Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018402855.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_5907.0, 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, 845
Length: 1409
ACGTcount: A:0.36, C:0.11, G:0.14, T:0.35
Warning! 40 characters in sequence are not A, C, G, or T
Found at i:286 original size:171 final size:170
Alignment explanation
Indices: 1--1055 Score: 1041
Period size: 171 Copynumber: 6.2 Consensus size: 170
* * *
1 AAATGGACTTTTCTTGTCAATGAATGCTTGTTCATTCATGTTTCACGAGGTAGACATGCAATTAT
1 AAATGGACTTTTCTTGTCAATGAATGCTTTTTC-TTCATGTTTCACAAGGTAGACATTCAATTAT
* * * * **
66 AGTCTGTTTTCACAAAAAATGTAAAAAACTTCAATTTAAAATCAATTATGGGATTATAAAACCGT
65 AGTCTGTTTTAACAAAAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACTAT
* * * * * *
131 TGAAAGTGAGTAATAAGCTTTTTCG-AGGAATGGGCGACTCT
130 TTAAAGCGAGTAATAAGCCTTTT-GAAGAAATGAGTGACTCT
* * * * *
172 AAATGGACTTTTCTTCTCAATGAATAGCTTTTTCTACACGTTTCCCAAGGTAGACAATCAATTAT
1 AAATGGACTTTTCTTGTCAATGAAT-GCTTTTTCTTCATGTTTCACAAGGTAGACATTCAATTAT
* *
237 AGTCTGTTTTAACAAAAAATGTAAAAAAATTCAACTGAAAATTAATTATGAGATTATAAAACTAT
65 AGTCTGTTTTAACAAAAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACTAT
*
302 TTAAAGTGAGTAATAAGCCTTTTGAAGAAATGAGTGACTCT
130 TTAAAGCGAGTAATAAGCCTTTTGAAGAAATGAGTGACTCT
343 AAATGGACTTTTCTTGTCAATGAATGCTTGTTTCTTCATGTTT-ACAGAGGTAGACATTCAATTA
1 AAATGGACTTTTCTTGTCAATGAATGCTT-TTTCTTCATGTTTCACA-AGGTAGACATTCAATTA
* * * * *
407 TAGTATGTTTTAATAAAAAATGTAAAAAAGTTTAACTTAAAATCAATTATGAGATTATAAAATTA
64 TAGTCTGTTTTAACAAAAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACTA
* * * *
472 TTAAAAGCGAATAATAAGCCTTTTGAAGAAATGGGTGACTAT
129 TTTAAAGCGAGTAATAAGCCTTTTGAAGAAATGAGTGACTCT
* * * * * * * *** *
514 AAATGAACGTTTCTTCTCAATCAATAGCTTTTTCTACGTATTTC-TTGGGATAGACATTAAATTA
1 AAATGGACTTTTCTTGTCAATGAAT-GCTTTTTCTTCATGTTTCACAAGG-TAGACATTCAATTA
* * * *
578 TTGTCTATTTTAA-AGAAAAATATAAAAAAGTTCAACTTAAAATCAATTATGAGATTATAAAACT
64 TAGTCTGTTTTAACA-AAAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACT
* *
642 ATTTAAGGCGAGTAATTAGCCTTTTGAA-AGAATGAGTGACTCT
128 ATTTAAAGCGAGTAATAAGCCTTTTGAAGA-AATGAGTGACTCT
* ***
685 AAATGGACTTTTCTTGTCAATGAATGCTTGTTTCTTCATATTT-ATTGTGGTAGACATTCAATTA
1 AAATGGACTTTTCTTGTCAATGAATGCTT-TTTCTTCATGTTTCA-CAAGGTAGACATTCAATTA
** * * ********** *
749 TAGAATGTTTTAATAAAAAATATAAAAAAATTCAACTTAAAATCAATTNNNNNNNNNNAAAACCA
64 TAGTCTGTTTTAACAAAAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACTA
* * * * *
814 TTTAAAGCGAGTAGTAAGCTTTTTGAAGGAATGGGTGGCTCT
129 TTTAAAGCGAGTAATAAGCCTTTTGAAGAAATGAGTGACTCT
