AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i158_CYD_operon_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 HI1157 71 ATP-binding protein protein (cydD) #2 HI1158 73 thioredoxin reductase (trxB) #3 HI1159 284 conserved hypothetical protein #4 HI1161 300 conserved hypothetical protein Motif number 1 TCTAACCAATTCCCCTCTTTTAACTCTTTT 1 15 1 TCCCCTCTTT 0.985753 -57 TAGAAAAAGTTCCCCTCTTTAAAAGAGTTA 1 35 0 TCCCCTCTTT 0.985753 -37 TCTAAAATCTTCCGCACTTTGCTAAAATCA 3 32 1 TCCGCACTTT 0.932806 -253 TGCCAAAAAATCCGCCGATTCTTTATGCGT 3 193 0 TCCGCCGATT 0.959295 -92 TCCCCCCATAAATGGGTGGA 4 1 1 TCCCCCCATA 0.997162 -300 TAATCTTGGCTCCACCCATTTATGGGGGGA 4 11 0 TCCACCCATT 0.991573 -290 TTCGGGCACCTTCCCCCACAAGCAGGGGAA 4 103 0 TTCCCCCACA 0.929577 -198 TGAACATTTATCCCCCCTCACCTTCGGCAG 4 228 1 TCCCCCCTCA 0.990403 -73 CTTCGGCAGCTCCCCCCATAAATGGGTGGA 4 249 1 TCCCCCCATA 0.997162 -52 TTATCTTGGCTCCACCCATTTATGGGGGGA 4 259 0 TCCACCCATT 0.991573 -42 ********** Masking position 1 Map Score: 23.6905 Number of sites scoring better than the average of aligned sites = 89 Number in coding regions = 69 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 Motif number 2 GCCAAAAAATCCGCCGATTCTTTATGCGTTGGCGCGTA 3 184 0 CCCCTTTGCG 0.993067 -101 AATCTTGGCTCCACCCATTTATGGGGGGA 4 2 0 CCCCTTGGGG 0.511061 -299 TGATAACTTGCCTTCTGCTTATTAGAGGTTTTAAAAAC 4 60 1 CCTCCTGAGG 0.977088 -241 TAAAAACTTGCCTTCCCCTGCTTGTGGGGGAAGGTGCC 4 91 1 CCTCCTTGGG 0.990248 -210 ATCCCTATATCCCCCTTCCCTTCGGGCACCTTCCCCCA 4 115 0 CCCCCTGGCA 0.994743 -186 GAACATTTATCCCCCCTCACCTTCGGCAGCTCCCCCCA 4 229 1 CCCCCTGGCA 0.996605 -72 TATCTTGGCTCCACCCATTTATGGGGGGAGCTGCCGAA 4 250 0 CCCCTTGGGG 0.511061 -51 ** ** * * **** Masking position 12 Map Score: 10.5808 Number of sites scoring better than the average of aligned sites = 37 Number in coding regions = 26 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 Motif number 3 CCCTCTTTAAAAGAGTTAAAAGAGGGGAATTG 1 21 0 AAAGTTAAAG 0.853733 -51 AAAGTTTATAATCAGTAAAATGCAACTTATTG 2 15 1 ATAGTAAAAG 0.853733 -59 GTAGTTAAGTAATAATATAATGCAATAAGTTG 2 37 0 AAAATATAAG 0.951361 -37 TAATAGAAATGGTAAAACGTTTCTAAAAT 3 8 1 AAGGTAAAAG 0.977252 -277 TATCCTTGTGAAAAAAATAATGGCTGATTTTA 3 54 0 AAAAAATAAG 0.713137 -231 TTTTTTTCACAAGGATAAAACATGGCTGATTT 3 69 1 AAGATAAAAA 0.783528 -216 CGTTGATCTCAACGATAAAAGGAAAATCAGCC 3 92 0 AAGATAAAAG 0.978695 -193 CAAGTTGCAGAACAATATCAAGGACAATTTAT 3 232 1 AAAATATCAG 0.882478 -53 TTACTTTTCCAAGAATAAATTGTCCTTGATAT 3 246 0 AAAATAAATG 0.951374 -39 TTATTCTTGGAAAAGTAAATTGTGAAAAAGAG 3 260 1 AAAGTAAATG 0.94818 -25 TAAAATAAATAATGATAACTTGCCTTCTGCTT 4 48 1 AAGATAACTG 0.875218 -253 ** ******* * Masking position 1 Map Score: 9.26398 Number of sites scoring better than the average of aligned sites = 337 Number in coding regions = 255 Number in noncoding regions = 82 Number of orfs with sites within 600 bp upstream = 61 Fraction of orfs with sites within 600 bp upstream = 0.00979762 Motif number 4 CTTGTGAAAAAAATAATGGCTGATTTTAGC 3 52 0 AAATAATGGC 0.885061 -233 TCACAAGGATAAAACATGGCTGATTTTCCT 3 75 1 AAAACATGGC 0.973514 -210 TTTTCCAAGAATAAATTGTCCTTGATATTG 3 244 0 ATAAATTGTC 0.772304 -41 TTAGAACCTCTAATCTTGGCTCCACCCATT 4 21 0 TAATCTTGGC 0.965785 -280 ATAAATAATGATAACTTGCCTTCTGCTTAT 4 52 1 ATAACTTGCC 0.971358 -249 AGAGGTTTTAAAAACTTGCCTTCCCCTGCT 4 83 1 AAAACTTGCC 0.977857 -218 ATATTATCAATTATCTTGGCTCCACCCATT 4 269 0 TTATCTTGGC 0.955904 -32 ********** Masking position 3 Map Score: 5.57936 Number of sites scoring better than the average of aligned sites = 293 Number in coding regions = 267 Number in noncoding regions = 26 Number of orfs with sites within 600 bp upstream = 20 Fraction of orfs with sites within 600 bp upstream = 0.00321234 Motif number 5 CTAACCAATTCCCCTCTTTTAACTCTTTTA 1 16 1 CCCCTCTTTT 0.990576 -56 AGAAAAAGTTCCCCTCTTTAAAAGAGTTAA 1 34 0 CCCCTCTTTA 0.96965 -38 CTAAAATCTTCCGCACTTTGCTAAAATCAG 3 33 1 CCGCACTTTG 0.949344 -252 TCGCTCTTTTTCACAATTTA 3 275 0 TCGCTCTTTT 0.942068 -10 AATCTTGGCTCCACCCATTTATGGGGGGA 4 10 0 CCACCCATTT 0.975197 -291 TATCTTGGCTCCACCCATTTATGGGGGGAG 4 258 0 CCACCCATTT 0.975197 -43 ********** Masking position 8 Map Score: 4.63082 Number of sites scoring better than the average of aligned sites = 850 Number in coding regions = 530 Number in noncoding regions = 320 Number of orfs with sites within 600 bp upstream = 236 Fraction of orfs with sites within 600 bp upstream = 0.0379056 Motif number 6 GGGGAACTTTTTCTATAATCACGACCAAAA 1 50 1 TTCTATAATC 0.967092 -22 GGTAAAACGTTTCTAAAATCTTCCGCACTT 3 21 1 TTCTAAAATC 0.986713 -264 TTCCGCACTTTGCTAAAATCAGCCATTATT 3 41 1 TGCTAAAATC 0.98768 -244 ACTGAAATACTGCAACAATCCTTAGGAAAA 3 135 1 TGCAACAATC 0.93461 -150 AGATTAGAGGTTCTAAAATAAATAATGATA 4 35 1 TTCTAAAATA 0.934339 -266 ********** Masking position 5 Map Score: 4.22277 Number of sites scoring better than the average of aligned sites = 69 Number in coding regions = 47 Number in noncoding regions = 22 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 7 AGGAAAAACCACTTGTCATCAATTTTTACG 3 158 1 ACTTGTCATC 0.921342 -127 GAACCTCTAATCTTGGCTCCACCCATTTAT 4 18 0 TCTTGGCTCC 0.98683 -283 AATAATGATAACTTGCCTTCTGCTTATTAG 4 55 1 ACTTGCCTTC 0.994727 -246 GGTTTTAAAAACTTGCCTTCCCCTGCTTGT 4 86 1 ACTTGCCTTC 0.994727 -215 CCTATATCCCCCTTCCCTTCGGGCACCTTC 4 120 0 CCTTCCCTTC 0.96208 -181 TTATCAATTATCTTGGCTCCACCCATTTAT 4 266 0 TCTTGGCTCC 0.98683 -35 ********** Masking position 4 Map Score: 8.26637 Number of sites scoring better than the average of aligned sites = 43 Number in coding regions = 26 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 8 TAGCAAAGTGCGGAAGATTTTAGAAACGTT 3 26 0 CGGAAGATTT 0.966211 -259 AAAAAAATAATGGCTGATTTTAGCAAAGTG 3 46 0 TGGCTGATTT 0.992338 -239 GGATAAAACATGGCTGATTTTCCTTTTATC 3 81 1 TGGCTGATTT 0.992338 -204 CATAAAGAATCGGCGGATTTTTTGGCACTA 3 196 1 CGGCGGATTT 0.994096 -89 ********** Masking position 7 Map Score: 4.14184 Number of sites scoring better than the average of aligned sites = 49 Number in coding regions = 38 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 9 TACTGATTATAAACTTTTTGC 2 2 0 AAACTTTTTG 0.733957 -72 CAATAAGTTGCATTTTACTGATTATAAACT 2 17 0 CATTTTACTG 0.954511 -57 CAGTAAAATGCAACTTATTGCATTATATTA 2 27 1 CAACTTATTG 0.962921 -47 CAACGAACAAAATCTTACTGAAATACTGCA 3 119 1 AATCTTACTG 0.924956 -166 ATATCAAGGACAATTTATTCTTGGAAAAGT 3 246 1 CAATTTATTC 0.86428 -39 CTCTTTTTCACAATTTACTTTTCCAAGAAT 3 262 0 CAATTTACTT 0.9014 -23 ATCACTCCAAAATTTTATTTCGCATATCCC 4 148 0 AATTTTATTT 0.740315 -153 ********** Masking position 2 Map Score: 1.17482 Number of sites scoring better than the average of aligned sites = 308 Number in coding regions = 260 Number in noncoding regions = 48 Number of orfs with sites within 600 bp upstream = 45 Fraction of orfs with sites within 600 bp upstream = 0.00722775 Motif number 10 ********** No masking Map Score: 1.43773e-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: 1.43773e-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: 1.43773e-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