AlignACE 3.0 10/20/99 AlignACE2 -i AP/AP_operons007_100.orf Parameter values: expect = 10 gcback = 0.38 minpass = 200 seed = 944249301 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 CTAGCCCGGGGGAGGGGTGGATAAGTCAAG 0 4 1 CCCTAGAGGCTAGGGGATAGTGTGGGGGTTTG 2 9 1 GGGTTACAGCCTCGGCGGCTGTGTGGACCGCTTCGC 1 97 1 TCTAGACAGGCTAGGGAGCCCTGAGGACCTCGCCTC 4 216 1 AAATATAACCCTTGGTCTGTGGGAGGGGGAATCTAA 4 107 1 CCCCGGTATACACGGGGGCTGTGAGGCCGTTCCGGC 1 45 1 GGCTGTAACCCCAGCGGCTCCGGAGCCGCCGGAACG 1 72 0 TTTATGCTCGCCAGACCGTAGGGCAGCTTAAGGTCT 1 252 0 GCTACTAAGCCCTAGGGCTACGGAGGAGGACGTTAG 4 267 1 AGGTTAGGAGCTCGGCCCAGCGAAGCGGTCCACACA 1 116 0 AAGAGGGTTTCCGGGGGATCGGGTTCC 0 61 1 TTAACGGCTCCCCGGGATAAAGAGGGTTTCCGGGGG 0 42 1 CCTAGCCTGTCTAGACCCTGCTGCAGTATATCCCTG 4 195 0 CCCTGAGGACCTCGCCTCGAGGATAGACTCTACGCT 4 234 1 TATTCTTAAGTTTGAGAATTGTGGGGTAATCATTTA 4 33 1 GCTCGCCAACTCTAGGCACCTATTATT 4 1 1 CCCGTGTATACCGGGGTTGCCAGCACCAGTCTTGAG 1 25 0 GATACCCCCTCCAGATTAGAGTATGCCGGGAAAACT 4 144 0 ** *** *** ** MAP Score: 26.5775 Motif 2 CTAGCCCGGGGGAGGGGTGGAT 0 2 1 AAGATTTAACGGCTCCCCGGGATAAAGAGG 0 37 1 GGGATAAAGAGGGTTTCCGGGGGATCGGGT 0 55 1 GTGTATACCGGGGTTGCCAGCACCAGTCTT 1 28 0 CCGCCGGAACGGCCTCACAGCCCCCGTGTA 1 53 0 CTGTGAGGCCGTTCCGGCGGCTCCGGAGCC 1 63 1 TAACCCCAGCGGCTCCGGAGCCGCCGGAAC 1 73 0 TGGGGTTACAGCCTCGGCGGCTGTGTGGAC 1 95 1 CAGCGAAGCGGTCCACACAGCCGCCGAGGC 1 105 0 TTTGAAGCTGGTCTCTCCAGCCAACGCCTA 1 187 0 GACCTTAAGCTGCCCTACGGTCTGGCGAGC 1 253 1 ATACCCTTTATGCTCGCCAGACCGTAGGGC 1 264 0 CTATCCCCTAGCCTCTAGGG 2 0 0 GTCCCTCCAGAGAGGCTTAA 3 0 1 AGAATAATAGGTGCCTAGAGTTGGCGAGC 4 9 0 GAATCTAATAGTTTTCCCGGCATACTCTAA 4 135 1 AATCTGGAGGGGGTATCCGGATTGCCGTCG 4 163 1 AGTATATCCCTGGCCGACGGCAATCCGGAT 4 177 0 GGTCTAGACAGGCTAGGGAGCCCTGAGGAC 4 214 1 TCGAGGCGAGGTCCTCAGGGCTCCCTAGCC 4 224 0 CCTGAGGACCTCGCCTCGAGGATAGACTCT 4 235 1 