AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_ecoli.txt -z/home/amcguire/genomes/ecoli.fna -irpoH_ecoli_bsub_100.orf -g0.5 -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 = 0.5 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 dnaK 300 chaperone Hsp70; DNA biosynthesis; autoregulated heat shock proteins #2 dnaJ 88 chaperone with DnaK; heat shock protein #3 clpP 245 ATP-dependent proteolytic subunit of clpA-clpP serine protease, heat shock protein F21.5 #4 clpX 125 ATP-dependent specificity component of clpP serine protease, chaperone #5 lon 187 DNA-binding, ATP-dependent protease La; heat shock K-protein #6 htpG 109 chaperone Hsp90, heat shock protein C 62.5 #7 gapA 300 glyceraldehyde-3-phosphate dehydrogenase A #8 clpB 129 heat shock protein #9 grpE 122 phage lambda replication; host DNA synthesis; heat shock protein; protein repair #10 rpsU 237 30S ribosomal subunit protein S21 #11 dnaG 110 DNA biosynthesis; DNA primase #12 rpoD 194 RNA polymerase, sigma(70) factor; regulation of proteins induced at high temperatures #13 hflB 99 degrades sigma32, integral membrane peptidase, cell division protein #14 ftsJ 125 cell division protein #15 ibpA 230 heat shock protein #16 hslV 92 heat shock protein hslVU, proteasome-related peptidase subunit #17 ftsN 91 essential cell division protein #18 cytR 155 regulator for deo operon, udp, cdd, tsx, nupC, and nupG #19 mopB 275 GroES, 10 Kd chaperone binds to Hsp60 in pres. Mg-ATP, suppressing its ATPase activity #20 mopA 43 GroEL, chaperone Hsp60, peptide-dependent ATPase, heat shock protein #21 yacA 103 similar to cell-cycle protein #22 ftsH 97 cell-division protein and general stress protein (class III heat-shock) #23 ctsR 300 transcriptional regulator #24 groES 196 class I heat-shock protein (molecular chaperonin) #25 groEL 46 class I heat-shock protein (molecular chaperonin) #26 clpE 300 ATP-dependent Clp protease-like #27 topA 187 DNA topoisomerase I #28 gid 75 glucose-inhibited division protein #29 codV 67 integrase/recombinase #30 yocM 66 similar to small heat-shock protein #31 sigA 198 RNA polymerase major sigma-43 factor (sigma-A) #32 dnaG 33 DNA primase #33 yqxD 157 alternate gene name: yqfM; similar to hypothetical proteins #34 rpsU 163 ribosomal protein S21 #35 dnaJ 199 heat-shock protein #36 dnaK 23 class I heat-shock protein (chaperonin) #37 grpE 71 heat-shock protein #38 hrcA 119 transcriptional regulator #39 lonA 180 class III heat-shock ATP-dependent Lon protease #40 clpX 272 ATP-dependent Clp protease ATP-binding