AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/alignace/lib/ORF_synecho.txt -z/skink1/amcguire/genomes/synecho.fna -ipurR_synecho_opreg_100.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 speA 180 arginine decarboxylase #2 purL 137 phosphoribosylformyl glycinamidine synthetase II #3 1651827 181 hypothetical protein #4 phdD 86 dihydrolipoamide dehydrogenase #5 1651830 57 hypothetical protein #6 ubiX 67 3-octaprenyl-4-hydroxybenzoate carboxy-lyase #7 gylA 300 serine hydroxymethyltransferase #8 purA 238 adenylosuccinate synthetase #9 purC 111 phosphoribosyl aminoidazole succinocarboxamide synthetase #10 codA 174 cytosine deaminase #11 1652679 207 hypothetical protein #12 gcvH 97 glycine decarboxylase complex H-protein #13 guaB 102 IMP dehydrogenase subunit #14 purD 111 glycinamide ribonucleotide synthetase #15 purB 109 adenylosuccinate lyase #16 gcvP 179 P protein of glycine cleavage complex #17 glnB 300 nitrogen regulatory protein P-II #18 pyrC 300 dihydroorotase #19 gcvT 168 aminomethyltransferase #20 purF 270 amidophosphoribosyltransferase #21 guaA 300 GMP synthetase #22 carB 46 carbamoyl-phosphate synthase, pyrimidine-specific, large chain #23 pyrR 300 pyrimidine operon regulatory protein PyrR #24 purM 133 phosphoribosyl formylglycinamidine cyclo-ligase #25 prsA 170 ribose-phosphate pyrophosphokinase #26 purE 100 phosphoribosylaminoimidazole carboxylase #27 pyrD 254 dihydroorotate dehydrogenase #28 speA 300 arginine decarboxylase #29 carA 50 carbamoyl-phosphate synthetase subunit A #30 purK 75 phosphoribosyl aminoimidazole carboxylase #31 1653935 195 hypothetical protein #32 1653950 142 hypothetical protein Motif number 1 TCTTGATTGCCATCGATCGCCGGGGAGTCCG 1 106 1 CTCGATCGCC 0.945207 -75 CGGGTTTGAAATCTGAGCCCCAACCCGGAAT 2 40 0 ACTGAGCCCC 0.837446 -98 TTCCACAAAGACCCGATCGCCAGGGGGGAA 3 10 0 ACCGATCGCC 0.985174 -172 CGAAGACAATGGGCGATCGCCAGGACGGGGG 4 12 1 GGCGATCGCC 0.910483 -75 GGACGGACTAACCCCGGCCCCTAGCCTAGGG 5 26 1 ACCCGGCCCC 0.841 -32 CTCGTCGCCCCACTGAGCGCCGATAACAATA 8 176 0 CCTGAGCGCC 0.958858 -63 TTTACCTTTTCCCTCGTCGCCCCACTGAGCG 8 188 0 CCTCGTCGCC 0.819334 -51 AAAACCGCCACGGCGATCGCCAAGGAAAATA 11 73 1 CGCGATCGCC 0.974917 -135 CTGTGTCCCGAACCGATCGCCGAAAGG 11 191 1 ACCGATCGCC 0.985174 -17 GCTCTGATCCCCACTGGATTAG 13 2 1 CCTGATCCCC 0.954939 -101 TGCCAAGGCGGCCCCATCCCCATAAAACTCG 16 44 0 GCCCATCCCC 0.954802 -136 CGTTTGGCAGCGCCCATGGCCGGAGATGAGG 17 97 0 CCCCATGGCC 0.866747 -204 TGAAGTAATTACCCGATCGCCGTCTCCAAGC 