AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/alignace/lib/ORF_synecho.txt -z/skink1/amcguire/genomes/synecho.fna -irpoN_synecho_opreg_100.orf -g0.48 -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 = 0.48 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 hypD 300 hydrogenase isoenzymes formation protein HypD #2 glnA 210 glutamate-ammonia ligase #3 hypB 60 hydrogenase expression/formation protein HypB #4 1652375 75 hypothetical protein #5 speB 300 agmatine ureohydrolase #6 hypE 48 hydrogenase expression/formation protein HypE #7 1652558 52 hypothetical protein #8 1652559 129 hypothetical protein #9 glnH 300 glutamine-binding periplasmic protein #10 opcA 163 OpcA #11 1652851 57 ABC transporter #12 hypB 182 hydrogenase isoenzymes formation protein HypB #13 hypA 149 hydrogenase expression/formation protein HypA #14 ndhI 110 NADH dehydrogenase subunit NdhI Motif number 1 ATGGCTCTTTGCCCACCCCCACCCTAGTTCG 1 91 0 GCCACCCCCA 0.994039 -210 AATTTCCCTAGCCCTCCTCCATAAGAGGCCG 1 178 0 GCCTCCTCCA 0.91657 -123 GTCATTTCTAGGCGATCGCCAGAATGGAGCC 2 83 1 GGCATCGCCA 0.987383 -128 CTCTCCCAAAGGCGATCGCCGATTATTTCAG 4 49 0 GGCATCGCCG 0.984681 -27 ACTTTTTATCGGCGATCGCCAAACTAAAGTT 5 42 0 GGCATCGCCA 0.987383 -259 TCTCGGACCAGCCATTCCCCACATCACCAGG 5 141 0 GCCTTCCCCA 0.98589 -160 CGTTCTACGGGCCTATCTCAACAATGGGGTC 8 14 1 GCCATCTCAA 0.840637 -116 TGGCACAAAAGCAAACCCCCACAGAATCCTA 9 93 0 GCAACCCCCA 0.916557 -208 GCCTCAATTTGCCTTCCCACACTGCCCAACC 9 129 1 GCCTCCCACA 0.782414 -172 GTTTGTTGATGGTCTCCGCCGCAATAATCCC 9 238 1 GGTTCCGCCG 0.721264 -63 GCCATGGTTTACCCATCCCCGGGGATTATCA 10 77 1 ACCATCCCCG 0.894967 -87 AAAATCCGGGGCCAAACCCCGCCAGTGTTGA 10 105 0 GCCAACCCCG 0.954934 -59 AATTACAACCGGCGATCGCCAAAAATCCGGG 10 126 0 GGCATCGCCA 0.987383 -38 TTCCAGACAGGGCAATCCCAGAACAATGCGG 13 105 0 GGCATCCCAG 0.944074 -45 TTAATCATTTGCTTATCCCAATCCCAAATCT 14 90 1 GCTATCCCAA 0.779933 -21 *** ******* Masking position 7 Map Score: 23.3623 Number of sites scoring better than the average of aligned sites = 5541 Number in coding regions = 5045 Number in noncoding regions = 496 Number of orfs with sites within 600 bp upstream = 423 Fraction of orfs with sites within 600 bp upstream = 0.0679409 Motif number 2 GGGCACTTGTCAAGAATCGGCCTCTTATGGA 1 161 1 CAAAATCGGC 0.97658 -140 GATGGCTCTGAAATAATCGGCGATCGCCTTT 4 42 1 AAAAATCGGC 0.76666 -34 TTGCCACTAGCTACACGGCGGGACAAAAGCC 5 199 1 CTAACGGCGG 0.636153 -102 CTTAAGTTTCCTAAAATGGGCAACTTTGCTT 7 24 0 CTAAATGGGC 0.953571 -29 GGGCCTATCTCAACAATGGGGTCTTGGACTA 8 22 1 CAAAATGGGG 0.987658 -108 GTCTCCGCCGCAATAATCCCCCTTGGGGGAA 9 249 1 CAAAATCCCC 