AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_ecoli.txt -z/home/amcguire/genomes/ecoli.fna -ifnr_ecoli_opreg_100.orf -g0.5 -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 = 0.5 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 cydA 300 cytochrome d terminal oxidase, polypeptide subunit I #2 pflA 191 pyruvate formate lyase activating enzyme 1 #3 pflB 54 formate acetyltransferase 1 #4 focA 300 probable formate transporter (formate channel 1) #5 ndh 300 respiratory NADH dehydrogenase #6 narK 300 nitrite extrusion protein #7 narG 300 nitrate reductase 1, alpha subunit #8 fdnG 231 formate dehydrogenase-N, nitrate-inducible, alpha subunit #9 ansB 175 periplasmic L-asparaginase II #10 nirB 261 nitrite reductase (NAD(P)H) subunit #11 nirC 300 nitrite reductase activity #12 nrfA 300 periplasmic cytochrome c(552): plays a role in nitrite reduction #13 nrfB 38 formate-dependent nitrite reductase; a penta-haeme cytochrome c #14 nrfE 79 formate-dependent nitrite reductase; possible assembly function Motif number 1 AGATAAATTGTTCTCGATCAAATTGGCTGA 1 6 1 AATTGTTTCA 0.954983 -295 TTTAGCTATAAATTGATCACCGTCGAAAAATGCAA 1 51 1 AATTGATTCG 0.954629 -250 TTAGATTTGACTGAAATCGTACAGTAAAA 2 5 1 ATTTGACTCG 0.641238 -187 ATAGATGAGAAATTGATATAGATCATATCTCGCCT 4 228 0 AATTGATTCA 0.986392 -73 GTCATACCAAAATTGATGTTAATCAAGTTTTGTTG 5 152 0 AATTGATTCA 0.986392 -149 CTTTATCTATCATTGATATTTATCATTACCCATAG 6 191 0 CATTGATTCA 0.913599 -110 GCTAAAGGCAATTTGATGTAAATCAAACGATAAGA 6 229 0 ATTTGATTCA 0.954983 -72 ACAGCGTGGGAATTGATAACGATCAAGAGTGATGG 7 197 0 AATTGATTCA 0.986392 -104 CGCCTTCGCAAATTGACCTACCTCAATAGCGGTAG 8 100 0 AATTGACTCA 0.954629 -132 TCACGTTGTAAATTGTTTAACGTCAAATTTCCCAT 9 103 1 AATTGTTTCA 0.954983 -73 GACTTAAGAAAATTTATACAAATCAGCAATATACC 10 140 1 AATTTATTCA 0.893831 -122 ATAAAGGTGAATTTGATTTACATCAATAAGCGGGG 10 188 1 ATTTGATTCA 0.954983 -74 ACGGCAGGGTAATTTTTGAAGGTCAGCAACAAAAG 12 39 1 AATTTTTTCA 0.711308 -262 ATGCACTTACAATTGATTAAAGACAACATTCACAG 12 158 1 AATTGATACA 0.877064 -143 ******* *** Masking position 4 Map Score: 18.5197 Number of sites scoring better than the average of aligned sites = 81 Number in coding regions = 46 Number in noncoding regions = 35 Number of orfs with sites within 600 bp upstream = 45 Fraction of orfs with sites within 600 bp upstream = 0.00722775 Motif number 2 AATTTGAGTTTTTATTAACATGTTTGCAAC 1 148 1 TTTATTAACA 0.897077 -153 AAGTGGATTTTTTATTTACTGCGTACTTCG 3 18 0 TTTATTTACT 0.560455 -37 ATGCTCCCTTTTAATTAACTGTTTTAGCGG 4 82 1 TTAATTAACT 0.815448 -219 GAGTAAATATTTGATTATCCAAATAAAAAT 4 156 0 TTGATTATCC 0.870042 -145 GCAACAAAACTTGATTAACATCAATTTTGG 5 151 1 TTGATTAACA 0.957078 -150 AACATAGCTCTTAATTAACAACAGGTTACA 