Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018399071.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_2346.0, 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: 3490
ACGTcount: A:0.25, C:0.09, G:0.09, T:0.24
Warning! 1163 characters in sequence are not A, C, G, or T
Found at i:3107 original size:172 final size:171
Alignment explanation
Indices: 2400--3490 Score: 555
Period size: 172 Copynumber: 6.4 Consensus size: 171
2390 NNTCTTCACC
* * * ** ** * * * *
2400 TTTCCCAAGGTAGCCATTCAATTATAGTCTGTTTTAATGAAAAATCTAAAAAAAAATGAACTTAC
1 TTTCTCAAGGTAGACATTCAATTATAGTCTGATTTAACCAAAAAAGT-AAAACAATTCAACTTAA
* * * ** * * * * *
2465 AATCAATTATTAGCTTATAAAACCATTTAAAGCGAGTAGTAAGCCTTTTAAAAAAATGAGAGACT
65 AATCAATTATGAGATTATGATGCCATTTAAAGCGAGTAATAAGGCTTTTGAAAGAATGGGAGACT
* * * *
2530 ATAAATTGACTTTT-TT-GCA-GAGGAATGCTTTTTTCTTCATG
130 ATAAATGGACTTTTCTTCCCATTA--AATGCTTTTTTCTTCAAG
* ** * * * *
2571 TTTCTCAAGGTTA-ACATTCAATTATTGTCTTTTTTAACTAAAAATGTACAAAGAATTCAAATTA
1 TTTCTCAAGG-TAGACATTCAATTATAGTCTGATTTAACCAAAAAAGTA-AAACAATTCAACTTA
*************** *
2635 AAATCAATTATGAGATNNNNNNNNNNNNNNNAGCGAGTAATAAGGCTTTTAAAAGAATGGGAGAC
64 AAATCAATTATGAGATTATGATGCCATTTAAAGCGAGTAATAAGGCTTTTGAAAGAATGGGAGAC
* * * *
2700 TATAAACGGACTTTTCTTACTATTAAATGCCTTTTTCTTCAAG
129 TATAAATGGACTTTTCTTCCCATTAAATGCTTTTTTCTTCAAG
* * * * * *
2743 TTTCTCAAGGTAGGCATTCAATTATAGTTTGCTTTAACCAAAAATGTAAAACTATTCGACTTAAA
1 TTTCTCAAGGTAGACATTCAATTATAGTCTGATTTAACCAAAAAAGTAAAACAATTCAACTTAAA
* *
2808 ATCACTTATGAGATTATGATGCCATTTAAAGCGAGTAATAAGGCTTTTGAAAGAATGGGAAACTA
66 ATCAATTATGAGATTATGATGCCATTTAAAGCGAGTAATAAGGCTTTTGAAAGAATGGGAGACTA
* * *
2873 TAAATGGTCTTTTCTTCCCAATGAATGCTTTTTTCTTCACA-
131 TAAATGGACTTTTCTTCCCATTAAATGCTTTTTTCTTCA-AG
********** *
2914 TTTCTNNNNNNNNNNATTCAATTATAGTCTGTTTTAACCAAAAACAG-AAAACAAATTCAACTTA
1 TTTCTCAAGGTAGACATTCAATTATAGTCTGATTTAACCAAAAA-AGTAAAAC-AATTCAACTTA
*********** * * * *
2978 AAATCAATTATGAGNNNNNNNNNNTATTTAAAGTGAGTAATAAGACTTTGGAAAGCATGGGAGAC
64 AAATCAATTATGAGATTATGATGCCATTTAAAGCGAGTAATAAGGCTTTTGAAAGAATGGGAGAC
* *
3043 TATAAATGGACTTTTCTTCCCATTTAATGCTTTTTTCTTCATG
129 TATAAATGGACTTTTCTTCCCATTAAATGCTTTTTTCTTCAAG
* * * * * * * **
3086 TTTCCCAAGGTTGACATTCAATTATAATCTAATTTAA-CAAAAAATGTCCAAAGACTTCAAAGTA
1 TTTCTCAAGGTAGACATTCAATTATAGTCTGATTTAACCAAAAAA-GT-AAAACAATTCAACTTA
* * * ********** * * **
3150 ATATCAATTTTTAGATTATNNNNNNNNNNAAAGTGAGTAATAGGGCTTTT-AAAGGAATGCAAGA
64 AAATCAATTATGAGATTATGATGCCATTTAAAGCGAGTAATAAGGCTTTTGAAA-GAATGGGAGA
* * * * * * *
3214 CTATAAATTGAGTTTTCTTGCTAATGAATGCTTTTGTT-TTCATG
128 CTATAAATGGACTTTTCTTCCCATTAAATGCTTTT-TTCTTCAAG
* * ** * * *
3258 TTTCCCAAGGTA-AGCATTCAATTATAGTCTGTTTTAATTAAAAATGTAAAAAAAATTAAACTTA
1 TTTCTCAAGGTAGA-CATTCAATTATAGTCTGATTTAACCAAAAAAGT-AAAACAATTCAACTTA
* ********** *
3322 AAATCAATTATGAGATTATTANNNNNNNNNNAGTGAGTAATAAGGCTTTTGAAAGAATGGGAGAC
64 AAATCAATTATGAGATTATGATGCCATTTAAAGCGAGTAATAAGGCTTTTGAAAGAATGGGAGAC
* * * * * * * *
3387 TATAAACGGACATTTCTTACCAATGAATGCTTCTTTCTTGATG
129 TATAAATGGACTTTTCTTCCCATTAAATGCTTTTTTCTTCAAG
* * * * * * * *
3430 TTTCTCAAGGTAAACAATCAATTACATTCTGTTTTAACTAAAAATGTAAAAAAATTCAACT
1 TTTCTCAAGGTAGACATTCAATTATAGTCTGATTTAACCAAAAAAGTAAAACAATTCAACT
Statistics
Matches: 708, Mismatches: 192, Indels: 40
0.75 0.20 0.04
Matches are distributed among these distances:
170 2 0.00
171 261 0.37
172 429 0.61
173 15 0.02
174 1 0.00
ACGTcount: A:0.35, C:0.12, G:0.13, T:0.34
Consensus pattern (171 bp):
TTTCTCAAGGTAGACATTCAATTATAGTCTGATTTAACCAAAAAAGTAAAACAATTCAACTTAAA
ATCAATTATGAGATTATGATGCCATTTAAAGCGAGTAATAAGGCTTTTGAAAGAATGGGAGACTA
TAAATGGACTTTTCTTCCCATTAAATGCTTTTTTCTTCAAG
Done.