Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018398804.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_2088.0, 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: 5167
ACGTcount: A:0.21, C:0.07, G:0.07, T:0.22
Warning! 2189 characters in sequence are not A, C, G, or T
Found at i:4059 original size:171 final size:169
Alignment explanation
Indices: 3738--4527 Score: 676
Period size: 171 Copynumber: 4.6 Consensus size: 169
3728 NNNNNNNNNN
* * * ** * *
3738 AATGAATGGCTTTTTCTACATGTTTCTCAAAACAAGCATTCT-ATTATAGTCTGTTTTAACGAAA
1 AATGAAT-GCTTTTTCTTCACGTTTCTCGAAGTAAACATT-TAATTATAGTCTGTTTTAACTAAA
* * * * * *
3802 AATGTAAAAAAAATT-ACTTAAAATCAATTATTAGAATATCAAATGATTTAAAACGAGTAATAAG
64 AATG-AAAAAAAATTCAATTAAAATCAATTATGAGATTATAAAATCATTTAAAACGAGTAATAAA
* * * *
3866 GCTCTTGAAAGAA-TGAGTGACTATAAATAAACTTTT-TTTCTC
128 CCTTTTGAAAGAATTG-GTGACTATAAATAGACTTTTCTTGC-C
* * * * * *
3908 AATGGATAGCTTTTTCTACACGTTTCTCGAATTAAATATTTAATTGTAATCTGTTTTAACTAAAA
1 AATGAAT-GCTTTTTCTTCACGTTTCTCGAAGTAAACATTTAATTATAGTCTGTTTTAACTAAAA
* * * *
3973 ATGAAAAAAAATTTAATTGAAAATCAATTATGAGGTCATAAAATCATTTAAAGCGAGTAATAAAC
65 ATGAAAAAAAATTCAATT-AAAATCAATTATGAGATTATAAAATCATTTAAAACGAGTAATAAAC
* *
4038 CTTTTGAAAGAATTGGTGACTATAAATGGACTTTTCTTGCT
129 CTTTTGAAAGAATTGGTGACTATAAATAGACTTTTCTTGCC
* * * * * * * *
4079 AATAAATGCCCTTTTGTCCACGTTTCTC-AAGGTAGATATTTAATTATAGTTTGTTTGAACTAAA
1 AATGAATG-CTTTTTCTTCACGTTTCTCGAA-GTAAACATTTAATTATAGTCTGTTTTAACTAAA
* * *
4143 AATGTAAAAACAAATTCAACTTAAAATCAATTATAAGATTATAAAATTATTTAAAGCGAGTAAT-
64 AATG-AAAAA-AAATTCAA-TTAAAATCAATTATGAGATTATAAAATCATTTAAAACGAGTAATA
* ** * *
4207 AACGCTTTTGAAAGAGTAAGAGACTATAAATTGACTTTTCTTGCC
126 AAC-CTTTTGAAAGAATTGGTGACTATAAATAGACTTTTCTTGCC
* * * * * * * * * * * * *
4252 AATGGATGCATTTTTCTTTACATTGCTTGAGGCAGACGTTTAATTATAGTTTGTTTCAGCCAAAA
1 AATGAATGC-TTTTTCTTCACGTTTCTCGAAGTAAACATTTAATTATAGTCTGTTTTAACTAAAA
* * *
4317 ATGAAAAAAAATTCAACTTAGAATCAATTATGAGATTATAAAACCATTTAAAACGAGTAATAAGG
65 ATGAAAAAAAATTCAA-TTAAAATCAATTATGAGATTATAAAATCATTTAAAACGAGTAATAA-A
* * * *
4382 CC-TTTGAAGGAATGGGTGACTATAAATAGATTTTTTTTGCC
128 CCTTTTGAAAGAATTGGTGACTATAAATAGACTTTTCTTGCC
* * * * * * * * * *
4423 AGTGAATACCTTTTTCTTCACGTTTGTTGAGGTTAACGTTCAATTATTGTCTGTTTTAATTAAAA
1 AATGAAT-GCTTTTTCTTCACGTTTCTCGAAGTAAACATTTAATTATAGTCTGTTTTAACTAAAA
* *
4488 ATGTAAAAAAATTCAACTGAAAATCAATTATGAGATTATA
65 ATGAAAAAAAATTCAA-TTAAAATCAATTATGAGATTATA
4528 GAGCCNNNNN
Statistics
Matches: 506, Mismatches: 98, Indels: 31
0.80 0.15 0.05
Matches are distributed among these distances:
169 11 0.02
170 61 0.12
171 280 0.55
172 22 0.04
173 129 0.25
174 3 0.01
ACGTcount: A:0.39, C:0.11, G:0.14, T:0.36
Consensus pattern (169 bp):
AATGAATGCTTTTTCTTCACGTTTCTCGAAGTAAACATTTAATTATAGTCTGTTTTAACTAAAAA
