Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018400755.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_3934.0, 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: 1847
ACGTcount: A:0.35, C:0.13, G:0.12, T:0.28
Warning! 239 characters in sequence are not A, C, G, or T
Found at i:507 original size:171 final size:170
Alignment explanation
Indices: 15--535 Score: 455
Period size: 171 Copynumber: 3.1 Consensus size: 170
5 AGCGAGTAAT
* * *** * * * * * *
15 AAGGCTTGAGGGGCTATAAAGGGACTTTTTTCTCTAATGGATA-CTTTTGCCTTACATTTCCTGA
1 AAGGCTTGAGTGACTATAAATAAACTTTTCTCCCTAATGGATAGCTTTTGCATCACGTTTCCTAA
* * * * *
79 GACAGACATTCAATTATAGCATACTTTAACAAAAAATATAAAAAAAACACAACTTAAAATCAATT
66 GGCTGACATTCAATTATAACATACTTGAAC-AAAAATATAAAAAAATC-CAACTTAAAATCAATT
*
144 ATAAGAAAATAAAACCATTTAAAGCGAGTAATAAGGCTTTCA
129 ATGAGAAAATAAAACCATTTAAAGCGAGTAATAAGGCTTTCA
* * * ** * ** *
186 GAGGCTTGAGTGATTGTAAATAAACTTTTCTCTATAATGGATGGC-TTCACATCATGTTT-CTCA
1 AAGGCTTGAGTGACTATAAATAAACTTTTCTCCCTAATGGATAGCTTTTGCATCACGTTTCCT-A
* * *
249 AGG-TAGACATTCAATTATAACATATTTTGATA-AAAAATGTAAAAAAATTCAACTTCAAAA-C-
65 AGGCT-GACATTCAATTATAACATA-CTTGA-ACAAAAATATAAAAAAATCCAACTT-AAAATCA
* * *
310 ATATATGAGAATATAAAACCATTTAAAGCAAGTAATAAGGCTTTAA
126 AT-TATGAGAAAATAAAACCATTTAAAGCGAGTAATAAGGCTTTCA
********** *
356 AAGGCTTGAGTGACTATANNNNNNNNNNTCTCCCTAATGGATAGCTTTTGCGTCACGTTTCCTAA
1 AAGGCTTGAGTGACTATAAATAAACTTTTCTCCCTAATGGATAGCTTTTGCATCACGTTTCCTAA
*
421 GGCTGACATTCAATTATAACATA-TTCGAACCAAAAATTTAAAAAAATCCAACTTAAAATCAATT
66 GGCTGACATTCAATTATAACATACTT-GAA-CAAAAATATAAAAAAATCCAACTTAAAATCAATT
* ** *
485 ATGAGAAAATAAAACAATTTAAATTGGGTAATAAGGCTTTCA
129 ATGAGAAAATAAAACCATTTAAAGCGAGTAATAAGGCTTTCA
*
527 AAGTCTTGA
1 AAGGCTTGA
536 NNNNNNNNNN
Statistics
Matches: 275, Mismatches: 60, Indels: 30
0.75 0.16 0.08
Matches are distributed among these distances:
169 5 0.02
170 83 0.30
171 177 0.64
172 9 0.03
173 1 0.00
ACGTcount: A:0.40, C:0.14, G:0.13, T:0.30
Consensus pattern (170 bp):
AAGGCTTGAGTGACTATAAATAAACTTTTCTCCCTAATGGATAGCTTTTGCATCACGTTTCCTAA
GGCTGACATTCAATTATAACATACTTGAACAAAAATATAAAAAAATCCAACTTAAAATCAATTAT
GAGAAAATAAAACCATTTAAAGCGAGTAATAAGGCTTTCA
Found at i:1057 original size:170 final size:171
Alignment explanation
Indices: 735--1646 Score: 772
Period size: 170 Copynumber: 5.3 Consensus size: 171
725 NNNNNNNNNN
* * * * *
735 CAAAAATGTAAAAAAAATCCAACTTAAAATTAATTTTCAGAATATGAAACCATTTAAAGCGAGTA
1 CAAAAATGT-AAAAAAATCCAACTTAAAACTAATTATGAGAATATAAAACCATTTAAAACGAGTA
* * * * *
