AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i303_mixed18_synecho_reg_300.orf -o303_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 RCY50877 115 Synechocystis #2 RCY07904 223 Synechocystis #3 RCY30559 209 Synechocystis #4 RCY45819 191 Synechocystis #5 RCY19151 224 Synechocystis #6 RCY38476 116 Synechocystis Motif number 1 CCGGTGGCGATCGCCCCTTGGCCAGGGGAATTC 2 103 1 TCGCCCCTCC 0.944114 -121 CCAGGGGAATTCTCCTCCAGTGCTTGCAAGGGA 2 124 1 TCTCCTCAGC 0.991777 -100 TTGATTGTATTTTCCTATATTGCCCCTCCCTTG 2 150 0 TTTCCTAAGC 0.9103 -74 TTACTCGACTTCGGCTCGACGGCGATCGAGTTG 2 180 0 TCGGCTCAGC 0.956673 -44 ATCGTCCCAAAAGCAGTGATTTAA 3 2 1 TCGTCCCAGC 0.958253 -208 TACGCAAAACTTTCCCCAAGGGGTCGTGATGTC 3 117 0 TTTCCCCAGG 0.987683 -93 CGAAGCCAATTTGCCCCCTAGGGTTCGGCAACG 4 62 1 TTGCCCCTGG 0.953097 -130 TTCAACGTCTTTCCCTCCAATGGTAATGGTGAT 4 152 0 TTCCCTCAGG 0.968977 -40 AGGGGATGGTTTTCCCCAATACTTTTAAGGGCT 5 26 0 TTTCCCCACT 0.863095 -199 GGGAAAACCATCCCCTCTTTTGCTGTCCTCAAC 5 43 1 TCCCCTCTGC 0.94946 -182 CCTCTTTTGCTGTCCTCAACGGGGCTTTTTGCC 5 56 1 TGTCCTCAGG 0.929802 -169 GTGCCCTCCCTCGCCCCCAAACTGAGGGCAACT 5 142 0 TCGCCCCACT 0.921527 -83 GGGCACAGATTCCGCTAAACTGGGGGGGATTGC 5 169 1 TCCGCTAAGG 0.612051 -56 CTGGTTTTGCTCTCCCCCATTGGTTTTGACTAC 6 14 1 TCTCCCCAGG 0.993224 -103 TTTTGACTACTTTTCCCGATCGCCGTTGAAGTG 6 37 1 TTTTCCCAGC 0.924941 -80 AGCAATTTCCTAGAATCCAGCAAAAATA 6 99 0 TTTCCTAACC 0.777194 -18 ******* * ** Masking position 1 Map Score: 19.3316 Number of sites scoring better than the average of aligned sites = 3369 Number in coding regions = 3071 Number in noncoding regions = 298 Number of orfs with sites within 600 bp upstream = 289 Fraction of orfs with sites within 600 bp upstream = 0.0464182 Motif number 2 TGGTTCACTACCCATTTTGGGTCATGGGCC 2 39 0 CCCATTTTGG 0.897575 -185 CGGTGGCGATCGCCCCTTGGCCAGGGGAAT 2 104 1 CGCCCCTTGG 0.921735 -120 GGGGAATTCTCCTCCAGTGCTTGCAAGGGA 2 127 1 CCTCCAGTGC 0.959739 -97 CTATATTGCCCCTCCCTTGCAAGCACTGGA 2 139 0 CCTCCCTTGC 0.986847 -85 ATTGTATTTTCCTATATTGCCCCTCCCTTG 2 150 0 CCTATATTGC 0.797588 -74 GACATCACGACCCCTTGGGGAAAGTTTTGC 3 117 1 CCCCTTGGGG 0.702516 -93 AAAAACTTCCCCTACTTTTGAGATACATAC 3 163 0 CCTACTTTTG 0.676065 -47 AGCCAATTTGCCCCCTAGGGTTCGGCAACG 4 65 1 CCCCCTAGGG 0.924756 -127 CGAAAGCGAGCCTTCTTTGGACATCAAGAT 4 119 0 CCTTCTTTGG 0.926139 -73 AACGTCTTTCCCTCCAATGGTAATGGTGAT 4 152 0 CCTCCAATGG 0.960442 -40 AAAACCATCCCCTCTTTTGCTGTCCTCAAC 5 46 1 CCTCTTTTGC 0.963159 -179 GAATCTGTGCCCTCCCTCGCCCCCAAACTG 5 151 0 CCTCCCTCGC 0.933902 -74 GTTTTGCTCTCCCCCATTGGTTTTGACTAC 6 17 1 CCCCCATTGG 0.987901 -100 ********** Masking position 1 Map Score: 14.3192 Number of sites scoring better than the average of aligned sites = 2917 Number in coding regions = 2603 Number in noncoding regions = 314 Number of orfs with sites within 600 bp upstream = 294 Fraction of orfs with sites within 600 bp upstream = 0.0472213 Motif number 3 TTTTAATTTCCGGTGGCGATCGCCCCTTGGC 2 94 1 CGGTGGCGTC 0.960463 -130 GACTTCGGCTCGACGGCGATCGAGTTGATTG 2 176 0 CGACGGCGTC 0.99662 -48 TTCGGCAACGCATCGGCGTTCCCTAGCTTAA 