AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00220_bsub_reg_100.orf -o00220_bsub_100.ace -a/home/amcguire/alignace/lib/ORF_bsub.txt -z/skink1/amcguire/genomes/bsub.fna -g0.44 -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 = 0.44 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 argC 206 N-acetylglutamate gamma-semialdehyde dehydrogenase #2 carA 70 carbamoyl-phosphate transferase-arginine (subunit A) #3 proB 300 gamma-glutamyl kinase #4 yodT 300 similar to adenosylmethionine-8-amino-7-oxononanoate aminotransferase #5 argG 169 argininosuccinate synthase #6 ureA 300 urease (gamma subunit) #7 ywhF 201 similar to spermidine synthase #8 rocF 73 arginase #9 rocE 222 amino acid permease #10 rocD 240 ornithine aminotransferase Motif number 1 ATTTCAGCCGCATAAAAAAACAGGCTGACC 1 14 0 CATAAAAAAA 0.966649 -193 TTTATAAATGAATAAAAATATTAAATATAC 1 118 1 AATAAAAATA 0.925201 -89 TTATAACATGAATAAAAATTAATTCAATCG 1 147 0 AATAAAAATT 0.698897 -60 GATATAAAGGCATAAAAATTCATTTTTATA 2 20 1 CATAAAAATT 0.844696 -51 AATAATTAATTATAAAAATGAATTTTTATG 2 30 0 TATAAAAATG 0.706188 -41 CTTTGCATAATATAAAAAAATCATTGAGCG 3 27 1 TATAAAAAAA 0.938421 -274 GCTCTTCTACAATAAAAAAACCCATTTCAT 3 266 0 AATAAAAAAA 0.925202 -35 AACTTTTTCACATAAAAAGAGCCTTCCTAA 4 211 0 CATAAAAAGA 0.885037 -90 TCAAGCCTTTTATAAAAAAAACTTCACCTA 5 44 0 TATAAAAAAA 0.938421 -126 AATTATATTTAATAAAAATACATTTTGTAT 5 105 0 AATAAAAATA 0.925201 -65 TTCTATTTTGTATAAAAATAAATTATATTT 5 125 0 TATAAAAATA 0.938418 -45 TAGAAATTTCCAGAAAAAAAGACATTTGTT 6 51 1 CAGAAAAAAA 0.797268 -250 ATAGTAGAAACATAAAAAAAGGGGGAACCC 7 14 0 CATAAAAAAA 0.966649 -188 CACTTCTTCTCATAAAGATACATTATACTA 9 98 0 CATAAAGATA 0.797267 -125 GCTTCTATTTTATAAAAAAACGGAGAGGAT 10 45 1 TATAAAAAAA 0.938421 -196 ********** Masking position 5 Map Score: 19.8002 Number of sites scoring better than the average of aligned sites = 706 Number in coding regions = 397 Number in noncoding regions = 309 Number of orfs with sites within 600 bp upstream = 313 Fraction of orfs with sites within 600 bp upstream = 0.050273 Motif number 2 GCTGGAGTCGTGCTGATTTTTTTTGAGCGGAA 1 68 1 TGCTGATTTT 0.970294 -139 AGGATTAGTAAGCAGACCTTTCTGTGACAGAG 3 63 1 AGCAGATTTC 0.956484 -238 ATTTGCTAGATGCTGAAATTTCAAAAGAGCCT 4 173 1 TGCTGATTTC 0.991436 -128 CCTAAATTTCAGGTGAAGTTTCATAGTATTTA 5 16 0 AGGTGATTTC 0.954841 -154 CCTGAAATTTAGGTGAAGTTTTTTTTATAAAA 5 35 1 AGGTGATTTT 0.856443 -135 AAACGCGTTAATCTGATCTTTCCGTGATCGAC 6 104 1 ATCTGATTTC 0.93183 -197 AAATAGGGAGTGCTGATTTTTCTGTTGTAAAT 9 49 0 TGCTGATTTC 0.991436 -174 GATAGCACCATGCAGATGTTCCAGCTTAGATC 9 172 1 TGCAGATTCC 0.870316 -51 ATTTTGCACTTGCTGAAATTTTCGCTCGAAAT 10 85 1 TGCTGATTTT 0.970294 -156 TGCAAAAACATTCTGATATTTCGAGCGAAAAT 10 102 0 TTCTGATTTC 0.952409 -139 ****** **** Masking position 6 Map Score: 13.6121 Number of sites scoring better than the average of aligned sites = 305 Number in coding regions = 283 