AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_ecoli.txt -z/home/amcguire/genomes/ecoli.fna -irhaS_ecoli_bsub_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 rhaD 300 rhamnulose-phosphate aldolase #2 rhaB_rhaS 287 rhaB: rhamnulokinase, rhaS: positive regulator for rhaBAD operon #3 rhaT 284 rhamnose transport #4 ybfI 230 similar to transcriptional regulator (AraC/XylS family) #5 ycxE 122 similar to hypothetical proteins #6 yfiD 154 similar to hypothetical proteins #7 yfiF 93 similar to transcriptional regulator (AraC/XylS family) #8 yulE 25 similar to L-rhamnose isomerase #9 yulB 56 similar to transcriptional regulator (DeoR family) #10 yuxG 137 alternate gene name: yulA; similar to sorbitol-6-phosphate 2-dehydrogenase Motif number 1 CGACGCTGTCGCGTCTTATCAGGC 1 1 0 GCGCATCGGC 0.999641 -300 AGACGCGACAGCGTCGCATCAGGCATTGATTGCC 1 19 1 GCGCATCGGC 0.999674 -282 TAAGGCACTTGTGCCGCATCCGGCAATCAATGCC 1 40 0 GTGCATCGGC 0.998528 -261 TGCGGCACAAGTGCCTTATCCGGCCTACAGGTCG 1 56 1 GTGCATCGGC 0.998528 -245 CGACGCTGTCGCGTCTTATCAGGCCTACAACTGT 1 93 0 GCGCATCGGC 0.999641 -208 AGACGCGACAGCGTCGCATCAGGCATTGATTGCC 1 111 1 GCGCATCGGC 0.999674 -190 ATGCGCACAAGTCGCTTATCAGGCCTACAGGTCG 1 147 1 GTCCATCGGC 0.986294 -154 CGACGCTGTCGCGTCTTATCAGGCCTACAACTAT 1 184 0 GCGCATCGGC 0.999641 -117 AGACGCGACAGCGTCGCATCAGGCATTGATTGCC 1 202 1 GCGCATCGGC 0.999674 -99 ATGCGCGCGAGCGCCTTATCCGGCCTACGGGTCG 1 240 1 GCGCATCGGC 0.999641 -61 AAAAGAGCTGCCGGAAAATCCGGCAGCTCTCAGG 5 24 0 CCGAATCGGC 0.959104 -99 AAACGAGAAAGCGGCATATCTGCTGCTTTCTTTT 10 13 1 GCGCATCGCT 0.959104 -125 *** * *** *** Masking position 8 Map Score: 56.4405 Number of sites scoring better than the average of aligned sites = 312 Number in coding regions = 49 Number in noncoding regions = 263 Number of orfs with sites within 600 bp upstream = 52 Fraction of orfs with sites within 600 bp upstream = 0.00835207 Motif number 2 CAGCGTCGCATCAGGCATTGATTGCCGGATG 1 27 1 TCAGGCATGA 0.993061 -274 AAGTGCCTTATCCGGCCTACAGGTCGGCAAC 1 64 1 TCCGGCCTCA 0.996568 -237 TCGCGTCTTATCAGGCCTACAACTGTTGCCG 1 88 0 TCAGGCCTCA 0.997167 -213 CAGCGTCGCATCAGGCATTGATTGCCGGATG 1 119 1 TCAGGCATGA 0.993061 -182 AAGTCGCTTATCAGGCCTACAGGTCGGCAAT 1 155 1 TCAGGCCTCA 0.997167 -146 TCGCGTCTTATCAGGCCTACAACTATTGCCG 1 179 0 TCAGGCCTCA 0.997167 -122 CAGCGTCGCATCAGGCATTGATTGCCGTGGA 1 210 1 TCAGGCATGA 0.993061 -91 GAGCGCCTTATCCGGCCTACGGGTCGTGCAT 1 248 1 TCCGGCCTCG 0.985496 -53 TTACGAAAAGTACGGCATTGATAATCATTTT 3 92 0 TACGGCATGA 0.921348 -193 ******** ** Masking position 8 Map Score: 24.6693 Number of sites scoring better than the average of aligned sites = 232 Number in coding regions = 42 Number in noncoding regions = 190 Number of orfs with sites within 600 bp upstream = 57 Fraction of orfs with