AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/alignace/lib/ORF_synecho.txt -z/skink1/amcguire/genomes/synecho.fna -irpoH_synecho_opreg_100.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 ftsH 165 cell division protein FtsH #2 dnaK 134 DnaK protein #3 ftsH 100 cell division protein FtsH #4 groES 113 10kD chaperonin #5 groEL 96 60kD chaperonin 1 #6 ftsH 131 cell division protein FtsH #7 gap1 300 glyceraldehyde 3-phosphate dehydrogenase #8 rpoD 300 RNA polymerase sigma factor #9 1652838 300 RNA polymerase sigma factor #10 dnaG 152 DNA primase #11 clpB 283 ClpB #12 clpB 300 ClpB protein #13 clpP 300 ATP-dependent Clp protease proteolytic subunit #14 1653656 99 ATP-dependent Clp protease proteolytic subunit #15 rpoD 300 RNA polymerase sigma factor #16 dnaK 205 DnaK protein #17 rps21 300 30S ribosomal protein S21 #18 clpC 300 ATP-dependent Clp protease regulatory subunit #19 ftsH 273 cell division protein FtsH #20 1001603 53 hypothetical protein #21 ycf43 300 hypothetical protein #22 groEL-2 162 60kD chaperonin 2 #23 dnaK 233 DnaK #24 grpE 217 heat shock protein GrpE #25 rpoD 300 RNA polymerase sigma factor #26 1001348 201 hypothetical protein #27 clpP 79 ATP-dependent protease ClpP #28 dnaJ 106 DnaJ #29 1001377 299 ATP-dependent Clp protease proteolytic subunit #30 gap2 254 glyceraldehyde-3-phosphate dehydrogenase (NADP+) (phosphorylating) #31 rpoDI 300 RNA polymerase sigma factor #32 htpG 300 heat shock protein Motif number 1 GCCCATTGGTTGGGGTTTTATGGTCTAGGTTGAAG 2 60 1 TGGGGTTGGC 0.986705 -75 TATAGGAGTTTGGGGCGGGACCCTGGGCAAACTTC 2 91 0 TGGGGGCCCG 0.812884 -44 CGTGGTTACCTGGGGAATAATTGGCAACAATGGTC 7 179 0 TGGGGTTTGC 0.986217 -122 CAAGCTTTATGGGGGATTTTTGCGTTTTTTATTG 8 10 1 TGGGGTTTGG 0.958225 -291 GGACGATTGATGGGGAATGACTGGGATCAATCCAC 8 131 0 TGGGGTCTGG 0.949477 -170 GCCTGTCCGATGGGGGCGTTTGGGACAACTGGAAA 8 167 0 TGGGGGTGGA 0.852043 -134 AAAGGGGCTTTGGGGCCTAGTTGAATGGCACAAAT 11 58 1 TGGGGTTTGA 0.899661 -226 ATCAATTTTAGGGGGTGGAATCCGGAGCTAGGAAG 11 217 0 GGGGGGTCCG 0.766623 -67 GCTTAGTCATTGGGGGTTCCTTGCCGGGGGACGCT 13 94 1 TGGGGTTTGC 0.986217 -207 GTTCCTTGCCGGGGGACGCTTGGGAACTCGCGATC 13 109 1 GGGGGGTGGA 0.780986 -192 TTACGTTCTGGGGGGCCGCTTTGCCCTAGGGAAAC 13 168 1 GGGGGGTTGC 0.964832 -133 TTTGACCTAAGGGGGCTTGGTTGGCAGGAAAGAAT 14 20 0 GGGGGTTTGC 0.977929 -80 GGTTCTAGGCTGGGGCGTTACCGCCGAAACCAATA 15 130 0 TGGGGTCCGC 0.981007 -171 TAGTGACGGTAGGGGCTTAGTTCTCGGAAGTGCAG 16 76 0 AGGGGTTTCC 0.809117 -130 GACGATACTCTGGGGGTTGCCCCACGGCACAATAG 17 20 1 TGGGGTCCCC 0.956081 -281 CCATTTTACTTGGGGAGCTTTTGGCCATATTAAAG 17 93 1 TGGGGCTTGC 0.940033 -208 ACTGCGTCTGTGGGGTTTTCCTCACCTCAACCGCC 18 161 0 TGGGGTCTCC 0.960814 -140 GGATTTAAATGGGGGAGTAACGGACGTTTAATGC 22 10 0 GGGGGTCGGC 0.974128 -153 TCAGTCATTTTGGGGGACATTCCACTGTCCCTCGT 23 14 1 TGGGGCTCCC 0.854064 -220 GATGGCCAAGTGGGGCTTAATGGTCTAAATTTGCA 23 143 1 TGGGGTTGGC 0.986705 -91 AACAGTTTGTAGGGGCAGCGCCGACAAAAAAATAG 25 218 1 AGGGGGCCGC 0.821141 -83 GATGCGGAGGTGGGGATTTCTGGGCAACCATCTGG 28 11 1 TGGGGTTGGC 0.986705 -96 CTTGAGCCTTGGGGGACTAACGCCCTAGGACAGGG 29 