AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i199_synecho_ctra_300.orf -o199_synecho_ctra_300.ace -a/home/amcguire/genomes/ORF_synecho.txt -z/home/amcguire/genomes/synecho.fna -g0.46 -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 = 0.46 maxlen = 30 weight = 0.8 exclude = 1 Purged sequences: RCT00303 21 Chlamydia_trachomatis RCY41239 17 Synechocystis RCT00768 16 Chlamydia_trachomatis RCT00493 16 Chlamydia_trachomatis RCT00497 18 Chlamydia_trachomatis RCT00769 20 Chlamydia_trachomatis RCT00490 17 Chlamydia_trachomatis Input sequences: #1 RCY25702 300 Synechocystis #2 RCY23794 104 Synechocystis #3 RCY53156 108 Synechocystis #4 RCY31741 108 Synechocystis #5 RCY09512 82 Synechocystis #6 RCY38222 137 Synechocystis #7 RCY33689 119 Synechocystis #8 RCY05922 107 Synechocystis #9 RCY14231 101 Synechocystis #10 RCY17023 68 Synechocystis #11 RCY34894 39 Synechocystis #12 RCY03648 59 Synechocystis #13 RCY03870 91 Synechocystis #14 RCY00359 106 Synechocystis #15 RCY25341 23 Synechocystis #16 RCY37057 40 Synechocystis #17 RCY34487 29 Synechocystis #18 RCY46798 32 Synechocystis #19 RCY53151 73 Synechocystis #20 RCY50421 39 Synechocystis #21 RCY31267 300 Synechocystis #22 RCY46651 107 Synechocystis #23 RCY25755 109 Synechocystis #24 RCY27247 105 Synechocystis #25 RCY39891 95 Synechocystis #26 RCY49697 163 Synechocystis #27 RCY03645 137 Synechocystis #28 RCY22631 194 Synechocystis #29 RCY51824 142 Synechocystis #30 RCY40141 87 Synechocystis #31 RCY11977 246 Synechocystis #32 RCY00456 110 Synechocystis #33 RCY08095 101 Synechocystis #34 RCY42619 279 Synechocystis #35 RCY23173 277 Synechocystis #36 RCY12795 137 Synechocystis #37 RCY36500 280 Synechocystis #38 RCY02337 187 Synechocystis #39 RCY08595 300 Synechocystis #40 RCY07893 147 Synechocystis #41 RCY44389 59 Synechocystis #42 RCY35764 206 Synechocystis #43 RCY36190 150 Synechocystis #44 RCY49047 96 Synechocystis #45 RCY44729 201 Synechocystis #46 RCY10129 213 Synechocystis #47 RCY17386 35 Synechocystis #48 RCY16852 164 Synechocystis #49 RCY20077 300 Synechocystis #50 RCY50281 225 Synechocystis #51 RCY44485 300 Synechocystis #52 RCY26391 300 Synechocystis #53 RCY23132 293 Synechocystis #54 RCY17020 157 Synechocystis #55 RCY50817 112 Synechocystis #56 RCY47116 56 Synechocystis #57 RCY14811 300 Synechocystis #58 RCY17622 25 Synechocystis #59 RCY16281 94 Synechocystis #60 RCY23988 96 Synechocystis #61 RCY23271 201 Synechocystis #62 RCY11277 49 Synechocystis #63 RCY29451 106 Synechocystis #64 RCT00126 206 Chlamydia_trachomatis #65 RCT00300 24 Chlamydia_trachomatis #66 RCT00301 300 Chlamydia_trachomatis #67 RCT00302 31 Chlamydia_trachomatis #68 RCT00304 22 Chlamydia_trachomatis #69 RCT00305 105 Chlamydia_trachomatis #70 RCT00306 300 Chlamydia_trachomatis #71 RCT00307 300 Chlamydia_trachomatis #72 RCT00308 300 Chlamydia_trachomatis #73 RCT00373 300 Chlamydia_trachomatis #74 RCT00374 86 Chlamydia_trachomatis #75 RCT00376 25 Chlamydia_trachomatis #76 RCT00377 292 Chlamydia_trachomatis #77 RCT00418 41 Chlamydia_trachomatis #78 RCT00419 49 Chlamydia_trachomatis #79 RCT00420 300 Chlamydia_trachomatis #80 