18 208 1 ACCGATCGCC 0.985174 -93 CGATCGCCGTCTCCAAGCCCCCTAAATCTTG 18 221 1 CCCAAGCCCC 0.933982 -80 TATTGAAAGTCCCCTAGCCCCCAATACTGGG 19 30 1 CCCTAGCCCC 0.95299 -139 TCTATACATTCCCCTGTCCCCTGACAACTAG 20 50 1 CCCTGTCCCC 0.877013 -221 AATTCCTGACTGCCGATCGCC 21 290 1 TCCGATCGCC 0.932411 -11 AATGCTCCAATCGCCTTGATTGTAT 23 5 1 CCCAATCGCC 0.963636 -296 AATCTTTATGGCTCCAGCCCCGGAGTTTACC 23 138 0 GTCCAGCCCC 0.571395 -163 TTTAAATGCCCCCCTAGCCCCCCAAGTTTGG 28 41 0 CCCTAGCCCC 0.95299 -260 AGGGGTTAAACAGCGATCGCCCCCTCAGAGT 28 205 1 CGCGATCGCC 0.974917 -96 ACTATGATGGATCCCATCGCCCAGACTGCTT 32 30 0 ACCCATCGCC 0.973515 -113 * ********* Masking position 10 Map Score: 35.4248 Number of sites scoring better than the average of aligned sites = 3773 Number in coding regions = 3467 Number in noncoding regions = 306 Number of orfs with sites within 600 bp upstream = 330 Fraction of orfs with sites within 600 bp upstream = 0.0530035 Motif number 2 GCTCGGCCAAGCTTGGGGAGCAATACTGCAGGT 3 48 1 GTGGGGAGAA 0.983797 -134 GCGATCGCCAGGACGGGGGTCAACTTTCCAGAG 4 24 1 GAGGGGGTAA 0.673351 -63 CAAGACTTTAGTTTAGGGGTTAAGGGCAACCTC 4 54 0 GTAGGGGTAA 0.615384 -33 CCGGCCCCTAGCCTAGGGGGGGAAATTTC 5 39 1 GCAGGGGGGA 0.853133 -19 TACAGTTTCCGTCTGGGAAGAAATTGTCAAGAG 7 77 0 GCGGGAAGAA 0.859652 -224 TGTAAACAGTGCTGGGGGCGGAAAGCACCGCGC 7 266 0 GTGGGGCGAA 0.984094 -35 GACCCCATTGGCCTAGGGAGAAAGAGGAGCCAA 9 15 0 GCAGGGAGAA 0.931905 -97 TGAAGTTTAAGGAAGGGGAAAAAGACTTTTAAC 18 250 1 GAGGGGAAAA 0.770466 -51 GTTGTCAGGGGACAGGGGAATGTATAGATTAGT 20 45 0 GCGGGGAAGT 0.720234 -226 TGCCTTCCCTGTCTGGCGGGAATCCACCAATTC 20 184 1 GCGGCGGGAT 0.855024 -87 TCTGCGCTAAGATGGGGGCGGAAAATTGCAGAA 21 106 0 GTGGGGCGAA 0.984094 -195 TTATACTGGAGGTGAGGGCGAATCCCCAGGCAC 21 258 0 GTAGGGCGAT 0.825919 -43 AACCTAAAGAGATTGGCGAGGAAAGAATCCGCT 25 65 1 GTGGCGAGAA 0.879664 -106 AATCTGCCATGACATGGGGGTAAA 25 157 1 GCTGGGGGAA 0.854482 -14 GGCTGCCCAGGGTAGGGAAAAAACCCTAGGGAT 27 185 0 GTGGGAAAAA 0.538334 -70 AGGAAGTTTTGATAGGGGCAGGACTGGTTACTA 27 221 0 GTGGGGCAGA 0.821115 -34 AGCCCCCCAAGTTTGGGGGGAAAGTATTAAAAG 28 24 0 GTGGGGGGAA 0.988468 -277 AACTTGGGGGGCTAGGGGGGCATTTAAAACAGA 28 44 1 GTGGGGGGAT 0.974224 -257 TGGAACAGACGACAGGGGCGAATCTGCTAAT 29 30 1 GCGGGGCGAT 0.972497 -21 CAGATTTTCAGACGGGGGAAGATAAATAAAACT 32 116 0 GCGGGGAAAT 0.89542 -27 * * ****** ** Masking position 6 Map Score: 18.5565 Number of sites scoring better than the average of aligned sites = 1874 Number in coding regions = 1626 Number in noncoding regions = 248 Number of orfs