AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i198_enolase_tpal_reg_300.orf -o198_tpal_300.ace -a/home/amcguire/alignace/lib/ORF_tpal.txt -z/skink1/amcguire/genomes/tpal.fna -g0.53 -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 = 0.53 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 RTP01184 26 AE000520 #2 RTP00603 27 AE000520 #3 RTP00604 95 AE000520 #4 RTP00605 80 AE000520 #5 RTP00606 87 AE000520 #6 RTP00607 300 AE000520 Motif number 1 GTGTGTGAGGGGACGCGTTTTT 2 16 0 GTGTGAGGGG 0.961509 -12 GCACGAGGAAGGGCGCGAAATTACTGACTA 3 13 0 GGGCGCGAAA 0.97071 -83 CCGTTTCCTTGCACGAGGAAGGGCGCGAAA 3 23 0 GCACGAGGAA 0.956231 -73 AGAACTTGCAGGATGAGGAGAGTGGCGATG 3 65 0 GGATGAGGAG 0.960016 -31 ACTTTCCTTGACATGCGCAGGCTTCTGGAG 4 14 1 ACATGCGCAG 0.830662 -67 TGCGGGAGCAGCGTGAGGTGTTCCAAGCGC 4 55 0 GCGTGAGGTG 0.985789 -26 AGTATGTGCGGGAGCAGCGTGAG 4 68 0 ATGTGCGGGA 0.782876 -13 TCGCGGCGCTGTGCGCGATTCGGGTGCCTT 5 38 0 GTGCGCGATT 0.734434 -50 GCTGCAGACAGCGCGAGAGATTGTCGCGGC 5 61 0 GCGCGAGAGA 0.911993 -27 TATGGGAAATGCATGCGATGGTGTCGCGCA 6 18 0 GCATGCGATG 0.96299 -283 GATCAGTTATGGGTGCGGTATGGGAAATGC 6 36 0 GGGTGCGGTA 0.983191 -265 TAGGAAGTGTGCATGCGGTGCCGCATATAC 6 88 1 GCATGCGGTG 0.989073 -213 GGTTTGGAATGAGCGCGGAAATAAAGAGGC 6 159 0 GAGCGCGGAA 0.956525 -142 CCAAAGGTACGCGTGCGCAGGCGATACTCA 6 190 1 GCGTGCGCAG 0.99222 -111 TACTCATCCAGGGCGCGCAGCATGTCTTCT 6 214 1 GGGCGCGCAG 0.988986 -87 GGCAAAGCGCGTACGCGGAGTTCTATTTTA 6 272 0 GTACGCGGAG 0.984963 -29 ********** Masking position 5 Map Score: 29.4488 Number of sites scoring better than the average of aligned sites = 3217 Number in coding regions = 2987 Number in noncoding regions = 230 Number of orfs with sites within 600 bp upstream = 156 Fraction of orfs with sites within 600 bp upstream = 0.0250562 Motif number 2 TTGAGAACTTGCAGGATGAGGAGAGTGGCG 3 68 0 GCAGGATGAG 0.897125 -28 CGTCTCTCCAGAAGCCTGCGCATGTCAAGG 4 19 0 GAAGCCTGCG 0.970552 -62 TGTTCCAAGCGCATGTTGCGTCTCTCCAGA 4 37 0 GCATGTTGCG 0.951987 -44 ATGTGCGGGAGCAGCGTGAGGTGTTCCAAG 4 58 0 GCAGCGTGAG 0.94121 -23 AGTAGAAAACACATACAGAGTAACAAAAGG 5 12 1 ACATACAGAG 0.766001 -76 GGCGGGGGCTGCAGACAGCGCGAGAGATTG 5 68 0 GCAGACAGCG 0.962255 -20 CACATCCTGCGCGACACCATC 6 2 1 ACATCCTGCG 0.992465 -299 TAGGAAGTGTGCATGCGGTGCCGCATATAC 6 88 1 GCATGCGGTG 0.915314 -213 CTGGATGAGTATCGCCTGCGCACGCGTACC 6 195 0 ATCGCCTGCG 0.851949 -106 CGGGTAGAAGACATGCTGCGCGCCCTGGAT 6 219 0 ACATGCTGCG 0.990684 -82 TATTTTACCGATATCCTGTGGCCTGACTTT 6 249 0 ATATCCTGTG 0.838918 -52 ********** Masking position 8 Map Score: 10.4593 Number of sites scoring better than the average of aligned sites = 1405 Number in coding regions = 1297 Number in noncoding regions = 108 Number of orfs with sites within 600 bp upstream = 77 Fraction of orfs with sites within 600 bp upstream = 0.0123675 Motif number 3 GTGTCTGCGCTTTTGCTTTTGGC 1 14 0 GTTGCGCTTT 0.992503 -13 GTGTGTGAGGGGACGCGTTTTTCTGTC 2 7 0 GGCGCGTTTT 0.99444 -21 TTGTTACTCTGTATGTGTTTTCTACTG 5 7 0 