AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_mpneu.txt -z/home/amcguire/genomes/mpneu.fna -inarP_mpneu_opreg_100.orf -g0.400 -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 = 0.4 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 1673774 300 B01_orf116L Protein #2 1673937 300 D02_orf128 Protein Motif number 1 CCAAAATTTTTATTTTTGCCGGTTTAACTGTTGTTA 1 10 1 TTATTTTGTA 0.974833 -291 TTAACTGTTGTTAATTTTTGAGACAAAGTTCTACCAG 1 34 1 TTATTTTGAA 0.925569 -267 ATTTGCACACTAATTTTTGGCGTCTTTTTGTTTTTTG 1 99 1 TAATTTTGTT 0.9663 -202 TGGCGTCTTTTTGTTTTTTGGGTAATTTAAATGATGT 1 116 1 TTGTTTTGTT 0.978599 -185 AAAAAGGTGAAAGTGTTTAAAGAGGTAGGCACCAACA 1 221 0 AAGGTTTGTA 0.895227 -80 AAGGGAAATTTTGCGTTTAATGGCAAAGACCTCCTTT 1 271 0 TTGGTTTGAA 0.902961 -30 GCGAGTCCAATTAATTTTTTAGGGTTTAAAAGAAATT 2 42 1 TTATTTTGTT 0.9782 -259 ACAGGAAAATTTAATTTTTAAGCCTAATGCTAATTTC 2 73 0 TTATTTTGAA 0.922755 -228 AGTGATGGCGTAGAGTTTTTAGTTTTTATTGTTGAAA 2 116 1 TAGGTTTGTT 0.955464 -185 TTTATTGTTGAAACTTTTTAAGCCTTTAATGGGTGTT 2 140 1 AAATTTTGTT 0.926924 -161 ATGGGTGTTGAAAAGTTTGTGGTAGTTTTTCAATTAA 2 168 1 AAAGTTTGTT 0.906954 -133 ACTGTCAGCATTGGTTTTTTAGTTGTTTTAAGTATTT 2 250 1 TTGTTTTGTT 0.978599 -51 GAAAAATATTTGTTTGGAAATAACAAATACTT 2 279 0 ATATTGTGTA 0.73879 -22 *** **** * ** Masking position 8 Map Score: 15.0929 Number of sites scoring better than the average of aligned sites = 221 Number in coding regions = 177 Number in noncoding regions = 44 Number of orfs with sites within 600 bp upstream = 34 Fraction of orfs with sites within 600 bp upstream = 0.00546097 Motif number 2 TATTTTTGCCGGTTTAACTGTTGTTAATTTT 1 21 1 GGTTAACTGT 0.969456 -280 TTTTTTAACTGGTAGAACTTTGTCTCAAAAA 1 48 0 GGTAAACTTT 0.956004 -253 ATTTTACGAGTTTAAAAGTGTCTTTTTTAAC 1 70 0 TTTAAAGTGT 0.91875 -231 TAAATGATTTTTTAAAACTGTCATTTTATTA 1 158 0 TTTAAACTGT 0.93097 -143 ATTGGAAAAAGGTGAAAGTGTTTAAAGAGGT 1 232 0 GGTGAAGTGT 0.97666 -69 GATTTATCGAGTTAAAACCGTTTTCATTAGC 2 13 1 GTTAAACCGT 0.911136 -288 ATGGCGTAGAGTTTTTAGTTTTTATTGTTGA 2 120 1 GTTTTAGTTT 0.828679 -181 AGTTTTTATTGTTGAAACTTTTTAAGCCTTT 2 136 1 GTTGAACTTT 0.957938 -165 TTGAAAAGTTTGTGGTAGTTTTTCAATTAAA 2 175 1 TGTGTAGTTT 0.637934 -126 TAGCGTTAACGTTACTACTGTCAGCATTGGT 2 234 1 GTTATACTGT 0.955921 -67 TTTTTTAGTTGTTTTAAGTATTTGTTATTTC 2 264 1 GTTTAAGTAT 0.786826 -37 **** ****** Masking position 7 Map Score: 9.81653 Number of sites scoring better than the average of aligned sites = 288 Number in coding regions = 252 Number in noncoding regions = 36 Number of orfs with sites within 600 bp upstream = 32 Fraction of orfs with sites within 600 bp upstream = 