AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/alignace/lib/ORF_bsub.txt -z/skink1/amcguire/genomes/bsub.fna -ilexA_bsub_opreg_300.orf -g0.435 -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 = 0.435 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 yerE 264 similar to hypothetical proteins #2 yerF 61 similar to ATP-dependent DNA helicase #3 spoIIIE 300 DNA translocase #4 pgsA 300 phosphatidylglycerophosphate synthase #5 recA 172 multifunctional SOS repair regulator #6 lexA 149 transcriptional regulator #7 dinG 125 ATP-dependent helicase #8 panB 245 ketopantoate hydroxymethyltransferase #9 ypjH 31 alternate gene name: jojH; similar to lipopolysaccharide biosynthesis-related protein #10 ypjD 300 alternate gene name: jojD #11 yqjW 165 similar to ATP/GTP-binding protein #12 recN 36 recN #13 ahrC 134 transcriptional regulator #14 yqiE 246 similar to hypothetical proteins #15 yqiC 85 similar to exodeoxyribonuclease VII (small subunit) #16 yqiB 137 similar to exodeoxyribonuclease VII (large subunit) #17 yqhZ 263 similar to transcription termination #18 accB 155 acetyl-CoA carboxylase subunit (biotin carboxyl carrier subunit) #19 spoIIIAC 22 spoIIIAC #20 spoIIIAA 75 spoIIIAA #21 yqhV 144 alternate gene name: yqgE #22 efp 24 elongation factor P #23 yqhS 86 similar to 3-dehydroquinate dehydratase #24 yqhR 226 yqhR #25 ruvB 250 Holliday junction DNA helicase #26 ruvA 138 Holliday junction DNA helicase #27 bofC 47 bofC #28 csbX 70 alpha-ketoglutarate permease #29 yrbE 237 similar to opine catabolism #30 ytpS 159 ytpS #31 ytpP 234 similar to thioredoxin H1 #32 uvrB 185 excinuclease ABC (subunit B) #33 csbA 300 putative membrane protein Motif number 1 AAATGGTTACATAAAAAGGGAGGCTGAGAG 1 9 0 AAAAAAGGAG 0.818768 -256 CTTTTTTCATAAAAAAAGAGAGCATATGGCAG 1 128 0 AAAAAAGGAG 0.818768 -137 CTCTTTTTTTATGAAAAAAGAATCAAAACACC 1 140 1 AGAAAAAGAA 0.925265 -125 CACATAGCGCGGAAAAACGGAAAAAGCCGTTA 1 193 0 GAAAAACGAA 0.750205 -72 GGAATCCTACAGAAAAAACGAGCCTGTAAACG 3 223 1 AAAAAAAGAG 0.896244 -78 AGAAGGAACGCTGAAAAAAGACGAAACCTATA 4 66 1 CGAAAAAGAC 0.841703 -235 GGGATTTGCCAAGAAAAAAGCGAACGCATATT 5 99 0 AGAAAAAGCG 0.885346 -74 CTGCCTTGATCCAAAAAAGGACTGGGACAGAG 8 108 1 CAAAAAAGAC 0.849029 -138 TGGCTTGCAGAAGAAAACGGCAGATCATCTCC 8 201 1 AGAAAACGCA 0.836954 -45 GTGGATGAAAAAGAAAACAGCAAACGTGCTTA 10 217 1 AGAAAACGCA 0.836954 -84 TTCGCATATAATGAAAAGCGAACATAAGTTCT 11 130 1 AGAAAAGGAA 0.866226 -36 