AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/alignace/lib/ORF_synecho.txt -z/skink1/amcguire/genomes/synecho.fna -igcvA_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 1652676 188 hypothetical protein #2 1652677 228 RNA-binding protein #3 1652678 127 amidase #4 1652679 207 hypothetical protein #5 gcvH 97 glycine decarboxylase complex H-protein #6 gcvP 179 P protein of glycine cleavage complex #7 gcvT 168 aminomethyltransferase #8 dnaK 205 DnaK protein #9 1001436 187 hypothetical protein #10 1001437 88 hypothetical protein #11 1001440 300 beta transducin-like protein Motif number 1 TTTTGCTTCAGACTGTTTTGGCACAGTTCAATCTTTATTCTG 1 130 0 GCGTTGGAAT 0.812881 -59 TTGACCGGGCGCTGGGGAGGGTTTTGGCTAAAATTTTCCCTT 2 17 1 GTGGGGGAAA 0.977853 -212 TTAACTCCTGGGCGGGGCTACGACCGCAGAAAAAAGGCCCAA 4 132 0 GCGGGCGAAA 0.984949 -76 CGGGACACAGGTCAGTGAGAGGAACGGTTAACTCCTGGGCGG 4 159 0 GCGTGGGAAC 0.970324 -49 AAGGATGAACGCCTGGACTGGATCTGTCAAAAAATGTTACAG 6 132 0 GCGGAGGAAA 0.994274 -48 AATGGCGGAGTAGGGAAAGGATGAACGCCTGGACT 6 155 0 GCGAGGGGAA 0.976742 -25 CCAATCCATTGCCTGGGGCCGACACGTTCACACTCTTATAGT 8 107 0 GCGGGGGACA 0.990623 -99 GAATAGCACTGACGGTTTCTGGGGAGTCGGAAGACATGTTAA 9 100 0 GCGTTGGGAA 0.922174 -88 AAAAAGCCTTGGCAGGACAGGTTCAGTTTAAAAGCTTATGGG 9 153 0 GCGGAGGAAA 0.994274 -35 GGAAAAAGCCGCCCGAATTTGTTTGGTAAAAACTTTGCCGCC 11 24 1 GCGAAGGAAA 0.971583 -277 CACTGCCAGGGACGGGGATAGGGGGGACTAAATCACCACTAA 11 103 0 GCGGGGGAAA 0.998378 -198 ACTGTGACAAGACTGGGCAAGCCTAGTCAAAAATAGCGAGGA 11 193 0 GCGGGGGAAA 0.998377 -108 * * *** * * *** Masking position 16 Map Score: 20.3491 Number of sites scoring better than the average of aligned sites = 303 Number in coding regions = 277 Number in noncoding regions = 26 Number of orfs with sites within 600 bp upstream = 34 Fraction of orfs with sites within 600 bp upstream = 0.00546097 Motif number 2 ATGCTTCTGGCATTTTTCCC 1 1 0 CATTTTTCCC 0.876673 -188 AAAATTTAATCCCTTTTCCTGGCGATCGTC 1 79 0 CCCTTTTCCT 0.893616 -110 AAAGGGATTAAATTTTTCCGGGAGTCGGGC 1 93 1 AATTTTTCCG 0.538925 -96 TTTTGGCTAAAATTTTCCCTTGTGAAGACA 2 38 1 AATTTTCCCT 0.757374 -191 ATGACTCAAACACCTTCCCTTCTACAACGA 3 45 0 CACCTTCCCT 0.772671 -83 GTGTTTGAGTCATCTTTCCTTTTTTGCTAG 3 62 1 CATCTTTCCT 0.787094 -66 GGTAAATCTGGCTCTTTCCCT 3 117 1 GCTCTTTCCC 0.939168 -11 TTGTTTAGCTGCTTTTCCGCAGGTCCAGCA 4 18 1 GCTTTTCCGC 0.890139 -190 GCCAAGGCGGCCCCATCCCCATAAAACTCG 6 44 0 CCCCATCCCC 0.713773 -136 CAGGCGTTCATCCTTTCCCTACTCCGCCAT 6 159 1 TCCTTTCCCT 0.624212 -21 CTGCATAATAGATTTTTCCTAAAAAAAGCA 7 105 0 GATTTTTCCT 0.89852 -64 AACCGTCAGTGCTATTCCGTGCTATTTCCC 9 125 1 GCTATTCCGT 0.534776 -63 GCTATTCCGTGCTATTTCCCCATAAGCTTT 9 135 1 