AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -a/home/amcguire/genomes/ORF_ecoli.txt -z/home/amcguire/genomes/ecoli.fna -intrC_ecoli_bsub_300.orf -g0.5 -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 = 0.5 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 glnP 138 glutamine high-affinity transport system; membrane component #2 glnH 300 periplasmic glutamine-binding protein; permease #3 glnL 285 histidine protein kinase sensor for GlnG regulator (nitrogen regulator II, NRII) #4 glnA 300 glutamine synthetase #5 yckK 114 similar to glutamine ABC transporter (glutamine-binding protein) #6 yclA 89 similar to transcriptional regulator (LysR family) #7 yfjN 300 similar to hypothetical proteins #8 yfjM 195 yfjM #9 yfjL 29 alternate gene name: yztA #10 acoA 231 acetoin dehydrogenase E1 component (TPP-dependent alpha subunit) #11 acoR 115 transcriptional regulator #12 spoVK 300 alternate gene name: spoVJ; disruption leads to the production of immature spores (stage V sporulation) #13 ynbA 220 similar to GTP-binding protein protease modulator #14 ynbB 187 similar to hypothetical proteins #15 glnR 110 transcriptional regulator #16 glnA 60 glutamine synthetase #17 yqiY 80 similar to amino acid ABC transporter (permease) #18 yqiX 268 similar to amino acid ABC transporter (binding protein) #19 yqiW 162 similar to hypothetical proteins from B. subtilis #20 yqiR 152 similar to transcriptional regulator (sigma-L-dependent) #21 glnQ 155 glutamine ABC transporter (ATP-binding protein) #22 glnH 21 glutamine ABC transporter (glutamine-binding protein) #23 glnM 60 glutamine ABC transporter (integral membrane protein) #24 ytmM 29 similar to amino acid ABC transporter (permease) #25 ytmL 21 similar to amino acid ABC transporter (permease) #26 ytmI 152 similar to hypothetical proteins from B. subtilis #27 yxeN 22 similar to amino acid ABC transporter (permease) #28 yxeM 24 similar to amino acid ABC transporter (binding protein) #29 yxeK 185 similar to monooxygenase #30 yxeI 154 similar to penicillin amidase #31 yxeH 39 similar to hypothetical proteins #32 yxeF 87 yxeF #33 rocR 240 transcriptional regulator (NtrC/NifA family) Motif number 1 CTTTTTACGGATAAAAAGCGCGAAGCATCAGAG 3 219 0 AAAAAAGCGA 0.931909 -67 GTGAAAGCGATCACAAAGGGACTCTGCAATACT 4 27 0 TACAAAGGGT 0.563441 -274 TTCACGGAGCATAAAAAGGGTTATCCAAAGGTC 4 55 1 AAAAAAGGGA 0.950972 -246 TAAATTGCCCCTAAAAGGCGTTATCATGCGCAC 4 174 0 CAAAAGGCGA 0.712485 -127 GCCGTAAAAAAGATAAAGCGAAATCTGTGCCAA 4 211 0 AATAAAGCGA 0.90955 -90 AAGGCTAACAAAATAAAGGGATTTTTACACAAT 8 31 1 AATAAAGGGT 0.892196 -165 TGGAGATATCATATAAAGGGGGAGAGGAAA 8 176 1 AATAAAGGGA 0.934433 -20 AGGCGCATGGATATAAGGCGCCTGCTTTTTTAT 11 24 1 AATAAGGCGT 0.904092 -92 TGTAGGGGAAAAATAAAGCGCTTTCAACAATAA 11 53 0 AATAAAGCGT 0.853792 -63 TCGATTGCTTTGAAAAGGCGGAAATACGAGCAA 13 39 0 TAAAAGGCGA 0.846176 -182 AACTAAGTTAAGAAAAGGAGGAAATTGAG 15 92 1 AAAAAGGAGA 0.909094 -19 TTTTCCTGTAAGAAAAGGAGACAAAGGCT 17 62 1 AAAAAGGAGA 0.909094 -19 TACTGCTTACAGAAAAAGGGGATTATATAACCA 19 37 0 AAAAAAGGGT 0.91846 -126 GGAAATGAAAAGATAAAGGGGTTTTCTGAAG 20 9 0 AATAAAGGGT 0.892196 -144 AAATTTTTTCATACAAAGGGGTATCGGG 20 135 1 AACAAAGGGA 0.899256 -18 CATCCCAATTTGATAAGGAGTGAATAGGCAG 23 40 1 TATAAGGAGA 0.646581 -21 AAATAGAAAAGGCGGGAAAATCAA 28 5 1 AAAAAGGCGA 0.956697 -20 TAAAAACATGATAAAAGGAGTATCGCC 29 169 1 AAAAAGGAGT 0.8531 -17 TAATCTGAATTGAAAAGGGGACTGATCAA 30 136 1 TAAAAGGGGT 0.819082 -19 GCATTCGCCCAAAAAAGGAGGAAAGA 32 72 1 AAAAAGGAGA 0.909094 -16 TTGAAACAGAAAACAAGGGGGAATTCAAAT 33 8 0 AACAAGGGGA 0.935104 -233 ACTTGCATTTATATAAAGGGAAAGCAGGATAAC 33 44 0 AATAAAGGGA 0.934433 -197 * ******** * Masking position 6 Map Score: 26.5588 Number of sites scoring better than the average of aligned sites = 233 Number in coding regions = 146 Number in noncoding regions = 87 Number of orfs with sites within 600 bp upstream = 97 Fraction of orfs with sites within 600 bp upstream = 0.0155798 Motif number 2 AAACGCACTGGCAGTTCCCTCTCCCCTATGGGG 1 27 1 GCTTCCCTTC 0.924641 -112 TGCCAGTTTTGCAACTCCTTGATTTTTCGAGAT 2 213 0 GCCTCCTTAT 0.982283 -88 AGCATTTCCTTTTTTCTATCCACG 2 287 0 GCTTCCTTTT 0.961832 -14 AAGAAAGCGCCTCCTTATCATACCTTTTA 6 71 0 GCCTCCTTTC 0.986184 -19 TTTGTGCGCCTCCTTCTATTTAGGGTTC 10 214 0 GCCTCCTTTA 0.931872 -18 TTATATCCATGCGCCTGCTTTTTCCTTTA 11 7 0 GCCTGCTTTT 0.965171 -109 TGGATATAAGGCGCCTGCTTTTTTATTGTTGAA 11 31 1 GCCTGCTTTT 0.965171 -85 TTCCTTGATCGCTCCTCCCTTACACGCCGTTTT 11 93 0 GCCTCCCTAC 0.96428 -23 ATGTGTCGAAACAATTGCTTTTTTCGGGAACAA 12 215 0 ACTTGCTTTT 0.650634 -86 ATACAACTGCTCCTTTATTTTCCTTCTG 19 6 1 ACCTCCTTAT 0.934951 -157 TGAAGACCTCTCCTTTTTCATCATCTGT 19 145 0 ACCTCCTTTT 0.961832 -18 CACTGCTCCCTCTCTTTTTAC 25 8 0 ACCTCCCTTC 0.924641 -14 ATCAATGCCGTTCCCTCATGGTCACGCAA 29 7 1 GCTTCCCTAT 0.905036 -179 CCTGCATCTCCTTCATGTCGTTTTCA 