AlignACE 3.0 10/20/99 AlignACE2 -i AP/AP_operons007_300.orf Parameter values: expect = 10 gcback = 0.38 minpass = 200 seed = 944249313 numcols = 10 undersample = 1 oversample = 1 Input sequences: #0 APE0914 78 103aa long hypothetical DNA-directed RNA polymerase subunit #1 APE1737 300 111aa long hypothetical 30S ribosomal protein S13 #2 APE1747 32 155aa long hypothetical 50S ribosomal protein L13 #3 APE1750 41 205aa long hypothetical 30S ribosomal protein S2 #4 APE2437 300 193aa long hypothetical deoxyribose-phosphate aldolase Motif 1 AGGCTGTAACCCCAGCGGCTCCGGAGCCGCCGGA 1 75 0 CTAGCCCGGGGGAGGGGTGGATAAGTCA 0 4 1 CCCTAGAGGCTAGGGGATAGTGTGG 2 1 1 AAAGAGGGTTTCCGGGGGATCGGGTTCC 0 60 1 TAGAGTCTATCCTCGAGGCGAGGTCCTCAGGGCT 4 232 0 CGCTACTAAGCCCTAGGGCTACGGAGGAGGACGT 4 266 1 ACCCTCTTTATCCCGGGGAGCCGTTAAATCTTGA 0 35 0 GGGTTACAGCCTCGGCGGCTGTGTGGACCGCTTC 1 97 1 AGGAGCTCGGCCCAGCGAAGCGGTCCACACAGCC 1 113 0 GCCTCACAGCCCCCGTGTATACCGGGGTTGCCAG 1 38 0 GCAAATATAACCCTTGGTCTGTGGGAGGGGGAAT 4 105 1 GAGGCGAGGTCCTCAGGGCTCCCTAGCCTGTCTA 4 218 0 CTGCAGTATATCCCTGGCCGACGGCAATCCGGAT 4 177 0 *** * **** ** MAP Score: 24.7423 Motif 2 CCCCGGTATACACGGGGGCTGTGAGGCCGTTCCGGCGG 1 45 1 CTAGCCCGGGGGAGGGGTGGATAAGTCAAGAT 0 4 1 TAAAGAGGGTTTCCGGGGGATCGGGTTCC 0 59 1 GGGTTACAGCCTCGGCGGCTGTGTGGACCGCTTCGCTG 1 97 1 AGGCTTAAGATGTGGGGGTGAAGTGAGCT 3 22 1 TCTAGACAGGCTAGGGAGCCCTGAGGACCTCGCCTCGA 4 216 1 CCCCCGTGTATACCGGGGTTGCCAGCACCAGTCTTGAG 1 25 0 TTTAACGGCTCCCCGGGATAAAGAGGGTTTCCGGGGGA 0 41 1 ACCCCAGCGGCTCCGGAGCCGCCGGAACGGCCTCACAG 1 63 0 CCCTAGAGGCTAGGGGATAGTGTGGGGGTTTG 2 9 1 GTGTGGACCGCTTCGCTGGGCCGAGCTCCTAACCTATA 1 117 1 TTAAGCTGCCCTACGGTCTGGCGAGCATAAAGGGTATT 1 257 1 GCTACTAAGCCCTAGGGCTACGGAGGAGGACGTTAGGA 4 267 1 TATGTTGGAATACAGGGATTAGGCGTTGGCTGGAGAGA 1 168 1 ACTCTAATCTGGAGGGGGTATCCGGATTGCCGTCGGCC 4 158 1 * ****** * * * MAP