TACGCTACTAAGCCCTAGGGCTACGGAGGA 4 264 1 ********** MAP Score: 23.7707 Motif 3 TATCCACCCCTCCCCCGGGCTAG 0 0 0 ACCCTCTTTATCCCGGGGAGCCGTTAAATCTTG 0 36 0 AAAGAGGGTTTCCGGGGGATCGGGTTCC 0 60 1 CAAGACTGGTGCTGGCAACCCCGGTATACACGG 1 27 1 AACCCCGGTATACACGGGGGCTGTGAGGCCGTT 1 43 1 CGGCTCCGGAGCCGCCGGAACGGCCTCACAGCC 1 61 0 AGGCTGTAACCCCAGCGGCTCCGGAGCCGCCGG 1 76 0 GGTCCACACAGCCGCCGAGGCTGTAACCCCAGC 1 93 0 AGGAGCTCGGCCCAGCGAAGCGGTCCACACAGC 1 114 0 CTATATCGACGCCTGCTATCCTGACTATATATT 1 215 0 CCTTAAGCTGCCCTACGGTCTGGCGAGCATAAA 1 255 1 CCCTAGAGGCTAGGGGATAGTGT 2 0 1 GTCCCTCCAGAGAGGCTTAAGATGT 3 2 1 ATCTTAATACACCTCCTAACCAGTGTAAATGAT 4 61 0 GATTCCCCCTCCCACAGACCAAGGGTTATATTT 4 107 0 TCCGGATACCCCCTCCAGATTAGAGTATGCCGG 4 151 0 ATCCCTGGCCGACGGCAATCCGGATACCCCCTC 4 169 0 GGTCCTCAGGGCTCCCTAGCCTGTCTAGACCCT 4 212 0 TGAGGACCTCGCCTCGAGGATAGACTCTACGCT 4 237 1 TCCTCCGTAGCCCTAGGGCTTAGTAGCGTAGAG 4 261 0 *** **** ** * MAP Score: 23.6828 Motif 4 CTAGCCCGGGGGAGGGGTGGATAAG 0 0 1 AACCCTCTTTATCCCGGGGAGCCGTTAAATCTTGA 0 35 0 CCGGGATAAAGAGGGTTTCCGGGGGATCGGGTTCC 0 53 1 GGGCAAATCTCAAGACTGGTGCTGGCAACCCCGGT 1 17 1 CAACCCCGGTATACACGGGGGCTGTGAGGCCGTTC 1 42 1 GGGGGCTGTGAGGCCGTTCCGGCGGCTCCGGAGCC 1 58 1 GTTCCGGCGGCTCCGGAGCCGCTGGGGTTACAGCC 1 73 1 GCTGGGGTTACAGCCTCGGCGGCTGTGTGGACCGC 1 93 1 CCCTGTATTCCAACATAGGGGAAGGCCTAATATAG 1 150 0 ACAGGGATTAGGCGTTGGCTGGAGAGACCAGCTTC 1 179 1 AATATATAGTCAGGATAGCAGGCGTCGATATAGAT 1 215 1 TAGAGGCTAGGGGATAGTGTGGGGGTTTG 2 13 1 CCCACATCTTAAGCCTCTCTGGAGGGAC 3 3 0 AGAGAGGCTTAAGATGTGGGGGTGAAGTGAGCT 3 18 1 ATCATTTACACTGGTTAGGAGGTGTATTAAGATGT 4 61 1 ATAACCCTTGGTCTGTGGGAGGGGGAATCTAATAG 4 111 1 CCGGCATACTCTAATCTGGAGGGGGTATCCGGATT 4 151 1 GCTGCAGTATATCCCTGGCCGACGGCAATCCGGAT 4 177 0 TAGCCTGTCTAGACCCTGCTGCAGTATATCCCTGG 4 194 0 CTAAGCCCTAGGGCTACGGAGGAGGACGTTAGGAA 4 271 1 **** ** ** ** MAP Score: 20.3013 Motif 5 