AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i225_Glutamyl_tRNA_synthase_mtub_reg_300.orf -a/home/amcguire/alignace/lib/ORF_mtub.txt -z/skink1/amcguire/genomes/mtub.fna -g0.66 -x5 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 = 0.66 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 gatB 29 gatB #2 pfkA 95 pfkA #3 gatC 84 gatC #4 Rv3371 191 hypothetical protein Rv3371 #5 otsB2 41 otsB2 #6 echA18 236 echA18 Motif number 1 CGTCGGGTGCTCAAACTAGG 1 1 1 CGTCGGGTGC 0.978029 -29 CGGCGAGCAGACACAGACTCG 2 2 1 GGCGAGCAGA 0.735809 -94 GGGCGAGGGGCGCCGGATGCGAGTCTGTGT 2 21 0 CGCCGGATGC 0.978867 -75 GCCGACCTGGCGCGAGCAGACACAGAATCG 2 54 0 CGCGAGCAGA 0.869445 -42 GCTCGCGCCAGGTCGGCGGCCGCGCGGCAA 2 67 1 GGTCGGCGGC 0.992847 -29 TCGGCGGCCGCGCGGCAAGATGAGGGT 2 79 1 CGCGGCAAGA 0.751178 -17 GGACGGCCGACGCCGGCTGCCGAAACGCCG 3 41 0 CGCCGGCTGC 0.997301 -44 AAGCCTAATGGGTGGCCGGACGGCCGACGC 3 58 0 GGTGGCCGGA 0.909077 -27 TTCCGCCCAGCTCGGCGGCCCGTTGCTCC 4 10 1 GCTCGGCGGC 0.947085 -182 TTCAGCACATCTTCACCTGCGAAACATGTT 4 89 1 CTTCACCTGC 0.714379 -103 CGCCGGACCGCACCGGAAGCAGAAGGCCCA 4 129 0 CACCGGAAGC 0.941206 -63 TTCCGGTGCGGTCCGGCGGACACTTATACC 4 141 1 GTCCGGCGGA 0.96786 -51 GACAAGTCCCCACCGTCGTTTTGCGAC 4 175 0 CCCCACCGTC 0.639615 -17 CGCCATCTCCGTCGGCGTTGACCCCC 5 7 1 CTCCGTCGGC 0.969188 -35 CCCACCCTCTCACGGGGGTCAACGCCGACG 5 20 0 CACGGGGGTC 0.919064 -22 GACGCGGTGCCGCCGCGGGCGATACGCTCC 6 11 1 CGCCGCGGGC 0.985226 -226 CCTCCTCGTTGACGGTCGGAGCGTATCGCC 6 28 0 GACGGTCGGA 0.674513 -209 ATGCAAACCACATGGCCGTCCTCCTCGTTG 6 47 0 CATGGCCGTC 0.845182 -190 CGGCCAGCATCTCCGGGTTCACCAATGCAA 6 71 0 CTCCGGGTTC 0.825912 -166 CTGTCGCCGCCGCGGCCAGCATCTCCGGGT 6 83 0 CGCGGCCAGC 0.9843 -154 CGGCGACAGACTTGGGCGGCATCAGGTCAG 6 104 1 CTTGGGCGGC 0.988007 -133 AGAGGACGCGCATAGGCGGCGCTGATCCCT 6 132 0 CATAGGCGGC 0.895387 -105 TCTTTATCGACACCGGGTGCTGCCAGAGAA 6 191 1 CACCGGGTGC 0.976163 -46 ACGCGGCACAGGTCGGCACC 6 227 1 GGTCGGCACC 0.7801 -10 ********** Masking position 5 Map Score: 38.6477 Number of sites scoring better than the average of aligned sites = 95720 Number in coding regions = 90490 Number in noncoding regions = 5230 Number of orfs with sites within 600 bp upstream = 1500 Fraction of orfs with sites within 600 bp upstream = 0.240925 Motif number 2 ATCGCACGGGCGAGGGGCGCCGGATGCGAGT 2 27 0 CGAGGGCGCC 0.916901 -69 