Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017569.1 Corchorus olitorius cultivar O-4 contig17602, 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: 4090
ACGTcount: A:0.33, C:0.16, G:0.15, T:0.36
Found at i:2894 original size:334 final size:330
Alignment explanation
Indices: 1--3368 Score: 3468
Period size: 332 Copynumber: 10.2 Consensus size: 330
* ** * *
1 GTAGG-AAAATGATATTAGAAGACGTAAAAAAATCTTCAATATTTTTGGCGTTGAATTAAATATA
1 GTAGGAAAAACGATATTAGAAG-CGTAAAAAACCCTTCAATA-TTTTGGAGTTGAATTATATATA
*
65 TCTCTATGAGTATTTCAGACTAAAAA-TGAAGGAAATATCGTTTCGGGTCTAATTTTTGACTAAA
64 TCTATATGAGTATTT-AG-CTAAAAATTG-AGGAAATAT--TTTCGGGTC-AATTTTTG-C-AAA
*
129 ATTTTAGCCGAAATCGTGTACTAACCATCACCGATTTTTTTGCTAAAAACGCATTTCGGGGCCCC
121 ATTTTAGCCGAAATCGTGTACTAACCATCA-CGA-TTTTTTGCTAAAAACGCGTTTCGGGGCCCC
*
194 GACTCAGTTTTGCATGATTTTCGGCATCGAGACTCCTTCAAATATCTATATTCATCTAATCAAAT
184 GACTCAGTTCTGCATGATTTTCGGCATCGAGACTCCTTCAAATATCTATATTCATCTAATCAAAT
* * * *
259 CTCAGCCACATTGCTTTTAAGAATTTTTTTTTACGAGCGTCTATATCTTATTTCAACTTTATTAG
249 CTCAGCCACATTGCATTTAAGAATTTGTTTTTACGAGCATCTATATCTTATTTCAACTTAATTAG
324 AAATTAATTCGGAAAAA
314 AAATTAATTCGGAAAAA
* *
341 GTAGGAAAAACGATATTAGAAGCGTAAAAAACCCTTAAATATTTCTGGCGTTGAATTATATATAT
1 GTAGGAAAAACGATATTAGAAGCGTAAAAAACCCTTCAATATTT-TGGAGTTGAATTATATATAT
* * *
406 CTCTATGAGTATTTCAGCTAAAAATTGAGTAAATATTTTTCGGGTCAATTTTTGCAAGATTTTAG
65 CTATATGAGTATTT-AGCTAAAAATTGAGGAAATA-TTTTCGGGTCAATTTTTGCAAAATTTTAG
* ***
471 CCGAAATCGTGTACGGTGTACTAACCATCACGATTTTTTGCTAAAAACACGTTTCGGGGCATTGA
128 CCGAAA-----T-C-GTGTACTAACCATCACGATTTTTTGCTAAAAACGCGTTTCGGGGCCCCGA
* * * ** * * *
536 CTCAGTTTTGCATGATTTTCGGCTTCAAGACTATTTCAAGTATCTATATTCATCTAGTCAAATTT
186 CTCAGTTCTGCATGATTTTCGGCATCGAGACTCCTTCAAATATCTATATTCATCTAATCAAATCT
* * ** * * * *
601 CAGCAAAATTGCATTTAAGTTTTTGTTTGTACGAGCATCTGA-ATCTTGTTTCGATTTAATTAGA
251 CAGCCACATTGCATTTAAGAATTTGTTTTTACGAGCATCT-ATATCTTATTTCAACTTAATTAGA
* *
665 AATTAATGCCGAAAAA
315 AATTAATTCGGAAAAA
* * * * ** * *
681 TTAATGAAAAACGATATGAAAATAGT-GAAAACTCCTCCAATCATTTTGGAG-TGAAATTATATA
1 GT-AGGAAAAACGATATTAGAAGCGTAAAAAAC-CCTTCAAT-ATTTTGGAGTTG-AATTATATA
* * * * * * * *
744 TAT-TACACGAGTATATTAGGC-GAAAATTGAGGAAAATTTTTTCGGATCATTTTTTACAGAATT
62 TATCTATATGAGTAT-TTA-GCTAAAAATTGAGG-AAATATTTTCGGGTCAATTTTTGCAAAATT
* * * * * *
807 TTAGCCGAAATCGTGTACTAACTATCACAATTTTTTACT-AAACCGCGTTTCGAGGCCCCGACAC
