AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i060_Diaminopimelate_Pathway_synecho_reg_100.orf -o060_synecho_100.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 RCY32906 29 Synechocystis #2 RCY06983 300 Synechocystis #3 RCY44336 300 Synechocystis #4 RCY38981 59 Synechocystis #5 RCY43130 300 Synechocystis Motif number 1 CATCCAGTGCTTGCCCTGGGTTAACGG 1 13 1 TTGCCCGGTC 0.978644 -17 ATGTTTGATGATGTCCAAGGTCAAATCTACGTCCA 2 87 0 ATGTCCGGTA 0.98006 -214 CCTGAACGTTTTCCCCTAGTTTGTACTGAATCTTA 2 122 1 TTCCCCGTTA 0.964739 -179 TTCACGGCGATCGCCCGTCGTCTGGGCTAGCAAAA 2 185 1 TCGCCCCGTG 0.941032 -116 ATCCCAACTGATCCCCTTGGTTTTGCTAGCCCAGA 2 205 0 ATCCCCGGTG 0.975351 -96 TGATCCCTTGTTGTCCATGCTACAACCATTTTCGA 2 257 0 TTGTCCGCTA 0.909607 -44 GAAAAGATTCTCGCCCTAGGAAAAAATGGCACCCG 3 32 0 TCGCCCGGAA 0.969811 -269 CATTATTGAATTGTCCAGCTAGAAAAATCATTGAT 3 110 0 TTGTCCCTAA 0.746778 -191 TTAGGGGGCAATGCCCTGCGTCACAATTAGTTTTT 3 155 1 ATGCCCCGTA 0.982779 -146 TCTGACTGCGTTGCCCATCTTTCGATCCCGATTAG 3 258 1 TTGCCCCTTA 0.9522 -43 CTCGGCAAATTTCTCCTAGGAGTAATTTGCCT 5 8 0 TTCTCCGGAA 0.953115 -293 TTCCGGGTTCAAGTCCCGGGTTCCGCATTCTAACT 5 73 0 AAGTCCGGTG 0.741866 -228 AAAGACCATCATCCCCCAGGATTGACTGGAAGTCA 5 186 1 ATCCCCGGAA 0.970385 -115 AAGTCGGCAGTTCCCCATGGTATCAAAAAAATTAA 5 250 0 TTCCCCGGTA 0.992776 -51 ****** *** * Masking position 6 Map Score: 17.7524 Number of sites scoring better than the average of aligned sites = 2494 Number in coding regions = 2275 Number in noncoding regions = 219 Number of orfs with sites within 600 bp upstream = 228 Fraction of orfs with sites within 600 bp upstream = 0.0366206 Motif number 2 TACAAACTAGGGGAAAACGTTCAGGATGTT 2 117 0 GGGAAAACGT 0.831195 -184 CAAAACCAAGGGGATCAGTTGGGATCAGTC 2 215 1 GGGATCAGTT 0.968451 -86 GGGATCAGTTGGGATCAGTCCTCCCTTTGG 2 225 1 GGGATCAGTC 0.988171 -76 TGGACAACAAGGGATCAGTCCGCTAGAAAC 2 275 1 GGGATCAGTC 0.988171 -26 ACCCCCCGGCGGGAAAAGATTCTCGCCCTA 3 49 0 GGGAAAAGAT 0.905402 -252 GCGGTTTAGGGGGCAATGCCCTGCGTCACA 3 150 1 GGGCAATGCC 0.85731 -151 TGGATGGGTTGGGAAAAATT 4 1 0 GGGAAAAATT 0.772182 -59 CCACCGCAAGCGGAACTGGCGGAATTGGTA 5 144 0 CGGAACTGGC 0.880165 -157 TGATACCATGGGGAACTGCCGACTTTTCCC 5 260 1 GGGAACTGCC 0.97722 -41 GATAGGGCCGGGGAAAAGTCGGCAGTTCCC 5 270 0 GGGAAAAGTC 0.990618 -31 GGTGATTTCGGGATAGGGCCGGGGAAAAG 5 282 0 GGGATAGGGC 0.941764 -19 ********** Masking position 3 Map Score: 11.896 Number of sites scoring better than the average of aligned sites = 1418 Number in coding regions = 1258 Number