122 0 GGGGGTCGCC 0.938398 -178 AACAAAAAAATGGGGCTTAATTGTGGTCTGACCAC 31 34 0 TGGGGTTTGG 0.958225 -267 ***** * *** * Masking position 5 Map Score: 42.2254 Number of sites scoring better than the average of aligned sites = 873 Number in coding regions = 788 Number in noncoding regions = 85 Number of orfs with sites within 600 bp upstream = 98 Fraction of orfs with sites within 600 bp upstream = 0.0157404 Motif number 2 CTATAATGGTTGGGCAAGTGCCTA 2 121 1 TGGGCATGCT 0.833735 -14 CAAGCTATCATGGGGGTTGGAGTTTTTCCCCTC 3 49 1 TGGGGGGGAT 0.894063 -52 CAGTAGTAATTTGGGAGAGGGTTTAGCACTCCC 4 66 0 TTGGGAGGGT 0.64299 -48 GTCTAGGGCTTGGGGATTGGAGTC 6 2 0 TGGGGAGGAT 0.975259 -130 AGGGATATGATGGGGAAAGGCCGATCAACCCGA 6 69 1 TGGGGAGGCG 0.961497 -63 AAGAAAAATCTGGCGATCGGGTTGATCGGCCTT 6 85 0 TGGCGAGGGT 0.933612 -47 AATCTTTCCTTGGCGATCGCCGTGGTTACCTGG 7 201 0 TGGCGAGCCT 0.977955 -100 CCCAGCTCCTTGGCCGCAGGATTAGGGAGAATG 7 248 0 TGGCCGGGAT 0.807469 -53 TAAGTAATGGTGGCGATCGCCCTGTTGCTTCAT 13 15 0 TGGCGAGCCT 0.977896 -286 ACGCTTAAATTTGGGAAGGGAATTTGGCTACAT 14 69 0 TTGGGAGGAT 0.824336 -31 TAAAAAAAATTGACGACTGCACTACCCTATTCT 15 239 1 TGACGAGCAT 0.467783 -62 ACTCCCCTTTTGACCAATGGCATACGGCTAGAT 16 23 1 TGACCAGGCT 0.757471 -183 AAAGAGGAACTTGGCATCGGACTATTGTGCCGT 17 43 0 TTGGCAGGAT 0.714982 -258 AGAAATATTTTGGCGATCGCCTGATGACC 18 7 0 TGGCGAGCCG 0.908315 -294 ACAGGGAATCTGGGCACAGGATTATGGCGGTTG 18 136 1 TGGGCAGGAT 0.954698 -165 AGCGGTGGAATGGCGAACTGCGTCTGTGGGGTT 18 179 0 TGGCGATGCT 0.897107 -122 GCTGTTGCCCTGGGTACAGCCGTGGGTGTAGGT 18 214 0 TGGGTAGCCT 0.690356 -87 GCCGAGCAAATGGCGATCGCCTAGCTAACTGCC 21 211 1 TGGCGAGCCA 0.713722 -90 TCTTAGAGCTTGGCGATCGCCCTGGATTTAAAT 22 35 0 TGGCGAGCCT 0.977896 -128 TTTAGCACTCTTGGCAGTGGAGTGCTAAGTCAG 22 87 0 TTGGCAGGAT 0.714995 -76 CTAAACTTAGTGGGGAATGGCGTTTTTTGTTCC 25 58 0 TGGGGAGGCT 0.991132 -243 AAAAAATCTATGGCCGATGGCAGGCTTTTCCAT 25 116 0 TGGCCGGGCG 0.723513 -185 ATCACTCCATTGGGCAACGGCGTTAATGCACTG 26 40 0 TGGGCAGGCT 0.98338 -162 TATAGACCACTGGCGATCGGCATGGTAACAGTA 26 107 0 TGGCGAGGCT 0.990466 -95 ATTTCGTTCCTCGGCACTGGCTTGGGTAATTCC 26 144 1 TCGGCAGGCT 0.762179 -58 CAAGCAAGAATGGCGATCGCCGTTGGGATTCGG 32 66 1 TGGCGAGCCT 0.977955 -235 TGGGCAAATCTGGGGAGCTGACTAGGTTCCTGG 32 221 1 TGGGGATGAT 0.767762 -80 ****** *** * Masking position 1 Map Score: 40.2528 Number of sites scoring better than the average of aligned sites = 2130 Number in coding regions = 1942 Number in noncoding regions = 188 Number of orfs with sites within 600 bp upstream = 199 Fraction of orfs with sites within 600 bp upstream = 0.0319627 Motif number 3 AGAAAAATCTGGCGATCGGGTTGATCGGCC 6 87 0 GGCGATCGGG 0.841237 -45 AGGTAACCACGGCGATCGCCAAGGAAAGAT 7 203 1 GGCGATCGCC 0.499998 -98 CTCCTCCAGAGGCTATCGTCTGGGTTAAGA 8 48 0 GGCTATCGTC 0.7882 -253 GAAGCAACAGGGCGATCGCCACCATTACTT 13 17 1 GGCGATCGCC 0.499998 -284 GGTCATCAGGCGATCGCCAAAATATTTC 18 9 1 GGCGATCGCC 0.499998 -292 TAGAGCAATGGGTGATCCCCGTTTTGATTA 18 72 0 GGTGATCCCC 0.807104 -229 AATATTTTGCGGTGATCCTCCCGGGGCGAG 19 62 1 GGTGATCCTC 0.781615 -212 CCGAGCAAATGGCGATCGCCTAGCTAACTG 21 212 1 GGCGATCGCC 0.499998 -89 TTAAATCCAGGGCGATCGCCAAGCTCTAAG 22 37 1 GGCGATCGCC 0.499998 -126 ATAGACCACTGGCGATCGGCATGGTAACAG 26 109 0 GGCGATCGGC 0.525653 -93 AAGCAAGAATGGCGATCGCCGTTGGGATTC 32 67 1 GGCGATCGCC 0.499998 -234 ********** Masking position 5 Map Score: 33.1483 Number of sites scoring better than the average of aligned sites = 5973 Number in coding regions = 5425 Number in noncoding regions = 548 Number of orfs with sites within 600 bp upstream = 344 Fraction of orfs with sites within 600 bp upstream = 0.0552522 Motif number 4 TAGGTTGAAGTTTGCCCAGGGTCCCGCCCCAA 2 85 1 TTTCCCAGGT 0.917607 -50 GGTTGGAGTTTTTCCCCTCTGCTGGAATTTTT 3 63 1 TTTCCCTTGC 0.883106 -38 GCTAAATTGCTTGACCCAGTGCAACACCCCGG 4 14 0 TTGCCCATGC 0.775293 -100 TCGATTAATTTTTACCGATCCTGACCTGTGTT 5 12 1 TTTCCGACCT 0.586958 -85 TTGCAGGATTTTTACCCATTCATCTATTGCAT 5 49 1 TTTCCCATCA 0.689274 -48 GACTCCAATCCCCAAGCCCTAGACTGAA 6 7 1 AATCCCAGCC 0.468418 -125 TTCCCCATCATATCCCTAAGGCAAGGCGATAT 6 54 0 TATCCTAGGC 0.491513 -78 TCAGTTACTCTTCTCCCAACCC 6 120 1 TTCCCCACCC 0.728718 -12 TTTGGTCGTATTTACCCATTGTGCCCAAATCC 7 147 1 TTTCCCATGT 0.873404 -154 TTTAAGTATTTTTTCCCATTCTCCCTAATCCT 7 232 1 TTTCCCATCT 0.915689 -69 GACATCCGACTTGCCCTAACGTTAACCCAGCT 7 274 0 TTGCCTACGT 0.260329 -27 TTATCCGTCATTTACCTAGCCCAGTCCGTCTC 8 203 1 TTTCCTACCC 0.884109 -98 ATGGCACAAATTTTCCTTCCCTGACTGTTTTT 11 82 1 TTTCCTTCCT 0.548163 -202 AGTGGTGGGGTTTACCCTTGCTCAACCAGGGG 11 168 0 TTTCCCTGCT 0.879754 -116 GGAAGGAGGGTTTTCCCAATGCAGTGGTGGGG 11 190 0 TTTCCCATGC 0.947655 -94 TCTCTGCAAGTTTCCCTAGGGCAAAGCGGCCC 13 180 0 TTTCCTAGGC 0.855086 -121 ACTCTGGGGGTTGCCCCACGGCACAATAGTCC 17 26 1 TTGCCCAGGC 0.847784 -275 TCGGATATTTATTCCCCTAGCTCCCTTTTGTT 17 251 1 ATTCCCTGCT 0.461038 -50 CACCCACGGCTGTACCCAGGGCAACAGCACAA 18 219 1 TGTCCCAGGC 0.683209 -82 GGGCAACTTGTTTTCCTTGCCCTGAAACC 21 282 1 TTTCCTTCCC 0.760966 -19 CCCATTCCTTTTTTCCCATTCTTCGACCCTGG 23 91 0 TTTCCCATCT 0.915689 -143 GCCCATTTTATATTCCCATTCCTTTTTTCCCA 23 105 0 TATCCCATCC 0.823594 -129 TGATGTAAACTATTCCCTAGCCAATGGTGACC 24 34 1 TATCCCTGCC 0.758747 -184 ATGCTACGGAATTACCCAAGCCAGTGCCGAGG 26 152 0 ATTCCCAGCC 0.843237 -50 GCCCTGTCAATTTACCTATTCCGGAGATTTCT 29 72 0 TTTCCTATCC 0.851947 -228 AAAAGTTTTTTTTCCCCACTCCTTGGACGCCG 29 221 1 TTTCCCATCC 0.966102 -79 TTTTTCTTAATTTTCCCTACCTTTCCCCGTAC 29 271 1 TTTCCCTCCT 0.857319 -29 TCCGTCGCTGTTTACCGTGGCCTCTGGGTTTT 30 105 0 TTTCCGTGCC 0.654549 -150 GTGGGAATCTTTTTCCCTTTCTCTCCGTCGCT 30 128 0 TTTCCCTTCT 0.819242 -127 GCATTCTGTTTTTCCCCAACGAAGAAGTTAGA 31 161 1 TTTCCCACGA 0.651339 -140 GCTCCCCAGATTTGCCCAGCGCCCCAGCAATG 32 207 0 TTTCCCACGC 0.960002 -94 *** **** *** Masking position 6 Map Score: 26.96 Number of sites scoring better than the average of aligned sites = 3032 Number in coding regions = 2682 Number in noncoding regions = 350 Number of orfs with sites within 600 bp upstream = 387 Fraction of orfs with sites within 600 bp upstream = 0.0621587 Motif number 5 TTTGAATTAACATCGTTCCCCAATCTGCTAA 2 6 1 AAACTCCCCC 0.970708 -129 TTGAAGTTTGCCCAGGGTCCCGCCCCAAACTCCTAT 2 89 1 CAGGTCCCCC 0.677222 -46 AGCAGAGGGGAAAAACTCCAACCCCCATGATAGCTT 