Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018398487.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_1782.0, 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, 934
Length: 1558
ACGTcount: A:0.28, C:0.09, G:0.10, T:0.26
Warning! 409 characters in sequence are not A, C, G, or T
Found at i:302 original size:170 final size:171
Alignment explanation
Indices: 1--344 Score: 397
Period size: 170 Copynumber: 2.0 Consensus size: 171
* * * *
1 CTTTTTCTTCACATTTCCTGAGACAGACATTCAATTAGAATCTGTTTTAGCTAAAAATATAAAAA
1 CTTTTTCTTCACATTTCCTGAGACAGACATTCAATTAGAATATATTTTAACAAAAAATATAAAAA
* * ** *
66 AATTCAACTTAAAATTAATTATGAGATTGTAAAAATATTTAAAATGAGTAATAAGGCTTACGAAG
66 AATTCAACTTAAAATCAATTATGAGATTATAAAAATATTTAAAATGAAAAATAAGACTTACGAAG
* * **
131 GCTTGAGTGACTGTAAATGGACTTTT-TTGCCAATGAATGG
131 GCATGAGTGACTATAAATGGACTTTTGTCACCAATGAATGG
* ** * *
171 CTTTTTCTTCATATTT-CTCGAGGTAGACATTCAATTATAATATATTTTAACAAAAAATGT-AAA
1 CTTTTTCTTCACATTTCCT-GAGACAGACATTCAATTAGAATATATTTTAACAAAAAATATAAAA
** * * * * * * *
234 ACGTTTAACCTTAAAATCAATTATGTGTTTATAAAACTATTTAAAGTGAAAAATAATACTTTCGA
65 AAATTCAA-CTTAAAATCAATTATGAGATTATAAAAATATTTAAAATGAAAAATAAGACTTACGA
*
299 AGGCATGAGTGACTATAAATGGACTTTTGTCACCAATGGATGG
129 AGGCATGAGTGACTATAAATGGACTTTTGTCACCAATGAATGG
342 CTT
1 CTT
345 NNNNNNNNNN
Statistics
Matches: 143, Mismatches: 28, Indels: 5
0.81 0.16 0.03
Matches are distributed among these distances:
169 10 0.07
170 119 0.83
171 14 0.10
ACGTcount: A:0.38, C:0.12, G:0.14, T:0.36
Consensus pattern (171 bp):
CTTTTTCTTCACATTTCCTGAGACAGACATTCAATTAGAATATATTTTAACAAAAAATATAAAAA
AATTCAACTTAAAATCAATTATGAGATTATAAAAATATTTAAAATGAAAAATAAGACTTACGAAG
GCATGAGTGACTATAAATGGACTTTTGTCACCAATGAATGG
Found at i:935 original size:170 final size:171
Alignment explanation
Indices: 648--977 Score: 445
Period size: 170 Copynumber: 1.9 Consensus size: 171
638 NNNNNAATAT
* * * *
648 AAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCTTTTAAAGAAAGTAATAAAGCTTTC
1 AAAAAATACAACTTAAAATCAATTATAAAATTATAAAACCATTTAAAGAAAGTAATAAAGCTTTC
* * * *
713 GAAGGCTTGAAAGACTATAAATAGACTTTTCTTGCTAGTGGATGGTTTTTGCTTCACGTTTCTT-
66 GAAGGCGTGAAAGACTATAAATAGACTTTTCTTGCCAGTGAATGGCTTTTGCTTCACGTTT-TTG
* *
777 AAGGTAGACATTCAATTATAA-CATATTTTAATCAAAAGTGTA
130 AAGGCAAACATTCAATTATAATC-TATTTTAATCAAAAGTGTA
* * *
819 AAAAAATACAACTTAAAATTAATTATAAAATTAT-AAACCATTTAAAGTAAGTAATAAGGCTTTC
1 AAAAAATACAACTTAAAATCAATTATAAAATTATAAAACCATTTAAAGAAAGTAATAAAGCTTTC
* * *
883 GAAGGCGTGAGCA-ACTATAAATGGACTTTTCTCT-CCAGTGAATGGCTTTTGCTTTACGTTTTT
66 GAAGGCGTGA-AAGACTATAAATAGACTTTTCT-TGCCAGTGAATGGCTTTTGCTTCACGTTTTT
946 GAAGGCAAACATTCAATTATAATCTATTTTAA
129 GAAGGCAAACATTCAATTATAATCTATTTTAA
978 CTAATAGTAC
Statistics
Matches: 139, Mismatches: 16, Indels: 9
0.85 0.10 0.05
Matches are distributed among these distances:
169 2 0.01
170 104 0.75
171 33 0.24
ACGTcount: A:0.39, C:0.12, G:0.14, T:0.35
Consensus pattern (171 bp):
AAAAAATACAACTTAAAATCAATTATAAAATTATAAAACCATTTAAAGAAAGTAATAAAGCTTTC
GAAGGCGTGAAAGACTATAAATAGACTTTTCTTGCCAGTGAATGGCTTTTGCTTCACGTTTTTGA
AGGCAAACATTCAATTATAATCTATTTTAATCAAAAGTGTA
Done.