AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i130_Transmembrane_Transport_4_synecho_reg_300.orf -o130_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 RCY28537 38 Synechocystis #2 RCY25783 171 Synechocystis #3 RCY43089 119 Synechocystis #4 RCY42092 106 Synechocystis #5 RCY13382 161 Synechocystis #6 RCY44868 300 Synechocystis #7 RCY30726 96 Synechocystis Motif number 1 TTCAACTGTTCAACCTGAGCAACTTGTGCCACGGTC 2 80 0 CACCACAACG 0.995684 -92 CCAAAGTAAGCTACCCATTAAAATAGGATTATCTTG 2 128 1 CTCCTAAAAG 0.891431 -44 TGGATGGGGTCAGCCAGAAAATCTAACCACATCAAA 3 63 0 CACCAAATCA 0.811039 -57 TGGCTGACCCCATCCAATAAAAAGAGTGACTAAATA 3 83 1 CACCTAAAAG 0.97864 -37 TTTAGTAACTCATCCGCAGAAAACTGACAACTTTTA 5 38 0 CACCAAAAAG 0.99315 -124 GTTTTTAAAACGCCCTAACCAGATAGCGTAAGCTTA 5 129 0 CGCCACAGAG 0.958792 -33 CAACCCTTAACACCCGTAACAAACCGTTACTTGATC 6 106 0 CACCACAAAG 0.996499 -195 CTAAATTTTCCACCCGAATCATCACGTCCGACATAG 6 189 0 CACCACATCG 0.988507 -112 CAACCCCTAACACCCGTAACAAACCGTTACCCATTA 7 37 0 CACCACAAAG 0.996499 -60 ** ** * **** * Masking position 11 Map Score: 11.4215 Number of sites scoring better than the average of aligned sites = 251 Number in coding regions = 228 Number in noncoding regions = 23 Number of orfs with sites within 600 bp upstream = 20 Fraction of orfs with sites within 600 bp upstream = 0.00321234 Motif number 2 GTTGAACAATGGCGATCGCCAAAGTAAGCT 2 110 1 GGCGATCGCC 0.499995 -62 AGGCGATCGCCTAGGAATTTG 3 2 1 GGCGATCGCC 0.499995 -118 CATTGTAATGGGCAAATTCCTAGGCGATCG 3 14 0 GGCAAATTCC 0.901743 -106 TAGATTTTCTGGCTGACCCCATCCAATAAA 3 74 1 GGCTGACCCC 0.957462 -46 TCCTCTAGAGGGCGATCGCCAAATGAAAAC 4 11 1 GGCGATCGCC 0.499995 -96 TGTGGTCTATGGCTAATTCCTAAAAGTTGT 5 18 1 GGCTAATTCC 0.973111 -144 GTATGCTGGTGGCTAATGCTTT 7 85 1 GGCTAATGCT 0.939586 -12 ********** Masking position 3 Map Score: 10.8561 Number of sites scoring better than the average of aligned sites = 5914 Number in coding regions = 5358 Number in noncoding regions = 556 Number of orfs with sites within 600 bp upstream = 336 Fraction of orfs with sites within 600 bp upstream = 0.0539672 Motif number 3 CCATGGGCCTTTGGGCGTAGCAAAAATTGA 1 11 1 TTGGGCGTAG 0.918776 -28 AGTTGCCTGAATTGGGTTTGACCGTGGCAC 2 61 1 ATTGGGTTTG 0.582978 -111 GGTAGCTTACTTTGGCGATCGCCATTGTTC 2 113 0 TTTGGCGATC 0.957266 -59 GGGCAAATTCCTAGGCGATCGCCT 3 5 0 CTAGGCGATC 0.916284 -115 TTGGTTTTCATTTGGCGATCGCCCTCTAGA 4 14 0 TTTGGCGATC 0.957266 -93 CAATTATTTTTTTGGCTTTGTCTGGTAAGC 5 104 1 TTTGGCTTTG 0.919072 -58 GCTATCTGGTTAGGGCGTTTTAAAAACTTT 5 138 1 TAGGGCGTTT 0.834775 -24 ACTTCGTAAACTAGGCGATGCTCTTGA 6 8 0 CTAGGCGATG 0.95467 -293 GTGTTAAGGGTTGGGGGTTTGTTGGATAAG 6 129 1 TTGGGGGTTT 0.888034 -172 TCACTAAAGGCGTTGAAACAAGCCC 7 6 1 AAAGGCGTTG 0.851906 -91 GTTACGGGTGTTAGGGGTTGGGGCTTGGTT 7 53 1 TTAGGGGTTG 0.966347 -44 ********** Masking position 5 Map Score: 8.4586 Number of sites scoring better than the average of aligned sites = 2240 Number in coding regions = 2011 Number in noncoding regions = 229 Number of orfs with sites within 600 bp upstream = 238 Fraction of orfs with sites within 600 bp upstream = 0.0382268 Motif number 4 CGCCAAAGTAAGCTACCCATTAAAATAGGA 2 126 1 AGCTACCCAT 0.925551 -46 TCGCCTAGGAATTTGCCCATTACAATGAAA 3 17 1 ATTTGCCCAT 0.781848 -103 AGTAGTATTTAGTCACTCTTTTTATTGGAT 3 94 0 AGTCACTCTT 0.96967 -26 GTTAAAATTAATTCACTCTTCTAAGCTGCA 4 46 1 ATTCACTCTT 0.912877 -61 CTCTGGATTTAGTAACTCATCCGCAGAAAA 5 51 0 AGTAACTCAT 0.904109 -111 TAGTTTACGAAGTCACCGATGATTTCATTC 6 25 1 AGTCACCGAT 0.945648 -276 AATCGAGAACCGACACTCATCAGCTTATCC 6 152 0 CGACACTCAT 0.842241 -149 AGTGATTATCATTCACCCTTCCTTCTGCCT 6 249 0 ATTCACCCTT 0.953674 -52 CGTAACAAACCGTTACCCATTAAGGGCTTG 7 29 0 CGTTACCCAT 0.958122 -68 ********** Masking position 10 Map Score: 5.13458 Number of sites