0.881024 -52 CCTAAAATGGGGTGACGGTCAC 10 2 1 CTAAATGGGG 0.966047 -162 CGGGGATTATCAACACTGGCGGGGTTTGGCC 10 96 1 CAAACTGGCG 0.905904 -68 CGGCGATCGCCAAAAATCCGGGGCCAAACCC 10 117 0 CAAAATCCGG 0.967271 -47 CAGAATGGAGCAACAAGCGCCCTTTGCTTAA 11 14 1 CAAAAGCGCC 0.833788 -44 TACAAAAATGGGGCTGGGAAATT 12 3 1 CAAAATGGGG 0.987659 -180 GGCAATCCCAGAACAATGCGGCGGAAAACCA 13 95 0 GAAAATGCGG 0.82703 -55 *** ******* Masking position 5 Map Score: 10.9622 Number of sites scoring better than the average of aligned sites = 966 Number in coding regions = 805 Number in noncoding regions = 161 Number of orfs with sites within 600 bp upstream = 159 Fraction of orfs with sites within 600 bp upstream = 0.0255381 Motif number 3 GTTCGTTTTTTATTCCCCAGGCAATGGCTCC 1 65 0 TATCCCCAGG 0.950123 -236 GATTCTTGACAAGTGCCCAGTCAAATGGGTA 1 148 0 AATGCCCAGT 0.922112 -153 TGTCCACTGTTACTGCCAAGAAACT 3 46 1 TATGCCAAGA 0.596388 -15 ACGGCGGGACAAAAGCCCGGGAGACTTTAAT 5 213 1 AAAGCCCGGG 0.957006 -88 AAACAACAAAATCTGCCCAGGAGTTATTAAT 5 265 0 ATTGCCCAGG 0.964359 -36 CCATAGCGAAAATTGTCCAGGCCGTGATTTT 8 62 0 AATGTCCAGG 0.974969 -68 AGAATCCTAAAATTCTCCGGGGGAAACGCAT 9 71 0 AATCTCCGGG 0.934283 -230 CCTTGGGGGAAAATGCCAAGGAACTACCGCC 9 269 1 AATGCCAAGG 0.943754 -32 CCAGTGTTGATAATCCCCGGGGATGGGTAAA 10 84 0 TATCCCCGGG 0.940016 -80 GGCGATCGCCAAAAATCCGGGGCCAAACCCC 10 116 0 AAAATCCGGG 0.585706 -48 ATGAGGTGGGATCTGTCCAGATCAAAGCCTC 13 22 1 ATTGTCCAGA 0.683722 -128 CTGGAAAATGAACTACCCAGAGTTAATCAT 13 130 1 AATACCCAGA 0.854871 -20 ** ******** Masking position 7 Map Score: 8.77805 Number of sites scoring better than the average of aligned sites = 1792 Number in coding regions = 1659 Number in noncoding regions = 133 Number of orfs with sites within 600 bp upstream = 157 Fraction of orfs with sites within 600 bp upstream = 0.0252168 Motif number 4 TTATGGAGGAGGGCTAGGGAAATTTGACATCACTT 1 185 1 GGTAGAAATT 0.959403 -116 CAAATTAGAGGGTGTTGACAAAGTTTGAAAGTGAT 1 213 0 GGTTGAAATT 0.924568 -88 CTGATTCCAAGGTTAACGAAAATTTTCAGTAACAG 1 259 0 GGAACAAATT 0.958866 -42 AATGTTAATGGGATTTGCGATGGTTTCCGTCATTT 2 55 1 GGTTGATGTT 0.760829 -156 GGCAATAATTAGTCAAGTTAAAGTTA 4 2 0 AGAAGAAATT 0.765773 -74 ATCGGCGATCGCCAAACTAAAGTTTAAAACCTGAC 5 31 0 GCAACAAGTT 0.741714 -270 AAACAGGCTAGGCTTTGTAAAGATTTTTGCCACTA 5 173 1 GGTTGAAGTT 0.934204 -128 AATTCTCCGGGGGAAACGCATAGTTTCGAGTCTAT 9 57 0 GGAACATATT 0.839304 -244 TACTGACCAAGGTTATGAAAAGTTTATTAAGTTTG 9 208 1 GGATGAAGTT 0.964759 -93 GGCCGACTAAGGTTAAGAACAGATTAAGCAAAGGG 11 33 0 GGAAGCAGTT 0.900607 -25 ACAATGCGGCGGAAAACCAAAACTTAGAAGCAAAA 13 79 0 GGAACAAATT 0.958866 -71 TTAGAAGCTGGGCTAAGACAAATTTCAGTGACATC 