Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018403309.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_981.0, 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: 2843
ACGTcount: A:0.26, C:0.09, G:0.10, T:0.27
Warning! 799 characters in sequence are not A, C, G, or T
Found at i:310 original size:171 final size:171
Alignment explanation
Indices: 119--540 Score: 526
Period size: 172 Copynumber: 2.5 Consensus size: 171
109 NNNNNNNNNN
* *
119 AGACATTCAATTCTAGTCTGTTTTAGCCAAAAATGTACAAAGAA-TCAAATTTAAGCCAATTTTG
1 AGACATTCAATTCTAGTCTGTTTTAACCAAAAATGTACAAAGAATTCAAATTTAA-TCAATTTTG
* * * * *******
183 AGATTTTAAAACTATTTAAAACGAATAATAAGGCTTTTGAAGGTATGGGTGACTATAANNNNNNN
65 AGATTATAAAACCATTTAAAACGAATAATAAGACTTTTAAAGGTATGGGTGACTATAAATTTACT
*** * *
248 NNNCTTGCCAATGAATACTTTTTTCTTCATGTTTCTT-AAGGT
130 TTTCTGGCCAATGAAAACTTTTTTCTTCATGTTT-TTGAAGGT
* * *
290 AGACAATCAATTCTAGTCTGTTTTAACTAAAAATATACAAAGAATTCAAATTTTAATCAATTTTG
1 AGACATTCAATTCTAGTCTGTTTTAACCAAAAATGTACAAAGAATTCAAA-TTTAATCAATTTTG
* * * * *
355 GGATTATAAAACCATTTAAAGCGAGTAATAAGATTTTTAAAGGTATTGGTGACTATAAATTTACT
65 AGATTATAAAACCATTTAAAACGAATAATAAGACTTTTAAAGGTATGGGTGACTATAAATTTACT
420 TTTCTGGCCAATGAAAACTTTTTTCTTCATGTTTTTGAAGGT
130 TTTCTGGCCAATGAAAACTTTTTTCTTCATGTTTTTGAAGGT
* * *
462 AAACATTCAATCCTAGTCTGTTTTAACC-AAAATGTACAAAGAATTTAAATTTAAATCAATTTTG
1 AGACATTCAATTCTAGTCTGTTTTAACCAAAAATGTACAAAGAATTCAAATTT-AATCAATTTTG
526 AGATTATAAAACCAT
65 AGATTATAAAACCAT
541 NNNNNNNNNN
Statistics
Matches: 214, Mismatches: 33, Indels: 8
0.84 0.13 0.03
Matches are distributed among these distances:
170 3 0.01
171 86 0.40
172 120 0.56
173 5 0.02
ACGTcount: A:0.37, C:0.12, G:0.13, T:0.36
Consensus pattern (171 bp):
AGACATTCAATTCTAGTCTGTTTTAACCAAAAATGTACAAAGAATTCAAATTTAATCAATTTTGA
GATTATAAAACCATTTAAAACGAATAATAAGACTTTTAAAGGTATGGGTGACTATAAATTTACTT
TTCTGGCCAATGAAAACTTTTTTCTTCATGTTTTTGAAGGT
Found at i:1120 original size:172 final size:171
Alignment explanation
Indices: 813--1208 Score: 424
Period size: 172 Copynumber: 2.3 Consensus size: 171
803 NNNNNNNNNN
* * * *
813 AATTTAAATCAATTTTGAGATTATGAAACCATTTAAAGTGAGTAATAAGGCTTTAGAAGGAGTGG
1 AATTAAAATCAATTTTGAGATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTAGAAGCAATGG
* * * * * * * *
878 GTGACTATAAATGGACTTCTCTTGCAAATGAATGATCTCTTCTTTATGTTCCTCAGAGTATACGT
66 GCGAATATAAATAGACTTCTCTTACAAATAAATAATCTCTTATTAATGTTCCTCAGAGTATACGT
943 TCAATTATA-ATATGTTTTAGCCAGAAAA-GTA-AAAACATTTTA
131 TCAATTATAGATAT-TTTTA-CCA-AAAATGTAGAAAACA-TTTA
* * * * * * *
985 ACTTAAAATCAATTTTGAAATTATCAAACTATCTAAAGTGATTAATAAGGCTTTTGAAGCAATGG
1 AATTAAAATCAATTTTGAGATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTAGAAGCAATGG
* * * * * *
1050 GCGAATATAAATAGACTTTTTTTACCAATAAATAATTTTTTATTAATGTTTCTCATG-GTATA-G
