AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00440_ecoli_reg_100.orf -o00440_ecoli_100.ace -a/home/amcguire/alignace/lib/ORF_ecoli.txt -z/skink1/amcguire/genomes/ecoli.fna -g0.51 -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 = 0.51 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 surA 52 survival protein #2 imp 254 organic solvent tolerance #3 prpB 238 putative phosphonomutase 2 #4 ybdL 108 putative aminotransferase #5 potF 300 periplasmic putrescine-binding protein; permease protein #6 ybjO 59 orf, hypothetical protein #7 ybjF 40 putative enzyme #8 cls 300 cardiolipin synthase, a major membrane phospholipid; novobiocin sensitivity #9 malX 174 PTS system, maltose and glucose-specific II ABC #10 cstC 300 acetylornithine delta-aminotransferase #11 ubiX 94 3-octaprenyl-4-hydroxybenzoate carboxy-lyase #12 purF 36 amidophosphoribosyltransferase = PRPP amidotransferase #13 cvpA 165 membrane protein required for colicin V production #14 ygcA 56 putative enzyme #15 yhdT 108 orf, hypothetical protein #16 nirC 300 nitrite reductase activity #17 yigN 140 putative alpha helix chain #18 ubiE 94 2-octaprenyl-6-methoxy-1,4-benzoquinone --> 2-octaprenyl-3-methyl-6-methoxy-1,4-benzoquinone Motif number 1 CAAATCGACACACGGATATCAGGGCTATCTCCCAC 2 19 1 CCGGTACAGC 0.898881 -236 CATTCAATGCCGTGCCTAACACCACTGACGCTATT 2 132 1 CTGCTACAAC 0.675453 -123 GACCGTTTGTCACGCGCAACGTTACCGATGATGGA 2 214 1 CCGCCACGAC 0.990007 -41 AGAACTTTCTCCCGGCCAGCACTGCTCGCTATATA 5 173 0 CCGGCACAGC 0.968319 -128 TACATAATGCCGCGCATGTCGCGGCATTGTTTTC 6 36 1 CCGCTGCGGC 0.977901 -24 TTTACGTCGGCTAGCCTGACGCTGCATGCGCCAGC 8 106 1 CAGCTGCGGC 0.837121 -195 ATTATACCCCCACCCCCGACGCTGACCAGTGCTTT 8 200 1 CCCCCGCGGA 0.952674 -101 TCTTTTTATTCACCCACATCGCAAACGTATTCACT 10 102 1 CCCCCACGAA 0.929116 -199 GCCAGACCGGCACCCTCAGCGAAGGCA 11 3 0 CCCCCACGGG 0.877166 -92 GGATTTCCTTCCCGCGCATCAATAAAAATGGCGCT 13 67 0 CCGCCACAAA 0.971185 -99 GCGCGCATTGCACGCCTGTCGGCAAATAACCCGCT 16 98 1 CCGCTGCGAA 0.921886 -203 GACCCACATACGCGCCCGCCATGGCGGAGCTGACC 16 142 0 CCGCCGCAGC 0.989542 -159 TACCAAAGGTCGCGCCCATCACCAAAGGGCGTACG 16 223 0 CCGCCACAAA 0.971185 -78 CAACAACTTACCCGCACAAAATAGAATTGTGCTGT 17 102 0 CCGCCAAAGA 0.785143 -39 GGGTAGAAATCTAGGGCATCGACGCCCAATCTGTT 18 32 1 CAGGCACGGC 0.85093 -63 CTCAATGCCTGCTCATCAAAAAATTGTTCCAG 18 73 0 CTGCCACAAA 0.796525 -22 * *** ** ** ** Masking position 1 Map Score: 17.9278 Number of sites scoring better than the average of aligned sites = 2826 Number in coding regions = 2697 Number in noncoding regions = 129 Number of orfs with sites within 600 bp upstream = 125 