AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i03010_synecho_reg_100.orf -o03010_synecho_100.ace -a/home/amcguire/alignace/lib/ORF_synecho.txt -z/skink1/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 ssr1604 198 rpmB, rpl28; 50S ribosomal protein L28. [SP:RL28_SYNY3] #2 ssl1784 164 rpsO, rps15; 30S ribosomal protein S15. [SP:RS15_SYNY3] #3 ssr1736 98 rpmF, rpl32; 50S ribosomal protein L32. [SP:RL32_SYNY3] #4 slr1050 135 hypothetical protein. #5 ssl3445 52 rpmE, rpl31; 50S ribosomal protein L31. [SP:RL31_SYNY3] #6 sll1821 64 rplM, rpl13; 50S ribosomal protein L13. [SP:RL13_SYNY3] #7 sll1819 77 rplQ, rpl17; 50S ribosomal protein L17. [SP:RL17_SYNY3] #8 sll1818 108 rpoA; DNA-directed RNA polymerase alpha chain (transcriptase alpha #9 sll1817 48 rpsK, rps11; 30S ribosomal protein S11. [SP:RS11_SYNY3] #10 sll1816 82 rpsM, rps13; 30S ribosomal protein S13. [SP:RS13_SYNY3] #11 sml0006 137 rpmJ, rpl36; 50S ribosomal protein L36. [SP:RL36_SYNY3] #12 sll1813 68 rplO, rpl15; 50S ribosomal protein L15. [SP:RL15_SYNY3] #13 sll1812 39 rpsE, rps5; 30S ribosomal protein S5. [SP:RS5_SYNY3] #14 sll1810 59 rplF, rpl6; 50S ribosomal protein L6. [SP:RL6_SYNY3] #15 sll1809 91 rpsH, rps8; 30S ribosomal protein S8. [SP:RS8_SYNY3] #16 sll1808 46 rplE, rpl5; 50S ribosomal protein L5. [SP:RL5_SYNY3] #17 sll1806 23 rplN, rpl14; 50S ribosomal protein L14. [SP:RL14_SYNY3] #18 sll1805 40 rplP, rpl16; 50S ribosomal protein L16. [SP:RL16_SYNY3] #19 sll1804 29 rpsC, rps3; 30S ribosomal protein S3. [SP:RS3_SYNY3] #20 ssl3432 32 rpsS, rps19; 30S ribosomal protein S19. [SP:RS19_SYNY3] #21 sll1802 49 rplB, rpl2; 50S ribosomal protein L2. [SP:RL2_SYNY3] #22 sll1800 39 rplD, rpl4; 50S ribosomal protein L4. [SP:RL4_SYNY3] #23 sll1799 300 rplC, rpl3; 50S ribosomal protein L3. [SP:RL3_SYNY3] #24 ssl2233 95 rpsT, rps20; 30S ribosomal protein S20. [SP:RS20_SYNY3] #25 sll1123 112 hypothetical protein. #26 sll1746 87 rplL, rpl12; 50S ribosomal protein L7/L12. [SP:RL7_SYNY3] #27 sll1745 246 rplJ, rpl10; 50S ribosomal protein L10. [SP:RL10_SYNY3] #28 sll1744 86 rplA, rpl1; 50S ribosomal protein L1. [SP:RL1_SYNY3] #29 sll1743 101 rplK, rpl11; 50S ribosomal protein L11. [SP:RL11_SYNY3] #30 sll1740 104 rplS, rpl19; 50S ribosomal protein L19. [SP:RL19_SYNY3] #31 slr1356 259 rps1a; 30S ribosomal protein S1 homolog A. [SP:RS1A_SYNY3] #32 sll1767 300 rpsF, rps6; 30S ribosomal protein S6. [SP:RS6_SYNY3] #33 sll1260 224 rpsB, rps2; 30S ribosomal protein S2. [SP:RS2_SYNY3] #34 sll1244 121 rplI, rpl9; 50S ribosomal protein L9. [SP:RL9_SYNY3] #35 slr1984 300 rps1b; 30S ribosomal protein S1 homolog B. [SP:RS1B_SYNY3] #36 slr1470 100 hypothetical protein. #37 sll1101 138 rpsJ, rps10; 30S ribosomal protein S10. [SP:RS10_SYNY3] #38 sll1097 150 rpsG, rps7; 30S ribosomal protein S7. [SP:RS7_SYNY3] #39 sll1096 96 rpsL, rps12; 30S ribosomal protein S12. [SP:RS12_SYNY3] #40 sll1095 111 