Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018402358.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_5438.0, 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: 2111
ACGTcount: A:0.32, C:0.12, G:0.13, T:0.33
Warning! 225 characters in sequence are not A, C, G, or T
Found at i:864 original size:171 final size:171
Alignment explanation
Indices: 163--1269 Score: 729
Period size: 171 Copynumber: 6.5 Consensus size: 171
153 NNNNNNNNNN
* * * * * *
163 TATGAGTGACTATAAATGGACTTTTCTTGCCAATGAAT-ACTTTTCTCTTCATGTTTTTCGAGGT
1 TATGGGTGACTATAAATTGACTTTTCTTGCCAATGAATGCCTTTT-TCTTCACGTTTCTCAAGGT
* * * * * * *
227 AGACATTCAATTCTAGTATGTTTT-AGCTAAAAATGACAAAAGAATTCAAATTTAAATCAATTTT
65 AGACATTCAATTATAGTCTGTTTTAATC-AAAAAAG-TAAAAGAATTCAACTTAAAATCAATTTT
********** * * *
291 GAG-NNNNNNNNNNCATTTAAAGTGAGTAACAAGGCTTTTAAAAG
128 G-GCATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTGAAGG
* * * * * *
335 AATGGGTGACGATAAATTGACTTTTCTTGCCAATGAATGCTTTTTTCTTTATGTTTCTCAAAGTA
1 TATGGGTGACTATAAATTGACTTTTCTTGCCAATGAATGCCTTTTTCTTCACGTTTCTCAAGGTA
* * * * *
400 GGCATTCAATTATTGTCTATTTTAA-CTAAAAATGTAAAA-ATATTCAACTTAAAATCAATTATG
66 GACATTCAATTATAGTCTGTTTTAATC-AAAAAAGTAAAAGA-ATTCAACTTAAAATCAATTTTG
* *************************
463 GCATTATAAAACTATTTANNNNNNNNNNNNNNNNNNNNNNNNN
129 GCATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTGAAGG
* * * * **
506 TATGGGTGAGTAAAAATAGACTTTTCTTGCCAATGAATGCTTTTTTCTTCATTTTTCTCAAGGTA
1 TATGGGTGACTATAAATTGACTTTTCTTGCCAATGAATGCCTTTTTCTTCACGTTTCTCAAGGTA
* * * * * * * *
571 TG-CATTTAATTCTAGTCTGTTTTAATCGAAAATGATAGAAGAATTAAAATTTAAATCAATTTTG
66 -GACATTCAATTATAGTCTGTTTTAATCAAAAAAG-TAAAAGAATTCAACTTAAAATCAATTTTG
** *
635 AAATTACAAAACCATTTAAAGTGAGTAATAAGGCTTTTGAAGG
129 GCATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTGAAGG
* * * *
678 AATGGGTGGCTATAAATTGACTTTTCTTGCCAATGAATGCCTTTTTATTTACGTTTCTCAAGGTA
1 TATGGGTGACTATAAATTGACTTTTCTTGCCAATGAATGCCTTTTTCTTCACGTTTCTCAAGGTA
*
743 GACATTCAATTATAGTCTGTTTTAA-CTAAAAAAGTAAAACAATTCAACTTAAAATCAATTTTGG
66 GACATTCAATTATAGTCTGTTTTAATC-AAAAAAGTAAAAGAATTCAACTTAAAATCAATTTTGG
* * * *
807 CATTATAAAACCATTTAAAGAGAGTATTGAGGCTTTGGAAGG
130 CATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTGAAGG
* * * * * *
849 TATGGGTGACTATAAATAGACTTTTCTTGCCAATGAATGCTTTTTTCTTTATGTTTGTAAAGGTA
1 TATGGGTGACTATAAATTGACTTTTCTTGCCAATGAATGCCTTTTTCTTCACGTTTCTCAAGGTA
* * * * * *
