AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i127_Transmembrane_Transport_1_tpal_reg_300.orf -o127_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 RTP00395 300 AE000520 #2 RTP00396 118 AE000520 #3 RTP01065 39 AE000520 #4 RTP00503 233 AE000520 #5 RTP01180 45 AE000520 #6 RTP01181 77 AE000520 Motif number 1 CCGACGCGCCAGTCACTCCT 1 1 1 CCGACGCGCC 0.9382 -300 AGTCACTCCTCCCCCCTGCTCCACCGCGCG 1 21 1 CCCCCCTGCT 0.909196 -280 CCCCCCTGCTCCACCGCGCGCAAAGACAAC 1 31 1 CCACCGCGCG 0.985975 -270 GCGGTTGGTACACCCCCGCCAGCAGCAATA 1 71 1 CACCCCCGCC 0.978612 -230 TGAGCATTGCCGCCGCCGCTAGCGCCCCTG 1 125 1 CGCCGCCGCT 0.775861 -176 CCGCCGCTAGCGCCCCTGCGCACACGGTCG 1 137 1 CGCCCCTGCG 0.819805 -164 GGATTTGTGGCGACCGTGTGCGCAGGGGCG 1 147 0 CGACCGTGTG 0.738124 -154 TACTACTGCACACACGCGCGGATTTGTGGC 1 166 0 CACACGCGCG 0.832741 -135 CCTCTGCGACCGCCCCTGCGTCTGTTCAGA 1 209 0 CGCCCCTGCG 0.819805 -92 CGCGTGACGCATCCTCTGCGACCGCCCCTG 1 221 0 ATCCTCTGCG 0.836066 -80 TCTCGCATGCAGCACGCGCGTGACGCATCC 1 237 0 AGCACGCGCG 0.721952 -64 GAACGACTTTCACCTGCACGTCCATATGGA 2 12 1 CACCTGCACG 0.902232 -107 CCATATGGAGACGACGTGCCACTTGAGCTA 2 33 1 ACGACGTGCC 0.694194 -86 CTCAACATCGTAGCCGCGCGCCTCCTGCAA 2 67 1 TAGCCGCGCG 0.873605 -52 TTGTTCCTCCTCCTGCGCGGTGTTCGTTG 2 100 0 CTCCTGCGCG 0.98735 -19 ACACGACAGACCGCGCGCGCAAGATCA 3 8 1 AGACCGCGCG 0.975611 -32 CTCTTTTTTGAGCATGTGCGGCTCAGTCCT 4 24 1 AGCATGTGCG 0.79581 -210 CGTTACCTAGATGCTGTGCCGTTTGATGGT 4 69 1 ATGCTGTGCC 0.662009 -165 ACGCGGTACACGCCTGTACCAGGCGTGTCA 4 159 0 CGCCTGTACC 0.851643 -75 ATAGAAAAGCCTGCCGCACGCAGAAATGCA 4 190 1 CTGCCGCACG 0.930557 -44 ********** Masking position 9 Map Score: 31.918 Number of sites scoring better than the average of aligned sites = 4713 Number in coding regions = 4353 Number in noncoding regions = 360 Number of orfs with sites within 600 bp upstream = 192 Fraction of orfs with sites within 600 bp upstream = 0.0308384 Motif number 2 CGACGCGCCAGTCACTCCTCCCCCCTGCTCCACC 1 12 1 GTCCCTCCCC 0.95197 -289 CTCAAAAGCGGTTGGTACACCCCCGCCAGCAGCA 1 64 1 GTGACACCCC 0.919112 -237 TTTCCGGTTCATTGGTATTGCTGCTGGCGGGGGT 1 82 0 ATGATTCTGC 0.930177 -219 AAATCCTGGCGTGAGCATTGCCGCCGCCGCTAGC 1 114 1 GTGATTCCGC 0.992784 -187 GACTACGGCGGTCCTTACTACTGCACACACGCGC 1 177 0 GTTACTCTGC 0.968284 -124 CCCTGCGTCTGTTCAGACTACGGCGGTCCTTACT 1 192 0 GTAACTCGGC 0.951655 -109 TTGTTCCTCCTCCTGCGCGGTGTTCG 2 103 0 GTCCCTCTGC 0.981187 -16 TGGGCTTCACGTTGGAACTGCTGCCATTGGCGTG 4 121 0 GTGACTCTGC 0.995724 -113 CCGCGTGATAGAAAAGCCTGCCGCACGCAGAAAT 4 183 1 GAACCTCCGC 0.930273 -51 TTGCACAACTGTTTGCATTTCTGCGTGCGGCAGG 4 199 0 GTGATTCTGC 0.988568 -35 TACCGAAAGAAAAAGGATTTCCGCAAAGCGCAGT 5 13 1 AAGATTCCGC 0.840546 -33 ** * *** **** Masking position 11 Map Score: 13.3104 Number of sites scoring better than the average of aligned sites = 289 Number in coding regions = 272 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 3 CAGGGGCGCTAGCGGCGGCGGCAATGCTCA 1 125 0 AGCGGCGGCG 0.917543 -176 GGGCGGTCGCAGAGGATGCGTCACGCGCGT 1 224 1 AGAGGATGCG 0.987713 -77 CGCGCGGCTACGATGTTGAGCTGTTAGCTC 2 57 0 CGATGTTGAG 0.883855 -62 GTTTTGATGTTGATCTTGCGCGCGCGGTCT 3 18 0 TGATCTTGCG 0.865947 -22 TGCTCAAAAAAGAGGCTGAGAAGCAGC 4 8 0 AGAGGCTGAG 0.977318 -226 GCCTCTTTTTTGAGCATGTGCGGCTCAGTC 4 22 1 TGAGCATGTG 0.891686 -212 CCCGTTACCTAGATGCTGTGCCGTTTGATG 4 67 1 AGATGCTGTG 0.986702 -167 TGAGCGTGCAAGATGAGGTGAAACAGGATC 6 12 1 AGATGAGGTG 0.952642 -66 TAAATCTGCCAGATCCTGTTTCACCTCATC 6 23 0 AGATCCTGTT 