Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018399229.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_2497.0, 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: 1793
ACGTcount: A:0.30, C:0.11, G:0.11, T:0.28
Warning! 343 characters in sequence are not A, C, G, or T
Found at i:797 original size:171 final size:159
Alignment explanation
Indices: 609--926 Score: 284
Period size: 171 Copynumber: 1.9 Consensus size: 159
599 NNNNNNNNNN
* * * *
609 CATTTAAAGCTAGTAATAA-GC-TTCTAAAGGCATGAGTAACTATAAATAAGGCTTTTCTGGCCA
1 CATTTAAAGCAAGTAATAAGGCTTTC-AAAGGCATGAGTAACCAAAAAT-AGACTTTTCTGGCCA
* * *
672 ATAAATGACTTTTTCTTCACATTT-CT-CGAGGTAGGCATTTAATTGTTATCTATTTTAACCAAA
64 ATAAATGACTTTTTCTTCACATTTCCTACGA--CAGACATTTAATTATTATCTATTTTAACCAAA
*
735 AATGTAAAGCAATTCAACTTAANNNNNNNNNNGATGTTATAAAAC
127 AATG-AAA-AAATTCAACTTAA----------GATGTTATAAAAC
* * * * *
780 CATTTAAAGCAAGTAATAAGGCTTTCAAAGGCGTGGGTGACCAAAAATAGACTTTTCTTGCTAAT
1 CATTTAAAGCAAGTAATAAGGCTTTCAAAGGCATGAGTAACCAAAAATAGACTTTTCTGGCCAAT
* * ** * *
845 GAATGGCTTTTTCTTCATGTTTCCTACGACAGACATTTAATTATTATTTGTTTTAACCAAAAATG
66 AAATGACTTTTTCTTCACATTTCCTACGACAGACATTTAATTATTATCTATTTTAACCAAAAATG
*
910 AAAAAATTCAACATAAG
131 AAAAAATTCAACTTAAG
927 GTCAATTATT
Statistics
Matches: 123, Mismatches: 20, Indels: 20
0.75 0.12 0.12
Matches are distributed among these distances:
159 1 0.01
169 11 0.09
170 3 0.02
171 81 0.66
172 21 0.17
173 6 0.05
ACGTcount: A:0.35, C:0.14, G:0.14, T:0.33
Consensus pattern (159 bp):
CATTTAAAGCAAGTAATAAGGCTTTCAAAGGCATGAGTAACCAAAAATAGACTTTTCTGGCCAAT
AAATGACTTTTTCTTCACATTTCCTACGACAGACATTTAATTATTATCTATTTTAACCAAAAATG
AAAAAATTCAACTTAAGATGTTATAAAAC
Found at i:1533 original size:170 final size:169
Alignment explanation
Indices: 1241--1793 Score: 606
Period size: 171 Copynumber: 3.2 Consensus size: 169
1231 NNNNNNNNNG
* * * *
1241 TTAAAATCAATTATGAGATTATAAAACCATTTAAAGTGAGTAATAAAGCTTTTCAAGGCATGGAT
1 TTAAAATTAATTATGAGATTAT-AAACCATTTAAAGCGAGTAATAAGGCTTTTCAAGGCAAGG-T
* * * * * *
1306 GACTCTAAATAGGCTTTTCTTGACAATGAATGGCTCTTGCTTCATGCTTT-TTGAGGTAGACATT
64 GACTATAAACAGGCTTTTCTTGTCAATGAATGGCTCTTTCTTCACG-TTTCTTGAGGTAAACATT
**********
1370 CAATTATTATCTATTTTAACNNNNNNNNNNAAAAAATTCAAC
128 CAATTATTATCTATTTTAACAAGAAATGCAAAAAAATTCAAC
*
1412 TTAAAATTAATTATGAGATTATAAACCATTTAAAACGAGTAATAAGGCTTTTCAAGGCAAGAGTG
1 TTAAAATTAATTATGAGATTATAAACCATTTAAAGCGAGTAATAAGGCTTTTCAAGGCAAG-GTG
* *
1477 ACTATAAACAGGCTTTTTTTGTCAATGAATGGCTCTTTCTTCACGTTTCATGAGGTAAACATTCA
65 ACTATAAACAGGCTTTTCTTGTCAATGAATGGCTCTTTCTTCACGTTTCTTGAGGTAAACATTCA
1542 ATTATTATCTATTTTAACAAGAAATGCAAAAAAATTCAAC
130 ATTATTATCTATTTTAACAAGAAATGCAAAAAAATTCAAC
********** *
1582 TTAAAATTAATTATCNNNNNNNNNNACCATTTAAAGCGAGTAATAAGGCTTTTCAAGGCGAGGGT
1 TTAAAATTAATTAT-GAGATTATAAACCATTTAAAGCGAGTAATAAGGCTTTTCAAGGC-AAGGT
* * * * *
1647 GACTATGAACAGGATTTTCTTATCAATGAATGGCTCTTTCTTCACATTTCTTGAGGCAAACATTC
64 GACTATAAACAGGCTTTTCTTGTCAATGAATGGCTCTTTCTTCACGTTTCTTGAGGTAAACATTC
* * * *
1712 AATTATTATCTGTTTCAACCAA-AACTGTAAAAAAATTCAAC
129 AATTATTATCTATTTTAA-CAAGAAATGCAAAAAAATTCAAC
* * *
1753 TTAAAATCAATTATGAGGTTATACAACCATTTAAAGTGAGT
1 TTAAAATTAATTATGAGATTATA-AACCATTTAAAGCGAGT
Statistics
Matches: 318, Mismatches: 58, Indels: 12
0.82 0.15 0.03
Matches are distributed among these distances:
169 3 0.01
170 134 0.42
171 176 0.55
172 5 0.02
ACGTcount: A:0.36, C:0.14, G:0.14, T:0.33
Consensus pattern (169 bp):
TTAAAATTAATTATGAGATTATAAACCATTTAAAGCGAGTAATAAGGCTTTTCAAGGCAAGGTGA
CTATAAACAGGCTTTTCTTGTCAATGAATGGCTCTTTCTTCACGTTTCTTGAGGTAAACATTCAA
TTATTATCTATTTTAACAAGAAATGCAAAAAAATTCAAC
Done.