AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i017_Glycolysis___PPS_synecho_reg_300.orf -o017_synecho_300.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 RCY22255 300 Synechocystis #2 RCY49058 126 Synechocystis #3 RCY53506 106 Synechocystis #4 RCY17695 300 Synechocystis #5 RCY44898 206 Synechocystis #6 RCY48136 300 Synechocystis #7 RCY07219 86 Synechocystis #8 RCY02847 174 Synechocystis #9 RCY27715 133 Synechocystis Motif number 1 CAAAACAGACCAATGGCCTTGCTTAGCCTAGCAT 1 124 1 CATGGCCGTT 0.886893 -177 AACTCTTTAACCCCGCCTCTGGTGGGGTTTTTCG 2 59 1 CCCGCCTGTG 0.962259 -68 GGGTCTGAAACCCCGCCCTTGAGGACGGCCTTGC 4 268 0 CCCGCCCGGG 0.989234 -33 GGTTAATTTCCTCTGGCCCAGGTGGAGGAACTGC 5 57 1 CCTGGCCGTG 0.991742 -150 TGCTTGGTGACCCTTTCCTCGGTGACCTAAACTG 5 139 1 CCTTTCCGTG 0.788599 -68 TGTAGTTTTTCAATGGCTTTGGGGCC 5 191 1 CATGGCTGGG 0.97652 -16 AATCCGCTGGCTATGCCTACGCTGGTTCAAATCC 6 48 0 CATGCCTGTG 0.981546 -253 AGCAATGGGTCGATGCCCGAGTGGTTAATGGGGG 6 91 0 CATGCCCGGG 0.992567 -210 TGCTGGGAATCGCTTCCTGTGTCGGGATTGGTTA 6 204 1 CCTTCCTGCG 0.898845 -97 ACAAGATTATCCATTCCCCAGAGGTTTCC 7 68 1 CATTCCCGGG 0.972593 -19 AAACAAGGAAAGACGCCCCAGGTGTTTTTTTATG 8 101 1 AACGCCCGTG 0.844601 -74 ACAGATGAAGCAATGGCGCTGGCGGATGGTA 8 154 1 CATGGCGGCG 0.924516 -21 TTACCATGGCCCGACCGACCGGGATTT 9 117 0 CATGGCCACG 0.866079 -17 * ****** * ** Masking position 7 Map Score: 14.6539 Number of sites scoring better than the average of aligned sites = 2228 Number in coding regions = 2122 Number in noncoding regions = 106 Number of orfs with sites within 600 bp upstream = 111 Fraction of orfs with sites within 600 bp upstream = 0.0178285 Motif number 2 CCTGCATCTTACAACGAAAAACCCCACCAGA 2 76 0 ACAAGAAAAA 0.853116 -51 GAACTGAGAAAGAAATTTTTCCT 3 3 1 ACTGGAAAGA 0.740617 -104 GAAAACTTTGCCAGAAAAAGAAAACTTTCGG 3 34 1 CCAGAAAAGA 0.965172 -73 GAAAAAACATCCGGCCAAAAATTGAGGACAA 4 197 0 CCGGCAAAAA 0.910177 -104 ATTTTATTAAACAGGAAAAAACATCCGGCCA 4 211 0 ACAGAAAAAA 0.941137 -90 GAAAGGGTCACCAAGCAAAAAGCTAAAATTC 5 125 0 CCAACAAAAA 0.932017 -82 GGCCCCAAAGCCATTGAAAAACTACACAAAA 5 186 0 CCATGAAAAA 0.926291 -21 TCTGACCAACCCAGAAAAAAATATTTTGACC 6 160 0 CCAGAAAAAA 0.980226 -141 TCCCAGCAAACCAGACAAAAATCTGACCAAC 6 181 0 CCAGCAAAAA 0.979834 -120 AGGCTTCAGACCTGGAAAAAAAC 8 3 0 CCTGAAAAAA 0.92481 -172 TGGAGTCGAAACAAGGAAAGACGCCCCAGGT 8 93 1 ACAAGAAAGA 0.764539 -82 CTAAAAATTGCCATAAAAAAACACCTGGGGC 8 115 0 CCATAAAAAA 0.907074 -60 **** ****** Masking position 7 Map Score: 12.3383 Number of sites scoring better than the average of aligned sites = 838 Number in coding regions = 706 Number in noncoding regions = 132 Number of orfs with sites within 600 bp upstream = 143 Fraction of orfs with sites within 600 bp upstream = 0.0229682 Motif number 3 GTAGATGCTAGGCTAAGCAAGGCCATTGGTC 1 131 0 GGCAAGCAAG 0.985434 -170 ATAATGACTACGGGAACCAAGTCCTATACTC 1 228 0 CGGAACCAAG 0.907288 -73 AGGTAAGGGCCCACCAAGAAGGGAAATC 2 109 