AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i127_Transmembrane_Transport_1_tpal_reg_100.orf -o127_tpal_100.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 AGGAGTGACTGGCGCGTCGG 1 1 0 GGCGCGTCGG 0.939123 -300 CGCGCGGTGGAGCAGGGGGGAGGAGTGACT 1 21 0 AGCAGGGGGG 0.910489 -280 GTTGTCTTTGCGCGCGGTGGAGCAGGGGGG 1 31 0 CGCGCGGTGG 0.986195 -270 TATTGCTGCTGGCGGGGGTGTACCAACCGC 1 71 0 GGCGGGGGTG 0.978945 -230 CAGGGGCGCTAGCGGCGGCGGCAATGCTCA 1 125 0 AGCGGCGGCG 0.778592 -176 CGACCGTGTGCGCAGGGGCGCTAGCGGCGG 1 137 0 CGCAGGGGCG 0.818054 -164 CGCCCCTGCGCACACGGTCGCCACAAATCC 1 147 1 CACACGGTCG 0.740995 -154 GCCACAAATCCGCGCGTGTGTGCAGTAGTA 1 166 1 CGCGCGTGTG 0.831292 -135 TCTGAACAGACGCAGGGGCGGTCGCAGAGG 1 209 1 CGCAGGGGCG 0.818054 -92 CAGGGGCGGTCGCAGAGGATGCGTCACGCG 1 221 1 CGCAGAGGAT 0.838251 -80 GGATGCGTCACGCGCGTGCTGCATGCGAGA 1 237 1 CGCGCGTGCT 0.720209 -64 TCCATATGGACGTGCAGGTGAAAGTCGTTC 2 12 0 CGTGCAGGTG 0.903637 -107 TAGCTCAAGTGGCACGTCGTCTCCATATGG 2 33 0 GGCACGTCGT 0.697586 -86 TTGCAGGAGGCGCGCGGCTACGATGTTGAG 2 67 0 CGCGCGGCTA 0.875365 -52 CAACGAACACCGCGCAGGAGGAGGAACAA 2 100 1 CGCGCAGGAG 0.987548 -19 TGATCTTGCGCGCGCGGTCTGTCGTGT 3 8 0 CGCGCGGTCT 0.975984 -32 AGGACTGAGCCGCACATGCTCAAAAAAGAG 4 24 0 CGCACATGCT 0.796098 -210 ACCATCAAACGGCACAGCATCTAGGTAACG 4 69 0 GGCACAGCAT 0.665587 -165 TGACACGCCTGGTACAGGCGTGTACCGCGT 4 159 1 GGTACAGGCG 0.853657 -75 TGCATTTCTGCGTGCGGCAGGCTTTTCTAT 4 190 0 CGTGCGGCAG 0.931586 -44 ********** Masking position 2 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 0.954158 -289 CTCAAAAGCGGTTGGTACACCCCCGCCAGCAGCA 1 64 1 GTGACACCCC 0.922675 -237 TTTCCGGTTCATTGGTATTGCTGCTGGCGGGGGT 1 82 0 ATGATTCTGC 0.933288 -219 AAATCCTGGCGTGAGCATTGCCGCCGCCGCTAGC 1 114 1 GTGATTCCGC 0.993124 -187 GACTACGGCGGTCCTTACTACTGCACACACGCGC 1 177 0 GTTACTCTGC 0.969752 -124 CCCTGCGTCTGTTCAGACTACGGCGGTCCTTACT 1 192 0 GTAACTCGGC 0.953857 -109 TTGTTCCTCCTCCTGCGCGGTGTTCG 2 103 0 GTCCCTCTGC 0.98207 -16 TGGGCTTCACGTTGGAACTGCTGCCATTGGCGTG 4 121 0 GTGACTCTGC 0.995923 -113 CCGCGTGATAGAAAAGCCTGCCGCACGCAGAAAT 4 183 1 GAACCTCCGC 0.93338 -51 TTGCACAACTGTTTGCATTTCTGCGTGCGGCAGG 4 199 0 GTGATTCTGC 0.989108 -35 TACCGAAAGAAAAAGGATTTCCGCAAAGCGCAGT 5 13 1 AAGATTCCGC 0.846995 -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 TGAGCATTGCCGCCGCCGCTAGCGCCCCTG 1 125 1 CGCCGCCGCT 0.909236 -176 ACGCGCGTGACGCATCCTCTGCGACCGCCC 1 224 0 CGCATCCTCT 0.986301 -77 GAGCTAACAGCTCAACATCGTAGCCGCGCG 2 57 1 CTCAACATCG 0.872054 -62 AGACCGCGCGCGCAAGATCAACATCAAAAC 3 18 1 CGCAAGATCA 0.85263 -22 GCTGCTTCTCAGCCTCTTTTTTGAGCA 