124 TTAGCCGAAATCGTGTACTAACCATCACGATTTTTTGCTAAAAACGCGTTTCGGGGCCCCGACTC
* *
871 AGTTCTGCTTGATTTTCGGCATCGAGACTCCTTCAAATATCTATATTTATCTAATCAAATCTCAG
189 AGTTCTGCATGATTTTCGGCATCGAGACTCCTTCAAATATCTATATTCATCTAATCAAATCTCAG
* * *
936 CCGCATTGCATTTAAGAATTTGTTTTTACGAGCGTCTATATCTTATTTCAACTTTATTAGAAATT
254 CCACATTGCATTTAAGAATTTGTTTTTACGAGCATCTATATCTTATTTCAACTTAATTAGAAATT
1001 AATTCGGAAAAA
319 AATTCGGAAAAA
*
1013 GTAGGAAAAACGATATTAGAAGCGTAAAAAACCCTTCAATATTTCTGGCGTTGAATTATATATAT
1 GTAGGAAAAACGATATTAGAAGCGTAAAAAACCCTTCAATATTT-TGGAGTTGAATTATATATAT
* *
1078 CTATATGAGTATTTCAGCTAAAAATTGAGGAAATATCATTCGGGTCAATTTTTGCAAAATTTTCG
65 CTATATGAGTATTT-AGCTAAAAATTGAGGAAATAT-TTTCGGGTCAATTTTTGCAAAATTTTAG
* * * * *
1143 CCAAAATCGTGTACTAACCATCACGATTTTTT-CTAAAAACGTGTTCCGGGGACCCGGCTCAGTT
128 CCGAAATCGTGTACTAACCATCACGATTTTTTGCTAAAAACGCGTTTCGGGGCCCCGACTCAGTT
* * *
1207 CTGCATGATTTTCGGCGTCGAGACTCCTTCAAATATCTATATTTATCTAATCAAATCTTAGCCAC
193 CTGCATGATTTTCGGCATCGAGACTCCTTCAAATATCTATATTCATCTAATCAAATCTCAGCCAC
*
1272 ATTGCATTTAAGAATTTGTTTTTACGAGCATCTATATCTTATTTCAACTAAATTAGAAATTAATT
258 ATTGCATTTAAGAATTTGTTTTTACGAGCATCTATATCTTATTTCAACTTAATTAGAAATTAATT
1337 CGGAAAAA
323 CGGAAAAA
* * * * *
1345 GTAGGAAAAACGATATTAGACGCGTAAAAATCCCTTCAATATTTTAAGAATCGAATTATATATAT
1 GTAGGAAAAACGATATTAGAAGCGTAAAAAACCCTTCAATATTTT-GGAGTTGAATTATATATAT
* * * *
1410 CTCTATAAGTATTTTAGCTAAAATTTGAGGAAATATCTTTAGGGTCAATTTTTGCAAAATTTTAG
65 CTATATGAGTA-TTTAGCTAAAAATTGAGGAAATAT-TTTCGGGTCAATTTTTGCAAAATTTTAG
* * * *
1475 CCGAAATTGTGTACGATGTACAAGCCATCACGATTTTTT-CTAAAAACGTGTTCCGGGGCCCCGG
128 CCGAAATCGTGTAC----T--AA-CCATCACGATTTTTTGCTAAAAACGCGTTTCGGGGCCCCGA
* *
1539 CTCAGTTCTGCATGATTTTCGGCGTCGAGACTCCTTCAAATATCTATATTTATCTAATCAAATCT
186 CTCAGTTCTGCATGATTTTCGGCATCGAGACTCCTTCAAATATCTATATTCATCTAATCAAATCT
* *
1604 CAGCCACAATGCATTTAAGAATTTGTTTTTACGAG---C-GT-TC-----T--A---AATTAGAA
251 CAGCCACATTGCATTTAAGAATTTGTTTTTACGAGCATCTATATCTTATTTCAACTTAATTAGAA
*
1654 ATTAATTCGAAAAAA
316 ATTAATTCGGAAAAA
* * * *
1669 GTAGGGAAAACGGTATGAGAAGCGTAAAAAACCCTTCAATATTTTTGGCA-TCGAATTATATATA
1 GTAGGAAAAACGATATTAGAAGCGTAAAAAACCCTTCAATA-TTTTGG-AGTTGAATTATATATA
* * *
1733 TCTCTATAAGTATTTTAGCTAAAATTTGAGGAAATATCTTTCGGGTCAATTTTTGCAAAATTTTA
64 TCTATATGAGTA-TTTAGCTAAAAATTGAGGAAATAT-TTTCGGGTCAATTTTTGCAAAATTTTA
* * * *
1798 GCCGAAATCGTGTACTATCCATCACGATTTTTTTACTAAAAACGCGTTTCGAGGCCCCGGCTCAG