GCTATTTCCC 0.808122 -53 TCCTGCCAAGGCTTTTTCCG 9 178 1 GCTTTTTCCG 0.938288 -10 GCACCATTGAGCTTATTCCCTCTACTTTTC 10 32 1 GCTTATTCCC 0.866599 -57 TATTCCCTCTACTTTTCCCTGATCTTCCGT 10 45 1 ACTTTTCCCT 0.889916 -44 ACTTTTCCCTGATCTTCCGTAGTTGCACTG 10 55 1 GATCTTCCGT 0.619356 -34 AATTCGGGCGGCTTTTTCCGCATTTCATCT 11 13 0 GCTTTTTCCG 0.938288 -288 TAACCCGGCTCATTATCCCGAATTTGCCAT 11 73 0 CATTATCCCG 0.646209 -228 ATTTAGTCCCCCCTATCCCCGTCCCTGGCA 11 112 1 CCCTATCCCC 0.808216 -189 GGTCGAATAGGCTTTTCCCTGCCCATAATT 11 264 1 GCTTTTCCCT 0.975964 -37 ********** Masking position 6 Map Score: 20.3501 Number of sites scoring better than the average of aligned sites = 3885 Number in coding regions = 3385 Number in noncoding regions = 500 Number of orfs with sites within 600 bp upstream = 483 Fraction of orfs with sites within 600 bp upstream = 0.0775779 Motif number 3 TGCCAACGACGATCGCCAGGAAAAGGGATT 1 72 1 GATCGCCAGG 0.854995 -117 TTAGCCAAAACCCTCCCCAGCGCCCGGTCA 2 18 0 CCCTCCCCAG 0.978692 -211 TCGGAGAGAAGCCTGCTAAGCGTAACCATA 2 169 0 GCCTGCTAAG 0.840646 -60 CTATCAGCAAGCCTGCCTAGCAAAAAAGGA 3 78 0 GCCTGCCTAG 0.969443 -50 GCCAGATTTACCTCCCCCAGTCTATCAGCA 3 99 0 CCTCCCCCAG 0.934986 -29 CCGCCACGGCGATCGCCAAGGAAAATAATT 4 77 1 GATCGCCAAG 0.927607 -131 GCGGTCGTAGCCCCGCCCAGGAGTTAACCG 4 147 1 CCCCGCCCAG 0.990726 -61 TAGGGGTCAGCATTGCCAAGGCGGCCCCAT 6 58 0 CATTGCCAAG 0.957337 -122 GGTTCCAATCCATTGCCTGGGGCCGACACG 8 123 0 CATTGCCTGG 0.790838 -83 CATGTCTTCCGACTCCCCAGAAACCGTCAG 9 104 1 GACTCCCCAG 0.949167 -84 ACTGAACCTGTCCTGCCAAGGCTTTTTCCG 9 168 1 TCCTGCCAAG 0.918307 -20 TCAGCGTTGACACTGCCAGGGACGGGGATA 11 125 0 CACTGCCAGG 0.956257 -176 TTTTGACTAGGCTTGCCCAGTCTTGTCACA 11 203 1 GCTTGCCCAG 0.984962 -98 ATAGGCTTTTCCCTGCCCATAATTGTACTA 11 270 1 CCCTGCCCAT 0.907471 -31 ********** Masking position 6 Map Score: 19.7488 Number of sites scoring better than the average of aligned sites = 1784 Number in coding regions = 1650 Number in noncoding regions = 134 Number of orfs with sites within 600 bp upstream = 153 Fraction of orfs with sites within 600 bp upstream = 0.0245744 Motif number 4 ATTAAATTTTTCCGGGAGTCGGGCCCTAAGGCA 1 99 1 TCGGAGCGGG 0.993365 -90 GGCCATCAAATTCTGGCGGCAGGTGCTATGATC 2 80 1 TCGGCGCAGG 0.9874 -149 CGGCGATCGGTTCGGGACACAGGTCAGTGAGAG 4 180 0 TCGGACCAGG 0.989476 -28 TTTCAGTCCTTTGTGGACCCAGGAACAACCCCT 5 20 1 TGGGACCAGG 0.989476 -78 ACCAAAAATATGGCGGAGGCAGGGGTTGTTCCT 5 40 0 TGGGAGCAGG 0.991487 -58 AATGGCGGAGTAGGGAAAGGATGAA 6 165 0 TGGGAGAGGG 0.96724 -15 TCCCCCAGTATTGGGGGCTAGGGGACTTTCAAT 7 31 0 TGGGGCAGGG 0.941308 -138 AGTGTGAACGTGTCGGCCCCAGGCAATGGATTG 8 115 1 TTGGCCCAGG 0.923798 -91 GCGTTGACACTGCCAGGGACGGGGATAGGGGGG 11 