AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i294_ecoli_bsub_100.orf -o294_ecoli_bsub_100.ace -a/home/amcguire/alignace/lib/ORF_ecoli.txt -z/skink1/amcguire/genomes/ecoli.fna -g0.47 -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 = 0.47 maxlen = 30 weight = 0.8 exclude = 1 Purged sequences: yqfA 21 yqfA Input sequences: #1 lpxC 100 UDP-3-O-acyl N-acetylglucosamine deacetylase; lipid A biosynthesis #2 rpsB 300 30S ribosomal subunit protein S2 #3 tsf 257 protein chain elongation factor EF-Ts #4 pyrH 146 uridylate kinase #5 frr 291 ribosome releasing factor #6 yaeM 91 putative ATP-binding component of a transport system #7 yaeS 185 orf, hypothetical protein #8 cdsA 120 CDP-diglyceride synthetase #9 yaeT 29 orf, hypothetical protein #10 hlpA 121 histone-like protein, located in outer membrane or nucleoid #11 fabZ 104 (3R)-hydroxymyristol acyl carrier protein dehydratase #12 dnaE 36 DNA polymerase III, alpha subunit #13 lnt 24 apolipoprotein N-acyltransferase, copper homeostasis protein, inner membrane #14 ybeX 89 putative transport protein #15 ybeZ 113 putative ATP-binding protein in pho regulon #16 plsX 110 glycerolphosphate auxotrophy in plsB background #17 fabH 67 3-oxoacyl-[acyl-carrier-protein] synthase III; acetylCoA ACP transacylase #18 acpP 210 acyl carrier protein #19 fabF 87 3-oxoacyl-[acyl-carrier-protein] synthase II #20 accD 155 acetylCoA carboxylase, carboxytransferase component, beta subunit #21 ucpA 62 putative oxidoreductase #22 yfeT 163 orf, hypothetical protein #23 rnc 271 RNase III, ds RNA #24 yhfB 125 similar to 3-oxoacyl- acyl-carrier protein synthase #25 yjaX 164 similar to 3-oxoacyl- acyl-carrier protein synthase #26 yjaY 22 similar to 3-oxoacyl- acyl-carrier protein synthase #27 ylpC 108 ylpC #28 acpA 83 acyl carrier protein #29 rncS 139 ribonuclease III #30 rpsB 143 ribosomal protein S2 #31 tsf 101 elongation factor Ts #32 smbA 145 uridylate kinase #33 yluA 130 similar to hypothetical proteins #34 yluB 61 similar to hypothetical proteins #35 cdd 118 cytidine/deoxycytidine deaminase #36 yqfF 78 yqfF #37 yqfC 56 yqfC #38 yqfB 24 yqfB #39 yqeZ 130 yqeZ #40 yrkA 300 similar to hemolysin-like #41 yttI 300 similar to acetyl-CoA carboxylase #42 ywpB 191 similar to hydroxymyristoyl-(acyl carrier protein) dehydratase Motif number 1 GCTCTTTGTGCTAAACTGGCCCGCCGAATGTA 1 37 1 CTAAACGCCC 0.742534 -64 GTTCGAGTTGCAGAAAGGCGGCAAGCTCGAGA 3 37 1 CAGAAAGGGC 0.928571 -221 ATATAAAAGTGAAAAAGGGGGCCATATGCAGG 3 190 0 GAAAAAGGGC 