Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018398988.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_2269.0, 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, 756
Length: 1261
ACGTcount: A:0.32, C:0.10, G:0.11, T:0.30
Warning! 211 characters in sequence are not A, C, G, or T
Found at i:1135 original size:343 final size:340
Alignment explanation
Indices: 418--1261 Score: 952
Period size: 343 Copynumber: 2.5 Consensus size: 340
408 NNNNNNNATG
* * * *
418 GGTGTCTATAAATAGACTTTTCTTGCCAATGAATGCCTTTTT-TT-ACGTTTCTCGAGATAGACA
1 GGTGACTATAAATAGACTTTTCTTGCCAATGAATGCTTTTTTCTTCACGTTTCTCAAGAGAGACA
* * * * ** *
481 TTGAATTATAATCTGTTTTGATAAAAAATGTAAACAAATTCAACCGTAAAATCAATTATGGCATT
66 TTCAATTATAGTTTGTTTTAACCAAAAATGTAAA-AAATTCAACC-TAAAATCAATTATTGCATT
* * *
546 ACAAAACCATTTAAAGCAAGTAATAAAGCTTTTGAAGGTACAAGTGACTATAAATAGACTTTTCT
129 ATAAAACTATTTAAAGCAAGTAATAAAGCTTTTAAAGGTACAAGTGACTATAAATAGACTTTTCT
* * * * * *
611 TACAAATGAATACTTTTTTCTTCATTTTTCTCAAGGTAGAAATTCAATTCTAGTCTATTTTAACC
194 TACAAATGAATACTTTTTTCGTCATGTTTCTAAAGGAAGAAATTCAATTATAGTCTATTTTAACA
* * * * *
676 AAAATGTACAAAGATTTCAAATGTAAATCAATTTTGAGATTATAAAACCATTTAAAGTGAGTAAT
259 AAAAAGTAAAAAGATTTCAAATGAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAAT
*
741 AAGGCTTTTGAAGAAAT
324 AAGGCTTTTAAAGAAAT
* * *
758 GAGTGACTATAAATGGACTTTTCTTGCTAATGAATACTTTTTTCTTCACGTTTCTCAAGAGAGAC
1 G-GTGACTATAAATAGACTTTTCTTGCCAATGAATGCTTTTTTCTTCACGTTTCTCAAGAGAGAC
* * *
823 ATTTAATTCTAGTTTGTTTTAACCAAAAATATAAAATAATTCAACCTAAAATCAATTATTGCATT
65 ATTCAATTATAGTTTGTTTTAACCAAAAATGTAAAA-AATTCAACCTAAAATCAATTATTGCATT
* ** * *** *
888 ATAAAACTATTTAAGGTGAGTACTAAAGCTTTTTAAAGGTATGGGTGACTATAAATGGAC-TTTC
129 ATAAAACTATTTAAAGCAAGTAATAAAGC-TTTTAAAGGTACAAGTGACTATAAATAGACTTTTC
* * * * *
952 TTGCCAATGAATGCTTCTTTT-GTCATGTTTCTAAAGGAAGACATTTAATTATAGTC-ATTTTTA
193 TTACAAATGAATACTT-TTTTCGTCATGTTTCTAAAGGAAGAAATTCAATTATAGTCTA-TTTTA
** * * *
1015 TTGAAAAAAGTAAAAAGA-TTCAACCT-AAAATCAATTATGATATTATAAAACTATTTAAAGCGA
256 -ACAAAAAAGTAAAAAGATTTCAA-ATGAAAATCAATTATGAGATTATAAAACCATTTAAAGCGA
**
1078 GTAATAAGGCTTTTTAAAGGTAT
319 GTAATAAGGC-TTTTAAAGAAAT
* * *
1101 AGGTGACTAT-AATAAGACTTTTCTTGCCAATGAATGCTTTTTTCTTCACATTTCTGAAG-GTAC
1 -GGTGACTATAAAT-AGACTTTTCTTGCCAATGAATGCTTTTTTCTTCACGTTTCTCAAGAG-AG
* * *
1164 ACATTCAATTATAGTTGGTTTTATCCAAAAATGTAAAAATATTTAACCTAAAATCAATTA-TGAC
63 ACATTCAATTATAGTTTGTTTTAACCAAAAATGTAAAAA-ATTCAACCTAAAATCAATTATTG-C
*
1228 ATTATAAAACTATTTAAAGCAAGTAATAAGGCTT
126 ATTATAAAACTATTTAAAGCAAGTAATAAAGCTT
Statistics
Matches: 421, Mismatches: 68, Indels: 28
0.81 0.13 0.05
Matches are distributed among these distances:
340 1 0.00
341 37 0.09
342 150 0.36
343 232 0.55
344 1 0.00
ACGTcount: A:0.38, C:0.13, G:0.13, T:0.37
Consensus pattern (340 bp):
GGTGACTATAAATAGACTTTTCTTGCCAATGAATGCTTTTTTCTTCACGTTTCTCAAGAGAGACA
TTCAATTATAGTTTGTTTTAACCAAAAATGTAAAAAATTCAACCTAAAATCAATTATTGCATTAT
