AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_rpxx.txt -z/home/amcguire/genomes/rpxx.fna -imetR_rpxx_opreg_100.orf -g0.290 -x5 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 = 0.29 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 RP716 300 unknown #2 RP743 79 SERINE HYDROXYMETHYLTRANSFERASE (glyA) #3 RP744 102 unknown Motif number 1 GAGTACTTTGATTCTCTAATAGAACCC 1 4 1 TCTTTTTTCT 0.993549 -297 ATATCTGATATTCTATTCTTAGCTAAGTTTAAAG 1 56 0 TCTATTTGCT 0.987582 -245 CAATAAAGCTTTCTTTTTTTATCTTAAGAGTATG 1 111 1 TCTTTTTTCT 0.993549 -190 ACTCTTTGACTACTATTGGGTTCTCGAAAGCCTT 1 192 1 TCTATGGTCT 0.960767 -109 TTCCATTGATTCCTATGTGTCTCTTTCTAATCCA 1 276 0 TCTATGTTCT 0.987591 -25 CGGTATCTAGTCGTTTATTTTTCTTTGTACTGTA 2 14 1 TGTTTTTTCT 0.984845 -66 TATAGGCTCTTTGTTTTGTTTGCTATTGCTATTC 3 23 1 TGTTTTTGCT 0.977643 -80 * **** ** *** Masking position 6 Map Score: 8.45618 Number of sites scoring better than the average of aligned sites = 65 Number in coding regions = 47 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 2 TGGGTTCTATTAGAGAATCAAAGTACTC 1 9 0 TAGAGAATCA 0.885735 -292 TAGCTAAGAATAGAATATCAGATATTAGAG 1 65 1 TAGAATATCA 0.925082 -236 TTTTTATCTTAAGAGTATGAGAAGAGAACA 1 126 1 AAGAGTATGA 0.978086 -175 CCTTACGAATAAGAGCATCATGTCTTAAAC 1 222 1 AAGAGCATCA 0.979839 -79 ATCATGTCTTAAACGCATCAACAAAGATGG 1 238 1 AAACGCATCA 0.966004 -63 TAAATACTAAAAACATATGAGGATGC 2 64 1 AAACATATGA 0.92666 -16 TTAAAGTAATAAACATATGAAATAAAGTAA 3 80 1 AAACATATGA 0.92666 -23 ********** Masking position 7 Map Score: 4.44887 Number of sites scoring better than the average of aligned sites = 143 Number in coding regions = 107 Number in noncoding regions = 36 Number of orfs with sites within 600 bp upstream = 17 Fraction of orfs with sites within 600 bp upstream = 0.00273049 Motif number 3 TCAGATATTAGAGTGCTTTAAATCTGCTTC 1 82 1 GAGTGCTTTA 0.956977 -219 GATAAAAAAAGAAAGCTTTATTGAAGCAGA 1 104 0 GAAAGCTTTA 0.763339 -197 GAGAAGAGAACATAGCCTTAATCTGACTAG 1 144 1 CATAGCCTTA 0.939516 -157 TTGGGTTCTCGAAAGCCTTACGAATAAGAG 1 207 1 GAAAGCCTTA 0.964089 -94 AACAAAGATGGAAAGATTTTGGATTAGAAA 1 257 1 GAAAGATTTT 0.871368 -44 ********** Masking position 8 Map Score: 2.38137 Number of sites scoring better than the average of aligned sites = 55 Number in coding regions = 43 Number in noncoding regions = 12 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 4 GATAATATTGGATATCTTTGGGTTCTATTA 1 27 0 GATATCTTTG 0.926212 -274 GATATCCAATATTATCTTTAAACTTAGCTA 1 41 1 ATTATCTTTA 0.898007 -260 GCTTTCTTTTTTTATCTTAAGAGTATGAGA 1 118 1 TTTATCTTAA 0.838472 -183 TAGTCGTTTATTTTTCTTTGTACTGTAGTA 2 21 1 TTTTTCTTTG 0.965979 -59 GTTTTTAGTATTTATCTGTATATGTGTTAC 2 48 0 TTTATCTGTA 0.884975 -32 TAGGCTCTTTGTTTTGTTTGCTATTGCTAT 3 25 1 GTTTTGTTTG 0.850185 -78 TTCATATGTTTATTACTTTAATATTAAAGT 3 71 0 TATTACTTTA 0.795175 -32 GGTTTACTTTATTTCATATGT 3 92 0 GTTTACTTTA 0.927569 -11 ********** Masking position 7 Map Score: 2.91007 Number of sites scoring better than the average of aligned sites = 702 Number in coding regions = 534 Number in noncoding regions = 168 Number of orfs with sites within 600 bp upstream = 104 Fraction of orfs with sites within 600 bp upstream = 0.0167041 Motif number 5 GCTTTAAATCTGCTTCAATAAAGCTTTCTT 1 96 1 TGCTTCAATA 0.980963 -205 GTATATGTGTTACTACAGTACAAAGAAAAA 2 31 0 TACTACAGTA 0.596943 -49 TAAGTGCTACAGTATAGGCTCTTT 3 5 1 TGCTACAGTA 0.88328 -98 ATATGTTTATTACTTTAATATTAAAGTTGA 3 68 0 TACTTTAATA 0.797789 -35 ********** Masking position 4 Map Score: 2.1887 Number of sites scoring better than the average of aligned sites = 81 Number in coding regions = 68 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 6 TCTTTGGGTTCTATTAGAGAATCAAAGTAC 1 13 0 CTATTAGAGA 0.920868 -288 TTTAAAGATAATATTGGATATCTTTGGGTT 1 33 0 ATATTGGATA 0.953597 -268 AGAATATCAGATATTAGAGTGCTTTAAATC 1 76 1 ATATTAGAGT 0.963969 -225 TCTTTGACTACTATTGGGTTCTCGAAAGCC 1 194 1 CTATTGGGTT 0.800982 -107 AGATGGAAAGATTTTGGATTAGAAAGAGAC 1 262 1 ATTTTGGATT 0.827444 -39 AAAGTTGAGTATATTAAATGAATAGCAATA 3 46 0 ATATTAAATG 0.827719 -57 CTCAACTTTAATATTAAAGTAATAAACATA 3 67 1 ATATTAAAGT 0.912577 -36 AGTAATAAACATATGAAATAAAGTAAACC 3 84 1 ATATGAAATA 0.685212 -19 ********** Masking position 4 Map Score: 1.79815 Number of sites scoring better than the average of aligned sites = 504 Number in coding regions = 345 Number in noncoding regions = 159 Number of orfs with sites within 600 bp upstream = 80 Fraction of orfs with sites within 600 bp upstream = 0.0128493 Motif number 7 TTTTTGAGATGCATCTGTCTAGTCAGATTA 1 162 0 GCATCTGTCT 0.981583 -139 CAAAATCTTTCCATCTTTGTTGATGCGTTT 1 248 0 CCATCTTTGT 0.95333 -53 ATTCCTATGTGTCTCTTTCTAATCCAAAAT 1 272 0 GTCTCTTTCT 0.971806 -29 GTATTTATCTGTATATGTGTTACTACAGTA 2 41 0 GTATATGTGT 0.905835 -39 CTACAGTATAGGCTCTTTGTTTTGTTTGCT 3 17 1 GGCTCTTTGT 0.976851 -86 ********** Masking position 6 Map Score: 0.226797 Number of sites scoring better than the average of aligned sites = 31 Number in coding regions = 21 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 8 ********** No masking Map Score: 3.08538e-14 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: 3.08538e-14 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 10 ********** No masking Map Score: 3.08538e-14 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