Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018401511.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_4638.0, 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: 1698
ACGTcount: A:0.37, C:0.15, G:0.14, T:0.33
Found at i:324 original size:172 final size:171
Alignment explanation
Indices: 1--1695 Score: 1638
Period size: 171 Copynumber: 9.9 Consensus size: 171
* * * *
1 GTGACTATAAATGGACTTTTCT-TC-TCAATGGATGGCTTTTACTTCATGTTTCCTAAGGCAGAC
1 GTGACTATAAATGGGCTTTTCTCTCTTC-AT-GATGGCTTTTGCTTCATGTTTCCCAAGGCAGTC
* * * * * *
64 ATTCAACTATAGCATATATTAACCAAAAATGTTAAAAAATCCAACTTAAAATAAATTATAAGAAT
64 ATTCAATTATAACATATTTTAACCAAAAATGTAAAAAAATCCAACTTAAAATCAATTATGAGAAT
* * * *
129 ACAAAACCATTTAAA-CTGAGTAATAAGGCTTTGAGAGGCTTGT
129 ATAAAACCATTTAAAGC-GAGTAATAAGGCTTTCAAAGGCTTGA
* *
172 GTGACTATAGATGGGCTTTTCTCTCTGTCA-GATGACTTTTGCTTCATGTTTCCCAAGGCAGTCA
1 GTGACTATAAATGGGCTTTTCTCTCT-TCATGATGGCTTTTGCTTCATGTTTCCCAAGGCAGTCA
* * * * *
236 TTTAATTATAATATATTTTTAACCAAAAATGTAAAAAAATCCAACTTAAATTTAATTATGTGAAT
65 TTCAATTATAACATA-TTTTAACCAAAAATGTAAAAAAATCCAACTTAAAATCAATTATGAGAAT
* *
301 ATAAAATCATTTAAAGCGAGTAATAAGGCTTTCAAAGACTTGA
129 ATAAAACCATTTAAAGCGAGTAATAAGGCTTTCAAAGGCTTGA
* ** * * * * *
344 GTGACTATAAATGGACTTTTC-C-CGACAATGGATGGCTTTTACCTCATGTTTCCTAAGGAAGAC
1 GTGACTATAAATGGGCTTTTCTCTCTTC-AT-GATGGCTTTTGCTTCATGTTTCCCAAGGCAGTC
* * * * *
407 ATTCAATTATAAAATATTTTAACCAAATATGTGAAAAAAATCTAACTTACAATCAATTACGAGAA
64 ATTCAATTATAACATATTTTAACCAAAAATGT-AAAAAAATCCAACTTAAAATCAATTATGAGAA
* * ** *
472 TACAAAACCATCTAAAATGAGTAATAAGGCTTTCAAAGGCTTGT
128 TATAAAACCATTTAAAGCGAGTAATAAGGCTTTCAAAGGCTTGA
* * * *
516 GTGACTA-AAGATGAGCTTTTCTCTTTGTCA-GATGGCTTTTGCTTCACGTCTCCCAAGGCAGTC
1 GTGACTATAA-ATGGGCTTTTCTCTCT-TCATGATGGCTTTTGCTTCATGTTTCCCAAGGCAGTC
* ** *
579 ATTCAATTACAACATAGGTTAACCAAAAATGTAAAAAAATCCAACTTAAAACCAATTATGAGAAT
64 ATTCAATTATAACATATTTTAACCAAAAATGTAAAAAAATCCAACTTAAAATCAATTATGAGAAT
* * ** *
644 GTAAAACAATTTAAAGTAAGTAATAAGGCTTTCAAAGGCTTGC
129 ATAAAACCATTTAAAGCGAGTAATAAGGCTTTCAAAGGCTTGA
* * * * * *
687 GTGACTATAAATGAGCTTTTCT-T-TTCAATGAATGGCTTTTGCTTCACGTTTCTCTAGGTAAAT
1 GTGACTATAAATGGGCTTTTCTCTCTTC-ATG-ATGGCTTTTGCTTCATGTTTCCCAAGG-CAGT
* * *
750 -ATTTAATTATAGC-TCATTTTAA-CAACAAATGTAAAAAAAACCAACTTAAAATCAATTATGAG
63 CATTCAATTATAACAT-ATTTTAACCAA-AAATGTAAAAAAATCCAACTTAAAATCAATTATGAG
* ** * * *
812 AACATAAAACCATTTAAATTGAGTAAGAAGGCTTTCAAATGCTTAA
126 AATATAAAACCATTTAAAGCGAGTAATAAGGCTTTCAAAGGCTTGA
* * * * * **
