Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018401294.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_4436.0, 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, 1000
Length: 2587
ACGTcount: A:0.25, C:0.09, G:0.10, T:0.23
Warning! 858 characters in sequence are not A, C, G, or T
Found at i:2554 original size:171 final size:170
Alignment explanation
Indices: 1819--2564 Score: 763
Period size: 171 Copynumber: 4.3 Consensus size: 170
1809 NNNNNNNNNN
*
1819 GGAATGGGTGACTATAAATGGACTTTTCTTCTCAATGAAT-GACTTTTTCTGCACATTTCCCCAA
1 GGAATGGGTGACTATAAATGGACTTTTCTTCTCAATGAATAG-CTTTTTTTGCACATTT-CCCAA
* * * *
1883 GACAGACAATCAATTATAGTCTGTTTTAACTAAAAATGTAAAAAAATTCAACTTAAAATCAATTA
64 GGCAGACAATCAATTATAGTATGTTTTAA-TAAAAAAGTAAAAAAAATCAACTTAAAATCAATTA
* * * *
1948 TGAGGTTATAAATCCGTTTAAAGCGAATAATAA-GCTTTTTGAA
128 TGAGATTATAAAACCGTTTAAAGCGAGTAATAAGGC-TTTCGAA
* * * * ** * *
1991 GGAATAGGTGACTCTAAATGGACTTTTCTTGTCAAAGAAT-GCTTGTTTCTT-CATGTTTCTCGA
1 GGAATGGGTGACTATAAATGGACTTTTCTTCTCAATGAATAGCTT-TTT-TTGCACATTTCCCAA
* * * * *
2054 GGTAGACATTCAATTATAGTATGTTTTAATCAAAAAAGTAAAAAAATTAAACTTAAAATTAATTA
64 GGCAGACAATCAATTATAGTATGTTTTAAT-AAAAAAGTAAAAAAAATCAACTTAAAATCAATTA
*
2119 TGAGATTATAAAACCAG-TTAAATCGAGTAATAAGGCTTTCGAA
128 TGAGATTATAAAACC-GTTTAAAGCGAGTAATAAGGCTTTCGAA
* * * ** * * * * * **
2162 AGAATGGGTCACTAAAAATGGTTTTTTCTTCCCAATGAATAACTTTTTCTACACCTTTCCTGAGG
1 GGAATGGGTGACTATAAATGGACTTTTCTTCTCAATGAATAGCTTTTTTTGCACATTTCCCAAGG
* * ** * * * *
2227 TAGGCTTTCAATTATAGTTTGTTTTAAAAAAAAAAGTAAAAAAAAATTCAACCTAAAATTAATTA
66 CAGACAATCAATTATAGTATGTTTT-AATAAAAAAGT-AAAAAAAA-TCAACTTAAAATCAATTA
* * *
2292 TAAGATTTTAAAACCATTTAAAGCG-GATAATAAGGCTTTCGAA
128 TGAGATTATAAAACCGTTTAAAGCGAG-TAATAAGGCTTTCGAA
* * *
2335 GGAATGAGTGACTATAAATAGACTTTTCTGT-TCAATGAATAGCTTTTTTTGCACGTTTCCCAAG
1 GGAATGGGTGACTATAAATGGACTTTTCT-TCTCAATGAATAGCTTTTTTTGCACATTTCCCAAG
* * * *
2399 GCAAACAATCACTTATAGCT-TGTTTTAATAGTAAATGTAAAAAAAATCAACTTAAAATCAATTA
65 GCAGACAATCAATTATAG-TATGTTTTAATA-AAAAAGTAAAAAAAATCAACTTAAAATCAATTA
* *
2463 CGAGATTATAAAACCGTTTAAAGCGAGTAATAA-GCTTTTTGAA
128 TGAGATTATAAAACCGTTTAAAGCGAGTAATAAGGC-TTTCGAA
* * *
2506 GGAATGTGTGACTATAAATGGAATTTTCTTCTCAATGAATGGCTTTTTTTGCACATTTC
1 GGAATGGGTGACTATAAATGGACTTTTCTTCTCAATGAATAGCTTTTTTTGCACATTTC
2565 TTGAGGCAAG
Statistics
Matches: 473, Mismatches: 83, Indels: 37
0.80 0.14 0.06
Matches are distributed among these distances:
170 5 0.01
171 269 0.57
172 73 0.15
173 124 0.26
174 2 0.00
ACGTcount: A:0.38, C:0.13, G:0.15, T:0.35
Consensus pattern (170 bp):
GGAATGGGTGACTATAAATGGACTTTTCTTCTCAATGAATAGCTTTTTTTGCACATTTCCCAAGG
CAGACAATCAATTATAGTATGTTTTAATAAAAAAGTAAAAAAAATCAACTTAAAATCAATTATGA
