Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397840.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_1140.0, 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: 16676
ACGTcount: A:0.18, C:0.07, G:0.06, T:0.19
Warning! 8346 characters in sequence are not A, C, G, or T
Found at i:7740 original size:170 final size:167
Alignment explanation
Indices: 7447--8003 Score: 579
Period size: 170 Copynumber: 3.3 Consensus size: 167
7437 NNNNNNNNNN
* * *
7447 TTTAAATGGTTTTATAATCTCATAATTGATTTTAAGCTGAAGTTTTTACAAGTTTTT-CTAAAAC
1 TTTAAATGATTTTATAATCTCATAATTGATTTTAAGCTGAATTTTTTAC-A-TTTTTGTTAAAAC
* ** * * * *
7511 AGACTATCATTGAATGGT-TGCCTCTACAAACGTGTAGGAAATCTCAATTATTTGCAAGAAAATT
64 AGACTATAATTGAAT-GTCTG-CTCTAGGAACGTGTAGAAAAACAC-ATTATTTGCAAGAAAAGT
* *
7575 CTATTTATAGTGTCTCATTTCTTGAAAAGCCTTATTACTCAT
126 CTATTTATAGTCTCTCATTCCTTGAAAAGCCTTATTACTCAT
* *
7617 TTTAAATGATTTTATAATCTCATAATTGATTTCAAGTTGAATTTTTTTAC-TTTTATGATTAAAA
1 TTTAAATGATTTTATAATCTCATAATTGATTTTAAGCTGAA-TTTTTTACATTTT-TG-TTAAAA
* *
7681 CAGACTATAATTGAATGTCTGCTCTAGGAACGTGTAGAAAAAGACATTCATTGGCAAGAAAAGTC
63 CAGACTATAATTGAATGTCTGCTCTAGGAACGTGTAGAAAAACACATT-ATTTGCAAGAAAAGTC
* * * * * * **
7746 CATTTGTAGTCACCCATTCCTTCAAAAGCCTTAATACTCGC
127 TATTTATAGTCTCTCATTCCTTGAAAAGCCTTATTACTCAT
* * * *
7787 TTTAAATGGTTTTATAATCTCATAATTGATTTTAAGCAGAATTTTTTACTTTTTTTGTTAAAGCA
1 TTTAAATGATTTTATAATCTCATAATTGATTTTAAGCTGAATTTTTTAC-ATTTTTGTTAAAACA
* * * * *
7852 GACTATAGTTGAATG-CTTGC-CTTAGGAAATGTGTAGAAAAACCCATTTATTTGAAAGAAAAGC
65 GACTATAATTGAATGTC-TGCTC-TAGG-AACGTGTAGAAAAACACA-TTATTTGCAAGAAAAGT
* * *
7915 CTATTTATGGTCTTTCATTCCTTCG-AAAGCCTTATTGCTCAT
126 CTATTTATAGTCTCTCATTCCTT-GAAAAGCCTTATTACTCAT
* *
7957 TTTAAAT-AGTTTTATAATCTCATAATTCATTTTAAGTTGAATTTTTT
1 TTTAAATGA-TTTTATAATCTCATAATTGATTTTAAGCTGAATTTTTT
8004 TACNNNNNNN
Statistics
Matches: 322, Mismatches: 51, Indels: 28
0.80 0.13 0.07
Matches are distributed among these distances:
168 6 0.02
169 40 0.12
170 241 0.75
171 35 0.11
ACGTcount: A:0.32, C:0.14, G:0.13, T:0.41
Consensus pattern (167 bp):
TTTAAATGATTTTATAATCTCATAATTGATTTTAAGCTGAATTTTTTACATTTTTGTTAAAACAG
ACTATAATTGAATGTCTGCTCTAGGAACGTGTAGAAAAACACATTATTTGCAAGAAAAGTCTATT
TATAGTCTCTCATTCCTTGAAAAGCCTTATTACTCAT
Found at i:9138 original size:170 final size:170
Alignment explanation
Indices: 8837--9151 Score: 397
Period size: 170 Copynumber: 1.9 Consensus size: 170
8827 AAACCTAATA
8837 ACTCGCTTTAAATGATTTTATAATCTCATAATTGATTTTAAGCTGAATTTTTTACATGTTTTTCT
1 ACTCGCTTTAAATGATTTTATAATCTCATAATTGATTTTAAGCTGAATTTTTTACATGTTTTTCT
* * * * * * *
8902 AAAACAGACTATCATTGAATGTTTGCCTCTACAAACGTGTAGAAAATCTCAATTATTTGTAAGAA
66 AAAACAAACTATAATTGAATGTCTGCCTCTACAAACGTGTAGAAAAACACAATTATTGGCAAGAA
* *
8967 AATTCTATTTATAGTGTCTCATTTCTTGAAAAGCCTTATT
131 AAGTCCATTTATAGTGTCTCATTTCTTGAAAAGCCTTATT
* * *
9007 ACTCGTTTTAAATGATTTTATAATCTCTTAATTGATTTTAAGTTGAATTTTTTTAC-T-TTTATG
1 ACTCGCTTTAAATGATTTTATAATCTCATAATTGATTTTAAGCTGAA-TTTTTTACATGTTT-T-
* * ** *
9070 AT-TAAAATAAACTATAATTGAATGTCTG-CTTTAGGAACGTGTAGAAAAAGAC-ATTCATTGGC
63 -TCTAAAACAAACTATAATTGAATGTCTGCCTCTACAAACGTGTAGAAAAACACAATT-ATTGGC
9132 AAGAAAAGTCCATTTATAGT
126 AAGAAAAGTCCATTTATAGT
9152 CACTCATTCC
Statistics
Matches: 123, Mismatches: 17, Indels: 10
0.82 0.11 0.07
Matches are distributed among these distances:
169 6 0.05
170 86 0.70
171 30 0.24
172 1 0.01
ACGTcount: A:0.34, C:0.12, G:0.12, T:0.42
Consensus pattern (170 bp):
ACTCGCTTTAAATGATTTTATAATCTCATAATTGATTTTAAGCTGAATTTTTTACATGTTTTTCT
AAAACAAACTATAATTGAATGTCTGCCTCTACAAACGTGTAGAAAAACACAATTATTGGCAAGAA
AAGTCCATTTATAGTGTCTCATTTCTTGAAAAGCCTTATT
Done.