Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018402795.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_5852.0, 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, 880
Length: 1468
ACGTcount: A:0.34, C:0.11, G:0.12, T:0.30
Warning! 182 characters in sequence are not A, C, G, or T
Found at i:397 original size:170 final size:172
Alignment explanation
Indices: 160--529 Score: 387
Period size: 170 Copynumber: 2.2 Consensus size: 172
150 NNNNNNNNNN
* **
160 GATTATAAAACCATTTAAGGTGAGTAATAAGGCTTTTGAAGGAATAGGAGACTACAAATGGACTT
1 GATTATAAAACCATTTAA-GCGAGTAATAAGGCCATTGAAGGAATAGGAGACTACAAATGGACTT
* ** * * *
225 TT-CTTTCTAGTGAAT-GCTTTGTTCTACACATTTCCTGAGACA-GACATTCAATTGTAGTCTGT
65 TTCCTTTC-AATGAATGGCTTT-TTCTACACATTTCCAAAGACATG-CATTCAAATATAGTCTGA
* * * *
287 TTTAACC-AAAGTG-TAAAAGAA-TTCAAAC-GAAAATTAATTATGA
127 TTTAACCAAAAATGAAAAAACAATTTC-AACTGAAAATGAATTATGA
* * ** * *
330 GATTATAAAACCATTTATAGCGAGTAGTAAGGCCATTGAAGGAAT-GAGTGACTATGAGTGTACT
1 GATTATAAAACCATTTA-AGCGAGTAATAAGGCCATTGAAGGAATAG-GAGACTACAAATGGACT
* * * *
394 TTTCCTTTCAATGAATGGCTTTTTCTCCACATTTCCAAAGCCATGCTTTCAAATATAGTGTGATT
64 TTTCCTTTCAATGAATGGCTTTTTCTACACATTTCCAAAGACATGCATTCAAATATAGTCTGATT
*
459 TAACCAAAAATGAAAAAACAATTTCAACTTAAAATGAATTATGA
129 TAACCAAAAATGAAAAAACAATTTCAACTGAAAATGAATTATGA
*
503 GATTATAAAATCATTTAAAGCGAGTAA
1 GATTATAAAACCATTT-AAGCGAGTAA
530 AAAAGATTTT
Statistics
Matches: 164, Mismatches: 26, Indels: 17
0.79 0.13 0.08
Matches are distributed among these distances:
169 1 0.01
170 97 0.59
171 17 0.10
172 9 0.05
173 39 0.24
174 1 0.01
ACGTcount: A:0.38, C:0.14, G:0.16, T:0.32
Consensus pattern (172 bp):
GATTATAAAACCATTTAAGCGAGTAATAAGGCCATTGAAGGAATAGGAGACTACAAATGGACTTT
TCCTTTCAATGAATGGCTTTTTCTACACATTTCCAAAGACATGCATTCAAATATAGTCTGATTTA
ACCAAAAATGAAAAAACAATTTCAACTGAAAATGAATTATGA
Found at i:570 original size:173 final size:168
Alignment explanation
Indices: 160--710 Score: 426
Period size: 173 Copynumber: 3.2 Consensus size: 168
150 NNNNNNNNNN
* * * *
160 GATTATAAAACCATTTAAGGTGAGTAATAAGGCTTTTGAAGGAATAGGAGACTACAAATGGACTT
1 GATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGGAGACTA-TAATGGACTT
* ** * * *
225 TTCTTTCTAGTGAAT-GCTTTGTTCTACACATTTCCTGAGACAGACATTCAATTGTAGTCTGTTT
65 TTCTTTC-AATGAATGGCTTT-TTCTACACATTTCCAAAGACAGACATTCAAATATAGTCTGATT
* * * *
289 TAACCAAAGTGTAAAAGAATTCAAACGAAAATTAATTATGA
128 TAACCAAAATGAAAAACAATTCAAACGAAAATGAATTATGA
* * ** * * * *
330 GATTATAAAACCATTTATAGCGAGTAGTAAGGCCATTGAAGGAATGAGTGACTATGAGTGTACTT
1 GATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGGAGACTAT-AATGGACTT
* * * *
395 TTCCTTTCAATGAATGGCTTTTTCTCCACATTTCCAAAGCCATG-CTTTCAAATATAGTGTGATT
65 TT-CTTTCAATGAATGGCTTTTTCTACACATTTCCAAAGACA-GACATTCAAATATAGTCTGATT
*
459 TAACCAAAAATGAAAAAACAATTTC-AACTTAAAATGAATTATGA
128 TAACC-AAAATG-AAAAACAA-TTCAAAC-GAAAATGAATTATGA
* * * * * *
503 GATTATAAAATCATTTAAAGCGAGTAAAAAAGATTTTAAAGGAATGGGAGAATATATATGGACTT
1 GATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGGAGACTATA-ATGGACTT
* * * * ********** * * *
568 TTCTTGCCAATGAATGCCTTTTTATTCACATTNNNNNNNNNNGACATTCAATTATAATCTGTTTT
65 TTCTT-TCAATGAATGGCTTTTTCTACACATTTCCAAAGACAGACATTCAAATATAGTCTGATTT
* ** * * *
633 AACCAATTATAT-AAAAATAATTGTACCTAAAATCAATTATGA
129 AACCAA--A-ATGAAAAACAATTCAAACGAAAATGAATTATGA
*
675 GATTATAAAACTATTTAAAGCGAGTAATAAGGCTTT
1 GATTATAAAACCATTTAAAGCGAGTAATAAGGCTTT
711 NNNNNNNNNN
Statistics
Matches: 297, Mismatches: 69, Indels: 28
0.75 0.18 0.07
Matches are distributed among these distances:
170 97 0.33
171 16 0.05
172 63 0.21
173 118 0.40
174 1 0.00
175 2 0.01
ACGTcount: A:0.38, C:0.13, G:0.15, T:0.33
Consensus pattern (168 bp):
GATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGGAGACTATAATGGACTTT
TCTTTCAATGAATGGCTTTTTCTACACATTTCCAAAGACAGACATTCAAATATAGTCTGATTTAA
CCAAAATGAAAAACAATTCAAACGAAAATGAATTATGA
Done.