Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018401451.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_4578.0, 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, 892
Length: 1487
ACGTcount: A:0.36, C:0.12, G:0.15, T:0.35
Warning! 20 characters in sequence are not A, C, G, or T
Found at i:294 original size:171 final size:171
Alignment explanation
Indices: 1--1487 Score: 1351
Period size: 171 Copynumber: 8.7 Consensus size: 171
* *
1 AGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGGAGACTGTAAACT-GAC
1 AGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAA-TGGAC
* * * * * *
65 TTTTCTTGCCAAAGAATGACATTTTT-TTCACGTTTTTTGAGGTAAACATTCTATTATAATTTGT
65 TTTTCTTGCCAATGAATG-CCTTTTTCTTCACGTTTCTTGAGGTAGACATTCAATTATAATCTGT
* * *
129 TTTAACCAAAAAAT-TAAAAAAATTTAACTTAAGATCAATTATG
129 TTTAACC-AAAAATGTAAAAAAATTGAACTTAAAATCAATTTTG
172 AGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGATA-GAATGGGTGACTATAAATGGAC
1 AGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGA-AGGAATGGGTGACTATAAATGGAC
* * * *
236 TTTTCATGCCAATGAATGCCTTTTTCTTCACGTTTCTTGAAGTAGCCATTCAATTATAATCTATT
65 TTTTCTTGCCAATGAATGCCTTTTTCTTCACGTTTCTTGAGGTAGACATTCAATTATAATCTGTT
* * * * * *
301 TTAGCCAATAATGTAAAAAAAATTGAACTTAGAATGATTTTTT
130 TTAACCAAAAATGT-AAAAAAATTGAACTTAAAATCAATTTTG
* * * **
344 AGATAATAAAACTATTTAAAGC--G-----AGGCTTTTGAAGCAATAAGTGACTATAAATGGACT
1 AGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATGGACT
* * * * * *
402 TTTCATGCCAATGAATGCCTTTTTCTTTACATTTCTCGAGGTAGCCATTCAATTATAATCTATTT
66 TTTCTTGCCAATGAATGCCTTTTTCTTCACGTTTCTTGAGGTAGACATTCAATTATAATCTGTTT
* * * *
467 TAACCAATAATGTAAAACAATTGAAGTTAAAATGAATTTTG
131 TAACCAAAAATGTAAAAAAATTGAACTTAAAATCAATTTTG
** * ** * *
508 AGAGAATAAAACTATTTAAAGCGAGTAATAAATCTTTTGAAGGAATGGGTGAATATAAATGGTCT
1 AGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATGGACT
* * *
573 TTTCTTGTCAATGAATGCCTTCTTCTTCATC-TTTCTT-ATCGTAGACATTCAATTATAATCTGT
66 TTTCTTGCCAATGAATGCCTTTTTCTTCA-CGTTTCTTGA-GGTAGACATTCAATTATAATCTGT
* * *
636 TCTAACCAAAAAAGTAAAAAACATTGAACATAAAATCAATTTTG
129 TTTAACCAAAAATGTAAAAAA-ATTGAACTTAAAATCAATTTTG
* * ** *
680 AGA-TAGTAACACTATTTAAAGTAAGTAGTAAGGCTTTTGAAGGAATGGGTGACTATAAATGGAC
1 AGATTA-TAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATGGAC
* *
744 TTTTCTTGCCAATGAATGCCTTTTTCTTCACGTTTCTCGAGGTTA-ACTTTCAATTATAAT-TCG
65 TTTTCTTGCCAATGAATGCCTTTTTCTTCACGTTTCTTGAGG-TAGACATTCAATTATAATCT-G
* * *
807 TTTTAAGCAAAAATGTAAAAAAAAAAGAATTGAAC-AAACAATCAATTATG
128 TTTTAACCAAAAATGT-----AAAAA-AATTGAACTTAA-AATCAATTTTG
* * * * * * * *
857 GGTTTATAAAACCATTTAAAGCGAGTGATAAGGCTTTGGATGGAATGGGAGACCATAAATAGACT
1 AGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATGGACT
* * * * * * * *
922 TTTCTTGTCAATAAAT--TTTCTTTCTTCACGTTTCTCGAGATAGATATTGAATTATAATCTCTT