with sites within 600 bp upstream = 238 Fraction of orfs with sites within 600 bp upstream = 0.0382268 Motif number 3 GTTGGGGCTCAGATTTCAAACCCGGTGGACACT 2 47 1 AGTCAAACCC 0.744337 -91 ACTTTGATGGGGTGTTAGAATCGGGCCACATTT 3 138 1 GGTAGAATCG 0.695837 -44 TCGGAAAACCGGGTCTAAAACCCCGTCTTTCAG 7 210 0 GGTAAAACCC 0.951748 -91 AGGCCAATGGGGTCATCAAACCCCACATCACCA 9 34 1 GGTCAAACCC 0.978284 -78 AGTCAGTAAAGGGCAGATAATCCGGCTATTATA 10 16 1 GGGATAATCC 0.589069 -159 GGTCCACAAAGGACTGAAAATCGTTTAA 12 6 0 GGGAAAATCG 0.582812 -92 CCAATGGAGCCGATTTAGACCCCGATGTGCTGT 18 174 1 CGTAGACCCC 0.862581 -127 TTTCAATACAGGTTTTAAAACCCAGAC 19 5 0 GGTAAAACCC 0.953906 -164 AATGACGAACGGGTCTAGACCCCTTAATCAATT 20 152 0 GGTAGACCCC 0.960019 -119 GGGATTCGAACCCCCGTTGAGTT 21 1 1 GGTCGAACCC 0.975386 -300 CAACAATCCCCGTATTCTACCCCAATACCTGAA 21 161 0 CGTCTACCCC 0.686628 -140 GACTACCCCTGGAGGTAAACTCCGGGGCTGGAG 23 125 1 GGTAAACTCC 0.881899 -176 CGCTATGATTGGATCGAAAACCCTGGGTTTGCT 25 94 1 GGGAAAACCC 0.951863 -77 GTCGGGTGCCCGGAAGCAAACCCAGGGTTTTCG 25 108 0 CGGCAAACCC 0.867549 -63 GTGCTGGAATGGGCTTCAAACCGTACTCCACTC 28 153 0 GGTCAAACCG 0.908283 -148 GGCAAGAATTGGTAATCGACTCCGGAAGTAACT 31 56 0 GGTCGACTCC 0.899263 -140 ** ******** Masking position 9 Map Score: 13.3442 Number of sites scoring better than the average of aligned sites = 894 Number in coding regions = 796 Number in noncoding regions = 98 Number of orfs with sites within 600 bp upstream = 103 Fraction of orfs with sites within 600 bp upstream = 0.0165435 Motif number 4 TGCCATCGATCGCCGGGGAGTCCGGGGCAGTTAC 1 113 1 CCCGGGTCCG 0.834598 -68 AAGGTAGAATGTGCCTAGTGTCCACCGGGTTTGA 2 62 0 GGCAGGTCCA 0.8207 -76 CCCCAAGCTTGGCCGAGCCGGCAGTTTCCACAAA 3 32 0 GCCGCGGCAG 0.843221 -150 GGCCTGGGGCTCCAAACGCTCAAA 3 168 0 GCCGGCTCCA 0.883159 -14 TACTCAGGTAGACCTCAGTGTCCGGATCTCGAAT 7 108 1 GCCAGGTCCG 0.986106 -193 GCAGAAAAAAGGCCCAAGGAGCAGGAACGCCGAG 11 115 0 GCCAGAGCAG 0.898731 -93 CTGTGCTGACGTCCAAAGGGTCAGATTATTTGGT 13 43 1 GCCAGGTCAG 0.977783 -60 AATTTTGGTAGGCCTAGGGGTCAGCATTGCCAAG 16 68 0 GCCGGGTCAG 0.98315 -112 CTGCTCTTTCGTCCGAAGAATCCGTTACCCTAGA 17 32 0 GCCAGATCCG 0.960829 -269 CCTCATCTCCGGCCATGGGCGCTGCCAAACGGTA 17 97 1 GCCGGCGCTG 0.858072 -204 TGACGACCATGGCCTTGCCGTCAGTTAGACCCAG 21 192 1 GCCGCGTCAG 0.902142 -109 ATCATACCACGCCCCCACTGTCCGGCAGGGTGAA 23 206 1 GCCACGTCCG 0.918123 -95 AGATTGCGGAGAGGTTTGAGGCCGGGAATTCTGG 24 49 0 GGGTGGGCCG 0.65963 -85 AGAGATTGGCGAGGAAAGAATCCGCTATGATTGG 25 72 1 GGGAGATCCG 0.796855 -99 CCTTAGTCGGGTGCCCGGAAGCAAACCCAGGGTT 