AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/alignace/lib/ORF_synecho.txt -z/skink1/amcguire/genomes/synecho.fna -icrp_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 pchR 242 regulatory protein PchR #2 ppiB 205 peptidyl-prolyl cis-trans isomerase B #3 1651883 300 hypothetical protein #4 1651928 300 hypothetical protein #5 1651929 48 hypothetical protein #6 1651991 238 hypothetical protein #7 1651992 65 hypothetical protein #8 1652008 255 hypothetical protein #9 1652009 95 hypothetical protein #10 lim 127 lipophilic protein #11 1652055 172 hypothetical protein #12 sulA 76 cell division inhibitor #13 malK 68 cytoplasmic membrane protein for maltose uptake #14 deoC 51 deoxyribose-phosphate aldolase #15 1652745 300 hypothetical protein #16 lacG 126 lactose transport system permease protein LacG #17 galE 73 UDP-glucose 4-epimerase #18 ilvG 300 acetohydroxy acid synthase #19 1653131 195 hypothetical protein #20 1653345 300 catabolite gene activator protein #21 glpD 145 glycerol-3-phosphate dehydrogenase #22 1653439 300 hypothetical protein #23 glpK 52 glycerol kinase #24 ycf27 154 regulatory components of sensory transduction system #25 1653613 187 hypothetical protein #26 leuA 185 2-isopropylmalate synthase #27 1001455 84 hypothetical protein #28 1001456 95 hypothetical protein #29 1001457 37 hypothetical protein #30 1001458 26 hypothetical protein #31 1001644 216 regulatory components of sensory transduction system #32 1001201 145 hypothetical protein #33 1001217 300 hypothetical protein #34 1001218 55 hypothetical protein #35 1001219 85 hypothetical protein #36 1001220 80 hypothetical protein #37 alr 265 alanine racemase #38 1001717 182 regulatory components of sensory transduction system #39 crtE 166 phytoene dehydrogenase #40 erg6 82 delta(24)-sterol C-methyltransferase #41 ppd 23 4-hydroxyphenylpyruvic acid dioxgenase (HPD) #42 1001727 56 aldehyde dehydrogenase #43 ycf27 190 regulatory components of sensory transduction system #44 1001829 221 hypothetical protein #45 devB 44 glucose-6-P-dehydrogenase #46 1653816 147 hypothetical protein #47 1653824 238 regulatory components of sensory transduction system #48 msiK 137 ATP binding protein responsible for multiple sugar import #49 fur 142 ferric uptake regulation protein Motif number 1 GTCCCCATTTCCCCTAGAAAGTTATCTAAA 2 92 1 CCCCTAGAAA 0.839829 -114 AATCTTTGACCCCCTGGAGAGGTGGCAGAG 3 15 1 CCCCTGGAGA 0.873963 -286 TTTTAGCTTACCCCTGGAGTAATTAGAGGA 4 186 0 CCCCTGGAGT 0.874113 -115 CCCCCAGCATCGGAGCCAAA 10 1 1 CCCCCAGCAT 0.955988 -127 TTTGGTATGGCCCCTAGAATTTGGCTCCGA 10 20 0 CCCCTAGAAT 0.839829 -108 AACCATTTTCCCCCTGGAGTGACAGAGGAA 11 64 0 CCCCTGGAGT 0.874113 -109 ACTCCTACTCCCCCCAGGGTC 12 66 1 CCCCCAGGGT 0.823132 -11 AATCCCCAGGAAAAAGTCGAGT 14 3 1 TCCCCAGGAA 0.652658 -49 TGAACGACTATCCATGGCAAGAACTGAGTC 