AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/alignace/lib/ORF_synecho.txt -z/skink1/amcguire/genomes/synecho.fna -ilexA_synecho_opreg_300.orf -g0.48 -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 = 0.48 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 1652528 300 hypothetical protein #2 cysK 69 cysteine synthase #3 zwf 106 glucose 6-phosphate dehydrogenase #4 uvrA 157 excinuclease ABC subunit A #5 1652539 167 hypothetical protein #6 recQ 98 ATP-dependent DNA helicase RecQ #7 1652541 289 hypothetical protein #8 cbiD 99 CbiD protein #9 1652543 89 hypothetical protein #10 1652544 73 hypothetical protein #11 1652545 111 hypothetical protein #12 1652546 105 DNA-damage-inducible protein #13 1652572 215 hypothetical protein #14 uvrD 165 DNA helicase II #15 1652585 76 hypothetical protein #16 1652675 188 hypothetical protein #17 lexA 215 SOS function regulatory protein #18 sdhB 293 succinate dehydrogenase iron- sulphur protein subunit #19 1652855 163 ABC transporter #20 ycf44 203 hypothetical protein #21 1653544 192 hypothetical protein #22 prk 300 phosphoribulokinase #23 recN 300 DNA repair protein RecN #24 uvrB 191 excinuclease ABC subunit B #25 ruvB 201 Holliday junction DNA helicase RuvB #26 1001814 300 hypothetical protein #27 recA 138 RecA Motif number 1 AATCTTGGCTGGCGATCGCCATTTACTTAGAA 4 84 0 GGCGATCGCT 0.995935 -74 TAAAATCTATGGCAATCCAGGTTAATGCTAGC 5 85 0 GGCAATCCGT 0.863461 -83 GGCAGGCAATGGGATTGATGATTTAC 6 83 0 GGCAATGGAT 0.955272 -16 CAAAAAATAGGGCGATGATCATAGAGCAATTA 8 13 0 GGCGATGACT 0.945966 -87 CCGTTTCCATGGCAATCGCCCTTCGTTGAGAG 14 68 0 GGCAATCGCT 0.993493 -98 CCCTTTTCCTGGCGATCGTCGTTGGCATAGCT 16 111 1 GGCGATCGCT 0.995935 -78 CAATCACAGCGGCGATCGCCTTCTGCTGGCCG 17 70 1 GGCGATCGCT 0.995935 -146 TAACATTCAGGGCAATCATACTAAAAAAGATA 17 138 0 GGCAATCAAT 0.827136 -78 GGATTTTAGGGGCGATCGCCTTGGGAATTTTA 18 119 1 GGCGATCGCT 0.995935 -175 TGGGTCGATGGGCAATGGACTTTGCCTTTGCT 19 92 0 GGCAATGGCT 0.988535 -72 CCGGCCCCATGGCAATGGAATTTGGCCGATGA 20 134 0 GGCAATGGAT 0.955272 -70 CCATGGGGCCGGCGATCGGGGCACAATGATAG 20 154 1 GGCGATCGGC 0.965157 -50 GGCGGCAAAGGAGCTATAGTCTGGG 24 177 0 GGCAAAGGGT 0.767729 -15 ATCCTACATTGGCGATCGCCGCCGGGTTGTTC 25 126 0 GGCGATCGCC 0.986134 -76 ******** * * Masking position 5 Map Score: 26.4753 Number of sites scoring better than