sites within 600 bp upstream = 0.00915516 Motif number 3 TGCCTGATGCGACGCTGTCGCGTCTTATCA 1 14 0 GACGCTGTCG 0.946837 -287 CAGGCCTACAACTGTTGCCGACCTGTAGGC 1 78 0 ACTGTTGCCG 0.966272 -223 TGCCTGATGCGACGCTGTCGCGTCTTATCA 1 106 0 GACGCTGTCG 0.946837 -195 CAGGCCTACAACTATTGCCGACCTGTAGGC 1 169 0 ACTATTGCCG 0.783776 -132 TGCCTGATGCGACGCTGTCGCGTCTTATCA 1 197 0 GACGCTGTCG 0.946837 -104 CTGTAAATTCGGTGTTGTCGGATGCACGAC 1 270 0 GGTGTTGTCG 0.960723 -31 ACTGGCCTCCTGATGTCGTCAACACGGC 2 9 1 CCTGATGTCG 0.858609 -279 ATTCATCTCCAGTATTGTCGGGCGGCCGAT 3 11 1 AGTATTGTCG 0.659945 -274 TAACCTTTCGCCTGTTGCCGCCGTTGTCGA 3 195 0 CCTGTTGCCG 0.981979 -90 GTGTAAAAATCGTGCTGTCGATTAACCTTT 3 217 0 CGTGCTGTCG 0.98159 -68 GGGATGCCTCCTGTCGGTGTGGTGGT 4 215 0 CCTCCTGTCG 0.946403 -16 CACGCTCCTGAGAGCTGCCGGATTTTCCGG 5 18 1 AGAGCTGCCG 0.926107 -105 GAACACAAAAAGAGCTGCCGGAAAATCCGG 5 35 0 AGAGCTGCCG 0.926107 -88 CTGCAATCCCCTTGCCGAAATAACGGC 7 8 1 CCCCTTGCCG 0.949695 -86 AATAAAAAATCCCCCTGCCGTTATTTCGGC 7 24 0 CCCCCTGCCG 0.971839 -70 TATGAGGAAGGGCGTTACCG 9 47 1 GGCGTTACCG 0.716452 -10 ********** Masking position 6 Map Score: 23.0454 Number of sites scoring better than the average of aligned sites = 5155 Number in coding regions = 4939 Number in noncoding regions = 216 Number of orfs with sites within 600 bp upstream = 172 Fraction of orfs with sites within 600 bp upstream = 0.0276261 Motif number 4 ATGCGACGCTGTCGCGTCTTATCAGGC 1 8 0 GTCGCGTCTT 0.994406 -293 ACGCGACAGCGTCGCATCAGGCATTGATTG 1 21 1 GTCGCATCAG 0.98553 -280 ATGCGACGCTGTCGCGTCTTATCAGGCCTA 1 100 0 GTCGCGTCTT 0.994406 -201 ACGCGACAGCGTCGCATCAGGCATTGATTG 1 113 1 GTCGCATCAG 0.98553 -188 ATGCGCACAAGTCGCTTATCAGGCCTACAG 1 147 1 GTCGCTTATC 0.81783 -154 ATGCGACGCTGTCGCGTCTTATCAGGCCTA 1 191 0 GTCGCGTCTT 0.994406 -110 ACGCGACAGCGTCGCATCAGGCATTGATTG 1 204 1 GTCGCATCAG 0.98553 -97 TAACGAGAAGGTCGCGAATTCAGGCGCTTT 2 231 1 GTCGCGAATT 0.84658 -57 ATCATTTTTCGTCGCGTCACATCTCCGACG 3 253 0 GTCGCGTCAC 0.991659 -32 ********** Masking position 2 Map Score: 19.2139 Number of sites scoring better than the average of aligned sites = 254 Number in coding regions = 110 Number in noncoding regions = 144 Number of orfs with sites within 600 bp upstream = 57 Fraction of orfs with sites within 600 bp upstream = 0.00915516 Motif number 5 CCTGACCTCGTGATTACTATTTCGCCGTGTTG 2 30 0 TGTTACATTT 0.74706 -258 TCAATAATAATTTTATCTTTTTTAATAAAAAT 4 65 0 TTTATCTTTT 0.917266 -166 GTTATTTGTCTGCTTTCGTTTAAGAATTTAAA 4 109 0 TGTTTCTTTA 0.890033 -122 AGGTCTTTTTTTGTTACAGTTTTATAGTACTT 6 28 1 TTTTACGTTT 0.910152 -127 TATAGTACTTTTATTTCATTTTCGTAAAATGT 6 50 1 TTTTTCTTTT 0.968929 -105 TCAAGTAATTTTGTTACATTTTACGAAAATGA 6 65 0 TTTTACTTTT 0.941771 -90 ATTAAGTAAGTGATAACATTTATCAAGGAGGA 6 129 1 TGTAACTTTA 0.598788 -26 