# HG changeset patch # User bgruening # Date 1501078445 14400 # Node ID 358f58401cd6d1abbc4c15b0fe49943e00619657 # Parent d788d1abe23817a8c9135129079d6c74a7a6bbf6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/trna_prediction commit cfb19d75629f02e0dea4475c16c016ed5510eb44 diff -r d788d1abe238 -r 358f58401cd6 aragorn.xml --- a/aragorn.xml Thu Jan 22 13:15:51 2015 -0500 +++ b/aragorn.xml Wed Jul 26 10:14:05 2017 -0400 @@ -1,41 +1,43 @@ - + prediction (Aragorn) aragorn - TRNAPRED_SCRIPT_PATH + python - - $gff3_output_file; -#end if -]]> + '$gff3_output_file' + #end if + ]]> - + @@ -58,18 +60,25 @@ - - - - - - + + + + + + + - + @@ -81,15 +90,53 @@ - - - - - + + + + + - + - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + @@ -101,7 +148,17 @@ .. _Aragorn: http://mbio-serv2.mbioekol.lu.se/ARAGORN/ ------ +**Input** + +As input a genome sequence FASTA file is needed. Select the right genetic code and the topology for your organism and choose what you want to have analyzed. + +By default, ARAGORN assumes that each sequence has a circular topology (search wraps around ends), that both strands should be searched, that the progress of the search is not reported, both tRNA and tmRNA genes are detected, and tRNA genes containing C‐loop introns are not detected. + +**Output** + +The output of Aragorn reports the proposed tRNA secondary structure and, for tmRNA genes, the secondary structure of the tRNA domain, the tmRNA gene sequence, the tag peptide and a list of organisms with matching tmRNA peptide tags. + +Optionally, your output can be converted to GFF3. **Example** @@ -189,16 +246,10 @@ tRNA GC range = 50.0% to 85.1% Number of tmRNA genes = 1 -------- - -**References** - -Dean Laslett and Bjorn Canback - -ARAGORN, a program to detect tRNA genes and tmRNA genes in nucleotide sequences Nucl. Acids Res. (2004) 32(1): 11-16 - -doi:10.1093/nar/gkh152 ]]> + + 10.1093/nar/gkh152 + diff -r d788d1abe238 -r 358f58401cd6 aragorn_out_to_gff3.py --- a/aragorn_out_to_gff3.py Thu Jan 22 13:15:51 2015 -0500 +++ b/aragorn_out_to_gff3.py Wed Jul 26 10:14:05 2017 -0400 @@ -1,165 +1,139 @@ #!/usr/bin/env python -import re - -def start_pattern(string): - return re.match(r'^[0-9]+\.$', string) \ - or string.startswith('Number of possible') \ - or string.startswith('Searching for') - -def blank_line(string): - return re.match(r'^\s*$', string) - -def blocks(iterable): - accumulator = [] - run_of_blanklines = 0 - for line in iterable: - # Count blank lines - if blank_line(line): - run_of_blanklines += 1 - else: - run_of_blanklines = 0 - - if start_pattern(line) or run_of_blanklines > 2 or 'Mean G+C' in line: - if accumulator: - yield accumulator - accumulator = [line] - else: - accumulator.append(line) - if accumulator: - yield accumulator +import sys -IMPORTANT_INFO = { - 'trna': re.compile(r'tRNA-(?P[A-Za-z]{3})$(?P[A-Za-z]{3})$'), - 'trna-alt': re.compile(r'tRNA-\?$(?P[^$]+)\)$(?P[A-Za-z]{2,})$'), - 'bases': re.compile(r'(?P[0-9]+) bases, %GC = (?P[0-9.]+)'), - 'sequence': re.compile(r'Sequence (?P[c]{0,1})\[(?P\d+),(?P\d+)\]'), - 'possible_pseudogene': re.compile(r'(?PPossible Pseudogene)'), -} -INFO_GROUPS = ('codon', 'anticodon', 'bases', 'gc', 'complement', 'start', 'end', 'pseudo') +full_gene_model = False +if '--full' in sys.argv: + full_gene_model = True -def important_info(block): - info = {} - for line in block: - for matcher in IMPORTANT_INFO: - matches = IMPORTANT_INFO[matcher].search(line) - if matches: - for group in INFO_GROUPS: - try: - info[group] = matches.group(group) - except: - pass - return info - -IMPORTANT_INFO_TMRNA = { - 'tag_peptide': re.compile(r'Tag peptide:\s+(?P[A-Z*]*)'), - 'location': re.compile(r'Location (?P[c]{0,1})\[(?P\d+),(?P\d+)\]'), -} -INFO_GROUPS_TMRNA = ('start', 'end', 'pep') - -def important_info_tmrna(block): - info = {} - for line in block: - for matcher in IMPORTANT_INFO_TMRNA: - matches = IMPORTANT_INFO_TMRNA[matcher].search(line) - if matches: - for group in INFO_GROUPS_TMRNA: - try: - info[group] = matches.group(group) - except: - pass - return info - -import fileinput +genome_id = None stdin_data = [] -for line in fileinput.input(): - stdin_data.append(line) - -possible_blocks = [line for line in blocks(stdin_data)] - -seqid = None -print '##gff-version-3' -# We're off to a GREAT start, if I'm accessing by index you just know that I'm going to do terrible -# awful things -for block_idx in range(len(possible_blocks)): - block = possible_blocks[block_idx] - data = None - fasta_defline = None - - if block[0].startswith('Searching for') or 'nucleotides in sequence' in block[-1]: - # Try and get a sequence ID out of it - try: - fasta_defline = block[-2].strip() - except: - # Failing that, ignore it. - pass - else: - # They DUPLICATE results in multiple places, including a fasta version - # in the 'full report'. - possible_ugliness = [x for x in block if x.startswith('>t')] - if len(possible_ugliness) > 0: - continue - - # However, if it didn't have one of those all important pieces of - # information, then it's either a different important piece of - # information, or complete junk - data = important_info(block) +KEY_ORDER = ('parent', 'source', 'type', 'start', 'end', 'score', 'strand', + '8', 'quals') - # I am not proud of any of this. We essentially say "if that block - # didn't come up with useful info, then try making it a tmrna" - if len(data.keys()) == 0: - data = important_info_tmrna(block) - # And if that fails, just none it. - if len(data.keys()) == 0: - data = None - else: - # But if it didn't, confirm that we're a tmRNA - data['type'] = 'tmRNA' - else: - # If we did have keys, and didn't pass through any of the tmRNA - # checks, we're tRNA - data['type'] = 'tRNA' - - # If we got a sequence ID in this block, set the defline - if 'nucleotides in sequence' in block[-1]: - try: - fasta_defline = block[-2].strip() - except: - pass +# Table of amino acids +aa_table = { + 'Ala' : 'A', + 'Arg' : 'R', + 'Asn' : 'N', + 'Asp' : 'D', + 'Cys' : 'C', + 'Gln' : 'Q', + 'Glu' : 'E', + 'Gly' : 'G', + 'His' : 'H', + 'Ile' : 'I', + 'Leu' : 'L', + 'Lys' : 'K', + 'Met' : 'M', + 'Phe' : 'F', + 'Pro' : 'P', + 'Ser' : 'S', + 'Thr' : 'T', + 'Trp' : 'W', + 'Tyr' : 'Y', + 'Val' : 'V', + 'Pyl' : 'O', + 'seC' : 'U', + '???' : 'X' } - # if a defline is available, try and extract the fasta header ID - if fasta_defline is not None: - try: - seqid = fasta_defline[0:fasta_defline.index(' ')] - except: - seqid = fasta_defline - - # If there's data - if data is not None and len(data.keys()) > 1: +def output_line(gff3): + print '\t'.join(str(gff3[x]) for x in KEY_ORDER) - # Deal with our