AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00310_bsub_reg_100.orf -o00310_bsub_100.ace -a/home/amcguire/alignace/lib/ORF_bsub.txt -z/skink1/amcguire/genomes/bsub.fna -g0.44 -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 = 0.44 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 ybxI 172 alternate gene name: ybdS; similar to beta-lactamase #2 ycbC 226 similar to 5-dehydro-4-deoxyglucarate dehydratase #3 ycbD 29 similar to aldehyde dehydrogenase #4 yckG 231 similar to D-arabino 3-hexulose 6-phosphate formaldehyde lyase #5 yhfI 151 similar to hypothetical proteins #6 yjmC 104 similar to malate dehydrogenase #7 cad 184 lysine decarboxylase #8 ylxY 117 alternate gene name: ymxI; similar to deacetylase #9 ymxG 39 similar to processing protease #10 pksF 300 pksF #11 penP 225 beta-lactamase precursor #12 odhB 29 2-oxoglutarate dehydrogenase complex (dihydrolipoamide transsuccinylase, E2 subunit) #13 odhA 227 2-oxoglutarate dehydrogenase (E1 subunit) #14 bfmBB 22 branched-chain alpha-keto acid dehydrogenase E2 subunit (lipoamide acyltransferase) #15 bfmBAA 73 branched-chain alpha-keto acid dehydrogenase E1 (2-oxoisovalerate dehydrogenase alpha subunit) #16 yqiS 124 similar to phosphate butyryltransferase #17 mmgA 137 acetyl-CoA acetyltransferase #18 yqhS 86 similar to 3-dehydroquinate dehydratase #19 yqhR 226 yqhR #20 bltD 168 spermine/spermidine acetyltransferase #21 yteI 185 similar to protease IV #22 yugK 103 similar to NADH-dependent butanol dehydrogenase #23 yugJ 229 similar to NADH-dependent butanol dehydrogenase #24 dhbE 28 2,3-dihydroxybenzoate-AMP ligase (enterobactin synthetase component E) #25 dhbC 25 isochorismate synthase #26 dhbA 193 2,3-dihydro-2,3-dihydroxybenzoate dehydrogenase #27 glyA 206 serine hydroxymethyltransferase #28 ywdH 167 alternate gene name: ipa-58r; similar to aldehyde dehydrogenase #29 dltA 300 D-alanyl-D-alanine carrier protein ligase (Dcl) #30 aldX 142 aldehyde dehydrogenase Motif number 1 AATAGAGGGTAAAAAGGAAGGCAGGGTAAGCGG 1 7 0 AAAAAGGCGT 0.941857 -166 AGGTAGTTAATCAAAACGAAGGGGAGAACAAA 1 151 1 TAAGAAGGGA 0.936541 -22 TTCTGATATTTTATAAAAAAGCGGTAAATCACTGTCC 2 62 0 TAAAAAGCGA 0.947376 -165 AAAAGCGCTTACAGATAGAGGCCGTATACACAAATAA 2 185 1 AAAGAGGCGT 0.92997 -42 CCAGAAAAAACACGAAAGGGGCAATGGGC 3 8 1 AAAAAAGGGA 0.942988 -22 TACAATGAAATCACTACAAAGGGGAAAGAGGGA 5 7 0 TATAAAGGGA 