AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/alignace/lib/ORF_synecho.txt -z/skink1/amcguire/genomes/synecho.fna -icpxR6_synecho_opreg_100.orf -g0.48 -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 = 0.48 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 ppiB 205 peptidyl-prolyl cis-trans isomerase B #2 hhoA 198 protease HhoA #3 lim 127 lipophilic protein #4 htrA 105 serine protease HtrA #5 1652523 300 regulatory components of sensory transduction system #6 1652728 300 hypothetical protein #7 1652730 69 hypothetical protein #8 1652731 32 hypothetical protein #9 1652734 59 hypothetical protein #10 icfg 99 ICFG #11 hhoB 113 protease HhoB #12 ycf27 154 regulatory components of sensory transduction system #13 1001717 182 regulatory components of sensory transduction system #14 ycf27 190 regulatory components of sensory transduction system #15 1001817 118 regulatory components of sensory transduction system #16 1653824 238 regulatory components of sensory transduction system Motif number 1 AACATAACAAACCCCCGTTTCTGCCCTGAATT 1 54 0 ACCCCTTTCT 0.879321 -152 GTTCAATTGGTCCCCATTTCCCCTAGAAAGTT 1 83 1 TCCCCTTCCC 0.945647 -123 CCACTCCGGCCCCCAAGTTTGCTTGGGCTAGT 2 54 1 CCCCATTTGC 0.985917 -145 ATAAAGTTTACCCCATATTTGTACGGTGCTTA 3 76 0 CCCCATTTGT 0.926964 -52 CCCTTCCCAATCCCATCTTTGCCC 3 114 1 TCCCATTTGC 0.969408 -14 AGAGTCAGATCCCCCAAGTGGCCACCAAGCTC 5 242 1 CCCCCGTGGC 0.975347 -59 TCGGAACTGACCCCCGCTTTGCTTAAATTAAA 6 246 1 CCCCCTTTGC 0.996311 -55 TTTAAAAATCCCCCCTGGTTCCCAACCTCGGA 7 17 1 CCCCCGTTCC 0.983401 -53 GATACCAAACCCCCAATTTGGCTATATGCTTA 12 37 1 CCCCATTGGC 0.972478 -118 CGAAAAAAATTCCCCCGTTTGCTATTGAGGGA 13 68 0 TCCCCTTTGC 0.991886 -115 ATTTTTTTCGTGCCCAATTTCCAGCCCTAGCG 13 90 1 TGCCCTTTCC 0.943175 -93 TGAAAATTAGCGCCCTGTTTCCCGCGGCATTT 14 91 0 CGCCCTTTCC 0.973453 -100 TGAATTTCATACCCCCTTTGGCAGACTGGGAA 15 42 0 ACCCCTTGGC 0.964073 -77 TACGATTTTCTCCCCCTTTTCTTCAATTTTAC 16 99 0 TCCCCTTTCT 0.94366 -140 ***** ***** Masking position 9 Map Score: 25.6399 Number of sites scoring better than the average of aligned sites = 784 Number in coding regions = 697 Number in noncoding regions = 87 Number of orfs with sites within 600 bp upstream = 101 Fraction of orfs with sites within 600 bp upstream = 0.0162223 Motif number 2 GTCAGTGGCGTGGAAAAGCTTTGAAAACGGA 2 99 1 TGGAAAAGCT 0.938047 -100 CGGATTCTTAGGTAAAATCGTCCCTGTTAGA 2 126 1 GGTAAAATCT 0.774581 -73 GTACAAATATGGGGTAAACTTTATCCTAAAC 3 84 1 