3 50 0 AAACCCCCCC 0.984209 -51 AAGCCCTAGACTGAAAACCATAGCCCAAAAATATCG 6 24 1 CAAACCGCCC 0.804734 -108 TGTTCCAGAACCAGATACCAGTCCCCGTGGCTAGAT 9 101 0 CGATCCCCCC 0.82992 -200 GCTTAAGTTGACAAGTATCTCTCCCCATCGTCACTC 10 101 1 AAGTTCCCCC 0.827935 -52 TGCCATTCAACTAGGCCCCAAAGCCCCTTTCTTGTA 11 52 0 CGGCCCGCCC 0.799779 -232 CATTGTCTAGCTCAAAGTCAGCCTCCGGCATCCTCT 11 118 1 CAAATCCTCC 0.565296 -166 CATCCTCTAGAAAGACTTCCATCCCCTGGTTGAGCA 11 146 1 AGACTCCCCC 0.91035 -138 AACCCTCCTTCCTAGCTCCGGATTCCACCCCCTAAA 11 210 1 CAGCCCTTCC 0.648876 -74 AATGGTCACAAAAAACGTCGACCTCCTAAGTAATGG 13 38 0 AAACTCCTCC 0.835788 -263 CCCCCCAGAACGTAATTTCGTCGCCCTTCTCTTGTT 13 147 0 CAATTCGCCC 0.686644 -154 TACCGCCGAAACCAATACCACGCTCCTACAGCCGCA 15 111 0 AAATCCCTCC 0.672232 -190 CAGAGAAAATATTATCGCCATTTCCCGGACTATAAT 17 139 0 AATCCCTCCC 0.529793 -162 CATAATTACGACAACCCCCTCGCCCCGGGAGGATCA 19 74 0 AACCCCCCCC 0.874856 -200 TCGGGGAACAAAAAACGCCATTCCCCACTAAGTTTA 25 54 1 AAACCCCCCC 0.984209 -247 TTACCCTTGACTTAACATCGAGTCCCAGTCACCCCC 25 267 1 CAACTCTCCC 0.904215 -34 TAGTCAGTGCATTAACGCCGTTGCCCAATGGAGTGA 26 36 1 AAACCCGCCC 0.941623 -166 TCCCCTGGCTCCCAATCCCTAGAAGCGGA 27 4 1 CGGCCCTCCC 0.786642 -76 ATACTACGGTAACAACACCATCTCCCC 27 63 1 AAACCCTCCC 0.93706 -17 ATGGTTGCCCAGAAATCCCCACCTCCGCATC 28 6 0 AAATCCCTCC 0.672232 -101 TGTTTACTGTAGCAAACTCTCGCCCCCAGATGGTTG 28 35 0 AAAATCCCCC 0.876545 -72 GACAGGGCAGATTAACCTCCTGCCCTCCCTGTCCTA 29 96 1 AAACTCCCCT 0.51368 -204 GACATCATAGCAAAAACTCTACCCCCAGGCATAGAC 30 69 1 CAAATCCCCC 0.894369 -186 GAGAAAGGGAAAAAGATTCCCACCCCCCCTTTGAAA 30 137 1 AAGATCCCCC 0.827935 -118 GATCTGACAACTCAGCTCCGAATCCCAACGGCGATC 32 80 0 CAGCCCTCCC 0.923267 -221 * *** ** **** Masking position 9 Map Score: 26.5499 Number of sites scoring better than the average of aligned sites = 1628 Number in coding regions = 1465 Number in noncoding regions = 163 Number of orfs with sites within 600 bp upstream = 171 Fraction of orfs with sites within 600 bp upstream = 0.0274655 Motif number 6 CCCAACCAATGGGCCAGGGTTTTACAGACAAATTA 2 39 0 GGCGGGTTTC 0.838039 -96 CTGGCCCATTGGTTGGGGTTTTATGGTCTAGGTTG 2 57 1 GGGGGTTTAG 0.734191 -78 CTATCATGGGGGTTGGAGTTTTTCCCCTCTGCTGG 3 53 1 GGGAGTTTTC 0.814865 -48 GTAGTAATTTGGGAGAGGGTTTAGCACTCCCACCT 4 62 0 GGGGGGTTAC 0.987515 -52 AATAAGGCCAGGCAGAAGGATTTTGAATACTAGAT 7 114 0 GGGAGGTTTG 0.965799 -187 CCAGCTCCTTGGCCGCAGGATTAGGGAGAATGGGA 7 245 0 GGGAGGTTAG 0.965799 -56 CCTGCGGCCAAGGAGCTGGGTTAACGTTAGGGCAA 7 261 1 AGGTGGTTAC 0.697606 -40 TTAGCTTACAAGAAAGGGGCTTTGGGGCCTAGTTG 11 46 1 AGAGGGTTTG 0.4415 -238 TTCCCAATGCAGTGGTGGGGTTTACCCTTGCTCAA 11 175 0 AGGGGGTTTC 0.9374 -109 TCCGGAGCTAGGAAGGAGGGTTTTCCCAATGCAGT 11 197 0 GGGAGGTTTC 0.983514 -87 ACAAGGGCCAAGATGAAGGATTACCGAATGGCACA 15 16 0 AGGAGGTTAC 0.918666 -285 TGTGGTTCTAGGCTGGGGCGTTACCGCCGAAACCA 15 133 0 GGGGGCTTAC 0.830643 -168 CAGGGAATCTGGGCACAGGATTATGGCGGTTGAGG 18 137 1 GGAAGGTTAG 0.759005 -164 GGCGAACTGCGTCTGTGGGGTTTTCCTCACCTCAA 18 166 0 GTGGGGTTTC 0.77734 -135 GTACAGCCGTGGGTGTAGGTTTAGCGGTGGAATGG 18 199 0 GGGAGGTTAC 0.983514 -102 GGGCACGCTGAGGTGATGGATTTAGATT 18 283 1 