4 8 1 CTCAGCCTCT 0.974742 -226 GACTGAGCCGCACATGCTCAAAAAAGAGGC 4 22 0 CACATGCTCA 0.880573 -212 CATCAAACGGCACAGCATCTAGGTAACGGG 4 67 0 CACAGCATCT 0.985176 -167 GATCCTGTTTCACCTCATCTTGCACGCTCA 6 12 0 CACCTCATCT 0.947415 -66 GATGAGGTGAAACAGGATCTGGCAGATTTA 6 23 1 AACAGGATCT 0.720374 -55 TATTTCCGTTCGCATCATCGGCACTAAATC 6 47 0 CGCATCATCG 0.974106 -31 ********** Masking position 3 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 CCGCTTTTGAGCGTGTTGTCTTTGCGCGCGGTGG 1 41 0 GCGTGTTTTG 0.752243 -260 CTGCTGGCGGGGGTGTACCAACCGCTTTTGAGCG 1 62 0 GGGTGTCACG 0.784687 -239 GAAAATCCTGGCGTGAGCATTGCCGCCGCCGCTA 1 112 1 GCGTGAATGC 0.703611 -189 TTTGTGGCGACCGTGTGCGCAGGGGCGCTAGCGG 1 140 0 CCGTGTGAGG 0.827371 -161 ACAAATCCGCGCGTGTGTGCAGTAGTAAGGACCG 1 169 1 GCGTGTGAGA 0.891444 -132 TGCAGCACGCGCGTGACGCATCCTCTGCGACCGC 1 226 0 GCGTGACTCT 0.833528 -75 TGCGTCACGCGCGTGCTGCATGCGAGAAAACGCA 1 240 1 GCGTGCCTGG 0.998207 -61 GTTTGTGGCAGTGTGTGCGTTTTCTCGCATGCAG 1 255 0 GTGTGTGTTC 0.380045 -46 TTATTTTCTTTGTGCTGCTTGGGTTTGTGGCAG 1 278 0 TTGTGCCTGG 0.75863 -23 TATGGAGACGACGTGCCACTTGAGCTAACAGCTC 2 36 1 ACGTGCCTGG 0.969232 -83 CATCGTAGCCGCGCGCCTCCTGCAAAAGCAACGA 2 72 1 GCGCGCCTGA 0.947515 -47 TGTTGATCTTGCGCGCGCGGTCTGTCGTGT 3 7 0 GCGCGCGTCG 0.961209 -33 GCTGCCATTGGCGTGCTTCATCGCGTCGCTCATT 4 102 0 GCGTGCCTCC 0.984843 -132 CCTGTACCAGGCGTGTCACTAGTGGGCTTCACGT 4 143 0 GCGTGTCAGG 0.991457 -91 CCTGGTACAGGCGTGTACCGCGTGATAGAAAAGC 4 166 1 GCGTGTCCGG 0.981232 -68 TTGCATTTCTGCGTGCGGCAGGCTTTTCTATCAC 4 187 0 GCGTGCCGGT 0.929967 -47 GTGAGCGTGCAAGATGAGGTGAAACAGG 6 5 1 GCGTGCGTGG 0.996485 -73 ****** * ** * Masking position 5 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 ACCCCCGCCAGCAGCAATACCAATGAACCGG 1 82 1 GCAGCAATCC 0.955324 -219 GCACACGGTCGCCACAAATCCGCGCGTGTGT 1 156 1 GCCACAAACC 0.991899 -145 CGCACACACTGCCACAAACCCAAGCAGCACA 1 270 1 GCCACAAACC 0.991903 -31 TAACAGCTCAACATCGTAGCCGCGCGCCTCC 2 61 1 ACATCGTACC 0.876951 -58 TCCTGCAAAAGCAACGAACACCGCGCAGGAG 2 89 1 GCAACGAAAC 0.949878 -30 CGCAAGATCAACATCAAAACCA 3 28 1 ACATCAAACC 0.972103 -12 ******** ** Masking position 5 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 0.980866 -291 CCTGCGCACACGGTCGCCACAAATCCGCGCGT 1 151 1 CGGTCCCCAA 0.932937 -150 CAGACTACGGCGGTCCTTACTACTGCACACAC 1 181 0 CGGTCTTCTA 0.985805 -120 ATGTGCGGCTCAGTCCTTGCTAGGCAGTGTCC 4 37 1 CAGTCTTCTA 0.988201 -197 ACGCCTGTACCAGGCGTGTCACTAGTGGGCTT 4 148 0 CAGGCTGCAC 0.932614 -86 CTGCGTGCGGCAGGCTTTTCTATCACGCGGTA 4 181 0 CAGGCTTCTA 0.985805 -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