AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i148_Rubredoxin_mjan_reg_300.orf -o148_mjan_300.ace -a/home/amcguire/genomes/ORF_mjan.txt -z/home/amcguire/genomes/mjan.fna -g0.31 -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 = 0.31 maxlen = 30 weight = 0.8 exclude = 1 Purged sequences: RMJ02153 57 M_jannaschii_chromosome Input sequences: #1 RMJ07936 89 M_jannaschii_chromosome #2 RMJ13354 75 M_jannaschii_chromosome #3 RMJ01522 39 M_jannaschii_chromosome #4 RMJ14619 28 M_jannaschii_chromosome #5 RMJ10200 71 M_jannaschii_chromosome #6 RMJ08904 180 M_jannaschii_chromosome #7 RMJ10274 104 M_jannaschii_chromosome #8 RMJ15352 128 M_jannaschii_chromosome #9 RMJ02377 221 M_jannaschii_chromosome #10 RMJ03320 214 M_jannaschii_chromosome #11 RMJ13235 109 M_jannaschii_chromosome #12 RMJ03131 268 M_jannaschii_chromosome #13 RMJ13030 263 M_jannaschii_chromosome #14 RMJ05742 210 M_jannaschii_chromosome #15 RMJ05650 213 M_jannaschii_chromosome #16 RMJ11762 83 M_jannaschii_chromosome #17 RMJ12007 203 M_jannaschii_chromosome #18 RMJ14441 286 M_jannaschii_chromosome #19 RMJ05775 271 M_jannaschii_chromosome #20 RMJ14343 124 M_jannaschii_chromosome #21 RMJ14151 93 M_jannaschii_chromosome #22 RMJ14817 43 M_jannaschii_chromosome #23 RMJ11840 197 M_jannaschii_chromosome #24 RMJ12613 227 M_jannaschii_chromosome #25 RMJ07178 197 M_jannaschii_chromosome #26 RMJ06181 270 M_jannaschii_chromosome #27 RMJ05205 170 M_jannaschii_chromosome #28 RMJ01354 84 M_jannaschii_chromosome Motif number 1 TTAACACATATTATAAATTTCTAAATCTTT 1 36 1 TTATAAATTT 0.66812 -54 TTTCTAAATCTTTTTAATTAATTGTAATTG 1 53 1 TTTTTAATTA 0.871847 -37 TTGGTTTTTATTTTATATTTGCTTTTCTT 2 10 0 TTTTATATTT 0.886955 -66 TTATTTTATCTTTTGTTTATTTAAGTTTTA 2 40 0 TTTTGTTTAT 0.412822 -36 CTCCCCTCCTTTTTATTTTATCTTTTGTTT 2 52 0 TTTTATTTTA 0.807146 -24 AATAAAATTATTTTAATTAAACTTTTTGGT 3 14 1 TTTTAATTAA 0.465184 -26 TCACATCGCGTTTTATTTAA 5 1 0 TTTTATTTAA 0.594301 -71 TTTTAGTTTATTATTTTTTACTTTATAAAA 6 19 0 TTATTTTTTA 0.713964 -162 AAGTTATTAGTTTTTAGTTTATTATTTTTT 6 30 0 TTTTTAGTTT 0.783161 -151 GTATTTGTGATTTTTTATATGCAAGTTATT 6 52 0 TTTTTTATAT 0.791227 -129 AGATAATCTTTTATTTATTAATTTAATTTA 7 17 1 TTATTTATTA 0.829282 -88 AATTCATATATTATATTTTTGATTTTAGAT 8 48 0 TTATATTTTT 0.630874 -81 TTTAAGTTCTTTATAAGTTATTTTTTGAGT 8 91 0 TTATAAGTTA 0.544798 -38 AATTCCCATTTTATTATTTTACTTAAATAC 9 67 1 TTATTATTTT 0.583425 -155 TTTTTGTCATTTTTATGTTTTTATTTGAAA 9 164 0 TTTTATGTTT 0.815071 -58 TAAATAAAAATTTTTAATTAAAT 10 4 0 TTTTTAATTA 0.871847 -211 TAATTAAAAATTTTTATTTAATTTTTATTT 10 14 1 TTTTTATTTA 0.774248 -201 TTTATTTAATTTTTATTTTTTAATTCTGTA 10 26 1 TTTTATTTTT 0.798174 -189 TATAATATTATTATATGTTTTATCACTTTA 10 90 1 TTATATGTTT 0.655736 -125 ATTTACTAATTTTTTAATTTGTTTTATTTA 10 121 1 TTTTTAATTT 0.8654 -94 TTTTAATTTGTTTTATTTATTGTTCAACAT 10 132 1 TTTTATTTAT 0.580585 -83 ATTTTGAATTAATTCATCACA 11 2 1 TTTTGAATTA 0.714617 -108 CCTTTTTAACTTTTTAATTATTACATTATA 11 83 0 TTTTTAATTA 0.871847 -27 CTTTTTTTACTTTTTTATTTTTTTAAGAAT 12 19 1 TTTTTTATTT 0.915456 -250 CTAATTTTTCTTATATATATATTACTTATC 12 79 0 TTATATATAT 0.539765 -190 AAAATTTTAGTTATTAATTAAATATATGTC 12 141 1 TTATTAATTA 0.742877 -128 ACGGTATATATTATTAATTATACGAATTTC 12 171 0 TTATTAATTA 0.742877 -98 TGAACTAAGATTTTTAATAAGGCTCACAAA 12 225 0 TTTTTAATAA 