RCT00441 300 Chlamydia_trachomatis #81 RCT00442 69 Chlamydia_trachomatis #82 RCT00472 300 Chlamydia_trachomatis #83 RCT00481 65 Chlamydia_trachomatis #84 RCT00482 20 Chlamydia_trachomatis #85 RCT00483 21 Chlamydia_trachomatis #86 RCT00484 55 Chlamydia_trachomatis #87 RCT00485 22 Chlamydia_trachomatis #88 RCT00488 21 Chlamydia_trachomatis #89 RCT00489 27 Chlamydia_trachomatis #90 RCT00495 32 Chlamydia_trachomatis #91 RCT00499 23 Chlamydia_trachomatis #92 RCT00502 300 Chlamydia_trachomatis #93 RCT00596 300 Chlamydia_trachomatis #94 RCT00853 300 Chlamydia_trachomatis #95 RCT00754 23 Chlamydia_trachomatis #96 RCT00765 300 Chlamydia_trachomatis #97 RCT00767 137 Chlamydia_trachomatis Motif number 1 CGACACAGATGTCGAGTGCCTCAG 2 91 1 GTCAGTGCCG 0.734893 -14 TGGCTATCACCTTTGCCCCGCAAGC 14 2 1 GGCATCACCG 0.984583 -105 GACGACCAGCGGCAATAACCTTTGGTCAACAGCT 21 181 0 GGCATAACCG 0.889872 -120 TCAGGAGGATGGCGATCGCCTAGGGTCTAATCCT 22 37 1 GGCATCGCCG 0.996892 -71 TTACCAGGGGGGCGATACCCCCAGA 23 2 0 GGCATACCCG 0.953857 -108 GAGGCTTTGGGCCGATCGCCACGGCCACTGATGC 26 37 0 GCCATCGCCG 0.980201 -127 GGCGATCGCCGACGTTAGTGTTCC 27 124 0 GGCATCGCCG 0.996892 -14 TACGACGCTTGGCGATCGCCATTGGCCGGAAACT 28 93 0 GGCATCGCCG 0.996892 -102 TCCTGACAGTGGCAAGGCCCAGCGGCTCAATATA 28 136 0 GGCAGGCCCG 0.938557 -59 AATGCCCCTTGGCGATCGCCGGGGCTGAAGCAGA 31 171 0 GGCATCGCCG 0.996892 -76 CTGGATTGCCGGCAATCCCCCCAGTCAATATTCC 34 242 1 GGCATCCCCG 0.993917 -38 CAACACCAATGGCGATCGCCATCGATGGGAATTG 35 30 1 GGCATCGCCG 0.996892 -248 GGTTGCGGAGGGCCGTCCCCCATGGTAACAGAGT 38 19 1 GGCGTCCCCG 0.948256 -169 TTGCCTTTCTGTCCATTGCCCCAGGTAAAAATTG 38 57 1 GTCATTGCCG 0.852997 -131 CGCCAAAATTGGCGATCGCCAGGGAGCAATTTTT 38 83 0 GGCATCGCCG 0.996892 -105 TTTCTGACTGGGCCAGCCCCACTGACTATTCAAC 40 65 1 GGCAGCCCCG 0.98735 -83 CGGCCAATGACCAGGGGCAGATTTTG 59 3 1 GCCATGACCG 0.658586 -92 ATGGAGCGTGGGCTAGTGCCTTAGGAATGCGTAG 94 91 1 GGCAGTGCCG 0.965258 -210 *** ****** * Masking position 9 Map Score: 37.3849 Number of sites scoring better than the average of aligned sites = 2416 Number in coding regions = 2193 Number in noncoding regions = 223 Number of orfs with sites within 600 bp upstream = 216 Fraction of orfs with sites within 600 bp upstream = 0.0346932 Motif number 2 GGTGTTCCCCCTCCACCAATCCCTGGAAAGTGGG 1 106 0 CTCCCACCCT 0.854915 -195 AATTCTAACGCTTCCCTTCACCCCGTAAGCCCAC 1 237 1 CTTCTCCCCC 0.897303 -64 TCTTCCCCCCATCCCTGTCCTGTTTA 4 3 1 TTCCCACCCT 0.742171 -106 GTTCCCTTCGTCCATCTACTCTCTGACCAAGCCC 14 65 1 TCCCTCCTCT 0.66451 -42 TAGGGTCTAATCCTCCTGCCCCCTTAATTGCCTT 22 57 1 TCCCTCCCCT 0.970098 -51 CTCTCCCCGGCCTTCCCTAACCCCAACCACCGCA 23 37 1 CCTCCACCCC 0.703204 -73 CCTGGATTACCCCGTCCCCAACCTCC 28 179 1 CCCCCCACCT 0.643617 -16 AATACGGAGCCCCTTCTCCTCCCTTTCTAAGCTA 29 79 1 CCCCTCCCCT 0.985166 -64 GGCTTTGCATCCTCACCACTCCCCTTGACCCC 29 121 1 CCTCCCCCCC 0.926005 -22 ATTTTTATTTCTCAGCTACGCCCTCGATATTTTT 34 129 1 CTCCTCCCCT 0.974351 -151 CCCTAAGGGTCTCCACTTCCCCCCAGACATTACA 39 94 1 CTCCTCCCCC 0.972583 -207 GTTGAGTTGCCCCCACGCCTCCCTGGGTTAGTTT 42 45 1 CCCCGCCCCT 0.887714 -162 GTGTAGCTGGCTTTACCACTCCCCTTACTTTCGG 43 55 1 CTTCCCCCCC 0.877428 -96 ACTGGAGTTATTTATCTCCGCCCCCCCACTTTCC 45 178 1 TTTCTCCCCC 