15 192 1 TCCATGGCAA 0.382148 -109 AACTATCAACCCCCTGGGATTATTCTGGGG 16 24 1 CCCCTGGGAT 0.934037 -103 AATAAAAATCCCCCCAGAATAATCCCAGGG 16 35 0 CCCCCAGAAT 0.846868 -92 ACAAACAATGCCACTGGCAATAGCCTGTGG 20 49 0 CCACTGGCAA 0.691492 -252 CCAGAAATGCTCCCTAGCAAGTGAAAAAAC 20 133 1 TCCCTAGCAA 0.845292 -168 ATTGATAGCCTCCCTAGGATGGCTCGGTCT 20 264 0 TCCCTAGGAT 0.650423 -37 ATTTACCCTGCCCATGGCAATAGTTTTAAG 22 14 0 CCCATGGCAA 0.699735 -287 TTGAGCTTTGCCCCCGGCGATCGCCTAGGG 22 140 1 CCCCCGGCGA 0.966016 -161 AATCCCTTACTCCCCAGCAATTTCAGCTTA 22 261 1 TCCCCAGCAA 0.852079 -40 GCACTTAGTCCCCCTTGCATAGGGAACCGC 25 22 0 CCCCTTGCAT 0.686676 -166 TCAGGTCTCCCCCCCGGCGAAAAAGCACTT 25 46 0 CCCCCGGCGA 0.966016 -142 CGGCCCATCCCACTGGCGATCGCCAATTT 25 169 0 CCACTGGCGA 0.595878 -19 GGCTACTTCATCCCCGGTAAAAAATCGTTA 28 25 0 TCCCCGGTAA 0.51916 -71 AATCTATCTGCCCCTAGCATCAGAGATTAA 32 63 0 CCCCTAGCAT 0.953691 -83 AAGTCAAAGTCCCCCAGCATCGGGAGATTT 33 23 1 CCCCCAGCAT 0.955988 -278 AGGGGCTTTGACCCTGGCATCATAGCACAC 33 224 0 ACCCTGGCAT 0.634332 -77 AGGGTCAAAGCCCCTGGTAAGCAATTGAAA 33 239 1 CCCCTGGTAA 0.794423 -62 AAGTTCCAGTTCCCTAGGATAGAAATTGGC 37 181 0 TCCCTAGGAT 0.650423 -85 GCTCCACTAATCCCCGGCGATGGAAGTTAA 39 49 0 TCCCCGGCGA 0.868124 -118 CGCCCTGTTTCCCGCGGCATTTTTATAGTA 43 83 0 CCCGCGGCAT 0.673834 -108 ********** Masking position 7 Map Score: 37.3224 Number of sites scoring better than the average of aligned sites = 2268 Number in coding regions = 2034 Number in noncoding regions = 234 Number of orfs with sites within 600 bp upstream = 263 Fraction of orfs with sites within 600 bp upstream = 0.0422422 Motif number 2 CAAGTAATACCATCTCCTATGGGACATTGA 1 10 1 CCATCTCCAT 0.906766 -233 ATTGCCATTCCCGTGCTGTCAGATT 2 5 1 CCATTCCCTG 0.725539 -201 TGTTAAGAGTTGATCGCCTTTAGGAATTCTC 6 159 0 TGATCGCCTT 0.599872 -80 TATCTACCTTCCATTTCCGGGATGGAAGCCC 8 166 0 CCATTTCCGG 0.566504 -90 GGCGATCGCCGGTTAGCTAAACT 9 3 1 CGATCGCCGT 0.961189 -93 AATCGCTGTCCCTTCCCCCATATTCCCGGTT 15 228 1 CCTTCCCCAT 0.721607 -73 CATAGGGAGCCCATCGCCGATTGAGTTAAAA 18 240 1 CCATCGCCAT 0.978204 -61 GCGATCGCCAATGCCAGTTGTG 21 2 1 CGATCGCCAT 0.967901 -144 TTGCCCCCGGCGATCGCCTAGGGATAAACAA 22 147 1 CGATCGCCAG 0.971403 -154 TCTGCCCCATCCCCATTGATACCAACG 24 7 1 CCATCCCCTT 0.94172 -148 ATCCCACTGGCGATCGCCAATTTTCGTTTAA 25 161 0 CGATCGCCAT 0.967901 -27 CTTTATCGTCCCATTGCCCTTTCTTCTCCCC 26 28 0 CCATTGCCTT 0.8221 -158 AAAGGCTACTTCATCCCCGGTAAAAAATCGT 28 27 0 TCATCCCCGT 0.567582 -69 CGTTTTGAGACCTTCCCCTTGGCTTAACCCA 31 134 1 CCTTCCCCTG 0.674306 -83 ATTTGCTATGCGATCGCCTAGTTTGCC 31 200 1 CGATCGCCAG 0.971403 -17 AGTCACAGGGCGATCGCCGTTAA 32 3 0 CGATCGCCTT 0.955316 -143 TAACCAATTTCCATTTCCTATCTAGGCTTTG 38 22 1 CCATTTCCAT 0.585474 -161 TAATTAACTTCCATCGCCGGGGATTAGTGGA 39 46 1 CCATCGCCGG 0.976485 -121 CTGACCGTGGCGATCGCCTGGAATGAATTTT 39 108 0 CGATCGCCGG 0.965397 -59 AGTCCACAATCTCCTAGGTAATT 41 7 1 