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bootstrap in the tree? #40

Closed marwa38 closed 1 year ago

marwa38 commented 2 years ago

Thanks very much for your paper on the workflow I am trying to find bootstrap in my tree so that I can have it in my tree graph but I haven't been successful yet, your advice is appreciated about which of the below 24 list is considered the bootstrap? I created the tree based on the paper as follows:

seqs <- getSequences(seqtab)
names(seqs) <- seqs # This propagates to the tip labels of the tree
alignment <- AlignSeqs(DNAStringSet(seqs), anchor=NA)
phang.align <- phyDat(as(alignment, "matrix"), type="DNA")
dm <- dist.ml(phang.align)
treeNJ <- NJ(dm) # Note, tip order != sequence order
fit = pml(treeNJ, data=phang.align)

negative edges length changed to 0!

fitGTR <- update(fit, k=4, inv=0.2)
fitGTR <- optim.pml(fitGTR, model="GTR", optInv=TRUE, optGamma=TRUE,
                      rearrangement = "stochastic", control = pml.control(trace = 0))
detach("package:phangorn", unload=TRUE)

a quick example of the tree I viewed using plot_tree image

here the structure of the final tree created before merging it into the phyloseq object dismiss the $data because it takes a space out of the 24 list shown below I don't know which one of these is considered the bootstrap, if this is to be figured out, I think bootstrap would be easily integrated into the tree plot as I need to do that.

