AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/alignace/lib/ORF_synecho.txt -z/skink1/amcguire/genomes/synecho.fna -iargR_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 argD 123 N-acetylornithine aminotransferase #2 argH 300 L-argininosuccinate lyase #3 argB 263 N-acetylglutamate kinase #4 carB 46 carbamoyl-phosphate synthase, pyrimidine-specific, large chain #5 pyrR 300 pyrimidine operon regulatory protein PyrR #6 argC 245 N-acetyl-gamma-glutamyl-phosphate reductase #7 argF 112 ornithine carbamoyltransferase chain f #8 carA 50 carbamoyl-phosphate synthetase subunit A #9 argG 233 argininosuccinate synthetase Motif number 1 GGTGACCCTACCCCTGCAGACCATATCCAAATT 1 72 1 CCCCCAGCCA 0.993158 -52 CAGACCATATCCAAATTTGGCCAGTCTAACGCG 1 88 1 CCAATTGCCA 0.948619 -36 CTGAGCAAAAACCATACTGTCCGTCAGCCAAGG 2 66 0 ACCACTGCCG 0.940387 -235 TAATCAAAGCCCAAATTTGCCCAGACTGGATAA 2 160 0 CCAATTGCCA 0.948619 -141 ACCAGTGAAACCCCGTATGCCCCAACCAAGCAC 2 201 0 CCCCATGCCC 0.906752 -100 CACAACGAAATCCCCCCATCCCA 2 288 1 TCCCCATCCA 0.678719 -13 AGTCAAGTCTTCCACATAGCCCAGCCGTTGTCT 3 25 1 TCCATAGCCA 0.860841 -239 ACTTTATCTAACCCTTCCGCCCGTAGAGATGGG 3 64 1 ACCCCCGCCG 0.947772 -200 GGAGCTAAAACCCATCTCGACCATTCACCTAGC 3 234 1 CCCATCGCCA 0.978207 -30 TCATACCACGCCCCCACTGTCCGGCAGGGTGAA 5 207 1 CCCCCTGCCG 0.994976 -94 CGGACCTAACCCCCGTCTAGCCATTGTACGCAA 6 55 1 CCCCCTACCA 0.953618 -191 TTTTTCCGGGATCCTTCTGCCCAGAGATATTGC 6 114 0 ATCCCTGCCA 0.880946 -132 AATTCTAATATCAAAATTGCCCAATGGCGAACT 6 169 0 TCAATTGCCA 0.754455 -77 TCACTGCCATCCCCCCAAGACCATTAACCGAGT 7 20 1 CCCCAAGCCA 0.961675 -93 TCGAATTAAGCCCCATTTTGCCATACTCGGTTA 7 44 0 CCCCTTTCCA 0.961919 -69 AGCCGTTATCCCCGATTGTCCAATGTGGTGGT 7 91 0 CCCCTTGCCA 0.99655 -22 AGCAGATTCGCCCCTGTCGTCTGTTCCACTAAT 8 25 0 CCCCTCGCTG 0.720301 -26 CTGAGATCGACTCCGTTTGACCATTCCACGGAC 9 32 0 CTCCTTGCCA 0.959661 -202 GTTAAAACAAACAATTCTGACCAAGACATTACT 9 169 1 ACAACTGCCA 0.851685 -65 **** *** *** Masking position 11 Map Score: 29.5883 Number of sites scoring better than the average of aligned sites = 2480 Number in coding regions = 2266 Number in noncoding regions = 214 Number of orfs with sites within 600 bp upstream = 208 Fraction of orfs with sites within 600 bp upstream = 0.0334083 Motif number 2 TTTGAGACATTTGCCAGTGGATATAACTGTGTCCCAGC 2 17 0 TGCTGTATCT 0.969916 -284 TGGGCAAATTTGGGCTTTGATTATTGGTTTTGTGCTTG 