Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018402315.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_5397.0, 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, 692
Length: 1154
ACGTcount: A:0.35, C:0.12, G:0.12, T:0.36
Warning! 50 characters in sequence are not A, C, G, or T
Found at i:634 original size:169 final size:161
Alignment explanation
Indices: 340--812 Score: 341
Period size: 169 Copynumber: 2.8 Consensus size: 161
330 NNNNNNNNNN
* *
340 TTTTATAATCTCAAAATTGATTTTAAGTTGAATATTTATACATTTTCAGTTAGAATAGATTATAA
1 TTTTATAATCTCAAAATTGATTTTAAGTTGAATATTTATACATTTTCAGTTAAAATAGATAATAA
* * * **
405 TTGAACGTCTACCAAGAGAAACGTAAAGAAAACGGTGTTCATTGGTAAGAAAAGTCCATTTATAG
66 TTGAACGTCCACCAAGAGAAACGTAAAGAAAAAGGTATTCATTGACAAGAAAAGTCCATTTATAG
* *
470 TTACCCA-TTCCTTCAAAAGNNNNNNNNNNCGCTTTAAATGA
131 TCA-CCATTTCCATCAAAAG----------CGCTTTAAATGA
* * *
511 TTTTATAATCT-AATAATTGATTTTAAGTTGAAT-TCTTTTA-TTTTTGA-TTAAAATAGATAAT
1 TTTTATAATCTCAA-AATTGATTTTAAGTTGAATAT-TTATACATTTTCAGTTAAAATAGATAAT
* * *
572 AATTGTACGTCCACCTTA-AGAAACTTAAAGAAAAAGGTATTCATTGACAAGAAAAGTCCATTTA
64 AATTGAACGTCCACC-AAGAGAAACGTAAAGAAAAAGGTATTCATTGACAAGAAAAGTCCATTTA
*
636 TAGTCACCATTTCCATCAAAAGCCTGATTACTCACTTTAAATGG
128 TAGTCACCATTTCCATCAAAAG-C-G--------CTTTAAATGA
* * * * * * *
680 TTTTATAATCTGAAAATTGATTTTAATTTGAATATTTTTATATTTTC-GATTAGAACAGATTATA
1 TTTTATAATCTCAAAATTGATTTTAAGTTGAATATTTATACATTTTCAG-TTAAAATAGATAATA
* ** * * * * * * * *
744 ATTTAATATCTACTAGGAGAAACATGAAGAAAAATGCATTCACT-AGCAAGAAAAGTCCATTTAT
65 ATTGAACGTCCACCAAGAGAAACGTAAAGAAAAAGGTATTCATTGA-CAAGAAAAGTCCATTTAT
*
808 TGTCA
129 AGTCA
813 GTCATTCCTT
Statistics
Matches: 245, Mismatches: 37, Indels: 40
0.76 0.11 0.12
Matches are distributed among these distances:
160 1 0.00
161 1 0.00
168 3 0.01
169 125 0.51
170 17 0.07
171 98 0.40
ACGTcount: A:0.38, C:0.12, G:0.12, T:0.36
Consensus pattern (161 bp):
TTTTATAATCTCAAAATTGATTTTAAGTTGAATATTTATACATTTTCAGTTAAAATAGATAATAA
TTGAACGTCCACCAAGAGAAACGTAAAGAAAAAGGTATTCATTGACAAGAAAAGTCCATTTATAG
TCACCATTTCCATCAAAAGCGCTTTAAATGA
Found at i:832 original size:171 final size:168
Alignment explanation
Indices: 169--874 Score: 444
Period size: 171 Copynumber: 4.1 Consensus size: 168
159 NNNNNNATGC
* * * *
169 TTTTATAATCTCATAATTTATTTTGAGTTGAATTTGTTTTCATTTTT-AGTTAAAACAGATAATA
