AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/alignace/lib/ORF_hinf.txt -z/skink1/amcguire/genomes/hinf.fna -inarL_hinf_opreg_300.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 HI0340 82 conserved hypothetical protein #3 HI0341 84 conserved hypothetical protein #4 HI0342 205 ferredoxin-type protein (napF) #5 HI0343 180 napD protein (napD) #6 HI0345 300 ferredoxin-type protein (napG) #7 HI0833 22 fumarate reductase, 15 kDa hydrophobic protein (frdC) #8 HI0835 181 fumarate reductase, flavoprotein subunit (frdA) #9 HI0936 108 cytochrome C-type biogenesis #10 HI0937 200 extragenic suppressor (suhB) #11 HI1047 253 anaerobic dimethyl sulfoxide reductase, chain A (dmsA) #12 HI1068 43 nitrite reductase, cytochrome C-type protein (nrfB) #13 HI1069 161 nitrite reductase, cytochrome C552 (nrfA) #14 HI1074 264 conserved hypothetical protein #15 HI1076 300 cytochrome D ubiquinol oxidase, subunit I (cydA) #16 HI1089 248 heme exporter ATP-binding protein A (ccmA) #17 HI1091 57 heme exporter protein C (ccmC) #18 HI1092 41 heme exporter protein D (ccmD) #19 HI1095 138 thiol:disulfide interchange protein (dsbE) Motif number 1 TTCCACTTTTACCGCACATTTTTTGAAGTC 6 215 0 ACCGCACATT 0.993764 -86 GTAAAAATCAACCGCACTTTATTTTCTCCC 6 264 1 ACCGCACTTT 0.998698 -37 CCAATTTTCCACCGCACTTTAACCATAAAT 10 19 1 ACCGCACTTT 0.998698 -182 TGAAAAATGCACCGCACTTTTTAGTGCAAA 12 12 1 ACCGCACTTT 0.998698 -32 CATTTTTTTAACCGCACTTT 14 255 1 ACCGCACTTT 0.998698 -10 GAGAAAAACCACCGCACTTTTATACGATGA 17 17 0 ACCGCACTTT 0.998698 -41 TTTTTACCGCACTTTTTCATTAACT 19 124 0 ACCGCACTTT 0.998698 -15 ********** Masking position 6 Map Score: 27.2183 Number of sites scoring better than the average of aligned sites = 1115 Number in coding regions = 700 Number in noncoding regions = 415 Number of orfs with sites within 600 bp upstream = 285 Fraction of orfs with sites within 600 bp upstream = 0.0457758 Motif number 2 CCAGAATACAAAACATTCTTGGTAAATATTGAAAAAGTTGGGGAGG 1 259 1 AATAAAAAAA 0.920331 -42 ACCTTGGAAAAAATTTGCCCTATTATACGAGAAAAATTGGTATAAT 2 16 1 AATATAAAAA 0.742021 -67 TGCCCCGTGAATGCAATAACAATGAATGATCTAAAACAAA 5 151 1 AGTAATAAAA 0.787558 -30 ATGCACAAGCACGTGGTTTACGTCATGGCGATAAAATTAAGATTTC 6 21 1 AGTATTAAAA 0.47999 -280 TAAAAGTGGAAAAGGCTGCGTAAAAACCATGTAAAAATCAACCGCA 6 234 1 AAAAATAAAA 0.941664 -67 AAAATCCGATACNTTTCCATCTTTAGACATAAAANACGTTATTAAT 8 63 1 ANTAGAAANA 0.776449 -119 TCCAATCAATAGAAAGTAAAAATAAATCCCCTAAAAGGGTAATATT 8 139 0 AATAATAAAA 0.949992 -43 TCGCTAATCAAGTATGTTTCATTAATAAAATTAAAAATAGCACCTT 9 37 0 ATTATTAAAA 0.526826 -72 TCTGTATCGCAAAGTTTTTCTGAAAACCTATAAAAACCACTGTTTT 10 86 1 AAAAAAAAAA 0.907545 -115 GAGATTTGCCAAAATAACTAGTTGAAAATCATAAAACAGTGGTTTT 10 118 0 AATAATAAAA 0.949992 -83 