AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i225_Glutamyl_tRNA_synthase_bsub_reg_300.orf -aORF_bsub.txt -zbsub.fna -g0.435 -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 = 0.435 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 yerL 300 alternate gene name: yedA; similar to hypothetical proteins #2 yerN 190 similar to pet112-like protein Motif number 1 GGTAACTTAACCTAACAAAGTATTCCCGG 1 7 1 TTACCACAAA 0.942935 -294 TAAGCTGGAAATACCGTTGCAAACCTAGAAGGG 1 66 1 ATACGTCAAA 0.919051 -235 CTAGAAGGGAATAAAGAATAAAACGCTTTCAAA 1 90 1 ATAAGAAAAA 0.902998 -211 CAAAAAATAATTAAAGTAAAAATATTCAGAAAA 1 119 1 TTAAGAAAAT 0.939227 -182 CTTCTCCTCATTTTAGTATAAAATATATAGGGT 1 166 1 TTTAGAAAAA 0.894894 -135 CAGGCCTGTGTTTTCGAAACAATACCCTATATA 1 189 0 TTTCGACAAT 0.949429 -112 AACAAGCCCTTTAAAGCAACAAAACGCCTTGAG 1 223 0 TTAAGACAAA 0.983016 -78 ATTATATGACTTAACGGAGAAATATGTGGAGGT 1 271 1 TTACGAAAAT 0.968103 -30 TCAAGTCCGATTACCGTTTCAAAGTTCAATTCT 2 20 0 TTACGTCAAA 0.972906 -171 *** ** * **** Masking position 11 Map Score: 8.18652 Number of sites scoring better than the average of aligned sites = 799 Number in coding regions = 671 Number in noncoding regions = 128 Number of orfs with sites within 600 bp upstream = 147 Fraction of orfs with sites within 600 bp upstream = 0.0236107 Motif number 2 TCGCTTGAATGGCCGGGAATACTTTGTTAG 1 22 0 GGCCGGGAAT 0.976123 -279 AGAAATATGTGGAGGTGGATCAT 1 288 1 GGAGGTGGAT 0.985855 -13 AACGGTAATCGGACTTGAAGTCCACGTTGA 2 35 1 GGACTTGAAG 0.960761 -156 CGCGCCGAATGGCGTTGGAGAGCTTGAGAA 2 87 0 GGCGTTGGAG 0.987686 -104 CATTCGGCGCGGAGGCGAATACGCAGACAA 2 106 1 GGAGGCGAAT 0.979528 -85 AAGCGTTATTGACCTCGGATATCCGGGCGT 2 134 1 GACCTCGGAT 0.920864 -57 GAACAAAGAAGCCGTTGAATTCGCA 2 176 1 GCCGTTGAAT 0.957686 -15 ********** Masking position 9 Map Score: 5.36309 Number of sites scoring better than the average of aligned sites = 626 Number in coding regions = 571 Number in noncoding regions = 55 Number of orfs with sites within 600 bp upstream = 53 Fraction of orfs with sites within 600 bp upstream = 0.00851269 Motif number 3 CTAGGTTTGCAACGGTATTTCCAGCTTATG 1 64 0 AACGGTATTT 0.942355 -237 TAAAGAATAAAACGCTTTCAAAAAATAATT 1 101 1 AACGCTTTCA 0.938191 -200 AAAGCAACAAAACGCCTTGAGACAGGCCTG 1 214 0 AACGCCTTGA 0.960121 -87 TGTTGCTTTAAAGGGCTTGTTTTTGATATG 1 235 1 AAGGGCTTGT 0.85096 -66 TGAACTTTGAAACGGTAATCGGACTTGAAG 2 25 1 AACGGTAATC 0.842235 -166 CAAGCTCTCCAACGCCATTCGGCGCGGAGG 2 91 1 AACGCCATTC 0.976069 -100 CGAGGTCAATAACGCTTGTCTGCGTATTCG 2 121 0 AACGCTTGTC 0.92697 -70 TGCGAATTCAACGGCTTCTTTGTTCAGAA 2 172 0 AACGGCTTCT 0.971813 -19 ********** Masking position 2 Map Score: 3.64289 Number of sites scoring better than the average of aligned