2 170 1 TGCTGTATGT 0.873882 -131 CCACATAGCCCAGCCGTTGTCTTTATCTACTTTATCTA 3 36 1 CGCTGTTTCT 0.986119 -228 CTGAACAGTTTTGACGTTGCCTTTAGCATTTAAACTGA 3 178 1 TGCTGTTTCA 0.861979 -86 AGCATTTAAACTGACAGGCAGTTTTGCTCCCCGGAGCT 3 202 1 CGCGCTTTCT 0.971206 -62 AGGTGAATGGTCGAGATGGGTTTTAGCTCCGGGGAGCA 3 226 0 TGGGGTTTCT 0.912493 -38 GATTCGGACCCGGATTTTTGGTCAATAAACCT 4 5 1 CGCGGTTTGT 0.971206 -42 GTAGTCTGGCTCGACTGTGATTATTGCCCATAATCCAG 5 93 0 TGCTGTATCC 0.925228 -208 TTTATGGCTCCAGCCCCGGAGTTTACCTCCAGGGGTAG 5 127 0 CGCGGTTTCT 0.993669 -174 GTACAATGGCTAGACGGGGGTTAGGTCCGATCATCAAT 6 46 0 TGCGGTAGCC 0.824343 -200 CTCCCCAGGACGGACTAGCAATATCTCTGGGCAGAAGG 6 97 1 CGCGCTATCT 0.960786 -149 CCTCGGCTATCTGTCAGGGGTTTTGCCTAGCCCGTTGA 9 114 0 CGCGGTTTCT 0.993669 -120 * * * ** *** ** Masking position 12 Map Score: 12.5293 Number of sites scoring better than the average of aligned sites = 707 Number in coding regions = 632 Number in noncoding regions = 75 Number of orfs with sites within 600 bp upstream = 84 Fraction of orfs with sites within 600 bp upstream = 0.0134918 Motif number 3 GGGTAGGGTCACCCCTCTGAAATAATTGTCT 1 54 0 ACCCCTCGAA 0.841418 -70 GGGTGACCCTACCCCTGCAGACCATATCCAA 1 71 1 ACCCCTGAGA 0.96395 -53 CACAGTTATATCCACTGGCAAATGTCTCAAA 2 24 1 TCCACTGCAA 0.731765 -277 TTAATATTTTTCCCCTCTCAAACTAACTACT 2 236 1 TCCCCTCCAA 0.958502 -65 GCTTATTTCTGCCCATCTCTACGGGCGGAAG 3 77 0 GCCCATCCTA 0.575496 -187 TGGCAATGGGTCCGCTGCAAGTTGTGCTTAT 3 102 0 TCCGCTGAAG 0.670139 -162 TCTCAGTAATGCCCCTGGCAATGGGTCCGCT 3 117 0 GCCCCTGCAA 0.978685 -147 CGGAGCTAAAACCCATCTCGACCATTCACCT 3 233 1 ACCCATCCGA 0.91381 -31 AGACCTCTGCACCGCCGACGGGTCTGGATTA 5 70 1 ACCGCCGCGG 0.909446 -231 GAGCCAGACTACCCCTGGAGGTAAACTCCGG 5 119 1 ACCCCTGAGG 0.941822 -182 CACCACCTGCACCGATGCCAAAAAGTTGTTT 5 276 0 ACCGATGCAA 0.825488 -25 ATCGGACCTAACCCCCGTCTAGCCATTGTAC 6 53 1 ACCCCCGCTA 0.910309 -193 CGCAAAGTTGACCGCTCCCCAGGACGGACTA 6 83 1 ACCGCTCCCA 0.832273 -163 ATCACTGCCATCCCCCCAAGACCATTAACCG 7 19 1 TCCCCCCAGA 0.746569 -94 TAGCAGATTCGCCCCTGTCGTCTGTTCCACT 8 28 0 GCCCCTGCGT 0.880204 -23 GCTAGGCAAAACCCCTGACAGATAGCCGAGG 9 121 1 ACCCCTGCAG 0.980255 -113 ******* *** Masking position 3 Map Score: 13.2609 Number of sites scoring better than the average of aligned sites = 2620 Number in coding regions = 2379 Number in noncoding regions = 241 Number of orfs with sites within 