Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018398920.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_2201.0, 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, 721
Length: 1203
ACGTcount: A:0.39, C:0.11, G:0.13, T:0.36
Warning! 10 characters in sequence are not A, C, G, or T
Found at i:341 original size:171 final size:169
Alignment explanation
Indices: 1--1203 Score: 949
Period size: 171 Copynumber: 7.0 Consensus size: 169
* * * * *
1 AAAAAAAATTGAACCTGAAATCAATTTTGAGATTATAAAACCATTTAAAGCGAGAAATAAAGCTT
1 AAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAAGCTT
* * ********** *
66 TTGAAGGAATGGGTGACTATAAATGGATTTTTTTTGCCAATNNNNNNNNNNTTCTTCATGTTTCT
66 TTGAAGGAATGGGTGACTATAAATGGACTTTTCTT-CCAATGAATGACTTTTTCTACAT-TTTCT
* * *
131 CAAGG-TAGACATTCAATTAT-TGCCTGTTTTTATAAAAAATGT
129 CAAGGCAAG-CATTCAATTATAT--CTATTTTAATAAAAAATGT
* * * *
173 ATAAATAA-TCAACTGAAAATCAATTATGTGATTATAAAACCATTTAAAGCGAGTAATAAAGCTT
1 AAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAAGCTT
* * *
237 TTGAAGGAATGGGTGATTATAAATGGACTTTTCTTCTTAATGAATGACTTTTTCTACATGTTTCC
66 TTGAAGGAATGGGTGACTATAAATGGACTTTTCTTC-CAATGAATGACTTTTTCTACAT-TTTCT
* *
302 CAAGGCAAGCATTTAATTATATCTATTTTAATAAAAAAATAT
129 CAAGGCAAGCATTCAATTATATCTATTTTAAT-AAAAAATGT
* * * *
344 AAAAACAATT-AACTTAAAATTAATTATGAGATTATAAAACCATTTAAAGTGAGTAAT-AAGTTG
1 AAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAAGCT-
* * ** *
407 TTTTAAGGAAT-GATAGACTATAAATAGG-CTTTTCTTCCAAAAAAATGGGCTTCTCTTCT-CAT
65 TTTGAAGGAATGGGT-GACTATAAAT-GGACTTTTCTTCC-AATGAAT-GACTT-T-TTCTACAT
* * * *
469 TTTC-CTAGGCAAGCAGTCAATTATGGTCTATTTTAACAAAAAA--T
124 TTTCTCAAGGCAAGCATTCAATTAT-ATCTATTTTAATAAAAAATGT
* * *
513 ATAAAAAATTCAACTT-AAATCAATTATGAGATTATAAAACTATTTAACGCGAGTAAT-AAGTCT
1 AAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAAG-CT
***** * * * * *
576 TTTGAAGGAATAAAACAATATAAATGGGCTTTGCTTGCTAATGAAT-ACTTTTTTCTTCACTTTT
65 TTTGAAGGAATGGGTGACTATAAATGGACTTTTCTT-CCAATGAATGAC-TTTTTCTACA-TTTT
** * ** *
640 CTTGAGGTCGA-CATTCAATTATAGTCTATTTTAACCAAAAATAT
127 CTCAAGG-CAAGCATTCAATTATA-TCTATTTTAATAAAAAATGT
* * * *
684 -AAAATAATTCAACTTAAAATCAATTATGATATTATAAAACCATTTAAAGTGAGTAATAAGGCTT
1 AAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAAGCTT
* * * * * * * *
748 TTAAAGGAATGGGTGATTATAAATTGACTTTTTTTCTAAATTAATGGCTTTTTTTGTAC-TTTTC