119 0 TCAGGGCGGG 0.908182 -182 * * **** **** Masking position 1 Map Score: 10.9146 Number of sites scoring better than the average of aligned sites = 283 Number in coding regions = 245 Number in noncoding regions = 38 Number of orfs with sites within 600 bp upstream = 33 Fraction of orfs with sites within 600 bp upstream = 0.00530035 Motif number 5 CCAAAACCCTCCCCAGCGCCCGGTCAACTGA 2 13 0 CCCAGCGCCC 0.935122 -216 CTGATCATAGCACCTGCCGCCAGAATTTGAT 2 84 0 CCCTGCCGCC 0.991583 -145 GGCGTTCCTGCTCCTTGGGCCTTTTTTCTGC 4 118 1 CCCTTGGGCC 0.9698 -90 GCAGGGGTTGTTCCTGGGTCCACAAAGGACT 5 24 0 TCCTGGGTCC 0.897161 -74 CCAGGAACAACCCCTGCCTCCGCCATATTTT 5 38 1 CCCTGCCTCC 0.969824 -60 GCAATGCTGACCCCTAGGCCTACCAAAATTT 6 72 1 CCCTAGGCCT 0.941826 -108 TATTGAAAGTCCCCTAGCCCCCAATACTGGG 7 30 1 CCCTAGCCCC 0.988778 -139 GAGAACTAAGCCCCTACCGTCACTATAAGAG 8 86 1 CCCTACCGTC 0.853394 -120 TCCAATCCATTGCCTGGGGCCGACACGTTCA 8 119 0 TCCTGGGGCC 0.969676 -87 GATTTAGTCCCCCCTATCCCCGTCCCTGGCA 11 111 1 CCCTATCCCC 0.919542 -190 TTGAAGCTAACGCCTAGGGCTTTCCTCGCTA 11 171 1 CCCTAGGGCT 0.95249 -130 * ********* Masking position 4 Map Score: 14.3618 Number of sites scoring better than the average of aligned sites = 960 Number in coding regions = 832 Number in noncoding regions = 128 Number of orfs with sites within 600 bp upstream = 117 Fraction of orfs with sites within 600 bp upstream = 0.0187922 Motif number 6 AATCTTTATTCTGCCTTAGGGCCCGACTCCCGGAAA 1 107 0 CTGCCTTGCA 0.966338 -82 TTACGCTTAGCAGGCTTCTCTCCGAAACCCACTCTC 2 174 1 CAGGCTTTCA 0.962755 -55 TTTCTTTTCTCTGGTTTTGGAGCTAATTT 2 210 1 CTGGTTTACA 0.972538 -19 TTTTGCTAGGCAGGCTTGCTGATAGACTGGGGGAGG 3 83 1 CAGGCTTGTA 0.882347 -45 ACTTTCAATACAGGTTTTAAAACCCAGAC 7 4 0 CAGGTTTACA 0.964869 -165 CTCGGAAGTGCAGGTTTCCGTACCTATGGGGGCATC 8 53 0 CAGGTTTTCA 0.952534 -153 GATTGGAACCATGGCTTTTCGGCCCATCGTTGTGTC 8 143 1 ATGGCTTGCA 0.902338 -63 AACCAAAAACCTGCTTTGCCAGCCTAAATCGCGCCC 9 11 0 CTGCTTTACA 0.915206 -177 ACTTTGCCGCCTGGTTTGATGGCAAATTCGGGATAA 11 55 1 CTGGTTTGCA 0.986523 -246 ******* * * * Masking position 7 Map Score: 4.57654 Number of sites scoring better than the average of aligned sites = 223 Number in coding regions = 196 Number in noncoding regions = 27 Number of orfs with sites within 600 bp upstream = 30 Fraction of orfs with sites within 600 bp upstream = 0.0048185 Motif number 7 CTTTTCCTGGCGATCGTCGTTGGCATAGCT 1 67 0 CGATCGTCGT 0.950174 -122 TTTTCCTTGGCGATCGCCGTGGCGGTTTTG 4 72 0 CGATCGCCGT 0.993244 -136 CCAAGGAGCAGGAACGCCGAGAAAAAGACA 4 106 0 GGAACGCCGA 0.951749 -102 GGCGGGGCTACGACCGCAGAAAAAAGGCCC 4 134 0 CGACCGCAGA 0.917939 -74 TGTCCCGAACCGATCGCCGAAAGG 4 194 1 CGATCGCCGA 