Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018399915.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_3148.0, 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: 3133
ACGTcount: A:0.33, C:0.11, G:0.11, T:0.30
Warning! 462 characters in sequence are not A, C, G, or T
Found at i:634 original size:169 final size:170
Alignment explanation
Indices: 459--767 Score: 415
Period size: 171 Copynumber: 1.8 Consensus size: 170
449 TTCCCTAGGC
* * * *
459 AAACATTTAATTATAATATTTTTTAACAAAAAATGTAAA-AACATTCAACTTAAAATCAATTATT
1 AAACATTTAAATATAATATGTTTTAACAAAAAATGTAAAGAA-ATACAACTTAAAATCAATTATG
* * * **
523 AGATGAT-AACCATTTAAAGTGAGTAATAAAGCTTTCAAATGTATGGGTGACTATAAAAGAACTT
65 ACATGATAAACCATTTAAAGCGAGTAATAAAGCTTTCAAATGCATCAGTGACTATAAAAGAACTT
587 TTCTTGCTAATGAATGGTTTTTTCTTCTCGTTTTCAGAGGT
130 TTCTTGCTAATGAATGGTTTTTTCTTCTCGTTTTCAGAGGT
* * * * *
628 AAACATTTAAATATCATCTGTTTTAAGAAAAAATGTAAAGAAATACAACTTAAATTTAATTATGA
1 AAACATTTAAATATAATATGTTTTAACAAAAAATGTAAAGAAATACAACTTAAAATCAATTATGA
* * * * *
693 CATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTCGAATGCATCAGTGACTATAAATGGACTT
66 CATGAT-AAACCATTTAAAGCGAGTAATAAAGCTTTCAAATGCATCAGTGACTATAAAAGAACTT
758 TTCTTGCTAA
130 TTCTTGCTAA
768 NNNNNNNNNN
Statistics
Matches: 118, Mismatches: 19, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
169 57 0.48
170 2 0.02
171 59 0.50
ACGTcount: A:0.41, C:0.11, G:0.12, T:0.36
Consensus pattern (170 bp):
AAACATTTAAATATAATATGTTTTAACAAAAAATGTAAAGAAATACAACTTAAAATCAATTATGA
CATGATAAACCATTTAAAGCGAGTAATAAAGCTTTCAAATGCATCAGTGACTATAAAAGAACTTT
TCTTGCTAATGAATGGTTTTTTCTTCTCGTTTTCAGAGGT
Found at i:1446 original size:170 final size:171
Alignment explanation
Indices: 1255--2332 Score: 492
Period size: 171 Copynumber: 6.3 Consensus size: 171
1245 ACGGATGGGT
* * *
1255 GACTATAGATGAACTTTTCTTGACAATGAATGGCCTTTTCTTTACGTTTCCCAATGTAGACATTC
1 GACTATAGATGAACATTTCTTGACAATGAATGGCATTTTCTTCACGTTTCCCAATGTAGACATTC
* * *
1320 AAATATTATCAGTTTTAA-TCAAAAATATAAAAAAA-TCAACTCAAAATCAATTACGAGATTATA
66 AAATATTATCAGTTTTAACT-AAAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGATTATA
** *** * * *
1383 AAACCATTTGCAGTGAGTAAT-AAGATTTTTGAAGACTTAAGC
130 AAACCATTTAAAACAACTAATAAAG-TTTTCGAAGACATAAGC
* * * ** * * * * *