hypothetical protein. #41 slr1678 107 rplU, rpl21; 50S ribosomal protein L21. [SP:RL21_SYNY3] #42 ssr2799 78 rpmA, rpl27; 50S ribosomal protein L27. [SP:RL27_SYNY3] #43 slr1679 110 hypothetical protein. #44 ssr0482 40 rpsP, rps16; 30S ribosomal protein S16. [SP:RS16_SYNY3] #45 slr0287 242 hypothetical protein. #46 sll0767 140 rplT, rpl20; 50S ribosomal protein L20. [SP:RL20_SYNY3] #47 ssl1426 96 rpmI, rpl35; 50S ribosomal protein L35. [SP:RL35_SYNY3] #48 sll0765 91 hypothetical protein. #49 tRNA-Ala-2 300 tRNA-Ala. #50 ssl0601 243 rpsU, rps21; 30S ribosomal protein S21. [SP:RS21_SYNY3] #51 slr0469 238 rpsD, rps4; 30S ribosomal protein S4. [SP:RS4_SYNY3] #52 slr0628 173 rpsN, rps14; 30S ribosomal protein S14. [SP:RS14_SYNY3] #53 ssr1398 96 rpmG, rpl33; 50S ribosomal protein L33. [SP:RL33_SYNY3] #54 ssr1399 265 rpsR, rps18; 30S ribosomal protein S18. [SP:RS18_SYNY3] Motif number 1 CCTGCTCCTTGCCATTGGGGGGTAAAACCACTG 1 93 0 GCTGGGGGGT 0.955367 -106 CTGTGGATTTGTCCATGGGAAGCTGTCTGGGAT 1 150 1 GCTGGGAAGC 0.774469 -49 GACAACCAAAGACGTTGGGGGGCAAATCATTCC 2 26 0 GCTGGGGGGC 0.985298 -139 CTTGGAAGTACGGACTGGGGGGTATATTGAAAA 4 21 0 CGTGGGGGGT 0.897147 -115 CTTCCAAGAAGCCATCGGGGTGAAGCCAACTGT 4 46 1 GCCGGGGTGA 0.883532 -90 CTAAAAAATTAACAACAGGGGGTTACTCTAAGG 7 42 0 ACCAGGGGGT 0.837534 -36 TAAACAGGACAGGGATGGGGGGAAGA 9 4 0 AGTGGGGGGA 0.926382 -45 AATGCTTCCCCTCAGTGGGGAGAGTTAATTTAA 11 44 1 CCTGGGGAGA 0.928111 -94 TTTAGTCGCGGCTCAGGGTGATTGGTCAGCA 15 9 1 CGCAGGGTGA 0.461057 -83 AGCATTCAGTATCCGCAGGGGGTCGTAAAAAAT 23 25 0 ACCAGGGGGT 0.837522 -276 CTTCGGCCCTAGCGGTAGGGAGAGTTAGTCCTA 23 110 0 ACTAGGGAGA 0.767088 -191 TCGTCGCTTTATGTCCGGGGAGCCTTTCTGCTT 23 243 1 AGCGGGGAGC 0.941302 -58 AAAAACAAATGACTTTGGGGTGAACAGGGTGAA 26 18 0 GCTGGGGTGA 0.85862 -70 CGATCAAACCCACCGCGGGGAGCGAGAATTTAC 29 33 0 CCCGGGGAGC 0.969938 -69 ACTCGTTAGGGTGGCCGGGGAGCTAGGGGTTAA 32 125 0 GGCGGGGAGC 0.958362 -176 AAAATTGGCGATCGCCAGGGAGCAATTTTTACC 34 74 0 ACCAGGGAGC 0.891666 -48 CTTAACCTTTAGGGGGAATCCCGCCAA 34 105 0 ACTAGGGGGA 0.865927 -17 CCTCCAAGCTGGGATTGGGGAGCCAAATACCAA 35 181 0 GGTGGGGAGC 0.948524 -120 GGTTGCCGGGAAGACTGGGGGGCTCAATGGCTC 36 43 1 AGTGGGGGGC 0.961797 -58 CATCTTGCGTATGATTGGGGGGTTTGTAAATTC 45 30 0 AGTGGGGGGT 0.88939 -213 ATTTACGCTTCCCCTTGGGAGGCAAAGAAATGG 45 102 0 CCTGGGAGGC 0.835788 -141 AATGGAGATTGTCAACGGGGGGAATGATAGAAT 50 127 1 GCCGGGGGGA 0.976659 -117 GTTCGAGTTTCCCTACAGGAAGCAATCAAAGCC 52 121 1 CCCAGGAAGC 0.472897 -53 * * ******** Masking position 8 Map Score: 29.4166 Number of sites scoring better than the average of aligned sites = 1969 Number in coding regions = 1751 Number in noncoding regions = 218 Number of orfs with sites within 600 bp upstream = 204 Fraction of orfs with sites within 600 bp upstream = 0.0327658 Motif number 2 AGCGATCGGCTGTAGTTTTT 1 189 0 AGCGATCGGC 0.838145 -10 CAAGGTGAGGGGCGATCGCCAAGGACAAAA 3 48 0 GGCGATCGCC 0.499996 -51 GCGGGGCAAAGGTGATAGCCA 16 2 0 GGTGATAGCC 0.852181 -45 GTTAATGAATGGCGATAGCGT 18 2 0 GGCGATAGCG 0.832396 -39 CAGTGGCCGTGGCGATCGGCCCAAAGCCTC 25 41 1 GGCGATCGGC 0.53201 -72 AATGCCCCTTGGCGATCGCCGGGGCTGAAG 27 175 0 GGCGATCGCC 0.499996 -72 CAATCCCAATAGTGATCGCCAAATTCCCTG 31 175 0 AGTGATCGCC 0.834849 -85 CAGTTTAGCAGGCGATCGCCCCGATTACCC 33 103 0 GGCGATCGCC 0.499996 -122 CGCCAAAATTGGCGATCGCCAGGGAGCAAT 34 81 0 GGCGATCGCC 0.499996 -41 TCTGGCTGTGGGTGATCGAGGCTTTGATTG 52 143 0 GGTGATCGAG 0.748415 -31 ********** Masking position 5 Map Score: 22.1791 Number of sites scoring better than the average of aligned sites = 6401 Number in coding regions = 5816 Number in noncoding regions = 585 Number of orfs with sites within 600 bp upstream = 377 Fraction of orfs with sites within 600 bp upstream = 0.0605525 Motif number 3 CAACCCCAACTTTTCAATATACCCC 4 4 1 CCCCATTTTC 0.768795 -132 TGACGCGACCTCCCTTATATCTCC 8 95 0 ACGCACTCCC 0.860017 -14 GTTCCCTACTTCGCCAGTACCCAAGGAGTTAC 28 58 1 TCGCATACCC 0.850092 -29 GAGAATTTACTTCCAATCTCCCACTAAAGGGT 29 11 0 TTCCACTCCC 0.859617 -91 CAATAGTGATCGCCAAATTCCCTGGGTTTTAA 31 167 0 CGCCATTCCC 0.940905 -93 ATGGGATTAACCCCTAGCTCCCCGGCCACCCT 32 119 1 CCCCACTCCC 0.989095 -182 CAGGCGATCGCCCCGATTACCCACGCTTACCA 33 93 0 CCCCATACCC 0.982813 -132 CTTTCCCAACTTTCCATTAGCCTAG 38 4 1 TCCCATTTCC 0.947244 -147 TAGGAGAACGATCCTAATTCCCACTATATTTA 39 71 1 ATCCATTCCC 0.897488 -26 TATCTCCGCCCCCCCACTTTCC 40 100 1 CCCCATTTCC 0.974375 -12 AGATACTACTACCCCATTACCCAGAGATAAAT 45 178 1 ACCCATACCC 0.94857 -65 ATTTTCCCCATCCCAACTTTCCATGGCACCCA 46 47 0 TCCCATTTCC 0.947244 -94 CATTCAAGCCTTCCAACTTCTCTTCTATGCGT 49 85 1 TTCCATTCTC 0.5285 -216 GAAAATATTATCGCCATTTCCCGGACTATAAT 50 82 0 TCGCATTCCC 0.949566 -162 GATATTTATTCCCCTAGCTCCCTTTTGTTGTT 50 197 1 CCCCACTCCC 0.989095 -47 AGTGAAACCTCCCCCATTTCCCCAGACAGAT 51 218 1 CCCCATTCCC 0.994761 -21 CAGTAAAAATCCCCCATTAACCTAGGTTTTGG 52 26 1 CCCCATAACC 0.776829 -148 ACTCCTCTGCACCCAAATTCCCCAAGGGGATA 54 18 1 ACCCATTCCC 0.983932 -248 **** * ***** Masking position 6 Map Score: 25.6048 Number of sites scoring better than the average of aligned sites = 899 Number in coding regions = 759 Number in noncoding regions = 140 Number of orfs with sites within 600 bp upstream = 134 Fraction of orfs with sites within 600 bp upstream = 0.0215226 Motif number 4 ACGCTATCTCAGTCAGAGGAAATTACGATTT 8 46 0 AGTCAGGGAA 0.861791 -63 ACAGCTTCATAGCCAGTGAATAACTAATTCA 23 189 0 AGCCAGGAAT 0.952414 -112 TCTTTGGCATAGCCAGTTAAATAAATAGTGG 27 39 0 AGCCAGTAAA 0.780368 -208 GCAGCTTAAAACCCAGGGAATTTGGCGATCA 31 162 1 ACCCAGGAAT 0.846654 -98 CATTTGGTGGAGTCAGGGAGAGTTTCTCTGA 35 144 1 AGTCAGGAGA 0.875775 -157 TACCAAAAAGAGTCAGAGAAACTCTCCCTGA 35 156 0 AGTCAGGAAA 0.967956 -145 TACCCAGGCAACTCAGTAAAACAGTTTTAAG 35 231 0 ACTCAGAAAA 0.725541 -70 GGGCTGGCCCAGTCAGAAAAAACTTACCGTA 37 53 0 AGTCAGAAAA 0.905514 -86 CTCGCTGGCTAGCCTGAAAAAAATTTGTTAA 41 36 0 AGCCTGAAAA 0.707938 -72 TTTTCAGGCTAGCCAGCGAGTTCTGATTGTA 41 47 1 AGCCAGGAGT 0.823684 -61 