in noncoding regions = 160 Number of orfs with sites within 600 bp upstream = 174 Fraction of orfs with sites within 600 bp upstream = 0.0279473 Motif number 3 TACCAGAGCGTTTTTAAACCA 2 1 0 TTTTTAACCA 0.926811 -300 CCCCTTGGTTTTGCTAGCCCAGACGACGGGC 2 197 0 TTGCTACCCA 0.972266 -104 CTACAACCATTTTCGACCCCAAAGGGAGGAC 2 242 0 TTTCGACCCA 0.993411 -59 TTTGGCTGATTTTTTACCCCAACAACTTTGA 3 195 1 TTTTTACCCA 0.978913 -106 GTTGCCCATCTTTCGATCCCGATTAGCTACT 3 267 1 TTTCGACCCG 0.978899 -34 AATTTTTCCCAACCCATCCATGGTTA 4 6 1 TTCCCACCCA 0.953628 -54 GGCTTAATTTTTTTGATACCATGGGGAACTG 5 247 1 TTTTGAACCA 0.952184 -54 ****** **** Masking position 6 Map Score: 6.30081 Number of sites scoring better than the average of aligned sites = 214 Number in coding regions = 176 Number in noncoding regions = 38 Number of orfs with sites within 600 bp upstream = 41 Fraction of orfs with sites within 600 bp upstream = 0.00658529 Motif number 4 CCAATTGATCATAATATAAGCCG 3 1 1 CCATTTCATA 0.98274 -300 AAGCCGGGTGCCATTTTTTCCTAGGGCGAGAAT 3 28 1 CCATTTCCTA 0.991568 -273 TGATTTAGTCCCATTCTCTCAAACCGGCCTGGG 3 81 0 CCATCTCAAA 0.967131 -220 TTAGTTAAGCCCAGTTGGTCAAAGTTGTTGGGG 3 211 0 CCATTTCAAA 0.977642 -90 AGGCAAATTACTCCTAGGAGAAATTT 5 4 1 CAATTTCCTA 0.938474 -297 AGCGCGTCTACCAATTCCGCCAGTTCCGCTTGC 5 136 1 CCATTGCCAG 0.949237 -165 CTGTTGACTTCCAGTCAATCCTGGGGGATGATG 5 192 0 CCATCTCCTG 0.981563 -109 *** ** ***** Masking position 3 Map Score: 4.68781 Number of sites scoring better than the average of aligned sites = 296 Number in coding regions = 262 Number in noncoding regions = 34 Number of orfs with sites within 600 bp upstream = 42 Fraction of orfs with sites within 600 bp upstream = 0.0067459 Motif number 5 CTGATCCCCTTGGTTTTGCTAGCCCAGACG 2 203 0 TGGTTTTGCT 0.992124 -98 ACTAAATCAATGATTTTTCTAGCTGGACAA 3 105 1 TGATTTTTCT 0.914631 -196 AATTCAATAATGGCTTTGCGGTTTAGGGGG 3 133 1 TGGCTTTGCG 0.983939 -168 CCGCTTGCGGTGGTTTTGCTTACCGAAAGA 5 161 1 TGGTTTTGCT 0.992124 -140 TGGGGGATGATGGTCTTTCGGTAAGCAAAA 5 174 0 TGGTCTTTCG 0.964526 -127 ********** Masking position 6 Map Score: 4.04103 Number of sites scoring better than the average of aligned sites = 234 Number in coding regions = 216 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 21 Fraction of orfs with sites within 600 bp upstream = 0.00337295 Motif number 6 ATGTCATTGAGCCAACCGCCAATCATTTTT 2 45 1 GCCAACCGCC 0.91873 -256 AGGAAAAAATGGCACCCGGCTTATATTATG 3 20 0 GGCACCCGGC 0.994584 -281 GGCCTGGGGGACCCCCCGGCGGGAAAAGAT 3 