Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018399163.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_2435.0, 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: 4088
ACGTcount: A:0.24, C:0.08, G:0.09, T:0.22
Warning! 1556 characters in sequence are not A, C, G, or T
Found at i:2767 original size:171 final size:170
Alignment explanation
Indices: 2396--2779 Score: 390
Period size: 171 Copynumber: 2.2 Consensus size: 170
2386 NNNNNNNNTT
* ** *
2396 TGTTTTAAAGAAAAATGTAAAAAAATTAAACTTAAAATCAATTATGAGATTAGAAAATTATTTAA
1 TGTTTTAAA-AAAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGATTAGAAAACCATCTAA
* * * *
2461 AGCGGGTAATAAGACTTTCGAAGGAATGGGAGACTATAAATGGACTTTTCTTCACAATCAATGGC
65 AGAGGGTAATAAGACTTTCGAAGGAATGAGAGACTATAAACGGACTTTTCTTCACAATCAATAGC
* * **
2526 TTTTTCTACACCTTTCCTAAGGCAGGCTTTCAATTATAGTC
130 TTTTTCTACACCTTTCCCAAGGCAGACACTCAATTATAGTC
************ * *
2567 TGNNNNNNNNNNNNNTATAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATCTAA
1 TG-TTTTAAAAAAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGATTAGAAAACCATCTAA
* * ** * *
2632 AGAGGGTAATAAGACTTTTGAAGGAATGAGTGACTATAAACGGACTTTTCTTCTTAATGAGTAGC
65 AGAGGGTAATAAGACTTTCGAAGGAATGAGAGACTATAAACGGACTTTTCTTCACAATCAATAGC
* * ** * *
2697 TTTTTTTGCATGTTTCCCAAGGTAGACACTCACTTATAGTC
130 TTTTTCTACACCTTTCCCAAGGCAGACACTCAATTATAGTC
*
2738 TGTTTTAACAAAAAATGTAAAATAATTCAACTTAAAATCAAT
1 TGTTTTAA-AAAAAATGTAAAAAAATTCAACTTAAAATCAAT
2780 NNNNNNNNNN
Statistics
Matches: 159, Mismatches: 52, Indels: 4
0.74 0.24 0.02
Matches are distributed among these distances:
171 159 1.00
ACGTcount: A:0.38, C:0.12, G:0.14, T:0.32
Consensus pattern (170 bp):
TGTTTTAAAAAAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGATTAGAAAACCATCTAAA
GAGGGTAATAAGACTTTCGAAGGAATGAGAGACTATAAACGGACTTTTCTTCACAATCAATAGCT
TTTTCTACACCTTTCCCAAGGCAGACACTCAATTATAGTC
Found at i:3001 original size:172 final size:171
Alignment explanation
Indices: 2807--3365 Score: 428
Period size: 171 Copynumber: 3.3 Consensus size: 171
2797 NNNNNNNNNN
*
2807 AGTAATAAGCTTTTTAAAGGAATGGGTGACTCTAAATGGACTTTTCTTGTCAAACAAT-GCTTGG
1 AGTAATAAGCCTTTTAAAGGAATGGGTGACTCTAAATGGACTTTTCTTGTCAAACAATGGCTT-G
* *
2871 TTCTT-CATATTTCTCGAGCTAGACAATCAATTATAGTATTTTTTAATCAAAAATGTAAAAACAA
65 TT-TTACATATTTCTCGAGCTAGACAATCAATTATAGTATGTTTTAATAAAAAATGTAAAAA-AA
* *
2935 TTCCACTTAAAATCAATTATGAGATTATAAAACCCTTTAAAGCG
128 TTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCG
* *** * * ** **
2979 AGTAATAAGCCTCTTAAAGGAATAAATGACTATAAATGAACTTTTCTTCCCAATGAATGGCTTGT
1 AGTAATAAGCCTTTTAAAGGAATGGGTGACTCTAAATGGACTTTTCTTGTCAAACAATGGCTTGT
* ********** * * * * *
3044 TTTACATGTNNNNNNNNNNAGACATTCAATTATAGTCTGTTTTAGTAAAAAATGTAAAAATATTT
66 TTTACATATTTCTCGAGCTAGACAATCAATTATAGTATGTTTTAATAAAAAATGTAAAAAAATTC
* **
3109 AACTTAAAATCAATTATGAGATTGTAAAAGTATTTAAAGCG
131 AACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCG
* * * * ** ******
3150 AGTAAAAAGTCTTTTGAAGGAATGGGTGACTCTAAATGGACTTTTCATGTCAATGAATGNNNNNN
1 AGTAATAAGCCTTTTAAAGGAATGGGTGACTCTAAATGGACTTTTCTTGTCAAACAATGGCTTGT
**** * * * * *
3215 NNNNCATGTTTCTCGAGATAGACATTCAATTATTGTCTGTTTTAA-AGAAAAA--TAAAAAAACG
66 TTTACATATTTCTCGAGCTAGACAATCAATTATAGTATGTTTTAATA-AAAAATGTAAAAAAA--
* * * * *
3277 TTCATCCTAAAATCAATTATGAGATTATCAAATCATTTAAACCG
128 TTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCG
* * ** *
3321 AGTAATAAGGCTTTCGAAA-GAATGGGTGACTAGAAATGGATTTTT
1 AGTAATAAGCCTTT-TAAAGGAATGGGTGACTCTAAATGGACTTTT
3366 TTTTCTCAAT
Statistics
Matches: 297, Mismatches: 84, Indels: 13
0.75 0.21 0.03
Matches are distributed among these distances:
169 7 0.02
170 1 0.00
171 193 0.65
172 92 0.31
173 4 0.01
ACGTcount: A:0.37, C:0.12, G:0.15, T:0.33
Consensus pattern (171 bp):
AGTAATAAGCCTTTTAAAGGAATGGGTGACTCTAAATGGACTTTTCTTGTCAAACAATGGCTTGT
TTTACATATTTCTCGAGCTAGACAATCAATTATAGTATGTTTTAATAAAAAATGTAAAAAAATTC
AACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCG
Done.