CTACCCCATTACCCAGAGATAAATTAGAAAA 45 186 1 ACCCAGGATA 0.691844 -57 TTTCCATGGCACCCAGCGGAAAAGTGAGCAA 46 31 0 ACCCAGGGAA 0.754392 -110 AAAAAACAACAGCCAGGAATATCTGAAAACC 49 266 1 AGCCAGAATA 0.720846 -35 TCAAAATTATAGTCCGGGAAATGGCGATAAT 50 77 1 AGTCCGGAAA 0.782417 -167 CATTAGTCCAAGCCAGAGAAAATATTATCGC 50 100 0 AGCCAGGAAA 0.9818 -144 AAATTGAATCAGTCAGGAAATGCTAAATATT 51 108 1 AGTCAGAAAT 0.780518 -131 GGTTTAACTCAGCCAGTAAAAATCCCCCATT 52 13 1 AGCCAGAAAA 0.944795 -161 GAAATTCATCGGTCAGAGAAATTTTGGTCGG 54 111 0 GGTCAGGAAA 0.762084 -155 GGCTAAGAATAGTCTGAGAATAAGAATAAGT 54 231 0 AGTCTGGAAT 0.61353 -35 ****** **** Masking position 6 Map Score: 15.5763 Number of sites scoring better than the average of aligned sites = 581 Number in coding regions = 506 Number in noncoding regions = 75 Number of orfs with sites within 600 bp upstream = 85 Fraction of orfs with sites within 600 bp upstream = 0.0136524 Motif number 5 CTTACTATATCACGTTTGCCGGAGGGCTCC 2 86 0 CACGTTTGCC 0.849608 -79 ATTAATTTTTTACCTTTGCCACCGTCAAAT 11 17 0 TACCTTTGCC 0.738324 -121 TGGCTATCACCTTTGCCCCGCAAGCAA 16 8 1 CACCTTTGCC 0.963351 -39 CTTGAGAGACCACCTTCGGCCCTAGCGGTA 23 126 0 CACCTTCGGC 0.889357 -175 GCGTTTCAATCAAGCTTTGCTTGAGAGACC 23 145 0 CAAGCTTTGC 0.540191 -156 ATTCAGGCTTCAACCTCGGCAGGTTAATTA 27 93 0 CAACCTCGGC 0.898144 -154 GGGAAAAAAGCAACTTTTGCAAAAGAGGGT 30 50 1 CAACTTTTGC 0.891821 -55 GTAACCCATCCAACATTGCCCAAAGTTTAG 32 38 1 CAACATTGCC 0.846757 -263 GAATTTTTGACAACCTTTCCAGTTTAGCAG 33 122 0 CAACCTTTCC 0.827554 -103 GGTAACAGAGTAACTTTGCCTTTCTGTCCA 34 36 1 TAACTTTGCC 0.823569 -86 TGGCGATCGCCAATTTTGGCGGGATTCCCC 34 90 1 CAATTTTGGC 0.873138 -32 GTCTTCCCGGCAACCTTGGCAATATTTATC 36 28 0 CAACCTTGGC 0.970454 -73 AACAACCAGTCAAATTTGGCTAGTATTGTA 41 85 0 CAAATTTGGC 0.796047 -23 AGTCTCTCGTCAATTTTGGCTAAAATGTCT 49 150 1 CAATTTTGGC 0.873138 -151 GGAACTTTTCCAACTTTGCCCTTATCTTAG 54 53 0 CAACTTTGCC 0.977522 -213 ********** Masking position 2 Map Score: 10.9641 Number of sites scoring better than the average of aligned sites = 951 Number in coding regions = 863 Number in noncoding regions = 88 Number of orfs with sites within 600 bp upstream = 109 Fraction of orfs with sites within 600 bp upstream = 0.0175072 Motif number 6 TTAACCCAGTGGTTTTACCCCCCAATGGCA 1 87 1 GGTTTTACCC 0.96699 -112 GCTCCTCTGTGGATTTGTCCATGGGAAGCT 1 144 1 GGATTTGTCC 0.927763 -55 GAATCTGGAATGATTTGCCCCCCAACGTCT 2 20 1 TGATTTGCCC 0.801475 -145 TTACAGCCTAGGTTTTTTCCACAGAGACT 2 146 1 GGTTTTTTCC 0.90333 -19 TTGGAGATTTGGATTTACCCGTACCCCTCT 5 11 1 GGATTTACCC 0.963853 -42 TCATCATAACTGATTTACCCTCTTTTGCAA 30 66 0 TGATTTACCC 0.876748 -39 TTCGACTATGGGATTAACCCCTAGCTCCCC 32 112 1 GGATTAACCC 0.616056 -189 TCTCCTATTCGGGTTTATCCTTCATCCAAG 33 196 0 GGGTTTATCC 0.763208 -29 GGGATTTACTGTTTTTACCCCTGTAACTCA 42 17 0 GTTTTTACCC 0.684617 -62 TGCCGGTTTTTTCCGTGGTGTTTA 44 27 0 GGTTTTTTCC 0.90333 -14 AACCCTAGCGGGATTTTCCCCATCCCAACT 46 61 0 GGATTTTCCC 0.97182 -80 CAACAAGCAAGGATTTTTCCGCTTTCCT 48 74 1 GGATTTTTCC 