1425 GACTATAAATGAACATTTCTTGTCAA-CAGATAACTTTTTCTTCACGTTTCTCAAGGAAGGCATT
1 GACTATAGATGAACATTTCTTGACAATGA-ATGGCATTTTCTTCACGTTTCCCAATGTAGACATT
* * * * *
1489 CTATTATAATACA-TTTTAACTAAAAATTGTAAAAAAATTTAACTTAAAATCAATTATGTGATTA
65 CAAATATTAT-CAGTTTTAACTAAAAA-TGTAAAAAAATTCAACTTAAAATCAATTATGAGATTA
** * * *
1553 TAAAACTGTTTAAAACAACTAATAAAGTTTTCGAAGGCATGAGT
128 TAAAACCATTTAAAACAACTAATAAAGTTTTCGAAGACATAAGC
* * *
1597 GACTATAGATG-GCTATTTCTT-ATCAATGAATGAG-ATTTGCTTCACTTTTCCCAATGTAGACA
1 GACTATAGATGAAC-ATTTCTTGA-CAATGAATG-GCATTTTCTTCACGTTTCCCAATGTAGACA
* * *
1659 ATCAAATATTATCAGTTTTAACTAAAAATGTAAAAAAATTCAACTTAAAATCAATTATGAAATGA
63 TTCAAATATTATCAGTTTTAACTAAAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGATTA
*********** * * * * ** * *
1724 TAAAACNNNNNNNNNNGAGTAATAAGGCTTTCAAAGATTTGAGT
128 TAAAACCATTTAAAACAACTAATAAAGTTTTCGAAGACATAAGC
* * * * * ** * ** *** * * *
1768 GACTATAAATGGACTTTTCTTGCCAATGGATAAC-TCTTGCTTCATATTTCTTGA-GGAAAGTAT
1 GACTATAGATGAACATTTCTTGACAATGAATGGCAT-TTTCTTCACGTTTCCCAATGTAGA-CAT
* * * * * * * *
1831 TCTATTATCATAT-A-TTTTAACAAAAAATGTAAAACAATTTAGCTTAAAACCAATCATGAGATT
64 TCAAATAT--TATCAGTTTTAACTAAAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGATT
* * * * *** * *
1894 ATAAAACCATTTAAAGCGACTAATAAGGCTTTCGAAGGTGTGAGT
127 ATAAAACCATTTAAAACAACTAATAAAGTTTTCGAAGACATAAGC
* * * * * *
1939 GACTATAGAT-AGACTTTTC-TCATCAATGGATGGCTTTTTCTTCATGTTTTCCAATGTAGACAT
1 GACTATAGATGA-ACATTTCTTGA-CAATGAATGGCATTTTCTTCACGTTTCCCAATGTAGACAT
* * * ********** *
2002 TCAAATATTATCTGTTGTGA-TAAAAATGTAAAAAAATTCAACTTNNNNNNNNNNATAAGATTAT
64 TCAAATATTATCAGTTTTAACTAAAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGATTAT
* * * * *
2066 AAAACCATTTAAAGCAAGTAATAAGGCTTTCGAAGACTTAAGC
129 AAAACCATTTAAAACAACTAATAAAGTTTTCGAAGACATAAGC
* * * ** * *
2109 GACTATA-AGTGGACGTTT-TT-ATCAATGGATAAC-TTTTGCTTCACGTTTCCCAAGGTAGACT
1 GACTATAGA-TGAACATTTCTTGA-CAATGAATGGCATTTT-CTTCACGTTTCCCAATGTAGACA
* * * * * * *
2170 TTCAATTACAATAT-A-TTGTAAC-AAACAAAGCAAAACAATTCAACTTAAAATCTATTATGAGA
63 TTCAA--ATATTATCAGTTTTAACTAAA-AATGTAAAAAAATTCAACTTAAAATCAATTATGAGA
* * * * * * * * * *
2232 TTAAAAAACTATTCAAAGCAAGTAATAAGGCTTTCGAAGGCATGAGT
125 TTATAAAACCATTTAAAACAACTAATAAAGTTTTCGAAGACATAAGC
* * * * *
2279 GACTATAGAT-AGCCTTTTCTTGACAATGAATAGCTTTTTCTTCATGTTTCCCAA
