AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i128_Transmembrane_Transport_2_tpal_reg_300.orf -o128_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 RTP00008 129 AE000520 #2 RTP00605 80 AE000520 #3 RTP00606 87 AE000520 #4 RTP00607 300 AE000520 Motif number 1 GTTTCTATACGCGCGGTAAGCGACATACGCCG 1 55 1 GCGCGGTGCG 0.990878 -75 AAAGAGGAAAGCGCTGGCCATACACCGGCGTA 1 80 0 GCGCTGGATA 0.953792 -50 AAAGTGTGCAGCCTAAAACCAGGCTTC 1 113 0 GTGCAGCAAA 0.740483 -17 CCAGAAGCCTGCGCATGTCAAGGAAAGTATC 2 10 0 GCGCATGAAG 0.953214 -71 GGTGTTCCAAGCGCATGTTGCGTCTCTCCAGA 2 37 0 GCGCATGGCG 0.992042 -44 GTATGTGCGGGAGCAGCGTGAGGTGTTCCAAG 2 58 0 GAGCAGCGAG 0.938098 -23 GATTGTCGCGGCGCTGTGCGCGATTCGGGTGC 3 41 0 GCGCTGTGCG 0.992426 -47 ACAATCTCTCGCGCTGTCTGCAGCCCCCGCC 3 67 1 GCGCTGTGCA 0.974135 -21 CGATGGTGTCGCGCAGGATGTG 4 1 0 GCGCAGGGTG 0.998131 -300 TCAGTTATGGGTGCGGTATGGGAAATGCATGC 4 32 0 GTGCGGTGGG 0.859983 -269 GCTAGGAAGTGTGCATGCGGTGCCGCATATAC 4 86 1 GTGCATGGTG 0.950684 -215 AGGTACGCGTGCGCAGGCGATACTCATCCAGG 4 194 1 GCGCAGGATA 0.975489 -107 CATGCTGCGCGCCCTGGATGAGTATCGCCTGC 4 206 0 GCCCTGGGAG 0.953018 -95 CATCCAGGGCGCGCAGCATGTCTTCTACCCGA 4 218 1 GCGCAGCGTC 0.968428 -83 ******* *** Masking position 4 Map Score: 22.4681 Number of sites scoring better than the average of aligned sites = 2468 Number in coding regions = 2315 Number in noncoding regions = 153 Number of orfs with sites within 600 bp upstream = 114 Fraction of orfs with sites within 600 bp upstream = 0.0183103 Motif number 2 AAGTGTGCAGCCTAAAACCAGGCTTCCAAAGAG 1 106 0 CCAAAAAGGC 0.991443 -24 ATACAGAGTAACAAAAGGCACCCGAATCGCGCA 3 24 1 ACAAAGACCC 0.946571 -64 CCGAAGATAACCAAATGGAACGCTAGGAAGTGT 4 65 1 CCAATGACGC 0.99195 -236 AGTTGGAACGCCGAAAAAAAAGATTAACAGCCT 4 130 1 CCAAAAAAGA 0.867924 -171 ATTCCAAACCCCCAAAGGTACGCGTGCGCAGGC 4 179 1 CCAAAGACGC 0.997999 -122 TGTCTTCTACCCGAAAGTCAGGCCACAGGATAT 4 236 1 CCAAAGAGGC 0.997089 -65 ** **** **** Masking position 5 Map Score: 5.2541 Number of sites scoring better than the average of aligned sites = 67 Number in coding regions = 61 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 5 Fraction of orfs with sites within 600 bp upstream = 0.000803084 Motif number 3 CTTTCCTCTTTGGAAGCCTGGTTTTAGGCTG 1 101 1 TGGAAGCTGG 0.992093 -29 TGCGTCTCTCCAGAAGCCTGCGCATGTCAAG 2 20 0 CAGAAGCTGC 0.95484 -61 AACATGCGCTTGGAACACCTCACGCTGCTCC 2 50 1 TGGAACCCTC 0.976175 -31 GATAACCAAATGGAACGCTAGGAAGTGTGCA 4 70 1 TGGAACCTAG 0.951004 -231 TAAGAATAGTTGGAACGCCGAAAAAAAAGAT 4 123 1 TGGAACCCGA 0.974228 -178 GACTTTCGGGTAGAAGACATGCTGCGCGCCC 4 224 0 TAGAAGCATG 0.903257 -77 GTCTTCTACCCGAAAGTCAGGCCACAGGATA 4 237 1 CGAAAGCAGG 0.847021 -64 ATCGGTAAAATAGAACTCCGCGTACGCGCTT 4 267 1 TAGAACCCGC 0.983237 -34 ****** **** Masking position 5 Map Score: 4.29957 Number of sites scoring better than the average of aligned sites = 201 Number in coding regions = 183 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 4 ATGTCGCTTACCGCGCGTATAGAAACTATT 1 51 0 CCGCGCGTAT 0.959511 -79 GGCCATACACCGGCGTATGTCGCTTACCGC 1 67 0 CGGCGTATGT 0.906767 -63 GGTGTATGGCCAGCGCTTTCCTCTTTGGAA 1 86 1 CAGCGCTTTC 0.848164 -44 CTCCAGAAGCCTGCGCATGTCAAGGAAAGT 2 14 0 CTGCGCATGT 0.983072 -67 GAGGTGTTCCAAGCGCATGTTGCGTCTCTC 2 41 0 AAGCGCATGT 0.877129 -40 CACGCTGCTCCCGCACATACT 2 70 1 CCGCACATAC 0.97705 -11 TGCGCGACACCATCGCATGCATTTCCCATA 4 18 1 CATCGCATGC 0.935341 -283 ATTTCCCATACCGCACCCATAACTGATCCG 4 38 1 CCGCACCCAT 0.778046 -263 GTATATGCGGCACCGCATGCACACTTCCTA 4 88 0 CACCGCATGC 0.955437 -213 GCATGCGGTGCCGCATATACCAACATAAGA 4 98 1 CCGCATATAC 0.894468 -203 CTCTTTATTTCCGCGCTCATTCCAAACCCC 4 161 1 CCGCGCTCAT 0.954059 -140 TGAGTATCGCCTGCGCACGCGTACCTTTGG 4 190 0 CTGCGCACGC 0.987362 -111 AAATAGAACTCCGCGTACGCGCTTTGCCAA 4 274 1 CCGCGTACGC 0.985643 -27 ********** Masking position 4 Map Score: 18.2201 Number of sites scoring better than the average of aligned sites = 2514 Number in coding regions = 2354 Number in noncoding regions = 160 Number of orfs with sites within 600 bp upstream = 115 Fraction of orfs with sites within 600 bp upstream = 0.0184709 Motif number 5 ********** No masking Map Score: -9.28379e-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 6 ********** No masking Map Score: -9.28379e-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 7 ********** No masking Map Score: -9.28379e-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