subunit (class III heat-shock protein) #41 gapB 205 glyceraldehyde-3-phosphate dehydrogenase #42 gap 46 glyceraldehyde-3-phosphate dehydrogenase #43 yvbQ 297 yvbQ #44 clpP 300 ATP-dependent Clp protease proteolytic subunit (class III heat-shock protein) #45 htpG 167 class III heat-shock protein (chaperonin) Motif number 1 CATTCATCAAAAAATTGTAATAAAAAGAAAAGATT 1 14 0 AAAAGAAAAA 0.69572 -287 AAATTTCTGCGCAAAAGCACAAAAAATTTTTGCAT 1 120 1 GCAAGAAAAA 0.629015 -181 AATTTTGCATGGAACCGTGCGAAAAGCCTCTTTCG 3 83 1 GGAAGGAAAA 0.799742 -163 TTCAACGCCGAGAATAGAGGAAAAATTAAAGGGGA 5 58 0 AGAAGGAAAA 0.633385 -130 TGGCTGCACCTAAATCGTGATGAAAATCACATTTT 7 73 1 TAAAGGGAAA 0.73581 -228 ATTTTAAAGGGCAATTACGATAAAAATGTGATTTT 7 95 0 GCAAAGAAAA 0.390537 -206 TGAATGCGAAAAAAACGCGGAGAAATTC 9 105 1 AAAAGGGAAA 0.830024 -18 TGCGCGGTAATAAAGCGAGGTAAAACAAGTC 10 7 0 TAAAGGAAAA 0.854582 -231 CAAAGCAGCAGCAATTGCAGTAAAATTCCGCACCA 10 152 1 GCAAGAAAAA 0.629015 -86 ACCTCTTATTACAACTGTGTTAAAAACAGCGTCAG 13 59 0 ACAAGGAAAA 0.767735 -41 CAATAGACCATAAACTGCAAAAAAAAGTCCGCTGA 15 70 1 TAAAGAAAAA 0.565989 -161 ATTTTTAGCAGATAGCGCGTGAAAACGGTTACAGA 18 71 0 GATAGGAAAA 0.542519 -85 CGGCGATGAAGAAATTGCGATGAAATGTGAGGTGA 19 89 1 GAAAGGGAAA 0.918618 -187 TGATCAGCACAAAATCGGGTGAAAACCCTGATTCA 19 121 0 AAAAGGAAAA 0.911533 -155 CTTCAAGGGGGAAAAAGAAAAAAAATTCTGATCAG 19 149 0 GAAAGAAAAA 0.840897 -127 AAGCTAACGGAAAAGGGAGCGGAAAAGAATGATGT 24 85 1 AAAAGGGAAA 0.830024 -112 TCAGCACTAAAGAGTGCTAACACAATTCTTAT 24 175 0 TAAAGGAACA 0.453447 -22 TCCTTGAAAAGACGAAGAAAACATGTTTTA 26 6 1 GAAAAGGAAA 0.486298 -295 TTTGACCAATGAAAGTGAATAAAAAGGTCTATTGG 26 245 0 GAAAGAAAAA 0.840897 -56 AAATATCTTGAAAAGAGAGAGAACACCTCTTGAGG 27 154 1 AAAAGGAACA 0.592605 -34 ATTATAATAAAAAATTGTGATAAAATGATTAATTT 33 89 1 AAAAGGAAAA 0.911533 -69 TTGCCCGGGATAAAAGGAATTGAAAAATCATAATT 35 125 1 TAAAGAGAAA 0.381971 -75 AACTCACCCAAAAAAAGCGCCAAAAACTTCATTGC 38 11 0 AAAAGGAAAA 0.911533 -109 CGTCTTTTTGGAAAGTATGGTAAAATGCAATACAT 40 171 1 GAAAAGAAAA 0.666383 -102 GCCGGTAAAAGAAAAAGTGAGACAAGATTAAGGGG 40 241 1 GAAAGGACAA 0.637369 -32 TATTTTTGGGGAAAATGGGAAAAAGAGACGACTTT 44 186 1 GAAAGGAAAG 0.637369 -115 GAATGAGTGAGAAAAAGAGTGAAAACAAATCCAAC 45 32 1 GAAAGGAAAA 0.959706 -136 **** * * **** Masking position 4 Map Score: 23.1197 Number of sites scoring better than the average of aligned sites = 791 Number in coding regions = 617 Number in noncoding regions = 174 Number of orfs with sites within 600 bp upstream = 183 Fraction of orfs with sites within 600 bp upstream = 0.0293929 Motif number 2 CAAAATTCATGACAAAAAAAAGCCCACCACCTGG 3 56 0 GCAAAAAACC 