25 112 0 GGCGGAGCAA 0.431433 -59 TACGCTATTAGCGGTTAGCCTCAGTTTAAAGTCA 26 46 1 GGGAGCTCAG 0.795639 -55 CAAGCTTGCTGAGCTGAGACTCAGTTAATCATTT 27 34 0 GGCAGCTCAG 0.91534 -221 CTCTCTTGGGGTCGGTGGTGTCCTCGTTCTTCAA 27 150 1 GCGGGGTCCT 0.599282 -105 ATTACCCCAAGTCGTTAGAGTCTGTTTTAAATGC 28 63 0 GCGAGGTCTG 0.835742 -238 ATCCCAACTTGCCCAGTGACTCTGAGGGGGCGAT 28 220 0 GCCTGCTCTG 0.695816 -81 TTCTATGGGGGCGCTTAGAAGCAGTCTGGGCGAT 32 12 1 GGCAGAGCAG 0.797623 -131 AAGCAGTCTGGGCGATGGGATCCATCATAGTCCC 32 30 1 GCGGGATCCA 0.629705 -113 ATCCATCATAGTCCCTTGGCTCAGCAGTTGCAAT 32 49 1 GCCTGCTCAG 0.876924 -94 * ** ** ***** Masking position 12 Map Score: 19.6442 Number of sites scoring better than the average of aligned sites = 1221 Number in coding regions = 1125 Number in noncoding regions = 96 Number of orfs with sites within 600 bp upstream = 111 Fraction of orfs with sites within 600 bp upstream = 0.0178285 Motif number 5 ACTGCCCCGGACTCCCCGGCGATCGATGGCAATC 1 110 0 ACTCGGCATC 0.61545 -71 TTCCCCCCTGGCGATCGGGTCTTTGT 3 3 1 CCCCGGCATC 0.977655 -179 GTGGAAACTGCCGGCTCGGCCAAGCTTGGGGAGC 3 35 1 CCGCGGCAAG 0.986083 -147 AAGTTGACCCCCGTCCTGGCGATCGCCCATTGTC 4 16 0 CCGCGGCATC 0.996219 -71 GAAATTTCCCCCCCTAGGCTAGGGGCCGGGGTT 5 35 0 CCCCGGCAGG 0.87343 -23 GCAATCAAAACCGCCACGGCGATCGCCAAGGAAA 11 67 1 CCGCGGCATC 0.996219 -141 GGCATTCCAACTGCCAAGGCAATGGCGTTTTCCA 15 24 0 CTGCGGCATG 0.97088 -86 GGGGATGGGGCCGCCTTGGCAATGCTGACCCCTA 16 54 1 CCGCGGCATG 0.996219 -126 TTGACAGATCCAGTCCAGGCGTTCATCCTTTCCC 16 144 1 CAGCGGCTTC 0.80345 -36 GACAACTAGACCGACTTGGCCAAGAACCAAACAC 20 72 1 CCGCGGCAAG 0.986083 -199 TCCCGCCAGACAGGGAAGGCAATGACGAACGGGT 20 171 0 CAGGGGCATG 0.880569 -100 GGTCTAACTGACGGCAAGGCCATGGTCGTCAACA 21 189 0 ACGCGGCATG 0.963359 -112 CCCCCACTGTCCGGCAGGGTGAACAGAGGAGACT 23 217 1 CCGCGGTAAC 0.800365 -84 CCCAGTGACTCTGAGGGGGCGATCGCTGTTTAAC 28 209 0 CTGGGGCATC 0.837282 -92 CCAATTCTTGCCGCCGAGGAAATCAGTGGAACAT 31 77 1 CCGCGGAATC 0.937147 -119 CGCTTAGAAGCAGTCTGGGCGATGGGATCCATCA 32 23 1 CAGCGGCATG 0.979497 -120 *** * *** *** Masking position 8 Map Score: 28.8891 Number of sites scoring better than the average of aligned sites = 599 Number in coding regions = 563 Number in noncoding regions = 36 Number of orfs with sites within 600 bp upstream = 41 Fraction of orfs with sites within 600 bp upstream = 0.00658529 Motif number 6 TTGAAATCTGAGCCCCAACCCGGAATACCT 2 36 0 AGCCCCAACC 0.839112 -102 GAGCGTTTGGAGCCCCAGGCC 3 171 1 AGCCCCAGGC 0.949672 -11 AGGACGGACTAACCCCGGCCCCTAGCCTAG 5 25 