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 3 CTCCAGCACAAAAACGTTGATGCGGTGCCGCATTT 1 40 0 AAAGTTGGGG 0.992107 -167 AAAAAATCATTGAGCGTTGAAGAGGATTAGTAAGC 3 41 1 TGGGTTGGGG 0.92726 -260 TTCATGCGGCAAAATGTTTCAGCGGTTCATTTTGC 3 96 0 AAAGTTTGGG 0.987471 -205 ATAAGGACGAAATGGGTTTCCGTGGTACCACCTTG 3 223 0 AAGGTTTGGG 0.982492 -78 TTTTTATGTGAAAAAGTTTTTGCGGGGAACGTCAT 4 223 1 AAAGTTTGGG 0.987471 -78 CAATATGGTAAAAGGGGTTTTGAGGTGGGAGC 4 279 1 AAGGGTTGGG 0.964826 -22 ACAAAATAGAAACACGGTTGAGAGGGGATTTTTAT 5 144 1 AAAGGTTGGG 0.9747 -26 GGAAAAAGTATAGAGGATGGCGGGGAAAAAGTAAA 7 91 0 TAAGATGGGG 0.938968 -111 GACATTATCTTAAATGTTGAGGTGGAATCACAG 8 51 1 TAAGTTGGGG 0.988486 -23 TTAGATCCAATACAAGTTGCTGAAGGGGTGCAGAA 9 197 1 TAAGTTGGAG 0.882359 -26 ** * **** * ** Masking position 8 Map Score: 12.5183 Number of sites scoring better than the average of aligned sites = 92 Number in coding regions = 77 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911 Motif number 4 CTGTTTTTTTATGCGGCTGAAATGCGGCAC 1 21 1 ATGCGGCTGA 0.928162 -186 TGCGGCTGAAATGCGGCACCGCATCAACGT 1 32 1 ATGCGGCACC 0.984339 -175 GGCAGGTTTCATGCGGCAAAATGTTTCAGC 3 108 0 ATGCGGCAAA 0.956572 -193 ACGACATTTTATGCGGGCCAAGTCCCAA 4 9 0 ATGCGGGCCA 0.967005 -292 ACGGATTTGGCTGCGGGACAAATACATTTG 4 93 1 CTGCGGGACA 0.937869 -208 TAGCAAATAAAAGCGGCTCCAACAATAATT 4 151 0 AAGCGGCTCC 0.945862 -150 TTCTTCGAGAATGGGGGTCATACGGTAAGA 6 198 0 ATGGGGGTCA 0.950252 -103 CGGAACAGTCAGGCGGGACATCACCTCCCT 6 228 0 AGGCGGGACA 0.949311 -73 TATAAAGCAGATGCGGCTACTACGAATTTG 6 258 0 ATGCGGCTAC 0.953702 -43 AACATAAAAAAAGGGGGAACCCGTT 7 6 0 AAGGGGGAAC 0.619404 -196 ATAATGTCCTATGCGGGTTATAACAAAGAT 8 29 0 ATGCGGGTTA 0.912258 -45 ********** Masking position 5 Map Score: 10.564 Number of sites scoring better than the average of aligned sites = 489 Number in coding regions = 447 Number in noncoding regions = 42 Number of orfs with sites within 600 bp upstream = 35 Fraction of orfs with sites within 600 bp upstream = 0.00562159 Motif number 5 GAAAATTTATAAATGAATAAAAATATTAAA 1 113 1 AAATGAATAA 0.601958 -94 TTAATTATAAAAATGAATTTTTATGCCTTT 2 25 0 AAATGAATTT 0.929661 -46 GACAAGTGTCTTTTTTCTTTGCA 3 4 1 AAGTGTCTTT 0.830918 -297 CAATTAACACAAATGTATTTGTCCCGCAGC 4 102 0 AAATGTATTT 0.919635 -199 GTACTTGTTAAAGTGTATACATACAAAATG 5 85 1 AAGTGTATAC 0.764505 -85 TATACATACAAAATGTATTTTTATTAAATA 5 100 1 AAATGTATTT 0.919635 -70 CTAAGATAACAAATGTCTTTTTTTCTGGAA 6 58 0 AAATGTCTTT 0.839789 -243 CGCTTACAATAAATGAATACAGCCTCGAAA 7 170 1 AAATGAATAC 0.804872 -32 TATACAAACGAAGTGAATATCCCGCCATGG 9 18 0 AAGTGAATAT 0.899709 -205 TTATGAGAAGAAGTGAATTTTATATTAAAT 9 113 1 AAGTGAATTT 0.937987 -110 GAGGATATGCAAAAGAATTTTGCACTTGCT 10 69 1 AAAAGAATTT 0.67369 -172 ********** Masking position 2 Map Score: 8.13984 Number of sites scoring better than the average of aligned sites = 270 Number in coding regions = 215 Number in noncoding regions = 55 Number of orfs with sites within 