str(fitGTR) List of 24 $ logLik : num -751575 $ inv : num 0.175 $ k : num 4 $ shape : num 0.968 $ Q : num [1:6] 0.905 2.009 1.01 0.873 2.279 ... $ bf : num [1:4] 0.27 0.224 0.221 0.285 $ rate : num 1 $ siteLik : num [1:1296, 1] -1.5 -1.31 -1.51 -1.26 -1.27 ... $ weight : int [1:1296] 1 2 3 3 1 2 1 1 1 1 ... $ g : num [1:4] 0.158 0.566 1.205 2.919 $ w : num [1:4] 0.206 0.206 0.206 0.206 $ eig :List of 3 ..$ values : num [1:4] -1.612 -1.46 -0.945 0 ..$ vectors: num [1:4, 1:4] -0.0221 -0.6764 -0.0368 0.7353 0.7141 ... ..$ inv : num [1:4, 1:4] -0.0207 0.6445 0.4995 0.5031 -0.7649 ... ..- attr(*, "class")= chr "eigen" $ data :List of 6579 ..$ TAGGGAATATTGCACAATGGAGGAAACTCTGATGCAGCGACGTCGCGTGAGGGAAGAAGGTTTTCGGATTGTAAACCTCTGTCTTTGGTGAAGAAAATGACGGTAACCAAAGAGGAAGCCACGGCTAACTACGTGCCAGCAGCCGCGGTAATACGTAGGTGGCAAGCGTTGTCCGGAATTACTGGGTGTAAAGGGAGCGTAGGCGGGGGAATAAGTTGAATGTTAAAACTATCGGCTCAACCGATAGCAGCGTTCAAAACTATTTCTCTTGAGTGGAGTAGAGGTAAGCGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGTTTACTGGGCTCTAACTGACGCTGAGGCTCGAAAGCGTGGGTAGCAAACA : int [1:1296] 18 18 18 18 18 18 18 18 18 18 ... ..$ TGGGGAATATTGGACAATGGGCGAAAGCCTGATCCAGCCATGCCGCGTGTGTGAAGAAGGTCTTCGGATTGTAAAGCACTTTAAGTTGGGAGGAAGGGCAGTAAATTAATACTTTGCTGTTTTGACGTTACCGACAGAATAAGCACCGGCTAACTCTGTGCCAGCAGCCGCGGTAATACAGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCGCGTAGGTGGTTCGTTAAGTTGGATGTGAAATCCCCGGGCTCAACCTGGGAACTGCATTCAAAACTGACGAGCTAGAGTATGGTAGAGGGTGGTGGAATTTCCTGTGTAGCGGTGAAATGCGTAGATATAGGAAGGAACACCAGTGGCGAAGGCGACCACCTGGACTGATACTGACACTGAGGTGCGAAAGCGTGGGGAGCAAACA : int [1:1296] 18 18 18 18 18 18 18 18 18 18 ... ..$ TGGGGAATATTGCACAATGGGGGAAACCCTGATGCAGCCATGCCGCGTGTGTGAAGAAGGCCTTCGGGTTGTAAAGCACTTTCAGCGAGGAGGAAAGGTTGATGCCTAATACGCATCAGCTGTGACGTTACTCGCAGAAGAAGCACCGGCTAACTCCGTGCCAGCAGCCGCGGTAATACGGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGTTGGATAAGTTAGATGTGAAAGCCCCGGGCTCAACCTGGGAATTGCATTTAAAACTGTCCAGCTAGAGTCTTGTAGAGGGGGGTAGAATTCCAGGTGTAGCGGTGAAATGCGTAGAGATCTGGAGGAATACCGGTGGCGAAGGCGGCCCCCTGGACAAAGACTGACGCTCAGGTGCGAAAGCGTGGGGAGCAAACA : int [1:1296] 18 18 18 18 18 18 18 18 18 18 ... ..$ TGGGGAATATTGCACAATGGGCGCAAGCCTGATGCAGCCATGCCGCGTGTATGAAGAAGGCCTTCGGGTTGTAAAGTACTTTCAGCGGGGAGGAAGGGAGTAAAGTTAATACCTTTGCTCATTGACGTTACCCGCAGAAGAAGCACCGGCTAACTCCGTGCCAGCAGCCGCGGTAATACGGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGTTTGTTAAGTCAGATGTGAAATCCCCGGGCTCAACCTGGGAACTGCATCTGATACTGGCAAGCTTGAGTCTCGTAGAGGGGGGTAGAATTCCAGGTGTAGCGGTGAAATGCGTAGAGATCTGGAGGAATACCGGTGGCGAAGGCGGCCCCCTGGACGAAGACTGACGCTCAGGTGCGAAAGCGTGGGGAGCAAACA : int [1:1296] 18 18 18 18 18 18 18 18 18 18 ... ..$ TGAGGAATATTGGTCAATGGGCGAGAGCCTGAACCAGCCAAGTCGCGTGAAGGAAGACTGTCCTAAGGATTGTAAACTTCTTTTATACGGGAATAACGGGCGATACGAGTATTGCATTGAATGTACCGTAAGAATAAGCATCGGCTAACTCCGTGCCAGCAGCCGCGGTAATACGGAGGATGCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGTAGGTTGTTCGGTAAGTCAGCGGTGAAACCTGAGCGCTCAACGTTCAGCCTGCCGTTGAAACTGCCGGGCTTGAGTTCAGCGGCGGCAGGCGGAATTCGTGGTGTAGCGGTGAAATGCATAGATATCACGAGGAACTCCGATTGCGAAGGCAGCTTGCCATACTGCGACTGACACTGAAGCACGAAGGCGTGGGTATCAAACA : int [1:1296] 18 18 18 18 18 18 18 18 18 18 ... ..$ TAGGGAATCTTCCGCAATGGGCGAAAGCCTGACGGAGCAACGCCGCGTGAGTGATGAAGGTCTTCGGATCGTAAAACTCTGTTATTAGGGAAGAACAAATGTGTAAGTAACTATGCACGTCTTGACGGTACCTAATCAGAAAGCCACGGCTAACTACGTGCCAGCAGCCGCGGTAATACGTAGGTGGCAAGCGTTATCCGGAATTATTGGGCGTAAAGCGCGCGTAGGCGGTTTTTTAAGTCTGATGTGAAAGCCCACGGCTCAACCGTGGAGGGTCATTGGAAACTGGAAAACTTGAGTGCAGAAGAGGAAAGTGGAATTCCATGTGTAGCGGTGAAATGCGCAGAGATATGGAGGAACACCAGTGGCGAAGGCGACTTTCTGGTCTGTAACTGACGCTGATGTGCGAAAGCGTGGGGATCAAACA : int [1:1296] 18 18 18 18 18 18 18 18 18 18 ... ..$ TAGGGAATCTTCGGCAATGGACGAAAGTCTGACCGAGCAACGCCGCGTGAGTGAAGAAGGTTTTCGGATCGTAAAGCTCTGTTGTAAGTCAAGAACGTGTGTGAGAGTGGAAAGTTCACACAGTGACGGTAGCTTACCAGAAAGGGACGGCTAACTACGTGCCAGCAGCCGCGGTAATACGTAGGTCCCGAGCGTTGTCCGGATTTATTGGGCGTAAAGGGAGCGCAGGCGGTCAGGAAAGTCTGGAGTAAAAGGCTATGGCTCAACCATAGTGTGCTCTGGAAACTGTCTGACTTGAGTGCAGAAGGGGAGAGTGGAATTCCATGTGTAGCGGTGAAATGCGTAGATATATGGAGGAACACCAGTGGCGAAAGCGGCTCTCTGGTCTGTCACTGACGCTGAGGCTCGAAAGCGTGGGTAGCGAACA : int [1:1296] 18 18 18 18 18 18 18 18 18 18 ... ..$ TAGGGAATCTTCCACAATGGGCGAAAGCCTGATGGAGCAACGCCGCGTGAGTGAAGAAGGGTTTCGGCTCGTAAAACTCTGTTGTTAAAGAAGAACGTATCTGATAGTAACTGATCAGGTAGTGACGGTATTTAACCAGAAAGCCACGGCTAACTACGTGCCAGCAGCCGCGGTAATACGTAGGTGGCAAGCGTTATCCGGATTTATTGGGCGTAAAGGGAGTGCAGGCGGTTATTTAAGTCTGATGTGAAAGCCTTCGGCTTAACCGGAGAAGGGCATCGGAAACTGGATAACTTGAGTACAGAAGAGGGTAGTGGAACTCCATGTGTAGCGGTGGAATGCGTAGATATATGGAAGAACACCAGTGGCGAAGGCGGCTACCTGGTCTGTAACTGACGCTGAGGCTCGAAAGCATGGGTAGCAAACA : int [1:1296] 18 18 18 18 18 18 18 18 18 18 ... ..$ TGGGGAATATTGGACAATGGGCGAAAGCCTGATCCAGCCATGCCGCGTGTGTGAAGAAGGTCTTCGGATTGTAAAGCACTTTAAGTTGGGAGGAAGGGCAGTAACCTAATACGTTATTGTTTTGACGTTACCGACAGAATAAGCACCGGCTAACTCTGTGCCAGCAGCCGCGGTAATACAGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCGCGTAGGTGGTTTGTTAAGTTGGATGTGAAAGCCCCGGGCTCAACCTGGGAACTGCATCCAAAACTGGCAAGCTAGAGTATGGTAGAGGGTGGTGGAATTTCCTGTGTAGCGGTGAAATGCGTAGATATAGGAAGGAACACCAGTGGCGAAGGCGACCACCTGGACTGATACTGACACTGAGGTGCGAAAGCGTGGGGAGCAAACA : int [1:1296] 18 18 18 18 18 18 18 18 18 18 ... ..$ TGGGGAATTTTCCGCAATGGGCGAAAGCCTGACGGAGCAATGCCGCGTGGAGGTAGAGGCCCCTGGGTCATGAACTTCTTTTCCCGGAGAAGAAAAAATGACGGTATCCGGGGAATAAGCATCGGCTAACTCTGTGCCAGCAGCCGCGGTAAGACAGAGGATGCAAGCGTTATCCGGAATGATTGGGCGTAAAGCGTCTGTAGGTGGCTTTTTAAGTTCGCTGTCAAATACCAGGGCTCAACCCTGGACAGGTGGTGAAAACTACTAAGCTAGAGTACGGTAGGGGCAGAGGGAATTTCCGGTGGAGCGATGAAATGCGTAGAGATCGGAAGGAACACCAACGGCGAAAGCACTCTGCTGGGCCGACACTGACACTGAGAGACGAAAGCTAGGGGAGCGAATG : int [1:1296] 18 18 18 18 18 18 18 18 18 18 ... ..$ TGGGGAATATTGCACAATGGGGGAAACCCTGATGCAGCCATGCCGCGTGTGTGAAGAAGGCCTTCGGGTTGTAAAGCACTTTCAGCGAGGAGGAAAGGTTGGTAGCTAATAACTGCCAACTGTGACGTTACTCGCAGAAGAAGCACCGGCTAACTCCGTGCCAGCAGCCGCGGTAATACGGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGTTGGATAAGTTAGATGTGAAAGCCCCGGGCTCAACCTGGGAATTGCATTTAAAACTGTCCAGCTAGAGTCTTGTAGAGGGGGGTAGAATTCCAGGTGTAGCGGTGAAATGCGTAGAGATCTGGAGGAATACCGGTGGCGAAGGCGGCCCCCTGGACAAAGACTGACGCTCAGGTGCGAAAGCGTGGGGAGCAAACA : int [1:1296] 18 18 18 18 18 18 18 18 18 18 ... ..$ TAGGGAATATTGGGCAATGGAGGCAACTCTGACCCAGCCATGCCGCGTGCAGGAAGAAGGCGTTATGCGTTGTAAACTGCTTTTATATAGGAAGAAATAGTCCTTGCGAGGAAAGTTGACGGTACTATATGAATAAGCACCGGCTAACTCCGTGCCAGCAGCCGCGGTAATACGGAGGGTGCAAGCGTTGTCCGGATTTATTGGGTTTAAAGGGTGCGTAGGCGGTTTATTAAGTCAGTGGTGAAAGACGGTCGCTCAACGATTGCAGTGCCATTGATACTGGTAGACTTGAGTGGGATTGAGGTAGCTGGAATGGATAGTGTAGCGGTGAAATGCATAGATATTATCCAGAACACCAATTGCGTAGGCAAGTTACTAAGTCTCAACTGACGCTGAGGCACGAAAGTGTGGGTATCAAACA : int [1:1296] 18 18 18 18 18 18 18 18 18 18 ... ..$ TAGGGAATCTTCCACAATGGACGAAAGTCTGATGGAGCAACGCCGCGTGAGTGAAGAAGGGTTTCGGCTCGTAAAACTCTGTTGTTAAAGAAGAACATATCTGAGAGTAACTGTTCAGGTATTGACGGTATTTAACCAGAAAGCCACGGCTAACTACGTGCCAGCAGCCGCGGTAATACGTAGGTGGCAAGCGTTGTCCGGATTTATTGGGCGTAAAGCGAGCGCAGGCGGTTTTTTAAGTCTGATGTGAAAGCCTTCGGCTCAACCGAAGAAGTGCATCGGAAACTGGGAAACTTGAGTGCAGAAGAGGACAGTGGAACTCCATGTGTAGCGGTGAAATGCGTAGATATATGGAAGAACACCAGTGGCGAAGGCGGCTGTCTGGTCTGTAACTGACGCTGAGGCTCGAAAGTATGGGTAGCAAACA : int [1:1296] 18 18 18 18 18 18 18 18 18 18 ... ..$ TGAGGAATATTGGTCAATCTGCGAAAGCGGGAACCAGCAACGCCGCGTGAAGGAAGAAGGCCCTCGGGTTGTAAACTTCTTTAGGGGAAGACGAGAAAGGACGGTATTCCCAAAATAAGCAACGGCAAACTACGTGCCAGCAGCCGCGGTAATACGTAGGTTGCGAGCGTTATCCGGATTTACTGGGCGTAAAGCGCTTGTAGGCGGTAATATAAGTTGGGCGTGAAACCTCTGGGCTTAACCCGGAGCATGCGCACAATACTGTAATACTAGAGGGTGTCAGAGGAAAACGGAATTCCCGGTGTAGTAGTGAAATGCGTAGATATCGGGAGGAACATCAGTGGCGAAGGCGGTTTTCTGGGACATTACTGACGCTGAGAAGCGACAGCTAGGGGAGCAAACA : int [1:1296] 18 18 18 18 18 18 18 18 18 18 ... ..$ TGGGGAATCTTGGACAATGGGCGAAAGCCCGATCCAGCAATATCGCGTGAGTGAAGAAGGGCAATGCCGCTTGTAAAGCTCTTTCGTCGAGTGCGCGATCATGACAGGACTCGAGGAAGAAGCCCCGGCTAACTCCGTGCCAGCAGCCGCGGTAAGACGGGGGGGGCAAGTGTTCTTCGGAATGACTGGGCGTAAAGGGCACGTAGGCGGTGAATCGGGTTGAAAGTGAAAGTCGCCAAAAAGTGGCGGAATGCTCTCGAAACCAATTCACTTGAGTGAGACAGAGGAGAGTGGAATTTCGTGTGTAGGGGTGAAATCCGTAGATCTACGAAGGAACGCCAAAAGCGAAGGCAGCTCTCTGGGTCCCTACCGACGCTGGGGTGCGAAAGCATGGGGAGCGAACA : int [1:1296] 18 18 18 18 18 18 18 18 18 18 ... ..$ TAGGGAATCTTCGGCAATGGACGCAAGTCTGACCGAGCAACGCCGCGTGAGTGAAGAAGGTTTTCGGATCGTAAAACTCTGTTGTTAGAGAAGAACAAGGATGAGAGTGGAAAGTTCATCCCTTGACGGTATCTAACCAGAAAGCCACGGCTAACTACGTGCCAGCAGCCGCGGTAATACGTAGGTGGCAAGCGTTGTCCGGATTTATTGGGCGTAAAGCGAGCGCAGGCGGTCTTTTAAGTCTGATGTGAAAGCCCCCGGCTTAACCGGGGAGGGTCATTGGAAACTGGGAGACTTGAGTGCAGAAGAGGAAAGCGGAATTCCATGTGTAGCGGTGAAATGCGTAGATATATGGAGGAACACCAGTGGCGAAGGCGGCTTTCTGGTCTGTAACTGACGCTGAGGCTCGAAAGCGTGGGGAGCAAACA : int [1:1296] 18 18 18 18 18 18 18 18 18 18 ... ..