AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i199_trans1_bbur_reg_300.orf -o199_borburg_300.ace -a/home/amcguire/genomes/ORF_borburg.txt -z/home/amcguire/genomes/borburg.fna -g0.28 -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 = 0.28 maxlen = 30 weight = 0.8 exclude = 1 Purged sequences: RBB00627 28 3615 RBB00621 17 3615 RBB00260 17 3615 RBB00253 17 3615 RBB00334 24 3615 Input sequences: #1 RBB00724 96 3615 #2 RBB00626 79 3615 #3 RBB00624 136 3615 #4 RBB00618 139 3615 #5 RBB00617 173 3615 #6 RBB00570 114 3615 #7 RBB00359 24 3615 #8 RBB00358 67 3615 #9 RBB00356 82 3615 #10 RBB00355 70 3615 #11 RBB00352 51 3615 #12 RBB00351 23 3615 #13 RBB00808 108 3615 #14 RBB00809 173 3615 #15 RBB00349 300 3615 #16 RBB00336 248 3615 #17 RBB00335 32 3615 #18 RBB00333 36 3615 #19 RBB00278 300 3615 #20 RBB00277 50 3615 #21 RBB00276 35 3615 #22 RBB00273 21 3615 #23 RBB00266 21 3615 #24 RBB00261 16 3615 #25 RBB00250 21 3615 #26 RBB00214 283 3615 #27 RBB00144 165 3615 #28 RBB00143 121 3615 Motif number 1 AACAATTTAATTTAATAATTACAAACTGTG 1 20 1 TTTAATAATT 0.75928 -77 TATTTATATATTTTATATTATACTAATATA 1 52 1 TTTTATATTA 0.762412 -45 TAAGTGATTCTTTAATAAGAGGTTATGTT 2 61 1 TTTAATAAGA 0.912072 -19 TTTAAAATTATAACATTTTA 3 1 1 TTTAAAATTA 0.741698 -136 TTTTAGCTTGTTTATTAAATAATTCAGGTT 3 26 1 TTTATTAAAT 0.750795 -111 ACTAAGTTTATTTAATAAAAATAAACTATT 3 57 0 TTTAATAAAA 0.821775 -80 TAAACTTAGTTTTTATATGATCTATTGTAT 3 77 1 TTTTATATGA 0.811015 -60 ATTCAATAAGTTTATTAAGACTTTAGGAGT 3 113 1 TTTATTAAGA 0.93818 -24 CAATAAAAATTTTTATAATATACAAAATGT 4 33 0 TTTTATAATA 0.766428 -107 TTATATATTTTTTATAAATAAGTGATAAAA 5 24 0 TTTATAAATA 0.821749 -150 ACACTATTTTATTATAAAGCTTTTTTT 5 157 0 TTTATTATAA 0.870998 -17 TTACACGAAGTTTTTTAAAAATGTAATTTA 6 23 0 TTTTTTAAAA 0.54199 -92 ATTTAATATTAACCCACCTTT 7 14 0 TTTAATATTA 0.876086 -11 TTGCTACCATTTTATTAATAGTTTCAAGAA 8 31 1 TTTATTAATA 0.91902 -37 CTTTGATATATTTTTAATTTT 9 2 0 TTTTTAATTT 0.43641 -81 AAAAGACTCCTTTTTTAAGACATAACAAGC 9 62 0 TTTTTTAAGA 0.86747 -21 TTTTATTATAAGAAGGGTAAA 12 2 1 TTTATTATAA 0.870998 -22 AGACGATTGCTTTTTAAATAGGTATTAAAT 15 14 1 TTTTTAAATA 0.670209 -287 TTTTTACTATTTTTTTATATTGGAGTTTTA 15 117 1 TTTTTTATAT 0.554683 -184 AAAGCCTAAATTTAAAATTTAGCATAAAAC 15 141 0 TTTAAAATTT 0.538363 -160 GTTTTGTTGTTTTAATATTTTTACATTGGT 15 172 1 TTTAATATTT 0.741699 -129 TGTCAAAATTTTTATAAATACTAACTTAAC 15 223 0 TTTATAAATA 0.821749 -78 CACACCTCAATTTAAAAAGTTGTCAAAATT 15 243 0 TTTAAAAAGT 0.631457 -58 AGGTGTGCATTTTATTATGTGTAGTTTATA 15 266 1 TTTATTATGT 0.84884 -35 TAATATGCATTTTAAAAAGATCAA 16 5 0 TTTAAAAAGA 0.808237 -244 AAGACATAGGTTTATAAAAAGGTTTTTGTT 16 107 0 TTTATAAAAA 0.743477 -142 TATAAGTAATTTTATTATAAGACATAGGTT 16 125 0 TTTATTATAA 0.870998 -124 ACCTAAGAGATTTATTATAAATAGGCAATA 16 191 1 TTTATTATAA 0.870998 -58 GCAATACTTATTTATAAAGAGAAGAATTAA 16 215 1 TTTATAAAGA 0.860438 -34 AGCTTTATTTTTTAATATTTTGTGCTT 19 8 1 TTTTTTAATA 0.831919 -293 AAAAATTGATTTTTTTATTTTTTTGATTAT 19 199 1 TTTTTTATTT 0.655955 -102 ATTTTCTTATTTTAATAAGAATAAATTTGT 19 237 1 TTTAATAAGA 0.912072 -64 TGTTAAAAATTTTTTAAAGAGATTAAATGT 19 264 1 TTTTTAAAGA 0.729706 -37 TAACTCTTACTTTATTATTATACTCCTAAG 26 19 0 TTTATTATTA 0.911798 -265 GTTTAAACTATTTTATATGAAATTTGACAG 26 149 0 TTTTATATGA 0.811015 -135 CTTCCAAATATTTAATAATATAAAACGATA 26 178 1 TTTAATAATA 0.885818 -106 TACAAAATTTTTTTTTAAAAATCTATCTTA 26 208 0 TTTTTTAAAA 0.54199 -76 CAATTATTTGTTTATTATTAATTTAA 27 7 0 TTTATTATTA 0.911798 -159 TTAACACAACTTTATTATGAGTGTCAATTA 27 31 0 TTTATTATGA 0.932554 -135 CGTCTTACAATTTAAAATGTTAACACAACT 27 50 0 TTTAAAATGT 0.609344 -116 ATGCTTTATTTTTAATATGTGAGGAA 27 150 1 TTTAATATGT 0.793413 -16 AATTTTATCATTTATTAAATTTAAGCTCAA 28 47 0 TTTATTAAAT 0.750795 -75 ********** Masking position 7 Map Score: 50.1203 Number of sites scoring better than the average of aligned sites = 2277 Number in coding regions = 1357 Number in noncoding regions = 920 Number of orfs with sites within 600 bp upstream = 152 Fraction of orfs with sites within 600 bp upstream = 0.0244137 Motif number 2 CAAACTGTGCTTATTTATATATTTTATATTATACT 1 41 1 TTATTATTTT 0.728036 -56 TAACTAGATTTAAATGTAAAATTTTGTTAAATTAG 2 22 1 TAATAATTTT 0.68238 -58 AATTATAACATTTTAGCTTGTTTATTAAATAATTC 3 16 1 TTTATTTTAT 0.680575 -121 TAATTCAGGTTAAATAGTTTATTTTTATTAAATAA 3 45 1 TAATTATTTT 0.727922 -92 GGTTTAAGATTATTTTTCAGTTACATT 4 3 1 TTTATTTTTT 0.878912 -137 ACATTTTGTATATTATAAAAATTTTTATTGTTGAA 4 33 1 TATAAATTTT 0.788976 -107 TAAAGTAAGGTATTATATATTTTTTATAAATAAGT 5 31 0 TATATTTTTT 0.878913 -143 TACCTTACTTTAATTGTAGCTTTTTCTCAAGATCA 5 54 1 TAATATTTTT 0.770195 -120 GCTTGTGTAGTAAGTAAAGTTTTTTTTTGCAAAAA 5 127 1 TAATATTTTT 0.770195 -47 GATACCTCCCTATAAATTACATTTTTAAAAAACTT 6 11 1 TATATATTTT 0.823186 -104 GTGTATATAATTACACGAAGTTTTTTAAAAATGTA 6 28 0 TTAAATTTTT 0.788975 -87 TTTTTAAGAATAAAAGCATTATTTTTTGTTTACAT 6 74 0 TAAAAATTTT 0.705505 -41 ACAACTTTGATATATTTTTAATTTT 9 1 0 TATTTATTTT 0.806707 -82 CATGACAGTGTTAGTCTTAATTTTTGAGTGCATGC 10 11 1 TTATTTTTTT 0.806707 -60 AAAATTAAATTTAGTACTTGTTTTTTTCTAAACAA 14 12 1 TTATTTTTTT 0.806707 -162 AAATAGGTATTAAATTAACATTTATTATAGGTCAT 15 29 1 TAATATTTAT 0.495809 -272 TATAGGTCATTATAAGATTATTTTTCAACGTTTTT 15 54 1 TATATTTTTT 0.878911 -247 AATTGTCAGTTATGAAATGATTTTTACTATTTTTT 15 97 1 TATATTTTTT 0.878913 -204 ATATTGGAGTTTTATGCTAAATTTTAAATTTAGGC 15 133 1 TTTTTATTTT 0.806707 -168 CAAATGTCGATTTAATATGCATTTTAAAAAGATCA 16 12 0 TTTATATTTT 0.823187 -237 TAAATCGACATTTGAAAACATTTTTTCCAACACTC 16 33 1 TTTAATTTTT 0.853565 -216 AAGGTTTTTGTTTATTTTAATTTATTTGCAGCAAT 16 84 0 TTTTTTTTAT 0.656352 -165 GACATAGGTTTATAAAAAGGTTTTTGTTTATTTTA 