0.701127 -44 AAAATAAATTTTAAGTAAATATTTTGAA 12 251 0 TTTTAAGTAA 0.492223 -18 ATTGTTTTAATTTTATTTTTCAAATATGTG 13 21 0 TTTTATTTTT 0.798174 -243 TAAGTAAATTTTATTTATATTGTGAAATAG 13 64 1 TTATTTATAT 0.618897 -200 TTATTATCAGTTATTTATTTTATTGTGTAA 13 163 0 TTATTTATTT 0.823917 -101 ATATTTGTAGTTATTAGTTATTTTATTATC 13 185 0 TTATTAGTTA 0.622891 -79 AAAACTTCTATTTTTTATTAACAATTATAC 14 13 1 TTTTTTATTA 0.919726 -198 ATTATACAAATTTTTTATTAGATTTATCTA 14 36 1 TTTTTTATTA 0.919726 -175 CTAAAAATCTTTTTATATTTTGGATTCCAG 14 97 1 TTTTATATTT 0.886955 -114 TGTTTATAGATTTTAAGTAATCTCTTGTAT 15 34 0 TTTTAAGTAA 0.492223 -180 TCAAACATTATTTTTTATTTATTTTGTATT 15 124 1 TTTTTTATTT 0.915456 -90 TTTTTATTTATTTTGTATTTTTGACAAGTT 15 135 1 TTTTGTATTT 0.799395 -79 AAGTTTTTGTTTATGTTTTTTTGGGATAAT 15 160 1 TTATGTTTTT 0.464679 -54 TGGCTTATCCTTTTTTGTTAAACCTTTCCT 16 31 0 TTTTTTGTTA 0.865542 -53 TTCATCTCATTTTTTTATTTTTTATTGTAA 18 15 1 TTTTTTATTT 0.915456 -272 ATTGGTAGTATTTTTAGTAATATCTTCACT 18 108 1 TTTTTAGTAA 0.572254 -179 AATATTTTATTTTTTTGTTA 19 1 0 TTTTTTGTTA 0.865542 -271 TTGTTATTACTTTTTAATAACCATTTAAGT 19 166 0 TTTTTAATAA 0.701127 -106 CAAATATTATTTTTGTTTAAAAGGAATATA 19 212 0 TTTTGTTTAA 0.42662 -60 ATTTTTTATTTTCATGGTTGT 20 2 1 TTTTTTATTT 0.915456 -123 TTAGTAAAATTTATATATTTGTTTTCTTAC 20 49 1 TTATATATTT 0.77223 -76 ATGAGGGCAGTTTTTATTTACCACAAAAAT 21 65 1 TTTTTATTTA 0.774248 -29 ATAATTATATATTTAAATTTTGAA 23 5 1 TTATATATTT 0.77223 -193 GTATGATAACTTTTGTTTTTATTGTTTTTA 23 36 1 TTTTGTTTTT 0.667618 -162 GTTTTTATTGTTTTTAGTAAAACCTCAATA 23 50 1 TTTTTAGTAA 0.572254 -148 ATCGAAAGGTTTATATATTATGAGTGTTAA 23 96 1 TTATATATTA 0.777783 -102 CAACCGTGAATTATTAATTTATAATTTTTT 23 147 1 TTATTAATTT 0.735335 -51 AATTATTTTTAATTGGTGAAAA 24 3 1 TTATTTTTAA 0.46479 -225 CGACTCAAAATTTTTTATATAGCTTTGCAT 24 34 0 TTTTTTATAT 0.791227 -194 ATTTTTATTGTTTTATTTTAATATACTGCT 24 153 1 TTTTATTTTA 0.807146 -75 TACTGCTGTTTTTTGTATTTTTAATGTTGT 24 176 1 TTTTGTATTT 0.799395 -52 TTATTTTGGATTTTATATTATAT 25 4 0 TTTTATATTA 0.89249 -194 TAACCTTTAATTTTTAATTTTATCTTTTAT 25 31 1 TTTTTAATTT 0.8654 -167 TAATTTTATCTTTTATTTTTTCATTTTTTT 25 45 1 TTTTATTTTT 0.798174 -153 TTTTTTCATTTTTTTTATTTTATATATTAT 25 60 1 TTTTTTATTT 0.915456 -138 TTAAAGAATATTTTTTATAAATGCAACTGA 25 153 0 TTTTTTATAA 0.79783 -45 TAATTTTTATTTTTATTTTTGCACTATATA 26 13 1 TTTTATTTTT 0.798174 -258 TAAATCCTGATTTTGTATTACCTACAATAT 26 79 0 TTTTGTATTA 0.808327 -192 TTATCATAAATTATAAATTATAATTAAAAA 27 15 1 TTATAAATTA 0.675477 -156 CACCAACAAATTTTTAATTATAATTTATAA 27 25 0 TTTTTAATTA 0.871847 -146 GAATGTATCTTTTTTTGTTTAATGCTACTG 27 127 0 TTTTTTGTTT 0.858811 -44 TTTTAAGAAATTATATATAATTACAATAAA 28 25 1 TTATATATAA 0.401763 -60 ACAATAAATGTTTTAAGTTAGAATAAAAAT 28 47 1 TTTTAAGTTA 0.734719 -38 ********** Masking position 4 Map Score: 71.7259 Number of sites scoring better than the average of aligned sites = 3559 Number in coding regions = 2346 Number in noncoding regions = 1213 Number of orfs with sites within 600 bp upstream = 594 Fraction of orfs with sites within 600 bp upstream = 0.0954064 Motif number 2 CCATTTTTATAAAGTAAAAAATAATAAACTA 6 15 1 AAGTAAAAAA 0.796561 -166 TAAGATAAATAATGACAAAAATAGCACAAAG 6 151 1 AAGACAAAAA 0.897984 -30 TATACTATCTAAAATCAAAAATATAATATAT 8 42 1 AAATCAAAAA 0.921986 -87 AAACGATAAAAAGGTGAAAAA 8 118 1 AAGTGAAAAA 0.951614 -11 