AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00440_synecho_reg_300.orf -o00440_synecho_300.ace -a/home/amcguire/genomes/ORF_synecho.txt -z/home/amcguire/genomes/synecho.fna -g0.48 -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 = 0.48 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 slr0723 78 hypothetical protein. #2 slr0724 83 sohA; HtaR suppressor protein. #3 slr0725 300 hypothetical protein. #4 slr1099 300 ubiX; 3-octaprenyl-4-hydroxybenzoate carboxy-lyase. [EC:4.1.1.-] #5 sll1909 77 prmA; probable methyltransferase. [EC:2.1.1.-] [SP:PRMA_SYNY3] #6 sll1908 260 serA; phosphoglycerate dehydrogenase. [EC:1.1.1.95] #7 slr1990 21 hypothetical protein. #8 slr1991 40 cyaA; adenylate cyclase. [EC:4.6.1.1] #9 slr1992 209 glutathione peroxidase. [EC:1.11.1.9] #10 slr1993 101 thl; acetyl coenzyme A acetyltransferase (thiolase). #11 slr1994 60 fabG; 3-oxoacyl-[acyl-carrier protein] reductase (3-ketoacyl-acyl #12 sll1906 60 428 aa (44.5 kD) bacteriochlorophyll synthase subunit. #13 sll1905 68 sensory transduction histidine kinase. #14 slr1998 32 hypothetical protein. #15 slr1999 38 hypothetical protein. #16 slr2000 257 hypothetical protein. #17 slr2001 147 pepE; peptidase E (alpha-aspartyl dipeptidase). [EC:3.4.-.-] #18 slr2002 32 hypothetical protein. #19 sll1902 300 hypothetical protein. #20 slr0095 161 hisB; O-methyltransferase. [EC:2.1.1.-] #21 slr0096 29 hisB; low affinity sulfate transporter. #22 slr0498 246 hisB; hypothetical protein. #23 sll0489 286 hisB; ABC transporter. #24 sll0488 116 hypothetical protein. #25 sll0487 109 hypothetical protein. #26 sll0486 173 hypothetical protein. #27 sll0485 247 hypothetical protein. #28 sll0484 130 ABC transporter. #29 slr0502 62 cobW; CobW. #30 slr0505 121 hypothetical protein. #31 slr0506 56 pcr; protochlorophyllide oxido-reductase. [EC:1.3.1.33] #32 sll0481 71 hypothetical protein. [SP:Y481_SYNY3] #33 sll0480 182 hypothetical protein. #34 slr0509 131 alkaline phosphatase-like. #35 slr0510 222 hypothetical protein. #36 ssr0871 55 transposase. #37 slr0511 300 transposase. Motif number 1 TCAAGAAATAGGGGATGGGCAAATATCTTC 2 27 1 GGGGATGGGC 0.973451 -57 GATTCCAAATGGCGATCGCCAGTGTGAAAG 3 272 1 GGCGATCGCC 0.499989 -29 CAGTGTCGGCGGCTGTGGGCAAAGTTTGGC 4 104 0 GGCTGTGGGC 0.917763 -197 AATGGGCTACGGAGATCGGCCCAGGATACT 6 230 1 GGAGATCGGC 0.895278 -31 AATCCCCCCCGGCGATCGCCTATGAGGATC 9 93 1 GGCGATCGCC 0.499989 -117 GATGATCCTTGGCGATCGCCAGTTTGGGAA 22 110 1 GGCGATCGCC 0.499989 -137 GAAATTGAGTGGCAATGGCTTTTTTCAGAA 23 26 1 GGCAATGGCT 0.908225 -261 CTATCCCCTAGGCGGTGGGCCGATATTAGG 