AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00410_bsub_reg_100.orf -o00410_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 ycbC 226 similar to 5-dehydro-4-deoxyglucarate dehydratase #2 ycbD 29 similar to aldehyde dehydrogenase #3 ycnG 106 similar to 4-aminobutyrate aminotransferase #4 panB 245 ketopantoate hydroxymethyltransferase #5 ywhF 201 similar to spermidine synthase #6 ywdH 167 alternate gene name: ipa-58r; similar to aldehyde dehydrogenase #7 aldX 142 aldehyde dehydrogenase Motif number 1 GGACAGTGATTTACCGCTTTTTTATAAAATAT 1 62 1 TTCGCTTTTT 0.8954 -165 TAAGTCAATATCTTTATTTTCTGATATTTTAT 1 85 0 TCTATTTTCT 0.921112 -142 GTAAGCGCTTTTATTAATTTTTCTTTCACATC 1 165 0 TTTAATTTTT 0.786025 -62 CATTGCCCCTTTCGTGTTTTTTCTGG 2 5 0 TTTGTTTTTT 0.89932 -25 TTTGTAGTTTCTCCTTCTGATA 3 1 1 TTTAGTTTCT 0.775977 -106 AAAGTACCAATTATAACTTTTTGATGGTATCA 3 28 0 TTAACTTTTT 0.810172 -79 AAAGTTATAATTGGTACTTTTCATCATACCAA 3 40 1 TTTACTTTTC 0.839468 -67 TATCCCCCTGTCGGTATTTTCTTATCATTCTG 3 80 0 TCTATTTTCT 0.921112 -27 TGCTGCAATGTCTATCTATTTTAATAATAGGT 4 74 0 TCTCTATTTT 0.681012 -172 TCCCTCTGTCCCAGTCCTTTTTTGGATCAAGG 4 111 0 CCTCCTTTTT 0.816677 -135 CGAGAAGGATTCTTCACTTTCTAAAGTTCGGC 4 151 0 TCCACTTTCT 0.917963 -95 AACGGGTTCCCCCTTTTTTTATGTTTCT 5 7 1 TTCCCTTTTT 0.933008 -195 ACAGGACGCATCTTTACTTTTTCCCCGCCATC 5 79 1 TCTACTTTTT 0.979739 -123 CCCGCCATCCTCTATACTTTTTCCTTAGGTGA 5 102 1 TCTACTTTTT 0.979739 -100 AAATGTTGTCTTCCTGCATTTTATCAAATTCC 6 31 1 TTTGCATTTT 0.769233 -137 AGATATGAGTTTGTTATTTTTTCTGACAAACC 6 75 1 TTTATTTTTT 0.946508 -93 TCCGTTTCTCCTTTTTGTAAGGTATG 6 152 0 TTTCCTTTTT 0.974549 -16 CTCATTTGCTTTCTTCTTTTCTCGGACCTATT 7 109 0 TTTCTTTTCT 0.902399 -34 ** ******** Masking position 9 Map Score: 16.5956 Number of sites scoring better than the average of aligned sites = 1982 Number in coding regions = 1502 Number in noncoding regions = 480 Number of orfs with sites within 600 bp upstream = 478 Fraction of orfs with sites within 600 bp upstream = 0.0767748 Motif number 2 CTTACAATTAAACAAAAGGATATATGGGAAG 1 129 1 ACAAAAGGAT 0.905183 -98 AAAAGGATATATGGGAAGGAGCGGATGTGAA 1 142 1 AGGGAAGGAG 0.944361 -85 ATACACAAATAACAGGAGGTTATGTTG 1 210 1 ACAGGAGGTT 0.965651 -17 TTTTGATGGTATCAGAAGGAGAAACTACAAA 3 11 0 ACAGAAGGAG 0.986994 -96 CCAAAGAGAAGTCAGAATGATAAGAAAATAC 3 68 1 GCAGAATGAT 0.856713 -39 AGAAAATACCGACAGGGGGATATTCAC 3 90 1 GCAGGGGGAT 0.977998 -17 AAAGGACTGGGACAGAGGGATGAAACTCGCC 4 123 1 GCAGAGGGAT 0.979394 -123 TTCCGTTACAACGAGAAGGATTCTTCACTTT 4 163 0 AGAGAAGGAT 0.986035 -83 TTCTCGTTGTAACGGAAGGTTTTTTGGCTTG 4 177 1 ACGGAAGGTT 0.920243 -69 TCCTCTAAACATGAGGAGGAGAAAAC 4 230 1 AGAGGAGGAG 0.976392 -16 AAGAAAGCAAATGAGGGGGATTTTACA 7 126 1 AGAGGGGGAT 0.976392 -17 * ********* Masking position 9 Map Score: 14.8048 Number of sites scoring better than the average of aligned sites = 683 Number