Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018400790.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_3966.0, 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: 4263
ACGTcount: A:0.23, C:0.07, G:0.09, T:0.22
Warning! 1693 characters in sequence are not A, C, G, or T
Found at i:3772 original size:170 final size:170
Alignment explanation
Indices: 3208--4263 Score: 842
Period size: 170 Copynumber: 6.2 Consensus size: 170
3198 NNNNNNNNNN
* * * *
3208 AAATCAATTATGAGATTATAAAATCATTTAGAGCGAGTAATAAGGCTTTTGAAGAAATA-ATAAC
1 AAATCAATTATGAGATTATAAAATCATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATAGGTAAC
* * ** * *
3272 TAT-AATGAACTTTTATTGCCAATGAATGTATTTTTCTTCATGTTTCTGGAGGTAGACATTCAAT
66 TATAAATGGACTTTTGTTGCCAATGAATGCCTTTTTCTTCACGTTTCTCGAGGTAGACATTCAAT
* * * *
3336 TATAGTCTGCTTTAACTAAAAATGTAAAAAAAATTGAACTTA
131 CATA-TCTGTTTTAACCAAAAAT-TTAAAAAAATTGAACTTA
* ********** * * *
3378 AAATCAATTTTGAGATTNNNNNNNNNNTTAAAGTGAGTAATAAGGCTTTCGAAGGAATGGGTGAC
1 AAATCAATTATGAGATTATAAAATCATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATAGGTAAC
* * * *
3443 TATAAATGGTCTTTTGTTGTCAATGAATGCCTTTTTCGTCATGTTTCAT-GAGGTAGACATTCAA
66 TATAAATGGACTTTTGTTGCCAATGAATGCCTTTTTCTTCACGTTTC-TCGAGGTAGACATTCAA
* *
3507 ACATAATCTGTTTTAATCAAAAAATGTTAAAAAAATTGAACTTA
130 TCAT-ATCTGTTTTAA-CCAAAAAT-TTAAAAAAATTGAACTTA
* ********** * *
3551 AAATCAATTTTGAGATTATAANNNNNNNNNNAGTGAATAATAAGGCTTTTGAAGGAATAGGTAAA
1 AAATCAATTATGAGATTATAAAATCATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATAGGTAAC
* * *
3616 TATAAATGGACTTTTGTTGCCAATGAATGCCATTTTC-TCACGTTTCTTGAGGTAGTCATTCAAT
66 TATAAATGGACTTTTGTTGCCAATGAATGCCTTTTTCTTCACGTTTCTCGAGGTAGACATTCAAT
* * * *
3680 TATGATCTATTTTAACCAATAATTTAAAAAAATTGAACCTA
131 CAT-ATCTGTTTTAACCAAAAATTTAAAAAAATTGAACTTA
* * * *
3721 AAATCAGTTACGAGATTATAAAATCATTTAAAGTGACTAATAAGGCTTTTGAAGCAATTA-G-AG
1 AAATCAATTATGAGATTATAAAATCATTTAAAGTGAGTAATAAGGCTTTTGAAGGAA-TAGGTA-
* * * * * * *
3784 ACTATAAACGGACTTTT-TCTGCTAATAAATGCTTTTTTCTTTACGTTTCTCGATGTAGATATTC
64 ACTATAAATGGACTTTTGT-TGCCAATGAATGCCTTTTTCTTCACGTTTCTCGAGGTAGACATTC
* * *
3848 AATCATAATCTGTTTTAACCAAAAATGTAAGAAAATTAAACTTA
128 AATCAT-ATCTGTTTTAACCAAAAATTTAAAAAAATTGAACTTA
* * * ** * * * * *
3892 AAATCAATTTTCATAAAATAAAATCATTTAAAGTGGGTAATAAGGCTTTTGATGGAGTGGGTGAC
1 AAATCAATTATGAGATTATAAAATCATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATAGGTAAC
* * ** * * *
3957 TATAAATAGACTTTTCTTGTTAATGAATGTCTTTTTCTTCACGTTTCTCAAGGTAGACATTCAAA
66 TATAAATGGACTTTTGTTGCCAATGAATGCCTTTTTCTTCACGTTTCTCGAGGTAGACATTCAAT
* * * * *
4022 AATAGTCTGTTTGAACTAAAAATAT-AAAAAATTCAACTTA
131 CATA-TCTGTTTTAACCAAAAATTTAAAAAAATTGAACTTA
* * * ** * *
4062 AAACCAATTATGAGATTATAAAA-CTATTTAAACTGATTAATAAGGCTTTTGAAAAAATAGATGA
1 AAATCAATTATGAGATTATAAAATC-ATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATAGGTAA
* * * * * **
4126 CTATAAATTGACTTTTCTT-CTCAATGAACTG-CTTTTT-TTATACGTTTC-CTAAGGCAGGGAT
65 CTATAAATGGACTTTTGTTGC-CAATGAA-TGCCTTTTTCTT-CACGTTTCTC-GAGGTAGACAT