0.810185 -24 TAAATCCATATCCCCCTTCCCCCCAGAGGGTATT 51 98 1 TCCCTCCCCC 0.968046 -203 TGGTCTGGACTTTCTCTTCACCCTCAGCTTTTCT 53 118 0 TTTCTCCCCT 0.820495 -176 TTGTCAGTCTCCCTACTTACCCCTTGAACATCAC 54 33 1 CCCCTACCCT 0.926327 -125 GTACCGGGAACCCCTCTGTGCCCAGCTACTGTG 66 10 0 CCCCTTCCCA 0.644497 -291 TTTTAAAAAATCCTTCTCCTCTCTTCTTTCTTAA 76 71 1 TCCCTCCTCT 0.66451 -222 AAACCGGCTGCCCTACTAACCCCAGACTTCAAGA 76 198 1 CCCCTACCCA 0.744137 -95 AACGATATTTTTCTTCCCCTCCCCTTTCCTCTTG 82 204 1 TTCCCCCCCC 0.9342 -97 TGAGGATATATTCCCCTATACCCTAACCTGGCCG 82 236 1 TTCCTTCCCT 0.686532 -65 AGTTCGACTCTACTTTACCCT 88 1 0 CTCCTTCCCT 0.817627 -21 AGCAAAGGGTTTCGACCTCTCCCAAAGATGTTAG 93 246 0 TTCCCCCCCA 0.778605 -55 AGAGACTGATTCTTACTACACCCTCACCACATAA 94 250 0 TCTCTCCCCT 0.888776 -51 *** ** * **** Masking position 6 Map Score: 24.3995 Number of sites scoring better than the average of aligned sites = 1166 Number in coding regions = 1001 Number in noncoding regions = 165 Number of orfs with sites within 600 bp upstream = 161 Fraction of orfs with sites within 600 bp upstream = 0.0258593 Motif number 3 ATGGATTATTCGATCGCCACACTT 1 287 1 CGATCGCCAC 0.983439 -14 ACGCTATCGCCATTCATTAACGC 16 4 1 CTATCGCCAT 0.882687 -37 AGACCCTAGGCGATCGCCATCCTCCTGAAA 22 35 0 CGATCGCCAT 0.990554 -73 GGCTTTGGGCCGATCGCCACGGCCACTGAT 26 39 0 CGATCGCCAC 0.983439 -125 GGCGATCGCCGACGTTAGTGTT 27 126 0 CGATCGCCGA 0.968506 -12 CGACGCTTGGCGATCGCCATTGGCCGGAAA 28 95 0 CGATCGCCAT 0.990554 -100 TCAGCCCCGGCGATCGCCAAGGGGCATTTT 31 177 1 CGATCGCCAA 0.982145 -70 GCGGTGGGTTTGATCGCCGTTAATTCACAT 33 50 1 TGATCGCCGT 0.807928 -52 CCATCGATGGCGATCGCCATTGGTGTTGGA 35 28 0 CGATCGCCAT 0.990554 -250 TGCTCCCTGGCGATCGCCAATTTTGGCGGG 38 89 1 CGATCGCCAA 0.982145 -99 GTCGTTAGTTCGATCGCCGGAGGTGAGCCA 45 21 0 CGATCGCCGG 0.947475 -181 GAAAAGTATGCGATCGCCATTTAAAAGTGG 51 253 1 CGATCGCCAT 0.990554 -48 ********** Masking position 3 Map Score: 26.6895 Number of sites scoring better than the average of aligned sites = 3528 Number in coding regions = 3185 Number in noncoding regions = 343 Number of orfs with sites within 600 bp upstream = 323 Fraction of orfs with sites within 600 bp upstream = 0.0518792 Motif number 4 GCTTCAATAAACAGGACAGGGATGGGGGGAAG 4 12 0 ACAGCAGGGA 0.911191 -97 TACCTGAGTAAAAGTGCGAGGGATGAAGCAAA 9 73 0 AAAGCGAGGG 0.531138 -29 GTCGTCGCTTTATGTCCGGGGAGCCTTTCTGC 21 209 1 TATGCGGGGA 0.674612 -92 TGTTATTCTAACAGTTTGGGGACGCCACGACA 25 19 0 ACAGTGGGGA 0.892947 -77 GGTACTTTGCACTGGACGAGGATACATGGGGG 28 25 0 ACTGCGAGGA 0.776792 -170 TTGGCCGGAAACTGCCCAGGGACTAATGCAGG 28 74 0 ACTGCAGGGA 0.949191 -121 TACGAGGAATATTGACTGGGGGGATTGCCGGC 34 249 0 ATTGTGGGGG 0.617318 -31 CTAGCGGCCAACAGTCCGGGCGCAACAGCAAG 36 45 1 ACAGCGGGCG 0.710615 -93 GATCTGTTGTAATGTCTGGGGGGAAGTGGAGA 39 103 0 AATGTGGGGG 0.900015 -198 GCAGATCTAGAAAGGTCGGGGAAAACGTATAG 42 106 1 AAAGCGGGGA 0.900254 -101 CTACACCTTCACTGGACAGGGGCGGCTAGGCT 43 29 0 ACTGCAGGGG 0.967872 -122 TGCCACAACGTCTGCCCAGGGGACTTTTTGCC 49 243 1 TCTGCAGGGG 0.791695 -58 ATCATATCACACTGCTTGGGGACACAAAGGTT 50 159 0 ACTGTGGGGA 0.938224 -67 GAATATCATAACTGATCGGGGGAATTTTTGCC 52 221 0 ACTGCGGGGG 0.98632 -80 CCCGCCGGATAATGGTTGGGGGGTTTGTTTTA 53 257 1 AATGTGGGGG 