AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i231_protease_clp_bsub_reg_100.orf -aORF_bsub.txt -zbsub.fna -g0.435 -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 = 0.435 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 lonA 180 class III heat-shock ATP-dependent Lon protease #2 lonB 151 Lon-like ATP-dependent protease #3 clpX 272 ATP-dependent Clp protease ATP-binding subunit (class III heat-shock protein) #4 tig 227 trigger factor (prolyl isomerase) #5 clpP 300 ATP-dependent Clp protease proteolytic subunit (class III heat-shock protein) Motif number 1 ACCCTATTTTGATAATAGGG 1 1 1 ACCCTATTTT 0.86515 -180 CTCGTAGTATACCCTTTCTTTCTGATATGA 1 61 0 ACCCTTTCTT 0.904842 -120 ATGGAACCATGCCGTTTATTGTACAAGGAT 1 109 1 GCCGTTTATT 0.971633 -72 CTTCCGGAAAAACGTTTATTCCCGTCTTCT 2 67 1 AACGTTTATT 0.714462 -85 AATGATTCGCGCCCTGTTTTATTAGTACTA 3 26 0 GCCCTGTTTT 0.984539 -247 AATCATTCGTGCCTTGTTTTCGTACAATTA 3 49 1 GCCTTGTTTT 0.876711 -224 ACAAAAAACAGCCCTGCATTAACTATATTG 3 102 0 GCCCTGCATT 0.928523 -171 ACACATTGTTACCGTCTTTTTGGAAAGTAT 3 159 1 ACCGTCTTTT 0.910697 -114 TCAAATAACAACCCTCTATTTCGAGAGGCC 5 95 1 ACCCTCTATT 0.954118 -206 ATTTCGAGAGGCCGTTTTTTAAATAGACAA 5 112 1 GCCGTTTTTT 0.96647 -189 ATGGTTTGAACCCCTGTATTTTTGGGGAAA 5 170 1 CCCCTGTATT 0.935681 -131 CTTTTTGTTTGACCTTTATTGACCAAAAAT 5 235 1 GACCTTTATT 0.890907 -66 ********** Masking position 5 Map Score: 13.4338 Number of sites scoring better than the average of aligned sites = 673 Number in coding regions = 518 Number in noncoding regions = 155 Number of orfs with sites within 600 bp upstream = 155 Fraction of orfs with sites within 600 bp upstream = 0.0248956 Motif number 2 TAATAGGGTTTTTTTCATGAAGGACATCTTT 1 23 1 TTTTTCTGAA 0.970347 -158 CAGGAGGTTTTTTTGCATGCAACTCTTCCGG 2 43 1 TTTTGCTGCA 0.904534 -109 GGAATAAACGTTTTTCCGGAAGAGTTGCATG 2 58 0 TTTTTCGGAA 0.977742 -94 ACATAAATTGTTTTTCAGGAGGGACCACC 2 133 1 TTTTTCGGAG 0.944028 -19 GAGTTATCTCTTTTTCTTGGGGCAATATAGT 3 80 1 TTTTTCTGGG 0.941795 -193 TCACTTTTTCTTTTACCGGCAGAGCAAAAGA 3 230 0 TTTTACGGCA 0.823374 -43 GGCAGCTTTGTTTTTGTTGGACGAAGCCGAA 4 150 1 TTTTTGTGGA 0.972489 -78 CTGAATAGATTTTTGGAGGGAAACAC 4 212 1 TTTTGGGGGA 0.953264 -16 AACCCCTGTATTTTTGGGGAAAATGGGAAAA 5 178 1 TTTTTGGGAA 0.973576 -123 TCAGGCCAGCTTTTTGTTTGACCTTTATTGA 5 226 1 TTTTTGTTGA 0.7554 -75 ACATGATACATTTTTGGTCAATAAAGGTCAA 5 243 0 TTTTTGTCAA 0.780475 -58 ****** **** Masking position 4 Map Score: 9.65443 Number of sites scoring better than the average of aligned sites = 903 Number in coding regions = 772 Number in noncoding regions = 131 Number of orfs with sites within 600 bp upstream = 137 Fraction of orfs with sites within 600 bp upstream = 0.0220045 Motif number 3 TTTCTGATATGAAAAAGGAAAAGATGTCCT 1 43 0 GAAAAAGGAA 0.975239 -138 CTGTTTTATAGAAAATGGAACCATGCCGTT 1 95 1 GAAAATGGAA 0.964897 -86 ATCTCCCATAGAAGACGGGAATAAACGTTT 2 76 0 GAAGACGGGA 0.961539 -76 ATTGCCCCAAGAAAAAGAGATAACTCATAA 3 76 0 GAAAAAGAGA 0.957148 -197 GCCGGTAAAAGAAAAAGTGAGACAAGATTA 3 241 1 GAAAAAGTGA 0.957148 -32 TATTTTTGGGGAAAATGGGAAAAAGAGACG 5 186 1 GAAAATGGGA 0.987856 -115 ********** Masking position 5 Map Score: 6.30202 Number of sites scoring better than the average of aligned sites = 170 Number in coding regions = 139 Number in noncoding regions = 31 Number of orfs with sites within 600 bp upstream = 33 Fraction of orfs with sites within 600 bp upstream = 0.00530035 Motif number 4 GTGACTGACACCTCCGTGACTTTAGTA 1 164 0 ACACCTCCGT 0.980326 -17 AGATAAGCACAAACCTCCTGAGTGGTAACA 2 11 1 AAACCTCCTG 0.955087 -141 GCATGCAAAAAAACCTCCTGAGTGTTACCA 2 33 0 AAACCTCCTG 0.955087 -119 TTTGCATGCAACTCTTCCGGAAAAACGTTT 2 54 1 ACTCTTCCGG 0.924774 -98 