AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i257_bsub_mtub_100.orf -o257_bsub_mtub_100.ace -a/home/amcguire/genomes/ORF_bsub.txt -z/home/amcguire/genomes/bsub.fna -g0.55 -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 = 0.55 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 groES 196 class I heat-shock protein (molecular chaperonin) #2 groEL 46 class I heat-shock protein (molecular chaperonin) #3 groEL2 293 groEL2 #4 groEL1 94 groEL1 #5 groES 266 groES Motif number 1 GTAACATAATCGGTACGGGGGTGAAAAAGC 1 59 1 CGGTACGGGG 0.989591 -138 CACTTGAAATTGGAAGGGAGATTCTTTATT 1 145 1 TGGAAGGGAG 0.515241 -52 CCTCGGCCCTCCGATCCGGGTGAGTATGTT 3 17 0 CCGATCCGGG 0.984371 -277 GCAAGAAGCCCCGCACCGGGTCATGCCCCT 3 60 0 CCGCACCGGG 0.996234 -234 TAGCACTCACCGGTCGCGAGTGCCAACGTT 3 116 0 CGGTCGCGAG 0.9893 -178 CCTGGCCTCACCGTCCCGACCTAGCACTCA 3 137 0 CCGTCCCGAC 0.966074 -157 AGGCCCGTCGTCGCAGCGAGTGGCAGCGAG 3 164 1 TCGCAGCGAG 0.85169 -130 TCGCAGCGAGTGGCAGCGAGGACAACTTGA 3 174 1 TGGCAGCGAG 0.86313 -120 CTTGAGCCGTCCGTCGCGGGCACTGCGCCC 3 199 1 CCGTCGCGGG 0.997604 -95 ATGAAACGGGGGTCACCGGGTGACGGCAAC 3 248 0 GGTCACCGGG 0.823678 -46 GTGATTCCTCCGGATCGGGGATGAAACGGG 3 268 0 CGGATCGGGG 0.956844 -26 AGAGCGTGTTCCGCCCCGGCGATCCCCGTG 4 12 1 CCGCCCCGGC 0.992844 -83 CTAACGCATGCCGCCCCGGAAATCACCCGT 4 48 0 CCGCCCCGGA 0.988794 -47 GGGCGGCATGCGTTAGCGGACTAGCCCTGC 4 62 1 CGTTAGCGGA 0.732835 -33 TTGCACCTGGCGTACCCGGACACGCTGGCA 5 19 1 CGTACCCGGA 0.850357 -248 GTCGCGGGTGCCGACGCAGGGGTTAGCCGA 5 112 0 CCGACGCAGG 0.895459 -155 CCTCGCGCCGTCGTCGCGGGTGCCGACGCA 5 124 0 TCGTCGCGGG 0.986455 -143 GTAATTCGGACGGTTCCGGGGCACGCCCCG 5 179 1 CGGTTCCGGG 0.992609 -88 AGTTGGCGGTCGGTCCGGGGCGTGCCCCGG 5 194 0 CGGTCCGGGG 0.995806 -73 CCGCCAACTCCGGTCCGGGCGAGCGTCCCG 5 215 1 CGGTCCGGGC 0.980341 -52 GTCCGGGCGAGCGTCCCGGGCTCTGATCCA 5 227 1 GCGTCCCGGG 0.989822 -40 ********** Masking position 8 Map Score: 46.9805 Number of sites scoring better than the average of aligned sites = 1518 Number in coding regions = 1355 Number in noncoding regions = 163 Number of orfs with sites within 600 bp upstream = 81 Fraction of orfs with sites within 600 bp upstream = 0.01301 Motif number 2 TCACCCGGATCGGAGGGCCGAGGACACGGT 3 24 1 CGGAGGGCCG 0.896556 -270 CACTCGCGACCGGTGAGTGCTAGGTCGGGA 3 124 1 CGGTGAGTGC 0.870259 -170 GTGCTAGGTCGGGACGGTGAGGCCAGGCCC 3 140 1 GGGACGGTGA 0.677051 -154 GAGGCCAGGCCCGTCGTCGCAGCGAGTGGC 3 158 1 CCGTCGTCGC 0.716487 -136 GTGCCCGCGACGGACGGCTCAAGTTGTCCT 3 192 0 CGGACGGCTC 0.976485 -102 CTTACGCTGGCCGGGCGCAGTGCCCGCGAC 3 211 0 CCGGGCGCAG 0.701126 -83 AGCGTAAGTAGCGGGGTTGCCGTCACCCGG 3 233 1 GCGGGGTTGC 0.914185 -61 GGGGATGAAACGGGGGTCACCGGGTGACGG 