0.914071 -68 TTATCAAAAAGGAGCCGCCTGAGGGC 4 5 1 CAAAAAGGCC 0.961707 -142 AAGATGGGCACAAAAAGAAGCCGCCCTCAGGC 4 27 0 CAAAAAAGCC 0.88106 -120 TCTTGAACGACAAAAACGCCGCTCAGTAGATC 6 13 1 CAAAAAGCGC 0.977951 -79 AGAATAAAAAGCAAAACGCCGCCAGCCGATCC 6 50 0 GCAAAAGCGC 0.715969 -42 GAAGCCTATACAAAAAAAAGCCGTGTAAAACC 7 120 0 CAAAAAAGCC 0.88106 -66 GATACTTCAGCAAAAGCGACCCCCA 8 4 0 CAAAAGGCCC 0.849086 -117 CCGGCGGCAACAGAAACAACGCCGCGATGACG 8 67 0 CAGAAAACGC 0.890118 -54 TCACGCCACAGGAAAAAGGCGCAAGCATTGCA 15 69 0 GGAAAAGCGC 0.715969 -45 TATACACTACGAAAACCATCGCGAAAGCGAGT 18 168 1 GAAAACACGC 0.653287 -43 CAGGTTCAGACAGAAAGGTCCCTA 20 142 1 CAGAAAGCCC 0.970462 -14 CTATGAAAAAGAAAAAGGAGGCTGAAAA 24 7 0 GAAAAAGGGC 0.914071 -119 CATTTTTGTACAGAACTGCCGCCTGCAGCACC 30 79 0 CAGAACGCGC 0.886453 -65 CAGTTCTGTACAAAAATGACCTAAGCGGAGGA 30 93 1 CAAAAAGCCT 0.66782 -51 CCTATACTGCCTGAAAAGAGCCGACTTAGCCG 32 27 0 CTGAAAGGCC 0.748347 -119 ATAGATAATAGTGAAAAGACCCTCTCATGTTT 33 27 1 GTGAAAGCCC 0.760954 -104 ACAGTATTAACAAAAAAACCCCCTGTAAACAT 33 53 0 CAAAAAACCC 0.939939 -78 AAATGGGCGTGAAAAAAAGCGCGCGATTATGT 35 47 1 GAAAAAACGC 0.868915 -72 TAAGCAATCATAAAAATGACCCGATAACGGGC 36 28 0 TAAAAAGCCC 0.750135 -51 ACAAAAAGAACCCCCTTTCATCT 37 44 0 CAAAAAACCC 0.939939 -13 ****** * *** Masking position 5 Map Score: 20.8576 Number of sites scoring better than the average of aligned sites = 860 Number in coding regions = 693 Number in noncoding regions = 167 Number of orfs with sites within 600 bp upstream = 160 Fraction of orfs with sites within 600 bp upstream = 0.0256987 Motif number 2 GAATTCTCGAGCTTGCCGCCTTTCTGCAACT 3 42 0 GCTTGCCGCT 0.933691 -216 GGGGCCATATGCAGGCCCCCTAACCAAACGT 3 174 0 GCAGGCCCCT 0.941071 -84 GAAGCCGCCCTCAGGCGGCTCCTTTTTGATA 4 12 0 TCAGGCGGCC 0.766212 -135 CGTTATTGTTGCAGGCAGTTTGGTCACGGCC 5 80 1 GCAGGCAGTT 0.953707 -212 GTTGCTGCGCGCTGGCCGTGACCAAACTGCC 5 93 0 GCTGGCCGTA 0.804841 -199 TTGCGGATCGGCTGGCGGCGTTTTGCTTTTT 6 46 1 GCTGGCGGCT 0.990187 -46 CCATTGTAACGCTGGTGGTCTGC 8 108 1 GCTGGTGGTT 0.706126 -13 TACGATTGCGGCAGGCCGTGTTATTATTGTC 11 55 1 GCAGGCCGTT 0.975886 -50 TTATTGCAATGCTTGCGCCTTTTTCCTGTGG 15 65 1 GCTTGCGCCT 0.736035 -49 CTGCGAGTTCGCTGGCAGCGTCCTG 17 5 0 GCTGGCAGCT 0.977306 -63 AAGATAAAACTCAGGCGGTCGAACGACCGCC 19 24 0 TCAGGCGGTG 0.717373 -64 ACTCTCCTGGGCTGGCAGCATAAATTCCGCT 22 138 0 GCTGGCAGCT 0.977306 -26 AGTTATTACAGCATGCCGCTTTTACGCGCGC 29 63 1 GCATGCCGCT 0.941201 -77 AGAGGGTGCTGCAGGCGGCAGTTCTGTACAA 30 75 1 GCAGGCGGCG 0.973148 -69 TCGGCTCTTTTCAGGCAGTATAGGGGACACA 32 35 1 TCAGGCAGTT 0.774196 -111 ********* * Masking position 5 Map Score: 15.3294 Number of sites scoring better than the average of aligned sites = 2353 Number in coding regions = 2265 Number in noncoding regions = 88 Number of orfs with sites within 600 bp upstream = 88 Fraction of orfs with sites within 600 bp upstream = 0.0141343 Motif number 3 TGCTAAACTGGCCCGCCGAATGTATAGTAC 1 45 1 GCCCGCCGAA 0.930603 -56 GATGTGATCTGCCCGGCATTAAACCGCACA 3 223 0 GCCCGGCATT 0.950889 -35 CAGACTTACGCCCCCGCGATACTTACGCGG 5 41 0 CCCCCGCGAT 0.909528 -251 GCAAAACGCCGCCAGCCGATCCGCAAGGAT 6 42 0 GCCAGCCGAT 0.879977 -50 TCTTTGCGTGGCCCGGCGATCTTATATTGA 10 61 0 GCCCGGCGAT 0.991202 -61 CCAGTCAAATGCCTGGCAAA 14 1 0 GCCTGGCAAA 0.674657 -89 TGGCAGACGTCCCCGCCGTTGGTGATTAAC 14 28 1 CCCCGCCGTT 0.962742 -62 TTCTCAGGCCTGCCGTTCCGGTGGGCC 15 8 1 GCCTGCCGTT 0.962481 -106 ACACGTCTAACCCTGGCGTTAGATGTC 16 94 1 CCCTGGCGTT 0.95254 -17 TCGAACGACCGCCTGGAGATGTTCAC 19 7 0 GCCTGGAGAT 0.770588 -81 ATTCCTTTAAGCCTGTCAATTCGGGATATA 22 62 0 GCCTGTCAAT 0.666583 -102 TAACGACATCCCCCGTCGTTGTGTATAGAA 23 83 1 CCCCGTCGTT 0.897238 -189 AAGGGCTAAAGCCCCGCGTTTCGGCGGGAC 29 24 0 GCCCCGCGTT 0.950083 -116 ********** Masking position 3 Map Score: 12.351 Number of sites scoring better than the average of aligned sites = 1548 Number in coding regions = 1469 Number in noncoding regions = 79 Number of orfs with sites within 600 bp upstream = 74 Fraction of orfs with sites within 600 bp upstream = 0.0118856 Motif number 4 TGGGATACGTGGAGGCATAACCCCAACTTTT 2 263 1 GGAGGATAAC 0.921345 -38 TGTCCTCCAGGGAGGGAAAAAATGATTCTAG 19 64 0 GGAGGAAAAA 0.978579 -24 TTCCCTCCCTGGAGGACAAAC 19 77 1 GGAGGCAAAC 0.839159 -11 ATGGTCTGTTGGGGGCAAAAATGGCATTATG 20 82 1 GGGGGAAAAA 0.914338 -74 TGACCTAAGCGGAGGAAAAAAACCATTATAT 30 109 1 GGAGGAAAAA 0.978579 -35 CATTATATTAGGAGGAAATAAC 30 132 1 GGAGGAATAA 0.935218 -12 AAACATATAAGGAGGAATACAA 31 90 1 GGAGGATACA 0.951846 -12 ATAAAAGGAAGGAGGGATACACCGCCC 39 114 1 GGAGGATACA 0.951846 -17 TTCACAAAAGGGAGGTAATCATTTGTTAAAG 41 205 1 GGAGGAATCA 0.922526 -96 ***** ***** Masking position 5 Map Score: 7.12332 Number of sites scoring better than the average of aligned sites = 45 Number in coding regions = 37 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 5 GAATTGACTGGAATTTGGGTTTCGAG 1 1 1 GTGATGGATT 0.950735 -100 AGTACACTTCGGTTGGATAGGTAATTTGGCGAGATA 1 70 1 GTGAAGGTTT 0.923203 -31 GGTGCAAATGGGATGGTAAGGAGTTTATT 10 103 1 GTGTAGGATT 0.966177 -19 TCACCGGCCTATAAGGAAATTATTCACGCCA 15 93 0 GCATAGGATT 0.733785 -21 GCGTGATGAAGCTTAGTGAGGATTTTCCCCAGGCAA 16 21 1 