AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i149_Thioredoxin_mjan_reg_300.orf -o149_mjan_300.ace -a/home/amcguire/genomes/ORF_mjan.txt -z/home/amcguire/genomes/mjan.fna -g0.31 -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 = 0.31 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 RMJ11103 99 M_jannaschii_chromosome #2 RMJ06689 196 M_jannaschii_chromosome #3 RMJ09620 165 M_jannaschii_chromosome #4 RMJ03965 39 M_jannaschii_chromosome #5 RMJ01109 243 M_jannaschii_chromosome #6 RMJ09316 300 M_jannaschii_chromosome #7 RMJ09765 160 M_jannaschii_chromosome Motif number 1 AATTTTATCCAAATTTTTATAAATAGTTTT 1 44 0 AAATTTTTAT 0.973165 -56 AATTTGGATAAAATTTTTATTATAAACTTA 1 59 1 AAATTTTTAT 0.973165 -41 CATATGTGTTAAAGTTATATTTTTCTGCTT 2 22 1 AAAGTTATAT 0.825324 -175 TAATTCATATGATTTTTTATTGTTTTTGGT 2 59 1 GATTTTTTAT 0.822011 -138 AAATCACAAAAAATTTAAATCATATCATAG 2 95 0 AAATTTAAAT 0.769677 -102 TTAAATCGAAAAGTATATATACTGGGGAAG 2 129 1 AAGTATATAT 0.890391 -68 GATAAATTTAATTTTTTTATTTT 3 4 0 ATTTTTTTAT 0.734536 -162 GCACATATAAAAATATATATCCTAATCATT 3 61 0 AAATATATAT 0.904279 -105 CATAAATTTAGATAAATCAATAA 3 153 0 AAATTTAGAT 0.832144 -13 TATTTCTTTCCATTTTTTATTTCAAC 4 7 0 CATTTTTTAT 0.822011 -33 ACTATCCCATTTTTATTTCTTTCCAT 4 24 0 CCATTTTTAT 0.704979 -16 ACTTTCTACTAAATTTATATAATATTGAAT 5 18 1 AAATTTATAT 0.980507 -226 ATTATTTGTGGTATTTATATACCCCCTATA 5 99 0 GTATTTATAT 0.759439 -145 GTATATATAGAATTATATATAAGAGCATTA 5 148 0 AATTATATAT 0.861548 -96 CACCTTATAGGAGTATATATAGAATTATAT 5 160 0 GAGTATATAT 0.7228 -84 CGTAACAACAAAGTATTTATTATATGAAAG 5 196 1 AAGTATTTAT 0.851086 -48 AGTTGGATTTACATTTATATATTAT 6 6 0 ACATTTATAT 0.914034 -295 GAAAAAATACAAATTTTTATAAAATATTGA 6 39 0 AAATTTTTAT 0.973165 -262 AAAAACCAAAAATTTTATATAGTCGATTAT 6 147 1 AATTTTATAT 0.953861 -154 AGGACTTTCACAGTTTATATATTAAGTGTT 6 224 1 CAGTTTATAT 0.894742 -77 GTTCCTTAAAAAATTTTTATCTCTGCGAAA 7 41 0 AAATTTTTAT 0.973165 -120 TGACCTCCTCATATTTATATTTTACCCTAA 7 127 0 ATATTTATAT 0.873133 -34 ********** Masking position 6 Map Score: 29.5883 Number of sites scoring better than the average of aligned sites = 1139 Number in coding regions = 703 Number in noncoding regions = 436 Number of orfs with sites within 600 bp upstream = 386 Fraction of orfs with sites within 600 bp upstream = 0.0619981 Motif number 2 TGAGCATATGTGTTAAAGTTATATTTTTCT 2 18 1 TGTTAAAGTT 0.867074 -179 TATTGTTTTTGGTGAAAGGCTATGATATGA 2 76 1 GGTGAAAGGC 0.974469 -121 AATCTCACCTGTGAATGGTTGTGTATGTT 2 178 0 TGTGAATGGT 0.77897 -19 GTATTTATTATATGAAAGTCTCTATCTAAT 5 208 1 TATGAAAGTC 0.949342 -36 AACTATACATTATTAAAGTCTCTCTATAGG 6 197 1 TATTAAAGTC 0.840959 -104 ATATATAAACTGTGAAAGTCCTATAGAGAG 6 216 0 TGTGAAAGTC 0.987942 -85 GAATCAATCCTCCGAAAGGTGGAGGGACTA 6 267 1 TCCGAAAGGT 0.905665 -34 TTTTTATCTCTGCGAAAGTCCTATTAAAAA 7 28 0 TGCGAAAGTC 0.98886 -133 AGGAACTGATGCCTAAAGGCATCCAACTGC 7 65 1 GCCTAAAGGC 0.802015 -96 ATATATGAACTGCGAAAGTCCTATTTAGGG 7 103 1 TGCGAAAGTC 0.98886 -58 ********** Masking position 5 Map Score: 11.5469 Number of sites scoring better than the average of aligned sites = 130 Number in coding regions = 65 Number in noncoding regions = 65 Number of orfs with sites within 600 bp