text: user5003: I have a data frame where the row names are the species names, and each column can either be an Amino-Acid character or "-".
  I wish to write it in a fasta format. Simple example of the format is:
  >UniRef90_A0A1V4QIJ3
  ------------------------------------------------------------
  --------------------------MDISTFSP-----PVAG-----------VE----
  ------ITAF-------------V------------------------------------
  LN--------G-------------------------------------------------
  ----EKIPA-----------------------------------------IVLSKD----
  ---LNPFL------------------Q-ELLDQEPAC-----------------------
  ------------EHDIGTCYG------------------------DA-------------
  --------------------------------------------------PC-----IS-
  -----------------------GPDAWNHSGFQC----Q---------VC---------
  ------------GLVKSWNL-------------------VGDFVVYRQE-----------
  >UniRef90_A0A0L9V5F8
  ------------------------------------------------------------
  RFHTLFRNEYGHLRVLQRFDQRSKQIQNLENYRLVEFKSKPNTLLLPHHADADFLLVVLN
  GRALLTLVNP-------------D---------------------------------G--
  RDSYILEQGHA-------------------------------------------------
  ----QKIPAGTIFFLVNPNDNENLRI------------------------IKIATPINNP
  HRFQDFFL-------------SSTEAQQSYLQG--FS-----------------------
  ----------------KNVLEASFDSEFKEINRVLFGEEGQQQQGEESQQEGVIVELERE
  QIRELIKHA-----------------------------------------KSSSRRSLS-
  -----------------------SQ-----DEPFNLRNRKP--------IY--SN-----
  ------------KF-GRWYEITPEKNP------------Q--------------------
  
  I can do it using the following for loop:
  for (n in row.names(df)){
      ss = do.call(paste, c(as.list(mu_df[1, ]), sep = ""))
      write.fasta(ss,
                    names=n,
                    as.string=TRUE,
                    open="a",
                    new_file_path)
  }
  
  Is there a faster way of writing it? I have to write millions of those files and I wish to optimize it.
  In order to create the data frame:
  structure(list(V1 = c("-", "-"), V2 = c("-", "-"), V3 = c("-", 
  "-"), V4 = c("-", "-"), V5 = c("-", "-"), V6 = c("-", "-"), V7 = c("-", 
  "-"), V8 = c("-", "-"), V9 = c("-", "-"), V10 = c("-", "-"), 
      V11 = c("-", "-"), V12 = c("-", "-"), V13 = c("-", "-"), 
      V14 = c("-", "-"), V15 = c("-", "-"), V16 = c("-", "-"), 
      V17 = c("-", "-"), V18 = c("-", "-"), V19 = c("-", "-"), 
      V20 = c("-", "-"), V21 = c("-", "-"), V22 = c("-", "-"), 
      V23 = c("-", "-"), V24 = c("-", "-"), V25 = c("-", "-"), 
      V26 = c("-", "-"), V27 = c("-", "-"), V28 = c("-", "-"), 
      V29 = c("-", "-"), V30 = c("-", "-"), V31 = c("-", "-"), 
      V32 = c("-", "-"), V33 = c("-", "-"), V34 = c("-", "-"), 
      V35 = c("-", "-"), V36 = c("-", "-"), V37 = c("-", "-"), 
      V38 = c("-", "-"), V39 = c("-", "-"), V40 = c("-", "-"), 
      V41 = c("-", "-"), V42 = c("-", "-"), V43 = c("-", "-"), 
      V44 = c("-", "-"), V45 = c("-", "-"), V46 = c("-", "-"), 
      V47 = c("-", "-"), V48 = c("-", "-"), V49 = c("-", "-"), 
      V50 = c("-", "-"), V51 = c("-", "-"), V52 = c("-", "-"), 
      V53 = c("-", "-"), V54 = c("-", "-"), V55 = c("-", "-"), 
      V56 = c("-", "-"), V57 = c("-", "-"), V58 = c("-", "-"), 
      V59 = c("-", "-"), V60 = c("-", "-"), V61 = c("-", "R"), 
      V62 = c("-", "F"), V63 = c("-", "H"), V64 = c("-", "T"), 
      V65 = c("-", "L"), V66 = c("-", "F"), V67 = c("-", "R"), 
      V68 = c("-", "N"), V69 = c("-", "E"), V70 = c("-", "Y"), 
      V71 = c("-", "G"), V72 = c("-", "H"), V73 = c("-", "L"), 
      V74 = c("-", "R"), V75 = c("-", "V"), V76 = c("-", "L"), 
      V77 = c("-", "Q"), V78 = c("-", "R"), V79 = c("-", "F"), 
      V80 = c("-", "D"), V81 = c("-", "Q"), V82 = c("-", "R"), 
      V83 = c("-", "S"), V84 = c("-", "K"), V85 = c("-", "Q"), 
      V86 = c("-", "I"), V87 = c("M", "Q"), V88 = c("D", "N"), 
      V89 = c("I", "L"), V90 = c("S", "E"), V91 = c("T", "N"), 
      V92 = c("F", "Y"), V93 = c("S", "R"), V94 = c("P", "L"), 
      V95 = c("-", "V"), V96 = c("-", "E"), V97 = c("-", "F"), 
      V98 = c("-", "K"), V99 = c("-", "S"), V100 = c("P", "K"), 
      V101 = c("V", "P"), V102 = c("A", "N"), V103 = c("G", "T"
      ), V104 = c("-", "L"), V105 = c("-", "L"), V106 = c("-", 
      "L"), V107 = c("-", "P"), V108 = c("-", "H"), V109 = c("-", 
      "H"), V110 = c("-", "A"), V111 = c("-", "D"), V112 = c("-", 
      "A"), V113 = c("-", "D"), V114 = c("-", "F"), V115 = c("V", 
      "L"), V116 = c("E", "L"), V117 = c("-", "V"), V118 = c("-", 
      "V"), V119 = c("-", "L"), V120 = c("-", "N"), V121 = c("-", 
      "G"), V122 = c("-", "R"), V123 = c("-", "A"), V124 = c("-", 
      "L"), V125 = c("-", "L"), V126 = c("-", "T"), V127 = c("I", 
      "L"), V128 = c("T", "V"), V129 = c("A", "N"), V130 = c("F", 
      "P"), V131 = c("-", "-"), V132 = c("-", "-"), V133 = c("-", 
      "-"), V134 = c("-", "-"), V135 = c("-", "-"), V136 = c("-", 
      "-"), V137 = c("-", "-"), V138 = c("-", "-"), V139 = c("-", 
      "-"), V140 = c("-", "-"), V141 = c("-", "-"), V142 = c("-", 
      "-"), V143 = c("-", "-"), V144 = c("V", "D"), V145 = c("-", 
      "-"), V146 = c("-", "-"), V147 = c("-", "-"), V148 = c("-", 
      "-"), V149 = c("-", "-"), V150 = c("-", "-"), V151 = c("-", 
      "-"), V152 = c("-", "-"), V153 = c("-", "-"), V154 = c("-", 
      "-"), V155 = c("-", "-"), V156 = c("-", "-"), V157 = c("-", 
      "-"), V158 = c("-", "-"), V159 = c("-", "-"), V160 = c("-", 
      "-"), V161 = c("-", "-"), V162 = c("-", "-"), V163 = c("-", 
      "-"), V164 = c("-", "-"), V165 = c("-", "-"), V166 = c("-", 
      "-"), V167 = c("-", "-"), V168 = c("-", "-"), V169 = c("-", 