1 GACTATAGATGA-ACATTTCTTGACAATGAATGGCATTTTCTTCACGTTTCCCAA
2333 AGTAANNNNN
Statistics
Matches: 678, Mismatches: 193, Indels: 73
0.72 0.20 0.08
Matches are distributed among these distances:
168 4 0.01
169 48 0.07
170 226 0.33
171 269 0.40
172 124 0.18
173 7 0.01
ACGTcount: A:0.38, C:0.14, G:0.13, T:0.33
Consensus pattern (171 bp):
GACTATAGATGAACATTTCTTGACAATGAATGGCATTTTCTTCACGTTTCCCAATGTAGACATTC
AAATATTATCAGTTTTAACTAAAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGATTATAA
AACCATTTAAAACAACTAATAAAGTTTTCGAAGACATAAGC
Found at i:1601 original size:342 final size:342
Alignment explanation
Indices: 176--2332 Score: 1147
Period size: 342 Copynumber: 6.3 Consensus size: 342
166 NNNNNNNNNN
* * * * * * * * * * *
176 TATGAGATTATAAAACCATTTAAAACGAGTAATACGGCCTTCGAAGACTTAAGTGACTATAAATG
1 TATGAGATTATAAAACTATTTAAAGCAACTAATAAGGCTTTCGAAGGCATGAGTGACTATAGATA
* * * * * * * * * *
241 GACTTTTCTTG-CCAATGGATGACTTTTAT-TTCATGTTTTCTAAGGCAGACATTCAATTACAAT
66 GACTTTTCTTGATCAATGAATGGCTTTT-TCTTCACGTTTCCCAATGTAGACATTCAA--ATATT
** * * * * *
304 AT-A-TTTTAAGAAAAAAATATATAAAAATTTAACTTAAAATGAATTACGAGATTATAAAACCAT
128 ATCAGTTTTAA-TCAAAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCAT
* ********** * *
367 TTAAAACGANNNNNNNNNNTTTCAAAGACTTAAGCGACTATAAATGGAC-TTCTCTCT-CCAATG
192 TTAAAGCGAGTAATAAGGCTTTCGAAGACTTAAGCGACTATAAATGGACATT-TCT-TGTCAATG
* * * * *
430 GATAACTTTTGCTTCATGTTTCCCTAGGCAA-ACATT-TAATTATAATATTTTTTAACAAAAAAT
255 GATAACTTTTGCTTCACGTTTCTCAAGG-AAGGCATTCT-ATTATAATATATTTTAAC-AAAAAT
*
493 GTAAAA-ACATTCAACTTAAAATCAAT
317 GTAAAACA-ATTTAACTTAAAATCAAT
* * * ** * * * * * * *
519 TATTAGATGAT--AACCATTTAAAGTGAGTAATAAAGCTTTCAAATGTATGGGTGACTATA-AAA
1 TATGAGATTATAAAACTATTTAAAGCAACTAATAAGGCTTTCGAAGGCATGAGTGACTATAGATA
* * * * * * * *
581 GAACTTTTCTTGCT-AATGAATGGTTTTTTCTTCTCGTTT-TCAGAGGTAAACATTTAAATATCA
66 G-ACTTTTCTTGATCAATGAATGGCTTTTTCTTCACGTTTCCCA-ATGTAGACATTCAAATATTA
* ** * * * * *
644 TCTGTTTTAAGAAAAAATGTAAAGAAATACAACTTAAATTTAATTATGACATTATAAAACCATTT
129 TCAGTTTTAATCAAAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTT
* * * * ***
709 AAAGCGAGTAATAAGGCTTTCGAATG-CATCAGTGACTATAAATGGACTTTTCTTG-CTAANNNN
194 AAAGCGAGTAATAAGGCTTTCGAA-GACTTAAGCGACTATAAATGGACATTTCTTGTC-AA-TGG
