AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i014_Glycolysis_1_synecho_reg_100.orf -o014_synecho_100.ace -a/home/amcguire/alignace/lib/ORF_synecho.txt -z/skink1/amcguire/genomes/synecho.fna -g0.48 -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 = 0.48 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 RCY09935 80 Synechocystis #2 RCY11182 235 Synechocystis #3 RCY06446 94 Synechocystis #4 RCY04603 188 Synechocystis #5 RCY37403 269 Synechocystis Motif number 1 AATTGTCTCACTACCCCCATGATTTACCTT 2 32 1 CTACCCCCAT 0.990361 -204 TTACCGTTATCTAATCCCCTTTGAAAAGGG 2 89 0 CTAATCCCCT 0.959127 -147 AAAAACTATCCTCACCCAATCAACTCTTCA 2 163 1 CTCACCCAAT 0.849432 -73 TCCGGGGCAACTCCTGCCCTAGACCGAGTA 3 11 0 CTCCTGCCCT 0.887323 -84 AGTGCCGGAACTAATTCCAGTTTATCTTCT 4 12 1 CTAATTCCAG 0.727151 -177 CAACGAGGAACTAACCCCCAAACTCAACTG 4 89 0 CTAACCCCCA 0.936966 -100 CAAAATTTGCCAACCCCCAGTTTACGTCGT 4 139 0 CAACCCCCAG 0.984992 -50 CAACGCTCCTCACAAGCCATAAATGTTAAC 5 13 1 CACAAGCCAT 0.720819 -257 AGCAAAAACTCTACCCCCAGGCATAGACAA 5 92 1 CTACCCCCAG 0.991096 -178 CAGGCATAGACAAAACCCAGAGGCCACGGT 5 109 1 CAAAACCCAG 0.917937 -161 AAAAGATTCCCACCCCCCCTTTGAAATTCG 5 162 1 CACCCCCCCT 0.981475 -108 ********** Masking position 7 Map Score: 11.8226 Number of sites scoring better than the average of aligned sites = 2537 Number in coding regions = 2252 Number in noncoding regions = 285 Number of orfs with sites within 600 bp upstream = 310 Fraction of orfs with sites within 600 bp upstream = 0.0497912 Motif number 2 CCAGTCAATGTTACCGCCGACAATGGAAAGCCCCA 1 13 0 TTCGCCGCTG 0.996674 -68 TAAACTGGAATTAGTTCCGGCACTG 4 1 0 TTTTCCGCTG 0.980391 -188 TAATTCCAGTTTATCTTCTCGATTGGACTAGATTG 4 23 1 TTCTTCTGTG 0.88573 -166 TGAAGCCGAATTAATGCCGCCCTGGCTTTCAATCT 4 52 0 TTTGCCGCGG 0.987809 -137 AGTTTGGGGGTTAGTTCCTCGTTGGTTAATGGTGA 4 95 1 TTTTCCTGGG 0.804567 -94 CAACCCCCAGTTTACGTCGTCCGGGGTCGTCACCA 4 124 0 TTCGTCGCGG 0.992116 -65 GCCATAAATGTTAACGTCTACAATCACCTGCCGGT 5 28 1 TTCGTCTCTC 0.879003 -242 CCGTCGCTGTTTACCGTGGCCTCTGGGTTTTGTCT 5 116 0 TTCGTGGCTG 0.956833 -154 CTTTTTCCCTTTCTCTCCGTCGCTGTTTACCGTGG 5 132 0 TTCTCCGCTG 0.993488 -138 ** ***** * ** Masking position 2 Map Score: 7.42011 Number of sites scoring better than the average of aligned sites = 1007 Number in coding regions = 937 Number in noncoding regions = 70 Number of orfs with sites within 600 bp upstream = 71 Fraction of orfs with sites within 600 bp upstream = 0.0114038 Motif number 3 CCATGATTTACCTTGGAAAGGAGAAAAATT 2 48 1 CCTTGGAAAG 0.974958 -188 TATCTAATCCCCTTTGAAAAGGGTTGGGTT 2 82 0 CCTTTGAAAA 0.993373 -154 GTAAATACAACCTTTGAAAACTGCCCTTAA 2 115 1 CCTTTGAAAA 0.993373 -121 GCAAAAGATGCCCTTGATAATACCATCAAA 3 45 0 CCCTTGATAA 0.953663 -50 TCCCACCCCCCCTTTGAAATTCGGGATCTA 5 169 1 CCTTTGAAAT 0.98345 -101 ********** Masking position 4 Map Score: 6.09658 Number of sites scoring better than the average of aligned sites = 50 Number in coding regions = 44 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 Motif number 4 TAAATGTCAAATAAACTTAACAAAATTAAACCA 1 45 0 AAAATTACAA 0.835348 -36 AGTCTGTTTAAAAAGTCTAAAAATTGTCTCAC 2 10 1 AAAATCTAAA 0.925656 -226 TGGAAAGGAGAAAAATTCTTAAACCCAACCCTT 2 61 1 AAAATCTAAA 0.925656 -175 TCCTCACCCAATCAACTCTTCACCCTGACATCA 2 171 1 ACAATCTCAC 0.891412 -65 TTGGTCAACAACTAATTTTTCCAACTATTTTTC 2 206 1 ATAATTTCCA 0.881309 -30 CACTACAGTTATAAAGTCTGCAAAAGATGCCCT 3 61 0 AAAATCTCAA 0.984431 -34 GAAGGTCACAACAAAATTTGCCAACCCCCAGTT 