Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018401916.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_5018.0, 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, 987
Length: 1645
ACGTcount: A:0.37, C:0.12, G:0.14, T:0.35
Warning! 40 characters in sequence are not A, C, G, or T
Found at i:438 original size:168 final size:171
Alignment explanation
Indices: 23--811 Score: 413
Period size: 171 Copynumber: 4.6 Consensus size: 171
13 TTTTTAACCA
* * * * * * *
23 AAAATGTAAAAAAATTCTACTTAAAATCAATTATGAGATTATGAAACTATTTAAACTGAGTAATA
1 AAAATGTAAAAAAATTCAACTGAAAATCAATTATAAAATTATAAAACCATTTAAAGTGAGTAATA
* * *
88 AAGCTTTTGAAGGAATGGGCGACAGT-AAATGGAC-TTTTCTTAAC-AATGAATGCCTTTTTTTT
66 AAGCTTTTGAAGGAATAGGTGA-A-TAAAATAGACTTTTTC-T-ACGAATGAATGCC-TTTTTTT
* * * ** * * * * *
150 TTTACGTTTCTTGAGATAGACATTCAGTTATA-AT-CTGTTTTA-CC
126 TTCACATTCCTCAAGGTAGACATTCAATTACAGATCCT-TCTAATCC
* * * * * **********
194 TAAAAATGTATAAAGAATTCAAACT-AAAATCGATTTTGAGATTATAAAACCANNNNNNNNNNGT
1 --AAAATGTA-AAAAAATTC-AACTGAAAATCAATTATAAAATTATAAAACCATTTAAAGTGAGT
* * *
258 AATAAGGCTTTTGAAGGAATAGGTG-ATGACAAATGGAC-TTTTCTTAC-CATGAATG-CTTTTT
62 AATAAAGCTTTTGAAGGAATAGGTGAAT-A-AAATAGACTTTTTC-TACGAATGAATGCCTTTTT
*
319 TTTT-ATC-TCTCCT-AAGGTAGACATTCAATTATA-ATCCGTTCTAAT-C
124 TTTTCA-CAT-TCCTCAAGGTAGACATTCAATTACAGATCC-TTCTAATCC
* * *
365 AAAA-GTATAAAAACTTCAATCT-AAAATCAATTATAAAATTATAAAGCCATTTAATGTGAGTAA
1 AAAATGTA-AAAAAATTCAA-CTGAAAATCAATTATAAAATTATAAAACCATTTAAAGTGAGTAA
* * *
428 TAAAGCTTTTGAAGGAATGGGTGAATATAATAGACTTTTTCTGCGAATGAATGCCTTTTTTTTTC
64 TAAAGCTTTTGAAGGAATAGGTGAATAAAATAGACTTTTTCTACGAATGAATGCCTTTTTTTTTC
* * * *
493 ACATTTCTCAAGGTAGACATTCAATTACAGTTTCTTTTAATCC
129 ACATTCCTCAAGGTAGACATTCAATTACAGATCCTTCTAATCC
* * ******
536 AAAATGTAAAAAAATTCAACTGAAAATCAATTATGACATTATAAAACCATTTAAAGTGANNNNNN
1 AAAATGTAAAAAAATTCAACTGAAAATCAATTATAAAATTATAAAACCATTTAAAGTGAGTAATA
**** * *
601 NNNNTTTTGAAGGAATAGGTGACTATAAAT-GAAC-TTTTCTTATCG-ATAAATG-CTTTTTTTT
66 AAGCTTTTGAAGGAATAGGTGAATA-AAATAG-ACTTTTTC-TA-CGAATGAATGCCTTTTTTTT
* * * * * * * *
662 TCACGTTTCTCTAGATAGACATTCAATTATA-AT-ATGTTTAAATCA
127 TCACATTCCTCAAGGTAGACATTCAATTACAGATCCT-TCT-AATCC
* * * * * * * *
707 AAAATGTGCAAAGAATCCAACTTAAAATTAATGT-TGAGATTATAAAACCATTTAAACTGAGTAA
1 AAAATGT-AAAAAAATTCAACTGAAAATCAAT-TATAAAATTATAAAACCATTTAAAGTGAGTAA
