AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_pyro.txt -z/home/amcguire/genomes/pyro.fna -icrp_pyro_opreg_100.orf -g0.419 -x5 Parameter values: expect = 5 ncols = 10 npass = 1000 maxnpass = 100 nruns = 1000 maxnruns = 100 repeat = 15 maxreps = 3 nread = 500 ncycles = 1 fragment = 1 psfact = 0.1 gcback = 0.419 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 PH0024 36 284aa long hypothetical sugar transport membrane protein #2 PH0025 169 426aa long hypothetical protein #3 PH0124 300 437aa long hypothetical protein #4 PH0194 60 375aa long hypothetical multiple sugar-binding transport ATP-binding protein #5 PH0206 132 544aa long hypothetical protein #6 PH0365 54 327aa long hypothetical galactose-1-phosphate uridyltransferase #7 PH0369 92 350aa long hypothetical galactokinase #8 PH0378 56 318aa long hypothetical UDP-glucose 4-epimerase #9 PH0857 300 394aa long hypothetical threonine synthase #10 PH0864 300 208aa long hypothetical transcription initiation factor IIB #11 PH1332 300 155aa long hypothetical protein #12 PH1337 300 197aa long hypothetical protein #13 PH1338 26 202aa long hypothetical protein #14 PH1340 58 120aa long hypothetical protein #15 PH1363 211 493aa long hypothetical protein #16 PH1463 40 438aa long hypothetical L-asparaginase #17 PH1497 109 197aa long hypothetical protein #18 PH1598 94 503aa long hypothetical pyrimidine-nucleoside phosphorylase #19 PH1742 55 306aa long hypothetical UDP-glucose 4-epimerase #20 PH1952 30 263aa long hypothetical protein #21 PH1953 110 705aa long hypothetical phosphoribosylformylglycinamidine synthase II Motif number 1 TTTCTCTATTTCTTTTTTATCTG 1 1 1 TTCTCTTTCT 0.779048 -36 CCTAAATCTTTATTTATTTTTCTGTTTTTGCCT 2 120 0 TTTTATTTCT 0.955966 -50 ATATGAGATATTTTTCATTTTTTGGACATGCAT 3 112 1 TTTTCTTTTT 0.820871 -189 CACTAATCGCTATTTAATTTTCTTTTAATAGCA 3 267 0 TTTTATTTCT 0.955966 -34 CCAGGAAATGTTTTTAGTCTTCTCATGCAATTT 4 23 1 TTTTACTTCT 0.932487 -38 GTCGAAAATTTTATTAAGTTTTTGACTATTATA 7 19 0 TATTATTTTT 0.656259 -74 CAACTCAGCGTATCTATCCTTTTTATAGTGAGG 9 16 1 TTCTACTTTT 0.803806 -285 AAGACGTCTTTCATGACCTTTCTCCAAGACAAG 9 220 0 TATGATTTCT 0.45219 -81 GAAGTTTAAATTTCAAATTTTTTAGAGAAAGGT 10 77 1 TTCAATTTTT 0.615601 -224 ATACGAGAGTTATTGAGCTTTCTAATAGTTTTT 11 66 1 TTTGATTTCT 0.853548 -235 AATCTCTCCATCTTTAATTTTCTTAAGGACAGT 11 220 1 TTTTATTTCT 0.955966 -81 ATCACGATATTCTCTATGCTTTTACTCTCGTAA 12 162 0 TTCTACTTTT 0.803806 -139 CTTCCGGCCTTCTTTAACCTTTTTTTGCTAACC 15 127 1 TTTTACTTTT 0.895572 -85 ATGTTGAATTTGTTTCAATTTTTGGAGGG 15 193 1 TTTTCTTTTT 0.820871 -19 ATATCCCCTCTCTTAACATTTTTCTGGGGGTAT 