      "-"), V170 = c("-", "-"), V171 = c("-", "-"), V172 = c("-", 
      "-"), V173 = c("-", "-"), V174 = c("-", "-"), V175 = c("-", 
      "-"), V176 = c("-", "-"), V177 = c("-", "-"), V178 = c("-", 
      "G"), V179 = c("-", "-"), V180 = c("-", "-"), V181 = c("L", 
      "R"), V182 = c("N", "D"), V183 = c("-", "S"), V184 = c("-", 
      "Y"), V185 = c("-", "I"), V186 = c("-", "L"), V187 = c("-", 
      "E"), V188 = c("-", "Q"), V189 = c("-", "G"), V190 = c("-", 
      "H"), V191 = c("G", "A"), V192 = c("-", "-"), V193 = c("-", 
      "-"), V194 = c("-", "-"), V195 = c("-", "-"), V196 = c("-", 
      "-"), V197 = c("-", "-"), V198 = c("-", "-"), V199 = c("-", 
      "-"), V200 = c("-", "-"), V201 = c("-", "-"), V202 = c("-", 
      "-"), V203 = c("-", "-"), V204 = c("-", "-"), V205 = c("-", 
      "-"), V206 = c("-", "-"), V207 = c("-", "-"), V208 = c("-", 
      "-"), V209 = c("-", "-"), V210 = c("-", "-"), V211 = c("-", 
      "-"), V212 = c("-", "-"), V213 = c("-", "-"), V214 = c("-", 
      "-"), V215 = c("-", "-"), V216 = c("-", "-"), V217 = c("-", 
      "-"), V218 = c("-", "-"), V219 = c("-", "-"), V220 = c("-", 
      "-"), V221 = c("-", "-"), V222 = c("-", "-"), V223 = c("-", 
      "-"), V224 = c("-", "-"), V225 = c("-", "-"), V226 = c("-", 
      "-"), V227 = c("-", "-"), V228 = c("-", "-"), V229 = c("-", 
      "-"), V230 = c("-", "-"), V231 = c("-", "-"), V232 = c("-", 
      "-"), V233 = c("-", "-"), V234 = c("-", "-"), V235 = c("-", 
      "-"), V236 = c("-", "-"), V237 = c("-", "-"), V238 = c("-", 
      "-"), V239 = c("-", "-"), V240 = c("-", "-"), V241 = c("-", 
      "-"), V242 = c("-", "-"), V243 = c("-", "-"), V244 = c("-", 
      "-"), V245 = c("E", "Q"), V246 = c("K", "K"), V247 = c("I", 
      "I"), V248 = c("P", "P"), V249 = c("A", "A"), V250 = c("-", 
      "G"), V251 = c("-", "T"), V252 = c("-", "I"), V253 = c("-", 
      "F"), V254 = c("-", "F"), V255 = c("-", "L"), V256 = c("-", 
      "V"), V257 = c("-", "N"), V258 = c("-", "P"), V259 = c("-", 
      "N"), V260 = c("-", "D"), V261 = c("-", "N"), V262 = c("-", 
      "E"), V263 = c("-", "N"), V264 = c("-", "L"), V265 = c("-", 
      "R"), V266 = c("-", "I"), V267 = c("-", "-"), V268 = c("-", 
      "-"), V269 = c("-", "-"), V270 = c("-", "-"), V271 = c("-", 
      "-"), V272 = c("-", "-"), V273 = c("-", "-"), V274 = c("-", 
      "-"), V275 = c("-", "-"), V276 = c("-", "-"), V277 = c("-", 
      "-"), V278 = c("-", "-"), V279 = c("-", "-"), V280 = c("-", 
      "-"), V281 = c("-", "-"), V282 = c("-", "-"), V283 = c("-", 
      "-"), V284 = c("-", "-"), V285 = c("-", "-"), V286 = c("-", 
      "-"), V287 = c("-", "-"), V288 = c("-", "-"), V289 = c("-", 
      "-"), V290 = c("-", "-"), V291 = c("I", "I"), V292 = c("V", 
      "K"), V293 = c("L", "I"), V294 = c("S", "A"), V295 = c("K", 
      "T"), V296 = c("D", "P"), V297 = c("-", "I"), V298 = c("-", 
      "N"), V299 = c("-", "N"), V300 = c("-", "P"), V301 = c("-", 
      "H"), V302 = c("-", "R"), V303 = c("-", "F"), V304 = c("L", 
      "Q"), V305 = c("N", "D"), V306 = c("P", "F"), V307 = c("F", 
      "F"), V308 = c("L", "L"), V309 = c("-", "-"), V310 = c("-", 
      "-"), V311 = c("-", "-"), V312 = c("-", "-"), V313 = c("-", 
      "-"), V314 = c("-", "-"), V315 = c("-", "-"), V316 = c("-", 
      "-"), V317 = c("-", "-"), V318 = c("-", "-"), V319 = c("-", 
      "-"), V320 = c("-", "-"), V321 = c("-", "-"), V322 = c("-", 
      "S"), V323 = c("-", "S"), V324 = c("-", "T"), V325 = c("-", 
      "E"), V326 = c("-", "A"), V327 = c("Q", "Q"), V328 = c("-", 
      "Q"), V329 = c("E", "S"), V330 = c("L", "Y"), V331 = c("L", 
      "L"), V332 = c("D", "Q"), V333 = c("Q", "G"), V334 = c("E", 
      "-"), V335 = c("P", "-"), V336 = c("A", "F"), V337 = c("C", 
      "S"), V338 = c("-", "-"), V339 = c("-", "-"), V340 = c("-", 
      "-"), V341 = c("-", "-"), V342 = c("-", "-"), V343 = c("-", 
      "-"), V344 = c("-", "-"), V345 = c("-", "-"), V346 = c("-", 
      "-"), V347 = c("-", "-"), V348 = c("-", "-"), V349 = c("-", 
      "-"), V350 = c("-", "-"), V351 = c("-", "-"), V352 = c("-", 
      "-"), V353 = c("-", "-"), V354 = c("-", "-"), V355 = c("-", 
      "-"), V356 = c("-", "-"), V357 = c("-", "-"), V358 = c("-", 
      "-"), V359 = c("-", "-"), V360 = c("-", "-"), V361 = c("-", 
      "-"), V362 = c("-", "-"), V363 = c("-", "-"), V364 = c("-", 
      "-"), V365 = c("-", "-"), V366 = c("-", "-"), V367 = c("-", 
      "-"), V368 = c("-", "-"), V369 = c("-", "-"), V370 = c("-", 
      "-"), V371 = c("-", "-"), V372 = c("-", "-"), V373 = c("E", 
      "-"), V374 = c("H", "-"), V375 = c("D", "-"), V376 = c("I", 
      "-"), V377 = c("G", "K"), V378 = c("T", "N"), V379 = c("C", 
      "V"), V380 = c("Y", "L"), V381 = c("G", "E"), V382 = c("-", 
      "A"), V383 = c("-", "S"), V384 = c("-", "F"), V385 = c("-", 
      "D"), V386 = c("-", "S"), V387 = c("-", "E"), V388 = c("-", 
      "F"), V389 = c("-", "K"), V390 = c("-", "E"), V391 = c("-", 
      "I"), V392 = c("-", "N"), V393 = c("-", "R"), V394 = c("-", 
      "V"), V395 = c("-", "L"), V396 = c("-", "F"), V397 = c("-", 
      "G"), V398 = c("-", "E"), V399 = c("-", "E"), V400 = c("-", 
      "G"), V401 = c("-", "Q"), V402 = c("-", "Q"), V403 = c("-", 
      "Q"), V404 = c("-", "Q"), V405 = c("-", "G"), V406 = c("D", 
      "E"), V407 = c("A", "E"), V408 = c("-", "S"), V409 = c("-", 
      "Q"), V410 = c("-", "Q"), V411 = c("-", "E"), V412 = c("-", 
      "G"), V413 = c("-", "V"), V414 = c("-", "I"), V415 = c("-", 
      "V"), V416 = c("-", "E"), V417 = c("-", "L"), V418 = c("-", 
      "E"), V419 = c("-", "R"), V420 = c("-", "E"), V421 = c("-", 
