AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00660_aful_reg_100.orf -o00660_aful_100.ace -a/home/amcguire/genomes/ORF_aful.txt -z/home/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 AF1540 143 succinyl-CoA synthetase, beta subunit (sucC-1) #2 AF1667 158 sulfate adenylyltransferase (sat) #3 AF1669 48 adenylylsulfate reductase, subunit B (aprB) #4 AF1671 64 coenzyme F390 synthetase (ftsA-2) #5 AF1720 182 acetolactate synthase, large subunit (ilvB-1) #6 AF1778 105 stage V sporulation protein (spoVG) #7 AF1779 57 2-hydroxyacid dehydrogenase, putative #8 AF2013 275 coenzyme F390 synthetase (ftsA-3) #9 AF2014 63 sugar transporter, putative #10 AF2100 106 acetolactate synthase, large subunit (ilvB-4) #11 AF2186 65 succinyl-CoA synthetase, beta subunit (sucC-2) #12 AF2187 174 A. fulgidus predicted coding region AF2187 Motif number 1 GAATTTCTTTTCCAAAAAATTTAAATAGTAAC 1 8 0 TCAAATTTAA 0.968405 -136 GAAAAGAAATTCCGAAAATTTTTTATATTGAAAAA 1 31 1 TCAAATTTTA 0.981425 -113 GTAGAAAATTTTTTGAACTCCTTTGC 2 2 1 TGAAATTTTA 0.927092 -157 TCTTTGAAAATTCGAAAACCTTTAATCATTAAAAT 2 79 1 TCAAACTTTA 0.962009 -80 TAAAATATTTTTCGAAACCTTTATATAAGGCTGTG 2 108 1 TCAAATTTAA 0.969105 -51 ATTTAGAAAAAAGAAAAATTTTAGAGCT 4 4 0 AGAAATTTAA 0.906728 -61 TTTTTTCTAAATCTAAAAGTTTTTATTGCATTGCC 4 27 1 ACAAATTTTA 0.976626 -38 GCACTGCTGCAAGCTAAGTTTTAAAAACTACTTAC 5 23 0 AGTAATTTAA 0.647739 -160 GCCTGGGCGAACCAAAACTTTTTAAAGCGCATGCT 5 67 1 ACAAATTTTA 0.975904 -116 GTTTCCTGCAATCAAAATTCTTATATACCACTTTG 6 46 1 ACAAACTTAA 0.91642 -60 TGGCTTTTGCTTCAAAACCTTTTTATCTTTTCTGG 7 20 1 TCAAATTTTA 0.981425 -38 ATGCGTTTGCAGCAAAAGGCTTTAAAAGCCACTGC 8 186 0 ACAAACTTTA 0.950563 -90 CATATTTATTTGCATAAAATTTTTAGCTTTTTAAT 9 26 1 TCTAATTTTA 0.911691 -38 AAATCAACCTTAGCAAACTTTTTAAAATTATAATC 10 71 1 TGAAATTTTA 0.956966 -36 * * *** **** * Masking position 7 Map Score: 23.5673 Number of sites scoring better than the average of aligned sites = 112 Number in coding regions = 39 Number in noncoding regions = 73 Number of orfs with sites within 600 bp upstream = 89 Fraction of orfs with sites within 600 bp upstream = 0.0142949 Motif number 2 ATTTAAATTTTTTGGAAAAGAAATTCCGAA 1 17 1 TTTGGAAAAG 0.919689 -127 AAATTTTTTATATTGAAAAATTGAGAATGT 1 46 1 TATTGAAAAA 0.823914 -98 TTTTGAATGTCTTTGAAAATTCGAAAACCT 2 70 1 CTTTGAAAAT 0.672279 -89 TATATAAAGGTTTCGAAAAATATTTTAATG 2 105 0 TTTCGAAAAA 0.794713 -54 TTATATAAGGCTGTGAAAAAAAATACATCA 2 128 1 CTGTGAAAAA 0.79067 -31 TTAATTTTTTTTTAGAAAAATGTATGAAAA 3 12 1 TTTAGAAAAA 0.935755 -37 AACTTTTAGATTTAGAAAAAAGAAAAATTT 4 18 0 TTTAGAAAAA 0.935755 -47 CCAGCATGCGCTTTAAAAAGTTTTGGTTCG 5 74 0 CTTTAAAAAG 0.745843 -109 GAAAAAGTTCTCTGGAAAAGAGTTCATTGT 5 117 1 TCTGGAAAAG 0.883701 -66 CTCTAACTCCTTTAGAAAAGAAGTAAAAGC 5 153 0 TTTAGAAAAG 0.959037 -30 CAGAATTGAACCCAGAAAAGATAAAAAGGT 7 36 0 CCCAGAAAAG 0.854421 -22 GAGCTGCAGTTCCAGAAAAGCTGACAGGTT 