AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i039_synecho_ctra_300.orf -o039_synecho_ctra_300.ace -a/home/amcguire/genomes/ORF_synecho.txt -z/home/amcguire/genomes/synecho.fna -g0.46 -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 = 0.46 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 RCY15392 300 Synechocystis #2 RCY11958 83 Synechocystis #3 RCY25664 83 Synechocystis #4 RCY14446 96 Synechocystis #5 RCY33821 135 Synechocystis #6 RCY24046 300 Synechocystis #7 RCY01084 222 Synechocystis #8 RCY12516 300 Synechocystis Motif number 1 ACCGTGGTTATTTTACCCCAAGCTCTGCGT 1 234 0 TTTTACCCCA 0.626341 -67 CACGGTTGACTGCTCCACCAACAATCCACT 1 258 1 TGCTCCACCA 0.881325 -43 CTGGCCAGGGATTTCCACCGCCTAGGATAC 2 49 0 ATTTCCACCG 0.929114 -35 GCCAGTCAATTTTGCCCCCT 2 74 1 TTTGCCCCCT 0.789288 -10 TTAGCTTTTTCCTCCCACCAATTATCCAAG 3 37 0 CCTCCCACCA 0.925406 -47 CGCCCCAAAGATTCTCACCATAACTTAGCT 3 61 0 ATTCTCACCA 0.809491 -23 ACTGCTTCCAACTGCCACCGCATCGAAACT 4 40 1 ACTGCCACCG 0.946203 -57 GATAAAAAGAACTGCCCCCAGTTTAGCCAA 4 70 0 ACTGCCCCCA 0.941292 -27 AGCCAGACAGTGTGCCCCCATGGGTTTTAA 5 47 1 TGTGCCCCCA 0.976035 -89 AAACACCTGTTGTCCCACCGAAAAACTATT 6 55 0 TGTCCCACCG 0.98158 -246 AGATCGGACTTTTTTCACCAGACCTAGTTC 6 112 0 TTTTTCACCA 0.867561 -189 AGGGTCTCCACTTCCCCCCAGACATTACAA 6 143 0 CTTCCCCCCA 0.917412 -158 ATAACTGAGGACTCCCACCGCCA 7 4 0 ACTCCCACCG 0.954499 -219 CCGCTCCAGTTCCCTCACCGGAACC 7 208 1 TCCCTCACCG 0.723249 -15 ACGACGCATTTGTTTCCCCACGTTTGTCCC 8 65 0 TGTTTCCCCA 0.903727 -236 GGGGGTTAGCTGTGCCACAAGTGCAAAATC 8 233 1 TGTGCCACAA 0.647156 -68 TTCATGGGATTTTTTCACCGGATTTTGCAC 8 253 0 TTTTTCACCG 0.881706 -48 CCCGCCCCTCTGTTCCCCCG 8 291 1 TGTTCCCCCG 0.975613 -10 ********** Masking position 6 Map Score: 21.3202 Number of sites scoring better than the average of aligned sites = 4548 Number in coding regions = 4154 Number in noncoding regions = 394 Number of orfs with sites within 600 bp upstream = 382 Fraction of orfs with sites within 600 bp upstream = 0.0613556 Motif number 2 TACTCTTTGCTAGGATAAATATCGGCATACTTAGG 1 34 1 TAGGAAACGG 0.739397 -267 GTTCATTAAATTTTAAAAAAATTTGTCCATTTTAA 1 136 0 TTTTAAATTG 0.831886 -165 AGACCTAGTTTTTGTGGATTAGTGGATTGTTGGTG 1 273 0 TTTGGAATGG 0.958342 -28 TTATTAAGAATTTTCAGACCCCTGGGATTCCTGTC 2 11 1 TTTTGACTGG 0.773287 -73 TCCAAGCGGCTTTGAAAAACCTTGGGTGGCCC 3 8 0 TTTGAACTGG 0.948907 -76 TCAAAGCCGCTTGGATAATTGGTGGGAGGAAAAAG 3 28 1 TTGGAAGTGG 0.7304 -56 ATAGACAAAGTTTTAAAACCCATGGGGGCACACTG 5 54 0 TTTTAACTGG 0.832171 -82 CCAAACAAGTTTGGCAAAACACCTGTTGTCCCACC 6 66 0 TTGGAAACTG 0.944985 -235 CCAAACTTGTTTGGAGGAGAATCTGGAACTAGGTC 6 87 1 TTGGGAACTG 0.921971 -214 TGTTGTAATGTCTGGGGGGAAGTGGAGACCCTTAG 6 141 1 TCTGGGATGG 0.572764 -160 GGAAAATTGATTTGGCAAATAGCTGCGCGACAACT 6 254 0 TTTGAAACTG 0.970966 -47 AATTTTCCCGTCTTTAAATTATCTGTTGCT 6 281 1 TCTTAAACTG 0.690349 -20 GTTACGATTCTTTGCTAAATAACTGAGGACTCCCA 7 17 0 TTTGAAACTG 0.970966 -206 CACGGAGGGCTTTTACAGAGATCGGTGAGCTATTG 