Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018402201.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_529.0, 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: 2408
ACGTcount: A:0.27, C:0.09, G:0.09, T:0.23
Warning! 754 characters in sequence are not A, C, G, or T
Found at i:275 original size:148 final size:148
Alignment explanation
Indices: 5--291 Score: 493
Period size: 148 Copynumber: 1.9 Consensus size: 148
1 ATTT
* * *
5 AAACCAAATTGAATCAAAATCATTTATAAGATTAGAAAACTGTTTAAAGATAGCAACAAGGATTT
1 AAACCAAATTCAATCAAAATCATTTATAAGATCAGAAAACTGTTTAAAGAGAGCAACAAGGATTT
* *
70 TTAAGACTTGAGTGACTATGGATGGACTTTTCTTGTCAATGGATGGCTTTTGCTTTATGTTGACC
66 TGAAGACTTGAGTGACTATGGATAGACTTTTCTTGTCAATGGATGGCTTTTGCTTTATGTTGACC
135 TGATGCACACCAAAAAAG
131 TGATGCACACCAAAAAAG
* *
153 AAACCAAATTCAATCAAAATCATTTATAAGATCAGAAAATTGTTTAAAGAGAGCAATAAGGATTT
1 AAACCAAATTCAATCAAAATCATTTATAAGATCAGAAAACTGTTTAAAGAGAGCAACAAGGATTT
* *
218 TGAAGACTTGAGTGACTATGGATAGACTTTTCTTGTCAATGGATGGCTTTTGTTTTATGTTTACC
66 TGAAGACTTGAGTGACTATGGATAGACTTTTCTTGTCAATGGATGGCTTTTGCTTTATGTTGACC
283 TGATGCACA
131 TGATGCACA
292 TAGAAAATTC
Statistics
Matches: 130, Mismatches: 9, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
148 130 1.00
ACGTcount: A:0.36, C:0.13, G:0.18, T:0.33
Consensus pattern (148 bp):
AAACCAAATTCAATCAAAATCATTTATAAGATCAGAAAACTGTTTAAAGAGAGCAACAAGGATTT
TGAAGACTTGAGTGACTATGGATAGACTTTTCTTGTCAATGGATGGCTTTTGCTTTATGTTGACC
TGATGCACACCAAAAAAG
Found at i:800 original size:168 final size:168
Alignment explanation
Indices: 433--1040 Score: 487
Period size: 170 Copynumber: 3.6 Consensus size: 168
423 TGTAATTAGG
* * * * * * * *
433 TGGCTTTTGCTTCATATTTC-CTTATGCAGAGATGAAATAATAATTTGATTTAACCAAAAAAGAA
1 TGGCTTTTGCTTCACATTTCTC-AATGCAAACATCAAATTATGATTTGTTTTAACC--AAAAGAA
** * * * * * *
497 AAAAAATTCAAGTTAAAATCATTTATAAAGTTATAAAACCACTTAAAACGACTAATAAGTCTTTC
63 AAAAAATT-ATTTTAAAATCATTTATAAAGATATAAAACCACTTAAAGCAAGTAACAAGGCTTTC
* * *
562 AAAGACATGAGTGATTATAAATAGACTTTTCTTATCAATGGA
127 GAAGGCATGAGTGACTATAAATAGACTTTTCTTATCAATGGA
* ** ** *
604 TGCCAATCACTTTC-TATTT-TCTAATGCAAACAAT-AAATTATGATTTGTTTTAACCAAAAGAA
1 TGGCTTTTGC-TTCACATTTCTC-AATGCAAAC-ATCAAATTATGATTTGTTTTAACCAAAAGAA
* *
666 AAAAAATTATTTTAATATCTTTTATAAAGATATAAAACCACTTAAAGCAAGTAACAAGGCTTTCG
63 AAAAAATTATTTTAAAATCATTTATAAAGATATAAAACCACTTAAAGCAAGTAACAAGGCTTTCG
* * * *
731 AAGGTATTAGTGACTATAAATGGGCTTTTCTTATCAATGGA
128 AAGGCATGAGTGACTATAAATAGACTTTTCTTATCAATGGA
** * * **
772 TGGCTTTTGCTTCACATTTCTCAATGCAAACATCAAATTATGACCTATTTGAACCAAAAGTGAAA
1 TGGCTTTTGCTTCACATTTCTCAATGCAAACATCAAATTATGATTTGTTTTAACCAAAAGAAAAA
* * * * *
837 AAATT-TTGATTCAAAATCATTTAT-ATGATTATAAAACAACATT-GAGCTAGTAGCAAGGCTTT
66 AAATTATT--TT-AAAATCATTTATAAAGA-TATAAAACCAC-TTAAAGCAAGTAACAAGGCTTT
* ** * **
899 TGAAGGCATGAGCAACTATAAATAGACTTTTCTTGTTGATGGA
126 CGAAGGCATGAGTGACTATAAATAGACTTTTCTTATCAATGGA
* * * * *
942 TAGCTTTTGAC-TCACGTTTCTCAATGCAAGCATCATATTATGATTTGTTTTAACTAAAAATGAA
1 TGGCTTTTG-CTTCACATTTCTCAATGCAAACATCAAATTATGATTTGTTTTAAC-CAAAA-GAA
* * * * *
1006 ATAAACTAAATTTAAAATTATTTAT-AAGATTATAA
63 AAAAAATTATTTTAAAATCATTTATAAAGA-TATAA
1041 NNNNNNNNNN
Statistics
Matches: 348, Mismatches: 74, Indels: 31
0.77 0.16 0.07
Matches are distributed among these distances:
167 7 0.02
168 129 0.37
169 22 0.06
170 133 0.38
171 45 0.13
172 11 0.03
173 1 0.00
ACGTcount: A:0.40, C:0.13, G:0.12, T:0.35
Consensus pattern (168 bp):
TGGCTTTTGCTTCACATTTCTCAATGCAAACATCAAATTATGATTTGTTTTAACCAAAAGAAAAA
AAATTATTTTAAAATCATTTATAAAGATATAAAACCACTTAAAGCAAGTAACAAGGCTTTCGAAG
GCATGAGTGACTATAAATAGACTTTTCTTATCAATGGA
Done.