AlignACE version 2.2 July 7, 1998 alignACE -i119_Spermidine_putrescine_Transport_ecoli_hinf_reg_300.orf -a/home/amcguire/alignace/lib/ORF_ecoli.txt -z/skink1/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 potF 300 periplasmic putrescine-binding protein; permease protein #2 potA 249 ATP-binding component of spermidine/putrescine transport #3 HI0498 254 spermidine/putrescine ABC transporter, periplasmic-binding protein (potD) #4 HI1344 72 spermidine/putrescine ABC transporter, periplasmic-binding protein (potD) #5 HI1345 25 spermidine/putrescine ABC transporter, permease protein (potC) #6 HI1347 268 spermidine/putrescine ABC transporter, ATP-binding protein (potA) Motif number 1 AATCTTTAAGAAAAGGTTAAAAACAGCAGATAAT 1 10 0 AAAATTAACA 0.877447 -291 AAATCGACACAAGAGAAGTGAAATAATCTTTAAGA 1 34 0 AAGAAGAATA 0.805115 -267 AATATGCATAAAAATTTGTTAAATACCGTTTTTTA 1 88 1 AAAATGAATA 0.968429 -213 GTCACACTGAAAGATATGCAATAAACGTGCATATT 1 233 0 AAGATGAAAA 0.933845 -68 ACAAACGAACAAAAGTTGTCACACTGAAAGATATG 1 250 0 AAAATGAACT 0.967728 -51 ATTAAGAAGCAAGAAAAGACAAATATTGCGTCAGG 2 41 1 AAGAAGAATA 0.805115 -209 TCCCTTAGGAAAAAACTGGCAAAATCTTACCCCGA 3 17 1 AAAATGAAAT 0.958834 -238 ATTTTTTTCTAAAAGGTTTGACATATTTCCCTTTC 3 50 0 AAAATTAATA 0.847589 -205 ACCTTTTAGAAAAAAATGCTATACTGCGCGCGCGC 3 68 1 AAAATGAACT 0.967728 -187 TCGGAGGTCAATAAATTGAAAAAATTCTTTGCTCA 3 136 1 ATAATGAAAT 0.696275 -119 TTAACAAAAGGTTTCACAAACCTTTGAATT 4 6 1 AAAATTAAAA 0.847589 -67 AGATATTTTTAAAAGGAGCGAGAAT 6 1 0 AAAAAGAAAT 0.872068 -268 TTAATTTTATAAATATTGTTATATATCAAGATGTT 6 62 0 AAATTGAATA 0.751185 -207 GAGTAGAAATAAAACCTGCAAGACTGCAGGGGCGA 6 229 0 AAAATGAACT 0.967728 -40 **** ** * *** Masking position 11 Map Score: 11.8454 Number of sites scoring better than the average of aligned sites = 419 Number in coding regions = 283 Number in noncoding regions = 136 Number of orfs with sites within 600 bp upstream = 163 Fraction of orfs with sites within 600 bp upstream = 0.0261805 Motif number 2 ATTATCTGCTGTTTTTAACCTTTTCT 1 7 1 TGCTGTTTTT 0.82719 -294 TTTGTTAAATACCGTTTTTTAATCCGAGCT 1 102 1 ACCGTTTTTT 0.702091 -199 AATAACTTTAGCCAGGGTTTGAGACTATAG 1 130 0 GCCAGGGTTT 0.827354 -171 GCAATAAACGTGCATATTTTTTATCGGCGC 1 221 0 TGCATATTTT 0.749414 -80 GGCTTACCGATGCGGGGTTTGTGGTTAACC 2 215 0 TGCGGGGTTT 0.890065 -35 TTTTTCCTAAGGGATTTTTT 3 1 0 GGGATTTTTT 0.738914 -254 GTAAGATTTTGCCAGTTTTTTCCTAAGGGA 3 17 0 GCCAGTTTTT 0.936651 -238 CGCGCAGTATAGCATTTTTTTCTAAAAGGT 3 68 0 AGCATTTTTT 0.878933 -187 GCGCAAAATTTGCGTGTTTTATGATGAACG 3 99 1 TGCGTGTTTT 0.935879 -156 GCACAATCAAGGCGTTTTTTT 4 62 1 GGCGTTTTTT 0.961373 -11 TTTTATGAACGGCAGTTTTTTACTTTCTAA 6 139 1 GGCAGTTTTT 0.977062 -130 CCTGCAGTCTTGCAGGTTTTATTTCTACTC 6 234 1 TGCAGGTTTT 0.961508 -35 ********** Masking position 8 Map Score: 10.852 Number of sites scoring better than the average of aligned sites = 2028 Number in coding regions = 1656 Number in noncoding regions = 372 Number of orfs with sites within 600 bp upstream = 349 Fraction of orfs with sites within 600 bp upstream = 0.0560553 Motif number 3 GCTGTTTTTAACCTTTTCTTAAAGATTATT 1 18 1 ACCTTTTCTT 0.969931 -283 AAGATTATTTCACTTCTCTTGTGTCGATTT 1 39 1 CACTTCTCTT 0.869941 -262 GGAGAAAGTTCTCTTTTCTTACACCGCGCC 1 196 1 CTCTTTTCTT 0.979161 -105 