AAAAAGAAATAATGAGAAAAAGATATTTCCT 9 35 0 AAGAGAAAAA 0.916331 -187 AGTTTCAAATAAAAACATAAAAATGACAAAA 9 162 1 AAAACATAAA 0.570493 -60 AAAACATAAAAATGACAAAAATAGTCCCAAC 9 173 1 AAGACAAAAA 0.897984 -49 TACAGAATTAAAAAATAAAAATTAAATAAAA 10 25 0 AAAATAAAAA 0.835466 -190 TAGTAAATATAAAGTGATAAAACATATAATA 10 98 0 AAGTGATAAA 0.798764 -117 ATAAATAAAACAAATTAAAAAATTAGTAAAT 10 121 0 CAATTAAAAA 0.52643 -94 ACATTAATCAAACATCATAAATATTAAGTAT 10 160 0 AAATCATAAA 0.704598 -55 TTGCCATAAAAAGGTGAAAAAT 10 203 1 AAGTGAAAAA 0.951614 -12 TAATAATTAAAAAGTTAAAAAGGTGAAAGC 11 90 1 AAGTTAAAAA 0.924219 -20 AAAAAATAAAAAAGTAAAAAAAGGATTAAAT 12 11 0 AAGTAAAAAA 0.796561 -258 AATATAATTAAAGGTGAAAAAATATGAAAGC 13 210 1 AAGTGAAAAA 0.951614 -54 ATTATCCCAAAAAAACATAAACAAAAACTTG 15 159 0 AAAACATAAA 0.570493 -55 GAGAAGTCATAAGGTGAAAAAACTCAAAGAA 17 159 1 AAGTGAAAAA 0.951614 -45 ATTTACAATAAAAAATAAAAAAATGAGATGA 18 16 0 AAAATAAAAA 0.835466 -271 AAAGGTGATAAATATGAAAAAAATAGCGATG 18 75 1 AAATGAAAAA 0.936323 -212 ATTAAAAAGTAATAACAAAAATAACAGTAAA 19 178 1 AAAACAAAAA 0.868095 -94 GAGGTGAGAAAATGTGGAAAAAACTGATGTT 19 241 1 AAGTGGAAAA 0.557486 -31 CACAACCATGAAAATAAAAAAT 20 2 0 AAATAAAAAA 0.745382 -123 AACTACCCTTCAGGTGAAAAA 20 114 1 CAGTGAAAAA 0.705673 -11 TTTTACTAAAAACAATAAAAACAAAAGTTAT 23 41 0 AAAATAAAAA 0.835466 -157 ATTGTATAAAAAAATTATAAATTAATAATTC 23 154 0 AAATTATAAA 0.647928 -44 ATTAAAATAAAACAATAAAAATGATATATCT 24 144 0 AAAATAAAAA 0.835466 -84 CAAAATCCACAACATTAAAAATACAAAAAAC 24 183 0 AAATTAAAAA 0.901171 -45 AATAAAAGATAAAATTAAAAATTAAAGGTTA 25 31 0 AAATTAAAAA 0.901171 -167 TAAAATAAAAAAAATGAAAAAATAAAAGATA 25 51 0 AAATGAAAAA 0.936323 -147 TATATAGTGCAAAAATAAAAATAAAAATTAA 26 12 0 AAAATAAAAA 0.835466 -259 CCAAAAGAAGAAGGTCAAAAATATATTTATA 26 164 1 AAGTCAAAAA 0.940501 -107 ** ******** Masking position 9 Map Score: 45.0363 Number of sites scoring better than the average of aligned sites = 1010 Number in coding regions = 773 Number in noncoding regions = 237 Number of orfs with sites within 600 bp upstream = 209 Fraction of orfs with sites within 600 bp upstream = 0.0335689 Motif number 3 TTCTAAATCTTTTTAATTAATTGTAATTGTTTTTT 1 54 1 TTTTTAATTA 0.881894 -36 TTTTATTGGTTTTTATTTTATATTTGCTTTTCTT 2 10 0 TTTTTTATTT 0.693717 -66 CTCCCCTCCTTTTTATTTTATCTTTTGTTTATTTA 2 47 0 TTTTTTATTT 0.693717 -29 ACCAAAAAGTTTAATTAAAATAATTTTATTATT 3 9 0 TTAAAAATTT 0.463452 -31 AGTTATTAGTTTTTAGTTTATTATTTTTTACTTTA 6 24 0 TTTTTTATTT 0.693717 -157 CTTTGTGCTATTTTTGTCATTATTTATCTTAGTCA 6 147 0 TTTTTATTTT 0.741885 -34 ACTTATAGATAATCTTTTATTTATTAA 7 3 1 TTATAAATTT 0.731135 -102 AGGAAATATCTTTTTCTCATTATTTCTTTTTCAAT 9 35 1 TTTTTATTTT 0.741885 -187 ATTTTATTATTTTACTTAAATACTACAATGCGATT 9 74 1 TTTATAATTA 0.703422 -148 TCCATTATACTTTATTACAATATTTTAAATGTAAA 9 116 0 TTTAAAATTT 0.703422 -106 AATTAAAAATTTTTATTTAATTTTTATTTTTTAAT 10 15 1 TTTTTAATTT 0.947452 -200 TATTTATGATGTTTGATTAATGTTTAAACTGTTAT 10 168 1 GTTTTAATTT 0.726603 -47 TTGGCAAAAATTTTAGTTATTAATTAAATATATGT 12 135 1 TTTTTATTTT 0.741885 -134 GTCGAAATTCGTATAATTAATAATATATACCGTAA 12 168 1 GTATTAATTA 0.286139 -101 ATAGCATAAATTTATTTGAATGGTTTGTGAGCCTT 12 202 1 TTTATAATTT 0.851348 -67 TTTGTGAGCCTTATTAAAAATCTTAGTTCAAAATA 12 225 1 TTATAAATTA 0.529671 -44 AAAATAAATTTTAAGTAAATATTTTGAACTAAGA 12 245 0 TTTATAATTT 0.851348 -24 TACTTAAAGATTTATATAAATTGTTTTAATTTTAT 13 35 