8 17 0 TCCAGAAAAG 0.867945 -259 TATCTGGCAGTATTAAAAAACGGTTTTCCC 8 53 1 TATTAAAAAA 0.400882 -223 TACTTCACCATCCTGAAAAACGAATGCGTT 8 214 0 TCCTGAAAAA 0.803435 -62 ATGATTATAATTTTAAAAAGTTTGCTAAGG 10 78 0 TTTTAAAAAG 0.76782 -29 AAACACAGCAGAGAAAAGAGAACGATCG 12 9 1 CAGAGAAAAG 0.66112 -166 CGTAACGCTGCTTAGAAAAACCGTTACAAG 12 37 1 CTTAGAAAAA 0.928575 -138 ********** Masking position 6 Map Score: 12.6312 Number of sites scoring better than the average of aligned sites = 908 Number in coding regions = 777 Number in noncoding regions = 131 Number of orfs with sites within 600 bp upstream = 146 Fraction of orfs with sites within 600 bp upstream = 0.02345 Motif number 3 TGGTGGGAGTGATGAAAAAGTTCTCTGGAAA 5 104 1 GATGAAAAGT 0.90049 -79 CTTTAGAAAAGAAGTAAAAGCTGTACTACAA 5 143 0 GAAGAAAAGC 0.969383 -40 AATTTTGATTGCAGGAAACGTTAGATTAAAT 6 34 0 GCAGAAACGT 0.940036 -72 AAAAGGTTTTGAAGCAAAAGCCAAACTCTTA 7 12 0 GAAGAAAAGC 0.969752 -46 GCAGCAAAAGGCTTTAAAAGCCACTGCCTTT 8 182 0 GCTTAAAAGC 0.55715 -94 AAAGCCTTTTGCTGCAAACGCATTCGTTTTT 8 198 1 GCTGAAACGC 0.982118 -78 AAATAAATATGCATAAAATGCACACT 9 6 0 GCATAAATGC 0.767606 -58 ATTTTGTCAGGCTGCAAGAGTTTAAAACCCA 10 44 0 GCTGAAGAGT 0.894934 -63 GCTATATCTGGCTGATATAGCCTTTTCTCGT 12 126 0 GCTGTATAGC 0.832039 -49 GCCAGATATAGCAGCAATAGCCATCGATTAT 12 145 1 GCAGAATAGC 0.972832 -30 **** ****** Masking position 7 Map Score: 9.9545 Number of sites scoring better than the average of aligned sites = 648 Number in coding regions = 611 Number in noncoding regions = 37 Number of orfs with sites within 600 bp upstream = 38 Fraction of orfs with sites within 600 bp upstream = 0.00610344 Motif number 4 GTTACTATTTAAATTTTTTGGAAAAG 1 5 1 CTATTAATTT 0.510645 -139 GCCTGCACATCCAACCACCTTTTAAGTTCGAT 1 79 0 CCACCACTTT 0.88732 -65 AATTCGAAAACCTTTAATCATTAAAATATTTT 2 87 1 CCTTAACATT 0.921259 -72 TCAACTCACCTCCAACCTTTTCATACATTT 3 29 0 CCTCAACTTT 0.896457 -20 GTTTTAAAAACTACTTACCTTTGTAGGAAA 5 9 0 CTATTACTTT 0.825391 -174 TTCTAACCCTCCTTTCAAATTTCGTTACTCTC 6 84 0 CCTTCAATTT 0.927218 -22 GCTTCAAAACCTTTTTATCTTTTCTGGGTTCA 7 28 1 CTTTTACTTT 0.930049 -30 AGAATCAACCTGTCAGCTTTTCTGGAACTG 8 9 1 CCTTCACTTT 0.982967 -267 GCCTGGTGATCCTCTCGGCTTTGGGAGCCGGT 8 124 0 CCTTCGCTTT 0.908317 -152 AAAGCCACTGCCTTTAATCATTACAGAGGGGC 8 165 0 CCTTAACATT 0.921259 -111 CCTTAGCAAACTTTTTAAAATTATAATCATAA 10 78 1 CTTTTAAATT 0.603533 -29 TAATTTACCACTTCGCAACATTAAAAC 11 49 1 CTTGCACATT 0.738595 -17 *** *** **** Masking position 11 Map Score: 6.04679 Number of sites scoring better than the average of aligned sites = 572 Number in coding regions = 499 Number in noncoding regions = 73 Number of orfs with sites within 600 bp upstream = 72 Fraction of orfs with sites within 600 bp upstream = 0.0115644 Motif number 5 GAACTCCTTTGCCTTTTATTTTCGAAGAGT 2 25 1 GCCTTTTATT 0.927084 -134 AAATTCGAAAACCTTTAATCATTAAAATAT 2 86 1 ACCTTTAATC 0.929247 -73 TTTTTTCACAGCCTTATATAAAGGTTTCGA 2 119 0 GCCTTATATA 0.725246 -40 CTCACCTCCAACCTTTTCATACATTTTTCT 3 25 0 ACCTTTTCAT 0.628986 -24 TTATTGCATTGCCTTAACTCTGCATC 4 49 1 GCCTTAACTC 0.964343 -16 TTGTAGTACAGCTTTTACTTCTTTTCTAAA 5 143 1 GCTTTTACTT 0.664097 -40 AAAAGCCACTGCCTTTAATCATTACAGAGG 8 168 0 GCCTTTAATC 0.97565 -108 TCGATTTAGAACCTTAAAACCTAAACTTAA 11 22 1 ACCTTAAAAC 0.685223 -44 GGCTGATATAGCCTTTTCTCGTCGAATTCT 12 118 0 GCCTTTTCTC 0.976677 -57 ********** Masking position 5 Map Score: 4.25278 Number of sites scoring better than the average of aligned sites = 452 Number in coding regions = 417 Number in noncoding regions = 35 Number of orfs with sites within 600 bp upstream = 35 Fraction of orfs with sites within 600 bp upstream = 0.00562159 Motif number 6 TTCTGCCTGCACATCCAACCACCTTTTAAGTTC 1 82 0 ACATCACCCC 0.96005 -62 AGGACTTCCGCCATTCTGCCTGCACATCCAACC 1 95 0 CCATCGCCGC 0.983309 -49 AAGGTAATTGCACTGCTGCAAGCTAAGTTTTAA 5 34 0 CACTCGCAGC 0.95592 -149 ACTTTTTCATCACTCCCACCACCAGCATGCGCT 5 92 0 CACTCACCCC 0.983995 -91 CACCAGGCTACCCTACGGCCCCTCTGTAATGAT 8 148 1 CCCTCGCCCT 0.979427 -128 TGAAGTATTTAAATCCTGCCTCCCTCATGACAG 8 237 1 AAATCGCCCC 0.985128 -39 ATGGGTTTTAAACTCTTGCAGCCTGACAAAATC 10 43 1 AACTTGCACC 0.81232 -64 AATAGGCAGAACCTTCTGCCCCCTCTACAACTT 12 82 1 ACCTCGCCCC 0.996293 -93 **** * *** ** Masking position 4 Map Score: 5.61287 Number of sites scoring better than the average of aligned sites = 500 Number in coding regions = 464 Number in noncoding regions = 36 Number of orfs with sites within 600 bp upstream = 31 Fraction of orfs with sites within 600 bp upstream = 0.00497912 Motif number 7 TAGAAAATTTTTTGAACTCCTTTGCCTTTTATTT 2 12 1 TTTAACTTTG 0.983639 -147 ACCGCGCAATTTTCAAACTCTTCGAAAATAAAAG 2 37 0 TTTAACTTCG 0.954204 -122 ATTGCGCGGTTTTGAATGTCTTTGAAAATTCGAA 2 61 1 TTTAACTTTG 0.983639 -98 TCTTTGAAAATTCGAAAACCTTTAATCATTAAAA 2 79 1 TTCAACTTTA 0.676713 -80 TTAAAATATTTTTCGAAACCTTTATATAAGGCTG 2 107 1 TTTGACTTTA 0.756145 -52 AATCTAAAAGTTTTTATTGCATTGCCTTAACTCT 4 36 1 TTTTACATTG 0.864288 -29 AGGTAAGTAGTTTTTAAAACTTAGCTTGCAGCAG 5 21 1 TTTTACTTAG 0.798465 -162 CAGCATGCGCTTTAAAAAGTTTTGGTTCGCCCAG 5 69 0 TTTAATTTTG 0.811807 -114 TCAAAATTCTTATATACCACTTTGTTTGAGAGTA 6 57 1 TATTACTTTG 0.768423 -49 AGGCAGTGGCTTTTAAAGCCTTTTGCTGCAAACG 8 184 1 TTTAACTTTT 0.840063 -92 AATTTTTAGCTTTTTAATTCTTTAAATTTCC 9 43 1 TTTTACTTTA 0.873149 -21 GCTGCAAGAGTTTAAAACCCATCGAATACGATTA 10 31 0 TTTAACATCG 0.809726 -76 ATGATTATAATTTTAAAAAGTTTGCTAAGGTTGA 10 74 0 TTTAAGTTTG 0.864744 -33 *** ** ***** Masking position 6 Map Score: 9.89946 Number of sites scoring better than the average of aligned sites = 236 Number in coding regions = 196 Number in noncoding regions = 40 Number of orfs with sites within 600 bp upstream = 44 Fraction of orfs with sites within 600 bp upstream = 0.00706714 Motif number 8 GAAACCTTTATATAAGGCTGTGAAAAAAAA 