66 TTTCTTGCCAATGAATGCCTT-TTTCTTCACGTTTCTTGAGGTAGACATTCAATTATAATCTGTT
* ** * * *
985 TTAACTAAATCTATAAAAATAATTCAACTTAAAATCACTTTTG
130 TTAACCAAAAATGTAAAAA-AATTGAACTTAAAATCAATTTTG
* * * * *
1028 AGATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTGAAGGACTGGGTGACAATGAATGGTCT
1 AGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATGGACT
* * * * * * * *
1093 TTTCTTGCCAAGGAATGCTTTTTTCTTCACATTTCATGAGGTAGGCTTTCAATTATAGTTTGTTT
66 TTTCTTGCCAATGAATGCCTTTTTCTTCACGTTTCTTGAGGTAGACATTCAATTATAATCTGTTT
* * * * * *
1158 TAAACAAAAATGCAAAAAAATTCAACTTAAATTTAATTATG
131 TAACCAAAAATGTAAAAAAATTGAACTTAAAATCAATTTTG
* * * **********
1199 AGATTATAAAACTATTTAAAGTGAGTAGTAAGGCTTTTGAANNNNNNNNNNACTATAAATGGACT
1 AGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATGGACT
* * * * **
1264 TTTCTTAG-CAATGAATG-CTTGTTTCTTCATGTTTCATGAGATACACATTTGATTATAATCTGT
66 TTTCTT-GCCAATGAATGCCTT-TTTCTTCACGTTTCTTGAGGTAGACATTCAATTATAATCTGT
********** *
1327 TTTAANNNNNNNNNNACAAAAAATTGAACTTAAAATCAATTTCG
129 TTTAACCAAAAATGTA-AAAAAATTGAACTTAAAATCAATTTTG
* * * * * *
1371 AAGATTATAAAACCATTTAAAGTGGGTAATAAGGCTTTTGAAAGAATAGGTGACTATAAATGAAG
1 -AGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATGGAC
* * * *
1436 TTGTCTTGCCAAAGAATGACTTTTTCTTCACGTTTCTTGAGGTAAACATTCA
65 TTTTCTTGCCAATGAATGCCTTTTTCTTCACGTTTCTTGAGGTAGACATTCA
Statistics
Matches: 1065, Mismatches: 210, Indels: 80
0.79 0.15 0.06
Matches are distributed among these distances:
164 45 0.04
165 103 0.10
166 1 0.00
170 16 0.02
171 419 0.39
172 248 0.23
173 93 0.09
174 3 0.00
175 4 0.00
176 44 0.04
177 86 0.08
178 3 0.00
ACGTcount: A:0.36, C:0.12, G:0.15, T:0.35
Consensus pattern (171 bp):
AGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATGGACT
TTTCTTGCCAATGAATGCCTTTTTCTTCACGTTTCTTGAGGTAGACATTCAATTATAATCTGTTT
TAACCAAAAATGTAAAAAAATTGAACTTAAAATCAATTTTG
Found at i:655 original size:336 final size:338
Alignment explanation
Indices: 30--1238 Score: 1091
Period size: 336 Copynumber: 3.5 Consensus size: 338
20 AGCGAGTAAT
* * * *
30 AAGGCTTTTGAAGGAATGGGAGACTGTAAACT-GACTTTTCTTGCCAAAGAATGACATTTTT-TT
1 AAGGCTTTTGAAGGAATGGGTGACTATAAA-TGGACTTTTCTTGCCAATGAATG-CCTTTTTCTT
* * * *
93 CACGTTTTTTGAGGTAAACATTCTATTATAATTTGTTTTAACCAAAAAAT-TAAAAAAATTTAAC
64 CACGTTTCTCGAGGT-AACATTCAATTATAA-TTGTTTTAACC-AAAAATGTAAAAAAATTGAAC
* ** *
157 TTAAGATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGATAGAATGGGT
126 TTAAAATCAATTATGAGAGAATAAAACCATTTAAAGCGAGTAATAAAGCTTTTGATAGAATGGGT
* * *
222 GACTATAAATGGACTTTTCATGCCAATGAATGCCTTTTTCTTCACGTTTCTTGAAGTAGCCATTC
191 GAATATAAATGGACTTTTCATGCCAATGAATGCCTTCTTCTTCACGTTTCTTGAAGTAGACATTC
* * * * * * * * *
287 AATTATAATCTATTTTAGCCAATAATGTAAAAAAAATTGAACTTAGAATGATTTTTTAGATAATA
256 AATTATAATCTATTCTAACCAAAAAAGTAAAAAAAATTGAACATAAAATCAATTTTGAGATAATA
*
352 AAACTATTT-A-AAG-CG
321 AAACTATTTAAGAAGTAG
* ** * *