the average of aligned sites = 6674 Number in coding regions = 6089 Number in noncoding regions = 585 Number of orfs with sites within 600 bp upstream = 388 Fraction of orfs with sites within 600 bp upstream = 0.0623193 Motif number 2 CTATTTTGGTGATGGCTAGGGGCAGGGCCAGT 1 13 0 GATGCTGGGG 0.905888 -288 CAGGTTAATGCTAGCATTGGGGCGGTTTCGGC 5 68 0 CTAGATGGGG 0.713296 -100 TTTTTCCGGTTTACTGGGGACAATAAGCT 6 8 1 GGTTACGGGG 0.704107 -91 TTTTCAGGAGCCTAGGGGATGGTTGGTA 7 7 1 GGAGCTGGGG 0.979695 -283 CCAAACTTGGGGAGCCAGGGGGGCTTTTCAAA 7 165 0 GGAGCAGGGG 0.958114 -125 CCTGGCTCCCCAAGTTTGGGGGAAGTTAAGTA 7 178 1 CAAGTTGGGG 0.923383 -112 CATTATTGGGGGATTTAGGGGGCAAAATAAAA 7 219 1 GGATTAGGGG 0.956733 -71 GTGCCTCCCCGGAATTGTGGGGTTTTCTTTAA 9 19 0 GGAATGGGGG 0.771004 -71 GGATCAACCGGTTTTTTTGGGGGTTATTCAAG 11 20 1 GTTTTTGGGG 0.845828 -92 ATTGCTTAATGATTTTGAGGGGG 14 2 0 GATTTGGGGG 0.714122 -164 ATAACAGTAACATTTTTCGGGGTAGTCTCAAT 17 22 1 CATTTTGGGG 0.857677 -194 AATTTAGATTGGATTTTAGGGGCGATCGCCTT 18 109 1 GGATTTGGGG 0.979011 -185 AAAATAGGCACAATTCTAGGGGGTTCTCGACA 18 195 1 CAATCTGGGG 0.913647 -99 CAAGATTGACCGATTCAAGGGGGGGCGCGCCC 22 24 0 CGATCAGGGG 0.931728 -277 AACCGAAGAGCGTTATCTGGGGTTGACCAGGA 22 125 1 CGTTTCGGGG 0.814872 -176 TCCTTCGGCCCTTGACAGGGGGTTAACAAGCC 22 180 1 CTTGCAGGGG 0.63537 -121 CAGTATTGGGGGATTTAGGGGGCGGAATAAAA 23 48 0 GGATTAGGGG 0.956733 -253 CTAAATCCCCCAATACTGGGGGACTTTCATTC 23 62 1 CAATCTGGGG 0.913647 -239 CCTAACCTCCCAAATTTGGGGGGAAACTGAAT 23 90 0 CAAATTGGGG 0.74908 -211 CCCAAATTTGGGAGGTTAGGGGAGCTTTTCGA 23 102 1 GGAGTTGGGG 0.980632 -199 TAACGCCTTGGGTAAATGGGGGAGAAGTACCT 25 40 1 GGTAATGGGG 0.704441 -162 GATCGCCAATGTAGGATGGGGGGATACTGACT 25 141 1 GTAGATGGGG 0.793454 -61 GGATGTATGGGGATTGCAGAAG 27 127 0 GGATTAGGGG 0.956733 -12 **** ** **** Masking position 9 Map Score: 27.44 Number of sites scoring better than the average of aligned sites = 1266 Number in coding regions = 1072 Number in noncoding regions = 194 Number of orfs with sites within 600 bp upstream = 180 Fraction of orfs with sites within 600 bp upstream = 0.028911 Motif number 3 AACTGGCCCTGCCCCTAGCCATCACCAAAA 1 12 1 GCCCCTAGCC 0.895559 -289 GTGGTCCTGGCTCCCTGAGCTAGCCCGCAA 1 127 1 CTCCCTGAGC 0.736617 -174 CCGCAGTTTCTCCCAGGGTGAGTAAGTTA 5 149 0 CTCCCAGGGT 0.924005 -19 TTACCAACCATCCCCTAGGCTCCTGAAAA 7 10 0 TCCCCTAGGC 0.975361 -280 