AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i017_tpal_bbur_300.orf -o017_tpal_bbur_300.ace -a/home/amcguire/genomes/ORF_tpal.txt -z/home/amcguire/genomes/synecho.fna -g0.40 -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 = 0.4 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 RTP00193 63 AE000520 #2 RTP00194 66 AE000520 #3 RTP01039 60 AE000520 #4 RTP00195 72 AE000520 #5 RTP00196 111 AE000520 #6 RTP00024 300 AE000520 #7 RBB00632 156 3615 #8 RBB00123 129 3615 #9 RBB00036 16 3615 #10 RBB00034 263 3615 Motif number 1 CGCAGCTAGCCGCGCAGGGTGGATTCGGCCTGG 1 41 0 CGCGCAGTGA 0.987771 -23 CCCCCTGTACCGCACGCTGCCGACACCCGCGCG 5 67 1 CGCACGGCGA 0.993447 -45 TGCCGACACCCGCGCGTCGCTGAATTCTCGGCG 5 84 1 CGCGCGGCGA 0.998933 -28 TGAAGGAACACACGCACGGCCAAAGCTACCGTC 6 48 0 CACGCAGCAA 0.988001 -253 ACTGTCAACACGCTCATTGCTGATACGCTCGAA 6 171 1 CGCTCAGCGA 0.989739 -130 TGAGATAGATCACGCGATGCGGAATCTGGACGG 6 227 1 CACGCGGCGA 0.996743 -74 AAGCTATAAACACGCTTAGCCAAAAATCAATAA 10 64 1 CACGCTGCAA 0.970223 -200 ****** ** ** Masking position 13 Map Score: 11.4804 Number of sites scoring better than the average of aligned sites = 5 Number in coding regions = 2 Number in noncoding regions = 3 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0 Motif number 2 CCAACGGCCTTGAGAACACCCTTACCGTTATAGC 6 136 0 TGAAACATTA 0.782341 -165 AAAGTATAAATATTAACAAAGTTAATATCAAGAA 7 39 1 TATAACATTA 0.978746 -118 GAATTAAAATAATAAAAATTGTTAAATGTTTTTT 7 70 1 AATAAAATTA 0.869335 -87 ATGTTTTTTTTAAAAAAAGTTTTAAGCTATAATA 7 95 1 TAAAAAATTA 0.775702 -62 ATACTTAACTTATTAATATTGTTAAATCAATTTT 7 128 0 TATAATATTA 0.849738 -29 ATCATTTTTTTATAAACAAAACTAGTATATAATA 8 17 0 TATAACACTA 0.951151 -113 TGCTAATCTTTATGAATATGTTTTTTGTGATATA 8 76 1 TATAATATTT 0.847357 -54 TTCAAATTGTTTTAAACAGTTTTACACAAATAAA 10 14 1 TTTAACATTA 0.830532 -250 GTTTTACACAAATAAAAAAGTTTAAAACAATTAA 10 32 1 AATAAAATTA 0.870002 -232 ACAATTAAGCTATAAACACGCTTAGCCAAAAATC 10 58 1 TATAACATTA 0.978746 -206 CTTAGCCAAAAATCAATAAATCTACCCTTAAAAT 10 78 1 AATAATACTA 0.819472 -186 AGCATCTTTCAATTAACAAAACTTACAAAATGCT 10 140 1 AATAACACTT 0.729475 -124 TTTTACACTATGTAAACAGCATTTTGTAAGTTTT 10 157 0 TGTAACATTT 0.782342 -107 TGTAAAATTATAACAATAATTTTACACTATAACA 10 184 1 TAAAATATTA 0.771383 -80 AGTGCATAAGAATTAATAATGTTATGGGTTGATT 10 217 0 AATAATATTA 0.914092 -47 *** **** *** Masking position 8 Map Score: 13.0011 Number of sites scoring better than the average of aligned sites = 315 Number in coding regions = 83 Number in noncoding regions = 232 Number of orfs with sites within 600 bp upstream = 4 Fraction of orfs with sites within 600 bp upstream = 0.000642467 Motif number 3 TTAGGGGTGATTATTATTTTGTA 7 1 0 TATTTTTTGA 0.929311 -156 TTAACTTTGTTAATATTTATACTTTACTTTTTA 7 31 0 TATATTATAT 0.613123 -126 TTAACAATTTTTATTATTTTAATTCTTGATATT 7 62 0 TATTTTTTAT 0.918753 -95 AATTGTTAAATGTTTTTTTTAAAAAAAGTTTTA 7 86 1 TTTTTTTTAA 0.864227 -71 TCTCCTTATTATATACTAGTTTTGT 8 3 1 TCTTTTATAA 0.830953 -127 AAATTAAATATCATTTTTTTATAAACAAAACTA 8 27 0 TATTTTTTAA 0.951984 -103 TTTTGTCTGCTAATCTTTATGAATATGTTTTTT 8 69 1 TATCTTATGA 0.731955 -61 CAATCTGGTCAATTTATTATATATCACAAAAAA 8 96 0 ATTTTTATAA 0.611325 -34 ACCTCTTTATTATGAT 9 1 0 