5 235 0 TTAATTAACA 0.933255 -66 TTAATAACCATTAATTAACAATTGGTTAAT 5 263 1 TTAATTAACA 0.933255 -38 CCCCCTTAAATTTATTAACCAATTGTTAAT 5 276 0 TTTATTAACC 0.890724 -25 ATCTTATCGTTTGATTTACATCAAATTGCC 6 228 1 TTGATTTACA 0.911681 -73 ATAAAACGTCTTAATTTACAGTCTGTTATG 7 110 1 TTAATTTACA 0.866186 -191 GTGGTGGCTGTTAATTATCCTAAAGGGGTA 7 139 1 TTAATTATCC 0.807623 -162 AAAGGTGAATTTGATTTACATCAATAAGCG 10 190 1 TTGATTTACA 0.911681 -72 CTGTAAACATTTGATTATCCTTTAAAAAAT 11 39 0 TTGATTATCC 0.870042 -262 ********** Masking position 4 Map Score: 13.5141 Number of sites scoring better than the average of aligned sites = 150 Number in coding regions = 93 Number in noncoding regions = 57 Number of orfs with sites within 600 bp upstream = 71 Fraction of orfs with sites within 600 bp upstream = 0.0114038 Motif number 3 TCCTTACAATAAACAGGTTTTTGTTGAAGCAAATTTGCATT 1 79 0 AAGTGTTGCA 0.909277 -222 AGGCTCCACGAAAGTGGGGCCTTTTTTAGCGCGAGAGCCTT 2 52 1 AAGTTTTGCG 0.952906 -140 AAATTAACAAATGAGTTGAATTTTTTCCGCATCCTCCGCTA 4 106 0 ATTTTTTGCA 0.903805 -195 ATAGGCCCGTAACTCGCATGGTTTTTATGCAAATACGGAGT 4 182 0 AAGTTTTGCA 0.98316 -119 TCACCCGGTAAAGTCGCCTATCTTTTCAGCAACAAAACTTG 5 123 1 AAGCTTTGCA 0.909277 -178 TTACATCGGTAAGGGTAGGGATTTTACAGCACCGTGAAAAA 6 119 1 AATTTTTGCA 0.963539 -182 GCACCGTGAAAAATCTCATAATTTTTATGAAGTCACTGTAC 6 147 1 AATTTTTGAA 0.654717 -154 TAGTTATTTAAACTATTAAGATTTTTATGCAGATGGGTATT 7 64 0 AATTTTTGCA 0.963539 -237 GCCGTTAAAAATTAAGCTGAATTTTATAGCATTTTTTTAAC 8 32 1 ATGTTTTGCA 0.954038 -200 TCAATTTGCGAAGGCGGATTATTTTGTGGCAAACAGATGTT 8 119 1 AAGTTTTGCA 0.98316 -113 CTAACAGTAAAATTCTGAATCTTTTTGCGCGAAATCAAAAA 8 161 0 AATTTTTGCG 0.901563 -71 AAACCCGCTCATTTTGTCTATTTTTTGCACAAACATGAAAT 10 84 1 ATGTTTTACA 0.59829 -178 ** * **** *** Masking position 1 Map Score: 9.14335 Number of sites scoring better than the average of aligned sites = 156 Number in coding regions = 110 Number in noncoding regions = 46 Number of orfs with sites within 600 bp upstream = 56 Fraction of orfs with sites within 600 bp upstream = 0.00899454 Motif number 4 AAAATGCAAATTTGCTTCAACAAAAACCTGTT 1 77 1 TTTGCCAACA 0.943602 -224 ACGTATATATTACGCCGCAAAATCCTTACAAT 1 110 0 TACGCCAAAA 0.800955 -191 CTTTAAGGTGACTGCCAAAACAGACTCGACGT 2 111 1 ACTGCAAACA 0.633625 -81 GCCTTCGAGCTGCGCACCAACACGGCCTCAGA 2 144 1 TGCGCCAACA 0.873558 -48 TTCCGCATCCTCCGCTAAAACAGTTAATTAAA 4 91 0 TCCGCAAACA 0.956158 -210 TTACTCCGTATTTGCATAAAAACCATGCGAGT 4 180 1 TTTGCAAAAA 0.912693 -121 CTCTCACAAATTCGCTCAAATAATAAACAATA 5 74 1 TTCGCAAATA 0.715435 -227 GCCTATCTTTTCAGCAACAAAACTTGATTAAC 5 138 1 TCAGCCAAAA 0.876478 -163 TTAATACCCATCTGCATAAAAATCTTAATAGT 7 62 1 TCTGCAAAAA 0.933463 -239 AGAACATCTGTTTGCCACAAAATAATCCGCCT 8 130 