in coding regions = 549 Number in noncoding regions = 134 Number of orfs with sites within 600 bp upstream = 142 Fraction of orfs with sites within 600 bp upstream = 0.0228076 Motif number 3 CAAACAGCCGGCTGACCAGGCTGTTTTTTT 1 13 1 GCTGACCAGG 0.808255 -214 GGCCGTATACACAAATAACAGGAGGTTATG 1 204 1 ACAAATAACA 0.3702 -23 CCAGAAAAAACACGAAAGGGGCAA 2 5 1 AAAAAACACG 0.35029 -25 TCTTTGGTATGATGAAAAGTACCAATTATA 3 45 0 GATGAAAAGT 0.442602 -62 GAGAAGTCAGAATGATAAGAAAATACCGAC 3 73 1 AATGATAAGA 0.423635 -34 CTGCCTTGATCCAAAAAAGGACTGGGACAG 4 108 1 CCAAAAAAGG 0.582867 -138 TTGGCTTGCAGAAGAAAACGGCAGATCATC 4 200 1 GAAGAAAACG 0.920982 -46 ACTATTATGAGAAAAAAAGATCGTTTTTAA 5 39 1 GAAAAAAAGA 0.780228 -163 TTTAAACATCGCAGAACAGGACGCATCTTT 5 64 1 GCAGAACAGG 0.94593 -138 TTCCTTAGGTGAAAATGAGATTTCAACCGA 5 122 1 GAAAATGAGA 0.482352 -80 GAGAATAAAAGCTGATAAGACGCTTACAAT 5 150 1 GCTGATAAGA 0.820122 -52 TAAAATGCAGGAAGACAACATTTATTTTTT 6 24 0 GAAGACAACA 0.760573 -144 TCAAATTCCTGCTGAAAACGCAGATATGAG 6 54 1 GCTGAAAACG 0.900711 -114 CGATTGACAAGCAGAAGAGATTTTTCACAT 6 112 1 GCAGAAGAGA 0.895061 -56 TTTCTGTAAGAAAGACAACGGTGAACCATC 7 65 0 AAAGACAACG 0.654588 -78 TGTCTTTCTTACAGAAAAGGTACCACCTTA 7 78 1 ACAGAAAAGG 0.917061 -65 AAAGAAGAAAGCAAATGAGGGGGATTTTAC 7 122 1 GCAAATGAGG 0.775217 -21 ********** Masking position 5 Map Score: 5.8525 Number of sites scoring better than the average of aligned sites = 6264 Number in coding regions = 5584 Number in noncoding regions = 680 Number of orfs with sites within 600 bp upstream = 616 Fraction of orfs with sites within 600 bp upstream = 0.0989399 Motif number 4 ACCAAACAGCCGGCTGACCAGGC 1 4 1 AAACAGCCGG 0.961492 -223 CGCAGCAAAAAAACAGCCTGGTCAGCCGGC 1 19 0 AAACAGCCTG 0.985567 -208 TTATTTGTGTATACGGCCTCTATCTGTAAG 1 192 0 ATACGGCCTC 0.982642 -35 AAAAGTAAAGATGCGTCCTGTTCTGCGATG 5 70 0 ATGCGTCCTG 0.899932 -132 CAATAAATGAATACAGCCTCGAAAGGGAGA 5 176 1 ATACAGCCTC 0.985567 -26 GAAGCACCCTCCAAAAAAATA 6 2 1 AAGCACCCTC 0.941422 -166 ********** Masking position 1 Map Score: 3.44278 Number of sites scoring better than the average of aligned sites = 279 Number in coding regions = 253 Number in noncoding regions = 26 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419 Motif number 5 TAAAGATATTGACTTATTGTTTATTTGTCT 1 101 1 GACTTATTGT 0.934956 -126 CTGCGAACTGCACCTATTATTAAAATAGAT 4 63 1 CACCTATTAT 0.941452 -183 CTGCAATGTCTATCTATTTTAATAATAGGT 4 74 0 TATCTATTTT 0.805032 -172 GTTTAAAAACGATCTTTTTTTCTCATAATA 5 41 0 GATCTTTTTT 0.794302 -161 AGGCTGTATTCATTTATTGTAAGCGTCTTA 5 165 0 CATTTATTGT 0.917797 -37 AGGAAGACAACATTTATTTTTTTGGAGGGT 6 16 0 CATTTATTTT 0.911837 -152 AAGGTATGGTGATTTATTATGTGAAAAATC 6 130 0 GATTTATTAT 0.931436 -38 TCTTTTCTCGGACCTATTATAAGGTGGTAC 7 97 0 GACCTATTAT 0.954793 -46 ********** Masking position 2 Map Score: 3.0286 Number of sites scoring better than the average of