Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018398541.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_1833.0, 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: 7479
ACGTcount: A:0.28, C:0.09, G:0.10, T:0.27
Warning! 2009 characters in sequence are not A, C, G, or T
Found at i:5501 original size:169 final size:165
Alignment explanation
Indices: 5085--5756 Score: 536
Period size: 171 Copynumber: 4.0 Consensus size: 165
5075 NNNNNNNNAT
5085 TTAAAGCGAGTAATAAGCCTTTTGAAGGAATAGGAGACTATAAATGGACTTTGT-TTGCCAATGA
1 TTAAAGCGAGTAATAAGCCTTTTGAAGGAATAGGAGACTATAAATGGACTTT-TCTTGCCAATGA
* * * * *
5149 ATGCTTATTTCTTCACATTTCCCAAGCTAGACATTCAATTATTATCTGTTTTAACTAAAATTTAA
65 ATGCTTATTTCTTCATATTTCTCGAGCTAGACATTCAATTATTGTCTGTTTTAACTAAAATGTAA
*
5214 GAAAATTCAACTTAAAATCAATTATGAGATTATAAA
130 AAAAATTCAACTTAAAATCAATTATGAGATTATAAA
***** * * **
5250 NNNNNNNNNNGCGAGTAATAAGACTTTTAAAGGAATAGGAGACTATAAATACACTTTTCTTGCCA
1 -----TTAAAGCGAGTAATAAGCCTTTTGAAGGAATAGGAGACTATAAATGGACTTTTCTTGCCA
* * * *
5315 ATAAATGCTTATTTCTTCATGTTTCTCGAGCTAGACATTTAATTATTGTCTGTTTGAACTAAAAT
61 ATGAATGCTTATTTCTTCATATTTCTCGAGCTAGACATTCAATTATTGTCTGTTTTAACTAAAAT
* * *****
5380 GTAAAAAAATTC-AGTTTAAATCAATTATGAGATTNNNNNNNNNN
126 GTAAAAAAATTCAACTTAAAATCAATTATGAGATT-----ATAAA
* * *
5424 TTAAAGTGAGTAATAAGCCTTTTGAAGGAAT-GGATGACAATAAATGGACTTTTCTTGTCAATGA
1 TTAAAGCGAGTAATAAGCCTTTTGAAGGAATAGGA-GACTATAAATGGACTTTTCTTGCCAATGA
* * * * * ****
5488 ATGCTTTTTTCTTCATATTTATTGAGATACACATTCAATTATTGTCTGTTTTAACTAAAANNNNN
65 ATGCTTATTTCTTCATATTTCTCGAGCTAGACATTCAATTATTGTCTGTTTTAACTAAAA-TGTA
******
5553 NNNNNTTTCAACTTAAAATCAATTATGAGATTATCAAACTA
129 AAAAAATTCAACTTAAAATCAATTATGAGATTAT--AA--A
* * * *
5594 TTTAAAGCGAGGAATAAG-CTTTTCGAAAGAAT-GGATAACTATAAATGGATTTTTCTT-CTCAA
1 -TTAAAGCGAGTAATAAGCCTTTT-GAAGGAATAGGA-GACTATAAATGGACTTTTCTTGC-CAA
* * * * * **
5656 TGAATGGCCT-TTTCTACATGTTT-TCTGAGGCAAG-CATTCAATTATAGTCCATTTTAA-TGAA
62 TGAAT-GCTTATTTCTTCATATTTCTC-GA-GCTAGACATTCAATTATTGTCTGTTTTAACT--A
*
5717 AAATGTAAAAAAATTCAACTTAAAATTAATTATGAGATTA
122 AAATGTAAAAAAATTCAACTTAAAATCAATTATGAGATTA
5757 NNNNNNNNNN
Statistics
Matches: 389, Mismatches: 92, Indels: 41
0.75 0.18 0.08
Matches are distributed among these distances:
168 3 0.01
169 120 0.31
170 126 0.32
171 131 0.34
172 9 0.02
ACGTcount: A:0.35, C:0.12, G:0.13, T:0.35
Consensus pattern (165 bp):
TTAAAGCGAGTAATAAGCCTTTTGAAGGAATAGGAGACTATAAATGGACTTTTCTTGCCAATGAA
TGCTTATTTCTTCATATTTCTCGAGCTAGACATTCAATTATTGTCTGTTTTAACTAAAATGTAAA
AAAATTCAACTTAAAATCAATTATGAGATTATAAA
Found at i:6466 original size:171 final size:162
Alignment explanation
Indices: 6272--6587 Score: 325
Period size: 172 Copynumber: 1.9 Consensus size: 162
6262 NNATTCAACT
* * ***
6272 TAAAATCAATTATGAGATTATAAACCCATTAAAAG-TGAGTAATAAAACTTCTGAAGGAATGGGT
1 TAAAATCAATTACGAGATTATAAAACCATTAAAAGCT-AGTAATAAAACTTCTGAAGGAATGAAA
* *
6336 GACTGT-AATGGACTTTTCTTGTTAATGAATG-TATTTTTCTTCAGGTTTC-TCAAGGTAGACAT
65 GACTATAAATGGACTTTTCTTGATAATGAATGCT-TTTTTCTTCAGGTTTCAT-AAGGTAGACAT
6398 TCAATTATAATCTATTTNNNNNNNNNNTGTAAAAGAATTTGAATC
128 TCAATTATAATCTATTT----------TGTAAAAGAATTTGAATC
