Origin IGS: gacttttcctccttaaattttaaggggaccagataaagaaaagaccttgctagtgcaaggcctcagttaaaatcgtacaacacaagagagcacacttaaaaagtctcctctagaaaattgtactattcttttatctgacaccttgtgagtctctctggactccccttaaaggttaaatttttactattatactctttcagctaaaaaaagtcaagtaaaaaacgaacattctacttgacttcaagaaa .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tttcttgaagtcaagtagaatgttcgttttttacttgactttttttagctgaaagagtataatagtaaaaatttaacctttaaggggagtccagagagactcacaaggtgtcagataaaagaatagtacaattttctagaggagactttttaagtgtgctctcttgtgttgtacgattttaactgaggccttgcactagcaaggtcttttctttatctggtccccttaaaatttaaggaggaaaagtc Mask Tandem Repeat Region ================================================ gacttttcctccttaaattttaaggggaccagataaagaaaagaccttgctagtgcaaggcctcagttaaaatcgtacaacacaagagagcacacttaaaaagtctcctctagaaaattgtactattcttttatctgacaccttgtgagtctctctggactccccttaaaggttaaatttttactattatactctttcagctaaaaaaagtcaagtaaaaaacgaacattctacttgacttcaagaaa Find is-nt database================================================ Query_seq: SMT_1359:SMT_1360|SMT_1359:SMT_1360:dihydroorotate dehydrogenase electron transfer subunit:lactoylglutathione lyase:<-<-:1338094..1338341 248 gacttttcctccttaaattttaaggggaccagataaagaaaagaccttgctagtgcaaggcctcagttaaaatcgtacaacacaagagagcacacttaaaaagtctcctctagaaaattgtactattcttttatctgacaccttgtgagtctctctggactccccttaaaggttaaatttttactattatactctttcagctaaaaaaagtcaagtaaaaaacgaacattctacttgacttcaagaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_1359:SMT_1360|SMT_1359:SMT_1360:dihydroorotate dehydrogenase electron transfer subunit:lactoylglutathione lyase:<-<-:1338094..1338341 248 gacttttcctccttaaattttaaggggaccagataaagaaaagaccttgctagtgcaaggcctcagttaaaatcgtacaacacaagagagcacacttaaaaagtctcctctagaaaattgtactattcttttatctgacaccttgtgagtctctctggactccccttaaaggttaaatttttactattatactctttcagctaaaaaaagtcaagtaaaaaacgaacattctacttgacttcaagaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_1359:SMT_1360|SMT_1359:SMT_1360:dihydroorotate dehydrogenase electron transfer subunit:lactoylglutathione lyase:<-<-:1338094..1338341 248 gacttttcctccttaaattttaaggggaccagataaagaaaagaccttgctagtgcaaggcctcagttaaaatcgtacaacacaagagagcacacttaaaaagtctcctctagaaaattgtactattcttttatctgacaccttgtgagtctctctggactccccttaaaggttaaatttttactattatactctttcagctaaaaaaagtcaagtaaaaaacgaacattctacttgacttcaagaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gacttttcctccttaaattttaaggggaccagataaagaaaagaccttgctagtgcaaggcctcagttaaaatcgtacaacacaagagagcacacttaaaaagtctcctctagaaaattgtactattcttttatctgacaccttgtgagtctctctggactccccttaaaggttaaatttttactattatactctttcagctaaaaaaagtcaagtaaaaaacgaacattctacttgacttcaagaaa Predict ORF larger than 30AA ================================================ gacttttcctccttaaattttaaggggaccagataaagaaaagaccttgctagtgcaaggcctcagttaaaatcgtacaacacaagagagcacacttaaaaagtctcctctagaaaattgtactattcttttatctgacaccttgtgagtctctctggactccccttaaaggttaaatttttactattatactctttcagctaaaaaaagtcaagtaaaaaacgaacattctacttgacttcaagaaa Predict Promoter with matrix: RpoD-15 score > 80================================================ Predict Promoter with matrix: RpoD-16 score > 80================================================ Predict Promoter with matrix: RpoD-17 score > 80================================================ PromScan Matrix: RpoD-17 Strand: - Score: 88 Start: 186 End: 215 .........................................................................................................................................................................................CTTGACTTTTTTTAGCTGAAAGAGTATAAT................................. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ gacttttcctccttaaattttaaggggaccagataaagaaaagaccttgctagtgcaaggcctcagttaaaatcgtacaacacaagagagcacacttaaaaagtctcctctagaaaattgtactattcttttatctgacaccttgtgagtctctctggactccccttaaaggttaaatttttactattatactctttcagctaaaaaaagtcaagtaaaaaacgaacattctacttgacttcaagaaa Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 100 HP_score: -10.0 Tail_Score: -5.06016 Start: 43 End: 62 Full_Region: tacgattttaactga ggccttgc acta gcaaggtc ttttctttatctggt ..........................................ggccttgcactagcaaggtc.......................................................................................................................................................................................... Find igs database================================================ Query_seq: SMT_1359:SMT_1360|SMT_1359:SMT_1360:dihydroorotate dehydrogenase electron transfer subunit:lactoylglutathione lyase:<-<-:1338094..1338341 248 gacttttcctccttaaattttaaggggaccagataaagaaaagaccttgctagtgcaaggcctcagttaaaatcgtacaacacaagagagcacacttaaaaagtctcctctagaaaattgtactattcttttatctgacaccttgtgagtctctctggactccccttaaaggttaaatttttactattatactctttcagctaaaaaaagtcaagtaaaaaacgaacattctacttgacttcaagaaa Intra-Species Hit: Count: 1 Min: 1 Max: 248 Len: 248 Subject: smit_SMT_1359_SMT_1360|dihydroorotate dehydrogenase electron transfer subunit:lactoylglutathione lyase|NEGATIVE:NEGATIVE|[1338094,1338341]|248 HSP 1 e-value: 1.0E-125 bit: 450.0 Len: 248 Query Start:1 Query End:248 Subject Strand: POSITIVE Subject Start: 1 Subject End: 248 gacttttcctccttaaattttaaggggaccagataaagaaaagaccttgctagtgcaaggcctcagttaaaatcgtacaacacaagagagcacacttaaaaagtctcctctagaaaattgtactattcttttatctgacaccttgtgagtctctctggactccccttaaaggttaaatttttactattatactctttcagctnnnnnnngtcaagtaaaaaacgaacattctacttgacttcaagaaa gacttttcctccttaaattttaaggggaccagataaagaaaagaccttgctagtgcaaggcctcagttaaaatcgtacaacacaagagagcacacttaaaaagtctcctctagaaaattgtactattcttttatctgacaccttgtgagtctctctggactccccttaaaggttaaatttttactattatactctttcagctaaaaaaagtcaagtaaaaaacgaacattctacttgacttcaagaaa Inter-species Hit: Count: 3 Min: 2 Max: 241 Len: 240 Subject: NC_008533_SPD_0850_SPD_0851|lactoylglutathione lyase:dihydroorotate dehydrogenase electron transfer subunit|POSITIVE:POSITIVE|[864461,864709]|249 HSP 1 e-value: 1.0E-102 bit: 371.0 Len: 240 Query Start:2 Query End:241 Subject Strand: NEGATIVE Subject Start: 9 Subject End: 248 .acttttcctccttaaattttaaggggaccagataaagaaaagaccttgctagtgcaaggcctcagttaaaatcgtacaacacaagagagcacacttaaaaagtctcctctagaaaattgtactattcttttatctgacaccttgtgagtctctctggactccccttaaaggttaaatttttactattatactctttcagctnnnnnnngtcaagtaaaaaacgaacattctacttgactt....... .acttttcctccttaaattttaaggggaccagataaagaaaagaccttgctagtgcaaggcctcagttaaaatcgtacaacacaagagagcacactcaaaaagtctcctctagaaaattgcactattcttttatctgacaccttgtgagtctctctggactccccttaaaggttgaatttttattagtatactctttcagctaaaaaaagtcaagtagaaaacgaatattctacttaactt....... Subject: NC_003098_spr0864_spr0865|Lactoylglutathione lyase:dihydroorotate