GGGGTAAACT 0.889537 -44 AACTAATTTGGTGCAAAGCATAGCATAATCT 6 141 0 GTGCAAAGCT 0.811084 -160 TTAGTTATCTTGGCAAATCATCT 6 288 1 TGGCAAATCT 0.961331 -13 AACTATGCACTGGCAAAACTTTGTTGT 10 7 0 TGGCAAAACT 0.936134 -93 CTGGGTTGAAGGGGAAAGAGTTTTCGTCCTT 11 31 1 GGGGAAAGAT 0.872269 -83 AACTGGAGCTGGGGAAATTGTCGCCAAAGGA 11 57 0 GGGGAAATTT 0.769752 -57 GGGGCAAAACTTAACCAATTTC 13 2 1 GGGCAAAACT 0.974761 -181 ATCGTTGAATTGGCAAAGCCTAGATAGGAAA 13 35 0 TGGCAAAGCT 0.966439 -148 TTGCTATTGAGGGAAAATCGTTGAATTGGCA 13 51 0 GGGAAAATCT 0.971783 -132 ATCTAAAACATGGGTAATCTTGTGCTGAAGC 14 14 0 TGGGTAATCT 0.838282 -177 GCCCTGGGACTGTGAAAGCCTTTATAATAGG 14 124 1 TGTGAAAGCT 0.706671 -67 GCTCAGGGGCTAAAACTAAAGGAAAAA 14 174 0 GGGCTAAAAT 0.507614 -17 TTGGCAGACTGGGAAAATCTTGGACAAATTC 15 26 0 GGGAAAATCT 0.971783 -93 AGAAAAGGGGGAGAAAATCGTAAAGAAATCG 16 109 1 GAGAAAATCT 0.660863 -130 ********* * Masking position 6 Map Score: 15.5341 Number of sites scoring better than the average of aligned sites = 1446 Number in coding regions = 1281 Number in noncoding regions = 165 Number of orfs with sites within 600 bp upstream = 179 Fraction of orfs with sites within 600 bp upstream = 0.0287504 Motif number 3 GGGCAGAAACGGGGGTTTGTTATGTTCAATTG 1 60 1 GGGGTTTGTA 0.964147 -146 TAGCAATTACGGAGATTAGATTTT 1 192 1 GGAGTTAGTT 0.934988 -14 CCGGGGTTGAGTCAATCCATCCCA 2 3 1 GGGGTGAGCA 0.733422 -196 ACTGACTTGTGGGCAATAGACTAGCCCAAGCA 2 73 0 GGGCATAGCT 0.707342 -126 ATATTTGTACGGTGCTTAGCCACTGTTACCCA 3 62 0 GGTGTTAGCA 0.769704 -66 TTGTTTTAGAGGGCTTTTTTTTGTAT 4 5 0 GGGCTTTTTT 0.753415 -101 ATAATATTGAGGGGCTTTTACTTAGTTTCGTC 5 52 1 GGGGTTTTCT 0.960181 -249 TGTTTCCATGGGAGTTTAGACTATGACTAACA 5 195 1 GGAGTTAGCT 0.942409 -106 TGGCCACTTGGGGGATCTGACTCTAACCAAGC 5 234 0 GGGGTCTGCT 0.874294 -67 AATTTAGTCGGGAGATTATGCTATGCTTTGCA 6 129 1 GGAGTTATCT 0.877972 -172 GTTCTGAACAGGTGAATTTTTTCAAGCCCGTC 6 209 1 GGTGATTTTT 0.584775 -92 TGGGAACCAGGGGGGATTTTTAAAAGTTAT 7 9 0 GGGGATTTTA 0.83607 -61 GGAGAATTGTTAATAGTCAGTG 11 102 0 GGAGATTGTA 0.829976 -12 TAGCCAAATTGGGGGTTTGGTATCGTTGGTAT 12 29 0 GGGGTTTGTA 0.964147 -126 ATAGCAAACGGGGGAATTTTTTTCGTGCCCAA 13 75 1 GGGGATTTTT 0.901395 -108 CAGCCCTAGCGGAGATTAGCTTTTTTCACCAT 13 111 1 GGAGTTAGTT 0.934988 -72 TGTTTTAGATGGAGTTTTTCTTGGTCATGATG 14 35 1 GGAGTTTTTT 0.899177 -156 **** **** ** Masking position 2 Map Score: 14.9397 Number of sites scoring better than the average of aligned sites = 1758 Number in coding regions = 1539 Number in noncoding regions = 219 