GACGTTAAAAGAAAAAAAAGCAGATGTACCGG 13 11 1 GAAAAAAGCA 0.866226 -124 ACATGAATGCAGAAAAAAGGAATAATAGCGCC 13 51 0 AAAAAAAGAA 0.92905 -84 AGCAGTTTATATGAAAAATGAAAAGGAAAAGC 14 128 1 AGAAAAAGAA 0.925265 -119 AAAAATGAAAAGGAAAAGCGCGTTTGTCTTTT 14 141 1 AGAAAAGGCG 0.801535 -106 AATCTCAGACATAAAAAAAGACAAACGCGCTT 14 156 0 AAAAAAAGAC 0.927664 -91 CAGACGTGAAAAAAAATGAAACATGACATT 15 9 1 AAAAAAAGAA 0.92905 -77 GAATGAGGGAAAAAAGCCCGCTAAACAA 18 7 1 GGAAAAAGCC 0.857062 -149 GTAGTAACCTATAAAAAAAGAAATTTCATACA 18 119 1 AAAAAAAGAA 0.92905 -37 AAAGGAAAAAAGAAGTCTGTTCCC 21 3 1 AGAAAAAGAA 0.925265 -142 GTTTTTGGGCACAAAAAAAGCCTGCTCCCATT 21 36 0 AAAAAAAGCC 0.923811 -109 TTTTTTGTGCCCAAAAACAGAATCTTTCTTTT 21 50 1 CAAAAACGAA 0.715756 -95 TAAAGTGTGCCCAAAAAATGAAATGTCAATAA 24 193 0 CAAAAAAGAA 0.851681 -34 ATTCTTTCACGAAAAAAAAGACATGAATACAT 26 29 0 GAAAAAAGAC 0.870254 -110 TCATTGTACCATAAAAACAGCCAAAGTCTTAT 26 92 0 AAAAAACGCC 0.841703 -47 AAACTGTTCAGGAAAAAGAGCCTAATTCTAGT 29 62 1 GAAAAAGGCC 0.768349 -176 TAAATCCGCCAAAAAAAACGAATCATGTGAAA 30 18 1 AAAAAAAGAA 0.92905 -142 TTATATTATCCTGAAAAATGCGGCCGTACTGG 33 30 1 CGAAAAAGCG 0.772014 -271 ATGATGTAATAAAAAAAGTGCCGCTGATTAGA 33 110 1 AAAAAAGGCC 0.863792 -191 TCTGATTATAGTAAAAAATGAAGAATCGGACA 33 248 0 GAAAAAAGAA 0.872589 -53 * ****** *** Masking position 6 Map Score: 37.3592 Number of sites scoring better than the average of aligned sites = 1159 Number in coding regions = 828 Number in noncoding regions = 331 Number of orfs with sites within 600 bp upstream = 338 Fraction of orfs with sites within 600 bp upstream = 0.0542885 Motif number 2 TATGAAATTGGAGGGGCTTT 4 291 1 GAGGGGCTTT 0.882002 -10 TACCCTGTTTGAAGGGATTTGCCAAGAAAA 5 114 0 GAAGGGATTT 0.560241 -59 CCCCCGATAAAGGGGGCTTTTCTT 7 5 0 AGGGGGCTTT 0.958695 -121 CCCCCTTTATCGGGGGTTTTCTTTTAAGAT 7 19 1 CGGGGGTTTT 0.833306 -107 TTTGAGAGTAAAACGGTTTTGCCGCTCCAT 7 49 1 AAACGGTTTT 0.56765 -77 TCGTTGTAACGGAAGGTTTTTTGGCTTGCA 8 180 1 GGAAGGTTTT 0.836176 -66 ATCTGGCTGAGGGCGGTTTTACAGGTATTA 10 48 0 GGGCGGTTTT 0.93398 -253 ATGGAAGGAAAAGGGGTTTTGTGTGATGCT 10 167 0 AAGGGGTTTT 0.810785 -134 CTAAAGCCAGGGCGGGTTTTCTTTAGTTAT 16 84 1 GGCGGGTTTT 0.97621 -54 CGGCTATGTAAGCCGGCTTTCTTCATGCTT 17 77 0 AGCCGGCTTT 0.919242 -187 CCGCTTGTTTAGCGGGCTTTTTTCCCTCAT 18 13 0 AGCGGGCTTT 0.965135 -143 CCGCTAAACAAGCGGGCTTTTTGCGTTGCT 18 28 1 AGCGGGCTTT 0.965135 -128 CCCAAATGGGAGCAGGCTTTTTTTGTGCCC 21 32 1 AGCAGGCTTT 0.846419 -113 TAGTTTTCTGGGACGGTTTTTAGTATACCA 30 119 0 GGACGGTTTT 0.913358 -41 