upstream = 49 Fraction of orfs with sites within 600 bp upstream = 0.00787022 Motif number 3 TTTTATAAATAGTTTTCCAAAAATAGAATATTAA 1 26 0 AGTTTTAAAT 0.682472 -74 TATTTATAAAAATTTGGATAAAATTTTTATTATA 1 49 1 AATTTGAAAT 0.794443 -51 CTAATTTTGAGCATATGTGTTAAAGT 2 3 1 AATTTTATAT 0.923678 -194 TTAAAGTTATATTTTTCTGCTTATACTTCTAATT 2 30 1 ATTTTTTTAT 0.814258 -167 TATGATTTAAATTTTTTGTGATTTGGAATTAAAT 2 101 1 ATTTTTATTT 0.842701 -96 TGATAAATTTAATTTTTTTATTTT 3 1 0 AATTTTTTTT 0.794042 -165 GATTGTTTAAAATTTGATAAATTTAATTTTTTTA 3 15 0 AATTTGATTT 0.87062 -151 AATTTTAAACAATCTTTTTTATTTTTAATGATTA 3 35 1 AATCTTATTT 0.638167 -131 TTCAGAATTCAATATTATATAAATTTAGTAGAAA 5 20 0 AATATTAAAT 0.51935 -224 ATAATATTGAATTCTGAAATTTATGATGGTTTTC 5 36 1 ATTCTGTTAT 0.554812 -208 GAGCATTAAGAATTTTAACATTTTGAAAACCATC 5 60 0 AATTTTTTTT 0.784315 -184 CACAAATAATATTTTTTTAGAAATCACCATAATG 5 119 1 ATTTTTAAAT 0.709111 -125 GTAACAACAAAGTATTTATTATATGAAAGTCTCT 5 197 1 AGTATTATAT 0.693194 -47 ATGTAAATCCAACTTGTTCAATATTTTATAAAAA 6 22 1 AACTTGATAT 0.583859 -279 ATTTTATAAAAATTTGTATTTTTTCGATATCTTA 6 44 1 AATTTGTTTT 0.824623 -257 TTATAGGATAATTATGTAAGATATCGAAAAAATA 6 60 0 ATTATGATAT 0.746133 -241 GGTTTTTCCGATTTTTTTGGATTTTTCGGGGGGG 6 120 0 ATTTTTATTT 0.842701 -181 GACTATATAAAATTTTTGGTTTTTCCGATTTTTT 6 137 0 AATTTTTTTT 0.794251 -164 AATAATGTATAGTTTGTTAATAATATGAGTTAAT 6 177 0 AGTTTGTAAT 0.608343 -124 ATTAAAAATAAGTTTGGGGGATATC 7 2 0 AGTTTGATAT 0.9072 -159 ATCCAACTGCATTATGAAATATATGAACTGCGAA 7 85 1 ATTATGATAT 0.746133 -76 ****** **** Masking position 5 Map Score: 15.8252 Number of sites scoring better than the average of aligned sites = 2049 Number in coding regions = 1612 Number in noncoding regions = 437 Number of orfs with sites within 600 bp upstream = 325 Fraction of orfs with sites within 600 bp upstream = 0.0522004 Motif number 4 TAATTTTGAGCATATGTGTTAAAGTTATAT 2 12 1 CATATGTGTT 0.855972 -185 AATAAAAAATCATATGAATTAGAAGTATAA 2 50 0 CATATGAATT 0.853636 -147 TATATATTTTTATATGTGCTATGGTTTTTA 3 72 1 TATATGTGCT 0.77798 -94 ACCCCCTATACATAGGAGCATTAAGAATTT 5 79 0 CATAGGAGCA 0.870936 -165 GATAACACCTTATAGGAGTATATATAGAAT 5 165 0 TATAGGAGTA 0.886984 -79 GTTTGTTAATAATATGAGTTAATATAATCG 6 170 0 AATATGAGTT 0.931491 -131 AAAGTCTCTCTATAGGACTTTCACAGTTTA 6 211 1 TATAGGACTT 0.945514 -90 ACTTATTTTTAATAGGACTTTCGCAGAGAT 7 23 1 AATAGGACTT 0.930202 -138 CATTATGAAATATATGAACTGCGAAAGTCC 7 94 1 TATATGAACT 0.774712 -67 TTTTACCCTAAATAGGACTTTCGCAGTTCA 7 108 0 AATAGGACTT 0.930202 -53 ********** Masking position 4 Map Score: 5.72187 Number of sites scoring better than the average of aligned sites = 221 Number in coding regions = 161 Number in noncoding regions = 60 Number of orfs with sites within 600 bp upstream = 53 Fraction of orfs with sites within 600 bp upstream = 0.00851269 Motif number 5 AAAAATTCCSCCCCCCCCCCCCCCCCCCCC 6 95 1 CCCCCCCCCC 0.998295 -206 CCCCCCCCCCCCCCCCCCCCCCGAAAAATC 6 105 1 CCCCCCCCCC 0.998295 -196 CCCTCCATAGTCCCTCCACCTTTCGGAGGA 6 274 0 TCCCTCCACC 0.985333 -27 GTATCTCCCCTCCATAGTCCCTC 6 288 0 TCTCCCCTCC 0.974423 -13 GATATCCCCCAAACTTATTTTTAA 7 5 1 TCCCCCAAAC 0.927918 -156 ********** Masking position 6 Map Score: 5.34627 Number of sites scoring better