Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018398915.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_2197.0, 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, 713
Length: 1189
ACGTcount: A:0.23, C:0.08, G:0.10, T:0.22
Warning! 446 characters in sequence are not A, C, G, or T
Found at i:324 original size:172 final size:161
Alignment explanation
Indices: 196--508 Score: 141
Period size: 171 Copynumber: 1.9 Consensus size: 161
186 NNNNNNNNNN
* * * * ** * *
196 AAAATTGAAATTTAAATCAATTTTGAG-ATTATAAAACCATTTAAAGTGAGTATTAAGTCTTTTG
1 AAAATTCAAATTTAAATAAATTATG-GCATTAAAAAACCATTTAAAGCAAGTAATAAGGCTTTTG
* * * * * *
260 AAGGAAT-GGATGTCTATAAATGGATTTTTCTTAG-CAATGACTGCCTTTTTCTTTACAT-TTCT
65 AAGGAATAGG-TGACCATAAATGGACTTTTCTT-GTCAATGAATGCATTTGTC-TT-CATATTCT
** *
322 CAAGATAGACATTCAATTATAGTCTATTTTAACAGAAAATTTAA
126 CAAGATAGACATTCAAACATAGTCTATTTTAAC--------CAA
* * * * * * * *
366 AACAATTCAACTTAAAATCAATTATGGTATTAGAAAACCATGTAAAGCGAGCAATAAGGCTTTTG
1 AA-AATTCAAATTTAAATAAATTATGGCATTAAAAAACCATTTAAAGCAAGTAATAAGGCTTTTG
* * * * * * * *
431 AAGGTAT-GAGTGACTATAAATGGGCTTCTCTTGCCAATGAATGCTTTTTTCTTCATGTTTCTCA
65 AAGGAATAG-GTGACCATAAATGGACTTTTCTTGTCAATGAATGCATTTGTCTTCAT-ATTCTCA
*
495 AGGTAGACATTCAA
128 AGATAGACATTCAA
509 NNNNNNNNNN
Statistics
Matches: 119, Mismatches: 18, Indels: 11
0.80 0.12 0.07
Matches are distributed among these distances:
169 3 0.03
170 6 0.05
171 109 0.92
172 1 0.01
ACGTcount: A:0.36, C:0.13, G:0.15, T:0.36
Consensus pattern (161 bp):
AAAATTCAAATTTAAATAAATTATGGCATTAAAAAACCATTTAAAGCAAGTAATAAGGCTTTTGA
AGGAATAGGTGACCATAAATGGACTTTTCTTGTCAATGAATGCATTTGTCTTCATATTCTCAAGA
TAGACATTCAAACATAGTCTATTTTAACCAA
Found at i:482 original size:171 final size:169
Alignment explanation
Indices: 13--508 Score: 462
Period size: 172 Copynumber: 2.9 Consensus size: 169
3 TGTTTAAATC
* * *
13 AAAAATGTAGAAAAATTCAACTTTAAATAAATTATGGCATTAAAAAACCATTTAAAGCAAGTAAT
1 AAAAATTTA-AAAAATTCAACTTTAAATCAATTATGG-ATTAAAAAACCATTTAAAGCGAGTAAT
* * *
78 ATGGCTTTTGAAGGTAT-AGGTGACCATAAATGGACTTTTCTTGTCAATGAATGCATTTGTC-TT
64 AAGGCTTTTGAAGGTATGA-GTGACTATAAATGGACTTTTCTTG-CAATGAATGCATTTTTCTTT
*
141 -CATGATTCTCAAGGTAGACATTCAAACCTAGTCTATTTTAACCA
127 ACAT--TTCTCAAGGTAGACATTCAAACATAGTCTATTTTAACCA
********* * * * * * *
185 ANNNNNNNNNNAAAATTGAAATTTAAATCAATTTTGAGATTATAAAACCATTTAAAGTGAGTATT
1 A-AAAATTTAAAAAATTCAACTTTAAATCAATTATG-GATTAAAAAACCATTTAAAGCGAGTAAT
* * * * * *
250 AAGTCTTTTGAAGGAATG-GATGTCTATAAATGGATTTTTCTTAGCAATGACTGCCTTTTTCTTT
64 AAGGCTTTTGAAGGTATGAG-TGACTATAAATGGACTTTTCTT-GCAATGAATGCATTTTTCTTT
* **
314 ACATTTCTCAAGATAGACATTCAATTATAGTCTATTTTAA-CA
127 ACATTTCTCAAGGTAGACATTCAAACATAGTCTATTTTAACCA
* * * * *
356 GAAAATTTAAAACAATTCAACTTAAAATCAATTATGGTATTAGAAAACCATGTAAAGCGAGCAAT
1 AAAAATTTAAAA-AATTCAACTTTAAATCAATTATGG-ATTAAAAAACCATTTAAAGCGAGTAAT
* * * *
421 AAGGCTTTTGAAGGTATGAGTGACTATAAATGGGCTTCTCTTGCCAATGAATGCTTTTTTCTTCA
64 AAGGCTTTTGAAGGTATGAGTGACTATAAATGGACTTTTCTTG-CAATGAATGCATTTTTCTTTA
**
486 TGTTTCTCAAGGTAGACATTCAA
128 CATTTCTCAAGGTAGACATTCAA
509 NNNNNNNNNN
Statistics
Matches: 252, Mismatches: 61, Indels: 23
0.75 0.18 0.07
Matches are distributed among these distances:
170 4 0.02
171 116 0.46
172 125 0.50
173 4 0.02
174 3 0.01
ACGTcount: A:0.36, C:0.13, G:0.15, T:0.34
Consensus pattern (169 bp):
AAAAATTTAAAAAATTCAACTTTAAATCAATTATGGATTAAAAAACCATTTAAAGCGAGTAATAA
GGCTTTTGAAGGTATGAGTGACTATAAATGGACTTTTCTTGCAATGAATGCATTTTTCTTTACAT
TTCTCAAGGTAGACATTCAAACATAGTCTATTTTAACCA
Done.