Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018401151.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_4304.0, 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: 3388
ACGTcount: A:0.27, C:0.10, G:0.09, T:0.29
Warning! 858 characters in sequence are not A, C, G, or T
Found at i:1059 original size:171 final size:172
Alignment explanation
Indices: 624--1618 Score: 551
Period size: 171 Copynumber: 5.8 Consensus size: 172
614 GCAGGAAAAA
** *
624 TCCATTTATAGTCACTCATTCCTTCAAAAGCCATATTACTCATTTTAAATGATTTCATAATCTAA
1 TCCATTTATAGTCACTCATTCCTTCAAAAGCCATATTACTCGCTTTAAATGATTTCATAATCTCA
* * * ** * *
689 TAATAGATTTTAAGTTGATTTTTTTTGTATTTTTGGTTAAAATAGACTATAGTTGAACATCTACC
66 TAATTGATTTTAAGTTGAATATTTTTACATTTTTTGTTAAAATAGACTATAGTTGAATATCTACC
* * *
754 TTGAGAAATATGAAAAAAAAGGCATTCACTGGCAAAAGAAAG
131 TAGAGAAACATGAAAAAAAAGGCATTCACTAGCAAAAGAAAG
* * ************
796 TCCATTTATAGTCACTCATTCCTTTAAAAGCCTTATTACTCGCTTTAAATNNNNNNNNNNNNTCA
1 TCCATTTATAGTCACTCATTCCTTCAAAAGCCATATTACTCGCTTTAAATGATTTCATAATCTCA
* *
861 TAATTGATTTTAAGTTGAATGTTTTTACATTTTTTGTTAAAATAGACTATAGTTGAATGTCTACC
66 TAATTGATTTTAAGTTGAATATTTTTACATTTTTTGTTAAAATAGACTATAGTTGAATATCTACC
* *
926 TAGAGAAACATGAAGAAAAAGGCATTCACTAGTAAAA-AAAG
131 TAGAGAAACATGAAAAAAAAGGCATTCACTAGCAAAAGAAAG
********** * *
967 TCCATTTATAGTCANNNNNNNNNNCAAAAGCCATATTACTCGCTTTAAATGGTTTTATAATCTCA
1 TCCATTTATAGTCACTCATTCCTTCAAAAGCCATATTACTCGCTTTAAATGATTTCATAATCTCA
* * * * * * * *
1032 GAATTGATTTTAAGCTGAATATTTTTACATTTTTTATTATAACAGACTATAATTGAATATTTCCC
66 TAATTGATTTTAAGTTGAATATTTTTACATTTTTTGTTAAAATAGACTATAGTTGAATATCTACC
* * * *
1097 GCA-AGAAACATGTAAAAAAAGTCATTCATTGAG-AATAA-AAA-
131 -TAGAGAAACATGAAAAAAAAGGCATTCACT-AGCAA-AAGAAAG
* * * * ********** * * * *
1138 TCTATTTATAGTCACCCATTCTTTCAAAAGCCTTATTACTNNNNNNNNNNGGTTTTATAATTTTA
1 TCCATTTATAGTCACTCATTCCTTCAAAAGCCATATTACTCGCTTTAAATGATTTCATAATCTCA
* * * * * * * * *
1203 TAATTGATTTTATGTTAAATATTTTTATATTTTTAGTTAAAACAGACTAGAATTAAATGTCTACC
66 TAATTGATTTTAAGTTGAATATTTTTACATTTTTTGTTAAAATAGACTATAGTTGAATATCTACC
** ** * *
1268 TCA-AGAAACATGAAGTAAAACACATTCATTA--ATAAGAAAAG
131 T-AGAGAAACATGAAAAAAAAGGCATTCACTAGCAAAAG-AAAG
* * * * * *
1309 TCTATTTATAGTCACACGTTCCTTCAAAAGCCTTATTACTCGCTTTAACT-AGTTTTATAATCTC
1 TCCATTTATAGTCACTCATTCCTTCAAAAGCCATATTACTCGCTTTAAATGA-TTTCATAATCTC
********** * * * * * * * *
1373 ATNNNNNNNNNNAAGTTGAATTTTTTTAGATTTTTGGTTAAAACAGACTATAATTGAATGTATAT
65 ATAATTGATTTTAAGTTGAATATTTTTACATTTTTTGTTAAAATAGACTATAGTTGAATATCTAC
* * * * * *
1438 CTTGAGAAACAT-AAAGAAAAAAGAATTCATTGGCAAGA-AAAG
130 CTAGAGAAACATGAAA-AAAAAGGCATTCACTAGCAAAAGAAAG
*** * * * ** *
1480 TTTGTTTATAGTCTC-CTATTTCTTCAAAAGCCTTATTACTCAATTTAAATTG-TTTTATAATCT
1 TCCATTTATAGTCACTC-ATTCCTTCAAAAGCCATATTACTCGCTTTAAA-TGATTTCATAATCT
* * * * * * * * * *
1543 CAAAATTGATTTTATGTTTAGTTTTTTTATTATTATTTT-TTAAAATATATTATAATTGAATGTC
64 CATAATTGATTTTAAGTTGAATATTTTTA-CATT-TTTTGTTAAAATAGACTATAGTTGAATATC
*
1607 TAGCTAGAGAAA
127 TACCTAGAGAAA
1619 NNNNNNNNNN
Statistics
Matches: 619, Mismatches: 187, Indels: 34
0.74 0.22 0.04
Matches are distributed among these distances:
168 2 0.00
169 1 0.00
170 7 0.01
171 424 0.68
172 180 0.29
173 5 0.01
ACGTcount: A:0.35, C:0.12, G:0.11, T:0.38
Consensus pattern (172 bp):
TCCATTTATAGTCACTCATTCCTTCAAAAGCCATATTACTCGCTTTAAATGATTTCATAATCTCA
TAATTGATTTTAAGTTGAATATTTTTACATTTTTTGTTAAAATAGACTATAGTTGAATATCTACC
TAGAGAAACATGAAAAAAAAGGCATTCACTAGCAAAAGAAAG
Done.