Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018400772.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_395.0, 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: 3039
ACGTcount: A:0.24, C:0.07, G:0.09, T:0.23
Warning! 1111 characters in sequence are not A, C, G, or T
Found at i:2013 original size:171 final size:172
Alignment explanation
Indices: 1695--2509 Score: 764
Period size: 171 Copynumber: 4.8 Consensus size: 172
1685 NTTTAAAACG
* * * * ** *
1695 AGTAATAAGGCTTTTGAAGGAACGGGTGACTACAAATACACTTTTCTTGCCAATGAATGCTTTTT
1 AGTAATAAGGCTTTTGAAGGAATGAGTGACTATAAATAGACTTTTCTTATCAATGAATGCCTTTT
* * ** * * * *
1760 TCTTTATGTTTCTGGAGATAAAGATTCAATTATAGTCTATTTTAATTAAAAATTTAAAAATATTC
66 TCTTCACGTTTCTCAAGATAAAGATTCAATTATAGTCTGTTTTAACTAAAAATGTAAAAAAATTC
*
1825 AACTCAAAA-CAAATTATGAGATTATAAAACT-ATTTAAAGGC
131 AACTTAAAATC-AATTATGAGATTATAAAACTAATTTAAAGGC
*
1866 AGTACTAAGGCTTTTGAAGGAATGAGTGACTATAAATAGACTTTT-TTATCAATGAATGCCTTTT
1 AGTAATAAGGCTTTTGAAGGAATGAGTGACTATAAATAGACTTTTCTTATCAATGAATGCCTTTT
* * *
1930 TCTTCACGTTTCTCAAGATAAAGATTCAATTATAGTTTTTTTTTAACCAAAAATGTAAAAAAATT
66 TCTTCACGTTTCTCAAGATAAAGATTCAATTATAG-TCTGTTTTAACTAAAAATGTAAAAAAATT
* * * *
1995 CAACTTAAAATTAATTATGAGATAAT-AAAGTAATTTAAAAAG-
130 CAACTTAAAATCAATTATGAGATTATAAAACTAATTT-AAAGGC
* * * * *
2037 AGTAGTAAGGCTTTTGAAGGAATGGGTGATTATAAATGGACTTTTCTTTAT-AATGAATGTCTTT
1 AGTAATAAGGCTTTTGAAGGAATGAGTGACTATAAATAGACTTTTC-TTATCAATGAATGCCTTT
* * * ** * * ** * *
2101 TTCTACATGTTTTTTGAGATGAATATTCAATTATAGTCTGTTTTAA-TGAATGATATAAAATAAT
65 TTCTTCACGTTTCTCAAGATAAAGATTCAATTATAGTCTGTTTTAACT-AAAAATGTAAAAAAAT
* *
2165 TCAACTTAAAATCAATTATGATATTATAAAA-TCATTTAAA-GC
129 TCAACTTAAAATCAATTATGAGATTATAAAACTAATTTAAAGGC
* * * * **
2207 GACTAATAAGGCTTTTGAAGGAAT-AGGTAACTATAAATGGACTTTTCTTCTCAATGAATGGTTT
1 -AGTAATAAGGCTTTTGAAGGAATGA-GTGACTATAAATAGACTTTTCTTATCAATGAATGCCTT
* * ** * * * * *
2271 TTTC-TGACATTT-TGCCAAGGCAAAAAGTAAATTATAGCCTGTTTTAACTAAAAATGTGAAAAA
64 TTTCTTCACGTTTCT--CAAGATAAAGATTCAATTATAGTCTGTTTTAACTAAAAATGTAAAAAA
* * **
2334 ATTCAGCTTAAAATCAATTCTGAGATTATAAAAC-AATTTAAAGTA
127 ATTCAACTTAAAATCAATTATGAGATTATAAAACTAATTTAAAGGC
* * *
2379 AGTAACAAGGCTTTTGAAGGAATAAGAGACTATAAATTA-ACTTTTCTTA-CAAATGAATGCCTT
1 AGTAATAAGGCTTTTGAAGGAATGAGTGACTATAAA-TAGACTTTTCTTATC-AATGAATGCCTT
* * ** * *
2442 TTTCTTCAC-TCTTCTCAAGGTATATG-TTCAATTATAGTCTGTTGAAACAAAAAATGTGAAAAA
64 TTTCTTCACGT-TTCTCAAGATA-AAGATTCAATTATAGTCTGTTTTAACTAAAAATGTAAAAAA
2505 ATTCA
127 ATTCA
2510 NNNNNNNNNN
Statistics
Matches: 524, Mismatches: 96, Indels: 48
0.78 0.14 0.07
Matches are distributed among these distances:
169 2 0.00
170 62 0.12
171 398 0.76
172 57 0.11
173 5 0.01
ACGTcount: A:0.39, C:0.11, G:0.14, T:0.37
Consensus pattern (172 bp):
AGTAATAAGGCTTTTGAAGGAATGAGTGACTATAAATAGACTTTTCTTATCAATGAATGCCTTTT
TCTTCACGTTTCTCAAGATAAAGATTCAATTATAGTCTGTTTTAACTAAAAATGTAAAAAAATTC
AACTTAAAATCAATTATGAGATTATAAAACTAATTTAAAGGC
Done.