25 14 1 GGCGGTGGGC 0.981444 -96 CCATTCCTCTGGCGATCGCCAAAGCTCCAG 25 77 1 GGCGATCGCC 0.499989 -33 AATTTGGACTAGCTATGGCCGTCACCATGA 33 50 1 AGCTATGGCC 0.70607 -133 CAGGGGAAATGGCAATGGGTTTATGCTCGC 33 109 0 GGCAATGGGT 0.902553 -74 TTTCCCCTGGGGCGAGGGGTAACTCACCTT 33 130 1 GGCGAGGGGT 0.900454 -53 CTTTTATAATGGCGATCGCCCTTTAATCAC 33 157 1 GGCGATCGCC 0.499989 -26 ATGGGGATAGGGGGATGGGTAACTGAAAAA 34 74 1 GGGGATGGGT 0.922957 -58 AAAGATCAGAGGCTATCGCTCTTCTATCAT 35 141 0 GGCTATCGCT 0.753753 -82 ********** Masking position 8 Map Score: 28.8316 Number of sites scoring better than the average of aligned sites = 7125 Number in coding regions = 6478 Number in noncoding regions = 647 Number of orfs with sites within 600 bp upstream = 420 Fraction of orfs with sites within 600 bp upstream = 0.067459 Motif number 2 AGTGGTCCCTCAGCCCATAAAACTAT 1 6 1 TCCCTCGCCC 0.933017 -73 TAAGTCCAAATCCCCCAACCTTGCCGGAGCT 4 222 0 TCCCCCACCT 0.776236 -79 TTAATTCCTCCCCCCATTGACTTGGACCCTT 5 21 0 CCCCCATGAC 0.787873 -57 TTTTTTAAACCCCCTTTAGCCAACTTTACTC 6 21 0 CCCCTTAGCC 0.710775 -240 TGGTTACTGTTCCCCCAGAGCAAAATCTTTT 6 51 0 TCCCCCGAGC 0.710094 -210 TGGTTTGGCCCCCCCAGTCCCAGGGAATCAG 6 165 1 CCCCCATCCC 0.964963 -96 CTAACGGTTATCCCCCAAGCCGCTAGAATGG 6 204 1 TCCCCCAGCC 0.971092 -57 ATTTCCAATGCCCCGCTTGCCAAATTAATCC 9 37 0 CCCCGCTGCC 0.89703 -173 ATAAACAAATCCCCCCCGGCGATCGCCTATG 9 86 1 CCCCCCGGCG 0.967666 -124 ACCAATAAAATACCCCGTGCCCAGGGCCGGG 9 131 1 TACCCCTGCC 0.830682 -79 TTGCAATCTTCACCCCGGCCCTGGGCACGGG 9 144 0 CACCCCGCCC 0.897605 -66 TTTTCCCCTCTTCACACCAAAATCA 15 24 0 CCCCTCTCAC 0.51698 -15 TCCGAGTCAGCCCCCAGGGTCAGGGAACCTT 17 109 1 CCCCCAGGTC 0.903365 -39 AGGTTTTCTTCCCCCTTGCTGGAGTCATTG 18 13 0 TCCCCCTGCT 0.93497 -20 CCGTCCACGTCCCCCATTACTAAATTCGATT 20 121 1 CCCCCATACT 0.549675 -41 CCATTCTTTGTCCCCATTGTCGCCGCACCGC 22 56 0 TCCCCATGTC 0.752736 -191 AATTGAAAAGTCCCCCTGGTTGCACAGAGGA 24 89 1 TCCCCCGGTT 0.739553 -28 CCGCTATCCCCTAGGCGGTGGGCCGAT 25 7 1 TCCCCTGGCG 0.808577 -103 GAAAATTTTGCCCCCATTCCTCTGGCGATCG 25 64 1 CCCCCATCCT 0.8313 -46 CCTGGTAATGTCCCTATGCCCGCAGTTTTGA 27 147 0 TCCCTAGCCC 0.825521 -101 ACCCCTTCGGCCATCAACAGAA 29 51 0 CCCCTTGGCC 0.912351 -12 TTTTGAACTGCCCCCCTGACCCCCCCAAGGC 31 15 1 CCCCCCGACC 0.972653 -42 ACCGATAAATTCCCCCCAGCCTTGGGGGGGT 31 33 0 TCCCCCAGCC 0.971092 -24 CATTGCCATTTCCCCTGGGGCGAGGGGTAAC 33 122 1 TCCCCTGGGC 0.807463 -61 AGTTACCCATCCCCCTATCCCCATGAACCTT 34 67 0 CCCCCTTCCC 0.952395 -65 ****** **** Masking position 4 Map Score: 25.1445 Number of sites scoring better than the average of aligned sites = 4371 Number in coding regions = 3848 Number in noncoding regions = 