TCCATAGTCAATTTGTTATTCCAAAGTTTATTAAAACATCAATCTA 11 91 1 ATAAGTAAAA 0.533253 -163 TCGTTCCCCCACAGTCAGATTGAAAAATAACTAAAACGAGTTAATT 11 214 0 AAAAATAAAA 0.941664 -40 GCTAGCGCGAAATGCACCATCAATAAAGAAAAAAAAGGTAAATTTG 14 66 1 ATAAAAAAAA 0.69794 -199 AAAAAAAGGTAAATTTGAGGAATAAATGATTTAAGAATTTTACCAA 14 95 1 AATAATAAGA 0.612749 -170 GTTGTTGAGAAAAAGATAAATGAGAAAAGTTAAAAAGGGTTCATTA 14 158 0 AAAAAAAAAA 0.907545 -107 ATTTTGGTAAATATTCTAGCATAGAAATTCGTAAAATTATTTTCCA 14 206 0 AAAAATAAAA 0.941664 -59 GTCAATTTGATCTAAGTCAATTAAATAAAATATAACAAAT 15 5 1 ATTAATAAAA 0.817239 -296 TTCTACTACTAAACATAAGGATAAAAAATAGTAAAAAATGCTATAT 15 88 0 AAAAATAAAA 0.941664 -213 TGACTTATCTACATAATTATTTTTAAAGGTTAAAAAAACACCAGTT 15 163 0 AATAAAAAAA 0.92033 -138 GTCTATAACCAAAATTGAGCAAATAATAGCAAAAAAATTGATTTAG 16 56 1 AAAAAAAAAA 0.907545 -193 AAAATTTAATAAATTCACTTTTTAAAAAAGGAAAAACATTTAATGA 16 103 0 AATAAAAAAA 0.92033 -146 CTTTAGAAGTAGATCGATAGGTTTATTGATTTAAAACAAAATTTAA 16 140 0 AATATTAAAA 0.825479 -109 AAAATATTCCTTATAAAAAATCGCTAAAAACTAACCGCA 18 13 0 AAAAATAAAA 0.941664 -29 TGGGTGGAGCAAAGTTAATGAAAAAGTGCGGTAAAAA 19 112 1 AAAAGTAAAA 0.829165 -27 * * * ** ***** Masking position 15 Map Score: 26.8607 Number of sites scoring better than the average of aligned sites = 414 Number in coding regions = 292 Number in noncoding regions = 122 Number of orfs with sites within 600 bp upstream = 115 Fraction of orfs with sites within 600 bp upstream = 0.0184709 Motif number 3 GTGTACGACACGCCCATCAATTTCGAGATC 1 118 0 CGCCCATCAA 0.891815 -183 GCGTGATTGCCTCACCCCAAGATGGTGTTA 1 224 0 CTCACCCCAA 0.963135 -77 GGTTGTGCTACGCCACCCATTTGTAATTTG 5 72 0 CGCCACCCAT 0.951507 -109 ACTTTATTTTCTCCCATCAATAAAAGAGGA 6 279 1 CTCCCATCAA 0.929386 -22 GAGAGCTACTCTCAACTCAATCTTAGCTTT 8 18 1 CTCAACTCAA 0.967608 -164 GATATCCTCCAATCAATAGAAAGTAA 8 166 0 CTCCAATCAA 0.933659 -16 TCCCTAATTACTCAACTCCAATCAGCTAAG 15 216 0 CTCAACTCCA 0.919774 -85 TCTCAACTCCTTTGTATAAAC 15 290 0 CTCAACTCCT 0.871129 -11 ATGAAATTTTCGCAACTCAAACACATAACT 16 186 0 CGCAACTCAA 0.949263 -63 TTCGCGACAGCTCCCCCCATAAATGGGTGG 19 89 1 CTCCCCCCAT 0.966994 -50 ATTAACTTTGCTCCACCCATTTATGGGGGG 19 101 0 CTCCACCCAT 0.969067 -38 ********** Masking position 3 Map Score: 11.1055 Number of sites scoring better than the average of aligned sites = 83 Number in coding regions = 53 Number in noncoding regions = 30 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 4 TTAGATTTTTTGATCTATAACAAATAAAGTTCA 4 83 1 TGACAAACAA 0.984074 -123 TTACGATGAATGAATGAAAACAACCCAAAATAG 4 133 0 TGATAAACAA 0.957809 -73 TAACAATGAATGATCTAAAACAAA 5 167 1 TGACAAACAA 0.984074 -14 ATTTGCAAGCTGACCTGCATCAAAGAAAGTGGT 6 140 0 TGACGATCAA 0.93256 -161 TCGGATTTTGTGATCTACCTCAAAAAAGCTAAG 8 39 0 TGACACTCAA 0.965732 -143 AAGTTTTACTTGAGCCAAATCAATTAATCATTA 