31 24 0 GCCTCCTTAT 0.982283 -16 ** ****** ** Masking position 6 Map Score: 16.4649 Number of sites scoring better than the average of aligned sites = 140 Number in coding regions = 104 Number in noncoding regions = 36 Number of orfs with sites within 600 bp upstream = 40 Fraction of orfs with sites within 600 bp upstream = 0.00642467 Motif number 3 ATCTGGTGCGCTAAAATTGTGCACTCAACACAG 2 115 0 CAAAAGTGCA 0.969165 -186 TTTTAGCGCACCAGATTGGTGCCCCAGAATGGT 2 132 1 CAGATGTGCC 0.975654 -169 GATTGGTGCCCCAGAATGGTGCATCTTCAGGGT 2 145 1 CAGAAGTGCA 0.97749 -156 CACATATATGAAAAAATCGTGCCAGTTTTGCAA 2 232 0 AAAAAGTGCC 0.816062 -69 CTATAATGCACTAAAATGGTGCAACCTGTTCAG 3 252 1 CAAAAGTGCA 0.969165 -34 CATTGAAGCACTATATTGGTGCAACATTCACAT 4 116 1 CATATGTGCA 0.810497 -185 AAAGATAAAGCGAAATCTGTGCCAACTTTTAAA 4 203 0 CAAATGTGCC 0.966673 -98 GCGACACGGCCAAAATAATTGCAGATTTCGTTA 4 242 1 CAAATTTGCA 0.812271 -59 ATTACCAACGCAAAATAATTGCCCTGTTA 7 7 0 CAAATTTGCC 0.840219 -294 TTATTTTAGTCAAGAATTGTGTAAAAATCCCTT 8 46 0 CAGAAGTGTA 0.725526 -150 ATTATAAATGCAAGAAGTGTGCCAGTCTTTTGA 10 178 0 CAGAAGTGCC 0.981404 -54 ACGAAGAGGCCAAAAAAAGTGCACGGCGAAGCA 19 71 1 CAAAAGTGCA 0.969165 -92 TATATAAATGCAAGTTCTGTGCCAAATCAAGAA 33 62 1 CAGTTGTGCC 0.797741 -179 AGGATATGCAAAAGAATTTTGCACTTGCTGAAA 33 159 0 AAGAATTGCA 0.477636 -82 * **** ***** Masking position 3 Map Score: 15.1501 Number of sites scoring better than the average of aligned sites = 171 Number in coding regions = 144 Number in noncoding regions = 27 Number of orfs with sites within 600 bp upstream = 29 Fraction of orfs with sites within 600 bp upstream = 0.00465789 Motif number 4 CGCATCTCGAAAAATCAAGGAGTTGCAAAA 2 210 1 AAAATCAAGG 0.739714 -91 CAAAAAGTTCAAAAGCAAGGCCACTAAGAA 7 87 1 AAAAGCAAGG 0.898971 -214 ACCAGAATATAAAAAATAGGGTAGATAATC 7 139 1 AAAAAATAGG 0.559009 -162 AAAGGCTAACAAAATAAAGGGATTTTTACA 8 30 1 AAAATAAAGG 0.837086 -166 GGATTTACCGAAAATCCAGGTTTATTTTAG 8 70 0 AAAATCCAGG 0.853573 -126 CTGCGTACAAAAAAGACCCGGATTTACCGA 8 89 0 AAAAGACCCG 0.584405 -107 TAAATTAGAGAAAAGACAGGCTGAGTAAAA 8 120 0 AAAAGACAGG 0.970588 -76 TTATTGTAAGAAAATAATGGTATATTTAGT 8 147 1 AAAATAATGG 0.56098 -49 ACATATGAGGAAAAGAGTGGGAAC 9 16 1 AAAAGAGTGG 0.822524 -14 GCATGCAAAAAAAAGACCGGATATCACCCG 10 54 0 AAAAGACCGG 0.961597 -178 TTACGGGCTCAAAAGACTGGCACACTTCTT 10 170 1 AAAAGACTGG 0.891381 -62 TAAAGGAAAAAGCAGGCGCATGGATA 11 7 1 AAAAAGCAGG 0.772015 -109 