AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i078_Lipopolysaccharide_Biosynthesis_3_synecho_reg_100.orf -o078_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 RCY50877 115 Synechocystis #2 RCY13382 161 Synechocystis #3 RCY24201 240 Synechocystis #4 RCY04335 82 Synechocystis #5 RCY28320 241 Synechocystis #6 RCY18066 196 Synechocystis #7 RCY33510 30 Synechocystis Motif number 1 CTTTTAGGAATTAGCCATAGACCACAAAAAAA 2 12 0 TTACCATAGC 0.955078 -150 GAATAAAATTTTCACCATAATTA 3 2 0 TTCCCATAAT 0.861294 -239 TTTTATTCTTTTCACCATTTTCCATTCTTCAC 3 26 1 TTCCCATTTC 0.889694 -215 TTTTCCATTCTTCACCCTACTTTTCAAACACG 3 43 1 TTCCCCTACT 0.908481 -198 TAATGAAAAATTATCCCTTGTCTTATGCTTTG 3 141 0 TTACCCTTGC 0.971452 -100 GCTGTTATTTTGCTCCCTAAATAGGCTGATTA 3 185 0 TGCCCCTAAT 0.88091 -56 TTCCAGATTTTTCTCCACTGCCGGATTAATGG 4 14 1 TTCCCACTGC 0.931516 -69 ACCGACCCATTGCTCCCTTGCCCT 5 3 0 TGCCCCTTGC 0.988511 -239 AACTGTTCACTGAACCCTAGACCCAACAACAT 5 201 1 TGACCCTAGC 0.962016 -41 ATCCCATTGGTTCACCATTGATGGATAAAAAG 6 75 0 TTCCCATTGT 0.963685 -122 TGTTATCCAAATCCCCCTAGCCTGCGGCGCTA 6 165 1 ATCCCCTAGC 0.954007 -32 *** ****** * Masking position 6 Map Score: 11.09 Number of sites scoring better than the average of aligned sites = 1347 Number in coding regions = 1166 Number in noncoding regions = 181 Number of orfs with sites within 600 bp upstream = 200 Fraction of orfs with sites within 600 bp upstream = 0.0321234 Motif number 2 TCCAGAGTTTTTTCCTGATTAAGAATTGAAC 2 74 1 TTTCCGATTA 0.973552 -88 TCTTTCCAGATTTTTCTCCACTG 4 3 1 TTTCCGATTT 0.96175 -80 TTTTTCTCCACTGCCGGATTAATGGTATTTT 4 21 1 CTGCCGATTA 0.965227 -62 GTTCACAGATTAAATTCCTCTT 4 71 0 TTCACGATTA 0.941333 -12 CCATCTCAACTTGCCTGATATGTTTATTGGT 5 55 0 TTGCCGATAT 0.951636 -187 TGCCCGTAAATTGACTGATTTCGTGTCATCA 5 103 0 TTGACGATTT 0.962926 -139 TACGCCATCATTTCTCGATTAGGTTTTAATG 5 140 1 TTTCTGATTA 0.850101 -102 ATGGTCAGTGTTGACCGATTCCTGCTTACTG 5 168 1 TTGACGATTC 0.921263 -74 CCGATTCCTGCTTACTGATAACTGTTCACTG 5 182 1 CTTACGATAA 0.747394 -60 CCAAAAGCTTTTCCCTGCTTTTTATCCATCA 6 58 1 TTCCCGCTTT 0.796978 -139 TGGTTCACCATTGATGGATAAAAAGCAGGGA 6 69 0 TTGATGATAA 0.700007 -128 ***** ***** Masking position 9 Map Score: 9.04112 Number of sites scoring better than the average of aligned sites = 779 Number in coding regions = 674 Number in noncoding regions = 105 Number of orfs with sites within 600 bp upstream = 104 Fraction of orfs with sites within 600 bp upstream = 0.0167041 Motif number 3 AAGCTTTGACCAACTGCTTTGACTCCGCCT 1 49 0 CAACTGCTTT 0.93727 -67 AGATAAATAACAACAACTTAAGCATT 1 100 1 CAACAACTTA 0.967537 -16 TAGGGCGTTTTAAAAACTTTATTT 2 148 1 TAAAAACTTT 0.786357 -14 CCCTGGGATTCAGCAACATAAAGGGA 3 225 1 CAGCAACATA 0.885976 -16 AATTTACGGGCAGATGCTTACGCCATCATT 5 122 1 CAGATGCTTA 0.835839 -120 ACCCTAGACCCAACAACATAACCGCTATCA 5 214 1 CAACAACATA 0.904031 -28 ATCAATTTACCAGAAACTTTGTGGGTAAAA 6 26 0 CAGAAACTTT 0.939094 -171 AATTGATTGCCAAAAGCTTTTCCCTGCTTT 6 49 1 CAAAAGCTTT 0.960105 -148 GATAACAAATTAACAGCTTTTACTGTACCT 