CAATCTCCAG 0.55996 -17 GAAGCCTTGACAATCCCCGTTGGTGATTTAT 46 27 1 CAATCCCCTT 0.652382 -121 ATGATGGATCCCATCGCCCAGACTGCTTCTA 49 106 1 CCATCGCCAG 0.980605 -37 ******** ** Masking position 4 Map Score: 28.8775 Number of sites scoring better than the average of aligned sites = 5335 Number in coding regions = 4894 Number in noncoding regions = 441 Number of orfs with sites within 600 bp upstream = 396 Fraction of orfs with sites within 600 bp upstream = 0.0636042 Motif number 3 AAGCCCTAACGGGCAAAATACCAGTGCAGTATATTTGT 1 102 0 GGGCAAATCA 0.617876 -141 ATAACTTTCTAGGGGAAATGGGGACCAATTGAACATAA 2 79 0 AGGGAAATAA 0.493132 -127 AAGGGCAGGCGAGGGAAAATCTCCTTCACCTCCTTTTT 4 94 1 GAGGAAAACA 0.89536 -207 GGAGTAATTAGAGGAAAATCTGACCAAACTGCTTCTAT 4 163 0 GAGGAAATAA 0.657796 -138 CAATCCTCTCAAGGAAGAAATTCAAACAGACGGTAGAA 8 119 1 AAGGAGAACA 0.553435 -137 CGGGGCAGTAGGGCCAGAAAACTTGCCATAGTCTTAGT 9 31 0 GGGCAGAACA 0.88865 -65 GTACAAATATGGGGTAAACTTTATCCTAAACCCTTCCC 10 84 1 GGGGAAACTA 0.603377 -44 TGTCACTCCAGGGGGAAAATGGTTGGAACCTGACAGAT 11 70 1 GGGGAAAAAA 0.970721 -103 GATAGAATAAAGGGCAGAAATATTAGAATAATTGAAGC 19 12 0 AGGGAGAAAA 0.827646 -184 GGATTTAGTTGAGGAAAAAAATTCCCAAGCTTGGAACC 20 12 1 GAGGAAAAAA 0.890903 -289 TCTCTGGAGTGGGGCACAACCAATTTAAGGTTTACTTA 20 169 1 GGGGACAAAA 0.818128 -132 CTGACTTAGGGGGGCAAAAACAATGTCAATCCAGGGAT 22 207 0 GGGGAAAACA 0.97202 -94 TTTTCGCCGGGGGGGAGACCTGAAACAAAAAGGTTTCT 25 53 1 GGGGAGACAA 0.916314 -135 GGGAAGCAGAGGGGGAGAAGAAAGGGCAATGGGACGAT 26 17 1 GGGGAGAACA 0.975823 -169 AATTTCCCCTGAGGAAGAAGCCATGGCAACAGCCAATG 31 65 0 GAGGAGAACA 0.908603 -152 TCTGATGCTAGGGGCAGATAGATTATAATTAATAGAGT 32 69 1 GGGGAGATAA 0.900667 -77 TGGGGGGAAACTAAGTCAAAGTCCCCCAGC 33 3 1 GGGGAAACAA 0.904071 -298 ATACTAAATGGAGCAAAAAAATTCGTCAGTAGTCATAA 35 22 1 GAGCAAAACA 0.628521 -64 TTGCTACCCTGAGGTAGAAAGACGCATAAAGAATATCT 37 56 0 GAGGAGAATA 0.604986 -210 GGGGCAAAACTTAACCAATTTCCATTTC 38 1 1 GGGGAAAAAA 0.970721 -182 TACCTTGCCCAGGGAAAAATTCATTCCAGGCGATCGCC 39 93 1 AGGGAAAACA 0.812409 -74 GCTCAGGGGCTAAAACTAAAGGAAAAAAACGATT 43 167 0 GGGCAAAAAA 0.867651 -24 ATAGCAAGTAGGAGAAGAAAAAAAGGAAAACTAAGAGT 44 96 0 GGAGAGAAAA 0.561121 -126 TTGAAGAAAAGGGGGAGAAAATCGTAAAGAAATCGGAA 47 105 1 GGGGAGAAAA 0.974696 -134 ATTTTCAGACGGGGGAAGATAAATAAAACTTTTTCTAG 49 18 1 GGGGAAGAAA 0.725874 -125 **** **** ** Masking position 6 Map Score: 24.5449 Number of sites scoring better than the average of aligned sites = 1312 Number in coding regions = 1111 Number in noncoding regions = 201 Number of orfs with sites within 600 bp upstream = 217 Fraction of orfs with sites within 600 bp upstream = 0.0348538 Motif number 4 CTACTCCTAATGCAAATTATTCCTAAATATT 1 163 0 TGCAATTATT 0.437685 -80 AGCAAATCCTGGGTAATTATTTTATAATCTA 3 176 1 GGGAATTATT 0.953358 -125 CCTTTTTTTTTGACAATTTTTGCCAGTGTGG 4 125 1 TGAAATTTTT 0.532966 -176 GGCAGGACCGCGGGAATTTTTTTAGCTTACC 4 