Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018398883.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_2165.0, 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:0.35, C:0.10, G:0.14, T:0.35
Warning! 77 characters in sequence are not A, C, G, or T
Found at i:689 original size:339 final size:342
Alignment explanation
Indices: 156--965 Score: 1085
Period size: 339 Copynumber: 2.4 Consensus size: 342
146 NNNNNNNNNN
* * * * * * *
156 AGCGAGTAATAAGGCTTTTGAAGAAATAAGAGACTATAAATAGACTTTTCTTGCGAATGAATACT
1 AGCGAGTAATAAGCCTTTTGAAGGAATAGGAGACTATAAATGGACTTTTCTTGCCAATGAATGCA
* *
221 TTTTTCTTTATGTTTCTCAAGGTAAAACATTCAATTATAGTCTGTTTTGACTAAAAATCTTAAAA
66 TTTTTCTTTATGTTTCTCAAGGT-AAACATTCAATTATAGTCTGTTTTAACTAAAAATCTAAAAA
* *
286 CATTCAACTTAAAATCAATTATGAGATTGTAAAACCATTTAAAGCAAGTGAAAAGGGTTTTGAAG
130 CATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCAAGTAAAAAGGGTTTTGAAG
* *
351 GAATGGGAGACTATAAATGGAC-TTCTCTTGCCAATGAATGCTTGTTTCTTGATGTTTCTCAAGA
195 GAATAGGAGACTATAAATGGACATT-TCTTGCCAATGAATGCTTGTTTCTTGACGTTTCTCAAGA
* * * *
415 AAGACATTCAATTATAATTTGTTTTAACCAATAATCTAATAAAATTTGACTTAAAATGAATTATT
259 AAGACATTCAATTATAATCTATTTTAACCAATAATCTAATAAAAATTGACTTAAAATGAATTACT
480 AGATTATAAAACAATTTAA
324 AGATTATAAAACAATTTAA
* * * * *
499 AGCGAGT-ATAAGTCTTTTGAAGGATTAGGAAATTGTAAATGGACTTTTCTTGCCAATGAATGC-
1 AGCGAGTAATAAGCCTTTTGAAGGAATAGGAGACTATAAATGGACTTTTCTTGCCAATGAATGCA
*
562 TTTTT-TTTATGTTTCTCAAGGTAAACATTGAATTATAGTCTGTTTTAACTAAAAATCTAAAAAC
66 TTTTTCTTTATGTTTCTCAAGGTAAACATTCAATTATAGTCTGTTTTAACTAAAAATCTAAAAAC
********** **
626 ATTCAANNNNNNNNNNATTATGAGATTATAAAACCATTTAAAGTGAGTAAAAAGGGTTTTGAAGG
131 ATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCAAGTAAAAAGGGTTTTGAAGG
* ** **
691 AATAGGAGATTATAAATGGACATTTCTTGCCAATGAATGCTTGTTTCTTGACGTTTCTTTAGGTA
196 AATAGGAGACTATAAATGGACATTTCTTGCCAATGAATGCTTGTTTCTTGACGTTTCTCAAGAAA
*
756 GACATTCAATTATAATCTATTTTAACCAATAATGTAATAAAAATTGACTTAAAATGAATTACTAG
261 GACATTCAATTATAATCTATTTTAACCAATAATCTAATAAAAATTGACTTAAAATGAATTACTAG
821 ATTATAAAACAATTTAA
326 ATTATAAAACAATTTAA
* * * * *
838 TGTGAGTAATAAGCCTTTTGAAGGAATGGGTGACTATAAATGGA-TTTTCTT-CTAAGTGAATGC
1 AGCGAGTAATAAGCCTTTTGAAGGAATAGGAGACTATAAATGGACTTTTCTTGCCAA-TGAATGC
* * * *
901 ATTTTTCTTCATGTTTCTCAAGGTAGATATTCAATTATAGTCTGTTTTAA-TGAAAAATATAAAA
65 ATTTTTCTTTATGTTTCTCAAGGTAAACATTCAATTATAGTCTGTTTTAACT-AAAAATCTAAAA
965 A
129 A
966 AANNNNNNNN
Statistics
Matches: 407, Mismatches: 54, Indels: 14
0.86 0.11 0.03
Matches are distributed among these distances:
338 3 0.01
339 241 0.59
340 54 0.13
341 56 0.14
342 46 0.11
343 7 0.02
ACGTcount: A:0.37, C:0.10, G:0.15, T:0.36
Consensus pattern (342 bp):
AGCGAGTAATAAGCCTTTTGAAGGAATAGGAGACTATAAATGGACTTTTCTTGCCAATGAATGCA
TTTTTCTTTATGTTTCTCAAGGTAAACATTCAATTATAGTCTGTTTTAACTAAAAATCTAAAAAC
ATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCAAGTAAAAAGGGTTTTGAAGG
AATAGGAGACTATAAATGGACATTTCTTGCCAATGAATGCTTGTTTCTTGACGTTTCTCAAGAAA
GACATTCAATTATAATCTATTTTAACCAATAATCTAATAAAAATTGACTTAAAATGAATTACTAG
ATTATAAAACAATTTAA
Found at i:859 original size:171 final size:171
Alignment explanation
Indices: 156--967 Score: 838
Period size: 171 Copynumber: 4.8 Consensus size: 171
146 NNNNNNNNNN
* * * * *
156 AGCGAGTAATAAGGCTTTTGAAGAAATAAGAGACTATAAATAGACTTTTCTTGCGAATGAATACT
1 AGCGAGTAATAAGGCTTTTGAAGGAATAGGAGACTATAAATGGACTTTTCTTGCCAATGAATGC-
* * * *
221 TTTTTCTTTATGTTTCTCAAGGTAAAACATTCAATTATAGTCTGTTTTGACTAAAAATCT--TAA
65 TTTTTCTTGATGTTTCTCAAGGT-AGACATTCAATTATAGTCTGTTTTAACCAAAAATCTAATAA
* * *
284 AACATTCAACTTAAAATCAATTATGAGATTGTAAAACCATTTAA
129 AA-ATTCAACTTAAAATGAATTATGAGATTATAAAACAATTTAA
* * * *
328 AGCAAGTGAA-AAGGGTTTTGAAGGAATGGGAGACTATAAATGGACTTCTCTTGCCAATGAATGC
1 AGCGAGT-AATAAGGCTTTTGAAGGAATAGGAGACTATAAATGGACTTTTCTTGCCAATGAATGC
** * * *
392 TTGTTTCTTGATGTTTCTCAAGAAAGACATTCAATTATAATTTGTTTTAACCAATAATCTAAT-A
65 TT-TTTCTTGATGTTTCTCAAGGTAGACATTCAATTATAGTCTGTTTTAACCAAAAATCTAATAA
** *
456 AAATTTGACTTAAAATGAATTATTAGATTATAAAACAATTTAA
129 AAATTCAACTTAAAATGAATTATGAGATTATAAAACAATTTAA
* * * * *
499 AGCGAGT-ATAAGTCTTTTGAAGGATTAGGAAATTGTAAATGGACTTTTCTTGCCAATGAATGCT
1 AGCGAGTAATAAGGCTTTTGAAGGAATAGGAGACTATAAATGGACTTTTCTTGCCAATGAATGCT
* * * * *
563 TTTT-TTTATGTTTCTCAAGGTAAACATTGAATTATAGTCTGTTTTAACTAAAAATCTAA-AAAC
66 TTTTCTTGATGTTTCTCAAGGTAGACATTCAATTATAGTCTGTTTTAACCAAAAATCTAATAAAA
********** *
626 ATTCAANNNNNNNNNNATTATGAGATTATAAAACCATTTAA
131 ATTCAACTTAAAATGAATTATGAGATTATAAAACAATTTAA
* * * * *
667 AGTGAGTAAAAAGGGTTTTGAAGGAATAGGAGATTATAAATGGACATTTCTTGCCAATGAATGCT
1 AGCGAGTAATAAGGCTTTTGAAGGAATAGGAGACTATAAATGGACTTTTCTTGCCAATGAATGCT
* ** * * * *
732 TGTTTCTTGACGTTTCTTTAGGTAGACATTCAATTATAATCTATTTTAACCAATAATGTAATAAA
66 T-TTTCTTGATGTTTCTCAAGGTAGACATTCAATTATAGTCTGTTTTAACCAAAAATCTAATAAA
*
797 AATT-GACTTAAAATGAATTACT-AGATTATAAAACAATTTAA
130 AATTCAACTTAAAATGAATTA-TGAGATTATAAAACAATTTAA
* * * * * *
838 TGTGAGTAATAAGCCTTTTGAAGGAATGGGTGACTATAAATGGA-TTTTCTT-CTAAGTGAATGC
1 AGCGAGTAATAAGGCTTTTGAAGGAATAGGAGACTATAAATGGACTTTTCTTGCCAA-TGAATGC
* * ** *
901 ATTTTTCTTCATGTTTCTCAAGGTAGATATTCAATTATAGTCTGTTTTAATGAAAAATATAA-AA
65 -TTTTTCTTGATGTTTCTCAAGGTAGACATTCAATTATAGTCTGTTTTAACCAAAAATCTAATAA
965 AAA
129 AAA
968 NNNNNNNNNN
Statistics
Matches: 518, Mismatches: 109, Indels: 29
0.79 0.17 0.04
Matches are distributed among these distances:
168 81 0.16
169 63 0.12
170 112 0.22
171 179 0.35
172 80 0.15
173 3 0.01
ACGTcount: A:0.37, C:0.10, G:0.15, T:0.36
Consensus pattern (171 bp):
AGCGAGTAATAAGGCTTTTGAAGGAATAGGAGACTATAAATGGACTTTTCTTGCCAATGAATGCT
TTTTCTTGATGTTTCTCAAGGTAGACATTCAATTATAGTCTGTTTTAACCAAAAATCTAATAAAA
ATTCAACTTAAAATGAATTATGAGATTATAAAACAATTTAA
Done.