0.939107 -18 ********** Masking position 5 Map Score: 10.8059 Number of sites scoring better than the average of aligned sites = 772 Number in coding regions = 685 Number in noncoding regions = 87 Number of orfs with sites within 600 bp upstream = 105 Fraction of orfs with sites within 600 bp upstream = 0.0168648 Motif number 7 AGAAGCCATCGGGGTGAAGCCAACTGTCCC 4 52 1 GGGGTGAAGC 0.756414 -84 AATCCATTTCGGCCTGAATCTGAGACCGTG 4 86 1 GGCCTGAATC 0.964286 -50 GCTGAAGGCCCCAAGCCTTTACTAAG 12 7 1 GGCCCCAAGC 0.954187 -62 CCTACCGCTAGGGCCGAAGGTGGTCTCTCA 23 124 1 GGGCCGAAGG 0.876394 -177 CGTGGCGATCGGCCCAAAGCCTCACTCCAC 25 48 1 GGCCCAAAGC 0.875588 -65 CCGAGGTTGAAGCCTGAATCAAGATTTGAG 27 104 1 AGCCTGAATC 0.640082 -143 GCGATCGCCGGGGCTGAAGCAGAGGATCAA 27 164 0 GGGCTGAAGC 0.969521 -83 AGTTAGGCTGGGCCTGAATCTATAGATCCA 31 212 0 GGCCTGAATC 0.964286 -48 GAAGACTGGGGGGCTCAATGGCTCCAGTGC 36 52 1 GGGCTCAATG 0.757367 -49 CCCCGATAATGGCCACAATCAATGTAATGC 49 11 1 GGCCACAATC 0.832559 -290 AGTATATCTAGGGCGCAATCTTCAGACCTA 49 233 1 GGGCGCAATC 0.725905 -68 ACTTTAATATGGCCAAAAGCTCCCCAAGTA 50 42 0 GGCCAAAAGC 0.757491 -202 CGGATAAGTCGGCCTGAAGGTGAGAATAAT 51 38 1 GGCCTGAAGG 0.940171 -201 ********** Masking position 7 Map Score: 9.66172 Number of sites scoring better than the average of aligned sites = 292 Number in coding regions = 261 Number in noncoding regions = 31 Number of orfs with sites within 600 bp upstream = 36 Fraction of orfs with sites within 600 bp upstream = 0.0057822 Motif number 8 TCGTCCCCTGTTAACCCAGTGGTTTTACCCCC 1 77 1 TTACCCAGGG 0.770293 -122 GTTTTTGTTGGTATCCCAGACAGCTTCCCATG 1 163 0 GTACCCAGCA 0.822568 -36 GTGAAGCCAACTGTCCCAGTCAATCCATTTCG 4 65 1 CTGCCCAGCA 0.958343 -71 TTGACCGACGCTATCTCAGTCAGAGGAAATTA 8 52 0 CTACTCAGCA 0.89067 -57 CCTGCGGTCTTTGGCATAGCCAGTTAAATAAA 27 45 0 TTGCATAGCA 0.386959 -202 CCTAATCACATTAACTTAGACATACATAAGCA 29 80 1 TTACTTAGCA 0.638547 -22 GGCAACTGAACTAGCCCAGACGATGATGGTTG 32 235 1 CTACCCAGCG 0.9583 -66 TCGGGTGTTTCTGCCACAGGCGGAAATTCCCT 33 166 1 CTGCACAGCG 0.704849 -59 TTTCTGTCCATTGCCCCAGGTAAAAATTGCTC 34 56 1 TTGCCCAGTA 0.684572 -66 GTCAGTGGGGCTGGCCCAGTCAGAAAAAACTT 37 59 0 CTGCCCAGCA 0.958343 -80 CAACTTTCCATTAGCCTAGCCGCCCCTGTCCA 38 17 1 TTACCTAGCG 0.832871 -134 GGGCAACGGTTTTCTCAGACAACATAACTTG 45 222 0 TTTCTCAGCA 0.696843 -21 CTCCAAAACACTTTCCCAGGTAAAGCTGAAAT 46 95 1 CTTCCCAGTA 0.491164 -46 CCTTTTGTTGTTAACCCAGGAGGTTTAAAACT 50 217 1 TTACCCAGAG 0.551454 -27 ACCTCCCCCATTTCCCCAGACAGAT 51 224 1 TTTCCCAGCA 0.887683 -15 TTGGTTTAACTCAGCCAGTAAAAATCC 52 6 1 TTACTCAGCA 0.877447 -168 AACTTTGCCCTTATCTTAGGCGTATCCCCTTG 54 40 0 TTACTTAGCG 0.591733 -226 AAGCCAATTTCTATCCTAGGGAACTGGAACTT 54 76 0 CTACCTAGGA 0.534347 -190 *** ***** ** Masking position 2 Map Score: 7.85939 Number of sites scoring better than the average of aligned sites = 867 Number in coding regions = 763 Number in noncoding regions = 104 Number of orfs with sites within 600 bp upstream = 128 Fraction of