14 36 0 GGAAGAAATT 0.978525 -75 ** *** *** ** Masking position 14 Map Score: 7.68543 Number of sites scoring better than the average of aligned sites = 646 Number in coding regions = 507 Number in noncoding regions = 139 Number of orfs with sites within 600 bp upstream = 163 Fraction of orfs with sites within 600 bp upstream = 0.0261805 Motif number 5 CGCCAGAATGGAGCCGCAAAAAATGGTAGCG 2 99 1 GGCCGCAAAA 0.96275 -112 GCAAAAAATGGTAGCGAAAAATACATTTTCT 2 114 1 GAGCGAAAAA 0.73164 -97 GATAGTCGACGCAGCGCAAAATCGTAATTTA 2 167 1 GAGCGCAAAA 0.954584 -44 CTGACTGCACTAAGGAGAAAAA 2 199 1 TAGGAGAAAA 0.61562 -12 GCCGTGTAGCTAGTGGCAAAAATCTTTACAA 5 187 0 TGTGGCAAAA 0.836586 -114 TAGCTACACGGCGGGACAAAAGCCCGGGAGA 5 206 1 GGGGACAAAA 0.947829 -95 TGAGGCAATTTTGGCACAAAAGCAAACCCCC 9 104 0 TGGCACAAAA 0.942498 -197 TTGGTCAGTATTGTCGCAAAAGCAGACTAAA 9 187 0 TGTCGCAAAA 0.897751 -114 ATAATCCCCCTTGGGGGAAAATGCCAAGGAA 9 261 1 TGGGGGAAAA 0.946228 -40 TTAATCAATGGAGCCAGAAAAGACAAACCTG 12 40 1 GGCCAGAAAA 0.865368 -143 CCAGAACAATGCGGCGGAAAACCAAAACTTA 13 88 0 GGGCGGAAAA 0.982888 -62 * ********* Masking position 8 Map Score: 7.79606 Number of sites scoring better than the average of aligned sites = 1394 Number in coding regions = 1255 Number in noncoding regions = 139 Number of orfs with sites within 600 bp upstream = 159 Fraction of orfs with sites within 600 bp upstream = 0.0255381 Motif number 6 TAATCGGCGATCGCCTTTGGGAGAGGTAAAA 4 55 1 TCCCTTTGGG 0.966633 -21 GCAGCTAATCTCTTTGTTGCAGGATGTAACAGT 6 24 0 TCTTGTTGCG 0.958159 -25 AAAGGTTTGCTTACCGTTGCCCGTTTGACTAGT 8 97 1 TTCCGTTGCG 0.930834 -33 GTACCGATCGACTTCGTTGCAAGCTTCATAGAC 9 30 1 ACTCGTTGCG 0.916769 -271 GCCGCAATAATCCCCCTTGGGGGAAAATGCCAA 9 255 1 TCCCCTTGGG 0.987496 -46 TCCTCATCGTTGGCGGTAGTTCCTTG 9 285 0 TCTCGTTGGG 0.991274 -16 GGGGTGACGGTCACTGTTGACGGATTACGGGGG 10 19 1 TCCTGTTGAG 0.918858 -145 AATAACCTTCCCCCTCGGGCGGAAATATTAA 12 162 0 TCCCCTCGGG 0.948614 -21 TCCCAGCTAATCTTTGTTGGAAGAGGA 14 5 0 TCTTGTTGGG 0.973861 -106 ** ******* * Masking position 7 Map Score: 6.04958 Number of sites scoring better than the average of aligned sites = 452 Number in coding regions = 412 Number in noncoding regions = 40 Number of orfs with sites within 600 bp upstream = 48 Fraction of orfs with sites within 600 bp upstream = 0.0077096 Motif number 7 TTTGCCCACCCCCACCCTAGTTCGTTTTTT 1 85 0 CCCACCCTAG 0.989085 -216 GTTCGTTTCGCCCAAATTAGAGGGTGTTGA 1 230 0 CCCAAATTAG 0.875842 -71 AGTGACCATACCCAACCCGCAAGTACTAAA 2 19 0 CCCAACCCGC 0.941585 -192 GCCCTAACCCACCGAGACTAAA 3 3 1 CCTAACCCAC 0.931436 -58 AACAATATCCCCTACCCTAGCTAGGGATGA 