Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018401980.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_5077.0, 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: 3338
ACGTcount: A:0.25, C:0.08, G:0.09, T:0.23
Warning! 1180 characters in sequence are not A, C, G, or T
Found at i:1901 original size:171 final size:171
Alignment explanation
Indices: 1590--2077 Score: 397
Period size: 171 Copynumber: 2.9 Consensus size: 171
1580 NNNNNNNNNN
* * * * * * * *
1590 TTCAACTTAAAATCAATTATGATATTATAAAACCATTTAAAGCGAGTAATAGGGTTTTTGAAGGA
1 TTCAACTTAAAATCAATTATGAGATAATAAAACCATTTAAAGCAAATAATAAGCTTTTCGAAGCA
**********
1655 ATCAATGACTCTAAATGGACTTTTCTTATCAATGAATGCTTGTTTCTTCACATTNNNNNNNNNNG
66 ATCAATGACTCTAAATGGACTTTTCTTATCAATGAATGCTTGTTTCTTCACATTTCTTGAGATAG
* *
1720 ACATTCAATTATAGTATGTTTTAACAAAAAATGCAAAATAA
131 ACAATCAATTATAGTATGTTTTAACAAAAAATGCAAAAAAA
* * *
1761 TTCAACTTAAAATCAATTTTGAGATAATAAAACTATTTAAAGTAAATAATAAGCTTTTCGAAGCA
1 TTCAACTTAAAATCAATTATGAGATAATAAAACCATTTAAAGCAAATAATAAGCTTTTCGAAGCA
** * * *
1826 ATGGATGACTCTAAATGGACTTTTCTTGTTAATGAATGCTTGTTT-TTACACGTTTCTTGAGATA
66 ATCAATGACTCTAAATGGACTTTTCTTATCAATGAATGCTTGTTTCTT-CACATTTCTTGAGATA
* * *
1890 TACAATCAATTATAGTCTGTTTTAACAAAAAATGTAAAAAAA
130 GACAATCAATTATAGTATGTTTTAACAAAAAATGCAAAAAAA
* * ********** * * * * * * *
1932 TTTAATTTAANNNNNNNNNNGAGATTATAAAACTATTTAAAGCGAGTAATAAACCTTTT-GAGGG
1 TTCAACTTAAAATCAATTATGAGATAATAAAACCATTTAAAGCAAATAAT-AAGCTTTTCGAAGC
*** * * * * *
1996 AATTGGTGACTCTAAATAGA-TTTTTTTATCAATAAATGCTTGTTTCTTCACATTTCTCGAGGTA
65 AATCAATGACTCTAAATGGACTTTTCTTATCAATGAATGCTTGTTTCTTCACATTTCTTGAGATA
* *
2060 GACATTTAATTATAGTAT
130 GACAATCAATTATAGTAT
2078 NNNNNNNNNN
Statistics
Matches: 250, Mismatches: 64, Indels: 7
0.78 0.20 0.02
Matches are distributed among these distances:
170 50 0.20
171 193 0.77
172 7 0.03
ACGTcount: A:0.36, C:0.11, G:0.12, T:0.36
Consensus pattern (171 bp):
TTCAACTTAAAATCAATTATGAGATAATAAAACCATTTAAAGCAAATAATAAGCTTTTCGAAGCA
ATCAATGACTCTAAATGGACTTTTCTTATCAATGAATGCTTGTTTCTTCACATTTCTTGAGATAG
ACAATCAATTATAGTATGTTTTAACAAAAAATGCAAAAAAA
Found at i:3075 original size:170 final size:170
Alignment explanation
Indices: 2655--3327 Score: 516