Fraction of orfs with sites within 600 bp upstream = 0.0200771 Motif number 2 GCCTAACACCACTGACGCTATTCGGACAGG 2 145 1 ACTGACGCTA 0.835836 -110 GCGCAACGTTACCGATGATGGAACAATAAA 2 227 1 ACCGATGATG 0.848755 -28 TTTTATTGTACCTGACGAAGTTGCGTGTTG 4 89 0 CCTGACGAAG 0.958291 -20 AATCGTCGCCCCTGATGATGTGAAGGTCAA 7 18 1 CCTGATGATG 0.978524 -23 GAATGCACTTCCTGATGCTGTGGATACGCA 8 42 1 CCTGATGCTG 0.990726 -259 CGTCGGCTAGCCTGACGCTGCATGCGCCAG 8 110 1 CCTGACGCTG 0.994165 -191 TACCCCCACCCCCGACGCTGACCAGTGCTT 8 204 1 CCCGACGCTG 0.991824 -97 TGACCTACTCCCTGATTATGTGACAGATAA 9 16 1 CCTGATTATG 0.799321 -159 ACGCATTGCCCGATGCCGCAAAGGCATA 13 9 1 CCCGATGCCG 0.952839 -157 AACGCCTCCTGACGCAACAACTTACCC 17 124 0 CCTGACGCAA 0.90298 -17 ********** Masking position 5 Map Score: 13.4513 Number of sites scoring better than the average of aligned sites = 1110 Number in coding regions = 1061 Number in noncoding regions = 49 Number of orfs with sites within 600 bp upstream = 47 Fraction of orfs with sites within 600 bp upstream = 0.00754899 Motif number 3 CGTTTGTCACGCGCAACGTTACCGATGATGG 2 217 1 GCGCACGTTA 0.98602 -38 AGCGCACCGCAAAGTTAAGAAA 3 2 1 GCGCACGCAA 0.967476 -237 TTGCAATGAAACGCGGTGAAACATTGCCTGA 3 66 1 ACGCGTGAAA 0.721482 -173 TTTTTTATCGGCGCGGTGTAAGAAAAGAGAA 5 204 0 GCGCGTGTAA 0.952158 -97 GCCGCGACATGCGCGGCATTATGTAGCCAGG 6 30 0 GCGCGCATTA 0.889645 -30 TGAGGGGCAATCGCGCCGAAATATGCGTATC 8 64 0 TCGCGCGAAA 0.720652 -237 CCTTTTGAAAGCGCATTGTTATGAGTTTACG 8 269 0 GCGCATGTTA 0.965549 -32 AAATCACATTACGCAACGATAATAGCGGGTA 9 71 0 ACGCACGATA 0.901767 -104 AGAATAAAAAACGCAATGTTATGCAGAAGTA 10 74 0 ACGCATGTTA 0.86086 -227 TTTCCTTCCCGCGCATCAATAAAAATGGCGC 13 68 0 GCGCACAATA 0.85246 -98 CCTGTTCGGGGCGCATTCTAACAGAAAAAGA 13 116 0 GCGCATCTAA 0.738581 -50 CGTGCAATGCGCGCAGCGTTAGCCGCACACT 16 81 0 GCGCACGTTA 0.98602 -220 TTCCTGCGAGGCGCTACGCAAAAATACAAAA 17 47 0 GCGCTCGCAA 0.824292 -94 ***** ***** Masking position 11 Map Score: 13.8169 Number of sites scoring better than the average of aligned sites = 1326 Number in coding regions = 1258 Number in noncoding regions = 68 Number of orfs with sites within 600 bp upstream = 82 Fraction of orfs with sites within 600 bp upstream = 0.0131706 Motif number 4 GGCTGCGGTCAATTGTGGGACATCGCCTATAA 2 81 1 AATTGTGGAA 0.887498 -174 TGTTGCAATGAAACGCGGTGAAACATTGCCTG 3 64 1 AAACGCGGGA 0.918965 -175 TTATTAAGGCAATTGTGGCACACCCCTTGCTT 3 172 1 AATTGTGGAA 0.887499 -67 GAAAACAATGCCGCGACATGCGCGGCAT 6 42 0 AATGCCGCAA 0.782604 -18 CTTGAGGGGCAATCGCGCCGAAATATGCGTAT 8 65 0 AATCGCGCGA 0.981965 -236 TGGCAAATAAAAACGCGGGAAAAGCACTGGTC 8 223 0 AAACGCGGAA 0.894181 -78 GGATTCAGTAAATTGCGCGAGAAGATAAAACG 