AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i293_mixed_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 HI0063 247 poly(A) polymerase (pcnB) #2 HI0393 48 conserved hypothetical GTP-binding protein #3 HI0394 166 peptidyl-tRNA hydrolase (pth) #4 HI0405 72 pyridoxine kinase, putative #5 HI0406 89 acetyl-CoA carboxylase, carboxyl transferase (accA) #6 HI0408 171 ABC transporter, ATP-binding protein (yebM) #7 HI0642 159 UDP-N-acetylglucosamine pyrophosphorylase (glmU) #8 HI1334 126 cell division protein (ftsJ) #9 HI1335 90 cell division protein (ftsH) #10 HI1336 111 dihydropteroate synthase (folP-1) #11 HI1337 37 mrsA protein (mrsA) #12 HI1603 207 conserved hypothetical protein #13 HI1604 24 phosphate permease, putative #14 HI1605 65 conserved hypothetical protein #15 HI1607 62 hemM protein (hemM) #16 HI1630 166 ribosomal protein L25 (rpL25) Motif number 1 GAAAAATACAAAAGTGCGGTTAAAATTAAC 1 22 1 AAAGTGCGGT 0.998946 -226 TAAATGCAAAAAAGTGCGGTTAATTTTAAC 1 40 0 AAAGTGCGGT 0.998946 -208 TTATAACGGAAAAGTGCGGTGACTTTTAAT 3 41 1 AAAGTGCGGT 0.998946 -126 TAACATTCTAAAAGAGCGGTGATTTTTACC 4 12 1 AAAGAGCGGT 0.99736 -61 TTAGATCAAAAAAGAGCGGTAAAAATCACC 4 29 0 AAAGAGCGGT 0.99736 -44 ATTCCTTGATAAAGTGCGGTCGATTTTTAC 5 50 1 AAAGTGCGGT 0.998946 -40 GAATTCTATAAAAATGCGTTATTTTCCCCA 6 126 1 AAAATGCGTT 0.920101 -46 TCCTAATAAAAAAGAGCGGTTGATTTTCTC 8 17 1 AAAGAGCGGT 0.99736 -110 AAAATGCGGTTAATTTTTAG 10 102 0 AAAATGCGGT 0.993204 -10 ATCTCAATAAAAAGTGCGGTTAATTTTAAC 14 14 1 AAAGTGCGGT 0.998946 -52 CATCACAACAAAAGTGCGGTTAAAATTAAC 14 32 0 AAAGTGCGGT 0.998946 -34 ********** Masking position 3 Map Score: 49.7467 Number of sites scoring better than the average of aligned sites = 1183 Number in coding regions = 748 Number in noncoding regions = 435 Number of orfs with sites within 600 bp upstream = 298 Fraction of orfs with sites within 600 bp upstream = 0.0478638 Motif number 2 ATGCAAAAAAGTGCGGTTAATTTTAACCGCACTT 1 33 0 GGCGGTTTTT 0.999172 -215 AAGTGCGGTTAGTTTTACAACCGTTT 2 3 1 GGCGGTTTTT 0.999172 -46 TAACGGAAAAGTGCGGTGACTTTTAATGATAAAT 3 44 1 GGCGGTTTTT 0.999172 -123 CATTCTAAAAGAGCGGTGATTTTTACCGCTCTTT 4 15 1 GGCGGTTTTT 0.999172 -58 CCTTGATAAAGTGCGGTCGATTTTTACGGTCTTT 5 53 1 GGCGGTTTTT 0.999172 -37 TAATAAAAAAGAGCGGTTGATTTTCTCAATGTTT 8 20 1 GGCGGTTTTT 0.999172 -107 AAAATGCGGTTAATTTTTAGAGTGATT 10 95 0 AGCGGTTTTT 0.991618 -17 