TTTGAAAAGCCCCCCTGGCTCCCCAAGTTT 7 165 1 CCCCCTGGCT 0.936627 -125 TTTCCCATTATCCCCTAGGCTGTGCCTCCC 9 42 0 TCCCCTAGGC 0.975361 -48 ATCACCTTTGTCCCCTGGGTAAAAAGCTAT 13 149 1 TCCCCTGGGT 0.984429 -67 AAAAAATAATTTCCCTTGGTTGATTGCTAA 14 109 1 TTCCCTTGGT 0.777776 -57 ACTCCTACTCCCCCCAGGGTC 15 2 0 CCCCCAGGGT 0.967949 -75 TCATTCGCTGCCCCCTGGGCATTAACCCAT 18 57 1 CCCCCTGGGC 0.959419 -237 TTTCCATACTTTCCATGGGTTAATGCCCAG 18 71 0 TTCCATGGGT 0.707448 -223 GCCACTAAAATTCCCAAGGCGATCGCCCCT 18 126 0 TTCCCAAGGC 0.874107 -168 CATATTGCTTTTCCCAGGGTATTTCCT 18 277 1 TTCCCAGGGT 0.922673 -17 GTGCCATGCTGCCCCGGGGTCGCAGATTAG 20 55 1 GCCCCGGGGT 0.641031 -149 CCGATCGCCGGCCCCATGGCAATGGAATTT 20 143 0 GCCCCATGGC 0.882494 -61 GGGTTAACAAGCCCATAGGCTCTGGTTTGT 22 199 1 GCCCATAGGC 0.703999 -102 GCCTTTCCTTTTCCCTGCGCC 25 191 1 TTCCCTGCGC 0.802676 -11 CAATTTGACCGCCCCTGGCCCTAGGATTAA 27 60 1 GCCCCTGGCC 0.937397 -79 ********** Masking position 4 Map Score: 23.5033 Number of sites scoring better than the average of aligned sites = 2664 Number in coding regions = 2397 Number in noncoding regions = 267 Number of orfs with sites within 600 bp upstream = 277 Fraction of orfs with sites within 600 bp upstream = 0.0444908 Motif number 4 CCAGGACCACAATCAGTGTTGGTAAAGAAAAACCGCC 1 100 0 AATTTGAAAG 0.870111 -201 GGCGATCGCCAGCCAAGATTAGCAAAGACAGTTTAAA 4 96 1 AGGTTGAAAG 0.970561 -62 AGGGTGAGTAAGTTAATGATTGTTAAGATTCGAGGTT 5 127 0 AGTATGTAAG 0.749942 -41 CCTTAAATTTAGAGAGTGTTTGAAAAGCCCCCCTGGC 7 147 1 AGTTTGAAAG 0.987126 -143 TAAATGTCTAAGAATCTGTTTGAAAAGTTTTATTTTG 7 241 0 AGTTTGAAAG 0.987126 -49 GGCACAGCCTAGGGGATAATGGGAAAGTTGCCATTTG 9 46 1 AGTATGAAAG 0.955185 -44 TGGGCAGTTTAGGTGTGCTTCGCAAAGATTTTTTATA 13 176 0 AGGTTGAAAG 0.970561 -40 CTTTTGCTTCAGACTGTTTTGGCACAGTTCAATCTTT 16 37 1 AGTTTGACAG 0.941143 -152 AAAACTTTTCAGAACATGTTTGGAAAGTTTTATTCCG 23 21 1 AGTTTGAAAG 0.987126 -280 TAACCTTATAAGAGCCTGTTCGAAAAGCTCCCCTAAC 23 116 0 AGTTTGAAAG 0.987126 -185 ** * ** * **** Masking position 10 Map Score: 11.2989 Number of sites scoring better than the average of aligned sites = 136 Number in coding regions = 48 Number in noncoding regions = 88 Number of orfs with sites within 600 bp upstream = 65 Fraction of orfs with sites within 600 bp upstream = 0.0104401 Motif number 5 ATTATTAGGTGTGAGGAAAAGCTAAAA 1 284 1 GGGAAAAGAA 0.962021 -17 