Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018400039.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_326.0, 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: 1702
ACGTcount: A:0.31, C:0.11, G:0.12, T:0.32
Warning! 248 characters in sequence are not A, C, G, or T
Found at i:866 original size:172 final size:169
Alignment explanation
Indices: 371--1239 Score: 466
Period size: 171 Copynumber: 5.1 Consensus size: 169
361 NNNNNNNNNN
* * * * * * * * **
371 AGCCTTATTGCTCGCTTTAAATAGTTTTATAATGTCATAATTGATTTTAAGTTGTATTCTTTTAC
1 AGCCTTATTACTCGCTTTAAATGGTTTTACAATCTCAAAATTAATTTAAATTTAAATT-TTTTAC
* * * * * * *
436 ATTTTTTGTTAAAACAGATTGTAATTGAATGTCTACCTCAAGAAACATGAAGAAAAGGATATTCA
65 ATTTTTGGTTAAAACAGATTATAATTGAATGTCTACCT-TAGGAACGTGAAGAAAAAGACATTCA
* **********
501 TTAGTAAGAAAAGTCCATTTNNNNNNNNNNATTCCTTCAAA
129 TTGGTAAGAAAAGTCCATTTATAATCACCCATTCCTTCAAA
* * * * * * *
542 AGCCTTATTACTCGCTATAAAAGATTTTACAATCTCATAATTGAATTTAAGTTGAAGTTTTTTAC
1 AGCCTTATTACTCGCTTTAAATGGTTTTACAATCTCAAAATT-AATTTAAATTTAAATTTTTTAC
********** * * * *
607 ATTTTTGGTTAANNNNNNNNNNAATTGAATGTTTACCTT-GAGAAAGATCAAGAAAAAGGCATTC
65 ATTTTTGGTTAAAACAGATTATAATTGAATGTCTACCTTAG-GAACG-TGAAGAAAAAGACATTC
** *
671 ATTGGTAAGAAATA-TTTATTTATAATCACCCATTGCTTCAAA
128 ATTGGTAAGAAA-AGTCCATTTATAATCACCCATTCCTTCAAA
*
713 AGCCTTATTGCTCGCTTTAAATGGTTTTACAATCTCAAAATTAATTTTAAATTTAAATTTATTTA
1 AGCCTTATTACTCGCTTTAAATGGTTTTACAATCTCAAAATTAA-TTTAAATTTAAATTT-TTTA
* *
778 CATTTTTAGTTAAAACAGATTATAATTGAATGTCTAGCTTAGGACACGTGAAGAAAAAGACATTC
64 CATTTTTGGTTAAAACAGATTATAATTGAATGTCTACCTTAGGA-ACGTGAAGAAAAAGACATTC
* * * **********
843 GTTGGAAAGAAAAGTCCATTTATAGTCACNNNNNNNNNNAAA
128 ATTGGTAAGAAAAGTCCATTTATAATCACCCATTCCTTCAAA
* * * * * * *
885 AGCCTTATTACTCACTTTAAGTGGTTGTATAATCTCAAAATTGATTTAAATTTGAATTTATTACA
1 AGCCTTATTACTCGCTTTAAATGGTTTTACAATCTCAAAATTAATTTAAATTTAAATTT-TT-TA
* * * * * * * * * *
950 CATTTTTGGATAAAATAGATTATAATTGAATGCCAACCTCATGAAACGTAAAGAACAAGCCTTTC
64 CATTTTTGGTTAAAACAGATTATAATTGAATGTCTACCTTA-GGAACGTGAAGAAAAAGACATTC
* ** * * *********
1015 ATTGGCAAGAAAAGTCTGTTTATAGTTANNNNNNNNNNT-AAA
128 ATTGGTAAGAAAAGTCCATTTATAATCA-CCCATTCCTTCAAA
** * * * * * * ** * *
1057 AGCCTTATTACTCATTTTAAATGATTTTATAATCTCATATTTGATTTTAGGTTGAATTTTTTGAT
1 AGCCTTATTACTCGCTTTAAATGGTTTTACAATCTCAAAATTAATTTAAATTTAAATTTTTT-AC
* * * * * * * *
1122 GTTTTTGGTTAAAACATATTATAATTGAATATTTGCCTTGGGAAACCTGAAGAAAAAGATATTCA
65 ATTTTTGGTTAAAACAGATTATAATTGAATGTCTACCTTAGG-AACGTGAAGAAAAAGACATTCA
* * * * *
1187 TTGGCAAGAAGAGTCCATTTATAGTCACCCATTTCTTCAAT
129 TTGGTAAGAAAAGTCCATTTATAATCACCCATTCCTTCAAA
1228 AGCCTTATTACT
1 AGCCTTATTACT
1240 TACNNNNNNN
Statistics
Matches: 525, Mismatches: 158, Indels: 30
0.74 0.22 0.04
Matches are distributed among these distances:
169 1 0.00
170 6 0.01
171 258 0.49
172 247 0.47
173 13 0.02
ACGTcount: A:0.34, C:0.12, G:0.13, T:0.36
Consensus pattern (169 bp):
AGCCTTATTACTCGCTTTAAATGGTTTTACAATCTCAAAATTAATTTAAATTTAAATTTTTTACA
TTTTTGGTTAAAACAGATTATAATTGAATGTCTACCTTAGGAACGTGAAGAAAAAGACATTCATT
GGTAAGAAAAGTCCATTTATAATCACCCATTCCTTCAAA
Done.