AGGTGGTTTG 0.52198 -18 AAGTTAAGACGGTCGTAGGATTTAGTGTAATCGGT 19 232 0 GGGAGGTTTG 0.965799 -42 CAGTTAACTAGACCGGAGGATTATCATTGTGAATA 24 75 0 GAGAGGTTAC 0.869345 -143 ATCTATGGCCGATGGCAGGCTTTTCCATTGACGGA 25 109 0 GAGAGGTTTC 0.869345 -192 GATGCGGAGGTGGGGATTTCTGGGCAACCA 28 6 1 GGGGGGATTC 0.829413 -101 GGACAGGGAGGGCAGGAGGTTAATCTGCCCTGTCA 29 95 0 GGGAGGTAAC 0.785751 -205 GGCTTCGTATGATGATGGGGTTACCCCCATTGCTG 32 180 1 GAAGGGTTAC 0.49592 -121 ** * *** *** * Masking position 8 Map Score: 21.3517 Number of sites scoring better than the average of aligned sites = 1021 Number in coding regions = 931 Number in noncoding regions = 90 Number of orfs with sites within 600 bp upstream = 97 Fraction of orfs with sites within 600 bp upstream = 0.0155798 Motif number 7 TCACCGGGGTGTTGCACTGGG 4 2 1 CACCGGGGTG 0.851295 -112 GCAAGACTATCATCTGGAGG 4 104 1 CATCTGGAGG 0.763296 -10 CAGACGATAGCCTCTGGAGGAGTATGTGCT 8 56 1 CCTCTGGAGG 0.895074 -245 TAATGCCTGTCCGATGGGGGCGTTTGGGAC 8 176 0 CCGATGGGGG 0.756164 -125 TTTTCTGTTTCCTTGGGTGGCCTTGTTGTT 9 233 1 CCTTGGGTGG 0.761089 -68 CACTCTCCTTCACCGGGGGGTGCTTTTTGC 10 49 1 CACCGGGGGG 0.958975 -104 AGACTTCCATCCCCTGGTTGAGCAAGGGTA 11 158 1 CCCCTGGTTG 0.438258 -126 ACGGCTTAGTCATTGGGGGTTCCTTGCCGG 13 91 1 CATTGGGGGT 0.506476 -210 CGGGATTTGACCTAAGGGGGCTTGGTTGGC 14 30 0 CCTAAGGGGG 0.756055 -70 GGTTTCCGTACCTATGGGGGCATCTAGCCG 16 47 0 CCTATGGGGG 0.951585 -159 CGGCGACGATACTCTGGGGGTTGCCCCACG 17 16 1 ACTCTGGGGG 0.730874 -285 TGGAGATTGTCAACGGGGGGAATGATAGAA 17 186 1 CAACGGGGGG 0.894421 -115 AACCCCCTCGCCCCGGGAGGATCACCGCAA 19 68 0 CCCCGGGAGG 0.88754 -206 TCTGGGCAACCATCTGGGGGCGAGAGTTTG 28 29 1 CATCTGGGGG 0.957278 -78 CCCAAATTACCCTTGGGGTGTCAGAGGCAT 29 19 1 CCTTGGGGTG 0.879846 -281 TTTACTTGAGCCTTGGGGGACTAACGCCCT 29 131 0 CCTTGGGGGA 0.61292 -169 TTTACCGTGGCCTCTGGGTTTTGTCTATGC 30 97 0 CCTCTGGGTT 0.552503 -158 TCCCGAATTTCAAAGGGGGGGTGGGAATCT 30 150 0 CAAAGGGGGG 0.730681 -105 TCTAGCAACGCCTAGGGGTGGCCTCAACTT 31 229 1 CCTAGGGGTG 0.900215 -72 ********** Masking position 6 Map Score: 15.1088 Number of sites scoring better than the average of aligned sites = 1684 Number in coding regions = 1515 Number in noncoding regions = 169 Number of orfs with sites within 600 bp upstream = 165 Fraction of orfs with sites within 600 bp upstream = 0.0265018 Motif number 8 AATTTGTCTGTAAAACCCTGGCCCATTGGTTG 2 40 1 TAACCCTGGC 0.739225 -95 TTATTCCCCAGGTAACCACGGCGATCGCCAAG 7 194 1 GAACCACGGC 0.883021 -107 ACCCAGCTCCTTGGCCGCAGGATTAGGGAGAA 7 250 0 TGCCGCAGGA 0.367798 -51 CAACAACAAGGCCACCCAAGGAAACAGAAAAC 9 232 0 GACCCAAGGA 0.334999 -69 AGTCTTTCTAGAGGATGCCGGAGGCTGACTTT 11 131 0 GGATGCCGGA 0.424882 -153 ACTGGCCAATTTTGACCACGGCTTAGTCATTG 13 74 1 TGACCACGGC 0.872999 -227 GAGTTCCCAAGCGTCCCCCGGCAAGGAACCCC 13 106 0 GTCCCCCGGC 0.71974 -195 CCCCCTTAGGTCAAATCCCGACCTTTTTAATG 14 40 1 TAATCCCGAC 0.477554 -60 AGGCTGGGGCGTTACCGCCGAAACCAATACCA 15 127 0 GACCGCCGAA 0.611577 -174 TGTGAACGTGTCGGCCCCAGGCAATGGATTGG 16 117 1 TGCCCCAGGC 0.781929 -89 GGCAATGGATTGGAACCATGGCTTTTCGGCCC 16 136 1 TAACCATGGC 0.38941 -70 CCCTTTTGTTGTTAACCCAGGAGGTTTAAAAC 