0 TTTGCCAAAA 0.935245 -102 TCTTTTTGATTTCGCGCAAAAAGATTCAGAAT 8 159 1 TTCGCAAAAA 0.933463 -73 TTGTCTATTTTTTGCACAAACATGAAATATCA 10 97 1 TTTGCAAACA 0.923722 -165 TTTTTGAAGGTCAGCAACAAAAGTTGATTAAT 12 51 1 TCAGCCAAAA 0.876478 -250 ***** ***** Masking position 9 Map Score: 9.28755 Number of sites scoring better than the average of aligned sites = 474 Number in coding regions = 409 Number in noncoding regions = 65 Number of orfs with sites within 600 bp upstream = 77 Fraction of orfs with sites within 600 bp upstream = 0.0123675 Motif number 5 TGAATGCACACAAAAACGGCGTAAAGAAAGGTTGCAA 1 171 0 CAAGGCGAAA 0.98451 -130 TCAGATGGGCCACATCTGGAGAAACACCGCA 2 171 1 CAAGGAGAAC 0.98451 -21 ACTGTTTTAGCGGAGGATGCGGAAAAAATTCAACTCA 4 99 1 CGATGCGAAA 0.837118 -202 GGTTTTTATGCAAATACGGAGTAAATATTTGATTATC 4 167 0 CAAGGAGAAA 0.970014 -134 AACCACACGGCAAATAAGGAGTAACTCTTTCCGGGTA 6 75 0 CAAGGAGAAC 0.98451 -226 GTAGCGTTCACGTAACTGGAGGAATGAA 9 158 1 CGAGGAGAAA 0.963877 -18 GTGAACAGTTCAGAACCGGCGATAATCACCAGCGTTA 11 264 0 CAAGGCGTAC 0.951655 -37 ACCGCCATTGCAACAATGGCGCAATTCGGATGAAGCC 12 271 1 CACGGCGAAC 0.966861 -30 CGTTCCGCCTCGCAAGGGGCGGAAAACACAATGGA 13 14 1 CGAGGCGAAC 0.990385 -25 ** * **** ** * Masking position 14 Map Score: 8.06723 Number of sites scoring better than the average of aligned sites = 212 Number in coding regions = 181 Number in noncoding regions = 31 Number of orfs with sites within 600 bp upstream = 33 Fraction of orfs with sites within 600 bp upstream = 0.00530035 Motif number 6 GATCAAATTGGCTGAAAGGCGGTAATTTAG 1 26 1 GCTGAAAGGC 0.937917 -275 TTATCAGAGGGCCGACAGGCTCCCACAGGA 7 273 1 GCCGACAGGC 0.981756 -28 CGCACCACTGCCTGACAGGCCAGTTAAAAA 8 65 0 CCTGACAGGC 0.904976 -167 CGACGATAGTGCCGTCCGGCATGAGCAA 10 9 0 GCCGTCCGGC 0.547288 -253 CGGCACTATCGTCGTCCGGCCTTTTCCTCT 10 25 1 GTCGTCCGGC 0.852119 -237 CGGGTTATTTGCCGACAGGCGTGCAATGCG 11 101 0 GCCGACAGGC 0.981756 -200 TGACCCAAAAGCCGAGCGGGTTATTTGCCG 11 117 0 GCCGAGCGGG 0.884567 -184 CCCTTGCGAGGCGGAACGGGG 13 2 0 GCGGAACGGG 0.866485 -37 ********** Masking position 4 Map Score: 7.29246 Number of sites scoring better than the average of aligned sites = 617 Number in coding regions = 593 Number in noncoding regions = 24 Number of orfs with sites within 600 bp upstream = 30 Fraction of orfs with sites within 600 bp upstream = 0.0048185 Motif number 7 CCATGTGAATGCACACAAAAACGGCGTAAAGAAAG 1 178 0 GCAAAAAGGC 0.989374 -123 ACAGTAAAAAGCGTACAATAAAGGCTCCACGAAAG 2 31 1 GCAAAAAGGC 0.98923 -161 AAAGGCTCTCGCGCTAAAAAAGGCCCCACTTTCGT 2 59 0 GCTAAAAGCC 0.920053 -133 AGTATAGATAGCTGACAAAAAAGGCTCTCGCGCTA 2 78 0 GCAAAAAGGC 0.989391 -114 CCTTCGAGCTGCGCACCAACACGGCCTCAGATGGG 2 145 1 GCACACAGGC 0.932681 -47 