Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018402039.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_5133.0, 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, 874
Length: 1457
ACGTcount: A:0.33, C:0.10, G:0.12, T:0.31
Warning! 209 characters in sequence are not A, C, G, or T
Found at i:535 original size:169 final size:169
Alignment explanation
Indices: 1--816 Score: 599
Period size: 169 Copynumber: 4.8 Consensus size: 169
* * * * *
1 CTTTTGAAGGAATGGGTGACTGTAAATAGACTTTTTTTTCTCAATGAGTAGCTTGTTTT-AGACG
1 CTTTTGAAGGATTGGGTGACTATAAATAGAC-TTTTCTTCTCAATGAATAGCTTTTTTTCA-A-G
** ** * * * *
65 TTTCTCAAGACAGGCATTCAATTATAGTCTATTTTAA-TAAAAAATATACAAAAATTCAATTTAA
63 TTTCTCAAGGTAAACATTCAATTATACTCTGTTTTAACT-AAAAATGTA-AAAAATTCAACTTAA
* **
129 AATCAATTATGAAATTATAAAATAATTTAAAATGAGTAATAAGG
126 AATCAATTATGAAATTATAAAACAATTTAAAGCGAGTAATAAGG
*********** * * ** * *
173 CTTTNNNNNNNNNNAGTGACTATAAATGGACTTTTTTTCTCAATGAATA-AATTTTTACATGTTT
1 CTTTTGAAGGATTGGGTGACTATAAATAGACTTTTCTTCTCAATGAATAGCTTTTTTTCAAGTTT
* ** ** * * ********* *
237 CTGAAGCCAGGCATTCAATTATAGTCTGTTTTAACCANNNNNNNNNNAAAATTCAACTCAAAATC
66 CTCAAGGTAAACATTCAATTATACTCTGTTTTAACTA-AAAATGTAAAAAATTCAACTTAAAATC
* ** *
302 AATTTTGGGA-TATAAAACAATTTAAAGTGAGTAATAAGG
130 AATTATGAAATTATAAAACAATTTAAAGCGAGTAATAAGG
* * * * *
341 CTTTTAAATG-TATGGGTGACTATAAATGGACTTTTCTTGC-CAATGAATTGCTTTTTTTCATGT
1 CTTTTGAAGGAT-TGGGTGACTATAAATAGACTTTTCTT-CTCAATGAATAGCTTTTTTTCAAGT
* * *
404 TTC-CTGAGGTAAACATTCGATTATTA-TCTGTTTTAACTAAAAATGTAAAAAATTCAACATAAA
64 TTCTC-AAGGTAAACATTCAATTA-TACTCTGTTTTAACTAAAAATGTAAAAAATTCAACTTAAA
* *
467 ATCAATTATGAAATTA-AGAAATAATTTAAAGCGAGTAATGAGG
127 ATCAATTATGAAATTATA-AAACAATTTAAAGCGAGTAATAAGG
* * * *
510 CTTTTGAAGGATTGGGTGGCTATAAACAGACTTTTCTTCTCAATGAATAGCTTTTTTGCACGTTT
1 CTTTTGAAGGATTGGGTGACTATAAATAGACTTTTCTTCTCAATGAATAGCTTTTTTTCAAGTTT
* * * ** *
575 CTCAAGGCAAGCATTCAATTATAGTCTACTTTAA-TAAGAAATGTTAAAAAAATCAACTTAAAAT
66 CTCAAGGTAAACATTCAATTATACTCTGTTTTAACTAA-AAATG-TAAAAAATTCAACTTAAAAT
* * **********
639 GAATTATGAGATTATAAAACAATTTNNNNNNNNNNATAAGG
129 CAATTATGAAATTATAAAACAATTTAAAGCGAGTAATAAGG
* **
680 CTTTTGAAGGACTAAGTGACTATAAATAGACTTTTCTTCTCAATGAATAGCTTTTTTTACAAGTT
1 CTTTTGAAGGATTGGGTGACTATAAATAGACTTTTCTTCTCAATGAATAGCTTTTTTT-CAAGTT
* * *
745 TCTCAAGGTAGACAATCAATTATACTCTGTTTTAACAAAAAATGTAAAATAATTCAACTTAAAAT
65 TCTCAAGGTAAACATTCAATTATACTCTGTTTTAACTAAAAATGTAAAA-AATTCAACTTAAAAT
810 CAATTAT
129 CAATTAT
817 AAGATTANNN
Statistics
Matches: 498, Mismatches: 126, Indels: 41
0.75 0.19 0.06
Matches are distributed among these distances:
168 91 0.18
169 202 0.41
170 108 0.22
171 77 0.15
172 20 0.04
ACGTcount: A:0.37, C:0.11, G:0.13, T:0.35
Consensus pattern (169 bp):
CTTTTGAAGGATTGGGTGACTATAAATAGACTTTTCTTCTCAATGAATAGCTTTTTTTCAAGTTT