11 166 0 TGACAATCAA 0.986564 -88 CCGCCTTAATTTATTTAAAACAACAATATACCT 13 45 1 TTATAAACAA 0.641406 -117 AAGATAAGCTTGATCAAGCTCAAACTTTAGCAT 13 95 1 TGACACTCAA 0.965732 -67 TTTATTTAATTGACTTAGATCAAATTGAC 15 7 0 TGATAATCAA 0.964257 -294 AAACATTTAATGATCTAAATCAATTTTTTTGCT 16 83 0 TGACAATCAA 0.986564 -166 ATAGGTTTATTGATTTAAAACAAAATTTAATAA 16 137 0 TGATAAACAA 0.95781 -112 *** * * ***** Masking position 3 Map Score: 16.6313 Number of sites scoring better than the average of aligned sites = 62 Number in coding regions = 42 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 17 Fraction of orfs with sites within 600 bp upstream = 0.00273049 Motif number 5 CCTTTTTGGATGCCTTTTTCTGCCGCTAAT 1 18 0 TGCCTTTTTC 0.739537 -283 GCGGCGATTATACCAATTTTTCTCGTATAA 2 38 0 TACCAATTTT 0.911512 -45 CAAAACAGCATAGCAATTTTGACTATGCTG 4 24 0 TAGCAATTTT 0.745971 -182 ATTGAAAAACTACCTATTTTGGGTTGTTTT 4 120 1 TACCTATTTT 0.911512 -86 GCTTAGTATTTACCACTTTCTTTGATGCAG 6 129 1 TACCACTTTC 0.860636 -172 ACGCAGCCTTTTCCACTTTTACCGCACATT 6 225 0 TTCCACTTTT 0.916905 -76 CTTCCTCTTTTATTGATGGGA 6 290 0 TTCCTCTTTT 0.916905 -11 AACTCAATCTTAGCTTTTTTGAGGTAGATC 8 31 1 TAGCTTTTTT 0.866405 -151 GTGGGCATTGTGCCATTTTTCGTTACAAAT 8 107 0 TGCCATTTTT 0.907251 -75 AACAACAATATACCTCTTTTTGAGTATTTT 13 63 1 TACCTCTTTT 0.955107 -99 TCCTCAAATTTACCTTTTTTTTCTTTATTG 14 86 0 TACCTTTTTT 0.957894 -179 TTACCAAAATTTCCATTTTTTTAACCGCAC 14 242 1 TTCCATTTTT 0.921869 -23 GTGATCTATATAGCATTTTTTACTATTTTT 15 81 1 TAGCATTTTT 0.866405 -220 TTAAATGTTTTTCCTTTTTTAAAAAGTGAA 16 106 1 TTCCTTTTTT 0.921869 -143 ********** Masking position 7 Map Score: 14.9319 Number of sites scoring better than the average of aligned sites = 351 Number in coding regions = 295 Number in noncoding regions = 56 Number of orfs with sites within 600 bp upstream = 47 Fraction of orfs with sites within 600 bp upstream = 0.00754899 Motif number 6 GCGATATGGTAAAAATTACTTCTCGTCGTG 1 47 1 AAAAATTACT 0.709045 -254 CAAATAATTGAAAAACTACCTATTTTGGGT 4 114 1 AAAAACTACC 0.963441 -92 CGCGGACGTAATAAACCACCTCGTGGCTTA 6 104 1 ATAAACCACC 0.944951 -197 AAAACCATGTAAAAATCAACCGCACTTTAT 6 256 1 AAAAATCAAC 0.850979 -45 GAATGGGTAGAAAAATCACTTGATCTGATT 10 49 1 AAAAATCACT 0.850979 -152 GAAAACCTATAAAAACCACTGTTTTATGAT 10 107 1 AAAAACCACT 0.945722 -94 AACATATTAGATAAACTAACACGCCACTAT 11 44 1 ATAAACTAAC 0.673944 -210 TTAAAGGTTAAAAAAACACCAGTTATTATA 15 157 0 AAAAAACACC 0.88901 -144 AATTAAAGAGAAAAACCACCGCACTTTTAT 17 24 0 AAAAACCACC 0.984064 -34 AAAAATCGCTAAAAACTAACCGCACT 18 7 0 AAAAACTAAC 0.881456 -35 ********** Masking position 5 Map Score: 7.59571 Number of sites scoring better than the average of aligned sites = 377 Number in coding regions = 301 Number in noncoding regions = 76 Number of orfs