16 16 1 TTTAATTTTT 0.770233 -25 ACCATAAGTCTTTTAAATCTTCTCAATTAACCA 17 48 0 TTTAACTTCT 0.774513 -62 ATGATCGATATTTTTAGGTTTCTCTTCGCATTA 18 48 1 TTTTATTTCT 0.955966 -47 AAATTTAAAATTTTTACATTTTTCTGGCAAATA 21 75 1 TTTTATTTTT 0.930939 -36 * **** ***** Masking position 10 Map Score: 19.0301 Number of sites scoring better than the average of aligned sites = 219 Number in coding regions = 172 Number in noncoding regions = 47 Number of orfs with sites within 600 bp upstream = 54 Fraction of orfs with sites within 600 bp upstream = 0.00867331 Motif number 2 AGATCCCTTATGCCCTAAATCTTTATTTATTT 2 134 0 TGCCCTATCT 0.907072 -36 GATCATTGCATCCCCTGCTTCTCCTGGAAAAT 3 57 1 TCCCCTCTCT 0.940507 -244 TTCCAGGAAATGTTTTTAGTCTTCTCATGCAA 4 21 1 TGTTTTATCT 0.462986 -40 GGATATCCCTTAACCCACTAGACCTTA 8 40 0 TCCCTTACCA 0.867856 -17 CTTCATAACATCTCCTGAATAAGGAGGAACGA 9 99 0 TCTCCTATAA 0.167893 -202 CGTAATTAAATCCTTTGATACTAGGGTTAGAA 10 235 1 TCCTTTAACT 0.579829 -66 GAGAAGAAAATGTTCTAACCCTAGTATCAAAG 10 247 0 TGTTCTACCT 0.7512 -54 TAGAACATTTTCTTCTCCCCCTAAGTTTAGGA 10 262 1 TCTTCTCCCT 0.83022 -39 ATCCGAAGTTCCCTTACTCCTAAACTTAGGG 10 280 0 TCCCTTCCCT 0.935048 -21 CTATCTATAATCCTTCTAACCTTTGTTTCCCA 11 14 1 TCCTTCACCT 0.650003 -287 AGAAGTTCAATCTCCTTCTCGTCGAGTGGAGA 11 107 1 TCTCCTCCGT 0.398982 -194 TTAAAAATTCTCCTCTCAGCCTCATGTATTCA 11 144 1 TCCTCTACCT 0.971708 -157 CCAGGATCCTTCCCTTTACCCTAATCTCTCCA 11 198 1 TCCCTTACCT 0.971708 -103 GCATCGAATATCTCCTTAGCCTTTAAAACCTC 12 25 0 TCTCCTACCT 0.958121 -276 ATATCTGCTTTCCCCTAATCCTTTGGGATAGC 12 66 0 TCCCCTACCT 0.98537 -235 CGGGGTAGAATCCCCTGAATATCTGCTTTCCC 12 84 0 TCCCCTATAT 0.756477 -217 ATATTCTCTATGCTTTTACTCTCGTAAATTCC 12 157 0 TGCTTTATCT 0.717367 -144 GGGATATATATCCTCAAAATCTGGTAAACCTT 12 269 0 TCCTCAATCT 0.579127 -32 CCATCCCTCCCTTTAGTCATCGTTCATCT 17 8 1 TCCCTTATCA 0.786216 -102 TCACCATAAGTCTTTTAAATCTTCTCAATTAA 17 51 0 TCTTTTATCT 0.769123 -59 ****** * *** Masking position 1 Map Score: 15.3722 Number of sites scoring better than the average of aligned sites = 1335 Number in coding regions = 1249 Number in noncoding regions = 86 Number of orfs with sites within 600 bp upstream = 94 Fraction of orfs with sites within 600 bp upstream = 0.015098 Motif number 3 ATTGCATCCCCTGCTTCTCCTGGAAAATTAT 3 61 1 CTGCTTTCCT 0.698283 -240 GGATATCCCTTAACCCACTAGACCTTA 8 40 0 CCCTTACCCA 0.628655 -17 TGGAAACTCATCGTTCCTCCTTATTCAGGAG 9 89 1 TCGTTCTCCT 0.615231 -212 TCCTAAATCACCCTTCTTCCTACTTCATTCT 9 180 0 CCCTTCTCCT 0.968714 -121 AAGACAAGTACCACTAGTCCTAAATCACCCT 9 197 0 CCACTATCCT 0.83725 -104 AGAACATTTTCTTCTCCCCCTAAGTTTAGGA 10 263 