0.86119 -145 CCCAAAAAACTGAAAAGGAAGGAGGCACTTGC 6 83 1 TAAGAAGGGA 0.936541 -22 TGCATAGGTATGATTACAAAGGTGGGAAAACAA 7 162 1 TATAAAGGGA 0.86119 -23 ATGAAAACATAAAAGGAGCCTGGGAGACCCG 8 5 1 AAAAAAGGGT 0.942988 -113 AAAAGCTTCAAAATAAAGAAGCCGGGTCTCCCAGGCT 8 27 0 AAAGAAGCGT 0.931316 -91 TTGAAGCTTTTCAAAAGCAGGCGGGTTCTACCTTGTC 8 53 1 TAACAGGCGT 0.865098 -65 TTCCTCCTATTCAAAGACAAGCTGCCTTCATCTG 9 8 0 TAACAAGCGT 0.867511 -32 AGAATAGAATCAACAAAAAAGCTGACAATGACTGTCA 11 62 0 CAAAAAGCGA 0.739546 -164 CTCGCAAAAACTAAGGGGGAAATGAAAAA 12 6 1 AAAAAGGGGA 0.941857 -24 TGGAACTTGCATAATAAAAGGCGGAGTCGAAACAAGA 16 85 1 AATAAGGCGT 0.848083 -40 GGCGGAGTCGAAACAAGAAAGGTGGTAACAG 16 104 1 AAAAAAGGGA 0.942988 -21 TGAATAGTTGTTAGAAGGAGGCTGTTTGACGCAGCCT 17 15 1 TAAGAGGCGT 0.935291 -123 TGAATGAATGAAAAAAGAAGGCTGCGTCAAACAGCCT 17 33 0 AAAAAGGCGT 0.941857 -105 CTAAACCTCTAGATTGACAGGCTGAAAAAATTGCCAT 19 80 1 AATCAGGCGA 0.670015 -147 GATACCGGGATAAGAAAAAAGGAGAATGTAGT 20 147 1 TAAAAAGGGT 0.947376 -22 AACTTAAATATGACAGCAAAGGGGAAATGGGAT 21 7 0 TAAAAAGGGA 0.947376 -179 GACAAAAAAGAAAAAGGGAAGCAGCCAAACGGCTATT 22 21 0 AAAGAAGCGA 0.931316 -83 CTGAATTTAAAGGAGGTTCATGAGA 25 2 1 TATAAAGGGT 0.86119 -24 CGCCGATATATTAATTTGAGGGAGATTAGGGAAAAAA 29 36 1 TATGAGGGGT 0.832806 -265 * * * ***** * * Masking position 9 Map Score: 27.2204 Number of sites scoring better than the average of aligned sites = 915 Number in coding regions = 694 Number in noncoding regions = 221 Number of orfs with sites within 600 bp upstream = 244 Fraction of orfs with sites within 600 bp upstream = 0.0391905 Motif number 2 TTACCCTGCCTTCCTTTTTACCCTCTATTTTCACGTTATCT 1 15 1 TTTTTTTCTT 0.633122 -158 CTGACCAGGCTGTTTTTTTGCTGCGCAGAATCCCGGCCGGA 2 24 1 TGTTTTTGAT 0.658452 -203 CATCACTTACTTACTTTTTTGCAGACTCTTTTTTCATTATA 4 55 1 TTTTTTTATT 0.931543 -177 AAAACAGTTATTGATTTTTGTAATCTGTTATATTACAATGA 5 36 0 TTTTTTTAAT 0.825162 -116 GATTATTTTAATGATTTTTATAGGTATATTTTCATAATATT 10 24 0 ATTTTTTGTT 0.842035 -277 AGTCATTGTCAGCTTTTTTGTTGATTCTATTCTTATGCCCT 11 66 1 AGTTTTTGTT 0.767483 -160 CCTTAATCCTATGCTTTTTGGCGTTTGTTTTTTCGAATGAT 13 12 1 ATTTTTTGTT 0.842035 -216 GATTAAATTTTTTGTTTTTTATAAAGGTTTTTTACTATTTT 13 50 1 TTTTTTTATT 0.931543 -178 TATCGTTGGAAGCGTTTTTATTACATAATTTTGACACAGCG 13 133 1 AGTTTTTATT 0.833435 -95 TTATTGACATTTCATTTTTTGGGCACACTTTAACTGGAGGT 19 193 1 TTTTTTTGTT 0.899765 -34 GCTTCCCTTTTTCTTTTTTGTCAACTTATGTTACAATGGAA 22 36 1 TTTTTTTAGT 0.760529 -68 AATGGAAAATCTGTTTTTTACCAGCATCATTTGGAGGTTTT 22 70 1 CTTTTTTATT 0.851927 -34 TCTCCTCCTTAGATTTTTTATTATGCAGAATGTCCTCACCA 23 195 0 AGTTTTTAAT 0.634427 -35 TTTGGATATGATTATTTTTATAATTGATAATGATAATCATT 26 77 1 ATTTTTTAAT 0.737018 -117 GTTATTAATATTCGTTTTTACCAATAAAAATTTAGATTTTT 27 84 1 TTTTTTTAAT 0.824716 -123 ATAAAAATTTAGATTTTTTAAAAATAATCTTTTACATCGGC 27 107 1 AGTTTTTATT 0.833399 -100 TATCCTGTTCTTTGTTTTTACCATCACTATTGTACATGGTT 27 154 0 TTTTTTTATT 0.931543 -53 AAGACAACATTTATTTTTTTGGAGGGTGCTTC 28 2 0 TTTTTTTATT 0.931543 -166 TATGAGTTTGTTATTTTTTCTGACAAACCTTGCGCGATTGA 28 78 1 TTTTTTTATT 0.931533 -90 TCCGTTTCTCCTTTTTGTAAGGTATGGTGATTTATTAT 28 140 0 CTTTTTTAGT 0.573156 -28 CACTTGACAGCGGGTTTTTCATACAGCTGTTTCATTAATTG 29 150 0 CGTTTTTATT 0.780828 -151 TACTGCTTGTTTTGTTTTTTATGTATGGTTTTCACACCGCG 29 220 1 TTTTTTTGTT 0.899765 -81 ** ***** * ** Masking position 9 Map Score: 18.0417 Number of sites scoring better than the average of aligned sites = 607 Number in coding regions = 472 Number in noncoding regions = 135 Number of orfs with sites within 600 bp upstream = 148 Fraction of orfs with sites within 600 bp upstream = 0.0237713 Motif number 3 TCTCTTTCGTTTGTTCTTCCTTTAAAAAAT 1 117 0 TTGTTCTTCC 0.889154 -56 TTTGTTCTCCCCTTCGTTTTG 1 162 0 TTGTTCTCCC 0.950153 -11 AGAAATCTGATTGTCTCTCCTCACAGTATC 4 118 1 TTGTCTCTCC 0.82902 -114 TCAAAAAAATTGGTCCTCCTTCAATATACC 5 115 0 TGGTCCTCCT 0.81583 -37 AATGTCCTCCTATCTTTTCAA 5 141 0 ATGTCCTCCT 0.859681 -11 TTGTTTTCCCACCTTTGTAA 7 175 0 TTGTTTTCCC 0.858914 -10 GGGTTCTACCTTGTCCTTCTCCTTCATAAT 8 75 1 TTGTCCTTCT 0.932155 -43 GTTCTGTCCCCCCCTCACCTCAC 8 105 0 CTGTCCCCCC 0.850519 -13 ATTTGTTCCTCCTATTCAAAGA 9 28 0 TTGTTCCTCC 0.82902 -12 TCTTATGCCCTTGTTCTCCCAACTTATAAA 11 96 1 TTGTTCTCCC 0.950153 -130 TTTTTCTCCTCCTTTTTCCTAAA 21 173 0 TTCTCCTCCT 0.89522 -13 GACATCTCCTCCTTAGATTTTTT 23 217 0 ATCTCCTCCT 0.615868 -13 AAAATAAATGTTGTCTTCCTGCATTTTATC 28 26 1 TTGTCTTCCT 0.912491 -142 AGTTATTCTCTCTCCAATTAGAAAT 29 286 0 TTCTCTCTCC 0.559245 -15 TGGTTCACCGTTGTCTTTCTTACAGAAAAG 30 67 1 TTGTCTTTCT 0.814409 -76 ********** Masking position 4 Map Score: 11.8562 Number of sites scoring better than the average of aligned sites = 492 Number in coding regions = 360 Number in noncoding regions = 132 Number of orfs with sites within 600 bp upstream = 123 Fraction of orfs with sites within 600 bp upstream = 0.0197559 Motif number 4 