TTCAACAATAAAAAAGCAGGCGCCTTATAT 11 34 0 AAAAAGCAGG 0.772015 -82 ATATAGAGAGAACAGAGAGGTGAAG 12 286 1 AACAGAGAGG 0.766284 -15 CCCAATATGCAAAAGAAAGGAACATCCATT 13 115 1 AAAAGAAAGG 0.941479 -106 AAAAAAGCGGCTCAACTTTT 17 1 1 AAAAAAGCGG 0.861448 -80 AGACGAACAACCCGGATGCTCAAAG 18 6 1 AACAACCCGG 0.517208 -263 TTATGCACAAAAAAACCCGGGCTGCTTTGA 18 30 0 AAAAACCCGG 0.858941 -239 AACCAGAAGGAAAATAAAGGAGCAGTTGTA 19 12 0 AAAATAAAGG 0.837086 -151 AGATGATGAAAAAGGAGAGGTCTTCA 19 147 1 AAAGGAGAGG 0.629351 -16 GTAAAAAGAGAGGGAGCAGTG 25 4 1 AAAAGAGAGG 0.949074 -18 TCTATTTTATAAAAAAACGGAGAGGATATG 33 184 0 AAAAAAACGG 0.842948 -57 ********** Masking position 2 Map Score: 17.6598 Number of sites scoring better than the average of aligned sites = 588 Number in coding regions = 456 Number in noncoding regions = 132 Number of orfs with sites within 600 bp upstream = 139 Fraction of orfs with sites within 600 bp upstream = 0.0223257 Motif number 5 ATTTACTTAATCAGCTGGAGATAGCAGATGG 2 4 0 TTGGAAGCAA 0.675712 -297 GATTGTGTGATGATGTGGATACAAAAAATTTACTTAAT 2 31 0 TTGGAAAAAA 0.920693 -270 CAGGGGATCGTCCCGTGGATAGAAAAAAGGAAATGCT 2 274 1 TTGGAAAAAA 0.920702 -27 AAGATTTTGTCTTATGAAAACCAAATACTTACTCATA 5 10 1 TTGAAAAAAA 0.840882 -105 TTCTGGTTGATTTTATTGAAATAAAAAATTAGCTTACA 5 73 0 TTTGAAAAAA 0.726994 -42 TAGATATTTTTCATATGGATATATCAGGAGTATGATTG 6 13 0 TTGGAATCAG 0.856171 -77 CTATTAAATCTATAATTAATACCTAAAAGGTATGATAA 6 48 1 TTTAAATAAA 0.462184 -42 TTTGCGTTGGTAATATGGAGAACTCATATGATATTCTA 7 26 1 TTGGAATCAA 0.886942 -275 TAATGGTATATTTAGTGGAGATATCATATAAAGGGGGA 8 161 1 TTGGAATCAA 0.886942 -35 GACAAATGAATCAGTTTGAGACAAAACGAGACACACGT 10 94 1 TTTGAAAAAG 0.66894 -138 AATCAGCCCGTTGTATGAAAAAGAAATAATGAGAAAGA 12 60 1 TTGAAAAAAA 0.840883 -241 TTCACGGACATGGGGTGGACAAACCATGAGATTTTGTT 12 131 0 TTGGAACCAG 0.612564 -170 AATCCTTACATCGTATTGACACATAATATAACATCACC 15 46 1 TTTGAATAAA 0.653748 -65 GTAAAATTCCTCCTCTTAAAAGGTAAAAATGTATATAG 16 30 0 TTTAAATAAA 0.462184 -31 AAATATTTTTTCCGCTGGACAATAAAGGAAATGAAAAG 20 30 0 TTGGAAAAAG 0.898063 -123 ATGATCAAACTTTTCTGAAAATTAAAAGTGAAAAAATG 21 91 0 TTGAAAAAAG 0.800397 -65 AAGGGTCTTTTCGCTTGAATAGAAAAAATTAATCTTAA 29 38 1 TTGAAAAAAA 0.840883 -148 CCTAGTCGTTTAATATGAATAAATCAAAATGTACCTTT 29 98 0 TTGAAATCAA 0.78121 -88 TGGGACTATAGCCTGAAAACGACATGAAGGAGATGC 31 9 1 TTGAAAACAG 0.79259 -31 * **** * *** * Masking position 6 Map Score: 12.1163 Number of sites scoring better than the average of aligned