CTCAAGGTAAACATTCAATTATACTCTGTTTTAACTAAAAATGTAAAAAATTCAACTTAAAATCA
ATTATGAAATTATAAAACAATTTAAAGCGAGTAATAAGG
Found at i:705 original size:170 final size:161
Alignment explanation
Indices: 507--823 Score: 352
Period size: 171 Copynumber: 1.9 Consensus size: 161
497 GCGAGTAATG
* ** * * *
507 AGGCTTTTGAAGGATTGGGTGGCTATAAACAGACTTTTCTTCTCAATGAATAGC-TTTTTTGCAC
1 AGGCTTTTGAAGGACTAAGTGACTATAAACAGACTTTTCTTCTCAATGAATAGCTTTTTTTACAA
* * * *
571 GTTTCTCAAGGCAAG-CATTCAATTATAGTCTACTTTAATAAGAAATGTTAAAA-AAATCAACTT
66 GTTTCTCAAGG-AAGACAATCAATTATACTCTACTTTAACAAAAAATG-TAAAATAAATCAACTT
* *
634 AAAATGAATTATGAGATTATAAAACAATTTNNNNNNNNNNATA
129 AAAATCAATTATAAGATTATAAAACAATTT----------ATA
*
677 AGGCTTTTGAAGGACTAAGTGACTATAAATAGACTTTTCTTCTCAATGAATAGCTTTTTTTACAA
1 AGGCTTTTGAAGGACTAAGTGACTATAAACAGACTTTTCTTCTCAATGAATAGCTTTTTTTACAA
* ** *
742 GTTTCTCAAGGTAGACAATCAATTATACTCTGTTTTAACAAAAAATGTAAAATAATTCAACTTAA
66 GTTTCTCAAGGAAGACAATCAATTATACTCTACTTTAACAAAAAATGTAAAATAAATCAACTTAA
807 AATCAATTATAAGATTA
131 AATCAATTATAAGATTA
824 NNNNNNNNNN
Statistics
Matches: 127, Mismatches: 17, Indels: 5
0.85 0.11 0.03
Matches are distributed among these distances:
170 56 0.44
171 71 0.56
ACGTcount: A:0.37, C:0.12, G:0.13, T:0.34
Consensus pattern (161 bp):
AGGCTTTTGAAGGACTAAGTGACTATAAACAGACTTTTCTTCTCAATGAATAGCTTTTTTTACAA
GTTTCTCAAGGAAGACAATCAATTATACTCTACTTTAACAAAAAATGTAAAATAAATCAACTTAA
AATCAATTATAAGATTATAAAACAATTTATA
Found at i:903 original size:170 final size:154
Alignment explanation
Indices: 674--994 Score: 281
Period size: 170 Copynumber: 2.0 Consensus size: 154
664 NNNNNNNNNN
* * *
674 ATAAGGCTTTTGAAGGACTAAGTGACTATAAATAGACTTTTCTTCTCAATGAATAGCTTTTTTTA
1 ATAAGACTTTTGAAGGAATAAGTGACTATAAATAGACTTTTCTTCTCAATGAATAGCTTTTTGTA
** * **
739 CAAGTTTCTCAAGG-TAGACAATCAATTATACT-CTGTTTTAACAAAAAATGTAAAAT-AATTCA
66 CAAGCCTCTCAAGGCAAG-CAATCAATTATA-TACTGTTTTAACAAAAAATAAAAAATAAATTCA
801 ACTTAAAATCAATTATAAGATTANNNNNNNNNNNNNNNNNNGTA
129 ACTTAAAATCAATTATAAGATTA------------------GTA
** * * * *
845 ATAAGACTTTTGAAGGAATGGGTGACTATAAATGGA-TTTTTTTCTCAATGAGTAGCTTTTTGTG
1 ATAAGACTTTTGAAGGAATAAGTGACTATAAATAGACTTTTCTTCTCAATGAATAGCTTTTTGTA
* *
909 CATGCCTCTCAAGGCAAGCATTCAATTATATACTGTTTTAACAAAAAATAAAAAATAAATTCAAC
66 CAAGCCTCTCAAGGCAAGCAATCAATTATATACTGTTTTAACAAAAAATAAAAAATAAATTCAAC
*
974 TTAAAATCAATTATGAGATTA
131 TTAAAATCAATTATAAGATTA
995 TNNNNNNNNN
Statistics
Matches: 130, Mismatches: 17, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
169 1 0.01
170 68 0.52
171 61 0.47
ACGTcount: A:0.37, C:0.12, G:0.12, T:0.33
Consensus pattern (154 bp):
ATAAGACTTTTGAAGGAATAAGTGACTATAAATAGACTTTTCTTCTCAATGAATAGCTTTTTGTA
CAAGCCTCTCAAGGCAAGCAATCAATTATATACTGTTTTAACAAAAAATAAAAAATAAATTCAAC
TTAAAATCAATTATAAGATTAGTA
Done.