1 AACCCCGGCC 0.981312 -33 GGGGGCGGAAAGCACCGCGCTTCTTGAGTA 7 256 0 AGCACCGCGC 0.616981 -45 TTTTTTCTGGAGCGCCACCCACGATCTCTT 8 58 0 AGCGCCACCC 0.818337 -181 CTGCGGTCGTAGCCCCGCCCAGGAGTTAAC 11 145 1 AGCCCCGCCC 0.98062 -63 ACCCAGGAACAACCCCTGCCTCCGCCATAT 12 36 1 AACCCCTGCC 0.911825 -62 GGAGTTATTTATCTCCGCCCCCCCACTTTC 14 12 0 ATCTCCGCCC 0.934684 -100 GGAGATAAATAACTCCAGTCAACTCCGGCC 14 26 1 AACTCCAGTC 0.52158 -86 AACTCCAGTCAACTCCGGCCATTCTGTTAA 14 36 1 AACTCCGGCC 0.965808 -76 AAAATGCCTCATCTCCGGCCATGGGCGCTG 17 91 1 ATCTCCGGCC 0.972068 -210 GTGAGGGCGAATCCCCAGGCACACCTCAGA 21 250 0 ATCCCCAGGC 0.908435 -51 TAATCTTTATGGCTCCAGCCCCGGAGTTTA 23 140 0 GGCTCCAGCC 0.827871 -161 CTAACCCAGAATTCCCGGCCTCAAACCTCT 24 44 1 ATTCCCGGCC 0.785451 -90 AGAGTTAACAATCTCCTGCCCGAATTTTAC 24 86 0 ATCTCCTGCC 0.87266 -48 ********** Masking position 5 Map Score: 14.5384 Number of sites scoring better than the average of aligned sites = 906 Number in coding regions = 841 Number in noncoding regions = 65 Number of orfs with sites within 600 bp upstream = 82 Fraction of orfs with sites within 600 bp upstream = 0.0131706 Motif number 7 TGTGGAAACTGCCGGCTCGGCCAAGCTTGGG 3 34 1 GCCGCTCGGC 0.827477 -148 CAGGACGGGGGTCAACTTTCCAGAGGTTGCC 4 32 1 GTCACTTTCC 0.705408 -55 GGGTTTTAGACCCGGTTTTCCGATAAACTTA 7 220 1 CCCGTTTTCC 0.864608 -81 CATCACCATGGTAATCTTTCCTTTCCTCCTA 9 59 1 GTAACTTTCC 0.433394 -53 GCAATTAGATGCCAATTTTCCTAGAACATTG 10 54 0 GCCATTTTCC 0.933869 -121 GATTTAGTTTGCCAGTTTGCCGTTGCATCAA 10 145 0 GCCATTTGCC 0.96251 -30 TTATTGTTTAGCTGCTTTTCCGCAGGTCCAG 11 15 1 GCTGTTTTCC 0.612998 -193 GTTGCCTTTAGCGGTTTTGCC 12 87 1 GCGGTTTGCC 0.809013 -11 ATCTCCGCCCCCCCACTTTCC 14 1 0 CCCCCTTTCC 0.778253 -111 AGGGCCAGTTCTCCAAATAACCGC 15 96 0 GCCATTCTCC 0.879711 -14 TGGGGATGGGGCCGCCTTGGCAATGCTGACC 16 53 1 GCCGCTTGGC 0.903032 -127 CAACCGCTCTGCCACCTCTCCAGGGAATTCT 21 65 1 GCCACTCTCC 0.929551 -236 CCATCTTAGCGCAGATTTGCCGTGGGTTATT 21 124 1 GCAGTTTGCC 0.920087 -177 TCTCAGCTCAGCAAGCTTGCCGATTATTGTA 27 49 1 GCAACTTGCC 0.936722 -206 AAACCGTACTCCACTCTTGCCGTGATAGAGT 28 138 0 CCACCTTGCC 0.669153 -163 AGTGAACTATCCCAACTTGCCCAGTGACTCT 28 231 0 CCCACTTGCC 0.9364 -70 ATTAGCAGATTCGCCCCTGTCGTCT 29 36 0 GCAGTTCGCC 0.855527 -15 **** ****** Masking position 7 Map Score: 11.8522 Number of sites scoring better than the average of aligned sites = 1094 Number in coding regions = 989 Number in noncoding regions = 105 Number of orfs with sites within 600 bp upstream = 112 Fraction of orfs with sites within 600 bp