Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018399497.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_2758.0, 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: 7856
ACGTcount: A:0.19, C:0.06, G:0.07, T:0.18
Warning! 3907 characters in sequence are not A, C, G, or T
Found at i:1960 original size:171 final size:162
Alignment explanation
Indices: 1761--2259 Score: 314
Period size: 171 Copynumber: 3.0 Consensus size: 162
1751 CAATTATTAC
* * * **
1761 ATTATAAACCTATTTAAAGCGGGTAATAAGGGTTTTAAAGGAAT-GAGTGACTATAAAT-AANNN
1 ATTATAAACCTATTTAAACCGAGTAATAAGGCTTTTAAAGGAATGGA-TGACTATAAATGAA-CT
******* * * * **
1824 NNNNNNNTCAATGAA-TGGCTTTTTTTGCACGTTTCCTAAGGTGGACATTCAATTATAGTCTGTT
64 TTTCTTCTCAATGAACAGGCTTTTTTTGCACATTTCCCAAGGCAGACATTCAATTATAGTCTGTT
1888 TTAATAAAAAATATAAAAAAATTCAACTTANNNNNNNNNNTGAG
129 TTAATAAAAAATATAAAAAAATTCAACTTA----------TGAG
* * * *
1932 ATTATAAAACC-ATTTAAACCGAGTAATAAGGCTTTTGAATGAATGGATGGCTATAAATGGACTT
1 ATTAT-AAACCTATTTAAACCGAGTAATAAGGCTTTTAAAGGAATGGATGACTATAAATGAACTT
*
1996 TTCTTCTCAATGAACAGGCTTTTTTTGCACATTTCCCAAGGCAGATATTCAATTATAGTCTGTTT
65 TTCTTCTCAATGAACAGGCTTTTTTTGCACATTTCCCAAGGCAGACATTCAATTATAGTCTGTTT
*
2061 TAATAAAAAATATAAAAANNNNNNNNNNAAATCAA-TTATGAG
130 TAATAAAAAATATAAAAA----------AATTCAACTTATGAG
* * * * * * * * *
2103 ATTATAAAACTATTGAAAGCGGGTGACAAGCCTTTTGAAGGAAT-GAGTAACTATAAAT-AGACT
1 ATTATAAACCTATTTAAACCGAGTAATAAGGCTTTTAAAGGAATGGA-TGACTATAAATGA-ACT
* * * * ** * * *
2166 TTTTTTCTCAATGAA-TGGTTTTTTTTACACATTTCTTAAGGTAGATAATCAATTATAGTCTGTT
64 TTTCTTCTCAATGAACAGGCTTTTTTTGCACATTTCCCAAGGCAGACATTCAATTATAGTCTGTT
* *
2230 TTAACAAAAAATGTAAACAAAA-TCAACTTA
129 TTAATAAAAAATATAAA-AAAATTCAACTTA
2260 AAATCANNNN
Statistics
Matches: 265, Mismatches: 44, Indels: 48
0.74 0.12 0.13
Matches are distributed among these distances:
160 4 0.02
161 5 0.02
170 63 0.24
171 114 0.43
172 70 0.26
181 3 0.01
182 6 0.02
ACGTcount: A:0.36, C:0.11, G:0.14, T:0.33
Consensus pattern (162 bp):
ATTATAAACCTATTTAAACCGAGTAATAAGGCTTTTAAAGGAATGGATGACTATAAATGAACTTT
TCTTCTCAATGAACAGGCTTTTTTTGCACATTTCCCAAGGCAGACATTCAATTATAGTCTGTTTT
AATAAAAAATATAAAAAAATTCAACTTATGAG
Found at i:3638 original size:172 final size:170
Alignment explanation
Indices: 3169--3680 Score: 570
Period size: 171 Copynumber: 3.0 Consensus size: 170
3159 NNNNNNNNNN
* * * *
3169 AAATCAATTATGAGATTATAACACTATTTAAAGCGAGTAATAAGCCTTTTGAAGAAATGGATGAC
1 AAATGAATTATGAGATTATAAAACTATTTAAAGCAAGTAATAAGCCTTTTGAAGGAATGG-TGAC
* * * ** * *
3234 TCTAAGTGAACTTTTCTGATAAATCAATGGC-TTTTTCTATACGTTT-TTTAAGATAGACATTCA
65 TATAAATGGACTTTTCTTCTCAATCAATGGCTTTTTTCTATACGTTTCTCTAAGATAGACATTCA
* * *
3297 ATTATTGTCTGTTTTAAAGAAATATGTAAAACAATTTAACTTA
130 ATTATTGTCTGTTTTAAA-AAA-ATATAAAAAAATTCAACTTA
* ** * *
3340 AAATCG-ATTATGAGATTATAAAACTATTTAAAGCATGTAATAAGGGTTTTGAGGGAATAAGTGA
1 AAAT-GAATTATGAGATTATAAAACTATTTAAAGCAAGTAATAAGCCTTTTGAAGGAAT-GGTGA
* * * * *
3404 CTATAAATGGACTTTTCTTCTCAATCAATGGTTTTTTTTGTATA--TTTC-CTGAGGTGGACATT
64 CTATAAATGGACTTTTCTTCTCAATCAATGG-CTTTTTTCTATACGTTTCTCTAAGATAGACATT
*
3466 CAATTATAGTCTGTTTTAATCAAAAATATAAAAAAAATTCAACTTA
128 CAATTATTGTCTGTTTTAA--AAAAATAT-AAAAAAATTCAACTTA
* * *
3512 AAATGAATTATAAGATTATAAAACTATTTAAAGCAAGTAATAATCCCTTTGAAGGAATGGTGACT
1 AAATGAATTATGAGATTATAAAACTATTTAAAGCAAGTAATAAGCCTTTTGAAGGAATGGTGACT
* *
3577 ATAAATGGACTTTTCTTCTCAATCAATGGCTTTTTTCTACACGTTTCTCT-AGTTAGACATTCAA
66 ATAAATGGACTTTTCTTCTCAATCAATGGCTTTTTTCTATACGTTTCTCTAAGATAGACATTCAA
** * *
3641 TTATTGTCAATTTTAAAGAAAAATCTTAAAAAATTCAACT
131 TTATTGTCTGTTTT-AA-AAAAATATAAAAAAATTCAACT
3681 NNNNNNNNNN
Statistics
Matches: 284, Mismatches: 44, Indels: 26
0.80 0.12 0.07
Matches are distributed among these distances:
170 9 0.03
171 160 0.56
172 101 0.36
173 14 0.05
ACGTcount: A:0.38, C:0.12, G:0.13, T:0.37
Consensus pattern (170 bp):
AAATGAATTATGAGATTATAAAACTATTTAAAGCAAGTAATAAGCCTTTTGAAGGAATGGTGACT
ATAAATGGACTTTTCTTCTCAATCAATGGCTTTTTTCTATACGTTTCTCTAAGATAGACATTCAA
TTATTGTCTGTTTTAAAAAAATATAAAAAAATTCAACTTA
Done.