AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i106_Potassium_Transport_kdp_operon_synecho_reg_300.orf -o106_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 RCY37413 300 Synechocystis #2 RCY34719 56 Synechocystis #3 RCY30401 142 Synechocystis #4 RCY19962 189 Synechocystis #5 RCY15566 231 Synechocystis Motif number 1 AGGGGAAAAGTTGCAGGGGT 1 1 1 AGGGGAAAAG 0.952072 -300 TTGTTTTAGTATGGGCGGGAAGACCCCTGC 1 23 0 ATGGGCGGGA 0.889965 -278 ATCATTTGGTATAGGCAAAAGCTAAACAAC 1 86 1 ATAGGCAAAA 0.921802 -215 CAACTTTAATATAGGTAAGGAAATTGCTTA 1 112 1 ATAGGTAAGG 0.846948 -189 TGGATAAATTAGGGGCGGAATTTGATTTTT 1 218 1 AGGGGCGGAA 0.909376 -83 GTTACTGGCTATGGGAAAAAAATCAAATTC 1 235 0 ATGGGAAAAA 0.907442 -66 AATCGGATTTAAGGGTAGAGAAAAGGTAGC 2 24 0 AAGGGTAGAG 0.77743 -33 AATCTTAGGTAAAAATCGGATTTA 2 43 0 TTAGGTAAAA 0.635721 -14 GAAAAATCTCTGGGGAAAGGGCACAATGGC 3 33 0 TGGGGAAAGG 0.920894 -110 AAGGAGAAAGTAGGGAAAAATCTCTGGGGA 3 47 0 TAGGGAAAAA 0.583963 -96 AAAGATGCTTTTAGGCAAAATATCAGGTTA 4 56 0 TTAGGCAAAA 0.858581 -134 ATTTTTTTGGGGGGGCAGGGGGCGTTTGAA 4 84 0 GGGGGCAGGG 0.96053 -106 GGGAAATTTAGGGGGCAAAATAAAACCTTT 4 147 1 GGGGGCAAAA 0.943462 -43 TTGAAACATCAGAGGCAAGGGT 5 3 0 AGAGGCAAGG 0.96451 -229 GGTGTAGCTCATAGGTAAGGGAAGTTGAAT 5 94 0 ATAGGTAAGG 0.846948 -138 CTAAGTTTTCATGGGCAGGACGATAGGTCG 5 148 0 ATGGGCAGGA 0.971953 -84 GGTGATGGGGCAGAGGGGATTTGCA 5 217 0 TGGGGCAGAG 0.969497 -15 ********** Masking position 5 Map Score: 22.0154 Number of sites scoring better than the average of aligned sites = 4695 Number in coding regions = 4072 Number in noncoding regions = 623 Number of orfs with sites within 600 bp upstream = 596 Fraction of orfs with sites within 600 bp upstream = 0.0957276 Motif number 2 TAAATACCTTTTAAATGCCCTTCTATACCT 1 153 1 TTAAATGCCC 0.964947 -148 GGGAAAAAAATCAAATTCCGCCCCTAATTT 1 223 0 TCAAATTCCG 0.97262 -78 TCTCCTTTACTCCAACTCCGATGTTTTCTA 3 70 1 TCCAACTCCG 0.919294 -73 AAAGCATCTTTCAAACGCCCCCTGCCCCCC 4 75 1 TCAAACGCCC 0.969876 -115 GGATTTTTACTTAACTTCCCCCTAATTTTT 4 108 0 TTAACTTCCC 0.970338 -82 TTTTGCCCCCTAAATTTCCCAATAATGGAG 4 137 0 TAAATTTCCC 0.825982 -53 GAGTTTGCATTCAACTTCCCTTACCTATGA 5 86 1 TCAACTTCCC 0.985415 -146 GGATCAAGGTTTCAATTCCCAACCCGGTGT 5 119 0 TTCAATTCCC 0.964947 -113 ********** Masking position 4 Map Score: 8.86685 Number of sites scoring better than the average of aligned sites = 684 Number in coding regions = 583 Number in noncoding regions = 101 Number of orfs with sites within 600 bp upstream = 84 Fraction of orfs with sites within 600 bp upstream = 0.0134918 Motif number 3 AGGGGCGGAATTTGATTTTTTTCCCATAGCC 1 228 1 TTGATTTTTT 0.819762 -73 TACCCTTAAATCCGATTTTTACCTAAGATT 2 37 1 TCGATTTTTA 0.743529 -20 GTCCGATGACTGCAAGGTTTTGCCATTGTGC 3 12 1 TGAAGGTTTT 0.854935 -131 TGCCCTTTCCCCAGAGATTTTTCCCTACTTT 3 40 1 CCGAGATTTT 0.92928 -103 TTACTCCAACTCCGATGTTTTCTACTTCTAA 3 76 1 TCGATGTTTT 0.970568 -67 GCGGCCAATGACGGAGGTTTTAGAAGTAGAA 3 95 0 ACGAGGTTTT 0.95101 -48 CCATTACTAACCTGATATTTTGCCTAAAAGC 4 49 1 CCGATATTTT 0.861207 -141 TTAACTTCCCCCTAATTTTTTTGGGGGGGCA 4 97 0 CCAATTTTTT 0.857193 -93 AGAGTTTTTTTGAAAGGTTTTATTTTGCCCC 4 158 0 TGAAGGTTTT 0.854935 -32 GGCAAAGTTTTAGAGTTTTTTTGAAAGGTT 4 170 0 TTGAGTTTTT 0.905942 -20 