367 -AGGCTTTTGAAGCAATAAGTGACTATAAATGGACTTTTCATGCCAATGAATGCCTTTTTCTTTA
1 AAGGCTTTTGAAGGAATGGGTGACTATAAATGGACTTTTCTTGCCAATGAATGCCTTTTTCTTCA
* * * * * *
431 CATTTCTCGAGGTAGCCATTCAATTATAATCTATTTTAACCAATAATGTAAAACAATTGAAGTTA
66 CGTTTCTCGAGGTA-ACATTCAATTATAAT-TGTTTTAACCAAAAATGTAAAAAAATTGAACTTA
* * * *
496 AAATGAATTTTGAGAGAATAAAACTATTTAAAGCGAGTAATAAATCTTTTGA-AGGAATGGGTGA
129 AAATCAATTATGAGAGAATAAAACCATTTAAAGCGAGTAATAAAGCTTTTGATA-GAATGGGTGA
* * * *
560 ATATAAATGGTCTTTTCTTGTCAATGAATGCCTTCTTCTTCATC-TTTCTT-ATCGTAGACATTC
193 ATATAAATGGACTTTTCATGCCAATGAATGCCTTCTTCTTCA-CGTTTCTTGA-AGTAGACATTC
* * *
623 AATTATAATCTGTTCTAACCAAAAAAGTAAAAAACATTGAACATAAAATCAATTTTGAGATAGTA
256 AATTATAATCTATTCTAACCAAAAAAGTAAAAAAAATTGAACATAAAATCAATTTTGAGATAATA
*
688 ACACTATTTAAAGTAAGTAG
321 AAACTATTT-AAG-AAGTAG
708 TAAGGCTTTTGAAGGAATGGGTGACTATAAATGGACTTTTCTTGCCAATGAATGCCTTTTTCTTC
1 -AAGGCTTTTGAAGGAATGGGTGACTATAAATGGACTTTTCTTGCCAATGAATGCCTTTTTCTTC
* *
773 ACGTTTCTCGAGGTTAACTTTCAATTATAATTCGTTTTAAGCAAAAATGTAAAAAAAAAAGAATT
65 ACGTTTCTCGAGG-TAACATTCAATTATAATT-GTTTTAACCAAAAATGT-----AAAAA-AATT
* * *** * * * *
838 GAAC-AAACAATCAATTATGGGTTTATAAAACCATTTAAAGCGAGTGATAAGGCTTTGGATGGAA
122 GAACTTAA-AATCAATTATGAGAGAATAAAACCATTTAAAGCGAGTAATAAAGCTTTTGATAGAA
* ** * * * * * *
902 TGGGAGACCATAAATAGACTTTTCTTGTCAATAAAT--TTTCTTTCTTCACGTTTCTCG-AGATA
186 TGGGTGAATATAAATGGACTTTTCATGCCAATGAATGCCTTC-TTCTTCACGTTTCTTGAAG-TA
* * * * * ** * * * *
964 GATATTGAATTATAATCTCTTTTAACTAAATCTA-TAAAAATAATTCAACTTAAAATCACTTTTG
249 GACATTCAATTATAATCTATTCTAACCAAA-AAAGTAAAAAAAATTGAACATAAAATCAATTTTG
* * * *
1028 AGATTATAAAACCATTTAAAGTGAGTAAT
313 AGATAATAAAACTATTT-AAG-AAGT-AG
* * * * * *
1057 AAGGCTTTTGAAGGACTGGGTGACAATGAATGGTCTTTTCTTGCCAAGGAATGCTTTTTTCTTCA
1 AAGGCTTTTGAAGGAATGGGTGACTATAAATGGACTTTTCTTGCCAATGAATGCCTTTTTCTTCA
* * * * * * *
1122 CATTTCAT-GAGGTAGGCTTTCAATTATAGTTTGTTTTAAACAAAAATGCAAAAAAATTCAACTT
66 CGTTTC-TCGAGGTA-ACATTCAATTATA-ATTGTTTTAACCAAAAATGTAAAAAAATTGAACTT
* * ** * * * *
1186 AAATTTAATTATGAGATTATAAAACTATTTAAAGTGAGTAGTAAGGCTTTTGA
128 AAAATCAATTATGAGAGAATAAAACCATTTAAAGCGAGTAATAAAGCTTTTGA
1239 ANNNNNNNNN
Statistics
Matches: 714, Mismatches: 123, Indels: 65
0.79 0.14 0.07
Matches are distributed among these distances:
335 16 0.02
336 258 0.36
337 1 0.00
338 1 0.00
340 3 0.00
341 1 0.00
342 50 0.07
343 104 0.15
344 2 0.00
347 7 0.01
348 186 0.26
349 85 0.12
ACGTcount: A:0.37, C:0.12, G:0.15, T:0.36
Consensus pattern (338 bp):
AAGGCTTTTGAAGGAATGGGTGACTATAAATGGACTTTTCTTGCCAATGAATGCCTTTTTCTTCA
CGTTTCTCGAGGTAACATTCAATTATAATTGTTTTAACCAAAAATGTAAAAAAATTGAACTTAAA
ATCAATTATGAGAGAATAAAACCATTTAAAGCGAGTAATAAAGCTTTTGATAGAATGGGTGAATA
TAAATGGACTTTTCATGCCAATGAATGCCTTCTTCTTCACGTTTCTTGAAGTAGACATTCAATTA
TAATCTATTCTAACCAAAAAAGTAAAAAAAATTGAACATAAAATCAATTTTGAGATAATAAAACT
ATTTAAGAAGTAG
Done.