$ TGGGGAATCTTAGACAATGGGGGAAACCCTGATCTAGCCATGCCGCGTGATCGATGAAGGCCTTAGGGTTGTAAAGATCTTTCAGATGGGAAGATAATGACGGTACCATCAGAAGAAGCCCCGGCTAACTCCGTGCCAGCAGCCGCGGTAATACGGAGGGGGCTAGCGTTATTCGGAATTACTGGGCGTAAAGCGCACGTAGGCGGATTGGATAGTTGGAGGTGAAATCCCAGGGCTCAACCTTGGAACTGCCTTCAAAACTTCCAGTCTTGAGTTCGAGAGAGGTGAGTGGAATTCCGAGTGTAGAGGTGAAATTCGTAGATATTCGGAGGAACACCAGTGGCGAAGGCGGCTCACTGGCTCGATACTGACGCTGAGGTGCGAAAGCGTGGGGAGCAAACA : int [1:1296] 18 18 18 18 18 18 18 18 18 18 ... ..$ TGGGGAATATTGCACAATGGGGGAAACCCTGATGCAGCAACGCCGCGTGAGTGATGACGGTCTTCGGATTGTAAAGCTCTGTCTTCAGGGACGATAATGACGGTACCTGAGGAGGAAGCCACGGCTAACTACGTGCCAGCAGCCGCGGTAATACGTAGGTGGCAAGCGTTGTCCGGATTTACTGGGCGTAAAGGGAGCGTAGGTGGATATTTAAGTGGGATGTGAAATACTCGGGCTTAACCTGGGTGCTGCATTCCAAACTGGATATCTAGAGTGCAGGAGAGGAAAGTAGAATTCCTAGTGTAGCGGTGAAATGCGTAGAGATTAGGAAGAATACCAGTGGCGAAGGCGACTTTCTGGACTGTAACTGACACTGAGGCTCGAAAGCGTGGGGAGCAAACA : int [1:1296] 18 18 18 18 18 18 18 18 18 18 ... ..$ TAGGGAATCTTCCACAATGGGCGCAAGCCTGATGGAGCAACGCCGCGTGAGTGAAGAAGGGTTTCGGCTCGTAAAACTCTGTTGTTAAAGAAGAACGTATCTGAGAGTAACTGTTCAGATAGTGACGGTATTTAACCAGAAAGCCACGGCTAACTACGTGCCAGCAGCCGCGGTAATACGTAGGTGGCAAGCGTTATCCGGATTTATTGGGCGTAAAGGGAGTGCAGGCGGTTATTTAAGTCTGATGTGAAAGCCTTCGGCTTAACCGGAGAAGGGCATCGGAAACTGGATAACTTGAGTGCAGAAGAGGGTAGTGGAACTCCATGTGTAGCGGTGGAATGCGTAGATATATGGAAGAACACCAGTGGCGAAGGCGGCTACCTAGTCTGTAACTGACGCTGAGGCTCGAAAGCATGGGTAGCAAACA : int [1:1296] 18 18 18 18 18 18 18 18 18 18 ... ..$ TCGAGAATAATTCACAATGGGGGAAACCCTGATGGTGCAACGCCGCGTGGAGGATGAAGGTCTTCGGATTGTAAACTCCTGTCATCCGGGAGTAAGACCTGGCGGTGAATAGCCGACAGGGTTGATAGTACCGGAAGAGGAAGGGACGGCTAACTTCGTGCCAGCAGCCGCGGTAATACGAAGGTCCCAAGCGTTGTTCGGAATCACTGGGCGTAAAGGGTGCGTAGGCGGTTTGGTAAGTCAGATGTGAAATCCCGGGGCTCAACCCCGGAACTGCATCCGATACTGCCAGACTAGAGGACTGGAGAGGTGACTGGAATTCTCGGTGTAGCAGTGAAATGCGTAGAGATCGAGAGGAACACTCGTGGCGAAGGCGAGTCACTGGACAGTATCTGACGCTGAGGCACGAAGGCCAGGGTAGCGAAAG : int [1:1296] 18 18 18 18 18 18 18 18 18 18 ... ..$ TGAAGAATCTCAAATATAAAATATATTTTGATTTGTATAATACTTTTTTGGTTACTACATGATTCCATATGTGTTATTTCATAGTTTTGTTGTCTTCACCATTATTCTACAATGTAGAAAATAGTAAAAAATAAAAAACCCATGAATTAGTAGTGTCCAAAACTTTAACTGGACTGTATATATATTTAAAATAATAAAATAAAAATTATGCCGACAATTACATCAATAGAAGCCGCAATGTTGAAGCTGATAACAAAAATAAAAGAAGAATATCCTGTTTCACTTGATTTAAAAACCAAGCATACCCCTTCTCCTCATCACCAAAGCTTTATTAAAATATCAAGTTTGGCAGCAGCAAAACAGTGAGTGGAAATCCCCTTTTATCCATATACAGTTGAAGTCGGAAGTTTACCGTCGTGGGACCCG : int [1:1296] 18 18 18 18 18 18 18 18 18 18 ... ..$ TAGGGAATCTTCCGCAATGGACGAAAGTCTGACGGAGCAACGCCGCGTGAGTGATGAAGGCTTTCGGGTCGTAAAACTCTGTTGTTAGGGAAGAACAAGTGCTAGTTGAATAAGCTGGCACCTTGACGGTACCTAACCAGAAAGCCACGGCTAACTACGTGCCAGCAGCCGCGGTAATACGTAGGTGGCAAGCGTTATCCGGAATTATTGGGCGTAAAGCGCGCGCAGGTGGTTTCTTAAGTCTGATGTGAAAGCCCACGGCTCAACCGTGGAGGGTCATTGGAAACTGGGAGACTTGAGTGCAGAAGAGGAAAGTGGAATTCCATGTGTAGCGGTGAAATGCGTAGAGATATGGAGGAACACCAGTGGCGAAGGCGACTTTCTGGTCTGTAACTGACACTGAGGCGCGAAAGCGTGGGGAGCAAACA : int [1:1296] 18 18 18 18 18 18 18 18 18 18 ... ..$ TGGGGAATATTGGACAATGGGCGAAAGCCTGATCCAGCCATGCCGCGTGTGTGAAGAAGGTCTTCGGATTGTAAAGCACTTTAAGTTGGGAGGAAGGGCAGTAAATTAATACTTTGCTGTTTTGACGTTACCGACAGAATAAGCACCGGCTAACTCTGTGCCAGCAGCCGCGGTAATACAGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCGCGTAGGTGGTTCGTTAAGTTGGATGTGAAATCCCCGGGCTCAACCTGGGAACTGCATTCAAAACTGTCGAGCTAGAGTATGGTAGAGGGTGGTGGAATTTCCTGTGTAGCGGTGAAATGCGTAGATATAGGAAGGAACACCAGTGGCGAAGGCGACCACCTGGACTGATACTGACACTGAGGTGCGAAAGCGTGGGGAGCAAACA : int [1:1296] 18 18 18 18 18 18 18 18 18 18 ... ..$ TGGGGAATCTTGCGCAATGGGCGAAAGCCTGACGCAGCAACGCCGCGTGCGGGATGAAGGCCTTCGGGTTGTAAACCGCTTTCAGCAGGGACGAAAATGACGGTACCTGCAGAAGAAGCCCCGGCTAACTACGTGCCAGCAGCCGCGGTAATACGTAGGGGGCAAGCGTTGTCCGGATTTATTGGGCGTAAAGAGCTCGTAGGCGGTTCCGTAAGTCGAGTGTGAAAAATCTGGGCTCAACCCAGTGGAGCACTCGATACTGCGGTGACTAGAGTACGGTAGAGGAGTGTGGAATTCCTGGTGTAGCGGTGAAATGCGCAGATATCAGGAGGAACACCAACGGCGAAGGCAGCACTCTGGGCCGGTACTGACGCTGAGGAGCGAAAGCGTGGGGAGCAAACA : int [1:1296] 18 18 18 18 18 18 18 18 18 18 ... ..$ TGGGGAATATTGGACAATGGGCGAAAGCCTGATCCAGCCATGCCGCGTGTGTGAAGAAGGTCTTCGGATTGTAAAGCACTTTAAGTTGGGAGGAAGGGCAGTTACCTAATACGTGATTGTTTTGACGTTACCGACAGAATAAGCACCGGCTAACTCTGTGCCAGCAGCCGCGGTAATACAGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCGCGTAGGTGGTTTGTTAAGTTGGATGTGAAATCCCCGGGCTCAACCTGGGAACTGCATTCAAAACTGACTGACTAGAGTATGGTAGAGGGTGGTGGAATTTCCTGTGTAGCGGTGAAATGCGTAGATATAGGAAGGAACACCAGTGGCGAAGGCGACCACCTGGACTAATACTGACACTGAGGTGCGAAAGCGTGGGGAGCAAACA : int [1:1296] 18 18 18 18 18 18 18 18 18 18 ... ..$ TGGGGAATATTGGACAATGGGCGAAAGCCTGATCCAGCCATGCCGCGTGTGTGAAGAAGGTCTTCGGATTGTAAAGCACTTTAAGTTGGGAGGAAGGGCAGTAAATTAATACTTTGCTGTTTTGACGTTACCGACAGAATAAGCACCGGCTAACTCTGTGCCAGCAGCCGCGGTAATACAGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCGCGTAGGTGGTTCGTTAAGTTGGATGTGAAAGCCCCGGGCTCAACCTGGGAACTGCATTCAAAACTGACGAGCTAGAGTATGGTAGAGGGTGGTGGAATTTCCTGTGTAGCGGTGAAATGCGTAGATATAGGAAGGAACACCAGTGGCGAAGGCGACCACCTGGACTGATACTGACACTGAGGTGCGAAAGCGTGGGGAGCAAACA : int [1:1296] 18 18 18 18 18 18 18 18 18 18 ... ..$ TAGGGAATATTGGGCAATGGACGGAAGTCTGACCCAGCCATGCCGCGTGCAGGAAGAAGGCGCTCAGCGTTGTAAACTGCTTTTGATGGGGAAGAAAGTGCGGGATGCGTCCTGTTTTGCCGGTACCCATCGAATAAGCACCGGCTAACTCCGTGCCAGCAGCCGCGGTAATACGGAGGGTGCAAGCGTTGTCCGGATTTATTGGGTTTAAAGGGTGCGTAGGTGGTTGAATAAGTCTGGTTTGAAAGTCAGTCGCTTAACGATTGAGGGTGGCTGGATACTGTTCAACTTGAATAATCTGGAGGTAGGCGGAACGGGTTGTGTAGCGGTGAAATGCATAGATATGACCCAGAACACCGATTGCGAAGGCAGCCTACTACGGATTGATTGACACTGAGGCACGAGAGCATGGGGAGCAAACA : int [1:1296] 18 18 18 18 18 18 18 18 18 18 ... ..$ TGGGGAATATTGCACAATGGGCGCAAGCCTGATGCAGCCATGCCGCGTGTGTGAAGAAGGCCTTCGGGTTGTAAAGCACTTTCAGCGAGGAGGAAGGGTTCAGTGTTAATAGCACTGTTCATTGACGTTACTCGCAGAAGAAGCACCGGCTAACTCCGTGCCAGCAGCCGCGGTAATACGGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGTTTGTTAAGTCAGATGTGAAATCCCCGCGCTTAACGTGGGAACTGCATTTGAAACTGGCAAGCTAGAGTCTTGTAGAGGGGGGTAGAATTCCAGGTGTAGCGGTGAAATGCGTAGAGATCTGGAGGAATACCGGTGGCGAAGGCGGCCCCCTGGACAAAGACTGACGCTCAGGTGCGAAAGCGTGGGGAGCAAACA : int [1:1296] 18 18 18 18 18 18 18 18 18 18 ... ..$ TGAGGAATATTGGACAATGGGTGAGAGCCTGATCCAGCCATCCCGCGTGAAGGACGACGGCCCTATGGGTTGTAAACTTCTTTTGTATAGGGATAAACCTACTCTCGTGAGAGTAGCTGAAGGTACTATACGAATAAGCACCGGCTAACTCCGTGCCAGCAGCCGCGGTAATACGGAGGGTGCAAGCGTTATCCGGATTTATTGGGTTTAAAGGGTCCGTAGGCGGATCTGTAAGTCAGTGGTGAAATCTCACAGCTTAACTGTGAAACTGCCATTGATACTGCAGGTCTTGAGTGTTGTTGAAGTAGCTGGAATAAGTAGTGTAGCGGTGAAATGCATAGATATTACTTAGAACACCAATTGCGAAGGCAGGTTACTAAGCAACAACTGACGCTGATGGACGAAAGCGTGGGGAGCGAACA : int [1:1296] 18 18 18 18 18 18 18 18 18 18 ... ..$ TGGGGAATTTTGGACAATGGGCGAAAGCCTGATCCAGCCATGCCGCGTGCAGGAAGAAGGCCTTCGGGTTGTAAACTGCTTTAGTCTAGGAAAAAGGGGTGCGAGGTTAATACCCTCGTGCTTTGATGGTACTGGAAGAATAAGCACCGGCTAACTACGTGCCAGCAGCCGCGGTAATACGTAGGGTGCGAGCGTTAATCGGAATTACTGGGCGTAAAGCGTGCGCAGGCGGTCTTGTAAGACAGTCGTGAAATCCCTGGGCTTAACCTAGGAACTGCGATTGTGACTGCAAGGCTAGAGTGTGTCAGAGGGGGGTGGAATTCCACGTGTAGCAGTGAAATGCGTAGAGATGTGGAGGAACACCGATGGCGAAGGCAGCCCCCTGGGATAACACTGACGCTCATGCACGAAAGCGTGGGGAGCAAACA : int [1:1296] 18 18 18 18 18 18 18 18 18 18 ... ..$ CATGGCCTTGTCTTAGCTGTTCTGAGGTGCCAGCTTGGCCCTCAGTGGTCTGAACAGAAGTGGACACCAGAGAAGCTCTGTGCAAGGAGTTGTGCCTAATGGAGGCCATGTCAACAGACACGTCAGCCAACATTTTAACACAATTAGAAAGCTCTTTCTGCAAGTGGTCTACAGTGTTAACCAGAGGAGAAAAAACTGAATTAACGTCCTTGAGAACCTCAGTGTGATGATGTTGCAAGCGCCACTGGAGAGTGGCAGTGAGTTGGGTTTGTTGGTAGTCAAACTGCCTGTCCATGGCACCAGTAACATCCCGTCTTCCACTCTCACTGAGCTCTGTCAGTGTGTGGGTTAGAGTGCTCAGTGAGTTTCTGAATTCCATGGCACTCTGTTGTTGCTCTTCACTCAGACATTTGAATTTATGGT : int [1:1296] 18 18 18 18 18 18 18 18 18 18 ... ..$ TAGGGAATCTTCCACAATGGACGAAAGTCTGATGGAGCAACGCCGCGTGAGTGAAGAAGGGTTTCGGCTCGTAAAGCTCTGTTGTTAAAGAAGAACGTGGGTAAGAGTAACTGTTTACCCAGTGACGGTATTTAACCAGAAAGCCACGGCTAACTACGTGCCAGCAGCCGCGGTAATACGTAGGTGGCAAGCGTTATCCGGATTTATTGGGCGTAAAGCGAGCGCAGGCGGTTTCTTAAGTCTAATGTGAAAGCCTTCGGCTCAACCGAAGAAGTGCATTGGAAACTGGGAAACTTGAGTGCAGAAGAGGATAGTGGAACTCCATGTGTAGCGGTGAAATGCGTAGATATATGGAAGAACACCAGTGGCGAAGGCGGCTATCTGGTCTGCAACTGACGCTGAGGCTCGAAAGCATGGGTAGCGAACA : int [1:1296] 18 18 18 18 18 18 18 18 18 18 ... ..$ TAGGGAATCTTCCGCAATGGGCGAAAGCTTGACGGAGCAACGCCGCGTGAGTGATGAAGGTCTTCGGATCGTAAAACTCTGTTATTAGGGAAGAACAAATGTGTAAGTAACTATGCACGTCTTGACGGTACCTAATCAGAAAGCCACGGCTAACTACGTGCCAGCAGCCGCGGTAATACGTAGGTGGCAAGCGTTATCCGGAATTATTGGGCGTAAAGCGCGCGTAGGCGGTTTTTTAAGTCTGATGTGAAAGCCCACGGCTCAACCGTGGAGGGTCATTGGAAACTGGAAAACTTGAGTGCAGAAGAGGAAAGTGGAATTCCATGTGTAGCGGTGAAATGCGCAGAGATATGGAGGAACACCAGTGGCGAAGGCGACTTTCTGGTCTGTAACTGACGCTGATGTGCGAAAGCGTGGGGATCAAACA : int [1:1296] 18 18 18 18 18 18 18 18 18 18 ... ..