17 273 1 GAACCCAGGA 0.756874 -28 ATTCCCTGTTTTTGACCCCGACAGTTAACAGA 18 113 0 TGACCCCGAC 0.924735 -188 CCGCTAAACCTACACCCACGGCTGTACCCAGG 18 207 1 TACCCACGGC 0.785441 -94 TTGCAAGACTGAAAACGCCGAAAATAGAACGA 23 45 0 GAACGCCGAA 0.686431 -189 TTTCCCATTCTTCGACCCTGGAGTGATCGGAG 23 80 0 TGACCCTGGA 0.68525 -154 AACTGCTGACCCCGAAAAACAATTGG 23 218 0 GGACCCCGAA 0.911989 -16 TATTGTCCAGGCAAACCCCGACTATAGTCGGA 25 187 1 GAACCCCGAC 0.930997 -114 TCGAGTCCCAGTCACCCCCGGACCTCC 25 284 1 GACCCCCGGA 0.932079 -17 TCCCCACTCCTTGGACGCCGGCTTGATCCCTG 29 233 1 TGACGCCGGC 0.89709 -67 GCCTGAACACTTAGATCCCGAATTTCAAAGGG 30 163 0 TGATCCCGAA 0.412467 -92 TTAATTGTGGTCTGACCACGACTTTTTTTCAC 31 21 0 TGACCACGAC 0.734338 -280 GAAGAAGTTAGAGAACCCCGAATCAATAGACT 31 181 1 GAACCCCGAA 0.884691 -120 * ********* Masking position 10 Map Score: 12.0343 Number of sites scoring better than the average of aligned sites = 2967 Number in coding regions = 2768 Number in noncoding regions = 199 Number of orfs with sites within 600 bp upstream = 218 Fraction of orfs with sites within 600 bp upstream = 0.0350145 Motif number 9 AAGCACCCCCCGGTGAAGGAGAGTGCAATTTGC 10 41 0 CGAAGGAGAG 0.982066 -112 CATCGTCACTCTTAGAAGGAGAGTAGGTTGATT 10 126 1 CGAAGGAGAG 0.982066 -27 GAATCCGGAGCTAGGAAGGAGGGTTTTCCCAAT 11 202 0 CGAAGGAGGG 0.9116 -82 CCTGGGTTAACAACAAAAGGGAGCTAGGGGAAT 17 261 0 CAAAAGGGAG 0.80618 -40 ATCAATTCCACGGCGTCGGGGAGCTAATCCTCC 19 168 1 CGTCGGGGAG 0.926092 -106 CAGGCTTTTCCATTGACGGAGAGCATTAAAGAC 25 96 0 CGACGGAGAG 0.986575 -205 GCTCCCAATCCCTAGAAGCGGAGAATATGGCAC 27 18 1 CGAAGCGGAG 0.895635 -62 GACTAACGCCCTAGGACAGGGAGGGCAGGAGGT 29 110 0 CGACAGGGAG 0.973141 -190 GGGTTAGGTACGGGGAAAGGTAGGGAAAATTAA 29 277 0 CGAAAGGTAG 0.680237 -23 CCACGGTAAACAGCGACGGAGAGAAAGGGAAAA 30 117 1 CGACGGAGAG 0.986575 -138 ATGTACTGAGCTAAAACAGAGAGGGCAAGACGA 30 230 1 CAACAGAGAG 0.80618 -25 * ********* Masking position 1 Map Score: 8.24471 Number of sites scoring better than the average of aligned sites = 226 Number in coding regions = 195 Number in noncoding regions = 31 Number of orfs with sites within 600 bp upstream = 39 Fraction of orfs with sites within 600 bp upstream = 0.00626405 Motif number 10 CGACCAAATAAGGCCAGGCAGAAGGATTTT 7 125 0 AGGCCAGGCA 0.87858 -176 CCTAATCCTGCGGCCAAGGAGCTGGGTTAA 7 255 1 CGGCCAAGGA 0.63617 -46 ACGCCCCCATCGGACAGGCATTATCCGTCA 8 183 1 CGGACAGGCA 0.761717 -118 TAGACCAATAAACCCAGGGAACGCCATGTT 8 245 0 AACCCAGGGA 0.84145 -56 GGCGCAAAAACAGTCAGGGAAGGAAAATTT 11 89 0 CAGTCAGGGA 0.881059 -195 CCATTAGTCCAAGCCAGAGAAAATATTATC 17 159 0 AAGCCAGAGA 0.761293 -142 GTCGGGGTCAAAAACAGGGAATCTGGGCAC 18 123 1 AAAACAGGGA 0.511382 -178 ACAACCCCCTCGCCCCGGGAGGATCACCGC 19 70 0 CGCCCCGGGA 0.7531 -204 AATAAAAGATAAGTCAGAGA 21 1 0 AAGTCAGAGA 0.473647 -300 GCCAAGCTCTAAGACCGGGAAACCGAACCT 22 54 1 AAGACCGGGA 0.905197 -109 GTGGAGTGCTAAGTCAGGTAAGGTTCGGTT 22 74 0 AAGTCAGGTA 0.5116 -89 TTACAATGGAGAGACCGGGATTATAGAACC 25 156 1 GAGACCGGGA 0.642616 -145 TAGTTTGCGGAGGCCCGGTATGCCTCTGAC 29 38 0 AGGCCCGGTA 0.722057 -262 CTAACGCCCTAGGACAGGGAGGGCAGGAGG 29 111 0 AGGACAGGGA 0.955878 -189 