Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018401138.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_4295.0, 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: 2742
ACGTcount: A:0.39, C:0.13, G:0.14, T:0.35
Found at i:293 original size:172 final size:170
Alignment explanation
Indices: 1--2742 Score: 2588
Period size: 171 Copynumber: 16.1 Consensus size: 170
* * * * *
1 TTATAAAATCATTTAAAGCGAGTAATAAGGCTTTCGAAAGAATGAGTG-CTATAAAAGGACATTT
1 TTATAAAACCATTTAAAGCGAGTAATAAGGCTTTCGAAGGCATGGGTGACTATAAATGGACATTT
* * *
65 CTTGTCAATGAATGGTTTTTTCTTCACATTTCTTAAGGCAAACAGTT-AATTATAATCTATTTTA
66 CTTGTCAATGAATGGCTTTTTCTTCACGTTTCTTGAGGCAAACA-TTCAATTATAATCTATTTTA
*
129 ACAAAAAATCCAAAAACAATTCAACCTAAAATCAATTATGAGA
130 ACAAAAAAT-TAAAAA-AATTCAACCTAAAATCAATTATGAGA
* *
172 TTATAAAACCATTTATAGCGAGTAATAAGGCTTAT-GAAGGCATAGGTGACTATAAATGGACATT
1 TTATAAAACCATTTAAAGCGAGTAATAAGGCTT-TCGAAGGCATGGGTGACTATAAATGGACATT
* * * * * *
236 TCTTGTCAATAAATGGCTTTTTCTTTACATTTCTTGAGGTAAACAATCAACTATAATCTATTTTA
65 TCTTGTCAATGAATGGCTTTTTCTTCACGTTTCTTGAGGCAAACATTCAATTATAATCTATTTTA
*
301 ACTAAAAATTAAAAACCAATTCAACCTAAAATCAATTATGAGA
130 ACAAAAAATTAAAAA--AATTCAACCTAAAATCAATTATGAGA
* * * *
344 TTATAAAACCATTTAAAGC-ACGTAATAAAGCTTTCGAAGGCGTGGGTGATTACAAATGGACATT
1 TTATAAAACCATTTAAAGCGA-GTAATAAGGCTTTCGAAGGCATGGGTGACTATAAATGGACATT
* *** * * * *
408 TCTTGTCAATGAATGGCTTTTTCTTCATGTTTCGCAAGGCAGACATTTAATTAGAATCTGTTTTA
65 TCTTGTCAATGAATGGCTTTTTCTTCACGTTTCTTGAGGCAAACATTCAATTATAATCTATTTTA
* *
473 ACCAAAAA-TATAAAAAATTCAA-CTTAAATCAATTATGAGA
130 ACAAAAAATTA-AAAAAATTCAACCTAAAATCAATTATGAGA
* * *
513 TTATAAAATCATTTAAAGTGAGTAATAAGGCTTTCGAAGGCATGGGTGACTATAAATGAACATTT
1 TTATAAAACCATTTAAAGCGAGTAATAAGGCTTTCGAAGGCATGGGTGACTATAAATGGACATTT
* * ** ** * * *
578 CTTATCAATGAATGGCTTTTTCTTCATGTTT-TCCAATACAGACACTCATTTATAATCTATTTTA
66 CTTGTCAATGAATGGCTTTTTCTTCACGTTTCT-TGAGGCAAACATTCAATTATAATCTATTTTA
* * * *
642 ACTAAAAATGTAAGAAAATTCAACTTAAAATCCATTATGAGA
130 ACAAAAAAT-TAAAAAAATTCAACCTAAAATCAATTATGAGA
* * * ** * * * *
684 TTATAAAACCATTTGAAGAGAGTAGTAAGGCTTTTAAAAGAATAGGTGGCTATAAATGGAC-TTT
1 TTATAAAACCATTTAAAGCGAGTAATAAGGCTTTCGAAGGCATGGGTGACTATAAATGGACATTT
* * * * * * * *
748 CTTTATGAATGAATAGCTTTTTCTTCATGTTTCCCT-AAGCAAACATTCAATTATAATATGTTTT
66 C-TTGTCAATGAATGGCTTTTTCTTCACGTTT-CTTGAGGCAAACATTCAATTATAATCTATTTT
** * * * *
812 AACCCAAATTGTAAGAAAATTCAACATAAAATCAATTTTGAGA
129 AACAAAAAAT-TAAAAAAATTCAACCTAAAATCAATTATGAGA
* * * * * * *
855 TTATAAAACTATTTAGAGCGTGTAATAAGGCTTTTGAAGGCATGGGCGACTATAAACGGACTTTT
