AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/alignace/lib/ORF_synecho.txt -z/skink1/amcguire/genomes/synecho.fna -imalT_synecho_opreg_300.orf -g0.48 -x5 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 = 0 Input sequences: #1 malQ 97 4-alpha-glucanotransferase #2 1651874 49 hypothetical protein #3 sulA 76 cell division inhibitor #4 malK 68 cytoplasmic membrane protein for maltose uptake #5 glgP 300 glycogen phosphorylase #6 1652666 300 glycogen phosphorylase #7 1652991 262 hypothetical protein #8 drgA 78 DrgA #9 aspS 129 aspartyl-tRNA synthetase #10 1652994 25 hypothetical protein #11 guaB 102 IMP dehydrogenase subunit #12 lacG 126 lactose transport system permease protein LacG #13 1653828 228 hypothetical protein #14 stpA 38 salt tolerance protein A #15 msiK 137 ATP binding protein responsible for multiple sugar import Motif number 1 TGGGTAGATCCTCTGGGGAACATTGACAGCA 3 10 1 CCTGGGGAAC 0.969783 -67 GACCCTGGGGGGAGTAGGAGTAAGT 3 62 0 CCGGGGGAGT 0.938763 -15 TAAGGGGTCACCGTTTGGGATAGAACCTGTAT 5 160 1 CCTTGGGATA 0.86034 -141 TCCATGATAACCACTGGCGATCGCCGCTTCTG 6 46 0 CCTGGCGATC 0.992147 -255 AACTAATCTGCCCTTTGCCATCAATTTCTAAT 6 97 0 CCTTGCCATC 0.887307 -204 TACACCTACCCCATCGGGCATTGTTAAGGACA 6 147 0 CCCGGGCATT 0.965465 -154 AAACTGGTTTTCGGTGGCGATCGGGCCTAGAA 7 118 0 TCTGGCGATC 0.941122 -145 AGGGGGGATCCCAATGGGCTTTAAACTGGTTT 7 140 0 CCTGGGCTTT 0.806888 -123 GGCTCATGGCCCAGGGGGGATCCCAATGGGCT 7 152 0 CCGGGGGATC 0.994957 -111 TAACCCTAATCCAGTGGGGATCAGAGC 11 6 0 CCTGGGGATC 0.996404 -97 CAACTATCAACCCCCTGGGATTATTCTGGGGG 12 23 1 CCCTGGGATT 0.946748 -104 CTGGGATTATTCTGGGGGGATTTTTATTGGGT 12 37 1 TCGGGGGATT 0.918691 -90 CATTCATTTTCCCTCGGCGATCGCCCTGTCTA 13 21 0 CCCGGCGATC 0.989005 -208 ** ******** Masking position 2 Map Score: 19.3346 Number of sites scoring better than the average of aligned sites = 1926 Number in coding regions = 1731 Number in noncoding regions = 195 Number of orfs with sites within 600 bp upstream = 225 Fraction of orfs with sites within 600 bp upstream = 0.0361388 Motif number 2 CCAATCCCCAAAATAGCCCC 4 1 1 CCAATCCCCA 0.966699 -68 CGTCAAGAGGCTGATCGCCGTTCTCAG 5 8 0 CTGATCGCCG 0.9912 -293 ATAACCACTGGCGATCGCCGCTTCTGCTTC 6 42 0 GCGATCGCCG 0.986499 -259 CCATCAATTTCTAATCACCGTAGTGAACAG 6 82 0 CTAATCACCG 0.9016 -219 GTACAGAAGCCCGATCGCCTTCTATAACCA 6 256 0 CCGATCGCCT 0.975472 -45 GGTTCTAGGCCCGATCGCCACCGAAAACCA 7 116 1 CCGATCGCCA 0.992415 -147 GCTCTGATCCCCACTGGATTAGG 11 4 1 CTGATCCCCA 0.953019 -99 TCTAGACAGGGCGATCGCCGAGGGAAAATG 13 19 1 GCGATCGCCG 0.986499 -210 GACCACCACCCCATTCTCCATTCATTTTCC 13 41 0 CCATTCTCCA 0.869661 -188 GGTGGTGAAGCCATTCTCCGTGGTCGAATT 15 15 1 CCATTCTCCG 0.939886 -123 CATTAAGTACCTAATCTCCGGGTAGTATGA 15 52 1 CTAATCTCCG 0.958594 -86 ********** Masking position 5 Map Score: 18.5919 Number of sites scoring better than the average of aligned sites = 3017 Number in coding regions = 2781 Number in