ACCCCAGCGGCTCCGGAGCCGCCGGAACGGCCTCACAGCC 1 61 0 CCCTAGAGGCTAGGGGATAGTGTGGGGGTT 2 0 1 CCCGGAAACCCTCTTTATCCCGGGGAGCCGTTAAATCTTG 0 36 0 TGCTGGCAACCCCGGTATACACGGGGGCTGTGAGGCCGTT 1 36 1 ACCCTTTATGCTCGCCAGACCGTAGGGCAGCTTAAGGTCT 1 252 0 AGACTCTACGCTACTAAGCCCTAGGGCTACGGAGGAGGAC 4 258 1 GCGAAGCGGTCCACACAGCCGCCGAGGCTGTAACCCCAGC 1 93 0 GAGGGGGTATCCGGATTGCCGTCGGCCAGGGATATACTGC 4 169 1 TGAAGCTGGTCTCTCCAGCCAACGCCTAATCCCTGTATTC 1 175 0 GTCCCTCCAGAGAGGCTTAAGATGTGGGGGTGAAGT 3 6 1 CTTGACTTATCCACCCCTCCCCCGGGCTAG 0 0 0 GCTCCCTAGCCTGTCTAGACCCTGCTGCAGTATATCCCTG 4 195 0 TCTAGACAGGCTAGGGAGCCCTGAGGACCTCGCCTCGAGG 4 216 1 AGATTCCCCCTCCCACAGACCAAGGGTTATATTTGCTTTA 4 101 0 TAATAGTTTTCCCGGCATACTCTAATCTGGAGGGGGTATC 4 140 1 *** **** ** * MAP Score: 19.5468 Motif 6 CTAGCCCGGGGGAGGGGTGGATAAGTCAAG 0 4 1 GGGTTACAGCCTCGGCGGCTGTGTGGACCGCTTCGC 1 97 1 TTTAACGGCTCCCCGGGATAAAGAGGGTTTCCGGGG 0 41 1 CCCCGGTATACACGGGGGCTGTGAGGCCGTTCCGGC 1 45 1 AGGCTGTAACCCCAGCGGCTCCGGAGCCGCCGGAAC 1 73 0 CGCTACTAAGCCCTAGGGCTACGGAGGAGGACGTTA 4 266 1 CCCTAGAGGCTAGGGGATAGTGTGGGGGTTTG 2 9 1 TCTAGACAGGCTAGGGAGCCCTGAGGACCTCGCCTC 4 216 1 TAAAGAGGGTTTCCGGGGGATCGGGTTCC 0 59 1 CCTTAAGCTGCCCTACGGTCTGGCGAGCATAAAGGG 1 255 1 AACCCTTGGTCTGTGGGAGGGGGAATCTAATAGTTT 4 113 1 ATACTCTAATCTGGAGGGGGTATCCGGATTGCCGTC 4 156 1 TATGTTGGAATACAGGGATTAGGCGTTGGCTGGAGA 1 168 1 *** **** * ** MAP Score: 17.7649 Motif 7 CTAGCCCGGGGGAGGGGTGGATAAGTCAAGATTTA 0 0 1 GATTTAACGGCTCCCCGGGATAAAGAGGGTTTCCGGGGGATCGGG 0 39 1 GGCCTCACAGCCCCCGTGTATACCGGGGTTGCCAGCACCAGTCTT 1 28 0 GAGGCTGTAACCCCAGCGGCTCCGGAGCCGCCGGAACGGCCTCAC 1 65 0 GGGTTACAGCCTCGGCGGCTGTGTGGACCGCTTCGCTGGGCCGAG 1 97 1 CCTTAAGCTGCCCTACGGTCTGGCGAGCATAAAGGGTATTGGATA 1 255 1 CCCTAGAGGCTAGGGGATAGTGTGGGGGTTTG 2 0 1 GTCCCTCCAGAGAGGCTTAAGATGTGGGGGTGAAGTGAG 3 4 1 GCAAATATAACCCTTGGTCTGTGGGAGGGGGAATCTAATAGTTTT 4 