****** * ** * * * * * * * * * *
772 NNNNNNTTT-CTTCATGTTTCTTGATGTAGACATTCAAATATTATCTTTTTTAATAGAAAATATA
256 ATAACTTTTGCTTCACGTTTCTCAAGGAAGGCATTCTATTATAATATATTTTAACA-AAAATGTA
* * *
836 AAAAAATTCAACTTAAAATTAAT
320 AAACAATTTAACTTAAAATCAAT
********** * ** * *
859 NNNNNNNNNNTAAAACGATTTAAAGTGAGTAAT-AGGACTTTCGAAGGCATGGGTGACTATAGAT
1 TATGAGATTATAAAACTATTTAAAGCAACTAATAAGG-CTTTCGAAGGCATGAGTGACTATAGAT
* * * ** * * * *
923 GGACTTTTCTT-ATCAATGAATGACTTTTTCTTTATATTTTCCAAAGTAAACATTTAAATATTAT
65 AGACTTTTCTTGATCAATGAATGGCTTTTTCTTCACGTTTCCCAATGTAGACATTCAAATATTAT
** * * * **********
987 TTGTTTTAACCAAAAATATAAAAAAATTCAACTTAAAATTAATTNNNNNNNNNNAAAACCATTTA
130 CAGTTTTAATCAAAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTA
* * * * *
1052 AAGCGAGTAATAAGGCTTTTGAAGACTTAAGTGAATATAAATAGACTTTTCTTGTCAATGGATAA
195 AAGCGAGTAATAAGGCTTTCGAAGACTTAAGCGACTATAAATGGACATTTCTTGTCAATGGATAA
* * * * * * **
1117 CTTTTGCTTCACATTTCCCATGGCAA-ACTTTCAATTATAATATATTTTAACAAAAAATACAAAA
260 CTTTTGCTTCACGTTTCTCAAGG-AAGGCATTCTATTATAATATATTTTAAC-AAAAATGTAAAA
* ************
1181 CAATTCAANNNNNNNNNNNN
323 CAATTTAACTTAAAATCAAT
***************************** * *
1201 NNNNNNNNNNNNNNNNNNNNNNNNNNNNNTAATAAGGCTTTTGAACGG-ATGGGTGACTATAGAT
1 TATGAGATTATAAAACTATTTAAAGCAACTAATAAGGCTTTCGAA-GGCATGAGTGACTATAGAT
* *
1265 -GAACTTTTCTTGA-CAATGAATGGCCTTTTCTTTACGTTTCCCAATGTAGACATTCAAATATTA
65 AG-ACTTTTCTTGATCAATGAATGGCTTTTTCTTCACGTTTCCCAATGTAGACATTCAAATATTA
* * *
1328 TCAGTTTTAATCAAAAATATAAAAAAA-TCAACTCAAAATCAATTACGAGATTATAAAACCATTT
129 TCAGTTTTAATCAAAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTT
** * ** * * **
1392 GCAGTGAGTAATAAGATTTTTGAAGACTTAAGCGACTATAAATGAACATTTCTTGTCAACAGATA
194 AAAGCGAGTAATAAGGCTTTCGAAGACTTAAGCGACTATAAATGGACATTTCTTGTCAATGGATA
* *
1457 ACTTTTTCTTCACGTTTCTCAAGGAAGGCATTCTATTATAATACATTTTAACTAAAAATTGTAAA
259 ACTTTTGCTTCACGTTTCTCAAGGAAGGCATTCTATTATAATATATTTTAAC-AAAAA-TGTAAA
*
1522 AAAATTTAACTTAAAATCAAT
322 ACAATTTAACTTAAAATCAAT
* * * * *
1543 TATGTGATTATAAAACTGTTTAAAACAACTAATAAAGTTTTCGAAGGCATGAGTGACTATAGAT-
1 TATGAGATTATAAAACTATTTAAAGCAACTAATAAGGCTTTCGAAGGCATGAGTGACTATAGATA
* * * * *
1607 GGCTATTTCTT-ATCAATGAATGAG-ATTTGCTTCACTTTTCCCAATGTAGACAATCAAATATTA
66 GACT-TTTCTTGATCAATGAATG-GCTTTTTCTTCACGTTTCCCAATGTAGACATTCAAATATTA
* * ****