AAAACTATTTAAAGCAAGTAATAAAGCTTTTAAAGGTACAAGTGACTATAAATAGACTTTTCTTA
CAAATGAATACTTTTTTCGTCATGTTTCTAAAGGAAGAAATTCAATTATAGTCTATTTTAACAAA
AAAGTAAAAAGATTTCAAATGAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAA
GGCTTTTAAAGAAAT
Found at i:1223 original size:172 final size:171
Alignment explanation
Indices: 418--1261 Score: 865
Period size: 171 Copynumber: 4.9 Consensus size: 171
408 NNNNNNNATG
* * * *
418 GGTGTCTATAAATAGACTTTTCTTGCCAATGAATGCCTTTTT-TT-ACGTTTCTCGAGATAGACA
1 GGTGACTATAAATAGACTTTTCTTGCCAATGAATGCTTTTTTCTTCACGTTTCTCAAGGTAGACA
* * * *
481 TTGAATTATAATCTGTTTTGAT-AAAAAATGTAAACAA-ATTCAACCGTAAAATCAATTATGGCA
66 TTCAATTATAGT-TGTTTT-ATCCAAAAATGTAAA-AAGATTCAACC-TAAAATCAATTATGACA
* * * * * *
544 TTACAAAACCATTTAAAGCAAGTAATAAAGC-TTTTGAAGGTACA
127 TTATAAAACTATTTAAAGCGAGTAATAAGGCTTTTTAAAGGTATA
* * * * ** *
588 AGTGACTATAAATAGACTTTTCTTACAAATGAATACTTTTTTCTTCATTTTTCTCAAGGTAGAAA
1 GGTGACTATAAATAGACTTTTCTTGCCAATGAATGCTTTTTTCTTCACGTTTCTCAAGGTAGACA
* * * * * * * *
653 TTCAATTCTAGTCTATTTTAACC-AAAATGTACAAAGATTTCAA-ATGTAAATCAATTTTGAGAT
66 TTCAATTATAGT-TGTTTTATCCAAAAATGTAAAAAGA-TTCAACCT-AAAATCAATTATGACAT
* * * **
716 TATAAAACCATTTAAAGTGAGTAATAAGGC-TTTTGAAGAAAT-
128 TATAAAACTATTTAAAGCGAGTAATAAGGCTTTTTAAAGGTATA
* * *
758 GAGTGACTATAAATGGACTTTTCTTGCTAATGAATACTTTTTTCTTCACGTTTCTCAAGAG-AGA
1 G-GTGACTATAAATAGACTTTTCTTGCCAATGAATGCTTTTTTCTTCACGTTTCTCAAG-GTAGA
* * * *
822 CATTTAATTCTAGTTTGTTTTAACCAAAAATATAAAATA-ATTCAACCTAAAATCAATTATTG-C
64 CATTCAATTATAG-TTGTTTTATCCAAAAATGTAAAA-AGATTCAACCTAAAATCAATTA-TGAC
* * * * *
885 ATTATAAAACTATTTAAGGTGAGTACTAAAGCTTTTTAAAGGTATG
126 ATTATAAAACTATTTAAAGCGAGTAATAAGGCTTTTTAAAGGTATA
* * * * *
931 GGTGACTATAAATGGAC-TTTCTTGCCAATGAATGCTTCTTTT-GTCATGTTTCTAAAGGAAGAC
1 GGTGACTATAAATAGACTTTTCTTGCCAATGAATGCTT-TTTTCTTCACGTTTCTCAAGGTAGAC
* ** * *
994 ATTTAATTATAGTCAT-TTTTATTGAAAAAAGTAAAAAGATTCAACCTAAAATCAATTATGATAT
65 ATTCAATTATAGT--TGTTTTATCCAAAAATGTAAAAAGATTCAACCTAAAATCAATTATGACAT
1058 TATAAAACTATTTAAAGCGAGTAATAAGGCTTTTTAAAGGTATA
128 TATAAAACTATTTAAAGCGAGTAATAAGGCTTTTTAAAGGTATA
* * *
1102 GGTGACTAT-AATAAGACTTTTCTTGCCAATGAATGCTTTTTTCTTCACATTTCTGAAGGTACAC
1 GGTGACTATAAAT-AGACTTTTCTTGCCAATGAATGCTTTTTTCTTCACGTTTCTCAAGGTAGAC
* *
1166 ATTCAATTATAGTTGGTTTTATCCAAAAATGTAAAAATATTTAACCTAAAATCAATTATGACATT
65 ATTCAATTATAGTT-GTTTTATCCAAAAATGTAAAAAGATTCAACCTAAAATCAATTATGACATT
*
1231 ATAAAACTATTTAAAGCAAGTAATAAGGCTT
129 ATAAAACTATTTAAAGCGAGTAATAAGGCTT
Statistics
Matches: 564, Mismatches: 84, Indels: 50
0.81 0.12 0.07
Matches are distributed among these distances:
170 48 0.09
171 315 0.56
172 199 0.35
173 2 0.00
ACGTcount: A:0.38, C:0.13, G:0.13, T:0.37
Consensus pattern (171 bp):
GGTGACTATAAATAGACTTTTCTTGCCAATGAATGCTTTTTTCTTCACGTTTCTCAAGGTAGACA
TTCAATTATAGTTGTTTTATCCAAAAATGTAAAAAGATTCAACCTAAAATCAATTATGACATTAT
AAAACTATTTAAAGCGAGTAATAAGGCTTTTTAAAGGTATA
Done.