AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i128_Transmembrane_Transport_2_hpyl_reg_300.orf -o128_hpyl_300.ace -a/home/amcguire/genomes/ORF_hpyl.txt -z/home/amcguire/genomes/hpyl.fna -g0.39 -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 = 0.39 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 RHP00941 240 AE000511 #2 RHP00942 139 AE000511 #3 RHP00952 74 AE000511 #4 RHP00954 21 AE000511 Motif number 1 TTATGGAGCGATTATAACACCATTAAGGAAATACAA 1 31 1 ATAACATTAA 0.987656 -210 TTTTCACAAAATCCTAAAATATTAAAGAAAATATTT 1 86 1 ATAAAATAAA 0.992423 -155 GTGGAGTATAATCTTAAAAAGTTAATGAAAAAATAT 1 116 0 ATAAAATAAT 0.959138 -125 AAAATTAAACCTAAAAACAGATTTAATTTACTATGC 1 177 0 CTAACATTAA 0.955069 -64 ATCCAACAAAATTTTAAAACACTTAAGGAGTTACGA 1 214 1 ATAAAATTAA 0.9879 -27 AGATAAAACGATACGAAAACTTTAAAACTAAGCGAA 2 71 0 ATAAAATAAA 0.992421 -69 AAAAAAATTAATTCAAAAATGATAAAAAGATAAAAC 2 98 0 ATAAAATAAA 0.99242 -42 ATGTTTGATTATTGTAACATACTAAATAAAACCATA 3 21 0 ATAACATAAA 0.992268 -54 ** **** **** Masking position 9 Map Score: 13.2322 Number of sites scoring better than the average of aligned sites = 207 Number in coding regions = 138 Number in noncoding regions = 69 Number of orfs with sites within 600 bp upstream = 70 Fraction of orfs with sites within 600 bp upstream = 0.0112432 Motif number 2 TAATCGCTCCATAAATCATACAAAAAGGATC 1 14 0 ATAAATATAC 0.899128 -227 TACAAGCAGTAAAAATGAAACTATTTTTCAC 1 62 1 AAAAATAAAC 0.991142 -179 ATTAACTTTTTAAGATTATACTCCACCATGT 1 126 1 TAAGATATAC 0.821591 -115 TTTGTTGGATCAAAATTAAACCTAAAAACAG 1 193 0 CAAAATAAAC 0.977245 -48 TCTTGGTTAAAAGAATTAAGCCGA 2 4 0 AAGAATAAGC 0.923261 -136 ATCAAAAAGAAAGGATTTAACCAAGAAAGAA 2 38 0 AAGGATTAAC 0.869758 -102 AAACTAAGCGAAGAATCAAAAAGAAAGGATT 2 52 0 AAGAATAAAA 0.906868 -88 AAAATGATAAAAAGATAAAACGATACGAAAA 2 88 0 AAAGATAAAC 0.989253 -52 AAATTAATTCAAAAATGATAAAAAGATAAAA 2 99 0 AAAAATATAA 0.846801 -41 TTGTAACATACTAAATAAAACCATAGGATAA 3 15 0 CTAAATAAAC 0.905857 -60 AGTATGTTACAATAATCAAACATTCTAACAT 3 34 1 AATAATAAAC 0.946351 -41 TCGGAATGTAAAGTTAAAACG 4 10 1 AAAGTTAAAC 0.914253 -12 ****** **** Masking position 6 Map Score: 14.4109 Number of sites scoring better than the average of aligned sites = 897 Number in coding regions = 724 Number in noncoding regions = 173 Number of orfs with sites within 600 bp upstream = 136 Fraction of orfs with sites within 600 bp upstream = 0.0218439 Motif number 3 ATTTTAGGATTTTGTGAAAAATAGTTTCAT 1 76 0 TTTGTGAAAA 0.910306 -165 TCCTAAAATATTAAAGAAAATATTTTTTCA 1 97 1 TTAAAGAAAA 0.788801 -144 TCTTAAAAAGTTAATGAAAAAATATTTTCT 1 111 0 TTAATGAAAA 0.878817 -130 