523 Number of orfs with sites within 600 bp upstream = 374 Fraction of orfs with sites within 600 bp upstream = 0.0600707 Motif number 3 CTATTTCTTGAGCAGGTTGAAGAACTT 2 6 0 AAGGTTGAAG 0.870481 -78 TTACAGTTGGGTGGAGGGTAAGAATC 4 5 1 ATGGGTGGAG 0.821254 -296 GTTGGCGCACATAAGGGAGAAATCG 5 63 1 AAGGGAGAAA 0.933314 -15 TTAAATGTTGAAAATGTTGAAATCGAAATGTT 10 32 1 AATGTTGAAA 0.768359 -70 TCTCCCCAGAATTAGGGAGGAGAAAATTAGGA 11 17 1 AAGGGAGGAG 0.904902 -44 AAAATAAGAAATTTGGGAGAAATATTTTGTGT 19 250 0 ATGGGAGAAA 0.776812 -51 TATTATCTTAATAATGGTGGAACAAAATAAGA 19 273 0 AATGGTGGAA 0.901169 -28 GGGGAAAAGATTGGTGAAATTGAGTGGCA 23 8 1 ATTGGTGAAA 0.842846 -279 ATTATTAAAAACCAGGGCGAAAATTTTGCCCC 25 46 1 AAGGGCGAAA 0.836534 -64 AGAATCGGCTACCATGGAGCAGAGAAACACAA 29 23 0 AATGGAGCAG 0.738019 -40 TTAGGATCGCACAATGTTGAAGCCGCTTTTGT 30 60 1 AATGTTGAAG 0.842118 -62 CGTTGGTTTAATCATGGTGACGGCCATAGCTA 33 59 0 AATGGTGACG 0.814742 -124 TGGGTAGGATAAAATGGAGAAGATAGTCTGAA 35 107 0 AATGGAGAAG 0.94698 -116 TAATTATGGTGAAAATTTTATTCT 36 3 1 AATGGTGAAA 0.955686 -53 TGAAGAATGGAAAATGGTGAAAAGAATAAAAT 36 25 0 AATGGTGAAA 0.955686 -31 AAAGTAGGGTGAAGAATGGAAAAT 36 42 0 AAGGGTGAAG 0.977627 -14 * ********* Masking position 1 Map Score: 12.0547 Number of sites scoring better than the average of aligned sites = 367 Number in coding regions = 275 Number in noncoding regions = 92 Number of orfs with sites within 600 bp upstream = 77 Fraction of orfs with sites within 600 bp upstream = 0.0123675 Motif number 4 TCTACAGATTCTTACCCTCCACCCAACTGTA 4 12 0 CTTACCCCCA 0.92372 -289 AAACTTTGCCCACAGCCGCCGACACTGGGCG 4 107 1 CACAGCCCCG 0.929192 -194 ATCAGAAGGACTTACCCTCAGAGCCTAAGTA 4 274 1 CTTACCCCAG 0.892332 -27 AGGAATTAATCTTCCCTACCGTTGGCGCACA 5 43 1 CTTCCCTCCG 0.757316 -35 GCCAACTTTACTCAGCCCCCGTA 6 3 0 CTCAGCCCCG 0.988129 -258 TAACTCCGCCTCCAGCTCAATTAT 9 4 1 CTCCGCCCCA 0.968851 -206 ATAAACAAATCCCCCCCGGCGATCGCCTATG 9 86 1 CCCCCCCGCG 0.822582 -124 ATTGATCCGAGTCAGCCCCCAGGGTCAGGGA 17 104 1 GTCAGCCCCA 0.740628 -44 TCATGGTTGTCTCCGCCACCGATCATTCCGA 22 149 0 CTCCGCCCCG 0.989735 -98 AATTTTAGTCCTTAGCCCCCGTCTGCGAAGT 24 62 0 CTTAGCCCCG 0.981136 -55 GTGAGTTACCCCTCGCCCCAGGGGAAATGGC 33 126 0 CCTCGCCCAG 0.892823 -57 TCCATTTTATCCTACCCACAATGATAGAAGA 35 121 1 CCTACCCCAA 0.62607 -102 ******* *** Masking position 6 Map Score: 8.25175 Number of sites scoring better than the average of aligned sites = 1321 Number in coding regions = 1247 Number in noncoding regions = 74 Number of orfs with sites within 600 bp upstream = 85 Fraction of orfs with sites within 600 bp upstream = 0.0136524 Motif number 5 GATCGCTCGGTGCGCCATGGTTGGGATTAG 