CGGCCGCCGACCTGGCGCGAGCAGACACAGA 2 58 0 CCTGCGCGAG 0.694872 -38 CTCATCTTGCCGCGCGGCCGCCGACCTGGCG 2 72 0 CGCGGGCCGC 0.766845 -24 ATGTATCCACGGCGTTTCGGCAGCCGGCGTC 3 32 1 GGCGTTCGGC 0.775152 -53 TGGCCGGACGGCCGACGCCGGCTGCCGAAAC 3 45 0 GCCGCGCCGG 0.829687 -40 AACGGGCCGCCGAGCTGGGCGGAA 4 4 0 CGAGTGGGCG 0.56878 -188 AGCTCGGCGGCCCGTTGCTCCACCCCACATT 4 19 1 CCCGTGCTCC 0.941992 -173 TTCTGCTTCCGGTGCGGTCCGGCGGACACTT 4 135 1 GGTGGGTCCG 0.72826 -57 GACACTTATACCTGGGGTCGCAAAACGACGG 4 159 1 CCTGGGTCGC 0.933869 -33 CATCTCCGTCGGCGTTGACCCCCGTGAGAGG 5 14 1 GGCGTGACCC 0.96681 -28 GAGCGTATCGCCCGCGGCGGCACCGCGTC 6 9 0 CCCGGGCGGC 0.504973 -228 GGCCGTCCTCCTCGTTGACGGTCGGAGCGTA 6 33 0 CTCGTGACGG 0.746964 -204 CATTGGTGAACCCGGAGATGCTGGCCGCGGC 6 74 1 CCCGAGATGC 0.71347 -163 GGAGATGCTGGCCGCGGCGGCGACAGACTTG 6 87 1 GCCGGGCGGC 0.501526 -150 TGATCCCTGACCTGATGCCGCCCAAGTCTGT 6 109 0 CCTGTGCCGC 0.987285 -128 GCGCATAGGCGGCGCTGATCCCTGACCTGAT 6 124 0 GGCGTGATCC 0.839798 -113 CCAGGTCACCGCAGAGGACGCGCATAGGCGG 6 143 0 GCAGGGACGC 0.950508 -94 ATCGACACCGGGTGCTGCCAGAGAACTCGAG 6 196 1 GGTGTGCCAG 0.774012 -41 CCAGAGAACTCGAGACGCGGCACAGGTCGGC 6 213 1 CGAGCGCGGC 0.698262 -24 **** ****** Masking position 4 Map Score: 26.2057 Number of sites scoring better than the average of aligned sites = 60382 Number in coding regions = 56684 Number in noncoding regions = 3698 Number of orfs with sites within 600 bp upstream = 1279 Fraction of orfs with sites within 600 bp upstream = 0.205429 Motif number 3 GCGCCGGATGCGAGTCTGTGTCTGCTCGCCG 2 10 0 CAGCTGTGTC 0.985005 -86 CTCGCCCGTGCGATTCTGTGTCTGCTCGCGCC 2 44 1 CATCTGTGTC 0.956889 -52 CTGCTCGCGCCAGGTCGGCGGCCGCGCGGCAA 2 65 1 CGGCGGCGGC 0.991901 -31 GGCCAACACTGTGGCACAACGATGT 3 4 1 CACCTGTGGC 0.992415 -81 CACTGTGGCACAACGATGTATCCACGGCGTTT 3 17 1 CACATGTATC 0.767007 -68 TTCCGCCCAGCTCGGCGGCCCGTTGCTCC 4 8 1 CGCCGGCGGC 0.995846 -184 TGCTGAACAACTGCGCTGTATCGAACAATTGT 4 64 0 CGCCTGTATC 0.983613 -128 TAAGTGTCCGCCGGACCGCACCGGAAGCAGAA 4 135 0 CGGCCGCACC 0.890766 -57 TCGCCCGCGGCGGCACCGCGTC 6 1 0 CGCCCGCGTC 0.996775 -236 ACGAGGAGGACGGCCATGTGGTTTGCATTGGT 6 49 1 CGCATGTGGT 0.679444 -188 TGATGCCGCCCAAGTCTGTCGCCGCCGCGGCC 6 96 0 CAGCTGTCGC 0.941006 -141 GGTCAGGGATCAGCGCCGCCTATGCGCGTCCT 6 128 1 CGCCCGCCTA 0.829081 -109 TTCTCTGGCAGCACCCGGTGTCGATAAAGACG 6 189 0 GACCGGTGTC 0.891859 -48 GGTGCCGACCTGTGCCGCGTCTCGAGTTCTC 