AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/alignace/lib/ORF_hinf.txt -z/skink1/amcguire/genomes/hinf.fna -inarP_hinf_opreg_100.orf -g0.38 -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 = 0.38 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 HI0007 300 formate dehydrogenase, beta subunit (fdxH) #2 HI0342 205 ferredoxin-type protein (napF) #3 HI0343 180 napD protein (napD) #4 HI0345 300 ferredoxin-type protein (napG) #5 HI0936 108 cytochrome C-type biogenesis #6 HI1068 43 nitrite reductase, cytochrome C-type protein (nrfB) #7 HI1069 161 nitrite reductase, cytochrome C552 (nrfA) #8 HI1089 248 heme exporter ATP-binding protein A (ccmA) #9 HI1091 57 heme exporter protein C (ccmC) #10 HI1092 41 heme exporter protein D (ccmD) #11 HI1095 138 thiol:disulfide interchange protein (dsbE) Motif number 1 TTTTTACCATATCGCCTTTTTGGATGCCTTT 1 31 0 ATCGCTTTTT 0.912192 -270 AACCACGGCGACCGCTTTAATATAGCCACGA 1 72 0 ACCGCTTAAT 0.966842 -229 TTCCACTTTTACCGCACATTTTTTGAAGTCG 4 214 0 ACCGCCATTT 0.970432 -87 GTAAAAATCAACCGCACTTTATTTTCTCCCA 4 264 1 ACCGCCTTTA 0.970432 -37 TGAAAAATGCACCGCACTTTTTAGTGCAAAC 6 12 1 ACCGCCTTTT 0.99522 -32 GCGGTATAAAACCGCCTTAATTTTGAGTATT 7 18 0 ACCGCTTAAT 0.966842 -144 GCGGTTTTATACCGCCTTAATTTATTTAAAA 7 34 1 ACCGCTTAAT 0.966842 -128 GAGAAAAACCACCGCACTTTTATACGATGAA 9 16 0 ACCGCCTTTT 0.99522 -42 TTTTTACCGCACTTTTTCATTAACTT 11 123 0 ACCGCCTTTT 0.99522 -16 ***** ***** Masking position 1 Map Score: 17.5367 Number of sites scoring better than the average of aligned sites = 784 Number in coding regions = 478 Number in noncoding regions = 306 Number of orfs with sites within 600 bp upstream = 233 Fraction of orfs with sites within 600 bp upstream = 0.0374237 Motif number 2 TTGTGCTACGCCACCCATTTGTAATTTGAA 3 70 0 CCACCCATTT 0.967038 -111 TCCACTTTTACCGCACATTTTTTGAAGTCG 4 214 0 CCGCACATTT 0.992416 -87 TAAAAATCAACCGCACTTTATTTTCTCCCA 4 265 1 CCGCACTTTA 0.97757 -36 GAAAAATGCACCGCACTTTTTAGTGCAAAC 6 13 1 CCGCACTTTT 0.995259 -31 AGAAAAACCACCGCACTTTTATACGATGAA 9 16 0 CCGCACTTTT 0.995259 -42 AATCCCCCTTCCGCCCTTCGGGCACCTTCC 11 40 0 CCGCCCTTCG 0.943874 -99 TAACTTTGCTCCACCCATTTATGGGGGGAG 11 99 0 CCACCCATTT 0.967038 -40 TTTTTACCGCACTTTTTCATTAACTT 11 123 0 CCGCACTTTT 0.995259 -16 ********** Masking position 8 Map Score: 16.9722 Number of sites scoring better than the average of aligned sites = 852 Number in coding regions = 534 Number in noncoding regions = 318 Number of orfs with sites within 600 bp upstream = 234 Fraction of orfs with sites within 600 bp upstream = 0.0375843 Motif number 3 TGTATTCTGGTGTTTGCGTGATTGCCTCACCCCAA 1 234 0 TGTTTTATTC 0.673556 -67 CCTCCCCAACTTTTTCAATATTTACCAAGAATGTT 1 270 0 TTTTTTTTTC 0.803425 -31 TTGCTATGCTGTTTTGTTTTAATCCCTTGCAAAAT 2 38 1 GTTTTTAATC 0.897539 -168 