AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00252_aful_reg_300.orf -o00252_aful_300.ace -a/home/amcguire/genomes/ORF_aful.txt -z/home/amcguire/genomes/aful.fna -g0.49 -x5 -e 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 = 0.49 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 AF0106 116 aspartate carbamoyltransferase, catalytic subunit (pyrB) #2 AF0841 80 adenylosuccinate synthetase (purA) #3 AF0842 65 A. fulgidus predicted coding region AF0842 #4 AF0883 71 argininosuccinate lyase (argH) #5 AF0916 59 glycyl-tRNA synthetase (glyS) #6 AF0919 30 conserved hypothetical protein #7 AF0920 36 aspartyl-tRNA synthetase (aspS) #8 AF1418 49 glycerol-3-phosphate cytidyltransferase (taqD) #9 AF1419 24 ribose-phosphate pyrophosphokinase (prsA-2) #10 AF1420 216 membrane protein #11 AF1421 49 conserved hypothetical protein #12 AF1422 35 aspartate racemase #13 AF1423 112 conserved hypothetical protein #14 AF1439 31 asparagine synthetase (asnB) #15 AF1442 54 conserved hypothetical protein #16 AF2242 61 adenylosuccinate lyase (purB) #17 AF2243 38 3-ketoacyl-CoA thiolase (fadA-3) #18 AF2244 300 acyl-CoA dehydrogenase (acd-11) #19 AF2252_AF2253 78 AF2252: argininosuccinate synthetase (argG), AF2253: molybdopterin-guanine dinucleotide biosynthesis protein B (mobB) #20 AF2254 207 ATP-dependent RNA helicase, DEAD-family (deaD) #21 AF2255 53 alanyl-tRNA synthetase (alaS) Motif number 1 ACCTCCTCTCCTTTTACGGTTTTAAACTTTCTCCCGTA 1 89 0 CTATTTAAAT 0.750558 -28 GCACCATAAGAAGATAACCTTTTAAGTTGCATTCTGCA 5 28 1 AGATTTAAGT 0.871449 -32 CTTACACCTTCAGGCAGTTTTTTAAGTTTAGCC 7 6 0 CGATTTAAGT 0.991723 -31 AATCCAAATTCAGGTAGGCATAAAAGTTTT 8 3 0 CGAATAAAGT 0.706625 -47 AATAGACTATCCGGGAAGCTTTGAAGCTGAGTGACAGA 10 52 0 CGATTTAAGT 0.991723 -165 AGTTATTCTGCTGGCAACGCTTCAAGACTTCGTGGATT 10 121 1 CGACTTAAGC 0.936719 -96 ATTGGTAGCACAGCAAACTTTTTAACATTCAAAGCAGA 11 14 1 CGATTTAACT 0.985437 -36 CATCACCCAACCTAAAAAATTTTAACCTCAACTTCAAG 13 20 0 CTATTTAACT 0.951096 -93 TTGGGTGATGCGCTAAATACTTCAAGACAGGCCTTTTA 13 48 1 CCACTTAAGC 0.779126 -65 GATGATGATGCGTAAACAATTTAAACTTTAAGGTTTAT 15 22 0 CTATTTAACT 0.951101 -33 GAGGAGCTTGCTGAAAGCATCTCAAGTTATGCTGTTGG 18 128 0 CGATCTAAGT 0.942052 -173 AGCTCCTCCACCTTCACCACTTCAAGTTTTCAACGGTG 18 158 1 CTACTTAAGT 0.940651 -143 TCTGAAAACCCAGGAAGTTTTTTAACTTTTGTTTAATC 19 15 1 CGATTTAACT 0.985437 -64 TTTGTTTAATCTCAAAAGATTTAAACCTCTCCGCATGA 19 42 1 CCATTTAACT 0.941606 -37 CTCTAGCGTTCAGACATGTTTAGAAGTTTAATTTGCAT 20 81 1 CGATTAAAGT 0.954118 -127 * * * *** *** * Masking position 6 Map Score: 19.1638 Number of sites scoring better than the average of aligned sites = 207 Number in coding regions = 177 Number in noncoding regions = 30 Number of orfs with sites within 600 bp upstream = 36 Fraction of orfs with sites within 600 bp upstream = 0.0057822 Motif number 2 TTCATAATTATTTAAGCTTTTGCTTGGTTA 1 42 1 TTTAAGCTTT 0.835687 -75 CTTTTACGGTTTTAAACTTTCTCCCGTATG 1 87 0 TTTAAACTTT 0.969921 -30 TCTATTAAACCTTAACTCAAACC 