16 100 0 TATAATTTTT 0.853562 -149 GTAAAATTAATATAAGTAATTTTATTATAAGACAT 16 130 0 TATAATTTAT 0.631132 -119 CTTATATTAATTTTACAATTTTTTTTCAAAAAAAA 16 149 1 TTTAATTTTT 0.853565 -100 ATCTCTTAGGTAAGAATATTTTTTTTGAAAAAAAA 16 167 0 TAAAATTTTT 0.788973 -82 TATTCTTACCTAAGAGATTTATTATAAATAGGCAA 16 184 1 TAAATATTAT 0.467113 -65 TAATGTAAAGTTTATATTAATTTTTAATGCTATTA 19 47 1 TTTTTTTTTT 0.866785 -254 ACTACGTGTTTTTCTAAAAAATTTTAATAGCTTTA 19 149 0 TTTTAATTTT 0.770197 -152 AAAAAATTGATTTTTTTATTTTTTTGATTATTTGT 19 198 1 TTTTATTTTT 0.839363 -103 TAAGAATAAATTTGTTAAAAATTTTTTAAAGAGAT 19 252 1 TTTTAATTTT 0.770197 -49 TTTAGTGAATTAACTCTTACTTTATTATTATACTC 26 24 0 TAATTTTTAT 0.550576 -260 TATTTGGAAGTTTAAACTATTTTATATGAAATTTG 26 153 0 TTTATTTTAT 0.680575 -131 TATAAAACGATATAAGATAGATTTTTAAAAAAAAA 26 196 1 TATATATTTT 0.823186 -88 ATCTTAGTAATTTTACAAAATTTTTTTTTAAAAAT 26 216 0 TTTAATTTTT 0.853565 -68 TGAGTGTCAATTATTTGTTTATTATTAATTTAA 27 9 0 TTATTATTAT 0.440021 -157 *** * * ***** Masking position 12 Map Score: 38.5655 Number of sites scoring better than the average of aligned sites = 5004 Number in coding regions = 3149 Number in noncoding regions = 1855 Number of orfs with sites within 600 bp upstream = 212 Fraction of orfs with sites within 600 bp upstream = 0.0340508 Motif number 3 AAATGTTTTATTAACTAGATTTAAATGTAA 2 6 1 TTTTTTAGAT 0.772646 -74 AATAGTTTATTTTTATTAAATAAACTTAGTTTTTA 3 57 1 TTTTTTAAAC 0.633397 -80 TTATAAAAATTTTTATTGTTGAAAAAAATTAGTCT 4 45 1 TTTTTTTAAA 0.935418 -95 GTAAGTAAAGTTTTTTTTTGCAAAAAAAGCTTTAT 5 136 1 TTTTTTTAAA 0.935418 -38 AAGCATTATTTTTTGTTTACATTATAAGAAATTGT 6 61 0 TTTTTTATAT 0.803911 -54 AAAATAATGCTTTTATTCTTAAAAAGAATAATTGA 6 84 1 TTTTTTTAAA 0.935418 -31 AACGCTCTCCTTTTCTTGAAACTATTAATAAAATG 8 38 0 TTTTTTATAT 0.803306 -30 TTTTATTATAAGAAGGGTAAATT 12 1 1 TTTTTTTAAG 0.777666 -23 TTTTCAACGTTTTTGTGGTCATAATTGTCAGTTAT 15 75 1 TTTTTGTAAT 0.668967 -226 TAGGCTTTAGTTTTGTTGTTTTAATATTTTTACAT 15 163 1 TTTTTTTAAT 0.956859 -138 TAAAAAGGTTTTTGTTTATTTTAATTTATTTGCAG 16 88 0 TTTGTTTAAT 0.892255 -161 ATTTTACAATTTTTTTTCAAAAAAAATATTCTTAC 16 158 1 TTTTTTAAAA 0.496202 -91 TTTTTTCCCATTTTATTCTTGTTAAA 17 2 0 TTTTTTTTAA 0.79825 -31 TATTTTGTGCTTTTCTTTAATTAATGTAAAGTTTA 19 26 1 TTTTTTAAAT 0.937144 -275 AAATTGATTTTTTTATTTTTTTGATTATTTGTAGC 19 201 1 TTTTTTTGAT 0.829326 -100 TTTGTAGCTATTTTCTTATTTTAATAAGAATAAAT 19 228 1 TTTTTTTAAT 0.956859 -73 TTTTGATTTTTCTAAAGGAGG 23 2 1 TTTGTTTAAA 0.848232 -20 GATTAAAACTTTTTATTTAGTGAATTAACTCTTAC 26 39 0 TTTTTTAAAT 0.939414 -245 TAGATTTTGATTTTATTGATTAAAACTTTTTATTT 26 56 0 TTTTTTAAAA 0.811041 -228 AATTTGACAGTTTGCTTGATTAAATTTGCATTAAT 26 124 0 TTTGTTAAAT 0.851062 -160 TTTTACAAAATTTTTTTTTAAAAATCTATCTTATA 26 206 0 TTTTTTTAAT 0.954842 -78 GTGTCAATTATTTGTTTATTATTAATTTAA 27 6 0 TTTGTTTTAA 0.59633 -160 **** ** * *** Masking position 6 Map Score: 27.999 Number of sites scoring better than the average of aligned sites = 944 Number in coding regions = 617 Number in noncoding regions = 327 Number of orfs with sites within 600 bp upstream = 89 Fraction of orfs with sites within 600 bp upstream = 0.0142949 Motif number 4 GTTTGTAATTATTAAATTAAATTGTTTTTGAATTT 1 11 0 ATTAATAATT 0.884511 -86 AAATAAACTATTTAACCTGAATTATTTAATAAACA 3 34 0 TTTAATAATT 0.870754 -103 ATTTTTATTAAATAAACTTAGTTTTTATATGATCT 3 65 1 AATAATAGTT 0.709232 -72 GGTTTAAGATTATTTTTCAGTTACATT 4 3 1 TTTAATATTT 0.671888 -137 AAAAGCTACAATTAAAGTAAGGTATTATATATTTT 5 43 0 ATTAATAGGT 0.96656 -131 CTTGAAAATAAGTGATATATTTGCTA 8 2 1 TTGAATAGTT 0.862867 -66 TGTTGTTAGAATTAAAGTGAGGCTTTAAA 13 90 1 ATTAATAGGT 0.96656 -19 GAAAATTAAATTTAGTACTTGTTTTTTTC 14 5 1 ATTAATAGTT 0.963826 -169 TATGCTAAATTTTAAATTTAGGCTTTAGTTTTGTT 15 145 1 TTTAATAGGT 0.962158 -156 TTGACAACTTTTTAAATTGAGGTGTGCATTTTATT 15 247 1 TTTAATAGGT 0.962158 -54 AAATTGTAAAATTAATATAAGTAATTTTATTATAA 16 135 0 ATTAATAGTT 0.962909 -114 CTTTTCTTTAATTAATGTAAAGTTTATATTAATTT 19 35 1 ATTAATAAGT 0.892569 -266 TTTTAAGTATATGAATTTGAGGTATTTTA 21 17 1 ATGAATAGGT 0.885838 -19 ATTTATTAAATTTAAGCTCAATCTTAGTTTGTTGG 28 33 0 TTTAATAATT 0.870754 -89 AATGATAAAATTTAACATTACTGCTAATATAGTAA 28 65 1 TTTAATACTT 0.752168 -57 ***** * *** * Masking position 10 Map Score: 13.889 Number of sites scoring better than the average of aligned sites = 93 Number in coding regions = 55 Number in noncoding regions = 38 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 5 TATATTTTATATTATACTAATATAGGTTAA 1 58 1 ATTATACTAA 0.186298 -39 ATTTAACAAAATTTTACATTTAAATCTAGT 2 24 0 ATTTTACATT 0.947465 -56 TTACCCACTAATTTAACAAAATTTTACATT 2 34 0 ATTTAACAAA 0.617757 -46 AACTTATTGAATTATACAATACAATAGATC 3 95 0 ATTATACAAT 0.796687 -42 TTTGTTGCATATTTTGCAATGCGATAGACC 4 104 1 ATTTTGCAAT 0.761367 -36 TTTATGCTAAATTTTAAATTTAGGCTTTAG 15 143 1 ATTTTAAATT 0.669961 -158 TGTTTTAATATTTTTACATTGGTGTTAATG 15 179 1 TTTTTACATT 0.582929 -122 ACATCACCACATTTTACATTAACACCAATG 15 195 0 ATTTTACATT 0.947465 -106 AAGAGTATTTTACAATATAAACTACA 15 285 0 ATTTTACAAT 0.905091 -16 TTTAATATGCATTTTAAAAAGATCAA 16 7 0 ATTTTAAAAA 0.505099 -242 ACTTATATTAATTTTACAATTTTTTTTCAA 16 148 1 ATTTTACAAT 0.905091 -101 ATTAATATAAACTTTACATTAATTAAAGAA 19 38 0 ACTTTACATT 0.674677 -263 AATTCTACACATTTTACAAAATATAGTCAA 19 118 0 ATTTTACAAA 0.914449 -183 TATCTTAGTAATTTTACAAAATTTTTTTTT 26 222 0 ATTTTACAAA 0.914449 -62 TTGTGTTAACATTTTAAATTGTAAGACGCA 27 52 1 ATTTTAAATT 0.669961 -114 AAATGATAAAATTTAACATTACTGCTAATA 28 64 1 ATTTAACATT 0.723661 -58 TTGTTGCATAATTTTACTATATTAGCAGTA 28 83 0 ATTTTACTAT 0.80102 -39 AACTAGGAGAATGTTACAATT 28 111 1 ATGTTACAAT 0.761367 -11 ********** Masking position 1 Map Score: 17.4922 