AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i216_Ribosomal_Operon_3_synecho_reg_300.orf -o216_synecho_300.ace -a/home/amcguire/alignace/lib/ORF_synecho.txt -z/skink1/amcguire/genomes/synecho.fna -g0.48 -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 = 0.48 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 RCY44131 300 Synechocystis #2 RCY51226 208 Synechocystis #3 RCY49691 112 Synechocystis #4 RCY12795 137 Synechocystis #5 RCY04561 102 Synechocystis #6 RCY30742 53 Synechocystis #7 RCY03877 300 Synechocystis #8 RCY26596 300 Synechocystis Motif number 1 CTGACTGTAACCCCTGTCCCCCAAAGGTCCCTG 1 60 1 CCCCTCCCCA 0.986218 -241 TTTTTGCCACCCCAGCTGCCCGATTGGGGGTGA 1 94 0 CCCAGGCCCA 0.969604 -207 GGTCAACCTACCCTCTGGCCCAGTGAACTATTC 1 158 0 CCCTCGCCCG 0.984345 -143 TTCTGTAGGCCACCTTGCCCCTGTCCACACCAC 1 240 1 CACCTCCCCG 0.90615 -61 GGAAATATGGCCCAGATCGCCAGTTAGGAACTG 2 19 0 CCCAGCGCCG 0.934784 -190 CCCTTTCTCTCCCTTTTCCCCCGGGGGAGTGAT 2 114 1 CCCTTCCCCG 0.987239 -95 GATTTTTAACCCCCACCCCTTAGTTATTGATC 2 187 0 CCCCCCCCTA 0.955199 -22 TTGCTTTTTTCCCACTTGCCTTGCTGTTGCGCC 4 63 0 CCCACGCCTG 0.932931 -75 GGCTAACGATCCCCGGATCACGGTAACAGGTTG 5 17 0 CCCCGTCACG 0.929965 -86 GGTTTAGATACCCACCTCAACAATCCAGTAATG 7 127 0 CCCACCAACA 0.751348 -174 GGACCCAGGCCTCTCCTCCCCAATGGCGATCGC 7 170 0 CTCTCCCCCA 0.799197 -131 TCGGTCCCATCCCCTAACCATGGGCGGACCCAG 7 195 0 CCCCTCCATG 0.953032 -106 GCCAGGGCAACCCTTTGCTACAGTTGAATTGGT 7 240 1 CCCTTCTACG 0.81212 -61 CTAAATTTATCCCCGGCCTACCGGATTTCTATC 8 34 0 CCCCGCTACG 0.952881 -267 TTGTCGTCAGCCACTCCCCACTAAATTTATCCC 8 54 0 CCACTCCACA 0.638818 -247 CACAAACTGACTCAGGAGCACAGACAGTCGGGA 8 109 0 CTCAGGCACG 0.809503 -192 TCCGAACTCTCCCCCGGGCACAAACTGACTCAG 8 127 0 CCCCCGCACA 0.970209 -174 ATTGGGAAAGCCCTGGTGCCATGGCTATCTGCG 8 172 1 CCCTGGCCAG 0.805142 -129 TTTTCAGGGGCCCAGCTCAATCGCCGCAGATAG 8 196 0 CCCAGCAATG 0.639992 -105 ***** **** * Masking position 1 Map Score: 20.8963 Number of sites scoring better than the average of aligned sites = 6182 Number in coding regions = 5560 Number in noncoding regions = 622 Number of orfs with sites within 600 bp upstream = 444 Fraction of orfs with sites within 600 bp upstream = 0.0713138 Motif number 2 CAGGGAAACTCCCAGGGGACAG 1 2 0 CCCAGGGACA 0.948691 -299 CTGGGAGTTTCCCTGGGAATATCTACGGCTT 1 18 1 CCCTGGGATA 0.933355 -283 GGGAATAGTTCACTGGGCCAGAGGGTAGGTT 1 156 1 CACTGGGCAG 0.974109 -145 TAATGTTGGACATTGGGTAAACTGAATATTT 1 201 0 CATTGGGAAA 0.89471 -100 CAGTGGTGTGGACAGGGGCAAGGTGGCCTAC 1 244 0 GACAGGGCAA 