sites = 182 Number in coding regions = 151 Number in noncoding regions = 31 Number of orfs with sites within 600 bp upstream = 35 Fraction of orfs with sites within 600 bp upstream = 0.00562159 Motif number 6 ACGATTGTGTGATGATGTGGATACAAAAAATTTACTT 2 34 0 GAGATGACAA 0.715068 -267 TTATTTAGCGTAAAACCTGATGAAAAAACAATCTTTA 2 75 0 TAAATGAAAA 0.898826 -226 ACAGGCTGAGTAAAAGCTGCGTACAAAAAAGACCCGG 8 98 0 TAAATGACAA 0.789748 -98 ATAATACTCTGACAAAATGATTAAAAACAAAATCTCA 12 106 1 GAAATGAAAA 0.974115 -195 GACAAACGCCTATCATGTGTCGAAACAATTGCTTTTT 12 225 0 TACATGAAAA 0.720569 -76 TCAAATCCAGGAGAAATTTTTAAAAAAT 15 2 0 GAAATTAAAA 0.898826 -109 TAAGCCTAAAGATAATTTTTAAAAATAGTATTGCATA 18 160 1 GAAATTAAAA 0.898826 -109 GCATAAAAATGAGAAACTGTTTAAAATACAAATTAAC 18 192 1 GAAATGAAAT 0.775032 -77 GCTATCATAAGAACAGATGATGAAAAAGGAGAGGTCT 19 133 1 GACATGAAAA 0.916132 -30 GTCAAGAGAAGAAAACGTGGTAACATAGGGTTGTGCA 20 69 1 GAAATGACAA 0.940868 -84 CCTCCTATCAGAAAATTTGACCAAAAAGTAAATGATC 21 123 0 GAAATGAAAA 0.974115 -33 GTATAAACAATAAAAGCTTAGTAAACAAATAGGAATT 26 98 1 TAAATTAAAA 0.677131 -55 GGGAAAGCAGGATAACATGTTGAAACAGAAAACAAGG 33 23 0 GAAATGAAAA 0.974115 -218 CCTTGTCCTCGAAAATTGTAGAAAACACACGAATTCT 33 91 0 GAAAGTAAAA 0.546563 -150 AATTTTCGAGGACAAGGTGCAAAAACATTCTGATATT 33 111 1 GAAATGAAAA 0.974115 -130 ** ** ** *** * Masking position 5 Map Score: 12.5997 Number of sites scoring better than the average of aligned sites = 196 Number in coding regions = 169 Number in noncoding regions = 27 Number of orfs with sites within 600 bp upstream = 38 Fraction of orfs with sites within 600 bp upstream = 0.00610344 Motif number 7 ACTGGCAGTTCCCTCTCCCCTATGGGGAGA 1 33 1 CCCTCTCCCC 0.980149 -106 CTCACCCTAATCCTCTCCCCATAGGGGAGA 1 46 0 TCCTCTCCCC 0.972781 -93 GGGTTTGCGCCCCTCACCCTAATCCTCTCC 1 58 0 CCCTCACCCT 0.906965 -81 CCTTTGTGATCGCTTTCACGGAGCATAAAA 4 41 1 CGCTTTCACG 0.791855 -260 TTTCCTCTCCCCCTTTATATGA 8 184 0 TCCTCTCCCC 0.972781 -12 GATCGCTCCTCCCTTACACGCCGTTTTCAT 11 90 0 CCCTTACACG 0.738711 -26 AGGAATCCTGCGCTTTCCCGAGAAATACTT 12 183 0 CGCTTTCCCG 0.95027 -118 ATTTTCAAAATGCTCATCCGTGATATGCGG 13 198 0 TGCTCATCCG 0.896223 -23 CTGCTTTCACCTCACCTATAT 21 2 1 TGCTTTCACC 0.766581 -154 GAGCATCGCCTGCTCATCCCGGGATGGTTG 23 11 0 TGCTCATCCC 0.911505 -50 GAGCAGGCGATGCTCATCCCAATTTGATAA 23 26 1 TGCTCATCCC 0.911505 -35 TCTTCTCCCCCCTCATCCGAAGAAATATA 24 11 0 CCCTCATCCG 0.911285 -19 CATGTTATCCTGCTTTCCCTTTATATAAAT 33 41 1 