Number of orfs with sites within 600 bp upstream = 207 Fraction of orfs with sites within 600 bp upstream = 0.0332477 Motif number 4 AAAATCGTCCCTGTTAGAATGGCAAAAGTGAAAA 2 139 1 CGTTATGGCA 0.988241 -60 TGCTTAGCCACTGTTACCCAGGCAGTAAAGACTT 3 48 0 CGTTCAGGCA 0.954574 -80 CCCCAAAATACTGTTTCCATGGGAGTTTAGACTA 5 184 1 CGTTCTGGGA 0.950905 -117 CAGTAACATTTCGTTACAGTGGCAATTTAGTCGG 6 106 1 TGTTATGGCA 0.984912 -195 TGATTACTTTTAGTTATCTTGGCAAATCATCT 6 279 1 TGTTCTGGCA 0.990434 -22 AACCTTTCCGTCCTTCCCGTGGCATCAACAT 8 12 1 TCTTCTGGCA 0.93767 -21 TGAGGGAAAATCGTTGAATTGGCAAAGCCTAGAT 13 41 0 TGTTATGGCA 0.984912 -142 CAATTTTACTTTGTTAGGATCGCATTTTTAATGC 16 74 0 TGTTGTCGCA 0.899566 -165 CGAAATGTAACAGTTTTAGTCGCATCAGCTAACT 16 143 0 CGTTATCGCA 0.962403 -96 * *** * ***** Masking position 5 Map Score: 8.40716 Number of sites scoring better than the average of aligned sites = 155 Number in coding regions = 139 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911 Motif number 5 GTCCACTTTAGATAACTTTCTAGGGGAAAT 1 98 0 GATAACTTTC 0.65658 -108 TTTAAAGTTGGTTAATTTACATAAACGATG 1 147 1 GTTAATTTAC 0.719743 -59 AGAGGACAGAGCTGCTTTTCAACAACAACC 5 95 1 GCTGCTTTTC 0.873795 -206 ATTGATCGTAGTTAATTTTCTAATTATTTT 5 126 0 GTTAATTTTC 0.919816 -175 AATGGGTCGAGCTGGATTTCCTCAGTAACA 6 84 1 GCTGGATTTC 0.79001 -217 ATTGTCTTAAATTTCCCTTTCCCTT 9 6 1 CTTAAATTTC 0.712465 -54 CATTTATGCGGTTGATTTTCAACTATGCAC 10 28 0 GTTGATTTTC 0.904614 -72 TTAGTAAGGAGCTAAATTACTTTTGGTAAA 10 72 1 GCTAAATTAC 0.83088 -28 GAAACAGGGCGCTAATTTTCAGGCCCTGGG 14 102 1 GCTAATTTTC 0.956334 -89 GAGATTTTCACCTGAATTTCATACCCCCTT 15 56 0 CCTGAATTTC 0.794957 -63 AGTCGCATCAGCTAACTTTCCGATTTCTTT 16 130 0 GCTAACTTTC 0.936521 -109 GACTAAAACTGTTACATTTCGCAACATGAA 16 156 1 GTTACATTTC 0.815665 -83 ********** Masking position 7 Map Score: 7.13687 Number of sites scoring better than the average of aligned sites = 463 Number in coding regions = 387 Number in noncoding regions = 76 Number of orfs with sites within 600 bp upstream = 82 Fraction of orfs with sites within 600 bp upstream = 0.0131706 Motif number 6 CTGACAGCACGGGAATGGCAAT 1 2 0 GGGAAGGCAA 0.933589 -204 AATTGCTAATGGCAACTGCCTTTCATCGTTT 1 169 0 GGCAATGCCT 0.662629 -37 GGGCAAAGATGGGATTGGGAAGGGTTTAGGA 3 107 0 GGGATGGGAA 0.968747 -21 AGTATTTTGGGGCAAATGGAAGCATTAAGAT 5 165 0 GGCAATGGAA 0.903246 -136 GGCCACTTGGGGGATCTGACTCTAACCAAGC 5 234 0 GGGATTGACT 0.640551 -67 GTGAATTGAAGGGAAAGGGAAATTTAAGACA 9 13 0 GGGAAGGGAA 0.981333 -47 GGTATCAATGGGGATGGGGCAGA 