Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018400482.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_3678.0, 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: 4566
ACGTcount: A:0.26, C:0.08, G:0.09, T:0.25
Warning! 1499 characters in sequence are not A, C, G, or T
Found at i:3918 original size:170 final size:170
Alignment explanation
Indices: 3580--4566 Score: 801
Period size: 170 Copynumber: 5.8 Consensus size: 170
3570 NNNNNNNNNN
* * * * *
3580 AATCGATTATGAGATTATAAAACCA-TTAAAGAG-GCTAATAAGTCTTTTGAAAGAATAAGAGAC
1 AATCAATTATGAGATTATAAAACCATTTAAAGTGAG-TAATAAGGCTTTTGAAGGAATAGGAGAC
* * * * *
3643 TATAAATAGACTTTTATTCTAAATAAAT-GAGTTTTTCTACAAGTTTTTTAAAGCAGGCATTCAA
65 TATAAATGGACTTTTCTTCCAAATAAATGGA-TTTTTCTACAGGTTTCTTAAAGCAGGCATTCAA
* * * * * *
3707 TTATGGTCTCTTTTAACAAAAAATATAAAACATTTAACTTAA
129 TTATAGTCTGTTTTAATAAAAAATGTAAAAAATTCAACTTAA
* * * * * *
3749 AATCAATTATAAGATTATAAAATCATTTAAAGTGAGTAATAAAGCTTTCGAAGGAATGGGAGAAT
1 AATCAATTATGAGATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATAGGAGACT
* * * * *
3814 ATAAATGGACTTTTCTTCCAAAGAAATGGATTTTTCTATAGGTTTCTTAAGGCAAGCATTTAATT
66 ATAAATGGACTTTTCTTCCAAATAAATGGATTTTTCTACAGGTTTCTTAAAGCAGGCATTCAATT
* *
3879 ATAGTCTGTTTTAATAAGAAATGTAAAAAACTCAACTTAA
131 ATAGTCTGTTTTAATAAAAAATGTAAAAAATTCAACTTAA
* * ********** * * *
3919 ATTCAATTATGAGATTATAAAACTATTTAAAGNNNNNNNNNNGGGTTTTGAAGGAATGGGTGACT
1 AATCAATTATGAGATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATAGGAGACT
* * * * * * *
3984 ATAAATGGACTTTTCTTGTC-TATAAATGTCATTTTT-T-CACGTTTCTTAACGTAGACATTCAA
66 ATAAATGGACTTTTCTT-CCAAATAAATG-GATTTTTCTACAGGTTTCTTAAAGCAGGCATTCAA
* *
4046 TTATAATCTGTTTTAACTAAAAAAT-TAAAAATAATTGAACTTAA
129 TTATAGTCTGTTTTAA-TAAAAAATGT-AAAA-AATTCAACTTAA
* * * * *
4090 AATAAATAATGAGATTATAAAACCATTTAAAGTGAG---TAAGGCTTTTGAAGAAAAAGGTGACT
1 AATCAATTATGAGATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATAGGAGACT
* * * * * *
4152 ATAAATGGACTTTTCTTCTAAATAAATGGATTTTTTTTCATGTTTCCTGAAGCAGGCATTCAATT
66 ATAAATGGACTTTTCTTCCAAATAAATGGATTTTTCTACAGGTTTCTTAAAGCAGGCATTCAATT
* *
4217 ATAGTCTGTTTTAATAAAAAATGT-ATAAATCTGAACTTAA
131 ATAGTCTGTTTTAATAAAAAATGTAAAAAAT-TCAACTTAA
* * ********** * * *
4257 AACCAATTATGAGATTACANNNNNNNNNNAAGCGAGTAATAAGGCTTTCGAAGGAATAGGAGAAT
