AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i197_replication1_synecho_reg_100.orf -o197_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 RCY05296 114 Synechocystis #2 RCY44021 99 Synechocystis #3 RCY07858 90 Synechocystis #4 RCY25948 41 Synechocystis #5 RCY21190 133 Synechocystis #6 RCY14244 51 Synechocystis #7 RCY52400 142 Synechocystis Motif number 1 CCCTAAAGTTCCGTCGGCTAAACCGCCCGAT 1 27 1 CCGTCGGTAA 0.774288 -88 GTTTGGTGGCGCTTTGGTCAATTGGGATCAA 1 65 1 GCTTTGGCAA 0.986891 -50 GTTCCGGAGCACTTCGGTCCAGTTGATCCCA 1 87 0 ACTTCGGCCA 0.95278 -28 GGACCGAAGTGCTCCGGAACACTCATA 1 98 1 GCTCCGGACA 0.978052 -17 ATTGAGGGCAACGCTGGCCCCTAC 2 4 0 ACGCTGGCCC 0.940636 -96 TCAATTTTTACCATTGGTCAAGTCTTTTCCT 2 30 1 CCATTGGCAA 0.952075 -70 ATACGCACGGGAAAAGGGGGGAAAG 2 85 0 GCACGGGAAA 0.85406 -15 GCCAATGTTAGCATTGGAAAGGCTGATTCTC 3 37 0 GCATTGGAAG 0.792046 -54 GGGAACCTGTGCGCTCGTCAATTCGCGGCCA 3 64 0 GCGCTCGCAA 0.906058 -27 GCCGCTGGGAACCTGTGCGCTC 3 79 0 CCGCTGGAAC 0.936513 -12 CATTCCCCACCCCCTGGAACAGTAACATTTT 5 71 1 CCCCTGGACA 0.919452 -63 GGACTAAATTACGTCGGGAAAAGAACCCCGT 5 112 0 ACGTCGGAAA 0.944137 -22 ATAGGCAATAACTGTGGGAAACTGAGAAAAA 7 54 0 ACTGTGGAAA 0.8494 -89 TGCCCCCTCAGCTCTGGGACAAATACCTGGT 7 85 1 GCTCTGGACA 0.986622 -58 AAGCCCAGAGACTTTGGACAATATGACCAGG 7 110 0 ACTTTGGCAA 0.971492 -33 AAGTCTCTGGGCTTTGGGCCTTTTGC 7 127 1 GCTTTGGCCT 0.88698 -16 ******* *** Masking position 7 Map Score: 15.6882 Number of sites scoring better than the average of aligned sites = 3888 Number in coding regions = 3577 Number in noncoding regions = 311 Number of orfs with sites within 600 bp upstream = 314 Fraction of orfs with sites within 600 bp upstream = 0.0504337 Motif number 2 CCACCAAACTTGGGAGATCGGGCGGTTTAGCCG 1 41 0 TGGGATCGGC 0.923653 -74 TTGGTCAATTGGGATCAACTGGACCGAAGTGCT 1 78 1 GGGAAACGGA 0.9924 -37 GCAAAGTGGGGAGGAGAATCAGCCTTTCCAATG 3 24 1 GAGGAATAGC 0.947217 -67 AACTAAACGGGGCAAAAATTGGCAATATTTTCT 4 14 0 GGCAAATGGC 0.975346 -28 CCAGTAACAGGGCGAGAACAGGAAGCATCATCC 5 26 1 GGCGAACGGA 0.991827 -108 GTTCCAGGGGGTGGGGAATGGGAACTCCATTGG 5 58 0 GTGGAATGGA 0.963377 -76 TTAGAGGGTGGGGGTTAACCGGCTAGGGATCTG 7 20 1 GGGGAACGGC 0.998719 -123 GTGGGAAACTGAGAAAAACCAGATCCCTAGCCG 7 39 0 GAGAAACAGA 0.854682 -104 CCAGAGCTGAGGGGGCAATAGGCAATAACTGTG 7 69 0 GGGGAATGGC 0.997496 -74 **** *** *** Masking position 7 Map Score: 13.5901 Number of sites scoring better than the average of aligned sites = 1202 Number in coding regions = 1088 Number in noncoding regions = 114 Number of orfs with sites within 600 bp upstream = 131 Fraction of orfs with sites within 600 bp upstream = 0.0210408 Motif number 3 GGGAAAGAAACCCTACCATTTTAGGGAGGTT 2 61 0 CCCTACCATT 0.967101 -39 AGGGTTTCTTTCCCCCCTTTTCCCGTGCGTA 2 78 1 TCCCCCCTTT 0.918978 -22 AGGCTGATTCTCCTCCCCACTTTGCCGGGTA 3 18 0 TCCTCCCCCT 