0.953011 -190 ACCATAAACTGCAAAAAAAAGTCCGCTGATAAGG 15 76 1 GAAAAAAGCC 0.8113 -155 ATCATTCCAATACAAACAATAACCATCTCGGAAG 22 22 0 TCAAAAAACC 0.743563 -76 TAAGATTAAAGTCAAATATAGTCAAAGTCAGTAA 23 264 1 GCAAAATGCA 0.929217 -37 AGACTTGAAAGTCAAAGATAGTCAGAGTATACTA 26 72 1 GCAAAATGCA 0.929217 -229 AAATCAATTGGTCAAAGATAGTCAAATATTCAGT 26 143 1 GCAAAATGCA 0.929217 -158 TATACTAATAGTCAAAGAAGGTCAAACCCAATAG 26 218 1 GCAAAAAGCA 0.975927 -83 ACTTTCATTGGTCAAAGATGATCAAATTATTAAG 26 264 1 GCAAAATACA 0.852331 -37 AATGTTGAAAGCCAAATAAAGACAGCTGCAAAAA 27 112 1 GCAAAAAGCA 0.975927 -76 AGGGAATAATGAAAAACAATAGCATCTTTGTGAA 33 49 1 GAAAAAAACA 0.624254 -109 TTCATCCTTGTACAATAAACGGCATGGTTCCATT 39 108 0 TCAATAAGCA 0.466525 -73 CTATATGTATGACAAAAAACAGCCCTGCATTAAC 40 109 0 GCAAAAAACC 0.953011 -164 TCCCGTCATAGCCAAAAAAAATCATTTCTGCTTT 43 215 0 GCAAAAAACA 0.946878 -83 GTCCCGCTATGACAAAAAACGTCCCGTCATAGCC 43 236 0 GCAAAAAGCC 0.978781 -62 GTCATAGCGGGACATATAATGTCCAGCAAAAAAG 43 257 1 GCATAAAGCC 0.787457 -41 GATAATTCCTTTCAAATAACAACCCTCTATTTCG 44 84 1 TCAAAAAACC 0.743563 -217 TACATTTTTGGTCAATAAAGGTCAAACAAAAAGC 44 234 0 GCAATAAGCA 0.859487 -67 * **** ** * ** Masking position 8 Map Score: 19.9293 Number of sites scoring better than the average of aligned sites = 319 Number in coding regions = 282 Number in noncoding regions = 37 Number of orfs with sites within 600 bp upstream = 42 Fraction of orfs with sites within 600 bp upstream = 0.0067459 Motif number 3 AAATTTTTGCATCTCCCCCTTGATGACGTGG 1 143 1 ATCCCCCCTT 0.970659 -158 AACCAGACGTTTCGCCCCTATTACAGACTCA 1 241 1 TTCCCCCTAT 0.892701 -60 GGGAGATAAAATCCCCCCTTTTTGGTTAACT 5 31 0 ATCCCCCTTT 0.953647 -157 GGGGGATTTTATCTCCCCTTTAATTTTTCCT 5 45 1 ATCCCCCTTT 0.953647 -143 ATGGGGATGTTTCCCCCACATTCAACGCCGA 5 82 0 TTCCCCACAT 0.672953 -106 CCTTGTCCCCATCTCTCCCACATCCTGTTTT 6 55 1 ATCCTCCCAC 0.749709 -55 TTCTACCGCCATCTCCCATATATCACCAAAT 14 48 1 ATCCCCATAT 0.619733 -78 AACCCTCAAAATCCCCCCCATCTATAATTGC 16 11 1 ATCCCCCCAT 0.944563 -82 TTTTTTTTCTTTTTCCCCCTTGAAGGGGCGA 19 159 1 TTTCCCCCTT 0.578592 -117 GGGATGAGGCTTCGCCCCTTCAAGGGGGAAA 19 170 0 TTCCCCCTTC 0.907099 -106 CGTTAGCTTTTTCACCCCCGTACCGATTATG 24 63 0 TTCCCCCCGT 0.83027 -134 TATGGATCCCTCCTTCCAAAGCTTGC 31 183 0 ATCCTCCTTC 0.783399 -16 TCTCTTTCCCTCCCTCCGAATACACC 34 148 0 TTCCTCCCTC 0.820353 -16 TCTTTCACCCCTTAATCTTGTCTC 40 259 0 TTCCCCCTTA 0.651694 -14 CAATATAAATATCTCTCACTTATTTAAAGGA 42 16 1 ATCCTCACTT 0.596756 -31 TCTTGATCGCTCCTTTACCATTATGT 45 152 0 ATCCTCCTTT 0.856807 -16 *** ******* Masking position 2 Map Score: 13.5774 Number of sites scoring better than the