ACAGGGCGCGAATCATTCGTGCCTTGTTTT 3 39 1 AATCATTCGT 0.839029 -234 TGCAATACATACTCGTTCGTTTCAAGAATC 3 196 1 ACTCGTTCGT 0.829812 -77 ATTCTAAAGCAATCATTCGGCTTCGTCCAA 4 166 0 AATCATTCGG 0.892616 -62 TGGAAGACCGACACAACCTGAATAGATTTT 4 195 1 ACACAACCTG 0.786545 -33 ACAGGGGTTCAAACCATCGTATGTCAGATT 5 157 0 AAACCATCGT 0.787543 -144 AATGCTCCTCCTTCACCTTTTAG 5 288 0 GCTCCTCCTT 0.816002 -13 ********** Masking position 4 Map Score: 3.63332 Number of sites scoring better than the average of aligned sites = 975 Number in coding regions = 831 Number in noncoding regions = 144 Number of orfs with sites within 600 bp upstream = 150 Fraction of orfs with sites within 600 bp upstream = 0.0240925 Motif number 5 ACCATGCCGTTTATTGTACAAGGATGAAAAA 1 114 1 TTATTGTACA 0.96926 -67 GTATGAACCATTATAATACAACTTTTTCATC 1 136 0 TTATAATACA 0.905029 -45 TGGTGCATAATAATAGTACTAATAAAACAGG 3 13 1 TAATAGTACA 0.96554 -260 AGATAACTCATAATTGTACGAAAACAAGGCA 3 58 0 TAATTGTACA 0.978438 -215 TCAGCACAACTAATTATACGATAATTCCTTT 5 65 1 TAATTATACA 0.952721 -236 ********* * Masking position 7 Map Score: 2.07766 Number of sites scoring better than the average of aligned sites = 21 Number in coding regions = 10 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 6 TCTTTTCCTTTTTCATATCAGAAAGAAAGGG 1 49 1 TTTCATTCAG 0.925765 -132 GATACATAAATTGTTTTTCAGGAGGGACCAC 2 130 1 TTGTTTTCAG 0.906153 -22 CATATAGAATGTGCAAGTCAGAAACACATTG 3 136 1 GTGCAATCAG 0.899905 -137 TGGACAGGCTTTGCAGTTCATTATTAACATC 4 96 1 TTGCAGTCAT 0.911789 -132 CTATATGCGCTCGTAGCTCAGTTGGATAGAG 5 17 0 TCGTAGTCAG 0.962921 -284 GTTCAAACCATCGTATGTCAGATTGCCAATT 5 150 0 TCGTATTCAG 0.969064 -151 AGAGACGACTTTGCATATCAGGCCAGCTTTT 5 209 1 TTGCATTCAG 0.989689 -92 ****** **** Masking position 10 Map Score: 2.43278 Number of sites scoring better than the average of aligned sites = 233 Number in coding regions = 213 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 7 ATACTAAAGTCACGGAGGTGTCAGTCAC 1 163 1 CACGGAGGTG 0.97223 -18 TGAGTGTTACCACTCAGGAGGTTTGTGCTT 2 15 0 CACTCAGGAG 0.993733 -137 TGAGTGGTAACACTCAGGAGGTTTTTTTGC 2 29 1 CACTCAGGAG 0.993733 -123 ********** Masking position 6 Map Score: 0.462495 Number of sites scoring better than the average of aligned sites = 23 Number in coding regions = 2 Number in noncoding regions = 21 Number of orfs with sites within 600 bp upstream = 3 Fraction of orfs with sites within 600 bp upstream = 0.00048185 Motif number 8 ********** No masking Map Score: -3.12396e-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 9 CTACGAGGAGACTGTTTTATAGAAAATGGAACCA 1 84 1 ACTGTTATAA 0.937771 -97 GTTGTATTATAATGGTTCATACTAAAGTCACGGA 1 145 1 AATGTCATAA 0.926909 -36 TTAATGCAGGGCTGTTTTTTGTCATACATATAGA 3 110 1 GCTGTTTTGA 0.804884 -163 ACGAGTATGTATTGCATTTTACCATACTTTCCAA 3 178 0 ATTGTTTTAA 0.665513 -95 AGCAAAAGAAAATGATTCTTGAAACGAACGAGTA 3 205 0 AATGTCTTGA 0.928926 -68 TTGAAAGCGCTATGTGTTATGTTATAATATAGTG 4 25 1 TATGTTATGA 0.844071 -203 ATTTGTGTATAACGGGTTATAAGAAATACGGTTG 4 64 1 AACGTTATAA 0.782237 -164 GCGCATATAGACTGCGTTATGAGAACGTCAGCAC 5 38 1 ACTGTTATGA 0.967328 -263 ATTGACCAAAAATGTATCATGTAACTACATACTT 5 252 1 AATGTCATGA 0.961413 -49 **** ***** * Masking position 7 Map Score: 0.134239 Number of sites scoring better than the average of aligned sites = 264 Number in coding regions = 221 Number in noncoding regions = 43 Number of orfs with sites within 600 bp upstream = 50 Fraction of orfs with sites within 600 bp upstream = 0.00803084 Motif number 10 ********** No masking Map Score: -3.12396e-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: -3.12396e-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: -3.12396e-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