4 158 0 TGCGCCATGG 0.958073 -143 TTAGCTCACCAAGGGTCCAAGTCA 5 5 1 CTCACCAAGG 0.6187 -73 CTCCCTTATGTGCGCCAACGGTAGGGAAGA 5 52 0 TGCGCCAACG 0.834128 -26 AAAACTTAAAATTGCCCTGGTTACTGTTCC 6 69 0 ATTGCCCTGG 0.722932 -192 TAAAATACCCCGTGCCCAGGGCCGGGGTGA 9 136 1 CGTGCCCAGG 0.946727 -74 ATTTAACCTATTTACCCAGGAGTCACC 10 8 0 TTTACCCAGG 0.765529 -94 GGATGTTTTCTGTGACAAGGTAGTA 12 46 1 TGTGACAAGG 0.778815 -15 GATCCGAGTCAGCCCCCAGGGTCAGGGAAC 17 107 1 AGCCCCCAGG 0.835376 -41 CAAACTGGCGATCGCCAAGGATCATCACCT 22 106 0 ATCGCCAAGG 0.898643 -141 CTTTTACCATTGTGCCAAGGGATGAATTTT 22 215 1 TGTGCCAAGG 0.970417 -32 AGGGGCATAATGTGCCCAGGTTGTTTACTC 23 251 1 TGTGCCCAGG 0.978862 -36 ATTTCCTCTGTGCAACCAGGGGGACTTTTC 24 93 0 TGCAACCAGG 0.667313 -24 GGGCAAAATTTTCGCCCTGGTTTTTAATAA 25 47 0 TTCGCCCTGG 0.911527 -63 ATCACGGCTAAGTTCCAAGGTGAGGGGTTT 27 225 0 AGTTCCAAGG 0.70056 -23 TGTGTTTCTCTGCTCCATGGTAGCCGATTC 29 24 1 TGCTCCATGG 0.778783 -39 ********** Masking position 6 Map Score: 9.29866 Number of sites scoring better than the average of aligned sites = 1449 Number in coding regions = 1340 Number in noncoding regions = 109 Number of orfs with sites within 600 bp upstream = 127 Fraction of orfs with sites within 600 bp upstream = 0.0203983 Motif number 6 AATTCAAACATTTCGTAAAAGTCTAAAATA 3 44 0 TTTCGTAAAA 0.69825 -257 AAAAATTAACATTGTTAAAACATTTTTGTT 3 242 1 ATTGTTAAAA 0.546606 -59 GGGGTATTTTATTGGTAAAAATCCGATCCT 9 117 0 ATTGGTAAAA 0.955171 -93 CCCTTGGCACAATGGTAAAAGCGAAACCAA 22 206 0 AATGGTAAAA 0.883385 -41 GGGGAAAAGATTGGTGAAATTGAGTGGCA 23 10 1 ATTGGTGAAA 0.907451 -277 ATACTGGAGTTTTGGGAAAACAGACTCTAA 23 99 0 TTTGGGAAAA 0.774415 -188 GGCATCGAGAAGTCGTAAAAGCAGCCC 24 8 0 AGTCGTAAAA 0.772505 -109 AATTGGGAAAAAACTGGAGCT 25 99 0 ATTGGGAAAA 0.900086 -11 GGATTTCGTAAAAATTTGTAAAA 28 4 1 TTTCGTAAAA 0.69825 -127 TTTCGTAAAAATTTGTAAAAATTAAATGGT 28 14 1 ATTTGTAAAA 0.604554 -117 GCAAATAGATAGTGGGAAAAAGAGCTTGTA 28 109 0 AGTGGGAAAA 0.834335 -22 ATTAATTGTTAGTGGTTAAACTTTGCCATT 30 28 1 AGTGGTTAAA 0.579774 -94 TCAACCATTGGTAAAACTGAATTTTG 30 106 0 ATTGGTAAAA 0.955171 -16 TAATTATGGTGAAAATTTTATTCT 36 5 1 TATGGTGAAA 0.570531 -51 AAGAATGGAAAATGGTGAAAAGAATAAAAT 36 25 0 AATGGTGAAA 0.777087 -31 ********** Masking position 8 Map Score: 8.15008 Number of sites scoring better than the average of aligned sites = 582 Number in coding regions = 488 Number in noncoding regions = 94 Number of orfs with sites within 600 bp upstream = 104 Fraction of orfs with sites within 600 bp upstream = 0.0167041 Motif number 7 GTCAACGAATGTGGAGGTTTGT 1 67 1 GTGGAGGTTT 0.925222 -12 CCCAACCTTGCCGGAGCTTTAGTGAAAATA 4 210 0 