average of aligned sites = 341 Number in coding regions = 279 Number in noncoding regions = 62 Number of orfs with sites within 600 bp upstream = 56 Fraction of orfs with sites within 600 bp upstream = 0.00899454 Motif number 4 AGACCCATTTTTACATCGTAGCCGATGAGGACGCG 15 128 1 TTATGTACCA 0.797727 -103 TGCGTAGATTTTCGATGGTAGCACAATCAGATTCG 19 47 1 TTATGTACAA 0.958287 -229 CACAACTATGTTCAATAGTACCATAGAAAATCATT 22 50 0 TTATGTACAA 0.958287 -48 TGTATTTTGGTTTATTGGTATCATAAAATTCCACT 23 104 1 TTTTGTACAA 0.922567 -197 GTGAAAAATTTTTTATCTTATCACTTGAAATTGGA 24 124 1 TTATTTACAT 0.643245 -73 AAAACATGTTTTACTTTGTAACAAATCAAAAATTT 26 28 1 TTTTGTACAA 0.922569 -273 GGAAGGGCTTTTAAATGGTATCACAAATCGCGCTC 29 27 0 TTATGTACAA 0.958287 -41 CCCATAATAGTTTATTCGTATCACACGATCCTTAA 33 129 0 TTTTGTACAA 0.922567 -29 CTCACATAAATTAGATTGTATCATTTTGAATTATG 35 153 0 TTATGTACAT 0.890922 -47 CGAGTATGTATTGCATTTTACCATACTTTCCAAAA 40 176 0 TTATTTACAA 0.835294 -97 GTTATAATCGTTGATTTTTATCAATATGTACTGGC 41 105 1 TTTTTTACAT 0.483245 -101 TATACTAATTTTAGATAGTAACAAATTAGGATGGC 41 158 1 TTATGTACAA 0.951905 -48 ** ** *** ** * Masking position 10 Map Score: 9.68456 Number of sites scoring better than the average of aligned sites = 20 Number in coding regions = 12 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 5 GCAAACGAGAGCAGGATCACCTGCT 6 5 1 AGAGAGCAGG 0.644804 -105 ATAATTTCAAGCGAGAGCAGGTGATCCTGCT 6 20 0 GGAGAGCAGG 0.740564 -90 ACCAGAGAAATGGGGATGAGGCTTCGCCCCT 19 182 0 TGGGATGAGG 0.709221 -94 TACCTGCTCATTGTGAGGAGGACATT 21 88 1 TGTGAGGAGG 0.924028 -16 AATAACCATCTCGGAAGCAGGCTGCCGA 22 8 0 TGGAAGCAGG 0.91227 -90 TGTGCTTACTGTGGGAGGAGGTAAGGA 22 81 1 GGGGAGGAGG 0.960157 -17 AGTCAAAGTCAGTAAAGGAGGGGGTTGA 23 283 1 ATAAAGGAGG 0.729078 -18 TACTTAAAACATTTGAGGAGGTCTTGTAAAC 25 26 1 ATTGAGGAGG 0.645359 -21 ATGATCAAATTATTAAGGAGGTTTTGGCAA 26 281 1 TTTAAGGAGG 0.825123 -20 CATACAACTATAGAAAGGAGGTTTGCCT 30 8 0 TGAAAGGAGG 0.947331 -59 GTTGCAAGCTTTGGAAGGAGGGATCCATA 31 180 1 TGGAAGGAGG 0.975452 -19 ATTGGTGTATTCGGAGGGAGGGAAAGAGA 34 145 1 TGGAGGGAGG 0.914292 -19 CTCCTTACACTTTGAGGGAGGTGAACACA 37 53 1 TTGAGGGAGG 0.817824 -19 CTCTCACTTATTTAAAGGAGGAAACAATC 42 28 1 TTAAAGGAGG 0.883303 -19 TTACCTAAAAGGTGAAGGAGGAGCATT 44 284 1 GTGAAGGAGG 0.903368 -17 * ********* Masking position 9 Map Score: 10.2706 Number of sites scoring better than the average of aligned sites = 117 Number in coding regions = 82 Number in noncoding regions = 35 Number of orfs with sites within 600 bp upstream = 43 Fraction of orfs with sites within 600 bp upstream = 0.00690652 Motif number 6 ATTCTCAGGCGCAAGCCGCTTACAGCGTTGTG 