Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018398206.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_1510.0, 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: 12808
ACGTcount: A:0.23, C:0.09, G:0.08, T:0.24
Warning! 4671 characters in sequence are not A, C, G, or T
Found at i:1691 original size:172 final size:161
Alignment explanation
Indices: 1433--1762 Score: 318
Period size: 172 Copynumber: 2.0 Consensus size: 161
1423 ATTATAACAT
* ** * **
1433 TATAAAACATTTTAAAGCGCGTAATAAGGCTTTTGAAGAAATGGGTGACTATAAATGGACTTTTC
1 TATAAAACATTTTAAAGCGAGTAATAAGGCTTTTGAAGAAATACGAGACTATAAATAAACTTTTC
* * * ** ** * *
1498 TTGCCAAGGAATACCTTTTTCTTTATGTTTCTTAAGTTAAACATTCAATTATAATCTGTTTTAAT
66 TTGCAAAGGAATACCTTTTTCTTCATGTTACACAAGGCAAACATTCAATTATAATCTATTTTAAA
*
1563 CAATAATGTAATAAAAATTGAACTTAAAAATA
131 CAAAAATGTAA-AAAAATTGAACTTAAAAATA
* * * *
1595 NNNNNNNNNNTATAAAACTTTTTAAAGTGAGTAATAAGGCTTTTGAAGGAGTACGAGACTATAAA
1 ----------TATAAAACATTTTAAAGCGAGTAATAAGGCTTTTGAAGAAATACGAGACTATAAA
* ** * *
1660 TAAACTTTTCTTGCAAATGAATATTTTTTTCTTCATGTTACACATGGCATACATTCAATTATAAT
56 TAAACTTTTCTTGCAAAGGAATACCTTTTTCTTCATGTTACACAAGGCAAACATTCAATTATAAT
* *
1725 CTATTTTAAAGAAAAATGTAAATAAATTGAACTTAAAA
121 CTATTTTAAACAAAAATGTAAAAAAATTGAACTTAAAA
1763 TCAAATATGA
Statistics
Matches: 131, Mismatches: 27, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
171 16 0.12
172 115 0.88
ACGTcount: A:0.38, C:0.10, G:0.12, T:0.36
Consensus pattern (161 bp):
TATAAAACATTTTAAAGCGAGTAATAAGGCTTTTGAAGAAATACGAGACTATAAATAAACTTTTC
TTGCAAAGGAATACCTTTTTCTTCATGTTACACAAGGCAAACATTCAATTATAATCTATTTTAAA
CAAAAATGTAAAAAAATTGAACTTAAAAATA
Found at i:3333 original size:171 final size:169
Alignment explanation
Indices: 3151--3625 Score: 465
Period size: 171 Copynumber: 2.8 Consensus size: 169
3141 NNNNNNNNNN
* * *
3151 ATAGTCACTCATTCCTTCAAAAGCCTTATTACTTGATTTAAATGGCTTTATAATCTAAAAATTGA
1 ATAGTCACTCATTCCTTCAAAAGCCTTATTACTCGCTTTAAATGGCTTTATAATCTAATAATTGA
*
3216 TTTTAAGTTGAATTGTTTTACGTTTTTAGTTAAAACAAACTATAATTAAATGCCTGCCTCAAGAA
66 TTTTAAGTTGAATT-TTTTA-GTTTTTAGTTAAAACAAACTATAATTGAATGCCTGCCTCAAGAA
* * * *
3281 ACGTGCAGAAAAAGCCTTTCA-TGGATAAAAAAAGT-TCATTT
129 ACATGCAGAAAAAGCCATTCACT-AAGAAAAAAAGTCT-ATTT
* * ********** * *
3322 ATAGTCACTCATTCCTTTAGAAGCCTTATTACTCGCTTTAAANNNNNNNNNNATCTTATAGTTGA
1 ATAGTCACTCATTCCTTCAAAAGCCTTATTACTCGCTTTAAATGGCTTTATAATCTAATAATTGA
* * *
3387 TTTTAAGTTGAAATTTTTTATGTTTTTGGTTAAAACAGACTATAATTGAATTCCTGCCT-AAGAA
66 TTTTAAGTTG-AATTTTTTA-GTTTTTAGTTAAAACAAACTATAATTGAATGCCTGCCTCAAG-A
* * * * **
3451 AACATGTATAGAAATCCATTCACTAAGAGGAAAAGTCTATTT
128 AACATGCAGAAAAAGCCATTCACTAAGAAAAAAAGTCTATTT
* * * * * *
3493 ATTGTCACCCATTCCTTCAAAAGCCTTATTACTCGCCTTAAATGGTTTTCTTATCTAATAATTGA
1 ATAGTCACTCATTCCTTCAAAAGCCTTATTACTCGCTTTAAATGGCTTTATAATCTAATAATTGA
* * *
3558 TTTTAAGTTGAATTTTTTTA-TATTTTAGTTAAAA-AAGACTATAATTGAATGTCTACCTCGAGA
66 TTTTAAGTTGAA-TTTTTTAGT-TTTTAGTTAAAACAA-ACTATAATTGAATGCCTGCCTCAAGA
3621 AACAT
128 AACAT
3626 AAGGAAAAAA
Statistics
Matches: 241, Mismatches: 55, Indels: 17
0.77 0.18 0.05
Matches are distributed among these distances:
169 2 0.01
170 40 0.17
171 193 0.80
172 6 0.02
ACGTcount: A:0.34, C:0.15, G:0.12, T:0.38
Consensus pattern (169 bp):
ATAGTCACTCATTCCTTCAAAAGCCTTATTACTCGCTTTAAATGGCTTTATAATCTAATAATTGA
TTTTAAGTTGAATTTTTTAGTTTTTAGTTAAAACAAACTATAATTGAATGCCTGCCTCAAGAAAC
ATGCAGAAAAAGCCATTCACTAAGAAAAAAAGTCTATTT
Done.