9 126 0 AATTGCGCAA 0.961616 -49 GTCAGAATGGCGCAGTAATTTCCAGTA 10 6 1 AATGGCGCGA 0.975847 -295 CATCAATAAAAATGGCGCTGAAAAAATATTCA 13 54 0 AATGGCGCGA 0.97647 -112 CAGGGCGTAAAATCGTGGGACACAT 13 151 1 AATCGTGGAA 0.925995 -15 CACAAAATAGAATTGTGCTGTACAAACGTCCA 17 91 0 AATTGTGCGA 0.926613 -50 ******** * * Masking position 2 Map Score: 9.62549 Number of sites scoring better than the average of aligned sites = 403 Number in coding regions = 367 Number in noncoding regions = 36 Number of orfs with sites within 600 bp upstream = 41 Fraction of orfs with sites within 600 bp upstream = 0.00658529 Motif number 5 CATTCTAAACAAACAGCGTAACTCGTTATT 8 17 0 AAACAGCGTA 0.763742 -284 TGGCAAATAAAAACGCGGGAAAAGCACTGG 8 225 0 AAACGCGGGA 0.908217 -76 AAAAGTGCATAAACGGCGGAGGCTAACTGG 10 184 0 AAACGGCGGA 0.98355 -117 GAACAGGATGACAGGGCGTAAAATCGTGGG 13 140 1 ACAGGGCGTA 0.925975 -26 TAAAGCGTCAAAAGGCCGGATTTTCCGGCC 15 17 1 AAAGGCCGGA 0.989809 -92 CAGTAATAAAAAAGGCCGGAAAATCCGGCC 15 30 0 AAAGGCCGGA 0.989809 -79 GCCCATCACCAAAGGGCGTACGGATGGATC 16 215 0 AAAGGGCGTA 0.979208 -86 CAAAAATACAAAAGGCCGAACGCGTCGGCC 17 30 0 AAAGGCCGAA 0.949081 -111 ********** Masking position 3 Map Score: 8.70688 Number of sites scoring better than the average of aligned sites = 176 Number in coding regions = 146 Number in noncoding regions = 30 Number of orfs with sites within 600 bp upstream = 26 Fraction of orfs with sites within 600 bp upstream = 0.00417604 Motif number 6 TTATCAACGCAAATAACAAGTTGATAACAAAG 3 209 1 AAAAAAAGTT 0.908061 -30 AGTATTTGGCAATCAAGACGTTTAGATGTCTA 4 36 0 AATAAACGTT 0.940507 -73 ATTATGTGACAGATAAAACGTTTTACCTTTTA 9 30 1 AGAAAACGTT 0.97692 -145 TTGCGCGAGAAGATAAAACGTTTTATCAAATT 9 114 0 AGAAAACGTT 0.97692 -61 GTGCATATAAAGTGAATACGTTTGCGATGTGG 10 115 0 AGTAAACGTT 0.939366 -186 CCTCTACAGTAAATAATTCGTTATTTATATGT 10 274 0 AAAAATCGTT 0.883788 -27 TCTAACAGAAAAAGAAAACGTTTGCGTAGGGA 13 99 0 AAAAAACGTT 0.977355 -67 ACAAAAAATAAAACAAAAAGTTTA 16 3 0 AAAAAAAGTT 0.908063 -298 *** ** ***** Masking position 6 Map Score: 7.14992 Number of sites scoring better than the average of aligned sites = 40 Number in coding regions = 26 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911 Motif number 7 ATCAGGGCTATCTCCCACAATATAAAGGTG 2 36 1 TCTCCCACAA 0.924413 -219 TTATAGGCGATGTCCCACAATTGACCGCAG 2 83 0 TGTCCCACAA 0.988259 -172 TTGATTTTATTGTTCCATCATCGGTAACGT 2 232 0 TGTTCCATCA 0.846368 -23 GGTTTAGTCTTGTTTCATAATTGTTGCAAT 3 43 1 TGTTTCATAA 0.69846 -196 AAGCAAGGGGTGTGCCACAATTGCCTTAAT 3 174 0 TGTGCCACAA 0.950736 -65 ACGTTTTATCTGTCACATAATCAGGGAGTA 9 21 0 TGTCACATAA 0.855611 -154 