$ TGGGGAATATTGGACAATGGGCGAAAGCCTGATCCAGCCATGCCGCGTGTGTGAAGAAGGTCTTCGGATTGTAAAGCACTTTAAGTTGGGAGGAAGGGTTGTAGATTAATACTCTGCAATTTTGACGTTACCGACAGAATAAGCACCGGCTAACTCTGTGCCAGCAGCCGCGGTAATACAGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCGCGTAGGTGGTTTGTTAAGTTGGATGTGAAATCCCCGGGCTCAACCTGGGAACTGCATTCAAAACTGACTGACTAGAGTATGGTAGAGGGTGGTGGAATTTCCTGTGTAGCGGTGAAATGCGTAGATATAGGAAGGAACACCAGTGGCGAAGGCGACCACCTGGACTAATACTGACACTGAGGTGCGAAAGCGTGGGGAGCAAACA : int [1:1296] 18 18 18 18 18 18 18 18 18 18 ... ..$ TGGGGAATTTTGGACAATGGGCGAAAGCCTGATCCAGCAATGCCGCGTGTGGGAAGAAGGCCTTCGGGTTGTAAACCACTTTTGTACGGAACGAAACGGTCTGCTTTAATACAGTGGGCTAATGACGGTACCGTAAGAATAAGCACCGGCTAACTACGTGCCAGCAGCCGCGGTAATACGTAGGGTGCGAGCGTTAATCGGAATTACTGGGCGTAAAGCGTGCGCAGGCGGTTATATAAGACAGTTGTGAAATCCCCGGGCTCAACCTGGGAATTGCATCTGTGACTGTATAGCTAGAGTACGGTAGAGGGGGATGGAATTCCGCGTGTAGCAGTGAAATGCGTAGATATGCGGAGGAACACCGATGGCGAAGGCAATCCCCTGGACCTGTACTGACGCTCATGCACGAAAGCGTGGGGAGCAAACA : int [1:1296] 18 18 18 18 18 18 18 18 18 18 ... ..$ TAGGGAATCTTCCACAATGGGCGCAAGCCTGATGGAGCAACGCCGCGTGTGTGATGAAGGCTTTCGGGTCGTAAAGCACTGTTGTATGGGAAGAAATGCTAAAATAGGGAATGATTTTAGTTTGACGGTACCATACCAGAAAGGGACGGCTAAATACGTGCCAGCAGCCGCGGTAATACGTATGTCCCGAGCGTTATCCGGATTTATTGGGCGTAAAGCGAGCGCAGACGGTTGATTAAGTCTGATGTGAAAGCCCGGAGCTCAACTCCGGAATGGCATTGGAAACTGGTTAACTTGAGTGTTGTAGAGGTAAGTGGAACTCCATGTGTAGCGGTGGAATGCGTAGATATATGGAAGAACACCAGTGGCGAAGGCGGCTTACTGGACAACAACTGACGTTGAGGCTCGAAAGTGTGGGTAGCAAACA : int [1:1296] 18 18 18 18 18 18 18 18 18 18 ... ..$ TGGGGAATATTGCACAATGGGGGAAACCCTGATGCAGCCATGCCGCGTGTGTGAAGAAGGCCTTCGGGTTGTAAAGCACTTTCAGCGAGGAGGAAAGGTTGATGCCTAATACGCATCAGCTGTGACGTTACTCGCAGAAGAAGCACCGGCTAACTCCGTGCCAGCAGCCGCGGTAATACGGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGTTGGATAAGTTAGATGTGAAAGCCCCGGGCTCAACCTGGGAATTGCATTTAAAACTGTCCAGCTAGAGTCTTGTAGAGGGGGGTAGAATTCCAGGTGTAGCGGTGAAATGCGTAGAGATCTGGAGGAATATCGGTGGCGAAGGCGGCCCCCTGGACAAAGACTGACGCTCAGGTGCGAAAGCGTGGGGAGCAAACA : int [1:1296] 18 18 18 18 18 18 18 18 18 18 ... ..$ TGGGGAATTTTGGACAATGGGCGAAAGCCTGATCCAGCCATACCGCGTGCGGGAAGAAGGCCTTCGGGTTGTAAACCGCTTTTGTCAGGGAAGAAATGCCTCGGGTTAATACCCTGGGGTGATGACGGTACCTGAAGAATAAGCACCGGCTAACTACGTGCCAGCAGCCGCGGTAATACGTAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGTGCGCAGGCGGTTCTATAAGACAGATGTGAAATCCCCGGGCTCAACCTGGGAACTGCATTTGTGACTGTAGAGCTAGAGTACGGTAGAGGGGGATGGAATTCCGCGTGTAGCAGTGAAATGCGTAGATATGCGGAGGAACACCGATGGCGAAGGCAATCCCCTGGACCTGTACTGACGCTCATGCACGAAAGCGTGGGGAGCAAACA : int [1:1296] 18 18 18 18 18 18 18 18 18 18 ... ..$ TAGGGAATCTTCGGCAATGGACGGAAGTCTGACCGAGCAACGCCGCGTGAGTGAAGAAGGTTTTCGGATCGTAAAGCTCTGTTGTTAGAGAAGAACGTTGGTAGGAGTGGAAAATCTACCAAGTGACGGTAACTAACCAGAAAGGGACGGCTAACTACGTGCCAGCAGCCGCGGTAATACGTAGGTCCCGAGCGTTGTCCGGATTTATTGGGCGTAAAGCGAGCGCAGGCGGTTCTTTAAGTCTGAAGTTAAAGGCAGTGGCTTAACCATTGTACGCTTTGGAAACTGGAGGACTTGAGTGCAGAAGGGGAGAGTGGAATTCCATGTGTAGCGGTGAAATGCGTAGATATATGGAGGAACACCGGTGGCGAAAGCGGCTCTCTGGTCTGTAACTGACGCTGAGGCTCGAAAGCGTGGGGAGCAAACA : int [1:1296] 18 18 18 18 18 18 18 18 18 18 ... ..$ TAGGGAATATTGCACAATGGAGGAAACTCTGATGCAGCGACGTCGCGTGAGGGAAGAAGGTTTTCGGATTGTAAACCTCTGTCTTTGGTGAAGAAAATGACGGTAACCAAAGAGGAAGCCACGGCTAACTACGTGCCAGCAGCCGCGGTAATACGTAGGTGGCAAGCGTTGTCCGGAATTACTGGGTGTAAAGGGAGCGTAGGCGGGGGAATAAGTTGAATCTTAAAACTATCGGCTCAACCGATAGCAGCGTTCAAAACTATTTCTCTTGAGTGGAGTAGAGGTAAGCGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGTTTACTGGGCTCTAACTGACGCTGAGGCTCGAAAGCGTGGGTAGCAAACA : int [1:1296] 18 18 18 18 18 18 18 18 18 18 ... ..$ TGGGGAATATTGCACAATGGGCGAAAGCCTGATGCAGCGACGCCGCGTGCGGGATGAAGGCCTTCGGGTTGTAAACCGCTTTTGATTGGGAGCAAGCGAGAGTGAGTGTACCTTTCGAATAAGCACCGGCTAACTACGTGCCAGCAGCCGCGGTAATACGTAGGGTGCAAGCGTTATCCGGAATTATTGGGCGTAAAGAGCTCGTAGGCGGTTTGTCGCGTCTGGTGTGAAAGTCCATCGCTTAACGGTGGATCTGCGCCGGGTACGGGCAGGCTAGAGTGCGACAGGGGAGACTGGAATTCCCGGTGTAACGGTGGAATGTGTAGATATCGGGAAGAACACCAATGGCGAAGGCAGGTCTCTGGGTCGTCACTGACGCTGAGGAGCGAAAGCGTGGGGAGCGAACA : int [1:1296] 18 18 18 18 18 18 18 18 18 18 ... ..$ TGGGGAATCTTAGACAATGGGCGCAAGCCTGATCTAGCCATGCCGCGTGATCGATGAAGGCCTTAGGGTTGTAAAGATCTTTCAGTGGGGAAGATAATGACTGTACCCACAGAAGAAGCCCCGGCTAACTCCGTGCCAGCAGCCGCGGTAATACGGAGGGGGCTAGCGTTGTTCGGAATTACTGGGCGTAAAGCGCACGTAGGCGGACTGGAAAGTCAGAGGTGAAATCCCAGGGCTCAACCTTGGAACTGCCTTTGAAACTCCCGGTCTTGAGGTCGAGAGAGGTGAGTGGAATTCCGAGTGTAGAGGTGAAATTCGTAGATATTCGGAGGAACACCAGTGGCGAAGGCGGCTCACTGGCTCGATACTGACGCTGAGGTGCGAAAGCGTGGGGAGCAAACA : int [1:1296] 18 18 18 18 18 18 18 18 18 18 ... ..$ TGGGGAATTTTCCGCAATGGGCGAAAGCCTGACGGAGCAATACCGCGTGAGGGATGACGGCCTATGGGTTGTAAACCTCTTTTTTCAGGGAGGAATCAATGACGTGTACCTGAGGAATAAGCATCGGCTAACTCCGTGCCAGCAGCCGCGGTAAGACGGAGGATGCAAGTGTTATCCGGAATCACTGGGCGTAAAGCGTCTGTAGGTGGTCAAATAAGTCAACTGTTAAATCTTGAGGCTCAACCTCAAAATCGCAGTCGAAACTATTCGACTAGAGTATAGTAGGGGTAAAGGGAATTTCCAGTGGAGCGGTGAAATGCGTAGAGATTGGAAAGAACACCGATGGCGAAGGCACTTTACTGGGCTATTACTAACACTGAGAGACGAAAGCTAGGGTAGCAAATG : int [1:1296] 18 18 18 18 18 18 18 18 18 18 ... ..$ TGGGGAATATTGGACAATGGGCGAAAGCCTGATCCAGCCATGCCGCGTGTGTGAAGAAGGTCTTCGGATTGTAAAGCACTTTAAGTTGGGAGGAAGAGCAGTAAATTAATACTTTGCTGTTTTGACGTTACCGACAGAATAAGCACCGGCTAACTCTGTGCCAGCAGCCGCGGTAATACAGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCGCGTAGGTGGTTCGTTAAGTTGGATGTGAAATCCCCGGGCTCAACCTGGGAACTGCATTCAAAACTGTCGAGCTAGAGTATGGTAGAGGGTGGTGGAATTTCCTGTGTAGCGGTGAAATGCGTAGATATAGGAAGGAACACCAGTGGCGAAGGCGACCACCTGGACTGATACTGACACTGAGGTGCGAAAGCGTGGGGAGCAAACA : int [1:1296] 18 18 18 18 18 18 18 18 18 18 ... ..$ TGGGGAATTTTCCGCAATGGGCGAAAGCCTGACGGAGCAATGCCGCGTGGAGGTGGAAGGCCTACGGGTCGTCAACTTCTTTTCTCGGAGAAGAAACAATGACGGTATCTGAGGAATAAGCATCGGCTAACTCTGTGCCAGCAGCCGCGGTAAGACAGAGGATGCAAGCGTTATCCGGAATGATTGGGCGTAAAGCGTCTGTAGGTGGCTTTTCAAGTCCGCCGTCAAATCCCAGGGCTCAACCCTGGACAGGCGGTGGAAACTACCAAGCTGGAGTACGGTAGGGGCAGAGGGAATTTCCGGTGGAGCGGTGAAATGCATTGAGATCGGAAAGAACACCAACGGCGAAAGCACTCTGCTGGGCCGACACTGACACTGAGAGACGAAAGCTAGGGGAGCAAATG : int [1:1296] 18 18 18 18 18 18 18 18 18 18 ... ..$ TGGGGAATATTGCACAATGGGCGGAAGCCTGATGCAGCAACGCCGCGTGCGGGATGACGGCCTTCGGGTTGTAAACCGCTTTCGCCTGTGACGAAGCGTGAGTGACGGTAATGGGTAAAGAAGCACCGGCTAACTACGTGCCAGCAGCCGCGGTGATACGTAGGGTGCGAGCGTTGTCCGGATTTATTGGGCGTAAAGGGCTCGTAGGTGGTTGATCGCGTCGGAAGTGTAATCTTGGGGCTTAACCCTGAGCGTGCTTTCGATACGGGTTGACTTGAGGAAGGTAGGGGAGAATGGAATTCCTGGTGGAGCGGTGGAATGCGCAGATATCAGGAGGAACACCAGTGGCGAAGGCGGTTCTCTGGGCCTTTCCTGACGCTGAGGAGCGAAAGCGTGGGGAGCGAACA : int [1:1296] 18 18 18 18 18 18 18 18 18 18 ... ..$ TGGGGAATTTTCCGCAATGGGCGAAAGCCTGACGGAGCAATGCCGCGTGAAGGTAGAAGGCCTACGGGTCATGAACTTCTTTTCCCGGAGAAGAAGCAATGACGGTATCCGGGGAATAAGCATCGGCTAACTCTGTGCCAGCAGCCGCGGTAAGACAGAGGATGCAAGCGTTATCCGGAATGATTGGGCGTAAAGCGTCTGTAGGTGGCTTTTTAAGTTCGCCGTCAAATCCCAGGGCTCAACCCTGGACAGGCGGTGGAAACTACCAAGCTGGAGTACGGTAGGGGCAGAGGGAATTTCCGGTGGAGCGGTGAAATGCGTAGAGATCGGAAAGAACACCAACGGCGAAAGCACTCTGCTGGGCCGACACTGACACTGAGAGACGAAAGCTAGGGGAGCGAATG : int [1:1296] 18 18 18 18 18 18 18 18 18 18 ... ..$ TTGGGAATCTTGCACAATGGGGGAAACCCTGATGCAGCGACGCCGCGTGGACGATGAAGGCCTTAGGGTTGTAAAGTCCTTTTTTGGGGAAAGACTTAGGACGGTACCCCAAGAATAAGCTCCGGCTAACTACGTGCCAGCAGCCGCGGTAAGACGTAGGGAGCAAGCGTTGTCCGGATTTACTGGGCGTAAAGAGCGCGTAGGCGGCTCGTTAAGTGTGAAGTGAAATCTCCAGTGCTCAACACGGAAACTGCTTTACATACTGGCGAGCTTGAGGAAAGCAGAGGTAACTGGAATTCCTGGTGTAGCGGTGAAATGCGTTGATATCAGGAGGAACACCCATGGCGAAGGCAGGTTACTGGGCTTTATCTGACGCTGAGGCGCGAAAGCGTGGGTAGCAAACA : int [1:1296] 18 18 18 18 18 18 18 18 18 18 ... ..$ TGGGGAATATTGGACAATGGGCGAAAGCCTGATCCAGCAATGCCGCGTGAGTGATGAAGGCCTTAGGGTTGTAAAGCTCTTTTACCCGGGATGATAATGACAGTACCGGGAGAATAAGCTCCGGCTAACTCCGTGCCAGCAGCCGCGGTAATACGGAGGGAGCTAGCGTTATTCGGAATTACTGGGCGTAAAGCGCACGTAGGCGGCTTTGTAAGTAAGAGGTGAAAGCCCAGAGCTCAACTCTGGAATTGCCTTTTAGACTGCATCGCTTGAATCATGGAGAGGTCAGTGGAATTCCGAGTGTAGAGGTGAAATTCGTAGATATTCGGAAGAACACCAGTGGCGAAGGCGGCTGACTGGACATGTATTGACGCTGAGGTGCGAAAGCGTGGGGAGCAAACA : int [1:1296] 18 18 18 18 18 18 18 18 18 18 ... ..$ TAGGGAATCTTCCGCAATGGGCGAAAGCCTGACGGAGCAACGCCGCGTGAGTGATGAAGGTCTTCGGATCGTAAAACTCTGTTATTAGGGAAGAACATATGTGTAAGTAACTGTGCACATCTTGACGGTACCTAATCAGAAAGCCACGGCTAACTACGTGCCAGCAGCCGCGGTAATACGTAGGTGGCAAGCGTTATCCGGAATTATTGGGCGTAAAGCGCGCGTAGGCGGTTTTTTAAGTCTGATGTGAAAGCCCACGGCTCAACCGTGGAGGGTCATTGGAAACTGGAAAACTTGAGTGCAGAAGAGGAAAGTGGAATTCCATGTGTAGCGGTGAAATGCGCAGAGATATGGAGGAACACCAGTGGCGAAGGCGACTTTCTGGTCTGTAACTGACGCTGATGTGCGAAAGCGTGGGGATCAAACA : int [1:1296] 18 18 18 18 18 18 18 18 18 18 ... ..$ TGGGGAATATTGGACAATGGGCGAAAGCCTGATCCAGCAATGCCGCGTGAGTGATGAAGGCCCTAGGGTTGTAAAGCTCTTTTACCCGGGATGATAATGACAGTACCGGGAGAATAAGCTCCGGCTAACTCCGTGCCAGCAGCCGCGGTAATACGGAGGGAGCTAGCGTTGTTCGGAATTACTGGGCGTAAAGCGCGCGTAGGCGGCTTTTTAAGTCAGAGGTGAAAGCCCGGGGCTCAACCCCGGAATTGCCTTTGAAACTGGGAAGCTAGAATCTTGGAGAGGTCAGTGGAATTCCGAGTGTAGAGGTGAAATTCGTAGATATTCGGAAGAACACCAGTGGCGAAGGCGACTGACTGGACAAGTATTGACGCTGAGGTGCGAAAGCGTGGGGAGCAAACA : int [1:1296] 18 18 18 18 18 18 18 18 18 18 ... ..