600 bp upstream = 275 Fraction of orfs with sites within 600 bp upstream = 0.0441696 Motif number 4 TAATTTCTTTTCCTTGGCTGACGGACAGTA 2 55 1 TCCTTGGCTG 0.96398 -246 GCCCAAATTTGCCCAGACTGGATAAAATTA 2 155 0 GCCCAGACTG 0.947287 -146 ATTGGTTTTGTGCTTGGTTGGGGCATACGG 2 192 1 TGCTTGGTTG 0.790027 -109 CTATGTGGAAGACTTGACTGTGACCGCCTT 3 14 0 GACTTGACTG 0.884204 -250 GCTAACAGTTGCCTTGATTGTGGCAAGATT 3 147 0 GCCTTGATTG 0.976163 -117 TGCTCCAATCGCCTTGATTGTATCGAATGA 5 13 1 GCCTTGATTG 0.976163 -288 GGGGTAGTCTGGCTCGACTGTGATTATTGC 5 104 0 GGCTCGACTG 0.970772 -197 ATCATACCACGCCCCCACTGTCCGGCAGGG 5 206 1 GCCCCCACTG 0.931345 -95 GCGAACTTGATCCCCGGTTTAGCAAAGATT 6 146 0 TCCCCGGTTT 0.647064 -100 AGCCGTTATCCCCGATTGTCCAATGTGG 7 95 0 TCCCCGATTG 0.957335 -18 GAAATCCTTTGCCTCGGCTATCTGTCAGGG 9 133 0 GCCTCGGCTA 0.910303 -101 ********** Masking position 9 Map Score: 9.29167 Number of sites scoring better than the average of aligned sites = 1066 Number in coding regions = 974 Number in noncoding regions = 92 Number of orfs with sites within 600 bp upstream = 108 Fraction of orfs with sites within 600 bp upstream = 0.0173466 Motif number 5 AAGATCAGGAGACAATTATTTCAGAGGGGTGACCC 1 45 1 GCAATTCAGA 0.977803 -79 GGCGGTCACAGTCAAGTCTTCCACATAGCCCAGCC 3 16 1 GCAAGTCACA 0.952867 -248 CCTTCCGCCCGTAGAGATGGGCAGAAATAAGCACA 3 76 1 GAGAGGCAGA 0.800301 -188 CCTTGATTGTGGCAAGATTCTCAGTAATGCCCCTG 3 131 0 GCAAGTCAGT 0.986052 -133 GTCAAAACTGTTCAGGGCTAACAGTTGCCTTGATT 3 158 0 TCAGGTCAGT 0.814731 -106 CTGGATTATGGGCAATAATCACAGTCGAGCCAGAC 5 93 1 GCAATTCAGT 0.95226 -208 CCCACTGTCCGGCAGGGTGAACAGAGGAGACTTTC 5 219 1 GCAGGGCAGA 0.987523 -82 GAAAAAAGACGCAAAGTAGGACAGAGTTAGACCAT 6 13 1 GAAAGGCAGA 0.950535 -233 TTGGGGGGATGGCAGTGATGTCAGAAA 7 3 0 GCAGTTCAGA 0.969102 -110 CCCATCGAATGTCAAGCTTTCCAGATAGAGCGTAT 9 70 0 GCAAGTCAGA 0.993636 -164 * **** * **** Masking position 13 Map Score: 9.60628 Number of sites scoring better than the average of aligned sites = 226 Number in coding regions = 199 Number in noncoding regions = 27 Number of orfs with sites within 600 bp upstream = 31 Fraction of orfs with sites within 600 bp upstream = 0.00497912 Motif number 6 GGTTTTAGCTCCGGGGAGCAAAACTGCCTGT 3 215 0 CCGGGGACAA 0.98138 -49 GACCAAAAATCCGGGTCCGAATC 4 3 0 CCGGGTCGAA 0.98733 -44 TGCACCGCCGACGGGTCTGGATTATGGGCAA 5 77 1 ACGGGTCGGA 0.916049 -224 GAGGTAAACTCCGGGGCTGGAGCCATAAAGA 