Period size: 171 Copynumber: 3.9 Consensus size: 170
2645 NNNNNNNNNN
* * * * *
2655 AGGAAT-GAGTGACACTAAATA-AACTTTTCTTGTCAATGAATGTTTGTTTCTGCACGTTTC-CA
1 AGGAATCG-GTGACTCTAAATAGAA-TTCTCTTATCAATGAATGCTTGTTTCTTCACGTTTCTC-
* * * **********
2717 GAGGTAAACAATCAATTATAGTCTGTTTTAACAAAAAATGTANNNNNNNNNNACTTAAAATCAAT
63 GAGGTAGACATTCAATTATAGTATGTTTTAAC-AAAAATGTAAAATAATTCAACTTAAAATCAAT
* * * * * *
2782 TATGAGGTTATAAAACTATTTAAAACAAATAATAAGCTTTTCGA
127 TATGAGATTATAAAACTATTTAAAGCGAGTAATAAGCCTTTCAA
* * * * * * ****
2826 AGGAATGGGTGACTCTAATTGGACTATTCT-TT-TCAATGAATACTTGTTTCCGT-ACGATNNNN
1 AGGAATCGGTGACTCTAAATAGA--ATTCTCTTATCAATGAATGCTTGTTT-CTTCACGTTTCTC
****** * * * **
2888 NNNNNNGACAATCAATTATAGTCTGTTTTAAAAAAAACATAAAATAATTCAACTTAAAACTC-AT
63 GAGGTAGACATTCAATTATAGTATGTTTTAACAAAAATGTAAAATAATTCAACTTAAAA-TCAAT
*
2952 TATGAGATTATAAAACTATTTAAAGCGAGTAGTAAGCCTTTCAA
127 TATGAGATTATAAAACTATTTAAAGCGAGTAATAAGCCTTTCAA
* * * *
2996 AGGAATCGGTGACTCTAAATAGAATTTTCTTATTAATGAATGCTTGTTTCTTCGCGTTTCTTGAG
1 AGGAATCGGTGACTCTAAATAGAATTCTCTTATCAATGAATGCTTGTTTCTTCACGTTTCTCGAG
* * * * *
3061 GTAGACATTCAATTATAGAATGCTTTCATCAAAAATGTAAAATTATTCAACTTAAAATCAATTAC
66 GTAGACATTCAATTATAGTATG-TTTTAACAAAAATGTAAAATAATTCAACTTAAAATCAATTAT
* * ** *
3126 GAGATTATAAAATTATTTAATGCGAGTAATAAGGTTTTCGA
130 GAGATTATAAAACTATTTAAAGCGAGTAATAAGCCTTTCAA
********** * *
3167 AGGAATNNNNNNNNNNAAATAGACTTCTCTTATCAATGAATGCTTGTTTCTTTACGTTTCTCGAG
1 AGGAATCGGTGACTCTAAATAGAATTCTCTTATCAATGAATGCTTGTTTCTTCACGTTTCTCGAG
* * * *
3232 GTCGACATTCAATTATAGTATGGTTTAATCAAAAATGTAAAACAATCCAACTT-AAATCAATTAT
66 GTAGACATTCAATTATAGTATGTTTTAA-CAAAAATGTAAAATAATTCAACTTAAAATCAATTAT
3296 GAGATTATAAAACTATTTAAAGCGAGTAATAA
130 GAGATTATAAAACTATTTAAAGCGAGTAATAA
3328 ACGTTTTGAA
Statistics
Matches: 388, Mismatches: 101, Indels: 27
0.75 0.20 0.05
Matches are distributed among these distances:
168 4 0.01
169 4 0.01
170 153 0.39
171 218 0.56
172 5 0.01
173 3 0.01
174 1 0.00
ACGTcount: A:0.37, C:0.12, G:0.13, T:0.33
Consensus pattern (170 bp):
AGGAATCGGTGACTCTAAATAGAATTCTCTTATCAATGAATGCTTGTTTCTTCACGTTTCTCGAG
GTAGACATTCAATTATAGTATGTTTTAACAAAAATGTAAAATAATTCAACTTAAAATCAATTATG
AGATTATAAAACTATTTAAAGCGAGTAATAAGCCTTTCAA
Done.