Score: 24.0443 Motif 3 CTAGCCCGGGGGAGGGGTGGAT 0 0 1 AGATTTAACGGCTCCCCGGGATAAAGAGGGTT 0 38 1 GGAACCCGATCCCCCGGAAACCCTCTTTA 0 59 0 CTGGTGCTGGCAACCCCGGTATACACGGGGGC 1 32 1 AACGGCCTCACAGCCCCCGTGTATACCGGGGT 1 44 0 GGCCGTTCCGGCGGCTCCGGAGCCGCTGGGGT 1 69 1 GCCGAGGCTGTAACCCCAGCGGCTCCGGAGCC 1 81 0 GCTGGGGTTACAGCCTCGGCGGCTGTGTGGAC 1 93 1 GGTTAGGAGCTCGGCCCAGCGAAGCGGTCCAC 1 119 0 TATATTAGGCCTTCCCCTATGTTGGAATACAG 1 151 1 GAGACCTTAAGCTGCCCTACGGTCTGGCGAGC 1 251 1 CAATACCCTTTATGCTCGCCAGACCGTAGGGC 1 264 0 CACTATCCCCTAGCCTCTAGGG 2 0 0 GTCCCTCCAGAGAGGCTTAAGA 3 0 1 AGCTCACTTCACCCCCACATCTTAAGCCTC 3 21 0 AAATATAACCCTTGGTCTGTGGGAGGGGGAAT 4 107 1 AATCCGGATACCCCCTCCAGATTAGAGTATGC 4 154 0 GCAGTATATCCCTGGCCGACGGCAATCCGGAT 4 177 0 GCCCTGAGGACCTCGCCTCGAGGATAGACTCT 4 233 1 TCTACGCTACTAAGCCCTAGGGCTACGGAGGA 4 262 1 TTCCTAACGTCCTCCTCCGTAGCCCTAGGGCT 4 274 0 ** **** **** MAP Score: 23.7178 Motif 4 AAGATTTAACGGCTCCCCGGGATAAAGAGG 0 37 1 ATACCCTTTATGCTCGCCAGACCGTAGGGC 1 264 0 TGGGGTTACAGCCTCGGCGGCTGTGTGGAC 1 95 1 GTCCCTCCAGAGAGGCTTAA 3 0 1 TTTGAAGCTGGTCTCTCCAGCCAACGCCTA 1 187 0 AGGTCCTCAGGGCTCCCTAGCCTGTCTAGA 4 216 0 GGGATAAAGAGGGTTTCCGGGGGATCGGGT 0 55 1 CCGTTCCGGCGGCTCCGGAGCCGCTGGGGT 1 71 1 GTGTATACCGGGGTTGCCAGCACCAGTCTT 1 28 0 GACCTTAAGCTGCCCTACGGTCTGGCGAGC 1 253 1 AGTATATCCCTGGCCGACGGCAATCCGGAT 4 177 0 AATCTGGAGGGGGTATCCGGATTGCCGTCG 4 163 1 CCGCCGGAACGGCCTCACAGCCCCCGTGTA 1 53 0 CTAGCCCGGGGGAGGGGTGGAT 0 2 1 GAATCTAATAGTTTTCCCGGCATACTCTAA 4 135 1 CTATCCCCTAGCCTCTAGGG 2 0 0 TACGCTACTAAGCCCTAGGGCTACGGAGGA 4 264 1 ATATAACCCTTGGTCTGTGGGAGGGGGAAT 4 109 1 TGTGTGGACCGCTTCGCTGGGCCGAGCTCC 1 116 1 CAGCGAAGCGGTCCACACAGCCGCCGAGGC 1 105 0 CTGCAGCAGGGTCTAGACAGGCTAGGGAGC 4 205 1 ********** MAP Score: 18.6395 Motif 5 CTAGCCCGGGGGAGGGGTGGATAAGTC 0 3 1 AAAGAGGGTTTCCGGGGGATCGGGTTCC 0 60 1 