204 0 CGGAATTTTT 0.88501 -97 CGATTTTGTCGGGAAAGTTCTCGCTTTATTT 4 255 0 GGGAAGTTCT 0.791301 -46 AGACCAGATCGGTTAATTATTCACTTGGAGT 8 69 1 GGTAATTATT 0.670986 -187 ACTAAGACTATGGCAAGTTTTCTGGCCCTAC 9 31 1 TGGAAGTTTT 0.827408 -65 GGGGAATTATTCGCTATAAAG 9 85 0 GGGAATTATT 0.953358 -11 GCAAGGACAGGGGCAATTACTCGACTTTTTC 14 20 0 GGGAATTACT 0.799551 -32 GATTATTCTGGGGGGATTTTTATTGGGTTTA 16 41 1 GGGGATTTTT 0.823347 -86 GTTCCAAGCTTGGGAATTTTTTTCCTCAACT 20 18 0 TGGAATTTTT 0.919598 -283 CTCTAACTTTGGGCAATTTTTAGGGGGTTTG 21 64 0 GGGAATTTTT 0.978883 -82 CATTCAGTCAGGATAATTTTTGCAGTTTTTT 22 91 1 GGAAATTTTT 0.822222 -210 TCTTCCTCAGGGGAAATTTTTTCTGGGCCAT 31 85 1 GGGAATTTTT 0.978883 -132 CAGCCGAACGGGGAAATTTTTTAACTCAAGG 32 122 0 GGGAATTTTT 0.978883 -24 AATGGAAATTGGTTAAGTTTTGCCCC 38 6 0 GGTAAGTTTT 0.659697 -177 ATAGCAAACGGGGGAATTTTTTTCGTGCCCA 38 75 1 GGGAATTTTT 0.978883 -108 GAATATTTACCGGGAAGTATTAATTAACTTC 39 26 1 CGGAAGTATT 0.587199 -141 CCGAAGTCGAGGCCAATTTTTTT 39 154 1 GGCAATTTTT 0.877361 -13 TGTTTTTTTATGGCAATTTTTAGGGCAGTCC 46 123 1 TGGAATTTTT 0.919598 -25 *** ******* Masking position 8 Map Score: 20.7547 Number of sites scoring better than the average of aligned sites = 876 Number in coding regions = 734 Number in noncoding regions = 142 Number of orfs with sites within 600 bp upstream = 144 Fraction of orfs with sites within 600 bp upstream = 0.0231288 Motif number 5 CATCTCCTATGGGACATTGAACTCTCATCG 1 21 1 GGGACATTGA 0.771421 -222 GGGCAGAAACGGGGGTTTGTTATGTTCAAT 2 60 1 GGGGGTTTGT 0.74719 -146 TAACTTTCTAGGGGAAATGGGGACCAATTG 2 86 0 GGGGAAATGG 0.798914 -120 GTCAAGGACCGGGGCAGTAGGGCCAGAAAA 9 48 0 GGGGCAGTAG 0.677428 -48 TCACTCCAGGGGGAAAATGGTTGGAACCTG 11 72 1 GGGAAAATGG 0.665082 -101 CCATGGATGGGGGTGTTTGGACTCAATGTT 11 113 1 GGGTGTTTGG 0.878898 -60 GACCCTGGGGGGAGTAGGAGTAAGTTA 12 60 0 GGGGGAGTAG 0.621649 -17 TAATCGAACCGGGAATATGGGGGAAGGGAC 15 235 0 GGGAATATGG 0.818297 -66 TGGCGGCAGGGGCTGTGGATTGGTTAGT 15 283 0 GGGGCTGTGG 0.975819 -18 GGGTAGTGGTGGGGCATTGGTCAACAAGGC 16 90 0 GGGGCATTGG 0.967148 -37 CCCTACCGGAGGAACTTTGGCGGGTAGCCT 18 14 0 GGAACTTTGG 0.582674 -287 GCAATTTTTAGGGGGTTTGGACAATGGTTA 21 53 0 GGGGGTTTGG 0.981215 -93 TAGCCAAATTGGGGGTTTGGTATCGTTGGT 24 31 0 GGGGGTTTGG 0.981215 -124 GGGGATGGGAGGGGGTTTAGCAACAAATTG 27 65 0 GGGGGTTTAG 0.860424 -20 CCGATGCTGGGGGACTTTGACTTAGTTTCC 33 16 0 GGGACTTTGA 0.884441 -285 TTGCTTACCAGGGGCTTTGACCCTGGCATC 33 233 0 GGGGCTTTGA 0.938697 -68 TATCCCCTTGGGGAATTTGGGTGCAGAGGA 37 237 1 GGGAATTTGG 0.90559 -29 TTCATCATCGGGGTGTATGGCAAGTGAAGC 40 51 1 GGGTGTATGG 0.773107 -32 TTCAGGCCCTGGGACTGTGAAAGCCTTTAT 43 119 1 GGGACTGTGA 0.82226 -72 GCTGAGCCAAGGGACTATGATGGATCCCAT 49 90 1 GGGACTATGA 0.782293 -53 ********** Masking position 8 Map Score: 19.5954 Number of sites scoring better than the average of aligned sites = 1742 Number in coding regions = 1567 Number in noncoding