* * * ***
856 AAATAGA--TTTCTTGTCAATGAATGCTTGTTTGTTCACGTTGT-TGGAGGTAGACATTCAATTA
1 AAATGGACTTTTCTTGTCAATGAATGCTT-TTTCTTCATGTT-TCACAAGGTAGACATTCAATTA
* ********** *
918 TAGTCTATTTTAATC-AAAAATGTAAAAANNNNNNNNNNAAAATCAATTATAAGATTATAAAACT
64 TAGTCTGTTTTAA-CAAAAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACT
* * *
982 ATTTAAAGCGAGTAATAAGCATTTTGAAGAAATGGGTGACTAT
128 ATTTAAAGCGAGTAATAAGCCTTTTGAAGAAATGAGTGACTCT
* *
1025 AAATGGACTTTTCTTCTCAATCAATGGCTTT
1 AAATGGACTTTTCTTGTCAATGAAT-GCTTT
1056 CGTGGCACGT
Statistics
Matches: 731, Mismatches: 134, Indels: 38
0.81 0.15 0.04
Matches are distributed among these distances:
169 128 0.18
170 16 0.02
171 568 0.78
172 19 0.03
ACGTcount: A:0.37, C:0.11, G:0.15, T:0.35
Consensus pattern (170 bp):
AAATGGACTTTTCTTGTCAATGAATGCTTTTTCTTCATGTTTCACAAGGTAGACATTCAATTATA
GTCTGTTTTAACAAAAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACTATT
TAAAGCGAGTAATAAGCCTTTTGAAGAAATGAGTGACTCT
Found at i:628 original size:342 final size:339
Alignment explanation
Indices: 1--1050 Score: 1209
Period size: 342 Copynumber: 3.1 Consensus size: 339
*
1 AAATGGACTTTTCTTGTCAATGAATGCTTG-TTCATTCATGTTT-CACGAGGTAGACATGCAATT
1 AAATGGACTTTTCTTGTCAATGAATGCTTGTTTC-TTCATGTTTACA-GAGGTAGACATTCAATT
* * * * * *
64 ATAGTCTGTTTTCACAAAAAATGTAAAAAACTTCAATTTAAAATCAATTATGGGATTATAAAACC
64 ATAGTATGTTTTAATAAAAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACC
* * * * *
129 GTTGAAAGTGAGTAATAAGCTTTTTCG-AGGAATGGGCGACTCTAAATGGACTTTTCTTCTCAAT
129 ATTAAAAGCGAGTAATAAGCTTTTT-GAAGGAATGGGTGACTCTAAAT-GACGTTTCTTCTCAAT
* *** * *
193 GAATAGCTTTTTCTACACGTTTCCCAAGGTAGACAATCAATTATAGTCTGTTTTAACAAAAAATG
192 GAATAGCTTTTTCT-CACGTTTTCTTGGGTAGACATTCAATTATAGTCTATTTTAA-AAAAAATG
* *
258 TAAAAAAATTCAACTGAAAATTAATTATGAGATTATAAAACTATTTAAAGTGAGTAATAAGCCTT
255 TAAAAAAATTCAACTGAAAATCAATTATGAGATTATAAAACTATTTAAAGCGAGTAATAAGCCTT
323 TTGAAGAAATGAGTGACTCT
320 TTGAAGAAATGAGTGACTCT
343 AAATGGACTTTTCTTGTCAATGAATGCTTGTTTCTTCATGTTTACAGAGGTAGACATTCAATTAT
1 AAATGGACTTTTCTTGTCAATGAATGCTTGTTTCTTCATGTTTACAGAGGTAGACATTCAATTAT
* * **
408 AGTATGTTTTAATAAAAAATGTAAAAAAGTTTAACTTAAAATCAATTATGAGATTATAAAATTAT
66 AGTATGTTTTAATAAAAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCAT
* * * * *
473 TAAAAGCGAATAATAAGCCTTTTGAAGAAATGGGTGACTATAAATGAACGTTTCTTCTCAATCAA
131 TAAAAGCGAGTAATAAGCTTTTTGAAGGAATGGGTGACTCTAAATG-ACGTTTCTTCTCAATGAA
* * *
538 TAGCTTTTTCT-ACGTATTTCTTGGGATAGACATTAAATTATTGTCTATTTTAAAGAAAAATATA
195 TAGCTTTTTCTCACGT-TTTCTTGGG-TAGACATTCAATTATAGTCTATTTTAAA-AAAAATGTA
* * * *