0 GGCCACCAAG 0.976944 -18 AAGCGTAAGTGGCCACACAATACGAGCATTC 3 83 1 GGCACACAAT 0.756931 -24 GTCTTAAGATGTGAACGCAAGGCCGTCCTCA 4 252 1 GTGACGCAAG 0.921974 -49 AAATTCTCCCGTTTCAGCAAGTTTTAGCAAC 5 100 0 GTTCAGCAAG 0.748937 -107 ACCGAGGAAAGGGTCACCAAGCAAAAAGCTA 5 131 0 GGGCACCAAG 0.981303 -76 ATGGCTAATCGTGAAAGCAATGGGTCGATGC 6 109 0 GTGAAGCAAT 0.884075 -192 GCCAATCCTAGGGTAACCAATCCCGACACAG 6 220 0 GGGAACCAAT 0.954038 -81 AAGATGGAGGGGAAAAACAAGATTATCCATT 7 52 1 GGAAAACAAG 0.862577 -35 AACATCTGGAGTCGAAACAAGGAAAGACGCC 8 87 1 GTCAAACAAG 0.923281 -88 *** ******* Masking position 9 Map Score: 7.51746 Number of sites scoring better than the average of aligned sites = 894 Number in coding regions = 809 Number in noncoding regions = 85 Number of orfs with sites within 600 bp upstream = 86 Fraction of orfs with sites within 600 bp upstream = 0.013813 Motif number 4 CCCAGTTATGGCTACCGGGA 4 1 0 GCTACCGGGA 0.933271 -300 GGACGAAACCTAAAGGGAAAACAGCTTT 5 9 1 CCTAAAGGGA 0.898469 -198 TTTCCTCTGGCCCAGGTGGAGGAACTGCTC 5 63 1 CCCAGGTGGA 0.818194 -144 AGCTACAAGGGCAAAAGGGATGGGCCGAGC 6 17 1 GCAAAAGGGA 0.865428 -284 AAGGGATGGGCCGAGCTGGATTTGAACCAG 6 31 1 CCGAGCTGGA 0.97491 -270 AAGAACTAGAGAGAGAGGGACAGTGGGTGC 6 273 0 GAGAGAGGGA 0.784574 -28 ATTCCTTTACCTAAACGGGAAACGACTCCA 7 23 1 CTAAACGGGA 0.760774 -64 GGAAACGACTCCAAGATGGAGGGGAAAAAC 7 40 1 CCAAGATGGA 0.926078 -47 GTCAAGGCTTCAGACCTGGAAAAAAAC 8 8 0 CAGACCTGGA 0.870957 -167 GTATAAATCACCAACGGGGATTGTCAAGGC 8 30 0 CCAACGGGGA 0.965835 -145 CATGGCCCGACCGACCGGGATTTCCAGACC 9 110 0 CCGACCGGGA 0.990676 -24 ********** Masking position 4 Map Score: 7.10523 Number of sites scoring better than the average of aligned sites = 1371 Number in coding regions = 1286 Number in noncoding regions = 85 Number of orfs with sites within 600 bp upstream = 103 Fraction of orfs with sites within 600 bp upstream = 0.0165435 Motif number 5 TCATTATTAGGTGTGAGGAAAAGCTAAAAAT 1 252 1 GTGTGGGAAA 0.963015 -49 TCTGGCAAAGTTTTCAGGAAAAATTTCTTTC 3 18 0 TTTTCGGAAA 0.941791 -89 AAAGTTTTCTTTTTCTGGCAAAGTTTTCAGG 3 31 0 TTTTCGGCAA 0.826626 -76 TGGGGTTGGTGTTGCGGGAAAAGCCTTGGCG 4 155 1 GTTGCGGAAA 0.940981 -146 TTTTGTCTGGTTTGCTGGGAATCGCTTCCTG 6 192 1 TTTGCGGGAA 0.83195 -109 GACTCCAAGATGGAGGGGAAAAACAAGATTA 7 46 1 TGGAGGGAAA 0.765518 -41 CTTAGGACAGGTGTGAGGAAATTAGAAAAAC 8 59 1 GTGTGGGAAA 0.963015 -116 CTAGCTTATTTTCGGAGGAAAT 9 2 0 TTCGGGGAAA 0.873591 -132 CACAGAGGCCTTGTCCGGAAAGGCTAATTTA 9 65 1 TTGTCGGAAA 0.976117 -69 CTGTTCAAACTGGTCTGGAAATCCCGGTCGG 9 99 1 TGGTCGGAAA 0.958563 -35 ***** ***** Masking position 10 Map Score: 6.98411 Number of sites scoring better than the average of aligned sites = 443 Number in coding regions = 354 Number in noncoding regions = 89 Number of orfs with sites within 600 bp upstream = 79 Fraction of orfs with sites within 600 bp upstream = 0.0126887 Motif number 6 ATCTTACAACGAAAAACCCCACCAGAGGCG 2 72 0 GAAAAACCCC 0.91609 -55 