AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i101_Iron_Transport_bsub_reg_100.orf -aORF_bsub.txt -zbsub.fna -g0.435 -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 = 0.435 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 yfmD 71 similar to ferrichrome ABC transporter (permease) #2 yfmC 108 similar to ferrichrome ABC transporter (binding protein) #3 yfiZ 130 similar to iron(III) dicitrate transport permease #4 yusV 217 similar to iron(III) dicitrate transport permease #5 yvrC 300 similar to iron-binding protein #6 fhuB_fhuD 97 fhuB: ferrichrome ABC transporter (permease), fhuD: ferrichrome ABC transporter (ferrichrome-binding protein) Motif number 1 TAAAAAAATATTGACATGATAAGCCATGCTATTATAG 2 29 1 TTCATATCAT 0.719969 -80 GTGTTACATGTGATAATGATTCTCATTACTAAATCTG 2 65 1 TGAATATCTT 0.991518 -44 CTCCCAATATTGAAATTCATTATCATTTAGATCATAA 3 18 1 TGATTATCTT 0.970144 -113 TGTTTGTTTTTGAGAATAATCCTCAATTAGGGATTGA 3 73 0 TGAATATCAT 0.98836 -58 GATCTAATTCTCCTAGTTATTTACTATGTAATGTTTG 3 104 0 TCAGTATCAT 0.896913 -27 ATTAGTTTTATGGACATAATTGACGTTTATGGGTTTT 4 22 0 TGCATATCTT 0.975911 -196 ACACTGACTTTGAAAATCATTTTCAATTAGTTTTATG 4 47 0 TGAATATCAT 0.98836 -171 TGGCTGAATATCGGAATCATTTGCATTGATGACAATT 4 120 1 TCAATATCTT 0.965345 -98 TATACAAGCCTGTCAGTCATATAGTATAATTACTCCG 5 24 1 TGAGTATGAT 0.795196 -277 GGCACCTATTTGACATTCGTATCCGTTTTTCGGAGTA 5 54 0 TGATTGTCTT 0.847982 -247 ACAGATGATGTGTAAACAATAGGCTTTTTTGTGTTGT 5 216 1 TGAACATCTT 0.952532 -85 TAATCACAGATGATAATGATTCTCTTTTTCATCTATC 6 33 0 TGAATATCTT 0.991518 -65 ** *** ** * ** Masking position 10 Map Score: 14.377 Number of sites scoring better than the average of aligned sites = 239 Number in coding regions = 186 Number in noncoding regions = 53 Number of orfs with sites within 600 bp upstream = 58 Fraction of orfs with sites within 600 bp upstream = 0.00931577 Motif number 2 CGAGGGGAATCCTTGCTTCTTCGTTTTTGCA 1 24 1 CCTTGCTCTT 0.60626 -48 ACATGATAAGCCATGCTATTATAGTGTTACA 2 42 1 CCATGCTTTA 0.916327 -67 TTTTCTATATACATGCTTTTAAGTCAATTGT 4 151 0 ACATGCTTTA 0.938954 -67 GCTCCTTTTTGCTGGCTTTTTAGCAGCACTA 4 193 0 GCTGGCTTTT 0.917604 -25 TATATGACTGACAGGCTTGTATATGTGTCCT 5 16 0 ACAGGCTGTA 0.9677 -285 TTGTTCACGGACCGGCACCTATTTGACATTC 5 73 0 ACCGGCACTA 0.932034 -228 TCCCTTTTAAGCCGGCTGTTGTTCACGGACC 5 91 0 GCCGGCTTTG 0.973094 -210 GCGGGACCGCACCGGCTTTTACCGGTTTCCC 5 118 0 ACCGGCTTTA 0.988975 -183 AGGCAGGTATCCTGGCTCTTGGCGCTTGGCC 5 159 0 CCTGGCTTTG 0.962275 -142 TGCTGATCAAACAGGCAGGTATCCTGGCTCT 5 171 0 ACAGGCAGTA 0.914174 -130 TGTGTAAACAATAGGCTTTTTTGTGTTGTTT 5 224 1 ATAGGCTTTT 0.723946 -77 TATCGTGTCAACCGGCACTTGCAGTGGTATA 6 68 0 ACCGGCATTG 0.963378 -30 ******* *** Masking position 10 Map Score: 11.1413 Number of sites scoring better than the average of aligned sites = 1351 Number in coding regions = 1194 Number in noncoding regions = 157 Number of orfs with sites within 600 bp upstream = 122 Fraction of orfs with sites within 600 bp upstream = 0.0195952 Motif number 3 GCGAGGGGAATCCTTGCTTCTTCGTTTTTG 1 23 1 TCCTTGCTTC 0.959907 -49 CCTTGCTTCTTCGTTTTTGCAACCAGACGC 1 34 1 TCGTTTTTGC 0.953849 -38 CAGTCTCACTTCCTTACTGCGTCTGGTTGC 1 52 0 TCCTTACTGC 0.954122 -20 GTCATTCTTCCTTTTTTCAGATTTAGTA 2 91 0 TCCTTTTTTC 0.985919 -18 TCAAAGTCAGTGTTTTCTGCTACAATGAGG 4 71 1 TGTTTTCTGC 0.868269 -147 AACCGCTCCTTTTTGCTGGCTTTTTA 4 202 0 TCCTTTTTGC 0.989028 -16 GACATTCGTATCCGTTTTTCGGAGTAATTA 5 50 0 TCCGTTTTTC 0.948971 -251 AATCTTTTCCTCCTAAACGAAC 5 289 0 TCTTTTCCTC 0.891686 -12 TGATAATGATTCTCTTTTTCATCTATCTTT 