4 52 0 GAAGCCGCTA 0.900343 -74 TGGCGTTGATGCCAGCGGCAAACCGAATTAAT 10 200 1 GCAGCGGCAA 0.901398 -38 AGAGCGATCGGGAAGCCCCCGACAGCCGCACT 12 31 1 GAAGCCCCGA 0.950589 -164 CGCACTGAGAGGCAGCGGCAAATATATAAGTA 12 57 1 GCAGCGGCAA 0.901398 -138 TAGCCGATGAGGACGCGCCTGATGGGTGTTCT 15 146 1 GACGCGCCGA 0.906977 -85 CTGGTCAAAGGCCCGCCGCTTAAGTAACATGG 17 35 1 GCCGCCGCTA 0.842503 -57 CCAAATTTTGGGCAACTGCGTAGATTTTCGAT 19 31 1 GCAACTGCTA 0.575063 -245 ATGGTGCAAACTGCAGAGCCTATGCTT 21 6 1 GAAACTGCGA 0.789924 -98 CATCTCGGAAGCAGGCTGCCGA 22 1 0 GAGGCTGCGA 0.689388 -97 TCTCACAGGGGGAAACCCCCGACTACCATCGG 23 22 0 GAAACCCCGA 0.848378 -279 TGTGAGAGTAGGACGCCGCCAAGCAAGCTTAA 23 47 1 GACGCCGCAA 0.870598 -254 GCCAAATAAAGACAGCTGCAAAAATAAAATTG 27 122 1 GCAGCTGCAA 0.851469 -66 AGTTCACATAGAAAACGCCTGAATGGACCGAA 31 122 1 GAAACGCCGA 0.824297 -77 GTTCTTTTCGGTCAGCTCCGGAAGCGGGGCTG 35 25 0 GCAGCTCCGA 0.908328 -175 GTTGGACACCCCTTATCAATTATGC 41 191 0 GACACCCCTA 0.554087 -15 ATCTTATACAGAAAGCGCCAAATGGTGCATCC 43 60 0 GAAGCGCCAA 0.879538 -238 * ******* ** Masking position 12 Map Score: 9.20292 Number of sites scoring better than the average of aligned sites = 1244 Number in coding regions = 1180 Number in noncoding regions = 64 Number of orfs with sites within 600 bp upstream = 57 Fraction of orfs with sites within 600 bp upstream = 0.00915516 Motif number 7 ATTTTTGCATCTCCCCCTTGATGACGTGGT 1 145 1 CTCCCCCTTG 0.970552 -156 GGGTCAAAACCTCTTCTTTGTTCTTTGTGC 4 106 0 CTCTTCTTTG 0.846415 -20 GGGATTTTATCTCCCCTTTAATTTTTCCTC 5 47 1 CTCCCCTTTA 0.741005 -141 GGTGATCCTGCTCTCGTTTGC 6 2 0 CTCTCGTTTG 0.8429 -108 GGATCACCTGCTCTCGCTTGAAATTATTCT 6 24 1 CTCTCGCTTG 0.895698 -86 CTTGAAATTATTCTCCCTTGTCCCCATCTC 6 40 1 TTCTCCCTTG 0.927995 -70 GTGTATACTCCTCACCCTTATAAAAGTCCC 10 97 1 CTCACCCTTA 0.744393 -141 GTGCCTCTCACCTTTGATTAATTCGG 10 222 0 CTCACCTTTG 0.929056 -16 TTTTTTCTTTTTCCCCCTTGAAGGGGCGAA 19 161 1 TTCCCCCTTG 0.914019 -115 TGATAACTCTCCTTTGAGAAAGTCCG 19 260 0 CTCTCCTTTG 0.961487 -16 GAGCCTATGCTTCTTCTTTGCTTGGAGGGG 21 26 1 TTCTTCTTTG 0.63997 -78 ATACAACTTTTTCATCCTTGTACAATAAAC 39 122 0 TTCATCCTTG 0.598782 -59 ********** Masking position 8 Map Score: 8.82184 Number of sites scoring better than the average of aligned sites = 205 Number in coding regions = 158 Number in noncoding regions = 47 Number of orfs with sites within 600 bp upstream = 53 Fraction of orfs with sites within 600 bp upstream = 0.00851269 Motif number 8 CCATTTAGTAGTCAACCGCAGTGAGTGAGTC 1 183 1 GTCACCGCAG 0.870046 -118 ACAAAGGCCCGTCACCGCCAGGTGGTGGGCT 3 39 1 GTCACGCCAG 0.978733 -207 TGCCGCTGGCATCAACGCCAGCTTATTTCAA 