ATGTGTCCCACGATTTTACGCCC 13 153 0 TGTCCCACGA 0.957184 -13 TGACCTTAATTGTCCCATAACGGAACTCC 14 10 0 TGTCCCATAA 0.981504 -47 ATCAAAAAATTGTTCCAGAAGTGTAACAGA 18 61 0 TGTTCCAGAA 0.903327 -34 ********** Masking position 7 Map Score: 6.46988 Number of sites scoring better than the average of aligned sites = 63 Number in coding regions = 53 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 8 AGCGCACCGCAAAGTTAAGAA 3 2 1 GCGCACCGCA 0.975936 -237 GAACTTTCTCCCGGCCAGCACTGCTCGCTA 5 177 0 CCGGCCAGCA 0.860701 -124 TTTTCTTACACCGCGCCGATAAAAAATATG 5 209 1 CCGCGCCGAT 0.892442 -92 TGAGGGGCAATCGCGCCGAAATATGCGTAT 8 65 0 TCGCGCCGAA 0.851184 -236 GCATGCGCCAGCGCCCCACTTCCGTTCTAC 8 129 1 GCGCCCCACT 0.890563 -172 GATTTCCTTCCCGCGCATCAATAAAAATGG 13 71 0 CCGCGCATCA 0.893743 -95 CTGTTAGAATGCGCCCCGAACAGGATGACA 13 123 1 GCGCCCCGAA 0.982021 -43 GGCGTGCAATGCGCGCAGCGTTAGCCGCAC 16 84 0 GCGCGCAGCG 0.936483 -217 ACCAAAGGTCGCGCCCATCACCAAAGGGCG 16 227 0 GCGCCCATCA 0.938993 -74 TTTTTGCGTAGCGCCTCGCAGGAAATGCCT 17 54 1 GCGCCTCGCA 0.921346 -87 AACAACTTACCCGCACAAAATAGAATTGTG 17 106 0 CCGCACAAAA 0.510812 -35 ********** Masking position 2 Map Score: 6.29516 Number of sites scoring better than the average of aligned sites = 2609 Number in coding regions = 2470 Number in noncoding regions = 139 Number of orfs with sites within 600 bp upstream = 143 Fraction of orfs with sites within 600 bp upstream = 0.0229682 Motif number 9 GACAGGTATGATAATGCAAATTATAGGCGATGTCCCAC 2 95 0 AATGCATGGC 0.880325 -160 GCACTATAACACGATGCTAGTATTTGGCAATCAAGACG 4 48 0 AATGCGAGGC 0.902619 -61 GTACCTGACGAAGTTGCGTGTTGAAGGCACTATAACAC 4 74 0 ATTGCGTGGC 0.989737 -35 GCCGATAAAAAATATGCACGTTTATTGCATATCTTTCA 5 223 1 AATGCGTTGC 0.983819 -78 CCCGCGTTTTTATTTGCCAGATGAATCCATATGCGTAA 8 236 1 TTTGCGTTCC 0.882861 -65 CTTCTGCATAACATTGCGTTTTTTATTCTTTTTATTCA 10 76 1 ATTGCTTTTC 0.661863 -225 GTATTCACTTTATATGCACTTTAAATGCATATGGTTTG 10 128 1 TATGCTTTGC 0.768953 -173 CTGTAAATGTAGATTGCAGGGTTCGTGCCAGCCAGTGA 10 215 0 ATTGCGTTGC 0.988891 -86 TTGCAGGCAGACTTTGCAGGATTTCGGCGGGAGTTGCA 11 47 0 ATTGCGTGGC 0.989737 -48 CACGCTCGGTAATTTGCTCGATCCATCCGTACGCCCTT 16 196 1 ATTGCGTTCC 0.96443 -105 * **** * * *** Masking position 5 Map Score: 4.42075 Number of sites scoring better than the average of aligned sites = 408 Number in coding regions = 366 Number in noncoding regions = 42 Number of orfs with sites within 600 bp upstream = 51 Fraction of orfs with sites within 600 bp upstream = 0.00819146 Motif number 10 CGACACACGGATATCAGGGCTATCTCCCACAA 2 24 1 ATTCAGGGCA 0.8638 -231 CGTACTCGTCATCTCTACGCTAGTGTTAATCC 2 173 0 ATTCTACGCA 0.941558 -82 