Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018399655.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_2902.0, 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, 701
Length: 1169
ACGTcount: A:0.32, C:0.11, G:0.10, T:0.32
Warning! 166 characters in sequence are not A, C, G, or T
Found at i:446 original size:171 final size:170
Alignment explanation
Indices: 5--513 Score: 554
Period size: 172 Copynumber: 3.0 Consensus size: 170
1 TGTT
* *
5 TTTATAATCTCATAATTGATTTTAAGTTGAATTGTTTTATATTTTTTATTGAAATAGATTATAAT
1 TTTATAATCTCATAATTGATTTTAAGTTAAATT-TTTTATATTTTTTATTAAAATAGATTATAAT
* * * * * ** *
70 TTAATGTCTGCCTCGAGAAACGTGAAGAAAAAGATATCCATTGGCGAGAAAAACCCATTTATGGT
65 TGAATGTCTACCTCAAGAAACGTGAAGAAAAAGATATCGATTGGCAAGAAAAGTCCATTTATAGT
* * *
135 CA-TGCATACCTTCAAAAAGCCTTATTACTTACTTTAAATGTG
130 CACT-CATGCCTTCAAAAA-CCTTATTACTCACTTTAAATATG
* * * ** * *
177 TTTATAATCTCATAATTGATTTTAAATTTAATTTTGTTATGTTTTTGGTTAAAACAGATAATAAT
1 TTTATAATCTCATAATTGATTTTAAGTTAAATTTT-TTATATTTTTTATTAAAATAGATTATAAT
* * *
242 TGAGTGTCTACCTTAAGAAACATGAAGAAAAAGATATCGATTGGCAAGAAAAGTCCATTTATAGT
65 TGAATGTCTACCTCAAGAAACGTGAAGAAAAAGATATCGATTGGCAAGAAAAGTCCATTTATAGT
* * **
307 CACTCATGCCTTCAAAAACTTTATTACTCGCTTTAAATANN
130 CACTCATGCCTTCAAAAACCTTATTACTCACTTTAAATATG
******** * * *
348 NNNNNNNNCTTATAATTGATTTTAAGTTAAATTTTTTATATTTTTTATAAAAATAAATTATAATT
1 TTTATAATCTCATAATTGATTTTAAGTTAAATTTTTTATATTTTTTATTAAAATAGATTATAATT
* *
413 GAATGTCTACCTCAAGAAACGTAAAGAAAAAAGATATCCG-TTGGCAAGAAAAGTCTATTTATAG
66 GAATGTCTACCTCAAGAAACGTGAAG-AAAAAGATAT-CGATTGGCAAGAAAAGTCCATTTATAG
* ** *
477 TCACCCATGCCTTCGGAAGCCTTATTACTCACTTTAA
129 TCACTCATGCCTTCAAAAACCTTATTACTCACTTTAA
514 NNNNNNNNNN
Statistics
Matches: 278, Mismatches: 55, Indels: 9
0.81 0.16 0.03
Matches are distributed among these distances:
170 45 0.16
171 107 0.38
172 125 0.45
173 1 0.00
ACGTcount: A:0.36, C:0.13, G:0.12, T:0.37
Consensus pattern (170 bp):
TTTATAATCTCATAATTGATTTTAAGTTAAATTTTTTATATTTTTTATTAAAATAGATTATAATT
GAATGTCTACCTCAAGAAACGTGAAGAAAAAGATATCGATTGGCAAGAAAAGTCCATTTATAGTC
ACTCATGCCTTCAAAAACCTTATTACTCACTTTAAATATG
Found at i:920 original size:171 final size:170
Alignment explanation
Indices: 621--980 Score: 508
Period size: 171 Copynumber: 2.1 Consensus size: 170
611 NNNNNNNNNN
* * * ** *
621 AGAAAAAGATATCCATTAGCAAGAAAAGTCTATTTATGGCCGTCCATGCCTTCGAAAGCCTTATT
1 AGAAAAAGATATCCATTAGCAAAAAAAGTCCATTTATAGCCACCCATACCTTCGAAAGCCTTATT
*
686 ACTCGCTTTAAGTGATTTTATAACCTCATAATTAATTTTAAGTAAAATTTTATTATATTTTTATT
66 ACTCGCTTTAACTGATTTTATAACCTCATAATTAATTTTAAGTAAAATTTTATTATATTTTTATT
* * * *
751 AAAACAAATTATAATTAAATGTCTACTTTGAGAAACATGA
131 AAAACAAATTATAATTAAATATCTACCTCGAGAAACATAA
* *
791 AGAAAAAGATATCCATTGGCAAAAGAAAGTCCATTTATAGCCACCCATACCTTTGAAAGCCTTAT
1 AGAAAAAGATATCCATTAGCAAAA-AAAGTCCATTTATAGCCACCCATACCTTCGAAAGCCTTAT
* * *
856 TACTCGCTTTAACTGATTTTATAACTTCATAATTGATTTTAAGTTGAATATTTTA-TAT-TTTTT
65 TACTCGCTTTAACTGATTTTATAACCTCATAATTAATTTTAAG-T-AAAATTTTATTATATTTTT
* * *
919 ATTAAAACAGATTATAATTGAATATTTACCTCGAGAAACATAA
128 ATTAAAACAAATTATAATTAAATATCTACCTCGAGAAACATAA
962 AGAAAAAGATATCCATTAG
1 AGAAAAAGATATCCATTAG
981 NNNNNNNNNN
Statistics
Matches: 167, Mismatches: 20, Indels: 5
0.87 0.10 0.03
Matches are distributed among these distances:
170 22 0.13
171 133 0.80
172 4 0.02
173 8 0.05
ACGTcount: A:0.39, C:0.14, G:0.11, T:0.36
Consensus pattern (170 bp):
AGAAAAAGATATCCATTAGCAAAAAAAGTCCATTTATAGCCACCCATACCTTCGAAAGCCTTATT
ACTCGCTTTAACTGATTTTATAACCTCATAATTAATTTTAAGTAAAATTTTATTATATTTTTATT
AAAACAAATTATAATTAAATATCTACCTCGAGAAACATAA
Done.