GAAAGCATAGTAAATTAAATCTGTTTTTAG 1 173 1 TAAATTAAAT 0.668608 -68 TAAAATTTTGTTGGATCAAAATTAAACCTA 1 200 0 TTGGATCAAA 0.642884 -41 AAGAACTCTCTTGGTTAAAAGAATTAAGCC 2 13 0 TTGGTTAAAA 0.97419 -127 GAGTTCTTTCTTGGTTAAATCCTTTCTTTT 2 35 1 TTGGTTAAAT 0.868644 -105 AAAATGATAAAAAGATAAAACGATACGAAA 2 89 0 AAAGATAAAA 0.727502 -51 TTAAAAAAAATTAATTCAAAAATGATAAAA 2 107 0 TTAATTCAAA 0.821436 -33 AAAAACCCCTTTATTAAAAAAAATTAATT 2 121 0 TTTATTAAAA 0.909878 -19 AATAAAACCATAGGATAAAAGC 3 3 0 TAGGATAAAA 0.929908 -72 TTGTAACATACTAAATAAAACCATAGGATA 3 16 0 CTAAATAAAA 0.582167 -59 TTTTATTTAGTATGTTACAATAATCAAACA 3 26 1 TATGTTACAA 0.703743 -49 TTATTCTCCTTATGTTAGAATGTTTGATTA 3 46 0 TATGTTAGAA 0.70378 -29 TCGGAATGTAAAGTTAAAACG 4 10 1 AAAGTTAAAA 0.838286 -12 ********** Masking position 9 Map Score: 10.05 Number of sites scoring better than the average of aligned sites = 1954 Number in coding regions = 1561 Number in noncoding regions = 393 Number of orfs with sites within 600 bp upstream = 285 Fraction of orfs with sites within 600 bp upstream = 0.0457758 Motif number 4 CATAAATCATACAAAAAGGATCGTT 1 6 0 ACAAAAAGGA 0.948074 -235 GATTATAACACCATTAAGGAAATACAAGCA 1 40 1 CCATTAAGGA 0.964287 -201 AATTTTAAAACACTTAAGGAGTTACGAT 1 223 1 CACTTAAGGA 0.963893 -18 AGGATTTAACCAAGAAAGAACTCTCTTGGT 2 28 0 CAAGAAAGAA 0.89233 -112 GAAGAATCAAAAAGAAAGGATTTAACCAAG 2 44 0 AAAGAAAGGA 0.971485 -96 CAAACATTCTAACATAAGGAGAATAACAAT 3 50 1 AACATAAGGA 0.94796 -25 ********** Masking position 6 Map Score: 2.88683 Number of sites scoring better than the average of aligned sites = 303 Number in coding regions = 229 Number in noncoding regions = 74 Number of orfs with sites within 600 bp upstream = 79 Fraction of orfs with sites within 600 bp upstream = 0.0126887 Motif number 5 TGAAAAAATATTTTCTTTAATATTTTAGGA 1 97 0 TTTTCTTTAA 0.90449 -144 AGAAAATATTTTTTCATTAACTTTTTAAGA 1 111 1 TTTTCATTAA 0.90449 -130 TAAATCTGTTTTTAGGTTTAATTTTGATCC 1 188 1 TTTAGGTTTA 0.867293 -53 GAAAGAACTCTCTTGGTTAAAAGAATTAAG 2 15 0 TCTTGGTTAA 0.987303 -125 GAGAGTTCTTTCTTGGTTAAATCCTTTCTT 2 33 1 TCTTGGTTAA 0.987303 -107 TCTTTTTGATTCTTCGCTTAGTTTTAAAGT 2 59 1 TCTTCGCTTA 0.938441 -81 ********** Masking position 3 Map Score: 3.3792 Number of sites scoring better than the average of aligned sites = 123 Number in coding regions = 109 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 6 ********** No masking Map Score: -6.37056e-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: -6.37056e-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 8 ********** No masking Map Score: -6.37056e-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