Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397645.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_5155.0, 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: 2727
ACGTcount: A:0.28, C:0.09, G:0.11, T:0.25
Warning! 742 characters in sequence are not A, C, G, or T
Found at i:378 original size:168 final size:170
Alignment explanation
Indices: 127--522 Score: 467
Period size: 170 Copynumber: 2.3 Consensus size: 170
117 TAACCCAAGC
* * *
127 TGAAAAAAGTTCTATTTAAAATCATTTATAAGATTATAAAACCATTTCAAGTAAGTAACTAGGCT
1 TGAAAAAAGTTCAATTTAAAATCATTTATAAGATTATAAAACCATTTAAAGTAAGTAACTAGACT
* * * * *
192 TTCGAAAGCTTGAGTGACTATAAA-TAAATTTTCTTGTAAATGGATGGCTTTCGCTTCACGTTTC
66 TTCGAAAGCATAAGTGACTATAAACGAAATTTTCTTGTAAATAGATGGATTTCGCTTCACGTTTC
** *
256 C-AATCCAAAAATCAAATTATGATCAATTTTAATGAAAAT
131 CTAATCCAAAAATCAAATTATGATCAATTTTAACCAAAAA
* * * * *
295 TTAAAAAAATTCAATTTGAAAAT-ATTTATAATATTATGAAACCATTTAAAGTGAGTAACTAGAC
1 TGAAAAAAGTTCAATTT-AAAATCATTTATAAGATTATAAAACCATTTAAAGTAAGTAACTAGAC
* * * * *
359 TTTTG-AAGCCATAAGTGACTATAAACGAACTTTTCTTGTCAATAGATGGATTTTGCTTCATGTT
65 TTTCGAAAG-CATAAGTGACTATAAACGAAATTTTCTTGTAAATAGATGGATTTCGCTTCACGTT
* ** * **
423 TCCTAATGCAACCATCAACTTATGATCTGTTTTAACCAAAAA
129 TCCTAATCCAAAAATCAAATTATGATCAATTTTAACCAAAAA
* * * *
465 TGAAAAAAGTTCAATCTAAAATCATTTGTAAGATTATAAAACCATTTCAAGCAAGTAA
1 TGAAAAAAGTTCAATTTAAAATCATTTATAAGATTATAAAACCATTTAAAGTAAGTAA
523 TTAGGCTTGT
Statistics
Matches: 187, Mismatches: 36, Indels: 8
0.81 0.16 0.03
Matches are distributed among these distances:
167 3 0.02
168 68 0.36
169 44 0.24
170 72 0.39
ACGTcount: A:0.40, C:0.13, G:0.12, T:0.35
Consensus pattern (170 bp):
TGAAAAAAGTTCAATTTAAAATCATTTATAAGATTATAAAACCATTTAAAGTAAGTAACTAGACT
TTCGAAAGCATAAGTGACTATAAACGAAATTTTCTTGTAAATAGATGGATTTCGCTTCACGTTTC
CTAATCCAAAAATCAAATTATGATCAATTTTAACCAAAAA
Found at i:548 original size:170 final size:168
Alignment explanation
Indices: 65--699 Score: 618
Period size: 169 Copynumber: 3.8 Consensus size: 168
55 TTTATCAGTG
* * * * * * **
65 GATGGCTTTTGCTTCACGTTTCCTGATGTAAACATTAATTTACAATCTGTTTTAACCCAAGCTGA
1 GATGGCTTTTGCTTCACGTTTCCTAATGCAAACATCAAATTATAATCTGTTTTAACCAAAAATGA
* *
130 AAAAAGTTCTATTTAAAATCATTTATAAGATTATAAAACCATTTCAAGTAAGTAACTAGGCTTTC
66 AAAAAGTTCAATCTAAAATCATTTATAAGATTATAAAACCATTTCAAGTAAGTAACTAGGCTTT-
* * * * *
195 GAAAGCTTGAGTGACTATAAATAAATTTTCTTGTAAATG
130 GAAGGCTTGAGTGACTATAAACAACTTTTCTTGTCAATA
* * * * ** ** * *
234 GATGGCTTTCGCTTCACGTTTCC-AATCCAAAAATCAAATTATGATCAATTTTAATGAAAATTTA
1 GATGGCTTTTGCTTCACGTTTCCTAATGCAAACATCAAATTATAATCTGTTTTAACCAAAAATGA
* * * * * * *
298 AAAAAATTCAATTTGAAAAT-ATTTATAATATTATGAAACCATTTAAAGTGAGTAACTAGACTTT
66 AAAAAGTTCAATCT-AAAATCATTTATAAGATTATAAAACCATTTCAAGTAAGTAACTAGGC-TT
* * *
362 TGAAGCCATAAGTGACTATAAACGAACTTTTCTTGTCAATA
129 TGAAGGCTTGAGTGACTATAAAC-AACTTTTCTTGTCAATA
* * * * *
403 GATGGATTTTGCTTCATGTTTCCTAATGCAACCATCAACTTATGATCTGTTTTAACCAAAAATGA
1 GATGGCTTTTGCTTCACGTTTCCTAATGCAAACATCAAATTATAATCTGTTTTAACCAAAAATGA
* * *
468 AAAAAGTTCAATCTAAAATCATTTGTAAGATTATAAAACCATTTCAAGCAAGTAATTAGGCTTGT
66 AAAAAGTTCAATCTAAAATCATTTATAAGATTATAAAACCATTTCAAGTAAGTAACTAGGCTT-T
* ****
533 GAAGGTTTGAGTGACTATAAACAGACTTTTCACAACAATA
130 GAAGGCTTGAGTGACTATAAACA-ACTTTTCTTGTCAATA
* * * * **
573 GGTGGCTTTTGCTTCA--TATTCCTAAGGTAAACATCAAATTATAATTTGTTTTAATAAAAAATG
1 GATGGCTTTTGCTTCACGT-TTCCTAATGCAAACATCAAATTATAATCTGTTTTAACCAAAAATG
* * *
636 AAAGCAA-TTCAAGCTAAAATCATTTATAAGATTATAAAA-C-TCTTCAAAGTAAGTAATTAGGC
65 AAA-AAAGTTCAATCTAAAATCATTTATAAGATTATAAAACCAT-TTC-AAGTAAGTAACTAGGC
698 TT
127 TT
700 ACGAACGGAT
Statistics
Matches: 378, Mismatches: 77, Indels: 22
0.79 0.16 0.05
Matches are distributed among these distances:
167 1 0.00
168 95 0.25
169 159 0.42
170 123 0.33
ACGTcount: A:0.38, C:0.14, G:0.13, T:0.35
Consensus pattern (168 bp):
GATGGCTTTTGCTTCACGTTTCCTAATGCAAACATCAAATTATAATCTGTTTTAACCAAAAATGA
AAAAAGTTCAATCTAAAATCATTTATAAGATTATAAAACCATTTCAAGTAAGTAACTAGGCTTTG
AAGGCTTGAGTGACTATAAACAACTTTTCTTGTCAATA
Done.