Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018400256.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_3465.0, 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: 4094
ACGTcount: A:0.23, C:0.08, G:0.08, T:0.21
Warning! 1639 characters in sequence are not A, C, G, or T
Found at i:1826 original size:171 final size:171
Alignment explanation
Indices: 1524--1992 Score: 435
Period size: 171 Copynumber: 2.7 Consensus size: 171
1514 NNNNNNAGTA
* * *
1524 AGTAATAA-AGCTTTTGAAGGAAT-AGGTGACTATAAATGGACTTTTCCTCTCAATCAAT-AGCT
1 AGTAATAAGA-CTTTTGAAGGAATGA-GTGACTATAAATAGACTTTTCTTCTCAATGAATGA-CT
* * * * *** * ** * * * *
1586 TTTTCTACACCTTTCTTGAGGCAGGCCTTCAATTATAGTCTGTTTTAA-AGAAAAATATAAAAAA
63 TTTTTTGCTCATTTCCCAAGGCAGACAATCACTAATAGTCTGTTTTAATA-AAAAATGTAAAATA
* * **********
1650 ATTCAACTTTAAATTAATTATGAGATTATANNNNNNNNNNAAGCG
127 ATTCAACTTCAAATCAATTATGAGATTATAAAACTATTTAAAGCG
* * * * *
1695 GGTAATAAGACTTTTGAAGGAATTAGTGACTATAAATTGACTTTTTTTCTCAATTAATGACTTTT
1 AGTAATAAGACTTTTGAAGGAATGAGTGACTATAAATAGACTTTTCTTCTCAATGAATGACTTTT
*
1760 TTTGCAT-GTTTCCCAAGGCAGACAATCACTAATAGTCTGTTTTAATAAAAAATGTAAAATAATT
66 TTTGC-TCATTTCCCAAGGCAGACAATCACTAATAGTCTGTTTTAATAAAAAATGTAAAATAATT
*
1824 CAACTTCAAATCAATTATGAGATTATAAAACTATTTAAAGCT
130 CAACTTCAAATCAATTATGAGATTATAAAACTATTTAAAGCG
**********
1866 AGTAATANNNNNNNNNNAGGAATGAGTGACTATAAATAGACTTTTCTTCTCAATGAATGACTTTT
1 AGTAATAAGACTTTTGAAGGAATGAGTGACTATAAATAGACTTTTCTTCTCAATGAATGACTTTT
*
1931 TTTGCTCATTTCCCAAGGCAGACAATCACTTATAGTCTGTTTTAATAAAAAATGTAAAATAA
66 TTTGCTCATTTCCCAAGGCAGACAATCACTAATAGTCTGTTTTAATAAAAAATGTAAAATAA
1993 NNNNNNNNNN
Statistics
Matches: 243, Mismatches: 49, Indels: 12
0.80 0.16 0.04
Matches are distributed among these distances:
170 1 0.00
171 238 0.98
172 4 0.02
ACGTcount: A:0.36, C:0.13, G:0.13, T:0.34
Consensus pattern (171 bp):
AGTAATAAGACTTTTGAAGGAATGAGTGACTATAAATAGACTTTTCTTCTCAATGAATGACTTTT
TTTGCTCATTTCCCAAGGCAGACAATCACTAATAGTCTGTTTTAATAAAAAATGTAAAATAATTC
AACTTCAAATCAATTATGAGATTATAAAACTATTTAAAGCG
Found at i:2404 original size:171 final size:160
Alignment explanation
Indices: 2218--2538 Score: 308
Period size: 171 Copynumber: 1.9 Consensus size: 160
2208 AGCAATAAGA
* * *
2218 CTTTTGAAAGAATGGGTGACAATAAATGGACTTTTGTT-CTCAATGAATGGCTT-TCTCTACGCG
1 CTTTTGAAAGAATGGGTGACAATAAAAGGACTTTTCTTGC-CAATGAAT-GCTTGTCTCTACACG
* * *
2281 TTTACT-GAGACAGACATTCAATTGTAGTCTATTTTA-AAAAAAGTGTTAAAAAAATTCAACTTA
64 TTT-CTCGAGACAGACATTCAATTATAGTATATTTTATAAAAAA-TG-TAAAAAAATCCAACTTA
2344 AAATCAATTATGAGATTATAAAACAATTTAAAGNNNNNNNNNNGC
126 AAATCAATTATGAGATTATAAAACAATTTAAAG----------GC
* ** * * * *
2389 CTTTTGAAGGAATGGGTGACTCTAAAAGGACTTTTCTTGCCAATGAATTCTTGTTTTTTCACGTT
1 CTTTTGAAAGAATGGGTGACAATAAAAGGACTTTTCTTGCCAATGAATGCTTGTCTCTACACGTT
* ** * *
2454 TTTCGAGGTAGACATTCAATTATAGTATGTTTTATTCAAAAATGTAAAAAAATCCAACTTAAAAT
66 TCTCGAGACAGACATTCAATTATAGTATATTTTA-TAAAAAATGTAAAAAAATCCAACTTAAAAT
2519 CAATTATGAGATTATAAAAC
130 CAATTATGAGATTATAAAAC
2539 CATTNNNNNN
Statistics
Matches: 127, Mismatches: 18, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
170 4 0.03
171 115 0.91
172 3 0.02
173 5 0.04
ACGTcount: A:0.36, C:0.12, G:0.15, T:0.34
Consensus pattern (160 bp):
CTTTTGAAAGAATGGGTGACAATAAAAGGACTTTTCTTGCCAATGAATGCTTGTCTCTACACGTT
TCTCGAGACAGACATTCAATTATAGTATATTTTATAAAAAATGTAAAAAAATCCAACTTAAAATC
AATTATGAGATTATAAAACAATTTAAAGGC
Done.