TCAATAAAAAGTGCGGTTAATTTTAACCGCACTT 14 17 1 GGCGGTTTTT 0.999172 -49 CAAGCCTTGAGAGCCGTGGATTATAGAATATCCT 16 63 0 GGCCGTTTAT 0.965084 -104 * ***** **** Masking position 7 Map Score: 33.6639 Number of sites scoring better than the average of aligned sites = 468 Number in coding regions = 285 Number in noncoding regions = 183 Number of orfs with sites within 600 bp upstream = 157 Fraction of orfs with sites within 600 bp upstream = 0.0252168 Motif number 3 CACTTTTGTATTTTTCAATAGAATGAA 1 5 0 TTTTAATAAA 0.520658 -243 TAACCGCACTTTTTTGCATTTAAAAATGCAGGA 1 48 1 TTTTCATTAA 0.880323 -200 TCCACTTGCCTTTTTCTTTACAAGAAAAGAGCC 1 84 1 TTTTTTTAAA 0.597164 -164 GAGTAAATTATTCTTACTTATATCAAAAATTTG 1 144 1 TTCTCTTAAT 0.812258 -104 AATTTTTCCCTTATTTTGAGTAAAAC 2 33 0 TTTTCTTATT 0.638315 -16 GGCTAAAATTTTTTAACAAAGAAGTAAAA 3 7 0 TTTTCAAAAA 0.577405 -160 TGTTAAAAAATTTTAGCCATTATAACGGAAAAG 3 22 1 TTTTCCATAT 0.43709 -145 TATATTTTCTCCTTTGTTGTATATTTA 4 56 0 TTTTCCTTGT 0.687149 -17 TTTGTTATCCTAAAAAGACCGTAAA 5 75 0 TGTTCCTAAA 0.671143 -15 TGAATAATGCTTTTTCCATAGGAATGAATTTTC 6 56 0 TTTTCATAGA 0.827135 -116 TCTCAAGATTTTCTCTCTTATGTCGAATATTTA 6 95 0 TTCTCTTAGT 0.693527 -77 CCCATCGGTTTTTTGAATTTTAAAGTGGTTAAA 7 18 0 TTTTATTTAA 0.796886 -142 AAACCATCGGTTTTTTCTTATATAAAAGTTTGT 7 51 1 TTTTCTTAAT 0.936517 -109 TTTGTTATAGTTTTTACTTAAAAACTTACCATT 7 79 1 TTTTCTTAAA 0.920192 -81 ACGGGTAATATTCTATCTTAGAAAGATAGCAAA 7 110 0 TTCTCTTAAA 0.902961 -50 AAATTTTCTCTTTATTCATCAATAAC 7 144 0 TTTTCTTTTT 0.586609 -16 TCAACCGCTCTTTTTTATTAGGAATCCTT 8 7 0 TTTTATTAGA 0.718317 -120 TGACGAAATTTTTTAACTTAGGAAAGGTAGGTT 9 54 1 TTTTCTTAGA 0.954231 -37 AAGGCTTTATTTTTTCCTAATGATTTTGTTCTT 10 33 1 TTTTCTAAGA 0.798544 -79 TTTTTTACCTTTCAAATTTTCTCGC 12 3 1 TTTTCTTTAA 0.97055 -205 CTCAATACACTTTTCGCTTTAAAAGCGAGAAAA 12 27 0 TTTTCTTTAA 0.970533 -181 AAGATAAACCTTTTTTCTTACAAATTTTTTTGA 12 110 1 TTTTCTTAAA 0.975996 -98 TTTTGAAAAATTTTAACTATCAACAAAAATCGG 12 137 1 TTTTCTATAA 0.858985 -71 TTTTTCCCCTTAAACATCACAACA 14 52 0 TTTTCCTTAA 0.921059 -14 TTTTCTAGGCTTTTTGATTTGAAAAGATTAAAA 16 12 0 TTTTATTTAA 0.796631 -155 GCCTGCGATTTTCTTTCTTTTAACATTAATTTA 16 130 1 TTCTCTTTAA 0.906239 -37 TTTAATGTTCTCTTTAAATTAATGTTAA 16 149 0 TGTTCTTTAA 0.823095 -18 **** **** ** Masking position 4 Map Score: 30.3048 Number of sites scoring better than the average of aligned sites = 960 Number in coding regions = 660 Number in noncoding regions = 300 Number of orfs with sites within 600 bp upstream = 254 Fraction of orfs with sites within 600 bp upstream = 0.0407967 Motif number 4 TACAAAAGTGCGGTTAAAATTAACCGCACT 1 28 1 CGGTTAAAAT 0.980628 -220 ACTCAAAATAAGGGAAAAATT 2 38 1 AGGGAAAAAT 0.701904 -11 TCCGTTATAATGGCTAAAATTTTTTAACAA 3 21 0 TGGCTAAAAT 0.906817 -146 CAAAAAAGAGCGGTAAAAATCACCGCTCTT 4 23 0 CGGTAAAAAT 0.918974 -50 CAACAATGGTTGGGGAAAATAACGCATTTT 6 136 0 TGGGGAAAAT 0.905059 -36 AATTTTAAAGTGGTTAAAATAGAAA 7 6 0 TGGTTAAAAT 0.96935 -154 TCAATAACAACGGGTAATATTCTATCTTAG 7 122 0 CGGGTAATAT 0.974031 -38 CGCCTATATTTGGGTACAATCTGTCAAATT 8 82 0 TGGGTACAAT 0.888691 -45 AAAATGCGGTTAATTTTTAGAGTGAT 10 96 0 CGGTTAATTT 0.713781 -16 AGTAAGCAACTGGGTAATATTTCCTAGTGT 12 74 0 TGGGTAATAT 0.959074 -134 TTTTTGTTGATAGTTAAAATTTTTCAAAAA 12 136 0 TAGTTAAAAT 0.675654 -72 CAACAAAAATCGGGTAATATGCGCACGAAT 12 157 1 CGGGTAATAT 0.974031 -51 AACAAAAGTGCGGTTAAAATTAACCGCACT 14 26 0 CGGTTAAAAT 0.980628 -40 ********** Masking position 6 Map Score: 17.6267 Number of sites scoring better than the average of aligned sites = 192 Number in coding regions = 145 Number in noncoding regions = 47 Number of orfs with sites within 600 bp upstream = 48 Fraction of orfs with sites within 600 bp upstream = 0.0077096 Motif number 5 TTTGCATTTAAAAATGCAGGAAAATCCACTTGC 1 60 1 AAAAGAGAAA 0.978763 -188 TTCCAACAACAAAACGGAGTAAATTATTCTTAC 1 128 1 AAAAGAGAAA 0.978763 -120 CGTTTTACTCAAAATAAGGGAAAAATT 2 32 1 AAAAAGGAAA 0.880832 -17 AAATTTTTTAACAAAGAAGTAAAA 3 2 0 ACAAGAGAAA 0.914939 -165 TATTGTAGCGAAAAAGCCTTAAATTCTCAATCT 3 114 0 AAAAGCTAAA 0.7597 -53 TTTAGATCAAAAAAGAGCGGTAAAAATCACCGC 4 27 0 AAAAACGTAA 0.663253 -46 TAAATATACAACAAAGGAGAAAATATA 4 56 1 ACAAGAGAAA 0.914939 -17 TGTTATCCTAAAAAGACCGTAAAAATCGACCGC 5 65 0 AAAAACGAAA 0.962998 -25 AATATTCGACATAAGAGAGAAAATCTTGAGAAT 6 97 1 ATAAAAGAAA 0.812581 -75 TTCTATCTTAGAAAGATAGCAAATGGTAAGTTT 7 100 0 GAAAAAGAAA 0.850377 -60 GTTATTGATGAATAAAGAGAAAATTT 7 144 1 AATAAAGAAA 0.793162 -16 AAACGACTACAAAAAATAGAAGATT 8 112 1 AAAAAAGAGA 0.850377 -15 ATTAGCAATGAAAAGCTATCAAAGCAA 9 5 0 AAAACATAAA 0.832475 -86 TTTTCGCTTTAAAAGCGAGAAAATTTGAAAGGT 12 17 0 AAAACAGAAA 0.973827 -191 TCAACAAAACATAGGAAATAAACT 13 6 1 AAAAAAGAAA 0.980647 -19 TTCAAATCAAAAAGCCTAGAAAAAAGTTTGATT 16 22 1 AAAGCAGAAA 0.806703 -145 AATTTTCCTAAAAACCGCTCAAAGACAAGCCTT 16 89 0 AAAACCTAAA 0.718494 -78 AATTAATGTTAAAAGAAAGAAAATCGCAGGCGA 