TAGGAGCTCGGCCCAGCGAAGCGGTCCACACAGC 1 114 0 AGGCTGTAACCCCAGCGGCTCCGGAGCCGCCGGA 1 75 0 ACCTTAAGCTGCCCTACGGTCTGGCGAGCATAAA 1 254 1 CGCTACTAAGCCCTAGGGCTACGGAGGAGGACGT 4 266 1 TGGGGTTACAGCCTCGGCGGCTGTGTGGACCGCT 1 95 1 ACCCTCTTTATCCCGGGGAGCCGTTAAATCTTGA 0 35 0 TGCAGTATATCCCTGGCCGACGGCAATCCGGATA 4 176 0 GCAAATATAACCCTTGGTCTGTGGGAGGGGGAAT 4 105 1 CGGCTCCGGAGCCGCCGGAACGGCCTCACAGCCC 1 60 0 GGCTAGGGAGCCCTGAGGACCTCGCCTCGAGGAT 4 224 1 CCCTAGAGGCTAGGGGATAGTGTG 2 0 1 AACCCCGGTATACACGGGGGCTGTGAGGCCGTTC 1 43 1 *** **** * ** MAP Score: 17.348 Motif 6 CTAGCCCGGGGGAGGGGTGGATAAGTCAAG 0 3 1 TTTAACGGCTCCCCGGGATAAAGAGGGTTTCCGGGGG 0 41 1 AAAGAGGGTTTCCGGGGGATCGGGTTCC 0 60 1 CCCCGGTATACACGGGGGCTGTGAGGCCGTTCCGGCG 1 45 1 TGAGGCCGTTCCGGCGGCTCCGGAGCCGCTGGGGTTA 1 66 1 TGGGGTTACAGCCTCGGCGGCTGTGTGGACCGCTTCG 1 95 1 GTGGACCGCTTCGCTGGGCCGAGCTCCTAACCTATAT 1 119 1 CAGGGATTAGGCGTTGGCTGGAGAGACCAGCTTCAAA 1 180 1 CCTTAAGCTGCCCTACGGTCTGGCGAGCATAAAGGGT 1 255 1 CCCTAGAGGCTAGGGGATAGTGTGGGG 2 0 1 GCAAATATAACCCTTGGTCTGTGGGAGGGGGAATCTA 4 105 1 ATCCGGATTGCCGTCGGCCAGGGATATACTGCAGCAG 4 177 1 GGATATACTGCAGCAGGGTCTAGACAGGCTAGGGAGC 4 198 1 GTAGAGTCTATCCTCGAGGCGAGGTCCTCAGGGCTCC 4 230 0 TCCTCCGTAGCCCTAGGGCTTAGTAGCGTAGAGTCTA 4 257 0 *** *** ** * * MAP Score: 15.5115 Motif 7 CTAGCCCGGGGGAGGGGTGGATAAGTCAAG 0 4 1 TTTAACGGCTCCCCGGGATAAAGAGGGTTTCCGGGG 0 41 1 AAGAGGGTTTCCGGGGGATCGGGTTCC 0 61 1 CCTCACAGCCCCCGTGTATACCGGGGTTGCCAGCAC 1 35 0 TGAGGCCGTTCCGGCGGCTCCGGAGCCGCTGGGGTT 1 66 1 CGAAGCGGTCCACACAGCCGCCGAGGCTGTAACCCC 1 96 0 GTGGACCGCTTCGCTGGGCCGAGCTCCTAACCTATA 1 119 1 CAGGGATTAGGCGTTGGCTGGAGAGACCAGCTTCAA 1 180 1 CCTTAAGCTGCCCTACGGTCTGGCGAGCATAAAGGG 1 255 1 CCCACACTATCCCCTAGCCTCTAGGG 2 0 0 ATAATAGGTGCCTAGAGTTGGCGAGC 4 0 0 GCAAATATAACCCTTGGTCTGTGGGAGGGGGAATCT 4 105 1 TCCCGGCATACTCTAATCTGGAGGGGGTATCCGGAT 4 149 1 ATCCGGATTGCCGTCGGCCAGGGATATACTGCAGCA 