AlignACE version 2.2 July 7, 1998 alignACE -i119_Spermidine_putrescine_Transport_ecoli_hinf_reg_100.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 ATTATCTGCTGTTTTTAACCTTTTCTTAAAGATT 1 10 1 TGTTAATTTT 0.87998 -291 TCTTAAAGATTATTTCACTTCTCTTGTGTCGATTT 1 34 1 TATTCTTCTT 0.808817 -267 TAAAAAACGGTATTTAACAAATTTTTATGCATATT 1 88 0 TATTCATTTT 0.969147 -213 AATATGCACGTTTATTGCATATCTTTCAGTGTGAC 1 233 1 TTTTCATCTT 0.935299 -68 CATATCTTTCAGTGTGACAACTTTTGTTCGTTTGT 1 250 1 AGTTCATTTT 0.968463 -51 CCTGACGCAATATTTGTCTTTTCTTGCTTCTTAAT 2 41 0 TATTCTTCTT 0.808817 -209 TCGGGGTAAGATTTTGCCAGTTTTTTCCTAAGGGA 3 17 0 ATTTCATTTT 0.959762 -238 GAAAGGGAAATATGTCAAACCTTTTAGAAAAAAAT 3 50 1 TATTAATTTT 0.850634 -205 GCGCGCGCGCAGTATAGCATTTTTTTCTAAAAGGT 3 68 0 AGTTCATTTT 0.968463 -187 TGAGCAAAGAATTTTTTCAATTTATTGACCTCCGA 3 136 0 ATTTCATTAT 0.701277 -119 AATTCAAAGGTTTGTGAAACCTTTTGTTAA 4 6 0 TTTTAATTTT 0.850634 -67 ATTCTCGCTCCTTTTAAAAATATCT 6 1 1 ATTTCTTTTT 0.874696 -268 AACATCTTGATATATAACAATATTTATAAAATTAA 6 62 1 TATTCAATTT 0.755601 -207 TCGCCCCTGCAGTCTTGCAGGTTTTATTTCTACTC 6 229 1 AGTTCATTTT 0.968463 -40 *** * ** **** Masking position 5 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 AAGAAAAGGTTAAAAACAGCAGATAAT 1 8 0 TAAAAACAGC 0.844033 -293 TAGCTCGGATTAAAAAACGGTATTTAACAA 1 103 0 TAAAAAACGG 0.877992 -198 CGCGCCGATAAAAAATATGCACGTTTATTG 1 220 1 AAAAATATGC 0.945577 -81 TGTCACACTGAAAGATATGCAATAAACGTG 1 239 0 AAAGATATGC 0.765916 -62 ATCCCTTAGGAAAAAACTGGCAAAATCTTA 3 16 1 AAAAAACTGG 0.88069 -239 AACCTTTTAGAAAAAAATGCTATACTGCGC 3 67 1 AAAAAAATGC 0.970693 -188 TCGTTCATCATAAAACACGCAAATTTTGCG 3 100 0 TAAAACACGC 0.944751 -155 GAATTTAAAATAGAATACGCCTTGACGCAC 4 36 1 TAGAATACGC 0.748939 -37 AAAAAAACGCCTTGATTGTG 4 63 0 AAAAAAACGC 0.972888 -10 CTTAGAAAGTAAAAAACTGCCGTTCATAAA 6 140 0 AAAAAACTGC 0.968726 -129 TGAGTAGAAATAAAACCTGCAAGACTGCAG 6 235 0 TAAAACCTGC 0.936551 -34 ********** Masking position 5 Map Score: 10.2368 Number of sites scoring better than the average of aligned sites = 826 Number in coding regions = 595 Number in noncoding regions = 231 Number of orfs with sites within 600 bp upstream = 222 Fraction of orfs with sites within 600 bp upstream = 0.0356569 Motif number 3 GCTGTTTTTAACCTTTTCTTAAAGATTATT 1 18 1 ACCTTTTCTT 0.972373 -283 AAGATTATTTCACTTCTCTTGTGTCGATTT 1 39 1 CACTTCTCTT 0.879492 -262 GGAGAAAGTTCTCTTTTCTTACACCGCGCC 1 196 1 CTCTTTTCTT 0.980868 -105 TCAGTGTGACAACTTTTGTTCGTTTGTTAA 1 258 1 AACTTTTGTT 0.889488 -43 ATCTCTTTCCTTCTGAAAGTTC 1 289 0 CTCTTTCCTT 0.931586 -12 CGCAATATTTGTCTTTTCTTGCTTCTTAAT 2 41 0 GTCTTTTCTT 0.95031 -209 TCACTCAAAAATCTTTTCCTTTCCACCACC 3 172 1 ATCTTTTCCT 0.918541 -83 GGTTTGTGAAACCTTTTGTTAA 4 3 0 ACCTTTTGTT 0.925662 -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 0.908988 -24 TGTTGTCACAAAAAGTGAGGGTGACTAC 2 9 0 AAAAGTGAGG 0.908988 -241 AGAAAAGACAAATATTGCGTCAGGTCACTT 2 52 1 AATATTGCGT 0.883272 -198 CGCGCGCGCAAAATTTGCGTGTTTTATGAT 3 94 1 AAATTTGCGT 0.883272 -161 GGAAGCCGCAAAAAGTGCGGTGGTGGAAAG 3 190 0 AAAAGTGCGG 0.987179 -65 AAAACGCCTTGATTGTGCGTCAAGGCGTAT 4 50 0 GATTGTGCGT 0.935783 -23 AAAATTCATCGAAAGTGCGGTTAAATTTCT 6 103 1 GAAAGTGCGG 0.98936 -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 0.708374 -294 GCTCGCTATATAAAAGCATCGCAAGAATAAC 1 154 0 TAAAAGCACG 0.984703 -147 CGGTTTGCCGTAGAATTACCGCCCTCATTAA 