1670 TCAGTTTTAA-CTAAAAATGTAAAAAAATTCAACTTAAAATCAATTATGAAATGATAAAACNNNN
129 TCAGTTTTAATC-AAAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATT
****** * * * * * *
1734 NNNNNNGAGTAATAAGGCTTTCAAAGATTTGAGTGACTATAAATGGACTTTTCTTGCCAATGGAT
193 TAAAGCGAGTAATAAGGCTTTCGAAGACTTAAGCGACTATAAATGGACATTTCTTGTCAATGGAT
* ** ** * * *
1799 AACTCTTGCTTCATATTTCTTGAGGAAAGTATTCTATTATCATATATTTTAACAAAAAATGTAAA
258 AACTTTTGCTTCACGTTTCTCAAGGAAGGCATTCTATTATAATATATTTTAAC-AAAAATGTAAA
* *
1864 ACAATTTAGCTTAAAACCAAT
322 ACAATTTAACTTAAAATCAAT
* * * **
1885 CATGAGATTATAAAACCATTTAAAGCGACTAATAAGGCTTTCGAAGGTGTGAGTGACTATAGATA
1 TATGAGATTATAAAACTATTTAAAGCAACTAATAAGGCTTTCGAAGGCATGAGTGACTATAGATA
* * * *
1950 GACTTTTC-TCATCAATGGATGGCTTTTTCTTCATGTTTTCCAATGTAGACATTCAAATATTATC
66 GACTTTTCTTGATCAATGAATGGCTTTTTCTTCACGTTTCCCAATGTAGACATTCAAATATTATC
* * * ********** *
2014 TGTTGTGAT-AAAAATGTAAAAAAATTCAACTTNNNNNNNNNNATAAGATTATAAAACCATTTAA
131 AGTTTTAATCAAAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAA
* * * *
2078 AGCAAGTAATAAGGCTTTCGAAGACTTAAGCGACTATAAGTGGACGTTT-TTATCAATGGATAAC
196 AGCGAGTAATAAGGCTTTCGAAGACTTAAGCGACTATAAATGGACATTTCTTGTCAATGGATAAC
* * * * * * * * *
2142 TTTTGCTTCACGTTTCCCAAGGTAGACTTTCAATTACAATATATTGTAACAAACAAAGCAAAACA
261 TTTTGCTTCACGTTTCTCAAGGAAGGCATTCTATTATAATATATTTTAACAAA-AATGTAAAACA
* *
2207 ATTCAACTTAAAATCTAT
325 ATTTAACTTAAAATCAAT
* * *
2225 TATGAGATTAAAAAACTATTCAAAGCAAGTAATAAGGCTTTCGAAGGCATGAGTGACTATAGATA
1 TATGAGATTATAAAACTATTTAAAGCAACTAATAAGGCTTTCGAAGGCATGAGTGACTATAGATA
* * *
2290 GCCTTTTCTTGA-CAATGAATAGCTTTTTCTTCATGTTTCCCAA
66 GACTTTTCTTGATCAATGAATGGCTTTTTCTTCACGTTTCCCAA
2333 AGTAANNNNN
Statistics
Matches: 1360, Mismatches: 410, Indels: 91
0.73 0.22 0.05
Matches are distributed among these distances:
339 11 0.01
340 309 0.23
341 304 0.22
342 587 0.43
343 149 0.11
ACGTcount: A:0.37, C:0.13, G:0.12, T:0.33
Consensus pattern (342 bp):
TATGAGATTATAAAACTATTTAAAGCAACTAATAAGGCTTTCGAAGGCATGAGTGACTATAGATA
GACTTTTCTTGATCAATGAATGGCTTTTTCTTCACGTTTCCCAATGTAGACATTCAAATATTATC
AGTTTTAATCAAAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAA
AGCGAGTAATAAGGCTTTCGAAGACTTAAGCGACTATAAATGGACATTTCTTGTCAATGGATAAC
TTTTGCTTCACGTTTCTCAAGGAAGGCATTCTATTATAATATATTTTAACAAAAATGTAAAACAA
TTTAACTTAAAATCAAT
Done.