AAACCTTAGATTTTTTGATCTATAACAAATAAAGT 2 78 1 TTTTTTTATA 0.870867 -128 ATTTTGGGTTGTTTTCATTCATTCATCGTAAACAC 2 135 1 GTTTTTATTA 0.96164 -71 TTTGTTTTAGATCATTCATTGTTATTGC 3 163 0 GTTTTTATTA 0.961655 -18 CAAGGTGCTATTTTTAATTTTATTAATGAAACATA 5 36 1 TTTTTTTATA 0.87086 -73 GTATATTGTTGTTTTAAATAAATTAAGGCGGTATA 7 41 0 GTTTTTAATA 0.949933 -121 AATATACCTCTTTTTGAGTATTTTAAAAGATAAGC 7 69 1 TTTTTTTTTA 0.898801 -93 ATTTCGTTGAGGTTTTGGTCTATAACCAAAATTGA 8 39 1 GGTTTTTATA 0.905781 -210 CAAAAAAATTGATTTAGATCATTAAATGTTTTTCC 8 85 1 GATTTTATTA 0.761144 -164 ATCATTAAATGTTTTTCCTTTTTTAAAAAGTGAAT 8 102 1 GTTTTTTTTA 0.961656 -147 ATTAAATTTTGTTTTAAATCAATAAACCTATCGAT 8 139 1 GTTTTTAATA 0.948729 -110 AAAGTGCGGTGGTTTTTCTCTTTAATTTTTAAGGA 9 27 1 GGTTTTTTTA 0.926797 -31 ***** * *** * Masking position 9 Map Score: 12.7112 Number of sites scoring better than the average of aligned sites = 319 Number in coding regions = 246 Number in noncoding regions = 73 Number of orfs with sites within 600 bp upstream = 63 Fraction of orfs with sites within 600 bp upstream = 0.0101189 Motif number 4 ACGACGAGAAGTAATTTTTACCATATCGCC 1 46 0 GTAATTTTTA 0.807109 -255 GACACGCCCATCAATTTCGAGATCTTTAAG 1 112 0 TCAATTTCGA 0.935245 -189 CCCAACTTTTTCAATATTTACCAAGAATGT 1 271 0 TCAATATTTA 0.601775 -30 TATGCTGTTTTCAATTTAGA 2 1 0 TCAATTTAGA 0.732533 -205 AAACAGCATAGCAATTTTGACTATGCTGTT 2 22 0 GCAATTTTGA 0.946914 -184 CAACCTTTAGTTAATTTCGATGCTTGTAAT 3 97 1 TTAATTTCGA 0.809742 -84 TTGAAGTCGGTTTCTTTTGAAATTGGGTCT 4 193 0 TTTCTTTTGA 0.459779 -108 CTATCAAGGTGCTATTTTTAATTTTATTAA 5 32 1 GCTATTTTTA 0.699011 -77 AAAATGCACCGCACTTTTTAGTGCAAACTA 6 15 1 GCACTTTTTA 0.915049 -29 CGCACTTTCTAGTTTGCACTA 6 33 0 GCACTTTCTA 0.866859 -11 TAAAACCGCCTTAATTTTGAGTATTATTAT 7 13 0 TTAATTTTGA 0.874743 -149 TATTATTTGCTCAATTTTGGTTATAGACCA 8 54 0 TCAATTTTGG 0.76581 -195 ATGATCTAAATCAATTTTTTTGCTATTATT 8 77 0 TCAATTTTTT 0.637547 -172 TTTAATAAATTCACTTTTTAAAAAAGGAAA 8 115 0 TCACTTTTTA 0.934997 -134 TAGAATACTGTCACTTTCTATTTTCCCTCT 8 223 1 TCACTTTCTA 0.896865 -26 GTTTTTCTCTTTAATTTTTAAGGATTTTTT 9 38 1 TTAATTTTTA 0.848209 -20 ********** Masking position 5 Map Score: 13.597 Number of sites scoring better than the average of aligned sites = 534 Number in coding regions = 386 Number in noncoding regions = 148 Number of orfs with sites within 600 bp upstream = 131 Fraction of orfs with sites within 600 bp upstream = 0.0210408 Motif number 5 AATTACTTCTCGTCGTGGCTATATTAAAGC 1 60 1 CGTCGTGGCT 0.994221 -241 TTAAAGCGGTCGCCGTGGTTACAAAACGTC 1 83 1 CGCCGTGGTT 0.939497 -218 ACGTGGTTTACGTCATGGCGATAAAATTAA 4 31 1 CGTCATGGCG 0.812006 -270 GATTTCATCTCGTCGAGGCGAAATGATTTC 4 61 1 CGTCGAGGCG 0.990265 -240 TAATAAACCACCTCGTGGCTTAGTATTTAC 4 112 1 CCTCGTGGCT 0.972865 -189 TCGTTTTTTTCGTTGATGCGCAGATAAAGT 5 82 0 CGTTGATGCG 0.859621 -27 AAACAGATTTCGTTGAGGTTTTGGTCTATA 