sites = 1650 Number in coding regions = 1511 Number in noncoding regions = 139 Number of orfs with sites within 600 bp upstream = 147 Fraction of orfs with sites within 600 bp upstream = 0.0236107 Motif number 4 TACTTTGTTAGGTTAAGTTACC 1 3 0 GGTTAAGTTA 0.907121 -298 GCCATTCAAGCGATGAAACATTGATCATAA 1 39 1 CGATGAAACA 0.852915 -262 CAACAAAACGCCTTGAGACAGGCCTGTGTT 1 210 0 CCTTGAGACA 0.977393 -91 CATATTTCTCCGTTAAGTCATATAATACTG 1 267 0 CGTTAAGTCA 0.973258 -34 TTGAAGTCCACGTTGAGTTAAAAACAAAAT 2 49 1 CGTTGAGTTA 0.988351 -142 GCGTTGGAGAGCTTGAGAAAATTTTTGATT 2 76 0 GCTTGAGAAA 0.821167 -115 ACAAAGAAGCCGTTGAATTCGCA 2 178 1 CGTTGAATTC 0.876871 -13 ********** Masking position 6 Map Score: 2.3475 Number of sites scoring better than the average of aligned sites = 474 Number in coding regions = 412 Number in noncoding regions = 62 Number of orfs with sites within 600 bp upstream = 42 Fraction of orfs with sites within 600 bp upstream = 0.0067459 Motif number 5 GTATTCCCGGCCATTCAAGCGATGAAACATT 1 30 1 CCATCAAGCG 0.932841 -271 ATTTTATACTAAAATGAGGAGAAGGAGAAAC 1 159 0 AAATGAGGAG 0.768069 -142 ATTGTTTCGAAAACACAGGCCTGTCTCAAGG 1 199 1 AAAACAGGCC 0.977754 -102 TGATCATATCAAAAACAAGCCCTTTAAAGCA 1 238 0 AAAACAAGCC 0.965168 -63 ACGCCATTCGGCGCGGAGGCGAATACGCAGA 2 102 1 GCGGGAGGCG 0.911033 -89 AGGCGAATACGCAGACAAGCGTTATTGACCT 2 118 1 GCAACAAGCG 0.979467 -73 TTTGTTCAGAACAGGCAGGACGCCCGGATAT 2 152 0 ACAGCAGGAC 0.955199 -39 CCTGTTCTGAACAAAGAAGCCGTTGAATTCG 2 168 1 ACAAGAAGCC 0.977564 -23 *** ******* Masking position 7 Map Score: 1.9241 Number of sites scoring better than the average of aligned sites = 1604 Number in coding regions = 1482 Number in noncoding regions = 122 Number of orfs with sites within 600 bp upstream = 99 Fraction of orfs with sites within 600 bp upstream = 0.0159011 Motif number 6 AATAAAACGCTTTCAAAAAATAATTAAAGT 1 106 1 TTTCAAAAAA 0.967324 -195 AAGTAAAAATATTCAGAAAAATATTTCGTT 1 132 1 ATTCAGAAAA 0.903695 -169 TAGGGTATTGTTTCGAAAACACAGGCCTGT 1 193 1 TTTCGAAAAC 0.954181 -108 ATACTGATCATATCAAAAACAAGCCCTTTA 1 243 0 TATCAAAAAC 0.969953 -58 TTAAAAACAAAATCAAAAATTTTCTCAAGC 2 66 1 AATCAAAAAT 0.892003 -125 ********** Masking position 7 Map Score: 0.756664 Number of sites scoring better than the average of aligned sites = 663 Number in coding regions = 516 Number in noncoding regions = 147 Number of orfs with sites within 600 bp upstream = 159 Fraction of orfs with sites within 600 bp upstream = 0.0255381 Motif number 7 ********** No masking Map Score: -8.78641e-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: -8.78641e-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: -8.78641e-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