4 177 1 AGGCGAGGTCCTCAGGGCTCCCTAGCCTGTCTAGAC 4 215 0 CGAGGATAGACTCTACGCTACTAAGCCCTAGGGCTA 4 251 1 GCTACTAAGCCCTAGGGCTACGGAGGAGGACGTTAG 4 267 1 *** ** * * * ** MAP Score: 14.093 Motif 8 GACTTATCCACCCCTCCCCCGGGCTAG 0 3 0 GTCAAGATTTAACGGCTCCCCGGGATAAAGAGGG 0 34 1 CGGGATAAAGAGGGTTTCCGGGGGATCGGGTTCC 0 54 1 CTGGCAACCCCGGTATACACGGGGGCTGTGAGGC 1 38 1 GGGCTGTGAGGCCGTTCCGGCGGCTCCGGAGCCG 1 60 1 TCCGGCGGCTCCGGAGCCGCTGGGGTTACAGCCT 1 75 1 CGCTGGGGTTACAGCCTCGGCGGCTGTGTGGACC 1 92 1 GGCTGTGTGGACCGCTTCGCTGGGCCGAGCTCCT 1 113 1 CCTTAAGCTGCCCTACGGTCTGGCGAGCATAAAG 1 255 1 CCACACTATCCCCTAGCCTCTAGGG 2 1 0 GTCCCTCCAGAGAGGCTTAAGATGTG 3 2 1 CAAATATAACCCTTGGTCTGTGGGAGGGGGAATC 4 106 1 TATCCGGATTGCCGTCGGCCAGGGATATACTGCA 4 176 1 AGCCCTGAGGACCTCGCCTCGAGGATAGACTCTA 4 232 1 AACGTCCTCCTCCGTAGCCCTAGGGCTTAGTAGC 4 267 0 **** * * * *** MAP Score: 13.1947 Motif 9 CGGAAACCCTCTTTATCCCGGGGAGCCGTTAAATCTTGA 0 35 0 GGGATAAAGAGGGTTTCCGGGGGATCGGGTTCC 0 55 1 TGGCAACCCCGGTATACACGGGGGCTGTGAGGCCGTTCC 1 39 1 GGGCTGTGAGGCCGTTCCGGCGGCTCCGGAGCCGCTGGG 1 60 1 TAGGTTAGGAGCTCGGCCCAGCGAAGCGGTCCACACAGC 1 114 0 CTTTATGCTCGCCAGACCGTAGGGCAGCTTAAGGTCTCC 1 250 0 AAATATAACCCTTGGTCTGTGGGAGGGGGAATCTAATAG 4 107 1 GGGGGTATCCGGATTGCCGTCGGCCAGGGATATACTGCA 4 171 1 TCCTCGAGGCGAGGTCCTCAGGGCTCCCTAGCCTGTCTA 4 218 0 CTCTACGCTACTAAGCCCTAGGGCTACGGAGGAGGACGT 4 261 1 * *** *** *** MAP Score: 12.244 Motif 10 CTAGCCCGGGGGAGGGGTGGATAAGT 0 2 1 GTCAAGATTTAACGGCTCCCCGGGATAAAGAGGG 0 34 1 CGGGATAAAGAGGGTTTCCGGGGGATCGGGTTCC 0 54 1 AAGACTGGTGCTGGCAACCCCGGTATACACGGGG 1 28 1 CCCGGTATACACGGGGGCTGTGAGGCCGTTCCGG 1 46 1 GGGCTGTGAGGCCGTTCCGGCGGCTCCGGAGCCG 1 60 1 TCCGGCGGCTCCGGAGCCGCTGGGGTTACAGCCT 1 75 1 CGCTGGGGTTACAGCCTCGGCGGCTGTGTGGACC 1 92 1 GGCTGTGTGGACCGCTTCGCTGGGCCGAGCTCCT 1 113 1 TACAGGGATTAGGCGTTGGCTGGAGAGACCAGCT 1 178 1 