* * * *
771 TAAGGCTTTTGAAAGAATGGGTGACTATAAATAGACTTTTT
64 TAAAGCTTTTGAAGGAATAGGTGAATA-AAATAGACTTTTT
812 TGTCAATGGA
Statistics
Matches: 484, Mismatches: 100, Indels: 64
0.75 0.15 0.10
Matches are distributed among these distances:
167 10 0.02
168 73 0.15
169 21 0.04
170 54 0.11
171 141 0.29
172 87 0.18
173 25 0.05
174 70 0.14
175 3 0.01
ACGTcount: A:0.37, C:0.12, G:0.13, T:0.35
Consensus pattern (171 bp):
AAAATGTAAAAAAATTCAACTGAAAATCAATTATAAAATTATAAAACCATTTAAAGTGAGTAATA
AAGCTTTTGAAGGAATAGGTGAATAAAATAGACTTTTTCTACGAATGAATGCCTTTTTTTTTCAC
ATTCCTCAAGGTAGACATTCAATTACAGATCCTTCTAATCC
Found at i:941 original size:170 final size:169
Alignment explanation
Indices: 386--1206 Score: 511
Period size: 171 Copynumber: 4.8 Consensus size: 169
376 AACTTCAATC
* * * * * * * *
386 TAAAATCAATTATAAAATTATAAAGCCATTTAATGTGAGTAATAAAGCTTTTGAAGGAATGGGTG
1 TAAAATTAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAAGAATGGGTG
* * * ** * * *
451 AATAT-AATAGACTTTT-TCTGCGAATGAATGCCTTTTTTTTTCACATTTCTCAAGGT-AGACAT
66 ACTATAAATAGACTTTTCT-TTC-AATGAATGCC-TTTTTCTTCATGTTTATCGAGGTAAG-CAA
* * * * ** ** *
513 TCAATTACAGTTTCTTTTAATCCAAAATGTAAAAAAATTCAACT
127 TCAATTATAATCTATTTTAATAGAAAAAATAAAAAAA-TCAAAT
* * * * ********** * *
557 GAAAATCAATTATGACATTATAAAACCATTTAAAGTGANNNNNNNNNNTTTTGAAGGAATAGGTG
1 TAAAATTAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAAGAATGGGTG
* * * * * * * * *
622 ACTATAAAT-GAACTTTTCTTATCGATAAATGCTTTTTTTTTCACGTTTCTCTAGAT-AGACATT
66 ACTATAAATAG-ACTTTTCTT-TCAATGAATGCCTTTTTCTTCATGTTTATCGAGGTAAG-CAAT
* * * ** * * *
685 CAATTATAATATGTTTAAATCA-AAAATGTGCAAAGAATCCAACT
128 CAATTATAATCTATTTTAAT-AGAAAAAAT-AAAAAAAT-CAAAT
729 TAAAATTAATGT-TGAGATTATAAAACCATTTAAA-CTGAGTAATAAGGCTTTTGAAAGAATGGG
1 TAAAATTAAT-TATGAGATTATAAAACCATTTAAAGC-GAGTAATAAGGCTTTTGAAAGAATGGG
* * **
792 TGACTATAAATAGACTTTT-TTGTCAATGGATGCCTTTGTCTTCATGTTTATCGAGGTGGGCAAT
64 TGACTATAAATAGACTTTTCTT-TCAATGAATGCCTTTTTCTTCATGTTTATCGAGGTAAGCAAT
* * *
856 CAATTATAATCTGTTTTCACTA-AAAAAATAAAAAAATTGAAAT
128 CAATTATAATCTATTTT-AATAGAAAAAATAAAAAAA-TCAAAT
* * * * * *
899 TAAAATCAATTATGAGATAATAAAACCTTTTAAAGCGAGTAATAACGCATTTGAAGGAATGGGAT
1 TAAAATTAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAAGAATGGG-T
* * * * * * *
964 -ACTATAAAT-GAAGTTTTCTTCCAAATGAATGGCTTTTTCTACATGTTTCTTGAGGTAAGCATT