12 3 0 GGGATGGGCA 0.966653 -152 TATATGCTTAGGGAAATGGCTTTTTGCCACG 12 59 1 GGGAATGGCT 0.968578 -96 AATCAAAGGAGGGTTGTGGATCTTGGAAACC 12 116 1 GGGTTTGGAT 0.711791 -39 AAGCCTAGATAGGAAATGGAAATTGGTTAAG 13 20 0 AGGAATGGAA 0.755304 -163 ATCTTAGCGGGGGAAGGAGATTTTCACCTGA 15 71 0 GGGAAGAGAT 0.777076 -48 ***** ***** Masking position 2 Map Score: 6.01906 Number of sites scoring better than the average of aligned sites = 2093 Number in coding regions = 1900 Number in noncoding regions = 193 Number of orfs with sites within 600 bp upstream = 204 Fraction of orfs with sites within 600 bp upstream = 0.0327658 Motif number 7 AGGACAAGGTCATTGTTTTAGAGGGCTTTT 4 19 0 CATTGTTTTA 0.904279 -87 CCCATGGAAACAGTATTTTGGGGCAAATGG 5 177 0 CAGTATTTTG 0.965277 -124 TCTAACCAAGCAGTGTTTTGTTAGTCATAG 5 215 0 CAGTGTTTTG 0.977749 -86 TTCAATTCACCATTATTTAGATTTTTGTAA 9 34 1 CATTATTTAG 0.81434 -26 TGTTAATAGTCAGTGTTTTAACTTTAACAA 11 87 0 CAGTGTTTTA 0.936927 -27 TTCACCATGTCATTATTTTGCCAAAAAGTT 13 135 1 CATTATTTTG 0.946565 -48 ********** Masking position 6 Map Score: 2.90848 Number of sites scoring better than the average of aligned sites = 100 Number in coding regions = 88 Number in noncoding regions = 12 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 8 GTTGAGTCAATCCATCCCAAGAAACCGTTCG 2 16 1 TCCATCCCAG 0.918131 -183 GTGTCAGTTTTTCAGGACAAGGTCATTGTTT 4 31 0 TTCAGGACAG 0.938348 -75 ACTGAGGAAATCCAGCTCGACCCATTTCGAC 6 79 0 TCCAGCTCAC 0.84886 -222 AATTCACCTGTTCAGAACCAGAATACTCCGC 6 196 0 TTCAGAACAG 0.848031 -105 CGACAATTTCCCCAGCTCCAGTTTGTTAAAG 11 65 1 CCCAGCTCAG 0.900312 -49 GTGCCCAATTTCCAGCCCTAGCGGAGATTAG 13 99 1 TCCAGCCCAG 0.991334 -84 TTAGCTTCAGCACAAGATTACCCATG 14 6 1 TTCAGCACAG 0.977283 -185 GGCGCTAATTTTCAGGCCCTGGGACTGTGAA 14 109 1 TTCAGGCCTG 0.908542 -82 TTCCTTTAGTTTTAGCCCCTGAGC 14 177 1 TTTAGCCCTG 0.733522 -14 ******** ** Masking position 4 Map Score: 2.67288 Number of sites scoring better than the average of aligned sites = 470 Number in coding regions = 425 Number in noncoding regions = 45 Number of orfs with sites within 600 bp upstream = 58 Fraction of orfs with sites within 600 bp upstream = 0.00931577 Motif number 9 GTTTCTGCCCTGAATTTGGTGTTCTTGGTA 1 40 0 TGAATTTGGT 0.732471 -166 AAGGATTTACAGAAATTTTCACTTTTGCCA 2 158 0 AGAAATTTTC 0.731713 -41 TATGGCCCCTAGAATTTGGCTCCGATGCTG 3 15 0 AGAATTTGGC 0.764255 -113 GACGACGGTATGAAATTTTTGTGTCAGTTT 4 52 0 TGAAATTTTT 0.699638 -54 TAGTTCTCTTTGAATTTTTCTTTCGGAGTG 6 167 1 