Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018402826.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_5880.0, 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, 875
Length: 1459
ACGTcount: A:0.25, C:0.11, G:0.07, T:0.27
Warning! 440 characters in sequence are not A, C, G, or T
Found at i:290 original size:171 final size:168
Alignment explanation
Indices: 1--556 Score: 533
Period size: 171 Copynumber: 3.2 Consensus size: 168
* *
1 AGTTGAATTTTTTTACATTTTTGGCTAAAACAAACTATAATTGAATGTCTACCTCAAGAAACATA
1 AGTTGAATTTTTTTACATGTTTGCCTAAAACAAACTATAATTGAATGTCTACCTCAAGAAA-ATA
* * * * * **
66 GAAAAAAAAGCATTCATTAGCAACAAAATTCTATTTATAGTTATCCTTTCCTTCAAAAGTCTTAT
65 GAAAAAAAGGCAATCATTAGCAACAAAATTC-ATTTATAGTCACCCATTCCTTCAAAAACCTTAT
* *
131 TACTCGCTTTAAACAGTTTTATAATTTCATAATTGATTTTA
129 TACTCACTTTAAAC-GTTTTATAATCTCATAATTGATTTTA
* * ** * *
172 AGTTGAATTTTTTTACATGTTTGCCTAAAACAGACAATAATTGAATGTCTGTCTCGAGAAAGGTA
1 AGTTGAATTTTTTTACATGTTTGCCTAAAACAAACTATAATTGAATGTCTACCTCAAGAAA-ATA
* *
237 GAAAAAAAGGCAATCATTAGTAAGAAAATTTCATTTATAGTCACCCATTCCTTCAAAAACCTTAT
65 GAAAAAAAGGCAATCATTAGCAACAAAA-TTCATTTATAGTCACCCATTCCTTCAAAAACCTTAT
********* *
302 TACTCACTTNNNNNNNNNNTATAATCTCAAAATTGATTTTA
129 TACTCACTT-TAAACGTTTTATAATCTCATAATTGATTTTA
** * * ** *
343 AGTTGAATTTTTTGTACAAT-TTTGGTTAAAACAAATTATAATTCAATGTCTACCTCTTGAAACT
1 AGTTGAATTTTTT-TAC-ATGTTTGCCTAAAACAAACTATAATTGAATGTCTACCTCAAGAAAAT
* * * * * * *
407 TGAAGAAAAAGACAGTCATT-GACAACAAAAGTCACTTTATAGTCACTCATTCTTTTAAAAACCT
64 AGAA-AAAAAGGCAATCATTAG-CAACAAAATTCA-TTTATAGTCACCCATTCCTTCAAAAACCT
* * *
471 TATTACTCATTTTAAGCGATTTTGTAATCTCATAATTGATTTTA
126 TATTACTCACTTTAAACG-TTTTATAATCTCATAATTGATTTTA
* * *
515 AGTTGAATTGTTTTGCATGTTT-CCTCAAAACAGACTATAATT
1 AGTTGAATTTTTTTACATGTTTGCCT-AAAACAAACTATAATT
557 TAATACCTTC
Statistics
Matches: 307, Mismatches: 68, Indels: 20
0.78 0.17 0.05
Matches are distributed among these distances:
170 3 0.01
171 176 0.57
172 126 0.41
173 2 0.01
ACGTcount: A:0.36, C:0.15, G:0.10, T:0.37
Consensus pattern (168 bp):
AGTTGAATTTTTTTACATGTTTGCCTAAAACAAACTATAATTGAATGTCTACCTCAAGAAAATAG
AAAAAAAGGCAATCATTAGCAACAAAATTCATTTATAGTCACCCATTCCTTCAAAAACCTTATTA
CTCACTTTAAACGTTTTATAATCTCATAATTGATTTTA
Found at i:652 original size:343 final size:331