0.988347 -73 AGTTCCCATTCCCCACCCCCTGGAACAGTAA 5 65 1 CCCCACCCCT 0.998123 -69 GCCGGTTAACCCCCACCCTCTAACATTTAAC 7 12 0 CCCCACCCCT 0.998123 -131 AAAACCAGATCCCTAGCCGGTTAACCCCCAC 7 27 0 CCCTAGCCGT 0.943706 -116 TTGCCTATTGCCCCCTCAGCTCTGGGACAAA 7 77 1 CCCCCTCACT 0.971071 -66 ******** ** Masking position 11 Map Score: 7.74629 Number of sites scoring better than the average of aligned sites = 717 Number in coding regions = 652 Number in noncoding regions = 65 Number of orfs with sites within 600 bp upstream = 74 Fraction of orfs with sites within 600 bp upstream = 0.0118856 Motif number 4 TCAAGTCTTTTCCTAACCTCCCTAAAATGG 2 47 1 TCCTAACCTC 0.972468 -53 GGGAAAGAAACCCTACCATTTTAGGGAGGT 2 62 0 CCCTACCATT 0.918605 -38 AGGGTTTCTTTCCCCCCTTTTCCCGTGCGT 2 78 1 TCCCCCCTTT 0.888499 -22 AGGCTGATTCTCCTCCCCACTTTGCCGGGT 3 19 0 TCCTCCCCAC 0.974731 -72 AGTTCCCATTCCCCACCCCCTGGAACAGTA 5 65 1 CCCCACCCCC 0.991602 -69 GCCGGTTAACCCCCACCCTCTAACATTTAA 7 13 0 CCCCACCCTC 0.996913 -130 GCCTATTGCCCCCTCAGCTCTGGGACAAAT 7 79 1 CCCTCAGCTC 0.944246 -64 ********** Masking position 3 Map Score: 5.1726 Number of sites scoring better than the average of aligned sites = 1408 Number in coding regions = 1242 Number in noncoding regions = 166 Number of orfs with sites within 600 bp upstream = 166 Fraction of orfs with sites within 600 bp upstream = 0.0266624 Motif number 5 CGGTCCAGTTGATCCCAATTGACCAAAGCGC 1 73 0 GATCCCATTG 0.99077 -42 TGGGGAATGGGAACTCCATTGGGATGATGCT 5 49 0 GAACTCATTG 0.994278 -85 GTCGGGAAAAGAACCCCGTTGATTCTACCAA 5 100 0 GAACCCGTTG 0.9921 -34 CTTAGTAGGAAAACTCTATTGGTGAGCGTGA 6 16 0 AAACTCATTG 0.977865 -36 ****** **** Masking position 9 Map Score: 2.16318 Number of sites scoring better than the average of aligned sites = 32 Number in coding regions = 25 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 4 Fraction of orfs with sites within 600 bp upstream = 0.000642467 Motif number 6 AGGGAAATTATGGCAAGGAA 1 1 0 TGGCAAGGAA 0.952116 -114 CCTCCCCACTTTGCCGGGTACAGTTTT 3 8 0 TTGCCGGGTA 0.892046 -83 ATGCTAACATTGGCCGCGAATTGACGAGCG 3 54 1 TGGCCGCGAA 0.984591 -37 ACCAGATCCCTAGCCGGTTAACCCCCACCC 7 25 0 TAGCCGGTTA 0.666833 -118 TTGGACAATATGACCAGGTATTTGTCCCAG 7 98 0 TGACCAGGTA 0.963132 -45 ********** Masking position 1 Map Score: 1.17637 Number of sites scoring better than the average of aligned sites = 639 Number in coding regions = 598 Number in noncoding regions = 41 Number of orfs with sites within 600 bp upstream = 51 Fraction of orfs with sites within 600 bp upstream = 0.00819146 Motif number 7 ********** No masking Map Score: -4.16788e-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: -4.16788e-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 9 ********** No masking Map Score: -4.16788e-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