0 TTTATAATTT 0.851348 -229 TATATAAATCTTTAAGTAAATTTTATTTATATTGT 13 52 1 TTTATAATTA 0.703422 -212 CTTCTATTTTTTATTAACAATTATACAAATTTTTT 14 17 1 TTATAAATTA 0.529671 -194 AATTGGGGTTTTATGGTGAATCTTATGAATAAAAT 14 149 1 TTATTAATTA 0.731135 -62 GTTTGAGATATTTTCCTCAATATTTGTATTTTATT 14 176 0 TTTTTAATTT 0.947452 -35 GTTTGAGAGATTTTCCTCAATATTTGGATTTTATC 15 95 0 TTTTTAATTT 0.947452 -119 TTTTGACAAGTTTTTGTTTATGTTTTTTTGGGATA 15 153 1 TTTTTTATTT 0.693717 -61 GCTTATCCTTTTTTGTTAAACCTTTCCTCTTCCTC 16 24 0 TTTTTAACTT 0.484079 -60 TTCCTCAAGTTTTACAAAATCTTTCTTAACTTCT 16 60 0 TTTTAAATTT 0.881894 -24 TTTTTATTTTTTATTGTAAATGGTTATGTATGTGA 18 26 1 TTATTAATTT 0.867835 -261 AACTTGGGTATTTTGCTGATTATTTTGAGTAGTTT 18 191 0 TTTTTATTTT 0.741885 -96 CTGGATGATATTTTGGATAATTCTTTTAATTGGAG 19 109 1 TTTTAAATTT 0.881894 -163 TTTACTGTTATTTTTGTTATTACTTTTTAATAACC 19 174 0 TTTTTATTTT 0.741885 -98 ATCAATTCTTTTTATAAAAATTGTAGGGGAGAGTT 21 29 1 TTTAAAATTA 0.495521 -65 TCGATTAAAAGTTTTTAAAATTATTGAGGTTTTAC 23 66 0 GTTTAAATTT 0.523954 -132 TTTATAATTTTTTTATACAATCCTTGTGCATAATA 23 164 1 TTTTAAATTT 0.881894 -34 CGAGTCTGTTTTATTCTGAATACTTACCAATATTA 24 107 1 TTATTAATTT 0.867835 -121 ATTTACAATCTTATAATTAATTATAATATATAAAA 25 77 0 TTATTAATTA 0.731117 -121 AAAATCAGGATTTATCATAATAATTATATCAACTA 26 95 1 TTTAAAATTT 0.703422 -176 TTTTTTATCATAAATTATAAATTATAATT 27 5 1 TTATTAATTA 0.731135 -166 ATGTATCTTTTTTTGTTTAATGCTACTGCTATGCA 27 120 0 TTTTTAATTA 0.881894 -51 **** * *** ** Masking position 2 Map Score: 45.4815 Number of sites scoring better than the average of aligned sites = 1344 Number in coding regions = 1025 Number in noncoding regions = 319 Number of orfs with sites within 600 bp upstream = 273 Fraction of orfs with sites within 600 bp upstream = 0.0438484 Motif number 4 ACCTCAAAAAACAATTACAATTAATTAAAA 1 64 0 ACAATTACAA 0.853216 -26 TAAAATAAAAACCAATAAAACTTAAATAAA 2 25 1 ACCAATAAAA 0.608497 -51 ATCGAACTTTACATTTAAAATATTGTAATA 9 109 1 ACATTTAAAA 0.851011 -113 CTATTAATTTACATATACAAATATATTCTT 12 43 0 ACATATACAA 0.820593 -226 AGGCTCACAAACCATTCAAATAAATTTATG 12 206 0 ACCATTCAAA 0.50329 -63 GAACGGGAGAACCAATACAAGAGATTACTT 15 20 1 ACCAATACAA 0.690482 -194 TGGATTTTATCCATTTACAACCACCGTCCT 15 76 0 CCATTTACAA 0.936679 -138 TCCAACACTTCCCTTTAAAATAAACTTCTC 15 191 0 CCCTTTAAAA 0.876384 -23 ACATACATAACCATTTACAATAAAAAATAA 18 29 0 CCATTTACAA 0.936679 -258 ATTTCCAAGCCCATTTCCAACTTGGGTATT 18 214 0 CCATTTCCAA 0.843267 -73 TTTTCCCGCTCCATTTCCAAGCCCATTTCC 18 226 0 CCATTTCCAA 0.843267 -61 TCCAGAAAATCCAAATAAAAGCAAATGGAA 19 84 0 CCAAATAAAA 0.803029 -188 AATGATTCCTCCAATTAAAAGAATTATCCA 19 122 0 CCAATTAAAA 0.879625 -150 CATATTTTCACCAATTAAAAATAATT 24 7 0 CCAATTAAAA 0.879625 -221 TTAATCACCCATATAAAACACATATTTA 25 180 0 CCATATAAAA 0.851852 -18 CTGAATATAAACCTATAAAAGATAATAATA 26 52 1 ACCTATAAAA 0.686729 -219 ATATCTGCAAACATTTACAATGTATTTGAC 26 230 0 ACATTTACAA 0.891284 -41 ********** Masking position 6 Map Score: 15.5803 Number of sites scoring better than the average of aligned sites = 298 Number in coding regions = 250 Number in noncoding regions = 48 Number of orfs with sites within 600 bp upstream = 41 Fraction of orfs with sites within 600 bp upstream = 0.00658529 Motif number 5 CAATAATCACCTTTAATAAACTGAC 4 14 0 ATCACCTTTA 0.921289 -15 TTCTATCACCTTTGTGCTATTTTT 6 167 0 ATCACCTTTG 