4 85 1 CATCGGCGTC 0.976529 -107 TAAACAAGTTCAACGTCTTTCCCTCCAATGG 4 162 0 CAACGTCTTC 0.927106 -30 TTGCTGTCCTCAACGGGGCTTTTTGCCATGG 5 62 1 CAACGGGGTT 0.949831 -163 GGAGAAACTACAACGGCGGCCATGGCAAAAA 5 81 0 CAACGGCGCC 0.995012 -144 AAAAACACTTCAACGGCGATCGGGAAAAGTA 6 44 0 CAACGGCGTC 0.994058 -73 ******** ** Masking position 5 Map Score: 10.6868 Number of sites scoring better than the average of aligned sites = 684 Number in coding regions = 632 Number in noncoding regions = 52 Number of orfs with sites within 600 bp upstream = 61 Fraction of orfs with sites within 600 bp upstream = 0.00979762 Motif number 4 ATCGTCCCAAAAGCAGTGATTTAA 3 4 1 GTCCCAAAGC 0.948517 -206 ACGCAAAACTTTCCCCAAGGGGTCGTGATGT 3 118 0 TTCCCCAAGG 0.991796 -92 CGCCGATGCGTTGCCGAACCCTAGGGGGCAA 4 72 0 TTGCCGAACC 0.910002 -120 GTAATGGTGATTCCCGAAAGCGAGCCTTCTT 4 132 0 TTCCCGAAGC 0.994942 -60 GGGGATGGTTTTCCCCAATACTTTTAAGGGC 5 27 0 TTCCCCAAAC 0.962283 -198 CTCTTTTGCTGTCCTCAACGGGGCTTTTTGC 5 57 1 GTCCTCAAGG 0.852795 -168 GGTTTTGCTCTCCCCCATTGGTTTTGACTAC 6 16 1 TCCCCCATGG 0.899257 -101 TTGACTACTTTTCCCGATCGCCGTTGAAGTG 6 39 1 TTCCCGATGC 0.984166 -78 ATAATAAAGATTCCCGAATCAAACCGTAAAA 6 71 0 TTCCCGAACA 0.915008 -46 ******** ** Masking position 7 Map Score: 6.81904 Number of sites scoring better than the average of aligned sites = 1001 Number in coding regions = 901 Number in noncoding regions = 100 Number of orfs with sites within 600 bp upstream = 105 Fraction of orfs with sites within 600 bp upstream = 0.0168648 Motif number 5 TATATTGCCCCTCCCTTGCAAGCACTGGAGGAGAATT 2 131 0 CCTCAACCTG 0.9981 -93 GGCTTCCCTACCACCTTTAAATCACTGCTTTTGGGAC 3 14 0 CCTAAACCTG 0.98791 -196 GCAACCACTGCTGACATTCCATTTCTGGCTAGGATTG 3 58 0 CCTCCATCTG 0.983413 -152 CGCTAAATACCCGTCAAGCAACCACTGCTGACATTCC 3 75 0 CCACAACCTG 0.992386 -135 TTACTGTTCACTATTTTTCAACCTCTGTAACTTTTGC 4 12 0 CTTCAACCTG 0.98791 -180 TGGCTTCGGACTGACATCCAATTACTGTTCACTATTT 4 33 0 CCTCAATCTG 0.994359 -159 * * * *** * *** Masking position 11 Map Score: 5.90167 Number of sites scoring better than the average of aligned sites = 69 Number in coding regions = 58 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 6 TTTGACCAACTGCTTTGACTCCGCCTCTGA 1 45 0 TGCTTTGACT 0.957643 -71 TACTGAACGAAGCTTTGACCAACTGCTTTG 1 58 0 AGCTTTGACC 0.93587 -58 AGTGAACCAAATCTTTTACTTGACTAACTT 2 60 1 ATCTTTTACT 0.879784 -164 TCCTGATAGCGGTTTTTACTCGACTTCGGC 2 198 0 GGTTTTTACT 0.933401 -26 TACAGATTGTATCTTTTACGCAAAACTTTC 3 136 0 ATCTTTTACG 0.858502 -74 CTCCCCCATTGGTTTTGACTACTTTTCCCG 6 25 1 GGTTTTGACT 0.944206 -92 GCCGTTGAAGTGTTTTTACGGTTTGATTCG 6 58 1 TGTTTTTACG 0.882563 -59 ********** Masking position 8 Map Score: 2.20333 Number of sites scoring better than the average of aligned sites = 447 Number in coding regions = 390 Number in noncoding regions = 57 Number of orfs with sites within 600 bp upstream = 65 Fraction of orfs with sites within 600 bp upstream = 0.0104401 Motif number 7 CACCTCGGGTTTGTAACAGT 1 1 1 CACCTCGGGT 0.954884 -115 TCCTATATTGCCCCTCCCTTGCAAGCACTG 2 141 0 CCCCTCCCTT 0.929652 -83 