AAGATGCAGGCAGATTTCCCTTCTTGGTGG 2 97 1 CAGATTTCCC 0.853726 -30 TAAAATAACTCACAATTCCCGAAAGTTTTC 3 53 0 CACAATTCCC 0.986808 -54 CACACAATACGAGCATTCCCC 3 96 1 GAGCATTCCC 0.950579 -11 AAGTTCTGTCCAAAATTCCTAAGTGAACCA 4 67 0 CAAAATTCCT 0.818393 -234 ACCAACCCCAGAAAATTCCCTCGGAGCAAA 4 135 0 GAAAATTCCC 0.951667 -166 TTTCCCGCAACACCAACCCCAGAAAATTCC 4 146 0 CACCAACCCC 0.962747 -155 AAAAATGGGTCTGAAACCCCGCCCTTGAGG 4 278 0 CTGAAACCCC 0.763172 -23 ATCCTAGGGTAACCAATCCCGACACAGGAA 6 217 0 AACCAATCCC 0.781871 -84 AGAAATTCCACAATTCCTTTACCTAAAC 7 9 1 CACAATTCCT 0.920182 -78 CTGAAGCCTTGACAATCCCCGTTGGTGATT 8 25 1 GACAATCCCC 0.979317 -150 ********** Masking position 8 Map Score: 8.09875 Number of sites scoring better than the average of aligned sites = 1448 Number in coding regions = 1305 Number in noncoding regions = 143 Number of orfs with sites within 600 bp upstream = 159 Fraction of orfs with sites within 600 bp upstream = 0.0255381 Motif number 7 TTGGTAAAGAAAAACCGCCTACAGCTTCTGC 1 58 0 AAAACGCCTA 0.822349 -243 CCAAGAAGGGAAATCTGCCTGCATCTTACAA 2 93 0 AAATCGCCTG 0.929208 -34 CCAGAAAAAGAAAACTTTCGGGAATTGTGAG 3 44 1 AAAACTTCGG 0.893908 -63 TAAACAGGAAAAAACATCCGGCCAAAAATTG 4 204 0 AAAACTCCGG 0.988499 -97 ACCTAAAGGGAAAACAGCTTTGATCGTAACC 5 18 1 AAAACGCTTT 0.736077 -189 TAAAGTTGCTAAAACTTGCTGAAACGGGAGA 5 96 1 AAAACTGCTG 0.842005 -111 GGCGGACTGTAAATCCGCTGGCTATGCCTAC 6 62 0 AAATCGCTGG 0.950707 -239 GGAAACCTCTGGGGAATGGATA 7 75 0 GAAACTCTGG 0.918298 -12 GGAAATTAGAAAAACATCTGGAGTCGAAACA 8 75 1 AAAACTCTGG 0.981783 -100 TTGCCATAAAAAAACACCTGGGGCGTCTTTC 8 108 0 AAAACCCTGG 0.951706 -67 ***** ***** Masking position 3 Map Score: 5.60134 Number of sites scoring better than the average of aligned sites = 659 Number in coding regions = 584 Number in noncoding regions = 75 Number of orfs with sites within 600 bp upstream = 81 Fraction of orfs with sites within 600 bp upstream = 0.01301 Motif number 8 ACGATGATGTTGATGGTTAATAACAGATTA 1 21 0 TGATGGTTAA 0.984316 -280 CCACAATCAGTGTTGGTAAAGAAAAACCGC 1 71 0 TGTTGGTAAA 0.930138 -230 GGTGACTATTTGTTGGTTCACTTAGGAATT 4 54 1 TGTTGGTTCA 0.941217 -247 GACAGAACTTTGGTGGTTAACCACACACTG 4 87 1 TGGTGGTTAA 0.973557 -214 TAAGGTGTTATGATGGCTAATCGTGAAAGC 6 122 0 TGATGGCTAA 0.958245 -179 ACCTTATTGTTGATGGTCAAAATATTTTTT 6 146 1 TGATGGTCAA 0.965841 -155 ********** Masking position 4 Map Score: 4.60688 Number of sites scoring better than the average of aligned sites = 98 Number in coding regions = 85 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 9 AGTCCGTCTTCTTAAGACACTTGTTTGAAA 2 16 1 CTTAAGACAC 0.835086 -111 CACTTAGGAATTTTGGACAGAACTTTGGTG 4 72 1 TTTTGGACAG 0.920917 -229 CGGCCAAAAATTGAGGACAAAAAAAGGCGA 4 187 0 TTGAGGACAA 0.907714 -114 GCGTTCACATCTTAAGACAATTAGAAAGAT 4 240 0 CTTAAGACAA 0.766 -61 AACCCCGCCCTTGAGGACGGCCTTGCGTTC 4 264 0 TTGAGGACGG 0.894043 -37 TTTTAGCAACTTTAGGAGAGCAGTTCCTCC 5 80 0 TTTAGGAGAG 0.914788 -127 