ATATACATAAGGAGGGATTTTTATT 31 6 0 GGAGGGATTT 0.864152 -229 ACGTTTTAAAAGCAGGTTTTTTATACACAA 32 50 1 AGCAGGTTTT 0.835537 -136 GAATCCCTGAGGAGGGTTTTTG 33 289 1 GGAGGGTTTT 0.962459 -12 ********** Masking position 8 Map Score: 19.0887 Number of sites scoring better than the average of aligned sites = 537 Number in coding regions = 365 Number in noncoding regions = 172 Number of orfs with sites within 600 bp upstream = 140 Fraction of orfs with sites within 600 bp upstream = 0.0224863 Motif number 3 GCCTATACAAAACATACGTTCTATCATAAACC 2 27 0 AACTAGTTCT 0.855167 -35 TGCGTTAAAAAATGTAAGTTCATACATAATGA 3 265 0 AATTAGTTCA 0.659301 -36 AAAAAATCCGAATATGCGTTCGCTTTTTTCTT 5 89 1 AATTGGTTCG 0.854716 -84 CTCCAACAGGAATGTTTGTTCGCATTTTTATA 6 14 1 AATTTGTTCG 0.909334 -136 AATTGACAGAAACGTTTGTTCGTATATACTGA 6 49 0 AACTTGTTCG 0.968356 -101 TTACAGTACAAACATAGGTTCGAAAAAACAAT 6 78 0 AACTAGTTCG 0.985419 -72 ATTATATGCGAAAGTATGTTCGTTTTATACTG 11 110 0 AAATAGTTCG 0.939239 -56 CTCTAAAAAGAACTTATGTTCGCTTTTCATTA 11 138 0 AACTAGTTCG 0.985419 -28 CAGCCGCTTCAAATTAGGATCGTTTTAGTGAT 14 74 0 AAATAGATCG 0.662629 -173 TAGAAAAGTTAACATATGTTCGCTTCTCTCTC 26 61 0 AACTAGTTCG 0.985419 -78 AAAACCACCGAACTTTAGTTCGTATTTTTAGT 32 96 1 AACTTGTTCG 0.968356 -90 *** ** ***** Masking position 2 Map Score: 11.4455 Number of sites scoring better than the average of aligned sites = 31 Number in coding regions = 17 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 17 Fraction of orfs with sites within 600 bp upstream = 0.00273049 Motif number 4 CTCTCAGCCTCCCTTTTTATGTAACCATTT 1 8 1 CCTCCTTTAT 0.917922 -257 GTCATACGTTCCTCCATTCGTTTGTTACCATTT 1 242 0 CCTCCTCGTT 0.860781 -23 ATTTGAATGACTTCCGCTTCATTCCCTTTCATT 3 76 0 CTTCCTTCTT 0.793801 -225 GATGACTTTTCTTCCTTTTTATTTACAATCTTT 4 225 0 CTTCCTTTTT 0.899529 -76 AAAGCCCCTCCAATTTCATACTCGGACGT 4 282 0 CCTCCTTTAT 0.917922 -19 TCTATTTTTTCCTCCTTTATGTTACCACTACAT 5 150 0 CCTCCTATTT 0.747163 -23 AGGAGATGATCTGCCGTTTTCTTCTGCAAGCCA 8 201 0 CTGCCTTTTT 0.821381 -45 GTTTTCTCCTCCTCATGTTTAGAGGAGATG 8 226 0 CCTCCATGTT 0.918549 -20 AAAGGGCCGCCCTCCCCTTGGTTTCGTGTTAAG 17 15 0 CCTCCTTGTT 0.979901 -249 AAGGGGAGGGCGGCCCTTTGGTTTTTTTACACG 17 29 1 CGGCCTTGTT 0.886868 -235 ACTCTCCCAACCTCCCATTTTTTTATATGATAT 21 119 0 CCTCCTTTTT 0.97186 -26 ATTATCAACCTGCCTATTTCTTTAGGATTGCT 24 10 1 CTGCCTTTTT 0.821381 -217 AATAAAAATCCCTCCTTATGTATATCCATCTGT 31 11 1 CCTCCATGAT 0.785028 -224 TATCGATACTCGTCCATTTGGATCATACCAAAC 31 173 0 CGTCCTTGAT 0.831715 -62 TTCATATCCCTCCAGTTGTTTATGTTCTTAC 31 214 0 CCTCCTTGTT 0.979901 -21 AAAAATAAGCCTCCGTTTCTTTAACGAAATCT 32 164 0 CCTCCTTCTT 0.936909 -22 AGTACCAGTACGGCCGCATTTTTCAGGATAATA 33 33 0 CGGCCATTTT 0.562264 -268 ***** *** ** Masking position 13 Map Score: 19.6355 Number of sites scoring better than the average of aligned sites = 389 Number in coding regions = 267 Number in noncoding regions = 122 Number of orfs with sites within 600 bp upstream = 145 Fraction of orfs with sites within 600 bp upstream = 0.0232894 Motif number 5 GTGTTCTACTGTGGAAATGGTTACATAAAA 1 25 0 GTGGAAATGG 0.739026 -240 CTCGTTATTCACTGAAAAAGGTGTTTTGAT 1 161 0 ACTGAAAAAG 0.667778 -104 GCGCGGAAAAACGGAAAAAGCCGTTAATCT 1 189 0 ACGGAAAAAG 0.735243 -76 TTCTAGTCGAAATGAAAGGGAATGAAGCGG 3 66 1 AATGAAAGGG 0.840688 -235 CACGTTTTGTACGGAAATGGAGCGGCAAAA 7 65 0 ACGGAAATGG 0.891591 -61 AGGGGCTGATGTGGAAAAGGGCATAAAGCA 10 12 1 GTGGAAAAGG 0.827672 -289 TATCTAATGGAAGGAAAAGGGGTTTTGTGT 10 173 0 AAGGAAAAGG 0.937168 -128 TATTATAGTGGATGAAAAAGAAAACAGCAA 10 210 1 GATGAAAAAG 0.686535 -91 TTATATGAAAAATGAAAAGGAAAAGCGCGT 14 134 1 AATGAAAAGG 0.915224 -113 TTGAAGAAGCGATGAAAGGGCTTGAGAGCA 15 40 1 GATGAAAGGG 0.843193 -46 AATAGAGTGAAAGGAAATGGTTAGCAATCC 24 35 0 AAGGAAATGG 0.897898 -192 GATTGTTGCTAATGAAATGGGAGTGGAA 25 233 1 AATGAAATGG 0.864227 -18 ATTGATTTTGGCTGAAAAGGGGTATGGTGT 33 194 1 GCTGAAAAGG 0.911411 -107 ********** Masking position 5 Map Score: 10.1584 Number of sites scoring better than the average of aligned sites = 685 Number in coding regions = 572 Number in noncoding regions = 113 Number of orfs with sites within 600 bp upstream = 110 Fraction of orfs with sites within 600 bp upstream = 0.0176678 Motif number 6 TTCTGATCAGTTATGTCTTTTTTATAGGTTTCGTC 4 85 0 TTATCTTTAT 0.669782 -216 TAAGATGACTTTTCTTCCTTTTTATTTACAATCTT 4 226 0 TTTCCTTTAT 0.853484 -75 TCTATTTTTTCCTCCTTTATGTTACCACTA 5 153 0 TTTTCTTTAT 0.908515 -20 AACAGGAATGTTTGTTCGCATTTTTATAATTTCAG 6 18 1 TTTGCTTTTT 0.901847 -132 GAAAAGCGCGTTTGTCTTTTTTTATGTCTGAGATT 14 153 1 TTTGTTTTAT 0.850565 -94 TTCTTTCTCCTTTGATCCTCTTTATCCGCTTGTCG 17 238 0 TTTGCTTTAT 0.978254 -26 TGCCAAAAAGTGTGAGCTTTTTTATTGACATTTCA 24 172 1 TGTGCTTTAT 0.876473 -55 TAAAAGAAAATTTGCGCGTGTTTATAGATGCGGCG 25 124 1 TTTGCTTTAT 0.978254 -127 TCTATAAGACTTTGGCTGTTTTTATGGTACAATGA 26 89 1 TTTGTTTTAT 0.850565 -50 TCTACACCTCTTTGCACACGTTTATGATTAGTTTG 27 21 0 TTTGCTTTAT 0.978254 -27 ATTCACCTTCTTTGCTCTATTTTATGCAGCTGTTT 29 14 1 TTTGCTTTAT 0.978254 -224 GATTCGTTTTTTTTGGCGGATTTATGGGAGT 30 7 0 TTTTCTTTAT 0.908515 -153 CCACCGAACTTTAGTTCGTATTTTTAGTGATTTTG 32 100 1 TTAGCTTTTT 0.652371 -86 **** * ***** Masking position 11 Map Score: 11.3446 Number of sites scoring better than the average of aligned sites = 150 Number in coding regions = 114 Number in noncoding regions = 36 Number of orfs with sites within 600 bp upstream = 43 Fraction of orfs with sites within 600 bp upstream = 0.00690652 Motif number 7 CGAGATTAACGGCTTTTTCCGTTTTTCCGC 1 187 1 GGCTTTTTCC 0.824882 -78 ACAACGAGAAGGATTCTTCACTTTCTAAAG 8 157 0 GGATTCTTCA 0.966796 -89 GCCCTTTCATCGCTTCTTCAAATGTCATGT 15 31 0 CGCTTCTTCA 0.978626 -55 GCACGATACCCGCTTCTTCAGGCTCCTAAA 16 59 1 CGCTTCTTCA 0.978626 -79 TCTACCGATTGGCTTCTTTAAAATGTATGA 20 41 0 GGCTTCTTTA 0.892685 -35 GGCTTCTTCCCCCTTGATCA 29 228 0 GGCTTCTTCC 0.976841 -10 CACGATTGTCCGATTCTTCATTTTTTACTA 33 242 1 CGATTCTTCA 0.947082 -59 CCCTCCTCAGGGATTCTTCATCTGATCTGA 33 275 0 GGATTCTTCA 0.966796 -26 ********** Masking position 5 Map Score: 8.70416 Number of sites scoring better than the average of aligned sites = 218 Number in coding regions = 201 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911 Motif number 8 TACATAAAAAGGGAGGCTGAGAG 1 1 0 GGGAGGAGAG 0.83089 -264 GTTTTCTTTTAAGATTTTGAGAGTAAAACGGTT 7 34 1 AAGATGAGAG 0.926103 -92 GCTAACATGTAAGAGGATGATAGGAGGTTTCGT 10 275 1 AAGAGGATAG 0.827199 -26 AGCGAAGCATAAGGATAGGAGAGTCATG 11 6 0 AAGGAGAGAG 0.952348 -160 AATATGATCCAAGGGTTTGAGAGAAGAAAAACA 11 53 0 AAGGGGAGAG 0.988685 -113 GAAGCGATGAAAGGGCTTGAGAGCATTGTATCA 15 45 1 AAGGGGAGAG 0.988685 -41 AAAAAAATGGGAGGTTGGGAGAGTGCT 21 128 1 GAGGTGAGAG 0.895761 -17 TTTTTCGTGAAAGAATGAGAGAGAAGCGAACAT 26 45 1 AAGAAGAGAG 0.926103 -94 AACGTGTGCAAAGAGGTGTAGAGG 27 34 1 AAGAGTAGAG 0.904506 -14 AGAAAACTATAAGGGAGTTAGAGATAAATT 30 140 1 AAGGGTAGAG 0.937907 -20 ***** ***** Masking position 10 Map Score: 6.94977 Number of sites scoring better than the average of aligned sites = 69 Number in coding regions = 54 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 9 GCGATGAAGTGGCAGCTCTTTAAAAGAAGGAACGCTG 4 42 1 GGCAGCTAAA 0.967206 -259 GCACCGGATATGCACCTAATCTGAAAATAAAAATCAA 4 134 1 TGCACCTAAA 0.926594 -167 AAAAAGTGATGGCACAAACCATAAAGATTGTAAATAA 4 203 1 GGCACAAAAA 0.697178 -98 GCCTGCGAACTGCACCTATTATTAAAATAGATAGACA 8 61 1 TGCACCTAAA 0.926594 -185 ATGAAAAAATTGCCGCTCCGATTAAAATAAAAAATAT 10 108 1 TGCCGCTAAA 0.899599 -193 TGTACATGAATGCAGAAAAAAGGAATAATAGCGCCCT 13 