3 252 0 CGGGGGTCAC 0.970661 -42 GGGGATCGCCGGGGCGGAACACGCTCTA 4 9 0 GGGGCGGAAC 0.820927 -86 GTGGTGAGCACGGGGATCGCCGGGGCGGAA 4 20 0 CGGGGATCGC 0.930976 -75 GGTGATTTCCGGGGCGGCATGCGTTAGCGG 4 51 1 GGGGCGGCAT 0.778639 -44 CCCGGACATTGCACCTGGCGTA 5 3 1 CGGACATTGC 0.722505 -264 CAGGAAGCAAGGGGGCGCCCTTGAGTGCTA 5 51 1 GGGGGCGCCC 0.959893 -216 GCTAACCCCTGCGTCGGCACCCGCGACGAC 5 115 1 GCGTCGGCAC 0.934654 -152 CGCCCTCGCGCCGTCGTCGCGGGTGCCGAC 5 127 0 CCGTCGTCGC 0.716487 -140 CGACGACGGCGCGAGGGCGCGGACGAATGC 5 138 1 GCGAGGGCGC 0.845334 -129 CCTGGTAATTCGGACGGTTCCGGGGCACGC 5 175 1 CGGACGGTTC 0.93654 -92 CGGACGGTTCCGGGGCACGCCCCGGACCGA 5 185 1 CGGGGCACGC 0.8441 -82 CCGGAGTTGGCGGTCGGTCCGGGGCGTGCC 5 198 0 CGGTCGGTCC 0.951033 -69 TCCGGTCCGGGCGAGCGTCCCGGGCTCTGA 5 223 1 GCGAGCGTCC 0.767924 -44 ATCCAAATAGTGGAGGGCTCCAATC 5 252 1 TGGAGGGCTC 0.758542 -15 ********** Masking position 3 Map Score: 24.0244 Number of sites scoring better than the average of aligned sites = 3157 Number in coding regions = 2919 Number in noncoding regions = 238 Number of orfs with sites within 600 bp upstream = 157 Fraction of orfs with sites within 600 bp upstream = 0.0252168 Motif number 3 TCAGCACTAAAGAGTGCTAACACAATTCTT 1 177 0 AGAGTGCTAA 0.990547 -20 TCGCCTATGCCGAGTGCAAGAAGCCCCGCA 3 75 0 CGAGTGCAAG 0.992719 -219 TCGGCATAGGCGAGTGCTAAGAATAACGTT 3 92 1 CGAGTGCTAA 0.995323 -202 TCACCGGTCGCGAGTGCCAACGTTATTCTT 3 110 0 CGAGTGCCAA 0.993179 -184 TCGCGACCGGTGAGTGCTAGGTCGGGACGG 3 127 1 TGAGTGCTAG 0.990504 -167 GTCGTCGCAGCGAGTGGCAGCGAGGACAAC 3 170 1 CGAGTGGCAG 0.984045 -124 TCTATACATGAGAGTGCTAGCACTCAAGGG 5 68 0 AGAGTGCTAG 0.996269 -199 TCTCATGTATAGAGTGCTAGATGGCAATCG 5 85 1 AGAGTGCTAG 0.996269 -182 ********** Masking position 3 Map Score: 23.0812 Number of sites scoring better than the average of aligned sites = 19 Number in coding regions = 15 Number in noncoding regions = 4 Number of orfs with sites within 600 bp upstream = 4 Fraction of orfs with sites within 600 bp upstream = 0.000642467 Motif number 4 GAGCGGAAAAGAATGATGTAAGCGTGAAAAATT 1 101 1 GAAAGTAAGC 0.91768 -96 TTTATTATAAGAATTGTGTTAGCACTCTTTAGT 1 169 1 GAAGGTTAGC 0.987326 -28 CGAGTGCTAAGAATAACGTTGGCACTCGCGACC 3 102 1 GAAAGTTGGC 0.967554 -192 CGCGACGGACGGCTCAAGTTGTCCTCGCTGCCA 3 184 0 GGCAGTTGTC 0.931097 -110 CACTGCGCCCGGCCAGCGTAAGTAGCGGGGTTG 3 219 1 GGCGGTAAGT 0.928176 -75 TTTCCGGGGCGGCATGCGTTAGCGGACTAGCCC 4 56 1 GGCGGTTAGC 0.996846 -39 CGGGTGCCGACGCAGGGGTTAGCCGATTGCCAT 5 105 0 CGCGGTTAGC 0.981245 -162 CGCTCGCCCGGACCGGAGTTGGCGGTCGGTCCG 5 207 0 GACGGTTGGC 0.994905 -60 *** * ****** Masking position 9 Map Score: 7.11134 Number of sites scoring better than the average of aligned