Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018400121.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_3338.0, 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, 980
Length: 1634
ACGTcount: A:0.30, C:0.08, G:0.10, T:0.27
Warning! 417 characters in sequence are not A, C, G, or T
Found at i:335 original size:171 final size:169
Alignment explanation
Indices: 1--446 Score: 462
Period size: 171 Copynumber: 2.6 Consensus size: 169
* * * * * *
1 ATGAATGCTTTTTTCTTTATGTTTCTCGAGGTAAAGATTCAATTATATTCTGTTTTAATTAAAAA
1 ATGAATGCCTTTTTCTTCATGTTTCTTGAGGTAAACATTCAATTATAGTCTGTTTTAATGAAAAA
* * * * **
66 TCTTAAAATATTCAACTTAAAACAAATTATAAGATTATAAAACTATTTAAAGCCAGTACTAAGGC
66 T-ATAAAAAATTCAACTTAAAATAAATTATGAGATTAT-AAACTATTTAAAAACAGTACTAAGGC
* * * * **
131 TTTTGAAGGAATGAGTGACTATGAATGGACTTTTTTTTGTCA
129 TTTTGAACGAATGAGTGACTATAAATAGAC-TTTTCTTCCCA
* * * * * *
173 ATGAACGCCTTTTTCTTCATGTTTCTTGAGATAAATATTGAATTATAGTGTATTTTAATGAAAAA
1 ATGAATGCCTTTTTCTTCATGTTTCTTGAGGTAAACATTCAATTATAGTCTGTTTTAATGAAAAA
* * * * * * * *
238 TGTAAAAAAATCAATTTAAAATTAATTATGAGATTATAAAGTAATTTAAAAAGAGTAGTAGGGCT
66 TATAAAAAATTCAACTTAAAATAAATTATGAGATTATAAACT-ATTTAAAAACAGTACTAAGGCT
* * *
303 TTTGACCGAATGGGTGATTATAAATAGACTTTTCTTCCCA
130 TTTGAACGAATGAGTGACTATAAATAGACTTTTCTTCCCA
* * * *
343 ATGAATGCCTTTTTCTGCATGTTTCTT-ATGGCAGACATTCAATTATAGTTTGTTTTAATGAAAA
1 ATGAATGCCTTTTTCTTCATGTTTCTTGA-GGTAAACATTCAATTATAGTCTGTTTTAATGAAAA
* *
407 ATATAGAAAAATTCAACCTAAAATCAATTATGAGATTATA
65 ATATA-AAAAATTCAACTTAAAATAAATTATGAGATTATA
447 GANNNNNNNN
Statistics
Matches: 224, Mismatches: 47, Indels: 7
0.81 0.17 0.03
Matches are distributed among these distances:
169 1 0.00
170 69 0.31
171 99 0.44
172 55 0.25
ACGTcount: A:0.37, C:0.10, G:0.14, T:0.39
Consensus pattern (169 bp):
ATGAATGCCTTTTTCTTCATGTTTCTTGAGGTAAACATTCAATTATAGTCTGTTTTAATGAAAAA
TATAAAAAATTCAACTTAAAATAAATTATGAGATTATAAACTATTTAAAAACAGTACTAAGGCTT
TTGAACGAATGAGTGACTATAAATAGACTTTTCTTCCCA
Found at i:1005 original size:171 final size:165
Alignment explanation
Indices: 694--1215 Score: 612
Period size: 171 Copynumber: 3.1 Consensus size: 165
684 NNNNNNNNNN
* * * ** *
694 AAAACAATTTAAAGCAAGTAATAAAGCTTTTGAAGGAATAAGAGACTATAAATTAACTTTTCTCG
1 AAAACAATTTAAAGCGAGTAATAAGGCTCTTGAAGGAATAAGAGACTATAAATGGACTTTTCTTG
* * ** * * *
759 CAAATGAATGCCTTTTTCTTCACTTTTCTTAAAGC-AGATGTTCAATTATAGTCAATTGAAACAA
66 CCAATGAATG-CTTTTT-TTCA-TTTTCTT--AGCTAAACATTCATTTATAGTCTATTTAAACAA
**
823 AAAATGTGAAAAAATTCAACTTAAAATTTATAATGAGATTAT
126 AAAA-GTGAAAAAATTCAACTTAAAATCAAT-ATGAGATTAT
*
865 AAAATAATTTAAAGCGAGTAATAAGGCTCTTGAAGGAATAAGAGACTATAAATGGACTTTTCTTG
1 AAAACAATTTAAAGCGAGTAATAAGGCTCTTGAAGGAATAAGAGACTATAAATGGACTTTTCTTG
*
930 CCAATGAATGCTTGTTTATTCATATTTCTTGAGCTAAACATTCATTTATAGTCTATTTTAACTAA
66 CCAATGAATGCTT-TTT-TTCAT-TTTCTT-AGCTAAACATTCATTTATAGTCTATTTAAAC-AA
995 AAAAGTGAAAAAATTCAACTTAAAATCAACTATGAGATTAT
126 AAAAGTGAAAAAATTCAACTTAAAATCAA-TATGAGATTAT
* * *
1036 AAAACAATTTAAAGCGACTAATAAGGC-CTTTGAAGGAATATGGGACTATAAATGGACTTTTCTT
1 AAAACAATTTAAAGCGAGTAATAAGGCTC-TTGAAGGAATAAGAGACTATAAATGGACTTTTCTT
* * *
1100 ACCAATGAATGC----TTT--TTTT-TTAGGTAAACATTCATTTATAGTCTATTTGAACAAAAAA
65 GCCAATGAATGCTTTTTTTCATTTTCTTAGCTAAACATTCATTTATAGTCTATTTAAAC-AAAAA
*
1158 AGTGAAAAAATTCAACTCAAAATCAATTATGAGATTAT
129 AGTGAAAAAATTCAACTTAAAATCAA-TATGAGATTAT
*
1196 AAAACGATTTAAAGCGAGTA
1 AAAACAATTTAAAGCGAGTA
1216 NNNNNNNNNN
Statistics
Matches: 314, Mismatches: 31, Indels: 23
0.85 0.08 0.06
Matches are distributed among these distances:
160 88 0.28
161 2 0.01
162 3 0.01
163 1 0.00
165 2 0.01
166 1 0.00
170 8 0.03
171 202 0.64
172 7 0.02
ACGTcount: A:0.42, C:0.12, G:0.13, T:0.33
Consensus pattern (165 bp):
AAAACAATTTAAAGCGAGTAATAAGGCTCTTGAAGGAATAAGAGACTATAAATGGACTTTTCTTG
CCAATGAATGCTTTTTTTCATTTTCTTAGCTAAACATTCATTTATAGTCTATTTAAACAAAAAAG
TGAAAAAATTCAACTTAAAATCAATATGAGATTAT
Done.