TTTTTTATGT 0.760199 -16 AGCTTCAAATTGTTTTAAACAGTTTTACA 10 7 1 AATTTTTTAA 0.788157 -257 GTTTATAGCTTAATTGTTTTAAACTTTTTTATT 10 42 0 TATTTTTTAA 0.951984 -222 TAGTGTAAAATTATTGTTATAATTTTACACTAT 10 180 0 TATTTTATAT 0.937076 -84 TGTTATGGGTTGATTGTTATAGTGTAAAATTAT 10 199 0 TATTTTATAT 0.937076 -65 ATAACATTATTAATTCTTATGCACTTATAGTAT 10 226 1 TATTTTATGA 0.945395 -38 * *** ***** * Masking position 7 Map Score: 11.5874 Number of sites scoring better than the average of aligned sites = 155 Number in coding regions = 46 Number in noncoding regions = 109 Number of orfs with sites within 600 bp upstream = 2 Fraction of orfs with sites within 600 bp upstream = 0.000321234 Motif number 4 AGGCCGAATCCACCCTGCGCGGCTAGCTGCG 1 43 1 CACCTCGCGG 0.960388 -21 AGTGCCATACCGCACACCGACCCCCTGTACCG 5 47 1 CGCCACGACC 0.95756 -65 CCCCCTGTACCGCACGCTGCCGACACCCGCGC 5 67 1 CGCCGTGCCG 0.996238 -45 TGCCGACACCCGCGCGTCGCTGAATTCTCGGC 5 84 1 CGCCGCGCTG 0.994667 -28 GTGGATGTCTCGCTCAGTGACGGTAGCTTTGG 6 30 1 CGCCATGACG 0.988498 -271 ACTGTCAACACGCTCATTGCTGATACGCTCGA 6 171 1 CGCCATGCTG 0.989855 -130 GGTATGGATGCGCTCAACCAGGGTGAGATAGA 6 204 1 CGCCACCAGG 0.95756 -97 TGAGATAGATCACGCGATGCGGAATCTGGACG 6 227 1 CACCGTGCGG 0.9838 -74 *** ** ***** Masking position 5 Map Score: 8.71836 Number of sites scoring better than the average of aligned sites = 131 Number in coding regions = 45 Number in noncoding regions = 86 Number of orfs with sites within 600 bp upstream = 3 Fraction of orfs with sites within 600 bp upstream = 0.00048185 Motif number 5 ACAGAAAGCCGGGGTCTCCATCGTCCATCT 3 20 1 GGGGTCTCCA 0.994578 -41 ATACTGAGCAGGGGTCTGGACAAAAGCATT 4 21 0 GGGGTCTGGA 0.97592 -52 GCGACGCGCGGGTGTCGGCAGCGTGCGGTA 5 74 0 GGTGTCGGCA 0.929159 -38 CTTCGACAGTGGGGTTTCCC 6 1 0 GGGGTTTCCC 0.966062 -300 TGTCGAAGTGGATGTCTCGCTCAGTGACGG 6 23 1 GATGTCTCGC 0.843518 -278 TTCCTTCAGGGGCGTCTACCgGAGAGTTCG 6 73 1 GGCGTCTACC 0.966795 -228 TGCTATGCTTGGCGTCTCCAT 6 290 1 GGCGTCTCCA 0.99213 -11 ********** Masking position 5 Map Score: 5.72996 Number of sites scoring better than the average of aligned sites = 223 Number in coding regions = 60 Number in noncoding regions = 163 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 6 GGTGGATTCGGCCTGGCGGAAAAGGTATAC 1 27 0 GCCTGGCGGA 0.937263 -37 CGCAGCTAGCCGCGCAGGGTGGATTCGGC 1 45 0 CCGCGCAGGG 0.863018 -19 CTGACCGTACCCCTGCTGGATAGTGTCTTT 2 13 1 CCCTGCTGGA 0.941632 -54 TGCTACCCAGCCGTGAAAGACACTATCCAG 2 28 0 CCGTGAAAGA 0.874113 -39 GTCCATCTTACCCCGCAGGAAATACAGGA 3 42 1 CCCCGCAGGA 0.919008 -19 cGGTAGACGCCCCTGAAGGAACACACGCAC 6 64 0 CCCTGAAGGA 0.964306 -237 CGCTCGAAATGCGTGATGGAGACAAGGAGC 6 106 1 GCGTGATGGA 0.935679 -195 ATCTATCTCACCCTGGTTGAGCGCATCCAT 6 207 0 CCCTGGTTGA 0.903505 -94 ********** Masking position 5 Map Score: 6.38353 Number of sites scoring better than the average of aligned sites = 1014 Number in coding regions = 298 Number in noncoding regions = 716 Number of orfs with sites within 600 bp upstream = 28 Fraction of orfs with sites within 600 bp upstream = 0.00449727 Motif number 7 TGGCACTCTTTTTAAGGTGAGTGTGCTCTTA 5 23 0 TTTAAGGGAG 0.935762 -89 ATACTTTACTTTTTAGGGGTGATTATTATTT 7 15 0 TTTTAGGGTG 0.903978 -142 TTTTTATTATTTTAATTCTTGATATTAACTT 