Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018402997.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_664.0, 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: 19692
ACGTcount: A:0.21, C:0.09, G:0.09, T:0.21
Warning! 7870 characters in sequence are not A, C, G, or T
Found at i:7082 original size:173 final size:172
Alignment explanation
Indices: 6649--7270 Score: 491
Period size: 171 Copynumber: 3.6 Consensus size: 172
6639 NNNNNTAACC
* *
6649 AAAAATATAAAAAAATTCAACTTAAAATCTATTATGAGATTATAAAACCTTTTAAAGCGAGTAAT
1 AAAAATATAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAAT
* * * *
6714 AAGGCTTTTC-AAGTG-GTGGGTGACTATAAACAGG-CTTTTCTTTTCAATGAATGGCTCTTTCT
66 AAGGC-TTTCGAAG-GCATGGGTGACTATAAA-TGGACTTTTCTTGTCAATGAATGGCTTTTTCT
********** * * *
6776 TCACGTNNNNNNNNNNAAACATTCAATTATTATCTATTTTAAC-C
128 TCACGTTTCTCAAGGTAAACATTTAATTATAATCTATTTTAACAA
* * *
6820 AAAAATATAAAATAATTCAACTTAAAATCAATTATGAGGTTATACAACCATTTAAAGCGAGTAAT
1 AAAAATATAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAAT
**************** * * *
6885 AANNNNNNNNNNNNNNNNGGTGACTATAAATGGACTTTTCCTGCCAATGAATGGCTTTTTCATCA
66 AAGGCTTTCGAAGGCATGGGTGACTATAAATGGACTTTTCTTGTCAATGAATGGCTTTTTCTTCA
* * *
6950 CGTTTCTTAAGGTAGACATTTAATTATAATCTGTTTTAACAA
131 CGTTTCTCAAGGTAAACATTTAATTATAATCTATTTTAACAA
* * * *
6992 AAAAATGTAAAATAAATTCAACTTAAAATCAATTATGAGGTTATAAATCCATTTTAAGCGAGTAA
1 AAAAATATAAAA-AAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAA
* * **********
7057 TAAGGCTTTCGAAGGCTTAGGTGACTATAANNNNNNNNNNCTTGTCAATGAATGGCTTTTTCTTC
65 TAAGGCTTTCGAAGGCATGGGTGACTATAAATGGACTTTTCTTGTCAATGAATGGCTTTTTCTTC
* ** * *
7122 ATGTTTCTCAAGGTACCCAATTAATTATAATCTATTTTAGCTAA
130 ACGTTTCTCAAGGTAAACATTTAATTATAATCTATTTTAAC-AA
* * * * * *
7166 AATAA-A-AAGAAAATTCAACTTAAAGTCAATTAAGAAATTATAAAACCATTCAAAGCGAGTAAT
1 AAAAATATAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAAT
* * *
7229 AAAGCTTTTGAAGGCATGGGTGACTATAAATGGACTTGTCTT
66 AAGGCTTTCGAAGGCATGGGTGACTATAAATGGACTTTTCTT
7271 NNNNNNNNNN
Statistics
Matches: 340, Mismatches: 105, Indels: 12
0.74 0.23 0.03
Matches are distributed among these distances:
170 2 0.01
171 200 0.59
172 14 0.04
173 118 0.35
174 6 0.02
ACGTcount: A:0.37, C:0.13, G:0.13, T:0.32
Consensus pattern (172 bp):
AAAAATATAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAAT
AAGGCTTTCGAAGGCATGGGTGACTATAAATGGACTTTTCTTGTCAATGAATGGCTTTTTCTTCA
CGTTTCTCAAGGTAAACATTTAATTATAATCTATTTTAACAA
Found at i:10569 original size:170 final size:171
Alignment explanation
Indices: 10315--10638 Score: 402
Period size: 170 Copynumber: 1.9 Consensus size: 171
10305 NNNNNNNNNN
* * * * ** *
10315 ATTATAATCTGTTTTAGCAAAAAATGTTAAACAATTCAAGTTAAAATCAATTATAAGATTATAAA
1 ATTATAATCTATTTTAACAAAAAATGATAAAAAATTCAACATAAAATCAATTAGAAGATTATAAA
* * * * *
10380 ACCAATTAAAGTAAGTAATAAGGCTTTTGGAGGCATAGGTGACTCTAAATAGGCTTTTCCTT-CC
66 ACCAATTAAAGTAAGTAATAAAGCTTTCGAAGGCATAGGTGACTATAAACAGGCTTTT-CTTGCC
10444 AATGAATGCCTCTTGCTTCATGTTTTTCGAGGTAGAAATTCA
130 AATGAATGCCTCTTGCTTCATGTTTTTCGAGGTAGAAATTCA
* * *
10486 ATTATTATCTATTTTAACCAAAAAT-ATAAAAAATTCAACATAAAATCAATTAGGAGATTATAAA
1 ATTATAATCTATTTTAACAAAAAATGATAAAAAATTCAACATAAAATCAATTAGAAGATTATAAA
* * * * * *
10550 GCCATTTAAAG-AGAGTAATAAAGCTTTCGAAGGCGTGGGTGACTATGAACAGGCTTTTCTTGTC
66 ACCAATTAAAGTA-AGTAATAAAGCTTTCGAAGGCATAGGTGACTATAAACAGGCTTTTCTTGCC