TCAGTGTGACAACTTTTGTTCGTTTGTTAA 1 258 1 AACTTTTGTT 0.880624 -43 ATCTCTTTCCTTCTGAAAGTTC 1 289 0 CTCTTTCCTT 0.925816 -12 CGCAATATTTGTCTTTTCTTGCTTCTTAAT 2 41 0 GTCTTTTCTT 0.946028 -209 TCACTCAAAAATCTTTTCCTTTCCACCACC 3 172 1 ATCTTTTCCT 0.911774 -83 GGTTTGTGAAACCTTTTGTTAA 4 3 0 ACCTTTTGTT 0.919436 -70 ********** Masking position 5 Map Score: 5.63756 Number of sites scoring better than the average of aligned sites = 142 Number in coding regions = 104 Number in noncoding regions = 38 Number of orfs with sites within 600 bp upstream = 41 Fraction of orfs with sites within 600 bp upstream = 0.00658529 Motif number 4 CTTTCCTTCTGAAAGTTCGTTAACAAACGA 1 277 0 GAAAGTTCGT 0.924602 -24 TGTTGTCACAAAAAGTGAGGGTGACTAC 2 9 0 AAAAGTGAGG 0.924602 -241 AGAAAAGACAAATATTGCGTCAGGTCACTT 2 52 1 AATATTGCGT 0.902827 -198 CGCGCGCGCAAAATTTGCGTGTTTTATGAT 3 94 1 AAATTTGCGT 0.902827 -161 GGAAGCCGCAAAAAGTGCGGTGGTGGAAAG 3 190 0 AAAAGTGCGG 0.989533 -65 AAAACGCCTTGATTGTGCGTCAAGGCGTAT 4 50 0 GATTGTGCGT 0.947068 -23 AAAATTCATCGAAAGTGCGGTTAAATTTCT 6 103 1 GAAAGTGCGG 0.991317 -166 ********** Masking position 2 Map Score: 4.9543 Number of sites scoring better than the average of aligned sites = 472 Number in coding regions = 422 Number in noncoding regions = 50 Number of orfs with sites within 600 bp upstream = 61 Fraction of orfs with sites within 600 bp upstream = 0.00979762 Motif number 5 AAGAAAAGGTTAAAAACAGCAGATAAT 1 7 0 TAAAAACACA 0.742753 -294 GCTCGCTATATAAAAGCATCGCAAGAATAAC 1 154 0 TAAAAGCACG 0.9871 -147 CGGTTTGCCGTAGAATTACCGCCCTCATTAA 2 171 1 TAGAATTACG 0.923806 -79 GTAAACGCAACGGATGGCTTAC 2 238 0 TAAACGCACG 0.977442 -12 TGTCCAGTTATAGACGTAAAGTTTGTTATTG 3 228 0 TAGACGTAAG 0.694093 -27 AAGATATTTTTAAAAGGAGCGAGAAT 6 6 0 TAAAAGGACG 0.966153 -263 ACAATATTTATAAAATTAACGAAGTAAAATT 6 78 1 TAAAATTACG 0.955379 -191 CTGCCGTTCATAAAAATAACGAGAAATTTAA 6 123 0 TAAAAATACG 0.955379 -146 ******** ** Masking position 4 Map Score: 3.19143 Number of sites scoring better than the average of aligned sites = 351 Number in coding regions = 313 Number in noncoding regions = 38 Number of orfs with sites within 600 bp upstream = 49 Fraction of orfs with sites within 600 bp upstream = 0.00787022 Motif number 6 ATTCTACGGCAAACCGCTTGAATCGCCAAT 2 157 0 AAACCGCTTG 0.974251 -93 GTTTGTGGTTAACCACCTTGGTGACTCTTA 2 199 0 AACCACCTTG 0.960054 -51 AAGGTTTGTGAAACCTTTTGTTAA 4 5 0 AAACCTTTTG 0.874675 -68 TTAAAATAGAATACGCCTTGACGCACAATC 4 40 1 ATACGCCTTG 0.961656 -33 AAAAAAACGCCTTGATTGTGCGTC 4 59 0 AAACGCCTTG 0.990091 -14 GAAAAATAGAAAACATCTTGATATATAACA 6 51 1 AAACATCTTG 0.966813 -218 ********** Masking position 8 Map Score: 3.79413 Number of sites scoring better than the average of aligned sites = 98 Number in coding regions = 86 Number in noncoding regions = 12 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 7 GATGCTTTTATATAGCGAGCAGTGCTGGCCGG 1 165 1 TAAGCGGCAG 0.977664 -136 AAGAGAACTTTCTCCCGGCCAGCACTGCTCGC 1 179 0 TCCCCGCCAG 0.98819 -122 TCTCTTTTCTTACACCGCGCCGATAAAAAATA 1 205 1 TAACCGGCCG 0.946492 -96 TGATAAATATTCCCGCTTGCAGGGGTAAAAGT 2 78 0 TCCGCTGCAG 0.991149 -172 CGCAAATTTTGCGCGCGCGCAGTATAGCATTT 3 81 0 GCCGCGGCAG 0.989341 -174 TGATGAACGATAACCCTCGGAGGTCAATAAAT 3 120 1 TACCCTGGAG 0.931929 -135 TTTTTATATGTCGCCCCTGCAGTCTTGCAGGT 