Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018402614.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_5685.0, 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, 813
Length: 1355
ACGTcount: A:0.30, C:0.12, G:0.11, T:0.30
Warning! 231 characters in sequence are not A, C, G, or T
Found at i:1111 original size:171 final size:171
Alignment explanation
Indices: 470--1354 Score: 771
Period size: 170 Copynumber: 5.2 Consensus size: 171
460 ATTCTTCAGT
* * * * * ** * *
470 CATTTTTAGTTAAAACAGACTAGAATTGAATGCCTCCCATAAGAAACATGAAGAAAAA-ATCATT
1 CATTTTTAGTTAAAAAAGACTATAATTGAATTCCTGCCTTGGGAAACGTGAAGAAAAAGGT-ATT
* * * * * * *
534 CATTGGCAAGCAAAGTCTATTCATAGTCACCCGTACC-TTCAAAAGCCTCATTACTCACTTTAAA
65 CATTGGCAAGAAAAGTCCATTTATAGTCACTCATTCCTTTCAAAAGCCTTATTACTCACTTTAAA
**
598 TGGTTTTATAATGC-CCTAATTGATTTTAAGTTGAATTTTTTA
130 TGGTTTTATAAT-CTCAAAATTGATTTTAAGTTGAATTTTTTA
* * * * * *** *
640 TATTTTTAGTTAAAACAGATTATAATAGAATGT-CTACCTCAAGAAACGTGAAGAAACAA-GAAT
1 CATTTTTAGTTAAAAAAGACTATAATTGAAT-TCCTGCCTTGGGAAACGTGAAGAAA-AAGGTAT
* * *
703 TCAATGAG-AAGAAAAGTCCATTTATAGCCACGCATT-CTTTCAAAAGCCTTATTACTCACTTTA
64 TCATTG-GCAAGAAAAGTCCATTTATAGTCACTCATTCCTTTCAAAAGCCTTATTACTCACTTTA
* * *
766 AATGGTTTTATAACCTCATAATTGATTTT-AGATTGATTTTTTTA
128 AATGGTTTTATAATCTCAAAATTGATTTTAAG-TTGAATTTTTTA
* * * * * * *
810 -ATGTTTTTGGTTAGAACAGATTATAATTGAATGT-TTGACTTGGGAAATGTGAAGAAAAAGGTA
1 CA--TTTTTAGTTAAAAAAGACTATAATTGAAT-TCCTGCCTTGGGAAACGTGAAGAAAAAGGTA
* ** ** **
873 TTCATTGGCAAGAAAA-TCCATTTCTAGTTGCTCAAGCC-TTCAAAAGCCTTATTACTCTTTTTA
63 TTCATTGGCAAGAAAAGTCCATTTATAGTCACTCATTCCTTTCAAAAGCCTTATTACTCACTTTA
*
936 AATGGCTTTATAATCTCAAAATTGATTTTAAGTTGAAATTTTTTA
128 AATGGTTTTATAATCTCAAAATTGATTTTAAGTTG-AATTTTTTA
* * * * * ** **
981 CATTTTTGGTTAAAAAA-AGCTATAATTGAATTCCTGCCCTGGGGAACGTAAAGCAAAAGCCAAC
1 CATTTTTAGTTAAAAAAGA-CTATAATTGAATTCCTGCCTTGGGAAACGTGAAGAAAAAGGTATT
*
1045 CTTTGGCACA-AAAAGTCCATTTATAGTCACTCATTCCTTT-AAAAGCCTTATTACTCACTTTAA
65 CATTGGCA-AGAAAAGTCCATTTATAGTCACTCATTCCTTTCAAAAGCCTTATTACTCACTTTAA
* * * **
1108 ATGGTTTTGTAATCTCAAAATTGATTTAAATTTGAATTCTTCAA
129 ATGGTTTTATAATCTCAAAATTGATTTTAAGTTGAATT-TTTTA
** * * * ** *
1152 TCATTTTTAGTTAAAGTAGACTAGAATTGAATGCCTACCTTGAAAAACATGAAGAAAAAGGTATT
1 -CATTTTTAGTTAAAAAAGACTATAATTGAATTCCTGCCTTGGGAAACGTGAAGAAAAAGGTATT
* * * *
1217 CATTGGCAAGAAAAGTCTATTTATAGTCACCCA-TACTTTCAAAAGCCTCATTACTCACTTTAAA
65 CATTGGCAAGAAAAGTCCATTTATAGTCACTCATTCCTTTCAAAAGCCTTATTACTCACTTTAAA
* **
1281 TAGTTTTATAATGC-CGTAATTGATTTTAAGTT-AATTTTTTTTA
130 TGGTTTTATAAT-CTCAAAATTGATTTTAAGTTGAA--TTTTTTA
* *
1324 CATTTTTAGTTAAAATAGACTACAATTGAAT
1 CATTTTTAGTTAAAAAAGACTATAATTGAAT
1355 G
Statistics
Matches: 580, Mismatches: 108, Indels: 53
0.78 0.15 0.07
Matches are distributed among these distances:
169 7 0.01
170 261 0.45
171 182 0.31
172 126 0.22
173 4 0.01
ACGTcount: A:0.36, C:0.15, G:0.13, T:0.36
Consensus pattern (171 bp):
CATTTTTAGTTAAAAAAGACTATAATTGAATTCCTGCCTTGGGAAACGTGAAGAAAAAGGTATTC
ATTGGCAAGAAAAGTCCATTTATAGTCACTCATTCCTTTCAAAAGCCTTATTACTCACTTTAAAT
GGTTTTATAATCTCAAAATTGATTTTAAGTTGAATTTTTTA
Done.