$ TGGGGAATCTTAGACAATGGGCGCAAGCCTGATCTAGCCATGCCGCGTGATCGATGAAGGCCTTAGGGTTGTAAAGATCTTTCAGGTGGGAAGATAATGACGGTACCACCAGAAGAAGCCCCGGCTAACTCCGTGCCAGCAGCCGCGGTAATACGGAGGGGGCTAGCGTTATTCGGAATTACTGGGCGTAAAGCGCACGTAGGCGGATCGGAAAGTCAGAGGTGAAATCCCAGGGCTCAACCCTGGAACTGCCTTTGAAACTCCCGATCTTGAGGTCGAGAGAGGTGAGTGGAATTCCGAGTGTAGAGGTGAAATTCGTAGATATTCGGAGGAACACCAGTGGCGAAGGCGGCTCACTGGCTCGATACTGACGCTGAGGTGCGAAAGCGTGGGGAGCAAACA : int [1:1296] 18 18 18 18 18 18 18 18 18 18 ... ..$ TAGGGAATCTTCGGCAATGGACGAAAGTCTGACCGAGCAACGCCGCGTGAGTGAAGAAGGTTTTCGGATCGTAAAACTCTGTTGGTAGAGAAGAACGTTGGTGAGAGTGGAAAGCTCATCAAGTGACGGTAACTACCCAGAAAGGGACGGCTAACTACGTGCCAGCAGCCGCGGTAATACGTAGGTCCCGAGCGTTGTCCGGATTTATTGGGCGTAAAGCGAGCGCAGGTGGTTTATTAAGTCTGGTGTAAAAGGCAGTGGCTCAACCATTGTATGCATTGGAAACTGGTAGACTTGAGTGCAGGAGAGGAGAGTGGAATTCCATGTGTAGCGGTGAAATGCGTAGATATATGGAGGAACACCGGTGGCGAAAGCGGCTCTCTGGCCTGTAACTGACACTGAGGCTCGAAAGCGTGGGGAGCAAACA : int [1:1296] 18 18 18 18 18 18 18 18 18 18 ... ..$ TGGGGAATATTGGACAATGGGGGGAACCCTGATCCAGCCATGCCGCGTGTGTGAAGAAGGCCTTATGGTTGTAAAGCACTTTAAGCGAGGAGGAGGCTCCTGTAGTTAATACCTACAGTGAGTGGACGTTACTCGCAGAATAAGCACCGGCTAACTCTGTGCCAGCAGCCGCGGTAATACAGAGGGTGCGAGCGTTAATCGGATTTACTGGGCGTAAAGCGTGCGTAGGCGGCTTTTTAAGTCGGATGTGAAATCCCCGAGCTTAACTTGGGAATTGCATTCGATACTGGGAAGCTAGAGTATGGGAGAGGATGGTAGAATTCCAGGTGTAGCGGTGAAATGCGTAGAGATCTGGAGGAATACCGATGGCGAAGGCAGCCATCTGGCCTAATACTGACGCTGAGGTACGAAAGCATGGGGAGCAAACA : int [1:1296] 18 18 18 18 18 18 18 18 18 18 ... ..$ TGGGGAATCTTGGACAATGGGCGAAAGCCCGATCCAGCAATATCGCGTGAGTGAAGAAGGGCAATGCCGCTTGTAAAGCTCTTTCGTCGAGTGCGCGATCATGACAGGACTCGAGGAAGAAGCCCCGGCTAACTCCGTGCCAGCAGCCGCGGTAAGACGGGGGGGGCAAGTGTTCTTCGGAATGACTGGGCGTAAAGGGCACGTAGGCGGTGAATCGGGTTGAAAGTTAAAGTCGCCAAAAACTGGTGGAATGCTCTCGAAACCAATTCACTTGAGTGAGACAGAGGAGAGTGGAATTTCGTGTGTAGGGGTGAAATCCGCAGATCTACGAAGGAACGCCAAAAGCGAAGGCAGCTCTCTGGGTCCCTACCGACGCTGGAGTGCGAAAGCATGGGGAGCGAACG : int [1:1296] 18 18 18 18 18 18 18 18 18 18 ... ..$ TGGGGAATATTGGACAATGGGCGAAAGCCTGATCCAGCAATGCCGCGTGAGTGATGAAGGCCTTAGGGTTGTAAAGCTCTTTTACCAGGGATGATAATGACAGTACCTGGAGAATAAGCTCCGGCTAACTTCGTGCCAGCAGCCGCGGTAATACGAGGGGAGCTAGCGTTGTTCGGAATTACTGGGCGTAAAGCGTGCGTAGGCGGTTACTCAAGTCAGAGGTGAAAGCCCGGGGCTCAACCCCGGAACGGCCTTTGAAACTAGGTAGCTAGAATCTTGGAGAGGTTAGTGGAATTCCGAGTGTAGAGGTGAAATTCGTAGATATTCGGAAGAACACCAGTGGCGAAGGCGACTAACTGGACAAGCATTGACGCTGAGGCACGAAAGCGTGGGGAGCAAACA : int [1:1296] 18 18 18 18 18 18 18 18 18 18 ... ..$ TAGGGAATCTTCCACAATGGGCGCAAGCCTGATGGAGCAACACCGCGTGAGTGAAGAAGGGTTTCGGCTCGTAAAGCTCTGTTGTTAAAGAAGAACACGTATGAGAGTAACTGTTCATACGTTGACGGTATTTAACCAGAAAGTCACGGCTAACTACGTGCCAGCAGCCGCGGTAATACGTAGGTGGCAAGCGTTATCCGGATTTATTGGGCGTAAAGAGAGTGCAGGCGGTTTTCTAAGTCTGATGTGAAAGCCTTCGGCTTAACCGGAGAAGTGCATCGGAAACTGGATAACTTGAGTGCAGAAGAGGGTAGTGGAACTCCATGTGTAGCGGTGGAATGCGTAGATATATGGAAGAACACCAGTGGCGAAGGCGGCTACCTGGTCTGCAACTGACGCTGAGACTCGAAAGCATGGGTAGCGAACA : int [1:1296] 18 18 18 18 18 18 18 18 18 18 ... ..$ TGGGGAATATTGGACAATGGGGGGAACCCTGATCCAGCCATGCCGCGTGTGTGAAGAAGGCCTTATGGTTGTAAAGCACTTTAAGCGAGGAGGAGGCTCTCTTGGTTAATACCCAAGATGAGTGGACGTTACTCGCAGAATAAGCACCGGCTAACTCTGTGCCAGCAGCCGCGGTAATACAGAGGGTGCGAGCGTTAATCGGATTTACTGGGCGTAAAGCGTGCGTAGGCGGCTTTTTAAGTCGGATGTGAAATCCCCGAGCTTAACTTGGGAATTGCATTCGATACTGGGAAGCTAGAGTATGGGAGAGGATGGTAGAATTCCAGGTGTAGCGGTGAAATGCGTAGAGATCTGGAGGAATACCGATGGCGAAGGCAGCCATCTGGCCTAATACTGACGCTGAGGTACGAAAGCATGGGGAGCAAACA : int [1:1296] 18 18 18 18 18 18 18 18 18 18 ... ..$ TGGGGAATATTGCACAATGGGCGCAAGCCTGATGCAGCCATGCCGCGTGTGTGAAGAAGGCCTTCGGGTTGTAAAGCACTTTCAGCGAGGAGGAAGGGCAGTGTGTTAATAGCACATTGCATTGACGTTACTCGCAGAAGAAGCACCGGCTAACTCCGTGCCAGCAGCCGCGGTAATACGGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGTTTGTTAAGTCAGATGTGAAATCCCCGCGCTTAACGTGGGAACTGCATTTGAAACTGGCAAGCTAGAGTCTTGTAGAGGGGGGTAGAATTCCAGGTGTAGCGGTGAAATGCGTAGAGATCTGGAGGAATACCGGTGGCGAAGGCGGCCCCCTGGACAAAGACTGACGCTCAGGTGCGAAAGCGTGGGGAGCAAACA : int [1:1296] 18 18 18 18 18 18 18 18 18 18 ... ..$ TAAGGAATATTGGTCAATGGAGGCAACTCTGAACCAGCCATGCCGCGTGCAGGAAGACAGCCCTCTGGGTCGTAAACTGCTTTTATTCGGGAATAAACCTACTTACGTGTAAGTAGCTGAATGTACCGAAGGAATAAGGATCGGCTAACTCCGTGCCAGCAGCCGCGGTAATACGGAGGATCCAAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGTAGGCGGCCTATTAAGTCAGGGGTGAAAGACGGTAGCTCAACTATCGCAGTGCCCTTGATACTGATGGGCTTGAATACACTAGAGGTAGGCGGAATGTGACAAGTAGCGGTGAAATGCATAGATATGTCACAGAACACCGATTGCGAAGGCAGCTTACTATGGTGTTATTGACGCTGAGGCACGAAAGCGTGGGGATCAAACA : int [1:1296] 18 18 18 18 18 18 18 18 18 18 ... ..$ TAAGGAATATTGGTCAATGGAGGCAACTCTGAACCAGCCATGCCGCGTGCAGGAAGACAGCCCTCTGGGTCGTAAACTGCTTTTATTCGGGAATAAACCTACTTACGTGTAAGTAGCTGAATGTACCGAAGGAATAAGGATCGGCTAACTCCGTGCCAGCAGCCGCGGTAATACGGAGGATCCAAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGTAGGCGGCCTATTAAGTCAGGGGTGAAAGACGGTAGCTCAACTATCGCAGTGCCCTTGATACTGATGGGCTTGAATACACTAGAGGTAGGCGGAATGTGACAAGTAGCGGTGAAATGCATAGATATGTCACAGAACACCGATTGCGAAGGCAGCTTACTATGGTGTCATTGACGCTGAGGCACGAAAGCGTGGGGATCAAACA : int [1:1296] 18 18 18 18 18 18 18 18 18 18 ... ..$ TGGGGAATTTTGGACAATGGACGCAAGTCTGATCCAGCAATGCCGCGTGCAGGACGAAGGCCTTCGGGTTGTAAACTGCTTTTGTACGGAACGAAACGGTCTTCTTTAATACAGAGGGCTAATGACGGTACCGTAAGAATAAGCACCGGCTAACTACGTGCCAGCAGCCGCGGTAATACGTAGGGTGCGAGCGTTAATCGGAATTACTGGGCGTAAAGCGTGCGCAGGCGGTTATATAAGTCAGATGTGAAATCCCCGGGCTCAACCTGGGACCTGCATTTGAGACTGTATAGCTAGAGTACGGTAGAGGGGGATGGAATTCCGCGTGTAGCAGTGAAATGCGTAGATATGCGGAGGAACACCGATGGCGAAGGCAATCCCCTGGACCTGTACTGACGCTCATGCACGAAAGCGTGGGGAGCAAACA : int [1:1296] 18 18 18 18 18 18 18 18 18 18 ... ..$ TGGGGAATATTGGACAATGGGCGAAAGCCTGATCCAGCCATGCCGCGTGTGTGAAGAAGGTCTTCGGATTGTAAAGCACTTTAAGTTGGGAGGAAGGGCAGTAAGTTAATACCTTGCTGTTTTGACGTTACCAACAGAATAAGCACCGGCTAACTTCGTGCCAGCAGCCGCGGTAATACGAAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCGCGTAGGTGGTTCAGCAAGTTGGATGTGAAATCCCCGGGCTCAACCTGGGAACTGCATCCAAAACTACTGAGCTAGAGTACGGTAGAGGGTGGTGGAATTTCCTGTGTAGCGGTGAAATGCGTAGATATAGGAAGGAACACCAGTGGCGAAGGCGACCACCTGGACTGATACTGACACTGAGGTGCGAAAGCGTGGGGAGCAAACA : int [1:1296] 18 18 18 18 18 18 18 18 18 18 ... ..$ TAGGGAATCTTCCACAATGGACGAAAGTCTGATGGAGCAACGCCGCGTGAGTGAAGAAGGTTTTCGGATCGTAAAACTCTGTTGTTGGAGAAGAACGTATTTGATAGTAACTGATCAGGTAGTGACGGTATCCAACCAGAAAGCCACGGCTAACTACGTGCCAGCAGCCGCGGTAATACGTAGGTGGCAAGCGTTGTCCGGATTTATTGGGCGTAAAGCGAGCGCAGGCGGTTTCTTAAGTCTGATGTGAAAGCCTTCGGCTCAACCGAAGAAGTGCATCGGAAACTGGGAAACTTGAGTGCAGAAGAGGACAGTGGAACTCCATGTGTAGCGGTGAAATGCGTAGATATATGGAAGAACACCAGTGGCGAAGGCGGCTGTCTGGTCTGTAACTGACGCTGAGGCTCGAAAGCATGGGTAGCAAACA : int [1:1296] 18 18 18 18 18 18 18 18 18 18 ... ..$ TGGGGAATATTGGACAATGGGCGAAAGCCTGATCCAGCCATGCCGCGTGTGTGAAGAAGGTCTTCGGATTGTAAAGCACTTTAAGTTGGGAGGAAGGGTTGTAGATTAATACTCTGCAATTTTGACGTTACCGACAGAATAAGCACCGGCTAACTCTGTGCCAGCAGCCGCGGTAATACAGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCGCGTAGGTGGTTCGTTAAGTTGGATGTGAAAGCCCCGGGCTCAACCTGGGAACTGCATTCAAAACTGACGAGCTAGAGTATGGTAGAGGGTGGTGGAATTTCCTGTGTAGCGGTGAAATGCGTAGATATAGGAAGGAACACCAGTGGCGAAGGCGACCACCTGGACTGATACTGACACTGAGGTGCGAAAGCGTGGGGAGCAAACA : int [1:1296] 18 18 18 18 18 18 18 18 18 18 ... ..$ TGGGGAATATTGGACAATGGGCGCAAGCCTGATCCAGCCATACCGCGTGGGTGAAGAAGGCCTTCGGGTTGTAAAGCCCTTTTGTTGGGAAAGAAATCCAGCTGGTTAATACCCGGTTGGGATGACGGTACCCAAAGAATAAGCACCGGCTAACTTCGTGCCAGCAGCCGCGGTAATACGAAGGGTGCAAGCGTTACTCGGAATTACTGGGCGTAAAGCGTGCGTAGGTGGTCGTTTAAGTCCGTTGTGAAAGCCCTGGGCTCAACCTGGGAACTGCAGTGGATACTGGACGACTAGAGTGTGGTAGAGGGTAGCGGAATTCCTGGTGTAGCAGTGAAATGCGTAGAGATCAGGAGGAACATCCATGGCGAAGGCAGCTACCTGGACCAACACTGACACTGAGGCACGAAAGCGTGGGGAGCAAACA : int [1:1296] 18 18 18 18 18 18 18 18 18 18 ... ..$ TAGGGAATCTTCCACAATGGACGAAAGTCTGATGGAGCAACGCCGCGTGAGTGAAGAAGGTTTTCGGATCGTAAAACTCTGTTGTTGGAGAAGAACACGTTTGAGAGTAACTGTTCAGACGTTGACGGTATCCAACCAGAAAGCCACGGCTAACTACGTGCCAGCAGCCGCGGTAATACGTAGGTGGCAAGCGTTATCCGGATTTATTGGGCGTAAAGCGAGCGCAGGCGGTTTCTTAAGTCTGATGTGAAAGCCTTCGGCTTAACCGAAGAAGTGCATCGGAAACTGGGGAACTTGAGTGCAGAAGAGGACAGTGGAACTCCATGTGTAGCGGTGAAATGCGTAGATATATGGAAGAACACCAGTGGCGAAGGCGGCTGTCTGGTCTGTAACTGACGCTGAGGCTCGAAAGCATGGGTAGCGAACA : int [1:1296] 18 18 18 18 18 18 18 18 18 18 ... ..$ TAGGGAATCTTCCACAATGGACGAAAGTCTGATGGAGCAACGCCGCGTGAGTGAAGAAGGTTTTCGGATCGTAAAACTCTGTTGTTGGAGAAGAACACGTTTGAGAGTAACTGTTCAGACGTTGACGGTATCCAACCAGAAAGCCACGGCTAACTACGTGCCAGCAGCCGCGGTAATACGTAGGTGGCAAGCGTTATCCGGATTTATTGGGCGTAAAGCGAGCGCAGGCGGTTTTTTAAGTCTGATGTGAAAGCCTTCGGCTTAACCGAAGAAGTGCATCGGAAACTGGGAAACTTGAGTGCAGAAGAGGACAGTGGAACTCCATGTGTAGCGGTGAAATGCGTAGATATATGGAAGAACACCAGTGGCGAAGGCGGCTGTCTGGTCTGTAACTGACGCTGAGGCTCGAAAGCATGGGTAGCGAACA : int [1:1296] 18 18 18 18 18 18 18 18 18 18 ... ..