CCTTTTTACCCTCTATTTTCACGTTATCTT 1 27 1 CTCTATTTTC 0.849562 -146 TTTTGATTAACTACCTTTTCTCTCTTTCGT 1 137 0 CTACCTTTTC 0.979216 -36 AAGTCAATATCTTTATTTTCTGATATTTTA 2 86 0 CTTTATTTTC 0.732212 -141 TTTTTGCAGACTCTTTTTTCATTATACTCA 4 70 1 CTCTTTTTTC 0.75166 -162 TGTTGATCCACTCCCTTTTCGAATTATTGT 4 212 0 CTCCCTTTTC 0.977808 -20 AATGTCCTCCTATCTTTTCAAAAAAATTG 5 133 0 CTATCTTTTC 0.949295 -19 CAAGTGCCTCCTTCCTTTTCAGTTTTTTGG 6 84 0 CTTCCTTTTC 0.955224 -21 CAGGCGGGTTCTACCTTGTCCTTCTCCTTC 8 70 1 CTACCTTGTC 0.881389 -48 ATTTTTATAGGTATATTTTCATAATATTCA 10 22 0 GTATATTTTC 0.632548 -279 TTGCCATAGCCTTGCTTTTCCTACATGCAT 19 110 1 CTTGCTTTTC 0.75608 -117 ATCAAATTAAGTACCTTTTCTTATTGTGCC 20 62 0 GTACCTTTTC 0.930705 -107 ACTACATTCTCCTTTTTTCTT 20 158 0 CTACATTCTC 0.705604 -11 TTTTTCTCCTCCTTTTTCCTAAACTCTC 21 168 0 CTCCTTTTTC 0.883947 -18 TTATAAGGTGGTACCTTTTCTGTAAGAAAG 30 81 0 GTACCTTTTC 0.930705 -62 ********** Masking position 6 Map Score: 11.649 Number of sites scoring better than the average of aligned sites = 530 Number in coding regions = 419 Number in noncoding regions = 111 Number of orfs with sites within 600 bp upstream = 143 Fraction of orfs with sites within 600 bp upstream = 0.0229682 Motif number 5 AAAACACGAAAGGGGCAATGGGC 3 17 1 AGGGGCAATG 0.921497 -13 GGATACTGTGAGGAGAGACAATCAGATTTCT 4 118 0 AGGAGAGACA 0.716582 -114 ATCACTACAAAGGGGAAAGAGGGA 5 4 0 AGGGGAAAGG 0.973432 -148 TAATCCCTTGAGGAGAGAGCGCATTATGGAT 10 60 1 AGGAGAGAGG 0.957701 -241 CCTCGCGAAAAGGAGAGATTGT 18 75 1 AGGAGAGATG 0.964677 -12 ATGACAGCAAAGGGGAAATGGGAT 21 4 0 AGGGGAAATG 0.977874 -182 AAAAAGGGGAAATAGCCGTTTGGCT 22 5 1 AGGGGAAATG 0.977874 -99 CCTTACAAAAAGGAGAAACGGA 28 156 1 AGGAGAAACG 0.958505 -12 ********* * Masking position 8 Map Score: 5.63214 Number of sites scoring better than the average of aligned sites = 164 Number in coding regions = 123 Number in noncoding regions = 41 Number of orfs with sites within 600 bp upstream = 46 Fraction of orfs with sites within 600 bp upstream = 0.00738837 Motif number 6 CATTATACTCACTCATAAAATCAAGCGAAAGAAATCTG 4 89 1 ATAAATCGGA 0.717752 -143 CTTCTCAACAAAAGAAGGAACCTATAGAATGAACAATA 4 180 1 AAAAACCTGA 0.935233 -52 TATAAAAATCATTAAAATAATCCCTTGAGGAGAGAGCG 10 43 1 ATAAATCTGA 0.936762 -258 CATTATGGATAAACAGAGAATCTTTGAAGTATTAATCA 10 81 1 AAAAATCTAA 0.749345 -220 TTGCGCTAGTAAACATAGAATCAATTGATCTTATATTT 11 125 0 AAAAATCTGA 0.976562 -101 ATTTCAAAGGTAATACAAAATCATTTGAATGAGGAGGC 