AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i210_trans4_synecho_reg_100.orf -o210_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 RCY46971 127 Synechocystis #2 RCY52311 104 Synechocystis #3 RCY11783 300 Synechocystis #4 RCY30106 164 Synechocystis #5 RCY30644 193 Synechocystis #6 RCY01064 148 Synechocystis #7 RCY25844 58 Synechocystis #8 RCY07234 110 Synechocystis #9 RCY43126 111 Synechocystis Motif number 1 GCCGACCAAAGGTTGATCACCGGGGAAATGGGCCT 1 31 0 GGTGATAGGG 0.973744 -97 GATAGGGTGATTAATGGGGGAGTGGGGAG 2 5 1 GGGGATAGGG 0.996268 -100 TGGGGGAGTGGGGAGATTAGGTCGGATGGCCACGA 2 25 1 GGGGATACGG 0.995103 -80 CCTCAGGGAGTGGTGAGAAGACGGGCTTCTAGTTG 3 19 0 TGGGAGAGGG 0.985561 -282 AGGGCATCCATGGTGATGGATAGGGAAAGGGTTTA 3 62 0 TGGGATGGGG 0.970537 -239 GTAAAGTATTGGGCGATAAATTTCGTTGCAATCTC 4 115 0 GGGGATATCG 0.967871 -50 ACTCCCTAAAGGGCGATCGCCGTGGGCCGGCCTTG 5 92 0 GGGGATGTGG 0.991446 -102 CGCAGTAGATGGGCTAGGAAAACGGGGTAAAATCA 5 132 1 GGGTAGACGG 0.944106 -62 TAGAAGGGGGGGTTGAGAAATTTTGGAGATTTTGT 6 66 0 GGTGAGATTG 0.892075 -83 CTTGCTACACTGGGGAGCGGACTTGGCCAACCCTA 8 37 1 TGGGAGGTTG 0.880122 -74 CTAACCTTGTGGGTGATCAAGTTGAACGAACCATT 8 69 1 GGGGATATGA 0.937012 -42 AGGGGGAGAATTGCTGGAGTTAAGGG 9 96 0 GGGGAGACTG 0.98314 -16 *** *** * *** Masking position 6 Map Score: 17.5764 Number of sites scoring better than the average of aligned sites = 1206 Number in coding regions = 1071 Number in noncoding regions = 135 Number of orfs with sites within 600 bp upstream = 144 Fraction of orfs with sites within 600 bp upstream = 0.0231288 Motif number 2 ATCAACCTTTGGTCGGCCCAGGGTTCGTCA 1 49 1 GGTCGGCCCA 0.981741 -79 ATGGTGTTAGGATCTGCTGAGAAGAAGAAA 1 79 1 GATCTGCTGA 0.820038 -49 AGATTAGGTCGGATGGCCACGAAGATTTGC 2 38 1 GGATGGCCAC 0.921403 -67 TGGCCACGAAGATTTGCTAAACTGGACGCA 2 51 1 GATTTGCTAA 0.777829 -54 GCAACGGTGCGGTCTGCCCCAATC 2 91 1 GGTCTGCCCC 0.978812 -14 AATCTGGAATGATTTGCCCCCCAACGTCTT 4 21 1 GATTTGCCCC 0.933361 -144 CACGTTTGCCGGAGGGCTCCTTTCCATCAC 4 76 0 GGAGGGCTCC 0.834883 -89 GAATTATACTGGCCTGCCAGAGCAGATCAA 5 60 1 GGCCTGCCAG 0.915921 -134 ATCAAGCCAAGGCCGGCCCACGGCGATCGC 5 85 1 GGCCGGCCCA 0.967803 -109 AACCGCAGTAGATGGGCTAGGAAAACGGGG 5 129 1 GATGGGCTAG 0.720164 -65 AGCCTGGACAGATTAGCCCAAACTCCCT 7 9 0 GATTAGCCCA 0.615106 -50 AGACCTGCTCCTCGGCAACAA 7 48 0 GACCTGCTCC 0.888052 -11 ACAAGGTTAGGGTTGGCCAAGTCCGCTCCC 8 49 0 GGTTGGCCAA 0.948264 -62 GGTTATTGGTTGGCTGGAATGGTTCGT 8 94 0 GGTTGGCTGG 0.871199 -17 TCGCCAAAGGGAACTGCTAAGGTTTTTGGT 9 60 1 GAACTGCTAA 0.747652 -52 TGGAGTTAAGGGGCGGCCACCAAAAACCTT 9 78 0 GGGCGGCCAC 0.906136 -34 AGGGGGAGAATTGCTGGAGTTAAGGGG 