CTCCGTATTTGCATAAAAACCATGCGAGTTACGGG 4 183 1 GCAAACCTGC 0.881976 -118 CGAGTTACGGGCCTATAAGCCAGGCGAGATATGAT 4 207 1 GCAAACCGGC 0.983178 -94 AAGTTTTGTTGCTGAAAAGATAGGCGACTTTACCG 5 128 0 GCAAAATGGC 0.958248 -173 TCAGCCAATAGCCGAGAATACTGCCATTCCAGAAT 6 30 0 GCAAAACGCC 0.981248 -271 GTCGTGAAAAACAATAAAAACCGCCATTGCAACAA 12 252 1 ACTAAACGCC 0.564169 -49 ** * ** ** *** Masking position 8 Map Score: 8.32439 Number of sites scoring better than the average of aligned sites = 490 Number in coding regions = 437 Number in noncoding regions = 53 Number of orfs with sites within 600 bp upstream = 57 Fraction of orfs with sites within 600 bp upstream = 0.00915516 Motif number 8 TGTAAGGATTTTGCGGCGTAATATATACGT 1 112 1 TTGCGGCGTA 0.851548 -189 ATGCACACAAAAACGGCGTAAAGAAAGGTT 1 175 0 AAACGGCGTA 0.917992 -126 GATTTTTTATTTACTGCGTACTTCGACAAC 3 13 0 TTACTGCGTA 0.885856 -42 TTTTATGCAAATACGGAGTAAATATTTGAT 4 171 0 ATACGGAGTA 0.961907 -130 CACACGGCAAATAAGGAGTAACTCTTTCCG 6 79 0 ATAAGGAGTA 0.940898 -222 ATCATTACCCATAGTGAGTACAGTGACTTC 6 175 0 ATAGTGAGTA 0.788315 -126 CAGATGGGTATTAAGGAGTATTCCCCATGG 7 46 0 TTAAGGAGTA 0.915783 -255 GAGCTAAGGGATAATGCGTAGCGTTCACGT 9 141 1 ATAATGCGTA 0.877501 -35 AATATACCCATTAAGGAGTATATAAAGGTG 10 167 1 TTAAGGAGTA 0.915783 -95 GCCCATCACCAAAGGGCGTACGGATGGATC 11 215 0 AAAGGGCGTA 0.85403 -86 ********** Masking position 9 Map Score: 6.18122 Number of sites scoring better than the average of aligned sites = 258 Number in coding regions = 148 Number in noncoding regions = 110 Number of orfs with sites within 600 bp upstream = 70 Fraction of orfs with sites within 600 bp upstream = 0.0112432 Motif number 9 AATAAAGTAACAATATCGATCGTATTTATT 4 46 0 CAATATCGAT 0.801861 -255 ATGTTATTCTCAATAGCGAAGAACATTTTC 5 200 1 CAATAGCGAA 0.946506 -101 ATACTTCAGCCAATAGCCGAGAATACTGCC 6 40 0 CAATAGCCGA 0.85812 -261 TAAACATTAGCAATGTCGATTTATCAGAGG 7 253 1 CAATGTCGAT 0.865213 -48 TGACCTACCTCAATAGCGGTAGAAAAACGC 8 92 0 CAATAGCGGT 0.973364 -140 TACGCGCCCGCCATGGCGGAGCTGACCCAA 11 139 0 CCATGGCGGA 0.939007 -162 GCCATTGTTGCAATGGCGGTTTTTATTGTT 12 261 0 CAATGGCGGT 0.98304 -40 GCCATTGCAACAATGGCGCAATTCGGATGA 12 274 1 CAATGGCGCA 0.942733 -27 ********** Masking position 3 Map Score: 4.71306 Number of sites scoring better than the average of aligned sites = 616 Number in coding regions = 593 Number in noncoding regions = 23 Number of orfs with sites within 600 bp upstream = 30 Fraction of orfs with sites within 600 bp upstream = 0.0048185 Motif number 10 GTCGAAAAATGCAAATTTGCTTCAACAAAA 1 72 1 GCAAATTTGC 0.484879 -229 GTTAAATATCGGTAATTTGTATTTAATAAA 4 22 1 GGTAATTTGT 0.901255 -279 AATATTTACTCCGTATTTGCATAAAAACCA 4 175 1 CCGTATTTGC 0.810092 -126 TATTATTTGAGCGAATTTGTGAGAGTGATA 