GTGTAGGATT 0.966177 -90 TATCGTCGCCGCCCGGTTTGGTCTTTCCCCAGTTGC 16 53 0 GCGTTGGTTT 0.638758 -58 GCGAAAGCGAGTTTTGATAGGAAATTTAAGAGT 18 188 1 GTGAAGGATT 0.979777 -23 AAAAAGAGAAGTGTAGATAGGAATCTATGAAAAAGA 24 27 0 GTGAAGGACT 0.901225 -99 TGGGCTTGATGTTTCAAGAGGAGGTTCTT 36 60 1 GTAAAGGATT 0.881854 -19 TCATGTGTATGATTTGAAAGGAGGTTCTAACACT 37 9 0 GTGAAGGATT 0.979777 -48 CTTTTCAAATGTACAGATTGGATCTTTGATGATTGC 42 129 1 GCGATGGATT 0.923588 -63 * * ** **** ** Masking position 16 Map Score: 6.96259 Number of sites scoring better than the average of aligned sites = 41 Number in coding regions = 25 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911 Motif number 6 CGAATGTATAGTACACTTCGGTTGGATAGGTA 1 61 1 GTACTTCGGT 0.694026 -40 ATCTTCGCTCGCTCATCCCGGTCACTTACTGA 3 86 0 GCTCCCCGGT 0.95559 -172 AACCAAACGTGTACTACCTGGTCTATAAGGGC 3 152 0 GTACCCTGGT 0.839732 -106 ACGTACTTTTGTACGCTCCGGTTGCTGCGCGC 5 112 0 GTACTCCGGT 0.95129 -180 AGGATGGCGAGCACTGCCCGGGGCCAAAATGG 5 145 1 GCACCCCGGG 0.907208 -147 GCAAAGAACTGCACCCTCCGGTGCAAATGGGA 10 84 1 GCACTCCGGT 0.98219 -38 CTTCAGATTCCGGTTTACTTAATC 12 23 0 TCAGTCCGGT 0.936332 -14 CAAGGTATCGTCGCCGCCCGGTTTGGTCTTTC 16 62 0 TCGCCCCGGT 0.856323 -49 GTACGCTCAGTCACTTTTCGGTTATATACCGT 17 46 0 TCACTTCGGT 0.751524 -22 GACCTTTCTGTCTGAACCTGGTTCGATGCCAG 20 130 0 TCTGCCTGGT 0.558834 -26 TTTAAGGTTGGCACCTCCAGGTTGCCACGGCA 23 126 1 GCACCCAGGT 0.911703 -146 ACACTAGATATTAGTATCTGGTACTAAAAAGA 24 76 0 TTAGTCTGGT 0.534819 -50 TGATCAATTATTAGTATCAGGTACTAATTCTA 25 96 0 TTAGTCAGGT 0.445172 -69 TTTTACGCGCGCTGTATCCGGTTTAGTCAGAG 29 82 1 GCTGTCCGGT 0.90908 -58 **** ****** Masking position 10 Map Score: 5.28842 Number of sites scoring better than the average of aligned sites = 983 Number in coding regions = 902 Number in noncoding regions = 81 Number of orfs with sites within 600 bp upstream = 78 Fraction of orfs with sites within 600 bp upstream = 0.0125281 Motif number 7 TCTGATGCTGTACACAGCGCCAACAATTAT 2 84 1 TACACAGCGC 0.910759 -217 ATTTGTGGTATAAAGCGCGCCGGACTTCCG 2 129 1 TAAAGCGCGC 0.977157 -172 TGCCCGGCATTAAACCGCACAGATATAAAA 3 214 0 TAAACCGCAC 0.855428 -44 TTTGGTCACGGCCAGCGCGCAGCAACCGGA 5 98 1 GCCAGCGCGC 0.926684 -194 CTAAACCGGATACAGCGCGCGTAAAAGCGG 29 78 0 TACAGCGCGC 0.988241 -62 GCACATCAGGTTCACCGCGCTTCTCTGACT 29 106 0 TTCACCGCGC 0.955777 -34 GGGCGTGAAAAAAAGCGCGCGATTATGTAA 35 51 1 AAAAGCGCGC 0.884605 -68 GAAGGAGGGATACACCGCCC 39 121 1 TACACCGCCC 0.945145 -10 AATCTCTTTTTCAACCGCGCTAAAATGTAA 42 86 0 TCAACCGCGC 0.967747 -106 ********** Masking position 4 Map Score: 6.83226 