Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007771.1 Hibiscus syriacus cultivar Beakdansim tig00110052_pilon, 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: 186237
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 2
Found at i:180314 original size:2 final size:2
Alignment explanation
Indices: 180304--180340 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
180294 TATATTACGT
180304 TA TA T- TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
180341 CCTATTTTCT
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:180558 original size:17 final size:17
Alignment explanation
Indices: 180526--180558 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
180516 TCCTTTTCCT
*
180526 TTTATTTATTTTTTTTC
1 TTTATTTATTATTTTTC
180543 TTTATTTATTATTTTT
1 TTTATTTATTATTTTT
180559 GTATATTATT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.15, C:0.03, G:0.00, T:0.82
Consensus pattern (17 bp):
TTTATTTATTATTTTTC
Found at i:184032 original size:311 final size:312
Alignment explanation
Indices: 182820--184361 Score: 2875
Period size: 310 Copynumber: 5.0 Consensus size: 312
182810 AGTCTACGTC
*
182820 CACTACCTTAGCTATCCACACTAAGGATTTTTCACAAATTCACTAATTTGTCTTTCTTTTGAGGA
1 CACTACCTTAGCTATCCACACTAAGGATTTTCCACAAATTCACTAATTTGTCTTTCTTTTGAGGA
* *
182885 CAAAGGGTAACCTTACAAACCATCAAGAATTATACCCCAAATTCTTGAGAACACTCTCTCCTAAA
66 CAAAGAGTAACCTTACAAACCATCAAGAATTATACCCCAAATTCTTGAGAACACTCTCTCCCAAA
182950 GAGAACAATACAAATTTGCAAACTTATAAGGAAATCCTCACAAGGTAGATTGTTTGCACAATTCT
131 GAGAACAATACAAATTTGCAAACTTATAAGGAAATCCTCACAAGGTAGATTGTTTGCACAATTCT
183015 AGAACAAAGAAAAGAACACTCAAGAATGAATACAATTGAGCACAATAAGTGTTCTTGAAAGCAAA
196 AGAACAAAGAAAAGAACACTCAAGAATGAATACAATTGAGCACAATAAGTGTTCTTGAAAGCAAA
183080 ATGAATATTGAATGAAAAATAGGCTTGAAATGCTCAAACTTAGGATTTTCCA
261 ATGAATATTGAATGAAAAATAGGCTTGAAATGCTCAAACTTAGGATTTTCCA
*
183132 CACTACCTTAGCTATCCACACTAAGGATTTTCCACAAATTCACTAATTTATCTTTCTTTTGAGGA
1 CACTACCTTAGCTATCCACACTAAGGATTTTCCACAAATTCACTAATTTGTCTTTCTTTTGAGGA
183197 CAAAGAGTAACCTTACAAACCATCAAGAATTATACCCC-AATTCTTGAGAACACTCTCTCCCAAA
66 CAAAGAGTAACCTTACAAACCATCAAGAATTATACCCCAAATTCTTGAGAACACTCTCTCCCAAA
*
183261 GAGAATAATACAAATTTGCAAACTTATAAGGAAATCCTCACAAGGTAGATTGTTTGCACAATTCT
131 GAGAACAATACAAATTTGCAAACTTATAAGGAAATCCTCACAAGGTAGATTGTTTGCACAATTCT
183326 AGAAC-AAGAAAAGAACACTCAAGAATGAATACAATTGAGCACAATAAGTGTTCTTGAAAGCAAA
196 AGAACAAAGAAAAGAACACTCAAGAATGAATACAATTGAGCACAATAAGTGTTCTTGAAAGCAAA
183390 ATGAATATTGAATGAAAAATAGGCTTGAAATGCTCAAACTTAGGATTTTCCA
261 ATGAATATTGAATGAAAAATAGGCTTGAAATGCTCAAACTTAGGATTTTCCA
