Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018398049.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_1358.0, 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: 4206
ACGTcount: A:0.19, C:0.08, G:0.06, T:0.20
Warning! 1961 characters in sequence are not A, C, G, or T
Found at i:1834 original size:170 final size:170
Alignment explanation
Indices: 1449--2474 Score: 617
Period size: 170 Copynumber: 6.0 Consensus size: 170
1439 NNNNNNNNNN
** * ** * * ** *
1449 GGTATTCATTGGCAAGAAAAGTCCATTTACAGTCACCCATTTCTTCAAAAGCTTTATTGTTTGCT
1 GGTATTCATTGGCAAGAAAAGTTTATTTATAGTCACTTATTCCTTCAAAAGCCTTATTACTCGCT
* * ********** *
1514 TTAAATTATTTTATAATCTCATAATTGATTTTAAG-TNNNNNNNNNNTACATATTTGGTTAAAAC
66 TTAAATGATTTTACAATCTCATAATTGATTTTAAGTTAAATCTTTTTTACAT-TTT-ATTAAAAC
* * * * * *
1578 AGACTATAATTGAATGTCTACCTCAAGAAACCTAAAAAAAGAA
129 ACAATATAATTGAATGTCTACCTCAAGAAACAT-GAAGAACAA
* ** *
1621 GGCATTCATTGGCAAGAATAA-TCCATTTATAGTCACCTATTCCTTCAAAAGCCTTATTACTCGC
1 GGTATTCATTGGCAAGAA-AAGTTTATTTATAGTCACTTATTCCTTCAAAAGCCTTATTACTCGC
*********** * *
1685 TTTANNNNNNNNNNTAATCTCATAATTGATTTTAAGTTGAA-CTTTTTTACATTTTAGTTAAAAT
65 TTTAAATGATTTTACAATCTCATAATTGATTTTAAGTTAAATCTTTTTTACATTTTA-TTAAAAC
* *
1749 ACATTATAATTGAATGTCTACCTCGAGAAACATGAAGAACAA
129 ACAATATAATTGAATGTCTACCTCAAGAAACATGAAGAACAA
**********
1791 GGTATTCATTGGCAAGAAAAGTTTATTTATAGTCACTTATTCCTTCAAAAGCCNNNNNNNNNNCT
1 GGTATTCATTGGCAAGAAAAGTTTATTTATAGTCACTTATTCCTTCAAAAGCCTTATTACTCGCT
* ** *
1856 TTAAATGATTTTACAATCTCATAATTGATTTTAAGTTAAATTTTTTTTATTTTTTATTAAAACAT
66 TTAAATGATTTTACAATCTCATAATTGATTTTAAGTTAAATCTTTTTTACATTTTATTAAAACAC
* * *
1921 AATATAATTGAATGTTTGCCTCTAGAAACATGAAGAACAA
131 AATATAATTGAATGTCTACCTCAAGAAACATGAAGAACAA
* **********
1961 GGTATTCATTGGCAAGAAAAGTTTATTTATAGTCACTCATTCCTTCAAAAGCNNNNNNNNNNGCT
1 GGTATTCATTGGCAAGAAAAGTTTATTTATAGTCACTTATTCCTTCAAAAGCCTTATTACTCGCT
* *
2026 TTAAATTG-TTTTATAATCTCATAATTGATTTTAAGTT-GAT-TTTTTTAAACATTTTTAGTTAA
66 TTAAA-TGATTTTACAATCTCATAATTGATTTTAAGTTAAATCTTTTTT--ACA-TTTTA-TTAA
* *
2088 AACA-AACTATAATTGACTGTTTACCTCAAGAAACATGAAGAGA-AA
126 AACACAA-TATAATTGAATGTCTACCTCAAGAAACATGAAGA-ACAA
* * * * ** ** * **
2133 TGCATTCATTTGCAGGAAAAGTCCA-TTATAGTCACCCATTCCTTCAAAAGGCTTATTGTTCGCT
1 GGTATTCATTGGCAAGAAAAGTTTATTTATAGTCACTTATTCCTTCAAAAGCCTTATTACTCGCT
* ********** * *
2197 TTAAATTG-TTTTATAATCTCATAATTGATNNNNNNNNNNAT-TTTTTTACATTTTTGGTTCAAA
66 TTAAA-TGATTTTACAATCTCATAATTGATTTTAAGTTAAATCTTTTTTACA-TTTT-ATTAAAA
* * * *
2260 CAGACTATAATTGAATGTGTACCT-AGAGAAACATGAAGAAAAA
128 CACAATATAATTGAATGTCTACCTCA-AGAAACATGAAGAACAA
* * ** * ** * * *
2303 TGCATTCATTGGCAAGAAAAGTCCATTTATACTCACCAATTCCTTCAAAAGCATTATT-TTCCAC
1 GGTATTCATTGGCAAGAAAAGTTTATTTATAGTCACTTATTCCTTCAAAAGCCTTATTACT-CGC
* * * * * *
2367 TTTAAATTG-TATTATAATCTCAGAATTGATTTTAAGTTGAAT-TGTTTTACATTTTTTTTAAAA
65 TTTAAA-TGATTTTACAATCTCATAATTGATTTTAAGTTAAATCTTTTTTACA-TTTTATTAAAA
* * *
2430 CA-AACTGTAATTGAATGTCTACCTCAAGAAACATAAAGAAAAA
128 CACAA-TATAATTGAATGTCTACCTCAAGAAACATGAAGAACAA
2473 GG
1 GG
2475 CATNNNNNNN
Statistics
Matches: 693, Mismatches: 140, Indels: 44
0.79 0.16 0.05
Matches are distributed among these distances:
168 6 0.01
169 7 0.01
170 334 0.48
171 190 0.27
172 152 0.22
173 4 0.01
ACGTcount: A:0.34, C:0.14, G:0.11, T:0.36
Consensus pattern (170 bp):
GGTATTCATTGGCAAGAAAAGTTTATTTATAGTCACTTATTCCTTCAAAAGCCTTATTACTCGCT
TTAAATGATTTTACAATCTCATAATTGATTTTAAGTTAAATCTTTTTTACATTTTATTAAAACAC
AATATAATTGAATGTCTACCTCAAGAAACATGAAGAACAA
Done.