6 30 0 TCTCTTTTTC 0.879069 -68 ********** Masking position 5 Map Score: 8.04787 Number of sites scoring better than the average of aligned sites = 1238 Number in coding regions = 1028 Number in noncoding regions = 210 Number of orfs with sites within 600 bp upstream = 238 Fraction of orfs with sites within 600 bp upstream = 0.0382268 Motif number 4 TTTAGTAAAGAAAGCTGCGTTT 2 2 0 AAGCTGCGTT 0.603031 -107 TGACATGATAAGCCATGCTATTATAGTGTTA 2 40 1 ACCATGCTAT 0.856417 -69 CGTTTTCTATATACATGCTTTTAAGTCAATT 4 153 0 AACATGCTTT 0.975044 -65 AACCGCTCCTTTTTGCTGGCTT 4 206 0 ACGCTCCTTT 0.858676 -12 TTCTGCGAGGACAGATGATGTGTAAACAATA 5 206 1 AAGATGATGT 0.83265 -95 CTACGACGGTAAAGATGCTGTAAACAACACA 5 245 0 AAGATGCTGT 0.785345 -56 TTACCGTCGTAGAGATGCTTTTTTAGTTCGT 5 264 1 AAGATGCTTT 0.967551 -37 ATCTCATACCTTCTTTCTAAAAGATA 6 6 1 AACCTTCTTT 0.830787 -92 * ********* Masking position 1 Map Score: 2.8466 Number of sites scoring better than the average of aligned sites = 575 Number in coding regions = 503 Number in noncoding regions = 72 Number of orfs with sites within 600 bp upstream = 66 Fraction of orfs with sites within 600 bp upstream = 0.0106007 Motif number 5 TTCCCCTCGCTTCTCATTTGTC 1 2 0 TTTCATTTGT 0.967023 -70 ATGAGAATCATTATCACATGTAACACTATAA 2 60 0 TTTCACATGT 0.844612 -49 GTGATAATGATTCTCATTACTAAATCTGAAA 2 74 1 TTTCATTACT 0.800184 -35 TTGAAATTCATTATCATTTAGATCATAATAA 3 27 1 TTTCATTTAG 0.865765 -104 CCATTTGATATGGTCATATATCCCTCATTGT 4 92 0 TGTCATATAT 0.818218 -126 TTTAAGTCAATTGTCATCAATGCAAATGATT 4 134 0 TTTCATCAAT 0.933236 -84 ATGATTCTCTTTTTCATCTATCTTTTAGAAA 6 24 0 TTTCATCTAT 0.974479 -74 AAGAGAATCATTATCATCTGTGATTATACCA 6 44 1 TTTCATCTGT 0.978773 -54 ** ******** Masking position 6 Map Score: 2.97421 Number of sites scoring better than the average of aligned sites = 495 Number in coding regions = 405 Number in noncoding regions = 90 Number of orfs with sites within 600 bp upstream = 104 Fraction of orfs with sites within 600 bp upstream = 0.0167041 Motif number 6 TACTATATGACTGACAGGCTTGTATATGTG 5 20 0 CTGACAGGCT 0.93678 -281 CTGTTGTTCACGGACCGGCACCTATTTGAC 5 77 0 CGGACCGGCA 0.991709 -224 GTTTCCCTTTTAAGCCGGCTGTTGTTCACG 5 95 0 TAAGCCGGCT 0.89848 -206 GTGGCGGGACCGCACCGGCTTTTACCGGTT 5 122 0 CGCACCGGCT 0.984847 -179 TCGTGCTGATCAAACAGGCAGGTATCCTGG 5 175 0 CAAACAGGCA 0.960325 -126 AAATATCGTGTCAACCGGCACTTGCAGTGG 6 72 0 TCAACCGGCA 0.953149 -26 ********** Masking position 5 Map Score: 1.49516 Number of sites scoring better than the average of aligned sites = 592 Number in coding regions = 536 Number in noncoding regions = 56 Number of orfs with sites within 600 bp upstream = 39 Fraction of orfs with sites within 600 bp upstream = 0.00626405 Motif number 7 TCCTCCCAATATTGAAATTCATTATCATTT 3 16 1 ATTGAAATTC 0.965993 -115 TCAATTAGGGATTGACACTCTTAACACTGC 3 58 0 ATTGACACTC 0.973636 -73 AAACACTGACTTTGAAAATCATTTTCAATT 4 56 0 TTTGAAAATC 0.941551 -162 CCGGCACCTATTTGACATTCGTATCCGTTT 5 63 0 TTTGACATTC 0.977748 -238 ********** Masking position 5 Map Score: 0.5415 Number of sites scoring better than the average of aligned sites = 58 Number in coding regions = 52 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 8 ********** No masking Map Score: -6.51267e-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 9 ********** No masking Map Score: -6.51267e-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 10 ********** No masking Map Score: -6.51267e-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