5 96 0 CCTACCCTAG 0.946931 -205 CCAGCCATTCCCCACATCACCAGGAATCGG 5 135 0 CCCACATCAC 0.89901 -166 CGATTAGACCCAACTTATCGTACCGATC 9 9 1 CCCAACTTAT 0.923694 -292 TCCCACACTGCCCAACCTAGAAAAACTGTA 9 143 1 CCCAACCTAG 0.985991 -158 CTGGACAGATCCCACCTCATAGAACTCGGT 13 12 0 CCCACCTCAT 0.952526 -138 ********** Masking position 4 Map Score: 6.89517 Number of sites scoring better than the average of aligned sites = 886 Number in coding regions = 795 Number in noncoding regions = 91 Number of orfs with sites within 600 bp upstream = 105 Fraction of orfs with sites within 600 bp upstream = 0.0168648 Motif number 8 TTATTTGGAGCCATTGCCTGGGGAATAAAA 1 59 1 CCATTGCCTG 0.882637 -242 TCCATTCTGGCGATCGCCTAGAAATGACGG 2 81 0 CGATCGCCTA 0.78701 -130 ACTTTAATGACCAGTGCTTAGGTGTTGTCA 5 236 1 CCAGTGCTTA 0.889401 -65 AAAATGGGCAACTTTGCTTATATCTTATCG 7 13 0 ACTTTGCTTA 0.832627 -40 TTGCTTTGCTTAAGTTTCCTAA 7 41 0 GCTTTGCTTA 0.931361 -12 TGGTTTAAAAGGTTTGCTTACCGTTGCCCG 8 90 1 GGTTTGCTTA 0.857553 -40 TACCGTTGCCCGTTTGACTAGTTACACATC 8 108 1 CGTTTGACTA 0.764357 -22 GATGGGTAAACCATGGCCTAGAATAATTGT 10 64 0 CCATGGCCTA 0.8928 -100 CAACAAGCGCCCTTTGCTTAATCTGTTCTT 11 24 1 CCTTTGCTTA 0.980674 -34 TTTTCTGGCTCCATTGATTAAATATCCAAT 12 31 0 CCATTGATTA 0.868051 -152 AACCTTTAATCATTTGCTTATCCCAATCCC 14 85 1 CATTTGCTTA 0.849998 -26 ********** Masking position 9 Map Score: 5.16052 Number of sites scoring better than the average of aligned sites = 692 Number in coding regions = 587 Number in noncoding regions = 105 Number of orfs with sites within 600 bp upstream = 121 Fraction of orfs with sites within 600 bp upstream = 0.0194346 Motif number 9 GAATCAGTTCGCCAAGTTTTAGCC 1 287 1 GCCAGTTTTA 0.960845 -14 GCTAATTGATGTCAGGTTTTAAACTTTAGTT 5 21 1 GTCAGTTTTA 0.706379 -280 TGTGTTCTGTGCTACTTTTTATCGGCGATCG 5 55 0 GCTATTTTTA 0.906556 -246 AGAGAAACAGGCTAGGCTTTGTAAAGATTTT 5 169 1 GCTAGCTTTG 0.936104 -132 GACAATTTTCGCTATGGTTTAAAAGGTTTGC 8 76 1 GCTAGGTTTA 0.967713 -54 ATTATTCTAGGCCATGGTTTACCCATCCCCG 10 67 1 GCCAGGTTTA 0.974739 -97 GCCAAACCCCGCCAGTGTTGATAATCCCCGG 10 95 0 GCCATGTTGA 0.82107 -69 GCAAAATCTAGCTATTCTTTAGGGTGCCTGC 13 54 0 GCTATCTTTA 0.938481 -96 TGACATCCCAGCTAATCTTTGTTGGAAGAGG 14 12 0 GCTATCTTTG 0.881751 -99 **** ****** Masking position 4 Map Score: 5.42834 Number of sites scoring better than the average of aligned sites = 328 Number in coding regions = 277 Number in noncoding regions = 51 Number of orfs with sites within 600 bp upstream = 63 Fraction of orfs with sites within 600 bp upstream = 0.0101189 Motif number 10 CGAAAATTTTCAGTAACAGTTCGTTTCGCC 1 248 0 CAGTAACAGT 0.979908 -53 