7 118 0 TTTTAGACGG 0.789914 -105 CCCTCCGTGCTTTGATGAGACGCGGATTTTATCCA 7 144 1 TTTGGACCGG 0.958423 -79 TAGTTTTACATTTGTTAACAATTTGTCGCTTGAAT 8 15 1 TTTGAAATTG 0.948808 -286 AATGCGTCGTTTTGTTAAACAACTGACGAAAAACA 8 85 1 TTTGAAACTG 0.970966 -216 **** ** * *** Masking position 1 Map Score: 16.4866 Number of sites scoring better than the average of aligned sites = 1102 Number in coding regions = 972 Number in noncoding regions = 130 Number of orfs with sites within 600 bp upstream = 141 Fraction of orfs with sites within 600 bp upstream = 0.022647 Motif number 3 GACAGGAATCCCAGGGGTCTGAAAATTCTT 2 16 0 CCAGGGGTCT 0.981273 -68 AATTGACTGGCCAGGGATTTCCACCGCCTA 2 55 0 CCAGGGATTT 0.911863 -29 GGGCCACCCAAGGTTTTTCAAAGCCGC 3 8 1 CCAAGGTTTT 0.97821 -76 CGTCGCCCCAAAGATTCTCACCATAAC 3 67 0 CCAAAGATTC 0.76916 -17 CCCAGTTTAGCCAAAGTTTCGATGCGGTGG 4 54 0 CCAAAGTTTC 0.861435 -43 CAGTGTGCCCCCATGGGTTTTAAAACTTTG 5 54 1 CCATGGGTTT 0.966934 -82 CCGGGTCAATCAATGGGTCTAATTTCTTAT 6 19 1 CAATGGGTCT 0.727454 -282 GGCAGTACCCCTAAGGGTCTCCACTTCCCC 6 156 0 CTAAGGGTCT 0.905677 -145 CACCTTTCAACCAAGGTTTTAGACTACCGA 6 193 0 CCAAGGTTTT 0.97821 -108 CGGATTTTATCCAACGGTCTCTCCGAGAAG 7 166 1 CCAACGGTCT 0.946542 -57 CGAGAAGGTATCAAGGTTCCCGCTCCAGTT 7 189 1 TCAAGGTTCC 0.801566 -34 TCTGTCTGCATCAAAGGTTTACCGGGGGTT 8 210 1 TCAAAGGTTT 0.783575 -91 ********** Masking position 3 Map Score: 11.2344 Number of sites scoring better than the average of aligned sites = 1433 Number in coding regions = 1306 Number in noncoding regions = 127 Number of orfs with sites within 600 bp upstream = 148 Fraction of orfs with sites within 600 bp upstream = 0.0237713 Motif number 4 TTCATTAAATTTTAAAAAAATTTGTCCATTTTAA 1 136 0 TTTAAAATTG 0.863458 -165 AGATGATGGACAAAGAGTTGATTGGGCGAG 5 116 0 TGGAAAATTG 0.972782 -20 CAAACAAGTTTGGCAAAACACCTGTTGTCCCACC 6 66 0 TGGAAAACTG 0.990913 -235 GCTTTGGATATGTTGAAACATCTTCACCTTTCAA 6 213 0 TGTAAAACTT 0.728871 -88 GAAAATTGATTTGGCAAATAGCTGCGCGACAACT 6 254 0 TTGAAAACTG 0.985587 -47 TTACGATTCTTTGCTAAATAACTGAGGACTCCCA 7 17 0 TTGAAAACTG 0.985587 -206 TGTTAACAAATGTAAAACTAACTG 8 1 0 TGTAACACTG 0.929729 -300 AGTTTTACATTTGTTAACAATTTGTCGCTTGAAT 8 16 1 TTGAACATTG 0.905987 -285 GGGACAAACGTGGGGAAACAAATGCGTCGTTTTG 8 65 1 TGGAAAAATG 0.933972 -236 ATGCGTCGTTTTGTTAAACAACTGACGAAAAACA 8 86 1 TTGAAAACTG 0.985587 -215 *** *** * *** Masking position 7 Map Score: 12.5923 Number of sites scoring better than the average of aligned sites = 255 Number in coding regions = 220 Number in noncoding regions = 35 Number of orfs with sites within 600 bp upstream = 41 Fraction of orfs with sites within 600 bp upstream = 0.00658529 Motif number 5 TGAGCACACGCAGAGCTTGGGGTAAAATAA 1 227 1 CAGAGCTTGG 0.943042 -74 GACAGACCTAGTTTTTGTGGAT 1 289 0 CAGACCTAGT 0.97925 -12 ATCAACTAGCCAGACAGTGTGCCCCCATGG 5 40 1 CAGACAGTGT 0.948329 -96 CTTTTTTCACCAGACCTAGTTCCAGATTCT 6 104 0 CAGACCTAGT 0.97925 -197 