Number of sites scoring better than the average of aligned sites = 504 Number in coding regions = 482 Number in noncoding regions = 22 Number of orfs with sites within 600 bp upstream = 26 Fraction of orfs with sites within 600 bp upstream = 0.00417604 Motif number 8 ATTAGGCTATTTTATTTGCCATTTTGGCCCCG 5 163 0 TTTTTTGCAT 0.916238 -129 TTTACACGGCTTTTTTTTGTATAGGCTTCAGT 7 123 1 TTTTTTTTAT 0.534954 -63 GTTCGACCACTTTTTTATCCAAAGTTTCGGGC 20 25 1 TTTTTATCAA 0.421481 -131 CAGCCTCCTTTTTCTTTTTCATAGATTCCTAT 24 15 1 TTTTTTTCAT 0.945843 -111 TCTATCCTATTTTTTTTCACATGGCAATATAT 25 68 0 TTTTTTCCAT 0.882485 -97 TTTACAAACCTTTTTTTCTCTTGCATAATAGA 32 94 1 TTTTTTCCTT 0.627219 -52 AATTCTTACATTTATTTTACATTTTTAGAAAT 35 19 1 TTTTTTTCAT 0.945843 -100 GCTATCACTTTATATTTTACATAATCGCGCGC 35 65 0 TATTTTTCAT 0.650173 -54 AAGATGTCCTTTTCTTTGCCAT 39 1 0 TTTTTTGCAT 0.916238 -130 AGAGATGTCTTTTTTTATACATAAAAAAATGA 39 39 1 TTTTTATCAT 0.781041 -92 CAGGTGTGTTTTTATTTTGCTTTCTTTTTTAA 40 89 1 TTTTTTTCTT 0.79646 -212 ACTATTGTACTTTTTTTGTCAAACGCTGTCAT 41 117 0 TTTTTTGCAA 0.690798 -184 AAGCATACTTTTTCTTTTTCGTGAATATATCC 41 235 0 TTTTTTTCGT 0.766843 -66 *** **** *** Masking position 6 Map Score: 3.25827 Number of sites scoring better than the average of aligned sites = 129 Number in coding regions = 87 Number in noncoding regions = 42 Number of orfs with sites within 600 bp upstream = 56 Fraction of orfs with sites within 600 bp upstream = 0.00899454 Motif number 9 TTTTCAGCCTCCTTTTTCTTTTTCATAG 24 8 1 CCTCCTTTTC 0.848768 -118 TTGTAAAAAACCTTCTTTTTAGTACCAGATA 24 63 1 CCTTCTTTTA 0.911119 -63 ACGCCTCCTTTCCATATACCATAC 25 4 1 CCTCCTTTCA 0.962997 -161 AGCAATTCACCTCCCCTCAAGTATTATAGT 28 64 0 CCTCCCCTCA 0.929543 -20 CCTTTTATCACCTTTTTTCAAGAAAAATGTG 31 39 1 CCTTTTTTCA 0.492465 -63 AAGAACCTCCTCTTGAAACATCAAGC 36 63 0 CCTCCTCTTA 0.94476 -16 AGTGTTAGAACCTCCTTTCAAATCATACACA 37 11 1 CCTCCTTTCA 0.962997 -46 ATAATAAGTGCCTTCTCTTCATACGTAACAA 39 85 0 CCTTCTCTTA 0.8795 -46 GTGTATCCCTCCTTCCTTTTATAATAAGTGC 39 105 0 CCTTCCTTTA 0.8795 -26 CAAATGATTACCTCCCTTTTGTGAAGGGTTC 41 199 0 CCTCCCTTTG 0.79984 -102 ********* * Masking position 8 Map Score: 4.7433 Number of sites scoring better than the average of aligned sites = 43 Number in coding regions = 27 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 10 TTGCGGATCGGCTGGCGGCGTTTTGCTTTT 6 46 1 GCTGGCGGCG 0.963807 -46 ACAACGCCGCGATGACGACGGGTATTAACA 8 54 0 GATGACGACG 0.932744 -67 AATCACCAACGGCGGGGACGTCTGCCAGTC 14 25 0 GGCGGGGACG 0.838708 -65 GTTGGTGATTAACGACGGCGTTTTGATTAA 14 45 1 