AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i150_ATP_synthase_1_mjan_reg_100.orf -o150_mjan_100.ace -a/home/amcguire/genomes/ORF_mjan.txt -z/home/amcguire/genomes/mjan.fna -g0.31 -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 = 0.31 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 RMJ14255 46 M_jannaschii_chromosome #2 RMJ07874 39 M_jannaschii_chromosome #3 RMJ02086 103 M_jannaschii_chromosome #4 RMJ01575 88 M_jannaschii_chromosome #5 RMJ04104 300 M_jannaschii_chromosome #6 RMJ09479 80 M_jannaschii_chromosome #7 RMJ15216 108 M_jannaschii_chromosome Motif number 1 ATTCCTTTCCTTAAAACTTTACAAACTCTT 1 11 1 TTAAAACTTT 0.939318 -36 ATAAAACCAATAAAAACGTTAA 2 28 1 TAAAAACGTT 0.884702 -12 TATTAAAAATATTTGATAGAGT 4 3 1 TTAAAAATAT 0.926289 -86 GAGTCAGAGATAAAAAATTTTATATACATA 4 29 1 TAAAAAATTT 0.927278 -60 TAACCCTATTTTAAAATATTACCAATAACT 4 57 1 TTAAAATATT 0.637869 -32 TTAAAAATTTCGTTTTTAAA 5 1 1 TTAAAAATTT 0.934579 -300 AATTTCGTTTTTAAAATTGTAATCTTTATT 5 16 1 TTAAAATTGT 0.876803 -285 TAATTTAAATTAATAAAGATTACAATTTTA 5 27 0 TAATAAAGAT 0.728807 -274 TAATTTAAATTAATAAATATTATTACCTAA 5 45 1 TAATAAATAT 0.828733 -256 TTACCTAAAATAAAAATGGTGCAGGGGAGG 5 67 1 TAAAAATGGT 0.779149 -234 AAATAGGTTTTTATAATTATGGGAAAACTT 5 248 0 TTATAATTAT 0.86263 -53 CGTTATAACATAAAAATTTAATGGTTATAG 6 11 0 TAAAAATTTA 0.825849 -70 AATTTTTATGTTATAACGTTGCTAATAATT 6 23 1 TTATAACGTT 0.787603 -58 CTTTTATAAGTAAAAATTATTAGCAACGTT 6 37 0 TAAAAATTAT 0.928524 -44 TTAAAACTAATTATAAATAAATTATGGTTT 7 50 0 TTATAAATAA 0.63674 -59 GTAAGAGATTTTAAAACTAATTATAAATAA 7 60 0 TTAAAACTAA 0.815104 -49 ATCTCTTACATAAAAATTTAGACCTTTTTG 7 81 1 TAAAAATTTA 0.825849 -28 ********** Masking position 5 Map Score: 17.061 Number of sites scoring better than the average of aligned sites = 2525 Number in coding regions = 1757 Number in noncoding regions = 768 Number of orfs with sites within 600 bp upstream = 524 Fraction of orfs with sites within 600 bp upstream = 0.0841632 Motif number 2 AGATTACGATAAAACCAATAAAAACGTTAA 2 20 1 AAAACCATAA 0.950428 -20 ACCCTATTGAAATACCGAATTCATTAGAGAG 3 31 0 AATACCAATT 0.870753 -73 CCTCCATAGGAAAACCCTATTGAAATACCGA 3 44 0 AAAACCTATT 0.908147 -60 TTTTATATACATAACCCTATTTTAAAATATT 4 46 1 ATAACCTATT 0.877503 -43 ATTTTAAAATATTACCAATAACTGCAGGTGG 4 64 1 ATTACCATAA 0.831975 -25 TTACAATTTTAAAAACGAAATTTTTAA 5 7 0 AAAAACAAAT 0.725797 -294 AATAAATATTATTACCTAAAATAAAAATGGT 5 56 1 ATTACCAAAA 0.905183 -245 TCTTTTGCACGAAACCGAAAAGTATATATAT 5 202 0 GAAACCAAAA 0.863872 -99 CATAATTATAAAAACCTATTTAAATAGGAAA 5 257 1 AAAACCATTT 0.908483 -44 CTATAACCATTAAATTTTTATGT 6 3 1 ATAACCTTAA 0.878346 -78 TAGCAACGTTATAACATAAAAATTTAATGGT 6 16 0 ATAACAAAAA 0.658321 -65 CTCTATAATCAAAACCATAATTTATTTATAA 7 39 1 AAAACCTAAT 0.950064 -70 ****** **** Masking position 4 Map Score: 8.8334 Number of sites scoring better than the average of aligned sites = 1004 Number in coding regions = 841 Number in noncoding regions = 163 