noncoding regions = 236 Number of orfs with sites within 600 bp upstream = 267 Fraction of orfs with sites within 600 bp upstream = 0.0428847 Motif number 3 CTCAACGATCAACACTGTCCCTGTTTTAATG 2 15 0 AACACTTCCC 0.882685 -35 TTAACTTACTCCTACTCCCCCCAGGGTC 3 59 1 CCTACTCCCC 0.982149 -18 CCAATCCCCAAAATAGCCCCAATGAAGAT 4 9 1 CAAAATGCCC 0.626399 -60 GATTTAGCCTACTTATTCCCCATTTTAAGGG 5 135 1 ACTTATCCCC 0.870752 -166 AACTGTCCTTAACAATGCCCGATGGGGTAGG 6 144 1 AACAATCCCG 0.826404 -157 CCAAGACTCTACACCTACCCCATCGGGCATT 6 157 0 ACACCTCCCC 0.883227 -144 TGGGGAATGAACAACCCTCCCATCTTATCGG 7 224 0 ACAACCTCCC 0.727622 -39 TTTAACGCTTACTTCTCACCCCTAACTCCTG 9 75 1 ACTTCTACCC 0.771821 -55 GTCAGCACAGCCTAATAACCCTAATCCAGTG 11 22 0 CCTAATACCC 0.842278 -81 TAAACCCAATAAAAATCCCCCCAGAATAATC 12 41 0 AAAAATCCCC 0.887376 -86 GGCCTTGTTGACCAATGCCCCACCACTACCC 12 89 1 ACCAATCCCC 0.977457 -38 CCAATGCCCCACCACTACCCGCTATTACCCC 12 100 1 ACCACTCCCG 0.969067 -27 AGTCGCTACGACCACCACCCCATTCTCCATT 13 49 0 ACCACCCCCC 0.958361 -180 GACATCCTAGCCTAATTTCCCAGACTTTAAG 13 151 0 CCTAATTCCC 0.842278 -78 TCTGAAAACTCCCTCTGGCCCGCGACAAAGA 13 194 1 CCCTCTGCCC 0.839197 -35 TAACCCCGTTCATACTACCCGGAGATTAGGT 15 60 0 CATACTCCCG 0.857968 -78 TCAAACGGTTAAAACTAACCGGTGTAACCCC 15 84 0 AAAACTACCG 0.556867 -54 ****** **** Masking position 9 Map Score: 12.8423 Number of sites scoring better than the average of aligned sites = 3587 Number in coding regions = 3254 Number in noncoding regions = 333 Number of orfs with sites within 600 bp upstream = 336 Fraction of orfs with sites within 600 bp upstream = 0.0539672 Motif number 4 GTAAAGTCATTTCTTGGCCCGTTGGATATG 1 42 1 TTCTTGGCCC 0.901967 -56 AGATTTTCCTTCCTAGGCTTGC 1 86 1 TCCTAGGCTT 0.792299 -12 TCTTTGTTCCTTCTGGACTTGGACTAGCTC 5 56 1 TTCTGGACTT 0.95264 -245 TAATGCTGTGCCTTTCCCTTATA 5 288 0 TGCTGTGCCT 0.88507 -13 CCGCTTCTGCTTCTAAGCTCAGCTTTTAGG 6 25 0 TTCTAAGCTC 0.765778 -276 GCGATCGGGCTTCTGTACTTTGAGCTAGCG 6 268 1 TTCTGTACTT 0.776648 -33 CTGGCCAAAGTGCTGGACCTTAACTAAGCG 7 87 0 TGCTGGACCT 0.95275 -176 TTTGGCCAGGTTCTAGGCCCGATCGCCACC 7 108 1 TTCTAGGCCC 0.968021 -155 TGGCCAATTTTTCTGGGCTCATGGCCCAGG 7 169 0 TTCTGGGCTC 0.980944 -94 AGTGGCTAATTGCTGAACCCGCTCCGACTC 9 42 1 TGCTGAACCC 0.801506 -88 TGTTACCCTGGTCTGGGCCTTGTTGACCAA 12 74 1 GTCTGGGCCT 0.961014 -53 CGATCGCCCTGTCTAGACTTCCACC 13 6 0 GTCTAGACTT 0.719198 -223 ********** Masking position 4 Map Score: 8.83725 Number of sites scoring better than the average of aligned sites = 1018 Number in coding regions = 935 Number in noncoding regions = 83 Number of orfs with sites within 600 bp upstream = 79 Fraction of orfs with sites within 600 bp upstream = 0.0126887 Motif number 5 CAGCGGATGAAGTGTGGCAACTCCTGGGAGAGCTA 5 80 0 ATGGCAATCT 0.984303 -221 ATGGGGAATAAGTAGGCTAAATCCTAAGTAATTAT 5 123 0 ATGCTAATCT 0.914408 -178 ACCATTAGTTACTCCGGCAATCCAGGCTCACAACA 6 222 0 ATGGCAACCG 0.989183 -79 TTTTTGAAAAACTTTGGCAAACCAGGTTATTCCCA 