9 95 0 GAATTGCTGG 0.519051 -17 ********** Masking position 6 Map Score: 15.8729 Number of sites scoring better than the average of aligned sites = 3032 Number in coding regions = 2822 Number in noncoding regions = 210 Number of orfs with sites within 600 bp upstream = 223 Fraction of orfs with sites within 600 bp upstream = 0.0358175 Motif number 3 CTTGTCCACCGGGTGTCGGGTA 1 3 0 GGGTGTCGGG 0.933747 -125 TTGATCACCGGGGAAATGGGCCTTGTCCAC 1 24 0 GGGAAATGGG 0.952684 -104 ACCTTTGGTCGGCCCAGGGTTCGTCAATGG 1 53 1 GGCCCAGGGT 0.792297 -75 TGATTAATGGGGGAGTGGGGAGATTAGGTC 2 18 1 GGGAGTGGGG 0.991065 -87 GGGAGTGGTGAGAAGACGGGCTTCTAGTTG 3 19 0 AGAAGACGGG 0.716014 -282 CAGCGCCTCAGGGAGTGGTGAGAAGACGGG 3 29 0 GGGAGTGGTG 0.927969 -272 GTGATGGATAGGGAAAGGGTTTATGGCAGC 3 55 0 GGGAAAGGGT 0.924419 -246 GGTAAGTTTCGGCAGAGGGCATCCATGGTG 3 82 0 GGCAGAGGGC 0.963429 -219 ATTAGTCAGGGGGACAGTGG 3 291 1 GGGACAGTGG 0.925075 -10 GGAGCCCTCCGGCAAACGTGATATAGTAAG 4 86 1 GGCAAACGTG 0.839503 -79 AGCCAAGGCCGGCCCACGGCGATCGCCCTT 5 89 1 GGCCCACGGC 0.855082 -105 AGATGGGCTAGGAAAACGGGGTAAAATCAG 5 138 1 GGAAAACGGG 0.938339 -56 ATTTTTCGAGGGCGGCGGGTTTAAGACCG 6 10 1 GGGCGGCGGG 0.961868 -139 AGGGAGTTTGGGCTAATCTGT 7 2 1 GGGAGTTTGG 0.74662 -57 ********** Masking position 2 Map Score: 11.6562 Number of sites scoring better than the average of aligned sites = 4142 Number in coding regions = 3707 Number in noncoding regions = 435 Number of orfs with sites within 600 bp upstream = 378 Fraction of orfs with sites within 600 bp upstream = 0.0607131 Motif number 4 CCGGGGAAATGGGCCTTGTCCACCGGGTGT 1 17 0 GGGCCTTGTC 0.934307 -111 GCCCAGGGTTCGTCAATGGTGTTAGGATCT 1 64 1 CGTCAATGGT 0.813225 -64 ATAGGGAAAGGGTTTATGGCAGCGCCTCAG 3 48 0 GGTTTATGGC 0.822455 -253 CTTTTTCCAGGGGCATTGTCCCCAAGAAAG 3 189 0 GGGCATTGTC 0.921736 -112 TGCCCCCCAACGTCTTTGGTTGTCGATAAC 4 35 1 CGTCTTTGGT 0.946086 -130 CGCCGTGGGCCGGCCTTGGCTTGATCTGCT 5 80 0 CGGCCTTGGC 0.987245 -114 GGTAATTGGCAATTAATTAA 6 139 0 GGTAATTGGC 0.928718 -10 CACTGGGGAGCGGACTTGGCCAACCCTAAC 8 44 1 CGGACTTGGC 0.946535 -67 GGTTATTGGTTGGCTGGAAT 8 101 0 GGTTATTGGT 0.872763 -10 TGGCGATCGCCTGCTTTGGCCGTTGAAAAG 9 36 0 CTGCTTTGGC 0.834721 -76 GAACTGCTAAGGTTTTTGGTGGCCGCCCCT 9 70 1 GGTTTTTGGT 0.872763 -42 ********** Masking position 7 Map Score: 9.371 Number of sites scoring better than the average of aligned sites = 3339 Number in coding regions = 3139 Number in noncoding regions = 200 Number of orfs with sites within 600 bp upstream = 206 Fraction of orfs with sites within 600 bp upstream = 0.0330871 Motif number 5 GTTAGCATTAGGAGTAAAACCATTTACTATT 