GGCAGGGGGATTTTTTATTTTTGTCCGCCTTG 7 35 1 TTTTTATTTT 0.812479 -59 GCATATCTGCTGCTTTCTTTTTTTGTTAAAAA 10 26 1 TGTTTCTTTT 0.973063 -112 TGAATCGTTTTTGTTTATTTTTGCTTTTTAAC 10 50 0 TTTTTATTTT 0.812479 -88 TCATTATATATGATTTCTGTTTGTTTTTGAAT 10 77 0 TGTTTCGTTT 0.957672 -61 ACCCTTTTATTTGTATCCGTTTTCATTATATA 10 99 0 TTTATCGTTT 0.874119 -39 ** **** **** Masking position 4 Map Score: 8.54011 Number of sites scoring better than the average of aligned sites = 419 Number in coding regions = 300 Number in noncoding regions = 119 Number of orfs with sites within 600 bp upstream = 144 Fraction of orfs with sites within 600 bp upstream = 0.0231288 Motif number 6 CATCAGGCATTGATTGCCGGATGCGGCACA 1 35 1 TGATTGCCGG 0.996493 -266 CATCAGGCATTGATTGCCGGATGCGCACAA 1 127 1 TGATTGCCGG 0.996493 -174 CATCAGGCATTGATTGCCGTGGATGCGCGC 1 218 1 TGATTGCCGT 0.986211 -83 CATCTTTCCCTGGTTGCCAATGGCCCATTT 2 192 1 TGGTTGCCAA 0.93464 -96 CTTAATGCCGTGATTGCCAGTAAATCGACA 3 171 1 TGATTGCCAG 0.992133 -114 ********** Masking position 5 Map Score: 7.84914 Number of sites scoring better than the average of aligned sites = 142 Number in coding regions = 128 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 7 GTTCTGTGTTCCTGTAAATTCGGTGTTGTCG 1 280 0 TTCTAAATTC 0.963002 -21 TTCACGCTGTATCTTGAAAAATCGACGTTTTTT 2 95 0 ATCTAAAATC 0.963002 -193 CTCACCGCATTTCCTGAAAATTCACGCTGTATC 2 115 0 TTCTAAATTC 0.963002 -173 TGAGCATCACATCACCACAATTCAGCAAATTGT 2 144 1 ATCCCAATTC 0.928209 -144 CTCGGGCATTTTCCTGCAAAACCATACCCTTAC 3 119 0 TTCTAAAACC 0.831542 -166 GAGGGTTAAAATCTTTTAAATTCTTAAACGAAA 4 95 1 ATCTAAATTC 0.969759 -136 CATACAAGAAATCCCCCAAAATCATGCTACACT 4 173 1 ATCCAAAATC 0.955495 -58 CCGGCGAATAATCACAACAATTCCAGCCAAAAT 5 64 1 ATCCCAATTC 0.928209 -59 TTGGGGAACCTTCTTTCAAAATGTATTTGCTGT 5 98 0 TTCTAAAATG 0.754283 -25 *** * ****** Masking position 9 Map Score: 5.23412 Number of sites scoring better than the average of aligned sites = 126 Number in coding regions = 84 Number in noncoding regions = 42 Number of orfs with sites within 600 bp upstream = 43 Fraction of orfs with sites within 600 bp upstream = 0.00690652 Motif number 8 GCACAAGTGCCTTATCCGGCCTACAGGTCG 1 60 1 CTTATCCGGC 0.941959 -241 GCGCGAGCGCCTTATCCGGCCTACGGGTCG 1 244 1 CTTATCCGGC 0.941959 -57 GTTCTGTGTTCCTGTAAATTCGGTG 1 286 0 GTGTTCCTGT 0.659129 -15 TTTTTACGTGGTTTTCCGTCGAAAATTTAA 2 70 0 GTTTTCCGTC 0.900629 -218 CCAATGGCCCATTTTCCTGTCAGTAACGAG 2 208 1 ATTTTCCTGT 0.706049 -80 AATGTGATCCTGCTGAATTTCAT 2 275 0 GTGATCCTGC 0.913952 -13 CATCTCCAGTATTGTCGGGCGGCCGATTGT 3 14 1 ATTGTCGGGC 0.762362 -271 CATCTCGGGCATTTTCCTGCAAAACCATAC 3 125 0 ATTTTCCTGC 0.957223 -160 GAGCTGCCGGATTTTCCGGCAGCTCTTTTT 5 29 1 ATTTTCCGGC 0.976136 -94 AGCTCTTTTTGTGTTCCGGCGAATAATCAC 5 49 1 GTGTTCCGGC 0.970528 -74 ACCTTTGTCCTGCACAGAGGTCT 6 4 