1 TTATAAAACCATTTAAAGCGAGTAATAAGGCTTTCGAAGGCATGGGTGACTATAAATGGACATTT
* * * ** * * *
920 CTTGTGAATGAATAAG-TATTTCTTCACGTTTCTTGAGATAAACATTTAATTATTATATATTTTA
66 CTTGTCAATGAAT-GGCTTTTTCTTCACGTTTCTTGAGGCAAACATTCAATTATAATCTATTTTA
* * *
984 ATC-AAAAATATAAAAATATTCAAGCTAAAATCAATTATAAGA
130 A-CAAAAAAT-TAAAAAAATTCAACCTAAAATCAATTATGAGA
* ** * * *
1026 TTATAAAAGCATTTAAAGCGAGTAATAAGGCTTTTAAAGGCATAGGTGACTATAAATGTACTTTT
1 TTATAAAACCATTTAAAGCGAGTAATAAGGCTTTCGAAGGCATGGGTGACTATAAATGGAC-ATT
* * * * * * * * *
1091 TTTTCTCAATAAATGGCTTTATCTTCATGTTTTGTTGTGGCAAATAGTT-AATTATAATCTGTTT
65 TCTTGTCAATGAATGGCTTTTTCTTCACG-TTTCTTGAGGCAAACA-TTCAATTATAATCTATTT
* * * * *
1155 GAACCAAAAATGTAAAACAATTTAACCTAAAATCAACTATGAGA
128 TAACAAAAAAT-TAAAAAAATTCAACCTAAAATCAATTATGAGA
* * *
1199 TTATAAAACCATTTAAAGCGAGTAATAAAGCTTTCGAAGGAATGGGTGACTATAAATAGACATTT
1 TTATAAAACCATTTAAAGCGAGTAATAAGGCTTTCGAAGGCATGGGTGACTATAAATGGACATTT
* * * * * *
1264 ATTGTCAATGAAT-GATTTTTCTTCATGTTTCTTGAGGCAGATAGTT-AATTGTAATCTATTTTA
66 CTTGTCAATGAATGGCTTTTTCTTCACGTTTCTTGAGGCAAACA-TTCAATTATAATCTATTTTA
*
1327 ACTAAAAATCTAAAACAAATTCAACCTAAAATCAATTATGAGA
130 ACAAAAAAT-TAAAA-AAATTCAACCTAAAATCAATTATGAGA
* * * *
1370 TTATGAAACCATTTATAGCGAGTAATAAGGCTTTCGAAGGTATGAGTGACTATAAATGGACATTT
1 TTATAAAACCATTTAAAGCGAGTAATAAGGCTTTCGAAGGCATGGGTGACTATAAATGGACATTT
* * ** * * *
1435 CTTGTCAATGAATAGCTTTTTCATT-ACATTTCTTGAGATAGACAGTCAACTATAATCTATTTTA
66 CTTGTCAATGAATGGCTTTTTC-TTCACGTTTCTTGAGGCAAACATTCAATTATAATCTATTTTA
* * *
1499 ACTAAAAATTAAAAAACAATTCAGCCTAAAATCAATTATGAAA
130 ACAAAAAATT-AAAAA-AATTCAACCTAAAATCAATTATGAGA
* * * *
1542 TTACAAAACCGTTTAAAGC-ACGTAATAAGGCTTTCGAAGGCATGGGTGGCTACAAATGGACATT
1 TTATAAAACCATTTAAAGCGA-GTAATAAGGCTTTCGAAGGCATGGGTGACTATAAATGGACATT
* * * * *
1606 TCTTGTCAATGAATGGCTTTTTCTTTATGTTTCCT-AGGGCAGACATTCAATTAGAATCTATTTT
65 TCTTGTCAATGAATGGCTTTTTCTTCACGTTTCTTGA-GGCAAACATTCAATTATAATCTATTTT
* *
1670 AACTAAAAA-TATAAAAAATTCAACTTAAAATCAATTATGAGA
129 AACAAAAAATTA-AAAAAATTCAACCTAAAATCAATTATGAGA
* * **
1712 TTATAAAATCATTTAAAGCGAGTAATAAGGCTTTCGAAGGCATGGGTGATTATAAATAAACATTT
1 TTATAAAACCATTTAAAGCGAGTAATAAGGCTTTCGAAGGCATGGGTGACTATAAATGGACATTT
* * * ** * * *
1777 CTTATCAATGAATGGCTTTTTCTTCACATTT-TCTAATACAGACACTAAATTATAATCTATTTTA
66 CTTGTCAATGAATGGCTTTTTCTTCACGTTTCT-TGAGGCAAACATTCAATTATAATCTATTTTA
* * *
1841 ACAAAAAATGTAAGAAAATTTAACCTAAAATCAATTATGAAA
130 ACAAAAAAT-TAAAAAAATTCAACCTAAAATCAATTATGAGA
* * * *
1883 TTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAAT-GG-CA-TATAAATAGAC-TTT
1 TTATAAAACCATTTAAAGCGAGTAATAAGGCTTTCGAAGGCATGGGTGACTATAAATGGACATTT
* * * * ** * * * * **