800 ATAAGGCTTTCAAAGGCTTGAGTGGCTGTAAATAGACTTTGCT-T-TACCATGGATGGC-TTTGC
65 ATAAGGCTTTCAAAGGCTTGAGTGACTATAAATAGACTTTTCTCTCTA--ATGGATGACTTTTCC
* * **
862 TTCATGTTTCTTAAGGCAAACATTCAATTATAACATATTCGAAC
128 TTCATGTTTCCTAAGGCAGACATTCAATTATAACATATTTTAAC
* *
906 CAAAAATTTAAAAAAATCCAACTTAAAACCAATTATGAGAGA-ATAAAACCATTTAAAACGAGTA
1 CAAAAATGTAAAAAAATCCAACTTAAAACTAATTATGAGA-ATATAAAACCATTTAAAACGAGTA
* *
970 ATAAGGCTTTCAAAAGCTTGAGTGGCTATAAAT-GACCTTTTCTCTCTAATGGAT-ACTTTTGCC
65 ATAAGGCTTTCAAAGGCTTGAGTGACTATAAATAGA-CTTTTCTCTCTAATGGATGACTTTT-CC
* * * *
1033 TT-ACT-TTTCCTAAGACAGACATTCAATTGTAGCATATTTTAAG
128 TTCA-TGTTTCCTAAGGCAGACATTCAATTATAACATATTTTAAC
* * **
1076 AAAAAATGTAAAAAAATCCAACTTAAAACTAATTATGAAAATATAAAACCATTTAAAGTGAGTAA
1 CAAAAATGTAAAAAAATCCAACTTAAAACTAATTATGAGAATATAAAACCATTTAAAACGAGTAA
* * * *
1141 TATGGCTTTTAAAGGCTTGAGTGACTATAAATAGACTTTTCTCTCCAATGGATGGCTTTTCCTTC
66 TAAGGCTTTCAAAGGCTTGAGTGACTATAAATAGACTTTTCTCTCTAATGGATGACTTTTCCTTC
* * * * **
1206 ATGTTTCCCATGGCAGACACTCAATCATGGCATATTTT-AC
131 ATGTTTCCTAAGGCAGACATTCAATTATAACATATTTTAAC
* * * * *
1246 ACAAAAATATGAAACAATCCAACTTAAAACTAATTATGAGAATATAAAACCATTTGAAACGAATA
1 -CAAAAATGTAAAAAAATCCAACTTAAAACTAATTATGAGAATATAAAACCATTTAAAACGAGTA
* * * * **
1311 ACAAGGCTTTCAACGGCTTGCGTGACTATAAATGGACTTTTCAAGTC-AATGGAT-AGCTTTTCC
65 ATAAGGCTTTCAAAGGCTTGAGTGACTATAAATAGACTTTTC-TCTCTAATGGATGA-CTTTTCC
* * * * * *
1374 TTCACGCTT-CTGGAGGTAGACATTCAATTATAATATATTTTAAT
128 TTCATGTTTCCT-AAGGCAGACATTCAATTATAACATATTTTAAC
* * ********** * *
1418 CAAAAATGTAAAAAAATTCTAACTTAAAACAAATTATNNNNNNNNNNAACTATTTAAATCGAGTA
1 CAAAAATGTAAAAAAA-TCCAACTTAAAACTAATTATGAGAATATAAAACCATTTAAAACGAGTA
* * ********** * **
1483 ATAAGGCTTTTAAAGGCTTGCGTGACTA-NNNNNNNNNNTTCTTCACTAATGGATAGA-TTTTGT
65 ATAAGGCTTTCAAAGGCTTGAGTGACTATAAATAGACTTTTC-TCTCTAATGGAT-GACTTTTCC
* ** * *
1546 TTCACGTTTCCTAAGATAGACATTCAATTATATCATATTTTAAG
128 TTCATGTTTCCTAAGGCAGACATTCAATTATAACATATTTTAAC
* * * * *
1590 CAAAAATGTAAAAAAATCCAACATAAAATTAATTAGGAAAATATAAAACCTTTTAAA
1 CAAAAATGTAAAAAAATCCAACTTAAAACTAATTATGAGAATATAAAACCATTTAAA
1647 GCCGCTTTTA
Statistics
Matches: 588, Mismatches: 131, Indels: 44
0.77 0.17 0.06
Matches are distributed among these distances:
169 4 0.01
170 233 0.40
171 224 0.38
172 124 0.21
173 2 0.00
174 1 0.00
ACGTcount: A:0.39, C:0.15, G:0.13, T:0.31
Consensus pattern (171 bp):
CAAAAATGTAAAAAAATCCAACTTAAAACTAATTATGAGAATATAAAACCATTTAAAACGAGTAA
TAAGGCTTTCAAAGGCTTGAGTGACTATAAATAGACTTTTCTCTCTAATGGATGACTTTTCCTTC
ATGTTTCCTAAGGCAGACATTCAATTATAACATATTTTAAC