with sites within 600 bp upstream = 59 Fraction of orfs with sites within 600 bp upstream = 0.00947639 Motif number 7 ATTGATGAATTTAATATAGAATATGCCTTC 3 38 1 TTAATATAGA 0.692707 -47 TGAACTTTATTTGTTATAGATCAAAAAATC 4 86 0 TTGTTATAGA 0.94563 -120 TTTGTTTTAGATCATTCATTG 5 170 0 TTGTTTTAGA 0.953851 -11 AAATTGACTATGGATTTAAAAATCCGTTAG 11 75 0 TGGATTTAAA 0.71036 -179 AGGTATATTGTTGTTTTAAATAAATTAAGG 13 48 0 TTGTTTTAAA 0.883635 -114 TTTTATTTAATTGACTTAGATCAAATTGAC 15 11 0 TTGACTTAGA 0.766111 -290 GATCACATTTTTGATATAAATACAAAAATA 15 57 0 TTGATATAAA 0.84065 -244 AAAACACCAGTTATTATAGAGATAATCCAA 15 145 0 TTATTATAGA 0.728231 -156 TGCTCAATTTTGGTTATAGACCAAAACCTC 16 47 0 TGGTTATAGA 0.869716 -202 AGCAAAAAAATTGATTTAGATCATTAAATG 16 83 1 TTGATTTAGA 0.94563 -166 TTATTAAATTTTGTTTTAAATCAATAAACC 16 137 1 TTGTTTTAAA 0.883635 -112 ********** Masking position 8 Map Score: 6.58557 Number of sites scoring better than the average of aligned sites = 192 Number in coding regions = 152 Number in noncoding regions = 40 Number of orfs with sites within 600 bp upstream = 25 Fraction of orfs with sites within 600 bp upstream = 0.00401542 Motif number 8 CCTTTTTCTGCCGCTAATTTTTCGC 1 3 0 CCGATTTTTC 0.941188 -298 ATTATGCCTCCCCAACTTTTTCAATATTTACC 1 279 0 CCCATTTTTC 0.972299 -22 CGTATAATAGGGCAAATTTTTTCCAAGGTTGAT 2 12 0 GGCATTTTTC 0.879367 -71 GTATAATCGCCGCCAATTTTTTCACGAACAAGA 2 55 1 CGCATTTTTC 0.985634 -28 CCACTTTTACCGCACATTTTTTGAAGTCGGTTT 6 210 0 CGCATTTTTG 0.879461 -91 ATGGTTTTTACGCAGCCTTTTCCACTTTTACCG 6 231 0 CGCCTTTTCC 0.916264 -70 ATCACAAAATCCGATACNTTTCCATCTTTAGAC 8 58 1 CCGANTTTCC 0.508029 -124 AAAACGCTCCAATTTTCCACCGCACTT 10 5 1 CGCCATTTTC 0.876147 -196 CGATCTGTATCGCAAAGTTTTTCTGAAAACCTA 10 83 1 CGCATTTTTC 0.985623 -118 GCTATAATGGCACGGAATTTTTCTGTTCTTTAA 10 164 1 CACATTTTTC 0.870568 -37 CTAAAAAGTGCGGTGCATTTTTCAT 12 3 0 CGGCTTTTTC 0.940446 -41 AGTGCGGTTAGTTTTTAGCGATTTTTT 18 5 1 CGGATTTTTA 0.691783 -37 TTTTTACCGCACTTTTTCATTAACTTTG 19 121 0 ACCATTTTTC 0.715789 -18 *** * ****** Masking position 9 Map Score: 9.93404 Number of sites scoring better than the average of aligned sites = 342 Number in coding regions = 286 Number in noncoding regions = 56 Number of orfs with sites within 600 bp upstream = 49 Fraction of orfs with sites within 600 bp upstream = 0.00787022 Motif number 9 ATGCTTGTAATGGCTGTGGGGCTTGTGTACAA 5 116 1 TGCTGGGGGC 0.996712 -65 TTTTTCAATCTGACTGTGGGGGAACGATATA 11 233 1 TGCTGGGGGG 0.99774 -21 TGCCTTCCCCTGCTTGCGGGGGAAGGTGCCCG 19 20 1 TGTTGGGGGG 0.988314 -119 CGGGGGAAGGTGCCCGAAGGGCGGAAGGGGGA 19 36 1 TGCCGAGGGC 0.963123 -103 TGTCGCGAAGTGACTGAGGGGGATACGTAATC 19 66 0 TGCTGGGGGG 0.99774 -73 ** *** ***** Masking position 1 Map Score: 4.55927 Number of sites scoring better than the