AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i119_Spermidine_putrescine_Transport_hinf_reg_100.orf -a/home/amcguire/alignace/lib/ORF_hinf.txt -z/skink1/amcguire/genomes/hinf.fna -g0.38 -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 = 0.38 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 HI0498 254 spermidine/putrescine ABC transporter, periplasmic-binding protein (potD) #2 HI1344 72 spermidine/putrescine ABC transporter, periplasmic-binding protein (potD) #3 HI1345 25 spermidine/putrescine ABC transporter, permease protein (potC) #4 HI1347 268 spermidine/putrescine ABC transporter, ATP-binding protein (potA) Motif number 1 AAAAAATCCCTTAGGAAAAAACTGGCAAAAT 1 7 1 TCCTAAAAAA 0.981699 -248 ATATGTCAAACCTTTTAGAAAAAAATGCTATACTG 1 59 1 CCTTAAAAAA 0.987857 -196 CCGAGGGTTATCGTTCATCATAAAACACGCAAATT 1 105 0 TCTTATAAAA 0.9869 -150 AATTCTTTGCTCACTCACTCAAAAATCTTTTCCTT 1 158 1 TCCTAAAAAA 0.981514 -97 GTTTCACAAACCTTTGAATTTAAAATAGAATACGC 2 21 1 CCTTATAAAA 0.987708 -52 ATTCTCGCTCCTTTTAAAAATATCTTTTT 4 5 1 TCCTCTAAAA 0.917978 -264 TCTATTTTTCTCGTTAAACTAAAAAAGATATTTTT 4 26 0 TCTTAAAAAA 0.986856 -243 GAATTTTACTTCGTTAATTTTATAAATATTGTTAT 4 75 0 TCTTATATAA 0.913641 -194 TAAAAAACTGCCGTTCATAAAAATAACGAGAAATT 4 126 0 CCTTAAAATA 0.919942 -143 GGACTTAATGCCTTAGAAAGTAAAAAACTGCCGTT 4 146 0 CCTAATAAAA 0.919938 -123 ** ** * ***** Masking position 12 Map Score: 13.9228 Number of sites scoring better than the average of aligned sites = 152 Number in coding regions = 111 Number in noncoding regions = 41 Number of orfs with sites within 600 bp upstream = 41 Fraction of orfs with sites within 600 bp upstream = 0.00658529 Motif number 2 AAAAAATCCCTTAGGAAAAAAC 1 1 1 AAAAATCCTT 0.930296 -254 ACCTTTTAGAAAAAAATGCTATACTGCGCGCG 1 68 1 AAAAATGCAT 0.950151 -187 GCGCGCGCGCAAAATTTGCGTGTTTTATGATG 1 93 1 AAAATTGCTG 0.897466 -162 CAATAAATTGAAAAAATTCTTTGCTCACTCAC 1 144 1 AAAAATTCTT 0.897527 -111 CGGAAGCCGCAAAAAGTGCGGTGGTGGAAAGG 1 189 0 AAAAATGCGT 0.990057 -66 AATTTAAAATAGAATACGCCTTGACGCACAAT 2 37 1 AGAATCGCTT 0.790075 -36 AAAAAAACGCCTTGATTGTGCGT 2 60 0 AAAAACGCTT 0.975277 -13 CGCTCCTTTTAAAAATATCTTTTTTAGTTTAA 4 16 1 AAAAAATCTT 0.709063 -253 TAAAATTCATCGAAAGTGCGGTTAAATTTCTC 4 102 1 CGAAATGCGT 0.936178 -167 TTAGAAAGTAAAAAACTGCCGTTCATAAAAAT 4 137 0 AAAAATGCGT 0.990058 -132 ATAAAACCTGCAAGACTGCAGGGGCGACATAT 4 224 0 CAAGATGCGG 0.73421 -45 ***** *** ** Masking position 3 Map Score: 9.35603 Number of sites scoring better than the average of aligned sites = 1627 Number in coding regions = 1188 Number in noncoding regions = 439 Number of orfs with sites within 600 bp upstream = 308 Fraction of orfs with sites within 600 bp upstream = 0.04947 Motif number 3 AGTTTTTTCCTAAGGGATTTTTT 1 4 0 TAAGGGATTT 0.954419 -251 CATTTTTTTCTAAAAGGTTTGACATATTTC 1 56 0 TAAAAGGTTT 0.827657 -199 GCGCGCGCAGTATAGCATTTTTTTCTAAAA 1 71 0 TATAGCATTT 0.709533 -184 AGTGAGTGAGCAAAGAATTTTTTCAATTTA 1 147 0 CAAAGAATTT 0.810735 -108 TTAACAAAAGGTTTCACAAACCTT 2 5 1 CAAAAGGTTT 0.884506 -68 GATTGTGCGTCAAGGCGTATTCTATTTTAA 2 40 0 CAAGGCGTAT 0.924285 -33 GACGCACAATCAAGGCGTTTTTTT 2 59 1 CAAGGCGTTT 0.988465 -14 CGTTTCTACGTAATGCATTT 3 16 1 TAATGCATTT 0.807422 -10 TGTTATATATCAAGATGTTTTCTATTTTTC 4 51 0 CAAGATGTTT 0.791104 -218 TTTTACTTTCTAAGGCATTAAGTCCTTTTC 4 156 1 TAAGGCATTA 0.794855 -113 ********** Masking position 8 Map Score: 6.0459 Number of sites scoring better than the average of aligned sites = 695 Number in coding regions = 617 Number in noncoding regions = 78 Number of orfs with sites within 600 bp upstream = 45 Fraction of orfs with sites within 600 bp upstream = 0.00722775 Motif number 4 ATCTTACCCCGAAAGGGAAATATGTCAAAC 1 40 1 GAAAGGGAAA 0.9793 -215 GTTTTATGATGAACGATAACCCTCGGAGGT 1 114 1 GAACGATAAC 0.891986 -141 TGCGGTGGTGGAAAGGAAAAGATTTTTGAG 1 175 0 GAAAGGAAAA 0.941128 -80 TTTTTAAAAGGAGCGAGAAT 4 1 0 GAGCGAGAAT 0.899466 -268 TTTTTTAGTTTAACGAGAAAAATAGAAAAC 4 35 1 TAACGAGAAA 0.969836 -234 TTCATAAAAATAACGAGAAATTTAACCGCA 4 118 0 TAACGAGAAA 0.969836 -151 TAATGCCTTAGAAAGTAAAAAACTGCCGTT 4 146 0 GAAAGTAAAA 0.854245 -123 ********** Masking position 8 Map Score: 3.3476 Number of sites scoring better than the average of aligned sites = 351 Number in coding regions = 308 Number in noncoding regions = 43 Number of orfs with sites within 600 bp upstream = 30 Fraction of orfs with sites within 600 bp upstream = 0.0048185 Motif number 5 AAGCCGCAAAAAGTGCGGTGGTGGAAAGGA 1 188 0 AAGTGCGGTG 0.989282 -67 AATTCATCGAAAGTGCGGTTAAATTTCTCG 4 105 1 AAGTGCGGTT 0.941955 -164 GAAAGTAAAAAACTGCCGTTCATAAAAATA 4 136 0 AACTGCCGTT 0.656922 -133 ********** Masking position 2 Map Score: 1.08028 Number of sites scoring better than the average of aligned sites = 694 Number in coding regions = 456 Number in noncoding regions = 238 Number of orfs with sites within 600 bp upstream = 177 Fraction of orfs with sites within 600 bp upstream = 0.0284292 Motif number 6 ********** No masking Map Score: -9.14168e-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: -9.14168e-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: -9.14168e-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