Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018398474.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_1770.0, 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: 14091
ACGTcount: A:0.21, C:0.07, G:0.08, T:0.21
Warning! 6184 characters in sequence are not A, C, G, or T
Found at i:12103 original size:171 final size:169
Alignment explanation
Indices: 11511--12104 Score: 567
Period size: 171 Copynumber: 3.5 Consensus size: 169
11501 NNNNNNNNNN
* * * *
11511 GACTTTTCTTGTCAATGAAT-GCTTGTTTCTTCACGTTTCTCAAGGTAGACATTCGATTATAGTA
1 GACTTTTCTTCTCAATGAATAGCTT-TTTCTTCACGTTTCCCAAGGTAGACATTCAATTATAGTT
* * * * * *
11575 TGTTTTAATCAAAAACGTAAAAAAACTAAACTTAAAATCAATTATGAGATTATAATACTATTTAA
65 TTTTTTAAGCAAAAA-ATAAAAAAATTAAACTTAAAATCAATTATGAAATTATAAAAC-ATTTAA
* * *
11640 AGCGAGTAATAAGCCTTTTGAAGGAATCG-GTGACTATAAATA
128 AGTGAGTAATAAGACTTTTGAAGGAAT-GAGTGACTATAAATG
* * * * * * * *
11682 GACTTTTTTTC-CAAATGAATGGCTTTTACTGT-ACATTTCTCGAGTTAGACATTCAATTTTTA-
1 GACTTTTCTTCTC-AATGAATAGCTTTTTCT-TCACGTTTCCCAAGGTAGACATTCAA-TTATAG
* * * * * * *
11744 TTTGTTTTAAAGCAAAAAGTAAAATAATTCATCCTAAATTCAATTAT-AAGATTATAAAATCATT
63 TTT-TTTTTAAGCAAAAAATAAAAAAATTAAACTTAAAATCAATTATGAA-ATTATAAAA-CATT
* * * *
11808 TAAACTGAGTAATAAGGCTTTAGAAGAAATGAGTGACTATAAATG
125 TAAAGTGAGTAATAAGACTTTTGAAGGAATGAGTGACTATAAATG
* * * * ** *
11853 GACTTTTGTTCTCAATGGATAAGCTTTTTCTACACGTTTCCCATGGTAGGTATTCAATTATAGTC
1 GACTTTTCTTCTCAATGAAT-AGCTTTTTCTTCACGTTTCCCAAGGTAGACATTCAATTATAGTT
* * * * *
11918 TATTTTAA-CAAAAAATAAATAAAATTTAACTTAAAATCAATCATGAAATTGTAAAACAATTAAA
65 TTTTTTAAGCAAAAAATAAA-AAAATTAAACTTAAAATCAATTATGAAATTATAAAAC-ATT-TA
11982 AAGTG-GCTAATAAGACTTTTGAAGGAATGAGTGACTATAAATG
127 AAGTGAG-TAATAAGACTTTTGAAGGAATGAGTGACTATAAATG
* * *
12025 GACTTTCCTTCTCAATGAATAGTTTTTTCTTCACGTTTCCCAAGGTAGACAATCAATTATAGTTT
1 GACTTTTCTTCTCAATGAATAGCTTTTTCTTCACGTTTCCCAAGGTAGACATTCAATTATAGTTT
12090 TTTTTAA-CAAAAAAT
66 TTTTTAAGCAAAAAAT
12105 GTAAAACAAT
Statistics
Matches: 340, Mismatches: 66, Indels: 34
0.77 0.15 0.08
Matches are distributed among these distances:
170 14 0.04
171 220 0.65
172 106 0.31
ACGTcount: A:0.38, C:0.13, G:0.13, T:0.36
Consensus pattern (169 bp):