sites = 158 Number in coding regions = 122 Number in noncoding regions = 36 Number of orfs with sites within 600 bp upstream = 17 Fraction of orfs with sites within 600 bp upstream = 0.00273049 Motif number 5 CACCGGGTCATGCCCCTCGTTCGACCGTGT 3 47 0 TGCCCCTCGT 0.955854 -247 GAGTGCAAGAAGCCCCGCACCGGGTCATGC 3 64 0 AGCCCCGCAC 0.982647 -230 CGGGGCTTCTTGCACTCGGCATAGGCGAGT 3 77 1 TGCACTCGGC 0.786146 -217 GGTGAGGCCAGGCCCGTCGTCGCAGCGAGT 3 155 1 GGCCCGTCGT 0.834723 -139 TTGTCCTCGCTGCCACTCGCTGCGACGACG 3 169 0 TGCCACTCGC 0.738852 -125 GTCCGTCGCGGGCACTGCGCCCGGCCAGCG 3 207 1 GGCACTGCGC 0.950795 -87 TGAAACGGGGGTCACCGGGTGACGGCAACC 3 247 0 GTCACCGGGT 0.743402 -47 ATCCGGAGGAATCACTTCGCA 3 283 1 ATCACTTCGC 0.737794 -11 CGCCCCGGCGATCCCCGTGCTCACCACGGG 4 23 1 ATCCCCGTGC 0.80064 -72 TTAGCGGACTAGCCCTGCGTAGAGGAGCCT 4 74 1 AGCCCTGCGT 0.971322 -21 CCCGGACATTGCACCTGGCGTACCCGGAC 5 10 1 TGCACCTGGC 0.939117 -257 CAATCGGCTAACCCCTGCGTCGGCACCCGC 5 109 1 ACCCCTGCGT 0.767253 -158 CGAATGCCGAATCACCTGGTAATTCGGACG 5 161 1 ATCACCTGGT 0.664609 -106 GTCCGGGGCGTGCCCCGGAACCGTCCGAAT 5 182 0 TGCCCCGGAA 0.690461 -85 TTCCGGGGCACGCCCCGGACCGACCGCCAA 5 192 1 CGCCCCGGAC 0.911908 -75 TTTGGATCAGAGCCCGGGACGCTCGCCCGG 5 229 0 AGCCCGGGAC 0.886296 -38 GATTGGAGCCCTCCACTATTTGGATC 5 251 0 AGCCCTCCAC 0.850306 -16 ********** Masking position 3 Map Score: 16.6755 Number of sites scoring better than the average of aligned sites = 2154 Number in coding regions = 1955 Number in noncoding regions = 199 Number of orfs with sites within 600 bp upstream = 115 Fraction of orfs with sites within 600 bp upstream = 0.0184709 Motif number 6 TAAGAATTGTGTTAGCACTCTTTAGTGCTG 1 176 1 GTTAGCACTC 0.960545 -21 GTGCGGGGCTTCTTGCACTCGGCATAGGCG 3 74 1 TCTTGCACTC 0.703288 -220 TAAGAATAACGTTGGCACTCGCGACCGGTG 3 109 1 GTTGGCACTC 0.991654 -185 ACCGTCCCGACCTAGCACTCACCGGTCGCG 3 128 0 CCTAGCACTC 0.959665 -166 AGTTGTCCTCGCTGCCACTCGCTGCGACGA 3 171 0 GCTGCCACTC 0.971799 -123 GCCGTCCGTCGCGGGCACTGCGCCCGGCCA 3 204 1 GCGGGCACTG 0.877656 -90 GTCACCGGGTGACGGCAACCCCGCTACTTA 3 237 0 GACGGCAACC 0.896373 -57 CGTGTTCCGCCCCGGCGATCCCCGTGCTCA 4 16 1 CCCGGCGATC 0.910132 -79 CGCATGCCGCCCCGGAAATCACCCGTGGTG 4 44 0 CCCGGAAATC 0.679909 -51 ACCCGGACACGCTGGCAACCAGGAAGCAAG 5 32 1 GCTGGCAACC 0.985698 -235 ACATGAGAGTGCTAGCACTCAAGGGCGCCC 5 63 0 GCTAGCACTC 0.986728 -204 TAGAGTGCTAGATGGCAATCGGCTAACCCC 5 94 1 GATGGCAATC 0.917946 -173 TAACCCCTGCGTCGGCACCCGCGACGACGG 5 117 1 GTCGGCACCC 0.976531 -150 CCGGACCGGAGTTGGCGGTCGGTCCGGGGC 5 203 0 GTTGGCGGTC 0.838411 -64 ********** Masking position 6 Map Score: 20.4967 Number of sites scoring better than the average of aligned sites = 1192 Number in coding