2 171 1 TAGAATTACG 0.910715 -79 GTAAACGCAACGGATGGCTTAC 2 238 0 TAAACGCACG 0.9733 -12 TGTCCAGTTATAGACGTAAAGTTTGTTATTG 3 228 0 TAGACGTAAG 0.656221 -27 AAGATATTTTTAAAAGGAGCGAGAAT 6 6 0 TAAAAGGACG 0.960023 -263 ACAATATTTATAAAATTAACGAAGTAAAATT 6 78 1 TAAAATTACG 0.947404 -191 CTGCCGTTCATAAAAATAACGAGAAATTTAA 6 123 0 TAAAAATACG 0.947404 -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 GCTATAGTCTCAAACCCTGGCTAAAGTTAT 1 129 1 CAAACCCTGG 0.902253 -172 GCTTGAATCGCCAATCTTTGTTGTGAATTA 2 142 0 CCAATCTTTG 0.897095 -108 AATTCTACGGCAAACCGCTTGAATCGCCAA 2 158 0 CAAACCGCTT 0.870664 -92 CATCGGTAAGCCATCCGTTGCGTTTAC 2 233 1 CCATCCGTTG 0.867909 -17 GGAAATATGTCAAACCTTTTAGAAAAAAAT 3 55 1 CAAACCTTTT 0.966906 -200 AAAGGTTTGTGAAACCTTTTGTTAA 4 6 0 GAAACCTTTT 0.834937 -67 AAAGGTTTCACAAACCTTTGAATTTAAAAT 4 17 1 CAAACCTTTG 0.937928 -56 TACTCAGTACCAAATCATTG 6 259 1 CAAATCATTG 0.836404 -10 ********** Masking position 3 Map Score: 2.53009 Number of sites scoring better than the average of aligned sites = 570 Number in coding regions = 544 Number in noncoding regions = 26 Number of orfs with sites within 600 bp upstream = 28 Fraction of orfs with sites within 600 bp upstream = 0.00449727 Motif number 7 CCGGCCAGCACTGCTCGCTATATAAAAGCATC 1 165 0 CTGCCGCTTA 0.975705 -136 GCGAGCAGTGCTGGCCGGGAGAAAGTTCTCTT 1 179 1 CTGGCGGGGA 0.987142 -122 TATTTTTTATCGGCGCGGTGTAAGAAAAGAGA 1 205 0 CGGCCGGTTA 0.941961 -96 ACTTTTACCCCTGCAAGCGGGAATATTTATCA 2 78 1 CTGCAGCGGA 0.990361 -172 AAATGCTATACTGCGCGCGCGCAAAATTTGCG 3 81 1 CTGCCGCGGC 0.988556 -174 ATTTATTGACCTCCGAGGGTTATCGTTCATCA 3 120 0 CTCCAGGGTA 0.92626 -135 ACCTGCAAGACTGCAGGGGCGACATATAAAAA 6 219 0 CTGCGGGGGA 0.991259 -50 **** **** ** Masking position 7 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 CAACTTTTGTTCGTTTGTTAACGAACTTTCAGAA 1 267 1 TCTTTTAACA 0.915834 -34 TTGTCTTTTCTTGCTTCTTAATAATGTTGTCACA 2 29 0 TTTTTTAATA 0.907831 -221 ATCGCCAATCTTTGTTGTGAATTACTGGCTTAGC 2 132 0 TTTTTGAATA 0.86924 -118 CGATGCGGGGTTTGTGGTTAACCACCTTGGTGAC 2 204 0 TTTGTTAACA 0.977644 -46 ATTTGCGTGTTTTATGATGAACGATAACCCTCGG 3 106 1 TTTGTGAACA 0.967065 -149 AAAATATCTTTTTTAGTTTAACGAGAAAAATAGA 6 27 1 TTAGTTAACA 0.900781 -242 TTAAGTCCTTTTCATTATTAACAATTCACTATAT 6 173 1 TTTTTTAACA 0.972899 -96 ** ** ***** * Masking position 10 Map Score: 0.815434 Number of sites scoring better than the average of aligned sites = 85 Number in coding regions = 62 Number in noncoding regions = 23 Number of orfs with sites within 600 bp upstream = 31 Fraction of orfs with sites within 600 bp upstream = 0.00497912 Motif number 9 CTCAAACCCTGGCTAAAGTTATTCTTGCGATGC 1 137 1 GGAAAGTATT 0.938936 -164 GTGCTGGCCGGGAGAAAGTTCTCTTTTCTTACA 1 186 1 GGAAAGTCTC 0.987869 -115 CGCTTGCAGGGGTAAAAGTGACCTGACGCAATA 2 64 0 GGAAAGTACC 0.916341 -186 CCCTGCAAGCGGGAATATTTATCAGCATTACCT 2 86 1 GGATATTATC 0.937229 -164 AAATTAACGAAGTAAAATTCATCGAAAGTGCGG 6 90 1 AGAAATTATC 0.902416 -179 TCGAAAGTGCGGTTAAATTTCTCGTTATTTTTA 6 111 1 GGAAATTCTC 0.949318 -158 ** ***** *** Masking position 7 Map Score: 0.0295425 Number of sites scoring better than the average of aligned sites = 159 Number in coding regions = 150 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 10 ********** 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 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