Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018400153.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_3369.0, 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: 2499
ACGTcount: A:0.27, C:0.08, G:0.09, T:0.25
Warning! 767 characters in sequence are not A, C, G, or T
Found at i:1378 original size:172 final size:169
Alignment explanation
Indices: 595--1569 Score: 569
Period size: 171 Copynumber: 5.7 Consensus size: 169
585 NNNNNNNNNT
** * *
595 TTTTTTTGCCAATGAATGCCTTTTTCTTTAAGTTTCTCAAGGTAGACAAGCAACTATCATCTGTT
1 TTTTTTTGCCAATGAAT-CCTTTTTCTTTAAGTTTCTCAAGGTAGACATTCAATTAT-ATCTATT
* * *
660 TTAATTAAAAATGTAAAAAAAACTCAACTTAAAATCAATTATGGGATTATAAAACCATTTAAAGT
64 TTAATCAAAAATGT-AAAAAAACTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGC
* * * *
725 GAGTAATAAGATTTTTAAAAGAATGGGCGACTATAAATGAAC
128 GAGTAATAAGACTTTTGAAAGAATGGGTGACTATAAATGGAC
* ** * * * * *
767 TTTTCTT-CTCAAT-AGATCGCTTTTTCTACACGTTT-TCTAAAGAAGACATTTAGTTATATTCT
1 TTTTTTTGC-CAATGA-ATC-CTTTTTCTTTAAGTTTCTC-AAGGTAGACATTCAATTATA-TCT
* * * * **********
829 ATTGTAATGAAAAATGT-AGAAAACTTCAACTTAAAATCAATTATGAAATTATNNNNNNNNNNAA
61 ATTTTAATCAAAAATGTAAAAAAAC-TCAACTTAAAATCAATTATGAGATTATAAAACCATTTAA
* * * **
893 AGTGAGTAATAAGCCTTTTGAAGGAATAAGTGACTATAAATGGAC
125 AGCGAGTAATAAGACTTTTGAAAGAATGGGTGACTATAAATGGAC
* * * * * * *
938 ATTTCTTGCCAATGAATACTTTTTTCTTCATA-TTTCTCGAGGTA-ATCATTTAACTATAATCTA
1 TTTTTTTGCCAATGAAT-CCTTTTTCTTTA-AGTTTCTCAAGGTAGA-CATTCAATTAT-ATCTA
* * * ** **
1001 ATATAACCAAAAATGTAAAATTA-T-AACTTAAAATCAATTATGAGATTATAAAAAGATTTAAAG
62 TTTTAATCAAAAATGTAAAAAAACTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAG
*********
1064 CGAGTAANNNNNNNNNNT-AAAGAATGGGTGACTATAAATGGAC
127 CGAGTAA-TAAGACTTTTGAAAGAATGGGTGACTATAAATGGAC
* * * *****
1107 CTTTTTGGCCAATGAATCCTTTGTTCTTCT-TGTTTCTCAAGGTAGACATTCAATTATANNNNNN
1 TTTTTTTGCCAATGAATCCTTT-TTCTT-TAAGTTTCTCAAGGTAGACATTCAATTATA-TCTAT
**** * * * *
1171 NNNNA-CTAAAAATGTAAAAGAATTCAACTTAAAATCAATTGTGAGATTATAAAACCATTTTAAG
63 TTTAATC-AAAAATGTAAAAAAACTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAG
* * * *
1235 CGAGTAATAAGGCTTTTGAAAGAATGTGTGATTATAAATGGATT
127 CGAGTAATAAGACTTTTGAAAGAATGGGTGACTATAAATGGA-C
* ** * *
1279 TTTTTTTGCCAATGAATGCCTTTTTCTTTAAGTCTCTCAAGGTAGACAAGCAATTATCATTTGTT
1 TTTTTTTGCCAATGAAT-CCTTTTTCTTTAAGTTTCTCAAGGTAGACATTCAATTAT-ATCTATT
**********
1344 TTAATCAAAAATGTAAAAAAACTCAACTTAAAATCAATTNNNNNNNNNNAAAACCATTTAAAGCG
64 TTAATCAAAAATGTAAAAAAACTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCG
* * * * *
1409 AGTAATAAGA-TTTTAAAAAGAATGGGCGACTATAAACGAAG
129 AGTAATAAGACTTTT-GAAAGAATGGGTGACTATAAATGGAC
* * ** * * * * *
1450 TTTTCTT-CTTAAT-AGATCACTTTTTCTACACGTTTC-CTAAAGAAGACATTTAGTTATATTCT
1 TTTTTTTGC-CAATGA-ATC-CTTTTTCTTTAAGTTTCTC-AAGGTAGACATTCAATTATA-TCT
* * *
1512 ATTTTAATGAAAAATGT-AGAAAACTTCAACTTAAAATCAATTATGAAATTATAAAACC
61 ATTTTAATCAAAAATGTAAAAAAAC-TCAACTTAAAATCAATTATGAGATTATAAAACC
1570 NNNNNNNNNN
Statistics
Matches: 594, Mismatches: 173, Indels: 73
0.71 0.21 0.09
Matches are distributed among these distances:
168 6 0.01
169 109 0.18
170 23 0.04
171 268 0.45
172 181 0.30
173 7 0.01
ACGTcount: A:0.38, C:0.12, G:0.12, T:0.34
Consensus pattern (169 bp):
TTTTTTTGCCAATGAATCCTTTTTCTTTAAGTTTCTCAAGGTAGACATTCAATTATATCTATTTT
AATCAAAAATGTAAAAAAACTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAG
TAATAAGACTTTTGAAAGAATGGGTGACTATAAATGGAC
Done.