$ TGGGGAATATTGGACAATGGGCGCAAGCCTGATCCAGCCATGCCGCGTGAGTGATGAAGGCCTTAGGGTTGTAAAGCTCTTTTGTCCGGGACGATAATGACGGTACCGGAAGAATAAGCCCCGGCTAACTTCGTGCCAGCAGCCGCGGTAATACGAAGGGGGCTAGCGTTGCTCGGAATCACTGGGCGTAAAGGGCGCGTAGGCGGCCATTCAAGTCGGGGGTGAAAGCCTGTGGCTCAACCACAGAATTGCCTTCGATACTGTTTGGCTTGAGTTTGGTAGAGGTTGGTGGAACTGCGAGTGTAGAGGTGAAATTCGTAGATATTCGCAAGAACACCAGTGGCGAAGGCGGCCAACTGGACCAACACTGACGCTGAGGCGCGAAAGCGTGGGGAGCAAACA : int [1:1296] 18 18 18 18 18 18 18 18 18 18 ... ..$ TAAGGAATATTGGTCAATGGAGGCAACTCTGAACCAGCCATGCCGCGTGCAGGAAGACGGCCCTCTGGGTTGTAAACTGCTTTTATTCGGGAATAAACCTATCTACGTGTAGATAGCTGAATGTACCGAAGGAATAAGGATCGGCTAACTCCGTGCCAGCAGCCGCGGTAATACGGAGGATCCAAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGTAGGCGGCCTATTAAGTCAGGGGTGAAAGACGGTAGCTCAACTATCGCAGTGCCCTTGATACTGATGGGCTTGAATGAACTAGAGGTAGGCGGAATGTGACAAGTAGCGGTGAAATGCATAGATATGTCACAGAACACCGATTGCGAAGGCAGCTTACTATGGTTTTATTGACGCTGAGGCACGAAAGCGTGGGGATCAAACA : int [1:1296] 18 18 18 18 18 18 18 18 18 18 ... ..$ TGAAGAATCTCAAATATAAAATATATTTTGATTTGTATAATACTTTTTTGGTTACTACATGATTCCATATGTGTTATTTCATAGTTTTGTTGTCTTCACCATTATTCTACAATGTAGAAAATAGTAAAAAAATAAAAAACCCATGAATTAGTAGTGTCCAAAACTTTAACTGGACTGTATATATATTTAAAATAATAAAATAAAAATTATGCCGACAATTACATCAATAGAAGCCGCAATGTTGAAGCTGATAACAAAAATAAAAGAAGAATATCCTGTTTCACTTGATTTAAAAACCAAGCATACCCCTTCTCCTCATCACCAAAGCTTTATTAAAATATCAAGTTTGGCAGCAGCAAAACAGTGAGTGGAAATCCCCTTTTATCCATATACAGTTGAAGTCGGAAGTTTACCGTCGTGGGACCCG : int [1:1296] 18 18 18 18 18 18 18 18 18 18 ... ..$ TAGGGAATCTTCGGCAATGGACGGAAGTCTGACCGAGCAACGCCGCGTGAGTGAAGAAGGTTTTCGGATCGTAAAGCTCTGTTGTAAGAGAAGAACGAGTGTGAGAGTGGAAAGTTCACACTGTGACGGTATCTTACCAGAAAGGGACGGCTAACTACGTGCCAGCAGCCGCGGTAATACGTAGGTCCCGAGCGTTGTCCGGATTTATTGGGCGTAAAGCGAGCGCAGGCGGTTAGATAAGTCTGAAGTTAAAGGCTGTGGCTTAACCATAGTACGCTTTGGAAACTGTTTAACTTGAGTGCAAGAGGGGAGAGTGGAATTCCATGTGTAGCGGTGAAATGCGTAGATATATGGAGGAACACCGGTGGCGAAAGCGGCTCTCTGGCTTGTAACTGACGCTGAGGCTCGAAAGCGTGGGGAGCAAACA : int [1:1296] 18 18 18 18 18 18 18 18 18 18 ... ..$ TGGGGAATTTTGGACAATGGGCGCAAGCCTGATCCAGCAATGCCGCGTGCAGGATGAAGGCCTTCGGGTTGTAAACTGCTTTTGTACGGAACGAAACGGCTCTTTCTAATAAAGGGAGCTAATGACGGTACCGTAAGAATAAGCACCGGCTAACTACGTGCCAGCAGCCGCGGTAATACGTAGGGTGCGAGCGTTAATCGGAATTACTGGGCGTAAAGCGTGCGCAGGCGGTTATGTAAGACAGATGTGAAATCCCCGGGCTCAACCTGGGACCTGCATTTGTGACTGCATAGCTAGAGTACGGTAGAGGGGGATGGAATTCCGCGTGTAGCAGTGAAATGCGTAGATATGCGGAGGAACACCGATGGCGAAGGCAATCCCCTGGACCTGTACTGACGCTCATGCACGAAAGCGTGGGGAGCAAACA : int [1:1296] 18 18 18 18 18 18 18 18 18 18 ... ..$ TGGGGAATTTTGGACAATGGGCGAAAGCCTGATCCAGCAATGCCGCGTGTGGGAAGAAGGCCTTCGGGTTGTAAACCACTTTTGTACGGAACGAAACGGTTCGCTTTAATACAGTGGGCTAATGACGGTACCGTAAGAATAAGCACCGGCTAACTACGTGCCAGCAGCCGCGGTAATACGTAGGGTGCGAGCGTTAATCGGAATTACTGGGCGTAAAGCGTGCGCAGGCGGTTATATAAGACAGTTGTGAAATCCCCGGGCTCAACCTGGGAATTGCATCTGTGACTGTATAGCTAGAGTACGGTAGAGGGGGATGGAATTCCGCGTGTAGCAGTGAAATGCGTAGATATGCGGAGGAACACCGATGGCGAAGGCAATCCCCTGGACCTGTACTGACGCTCATGCACGAAAGCGTGGGGAGCAAACA : int [1:1296] 18 18 18 18 18 18 18 18 18 18 ... ..$ TGGGGAATCTTCCGCAATGGACGAAAGTCTGACGGAGCAACGCCGCGTGAGTGATGAAGGTCTTCGGATTGTAAAGCTCTGTTAATCGGGACGAAAGAGCCTAGTGTGAATAATGCTAGGAAGTGACGGTACCGGAATAGAAAGCCACGGCTAACTACGTGCCAGCAGCCGCGGTAATACGTAGGTGGCAAGCGTTGTCCGGAATTATTGGGCGTAAAGCGCGCGCAGGCGGATCTGCCAGTCTGTCTTAAAAGTTCGGGGCTTAACCCCGTGATGGGATGGAAACTACAGATCTAGAGTATCGGAGAGGAAAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAAGAACACCAGTGGCGAAGGCGACTTTCTGGACGAAAACTGACGCTGAGGCGCGAAAGCCAGGGGAGCGAACG : int [1:1296] 18 18 18 18 18 18 18 18 18 18 ... ..$ TGGGGAATATTGGACAATGGGCGCAAGCCTGATCCAGCAATTCCGCGTGGGTGAAGAAGGTCTTCGGATTGTAAAGCCCTTTCGACAGGGACGATGATGACGGTACCTGTAGAAGAAGCCCCGGCTAACTTCGTGCCAGCAGCCGCGGTAATACGAAGGGGGCTAGCGTTGCTCGGAATGACTGGGCGTAAAGGGCGCGTAGGCGGCACAACTAGTCAGGCGTGAAATTCCTGGGCTTAACCTGGGGGCTGCGTTTGATACGGTTGGGCTAGAGGATGGAAGAGGCTCGTGGAATTCCCAGTGTAGAGGTGAAATTCGTAGATATTGGGAAGAACACCGGTGGCGAAGGCGGCGAGCTGGTCCATTACTGACGCTGAGGCGCGAAAGCGTGGGGAGCAAACA : int [1:1296] 18 18 18 18 18 18 18 18 18 18 ... ..$ TGGGGAATTTTGGACAATGGGCGAAAGCCTGATCCAGCCATACCGCGTGCGGGAAGAAGGCCTTCGGGTTGTAAACCGCTTTTGTCAGGGAAGAAATACCTCGGGCTAATACCCTGGGGTGATGACGGTACCTGAAGAATAAGCACCGGCTAACTACGTGCCAGCAGCCGCGGTAATACGTAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGTGCGCAGGCGGTTCTATAAGACAGATGTGAAATCCCCGGGCTCAACCTGGGAACTGCATTTGTGACTGTAGAGCTAGAGTACGGTAGAGGGGGATGGAATTCCGCGTGTAGCAGTGAAATGCGTAGATATGCGGAGGAACACCGATGGCGAAGGCAATCCCCTGGACCTGTACTGACGCTCATGCACGAAAGCGTGGGGAGCAAACA : int [1:1296] 18 18 18 18 18 18 18 18 18 18 ... ..$ TAGGGAATCTTCCACAATGGACGCAAGTCTGATGGAGCAACGCCGCGTGAGTGAAGAAGGTTTTCGGATCGTAAAGCTCTGTTGTTGGTGAAGAAGGATAGAGGCAGTAACTGGTCTTTATTTGACGGTAATCAACCAGAAAGTCACGGCTAACTACGTGCCAGCAGCCGCGGTAATACGTAGGTGGCAAGCGTTGTCCGGATTTATTGGGCGTAAAGCGAGCGCAGGCGGAATGATAAGTCTGATGTGAAAGCCCACGGCTCAACCGTGGAACTGCATCGGAAACTGTCATTCTTGAGTGCAGAAGAGGAGAGTGGAACTCCATGTGTAGCGGTGGAATGCGTAGATATATGGAAGAACACCAGTGGCGAAGGCGGCTCTCTGGTCTGCAACTGACGCTGAGGCTCGAAAGCATGGGTAGCGAACA : int [1:1296] 18 18 18 18 18 18 18 18 18 18 ... ..$ GCGGTCGACGTCACCGGCTTTCTAGCTATCGCCGCTCAATTTTTCATTGTTCCATTTGTTTTGTCTTGTTCCCTGCACACCTGGTTTACATTCCCCAATCACACTGCATGTATTTATTCCTCTGTTCCCCCACATGTCTTTGTGTGAAATTGTTTTGTGTTACATGTTTGAGGTTACGCGCCAGCCTGGTGTTTATGATCCATGTTATTGCACGTAGTATGTTTATTTGATATCATTAGCTTTTGTGACTGTGTTTTGTGCTCTGCACTTTTGCTATTGTGGCTGGATGTTTTGACGCAGTTGCGTCCGTCTGCTGTTTTCTCCTGCCTCAATAAAGTGTGCGCCTGTTCGCAAATCTCGGCTCTCCTGCGCCTGACTTCACTACCAGTACGTGCCCAACATCCTGACAGAATTTCACACCACCCATGGAGTCAGCA : int [1:1296] 18 18 18 18 18 18 18 18 18 18 ... ..$ TGGGGAATATTGCACAATGGGCGGAAGCCTGATGCAGCGACGCCGCGTGAGGGATGACGGCCTTCGGGTTGTAAACCTCTTTCAGCACGGAAGAAGCGAGAGTGACGGTACGTGCAGAAGAAGCGCCGGCTAACTACGTGCCAGCAGCCGCGGTAATACGTAGGGCGCAAGCGTTGTCCGGAATTATTGGGCGTAAAGAGCTCGTAGGCGGTTTGTCGCGTCTGCTGTGAAAGCCCGGGGCTTAACCCCGGGTGTGCAGTGGGTACGGGCAGACTTGAGTGCAGTAGGGGAGACTGGAATTCCTGGTGTAGCGGTGAAATGCGCAGATATCAGGAGGAACACCGATGGCGAAGGCAGGTCTCTGGGCTGTTACTGACGCTGAGGAGCGAAAGCATGGGGAGCGAACA : int [1:1296] 18 18 18 18 18 18 18 18 18 18 ... ..$ TAAGGAATATTGCGCAATGGACGAAAGTCTGACGCAGCGACGCCGCGTGGGGGATGAAGGTCTTCGGATTGTAAACCCCTTTCGGGAGGGAAGATGGAGTGGGTAACCACTTGGACGGTACCTCCAGAAGCAGCCACGGCTAACTTCGTGCCAGCAGCCGCGGTAATACGAAGGTGGCAAGCGTTGTTCGGATTCACTGGGCGTACAGGGAGCGTAGGCGGTTGGGTAAGCCCTCCGTGAAATCTCCGGGCCTAACCCGGAAAGTGCAGAGGGGACTGCTCAGCTAGAGGATGGGAGAGGAGCGCGGAATTCCCGGTGTAGCGGTGAAATGCGTAGAGATCGGGAGGAAGGCCGGTGGCGAAGGCGGCGCTCTGGAACATTTCTGACGCTGAGGCTCGAAAGCGTGGGGAGCAAACA : int [1:1296] 18 18 18 18 18 18 18 18 18 18 ... ..$ TGGGGAATATTGCACAATGGGCGGAAGCCTGATGCAGCGACGCCGCGTGAGGGATGAAGGCCTTCGGGTTGTAAACCTCTTTCAGCAGGGACGAAGCGTGAGTGACGGTACCTGCAGAAGAAGCACCGGCTAACTACGTGCCAGCAGCCGCGGTAATACGTAGGGTGCGAGCGTTGTCCGGAATTACTGGGCGTAAAGAGTTCGTAGGCGGTTTGTCGCGTCGTTTGTGAAAACCCGGGGCTCAACTTCGGGCTTGCAGGCGATACGGGCAGACTTGAGTGTTTCAGGGGAGACTGGAATTCCTGGTGTAGCGGTGAAATGCGCAGATATCAGGAGGAACACCGGTGGCGAAGGCGGGTCTCTGGGAAACAACTGACGCTGAGGAACGAAAGCGTGGGTAGCAAACA : int [1:1296] 18 18 18 18 18 18 18 18 18 18 ... ..$ TGGGGAATATTGCACAATGGGCGCAAGCCTGATGCAGCCATGCCGCGTGTATGAAGAAGGCCTTCGGGTTGTAAAGTACTTTCAGCGGGGAGGAAGGTGTTGTGGTTAATAACCACAGCAATTGACGTTACCCGCAGAAGAAGCACCGGCTAACTCCGTGCCAGCAGCCGCGGTAATACGGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGTCTGTCAAGTCGGATGTGAAATCCCCGGGCTCAACCTGGGAACTGCATTCGAAACTGGCAGGCTAGAGTCTTGTAGAGGGGGGTAGAATTCCAGGTGTAGCGGTGAAATGCGTAGAGATCTGGAGGAATACCGGTGGCGAAGGCGGCCCCCTGGACAAAGACTGACGCTCAGGTGCGAAAGCGTGGGGAGCAAACA : int [1:1296] 18 18 18 18 18 18 18 18 18 18 ... ..$ TGGGGAATATTGCACAATGGGGGAAACCCTGATGCAGCCATGCCGCGTGTGTGAAGAAGGCCTTCGGGTTGTAAAGCACTTTCAGCGAGGAGGAAAGGTTGGCGCCTAATACGTGTCAACTGTGACGTTACTCGCAGAAGAAGCACCGGCTAACTCCGTGCCAGCAGCCGCGGTAATACGGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGTTGGATAAGTTAGATGTGAAAGCCCCGGGCTCAACCTGGGAATTGCATTTAAAACTGTCCAGCTAGAGTCTTGTAGAGGGGGGTAGAATTCCAGGTGTAGCGGTGAAATGCGTAGAGATCTGGAGGAATACCGGTGGCGAAGGCGGCCCCCTGGACAAAGACTGACGCTCAGGTGCGAAAGCGTGGGGAGCAAACA : int [1:1296] 18 18 18 18 18 18 18 18 18 18 ... ..$ CTGGTCCCAGTTCCTCCCGTCTCTCTCGATGACCTTCTTCAGCATCTGCTTTAGGGTCTTATTGAAGAATTTGACTAGCACGTCCGTTTGTGGGATGGTACACACTGGTCCTCACCTGTTCAAATCGTAAAAGATTGCATTACACAAGACATGAATGTGGTGCCCTGGTCGTCAGGATTTCCCACGGCAATACCCACCCAGCTGAATAAATGGAAGAGCTCCTGTGTGGTACCTTTCGCTGCCGCTGTGTGTAATGGGATTGCCTCCGGATACGGCTGGCATATTCCACGATTACCAGGATGTATTGATGTCCCCTCGGGGTCTTCACCAACGGACCCACCAGAACCAAAGGGTTTCTATAATGTGCCCTCGGGGCTGTGATCTGGCACTC : int [1:1296] 18 18 18 18 18 18 18 18 18 18 ... ..$ TAGGGAATATTGGTCAATGGGGGCAACCCTGAACCAGCCATGCCGCGTGCAGGAATAAGGCCCTATGGGTCGTAAACTGCTTTTGAACGGGAAGAAATCTATTTACGTGTAAATAGTTGACGGTACCGTTAGAATAAGGATCGGCTAACTTCGTGCCAGCAGCCGCGGTAATACGAAGGATCCAAGCGTTGTCCGGATTTACTGGGTTTAAAGGGTGCGTAGGCGGACTTATAAGTCAGTGGTGAAAGCCTTCAGCTTAACTGAAGAACTGCCATTGAAACTGTAAGTCTCGAGTTCGGTTGAGGTCATTGGAATGTAACATGTAGCGGTGAAATGCATAGATATGTTACAGAACACCGATTGCGAAGGCAGATGACTAAACCGAAACTGACGCTGAGGCACGAAAGCGTGGGGATCAAACA : int [1:1296] 18 18 18 18 18 18 18 18 18 18 ... ..