* * *** * *
4187 TCAATTATAATATGTTTTAATGTAAAATATAAAAAAATTCAACTTA
126 TCAATCAT-ATCTGTTTTAACCAAAAATTTAAAAAAATTGAACTTA
* *
4233 AAATCAATTATGAGGTTATAAAACCATTTAA
1 AAATCAATTATGAGATTATAAAATCATTTAA
Statistics
Matches: 713, Mismatches: 151, Indels: 43
0.79 0.17 0.05
Matches are distributed among these distances:
169 6 0.01
170 262 0.37
171 234 0.33
172 98 0.14
173 113 0.16
ACGTcount: A:0.38, C:0.11, G:0.14, T:0.36
Consensus pattern (170 bp):
AAATCAATTATGAGATTATAAAATCATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATAGGTAAC
TATAAATGGACTTTTGTTGCCAATGAATGCCTTTTTCTTCACGTTTCTCGAGGTAGACATTCAAT
CATATCTGTTTTAACCAAAAATTTAAAAAAATTGAACTTA
Found at i:4079 original size:341 final size:341
Alignment explanation
Indices: 3588--4241 Score: 764
Period size: 341 Copynumber: 1.9 Consensus size: 341
3578 NNNNAGTGAA
* *
3588 TAATAAGGCTTTTGAAGGAATAGGTAAATATAAATGGACTTTTGTTGCCAATGAATGCCATTTTC
1 TAATAAGGCTTTTGAAGGAATAGGTAAATATAAATAGACTTTTCTTGCCAATGAATGCCATTTTC
** * ** * * * *
3653 TCACGTTTCTTGAGGTAGTCATTCAATTATGATCTATTTTAACCAATAATTTAAAAAAATTGAAC
66 TCACGTTTCTCAAGGTAGACATTCAAAAATGATCTATTTGAACCAAAAATATAAAAAAATTCAAC
* * * * *
3718 CTAAAATCAGTTACGAGATTATAAAA-TCATTTAAAGTGACTAATAAGGCTTTTGAAGCAATTAG
131 CTAAAACCAATTACGAGATTATAAAACT-ATTTAAACTGACTAATAAGGCTTTTGAA-AAAATAG
* * * *
3782 A-GACTATAAACGGACTTTTTCTGCT-AAT-AAATGCTTTTTTCTTTACGTTT-CTCGATGTAGA
194 ATGACTATAAACGGAC-TTTTCTGCTCAATGAAATGCTTTTTT-TATACGTTTCCT-AAGGCAGA
* * * *
3843 TATTCAATCATAATCTGTTTTAACCAAAAATGTAAGAAAATTAAACTTAAAATCAATTTTCATAA
256 GATTCAATCATAATATGTTTTAACCAAAAATATAAAAAAATTAAACTTAAAATCAATTTTCATAA
3908 AATAAAATCATTTAAAGTGGG
321 AATAAAATCATTTAAAGTGGG
* * * * * ** * *
3929 TAATAAGGCTTTTGATGGAGTGGGTGACTATAAATAGACTTTTCTTGTTAATGAATGTCTTTTTC
1 TAATAAGGCTTTTGAAGGAATAGGTAAATATAAATAGACTTTTCTTGCCAATGAATGCCATTTTC
* *
3994 TTCACGTTTCTCAAGGTAGACATTCAAAAAT-AGTCTGTTTGAACTAAAAATAT-AAAAAATTCA
66 -TCACGTTTCTCAAGGTAGACATTCAAAAATGA-TCTATTTGAACCAAAAATATAAAAAAATTCA
* * *
4057 ACTTAAAACCAATTATGAGATTATAAAACTATTTAAACTGATTAATAAGGCTTTTGAAAAAATAG
129 ACCTAAAACCAATTACGAGATTATAAAACTATTTAAACTGACTAATAAGGCTTTTGAAAAAATAG
** * * *
4122 ATGACTATAAATTGACTTTTCTTCTCAATGAACTGCTTTTTTTATACGTTTCCTAAGGCAGGGAT
194 ATGACTATAAACGGACTTTTCTGCTCAATGAAATGCTTTTTTTATACGTTTCCTAAGGCAGAGAT
* *** *
4187 TCAATTATAATATGTTTTAATGTAAAATATAAAAAAATTCAACTTAAAATCAATT
259 TCAATCATAATATGTTTTAACCAAAAATATAAAAAAATTAAACTTAAAATCAATT
4242 ATGAGGTTAT
Statistics
Matches: 258, Mismatches: 48, Indels: 14
0.81 0.15 0.04
Matches are distributed among these distances:
340 14 0.05
341 190 0.74
342 54 0.21
ACGTcount: A:0.38, C:0.12, G:0.13, T:0.37
Consensus pattern (341 bp):
TAATAAGGCTTTTGAAGGAATAGGTAAATATAAATAGACTTTTCTTGCCAATGAATGCCATTTTC
TCACGTTTCTCAAGGTAGACATTCAAAAATGATCTATTTGAACCAAAAATATAAAAAAATTCAAC
CTAAAACCAATTACGAGATTATAAAACTATTTAAACTGACTAATAAGGCTTTTGAAAAAATAGAT
GACTATAAACGGACTTTTCTGCTCAATGAAATGCTTTTTTTATACGTTTCCTAAGGCAGAGATTC
AATCATAATATGTTTTAACCAAAAATATAAAAAAATTAAACTTAAAATCAATTTTCATAAAATAA
AATCATTTAAAGTGGG
Done.