183442 CACTACCTTAGCTATCCACACTAAGGA-TTTCCACAAATTCACTAATTTGTCTTTCTTTTGAGGA
1 CACTACCTTAGCTATCCACACTAAGGATTTTCCACAAATTCACTAATTTGTCTTTCTTTTGAGGA
183506 CAAAGAGTAACCTTACAAACCATCAAGAATTATACCCCAAATTCTTGAGAACACTCTCTCCCAAA
66 CAAAGAGTAACCTTACAAACCATCAAGAATTATACCCCAAATTCTTGAGAACACTCTCTCCCAAA
*
183571 GAGAACAATACAAATTTGTAAACTTATAAGGAAATCCTCACAAGGTAGATTGTTTGCACAATTCT
131 GAGAACAATACAAATTTGCAAACTTATAAGGAAATCCTCACAAGGTAGATTGTTTGCACAATTCT
*
183636 AGAACAAAGAAAAGAACACTCAATAATGAATACAATTGAGCACAATAAG-GTTCTTGAAAGCAAA
196 AGAACAAAGAAAAGAACACTCAAGAATGAATACAATTGAGCACAATAAGTGTTCTTGAAAGCAAA
*
183700 ATGAATATTGAATGAAAAATAGGCTTGAAATACTCAAACTTAGGATTTTCCA
261 ATGAATATTGAATGAAAAATAGGCTTGAAATGCTCAAACTTAGGATTTTCCA
* *
183752 CACTACCTTAGTTATCCACACTAAGGATTTTCCACAAATTCACTAATTTATCTTTCTTTTGAGGA
1 CACTACCTTAGCTATCCACACTAAGGATTTTCCACAAATTCACTAATTTGTCTTTCTTTTGAGGA
* *
183817 CAAAGAGTAAACTTACAAACCATCAAGAATTATACCCCAAATTCTTGAGAACACTCTTTCCCAAA
66 CAAAGAGTAACCTTACAAACCATCAAGAATTATACCCCAAATTCTTGAGAACACTCTCTCCCAAA
183882 GAG-ACAATACAAATTTGCAAACTTATAAGGAAATCCTCACAAGGTAGATTGTTTGCACAATTCT
131 GAGAACAATACAAATTTGCAAACTTATAAGGAAATCCTCACAAGGTAGATTGTTTGCACAATTCT
183946 AGAACAAAGAAAAGAACACTCAAGAATGAATACAATTGAGCACAATAAGTGTTCTTGAAAGCAAA
196 AGAACAAAGAAAAGAACACTCAAGAATGAATACAATTGAGCACAATAAGTGTTCTTGAAAGCAAA
184011 ATGAATATTGAATGAAAAATAGGCTTGAAATGCTCAAACTTAGGATTTTCCA
261 ATGAATATTGAATGAAAAATAGGCTTGAAATGCTCAAACTTAGGATTTTCCA
*
184063 CACTACCTTAGTTATCCACACTAAGGATTTTCCAC-AATTCACTAATTTGTCTTTCTTTTGAGGA
1 CACTACCTTAGCTATCCACACTAAGGATTTTCCACAAATTCACTAATTTGTCTTTCTTTTGAGGA
184127 C-AAGAGTAACCTTACAAACCATCAAGAATTATACCCCAAATTCTTGAGAAACACTCTCTCCCAA
66 CAAAGAGTAACCTTACAAACCATCAAGAATTATACCCCAAATTCTTGAG-AACACTCTCTCCCAA
* *
184191 ATAGAACAATACAAATTTGCAAACTTATAAGGAAATCCTCACATGGTAGATTGTTTGCACAATTC
130 AGAGAACAATACAAATTTGCAAACTTATAAGGAAATCCTCACAAGGTAGATTGTTTGCACAATTC
184256 TAGAACAAAG-AAAGAACACTCAAGAATGAATACAATTGAGCACAATAAGTGTTCTTGAAAGCAA
195 TAGAACAAAGAAAAGAACACTCAAGAATGAATACAATTGAGCACAATAAGTGTTCTTGAAAGCAA
*
184320 AATGAATATTGAATGAAAAATAGGATTGAAATGCTCAAACTT
260 AATGAATATTGAATGAAAAATAGGCTTGAAATGCTCAAACTT
184362 GAGGTTTGAT
Statistics
Matches: 1201, Mismatches: 23, Indels: 14
0.97 0.02 0.01
Matches are distributed among these distances:
309 120 0.10
310 573 0.48
311 408 0.34
312 100 0.08
ACGTcount: A:0.41, C:0.19, G:0.13, T:0.27
Consensus pattern (312 bp):
CACTACCTTAGCTATCCACACTAAGGATTTTCCACAAATTCACTAATTTGTCTTTCTTTTGAGGA
CAAAGAGTAACCTTACAAACCATCAAGAATTATACCCCAAATTCTTGAGAACACTCTCTCCCAAA
GAGAACAATACAAATTTGCAAACTTATAAGGAAATCCTCACAAGGTAGATTGTTTGCACAATTCT
