Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018399952.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_3180.0, 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: 3353
ACGTcount: A:0.24, C:0.09, G:0.09, T:0.23
Warning! 1161 characters in sequence are not A, C, G, or T
Found at i:1197 original size:171 final size:172
Alignment explanation
Indices: 838--1214 Score: 436
Period size: 172 Copynumber: 2.2 Consensus size: 172
828 NNNNNNGAGC
* * * * *
838 ATTCATTGGCAAGAGAAGTCCATTTATAGTCACTTATTCCTTCAAAAGCCTTATTACACACTTTA
1 ATTCATTGGCAAGAAAAGTCTATTTATAGTCACCTATACCTTCAAAAGCATTATTACACACTTTA
* *
903 AATGATTTTATAATCTCAAAATTGATTTAAATTTGAATTTTTTCTACATTTCTAGTTAAAACAGA
66 AATAATTTTATAATCTCAAAATTGATTTAAATTTGAATTTTTTCTACATTTCTAGGTAAAACAGA
* * ***
968 CTCGAATTGAATGTCTACCATGAGAAATATGAAGAAAAANNN
131 CTAGAATTGAATGTCTACCATGAGAAACATGAAGAAAAAAGT
******* * * *
1010 NNNNNNNGGCAAGAAAAGTCTATTTATAGTCACCTATACCTTTAAAAGCATTATTACTCGCTTTA
1 ATTCATTGGCAAGAAAAGTCTATTTATAGTCACCTATACCTTCAAAAGCATTATTACACACTTTA
* * ** * * *
1075 AATAATTTTGTAATGTCGTAATTGATTTTAAA-TTGAATTGTTTT-TATATTT-TTGGTCAAACA
66 AATAATTTTATAATCTCAAAATTGA-TTTAAATTTGAATT-TTTTCTACATTTCTAGGTAAAACA
*
1137 GACTAGAATTGAATGTCTACCATGATAAACATGAAGAAAAAAGT
129 GACTAGAATTGAATGTCTACCATGAGAAACATGAAGAAAAAAGT
*
1181 ATTCATTGGAAAGAAAAGTCTATTTATAGTCACC
1 ATTCATTGGCAAGAAAAGTCTATTTATAGTCACC
1215 CANNNNNNNN
Statistics
Matches: 165, Mismatches: 38, Indels: 5
0.79 0.18 0.02
Matches are distributed among these distances:
171 72 0.44
172 83 0.50
173 10 0.06
ACGTcount: A:0.37, C:0.13, G:0.12, T:0.35
Consensus pattern (172 bp):
ATTCATTGGCAAGAAAAGTCTATTTATAGTCACCTATACCTTCAAAAGCATTATTACACACTTTA
AATAATTTTATAATCTCAAAATTGATTTAAATTTGAATTTTTTCTACATTTCTAGGTAAAACAGA
CTAGAATTGAATGTCTACCATGAGAAACATGAAGAAAAAAGT
Found at i:3237 original size:172 final size:162
Alignment explanation
Indices: 2939--3248 Score: 327
Period size: 172 Copynumber: 1.9 Consensus size: 162
2929 TAAATTTGAA
* * *
2939 TTCTTTGTACATTTTTGGTTAAAACAGATGAGGATTGAATGTATACCTTCAAAAACATGAAGAAA
1 TTCTTTGTACATTTTTAGTTAAAACAGATGAGAATTGAATGTATACCTACAAAAACATGAAGAAA
** * ** * * *
3004 AAAGTATTCATTGGCAAGAAAAGTCCAATTATAGTCACACATTTCTTTAAGAGCCTTATTACTCA
66 AAAACATTCATTGGCAAGAAAAATCCAATTATAGTCACACATAGCTTCAAAAGCATTATTACTCA
*
3069 GTTTAAATGGTTTTATAATCTAAAAATTGATT
131 CTTTAAATGGTTTTATAATCTAAAAATTGATT
* * *
3101 NNNNNNNNNNTTCTTTGTACATTTTTAGTTAAAGCAGACT-AGAATTGAATGTCTACC-ACGAGA
1 ----------TTCTTTGTACATTTTTAGTTAAAACAGA-TGAGAATTGAATGTATACCTAC-AAA
* * * *
3164 AACATGAAGAAAAAAACATTTATTGGGAAGAAAAATCCATTTATAGTCACCCATAGCTTCAAAAG
54 AACATGAAGAAAAAAACATTCATTGGCAAGAAAAATCCAATTATAGTCACACATAGCTTCAAAAG
3229 CATTATTACTCACTTTAAAT
119 CATTATTACTCACTTTAAAT
3249 AATTTTGTAA
Statistics
Matches: 117, Mismatches: 19, Indels: 4
0.84 0.14 0.03
Matches are distributed among these distances:
171 1 0.01
172 115 0.98
173 1 0.01
ACGTcount: A:0.37, C:0.14, G:0.13, T:0.33
Consensus pattern (162 bp):
TTCTTTGTACATTTTTAGTTAAAACAGATGAGAATTGAATGTATACCTACAAAAACATGAAGAAA
AAAACATTCATTGGCAAGAAAAATCCAATTATAGTCACACATAGCTTCAAAAGCATTATTACTCA
CTTTAAATGGTTTTATAATCTAAAAATTGATT
Done.