AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i113_Amino_Acid_Transport_4_hinf_reg_300.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 HI0883 300 amino acid carrier protein, putative Motif number 1 GTGGGGTCAATTTCCCGCTCTCCAGCTACCTT 1 12 0 TTTCCGCCTC 0.996411 -289 ACCTGAAAGATTTTACATCGTCGGTGTGGGGT 1 37 0 TTTACATGTC 0.936536 -264 GATTGAAAAATTAACCGCTCTTTTGCGCTTCG 1 129 0 TTACCGCCTT 0.965025 -172 AGCGGTTAATTTTTCAATCGTTTTTCAAACGC 1 142 1 TTTCAATGTT 0.902947 -159 TTCAATCGTTTTTCAAACGCTCAGGCAAAAGG 1 154 1 TTTAAACCTC 0.916545 -147 TAGATTGTCTTTTGCCCCTGTCCTTTTGCCTG 1 175 0 TTTCCCCGTC 0.988181 -126 AAAATAAATAATTTCCACACTTACAATAGATT 1 201 0 ATTCCACCTT 0.965694 -100 TATTTATTTTTTTACCGCACTTTCTTTTCCAT 1 223 1 TTTCCGCCTT 0.994319 -78 CCGCACTTTCTTTTCCATTGTATCTTTTCGTC 1 237 1 TTTCCATGTA 0.934899 -64 *** **** *** Masking position 2 Map Score: 10.197 Number of sites scoring better than the average of aligned sites = 1362 Number in coding regions = 990 Number in noncoding regions = 372 Number of orfs with sites within 600 bp upstream = 248 Fraction of orfs with sites within 600 bp upstream = 0.039833 Motif number 2 GGGTCAATTTCCCGCTCTCCAGCTACCTTC 1 11 0 CCCGCTCTCC 0.99635 -290 CGGGAAATTGACCCCACACCGACGATGTAA 1 27 1 ACCCCACACC 0.985457 -274 TGAAAAATTAACCGCTCTTTTGCGCTTCGG 1 128 0 ACCGCTCTTT 0.989204 -173 ATTGTCTTTTGCCCCTGTCCTTTTGCCTGA 1 174 0 GCCCCTGTCC 0.981556 -127 TTATTTTTTTACCGCACTTTCTTTTCCATT 1 226 1 ACCGCACTTT 0.984604 -75 ********** Masking position 5 Map Score: 3.94068 Number of sites scoring better than the average of aligned sites = 164 Number in coding regions = 130 Number in noncoding regions = 34 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419 Motif number 3 AATTGACCCCACACCGACGATGTAAAATCT 1 32 1 ACACCGACGA 0.974551 -269 TTAGAAATGGACGCCGAAGCGCAAAAGAGC 1 115 1 ACGCCGAAGC 0.993167 -186 CGTTTTTCAAACGCTCAGGCAAAAGGACAG 1 160 1 ACGCTCAGGC 0.976942 -141 CAAAATAAACACGACAAGAAGACGAAAAGA 1 259 0 ACGACAAGAA 0.921593 -42 TTTGATTTAAACGACGAGGAATCACA 1 285 1 ACGACGAGGA 0.995738 -16 ********** Masking position 7 Map Score: 2.50377 Number of sites scoring better than the average of aligned sites = 120 Number in coding regions = 106 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 Motif number 4 CGTCCATTTCTAAAATGGATCTCTCCAAGG 1 98 0 TAAAATGGAT 0.983461 -203 TTTCCACACTTACAATAGATTGTCTTTTGC 1 192 0 TACAATAGAT 0.982893 -109 GACGAAAAGATACAATGGAAAAGAAAGTGC 1 239 0 TACAATGGAA 0.982854 -62 ********** Masking position 5 Map Score: 1.54986 Number of sites scoring better than the average of aligned sites = 11 Number in coding regions = 10 Number in noncoding regions = 1 Number of orfs with sites within 600 bp upstream = 1 Fraction of orfs with sites within 600 bp upstream = 0.000160617 Motif number 5 AAACGATTGAAAAATTAACCGCTCTTTTGC 1 135 0 AAAATTAACC 0.927853 -166 GTGCGGTAAAAAAATAAATAATTTCCACAC 1 213 0 AAAATAAATA 0.947772 -88 GATACAATGGAAAAGAAAGTGCGGTAAAAA 1 231 0 AAAAGAAAGT 0.919976 -70 CAAGAAGACGAAAAGATACAATGGAAAAGA 1 245 0 AAAAGATACA 0.95946 -56 CGTTTAAATCAAAATAAACACGACAAGAAG 1 268 0 AAAATAAACA 0.986325 -33 ********** Masking position 4 Map Score: 1.44507 Number of sites scoring better than the average of aligned sites = 322 Number in coding regions = 240 Number in noncoding regions = 82 Number of orfs with sites within 600 bp upstream = 82 Fraction of orfs with sites within 600 bp upstream = 0.0131706 Motif number 6 TCCAAGGGTTCGTCCAGTAACAGTCCCTGC 1 75 0 CGTCCAGTAA 0.972511 -226 TGCGCTTCGGCGTCCATTTCTAAAATGGAT 1 108 0 CGTCCATTTC 0.975292 -193 CTTTTGCCCCTGTCCTTTTGCCTGAGCGTT 1 169 0 TGTCCTTTTG 0.961691 -132 TTCGTCTTCTTGTCGTGTTTATTTTGATTT 1 263 1 TGTCGTGTTT 0.926212 -38 TGTGATTCCTCGTCGTTTAAATCAAAATAA 1 281 0 CGTCGTTTAA 0.969917 -20 ********** Masking position 3 Map Score: 0.175338 Number of sites scoring better than the average of aligned sites = 156 Number in coding regions = 143 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 7 ********** No masking Map Score: 7.91135e-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: 7.91135e-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 9 ********** No masking Map Score: 7.91135e-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