5 136 1 CCGGGGCGGA 0.995258 -165 CTAGTCCGTCCTGGGGAGCGGTCAACTTTGC 6 84 0 CTGGGGACGG 0.75803 -162 TAGCAATATCTCTGGGCAGAAGGATCCCGGA 6 112 1 TCTGGGCGAA 0.866936 -134 CTTTGCTAAACCGGGGATCAAGTTCGCCATT 6 149 1 CCGGGGACAA 0.98138 -97 GCAGTAATGTCTTGGTCAGAATTGTTTGTTT 9 173 0 CTTGGTCGAA 0.817882 -61 ******* *** Masking position 5 Map Score: 3.57951 Number of sites scoring better than the average of aligned sites = 1064 Number in coding regions = 999 Number in noncoding regions = 65 Number of orfs with sites within 600 bp upstream = 85 Fraction of orfs with sites within 600 bp upstream = 0.0136524 Motif number 7 GTTAGACTGGCCAAATTTGGATATGGTCTG 1 88 0 CCAAATTTGG 0.429034 -36 ATATCCACTGGCAAATGTCTCAAATAATTT 2 31 1 GCAAATGTCT 0.869748 -270 TCCAGTCTGGGCAAATTTGGGCTTTGATTA 2 163 1 GCAAATTTGG 0.877522 -138 GTGATAGTTAGCAAATGATGGCGGAGTAGT 2 261 0 GCAAATGATG 0.877537 -40 CGTCGGCGGTGCAGAGGTCTTTTACGGATA 5 60 0 GCAGAGGTCT 0.76544 -241 GAAAAAAGACGCAAAGTAGGACAGAGTTAG 6 13 1 GCAAAGTAGG 0.931249 -233 GCCATTGTACGCAAAGTTGACCGCTCCCCA 6 74 1 GCAAAGTTGA 0.822187 -172 CCCCGGTTTAGCAAAGATTTTTTCCGGGAT 6 135 0 GCAAAGATTT 0.744893 -111 CTCTGCAAAGGTTGCTTCTGGGTC 9 5 1 GCAAAGGTTG 0.97374 -229 GATAGCCGAGGCAAAGGATTTCGGCAGTGT 9 141 1 GCAAAGGATT 0.895249 -93 ********** Masking position 5 Map Score: 2.68505 Number of sites scoring better than the average of aligned sites = 1075 Number in coding regions = 952 Number in noncoding regions = 123 Number of orfs with sites within 600 bp upstream = 126 Fraction of orfs with sites within 600 bp upstream = 0.0202377 Motif number 8 TTTTGCTCAGAATATCAGTGCGATTAAATCC 2 89 1 AATATCATGC 0.932713 -212 AGTCAGCGAGGATATCAATGGATTTAATCGC 2 108 0 GATATCATGG 0.974096 -193 GTTAGGTCCGATCATCAATGGTCTAACTCTG 6 34 0 ATCATCATGG 0.886452 -212 ACGGACTAGCAATATCTCTGGGCAGAAGGAT 6 106 1 AATATCTTGG 0.79079 -140 TTTCTGACATCACTGCCATCCCCCCA 7 6 1 GACATCATGC 0.983369 -107 AGGACAATTTGACATTAGTGGAACAGACGAC 8 12 1 GACATTATGG 0.954928 -39 TTCTGACCAAGACATTACTGCTAGAATGGCA 9 183 1 GACATTATGC 0.941623 -51 ******* *** Masking position 4 Map Score: 2.67129 Number of sites scoring better than the average of aligned sites = 297 Number in coding regions = 270 Number in noncoding regions = 27 Number of orfs with sites within 600 bp upstream = 32 Fraction of orfs with sites within 600 bp upstream = 0.00513974 Motif number 