Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018403272.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_946.0, 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: 12375
ACGTcount: A:0.21, C:0.08, G:0.06, T:0.22
Warning! 5409 characters in sequence are not A, C, G, or T
Found at i:6753 original size:169 final size:161
Alignment explanation
Indices: 6535--6866 Score: 294
Period size: 171 Copynumber: 2.0 Consensus size: 161
6525 ATTGTTTTTT
* * * * * *
6535 ATTCACATAATTAATTTTAAGTTGAATTTTTTTATATTTTCTCTTAAAACAGAATAT-A-TGAAT
1 ATTCTCATAATTAATTTTAAGTTAAATTATTTTACATTTTCTATTAAAACAGAATATAATTAAAT
* * * ** * * * *
6598 GTTTATCTGAAGCAACGT-AAAGACAAAAGCATTCATTGGCAAGAAAAGTCCATTTATGGTCATC
66 ATCTACCACAAGAAACGTGAAAGA-AAAAGCATTCATGGGCAAGAAAAGTACATTTATAGTCATC
* * *
6662 CATTCCTTTAAAAGCCTTATTACTTGCTTTAA
130 CAGTCCTTCAAAAGCCTTATTACTCGCTTTAA
* *
6694 ATNNNNNNNNNNTCTCATAATTGATTTTAAGTTAAATTATTTTACATTTT-TAATTAAAACAGAC
1 AT----------TCTCATAATTAATTTTAAGTTAAATTATTTTACATTTTCT-ATTAAAACAGAA
* ** *
6758 TATAATTAAATATCTACCACAAGAAATGTGAATTAAAAAGCATTTATGGGCAAGAAAAGTACATT
55 TATAATTAAATATCTACCACAAGAAACGTGAAAGAAAAAGCATTCATGGGCAAGAAAAGTACATT
* *
6823 TATAGTCTTCTAGTCCTTCAAAAGCCTTATTACTCGCTTTAA
120 TATAGTCATCCAGTCCTTCAAAAGCCTTATTACTCGCTTTAA
6865 AT
1 AT
6867 GATTTTATAA
Statistics
Matches: 133, Mismatches: 26, Indels: 16
0.76 0.15 0.09
Matches are distributed among these distances:
159 2 0.02
168 1 0.01
169 46 0.35
170 1 0.01
171 80 0.60
172 3 0.02
ACGTcount: A:0.36, C:0.14, G:0.10, T:0.37
Consensus pattern (161 bp):
ATTCTCATAATTAATTTTAAGTTAAATTATTTTACATTTTCTATTAAAACAGAATATAATTAAAT
ATCTACCACAAGAAACGTGAAAGAAAAAGCATTCATGGGCAAGAAAAGTACATTTATAGTCATCC
AGTCCTTCAAAAGCCTTATTACTCGCTTTAA
Found at i:9962 original size:171 final size:171
Alignment explanation
Indices: 9435--10366 Score: 650
Period size: 171 Copynumber: 5.5 Consensus size: 171
9425 NNNNNNNNNN
* * *
9435 AAACATGAAGAAAAGATCATTCATTGACAAGAAAAGTCCATTTATAGTCACCCCTTCTTTCAAAA
1 AAACATGAAGAAAAAAACATTCATTGACAAGAAAAGTCCATTTATAGTCACCCATTCTTTCAAAA
* * * *
9500 GCCTTATTATTCACTTTAAATAGTTTTCTAATCT-AT-ATATGATTTTAAG-TAAATTTTTTTTA
66 GCCTTATTACTCACTTTAAATAATTTTATAATCTAATAAT-TGATTTTAAGTTCAA-TTTTTTTA
* * * *
9562 CAATTTTTATTAAAACTGACTATAATTGAATGTTTGTC-TTGGG
129 CATTTTTTATTAAAACAGACTATAATTGAATGTCTG-CATTGAG