than the average of aligned sites = 34 Number in coding regions = 12 Number in noncoding regions = 22 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 6 TTTTAGCCTATAATTTAATATTCTATTTTT 1 12 1 TAATTTAATA 0.922591 -88 AAAAACCTCTTAAGTTTATAATAAAAATTT 1 69 0 TAAGTTTATA 0.900483 -31 ATATACTGGGGAAGTTAATAATATAGTTCG 2 145 1 GAAGTTAATA 0.943268 -52 TAAATTTAGATAAATCAATAAAGTGCTCCT 3 144 0 TAAATCAATA 0.829044 -22 AACTTTCTACTAAATTTATATAATATTGAA 5 17 1 TAAATTTATA 0.753541 -227 ATAAATTTCAGAATTCAATATTATATAAAT 5 30 0 GAATTCAATA 0.923534 -214 CTCTTATATATAATTCTATATATACTCCTA 5 153 1 TAATTCTATA 0.867945 -91 GAAAAACCAAAAATTTTATATAGTCGATTA 6 146 1 AAATTTTATA 0.593351 -155 GTTAATAATATGAGTTAATATAATCGACTA 6 166 0 TGAGTTAATA 0.742938 -135 CCTATAGAGAGACTTTAATAATGTATAGTT 6 197 0 GACTTTAATA 0.729241 -104 TAAATATGAGGAGGTCAATAATAGTGTATA 7 140 1 GAGGTCAATA 0.764307 -21 ********** Masking position 8 Map Score: 4.24596 Number of sites scoring better than the average of aligned sites = 618 Number in coding regions = 476 Number in noncoding regions = 142 Number of orfs with sites within 600 bp upstream = 136 Fraction of orfs with sites within 600 bp upstream = 0.0218439 Motif number 7 ATAATTTAATATTCTATTTTTGGAAAACTATTT 1 21 1 ATTCTTTTTG 0.95031 -79 ATATGATTTTTTATTGTTTTTGGTGAAAGGCTA 2 65 1 TTATTTTTTG 0.943371 -132 TAAACAATCTTTTTTATTTTTAATGATTAGGAT 3 40 1 TTTTTTTTTA 0.780043 -126 TATGGTTTTTATTCTTCTTTTAGTATATTTTCT 3 91 1 ATTCTCTTTG 0.817132 -75 CTTTTAGTATATTTTCTTTGTTGAGGTGGTTAA 3 107 1 ATTTTTTTTG 0.975078 -59 ACTATCCCATTTTTATTTCTTTCCATTTTTTA 4 18 0 TTTTTTTTTT 0.780043 -22 TTCTAAAAAAATATTATTTGTGGTATTTATATA 5 108 0 ATATTTTTTG 0.95354 -136 GGGGGGGGAATTTTTTTTATAGGATAATTATG 6 78 0 ATTTTTTTTG 0.975078 -223 TCCCCCAAACTTATTTTTAATAGGACTTTCGCA 7 15 1 TTATTTTATG 0.724205 -146 ***** *** * * Masking position 8 Map Score: 3.4044 Number of sites scoring better than the average of aligned sites = 377 Number in coding regions = 286 Number in noncoding regions = 91 Number of orfs with sites within 600 bp upstream = 89 Fraction of orfs with sites within 600 bp upstream = 0.0142949 Motif number 8 TATTATAAACTTAAGAGGTTTTTAAGGTGT 1 76 1 TTAAGAGGTT 0.715998 -24 TAAGAGGTTTTTAAGGTGTTAGT 1 87 1 TTAAGGTGTT 0.972842 -13 ATTTTCTTTGTTGAGGTGGTTAAATGGAGG 3 117 1 TTGAGGTGGT 0.976959 -49 ATTCTGAAATTTATGATGGTTTTCAAAATG 5 46 1 TTATGATGGT 0.860484 -198 AAAATATTATTTGTGGTATTTATATACCCC 5 104 0 TTGTGGTATT 0.70965 -140 TATAAGAGCATTATGGTGATTTCTAAAAAA 5 131 0 TTATGGTGAT 0.871581 -113 ATATACTCCTATAAGGTGTTATCACGTAAC 5 172 1 ATAAGGTGTT 0.929148 -72 AAATATAAATATGAGGAGGTCAATAATAGT 7 135 1 ATGAGGAGGT 0.763177 -26 ********** Masking position 2 Map Score: 1.23101 Number of sites scoring better than the average of aligned sites = 299 Number in coding regions = 230 Number in noncoding regions = 69 Number of orfs with sites within 600 bp upstream = 82 Fraction of orfs with sites within 600 bp upstream = 0.0131706 Motif number 9 ********** No masking Map Score: 2.97961e-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: 2.97961e-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: 2.97961e-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