CCGGAGCTTT 0.952407 -91 GCCAAACCATAGGGAGTTTTCCCTAGAAAG 6 144 0 AGGGAGTTTT 0.773913 -117 CCCTAATTCTGGGGAGATTTTTT 11 4 0 GGGGAGATTT 0.753235 -57 GGTTAGAATACGGGATGTTTTCTGTGACAA 12 34 1 CGGGATGTTT 0.872178 -27 GACCGCAATACTGGAGTTTTGGGAAAACAG 23 106 0 CTGGAGTTTT 0.890262 -181 TGGGAAAAAACTGGAGCTTTGGCGATCGCC 25 87 0 CTGGAGCTTT 0.967468 -23 CACTTATTATATGGAGCTTTTAACTAAGTT 27 33 0 ATGGAGCTTT 0.906947 -215 CTATCTAGGGGCGGATCTTTAAGTTTAGCC 28 46 1 GCGGATCTTT 0.694804 -85 CGCTTTTGTGAAGGAGCTTTAAGCAAAATT 30 83 1 AAGGAGCTTT 0.706269 -39 TCCCCAGAATCGGGATGTTTGAATGTGGCC 34 19 1 CGGGATGTTT 0.872178 -113 AATAGGAAAGCTGGAGGTTTATTTAAGGTC 35 177 1 CTGGAGGTTT 0.960014 -46 ********** Masking position 5 Map Score: 7.67535 Number of sites scoring better than the average of aligned sites = 313 Number in coding regions = 230 Number in noncoding regions = 83 Number of orfs with sites within 600 bp upstream = 71 Fraction of orfs with sites within 600 bp upstream = 0.0114038 Motif number 8 TACCCCAATCTTGAGAGATTGAGAGAAAAATTAACAT 3 217 1 TTAAGAAGAA 0.680423 -84 GTCCCAGGGAATCAGAAATATTGCTAACGGTTATCCC 6 181 1 ATAAAATGAA 0.815143 -80 TATTAGTATGATCAAAAAATCAGCCAAGTAATGAAAT 19 41 0 ATAAAAAGAA 0.925388 -260 TAACAGATTATTGAAAAAATGAGCAAATCTAGAAGCT 23 175 1 TTAAAAAGAA 0.925382 -112 CAAATAATGGATTATTAATCTAGTTAAAACAAAGTGT 26 58 0 ATATAAAGAA 0.589581 -116 CGCTGATAACAAATAAAGCCAATGCTTAAATC 26 152 0 ATAAAAAGAA 0.925389 -22 ATTAACCGACATTAAAAACTTAGTTAAAAGCTCCATA 27 17 1 ATAAAAAGAA 0.925204 -231 ACATTGTGCGATCCTAAAGAATGGCAAAGTTTAACCA 30 40 0 ATCAAATGAA 0.711414 -82 GTATAATTCATTGACAAATACTGCGAAGGATACAGAG 35 25 0 TTAAAATGAA 0.814627 -198 CCTCTGATCTTTCATAAAAATAGGAAAGCTGGAGGTT 35 159 1 TTAAAAAGAA 0.925285 -64 TCAAGCGATTTTCCAAAAGGAAGCCAAACACTACAAT 37 87 1 TTCAAAAGAA 0.873957 -214 AAACACTTTCTTACAAAAAGTAGATAAAATTGCATGG 37 266 0 TTCAAAAGAA 0.873951 -35 ** * *** ** ** Masking position 8 Map Score: 5.20548 Number of sites scoring better than the average of aligned sites = 104 Number in coding regions = 74 Number in noncoding regions = 30 Number of orfs with sites within 600 bp upstream = 29 Fraction of orfs with sites within 600 bp upstream = 0.00465789 Motif number 9 CTCTCAATCTCTCAAGATTGGGGTATTTAGA 3 211 0 CTCAAGATGG 0.861497 -90 AACGGCTAATCCCAACCATGGCGCACCGAGC 4 153 1 CCCAACCTGG 0.743493 -148 AGGGAGTTTTCCCTAGAAAGCCTAGAAGTTT 6 133 0 CCCTAGAAGC 0.840962 -128 GACTATCATTCTCAAGCTAGGCCTCTGACTG 17 54 1 CTCAAGCAGG 0.939173 -94 CCATGACCCAAGGCAGGTAAGGTTCCC 17 131 0 CCCAAGGAGG 0.973294 -17 AGCAATGACTCCAGCAAGGGGGAAGAAAA 18 9 1 CTCCAGCAGG 0.869092 -24 TGTAAACTGACCCAATCAAGCGACCGCAATA 23 126 0 