AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_pyro.txt -z/home/amcguire/genomes/pyro.fna -irpoN_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 PH0359 300 443aa long hypothetical glutamine synthetase #2 PH0879 300 367aa long hypothetical hydrogenase expression/formation protein hypD #3 PH1353 66 679aa long hypothetical formate dehydrogenase #4 PH1354 28 196aa long hypothetical protein #5 PH1429 288 147aa long hypothetical protein #6 PH1433 59 118aa long hypothetical protein #7 PH1437 45 427aa long hypothetical NADH-ubiquinone oxidoreductase subunit #8 PH1439 300 321aa long hypothetical NADH-ubiquinone oxidoreductase subunit #9 PH1454 265 241aa long hypothetical protein #10 PH1581 75 139aa long hypothetical protein #11 PH1815 24 284aa long hypothetical cobalt transport ATP-binding protein Motif number 1 TTCCATAAAGGAAGGCGAATA 1 1 0 GAAGGGAATA 0.816605 -300 CAGCAAGTAAGAGGGTTAGGAAGGCAAGTAA 1 100 0 GAGGGTAGGA 0.940671 -201 AGTTGATTTTGGAGGTGTGAAAAGGGAGGTT 2 136 1 GGAGGGTGAA 0.723452 -165 CTCAGCCCTTGGAGGTGAGTGA 2 289 1 GGAGGGAGTG 0.954234 -12 ATTTGGTCTAGGCGGTGAAGATTGGAAAAGA 5 90 1 GGCGGGAAGA 0.87911 -199 ACACGGACTCGAAGACGTGGGTGGAATGAAC 5 150 1 GAAGAGTGGG 0.926081 -139 GGCCCTGGAGGAGGGAGAGGA 5 278 1 GAGGGGAGGA 0.993275 -11 TATCTCCTGAGGAGGGGAGGTAA 7 33 1 GGAGGGAGGT 0.958823 -13 GGAAGAAGGGTAGGGATGGTCCCGT 8 5 1 GAAGGTAGGG 0.954926 -296 CCGTCAGATGGAAGATGAGGGAACCAACTTT 8 32 1 GAAGAGAGGG 0.978989 -269 TCCTACTCCCGCGGGAGTGGGATCCCCTTTT 8 261 0 GCGGGGTGGG 0.909638 -40 GGATGCATTAGGGGGTGAGGAT 8 289 1 GGGGGGAGGA 0.992612 -12 TTTTAATGGCGAAGATGAAGACAGCACCGCT 9 202 0 GAAGAGAAGA 0.9005 -64 GTATGAAAGCGAGGAGGAAGAGAAACCTGGT 9 243 1 GAGGAGAAGA 0.891677 -23 GATGCTCCCAAGGAGAGGGGAGTA 11 9 1 CAAGGGAGGG 0.943026 -16 ***** ***** Masking position 4 Map Score: 18.5275 Number of sites scoring better than the average of aligned sites = 1164 Number in coding regions = 1049 Number in noncoding regions = 115 Number of orfs with sites within 600 bp upstream = 110 Fraction of orfs with sites within 600 bp upstream = 0.0176678 Motif number 2 TGAAATTAAAGGAAACATCGGGATAGTTGATTTTGG 2 112 1 GACATGGAAG 0.98777 -189 TGGACTAAGAGCAACCATAAGAGCAGCAAATATTAT 5 40 0 GACATAGGAG 0.870349 -249 GGTCTAGGCGGTGAAGATTGGAAAAGATATCGCTAT 5 94 1 GAGATGGAAG 0.97637 -195 GTTTTATGTAGTAATCATCGGTATAGCGATATCTTT 5 116 0 GACATGGAAG 0.98777 -173 ACACGGACTCGAAGACGTGGGTGGAATGAACATAGT 5 150 1 GGCGTGGGAA 0.925305 -139 CAGAGGTTACGATACCATTGGAGAAGCAACGGTTTT 5 207 1 GACATGGGAG 0.989425 -82 GGAAGAAGGGTAGGGATGGTCCCGTCAGA 8 4 1 AAGGTGGAGG 0.738584 -297 TCACAATAGCGAAGGGATTGGAAGGAAATCAACTAG 