      "Q"), V422 = c("-", "I"), V423 = c("-", "R"), V424 = c("-", 
      "E"), V425 = c("-", "L"), V426 = c("-", "I"), V427 = c("-", 
      "K"), V428 = c("-", "H"), V429 = c("-", "A"), V430 = c("-", 
      "-"), V431 = c("-", "-"), V432 = c("-", "-"), V433 = c("-", 
      "-"), V434 = c("-", "-"), V435 = c("-", "-"), V436 = c("-", 
      "-"), V437 = c("-", "-"), V438 = c("-", "-"), V439 = c("-", 
      "-"), V440 = c("-", "-"), V441 = c("-", "-"), V442 = c("-", 
      "-"), V443 = c("-", "-"), V444 = c("-", "-"), V445 = c("-", 
      "-"), V446 = c("-", "-"), V447 = c("-", "-"), V448 = c("-", 
      "-"), V449 = c("-", "-"), V450 = c("-", "-"), V451 = c("-", 
      "-"), V452 = c("-", "-"), V453 = c("-", "-"), V454 = c("-", 
      "-"), V455 = c("-", "-"), V456 = c("-", "-"), V457 = c("-", 
      "-"), V458 = c("-", "-"), V459 = c("-", "-"), V460 = c("-", 
      "-"), V461 = c("-", "-"), V462 = c("-", "-"), V463 = c("-", 
      "-"), V464 = c("-", "-"), V465 = c("-", "-"), V466 = c("-", 
      "-"), V467 = c("-", "-"), V468 = c("-", "-"), V469 = c("-", 
      "-"), V470 = c("-", "-"), V471 = c("P", "K"), V472 = c("C", 
      "S"), V473 = c("-", "S"), V474 = c("-", "S"), V475 = c("-", 
      "R"), V476 = c("-", "R"), V477 = c("-", "S"), V478 = c("I", 
      "L"), V479 = c("S", "S"), V480 = c("-", "-"), V481 = c("-", 
      "-"), V482 = c("-", "-"), V483 = c("-", "-"), V484 = c("-", 
      "-"), V485 = c("-", "-"), V486 = c("-", "-"), V487 = c("-", 
      "-"), V488 = c("-", "-"), V489 = c("-", "-"), V490 = c("-", 
      "-"), V491 = c("-", "-"), V492 = c("-", "-"), V493 = c("-", 
      "-"), V494 = c("-", "-"), V495 = c("-", "-"), V496 = c("-", 
      "-"), V497 = c("-", "-"), V498 = c("-", "-"), V499 = c("-", 
      "-"), V500 = c("-", "-"), V501 = c("-", "-"), V502 = c("-", 
      "-"), V503 = c("-", "-"), V504 = c("G", "S"), V505 = c("P", 
      "Q"), V506 = c("D", "-"), V507 = c("A", "-"), V508 = c("W", 
      "-"), V509 = c("N", "-"), V510 = c("H", "-"), V511 = c("S", 
      "D"), V512 = c("G", "E"), V513 = c("F", "P"), V514 = c("Q", 
      "F"), V515 = c("C", "N"), V516 = c("-", "L"), V517 = c("-", 
      "R"), V518 = c("-", "N"), V519 = c("-", "R"), V520 = c("Q", 
      "K"), V521 = c("-", "P"), V522 = c("-", "-"), V523 = c("-", 
      "-"), V524 = c("-", "-"), V525 = c("-", "-"), V526 = c("-", 
      "-"), V527 = c("-", "-"), V528 = c("-", "-"), V529 = c("-", 
      "-"), V530 = c("V", "I"), V531 = c("C", "Y"), V532 = c("-", 
      "-"), V533 = c("-", "-"), V534 = c("-", "S"), V535 = c("-", 
      "N"), V536 = c("-", "-"), V537 = c("-", "-"), V538 = c("-", 
      "-"), V539 = c("-", "-"), V540 = c("-", "-"), V541 = c("-", 
      "-"), V542 = c("-", "-"), V543 = c("-", "-"), V544 = c("-", 
      "-"), V545 = c("-", "-"), V546 = c("-", "-"), V547 = c("-", 
      "-"), V548 = c("-", "-"), V549 = c("-", "-"), V550 = c("-", 
      "-"), V551 = c("-", "-"), V552 = c("-", "-"), V553 = c("G", 
      "K"), V554 = c("L", "F"), V555 = c("V", "-"), V556 = c("K", 
      "G"), V557 = c("S", "R"), V558 = c("W", "W"), V559 = c("N", 
      "Y"), V560 = c("L", "E"), V561 = c("-", "I"), V562 = c("-", 
      "T"), V563 = c("-", "P"), V564 = c("-", "E"), V565 = c("-", 
      "K"), V566 = c("-", "N"), V567 = c("-", "P"), V568 = c("-", 
      "-"), V569 = c("-", "-"), V570 = c("-", "-"), V571 = c("-", 
      "-"), V572 = c("-", "-"), V573 = c("-", "-"), V574 = c("-", 
      "-"), V575 = c("-", "-"), V576 = c("-", "-"), V577 = c("-", 
      "-"), V578 = c("-", "-"), V579 = c("-", "-"), V580 = c("V", 
      "Q"), V581 = c("G", "-"), V582 = c("D", "-"), V583 = c("F", 
      "-"), V584 = c("V", "-"), V585 = c("V", "-"), V586 = c("Y", 
      "-"), V587 = c("R", "-"), V588 = c("Q", "-"), V589 = c("E", 
      "-"), V590 = c("-", "-"), V591 = c("-", "-"), V592 = c("-", 
      "-"), V593 = c("-", "-"), V594 = c("-", "-"), V595 = c("-", 
      "-"), V596 = c("-", "-"), V597 = c("-", "-"), V598 = c("-", 
      "-"), V599 = c("-", "-"), V600 = c("-", "-")), class = "data.frame", row.names = c("UniRef90_A0A1V4QIJ3", 
  "UniRef90_A0A0L9V5F8"))
  
  
  user2108: Update
  It seems that part of the desired behavior is to write the sequences in the alignment separately. I am not sure that I understand why it is necessary to write them separately. Generally it is inadvisable to write many small files rather than one big file, based purely on issues of performance; you are likely to hit the I/O bound on performance very quickly, and that will be much slower.
  One solution that has been suggested previously for this kind of problem is to write the whole alignment to a single file, and then post-process that filed in a second step to extract the sequences of interest. This could be as trivial as a samtools faidx call from the shell, or you could work with it in seqinr as suggested in the previous answer.
  Of course, it seems like it would be simpler for most purposes to just have the big alignment file and use e.g. samtools indexing / faidx / biopython / whatever to extract the sequences of interest. But it seems that that is specifically not desired in this case.
  Original answer
  I would strongly suggest using the seqinr package, which is optimized for solving exactly these problems. See e.g. this similar question.
  You will be able to read in an alignment (or whatever), cast it to as.matrix.alignment, do whatever your analysis is, then cast it back to as.alignment, which can then be passed to write.fasta to write the files.
  Whenever possible it is preferable to work with such libraries, which handle these utility functions well, fast, and easy.