914 GGCATTCAATTCTAGTCTGTTTTAATCAAAAATGAG-AGAAGAATTTAAATTTAAATCAATTTTG
66 GACATTCAATTATAGTCTGTTTTAATCAAAAA--AGTAAAAGAATTCAACTTAAAATCAATTTTG
* *
978 AG-ATGAAAAAACCATTTAAAGTGAGTAATAAGGCTTTTGAAGG
129 -GCATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTGAAGG
* * * * * * * * * *
1021 TTTGAGTGAATATAAA-TGAATTTT-TGTGCCAATTG-TTGGCTTTTGCTTCACGTTCCTTACGG
1 TATGGGTGACTATAAATTGACTTTTCT-TGCCAA-TGAATGCCTTTTTCTTCACGTTTCTCAAGG
* * * * * * *
1083 CAGGA-ACTCAATTATAGCCTTTTTTAATAAAAAAATGTAAAAAAATTCACCTTAAAATCAA-TT
64 TA-GACATTCAATTATAGTCTGTTTTAATCAAAAAA-GTAAAAGAATTCAACTTAAAATCAATTT
* * *
1146 TGGAGATTATAAAGCC-TATTAAAGTGAGTAATAAGGCTTTCGAAGG
127 TGG-CATTATAAAACCAT-TTAAAGTGAGTAATAAGGCTTTTGAAGG
* * * * * * *
1192 CT-TGAGTAACTATAAATGGACTTTTCTTGCCAAT-AAGTTCCGTTTTCTTCACTTTTCTAAAGG
1 -TATGGGTGACTATAAATTGACTTTTCTTGCCAATGAA-TGCCTTTTTCTTCACGTTTCTCAAGG
*
1255 TA-AAATTCAATTATA
64 TAGACATTCAATTATA
1270 ATCTAATCTA
Statistics
Matches: 711, Mismatches: 196, Indels: 57
0.74 0.20 0.06
Matches are distributed among these distances:
169 2 0.00
170 10 0.01
171 386 0.54
172 303 0.43
173 10 0.01
ACGTcount: A:0.34, C:0.12, G:0.15, T:0.36
Consensus pattern (171 bp):
TATGGGTGACTATAAATTGACTTTTCTTGCCAATGAATGCCTTTTTCTTCACGTTTCTCAAGGTA
GACATTCAATTATAGTCTGTTTTAATCAAAAAAGTAAAAGAATTCAACTTAAAATCAATTTTGGC
ATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTGAAGG
Found at i:1016 original size:343 final size:342
Alignment explanation
Indices: 163--1225 Score: 1037
Period size: 343 Copynumber: 3.1 Consensus size: 342
153 NNNNNNNNNN
* * * * *
163 TATGAGTGACTATAAATGGACTTTTCTTGCCAATGAATACTTTTCTCTTCATGTTTTTCGAGGTA
1 TATGAGTGACTATAAATAGACTTTTCTTGCCAATGAATGCTTTTTTCTTCATGTTTCTCAAGGTA
* * * * *
228 GACATTCAATTCTAGTATGTTTT-AGCTAAAAATGACAAAAGAATTCAAATTTAAATCAATTTTG
66 GGCATTCAATTCTAGTCTGTTTTAATC-AAAAATGACAGAAGAATTAAAATTTAAATCAATTTTG
********** * * * *
292 AGNNNNNNNNNNCATTTAAAGTGAGTAACAAGGCTTTTAAAAGAATGGGTGACGATAAATTGACT
130 AGATGAAAAAACCATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATTGACT
* * * * *
357 TTTCTTGCCAATGAATGCTTTTTTCTTTATGTTTCTCAAAGTAGGCATTCAATTATTGTCTATTT
195 TTTCTTGCCAATGAATGCCTTTTTCTTTACGTTTCTCAAGGTAGACATTCAATTATAGTCTATTT
* * * ******
422 TAACTAAAAATGTAAAAATATTCAACTTAAAATCAATTATGGCATTATAAAACTATTTANNNNNN
260 TAACTAAAAAAGTAAAAA-ATTCAACTTAAAATCAATTTTGGCATTATAAAACCATTTAAAGAGA
*******************
487 NNNNNNNNNNNNNNNNNNN
324 GTAATAAGGCTTTCGAAGG
