Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018398659.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_1944.0, 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: 2303
ACGTcount: A:0.25, C:0.10, G:0.09, T:0.27
Warning! 653 characters in sequence are not A, C, G, or T
Found at i:2283 original size:172 final size:172
Alignment explanation
Indices: 1456--2290 Score: 901
Period size: 171 Copynumber: 4.9 Consensus size: 172
1446 NNNTAAATTG
* * * * *
1456 TTTTATAATCTCATAATTGATTTTGAGTTGAGTTT-TTTTATATTTTTAGTTAAAATAGGCTATA
1 TTTTATAATCTCATAATTGATTTTAAGTTGAATTTGTTTTACATTTTTAGTTAAAACAGACTATA
** * *
1520 ATTGAATGTCTACCTTAAAAAATATGAATAAAAATG-CATTCATTGGCAAGAAAAGTCCATTTAT
66 ATTGAATGTCTACCTCGAGAAATATGAAGAAAAA-GACATTCATTGGCAAGAAAAGTCCATTTAT
* * * *
1584 AGTCACCAATTCCTTCAAAAGCTTTATTACTCGCTTTAAATTA
130 AGTCACCCATTCCTTCAAAAGCCTTATTACTCACTTTAAATGA
* *
1627 TTTTAGAATCTCATAATTGATTTTAAGTTGAA-TTGTTTTACATTTTTAGTTAAAGCAGACTATA
1 TTTTATAATCTCATAATTGATTTTAAGTTGAATTTGTTTTACATTTTTAGTTAAAACAGACTATA
* * * ** * *
1691 ATT-AAAGTTTTAGCTCGAGAAACCTGAAGAAACAAG-TATTCATTGGCAAGACAAGTCCATTTA
66 ATTGAATG-TCTACCTCGAGAAATATGAAGAAA-AAGACATTCATTGGCAAGAAAAGTCCATTTA
* ** * * * * *
1754 TAGTCTCTTATTCCATCTAAAGCCTTATTACACGCTTTAAATGG
129 TAGTCACCCATTCCTTCAAAAGCCTTATTACTCACTTTAAATGA
* * * * * * * * *
1798 TTATGTAATCTCAAAATTGATTTTAAATTGAA-TAGTTTTAGATTTTTGGTTAAAACAGGCCATA
1 TTTTATAATCTCATAATTGATTTTAAGTTGAATTTGTTTTACATTTTTAGTTAAAACAGACTATA
* * * * * * * * *
1862 ATTGAATGTTTACCTTGAGAAACATAAAGAAAAAAACATTCATTAGTAAAAAAAGTCCATTTGTA
66 ATTGAATGTCTACCTCGAGAAATATGAAGAAAAAGACATTCATTGGCAAGAAAAGTCCATTTATA
* ** * * * *
1927 GTCTCGTATTTCTTTAAAAGCCTTATAACTCACTTTAAATGG
131 GTCACCCATTCCTTCAAAAGCCTTATTACTCACTTTAAATGA
* * * * * * *
1969 TTTTATAATCTCAAAATTGATTTTAGGTTCAATTTTTTTTACATTATTAGTTAAAACATATTATA
1 TTTTATAATCTCATAATTGATTTTAAGTTGAATTTGTTTTACATTTTTAGTTAAAACAGACTATA
* * * *
2034 ATTGAATGTCTAGCTCAAAAAATATGAAGAAAAAGACATTCATTGGCAAGAAAAGTCCATTCATA
66 ATTGAATGTCTACCTCGAGAAATATGAAGAAAAAGACATTCATTGGCAAGAAAAGTCCATTTATA
* * * **
2099 GTGACTCATTCCTTCAACAGCCTTCGTACTCACTTTAAAAT-A
131 GTCACCCATTCCTTCAAAAGCCTTATTACTCACTTT-AAATGA
* *
2141 TTTTATAATCTCATAATTGATTTTGAGTTGAATTTGTTTTATATTTTTAGTTAAAACAGACTATA
1 TTTTATAATCTCATAATTGATTTTAAGTTGAATTTGTTTTACATTTTTAGTTAAAACAGACTATA
* *
2206 ATTGAATGTCTACCTCGAGAAATATGAAGAAAAAGACATTCATTGGCGAGAAAAGTCAATTTATA
66 ATTGAATGTCTACCTCGAGAAATATGAAGAAAAAGACATTCATTGGCAAGAAAAGTCCATTTATA
*
2271 GTCACCCATTCCTTCTAAAG
131 GTCACCCATTCCTTCAAAAG
2291 TGCTTCTACT
Statistics
Matches: 542, Mismatches: 115, Indels: 13
0.81 0.17 0.02
Matches are distributed among these distances:
170 7 0.01
171 294 0.54
172 237 0.44
173 4 0.01
ACGTcount: A:0.36, C:0.13, G:0.12, T:0.38
Consensus pattern (172 bp):
TTTTATAATCTCATAATTGATTTTAAGTTGAATTTGTTTTACATTTTTAGTTAAAACAGACTATA
ATTGAATGTCTACCTCGAGAAATATGAAGAAAAAGACATTCATTGGCAAGAAAAGTCCATTTATA
GTCACCCATTCCTTCAAAAGCCTTATTACTCACTTTAAATGA
Done.