AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i251_chemotaxis_tpal_reg_100.orf -o251_tpal_100.ace -a/home/amcguire/alignace/lib/ORF_tpal.txt -z/skink1/amcguire/genomes/tpal.fna -g0.53 -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 = 0.53 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 RTP00897 300 AE000520 #2 RTP00899 21 AE000520 #3 RTP00159 29 AE000520 #4 RTP00160 86 AE000520 #5 RTP00980 169 AE000520 #6 RTP00594 46 AE000520 Motif number 1 CCGTTTAGGGGTTGGCGGGCACAAGGGGGA 1 23 0 GTTGGCGGGC 0.932075 -278 TTCACGTAATGAAAGCAGGAACCCGTTTAG 1 45 0 GAAAGCAGGA 0.968414 -256 TCAGTGTATTGAATGCGGCAACTGCATTTG 1 192 0 GAATGCGGCA 0.951625 -109 CGTAAAAGCGATGTGCAGGATCGCCTCAGT 1 217 0 ATGTGCAGGA 0.972763 -84 AGGAGCGCGTGTATGCAGGCATGGAGAGAA 1 258 0 GTATGCAGGC 0.992008 -43 GTTAAGGAACAAAGGCAGGATCAGGAGCGC 1 280 0 AAAGGCAGGA 0.935306 -21 GAGACGAATAGTTTGCAGCAGCCTCTTT 3 12 1 GTTTGCAGCA 0.960811 -18 CGCGAACTGAGTGTGCAGGCGGCGAACGGT 5 36 0 GTGTGCAGGC 0.991876 -134 TCCGCAACCTGAATGAAGGAGATGCCGTTC 5 106 1 GAATGAAGGA 0.937295 -64 CCTTGGTCTGCGTGCAGGAAATATTATCA 6 10 1 GCGTGCAGGA 0.985572 -37 ********** Masking position 5 Map Score: 14.9039 Number of sites scoring better than the average of aligned sites = 531 Number in coding regions = 488 Number in noncoding regions = 43 Number of orfs with sites within 600 bp upstream = 33 Fraction of orfs with sites within 600 bp upstream = 0.00530035 Motif number 2 ATTAGGAAGTCATCCCCCTTGTGC 1 3 1 TAGGAGCATC 0.876077 -298 GTAATGAAAGCAGGAACCCGTTTAGGGGTTGG 1 38 0 CAGGACCGTT 0.980715 -263 CATTTTCCCCCAGGGTAACGCGTGCGGAGCAT 1 145 0 CAGGGACGCG 0.928315 -156 GAAAATGAAACTCGATCACGCCCAAATGCAGT 1 170 1 CTCGACCGCC 0.923715 -131 AAGCGATGTGCAGGATCGCCTCAGTGTATTGA 1 210 0 CAGGACCCTC 0.977514 -91 AAGGCAGGATCAGGAGCGCGTGTATGCAGGCA 1 267 0 CAGGACCGTG 0.897507 -34 ATCTACTCCGCAGAAGACCGTCTCT 5 4 0 CAGAAACGTC 0.980671 -166 CGCGAATGCGCTGGATAACGTCGGTGGTCTCC 5 62 1 CTGGAACGTC 0.988004 -108 GGCGTTTTTACAGGAGACCACCGACGTTATCC 5 74 0 CAGGAACACC 0.985729 -96 TACAAACGCGCAGAACGGCATCTCCTTCATTC 5 116 0 CAGAAGCATC 0.933301 -54 ***** * **** Masking position 9 Map Score: 11.2771 Number of sites scoring better than the average of aligned sites = 340 Number in coding regions = 313 Number in noncoding regions = 27 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419 Motif number 3 GAAGTCATCCCCCTTGTGCCCGCCAACCCCT 1 16 1 CCTTGTGCCC 0.989026 -285 CCGACTACATCCATGCTCCGCACGCGTTACC 1 133 1 CCTGCTCCGC 0.99696 -168 TGATCGAGTTTCATTTTCCCCCAGGGTAACG 1 157 0 TCTTTTCCCC 0.877452 -144 CGCTGAGATACAATTCTCTCCATGCCTGCAT 1 245 1 CATTCTCTCC 0.944337 -56 GGAGTAGATACCGTTCGCCGCCTGCACACTC 5 27 1 CCTTCGCCGC 0.988873 -143 TGGATAACGTCGGTGGTCTCCTGTAAAAACG 5 73 1 CGTGGTCTCC 0.949402 -97 GAAGGAGATGCCGTTCTGCGCGTTTGTAGAC 5 120 1 CCTTCTGCGC 0.991623 -50 CCTTGGTCTGCGTGCAGGAAA 6 1 1 CCTGGTCTGC 0.989858 -46 ** ******** Masking position 4 Map Score: 8.27865 Number of sites scoring better than the average of aligned sites = 380 Number in coding regions = 339 Number in noncoding regions = 41 Number