Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018399260.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_2528.0, 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: 2383
ACGTcount: A:0.20, C:0.06, G:0.08, T:0.19
Warning! 1122 characters in sequence are not A, C, G, or T
Found at i:1396 original size:171 final size:162
Alignment explanation
Indices: 1092--1409 Score: 415
Period size: 171 Copynumber: 1.9 Consensus size: 162
1082 NNNNNNTATT
* *
1092 AGATTATAAAAATATTTAAAGCAAGTAATAAGGCCTTTGAGGGAATGAGATGCTATAAATAGAGT
1 AGATTATAAAAATATTTAAAGCAAGTAATAAGGCATTTGAGGGAATGAGAAGCTATAAATAGAGT
* * * * * *
1157 TTTCTTGCCAATGAATGATTTTTTCTTCATATTTCTCGAGATAGATAGTCAGTTATTGTCTATTT
66 TTTCTTGCCAATGAATGATTTTTTCTTCATATTGCTCAAGACAGACAGTCAATTATAGTCTATTT
1222 TAAT-AAAAATATAAAAAAAATTTAAGTTAAA
131 TAATGAAAAATATAAAAAAAATTTAAGTTAAA
1253 NNNNNNNNNNAGATTATAAAAATATTTAAAGCAAGTAATAAGGCATTTGAGGGAATGAGAAGCTA
1 ----------AGATTATAAAAATATTTAAAGCAAGTAATAAGGCATTTGAGGGAATGAGAAGCTA
* *
1318 TAAATAGAGTTTTCTTGCCAATGAATGATTTTTTCTTCACT-TTGCTTAAGACAGACATTCAATT
56 TAAATAGAGTTTTCTTGCCAATGAATGATTTTTTCTTCA-TATTGCTCAAGACAGACAGTCAATT
* *
1382 ATAGTCTGTTTTAATGAAAAATGTAAAA
120 ATAGTCTATTTTAATGAAAAATATAAAA
1410 CAATTGAACN
Statistics
Matches: 133, Mismatches: 12, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
171 121 0.91
172 12 0.09
ACGTcount: A:0.39, C:0.08, G:0.15, T:0.35
Consensus pattern (162 bp):
AGATTATAAAAATATTTAAAGCAAGTAATAAGGCATTTGAGGGAATGAGAAGCTATAAATAGAGT
TTTCTTGCCAATGAATGATTTTTTCTTCATATTGCTCAAGACAGACAGTCAATTATAGTCTATTT
TAATGAAAAATATAAAAAAAATTTAAGTTAAA
Found at i:2335 original size:171 final size:160
Alignment explanation
Indices: 2061--2383 Score: 306
Period size: 171 Copynumber: 1.9 Consensus size: 160
2051 TAAAACCATT
* * * *
2061 TAAAGCGAGTAATAAGGCTTTTGAAGGATGAAAGGCTATACATAGACTTTTCTTACCAATGAATG
1 TAAAGTGAGTAATAAGGCTTTTGAAGGATGAAAGACTATAAATAGACTTTTCTTACAAATGAATG
* * * * *
2126 CTTTTTTCTTCACAGTTATCGAGGTAAACATTTAATTATAGCCTAG-TTTAATGAAAAATGTAAA
66 CTTTTGTCTTCACAGTTATCGAGATAAACAGTTAATTATAGCCT-GTTTTAATCAAAAATGCAAA
* *
2190 AATATTCAACTTAAAATTAATTATGAGATTA
130 AAAATTCAACTTAAAATCAATTATGAGATTA
* *** *
2221 TAAANNNNNNNNNNGTGAGTAATATGGCTTTTGAAGGAATGGGTGACTATAAATGGACTTTTCTT
1 TAAA----------GTGAGTAATAAGGCTTTTGAAGG-ATGAAAGACTATAAATAGACTTTTCTT
** * * * * * * *
2286 GGAAATGAATGCTTTTGTCTTCATATTTCTCGAGATAGACAGTTAATTATTGTCTGTTTTAATCT
55 ACAAATGAATGCTTTTGTCTTCACAGTTATCGAGATAAACAGTTAATTATAGCCTGTTTTAATCA
2351 AAAATGCAAAAAAATTCAACTTAAAATCAATTA
120 AAAATGCAAAAAAATTCAACTTAAAATCAATTA
Statistics
Matches: 126, Mismatches: 25, Indels: 13
0.77 0.15 0.08
Matches are distributed among these distances:
160 4 0.03
170 22 0.17
171 100 0.79
ACGTcount: A:0.36, C:0.11, G:0.15, T:0.35
Consensus pattern (160 bp):
TAAAGTGAGTAATAAGGCTTTTGAAGGATGAAAGACTATAAATAGACTTTTCTTACAAATGAATG
CTTTTGTCTTCACAGTTATCGAGATAAACAGTTAATTATAGCCTGTTTTAATCAAAAATGCAAAA
AAATTCAACTTAAAATCAATTATGAGATTA
Done.