CTAGAGGCTAGGGGATAGTGTGGGGGTTTG 2 12 1 TATAACCCTTGGTCTGTGGGAGGGGGAATCTAAT 4 110 1 TATCCGGATTGCCGTCGGCCAGGGATATACTGCA 4 176 1 TAGACAGGCTAGGGAGCCCTGAGGACCTCGCCTC 4 218 1 ACTAAGCCCTAGGGCTACGGAGGAGGACGTTAGG 4 270 1 **** *** *** MAP Score: 7.9827 Motif 11 CTAGCCCGGGGGAGGGGTGGATAAGTCAAG 0 4 1 TTAACGGCTCCCCGGGATAAAGAGGGTTTCCGGGGG 0 42 1 AAGAGGGTTTCCGGGGGATCGGGTTCC 0 61 1 CCTCACAGCCCCCGTGTATACCGGGGTTGCCAGCAC 1 35 0 GTTCCGGCGGCTCCGGAGCCGCTGGGGTTACAGCCT 1 73 1 GGGTTACAGCCTCGGCGGCTGTGTGGACCGCTTCGC 1 97 1 GCTGTGTGGACCGCTTCGCTGGGCCGAGCTCCTAAC 1 114 1 TTAAGCTGCCCTACGGTCTGGCGAGCATAAAGGGTA 1 257 1 CCCTAGAGGCTAGGGGATAGTGTGGGGGTTTG 2 9 1 TCCAGAGAGGCTTAAGATGTGGGGGTGAAGTGAGCT 3 15 1 AAATATAACCCTTGGTCTGTGGGAGGGGGAATCTAA 4 107 1 CCGGCATACTCTAATCTGGAGGGGGTATCCGGATTG 4 151 1 TCTAGACAGGCTAGGGAGCCCTGAGGACCTCGCCTC 4 216 1 TAACGTCCTCCTCCGTAGCCCTAGGGCTTAGTAGCG 4 266 0 ** *** *** ** MAP Score: 7.58154 Motif 12 CTAGCCCGGGGGAGGGGTGGATAAGTC 0 4 1 TTAACGGCTCCCCGGGATAAAGAGGGTTTCCGG 0 42 1 AAGAGGGTTTCCGGGGGATCGGGTTCC 0 61 1 CCCGTGTATACCGGGGTTGCCAGCACCAGTCTT 1 28 0 TGAGGCCGTTCCGGCGGCTCCGGAGCCGCTGGG 1 66 1 TCCGGAGCCGCTGGGGTTACAGCCTCGGCGGCT 1 84 1 AGGTTAGGAGCTCGGCCCAGCGAAGCGGTCCAC 1 119 0 TAGGCGTTGGCTGGAGAGACCAGCTTCAAATAT 1 187 1 GCCCTACGGTCTGGCGAGCATAAAGGGTATTGG 1 264 1 CCCTAGAGGCTAGGGGATAGTGTGG 2 2 1 AACCCTTGGTCTGTGGGAGGGGGAATCTAATAG 4 113 1 ATCCCTGGCCGACGGCAATCCGGATACCCCCTC 4 169 0 TCTAGACAGGCTAGGGAGCCCTGAGGACCTCGC 4 216 1 CCCTGAGGACCTCGCCTCGAGGATAGACTCTAC 4 234 1 CTACTAAGCCCTAGGGCTACGGAGGAGGACGTT 4 268 1 ****** **** MAP Score: 4.86121 Motif 13 ATCCACCCCTCCCCCGGGCTAG 0 0 0 AAAGAGGGTTTCCGGGGGATCGGGTTCC 0 60 1 GCCTCACAGCCCCCGTGTATACCGGGGTTGCC 1 40 0 GTGAGGCCGTTCCGGCGGCTCCGGAGCCGCTG 1 65 1 AGGCTGTAACCCCAGCGGCTCCGGAGCCGCCG 1 77 0 AGGAGCTCGGCCCAGCGAAGCGGTCCACACAG 1 115 0 GCTGGTCTCTCCAGCCAACGCCTAATCCCTGT 1 179 