Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018401521.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_4647.0, 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, 810
Length: 1351
ACGTcount: A:0.28, C:0.11, G:0.11, T:0.30
Warning! 269 characters in sequence are not A, C, G, or T
Found at i:780 original size:171 final size:171
Alignment explanation
Indices: 426--1128 Score: 788
Period size: 171 Copynumber: 4.1 Consensus size: 171
416 NNNNNAATAG
** * * *
426 GTGACTATAAATGGACTTTTCTTGTAAATTAATTCCTTTTTCTTCACGTTTATTGTGGTAGACAT
1 GTGACTATAAATGGACTTTTCTTGCCAATGAATTCCTTTTTCTTCACGTTTCTTGAGGTAGACAT
* * *
491 TCAATTATAGTCTGTTTTAACTAAAAATGTAAAAAATATTCAACTTAAAGTCAGTTATGAGATTA
66 TCAATTATAGTCTGTTTTAACCAAAAATGTTAAAAATATTCAACTTAAAATCAGTTATGAGATTA
* * * *
556 TAAAACCTTTTAAAGC-ACGTAATAAGCCTTCTTAAAGAATGG
131 TAAAACCATTTAAAGCGA-GTAATAAACCTT-TTAAGGAATGT
* * * **
598 GTGAGTATAAATGGACTTTTCTTGCCAATGAATGCCTTTTTATTCAAATTTCTTGAGGTAGACAT
1 GTGACTATAAATGGACTTTTCTTGCCAATGAATTCCTTTTTCTTCACGTTTCTTGAGGTAGACAT
* *
663 TCAATTATTGTCTGTTTTAACCAAAAAT-TTAAAAATATTCAACTTAAAATCTGTTATGAGATTA
66 TCAATTATAGTCTGTTTTAACCAAAAATGTTAAAAATATTCAACTTAAAATCAGTTATGAGATTA
*
727 TAAAAGCATTTAAAGCGAGTAATAAACCTTTTGAAGGAATGT
131 TAAAACCATTTAAAGCGAGTAATAAACCTTTT-AAGGAATGT
* * ** *
769 GTGACTATAAATGGACTTTTCTTGTCAATGAATTCATTTTTCTTCACGTTTCTCAAGGTAGGCAT
1 GTGACTATAAATGGACTTTTCTTGCCAATGAATTCCTTTTTCTTCACGTTTCTTGAGGTAGACAT
* * * *
834 TCAATTATAGTCTGTTTTAAACAAAAATGTTGAAAACT-TT-AACCTAAAATCAGTAATGAGATT
66 TCAATTATAGTCTGTTTTAACCAAAAATGTT-AAAAATATTCAACTTAAAATCAGTTATGAGATT
* * * *
897 ATAGAACCAATTAAAACGAGTAATAAGCCTTTTTAAGGAATAG-
130 ATAAAACCATTTAAAGCGAGTAATAAACC-TTTTAAGGAAT-GT
* * * *
940 GTGACTATAAATAGACTTTTCTTGCCAATGAATT-CTTGTTTCTTTATGTTTCTCT-AGGTACAC
1 GTGACTATAAATGGACTTTTCTTGCCAATGAATTCCTT-TTTCTTCACGTTTCT-TGAGGTAGAC
* * *
1003 ATTCAATTATTA-T-T-TTTTGCAACC-AAAGTG-TAAAACA-ATTCAACTTACAATCAGTTATA
64 ATTCAATTA-TAGTCTGTTTT--AACCAAAAATGTTAAAA-ATATTCAACTTAAAATCAGTTATG
* * *
1062 AGATTATAAAATCATTTAAAGCTACTAATAAACCTTTTAAAGGAAT-T
125 AGATTATAAAACCATTTAAAGCGAGTAATAAACCTTTT-AAGGAATGT
1109 GGTGACTATAAATGG-CTTTT
1 -GTGACTATAAATGGACTTTT
1129 TTCTTCATGT
Statistics
Matches: 450, Mismatches: 64, Indels: 37
0.82 0.12 0.07
Matches are distributed among these distances:
168 4 0.01
169 16 0.04
170 71 0.16
171 261 0.58
172 93 0.21
173 5 0.01
ACGTcount: A:0.36, C:0.13, G:0.14, T:0.38
Consensus pattern (171 bp):
GTGACTATAAATGGACTTTTCTTGCCAATGAATTCCTTTTTCTTCACGTTTCTTGAGGTAGACAT
TCAATTATAGTCTGTTTTAACCAAAAATGTTAAAAATATTCAACTTAAAATCAGTTATGAGATTA