average of aligned sites = 8 Number in coding regions = 5 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 ATTTTTACCATATCGCCTTTTTGGATGCCTTT 1 31 0 TACGCCTTTT 0.969647 -270 CTTTGCCATTTAATGCCTTCATATTCCAGTGA 1 165 0 TATGCCTTAT 0.873679 -136 ACGAATACCTTAACACCATCTTGGGGTGAGGC 1 214 1 TACACCATTT 0.714741 -87 TGCCTTCAAATATAACCTTAATAGGAGAAATA 3 61 1 TAAACCTTAT 0.661189 -24 ATCTTAATTTTATCGCCATGACGTAAACCACG 6 32 0 TACGCCATAC 0.803533 -269 AAATTAAAAATAGCACCTTGATAGGTGCTATT 9 24 0 TACACCTTAT 0.952167 -85 CATACTTGATTAGCGACTTTATCTGCGCATCA 9 67 1 TACGACTTAT 0.860408 -42 GGCGGTATAAAACCGCCTTAATTTTGAGTATT 13 18 0 AACGCCTTAT 0.917503 -144 GGCGGTTTTATACCGCCTTAATTTATTTAAAA 13 33 1 TACGCCTTAT 0.986024 -129 TTATTTAAGGCATCGCCTTGTTAATCATTGTT 15 246 1 CACGCCTTTT 0.88185 -55 ** ****** ** Masking position 9 Map Score: 3.97889 Number of sites scoring better than the average of aligned sites = 210 Number in coding regions = 183 Number in noncoding regions = 27 Number of orfs with sites within 600 bp upstream = 20 Fraction of orfs with sites within 600 bp upstream = 0.00321234 Motif number 11 TAATCCCTTGCAAAATTCATTAAACCTTAGATTT 4 57 1 CAAATTAAAA 0.972904 -149 TTACAAGCATCGAAATTAACTAAAGGTTGTGCTA 5 92 0 CGAATTAAAA 0.905096 -89 TGCGACAGACCCAATTTCAAAAGAAACCGACTTC 6 187 1 CCAATTAAGA 0.90751 -114 TCAAAAGAAACCGACTTCAAAAAATGTGCGGTAA 6 203 1 CCGATTAAAA 0.828015 -98 TTTGTTATTCCAAAGTTTATTAAAACATCAATCT 11 102 1 CAAATTAAAA 0.972904 -152 AAGAATTTTACCAACTAAATAAAAGGGTTCATAA 14 127 1 CCAATAAAAA 0.764615 -138 GGTCTATAACCAAAATTGAGCAAATAATAGCAAA 16 55 1 CAAATTAAAA 0.972904 -194 TGATTTAAAACAAAATTTAATAAATTCACTTTTT 16 126 0 CAAATTAAAA 0.972904 -123 TTGAGTTGCGAAAATTTCATCAAATATTAGAATA 16 196 1 AAAATTAAAA 0.846901 -53 AAAAATCCTTAAAAATTAAAGAGAAAAACCACCG 17 33 0 AAAATTAAGA 0.679801 -25 ATGGGTGGAGCAAAGTTAATGAAAAAGTGCGGTA 19 111 1 CAAATTAAAA 0.972904 -28 **** ** * *** Masking position 9 Map Score: 8.77927 Number of sites scoring better than the average of aligned sites = 105 Number in coding regions = 74 Number in noncoding regions = 31 Number of orfs with sites within 600 bp upstream = 28 Fraction of orfs with sites within 600 bp upstream = 0.00449727 Motif number 12 TGTTATAGATCAAAAAATCTAAGGTTTAATGAATTT 4 69 0 CAAAATAGTT 0.970174 -137 GAAAACAACCCAAAATAGGTAGTTTTTCAATTATTT 4 115 0 CAAAATATTT 0.700021 -91 CGATTCGTTTCAAATTACAAATGGGTGGCGTAGCAC 5 62 1 CAATAAAGGT 0.800318 -119 TACGTCATGGCGATAAAATTAAGATTTCATCTCGTC 6 39 1 CATAATAGTT 0.879343 -262 TGATCTACCTCAAAAAAGCTAAGATTGAGTTGAGAG 8 26 0 CAAAATAGTT 0.970174 -156 TTTTTCGTTACAAATTAATAACGTTTTTATGTCTA 8 86 0 CAATAAAGT 0.258008 -96 GATAAAGTCGCTAATCAAGTATGTTTCATTAATAAA 9 54 0 CAATATAGTT 0.970174 -55 ATTTTTCTACCCATTCATTTATGGTTAAAGTGCGGT 10 29 0 CATTATAGTT 