66 TTGAAGGAATGGGTGACTATAAATGGACTTTTCTTC-CAATGAATGAC--TTTTTCTACATTTTC
** * * * * * *
812 TTGACGTAGGCATTCAATTATAGTCTATTTTAATGAGAAAGGT
128 TCAAGGCAAGCATTCAATTATA-TCTATTTTAATAAAAAATGT
* * * * *
855 AAAAAAAATTCAACTTTAAATCAATTACGAAATTATAAAACCATTTAAAGCGATTAATAAGGCTT
1 AAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAAGCTT
* * * * * *
920 TTGAAAGAATGGGTGACAATGAATGGACTTTTCTTCTCAATGAAT-AGCTTTTTCTATAGGTTTG
66 TTGAAGGAATGGGTGACTATAAATGGACTTTTCTTC-CAATGAATGA-CTTTTTCTACA-TTTTC
*
984 TCAAGGCAAGCACTCAATTATAATCTATTTTAATAAAAAATGT
128 TCAAGGCAAGCATTCAATTAT-ATCTATTTTAATAAAAAATGT
* * * * *
1027 -AAAAAGATTCAACTTAAATTCAATTATAAGATTATAAAA-AATTTAAAGCAAGTAAT-AAGACT
1 AAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAAG-CT
* * * ** *
1089 TTTGAAGGAATGGATGACTATAAATAGAGTTTTCTTACCAATGAATCCCTTTTTCTTCATATTTC
65 TTTGAAGGAATGGGTGACTATAAATGGACTTTTCTT-CCAATGAATGACTTTTTCTACAT-TTTC
* * *
1154 TCAAGG-TAGACATTCAATTATTGTCTGTTTTAACT-AAAAATGT
128 TCAAGGCAAG-CATTCAATTA-TATCTATTTTAA-TAAAAAATGT
1197 AAAAAAA
1 AAAAAAA
Statistics
Matches: 827, Mismatches: 159, Indels: 91
0.77 0.15 0.08
Matches are distributed among these distances:
166 4 0.00
167 4 0.00
168 9 0.01
169 112 0.14
170 144 0.17
171 374 0.45
172 163 0.20
173 13 0.02
174 4 0.00
ACGTcount: A:0.39, C:0.11, G:0.13, T:0.36
Consensus pattern (169 bp):
AAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAAGCTT
TTGAAGGAATGGGTGACTATAAATGGACTTTTCTTCCAATGAATGACTTTTTCTACATTTTCTCA
AGGCAAGCATTCAATTATATCTATTTTAATAAAAAATGT
Found at i:662 original size:340 final size:336
Alignment explanation
Indices: 172--1129 Score: 965
Period size: 340 Copynumber: 2.8 Consensus size: 336
162 ATAAAAAATG
* * *
172 TATAAATAA-TCAACTGAAAATCAATTATGTGATTATAAAACCATTTAAAGCGAGTAATAAAGCT
1 TATAAAAAATTCAACT-TAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAAT-AAGCT
* ** * *
236 TTTGAAGGAATGGGTGATTATAAATGGACTTTTCTTCTTAATGAATGACTTTTTCTACATGTTTC
64 TTTGAAGGAATGAGACAATATAAATGGACTTTTCTTC-TAATGAAT-ACTTTTTCTTCAT-TTTC
* *
301 CCAAGGCAAGCATTTAATTATATCTATTTTAATAAAAAAATATAAAAACAATT-AACTTAAAATT
126 TCAAGGCAAGCATTCAATTATATCTATTTTAAT-AAAAAATATAAAAA-AATTCAACTTAAAATT
365 AATTATGAGATTATAAAACCATTTAAAGTGAGTAATAAGTTGTTTTAAGGAAT-GATAGACTATA
189 AATTATGAGATTATAAAACCATTTAAAGTGAGTAATAAG-TGTTTTAAGGAATGGAT-GACTATA
*
429 AATAGGCTTTTCTTCCAAAAAAATGGGCTTCTCTTCT-CATTTTCCT-AGGCAAGCAGTCAATTA
