AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i101_Iron_Transport_mjan_reg_300.orf -o101_mjan_300.ace -a/home/amcguire/genomes/ORF_mjan.txt -z/home/amcguire/genomes/mjan.fna -g0.31 -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 = 0.31 maxlen = 30 weight = 0.8 exclude = 1 Purged sequences: RMJ06212 36 M_jannaschii_chromosome Input sequences: #1 RMJ14763 300 M_jannaschii_chromosome #2 RMJ07770 261 M_jannaschii_chromosome #3 RMJ04644 134 M_jannaschii_chromosome #4 RMJ10046 23 M_jannaschii_chromosome #5 RMJ15227 18 M_jannaschii_chromosome Motif number 1 AGGCTTTCTTTATGATTCAAAAAAATGCGTAAGT 1 78 1 TATATAAAAA 0.979092 -223 AAATCTTTAAAATCTTTAAAAAAATTTTGAATTC 1 140 0 AATTTAAAAA 0.960413 -161 ATTAAAATGATAAAATTAAAAAAATCTTTAAAAT 1 161 0 TAAATAAAAA 0.979271 -140 ATGTTAAAATAATAATATTAAAATGATAAAATTA 1 177 0 AATATAAAAT 0.884091 -124 TTTTATCCTAAAAATTACTAAAAAATGTTAAAAT 1 201 0 AAATTAAAAA 0.96053 -100 ATAGCTGTAGTAATATATTAACAAAAAGGTTGGT 1 270 1 TAAATAACAA 0.921865 -31 AAATTAAAAATAAAGTCCAAAAAATAAAACTTAA 2 27 0 TAAGTAAAAA 0.898972 -235 GCCCTCCAATTAAAATTTTAAAATTAAAAATAAA 2 47 0 TAAATAAAAT 0.884091 -215 CCATTAATATTATTTTATCTAAAACTTTTGATAA 2 102 0 TATTTTAAAA 0.856945 -160 AGTCTGATTTAAATTTAATTAAAACCTAATATCT 2 227 0 AAATTTAAAA 0.858191 -35 AAATTATATAAAAAATAGAAAAAAG 3 2 0 AAAATAAAAA 0.979274 -133 AAAATACATCAATATTCATAAAAATTATATAAAA 3 23 0 AATTTAAAAA 0.960528 -112 GTTTATCAAAAATAATCGTTAAAAATACATCAAT 3 44 0 AATATTAAAA 0.921571 -91 AAAATATATATTAGATATTAAAAATTTTTGTTCA 3 84 1 TTAATAAAAA 0.801702 -51 TTTTAGGCTATATGATATGAACAAAAATTTTTAA 3 101 0 TATATAACAA 0.921865 -34 AATAATTCAAAAAATGTGATAGT 4 1 1 AATATAAAAA 0.979245 -23 *** ** ***** Masking position 6 Map Score: 22.4551 Number of sites scoring better than the average of aligned sites = 1318 Number in coding regions = 942 Number in noncoding regions = 376 Number of orfs with sites within 600 bp upstream = 296 Fraction of orfs with sites within 600 bp upstream = 0.0475426 Motif number 2 AAATCTTTAAAAAAATTTTGAATTCCTCACAG 1 133 0 AAAATTTTAA 0.968741 -168 TAAAATTAAAAAAATCTTTAAAATCTTTAAAA 1 153 0 AAAACTTTAA 0.930195 -148 TAATAATATTAAAATGATAAAATTAAAAAAAT 1 170 0 AAAAGATAAA 0.933494 -131 AAATTACTAAAAAATGTTAAAATAATAATATT 1 192 0 AAAAGTTAAA 0.971078 -109 GATAAAATAGAAAATTTTATATACCTATTACT 1 228 1 AAAATTTAAT 0.976084 -73 TCCAAAAAATAAAACTTAAAATAAGATAATAA 2 14 0 AAAATTAAAT 0.884511 -248 CCCTCCAATTAAAATTTTAAAATTAAAAATAA 2 48 0 AAAATTTAAA 0.976085 -214 AACTTTTGATAAAATGTTTGAATCTATTATTA 2 82 0 AAAAGTTTAA 0.962257 -180 TATTTTATCTAAAACTTTTGATAAAATGTTTG 2 94 0 AAAATTTTAT 0.968741 -168 CACTTGTTAGAAAAAGATTTATACTAAATAAG 2 197 1 AAAAGATTAT 0.913823 -65 AAATTTAATTAAAACCTAATATCTTATTTAGT 2 219 0 AAAACTAAAT 0.767072 -43 AATATTCATAAAAATTATATAAAAAATAGAAA 3 15 0 AAAATATAAA 0.944635 -120 TAAACTACCGAAAAATATATATTAGATATTAA 3 73 1 AAAATATAAT 0.944511 -62 GATATGAACAAAAATTTTTAATATCTAATATA 3 90 0 AAAATTTTAT 0.968741 -45 **** **** ** Masking position 4 Map Score: 24.2371 Number of sites scoring better than the average of aligned sites = 1112 Number in coding regions = 680 Number in noncoding regions = 432 