Alignment explanation
Indices: 1--654 Score: 705
Period size: 343 Copynumber: 1.9 Consensus size: 331
* *
1 AGTTGAATTTTTTTACATTTTTGGCTAAAACAAACTATAATTGAATGTCTACCTCAAGAAACATA
1 AGTTGAATTTTTTTACAATTTTGGCTAAAACAAACTATAATTCAATGTCTACCTCAAGAAACATA
* * * * **
66 GAAAAAAAAGCATTCATTAGCAACAAAATTCTATTTATAGTTATCCTTTCCTTCAAAAGTCTTAT
66 GAAAAAAAAGCAGTCATTAGCAACAAAAGTCTATTTATAGTCATCCATTCCTTCAAAAACCTTAT
* * *
131 TACTCGCTTTAAACAGTTTTATAATTTCATAATTGATTTTAAGTTGAATTTTTTTACATGTTTGC
131 TACTCACTTTAAACAGTTTTATAATCTCATAATTGATTTTAAGTTGAATTGTTTTACATGTTTGC
** * *
196 CTAAAACAGACAATAATTGAATGTCTGTCTCGAGAAAGGTAGAAAAAAAGGCAATCATTAGTAAG
196 CTAAAACAGACAATAATTGAATACCTGTCTCGAGAAAGGTAG-AAAAAAGCCAATCATTAGAAAG
* * *
261 AAAATTTCATTTATAGTCACCCATTCCTTCAAAAACCTTATTACTCACTTNNNNNNNNNNTATAA
260 AAAAGTCCATCTATAGTCACCCATTCCTTCAAAAACCTTATTACTCACTT----------TATAA
326 TCTCAAAATTGATTTTA
315 TCTCAAAATTGATTTTA
* * **
343 AGTTGAATTTTTTGTACAATTTTGGTTAAAACAAATTATAATTCAATGTCTACCTCTTGAAAC-T
1 AGTTGAATTTTTT-TACAATTTTGGCTAAAACAAACTATAATTCAATGTCTACCTCAAGAAACAT
* * * *
407 TGAAGAAAAAGACAGTCATT-GACAACAAAAGTC-ACTTTATAGTCA-CTCATTCTTTTAAAAAC
65 AGAAAAAAAAG-CAGTCATTAG-CAACAAAAGTCTA-TTTATAGTCATC-CATTCCTTCAAAAAC
* * * *
469 CTTATTACTCATTTTAAGC-GATTTTGTAATCTCATAATTGATTTTAAGTTGAATTGTTTTGCAT
126 CTTATTACTCACTTTAAACAG-TTTTATAATCTCATAATTGATTTTAAGTTGAATTGTTTTACAT
* * * * *
533 GTTT-CCTCAAAACAGACTATAATTTAATACCT-TCCTTGGGAAACGTGTAG-AAAAAGCCATTC
190 GTTTGCCT-AAAACAGACAATAATTGAATACCTGT-CTCGAGAAA-G-GTAGAAAAAAGCCAATC
** *
595 ATTTA-AAAGAAAAGTCCATCTATAGTCTTCCATTCCTTCAAAAGCCTTATTACTCACTTT
251 A-TTAGAAAGAAAAGTCCATCTATAGTCACCCATTCCTTCAAAAACCTTATTACTCACTTT
655 NNNNNNNNNN
Statistics
Matches: 263, Mismatches: 38, Indels: 31
0.79 0.11 0.09
Matches are distributed among these distances:
333 1 0.00
342 31 0.12
343 223 0.85
344 4 0.02
345 4 0.02
ACGTcount: A:0.36, C:0.16, G:0.11, T:0.37
Consensus pattern (331 bp):
AGTTGAATTTTTTTACAATTTTGGCTAAAACAAACTATAATTCAATGTCTACCTCAAGAAACATA
GAAAAAAAAGCAGTCATTAGCAACAAAAGTCTATTTATAGTCATCCATTCCTTCAAAAACCTTAT
TACTCACTTTAAACAGTTTTATAATCTCATAATTGATTTTAAGTTGAATTGTTTTACATGTTTGC
CTAAAACAGACAATAATTGAATACCTGTCTCGAGAAAGGTAGAAAAAAGCCAATCATTAGAAAGA
AAAGTCCATCTATAGTCACCCATTCCTTCAAAAACCTTATTACTCACTTTATAATCTCAAAATTG
ATTTTA
Done.