aligned sites = 232 Number in coding regions = 186 Number in noncoding regions = 46 Number of orfs with sites within 600 bp upstream = 51 Fraction of orfs with sites within 600 bp upstream = 0.00819146 Motif number 6 ATGAAAAGTACCAATTATAACTTTTTGATG 3 34 0 CCAATTATAA 0.968608 -73 GCGAACTGCACCTATTATTAAAATAGATAG 4 65 1 CCTATTATTA 0.968608 -181 AAAGACACCTCCAATCATTAGACAGATCTT 7 12 1 CCAATCATTA 0.947641 -131 TTTTCTCGGACCTATTATAAGGTGGTACCT 7 95 0 CCTATTATAA 0.968608 -48 ********** Masking position 5 Map Score: 1.38134 Number of sites scoring better than the average of aligned sites = 38 Number in coding regions = 28 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 7 ACCAAACAGCCGGCTGACCAGGCT 1 5 1 AACAGCCGGC 0.957755 -222 GCAGCAAAAAAACAGCCTGGTCAGCCGGCT 1 18 0 AACAGCCTGG 0.983395 -209 TAAATCACTGTCCGGCCGGGATTCTGCGCA 1 45 0 TCCGGCCGGG 0.815831 -182 TATTTGTGTATACGGCCTCTATCTGTAAGC 1 191 0 TACGGCCTCT 0.940255 -36 AATAAATGAATACAGCCTCGAAAGGGAGAT 5 177 1 TACAGCCTCG 0.983206 -25 ********** Masking position 5 Map Score: 0.452012 Number of sites scoring better than the average of aligned sites = 186 Number in coding regions = 169 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 8 AAGCGGTAAATCACTGTCCGGCCGGGATTC 1 51 0 TCACTGTCCG 0.941673 -176 GCCCATTGCCCCTTTCGTGTTTTTTCTG 2 12 0 CCCCTTTCGT 0.974366 -18 GTGAATATCCCCCTGTCGGTATTTTCTTA 3 88 0 CCCCTGTCGG 0.992506 -19 CATCCCTCTGTCCCAGTCCTTTTTTGGATC 4 115 0 TCCCAGTCCT 0.943037 -131 TTGTCATCTCCCTTTCGAGGCTGTATTC 5 184 0 TCCCTTTCGA 0.952308 -18 ********** Masking position 7 Map Score: 0.350402 Number of sites scoring better than the average of aligned sites = 160 Number in coding regions = 137 Number in noncoding regions = 23 Number of orfs with sites within 600 bp upstream = 21 Fraction of orfs with sites within 600 bp upstream = 0.00337295 Motif number 9 GGGAAGGAGCGGATGTGAAAGAAAAATTAA 1 154 1 GGATGTGAAA 0.965835 -73 GATGGTATCAGAAGGAGAAACTACAAA 3 8 0 GAAGGAGAAA 0.917954 -99 GAAGTCAGAATGATAAGAAAATACCGACAG 3 75 1 TGATAAGAAA 0.798136 -32 CTAAACATGAGGAGGAGAAAAC 4 234 1 GGAGGAGAAA 0.977999 -12 GTTTCTACTATTATGAGAAAAAAAGATCGT 5 33 1 TTATGAGAAA 0.950945 -169 TACTTTTTCCTTAGGTGAAAATGAGATTTC 5 116 1 TTAGGTGAAA 0.947308 -86 TGGTGATTTATTATGTGAAAAATCTCTTCT 6 124 0 TTATGTGAAA 0.937057 -44 ********** Masking position 3 Map Score: 6.03818 Number of sites scoring better than the average of aligned sites = 438 Number in coding regions = 328 Number in noncoding regions = 110 Number of orfs with sites within 600 bp upstream = 119 Fraction of orfs with sites within 600 bp upstream = 0.0191134 Motif number 10 ********** No masking Map Score: -3.14527e-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: -3.14527e-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: -3.14527e-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