16 128 0 AAAAAAGAAA 0.980647 -39 **** * ** *** Masking position 13 Map Score: 21.8208 Number of sites scoring better than the average of aligned sites = 434 Number in coding regions = 315 Number in noncoding regions = 119 Number of orfs with sites within 600 bp upstream = 116 Fraction of orfs with sites within 600 bp upstream = 0.0186315 Motif number 6 CGCGTGATTTATCATTAAAAGTCACCGCACTTT 3 51 0 ATCTTAAAAC 0.979902 -116 ATCAAAAAAGAGCGGTAAAAATCACCGCTCTTT 4 22 0 AGCGTAAAAC 0.864373 -51 TTTGTTATCCTAAAAAGACCGTAAAAATC 5 71 0 ATCTAAAAAC 0.861009 -19 TGGAAAAAGCATTATTCAAACGCTTAAATATTC 6 71 1 ATTTTCAAAC 0.837642 -101 ACCATTTGCTATCTTTCTAAGATAGAATATTAC 7 106 1 ATCTTCTAAT 0.749305 -54 GCTAATTGAAATCAGTAAAAAACATTGAGAAAA 8 40 0 ATCGTAAAAC 0.968313 -87 TTTGGGTACAATCTGTCAAATTCAAGCCGAAGC 8 71 0 ATCGTCAAAC 0.976196 -56 ATCGTTCAAAGTCTAACCTACCT 9 78 0 ATCTTCAAAC 0.984943 -13 TTAATTTTTTATCGTTATAAAACCA 11 3 0 ATCTTATAAC 0.923697 -35 TTTTTTACCTTTCAAATTTTCTCGCTTTT 12 7 1 ACCTTCAAAT 0.771536 -201 ATTAAACTAAATCCTTAAAATATGCGAGCTTAT 15 33 1 ATCTTAAAAT 0.923303 -30 *** ****** * Masking position 9 Map Score: 8.23191 Number of sites scoring better than the average of aligned sites = 151 Number in coding regions = 130 Number in noncoding regions = 21 Number of orfs with sites within 600 bp upstream = 20 Fraction of orfs with sites within 600 bp upstream = 0.00321234 Motif number 7 CTCCGTTTTGTTGTTGGAAATAAATGACTTG 1 116 0 TTGTTGAAAT 0.617685 -132 TATCAAAAATTTGTTTGGCAAGAAGACAAAA 1 164 1 TTGTTGGCAA 0.938939 -84 AATGAGCACTTGTTTTGGCAACCTCTTTTGA 1 198 0 TGTTTGGCAA 0.918276 -50 TGGTTTTCACTGGTTGGGCAAGC 5 3 0 TGGTTGGCAA 0.946872 -87 TTTTACGGTCTTTTTAGGATAACAAA 5 74 1 TTTTTGGATA 0.648683 -16 TTTTCAACAATGGTTGGGGAAAATAACGCAT 6 139 0 TGGTTGGGAA 0.869257 -33 CCGCTCTTTTTTATTAGGAATCCTT 8 5 0 TTATTGGAAT 0.779921 -122 ATCAAAGCCTTTCTTCGGAAAGGCTTTATTT 10 14 1 TTCTTGGAAA 0.886566 -98 AAGAACAAAATCATTAGGAAAAAATAAAGCC 10 35 0 TCATTGGAAA 0.821699 -77 TCTTACAAATTTTTTTGAAAAATTTTAACTA 12 125 1 TTTTTGAAAA 0.831594 -83 CTAGGCTTTTTGATTTGAAAAGATTAAAAT 16 10 0 TGATTGAAAA 0.85245 -157 GAAAAAAGTTTGATTTGAAAATAAGGATATT 16 40 1 TGATTGAAAA 0.85245 -127 CTTTGAGCGGTTTTTAGGAAAATTGCTGGGT 16 98 1 TTTTTGGAAA 0.94547 -69 ***** ***** Masking position 5 Map Score: 8.73165 Number of sites scoring better than the average of aligned sites = 254 Number in coding regions = 210 Number in noncoding regions = 44 Number of orfs with sites within 600 bp upstream = 40 Fraction of orfs with sites within 600 bp upstream = 0.00642467 Motif number 8 TTGTAGCGAAAAAGCCTTAAATTCTCAATC 3 115 0 AAAGCCTTAA 0.962188 -52 GCCACAGTTTAATTCCTTGATAAAGTGCGG 5 39 1 AATTCCTTGA 0.891356 -51 CTCATCAAAGCCTTTCTTCGGAAAGG 10 7 1 AAAGCCTTTC 0.953805 -105 AGGAAAAAATAAAGCCTTTCCGAAGAAAGG 10 21 0 AAAGCCTTTC 0.953805 -91 AATAAAATTCCTTTAATTTTTTATC 11 23 0 AATTCCTTTA 0.839168 -15 CAATTAAACTAAATCCTTAAAATATGCGAG 15 31 1 AAATCCTTAA 0.908648 -32 TTCAAATCAAAAAGCCTAGAAAAAAGTTTG 16 22 1 AAAGCCTAGA 0.911305 -145 CGCTCAAAGACAAGCCTTGAGAGCCGTGGA 16 77 0 CAAGCCTTGA 0.938379 -90 ********** Masking position 2 Map Score: 5.24675 Number of sites scoring better than the average of aligned sites = 191 Number in coding regions = 154 Number in noncoding regions = 37 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 9 TACTTATATCAAAAATTTGTTTGGCAAGAA 1 158 1 AAAAATTTGT 0.937067 -90 AGAATTCTATAAAAATGCGTTATTTTCCCC 6 125 1 AAAAATGCGT 0.926649 -47 TTTCTTATATAAAAGTTTGTTATAGTTTTT 7 64 1 AAAAGTTTGT 0.964212 -96 CCTAAGTTAAAAAATTTCGTCACAAGATAC 9 46 0 AAAATTTCGT 0.925811 -45 AATTTTTCAAAAAAATTTGTAAGAAAAAAG 12 119 0 AAAAATTTGT 0.937067 -89 TTAAGGGGTTAAAAATTCGTGCGCATATTA 12 171 0 AAAAATTCGT 0.974671 -37 AAGCCTAGAAAAAAGTTTGATTTGAAAATA 16 33 1 AAAAGTTTGA 0.854108 -134 ********** Masking position 4 Map Score: 6.6228 Number of sites scoring better than the average of aligned sites = 71 Number in coding regions = 49 Number in noncoding regions = 22 Number of orfs with sites within 600 bp upstream = 26 Fraction of orfs with sites within 600 bp upstream = 0.00417604 Motif number 10 TTTAACCGCACTTTTGTATTTTTCAATAGAAT 1 14 0 CTTTGTTTTT 0.650125 -234 AATGACTTGGCTCTTTTCTTGTAAAGAAAAAG 1 93 0 CTTTTTTTGT 0.776993 -155 ATAATTTACTCCGTTTTGTTGTTGGAAATAAA 1 123 0 CCTTTTTTGT 0.722887 -125 TTTTGGCAACCTCTTTTGATTTTTTTGTCTTC 1 185 0 CTTTTTATTT 0.689035 -63 CAATAAATTACCTCTTTGTTTCCGCCTTATAG 3 84 1 CCCTTTTTTC 0.851351 -83 CTACAATACGCCACTATTTTTTACATCATCAA 3 139 1 CCCTATTTTT 0.91393 -28 GTGATTTTTACCGCTCTTTTTTGATCTAAATA 4 30 1 CCCTCTTTTT 0.897992 -43 TATATTTTCTCCTTTGTTGTATATTTAGAT 4 53 0 CTCTTTTTGT 0.922956 -20 ATGCTGAAAACTTTTTTATTTTAGGG 6 5 0 CTTTTTTTTT 0.899092 -167 AACTTACCATTTGCTATCTTTCTAAGATAGAA 7 101 1 TTCTATTTTC 0.507379 -59 AGAAAATCAACCGCTCTTTTTTATTAGGAATC 