AGAACAAAGAAAAGAACACTCAAGAATGAATACAATTGAGCACAATAAGTGTTCTTGAAAGCAAA
ATGAATATTGAATGAAAAATAGGCTTGAAATGCTCAAACTTAGGATTTTCCA
Found at i:184033 original size:621 final size:622
Alignment explanation
Indices: 182820--184361 Score: 2889
Period size: 621 Copynumber: 2.5 Consensus size: 622
182810 AGTCTACGTC
*
182820 CACTACCTTAGCTATCCACACTAAGGATTTTTCACAAATTCACTAATTTGTCTTTCTTTTGAGGA
1 CACTACCTTAGCTATCCACACTAAGGATTTTCCACAAATTCACTAATTTGTCTTTCTTTTGAGGA
* *
182885 CAAAGGGTAACCTTACAAACCATCAAGAATTATACCCCAAATTCTTGAGAACACTCTCTCCTAAA
66 CAAAGAGTAACCTTACAAACCATCAAGAATTATACCCCAAATTCTTGAGAACACTCTCTCCCAAA
182950 GAGAACAATACAAATTTGCAAACTTATAAGGAAATCCTCACAAGGTAGATTGTTTGCACAATTCT
131 GAGAACAATACAAATTTGCAAACTTATAAGGAAATCCTCACAAGGTAGATTGTTTGCACAATTCT
183015 AGAACAAAGAAAAGAACACTCAAGAATGAATACAATTGAGCACAATAAGTGTTCTTGAAAGCAAA
196 AGAACAAAGAAAAGAACACTCAAGAATGAATACAATTGAGCACAATAAGTGTTCTTGAAAGCAAA
183080 ATGAATATTGAATGAAAAATAGGCTTGAAATGCTCAAACTTAGGATTTTCCACACTACCTTAGCT
261 ATGAATATTGAATGAAAAATAGGCTTGAAATGCTCAAACTTAGGATTTTCCACACTACCTTAGCT
*
183145 ATCCACACTAAGGATTTTCCACAAATTCACTAATTTATCTTTCTTTTGAGGACAAAGAGTAACCT
326 ATCCACACTAAGGATTTTCCACAAATTCACTAATTTATCTTTCTTTTGAGGACAAAGAGTAAACT
*
183210 TACAAACCATCAAGAATTATACCCCAATTCTTGAGAACACTCTCTCCCAAAGAGAATAATACAAA
391 TACAAACCATCAAGAATTATACCCCAATTCTTGAGAACACTCTCTCCCAAAGAGAACAATACAAA
183275 TTTGCAAACTTATAAGGAAATCCTCACAAGGTAGATTGTTTGCACAATTCTAGAACAAGAAAAGA
456 TTTGCAAACTTATAAGGAAATCCTCACAAGGTAGATTGTTTGCACAATTCTAGAACAAGAAAAGA
183340 ACACTCAAGAATGAATACAATTGAGCACAATAAGTGTTCTTGAAAGCAAAATGAATATTGAATGA
521 ACACTCAAGAATGAATACAATTGAGCACAATAAGTGTTCTTGAAAGCAAAATGAATATTGAATGA
183405 AAAATAGGCTTGAAATGCTCAAACTTAGGATTTTCCA
586 AAAATAGGCTTGAAATGCTCAAACTTAGGATTTTCCA
183442 CACTACCTTAGCTATCCACACTAAGGA-TTTCCACAAATTCACTAATTTGTCTTTCTTTTGAGGA
1 CACTACCTTAGCTATCCACACTAAGGATTTTCCACAAATTCACTAATTTGTCTTTCTTTTGAGGA
183506 CAAAGAGTAACCTTACAAACCATCAAGAATTATACCCCAAATTCTTGAGAACACTCTCTCCCAAA
66 CAAAGAGTAACCTTACAAACCATCAAGAATTATACCCCAAATTCTTGAGAACACTCTCTCCCAAA
*
183571 GAGAACAATACAAATTTGTAAACTTATAAGGAAATCCTCACAAGGTAGATTGTTTGCACAATTCT
131 GAGAACAATACAAATTTGCAAACTTATAAGGAAATCCTCACAAGGTAGATTGTTTGCACAATTCT
*
183636 AGAACAAAGAAAAGAACACTCAATAATGAATACAATTGAGCACAATAAG-GTTCTTGAAAGCAAA
196 AGAACAAAGAAAAGAACACTCAAGAATGAATACAATTGAGCACAATAAGTGTTCTTGAAAGCAAA
* *
183700 ATGAATATTGAATGAAAAATAGGCTTGAAATACTCAAACTTAGGATTTTCCACACTACCTTAGTT
261 ATGAATATTGAATGAAAAATAGGCTTGAAATGCTCAAACTTAGGATTTTCCACACTACCTTAGCT
183765 ATCCACACTAAGGATTTTCCACAAATTCACTAATTTATCTTTCTTTTGAGGACAAAGAGTAAACT
326 ATCCACACTAAGGATTTTCCACAAATTCACTAATTTATCTTTCTTTTGAGGACAAAGAGTAAACT