CAGAGGCGGGGTTAAAGAGTTATTAGAGTTTAACT 2 45 0 GGAAAGAGAA 0.818146 -25 TGAAAACTTTGCCAGAAAAAGAAAACTTTCGGGAATT 3 33 1 GCAAAAAGAT 0.856857 -74 GTTTAAAATCGTGAAGAAAAGTTAAGAGCCTTGTCTC 4 126 1 GGGAAAAGAA 0.962021 -32 GGTGCAGGGAAAAAAAGATGAATAAATGTCTAA 7 267 0 GGAAAAAGGT 0.759334 -23 GGCCGAGTTGAAAAGCAACAATATTAAAGAT 13 5 1 GGGAAAAGAA 0.962021 -211 CTTTGTCCCCTGGGTAAAAAGCTATAAAAAATCTTTG 13 154 1 TGAAAAAGAA 0.928463 -62 AACGACGATCGCCAGGAAAAGGGATTAAATTTTTCCG 16 97 0 GCGAAAAGAA 0.928065 -92 CTGTGATTGAGGGCGAAAAAGCAAAATTGAGACTACC 17 42 0 GGAAAAAGAT 0.921586 -174 AGGGCAATCATACTAAAAAAGATACAAAATTTTACAT 17 125 0 TCAAAAAGAA 0.868601 -91 GCTCTAGGACTGGGTGAAAAGTAGTCATGGTTACCCA 18 14 1 TGGAAAAGGA 0.741048 -280 GTCAAAGACTTGGGAAAATAGGCACAATTCTAGGGGG 18 181 1 TGAAATAGAA 0.560904 -113 GGGGGTTCTCGACAAAAAAAGCCAGCAACGGGGTCTT 18 213 1 GCAAAAAGAA 0.940149 -81 ACATAACGTTTTGCCAAAAAGACAAATAAAAAGTAGC 26 122 0 TGAAAAAGAT 0.831819 -179 CCTAAAGTACTGCCAAAAAAGTAATAAGTACGCTGCT 26 259 0 TCAAAAAGAA 0.868601 -42 * * ****** * * Masking position 8 Map Score: 10.3629 Number of sites scoring better than the average of aligned sites = 320 Number in coding regions = 263 Number in noncoding regions = 57 Number of orfs with sites within 600 bp upstream = 65 Fraction of orfs with sites within 600 bp upstream = 0.0104401 Motif number 6 CCCCTAGCCATCACCAAAATAGCAACTATAAT 1 23 1 TCACAAAAAG 0.68711 -278 CCTGAGCTAGCCCGCAAAACAGACCAATGGCC 1 140 1 CCCCAAAAAG 0.97431 -161 TACTTAACTTCCCCCAAACTTGGGGAGCCAGG 7 178 0 CCCCAAACTG 0.914834 -112 CCCCCTAAATCCCCCAATAATGGGTGACTTTT 7 209 0 CCCCAATATG 0.96559 -81 ACTTGAATAACCCCCAAAAAAACCGGTTGATC 11 21 0 CCCCAAAAAA 0.714122 -91 AGTTCCGCAAAAATGGGCAGTTTAG 13 201 0 TCCCAAAATG 0.930314 -15 ATTGAGACTACCCCGAAAAATGTTACTGTTAT 17 22 0 CCCGAAAATG 0.860634 -194 TAATCACATCAATATTGACTTAACCAC 20 6 1 ACACAATATG 0.391382 -198 AAATCAAACCCCAACAAAAATCGTGGCGGAAC 21 85 0 CCACAAAATC 0.696592 -108 AACATCCCTCAAAAATGCAAAACTGAT 22 284 0 CCCCAAAATG 0.986602 -17 CCCCCTAAATCCCCCAATACTGGGGGACTTTC 23 58 1 CCCCAATATG 0.96559 -243 ATTCAGTTTCCCCCCAAATTTGGGAGGTTAGG 23 90 1 CCCCAAATTG 0.878752 -211 GATTAATTGATCAACAATAAAGCACTGTGCGA 24 39 1 TCACAATAAG 0.455591 -153 TCGGAACATCCCAGCAAAAAAGCCTCCAGCCC 25 96 0 CCACAAAAAG 0.923739 -106 GAGTCATTGCCCCACAAAAGTTAAGATAACAT 26 155 0 CCCCAAAATT 0.829065 -146 *** ***** ** Masking position 