ACCCTTGCCTCTGATGTTTCAAGCAAAAAT 5 10 1 TCGATGTTTC 0.960341 -222 CCATGGTTAGCCAGAGTTTGCATTCAACTTC 5 73 1 CCGAGTTTGC 0.793591 -159 GATAGGTCGGATCAAGGTTTCAATTCCCAAC 5 126 0 ATAAGGTTTC 0.527045 -106 CGTTGAACGGTCTAAGTTTTCATGGGCAGGA 5 158 0 TCAAGTTTTC 0.919002 -74 ** ******** Masking position 5 Map Score: 8.01465 Number of sites scoring better than the average of aligned sites = 1296 Number in coding regions = 1078 Number in noncoding regions = 218 Number of orfs with sites within 600 bp upstream = 217 Fraction of orfs with sites within 600 bp upstream = 0.0348538 Motif number 4 GTCTTCCCGCCCATACTAAAACAAAAAAGATA 1 29 1 CCATCTAAAC 0.879751 -272 TTGGTATAGGCAAAAGCTAAACAACTTTAATA 1 91 1 CAAAGCAAAC 0.716692 -210 CAAAACCTTGCAGTCATCGGACA 3 2 0 CAGTATGGAC 0.745058 -141 GGAAAGGGCACAATGGCAAAACCTTGCAGTCA 3 18 0 CAATGCAAAC 0.910679 -125 TCTAAAACCTCCGTCATTGGCCGCATCATCTT 3 102 1 CCGTATGGCC 0.938 -41 TTTTTATGCTCCATTACTAACCTGATATTTTG 4 39 1 CCATACAACC 0.94535 -151 TAGGCGATCGCCGTGGTGAACCACAAGAATTT 5 37 0 CCGTGTAACC 0.981406 -195 CGCCTACGGGCCATGGTTAGCCAGAGTTTGCA 5 63 1 CCATGTAGCC 0.973532 -169 ATCAAGGTTTCAATTCCCAACCCGGTGTAGCT 5 115 0 CAATCCAACC 0.872785 -117 CTGCCTCGGTCCGTCGTTGAACGGTCTAAGTT 5 171 0 CCGTGTGAAC 0.962897 -61 CAACGACGGACCGAGGCAGGCCCCTCTGCTTT 5 184 1 CCGAGCGGCC 0.938915 -48 **** ** **** Masking position 1 Map Score: 7.06042 Number of sites scoring better than the average of aligned sites = 2284 Number in coding regions = 2085 Number in noncoding regions = 199 Number of orfs with sites within 600 bp upstream = 219 Fraction of orfs with sites within 600 bp upstream = 0.0351751 Motif number 5 AAGACCCCTGCAACTTTTCCCCT 1 3 0 CAACTTTCCC 0.911501 -298 AATTCCGCCCCTAATTTATCCATATCATCAG 1 209 0 CTAATTTTCC 0.960079 -92 AGATTTTTCCCTACTTTCTCCTTTACTCCAA 3 54 1 CTACTTTTCC 0.986144 -89 ATCTTGCTGGCGACTTTATGCAAT 3 129 1 CGACTTTTGC 0.987152 -14 GTGAACCACAAGAATTTTTGCTTGAAACATC 5 23 0 AGAATTTTGC 0.800649 -209 GCAGGCCCCTCTGCTTTCTGCAAATCCCCTC 5 199 1 CTGCTTTTGC 0.962996 -33 ******* *** Masking position 6 Map Score: 1.1596 Number of sites scoring better than the average of aligned sites = 255 Number in coding regions = 227 Number in noncoding regions = 28 Number of orfs with sites within 600 bp upstream = 35 Fraction of orfs with sites within 600 bp upstream = 0.00562159 Motif number 6 CACAAGGTATAGAAGGGCATTTAAAAGGTA 1 157 0 AGAAGGGCAT 0.92372 -144 AAACAGGATAAGTGGGGGTTACTGGCTATG 1 252 0 AGTGGGGGTT 0.984421 -49 TTGGGGGGGCAGGGGGCGTTTGAAAGATGC 4 78 0 AGGGGGCGTT 0.963652 -112 TGCAGAAAGCAGAGGGGCCTGCCTCGGTCC 5 191 0 AGAGGGGCCT 0.989355 -41 GTGATGGGGCAGAGGGGATTTGCAGAAAGC 5 211 0 AGAGGGGATT 0.983203 -21 ********** Masking position 1 Map Score: 1.2023 Number of sites scoring better than the average of aligned sites = 274 Number in coding regions = 192 Number in noncoding regions = 82 Number of orfs with sites within 600 bp upstream = 71 Fraction of orfs with sites within 600 bp upstream = 0.0114038 Motif number 7 ********** No masking Map Score: -6.79689e-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: -6.79689e-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: -6.79689e-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