1944 -TTATCCCAATGGATGGCTTTTGCTTTACGTTTCTCAAGGTAGATATTCAATGATAATAAATTTT
66 CTTGT--CAATGAATGGCTTTTTCTTCACGTTTCTTGAGGCAAACATTCAATTATAATCTATTTT
2008 AACAAAAAATGT-----AA---AA--TAAAATCAATTATGAGA
129 AACAAAAAAT-TAAAAAAATTCAACCTAAAATCAATTATGAGA
* * * ** * *
2041 TTATAAGACCATTTAAAG-TATGTAATAAAGCTTTCGAAGGTTTGGGTGACTATAAATGAACTTT
1 TTATAAAACCATTTAAAGCGA-GTAATAAGGCTTTCGAAGGCATGGGTGACTATAAATGGACATT
* * ** ** * *
2105 TCATGACAATGAATGATTTTTTCTTCACGTTTCTCAAGGCAGACAGTCAATTATAATCTATTTTA
65 TCTTGTCAATGAATGGCTTTTTCTTCACGTTTCTTGAGGCAAACATTCAATTATAATCTATTTTA
* * * *
2170 ATAAAAAATCTAAAAATAATTTAACTTAAAATTAATTATGAGA
130 ACAAAAAAT-TAAAAA-AATTCAACCTAAAATCAATTATGAGA
* * * * * * *
2213 TTATAAAACTATTTAATGTGCGTAATAAGACTTTCGAAGGTATGGGTGACTACAAATGGACATTT
1 TTATAAAACCATTTAAAGCGAGTAATAAGGCTTTCGAAGGCATGGGTGACTATAAATGGACATTT
* ** * * * * *
2278 CTTGTCAATGAATGGCTTTTTCTTTACGTTTCTCAAGGTAAAAATTCAACTAGAATCTGTTTTAA
66 CTTGTCAATGAATGGCTTTTTCTTCACGTTTCTTGAGGCAAACATTCAATTATAATCTATTTTAA
* *
2343 TCACAAACA-T-AAAAAATTCAACTTAAAATCAATTATGAGA
131 -CA-AAAAATTAAAAAAATTCAACCTAAAATCAATTATGAGA
* * * *
2383 TTATAAAACTATTTAAAGCGAGTAATAAGGCTTTCGAACGTATAGGTGACTATAAATGGACATTT
1 TTATAAAACCATTTAAAGCGAGTAATAAGGCTTTCGAAGGCATGGGTGACTATAAATGGACATTT
* * * *** * *
2448 TTTGTCCATGAATGGCTTTTTCTTCATGTTTCTTGATATAGACACTCAATTATAATCTATTTTAA
66 CTTGTCAATGAATGGCTTTTTCTTCACGTTTCTTGAGGCAAACATTCAATTATAATCTATTTTAA
* *
2513 C-AAAAATTGTAAGAAATTCAACCTAAAATCAATTATGAGA
131 CAAAAAATT-AAAAAAATTCAACCTAAAATCAATTATGAGA
* * **
2553 TTATAAAACTATTTAAAAG-GAGTAATAAGGCTTTAGAAGAAAT-GG-G-CTATAAATGGAC-TT
1 TTATAAAACCATTT-AAAGCGAGTAATAAGGCTTTCGAAGGCATGGGTGACTATAAATGGACATT
* * ** * * * *
2613 TCTTTGCCAATGAATGG-TTTTTCTTCATGTTT-TCCCAAGCAAACATTTAATTATAATATGTTT
65 TC-TTGTCAATGAATGGCTTTTTCTTCACGTTTCT-TGAGGCAAACATTCAATTATAATCTATTT
* * *
2676 TAACCAAAAATGTAAAAAAACTCAA-CTCAAAATCAATTATGAGG
128 TAACAAAAAAT-TAAAAAAATTCAACCT-AAAATCAATTATGAGA
*
2720 TTATAAAATCATTTAAAGCGAGT
1 TTATAAAACCATTTAAAGCGAGT
Statistics
Matches: 2141, Mismatches: 358, Indels: 148
0.81 0.14 0.06
Matches are distributed among these distances:
157 1 0.00
158 51 0.02
159 2 0.00
160 3 0.00
161 66 0.03
162 3 0.00
163 3 0.00
165 1 0.00
166 51 0.02
167 79 0.04
168 67 0.03
169 139 0.06
170 403 0.19
171 577 0.27
172 576 0.27
173 113 0.05
174 6 0.00
ACGTcount: A:0.39, C:0.13, G:0.14, T:0.35
Consensus pattern (170 bp):
TTATAAAACCATTTAAAGCGAGTAATAAGGCTTTCGAAGGCATGGGTGACTATAAATGGACATTT
CTTGTCAATGAATGGCTTTTTCTTCACGTTTCTTGAGGCAAACATTCAATTATAATCTATTTTAA
CAAAAAATTAAAAAAATTCAACCTAAAATCAATTATGAGA
Done.