TGCTTTCCCT 0.790489 -200 ********** Masking position 4 Map Score: 9.77632 Number of sites scoring better than the average of aligned sites = 727 Number in coding regions = 543 Number in noncoding regions = 184 Number of orfs with sites within 600 bp upstream = 122 Fraction of orfs with sites within 600 bp upstream = 0.0195952 Motif number 8 ATCACCGTGTAGGCCGGATAAGACGCATTTG 3 93 0 AGGCCGGATA 0.982378 -193 ATGATGTGGTAGGCCGGAGCAGGTGAGTCGC 3 122 1 AGGCCGGAGA 0.928694 -164 GAGAAAAGACAGGCTGAGTAAAAGCTGCGTA 8 112 0 AGGCTGAGTA 0.877946 -84 TCATTGTCAAAGGCCGGGTGATATCCGGTCT 10 40 1 AGGCCGGGTA 0.986258 -192 CAGGTATCTTAGGGCGGGTAATACGTTTCGT 12 24 1 AGGGCGGGTA 0.912496 -277 TGCTCAAAGCAGCCCGGGTTTTTTTGTGCAT 18 27 1 AGCCCGGGTT 0.845371 -242 TCATGTTTTTAGGCTGAATAATGCGAAAAAT 29 149 0 AGGCTGAATA 0.848189 -37 AGCCTTTAGAAGGCTGGATTTTTTA 30 5 0 AGGCTGGATT 0.937043 -150 AGCCTTCTAAAGGCTGGATCTTTTCGTTTTA 30 21 1 AGGCTGGATT 0.93704 -134 ********* * Masking position 1 Map Score: 6.60964 Number of sites scoring better than the average of aligned sites = 351 Number in coding regions = 163 Number in noncoding regions = 188 Number of orfs with sites within 600 bp upstream = 77 Fraction of orfs with sites within 600 bp upstream = 0.0123675 Motif number 9 AGCATTTCCTTTTTTCTATCCAC 2 288 0 AGCTTTCTTT 0.760724 -13 AAAAAAAGTTATCCTTTAGATTTGTAAGCTAAT 5 51 1 ATCTTTATTT 0.844543 -64 TATCTACCCTATTTTTTATATTCTGGTTAACTG 7 133 0 ATTTTTATTC 0.508765 -168 CAAAAATCAAATCCTTTCATTATGGGATACGGC 7 276 0 ATCTTTCTAT 0.682042 -25 CTTCTTTCTCATTATTTCTTTTTCATACAACGG 12 67 0 ATTTTTCTTT 0.924368 -234 TTTCTCCTGAATCGTTTCTTGTTCGTTCAAATG 13 141 0 ATCTTTCGTT 0.772802 -80 GCGGTCTACCATCGTTTCCGATTTGATTCTGGA 14 55 0 ATCTTTCATT 0.696508 -133 TGCTATATACATTTTTACCTTTTAAGAGGAGGA 16 28 1 ATTTTACTTT 0.511187 -33 AAACCCCTTTATCTTTTCATTTCCTTTATTGTC 20 18 1 ATCTTTCTTC 0.907435 -135 ACAAGGAATTATTCTTTATGTTTCTTTAGTCAG 21 44 1 ATTTTTATTT 0.725918 -112 AGTCATGGACATTTTTTCACTTTTAATTTTCAG 21 82 1 ATTTTTCTTT 0.924368 -74 GAAAAGTTTGATCATTTACTTTTTGGTCAAATT 21 114 1 ATCTTTATTT 0.844544 -42 GTTAAGATTAATTTTTTCTATTCAAGCGAAAAG 29 44 0 ATTTTTCTTC 0.826968 -142 TAAAGGCTGGATCTTTTCGTTTTATTTGATGTA 30 28 1 ATCTTTCTTT 0.961641 -127 TCTTTTGCATATCCTCTCCGTTTTTTTATAAAA 33 177 1 ATCTCTCTTT 0.760724 -64 TTTTCTTAATATTGCTTCTATTTTATAAAAAAA 33 197 0 ATTCTTCTTT 0.607838 -44 *** **** *** Masking position 1 Map Score: 7.64033 Number of sites