105 1 GCAGCAGGGTCTAGACAGGCTAGGGAGCCCTGAGGACCTCGCCTC 4 207 1 CGCTACTAAGCCCTAGGGCTACGGAGGAGGACGTTAGGAATCTT 4 266 1 *** * * *** * * MAP Score: 11.4113 Motif 8 CTAGCCCGGGGGAGGGGTGGATA 0 0 1 TCAAGATTTAACGGCTCCCCGGGATAAAGAGGG 0 35 1 GGAACCCGATCCCCCGGAAACCCTCTTT 0 60 0 TAGGGCAAATCTCAAGACTGGTGCTGGCAACCC 1 15 1 AAGACTGGTGCTGGCAACCCCGGTATACACGGG 1 28 1 GGAACGGCCTCACAGCCCCCGTGTATACCGGGG 1 45 0 CCAGCGGCTCCGGAGCCGCCGGAACGGCCTCAC 1 65 0 AAGCGGTCCACACAGCCGCCGAGGCTGTAACCC 1 97 0 AGGTTAGGAGCTCGGCCCAGCGAAGCGGTCCAC 1 119 0 ATATTTGAAGCTGGTCTCTCCAGCCAACGCCTA 1 187 0 TTTATGCTCGCCAGACCGTAGGGCAGCTTAAGG 1 255 0 TACGGTCTGGCGAGCATAAAGGGTATTGGATAC 1 268 1 ACACTATCCCCTAGCCTCTAGGG 2 0 0 CCCCACATCTTAAGCCTCTCTGGAGGGAC 3 6 0 TTCCCCCTCCCACAGACCAAGGGTTATATTTGC 4 105 0 CCGGCATACTCTAATCTGGAGGGGGTATCCGGA 4 151 1 CCTAGCCTGTCTAGACCCTGCTGCAGTATATCC 4 198 0 GCGAGGTCCTCAGGGCTCCCTAGCCTGTCTAGA 4 216 0 CCCTGAGGACCTCGCCTCGAGGATAGACTCTAC 4 234 1 CTCTACGCTACTAAGCCCTAGGGCTACGGAGGA 4 261 1 * ** *** **** MAP Score: 10.9306 Motif 9 CTAGCCCGGGGGAGGGGTGGA 0 0 1 CAAGATTTAACGGCTCCCCGGGATAAAGAGG 0 36 1 CAACCCCGGTATACACGGGGGCTGTGAGGCC 1 42 1 GCCGTTCCGGCGGCTCCGGAGCCGCTGGGGT 1 70 1 CCGAGGCTGTAACCCCAGCGGCTCCGGAGCC 1 81 0 CTGGGGTTACAGCCTCGGCGGCTGTGTGGAC 1 94 1 GTTAGGAGCTCGGCCCAGCGAAGCGGTCCAC 1 119 0 AGACCTTAAGCTGCCCTACGGTCTGGCGAGC 1 252 1 AATACCCTTTATGCTCGCCAGACCGTAGGGC 1 264 0 ACTATCCCCTAGCCTCTAGGG 2 0 0 AGGCTAGGGGATAGTGTGGGGGTTTG 2 16 1 CCACATCTTAAGCCTCTCTGGAGGGAC 3 6 0 GCTCGCCAACTCTAGGCACCTATTATT 4 6 1 CAGGGATATACTGCAGCAGGGTCTAGACAGG 4 195 1 TCGAGGCGAGGTCCTCAGGGCTCCCTAGCCT 4 223 0 CTGAGGACCTCGCCTCGAGGATAGACTCTAC 4 236 1 CCTCGAGGATAGACTCTACGCTACTAAGCCC 4 248 1 CTACGCTACTAAGCCCTAGGGCTACGGAGGA 4 263 1 ****** **** MAP Score: 10.9273 Motif 10 CTAGCCCGGGGGAGGGGTGGATAAG 0 1 1 AGTCAAGATTTAACGGCTCCCCGGGATAAAGAGG 0 33 1 