252 AATAGGCTTTTCTTCCAAAAAAAT-GGCTTCTCTTCTAC-TTTTCCTGACGCAAGCAGTCAATTA
*
492 TGGTCTATTTTAA-CA-AAAAA
315 TAGTCTATTTTAATCAGAAAAA
* *
512 TATAAAAAATTCAACTTAAATCAATTATGAGATTATAAAACTATTTAACGCGAGTAATAAGTCTT
1 TATAAAAAATTCAACTTAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAG-CTT
* * * *
577 TTGAAGGAATAAAACAATATAAATGGGCTTTGCTTGCTAATGAATACTTTTTTCTTCACTTTTCT
65 TTGAAGGAATGAGACAATATAAATGGACTTTTCTT-CTAATGAATAC-TTTTTCTTCA-TTTTCT
** * ** * *
642 TGAGGTCGA-CATTCAATTATAGTCTATTTTAACCAAAAATATAAAATAATTCAACTTAAAATCA
127 CAAGG-CAAGCATTCAATTATA-TCTATTTTAATAAAAAATATAAAAAAATTCAACTTAAAATTA
* * *
706 ATTATGATATTATAAAACCATTTAAAGTGAGTAATAAG-GCTTTTAAAGGAATGGGTGATTATAA
190 ATTATGAGATTATAAAACCATTTAAAGTGAGTAATAAGTG-TTTT-AAGGAATGGATGACTATAA
* * * * ** * * * * * * *
770 ATTGACTTTTTTTCTAAATTAATGGCTTTTTTTGTACTTTTCTTGACGTAGGCATTCAATTATAG
253 ATAGGCTTTTCTTCCAAAAAAATGGCTTCTCTTCTACTTTTCCTGACGCAAGCAGTCAATTATAG
* **
835 TCTATTTTAATGAGAAAGG
318 TCTATTTTAATCAGAAAAA
* * * *
854 TAAAAAAAATTCAACTTTAAATCAATTACGAAATTATAAAACCATTTAAAGCGATTAATAAGGCT
1 TATAAAAAATTCAAC-TTAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAA-GCT
* * * *
919 TTTGAAAGAATGGGTGAC-A-ATGAATGGACTTTTCTTCTCAATGAATAGCTTTTTCTAT-AGGT
64 TTTGAAGGAAT--GAGACAATATAAATGGACTTTTCTTCT-AATGAATA-CTTTTTCT-TCA-TT
* * * *
981 TTGTCAAGGCAAGCACTCAATTATAATCTATTTTAATAAAAAATGTAAAAAGATTCAACTT-AAA
123 TTCTCAAGGCAAGCATTCAATTAT-ATCTATTTTAATAAAAAATATAAAAAAATTCAACTTAAAA
* * ** **
1045 TTCAATTATAAGATTATAAAA-AATTTAAAGCAAGTAATAAGACTTTTGAAGGAATGGATGACTA
187 TT-AATTATGAGATTATAAAACCATTTAAAGTGAGTAATAAGTGTTTT-AAGGAATGGATGACTA
1109 TAAATAGAG-TTTTCTTACCAA
250 TAAATAG-GCTTTTCTT-CCAA
1130 TGAATCCCTT
Statistics
Matches: 507, Mismatches: 83, Indels: 53
0.79 0.13 0.08
Matches are distributed among these distances:
338 1 0.00
339 28 0.06
340 228 0.45
341 23 0.05
342 72 0.14
343 148 0.29
344 5 0.01
345 2 0.00
ACGTcount: A:0.40, C:0.11, G:0.13, T:0.36
Consensus pattern (336 bp):
TATAAAAAATTCAACTTAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGCTTT
TGAAGGAATGAGACAATATAAATGGACTTTTCTTCTAATGAATACTTTTTCTTCATTTTCTCAAG
GCAAGCATTCAATTATATCTATTTTAATAAAAAATATAAAAAAATTCAACTTAAAATTAATTATG
AGATTATAAAACCATTTAAAGTGAGTAATAAGTGTTTTAAGGAATGGATGACTATAAATAGGCTT
TTCTTCCAAAAAAATGGCTTCTCTTCTACTTTTCCTGACGCAAGCAGTCAATTATAGTCTATTTT
AATCAGAAAAA
Done.