0 CTTAAGGTCTCCATCTATATCGACGCCTGCTA 1 230 0 CAAACCCCCACACTATCCCCTAGCCTCT 2 14 0 GTCCCTCCAGAGAGGCTTAAGATG 3 2 1 AATCCGGATACCCCCTCCAGATTAGAGTATGC 4 154 0 GGCTAGGGAGCCCTGAGGACCTCGCCTCGAGG 4 224 1 GAGGACCTCGCCTCGAGGATAGACTCTACGCT 4 238 1 CCTAACGTCCTCCTCCGTAGCCCTAGGGCTTA 4 272 0 *** *** **** MAP Score: 4.16035 Motif 14 ACTTATCCACCCCTCCCCCGGGCTAG 0 2 0 AACCCGATCCCCCGGAAACCCTCTTTATCCCGGG 0 52 0 TACCGGGGTTGCCAGCACCAGTCTTGAGATTTGC 1 19 0 CGGCCTCACAGCCCCCGTGTATACCGGGGTTGCC 1 40 0 CGGCTCCGGAGCCGCCGGAACGGCCTCACAGCCC 1 60 0 TTCCGGCGGCTCCGGAGCCGCTGGGGTTACAGCC 1 74 1 GGTCCACACAGCCGCCGAGGCTGTAACCCCAGCG 1 92 0 AGGAGCTCGGCCCAGCGAAGCGGTCCACACAGCC 1 113 0 CCTATATTAGGCCTTCCCCTATGTTGGAATACAG 1 149 1 ATCGACGCCTGCTATCCTGACTATATATTTGAAG 1 210 0 ACCTTAAGCTGCCCTACGGTCTGGCGAGCATAAA 1 254 1 CACACTATCCCCTAGCCTCTAGGG 2 0 0 CAAACCCCCACACTATCCCCTAGCCTCT 2 14 0 GTCCCTCCAGAGAGGCTTAAGATGTG 3 2 1 GCTCGCCAACTCTAGGCACCTATTA 4 1 1 TATTAGATTCCCCCTCCCACAGACCAAGGGTTAT 4 111 0 ATCCGGATACCCCCTCCAGATTAGAGTATGCCGG 4 151 0 TATATCCCTGGCCGACGGCAATCCGGATACCCCC 4 171 0 CTCAGGGCTCCCTAGCCTGTCTAGACCCTGCTGC 4 207 0 GGCTAGGGAGCCCTGAGGACCTCGCCTCGAGGAT 4 224 1 GAGGACCTCGCCTCGAGGATAGACTCTACGCTAC 4 238 1 CTCCTCCGTAGCCCTAGGGCTTAGTAGCGTAGAG 4 261 0 *** ** * **** MAP Score: 4.1079 Motif 15 CTTGACTTATCCACCCCTCCCCCGGGCTAG 0 0 0 CCGGAGCCGCCGGAACGGCCTCACAGCCCCCGTGTATACC 1 49 0 GAGGCTGTAACCCCAGCGGCTCCGGAGCCGCCGGAACGGC 1 70 0 GCGAAGCGGTCCACACAGCCGCCGAGGCTGTAACCCCAGC 1 93 0 ATATAGTCAGGATAGCAGGCGTCGATATAGATGGAGACCT 1 218 1 TATCCAATACCCTTTATGCTCGCCAGACCGTAGGGCAGCT 1 260 0 CCCTAGAGGCTAGGGGATAGTGTGGGGGTT 2 0 1 GTCCCTCCAGAGAGGCTTAAGATGTGGGGGTGAAGTG 3 7 1 GCAAATATAACCCTTGGTCTGTGGGAGGGGGAATCTAATA 4 105 1 GAGGGGGTATCCGGATTGCCGTCGGCCAGGGATATACTGC 4 169 1 GAGGCGAGGTCCTCAGGGCTCCCTAGCCTGTCTAGACCCT 4 212 0 ** **** *** * MAP Score: 0.737918