0.00513974 Motif number 3 TTTTTTGGGTAATTTAAATGATGTATGCGT 1 129 1 AATTTAAATG 0.820267 -172 CTGCCCAAATAAAATAAATGATTTTTTAAA 1 173 0 AAAATAAATG 0.919449 -128 AAACCCTAAAAAATTAATTGGACTCGCTAA 2 39 0 AAATTAATTG 0.762228 -262 TTAGGCTTAAAAATTAAATTTTCCTGTTAT 2 83 1 AAATTAAATT 0.511933 -218 TTGGTTAGGAAATTTAATTGAAAAACTACC 2 188 0 AATTTAATTG 0.751108 -113 GAAAAATATTTGTTTGGAAATA 2 289 0 AAAATATTTG 0.83403 -12 ********** Masking position 5 Map Score: 5.44856 Number of sites scoring better than the average of aligned sites = 68 Number in coding regions = 49 Number in noncoding regions = 19 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 4 TTAACAACAGTTAAACCGGCAAAAATAAAAATT 1 15 0 TTAACCGGAA 0.965325 -286 AAGTGTCTTTTTTAACTGGTAGAACTTTGTCTC 1 53 0 TTAACTGGAA 0.976949 -248 AAAGACACTTTTAAACTCGTAAAATTTGCACAC 1 76 1 TTAACTCGAA 0.990672 -225 TATTTGGGCAGTCAACTCGCTCAGTGACCTGTT 1 192 1 GTAACTCGTA 0.974673 -109 GCCTACCTCTTTAAACACTTTCACCTTTTTCCA 1 228 1 TTAACACTTA 0.882168 -73 TGAAAACGGTTTTAACTCGATAAATCTA 2 6 0 TTAACTCGTA 0.99304 -295 AAAAAATTAATTGGACTCGCTAATGAAAACGGT 2 29 0 TTGACTCGTA 0.974627 -272 CTAATTTCTTTTAAACCCTAAAAAATTAATTGG 2 48 0 TTAACCCTAA 0.956439 -253 ** ****** * * Masking position 5 Map Score: 9.23641 Number of sites scoring better than the average of aligned sites = 50 Number in coding regions = 44 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 4 Fraction of orfs with sites within 600 bp upstream = 0.000642467 Motif number 5 CCAAAATTTTTATTTTTGCCGGTTTA 1 7 1 TTTTTATTTT 0.964073 -294 GGTTTAACTGTTGTTAATTTTTGAGACAAA 1 31 1 TTGTTAATTT 0.824978 -270 TTTTGGCGTCTTTTTGTTTTTTGGGTAATT 1 113 1 TTTTTGTTTT 0.963373 -188 TTTAAAAAATCATTTATTTTATTTGGGCAG 1 173 1 CATTTATTTT 0.816271 -128 GAGTTTTTAGTTTTTATTGTTGAAACTTTT 2 128 1 TTTTTATTGT 0.876959 -173 ATTGGTTTTTTAGTTGTTTTAAGTATTTGT 2 259 1 TAGTTGTTTT 0.94142 -42 TTTTAAGTATTTGTTATTTCCAAACAAATA 2 275 1 TTGTTATTTC 0.890028 -26 GAAAAATATTTGTTTGGAAATAACAA 2 285 0 TATTTGTTTG 0.834572 -16 ********** Masking position 5 Map Score: 4.39477 Number of sites scoring better than the average of aligned sites = 155 Number in coding regions = 101 Number in noncoding regions = 54 Number of orfs with sites within 600 bp upstream = 42 Fraction of orfs with sites within 600 bp upstream = 0.0067459 Motif number 6 ********** No masking Map Score: 1.30983e-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 7 ********** No masking Map Score: 1.30983e-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 8 ********** No masking Map Score: 1.30983e-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