orfs with sites within 600 bp upstream = 0.0205589 Motif number 9 CTCTGTGGATTTGTCCATGGGAAGCTGTCT 1 148 1 TTGTCCATGG 0.75601 -51 TTGCCCCCCAACGTCTTTGGTTGTCGATAA 2 34 1 ACGTCTTTGG 0.761238 -131 CAAAACCGTTTTGTCCTTGGCGATCGCCCC 3 40 1 TTGTCCTTGG 0.875419 -59 GCCTGATTTTCTTTGGCAACACTGCA 11 122 0 TTTTCTTTGG 0.553329 -16 AGTAATTTCCTTGGATGTTAATGG 13 26 0 ATTTCCTTGG 0.911998 -14 ACGGCCACTGATGCCCTTGGATCCGATTAT 25 21 0 ATGCCCTTGG 0.898878 -92 TCGGGTTTCACCTCCTTGGGGTTGGGATA 27 228 0 ACCTCCTTGG 0.937031 -19 GGATTTGGTAACTCCTTGGGTACTGGCGA 28 68 0 AACTCCTTGG 0.593304 -19 TGATCGCCAAATTCCCTGGGTTTTAAGCTG 31 163 0 ATTCCCTGGG 0.588024 -97 TACCAAAAGCCTGTCCATGGACTGCAATAC 32 78 0 CTGTCCATGG 0.718768 -223 AATAACAGTGTCTTCCATGGCAACTGAACT 32 217 1 TCTTCCATGG 0.750761 -84 ACAGGCGGAAATTCCCTTGGATGAAGGATA 33 181 1 ATTCCCTTGG 0.879722 -44 CGGAGGGCCGTCCCCCATGGTAACAGAGTA 34 18 1 TCCCCCATGG 0.720959 -104 CCATTTACGCTTCCCCTTGGGAGGCAAAGA 45 107 0 TTCCCCTTGG 0.832196 -136 CCCATCCCAACTTTCCATGGCACCCAGCGG 46 43 0 CTTTCCATGG 0.677725 -98 CTTGTTGTGAACTTCTATGGCTATAATAGC 48 51 0 ACTTCTATGG 0.536344 -41 AGAGTTTTAAACCTCCTGGGTTAACAACAA 50 221 0 ACCTCCTGGG 0.74385 -23 AAACTGCGAAACTTCTTTGGAAGTTAATAT 51 134 0 ACTTCTTTGG 0.724013 -105 TCTTAGGCGTATCCCCTTGGGGAATTTGGG 54 29 0 ATCCCCTTGG 0.898878 -237 TTTTTCCGTCTTTGGGCTAAGAATA 54 251 0 CCGTCTTTGG 0.594684 -15 ********** Masking position 5 Map Score: 13.8115 Number of sites scoring better than the average of aligned sites = 1671 Number in coding regions = 1504 Number in noncoding regions = 167 Number of orfs with sites within 600 bp upstream = 183 Fraction of orfs with sites within 600 bp upstream = 0.0293929 Motif number 10 GGGAAAGTTATCGACAACCAAAGACGTTGG 2 41 0 TCGACAACCA 0.815374 -124 ATCACCCTGAGCCGCGACTAAA 15 3 0 GCCGCGACTA 0.611513 -89 CGGACATAAAGCGACGACCAGCGGCAATAA 23 230 0 GCGACGACCA 0.960102 -71 GTTTGGGGACGCCACGACAATGGTCAC 24 8 0 GCCACGACAA 0.913464 -88 TGGGCCGATCGCCACGGCCACTGATGCCCT 25 34 0 GCCACGGCCA 0.926485 -79 GCGACGACAATTTCCGAGTC 27 1 1 GCGACGACAA 0.89498 -246 CAGTCCGGGCGCAACAGCAAGGCAAGTGGG 30 23 1 GCAACAGCAA 0.754044 -82 TCAGGCAGGCGCAGCAACCATCATCGTCTG 32 251 0 GCAGCAACCA 0.92524 -50 TTAATCCAAATCGACGACAATCTTCAGTCA 33 40 0 TCGACGACAA 0.629165 -185 GGGACGGCCCTCCGCAACCAG 34 2 0 TCCGCAACCA 0.767797 -120 ATTTCCTCAAGCAACAACAACATTTGGTGG 35 124 1 GCAACAACAA 0.878803 -177 GACAACAACCAGTCAAATTTG 41 97 0 ACAACAACCA 0.739911 -11 CCCGATAATGGCCACAATCAATGTAATGCC 49 12 1 GCCACAATCA 0.608568 -289 TAGCCAAAAAACAACAGCCAGGAATATCTG 49 261 1 ACAACAGCCA 0.546034 -40 AAAGAAAAATGCAGCAACCACAAAAGCCAC 54 148 1 GCAGCAACCA 0.92524 -118 ********** Masking position 10 Map Score: 7.68807 Number of sites scoring better than the average of aligned sites = 826 Number in coding regions = 779 Number in noncoding regions = 47 Number of orfs with sites within 600 bp upstream = 53 Fraction of orfs with sites within 600 bp upstream = 0.00851269 Motif number 11 