TAAAACCATTTAAAGCGAGTAATAAACCTTTTAAGGAATGT
Found at i:1133 original size:342 final size:342
Alignment explanation
Indices: 425--1128 Score: 899
Period size: 342 Copynumber: 2.1 Consensus size: 342
415 NNNNNNAATA
* * ***
425 GGTGACTATAAATGGACTTTTCTTGTAAATTAATTCCTTTTTCTTCACGTTTATTGTGGTAGACA
1 GGTGACTATAAATGGACTTTTCTTGTAAATGAATTCATTTTTCTTCACGTTTATCAAGGTAGACA
* * *
490 TTCAATTATAGTCTGTTTTAACTAAAAATGTAAAAAATATTCAACTTAAAGTCAGTTATGAGATT
66 TTCAATTATAGTCTGTTTTAACTAAAAATGTAAAAAATATTCAACCTAAAATCAGTAATGAGATT
** * * * *
555 ATAAAACCTTTTAAAGCACGTAATAAGCCTTCTTAAAGAATGGGTGAGTATAAATGGACTTTTCT
131 ATAAAACCAATTAAAACACGTAATAAGCCTTCTTAAAGAATAGGTGACTATAAATAGACTTTTCT
* *
620 TGCCAATGAATGCCTTTTTATTCAAATTTCTTGAGGTAGACATTCAATTATTGTCTGTTTTAACC
196 TGCCAATGAATGCCTTTTTATTCAAATTTCTTGAGGTACACATTCAATTATTATCTGTTTTAACC
* * * *
685 AAAAATTTAAAAATATTCAACTTAAAATCTGTTATGAGATTATAAAAGCATTTAAAGCGAGTAAT
261 AAAAATGTAAAAATATTCAACTTAAAATCAGTTATAAGATTATAAAAGCATTTAAAGCGACTAAT
*
750 AAACCTTTTGAAGGAAT
326 AAACCTTTTAAAGGAAT
* * *
767 GTGTGACTATAAATGGACTTTTCTTGTCAATGAATTCATTTTTCTTCACGTTTCTCAAGGTAGGC
1 G-GTGACTATAAATGGACTTTTCTTGTAAATGAATTCATTTTTCTTCACGTTTATCAAGGTAGAC
* *
832 ATTCAATTATAGTCTGTTTTAAAC-AAAAATGTTGAAAACT-TT-AACCTAAAATCAGTAATGAG
65 ATTCAATTATAGTCTGTTTT-AACTAAAAATG-TAAAAAATATTCAACCTAAAATCAGTAATGAG
* * *
894 ATTATAGAACCAATTAAAACGA-GTAATAAGCCTTTTTAAGGAATAGGTGACTATAAATAGACTT
128 ATTATAAAACCAATTAAAAC-ACGTAATAAGCCTTCTTAAAGAATAGGTGACTATAAATAGACTT
* * * **
958 TTCTTGCCAATGAAT-TCTTGTTTCTTTATGTTTCTCT-AGGTACACATTCAATTATTAT-T-TT
192 TTCTTGCCAATGAATGCCTT-TTTATTCAAATTTCT-TGAGGTACACATTCAATTATTATCTGTT
* * *
1019 TTGCAACC-AAAGTGTAAAACA-ATTCAACTTACAATCAGTTATAAGATTATAAAATCATTTAAA
255 TT--AACCAAAAATGTAAAA-ATATTCAACTTAAAATCAGTTATAAGATTATAAAAGCATTTAAA
*
1082 GCTACTAATAAACCTTTTAAAGGAATT
317 GCGACTAATAAACCTTTTAAAGGAA-T
1109 GGTGACTATAAATGG-CTTTT
1 GGTGACTATAAATGGACTTTT
1129 TTCTTCATGT
Statistics
Matches: 314, Mismatches: 38, Indels: 22
0.84 0.10 0.06
Matches are distributed among these distances:
340 9 0.03
341 87 0.28
342 123 0.39
343 86 0.27
344 9 0.03
ACGTcount: A:0.36, C:0.13, G:0.14, T:0.38
Consensus pattern (342 bp):
GGTGACTATAAATGGACTTTTCTTGTAAATGAATTCATTTTTCTTCACGTTTATCAAGGTAGACA
TTCAATTATAGTCTGTTTTAACTAAAAATGTAAAAAATATTCAACCTAAAATCAGTAATGAGATT
ATAAAACCAATTAAAACACGTAATAAGCCTTCTTAAAGAATAGGTGACTATAAATAGACTTTTCT
TGCCAATGAATGCCTTTTTATTCAAATTTCTTGAGGTACACATTCAATTATTATCTGTTTTAACC
AAAAATGTAAAAATATTCAACTTAAAATCAGTTATAAGATTATAAAAGCATTTAAAGCGACTAAT
AAACCTTTTAAAGGAAT
Done.