65 GACTATAAATAG-ACTTTTCTTTC-AATGAATGCCTTTTTCTTCATGTTTATCGAGGTAAGCAAT
* * *
1027 CAATTATACTCTATTTTAATAGAAAATATAAAAAAATCAACT
128 CAATTATAATCTATTTTAATAGAAAAAATAAAAAAATCAAAT
* ** *
1069 TAAAATTAATGATGAGATTATAAAACCATTTAAAGAAAGTAATAAGGCTTTTG-AAGAAATGTGT
1 TAAAATTAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAAG-AATGGGT
* * * * * *
1133 GGCTATAACTAAACTTTTCTTTCCAATGAATGCCTTTTTCTTTA-GCTTTCTCGAGGT-AGAAAT
65 GACTATAAATAGACTTTTCTTT-CAATGAATGCCTTTTTCTTCATG-TTTATCGAGGTAAGCAA-
1196 TCAATTATAAT
127 TCAATTATAAT
1207 ATGTTATAAC
Statistics
Matches: 509, Mismatches: 115, Indels: 53
0.75 0.17 0.08
Matches are distributed among these distances:
169 9 0.02
170 185 0.36
171 220 0.43
172 91 0.18
173 4 0.01
ACGTcount: A:0.38, C:0.11, G:0.14, T:0.35
Consensus pattern (169 bp):
TAAAATTAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAAGAATGGGTG
ACTATAAATAGACTTTTCTTTCAATGAATGCCTTTTTCTTCATGTTTATCGAGGTAAGCAATCAA
TTATAATCTATTTTAATAGAAAAAATAAAAAAATCAAAT
Found at i:1404 original size:342 final size:339
Alignment explanation
Indices: 256--1418 Score: 827
Period size: 342 Copynumber: 3.4 Consensus size: 339
246 NNNNNNNNNN
* * * *
256 GTAATAAGGCTTTTGAAGGAATAGGTGA-TGACAAATGGACTTTTCTTACC-ATGAATGCTTTTT
1 GTAATAACGCTTTTGAAGGAATGGGTGACT-ATAAATGAACTTTTCTT-CCAATGAATGCTTTTT
* ** * * * * * * **
319 TTTTA--TCTCTCCTAAGGTAGACATTCAATTATAATCCGTTCTAATCAAAAGTAT-AAAAACTT
64 CTACACGTTTCT-C-GAGGTAGACATTCAATTATAATCTGTTTTAATCAAAAATGTGAAAAAAAT
* * * * * **** * *
381 CAA-TCTAAAATCAATTATAAAATTATAAAGCCATTTAATGTGAGTAATAAAGCTTTTGAAGGAA
127 CAACT-TAAAATTAATGATGAGATTATAAAACCATTTAAACAAAGTAATAAGGCTTTTGAAAGAA
* * * * ** * *
445 TGGGTGAATAT-AATAGACTTTTTCTG-CGAATGAATGCCTTTTTTTTTCACATTTCTCAAGGT-
191 TGGGTGACTATAAATAAACTTTTT-TGTC-AATGAATGCC-TTTGTCTTCATGTTTATCGAGGTG
* * * * * * ** * *
507 AGACATTCAATTACAGTTTCTTTTAATCC-AAAATGTAAAAAAATTCAACTGAAAATCAATTATG
253 AGA-AATCAATTATAATATGTTATAA-CCAAAAAAATAAAAAAATTCAAATTAAAATCAATTATG
* * * *
571 ACATTATAAAACCATTTAAAGTGA
316 AGATAATAAAACCTTTTAAAGCGA
********** * * * *
595 NNNNNNNNNNTTTTGAAGGAATAGGTGACTATAAATGAACTTTTCTTATCGATAAATGCTTTTTT
1 GTAATAACGCTTTTGAAGGAATGGGTGACTATAAATGAACTTTTCTT-CCAATGAATGC-TTTTT
* * * * * * * *
660 TTTCACGTTTCTCTAGATAGACATTCAATTATAATATGTTTAAATCAAAAATGTGCAAAGAATCC
64 CTACACGTTTCTCGAGGTAGACATTCAATTATAATCTGTTTTAATCAAAAATGTGAAAAAAAT-C
