Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018399194.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_2463.0, 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: 3898
ACGTcount: A:0.23, C:0.09, G:0.08, T:0.25
Warning! 1364 characters in sequence are not A, C, G, or T
Found at i:3328 original size:173 final size:171
Alignment explanation
Indices: 2592--3328 Score: 538
Period size: 172 Copynumber: 4.3 Consensus size: 171
2582 AGAAAACCCT
* * * * * * *
2592 ATTTATAGTCTCTCATT-ATTTCAAAAGCCTTATTCCTCGCTTTAAAT-AGTTTTATATTCTCAT
1 ATTTATAGTCACTTATTCCTTTCAAAAGCCTTATTACTCACTTTAAATGA-TTTTATAATCTCAA
* * * *
2655 AATTGAATTTAAGTTGAATTTTTTTTATATTTTTAGTTAAAACAGACCATAATTGAATGTCTATC
65 AATTGATTTTATGTTCAA-TTTTTTTA-ATTTTTAGTTAAAACAGACCATAATTGAATGTCTACC
* * * * *
2720 T-TATGAAACGTGAAAAAACAAGCATTTATTAGTAAGAAAAGTCC
128 TCGA-GAAACGTGAAAAAAAAAGCATTCATTGGCAAGAAAAGTCC
* * * *
2764 ATTTATAGTCACCTATTCCTTT-AAAAGCCTCATTACCCA-TATTAAATGATTTTATTATCTCAA
1 ATTTATAGTCACTTATTCCTTTCAAAAGCCTTATTACTCACT-TTAAATGATTTTATAATCTCAA
********* * * * *
2827 AATTGATTTTATGTTCAATTATTNNNNNNNNNNTAATTAAGATAAACCATAATTGAATGTCTACC
65 AATTGATTTTATGTTCAATT-TT-TTTAATTTTTAGTTAAAACAGACCATAATTGAATGTCTACC
* *
2892 TCGAGAAACGTGAATAAAAAAGCATTCATTGACAAGAAAAGTCC
128 TCGAGAAACGTGAAAAAAAAAGCATTCATTGGCAAGAAAAGTCC
* * * *
2936 ATTTATAGTCTCATATTCCTTT-AAAAGCCTTATTACTCAATTTAAATGATTTTATTATCTCAAA
1 ATTTATAGTCACTTATTCCTTTCAAAAGCCTTATTACTCACTTTAAATGATTTTATAATCTCAAA
********** * * * *
3000 ATTGATTTTATGNNNNNNNNNNTTAATATTTTTGATTAAAACAGACTATAATTGAATGACCACCT
66 ATTGATTTTATGTTCAATTTTTTTAAT-TTTTAG-TTAAAACAGACCATAATTGAATGTCTACCT
* * * *
3065 CGAGAAACATGAAGAGAACAAACCATTCATTGGTAAGAAAAGTCC
129 CGAGAAACGTGAA-A-AAAAAAGCATTCATTGGCAAGAAAAGTCC
* * * ********** * * *
3110 ATTTATAGTCTCTCATTTC-TTCANNNNNNNNNNTACTCGCTTTAAATGAATTTATAATCTCATA
1 ATTTATAGTCACTTATTCCTTTCAAAAGCCTTATTACTCACTTTAAATGATTTTATAATCTCAAA
* * * * ** *
3174 ATTGATTTTAGGTTTAATTTTTTTACCTTATTAGTTAAAACAGATTATAATTGAATGTGTACCTC
66 ATTGATTTTATGTTCAATTTTTTTA-ATTTTTAGTTAAAACAGACCATAATTGAATGTCTACCTC
* *
3239 GAGAAACGTGAAAAAAAAAAGACATTTACTGGCAAGAAAAGTCC
130 GAGAAACGTG-AAAAAAAAAG-CATTCATTGGCAAGAAAAGTCC
3283 ATTTAT-GTTCACTTATT-CTTTCAAAAGCCTTATTACTCACTTTAAA
1 ATTTATAG-TCACTTATTCCTTTCAAAAGCCTTATTACTCACTTTAAA
3329 GNNNNNNNNN
Statistics
Matches: 423, Mismatches: 125, Indels: 33
0.73 0.22 0.06
Matches are distributed among these distances:
170 1 0.00
171 4 0.01
172 236 0.56
173 93 0.22
174 88 0.21
175 1 0.00
ACGTcount: A:0.35, C:0.14, G:0.10, T:0.37
Consensus pattern (171 bp):
ATTTATAGTCACTTATTCCTTTCAAAAGCCTTATTACTCACTTTAAATGATTTTATAATCTCAAA
ATTGATTTTATGTTCAATTTTTTTAATTTTTAGTTAAAACAGACCATAATTGAATGTCTACCTCG
AGAAACGTGAAAAAAAAAGCATTCATTGGCAAGAAAAGTCC
Done.