0.742026 -55 GATTTAGTGCCGATGATGCGAACGGAAATA 6 47 1 CGATGATGCG 0.976743 -31 ********** Masking position 8 Map Score: 8.50372 Number of sites scoring better than the average of aligned sites = 500 Number in coding regions = 471 Number in noncoding regions = 29 Number of orfs with sites within 600 bp upstream = 25 Fraction of orfs with sites within 600 bp upstream = 0.00401542 Motif number 4 CCACCGCGCGCAAAGACAACACGCTCAAAAGCGG 1 41 1 CAAAACACGC 0.752243 -260 CGCTCAAAAGCGGTTGGTACACCCCCGCCAGCAG 1 62 1 CGTGACACCC 0.784687 -239 TAGCGGCGGCGGCAATGCTCACGCCAGGATTTTC 1 112 0 GCATTCACGC 0.703611 -189 CCGCTAGCGCCCCTGCGCACACGGTCGCCACAAA 1 140 1 CCTCACACGG 0.827371 -161 CGGTCCTTACTACTGCACACACGCGCGGATTTGT 1 169 0 TCTCACACGC 0.891444 -132 GCGGTCGCAGAGGATGCGTCACGCGCGTGCTGCA 1 226 1 AGAGTCACGC 0.833528 -75 TGCGTTTTCTCGCATGCAGCACGCGCGTGACGCA 1 240 0 CCAGGCACGC 0.998207 -61 CTGCATGCGAGAAAACGCACACACTGCCACAAAC 1 255 1 GAACACACAC 0.380045 -46 CTGCCACAAACCCAAGCAGCACAAAGAAAATAA 1 278 1 CCAGGCACAA 0.75863 -23 GAGCTGTTAGCTCAAGTGGCACGTCGTCTCCATA 2 36 0 CCAGGCACGT 0.969232 -83 TCGTTGCTTTTGCAGGAGGCGCGCGGCTACGATG 2 72 0 TCAGGCGCGC 0.947515 -47 ACACGACAGACCGCGCGCGCAAGATCAACA 3 7 1 CGACGCGCGC 0.961209 -33 AATGAGCGACGCGATGAAGCACGCCAATGGCAGC 4 102 1 GGAGGCACGC 0.984843 -132 ACGTGAAGCCCACTAGTGACACGCCTGGTACAGG 4 143 1 CCTGACACGC 0.991457 -91 GCTTTTCTATCACGCGGTACACGCCTGTACCAGG 4 166 0 CCGGACACGC 0.981232 -68 GTGATAGAAAAGCCTGCCGCACGCAGAAATGCAA 4 187 1 ACCGGCACGC 0.929967 -47 CCTGTTTCACCTCATCTTGCACGCTCAC 6 5 0 CCACGCACGC 0.996485 -73 * ** * ****** Masking position 10 Map Score: 20.6254 Number of sites scoring better than the average of aligned sites = 1592 Number in coding regions = 1479 Number in noncoding regions = 113 Number of orfs with sites within 600 bp upstream = 91 Fraction of orfs with sites within 600 bp upstream = 0.0146161 Motif number 5 CCGGTTCATTGGTATTGCTGCTGGCGGGGGT 1 82 0 GGATTGCTGC 0.94952 -219 ACACACGCGCGGATTTGTGGCGACCGTGTGC 1 156 0 GGTTTGTGGC 0.990802 -145 TGTGCTGCTTGGGTTTGTGGCAGTGTGTGCG 1 270 0 GGTTTGTGGC 0.990805 -31 GGAGGCGCGCGGCTACGATGTTGAGCTGTTA 2 61 0 GGTACGATGT 0.862432 -58 CTCCTGCGCGGTGTTCGTTGCTTTTGCAGGA 2 89 0 GTTTCGTTGC 0.943409 -30 TGGTTTTGATGTTGATCTTGCG 3 28 0 GGTTTGATGT 0.968406 -12 ** ******** Masking position 7 Map Score: 1.51244 Number of sites scoring better than the average of aligned sites = 129 Number in coding regions = 122 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 Motif number 6 CCGACGCGCCAGTCACTCCTCCCCCCTGCTC 1 10 1 CAGTCCTCTC 0.981612 -291 CCTGCGCACACGGTCGCCACAAATCCGCGCGT 1 151 1 CGGTCCCCAA 0.93615 -150 CAGACTACGGCGGTCCTTACTACTGCACACAC 1 181 0 CGGTCTTCTA 0.98652 -120 ATGTGCGGCTCAGTCCTTGCTAGGCAGTGTCC 4 37 1 CAGTCTTCTA 0.988797 -197 ACGCCTGTACCAGGCGTGTCACTAGTGGGCTT 4 148 0 CAGGCTGCAC 0.935808 -86 CTGCGTGCGGCAGGCTTTTCTATCACGCGGTA 4 181 0 CAGGCTTCTA 0.98652 -53 ***** ** *** Masking position 5 Map Score: 1.30885 Number of sites scoring better than the average of aligned sites = 33 Number in coding regions = 31 Number in noncoding regions = 2 Number of orfs with sites within 600 bp upstream = 1 Fraction of orfs with sites within 600 bp upstream = 0.000160617 Motif number 7 ********** No masking Map Score: 1.56563e-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: 1.56563e-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: 1.56563e-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