Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018398795.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_2078.0, 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, 885
Length: 1475
ACGTcount: A:0.38, C:0.12, G:0.12, T:0.35
Warning! 50 characters in sequence are not A, C, G, or T
Found at i:503 original size:171 final size:171
Alignment explanation
Indices: 2--1475 Score: 933
Period size: 171 Copynumber: 8.6 Consensus size: 171
1 T
* ** * * *
2 CAATGAATATCTTTTTCTTCACATTTCTCAAGGTAAACATTCAA-TATTAATCTGTTTTAATAAA
1 CAATGAATAGCTTTTTCTTCAGTTTTCTCAAAGCAAACATTCAATTA-TAATCTGTTTTAATTAA
* * * * * * *
66 AAATAT-AAATAATTCAA-TGTAAAATCGATTATGAGGTTATAAAATCATTTAAAACGAGTAATA
65 AAATGTAAAAAAATTTAACT-TAAAATCAATTATGAGATTATAAAAACATTTAAAGCGAGTAATA
* * ********** *
129 AGGCTTTCGAANNNNNNNNNNACTATAAATAGACTTTTCTTGC
129 AGACTTTCAAAGGCATGGGTGACTATAAATGGACTTTTCTTGC
* * * * * * **
172 CAATGGATATCTTTTTCTTCAAGTTTTGT-AAGGCAGACATTCAATTACT-TTCTGTTTTAACAA
1 CAATGAATAGCTTTTTCTTC-AGTTTTCTCAAAGCAAACATTCAATTA-TAATCTGTTTTAA-TT
* * * * * ** * * **
235 AAAAATATATAAAAATTTAAGTTAAAGTTAATTACAAGATTCTAAAAACATTT-TAGTTACGTAA
63 AAAAATGTAAAAAAATTTAACTTAAAATCAATTATGAGATTATAAAAACATTTAAAGCGA-GTAA
* ** ********** *
299 TAAGGCTTTTGAANNNNNNNNNNACAATAAATGGACTTTTCTTGC
127 TAAGACTTTCAAAGGCATGGGTGACTATAAATGGACTTTTCTTGC
* * * * * *
344 CAATGAATGGCTTTTTCTTTAGGTTTTC-CTAGGCAAACATT-AAGTTATTATTTGTTTTAATTA
1 CAATGAATAGCTTTTTCTTCA-GTTTTCTCAAAGCAAACATTCAA-TTATAATCTGTTTTAATTA
* * * *
407 AAAATGTAAAAACATTTTGA-TTGAAATTAATTATGAGATTATAAAAACATTTAAAGCGAGTAAT
64 AAAATGTAAAAA-AATTTAACTTAAAATCAATTATGAGATTATAAAAACATTTAAAGCGAGTAAT
* * *
471 AAGACTTTTAAAGGCATCGGTGACTATAAATGGGCTTTTCTTGC
128 AAGACTTTCAAAGGCATGGGTGACTATAAATGGACTTTTCTTGC
* ** * * * ** *
515 CAATGAATATCTTTTTCTTCACATTTCTCAAGGCAAACATTCAATTCTTATCTGTTTTAACCAAG
1 CAATGAATAGCTTTTTCTTCAGTTTTCTCAAAGCAAACATTCAATTATAATCTGTTTTAATTAAA
* * * *
580 AATGTAAAAAAATTTGACTTAAAATCAATTATGAGATTAAAAAAATATTTAAGGCGAGTAATAAG
66 AATGTAAAAAAATTTAACTTAAAATCAATTATGAGATTATAAAAACATTTAAAGCGAGTAATAAG
************ * *
645 GNNNNNNNNNNTATGGGTGACTATAAATGGACTTCTCTAGC
131 ACTTTCAAAGGCATGGGTGACTATAAATGGACTTTTCTTGC
* * * *
686 CACTGTATATCTTTTTCTTCACG-TTTCTCAAAGCATAA-ATTCAATTATAATCTGTTTTAATAA