1 TTTTATAATCT-AAAATTGATTTTAAGTTGAA-TTCTTTT-ATTTTTGA-TTAAAACAGATAATA
* * *** * * ** * * *
233 ATTGAACATCTACCTTAAGAAGTGTAAATAAAAAGGCATTCATTGGTAGGAAAAGTTCTTTTATA
62 ATTGTACATCCACCTTAAGAAACATAAAGAAAAAGGCATTCATAGACAAGAAAAGTCCATTTATA
* **********
298 GTCACTCA-TTCCATCAAAAGCCTTATTACTCANNNNNNNNNN
127 GTCAC-CATTTCCATCAAAAGCCTGATTACTCACTTTAAATGA
* * * * * *
340 TTTTATAATCTCAAAATTGATTTTAAGTTGAATAT-TTATACATTTTCAGTTAGAATAGATTATA
1 TTTTATAATCT-AAAATTGATTTTAAGTTGAAT-TCTTTTA-TTTTTGA-TTAAAACAGATAATA
* * * * * * ** * **
404 ATTGAACGTCTACC-AAGAGAAACGTAAAGAAAACGGTGTTCATTGGTAAGAAAAGTCCATTTAT
62 ATTGTACATCCACCTTA-AGAAACATAAAGAAAAAGGCATTCATAGACAAGAAAAGTCCATTTAT
* * ********** *
468 AGTTACCCA-TTCCTTCAAAAGNNNNNNNNNNCGCTTTAAATGA
126 AGTCA-CCATTTCCATCAAAAGCCTGATTACTCACTTTAAATGA
*
511 TTTTATAATCTAATAATTGATTTTAAGTTGAATTCTTTTATTTTTGATTAAAATAGATAATAATT
1 TTTTATAATCTAA-AATTGATTTTAAGTTGAATTCTTTTATTTTTGATTAAAACAGATAATAATT
* * * *
576 GTACGTCCACCTTAAGAAACTTAAAGAAAAAGGTATTCATTGACAAGAAAAGTCCATTTATAGTC
65 GTACATCCACCTTAAGAAACATAAAGAAAAAGGCATTCATAGACAAGAAAAGTCCATTTATAGTC
*
641 ACCATTTCCATCAAAAGCCTGATTACTCACTTTAAATGG
130 ACCATTTCCATCAAAAGCCTGATTACTCACTTTAAATGA
* * *
680 TTTTATAATCTGAAAATTGATTTTAATTTGAATAT-TTTTATATTTTCGATTAGAACAGATTATA
1 TTTTATAATCT-AAAATTGATTTTAAGTTGAAT-TCTTTTAT-TTTT-GATTAAAACAGATAATA
* * * *
744 ATT-TAATATCTA-C-TAGGAGAAACATGAAGAAAAATGCATTCACTAG-CAAGAAAAGTCCATT
62 ATTGT-ACATCCACCTTA--AGAAACATAAAGAAAAAGGCATTCA-TAGACAAGAAAAGTCCATT
* * * * * *
805 TATTGTCAGTCA-TTCCTTCAGAAGCCTGATTGCTTACTTTAAATGA
123 TATAGTCA-CCATTTCCATCAAAAGCCTGATTACTCACTTTAAATGA
*
851 TTTTATAATCTCATAATTGATTTT
1 TTTTATAATCT-AAAATTGATTTT
875 NNNNNNNNNN
Statistics
Matches: 427, Mismatches: 90, Indels: 36
0.77 0.16 0.07
Matches are distributed among these distances:
168 3 0.01
169 130 0.30
170 27 0.06
171 262 0.61
172 5 0.01
ACGTcount: A:0.36, C:0.12, G:0.12, T:0.37
Consensus pattern (168 bp):
TTTTATAATCTAAAATTGATTTTAAGTTGAATTCTTTTATTTTTGATTAAAACAGATAATAATTG
TACATCCACCTTAAGAAACATAAAGAAAAAGGCATTCATAGACAAGAAAAGTCCATTTATAGTCA
CCATTTCCATCAAAAGCCTGATTACTCACTTTAAATGA
Found at i:847 original size:340 final size:342
Alignment explanation
Indices: 169--874 Score: 767
Period size: 340 Copynumber: 2.1 Consensus size: 342
159 NNNNNNATGC
* * *
