Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018402936.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_5982.0, 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, 834
Length: 1390
ACGTcount: A:0.33, C:0.13, G:0.11, T:0.37
Warning! 94 characters in sequence are not A, C, G, or T
Found at i:321 original size:171 final size:171
Alignment explanation
Indices: 1--1103 Score: 599
Period size: 171 Copynumber: 6.5 Consensus size: 171
* * * * * * * *
1 ATTTTAAGTTAAATTTTTTTACATTTTT-ATTTAAAACAGACAATAATTGATTGTCTATCTCGAA
1 ATTTTAAGTTGAATTATTTTATATTTTTGA-TTAAAATAGATAATAATTGAATGTCTACCTCGAG
* * * * * * * * *******
65 AAACATGAAGACAAAAGCATTCATTGACAAGAAATGTCCATTTATAGTCACCTATTCCNNNNNNN
65 AAACGTAAAGAAAAAAGCATTCAATGATAAGAAAAGTTCATTTATAGTCACCCATTCCTTCAAAA
*** * *
130 NNNTTATTACTCACTTTAAATGGTTTTATAATCTAATAATTC
130 GCCTTATTACTCACTTTAAATGGTTTTATAATCTCATAATTG
* * * * *
172 ATTTTAAGTTGAATTATTTTATATTTTTGATTGAAATAGATAATAATTTACTGTCTATCTTGAGA
1 ATTTTAAGTTGAATTATTTTATATTTTTGATTAAAATAGATAATAATTGAATGTCTACCTCGAGA
* * *
237 AACGTAAAGAAAAAAGTATTCAATGGTAAGAAAAGTTCATTTATAGTCACTCATTCCTTCAAAAG
66 AACGTAAAGAAAAAAGCATTCAATGATAAGAAAAGTTCATTTATAGTCACCCATTCCTTCAAAAG
* * * *
302 CCTTATTAATCTCTTTAAATGATTTTCTAATCTCATAATTG
131 CCTTATTACTCACTTTAAATGGTTTTATAATCTCATAATTG
********* * * * * *
343 ATTTT-AGNNNNNNNNNNTTTACATTTTTGATTAAAACAGATTATAATTGAATATTTACCTCGAG
1 ATTTTAAG-TTGAATTATTTTATATTTTTGATTAAAATAGATAATAATTGAATGTCTACCTCGAG
* * * * * *
407 AAACGTGAAGACAAAAGCATTCATTCACAA-AAAAGTCCATTTATAGTCACCCATTCCTTCAAAA
65 AAACGTAAAGAAAAAAGCATTCAATGATAAGAAAAGTTCATTTATAGTCACCCATTCCTTCAAAA
* ********** *
471 GCCTTATTAATCNNNNNNNNNNGTTTTCTAATCTCATAATTG
130 GCCTTATTACTCACTTTAAATGGTTTTATAATCTCATAATTG
** * * * ********** * *
513 ATTTTGGGTTGAGTTGTTTTAAATTTTTGATTAAANNNNNNNNNNATTGAATATTTACCTCGAGA
1 ATTTTAAGTTGAATTATTTTATATTTTTGATTAAAATAGATAATAATTGAATGTCTACCTCGAGA
* * ********** *
578 AACGTAAAGACAAAAGCATTCATTGATAAGAAAAG-TCTATTTATANNNNNNNNNNCCTTTAAAA
66 AACGTAAAGAAAAAAGCATTCAATGATAAGAAAAGTTC-ATTTATAGTCACCCATTCCTTCAAAA
* * * * *
642 GCCTTATTACTCGCTTTAAATCGTTTGATAATCTAATAATTC
130 GCCTTATTACTCACTTTAAATGGTTTTATAATCTCATAATTG
* * * * * *
684 ATTTTAACTTGAATTGTTTTATATTTTTGATTGAAATAGACAATAATTGACTGTCTATCTCGAGA
1 ATTTTAAGTTGAATTATTTTATATTTTTGATTAAAATAGATAATAATTGAATGTCTACCTCGAGA
* * ** * ** * ********
749 AACATGAAGACGAAAGAATTCAATGGCAAGAAAAGTTCATTTATAGTCACCCATTTCNNNNNNNN
66 AACGTAAAGAAAAAAGCATTCAATGATAAGAAAAGTTCATTTATAGTCACCCATTCCTTCAAAAG
** * * * *
814 NNTTATTACTCGCTTTAAATAGTTTTCTATTCTCATAATTG
131 CCTTATTACTCACTTTAAATGGTTTTATAATCTCATAATTG
* * * * * *
855 ATTTTTAGTTGAATT-TTTTTTATTTTT-ATTTAAAACAGAAAATAATTGAATGTCTATCTCTAG
1 ATTTTAAGTTGAATTATTTTATATTTTTGA-TTAAAATAGATAATAATTGAATGTCTACCTCGAG
* * * * * * * * *
918 AAATGTTAAGGAAAAAA-TATTC-ATTATCAACAAAAGTCCATTTCTAGTCGCTCATTCCTAT-A
65 AAACG-TAAAGAAAAAAGCATTCAATGAT-AAGAAAAGTTCATTTATAGTCACCCATTCCT-TCA
* * * *
980 AAAGCCTTATTACTCACTTTAGATGATTTTATAATGTCATATTTG
127 AAAGCCTTATTACTCACTTTAAATGGTTTTATAATCTCATAATTG
* * * * * *
1025 ATTCTAAGTTAAATTCA-TTTACATTTTTCAGTAAAATAGACT-ATAATTGAATGTCTACCTCAA
1 ATTTTAAGTTGAATT-ATTTTATATTTTTGATTAAAATAGA-TAATAATTGAATGTCTACCTCGA
*
1088 GAAACGTGAAGAAAAA
64 GAAACGTAAAGAAAAA
1104 CACATTNNNN
Statistics
Matches: 683, Mismatches: 235, Indels: 29
0.72 0.25 0.03
Matches are distributed among these distances:
169 3 0.00
170 256 0.37
171 420 0.61
172 4 0.01
ACGTcount: A:0.35, C:0.13, G:0.10, T:0.37
Consensus pattern (171 bp):
ATTTTAAGTTGAATTATTTTATATTTTTGATTAAAATAGATAATAATTGAATGTCTACCTCGAGA
AACGTAAAGAAAAAAGCATTCAATGATAAGAAAAGTTCATTTATAGTCACCCATTCCTTCAAAAG
CCTTATTACTCACTTTAAATGGTTTTATAATCTCATAATTG
Done.