ACATTTAGATCAGTGACCATACCCAACCCG 2 30 0 CAGTGACCAT 0.906329 -181 AGTTTCTTGGCAGTAACAGTGGACAAGTTA 3 41 0 CAGTAACAGT 0.979908 -20 GTTCTTGGCCGTAACTGTTACATCCTGC 6 9 1 CCGTAACTGT 0.946903 -40 AATCCGTCAACAGTGACCGTCACCCCATTT 10 15 0 CAGTGACCGT 0.984263 -149 GAATAATTGTCAGTAAGTGTCGCCCCCGTA 10 44 0 CAGTAAGTGT 0.917917 -120 ********** Masking position 6 Map Score: 3.51711 Number of sites scoring better than the average of aligned sites = 102 Number in coding regions = 90 Number in noncoding regions = 12 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 11 AAAGTGATGTCAAATTTCCCTAGCCCTCCT 1 191 0 CAAATTTCCC 0.909522 -110 TTTTGCGGCTCCATTCTGGCGATCGCCTAG 2 90 0 CCATTCTGGC 0.913478 -121 TTCAGAGCCATCAATTTGGCAATAATTAGT 4 24 0 TCAATTTGGC 0.885867 -52 AAGATATAAGCAAAGTTGCCCATTTTAGGA 7 17 1 CAAAGTTGCC 0.764623 -36 ACGGCCTGGACAATTTTCGCTATGGTTTAA 8 68 1 CAATTTTCGC 0.893938 -62 CAAATTGAGGCAATTTTGGCACAAAAGCAA 9 110 0 CAATTTTGGC 0.93533 -191 CAAAATTGCCTCAATTTGCCTTCCCACACT 9 122 1 TCAATTTGCC 0.902508 -179 TAGTTCCTTGGCATTTTCCCCCAAGGGGGA 9 265 0 GCATTTTCCC 0.759871 -36 GCTTGTTGCTCCATTCTGCCA 11 2 0 CCATTCTGCC 0.926427 -56 GATTAAATATCCAATTTCCCAGCCCCATTT 12 16 0 CCAATTTCCC 0.950297 -167 GCCCAGCTTCTAACTTTGGCCGACTTAAAC 14 58 1 TAACTTTGGC 0.598741 -53 ********** Masking position 3 Map Score: 6.87937 Number of sites scoring better than the average of aligned sites = 1396 Number in coding regions = 1231 Number in noncoding regions = 165 Number of orfs with sites within 600 bp upstream = 185 Fraction of orfs with sites within 600 bp upstream = 0.0297141 Motif number 12 AATTTTCGTTAACCTTGGAATCAGTTCGCC 1 270 1 AACCTTGGAA 0.874492 -31 AACTTTTCATAACCTTGGTCAGTATTGTCG 9 202 0 AACCTTGGTC 0.988391 -99 GGGATGGGTAAACCATGGCCTAGAATAATT 10 66 0 AACCATGGCC 0.965702 -98 ATCTGTTCTTAACCTTAGTCGGCC 11 44 1 AACCTTAGTC 0.945879 -14 AGAAAAGACAAACCTGGGTCTCCACCATCA 12 55 1 AACCTGGGTC 0.975877 -128 CCCAGCTTCTAACTTTGGCCGACTTAAACC 14 59 1 AACTTTGGCC 0.950046 -52 ********** Masking position 2 Map Score: 3.7846 Number of sites scoring better than the average of aligned sites = 298 Number in coding regions = 266 Number in noncoding regions = 32 Number of orfs with sites within 600 bp upstream = 39 Fraction of orfs with sites within 600 bp upstream = 0.00626405 Motif number 13 ********** No masking Map Score: 5.57309e-12 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 14 ********** No masking Map Score: 5.57309e-12 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 15 ********** No masking Map Score: 5.57309e-12 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