AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00740_bsub_reg_300.orf -o00740_bsub_300.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 ylxS 300 alternate gene name: ymxA; similar to hypothetical proteins #2 nusA 34 nusA #3 truB 81 tRNA pseudouridine 55 synthase #4 ribH 32 riboflavin synthase (beta subunit) #5 ypuE 258 ypuE #6 ypuD 234 ypuD #7 sipS 266 type I signal peptidase Motif number 1 CTGTTCAATACAAAAGAGCGGGTTTCCCCA 1 165 0 CAAAAGAGCG 0.954992 -136 AACCCTGCTTCAAAAGAGCAGGGGCTAAAA 1 228 0 CAAAAGAGCA 0.962676 -73 AAAAAGAGAGGATAGGCGTA 3 1 1 AAAAAGAGAG 0.949206 -81 TTATAAACGAAGAAAGAGGACAGACGATAT 3 30 0 AGAAAGAGGA 0.942361 -52 GAAAAAAACTCAAAAGAAGGAGTGAAAGGC 3 60 1 CAAAAGAAGG 0.860184 -22 ACAAATATCACAAAAAAGGATGGGAATCAT 4 13 1 CAAAAAAGGA 0.935306 -20 ACAATTTGAGAAAAACAAAACATCACCCTT 5 32 0 AAAAACAAAA 0.639525 -227 AAAAAGATATAAAAAAAGCAGCCCCAATGG 6 25 0 AAAAAAAGCA 0.904779 -210 GTCATCCCCTAAAAACAGAACATAAATTCG 6 59 1 AAAAACAGAA 0.88934 -176 TTTATTCATGAAAAAAAGGAATAACTCATA 6 179 1 AAAAAAAGGA 0.925819 -56 TGGACTCAGAAGAAAGAGAGTTCTCATATG 7 54 0 AGAAAGAGAG 0.912641 -213 TATCACGAATCGAAAAAAAATCCCATTAGG 7 209 0 CGAAAAAAAA 0.580861 -58 ********** Masking position 5 Map Score: 10.1385 Number of sites scoring better than the average of aligned sites = 2109 Number in coding regions = 1597 Number in noncoding regions = 512 Number of orfs with sites within 600 bp upstream = 479 Fraction of orfs with sites within 600 bp upstream = 0.0769354 Motif number 2 TACCGAGGCAAAGAGTGGGGAAACCCGCTCT 1 150 1 AAGAGTGGGA 0.970837 -151 GGTTTTTATGCAGAGTGACGAGACGAATATG 1 254 1 CAGAGTGAGA 0.929637 -47 TCGACAGCACAAGGAGGAAGAAC 1 288 1 AAGGAGGAGA 0.951355 -13 CAAATGTTTTAAGGGGGGAGACCGTTAA 2 17 1 AAGGGGGGGA 0.980257 -18 CTTATAAACGAAGAAAGAGGACAGACGATAT 3 30 0 AAGAAAGAGA 0.701484 -52 TATCACAAAAAAGGATGGGAATCAT 4 18 1 AAGGATGGAA 0.882262 -15 CTTCGATCCGAAAGGTGATGTTTT 5 4 0 AAAGGTGAGT 0.787637 -255 TTTCGGATCGAAGGGTGATGTTTTGTTTTTC 5 22 1 AAGGGTGAGT 0.976986 -237 ATCTTCGGGGCAGGGTGGAAATCCCGACCGG 5 133 1 CAGGGTGGAA 0.883042 -126 ATCGTATATAAAGCATGAGGTTACGGGCAGT 7 11 0 AAGCATGAGT 0.776927 -256 ******** ** Masking position 2 Map Score: 5.04319 Number of sites scoring better than the average of aligned sites = 865 Number in coding regions = 613 Number in noncoding regions = 252 Number of orfs with sites within 600 bp upstream = 226 Fraction of orfs with sites within 600 bp upstream = 0.0362994 Motif number 3 TTGCGCTTATGTATGCATAGAAGC 1 2 0 GTATGCAAAG 0.791145 -299 ACCATATTTTTATTGCAAATGGATATACGCTTA 1 85 0 TATTGCAAGA 0.813792 -216 CGCTCTTTTGTATTGAACAGGAGAATTTTGTCT 1 175 1 TATTGAAAGG 0.932154 -126 GCCCCTGCTCTTTTGAAGCAGGGTTTTTATGCA 1 233 1 TTTTGAACGG 0.761199 -68 TCACGGGCTCTAAAGCAAATGTGCTTTACTACC 5 165 0 TAAAGCAAGG 0.893331 -94 CACCGCGTGCTTATGCACACGGGTCACGGGCTC 5 188 0 TTATGCAAGG 0.987835 -71 GAAAAGAAATTTTTGCAGAAATGTGAAACATAT 6 99 1 TTTTGCAAAG 0.944194 -136 GGTTTTTTATTCATGAAAAAAAGGAATAACTCA 