1 TTTGTCCTGC 0.9288 -151 TTTATCCTCCTTGATAAATG 6 145 0 TTTATCCTCC 0.720249 -10 ATTTTTTATTTTTGTCCGCCTTGTTATGAT 7 44 1 TTTGTCCGCC 0.881867 -50 TCCTCATATCGTAGTCCGTCTTATATTTTT 9 25 0 GTAGTCCGTC 0.655064 -32 ATTTGATATTCCTCCATACCCTTTT 10 123 0 ATATTCCTCC 0.610824 -15 ********** Masking position 5 Map Score: 14.6594 Number of sites scoring better than the average of aligned sites = 2788 Number in coding regions = 2420 Number in noncoding regions = 368 Number of orfs with sites within 600 bp upstream = 250 Fraction of orfs with sites within 600 bp upstream = 0.0401542 Motif number 9 ATTGATTGCCGGATGCGCACAAGTCGCTTA 1 135 1 GGATGCGCAC 0.990915 -166 TGATTGCCGTGGATGCGCGCGAGCGCCTTA 1 228 1 GGATGCGCGC 0.994197 -73 CGGTGTTGTCGGATGCACGACCCGTAGGCC 1 261 0 GGATGCACGA 0.944898 -40 TGTGGTGATGTGATGCTCACCGCATTTCCT 2 133 0 TGATGCTCAC 0.959793 -155 ATGAACGTGATGATGTTCACAATTTGCTGA 2 165 0 TGATGTTCAC 0.786927 -123 AAGAATGCACGCTCCTGAGAGC 5 3 1 GAATGCACGC 0.944669 -120 ********** Masking position 4 Map Score: 3.96785 Number of sites scoring better than the average of aligned sites = 290 Number in coding regions = 270 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 21 Fraction of orfs with sites within 600 bp upstream = 0.00337295 Motif number 10 GCGGTGAGCATCACATCACCACAATTCAGC 2 140 1 TCACATCACC 0.960506 -148 ATTCATCTCCAGTATTGTCG 3 1 1 ATTCATCTCC 0.881907 -284 GTGATTTGCTTCACATCTCGGGCATTTTCC 3 138 0 TCACATCTCG 0.982121 -147 CGATTTTTACACTCATCTCGTCGGAGATGT 3 235 1 ACTCATCTCG 0.96397 -50 TTTCGTCGCGTCACATCTCCGACGAGATGA 3 247 0 TCACATCTCC 0.987656 -38 ********** Masking position 5 Map Score: 2.20168 Number of sites scoring better than the average of aligned sites = 73 Number in coding regions = 58 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911 Motif number 11 CGGAAAACCACGTAAAAAACGTCGATTTTTCAA 2 82 1 CGAAAAACGC 0.989428 -206 TTACGACCAGTCTAAAAAGCGCCTGAATTCGCG 2 243 0 TCAAAAGCGC 0.929674 -45 CATACCCTTACGAAAAGTACGGCATTGATAATC 3 97 0 CGAAATACGC 0.976028 -188 TTTCTCTATTCCTAAACAGCAACATCATACAAG 4 148 1 CCAAAAGCAC 0.96528 -83 AAAGAGCTGCCGGAAAATCCGGCAGCTCTCAGG 5 24 0 CGAAATCCGC 0.948298 -99 ACAATTCCAGCCAAAATAACAGCAAATACATTT 5 80 1 CCAAAAACAC 0.971044 -43 AATCCCCTTGCCGAAATAACGGCAGGGGGATTT 7 15 1 CCAAAAACGC 0.991931 -79 ** *** **** * Masking position 6 Map Score: 4.17354 Number of sites scoring better than the average of aligned sites = 174 Number in coding regions = 164 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 12 TGAATTTTCAGGAAATGCGGTGAGCATCAC 2 124 1 GGAAATGCGG 0.816789 -164 TTGGCAACCAGGGAAAGATGAACGTGATGA 2 182 0 GGGAAAGATG 0.756729 -106 CGAGAAGGTCGCGAATTCAGGCGCTTTTTA 2 234 1 GCGAATTCAG 0.765201 -54 TGTTAATGCCGCGTAAGCAGTTGGTTCATT 3 41 1 GCGTAAGCAG 0.965452 -244 AAAATGATGAGGATAAGAAG 