regions = 175 Number of orfs with sites within 600 bp upstream = 190 Fraction of orfs with sites within 600 bp upstream = 0.0305172 Motif number 6 ACCAAATTCAGGGCAGAAACGGGGGTTTGTTATG 2 50 1 GGGAGAGGGG 0.995407 -156 GCCCGCCGATGGGCAGGACCGCGGGAATTTTTTT 4 212 0 GGGAGAGCGG 0.954871 -89 AAGGAAAGTGGTCAAGGACCGGGGCAGTAGGGCC 9 54 0 GTCAGAGGGG 0.895668 -42 GACCCTGGGGGGAGTAGGAGTAAGTTAAAA 12 57 0 GGGGGGGGAG 0.833265 -20 GGGATGAAATGGCAAGGACAGGGGCAATTACTCG 14 28 0 GGCAGAGGGG 0.985476 -24 GGGTAATAGCGGGTAGTGGTGGGGCATTGGTCAA 16 96 0 GGGAGGGGGG 0.993756 -31 TTTATCCCTAGGCGATCGCCGGGGGCAAAGCTCA 22 141 0 GGCATGGGGG 0.934732 -160 TGAAATTGCTGGGGAGTAAGGGATTTTCAACTCT 22 252 0 GGGAGAGGAT 0.739729 -49 TTGGTATCGTTGGTATCAATGGGGATGGGGCAGA 24 11 0 TGGATAGGGG 0.88742 -144 GGGCTAGGGAAGCAGAGGGGGAGAAGAAAG 26 7 1 GGGAGAGGGG 0.995407 -179 GGGGATGGGAGGGGGTTTAGCAAC 27 71 0 GGGATGGGGG 0.978608 -14 TTCCATCGCCGGGGATTAGTGGAGCACGATCCTC 39 54 1 GGGATAGGAG 0.925392 -113 CAAAGTAAAATTGAAGAAAAGGGGGAGAAAATCG 47 95 1 TTGAGAGGGG 0.77627 -144 *** ** * **** Masking position 11 Map Score: 16.1594 Number of sites scoring better than the average of aligned sites = 703 Number in coding regions = 641 Number in noncoding regions = 62 Number of orfs with sites within 600 bp upstream = 70 Fraction of orfs with sites within 600 bp upstream = 0.0112432 Motif number 7 AAATGTGCTGTGGCGATTGGGACAACCTTG 1 67 0 TGGCGATTGG 0.955266 -176 TTAGCAATTACGGAGATTAGATTTT 2 191 1 CGGAGATTAG 0.914219 -15 GGGGCTATTTTGGGGATTGG 13 1 0 TGGGGATTGG 0.942055 -68 GGGGAAGGGACAGCGATTAGGATAGACTCA 15 216 0 CAGCGATTAG 0.629064 -85 TTAACTCAATCGGCGATGGGCTCCCTATGG 18 239 0 CGGCGATGGG 0.870445 -62 TCAAAAAGACTGGAAAATGGGATCAAACAA 22 57 0 TGGAAAATGG 0.677772 -244 TTGGTATCAATGGGGATGGGGCAGA 24 6 0 TGGGGATGGG 0.802354 -149 GTAAAATCGGTAGCGATTGGTTTCCCCTTA 26 79 0 TAGCGATTGG 0.822303 -107 AGACCTATGTAGAAAATGGAAAGCTGAGC 28 77 0 TAGAAAATGG 0.313099 -19 TTCCCTAGGATAGAAATTGGCTTACTCCGA 37 172 0 TAGAAATTGG 0.647004 -94 AGATAGGAAATGGAAATTGGTTAAGTTTTG 38 15 0 TGGAAATTGG 0.89427 -168 CCGCTAGGGCTGGAAATTGGGCACGAAAAA 38 93 0 TGGAAATTGG 0.89427 -90 CCAGCCCTAGCGGAGATTAGCTTTTTTCAC 38 110 1 CGGAGATTAG 0.914219 -73 CTTCCATCGCCGGGGATTAGTGGAGCACGA 39 53 1 CGGGGATTAG 0.856283 -114 AATTCGACCACGGAGAATGGCTTCACCACC 48 15 0 CGGAGAATGG 0.901116 -123 TCATACTACCCGGAGATTAGGTACTTAATG 48 52 0 CGGAGATTAG 0.914219 -86 ********** Masking position 6 Map Score: 12.8563 Number of sites scoring better than the average of aligned sites = 1252 Number in coding regions = 1134 Number in noncoding regions = 118 Number of orfs with sites within 600 bp upstream = 133 Fraction of orfs with sites within 600 bp upstream = 0.021362 Motif number 8 TGAAAACCTGCATTGTGCTGTCAATGTTCCC 12 26 0 CATTTGCTGT 0.951691 -51 AGGAAATTGCCATTATGCTTTTTCAGAGAGA 15 18 0 CATTTGCTTT 0.969187 -283 GTTATCGAGAAATTAAGCTGTGAGCGTTATT 