49 0 TGCAGAAAAA 0.616826 -86 TAAGCATTCCTGCACCATAACTAAAGAAAACCCGCCC 16 93 0 TGCACCAAAA 0.926594 -45 CACACTTTTTGGCAGCTGCGAGTAAAATTTGAAAATA 24 149 0 GGCAGCTAAA 0.967206 -78 GGCACCTCCAGTTAAAGTGTGCCCAAA 24 210 0 GGCACCTAAG 0.770956 -17 CAGTATATCGGGCAGCATAAGGTAAAAGAAAATTTGC 25 102 1 GGCAGCAAAA 0.967206 -149 GTCTCATTTTCGCCGCATCTATAAACACGCGCAAATT 25 132 0 CGCCGCAAAA 0.704128 -119 CTCTATTTTATGCAGCTGTTTATAGGAAAATCATAAA 29 28 1 TGCAGCTAGA 0.801139 -210 GTACCAGTACGGCCGCATTTTTCAGGATAATATAACC 33 28 0 GGCCGCAAGA 0.803527 -273 ATAAAAAAAGTGCCGCTGATTAGAACAGCGGCACCAT 33 118 1 TGCCGCTAAA 0.899599 -183 TTAGAACAGCGGCACCATGGAATAAGTTTTGACCGGC 33 137 1 GGCACCAAAT 0.800187 -164 AGTTTTGACCGGCACCAAAATGCAAATATGGTGATTG 33 161 1 GGCACCAAAT 0.800187 -140 ******* ** * Masking position 14 Map Score: 10.6495 Number of sites scoring better than the average of aligned sites = 473 Number in coding regions = 426 Number in noncoding regions = 47 Number of orfs with sites within 600 bp upstream = 48 Fraction of orfs with sites within 600 bp upstream = 0.0077096 Motif number 10 AAGAATCAAAACACCTTTTTCAGTGAATAA 1 157 1 ACACCTTTTT 0.844686 -108 TAGAAGCGGTACACCTTTATATTCAATTTG 3 41 0 ACACCTTTAT 0.902192 -260 TTTTCGCACCTCAAAACGTCGATTT 6 135 0 GCACCTCAAA 0.789931 -15 TAAAATGGACACCTCAATTCTTGCATAC 7 108 0 ACACCTCAAT 0.936839 -18 ACACACCTCTAAAAAGAACTTA 11 154 0 ACACCTCTAA 0.956438 -12 ACAGCATTACACCTCTTATCTTTGTTAG 12 19 0 ACACCTCTTA 0.928291 -18 GTAAGCACCTCTATTTCCAAGCTT 13 121 0 GCACCTCTAT 0.941217 -14 ATATTTTCACACACCTTAATATGATTATTC 17 131 0 ACACCTTAAT 0.786056 -133 TGTACAGGAAACACCGCTAAACCTCTAGAT 24 64 1 ACACCGCTAA 0.805247 -163 GCAAATTCACCTCTTTGACTGTTCTT 26 123 0 TCACCTCTTT 0.775842 -16 CCTCTACACCTCTTTGCACACGTTT 27 33 0 ACACCTCTTT 0.956438 -15 ********** Masking position 3 Map Score: 8.36875 Number of sites scoring better than the average of aligned sites = 152 Number in coding regions = 94 Number in noncoding regions = 58 Number of orfs with sites within 600 bp upstream = 63 Fraction of orfs with sites within 600 bp upstream = 0.0101189 Motif number 11 CTTCTTTTAAAGAGCTGCCACTTCATCGCG 4 41 0 AGAGCTGCCA 0.834433 -260 GTACGGAAATGGAGCGGCAAAACCGTTTTA 7 57 0 GGAGCGGCAA 0.96104 -69 TATTTTAATCGGAGCGGCAATTTTTTCATT 10 107 0 GGAGCGGCAA 0.96104 -194 CTAATTTGAAGCGGCTGCACGAGGGTATGG 14 89 1 GCGGCTGCAC 0.913628 -158 AACCAAGGGGAGGGCGGCCCTTTGGTTTTT 17 25 1 AGGGCGGCCC 0.960647 -239 AATTTTACTCGCAGCTGCCAAAAAGTGTGA 24 157 1 GCAGCTGCCA 0.893656 -70 TTTCCGAGTCCGGGCGGCCCGTACAGAAGA 25 188 0 CGGGCGGCCC 0.935218 -63 GCTGTTCTAATCAGCGGCACTTTTTTTATT 33 117 0 TCAGCGGCAC 0.882326 -184 GCTGATTAGAACAGCGGCACCATGGAATAA 33 132 1 ACAGCGGCAC 0.949863 -169 ********** Masking position 5 Map Score: 4.23054 Number of sites scoring better than the average of aligned sites = 456 Number in coding regions = 430 Number in noncoding regions = 26 Number of orfs with sites within 600 bp upstream = 32 Fraction of orfs with sites within 600 bp upstream = 0.00513974 Motif number 12 ACCATTTAAACATTATAACAAATTCACATAGC 1 217 0 CATTTACAAA 0.939644 -48 ACAAAACATACGTTCTATCATAAACCAAATCC 2 21 0 CGTTTACATA 0.916749 -41 AGGATTCCCCTATTATAGCATATTTTGCCCTT 3 199 0 TATTTACATA 0.818549 -102 AAACTGCTTACATTTTACCATACCCTCGTGCA 14 104 0 CATTTACATA 0.972607 -143 GGCTTGAGAGCATTGTATCAAAGCTTGAAGAG 15 58 1 CATTTACAAA 0.939644 -28 TTCTCGTGAACATTTTATCATACTGGAAAAGG 23 19 0 CATTTACATA 0.972607 -68 GACTGTTCTTCATTGTACCATAAAAACAGCCA 26 101 0 CATTTACATA 0.972607 -38 **** ** **** Masking position 7 Map Score: 3.87693 Number of sites scoring better than the average of aligned sites = 25 Number in coding regions = 5 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 27 Fraction of orfs with sites within 600 bp upstream = 0.00433665 Motif number 13 TGAATAACGAGATTAACGGCTTTTTCCGTTT 1 180 1 GATTACGGCT 0.924639 -85 AATTTGTTCACCCGCCTATACAAAAC 2 46 0 GTTCACCGCC 0.841113 -16 GAAAGCAGCCGTTTACAGGCTCGTTTTTTCT 3 233 0 GTTTAAGGCT 0.669847 -68 GAGTAAAACGGTTTTGCCGCTCCATTTCCGT 7 54 1 GTTTTCCGCT 0.720312 -72 GTTTAGAGGAGATGATCTGCCGTTTTCTTCT 8 209 0 GATGACTGCC 0.534574 -37 CTGAAAGTGAGTTGATCCGCT 14 236 1 GTTGACCGCT 0.948165 -11 CAGGCGAAATGTTTACCCGCCTTGAATATGA 16 28 1 GTTTACCGCC 0.95773 -110 CTTTGATCCTCTTTATCCGCTTGTCGTTAAG 17 233 0 CTTTACCGCT 0.684604 -31 AAGCCCGCTTGTTTAGCGGGCTTTTTTCCCT 18 16 0 GTTTACGGGC 0.75395 -140 GATGTTCATGGATGAACGGCTCGTCTCAAGT 25 14 1 GATGACGGCT 0.909858 -237 CTAAACAAGGGCTTAGCGGCTTTTCACATGA 30 40 0 GCTTACGGCT 0.9298 -120 CTAAGCCCTTGTTTAGCGGCTTGGTTTCTGC 30 55 1 GTTTACGGCT 0.968557 -105 GTATACCACTGCTGGTCGGCCCAGAAAAGAT 30 96 0 GCTGGCGGCC 0.655892 -64 ***** ***** Masking position 3 Map Score: 4.47969 Number of sites scoring better than the average of aligned sites = 572 Number in coding regions = 530 Number in noncoding regions = 42 Number of orfs with sites within 600 bp upstream = 38 Fraction of orfs with sites within 600 bp upstream = 0.00610344 Motif number 14 