6 216 0 CGTCCGCGTC 0.981626 -21 * ** ******* Masking position 8 Map Score: 20.1983 Number of sites scoring better than the average of aligned sites = 17629 Number in coding regions = 16434 Number in noncoding regions = 1195 Number of orfs with sites within 600 bp upstream = 763 Fraction of orfs with sites within 600 bp upstream = 0.122551 Motif number 4 AGGGGCGCCGGATGCGAGTCTGTGTCTGCT 2 16 0 GATGCGAGTC 0.887141 -80 TCGCACGGGCGAGGGGCGCCGGATGCGAGT 2 27 0 GAGGGGCGCC 0.956461 -69 CCCTCATCTTGCCGCGCGGCCGCCGACCTG 2 75 0 GCCGCGCGGC 0.49979 -21 CACAACGATGTATCCACGGCGTTTCGGCAG 3 25 1 TATCCACGGC 0.928248 -60 GCCCGCGGCGGCACCGCGTC 6 1 0 GCACCGCGTC 0.909623 -236 CCGGAGATGCTGGCCGCGGCGGCGACAGAC 6 85 1 TGGCCGCGGC 0.969085 -152 TCAGGTCAGGGATCAGCGCCGCCTATGCGC 6 125 1 GATCAGCGCC 0.899729 -112 CAGCGCCGCCTATGCGCGTCCTCTGCGGTG 6 138 1 TATGCGCGTC 0.962964 -99 GCTGGTAGCTTAGGCACGTCTTTATCGACA 6 173 1 TAGGCACGTC 0.940797 -64 CAGAGAACTCGAGACGCGGCACAGGTCGGC 6 214 1 GAGACGCGGC 0.970436 -23 ********** Masking position 10 Map Score: 10.6149 Number of sites scoring better than the average of aligned sites = 10287 Number in coding regions = 9417 Number in noncoding regions = 870 Number of orfs with sites within 600 bp upstream = 554 Fraction of orfs with sites within 600 bp upstream = 0.0889817 Motif number 5 GGCCAACACTGTGGCACAACGATGTATCC 3 10 1 TGTGGCACAA 0.968672 -75 TTCCACAGTATATCGAACAATTGTTCGATA 4 48 1 TATCGAACAA 0.968402 -144 AACTGCGCTGTATCGAACAATTGTTCGATA 4 58 0 TATCGAACAA 0.968402 -134 GGTGAAGATGTGCTGAACAACTGCGCTGTA 4 76 0 TGCTGAACAA 0.921232 -116 TTATACCTGGGGTCGCAAAACGACGGTGGG 4 164 1 GGTCGCAAAA 0.919258 -28 CCTGACCTGATGCCGCCCAAGTCTGTCGCC 6 105 0 TGCCGCCCAA 0.970909 -132 CAGCACCCGGTGTCGATAAAGACGTGCCTA 6 183 0 TGTCGATAAA 0.88319 -54 ********** Masking position 9 Map Score: 4.05005 Number of sites scoring better than the average of aligned sites = 909 Number in coding regions = 830 Number in noncoding regions = 79 Number of orfs with sites within 600 bp upstream = 74 Fraction of orfs with sites within 600 bp upstream = 0.0118856 Motif number 6 ********** No masking Map Score: -3.24418e-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: -3.24418e-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: -3.24418e-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