6 Map Score: 13.1369 Number of sites scoring better than the average of aligned sites = 673 Number in coding regions = 544 Number in noncoding regions = 129 Number of orfs with sites within 600 bp upstream = 99 Fraction of orfs with sites within 600 bp upstream = 0.0159011 Motif number 7 TGATGGCTAGGGGCAGGGCCAGTTT 1 1 0 GGGCAGCAGT 0.917684 -300 GCTAGCATTGGGGCGGTTTCGGCATTGGTTACAAT 5 56 0 GGGCGGTGGT 0.971683 -112 CCCCAAACTTGGGGAGCCAGGGGGGCTTTTCAAAC 7 164 0 GGGGAGAGGG 0.752546 -126 GGGATTTAGGGGGCAAAATAAAACTTTTCAAACAG 7 228 1 GGGCAATAAT 0.61592 -62 TAACCAGATTGGGCAGAGATAGACTGAGACAAATT 8 65 0 GGGCAGAAGT 0.979471 -35 CCACAATTCCGGGGAGGCACAGCCTAGGGGATAAT 9 31 1 GGGGAGAAGT 0.945785 -59 TAAATAAATTGGGCAAGTAGAGAATAATTAGCTTA 11 62 0 GGGCAAAAGT 0.787859 -50 AGGGCAGATTAGACTGCTCTTCTCAC 12 90 0 GGGCAGTGAG 0.78215 -16 CCGCAAAAATGGGCAGTTTAGGTGTGCTTCGCAAA 13 187 0 GGGCAGTGGT 0.983048 -29 GACCCTGGGGGGAGTAGGAGTAAGTTAAAAT 15 7 1 GGGGGGTGGT 0.926204 -70 TCGGGCCCTAAGGCAGAATAAAGATTGAACTGTGC 16 58 0 AGGCAGTAAT 0.462951 -131 ACATTTTTCGGGGTAGTCTCAATTTTGCTTTTTCG 17 31 1 GGGTAGTAAT 0.53827 -185 AATGCCCAGGGGGCAGCGAATGATTTGGATGGGTA 18 45 0 GGGCAGATGT 0.933174 -249 CTCTGGATTAGGGCAGGAAAATGGTCCGGCCTTGG 19 59 0 GGGCAGAATT 0.758616 -105 TGCGACCCCGGGGCAGCATGGCACTAGGGCCCCGG 20 44 0 GGGCAGTGCT 0.849873 -160 GGGATTTAGGGGGCGGAATAAAACTTTCCAAACAT 23 36 0 GGGCGGTAAT 0.924195 -265 TCCCAAATTTGGGGGGAAACTGAATGAAAGTCCCC 23 80 0 GGGGGGATGT 0.751387 -221 TGGGATAATAGGGCTGATTAAAGATAACTATCGTG 24 146 0 GGGCTGTAAT 0.653511 -46 AATGTAGGATGGGGGGATACTGACTAGAACCGACT 25 148 1 GGGGGGATGT 0.751386 -54 AAAAGGTTTAGGGCAGTCTTAGTTTGTTGACTATC 26 44 1 GGGCAGTAGT 0.984835 -257 ****** * ** * Masking position 3 Map Score: 18.5556 Number of sites scoring better than the average of aligned sites = 906 Number in coding regions = 800 Number in noncoding regions = 106 Number of orfs with sites within 600 bp upstream = 105 Fraction of orfs with sites within 600 bp upstream = 0.0168648 Motif number 8 AAAGTTTTCAGGAAAAATTTCTTTCTCAGTTC 3 11 0 GAAAAATTTT 0.87746 -96 TCTTTTTCTGGCAAAGTTTTCAGGAAAAATTT 3 23 0 GAAAGTTTTA 0.870694 -84 GAATCTGTTTGAAAAGTTTTATTTTGCCCCCT 7 235 0 GAAAGTTTTT 0.919384 -55 AATCAGTAGCGAGAAAATTTGTCTCAGTCTAT 8 50 1 GGAAAATTTT 0.81804 -50 GGTGTGCTTCGCAAAGATTTTTTATAGCTTTT 13 170 0 GAAAGATTTT 0.905941 -46 