9 TTTAAGATCAGGAGACAATTATTTCAGAGGGG 1 42 1 GGAACATTAT 0.984998 -82 TGACTGGCTGGGACACAGTTATATCCACTGGC 2 11 1 GGAACATTAT 0.984998 -290 TGCCCAGACTGGATAAAATTATTCCAGGCATT 2 144 0 GGAAAATTAT 0.966822 -157 GGTCTTTTACGGATACAATTTTAGAGACTGCA 5 43 0 GGAACATTTT 0.978642 -258 GAAGGATCCCGGAAAAAATCTTTGCTAAACCG 6 130 1 GGAAAATCTT 0.901588 -116 *** *** **** Masking position 7 Map Score: 1.24607 Number of sites scoring better than the average of aligned sites = 21 Number in coding regions = 14 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 10 CTTAAATCGACTGACCTGTTTTAAGTGAGG 1 18 0 CTGACCTGTT 0.857133 -106 GGGGGGCTCCTAACGCGTTAGACTGGCCA 1 105 0 CTAACGCGTT 0.864925 -19 CTCAAACTAACTACTCCGCCATCATTTGCT 2 252 1 CTACTCCGCC 0.891069 -49 TCTACTTTATCTAACCCTTCCGCCCGTAGA 3 61 1 CTAACCCTTC 0.823966 -203 GCCCATAATCCAGACCCGTCGGCGGTGCAG 5 76 0 CAGACCCGTC 0.805004 -225 AGAGATATTGCTAGTCCGTCCTGGGGAGCG 6 95 0 CTAGTCCGTC 0.950061 -151 ACCAATTTCACTAATCTGTTGGCATTATTT 6 212 1 CTAATCTGTT 0.897431 -34 ACGACAGGGGCGAATCTGCTAAT 8 38 1 CGAATCTGCT 0.647757 -13 AAACTGAGATCGACTCCGTTTGACCATTCC 9 38 0 CGACTCCGTT 0.895651 -196 GGGGTTTTGCCTAGCCCGTTGAATCTCACA 9 106 0 CTAGCCCGTT 0.96552 -128 ********** Masking position 1 Map Score: 1.32091 Number of sites scoring better than the average of aligned sites = 1004 Number in coding regions = 904 Number in noncoding regions = 100 Number of orfs with sites within 600 bp upstream = 109 Fraction of orfs with sites within 600 bp upstream = 0.0175072 Motif number 11 ATTGTCTCCTGATCTTAAATCGACTGACCTG 1 30 0 GTCTTAAATC 0.964646 -94 GAATATCAGTGCGATTAAATCCATTGATATC 2 98 1 GGATTAAATC 0.904899 -203 GCTGCAAGTTGTGCTTATTTCTGCCCATCTC 3 89 0 GGCTTATTTC 0.924591 -175 GGTTCTCAAATCTCAAATAATG 6 234 0 GTCTCAAATC 0.92015 -12 TGGCAAAATGGGGCTTAATTCGATCGATGTT 7 54 1 GGCTTAATTC 0.980276 -59 TAATTCGATCGATGTTAATTCGACCACCACA 7 69 1 GTGTTAATTC 0.899365 -44 * ********* Masking position 5 Map Score: 0.182255 Number of sites scoring better than the average of aligned sites = 90 Number in coding regions = 74 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911 Motif number 12 ********** No masking Map Score: -1.46782e-13 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: -1.46782e-13 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: -1.46782e-13 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