Number of orfs with sites within 600 bp upstream = 156 Fraction of orfs with sites within 600 bp upstream = 0.0250562 Motif number 3 ATTACCAATAACTGCAGGTGGAAGT 4 74 1 ACTGCAGGTG 0.955694 -15 AAATAAAAATGGTGCAGGGGAGGGGATTTG 5 74 1 GGTGCAGGGG 0.998881 -227 GTCCCGTAGGGGTTCGGGGGTTCAAATCCC 5 96 0 GGTTCGGGGG 0.987194 -205 ATTCGCTTGCGGTGCAGGGGTCGCCAAGCC 5 154 0 GGTGCAGGGG 0.998881 -147 TACTTATAAAAGTGGAGAGGGATTTACATG 6 55 1 AGTGGAGAGG 0.955694 -26 ********** Masking position 3 Map Score: 5.93813 Number of sites scoring better than the average of aligned sites = 21 Number in coding regions = 11 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 Motif number 4 AACAAGATACTAATTGCCTCTCTAATGAATTC 3 14 1 TAATGCCTCC 0.978608 -90 AACTTCTCTGTAATTCTCGCCCTCCATAGGAA 3 63 0 TAATCTCGCC 0.981854 -41 TCGGGGGTTCAAATCCCCTCCCCTGCACCATT 5 81 0 AAACCCCTCC 0.969562 -220 GACCGGATCTTAAGTCCGGCGCCTTTGGCCAG 5 123 1 TAATCCGGCC 0.968538 -178 ATCTATTCTATAATTCGCTTGCGGTGCAGGGG 5 164 0 TAATCGCTTC 0.94855 -137 TCTCTGCATGTAAATCCCTCTCCACTTTTATA 6 59 0 TAATCCCTCC 0.995815 -22 AATTAGTTTTAAAATCTCTTACATAAAAATTT 7 68 1 AAATCTCTTC 0.905144 -41 *** ****** * Masking position 3 Map Score: 4.59725 Number of sites scoring better than the average of aligned sites = 189 Number in coding regions = 173 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 5 ATCATCACCTCAAATAAAGAGTTTGTAA 1 29 0 CCTAAATAAA 0.96374 -18 TTCTCGCCCTCCATAGGAAAACCCTATTGAA 3 51 0 CCAAGGAAAA 0.832653 -53 TTTGATAGAGTCAGAGATAAAAAATTTTATA 4 22 1 TCAAGATAAA 0.950411 -67 AATATTATTACCTAAAATAAAAATGGTGCAG 5 60 1 CCTAAATAAA 0.963739 -241 CGGTTTCGTGCAAAAGATAAATATATATTAA 5 216 1 CAAAGATAAA 0.918131 -85 CATATTTCCTCCTGAGGTAAAGT 5 288 1 CCTAGGTAAA 0.978042 -13 TTAGCAACGTTATAACATAAAAATTTAATGG 6 17 0 TATACATAAA 0.786075 -64 TTTTAAAATCTCTTACATAAAAATTTAGACC 7 74 1 TCTACATAAA 0.941407 -35 *** ******* Masking position 5 Map Score: 4.96349 Number of sites scoring better than the average of aligned sites = 377 Number in coding regions = 317 Number in noncoding regions = 60 Number of orfs with sites within 600 bp upstream = 56 Fraction of orfs with sites within 600 bp upstream = 0.00899454 Motif number 6 ATAGGAAAACCCTATTGAAATACCGAATTC 3 40 0 CCTATTGAAA 0.976882 -64 TATACATAACCCTATTTTAAAATATTACCA 4 51 1 CCTATTTTAA 0.966115 -38 TTAAAAATTTCGTTTTTAAAATTGTAATCT 5 11 1 CGTTTTTAAA 0.914059 -290 ATTATAAAAACCTATTTAAATAGGAAACAT 5 261 1 CCTATTTAAA 0.986304 -40 ********** Masking position 5 Map Score: 1.33897 Number of sites scoring better than the average of aligned sites = 68 Number in coding regions = 53 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 7 ********** No masking Map Score: 1.65857e-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 8 ********** No masking Map Score: 1.65857e-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 9 ********** No masking Map Score: 1.65857e-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