0.782683 -14 TTTTTCACCTTTTTATCGTTTAA 8 116 0 TTCACCTTTT 0.973303 -13 CATTTTAATTCACCTGATCAATTAGTCA 9 204 0 TTCACCTGAT 0.879952 -18 ATTTTTCACCTTTTTATGGCAAAT 10 201 0 TTCACCTTTT 0.973303 -14 GCTTTCACCTTTTTAACTTTTTA 11 97 0 TTCACCTTTT 0.973303 -13 TTCATATTTTTTCACCTTTAATTATATTTG 13 208 0 TTCACCTTTA 0.973303 -56 ATTCATAAGATTCACCATAAAACCCCAATT 14 149 0 TTCACCATAA 0.839219 -62 TTTGAGTTTTTTCACCTTATGACTTCTCAT 17 157 0 TTCACCTTAT 0.958835 -47 TTTCATATTTATCACCTTTAATGGTTGAGA 18 64 0 ATCACCTTTA 0.921289 -223 ATGCTTTCTTTTCACCATTTCCATTTGCTT 19 66 1 TTCACCATTT 0.890933 -206 TTTTTCACCTGAAGGGTAGTTAT 20 112 0 TTCACCTGAA 0.879043 -13 TATTTCACCCTAAGACTTTTAAT 26 258 0 TTCACCCTAA 0.814374 -13 ********** Masking position 4 Map Score: 17.3391 Number of sites scoring better than the average of aligned sites = 48 Number in coding regions = 26 Number in noncoding regions = 22 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 6 AATTAATAAATAAAAGATTATCTATAAGT 7 7 0 TAAAATATCT 0.730523 -98 TTTAAGTTCTTTATAAGTTATTTTTTGAGTGGT 8 88 0 TATAGTATTT 0.684936 -41 GAAATAATGAGAAAAAGATATTTCCTCCGAAAA 9 28 0 GAAAGTATTT 0.763151 -194 TGTTTTTATTTGAAACTATATATCGTTTTCCAT 9 146 0 TAAATTATAT 0.50477 -76 GATTAATGTTTAAACTGTTATTTGCCATAAAAA 10 182 1 TAACGTATTT 0.763153 -33 AAATATTTACTTAAAATTTATTTT 12 255 1 TAAATTATTT 0.844512 -14 ATTTATATTGTGAAATAGTATTTTCAAATTTAG 13 76 1 TAAAATATTT 0.945018 -188 ATCCAAAATATAAAAAGATTTTTAGCCAGATAT 14 89 0 TAAAGTTTTT 0.68492 -122 GGAAAATATCTCAAACATTATTTTTT 14 195 1 TAAAATATTT 0.945021 -16 GGAAAATCTCTCAAACATTATTTTTTATTTATT 15 114 1 TAAAATATTT 0.945021 -100 TTTTCTCACCTCAAATATTATTTTTGTTTAAAA 19 220 0 TAAAATATTT 0.945021 -52 CTTACCAATATTAAAAGATATATCATTTTTATT 24 129 1 TAAAGTATAT 0.816728 -99 AAATTAAAAATTAAAGGTTATTTTGGATTTTAT 25 18 0 TAAAGTATTT 0.959592 -180 AAACACATATTTAAAGAATATTTTTTATAAATG 25 160 0 TAAAATATTT 0.945018 -38 ACTATCACATAAAAAACTATTTTTATTCTAAC 28 63 0 TAAAATATTT 0.945002 -22 * *** * ***** Masking position 3 Map Score: 11.4691 Number of sites scoring better than the average of aligned sites = 208 Number in coding regions = 149 Number in noncoding regions = 59 Number of orfs with sites within 600 bp upstream = 67 Fraction of orfs with sites within 600 bp upstream = 0.0107613 Motif number 7 TTGTAATTGTTTTTTGAGGTGGAAAT 1 74 1 TTTTTGAGGG 0.934292 -16 TATAAGTTATTTTTTGAGTGGTTTTACTACCT 8 78 0 TTTTTGAGGT 0.976206 -51 ATTTACTAATTTTTTAATTTGTTTTATTTATT 10 121 1 TTTTTAATGT 0.740999 -94 GTGTTTATAGATTTTAAGTAATCTCTTGTATT 15 33 0 ATTTTAAGAT 0.720688 -181 TTATTTTGTATTTTTGACAAGTTTTTGTTTAT 15 142 1 TTTTTGACGT 0.841585 -72 TAGTTTGAACATTTTGAGCTGTTTCTGTATTC 18 165 0 ATTTTGAGGT 0.976206 -122 TTTGCTGATTATTTTGAGTAGTTTGAACATTT 18 183 0 ATTTTGAGGT 0.976206 -104 AATTATTTTTAATTGGTGAAAATATGC 24 6 1 TTTTTAATGT 0.740999 -222 TATATAAAAAATTTTGAGTCGTCATGGTTTGC 24 43 1 ATTTTGAGGT 0.976206 -185 AATGTTGTGGATTTTGAGATGGGTAAAGTATC 24 198 1 ATTTTGAGGG 0.934292 -30 AAAGGTAGTTATTTTAAGATGTGATAGTGCGG 27 65 1 ATTTTAAGGT 0.948903 -106 ATCACATCCCTTTTTAAGAAATTATATATAAT 28 14 1 TTTTTAAGAT 0.720688 -71 ******** ** Masking position 7 Map Score: 8.64955 Number of sites scoring better than the average of aligned sites = 80 Number in coding regions = 63 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 8 AACTTTCAATGAAATTACTATATATTTAACAC 