0.900015 -37 CGGCCAATGACCAGGGGCAGATTTTGT 59 6 1 AATGCAGGGG 0.917166 -89 GAAAATGTTCACAGACCAGGGAAA 60 3 0 ACAGCAGGGA 0.911191 -94 CCCTAGACTGACTGCCCAGGGAAAAATTCACT 61 129 0 ACTGCAGGGA 0.949191 -73 GTTGGAATGATTGGGGACAGTCTAGTT 62 33 0 AATGTGGGGA 0.848071 -17 GATACTAATGACAGGATAGGGGATA 64 4 0 ACAGTAGGGG 0.848944 -203 **** ****** Masking position 4 Map Score: 19.731 Number of sites scoring better than the average of aligned sites = 605 Number in coding regions = 552 Number in noncoding regions = 53 Number of orfs with sites within 600 bp upstream = 61 Fraction of orfs with sites within 600 bp upstream = 0.00979762 Motif number 5 AGTAATTTCCTTGGATGTTAATGGG 11 25 0 TTTCCTTGGA 0.84104 -15 GCACCGTCCTTTCCCTTGGGAAGGCCAAAT 24 11 1 TTCCCTTGGG 0.925989 -95 GATTTTTCCCTGGGCAACTATGCG 29 5 1 TTTCCCTGGG 0.968472 -138 TCGGGTTTCACCTCCTTGGGGTTGGGATAG 31 227 0 CCTCCTTGGG 0.919224 -20 GGATTTGGTAACTCCTTGGGTACTGGCGAA 32 67 0 ACTCCTTGGG 0.756357 -44 GGGAGCAATTTTTACCTGGGGCAATGGACA 38 66 0 TTTACCTGGG 0.74114 -122 TGCCCCCACGCCTCCCTGGGTTAGTTTTCA 42 52 1 CCTCCCTGGG 0.910409 -155 GCCTCCCGTTTTCCCTTGGGAAAGAGAGAG 42 149 1 TTCCCTTGGG 0.925989 -58 GGGGCAAAAAGTCCCCTGGGCAGACGTTGT 49 247 0 GTCCCCTGGG 0.699698 -54 ATCGCATACTTTTCCTTGGAGGCACAAACA 51 237 0 TTTCCTTGGA 0.84104 -64 TTTCCCTGGTCTGTGAACAT 60 1 1 TTTCCCTGGT 0.65155 -96 AAAGTGAATTTTTCCCTGGGCAGTCAGTCT 61 127 1 TTTCCCTGGG 0.968472 -75 CATAAAAATCTTTCCTTGGGATCTTGAAGA 63 84 0 TTTCCTTGGG 0.971751 -23 GGTGCTGCAGCTTCATTGGGTGCCCAAGCC 72 222 1 CTTCATTGGG 0.608097 -79 ATGCAAAAACATTCCTTGGGGGTTTGAGAA 76 231 1 ATTCCTTGGG 0.895126 -62 ACTAGTGGAGCTTCCTTGGAAGAAAACTTA 92 18 0 CTTCCTTGGA 0.827951 -283 AATATGCCTTACTTGGGCTCTTAAAAA 94 284 0 CTTACTTGGG 0.744653 -17 ********** Masking position 7 Map Score: 15.5518 Number of sites scoring better than the average of aligned sites = 615 Number in coding regions = 533 Number in noncoding regions = 82 Number of orfs with sites within 600 bp upstream = 91 Fraction of orfs with sites within 600 bp upstream = 0.0146161 Motif number 6 GTACAGATGTTTTGGCGCGGTGTTCCCCCTCCACCA 1 122 0 TTTGGGTTTC 0.837705 -179 GACCATGAAGTTTGTAATGGAAATCCGCCCTCAGTA 1 185 0 TTTGGGAATC 0.643887 -116 GAAACTGAATCCTGAGGTGGGCTTACGGGGTGAAGG 1 251 0 CCTGGGGTTC 0.78564 -50 GGCTTTTAAGTCTGATCAGGAATTGCGGTCATCCCC 21 27 1 TCTGGGATTC 0.923507 -274 TGCAACTTGCTTTGGCTAGGGATCGCAAGATCTCCC 26 135 1 TTTGGGGTCC 0.909721 -29 TGGCAAAACCATTGAGTTGGATTTACTGAACAAAAC 27 52 1 ATTGGGATTC 0.683784 -86 AAGATTTGAGTTTGTTGGGGATTTGCTTCCTTGACA 31 124 1 TTTGGGATTC 0.961937 -123 CTTGCTCAAACTTGAGCCTGGATTGCCGGCAATCCC 34 225 1 CTTGTGGTTC 0.490141 -55 TTGATACAGGTTTGGGGTTGAGTTGCCCCCACGCCT 42 29 1 TTTGTGATTC 0.760004 -178 ATGATGAAAATTTGTCGATGATTTTCTTATCTATTA 44 37 1 TTTGTGATTC 0.760004 -60 CATTCCTAGGTTTGGCTCGGGATTACCATTTGAAAG 53 34 0 TTTGGGGTTC 0.957568 -260 CCTCAGCTTTTCTGTTAGGGTGTCTCCCATTAAGTC 53 95 0 TCTGGGTTCC 0.524053 -199 TCTGTCAGTTTGTGGTCTGGACTTTCTCTTCACCCT 53 128 0 TGTGGGATTC 0.77421 -166 AAAATTCTCCTTTGCAAAGGAATTCCGATAGATTTT 61 67 0 TTTGGGATTC 0.961937 -135 ATGAATATTTTTGGCTTTGGATTTTCCATCTATTGT 70 206 1 TTGGGGATTC 0.728247 -95 TGTGAATATTCTTGAGTAGGATTCACAACAACTTTC 79 14 1 CTTGGGATCC 