TCCATGGGAAGCTGTCTGGGATACCAACAA 1 161 1 GCTGTCTGGG 0.784435 -38 CTATATCACGTTTGCCGGAGGGCTCCTTTC 2 82 0 TTTGCCGGAG 0.906599 -83 TCAATCAAGCTTTGCTTGAGAGACCACCTT 23 140 0 TTTGCTTGAG 0.790764 -161 AAGATTTGAGTTTGTTGGGGATTTGCTTCC 27 124 1 TTTGTTGGGG 0.71561 -123 ACTCGTTAGGGTGGCCGGGGAGCTAGGGGT 32 128 0 GTGGCCGGGG 0.865164 -173 GGGAGCAATTTTTACCTGGGGCAATGGACA 34 60 0 TTTACCTGGG 0.845282 -62 AAATGTTGTTGTTGCTTGAGGAAATCTCAG 35 119 0 GTTGCTTGAG 0.858457 -182 GTTTTACTGAGTTGCCTGGGTACCCTGTTT 35 240 1 GTTGCCTGGG 0.979741 -61 TATTGCCAAGGTTGCCGGGAAGACTGGGGG 36 34 1 GTTGCCGGGA 0.728078 -67 TCCAAGTTATGTTGTCTGAGAAAACCGTTG 45 220 1 GTTGTCTGAG 0.816167 -23 TAATTTCAGCTTTACCTGGGAAAGTGTTTT 46 99 0 TTTACCTGGG 0.845282 -42 AGCTCTCCATTTTACTTGGGGAGCTTTTGG 50 30 1 TTTACTTGGG 0.659258 -214 ATCTGTCTGGGGAAATGGGGG 51 228 0 TCTGTCTGGG 0.693961 -11 CCTAATCATAGTTGCTGGAGTCTGACCCAC 52 90 0 GTTGCTGGAG 0.846541 -84 ********** Masking position 8 Map Score: 7.60696 Number of sites scoring better than the average of aligned sites = 1499 Number in coding regions = 1352 Number in noncoding regions = 147 Number of orfs with sites within 600 bp upstream = 162 Fraction of orfs with sites within 600 bp upstream = 0.0260199 Motif number 12 TACGGACTGGGGGGTATATTGAAAAGTTGG 4 16 0 GGGGTATATT 0.655067 -120 TTATTAAGCGGGGGTATTTTTGAAAACT 6 47 1 GGGGTATTTT 0.855395 -18 AAAGACCGCAGGAGCAATTAGGGTTGCTTA 27 65 1 GGAGCAATTA 0.515859 -182 CGATCGCCAAGGGGCATTTTTATTGTGTGT 27 187 1 GGGGCATTTT 0.930207 -60 CGATCGCCAGGGAGCAATTTTTACCTGGGG 34 69 0 GGAGCAATTT 0.768458 -53 ATCCCAGCTTGGAGGATAATGCTCGAAGCG 35 199 1 GGAGGATAAT 0.654829 -102 TCCAAATTCTGGGGGATTTACTGTTTTTAC 42 29 0 GGGGGATTTA 0.916568 -50 CCCAGAATTTGGAGGATTTTAAGCATTCTA 42 46 1 GGAGGATTTT 0.948469 -33 TAGAACCCTAGCGGGATTTTCCCCATCCCA 46 64 0 GCGGGATTTT 0.769609 -77 GCCCTGTTGAGGAGGAATAAATGGCAACAA 49 196 0 GGAGGAATAA 0.467591 -105 GGAGTTTACAGGAGGATTATTCTCACCTTC 51 53 0 GGAGGATTAT 0.855264 -186 CTAGGTTAATGGGGGATTTTTACTGGCTGA 52 21 0 GGGGGATTTT 0.971606 -153 CCTAGGTTTTGGGGGAAATTGATCAGATTG 52 46 1 GGGGGAAATT 0.835683 -128 ********** Masking position 6 Map Score: 5.70744 Number of sites scoring better than the average of aligned sites = 1365 Number in coding regions = 1096 Number in noncoding regions = 269 Number of orfs with sites within 600 bp upstream = 201 Fraction of orfs with sites within 600 bp upstream = 0.032284 Motif number 13 AGCGATCGGCTGTAGTTTTTGTTGGTATC 1 180 0 GGCTGTGTTT 0.93066 -19 GGATACTGAATGCTTAGGCTTTTAAGTCTGAT 23 44 1 TGCTTAGTTT 0.638961 -257 TATTGCCGCTGGTCGTCGCTTTATGTCCGGGG 23 231 1 GGTCGTGTTT 0.859969 -70 CAAAGTCATTTGTTTTTGGTTTGTCTAATCAG 26 34 1 TGTTTTGTTT 0.560938 -54 GATTTGAGTTTGTTGGGGATTTGCTTCCTTGA 27 126 1 TGTTGGGTTT 0.709496 -121 AATCTACAGAGGTTGAGGCTTTGTTTTTATAG 31 80 0 GGTTGAGTTT 0.878336 -180 CAGTGGTAATTGCTGATGGTTTTCAAAATGGC 31 115 1 TGCTGAGTTT 0.927208 -145 GGTTTTAAGCTGCTCAGGGTTTTTTCTTGCCA 31 143 0 TGCTCAGTTT 0.732445 -117 GACTGAAGATTGTCGTCGATTTGGATTAAAGG 