3 275 1 GGATAAGAAG 0.547688 -10 AAATTCTTAAACGAAAGCAGACAAATAACG 4 112 1 ACGAAAGCAG 0.915316 -119 TTTAGGAATAGAGAAAGCAGACCGTTATTT 4 134 0 GAGAAAGCAG 0.978079 -97 TTTCGGCAAGGGGATTGCAG 7 1 0 GGGATTGCAG 0.895302 -93 TGAAACGAGAAAGCGGCATATCTGCT 10 7 1 GAGAAAGCGG 0.950458 -131 TTAACAAAAAAAGAAAGCAGCAGATATGCC 10 25 0 AAGAAAGCAG 0.872998 -113 ACAAATAAAAGGGTATGGAGGAATATCAAA 10 117 1 GGGTATGGAG 0.795711 -21 ********** Masking position 10 Map Score: 4.66205 Number of sites scoring better than the average of aligned sites = 1797 Number in coding regions = 1674 Number in noncoding regions = 123 Number of orfs with sites within 600 bp upstream = 142 Fraction of orfs with sites within 600 bp upstream = 0.0228076 Motif number 13 TATCCGGCCTACAGGTCGGCAACAGTTGTA 1 72 1 ACAGGTCGGC 0.99274 -229 TATCAGGCCTACAGGTCGGCAATAGTTGTA 1 163 1 ACAGGTCGGC 0.99274 -138 TATCCGGCCTACGGGTCGTGCATCCGACAA 1 256 1 ACGGGTCGTG 0.975885 -45 CGCTTTTTAGACTGGTCGTAATGAAATTCA 2 255 1 ACTGGTCGTA 0.948514 -33 ********** Masking position 6 Map Score: 0.886012 Number of sites scoring better than the average of aligned sites = 51 Number in coding regions = 46 Number in noncoding regions = 5 Number of orfs with sites within 600 bp upstream = 2 Fraction of orfs with sites within 600 bp upstream = 0.000321234 Motif number 14 TGTGACGCGACGAAAAATGATGAGGATAAG 3 262 1 CGAAAAATGA 0.632862 -23 TAAATTTTTATTAAAAAAGATAAAATTATT 4 62 1 TTAAAAAAGA 0.41971 -169 TTCGCCGGAACACAAAAAGAGCTGCCGGAA 5 42 0 CACAAAAAGA 0.905828 -81 CAATTCCAGCCAAAATAACAGCAAATACAT 5 81 1 CAAAATAACA 0.598081 -42 AAAACTGTAACAAAAAAAGACCTCTGTGCA 6 21 0 CAAAAAAAGA 0.976286 -134 ACAAGGCGGACAAAAATAAAAAATCCCCCT 7 38 0 CAAAAATAAA 0.854888 -56 TGCTTTTTAACAAAAAAAGAAAGCAGCAGA 10 31 0 CAAAAAAAGA 0.976286 -107 TGTTAAAAAGCAAAAATAAACAAAAACGAT 10 49 1 CAAAAATAAA 0.854888 -89 AAAAACGATTCAAAAACAAACAGAAATCAT 10 70 1 CAAAAACAAA 0.831979 -68 ********** Masking position 5 Map Score: 1.15067 Number of sites scoring better than the average of aligned sites = 341 Number in coding regions = 249 Number in noncoding regions = 92 Number of orfs with sites within 600 bp upstream = 109 Fraction of orfs with sites within 600 bp upstream = 0.0175072 Motif number 15 TAATCATTTTCAATATCATTTAATTAACTA 3 72 0 CAATATCATT 0.794995 -213 TCCTGCAAAACCATACCCTTACGAAAAGTA 3 111 0 CCATACCCTT 0.99036 -174 CCTATCTGTTCCAAACCATTATAACTGAAA 4 21 1 CCAAACCATT 0.932701 -210 CTGCAATCCCCTTGCCGAAATAA 7 4 1 CAATCCCCTT 0.953576 -90 TGATATTCCTCCATACCCTTTTATTTGTAT 10 115 0 CCATACCCTT 0.99036 -23 ********** Masking position 3 Map Score: 1.82119 Number of sites scoring better than the average of aligned sites = 44 Number in coding regions = 40 Number in noncoding regions = 4 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701