TGAAAAAAAATTCAATTAAAATCAATTATGAGATTATAAAATCATTTAAAACGAGTAATAAACCT
TTTGAAAGAATTGGTGACTATAAATAGACTTTTCTTGCC
Found at i:4447 original size:344 final size:343
Alignment explanation
Indices: 3774--4527 Score: 831
Period size: 344 Copynumber: 2.2 Consensus size: 343
3764 TCAAAACAAG
* * *
3774 CATTCTATTATAGTCTGTTTTAACGAAAAATGTAAAAAAAATT--ACTTAAAATCAATTATTAGA
1 CATTCAATTATAGTCTGTTTTAACTAAAAATGTAAAAAAAATTCAACTTAAAATCAATTATAAGA
* * * * *
3837 ATATCAAATGATTTAAAACGAGTAATAAGGCTCTTGAAAGAATGAGTGACTATAAATAAACTTTT
66 TTATAAAATGATTTAAAACGAGTAATAACGCTCTTGAAAGAATAAGAGACTATAAATAAACTTTT
* * * ** * * *
3902 TTTCTCAATGGATAGCTTTTTCTACACGTTTCTCGAATTAAATATTTAATTGTAATCTGTTTTAA
131 TTGCTCAATGGATAGCTTTTTCTACACATTGCTCGAAGCAAACATTTAATTATAATCTGTTTCAA
* * * * *
3967 CTAAAAATGAAAAAAAATTTAATTGAAAATCAATTATGAGGTCATAAAATCATTTAAAGCGAGTA
196 CCAAAAATGAAAAAAAATTCAATTGAAAATCAATTATGAGATCATAAAACCATTTAAAACGAGTA
* * * * *
4032 ATAAACCTTTTGAAAGAATTGGTGACTATAAATGGACTTTTCTTGCTAATAAATGCCCTTTTGTC
261 ATAAACCTTTTGAAAGAATGGGTGACTATAAATAGACTTTTCTTGCCAATAAATACCCTTTTCTC
4097 CACGTTTCTCAAGG-TAGA
326 CACGTTTCTCAAGGTTA-A
* * * *
4115 TATTTAATTATAGTTTGTTTGAACTAAAAATGTAAAAACAAATTCAACTTAAAATCAATTATAAG
1 CATTCAATTATAGTCTGTTTTAACTAAAAATGTAAAAA-AAATTCAACTTAAAATCAATTATAAG
* * * * **
4180 ATTATAAAATTATTTAAAGCGAGTAATAACGCTTTTGAAAGAGTAAGAGACTATAAATTGACTTT
65 ATTATAAAATGATTTAAAACGAGTAATAACGCTCTTGAAAGAATAAGAGACTATAAATAAACTTT
** * * * * * *
4245 TCTTGC-CAATGGAT-GCATTTTTCTTTACATTGCTTGAGGCAGACGTTTAATTATAGTTTGTTT
130 T-TTGCTCAATGGATAGC-TTTTTCTACACATTGCTCGAAGCAAACATTTAATTATAATCTGTTT
* * *
4308 CAGCCAAAAATGAAAAAAAATTCAACTT-AGAATCAATTATGAGATTATAAAACCATTTAAAACG
193 CAACCAAAAATGAAAAAAAATTCAA-TTGAAAATCAATTATGAGATCATAAAACCATTTAAAACG
* * * * * * *
4372 AGTAATAAGGCC-TTTGAAGGAATGGGTGACTATAAATAGATTTTTTTTGCCAGTGAATACCTTT
257 AGTAATAA-ACCTTTTGAAAGAATGGGTGACTATAAATAGACTTTTCTTGCCAATAAATACCCTT
* * **
4436 TTCTTCACGTTTGTTGAGGTTAA
321 TTCTCCACGTTTCTCAAGGTTAA
* * * * *
4459 CGTTCAATTATTGTCTGTTTTAATTAAAAATGT-AAAAAAATTCAACTGAAAATCAATTATGAGA
1 CATTCAATTATAGTCTGTTTTAACTAAAAATGTAAAAAAAATTCAACTTAAAATCAATTATAAGA
4523 TTATA
66 TTATA
4528 GAGCCNNNNN
Statistics
Matches: 338, Mismatches: 67, Indels: 15
0.80 0.16 0.04
Matches are distributed among these distances:
341 32 0.09
342 35 0.10
343 6 0.02
344 256 0.76
345 9 0.03
ACGTcount: A:0.39, C:0.11, G:0.14, T:0.36
Consensus pattern (343 bp):
CATTCAATTATAGTCTGTTTTAACTAAAAATGTAAAAAAAATTCAACTTAAAATCAATTATAAGA
TTATAAAATGATTTAAAACGAGTAATAACGCTCTTGAAAGAATAAGAGACTATAAATAAACTTTT
TTGCTCAATGGATAGCTTTTTCTACACATTGCTCGAAGCAAACATTTAATTATAATCTGTTTCAA
CCAAAAATGAAAAAAAATTCAATTGAAAATCAATTATGAGATCATAAAACCATTTAAAACGAGTA
ATAAACCTTTTGAAAGAATGGGTGACTATAAATAGACTTTTCTTGCCAATAAATACCCTTTTCTC
CACGTTTCTCAAGGTTAA
Done.