CCGGGATAAAGAGGGTTTCCGGGGGATCGGGTTC 0 53 1 GGCAAATCTCAAGACTGGTGCTGGCAACCCCGGT 1 18 1 AACCCCGGTATACACGGGGGCTGTGAGGCCGTTC 1 43 1 GGGGCTGTGAGGCCGTTCCGGCGGCTCCGGAGCC 1 59 1 TTCCGGCGGCTCCGGAGCCGCTGGGGTTACAGCC 1 74 1 CCGCTGGGGTTACAGCCTCGGCGGCTGTGTGGAC 1 91 1 CGGCTGTGTGGACCGCTTCGCTGGGCCGAGCTCC 1 112 1 ATACAGGGATTAGGCGTTGGCTGGAGAGACCAGC 1 177 1 TAAGCTGCCCTACGGTCTGGCGAGCATAAAGGGT 1 258 1 CCCTAGAGGCTAGGGGATAGTGTGGGG 2 3 1 CCAGAGAGGCTTAAGATGTGGGGGTGAAGTGAGC 3 16 1 TAATCATTTACACTGGTTAGGAGGTGTATTAAGA 4 59 1 ATATAACCCTTGGTCTGTGGGAGGGGGAATCTAA 4 109 1 CGGCATACTCTAATCTGGAGGGGGTATCCGGATT 4 152 1 GTATCCGGATTGCCGTCGGCCAGGGATATACTGC 4 175 1 TACTAAGCCCTAGGGCTACGGAGGAGGACGTTAG 4 269 1 *** * ** ** ** MAP Score: 10.2003 Motif 11 CTAGCCCGGGGGAGGGGTGGATAAGTC 0 4 1 TCAAGATTTAACGGCTCCCCGGGATAAAGAGGG 0 35 1 CGGGATAAAGAGGGTTTCCGGGGGATCGGGTTC 0 54 1 CTGGCAACCCCGGTATACACGGGGGCTGTGAGG 1 38 1 GGGCTGTGAGGCCGTTCCGGCGGCTCCGGAGCC 1 60 1 TCCGGCGGCTCCGGAGCCGCTGGGGTTACAGCC 1 75 1 CGCTGGGGTTACAGCCTCGGCGGCTGTGTGGAC 1 92 1 GGCTGTGTGGACCGCTTCGCTGGGCCGAGCTCC 1 113 1 CCTTAAGCTGCCCTACGGTCTGGCGAGCATAAA 1 255 1 CTAGAGGCTAGGGGATAGTGTGGGGGTTTG 2 12 1 TCTTAAGTTTGAGAATTGTGGGGTAATCATTTA 4 36 1 TATCCGGATTGCCGTCGGCCAGGGATATACTGC 4 176 1 TACTGCAGCAGGGTCTAGACAGGCTAGGGAGCC 4 203 1 AGACAGGCTAGGGAGCCCTGAGGACCTCGCCTC 4 219 1 ACTAAGCCCTAGGGCTACGGAGGAGGACGTTAG 4 270 1 **** * *** ** MAP Score: 9.46232 Motif 12 CTAGCCCGGGGGAGGGGTGGATAAGT 0 1 1 AAACCCTCTTTATCCCGGGGAGCCGTTAAATCTTG 0 36 0 GGAACCCGATCCCCCGGAAACCCTCTTTATCC 0 56 0 AGCCCCCGTGTATACCGGGGTTGCCAGCACCAGTC 1 30 0 CCGCCGGAACGGCCTCACAGCCCCCGTGTATACCG 1 48 0 CTGTGAGGCCGTTCCGGCGGCTCCGGAGCCGCTGG 1 63 1 GCGGCTCCGGAGCCGCTGGGGTTACAGCCTCGGCG 1 79 1 TGGGGTTACAGCCTCGGCGGCTGTGTGGACCGCTT 1 95 1 GTTAGGAGCTCGGCCCAGCGAAGCGGTCCACACAG 1 115 0 ATTAGGCGTTGGCTGGAGAGACCAGCTTCAAATAT 1 185 1 