0.793229 -287 TTTTGCGATTTTTGGTGTGGGATTTCTTAGCGTCAA 92 77 1 TTTGGGGTTC 0.957568 -224 AGGAGGCTGTTTTGCTAGGGGCTCTCATTTCTAAGT 94 211 1 TTTGGGGTCC 0.909721 -90 TCTGACGGGGATTTACTGTTCACTTT 97 1 1 TCTGGGATTC 0.923507 -137 **** *** ** * Masking position 10 Map Score: 13.8591 Number of sites scoring better than the average of aligned sites = 192 Number in coding regions = 170 Number in noncoding regions = 22 Number of orfs with sites within 600 bp upstream = 26 Fraction of orfs with sites within 600 bp upstream = 0.00417604 Motif number 7 CAGGACAGGGATGGGGGGAAGA 4 3 0 ATGGGGGGAA 0.772811 -106 ACTCTCCCCACTGAGGGGAAGCATTAATTT 6 39 0 CTGAGGGGAA 0.828208 -99 CTCTCCCAGGCTATGGGGAAGGATTTTGGT 9 19 0 CTATGGGGAA 0.864278 -83 GCAAGGCAATTAAGGGGGCAGGAGGATTAG 22 63 0 TAAGGGGGCA 0.651442 -45 AAGATTGAGATTAGGGGGCAAGGCAATTAA 22 80 0 TTAGGGGGCA 0.86461 -28 AATGGGTAGATTGAGGGGAACACTAACGTC 27 108 1 TTGAGGGGAA 0.694799 -30 GGAATATTGACTGGGGGGATTGCCGGCAAT 34 246 0 CTGGGGGGAT 0.76056 -34 ATCTTAACCTTTAGGGGGAATCCCGCCAAA 38 110 0 TTAGGGGGAA 0.937904 -78 GTTGTAATGTCTGGGGGGAAGTGGAGACCC 39 100 0 CTGGGGGGAA 0.971987 -201 GCAACTAAATCTAGGGGGAATTTTCCTGAA 42 78 0 CTAGGGGGAA 0.969684 -129 AAACCAAGACCAATGGGGAAGCTCGAAACT 51 14 0 CAATGGGGAA 0.650797 -287 ACAATACCCTCTGGGGGGAAGGGGGATATG 51 104 0 CTGGGGGGAA 0.971987 -197 CCTCTCAAAACGAGGGGGAAAAACGAAAAA 69 60 0 CGAGGGGGAA 0.84594 -46 AAGAATTCGCTTATGGGGCAAGATCACCGA 70 47 1 TTATGGGGCA 0.559742 -254 AAACCAGACCTAAGGGGGAATAAAAGACAA 96 37 0 TAAGGGGGAA 0.815511 -264 ********** Masking position 5 Map Score: 13.1163 Number of sites scoring better than the average of aligned sites = 727 Number in coding regions = 602 Number in noncoding regions = 125 Number of orfs with sites within 600 bp upstream = 116 Fraction of orfs with sites within 600 bp upstream = 0.0186315 Motif number 8 GTAACTGAACTCCTAAAAAATTAACAACAG 2 57 0 TCCTAAAAAA 0.955814 -48 GTTAATGACCTCCTAAAAATAAAGCGGAAT 7 97 0 TCCTAAAAAT 0.891815 -23 GGCGTTTTCCTAAAAAAATCGGA 15 7 0 TCCTAAAAAA 0.955814 -17 CCAGCTTTGTTCCTAAAATACCGATAGACA 21 279 0 TCCTAAAATA 0.66446 -22 ATCGCCATCCTCCTGAAAAACTAACGGGAA 22 23 0 TCCTGAAAAA 0.787844 -85 TGGGGTATATCCTCAAAAAGGGTAGATTT 46 10 1 TCCTCAAAAA 0.787844 -204 GATGAATCTGCCCTAAAAATAAAGTTTGGC 52 194 1 CCCTAAAAAT 0.705256 -107 CCGTTTATCCTTAAAAATACTGAAACT 57 284 0 TCCTTAAAAA 0.815436 -17 ATCATCCTAATAAACTATCTTGTA 64 193 0 TCCTAATAAA 0.66446 -14 TCCTAAAAAAACCTAAAAAACATTCTATCT 72 281 0 ACCTAAAAAA 0.697154 -20 TCCTAAAAAAACCTAAAAAA 72 291 0 TCCTAAAAAA 0.955814 -10 AACAAGCCTTCCCTAAAAATAATTAATAAA 79 130 0 CCCTAAAAAT 0.705256 -171 AATCCTTGCTTCCTAAAAAAGAAGTTGACT 82 146 1 TCCTAAAAAA 0.955814 -155 AACACTCTCTCCTAAAAATTA 85 3 0 TCCTAAAAAT 0.891815 -19 CTTATTTTATTCCTTAAAAAACATCGCCTC 93 159 0 TCCTTAAAAA 0.815436 -142 ********** Masking position 6 Map Score: 11.0476 Number of sites scoring better than the average of aligned sites = 31 Number in coding regions = 18 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 9 TCGACAATTCTAACGCTTCCCTTCACCCCGT 1 232 1 TAAGCTTCCC 0.55142 -69 GGTAAAAAATTAATGCTTCCCCTCAGTGGGG 6 33 1 TAAGCTTCCC 0.55142 -105 AATATTAAATTAACTCTCCCCACTGAGGGGA 6 50 0 TAATCTCCCC 0.85188 -88 