* * * *
506 TATGGGTGAGTAAAAATAGACTTTTCTTGCCAATGAATGCTTTTTTCTTCATTTTTCTCAAGGTA
1 TATGAGTGACTATAAATAGACTTTTCTTGCCAATGAATGCTTTTTTCTTCATGTTTCTCAAGGTA
* * * *
571 TGCATTTAATTCTAGTCTGTTTTAATCGAAAATGATAGAAGAATTAAAATTTAAATCAATTTTGA
66 GGCATTCAATTCTAGTCTGTTTTAATCAAAAATGACAGAAGAATTAAAATTTAAATCAATTTTGA
* * * *
636 AATTACAAAACCATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATGGGTGGCTATAAATTGACTT
131 GATGAAAAAACCATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATTGACTT
* *
701 TTCTTGCCAATGAATGCCTTTTTATTTACGTTTCTCAAGGTAGACATTCAATTATAGTCTGTTTT
196 TTCTTGCCAATGAATGCCTTTTTCTTTACGTTTCTCAAGGTAGACATTCAATTATAGTCTATTTT
766 AACTAAAAAAGTAAAACAATTCAACTTAAAATCAATTTTGGCATTATAAAACCATTTAAAGAGAG
261 AACTAAAAAAGTAAAA-AATTCAACTTAAAATCAATTTTGGCATTATAAAACCATTTAAAGAGAG
* * *
831 TATTGAGGCTTTGGAAGG
325 TAATAAGGCTTTCGAAGG
* * * *
849 TATGGGTGACTATAAATAGACTTTTCTTGCCAATGAATGCTTTTTTCTTTATGTTTGTAAAGGTA
1 TATGAGTGACTATAAATAGACTTTTCTTGCCAATGAATGCTTTTTTCTTCATGTTTCTCAAGGTA
* *
914 GGCATTCAATTCTAGTCTGTTTTAATCAAAAATGAGAGAAGAATTTAAATTTAAATCAATTTTGA
66 GGCATTCAATTCTAGTCTGTTTTAATCAAAAATGACAGAAGAATTAAAATTTAAATCAATTTTGA
** * * *
979 GATGAAAAAACCATTTAAAGTGAGTAATAAGGCTTTTGAAGGTTTGAGTGAATATAAA-TGAATT
131 GATGAAAAAACCATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATTGACTT
* * * * * * * * * * *
1043 TT-TGTGCCAATTG-TTGGCTTTTGCTTCACGTTCCTTACGGCAGGA-ACTCAATTATAGCCTTT
196 TTCT-TGCCAA-TGAATGCCTTTTTCTTTACGTTTCTCAAGGTA-GACATTCAATTATAGTCTAT
* * *
1105 TTTAA-TAAAAAAATGTAAAAAAATTCACCTTAAAATCAA-TTTGGAGATTATAAAGCC-TATTA
258 TTTAACT-AAAAAA-GT-AAAAAATTCAACTTAAAATCAATTTTGG-CATTATAAAACCAT-TTA
*
1167 AAGTGAGTAATAAGGCTTTCGAAGG
318 AAGAGAGTAATAAGGCTTTCGAAGG
* *
1192 CT-TGAGTAACTATAAATGGACTTTTCTTGCCAAT
1 -TATGAGTGACTATAAATAGACTTTTCTTGCCAAT
1226 AAGTTCCGTT
Statistics
Matches: 598, Mismatches: 111, Indels: 22
0.82 0.15 0.03
Matches are distributed among these distances:
341 2 0.00
342 64 0.11
343 524 0.88
344 8 0.01
ACGTcount: A:0.34, C:0.11, G:0.15, T:0.36
Consensus pattern (342 bp):
TATGAGTGACTATAAATAGACTTTTCTTGCCAATGAATGCTTTTTTCTTCATGTTTCTCAAGGTA
GGCATTCAATTCTAGTCTGTTTTAATCAAAAATGACAGAAGAATTAAAATTTAAATCAATTTTGA
GATGAAAAAACCATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATTGACTT
TTCTTGCCAATGAATGCCTTTTTCTTTACGTTTCTCAAGGTAGACATTCAATTATAGTCTATTTT
AACTAAAAAAGTAAAAAATTCAACTTAAAATCAATTTTGGCATTATAAAACCATTTAAAGAGAGT
AATAAGGCTTTCGAAGG
Done.