1 CTTCTCCCCT 0.832095 -38 ATCCGAAGTTCCCTTACTCCTAAACTTAGGG 10 280 0 CCCTTATCCT 0.942128 -21 TAAAAATTCTCCTCTCAGCCTCATGTATTCA 11 145 1 CCTCTCGCCT 0.857721 -156 CAGGATCCTTCCCTTTACCCTAATCTCTCCA 11 199 1 CCCTTTCCCT 0.951889 -102 CATCGAATATCTCCTTAGCCTTTAAAACCTC 12 25 0 CTCCTTGCCT 0.806798 -276 TATCTGCTTTCCCCTAATCCTTTGGGATAGC 12 66 0 CCCCTATCCT 0.970924 -235 AACTTCGACTTCCCTTTCCCTGGGATCGGGG 12 111 0 TCCCTTCCCT 0.897902 -190 TTTTCATTTCTCCCTCTTCCTTTGCTTTCAT 12 223 0 TCCCTCTCCT 0.932264 -78 TTCAGCTTGGCTCTTTGCCCTTGCAACCTTT 15 74 0 CTCTTTCCCT 0.851947 -138 CCTTTTATTCCTCCTTTCGCTT 20 2 1 CTTTTATCCT 0.511051 -29 GAAATGTCAATCACTCACCCTAAATCCTATC 21 24 0 TCACTCCCCT 0.720431 -87 ****** **** Masking position 5 Map Score: 12.7524 Number of sites scoring better than the average of aligned sites = 1052 Number in coding regions = 987 Number in noncoding regions = 65 Number of orfs with sites within 600 bp upstream = 72 Fraction of orfs with sites within 600 bp upstream = 0.0115644 Motif number 4 TCCCCTGCTTCTCCTGGAAAATTATGTAGC 3 67 1 CTCCTGGAAA 0.966913 -234 CTAAAAACATTTCCTGGAAAAACATTGCT 4 10 0 TTCCTGGAAA 0.987042 -51 GAAAGAAAAATTCCTGGAAACTCATCGTTC 9 75 1 TTCCTGGAAA 0.987042 -226 TCCTACTTCATTCTTGGAAATCAGGAACTA 9 164 0 TTCTTGGAAA 0.936411 -137 AAATTTAAACTTCAAGGAAACTGTTGTTTT 10 60 0 TTCAAGGAAA 0.865046 -241 ATTGTGGATTTTCCTGGGAAACAAAGGTTA 11 30 0 TTCCTGGGAA 0.903431 -271 TCTACCCCGATCCCAGGGAAAGGGAAGTCG 12 107 1 TCCCAGGGAA 0.891929 -194 ********** Masking position 9 Map Score: 7.18118 Number of sites scoring better than the average of aligned sites = 113 Number in coding regions = 100 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 5 TTAGTTTTGTTTTCAAAGGCAAAAACAGAAA 2 104 1 TTTCAAGGCA 0.89003 -66 AACGTTCCAATTTCAAAAGCTGTTCATGTCT 3 231 1 TTTCAAAGCT 0.952418 -70 TTTAATTTTCTTTTAATAGCACATTAAGACA 3 257 0 TTTTAAAGCA 0.657523 -44 CGAAACACTTTTTAAATACCCCGAATAACTT 5 53 1 TTTAAAACCC 0.576357 -80 ACTATCCTCCTTTAAAGTGCTATGTTCTTCA 9 126 0 TTTAAATGCT 0.798059 -175 CAAAGACGTCTTTCATGACCTTTCTCCAAGA 9 224 0 TTTCATACCT 0.53729 -77 GAAGGTAAACTTTAAATACCTTTCTCTAAAA 10 96 0 TTTAAAACCT 0.887955 -205 AGAGGAGAATTTTTAATGACTTCTCCACTCG 11 129 0 TTTTAAGACT 0.610411 -172 CCTCCCGAGGTTTTAAAGGCTAAGGAGATAT 12 19 1 TTTTAAGGCT 0.900631 -282 TCGGAACTTTTTTAAAGAGCTCCTTATGCAG 15 24 0 TTTAAAAGCT 0.925958 -188 AAAATAAAGGTTGCAAGGGCAAAGAGCCAAG 15 69 1 TTGCAAGGCA 0.684814 -143 GTCTTTGATTTTGCAATTGCTTCCGGCCTTC 15 108 1 TTGCAATGCT 0.629364 -104 ATTGAGAAGATTTAAAAGACTTATGGTGAAG 17 54 1 TTTAAAGACT 0.749177 -56 TCTTTCAACACCTCAATACTTAA 18 82 0 TTTCAAACCT 0.926924 -13 