$ TAGGGAATCTTCCGCAATGGACGAAAGTCTGACGGAGCAACGCCGCGTGAGTGAAGAAGGTTTTCGGATCGTAAAACTCTGTTGTTAAAGAAGAACAAGGATGAGAGTAACTGCTCATCCCCTGACGGTATTTAACCAGAAAGCCACGGCTAACTACGTGCCAGCAGCCGCGGTAATACGTAGGTGGCAAGCGTTGTCCGGATTTATTGGGCGTAAAGCGAGCGCAGGCGGTTCTTTAAGTCTGATGTGAAAGCCCCCGGCTCAACCGGGGAGGGTCATTGGAAACTGGAGAACTTGAGTGCAGAAGAGGAGAGTGGAATTCCACGTGTAGCGGTGAAATGCGTAGATATGTGGAGGAACACCAGTGGCGAAGGCGACTCTCTGGTCTGTAACTGACGCTGAGGCTCGAAAGCGTGGGGAGCAAACA : int [1:1296] 18 18 18 18 18 18 18 18 18 18 ... ..$ TAGGGAATCTTCGGCAATGGACGCAAGTCTGACCGAGCAACGCCGCGTGAGTGAAGAAGGTTTTCGGATCGTAAAACTCTGTTGTTAGAAAAGAACAAGGATGAGAGTGGAAAGTTCATCCCTTGACGGTATCTAACCAGAAAGCCACGGCTAACTACGTGCCAGCAGCCGCGGTAATACGTAGGTGGCAAGCGTTGTCCGGATTTATTGGGCGTAAAGCGAGCGCAGGCGGTCTTTTAAGTCTGATGTGAAAGCCCCCGGCTTAACCGGGGAGGGTCATTGGAAACTGGGAGACTTGAGTGCAGAAGAGGAAAGCGGAATTCCATGTGTAGCGGTGAAATGCGTAGATATATGGAGGAACACCAGTGGCGAAGGCGGCTTTCTGGTCTGTAACTGACGCTGAGGCTCGAAAGCGTGGGGAGCAAACA : int [1:1296] 18 18 18 18 18 18 18 18 18 18 ... ..$ TAGGGAATCTTCCACAATGGGCGAAAGCCTGATGGAGCAACGCCGCGTGTGTGATGAAGGCTTTCGGGTCGTAAAGCACTGTTGTATGGGAAGAACAGCTAGAATAGGGAATGATTTTAGTTTGACGGTACCATACCAGAAAGGGACGGCTAAATACGTGCCAGCAGCCGCGGTAATACGTATGTCCCGAGCGTTATCCGGATTTATTGGGCGTAAAGCGAGCGCAGACGGTTGATTAAGTCTGATGTGAAAGCCCGGAGCTCAACTCCGGAATGGCATTGGAAACTGGTTAACTTGAGTGCAGTAGAGGTAAGTGGAACTCCATGTGTAGCGGTGGAATGCGTAGATATATGGAAGAACACCAGTGGCGAAGGCGGCTTACTGGACTGTAACTGACGTTGAGGCTCGAAAGTGTGGGTAGCAAACA : int [1:1296] 18 18 18 18 18 18 18 18 18 18 ... ..$ TGGGGAATATTGGACAATGGGGGAAACCCTGATCCAGCCATGCCGCGTGTGTGAAGAAGGCCTTTTGGTTGTAAAGCACTTTAAGCGAGGAGGAGGCTACCCTGACTAATATTCAGGAGTAGTGGACGTTACTCGCAGAATAAGCACCGGCTAACTCTGTGCCAGCAGCCGCGGTAATACAGAGGGTGCGAGCGTTAATCGGAATTACTGGGCGTAAAGCGCGCGTAGGCGGTTTATTAAGTCGGATGTGAAATCCCTGAGCTTAACTTAGGAATTGCATTCGATACTGGTAAGCTAGAGTATGGGAGAGGAAGGTAGAATTCCAGGTGTAGCGGTGAAATGCGTAGAGATCTGGAGGAATACCGATGGCGAAGGCAGCCTTCTGGCCTAATACTGACGCTGAGGTGCGAAAGCATGGGGAGCAAACA : int [1:1296] 18 18 18 18 18 18 18 18 18 18 ... ..$ TAGGGAATATTGGGCAATGGATGCAAGTCTGACCCAGCCATGCCGCGTGCAGGAAGAAGGTCCTCTGGATTGTAAACTGCTTTTGTCGGGGAAGAATAGGCATCTTGCGAGGTGTTGTGACGGTACCCGATGAATAAGCCACGGCTAACTACGTGCCAGCAGCCGCGGTAATACGTAGGTGGCAAGCGTTGTCCGGATTTATTGGGTTTAAAGGGTGCGTAGGTGGTTTGCTAAGTCAGTGGTGAAAGCTGGTTGCTCAACAATCAAGTTGCCATTGATACTGTCAGACTTGAGAGAAGTGGAGGCTCATGGAATGGATGGTGTAGCGGTGAAATGCATAGATATCATCCAGAACGTCGATTGCGAAGGCAGTGGGCTGTACTTTTTCTGACACTGAGGCACGAAAGCGTGGGGATCAAACA : int [1:1296] 18 18 18 18 18 18 18 18 18 18 ... ..$ TGGGGAATATTGCACAATGGGGGAAACCCTGATGCAGCAACGCCGCGTGAGTGATGAAGGCCTTCGGGTTGTAAAGCTCTGTCTTTGGGGACGATAATGACGGTACCCAAGGAGGAAGCCACGGCTAACTACGTGCCAGCAGCCGCGGTAATACGTAGGTGGCAAGCGTTGTCCGGATTTACTGGGCGTAAAGGGAGCGTAGGCGGATTTTTAAGTGGGATGTGAAATACCCGGGCTCAACTTGGGTGCTGCATTCCAAACTGGAAGTCTAGAGTGCAGGAGAGGAAAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGAGATTAGGAAGAACACCAGTGGCGAAGGCGACTTTCTGGACTGTAACTGACGCTGAGGCTCGAAAGCGTGGGGAGCAAACA : int [1:1296] 18 18 18 18 18 18 18 18 18 18 ... ..$ TGGGGAATATTGGACAATGGGCGCAAGCCTGATCCAGCCATACCGCGTGGGTGAAGAAGGCCTTCGGGTTGTAAAGCCCTTTTGTTGGGAAAGAAATCCAGCTGGCTAATACCCGGTTGGGATGACGGTACCCAAAGAATAAGCACCGGCTAACTTCGTGCCAGCAGCCGCGGTAATACGAAGGGTGCAAGCGTTACTCGGAATTACTGGGCGTAAAGCGTGCGTAGGTGGTCGTTTAAGTCCGTTGTGAAAGCCCTGGGCTCAACCTGGGAACTGCAGTGGATACTGGACGACTAGAGTGTGGTAGAGGGTAGCGGAATTCCTGGTGTAGCAGTGAAATGCGTAGAGATCAGGAGGAACATCCATGGCGAAGGCAGCTACCTGGACCAACACTGACACTGAGGCACGAAAGCGTGGGGAGCAAACA : int [1:1296] 18 18 18 18 18 18 18 18 18 18 ... ..$ TGGGGAATATTGGACAATGGGCGAAAGCCTGATCCAGCAATGCCGCGTGAGTGATGAAGGCCTTAGGGTTGTAAAGCTCTTTTACCAGGGATGATAATGACAGTACCTGGAGAATAAGCTCCGGCTAACTCCGTGCCAGCAGCCGCGGTAATACGGAGGGAGCTAGCGTTGTTCGGAATTACTGGGCGTAAAGCGCACGTAGGCGGCTACTCAAGTCAGAGGTGAAAGCCCGGGGCTCAACCCCGGAACTGCCTTTGAAACTAGGTAGCTAGAATCTTGGAGAGGTCAGTGGAATTCCGAGTGTAGAGGTGAAATTCGTAGATATTCGGAAGAACACCAGTGGCGAAGGCGACTGACTGGACAAGTATTGACGCTGAGGTGCGAAAGCGTGGGGAGCAAACA : int [1:1296] 18 18 18 18 18 18 18 18 18 18 ... ..$ TGGGGAATTTTGGACAATGGGCGCAAGCCTGATCCAGCCATGCCGCGTGCGGGAAGAAGGCCTTCGGGTTGTAAACCGCTTTTGTCAGGGAAGAAATCCTTTGAACTAATACTTCGGAGGGATGACGGTACCTGAAGAATAAGCACCGGCTAACTACGTGCCAGCAGCCGCGGTAATACGTAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGTGCGCAGGCGGTTATGCAAGACAGATGTGAAATCCCCGGGCTCAACCTGGGAACTGCATTTGTGACTGCATAGCTAGAGTACGGTAGAGGGGGATGGAATTCCGCGTGTAGCAGTGAAATGCGTAGATATGCGGAGGAACACCGATGGCGAAGGCAATCCCCTGGACCTGTACTGACGCTCATGCACGAAAGCGTGGGGAGCAAACA : int [1:1296] 18 18 18 18 18 18 18 18 18 18 ... ..$ GTGCACGCGCCTAAGCCCATTGTCCCTTGATCGGCCACTTGAGAAAGGCGATAATGTGTTTCAGCCTGGGGCTGGAATGACGACATTCAGGTTTTTCCCGGGCTCTGAGAGCCTATTGGAGCTGTGGGAAGTGTCACGTTACCGCAGAGATCCTAAATTTTGGAAAGAGATGTCAAAGAAAGACAATAAATGGTCAGACAGGCCACTTCCTGTAAAGGAATCTCTCAGGTTTTGAAAAGCCAATAATTATATGCATATTCTAGTTACTGGGCAGGAGTAGTAACCAGATTAAATCGGGTACGTTTTTTATCCAGCCGTGTCAATACTGCCCCCTAGCCCTAACAGGTTAAAGAATAGCCAGGCATCTTTTACTAATAGAATGACGTCAATATCC : int [1:1296] 18 18 18 18 18 18 18 18 18 18 ... ..$ TGGGGAATTTTCCGCAATGGGCGAAAGCCTGACGGAGCAATACCGCGTGAGGGAAGAATGCCTATGGGTTGTAAACCTCTTTTTTCAGGGAGGAATAAAATGACGTGTACCTGAAGAATAAGCATCGGCTAACTCCGTGCCAGCAGCCGCGGTAAGACGGAGGATGCAAGTGTTATCCGGAATCACTGGGCGTAAAGCGTCTGTAGGTGGTTTAATAAGTCAACTGTTAAATCTTGATGGCTCAACTTCAAAATCGCAGTCGAAACTATTAGACTAGAGTATAGTAGAGGTAAAGGGAATTTCCAGTGGAGCGGTGAAATGCGTAGATATTGGAAAGAACACCGATGGCGAAAGCACTTTACTGGGCTATTACTAACACTCAGAGACGAAAGCTAGGGTAGCAAATG : int [1:1296] 18 18 18 18 18 18 18 18 18 18 ... ..$ TGGGGAATTGTTCGCAATGGGCGCAAGCCTGACGACGCAACGCCGCGTGGAGGATGAAGGTCTTCGGATTGTAAACTCCTGTTGATCGGGACGAAAAGCCTCAACCTAATACGTTGGGGACTGACGGTACCGGTTGAGGAAGCCACGGCTAACTCTGTGCCAGCAGCCGCGGTAATACAGAGGTGGCAAGCGTTGTTCGGAATTACTGGGCGTAAAGGGCGCGTAGGCGGCCTTCTAAGTCGGACGTGAAAGCCCCAGGCTTAACCTGGGAACTGCGTCCGATACTGGGAGGCTTGGATTCGGGAGAGGGATGTGGAATTCCAGGTGTAGCGGTGAAATGCGTAGATATCTGGAGGAACACCGGTGGCGAAGGCGGCATCCTGGACCGAGATCGACGCTGAGGCGCGAAAGCTAGGGGAGCAAACG : int [1:1296] 18 18 18 18 18 18 18 18 18 18 ... ..$ TTGGGAATCTTGGACAATGGGGGAAACCCTGATCCAGCCATGCCGCGTGAGTGATGAAGGCCTTCGGGTTGTAAAACTCTTTCGCGCACGACGATAATGACGGTAGTGCGAGAAGAAGCTCCGGCTAACTTCGTGCCAGCAGCCGCGGTAATACGAAGGGGGCTAGCGTTGTTCGGAATTACTGGGCGTAAAGCGCGCGCAGGCGGTCTTCCAAGTCAGTGGTGAAAGCCCGGAGCTCAACTCCGGAACTGCCATTGAAACTGTGAGACTTGAGTATGAGAGAGGTGAGTGGAATTCCCAGTGTAGAGGTGAAATTCGTAGATATTGGGAAGAACACCGGTGGCGAAGGCGGCTCACTGGCTCATTACTGACGCTCAGGCGCGACAGCGTGGGGATCAAACA : int [1:1296] 18 18 18 18 18 18 18 18 18 18 ... .. [list output truncated] ..- attr(, "weight")= int [1:1296] 1 2 3 3 1 2 1 1 1 1 ... ..- attr(, "nr")= int 1296 ..- attr(, "nc")= num 4 ..- attr(, "index")= int [1:1563] 1 2 3 2 4 3 4 3 4 5 ... ..- attr(, "levels")= chr [1:4] "a" "c" "g" "t" ..- attr(, "allLevels")= chr [1:18] "a" "c" "g" "t" ... ..- attr(, "type")= chr "DNA" ..- attr(, "contrast")= num [1:18, 1:4] 1 0 0 0 0 1 1 1 0 0 ... .. ..- attr(, "dimnames")=List of 2 .. .. ..$ : NULL .. .. ..$ : chr [1:4] "a" "c" "g" "t" ..- attr(, "class")= chr "phyDat" $ model : chr "GTR" $ INV :Formal class 'dgCMatrix' [package "Matrix"] with 6 slots .. ..@ i : int [1:201] 1 5 53 87 117 127 130 186 211 214 ... .. ..@ p : int [1:5] 0 53 103 145 201 .. ..@ Dim : int [1:2] 1296 4 .. ..@ Dimnames:List of 2 .. .. ..$ : NULL .. .. ..$ : NULL .. ..@ x : num [1:201] 1 1 1 1 1 1 1 1 1 1 ... .. ..@ factors : list() $ ll.0 : num [1:1296, 1] 0.0392 0.0472 0.0387 0.0498 0.0498 ... ..- attr(, "dimnames")=List of 2 .. ..$ : NULL .. ..$ : NULL $ tree :List of 4 ..$ edge : int [1:13155, 1:2] 7250 7250 11522 11522 10189 10189 8542 8542 7624 7624 ... ..$ edge.length: num [1:13155] 7.42e-02 1.90e-01 1.00e-08 3.83e-03 1.32e-01 ... ..$ tip.label : chr [1:6579] "TAGGGAATATTGCACAATGGAGGAAACTCTGATGCAGCGACGTCGCGTGAGGGAAGAAGGTTTTCGGATTGTAAACCTCTGTCTTTGGTGAAGAAAATGACGGTAACCAAA"| truncated "TGGGGAATATTGGACAATGGGCGAAAGCCTGATCCAGCCATGCCGCGTGTGTGAAGAAGGTCTTCGGATTGTAAAGCACTTTAAGTTGGGAGGAAGGGCAGTAAATTAATA"| truncated "TGGGGAATATTGCACAATGGGGGAAACCCTGATGCAGCCATGCCGCGTGTGTGAAGAAGGCCTTCGGGTTGTAAAGCACTTTCAGCGAGGAGGAAAGGTTGATGCCTAATA"| truncated "TGGGGAATATTGCACAATGGGCGCAAGCCTGATGCAGCCATGCCGCGTGTATGAAGAAGGCCTTCGGGTTGTAAAGTACTTTCAGCGGGGAGGAAGGGAGTAAAGTTAATA"| truncated ... ..$ Nnode : int 6577 ..- attr(, "class")= chr "phylo" ..- attr(*, "order")= chr "postorder" $ lv : num [1:1296, 1:4] 0.224 0.27 0.221 0.285 0.284 ... $ call : language pml(tree = treeNJ, data = phang.align, k = 4, inv = 0.174896258961264, bf = c(0.269859436060646, 0.22404764639921| truncated ... $ df : num 13165 $ wMix : num 0 $ llMix : num 0 $ Mkv : logi FALSE $ site.rate: chr "gamma"

