Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018400708.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_3889.0, 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: 2658
ACGTcount: A:0.25, C:0.09, G:0.09, T:0.27
Warning! 820 characters in sequence are not A, C, G, or T
Found at i:441 original size:175 final size:166
Alignment explanation
Indices: 5--797 Score: 501
Period size: 171 Copynumber: 4.7 Consensus size: 166
1 CATG
* * * *
5 TTTGGTTAAAACAGACAATAATTGAATGTCTTCCTTGA-AAACATGAAGAAAAATGCATTCATTG
1 TTTGGTTAAAACAGACTATAATTGAATGTCTACCTTGAGAAACATGAAGAGAAACGCATTCATTG
* * * * * * *
69 CCAAGAACAGTCAACTTATAGTCACCTATTCCT-TCAAAAGTCTTATTACTCATTTTTAATGGTT
66 ACAAGAAAAGTCTATTTATAGTCACCCATT-CTATCAAAAGCCTTATTACTCA-CTTTAAT-GTT
********* *
133 TTATAATCTCAAAATTGATNNNNNNNNNNAATTTTTTTATATT
128 TTATAATCTC--AA-TGAT-TTTAAGTTCAATTTTTTTACATT
* * * ** * * *
176 TTTGGTTAAAATC-GATTATAATTAAATGTCTACATAAAGAAACATGAAGAAAAATGTATTCATT
1 TTTGGTTAAAA-CAGACTATAATTGAATGTCTACCTTGAGAAACATGAAGAGAAACGCATTCATT
* **********
240 GGCAAGAAAANNNNNNNNNNAGTCACCCATTCTATCAAAAGCCTTATTACTCACTTTATATGATT
65 GACAAGAAAAGTCTATTTATAGTCACCCATTCTATCAAAAGCCTTATTACTCACTTTA-ATG-TT
305 TTATAATCTCAAAATTGATTTTAAGTTCAATGTTTTTTTTTACATT
128 TTATAATCTC--AA-TGATTTTAAGTTCAA----TTTTTTTACATT
** *
351 TTTGGTTAAAATTGACTATAATTGAATGTCTA-CTGTGAGAAACATGAAG-GAAAACTCATTCAT
1 TTTGGTTAAAACAGACTATAATTGAATGTCTACCT-TGAGAAACATGAAGAG-AAACGCATTCAT
** * *
414 TGGTAAGAAAAGTTTATTTATAGTCACCAATTCCT-TCAAAAGCCTTATTACTCACTTTCAATTG
64 TGACAAGAAAAGTCTATTTATAGTCACCCATT-CTATCAAAAGCCTTATTACTCACTTT-AA-TG
* * * * *
478 TTTTACAATCTCTATGTTTTTAGGTTGAATTTTTTTACATT
126 TTTTATAATCTCAATGATTTTAAGTTCAATTTTTTTACATT
* ** * *
519 TTTTGTTAAAACAGTTTATAATTGAATGTCTACCTTGAGAAGCATGAAGAGAAAGGCATTCATTG
1 TTTGGTTAAAACAGACTATAATTGAATGTCTACCTTGAGAAACATGAAGAGAAACGCATTCATTG
* * *
584 ACAAGAAAAGTCTATTTATAGTCACCCATTC-ATTCAAAAGGCTTTTTACTCGCTTTAAATGGTT
66 ACAAGAAAAGTCTATTTATAGTCACCCATTCTA-TCAAAAGCCTTATTACTCACTTT-AAT-GTT
******* * * *
648 TTATANNNNNNNNNNTGATTTTAGGTTGAATTTTTTTACAGT
128 TTATA---ATCTCAATGATTTTAAGTTCAATTTTTTTACATT
* * * * * * *
690 ATTAGTTAGAACAGATTATAATTGAATGTCTACATTG-GAAAACGTGAAGAG-AATG-ATTTTCA
1 TTTGGTTAAAACAGACTATAATTGAATGTCTACCTTGAG-AAACATGAAGAGAAACGCA--TTCA
* * *
752 TTGACAAAAAAAGTCAATTTGTAGTCACCCATTCCT-TCAAAAGCCT
63 TTGACAAGAAAAGTCTATTTATAGTCACCCATT-CTATCAAAAGCCT
798 CNNNNNNNNN
Statistics
Matches: 496, Mismatches: 98, Indels: 56
0.76 0.15 0.09
Matches are distributed among these distances:
167 2 0.00
168 119 0.24
169 4 0.01
170 4 0.01
171 148 0.30
172 97 0.20
173 1 0.00
174 1 0.00
175 115 0.23
176 5 0.01
ACGTcount: A:0.34, C:0.13, G:0.12, T:0.37
Consensus pattern (166 bp):
TTTGGTTAAAACAGACTATAATTGAATGTCTACCTTGAGAAACATGAAGAGAAACGCATTCATTG
ACAAGAAAAGTCTATTTATAGTCACCCATTCTATCAAAAGCCTTATTACTCACTTTAATGTTTTA
TAATCTCAATGATTTTAAGTTCAATTTTTTTACATT
Done.