66 GCGAATATAAATAGACTTCTCTTACAAATAAATAATCTCTTATTAATGTTCCTCA-GAGTATACG
* *
1113 ATTCAATTGTAGTGTATTTTTACCAAAAATGTAGAAAACATTTA
130 -TTCAATTATAG-ATATTTTTACCAAAAATGTAGAAAACATTTA
* * *
1157 AATTTAAATCAATTTTGAGATTATAAAACCATTTAAACTAAGTAATAAGGCT
1 AATTAAAATCAATTTTGAGATTATAAAACCATTTAAAGTGAGTAATAAGGCT
1209 CNNNNNNNNN
Statistics
Matches: 183, Mismatches: 35, Indels: 12
0.80 0.15 0.05
Matches are distributed among these distances:
171 5 0.03
172 163 0.89
173 12 0.07
174 3 0.02
ACGTcount: A:0.39, C:0.11, G:0.14, T:0.37
Consensus pattern (171 bp):
AATTAAAATCAATTTTGAGATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTAGAAGCAATGG
GCGAATATAAATAGACTTCTCTTACAAATAAATAATCTCTTATTAATGTTCCTCAGAGTATACGT
TCAATTATAGATATTTTTACCAAAAATGTAGAAAACATTTA
Found at i:2055 original size:172 final size:170
Alignment explanation
Indices: 1604--2158 Score: 472
Period size: 172 Copynumber: 3.2 Consensus size: 170
1594 NNNNNAGAAA
*
1604 AAAAATTTGAACTTAAAATCAATTTTGAGATTGTAAAACCATCTAAAGTGATTAATAAGGCATTT
1 AAAAA-TTGAACTTAAAATCAATTTTGAGATTATAAAACCATCTAAAGTGATTAATAAGGCATTT
* * *
1669 AAAGCAATGGGTGACTATAAATAGACTTTTTTCGCCAATGAATATTTTTTTCTTCATGTTTCTCA
65 GAAGCAATGGGTGACTATAAATAGACTTTTTTC-ACAATGAATATTCTTTTCTTCATGTTTCTCA
* * * * ** *
1734 TGGTATAGATTCAATTCTTGTGTATTTTAACAAAAAATGTAC
129 GGGTAGACATTCAATTATAATATATTTTAACAAAAAATGTAC
* * * ********** * * *
1776 AAAACATTCAAATTTAAATCAATTTTGNNNNNNNNNNACCATTTAAAGTGAGTAATAAGGCTTTT
1 AAAA-ATTGAACTTAAAATCAATTTTGAGATTATAAAACCATCTAAAGTGATTAATAAGGCATTT
* * *
1841 GAAGGAGTGGGTGACTATAAAT-GTACTTCTCTT-ACAAATGAATGATCTCTTTT-TT-ATGTTT
65 GAAGCAATGGGTGACTATAAATAG-ACTT-TTTTCAC-AATGAAT-AT-TCTTTTCTTCATGTTT
* **********
1902 CTCAGGGTAGACATTCAATTATAATATGTTTTAACTANNNNNNNNNN
125 CTCAGGGTAGACATTCAATTATAATATATTTTAAC-AAAAAATGTAC
* *
1949 AAAAATTGAACTTAAAATCAATTTTGAGATTATAACATCATCTAAAGTGATTAATAAGGCATTTG
1 AAAAATTGAACTTAAAATCAATTTTGAGATTATAAAACCATCTAAAGTGATTAATAAGGCATTTG
*
2014 AAGCAATGGGTGACTATAAATAGACTTTTTTCATCAATGAATACTT-TTTTCTTCATCTTTCTCA
66 AAGCAATGGGTGACTATAAATAGACTTTTTTCA-CAATGAATA-TTCTTTTCTTCATGTTTCTCA
* * * * * *
2078 TGGTATAGATTCAATTCTAGTCTATTTTAACAAAAAATGTAC
129 GGGTAGACATTCAATTATAATATATTTTAACAAAAAATGTAC
* * * * *
2120 ACAACATTCAAATTTAAATTAATTTTGAGATTATAAAAC
1 A-AAAATTGAACTTAAAATCAATTTTGAGATTATAAAAC
2159 TATTTAAACT
Statistics
Matches: 284, Mismatches: 85, Indels: 28
0.72 0.21 0.07
Matches are distributed among these distances:
170 4 0.01
171 11 0.04
172 249 0.88
173 15 0.05
174 5 0.02
ACGTcount: A:0.36, C:0.12, G:0.12, T:0.37
Consensus pattern (170 bp):
AAAAATTGAACTTAAAATCAATTTTGAGATTATAAAACCATCTAAAGTGATTAATAAGGCATTTG
AAGCAATGGGTGACTATAAATAGACTTTTTTCACAATGAATATTCTTTTCTTCATGTTTCTCAGG
GTAGACATTCAATTATAATATATTTTAACAAAAAATGTAC
Done.