CCCGACTCCCGGAAAAATTTAATCCCTTTTCC 16 88 1 GAAAAATTTA 0.808637 -101 CGGAAGAAATGTAAAATTTTGTATCTTTTTTA 17 117 1 GAAAATTTTT 0.889642 -99 CTGGGGTGAGGAGAAATTTTCTAGGAAACCGG 22 245 1 GGAAATTTTT 0.842194 -56 AACATGTTCTGAAAAGTTTTTAAATTTGCT 23 9 0 GAAAGTTTTA 0.870694 -292 GAACATGTTTGGAAAGTTTTATTCCGCCCCCT 23 32 1 GAAAGTTTTT 0.919384 -269 AGATGCTCGGGAGAAAATTTTAACTTAATCCT 27 82 0 GGAAAATTTA 0.726082 -57 * ******** * Masking position 5 Map Score: 6.42114 Number of sites scoring better than the average of aligned sites = 295 Number in coding regions = 201 Number in noncoding regions = 94 Number of orfs with sites within 600 bp upstream = 89 Fraction of orfs with sites within 600 bp upstream = 0.0142949 Motif number 9 GTCTTTGCTAATCTTGGCTGGCGATCGCCAT 4 94 0 ATCTGGCTGG 0.937728 -64 AAATCCCCCAATAATGGGTGACTTTTACTTA 7 204 0 ATATGGGTGA 0.818883 -86 GACCCTGGGGGGAGTAGGAGTA 15 2 1 ACCTGGGGGG 0.779013 -75 TTTCCTGGCGATCGTCGTTGGCATAGCTCGA 16 115 1 ATCTCGTTGG 0.38225 -74 GGGAAAAGCAATATGGGCGGAGGCTACCTCA 18 261 0 ATAGGGCGGA 0.868412 -33 CTAGACTCTAATCCTGTGGGAAATTCTACCC 20 90 0 ATCTGTGGGA 0.689294 -114 CCCAACAAAAATCGTGGCGGAACCACAGCCA 21 77 0 ATCTGGCGGA 0.973294 -116 TCTTCACAACATCCGGGTTGAGCTTATTTCT 21 162 1 ATCGGGTTGA 0.825312 -31 CCAACACGCCATCTGGGGTGAGGAGAAATTT 22 233 1 ATCGGGGTGA 0.953823 -68 AAATCCCCCAATACTGGGGGACTTTCATTCA 23 64 1 ATATGGGGGA 0.878872 -237 AACCTCCCAAATTTGGGGGGAAACTGAATGA 23 88 0 ATTGGGGGGA 0.723135 -213 TAATGGACTTATCGGGGCGGACATCGGTAAA 23 155 1 ATCGGGCGGA 0.970716 -146 AAAGATAACTATCGTGGCTGGCCATTCAGCG 24 131 0 ATCTGGCTGG 0.937728 -61 CATAGTGCCAATCTTCGCTGAATTCGATGAT 26 218 1 ATCTCGCTGA 0.803149 -83 *** ******* Masking position 1 Map Score: 9.85188 Number of sites scoring better than the average of aligned sites = 787 Number in coding regions = 711 Number in noncoding regions = 76 Number of orfs with sites within 600 bp upstream = 89 Fraction of orfs with sites within 600 bp upstream = 0.0142949 Motif number 10 TCTTTGCTAATCTTGGCTGGCGATCGCCATT 4 93 0 TCTTGCTGGC 0.868698 -65 ACCCCACAATTCCGGGGAGGCACAGCCTAGG 9 28 1 TCCGGGAGGC 0.79379 -62 TTATGTACAATGGGAGCAGGCAGAGCCAAGC 13 57 0 TGGGGCAGGC 0.963632 -159 TTCCTGGCGATCGTCGTTGGCATAGCTCGAT 16 116 1 TCGTGTTGGC 0.91259 -73 GAAGCATCGATGGTTGGTGGATCATTTGTTG 16 155 0 TGGTGGTGGA 0.793512 -34 TTGGGAATTTTAGTGGCAGGCTTAGTGATGT 18 139 1 TAGTGCAGGC 