flags/notes. - if data['type'] == 'tRNA': - # Are these acceptable GFF3 tags? - notes = { - 'Codon': data['codon'], - 'Anticodon': data['anticodon'], - } - if 'pseudo' in data: - notes['Note'] = 'Possible pseudogene' - else: - notes = { - 'Note': 'Tag peptide: ' + data['pep'] + '' +print '##gff-version 3' +for line in sys.stdin: + if line.startswith('>'): + genome_id = line[1:].strip() + if ' ' in genome_id: + genome_id = genome_id[0:genome_id.index(' ')] + else: + data = line.split() + if len(data) == 5: + # Parse data + strand = '-' if data[2].startswith('c') else '+' + start, end = data[2][data[2].index('[') + 1:-1].split(',') + + gff3 = { + 'parent': genome_id, + 'source': 'aragorn', + 'start': int(start), + 'end': int(end), + 'strand': strand, + 'score': '.', + '8': '.', } - notestr = ';'.join(['%s="%s"' % (k,v) for k,v in notes.iteritems()]) + aa_long = data[1][5:] + aa_short = aa_table[aa_long] + anticodon = data[4][1:data[4].index(")")].upper().replace("T", "U") + name = 'trn{}-{}'.format(aa_short, anticodon) + + if not full_gene_model: + gff3.update({ + 'type': 'tRNA', + 'quals': 'ID=tRNA{0}.{1};Name={name};product={2}'.format(genome_id, *data, name = name), + }) + output_line(gff3) + else: + gff3.update({ + 'type': 'gene', + 'quals': 'ID=gene{0}.{1};Name={name};product={2}'.format(genome_id, *data, name = name), + }) + output_line(gff3) + gff3.update({ + 'type': 'tRNA', + 'quals': 'ID=tRNA{0}.{1};Parent=gene{0}.{1};Name={name};product={2}'.format(genome_id, *data, name = name), + }) + output_line(gff3) + + # If no introns + if ')i(' not in data[4]: + gff3['type'] = 'exon' + gff3['quals'] = 'Parent=tRNA{0}.{1}'.format(genome_id, *data) + output_line(gff3) + else: + intron_location = data[4][data[4].rindex('(') + 1:-1].split(',') + intron_start, intron_length = map(int, intron_location) + if strand == '+': + original_end = gff3['end'] + else: + original_end = gff3['start'] - print '\t'.join([ - seqid, - 'aragorn', - data['type'], - data['start'], - data['end'], - '.', - '.', - '.', - notestr - ]) + # EXON + gff3.update({ + 'type': 'exon', + 'quals': 'Parent=tRNA{0}.{1}'.format(genome_id, *data), + }) + if strand == '+': + gff3['end'] = gff3['start'] + intron_start - 2 + else: + gff3['start'] = gff3['end'] - intron_start + 2 + + output_line(gff3) + + # INTRON + gff3.update({ + 'type': 'intron', + 'quals': 'Parent=tRNA{0}.{1}'.format(genome_id, *data), + }) + if strand == '+': + gff3['start'] = gff3['end'] + 1 + gff3['end'] = gff3['start'] + intron_length + 2 + else: + gff3['end'] = gff3['start'] - 1 + gff3['start'] = gff3['end'] - intron_length + 1 + + output_line(gff3) + + # EXON + gff3.update({ + 'type': 'exon', + 'quals': 'Parent=tRNA{0}.{1}'.format(genome_id, *data), + }) + if strand == '+': + gff3['start'] = gff3['end'] + 1 + gff3['end'] = original_end + else: + gff3['end'] = gff3['start'] - 1 + gff3['start'] = original_end + + output_line(gff3) diff -r d788d1abe238 -r 358f58401cd6 readme.rst --- a/readme.rst Thu Jan 22 13:15:51 2015 -0500 +++ b/readme.rst Wed Jul 26 10:14:05 2017 -0400 @@ -67,6 +67,8 @@ - v0.1: Initial public release - v0.2: added options, upgrade to 1.2.36, tool-dependency - v0.3: add unit tests, documentation improvements + - v0.4: added gff3 parser + - v0.5: improved gff3 parser, now handles introns and full gene model diff -r d788d1abe238 -r 358f58401cd6 tRNAscan.py --- a/tRNAscan.py Thu Jan 22 13:15:51 2015 -0500 +++ b/tRNAscan.py Wed Jul 26 10:14:05 2017 -0400 @@ -8,13 +8,12 @@ from Bio.SeqRecord import SeqRecord import subprocess - def main(args): """ Call from galaxy: tRNAscan.py $organism $mode $showPrimSecondOpt $disablePseudo $showCodons $tabular_output $inputfile $fasta_output - tRNAscan-SE $organism $mode $showPrimSecondOpt $disablePseudo $showCodons -d -Q -y -q -b -o $tabular_output $inputfile; + tRNAscan-SE $organism $mode $showPrimSecondOpt $disablePseudo $showCodons -Q -y -q -b -o $tabular_output $inputfile; """ cmd = """tRNAscan-SE -Q -y -q -b %s""" % ' '.join( args[:-1] ) child = subprocess.Popen(cmd.split(), diff -r d788d1abe238 -r 358f58401cd6 tRNAscan.xml --- a/tRNAscan.xml Thu Jan 22 13:15:51 2015 -0500 +++ b/tRNAscan.xml Wed Jul 26 10:14:05 2017 -0400 @@ -1,38 +1,50 @@ - + (tRNAscan) - tRNAscan-SE - biopython + trnascan-se + infernal + biopython + python - - + + - + - + - + @@ -45,37 +57,34 @@ - + - + - + Cove mode, but is much slower (by approx. 250 - to 3,000 fold). Output format and other program defaults are - otherwise identical to the normal analysis. + Directs tRNAscan-SE to analyze sequences using Cove analysis only. + This option allows a slightly more sensitive search than the default + tRNAscan + EufindtRNA -> Cove mode, but is much slower (by approx. 250 + to 3,000 fold). Output format and other program defaults are + otherwise identical to the normal analysis. - search using Eukaryotic tRNA finder (EufindtRNA) only: - This option runs EufindtRNA alone to search for tRNAs. Since Cove is - not being used as a secondary filter to remove false positives, this - run mode defaults to "Normal" parameters which more closely - approximates the sensitivity and selectivity of the original algorithm - describe by Pavesi and colleagues. + This option runs EufindtRNA alone to search for tRNAs. Since Cove is + not being used as a secondary filter to remove false positives, this + run mode defaults to "Normal" parameters which more closely + approximates the sensitivity and selectivity of the original algorithm + describe by Pavesi and colleagues. - search using tRNAscan only (defaults to strict search parameters) - Directs tRNAscan-SE to use only tRNAscan to analyze sequences. This - mode will cause tRNAscan to default to using "strict" parameters - (similar to tRNAscan version 1.3 operation). This mode of operation - is faster (about 3-5 times faster than default mode analysis), but - will result in approximately 0.2 to 0.6 false positive tRNAs per Mbp, - decreased sensitivity, and less reliable prediction of anticodons, - tRNA isotype, and introns. + Directs tRNAscan-SE to use only tRNAscan to analyze sequences. This + mode will cause tRNAscan to default to using "strict" parameters + (similar to tRNAscan version 1.3 operation). This mode of operation + is faster (about 3-5 times faster than default mode analysis), but + will result in approximately 0.2 to 0.6 false positive tRNAs per Mbp, + decreased sensitivity, and less reliable prediction of anticodons, + tRNA isotype, and introns. - search using Infernal cm analysis only (max sensitivity, very slow) @@ -157,56 +166,54 @@ - search using Infernal and new cm models instead of Cove ------ **disable