Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018398581.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_1871.0, 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: 2602
ACGTcount: A:0.24, C:0.07, G:0.09, T:0.23
Warning! 957 characters in sequence are not A, C, G, or T
Found at i:2096 original size:171 final size:172
Alignment explanation
Indices: 1768--2600 Score: 821
Period size: 171 Copynumber: 4.9 Consensus size: 172
1758 NNNNNNNNNN
* * * * * * *
1768 TAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGAAATGAGAG-G-CTATAAATGAACTTTTT
1 TAAAATCATTTAAAGTGAGTAATAAGGCTTTTAAAGGAAT-AGGGTGACTATAAATGGACTTTTC
** * * ** * *
1831 TTACCAATCACTGTTTTTTTCTTCACATTTCT-AGAGGTAAACATTCAATTATAGCCTGTTTTAA
65 TTGTCAATGAATACTTTTTTCTTCACATTTCTCA-AGGCAAACATTCAATTATAGTCTGTTTTAA
* * *
1895 TGAAAAATGTAAAAATATTTAACTTAAAATCAATTACGAGATTA
129 TCAAAAATGTAAAAAAATTCAACTTAAAATCAATTACGAGATTA
* * *
1939 TAAAA-CTATTTGAAGTGAGTAATATGGCTTTTAAAAGAA-AGGGTGACTATAAATGGACTTTTC
1 TAAAATC-ATTTAAAGTGAGTAATAAGGCTTTTAAAGGAATAGGGTGACTATAAATGGACTTTTC
*
2002 TTGTCAATGAATACTTTTTTCTTCACATTTCTCAAGGCAAATATTCAATTATAGTCTGTTTTAAT
65 TTGTCAATGAATACTTTTTTCTTCACATTTCTCAAGGCAAACATTCAATTATAGTCTGTTTTAAT
* *
2067 CAAAAATATAAAAAAATTCAACCTAAAATCAATTACGAGATTA
130 CAAAAATGTAAAAAAATTCAACTTAAAATCAATTACGAGATTA
* * * * *
2110 GAAAACCATTTAAAGCGAGTAACAAGGCTTTTGAAGGAAT-GGGTGACTATAAATGGACTTTTCT
1 TAAAATCATTTAAAGTGAGTAATAAGGCTTTTAAAGGAATAGGGTGACTATAAATGGACTTTTCT
** * * * * * * * * *
2174 TGTCTTTCAATGCTTTTATCTTCACGTTTCTCGA-GAAAGACAGTCAATTATTGTCTCTTTTAAT
66 TGTCAATGAATACTTTTTTCTTCACATTTCTCAAGGCAA-ACATTCAATTATAGTCTGTTTTAAT
* * **
2238 AAAAAATGTACAAAAATTCAACTTAAAATCAATTATTAGATTGA
130 CAAAAATGTAAAAAAATTCAACTTAAAATCAATTACGAGATT-A
* * ** *
2282 -AAAATCATTTAAAATGAGTAATAAGGCTTTTGAAGGAATACAAG-G-CTATAAATAGACTTTTC
1 TAAAATCATTTAAAGTGAGTAATAAGGCTTTTAAAGGAATA-GGGTGACTATAAATGGACTTTTC
* * * * * * * *
2344 TTGCCAATGAAT-GTCTTTTTCTTCACTTTTCTCGAGCCAGACATTCAATTGTAATCTGTTTTAA
65 TTGTCAATGAATACT-TTTTTCTTCACATTTCTCAAGGCAAACATTCAATTATAGTCTGTTTTAA
** * * * **
2408 AGAAAAATGTAAAAAAATTGAAATTAAAATTAATTATAAGATTA
129 TCAAAAATGTAAAAAAATTCAACTTAAAATCAATTACGAGATTA
* * *
2452 TAAAATCATTCAAAGTGTGTAATAAAGCTTTTAAAGGAATA-GGTGACTATAAATGGACTTTTCT
1 TAAAATCATTTAAAGTGAGTAATAAGGCTTTTAAAGGAATAGGGTGACTATAAATGGACTTTTCT
* * * ** * *
2516 TGAT-AATGAATACTTTTTCCTTTACATTTTTCAAGATAGACATTCAATTATTA-ACTGTTTTAA
66 TG-TCAATGAATACTTTTTTCTTCACATTTCTCAAGGCAAACATTCAATTA-TAGTCTGTTTTAA
2579 TCAAAAATGTAAAAAAATTCAA
129 TCAAAAATGTAAAAAAATTCAA
2601 GT
Statistics
Matches: 546, Mismatches: 98, Indels: 36
0.80 0.14 0.05
Matches are distributed among these distances:
169 4 0.01
170 8 0.01
171 525 0.96
172 8 0.01
173 1 0.00
ACGTcount: A:0.39, C:0.12, G:0.13, T:0.36
Consensus pattern (172 bp):
TAAAATCATTTAAAGTGAGTAATAAGGCTTTTAAAGGAATAGGGTGACTATAAATGGACTTTTCT
TGTCAATGAATACTTTTTTCTTCACATTTCTCAAGGCAAACATTCAATTATAGTCTGTTTTAATC
AAAAATGTAAAAAAATTCAACTTAAAATCAATTACGAGATTA
Done.