upstream = 0.0179891 Motif number 8 GGCTATTATACTGGTCAATGTTCTAGGAAAA 10 39 1 CTGGTCATGT 0.772272 -136 CTGATCCCCACTGGATTAGGGTTATTAGGCT 13 14 1 CTGGATAGGG 0.967407 -89 AACGCCTGGACTGGATCTGTCAAAAAATGTT 16 136 0 CTGGATTGTC 0.448001 -44 GTGCAATGATCTGGTTGTTGTCTTATTTATA 17 185 0 CTGGTTTTGT 0.68321 -116 CAAAATTGCGCTGGTTAATGCAGGGATCGTT 17 277 1 CTGGTTATGC 0.878391 -24 TAATCATAAGCTGGTTTAGGTTTAGTTAAAA 18 276 0 CTGGTTAGGT 0.948835 -25 AAAAATCCCCCTGGTTAAAGGAGGATTATCG 19 72 0 CTGGTTAAGG 0.775674 -97 GGCAATCTTCCTGGATCAGGGTAGAGAAAAA 20 247 0 CTGGATAGGG 0.967407 -24 GTCAATAAACCTGGATATGGGAACGG 22 31 1 CTGGATTGGG 0.896765 -16 GCCGACGGGTCTGGATTATGGGCAATAATCA 23 83 1 CTGGATATGG 0.921843 -218 GCCGGGAATTCTGGGTTAGGCTCAGCAATAA 24 32 0 CTGGGTAGGC 0.937473 -102 ATTGTTAACTCTGGTTAAGTTTCAGTGGGTA 24 104 1 CTGGTTAGTT 0.77075 -30 CTCAGAGTCACTGGGCAAGTTGGGATAGTTC 28 228 1 CTGGGCAGTT 0.560667 -73 TAGAAGCAGTCTGGGCGATGGGATCCATCAT 32 27 1 CTGGGCATGG 0.841777 -116 ****** **** Masking position 2 Map Score: 8.43005 Number of sites scoring better than the average of aligned sites = 834 Number in coding regions = 762 Number in noncoding regions = 72 Number of orfs with sites within 600 bp upstream = 91 Fraction of orfs with sites within 600 bp upstream = 0.0146161 Motif number 9 TTTTGCTTCACCTGCAGTATTGCTCCCCAA 3 60 0 CCTGCAGTAT 0.91163 -122 ACTCAGGTAGACCTCAGTGTCCGGATCTCG 7 109 1 ACCTCAGTGT 0.646614 -192 CTTTCCGCCCCCAGCACTGTTTACAGGAAG 7 274 1 CCAGCACTGT 0.744493 -27 AAATTTTTCCCCTGCAGGGTAACGCAAAGT 10 96 1 CCTGCAGGGT 0.75598 -79 TATCTCCGCCCCCCCACTTTCC 14 3 0 CCCCCACTTT 0.83698 -109 GAATCTGATTCCCCCAGTATTGGGGGCTAG 19 43 0 CCCCCAGTAT 0.972761 -126 CAGTGCCCACACCGCAGTGTTTGGTTCTTG 20 92 0 ACCGCAGTGT 0.905118 -179 TTCGCCCTCACCTCCAGTATAAATTCCTGA 21 269 1 CCTCCAGTAT 0.938424 -32 TCATACCACGCCCCCACTGTCCGGCAGGGT 23 207 1 CCCCCACTGT 0.970747 -94 TATTAAAAGTCCCCCAGTATTG 28 3 0 CCCCCAGTAT 0.972761 -298 TCTCAATAAGACTCCACTATTGCAACTGCT 32 71 0 ACTCCACTAT 0.687494 -72 ********** Masking position 6 Map Score: 5.79788 Number of sites scoring better than the average of aligned sites = 549 Number in coding regions = 464 Number in noncoding regions = 85 Number of orfs with sites within 600 bp upstream = 89 Fraction of orfs with sites within 600 bp upstream = 0.0142949 Motif number 10 ATCAGAAGATTACTCAGTCAAGCAAAAAGCACC 1 67 0 TCCAGTCAGC 0.894764 -114 GTGGACACTAGGCACATTCTACCTTGAACTATC 2 71 1 GCCATTCACC 0.968845 -67 TCCAGGCTCATTTTATCTGACATTGCC 2 121 0 GCCATTTATC 0.659726 -17 