GTTGTGTTTT 0.940854 -81 TGCGCGATTCGGGTGCCTTTTGTTACTCTGT 5 26 0 GGTGCCTTTT 0.966068 -62 TCGCGGCGCTGTGCGCGATTCGGGTGCCTTT 5 37 0 GTCGCGATTC 0.947463 -51 GATCAGTTATGGGTGCGGTATGGGAAATGCA 6 35 0 GGTGCGGTAT 0.947465 -266 AGAACTCCGCGTACGCGCTTTGCCAAAGCAA 6 278 1 GTCGCGCTTT 0.993784 -23 ** ******** Masking position 9 Map Score: 6.82004 Number of sites scoring better than the average of aligned sites = 205 Number in coding regions = 193 Number in noncoding regions = 12 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 4 CAACATGCGCTTGGAACACCTCACGCTGCT 4 49 1 TTGGAACACC 0.990813 -32 AGATAACCAAATGGAACGCTAGGAAGTGTG 6 69 1 ATGGAACGCT 0.986667 -232 ATAAGAATAGTTGGAACGCCGAAAAAAAAG 6 122 1 TTGGAACGCC 0.996612 -179 TATCGGTAAAATAGAACTCCGCGTACGCGC 6 266 1 ATAGAACTCC 0.964454 -35 ********** Masking position 5 Map Score: 3.45448 Number of sites scoring better than the average of aligned sites = 17 Number in coding regions = 15 Number in noncoding regions = 2 Number of orfs with sites within 600 bp upstream = 3 Fraction of orfs with sites within 600 bp upstream = 0.00048185 Motif number 5 GTGTGTGAGGGGACGCGTTTTT 2 16 0 GTGGTGGGGG 0.917646 -12 GAGTGGCGATGAGCTTGACGAGTCCGTTTCCT 3 44 0 GAGTTGCGAG 0.989259 -52 GCAGGATGAGGAGAGTGGCGATGAGCTTGACG 3 56 0 GAGGTGCGAT 0.968192 -40 CCAGAAGCCTGCGCATGTCAAGGAAAGTATC 4 10 0 GCGATGCAAG 0.925487 -71 GGTGTTCCAAGCGCATGTTGCGTCTCTCCAGA 4 37 0 GCGATGTGCG 0.972631 -44 AGTATGTGCGGGAGCAGCGTGAGGTGTTC 4 62 0 GCGGAGAGCG 0.949616 -19 GACAGCGCGAGAGATTGTCGCGGCGCTGTGCG 5 53 0 GAGTTGCGCG 0.994771 -35 AAATGCATGCGATGGTGTCGCGCAGGATGTG 6 10 0 GATGTGCGCG 0.984342 -291 *** *** **** Masking position 7 Map Score: 4.42552 Number of sites scoring better than the average of aligned sites = 911 Number in coding regions = 833 Number in noncoding regions = 78 Number of orfs with sites within 600 bp upstream = 71 Fraction of orfs with sites within 600 bp upstream = 0.0114038 Motif number 6 GTCTGCGCTTTTGCTTTTGGCGTC 1 5 0 TTGCTTTTGG 0.975056 -22 CGCGATTCGGGTGCCTTTTGTTACTCTGTA 5 25 0 GTGCCTTTTG 0.836206 -63 TTCCATTTGGTTATCTTCGGATCAGTTATG 6 55 0 TTATCTTCGG 0.952375 -246 CTTCCTAGCGTTCCATTTGGTTATCTTCGG 6 65 0 TTCCATTTGG 0.89369 -236 CTGTTAATCTTTTTTTTCGGCGTTCCAACT 6 130 0 TTTTTTTCGG 0.871087 -171 CTGCGCACGCGTACCTTTGGGGGTTTGGAA 6 180 0 GTACCTTTGG 0.976932 -121 TCCTGTGGCCTGACTTTCGGGTAGAAGACA 6 236 0 TGACTTTCGG 0.904097 -65 TTTTGCTTTGGCAAAGCGCGT 6 290 0 TTTGCTTTGG 0.922883 -11 ********** Masking position 6 Map Score: 2.33962 Number of sites scoring better than the average of aligned sites = 258 Number in coding regions = 233 Number in noncoding regions = 25 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 7 ********** No masking Map Score: 1.65089e-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 8 ********** No masking Map Score: 1.65089e-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 9 ********** No masking Map Score: 1.65089e-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