** * * * * **********
9605 AAACATGAAG-AAAAAGTATTAATTGGCAACAAAAGTCCATTTATAGTCACCTANNNNNNNNNNA
1 AAACATGAAGAAAAAAACATTCATTGACAAGAAAAGTCCATTTATAGTCACCCATTCTTTCAAAA
* * * * * * * *
9669 GTCTTATTACTCGCTTTAAATGACTTTGTAATCTCATAATTGATTTTAAGTTGAATTTTTTAACA
66 GCCTTATTACTCACTTTAAATAATTTTATAATCTAATAATTGATTTTAAGTTCAATTTTTTTACA
** ********
9734 TTTTTCGTTAAAACAGACTATAATTGAATGTCTNNNNNNNN
131 TTTTTTATTAAAACAGACTATAATTGAATGTCTGCATTGAG
** * * * * *
9775 NNATA-GAAAGAAAAAAACATTCATTGATAAGAAAAGTCTATTTATAGTCACCCATTCCTTCAAC
1 AAACATG-AAGAAAAAAACATTCATTGACAAGAAAAGTCCATTTATAGTCACCCATTCTTTCAAA
* *
9839 AGCCTTTTTACTCA-TTCTAAATAATTTTATAATCTCATAATTGATTTTAAGTTCAATTTGTTTT
65 AGCCTTATTACTCACTT-TAAATAATTTTATAATCTAATAATTGATTTTAAGTTCAATTT-TTTT
* *
9903 GCATTTTTTATTGAAACAGACTATAATTGAATGTCTGCATTGAG
128 ACATTTTTTATTAAAACAGACTATAATTGAATGTCTGCATTGAG
* * * ** * *
9947 AAGCATGAA-AAAAAAAGCATTTATT-AGCAAGAAATGTCTGTTTATAGCCTCCCATTCTTTCAA
1 AAACATGAAGAAAAAAA-CATTCATTGA-CAAGAAAAGTCCATTTATAGTCACCCATTCTTTCAA
* * ** ********** *
10010 AAGCCTCATTAATCACTTTAAATGGTTTTATAATCTAATAATTNNNNNNNNNNTCAATATTTTTA
64 AAGCCTTATTACTCACTTTAAATAATTTTATAATCTAATAATTGATTTTAAGTTCAATTTTTTTA
* * * *
10075 TATTTTTTATTAAAATAGGCTATAATTGAATATCTGCATTGAG
129 CATTTTTTATTAAAACAGACTATAATTGAATGTCTGCATTGAG
* ** ** * *
10118 AAACATGAA-AAAAAAAGCATTCATT-AGCAAGAAATGTCTGTTTGCAGCCTCCCATTCTTTCAA
1 AAACATGAAGAAAAAAA-CATTCATTGA-CAAGAAAAGTCCATTTATAGTCACCCATTCTTTCAA
**********
10181 AAGCCTTATTACTCACTTTAAANNNNNNNNNNATCTAATAATTGATTTTAAGTTCAATTTTTTTA
64 AAGCCTTATTACTCACTTTAAATAATTTTATAATCTAATAATTGATTTTAAGTTCAATTTTTTTA
* ** * * *
10246 TATTTTTTTATTAAATTAGGCTATAATTGAATATCT--ATCTTAGG
129 CA-TTTTTTATTAAAACAGACTATAATTGAATGTCTGCAT-TGA-G
* * * * *
10290 AAACGTGAAGAAAAGATCATTTATTGACAAGAAAAGTCCATTTATAGTCACGCATTCCTTT-AAA
1 AAACATGAAGAAAAAAACATTCATTGACAAGAAAAGTCCATTTATAGTCACCCATT-CTTTCAAA
10354 AGCCTTATTACTC
65 AGCCTTATTACTC
10367 GCTTNNNNNN
Statistics
Matches: 588, Mismatches: 156, Indels: 34
0.76 0.20 0.04
Matches are distributed among these distances:
169 64 0.11
170 68 0.12
171 244 0.41
172 199 0.34
173 13 0.02
ACGTcount: A:0.35, C:0.13, G:0.10, T:0.37
Consensus pattern (171 bp):
AAACATGAAGAAAAAAACATTCATTGACAAGAAAAGTCCATTTATAGTCACCCATTCTTTCAAAA
GCCTTATTACTCACTTTAAATAATTTTATAATCTAATAATTGATTTTAAGTTCAATTTTTTTACA
TTTTTTATTAAAACAGACTATAATTGAATGTCTGCATTGAG
Done.