AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i100_synecho_ctra_300.orf -o100_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 RCY32683 300 Synechocystis #2 RCY15084 118 Synechocystis #3 RCY05328 25 Synechocystis #4 RCY34497 112 Synechocystis #5 RCY24958 106 Synechocystis Motif number 1 ACCCCTTGCCGACAACGGTGGAATTACTCTT 1 133 0 GACAACGTGG 0.913234 -168 AACTCCGTTGGCCCATCCCGGCCCTGAATGG 1 218 1 GCCCATCCGG 0.991429 -83 GGAAAACCCTGCCATTCAGGGCCGGGATGGG 1 229 0 GCCATTCGGG 0.996326 -72 GGAGTAATGCCATCGCCAGAAGCCCAAAG 2 9 1 GCCATCGCAG 0.936639 -110 AAATTTCTTCGCCAATCATAGGGGATCTTTG 2 35 0 GCCAATCTAG 0.977881 -84 ACGAAACCGTGCCAATCAGGGCATTGTAAAC 2 79 0 GCCAATCGGG 0.997705 -40 GCCCCATTTTGCCATACTCGGTTAATGGTCT 4 37 0 GCCATACCGG 0.985279 -76 CACCACATTGGACAATCGGGGATAACGGCT 4 93 1 GACAATCGGG 0.99006 -20 ******* *** Masking position 3 Map Score: 11.4109 Number of sites scoring better than the average of aligned sites = 794 Number in coding regions = 745 Number in noncoding regions = 49 Number of orfs with sites within 600 bp upstream = 65 Fraction of orfs with sites within 600 bp upstream = 0.0104401 Motif number 2 ACTTTAATCAATACTACTGAT 1 2 1 CTTTAATCAA 0.86457 -299 ATCAATGTTTGTTAAATCGTAAAGTAGAGT 1 33 1 GTTAAATCGT 0.979306 -268 GCCGCAAATCCTTAAATCCTTAGAAAGCTT 1 67 1 CTTAAATCCT 0.970139 -234 GGCCAACGGAGTTTAATCCTGATTCTAATG 1 201 0 GTTTAATCCT 0.94569 -100 CAAAATGGGGCTTAATTCGATCGATGTTAA 4 57 1 CTTAATTCGA 0.962067 -56 TTCGATCGATGTTAATTCGACCACCACATT 4 72 1 GTTAATTCGA 0.962067 -41 ********** Masking position 5 Map Score: 3.34241 Number of sites scoring better than the average of aligned sites = 141 Number in coding regions = 118 Number in noncoding regions = 23 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 3 CATAACTCTACTTTACGATTTAACAAACAT 1 37 0 CTTTACGATT 0.805492 -264 TGTGCCTGTACTTTGTCATTAGAATCAGGA 1 185 1 CTTTGTCATT 0.973248 -116 CACGGGAAAACCCTGCCATTCAGGGCCGGG 1 234 0 CCCTGCCATT 0.924973 -67 GGGCTTCTGGCGATGGCATTACTCC 2 6 0 CGATGGCATT 0.855842 -113 CATAGGGGATCTTTGGGCTTCTGGCGATGG 2 20 0 CTTTGGGCTT 0.928386 -99 CTCAAAATTTCTTCGCCAATCATAGGGGAT 2 40 0 CTTCGCCAAT 0.863104 -79 GCATTGTAAACTTTGGCATTCTCAAAATTT 2 60 0 CTTTGGCATT 0.990797 -59 AAAAATCTTTCCTTGGGATCTTGAAGATTT 5 17 1 CCTTGGGATC 0.938868 -90 AAACCTCCATCTTCGTCATCTCAATTTAAT 5 85 1 CTTCGTCATC 0.896824 -22 ********** Masking position 1 Map Score: 4.09833 Number of sites scoring better than the average of aligned sites = 1926 Number in coding regions = 1759 Number in noncoding regions = 167 Number of orfs with sites within 600 bp upstream = 185 Fraction of orfs with sites within 600 bp upstream = 0.0297141 Motif number 4 ACAAACATTGATAATCAGTAGTATTGATTAA 1 14 0 ATATCAGTAG 0.839265 -287 TAGAAAGCTTAATCTACCTAGGGACTACGGA 1 87 1 AACTACCTAG 0.915146 -214 AGAGGGGGAAATTATCCGTAGTCCCTAGGTA 1 101 0 ATATCCGTAG 0.975762 -200 AACACAGAGCAAAACCCCTTGCCGACAACGG 1 146 0 AAACCCCTTG 0.952732 -155 AATCAGGATTAAACTCCGTTGGCCCATCCCG 1 207 1 AACTCCGTTG 0.964953 -94 CATCACTGCCATCCCCCCAAGACCATTAACC 4 18 1 ATCCCCCAAG 0.94922 -95 GAAAATCTTCAAGATCCCAAGGAAAGATTTT 5 18 0 AAATCCCAAG 0.967693 -89 ** ******** Masking position 1 Map Score: 1.90301 Number of sites scoring better than the average of aligned sites = 765 Number in coding regions = 614 Number in noncoding regions = 151 Number of orfs with sites within 600 bp upstream = 153 Fraction of orfs with sites within 600 bp upstream = 0.0245744 Motif number 5 ACCCTGCCATTCAGGGCCGGGATGGGCCAAC 1 224 0 TCAGGCCGGG 0.99123 -77 ACCGTGCCAATCAGGGCATTGTAAACTTTGG 2 74 0 TCAGGCATTG 0.969347 -45 ACGGTTTCGTTCACGGTCTGGTTATCTGC 2 100 1 TCAGGTCTGG 0.994821 -19 CATACTCGGTTAATGGTCTTGGGGGGATGGC 4 25 0 TAAGGTCTTG 0.969621 -88 *** ******* Masking position 3 Map Score: 0.377273 Number of sites scoring better than the average of aligned sites = 126 Number in coding regions = 116 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 6 ********** No masking Map Score: -5.09159e-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 7 ********** No masking Map Score: -5.09159e-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: -5.09159e-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