  • attr(*, "class")= chr "pml"

> sessionInfo()

R version 4.1.0 (2021-05-18) Platform: x86_64-conda-linux-gnu (64-bit) Running under: Ubuntu 20.04.3 LTS

Matrix products: default BLAS/LAPACK: /home/r01mt19/.conda/envs/updatedR/lib/libopenblasp-r0.3.18.so

locale: [1] LC_CTYPE=en_GB.UTF-8 LC_NUMERIC=C LC_TIME=en_GB.UTF-8 LC_COLLATE=en_GB.UTF-8
[5] LC_MONETARY=en_GB.UTF-8 LC_MESSAGES=en_GB.UTF-8 LC_PAPER=en_GB.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C

attached base packages: [1] stats graphics grDevices utils datasets methods base

other attached packages: [1] microbiome_1.14.0 ggplot2_3.3.5 ape_5.5 data.table_1.14.2 magrittr_2.0.1 phyloseq_1.36.0

loaded via a namespace (and not attached): [1] Rcpp_1.0.7 lattice_0.20-45 tidyr_1.1.4 Biostrings_2.60.2 assertthat_0.2.1
[6] digest_0.6.28 foreach_1.5.1 utf8_1.2.2 R6_2.5.1 GenomeInfoDb_1.28.4
[11] plyr_1.8.6 stats4_4.1.0 pillar_1.6.4 zlibbioc_1.38.0 rlang_0.4.12
[16] rstudioapi_0.13 vegan_2.5-7 S4Vectors_0.30.2 Matrix_1.3-2 labeling_0.4.2
[21] splines_4.1.0 Rtsne_0.15 stringr_1.4.0 igraph_1.2.7 RCurl_1.98-1.5
[26] munsell_0.5.0 compiler_4.1.0 pkgconfig_2.0.3 BiocGenerics_0.38.0 multtest_2.48.0
[31] mgcv_1.8-38 biomformat_1.20.0 tidyselect_1.1.1 tibble_3.1.6 GenomeInfoDbData_1.2.6 [36] IRanges_2.26.0 codetools_0.2-18 fansi_0.5.0 permute_0.9-5 crayon_1.4.2
[41] dplyr_1.0.7 withr_2.4.2 MASS_7.3-54 bitops_1.0-7 rhdf5filters_1.4.0
[46] grid_4.1.0 nlme_3.1-153 jsonlite_1.7.2 gtable_0.3.0 lifecycle_1.0.1
[51] DBI_1.1.1 scales_1.1.1 stringi_1.7.5 farver_2.1.0 XVector_0.32.0
[56] reshape2_1.4.4 ellipsis_0.3.2 generics_0.1.1 vctrs_0.3.8 Rhdf5lib_1.14.2
[61] iterators_1.0.13 tools_4.1.0 ade4_1.7-18 Biobase_2.52.0 glue_1.5.0
[66] purrr_0.3.4 parallel_4.1.0 survival_3.2-13 yaml_2.2.1 colorspace_2.0-2
[71] rhdf5_2.36.0 cluster_2.1.2

benjjneb commented 2 years ago

See the documentation on Estimating phylogenetic trees with phangorn.

There is an additional step you need to perform (bootstrap.pml) to get bootstrap confidence estimates.

marwa38 commented 2 years ago

Thanks again @benjjneb

It takes about 5 days to run bootstrap (bold) in the code as follows 

seqs <- getSequences(seqtab.nochim2) #extract sequences from dada2 output
names(seqs) <- seqs # This propagates to the tip labels of the tree
alignment <- AlignSeqs(DNAStringSet(seqs), anchor=NA) 
#change sequence alignment output into a phyDat structure 
phang.align <- phyDat(as(alignment, "matrix"), type="DNA") 
dm <- dist.ml(phang.align) #create distance matrix
#reconstruct unrooted tree 
treeNJ <- NJ(dm) # Note, tip order != sequence order #perform neighbor joining 
fit <- pml(treeNJ, data=phang.align) #internal maxiumum likelihood
fit <- pml(treeNJ, data=phang.align)
fitJC  <- optim.pml(fit, TRUE)
**bs = bootstrap.pml(fitJC, bs=100, optNni=TRUE,
    control = pml.control(trace = 0))**

I need to run this on fitGTR, is there a difference between bootstrapping fitJC vs fitGTR?

fitGTR <- update(fit, k=4, inv=0.2)
fitGTR <- optim.pml(fitGTR, model="GTR", optInv=TRUE, optGamma=TRUE,
                    rearrangement = "stochastic", control = pml.control(trace = 0))

Thanks very much

benjjneb commented 2 years ago

is there a difference between bootstrapping fitJC vs fitGTR?

I would presume yes.

For larger trees, the phangorn implemantations get slow enough to be unwieldy to unusuable for microbiome datasets. You may want to consider using an external program such as RaxML to do the tree-ing part of the analysis.