GACTTTTCTTCTCAATGAATAGCTTTTTCTTCACGTTTCCCAAGGTAGACATTCAATTATAGTTT
TTTTTAAGCAAAAAATAAAAAAATTAAACTTAAAATCAATTATGAAATTATAAAACATTTAAAGT
GAGTAATAAGACTTTTGAAGGAATGAGTGACTATAAATG
Found at i:12611 original size:171 final size:171
Alignment explanation
Indices: 12325--12924 Score: 717
Period size: 171 Copynumber: 3.5 Consensus size: 171
12315 NNNNNNNNNN
** *
12325 TTTTGAAGGAATAAGTGACTCTAAAT-AGACTTTTCTTGTCAATGAATGCTTGTTTCCTT-ATGT
1 TTTTGAAGGAATGGGTGACTCTAAATGA-ACTTTTCTTGTCAATGAATGCTTGTTT-CTTCACGT
* * * * * * *
12388 TTC-CTAAGGTAGACATTCAATTATCGCCCGTTTTAGCAAAAAATGAAAAAAAATTCAACATAAA
64 TTCTC-GAGGTAGACATTCAATTATAGTCTGTTTTAACAAAAAATGTAAAAAAATTCAACTTAAA
* *
12452 ATGAATTATAAGATTATAAAACTATTTAAAGCGAGTAATAAGCC
128 ATCAATTATGAGATTATAAAACTATTTAAAGCGAGTAATAAGCC
* *
12496 TTTTGAAGGAATGGGTGACTCTAAATGAACTTTTATTGTCAATAAATGCTTGTTTCTTCACGTTT
1 TTTTGAAGGAATGGGTGACTCTAAATGAACTTTTCTTGTCAATGAATGCTTGTTTCTTCACGTTT
* *
12561 CTCGAGGTAGACATTTAATTATAGTATGTTTTAATC-AAAAATGTAAAAAAATTCAACTTAAAAT
66 CTCGAGGTAGACATTCAATTATAGTCTGTTTTAA-CAAAAAATGTAAAAAAATTCAACTTAAAAT
* * * *
12625 CAATTATGGGATTATAAAACCT-TTTAAAACCAGTAATAAGCT
130 CAATTATGAGATTATAAAA-CTATTTAAAGCGAGTAATAAGCC
* * * * * * *
12667 TTTTGAAGGAATTGGGTGATTCTAAATGGACATTTCTTGTCAATGAATGATTTTTTCTACAAGTT
1 TTTTGAAGGAA-TGGGTGACTCTAAATGAACTTTTCTTGTCAATGAATGCTTGTTTCTTCACGTT
* * * *
12732 T-TCCATGGTAAACAATCAATTATAGTCTGTTTTAACAAAAAATATAAAAAAATTCAACTTAAAA
65 TCTCGA-GGTAGACATTCAATTATAGTCTGTTTTAACAAAAAATGTAAAAAAATTCAACTTAAAA
* * *
12796 TTAATTATGAGATTATAAAATTATTTAAAGCGAGTAATATGCC
129 TCAATTATGAGATTATAAAACTATTTAAAGCGAGTAATAAGCC
* ** * * * * *
12839 TTCTGAAATAATGGGTGACTCTAAATGGACTTTTCTTATAAATGAATGCTTGTTTCTTCACATTC
1 TTTTGAAGGAATGGGTGACTCTAAATGAACTTTTCTTGTCAATGAATGCTTGTTTCTTCACGTTT
12904 CTCGAGGTAGACATTCAATTA
66 CTCGAGGTAGACATTCAATTA
12925 NNNNNNNNNN
Statistics
Matches: 361, Mismatches: 58, Indels: 20
0.82 0.13 0.05
Matches are distributed among these distances:
170 3 0.01
171 212 0.59
172 146 0.40
ACGTcount: A:0.37, C:0.12, G:0.14, T:0.36
Consensus pattern (171 bp):
TTTTGAAGGAATGGGTGACTCTAAATGAACTTTTCTTGTCAATGAATGCTTGTTTCTTCACGTTT
CTCGAGGTAGACATTCAATTATAGTCTGTTTTAACAAAAAATGTAAAAAAATTCAACTTAAAATC
AATTATGAGATTATAAAACTATTTAAAGCGAGTAATAAGCC
Done.