602 AAAAAGTTCAACTTAAAATCAATTATGAGATTATAAAACTATTTAAGGCGAGTAATTAGCCTTTT
257 AAAAAATTCAACTGAAAATCAATTATGAGATTATAAAACTATTTAAAGCGAGTAATAAGCCTTTT
667 GAA-AGAATGAGTGACTCT
322 GAAGA-AATGAGTGACTCT
* ** *
685 AAATGGACTTTTCTTGTCAATGAATGCTTGTTTCTTCATATTTATTGTGGTAGACATTCAATTAT
1 AAATGGACTTTTCTTGTCAATGAATGCTTGTTTCTTCATGTTTACAGAGGTAGACATTCAATTAT
* * **********
750 AGAATGTTTTAATAAAAAATATAAAAAAATTCAACTTAAAATCAATTNNNNNNNNNNAAAACCAT
66 AGTATGTTTTAATAAAAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCAT
* * * *
815 TTAAAGCGAGTAGTAAGCTTTTTGAAGGAATGGGTGGCTCTAAAT-A-GATTTCTTGTCAATGAA
131 TAAAAGCGAGTAATAAGCTTTTTGAAGGAATGGGTGACTCTAAATGACG-TTTCTTCTCAATGAA
* * * *
878 T-GCTTGTTTGTTCACGTTGT-TGGAGGTAGACATTCAATTATAGTCTATTTTAATCAAAAATGT
195 TAGCTT-TTT-CTCACGTTTTCTTG-GGTAGACATTCAATTATAGTCTATTTTAA-AAAAAATGT
********** * *
941 AAAAANNNNNNNNNNAAAATCAATTATAAGATTATAAAACTATTTAAAGCGAGTAATAAGCATTT
256 AAAAAAATTCAACTGAAAATCAATTATGAGATTATAAAACTATTTAAAGCGAGTAATAAGCCTTT
* *
1006 TGAAGAAATGGGTGACTAT
321 TGAAGAAATGAGTGACTCT
* *
1025 AAATGGACTTTTCTTCTCAATCAATG
1 AAATGGACTTTTCTTGTCAATGAATG
1051 GCTTTCGTGG
Statistics
Matches: 604, Mismatches: 89, Indels: 32
0.83 0.12 0.04
Matches are distributed among these distances:
339 5 0.01
340 146 0.24
341 15 0.02
342 433 0.72
343 5 0.01
ACGTcount: A:0.37, C:0.11, G:0.15, T:0.35
Consensus pattern (339 bp):
AAATGGACTTTTCTTGTCAATGAATGCTTGTTTCTTCATGTTTACAGAGGTAGACATTCAATTAT
AGTATGTTTTAATAAAAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCAT
TAAAAGCGAGTAATAAGCTTTTTGAAGGAATGGGTGACTCTAAATGACGTTTCTTCTCAATGAAT
AGCTTTTTCTCACGTTTTCTTGGGTAGACATTCAATTATAGTCTATTTTAAAAAAAATGTAAAAA
AATTCAACTGAAAATCAATTATGAGATTATAAAACTATTTAAAGCGAGTAATAAGCCTTTTGAAG
AAATGAGTGACTCT
Found at i:1117 original size:511 final size:511
Alignment explanation
Indices: 80--1094 Score: 1223
Period size: 513 Copynumber: 2.0 Consensus size: 511
70 TGTTTTCACA
* * * * *
80 AAAAATGTAAAAAACTTCAATTTAAAATCAATTATGGGATTATAAAACCGTTGAAAGTGAGTAAT
1 AAAAATATAAAAAACTTCAACTTAAAATCAATTATGAGATTATAAAACCATTGAAAGCGAGTAAT
* * *
145 AAGCTTTTTCGAGGAATGGGCGACTCTAAATGGACTTTTCTTCTCAATGAATAGCTTTTTCTACA
66 AAGCCTTTTCGAAGAATGAGCGACTCTAAATGGACTTTTCTTCTCAATGAATAGCTTTTTCTACA
* * ** *
210 CGTTTCCCAAGGTAGACAATCAATTATAGTCTGTTTTAACAAAAAATGTAAAAAAATTCAACTGA
131 CATTTACCAAGGTAGACAATCAATTATAGAATGTTTTAACAAAAAATATAAAAAAATTCAACTGA
* * *
275 AAATTAATTATGAGATTATAAAACTATTTAAAGTGAGTAATAAGCCTTTTGAAGAAATGAGTGAC
196 AAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGCCTTTTGAAGAAATGAGTGAC
* *
340 TCTAAATGGACTTTTCTTGTCAATGAATGCTTGTTTCTTCATGTTTACAGAGGTAGACATTCAAT