TGCTTTGTCTTTATCAACGCAAATAACAAGTT 3 199 1 TTTCAACGCA 0.9545 -40 GGATACGCATATTTCGGCGCGATTGCCCCTCA 8 63 1 ATTCGGCGCA 0.937775 -238 ATTGCCCCTCAAGCCAACGCGATTTACGTCGG 8 84 1 AACCAACGCA 0.828607 -217 TTTACTGGAAATTACTGCGCCATTCTGAC 10 8 0 ATACTGCGCA 0.903898 -293 GCAATCTACATTTACAGCGCAAACATTACTTA 10 236 1 TTACAGCGCA 0.924512 -65 GCTGAAAAAATATTCAACGCCATCGACTTTTT 13 38 0 TATCAACGCA 0.85362 -128 GTTGAATATTTTTTCAGCGCCATTTTTATTGA 13 52 1 TTTCAGCGCA 0.970976 -114 CGGGAAGGAAATCCCTACGCAAACGTTTTCTT 13 88 1 ATCCTACGCA 0.901209 -78 ** ******* * Masking position 12 Map Score: 5.59731 Number of sites scoring better than the average of aligned sites = 599 Number in coding regions = 566 Number in noncoding regions = 33 Number of orfs with sites within 600 bp upstream = 41 Fraction of orfs with sites within 600 bp upstream = 0.00658529 Motif number 11 CAGCCGGAAAACGGTAAAAGCACCTTTATATT 2 54 0 ACGTAAAGCA 0.910091 -201 AAATAAAAACGCGGGAAAAGCACTGGTCAGCG 8 219 0 GCGGAAAGCA 0.991383 -82 TCAGAATGGCGCAGTAATTTCCAGTAAATTTC 10 12 1 GCGTAATTCC 0.765808 -289 CTTTATATGCACTTTAAATGCATATGGTTTGG 10 135 1 ACTTAAAGCA 0.636346 -166 TAATGTTTGCGCTGTAAATGTAGATTGCAGGG 10 232 0 GCGTAAAGTA 0.836489 -69 CAGGATTTCGGCGGGAGTTGCAAGTCAGGGTG 11 37 0 GCGGAGTGCA 0.86961 -58 ATTGCCCGATGCCGCAAAGGCATAAAAAGTCG 13 15 1 GCGCAAAGCA 0.963474 -151 AATAAAAAAGGCCGGAAAATCCGGCCTTTTGA 15 24 0 GCGGAAATCC 0.958527 -85 AAATTACCGAGCGTGAAAATCAGGATGATCCC 16 179 0 GCTGAAATCA 0.848747 -122 GTAGCGCCTCGCAGGAAATGCCTTTCCAACTG 17 61 1 GCGGAAAGCC 0.987939 -80 ** ***** *** Masking position 6 Map Score: 3.91795 Number of sites scoring better than the average of aligned sites = 1384 Number in coding regions = 1292 Number in noncoding regions = 92 Number of orfs with sites within 600 bp upstream = 87 Fraction of orfs with sites within 600 bp upstream = 0.0139737 Motif number 12 CGTTTGTCACGCGCAACGTTACCGATGATG 2 217 1 GCGCAACGTT 0.985218 -38 TTAACGTTTCAGGCAATGTTTCACCGCGTT 3 75 0 AGGCAATGTT 0.634904 -164 GCCGCGACATGCGCGGCATTATGTAGCCAG 6 31 0 GCGCGGCATT 0.896175 -29 ACATCATCAGGGGCGACGATTATACACA 7 9 0 GGGCGACGAT 0.950645 -32 CCTTTTGAAAGCGCATTGTTATGAGTTTAC 8 270 0 GCGCATTGTT 0.89664 -31 AAATCACATTACGCAACGATAATAGCGGGT 9 72 0 ACGCAACGAT 0.919705 -103 GTCAGAATGGCGCAGTAATTTCCAGTAAA 10 10 1 GCGCAGTAAT 0.74468 -291 AGAATAAAAAACGCAATGTTATGCAGAAGT 10 75 0 ACGCAATGTT 0.792281 -226 AAGTCTGACAGGGCAACTATTT 11 83 1 GGGCAACTAT 0.720008 -12 TTTCCTTCCCGCGCATCAATAAAAATGGCG 13 69 0 GCGCATCAAT 0.865826 -97 CGTGCAATGCGCGCAGCGTTAGCCGCACAC 16 82 0 GCGCAGCGTT 0.979362 -219 TTGGTGATGGGCGCGACCTTTGGTATCGCC 16 233 1 GCGCGACCTT 0.876713 -68 GTAACAGATTGGGCGTCGATGCCCTAGATT 