7 48 1 ATGGCAACCG 0.989183 -215 AGCCCAGAAAAATTGGCCAATTCTTCTTCCGGGTT 7 180 1 ATGCCAATCT 0.988004 -83 TCTTATCGGTAGTGGGCCAACCCGGAAGAAGAATT 7 198 0 ATGCCAACCG 0.991743 -65 TTCCCCAAACAATCCGCCAAATCCT 7 248 1 ATGCCAATCT 0.988004 -15 * * ***** ** * Masking position 9 Map Score: 6.44881 Number of sites scoring better than the average of aligned sites = 139 Number in coding regions = 124 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 17 Fraction of orfs with sites within 600 bp upstream = 0.00273049 Motif number 6 TTAAAATTTGGTTACCATTGCTAACTTTTG 5 244 0 GTTACCATTG 0.91183 -57 ATCGCCAGTGGTTATCATGGACAATCTGTT 6 57 1 GTTATCATGG 0.951891 -244 CTACTCTAAAGTTAGCATCGCTGTTGTGAG 6 201 1 GTTAGCATCG 0.96836 -100 CATCGCTGTTGTGAGCCTGGATTGCCGGAG 6 216 1 GTGAGCCTGG 0.949448 -85 TGTACTTTGAGCTAGCGTCGGCTAGCCTGG 6 281 1 GCTAGCGTCG 0.931101 -20 GCTAGCGTCGGCTAGCCTGG 6 291 1 GCTAGCCTGG 0.985777 -10 CATTTTCCTAGCTATCATTGCTAAAACACT 8 59 1 GCTATCATTG 0.867607 -20 GGGTTTATTTGTTACCCTGGTCTGGGCCTT 12 65 1 GTTACCCTGG 0.973656 -62 ********** Masking position 4 Map Score: 5.64038 Number of sites scoring better than the average of aligned sites = 252 Number in coding regions = 219 Number in noncoding regions = 33 Number of orfs with sites within 600 bp upstream = 40 Fraction of orfs with sites within 600 bp upstream = 0.00642467 Motif number 7 GCACATCTTGACAGTAGCGCCG 1 3 1 ACATCTTGAC 0.897013 -95 TTACATCAAGGCATCCTAGCATCTTCATTG 4 30 0 GCATCCTAGC 0.977655 -39 ACGGCGATCAGCCTCTTGACGCATTCGTGC 5 17 1 GCCTCTTGAC 0.855454 -284 CTGTATCTCTGCAACCTAGCGGTTTGTTAT 5 186 1 GCAACCTAGC 0.860257 -115 CTTTTGTATGACTTCTTAACAAAACACCGA 5 220 0 ACTTCTTAAC 0.794479 -81 CGCCGCTTCTGCTTCTAAGCTCAGCTTTTA 6 27 0 GCTTCTAAGC 0.730614 -274 AACAACCCTCCCATCTTATCGGTAGTGGGC 7 216 0 CCATCTTATC 0.800549 -47 GCGACTATCACCATCTTAGCCTGACCTGAC 13 74 1 CCATCTTAGC 0.962887 -155 GCTCTGAGTGACATCCTAGCCTAATTTCCC 13 161 0 ACATCCTAGC 0.944789 -68 TTAATTTTTCGCATCTTGACTGAACTG 14 8 0 GCATCTTGAC 0.957049 -31 ********** Masking position 5 Map Score: 6.14238 Number of sites scoring better than the average of aligned sites = 219 Number in coding regions = 187 Number in noncoding regions = 32 Number of orfs with sites within 600 bp upstream = 39 Fraction of orfs with sites within 600 bp upstream = 0.00626405 Motif number 8 AAGAAATGACTTTACTGGTTTTGGCGGCGC 1 27 0 TTTACTGGTT 0.91701 -71 CTGTCCCTGTTTTAATGGTTG 2 2 0 TTTAATGGTT 0.960828 -48 TATTCCCCATTTTAAGGGGTCACCGTTTGG 5 148 1 TTTAAGGGGT 0.969674 -153 TAAGCTCAGCTTTTAGGGTTGACTAGTGAA 6 12 0 TTTTAGGGTT 0.833796 -289 TGGGGGGATTTTTATTGGGTTTATTTGTTA 12 49 1 TTTATTGGGT 0.921401 -78 AGATTAGGTACTTAATGGGTACTTAATTCG 15 39 0 CTTAATGGGT 0.933786 -99 ********** Masking position 3 Map Score: 0.809608 Number of sites scoring better than the average of aligned sites = 87 Number in coding regions = 70 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 9 