5 69 0 GCGAATTTGT 0.844065 -232 AAGAGTTACTCCTTATTTGCCGTGTGGTTA 6 83 1 CCTTATTTGC 0.897137 -218 TGGGTATATTGCTGATTTGTATAAATTTTC 10 147 0 GCTGATTTGT 0.835877 -115 AAGCCGAGCGGGTTATTTGCCGACAGGCGT 11 109 0 GGTTATTTGC 0.963381 -192 TTTCACGCTCGGTAATTTGCTCGATCCATC 11 193 1 GGTAATTTGC 0.952828 -108 TTACCCTGCCGTTTATTTGCACAATTCTAC 12 21 0 GTTTATTTGC 0.834708 -280 TTCACAGTGTGGTTATTTGTTACACATAGG 12 186 1 GGTTATTTGT 0.918378 -115 ********** Masking position 5 Map Score: 5.1054 Number of sites scoring better than the average of aligned sites = 356 Number in coding regions = 312 Number in noncoding regions = 44 Number of orfs with sites within 600 bp upstream = 45 Fraction of orfs with sites within 600 bp upstream = 0.00722775 Motif number 11 TAACTCTTTCCGGGTATGGGTATACTTCAGCCA 6 58 0 CGATGGGTAT 0.940052 -243 GTCACTGTACTCACTATGGGTAATGATAAATAT 6 178 1 TCATGGGTAA 0.970111 -123 TAAGGAGTATTCCCCATGGGTAACATATTAATG 7 32 0 TCATGGGTAA 0.970111 -269 AAGATTTTTATGCAGATGGGTATTAAGGAGTAT 7 55 0 TGATGGGTAT 0.935375 -246 TGTTAATTATCCTAAAGGGGTATCTTAGGAATT 7 147 1 CCAGGGGTAT 0.973444 -154 CTTTCCTCTTTTTTCAGGGGTATTACTGCGCGA 8 207 0 TTAGGGGTAT 0.790716 -25 ATCCCTTAGCTCTGTATGGGAAATTTGACGTTA 9 120 0 TCATGGGAAA 0.820373 -56 TTTATATACTCCTTAATGGGTATATTGCTGATT 10 160 0 CCATGGGTAT 0.980946 -102 ACTGACTAACTCTAAAGTGGTATTTTACATGCA 12 130 1 TCAGTGGTAT 0.747217 -171 ACATTGCTCGCCCCTATGTGTAACAAATAACCA 12 195 0 CCATGTGTAA 0.754436 -106 ** ******** Masking position 6 Map Score: 4.77694 Number of sites scoring better than the average of aligned sites = 157 Number in coding regions = 138 Number in noncoding regions = 19 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 12 GGTAAAGTCGCCTATCTTTTCAGCAACAAA 5 129 1 CCTATCTTTT 0.712245 -172 TGCTTTCCTCTTTTTTCAGGGGTATT 8 216 0 CCTCTTTTTT 0.953559 -16 TCCTCTATTTTAAGACGGCAT 9 2 1 CCTCTATTTT 0.953559 -174 CCGGCCTTTTCCTCTCTTCCCCCGCTACGT 10 40 1 CCTCTCTTCC 0.952173 -222 CCGCTACGTGCATCTATTTCTATAAACCCG 10 61 1 CATCTATTTC 0.784337 -201 TTTTGCCTCGATTTCTTTTCTATTA 10 247 0 CCTCGATTTC 0.896376 -15 TCAGTATCTTCCTCTTTTTCAACAGCATGC 12 105 0 CCTCTTTTTC 0.97021 -196 CCAGAAACCACCTCTTTTCTGGC 14 4 0 CCTCTTTTCT 0.920805 -76 ********** Masking position 7 Map Score: 3.27594 Number of sites scoring better than the average of aligned sites = 123 Number in coding regions = 98 Number in noncoding regions = 25 Number of orfs with sites within 600 bp upstream = 28 Fraction of orfs with sites within 600 bp upstream = 0.00449727 Motif number 13 TTTTATTAACATGTTTGCAACCTTTCTTTACGCC 1 157 1 ATGTGACCTT 0.970051 -144 CTATTGGGGCATGCGTGTGACCCTTTCTAACGGG 1 239 1 ATGTGACCCT 0.970832 -62 ATGCCTGATGCGCTTCTTATCAGG 5 1 1 ATGTGGCGCT 0.961308 -300 TGAGAATAACATGAATGGTGCATTGGTCATACCA 5 178 0 ATGTGGCATT 0.902847 -123 TTAATGAATGTGACGATACATTCTGGA 6 4 1 ATGTGACGAT 0.902843 -297 ACTCGTTTCGATGTCTGCCACCTTAGTGTCTGTA 6 264 0 ATGTGACCTT 0.979691 -37 CAGGCGTGCAATGCGCGCAGCGTTAGCCGCACAC 11 82 0 ATGCGGCGTT 0.954341 -219 CCCTTTGGTGATGGGCGCGACCTTTGGTATCGCC 11 229 1 ATGCGACCTT 0.951436 -72 *** ** ***** Masking position 1 Map Score: 2.92665 Number of sites scoring better than the average of aligned sites = 70 Number in coding regions = 64 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 Motif number 14 TTTCATTGCTGTAACCTGTTGTTAATTAAGAGCT 5 226 1 GACTGTGTTA 0.842624 -75 TACTCCTTATTTGCCGTGTGGTTAGTCGCTTTAC 6 89 1 TCCTGTGTTA 0.970964 -212 ATGAGATTTTTCACGGTGCTGTAAAATCCCTACC 6 132 0 TCGTGCGTAA 0.772399 -169 TAAGACGTTTTATACCTGTAGTTATTTAAACTAT 7 89 0 TACTGTGTTA 0.939206 -212 TCGTTATCAATTCCCACGCTGTTTCAGAGCGTTA 7 210 1 TCCCGCGTTT 0.743568 -91 TTTCAGAGCGTTACCTTGCCCTTAAACATTAGCA 7 231 1 TCCTGCCTTA 0.941872 -70 CCTTCAAAAATTACCCTGCCGTTTATTTGCACAA 12 27 0 TCCTGCGTTT 0.94411 -274 AATTCTTTGAGGAACATGCAGTTATGCATGCTGT 12 80 1 GACTGCGTTA 0.92205 -221 AAAGTGGTATTTTACATGCACTTACAATTGATTA 12 143 1 TACTGCCTTA 0.880028 -158 AAGACAACATTCACAGTGTGGTTATTTGTTACAC 12 177 1 TCATGTGTTA 0.765699 -124 GTCATGACAGTGTAGGTGCGGTTACTGTCGTGAA 12 226 1 TAGTGCGTTA 0.930038 -75 GTCGGTTTTCTGGCGTTGTTGTTAAGTCTCGGGG 14 51 1 TCGTGTGTTA 0.93004 -29 * ** *** **** Masking position 12 Map Score: 4.90567 Number of sites scoring better than the average of aligned sites = 467 Number in coding regions = 426 Number in noncoding regions = 41 Number of orfs with sites within 600 bp upstream = 50 Fraction of orfs with sites within 600 bp upstream = 0.00803084 Motif number 15 GGCGTAAAGAAAGGTTGCAAACATGTTAATAAA 1 158 0 AAGGTGCACA 0.952286 -143 CCCGTTAGAAAGGGTCACACGCATGCCCCAATA 1 240 0 AGGGTACCCA 0.854651 -61 TCTATACTTTAAGGTGACTGCCAAAACAGACTC 2 105 1 AAGGTACGCA 0.978668 -87 TCCACTTAAGAAGGTAGGTGTTAC 3 41 1 AAGGTGGGTA 0.89541 -14 TACAGACACTAAGGTGGCAGACATCGAAACGAG 6 264 1 AAGGTGCGCA 0.986516 -37 GTTTAAGGGCAAGGTAACGCTCTGAAACAGCGT 7 225 0 AAGGTACCCT 0.798704 -76 GGAGATCTACAAAGTTAGAGGCAGGTAACAAAA 9 61 0 AAAGTAGGCA 0.730689 -115 CTGAATCGTTAAGGTAGGCGGTAATAGAAAAGA 10 226 1 AAGGTGGGTA 0.89541 -36 GGCGATACCAAAGGTCGCGCCCATCACCAAAGG 11 230 0 AAGGTGCCCA 0.978241 -71 GTAATTTTTGAAGGTCAGCAACAAAAGTTGATT 12 47 1 AAGGTAGACA 0.894422 -254 ***** ** * ** Masking position 5 Map Score: 5.46423 Number of sites scoring better than the average of aligned sites = 263 Number in coding regions = 238 Number in noncoding regions = 25 Number of orfs with sites within 600 bp upstream = 28 Fraction of orfs with sites within 600 bp upstream = 0.00449727