18 39 0 GGGCGTCGAT 0.897136 -56 ********** Masking position 10 Map Score: 9.66885 Number of sites scoring better than the average of aligned sites = 2458 Number in coding regions = 2337 Number in noncoding regions = 121 Number of orfs with sites within 600 bp upstream = 138 Fraction of orfs with sites within 600 bp upstream = 0.0221651 Motif number 13 ACCGATGATGGAACAATAAAATCAACGT 2 237 1 GAAAATAAAA 0.963443 -18 ACTTCGTCAGGTACAATAAAA 4 98 1 GTAAATAAAA 0.906085 -11 GCGGGTATAAGATAAATAAAAGGTAAAACGT 9 47 0 GATAATAAAA 0.825262 -128 TTATGCAGAAGTAAAATATAATTCTGGAATT 10 56 0 GTAAATATAA 0.63356 -245 GGGTGAATAAAAAGAATAAAAAACGCAATGT 10 86 0 AAAAATAAAA 0.911517 -215 CATTCTAACAGAAAAAGAAAACGTTTGCGTA 13 103 0 GAAAAGAAAA 0.874998 -63 AAATAAAAACAAAAAATAAAACAAAAAGTTT 16 12 0 AAAAATAAAA 0.911517 -289 ATTATCCTTTAAAAAATAAAAACAAAAAATA 16 25 0 AAAAATAAAA 0.911517 -276 *** ******* Masking position 6 Map Score: 2.66607 Number of sites scoring better than the average of aligned sites = 38 Number in coding regions = 16 Number in noncoding regions = 22 Number of orfs with sites within 600 bp upstream = 25 Fraction of orfs with sites within 600 bp upstream = 0.00401542 Motif number 14 CGTACTCGTCATCTCTACGCTAGTGTTAAT 2 175 0 ATCTCTACGC 0.94144 -80 TGCCAGATGAATCCATATGCGTAAACTCAT 8 250 1 ATCCATATGC 0.960115 -51 GTTATAACCAAACCATATGCATTTAAAGTG 10 144 0 AACCATATGC 0.879758 -157 CGGGAAGGAAATCCCTACGCAAACGTTTTC 13 88 1 ATCCCTACGC 0.988221 -78 TGCTCGATCCATCCGTACGCCCTTTGGTGA 16 210 1 ATCCGTACGC 0.978535 -91 ********** Masking position 6 Map Score: 1.20118 Number of sites scoring better than the average of aligned sites = 47 Number in coding regions = 42 Number in noncoding regions = 5 Number of orfs with sites within 600 bp upstream = 5 Fraction of orfs with sites within 600 bp upstream = 0.000803084 Motif number 15 ACTGACGCTATTCGGACAGGATTAACACTA 2 155 1 TTCGGACAGG 0.95609 -100 CAAGAATAACTTTAGCCAGGGTTTGAGACT 5 134 0 TTTAGCCAGG 0.894069 -167 CGCGGCATTATGTAGCCAGGTTGGCAAATT 6 20 0 TGTAGCCAGG 0.910653 -40 CTGCCTGCAAGTCTGACAGGGCAACTATTT 11 75 1 GTCTGACAGG 0.945746 -20 GCCCCGAACAGGATGACAGGGCGTAAAATC 13 135 1 GGATGACAGG 0.801343 -31 GCGGGTTATTTGCCGACAGGCGTGCAATGC 16 102 0 TGCCGACAGG 0.963362 -199 CGCGTCGGCCTTCAGACAGGAGAAGAGAA 17 10 0 TTCAGACAGG 0.973767 -131 ********** Masking position 8 Map Score: 0.975222 Number of sites scoring better than the average of aligned sites = 468 Number in coding regions = 418 Number in noncoding regions = 50 Number of orfs with sites within 600 bp upstream = 56 Fraction of orfs with sites within 600 bp upstream = 0.00899454