1 AATCAATTATGAGATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATAGGAGACT
* **
4322 ATAAATAGACTTTTCTTCCAAATAAATGGGCTTTTCTACAGGTTTCTTAAAGCAGGCATTCAATT
66 ATAAATGGACTTTTCTTCCAAATAAATGGATTTTTCTACAGGTTTCTTAAAGCAGGCATTCAATT
* * *
4387 ATTGTCTGTTTTAATGAGAAATGTAAAAAATTCAACTTAA
131 ATAGTCTGTTTTAATAAAAAATGTAAAAAATTCAACTTAA
* ********** * ** *
4427 ATTNNNNNNNNNNATTATAAAACCATTTAAAGTGAGTAATAAGGTTTTTGAAACAATAGGCGACT
1 AATCAATTATGAGATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATAGGAGACT
* * ** * * * * *
4492 ATAAATGGACTTTTCTTGCC-TATGAATGCCTTTTTCTTCATGTTTCTTAATGTAGACATTCAAT
66 ATAAATGGACTTTTCTT-CCAAATAAATGGATTTTTCTACAGGTTTCTTAAAGCAGGCATTCAAT
*
4556 TATAATCTGTT
130 TATAGTCTGTT
Statistics
Matches: 633, Mismatches: 167, Indels: 35
0.76 0.20 0.04
Matches are distributed among these distances:
166 3 0.00
167 38 0.06
168 52 0.08
169 91 0.14
170 394 0.62
171 55 0.09
ACGTcount: A:0.38, C:0.10, G:0.14, T:0.35
Consensus pattern (170 bp):
AATCAATTATGAGATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATAGGAGACT
ATAAATGGACTTTTCTTCCAAATAAATGGATTTTTCTACAGGTTTCTTAAAGCAGGCATTCAATT
ATAGTCTGTTTTAATAAAAAATGTAAAAAATTCAACTTAA
Found at i:4499 original size:508 final size:510
Alignment explanation
Indices: 3588--4566 Score: 1169
Period size: 508 Copynumber: 1.9 Consensus size: 510
3578 NNAATCGATT
* *
3588 ATGAGATTATAAAACCATTAAAGAGGCTAATAAGTCTTTTGAAAGAATAAGAGACTATAAATAGA
1 ATGAGATTATAAAACCATTAAAGAGGC-AATAAGGCTTTTGAAAGAAAAAGAGACTATAAATAGA
** *
3653 CTTTTATTCTAAATAAATGAGTTTTTCTACAAGTTTTTTAAAGCAGGCATTCAATTATGGTCTCT
65 CTTTTATTCTAAATAAATGAGTTTTTCTACAAGTTTCCTAAAGCAGGCATTCAATTATAGTCTCT
* * * *
3718 TTTAACAAAAAATATAAAACATTTAACTTAAAATCAATTATAAGATTATAAAATCATTTAAAGTG
130 TTTAACAAAAAATATAAAACATTGAACTTAAAACCAATTATAAGATTACAAAATCATTTAAAGCG
* * *
3783 AGTAATAAAGCTTTCGAAGGAATGGGAGAATATAAATGGACTTTTCTTCCAAAGAAATGGATTTT
195 AGTAATAAAGCTTTCGAAGGAATAGGAGAATATAAATAGACTTTTCTTCCAAAGAAATGGACTTT
* * *
3848 TCTATAGGTTTCTTAAGGCAAGCATTTAATTATAGTCTGTTTTAATAAGAAATGTAAAAAACTCA
260 TCTACAGGTTTCTTAAAGCAAGCATTCAATTATAGTCTGTTTTAATAAGAAATGTAAAAAACTCA
* ********** ** *
3913 ACTTAAATTCAATTATGAGATTATAAAACTATTTAAAGNNNNNNNNNNGGGTTTTGAAGGAATGG