0.879343 -172 GTTAGTTTATCTAATATGTTAAGTTTAACTATTATT 11 28 0 CAATTTAGTT 0.790249 -226 CGTAAGATACCAAAAGAAAAAAGTTTTTCTACTCGC 13 131 0 CAAAAAAGTT 0.920411 -31 TTACTCAACTCCAATCAGCTAAGTTTAAATTGACTT 15 203 0 CAATATAGTT 0.970174 -98 CGATCTACTTCTAAAGAGTTATGTGTTTGAGTTGCG 16 170 1 CAAAATAGGT 0.918521 -79 * *** * ** * ** Masking position 11 Map Score: 11.3898 Number of sites scoring better than the average of aligned sites = 84 Number in coding regions = 59 Number in noncoding regions = 25 Number of orfs with sites within 600 bp upstream = 34 Fraction of orfs with sites within 600 bp upstream = 0.00546097 Motif number 13 TTGTACACAAGCCCCACAGCCATTACAAGCA 5 117 0 GCCCCACAGC 0.983855 -64 TATATCGTTCCCCCACAGTCAGATTGAAAA 11 234 0 CCCCCACAGC 0.995363 -20 CGGGCACCTTCCCCCGCAAGCAGGGGAAGGC 19 21 0 CCCCCGCAAC 0.971894 -118 ATACGTAATCCCCCTTCCGCCCTTCGGGCAC 19 45 0 CCCCTTCCGC 0.948805 -94 GATTACGTATCCCCCTCAGTCACTTCGCGAC 19 66 1 CCCCCTCAGC 0.995363 -73 ********* * Masking position 7 Map Score: 1.55519 Number of sites scoring better than the average of aligned sites = 8 Number in coding regions = 4 Number in noncoding regions = 4 Number of orfs with sites within 600 bp upstream = 4 Fraction of orfs with sites within 600 bp upstream = 0.000642467 Motif number 14 CTTTAATATAGCCACGACGAGAAGTAATTT 1 59 0 GCCACGACGA 0.981156 -242 ACGTTTTGTAACCACGGCGACCGCTTTAAT 1 82 0 ACCACGGCGA 0.865595 -219 AAATCATTTCGCCTCGACGAGATGAAATCT 6 60 0 GCCTCGACGA 0.989467 -241 AAGCTGACCTGCATCAAAGAAAGTGGTAAA 6 137 0 GCATCAAAGA 0.763764 -164 CTTTATCTGCGCATCAACGAAAAAAACGAC 9 83 1 GCATCAACGA 0.954326 -26 ATAGACCAAAACCTCAACGAAATCTGTTTT 16 32 0 ACCTCAACGA 0.954326 -217 ********** Masking position 10 Map Score: 1.53774 Number of sites scoring better than the average of aligned sites = 31 Number in coding regions = 28 Number in noncoding regions = 3 Number of orfs with sites within 600 bp upstream = 2 Fraction of orfs with sites within 600 bp upstream = 0.000321234 Motif number 15 ATATGCCTTCAAATATAACCTTAATAGGAGA 3 58 1 AAATATAACT 0.577954 -27 ATCCTCCAATCAATAGAAAGTAAAAATAAAT 8 158 0 CAATAGAAGT 0.951352 -24 TTTATAAGCACAATAGCACCTATCAAGGTGC 9 13 1 CAATAGCACT 0.871902 -96 ATAAAATTAAAAATAGCACCTTGATAGGTGC 9 28 0 AAATAGCACT 0.874122 -81 TTTTAGTGCAAACTAGAAAGTGCG 12 30 1 AACTAGAAGT 0.841251 -14 GGAGAAATAGAATGTTATATGCGAT 14 5 1 AAATAGAAGT 0.95227 -260 CTGTTTTTAACAATAGAAGGAATACATT 16 8 0 CAATAGAAGA 0.778003 -241 TACAGAGGGAAAATAGAAAGTGACAGTATTC 16 225 0 AAATAGAAGT 0.952271 -24 ******** ** Masking position 5 Map Score: 0.864422 Number of sites scoring better than the average of aligned sites = 69 Number in coding regions = 50 Number in noncoding regions = 19 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802