CCCGAAATCGTTTAAATGCCTCAAATTTTTA 19 18 1 TTTAAAGCCT 0.916312 -38 ****** **** Masking position 5 Map Score: 7.27954 Number of sites scoring better than the average of aligned sites = 372 Number in coding regions = 329 Number in noncoding regions = 43 Number of orfs with sites within 600 bp upstream = 53 Fraction of orfs with sites within 600 bp upstream = 0.00851269 Motif number 6 CATTTTTAATTGGTAAATTTAAGCCCTTT 2 8 0 TGTAAATTTA 0.778532 -162 ATGTTTCCTATGGAAAATTTGACAATAACGTT 3 205 1 TGAAAATTTA 0.961008 -96 TACTTTGAACTAAACAATTTTAAGGTTGGTGA 6 29 1 TAACAATTTA 0.870236 -26 ACTATAATAGTCAAAAACTTAATAAAATTTTC 7 17 1 TAAAAACTTA 0.765163 -76 ACTCACATTGTCGAAAATTTTATTAAGTTTTT 7 29 0 TGAAAATTTA 0.961008 -64 TACCTTTCTCTAAAAAATTTGAAATTTAAACT 10 79 0 TAAAAATTTA 0.924061 -222 CGAAGTAGAAACTTTCAACGAGATATT 11 284 0 TGAAACTTTA 0.91436 -17 ATGTAGAAACTGGACACTTTAAGATGATCGAT 18 25 1 TGACACTTTA 0.822028 -70 CCCCTAATTATTAAAAATTTGAGGCATTTAAA 19 28 0 TAAAAATTTA 0.924061 -28 AAAATAAATCTTAAAAATTTAAAATTTTTACA 21 61 1 TAAAAATTTA 0.924061 -50 * ******** * Masking position 6 Map Score: 7.91169 Number of sites scoring better than the average of aligned sites = 84 Number in coding regions = 43 Number in noncoding regions = 41 Number of orfs with sites within 600 bp upstream = 56 Fraction of orfs with sites within 600 bp upstream = 0.00899454 Motif number 7 TTCTCTATTTCTTTTTTATCTGGGAGGGCG 1 12 1 CTTTTTTATC 0.908276 -25 ATTATGTTAGCTTTGTTATCTGTTTTTAAT 2 62 1 CTTTGTTATC 0.940143 -108 TAGGCATTAGTTTTGTTTTCAAAGGCAAAA 2 98 1 TTTTGTTTTC 0.866456 -72 TTTCCAGGAATTTTTCTTTCCTTCTAGAGC 9 65 0 TTTTTCTTTC 0.744405 -236 AAACTGTTGTTTTTATTATCTTCCACTTTT 10 43 0 TTTTATTATC 0.599595 -258 TCCTTCTAACCTTTGTTTCCCAGGAAAATC 11 24 1 CTTTGTTTCC 0.843078 -277 CTCCCTCTTCCTTTGCTTTCATAAATTCTC 12 215 0 CTTTGCTTTC 0.942437 -86 TTTTCTCACTCTTTTCTATCGGAACTTTTT 15 43 0 CTTTTCTATC 0.875783 -169 CCCTTGCAACCTTTATTTTCTCACTCTTTT 15 58 0 CTTTATTTTC 0.885975 -154 CTTCTTTAACCTTTTTTTGCTAACCTAATG 15 135 1 CTTTTTTTGC 0.772063 -77 ********** Masking position 4 Map Score: 4.8646 Number of sites scoring better than the average of aligned sites = 250 Number in coding regions = 223 Number in noncoding regions = 27 Number of orfs with sites within 600 bp upstream = 31 Fraction of orfs with sites within 600 bp upstream = 0.00497912 Motif number 8 TAATTCGTCCTCTAAGGGGGGTGAAAG 5 116 1 TCTAAGGGGG 0.913822 -17 ACATCTCCTGAATAAGGAGGAACGATGAGT 9 94 0 AATAAGGAGG 0.968678 -207 AAGTATATATAATATGGGGGATCCAAGATT 10 128 1 AATATGGGGG 0.929878 -173 TTACTCCTAAACTTAGGGGGAGAAGAAAAT 10 268 0 ACTTAGGGGG 0.949235 -33 