11 195 1 TAAAATCTGA 0.828353 -31 ATAAAAAACAAAAAATTTAATCATTCGAAAAAACAAAC 13 34 0 AAAAATCTGA 0.976562 -194 ATTTCAAGATAGTGAATCAATCACTTGATTATTTAAGT 13 184 1 ATAAATCTGA 0.936762 -44 ACAGAATGAATTGCTGGAGGGATACAAC 24 1 1 AAAAATTTGA 0.852702 -28 CTGCGCCTTGAAAAACGCAATCTATTGATAATGATTAT 26 109 0 AAAAATCTGA 0.976562 -85 AGATTAGGGAAAAAATGAAACTTTTTGAGCATCTGATC 29 58 1 AAAAACTTGA 0.667364 -243 AAAAGACACCTCCAATCATTAGACAGATCTTAG 30 6 1 AACAATCTGA 0.87734 -137 * * * **** * ** Masking position 9 Map Score: 6.70252 Number of sites scoring better than the average of aligned sites = 55 Number in coding regions = 42 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 7 CGGTAAATCACTGTCCGGCCGGGATTCTGCGCAGC 2 43 0 CTGTCCGCAT 0.822246 -184 CTTTCACATCCGCTCCTTCCCATATATCCTTTTGT 2 140 0 CGCTCCTCAT 0.97132 -87 ATCTGATTGTCTCTCCTCACAGTATCCTCCAAGTA 4 122 1 CTCTCCTCAT 0.985313 -110 TTTTTGGGCACTCTCCAAGCGAAACCCCTACAAAC 6 56 0 CTCTCCACAC 0.916502 -49 CTGTCCCCCCCTCACCTCACATTATGAAGGAGAAG 8 90 0 CTCACCTCAT 0.965571 -28 ATAATGCGCTCTCTCCTCAAGGGATTATTTTAATG 10 52 0 CTCTCCTAAT 0.815453 -249 CTACAGAGTCAGCTCCTAGCTCAACTAACTGATCT 10 171 0 AGCTCCTCAC 0.846611 -130 CCAATAACACTCCAATCACAATTGATAAAGCT 11 8 1 CACTCCACAT 0.7519 -218 CTTCTTTCCCAGCACCTTGCAAAATAAAACCATCT 23 124 1 AGCACCTCAT 0.833718 -106 GCAATCAGCTCTCACCGATCAGCATACCAGATGGT 23 152 0 CTCACCGCAT 0.914993 -78 ATTATGCAGAATGTCCTCACCACATGTAAAGCAAT 23 182 0 ATGTCCTCAT 0.810176 -48 GACATCTCCTCCTTAGATTTTTTATTAT 23 212 0 ATCTCCTTAT 0.610099 -18 CAGCGAGATCCTCTCCTATCCGTATCCTGTTCTTT 27 182 0 CTCTCCTCAT 0.985313 -25 CACATAATAAATCACCATACCTTACAAAAAGGAGA 28 137 1 ATCACCACAC 0.619044 -31 ******* * ** Masking position 14 Map Score: 7.73861 Number of sites scoring better than the average of aligned sites = 234 Number in coding regions = 175 Number in noncoding regions = 59 Number of orfs with sites within 600 bp upstream = 60 Fraction of orfs with sites within 600 bp upstream = 0.00963701 Motif number 8 ATTGTTTATTTGTCTTACAATTAAACAAAAG 2 116 1 TTCTTACAAT 0.844897 -111 TGTAATCTGTTATATTACAATGAAATCACTA 5 28 0 TTATTACAAT 0.778842 -124 CAATAACTGTTTTGATACAATGTTTAAAACA 5 64 1 TTGATACAAT 0.91353 -88 CATAATAGTGTGTATTAAAATCAGTTTCTCA 7 133 0 TTATTAAAAT 0.687528 -52 CGCAAAGGGGTTTGTTACACTAACTGTCATG 11 158 1 TTGTTACACT 0.777338 -68 TTTCGAACGCTGTGTCAAAATTATGTAATAA 13 150 0 TTGTCAAAAT 0.815195 -78 CCTTTTCCAGTATGATAAAATGTTCACGAGA 