169 TTTTATAATCTCATAATTTATTTTGAGTTGAATTTGTTTTCATTTTTAGTTAAAACAGATAATAA
1 TTTTATAATCTCATAATTGATTTTAAGTTGAATTTCTTTTCATTTTTAGTTAAAACAGATAATAA
* * * ** * * *
234 TTGAACATCTACCTTAAGAAGTGTAAATAAAAAGGCATTCATTGGTAGGAAAAGTTCTTTTATAG
66 TTGAACATCCACCTTAAGAACTGTAAAGAAAAAGGCATTCATTGACAAGAAAAGTCCATTTATAG
* **********
299 TCACTCATTCCATCAAAAGCCTTATTACTCANNNNNNNNNNTTTTATAATCTCAAAATTGATTTT
131 TCACTCATTCCATCAAAAGCCTGATTACTCACTTTAAATGGTTTTATAATCTCAAAATTGATTTT
* * *
364 AAGTTGAATATTTATACATTTTCAGTTAGAATAGATTATAATTGAACGTCTACCAAGAGAAACGT
196 AAGTTGAATATTTATACATTTTCAGTTAGAACAGATTATAATTGAACATCTACCAAGAGAAACAT
* ** * * * * *****
429 AAAGAAAACGGTGTTCATTGGTAAGAAAAGTCCATTTATAGTTACCCATTCCTTCAAAAGNNNNN
261 AAAGAAAAAGGCATTCACTAGCAAGAAAAGTCCATTTATAGTCACCCATTCCTTCAAAAGCCTGA
***** *
494 NNNNNCGCTTTAAATGA
326 TTGCTCACTTTAAATGA
* *
511 TTTTATAATCTAATAATTGATTTTAAGTTGAA-TTCTTTT-ATTTTT-GATTAAAATAGATAATA
1 TTTTATAATCTCATAATTGATTTTAAGTTGAATTTCTTTTCATTTTTAG-TTAAAACAGATAATA
* * *
573 ATTGTACGTCCACCTTAAGAAACT-TAAAGAAAAAGGTATTCATTGACAAGAAAAGTCCATTTAT
65 ATTGAACATCCACCTTAAG-AACTGTAAAGAAAAAGGCATTCATTGACAAGAAAAGTCCATTTAT
*
637 AGTCAC-CATTTCCATCAAAAGCCTGATTACTCACTTTAAATGGTTTTATAATCTGAAAATTGAT
129 AGTCACTCA-TTCCATCAAAAGCCTGATTACTCACTTTAAATGGTTTTATAATCTCAAAATTGAT
* * * * * * *
701 TTTAATTTGAATATTTTTATATTTTC-GATTAGAACAGATTATAATTTAATATCTACTAGGAGAA
193 TTTAAGTTGAATATTTATACATTTTCAG-TTAGAACAGATTATAATTGAACATCTACCAAGAGAA
* * * ** *
765 ACATGAAGAAAAATGCATTCACTAGCAAGAAAAGTCCATTTATTGTCAGTCATTCCTTCAGAAGC
257 ACATAAAGAAAAAGGCATTCACTAGCAAGAAAAGTCCATTTATAGTCACCCATTCCTTCAAAAGC
*
830 CTGATTGCTTACTTTAAATGA
322 CTGATTGCTCACTTTAAATGA
851 TTTTATAATCTCATAATTGATTTT
1 TTTTATAATCTCATAATTGATTTT
875 NNNNNNNNNN
Statistics
Matches: 296, Mismatches: 64, Indels: 10
0.80 0.17 0.03
Matches are distributed among these distances:
339 4 0.01
340 254 0.86
341 9 0.03
342 29 0.10
ACGTcount: A:0.36, C:0.12, G:0.12, T:0.37
Consensus pattern (342 bp):
TTTTATAATCTCATAATTGATTTTAAGTTGAATTTCTTTTCATTTTTAGTTAAAACAGATAATAA
TTGAACATCCACCTTAAGAACTGTAAAGAAAAAGGCATTCATTGACAAGAAAAGTCCATTTATAG
TCACTCATTCCATCAAAAGCCTGATTACTCACTTTAAATGGTTTTATAATCTCAAAATTGATTTT
AAGTTGAATATTTATACATTTTCAGTTAGAACAGATTATAATTGAACATCTACCAAGAGAAACAT
AAAGAAAAAGGCATTCACTAGCAAGAAAAGTCCATTTATAGTCACCCATTCCTTCAAAAGCCTGA
TTGCTCACTTTAAATGA
Done.