*
183830 TACAAACCATCAAGAATTATACCCCAAATTCTTGAGAACACTCTTTCCCAAAGAG-ACAATACAA
391 TACAAACCATCAAGAATTATACCCC-AATTCTTGAGAACACTCTCTCCCAAAGAGAACAATACAA
183894 ATTTGCAAACTTATAAGGAAATCCTCACAAGGTAGATTGTTTGCACAATTCTAGAACAAAGAAAA
455 ATTTGCAAACTTATAAGGAAATCCTCACAAGGTAGATTGTTTGCACAATTCTAGAAC-AAGAAAA
183959 GAACACTCAAGAATGAATACAATTGAGCACAATAAGTGTTCTTGAAAGCAAAATGAATATTGAAT
519 GAACACTCAAGAATGAATACAATTGAGCACAATAAGTGTTCTTGAAAGCAAAATGAATATTGAAT
184024 GAAAAATAGGCTTGAAATGCTCAAACTTAGGATTTTCCA
584 GAAAAATAGGCTTGAAATGCTCAAACTTAGGATTTTCCA
*
184063 CACTACCTTAGTTATCCACACTAAGGATTTTCCAC-AATTCACTAATTTGTCTTTCTTTTGAGGA
1 CACTACCTTAGCTATCCACACTAAGGATTTTCCACAAATTCACTAATTTGTCTTTCTTTTGAGGA
184127 C-AAGAGTAACCTTACAAACCATCAAGAATTATACCCCAAATTCTTGAGAAACACTCTCTCCCAA
66 CAAAGAGTAACCTTACAAACCATCAAGAATTATACCCCAAATTCTTGAG-AACACTCTCTCCCAA
* *
184191 ATAGAACAATACAAATTTGCAAACTTATAAGGAAATCCTCACATGGTAGATTGTTTGCACAATTC
130 AGAGAACAATACAAATTTGCAAACTTATAAGGAAATCCTCACAAGGTAGATTGTTTGCACAATTC
184256 TAGAACAAAG-AAAGAACACTCAAGAATGAATACAATTGAGCACAATAAGTGTTCTTGAAAGCAA
195 TAGAACAAAGAAAAGAACACTCAAGAATGAATACAATTGAGCACAATAAGTGTTCTTGAAAGCAA
*
184320 AATGAATATTGAATGAAAAATAGGATTGAAATGCTCAAACTT
260 AATGAATATTGAATGAAAAATAGGCTTGAAATGCTCAAACTT
184362 GAGGTTTGAT
Statistics
Matches: 898, Mismatches: 17, Indels: 11
0.97 0.02 0.01
Matches are distributed among these distances:
620 317 0.35
621 547 0.61
622 34 0.04
ACGTcount: A:0.41, C:0.19, G:0.13, T:0.27
Consensus pattern (622 bp):
CACTACCTTAGCTATCCACACTAAGGATTTTCCACAAATTCACTAATTTGTCTTTCTTTTGAGGA
CAAAGAGTAACCTTACAAACCATCAAGAATTATACCCCAAATTCTTGAGAACACTCTCTCCCAAA
GAGAACAATACAAATTTGCAAACTTATAAGGAAATCCTCACAAGGTAGATTGTTTGCACAATTCT
AGAACAAAGAAAAGAACACTCAAGAATGAATACAATTGAGCACAATAAGTGTTCTTGAAAGCAAA
ATGAATATTGAATGAAAAATAGGCTTGAAATGCTCAAACTTAGGATTTTCCACACTACCTTAGCT
ATCCACACTAAGGATTTTCCACAAATTCACTAATTTATCTTTCTTTTGAGGACAAAGAGTAAACT
TACAAACCATCAAGAATTATACCCCAATTCTTGAGAACACTCTCTCCCAAAGAGAACAATACAAA
TTTGCAAACTTATAAGGAAATCCTCACAAGGTAGATTGTTTGCACAATTCTAGAACAAGAAAAGA
ACACTCAAGAATGAATACAATTGAGCACAATAAGTGTTCTTGAAAGCAAAATGAATATTGAATGA
AAAATAGGCTTGAAATGCTCAAACTTAGGATTTTCCA
Found at i:184640 original size:19 final size:19
Alignment explanation
Indices: 184616--184652 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
184606 CCGTTACACA
184616 GGGGGGAATCGGTACCCTT
1 GGGGGGAATCGGTACCCTT
*
184635 GGGGGGAATCGGTTCCCT
1 GGGGGGAATCGGTACCCT
184653 CCGAGCATAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.14, C:0.22, G:0.43, T:0.22
Consensus pattern (19 bp):
GGGGGGAATCGGTACCCTT
Done.