pseudogene checking** - Manually disable checking tRNAs for poor primary or secondary - structure scores often indicative of eukaryotic pseudogenes. This - will slightly speed the program and may be necessary for non-eukaryotic - sequences that are flagged as possible pseudogenes but are known to be - functional tRNAs. + Manually disable checking tRNAs for poor primary or secondary + structure scores often indicative of eukaryotic pseudogenes. This + will slightly speed the program and may be necessary for non-eukaryotic + sequences that are flagged as possible pseudogenes but are known to be + functional tRNAs. ------ **Show both primary and secondary structure score components to covariance model bit scores** - This option displays the breakdown of the two components of the - covariance model bit score. Since tRNA pseudogenes often have one - very low component (good secondary structure but poor primary sequence - similarity to the tRNA model, or vice versa), this information may be - useful in deciding whether a low-scoring tRNA is likely to be a - pseudogene. The heuristic pseudogene detection filter uses this - information to flag possible pseudogenes -- use this option to see why - a hit is marked as a possible pseudogene. The user may wish to - examine score breakdowns from known tRNAs in the organism of interest - to get a frame of reference. + This option displays the breakdown of the two components of the + covariance model bit score. Since tRNA pseudogenes often have one + very low component (good secondary structure but poor primary sequence + similarity to the tRNA model, or vice versa), this information may be + useful in deciding whether a low-scoring tRNA is likely to be a + pseudogene. The heuristic pseudogene detection filter uses this + information to flag possible pseudogenes -- use this option to see why + a hit is marked as a possible pseudogene. The user may wish to + examine score breakdowns from known tRNAs in the organism of interest + to get a frame of reference. ------ + **Show codons instead of tRNA anticodons** - This option causes tRNAscan-SE to output a tRNA's corresponding codon - in place of its anticodon. + This option causes tRNAscan-SE to output a tRNA's corresponding codon + in place of its anticodon. ------ + **Example** -* input: +**input** - >CELF22B7 C.aenorhabditis elegans (Bristol N2) cosmid F22B7 - GATCCTTGTAGATTTTGAATTTGAAGTTTTTTCTCATTCCAAAACTCTGT - GATCTGAAATAAAATGTCTCAAAAAAATAGAAGAAAACATTGCTTTATAT - TTATCAGTTATGGTTTTCAAAATTTTCTGACATACCGTTTTGCTTCTTTT - TTTCTCATCTTCTTCAAATATCAATTGTGATAATCTGACTCCTAACAATC - GAATTTCTTTTCCTTTTTCTTTTTCCAACAACTCCAGTGAGAACTTTTGA - ATATCTTCAAGTGACTTCACCACATCAGAAGGTGTCAACGATCTTGTGAG - AACATCGAATGAAGATAATTTTAATTTTAGAGTTACAGTTTTTCCTCCGA - ..... + >CELF22B7 C.aenorhabditis elegans (Bristol N2) cosmid F22B7 + GATCCTTGTAGATTTTGAATTTGAAGTTTTTTCTCATTCCAAAACTCTGT + GATCTGAAATAAAATGTCTCAAAAAAATAGAAGAAAACATTGCTTTATAT + TTATCAGTTATGGTTTTCAAAATTTTCTGACATACCGTTTTGCTTCTTTT + TTTCTCATCTTCTTCAAATATCAATTGTGATAATCTGACTCCTAACAATC + GAATTTCTTTTCCTTTTTCTTTTTCCAACAACTCCAGTGAGAACTTTTGA + ATATCTTCAAGTGACTTCACCACATCAGAAGGTGTCAACGATCTTGTGAG + AACATCGAATGAAGATAATTTTAATTTTAGAGTTACAGTTTTTCCTCCGA + ..... -* output: +**output** ======== ====== ===== ====== ==== ========== ====== ====== ========== ========== @@ -222,17 +229,9 @@ ======== ====== ===== ====== ==== ========== ====== ====== ========== ========== -------- - -**References** - -Todd M. Lowe and Sean R. Eddy - -tRNAscan-SE: A Program for Improved Detection of Transfer RNA Genes in Genomic Sequence Nucl. Acids Res. (1997) 25(5): 0955-964 - -doi:10.1093/nar/25.5.0955 - - ]]> + + 10.1093/nar/25.5.0955 + diff -r d788d1abe238 -r 358f58401cd6 test-data/aragorn_tansl-table-11_introns.gff3 --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/aragorn_tansl-table-11_introns.gff3 Wed Jul 26 10:14:05 2017 -0400 @@ -0,0 +1,32 @@ +##gff-version 3 +genome_with_introns aragorn gene 1533 4118 . - . ID=genegenome_with_introns.1;Name=trnK-UUU;product=tRNA-Lys +genome_with_introns aragorn tRNA 1533 4118 . - . ID=tRNAgenome_with_introns.1;Parent=genegenome_with_introns.1;Name=trnK-UUU;product=tRNA-Lys +genome_with_introns aragorn exon 4081 4118 . - . Parent=tRNAgenome_with_introns.1 +genome_with_introns aragorn intron 1569 4080 . - . Parent=tRNAgenome_with_introns.1 +genome_with_introns aragorn exon 1533 1568 . - . Parent=tRNAgenome_with_introns.1 +genome_with_introns aragorn gene 6453 6524 . - . ID=genegenome_with_introns.2;Name=trnQ-UUG;product=tRNA-Gln +genome_with_introns aragorn tRNA 6453 6524 . - . ID=tRNAgenome_with_introns.2;Parent=genegenome_with_introns.2;Name=trnQ-UUG;product=tRNA-Gln +genome_with_introns aragorn exon 6453 6524 . - . Parent=tRNAgenome_with_introns.2 +genome_with_introns aragorn gene 7730 7819 . - . ID=genegenome_with_introns.3;Name=trnS-GCU;product=tRNA-Ser +genome_with_introns aragorn tRNA 7730 7819 . - . ID=tRNAgenome_with_introns.3;Parent=genegenome_with_introns.3;Name=trnS-GCU;product=tRNA-Ser +genome_with_introns aragorn exon 7730 7819 . - . Parent=tRNAgenome_with_introns.3 +genome_with_introns aragorn gene 12356 12431 . + . ID=genegenome_with_introns.4;Name=trnP-UGG;product=tRNA-Pro +genome_with_introns aragorn tRNA 12356 12431 . + . ID=tRNAgenome_with_introns.4;Parent=genegenome_with_introns.4;Name=trnP-UGG;product=tRNA-Pro +genome_with_introns aragorn exon 12356 12431 . + . Parent=tRNAgenome_with_introns.4 +genome_with_introns aragorn gene 12597 12670 . + . ID=genegenome_with_introns.5;Name=trnW-CCA;product=tRNA-Trp +genome_with_introns aragorn tRNA 12597 12670 . + . ID=tRNAgenome_with_introns.5;Parent=genegenome_with_introns.5;Name=trnW-CCA;product=tRNA-Trp +genome_with_introns aragorn exon 12597 12670 . + . Parent=tRNAgenome_with_introns.5 +genome_with_introns aragorn gene 22050 22123 . - . ID=genegenome_with_introns.6;Name=trnR-CCG;product=tRNA-Arg +genome_with_introns aragorn tRNA 22050 22123 . - . ID=tRNAgenome_with_introns.6;Parent=genegenome_with_introns.6;Name=trnR-CCG;product=tRNA-Arg +genome_with_introns aragorn exon 22050 22123 . - . Parent=tRNAgenome_with_introns.6 +genome_with_introns aragorn gene 26588 26660 . - . ID=genegenome_with_introns.7;Name=trnM-CAU;product=tRNA-Met +genome_with_introns aragorn tRNA 26588 26660 . - . ID=tRNAgenome_with_introns.7;Parent=genegenome_with_introns.7;Name=trnM-CAU;product=tRNA-Met +genome_with_introns aragorn exon 26588 26660 . - . Parent=tRNAgenome_with_introns.7 +genome_with_introns aragorn gene 26850 27468 . + . ID=genegenome_with_introns.8;Name=trnY-AUA;product=tRNA-Tyr +genome_with_introns aragorn tRNA 26850 27468 . + . ID=tRNAgenome_with_introns.8;Parent=genegenome_with_introns.8;Name=trnY-AUA;product=tRNA-Tyr +genome_with_introns aragorn exon 26850 26884 . + . Parent=tRNAgenome_with_introns.8 +genome_with_introns aragorn intron 26885 27410 . + . Parent=tRNAgenome_with_introns.8 +genome_with_introns aragorn exon 27411 27468 . + . Parent=tRNAgenome_with_introns.8 +genome_with_introns aragorn gene 29759 29833 . + . ID=genegenome_with_introns.9;Name=trnH-GUG;product=tRNA-His +genome_with_introns aragorn tRNA 29759 29833 . + . ID=tRNAgenome_with_introns.9;Parent=genegenome_with_introns.9;Name=trnH-GUG;product=tRNA-His +genome_with_introns aragorn exon 29759 29833 . + . Parent=tRNAgenome_with_introns.9 diff -r d788d1abe238 -r 358f58401cd6 test-data/aragorn_tansl-table-1_tmRNA_tRNA.gff3 --- a/test-data/aragorn_tansl-table-1_tmRNA_tRNA.gff3 Thu Jan 22 13:15:51 2015 -0500 +++ b/test-data/aragorn_tansl-table-1_tmRNA_tRNA.gff3 Wed Jul 26 10:14:05 2017 -0400 @@ -1,2 +1,2 @@ -##gff-version-3 -gi|240255695:23036500-23037000 aragorn tRNA 381 453 . . . Anticodon=tgc;Codon=Ala +##gff-version 3 +gi|240255695:23036500-23037000 aragorn tRNA 381 453 . + . ID=tRNAgi|240255695:23036500-23037000.1;Name=trnA-UGC;product=tRNA-Ala diff -r d788d1abe238 -r 358f58401cd6 test-data/aragorn_tansl-table-1_tmRNA_tRNA.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/aragorn_tansl-table-1_tmRNA_tRNA.txt Wed Jul 26 10:14:05 2017 -0400 @@ -0,0 +1,70 @@ +------------------------------ +ARAGORN v1.2.36 Dean Laslett +------------------------------ + +Please reference the following paper if you use this +program as part of any published research. + +Laslett, D. and Canback, B. (2004) ARAGORN, a +program for the detection of transfer RNA and +transfer-messenger RNA genes in nucleotide sequences. +Nucleic Acids Research, 32;11-16. + + +Searching for tRNA genes with no introns +Searching for tmRNA genes +Assuming circular topology, search wraps around ends +Searching both strands +Using standard genetic code + + +gi|240255695:23036500-23037000 Arabidopsis thaliana chromosome 3, complete sequence +501 nucleotides in sequence +Mean G+C content = 43.1% + +1. + + + + a + g-c + g-c + g+t + g-c + a-t + t-a + g-c tt + t gtccc a + ta a !!!!! g + a ctcg caggg c + t !!!! a tt + g gagc c + gta g g + c-gag + t-a + c-g + g-c + c-g + t t + t a + tgc + + + + tRNA-Ala(tgc) + 73 bases, %GC = 56.2 + Sequence [381,453] + + + +>tRNA-Ala(tgc) [381,453] +ggggatgtagctcatatggtagagcgctcgctttgcatgcgagaggcaca +gggttcgattccctgcatctcca + + + + +Number of tmRNA genes = 0 + + +Configuration: aragorn /tmp/tmpx1qAPk/files/000/dataset_3.dat -gc1 -m -t -c -o /tmp/tmpx1qAPk/files/000/dataset_4.dat -fasta diff -r d788d1abe238 -r 358f58401cd6 test-data/genome_with_introns.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/genome_with_introns.fa Wed Jul 26 10:14:05 2017 -0400 @@ -0,0 +1,2 @@ +>genome_with_introns +TTATCCACCTATTGAAATAGATTCAACAGCAGCTAGATCCAGAGGAAAGTTATGAGCATTACGTTCGTGCATAACTTCCATACCTAGGTTAGCACGATTAATGATATCGGCCCAAGTGTTAATTACACGACCTTGACTGTCAACTACAGATTGGTTGAAATTGAATCCATTTAGGTTGAAAGCCATAGTGCTTATGCCTAGAGCGGTAAACCAGATACCTGCTACGGGCCAAGCAGCTAAGAAGAAATGTAAAGAACGGGAGTTGTTGAAACTAGCATACTGGAAGATCAATCGGCCGAAATAACCGTGAGCAGCCACAATATTGTAGGTTTCTTCCTCCTGACCAAATTTGTAACCTGCATTTGCGGACTGATTCTCAGTAGTTTCCCTGATCAAACTAGAAGTTACCAAAGAACCATGCATAGCACTGAATAGAGAGCCGCCGAATACACCAGCTACACCCAACATGTGGAATGGATGCATAAGGATATTGTGCTCAGCCTGGAATACAATCATGAAATTGAAAGTACCAGAGATTCCTAGAGGCATACCGTCAGAGAAGCTTCCTTGACCAATAGGGTAGATCAAGAAAACGGCACTAGCAGCTGCAACAGGAGCTGAGTATGCAACAGCAATCCAAGGACGCATACCTAGACGGAAGCTAAGCTCCCACTCACGACCCATATAGCAAGCTACACCAAGTAGGAAGTGTAGAACGATTAGCTCGTAAGGACCCCCGTTGTATAGCCATTCATCGACGGAAGCTGCTTCCCAGATGGGATAGAAGTGCAAACCGATAGCTGCAGAGGTAGGAATAATGGCACCGGAGATAATATTGTTTCCATAAAGAAGAGAACCGGAAACGGGCTCACGAATACCATCAATATCTACCGGAGGAGCTGCGATGAAAGCAATAATGAATACAGAGGTTGCGGTCAATAGGGTAGGGATCATCAAAACACCGAACCATCCAATGTAAAGACGGTTTTCGGTGCTAGTGATCCAGTCGCAGAAGCGACCCCATAAATTTGCGCTTTCGCGTCTTTCTATAATTGCGGTCATGGTCAAAACTTCGTTTATAAAATCATCAGAGGCTCCCAAGCATAAGGCTTGTTATTTGACAGTATAATATGATCCATGTATCAATGTCAACTAATATCCGGGATAGAATATAGTATTTGAGATAGACTCTCTATTTTTTCGCATATATTACACACTCTATAGATCTATCTGTGGTTAGATACTCCATCAAATTCTTCCATTCCTGGTTACAGGAATGGAAGATCCGTTGTAATGAGAACGGATAGGCAGTGGAGATAAAAATTTTGTTGTTCGCTATAACGAAGTGCAATGCGATTCTGGAACCGAATTCTGAATAAATTAATATGAGTGGGATATTAATTCTTCATCACCTTTCCGGAGAACCCATAGTGCGATAGTTCGTTACCTGTGAATAGGAACAAATAGGAAAAGGAACTTGATTGGATCCAGAACCAGAATAAGTGGACAGAGGTCCCTATCAGAAATTTGATCCGGGTTGCCCGGGACTCGAACCCGGAGCTCGTCGGATGGAGTGGATTATCTGCTCCTTCAGTATCAGTAAGAGCGAGAAATCTCTCCCCAAACCGTGCTTGCAATTCTCATCGCACACGGCTTTCCCCATGTAATGTATCTATTTCCTAATCATTTTAGTTCTCGGATGGCAAAATAAAAATGATTCTGAATCGAGGCAATGACTCAAAGAGCATTTCATTGGTCAAATAAGTTTTCTATTTTCAGATCCTGTATCTTTTGCCAGGAATGGGCTAGGGGATTTATCTGGGGAATATCTGAATGCCAAATTCGTTCTCTCTGTGAACGGGCCGCCGCTTTTGATGAAAAAGGCGGAGAATCCAATTCTCGTTCTTTTGAAAACGATTTTTTAAAGAGTTCTGGACCTAATTCCTTCCGAACTACACGTATCGTACTTTTATGTTTACAGGCTAAAGTTTTAGCACATGATAATGAAAGTATATACTTTATACGATATAAACCATCTCGACCAAAGGATCCACTGTAGTAATGAAAAAGATTTCTCCAAATTCGATCGAATCGATCCAGGATATCATCATCTGTTAGACTGGTCCAAGACAATTTACTAATTGGCCGCCCTGATATATCACAGAATTTTTCTCTAGACAATAATCCAATTATTGGTACAATCGGAACTATTGGATCAAATTCATCGGTAATAAGATCGGCAATGAATAACTCATCTAGCATTTTAGTCTTGACCAAAAGAGGTTTCATCCGAAACCTCAGAAAATAACCTAAAGAAGAAGAACAATTCTTGGATAATTGATGAGAACATACCCTATATGGTTCGTTCCAAAGATGGAAATAACATTGCCGAAAAATTGGAAGATAATATCTATATTTTTTCACTAGGAGATTAGTACCCTTTATAGCTATAATAGATCTTTCTCCATATCTAACATAGTGAATGTTAGGATCCTTCAACGACCAGATACTTTGAAATGAATTTCGACGAGAAAATAGAAAAATATTTTTTATTTTTCGATGAAAATGAGTTCGCTGAGGGAAAGACCCATGAGATAACGATCGTGAATGAGAGGATCGTTTAAGAAGGGAAACTAAAATGGATTCGCATTCATAGACATAATTATTCCACAGGAACAGGAAGAATCTCGTATTTACTTTCGGGACGACAATAATCGATCTTTGTAAACTCTCTGAACTATTTCGATATTCATAGAGAATAGATCGTAATGGGTGCAAGGAGGGAGCATCTCCGATCCAGCGACGAAAGGTTCGAACCAAAATTTCTGGATGAATAGAATAGGGTATTCGTGTATCTGATACATAATTTGAATGCGGGAATTTATCCTCCAAGAAGGGAAATATTGAATGGATCGACCGGAAACTCTTCCATTCATTCATCCCTTCCACAGAATATTTTGACCGTATAGAGAACGGAACTTCCAGGACCAATGTCAGTCCTTCTAGTACCGATTCAGAATAGGAACTCTTCTTGCGATCAACTAATGGATTTGGATCACAATTCACGAATAAAACAATTGAATGATTCTGTTGACGTATTTGACCAATCAAACGTTTTACAGTTAGGAAACTGAACTGATCATTGGAACTTAAATGTTCCATCGGTTCGGAGGAACTCGATCCATCCAAATAATGATCATGAGAAATTGCGTAAAGATCTTCCTGAAAAAAGAGTGGATATAAAAAGCATTGTTGCCAAGAGCTATCTTCCTTTCCGTATCTATGGAACTCATCCATTTTCAAACCTCAGTTATGGCCCTCGTTCATGAGAATAACCTCTTAAATTCTGAGATAATACAATACATGGTGCGATCTAGTCGGGACAAGATAGGAAAAAGATAGATGATATAAAGATTCTATCTTCTATTCAGCAGATTTACTACCCAAGGATCTCGTTCGTCATGAGGAAGAACGAAAATCTTTTATCCTGGCAACCGATCGCTCTCCTGACTCATGGAATAAATAAACCTGGTCAGTACACTATTTATCTTACACATCTGTACTCGAGTACTTAGGACTCATTGTGAGTGTATAAATCCCTGATCTACTCAGGGAAAACCTCCCGATATCGGGTACTAAAATGCTCTTAACTTCTGATCAGTAAAGGGAATTCCTCGCTCGTTTAATTGGAACGAGGAACAGAAGCTCGTTTCTCTGGGTCTACTTATGATTCAAGTCATATAGCTTTCTCCATTGACTCATTCGACTTAACCGCGAATTGATTCGATCCTATTCACAATTATCACATTTGATCCGAAAGGATGATCATATTATACATCCACCTAGGTATATAATAGACATTTCCCACCCATTTGATTCCTTGAATTAGATCCGGTCCTGATCGAATAATATCAGGTATCCTAAAAATCATATCAGGTATCATAAAGATCATATGTTGGAACGACATGCTGTTTTTTCCGTTAATTCTACTTCGAGGATCAGTCGTAGTCTTCCAAACTTTACCGATGGTATCGACGAGTTTTCTACTTCATTCAAATGTGTAAAAGACCTTAGTCGCACTTAAAAGCCGAGTACTCTACCATTGAGTTAGCAACCCATATTTCAAATAGATATTGAGGATATATATACGATCGAAGTGGAATGCGAGGTTACTCAATATGAACCGGTAAATAGAATCTTACCAATCGTTGTTGTTAAATAACAACGGGAGGGATCAAAAACCTATGTGAATGACCAAATAATTCACTCATCAGTTCATATATGTATATGAATAATTTCGATCCACCATTCCAGAATAAAGTAATCTAGGTTATGAATAAATGATCCGTCGACAGAATTATCATGATTGGATAGGATCACTGATAAATGATGAACCTAAGATATCTATTTCTATTGTGAATGGACGAATTATATCGACACAATACACTATTGTCAATCCAGAATAAAAGATAAATGAATTGTTGGATGTCATAATCCATATCCACGAAACCGATTATGTAAAGTCGCACGTTGCTTTCTACCACATCGTTTCAGACGATGTTTTTAAGATCTCGAATCATGATTGATACGTGATTATGAATAGTCATTAACTCAATTGATATGAGAGGAATAGGTATCGAATTGGATCCACTCTTTTTGTATAGAATACACTCAATGTAATAAATGAATTGATATTGATCAGGTACTTAACTTAATGCTTCTTTAGCTGCGTGCATTACCTCGACAGTAACGTTCAAAATGCCCTTTCGTCGTGCAAATTTTTCTGTGTTTCTCTTTACTTCGTCCCTGACAAAACGGGGGATTTTATTCAATTCTAGTCGACTTTCAGGATTCCAAATTGGACTCATATCCGTGGATAATGATTTAGTCGTTATTTCCTTCGTATCATGACCACAAAAAATCTCTAGAAGATGATCCTCCATACCCAGAGCGAATGAGTTATAAACTGGATCAGCTATTTGATTAGTACCTTCGTAACCCAGGAAGGGTCGATATCCCAAGGAAAAATTTTGGATATGAGCTGGTGCGGAAATAACTCCACAGGGAATCTCAAGACGTTTACCAATATGACGTTCCATTTGAGTACCAAATATTGCAGAGGGTTCCACGCGAGCGATAATATCTCCTACTTCAGCATGATCATCTGTGATGATTATCTCATCACAAAAATCTTTAATTTGCTCTTTGAACCATTCTGCATCATGTTTACAATAAGTACCTGTACAACTCACACGAATTCCCATCTCTCTAGCAAGTATCTTAGTGATTGAAGCAGCATGAGTTGCATCACCAAAAACGACTGTTTCTTTCCCCGTAAAATTCTGACAATCGATAGATCTTGAGAACCAAGCAGCTTGGGAAACGAATCGAGTTTGTCCATCGATATAGGATTCGTAATCAACCCTTTTGCTTGATAAAATAGGAGCCGCCAAGGTATCAATATATTTCTTTATCTGTCGAATGCACTCGGCCATATCTACAGCTCCCATAGGAGTTGTAGATACATAAGGCATCCCAAATTCTTTATTCAAATACATTGCTGTCATTAAGCCCACTTCACGATAAGGAATTAAATTGAACCGAGCTTTTGGTAAATTTTTTGAATCCTCTACAGATCCTCCTTCAGGAATTATTTGATTAATTCTGATGTCCAGATCTTTTAATAAACGTCTCAACTCACGACAATCGTGTCGATTATGAAAGCCCAAAGTAAGAATCCCAATTATATTTACAGAAGGTGCATCTGTTACGAATTGATCCAATGTTTCTTGTCTATAGGATTTCTCCAAATAATATCGAACCACCTGTTCCAAAGTTCTATCCGCTGCCTGAATTTCATTCACTTGATAATGATCCACATCCGCAAAAATGACGTTGCAATCGGAGATTATGGATGCTCTATCCACAAAGTTTTTTAAATCCTCTTGCAAGATACTAGAGGTACATGTAGGTGTCAATATGATCAGATCGGGACCTTCCTCCTTATCTTTTCGAAGAATATTATCCACAACTCTTTTTCGAGATCCACGTGCTAGTACGTGACGATCTACTATACTAGCAGTTGCAGGAGTAAAATTTCTTTCCCGTTCTAACATAGAGCGCATTACATTAAAATAATCATCTCCTAGAGGAGCATGCATAATGGCATGGACATTTTTGAATGAACTAGCTACTCGTAGAGTTCCAATATGAGCAGGACCAGCATACATCCAATGGGCTAATTTCATAAATTGAACCTTATCTCAAATTGATCCGTATTCCCATCTTGCACCACAGAGATATCCCTTTATCCCTTCCCTATTGTAATCACATTCCCTTCTGATAAGTATGGTGAAATTATGATAAAAAGTAGAACGAAATTTTGGATTTATCTTTACGAAAGAAAAAAAGGAAGAGGGAGAGAACAGAAAACAGGAACCAATGAAATAAGTCTGGGACGGAAGGATTCGAACCTCCGAATAACAGGATCAAAACCTGCTGCCTTACCGCTTGGCCACGCCCCATTCCCATCCTATTTCCCTATTCATATGCTAATGAATACTTATATTCAATTTTTTGTCAACTCATTAGGATCCAAGATTCATTAGATAAGATCCTAATTGGGCTGGAAAATTTTGTGGATATTTTGATAAAATAGGTTATTGATGGAATTGGACATAATAGGAAAAACAGAAAAAGGGACAAGAATATCCATTCATTGATCATTTTCTATTAGATTGGGTAAAATATTGTATGTATGAAAGAATCATCCCTTCCAACCCCAAGTCCGGTCAAACTTGCCGAAGAGCTTCTCGATCGATTTGATCAATCAAAGACTTTTCTGGCTTTACCCCCCCTAATTTTTTTTTGGAGAAGAAAAATGCCAGTTATGCTCAATATTTTTCTAGATGATGCCTTTATCTATTCAAATAATATCTTTTTTGGAAAATTACCTGAGGCTTATGCGATTTCCGATCCAATTGTCGATGTAATGCCAATTATTCCTGTTCTCTCTTTTCTCTTAGCCTTTGTTTGGCAAGCTGCTGTAAGTTTTCGATAAAAAGTATCCCCTTTTTTCCTTTTGAAAGTTTTAAGATCGCTGTCATTGATCCAATTTTTGTATAACTCTTTACATTTTTTGTGACAGAAGTTCTATCCTTGCTCCACCCGATGATACCAGATCCAGATACCTTATCTGCTCCCGACTAAAAACTTTTCCACTCACCTTCATCAATTCCTTTCCTTTCAATCCCATCGCTCACTTCGGATCGGGCTATTTGTTCACGTATTGATACGAATGATATATTTTCATAAAGATTCGATAAATATCTGGTTGATCCAAAAAAGAAGAAGGGAAAAAAGACCATTTTGAAAACAAAGAGATAAATTATCTCCTTCTTTCAATTTGATTTTCACACGTGATCCGGAGAAATCGTGATTTTTATGAATCATACTATTGTTTGGTATTCAAGTATTCATATATTATACAAAGATTGATGATTTATTCTGTTGTACTTATAATTAGGATCCCGGAGATTACGTAATGCTTACTCTTAAGCTGTTCGTTTACACAGTAGTGATATTTTTCATTTCTCTTTTTATCTTTGGATTTCTATCGAACGATCCAGGACGTAATCCCGGACGTAAAGAATAGTGAAAAAAAGTATCTAGGTTAATGAGTCTTTTCCGTTCCGTAGAAAGATTCGGAGTTATCCGCAATAGTGACCGAACGGAGAGAGAGGGATTCGAACCCTCGGTACGGATAATCCGTACTACGGATTAGCAATCCGCCGCTTTGGTCCGCTCAGCCATCTCTCCAAGATGGAAAAGTTCTTGTTTAACAAAATGAATGGTGGAGTAAAGGTGTATACCATAGCATGTACGGATTGTATCGACAATATAACGAATATTGCAATTATTCAGTTAGAAAAACGAATCTGGCGAATCGTATTTTTCATTTCGTTTCAAAAAATTTTGCCTTTTTTCTGACCTGCCTGGCCTGGCCTTAACAAACCACCCTTGTCCTTTCAATTTTTTTTTTTTTTCTTTTTTTTTTCTATGTTTCTTTCTTTGGCTCTCTAGTCCTTTTATATGGTATGATATTGTTCATAGTTACTGAGGGCTATTCCTGACGAAGTTACACAGATGGGGAAGAAGAAGAAAAATGGAGCGGCAGATGAAGAAGAGAAAATAGAAGAGAAGAAAAGTGATTGATCTCGACAACATTTTATTCATACATCCATCAAGTCGATGGGATCATAGAGGTGAAAGAAACCCAAATGAATCTAGAAGTTATTGCGCAGCTCACTGTTCTGACTCTGACGGTTGTATCGGGCCCATTAGTCATTGTTTTATTAGCAGTTCGCAAAGGTAATCTATAATTACAATGAGCCATCGCCGGGAATGAAATACTTTGGTAAATAGTATTTCATCCCCGGCGATGGAGATTCATGTAATAATGAAAACGAGGTAATGATTGATAGAAACTTTCAATAGAGGTTGATAACTCCTCATCTTCCTATCGGTTGGACAAAAGATCGATCCGTATGTTACAATCGGATCGTGGCGGGTATAGTTTAGTGGTAAAAGTGTGATTCGTTACATTATCAACTCGAATAATTGAAGGATCTTTTACATGGATCTTTGATCCATCTAAAGCTCTATTTCCAAATAGGTGAAAAACCTTTCCTATGAAGAAATACTATCCATCCAAGATGGAAGAGTTCATGTGTGACACAACTTCATATACTTTACGTTCCCATATTAGAGTATAGTGCTTCACTTCTTTCCATTAAAACAAATGCCCGTTGGTGTTCCAAAAGTTCCTTTCCGAGCCCCTGGAGATGAAGATGCAAATTGGGTCGACTTATACAACCGACTTTATCGAGAGAGATTACTTTTTTTGGCTCAGGATATCAATCACGAGATTGCAAATCAACTCATGGGTCTCATGGTATATTTGAGTGCAGAAGATGCAAATAAAGATATGTTCTCATTTCTCAACTGTCCCGGTGGATCAGTAATACCGGGAGTAGGTCTTTTCGATATTATGCAAATAATAGTACCAGATGTACATACAATATGTATGGGGATAGCTGCTTCAATGGGATCTTTCATCCTAATCGGGGGAGAAATTACTAAACGTATAGCATTACCTCACGCTAGGGTTATGATCCACCAACCTGCTAGTTCCTATTATGACGGACCGGCCGCAGATTTTCATACCGAATCGAAACACGTAACGATGCTTCGCGATTACATAACAAAATGTTATATAGAAAGAACGGGCAACCTCGGAGAGGTCATTCAACGGGACCTGGACAGAGATGTTTTTATGTCAGCAACAGAAGCCCGAGCTTATGGCATTGTTGATGCCGTAGCGGAAGGTTGATCTCATATCGGAAGATCCTCTTTTTCATTGATTTTTATAATGAACTGTAAACTGATCTTTTCTTTTTCTTAAAAAAAAAGGGGAAAGGGAAAGTGATTCATTTCATAATAACCTTATATGGTTAGGATCAATCCGAACCAGTTGATTCCGCATACAATACAGCTAGAATGCCCACTATTCAACAACTTATTAGAAAAGCAAGACAGCCAATAGAGAATAGAAAAAAATCTCCTGCTCTTCGAGGATGTCCTCAGCGTAGAGGAGTATGTGCTAGGGTGTATGTGCGACTCGTTCGGATCAGAAGCTGAAAGAGACTGGGAAATTCTTACAACGAAATAAGAGAAGAATTTTCCCGCCATAATAAAGTAAAGATCCATCATCTAACCTTACCGGGGATGAAATTTATGGTTTCCATTGGTGCAAACCCAATCACCTTGATGTGGGATGAAAAGCAATTCCTCATTGGTAGCGAATGGTCATCAATCCATTGAGCGGGGAAATCATGCAAATTGAAGAAGCATAAAGTTTATGCTCATATTGCCGCGAGAACGGAACAACAGGGTCAGCTACCTGGCCAACCCCAGAATTACATGTCGTTACTGTATGAATAGATCTTGTAATGAGAGTATTTATTACTTGATGATTCAAGAGTAGAGCTGGAGATGGTAAACCGTACAAGTTACCGATAACATACTCATCTCATATTTCGGAAATGAATAAGAGGCTCCGGCGTATGGAGAGGACCTTACCGTTGGAGAAAGAACCATAGAAACGATGAAACCCATGATTTTTTCTCATTCTCAGTACAAGGTCCGAGCCCTTGCTTACCCGGAAGATGCCTATCCAAAGGGAATTATGGTTGGGAAGGTTGCAGTAGCAAAAGCCATTGGAACTTTTATTTTCTAAATAAGAAGAATCAGTGTTATTCTCAATGGACCAAACAAATGACTAACCAATAAAAAGATTAGCGATTCATGAGAGTAAACGTCAATGACCAGAGTGAAACGTGGATATATAGCTCGAAAACGTCGGAAAAAGATTCTTGCATTTGTATCAGGCTCTCGAGGGGCCCATTCGAAACTTTTTCGAACTGCTAACCAACGGAAAGCTAGAGCCTTAGTTTCCGCCCACCGAGATAGAGGTAAACGCAAGAGAGATCTTCGTCGTTTGTGGATTACTCGAATTAATGCAGCAGCCCGTGCCAATGGAGTCTCTTATAACAGATTCATCCAATATTTGTACAAGAGGCAGTTGCTTCCAAATCGTAAAACACTTGCACAAATAGCTGTATTAGATAGTAATTGCTTTTCCACCATCTTGAAGAACTTATCGTGTGATGAAATAGGTTAGGTATAGATGAAAGAAATAGGTAAAGATGGAATGGATAGAAAGATTCTCCCGGAGAATTCCCTCCGGGAAGGTCAAAACATTGAAAAATTTTTCAATATTGGAAATGAATGAAACGAAAAGACTTCAATCAAATTTTTTTCCAAGAATGAAATTCTGTCAACTTTTTCGACAATAGACTAAAGATCTGCATCTTTATCGAACAGATATCCCAGCTCCGATTTGATTAAGGAGTAGGTTCATTTCCATTCCATGGATGAATTTAGTTTTCATTATAAAGAAAGGGTAACAAAGATGGAATACGAGCTCGTTTAATAGCGTTAGTAATGAGACGTTGTTGTTTTGAGGTTAATCTATTCACTCGGCCAGATAATATTTTTCCTTGCTCGCTAATAAATCGACTAATTAGGCTCATATTTTTATAATCAATCCGATCTCCCGACCTAATTGGTGACAAATGTCTACGAATTGGTGTCAAATGTCTACGAATTGGTGTCAAATGTCTACGAAAATATCGCTTGGGTTTATCCATAGTTTGTTTCATGAACCTTTTGAATACTATTTATTCCAAATCTTTCGAAAATATCGTTCCATTAAAGATCTTGTTGAAATACCATTTCTTTTTATATCTGTGATCTATTTCTATCCCTGGGTAGGAGTAGTACGTTTAATCTCGTTTTTTTATCTCTCCGTGAATGGTATGCTTGTAACAATAGGGACAAAATTTATTTGATTCCAATCGAATAGGTGTATTGCGTCGATTTTTCCGAGTCGTATATCTAGAAATCCCCGGGAATCTTTTATAAACACTATCTTGGGTACAACTAGTGCACTCCAAAGTAATTGTTACTCTTACATCTCCGCTCTTGGCCATAAACTTATTCTGGATATTGGGTCTACTTTGCTTTTCGATCTGAAAAAGAGGGAAAAAGGGATAGAAGTTGATAGACGGAGATCCCACGATAAAACATTTGAAAGTAAAAAAATGATTGATCAGGAGTTTTTAGTTTTACTTACAAAATTGAATGTGGAAAGAACCTTTGGATCTATATTTCTACTTTGATTCTACCCCCCCCCATTTCATCTCCAAACTTAGATCTATTTTGGGCTGAATCAACTAATTTCTCCAAGAGGTAGGAGAAGTCAATCTAGCACAATCTTTTTCCCTTGACTTTAAGGGGAGGACAACAATTAAAAAAAAGCAAAAGTAAGAGCATCTGGAAAAAAACGATTGATTTCTATCAATAGACCGGCTAAAAAAATGAACGATGAAATAGCTAACACAGGCGCTGTGGAAAGATAGGTCTTTAGATCTTGCATTGTAAATTCTCCTTATCGATCATAATGTGTAAGTGATTCAACCGTATCAATAGTTACGAATCCTAGGAAAAACTCGGAACTGATGAATATATGTATAATGTGATCCAGGCTGTGGTCCTATTTATAGAACAGAAAAAAGATGTTTCATCACCAAATTTTGCTAATTAATCTTCTAGATAATAGACCCTACATGCATGTATAAAGTCTTTTCATTCACGAGACCGAAGAGAAATGAAGGTGGAAAAATGTGGGAAACAGATTTCGAATTCTATAAAATAACATTGTCTAATGATTAGAAGGGATGTAGCGCAGCTTGGTAGCGTATTTGTTTTGGGTACAAAATGTCGCAGGTTCAAATCCTGTCATCCCTACCTTTCCCTTCTTTTCTATGGAAAGAGAAAGGAACGAAAGATCATTTTATATCGATTCGAATGGATCAATCAAATAATTGAATCGTATCAGATGCGAAAGTGTTTGACTCTAAGAGTATAAACGAAAAGATTTTGTTCCTTTCCTTTCTCTCCGGATGTTAAATAAAGCGCTCTTAGTTCAGTTCGGTAGAACGTAGGTCTCCAAAACCTGATGCCGTAGGTTCAAATCCTACAGAGCGTGATTCTGTTCCTATCAAACCCAACCTTCTAAATTATCGAGAATTCATTCCAATTGGAACGAGCAATGGAATCTGACCTCCCAGGAAAAGTAGGAGGTCAATGAAATTGAAGGATATTCCCGGATCAAATATCCAATTGATCACCACGTCGGTATTGTGAATATGCAGTTACGGATAATCCGGCCAAAGTTATAGGAATTAGACCTAACACAATTCCGGATGGCAAAGCCTCAATCATTTCGATTCAACGGAATAAGTAGGGATAATAGCTATCCTGGATAGTACCCTGAATTTGCTATGAATCTCAATGATCAGAAATTGATATAGAGAGAATCAACGAAATTATTGAAATTGATATAGTGAACTGAGAGGGTTTCCCCTTCCTTCATTTCGAATAAGTTGTATCTTGCTCGAGCTAATGAATAGGACTAGGGTGAAAATGATAGAAGCCAACAAGAAACCGAAATAACTAATTATAGTTATAGTAGGCGTGGAAGGACTGAATGAAATATGGTTTATACATATCTTCATGAGACAATTACCTAAATTTTGCTTTTCGTAACCTTGAGATCAGAATACAAAAGATCAATTGTCCCAATTCGTACCAATTAAGGATCCTATATCTACTATAGGATATGTATGAACGAACATGGATGAGAGGAAATCTATGGTAGATATCTCTTCATTATCCTAGAAATCCTCACATTCATCGAGCAACTAATTAATAGCACCCGCGAACTCCTTCACAAATTGTCAAACGTAATCTTCTTACAGGGTGAATGAATTATAAATAAGTACGATTGGATCATCTGGCATTATCTTCGATACCAGTAGCTATCGGTTGGATTGGAAGAAACCTCTTCTACAGACATAGCAAAGTTTTGTGAATTTCACGTTTAGGTATAAGAATATTAATATCCAGTTTGTCCTTTCATTTCTAGATCTTATTGATCCAGATCATTGGACCCTCTAGATGGATTTTTTCAATATTCATTCTTAGAGCCAGTAGAGCCCGCAAGAATTCCACCTATTGCAAGGAATAACTCGTAATTTAACATACCTAAAAGTGACTAGGTTCTATTGCACTATCCACTTGGGTTTATCTAATTAGTAACATCTACTCGTTAATACAAGGTACTATATAATAAGTCCGTGGCATAACTCCACCTGCGCCGGATACTATTGGAAGAGCAACATACATCTGCGTAGCACCAATGATCCCCGTGCAATCTTAATTACTGGAATCATCTACACGGACATAATGTCATGTCGGAATGAAAAAAGGAAGGGGTCAAAGTATCATATTCTGGATTGGTTGGATTGATAGTGATTAATACCCTTTGCAAGCGGCACTCATCCTTTTTTCGGTTCTACAGCCTAGAAGCTAATTCCAATCGAAAATTTCCAGGGTTATGCAATTGTTACAACATCGATTGAGGGAGTTCCTTACACCCGAACCTCGGAATATGCAATATTCTCTTATTTCTGTTGGGATTAAGTCCATCAAACAGAGATGGACTAACTGCTGGCAGGAACAGAATCATTCTATTCCGTTCCTTCTCGATACTCATCAAAATTGTATTGCTGTGTCAGAAGAAAGCTAGCTATACTGGTCCAGTAGACTTCAAAGATACCCTTGGTATAACATTGACAATCGAACAAGGATTGGAGAAGATATCAGTAGTTTTCCATTTCCTGATCTCTATCTTTCATGGGATCAATTCCCCCTTGACTGACTTTAAAATAATATATGGAGCTGAGCATGTCTGGGAATACGGGAGAACGCTCCTTTGCTGACATTATTACTAGTATTAGATACTGGGTTATCCATAGCATTACCATACCTTCTCTATTCATTGCAGGTTGGTTATTTGTCAGCACGGGTTTGGCTTATGATGTGTTCGGGAGCCCCCGGCCGAATGAGTATTTCACAGAAAGTCGACAAGAGGTTCCATTAGTAACTGGCCGTTTCGATTCGTTAGAGCAACTCGATGAATTTACTAGATCTTTTTAGGAGGCACTAATGACTATAGATAGAACTTATCCGATTTTTACAGTTAGATGGTTGGCCATTCACGGGCTAGCTGTCCCTACAGTTTTTTTCTCGGGATCAATCTCGGCAATGCAGTTCATCCAGCGATAAACTCTATATTAAAGGAAGAGGAAGTATGTAGATATGACACAATTGAATCCGAACAACCAAAATGTTGAATTGAATCGTACCAGTCTCTACTGGGGGTTGCTACTAATTTTTGTACTTGCTGTTCTATTCTCTAATTATTTGTTTAATTAGGAACAATGAGAATATTATCACTCCATTCGAAGAGATCCAATACTAATAATTATCTATGCTATGACTGTTTATGTCTCGAGCATGACCACTTAAGAAAATGTGAAAGGGAGTAAGAGAAATGGCCGATACCACTGGAAGGATCCCTCTTTGGTTGATAGGTACTGTAACTGGTATTATCGTGATTGGTCTACTGGGTATCTTTTTCTATGGTTCATATTCCGGATCAGGGTCATCCCTATAGTAGGGGAAATGCACTTACTATGGGAATACTATACATGCGAAAGTGACAAATAAATAAGGCCTTACCCTTCTTTTAAGGGTAAGGTCTTATCGAAATCTCTTTTTTAGATTCTCTTCTATATTAATATTAATTAGAAGAGAAGATTCGCACAAATACAATGACTCTGTTACTTCATTCAATGCCTTTCAGTCAAGTTATGAGCCAATTTATTCTATGATAAAAAAAAAATTTTTGATCGATCCAATTTCAATCTCTGTCGAAGGAACAACGGAGAAACGGAGAATATTTATTACTAAATATTTGTTCATTTCTCTGGTGGGAGATTATTCGAAGTTTTTCTAAAAACCCGAACTATGAGAATCTTAATGTGCGAATAGAATATTTTCTTCTCTTATTTTGGCTTACAAAAGAAAAGAGGAGGAAAAACACCTTTAATTCATTTTCTCTCATTAGGAACGAACCCTATCAAAAGGTGGGTTGTTTTGCTCAATGAGTGATATTACCCCTTACTTTTCTGCTCTTCCTTCTTTAGGAATTTGAAGGTTCCTCAATATAACGTACAAAATAATCGTCAATTTACGAAGGAATTGATGAACAGGACAGGATCGGAAACCCAATGAGTTCCTCTTATCTCGACGAGAAATCGGAGAATTTATTCGACGAATAATAATGGGATAGGATAAAGAATGGGATTAGAGAAGATAGGAATCTTCTCCAAGATTGCTTAGTTATTCTCCTAATCTCTCCTTCCTGCGATCTATCTCTATTTTCCGGATTTTTTCTTTTGAAAATGGGCAAGGAAAGGAGGGAATGGCATGTATATAGTACACGATCTAGAAAGCATATGGGGATCGTTCGACAAGTTGATCTGTTCCAGTGCTTATTGAGTCACTCCCTATTTGAAATGTAGATATGTCTACATGAACATTTTCCCAAGAATATATAAGGGAGAAGGAGGAGAAAAGGTTCTCCATCTCCGAAGGGGTATTCATTTTTGATTCAATCAGTCAACTTCATGTTCGGAAATCTATGGACCTGAAGATTCATCTCGGCCAATTGAACTTTCTCAAATTGTTTCTTCTTAAGGACCAAAAATATCTGTGCCAGAATGACAGATGCTAAGAATAATAAAAGACCTTTAACACGTAATGGATCTTGAAGTACTATCTCTGCATCTCCTTGACCAAATCCACCCACATTAGGGTTATTCGTTAATGGCTGATCGACCTTGATCAATTCGCCCTCTGAAATAAGAAGTTCCGGTCCCGGAGGTACAATGTCAACCACTTGCCCACCGTCTGATGTATTATCGATAGTTATCTCATATCCACCCTTTTCTTTACGTAAAATTTTGCTCACTCTTCCTGTTGCTGAAGCGCTATAGACCGTATTGTTGCTCTTACTCCCGTCGGGATAAATTTGTCCTCTCCCTCTATTACCACCCAAATATATAGGATATTTCAGGAAGTGAGCTTCTTTATCAGTAGCAGGATCTGGGGAAAGGATGGGGAACACAAGTTCACTATATTTTTGCCCAGGAACAGGACCTATTACAATAATGTTTTTTTGATTGGGACGATAGTTCTGAAAATAAAGATTACCCATCTTTTGTCTAATCTCAGGAGAAATACGATCCGGAGGGGCTAATTCAAAGCCCTCGGGTAAAATTAGAACAGCTCCTACATTTAAAGCCCCTTTCTTACCATTAGCAAGAACTTGTTTCATTTGCGTATCATAGGGGATCTTAACAACTGCTTCAAATACGGTATTGGGAAGCACGGACTGTGGAACCTCAATATCCACAGGTTTTTTGGCCAAGTGACAATTGGCACATACAATACGTCCAGTTGCTTCTCGGGGATTTTCATAACCCTGCTGTGCAAAAATGGGATATGCATTCGAAATGGATGTCCGAGTTATGATATGTATCATCACCAGGACGGAAATTAACCGAGTCATCTTTTTTTTTAAGTCATAAGTATTTCTATTTTGCATGGTTCAATTATTGGTTCCAAATCATTTTTCGGGTGAGAGTAGGTAGCTATCATAGTTACCTGTCAAAAATTCTGCTACTATATTGATTGAACCAAACCTAAAAGTAAGAAATCGGAAGTCTCGCACCAGGAGAAGAATGAGGGGGAGGAATAGCTAATTCCTGAACAAAGAAAACACTTTATTATTCTGTTTCAATTCTTTCGGTCGGAGAAAACAACCTATTCTTTATTCATTCATCGAATGATAAATTACTACAAGTGAAGGAGATATACGATTGAAACGACGGAAGATCCAATATTTGAGAATCGTATCTAAGATGACTGGAAAAGTTGAAACAAGACCAGATATGATTCGTTCGTTATGGGCAAAGCCAAAATTTTCGGAGATCGAATCGATCATCAGTTCCCAACCATGGGGTGAATGAAACCCAATACATAGATCGGTTGCTAAAAGAATGAGAAAAGCTTTCATTGTATCGCTCAGACTATAGAAGAATTCTTGGATCCAAGAATTGAGAATGCCAAGTTTATTCTTACCCAGAATGAGATAAGCACTTATAAAAGCAAAACCTATTAGATTTGTTAATAAATGTGAGATTATCTTAATACAATCTTCATTGTACATTTCGACCAATTGGATTGTTTCTTTGTGAATCTCTATACGAAGATCTTTTGAATCTGTTCCCGAAGAATCTTCCACCATTCTTTCTAACAGGAATAGTTCTTCTATTTTCTCAAATCTTCCCAGAACATTTTCTTCCTGGAGATAATCAAAAATTTTCTGAGATTGACCCGTATTCCACCAATTTGTAACCCAAGGTTCCAAACCTTTCCGTAATGAAATAGGAATGACCCAAGGCAGTACCACTAAACATGCAAGATATCGTAGGGAAGCTGATGCTTTATATTCGGCCACTTCCAATTCGTGAATCGCTAACGAACCTGATTCACTCGTCAGTTCTGTCCGAAATCTAGACAAAGTACGAGTGATAGAATGAGGTATGGGATCCATAAATTTATCTATTGTGTAATTGTTTGACCCTGAGAAAAAAGATCCTCAGAGAAAAAAGAAAAAGGTTCGCTCCAAATGAGTGAGACGGAGCATAAGAAGATCATTCCCCGATATCCGATCCAGATCGTTTCTATCTGGATCAATTATCTATTCATTTTTTCTATCTTATTCTTTTTTAGAAGAATAACTTGAAGTAACATAAGTCGTTTTATTCATTGTAAAGATCCTTTGAATCCTGATCACTCGATCGATCCTTTACGAATCTTTCCCCAGTTATCTCCAAAGATGACAAACAAAATGAGAGAACGACGAAATCATATAAGAATAAATTGGATCGTGATGAAGAACGGGGATGAGAGGAAAAAACGTTCTAGTTTTAGGGAAACCGGACCACTATATCTAGTCATTGTTCTTTCTGATCCATCATATCCATCTACTGGCTCACTCGCCCTCTCTAGGATAGGAAATGATATGGCGTGTTCAGGAACTACCAAAATAATCTTGGTCTGATTCATTCCATAAACATAAATATCATTTAGTAGGAATTAACTAAATGATATTTTTCCCGGACAAATACCAACCAGTTCTATTGTAACTTATAGCTCTTTCTATATTACCTATTCCTATACTATTTTTTAAAAAATAGTATATTGTTCATAAAGATCCTATATCGTTCCATTTCCATACAATTAGATTTCAATATTTATTGAAATTGATATGTATGGAAATCTAAAAATTTCCTGATTGGATATTGATTCATGTTCCTTGATTCGATCCATATAAAAATGTCGATCAATTTGAATTTATGTTGAGTATAAAGAACCCCTTGGTTCATTTCAAAACCCTTCAATGGATACACGCAAGAAACGGGCTGATTCAGCAGCTTTCTGTTCGATCTCCCTTAGGTTCAAATTATCACCAGTACGAGCTAAAGGAATGTCTTGTCGGCCCTTTATTTCCATATAAAGAACACGACGAGGGGAAATACCTTCTTGAATTTCCATTTTAATCATCTGAATATCCTTCATAAGAAATCGTGGGAAAATACGACGATTTTTTCCGGGAAATCCCCAACGAAAAAGACATACAATTCCTTTTCTTTTATCAAACTTATTATAGCCACTACCCACATCGAACAAAATTGTGCACCACAGATAAGAGCTAATGAACAGACCTGCAATACCATAAAAACACATTACAATTCCTTGTGGAACAAAGAGTATTTCCTGAGATGACAATAGGGGTATCAGGTTCTCACCAAAATAACTCGAAATCCCGACTAGGAAAAATCCTAGTGAACCCAGAAAGAGGATACAAGCCCAAAAGAAATTACTTCTTTTTCGAGACCCTGTTATAGGTTCTATCCAGAGCCATTTGGATCGATTATTCATAAAAAATCGTATTCAATTCCATCCTATTGAAGTTGAGGGAATAGCCCACTTTTTCATCCTTTGGTTCCCAAACTCTTATGAACTAGCTATCTATATACATAGCTAACATTTCAGTCAAGTCAGTCAAGTTTGTCTTCTTGTCCATTCTTACTATCAATTTCAAATAGGTCCTTCCCAAAATTATCAATTTGTTAAACAAAACTGAATCAGTGGAGTTAAAATATCTCTAGGAATCGATATGTATACCATATGCAAAAAATATAACCAACCATATGAAAATATTGACCAATACCTATTTATTGACACATGTGTATATCCGATATGTATATGGATATGAATATGAATAGATATATAAATTCGCTATATCTAGAATATAATGGTAAGATCTATCCATATTCAAGTATGAATGAGTCTAAATAAATATATATATTTATTTATTTCTATTTAGACCTATCTTGTATCTATAAGAGTTCTATCTTATATCATCTGAAATAGATATAGAGATTTATATCTGTTCTGCAATTGAACAGATCCAAACCTATTTATTAAATCTAATTTGATCAGATTCAAAAAATATCGTCATTCTGAATATACAGATGGAAAAGAACCATTGTAATTGCCGGAAGTAATAAGCCGACTAAAGGCACGAAAAAAGAAGGTAGGTTAGGAATTATCATAGAACGAGTACCTTACTTACTCAATGAAATGTTTATCCATATGATTATAAGATAAAATAAGTGATGGGACCAAATGAGCGGTCCCATTTGTCCTTCTTCATAGAATACATGTACGCAAATGTTCGTTGTTCCTTTCCCCGTCTCTTCCAAAAATACTGAAAAAGCATTTGAAGTTGGATTCAAAATTGTTTTTGAATAAGATCCCGACGAGTTCAACAATGAGGATCTGTATCTATATATACAATACATATATATCTATATATATATTGTATATATAGATCCTTTACAACACTTATTAATATTATATAAGTTAAATAGTGGAAGAACATGAATCCTGACAAAAATTTATCTGATTTCGAAAAGCGGAAAATTGGCTATATTTATTGTTAGTATAGGATCGAGGATCATAAATTGTTGGTAAGAAGGGGGTAAAAAGCGATTCTCTTAGAGAAATCCTTATTTTGCCGCAATAAGAAACTGTATCACTGTCACTTCCGTTACAAGGAACTCGATTTGATCATTTTTCCTTATAAGGAACTAAACGTTCATTTTTTTTTCTTTACGAGGAAGACTGTAAAGCTGAAATAGTTCACTTAGAACACCTTTTAAGAGATTACGTGGAACGATCAGATCAAATAAACCATGGCCAAATAAATGCTCAGTCACCTGAAAATCTTCAATCACTTTCTGACCTAATGTCTGTTCGATTACTCTTTTACCTGCAAATGCAATGTACGCTTTAGGTTCGGCAATAATGATATCTCCCAACATGCCAAAACTAGCAGTAACTCCACCGGTTGTCGGAGACGTCAGAATCGATACATATAACAACCTTTTATCCTTCTGATGAATATATAACGCAGAAGCTATTTTAGCCATTTGCATTGAACTAAAACTTCCTTCTTGCATGCGTGCTCCTCCGGAAGCACACACCATAATGACTGGAAGAGATTCCTCGGTAGCGCGCTCGATCAGACGGGTTATTTTCTCGCCTACTACAGAGCCCATACTACCTCCCATGAACTTAAAATCCATAACTCCGAGTGCGATAGGAAGACCATTTAATTGACCTATGCCTGTTTGAATAGCATCAGTTAAACCTGTCTCTATTTGACAGAAAGTGATATGATCCTTATAAGATTCATCCTCAGAATGAAGAGGATCAGAATGAGCAGGTTCATTCTCAGAATGAAATTGAAGAACATCTAGAGTGTACATGTCTTCATCCATAGGATGCCGAGTGCCGCGATCAATTGGAAGTTCTATTCTATCTGAACTATTCATTTGCAGATAATATCCACATTCTTCACAAACACTTTTATTCTCTCTCAAGAATCTGATATAGAGCAAGCTCTCGCAATTATCGCATTGAACCCATAATCTATTAATTTTAACGTAATCAATACTTAGATTCTTGTTCCTCTCCATCTCATTGACGTCCTTACTATCCCTTTCGACCGAATTTTTTAGTAATCCAGTTATTTTACGCCTGTCTTCGAACCACTCCCTTATAGACATAGAGTTTTCCATATAAAGGTGAAGATTGTTACTTTTCCTATCTTATTTTGTATGAAGAGAAGTCGTATAAATAAAATGATTCAATTTCTCAATGAATAGTGAAATGAATCATGGATAAATCATCTCCATTCATTATTGATTAGGAATCCGAAGTATCAATCCGGGATTATGATAGAACCCTTTATTCTTTTATAAAGAAAGATTATCTCCTATGCCGCGATGAAAAGGAATTTTCATCCCAAATACAAAATCTTTTGGGCTAGAAGGGATTTGAACCCTTGACTTCATGGTCCGGAACCATGAGCTCTGATCCACTGAGCTACCAACCCTATCGAATGATCTATAAGATAAATGTAAAGGATGAATAGGATTCGTTATCGAATCCTTGACCCCAAAAAATTTTCATCGACTCACTCTGTTTTAGATATTTTACCTCGGAAATATATCAATATCTATATATCAATATATATATATCAATATATATAGATATTGATATATAGATATTGATATATAGAAATCCCAGATATTGATATCTGAAATCCCATATCTCCGTTCACGATTTGGCCTAATCTTTGTGGTAGCGGTAAAAGATTGGGCCGAGTCCGATTGGTAGAACGAAAGTCACTGGATCACAAGGTATCTATTGCCTCAAATTGTATCTATTGCCTCAAATTCAAATTTGATCTCCTTCCATATTTCACAAGCAGCAGCTAGTTCAGGACTCCATTTACTAGCTTCACGGATCACTTCATTACCTTCACGAGCAAGATCACGTCCTTCATTACGAGCTTGTACACAAGCTTCTAGAGCAACTCGATTAGCTACTGCACCAGGTGCATTTCCCCAAGGGTGTCCCAAAGTTCCCCCACCAAACTGTAGTACGGAATCATCCCCAAAGATCTCGGTCAGAGCAGGCATATGCCAAACGTGAATACCTCCTGAAGCTACGGGCAGGACACCTGGCATAGATACCCAATCTTGAGTGAAGTAAATACCACGACTTCGATCTTTTTCGATAAAATCATCACGCAGTAGATCAACAAACCCTAAAGTGACGTCTCGTTCCCCTTCAAGTTTACCTACTACAGTACCGCCGTGAATATGATCTCCACCGGACATACGCAATGCTTTAGCCAGTACACGGAAGTGCATACCATGATTTTTTTGTCTGTCAATCACTGCATGCATCGCGCGGTGAATGTGAAGAAGTAGGCCGTTGTCTCGGCAATAATGAGCCAAAGAAGTATTTGCGGTAAAACCTCCCGTCAGATAGTCATGCATAACGATAGGAACTCCCAATTCTCTTGCAAATATTGCCCTTTTCATCATTTCTTCACATGTACCTGCAGTAGCATTCAAGTAATGTCCCTTAATTTCACCCGTCTCAGCCTGAGCTTTATAAATTGCTTCCGCACAAAAGACAAAACGATCTCTCCAGCGCATGAATGGTTGGGAATTTACGTTCTCATCATCCTTGGTAAAATCGAGTCCACCACGGAGACATTCGTAAACTGCTCTACCATAGTTCTTGGCCGATAGACCCAATTTTGGTTTGATAGTACATCCCAATAAAGGACGGCCATATTTGTTCAATTTATCTCTTTCAACTTGGATACCATGAGGTGGACCTTGAAATGTTTTGGAATAAGCAGGGGGAATCCGCAAATCTTCCAAACGTAGAGCCCGTAGGGCCTTGAATCCAAATACATTACCTACAATGGAAGTGAACAAGTTAGTAACAGAACCTTCTTCGAAAAGGTCTAAGGGGTAAGCTACATAGGCAATAAATTGAGTTTCCTCTCCAGGAACGGGCTCGATGTCATAGCATCGCCCCTTGTAACGATCAAGACTAGTAAGTCCATCGGTCCAAACAGTGGTCCATGTACCGGTGGAAGATTCAGCAGCTACTGCTGCTCCCGCTTCCTCGGGCGGCACCCCTGGTTGAGGAGTTACTCGGAATGCTGCCAAAATATCCGTATCTTTGGTCTGATATTCAGGAGTATAATAAGTTAATCTGTAATCTTTAACACCAGCTTTAAATCCGACACTAGCTTTAGTCTCTGTTTTTGGTGACATAAGTCCCTCCTTTATTAATAATTATCTCTCGCAAGGACGAGGTCTGCTCGACATGGATCGAACATAAACAATCAATTTTGACAGAACTATCCTACAAAAAAATCGTCCGTTATTGGACAATAAGATCTGCTAGGTACACTCTCATTGTATAATGTTCTTTATGTATGATGCAACCCAATCTTTGCTCTTTAAGTTCTTCCTCCATGGATTGACCCGAGCACCTTTCAGCGGTTAAACTAGTTCATGAATGAACTTAAGGAACCGAATCGACCTTTGACCATAATGGTGCGAATTGTCTATATGAAAATAAATATAGAATAGGGAACAGATGTGCGTACGAAGAGAAGAGATAACGACCGACCAATGAGAGAAAGGTCATGAATAGGGTTCAAGTTTCACATTTCACAGATGATCTGGACATAATTTTTAAGTATTTTCGGTTTTAGTTATGGAGAATTTGGTTCTAGTTATAAATAAAAAAATCGAAGACTTCCTCATTATCCTTATCCATCTACTTACTTCATATTCCAAATATGAATGGATTCGAACTTTTCCATAAAGTAGGATATTACTAAGGTGGTAACTCCCATTCATTATTTACTGATCTGATCGACCCGATACGGAACATTTTTGTTATTGATGATATTGGCAAAATCATATTTATATATATATATATAAAATCTTCATGGAATTTCTTTCCTTTTTTGTATGAGAACCAATCCTCTTGTTCTTGGGGTTTCCGCACTTGTAGAAAAAAATGTGGGACGTATAGCTCAAATCATTGGCCCAGTACTGGATGTCTCTTTTCCTCCAGGTAATATGCCTAATATTTACAATTCATTAATAGTTAAGGGTCAAGGTACAGCCGGTCAGGAAATTCAGGTTACTTGTGAGGTACAGCAATTATTAGGAAATCATAAGGTTAGAGCTGTAGCTATGAGTGCTACAGATGGTTTGACGAGAGGAATGAGAGTGATTGACACGGGAGCTCCTCTTAGTGTTCCAGTTGGTGGAGCTACTCTCGGACGAATTTTCAATGTTCTTGGCGAACCTGTTGATAATTTGGGTCCCGTAGATGCTCGCATAACATCTCCTATTCATAGATCTGCTCCCGCCTTTACAGAGTTGGATACAAAATTATCTATCTTCGAAACAGGCATTAAAGTAGTAGATCTTTTGGCTCCTTACCGCCGTGGGGGAAAAATCGGTTTATTTGGAGGAGCTGGAGTGGGTAAAACAGTACTCATTATGGAGTTGATTAACAACATTGCTAAGGCTCATGGAGGGGTATCTGTATTTGGAGGAGTAGGAGAACGTACTCGTGAAGGGAATGATCTTTACATGGAAATGAAAGAATCGGGAGTAATTGATGAACAAAACATCTCAGAATCAAAAGTGGCTCTGGTCTATGGTCAGATGAATGAACCACCAGGAGCTCGTATGAGAGTCGGTTTAACTGCTCTAACCATGGCCGAATATTTCCGAGATGTCAATGAGCAAGACGTACTATCATTTATTGATAACATCTTCCGCTTTGTCCAAGCGGGATCAGAGGTATCCGCCCTATTAGGTAGAATGCCTTCCGCCGTGGGTTATCAGCCAACTCTTGCCACGGAAATGGGAACTTTGCAAGAGAGAATTACTTCCACAAAAAGGGGATCGATAACCTCGATTCAAGCAGTTTATGTACCTGCTGACGACTTGACTGACCCCGCTCCTGCTACGACATTTGCACATTTAGATGCTACTACCGTACCATCGAGAGGATTAGCTGCCAAGGGTATCTATCCAGCAGTGGATCCTTTAGATTCAACATCGACTATGCTCCAACCTTGGATCGTAGGCGAAGAACATTACGAAACTGCACAAGGGGTTAAGCAAACTTTACAACGTTATAAGGAACTTCAAGACATTATAGCTATTCCTGGACTGGATGAATTATCGGAGGAAGATCGTTTAATCGTAGCAAGAGCAAGAAAAATTGAACGTTTCTTATCACAACCCTTTTTCGTAGCAGAGGTATTCACAGGTTTCCCGGGCAAATATGTTGGTCTCATGGAAACCATTAGAGGGTTTCAAATGATCCTTTCCGGAGAATTAGATGGTATTACCGAACAGTCTTTTTATTTAGTGGGTAACATTGATGAAGCTACCGCGAAGGCTATGAACTCCAAAACGGAAAGTTAATTCTGAAAATGACCTTAAATCTTCGTGTACTGTCTCCTAATCGAGTCATTTGGGATTCAGAAGTTCAAGAAATAATCTTATCTACTAATAGTGGTCAAATTGGCGTATTACCCAATCATGCTTCACTTGTGGCAGCTGTAGATATAGGAGTTATGAAAATACGTCTTAATGGGCAGTGGTCCACTATGGCTTTGATGGGCGGTTTCGCCAAGATAGACAATGATAGAATCACCGTATTGGTAAATAATGCAGAGAGAGATGTTGACATCGATCTCAAAGAAGCCCAGGAAACCTTTAAAGTAGCTAAAGCTGACTTAGCTCGAGCCGAAGGCAAAAGACAAGCAATTGAGGCTGATGTAGCTCCGAAAAGAGCTAGAACACGATTAGAAGCTATCAGTGCTAGCCCCCCCGTCTCTAATTAAACATTTCCTATAAATATCTGAAAATGGATTCAATGTTCCGCCTCGATCCAAACAAGTGGAGTCAAACTTATTAGATGCCATCGACTCTTCAATGGTATCTAATAAGTTTACCTACTATTGGATTTGAACCAACGACTCTCGCCGTATGAAAGCGATACTCTAACCACTGAGTTAAGTGGGTCATTTATTCTCATAGGTAGAGTTGGACTTATAAACGATTCTATATGGAATTCAATGTATAGACAATGTGTCCCTGGCACAGATCGAACTTATTGGAACGTATTGGATCATAGTATCGGATCATGAAATATCTACCTTGACAGAAAGTGATCCATCTGGTTAGTATAGTAGTGTATCACCAAGACTGGGAAGGGCTATAGCTCAGCAAGGTAGAGCACCTCGTTTACACGTGCGCCAATGGTTTTCGGGAGAGTTTATCGATTCGTCCGATCCACGAAATAGATTCTATGTGAAAAAGTCTTACTCTATCAATGTGTTTCTCTGGGGAACAATAGCATGACAAAGATGAAGTTCGATCCGATTCGAATTACGAATCTAATTGATATGGTCAATCCCAGCTCCGTTCAATGCCAGGCATAATGAGTATAATACGGGGACCTCAAAATAGATTCTTTTCGCTCTATGACACTTTTAGGTGTATGAAGTGTCATATTTTCTTTTTGGAGCGCTAGAGGAGACTCTATTTGAGTCAATCTATGCCCGAGCAAGGCAGACCTACGTCAAGGAAACCTTTTGAATCACTTTGGGATTGCTTCCGAAGGGTAAGAATTTGGAGCACACGGAGCCATATTAGTATCTTTCCTGGAAAGAGGAGAATGGCAGACTAACCGATCTTTCCATCAGTTAATGAAAGAGCCCAATGCGATAAAATGCATGTTGGGTTCTTGGAACAGTTCAAATTATTTTGATAATAAGAACTTTGATCTGTTCTACCGAGAAGGTCTACGGTTCGAGCCCGTATAGCCCTATACATTCCACTAAGTTACACTACTCTTATATATATCCCCTCATAGTCCCTATGACTTGGACTTTCAAAGTCTTTCGGATCATATCAATATCTTGTCCTTATCAAGATCGATGGATGGGAACGTTGGAACAGGGCAGGCAGATTAGTATTTCTCATCGATCGATCTTGATCCGATACCAGATGATCGGGCCTATAAACCCTTTTTTTTTTCGAGGCACTTATAGATAGATTCTATCTCAAAATATAGATAGAGGATTGAGGTATTCAATACTATCTATATTACTTGGATTTGTACAATGTTTGTTATAATTCCCATTATAACATCGTCTAGTTCGGAACCGCTTTTGTTCATTTTTATCGCTAGTTCTTCGAAAAACTCGGGAGTTCTCTGGAATAGAATATGTTGAAAGCAATCCATATTCCAGTCAAAGTATCGATCGGACATGTGGCTTTTAGCTCCATCCAAATGCAACGCATTCCGTTGGGGTTGAACGAACGAAGTACTCTTCCGTTCAATCGAAAATCCCGGGTCTATCCCTTTGCTAAAGATCGGGGCGAAGATCTTGATCCACTAGGATTCTACACAATATGTTATGTGTGGTAAATCGAACCTATTCTTGAACCATAGAAGTGGGAAGTACTACGGCCGAATACCTGGAAAGGTCAATTCTCTGGAGTTGATCCATCCTAGCTAAAGGCGAACCTTTGGTTTGTTTTCTTTCTCCACCTAAGATCATCACATGGTTTTTTAGACCCAATATTTTCATATTGGGACAAACACTCTTTCCTCTAGTTCCGTTCTGTTAACATACCAAAAAAATGCAATCTATCGGCTACGCATATTGGATCTATATCTGGACCAACGTTTGCATAAATCTACCCCACTATTCTATAGAATACACATATTTCATGGAATGCGTTCTGAAACAATAGAAAAAAGAAATCTGTTGGAATGAAACTATTACCCCTTGCTCATCAATTTTGTGGACTGCGACCCAAAAGAAGCCCTGTTCTGCCCCGTTACAAATAGTCGGCTAGACAATAGATCTGTCCGAAATGATATTATATCGGAATGAGCCCAGGCTCATAACGAACTTAAACGTGAAAGATTTGATACGTTCCACGGATCGATTGGCGTCTACCAATCCTGTTCCGATTGACCTGTATCAACCATTAAAACGAATGAACTGAAAGACAACGGATTTATTTTTATTTGATTAATCGAACGGAACCGATTTCATATTTGTCATATGTTGAATGCATAGTACTGCTTTCATTTCTGAAGAAACTGAATCCTTCGAACCTTACTCATTCCCCGGTCACTCGATCCTTTTATCCCTTTTGCTACTATAAGATCTGGACAGTACGAATGTAAAAGATCTACTCCTCAACCCGTTCCAGTAAAAACATAAAGAAACGCATGTTCTAATTCTTTGATACTTCCTTCGTTCCAACCAAATCTTTGACGACAGAGATTCCCCTTTTCTCATTCGTCTTCTTTCAATACTGTAAAATGTTCACTATCTCCATTGATAGATGAGCCTCTAAATTTGTATATTTGTCCCATCACCTGCATAATAATATAAAAAAGAATTTGATTGGTCTTCTAACCGTGCATGTAAGATGGCAAAATTTTCCAGATTGGATGCAAAGCCCTATCTTTTCTAATACGAGAAGGATACGAGTTCCAAGGGTCTAGATTTCATTGAATCTGAATATGTAACAAGCGGATAGGGTCGAACTTGTCGACGCAGCCGCAGCCTCGATCATTTGAAACAACGACCCTCCGATTAAATACCCCGCCCAGAGTTGTTCGGGCGGACAAGATCTGAGTATCAAGATAAAACATAAAAGAAATCCCAAGATAGATCTCTTTCAATTTACACCGAACCATGTTCATGTTGATGGCCCGTTCGTTTCGTTACAACTCGAATAACGTGGGATCTACCGAACCAATCTGCAAAACTGCGTTTTTTTAGAACAAAATGATAATCTGACTGGAAGGGAAGAAACGATCGTTATCGTCCATGGGTGAATGGACAAAGGATCGATACGAAAAAAGAAAGATTATTCACGTTCGAAAGAACTGAGGAAGGATGGGATCGGGATATGTCTCCGGAATAAATATAAAATACTTAAGAAAAACTTGTTCGATAGTTGGTTGGGAATTAGTCATCGATCTTGCTTTGATCCCCTGTAAGAGGTCGCCGACCCACATACAGACGTTAGCCTCGTCATTTCTTCCAAGAAGAAATGACTGTAGATAGAGACAATTGGTTTGTTTTTCCGGGGCGGACGTAGCCAAGTGGACCAAGGCAGTGGATTGTGAATCCACCACGCGCGGGTTCAATTCCCGTCGTTCGCCCATAAAATAAAAGAAAAAACGGACTGGATTCAGTGTCATTTTCTTATTTCGGTGTCCATATTTCTATCTATTACATAGATAGAGAAATGGACACCCGGGCCTTCTTTCTTCGTAGGAAAAATGAGCCCTTTATCGGACTTGAACCGATGACTTACGCCTTACCATGGC diff -r d788d1abe238 -r 358f58401cd6 tool_dependencies.xml --- a/tool_dependencies.xml Thu Jan 22 13:15:51 2015 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,15 +0,0 @@ - - - - - - - - - - - - - $REPOSITORY_INSTALL_DIR - -