AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i164_NIF1_aful_reg_300.orf -o164_aful_300.ace -a/home/amcguire/alignace/lib/ORF_aful.txt -z/skink1/amcguire/genomes/aful.fna -g0.49 -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 = 0.49 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 RAG04733 300 Archaeoglobus_fulgidus #2 RAG12654 142 Archaeoglobus_fulgidus #3 RAG07415 102 Archaeoglobus_fulgidus Motif number 1 GTATCGTCAGCTTATGAAACGTTCTGAACCATC 1 20 0 CTTATGAAAT 0.901392 -281 GTTTCATAAGCTGACGATACGTTTCATCTCCAA 1 33 1 CTGACGATAT 0.93798 -268 CTCGGCAGGCTGGATGAAAATGTTGATAAAGTA 1 142 0 TGGATGAAAT 0.81503 -159 ACTATTTTTTTTCCCGAAACTTTTAAATAGTTA 1 260 1 TTCCCGAAAT 0.961982 -41 GGACAATTCCTGCAGGAAATTGTTGCATAATAA 2 15 1 TGCAGGAAAT 0.961982 -128 GGTATCGACACTCCCGAAAGGCTCTACGCCCCA 2 108 1 CTCCCGAAAT 0.988972 -35 CTTATTAACACTCAGGAAAAATTGCTTCG 3 7 0 CTCAGGAAAT 0.995228 -96 ATAAGGTTGACTGAGGCAATCCTTACACTCCAG 3 35 1 CTGAGGCAAT 0.957293 -68 TCCAGGAAAACTCACGAAACATTAAATAGCTCA 3 63 1 CTCACGAAAT 0.995228 -40 CATTAAATAGCTCAGGAAAGCGTTAACCATT 3 82 1 CTCAGGAAAT 0.995228 -21 ********* * Masking position 9 Map Score: 14.0969 Number of sites scoring better than the average of aligned sites = 264 Number in coding regions = 235 Number in noncoding regions = 29 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 2 GAAACTATTTTTTTTCCCGAAACTTTTAAAT 1 257 1 TTTTCCCGAA 0.771774 -44 TGCAACAATTTCCTGCAGGAATTGTCCTTCC 2 11 0 TCTGCAGGAA 0.901255 -132 CTAAGCGAACTCTCGCAGGGAGACGAGCGGT 2 80 1 TCCGCAGGGA 0.941564 -63 AGCGGTATCGACACTCCCGAAAGGCTCTACG 2 105 1 ACCTCCCGAA 0.989642 -38 AACCTTATTAACACTCAGGAAAAATTGCTTC 3 12 0 ACCTCAGGAA 0.99203 -91 GGCAATCCTTACACTCCAGGAAAACTCACGA 3 49 1 ACCTCCAGGA 0.93144 -54 CACTCCAGGAAAACTCACGAAACATTAAATA 3 60 1 AACTCACGAA 0.96377 -43 AAACATTAAATAGCTCAGGAAAGCGTTAACC 3 79 1 TACTCAGGAA 0.971668 -24 ** ******** Masking position 11 Map Score: 6.52641 Number of sites scoring better than the average of aligned sites = 662 Number in coding regions = 620 Number in noncoding regions = 42 Number of orfs with sites within 600 bp upstream = 35 Fraction of orfs with sites within 600 bp upstream = 0.00562159 Motif number 3 TCGTTTTATCTGCAACTATTGTCTTAAATA 1 72 1 TGCAACTATT 0.976066 -229 TCTCGTGGCAGGTAATTATTTTTCATTTTG 1 215 1 GGTAATTATT 0.962823 -86 CTCCCTATGTGGAAACTATTTTTTTTCCCG 1 246 1 GGAAACTATT 0.974111 -55 ACATTGTTAAGGTAACTATTTAAAAGTTTC 1 275 0 GGTAACTATT 0.989589 -26 TCTTTTATTATGCAACAATTTCCTGCAGGA 2 22 0 TGCAACAATT 0.925346 -121 GGTTGACTGAGGCAATCCTTACACTCCAGG 3 39 1 GGCAATCCTT 0.912304 -64 TCAGGAAAGCGTTAACCATT 3 93 1 GTTAACCATT 0.910901 -10 ********** Masking position 5 Map Score: 6.84543 Number of sites scoring better than the average of aligned sites = 186 Number in coding regions = 172 