Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018398513.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_1806.0, 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: 4693
ACGTcount: A:0.19, C:0.06, G:0.08, T:0.19
Warning! 2277 characters in sequence are not A, C, G, or T
Found at i:683 original size:170 final size:168
Alignment explanation
Indices: 328--746 Score: 428
Period size: 170 Copynumber: 2.4 Consensus size: 168
318 NNNNNNNNNN
* * *
328 AACATTCAATTATAATCTGTTCTAATAAAAAATATAAAAAAGTTCAACTTAAAAATATTTATGAG
1 AACATTCAATTATAATCTGTTTTAATAAAAAATA-AAAAAA-TTCAAATT-AAAATAATTATGAG
* * * * *
393 ATTACAAAA-CTATTTAAAGCGAGTAGTAAGGCTTTCGAAGGCATGAGTGATAAAAAATGGACTT
63 GTTACAAAATC-ATTTAAAGCGAGTAATAAGGCTTTCAAAGACATGAGTGATAAAAAACGGACTT
** * * * **
457 CTCTTGCCAATGGATATCATTTTCTTTATGTTTTTTGAGGNN
127 CTCTTGCCAATGGATATCATTTTCTCCACGTTTCTCGAGGTA
********
499 NNNNNNNNATTATAATCTGTTTTAATAACAAAATAAAAAAATTCAAATTAAAATGAATTATGAGG
1 AACATTCAATTATAATCTGTTTTAATAA-AAAATAAAAAAATTCAAATTAAAAT-AATTATGAGG
** * * * *
564 TTGTAAAATCATTTAAAGTGAGTAATAAGGCTTTCAAAGACATGGGTGACT-ATAAACGGACTTT
64 TTACAAAATCATTTAAAGCGAGTAATAAGGCTTTCAAAGACATGAGTGA-TAAAAAACGGACTTC
*
628 TCTTGTCAATGGATATCATTTTCTCCACGTTTCTCGAGGTA
128 TCTTGCCAATGGATATCATTTTCTCCACGTTTCTCGAGGTA
* ** *
669 AACATTCAATTATAATCTATTTTGTTAAAAATTATAAAAAAATTAAAATTAAAATCAATTATGAG
1 AACATTCAATTATAATCTGTTTTAATAAAAA--ATAAAAAAATTCAAATTAAAAT-AATTATGAG
734 GTTACAAAATCAT
63 GTTACAAAATCAT
747 NNNNNNNNNN
Statistics
Matches: 197, Mismatches: 45, Indels: 12
0.78 0.18 0.05
Matches are distributed among these distances:
169 8 0.04
170 115 0.58
171 68 0.35
172 6 0.03
ACGTcount: A:0.40, C:0.11, G:0.13, T:0.34
Consensus pattern (168 bp):
AACATTCAATTATAATCTGTTTTAATAAAAAATAAAAAAATTCAAATTAAAATAATTATGAGGTT
ACAAAATCATTTAAAGCGAGTAATAAGGCTTTCAAAGACATGAGTGATAAAAAACGGACTTCTCT
TGCCAATGGATATCATTTTCTCCACGTTTCTCGAGGTA
Found at i:3647 original size:171 final size:171
Alignment explanation
Indices: 3304--3724 Score: 441
Period size: 171 Copynumber: 2.5 Consensus size: 171
3294 NNNNNNNNNN
* * * *
3304 ATTATGAGGTTATAAAATCATTTAAAGCGAGTAATAAGGCTTTCGAAGGCTTAGTTGAGTATAAA
1 ATTATGAGATTATAAAATCATTTAAAGCGAGTAATAAGGCTTTCGAAGGCATAGGTGACTATAAA
* * * * * *
3369 TGAACTTTTCTTGCCAATGGATATCTTTTTCTTGACATTTTTCGAGGCAGACATTCAATTATATT
66 TGAACTTTTCTTGCCAATGAATATCTTTTGCTTCACATTTCTCGAGGCAAACATTCAATTATAAT
* **********
3434 CTGTTTTAATAAAAAATATAAAAAAANNNNNNNNNNAATCA
131 CTATTTTAATAAAAAATATAAAAAAATTCAGCTTAAAATCA
* * * * *
3475 ATTATGAGATTATCAAATCATTTAAAGCGAGTAATGATGCTTTCGAAGGCATGGGTGACTATGAA
1 ATTATGAGATTATAAAATCATTTAAAGCGAGTAATAAGGCTTTCGAAGGCATAGGTGACTATAAA
* * * *
3540 TGAACTTTTTTTGTCAATGAATATCTTTTGCTTCACGTTTCTCGAGGTAAACATTCAATTATAAT
66 TGAACTTTTCTTGCCAATGAATATCTTTTGCTTCACATTTCTCGAGGCAAACATTCAATTATAAT
* *
3605 CTATTTTTATAAAAAATATAAAAACATTCAGCTTAAAATCA
131 CTATTTTAATAAAAAATATAAAAAAATTCAGCTTAAAATCA
** * * * * *
3646 ATTATGAGGCTCTAAAAACATTT-AAGCCGAGCAATAAGGCTTTTGAAGGCAT-GAATGACTATA
1 ATTATGAGATTATAAAATCATTTAAAG-CGAGTAATAAGGCTTTCGAAGGCATAG-GTGACTATA
* *
3709 AATGGACTTCTCTTGC
64 AATGAACTTTTCTTGC
3725 TAACGGATGT
Statistics
Matches: 201, Mismatches: 47, Indels: 4
0.80 0.19 0.02
Matches are distributed among these distances:
170 4 0.02
171 197 0.98
ACGTcount: A:0.35, C:0.13, G:0.15, T:0.34
Consensus pattern (171 bp):
ATTATGAGATTATAAAATCATTTAAAGCGAGTAATAAGGCTTTCGAAGGCATAGGTGACTATAAA
TGAACTTTTCTTGCCAATGAATATCTTTTGCTTCACATTTCTCGAGGCAAACATTCAATTATAAT
CTATTTTAATAAAAAATATAAAAAAATTCAGCTTAAAATCA
Done.