AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i224_tpal_bbur_100.orf -o224_tpal_bbur_100.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 Purged sequences: RBB00392 26 3615 Input sequences: #1 RTP00323 174 AE000520 #2 RTP00235 300 AE000520 #3 RTP00092 41 AE000520 #4 RTP00091 24 AE000520 #5 RTP00090 84 AE000520 #6 RTP00984 143 AE000520 #7 RBB00708 44 3615 #8 RBB00707 79 3615 #9 RBB00462 198 3615 Motif number 1 ACCCCATTACCTACCTCTTCACCTGCACAGTCACAA 1 49 0 CACCTTCTGC 0.9901 -126 TTACACAAGGCGCGCGTATGCACTGCTGGCAAATAT 1 146 1 CCCTATCTGC 0.903125 -29 GACAGTTCCAGAACCACTGGTGTTGCAGGCG 2 6 0 GACCTGTTGC 0.807709 -295 CTGGAACTGTCGAGCTGGCAGCTTGCAGACCTACGC 2 31 1 CACGGCTTGC 0.884484 -270 CACTGTACACCACGCCGGTCTGCTGCGCCCGGAGAT 2 87 1 CCCGGTCTGC 0.995819 -214 TGTGCGTATAGCACCTGTTTGTCTGCCACGTAGCTT 2 177 0 GACGTTCTGC 0.974175 -124 AAGCGGGGTCCCCACCCGTCATCTGCGTTACACAGC 2 234 0 CCCCGTCTGC 0.994847 -67 ACGGGTGGGGACCCCGCTTTGCCTGCGAAGCGCAGA 2 251 1 ACCCTTCTGC 0.963193 -50 AAAAGACGCGCACTCCGTTTTTCTGCGCTTCGCAGG 2 272 0 CCCGTTCTGC 0.996567 -29 TTTGATTATGCACCCTGTGCTCTTGCA 5 2 0 CCCGTGTTGC 0.97563 -83 * * * *** **** Masking position 14 Map Score: 10.81 Number of sites scoring better than the average of aligned sites = 254 Number in coding regions = 78 Number in noncoding regions = 176 Number of orfs with sites within 600 bp upstream = 1 Fraction of orfs with sites within 600 bp upstream = 0.000160617 Motif number 2 TTTTTTTCTTACCTCTTTGTCGCGGTTTTT 1 90 1 ACCTCTTTGT 0.987851 -85 TGCGTATAGCACCTGTTTGTCTGCCACGTA 2 181 0 ACCTGTTTGT 0.949096 -120 GGGTGGGGACCCCGCTTTGCCTGCGAAGCG 2 253 1 CCCGCTTTGC 0.976393 -48 GACGCGCACTCCGTTTTTCTGCGCTTCGCA 2 274 0 CCGTTTTTCT 0.853449 -27 GTACTGCTATCCCTCTTTCTATTTTTTCTC 5 46 0 CCCTCTTTCT 0.992307 -39 GAGAGATGATACCGCTTTCTGCACGTATTA 6 21 1 ACCGCTTTCT 0.978745 -123 ATGAGAAAATCCCTTTTTGTAAGAGCGTTC 6 86 0 CCCTTTTTGT 0.972365 -58 GCTCTAACAAACCTCTTGCCATAATTTAAA 9 151 0 ACCTCTTGCC 0.924418 -48 ********** Masking position 6 Map Score: 7.84952 Number of sites scoring better than the average of aligned sites = 281 Number in coding regions = 80 Number in noncoding regions = 201 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 3 TTATTAGTTTTTTATAGTTATAAA 7 5 1 TAGTTTTTTA 0.901072 -40 AGTTATAAAATAGTTTTTAAGGAATATTT 7 26 1 TAGTTTTTAA 0.952642 -19 CTGTGTAATATAATTTATAATTTAATTAT 8 61 1 TAATTTATAA 0.945671 -19 TATGACATTTTAATTTTATATTTGTTTTTT 9 23 1 TAATTTTATA 0.791994 -176 AATTATTAAATTGTTTAAAAAAACAAATAT 9 40 0 TTGTTTAAAA 0.804911 -159 AACAATTTAATAATTTATTATTAAAAATAA 9 55 1 TAATTTATTA 0.887053 -144 CCTTTTCGGGTTATTTTTAATAATAAATTA 9 65 0 TTATTTTTAA 0.892787 -134 ATTGCTTTTGTTATTTTTAAGAAAAAATAT 9 99 1 TTATTTTTAA 0.892787 -100 ACTACTACGATAGATTATAATATTTTTTCT 9 118 0 TAGATTATAA 0.738913 -81 CCTCTTGCCATAATTTAAAATAACTACTAC 9 140 0 TAATTTAAAA 0.89359 -59 ********** Masking position 5 Map Score: 7.67474 Number of sites scoring better than the average of aligned sites = 360 Number in coding regions = 113 Number in noncoding regions = 247 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 Motif number 4 