regions = 1080 Number in noncoding regions = 112 Number of orfs with sites within 600 bp upstream = 80 Fraction of orfs with sites within 600 bp upstream = 0.0128493 Motif number 7 GCTTTTTCACCCCCGTACCGATTATGTTAC 1 59 0 CCCCGTACCG 0.748927 -138 CATCATTCTTTTCCGCTCCCTTTTCCGTTA 1 89 0 TTCCGCTCCC 0.830208 -108 GTCCTCGGCCCTCCGATCCGGGTGAGTATG 3 19 0 CTCCGATCCG 0.797774 -275 GTTCGACCGTGTCCTCGGCCCTCCGATCCG 3 29 0 GTCCTCGGCC 0.783678 -265 GTGCAAGAAGCCCCGCACCGGGTCATGCCC 3 62 0 CCCCGCACCG 0.975644 -232 CGACGGGCCTGGCCTCACCGTCCCGACCTA 3 144 0 GGCCTCACCG 0.855322 -150 CGCTGCCACTCGCTGCGACGACGGGCCTGG 3 162 0 CGCTGCGACG 0.541101 -132 GGCTCAAGTTGTCCTCGCTGCCACTCGCTG 3 177 0 GTCCTCGCTG 0.596053 -117 CGGGCGCAGTGCCCGCGACGGACGGCTCAA 3 200 0 GCCCGCGACG 0.969969 -94 TACTTACGCTGGCCGGGCGCAGTGCCCGCG 3 213 0 GGCCGGGCGC 0.783297 -81 GAAGTGATTCCTCCGGATCGGGGATGAAAC 3 271 0 CTCCGGATCG 0.881739 -23 GCACGGGGATCGCCGGGGCGGAACACGCTC 4 13 0 CGCCGGGGCG 0.751257 -82 CACGGGTGATTTCCGGGGCGGCATGCGTTA 4 47 1 TTCCGGGGCG 0.907326 -48 CGCAGGGCTAGTCCGCTAACGCATGCCGCC 4 63 0 GTCCGCTAAC 0.532882 -32 CAGGCTCCTCTACGCAGGGCTAGT 4 81 0 CTCCTCTACG 0.751903 -14 TTGCCAGCGTGTCCGGGTACGCCAGGTGCA 5 20 0 GTCCGGGTAC 0.541109 -247 TAACCCCTGCGTCGGCACCCGCGACGACGG 5 117 1 GTCGGCACCC 0.730214 -150 TTCGGCATTCGTCCGCGCCCTCGCGCCGTC 5 142 0 GTCCGCGCCC 0.974639 -125 CCGGGGCGTGCCCCGGAACCGTCCGAATTA 5 180 0 CCCCGGAACC 0.882054 -87 TTGGCGGTCGGTCCGGGGCGTGCCCCGGAA 5 192 0 GTCCGGGGCG 0.969474 -75 CGACCGCCAACTCCGGTCCGGGCGAGCGTC 5 212 1 CTCCGGTCCG 0.978335 -55 TTGGATCAGAGCCCGGGACGCTCGCCCGGA 5 228 0 GCCCGGGACG 0.978434 -39 ********** Masking position 3 Map Score: 34.6481 Number of sites scoring better than the average of aligned sites = 2404 Number in coding regions = 2231 Number in noncoding regions = 173 Number of orfs with sites within 600 bp upstream = 108 Fraction of orfs with sites within 600 bp upstream = 0.0173466 Motif number 8 ********** No masking Map Score: -1.24102e-12 Number of sites scoring better than the average of aligned sites = 0 Number in coding regions = 0 Number in noncoding regions = 0 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0 Motif number 9 ********** No masking Map Score: -1.24102e-12 Number of sites scoring better than the average of aligned sites = 0 Number in coding regions = 0 Number in noncoding regions = 0 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0 Motif number 10 ********** No masking Map Score: -1.24102e-12 Number of sites scoring better than the average of aligned sites = 0 Number in coding regions = 0 Number in noncoding regions = 0 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0