Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018398330.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_1630.0, 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: 3559
ACGTcount: A:0.30, C:0.09, G:0.10, T:0.28
Warning! 805 characters in sequence are not A, C, G, or T
Found at i:303 original size:171 final size:172
Alignment explanation
Indices: 1--381 Score: 559
Period size: 171 Copynumber: 2.2 Consensus size: 172
* *
1 TTTTAGCCAAAAATGTAAAAAAAATTTAACTTAAAATCAATTATGAAATTATAAGAACATTTAAA
1 TTTTAGCTAAAAATATAAAAAAAATTTAACTTAAAATCAATTATGAAATTATAAGAACATTTAAA
* * * * *
66 GCGAGTAATCAGGCTTTCGAAGGCATGGGTGATTATAAATGGACTTTTCTCGTCAATGGATATCT
66 GCGAGTAATAAGACTTTCGAAGGCATGGATGACTATAAATGGACTTTTCTCGTCAATAGATATCT
* * * *
131 TTTTCTTCACGTTTCTCGAGGTAGATATTAAATTATTATCTC
131 TTTTCTTCACGTTTCTCAAGGTAGACATTAAATTATAATCTA
* *
173 TTTTAGCTAAAAATAT-AAAAAAATTTAACTTAAAATCAATTATGAGATTATAATAACATTTAAA
1 TTTTAGCTAAAAATATAAAAAAAATTTAACTTAAAATCAATTATGAAATTATAAGAACATTTAAA
* * *
237 GCGAGTAATAAGACTTTCGAAGGCTTGGATGACTATAAGTGGACTTTTCTTGTCAATAGATATCT
66 GCGAGTAATAAGACTTTCGAAGGCATGGATGACTATAAATGGACTTTTCTCGTCAATAGATATCT
* * *
302 TTTTCTTCACGTTTCTTAAGGTAGGCATTTAATTATAATCTA
131 TTTTCTTCACGTTTCTCAAGGTAGACATTAAATTATAATCTA
*
344 TTTTA-ATAAAAAATATAAAAAAAATTTAACTTAAAATC
1 TTTTAGCT-AAAAATATAAAAAAAATTTAACTTAAAATC
382 NNNNNNNNNN
Statistics
Matches: 187, Mismatches: 20, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
170 1 0.01
171 151 0.81
172 35 0.19
ACGTcount: A:0.39, C:0.11, G:0.13, T:0.37
Consensus pattern (172 bp):
TTTTAGCTAAAAATATAAAAAAAATTTAACTTAAAATCAATTATGAAATTATAAGAACATTTAAA
GCGAGTAATAAGACTTTCGAAGGCATGGATGACTATAAATGGACTTTTCTCGTCAATAGATATCT
TTTTCTTCACGTTTCTCAAGGTAGACATTAAATTATAATCTA
Found at i:1464 original size:158 final size:148
Alignment explanation
Indices: 1171--1463 Score: 338
Period size: 158 Copynumber: 1.9 Consensus size: 148
1161 NNNNNNGAGG
* * **
1171 TTATAAAATTATTCAAAGCGAGTAATAAAGCTTTCAAAGGCATATGTGGCTATAAATGGACTTTT
1 TTATAAAATCATTCAAAGCGAGTAATAAAGCTTTCAAAGGCATAGGTAACTATAAATGGACTTTT
* *
1236 CTTGTCAATGGATATCTTTTGCTTCACGTTTCTCGAGGTAGACATTCAATTATAATATGTTTTAA
66 CTTGTCAATGGATATATTTTGCTTCACGTTTCTCAAGGTAGACATTCAATTATAATATGTTTTAA
1301 TAAAAANNNNNNNNNNTCAATTTTGAGA
131 TAAAAA----------TCAATTTTGAGA
* * * * * *
1329 TTATAAAATCATTTAAAGTGAGTAATAAGGCTTTCGAAGTCATGGGTAACTATAAATGGACTTTT
1 TTATAAAATCATTCAAAGCGAGTAATAAAGCTTTCAAAGGCATAGGTAACTATAAATGGACTTTT
* * *
1394 CTTG-CTAATGGATATATTTT-TTTCAGGTTTTTCAAGGTAGACATTCAATTATAATATGTTTTA
66 CTTGTC-AATGGATATATTTTGCTTCACGTTTCTCAAGGTAGACATTCAATTATAATATGTTTTA
1457 ATAAAAA
130 ATAAAAA
1464 ATATAAAAAA
Statistics
Matches: 119, Mismatches: 15, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
157 47 0.39
158 72 0.61
ACGTcount: A:0.34, C:0.10, G:0.15, T:0.38
Consensus pattern (148 bp):
TTATAAAATCATTCAAAGCGAGTAATAAAGCTTTCAAAGGCATAGGTAACTATAAATGGACTTTT