CTTTTAGCAGTTTAGGTCACCGAGGAAAGG 5 150 0 TTTAGGTCAC 0.848187 -57 GTGATTTATACTTAGGACAGGTGTGAGGAA 8 49 1 CTTAGGACAG 0.983846 -126 TATGGCAATTTTTAGGGCAGTCCACAGATG 8 131 1 TTTAGGGCAG 0.951513 -44 ********** Masking position 2 Map Score: 3.50091 Number of sites scoring better than the average of aligned sites = 219 Number in coding regions = 173 Number in noncoding regions = 46 Number of orfs with sites within 600 bp upstream = 53 Fraction of orfs with sites within 600 bp upstream = 0.00851269 Motif number 10 GCTCAGGGAGCCAGGACCACAATCAGTGTT 1 87 0 CCAGGACCAC 0.84023 -214 CCTGAGCTAGCCCGCAAAACAGACCAATGG 1 110 1 CCCGCAAAAC 0.975705 -191 TTTTAGCTTTTCCTCACACCTAATAATGAC 1 251 0 TCCTCACACC 0.931562 -50 AAGAAATTTTTCCTGAAAACTTTGCCAGAA 3 20 1 TCCTGAAAAC 0.842808 -87 CAAGGCTTTTCCCGCAACACCAACCCCAGA 4 153 0 CCCGCAACAC 0.951528 -148 TCACGATTAGCCATCATAACACCTTATTGT 6 126 1 CCATCATAAC 0.67064 -175 GAAGCGATTCCCAGCAAACCAGACAAAAAT 6 190 0 CCAGCAAACC 0.915658 -111 TTTTCTAATTTCCTCACACCTGTCCTAAGT 8 58 0 TCCTCACACC 0.931562 -117 AATTAGCCTTTCCGGACAAGGCCTCTGTGA 9 64 0 TCCGGACAAG 0.708263 -70 ********** Masking position 6 Map Score: 2.04414 Number of sites scoring better than the average of aligned sites = 1105 Number in coding regions = 1030 Number in noncoding regions = 75 Number of orfs with sites within 600 bp upstream = 74 Fraction of orfs with sites within 600 bp upstream = 0.0118856 Motif number 11 GGTCTGTTTTGCGGGCTAGCTCAGGGAGCCA 1 104 0 GGGGCTAGCT 0.883412 -197 AGTGTCTTAAGAAGACGGACTCAGGC 2 6 0 GAGACGGACT 0.947866 -121 GGGATGGGATGTGGAGGGGCATAGGAGGTGA 4 28 1 GGGAGGGGCA 0.940305 -273 CCCCGCCCTTGAGGACGGCCTTGCGTTCACA 4 261 0 GGGACGGCCT 0.993434 -40 TCTGGCCCAGGTGGAGGAACTGCTCTCCTAA 5 68 1 GGGAGGAACT 0.94164 -139 AGTGGTTAATGGGGGCGGACTGTAAATCCGC 6 75 0 GGGGCGGACT 0.989509 -226 TGCTTCATCTGTGGACTGCCCTAAAAATTGC 8 135 0 GGGACTGCCC 0.937709 -40 * ********* Masking position 4 Map Score: 1.42807 Number of sites scoring better than the average of aligned sites = 241 Number in coding regions = 225 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 12 TTGTGGTCCTGGCTCCCTGAGCTAGCCCGCA 1 95 1 GGCTCCCGAG 0.983482 -206 TATAGGACTTGGTTCCCGTAGTCATTATTAG 1 231 1 GGTTCCCTAG 0.994254 -70 ACTATTTGTTGGTTCACTTAGGAATTTTGGA 4 58 1 GGTTCACTAG 0.987147 -243 ACCGAGGAAAGGGTCACCAAGCAAAAAGCTA 5 131 0 GGGTCACAAG 0.946892 -76 TGTCGGGATTGGTTACCCTAGGATTGGCTCG 6 223 1 GGTTACCTAG 0.970725 -78 ******* *** Masking position 4 Map Score: 0.970815 Number of sites scoring better than the average of aligned sites = 71 Number in coding regions = 58 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 13 ********** No masking Map Score: 2.40407e-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 14 ********** No masking Map Score: 2.40407e-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 15 ********** No masking Map Score: 2.40407e-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