AACGACGGCG 0.736087 -45 GACCAAACCGGGCGGCGACGATACCTTGAC 16 66 1 GGCGGCGACG 0.978025 -45 CTGCGAGTTCGCTGGCAGCGTCCTG 17 6 0 GCTGGCAGCG 0.933337 -62 TCGCCATAACGGCGACAACGTGAACGAAGA 23 17 0 GGCGACAACG 0.961587 -255 TCGCCGTTATGGCGACAACGTGAATTATTT 23 32 1 GGCGACAACG 0.961587 -240 AACCTTTTTGGGTGACGGAGGAATCTC 33 114 1 GGTGACGGAG 0.841698 -17 AAACGACAAGGTTGACAGCGCATTCAAAAA 41 18 0 GTTGACAGCG 0.845887 -283 TCGAATTGAGGATGACAGCGTTTGACAAAA 41 106 1 GATGACAGCG 0.932744 -195 ********** Masking position 4 Map Score: 6.61444 Number of sites scoring better than the average of aligned sites = 2082 Number in coding regions = 2016 Number in noncoding regions = 66 Number of orfs with sites within 600 bp upstream = 68 Fraction of orfs with sites within 600 bp upstream = 0.0109219 Motif number 11 CTGCAACAATAACGCCTTATAACCAGACTTACG 5 61 0 ACGCCTAAAC 0.959134 -231 TTGCTGAAGTATCGCCTGATATCTGCTTTTGTG 8 23 1 ACGCCTAATC 0.975494 -98 AGTTAGGAAGAACGCATAATAACG 9 16 1 ACGCATAAAC 0.783352 -14 TCTTATATTGATCGCCTAAAGTCATCGCTACAC 10 39 0 ACGCCTAGTC 0.882303 -83 TTGAGGCCTTACCCCCCAATAACGCAAATCATT 18 77 0 ACCCCCAAAC 0.79719 -134 GATAAGAGGGACTGCCTTTTATCACCTTTTTTC 31 25 1 ATGCCTTATC 0.788457 -77 TAACAAAAAAACCCCCTGTAAACATGAGAGGGT 33 45 0 ACCCCTTAAC 0.915705 -86 GAATGACCCGATCGCCCGTTATCGGGTCATTTT 36 15 1 ACGCCCTATC 0.953139 -64 ACAAAAAGAACCCCCTTTCATCTCATGTGTAT 37 35 0 ACCCCTTATC 0.948519 -22 TAAGCCTTAAAACGCCACTAATCGTTAGTTGAA 40 118 1 ACGCCATATC 0.881754 -183 GGTTCTCTTCACCGCATGTCATCAAACAGATAG 41 171 0 ACGCATTATC 0.879336 -130 * ***** * *** Masking position 1 Map Score: 4.68813 Number of sites scoring better than the average of aligned sites = 365 Number in coding regions = 334 Number in noncoding regions = 31 Number of orfs with sites within 600 bp upstream = 32 Fraction of orfs with sites within 600 bp upstream = 0.00513974 Motif number 12 AGATTGTCGCTTCCGTCCAGTCTGTGTATACGA 2 166 0 TTCCGTGTCT 0.963494 -135 TCGGCACATATTCCGGGGTGCCCTTTGGGGTCG 2 224 1 TTCCGGGCCC 0.960355 -77 TGATGTAAGCTCCCGGGAATTCTCGAGCTTGCC 3 56 0 TCCCGGTTCT 0.794196 -202 TCGCCAAACTTTACGGCCTGTCTCATTCTTACG 11 26 1 TTACGGGTCT 0.887573 -79 AGGCCTGCCGTTCCGGTGGGCCTTGTTTTTTCT 15 16 1 TTCCGGGCCT 0.990447 -98 TGCAACTAAATCCCGGCAGGTCTTACCACGATT 18 120 0 TCCCGGGTCT 0.975225 -91 GACTCAATGATTCCTTTAAGCCTGTCAATTCGG 22 68 0 TTCCTTGCCT 0.769115 -96 AAAAGTATGCTTCCGTACCGTCTGATCAAGCGA 41 255 1 TTCCGTGTCT 0.963492 -46 AAGCACGATGTTCCGGAAGGCATT 41 287 1 TTCCGGGCAT 0.910427 -14 ****** **** Masking position 1 Map Score: 3.42432 Number of sites scoring