scoring better than the average of aligned sites = 204 Number in coding regions = 164 Number in noncoding regions = 40 Number of orfs with sites within 600 bp upstream = 48 Fraction of orfs with sites within 600 bp upstream = 0.0077096 Motif number 10 GCACCATTCTGGGGCACCAATCTGGTGCGCT 2 136 0 GGGCACCAAT 0.969867 -165 ATACCCTGAAGATGCACCATTCTGGGGCACC 2 149 0 GTGCACCATT 0.98137 -152 GCAAAAACGTGATGCACGATTTATAGGGCAA 2 179 0 GTGCACGATT 0.970041 -122 AGTTGCAAAACTGGCACGATTTTTTCATATA 2 230 1 CGGCACGATT 0.840069 -71 TCCTGAACAGGTTGCACCATTTTAGTGCATT 3 256 0 GTGCACCATT 0.98137 -30 CGATGTGAATGTTGCACCAATATAGTGCTTC 4 120 0 GTGCACCAAT 0.970446 -181 TTCTATTTAGGGTTCACCATTATAAATGCAA 10 198 0 GTTCACCATT 0.854707 -34 CATTGGCACAGTGGCACGCATTCGCCCAAAA 32 55 1 GGGCACGCAT 0.840117 -33 * ********* Masking position 6 Map Score: 5.32382 Number of sites scoring better than the average of aligned sites = 132 Number in coding regions = 125 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 Motif number 11 TGTTTTAGTTGCCGTGGAAACTTTTCGCCTGTC 3 12 1 GCCTGGAAAT 0.963851 -274 ATATAGTGCTTCAATGGAAACATTAAGCACCAT 4 99 0 TCATGGAAAT 0.960999 -202 CGTATTTATTTCCTTGGAAATCTTT 10 3 0 TCCTGGAAAT 0.986472 -229 TATTCATATATCCTTGGAAATTTATGCACAAAA 18 48 0 TCCTGGAAAT 0.986472 -221 TCAGAAGAGATCACTGGAAAGATAAGCCTAAAG 18 138 1 TCATGGAAAT 0.960999 -131 AAAGAATAATTCCTTGTAAACCTCAAAAGATAT 21 28 0 TCCTGTAAAT 0.918573 -128 *** ****** * Masking position 8 Map Score: 2.21461 Number of sites scoring better than the average of aligned sites = 7 Number in coding regions = 4 Number in noncoding regions = 3 Number of orfs with sites within 600 bp upstream = 5 Fraction of orfs with sites within 600 bp upstream = 0.000803084 Motif number 12 TCAGGGTATTGCCCTATAAATCGTGCATCACGT 2 171 1 GCCCATATCG 0.732115 -130 AGCACATCACGCCGGATGCGACGCAAATGCGTC 3 70 1 GCCGATGACG 0.991269 -216 CACCGTGTAGGCCGGATAAGACGCATTTGCGTC 3 89 0 GCCGATGACG 0.991269 -197 TCGTGGTGCAGCCCTTTTGCACGATGGTGCGCA 4 148 1 GCCCTTCACG 0.92022 -153 TCAAGCGGATGCCGATTGTGACAAACGCCTATC 12 248 0 GCCGTTGACA 0.947768 -53 TCAGGAGAAAGCCATTTTAGTCGGATGTCAGCT 13 164 1 GCCATTGTCG 0.862446 -57 GATGTCAGCTGCCGCATATCACGGATGAGCATT 13 187 1 GCCGATCACG 0.975708 -34 CTTGGACATAGCCGGATATGTCATACTGTTCAT 14 107 0 GCCGATGTCA 0.921426 -81 AAAGTCATTTGCCGATATGGACGTTTCCTTGCT 19 103 1 GCCGTAGACG 0.935594 -60 **** ** **** Masking position 3 Map Score: 3.98631 Number of sites