127 GCCGAAATCGTGTACTAACCATCACGA-TTTTTTGCTAAAAACGCGTTTCGGGGCCCCGACTCAG
* *
1863 TTCTGCATGATTTTCGGCGTCAAGACTCCTTCAAATATCTATATTCATCTAATCAAATCTCAGCC
191 TTCTGCATGATTTTCGGCATCGAGACTCCTTCAAATATCTATATTCATCTAATCAAATCTCAGCC
* *
1928 ACATTGCATTTAAGAATTTGTTTTTACGAGCGTCTATATCTTATTTCAACTTTATTAGAAATTAA
256 ACATTGCATTTAAGAATTTGTTTTTACGAGCATCTATATCTTATTTCAACTTAATTAGAAATTAA
*
1993 TTCGGAGAAA
321 TTCGGAAAAA
* * *
2003 GTAGGAAAAACGATATTAGAAGCATAAAAAACCCTTCAATATTTCTGGCGTTGAATTATATATAA
1 GTAGGAAAAACGATATTAGAAGCGTAAAAAACCCTTCAATATTT-TGGAGTTGAATTATATATAT
* *
2068 CTCTATGAGTATTTCAGCTAAAAAATTGAGGAAATATCTTTCGTGTCAATTTTTGCAAAAATTTT
65 CTATATGAGTATTT-AGCT-AAAAATTGAGGAAATAT-TTTCGGGTCAATTTTTGC-AAAATTTT
* * * *
2133 AGCCGTAATCGTGTACTAACCATCACGATTTTTTGCTAAAAACGCGTTTCGAGGCACTGACTCAG
126 AGCCGAAATCGTGTACTAACCATCACGATTTTTTGCTAAAAACGCGTTTCGGGGCCCCGACTCAG
* * *
2198 TTCTGCATGATTTTCGGCTTCGAGA---C-T---ATTTC-A-AGT-ATCT-AT----T-TCAGCC
191 TTCTGCATGATTTTCGGCATCGAGACTCCTTCAAATATCTATATTCATCTAATCAAATCTCAGCC
* * ** * * *
2247 AAATTCCATTTAA-TTTTTGTTTTTACGAGCATCTGAT-TCTTGTTTCGATTTAATTAGAAATTA
256 ACATTGCATTTAAGAATTTGTTTTTACGAGCATCT-ATATCTTATTTCAACTTAATTAGAAATTA
* *
2310 ATACCGAAAAA
320 ATTCGGAAAAA
* * * * * ** *
2321 TTAATGAAAAACGATATGA-AACGAGTGAAAAGTCCTCCAATCATTTTGGAG-TGAAATTATATA
1 GT-AGGAAAAACGATATTAGAA-GCGTAAAAAACCCTTCAAT-ATTTTGGAGTTG-AATTATATA
*** * * * * *
2384 TAT-TACCCGAGTATATTAGGC-GAAAATAGAGGAAA-ATTTTTCGGATCATTTTTTGCAGAATT
62 TATCTATATGAGTAT-TTA-GCTAAAAATTGAGGAAATA-TTTTCGGGTCAATTTTTGCAAAATT
* * * *
2446 TTAGCCGAAATCAG-GTACTAACCTTCATGATTTTTTTGCTAAAAACTCGTTACGGGGCCCCGAC
124 TTAGCCGAAATC-GTGTACTAACCATCACGA-TTTTTTGCTAAAAACGCGTTTCGGGGCCCCGAC
*
2510 TCAGTTCTGCATGATTTTCGGCATCGAGACTCCTTCAAATATCTATATTCATCTAATCAAATTTC
187 TCAGTTCTGCATGATTTTCGGCATCGAGACTCCTTCAAATATCTATATTCATCTAATCAAATCTC
* * * * * * * *
2575 AGCCGA-ATTGCATTTAAGGATTTGTTTTTAAGAGCTTCTGA-ATCATGTTTCGAGTTAATTATA
252 AGCC-ACATTGCATTTAAGAATTTGTTTTTACGAGCATCT-ATATCTTATTTCAACTTAATTAGA
2638 AATTAATTCGGAAAAA
315 AATTAATTCGGAAAAA
* * ** * * * *** * *
2654 TTAATGAAAAATAATATCAAAAGCGTGAAATGTCCTCCAATCATTTTGGAGTTAAATTATATATA
1 GT-AGGAAAAACGATATTAGAAGCGTAAAAAACCCTTCAAT-ATTTTGGAGTTGAATTATATATA
* * *
2719 T-TAT-TGAGTATATTAGGC-AAAAATTGAGGAGAA-ATTTCTCGGATCATTTTTTTGCAGAATT
64 TCTATATGAGTAT-TTA-GCTAAAAATTGAGGA-AATATTT-TCGGGTCA-ATTTTTGCAAAATT