GATTATAAAACCGTTTAAAGCGAGTAATAAGGCTTTCGAA
Found at i:2586 original size:344 final size:341
Alignment explanation
Indices: 1819--2587 Score: 865
Period size: 344 Copynumber: 2.2 Consensus size: 341
1809 NNNNNNNNNN
* ** *
1819 GGAATGGGTGACTATAAATGGACTTTTCTTCTCAATGAATGACTTTTTCTGCACATTTCCCCAAG
1 GGAATGGGTGACTATAAATGGAATTTTCTTCTCAATGAATGACTTTTTCTGCACATTTCCTGAGG
* * ** * *
1884 ACAGACAATCAATTATAGTCTGTTTTAACTAAAAATGTAAAAAAATTCAACTTAAAATCAATTAT
66 A-AG-CATTTAATTATAGTCTGTTTTAAAAAAAAAAGTAAAAAAATTCAACCTAAAATCAATTAT
* * * * * * *
1949 GAGGTTATAAATCCGTTTAAAGCGAATAATAAGCTTTTTGAAGGAATAGGTGACTCTAAATGGAC
129 AAGATTATAAAACCATTTAAAGCGAATAATAAGCTTTTCGAAGGAATAGGTGACTATAAATAGAC
* * * * * *
2014 TTTTCTTGTCAAAGAATGCTTGTTTCTTCATGTTTCTCGAGGTAGACATTCAATTATAGTATGTT
194 TTTTCTTGTCAAAGAATGCTTGTTTCTTCACGTTTCCCAAGGCAAACAATCAATTATAGTATGTT
* * * *
2079 TTAATCAAAAAAGTAAAAAAATTAAACTTAAAATTAATTATGAGATTATAAAACCAGTTAAATCG
259 TTAATCAAAAAAGTAAAAAAAATAAACTTAAAATCAATTACGAGATTATAAAACCAGTTAAAGCG
2144 AGTAATAAGGCTTTCGAA
324 AGTAATAAGGCTTTCGAA
* * * ** * * * *
2162 AGAATGGGTCACTAAAAATGGTTTTTTCTTCCCAATGAATAACTTTTTCTACACCTTTCCTGAGG
1 GGAATGGGTGACTATAAATGGAATTTTCTTCTCAATGAATGACTTTTTCTGCACATTTCCTGAGG
* * *
2227 TAGGC-TTTCAATTATAGTTTGTTTTAAAAAAAAAAGTAAAAAAAAATTCAACCTAAAATTAATT
66 -AAGCATTT-AATTATAGTCTGTTTTAAAAAAAAAAGT--AAAAAAATTCAACCTAAAATCAATT
* *
2291 ATAAGATTTTAAAACCATTTAAAGCGGATAATAAGGC-TTTCGAAGGAAT-GAGTGACTATAAAT
127 ATAAGATTATAAAACCATTTAAAGCGAATAATAA-GCTTTTCGAAGGAATAG-GTGACTATAAAT
* *
2354 AGACTTTTC-TGTTCAATGAATAGCTT-TTT-TTGCACGTTTCCCAAGGCAAACAATCACTTATA
190 AGACTTTTCTTG-TCAAAGAAT-GCTTGTTTCTT-CACGTTTCCCAAGGCAAACAATCAATTATA
* * *
2416 GCT-TGTTTTAAT-AGTAAATGTAAAAAAAATCAACTTAAAATCAATTACGAGATTATAAAACC-
252 G-TATGTTTTAATCA-AAAAAGTAAAAAAAATAAACTTAAAATCAATTACGAGATTATAAAACCA
*
2478 GTTTAAAGCGAGTAATAA-GCTTTTTGAA
315 G-TTAAAGCGAGTAATAAGGC-TTTCGAA
* * * *
2506 GGAATGTGTGACTATAAATGGAATTTTCTTCTCAATGAATGGCTTTTTTTGCACATTTCTTGAGG
1 GGAATGGGTGACTATAAATGGAATTTTCTTCTCAATGAATGACTTTTTCTGCACATTTCCTGAGG
2571 CAAGCATTTAATTATAG
66 -AAGCATTTAATTATAG
Statistics
Matches: 351, Mismatches: 61, Indels: 27
0.80 0.14 0.06
Matches are distributed among these distances:
341 1 0.00
342 25 0.07
343 63 0.18
344 252 0.72
345 10 0.03
ACGTcount: A:0.38, C:0.13, G:0.15, T:0.35
Consensus pattern (341 bp):
GGAATGGGTGACTATAAATGGAATTTTCTTCTCAATGAATGACTTTTTCTGCACATTTCCTGAGG
AAGCATTTAATTATAGTCTGTTTTAAAAAAAAAAGTAAAAAAATTCAACCTAAAATCAATTATAA
GATTATAAAACCATTTAAAGCGAATAATAAGCTTTTCGAAGGAATAGGTGACTATAAATAGACTT
TTCTTGTCAAAGAATGCTTGTTTCTTCACGTTTCCCAAGGCAAACAATCAATTATAGTATGTTTT
AATCAAAAAAGTAAAAAAAATAAACTTAAAATCAATTACGAGATTATAAAACCAGTTAAAGCGAG
TAATAAGGCTTTCGAA
Done.