Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018400902.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_4066.0, 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, 789
Length: 1316
ACGTcount: A:0.34, C:0.13, G:0.12, T:0.35
Warning! 81 characters in sequence are not A, C, G, or T
Found at i:297 original size:172 final size:163
Alignment explanation
Indices: 9--347 Score: 491
Period size: 172 Copynumber: 2.0 Consensus size: 163
1 TAAATTGT
* *
9 TTTATAATGTCATAATTGATTTTAAGTTAAATTTTTTTTACATTTTCGTTTAAAACAAACTATAA
1 TTTATAATGTCATAATTGATTTTAAGTTAAATTATTTTTACATTTTCGGTTAAAACAAACTATAA
*
74 TTGAATGTTTACCTAGAGAAATGTGTAGAAAAAGCCAATCATTGAGAAAAAAAAGCCCATTTATA
66 TTGAATGTCTACCTAGAGAAATGTGTAGAAAAAGCCAATCATTGAGAAAAAAAAGCCCATTTATA
* *
139 GTCACCTATTCCTTCGAAAGCCTTATTACTCGC
131 GTCACCCATTCCTTCAAAAGCCTTATTACTCGC
*
172 TNNNNNNNNNNTTATAATGTCATAATTGATTTTAAGTTGAA-TATTTTTACATTTTCGGTTAAAA
1 T----------TTATAATGTCATAATTGATTTTAAGTTAAATTATTTTTACATTTTCGGTTAAAA
* *
236 CAGACTATAATTGAATGTCTACTTAGAGAAATGTGTAGAAAAAGCCAATCATTGAGAAAAAAAAG
56 CAAACTATAATTGAATGTCTACCTAGAGAAATGTGTAGAAAAAGCCAATCATTGAGAAAAAAAAG
* *
301 CCCGTTTATAGTCACCCATTCCTTCAAAAGCCTTATTACTCAC
121 CCCATTTATAGTCACCCATTCCTTCAAAAGCCTTATTACTCGC
344 TTTA
1 TTTA
348 AATTGTTTTA
Statistics
Matches: 156, Mismatches: 10, Indels: 21
0.83 0.05 0.11
Matches are distributed among these distances:
162 3 0.02
163 1 0.01
172 123 0.79
173 29 0.19
ACGTcount: A:0.36, C:0.14, G:0.12, T:0.35
Consensus pattern (163 bp):
TTTATAATGTCATAATTGATTTTAAGTTAAATTATTTTTACATTTTCGGTTAAAACAAACTATAA
TTGAATGTCTACCTAGAGAAATGTGTAGAAAAAGCCAATCATTGAGAAAAAAAAGCCCATTTATA
GTCACCCATTCCTTCAAAAGCCTTATTACTCGC
Found at i:1238 original size:172 final size:171
Alignment explanation
Indices: 390--1316 Score: 756
Period size: 171 Copynumber: 5.4 Consensus size: 171
380 NNNNNNNNNN
* * *
390 TCACATTTTTGGTTAAAACAGACTATAATTGAATGTGTACCTTGAGAAACATGAGGAAA-AAGGC
1 TCACATTTTTGATTAAAACAGACTATAATTGAATGTCTACCTTGAGAAACATGAAGAAACAA-GC
* * * **********
454 ATTAATTGGCAAGCAAAAGTCTATTTATAGTCACCCATTCCTTNNNNNNNNNNATTACTCGCTTT
65 ATTCATTGGCAAG-AAAAGTCTATTTATAGTCTCTCATTCCTTCAAAAGCCTTATTACTCGCTTT
** * *
519 AAAT-GATTTTATAATCTCATAATTTATTTTAAATTGAATTTTT
129 GTATAG-TTTTATAATCTCATAATTGATTTTAAGTTGAATTTTT
