTT-G-GCCAAAAATCATGCAAAATTGAGCCGGGGC
1 GTTAGATGAATATAGATATTTCAAAGAGTCTTGGCGCCAAAAATTATGCAAAACTGAGCCGGGGC
* * *
852 TCCGGAACGCGTTTTTAGCCAAAAATC-GTGAT-GGTTATTACACGATTTCGGC-ATAAATTTTG
66 CCCGAAACGCGTTTTTAGCCAAAAA-CAGTGATGGGTAATT-CACGATTTCGGCTA-AAATTTTG
* * *
914 CAAAAATTGACCCGAAAGATTTTTCCTCAATTTTTAGCAACAATATTACTCTTAAAAAATATATA
128 CAAAAATTGAACCGAAAGATTTTTCCTCAATTTTTAGCTAC-A-A-TACTCATAAAAAA-ATATA
* * *
979 ATTTAACGCCAAAAAGATTGAA--A-----A--CTTCTAATATCGTTTATTCTATTTGTTT-GAA
189 ATTTAACGTCAAAAAGATTGAAGGATTTTCACGCTTCTAATATCGTTTTTTCTATTTTTTTCGAA
** * *
1034 TTAATTTCTTGTTAAATCGAAACATA-ATTCAGATGCTCGTAAAAA-AGATCCTTAAATTCAATG
254 TTAATTTCTAATTAAATCGAAACA-AGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATG
* *
1097 TGGCTGATATTTA
318 TGGCTGAAATTTG
* * * * *
1110 GTAAGATGAATATAGATATTTC-AAGCTGTCATGGAGCCAAAAATCATAAATCATGCAAAATTG-
1 GTTAGATGAATATAGATATTTCAAAG-AGTCTTGGCGCC-AAAA--AT---T-ATGCAAAACTGA
* * * * * * * * *
1173 GTCCGAGGCCCCGAAACGCGTTTTTAGCCAAAAACCGCGATAGTTAGTACACGATCTCTGCTAAA
58 G-CCGGGGCCCCGAAACGCGTTTTTAGCCAAAAACAGTGATGGGTAATTCACGATTTCGGCTAAA
* * * * * *
1238 ATTTTGC-AAATTTGACCCGAAAGATTTTT-GTACAATTTTTAG-TCACAACACTTATAAAAATA
122 ATTTTGCAAAAATTGAACCGAAAGATTTTTCCT-CAATTTTTAGCT-ACAATACTCATAAAAAAA
* * * * * *
1300 TATAATTCAACGACAAAAAGATTGAAGGGATTTTCACACTTCTAATATCGTTTTGTTTTGTTTTG
185 TATAATTTAACGTCAAAAAGATTGAA-GGATTTTCACGCTTCTAATATCGTTTT-TTCTATTTTT
* * *
1365 TTCTGAATTAATCTTTTAATTAAATCCAAACAAGATTTAGATGCTCGTAAAAACAAATCCTTAAA
248 TTC-GAATTAAT-TTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAA
1430 TCCAATGTGGCTGAAATTTG
311 TCCAATGTGGCTGAAATTTG
* *
1450 GTTAGATGAATATAGATATTTCAAGGAGTCTTGGCGTCAAAAATTATGCAAAACTGAGCCGGGGC
1 GTTAGATGAATATAGATATTTCAAAGAGTCTTGGCGCCAAAAATTATGCAAAACTGAGCCGGGGC
* * * ** * *
1515 ACCGAAACGTGTTCTTAGCTTAAAACAGTGATGGGTAATTCACGATTTCGGCTAAAATTTTGTAG
66 CCCGAAACGCGTTTTTAGCCAAAAACAGTGATGGGTAATTCACGATTTCGGCTAAAATTTTGCAA
* * *
1580 AAATTAAACTGAATG-TTTTTCCCTCAA-TTTTAGCTACAATACTCATAAAAAAATATAATTTAA
131 AAATTGAACCGAAAGATTTTT-CCTCAATTTTTAGCTACAATACTCATAAAAAAATATAATTTAA
** * * *
1643 TTTCAAAAATATTGAAGGACTTTTCACGCTTATAATATAGTTTTTTCTATTTTTATTCGAATTAA
195 CGTCAAAAAGATTGAAGGA-TTTTCACGCTTCTAATATCGTTTTTTCTATTTTT-TTCGAATTAA
* * *
1708 ATTCTAATTAAATCGAAACAAGATTCAGATGCTCTTAAAAACAAATCCTTAAATCCAATGTGTCT
258 TTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCT
1773 GAAATTTG
323 GAAATTTG
* * * *
1781 GTTAGATTAATATAGATATTTCATATAGTCTTGGTGCCAAAAATTATGCAAAAC
1 GTTAGATGAATATAGATATTTCAAAGAGTCTTGGCGCCAAAAATTATGCAAAAC
1835 AAAGTTAGGG
Statistics
Matches: 851, Mismatches: 141, Indels: 107
0.77 0.13 0.10
Matches are distributed among these distances:
320 3 0.00
321 45 0.05
322 45 0.05
323 10 0.01
324 23 0.03
325 25 0.03
326 12 0.01
327 5 0.01
328 54 0.06
329 73 0.09
330 99 0.12
331 121 0.14
332 29 0.03
333 143 0.17
334 34 0.04
335 16 0.02
336 8 0.01
337 2 0.00
338 9 0.01
339 37 0.04
340 56 0.07
341 2 0.00
ACGTcount: A:0.37, C:0.15, G:0.14, T:0.34
Consensus pattern (330 bp):
GTTAGATGAATATAGATATTTCAAAGAGTCTTGGCGCCAAAAATTATGCAAAACTGAGCCGGGGC
CCCGAAACGCGTTTTTAGCCAAAAACAGTGATGGGTAATTCACGATTTCGGCTAAAATTTTGCAA
AAATTGAACCGAAAGATTTTTCCTCAATTTTTAGCTACAATACTCATAAAAAAATATAATTTAAC
GTCAAAAAGATTGAAGGATTTTCACGCTTCTAATATCGTTTTTTCTATTTTTTTCGAATTAATTT
CTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAA
ATTTG
Done.