Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018398161.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_1465.0, 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: 2855
ACGTcount: A:0.23, C:0.08, G:0.07, T:0.23
Warning! 1119 characters in sequence are not A, C, G, or T
Found at i:413 original size:170 final size:169
Alignment explanation
Indices: 109--478 Score: 395
Period size: 170 Copynumber: 2.2 Consensus size: 169
99 ATTTACTTTA
* * *
109 AAGAAAAGTCCATTTATAGTCTCTCATTCCCTTAAAAGCCATATTGCTCTCTGTAAATGGCTTTA
1 AAGAAAAGTCCATTTATAGTCTCTCATT-CATTAAAAGCCATATTACTCGCTGTAAATGGCTTTA
* * * * * * **
174 TCATATCAAAATTGATTTTAAGTTCAATTTTTTAACTTTTTTCGCTAAAACAGATTATAATTAAA
65 TAAGATCAAAACTGATTTCAAGTTAAATTTTTTAAC-TTTTTCGCTAAAACAAACCATAATTAAA
* * * * * *
239 TGTCTACATTA-AGAAACGCGAGGAAAAATGTATTCATTGGC
129 TGTCTAC-CTAGAGAAACACAAAGAAAAAAGCATTCATTGGC
* * *
280 AA-AAAAGTCCATTTATAGTCTCTCATTCATTCAAAAGCCTTATTACTCGCTTTAAATGGTTTTA
1 AAGAAAAGTCCATTTATAGTCTCTCATTCATT-AAAAGCCATATTACTCGCTGTAAATGGCTTTA
* * * * * *
344 TAAGCTCATAACTGATTTCAAGTTAAAATTTTTTACAC-TTTTGGTTGAAACAAACCATAATTGA
65 TAAGATCAAAACTGATTTCAAGTT-AAATTTTTTA-ACTTTTTCGCTAAAACAAACCATAATTAA
* *
408 ATGTCTACCTAGAGAAACATAAAGAAAAAAGCATTCATTGTC
128 ATGTCTACCTAGAGAAACACAAAGAAAAAAGCATTCATTGGC
* *
450 AAGAAAAGTCGATTTATAGTCTCTTATTC
1 AAGAAAAGTCCATTTATAGTCTCTCATTC
479 CNNNNNNNNN
Statistics
Matches: 164, Mismatches: 30, Indels: 10
0.80 0.15 0.05
Matches are distributed among these distances:
169 5 0.03
170 122 0.74
171 35 0.21
172 2 0.01
ACGTcount: A:0.36, C:0.16, G:0.12, T:0.36
Consensus pattern (169 bp):
AAGAAAAGTCCATTTATAGTCTCTCATTCATTAAAAGCCATATTACTCGCTGTAAATGGCTTTAT
AAGATCAAAACTGATTTCAAGTTAAATTTTTTAACTTTTTCGCTAAAACAAACCATAATTAAATG
TCTACCTAGAGAAACACAAAGAAAAAAGCATTCATTGGC
Found at i:1161 original size:171 final size:171
Alignment explanation
Indices: 786--1220 Score: 479
Period size: 171 Copynumber: 2.5 Consensus size: 171
776 ACTTAAAAAA
* * * * * * *
786 AAAAGTCCATTTACAGTCTTCCATACCTTCAAAAGCCCTATTACTACCCTTT-AATAGTTTTGTA
1 AAAAGTCCATTTATAGTCTCCCATTCCTTCAAAAGCCTTATTACT-CGCTTTAAATGGTTTTATA
* * * * *
850 ATCTCATAATTG-TATTTAATTTGAATTTTTTTTACATTTTTTATTAAAATAGACTAGAATTGAA
65 ATCTCATAATTGAT-TTTAAGTTGAA-TTTTTTGACAGTTTTGATTAAAACAGACTAGAATTGAA
** * *
914 TGCTTGCCTTGGAAAACGTGTAGAAAAAGCCATTCATTGACAAG
128 TGCTTGCCTAAGAAAACATGAAGAAAAAGCCATTCATTGACAAG
* *
958 AAAAGTACATTTATAGTCTCTCATTCCTTCAAAAGCCTTATTACTCGCTTTAAATGGTTTTATAA
1 AAAAGTCCATTTATAGTCTCCCATTCCTTCAAAAGCCTTATTACTCGCTTTAAATGGTTTTATAA
* * * *
1023 TCTCATAACTGATTTTAAGTTGAATTTTTTGACAGTTTTGGTTAAAACAGATTATAATTGAATGT
66 TCTCATAATTGATTTTAAGTTGAATTTTTTGACAGTTTTGATTAAAACAGACTAGAATTGAATG-
* **
1088 CTATGTC-AAG-AAACATGAAGAAAAAAG-CATTCATT-AGGGAG
130 CT-TGCCTAAGAAAACATGAAG-AAAAAGCCATTCATTGA-CAAG
* * * *
1129 AAAAGTCCATTTATAGACTCCCATTTCTTCAAAA-ACTTTTGTACTCGCTTTAAATGGTTTTATA
1 AAAAGTCCATTTATAGTCTCCCATTCCTTCAAAAGCCTTAT-TACTCGCTTTAAATGGTTTTATA
*
1193 ATCTCATAATTCATTTTAAGTTGAATTT
65 ATCTCATAATTGATTTTAAGTTGAATTT
1221 GTTNNNNNNN
Statistics
Matches: 223, Mismatches: 33, Indels: 15
0.82 0.12 0.06
Matches are distributed among these distances:
170 5 0.02
171 135 0.61
172 79 0.35
173 4 0.02
ACGTcount: A:0.34, C:0.15, G:0.12, T:0.39
Consensus pattern (171 bp):
AAAAGTCCATTTATAGTCTCCCATTCCTTCAAAAGCCTTATTACTCGCTTTAAATGGTTTTATAA
TCTCATAATTGATTTTAAGTTGAATTTTTTGACAGTTTTGATTAAAACAGACTAGAATTGAATGC
TTGCCTAAGAAAACATGAAGAAAAAGCCATTCATTGACAAG
Done.