4 147 0 AAAATTTCCA 0.976434 -42 ACATCATAGCAAAAACTCTACCCCCAGGCATAG 5 85 1 AAAATCTCCC 0.975485 -185 AGAGAAAGGGAAAAAGATTCCCACCCCCCCTTT 5 151 1 AAAAATTCCA 0.867228 -119 * *** *** *** Masking position 5 Map Score: 3.92304 Number of sites scoring better than the average of aligned sites = 699 Number in coding regions = 579 Number in noncoding regions = 120 Number of orfs with sites within 600 bp upstream = 139 Fraction of orfs with sites within 600 bp upstream = 0.0223257 Motif number 5 AAGTCTAAAAATTGTCTCACTACCCCCATGATT 2 23 1 ATTGCTACAC 0.981111 -213 CTGACATCAGATTGGTCAACAACTAATTTTTCC 2 195 1 ATTGTCACAC 0.980168 -41 TTTTCCAACTATTTTTCCAATACC 2 222 1 ATTTTCAAAC 0.832317 -14 GGTTATTGCCTCACTACAGTTATAAAG 3 78 0 ATTGCTACAC 0.981153 -17 CCCAAACTCAACTGCTTGAAGCCGAATTAATGC 4 70 0 ACTGTTAACC 0.780286 -119 TCACAACAAAATTTGCCAACCCCCAGTTTACGT 4 142 0 ATTTCCACCC 0.919393 -47 CGCACCTGTAATTGAGCGACATCATAGCAAAAA 5 67 1 ATTGGCACTC 0.917348 -203 ATCATATCCTATTGCCTGAACACTTAGATCCCG 5 190 0 ATTGCTAAAC 0.963635 -80 CCTTAAATGTACTGAGCTAAAACAGAGAGGGCA 5 239 1 ACTGGCAAAC 0.930077 -31 **** ** ** ** Masking position 9 Map Score: 5.04298 Number of sites scoring better than the average of aligned sites = 635 Number in coding regions = 558 Number in noncoding regions = 77 Number of orfs with sites within 600 bp upstream = 83 Fraction of orfs with sites within 600 bp upstream = 0.0133312 Motif number 6 CAACTCTTCACCCTGACATCAGATTGGTCA 2 183 1 CCCTGACATC 0.961172 -53 TCAAAAACATCCGGGGCAACTCCTGCCCTA 3 20 0 CCGGGGCAAC 0.989981 -75 ATGGTATTATCAAGGGCATCTTTTGCAGAC 3 49 1 CAAGGGCATC 0.939247 -46 AGATTGAAAGCCAGGGCGGCATTAATTCGG 4 52 1 CCAGGGCGGC 0.978022 -137 TGGTGACGACCCCGGACGACGTAAACTGGG 4 124 1 CCCGGACGAC 0.970193 -65 AAACTCTACCCCCAGGCATAGACAAAACCC 5 97 1 CCCAGGCATA 0.869707 -173 TCGCTGTTTACCGTGGCCTCTGGGTTTTGT 5 118 0 CCGTGGCCTC 0.965593 -152 ********** Masking position 5 Map Score: 3.50338 Number of sites scoring better than the average of aligned sites = 1477 Number in coding regions = 1405 Number in noncoding regions = 72 Number of orfs with sites within 600 bp upstream = 84 Fraction of orfs with sites within 600 bp upstream = 0.0134918 Motif number 7 ********** No masking Map Score: -6.939e-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: -6.939e-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 CTTAACAAAATTAAACCAGTCAATGTTACCG 1 32 0 TAAACCAGTC 0.976038 -49 TTAAAAAGTCTAAAAATTGTCTCACTACCCC 2 18 1 TAAAATTGTC 0.785471 -218 GAAAAATTCTTAAACCCAACCCTTTTCAAAG 2 70 1 TAACCCAACC 0.901996 -166 TAGATAACGGTAAATACAACCTTTGAAAACT 2 106 1 TAATACAACC 0.873475 -130 ATACAACCTTTGAAAACTGCCCTTAAAACGC 2 119 1 TAAAACTGCC 0.940085 -117 TTTTTAGCAATAAAAACTATCCTCACCCAAT 2 152 1 TAAAACTATC 0.909847 -84 GCCCTGGCTTTCAATCTAGTCCAATCGAGAA 4 38 0 TAATCTAGTC 0.802096 -151 GGATTATTAATGACACCAATCATATCCTATT 5 210 0 TACACCAATC 0.872136 -60 * ********* Masking position 3 Map Score: 0.653197 Number of sites scoring better than the average of aligned sites = 686 Number in coding regions = 604 Number in noncoding regions = 82 Number of orfs with sites within 600 bp upstream = 92 Fraction of orfs with sites within 600 bp upstream = 0.0147767 Motif number 10 ********** No masking Map Score: -6.939e-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: -6.939e-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: -6.939e-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