TGTTAAACTGCATAAGGAGCTCTTTAAAAA 15 17 1 CATAAGGAGC 0.826741 -195 AATTTTTAATAATTAGGGGCCCCAT 19 41 1 AATTAGGGGC 0.921417 -15 TTTTCTGGCAAATAAGGAGGTGTCACG 21 94 1 AATAAGGAGG 0.968678 -17 ********** Masking position 3 Map Score: 2.42081 Number of sites scoring better than the average of aligned sites = 108 Number in coding regions = 85 Number in noncoding regions = 23 Number of orfs with sites within 600 bp upstream = 25 Fraction of orfs with sites within 600 bp upstream = 0.00401542 Motif number 9 AACAGCTTTTGAAATTGGAACGTTATTGTCAA 3 223 0 GAATTGGACG 0.928793 -78 TCCTTATTCAGGAGATGTTATGAAGAACATAG 9 106 1 GAGATGTATG 0.82705 -195 TGGGAGTTTTGAAGTTGGGACGGGTAATTGAC 9 253 1 GAGTTGGACG 0.988279 -48 AAGGGAAGTCGAAGTTGTCACGTTGCTTAGCG 12 126 1 GAGTTGTACG 0.990263 -175 ATATCTCTTTGCAGTTATCACGATATTCTCTA 12 179 0 GAGTTATACG 0.940239 -122 TGGCAAATAAGGAGGTGTCACG 21 99 1 GAGGTGTACG 0.978639 -12 * ****** *** Masking position 6 Map Score: 0.999234 Number of sites scoring better than the average of aligned sites = 29 Number in coding regions = 26 Number in noncoding regions = 3 Number of orfs with sites within 600 bp upstream = 4 Fraction of orfs with sites within 600 bp upstream = 0.000642467 Motif number 10 TTTCTCTATTTCTTTTTTATCTGGG 1 3 1 TCTTTTCTTT 0.840214 -34 TTTAGGAAGATACATTTTTAATTGGTAAATTTA 2 19 0 TATTTTAATT 0.870187 -151 AGCTTTGTTATCTGTTTTTAATGTAAATTAGGC 2 70 1 TCTTTTAATG 0.888316 -100 ATGCCCTAAATCTTTATTTATTTTTCTGTTTTT 2 124 0 TCTTTTATTT 0.914949 -46 ATAACACTAATCGCTATTTAATTTTCTTTTAAT 3 271 0 TCTTTTAATT 0.971463 -30 AATTTTAGTGTACTTTCTTAATTCGTCCTCTAA 5 98 1 TATCTTAATT 0.766172 -35 CCCTAATCTCTCCATCTTTAATTTTCTTAAGGA 11 216 1 TCTTTTAATT 0.971463 -85 TAAGTAATTCTCTCTTTTTCATTTCTCCCTCTT 12 236 0 TCTTTTCATT 0.943311 -65 TTTCAACACCTCAATACTTAATTAATGCGAAGA 18 70 0 TCTCTTAATT 0.943311 -25 ** * ******* Masking position 8 Map Score: 3.44262 Number of sites scoring better than the average of aligned sites = 61 Number in coding regions = 49 Number in noncoding regions = 12 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 11 GTTAGATATTAATTTCTCTCAGAATAGGTA 5 23 0 AATTTCTCTC 0.897054 -110 GTCCCAACTTCAAAACTCCCAAAGACGTCT 9 244 0 CAAAACTCCC 0.822286 -57 CCGAACACATATCTCCCAAGGCTATCA 10 8 1 CATATCTCCC 0.956822 -293 TAGAAAGCTCAATAACTCTCGTATGTACAA 11 60 0 AATAACTCTC 0.71983 -241 AAGTCATTAAAAATTCTCCTCTCAGCCTCA 11 138 1 AAATTCTCCT 0.709097 -163 TCCCTTTACCCTAATCTCTCCATCTTTAAT 11 208 1 CTAATCTCTC 0.638421 -93 TAGTGCATCGAATATCTCCTTAGCCTTTAA 12 31 0 AATATCTCCT 0.774883 -270 AATTCTCTCGCATATCTCTTTGCAGTTATC 12 192 0 CATATCTCTT 0.803551 -109 