AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i103_Ferrous_Iron_Transporter_synecho_reg_300.orf -o103_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 RCY32435 100 Synechocystis #2 RCY33367 108 Synechocystis #3 RCY00914 273 Synechocystis #4 RCY13728 55 Synechocystis Motif number 1 CCCCATGATAGCTTGGGTCTTTGATTAACAA 1 33 0 GCTGGGTCTT 0.919052 -68 TATCATGGGGGTTGGAGTTTTTCCCCTCTGC 1 54 1 GTGGAGTTTT 0.950884 -47 TTTCCCCTCTGCTGGAATTTTTTTAGTTTAA 1 73 1 GCGGAATTTT 0.995841 -28 TACCGCCCTTGGGGGAGTTTTCCGGTTTTCT 2 59 0 GGGGAGTTTT 0.966323 -50 TCCCCCAAGGGCGGTAAATTTTGGGGTGTAT 2 74 1 GCGTAAATTT 0.929104 -35 CTCCCAGCAGGGATTTTCTTTAACTCG 3 7 1 GCGGGATTTT 0.997388 -267 CCAAATAGTTGCGGAGATTTTTGGCGATCTA 3 75 1 GCGAGATTTT 0.977083 -199 TCTGTCTTGGGCAGGACTTTTCCATAGGTTG 3 123 1 GCGGACTTTT 0.986607 -151 TCCATAGGTTGCATGGAATTTAATCAATGGT 3 143 1 GCTGGAATTT 0.948313 -131 CACAATTATTCCAGTGATTTTTGATATTTAT 3 187 1 CCGTGATTTT 0.906848 -87 ** ******** Masking position 10 Map Score: 14.3852 Number of sites scoring better than the average of aligned sites = 1451 Number in coding regions = 1274 Number in noncoding regions = 177 Number of orfs with sites within 600 bp upstream = 174 Fraction of orfs with sites within 600 bp upstream = 0.0279473 Motif number 2 AAAACTCCAACCCCCATGATAGCTTGGGTC 1 45 0 CCCCCATGAT 0.817349 -56 TGGAGTTTTTCCCCTCTGCTGGAATTTTTT 1 66 1 CCCCTCTGCT 0.942421 -35 CCCCCTATCTGTGCAATGTC 2 1 1 CCCCCTATCT 0.979227 -108 CCGGAAAACTCCCCCAAGGGCGGTAAATTT 2 65 1 CCCCCAAGGG 0.959815 -44 CTCCCAGCAGGGATTTTCTTTA 3 3 1 CCCAGCAGGG 0.604619 -271 GGACCTAAGCCCCGGTTTGTTAAATCATTA 3 46 0 CCCGGTTTGT 0.801356 -228 CGCCAAAAATCTCCGCAACTATTTGGGACC 3 71 0 CTCCGCAACT 0.80591 -203 CAGCAATGCTCCCAGCATCTGTCTTGGGCA 3 106 1 CCCAGCATCT 0.969602 -168 TTGGCAATGACTCACCATCTCCGCC 4 6 0 CTCACCATCT 0.872329 -50 ACTGGACTGACCCCCTTTGGCAATGACTCA 4 22 0 CCCCCTTTGG 0.948706 -34 ********** Masking position 3 Map Score: 5.27725 Number of sites scoring better than the average of aligned sites = 4523 Number in coding regions = 3992 Number in noncoding regions = 531 Number of orfs with sites within 600 bp upstream = 439 Fraction of orfs with sites within 600 bp upstream = 0.0705108 Motif number 3 GGGGTGTATTACTATGGCTTAGT 2 96 1 ACTATGGCTT 0.939497 -13 CTCCCAGCAGGGATTTTCTTTAACT 3 6 1 AGCAGGGATT 0.98092 -268 CTCGGTCAACACTAATGATTTAACAAACCG 3 34 1 ACTAATGATT 0.752211 -240 GATTTAACAAACCGGGGCTTAGGTCCCAAA 3 50 1 ACCGGGGCTT 0.956093 -224 AGATGCTGGGAGCATTGCTGTAGATCGCCA 3 96 0 AGCATTGCTG 0.874805 -178 TTCCATAGGTTGCATGGAATTTAATCAATG 3 142 1 TGCATGGAAT 0.736353 -132 ATAATCACTTACCATTGATTAAATTCCATG 3 154 0 ACCATTGATT 0.977612 -120 TCACAATTATTCCAGTGATTTTTGATATTT 3 186 1 TCCAGTGATT 0.95075 -88 ********** Masking position 7 Map Score: 3.09728 Number of sites scoring better than the average of aligned sites = 2087 Number in coding regions = 1903 Number in noncoding regions = 184 Number of orfs with sites within 600 bp upstream = 191 Fraction of orfs with sites within 600 bp upstream = 0.0306778 Motif number 4 TTAGGTCCCAAATAGTTGCGGAGATTTTTG 3 68 1 AATAGTTGCG 0.992247 -206 AAATCACTGGAATAATTGTGAGTATAATCA 3 177 0 AATAATTGTG 0.968458 -97 ATGCTAACTTAATAGTTGAGAATTATTTGC 3 230 1 AATAGTTGAG 0.988556 -44 ********** Masking position 4 Map Score: 0.89238 Number of sites scoring better than the average of aligned sites = 21 Number in coding regions = 17 Number in noncoding regions = 4 Number of orfs with sites within 600 bp upstream = 3 Fraction of orfs with sites within 600 bp upstream = 0.00048185 Motif number 5 GCTATCATGGGGGTTGGAGTTTTTCCCCTCT 1 52 1 GGGTGGAGTT 0.9852 -49 GATTGTACGAGGATCGGACATTGCACAGATA 2 16 0 GGATGGACAT 0.983685 -93 CCGGTTTTCTGGGTTGAAAATAGATTGTACG 2 38 0 GGGTGAAAAT 0.938184 -71 ACTCCCCCAAGGGCGGTAAATTTTGGGGTGT 2 72 1 GGGCGTAAAT 0.959783 -37 CATCTGTCTTGGGCAGGACTTTTCCATAGGT 3 121 1 GGGCGGACTT 0.996449 -153 CTGGACGACTGGACTGGACTGACCCCCTTTG 4 33 0 GGACGGACTG 0.971965 -23 **** ****** Masking position 8 Map Score: 3.94611 Number of sites scoring better than the average of aligned sites = 522 Number in coding regions = 471 Number in noncoding regions = 51 Number of orfs with sites within 600 bp upstream = 55 Fraction of orfs with sites within 600 bp upstream = 0.00883392 Motif number 6 ********** No masking Map Score: -8.21797e-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: -8.21797e-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: -8.21797e-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