AAAGAATCAAAACACCTTTTTCAGTGAATAAC 1 156 1 AACACTTTTC 0.84622 -109 CCCCTATTATAGCATATTTTGCCCTTAAAAAA 3 193 0 AGCATTTTTC 0.786296 -108 GGTTTGTGCCATCACTTTTTTCGGATCGAGTT 4 191 0 ATCACTTTTC 0.864405 -110 TATCAGAGAAATCATGTTTTCTTAGGAGGATA 5 25 0 ATCATTTTTT 0.919343 -148 ACAAAAGTGTAACACGTTTTGTACGGAAATGG 7 75 0 AACACTTTTT 0.819096 -51 TAGATTAAAAAACATATTTTTTATTTTAATCG 10 126 0 AACATTTTTT 0.907739 -175 AAACCCTTGGATCATATTTTCTGTCAGACAAG 11 68 1 ATCATTTTTT 0.919343 -98 AATGTCATGTTTCATTTTTTTTCACGTCTG 15 9 0 TTCATTTTTT 0.769364 -77 AAGAGATCATAACATATTTTTTTCGTATCCGC 17 196 0 AACATTTTTT 0.907739 -68 ACGAGAAGTGAACATTTTTTACATGAGAAACC 23 44 1 AACATTTTTC 0.922826 -43 GAGACGCTGGATCATGTTCTTCTGTACGGGCC 25 171 1 ATCATTTCTC 0.668957 -80 CATTATCATTATCATATTTTATTTGCATTATC 31 86 0 ATCATTTTTT 0.919342 -149 TTTATGTTCTTACATGTTTTTTATCGATACTC 31 195 0 TACATTTTTT 0.742234 -40 TGTCCGATTCTTCATTTTTTACTATAATCAGA 33 248 1 TTCATTTTTC 0.802143 -53 ***** **** * Masking position 4 Map Score: 10.2861 Number of sites scoring better than the average of aligned sites = 274 Number in coding regions = 215 Number in noncoding regions = 59 Number of orfs with sites within 600 bp upstream = 75 Fraction of orfs with sites within 600 bp upstream = 0.0120463 Motif number 15 CGATACAGGACTCACCATGCAGGTACTGCC 1 103 1 CTCACCATGC 0.690703 -162 CCAATGCATTTTCTGCATCCGGACATTTCA 3 122 1 TTCTGCATCC 0.770618 -179 TGCCGTTTTCTTCTGCAAGCCAAAAAACCT 8 193 0 TTCTGCAAGC 0.967433 -53 TTAATCTAATTTCTCCAAGCATCACACAAA 10 150 1 TTCTCCAAGC 0.90048 -151 TATTCCTTTTTTCTGCATTCATGTACAATG 13 59 1 TTCTGCATTC 0.693882 -76 TTATTGTCAGCTCGGCATGCAAAAGACATG 14 186 1 CTCGGCATGC 0.767592 -61 TCAACTCACTTTCAGCATGAATTTCTGCAA 14 221 0 TTCAGCATGA 0.742824 -26 ATCTCCCTCTTCAAGCTTTGATACAA 15 70 0 CTCTTCAAGC 0.860877 -16 CGATACCCGCTTCTTCAGGCTCCTAAAGCC 16 62 1 TTCTTCAGGC 0.805351 -76 TAAGCCGGCTTTCTTCATGCTTTGAAATAA 17 69 0 TTCTTCATGC 0.939677 -195 ATAGCCGAGTTTCTTCATGAACGTGAAATC 17 100 1 TTCTTCATGA 0.738503 -164 ACAAGACTACTTCAGCAAGCTAGAGCATAT 21 93 1 TTCAGCAAGC 0.932214 -52 AGGATTACAATTCAGCAAGCTTGGGTACAT 28 17 1 TTCAGCAAGC 0.932214 -54 AGTAGCCTTCTTCTTCAAGACCAGATACAC 29 92 0 TTCTTCAAGA 0.709116 -146 ********** Masking position 7 Map Score: 10.0714 Number of sites scoring better than the average of aligned sites = 818 Number in coding regions = 762 Number in noncoding regions = 56 Number of orfs with sites within 600 bp upstream = 55 Fraction of orfs with sites within 600 bp upstream = 0.00883392