1 CAATGAATAGCTTTTTCTTCA-GTTTTCTCAAAGCA-AACATTCAATTATAATCTGTTTTAATTA
** * *
749 AAAAAATAAAAAAATTTAACTTAAAATCAATTATGAGATTATAAACACATTTAAGGCGAGTAATA
64 AAAATGTAAAAAAATTTAACTTAAAATCAATTATGAGATTATAAAAACATTTAAAGCGAGTAATA
* * * * *
814 AGGCTTTCGAAGGCATGGGTGAATATAAATGGATTTTTCTTAC
129 AGACTTTCAAAGGCATGGGTGACTATAAATGGACTTTTCTTGC
* *
857 CAATGGATATG-TTTTTCTTCA-TATTTCTCGAAGCAAACATTCAATTATAATCTGTTTTAA-TA
1 CAATGAATA-GCTTTTTCTTCAGT-TTTCTCAAAGCAAACATTCAATTATAATCTGTTTTAATTA
* * * * * *
919 GAAACTGT-AAAAAATTTAACTTAAAATTAATTATGAGGTTATAAAATCATTTAAACCAAGTAAT
64 -AAAATGTAAAAAAATTTAACTTAAAATCAATTATGAGATTATAAAAACATTTAAAGCGAGTAAT
* * * *
983 AAGACTTTCAAATGCATGGGTAACTATAAATGGACATTTGTTGC
128 AAGACTTTCAAAGGCATGGGTGACTATAAATGGACTTTTCTTGC
* ** * * ***
1027 CAATGAATGGCTTTTT-TTCCACATTTGTC-AAGTCAAACATTCAATTATTATCTGTTTTACCCA
1 CAATGAATAGCTTTTTCTT-CAGTTTTCTCAAAG-CAAACATTCAATTATAATCTGTTTTAATTA
* * ********** * *
1090 AAAATGTAAAAAAA-TCAACTTAAAATCATTTANNNNNNNNNNAAACCATTTAAAGTGAGTAATA
64 AAAATGTAAAAAAATTTAACTTAAAATCAATTATGAGATTATAAAAACATTTAAAGCGAGTAATA
** ** * * * * **
1154 AGGGTTTTGAAGACATGAGTCACTATAAGTAAACTTTTCTTGC
129 AGACTTTCAAAGGCATGGGTGACTATAAATGGACTTTTCTTGC
* * * *
1197 CAATGAATATCTTTTTCTTCA-TGTTTCT-AAAGGAAGACATTCAATTTTAATCTGTTTTAATAA
1 CAATGAATAGCTTTTTCTTCAGT-TTTCTCAAAGCAA-ACATTCAATTATAATCTGTTTTAATTA
* *
1260 AAAAAGTAAAAAAATTCT-ACTTAAAGTCAATTATGAGATTATAAAAACATTTAAAGC-ATGTAA
64 AAAATGTAAAAAAATT-TAACTTAAAATCAATTATGAGATTATAAAAACATTTAAAGCGA-GTAA
* ** **********
1323 TAAGGCTTTTGAAGGCATGGGTGACTATAANNNNNNNNNNCTTGC
127 TAAGACTTTCAAAGGCATGGGTGACTATAAATGGACTTTTCTTGC
* * * * ** *
1368 CAATGAATATCTTTTTCTTCA-TGTTTCCCAAGGTAGTCATTCAATTATAATCTGTTTTAATAAA
1 CAATGAATAGCTTTTTCTTCAGT-TTTCTCAAAGCAAACATTCAATTATAATCTGTTTTAATTAA
* * *
1432 AAATCTAAAAACATTCAACTTAAAATCAATTATGAGATTATAAA
65 AAATGTAAAAAAATTTAACTTAAAATCAATTATGAGATTATAAA
Statistics
Matches: 1026, Mismatches: 241, Indels: 73
0.77 0.18 0.05
Matches are distributed among these distances:
169 8 0.01
170 311 0.30
171 570 0.56
172 136 0.13
173 1 0.00
ACGTcount: A:0.38, C:0.12, G:0.12, T:0.35
Consensus pattern (171 bp):
CAATGAATAGCTTTTTCTTCAGTTTTCTCAAAGCAAACATTCAATTATAATCTGTTTTAATTAAA
AATGTAAAAAAATTTAACTTAAAATCAATTATGAGATTATAAAAACATTTAAAGCGAGTAATAAG
ACTTTCAAAGGCATGGGTGACTATAAATGGACTTTTCTTGC
Done.