AAGAAAAAGGCGGACAGGGATCAAGCCGGC 29 249 0 CGGACAGGGA 0.94679 -51 TCATCATACGAAGCCAGGGACAGTTTACTC 32 165 0 AAGCCAGGGA 0.969664 -136 ********** Masking position 10 Map Score: 7.48605 Number of sites scoring better than the average of aligned sites = 1064 Number in coding regions = 955 Number in noncoding regions = 109 Number of orfs with sites within 600 bp upstream = 119 Fraction of orfs with sites within 600 bp upstream = 0.0191134 Motif number 11 TGGGGGTTGGAGTTTTTCCCCTCTGCTGGA 3 59 1 AGTTTTTCCC 0.671015 -42 TCCAGATGATAGTCTTGCAAGGTCAGTAGT 4 92 0 AGTCTTGCAA 0.783794 -22 CAATTCTTTAAGTTTTGTAAAGTTTTTTGT 8 88 0 AGTTTTGTAA 0.716227 -213 AAAAAACTAAAGTTTTGCCATTTTTGGAAA 9 59 1 AGTTTTGCCA 0.958567 -242 GTTTCCGTTTAGTTTTTTCAACCT 9 287 1 AGTTTTTTCA 0.511019 -14 TTGCCAAATCAGTTTTGCCAGCAAAGAAGA 12 14 0 AGTTTTGCCA 0.958567 -287 TTATCCCCTCAGCTTTGTCCCTTTAAAATT 12 146 0 AGCTTTGTCC 0.698896 -155 ATGGATGAGCAGTTTTGCCCATATCCCTCA 12 270 1 AGTTTTGCCC 0.950005 -31 TTGACAACGGAGTTTTGTAACAAAATCTTA 19 130 0 AGTTTTGTAA 0.716227 -144 CGGCGTTTTCAGTCTTGCAAAAACTCCGAT 23 57 1 AGTCTTGCAA 0.783794 -177 TTCCCCACTAAGTTTAGTCAACGTCTTTAA 25 74 1 AGTTTAGTCA 0.471259 -227 ACACTACAGAAGCCTTGTCAATTATTGTTA 28 68 1 AGCCTTGTCA 0.630751 -39 GTTCGTCTTGCCCTCTCTGTTTT 30 242 0 CGTCTTGCCC 0.609126 -13 TCAGCTCCCCAGATTTGCCCAGCGCCCCAG 32 212 0 AGATTTGCCC 0.669108 -89 GGTTCCTGGAAGTTTTGCTAATCCACTAAA 32 245 1 AGTTTTGCTA 0.645757 -56 ********** Masking position 5 Map Score: 5.33194 Number of sites scoring better than the average of aligned sites = 730 Number in coding regions = 613 Number in noncoding regions = 117 Number of orfs with sites within 600 bp upstream = 132 Fraction of orfs with sites within 600 bp upstream = 0.0212014 Motif number 12 ACCCTGGCCCATTGGTTGGGGTTTTATGGTCTAG 2 54 1 ATTGTTGGTT 0.472172 -81 GTTTTATGGTCTAGGTTGAAGTTTGCCCAGGGTC 2 74 1 CTAGTTGATT 0.786156 -61 AACCCCCATGATAGCTTGGGTCTTTGATTAACAA 3 33 0 ATAGTTGGCT 0.927419 -68 ATTTTGAATACTAGATTGTGGGTTGTGATATGTC 7 96 0 CTAGTTGGGT 0.96252 -205 GTCCCCGTGGCTAGATTGTGTCATTGATTTTCCA 9 83 0 CTAGTTGGCT 0.983017 -218 TCAGACTAGCTTGAGGGATATGGGCAAAA 12 282 0 CTAGTTGGGT 0.96252 -19 TTTTGTGGTTCTAGGCTGGGGCGTTACCGCCGAA 15 137 0 CTAGCTGGCT 0.908565 -164 AACGAATTTGCTAGTTTGAAAGGTAATCGTTTAA 19 22 0 CTAGTTGAGT 0.892278 -252 AAGTGTACAACTAGGTTTCACCTTATAAAG 24 198 1 CTAGTTTACT 0.572573 -20 AGTATTCTCCCTAGATTGTGCCATATTCTCCGCT 27 34 0 CTAGTTGGCT 0.983017 -46 AAAAGACTTCATTGATTGTAGCCTCGATAACAAA 31 63 0 ATTGTTGACT 0.594366 -238 GATCGCCATTCTTGCTTGGGGCATTAAAACCCGC 32 50 0 CTTGTTGGCT 0.953659 -251 **** *** * * * Masking position 7 Map Score: 6.14373 Number of sites scoring better than the average of aligned sites = 134 Number in coding regions = 109 Number in noncoding regions = 25 Number of orfs with sites within 600 bp upstream = 28 Fraction of orfs with sites within 600 bp upstream = 0.00449727 Motif number 13 TAAGAAGGCAATAAAAAACGCAAAAATCCC 8 23 0 ATAAAAAACG 0.702562 -278 TATGTGCTTCACAAAAAACTTTACAAAACT 8 78 1 ACAAAAAACT 0.919479 -223 GATAGATATTAAAAAAAACTAAAGTTTTGC 9 47 1 AAAAAAAACT 0.789142 -254 