Found at i:1364 original size:341 final size:341
Alignment explanation
Indices: 736--1454 Score: 860
Period size: 341 Copynumber: 2.1 Consensus size: 341
726 NNNNNNNNNC
* * * *
736 AAAAATGTAAAAAAAATCCAACTTAAAATTAATTTTCAGAATATGAAACCATTTAAAGCGAGTAA
1 AAAAATGT-AAAAAAATCCAACTTAAAACTAATTATCAAAATATAAAACCATTTAAAGCGAGTAA
* * * *
801 TAAGGCTTTCAAAGGCTTGAGTGGCTGTAAATAGACTTTGCTTTACCATGGATGGCTTTGCTTCA
65 TAAGGCTTTCAAAGGCTTGAGTGACTATAAATAGACTTTGCTCTACCATGGATGGCTTTCCTTCA
** * * *
866 TGTTTCTTAAGGCAAACATTCAATTATAACATATTCGAACCAAAAATTTAAAAAAATCCAACTTA
130 TGTTTCCCAAGGCAAACACTCAATCATAACATATTCGAACCAAAAATATAAAAAAATCCAACTTA
* * *
931 AAACCAATTATGAGAGAATAAAACCATTTAAAACGAGTAATAAGGCTTTCAAAAGCTTGAGTGGC
195 AAACCAATTATGAGAGAATAAAACCATTTAAAACGAATAACAAGGCTTTCAAAAGCTTGAGTGAC
* **
996 TATAAATGACCTTTTCTCTCTAATGGATA-CTTTTGCCTT-ACTTTTCCT-AAGACAGACATTCA
260 TATAAATGACCTTTTCACTCTAATGGATAGCTTTT-CCTTCACGCTT-CTGAAGACAGACATTCA
* *
1058 ATTGTAGCATATTTTAAGA
323 ATTATAACATATTTTAAGA
* *
1077 AAAAATGTAAAAAAATCCAACTTAAAACTAATTATGAAAATATAAAACCATTTAAAGTGAGTAAT
1 AAAAATGTAAAAAAATCCAACTTAAAACTAATTATCAAAATATAAAACCATTTAAAGCGAGTAAT
* * *
1142 ATGGCTTTTAAAGGCTTGAGTGACTATAAATAGACTTTTCTCT-CCAATGGATGGCTTTTCCTTC
66 AAGGCTTTCAAAGGCTTGAGTGACTATAAATAGACTTTGCTCTACC-ATGGATGGC-TTTCCTTC
* * ** ** * *
1206 ATGTTTCCCATGGCAGACACTCAATCATGGCATATT-TTACACAAAAATATGAAACAATCCAACT
129 ATGTTTCCCAAGGCAAACACTCAATCATAACATATTCGAAC-CAAAAATATAAAAAAATCCAACT
* * ** *
1270 TAAAACTAATTATGAGA-ATATAAAACCATTTGAAACGAATAACAAGGCTTTCAACGGCTTGCGT
193 TAAAACCAATTATGAGAGA-ATAAAACCATTTAAAACGAATAACAAGGCTTTCAAAAGCTTGAGT
* * **
1334 GACTATAAATGGA-CTTTTCAAGTC-AATGGATAGCTTTTCCTTCACGCTTCTGGAGGTAGACAT
257 GACTATAAAT-GACCTTTTC-ACTCTAATGGATAGCTTTTCCTTCACGCTTCTGAAGACAGACAT
* **
1397 TCAATTATAATATATTTTAATC
320 TCAATTATAACATATTTTAAGA
* *
1419 AAAAATGTAAAAAAATTCTAACTTAAAACAAATTAT
1 AAAAATGTAAAAAAA-TCCAACTTAAAACTAATTAT
1455 NNNNNNNNNN
Statistics
Matches: 320, Mismatches: 48, Indels: 18
0.83 0.12 0.05
Matches are distributed among these distances:
339 2 0.01
340 100 0.31
341 147 0.46
342 53 0.17
343 18 0.06
ACGTcount: A:0.40, C:0.16, G:0.13, T:0.31
Consensus pattern (341 bp):
AAAAATGTAAAAAAATCCAACTTAAAACTAATTATCAAAATATAAAACCATTTAAAGCGAGTAAT
AAGGCTTTCAAAGGCTTGAGTGACTATAAATAGACTTTGCTCTACCATGGATGGCTTTCCTTCAT
GTTTCCCAAGGCAAACACTCAATCATAACATATTCGAACCAAAAATATAAAAAAATCCAACTTAA
AACCAATTATGAGAGAATAAAACCATTTAAAACGAATAACAAGGCTTTCAAAAGCTTGAGTGACT
ATAAATGACCTTTTCACTCTAATGGATAGCTTTTCCTTCACGCTTCTGAAGACAGACATTCAATT
ATAACATATTTTAAGA
Done.