of orfs with sites within 600 bp upstream = 41 Fraction of orfs with sites within 600 bp upstream = 0.00658529 Motif number 4 TTGTGCCCGCCAACCCCTAAACGGGTTCCT 1 29 1 CAACCCCTAA 0.982451 -272 CGTGTTTGATCAAACACAAAAATTTCAGTC 1 95 1 CAAACACAAA 0.924033 -206 TGCCGCATTCAATACACTGAGGCGATCCTG 1 202 1 AATACACTGA 0.852347 -99 AGCCCTCTTCCATCCAGTAATACGAAGCCT 4 23 0 CATCCAGTAA 0.874336 -64 TTTGGGGTTGAAACCACTGATAATAATTCC 4 59 0 AAACCACTGA 0.979856 -28 TCAGTGGTTTCAACCCCAAAAATTAAGG 4 69 1 CAACCCCAAA 0.967746 -18 CGCCTGGTTCAAACCACGGATCTGGCTCCG 5 150 1 AAACCACGGA 0.956356 -20 ********** Masking position 2 Map Score: 3.97341 Number of sites scoring better than the average of aligned sites = 152 Number in coding regions = 142 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 5 CGGGCACAAGGGGGATGACTTCCTAAT 1 6 0 GGGAGACTTC 0.93167 -295 AACAAAGGCAGGATCAGGAGCGCGTGTATGCA 1 271 0 GGACGGAGCG 0.866422 -30 TTGCAAAGGAAAAGGCTTCGTATTACTGG 4 8 1 GGAAGGCTTC 0.988529 -79 TTACTGGATGGAAGAGGGCTTGACGGGGAATT 4 33 1 GAAAGGCTTG 0.955115 -54 AGAGACGGTCTTCTGCGGAGTAG 5 2 1 GAGCGTCTTC 0.892991 -168 CCTGAATGAAGGAGATGCCGTTCTGCGCGTTT 5 113 1 GGAAGCCGTT 0.845028 -57 TCCGTGGTTTGAACCAGGCGTCTACAAACGCG 5 138 0 GAACGGCGTC 0.986736 -32 TTCAAACCACGGATCTGGCTCCG 5 157 1 GGACGGCTCC 0.783785 -13 *** * ****** Masking position 7 Map Score: 2.57585 Number of sites scoring better than the average of aligned sites = 365 Number in coding regions = 334 Number in noncoding regions = 31 Number of orfs with sites within 600 bp upstream = 21 Fraction of orfs with sites within 600 bp upstream = 0.00337295 Motif number 6 CGTGCGATTGGCAAGCGCAATATTCACGTA 1 67 0 GCAAGCGCAA 0.966108 -234 ACTACATCCATGCTCCGCACGCGTTACCCT 1 136 1 TGCTCCGCAC 0.878822 -165 ATTGAATGCGGCAACTGCATTTGGGCGTGA 1 185 0 GCAACTGCAT 0.861307 -116 ACTGAGGCGATCCTGCACATCGCTTTTACG 1 217 1 TCCTGCACAT 0.891867 -84 AAAGAGGCTGCTGCAAACTATTCGTC 3 14 0 GCTGCTGCAA 0.639795 -16 CGAAGCCTTTTCCTTTGCAA 4 1 0 TCCTTTGCAA 0.78416 -86 ATCAGTGGTTTCAACCCCAAAAATTAAGG 4 68 1 TCAACCCCAA 0.785615 -19 ACCGTTCGCCGCCTGCACACTCAGTTCGCG 5 36 1 GCCTGCACAC 0.9342 -134 ACCGACGTTATCCAGCGCATTCGCGAACTG 5 57 0 TCCAGCGCAT 0.971427 -113 CTGTAAAAACGCCTCCGCAACCTGAATGAA 5 93 1 GCCTCCGCAA 0.992522 -77 ********** Masking position 9 Map Score: 3.57706 Number of sites scoring better than the average of aligned sites = 2002 Number in coding regions = 1898 Number in noncoding regions = 104 Number of orfs with sites within 600 bp upstream = 88 Fraction of orfs with sites within 600 bp upstream = 0.0141343 Motif number 7 GGGTTGAAACCACTGATAATAATTCCCCGT 4 55 0 CACTGATAAT 0.99151 -32 ACAACACGCTCACTGATAATATTTCCTGCA 6 23 0 CACTGATAAT 0.99151 -24 ********** Masking position 6 Map Score: 0.0887949 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: 1.82142e-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 9 ********** No masking Map Score: 1.82142e-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 10 ********** No masking Map Score: 1.82142e-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