0.826397 -57 CTGTCCACACCACTGGGACCGCTTTGGGATG 1 260 1 CACTGGGCCG 0.974579 -41 GTATCACTCCCCCGGGGGAAAAGGGAGAGAA 2 118 0 CCCGGGGAAA 0.965597 -91 TAATAGGAAAGACTGGGCTAATAAACCGTCG 5 52 1 GACTGGGTAA 0.864093 -51 CGGCGATCGCCATTGGGGAGGAGAGGCCTGG 7 168 1 CATTGGGAGG 0.732305 -133 GGGAGGAGAGGCCTGGGTCCGCCCATGGTTA 7 183 1 GCCTGGGCCG 0.966208 -118 CAAAGGGTTGCCCTGGCCAGAGAATCTGATC 7 226 0 CCCTGGCAGA 0.762102 -75 AATCCGGTAGGCCGGGGATAAATTTAGTGGG 8 40 1 GCCGGGGTAA 0.763592 -261 CCGAACTCTCCCCCGGGCACAAACTGACTCA 8 128 0 CCCCGGGACA 0.939544 -173 TCCTTGACCCCATTGGGAAAGCCCTGGTGCC 8 161 1 CATTGGGAAG 0.86417 -140 ATTGGGAAAGCCCTGGTGCCATGGCTATCTG 8 172 1 CCCTGGTCCA 0.823289 -129 AATAAAAATAGACTGGGAAAAATTTCGCGTT 8 276 0 GACTGGGAAA 0.962441 -25 ******* *** Masking position 6 Map Score: 17.5347 Number of sites scoring better than the average of aligned sites = 3401 Number in coding regions = 3098 Number in noncoding regions = 303 Number of orfs with sites within 600 bp upstream = 319 Fraction of orfs with sites within 600 bp upstream = 0.0512367 Motif number 3 AATTGCGCTGCTTTATCGGGGAAATATGGCC 2 40 0 CTTTTCGGGG 0.921405 -169 ATCAATAACTAAGGGGTGGGGGTTAAAAATC 2 188 1 AAGGGTGGGG 0.900189 -21 AAAGCTGAAAAATTAGTGGGGCAAATTGATT 6 25 1 AATTGTGGGG 0.983803 -29 TGGGTCCGCCCATGGTTAGGGGATGGGACCG 7 196 1 CATGTTAGGG 0.897288 -105 GAAAACATTCAATTTTTAGGGATAGAAATCC 8 14 1 AATTTTAGGG 0.966142 -287 CCGGGGATAAATTTAGTGGGGAGTGGCTGAC 8 51 1 ATTTGTGGGG 0.976464 -250 ATCTGCGGCGATTGAGCTGGGCCCCTGAAAA 8 198 1 ATTGGCTGGG 0.764909 -103 TAGGGTCGTAAATTTTCAGGGGCCCAGCTCA 8 210 0 AATTTCAGGG 0.953089 -91 TTGGGGCCAGAATTTTTAGGGTCGTAAATTT 8 226 0 AATTTTAGGG 0.966142 -75 ATTCTAACCTATTTTTTGGGGCCAGAATTTT 8 241 0 ATTTTTGGGG 0.97455 -60 **** ****** Masking position 9 Map Score: 9.50458 Number of sites scoring better than the average of aligned sites = 491 Number in coding regions = 433 Number in noncoding regions = 58 Number of orfs with sites within 600 bp upstream = 60 Fraction of orfs with sites within 600 bp upstream = 0.00963701 Motif number 4 ACCCTAGAGAGGAAAATATTCAGTTTACCCAATGTC 1 188 1 GAAAATCTTT 0.991043 -113 AAGCTTAGTTGCAAAAACCGCCCTTTCTCTCCCTTT 2 94 1 GAAAACCTTT 0.971465 -115 TTAAAGTTATGGAAAAATTTCGTTTTACAACGTATC 2 144 0 GAAAATCTTT 0.991043 -65 ACCCTCTTTTGCAAAAGTTGCTTTTTTCCCACTTGC 4 77 0 GAAAATCTTT 0.991043 -61 CAGTTATGATGAGAAATTGTCAGTTTTTACT 4 117 1 GGAAAGCTTT 0.950687 -21 TAAACTAAGGGTGTAATTTACCCTTTTTTCAACCAG 7 42 1 GGTAATCTTT 0.91822 -259 GAGGAAAACATTCAATTTTTAGGGATAG 8 3 1 GAAAATCTTT 0.991043 -298 AATAGACTGGGAAAAATTTCGCGTTTATCATTCTAA 8 265 0 GAAAATGTTT 0.948219 -36 * **** * * *** Masking position 6 Map Score: 9.03016 Number of sites scoring better than the average of aligned sites = 66 Number in coding regions = 48 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 20 Fraction of orfs with sites within 600 bp upstream = 0.00321234 Motif number 5 GCTATAGTTGTGACCGTTTTTTGCCACCCCAG 1 112 0 TACCTTTTTT 0.981095 -189 CCTCAATCCTTAACCTACTTTTAACTG 3 6 0 TACCACTTTT 0.97506 -107 CATAACTGATTTACCCTCTTTTGCAAAAGTTG 4 93 0 TACCTCTTTT 0.982463 -45 AGGGTGTAATTTACCCTTTTTTCAACCAGAGT 7 49 1 TACCTTTTTT 0.981095 -252 TTTATCATTCTAACCTATTTTTTGGGGCCAGA 8 246 0 TACCATTTTT 0.97313 -55 * *** ****** Masking position 9 Map Score: 3.94244 Number of sites scoring better than the average of aligned sites = 45 Number in coding regions = 34 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 6 TAGATATTCCCAGGGAAACTCCCAGGGGAC 1 13 0 CAGGGAAACT 0.9426 -288 CAAATCGAATCAGCAAAACTTCTTTGTGAG 3 53 0 CAGCAAAACT 0.992269 -60 AATTATGATCCAGCAAAACTGCATTCTAGC 4 20 1 CAGCAAAACT 0.992269 -118 GACAATTTCTCATCATAACTGATTTACCCT 4 108 0 CATCATAACT 0.907571 -30 CAATAATGGACAACAAAACTCTGGTTGAAA 7 68 0 CAACAAAACT 0.969975 -233 ********** Masking position 7 Map Score: 3.63287 Number of sites scoring better than the average of aligned sites = 49 Number in coding regions = 41 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 7 TGGTGTGGACAGGGGCAAGGTGGCCTACAG 1 242 0 AGGGGCAAGG 0.966113 -59 GCCAGTTAGGAACTGCTAGGAAC 2 4 0 AACTGCTAGG 0.93011 -205 ACAGAACTATATCGGCAAGGAAAACC 3 97 1 ATCGGCAAGG 0.991696 -16 GTCCGGGCGCAACAGCAAGGCAAGTGGGAA 4 58 1 AACAGCAAGG 0.987214 -80 CCTTCGAGTGATCAGCAAGGTCATTACTGG 7 106 1 ATCAGCAAGG 0.987214 -195 ********** Masking position 8 Map Score: 3.18131 Number of sites scoring better than the average of aligned sites = 70 Number in coding regions = 59 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 8 ATGTTGTAATGTTGGACATTGGGTAAACTG 1 208 0 GTTGGACATT 0.924755 -93 ACCGCTTTGGGATGGCCTTTTGAGGAATAT 1 277 1 GATGGCCTTT 0.95523 -24 ATATGGCCCAGATCGCCAGTTAGGAACTGC 2 18 0 GATCGCCAGT 0.949786 -191 CGCCCGGACTGTTGGCCGCTAGAATGCAGT 4 37 0 GTTGGCCGCT 0.942547 -101 CCAGAGTTTTGTTGTCCATTATTGGTTTCT 7 74 1 GTTGTCCATT 0.924755 -227 ATTACACGGCGATCGCCATTGGGGAGGAGA 7 162 1 GATCGCCATT 0.973266 -139 ********** Masking position 3 Map Score: 0.884852 Number of sites scoring better than the average of aligned sites = 683 Number in coding regions = 622 Number in