33 41 1 TGTCGTGTTT 0.871001 -184 GATGAAAATTTGTCGATGATTTTCTTATCTAT 39 39 1 TGTCGAGTTT 0.853551 -58 AAAAATCTGTTGCTCAAGTTTTAATTTATTCT 43 32 1 TGCTCAGTTT 0.732445 -79 CAAAGAAATGGGTCGTTGTTTTTGTATCTATA 45 81 0 GGTCGTGTTT 0.859969 -162 AGATATTCCTGGCTGTTGTTTTTTGGCTAGGT 49 258 0 GGCTGTGTTT 0.93066 -43 TACGGGGAAATGCAGTGGCTTTTGTGGTTGCT 54 160 0 TGCAGTGTTT 0.674939 -106 ****** * *** Masking position 10 Map Score: 5.89584 Number of sites scoring better than the average of aligned sites = 401 Number in coding regions = 334 Number in noncoding regions = 67 Number of orfs with sites within 600 bp upstream = 54 Fraction of orfs with sites within 600 bp upstream = 0.00867331 Motif number 14 AGGACAAAACGGTTTTGGGAAAAATAATTGAA 3 25 0 GGTTGGGAAA 0.973481 -74 GGATGTTAATGGGTTTGGTTAACGTTG 13 6 0 GGTTGGTTAA 0.793118 -34 AGTATCCGCAGGGGGTCGTAAAAAATAGCAGT 23 19 0 GGGTCGTAAA 0.659169 -282 ACTCCACAACGGTCTTGGTAAATTTTTGTCTA 25 71 1 GGTTGGTAAA 0.972991 -42 TCACCTCCTTGGGGTTGGGATAGCAAGCATTA 27 218 0 GGTTGGGATA 0.796189 -29 GGATTTGGTAACTCCTTGGGTA 28 75 0 GGTTGGTAAC 0.850343 -12 CAACAGCAAGGCAAGTGGGAAAAAAGCAACTT 30 34 1 GCGTGGGAAA 0.799308 -71 CCATGGACAGGCTTTTGGTAAAGGTTCGACTA 32 88 1 GCTTGGTAAA 0.885614 -213 AAAGACTGCGCGAGTTGGGAAACCGCCACTGA 35 91 1 CGTTGGGAAA 0.78183 -210 CGAAAGTAAGGGGAGTGGTAAAGCCAGCTACA 38 56 0 GGGTGGTAAA 0.947879 -95 AGGGGGCAGACGTTGGTAAACACCACGGAA 44 9 1 GATTGGTAAA 0.739482 -32 GTATGATTGGGGGGTTTGTAAATTCTGAAATA 45 23 0 GGTTTGTAAA 0.721048 -220 ATGGAAAGTTGGGATGGGGAAAATCCCGCTAG 46 55 1 GGTGGGGAAA 0.852723 -86 ** ******** Masking position 8 Map Score: 6.16341 Number of sites scoring better than the average of aligned sites = 646 Number in coding regions = 574 Number in noncoding regions = 72 Number of orfs with sites within 600 bp upstream = 75 Fraction of orfs with sites within 600 bp upstream = 0.0120463 Motif number 15 GAGAAGTTCACCTTTCCATTCTGCGTTATC 1 27 1 CCTTTCCATT 0.953658 -172 GGTTCCTGCTCCTTGCCATTGGGGGGTAAA 1 100 0 CCTTGCCATT 0.919974 -99 CCGGAGGGCTCCTTTCCATCACGAAAAGGG 2 68 0 CCTTTCCATC 0.79489 -97 TCCCCCCATCCCTGTCCTGTTTATTGAAGC 9 14 1 CCTGTCCTGT 0.858479 -35 TGTTTAAACCTGTTCATTTTGTACACTC 31 9 1 CCTGTTCATT 0.820669 -251 CAGGGTTTTTTCTTGCCATTTTGAAAACCA 31 131 0 TCTTGCCATT 0.639296 -129 TTACCAAAAGCCTGTCCATGGACTGCAATA 32 79 0 CCTGTCCATG 0.860453 -222 TTTTTGACAACCTTTCCAGTTTAGCAGGCG 33 119 0 CCTTTCCAGT 0.944158 -106 ACTTTGCCTTTCTGTCCATTGCCCCAGGTA 34 48 1 TCTGTCCATT 0.835365 -74 CTTTCCCAACTTTCCATTAGCCTAGCCG 38 9 1 ACTTTCCATT 0.642589 -142 CCTAGCCGCCCCTGTCCAGTGAAGGTGTAG 38 31 1 CCTGTCCAGT 0.959969 -120 TTTCCCTGGTCTGTGAACATTTTC 53 83 0 CCTGGTCTGT 0.320335 -14 ********** Masking position 3 Map Score: 5.11093 Number of sites scoring better than the average of aligned sites = 346 Number in coding regions = 301 Number in noncoding regions = 45 Number of orfs with sites within 600 bp upstream = 43 Fraction of orfs with sites within 600 bp upstream = 0.00690652