18 19 1 TTGATAAAAT 0.868445 -68 ATCCAGTATTTGTGATAAAATACCTTTGGCC 21 52 1 TTGATAAAAT 0.868445 -134 TTTGTCAACTTATGTTACAATGGAAAATCTG 22 52 1 TTGTTACAAT 0.953199 -52 GATTCTCCAATATGTCACAATCTATAACTGT 23 41 0 TTGTCACAAT 0.875925 -189 TTTATTTCACTATCTTAAAATAAAAGAAAAG 27 29 0 TTCTTAAAAT 0.772905 -178 TCAGCAGGAATTTGATAAAATGCAGGAAGAC 28 38 0 TTGATAAAAT 0.868445 -130 * ********* Masking position 7 Map Score: 6.35744 Number of sites scoring better than the average of aligned sites = 168 Number in coding regions = 96 Number in noncoding regions = 72 Number of orfs with sites within 600 bp upstream = 97 Fraction of orfs with sites within 600 bp upstream = 0.0155798 Motif number 9 TAAGCGCTTTTTGATTATTTTTTAAAGGAA 1 101 1 TTGATTATTT 0.915632 -72 TATTGACTTATTGTTTATTTGTCTTACAAT 2 107 1 TTGTTTATTT 0.631113 -120 ATATAATATAAAGAATATTTAAAATAATTT 6 13 1 AAGAATATTT 0.529866 -92 AATCAATCACTTGATTATTTAAGTTGGGGG 13 198 1 TTGATTATTT 0.915632 -30 ATCTCCTCCTTAGATTTTTTATTATGCAGA 23 207 0 TAGATTTTTT 0.735708 -23 ACATTTGGATATGATTATTTTTATAATTGA 26 74 1 ATGATTATTT 0.898053 -120 AATAAAAATTTAGATTTTTTAAAAATAATC 27 106 1 TAGATTTTTT 0.735708 -101 GCCGATGTAAAAGATTATTTTTAAAAAATC 27 118 0 AAGATTATTT 0.8773 -89 CGACAATCACATGATTATTTGACGATCAGA 29 89 0 ATGATTATTT 0.898053 -212 ********** Masking position 6 Map Score: 3.12333 Number of sites scoring better than the average of aligned sites = 120 Number in coding regions = 93 Number in noncoding regions = 27 Number of orfs with sites within 600 bp upstream = 33 Fraction of orfs with sites within 600 bp upstream = 0.00530035 Motif number 10 ACCAAACAGCCGGCTGACCAGGCTGTTTTTTT 2 10 1 CCGGTACCGG 0.902589 -217 TAAAAGGAGCCTGGGAGACCCGGCTTCTTTATT 8 20 1 CTGGAACCGG 0.70193 -98 CACGAATGTTTCGGTATACCTGGTATGACAGCA 16 36 1 TCGGAACCGG 0.976101 -89 TTTAGCAATATCAGGATACCGGGATAAGAAAAA 20 133 1 TCAGAACCGG 0.887219 -36 TAACGGGCTGCCGGCAAACGTGGTACACTTATG 21 82 0 CCGGAACGGG 0.988693 -104 TGAGAAAGCTCCGGCTTAACGGGCTGCCGGCAA 21 98 0 CCGGTAACGG 0.854078 -88 AATATATGAACCGGTATTCGCGGTGTGAAAACC 29 246 0 CCGGATCGGG 0.827806 -55 **** * *** ** Masking position 4 Map Score: 2.80306 Number of sites scoring better than the average of aligned sites = 84 Number in coding regions = 67 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 11 TTCGTTTGTTCTTCCTTTAAAAAATAATCAAA 1 110 0 CTTCCTTTAA 0.65887 -63 ATAGAATCCCCCCTTAGTAACCTTTTTGT 4 8 1 CCCCCCTTAA 0.864351 -224 AAAAATTGGTCCTCCTTCAATATACCCATTTT 5 109 0 CCTCCTTCAA 0.97306 -43 GCAAGTGCCTCCTTCCTTTTCAGTTTTTT 6 86 0 CCTCCTTCCT 0.845586 -19 TGTAGATTTACTTCCCTTAAGAGAAAGCATCT 7 24 1 CTTCCCTTAA 0.714555 -161 ACCTTGTCCTTCTCCTTCATAATGTGAGGTGA 8 82 1 TCTCCTTCAA 0.828294 -36 GTTCTGTCCCCCCCTCACCTCACATTATGA 8 98 0 CCCCCCTCAT 0.952983 -20 CAGGCCTCCTCATTCAAATGATTTTGTAT 11 207 0 CCTCATTCAT 0.810879 -19 GATTGTATCCTCCCTTACGTCT 14 3 0 CCTCCCTTAT 0.959794 -20 TCAAGCCCCTCCTTTATGCTTTTAAAAAT 15 55 0 CCTCCTTTAC 0.876068 -19 CGTCAAACAGCCTCCTTCTAACAACTATTCAT 17 14 0 CCTCCTTCTC 0.586443 -124 GGTTTCACCTCATTCAGAAGATAGACAGC 17 119 0 CCTCATTCAA 0.770986 -19 GTTTTGCAACCTCCTCCATGAATTATTAAAA 23 10 1 CCTCCTCCAA 0.802032 -220 GGCAGGCCAGCTTCCCTCATATGGAGAATGCA 23 78 0 CTTCCCTCAT 0.888428 -152 GCTGGCCTGCCCTCGCTTATATCAGCTTCTTT 23 99 1 CCTCGCTTAT 0.651584 -131 TCTCATGAACCTCCTTTAAATTCAG 25 5 0 CCTCCTTTAT 0.948502 -21 TTTTCCCTAATCTCCCTCAAATTAATATATCG 29 39 0 TCTCCCTCAT 0.888428 -262 TGTAAAATCCCCCTCATTTGCTTTCTTCT 30 124 0 TCCCCCTCAT 0.730241 -19 ********* * Masking position 4 Map Score: 12.9084 Number of sites scoring better than the average of aligned sites = 631 Number in coding regions = 441 Number in noncoding regions = 190 Number of orfs with sites within 600 bp upstream = 236 Fraction of orfs with sites within 600 bp upstream = 0.0379056 Motif number 12 CCCGCCTGCTTTTGAAAAGCTTCAAAATAAAGA 8 45 0 TTTGAAGCTC 0.989572 -73 TTGTATTACCTTTGAAATGTTTCCCATGACAGT 11 180 0 TTTGAAGTTC 0.947874 -46 AGCAATTGGAGAAGCTGCGCTTGCCGCA 15 6 1 TTGGAAGCTC 0.977142 -68 AGGTACTTAATTTGATAGGCTACATGTTGCTTG 20 76 1 TTTGAAGCTC 0.989572 -93 GAAGGGAATTTTTGATATGCTGCAATTAATGAA 29 128 1 TTTGAAGCTC 0.989572 -173 ***** * *** * Masking position 7 Map Score: 1.83674 Number of sites scoring better than the average of aligned sites = 43 Number in coding regions = 38 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 13 TTTGTTCTTCCTTTAAAAAATAATCAAAAA 1 108 0 CTTTAAAAAA 0.929883 -65 ACCCATTTTTCTTGAAAAAAGCATGTTTTA 5 88 0 CTTGAAAAAA 0.945393 -64 ATATTATGAACTTGAAAGAATGTAAAGAAC 7 73 0 CTTGAAAGAA 0.801864 -112 GTTCTCCCAACTTATAAAAATATAAGATCA 11 108 1 CTTATAAAAA 0.592081 -118 AGTAAAAAACCTTTATAAAAAACAAAAAAT 13 56 0 CTTTATAAAA 0.6284 -172 GATTCACTATCTTGAAATAACTTTCGAACG 13 172 0 CTTGAAATAA 0.82803 -56 CTCCTTTATGCTTTTAAAAATGAATGGCTT 15 46 0 CTTTTAAAAA 0.763516 -28 TCAGCCTTGCCTTTAAAAAAATATTTGTCA 26 18 1 