15 101 0 AATTAGCTGT 0.642325 -200 TTGTTTGTGCCATTTTGATTTGGTTTGCCCA 20 71 1 CATTTGATTT 0.828933 -230 GTTTTGATAACATTGAGCTTTGCCCCCGGCG 22 128 1 CATTAGCTTT 0.886418 -173 GGGCCTTGCAAATTTTGCTTTTGTTTAAACG 25 137 1 AATTTGCTTT 0.920357 -51 TTTAGCAACAAATTGTGATGTTTGCTACCAA 27 49 0 AATTTGATGT 0.527197 -36 GTGGTTGCTGCATTTTTCTTTACTCGTGAAA 37 118 1 CATTTTCTTT 0.712504 -148 AATGTTAATTATGCTTTAGTAACGCAC 42 40 0 AATTTGCTTT 0.920356 -17 ATCCTGATTTCATTTTGCTTTGCCAGACTGG 44 169 1 CATTTGCTTT 0.969187 -53 AGCCCATTGTGCTTTTCTCTATCAA 47 224 0 CATTTGCTTT 0.969187 -15 **** ****** Masking position 2 Map Score: 8.53507 Number of sites scoring better than the average of aligned sites = 93 Number in coding regions = 70 Number in noncoding regions = 23 Number of orfs with sites within 600 bp upstream = 29 Fraction of orfs with sites within 600 bp upstream = 0.00465789 Motif number 9 TATAAAATAATTACCCAGGATTTGCTTGGG 3 172 0 TTACCCAGGA 0.832011 -129 TTAGCCACTGTTACCCAGGCAGTAAAGACT 10 49 0 TTACCCAGGC 0.974479 -79 GGTTTATTTGTTACCCTGGTCTGGGCCTTG 16 66 1 TTACCCTGGT 0.889969 -61 TGTCGACTATTAACCCAAGCTGTTGCCTCG 17 54 0 TAACCCAAGC 0.828507 -20 TCATCTATCTAAACCCAGGTCCCAGTAAAT 18 147 1 AAACCCAGGT 0.83835 -154 TAGGGAATTCAAACCCAGGTAAACAAGATG 20 207 1 AAACCCAGGT 0.83835 -94 CATTGGAGCATTACCCAGCC 21 136 1 TTACCCAGCC 0.881977 -10 AAAAATCAATTTACCCTGCCCATGGCAATA 22 22 0 TTACCCTGCC 0.686229 -279 GAAAATATCACCCAGGTAATTACAGGT 31 8 1 TCACCCAGGT 0.894781 -209 CCCCTTGGCTTAACCCAGGTTGAAAGCCGC 31 148 1 TAACCCAGGT 0.96508 -69 CCAGGGGCTTTGACCCTGGCATCATAGCAC 33 226 0 TGACCCTGGC 0.774698 -75 ATTGATAACCTAACCCAAGTTA 42 3 0 TAACCCAAGT 0.777619 -54 CAGCACAAGATTACCCATGTTTTAGATGGA 43 18 1 TTACCCATGT 0.66477 -173 CAACATGAATTAACCCAGACCTGTTCACCC 47 177 1 TAACCCAGAC 0.732602 -62 ********** Masking position 3 Map Score: 9.86913 Number of sites scoring better than the average of aligned sites = 574 Number in coding regions = 520 Number in noncoding regions = 54 Number of orfs with sites within 600 bp upstream = 60 Fraction of orfs with sites within 600 bp upstream = 0.00963701 Motif number 10 TGCTCAATAAATTAAACCCATCAAATATTTAGGAA 1 140 1 ATAACCCAAA 0.924101 -103 TTGCCTCTTGAAGAAACCCATTAAA 7 1 0 AAAACCCAAA 0.974309 -65 CAATCCCCAAAATAGCCCCAATGAAGATGCTAGGA 13 12 1 AAAGCCCAAA 0.856764 -57 ATTTCTCGATAACAAGCCCATTTTAGGGTTTAGGT 15 119 1 AAAACCCATA 0.80142 -182 CAGGGTAACAAATAAACCCAATAAAAATCCCCCCA 16 49 0 AAAACCCAAA 0.974309 -78 TCAATTTATTAACTAGCCCAAAAAACGATACCGCC 18 61 0 AATACCCAAA 0.80142 -240 ATAAAGAGAAAAAAAGCCCTTTAAAATGATAGAAT 19 42 0 AAAACCCTAA 0.81456 -154 TTATAGGGAATTCAAACCCAGGTAAACAAGATGTT 20 204 1 TTAACCCAAA 0.713199 -97 ATTGAATGGAAAAAAGCCCCCTAAACTCTAACTTT 21 85 0 AAAACCCCAA 0.86685 -61 TAATTAAACGATTAAACCCATTCAAATTCATTGGC 31 37 1 ATAACCCAAA 0.924101 -180 TAAGGTTATTAATAACTCCAAAAAAGCAACAAAAA 33 186 0 AAAATCCAAA 0.827535 -115 