600 bp upstream = 57 Fraction of orfs with sites within 600 bp upstream = 0.00915516 Motif number 6 ATCGTGATAAGAAAGGATGAAAACAGCATGTAT 4 41 1 GAAGGTGAAA 0.932324 -260 ATCGACAGGGGAACGGTTGTTGACCATGGCAAG 6 130 1 GAAGGTGTGA 0.994017 -171 GTTGACCATGGCAAGGCTGATGAAGAAACGGCA 6 148 1 GCAGGTGTGA 0.983806 -153 CATTCTCGAAGAAAGGGAGGTGATGTCCCGCCT 6 215 1 GAAGGAGTGA 0.988895 -86 ATACAGCCTCGAAAGGGAGATGACAA 7 186 1 GAAGGAGTGA 0.988895 -16 ACAAGTTGCTGAAGGGGTGCAGAAT 9 208 1 GAAGGTGAGA 0.988895 -15 *** ** ** *** Masking position 3 Map Score: 6.22307 Number of sites scoring better than the average of aligned sites = 63 Number in coding regions = 49 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 21 Fraction of orfs with sites within 600 bp upstream = 0.00337295 Motif number 7 GAAACCTGCCGAACCTGCCTTGGAGTCCTA 3 128 1 GAACCTGCCT 0.980576 -173 AATTTCAAAAGAGCCTTCCTTATTAGGAAG 4 189 1 GAGCCTTCCT 0.980312 -112 CACATAAAAAGAGCCTTCCTAATAAGGAAG 4 203 0 GAGCCTTCCT 0.980312 -98 AGGCGGGACATCACCTCCCTTTCTTCGAGA 6 218 0 TCACCTCCCT 0.974299 -83 TTGTCATCTCCCTTTCGAGGCTG 7 189 0 TCATCTCCCT 0.854326 -13 TGTATGAACCTCCCTCAATTATTTT 10 6 1 GAACCTCCCT 0.992665 -235 ********** Masking position 6 Map Score: 4.33541 Number of sites scoring better than the average of aligned sites = 98 Number in coding regions = 69 Number in noncoding regions = 29 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 8 TGCGGTGCCGCATTTCAGCCGCATAAAAAAA 1 24 0 CATTTCACCG 0.949546 -183 ATGCGCCTAGGTTTTCCCCCTAGGACTCCAA 3 147 0 GTTTTCCCCT 0.959495 -154 CACGGAAACCCATTTCGTCCTTATGAATCAG 3 234 1 CATTTCGCCT 0.916576 -67 TAAAAAAACCCATTTCATCCTGATTCATAAG 3 253 0 CATTTCACCT 0.967792 -48 CATACATGCTGTTTTCATCCTTTCTTATCAC 4 44 0 GTTTTCACCT 0.936926 -257 CTGTAGTCCTCCTTCTTTTGTCA 6 288 0 GTAGTCCCCT 0.692857 -13 CGCATCTTTACTTTTTCCCCGCCATCCTCTA 7 85 1 CTTTTTCCCG 0.814238 -117 GTTGAAATCTCATTTTCACCTAAGGAAAAAG 7 118 0 CATTTTCCCT 0.922298 -84 GTGAAAATGAGATTTCAACCGAGAATAAAAG 7 130 1 GATTTCACCG 0.940404 -72 TCTGTTTCAACATGTTATCCTGCTTTCCCTT 10 200 0 CATGTTACCT 0.740708 -41 ATTTGAATTCCCCCTTGTTTTCTGT 10 226 0 GAATTCCCCT 0.908832 -15 ******* *** Masking position 5 Map Score: 8.66621 Number of sites scoring better than the average of aligned sites = 645 Number in coding regions = 521 Number in noncoding regions = 124 Number of orfs with sites within 600 bp upstream = 127 Fraction of orfs with sites within 600 bp upstream = 0.0203983 Motif number 9 AATTCAATCGTATATTTAATATTTTTATTCA 1 126 0 TATATTTATA 0.948965 -81 TTAATAAAAATACATTTTGTATGTATACACT 5 96 0 TACATTTGTA 0.849025 -74 AAAAATAAATTATATTTAATAAAAATACATT 5 111 0 TATATTTATA 0.948965 -59 CAACCGTGTTTCTATTTTGTATAAAAATAAA 5 133 0 TCTATTTGTA 0.960423 -37 AGAGTCTCTATCTATTTAATATAAAATTCAC 9 125 0 TCTATTTATA 0.966992 -98 TAATATTGCTTCTATTTTATAAAAAAACGGA 10 38 1 TCTATTTATA 0.966893 -203 ******* *** Masking position 6 Map Score: 2.19005 Number of sites