Number of sites scoring better than the average of aligned sites = 285 Number in coding regions = 177 Number in noncoding regions = 108 Number of orfs with sites within 600 bp upstream = 53 Fraction of orfs with sites within 600 bp upstream = 0.00851269 Motif number 6 AATTACTCCTAAAGTCTTAATA 3 125 0 ATACTCCTAA 0.851992 -12 TACTAAAACTCCTTATGGTCTATCG 4 125 0 AAACTCCTTA 0.975216 -15 TAAAAGACTCCTTTTTTAAGACAT 9 69 0 AAACTCCTTT 0.833323 -14 ATTAACTCCTTATATATTTTCA 10 59 0 TTACTCCTTA 0.891491 -12 ATAATCTCCTTATGGTAGTAAC 11 40 0 TATCTCCTTA 0.929523 -12 AATTCCCTATAAAACTCTTTATTATCTTAGT 14 50 0 AAACTCTTTA 0.871825 -124 ATAACAAAACTCCTAACTACCAATAA 14 158 0 AAACTCCTAA 0.958677 -16 CATTTTTTCCAACACTCATTAAATTCCTCAT 16 51 1 AAACTCATTA 0.794133 -198 TACTTACATTTAATCTCTTTAAAAAATTTTT 19 268 0 TATCTCTTTA 0.695106 -33 TTTATTCTCCTAAACTTTAGAGA 20 38 0 TATCTCCTAA 0.886058 -13 ACTTTATTATTATACTCCTAAGATAATTAT 26 10 0 TAACTCCTAA 0.951275 -274 ** ******** Masking position 6 Map Score: 9.02186 Number of sites scoring better than the average of aligned sites = 106 Number in coding regions = 60 Number in noncoding regions = 46 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 7 AACTAGATTTAAATGTAAAATTTTGTTAAA 2 23 1 AAATGTAAAA 0.630591 -57 AAATGTAAAATTTTGTTAAATTAGTGGGTA 2 33 1 TTTTGTTAAA 0.676539 -47 TGATCTATTGTATTGTATAATTCAATAAGT 3 94 1 TATTGTATAA 0.462381 -43 ACATTTTGTATATTATAAAAATTTTTATTG 4 33 1 TATTATAAAA 0.650677 -107 TTTATCACTTATTTATAAAAAATATATAAT 5 25 1 ATTTATAAAA 0.559251 -149 TAAAGTTTTTTTTTGCAAAAAAAGCTTTAT 5 141 1 TTTTGCAAAA 0.399476 -33 TTACACGAAGTTTTTTAAAAATGTAATTTA 6 23 0 TTTTTTAAAA 0.518131 -92 ATAATGCTTTTATTCTTAAAAAGAATAATT 6 87 1 TATTCTTAAA 0.380095 -28 GCCTCACTTTAATTCTAACAACAGGTCAGG 13 83 0 AATTCTAACA 0.322909 -26 AATATAAAAAAATAGTAAAAATCATTTCAT 15 108 0 AATAGTAAAA 0.532753 -193 ACATTAACACCAATGTAAAAATATTAAAAC 15 180 0 CAATGTAAAA 0.243266 -121 ACATTGGTGTTAATGTAAAATGTGGTGATG 15 194 1 TAATGTAAAA 0.703123 -107 TTAAGTTAGTATTTATAAAAATTTTGACAA 15 224 1 ATTTATAAAA 0.559251 -77 GTGTAGTTTATATTGTAAAATACTCTT 15 284 1 TATTGTAAAA 0.939064 -17 TTTGAAAAAAAATTGTAAAATTAATATAAG 16 149 0 AATTGTAAAA 0.920013 -100 AGAATATTTTTTTTGAAAAAAAATTGTAAA 16 160 0 TTTTGAAAAA 0.417281 -89 ATTGACTATATTTTGTAAAATGTGTAGAAT 19 117 1 TTTTGTAAAA 0.827105 -184 CACTACGTGTTTTTCTAAAAAATTTTAATA 19 155 0 TTTTCTAAAA 0.774156 -146 GTGCGGGTCAATTTCTAAAAAATTGATTTT 19 182 1 ATTTCTAAAA 0.733395 -119 ATAAGAATAAATTTGTTAAAAATTTTTTAA 19 251 1 ATTTGTTAAA 0.612106 -50 TACAAAATTTTTTTTTAAAAATCTATCTTA 26 208 0 TTTTTTAAAA 0.518131 -76 TAAAAAAAAATTTTGTAAAATTACTAAGAT 26 221 1 TTTTGTAAAA 0.827105 -63 TAACATTTTAAATTGTAAGACGCAGGGTAG 27 58 1 AATTGTAAGA 0.500328 -108 TTACTGCTAATATAGTAAAATTATGCAACA 28 82 1 TATAGTAAAA 0.612595 -40 AATTGTAACATTCTCCTAGT 28 112 0 