CTGATTGATGCAACTCTGCCCGTAAAAATAG 8 17 0 CAATCTGCCC 0.854927 -91 ATGGTAACCAAAATCCTTCCCCATAGCCTGG 9 13 1 AAACCTTCCC 0.873038 -89 AAACAAGCAGAAAGGCTCCCCGGACATAAAG 21 216 0 AAAGCTCCCC 0.887113 -85 CCCCCCTGGTAACCTCTCCCCGGCCTTCCCT 23 24 1 AACTCTCCCC 0.898842 -86 CGAAGTAGGGAACTTCTCCCCGAAATAAATG 32 40 0 AACTCTCCCC 0.898842 -71 ACCTTTACCAAAAGCCTGTCCATGGACTGCA 37 62 0 AAACCTGTCC 0.657855 -219 TAAGGGTCTCCACTTCCCCCCAGACATTACA 39 97 1 CACTCCCCCC 0.389831 -204 AAATATCTAGAAAGTCTGCCCAGTTCATTAC 46 192 0 AAATCTGCCC 0.923352 -22 TTTGTATATTAAAGTCGCCCCGGCTGGTTGA 49 59 1 AAATCGCCCC 0.599583 -242 ACAATGCCACAACGTCTGCCCAGGGGACTTT 49 239 1 AACTCTGCCC 0.850952 -62 AGGGTCAGCCCAAGTCTGTCCTGGACACGTA 50 42 1 CAATCTGTCC 0.566673 -184 CCGAATTTTGCGACTCTCCCCGTATTTGATC 52 68 1 CGATCTCCCC 0.662575 -233 GACTATGGGATGAATCTGCCCTAAAAATAAA 52 186 1 TGATCTGCCC 0.441709 -115 TTACCATTTGAAAGGCTTCCCCGAATTTGAG 53 17 0 AAAGCTTCCC 0.800289 -277 ATTAAGTCTCTACACCTTCCCAGAAACACCA 53 72 0 TACCCTTCCC 0.499927 -222 AAAAAGAAAAAAATTCCCCCCGCCGGATAAT 53 239 1 AAATCCCCCC 0.733739 -55 GTCTTGGGACAAAATCTGCCCCTGGTCATTG 59 15 0 AAATCTGCCC 0.923352 -80 TGACATAAAAATCTTTCCTTGGGATCTT 63 89 0 AAATCTTTCC 0.679645 -18 TCTTATAAAAAAAGCCTTTCCTAATTAAAAT 64 71 1 AAACCTTTCC 0.604106 -136 TAACTTCTCTCCAACAAGTGTT 65 13 0 AACTCTCTCC 0.663499 -12 TTTCTTAAAACAAGCCTTCCCTAAAAATAAT 79 137 0 CAACCTTCCC 0.770845 -164 ATTGCAAACAAGAGCCTTCCCGGATAAAGGA 94 53 0 AGACCTTCCC 0.595506 -248 GCCCCAATCGAAAATCTCTCCTATTCAATAA 96 79 0 AAATCTCTCC 0.806218 -222 ACATACGAAGAAATCCTCTCCAAGCAAGCGT 96 165 0 AAACCTCTCC 0.749525 -136 *** ******* Masking position 6 Map Score: 16.3732 Number of sites scoring better than the average of aligned sites = 1076 Number in coding regions = 912 Number in noncoding regions = 164 Number of orfs with sites within 600 bp upstream = 186 Fraction of orfs with sites within 600 bp upstream = 0.0298747 Motif number 10 TCGGGTTTCACCTCCTTGGGGTTGG 31 232 0 GGGTTTCTCC 0.915777 -15 CCTGATGTCGGGGGTTCAAGTCCTCCAGGGCGC 35 167 1 GGGGTTCTCC 0.985936 -111 CAATGTTGGATGGGTTACCGTCCCC 37 3 0 TGGGTTATCC 0.579102 -278 TTGATTGACCCGGTTTCCCATCCAGGGGCCGAT 39 240 1 CGGTTTCTCC 0.721556 -61 AGCAGTTGTAGAGGTTACAGTCCATGAAAGTGG 45 91 0 GAGGTTATCC 0.801685 -111 TCTATCCACTGAGCTACGTGTCCAGGACAGACT 50 54 0 GAGCTACTCC 0.608622 -172 GATAGAGCATCAGGTTCCGGTCCTGAGGGTCGG 50 81 1 CAGGTTCTCC 0.883907 -145 CTGAGGGTCGGGGGTTCGAATCCCTCCGTGTTC 50 103 1 GGGGTTCTCC 0.986029 -123 CCGAAGGTCGGTGGTTCAAATCCGCCTCCCGCC 53 199 1 GTGGTTCTCC 0.887415 -95 CAAGTGGCCGTAGGTTCAATTCCTATTCTGGGC 71 232 1 TAGGTTCTCC 0.831145 -69 TTTAAGGGGTACGCGTCCTTAGCAGGGA 82 6 1 GGGGTACTCC 0.935135 -295 GAGGTTCGAATCCTTCCACCCCA 96 1 1 GAGGTTCTCC 0.969651 -300 ATGGCCTTAAGGGCTTCTTTTCCCTCAACCGGA 96 237 0 GGGCTTCTCC 0.943886 -64 ******* *** Masking position 5 Map Score: 10.0562 Number of sites scoring better than the average of aligned sites = 142 Number in coding regions = 115 Number in noncoding regions = 27 Number of orfs with sites within 600 bp upstream = 36 Fraction of orfs with sites within 600 bp upstream = 0.0057822 Motif number 11 ACTTCATGGTCAATGGCAAACCTCGACAAT 1 210 1 CAATGGCAAA 0.446168 -91 CATCTGTGTCGCATGGTAACTGAACTCCTA 