6 219 1 TCCCCCGCAG 0.991974 -50 ** **** **** Masking position 6 Map Score: 2.67604 Number of sites scoring better than the average of aligned sites = 618 Number in coding regions = 585 Number in noncoding regions = 33 Number of orfs with sites within 600 bp upstream = 37 Fraction of orfs with sites within 600 bp upstream = 0.00594282 Motif number 8 TTTCAGTGTGACAACTTTTGTTCGTTTGTT 1 256 1 ACAACTTTTG 0.667299 -45 GCTTGAATCGCCAATCTTTGTTGTGAATTA 2 142 0 CCAATCTTTG 0.962156 -108 CATCGGTAAGCCATCCGTTGCGTTTAC 2 233 1 CCATCCGTTG 0.814832 -17 GGAAATATGTCAAACCTTTTAGAAAAAAAT 3 55 1 CAAACCTTTT 0.934897 -200 TAAATTGAAAAAATTCTTTGCTCACTCACT 3 147 1 AAATTCTTTG 0.797343 -108 CACTCACTCAAAAATCTTTTCCTTTCCACC 3 169 1 AAAATCTTTT 0.800147 -86 AAAGGTTTGTGAAACCTTTTGTTAA 4 6 0 GAAACCTTTT 0.826361 -67 AAAGGTTTCACAAACCTTTGAATTTAAAAT 4 17 1 CAAACCTTTG 0.936578 -56 TACTCAGTACCAAATCATTG 6 259 1 CAAATCATTG 0.838871 -10 ********** Masking position 3 Map Score: 3.57195 Number of sites scoring better than the average of aligned sites = 547 Number in coding regions = 501 Number in noncoding regions = 46 Number of orfs with sites within 600 bp upstream = 51 Fraction of orfs with sites within 600 bp upstream = 0.00819146 Motif number 9 TAAGAAAAGGTTAAAAACAGCAGATAAT 1 9 0 TTAAAAACAG 0.679516 -292 GCAAATATGCATAAAAATTTGTTAAATACC 1 85 1 ATAAAAATTT 0.579674 -216 ACCGCGCCGATAAAAAATATGCACGTTTAT 1 218 1 TAAAAAATAT 0.729034 -83 GTTGTCACACTGAAAGATATGCAATAAACG 1 241 0 TGAAAGATAT 0.732839 -60 AAGCAAGAAAAGACAAATATTGCGTCAGGT 2 47 1 AGACAAATAT 0.738707 -203 AAGGTAATGCTGATAAATATTCCCGCTTGC 2 90 0 TGATAAATAT 0.795774 -160 CAAACCTTTTAGAAAAAAATGCTATACTGC 3 65 1 AGAAAAAAAT 0.634882 -190 AACCTTTGAATTTAAAATAGAATACGCCTT 4 29 1 TTTAAAATAG 0.567915 -44 CTCGCTCCTTTTAAAAATATCTTTTTTAGT 6 14 1 TTAAAAATAT 0.937547 -255 TAGTTTAACGAGAAAAATAGAAAACATCTT 6 40 1 AGAAAAATAG 0.925094 -229 TTCGTTAATTTTATAAATATTGTTATATAT 6 71 0 TTATAAATAT 0.770637 -198 ACTGCCGTTCATAAAAATAACGAGAAATTT 6 125 0 ATAAAAATAA 0.671343 -144 GGGGCGACATATAAAAATAGACGCCTATGA 6 206 0 ATAAAAATAG 0.914245 -63 ********** Masking position 5 Map Score: 3.74909 Number of sites scoring better than the average of aligned sites = 685 Number in coding regions = 480 Number in noncoding regions = 205 Number of orfs with sites within 600 bp upstream = 229 Fraction of orfs with sites within 600 bp upstream = 0.0367812 Motif number 10 GTAGTCACCCTCACTTTTTGTGACAA 2 7 1 ACCCTCACTT 0.946018 -243 AATATTGCGTCAGGTCACTTTTACCCCTGC 2 62 1 CAGGTCACTT 0.891093 -188 TCCTTTCCACCACCGCACTTTTTGCGGCTT 3 188 1 CACCGCACTT 0.988134 -67 CGAGAAATTTAACCGCACTTTCGATGAATT 6 105 0 AACCGCACTT 0.965547 -164 TATTTTTATGAACGGCAGTTTTTTACTTTC 6 136 1 AACGGCAGTT 0.875302 -133 ********** Masking position 7 Map Score: 0.403536 Number of sites scoring better than the average of aligned sites = 113 Number in coding regions = 103 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 11 ********** No masking Map Score: -3.54318e-12 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 12 ********** No masking Map Score: -3.54318e-12 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 13 ********** No masking Map Score: -3.54318e-12 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