CTTTAAAAAA 0.929883 -176 ACTGCTGCGCCTTGAAAAACGCAATCTATT 26 121 0 CTTGAAAAAC 0.765363 -73 ATTTCACTATCTTAAAATAAAAGAAAAGAC 27 27 0 CTTAAAATAA 0.619337 -180 AAAAGATTATTTTTAAAAAATCTAAATTTT 27 110 0 TTTTAAAAAA 0.498929 -97 ********** Masking position 7 Map Score: 2.73065 Number of sites scoring better than the average of aligned sites = 343 Number in coding regions = 276 Number in noncoding regions = 67 Number of orfs with sites within 600 bp upstream = 70 Fraction of orfs with sites within 600 bp upstream = 0.0112432 Motif number 14 TCTGATATTTTATAAAAAAGCGGTAAATCACTG 2 65 0 TTAAAAACGG 0.744601 -162 CATGCTTTTTTCAAGAAAAATGGGTATATTGAA 5 93 1 TAAGAAATGG 0.757614 -59 TCCTATCTTTTCAAAAAAATTGGTCCTCCTTCA 5 122 0 TAAAAAATGG 0.943174 -30 AGGAAGCACCTCGCAAATATTGGTGATTAATAC 10 109 0 TGCAAAATGG 0.943109 -192 CTATCCGGGGTGAAAAACATCGGTGAATTAGCT 10 268 1 TAAAAAACGG 0.921982 -33 TAGAATCAAATTGCAAACAGTGGTAAAATATCG 13 105 1 TGCAAAATGG 0.94311 -123 TTTATGCTTTTAAAAATGAATGGCTTTGCCATC 15 39 0 TAAAATATGG 0.678344 -35 CGAGTAAAATTTGAAAATAACGGGTATAATGCA 19 135 0 TGAAAAACGG 0.949611 -92 AGGTATTTTATCACAAATACTGGATGGCAGAAA 21 44 0 TACAAAATGG 0.912246 -142 CTTAAAATAAAAGAAAAGACTGGCTATGCAGTC 27 14 0 AGAAAAATGG 0.770805 -193 CATGTGATTGTCGAAAAAACGGGAAGGGAATTT 29 106 1 TGAAAAAGGG 0.875469 -195 * ***** * *** Masking position 6 Map Score: 3.80505 Number of sites scoring better than the average of aligned sites = 239 Number in coding regions = 200 Number in noncoding regions = 39 Number of orfs with sites within 600 bp upstream = 46 Fraction of orfs with sites within 600 bp upstream = 0.00738837 Motif number 15 TTCTTTCACATCCGCTCCTTCCCATATATCCTT 2 144 0 TCCCTCTTCC 0.966626 -83 ATACGTATCATCACTTACTTACTTTTTTGCAGA 4 47 1 TCATTCTTCT 0.945227 -185 GTCTACAGAGTCAGCTCCTAGCTCAACTAACTG 10 175 0 TCACTCTACT 0.939414 -126 CTCGCTTATATCAGCTTCTTTCCCAGCACCTTG 23 110 1 TCACTCTTCC 0.977294 -120 ATCATCAATTCCTTTCTTCGCTCTAAA 26 177 0 TCATTCTTCT 0.945227 -17 CAGCGAGATCCTCTCCTATCCGTATCCTGTT 27 186 0 TCCCTCTACC 0.926469 -21 AAAATCCCCCTCATTTGCTTTCTTCTTTTCTCG 30 117 0 TCATTCTTCT 0.945227 -26 *** ** *** ** Masking position 6 Map Score: 1.18993 Number of sites scoring better than the average of aligned sites = 105 Number in coding regions = 75 Number in noncoding regions = 30 Number of orfs with sites within 600 bp upstream = 21 Fraction of orfs with sites within 600 bp upstream = 0.00337295