8 74 1 GGGATGGAGA 0.795306 -227 ACTAGCCGATGTCGTCGTTGCAATAGCCTCTATAGA 8 105 1 GGCGTGCAAG 0.942992 -196 AAGCTGTACCGATAGGGTAGCCGTAGTGAAAGAAGG 8 150 1 GAGGTGCGAG 0.922579 -151 TTTGCTAGCTGCTACCGTGGGAATGGCCGCGGTCAG 9 87 1 GACGTGGAGG 0.987174 -179 AATGACGGAAGCGGCCATAGGAGCGGCCCTGAGCGG 9 171 1 GGCATGGGGG 0.984452 -95 * * *** ** * ** Masking position 8 Map Score: 11.6165 Number of sites scoring better than the average of aligned sites = 417 Number in coding regions = 400 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 3 CTTGACTCTCGGAAGTGCTCCCTGACTATTAGAGA 1 49 0 GGAATCTCGA 0.976107 -252 AAAAAGCTAAGGAAATACTTGAAGCTTGGGAGGAA 2 249 1 GGAATCTAGC 0.893205 -52 AAGCTTGGGAGGAAGTTTTCTCAGCCCTTGGAGGT 2 270 1 GGAATTTCGC 0.983615 -31 TCTCATTGATGATAATATTTGCTGCTCTTATGGTT 5 29 1 GATATTTCGC 0.930741 -260 GAGAAGCAACGGTTTTATTCACGGCAATAGCCGGA 5 227 1 GGTTTTTCGC 0.955573 -62 TAATATCCCAGAGATTTCTTGCAGCTGGTATC 6 8 0 GAGATCTCGC 0.926312 -52 AAGGCAAGAAGATTATCCTAACCGAAAAAGATCTG 8 182 1 GATTTCTCGA 0.862008 -119 TTTCTGAATTGAAAGTTTTAGCAGATCTTTTTCGG 8 203 0 GAAATTTCGA 0.916197 -98 TTTTACTTCTGGATTTATTTCCCGAGTTTTCTGAA 8 230 0 GGATTTTCGA 0.945942 -71 TTGAATGGAGGGATTTGCTAGCTGCTACCGTGGGA 9 74 1 GGATTCTCGC 0.984937 -192 **** * ** * ** Masking position 9 Map Score: 8.2831 Number of sites scoring better than the average of aligned sites = 127 Number in coding regions = 115 Number in noncoding regions = 12 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 4 TATCATAATTTTGTCAATTTAAAGCACAATAACC 1 138 1 TTGAATAAAG 0.964771 -163 ATTTGGTATATTGTTCACTAAAAGCGGATGATCA 1 258 1 TTGCATAAAG 0.940777 -43 TTTAGACATTTTTAAAACCAAAAGTTTTCAACCT 2 16 0 TTTAACAAAG 0.873453 -285 CAGGAAAGGTTCTTGAAATTAAAGGAAACATCGG 2 99 1 TCTAATAAAG 0.93634 -202 TTCCCGAGTTTTCTGAATTGAAAGTTTTAGCAGA 8 213 0 TTCAATAAAG 0.975295 -88 GGGAAATAAATCCAGAAGTAAAAGGGGATCCCAC 8 242 1 TCCAATAAAG 0.958574 -59 TGTCTTCATCTTCGCCATTAAAAGGACGTACAGG 9 210 1 TTCCATAAAG 0.958572 -56 TATATTATAGTTTAAAAATGAAAGGGATTACATT 10 28 0 TTTAATAAAG 0.962915 -48 *** ** * **** Masking position 7 Map Score: 4.09076 Number of sites scoring better than the average of aligned sites = 74 Number in coding regions = 60 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 17 Fraction of orfs with sites within 600 bp upstream = 0.00273049 Motif number 5 GTATATTAGTGGGTAGAAGATTTCTTCGTCTA 1 197 1 GGTAGAAGTT 0.98284 -104 GGAAACATCGGGATAGTTGATTTTGGAGGTGT 2 122 1 GGTAGTTGTT 0.971248 -179 CTCTTACATCGGTTAGAAGGTCAAGTCTAACC 2 163 0 GGTAGAAGTC 0.946304 -138 CTTGAAGCTTGGGAGGAAGTTTTCTCAGCCCT 2 266 1 GGAGGAAGTT 0.931198 -35 