TTTCAGTGCGGATCGCACTACCC 1 4 1 CAGTGCGGAT 0.926725 -171 TTTACACAAGGCGCGCGTATGCACTGCTGG 1 145 1 GCGCGCGTAT 0.980302 -30 TGTGCATCGACTGCGCGTAGGTCTGCAAGC 2 51 0 CTGCGCGTAG 0.780725 -250 CAGTGTGGTCCTGTGCATCGACTGCGCGTA 2 62 0 CTGTGCATCG 0.76528 -239 CCGGTCTGCTGCGCCCGGAGATTGCCATCA 2 101 1 GCGCCCGGAG 0.790722 -200 ATCAAAACTGGTATGCGGATATGGAAAGCT 2 152 1 GTATGCGGAT 0.745469 -149 GCGTTCCCTGGTGTGCGTATAGCACCTGTT 2 194 0 GTGTGCGTAT 0.981635 -107 CTCCGTTTTTCTGCGCTTCGCAGGCAAAGC 2 266 0 CTGCGCTTCG 0.861086 -35 GAAAAACGGAGTGCGCGTCTTTTGGT 2 285 1 GTGCGCGTCT 0.984554 -16 ATACCGCTTTCTGCACGTATTACGAGCATC 6 29 1 CTGCACGTAT 0.913762 -115 GTATATGATGCATTGCGTATGGAACGCTCT 6 65 1 CATTGCGTAT 0.638234 -79 ********** Masking position 6 Map Score: 6.67357 Number of sites scoring better than the average of aligned sites = 227 Number in coding regions = 66 Number in noncoding regions = 161 Number of orfs with sites within 600 bp upstream = 5 Fraction of orfs with sites within 600 bp upstream = 0.000803084 Motif number 5 TTTCAGTGCGGATCGCACTACCCATGACGACATG 1 11 1 GACGCACTCA 0.993998 -164 GCAGACCTACGCGCAGTCGATGCACAGGACCACA 2 55 1 GCCAGTCGCA 0.920449 -246 CGATGCACAGGACCACACTGTACACCACGCCGGT 2 72 1 GACACACTCA 0.994116 -229 GCACACCAGGGAACGCACGATACACTGCTGTGTA 2 208 1 GACGCACGCA 0.993878 -93 TGCAAGAGCACAGGGTGCATAATCAAAAT 5 6 1 GACACAGGCA 0.964802 -79 ATTGCGTATGGAACGCTCTTACAAAAAGGGATTT 6 76 1 GACGCTCTAA 0.920182 -68 ATTTTCTCATGAACAAACTACACACATGATTTTA 6 106 1 GACAAACTCA 0.963153 -38 CATGATTTTAGAACAGTCTGGACA 6 130 1 GACAGTCTCA 0.977995 -14 ** ****** ** Masking position 14 Map Score: 6.46016 Number of sites scoring better than the average of aligned sites = 121 Number in coding regions = 28 Number in noncoding regions = 93 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 6 ATCGCACTACCCATGACGACATGACCATTG 1 22 1 CCATGACGAC 0.959909 -153 GACGACATGACCATTGTGACTGTGCAGGTG 1 36 1 CCATTGTGAC 0.970701 -139 CCGGAGATTGCCATCATGACTCCCATTATG 2 115 1 CCATCATGAC 0.98988 -186 ATCATGACTCCCATTATGGCTGACCATCAA 2 127 1 CCATTATGGC 0.986861 -174 TTATGGCTGACCATCAAAACTGGTATGCGG 2 140 1 CCATCAAAAC 0.909468 -161 AACTCCTATACCATTATAGCAAAGCTCTAA 9 174 0 CCATTATAGC 0.962095 -25 ********** Masking position 4 Map Score: 4.44268 Number of sites scoring better than the average of aligned sites = 130 Number in coding regions = 45 Number in noncoding regions = 85 Number of orfs with sites within 600 bp upstream = 2 Fraction of orfs with sites within 600 bp upstream = 0.000321234 Motif number 7 CGTCATGGGTAGTGCGATCCGCACTGAAA 1 10 0 AGTGCGATCC 0.990942 -165 CGTGGTGTACAGTGTGGTCCTGTGCATCGA 2 71 0 AGTGTGGTCC 0.96325 -230 AGCAGTGTATCGTGCGTTCCCTGGTGTGCG 2 207 0 CGTGCGTTCC 0.979702 -94 TCGCAGGCAAAGCGGGGTCCCCACCCGTCA 2 249 0 AGCGGGGTCC 0.945947 -52 TGTTGTCAGTACTGCTATCCCTCTTTCTAT 5 54 0 ACTGCTATCC 0.851729 -31 CCTTTTTGTAAGAGCGTTCCATACGCAATG 6 75 0 AGAGCGTTCC 0.987985 -69 GAGGTTTGTTAGAGCTTTGCTATAATGGTA 9 166 1 AGAGCTTTGC 0.81521 -33 ********** Masking position 8 Map Score: 3.84706 Number of sites scoring better than the average of aligned sites = 156 Number in coding regions = 