Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018400956.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_4117.0, 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, 651
Length: 1085
ACGTcount: A:0.36, C:0.11, G:0.14, T:0.35
Warning! 40 characters in sequence are not A, C, G, or T
Found at i:800 original size:340 final size:332
Alignment explanation
Indices: 373--995 Score: 695
Period size: 340 Copynumber: 1.9 Consensus size: 332
363 AGCGAGTAAT
* * * * *
373 AAGGCTTTTGAAGGAATTGGTAACTATAAATGGACTTTTTTTGCCAATGAATGCATTTTTCTTCA
1 AAGGCTCTTGAAGGAATGGGTAACTATAAATCGACTTTTCTTGCCAATGAATGCATTTTTCTACA
* *
438 TGTTTCTTGAAGTAGACATTTAATTATAATTTGTTTTAACAAAAAACGTAAAGAAATT-AGACTT
66 TGTTTCTTGAAGTAGACATTTAATTATAATTTATTTTAACAAAAAACATAAAGAAATTCA-ACTT
* ********** *
502 AAAATTAATTTTGAGATTATAAAACCATNNNNNNNNNNTAATAA-AGCTTTTGAAGGAATGGATG
130 AAAATTAATTATGAGATTATAAAACCATTTAAACCGAATAATAAGA-CTTTTGAAAGAATGGATG
* * * *
566 ACTAT-AGTGGACTTTTCTTGCCAATGAAAGAGTTTTT-TTCATGTTTCTTGAGATAGACATTCA
194 ACTATAAATGGACCTTTCTTGCCAATGAAAGACTTTTTCGTCATGTTTCTTGAGATAGACATTCA
* *
629 ATTATTGTCTGTTTTAACCAAAAATATNNNNNNNNNNAACTTCAAATCAGTTATGAGATTATAAA
259 ATTATAGTCTATTTTAACCAAAAATAT----------AACTTCAAATCAGTTATGAGATTATAAA
694 ACTATTTAAAGCAAATAAC
314 ACTATTTAAAGCAAATAAC
* * *
713 AAGGCTCTTGAAGGAATGGGTGAGTATAAATCGACTTTTCTT-CTTAATGAATGGC-TTTTTCTA
1 AAGGCTCTTGAAGGAATGGGTAACTATAAATCGACTTTTCTTGC-CAATGAAT-GCATTTTTCTA
* * * * *
776 CATGTTT-TCT-AAGGTAGGCATTTAATTATAGTTTATTTTAATAAAAAATATAAATAAATTCAA
64 CATGTTTCT-TGAA-GTAGACATTTAATTATAATTTATTTTAACAAAAAACATAAAGAAATTCAA
* *
839 CTTAAAATTAATTATGAGATTGTAAAACCATTTAAACCGAATAATAAGACTTTTGAAAGAATGGG
127 CTTAAAATTAATTATGAGATTATAAAACCATTTAAACCGAATAATAAGACTTTTGAAAGAATGGA
* * *
904 TGACTATAAATGGACCTTTCTTGCCAATGAATGTCTTTTTCGTCATGTTTCTTGAGATAGATATT
192 TGACTATAAATGGACCTTTCTTGCCAATGAAAGACTTTTTCGTCATGTTTCTTGAGATAGACATT
*
969 CAATTATAGTCTATTTTAACTAAAAAT
257 CAATTATAGTCTATTTTAACCAAAAAT
996 GTAAAAAAAA
Statistics
Matches: 236, Mismatches: 39, Indels: 14
0.82 0.13 0.05
Matches are distributed among these distances:
339 4 0.02
340 155 0.66
341 31 0.13
342 46 0.19
ACGTcount: A:0.35, C:0.10, G:0.14, T:0.37
Consensus pattern (332 bp):
AAGGCTCTTGAAGGAATGGGTAACTATAAATCGACTTTTCTTGCCAATGAATGCATTTTTCTACA
TGTTTCTTGAAGTAGACATTTAATTATAATTTATTTTAACAAAAAACATAAAGAAATTCAACTTA
AAATTAATTATGAGATTATAAAACCATTTAAACCGAATAATAAGACTTTTGAAAGAATGGATGAC
TATAAATGGACCTTTCTTGCCAATGAAAGACTTTTTCGTCATGTTTCTTGAGATAGACATTCAAT
TATAGTCTATTTTAACCAAAAATATAACTTCAAATCAGTTATGAGATTATAAAACTATTTAAAGC
AAATAAC
Found at i:1065 original size:171 final size:171
Alignment explanation
Indices: 1--1085 Score: 760
Period size: 171 Copynumber: 6.4 Consensus size: 171
* * * * * *
1 GAGAATATAAAACCATTTAAAGCGAGTGATAAGCCTTTTGAAGGAATGAGTGACCATAAATGAAC
1 GAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATGGAC
* ** ********* * * *
