Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018401567.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_4691.0, 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: 2202
ACGTcount: A:0.26, C:0.10, G:0.08, T:0.28
Warning! 620 characters in sequence are not A, C, G, or T
Found at i:501 original size:171 final size:169
Alignment explanation
Indices: 199--866 Score: 758
Period size: 171 Copynumber: 3.9 Consensus size: 169
189 TCCTTTTAAG
* * * * * *
199 TTGATTTTAAGTTGAATTGTTTTACATTTTTAGTTAAAACAGACTATAATTAAATGCTTGCCTCA
1 TTGATTTTAAGTTGAATTATTTTACATTTTTAATTAAAACAGACTATAATTGAATGTTTACCTCT
* * *
264 AGAAAGATGCAA-AAAAAGCTATTCATTGAGAAAAAAAATCCATTTATAGTCACCCATTCCTTCA
66 AGAAACATG-AAGAAAAAGC-ATTCATTGAGAAGAAAAGTCCATTTATAGTCA-CCATTCCTTCA
*
328 AAAGGTTTAATACTCGCTTTAAATAGTTTTATAATCTCATAA
128 AAAGGCTTAATACTCGCTTTAAATAGTTTTATAATCTCATAA
*
370 TTGATTTTAAGTTGAA-TATTTTTACATTTTTAATTAAAACATACTATAATTGAATGTTTACCTC
1 TTGATTTTAAGTTGAATTA-TTTTACATTTTTAATTAAAACAGACTATAATTGAATGTTTACCTC
* * *
434 TAGAAACATGAAGAAACAAGCATTCATTGATAAGAAAAGTCCATTTAGAGTCATCCATTCATTCA
65 TAGAAACATGAAGAAA-AAGCATTCATTGAGAAGAAAAGTCCATTTATAGTCA-CCATTCCTTCA
*
499 AAAAGCTT-ATGACTCGCTTTAAA-AGATTTTATAATCTCATAA
128 AAAGGCTTAAT-ACTCGCTTTAAATAG-TTTTATAATCTCATAA
* ** * *
541 TTGATTTTAAGTTGAATTTTTTTACATTTTTTGTTAAAACAGACTATAATTGATTGTCTACCT-T
1 TTGATTTTAAGTTGAATTATTTTACATTTTTAATTAAAACAGACTATAATTGAATGTTTACCTCT
* ** *
605 AGGAAACATGCAGAAAAAGCCATTCATTGAGAAGAAAAGTTTATTTATAGTCACTCATTCCTTTA
66 A-GAAACATGAAGAAAAAG-CATTCATTGAGAAGAAAAGTCCATTTATAGTCAC-CATTCCTTCA
* * *
670 AAAGGCTTATTACTCGCTTTTAATGGTTTTATAATCTCATAA
128 AAAGGCTTAATACTCGCTTTAAATAGTTTTATAATCTCATAA
* * * *** *
712 TTGATTTTAAATTGAATTATTTTACATTTTTTATTAAAATAGACTATAATTGAATACCTGCCT-T
1 TTGATTTTAAGTTGAATTATTTTACATTTTTAATTAAAACAGACTATAATTGAATGTTTACCTCT
* * * *
776 GGAAAACATGCAA-AAAAAGCCTATTCATTGAGAAAAAAAGTTCATTTATAGCCACCCATT-CTC
66 AG-AAACATG-AAGAAAAAG-C-ATTCATTGAGAAGAAAAGTCCATTTATAGTCA-CCATTCCT-
* * *
839 TCAAAAGTCTTATTACTCGGTTTAAATA
125 TCAAAAGGCTTAATACTCGCTTTAAATA
867 NNNNNNNNNN
Statistics
Matches: 430, Mismatches: 51, Indels: 31
0.84 0.10 0.06
Matches are distributed among these distances:
170 14 0.03
171 351 0.82
172 64 0.15
173 1 0.00
ACGTcount: A:0.37, C:0.14, G:0.11, T:0.38
Consensus pattern (169 bp):
TTGATTTTAAGTTGAATTATTTTACATTTTTAATTAAAACAGACTATAATTGAATGTTTACCTCT
AGAAACATGAAGAAAAAGCATTCATTGAGAAGAAAAGTCCATTTATAGTCACCATTCCTTCAAAA
GGCTTAATACTCGCTTTAAATAGTTTTATAATCTCATAA
Done.