AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_mjan.txt -z/home/amcguire/genomes/mjan.fna -icytR_mjan_opreg_300.orf -g0.314 -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 = 0.314 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 MJ0667 91 thymidine phosphorylase (deoA) #2 MJ0703 24 phosphoribosylformimino-5-aminoimidazole carboxamide ribotide isomerase (hisA2) #3 MJ0703.1 125 M. jannaschii predicted coding region MJ0703.1 #4 MJ0704 95 M. jannaschii predicted coding region MJ0704 Motif number 1 AACTTTATATATTTTCTTTAATATTACTTC 1 25 0 ATTTTCTTTA 0.958125 -67 AAATTTTTATATTTTCTAAACTTTATATAT 1 43 0 ATTTTCTAAA 0.836326 -49 TTTATCTATTAAATTTTTATATTTTCTAAA 1 53 0 AAATTTTTAT 0.673367 -39 AATCACCACTAATTTCTTTATCTATTAAAT 1 69 0 AATTTCTTTA 0.943247 -23 GTTTCCCTCTAAATTATTATTTA 2 4 0 AAATTATTAT 0.612324 -21 AAAATAAACACTACTTTTTACAGAAACATA 3 47 1 CTACTTTTTA 0.655672 -79 ACTATAACACCATCTTTTAAATATGTTTCT 3 68 0 CATCTTTTAA 0.882371 -58 GTATAGAACTATTTTATTATTTTT 3 112 1 ATTTTATTAT 0.859582 -14 AGTTATAATAATTTTTTTAA 4 1 0 ATTTTTTTAA 0.957363 -95 AATAGATATCCATTTATTAAAATCTCCTAC 4 49 0 CATTTATTAA 0.911541 -47 ATGGATATCTATTCTCTTAATTGCTTATGC 4 66 1 ATTCTCTTAA 0.961032 -30 ATTGCTTATGCTTTTCTTTAC 4 85 1 CTTTTCTTTA 0.949553 -11 ********** Masking position 5 Map Score: 12.2382 Number of sites scoring better than the average of aligned sites = 3155 Number in coding regions = 2648 Number in noncoding regions = 507 Number of orfs with sites within 600 bp upstream = 380 Fraction of orfs with sites within 600 bp upstream = 0.0610344 Motif number 2 TTAAATCACCACTAATTTCTTT 1 80 0 TAATCACCAC 0.952089 -12 AGTTTCCCTCTAAATTATTATTTA 2 4 0 TAATTATTAT 0.7577 -21 TAAAGTTCTATCAGTTGATGA 3 1 1 TAAGTTCTAT 0.932561 -125 CACTACTTTTTACAGAAACATATTTAAAAGA 3 55 1 TAAGAAACAT 0.935704 -71 TTCATCCAACTATAACACCATCTTTTAAATA 3 75 0 TAAACACCAT 0.962349 -51 GAAGTTGAGGTATAGAACTATTTTATTATTT 3 103 1 TAAGAACTAT 0.978517 -23 ATTAAGAGAATAGATATCCATTTATTAAAAT 4 56 0 TAATATCCAT 0.962998 -40 ** ******** Masking position 4 Map Score: 1.6045 Number of sites scoring better than the average of aligned sites = 466 Number in coding regions = 388 Number in noncoding regions = 78 Number of orfs with sites within 600 bp upstream = 67 Fraction of orfs with sites within 600 bp upstream = 0.0107613 Motif number 3 ATTTTCTAAACTTTATATATTTTCTTTAATA 1 32 0 CTTTATTATT 0.980534 -60 TCTATTAAATTTTTATATTTTCTAAACTTTA 1 48 0 TTTTATTTTT 0.970207 -44 CCACTAATTTCTTTATCTATTAAATTTTTAT 1 63 0 CTTTATTATT 0.980534 -29 AGTTCTATCAGTTGATGAATTCAATCTAATG 3 14 1 GTTGATAATT 0.908017 -112 AAAAAGTAGTGTTTATTTTTTCATTAGATTG 3 35 0 GTTTATTTTT 0.980534 -91 TATAGAACTATTTTATTATTTTT 3 113 1 TTTTATATTT 0.94581 -13 ****** **** Masking position 6 Map Score: 6.36631 Number of sites scoring better than the average of aligned sites = 744 Number in coding regions = 523 Number in noncoding regions = 221 Number of orfs with sites within 600 bp upstream = 189 Fraction of orfs with sites within 600 bp upstream = 0.0303566 Motif number 4 ********** No masking Map Score: -8.2833e-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 5 ********** No masking Map Score: -8.2833e-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 6 ********** No masking Map Score: -8.2833e-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