AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i105_Manganese_Transport_ecoli_hinf_reg_300.orf -a/home/amcguire/genomes/ORF_ecoli.txt -z/home/amcguire/genomes/ecoli.fna -g0.46 -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 = 0.46 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 fecB 38 citrate-dependent iron transport, periplasmic protein #2 fecA 86 outer membrane receptor; citrate-dependent iron transport, outer membrane receptor #3 fecI 291 probable RNA polymerase sigma factor #4 HI0362 300 iron (chelated) ABC transporter, periplasmic-binding protein (yfeA) Motif number 1 CGTTCGACTCATAGCTGAACACAACAAAAAT 2 51 1 AAGCTGAACA 0.985262 -36 GATGTCAATAATAGCAGACCACATCATGAGT 3 93 1 AAGCAGACCA 0.986928 -199 TTCCAATTGTAATGATAACCATTCTCATATT 3 232 1 ATGATAACCA 0.805303 -60 AGAAAAAGTCACTGTAGAACAGCCT 4 5 0 ATGTAGAACA 0.805301 -296 ACAAACCAAAACAACTGACCAAGAAAAAGTC 4 26 0 AAACTGACCA 0.974546 -275 CTAAAATGACAGAACAAACCAAAACAACTGA 4 39 0 AAACAAACCA 0.952838 -262 AGCCAAGACTATTGCTGAACTTAATACTAAC 4 86 1 ATGCTGAACT 0.877199 -215 TGCTGAACTTAATACTAACCAAAATGTTTTG 4 98 1 ATACTAACCA 0.952838 -203 GTATGAAAAAAGAACAAAACATTTTGGTTAG 4 112 0 AAACAAAACA 0.937714 -189 AATCATTCCCATTCCAAAACAATATAAAAAG 4 193 1 ATCCAAAACA 0.850907 -108 TAATTGTTCAATAGCTCAACAATTATTCATC 4 240 0 AAGCTCAACA 0.938757 -61 * ********* Masking position 8 Map Score: 10.4374 Number of sites scoring better than the average of aligned sites = 1122 Number in coding regions = 1046 Number in noncoding regions = 76 Number of orfs with sites within 600 bp upstream = 81 Fraction of orfs with sites within 600 bp upstream = 0.01301 Motif number 2 AATCGAAATAAGAATTATTTTCC 2 4 0 AGAATTATTT 0.933242 -83 ACCTTCCCCATCATCATTTTTGTTGTGTT 2 68 0 ATCATCATTT 0.913879 -19 CCTTAAAATCACCATCATACACTAAATCAG 3 18 1 ACCATCATAC 0.798748 -274 AATTGTAATGATAACCATTCTCATATTAAT 3 236 1 ATAACCATTC 0.908805 -56 AGATTTATTTATAATTATTTCGTACAAAAT 4 152 0 ATAATTATTT 0.944014 -149 TCAAAATAATAGATTTATTTATAATTATTT 4 162 0 AGATTTATTT 0.687856 -139 TATTATTTTGATAATCATTCCCATTCCAAA 4 181 1 ATAATCATTC 0.977092 -120 CAATAGCTCAACAATTATTCATCGGAGATA 4 233 0 ACAATTATTC 0.975614 -68 GAGCTATTGAACAATTATTCAGGCATTCAA 4 254 1 ACAATTATTC 0.975614 -47 ********** Masking position 7 Map Score: 7.25753 Number of sites scoring better than the average of aligned sites = 282 Number in coding regions = 205 Number in noncoding regions = 77 Number of orfs with sites within 600 bp upstream = 93 Fraction of orfs with sites within 600 bp upstream = 0.0149374 Motif number 3 TTATTTCGATTGTCCTTTTTACCCTTCTCG 2 23 1 TGTCCTTTTT 0.991499 -64 ATTTTTAACATGTTGTTTTTCTAAGTGTTA 3 181 0 TGTTGTTTTT 0.936312 -111 TGGTTTGTTCTGTCATTTTAGGTTTATCAT 4 49 1 TGTCATTTTA 0.878671 -252 CAAAATGTTTTGTTCTTTTTTCATACATTC 4 117 1 TGTTCTTTTT 0.975254 -184 GCATTCAATCTATCTTTTTTAAATAAGGAC 4 276 1 TATCTTTTTT 0.819539 -25 AAGATGTCCTTATTTAAAAAAGAT 4 287 0 TGTCCTTATT 0.966413 -14 ********** Masking position 6 Map Score: 4.3639 Number of sites scoring better than the average of aligned sites = 135 Number in coding regions = 88 Number in noncoding regions = 47 Number of orfs with sites within 600 bp upstream = 62 Fraction of orfs with sites within 600 bp upstream = 0.00995824 Motif number 4 CAAAAATGATGATGGGGAAGGT 2 75 1 GATGGGGAAG 0.988395 -12 TTTAGTGTATGATGGTGATTTTAAGGTGCT 3 14 0 GATGGTGATT 0.971545 -278 TGCCCTAAAGGATGGGGATTTCGGTAATGC 3 58 0 GATGGGGATT 0.990198 -234 GGTAGGTATAAAATGGGATGGAGCCTCTGC 3 148 0 AAATGGGATG 0.893381 -144 AGTCTTGGCTGCTTGTGATGATAAACCTAA 4 66 0 GCTTGTGATG 0.925849 -235 TATTGTTTTGGAATGGGAATGATTATCAAA 4 187 0 GAATGGGAAT 0.948617 -114 ********** Masking position 8 Map Score: 3.44984 Number of sites scoring better than the average of aligned sites = 580 Number in coding regions = 541 Number in noncoding regions = 39 Number of orfs with sites within 600 bp upstream = 44 Fraction of orfs with sites within 600 bp upstream = 0.00706714 Motif number 5 AAAATCACCATCATACACTAAATCAGTAAG 3 22 1 TCATACACTA 0.892095 -270 GACCACATCATGAGTCATTCTGACCGACAC 3 109 1 TGAGTCATTC 0.943849 -183 AATTAACTTTTGATGCACTCCGC 3 279 1 TGATGCACTC 0.978519 -13 TGTTCTTTTTTCATACATTCAATACATTTT 4 127 1 TCATACATTC 0.975523 -174 GAACAATTATTCAGGCATTCAATCTATCTT 4 262 1 TCAGGCATTC 0.98511 -39 ********** Masking position 7 Map Score: 1.27572 Number of sites scoring better than the average of aligned sites = 100 Number in coding regions = 85 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 6 ********** No masking Map Score: -2.95996e-13 Number of sites scoring better than the average of aligned sites = 0 Number in coding regions = 0 Number in noncoding regions = 0 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0 Motif number 7 ********** No masking Map Score: -2.95996e-13 Number of sites scoring better than the average of aligned sites = 0 Number in coding regions = 0 Number in noncoding regions = 0 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0 Motif number 8 ********** No masking Map Score: -2.95996e-13 Number of sites scoring better than the average of aligned sites = 0 Number in coding regions = 0 Number in noncoding regions = 0 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0