10 189 0 ATCACGCCAG 0.767557 -49 TGGCGTTGATGCCAGCGGCAAACCGAATTAA 10 200 1 GCCACGGCAA 0.802333 -38 CGCACTGAGAGGCAGCGGCAAATATATAAGT 12 57 1 GGCACGGCAA 0.881935 -138 GTCAAATATAGTCAAAGTCAGTAAAGGAGGG 23 274 1 GTCAAGTCAG 0.900861 -27 GTCAAAGAAGGTCAAACCCAATAGACCTTTT 26 228 1 GTCAACCCAA 0.842137 -73 TTCGCACATTGTTAAAGGCAGTTCACATAGA 31 103 1 GTTAAGGCAG 0.658652 -96 ATTCCCTTTTGGCACAGCCAAAAACCCAGGA 33 25 0 GGCAAGCCAA 0.905002 -133 TGATTAGAAAGTCAAAGTCAGGCATCTCTTG 35 78 1 GTCAAGTCAG 0.900861 -122 AAGAAAAAAAGTCAAAGCCAAGAGATGCCTG 35 96 0 GTCAAGCCAA 0.961273 -104 AAAACGTCCCGTCATAGCCAAAAAAAATCAT 43 224 0 GTCAAGCCAA 0.961273 -74 **** ****** Masking position 4 Map Score: 6.07318 Number of sites scoring better than the average of aligned sites = 1019 Number in coding regions = 985 Number in noncoding regions = 34 Number of orfs with sites within 600 bp upstream = 35 Fraction of orfs with sites within 600 bp upstream = 0.00562159 Motif number 9 GTTATGGGTACGGCATCACCATATTTCAAG 3 148 0 CGGCATCACC 0.907136 -98 TACTTATCCAGGGCGGCACAACGCTGTAAG 4 36 1 GGGCGGCACA 0.889565 -90 CTCGACGAAATGGCTGCACCTAAATCGTGA 7 63 1 TGGCTGCACC 0.838904 -238 AGGGTTTCAAGGGAAGCACTCACATTGTCA 9 40 0 GGGAAGCACT 0.858567 -83 GCATTCCTTTCGGAAGCACGGCCTTACAAC 11 50 0 CGGAAGCACG 0.895102 -61 AAGAGCGATCGGGAAGCCCCCGACAGCCGC 12 30 1 GGGAAGCCCC 0.906964 -165 TAGACTGAGGGGGCAGCACGAAACGTTAAA 15 38 0 GGGCAGCACG 0.974873 -193 ACGTAAGCTCCGGCGTCACCCATAACAGAT 19 229 1 CGGCGTCACC 0.846916 -47 TTTTATCGAAGGGCAGCACCTGTCCTTCTC 37 26 1 GGGCAGCACC 0.990962 -46 TGTTTATATTGGGATGCACCATTTGGCGCT 43 49 1 GGGATGCACC 0.944852 -249 ********** Masking position 7 Map Score: 5.53932 Number of sites scoring better than the average of aligned sites = 397 Number in coding regions = 376 Number in noncoding regions = 21 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911 Motif number 10 ATTAGTTAACCAAAAAGGGGGGATTTTATCT 5 28 1 CAAAAAGGGG 0.876883 -160 TATTCACTAACAAATAGCTGGTGGAATAT 7 282 1 CAAATAGCGG 0.866669 -19 CACCATTTTGAAATAAGCTGGCGTTGATGCC 10 182 1 AAATAAGCGG 0.707425 -56 TCATAAACGAAAATAAGCCGCGCATTCCTTT 11 70 0 AAATAAGCGC 0.646327 -41 CCGACAGCCGCACTGAGAGGCAGCGGCAAAT 12 49 1 CACTGAGAGC 0.633341 -146 CATATATCACCAAATAGGCGCGTAAAAATTT 14 64 1 CAAATAGGGC 0.59942 -62 GTCCTCCTCACAATGAGCAGGTATTTTAAAG 21 80 0 CAATGAGCGG 0.91647 -24 AAACCCAGCTCAATGAGCTGGGTTTTTTGTA 23 77 1 CAATGAGCGG 0.91647 -224 TCTTTTAACACACAAAGAAGGTGAGCAAGAC 28 22 0 CACAAAGAGG 0.829666 -54 ATACAAACTTCACAAAGATGCTATTGTTTTT 33 60 0 CACAAAGAGC 0.786388 -98 CCATACTTTCCAAAAAGACGGTAACAATGTG 40 160 0 CAAAAAGAGG 