* * * * *
2780 TTAGTCGAAATTGCGTACTAACCATCAAGATTTTTTTGCTAAAAACGCGTTTAGGGGCCCCGACT
124 TTAGCCGAAATCGTGTACTAACCATCACGA-TTTTTTGCTAAAAACGCGTTTCGGGGCCCCGACT
* * *
2845 CAGTTCTGCATGATTTTCGGCATCGAGACTCCTTGAAATATCCATATTCATTTAATCAAATCTCA
188 CAGTTCTGCATGATTTTCGGCATCGAGACTCCTTCAAATATCTATATTCATCTAATCAAATCTCA
*
2910 GCCACATTGCATTGAAGAATTTGTTTTTACGAGCATCTATATCTTATTTCAACTTAATTAGAAAT
253 GCCACATTGCATTTAAGAATTTGTTTTTACGAGCATCTATATCTTATTTCAACTTAATTAGAAAT
* *
2975 TAATTTGGAAAAT
318 TAATTCGGAAAAA
* ** *
2988 GTAGGAAAAACGATATTAGAAGCGTAAAAAACCCGTCAATATTTTTTACGATGAATTATATATAT
1 GTAGGAAAAACGATATTAGAAGCGTAAAAAACCCTTCAATATTTTGGA-GTTGAA-T-TATATAT
* *
3053 ATCTCTATGAGTATTTTAACTAAAAATTGAGGAAATATCTTTCGGGTCAATTTTTGCAAAATTTT
63 ATCTATATGAGTA-TTTAGCTAAAAATTGAGGAAATAT-TTTCGGGTCAATTTTTGCAAAATTTT
* *
3118 A---G----C-----CT-----TCACGATTTTTTGCTAAAAACGTGTTCCGGGGCCCC-AGCTCA
126 AGCCGAAATCGTGTACTAACCATCACGATTTTTTGCTAAAAACGCGTTTCGGGGCCCCGA-CTCA
* ** * * * *
3165 GTTTTGCATGATTTTCGGTGTCAAAACTCCTTCAAATATCTATATTCATCGAATCAAATCTCATC
190 GTTCTGCATGATTTTCGGCATCGAGACTCCTTCAAATATCTATATTCATCTAATCAAATCTCAGC
* * * * * * *
3230 CACACTGCATTTAAGGATTTGTTTTTACGACCATCTGA-ATATTGTTTCGATTTAATTAGAAATT
255 CACATTGCATTTAAGAATTTGTTTTTACGAGCATCT-ATATCTTATTTCAACTTAATTAGAAATT
* ***
3294 ATTTTAAAAAATA
319 AATTCGGAAAA-A
* * * * * * *
3307 ATTGGAAAAATGATATTAAAAGCGTGAAAATA-CCATCAATATTTTTGATGTTGAATTATATA
1 GTAGGAAAAACGATATTAGAAGCGT-AAAAAACCCTTCAATATTTTGGA-GTTGAATTATATA
3369 GATTTTTTAT
Statistics
Matches: 2593, Mismatches: 324, Indels: 245
0.82 0.10 0.08
Matches are distributed among these distances:
315 30 0.01
316 73 0.03
317 29 0.01
318 217 0.08
319 231 0.09
320 12 0.00
322 1 0.00
323 5 0.00
324 158 0.06
325 11 0.00
326 6 0.00
327 4 0.00
328 4 0.00
329 2 0.00
330 4 0.00
331 57 0.02
332 540 0.21
333 188 0.07
334 289 0.11
335 116 0.04
336 57 0.02
337 38 0.01
338 14 0.01
339 154 0.06
340 266 0.10
341 68 0.03
342 19 0.01
ACGTcount: A:0.33, C:0.16, G:0.15, T:0.35
Consensus pattern (330 bp):
GTAGGAAAAACGATATTAGAAGCGTAAAAAACCCTTCAATATTTTGGAGTTGAATTATATATATC
TATATGAGTATTTAGCTAAAAATTGAGGAAATATTTTCGGGTCAATTTTTGCAAAATTTTAGCCG
AAATCGTGTACTAACCATCACGATTTTTTGCTAAAAACGCGTTTCGGGGCCCCGACTCAGTTCTG
CATGATTTTCGGCATCGAGACTCCTTCAAATATCTATATTCATCTAATCAAATCTCAGCCACATT
GCATTTAAGAATTTGTTTTTACGAGCATCTATATCTTATTTCAACTTAATTAGAAATTAATTCGG
AAAAA
Done.