CCCAATCAGC 0.658663 -161 ACCAGGTAAACCCCAGAGAGGCAAAGGCATA 27 172 1 CCCCAGAAGG 0.941132 -76 AAAGATCCGCCCCTAGATAGCCACCATTTAA 28 35 0 CCCTAGAAGC 0.840962 -96 TTGTGCGATCCTAAAGAATGGCAAAGTTTAA 30 43 0 CTAAAGATGG 0.463582 -79 CCCTGACCCCCCCAAGGCTGGGGGGAATTTA 31 28 1 CCCAAGGTGG 0.949753 -29 AATCCCTCCCAAAGGTAGCTCTAGCTCTA 32 9 1 CCAAAGGAGC 0.721493 -63 ******* *** Masking position 5 Map Score: 2.5885 Number of sites scoring better than the average of aligned sites = 787 Number in coding regions = 671 Number in noncoding regions = 116 Number of orfs with sites within 600 bp upstream = 129 Fraction of orfs with sites within 600 bp upstream = 0.0207196 Motif number 10 ACCCAGGTAGACTTCTCAAATATACTCTTTA 3 157 0 ACTTCCAAAT 0.916434 -144 TAGTCCCTTTAGTTCACAAATTTCTCAACAT 10 59 0 AGTTCCAAAT 0.849785 -43 TCGCCCCAATAGTTGTCAAACTGCCCACAAA 16 96 0 AGTTGCAAAC 0.913748 -162 CGACAGAACCACTTCCCAAACTGGCGATCGC 22 121 0 ACTTCCAAAC 0.971038 -126 ATAAACTGAAACTTCGCAGACGGGGGCTAAG 24 52 1 ACTTCCAGAC 0.886816 -65 CACAATTAAAACTTGGCAAATAAGCTTTGAC 27 104 0 ACTTGCAAAT 0.86513 -144 TCAGGGGGGCAGTTCAAAAACGA 31 3 0 AGTTCAAAAC 0.772884 -54 AATTTTTATACTTGAAAAACCAGCATTATT 37 10 1 ACTTGAAAAC 0.802276 -291 AACTTTTCAAACACTTTCTTAC 37 289 0 ACTTTCAAAC 0.838356 -12 ***** ***** Masking position 4 Map Score: 1.94932 Number of sites scoring better than the average of aligned sites = 154 Number in coding regions = 52 Number in noncoding regions = 102 Number of orfs with sites within 600 bp upstream = 74 Fraction of orfs with sites within 600 bp upstream = 0.0118856 Motif number 11 GTCAACTCTTGTCATTATTC 7 12 0 GTCAACTCTT 0.940906 -10 TTTATTTGTTGTCAAAGCTTGAAATTTCCA 9 61 0 GTCAAAGCTT 0.970788 -149 TGTCAACTCTTAGGGGTTCAG 16 2 1 GTCAACTCTT 0.940906 -256 TACTGCCATGGTCAAAGCTAGTTAAATTTA 16 191 1 GTCAAAGCTA 0.909917 -67 TTTAGGATTAGTCAAAGCTTATTTGCCAAG 27 94 1 GTCAAAGCTT 0.970788 -154 ********** Masking position 5 Map Score: 1.56512 Number of sites scoring better than the average of aligned sites = 32 Number in coding regions = 26 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 Motif number 12 CACACTGGCGATCGCCATTTGGAATCAACA 3 268 0 ATCGCCATTT 0.950014 -33 ATCCTTGGCGATCGCCAGTTTGGGAAGTGG 22 114 1 ATCGCCAGTT 0.874204 -133 GAAAAAAGCCATTGCCACTCAATTTCACCA 23 22 0 ATTGCCACTC 0.900486 -265 GTGGTTAAACTTTGCCATTCTTTAGGATCG 30 39 1 TTTGCCATTC 0.837074 -83 GCCTTTATCAATTGCCATTCCAGTTTGAAA 32 41 1 ATTGCCATTC 0.961161 -31 GCATAAACCCATTGCCATTTCCCCTGGGGC 33 113 1 ATTGCCATTT 0.940257 -70 TTAAAGGGCGATCGCCATTATAAAAGGTGA 33 153 0 ATCGCCATTA 0.882655 -30 ********** Masking position 7 Map Score: 1.87451 Number