* *
10614 AATGAATGGCTCTTTCTTCATGTTT
130 AATGAATGCCTCTTGCTTCATGTTT
10639 NNNNNNNNNN
Statistics
Matches: 128, Mismatches: 23, Indels: 5
0.82 0.15 0.03
Matches are distributed among these distances:
169 4 0.03
170 103 0.80
171 21 0.16
ACGTcount: A:0.37, C:0.13, G:0.15, T:0.34
Consensus pattern (171 bp):
ATTATAATCTATTTTAACAAAAAATGATAAAAAATTCAACATAAAATCAATTAGAAGATTATAAA
ACCAATTAAAGTAAGTAATAAAGCTTTCGAAGGCATAGGTGACTATAAACAGGCTTTTCTTGCCA
ATGAATGCCTCTTGCTTCATGTTTTTCGAGGTAGAAATTCA
Found at i:11412 original size:171 final size:170
Alignment explanation
Indices: 11125--12005 Score: 673
Period size: 171 Copynumber: 5.1 Consensus size: 170
11115 NNNNNNNNNN
* * *
11125 CATGGGTGACTATAAATGGACTTGTCTTGCAAATGAATGGCTTTTTCTTCATGTATCTTGAGGTA
1 CATGGGTGACTATAAATGGACTT-TCTTGCCAATGAATGGCTTTTTCTTCACGTTTCTTGAGGTA
** * * * * *
11190 GAGGTTTAATTATAATCTATTTGAGCCAAAAATGCAAAAACAATT-AACTTAAAATTAATGATGA
65 GACATTTAATTATCATCTATTTTAACCAAAAATGC-AAAACAATTCAACTTAAAATCAATTATGA
* ********** *
11254 GATTATAAAATCATTTAAANNNNNNNNNNAGGCTTTCGAAGG
129 GGTTATAAAATCATTTAAAGCGAGTAATAAGGCTTCCGAAGG
* * *
11296 CATGGGTGACGATAAATGAACTTTACTTGCCAATGAATGGCTTTTTCTTCACGTTTCTTGATGTA
1 CATGGGTGACTATAAATGGACTTT-CTTGCCAATGAATGGCTTTTTCTTCACGTTTCTTGAGGTA
* * *
11361 AACATTCAATTATCATCTATTTTAACCAAAAAAGCAAAACAATTCAACTTAAAATCAATTATGAG
65 GACATTTAATTATCATCTATTTTAACCAAAAATGCAAAACAATTCAACTTAAAATCAATTATGAG
* * *
11426 GCTATACAACCATTTAAAGCGAGTAATAAGGCTTCCGAAGG
130 GTTATAAAATCATTTAAAGCGAGTAATAAGGCTTCCGAAGG
** **
11467 TGTGGGTGACTATAAATGGACTTTTCCTT-CCAATGAATGGCTTTTTCTTCACGTTTCTCAAGGT
1 CATGGGTGACTATAAATGGAC-TTT-CTTGCCAATGAATGGCTTTTTCTTCACGTTTCTTGAGGT
* * * *
11531 AGACATTTAATTA-CAATCTGTTTTCACCAAAAATGTAAAA-AGATTCAAGTTAAAATCAATTAT
64 AGACATTTAATTATC-ATCTATTTTAACCAAAAATGCAAAACA-ATTCAACTTAAAATCAATTAT
* * **
11594 GAGGTTAT-AAATCCATTTAAAGCGTGTAATAAGTCTTTTGAAGG
127 GAGGTTATAAAAT-CATTTAAAGCGAGTAATAAGGCTTCCGAAGG
* * * * ********** * **
11638 CTTAGGTGACTGTAAATAGG-CTTTTCTTGTCAATGNNNNNNNNNNTCTTCATGTTTCTCAAGGT
1 CATGGGTGACTATAAAT-GGAC-TTTCTTGCCAATGAATGGCTTTTTCTTCACGTTTCTTGAGGT
* * * ** * **
11702 ACACAATTAATTA-CAATCTATTTTAA-CTAAAATAAAAAAAGAATTCAACTTAATGTCAATTAT
64 AGACATTTAATTATC-ATCTATTTTAACCAAAAAT-GCAAAACAATTCAACTTAAAATCAATTAT
** * ********** **
11765 GAAATTATAAAACCATTTAAAGNNNNNNNNNNGGCTTTTGAAGG
127 GAGGTTATAAAATCATTTAAAGCGAGTAATAAGGCTTCCGAAGG
* * *
11809 CATGGGTGACTATAAATGGACTTGTCTTGCAAAATGAACGGCTTTTTCTTCACGTTTCTCGAGGT
1 CATGGGTGACTATAAATGGACTT-TCTTGC-CAATGAATGGCTTTTTCTTCACGTTTCTTGAGGT
* * * * * *
11874 AGAGATTTAATTATAATGTATTTGAACCAAAAATGCAAAATACATTCAACTTAAAATTAATTATG
64 AGACATTTAATTATCATCTATTTTAACCAAAAATGCAAAACA-ATTCAACTTAAAATCAATTATG
* * * * *
11939 AGATTATAAAA-CTACTTAAAGTGAGAAATAAGGCTTTCGAAGG
128 AGGTTATAAAATC-ATTTAAAGCGAGTAATAAGGCTTCCGAAGG
*
11982 CATGAGTGACTATAAATGGACTTT
1 CATGGGTGACTATAAATGGACTTT
12006 ACNNNNNNNN
Statistics
Matches: 555, Mismatches: 137, Indels: 35
0.76 0.19 0.05
Matches are distributed among these distances:
170 27 0.05
171 394 0.71
172 59 0.11
173 75 0.14
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.33
Consensus pattern (170 bp):
CATGGGTGACTATAAATGGACTTTCTTGCCAATGAATGGCTTTTTCTTCACGTTTCTTGAGGTAG
ACATTTAATTATCATCTATTTTAACCAAAAATGCAAAACAATTCAACTTAAAATCAATTATGAGG
TTATAAAATCATTTAAAGCGAGTAATAAGGCTTCCGAAGG
Done.