2 4 1 ATTAAACCTT 0.786412 -77 TCAGGCAGTTTTTTAAGTTTAGCC 7 5 0 TTTTAAGTTT 0.74748 -32 ACAGCAAACTTTTTAACATTCAAAGCAGAA 11 23 1 TTTTAACATT 0.796607 -27 ACCTAAAAAATTTTAACCTCAACTTCAAGC 13 19 0 TTTTAACCTC 0.919526 -94 GCGTAAACAATTTAAACTTTAAGGTTTATG 15 21 0 TTTAAACTTT 0.969921 -34 TATCGCCCCCTGTTAACTTCGCTTC 16 47 1 TGTTAACTTC 0.763241 -15 TTTGTGATTATTTAAATTTTGCCAAGTTAA 18 271 0 TTTAAATTTT 0.698223 -30 CCAGGAAGTTTTTTAACTTTTGTTTAATCT 19 24 1 TTTTAACTTT 0.96532 -55 TCTCAAAAGATTTAAACCTCTCCGCATGAC 19 51 1 TTTAAACCTC 0.929761 -28 CACTCCTTAATTTTAACTTTACAAAACTTT 20 28 0 TTTTAACTTT 0.96532 -180 CGAGATGCAAATTAAACTTCTAAACATGTC 20 93 0 ATTAAACTTC 0.828653 -115 ********** Masking position 5 Map Score: 14.8074 Number of sites scoring better than the average of aligned sites = 170 Number in coding regions = 102 Number in noncoding regions = 68 Number of orfs with sites within 600 bp upstream = 83 Fraction of orfs with sites within 600 bp upstream = 0.0133312 Motif number 3 CCAACCACCTCATGTTTTATCACT 3 52 0 CCACCTCATG 0.885632 -14 GCTCTTACACCTTCAGGCAGTTTTTTA 7 20 0 CACCTTCAGG 0.952818 -17 ATCTCCAATCCAAATTCAGGTAGGCATAAA 8 17 0 CAAATTCAGG 0.84955 -33 CTGTCCAAATTCAACTGCGGGCTCG 10 6 1 CAAATTCAAC 0.67699 -211 CTCTGTCACTCAGCTTCAAAGCTTCCCGGA 10 51 1 CAGCTTCAAA 0.653569 -166 TCTGCTGGCAACGCTTCAAGACTTCGTGGA 10 127 1 ACGCTTCAAG 0.908547 -90 ATCTCAATATCAAACTCATGAAAAACCTTA 10 172 1 CAAACTCATG 0.490633 -45 ATTTTAACCTCAACTTCAAGCAAAATCCA 13 10 0 CAACTTCAAG 0.96808 -103 GATGCGCTAAATACTTCAAGACAGGCCTTT 13 54 1 ATACTTCAAG 0.644108 -59 GGATACCCTTCAACTATGAGTTAT 14 18 0 ACCCTTCAAC 0.775203 -14 AGAGCTGTTTCCGCCTCAGGCTGAGGCGGT 18 74 0 CCGCCTCAGG 0.942253 -227 TCCACCTTCACCACTTCAAGTTTTCAACGG 18 164 1 CCACTTCAAG 0.979815 -137 AGACTTATATACCCTTCAGCCAAGCGTTGG 20 154 1 ACCCTTCAGC 0.763313 -54 ********** Masking position 8 Map Score: 7.51723 Number of sites scoring better than the average of aligned sites = 1534 Number in coding regions = 1453 Number in noncoding regions = 81 Number of orfs with sites within 600 bp upstream = 59 Fraction of orfs with sites within 600 bp upstream = 0.00947639 Motif number 4 AATTATTTAAGCTTTTGCTTGGTTATATCA 1 47 1 GCTTTTGCTT 0.894333 -70 TCTCCCGTATGCTATTGCACTTGATATAAC 1 68 0 GCTATTGCAC 0.747265 -49 GCTCTGCCATCATCTCCAAA 4 1 1 GCTCTGCCAT 0.82038 -71 GCTCTTACACCTTCAGGCAG 7 27 0 GCTCTTACAC 0.742088 -10 GACCCTTTTCTTCATCTCCAATC 8 37 0 CCTTTTCTTC 0.612423 -13 AAGCCCTTCCTCTTTTTTTGAT 9 3 1 GCCCTTCCTC 0.917657 -22 CTCCATCAGGGCTATTCGTTTTGTCAAGTT 10 95 1 GCTATTCGTT 0.702288 -122 AAAGGTTACTCCTTTTCGTTAAAAAGAAAA 16 17 0 CCTTTTCGTT 0.766461 -45 CCGGAAAAGACCTTCTCCACCGCCTCAGCC 18 56 1 CCTTCTCCAC 0.891501 -245 GGCGGAAACAGCTCTTCTATACCCTCCTCC 18 89 1 GCTCTTCTAT 0.823853 -212 TCTTCTATACCCTCCTCCTTTAAAATGCCA 18 101 1 CCTCCTCCTT 0.941204 -200 CTTTCAGCAAGCTCCTCCACCTTCACCACT 18 149 1 GCTCCTCCAC 0.967734 -152 ATTAAAAATTGCTCCTCGTTAAACTCATGA 18 197 1 GCTCCTCGTT 0.907743 -104 TATATCTCTTGCCTTTGCTTATTTCGATG 21 10 0 GCCTTTGCTT 0.694389 -44 CGGATGCCTTCTGCATTGGATGTTTA 21 38 0 CCTTCTGCAT 0.756956 -16 ********** Masking position 2 Map Score: 6.60292 Number of sites scoring better than the average of aligned sites = 3159 Number in coding regions = 2988 Number in noncoding regions = 171 Number of orfs with sites within 600 bp upstream = 124 Fraction of orfs with sites within 600 bp upstream = 0.0199165 Motif number 5 GCACTCAGTTTGTGCAGAGGTTATTAATT 4 53 0 TCTTGTGCGG 0.94411 -19 AAGGTTATCTTCTTATGGTGCCGCGCAGCCACTAA 5 14 0 TCATGTGCGG 0.967519 -46 ATTCGTTTTGTCAAGTTATTCTGCTGGCAACGCTT 10 108 1 TCGTATTCGT 0.886914 -109 CAAAGCTTTATCTTGTTAGGCGATTAGTCTATTT 12 12 1 TCGTAGGCAT 0.940283 -24 TGATGTTGTTCTGGTTGGGCCGATAAAAATTTAC 13 89 0 TCGTGGGCGT 0.990925 -24 TGAAAGCATCTCAAGTTATGCTGTTGGCATTTTAA 18 120 0 TCGTATGCGT 0.985962 -181 ACAATCCCGTCATGCGGAGAGGTTTAAAT 19 60 0 TCGTATGCGG 0.985681 -19 GAGTCTCGGCTCAAATCGGGCGAATCCACTCCTTA 20 49 0 TCATGGGCAT 0.872008 -159 ** ** **** * * Masking position 6 Map Score: 3.89652 Number of sites scoring better than the average of aligned sites = 121 Number in coding regions = 111 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 6 GCGATTTTTGGAAAAATGGTAGGTTTGAGTT 2 24 0 GAAAAAGGTA 0.883352 -57 TTCAGGTAGGCATAAAAGTTTT 8 2 0 CATAAAGTTT 0.844278 -48 TCAAACTCATGAAAAACCTTATTAGCCTCTT 10 181 1 GAAAAACTTA 0.849466 -36 CGCCTAACAAGATAAAGCTTTGG 12 3 0 GATAAACTTT 0.925719 -33 TGGTTGGGCCGATAAAAATTTACCGCTAAAA 13 81 0 GATAAAATTT 0.846887 -32 GTCTTTCTATCATAAACCTTAAAGTTTAAAT 15 11 1 CATAAACTTA 0.601425 -44 AACAGGGGGCGATAAAAGGTTACTCCTTTTC 16 30 0 GATAAAGGTT 0.94358 -32 TTTATTATTTGAAAAACGTTTGCAGGGTGAT 17 15 1 GAAAAAGTTT 0.952998 -24 TTAAACAATTGAAAAAGGATTTAAATAGAAC 18 244 0 GAAAAAGATT 0.808039 -57 CTTTCACCATGAAAAAGAGTT 20 1 0 GAAAAAAGTT 0.820218 -207 ****** **** Masking position 6 Map Score: 4.53791 Number of sites scoring better than the average of aligned sites = 264 Number in coding regions = 196 Number in noncoding regions = 68 Number of orfs with sites within 600 bp upstream = 86 Fraction of orfs with sites within 600 bp upstream = 0.013813 Motif number 7 ACCTCCTCTCCTTTTACGGTT 1 106 0 CCTCCTCTCC 0.919869 -11 GCTCTGCCATCATCTCCAAAACATAAA 4 8 1 CATCATCTCC 0.969478 -64 GACCCTTTTCTTCATCTCCAATCCAAATT 8 31 0 CTTCATCTCC 0.986489 -19 AAAATTTTAACCTCAACTTCAAGCAAAATC 13 13 0 CCTCAACTTC 0.838495 -100 ATTGTTTACGCATCATCATCTTATC 15 40 1 CATCATCATC 0.743409 -15 AAAAGACCTTCTCCACCGCCTCAGCCTGAG 18 60 1 CTCCACCGCC 0.933943 -241 CAGCAAGCTCCTCCACCTTCACCACTTCAA 18 153 1 CTCCACCTTC 0.964405 -148 GTTTGAATCCCTCAATCTTCGACTCTCTCC 20 122 0 CTCAATCTTC 0.842343 -86 CAACGTTCCACTCTATCTCCCAACGCTTGG 20 173 0 CTCTATCTCC 0.913023 -35 ********** Masking position 7 Map Score: 3.64293 Number of sites scoring better than the average of aligned sites = 1404 Number in coding regions = 1347 Number in noncoding regions = 57 Number of orfs with sites within 600 bp upstream = 45 Fraction of orfs with sites within 600 bp upstream = 0.00722775 Motif number 