AATTGTAACA 0.648228 -10 ********** Masking position 10 Map Score: 12.5444 Number of sites scoring better than the average of aligned sites = 796 Number in coding regions = 537 Number in noncoding regions = 259 Number of orfs with sites within 600 bp upstream = 64 Fraction of orfs with sites within 600 bp upstream = 0.0102795 Motif number 8 TTATATTATACTAATATAGGTTAATAAGTA 1 64 1 CTAATATAGG 0.956045 -33 AAACAATCAACTAAGATAATAAAGAGTTTT 14 41 1 CTAAGATAAT 0.948965 -133 AATTGTAAAATTAATATAAGTAATTTTATT 16 139 0 TTAATATAAG 0.705682 -110 TATTATACTCCTAAGATAATTAT 26 4 0 CTAAGATAAT 0.948965 -280 GATATATTCCCTAATATAAGGATATACATT 26 97 1 CTAATATAAG 0.919287 -187 TGTAAAATTACTAAGATAGTTAATCTTCTA 26 234 1 CTAAGATAGT 0.957398 -50 AACATTACTGCTAATATAGTAAAATTATGC 28 78 1 CTAATATAGT 0.948965 -44 ********** Masking position 6 Map Score: 4.05235 Number of sites scoring better than the average of aligned sites = 67 Number in coding regions = 35 Number in noncoding regions = 32 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 Motif number 9 TAACAAAATTTTACATTTAAATCTAGTTAAT 2 20 0 TTACATTTAA 0.667074 -60 TTTAAAATTATAACATTTTAGC 3 2 1 TTAAAATTTA 0.643795 -135 AAAAAAAGCTTTATAATAAAATAGTGT 5 157 1 TTATAATAAA 0.562798 -17 TCCCTATAAATTACATTTTTAAAAAACTTCG 6 17 1 TTACATTTTA 0.54193 -98 TATTTTTTGTTTACATTATAAGAAATTGTGT 6 59 0 TTACATTAAA 0.725698 -56 TTTACCCTTCTTATAATAAAA 12 1 0 TTATAATAAA 0.562798 -23 TAAATAGGTATTAAATTAACATTTATTATAG 15 28 1 TTAAATTACA 0.859134 -273 TGTAAAAATATTAAAACAACAAAACTAAAGC 15 166 0 TTAAAACACA 0.455295 -135 TCACCACATTTTACATTAACACCAATGTAAA 15 191 0 TTACATTACA 0.845057 -110 AAGAGTATTTTACAATATAAACTACACATA 15 281 0 TTACAATAAA 0.783682 -20 AACCTATGTCTTATAATAAAATTACTTATAT 16 125 1 TTATAATAAA 0.562798 -124 ATTACTTATATTAATTTTACAATTTTTTTTC 16 145 1 TTAATTTTCA 0.218579 -104 ACCCTTAAAATAACAAATATTTAAA 18 5 1 TTAAAATACA 0.892487 -32 TTTAATAGCTTTAAAATTCTACACATTTTAC 19 131 0 TTAAAATTTA 0.643795 -170 TTTATTCTTATTAAAATAAGAAAATAGCTAC 19 231 0 TTAAAATAGA 0.546993 -70 ATTCATATACTTAAAATATCAT 21 2 0 TTAAAATACA 0.883818 -34 GTTTGCTTGATTAAATTTGCATTAATGTATA 26 119 0 TTAAATTTCA 0.804237 -165 ATAAAATAGTTTAAACTTCCAAATATTTAAT 26 163 1 TTAAACTTCA 0.490664 -121 TTAAATTAATAATAAACAAAT 27 1 1 TTAAATTATA 0.66317 -165 ACCCTGCGTCTTACAATTTAAAATGTTAACA 27 55 0 TTACAATTAA 0.681295 -111 ******** ** Masking position 2 Map Score: 8.8693 Number of sites scoring better than the average of aligned sites = 980 Number in coding regions = 606 Number in noncoding regions = 374 Number of orfs with sites within 600 bp upstream = 104 Fraction of orfs with sites within 600 bp upstream = 0.0167041 Motif number 10 AAATTCAAAAACAATTTAATTTAATAATTAC 1 11 1 ACAATTAATT 0.523098 -86 ATTCAGGTTAAATAGTTTATTTTTATTAAAT 3 47 1 AATATTTATT 0.684985 -90 