Number of orfs with sites within 600 bp upstream = 310 Fraction of orfs with sites within 600 bp upstream = 0.0497912 Motif number 3 TTATCATTTTAATATTATTATTTTAACATT 1 182 1 AATATTATTA 0.840265 -119 TTTTTGTTAATATATTACTACAGCTATAGA 1 267 0 TATATTACTA 0.802459 -34 TCTTTATTATCTTATTTTAAGTTTTAT 2 8 1 TATCTTATTT 0.890554 -254 TATTTTAAGTTTTATTTTTTGGACTTTATT 2 23 1 TTTATTTTTT 0.860725 -239 TTTTTTGGACTTTATTTTTAATTTTAAAAT 2 37 1 TTTATTTTTA 0.860725 -225 AATGTTTGAATCTATTATTATGCCCTCCAA 2 72 0 TCTATTATTA 0.91718 -190 CTCTTCCATTAATATTATTTTATCTAAAAC 2 111 0 AATATTATTT 0.840266 -151 TAAAACCTAATATCTTATTTAGTATAAATC 2 212 0 TATCTTATTT 0.890554 -50 CTTTTTTCTATTTTTTATATAATTTT 3 7 1 TCTATTTTTT 0.905298 -128 CTATTTTTTATATAATTTTTATGAATATTG 3 18 1 TATAATTTTT 0.702703 -117 TGAATATTGATGTATTTTTAACGATTATTT 3 39 1 TGTATTTTTA 0.838563 -96 ATATCTAATATATATTTTTCGGTAGTTTAT 3 72 0 TATATTTTTC 0.872461 -63 TAATAGTATATTATTAGT 5 7 1 TATATTATTA 0.962624 -12 ********** Masking position 6 Map Score: 13.3057 Number of sites scoring better than the average of aligned sites = 1641 Number in coding regions = 1159 Number in noncoding regions = 482 Number of orfs with sites within 600 bp upstream = 383 Fraction of orfs with sites within 600 bp upstream = 0.0615162 Motif number 4 TATAGCCTCTGCGTAAGTTCCATTGTGGGA 1 22 0 GCGTAAGTTC 0.996616 -279 TCAAAAAAATGCGTAAGTTCTATTGAATAG 1 94 1 GCGTAAGTTC 0.996616 -207 TTTCAGACCAGTGTATGTTCCTCCACTTGT 2 174 1 GTGTATGTTC 0.983908 -88 ********** Masking position 5 Map Score: 3.00821 Number of sites scoring better than the average of aligned sites = 3 Number in coding regions = 1 Number in noncoding regions = 2 Number of orfs with sites within 600 bp upstream = 2 Fraction of orfs with sites within 600 bp upstream = 0.000321234 Motif number 5 ATTTTCTATTTTATCCTAAAAATTACTAAA 1 213 0 TTATCCTAAA 0.851467 -88 ATAGTAATAGGTATATAAAATTTTCTATTT 1 232 0 GTATATAAAA 0.636966 -69 TAGTAATATATTAACAAAAAGGTTGGTGTT 1 277 1 TTAACAAAAA 0.94375 -24 AAAATAAAACTTAAAATAAGATAATAAAGA 2 11 0 TTAAAATAAG 0.636963 -251 TTCAAACATTTTATCAAAAGTTTTAGATAA 2 92 1 TTATCAAAAG 0.940895 -170 TAATATTATTTTATCTAAAACTTTTGATAA 2 102 0 TTATCTAAAA 0.950659 -160 CCTCCACTTGTTAGAAAAAGATTTATACTA 2 193 1 TTAGAAAAAG 0.689746 -69 AGAAAAAGATTTATACTAAATAAGATATTA 2 205 1 TTATACTAAA 0.750724 -57 TGATTTAAATTTAATTAAAACCTAATATCT 2 227 0 TTAATTAAAA 0.595998 -35 TTCATAAAAATTATATAAAAAATAGAAAAA 3 13 0 TTATATAAAA 0.905098 -122 TTTCGGTAGTTTATCAAAAATAATCGTTAA 3 56 0 TTATCAAAAA 0.965964 -79 CTATATGATATGAACAAAAATTTTTAATAT 3 98 0 TGAACAAAAA 0.742422 -37 ********** Masking position 3 Map Score: 7.6369 Number of sites scoring better than the average of aligned sites = 1316 Number in coding regions = 1084 Number in noncoding regions = 232 Number of orfs with sites within 600 bp upstream = 225 Fraction of orfs with sites within 600 bp upstream = 0.0361388 Motif number 6 ********** No masking Map Score: 4.92707e-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: 4.92707e-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: 4.92707e-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