AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i079_Phospholipid_Biosynthesis_mjan_reg_300.orf -o079_mjan_300.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 RMJ01130 162 M_jannaschii_chromosome #2 RMJ14570 123 M_jannaschii_chromosome #3 RMJ05488 49 M_jannaschii_chromosome #4 RMJ00515 41 M_jannaschii_chromosome #5 RMJ05845 54 M_jannaschii_chromosome #6 RMJ03243 87 M_jannaschii_chromosome Motif number 1 TTCAATTTTGATGAAACTTTTTCTAAAAGT 1 22 1 ATGAAACTTT 0.870549 -141 GAGGTTTTAAAAGAAACTTTTAGAAAAAGT 1 37 0 AAGAAACTTT 0.902514 -126 GGATTATCCTAATAAATTATAGTAATCTTT 1 94 0 AATAAATTAT 0.93623 -69 ATCCTGCCTTATTAAAAAATAGCAAGTTAC 1 120 1 ATTAAAAAAT 0.923286 -43 ATATTCAATAAATAAACTATCCGACGATAA 2 59 0 AATAAACTAT 0.97076 -65 AATCCATACATTAAAAAATCCATTGAGGA 3 10 1 ATTAAAAAAT 0.923286 -40 CTGAAATAAAAATTAAATCTTCCT 3 36 0 AATAAAAATT 0.923286 -14 AATAAAATTTTTATTGTTAA 4 1 1 AATAAAATTT 0.971321 -41 TTTTATTGTTAATAAAATTTTGCTGGTGAA 4 19 1 AATAAAATTT 0.971321 -23 AAAATCCCTCAAAAAAATAT 5 1 0 AAAAAAATAT 0.867755 -54 AATCAAACAAATTAAATTAACTTCCAGCTC 5 33 0 ATTAAATTAA 0.705765 -22 TAGTGAAAACATTAAAATAACTATCTAAGT 6 58 1 ATTAAAATAA 0.883595 -30 ********** Masking position 5 Map Score: 16.1549 Number of sites scoring better than the average of aligned sites = 1208 Number in coding regions = 821 Number in noncoding regions = 387 Number of orfs with sites within 600 bp upstream = 337 Fraction of orfs with sites within 600 bp upstream = 0.0541279 Motif number 2 AAAGCTTTTTAATTTGGAACGCTATAAAAAGATT 1 67 1 AATTAAGCTA 0.93523 -96 AGATTACTATAATTTATTAGGATAATCCTGCCTT 1 96 1 AATTTAGATA 0.809093 -67 GCCTTATTAAAAAATAGCAAGTTACTAAAGAATT 1 125 1 AAATCAGTTA 0.852046 -38 GTTACTAAAGAATTTCTAAAGTGATATA 1 145 1 AATTAAGTGA 0.978186 -18 AATAAAATTTTTATTGTTAATAAAATTTT 4 6 1 AATTATGTTA 0.985288 -36 TTGTTAATAAAATTTTGCTGGTGAAATT 4 24 1 AATTCTGTGA 0.973805 -18 GCTGGAAGTTAATTTAATTTGTTTGATTGA 5 35 1 AATTTTGTTT 0.821194 -20 ACCCTACATCCAATTACATAGTGAAAACATTAAA 6 40 1 CATTATGTGA 0.928098 -48 GGTATCACCAACTTAGATAGTTATTTTAATGTT 6 65 0 AATTATGTTA 0.985281 -23 ** ** ** **** Masking position 5 Map Score: 4.92975 Number of sites scoring better than the average of aligned sites = 235 Number in coding regions = 179 Number in noncoding regions = 56 Number of orfs with sites within 600 bp upstream = 59 Fraction of orfs with sites within 600 bp upstream = 0.00947639 Motif number 3 TTTGATGAAACTTTTTCTAAAAGTTTCTTTT 1 28 1 CTTTTTCTAA 0.955796 -135 CTAAAAGTTTCTTTTAAAACCTCAAAGCTTT 1 44 1 CTTTTAAAAC 0.956616 -119 TTATAGTAATCTTTTTATAGCGTTCCAAATT 1 77 0 CTTTTTATAC 0.974808 -86 ATAATCCTGCCTTATTAAAAAATAGCAAGTT 1 117 1 CTTATTAAAA 0.802083 -46 TTCTTAGTTGCTTTAACTAAAGTCCAACATT 2 11 1 CTTTAACTAA 0.879439 -113 TAACTTCCAGCTCTTAAAATCCCTCAAAAAA 5 15 0 CTCTTAAAAC 0.876664 -40 AAACCACAACCTTTATATACACCCTACATCC 6 20 1 CTTTATATAA 0.933842 -68 ********* * Masking position 9 Map Score: 1.86641 Number of sites scoring better than the average of aligned sites = 791 Number in coding regions = 662 Number in noncoding regions = 129 Number of orfs with sites within 600 bp upstream = 118 Fraction of orfs with sites within 600 bp upstream = 0.0189528 Motif number 4 CAAAATTGAATATATATCTTA 1 2 0 TATATATCTT 0.61287 -161 GAAACTTTTAGAAAAAGTTTCATCAAAATT 1 25 0 GAAAAAGTTT 0.821086 -138 CGTTCCAAATTAAAAAGCTTTGAGGTTTTA 1 58 0 TAAAAAGCTT 0.958456 -105 TGGAACGCTATAAAAAGATTACTATAATTT 1 81 1 TAAAAAGATT 0.955299 -82 AAAAACATGGCATAAATGTTGGACTTTAGT 2 26 0 CATAAATGTT 0.812045 -98 TCCAGTCTTATAAACATATTCAATAAATAA 2 74 0 TAAACATATT 0.884075 -50 TTATTAACAATAAAAATTTTATT 4 4 0 TAAAAATTTT 0.903781 -38 TCAATCAAACAAATTAAATTAACTT 5 40 0 CAAACAAATT 0.567702 -15 GTAGGGTGTATATAAAGGTTGTGGTTTGGT 6 17 0 TATAAAGGTT 0.923677 -71 ********** Masking position 6 Map Score: 2.73027 Number of sites scoring better than the average of aligned sites = 1197 Number in coding regions = 863 Number in noncoding regions = 334 Number of orfs with sites within 600 bp upstream = 298 Fraction of orfs with sites within 600 bp upstream = 0.0478638 Motif number 5 TATATTCAATTTTGATGAAACTTTTTCTAA 1 18 1 TTTGATGAAA 0.921645 -145 AATGTTGGACTTTAGTTAAAGCAACTAAGA 2 12 0 TTTAGTTAAA 0.711857 -112 AGAAGGAAGAGCTGATTATATTTTA 2 109 1 GCTGATTATA 0.852253 -15 ATAAAATTTTGCTGGTGAAATT 4 30 1 GCTGGTGAAA 0.986356 -12 AAGGTTGTGGTTTGGTGAGAGA 6 3 0 TTTGGTGAGA 0.969038 -85 AACTATCTAAGTTGGTGATACC 6 76 1 GTTGGTGATA 0.983879 -12 ********** Masking position 6 Map Score: 3.05471 Number of sites scoring better than the average of aligned sites = 408 Number in coding regions = 314 Number in noncoding regions = 94 Number of orfs with sites within 600 bp upstream = 121 Fraction of orfs with sites within 600 bp upstream = 0.0194346 Motif number 6 ********** No masking Map Score: -5.94424e-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 7 ********** No masking Map Score: -5.94424e-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: -5.94424e-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