GTATAATTCAATAAGTTTATTAAGACTTTAG 3 108 1 ATAATTTATT 0.604664 -29 TATAAAAGAGACTAATTTTTTTCAACAATAA 4 57 0 ACTATTTTTT 0.942011 -83 ACACTATTTTATTATAAAGCTTT 5 161 0 ACTATTTATT 0.938729 -13 TATATTTGCTACCATTTTATTAATAGTTTCA 8 26 1 ACCATTTATT 0.905679 -42 TAAAAGACTCCTTTTTTAAGACATAAC 9 66 0 ACTCTTTTTT 0.655686 -17 TAAATTTAGTACTTGTTTTTTTCTAAACAAT 14 17 1 ACTTTTTTTT 0.562336 -157 AATGATTTTTACTATTTTTTTATATTGGAGT 15 112 1 ACTATTTTTT 0.944338 -189 AAAAATTTTGACAACTTTTTAAATTGAGGTG 15 240 1 ACAATTTTTA 0.693784 -61 TATTAATTTTACAATTTTTTTTCAAAAAAAA 16 153 1 ACAATTTTTT 0.944334 -96 CTTAGGTAAGAATATTTTTTTTGAAAAAAAA 16 167 0 AATATTTTTT 0.706452 -82 TTACTTTTTTCCCATTTTATTCTTGTTAAA 17 10 0 CCCATTTATT 0.504512 -23 AAATAAAAAAATCAATTTTTTAGAAATTGAC 19 188 0 ATCATTTTTT 0.514748 -113 AAAATTTTTAACAAATTTATTCTTATTAAAA 19 246 0 ACAATTTATT 0.936165 -55 TAAATTTGTTAAAAATTTTTTAAAGAGATTA 19 258 1 AAAATTTTTT 0.621541 -43 GGAAGTTTAAACTATTTTATATGAAATTTGA 26 152 0 ACTATTTATA 0.671692 -132 TAGTAATTTTACAAAATTTTTTTTTAAAAAT 26 216 0 ACAAATTTTT 0.529216 -68 AAATGTTAACACAACTTTATTATGAGTGTCA 27 35 0 ACAATTTATT 0.938725 -131 **** ****** Masking position 7 Map Score: 13.7585 Number of sites scoring better than the average of aligned sites = 221 Number in coding regions = 134 Number in noncoding regions = 87 Number of orfs with sites within 600 bp upstream = 21 Fraction of orfs with sites within 600 bp upstream = 0.00337295 Motif number 11 CTGTGCTTATTTATATATTTTATATTATAC 1 45 1 TTATATATTT 0.927456 -52 CTATTTAACCTGAATTATTTAATAAACAAG 3 32 0 TGAATTATTT 0.536487 -105 ATAATTCAGGTTAAATAGTTTATTTTTATT 3 44 1 TTAAATAGTT 0.700257 -93 AAGTAAGGTATTATATATTTTTTATAAATA 5 34 0 TTATATATTT 0.927456 -140 TGAAAATAAGTGATATATTTGCTACCATTT 8 13 1 TGATATATTT 0.903734 -55 ATAACAACTTTGATATATTTTTAATTTT 9 9 0 TGATATATTT 0.903734 -74 ATTAACTCCTTATATATTTTCATTTCACA 10 52 0 TTATATATTT 0.927456 -19 GTTTTGTTGTTTTAATATTTTTACATTGGT 15 172 1 TTTAATATTT 0.751568 -129 ATACTCCTGTTTAAATATTTGTTATTTTAA 18 15 0 TTAAATATTT 0.936756 -22 AGCTTTATTTTTTAATATTTTGTGCTTTTC 19 11 1 TTTAATATTT 0.751568 -290 AATAAATTTGTTAAAAATTTTTTAAAGAGA 19 256 1 TTAAAAATTT 0.611839 -45 ATCTACTAAATGATATATTCCCTAATATAA 26 86 1 TGATATATTC 0.596899 -198 TTTTATATTATTAAATATTTGGAAGTTTAA 26 173 0 TTAAATATTT 0.936756 -111 ********** Masking position 7 Map Score: 12.8522 Number of sites scoring better than the average of aligned sites = 301 Number in coding regions = 193 Number in noncoding regions = 108 Number of orfs with sites within 600 bp upstream = 33 Fraction of orfs with sites within 600 bp upstream = 0.00530035 Motif number 12 AAGTTTATTAAGACTTTAGGAGTAATT 3 120 1 AGACTTTAGG 0.970532 -17 ATTGAGTTTAAAAGTTTAAGCGTATTGACT 19 94 1 AAAGTTTAAG 0.904305 -207 GTTAAGACTTTAAGGATATATTAA 20 5 1 AGACTTTAAG 0.935968 -46 