42 Number in noncoding regions = 114 Number of orfs with sites within 600 bp upstream = 1 Fraction of orfs with sites within 600 bp upstream = 0.000160617 Motif number 8 CAAAGAGGTAAGAAAAAAATAGCAACCCCA 1 79 0 AGAAAAAAAT 0.804374 -96 GAATACGTCGAAAACAAAAACCGCGACAAA 1 105 0 AAAACAAAAA 0.92051 -70 AATATCCCAGAGAAAAAATAGAAAGAGGGA 5 37 1 AGAAAAAATA 0.962672 -48 ATAACTATAAAAAACTAATAA 7 2 0 AAAACTAATA 0.757897 -43 AAAAGCCTTAAGTAAAAAAAGGACACTAA 8 10 0 AGTAAAAAAA 0.804374 -70 ATTGTTTAAAAAAACAAATATAAAATTAAA 9 31 0 AAAACAAATA 0.937806 -168 GTTATTTTTAAGAAAAAATATTATAATCTA 9 108 1 AGAAAAAATA 0.962672 -91 ********** Masking position 4 Map Score: 2.47064 Number of sites scoring better than the average of aligned sites = 229 Number in coding regions = 55 Number in noncoding regions = 174 Number of orfs with sites within 600 bp upstream = 3 Fraction of orfs with sites within 600 bp upstream = 0.00048185 Motif number 9 AGAAAAAAATAGCAACCCCATTACCTACCTCT 1 67 0 AGCAACCCTT 0.992579 -108 CGCCTGCAACACCAGTGGTTCTGGAA 2 5 1 TGCAACCCGT 0.942156 -296 ACGTATTACGAGCATCGCCGATGTATATGATG 6 43 1 AGCATCCCAT 0.965238 -101 TTTGTTCATGAGAAAATCCCTTTTTGTAAGAG 6 91 0 AGAAAACCTT 0.893617 -53 AACAATTTAAAGCAAAAGCCTTAAGTAAAAAA 8 21 0 AGCAAAGCTT 0.964697 -59 TCTTAAAAATAACAAAAGCAATTTATCCTTTT 9 89 0 AACAAAGCAT 0.779954 -110 AAAGCAACTCCTATACCATTATAG 9 185 0 AGCAACCCAT 0.992579 -14 ****** ** ** Masking position 4 Map Score: 2.44237 Number of sites scoring better than the average of aligned sites = 395 Number in coding regions = 109 Number in noncoding regions = 286 Number of orfs with sites within 600 bp upstream = 2 Fraction of orfs with sites within 600 bp upstream = 0.000321234 Motif number 10 TTTCTCTGGGATATTTTGATTATGCACCCT 5 22 0 ATATTTTGAT 0.82156 -63 GAAACATTCAACAATTTAAAGCAAAAGCCT 8 32 0 ACAATTTAAA 0.911003 -48 AATATAATTTATAATTTAATTAT 8 67 1 ATAATTTAAT 0.950845 -13 ATATATTATGACATTTTAATTTTATATTTG 9 17 1 ACATTTTAAT 0.947563 -182 GTTTTTTTAAACAATTTAATAATTTATTAT 9 46 1 ACAATTTAAT 0.95922 -153 TTAAGAAAAAATATTATAATCTATCGTAGT 9 115 1 ATATTATAAT 0.756225 -84 ACCTCTTGCCATAATTTAAAATAACTACTA 9 141 0 ATAATTTAAA 0.894464 -58 ********** Masking position 3 Map Score: 4.82535 Number of sites scoring better than the average of aligned sites = 65 Number in coding regions = 18 Number in noncoding regions = 47 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0 Motif number 11 TTTCGACGTATTCTGTTTAAAGTTTTACAC 1 122 1 TTCTGTTTAA 0.966652 -53 CACGATACACTGCTGTGTAACGCAGATGAC 2 223 1 TGCTGTGTAA 0.985182 -78 TGTTGAATGTTTCTGTGTAATATAATTTAT 8 49 1 TTCTGTGTAA 0.987498 -31 ********** Masking position 9 Map Score: 0.210528 Number of sites scoring better than the average of aligned sites = 5 Number in coding regions = 1 Number in noncoding regions = 4 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: 1.73616e-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 13 ********** No masking Map Score: 1.73616e-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 14 ********** No masking Map Score: 1.73616e-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