AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00472_synecho_reg_100.orf -o00472_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 slr0884 300 gap1; glyceraldehyde 3-phosphate dehydrogenase 1 (gapdh 1) (GAP-1). #2 ssr1391 77 hypothetical protein. #3 slr0820 145 glucosyltransferase. #4 slr0776 107 lpxD; UDP-3-o-[3-hydroxymyristoyl] glucosamine n-acyltransferase. Motif number 1 ACTCACAATGCCTGGGCCACTAGCCCAAGTGAG 1 26 0 CCTGGGCAAG 0.98521 -275 GGAATTTTTACCATGACCGCCGATCAACTGTTG 1 72 1 CCATGACGGA 0.890928 -229 TAGCAAAATACCAGGGACAAGGAGGACAACTAA 1 108 0 CCAGGGCAGA 0.996037 -193 TCTAGATTTACCGGGGTAATAAAGTAATCCCGG 1 199 0 CCGGGGAAAA 0.955242 -102 GTTATCAAGCCCAGGAAAATCAGAGCAGTCATC 1 262 0 CCAGGAAAAG 0.975444 -39 ATTGCGCCCCCCAGGGACAACGG 2 1 0 CCAGGGCAGG 0.98572 -77 TTTCCCTGGGTAATGGAAAGGGTAGGC 2 61 0 CCTGGGAAGA 0.992304 -17 GATTGTCAGTCCAGGAAAGTAGAGCAAAATCTT 3 106 0 CCAGGAAGGA 0.968672 -40 AATCGGTCAGCCTTGCCCAAAGGGAAAATAAAG 4 15 0 CCTTGCCAGG 0.897019 -93 GATAATTGAACCAAGAAAAAGAAACTCCCCACC 4 50 1 CCAAGAAAAA 0.853559 -58 AACTCCCCACCCTAGGTAACTGGGATGGGGTTT 4 72 1 CCTAGGAAGG 0.965826 -36 ****** ** ** Masking position 2 Map Score: 15.5573 Number of sites scoring better than the average of aligned sites = 2784 Number in coding regions = 2556 Number in noncoding regions = 228 Number of orfs with sites within 600 bp upstream = 251 Fraction of orfs with sites within 600 bp upstream = 0.0403148 Motif number 2 ACTAATTCAAAAAACTCACAATGCCTGGGC 1 42 0 AAAACTCACA 0.948404 -259 CGGTCATGGTAAAAATTCCACTAATTCAAA 1 61 0 AAAAATTCCA 0.92283 -240 GACAAGGAGGACAACTAACATCAACAGTTG 1 96 0 ACAACTAACA 0.901638 -205 GGGCGGATAGCAAAATACCAGGGACAAGGA 1 118 0 CAAAATACCA 0.927926 -183 CCCCTTTAGCAAAACTACCCATCACTAGGG 1 145 0 AAAACTACCC 0.98743 -156 TGATAACTTAACAAATACCAAAC 1 288 1 ACAAATACCA 0.959504 -13 AGCCATGAATAAAACTACCCATTGATGGAA 3 32 1 AAAACTACCC 0.98743 -114 CCAAGAAAAAGAAACTCCCCACCCTAGGTA 4 60 1 GAAACTCCCC 0.953381 -48 ACCTGCAACGAAAAACCCCATCCCAGTTAC 4 87 0 AAAAACCCCA 0.917361 -21 ********** Masking position 4 Map Score: 10.741 Number of sites scoring better than the average of aligned sites = 869 Number in coding regions = 745 Number in noncoding regions = 124 Number of orfs with sites within 600 bp upstream = 122 Fraction of orfs with sites within 600 bp upstream = 0.0195952 Motif number 3 CCATAGGGTTTGTCCCTCACTTGGGCT 1 8 1 GTTTGTCCCT 0.97365 -293 TAGTTGTCCTCCTTGTCCCTGGTATTTTGC 1 109 1 CCTTGTCCCT 0.995346 -192 CCGTTGTCCCTGGGGGGCGCA 2 2 1 CGTTGTCCCT 0.98762 -76 TCTAAGCCTACCCTTTCCATTACCCAGGGA 2 56 1 CCCTTTCCAT 0.943829 -22 AGACTCAATCGCTTTTCCATCAATGGGTAG 3 46 0 GCTTTTCCAT 0.969276 -100 AAAGCTTTATTTTCCCTTTGGGCAAGG 4 8 1 TATTTTCCCT 0.896001 -100 ********** Masking position 6 Map Score: 4.80793 Number of sites scoring better than the average of aligned sites = 445 Number in coding regions = 376 Number in noncoding regions = 69 Number of orfs with sites within 600 bp upstream = 86 Fraction of orfs with sites within 600 bp upstream = 0.013813 Motif number 4 CCATAGGGTTTGTCCCTCACTT 1 3 1 ATAGGGTTTG 0.973146 -298 TCAACAGTTGATCGGCGGTCATGGTAAAAA 1 76 0 ATCGGCGGTC 0.889101 -225 TAGTTTTGCTAAAGGGGGTTAACTAAACAT 1 158 1 AAAGGGGGTT 0.9218 -143 GAGACAAGTCATAGGCTGTTGGACGATGAC 1 238 1 ATAGGCTGTT 0.93814 -63 GCAATGAACGATCGCCGTTGCGTTCAATCT 2 29 1 ATCGCCGTTG 0.946334 -49 CATTGATGGAAAAGCGATTGAGTCTCTTTT 3 51 1 AAAGCGATTG 0.804481 -95 TCTTTGAGAAATAGGCGTTTCAGCCTTTTA 3 80 0 ATAGGCGTTT 0.974062 -66 ATTAGAAAATATAGCGATTGTCAGTCCAGG 3 124 0 ATAGCGATTG 0.92875 -22 GGTAACTGGGATGGGGTTTTTCGTTGCAGG 4 86 1 ATGGGGTTTT 0.875485 -22 ********** Masking position 9 Map Score: 4.5208 Number of sites scoring better than the average of aligned sites = 982 Number in coding regions = 881 Number in noncoding regions = 101 Number of orfs with sites within 600 bp upstream = 112 Fraction of orfs with sites within 600 bp upstream = 0.0179891 Motif number 5 GGCCACTAGCCCAAGTGAGGGACAAACCCTA 1 14 0 CCAGTGAGGG 0.989885 -287 GGGCTAGTGGCCCAGGCATTGTGAGTTTTTT 1 33 1 CCAGGCATTG 0.948378 -268 TGCTATCCGCCCTAGTGATGGGTAGTTTTGC 1 136 1 CCAGTGATGG 0.996503 -165 AATAAAACTACCCATTGATGGAAAAGCGATT 3 39 1 CCATTGATGG 0.984353 -107 ATCCCAGTTACCTAGGGTGGGGAGTTTCTTT 4 67 0 CCAGGGTGGG 0.980268 -41 ** ******** Masking position 4 Map Score: 5.46462 Number of sites scoring better than the average of aligned sites = 201 Number in coding regions = 179 Number in noncoding regions = 22 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911 Motif number 6 ********** No masking Map Score: 2.65333e-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 7 ********** No masking Map Score: 2.65333e-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 8 ********** No masking Map Score: 2.65333e-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