6 142 0 TAACAGCTTT 0.903012 -55 ********** Masking position 2 Map Score: 6.6353 Number of sites scoring better than the average of aligned sites = 634 Number in coding regions = 548 Number in noncoding regions = 86 Number of orfs with sites within 600 bp upstream = 89 Fraction of orfs with sites within 600 bp upstream = 0.0142949 Motif number 4 TCAGAGGCGGAGTCAAAGCAGTTGGTCAAA 1 45 1 AGTCAAAGCA 0.833579 -71 CAAAGCAGTTGGTCAAAGCTTCGTTCAGTA 1 58 1 GGTCAAAGCT 0.98495 -58 TTCTTAATCAGGAAAAAACTCTGGATTTAG 2 69 0 GGAAAAAACT 0.927551 -93 TAAGCTTACCAGACAAAGCCAAAAAAATAA 2 107 0 AGACAAAGCC 0.912966 -55 CCGGCAGTGGAGAAAAATCTGGAAAGA 4 8 0 AGAAAAATCT 0.683798 -75 GGTTAGGGAAGGCAAAAGCCACCACCAATA 5 32 1 GGCAAAAGCC 0.91797 -210 AGCAGGAATCGGTCAACACTGACCATTAAA 5 164 0 GGTCAACACT 0.817399 -78 GAAACTTTGTGGGTAAAACTTTCTTTACTC 6 14 0 GGGTAAAACT 0.773191 -183 ATAAAAAGCAGGGAAAAGCTTTTGGCAATC 6 53 0 GGGAAAAGCT 0.976838 -144 GGTGAGGTACAGTAAAAGCTGTTAATTTGT 6 138 1 AGTAAAAGCT 0.955944 -59 ********** Masking position 5 Map Score: 6.43406 Number of sites scoring better than the average of aligned sites = 1367 Number in coding regions = 1202 Number in noncoding regions = 165 Number of orfs with sites within 600 bp upstream = 177 Fraction of orfs with sites within 600 bp upstream = 0.0284292 Motif number 5 AACGAAACTGTTACAAACCCGAGGTG 1 6 0 TTACAACCCG 0.955201 -110 TGAACTAGTGTAACGAAACTGTTACAAACCC 1 17 0 TAACAAACTG 0.843403 -99 CTGGATTTAGTAACTCATCCGCAGAAAACTG 2 48 0 TAACCATCCG 0.958421 -114 TCTTTAGGGTTACGACACCCGAAAAAATACC 4 44 0 TACGCACCCG 0.936937 -39 GGCTTTTGCCTTCCCTAACCGACCCATTGCT 5 21 0 TTCCTAACCG 0.923535 -221 CTAGACCCAACAACATAACCGCTATCAAGAT 5 217 1 CAACTAACCG 0.899397 -25 GCTTTTACTGTACCTCACCCGATGTGCCCAA 6 126 0 TACCCACCCG 0.988983 -71 TTTATTTAACCAAATCGTTCTTTCTTT 7 7 1 TAACAAATCG 0.843403 -24 **** ****** Masking position 7 Map Score: 1.97084 Number of sites scoring better than the average of aligned sites = 520 Number in coding regions = 482 Number in noncoding regions = 38 Number of orfs with sites within 600 bp upstream = 44 Fraction of orfs with sites within 600 bp upstream = 0.00706714 Motif number 6 AATAACAACAACTTAAGCATT 1 105 1 ACTTAAGCAT 0.887121 -11 TAACCAGATAGCGTAAGCTTACCAGACAAA 2 120 0 GCGTAAGCTT 0.96562 -42 TGAAAAGTAGGGTGAAGAATGGAAAATGGT 3 39 0 GGTGAAGAAT 0.853466 -202 AGAAATGATGGCGTAAGCATCTGCCCGTAA 5 125 0 GCGTAAGCAT 0.989294 -117 AGGGGAAGCATAGCGCCGCAG 6 186 0 GGGGAAGCAT 0.985608 -11 ********** Masking position 5 Map Score: 0.937681 Number of sites scoring better than the average of aligned sites = 107 Number in coding regions = 95 Number in noncoding regions = 12 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 7 ********** No masking Map Score: -1.09891e-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 8 ********** No masking Map Score: -1.09891e-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: -1.09891e-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