66 TTTTTTTGCCAATGAATCCCTTTTTCTTNNNNNNNNNNT-AGGTAGACATTCAATTATAGTTTGT
66 TTTTCTTGCCAATGAATGTCTTTTTCTT-CATGTTTCTTGAGATAGACATTCAATTATAGTCTAT
* ** *
130 TTTAACCAAAAA-AGTAAAAAAATTTCTCTTAAAATCT-CTTAT
130 TTTAACCAAAAATA-TAAAAAAAATTAACTTAAAAT-TAGTTAT
* **
172 GAGATTATAAAACCATTTAAAGCGAGAAATAAACCTTTCT-AAGGAATGGGTGACTATAAATGGA
1 GAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTT-TGAAGGAATGGGTGACTATAAATGG-
* * * * * * * * * *
236 ATTTTTCTCGACAATGTATATTTTTTTCTTCAGGTTT-TTGAAGGTACATATTCAATTACTA-TC
64 ACTTTTCTTGCCAATGAATGTCTTTTTCTTCATGTTTCTTG-AGATAGACATTCAATTA-TAGTC
* *
299 TA-TTTAACCAAAAATATAAAAAAATTTAACTTAAAATCAGTTAT
127 TATTTTAACCAAAAATATAAAAAAAATTAACTTAAAATTAGTTAT
********** * * *
343 NNNNNNNNNNAACCATTTAGAGCGAGTAATAAGGCTTTTGAAGGAATTGGTAACTATAAATGGAC
1 GAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATGGAC
* * * * *
408 TTTTTTTGCCAATGAATG-CATTTTTCTTCATGTTTCTTGA-AGTAGACATTTAATTATAATTTG
66 TTTTCTTGCCAATGAATGTC-TTTTTCTTCATGTTTCTTGAGA-TAGACATTCAATTATAGTCTA
* ** * * *
471 TTTTAACAAAAAACGT-AAAGAAATTAGACTTAAAATTAATTTT
129 TTTTAACCAAAAATATAAAAAAAATTA-ACTTAAAATTAGTTAT
********** * * *
514 GAGATTATAAAACCATNNNNNNNNNNTAATAAAGCTTTTGAAGGAATGGATGACTAT-AGTGGAC
1 GAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATGGAC
* ** * *
578 TTTTCTTGCCAATGAAAGAGTTTTT-TTCATGTTTCTTGAGATAGACATTCAATTATTGTCTGTT
66 TTTTCTTGCCAATGAATGTCTTTTTCTTCATGTTTCTTGAGATAGACATTCAATTATAGTCTATT
********** * *
642 TTAACCAAAAATATNNNNNNNNNNAACTTCAAATCAGTTAT
131 TTAACCAAAAATATAAAAAAAATTAACTTAAAATTAGTTAT
* * * * * * *
683 GAGATTATAAAACTATTTAAAGCAAATAACAAGGCTCTTGAAGGAATGGGTGAGTATAAATCGAC
1 GAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATGGAC
* * * * * * * *
748 TTTTCTT-CTTAATGAATGGCTTTTTCTACATGTTT-TCTAAGGTAGGCATTTAATTATAGTTTA
66 TTTTCTTGC-CAATGAATGTCTTTTTCTTCATGTTTCT-TGAGATAGACATTCAATTATAGTCTA
** * *
811 TTTTAATAAAAAATAT-AAATAAATTCAACTTAAAATTAATTAT
129 TTTTAACCAAAAATATAAAAAAAATT-AACTTAAAATTAGTTAT
* * * * *
854 GAGATTGTAAAACCATTTAAACCGAATAATAAGACTTTTGAAAGAATGGGTGACTATAAATGGAC
1 GAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATGGAC
* * *
919 CTTTCTTGCCAATGAATGTCTTTTTCGTCATGTTTCTTGAGATAGATATTCAATTATAGTCTATT
66 TTTTCTTGCCAATGAATGTCTTTTTCTTCATGTTTCTTGAGATAGACATTCAATTATAGTCTATT
* * * * *
984 TTAACTAAAAATGTAAAAAAAATTGACTTAAAATTATTTAC
131 TTAACCAAAAATATAAAAAAAATTAACTTAAAATTAGTTAT
* ** * * *
1025 GAGATTTTAAAACCATTTAAAATGAGCAATAAGGCTTTTGAAAGAGTGGGTGACTATAAAT
1 GAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAAT
Statistics
Matches: 693, Mismatches: 196, Indels: 50
0.74 0.21 0.05
Matches are distributed among these distances:
169 100 0.14
170 106 0.15
171 434 0.63
172 51 0.07
173 2 0.00
ACGTcount: A:0.36, C:0.11, G:0.14, T:0.35
Consensus pattern (171 bp):
GAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATGGAC
TTTTCTTGCCAATGAATGTCTTTTTCTTCATGTTTCTTGAGATAGACATTCAATTATAGTCTATT
TTAACCAAAAATATAAAAAAAATTAACTTAAAATTAGTTAT
Done.