AACAAGTTGGGAAAAGTTGGTTCCCTCATCTT 8 43 0 GAAAGTTGTT 0.770907 -258 CGACGACATCGGCTAGTTGATTTCCTTCCAAT 8 90 0 GGTAGTTGTT 0.971248 -211 AGTGAAAGAAGGCAAGAAGATTATCCTAACCG 8 174 1 GGAAGAAGTT 0.977771 -127 ** ****** ** Masking position 11 Map Score: 3.40676 Number of sites scoring better than the average of aligned sites = 61 Number in coding regions = 53 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 6 TTCCGAGAGTCAAGGCTATATAAACTAAGT 1 70 1 CAAGGCTATA 0.886336 -231 AGAGGGTTAGGAAGGCAAGTAAACTTAGTT 1 92 0 GAAGGCAAGT 0.962396 -209 CCTTTCCTGGGACGGCAAGACACATTAGCT 2 78 0 GACGGCAAGA 0.989118 -223 CGGTTTTATTCACGGCAATAGCCGGAGCTG 5 236 1 CACGGCAATA 0.96515 -53 CGTAGTGAAAGAAGGCAAGAAGATTATCCT 8 171 1 GAAGGCAAGA 0.988263 -130 ********** Masking position 8 Map Score: 1.97852 Number of sites scoring better than the average of aligned sites = 27 Number in coding regions = 24 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 7 CCCTCTTACTTGCTGGGGCTTTTATCATAATTT 1 116 1 TGCGGCTTTT 0.93971 -185 TTATCTAATGATCATCCGCTTTTAGTGAACAAT 1 267 0 ATCCGCTTTT 0.907633 -34 CTATAACGTAATCACCAGCTCTTACATCGGTTA 2 180 0 ATCAGCTCTT 0.970107 -121 CTTCAAGTATTTCCTTAGCTTTTTCCTCGTCGA 2 240 0 TTCAGCTTTT 0.953787 -61 ATGAGAGAAATGCCAAAGCTCTTT 5 2 0 TGCAGCTCTT 0.980944 -287 TCATCGGTATAGCGATATCTTTTCCAATCTTCA 5 105 0 AGCATCTTTT 0.878042 -184 CAATAGCCGGAGCTGTAGCTCTTCTAAGGCCCT 5 251 1 AGCAGCTCTT 0.9853 -38 *** ******* Masking position 10 Map Score: 1.75904 Number of sites scoring better than the average of aligned sites = 170 Number in coding regions = 157 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 8 TCATGAACATTGAACATTAGACGAAGAAAT 1 216 0 TGAACATTAG 0.848515 -85 TAATGTTCAATGTTCATGAGTAAAGACTTA 1 227 1 TGTTCATGAG 0.840952 -74 TAAAAGCGGATGATCATTAGATAACTATTC 1 276 1 TGATCATTAG 0.964261 -25 ATTAGATAACTATTCACTAG 1 291 1 TATTCACTAG 0.86738 -10 AACTATAACGTAATCACCAGCTCTTACATC 2 185 0 TAATCACCAG 0.925728 -116 TTTTATGTAGTAATCATCGGTATAGCGATA 5 121 0 TAATCATCGG 0.850732 -168 ATTGCGGATATAATCATTAGGAGAACAATT 9 36 0 TAATCATTAG 0.957159 -230 ********** Masking position 6 Map Score: 1.06039 Number of sites scoring better than the average of aligned sites = 31 Number in coding regions = 26 Number in noncoding regions = 5 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 Motif number 9 ********** No masking Map Score: 4.08805e-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 10 ********** No masking Map Score: 4.08805e-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 11 ********** No masking Map Score: 4.08805e-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