scoring better than the average of aligned sites = 27 Number in coding regions = 17 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 10 TTGCGGGGAACGTCATGCCGCCATTTGGACA 4 242 1 CGCATGCCGC 0.993393 -59 GATGAAGAAACGGCATGCCGCTTTGAAAGGC 6 166 1 CGCATGCCGC 0.993392 -135 GTGAATATCCCGCCATGGTGCGGAT 9 5 0 CGCATGGTGC 0.995095 -218 GCTGGAACATCTGCATGGTGCTATCCCAGTT 9 166 0 CTCATGGTGC 0.974919 -57 CAATTTTCGAGGACAAGGTGCAAAAACATTC 10 121 0 GGCAAGGTGC 0.945788 -120 ** ******** Masking position 5 Map Score: 3.27128 Number of sites scoring better than the average of aligned sites = 86 Number in coding regions = 80 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 11 TGGGTTTTTTTATTGTAGAAGAGCCGCGGA 3 272 1 TATTGTAGAA 0.962315 -29 TTCAGATTTTAATTGTCGAACTAGTCAGAC 6 12 1 AATTGTCGAA 0.942805 -289 TCAGACAAGTTATTATAGAAATTTCCAGAA 6 36 1 TATTATAGAA 0.830292 -265 TTTTTCTCATAATAGTAGAAACATAAAAAA 7 25 0 AATAGTAGAA 0.917505 -177 TGTCCTCGAAAATTGTAGAAAACACACGAA 10 137 1 AATTGTAGAA 0.973399 -104 ********** Masking position 6 Map Score: 0.872515 Number of sites scoring better than the average of aligned sites = 44 Number in coding regions = 33 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 12 GGAATTCCCATTGAACAGAAAATTTATAAAT 1 96 1 TTAACAGAAA 0.933871 -111 TTTTGCTCTCTGTCACAGAAAGGTCTGCTTA 3 71 0 TGCACAGAAA 0.984946 -230 ATCAAGGTGGTACCACGGAAACCCATTTCGT 3 221 1 TACACGGAAA 0.899754 -80 GCAAAAACTTTTTCACATAAAAAGAGCCTTC 4 215 0 TTCACATAAA 0.790343 -86 TGTATAAATTTACAACAGAAAAATCAGCACT 9 42 1 TAAACAGAAA 0.933879 -181 ATTCTTGATTTGGCACAGAACTTGCATTTAT 10 166 1 TGCACAGAAC 0.952882 -75 GATAACATGTTGAAACAGAAAACAAGGGGGA 10 212 1 TGAACAGAAA 0.969533 -29 ** ******** Masking position 5 Map Score: 2.4919 Number of sites scoring better than the average of aligned sites = 129 Number in coding regions = 110 Number in noncoding regions = 19 Number of orfs with sites within 600 bp upstream = 20 Fraction of orfs with sites within 600 bp upstream = 0.00321234 Motif number 13 TATTCATCAAGAGGTGGGCTGTTAG 2 56 1 GAGGTGGGCT 0.961915 -15 GGCGTTACAGGAGAGCGGAGCGTGCACAAG 3 183 1 GAGAGCGGAG 0.857239 -118 AAGGGGTTTTGAGGTGGGAGC 4 290 1 GAGGTGGGAG 0.978939 -11 AAACACGGTTGAGAGGGGATTTTTATC 5 153 1 GAGAGGGGAT 0.974949 -17 CTTAAATGTTGAGGTGGAATCACAG 8 59 1 GAGGTGGAAT 0.949605 -15 GAAAATAATTGAGGGAGGTTCATACA 10 7 0 GAGGGAGGTT 0.844838 -234 AACAGAAAACAAGGGGGAATTCAAAT 10 225 1 AAGGGGGAAT 0.834658 -16 ********** Masking position 2 Map Score: 1.18072 Number of sites scoring better than the average of aligned sites = 196 Number in coding regions = 106 Number in noncoding regions = 90 Number of orfs with sites within 600 bp upstream = 101 Fraction of orfs with sites within 600 bp upstream = 0.0162223 Motif number 14 ********** No masking Map Score: -4.44557e-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: -4.44557e-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