TTTCGAAAAATAAAAACCCAACTAATTACGCTAGC 36 17 0 TAAACCCAAA 0.885658 -64 CATGACCAAGAAAAACTCCATCTAAAACATGGGTA 43 29 0 AAAATCCAAA 0.827535 -162 ** ** **** ** Masking position 15 Map Score: 8.96903 Number of sites scoring better than the average of aligned sites = 138 Number in coding regions = 107 Number in noncoding regions = 31 Number of orfs with sites within 600 bp upstream = 31 Fraction of orfs with sites within 600 bp upstream = 0.00497912 Motif number 11 ATATAATCCAGGGCACACCAGCAACGGCCC 3 145 1 GGGCACACCA 0.869199 -156 AATTACTCCAGGGGTAAGCTAAAAAAATTC 4 192 1 GGGGTAAGCT 0.697946 -109 TGGGTAACAGTGGCTAAGCACCGTACAAAT 10 62 1 TGGCTAAGCA 0.843624 -66 GGGCAAAGATGGGATTGGGA 10 118 0 GGGCAAAGAT 0.840647 -10 TATTTGACTCGGGCTAACAAAAACAGGGAT 15 162 1 GGGCTAACAA 0.7641 -139 TGAACCGAGTGGGCAAACCAAATCAAAATG 20 81 0 GGGCAAACCA 0.963782 -220 CTTTTAATTCTGGCAAACAATGGTTGAAAC 20 236 0 TGGCAAACAA 0.667392 -65 CGATCGCCGGGGGCAAAGCTCAATGTTATC 22 133 0 GGGCAAAGCT 0.953161 -168 AACGCATTAAGGGGAAACCAATCGCTACCG 26 72 1 GGGGAAACCA 0.865523 -114 TGGGGGGAAACTAAGTCAAAGTC 33 4 1 GGGGAAACTA 0.472095 -297 TTCCGTCTTTGGGCTAAGAATAGTCTGAGA 37 14 1 GGGCTAAGAA 0.827852 -252 CCTAAGATAAGGGCAAAGTTGGAAAAGTTC 37 205 0 GGGCAAAGTT 0.738727 -61 GGGGCAAAACTTAACCAATTT 38 2 1 GGGCAAAACT 0.640015 -181 ATCGTTGAATTGGCAAAGCCTAGATAGGAA 38 36 0 TGGCAAAGCC 0.683953 -147 AATTCCAGTCTGGCAAAGCAAAATGAAATC 44 174 0 TGGCAAAGCA 0.919946 -48 CATAGTCCCTTGGCTCAGCAGTTGCAATAG 49 79 0 TGGCTCAGCA 0.573955 -64 ********** Masking position 7 Map Score: 8.64574 Number of sites scoring better than the average of aligned sites = 1074 Number in coding regions = 939 Number in noncoding regions = 135 Number of orfs with sites within 600 bp upstream = 150 Fraction of orfs with sites within 600 bp upstream = 0.0240925 Motif number 12 CTAATGCAAATTATTCCTAAATATTTGATGGGT 1 155 0 TTTTCCTAAA 0.806432 -88 CAATTTTTCTCTCTGAAAAAGCATAATGG 15 7 1 TTTCTCTAAA 0.806404 -294 GTGAGCGTTATTGTCCCTGAAGATATTTTGACG 15 80 0 TTTCCCTAAA 0.973876 -221 TAAATTGAAATCCTCCCTGAAGAAGGTCAACTT 18 88 1 TCTCCCTAAA 0.954785 -213 AACCCTCCTCCCTAAACATTGATAGCCT 20 283 0 TCTCCCTAAA 0.954805 -18 GTCTTGGGAGTTATCCCTCATAATTCGAGCTAA 33 88 1 TTTCCCTATA 0.869887 -213 CTTGTCCCTAAATACTAAATGGAG 35 2 1 TTTCCCTAAA 0.973896 -84 AATTCAACGATTTTCCCTCAATAGCAAACGGGG 38 55 1 TTTCCCTAAA 0.973895 -128 ** ***** ** * Masking position 10 Map Score: 4.67795 Number of sites scoring better than the average of aligned sites = 30 Number in coding regions = 21 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 13 GGGCGCATTCGACCACTCTGCCACCTCTCCA 3 29 0 GACCATCTGC 0.983656 -272 AGGAAAATCTGACCAAACTGCTTCTATTTTG 4 159 0 GACCAACTGC 0.963855 -142 GATTTGGTTTGCCCACTCGGTTCATGGTAAC 20 87 1 GCCCATCGGT 0.906794 -214 GTATGTCGGCGACCAGTCGGCTCAGCTTTCC 28 58 1 GACCATCGGC 0.965421 -38 TTCAACTATTGCCCATTCTGCATCGCTCAGG 44 14 