Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018399535.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_2794.0, 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, 737
Length: 1229
ACGTcount: A:0.31, C:0.11, G:0.10, T:0.34
Warning! 166 characters in sequence are not A, C, G, or T
Found at i:303 original size:170 final size:160
Alignment explanation
Indices: 16--342 Score: 320
Period size: 170 Copynumber: 2.0 Consensus size: 160
6 TAAAACATAC
* * * **
16 TATAATTGAATGTCTACCTTGAGAAACATGAAGAAAAAAAATTCATTGGCAAGCAAAGTTTATTT
1 TATAATTGAATGCCTACCTAGAGAAACATGAAGAAAAAAAATTCATTGGCAAGAAAAGTCCATTT
* * ** * *
81 ATGGTCTCCCATTCCTTCAAAAGCCTTATCACTTGCTTTAAATGGCTTTATAATCTTATAATTAA
66 ATAGTCTCCCATTCCTTCAAAAGCCTTATCAATCACTTTAAATGGCTTTATAATCTAAGAATTAA
*
146 TTTTAAGTTGAATTGTTTTATATTTTTCAT
131 TTTTAAGTTAAATTGTTTTATATTTTTCAT
* * *
176 TNNNNNNNNNNATAATTGAATGCCTACCTA-AGGAAACATGTAGAAAAAGTAGTTCATTGAG-AA
1 T----------ATAATTGAATGCCTACCTAGA-GAAACATGAAGAAAAA-AAATTCATTG-GCAA
* *
239 GAAAAGTCCATTTATAGTCAT-CCATTCCTTCAAAAG-CTTATTAATCACTTTAAATGGTTTTAT
53 GAAAAGTCCATTTATAGTC-TCCCATTCCTTCAAAAGCCTTATCAATCACTTTAAATGGCTTTAT
* * *
302 AATCTAAGAATTGATTTTTAGTTAAATTTTTTTATATTTTT
117 AATCTAAGAATTAATTTTAAGTTAAATTGTTTTATATTTTT
343 GGTTAAAACA
Statistics
Matches: 133, Mismatches: 20, Indels: 18
0.78 0.12 0.11
Matches are distributed among these distances:
160 1 0.01
169 1 0.01
170 89 0.67
171 40 0.30
172 2 0.02
ACGTcount: A:0.34, C:0.12, G:0.12, T:0.39
Consensus pattern (160 bp):
TATAATTGAATGCCTACCTAGAGAAACATGAAGAAAAAAAATTCATTGGCAAGAAAAGTCCATTT
ATAGTCTCCCATTCCTTCAAAAGCCTTATCAATCACTTTAAATGGCTTTATAATCTAAGAATTAA
TTTTAAGTTAAATTGTTTTATATTTTTCAT
Found at i:854 original size:172 final size:173
Alignment explanation
Indices: 661--1035 Score: 441
Period size: 173 Copynumber: 2.2 Consensus size: 173
651 NNNNNNNNNN
* * ** * *
661 AAGCCTTATTAGTCGCTTTAAATGGTTTTATAATCTCGTAACTGATTTTTTA-TTTAATTTTTTT
1 AAGCCTTATTACTCACTTTAAATGGTTTTATAATCTCAAAACTGA-TTTTAAGTTCAATTTTTTT
*
725 TACATTATTT-GTGAAAATAGATTATATTTGAATGTCTACCTCAAGAAACATGAGGAAAATGACA
65 TACATTATTTGGTGAAAATAGATTATATTTGAATGTCTACCTCAAGAAACATGAGGAAAAAGACA
* *
789 TTCATTGACAACAAAAGTCCATCTATATTCACCTATTCCTTCGA
130 TTCATTGACAACAAAAGTCCATCTATAGTCACCTATTCCTTCAA
* *
833 AAGCCTTATTATTCACTTTAAATTGG-TTTATAATCTCAAAATTGATTTTAAGTTCAATTTTTTT
1 AAGCCTTATTACTCACTTTAAA-TGGTTTTATAATCTCAAAACTGATTTTAAGTTCAATTTTTTT
* * * * * *** * * **
897 TATATTTTTTGGTTAAAATAGATTATATTTGAATTTTTACCTTGTGAAACGTGATGAAAAAGGTA
65 TACATTATTTGGTGAAAATAGATTATATTTGAATGTCTACCTCAAGAAACATGAGGAAAAAGACA
** * ** * *
962 TTCATTGGTAAGAAAAGTCTGTTTATAGTCACTTATTCCTTCAA
130 TTCATTGACAACAAAAGTCCATCTATAGTCACCTATTCCTTCAA
1006 AAGCCTTATTACTCACTTTAAATGGTTTTA
1 AAGCCTTATTACTCACTTTAAATGGTTTTA
1036 NNNNNNNNNN
Statistics
Matches: 169, Mismatches: 30, Indels: 7
0.82 0.15 0.03
Matches are distributed among these distances:
171 5 0.03
172 58 0.34
173 106 0.63
ACGTcount: A:0.33, C:0.13, G:0.12, T:0.43
Consensus pattern (173 bp):
AAGCCTTATTACTCACTTTAAATGGTTTTATAATCTCAAAACTGATTTTAAGTTCAATTTTTTTT
ACATTATTTGGTGAAAATAGATTATATTTGAATGTCTACCTCAAGAAACATGAGGAAAAAGACAT
TCATTGACAACAAAAGTCCATCTATAGTCACCTATTCCTTCAA
Done.