6 174 1 TCATGAAAAG 0.770264 -61 ATGAATCTATTCATTCATATGAGTTATTCCTTT 6 193 0 TCATTCAAGG 0.893824 -42 GATCTAAAGATTTTGCATATGAGAACTCTCTTT 7 39 1 TTTTGCAAGG 0.985577 -228 ATGAATCGCATAATTCAGAAGCGATGGACTCAG 7 75 0 TAATTCAAGG 0.910349 -192 ******* * * * Masking position 7 Map Score: 5.04944 Number of sites scoring better than the average of aligned sites = 908 Number in coding regions = 801 Number in noncoding regions = 107 Number of orfs with sites within 600 bp upstream = 117 Fraction of orfs with sites within 600 bp upstream = 0.0187922 Motif number 4 GCTTAGGTATGAAGGTAAGCGTATATCCATT 1 70 1 GAAGGAAGCG 0.866797 -231 GAGGCAAAGAGTGGGGAAACCCGCTCTTTTG 1 154 1 GTGGGAAACC 0.932783 -147 GACAGCACAAGGAGGAAGAAC 1 290 1 GGAGGAGAAC 0.909151 -11 AATGTTTTAAGGGGGGAGACCGTTAA 2 19 1 GGGGGAGACC 0.989456 -16 AAAAAGAGAGGATAGGCGTATATCGTCT 3 8 1 GAGGAAGGCG 0.959766 -74 AACGAAGAAAGAGGACAGACGATATACGCCT 3 24 0 GAGGAAGACG 0.976812 -58 TGAAAGTCTGGATGGGAGAAGG 5 247 1 GATGGAGAAG 0.917609 -12 TAGGCATGATGTGGGTAGAAGATGAAGATTA 7 152 1 GTGGGAGAAG 0.974738 -115 ***** ***** Masking position 7 Map Score: 3.39465 Number of sites scoring better than the average of aligned sites = 359 Number in coding regions = 296 Number in noncoding regions = 63 Number of orfs with sites within 600 bp upstream = 54 Fraction of orfs with sites within 600 bp upstream = 0.00867331 Motif number 5 CAAGTGACAGAAACTCTAATATTACGATGGCACTTTT 1 34 0 AATAATACGA 0.980167 -267 ATTTCCAATAAAACTATACCATAACCATATTTTTATT 1 104 0 AATAATACCA 0.975549 -197 TTGCCTCGGTAATCGTTAGCATTTCCAATAAAACTAT 1 124 0 AATAATTCCA 0.954399 -177 CTAAAAAGTAAACGATGAACATGTCGAGACAAAATTC 1 197 0 AAGAATTCGA 0.873187 -104 AGAGTGACGAGACGAATATGAGATCGACAGCACAAGG 1 265 1 GATAAGTCGA 0.860997 -36 CTTTAAAAAGGATCGCTATAATAACCAATAAGGACAA 5 81 1 GATAATACCA 0.951225 -178 AATTCTCGTAAATAATTAATATAACGATGCATAACGG 6 134 0 AATAATACGA 0.980167 -101 AATCGAAAAAAAATCCCATTAGGACCATTGAAGTGAT 7 195 0 AACAAGACCA 0.838187 -72 AACGGTCTTCAATTTATGTTATCACGAATCGAAAAAA 7 221 0 AATGATACGA 0.920297 -46 ** ** ** **** Masking position 11 Map Score: 2.59421 Number of sites scoring better than the average of aligned sites = 74 Number in coding regions = 61 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 6 TATCCATTTGCAATAAAAATATGGTTATGGTATA 1 93 1 CAAAAAATGG 0.927543 -208 TTCTCCTGTTCAATACAAAAGAGCGGGTTTCCCC 1 166 0 CAAAAAAAGC 0.895514 -135 TGAATACAAATGTTTTAAGGGGGGA 2 2 1 GAAAAAATTT 0.901745 -33 ACCCTGCCCCGAAGATACAATCTTTATTCATTTG 5 115 0 GAAAACAATT 0.846795 -144 CCTAAAAACAGAACATAAATTCGTATATCTATAG 6 66 1 GAAAAAATGT 0.965522 -169 TATATCTATAGAAAAGAAATTTTTGCAGAAATGT 6 89 1 GAAAAAATTT 0.901745 -146 TTTTTTTCATGAATAAAAAACCGTAAATTCTCGT 6 162 0 GAAAAAAAGT 0.971832 -73 TTATGATCGACAAGAAAAAATAGGCATGATGTGG 7 132 1 CAAAAAAAGG 0.94038 -135 TGATTTCCTCCAATAAACAACGGTCTTCAATTTA 7 242 0 CAAAACAAGT 0.931578 -25 *** * **** ** Masking position 7 Map Score: 3.80712 Number of sites scoring