1 GCCCATCTGC 0.98107 -208 AGCCCATTGTGCTTTTCTCTAT 47 227 0 GCCCATGTGC 0.739775 -12 GGATCCCATCGCCCAGACTGCTTCTAAGCGC 49 111 1 GCCCAACTGC 0.981697 -32 ***** ***** Masking position 5 Map Score: 5.5243 Number of sites scoring better than the average of aligned sites = 86 Number in coding regions = 76 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 14 TATATCCCATCAATTAAAAGTGAAAGTTAAGCAAGCG 3 113 0 CAAAATAAAT 0.956041 -188 TAAACGTTCGCAAATAAATATTTAAGTTCTCGTAATT 6 211 0 CAAAATTAAT 0.829724 -28 CATTATTTTCCAAATAAATTTTTAAGTCACTACCAGC 19 119 0 CAAAATTAAT 0.829724 -77 GAATTCCCTATAAGTAAACCTTAAATTGGTTGTGCCC 20 180 0 TAAAATAAAT 0.751352 -121 GATCAAACAACAAGAAAAAATCAATTTACCCTGCCCA 22 30 0 CAAAATAATT 0.715832 -271 AAAATAAGCTCAAAATAAGCTGAAATTGCTGGGGAGT 22 269 0 CAAAATAAAT 0.956041 -32 CGAGCTAACTCAATCAAAACTTAAAGTTTACAGAAAC 33 113 1 CAAAATAAAT 0.956041 -188 GGTGATAATCAAGGGATGTTAAAAATTAGTAAAAGC 33 275 0 CAAATTAAAT 0.715832 -26 GGGTGTATGGCAAGTGAAGCTCAAAATGATAA 40 61 1 CAAAATAAAT 0.956041 -22 TCCAGTCTGGCAAAGCAAAATGAAATCAGGATGAAAT 44 164 0 CAAAATAAAC 0.788741 -58 ATAAAGTTAGTAATTAAACTTAAAAGTTGTTTAATGT 47 13 1 TAAAATAAAT 0.751351 -226 AATTACGATACAACAAAAAATTAAAATCAAACGGTTA 48 104 0 CAAAATAAAT 0.956041 -34 *** ** * *** * Masking position 7 Map Score: 6.51877 Number of sites scoring better than the average of aligned sites = 40 Number in coding regions = 24 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 17 Fraction of orfs with sites within 600 bp upstream = 0.00273049 Motif number 15 CTGGTATTTTGCCCGTTAGGGCTTTGCTCAATA 1 116 1 GCCCGTGGCT 0.823922 -127 CATAACAAACCCCCGTTTCTGCCCTGAATTTGG 2 51 0 CCCCGTTGCC 0.881566 -155 AAAATCTAATCTCCGTAATTGCTAATGGCAACT 2 183 0 CTCCGATGCT 0.833851 -23 TCTATTTTGCCTCCACACTGGCAAAAATTGTCA 4 135 0 CTCCAAGGCA 0.554819 -166 CAACTCTTAACACCAATCATGCTAACCGTATAA 6 178 1 CACCATTGCT 0.619871 -61 GCCAAAGTTCCTCCGGTAGGGGTGATATATTTC 18 23 1 CTCCGTGGGT 0.736968 -278 CTGGGTAATGCTCCAATGAGGAATAAATCGTGC 21 121 0 CTCCATGGAA 0.456628 -25 GATACCAAACCCCCAATTTGGCTATATGCTTAG 24 37 1 CCCCATGGCT 0.959147 -118 CATCCTAAGGCCCCATTGCGGCTTTCAACCTGG 31 162 0 CCCCATGGCT 0.959139 -55 CACTGCATTTCCCCGTATTTGCTACCCTGAGGT 37 79 0 CCCCGATGCT 0.914001 -187 AAAAGCTAATCTCCGCTAGGGCTGGAAATTGGG 38 102 0 CTCCGTGGCT 0.963435 -81 TTGCCATACACCCCGATGATGAACCATAGGCAT 40 41 0 CCCCGTTGAA 0.749729 -42 CCTTGACAATCCCCGTTGGTGATTTATACTTAG 46 31 1 CCCCGTTGAT 0.877541 -117 ACCGGTGTAACCCCGTTCATACTACCCGGAGAT 48 65 0 CCCCGTTACT 0.691023 -73 CTCAATAAGACTCCACTATTGCAACTGCTGAGC 49 64 1 CTCCATTGCA 0.76655 -79 ***** * **** Masking position 4 Map Score: 6.59978 Number of sites scoring better than the average of aligned sites = 775 Number in coding regions = 725 Number in noncoding regions = 50 Number of orfs with sites within 600 bp upstream = 55 Fraction of orfs with sites within 600 bp upstream = 0.00883392