8 14 0 CCCTCTTTTT 0.897992 -113 AATCTTCTATTTTTTGTAGTCGTTT 8 112 0 CTCTATTTTT 0.934134 -15 AATAAAATTCCTTTAATTTTTTATCGTTA 11 19 0 TTCTTTATTT 0.689035 -19 AGTTTATTTCCTATGTTTTGTTGA 13 6 0 TTCTATTTTT 0.804872 -19 TTGAGTAAAGTTACTTTTATTTG 15 2 0 TTCTTTATTT 0.689035 -61 CGCCTGCGATTTTCTTTCTTTTAACATTAATT 16 129 1 TTCTTTTTTT 0.899092 -38 ** **** **** Masking position 7 Map Score: 11.9115 Number of sites scoring better than the average of aligned sites = 649 Number in coding regions = 488 Number in noncoding regions = 161 Number of orfs with sites within 600 bp upstream = 135 Fraction of orfs with sites within 600 bp upstream = 0.0216833 Motif number 11 TTGGCTATTAGAACGCTCAACTCGT 1 233 0 GCATTAAACG 0.990278 -15 AAAAATTTTAGCCATTATAACGGAAAAGTGCG 3 27 1 GCATTAAACG 0.990278 -140 TCTTTATTCATCAATAACAACGGGTAATATTC 7 130 0 TCATAAAACG 0.795409 -30 ATTTTGGTGGGCGATTATAGCGAAATACATCC 10 66 0 GCATTAAGCG 0.988297 -46 TGGTTTTATAACGATAAAAAATT 11 2 1 GGTTTAAACG 0.925387 -36 AAATTTTCTCGCTTTTAAAGCGAAAAGTGTAT 12 24 1 GCTTTAAGCG 0.977962 -184 ** **** **** Masking position 7 Map Score: 3.38821 Number of sites scoring better than the average of aligned sites = 41 Number in coding regions = 23 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 12 CAACAACAAAACGGAGTAAATTATTCTTAC 1 131 1 ACGGAGTAAA 0.911648 -117 TTTCCCTTATTTTGAGTAAAACGGTTGTAA 2 25 0 TTTGAGTAAA 0.954707 -24 ATATACAACAAAGGAGAAAATATA 4 59 1 AAGGAGAAAA 0.812724 -14 TCAACAATGGTTGGGGAAAATAACGCATTT 6 137 0 TTGGGGAAAA 0.847376 -35 ATGGTAAGTTTTTAAGTAAAAACTATAACA 7 81 0 TTTAAGTAAA 0.700837 -79 AGTAAAAAACATTGAGAAAATCAACCGCTC 8 30 0 ATTGAGAAAA 0.929471 -97 ACCCCTTAATTTGGAGTAAATCACTT 12 192 1 TTGGAGTAAA 0.971038 -16 ATTTAGTTTAATTGAGTAAAGTTACTTTTA 15 15 0 ATTGAGTAAA 0.954832 -48 ********** Masking position 8 Map Score: 3.8468 Number of sites scoring better than the average of aligned sites = 182 Number in coding regions = 126 Number in noncoding regions = 56 Number of orfs with sites within 600 bp upstream = 59 Fraction of orfs with sites within 600 bp upstream = 0.00947639 Motif number 13 ********** No masking Map Score: -4.24661e-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 14 ********** No masking Map Score: -4.24661e-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 15 ********** No masking Map Score: -4.24661e-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