858 GTGACTATAAATGGACTTTTCTCTC-CCATGGTTGGGTTTTGCTTCATGTGTCCCTGGGCAGTCA
1 GTGACTATAAATGGGCTTTTCTCTCTTCAT-GATGGCTTTTGCTTCATGTTTCCCAAGGCAGTCA
* * * *
922 TTCAATTATAACATATTTGAACTAAAAATGTAAACAAATCCAACATAAAATCAATTATGAGAATA
65 TTCAATTATAACATATTTTAACCAAAAATGTAAAAAAATCCAACTTAAAATCAATTATGAGAATA
* * *
987 TAAAACCATTCACAGCGAGTAATACGGCTTTCAAAGGCTTGA
130 TAAAACCATTTAAAGCGAGTAATAAGGCTTTCAAAGGCTTGA
** * * ** * *
1029 GTGACTATAAATATAG-TTTTCTCTC-TAATGCATGGCTTTTGGTTCACATTTCTCGAGGCAGAT
1 GTGACTATAAAT-GGGCTTTTCTCTCTTCATG-ATGGCTTTTGCTTCATGTTTCCCAAGGCAG-T
* * * * * * * *
1092 -ATTCAATTATAACGTATTTTAACTAAAAGTGCACAAAAATCCAACTTAGAACCAATTATGAAAA
63 CATTCAATTATAACATATTTTAACCAAAAATGTAAAAAAATCCAACTTAAAATCAATTATGAGAA
* * *
1156 TATAAAATCATTTAAAGCGAGTAATAAGGTTTTCAAAAGCTTGA
128 TATAAAACCATTTAAAGCGAGTAATAAGGCTTTCAAAGGCTTGA
** * * * ** * * * ***
1200 GTGACTATAAATGGATTTTTTTCTC-CCATGGATGGCTTTTGCGTCACATTTCTCGAGGTAAAAA
1 GTGACTATAAATGGGCTTTTCTCTCTTCAT-GATGGCTTTTGCTTCATGTTTCCCAAGGCAGTCA
* * ** * *
1264 TTCAACTATAGCATATTTTAAATAGAAATGTAAAAAAATCCAAGTTAAAATCAATTATGAGAATA
65 TTCAATTATAACATATTTTAACCAAAAATGTAAAAAAATCCAACTTAAAATCAATTATGAGAATA
* *
1329 TAAAACCATTTAAAGTGAGTAATAAGGCTTTCAAGGGCTTGA
130 TAAAACCATTTAAAGCGAGTAATAAGGCTTTCAAAGGCTTGA
* * * *
1371 GTGACTATAAATGGAACTTTTCTCTCCT-ATGGATGGCTTTTGCTTCATGTTTCCCAATGTAGAT
1 GTGACTATAAATGG-GCTTTTCTCTCTTCAT-GATGGCTTTTGCTTCATGTTTCCCAAGGCAG-T
* * * *
1435 -ATTTC-ATTATAGCATATTTTCACCAAAAATGTAAAAAAATTTCAACTTAGAATCAATTATGAG
63 CA-TTCAATTATAACATATTTTAACCAAAAATGTAAAAAAA-TCCAACTTAAAATCAATTATGAG
* * *** *
1498 AATCTAAAACTATTTAAAGCGAGTAATAAGGCTTTTTGAGGCTTTA
126 AATATAAAACCATTTAAAGCGAGTAATAAGGCTTTCAAAGGCTTGA
* * * * * **
1544 GTGACTATAAATGGACATTTCTCTC-CCATGGATGGCTTTTACTTCATGTTTCCTAAGGCAAACA
1 GTGACTATAAATGGGCTTTTCTCTCTTCAT-GATGGCTTTTGCTTCATGTTTCCCAAGGCAGTCA
* * **
1608 TTCAATTATAGCATATTTTAACCAAAATTGT--AAAAATCCAACTTAAAATCAATTGCGAGAATA
65 TTCAATTATAACATATTTTAACCAAAAATGTAAAAAAATCCAACTTAAAATCAATTATGAGAATA
* *
1671 TAAAACCATTGAAAGTGAGTAATAA
130 TAAAACCATTTAAAGCGAGTAATAA
1696 TGC
Statistics
Matches: 1257, Mismatches: 227, Indels: 82
0.80 0.14 0.05
Matches are distributed among these distances:
168 2 0.00
169 47 0.04
170 16 0.01
171 695 0.55
172 415 0.33
173 78 0.06
174 3 0.00
175 1 0.00
ACGTcount: A:0.37, C:0.15, G:0.14, T:0.33
Consensus pattern (171 bp):
GTGACTATAAATGGGCTTTTCTCTCTTCATGATGGCTTTTGCTTCATGTTTCCCAAGGCAGTCAT
TCAATTATAACATATTTTAACCAAAAATGTAAAAAAATCCAACTTAAAATCAATTATGAGAATAT
AAAACCATTTAAAGCGAGTAATAAGGCTTTCAAAGGCTTGA
Done.