1 9 1 ATGAAATATA 0.567382 -81 ATAAAAACCAATAAAACTTAAATAAACAAAAGAT 2 29 1 ATAAAACATA 0.616187 -47 TAAACAAAAGATAAAATAAAAAGGAGGGGAGAAA 2 51 1 ATAAAATAGG 0.401442 -25 AATAATAAAATTATTTTAATTAAACTTT 3 5 1 ATAAAATTTA 0.706963 -35 ATTTCGCATAATATAATGAAATTAAAGACGATTA 6 84 0 ATATAATTTA 0.405591 -97 AAGTAAAATAATAAAATGGGAATTGAAAAAGAAA 9 57 0 ATAAAATATT 0.531404 -165 GAATTAAAAAATAAAAATTAAATAAAAATTTTTA 10 18 0 ATAAAAAATA 0.814495 -197 TCTGGGTATTATAATATTATTATATGTTTTATCA 10 81 1 ATAATATATA 0.618274 -134 AATCACGATTATATAATATTAATGGTTCGAAATT 11 41 0 ATATAATATG 0.712045 -69 GATATGAGTAATAAAATATCGATATTGGCAAAAA 12 111 1 ATAAAATATA 0.94858 -158 TATTTGAAAAATAAAATTAAAACAATTTATATAA 13 25 1 ATAAAATACA 0.585946 -239 CACAATATAAATAAAATTTACTTAAAGATTTATA 13 54 0 ATAAAATTTA 0.706963 -210 TAAATCTAATAAAAAATTTGTATAATTGTTAATA 14 28 0 AAAAAATATA 0.627376 -183 AAATAGGAGGATAAAAATTAGATAAATCTAATAA 14 50 0 ATAAAAAATA 0.814495 -161 AATCTTATGAATAAAATACAAATATTGAGGAAAA 14 167 1 ATAAAATATA 0.94858 -44 TTGTAAATGGATAAAATCCAAATATTGAGGAAAA 15 86 1 ATAAAATATA 0.94858 -128 ATAAATATGAAAAAAATAGCGATGATATTGGTAG 18 82 1 AAAAAATATG 0.443809 -205 TAACAAAAAAATAAAATATTTATGGTGTGACATA 19 11 1 ATAAAATATG 0.897361 -261 AATATCATCCAGAAAATCCAAATAAAAGCAAATG 19 87 0 AGAAAATATA 0.585946 -185 TCACAACTTAGTAAAATTTATATATTTGTTTTCT 20 42 1 GTAAAATATA 0.567382 -83 AATATAATTGGTATGTAGTAGAGGT 22 2 1 ATATAATATG 0.712045 -42 CAAGGATTGTATAAAAAAATTATAAATTAATAAT 23 156 0 ATAAAAAATA 0.814495 -42 ATCCTTGTGCATAATATTGACATAG 23 183 1 ATAATATATA 0.618274 -15 AAATAAAACAATAAAAATGATATATCTTTTAATA 24 137 0 ATAAAAAATA 0.814495 -91 ATTATAATATATAAAATAAAAAAAATGAAAAAAT 25 59 0 ATAAAATAAA 0.488441 -139 TTAATCACCCATATAAAACACATATTTAAAGAAT 25 174 0 ATATAAAATA 0.553936 -24 AAGATAGTTGATATAATTATTATGATAAATCCTG 26 100 0 ATATAATATG 0.712045 -171 AAGAAATTATATATAATTACAATAAATGTTTTAA 28 29 1 ATATAATATA 0.839165 -56 ******* *** Masking position 6 Map Score: 19.9606 Number of sites scoring better than the average of aligned sites = 496 Number in coding regions = 317 Number in noncoding regions = 179 Number of orfs with sites within 600 bp upstream = 181 Fraction of orfs with sites within 600 bp upstream = 0.0290716 Motif number 9 CATATAAAAAATCACAAATACGATAATCGT 6 61 1 ATCACAAATA 0.822887 -120 ACTATCTAAAATCAAAAATATAATATATGA 8 45 1 ATCAAAAATA 0.879559 -84 ATAATTGTTAATAAAAAATAGAAGTTTTTA 14 11 0 ATAAAAAATA 0.819311 -200 AAACTCTGGAATCCAAAATATAAAAAGATT 14 102 0 ATCCAAAATA 0.935942 -109 TACAAAATAAATAAAAAATAATGTTTGAGA 15 122 0 ATAAAAAATA 0.819311 -92 CTTGTCAAAAATACAAAATAAATAAAAAAT 15 133 0 ATACAAAATA 0.900714 -81 CTTCTCAATTATCCCAAAAAAACATAAACA 15 167 0 ATCCCAAAAA 0.882246 -47 ACCATTTACAATAAAAAATAAAAAAATGAG 18 20 0 ATAAAAAATA 0.819311 -267 CCAAAATATCATCCAGAAAATCCAAATAAA 19 95 0 ATCCAGAAAA 0.569134 -177 TAAAAGAATTATCCAAAATATCATCCAGAA 19 107 0 ATCCAAAATA 0.935942 -165 TTAAAAAGTAATAACAAAAATAACAGTAAA 19 179 1 ATAACAAAAA 0.699265 -93 TTGATGTTTAATACCAAAAATTT 21 4 0 ATACCAAAAA 0.823071 -90 GATATCAATCCCAAAAATACCTCTACT 22 27 0 ATCCCAAAAA 0.882246 -17 AACATTAAAAATACAAAAAACAGCAGTATA 24 174 0 ATACAAAAAA 0.879693 -54 TGGGTAAAGTATCCAAAAAAT 24 217 1 ATCCAAAAAA 0.921731 -11 ATAATATAAAATCCAAAATAACCTTTAATT 25 13 1 ATCCAAAATA 0.935942 -185 AATATATAAAATAAAAAAAATGAAAAAATA 25 58 0 ATAAAAAAAA 0.785167 -140 