Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018402485.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_556.0, 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: 14507
ACGTcount: A:0.19, C:0.07, G:0.06, T:0.19
Warning! 7089 characters in sequence are not A, C, G, or T
Found at i:13275 original size:141 final size:129
Alignment explanation
Indices: 13089--13356 Score: 299
Period size: 141 Copynumber: 2.0 Consensus size: 129
13079 ATAAATGGAC
*
13089 TTTTCTTGCCAATGGATATCTGTTTCTTCCTGTTTCTTAAGGTAGACATTCAATTATAATCA-GT
1 TTTTCTTGCCAATGGATATCTGTTTCTTCCCGTTTCTTAAGGTAGACATTCAATTATAAT-ATGT
13153 TTCAATAAAAAATAGAGAAAAACTCAAATTAAAATCAATTATGAGGTTATAAAATCATTTAAAGC
65 TTCAAT-AAAAATAGA-AAAAACTCAAATTAAAATCAATTATGAGGTTATAAAATCATTTAAAGC
13218 AA
128 AA
* *
13220 NNNNNNNNNNTTTTCTTGCTAATGGATATCT-TTT-TTCTCACGTTTCTTGAGGTAGACATTCAA
1 ----------TTTTCTTGCCAATGGATATCTGTTTCTTC-C-CGTTTCTTAAGGTAGACATTCAA
** * * * *
13283 TTATAATATGTTTTTATAAAAATATAAAAGATTCAAGTTAAAATCAATTATGAGGTTATAAAATC
54 TTATAATATGTTTCAATAAAAATAGAAAAAACTCAAATTAAAATCAATTATGAGGTTATAAAATC
13348 ATTTAAAGC
119 ATTTAAAGC
13357 GAGTAGTAAG
Statistics
Matches: 115, Mismatches: 9, Indels: 8
0.87 0.07 0.06
Matches are distributed among these distances:
139 48 0.42
140 13 0.11
141 54 0.47
ACGTcount: A:0.37, C:0.11, G:0.11, T:0.37
Consensus pattern (129 bp):
TTTTCTTGCCAATGGATATCTGTTTCTTCCCGTTTCTTAAGGTAGACATTCAATTATAATATGTT
TCAATAAAAATAGAAAAAACTCAAATTAAAATCAATTATGAGGTTATAAAATCATTTAAAGCAA
Found at i:14285 original size:171 final size:172
Alignment explanation
Indices: 13924--14394 Score: 610
Period size: 171 Copynumber: 2.7 Consensus size: 172
13914 TGGATGACGA
* * *** *
13924 TAAATGGACTTTTCTTACTAATGGATATCTTTTTCTTCGTATTTCTCAAGGTAAATATTCAATTA
1 TAAATGGACTTTTCTTGCCAATGGATATCTTTTTCTTCACGTTTCTCAAGGTAGATATTCAATTA
* *
13989 TAATCTATTTTAATAAAAAAATATATAAAAGTTCAACTTTAAACTAATTATGAGATTAAAAAAAG
66 TAATCTATTTTAAT-AAAAAATATAAAAAAATTCAACTTTAAACTAATTATGAGATTAAAAAAAG
* *
14054 CATTTAAAGTAAGTAATTAGGCTTTCGAAAGCATAGGTGACCC
130 CATTTAAAGCAAGTAATAAGGCTTTCGAAAGCATAGGTGACCC
*
14097 TATATGGACTTTTCTTGCCAATGGATATCTTTTTCTTCACGTTTC-CTAAGGTAGATATTCAATT
1 TAAATGGACTTTTCTTGCCAATGGATATCTTTTTCTTCACGTTTCTC-AAGGTAGATATTCAATT
* * *********
14161 TTAATCTATTTTAATAAAAAATATAGAAAAATTCAACTTTAAACTAATTATGAGA-NNNNNNNNN
65 ATAATCTATTTTAATAAAAAATATAAAAAAATTCAACTTTAAACTAATTATGAGATTAAAAAAAG
* * *
14225 NATTTAAAGCAAGTAATAAGGCTTTCGAAAGCATGGGTGACCT
130 CATTTAAAGCAAGTAATAAGGCTTTCGAAAGCATAGGTGACCC
*
14268 TAAATGGACTTTTCTTGCCATTGGATATCTTTTTCTTCACGTTTCTCAAGGTAGATATTCAATTA
1 TAAATGGACTTTTCTTGCCAATGGATATCTTTTTCTTCACGTTTCTCAAGGTAGATATTCAATTA
* * *
14333 TAATCT-TTATTAATAAAAAATATAAAAAAATTCAA-ATTAAA-TCAATTATGAGGTTATAAAAA
66 TAATCTATT-TTAATAAAAAATATAAAAAAATTCAACTTTAAACT-AATTATGAGATTAAAAAAA
14395 NNNNNNNNNN
Statistics
Matches: 255, Mismatches: 38, Indels: 12
0.84 0.12 0.04
Matches are distributed among these distances:
169 1 0.00
170 16 0.06
171 129 0.51
172 40 0.16
173 69 0.27
ACGTcount: A:0.38, C:0.12, G:0.11, T:0.37
Consensus pattern (172 bp):
TAAATGGACTTTTCTTGCCAATGGATATCTTTTTCTTCACGTTTCTCAAGGTAGATATTCAATTA
TAATCTATTTTAATAAAAAATATAAAAAAATTCAACTTTAAACTAATTATGAGATTAAAAAAAGC
ATTTAAAGCAAGTAATAAGGCTTTCGAAAGCATAGGTGACCC
Done.