better than the average of aligned sites = 449 Number in coding regions = 360 Number in noncoding regions = 89 Number of orfs with sites within 600 bp upstream = 108 Fraction of orfs with sites within 600 bp upstream = 0.0173466 Motif number 7 ATGAAGGTAAGCGTATATCCATTTGCAATA 1 78 1 GCGTATATCC 0.952364 -223 GAGAGGATAGGCGTATATCGTCTGTCCTCT 3 16 1 GCGTATATCG 0.952412 -66 TCCTCTTTCTTCGTTTATAAGAAAAAAACT 3 40 1 TCGTTTATAA 0.865886 -42 GAACATAAATTCGTATATCTATAGAAAAGA 6 76 1 TCGTATATCT 0.942155 -159 CCGTAAATTCTCGTAAATAATTAATATAAC 6 146 0 TCGTAAATAA 0.865886 -89 AATCTTTAGATCGTATATAAAGCATGAGGT 7 21 0 TCGTATATAA 0.963093 -246 ********** Masking position 4 Map Score: 1.45048 Number of sites scoring better than the average of aligned sites = 79 Number in coding regions = 62 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 8 TCGATCCGAAAGGTGATGTTTT 5 2 0 AGGTGATGTT 0.827816 -257 TCGGATCGAAGGGTGATGTTTTGTTTTTCTC 5 24 1 GGGTGATGTT 0.944565 -235 AGCACGCGGTGGATTCAGTTTAAGCTGAAGC 5 210 1 GGATTCAGTT 0.932941 -49 TTTCACTGTCGGCTTCAGCTTAAACTGAATC 5 221 0 GGCTTCAGTT 0.956648 -38 AGCCCCAATGGGAAGCTGCTTGATC 6 5 0 GGAAGCTGTT 0.936554 -230 TTCCCATTGGGGCTGCTTTTTTTATATCTTT 6 22 1 GGCTGCTTTT 0.818764 -213 ATGCATAACGGGAATATGTTTCACATTTCTG 6 114 0 GGAATATGTT 0.798857 -121 GATTCATATTGGCTGGAGGTTTAGAA 6 219 1 GGCTGGAGTT 0.96432 -16 TCGTATATAAAGCATGAGGTTACGGGCAGT 7 10 0 AGCATGAGTT 0.595721 -257 TGTGGGTAGAAGATGAAGATTAACAGTTTGT 7 161 1 AGATGAAGTT 0.852923 -106 ******** ** Masking position 10 Map Score: 3.19925 Number of sites scoring better than the average of aligned sites = 1640 Number in coding regions = 1481 Number in noncoding regions = 159 Number of orfs with sites within 600 bp upstream = 152 Fraction of orfs with sites within 600 bp upstream = 0.0244137 Motif number 9 GCTAAAAAGTAAACGATGAACATGTCGAGA 1 205 0 AAACGATGAA 0.929706 -96 ATGCAGAGTGACGAGACGAATATGAGATCG 1 261 1 ACGAGACGAA 0.826313 -40 TTTTTCTTATAAACGAAGAAAGAGGACAGA 3 36 0 AAACGAAGAA 0.733034 -46 AACTCAAAAGAAGGAGTGAAAGGCAA 3 66 1 AAGGAGTGAA 0.745852 -16 TTTTTAAAGTACGCAATGAAATAAACTTAC 5 60 0 ACGCAATGAA 0.956812 -199 GTGCATAAGCACGCGGTGGATTCAGTTTAA 5 203 1 ACGCGGTGGA 0.947847 -56 CATAATTCAGAAGCGATGGACTCAGAAGAA 7 70 0 AAGCGATGGA 0.970365 -197 AAAATATTGAAAGAAATGAATCGCATAATT 7 93 0 AAGAAATGAA 0.860451 -174 ********** Masking position 1 Map Score: 1.02522 Number of sites scoring better than the average of aligned sites = 1209 Number in coding regions = 1090 Number in noncoding regions = 119 Number of orfs with sites within 600 bp upstream = 90 Fraction of orfs with sites within 600 bp upstream = 0.0144555 Motif number 10 ********** No masking Map Score: -3.88366e-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 11 ********** No masking Map Score: -3.88366e-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 12 ********** No masking Map Score: -3.88366e-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