GAGCTATTGGCAGTCATCGTACTCCATCAC 7 97 0 CAGTCATCGT 0.897526 -126 AGGGCTTTTACAGAGATCGGTGAGCTATTG 7 118 0 CAGAGATCGG 0.953152 -105 ACCTTTGATGCAGACAGAGGAGACGATACA 8 198 0 CAGACAGAGG 0.969473 -103 ********** Masking position 2 Map Score: 4.68613 Number of sites scoring better than the average of aligned sites = 79 Number in coding regions = 62 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 21 Fraction of orfs with sites within 600 bp upstream = 0.00337295 Motif number 6 TTTTAAAAAAATTTGTCCATTTTAAAAATT 1 131 0 ATTTGTCCAT 0.911085 -170 CCAATCAACTCTTTGTCCATCATCT 5 121 1 CTTTGTCCAT 0.731297 -15 ACATATCCAAAGCCGTCGCTAGTTGTCGCG 6 234 1 AGCCGTCGCT 0.891389 -67 AGCCGTCGCTAGTTGTCGCGCAGCTATTTG 6 244 1 AGTTGTCGCG 0.889216 -57 TCTTTAAATTATCTGTTGCT 6 291 1 ATCTGTTGCT 0.853784 -10 GAATCGTAACAATTGTCGATTCAGGCTTTA 7 42 1 AATTGTCGAT 0.804987 -181 TTTGTTAACAATTTGTCGCTTGAATCTCAT 8 25 1 ATTTGTCGCT 0.983784 -276 GTTTCCCCACGTTTGTCCCTATGTCCTTAA 8 54 0 GTTTGTCCCT 0.89252 -247 GACCGGTTATATTCGTTGCTGCAGGCTGTA 8 172 1 ATTCGTTGCT 0.853787 -129 ********** Masking position 6 Map Score: 1.56245 Number of sites scoring better than the average of aligned sites = 371 Number in coding regions = 326 Number in noncoding regions = 45 Number of orfs with sites within 600 bp upstream = 57 Fraction of orfs with sites within 600 bp upstream = 0.00915516 Motif number 7 TCAACTAGCCAGACAGTGTGCCCCCATGGG 5 41 1 AGACAGTGTG 0.817804 -95 AGATGATGGACAAAGAGTTGATTGGGC 5 119 0 GGACAAAGAG 0.878755 -17 TCTCATCAAAGCACGGAGGGCTTTTACAGA 7 134 0 GCACGGAGGG 0.945203 -89 ATCTCATTAAGGACATAGGGACAAACGTGG 8 48 1 GGACATAGGG 0.98804 -253 AATTCAATGGGGACATTGGGGACATTATTT 8 141 0 GGACATTGGG 0.972928 -160 CCTTTGATGCAGACAGAGGAGACGATACAG 8 197 0 AGACAGAGGA 0.896385 -104 CGGGGGAACAGAGGGGCGGGGAGGT 8 286 0 GAACAGAGGG 0.974242 -15 ********** Masking position 3 Map Score: 2.42408 Number of sites scoring better than the average of aligned sites = 430 Number in coding regions = 382 Number in noncoding regions = 48 Number of orfs with sites within 600 bp upstream = 55 Fraction of orfs with sites within 600 bp upstream = 0.00883392 Motif number 8 TACATAGTTTAGGTTTCAGACTATTATTGCCA 1 191 0 AGGTTAGACT 0.988913 -110 CTTTCAACCAAGGTTTTAGACTACCGAAAAGC 6 188 0 AGGTTAGACT 0.988913 -113 ATTATTTAATAGGTTAAAGACTTTTTTCTGTT 8 116 0 AGGTTAGACT 0.988913 -185 ***** ***** Masking position 8 Map Score: 0.621939 Number of sites scoring better than the average of aligned sites = 6 Number in coding regions = 3 Number in noncoding regions = 3 Number of orfs with sites within 600 bp upstream = 5 Fraction of orfs with sites within 600 bp upstream = 0.000803084 Motif number 9 ********** No masking Map Score: -1.43997e-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: -1.43997e-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 11 ********** No masking Map Score: -1.43997e-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