* * * ** * *
6443 TAAAATCAATTACGGGATTATAAAACTATTTAAAGCTAGTAATAAGGCTTTTGATGGAATGAAAG
1 TAAAATCAATTACGAGATTATAAAACCATTAAAAGCTAGTAATAAAACTTCTGAAGGAATGAAAG
* * *
6508 ACTATAAATGGACTTTTCTTGATAATGAATGCTTTTTTCTTTATGTTTCATGAGGTAGACATTCA
66 ACTATAAATGGACTTTTCTTGATAATGAATGCTTTTTTCTTCAGGTTTCATAAGGTAGACATTCA
*
6573 ATTATAGTCTATTTT
131 ATTATAATCTATTTT
6588 ANNNNNNNNN
Statistics
Matches: 123, Mismatches: 18, Indels: 17
0.78 0.11 0.11
Matches are distributed among these distances:
162 1 0.01
171 55 0.45
172 65 0.53
173 2 0.02
ACGTcount: A:0.34, C:0.10, G:0.16, T:0.37
Consensus pattern (162 bp):
TAAAATCAATTACGAGATTATAAAACCATTAAAAGCTAGTAATAAAACTTCTGAAGGAATGAAAG
ACTATAAATGGACTTTTCTTGATAATGAATGCTTTTTTCTTCAGGTTTCATAAGGTAGACATTCA
ATTATAATCTATTTTGTAAAAGAATTTGAATC
Found at i:6694 original size:171 final size:164
Alignment explanation
Indices: 6268--6927 Score: 396
Period size: 171 Copynumber: 3.9 Consensus size: 164
6258 NNNNNNATTC
* * * * ** *
6268 AACTTAAAATCAATTATGAGATTATAAACCCATTAAAAGTGAGTAATAAAACTTCTGAAGGAATG
1 AACTTAAAATCAATTATGAGATTATAAAACTATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATG
* *
6333 GGTGACTGT-AATGGACTTTTCTTGTTAATGAATGTATTTTTCTTCAGGTTTCTCAAGGTAGACA
66 GGTGACTATAAATGGACTTTTCTTGATAATGAATGTATTTTTCTTCAGGTTTCTCAAGGTAGACA
** *
6397 TTCAATTATAATCTATTTNNNNNNNNNNTGTAAAAGAATTTG
131 TTCAATTATAATCTATTT--------TATGTAAAAAAATTTG
* * * *
6439 AA-TCTAAAATCAATTACGGGATTATAAAACTATTTAAAGCTAGTAATAAGGCTTTTGATGGAAT
1 AACT-TAAAATCAATTATGAGATTATAAAACTATTTAAAGCGAGTAATAAGGCTTTTGAAGGAAT
*** * * *
6503 GAAAGACTATAAATGGACTTTTCTTGATAATGAATGCT-TTTTTCTTTATGTTTCAT-GAGGTAG
65 GGGTGACTATAAATGGACTTTTCTTGATAATGAATG-TATTTTTCTTCAGGTTTC-TCAAGGTAG
* **
6566 ACATTCAATTATAGTCTATTTTANNNNNNNNNNTAAAAAAATTT-
128 ACATTCAATTATAATCTATTTTA--------TGTAAAAAAATTTG
* * * *
6610 AACTTAAAATCAATTGTGAGATTATAAAATTATTTAAAGCGAGAAATGAGGCTTTTGAAGGAATG
1 AACTTAAAATCAATTATGAGATTATAAAACTATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATG
* * ** * **
6675 GGTGACTATAAATGGACTTTTCCT-ATCAATG--TGGCT-TTTTTC-ACAAATTTCCCAACTTAG
66 GGTGACTATAAATGGACTTTTCTTGAT-AATGAAT-G-TATTTTTCTTCAGGTTTCTCAAGGTAG
* * * *
6735 GCATTCAATTATAGTCTGTTTTAACAAAAAATGTAAAAACAA--TC
128 ACATTCAATTATAATCTATTTT--------ATGTAAAAA-AATTTG
* * * *
6779 AA-TTGAAAATCAATTATGAGATTATAAATCCATTTAAAGCGAGCAATAAGG-TTTTGAAAGAAT
1 AACTT-AAAATCAATTATGAGATTATAAAACTATTTAAAGCGAGTAATAAGGCTTTTGAAGGAAT
* * * ** *** * * * *
6842 GAGTTACTATAAATGGACTTTCCTTGCCAATGAATACCTGTTTCTTCATGTTTCT-AGTGGTAGC
65 GGGTGACTATAAATGGACTTTTCTTGATAATGAATGTATTTTTCTTCAGGTTTCTCA-AGGTAGA
* *
6906 CATTCAATTATAGTCTAATTTA
129 CATTCAATTATAATCTATTTTA
6928 ACCAAAAATG
Statistics
Matches: 381, Mismatches: 75, Indels: 75
0.72 0.14 0.14
Matches are distributed among these distances:
162 1 0.00
168 39 0.10
169 84 0.22
170 43 0.11
171 136 0.36
172 75 0.20
173 2 0.01
177 1 0.00
ACGTcount: A:0.35, C:0.11, G:0.15, T:0.35
Consensus pattern (164 bp):
AACTTAAAATCAATTATGAGATTATAAAACTATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATG
GGTGACTATAAATGGACTTTTCTTGATAATGAATGTATTTTTCTTCAGGTTTCTCAAGGTAGACA
TTCAATTATAATCTATTTTATGTAAAAAAATTTG
Done.