CTTGTCAATGGATATATTTTGCTTCACGTTTCTCAAGGTAGACATTCAATTATAATATGTTTTAA
TAAAAATCAATTTTGAGA
Found at i:2331 original size:169 final size:169
Alignment explanation
Indices: 1586--2453 Score: 592
Period size: 169 Copynumber: 5.1 Consensus size: 169
1576 NNNATTTAAT
* * * * **
1586 TTAAAATCAATTATGAGATTATAAAAATATTTAAAGTGAGTAATAAGG-TATTTTAAGGCATGGG
1 TTAAAATCAATTACGAGATTATAAAAAAATTTAAAGCGAGTAAAAAGGCT-TTCGAAGGCATGGG
* * ** * * * * * *
1650 CGACTCTAAATATACTTTTCCA-ACAAATGCATATATTTTTCTTCACGTTTCCTAAGGCAGACAT
65 TGACTATAAATGGACTTTT-CATACCAATGGATATCTTTTTCTTCATGTTTCTTAAGGTAGACAT
* * **
1714 TAAATTATTATCTATTTTAGCCAAAAATATAAAAAAATTCAAC
129 TCAATTATTATCTGTTTTAATCAAAAAT-TAAAAAAA-TCAAC
* * *********** * * * **
1757 TTAAAATCAA-TATGTGNNNNNNNNNNCATTTAAAGCGAATAATAAGGCTTTCGAAGGAATGAAT
1 TTAAAATCAATTACGAGATTATAAAAAAATTTAAAGCGAGTAAAAAGGCTTTCGAAGGCATGGGT
* * * * * * ****
1821 GACTATACATGAACTTTTCTTACTAATGGATAT-TTTTTCTTCACGTTT-TCTGAGGTAGANNNN
66 GACTATAAATGGACTTTTCATACCAATGGATATCTTTTTCTTCATGTTTCT-TAAGGTAGACATT
****** * * **
1884 NNNNNNTTATCTATTTTAACCAAAAA-TAAAAAAATTGAC
130 CAATTATTATCTGTTTTAATCAAAAATTAAAAAAATCAAC
* * * *
1923 TTAAAATCAATTATGAGATTATAAAAACATTTAAAGGGAGTGAAAAGGCTTTTGCTGAA-G--TG
1 TTAAAATCAATTACGAGATTATAAAAAAATTTAAAGCGAGTAAAAAGGC-TTT-C-GAAGGCATG
* *********** * *
1985 GGTGACTATAAATGAACTTTTNNNNNNNNNNAATATCTTTTTCTTCATGTTTCCTAAGGTAGATA
63 GGTGACTATAAATGGACTTTTCATACCAATGGATATCTTTTTCTTCATGTTTCTTAAGGTAGACA
* * * **
2050 TTTAATTAATATCCGTTTTAA-CTAACAACGTAAAAAAATTCAAC
128 TTCAATTATTATCTGTTTTAATC-AA-AAATTAAAAAAA-TCAAC
** * * * *
2094 TTAAAATCAATTTTGAGATTATAAAAATATTTAAAGTGAGTAAAAAGGCTTTTGAAGGTATGGGT
1 TTAAAATCAATTACGAGATTATAAAAAAATTTAAAGCGAGTAAAAAGGCTTTCGAAGGCATGGGT
* * * * * *
2159 GACTTTAAATGGACTTTTCTTGCTAATGGATATCTTTTTCCTCACGTTTCTTAAGGTAGACATTC
66 GACTATAAATGGACTTTTCATACCAATGGATATCTTTTTCTTCATGTTTCTTAAGGTAGACATTC
*
2224 AATTATTATATGTTTTAATCAAAAATTAAAAAAATCAAC
131 AATTATTATCTGTTTTAATCAAAAATTAAAAAAATCAAC
* *
2263 TTAAAATCAATTACGAG-TTGATAAAAACAATTT-AAGCGAGTAATAAGGCTTTCGAAGGCATTG
1 TTAAAATCAATTACGAGATT-ATAAAAA-AATTTAAAGCGAGTAAAAAGGCTTTCGAAGGCATGG
* * *
2326 GTGACTATAAATGGACTTTTCATACCAATGGATATCTTTTTCTTCATATTT-TTCTAGGTACACA
64 GTGACTATAAATGGACTTTTCATACCAATGGATATCTTTTTCTTCATGTTTCTT-AAGGTAGACA
*
2390 TTCAATTATTATCTGTTTTAATAAAAAATGTAAAAAAAATCAAC
128 TTCAATTATTATCTGTTTTAATCAAAAAT-T-AAAAAAATCAAC
*
2434 TTAAAATCAATTATGAGATT
1 TTAAAATCAATTACGAGATT
2454 NNNNNNNNNN
Statistics
Matches: 535, Mismatches: 139, Indels: 45
0.74 0.19 0.06
Matches are distributed among these distances:
166 13 0.02
167 56 0.10
168 44 0.08
169 178 0.33
170 85 0.16
171 156 0.29
172 3 0.01
ACGTcount: A:0.37, C:0.11, G:0.13, T:0.35
Consensus pattern (169 bp):
TTAAAATCAATTACGAGATTATAAAAAAATTTAAAGCGAGTAAAAAGGCTTTCGAAGGCATGGGT
GACTATAAATGGACTTTTCATACCAATGGATATCTTTTTCTTCATGTTTCTTAAGGTAGACATTC
AATTATTATCTGTTTTAATCAAAAATTAAAAAAATCAAC
Done.