AGTTGCATTTATAAAAAATATTCTTTAAAT 25 155 1 ATAAAAAATA 0.819311 -43 ********** Masking position 2 Map Score: 26.7556 Number of sites scoring better than the average of aligned sites = 278 Number in coding regions = 232 Number in noncoding regions = 46 Number of orfs with sites within 600 bp upstream = 44 Fraction of orfs with sites within 600 bp upstream = 0.00706714 Motif number 10 TATGTGTTAAATATATAGTAATTTCATTGA 1 16 0 ATATATAGTA 0.794297 -74 TATATATTTAACACATATTATAAATTTCTA 1 29 1 ACACATATTA 0.847146 -61 TTACATATAGACATATACTTCACATCGCGT 5 20 0 ACATATACTT 0.825347 -52 ATTTTTCGTTATACATAGTAATCAAACTAA 7 73 0 ATACATAGTA 0.739272 -32 TTAGAAAGTTATATATACTATCTAAAATCA 8 29 1 ATATATACTA 0.74618 -100 ATGGAAAACGATATATAGTTTCAAATAAAA 9 146 1 ATATATAGTT 0.711555 -76 AAGTGATAAAACATATAATAATATTATAAT 10 88 0 ACATATAATA 0.650599 -127 TTTTTCTTATATATATATTACTTATCCTAA 12 75 0 ATATATATTA 0.749909 -194 ACGAATTTCGACATATATTTAATTAATAAC 12 150 0 ACATATATTT 0.826118 -119 TTCCAATATACACATATTTGAAAAATAAA 13 10 1 ACACATATTT 0.779758 -254 CTTTTTAACTACATATAGTAGTGTAAGAAA 20 71 0 ACATATAGTA 0.906691 -54 TTAAAAAGATACATATACTATAACTACCCT 20 93 1 ACATATACTA 0.880924 -32 CCCATATAAAACACATATTTAAAGAATATT 25 171 0 ACACATATTT 0.779758 -27 ********** Masking position 5 Map Score: 7.12536 Number of sites scoring better than the average of aligned sites = 64 Number in coding regions = 54 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 11 AAGCAAATATAAAATAAAAACCAATAAAAC 2 16 1 AAAATAAAAA 0.867751 -60 CAATAAAACTTAAATAAACAAAAGATAAAA 2 37 1 TAAATAAACA 0.276941 -39 AACAAAAGATAAAATAAAAAGGAGGGGAGA 2 53 1 AAAATAAAAA 0.867751 -23 AAGTTTAATTAAAATAATTTTATTATT 3 8 0 AAAATAATTT 0.484574 -32 AAAGTAAAAAATAATAAACTAAAAACTAAT 6 25 1 ATAATAAACT 0.19625 -156 AACCACTCAAAAAATAACTTATAAAGAACT 8 87 1 AAAATAACTT 0.521361 -42 GTATTTAAGTAAAATAATAAAATGGGAATT 9 67 0 AAAATAATAA 0.712967 -155 ACAGAATTAAAAAATAAAAATTAAATAAAA 10 25 0 AAAATAAAAA 0.867751 -190 ATTACATTATAAAATAAACAATCACGATTA 11 64 0 AAAATAAACA 0.8986 -46 TATTCTTAAAAAAATAAAAAAGTAAAAAAA 12 20 0 AAAATAAAAA 0.867751 -249 AAAATAAATTTTAAGTAAAT 12 259 0 AAAATAAATT 0.712965 -10 ACATATTTGAAAAATAAAATTAAAACAATT 13 22 1 AAAATAAAAT 0.807058 -242 CTTACACAATAAAATAAATAACTGATAATA 13 162 1 AAAATAAATA 0.795768 -102 AACTGATAATAAAATAACTAATAACTACAA 13 181 1 AAAATAACTA 0.630814 -83 CAAACTTTATAATATAAACTCTGGAATCCA 14 117 0 AATATAAACT 0.201596 -94 AAAAAATAATGTTTGAGATATT 14 199 0 AAAATAATGT 0.314895 -12 AAATAAATAAAAAATAATGTTTGAGAGATT 15 118 0 AAAATAATGT 0.314895 -96 TCAAAAATACAAAATAAATAAAAAATAATG 15 129 0 AAAATAAATA 0.795768 -85 ATCCCAAAAAAACATAAACAAAAACTTGTC 15 157 0 AACATAAACA 0.369896 -57 ACTTCCCTTTAAAATAAACTTCTCAATTAT 15 185 0 AAAATAAACT 0.849611 -29 TTTACAATAAAAAATAAAAAAATGAGATGA 18 16 0 AAAATAAAAA 0.867751 -271 CAAACTACTCAAAATAATCAGCAAAATACC 18 190 1 AAAATAATCA 0.770367 -97 AATAATCAGCAAAATACCCAAGTTGGAAAT 18 202 1 AAAATACCCA 0.199319 -85 TAACAAAAAAATAAAATATTTATGGTG 19 8 1 AAAATAAAAT 0.807058 -264 CTTTTAAACAAAAATAATATTTGAGGTGAG 19 219 1 AAAATAATAT 0.612924 -53 CACAACCATGAAAATAAAAAAT 20 3 0 AAAATAAAAA 0.867751 -122 ATTTACCACAAAAATAATCAAAGA 21 80 1 AAAATAATCA 0.770367 -14 TATAAAATCCAAAATAACCTTTAATTTTTA 25 17 1 AAAATAACCT 0.712429 -181 TATAATATATAAAATAAAAAAAATGAAAAA 25 61 0 AAAATAAAAA 0.867751 -137 TGCAAAAATAAAAATAAAAATTAAT 