0.877017 -155 GATTAAGACCCCGTTGCTGGCTTTTTTTGTC 18 223 0 CCGTGCTGGC 0.966687 -71 AAAAGCAATATGGGCGGAGGCTACCTCACAG 18 258 0 TGGGGGAGGC 0.95534 -36 TAACAAAACACGGTGGGTGGCCTGTCTGTCT 24 70 0 CGGTGGTGGC 0.949782 -122 AAGATAACTATCGTGGCTGGCCATTCAGCGG 24 130 0 TCGTGCTGGC 0.985398 -62 **** ****** Masking position 6 Map Score: 3.78633 Number of sites scoring better than the average of aligned sites = 512 Number in coding regions = 486 Number in noncoding regions = 26 Number of orfs with sites within 600 bp upstream = 30 Fraction of orfs with sites within 600 bp upstream = 0.0048185 Motif number 11 AATTCCGGGGAGGCACAGCCTAGGGGATAA 9 35 1 AGGCACAGCC 0.97163 -55 CAATGGGAGCAGGCAGAGCCAAGCTCTCAC 13 51 0 AGGCAGAGCC 0.97163 -165 ACTGTGAGGTAGCCTCCGCCCATATTGCTT 18 257 1 AGCCTCCGCC 0.900957 -37 ATCGTGGCGGAACCACAGCCATGGCCACCA 21 68 0 AACCACAGCC 0.955737 -125 CCCCAGAAATAAGCTCAACCCGGATGTTGT 21 167 0 AAGCTCAACC 0.736892 -26 CCAGAGATATAGCCTGACCCTCTGAATACT 22 91 0 AGCCTGACCC 0.868146 -210 TGGAGAGACAAACCAGAGCCTATGGGCTTG 22 206 0 AACCAGAGCC 0.955737 -95 GAACCGACTCAAGCTGAGCCTTTCCTTTTC 25 174 1 AAGCTGAGCC 0.955737 -28 ********** Masking position 1 Map Score: 3.94163 Number of sites scoring better than the average of aligned sites = 220 Number in coding regions = 191 Number in noncoding regions = 29 Number of orfs with sites within 600 bp upstream = 37 Fraction of orfs with sites within 600 bp upstream = 0.00594282 Motif number 12 AACTCTAATAACTCTTTAACCCCGCCTCTG 2 50 1 ACTCTTACCC 0.874663 -20 TCTCCCGGTAAATCATCAATCCCATTGCCTGCC 6 76 1 AATCTCACCC 0.988115 -23 TTTATATCTAAATCATTAATCCCAGTTACCAAC 7 32 0 AATCTTACCC 0.957769 -258 ATAGGACAAGAATCTTCTATCCCATGGTCCGGT 12 13 0 AATCTCACCC 0.988115 -93 CCCATTGACTAATCTGCGACCCCGGGGCAGCAT 20 60 0 AATCGCACCC 0.982439 -144 AGCCCTCGATAATCCGCTAACCTGAAATTAGGT 25 68 0 AATCGCACCT 0.878884 -134 CCCAGCAAAAAAGCCTCCAGCCCTCGATAATCC 25 86 0 AAGCTCACCC 0.962379 -116 **** ** * *** Masking position 9 Map Score: 3.42433 Number of sites scoring better than the average of aligned sites = 42 Number in coding regions = 34 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 13 GGCTTAAAACCCAGAACAGTTTACGAAATT 4 51 0 CCAGAACAGT 0.660294 -107 ATGGGAGCAGGCAGAGCCAAGCTCTCACTC 13 49 0 GCAGAGCCAA 0.769439 -167 TCACCCAGTCCTAGAGCATA 18 1 0 CTAGAGCATA 0.77083 -293 CTGCCCTAATCCAGAGCAAAGGCAAAGTCC 