TGAATTTTTC 0.856364 -134 TCTGAACAGGTGAATTTTTTCAAGCCCGTC 6 211 1 TGAATTTTTT 0.72964 -90 CTGGAGCTGGGGAAATTGTCGCCAAAGGAC 11 56 0 GGAAATTGTC 0.95072 -58 GATAGGAAATGGAAATTGGTTAAGTTTTGC 13 14 0 GGAAATTGGT 0.865432 -169 AGCAAACGGGGGAATTTTTTTCGTGCCCAA 13 77 1 GGAATTTTTT 0.880149 -106 CGCTAGGGCTGGAAATTGGGCACGAAAAAA 13 92 0 GGAAATTGGG 0.701675 -91 TGTTTTAGATGGAGTTTTTCTTGGTCATGA 14 35 1 GGAGTTTTTC 0.836783 -156 CCTCAAATTGGGAATTTGTCCAAGATTTTC 15 15 1 GGAATTTGTC 0.957299 -104 AGCGGGGGAAGGAGATTTTCACCTGAATTT 15 67 0 GGAGATTTTC 0.81556 -52 ********** Masking position 3 Map Score: 8.17566 Number of sites scoring better than the average of aligned sites = 1416 Number in coding regions = 1253 Number in noncoding regions = 163 Number of orfs with sites within 600 bp upstream = 195 Fraction of orfs with sites within 600 bp upstream = 0.0313203 Motif number 10 ATTTGGTGTTCTTGGTAGTGAAATCTGACA 1 27 0 CTTGGTAGTG 0.975004 -179 AATCTCCGTAATTGCTAATGGCAACTGCCT 1 179 0 ATTGCTAATG 0.783518 -27 TCTGTAAATCCTTGCTAATGCGTATTTGGA 2 175 1 CTTGCTAATG 0.949667 -24 TCGTCTCAATGTTGGTAGAGGACAGAGCTG 5 79 1 GTTGGTAGAG 0.93997 -222 AATCTAAATTCTTGCTAGAGTTGAGAAAAC 5 275 1 CTTGCTAGAG 0.967647 -26 TGGAGTTTTTCTTGGTCATGATGCTCGCAA 14 44 1 CTTGGTCATG 0.851479 -147 GTAAGCTGAGGTTGATAGAGAAAAGCACAA 16 213 1 GTTGATAGAG 0.797594 -26 ********** Masking position 6 Map Score: 0.991571 Number of sites scoring better than the average of aligned sites = 180 Number in coding regions = 149 Number in noncoding regions = 31 Number of orfs with sites within 600 bp upstream = 37 Fraction of orfs with sites within 600 bp upstream = 0.00594282 Motif number 11 ATTCCATTGGACAACTTTTAGTTTGTCCAC 5 14 1 ACAACTTTTA 0.950416 -287 AATTAAACTGATTACTTTTAGTTATCTTGG 6 271 1 ATTACTTTTA 0.925329 -30 ATAACTTTTAAAAATCCCCC 7 1 1 ATAACTTTTA 0.946684 -69 AAGGAGCTAAATTACTTTTGGTAAATTAAA 10 77 1 ATTACTTTTG 0.848079 -23 TGGACATTAAACAACTTTTAAGTTTAATTA 16 23 0 ACAACTTTTA 0.950416 -216 ********** Masking position 6 Map Score: 0.867376 Number of sites scoring better than the average of aligned sites = 43 Number in coding regions = 32 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 12 ********** No masking Map Score: -1.32571e-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 13 ********** No masking Map Score: -1.32571e-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 14 ********** No masking Map Score: -1.32571e-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