8 GCTATTGCACTTGATATAACCAAGCAAAAGCT 1 56 0 TTGAAAACCA 0.804618 -61 GAATTTGGATTGGAGATGAAGAAAAGGGTC 8 30 1 TGGAAGAAGA 0.792885 -20 GAATCAAAAAAAGAGGAAGGGCTT 9 11 0 ATCAAAAAGA 0.94071 -14 GCAGAATAACTTGACAAAACGAATAGCCCTGA 10 100 0 TTGAAAACGA 0.961462 -117 ATTGAGATATTGCAGAAAACGAATCCACGAAG 10 148 0 TGCAAAACGA 0.933895 -69 TTTAAGGTTTATGATAGAAAGAC 15 2 0 ATGAAAAAGA 0.94071 -53 AATTTAAATAATCACAAAAAGAGCCTGC 18 283 1 ATCAAAAAGA 0.94071 -18 GATTGAGGGATTCAAACAAAGACTTATATACC 20 135 1 TTCAAAAAGA 0.962197 -73 **** * ***** Masking position 6 Map Score: 1.91 Number of sites scoring better than the average of aligned sites = 95 Number in coding regions = 80 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 9 TTATTTAAGCTTTTGCTTGGTTATATCAAG 1 49 1 TTTTGCTTGG 0.813262 -68 GCAAATGTATTTATGTTTTGGAGATGATGG 4 17 0 TTATGTTTTG 0.795346 -55 TTAAGTTGCATTCTGCACTGC 5 49 1 TTCTGCACTG 0.956531 -11 AATGCAATTCTGCTTTGAATGTTAAAA 11 33 0 TTCTGCTTTG 0.976683 -17 TGATGTTGTTCTGGTTGGGCCGA 13 100 0 TGTTGTTCTG 0.847764 -13 AGTGGAACGTTGCTGTTCTGTTCTCTG 20 191 1 TGCTGTTCTG 0.942793 -17 CGGATGCCTTCTGCATTGGATGTTTATA 21 36 0 TTCTGCATTG 0.947976 -18 ********** Masking position 4 Map Score: 1.53995 Number of sites scoring better than the average of aligned sites = 220 Number in coding regions = 199 Number in noncoding regions = 21 Number of orfs with sites within 600 bp upstream = 17 Fraction of orfs with sites within 600 bp upstream = 0.00273049 Motif number 10 ACCAAATAAACCCCTGCGAAGGACTGTCAG 2 57 1 CCCCTGCGAA 0.983056 -24 GCTCTGCCATCATCTCCAAAACATAAATAC 4 11 1 CATCTCCAAA 0.872216 -61 GAATTAATAACCTCTGCACAAACTGAGTGC 4 52 1 CCTCTGCACA 0.985912 -20 TCTATCACCCTGCAAACGTTTTTCAA 17 23 0 ACCCTGCAAA 0.915445 -16 AACCTCTGAAAACCCAGGAAGT 19 3 1 CCTCTGAAAA 0.928872 -76 AAGATTTAAACCTCTCCGCATGACGGGATT 19 57 1 CCTCTCCGCA 0.968077 -22 ********** Masking position 5 Map Score: 1.45913 Number of sites scoring better than the average of aligned sites = 271 Number in coding regions = 255 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 17 Fraction of orfs with sites within 600 bp upstream = 0.00273049 Motif number 11 TTATGGTGCCGCGCAGCCACTAAAAT 5 7 0 GCGCAGCCAC 0.985974 -53 ATTGCAGAAAACGAATCCACGAAGTCTTGA 10 142 0 ACGAATCCAC 0.957064 -75 GAAGTATTTAGCGCATCACCCAACCTAAAA 13 41 0 GCGCATCACC 0.967369 -72 TAAATTGTTTACGCATCATCATCTTATC 15 37 1 ACGCATCATC 0.871429 -18 CTTTCAGCAAGCTCCTCCACCTTCACCACT 18 149 1 GCTCCTCCAC 0.91693 -152 CTCAAATCGGGCGAATCCACTCCTTAATTT 20 45 0 GCGAATCCAC 0.984483 -163 ********** Masking position 7 Map Score: 1.942 Number of sites scoring better than the average of aligned sites = 89 Number in coding regions = 79 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 12 ********** No masking Map Score: -1.51813e-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 13 ********** No masking Map Score: -1.51813e-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: -1.51813e-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