2 72 0 GCATGGTAAC 0.85201 -33 CAATGGTAACCAAAATCCTT 9 1 1 CAATGGTAAC 0.884071 -101 GGTATCGCCCCCCTGGTAACCTCTCCCCGG 23 17 1 CCCTGGTAAC 0.811006 -93 GACGCCACGACAATGGTCAC 25 1 0 CAATGGTCAC 0.873995 -95 GGGCCGATCGCCACGGCCACTGATGCCCTT 26 33 0 CCACGGCCAC 0.780219 -131 ACAGTGTCTTCCATGGCAACTGAACTAGCC 37 201 1 CCATGGCAAC 0.963972 -80 GGGCCGTCCCCCATGGTAACAGAGTAACTT 38 28 1 CCATGGTAAC 0.967124 -160 AGTTAAATTTCCATGGCAACA 40 137 1 CCATGGCAAC 0.963972 -11 TGTTTTCTTCCCATGGTCAAAGGTAAAAAA 51 197 0 CCATGGTCAA 0.756549 -104 TACTTTACTGCAATGGTCACAACTAGATGA 52 107 0 CAATGGTCAC 0.873995 -194 AATTAAAATGGCATGGTCACAGATGTGAAA 57 214 1 GCATGGTCAC 0.839653 -87 TAAGAAAAAACCATTGCAACAGAAATATTC 66 95 0 CCATTGCAAC 0.619585 -206 TAAAACACGCTCATGGTAACATGATCTTCT 80 94 1 TCATGGTAAC 0.678532 -207 ********** Masking position 9 Map Score: 8.09123 Number of sites scoring better than the average of aligned sites = 557 Number in coding regions = 504 Number in noncoding regions = 53 Number of orfs with sites within 600 bp upstream = 63 Fraction of orfs with sites within 600 bp upstream = 0.0101189 Motif number 12 GAACACCGCGCCAAAACATCTGTACACCTG 1 133 1 CCAAAACATC 0.409403 -168 AAATCCTTCCCCATAGCCTGGGAGAGAGCG 9 23 1 CCATAGCCTG 0.70408 -79 GCTGAAGGCCCCAAGCCTTTACTAAGTGA 10 10 1 CCCAAGCCTT 0.703294 -59 GGCGATCGGCCCAAAGCCTCACTCCACAAC 26 51 1 CCAAAGCCTC 0.931938 -113 TCCAGGCCCTCCCAATCCTGACAGTGGCAA 28 155 0 CCCAATCCTG 0.887946 -40 ATTACCCCGTCCCCAACCTCC 28 184 1 CCCCAACCTC 0.795693 -11 ACGCAGGTCTCCAAAACCTGATGTCGGGGG 35 151 1 CCAAAACCTG 0.918264 -127 GAACCTTTACCAAAAGCCTGTCCATGGACT 37 65 0 CAAAAGCCTG 0.475452 -216 TGGAGCAATTCACAAACCTCCATCTTAACC 38 131 0 CACAAACCTC 0.716662 -57 GCAACTCAACCCCAAACCTGTATCAATGTT 42 25 0 CCCAAACCTG 0.961063 -182 TTGAGTTGCCCCCACGCCTCCCTGGGTTAG 42 46 1 CCCACGCCTC 0.761335 -161 ATTAATAATTCCCAAACGTCCCATTATACC 48 126 0 CCCAAACGTC 0.80598 -39 TGCTCTTAAGCCAAAACCACAATCCACTTT 52 34 1 CCAAAACCAC 0.500016 -267 TTCAGTTTAACCAAAACCTCTACTGAGTTC 54 86 0 CCAAAACCTC 0.933235 -72 TATCCCCTATCCTGTCATTAGTAT 64 5 1 CCCTATCCTG 0.631434 -202 TCATTGGGTGCCCAAGCCTGTTTTTTTGTT 72 234 1 CCCAAGCCTG 0.960284 -67 TTCCCCTATACCCTAACCTGGCCGAGAGAG 82 246 1 CCCTAACCTG 0.84218 -55 GATGTTAGCTCCAAAACGTCTCGCTATTCT 93 224 0 CCAAAACGTC 0.654073 -77 GCTGAGAAAGCCCAATCCTCCGGGTCAGCA 93 277 1 CCCAATCCTC 0.907914 -24 ********** Masking position 7 Map Score: 12.5962 Number of sites scoring better than the average of aligned sites = 650 Number in coding regions = 577 Number in noncoding regions = 73 Number of orfs with sites within 600 bp upstream = 85 Fraction of orfs with sites within 600 bp upstream = 0.0136524 Motif number 13 GACAGTTAAATTTTTTGCTAACAGCTTTTTTGAGCAAA 3 11 1 TTTTTAAATT 0.846833 -98 GTTGATTTTCCTCTAAATAAGTTCAATAAATTT 5 60 0 TTTTCAATTT 0.470379 -23 GGTTGCAATATTTTTGGTCAACTGTATTGATCAACTGG 24 41 1 TTTTTAATTT 0.819856 -65 GACAGTGCTATTTTTGTGCAACTTGCTTTGGCTAGGGA 26 119 1 TTTTTAATTT 0.819856 -45 GCTAGTCATGGTTTTAGCGAATAACAGTGTCTTCCATG 37 178 1 GTTTTAAAGT 0.410652 -103 GACAACAGGTGTTTTGCCAAACTTGTTTGGAGGAGAAT 39 163 0 GTTTTAATTT 0.656074 -138 ATCGGGGGAATTTTTGCCAAACTTTATTTTTAGGGCAG 52 201 0 TTTTTAATTT 0.819856 -100 