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 4 AACGTTTCATAAGCTGACGATACGTTTCAT 1 30 1 AAGCTGACGA 0.976299 -271 AGCGGTATCGACACTCCCGAAAGGCTCTAC 2 105 1 ACACTCCCGA 0.984925 -38 AACCTTATTAACACTCAGGAAAAATTGCTT 3 13 0 ACACTCAGGA 0.990057 -90 CACTCCAGGAAAACTCACGAAACATTAAAT 3 60 1 AAACTCACGA 0.992612 -43 AAACATTAAATAGCTCAGGAAAGCGTTAAC 3 79 1 TAGCTCAGGA 0.968015 -24 ********** Masking position 5 Map Score: 4.31212 Number of sites scoring better than the average of aligned sites = 94 Number in coding regions = 88 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 5 TTCTGAACCATCTGGCAGCTT 1 1 0 TCTGCAGCTT 0.956186 -300 TGTCCTAAAATCTGAAATCCTACTTTATCAA 1 122 1 TCTGAATCCT 0.90697 -179 ATCAACATTTTCATCCAGCCTGCCGAGTTAC 1 148 1 TCATCAGCCT 0.952686 -153 CTATTTTTTTTCCCGAAACTTTTAAATAGTT 1 261 1 TCCCAAACTT 0.870827 -40 TGTAGATTACTCTCTCAACCTCTGTCTCTTT 2 47 0 TCTCCAACCT 0.988638 -96 CTGCGAGAGTTCGCTTAGCCTGTAGATTACT 2 67 0 TCGCTAGCCT 0.92191 -76 AAGGATTGCCTCAGTCAACCTTATTAACACT 3 28 0 TCAGCAACCT 0.98513 -75 CCAGGAAAACTCACGAAACATTAAATAGCTC 3 64 1 TCACAAACAT 0.866981 -39 **** ****** Masking position 7 Map Score: 3.44368 Number of sites scoring better than the average of aligned sites = 894 Number in coding regions = 828 Number in noncoding regions = 66 Number of orfs with sites within 600 bp upstream = 54 Fraction of orfs with sites within 600 bp upstream = 0.00867331 Motif number 6 CTGAAATCCTACTTTATCAACATTTTCATC 1 133 1 ACTTTATCAA 0.971638 -168 CAAAGCAAGCCCTTTAATAAATCCAGGTAA 1 175 0 CCTTTAATAA 0.928521 -126 TTAAATAGTTACCTTAACAATGTTAAGTT 1 282 1 ACCTTAACAA 0.981471 -19 GCCTCAGTCAACCTTATTAACACTCAGGAA 3 22 0 ACCTTATTAA 0.971638 -81 ********** Masking position 5 Map Score: 0.829949 Number of sites scoring better than the average of aligned sites = 49 Number in coding regions = 40 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 7 GCTGACGATACGTTTCATCTCCAAAATCAATCG 1 42 1 CGTTATCTCA 0.988827 -259 CAAAATCAATCGTTTTATCTGCAACTATTGTCT 1 63 1 CGTTATCTCA 0.988827 -238 TCCAGCCTGCCGAGTTACCTGGATTTATTAAAG 1 161 1 CGGTACCTGA 0.943566 -140 CTGCCACGAGAGGATGATCACCAAAGCAAGCCC 1 193 0 AGATATCACA 0.906518 -108 AGAGGTTGAGAGAGTAATCTACAGGCTAAGCGA 2 55 1 AGGTATCTCA 0.992171 -88 CAGGGAGACGAGCGGTATCGACACTCCCGAAAG 2 95 1 AGGGATCGCA 0.954317 -48 ** ** **** ** Masking position 7 Map Score: 0.601658 Number of sites scoring better than the average of aligned sites = 72 Number in coding regions = 65 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 8 ********** No masking Map Score: -8.21797e-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 9 ********** No masking Map Score: -8.21797e-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 10 ********** No masking Map Score: -8.21797e-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