AGTAATGGTCACAAAAAACGTCGACCTCCT 13 47 0 ACAAAAAACG 0.947945 -254 AATCTCAAATAAAAAAAAAGAAATAAAAGA 21 22 0 AAAAAAAAAG 0.627419 -279 CTAAAAAGTTACAAATAACGTCAAAGGTGG 22 140 0 ACAAATAACG 0.719286 -23 TGGTCGGGGAACAAAAAACGCCATTCCCCA 25 51 1 ACAAAAAACG 0.947945 -250 GGCAGCGCCGACAAAAAAATAGACAATTAA 25 231 1 ACAAAAAAAT 0.763146 -70 AGGAGTGGGGAAAAAAAACTTTTCCTTTAC 29 214 0 AAAAAAAACT 0.789142 -86 AGCCTCGATAACAAAAAAATGGGGCTTAAT 31 48 0 ACAAAAAAAT 0.763146 -253 ********** Masking position 5 Map Score: 4.47318 Number of sites scoring better than the average of aligned sites = 54 Number in coding regions = 37 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 14 GTCAAGCAATTTAGCTAAATTAGCACTCGTGAGG 4 31 1 TTACAATTGC 0.683025 -83 TTCTGCGTAGGGGTCAAGATTAGCCCTTAGCTTA 11 20 1 GGGCAATTGC 0.952736 -264 AAAATTTTCTATATTGGCTATTGGGTGT 11 266 0 TTTCAATTGC 0.844832 -18 GACTAAGCCGTGGTCAAAATTGGCCAGTAATGGT 13 68 0 TGGCAATTGC 0.981316 -233 TTCCCGAACCTTGTCACCATTTGCGGCGTCTAAA 15 182 1 TTGCCATTGC 0.881037 -119 CCATAATCCTGTGCCCAGATTCCCTGTTTTTGAC 18 129 0 GTGCAATTCC 0.664468 -172 TGGGGCTTAATGGTCTAAATTTGCATCAAAAGAC 23 153 1 TGGCAATTGC 0.981316 -81 TAATCACCGATGGTCACCATTGGCTAGGGAATAG 24 43 0 TGGCCATTGC 0.952736 -175 CTCCCTAGATTGTGCCATATTCTCCGCTTCTAGG 27 28 0 TGTCAATTTC 0.592304 -52 CCCGTTGGCCCAAATTACCCTTGGGGTGT 29 6 1 TGGCAATTCC 0.933529 -294 TCCTAAGTCGTGTACAAAATTAGCTGGTCAGTCA 31 259 0 TGTCAATTGC 0.936786 -42 *** * * *** ** Masking position 9 Map Score: 4.61825 Number of sites scoring better than the average of aligned sites = 238 Number in coding regions = 210 Number in noncoding regions = 28 Number of orfs with sites within 600 bp upstream = 39 Fraction of orfs with sites within 600 bp upstream = 0.00626405 Motif number 15 TACACTCACTATTGGAGAGTTCTAGC 1 150 1 ATTGGAGAGT 0.405491 -16 TTAGGGATATGATGGGGAAAGGCCGATCAA 6 67 1 GATGGGGAAA 0.618678 -65 ACGGACGATTGATGGGGAATGACTGGGATC 8 138 0 GATGGGGAAT 0.757765 -163 ACCCCCCGGTGAAGGAGAGTGCAATTTGCA 10 40 0 GAAGGAGAGT 0.910012 -113 TAAGAGTGACGATGGGGAGAGATACTTGTC 10 110 0 GATGGGGAGA 0.942067 -43 GTCACTCTTAGAAGGAGAGTAGGTTGATTT 10 130 1 GAAGGAGAGT 0.910012 -23 CCGGAGCTAGGAAGGAGGGTTTTCCCAATG 11 201 0 GAAGGAGGGT 0.561874 -83 CCATTGGTCAAAAGGGGAGTTAACGCCACG 16 13 0 AAAGGGGAGT 0.778949 -193 CCCCAAGTAAAATGGAGAGCTTCAGATCAA 17 78 0 AATGGAGAGC 0.776583 -223 ATTCCACGGCGTCGGGGAGCTAATCCTCCA 19 172 1 GTCGGGGAGC 0.774023 -102 CTCCGAATCCGATCGGGAGTTATGACGATG 24 139 0 GATCGGGAGT 0.724465 -79 GACGGGAAGTGTTCTCTCTA 25 1 1 GACGGGAAGT 0.576869 -300 CTTTTCCATTGACGGAGAGCATTAAAGACG 25 95 0 GACGGAGAGC 0.929555 -206 AAAGGTTTACAATGGAGAGACCGGGATTAT 25 150 1 AATGGAGAGA 0.68666 -151 CGCTTCTAGGGATTGGGAGCCAGGGGA 27 8 0 GATTGGGAGC 0.593399 -72 GGTAAACAGCGACGGAGAGAAAGGGAAAAA 30 121 1 GACGGAGAGA 0.892695 -134 ********** Masking position 5 Map Score: 5.35169 Number of sites scoring better than the average of aligned sites = 745 Number in coding regions = 632 Number in noncoding regions = 113 Number of orfs with sites within 600 bp upstream = 115 Fraction of orfs with sites within 600 bp upstream = 0.0184709