8 33 1 CGTTGAGGTT 0.914273 -216 ********** Masking position 8 Map Score: 6.24244 Number of sites scoring better than the average of aligned sites = 87 Number in coding regions = 73 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 4 Fraction of orfs with sites within 600 bp upstream = 0.000642467 Motif number 6 CCCCAAGATGGTGTTAAGGTATTCGTAGAGA 1 209 0 GTGTTAAGGA 0.806866 -92 ACACCATCTTGGGGTGAGGCAATCACGCAAA 1 226 1 GGGGTGAGGA 0.98042 -75 ATTGAAAAAGTTGGGGAGGCATAAT 1 286 1 TTGGGGAGGA 0.848295 -15 GTCGCATCTAGTGTTAAGCTATTTGCAAGCT 4 162 0 GTGTTAAGCA 0.682842 -139 CCCCGCAAGCAGGGGAAGGCAAGAATAAAA 11 10 0 AGGGGAAGGA 0.929836 -129 CCCTGCTTGCGGGGGAAGGTGCCCGAAGGGC 11 27 1 GGGGGAAGGG 0.989887 -112 GTGCCCGAAGGGCGGAAGGGGGATTACGTAT 11 45 1 GGCGGAAGGG 0.93431 -94 ACCCATTTATGGGGGGAGCTGTCGCGAAGTG 11 86 0 GGGGGGAGCG 0.984836 -53 CCCCATAAATGGGTGGAGCAAAGTTAATGAA 11 103 1 GGGTGGAGCA 0.962694 -36 ********* * Masking position 7 Map Score: 5.08922 Number of sites scoring better than the average of aligned sites = 126 Number in coding regions = 69 Number in noncoding regions = 57 Number of orfs with sites within 600 bp upstream = 17 Fraction of orfs with sites within 600 bp upstream = 0.00273049 Motif number 7 TCTACGAATACCTTAACACCATCTTGGGGT 1 211 1 CCTTAACACC 0.766086 -90 GAGGCAATCACGCAAACACCAGAATACAAA 1 241 1 CGCAAACACC 0.97584 -60 ATTCATTCATCGTAAACACATAATCCGTTG 2 151 1 CGTAAACACA 0.874885 -55 ATCGCCATGACGTAAACCACGTGCTTGTGC 4 23 0 CGTAAACCAC 0.946655 -278 TACTCGCGGACGTAATAAACCACCTCGTGG 4 100 1 CGTAATAAAC 0.853784 -201 GAAAAGGCTGCGTAAAAACCATGTAAAAAT 4 242 1 CGTAAAAACC 0.97319 -59 TGCGCATCAACGAAAAAAACGACGACATT 5 90 1 CGAAAAAAAC 0.793229 -19 TATAAAAAATCGCTAAAAACTAACCGCACT 10 11 0 CGCTAAAAAC 0.767799 -31 GAGGGGGATACGTAATCCCCCTTCCGCCCT 11 53 0 CGTAATCCCC 0.916789 -86 ********** Masking position 5 Map Score: 3.88541 Number of sites scoring better than the average of aligned sites = 179 Number in coding regions = 162 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 8 TTTTGACTATGCTGTTTTCAATTTAGA 2 7 0 GCTGTTTTAA 0.971013 -199 GCTATGCTGTTTTGTTTTAATCCCTTGCAAA 2 40 1 TTTGTTTTAT 0.908829 -166 CCTATTTTGGGTTGTTTTCATTCATTCATCG 2 132 1 GTTGTTTTAT 0.927713 -74 TTTGTTTTAGATCATTCATTG 3 170 0 TTTGTTTTGA 0.880527 -11 TTGAAGTCGGTTTCTTTTGAAATTGGGTCTG 4 192 0 TTTCTTTTAA 0.839252 -109 CTATCAAGGTGCTATTTTTAATTTTATTAAT 5 32 1 GCTATTTTAA 0.789064 -77 GAGGTATATTGTTGTTTTAAATAAATTAAGG 7 48 0 GTTGTTTTAA 0.975968 -114 CTCAACGAAATCTGTTTTTAACAATAGAAGG 8 19 0 TCTGTTTTAA 0.96299 -230 TTTATTAAATTTTGTTTTAAATCAATAAACC 8 136 1 TTTGTTTTAA 0.969269 -113 ******** ** Masking position 6 Map Score: 7.67919 Number of sites scoring better than the average of aligned sites = 117 Number in coding regions = 89 Number in noncoding regions = 28 Number of orfs