* **
725 AACTTAAAATTAATGTTGAGATTATAAAACCATTTAAACTGAGTAATAAGGCTTTTGAAAGAATG
128 AACTTAAAATTAATGATGAGATTATAAAACCATTTAAACAAAGTAATAAGGCTTTTGAAAGAATG
* * * *
790 GGTGACTATAAATAGACTTTTTTGTCAATGGATGCCTTTGTCTTCATGTTTATCGAGGTGGGCAA
193 GGTGACTATAAATAAACTTTTTTGTCAATGAATGCCTTTGTCTTCATGTTTATCGAGGTGAGAAA
* * * * *
855 TCAATTATAATCTGTTTTCACTAAAAAAATAAAAAAATTGAAATTAAAATCAATTATGAGATAAT
258 TCAATTATAATATGTTATAACCAAAAAAATAAAAAAATTCAAATTAAAATCAATTATGAGATAAT
920 AAAACCTTTTAAAGCGA
323 AAAACCTTTTAAAGCGA
* *
937 GTAATAACGCATTTGAAGGAATGGGAT-ACTATAAATGAAGTTTTCTTCCAAATGAATGGCTTTT
1 GTAATAACGCTTTTGAAGGAATGGG-TGACTATAAATGAACTTTTCTTCC-AATGAAT-GCTTTT
* * * * *
1001 TCTACATGTTTCTTGAGGTA-AGCATTCAATTATACTCTATTTTAAT-AGAAAATAT-AAAAAAA
63 TCTACACGTTTCTCGAGGTAGA-CATTCAATTATAATCTGTTTTAATCA-AAAATGTGAAAAAAA
*
1063 TCAACTTAAAATTAATGATGAGATTATAAAACCATTTAAAGAAAGTAATAAGGCTTTTG-AAGAA
126 TCAACTTAAAATTAATGATGAGATTATAAAACCATTTAAACAAAGTAATAAGGCTTTTGAAAG-A
* * * * * *
1127 ATGTGTGGCTATAACTAAACTTTTCTT-TCCAATGAATGCCTTTTTCTTTA-GCTTTCTCGAGGT
190 ATGGGTGACTATAAATAAACTTTT-TTGT-CAATGAATGCCTTTGTCTTCATG-TTTATCGAGGT
** * * * *
1190 -AGAAATTCAATTATAATATGTTATAACCAAAAATGTACAAAGAATTCAACTTATAATCAATTTT
252 GAGAAA-TCAATTATAATATGTTATAACCAAAAAAATA-AAAAAATTCAAATTAAAATCAATTAT
* * *
1254 TAGATTATAAAA-CTATTTAAAGCGN
315 GAGATAATAAAACCT-TTTAAAGCGA
********* * * *
1279 NNNNNNNNNCTTTTGAAGGAGTGGGTGACTATAAATGGACTTTTTTTGCCAATGAATGTCTTTTT
1 GTAATAACGCTTTTGAAGGAATGGGTGACTATAAATGAACTTTTCTT-CCAATGAATG-CTTTTT
* * * *
1344 CTACACATTTCTCGAGGTAGACATTCAACTATAAGCTGTTTTAA-CCAAAATGTGAAAAAAAATT
64 CTACACGTTTCTCGAGGTAGACATTCAATTATAATCTGTTTTAATCAAAAATGTG-AAAAAAA-T
*
1408 GAACTTAAAAT
127 CAACTTAAAAT
1419 CAATTTTGAN
Statistics
Matches: 647, Mismatches: 145, Indels: 59
0.76 0.17 0.07
Matches are distributed among these distances:
339 38 0.06
340 88 0.14
341 117 0.18
342 288 0.45
343 91 0.14
344 25 0.04
ACGTcount: A:0.37, C:0.12, G:0.14, T:0.35
Consensus pattern (339 bp):
GTAATAACGCTTTTGAAGGAATGGGTGACTATAAATGAACTTTTCTTCCAATGAATGCTTTTTCT
ACACGTTTCTCGAGGTAGACATTCAATTATAATCTGTTTTAATCAAAAATGTGAAAAAAATCAAC
TTAAAATTAATGATGAGATTATAAAACCATTTAAACAAAGTAATAAGGCTTTTGAAAGAATGGGT
GACTATAAATAAACTTTTTTGTCAATGAATGCCTTTGTCTTCATGTTTATCGAGGTGAGAAATCA
ATTATAATATGTTATAACCAAAAAAATAAAAAAATTCAAATTAAAATCAATTATGAGATAATAAA
ACCTTTTAAAGCGA
Done.