* * * * * *
562 TTACATTTTTGGTTAAAACAGACTGTAAGTAAATGTCTACCTTGAGAAACATGAAGAAATAAGCA
1 TCACATTTTTGATTAAAACAGACTATAATTGAATGTCTACCTTGAGAAACATGAAGAAACAAGCA
* * ****
627 TTCATTGGCAACAAAAGTCTATTTATAGTCTCTTATTCCTTCAAAAGCCTTATTACTCGCTNNNN
66 TTCATTGGCAAGAAAAGTCTATTTATAGTCTCTCATTCCTTCAAAAGCCTTATTACTCGCTTTGT
****** *
692 NNNNNNTTATACTCTCATAATTGATTTTAAGTTGAATTTTT
131 ATAGTTTTATAATCTCATAATTGATTTTAAGTTGAATTTTT
* * * *
733 TCACATTTTTGATTAAACCAGACTATAATTGAATGTCTACCTTGGGAAACATGAAGAACCAATCA
1 TCACATTTTTGATTAAAACAGACTATAATTGAATGTCTACCTTGAGAAACATGAAGAAACAAGCA
* *
798 TTCATTTGG-AAGAAAAGTAC-ATTTGTAGTCTCTTATTCCTTCAAAAGCCTTATTACTCGCTTT
66 TTCA-TTGGCAAGAAAAGT-CTATTTATAGTCTCTCATTCCTTCAAAAGCCTTATTACTCGCTTT
* * * * *
861 GTATTGTTTTGTAATCTCAAAATTAATTTTAAGTTGAATATTT
129 GTATAGTTTTATAATCTCATAATTGATTTTAAGTTGAATTTTT
* * ** *
904 TCACTTTTTTTGATTAAAACAGACTATAATTGAAAGTCTACCTT-ACGAAATGTGAACAAACAAG
1 TCAC-ATTTTTGATTAAAACAGACTATAATTGAATGTCTACCTTGA-GAAACATGAAGAAACAAG
* * * ********
968 CATTTATTAGCAAGAAAAGTCTATTTATAGTCTCTCATTTCTTCAAAAGCCTTATTANNNNNNNN
64 CATTCATTGGCAAGAAAAGTCTATTTATAGTCTCTCATTCCTTCAAAAGCCTTATTACTCGCTTT
** * * *
1033 NNATGGTTTTATAATCTCATAATTGAATTTAAGTTGAGTTTTT
129 GTATAGTTTTATAATCTCATAATTGATTTTAAGTTGAATTTTT
* * * * * * *
1076 TTATATTTTTGGTTAAAAGAGTCTATAATTGAATGTCTACCTCGAGAAACGTGAAGAAA-AAGGC
1 TCACATTTTTGATTAAAACAGACTATAATTGAATGTCTACCTTGAGAAACATGAAGAAACAA-GC
* * *******
1140 ATTCATTGGTAAAAAAAAGTCTATTTATAGTCAT-TCATTCCTTCAAAAGCCTTATTANNNNNNN
65 ATTCATTGG-CAAGAAAAGTCTATTTATAGTC-TCTCATTCCTTCAAAAGCCTTATTACTCGCTT
*** * *
1204 NNNATAGTTTTACAATCTCATAATTGATTTTAAGTTGAA-TTTA
128 TGTATAGTTTTATAATCTCATAATTGATTTTAAGTTGAATTTTT
* * * * * * * * * * * *
1247 TCTAGAGTTTAG-CTAAAACAGACTATAATTAAATATTTACCTCGAGATACATAAAGAAAAAAGT
1 TC-ACATTTTTGATTAAAACAGACTATAATTGAATGTCTACCTTGAGAAACATGAAGAAACAAGC
1311 ATTCAT
65 ATTCAT
Statistics
Matches: 616, Mismatches: 125, Indels: 29
0.80 0.16 0.04
Matches are distributed among these distances:
170 2 0.00
171 316 0.51
172 295 0.48
173 3 0.00
ACGTcount: A:0.34, C:0.13, G:0.12, T:0.36
Consensus pattern (171 bp):
TCACATTTTTGATTAAAACAGACTATAATTGAATGTCTACCTTGAGAAACATGAAGAAACAAGCA
TTCATTGGCAAGAAAAGTCTATTTATAGTCTCTCATTCCTTCAAAAGCCTTATTACTCGCTTTGT
ATAGTTTTATAATCTCATAATTGATTTTAAGTTGAATTTTT
Done.