19 78 1 CCAGAGCAAA 0.868567 -86 ATATCTCTGGCTAGAACCGAAGAGCGTTAT 22 111 1 CTAGAACCGA 0.950369 -190 GAGAGACAAACCAGAGCCTATGGGCTTGTT 22 204 0 CCAGAGCCTA 0.952749 -97 GGGATACTGACTAGAACCGACTCAAGCTGA 25 161 1 CTAGAACCGA 0.950369 -41 GCACTATGCAACAGAGCCGATAAACCAGCC 26 196 0 ACAGAGCCGA 0.891939 -105 GCTAAAGATCCTAGAACCGAGGTAACG 27 8 0 CTAGAACCGA 0.950369 -131 ********** Masking position 5 Map Score: 2.49866 Number of sites scoring better than the average of aligned sites = 291 Number in coding regions = 259 Number in noncoding regions = 32 Number of orfs with sites within 600 bp upstream = 37 Fraction of orfs with sites within 600 bp upstream = 0.00594282 Motif number 14 CTGATTGTGGTCCTGGCTCCCTGAGCTAGCC 1 121 1 TCTGGCTCCC 0.944159 -180 TGACCAACTTTGCAGTCTCCCGGTAAATCAT 6 61 1 TCAGTCTCCC 0.975051 -38 TGAAAAGCCCCCCTGGCTCCCCAAGTTTGGG 7 167 1 CCTGGCTCCC 0.838778 -123 GGTCTACTGTCTCCCTCCAAATGGC 9 75 0 TCTGTCTCCC 0.9752 -15 TTTCGCTCTTTTCCGTTTCCATGGCAATCGC 14 81 0 TCCGTTTCCA 0.614902 -85 CTGCCTTAGGGCCCGACTCCCGGAAAAATTT 16 77 1 GCCGACTCCC 0.890197 -112 GGGACTTTCATTCAGTTTCCCCCCAAATTTG 23 81 1 TCAGTTTCCC 0.943761 -220 TTATCGTAACGACAGTTTCCCATAGCATAAC 23 256 1 GCAGTTTCCC 0.947864 -45 TGGGTGGCCTGTCTGTCTCGCACAGTGCTTT 24 57 0 GCTGTCTCGC 0.832641 -135 GTCGGTTCTAGTCAGTATCCCCCCATCCTAC 25 151 0 GCAGTATCCC 0.846764 -51 AGCTGAGCCTTTCCTTTTCCCTGCGCC 25 185 1 TCCTTTTCCC 0.614902 -17 * ********* Masking position 8 Map Score: 4.18377 Number of sites scoring better than the average of aligned sites = 374 Number in coding regions = 326 Number in noncoding regions = 48 Number of orfs with sites within 600 bp upstream = 52 Fraction of orfs with sites within 600 bp upstream = 0.00835207 Motif number 15 GAACATTGACAGCACAATGCAGGTTTTCAT 15 40 0 AGCACAATGC 0.956911 -37 AGACTGTTTTGGCACAGTTCAATCTTTATT 16 47 1 GGCACAGTTC 0.948483 -142 TGGGAAAATAGGCACAATTCTAGGGGGTTC 18 191 1 GGCACAATTC 0.956911 -103 CGGCGATCGGGGCACAATGATAGGGCTATC 20 163 1 GGCACAATGA 0.910454 -41 TCAACAATAAAGCACTGTGCGAGACAGACA 24 49 1 AGCACTGTGC 0.907984 -143 AGCGAAGATTGGCACTATGCAACAGAGCCG 26 207 0 GGCACTATGC 0.972395 -94 ********** Masking position 4 Map Score: 1.77576 Number of sites scoring better than the average of aligned sites = 109 Number in coding regions = 103 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432