0.994803 -14 TTAGTCCCCCCTATCCCCGTCCCTGGCAGT 11 114 1 CTATCCCCGT 0.885193 -187 AGAATTGAAGCTAACGCCTAGGGCTTTCCT 11 167 1 CTAACGCCTA 0.784041 -134 ********** Masking position 3 Map Score: 4.03607 Number of sites scoring better than the average of aligned sites = 2606 Number in coding regions = 2387 Number in noncoding regions = 219 Number of orfs with sites within 600 bp upstream = 233 Fraction of orfs with sites within 600 bp upstream = 0.0374237 Motif number 8 GGCCCTAAGGCAGAATAAAGATTGAACTGT 1 120 1 CAGAATAAAG 0.896919 -69 GCTCCAAAACCAGAGAAAAGAAAGAGAGTG 2 203 0 CAGAGAAAAG 0.978507 -26 GCTACGACCGCAGAAAAAAGGCCCAAGGAG 4 128 0 CAGAAAAAAG 0.982205 -80 CTAAAAAAAGCACAAAAAATCCCCCTGGTT 7 87 0 CACAAAAAAT 0.722289 -82 TAGATTTTTCCTAAAAAAAGCACAAAAAAT 7 97 0 CTAAAAAAAG 0.703583 -72 CTAATAATTCCAAAAAAAACCAAAAACCTG 9 34 0 CAAAAAAAAC 0.713637 -154 AATTATTAGTCACAAAAAAGCTGTCGTATA 9 55 1 CACAAAAAAG 0.958832 -133 TACGGAAGATCAGGGAAAAGTAGAGGGAAT 10 46 0 CAGGGAAAAG 0.956997 -43 CAATTATGGGCAGGGAAAAGCCTATTCGAC 11 265 0 CAGGGAAAAG 0.956997 -36 ********** Masking position 7 Map Score: 7.48735 Number of sites scoring better than the average of aligned sites = 340 Number in coding regions = 268 Number in noncoding regions = 72 Number of orfs with sites within 600 bp upstream = 73 Fraction of orfs with sites within 600 bp upstream = 0.011725 Motif number 9 AACAGTCTGAAGCAAAAGAGATTATCAGAT 1 155 1 AGCAAAAGAG 0.815837 -34 AAGACATCTAGACAAATTGGCCATCAAATT 2 62 1 GACAAATTGG 0.760754 -167 TGAAGCTGCAATCAAAACCGCCACGGCGAT 4 60 1 ATCAAAACCG 0.738757 -148 AACCGCTAAAGGCAACAGCGTTGTTAGTTT 5 73 0 GGCAACAGCG 0.923093 -25 GGCAAAACCGCTAAAGGCAA 5 88 0 GGCAAAACCG 0.977687 -10 CGGCAAATGGGAAACGTTTTA 6 2 1 GGCAAATGGG 0.966344 -178 TATGCCATTGGTCAAAAGGGGAGTTAACGC 8 17 0 GTCAAAAGGG 0.890003 -189 GATTTAGGCTGGCAAAGCAGGTTTTTGGTT 9 17 1 GGCAAAGCAG 0.813804 -171 GTTTTTACCAAACAAATTCGGGCGGCTTTT 11 27 0 AACAAATTCG 0.593449 -274 CTGGTTTGATGGCAAATTCGGGATAATGAG 11 65 1 GGCAAATTCG 0.95766 -236 ********** Masking position 5 Map Score: 2.89367 Number of sites scoring better than the average of aligned sites = 1120 Number in coding regions = 1014 Number in noncoding regions = 106 Number of orfs with sites within 600 bp upstream = 124 Fraction of orfs with sites within 600 bp upstream = 0.0199165 Motif number 10 ATTCTGCCTTAGGGCCCGACTCCCGGAAAA 1 106 0 AGGGCCCGAC 0.95414 -83 TTTATGGGGATGGGGCCGCCTTGGCAATGC 6 49 1 TGGGGCCGCC 0.992078 -131 CCCCCAATACTGGGGGAATCAGATTCGATA 7 47 1 TGGGGGAATC 0.832083 -122 TCCGTACCTATGGGGGCATCTAGCCGTATG 8 43 0 TGGGGGCATC 0.955861 -163 ATCCATTGCCTGGGGCCGACACGTTCACAC 8 116 0 TGGGGCCGAC 0.982705 -90 