  
original_text: 5003: <p>I have a data frame where the row names are the species names, and each column can either be an Amino-Acid character or &quot;-&quot;.</p>
  <p>I wish to write it in a <a href="https://en.wikipedia.org/wiki/FASTA_format" rel="nofollow noreferrer">fasta format</a>. Simple example of the format is:</p>
  <pre><code>&gt;UniRef90_A0A1V4QIJ3
  ------------------------------------------------------------
  --------------------------MDISTFSP-----PVAG-----------VE----
  ------ITAF-------------V------------------------------------
  LN--------G-------------------------------------------------
  ----EKIPA-----------------------------------------IVLSKD----
  ---LNPFL------------------Q-ELLDQEPAC-----------------------
  ------------EHDIGTCYG------------------------DA-------------
  --------------------------------------------------PC-----IS-
  -----------------------GPDAWNHSGFQC----Q---------VC---------
  ------------GLVKSWNL-------------------VGDFVVYRQE-----------
  &gt;UniRef90_A0A0L9V5F8
  ------------------------------------------------------------
  RFHTLFRNEYGHLRVLQRFDQRSKQIQNLENYRLVEFKSKPNTLLLPHHADADFLLVVLN
  GRALLTLVNP-------------D---------------------------------G--
  RDSYILEQGHA-------------------------------------------------
  ----QKIPAGTIFFLVNPNDNENLRI------------------------IKIATPINNP
  HRFQDFFL-------------SSTEAQQSYLQG--FS-----------------------
  ----------------KNVLEASFDSEFKEINRVLFGEEGQQQQGEESQQEGVIVELERE
  QIRELIKHA-----------------------------------------KSSSRRSLS-
  -----------------------SQ-----DEPFNLRNRKP--------IY--SN-----
  ------------KF-GRWYEITPEKNP------------Q--------------------
  </code></pre>
  <p>I can do it using the following for loop:</p>
  <pre><code>for (n in row.names(df)){
      ss = do.call(paste, c(as.list(mu_df[1, ]), sep = &quot;&quot;))
      write.fasta(ss,
                    names=n,
                    as.string=TRUE,
                    open=&quot;a&quot;,
                    new_file_path)
  }
  </code></pre>
  <p>Is there a faster way of writing it? I have to write millions of those files and I wish to optimize it.</p>
  <p>In order to create the data frame:</p>
  <pre><code>structure(list(V1 = c(&quot;-&quot;, &quot;-&quot;), V2 = c(&quot;-&quot;, &quot;-&quot;), V3 = c(&quot;-&quot;, 
  &quot;-&quot;), V4 = c(&quot;-&quot;, &quot;-&quot;), V5 = c(&quot;-&quot;, &quot;-&quot;), V6 = c(&quot;-&quot;, &quot;-&quot;), V7 = c(&quot;-&quot;, 
  &quot;-&quot;), V8 = c(&quot;-&quot;, &quot;-&quot;), V9 = c(&quot;-&quot;, &quot;-&quot;), V10 = c(&quot;-&quot;, &quot;-&quot;), 
      V11 = c(&quot;-&quot;, &quot;-&quot;), V12 = c(&quot;-&quot;, &quot;-&quot;), V13 = c(&quot;-&quot;, &quot;-&quot;), 
      V14 = c(&quot;-&quot;, &quot;-&quot;), V15 = c(&quot;-&quot;, &quot;-&quot;), V16 = c(&quot;-&quot;, &quot;-&quot;), 
      V17 = c(&quot;-&quot;, &quot;-&quot;), V18 = c(&quot;-&quot;, &quot;-&quot;), V19 = c(&quot;-&quot;, &quot;-&quot;), 
      V20 = c(&quot;-&quot;, &quot;-&quot;), V21 = c(&quot;-&quot;, &quot;-&quot;), V22 = c(&quot;-&quot;, &quot;-&quot;), 
      V23 = c(&quot;-&quot;, &quot;-&quot;), V24 = c(&quot;-&quot;, &quot;-&quot;), V25 = c(&quot;-&quot;, &quot;-&quot;), 
      V26 = c(&quot;-&quot;, &quot;-&quot;), V27 = c(&quot;-&quot;, &quot;-&quot;), V28 = c(&quot;-&quot;, &quot;-&quot;), 
      V29 = c(&quot;-&quot;, &quot;-&quot;), V30 = c(&quot;-&quot;, &quot;-&quot;), V31 = c(&quot;-&quot;, &quot;-&quot;), 
      V32 = c(&quot;-&quot;, &quot;-&quot;), V33 = c(&quot;-&quot;, &quot;-&quot;), V34 = c(&quot;-&quot;, &quot;-&quot;), 
      V35 = c(&quot;-&quot;, &quot;-&quot;), V36 = c(&quot;-&quot;, &quot;-&quot;), V37 = c(&quot;-&quot;, &quot;-&quot;), 
      V38 = c(&quot;-&quot;, &quot;-&quot;), V39 = c(&quot;-&quot;, &quot;-&quot;), V40 = c(&quot;-&quot;, &quot;-&quot;), 
      V41 = c(&quot;-&quot;, &quot;-&quot;), V42 = c(&quot;-&quot;, &quot;-&quot;), V43 = c(&quot;-&quot;, &quot;-&quot;), 
      V44 = c(&quot;-&quot;, &quot;-&quot;), V45 = c(&quot;-&quot;, &quot;-&quot;), V46 = c(&quot;-&quot;, &quot;-&quot;), 
      V47 = c(&quot;-&quot;, &quot;-&quot;), V48 = c(&quot;-&quot;, &quot;-&quot;), V49 = c(&quot;-&quot;, &quot;-&quot;), 
      V50 = c(&quot;-&quot;, &quot;-&quot;), V51 = c(&quot;-&quot;, &quot;-&quot;), V52 = c(&quot;-&quot;, &quot;-&quot;), 
      V53 = c(&quot;-&quot;, &quot;-&quot;), V54 = c(&quot;-&quot;, &quot;-&quot;), V55 = c(&quot;-&quot;, &quot;-&quot;), 
      V56 = c(&quot;-&quot;, &quot;-&quot;), V57 = c(&quot;-&quot;, &quot;-&quot;), V58 = c(&quot;-&quot;, &quot;-&quot;), 
      V59 = c(&quot;-&quot;, &quot;-&quot;), V60 = c(&quot;-&quot;, &quot;-&quot;), V61 = c(&quot;-&quot;, &quot;R&quot;), 
      V62 = c(&quot;-&quot;, &quot;F&quot;), V63 = c(&quot;-&quot;, &quot;H&quot;), V64 = c(&quot;-&quot;, &quot;T&quot;), 
      V65 = c(&quot;-&quot;, &quot;L&quot;), V66 = c(&quot;-&quot;, &quot;F&quot;), V67 = c(&quot;-&quot;, &quot;R&quot;), 
      V68 = c(&quot;-&quot;, &quot;N&quot;), V69 = c(&quot;-&quot;, &quot;E&quot;), V70 = c(&quot;-&quot;, &quot;Y&quot;), 
      V71 = c(&quot;-&quot;, &quot;G&quot;), V72 = c(&quot;-&quot;, &quot;H&quot;), V73 = c(&quot;-&quot;, &quot;L&quot;), 
      V74 = c(&quot;-&quot;, &quot;R&quot;), V75 = c(&quot;-&quot;, &quot;V&quot;), V76 = c(&quot;-&quot;, &quot;L&quot;), 
      V77 = c(&quot;-&quot;, &quot;Q&quot;), V78 = c(&quot;-&quot;, &quot;R&quot;), V79 = c(&quot;-&quot;, &quot;F&quot;), 
      V80 = c(&quot;-&quot;, &quot;D&quot;), V81 = c(&quot;-&quot;, &quot;Q&quot;), V82 = c(&quot;-&quot;, &quot;R&quot;), 
      V83 = c(&quot;-&quot;, &quot;S&quot;), V84 = c(&quot;-&quot;, &quot;K&quot;), V85 = c(&quot;-&quot;, &quot;Q&quot;), 
      V86 = c(&quot;-&quot;, &quot;I&quot;), V87 = c(&quot;M&quot;, &quot;Q&quot;), V88 = c(&quot;D&quot;, &quot;N&quot;), 
      V89 = c(&quot;I&quot;, &quot;L&quot;), V90 = c(&quot;S&quot;, &quot;E&quot;), V91 = c(&quot;T&quot;, &quot;N&quot;), 