TTGCTTTCATAAATTCTCTCGCATATCTCT 12 203 0 AAATTCTCTC 0.879994 -98 CTCTCTTTTTCATTTCTCCCTCTTCCTTTG 12 230 0 CATTTCTCCC 0.949105 -71 AACCTTTAAGTAATTCTCTCTTTTTCATTT 12 245 0 TAATTCTCTC 0.644009 -56 ********** Masking position 7 Map Score: 4.65206 Number of sites scoring better than the average of aligned sites = 372 Number in coding regions = 348 Number in noncoding regions = 24 Number of orfs with sites within 600 bp upstream = 31 Fraction of orfs with sites within 600 bp upstream = 0.00497912 Motif number 12 AATGTATCTTCCTAAAATTCAAATCTATTA 2 36 1 CCTAAAATTC 0.646833 -134 AAAACTAATGCCTAATTTACATTAAAAACA 2 82 0 CCTAATTTAC 0.752282 -88 TCCCTTATGCCCTAAATCTTTATTTATTTT 2 133 0 CCTAAATCTT 0.95307 -37 TGGAAAGCAACCTAATTCTCACCTCAACAG 3 166 0 CCTAATTCTC 0.955 -135 TACCACTAGTCCTAAATCACCCTTCTTCCT 9 190 0 CCTAAATCAC 0.905408 -111 TCTGCTTTCCCCTAATCCTTTGGGATAGCT 12 65 0 CCTAATCCTT 0.814065 -236 CTTTCCTAAATTTTCAGGCGATTT 17 96 0 CCTAAATTTT 0.888123 -14 ATGGGGCCCCTAATTATTAAAAATTTGA 19 38 0 CCTAATTATT 0.718315 -18 AATCACTCACCCTAAATCCTATCAACTGAA 21 17 0 CCTAAATCCT 0.862048 -94 ********** Masking position 5 Map Score: 2.17181 Number of sites scoring better than the average of aligned sites = 134 Number in coding regions = 116 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 21 Fraction of orfs with sites within 600 bp upstream = 0.00337295 Motif number 13 GCATCCCCTGCTTCTCCTGGAAAATTATGTA 3 64 1 CTTTCCTGGA 0.978385 -237 AATTATGTAGCTTCTATTGGAAGATTATATG 3 86 1 CTTTATTGGA 0.956152 -215 AGATATTTTTCATTTTTTGGACATGCATTTG 3 117 1 CATTTTTGGA 0.819073 -184 AGACTAAAAACATTTCCTGGAAAAACATTGC 4 12 0 CATTCCTGGA 0.943088 -49 CCCCGAATAACTTACATTGGACTTTTCAATT 5 71 1 CTTCATTGGA 0.852764 -62 ACTAGTGGTACTTGTCTTGGAGAAAGGTCAT 9 210 1 CTTTCTTGGA 0.987645 -91 CCTCCATTAACTTTTCTTGGTCAATTACCCG 9 273 0 CTTTCTTGGT 0.934747 -28 AACTGGACACCTAATCTTGGATCCCCCATAT 10 139 0 CTATCTTGGA 0.934747 -162 *** ******* Masking position 8 Map Score: 5.82834 Number of sites scoring better than the average of aligned sites = 107 Number in coding regions = 97 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 14 ********** No masking Map Score: 3.71857e-12 Number of sites scoring better than the average of aligned sites = 0 Number in coding regions = 0 Number in noncoding regions = 0 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0 Motif number 15 ********** No masking Map Score: 3.71857e-12 Number of sites scoring better than the average of aligned sites = 0 Number in coding regions = 0 Number in noncoding regions = 0 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0