with sites within 600 bp upstream = 28 Fraction of orfs with sites within 600 bp upstream = 0.00449727 Motif number 9 AAAACAACCCAAAATAGGTAGTTTTTCAAT 2 120 0 AAAATAGGTA 0.900766 -86 CTGCATCAAAGAAAGTGGTAAATACTAAGC 4 129 0 GAAAGTGGTA 0.902754 -172 AATGTGCGGTAAAAGTGGAAAAGGCTGCGT 4 225 1 AAAAGTGGAA 0.962105 -76 TCCCATCAATAAAAGAGGAAG 4 290 1 AAAAGAGGAA 0.979326 -11 AAAATACTCAAAAAGAGGTATATTGTTGTT 7 63 0 AAAAGAGGTA 0.979326 -99 TTCACTTTTTAAAAAAGGAAAAACATTTAA 8 106 0 AAAAAAGGAA 0.900766 -143 ********** Masking position 4 Map Score: 4.38054 Number of sites scoring better than the average of aligned sites = 85 Number in coding regions = 68 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 10 GGATGCCTTTTTCTGCCGCTAATTTTTCGC 1 8 0 TTCGCCTAAT 0.968375 -293 CACGGTTACCTTTGCCATTTAATGCCTTCATAT 1 173 0 TTTCCATAAT 0.908716 -128 TCTTGGCAAGTTCGGCATTCAATACGGTGCAAT 3 12 0 TTCGCACAAT 0.920797 -169 GCCAAGATAATTGTCCAGCTAATGCGATTCGTT 3 38 1 TTGCCATAAT 0.957318 -143 AACCACGTGCTTGTGCATCTAATGGGTG 4 6 0 TTGGCATAAT 0.947665 -295 GCACTTTATTTTCTCCCATCAATAAAAGAGGAA 4 277 1 TTCCCCCAAT 0.948822 -24 ATAACCAAAATTGAGCAAATAATAGCAAAAAAA 8 60 1 TTGGCATAAT 0.947665 -189 ACTTTCTATTTTCCCTCTGTAATT 8 235 1 TTCCTCTAAT 0.881918 -14 GTGCGGTGGTTTTTCTCTTTAATTTTTAAGGAT 9 30 1 TTTCTCTAAT 0.716206 -28 *** *** **** Masking position 11 Map Score: 3.80486 Number of sites scoring better than the average of aligned sites = 197 Number in coding regions = 172 Number in noncoding regions = 25 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 11 CCATATCGCCTTTTTGGATGCCTTTTTCTGC 1 25 0 TTTTTGATGC 0.922969 -276 GGTTTAATGAATTTTGCAAGGGATTAAAACA 2 52 0 ATTTTGAAGG 0.880321 -154 CTTTCAAATATTTCTGAATGCTTCTGTAGGC 2 180 0 TTTCTGATGC 0.714186 -26 CATTCAGAAATATTTGAAAGACATT 2 191 1 TATTTGAAGA 0.712917 -15 AGTGTTAAGCTATTTGCAAGCTGACCTGCAT 4 153 0 TATTTGAAGC 0.880321 -148 GTGCGGTTGATTTTTACATGGTTTTTACGCA 4 250 0 TTTTTAATGG 0.882539 -51 TTTTTATAAGCACAATAGCAC 5 1 1 TTTTTAAAGC 0.943159 -108 CTTTTTGAGTATTTTAAAAGATAAGCTTGAT 7 78 1 ATTTTAAAGA 0.609072 -84 TGTTTTTCCTTTTTTAAAAAGTGAATTTATT 8 111 1 TTTTTAAAAG 0.591157 -138 TTTTAGCGATTTTTTATAAGGAATATTTT 10 23 1 TTTTTAAAGG 0.943159 -19 ****** **** Masking position 5 Map Score: 1.89144 Number of sites scoring better than the average of aligned sites = 436 Number in coding regions = 367 Number in noncoding regions = 69 Number of orfs with sites within 600 bp upstream = 63 Fraction of orfs with sites within 600 bp upstream = 0.0101189 Motif number 12 ********** No masking Map Score: 6.31205e-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 13 ********** No masking Map Score: 6.31205e-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 14 ********** No masking Map Score: 6.31205e-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