scoring better than the average of aligned sites = 810 Number in coding regions = 416 Number in noncoding regions = 394 Number of orfs with sites within 600 bp upstream = 101 Fraction of orfs with sites within 600 bp upstream = 0.0162223 Motif number 13 ATATGTCATACTGTTCATTTTCTTCATTAAAAT 14 92 0 CTTTCATTTT 0.925839 -96 GTCTTTATATTTCCTTCCTACATAT 14 173 0 CTTATATTTT 0.599658 -15 TTTTTTTGGCCTCTTCGTTTACTGCTTACAGAA 19 56 0 CTTTCGTTTT 0.974419 -107 ACCCCTTTATCTTTTCATTTCCTTTATTGTCCA 20 20 1 CTTTCATTTT 0.925839 -133 AGGAATTATTCTTTATGTTTCTTTAGTCAGTCA 21 47 1 CTTATGTTTT 0.820476 -109 TATATAATTCCTATTTGTTTACTAAGCTTTTAT 26 107 0 CTTTTGTTTT 0.925839 -46 TCCTATATTCCTAGTCGTTTAATATGAATAAAT 29 112 0 CTGTCGTTTT 0.898989 -74 AAGGCTGGATCTTTTCGTTTTATTTGATGTAAT 30 30 1 CTTTCGTTTT 0.974419 -125 TTTGCATATCCTCTCCGTTTTTTTATAAAATAG 33 180 1 CTTCCGTTTT 0.921389 -61 ** ******* * Masking position 8 Map Score: 3.13446 Number of sites scoring better than the average of aligned sites = 39 Number in coding regions = 33 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 14 TCTCCAACGTGAAGTTTGTCAGCTATCTGT 3 153 1 GAAGTTTGTC 0.832974 -133 AACTGGCGCTGACCTTCGTCTTTCTTAGTG 7 108 0 GACCTTCGTC 0.919513 -193 GATATCACCCGGCCTTTGACAATGATCGAC 10 35 0 GGCCTTTGAC 0.886948 -197 GACAGTTTGAGACGTGTGTCTCGTTTTGTC 10 113 0 GACGTGTGTC 0.921475 -119 ACACATGATAGGCGTTTGTCACAATCGGCA 12 242 1 GGCGTTTGTC 0.977633 -59 AGCCTTTGTCTCCTTTTCTT 17 71 0 AGCCTTTGTC 0.850268 -10 CTTTGTCTTGGACGTTTGTCAATGAGTTAA 29 72 0 GACGTTTGTC 0.97727 -114 AATCAAAATGTACCTTTGTCTTGGACGTTT 29 85 0 TACCTTTGTC 0.852797 -101 ********** Masking position 5 Map Score: 2.95008 Number of sites scoring better than the average of aligned sites = 169 Number in coding regions = 159 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 15 AACCTGTTCAGGAGACTGCTTT 3 274 1 GGAGACTGCT 0.974015 -12 TCTTCACTTTGGAGACAGTTTGAGACGTGT 10 126 0 GGAGACAGTT 0.884884 -106 GTGAAGATGAGAAGACTGATTTTACGGGCT 10 149 1 GAAGACTGAT 0.9245 -83 GAATTGAAAAGGGGACTGATCAA 30 142 1 GGGGACTGAT 0.966428 -13 TCACCCACAAGGAGACTGATCAC 32 4 0 GGAGACTGAT 0.984592 -84 ********** Masking position 5 Map Score: 0.542882 Number of sites scoring better than the average of aligned sites = 14 Number in coding regions = 10 Number in noncoding regions = 4 Number of orfs with sites within 600 bp upstream = 3 Fraction of orfs with sites within 600 bp upstream = 0.00048185