26 6 0 AAAATAAAAA 0.867751 -265 ATCACATCTTAAAATAACTACCTTTGTCAC 27 60 0 AAAATAACTA 0.630814 -111 ********** Masking position 5 Map Score: 36.6577 Number of sites scoring better than the average of aligned sites = 1220 Number in coding regions = 774 Number in noncoding regions = 446 Number of orfs with sites within 600 bp upstream = 346 Fraction of orfs with sites within 600 bp upstream = 0.0555734 Motif number 12 CTTTCAATGAAATTACTATATATTTAACACATA 1 13 1 ATTATAATAT 0.703701 -77 ACATATTATAAATTTCTAAATCTTTTTAATTAA 1 41 1 ATTTTAATCT 0.505247 -49 AATTTCTATTTAAAAAATTTAGAAAGTTAT 8 8 1 ATTAAAATTT 0.784641 -121 CGAACTTTACATTTAAAATATTGTAATAAAGTA 9 111 1 ATTAAAATTG 0.651746 -111 CAAATTAAAAAATTAGTAAATATAAAGTGATAA 10 109 0 ATTATAATAT 0.703698 -106 ATATAAGAAAAATTAGAAGATATGAGTAATAAA 12 93 1 ATTAAAATAT 0.856186 -176 ACCTCTGCTAAATTTGAAAATACTATTTCACAA 13 83 0 ATTTAAATAC 0.518643 -181 TAACTATTCGAATTTCAACATATCTATTTAAAT 13 116 0 ATTTAAATAT 0.880757 -148 TTATCCTCCTATTTTTAAAATATCTGGCTAAAA 14 70 1 ATTTAAATAT 0.880015 -141 TATTTTGAGTAGTTTGAACATTTTGAGCTGTTT 18 173 0 ATTTAAATTT 0.81886 -114 AACTTAGTAAAATTTATATATTTGTTTTCTTAC 20 46 1 ATTTTAATTT 0.643289 -79 ATACTTTCAAAATTTAAATATATAATTAT 23 7 0 ATTTAAATAT 0.880751 -191 ACGACTCAAAATTTTTTATATAGCTTTGCATAT 24 32 0 ATTTTAATAG 0.602133 -196 TCTTATAATTAATTATAATATATAAAATAAAAA 25 71 0 ATTAAAATAT 0.85583 -127 TATTATAATTAATTATAAGATTGTAAATCAGCA 25 84 1 ATTAAAATTG 0.651746 -114 AATATCACTCACTTTGAAGATAGTTGATATAAT 26 117 0 ATTTAAATAG 0.791395 -154 TCACCCTAAGACTTTTAATATCTGCAAACATTT 26 244 0 ATTTAAATCT 0.719076 -27 TTTTATTCTAACTTAAAACATTTATTGTAATTA 28 42 0 ATTAAAATTT 0.784653 -43 * *** ** **** Masking position 4 Map Score: 12.7515 Number of sites scoring better than the average of aligned sites = 635 Number in coding regions = 445 Number in noncoding regions = 190 Number of orfs with sites within 600 bp upstream = 192 Fraction of orfs with sites within 600 bp upstream = 0.0308384 Motif number 13 AATAGCACAAAGGTGATAGAA 6 170 1 AGGTGATAGA 0.911481 -11 ATGGTTATGTATGTGATTGTCTCAACCATT 18 45 1 ATGTGATTGT 0.908717 -242 TTATTTTAAGATGTGATAGTGCGGCAAAAA 27 73 1 ATGTGATAGT 0.970373 -98 TTAAAAAGGGATGTGATAGA 28 1 0 ATGTGATAGA 0.958085 -84 ATAGTTTTTTATGTGATAGT 28 75 1 ATGTGATAGT 0.970373 -10 ********** Masking position 6 Map Score: 1.95639 Number of sites scoring better than the average of aligned sites = 13 Number in coding regions = 8 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 14 GATTAATGATATATACCTCTAACTGACTAA 6 124 1 ATATACCTCT 0.810905 -57 ATATCTATTTAAATACCTCTGCTAAATTTG 13 100 0 AAATACCTCT 0.953823 -164 CATCAACCTTAACTCCCTCTGGGTTCATTG 17 99 1 AACTCCCTCT 0.909042 -105 CATATACTATAACTACCCTTCAGGTGAAAA 20 104 1 AACTACCCTT 0.856369 -21 TCAATCCCAAAAATACCTCTACTACATACC 22 20 0 AAATACCTCT 0.953823 -24 GAGTGATATTAATTACCCCTATCTCCAAAA 26 140 1 AATTACCCCT 0.84618 -131 ATCTTAAAATAACTACCTTTGTCACAATAT 27 55 0 AACTACCTTT 0.898584 -116 ********** Masking position 1 Map Score: 0.515396 Number of sites scoring better than the average of aligned sites = 51 Number in coding regions = 47 Number in noncoding regions = 4 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 Motif number 15 ********** No masking Map Score: 1.31617e-11 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