325 ACTTAAATTCAATTATGAGATTATAAAACCATTTAAAGTGAGTAATAAGGGTTTTGAAACAATAG
* * *
3978 GTGACTATAAATGGACTTTTCTTGTCTATAAATGTCATTTT-TTCACGTTTCTTAACGTAGACAT
390 GCGACTATAAATGGACTTTTCTTGCCTATAAATGCCATTTTCTTCACGTTTCTTAACGTAGACAT
4042 TCAATTATAATCTGTTTTAACTAAAAAATTAAAAATAATTGAACTTAAAATAAATA
455 TCAATTATAATCTGTTTTAACTAAAAAATTAAAAATAATTGAACTTAAAATAAATA
* * * *
4098 ATGAGATTATAAAACCATTTAAAG-TG-AGTAAGGCTTTTG-AAGAAAAAGGTGACTATAAATGG
1 ATGAGATTATAAAACCA-TTAAAGAGGCAATAAGGCTTTTGAAAGAAAAA-GAGACTATAAATAG
* * * * *
4160 ACTTTTCTTCTAAATAAATG-GATTTTTTTTCATGTTTCCTGAAGCAGGCATTCAATTATAGTCT
64 ACTTTTATTCTAAATAAATGAG-TTTTTCTACAAGTTTCCTAAAGCAGGCATTCAATTATAGTCT
* * * * * **********
4224 GTTTTAATAAAAAATGTATAA-ATCTGAACTTAAAACCAATTATGAGATTACANNNNNNNNNNAA
128 CTTTTAACAAAAAATATAAAACAT-TGAACTTAAAACCAATTATAAGATTACAAAATCATTTAAA
* * *
4288 GCGAGTAATAAGGCTTTCGAAGGAATAGGAGAATATAAATAGACTTTTCTTCCAAATAAATGGGC
192 GCGAGTAATAAAGCTTTCGAAGGAATAGGAGAATATAAATAGACTTTTCTTCCAAAGAAATGGAC
* * * *
4353 TTTTCTACAGGTTTCTTAAAGCAGGCATTCAATTATTGTCTGTTTTAATGAGAAATGTAAAAAAT
257 TTTTCTACAGGTTTCTTAAAGCAAGCATTCAATTATAGTCTGTTTTAATAAGAAATGTAAAAAAC
********** *
4418 TCAACTTAAATTNNNNNNNNNNATTATAAAACCATTTAAAGTGAGTAATAAGGTTTTTGAAACAA
322 TCAACTTAAATTCAATTATGAGATTATAAAACCATTTAAAGTGAGTAATAAGGGTTTTGAAACAA
* * * *
4483 TAGGCGACTATAAATGGACTTTTCTTGCCTATGAATGCCTTTTTCTTCATGTTTCTTAATGTAGA
387 TAGGCGACTATAAATGGACTTTTCTTGCCTATAAATGCCATTTTCTTCACGTTTCTTAACGTAGA
4548 CATTCAATTATAATCTGTT
452 CATTCAATTATAATCTGTT
Statistics
Matches: 386, Mismatches: 78, Indels: 11
0.81 0.16 0.02
Matches are distributed among these distances:
507 10 0.03
508 315 0.82
509 37 0.10
510 18 0.05
511 6 0.02
ACGTcount: A:0.38, C:0.10, G:0.14, T:0.35
Consensus pattern (510 bp):
ATGAGATTATAAAACCATTAAAGAGGCAATAAGGCTTTTGAAAGAAAAAGAGACTATAAATAGAC
TTTTATTCTAAATAAATGAGTTTTTCTACAAGTTTCCTAAAGCAGGCATTCAATTATAGTCTCTT
TTAACAAAAAATATAAAACATTGAACTTAAAACCAATTATAAGATTACAAAATCATTTAAAGCGA
GTAATAAAGCTTTCGAAGGAATAGGAGAATATAAATAGACTTTTCTTCCAAAGAAATGGACTTTT
CTACAGGTTTCTTAAAGCAAGCATTCAATTATAGTCTGTTTTAATAAGAAATGTAAAAAACTCAA
CTTAAATTCAATTATGAGATTATAAAACCATTTAAAGTGAGTAATAAGGGTTTTGAAACAATAGG
CGACTATAAATGGACTTTTCTTGCCTATAAATGCCATTTTCTTCACGTTTCTTAACGTAGACATT
CAATTATAATCTGTTTTAACTAAAAAATTAAAAATAATTGAACTTAAAATAAATA
Done.