      V92 = c(&quot;F&quot;, &quot;Y&quot;), V93 = c(&quot;S&quot;, &quot;R&quot;), V94 = c(&quot;P&quot;, &quot;L&quot;), 
      V95 = c(&quot;-&quot;, &quot;V&quot;), V96 = c(&quot;-&quot;, &quot;E&quot;), V97 = c(&quot;-&quot;, &quot;F&quot;), 
      V98 = c(&quot;-&quot;, &quot;K&quot;), V99 = c(&quot;-&quot;, &quot;S&quot;), V100 = c(&quot;P&quot;, &quot;K&quot;), 
      V101 = c(&quot;V&quot;, &quot;P&quot;), V102 = c(&quot;A&quot;, &quot;N&quot;), V103 = c(&quot;G&quot;, &quot;T&quot;
      ), V104 = c(&quot;-&quot;, &quot;L&quot;), V105 = c(&quot;-&quot;, &quot;L&quot;), V106 = c(&quot;-&quot;, 
      &quot;L&quot;), V107 = c(&quot;-&quot;, &quot;P&quot;), V108 = c(&quot;-&quot;, &quot;H&quot;), V109 = c(&quot;-&quot;, 
      &quot;H&quot;), V110 = c(&quot;-&quot;, &quot;A&quot;), V111 = c(&quot;-&quot;, &quot;D&quot;), V112 = c(&quot;-&quot;, 
      &quot;A&quot;), V113 = c(&quot;-&quot;, &quot;D&quot;), V114 = c(&quot;-&quot;, &quot;F&quot;), V115 = c(&quot;V&quot;, 
      &quot;L&quot;), V116 = c(&quot;E&quot;, &quot;L&quot;), V117 = c(&quot;-&quot;, &quot;V&quot;), V118 = c(&quot;-&quot;, 
      &quot;V&quot;), V119 = c(&quot;-&quot;, &quot;L&quot;), V120 = c(&quot;-&quot;, &quot;N&quot;), V121 = c(&quot;-&quot;, 
      &quot;G&quot;), V122 = c(&quot;-&quot;, &quot;R&quot;), V123 = c(&quot;-&quot;, &quot;A&quot;), V124 = c(&quot;-&quot;, 
      &quot;L&quot;), V125 = c(&quot;-&quot;, &quot;L&quot;), V126 = c(&quot;-&quot;, &quot;T&quot;), V127 = c(&quot;I&quot;, 
      &quot;L&quot;), V128 = c(&quot;T&quot;, &quot;V&quot;), V129 = c(&quot;A&quot;, &quot;N&quot;), V130 = c(&quot;F&quot;, 
      &quot;P&quot;), V131 = c(&quot;-&quot;, &quot;-&quot;), V132 = c(&quot;-&quot;, &quot;-&quot;), V133 = c(&quot;-&quot;, 
      &quot;-&quot;), V134 = c(&quot;-&quot;, &quot;-&quot;), V135 = c(&quot;-&quot;, &quot;-&quot;), V136 = c(&quot;-&quot;, 
      &quot;-&quot;), V137 = c(&quot;-&quot;, &quot;-&quot;), V138 = c(&quot;-&quot;, &quot;-&quot;), V139 = c(&quot;-&quot;, 
      &quot;-&quot;), V140 = c(&quot;-&quot;, &quot;-&quot;), V141 = c(&quot;-&quot;, &quot;-&quot;), V142 = c(&quot;-&quot;, 
      &quot;-&quot;), V143 = c(&quot;-&quot;, &quot;-&quot;), V144 = c(&quot;V&quot;, &quot;D&quot;), V145 = c(&quot;-&quot;, 
      &quot;-&quot;), V146 = c(&quot;-&quot;, &quot;-&quot;), V147 = c(&quot;-&quot;, &quot;-&quot;), V148 = c(&quot;-&quot;, 
      &quot;-&quot;), V149 = c(&quot;-&quot;, &quot;-&quot;), V150 = c(&quot;-&quot;, &quot;-&quot;), V151 = c(&quot;-&quot;, 
      &quot;-&quot;), V152 = c(&quot;-&quot;, &quot;-&quot;), V153 = c(&quot;-&quot;, &quot;-&quot;), V154 = c(&quot;-&quot;, 
      &quot;-&quot;), V155 = c(&quot;-&quot;, &quot;-&quot;), V156 = c(&quot;-&quot;, &quot;-&quot;), V157 = c(&quot;-&quot;, 
      &quot;-&quot;), V158 = c(&quot;-&quot;, &quot;-&quot;), V159 = c(&quot;-&quot;, &quot;-&quot;), V160 = c(&quot;-&quot;, 
      &quot;-&quot;), V161 = c(&quot;-&quot;, &quot;-&quot;), V162 = c(&quot;-&quot;, &quot;-&quot;), V163 = c(&quot;-&quot;, 
      &quot;-&quot;), V164 = c(&quot;-&quot;, &quot;-&quot;), V165 = c(&quot;-&quot;, &quot;-&quot;), V166 = c(&quot;-&quot;, 
      &quot;-&quot;), V167 = c(&quot;-&quot;, &quot;-&quot;), V168 = c(&quot;-&quot;, &quot;-&quot;), V169 = c(&quot;-&quot;, 
      &quot;-&quot;), V170 = c(&quot;-&quot;, &quot;-&quot;), V171 = c(&quot;-&quot;, &quot;-&quot;), V172 = c(&quot;-&quot;, 
      &quot;-&quot;), V173 = c(&quot;-&quot;, &quot;-&quot;), V174 = c(&quot;-&quot;, &quot;-&quot;), V175 = c(&quot;-&quot;, 
      &quot;-&quot;), V176 = c(&quot;-&quot;, &quot;-&quot;), V177 = c(&quot;-&quot;, &quot;-&quot;), V178 = c(&quot;-&quot;, 
      &quot;G&quot;), V179 = c(&quot;-&quot;, &quot;-&quot;), V180 = c(&quot;-&quot;, &quot;-&quot;), V181 = c(&quot;L&quot;, 
      &quot;R&quot;), V182 = c(&quot;N&quot;, &quot;D&quot;), V183 = c(&quot;-&quot;, &quot;S&quot;), V184 = c(&quot;-&quot;, 
      &quot;Y&quot;), V185 = c(&quot;-&quot;, &quot;I&quot;), V186 = c(&quot;-&quot;, &quot;L&quot;), V187 = c(&quot;-&quot;, 
      &quot;E&quot;), V188 = c(&quot;-&quot;, &quot;Q&quot;), V189 = c(&quot;-&quot;, &quot;G&quot;), V190 = c(&quot;-&quot;, 
      &quot;H&quot;), V191 = c(&quot;G&quot;, &quot;A&quot;), V192 = c(&quot;-&quot;, &quot;-&quot;), V193 = c(&quot;-&quot;, 
      &quot;-&quot;), V194 = c(&quot;-&quot;, &quot;-&quot;), V195 = c(&quot;-&quot;, &quot;-&quot;), V196 = c(&quot;-&quot;, 
      &quot;-&quot;), V197 = c(&quot;-&quot;, &quot;-&quot;), V198 = c(&quot;-&quot;, &quot;-&quot;), V199 = c(&quot;-&quot;, 
      &quot;-&quot;), V200 = c(&quot;-&quot;, &quot;-&quot;), V201 = c(&quot;-&quot;, &quot;-&quot;), V202 = c(&quot;-&quot;, 
      &quot;-&quot;), V203 = c(&quot;-&quot;, &quot;-&quot;), V204 = c(&quot;-&quot;, &quot;-&quot;), V205 = c(&quot;-&quot;, 
      &quot;-&quot;), V206 = c(&quot;-&quot;, &quot;-&quot;), V207 = c(&quot;-&quot;, &quot;-&quot;), V208 = c(&quot;-&quot;, 
      &quot;-&quot;), V209 = c(&quot;-&quot;, &quot;-&quot;), V210 = c(&quot;-&quot;, &quot;-&quot;), V211 = c(&quot;-&quot;, 
      &quot;-&quot;), V212 = c(&quot;-&quot;, &quot;-&quot;), V213 = c(&quot;-&quot;, &quot;-&quot;), V214 = c(&quot;-&quot;, 
      &quot;-&quot;), V215 = c(&quot;-&quot;, &quot;-&quot;), V216 = c(&quot;-&quot;, &quot;-&quot;), V217 = c(&quot;-&quot;, 
      &quot;-&quot;), V218 = c(&quot;-&quot;, &quot;-&quot;), V219 = c(&quot;-&quot;, &quot;-&quot;), V220 = c(&quot;-&quot;, 
      &quot;-&quot;), V221 = c(&quot;-&quot;, &quot;-&quot;), V222 = c(&quot;-&quot;, &quot;-&quot;), V223 = c(&quot;-&quot;, 
      &quot;-&quot;), V224 = c(&quot;-&quot;, &quot;-&quot;), V225 = c(&quot;-&quot;, &quot;-&quot;), V226 = c(&quot;-&quot;, 
      &quot;-&quot;), V227 = c(&quot;-&quot;, &quot;-&quot;), V228 = c(&quot;-&quot;, &quot;-&quot;), V229 = c(&quot;-&quot;, 
      &quot;-&quot;), V230 = c(&quot;-&quot;, &quot;-&quot;), V231 = c(&quot;-&quot;, &quot;-&quot;), V232 = c(&quot;-&quot;, 
      &quot;-&quot;), V233 = c(&quot;-&quot;, &quot;-&quot;), V234 = c(&quot;-&quot;, &quot;-&quot;), V235 = c(&quot;-&quot;, 
      &quot;-&quot;), V236 = c(&quot;-&quot;, &quot;-&quot;), V237 = c(&quot;-&quot;, &quot;-&quot;), V238 = c(&quot;-&quot;, 
      &quot;-&quot;), V239 = c(&quot;-&quot;, &quot;-&quot;), V240 = c(&quot;-&quot;, &quot;-&quot;), V241 = c(&quot;-&quot;, 
      &quot;-&quot;), V242 = c(&quot;-&quot;, &quot;-&quot;), V243 = c(&quot;-&quot;, &quot;-&quot;), V244 = c(&quot;-&quot;, 
      &quot;-&quot;), V245 = c(&quot;E&quot;, &quot;Q&quot;), V246 = c(&quot;K&quot;, &quot;K&quot;), V247 = c(&quot;I&quot;, 
      &quot;I&quot;), V248 = c(&quot;P&quot;, &quot;P&quot;), V249 = c(&quot;A&quot;, &quot;A&quot;), V250 = c(&quot;-&quot;, 
      &quot;G&quot;), V251 = c(&quot;-&quot;, &quot;T&quot;), V252 = c(&quot;-&quot;, &quot;I&quot;), V253 = c(&quot;-&quot;, 
      &quot;F&quot;), V254 = c(&quot;-&quot;, &quot;F&quot;), V255 = c(&quot;-&quot;, &quot;L&quot;), V256 = c(&quot;-&quot;, 
      &quot;V&quot;), V257 = c(&quot;-&quot;, &quot;N&quot;), V258 = c(&quot;-&quot;, &quot;P&quot;), V259 = c(&quot;-&quot;, 
      &quot;N&quot;), V260 = c(&quot;-&quot;, &quot;D&quot;), V261 = c(&quot;-&quot;, &quot;N&quot;), V262 = c(&quot;-&quot;, 
      &quot;E&quot;), V263 = c(&quot;-&quot;, &quot;N&quot;), V264 = c(&quot;-&quot;, &quot;L&quot;), V265 = c(&quot;-&quot;, 
      &quot;R&quot;), V266 = c(&quot;-&quot;, &quot;I&quot;), V267 = c(&quot;-&quot;, &quot;-&quot;), V268 = c(&quot;-&quot;, 
      &quot;-&quot;), V269 = c(&quot;-&quot;, &quot;-&quot;), V270 = c(&quot;-&quot;, &quot;-&quot;), V271 = c(&quot;-&quot;, 
      &quot;-&quot;), V272 = c(&quot;-&quot;, &quot;-&quot;), V273 = c(&quot;-&quot;, &quot;-&quot;), V274 = c(&quot;-&quot;, 
      &quot;-&quot;), V275 = c(&quot;-&quot;, &quot;-&quot;), V276 = c(&quot;-&quot;, &quot;-&quot;), V277 = c(&quot;-&quot;, 
      &quot;-&quot;), V278 = c(&quot;-&quot;, &quot;-&quot;), V279 = c(&quot;-&quot;, &quot;-&quot;), V280 = c(&quot;-&quot;, 
      &quot;-&quot;), V281 = c(&quot;-&quot;, &quot;-&quot;), V282 = c(&quot;-&quot;, &quot;-&quot;), V283 = c(&quot;-&quot;, 
      &quot;-&quot;), V284 = c(&quot;-&quot;, &quot;-&quot;), V285 = c(&quot;-&quot;, &quot;-&quot;), V286 = c(&quot;-&quot;, 
      &quot;-&quot;), V287 = c(&quot;-&quot;, &quot;-&quot;), V288 = c(&quot;-&quot;, &quot;-&quot;), V289 = c(&quot;-&quot;, 
      &quot;-&quot;), V290 = c(&quot;-&quot;, &quot;-&quot;), V291 = c(&quot;I&quot;, &quot;I&quot;), V292 = c(&quot;V&quot;, 
      &quot;K&quot;), V293 = c(&quot;L&quot;, &quot;I&quot;), V294 = c(&quot;S&quot;, &quot;A&quot;), V295 = c(&quot;K&quot;, 
      &quot;T&quot;), V296 = c(&quot;D&quot;, &quot;P&quot;), V297 = c(&quot;-&quot;, &quot;I&quot;), V298 = c(&quot;-&quot;, 
      &quot;N&quot;), V299 = c(&quot;-&quot;, &quot;N&quot;), V300 = c(&quot;-&quot;, &quot;P&quot;), V301 = c(&quot;-&quot;, 
      &quot;H&quot;), V302 = c(&quot;-&quot;, &quot;R&quot;), V303 = c(&quot;-&quot;, &quot;F&quot;), V304 = c(&quot;L&quot;, 
      &quot;Q&quot;), V305 = c(&quot;N&quot;, &quot;D&quot;), V306 = c(&quot;P&quot;, &quot;F&quot;), V307 = c(&quot;F&quot;, 
      &quot;F&quot;), V308 = c(&quot;L&quot;, &quot;L&quot;), V309 = c(&quot;-&quot;, &quot;-&quot;), V310 = c(&quot;-&quot;, 
      &quot;-&quot;), V311 = c(&quot;-&quot;, &quot;-&quot;), V312 = c(&quot;-&quot;, &quot;-&quot;), V313 = c(&quot;-&quot;, 
      &quot;-&quot;), V314 = c(&quot;-&quot;, &quot;-&quot;), V315 = c(&quot;-&quot;, &quot;-&quot;), V316 = c(&quot;-&quot;, 
      &quot;-&quot;), V317 = c(&quot;-&quot;, &quot;-&quot;), V318 = c(&quot;-&quot;, &quot;-&quot;), V319 = c(&quot;-&quot;, 
      &quot;-&quot;), V320 = c(&quot;-&quot;, &quot;-&quot;), V321 = c(&quot;-&quot;, &quot;-&quot;), V322 = c(&quot;-&quot;, 
      &quot;S&quot;), V323 = c(&quot;-&quot;, &quot;S&quot;), V324 = c(&quot;-&quot;, &quot;T&quot;), V325 = c(&quot;-&quot;, 
      &quot;E&quot;), V326 = c(&quot;-&quot;, &quot;A&quot;), V327 = c(&quot;Q&quot;, &quot;Q&quot;), V328 = c(&quot;-&quot;, 
      &quot;Q&quot;), V329 = c(&quot;E&quot;, &quot;S&quot;), V330 = c(&quot;L&quot;, &quot;Y&quot;), V331 = c(&quot;L&quot;, 
      &quot;L&quot;), V332 = c(&quot;D&quot;, &quot;Q&quot;), V333 = c(&quot;Q&quot;, &quot;G&quot;), V334 = c(&quot;E&quot;, 
      &quot;-&quot;), V335 = c(&quot;P&quot;, &quot;-&quot;), V336 = c(&quot;A&quot;, &quot;F&quot;), V337 = c(&quot;C&quot;, 
      &quot;S&quot;), V338 = c(&quot;-&quot;, &quot;-&quot;), V339 = c(&quot;-&quot;, &quot;-&quot;), V340 = c(&quot;-&quot;, 
      &quot;-&quot;), V341 = c(&quot;-&quot;, &quot;-&quot;), V342 = c(&quot;-&quot;, &quot;-&quot;), V343 = c(&quot;-&quot;, 
      &quot;-&quot;), V344 = c(&quot;-&quot;, &quot;-&quot;), V345 = c(&quot;-&quot;, &quot;-&quot;), V346 = c(&quot;-&quot;, 
      &quot;-&quot;), V347 = c(&quot;-&quot;, &quot;-&quot;), V348 = c(&quot;-&quot;, &quot;-&quot;), V349 = c(&quot;-&quot;, 
      &quot;-&quot;), V350 = c(&quot;-&quot;, &quot;-&quot;), V351 = c(&quot;-&quot;, &quot;-&quot;), V352 = c(&quot;-&quot;, 
      &quot;-&quot;), V353 = c(&quot;-&quot;, &quot;-&quot;), V354 = c(&quot;-&quot;, &quot;-&quot;), V355 = c(&quot;-&quot;, 
      &quot;-&quot;), V356 = c(&quot;-&quot;, &quot;-&quot;), V357 = c(&quot;-&quot;, &quot;-&quot;), V358 = c(&quot;-&quot;, 
      &quot;-&quot;), V359 = c(&quot;-&quot;, &quot;-&quot;), V360 = c(&quot;-&quot;, &quot;-&quot;), V361 = c(&quot;-&quot;, 
      &quot;-&quot;), V362 = c(&quot;-&quot;, &quot;-&quot;), V363 = c(&quot;-&quot;, &quot;-&quot;), V364 = c(&quot;-&quot;, 
      &quot;-&quot;), V365 = c(&quot;-&quot;, &quot;-&quot;), V366 = c(&quot;-&quot;, &quot;-&quot;), V367 = c(&quot;-&quot;, 
      &quot;-&quot;), V368 = c(&quot;-&quot;, &quot;-&quot;), V369 = c(&quot;-&quot;, &quot;-&quot;), V370 = c(&quot;-&quot;, 