261 TCTAAATAGAC-TTTCTTGTCAATGAATGCTTGTTTCTTCACGTTTACAGAGGTAGACATTCAAT
* * *
405 TATAGTATGTTTTAATAAAAAATGTAAAAAAGTTTAACTTAAAATCAATTATGAGATTATAAAAT
325 TATAGTATATTTTAATAAAAAATGTAAAAAAGTTTAACTTAAAATCAATTATAAGATTATAAAAC
*
470 TATTAAAAGCGAATAATAAGCCTTTTGAAGAAATGGGTGACTATAAATGAACGTTTCTTCTCAAT
390 TATTAAAAGCGAATAATAAGCATTTTGAAGAAATGGGTGACTATAAATGAACGTTTCTTCTCAAT
* *
535 CAATAGCTTTTTCTACGTATTTCTTGGGATAGACATTAAATTATTGTCTATTTTAAAG
455 CAATAGCTTTTGCTACG-ATTTCTTGAGATAGACATTAAATTATTGTCTATTTTAAAG
* * * *
593 AAAAATATAAAAAAGTTCAACTTAAAATCAATTATGAGATTATAAAACTATTTAAGGCGAGTAAT
1 AAAAATATAAAAAACTTCAACTTAAAATCAATTATGAGATTATAAAACCATTGAAAGCGAGTAAT
* * * *
658 TAGCCTTTT-GAAAGAATGAGTGACTCTAAATGGACTTTTCTTGTCAATGAAT-GCTTGTTTCTT
66 AAGCCTTTTCG-AAGAATGAGCGACTCTAAATGGACTTTTCTTCTCAATGAATAGCTT-TTTCTA
* **** * *
721 CATATTTATTGTGGTAGACATTCAATTATAGAATGTTTTAATAAAAAATATAAAAAAATTCAACT
129 CACATTTACCAAGGTAGACAATCAATTATAGAATGTTTTAACAAAAAATATAAAAAAATTCAACT
* ********** * * * *
786 TAAAATCAATTNNNNNNNNNNAAAACCATTTAAAGCGAGTAGTAAGCTTTTTGAAGGAATGGGTG
194 GAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGCCTTTTGAAGAAATGAGTG
* * **
851 GCTCTAAATAGA-TTTCTTGTCAATGAATGCTTGTTTGTTCACGTTGT-TGGAGGTAGACATTCA
259 ACTCTAAATAGACTTTCTTGTCAATGAATGCTTGTTTCTTCACGTT-TACAGAGGTAGACATTCA
* * **********
914 ATTATAGTCTATTTTAATCAAAAATGTAAAAANNNNNNNNNNAAAATCAATTATAAGATTATAAA
323 ATTATAGTATATTTTAATAAAAAATGTAAAAAAGTTTAACTTAAAATCAATTATAAGATTATAAA
* * * *
979 ACTATTTAAAGCGAGTAATAAGCATTTTGAAGAAATGGGTGACTATAAATGGACTTTTCTTCTCA
388 ACTATTAAAAGCGAATAATAAGCATTTTGAAGAAATGGGTGACTATAAATGAACGTTTCTTCTCA
* * *
1044 ATCAATGGCTTTCGTGGC-ACG-TTTCTTGAGTTAGACATTCAATTATTGTCT
453 ATCAATAGCTTT--T-GCTACGATTTCTTGAGATAGACATTAAATTATTGTCT
1095 GTTTNNNNNN
Statistics
Matches: 419, Mismatches: 77, Indels: 14
0.82 0.15 0.03
Matches are distributed among these distances:
511 193 0.46
512 6 0.01
513 219 0.52
514 1 0.00
ACGTcount: A:0.37, C:0.11, G:0.15, T:0.35
Consensus pattern (511 bp):
AAAAATATAAAAAACTTCAACTTAAAATCAATTATGAGATTATAAAACCATTGAAAGCGAGTAAT
AAGCCTTTTCGAAGAATGAGCGACTCTAAATGGACTTTTCTTCTCAATGAATAGCTTTTTCTACA
CATTTACCAAGGTAGACAATCAATTATAGAATGTTTTAACAAAAAATATAAAAAAATTCAACTGA
AAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGCCTTTTGAAGAAATGAGTGAC
TCTAAATAGACTTTCTTGTCAATGAATGCTTGTTTCTTCACGTTTACAGAGGTAGACATTCAATT
ATAGTATATTTTAATAAAAAATGTAAAAAAGTTTAACTTAAAATCAATTATAAGATTATAAAACT
ATTAAAAGCGAATAATAAGCATTTTGAAGAAATGGGTGACTATAAATGAACGTTTCTTCTCAATC
AATAGCTTTTGCTACGATTTCTTGAGATAGACATTAAATTATTGTCTATTTTAAAG
Done.