GGAAACTGCCGGCTCGGCCAAGCTTGGGGAGCA 3 37 1 GCCGGCCAGC 0.841467 -145 TTAGAATCGGGCCACATTTGAGCGTTTGGAGCC 3 152 1 GCCATTTAGC 0.945539 -30 GTTAATCGTTAACCCATACTAGCAAAGAAGCAG 20 119 0 ACCATACAGC 0.825032 -152 TTTCGAGTCTGCCGCATTCAACCGCTCTGCCAC 21 47 1 GCCATTCACC 0.968844 -254 ATGGGCAATAATCACAGTCGAGCCAGACTACCC 23 100 1 ACCAGTCAGC 0.965486 -201 GATTAACTGAGTCTCAGCTCAGCAAGCTTGCCG 27 38 1 GCCAGCTAGC 0.874712 -217 TACGGTTTGAAGCCCATTCCAGCACTTTATCAT 28 161 1 ACCATTCAGC 0.96765 -140 CTCCGGAAGTAACTCATTCAACCAAAGATTTGT 31 37 0 ACCATTCACC 0.929928 -159 * * ***** *** Masking position 11 Map Score: 4.12028 Number of sites scoring better than the average of aligned sites = 146 Number in coding regions = 123 Number in noncoding regions = 23 Number of orfs with sites within 600 bp upstream = 30 Fraction of orfs with sites within 600 bp upstream = 0.0048185 Motif number 11 GAAGCGCGGTGCTTTCCGCCCCCAGCACTG 7 263 1 GCTTTCCGCC 0.973988 -38 TGGAGTTATTTATCTCCGCCCCCCCACTTT 14 13 0 TATCTCCGCC 0.816869 -99 ATCTGACGATGGTTGCCGCCAAATAGTAAA 15 61 1 GGTTGCCGCC 0.976721 -49 GGAATTGGTGGATTCCCGCCAGACAGGGAA 20 188 0 GATTCCCGCC 0.953152 -83 GATCCAGGAAGATTGCCGCC 20 261 1 GATTGCCGCC 0.986232 -10 GATTTCTGCAATTTTCCGCCCCCATCTTAG 21 103 1 ATTTTCCGCC 0.822649 -198 CAAAACTTCCTTTTGCCGCCCT 27 243 1 TTTTGCCGCC 0.960328 -12 GATTACCAATTCTTGCCGCCGAGGAAATCA 31 72 1 TCTTGCCGCC 0.973988 -124 ********** Masking position 3 Map Score: 5.57132 Number of sites scoring better than the average of aligned sites = 267 Number in coding regions = 247 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 25 Fraction of orfs with sites within 600 bp upstream = 0.00401542 Motif number 12 TTTCCACAAAGACCCGATCGCCAGGGGGGA 3 12 0 GACCCGATCG 0.989088 -170 CCTGTGTCCCGAACCGATCGCCGAAAGG 11 190 1 GAACCGATCG 0.921612 -18 CAAATAATCTGACCCTTTGGACGTCAGCAC 13 45 0 GACCCTTTGG 0.89129 -58 ACTATTCAATGACCCAATGGAGCCGATTTA 18 161 1 GACCCAATGG 0.914353 -140 ATGAAGTAATTACCCGATCGCCGTCTCCAA 18 207 1 TACCCGATCG 0.921612 -94 AAGGGGTCTAGACCCGTTCGTCATTGCCTT 20 160 1 GACCCGTTCG 0.985838 -111 CCATAATCCAGACCCGTCGGCGGTGCAGAG 23 74 0 GACCCGTCGG 0.942221 -227 ********** Masking position 2 Map Score: 4.37727 Number of sites scoring better than the average of aligned sites = 70 Number in coding regions = 65 Number in noncoding regions = 5 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 Motif number 13 GTTCTATGTTACCACTGACCCTGAATTTG 7 9 0 ACCACTGACC 0.889853 -292 TTGACCACGGAACGCCGAGAATTT 8 4 1 ACCACGGACG 0.608796 -235 CCCTCGTCGCCCCACTGAGCGCCGATAACAA 8 178 0 CCCACTGACG 0.70876 -61 ATCCGCTGATCGACTTAATAAG 8 227 0 TCCGCTGACG 0.810686 -12 GGAACGGTTAACTCCTGGGCGGGGCTACGAC 11 150 0 ACTCCTGGCG 0.791605 -58 GGCAAAACCGCTAAAGGCAACAGCGTT 12 81 0 ACCGCTAAGG 0.82509 -17 TGGCATTCCAACTGCCAAGGCAATGGCGTTT 15 28 0 ACTGCCAAGC 0.386641 -82 GGCAATGCTGACCCCTAGGCCTACCAAAATT 16 71 1 ACCCCTAGCC 0.853853 -109 GTATTGAAAGTCCCCTAGCCCCCAATACTGG 19 29 1 TCCCCTAGCC 0.503469 -140 TAAATTCCTGACTGCCGATCGCC 21 288 1 ACTGCCGACG 0.787223 -13 AGACCTCTGCACCGCCGACGGGTCTGGATTA 23 70 1 ACCGCCGAGG 0.910866 -231 GAGCCAGACTACCCCTGGAGGTAAACTCCGG 23 119 1 ACCCCTGGGG 0.912698 -182 GAACGAGGACACCACCGACCCCAAGAGAGCT 27 148 0 ACCACCGACC 0.858129 -107 TTTTAAATGCCCCCCTAGCCCCCCAAGTTTG 28 42 0 CCCCCTAGCC 0.610658 -259 CAGTTTACTTACCGCTGGAGCAAGCC 28 285 1 ACCGCTGGGC 0.915695 -16 GCGCGGGCATACCCCCAATGGCAGGGAGAGG 31 113 0 ACCCCCAAGG 0.752513 -83 CACTATTGCAACTGCTGAGCCAAGGGACTAT 32 56 0 ACTGCTGACC 0.814945 -87 ******** ** Masking position 5 Map Score: 5.77792 Number of sites scoring better than the average of aligned sites = 1647 Number in coding regions = 1502 Number in noncoding regions = 145 Number of orfs with sites within 600 bp upstream = 150 Fraction of orfs with sites within 600 bp upstream = 0.0240925 Motif number 14 GCCAATGGGGTCATCAAACCCCACATCACCA 9 36 1 TCATCAACCC 0.720724 -76 GTCCAGGCGTTCATCCTTTCCCTACTCCGCC 16 156 1 TCATCTTTCC 0.686958 -24 ACCAACGATCCCTGCATTAACC 17 289 0 CCAACATCCC 0.929061 -12 TTTTTGAATATCAACTATTCCATCTTGATTA 18 49 0 TCAACATTCC 0.959366 -252 TGGCGGGAATCCACCAATTCCCATAGTCTAA 20 197 1 CCACCATTCC 0.684875 -74 GAAATCCTTCTCAAGAATTCCCTGGAGAGGT 21 78 0 TCAAGATTCC 0.849087 -223 GCCATGGTCGTCAACAATCCCCGTATTCTAC 21 174 0 TCAACATCCC 0.97422 -127 GTTAATCATTTCAACCCTCCCAGCGGACGGC 27 14 0 TCAACCTCCC 0.959462 -241 CCTGCCCCTATCAAAACTTCCTTTTGCCGCC 27 232 1 TCAAACTTCC 0.563688 -23 CCAACTACAGTGAACTATCCCAACTTGCCCA 28 239 0 TGAACATCCC 0.890369 -62 TGAATTCAGGTCATCGCTTCCCCA 31 182 1 TCATCCTTCC 0.897106 -14 CAAGGGACTATGATGGATCCCATCGCCCAGA 32 36 0 TGATGATCCC 0.532951 -107 ***** ***** Masking position 3 Map Score: 2.4402 Number of sites scoring better than the average of aligned sites = 522 Number in coding regions = 470 Number in noncoding regions = 52 Number of orfs with sites within 600 bp upstream = 65 Fraction of orfs with sites within 600 bp upstream = 0.0104401 Motif number 15 ********** No masking Map Score: 1.21035e-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