AGGGCAGATTAGTTTTCTGTCACTGTGTCAACT 6 115 1 AGTTCTGCAC 0.876615 -186 GAGTAGTGTAAGGTCTCTGCCAAGACTCTACAC 6 174 0 AGTTCTGCAA 0.963963 -127 CGTTTGTCCTAGATTTTTAGCAAAAGTTTTCCC 7 11 0 AGTTTTACAA 0.965328 -252 AGTGTTTTAGCAATGATAGCTAG 8 66 0 AGGTTTACAA 0.940356 -13 CTAAGGTTTGGTGTTTAGCAATTTAGTGTTG 9 9 1 TGTTTTACAA 0.83304 -121 AGAGGTGTTAATCAAGCAAAATTTC 9 115 0 AGTTTAACAA 0.94552 -15 GGCCAGAGGGAGTTTTCAGACAAGCTCTGAGTG 13 181 0 AGTTCAGCAA 0.94342 -48 AGGGATTAATCAAATCTTTGTCG 13 216 0 AGGTTAACAA 0.907645 -13 ** * **** *** Masking position 12 Map Score: 1.32019 Number of sites scoring better than the average of aligned sites = 191 Number in coding regions = 148 Number in noncoding regions = 43 Number of orfs with sites within 600 bp upstream = 50 Fraction of orfs with sites within 600 bp upstream = 0.00803084 Motif number 10 CAGGGACAGTGTTGATCGTTGAGCCCTTTCT 2 23 1 GTTGATCGTG 0.965194 -27 GCGTCAAGAGGCTGATCGCCGTTCTCAG 5 8 0 GCTGATCGCG 0.943166 -293 GATAACCACTGGCGATCGCCGCTTCTGCTTC 6 42 0 GGCGATCGCG 0.977331 -259 GATCGCCAGTGGTTATCATGGACAATCTGTT 6 56 1 GGTTATCATG 0.704719 -245 AGTAACTAATGGTGGTTATAGAAGGCGATCG 6 244 1 GGTGGTTATG 0.692147 -57 ATCCCAGGGGGTTGATAGTTGCAATGGCAAG 12 13 0 GTTGATAGTG 0.863809 -114 GGTAATAGCGGGTAGTGGTGGGGCATTGGTC 12 98 0 GGTAGTGGTG 0.653946 -29 GTCTAGACAGGGCGATCGCCGAGGGAAAATG 13 18 1 GGCGATCGCG 0.977331 -211 AGAATGGGGTGGTGGTCGTAGCGACTATCAC 13 54 1 GGTGGTCGTG 0.990125 -175 AGGCTAAGATGGTGATAGTCGCTACGACCAC 13 65 0 GGTGATAGTG 0.969889 -164 ********* * Masking position 6 Map Score: 6.52447 Number of sites scoring better than the average of aligned sites = 2863 Number in coding regions = 2667 Number in noncoding regions = 196 Number of orfs with sites within 600 bp upstream = 234 Fraction of orfs with sites within 600 bp upstream = 0.0375843 Motif number 11 GACTTCTTAACAAAACACCGAAAAAATAACA 5 210 0 CAAAACACCA 0.908548 -91 TCTGCCAAGACTCTACACCTACCCCATCGGG 6 161 0 CTCTACACCA 0.977495 -140 AGAGACCTTACACTACTCTAAAGTTAGCATC 6 189 1 CACTACTCTA 0.794849 -112 AATCCAGGCTCACAACAGCGATGCTAACTTT 6 208 0 CACAACAGCA 0.877883 -93 GAGAAGAGAACTCAAAACTTAAATATAAAGA 8 23 0 CTCAAAACTA 0.75257 -56 GTTTTGAGTTCTCTTCTCCTAATCATTTTCC 8 36 1 CTCTTCTCCA 0.74023 -43 CACTAAATTGCTAAACACCAAACCTTAG 9 8 0 CTAAACACCA 0.94096 -122 CAATTAGCCACTCAACACTAAATTGCTAAAC 9 23 0 CTCAACACTA 0.964586 -107 ********* * Masking position 11 Map Score: 0.314324 Number of sites scoring better than the average of aligned sites = 352 Number in coding regions = 326 Number in noncoding regions = 26 Number of orfs with sites within 600 bp upstream = 30 Fraction of orfs with sites within 600 bp upstream = 0.0048185 Motif number 12 ********** No masking Map Score: 3.55515e-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: 3.55515e-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 14 ********** No masking Map Score: 3.55515e-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