Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018402029.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_5124.0, 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: 2343
ACGTcount: A:0.28, C:0.09, G:0.09, T:0.26
Warning! 648 characters in sequence are not A, C, G, or T
Found at i:870 original size:170 final size:158
Alignment explanation
Indices: 573--1248 Score: 430
Period size: 171 Copynumber: 4.0 Consensus size: 158
563 ATAAAACCAT
* *
573 TTAAAGTGAGTAATAAGGCTTTTAATGGAATGGGTGACTATAAA-ATGAACTTTTCTTGCCAATA
1 TTAAAGTGAGTAATAAGGCTTTGAA-GGAATGGGTGACTATAAATA-GAA-TTTTCTTGCCAATG
* * *
637 AATACCTTTTTCTTCACGTTTCCTAAGGTAAACATGT-AATTATAATCTGTTGTAACTAAAAATG
63 AATACCTTTTTC-T-ACGTTTCCTAAGGTAGACAT-TCAATTATAATCTGTTCTAACAAAAAATG
701 TAAAACAATTCAACCTAAAATCAATTATGAAATTA
125 TAAAA-AATTCAACCTAAAATCAATTATGAAATTA
* *
736 NNNNNNNNNNTAAAGTGAGTAATAAGGCTTTGGAAGGAATGGGTGAATATAAATAGAATTTTCTT
1 ---------TTAAAGTGAGTAATAAGGCTTT-GAAGGAATGGGTGACTATAAATAGAATTTTCTT
* * * *
801 GCCAATGAATGCCTTTTTCTAACGTTTCCTAAGGGAGACCTTCAATTATAATCTGTTCTAACCAA
56 GCCAATGAATACCTTTTTCT-ACGTTTCCTAAGGTAGACATTCAATTATAATCTGTTCTAACAAA
* * * *
866 AAATGTTCAAATATTCAACCTAAAATTAATTATGAAATTNNNNNNNNNN
120 AAATG-TAAAAAATTCAACCTAAAATCAATTATGAAATT---------A
* * * * *
915 TTAAAGTGAGCAATAAGGCTTTTGACGGAATGGATGACTATAAATAGACTTTACTTGCCAATGAA
1 TTAAAGTGAGTAATAAGGC-TTTGAAGGAATGGGTGACTATAAATAGAATTTTCTTGCCAATGAA
** * * *
980 TATTTTTTTCTTCATGTCTCTCAAGGTAGACATTCAATTATAAAT-TGTTCTAACAAAAAATGTA
65 TACCTTTTTCTACGTTTC-CT-AAGGTAGACATTCAATTAT-AATCTGTTCTAACAAAAAATGTA
*** * * *
1044 AAAGAATTCAACCTANNNNNNNNNNTGAGATTATAAAACTA
127 AAA-AATTCAACCTA-------AAATCA-ATTATGAAATTA
** * * * *
1085 TTTAAAGTGAGTAATATCA-TTTTTAAAAGAATGGGTGACTATAAAT-GAACTTTTTTTGCTAAT
1 -TTAAAGTGAGTAATA--AGGCTTTGAAGGAATGGGTGACTATAAATAGAA-TTTTCTTGCCAAT
* ** * *
1148 GAATGCCTTTTTCTTCATATTTCTCCAA-GTAGACATTCAATTATAATCTGTT-TGAACTAAAAA
62 GAATACCTTTTTC-T-ACGTTTC-CTAAGGTAGACATTCAATTATAATCTGTTCT-AACAAAAAA
* * * * *
1211 TATAAAAAAATTCAGCTTAAAATCAATTTTGAGATTA
123 TGT-AAAAAATTCAACCTAAAATCAATTATGAAATTA
1248 T
1 T
1249 AAAACCATTT
Statistics
Matches: 399, Mismatches: 70, Indels: 80
0.73 0.13 0.15
Matches are distributed among these distances:
162 1 0.00
163 8 0.02
164 2 0.01
169 5 0.01
170 143 0.36
171 168 0.42
172 51 0.13
173 10 0.03
178 2 0.01
179 9 0.02
ACGTcount: A:0.37, C:0.12, G:0.13, T:0.34
Consensus pattern (158 bp):
TTAAAGTGAGTAATAAGGCTTTGAAGGAATGGGTGACTATAAATAGAATTTTCTTGCCAATGAAT
ACCTTTTTCTACGTTTCCTAAGGTAGACATTCAATTATAATCTGTTCTAACAAAAAATGTAAAAA
ATTCAACCTAAAATCAATTATGAAATTA
Done.