Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018398321.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_1621.0, 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: 1928
ACGTcount: A:0.27, C:0.08, G:0.09, T:0.24
Warning! 617 characters in sequence are not A, C, G, or T
Found at i:1317 original size:170 final size:171
Alignment explanation
Indices: 1035--1928 Score: 1016
Period size: 171 Copynumber: 5.2 Consensus size: 171
1025 CAAAAGTGCA
* * *
1035 AAAAAAATT-AACTTAAAATGAATTATGAGATTATAAATCTATTTAAAGCGAGTAATAAGGCTTT
1 AAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTT
* * ** * **
1099 TGAAGGAATGGGTGACTATAAAT-GAACTTTTCTCATCAATGAATGGCTTTTTCTACATGTTTCT
66 TGAAGGAATAGGAGACTATAAATAG-ACTTTTCTTGTCAATAAATGGCTTTTTCTACACATTTCT
* * *
1163 TGAGGCAAGCACTCAGTTATAGTCTGTTTTAATGAAAAATGT
130 TAAGGCAAGCATTCAATTATAGTCTGTTTTAATGAAAAATGT
* * *
1205 AAAAAAAATCAACCTAAAATCAATTATGAGATTATAAAACCATTTAAAGCAAGTAATAAGG-TTT
1 AAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTT
* * * *
1269 AGAAGGAATAGGAGACTATAAATAGACTTTTCTTGTGAATGAATGGCTTTTTCTACACATTTCCT
66 TGAAGGAATAGGAGACTATAAATAGACTTTTCTTGTCAATAAATGGCTTTTTCTACACATTTCTT
*
1334 AAGGCAAGCATTCAATTATAGTCTGTTTTAATGAAAAATAT
131 AAGGCAAGCATTCAATTATAGTCTGTTTTAATGAAAAATGT
* * * *
1375 AAAAATAATTCAAGTT-AAATACAATTATGAGATTACAAAATCATTTAAAGCTAGTAATAAGGCT
1 AAAAA-AATTCAACTTAAAAT-CAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCT
* * * * * * **
1439 TTTGAAGGTATAAGAGACTGTAAATAGATTTTTCTT-CCAAATAAATGGCTTTCTCTACATGTTT
64 TTTGAAGGAATAGGAGACTATAAATAGACTTTTCTTGTC-AATAAATGGCTTTTTCTACACATTT
* * *
1503 CTCAAGGTAAACATTCAATTATAGTCTGTTTTAATGAAAAATGT
128 CTTAAGGCAAGCATTCAATTATAGTCTGTTTTAATGAAAAATGT
* *
1547 CAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGTGAGTAATAAGGCTTT
1 AAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTT
* * * * * *
1612 TGAAGGAAT-GAGAGACTATAAATGGACTTTTATTGGCAATAAATGTCTTTTTTTTCACATTTCT
66 TGAAGGAATAG-GAGACTATAAATAGACTTTTCTTGTCAATAAATGGCTTTTTCTACACATTTCT
* * * * *
1676 TGAGG-TAGACATTCAATTATGGTTTGTTTTAACT-AAAAGTGT
130 TAAGGCAAG-CATTCAATTATAGTCTGTTTTAA-TGAAAAATGT
* * * ** *
1718 AAAAGAATTCAACTTAAAAAATCAATTATAAGATAATAAAATGATTTAAAGTGAGTAATAAGGCT
1 AAAAAAATTCAACTT--AAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCT
* * **
1783 TTTGAAAGAATAGGTGACTATAAATAGACTTTTCTTGTCAATAAAT-GCATTTTTCTTTACATTT
64 TTTGAAGGAATAGGAGACTATAAATAGACTTTTCTTGTCAATAAATGGC-TTTTTCTACACATTT
** * * * ** **
1847 CCCAAGGTAAACATTCAATTATAGTCTATTTTAACCAAAAAAAT
128 CTTAAGGCAAGCATTCAATTATAGTCTGTTTTAATGAAAAATGT
1891 -AAAAAATTCAACTTAAAATCAATTATGAGATTATAAAA
1 AAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAA
Statistics
Matches: 611, Mismatches: 96, Indels: 34
0.82 0.13 0.05
Matches are distributed among these distances:
170 134 0.22
171 234 0.38
172 116 0.19
173 125 0.20
174 2 0.00
ACGTcount: A:0.41, C:0.11, G:0.14, T:0.34
Consensus pattern (171 bp):
AAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTT
TGAAGGAATAGGAGACTATAAATAGACTTTTCTTGTCAATAAATGGCTTTTTCTACACATTTCTT
AAGGCAAGCATTCAATTATAGTCTGTTTTAATGAAAAATGT
Done.