GACATCACGACCCCTTGGGGAAAGTTTTGC 3 117 1 CCCCTTGGGG 0.75511 -93 GCCAATTTGCCCCCTAGGGTTCGGCAACGC 4 66 1 CCCCTAGGGT 0.849317 -126 GGAAAACCATCCCCTCTTTTGCTGTCCTCA 5 44 1 CCCCTCTTTT 0.857467 -181 GTTGTAGTTTCTCCCCAGTTAATCACAGCA 5 98 1 CTCCCCAGTT 0.881378 -127 TTGCTGAGTTGCCCTCAGTTTGGGGGCGAG 5 136 1 GCCCTCAGTT 0.95187 -89 CATTGCAATCCCCCCCAGTTTAGCGGAATC 5 176 0 CCCCCCAGTT 0.985189 -49 TTTGCTCTCCCCCATTGGTTTTGACTACTT 6 19 1 CCCATTGGTT 0.862961 -98 ********** Masking position 3 Map Score: 3.48718 Number of sites scoring better than the average of aligned sites = 1526 Number in coding regions = 1382 Number in noncoding regions = 144 Number of orfs with sites within 600 bp upstream = 154 Fraction of orfs with sites within 600 bp upstream = 0.024735 Motif number 8 AATGCTTAAGTTGTTGTTATTTA 1 103 0 GCTTAAGTTG 0.945669 -13 TCATTCTTGGGCTAAAAAAAGCCAGGCCCA 2 15 1 GCTAAAAAAA 0.628687 -209 GAAATTAAAAGATTAAGTTAGTCAAGTAAA 2 74 0 GATTAAGTTA 0.732415 -150 GGCAAAAGTTACAGAGGTTGA 4 2 1 GCAAAAGTTA 0.899847 -190 GCGTTCCCTAGCTTAAATTATCTTGATGTC 4 100 1 GCTTAAATTA 0.914825 -92 CTTAAATAGTGGTTAAGTAAAGAAACATTG 5 201 0 GGTTAAGTAA 0.901942 -24 ATTGCTTAAATAGTGGTTAAGTA 5 212 0 GCTTAAATAG 0.91607 -13 ACGGCGATCGGGAAAAGTAGTCAAAACCAA 6 33 0 GGAAAAGTAG 0.763611 -84 CTAGAATCCAGCAAAAATAATAAAGATTCC 6 88 0 GCAAAAATAA 0.849263 -29 ********** Masking position 5 Map Score: 2.77992 Number of sites scoring better than the average of aligned sites = 444 Number in coding regions = 350 Number in noncoding regions = 94 Number of orfs with sites within 600 bp upstream = 101 Fraction of orfs with sites within 600 bp upstream = 0.0162223 Motif number 9 GTAACGAAACTGTTACAAACCCGAGGTG 1 9 0 TGTTACAAAC 0.857038 -107 CAATATAGGAAAATACAATCAACTCGATCG 2 161 1 AAATACAATC 0.896665 -63 TTTGCGTAAAAGATACAATCTGTATGTATC 3 142 1 AGATACAATC 0.978395 -68 CCTACTTTTGAGATACATACAGATTGTATC 3 153 0 AGATACATAC 0.978395 -57 TTTCTTGTCAAGATACATACTGTCTGA 3 193 1 AGATACATAC 0.978395 -17 ********** Masking position 5 Map Score: 2.40221 Number of sites scoring better than the average of aligned sites = 35 Number in coding regions = 25 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 10 ACCCATTTTGGGTCATGGGCCTGGCTTTTT 2 30 0 GGTCATGGGC 0.686498 -194 ATCGCCCCTTGGCCAGGGGAATTCTCCTCC 2 112 1 GGCCAGGGGA 0.926335 -112 TTAAGGGCTGGGCCCTGAGAACAC 5 5 0 GGCCCTGAGA 0.959191 -220 CTACAACGGCGGCCATGGCAAAAAGCCCCG 5 75 0 GGCCATGGCA 0.568381 -150 ********** Masking position 4 Map Score: 0.577637 Number of sites scoring better than the average of aligned sites = 516 Number in coding regions = 467 Number in noncoding regions = 49 Number of orfs with sites within 600 bp upstream = 58 Fraction of orfs with sites within 600 bp upstream = 0.00931577 Motif number 11 ********** No masking Map Score: -1.94446e-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 12 ********** No masking Map Score: -1.94446e-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 13 ********** No masking Map Score: -1.94446e-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