7 57 0 TTTAATTTTG 0.929214 -100 GTTAAATCAATTTTATTATAGCTTAAAACTT 7 111 0 TTTTATTTAG 0.848233 -46 AAAAATGATATTTAATTTGAGCTTAATTTTT 8 42 1 TTTAATTGAG 0.932048 -88 TTAATTTGAGCTTAATTTTTGTCTGCTAATC 8 53 1 CTTAATTTTG 0.754113 -77 TTTTAAACTTTTTTATTTGTGTAAAACTGTT 10 28 0 TTTTATTGTG 0.898634 -236 TGTTTTTGATTTTAAGGGTAGATTTATTGAT 10 89 0 TTTAAGGTAG 0.918797 -175 AACAGCATTTTGTAAGTTTTGTTAATTGAAA 10 146 0 TGTAAGTTTG 0.797924 -118 ******* *** Masking position 5 Map Score: 2.59041 Number of sites scoring better than the average of aligned sites = 248 Number in coding regions = 81 Number in noncoding regions = 167 Number of orfs with sites within 600 bp upstream = 2 Fraction of orfs with sites within 600 bp upstream = 0.000321234 Motif number 8 GTTAAATGTTTTTTTTAAAAAAAGTTTTAA 7 90 1 TTTTTTAAAA 0.699562 -67 AATTTTATTATAGCTTAAAACTTTTTTTAA 7 104 0 TAGCTTAAAA 0.879683 -53 TAAACAAAACTAGTATATAATAAGGAGA 8 9 0 TAGTATATAA 0.709124 -121 TATACTAGTTTTGTTTATAAAAAAATGATA 8 22 1 TTGTTTATAA 0.889033 -108 AGCTTCAAATTGTTTTAAACAGTTTTACA 10 10 1 TTGTTTTAAA 0.800137 -254 ACTTTTTTATTTGTGTAAAACTGTTTAAAA 10 23 0 TTGTGTAAAA 0.960552 -241 ACAAATAAAAAAGTTTAAAACAATTAAGCT 10 39 1 AAGTTTAAAA 0.831453 -225 GCTGTTTACATAGTGTAAAATTATAACAAT 10 171 1 TAGTGTAAAA 0.968399 -93 TTGATTGTTATAGTGTAAAATTATTGTTAT 10 193 0 TAGTGTAAAA 0.968399 -71 ********** Masking position 6 Map Score: 6.22614 Number of sites scoring better than the average of aligned sites = 110 Number in coding regions = 29 Number in noncoding regions = 81 Number of orfs with sites within 600 bp upstream = 2 Fraction of orfs with sites within 600 bp upstream = 0.000321234 Motif number 9 TCGTTCTGCGCCTCAAACTCGTCTTCT 4 56 0 TGCGCCTCAA 0.987667 -17 AAAGAGCGCACCTAAGAGCACACTC 5 5 1 AGCGCACCAA 0.975879 -107 ACGCATTTCGAGCGCCTCGAACTCTCcGGTA 6 89 0 AGCGCCTCAA 0.99506 -212 ACCCTGGTTGAGCGCATCCATACCTTCGAGC 6 197 0 AGCGCATCAT 0.984294 -104 TGCTATGCTTGGCGTCTCCAT 6 290 1 GGCGTCTCAT 0.940737 -11 ******** ** Masking position 10 Map Score: 1.63059 Number of sites scoring better than the average of aligned sites = 55 Number in coding regions = 12 Number in noncoding regions = 43 Number of orfs with sites within 600 bp upstream = 1 Fraction of orfs with sites within 600 bp upstream = 0.000160617 Motif number 10 ATTCGGCCTGGCGGAAAAGGTATACAGACA 1 22 0 GCGGAAAAGG 0.935648 -42 CTATCCAGCAGGGGTACGGTCAGGT 2 6 0 GGGGTACGGT 0.977078 -61 TATTTCCTGCGGGGTAAGATGGACGATGGA 3 36 0 GGGGTAAGAT 0.862255 -25 GGGTCGGTGTGCGGTATGGCACTCTTTTTA 5 40 0 GCGGTATGGC 0.959749 -72 TCGGCAGCGTGCGGTACAGGGGGTCGGTGT 5 60 0 GCGGTACAGG 0.981028 -52 GAGCGCTATAACGGTAAGGGTGTTCTCAAG 6 132 1 ACGGTAAGGG 0.96414 -169 ********** Masking position 6 Map Score: 0.434941 Number of sites scoring better than the average of aligned sites = 632 Number in coding regions = 173 Number in noncoding regions = 459 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 11 ********** No masking Map Score: 8.47978e-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 12 ********** No masking Map Score: 8.47978e-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: 8.47978e-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