      &quot;-&quot;), V371 = c(&quot;-&quot;, &quot;-&quot;), V372 = c(&quot;-&quot;, &quot;-&quot;), V373 = c(&quot;E&quot;, 
      &quot;-&quot;), V374 = c(&quot;H&quot;, &quot;-&quot;), V375 = c(&quot;D&quot;, &quot;-&quot;), V376 = c(&quot;I&quot;, 
      &quot;-&quot;), V377 = c(&quot;G&quot;, &quot;K&quot;), V378 = c(&quot;T&quot;, &quot;N&quot;), V379 = c(&quot;C&quot;, 
      &quot;V&quot;), V380 = c(&quot;Y&quot;, &quot;L&quot;), V381 = c(&quot;G&quot;, &quot;E&quot;), V382 = c(&quot;-&quot;, 
      &quot;A&quot;), V383 = c(&quot;-&quot;, &quot;S&quot;), V384 = c(&quot;-&quot;, &quot;F&quot;), V385 = c(&quot;-&quot;, 
      &quot;D&quot;), V386 = c(&quot;-&quot;, &quot;S&quot;), V387 = c(&quot;-&quot;, &quot;E&quot;), V388 = c(&quot;-&quot;, 
      &quot;F&quot;), V389 = c(&quot;-&quot;, &quot;K&quot;), V390 = c(&quot;-&quot;, &quot;E&quot;), V391 = c(&quot;-&quot;, 
      &quot;I&quot;), V392 = c(&quot;-&quot;, &quot;N&quot;), V393 = c(&quot;-&quot;, &quot;R&quot;), V394 = c(&quot;-&quot;, 
      &quot;V&quot;), V395 = c(&quot;-&quot;, &quot;L&quot;), V396 = c(&quot;-&quot;, &quot;F&quot;), V397 = c(&quot;-&quot;, 
      &quot;G&quot;), V398 = c(&quot;-&quot;, &quot;E&quot;), V399 = c(&quot;-&quot;, &quot;E&quot;), V400 = c(&quot;-&quot;, 
      &quot;G&quot;), V401 = c(&quot;-&quot;, &quot;Q&quot;), V402 = c(&quot;-&quot;, &quot;Q&quot;), V403 = c(&quot;-&quot;, 
      &quot;Q&quot;), V404 = c(&quot;-&quot;, &quot;Q&quot;), V405 = c(&quot;-&quot;, &quot;G&quot;), V406 = c(&quot;D&quot;, 
      &quot;E&quot;), V407 = c(&quot;A&quot;, &quot;E&quot;), V408 = c(&quot;-&quot;, &quot;S&quot;), V409 = c(&quot;-&quot;, 
      &quot;Q&quot;), V410 = c(&quot;-&quot;, &quot;Q&quot;), V411 = c(&quot;-&quot;, &quot;E&quot;), V412 = c(&quot;-&quot;, 
      &quot;G&quot;), V413 = c(&quot;-&quot;, &quot;V&quot;), V414 = c(&quot;-&quot;, &quot;I&quot;), V415 = c(&quot;-&quot;, 
      &quot;V&quot;), V416 = c(&quot;-&quot;, &quot;E&quot;), V417 = c(&quot;-&quot;, &quot;L&quot;), V418 = c(&quot;-&quot;, 
      &quot;E&quot;), V419 = c(&quot;-&quot;, &quot;R&quot;), V420 = c(&quot;-&quot;, &quot;E&quot;), V421 = c(&quot;-&quot;, 
      &quot;Q&quot;), V422 = c(&quot;-&quot;, &quot;I&quot;), V423 = c(&quot;-&quot;, &quot;R&quot;), V424 = c(&quot;-&quot;, 
      &quot;E&quot;), V425 = c(&quot;-&quot;, &quot;L&quot;), V426 = c(&quot;-&quot;, &quot;I&quot;), V427 = c(&quot;-&quot;, 
      &quot;K&quot;), V428 = c(&quot;-&quot;, &quot;H&quot;), V429 = c(&quot;-&quot;, &quot;A&quot;), V430 = c(&quot;-&quot;, 
      &quot;-&quot;), V431 = c(&quot;-&quot;, &quot;-&quot;), V432 = c(&quot;-&quot;, &quot;-&quot;), V433 = c(&quot;-&quot;, 
      &quot;-&quot;), V434 = c(&quot;-&quot;, &quot;-&quot;), V435 = c(&quot;-&quot;, &quot;-&quot;), V436 = c(&quot;-&quot;, 
      &quot;-&quot;), V437 = c(&quot;-&quot;, &quot;-&quot;), V438 = c(&quot;-&quot;, &quot;-&quot;), V439 = c(&quot;-&quot;, 
      &quot;-&quot;), V440 = c(&quot;-&quot;, &quot;-&quot;), V441 = c(&quot;-&quot;, &quot;-&quot;), V442 = c(&quot;-&quot;, 
      &quot;-&quot;), V443 = c(&quot;-&quot;, &quot;-&quot;), V444 = c(&quot;-&quot;, &quot;-&quot;), V445 = c(&quot;-&quot;, 
      &quot;-&quot;), V446 = c(&quot;-&quot;, &quot;-&quot;), V447 = c(&quot;-&quot;, &quot;-&quot;), V448 = c(&quot;-&quot;, 
      &quot;-&quot;), V449 = c(&quot;-&quot;, &quot;-&quot;), V450 = c(&quot;-&quot;, &quot;-&quot;), V451 = c(&quot;-&quot;, 
      &quot;-&quot;), V452 = c(&quot;-&quot;, &quot;-&quot;), V453 = c(&quot;-&quot;, &quot;-&quot;), V454 = c(&quot;-&quot;, 
      &quot;-&quot;), V455 = c(&quot;-&quot;, &quot;-&quot;), V456 = c(&quot;-&quot;, &quot;-&quot;), V457 = c(&quot;-&quot;, 
      &quot;-&quot;), V458 = c(&quot;-&quot;, &quot;-&quot;), V459 = c(&quot;-&quot;, &quot;-&quot;), V460 = c(&quot;-&quot;, 
      &quot;-&quot;), V461 = c(&quot;-&quot;, &quot;-&quot;), V462 = c(&quot;-&quot;, &quot;-&quot;), V463 = c(&quot;-&quot;, 
      &quot;-&quot;), V464 = c(&quot;-&quot;, &quot;-&quot;), V465 = c(&quot;-&quot;, &quot;-&quot;), V466 = c(&quot;-&quot;, 
      &quot;-&quot;), V467 = c(&quot;-&quot;, &quot;-&quot;), V468 = c(&quot;-&quot;, &quot;-&quot;), V469 = c(&quot;-&quot;, 
      &quot;-&quot;), V470 = c(&quot;-&quot;, &quot;-&quot;), V471 = c(&quot;P&quot;, &quot;K&quot;), V472 = c(&quot;C&quot;, 
      &quot;S&quot;), V473 = c(&quot;-&quot;, &quot;S&quot;), V474 = c(&quot;-&quot;, &quot;S&quot;), V475 = c(&quot;-&quot;, 
      &quot;R&quot;), V476 = c(&quot;-&quot;, &quot;R&quot;), V477 = c(&quot;-&quot;, &quot;S&quot;), V478 = c(&quot;I&quot;, 
      &quot;L&quot;), V479 = c(&quot;S&quot;, &quot;S&quot;), V480 = c(&quot;-&quot;, &quot;-&quot;), V481 = c(&quot;-&quot;, 
      &quot;-&quot;), V482 = c(&quot;-&quot;, &quot;-&quot;), V483 = c(&quot;-&quot;, &quot;-&quot;), V484 = c(&quot;-&quot;, 
      &quot;-&quot;), V485 = c(&quot;-&quot;, &quot;-&quot;), V486 = c(&quot;-&quot;, &quot;-&quot;), V487 = c(&quot;-&quot;, 
      &quot;-&quot;), V488 = c(&quot;-&quot;, &quot;-&quot;), V489 = c(&quot;-&quot;, &quot;-&quot;), V490 = c(&quot;-&quot;, 
      &quot;-&quot;), V491 = c(&quot;-&quot;, &quot;-&quot;), V492 = c(&quot;-&quot;, &quot;-&quot;), V493 = c(&quot;-&quot;, 
      &quot;-&quot;), V494 = c(&quot;-&quot;, &quot;-&quot;), V495 = c(&quot;-&quot;, &quot;-&quot;), V496 = c(&quot;-&quot;, 
      &quot;-&quot;), V497 = c(&quot;-&quot;, &quot;-&quot;), V498 = c(&quot;-&quot;, &quot;-&quot;), V499 = c(&quot;-&quot;, 
      &quot;-&quot;), V500 = c(&quot;-&quot;, &quot;-&quot;), V501 = c(&quot;-&quot;, &quot;-&quot;), V502 = c(&quot;-&quot;, 
      &quot;-&quot;), V503 = c(&quot;-&quot;, &quot;-&quot;), V504 = c(&quot;G&quot;, &quot;S&quot;), V505 = c(&quot;P&quot;, 
      &quot;Q&quot;), V506 = c(&quot;D&quot;, &quot;-&quot;), V507 = c(&quot;A&quot;, &quot;-&quot;), V508 = c(&quot;W&quot;, 
      &quot;-&quot;), V509 = c(&quot;N&quot;, &quot;-&quot;), V510 = c(&quot;H&quot;, &quot;-&quot;), V511 = c(&quot;S&quot;, 