2 121 1 TATAAGGCTG 0.903328 -38 TTTTAAAACTTAGCTTGCAGCAGTGCAATT 5 32 1 TAGCTTGCAG 0.881765 -151 GCTCAGACAGTATCTGGCAGTATTAAAAAA 8 43 1 TATCTGGCAG 0.983715 -233 GATAAAGTGTATCTTTCTGTCATGAGGGA 8 257 0 TATCTTTCTG 0.854889 -19 AGGTTGATTTTGTCAGGCTGCAAGAGTTTA 10 51 0 TGTCAGGCTG 0.956683 -56 ATTGCTGCTATATCTGGCTGATATAGCCTT 12 133 0 TATCTGGCTG 0.991199 -42 ********** Masking position 1 Map Score: 2.55436 Number of sites scoring better than the average of aligned sites = 144 Number in coding regions = 131 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 9 ACCACCCCATTTTCAACGAAACCAAA 1 128 0 CCCCATTCAA 0.985421 -16 TTCTAACCCTCCTTTCAAATTTCGTTAC 6 88 0 CCCTCTTCAA 0.980938 -18 AACGGTTTTCCCGCCAGTTCAATGATGGGGCC 8 71 1 CCGCCTTCAA 0.987058 -205 GGAGCCGGTGACCCGAGTTCAAATCTCGGCGG 8 101 0 ACCCGTTCAA 0.950487 -175 GAACCTTCTGCCCCCTCTACAACTTAATAGAA 12 90 1 CCCCCTACAA 0.987897 -85 ***** ***** Masking position 8 Map Score: 0.24243 Number of sites scoring better than the average of aligned sites = 121 Number in coding regions = 117 Number in noncoding regions = 4 Number of orfs with sites within 600 bp upstream = 4 Fraction of orfs with sites within 600 bp upstream = 0.000642467 Motif number 10 CCTTTTAAGTTCGATTTAACATTCTCAATTTTT 1 61 0 TCGATTTCTT 0.985469 -83 GCGTGGTAATTTAATCTAACGTTTCCTGCAATC 6 26 1 TTAATCTCTT 0.741333 -80 TTTATTCTTTTTGATTAATCGTATTCGATGGGT 10 16 1 TTGATTACTA 0.747827 -91 ACTCGATTTATGATTATAATTTTAA 10 92 0 TCGATTTGTT 0.928762 -15 AGGTTCTAAATCGATCTGCCTTTCT 11 3 0 TCGATCTCTT 0.978557 -63 GTTCTGCCTATTGATTTGTCTTTGAGTCTTGTA 12 61 0 TTGATTTCTT 0.970445 -114 GCAATAGCCATCGATTATGCTTTATCC 12 158 1 TCGATTACTT 0.967215 -17 ******* * ** Masking position 4 Map Score: 0.809553 Number of sites scoring better than the average of aligned sites = 54 Number in coding regions = 41 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 11 CGAACTTAAAAGGTGGTTGGATGTGCAGGC 1 81 1 AGGTGGTTGG 0.890193 -63 ATGTATGAAAAGGTTGGAGGTGAGTTGA 3 31 1 AGGTTGGAGG 0.957475 -18 TTTAAAGCGCATGCTGGTGGTGGGAGTGAT 5 87 1 ATGCTGGTGG 0.956216 -96 GAAATTTGAAAGGAGGGTTAGAA 6 93 1 AGGAGGGTTA 0.849043 -13 GCCGTAGGGTAGCCTGGTGATCCTCTCGGC 8 137 0 AGCCTGGTGA 0.881683 -139 TTCGTTTTTCAGGATGGTGAAGTATTTAAA 8 220 1 AGGATGGTGA 0.972905 -56 TCTTTCTGTCATGAGGGAGGCAGGATTTAA 8 245 0 ATGAGGGAGG 0.914001 -31 ********** Masking position 1 Map Score: 0.178144 Number of sites scoring better than the average of aligned sites = 934 Number in coding regions = 890 Number in noncoding regions = 44 Number of orfs with sites within 600 bp upstream = 33 Fraction of orfs with sites within 600 bp upstream = 0.00530035 Motif number 12 ********** No masking Map Score: 1.80068e-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: 1.80068e-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: 1.80068e-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