scoring better than the average of aligned sites = 311 Number in coding regions = 250 Number in noncoding regions = 61 Number of orfs with sites within 600 bp upstream = 68 Fraction of orfs with sites within 600 bp upstream = 0.0109219 Motif number 5 CCATGGCAACAAACAAATGGTTTTAT 2 3 1 AGCACAACAA 0.979824 -169 ATCCTTCAATAGCTCATAAAACCATTTGTTTGTT 2 18 0 ACCAAAACCA 0.909982 -154 TTTCTGGCTGACCCCATCCAATAAAAAGAGTGAC 3 79 1 ACCACAATAA 0.93987 -41 AGATAGCGTAAGCTTACCAGACAAAGCCAAAAAA 5 111 0 ACTACGACAA 0.962316 -51 GGTAATGATAACGACAACTGACAACACGAATGAA 6 48 0 AGCACGACAA 0.959576 -253 CCCAACCCTTAACACCCGTAACAAACCGTTACTT 6 110 0 ACCCGAACAA 0.965002 -191 GACACTCATCAGCTTATCCAACAAACCCCCAACC 6 137 0 ACTACAACAA 0.981221 -164 CCCAACCCCTAACACCCGTAACAAACCGTTACCC 7 41 0 ACCCGAACAA 0.965002 -56 ATTAGCCACCAGCATACCCAACCAAGCCCCAACC 7 68 0 ACTACAACCA 0.962324 -29 * * ** * ***** Masking position 11 Map Score: 6.6021 Number of sites scoring better than the average of aligned sites = 381 Number in coding regions = 336 Number in noncoding regions = 45 Number of orfs with sites within 600 bp upstream = 60 Fraction of orfs with sites within 600 bp upstream = 0.00963701 Motif number 6 CCTTTGGGCGTAGCAAAAATTGACCTCAAGT 1 18 1 TAGCAAAATG 0.974229 -21 TTAAATACAGTTGCCTGAATTGGGTTTGACCG 2 53 1 TTGCCTAATG 0.988396 -119 TCTAAAACGGTAGCCATAATGGTGCAGCTTAG 4 66 0 TAGCCAAATG 0.988396 -41 TCATTACCGATAGCATTAATCGTATTTCGGTC 6 74 1 TAGCATAATG 0.981874 -227 CATGTACTTTTTGCCTAAATTTTCCACCCGAA 6 207 0 TTGCCTAATT 0.94227 -94 ****** *** * Masking position 8 Map Score: 1.70373 Number of sites scoring better than the average of aligned sites = 129 Number in coding regions = 114 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911 Motif number 7 CCATGGGCCTTTGGGCGTAGCAAAAATTG 1 10 1 TTTGGGCGTA 0.95638 -29 CGCTATCTGGTTAGGGCGTTTTAAAAACTT 5 137 1 TTAGGGCGTT 0.969287 -25 AACGGTTTGTTACGGGTGTTAAGGGTTGGG 6 114 1 TACGGGTGTT 0.987646 -187 GACGTGATGATTCGGGTGGAAAATTTAGGC 6 197 1 TTCGGGTGGA 0.973328 -104 AACGGTTTGTTACGGGTGTTAGGGGTTGGG 7 45 1 TACGGGTGTT 0.987646 -52 ********** Masking position 1 Map Score: 3.03181 Number of sites scoring better than the average of aligned sites = 27 Number in coding regions = 21 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 8 CTGTATTTAAAATCCTTCAATAGCTCATAA 2 33 0 AATCCTTCAA 0.951397 -139 GCCATTGTTCAACTGTTCAACCTGAGCAAC 2 93 0 AACTGTTCAA 0.926339 -79 AATGAAAACCAATTGTTAAAATTAATTCAC 4 32 1 AATTGTTAAA 0.92077 -75 GTCTATGGCTAATTCCTAAAAGTTGTCAGT 5 22 1 AATTCCTAAA 0.868671 -140 CCAAAAAAATAATTGTTCAATTCTTAATCA 5 89 0 AATTGTTCAA 0.971746 -73 GGTGAATGATAATCACTCAACACGTTTGTA 6 262 1 AATCACTCAA 0.856109 -39 ********** Masking position 7 Map Score: 0.964783 Number of sites scoring better than the average of aligned sites = 212 Number in coding regions = 177 Number in noncoding regions = 35 Number of orfs with sites within 600 bp upstream = 37 Fraction of orfs with sites within 600 bp upstream = 0.00594282 Motif number 9 ACGGTTTGTTACGGGTGTTAAGGGTTGGGG 6 115 1 ACGGGTGTTA 0.993037 -186 ACGTGATGATTCGGGTGGAAAATTTAGGCA 6 198 1 TCGGGTGGAA 0.974716 -103 ACGGTTTGTTACGGGTGTTAGGGGTTGGGG 7 46 1 ACGGGTGTTA 0.993037 -51 ********** Masking position 10 Map Score: 0.541894 Number of sites scoring better than the average of aligned sites = 11 Number in coding regions = 8 Number in noncoding regions = 3 Number of orfs with sites within 600 bp upstream = 3 Fraction of orfs with sites within 600 bp upstream = 0.00048185 Motif number 10 ********** No masking Map Score: 2.54618e-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 11 ********** No masking Map Score: 2.54618e-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: 2.54618e-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