better than the average of aligned sites = 306 Number in coding regions = 285 Number in noncoding regions = 21 Number of orfs with sites within 600 bp upstream = 25 Fraction of orfs with sites within 600 bp upstream = 0.00401542 Motif number 13 CGGAATATGTGCCGATACGTGTGTGTTGTT 2 209 0 GCCGATACGT 0.950126 -92 ATTTCGCGCCGCAGATGCGTTATCTTCGCT 3 109 0 GCAGATGCGT 0.908791 -149 AACGCCGCCAGCCGATCCGCAAGGATCTAC 6 38 0 GCCGATCCGC 0.902201 -54 GCTTCATCACGCAGATGCGTGA 16 3 0 GCAGATGCGT 0.908791 -108 TAAAAAAGTGGTCGAACCGCGGAGTTACTT 20 12 0 GTCGAACCGC 0.833507 -144 GAATTAGTGAGCTGATCCGCAGCAATATT 21 44 1 GCTGATCCGC 0.862056 -19 TAAAAGTCCCGCCGAAACGCGGGGCTTTAG 29 19 1 GCCGAAACGC 0.944767 -121 ********** Masking position 5 Map Score: 2.2401 Number of sites scoring better than the average of aligned sites = 452 Number in coding regions = 435 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 14 TGTGTGCACCTCACCTTTTT 26 1 0 TCACCTTTTT 0.965713 -22 GTCCCTCTTATCACCTTTTGAATAGG 31 7 0 TCACCTTTTG 0.932283 -95 CTGCCTTTTATCACCTTTTTTCAAGAAAAA 31 36 1 TCACCTTTTT 0.965713 -66 TATGTATATTACACATTTTTCTTGAAAAAA 31 51 0 ACACATTTTT 0.818147 -51 AGTATAGGGGACACATTTTGTGTTCCCTAT 32 51 1 ACACATTTTG 0.687536 -95 CTATATTTACAAACCTTTTTTTCTCTTGCA 32 89 1 AAACCTTTTT 0.818147 -57 GCAGGGAATGTAACCTTTTTGGGTGACGGA 33 103 1 TAACCTTTTT 0.847234 -28 ATGTAAATAATCATCTTTTTCCGTATGGAG 40 167 0 TCATCTTTTT 0.758757 -134 CCTCAATTCGACAACTTTTTATTCGATGAC 41 87 0 ACAACTTTTT 0.71846 -214 ********** Masking position 6 Map Score: 2.60516 Number of sites scoring better than the average of aligned sites = 136 Number in coding regions = 101 Number in noncoding regions = 35 Number of orfs with sites within 600 bp upstream = 39 Fraction of orfs with sites within 600 bp upstream = 0.00626405 Motif number 15 CATTTCGTATACACAGACTGGACGGAAGCGAC 2 162 1 AACAGACTGA 0.952815 -139 CCAGACAGTCACACACAGTGGAAGTGTGCTAA 5 237 0 AACACAGTGA 0.884108 -55 AACTTGTCTCAGTCAGACCAGACAGTCACACA 5 254 0 ATCAGACCGA 0.933038 -38 GAAACATCCAGAGTTGAGACAGAATAA 6 75 0 ACCAGAGTGA 0.819438 -17 TCAGCACACGAAACAGACCTGATATACATGGT 23 220 0 AACAGACCGA 0.969724 -52 GGTATTATTGAAACACACCAGAAAATTCAGGT 40 62 1 AACACACCGA 0.95166 -239 AGCAAAATAAAAACACACCTGAATTTTCTGGT 40 78 0 AACACACCGA 0.95166 -223 TATTTACATCATTCAGAGTTGATTTTAGGTTC 40 188 1 ATCAGAGTGA 0.843736 -113 * ******* ** Masking position 7 Map Score: 2.02957 Number of sites scoring better than the average of aligned sites = 51 Number in coding regions = 43 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555