AATACTCTCTAAAGTTTAGGAGAATAAA 20 33 1 AAAGTTTAGG 0.955141 -18 AAGGAGAGTTTAGGCTATTTC 25 5 1 AGAGTTTAGG 0.979581 -17 ********** Masking position 5 Map Score: 1.66314 Number of sites scoring better than the average of aligned sites = 20 Number in coding regions = 11 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 Motif number 13 TTTATTTAATAAAAATAAACTATTTAACCT 3 51 0 AAAAATAAAC 0.792486 -86 AGAAAAAGCTACAATTAAAGTAAGGTATTA 5 51 0 ACAATTAAAG 0.700615 -123 AATGTAAACAAAAAATAATGCTTTTATTCT 6 73 1 AAAAATAATG 0.736635 -42 AAAATTAAAAATATATCAAA 9 1 1 AAAATTAAAA 0.702075 -82 GCATGCACTCAAAAATTAAGACTAACACTG 10 16 0 AAAAATTAAG 0.736635 -55 ACCTGTTGTTAGAATTAAAGTGAGGCTTTA 13 87 1 AGAATTAAAG 0.700615 -22 GAAAATTAAATTTAGTACTTG 14 2 1 AAAATTAAAT 0.702075 -172 TTAAAACAACAAAACTAAAGCCTAAATTTA 15 157 0 AAAACTAAAG 0.859962 -144 CAAAATATTAAAAAATAAAGCT 19 3 0 AAAAATAAAG 0.963348 -298 AAATAATCAAAAAAATAAAAAAATCAATTT 19 201 0 AAAAATAAAA 0.819612 -100 GGTTTTGGAGAAAAATAAAT 22 12 1 AAAAATAAAT 0.819612 -10 TTAGGAGTATAATAATAAAGTAAGAGTTAA 26 20 1 AATAATAAAG 0.736635 -264 CTCACATATTAAAAATAAAGCATAGCAGGG 27 143 0 AAAAATAAAG 0.963348 -23 ********** Masking position 4 Map Score: 8.42742 Number of sites scoring better than the average of aligned sites = 263 Number in coding regions = 158 Number in noncoding regions = 105 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419 Motif number 14 ACACTGTACTTATTAACCTATATTAGTATAATA 1 67 0 TATACCTATT 0.76719 -30 GATACCTCCCTATAAATTACATTTT 6 3 1 TACCCCTATA 0.971327 -112 CCGTTGGAACTACTGACCTATTATTTA 13 5 0 TATACCTATA 0.954346 -104 ATAAGGGCACTAATTCCCTATAAAACTCTTTAT 14 59 0 TATCCCTATA 0.945177 -115 ACAAAACTCCTAACTACCAATAAAAGCCCTCAA 14 148 0 TACACCAATA 0.928461 -26 AATAATCTTATAATGACCTATAATAAATGTTAA 15 43 0 TATACCTATA 0.954346 -258 AATAAGAAAATAGCTACAAATAATCAAAAAAAT 19 215 0 TACACAAATA 0.718756 -86 ACATCCCCCTATTAAA 24 3 0 CACCCCTATA 0.88783 -14 GTTAATCTTCTACCCACATATCATCAGGAGGGA 26 252 1 TACACATATA 0.889956 -32 ** * ****** * Masking position 10 Map Score: 2.85159 Number of sites scoring better than the average of aligned sites = 29 Number in coding regions = 13 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 Motif number 15 TTAATATTAACCCACCTTTCAG 7 3 0 CCCACCTTTC 0.946393 -22 TTATCAACGCTCTCCTTTTCTTGAAACTA 8 49 0 CTCTCCTTTT 0.764189 -19 AATTTACCCTTCTTATAATAAAA 12 8 0 CCCTTCTTAT 0.858085 -16 GGGTTCGAATCCCTCCTGACCTGTTGTTAG 13 69 1 CCCTCCTGAC 0.980751 -40 ACCGACGACCCCCACCTTACCATGGTGGTG 14 108 0 CCCACCTTAC 0.970535 -66 TAGACTTTGTCCCTCCTGATGATATGTGGG 26 264 0 CCCTCCTGAT 0.970062 -20 ********** Masking position 7 Map Score: 1.66538 Number of sites scoring better than the average of aligned sites = 22 Number in coding regions = 7 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432