of sites scoring better than the average of aligned sites = 248 Number in coding regions = 218 Number in noncoding regions = 30 Number of orfs with sites within 600 bp upstream = 36 Fraction of orfs with sites within 600 bp upstream = 0.0057822 Motif number 13 GACGGGAGGTGGTTAATTGATAAGCGGTTG 4 56 0 GGTTAATTGA 0.957703 -245 TAATAAGCAAGATTAATTTAAAGTAACAAA 6 96 0 GATTAATTTA 0.733995 -165 CGCTCACACTGGTTAATTGAACTTAAATTT 16 224 0 GGTTAATTGA 0.957703 -34 TACTAAATTCGATTAATCGAGAATTGGATA 20 138 1 GATTAATCGA 0.840388 -24 ACTGACCCCAGATTAATTGAGCTAGATTTA 26 128 1 GATTAATTGA 0.935064 -46 TTTTAATGTCGGTTAATTAATCT 27 4 0 GGTTAATTAA 0.812693 -244 ********** Masking position 5 Map Score: 0.685866 Number of sites scoring better than the average of aligned sites = 55 Number in coding regions = 44 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 14 CAGGGCAATTTTAAGTTTTGTTACTTTAAAT 6 80 1 TTAATTTTGT 0.615693 -181 TCAAAGCTAGTTAAATTTAGTCAAATTTAAG 16 202 1 TTAATTTAGT 0.852145 -56 GTTCACATCTTTAATTCTAACTATTAGTATG 19 68 0 TTAATCTAAC 0.83154 -233 ATTTTGTGTTTTAACTATAGCAAAAAGTGAG 19 228 0 TTAATATAGC 0.882044 -73 GTTTAGTTGTTTAACTATAACCTATTACACT 26 32 1 TTAATATAAC 0.761402 -142 AAGCCAATGCTTAAATCTAGCTCAATTAATC 26 138 0 TTAATCTAGC 0.920424 -36 TATGGGTTAGTTAAGTTTAATGCTATGCCTT 27 195 0 TTAATTTAAT 0.710944 -53 TAGCCACCATTTAATTTTTACAAATTTTTAC 28 18 0 TTAATTTTAC 0.707854 -113 GGGCGGATCTTTAAGTTTAGCCGTGGTTTTC 28 54 1 TTAATTTAGC 0.953328 -77 GATTTTGATGTTAACTTTAGCTGGTTGTAAA 37 134 1 TTAATTTAGC 0.953328 -167 **** ****** Masking position 6 Map Score: 2.03157 Number of sites scoring better than the average of aligned sites = 113 Number in coding regions = 79 Number in noncoding regions = 34 Number of orfs with sites within 600 bp upstream = 42 Fraction of orfs with sites within 600 bp upstream = 0.0067459 Motif number 15 GGCATTGCCGCCAGAAAAGCTGACGGGAGG 4 77 0 CCAGAAAAGC 0.947655 -224 CACCGAGCGATCACTAAAGCCTTTGTCCCC 4 176 1 TCACTAAAGC 0.938924 -125 CCAACTATTTTCACTAAAGCTCCGGCAAGG 4 205 1 TCACTAAAGC 0.938924 -96 GTCAAACTGCCCACAAAAACTCTTGGCATG 16 83 0 CCACAAAAAC 0.755167 -175 ATGGCTTTTTTCAGAACAGCCTTAATCCAT 23 40 1 TCAGAACAGC 0.907726 -247 GATGAGTCACTCAGAATAGCTTCTAGATTT 23 199 0 TCAGAATAGC 0.869065 -88 TAAAGCTCCTTCACAAAAGCGGCTTCAACA 30 74 0 TCACAAAAGC 0.972481 -48 ********** Masking position 6 Map Score: 0.829195 Number of sites scoring better than the average of aligned sites = 95 Number in coding regions = 56 Number in noncoding regions = 39 Number of orfs with sites within 600 bp upstream = 32 Fraction of orfs with sites within 600 bp upstream = 0.00513974