GACCTTAAGCTGCCCTACGGTCTGGCGAGCATAAA 1 253 1 CCCTAGAGGCTAGGGGATAGTGTGGGGGTT 2 5 1 GTCCCTCCAGAGAGGCTTAAGATGT 3 0 1 AGAGGCTTAAGATGTGGGGGTGAAGTGAGCT 3 20 1 AGAATAATAGGTGCCTAGAGTTGGCGAGC 4 4 0 TATAACCCTTGGTCTGTGGGAGGGGGAATCTAATA 4 110 1 AGTATATCCCTGGCCGACGGCAATCCGGATACCCC 4 172 0 AGGGATATACTGCAGCAGGGTCTAGACAGGCTAGG 4 196 1 TCGAGGCGAGGTCCTCAGGGCTCCCTAGCCTGTCT 4 219 0 GCGTAGAGTCTATCCTCGAGGCGAGGTCCTCAGGG 4 234 0 CCTCCTCCGTAGCCCTAGGGCTTAGTAGCGTAGAG 4 261 0 ****** *** * MAP Score: 6.76996 Motif 13 AAGATTTAACGGCTCCCCGGGATAAAGAGGGTTTCCGGGGG 0 37 1 GATCTTAGGGCAAATCTCAAGACTGGTGCTGGCAACCCCG 1 9 1 GGGCTGTGAGGCCGTTCCGGCGGCTCCGGAGCCGCTGGGGT 1 60 1 AGCCGCTGGGGTTACAGCCTCGGCGGCTGTGTGGACCGCTT 1 89 1 GCGGCTGTGTGGACCGCTTCGCTGGGCCGAGCTCCTAACCT 1 111 1 GGAATACAGGGATTAGGCGTTGGCTGGAGAGACCAGCTTCA 1 174 1 GAGACCTTAAGCTGCCCTACGGTCTGGCGAGCATAAAGGGT 1 251 1 CCCTAGAGGCTAGGGGATAGTGTGGGGGTTTG 2 8 1 TAGTTTTCCCGGCATACTCTAATCTGGAGGGGGTATCCGGA 4 143 1 GGGGGTATCCGGATTGCCGTCGGCCAGGGATATACTGCAGC 4 171 1 TACTGCAGCAGGGTCTAGACAGGCTAGGGAGCCCTGAGGAC 4 203 1 * ** *** ** * * MAP Score: 2.92912 Motif 14 CTAGCCCGGGGGAGGGGTGGATAAGTC 0 4 1 GTCAAGATTTAACGGCTCCCCGGGATAAAGAGG 0 34 1 AAGAGGGTTTCCGGGGGATCGGGTTCC 0 61 1 AAGACTGGTGCTGGCAACCCCGGTATACACGGG 1 28 1 CCCCGGTATACACGGGGGCTGTGAGGCCGTTCC 1 45 1 CCCAGCGGCTCCGGAGCCGCCGGAACGGCCTCA 1 66 0 CGCTGGGGTTACAGCCTCGGCGGCTGTGTGGAC 1 92 1 GGAGCTCGGCCCAGCGAAGCGGTCCACACAGCC 1 113 0 GTCTCCATCTATATCGACGCCTGCTATCCTGAC 1 223 0 GGAGACCTTAAGCTGCCCTACGGTCTGGCGAGC 1 250 1 ACACTATCCCCTAGCCTCTAGGG 2 0 0 CAAATATAACCCTTGGTCTGTGGGAGGGGGAAT 4 106 1 TCTAATCTGGAGGGGGTATCCGGATTGCCGTCG 4 160 1 TGCAGTATATCCCTGGCCGACGGCAATCCGGAT 4 177 0 CCTAGCCTGTCTAGACCCTGCTGCAGTATATCC 4 198 0 TCTAGACAGGCTAGGGAGCCCTGAGGACCTCGC 4 216 1 CTCTACGCTACTAAGCCCTAGGGCTACGGAGGA 4 261 1 * **** * **** MAP Score: 2.43847