noncoding regions = 61 Number of orfs with sites within 600 bp upstream = 73 Fraction of orfs with sites within 600 bp upstream = 0.011725 Motif number 9 CTGTCCCCTGGGAGTTTCCCTGGG 1 3 1 GCCCTGGGAG 0.97221 -298 GGTGAACAGGGACCTTTGGGGGACAGGGGTTA 1 67 0 GCCTTGGGGG 0.99353 -234 CACCCCAGCTGCCCGATTGGGGGTGAACAGGG 1 88 0 GCCGTTGGGG 0.994898 -213 ACACCACTGGGACCGCTTTGGGATGGCCTTTT 1 266 1 GCCGTTTGGG 0.990059 -35 GCTTTGGGATGGCCTTTTGAGGAATATATTT 1 280 1 GCCTTTGAGG 0.967188 -21 CGGAATCCTTGACCCCATTGGGAAAGCCCTGG 8 156 1 GCCCATTGGG 0.96089 -145 * *** ****** Masking position 4 Map Score: 3.85087 Number of sites scoring better than the average of aligned sites = 314 Number in coding regions = 281 Number in noncoding regions = 33 Number of orfs with sites within 600 bp upstream = 29 Fraction of orfs with sites within 600 bp upstream = 0.00465789 Motif number 10 TTAATTAAAGTTATGGAAAAATTTCGTTTT 2 154 0 TTATGGAAAA 0.92695 -55 TGCTGGATCATAATTGAAAAGCCG 4 5 0 TAATTGAAAA 0.93228 -133 CTTGACTTTACTGAAAAGCTGAAAAAT 6 8 1 TTACTGAAAA 0.927108 -46 TGGGGCAAATTGATTGAAAAAAT 6 41 1 TGATTGAAAA 0.974054 -13 CGGTTAATTATTATTGAAAACGTCC 7 6 0 TTATTGAAAA 0.971885 -295 AACAAAACTCTGGTTGAAAAAAGGGTAAAT 7 57 0 TGGTTGAAAA 0.932111 -244 ********** Masking position 7 Map Score: 4.03331 Number of sites scoring better than the average of aligned sites = 65 Number in coding regions = 49 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 11 GCTGGAGAAAGCCGTAGATATTCCCAGGGAA 1 26 0 GCCGAGATAT 0.952527 -275 CAACTGAGATGACGGGAATAGTTCACTGGGC 1 143 1 GACGGAATAG 0.907969 -158 CGGACTGTTGGCCGCTAGAATGCAGTTTTGC 4 32 0 GCCGTAGAAT 0.761161 -106 GGGATCGTTAGCCGATAATAGGAAAGACTGG 5 37 1 GCCGTAATAG 0.986006 -66 GTTCCGTCCCGCCGTTAAAAGTCT 7 287 1 GCCGTAAAAG 0.968406 -14 AATCCGGTAGGCCGGGGATAAATTTAGTGGG 8 40 1 GCCGGGATAA 0.946239 -261 CAGCTCAATCGCCGCAGATAGCCATGGCACC 8 186 0 GCCGAGATAG 0.983438 -115 **** ****** Masking position 10 Map Score: 2.08579 Number of sites scoring better than the average of aligned sites = 299 Number in coding regions = 272 Number in noncoding regions = 27 Number of orfs with sites within 600 bp upstream = 30 Fraction of orfs with sites within 600 bp upstream = 0.0048185 Motif number 12 ********** No masking Map Score: 2.60302e-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 13 ********** No masking Map Score: 2.60302e-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 14 ********** No masking Map Score: 2.60302e-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