TAGGAAAGGCTTTTTTTATAAGAACCTTTCGTTCAATA 64 56 0 TTTTTAAATT 0.846833 -151 CGTATAAAATTTTTTCGATAAAAGATTTTAATTAGGAA 64 88 0 TTTTTAAATT 0.846833 -119 AGTTTTTATTTTTTTTCGAAACAGAAGTCGTATAAAAT 64 116 0 TTTTTAAAGT 0.624398 -91 GCTGCTTGTTTTTTTACAAAAGATACTTTCTTAAGAAA 70 83 0 TTTTTAAATT 0.846833 -218 CGTCAAGATTGTTTTGATGAATATTTTTGGCTTTGGAT 70 190 1 GTTTTAAATT 0.698559 -111 TTTCCTTCTGTTTTTTGACAAGTTGTTTGACATTTTCT 72 140 1 TTTTTAATTT 0.819856 -161 TCTTGCAGCTTTTTTTTAAAAAATCCTTCTCCTCTCTT 76 58 1 TTTTTAAATT 0.846833 -235 TGATAAAATGTTTTCTTCGAATACTGTTAGTTCAAAAA 79 73 0 TTTTCAAATT 0.518985 -228 ATTTAACTCTTTTTTTATTAATTATTTTTAGGGAAGGC 79 117 1 TTTTTAATTT 0.819856 -184 GGGAAGGCTTGTTTTAAGAAAATCTTTTGGAGGAAATG 79 147 1 GTTTTAATTT 0.656074 -154 GGAGGAAATGTTTTTTAATAAAATTGTTATAGAGATCG 79 175 1 TTTTTAAATT 0.846833 -126 TGAGATTTTTTAAATAAGAAGAGTTTTTTTAGCA 93 7 1 TTTTTAAAGT 0.624398 -294 AAACTGATTATTTTTCAGTAACTTTTTTTCAAAAAGTG 97 31 0 TTTTTAATTT 0.819856 -107 ***** ** * ** Masking position 4 Map Score: 13.0947 Number of sites scoring better than the average of aligned sites = 122 Number in coding regions = 83 Number in noncoding regions = 39 Number of orfs with sites within 600 bp upstream = 41 Fraction of orfs with sites within 600 bp upstream = 0.00658529 Motif number 14 TCCTCTGACTGAGATAGCGTCGGTCAAGCT 3 57 1 GAGATAGCGT 0.941251 -52 CATAGCCTGGGAGAGAGCGATAATAGGTTA 9 34 1 GAGAGAGCGA 0.962468 -68 TTAATGAATGGCGATAGCGT 16 1 0 GCGATAGCGT 0.78918 -40 CCTTGGGAAAGAGAGAGCTTGTTTTTGGTC 42 162 1 GAGAGAGCTT 0.941252 -45 CATCATACAAGAGAGAGCGTTGGACTATTT 57 241 0 GAGAGAGCGT 0.979954 -60 CCGGAAACTCGAGAGAGCGATTATATCGAC 72 183 0 GAGAGAGCGA 0.962468 -118 TAACCTGGCCGAGAGAGCTTCCTTTACCAA 82 259 1 GAGAGAGCTT 0.941252 -42 TAATTTTTAGGAGAGAGTGTT 85 11 1 GAGAGAGTGT 0.827364 -11 CCAATAACTAGAGATAGCTACTCTATAAGA 97 87 0 GAGATAGCTA 0.73365 -51 ********** Masking position 6 Map Score: 7.57711 Number of sites scoring better than the average of aligned sites = 19 Number in coding regions = 13 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 15 CTGGCTATGAAGCTGTTGACCAAAGGTTATTGCCG 21 171 1 ACTTTGCCAG 0.800195 -130 ATTGTACGATATTTATCGGCCCCTGGATGGGAAAC 39 252 0 ATTTCGCCCG 0.816986 -49 TAATTTGCTTAACTATCGGCCCGAATTGTACTTTT 46 70 1 ACTTCGCCGA 0.808204 -144 TGCCCAGGGGACTTTTTGCCCCGATTAACCTAGAC 49 255 1 ATTTTGCCGT 0.690291 -46 CTTAAGAGCAATTTTTTGTCCCGAGCTGGTCTT 52 9 0 ATTTTGCCGG 0.96228 -292 TTACATCTTGCGACCTGAGCCCGACGAGC 52 282 0 ACTGCGCCGG 0.75067 -19 TTTTCACAAAACTTCTTGACCGGGGTTGAAAGTGA 61 99 1 ATTTTGCCGG 0.96228 -103 GGGACAGTCTAGTTCTCGACCAGTGGAGCAGATAT 62 12 0 ATTTCGCCGG 0.949323 -38 TGCTACCAATATCTTTTGCCCAGAATAGGAATTGA 71 247 0 ACTTTGCCGA 0.851602 -54 AAGCTGCAGCACCTGTTGTCCTCCGGAAACTCGAG 72 200 0 ACTTTGCCCG 0.861012 -101 CGAGCGCTAAAATTCTTGACCAGTGGAGACGGTTT 74 24 1 ATTTTGCCGG 0.96228 -63 AAAATAACAATTTTTGACCTAAGATGCTTATAT 86 9 1 ATTTTGCCAG 0.79717 -47 GCAAAAGGGTACTTCTTGTCCGGTAGGAGGAGGCT 94 184 1 ATTTTGCCGA 0.849208 -117 * ** *** ** * * Masking position 1 Map Score: 6.92215 Number of sites scoring better than the average of aligned sites = 97 Number in coding regions = 86 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863