      &quot;D&quot;), V512 = c(&quot;G&quot;, &quot;E&quot;), V513 = c(&quot;F&quot;, &quot;P&quot;), V514 = c(&quot;Q&quot;, 
      &quot;F&quot;), V515 = c(&quot;C&quot;, &quot;N&quot;), V516 = c(&quot;-&quot;, &quot;L&quot;), V517 = c(&quot;-&quot;, 
      &quot;R&quot;), V518 = c(&quot;-&quot;, &quot;N&quot;), V519 = c(&quot;-&quot;, &quot;R&quot;), V520 = c(&quot;Q&quot;, 
      &quot;K&quot;), V521 = c(&quot;-&quot;, &quot;P&quot;), V522 = c(&quot;-&quot;, &quot;-&quot;), V523 = c(&quot;-&quot;, 
      &quot;-&quot;), V524 = c(&quot;-&quot;, &quot;-&quot;), V525 = c(&quot;-&quot;, &quot;-&quot;), V526 = c(&quot;-&quot;, 
      &quot;-&quot;), V527 = c(&quot;-&quot;, &quot;-&quot;), V528 = c(&quot;-&quot;, &quot;-&quot;), V529 = c(&quot;-&quot;, 
      &quot;-&quot;), V530 = c(&quot;V&quot;, &quot;I&quot;), V531 = c(&quot;C&quot;, &quot;Y&quot;), V532 = c(&quot;-&quot;, 
      &quot;-&quot;), V533 = c(&quot;-&quot;, &quot;-&quot;), V534 = c(&quot;-&quot;, &quot;S&quot;), V535 = c(&quot;-&quot;, 
      &quot;N&quot;), V536 = c(&quot;-&quot;, &quot;-&quot;), V537 = c(&quot;-&quot;, &quot;-&quot;), V538 = c(&quot;-&quot;, 
      &quot;-&quot;), V539 = c(&quot;-&quot;, &quot;-&quot;), V540 = c(&quot;-&quot;, &quot;-&quot;), V541 = c(&quot;-&quot;, 
      &quot;-&quot;), V542 = c(&quot;-&quot;, &quot;-&quot;), V543 = c(&quot;-&quot;, &quot;-&quot;), V544 = c(&quot;-&quot;, 
      &quot;-&quot;), V545 = c(&quot;-&quot;, &quot;-&quot;), V546 = c(&quot;-&quot;, &quot;-&quot;), V547 = c(&quot;-&quot;, 
      &quot;-&quot;), V548 = c(&quot;-&quot;, &quot;-&quot;), V549 = c(&quot;-&quot;, &quot;-&quot;), V550 = c(&quot;-&quot;, 
      &quot;-&quot;), V551 = c(&quot;-&quot;, &quot;-&quot;), V552 = c(&quot;-&quot;, &quot;-&quot;), V553 = c(&quot;G&quot;, 
      &quot;K&quot;), V554 = c(&quot;L&quot;, &quot;F&quot;), V555 = c(&quot;V&quot;, &quot;-&quot;), V556 = c(&quot;K&quot;, 
      &quot;G&quot;), V557 = c(&quot;S&quot;, &quot;R&quot;), V558 = c(&quot;W&quot;, &quot;W&quot;), V559 = c(&quot;N&quot;, 
      &quot;Y&quot;), V560 = c(&quot;L&quot;, &quot;E&quot;), V561 = c(&quot;-&quot;, &quot;I&quot;), V562 = c(&quot;-&quot;, 
      &quot;T&quot;), V563 = c(&quot;-&quot;, &quot;P&quot;), V564 = c(&quot;-&quot;, &quot;E&quot;), V565 = c(&quot;-&quot;, 
      &quot;K&quot;), V566 = c(&quot;-&quot;, &quot;N&quot;), V567 = c(&quot;-&quot;, &quot;P&quot;), V568 = c(&quot;-&quot;, 
      &quot;-&quot;), V569 = c(&quot;-&quot;, &quot;-&quot;), V570 = c(&quot;-&quot;, &quot;-&quot;), V571 = c(&quot;-&quot;, 
      &quot;-&quot;), V572 = c(&quot;-&quot;, &quot;-&quot;), V573 = c(&quot;-&quot;, &quot;-&quot;), V574 = c(&quot;-&quot;, 
      &quot;-&quot;), V575 = c(&quot;-&quot;, &quot;-&quot;), V576 = c(&quot;-&quot;, &quot;-&quot;), V577 = c(&quot;-&quot;, 
      &quot;-&quot;), V578 = c(&quot;-&quot;, &quot;-&quot;), V579 = c(&quot;-&quot;, &quot;-&quot;), V580 = c(&quot;V&quot;, 
      &quot;Q&quot;), V581 = c(&quot;G&quot;, &quot;-&quot;), V582 = c(&quot;D&quot;, &quot;-&quot;), V583 = c(&quot;F&quot;, 
      &quot;-&quot;), V584 = c(&quot;V&quot;, &quot;-&quot;), V585 = c(&quot;V&quot;, &quot;-&quot;), V586 = c(&quot;Y&quot;, 
      &quot;-&quot;), V587 = c(&quot;R&quot;, &quot;-&quot;), V588 = c(&quot;Q&quot;, &quot;-&quot;), V589 = c(&quot;E&quot;, 
      &quot;-&quot;), V590 = c(&quot;-&quot;, &quot;-&quot;), V591 = c(&quot;-&quot;, &quot;-&quot;), V592 = c(&quot;-&quot;, 
      &quot;-&quot;), V593 = c(&quot;-&quot;, &quot;-&quot;), V594 = c(&quot;-&quot;, &quot;-&quot;), V595 = c(&quot;-&quot;, 
      &quot;-&quot;), V596 = c(&quot;-&quot;, &quot;-&quot;), V597 = c(&quot;-&quot;, &quot;-&quot;), V598 = c(&quot;-&quot;, 
      &quot;-&quot;), V599 = c(&quot;-&quot;, &quot;-&quot;), V600 = c(&quot;-&quot;, &quot;-&quot;)), class = &quot;data.frame&quot;, row.names = c(&quot;UniRef90_A0A1V4QIJ3&quot;, 
  &quot;UniRef90_A0A0L9V5F8&quot;))
  </code></pre>
   2108: <p><strong>Update</strong></p>
  <p>It seems that part of the desired behavior is to write the sequences in the alignment <em>separately</em>. I am not sure that I understand why it is necessary to write them separately. Generally it is inadvisable to write many small files rather than one big file, based purely on issues of performance; you are likely to hit the I/O bound on performance very quickly, and that will be much slower.</p>
  <p>One solution that <a href="https://stackoverflow.com/questions/55305833/extracting-subset-alignment-based-in-sequence-name-using-seqinr">has been suggested previously for this kind of problem</a> is to write the whole alignment to a single file, and then post-process that filed in a second step to extract the sequences of interest. This could be as trivial as a <code>samtools faidx</code> call from the shell, or you could work with it in seqinr as suggested in the previous answer.</p>
  <p>Of course, it seems like it would be simpler for most purposes to just have the big alignment file and use e.g. samtools indexing / faidx / biopython / whatever to extract the sequences of interest. But it seems that that is specifically not desired in this case.</p>
  <p><strong>Original answer</strong></p>
  <p>I would strongly suggest using the <a href="https://cran.r-project.org/web/packages/seqinr/index.html" rel="nofollow noreferrer">seqinr</a> package, which is optimized for solving exactly these problems. See e.g. <a href="https://www.biostars.org/p/270009/" rel="nofollow noreferrer">this similar question</a>.</p>
  <p>You will be able to read in an alignment (or whatever), cast it to as.matrix.alignment, do whatever your analysis is, then cast it back to as.alignment, which can then be passed to write.fasta to write the files.</p>
  <p>Whenever possible it is preferable to work with such libraries, which handle these utility functions well, fast, and easy.</p>
  