3 130 1 GGAGTAAAAC 0.969117 -171 AAGCTTTCTTGGGGACAATGCCCCTGGAAAA 3 186 1 GGGGACAATC 0.94152 -115 GACAATGCCCCTGGAAAAAGCTAGTGCTCTG 3 199 1 CTGGAAAAAC 0.858032 -102 AAAGACGTTGGGGGGCAAATCATTCCAGATT 4 21 0 GGGGGCAAAC 0.97849 -144 AGTCTCTGTGGAAAAAACCTAGGCTGTA 4 147 0 GTGGAAAAAC 0.969172 -18 CGCCCTTTAGGGAGTAAAACCGCAGTAGATG 5 112 1 GGAGTAAAAC 0.969117 -82 CTAGGAAAACGGGGTAAAATCAGCAAGTATT 5 145 1 GGGGTAAAAC 0.991397 -49 ********* * Masking position 7 Map Score: 5.70366 Number of sites scoring better than the average of aligned sites = 705 Number in coding regions = 620 Number in noncoding regions = 85 Number of orfs with sites within 600 bp upstream = 96 Fraction of orfs with sites within 600 bp upstream = 0.0154192 Motif number 6 GTTTCTTCTTCTCAGCAGATCCTAACACCA 1 80 0 CTCAGCAGAT 0.957328 -48 AAACTGGACGCAGAGTAGATACGCAACGGT 2 69 1 CAGAGTAGAT 0.981696 -36 GAAAGCTTTGCGGAGTCGATAAGGTGAAGC 3 164 0 CGGAGTCGAT 0.97394 -137 ACTGGCCTGCCAGAGCAGATCAAGCCAAGG 5 67 1 CAGAGCAGAT 0.983021 -127 GGAGTAAAACCGCAGTAGATGGGCTAGGAA 5 122 1 CGCAGTAGAT 0.982745 -72 ********** Masking position 4 Map Score: 3.63047 Number of sites scoring better than the average of aligned sites = 44 Number in coding regions = 38 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 7 GATTTGAATCTGGAATGATTTGCCCCCCAA 4 15 1 TGGAATGATT 0.986686 -150 GACCGGATTTTTGAATGATTGCTCAGTATC 6 35 1 TTGAATGATT 0.949115 -114 AGTCCGAGCCTGGACAGATTAGCCCAAACT 7 15 0 TGGACAGATT 0.945067 -44 ATTGGTTGGCTGGAATGGTTCGTTCAACTT 8 87 0 TGGAATGGTT 0.977513 -24 ********** Masking position 4 Map Score: 0.33808 Number of sites scoring better than the average of aligned sites = 71 Number in coding regions = 64 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 8 AAGAAGAAACGTCATAGCACATAAGGAAAA 1 100 1 GTCATAGCAC 0.964079 -28 CTAGAAGCCCGTCTTCTCACCACTCCCTGA 3 22 1 GTCTTCTCAC 0.916503 -279 CTAGTGCTCTGTCTGTGCACCTAGTCTTTG 3 219 1 GTCTGTGCAC 0.986844 -82 TGTGCACCTAGTCTTTGCACTCACATAAAC 3 232 1 GTCTTTGCAC 0.985826 -69 AAACTAATCGGTCAGGGCAAAAAAATCGTT 6 106 0 GTCAGGGCAA 0.894194 -43 ********** Masking position 2 Map Score: 0.505105 Number of sites scoring better than the average of aligned sites = 50 Number in coding regions = 43 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 Motif number 9 ********** No masking Map Score: 2.51122e-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 10 ********** No masking Map Score: 2.51122e-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 11 ********** No masking Map Score: 2.51122e-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