0.913677 -113 GCGTAAGAACCAAAAAGCAGCCAGCGCTCCG 41 30 0 CAAAAAGCGC 0.946447 -176 AAAGGTCAAACAAAAAGCTGGCCTGATATGC 44 221 0 CAAAAAGCGG 0.958989 -80 ATTCTCATAAAAAAGAGAGGCTTCA 45 5 0 AAAAGAGAGC 0.544029 -163 ******** ** Masking position 6 Map Score: 4.85986 Number of sites scoring better than the average of aligned sites = 638 Number in coding regions = 583 Number in noncoding regions = 55 Number of orfs with sites within 600 bp upstream = 55 Fraction of orfs with sites within 600 bp upstream = 0.00883392 Motif number 11 TGACACGGGCGAAGGGGAATTTCCTCTCCGCC 2 36 1 GAAGGGGATT 0.913207 -53 CCCCGAATTTTAAAGGGCAATTACGATAAAAA 7 104 0 TAAAGGGCTT 0.730951 -197 GGCCTTTTTTGAAAGGGACTTTTATAAGGGTG 10 109 0 GAAAGGGATT 0.955605 -129 AATTATAGATGGGGGGGATTTTGAGGGTT 16 8 0 GGGGGGGATT 0.82847 -85 ACTTGAAATTGGAAGGGAGATTCTTTATTATA 24 146 1 GGAAGGGATT 0.9769 -51 TACCTCCCCAGGAAGGGCTTTTAAATGGTATC 29 40 0 GGAAGGGCTT 0.981964 -28 CCTTCCCGTAGAAAGGGCTGTTTCATTAAAGC 43 15 0 GAAAGGGCTT 0.965172 -283 CCTTTCTACGGGAAGGGCTGTTTATATTGGGA 43 31 1 GGAAGGGCTT 0.981965 -267 CAGCAAAAAAGGAAGGAACGTTTGAGTC 43 280 1 GGAAGGAATT 0.805673 -18 ******** ** Masking position 11 Map Score: 5.22293 Number of sites scoring better than the average of aligned sites = 99 Number in coding regions = 83 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 12 CCATATCGCGAAATTTCTGCGCAAAAGCACAA 1 110 1 AAATCTGCGC 0.588533 -191 ATTGCCCTTTAAAATTCGGGGCGCCGACCCCA 7 115 1 AAATCGGGGC 0.924897 -186 ATGAATGCGAAAAAAACGCGGAGAAATTC 9 104 1 AAAACGCGGA 0.615023 -19 AGTCCCTTTCAAAAAAGGCCGCGGTGCTTTAC 10 121 1 AAAAGGCCGC 0.962773 -117 TTCATAAACGAAAATAAGCCGCGCATTCCTTT 11 70 0 AAAAAGCCGC 0.742798 -41 ATGAATTGCTAAAAATCGGGGCCT 11 97 1 AAATCGGGGC 0.924897 -14 TAAACTGCAAAAAAAAGTCCGCTGATAAGGCT 15 80 1 AAAAGTCCGC 0.750233 -151 ACCCCGTACAAAAGTACGGGGCATAATGCAAT 16 37 0 AAAACGGGGC 0.967169 -56 CAGTTGCCCAAAATTTGGGCGCAATCGGACAT 19 17 0 AAATGGGCGC 0.93466 -259 CAAAGTCAGTAAAGGAGGGGGTTGA 23 286 1 AAAAGGGGGT 0.710582 -15 ATTGATTTTTAAAAAAGGCCGGTTTGTTTGAC 26 119 0 AAAAGGCCGG 0.733354 -182 AAAGTATGTTAAGACAGGGGGCTTCAA 30 50 1 AAGAGGGGGC 0.833097 -17 TAGTACTAATAAAACAGGGCGCGAATCATTCG 40 26 1 AAAAGGGCGC 0.971605 -247 TTGCTGGATAAAACGACGCGGCATGAAAACTC 43 113 1 AAAACGCGGC 0.957017 -185 *** ******* Masking position 2 Map Score: 7.88458 Number of sites scoring better than the average of aligned sites = 519 Number in coding regions = 452 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 13 CAAAGAAGAGGTTTTGACCC 4 116 1 GTTTTGACCC 0.775399 -10 TTCTGTAACCGTTTTCACGCGCTATCTGCT 18 70 1 GTTTTCACGC 0.964563 -86 GTGAATCAGGGTTTTCACCCGATTTTGTGC 19 120 1 GTTTTCACCC 0.970117 -156 ATTTTTTTTCTTTTTCCCCCTTGAAGGGGC 19 158 1 TTTTTCCCCC 0.808793 -118 TTCCGTTAGCTTTTTCACCCCCGTACCGAT 24 67 0 TTTTTCACCC 0.953014 -130 AGATAAAAAATTTTTCACGCTTACATCATT 24 112 0 TTTTTCACGC 0.944463 -85 GCTTTGACTTTTTTTCTTGCCCGGGATAAA 35 109 1 TTTTTCTTGC 0.576447 -91 ATAATACAACTTTTTCATCCTTGTACAATA 39 125 0 TTTTTCATCC 0.86741 -56 TCTTTCACCCCTTAATCTTG 40 263 0 TCTTTCACCC 0.776882 -10 TGCATCTTATGTTTTCTTGCACAGAATATC 41 63 0 GTTTTCTTGC 0.685368 -143 TATTCGCAGAGTTTTCATGCCGCGTCGTTT 43 123 0 GTTTTCATGC 0.897743 -175 AGTTGGATTTGTTTTCACTCTTTTTCTCAC 45 38 0 GTTTTCACTC 0.808093 -130 ********** Masking position 5 Map Score: 7.96493 Number of sites scoring better than the average of aligned sites = 312 Number in coding regions = 273 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 14 ACCGCGCAGTGTAGGACCAATGCGGGTTGA 10 34 1 GTAGGACCAA 0.769558 -204 AGCGGCGGGCCTTTGACCAGTCACGGCAGT 17 25 0 CTTTGACCAG 0.8427 -67 AGGCCGGTTTGTTTGACCAACTTTGATTAA 26 106 0 GTTTGACCAA 0.952764 -195 ATTTGACTATCTTTGACCAATTGATTTTTA 26 140 0 CTTTGACCAA 0.952764 -161 ATTTGATCATCTTTGACCAATGAAAGTGAA 26 261 0 CTTTGACCAA 0.952764 -40 ATTATCGTTTGACAAACGGTATTGTA 27 7 1 GTTTGACAAA 0.887441 -181 CATTCTATATGTATGACAAAAAACAGCCCT 40 117 0 GTATGACAAA 0.830929 -156 ATATGTCCCGCTATGACAAAAAACGTCCCG 43 244 0 CTATGACAAA 0.830929 -54 ********** Masking position 6 Map Score: 2.7398 Number of sites scoring better than the average of aligned sites = 35 Number in coding regions = 32 Number in noncoding regions = 3 Number of orfs with sites within 600 bp upstream = 4 Fraction of orfs with sites within 600 bp upstream = 0.000642467 Motif number 15 ATGGGTACGGCATCACCATATTTCAAGCAT 3 145 0 CATCACCATA 0.821349 -101 TTAACCATTCCCATACAATTAGTTA 5 6 1 CATTCCCATA 0.938912 -182 GTGGGGGAAACATCCCCATATACTGACGTA 5 94 1 CATCCCCATA 0.979122 -94 CCCTGAAACTGATCCCCATAATAAGCGAAG 9 66 1 GATCCCCATA 0.872025 -57 GGCGAAGCCTCATCCCCATTTCTCTGGTCA 19 185 1 CATCCCCATT 0.936787 -91 CATAGAAAATCATTCCAATACAAACAATAA 22 34 0 CATTCCAATA 0.834362 -64 TCAATTATGCCATCCTAATTTGTTACTATC 41 171 0 CATCCTAATT 0.488858 -35 CCAAATGGTGCATCCCAATATAAACAGCCC 43 45 0 CATCCCAATA 0.938912 -253 TTTTCTCACTCATTCTCATAAAAAAGAGAG 45 17 0 CATTCTCATA 0.751647 -151 ********** Masking position 3 Map Score: 4.55868 Number of sites scoring better than the average of aligned sites = 177 Number in coding regions = 150 Number in noncoding regions = 27 Number of orfs with sites within 600 bp upstream = 29 Fraction of orfs with sites within 600 bp upstream = 0.00465789