59 0 ACCCCCCGGC 0.97726 -242 TCCCATTCTCTCAAACCGGCCTGGGGGACC 3 76 0 TCAAACCGGC 0.972983 -225 AGGTTTACTATCAACTCGGCAAATTTCTCC 5 27 0 TCAACTCGGC 0.946188 -274 GTTAGAATGCGGAACCCGGGACTTGAACCC 5 74 1 GGAACCCGGG 0.964035 -227 ACCCGGGACTTGAACCCGGAAGTCCTTACG 5 87 1 TGAACCCGGA 0.963515 -214 AAGACCATCATCCCCCAGGATTGACTGGAA 5 187 1 TCCCCCAGGA 0.811599 -114 ********** Masking position 8 Map Score: 5.2947 Number of sites scoring better than the average of aligned sites = 1276 Number in coding regions = 1194 Number in noncoding regions = 82 Number of orfs with sites within 600 bp upstream = 84 Fraction of orfs with sites within 600 bp upstream = 0.0134918 Motif number 7 TCCTGAACGTTTTCCCCTAGTTTGTACTGA 2 121 1 TTTCCCCTAG 0.821162 -180 AGTTGGGATCAGTCCTCCCTTTGGGGTCGA 2 231 1 AGTCCTCCCT 0.831747 -70 ACAAGGGATCAGTCCGCTAGAAACATGCCC 2 281 1 AGTCCGCTAG 0.96643 -20 CCCGCCGGGGGGTCCCCCAGGCCGGTTTGA 3 66 1 GGTCCCCCAG 0.988771 -235 AGCTTACTCCTCCAGTAGCTAATCG 3 286 0 ACTCCTCCAG 0.958524 -15 GCGTCTACCAATTCCGCCAGTTCCGCTTGC 5 139 1 ATTCCGCCAG 0.977026 -162 GAAAGACCATCATCCCCCAGGATTGACTGG 5 185 1 CATCCCCCAG 0.94405 -116 AAAAGTCGGCAGTTCCCCATGGTATCAAAA 5 257 0 AGTTCCCCAT 0.860156 -44 ********** Masking position 3 Map Score: 3.77339 Number of sites scoring better than the average of aligned sites = 1399 Number in coding regions = 1234 Number in noncoding regions = 165 Number of orfs with sites within 600 bp upstream = 157 Fraction of orfs with sites within 600 bp upstream = 0.0252168 Motif number 8 GGTCGAAAATGGTTGTAGCATGGACAACAA 2 255 1 GGTTGTAGCA 0.88895 -46 GGGCATGTTTCTAGCGGACTGATCCC 2 285 0 GTTTCTAGCG 0.972157 -16 GGCGGGAAAAGATTCTCGCCCTAGGAAAAA 3 42 0 GATTCTCGCC 0.939223 -259 AGGACTTCCGGGTTCAAGTCCCGGGTTCCG 5 83 0 GGTTCAAGTC 0.887988 -218 GCTAGATTCAGGTTCTAGTGTTCGTAAGGA 5 109 0 GGTTCTAGTG 0.979107 -192 ACTAGAACCTGAATCTAGCGCGTCTACCAA 5 120 1 GAATCTAGCG 0.938227 -181 ********** Masking position 4 Map Score: 0.215837 Number of sites scoring better than the average of aligned sites = 239 Number in coding regions = 195 Number in noncoding regions = 44 Number of orfs with sites within 600 bp upstream = 51 Fraction of orfs with sites within 600 bp upstream = 0.00819146 Motif number 9 ********** No masking Map Score: -2.90369e-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: -2.90369e-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 11 ********** No masking Map Score: -2.90369e-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