CCATGGCTTTTCGGCCCATCGTTGTGTCTT 8 151 1 TCGGCCCATC 0.894711 -55 GTGACAAGACTGGGCAAGCCTAGTCAAAAA 11 202 0 TGGGCAAGCC 0.819206 -99 GTCTTGTCACAGTGCCCACCGTCAATTAAG 11 222 1 AGTGCCCACC 0.764171 -79 ********** Masking position 4 Map Score: 2.19235 Number of sites scoring better than the average of aligned sites = 854 Number in coding regions = 803 Number in noncoding regions = 51 Number of orfs with sites within 600 bp upstream = 62 Fraction of orfs with sites within 600 bp upstream = 0.00995824 Motif number 11 AATCCCTTTTCCTGGCGATCGTCGTTGGCAT 1 71 0 CCGGCGATCG 0.850609 -118 TTAAATTTTTCCGGGAGTCGGGCCCTAAGGC 1 100 1 CCGGAGTCGG 0.885166 -89 CTGATAGACTGGGGGAGGTAAATCTGGCTCT 3 101 1 GGGGAGGTAA 0.553257 -27 GTAGCCCCGCCCAGGAGTTAACCGTTCCTCT 4 153 1 CCGGAGTTAA 0.982832 -55 CAGATCCAGTCCAGGCGTTCATCCTTTCCCT 6 148 1 CCGGCGTTCA 0.978082 -32 AATGGTTCCAGGAATCAAAAATCAAAGA 7 151 0 CCGGAATCAA 0.780755 -18 TGCGTGGCGTTAACTCCCCTTTT 8 3 1 CGGGCGTTAA 0.965286 -203 TTACTTGTTAACGGGAGTTAATTAAAATT 8 187 1 ACGGAGTTAA 0.848765 -19 TGCCATCAAACCAGGCGGCAAAGTTTTTACC 11 48 0 CCGGCGGCAA 0.969487 -253 GAGGAAAGCCCTAGGCGTTAGCTTCAATTCT 11 167 0 CTGGCGTTAG 0.878914 -134 ** ******** Masking position 5 Map Score: 1.7699 Number of sites scoring better than the average of aligned sites = 1803 Number in coding regions = 1676 Number in noncoding regions = 127 Number of orfs with sites within 600 bp upstream = 157 Fraction of orfs with sites within 600 bp upstream = 0.0252168 Motif number 12 AAAATTTAATCCCTTTTCCTGGCGATCGTCG 1 78 0 CCTTTTCCTG 0.706015 -111 TGCACTAACACTCATAACAAGTGCGTCTACC 2 133 0 CTATAACAAG 0.802557 -96 GTTTTTGCCTAATTACCTGAATTTAAGAT 3 9 1 CTATTACCTG 0.862856 -119 CGATAATCCTCCTTTAACCAGGGGGATTTTT 7 72 1 CCTTAACCAG 0.966975 -97 TAATTAACTCCCGTTAACAAGTAAGAATATA 8 180 0 CCTTAACAAG 0.905486 -26 CCAAAAAAAACCAAAAACCTGCTTTGCCAGC 9 24 0 CCAAAACCTG 0.860501 -164 ATGGTATTAGCCTTTAACATGTCTTCCGACT 9 87 1 CCTTAACATG 0.940419 -101 TCCCCATAAGCTTTTAAACTGAACCTGTCCT 9 151 1 CTTTAAACTG 0.698677 -37 TAAATCACCACTAATAACCCGGCTCATTATC 11 86 0 CTATAACCCG 0.879249 -215 ** ******** Masking position 1 Map Score: 0.795517 Number of sites scoring better than the average of aligned sites = 595 Number in coding regions = 531 Number in noncoding regions = 64 Number of orfs with sites within 600 bp upstream = 80 Fraction of orfs with sites within 600 bp upstream = 0.0128493 Motif number 13 ********** No masking Map Score: -1.80945e-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: -1.80945e-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 15 ********** No masking Map Score: -1.80945e-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