dehydrogenase electron transfer subunit|POSITIVE:POSITIVE|[856931,857179]|249 HSP 1 e-value: 1.0E-102 bit: 371.0 Len: 240 Query Start:2 Query End:241 Subject Strand: NEGATIVE Subject Start: 9 Subject End: 248 .acttttcctccttaaattttaaggggaccagataaagaaaagaccttgctagtgcaaggcctcagttaaaatcgtacaacacaagagagcacacttaaaaagtctcctctagaaaattgtactattcttttatctgacaccttgtgagtctctctggactccccttaaaggttaaatttttactattatactctttcagctnnnnnnngtcaagtaaaaaacgaacattctacttgactt....... .acttttcctccttaaattttaaggggaccagataaagaaaagaccttgctagtgcaaggcctcagttaaaatcgtacaacacaagagagcacactcaaaaagtctcctctagaaaattgcactattcttttatctgacaccttgtgagtctctctggactccccttaaaggttgaatttttattagtatactctttcagctaaaaaaagtcaagtagaaaacgaatattctacttaactt....... Subject: NC_003028_SP_0962_SP_0963|lactoylglutathione lyase:dihydroorotate dehydrogenase electron transfer subunit|POSITIVE:POSITIVE|[908955,909251]|297 HSP 1 e-value: 2.0E-99 bit: 363.0 Len: 240 Query Start:2 Query End:241 Subject Strand: NEGATIVE Subject Start: 9 Subject End: 248 .acttttcctccttaaattttaaggggaccagataaagaaaagaccttgctagtgcaaggcctcagttaaaatcgtacaacacaagagagcacacttaaaaagtctcctctagaaaattgtactattcttttatctgacaccttgtgagtctctctggactccccttaaaggttaaatttttactattatactctttcagctnnnnnnngtcaagtaaaaaacgaacattctacttgactt....... .acttttcctccttaaattttaaggggaccagataaagaaaagaccttgctagtgcaaggcctcagttaaaatcgtacaacacaagagagcacactcaaaaagtctcctctagaaaattgcaccattcttttatctgacaccttgtgagtctctctggactccccttaaaggttgaatttttattagtatactctttcagctaaaaaaagtcaagtagaaaacgaatattctacttaactt....... Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ ACUUUUCCUCCUUAAAUUUUAAGGGGACCAGAUAAAGAAAAGACCUUGCUAGUGCAAGGCCUCAGUUAAAAUCGUACAACACAAGAGAGCACACUUAAAAAGUCUCCUCUAGAAAAUUGUACUAUUCUUUUAUCUGACACCUUGUGAGUCUCUCUGGACUCCCCUUAAAGGUUAAAUUUUUACUAUUAUACUCUUUCAGCUAAAAAAAGUCAAGUAAAAAACGAACAUUCUACUUGACUU ...........((((.((((((((((..(((((((((((.((.((((((....)))))).))...........((((((......((((...(((.....)))...))))......))))))..))).))))))))..........(((((....))))))))))))))).))))...............................((((((((((.((........)).)))))))))) (-57.30) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAGUCAAGUAGAAUGUUCGUUUUUUACUUGACUUUUUUUAGCUGAAAGAGUAUAAUAGUAAAAAUUUAACCUUUAAGGGGAGUCCAGAGAGACUCACAAGGUGUCAGAUAAAAGAAUAGUACAAUUUUCUAGAGGAGACUUUUUAAGUGUGCUCUCUUGUGUUGUACGAUUUUAACUGAGGCCUUGCACUAGCAAGGUCUUUUCUUUAUCUGGUCCCCUUAAAAUUUAAGGAGGAAAAGU (((((((((((((........)))))))))))))......(((.....))).............(((((..((((((((((..(((((((.(((.....))).)).....((((((..(((((((.....((((.(.(((.....))).).)))).....)))))))..........((((((((((....)))))))))))))))).)))))))))))))))..))))).......... (-73.40) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 946 90 41 182 133 smit:SMT_1359|5end_dihydroorotate_dehydrogenase_electron_transfer_subunit_1338003..1338233_NEGATIVE 327 159 122 231 193 smit:SMT_434|5end_orotidine_5'-phosphate_decarboxylase_376107..376337_POSITIVE 290 179 131 124 70 smit:SMT_1221|5end_choline_binding_protein_A_1185539..1185769_NEGATIVE 283 73 36 216 171 smit:SMT_1149|5end_hypothetical_protein_1094270..1094500_NEGATIVE 280 167 133 122 84 smit:SMT_461|5end_mannose-6-phosphate_isomerase_399379..399609_POSITIVE 279 60 20 61 9 smit:SMT_941|5end_hypothetical_protein_893558..893788_NEGATIVE 279 85 48 184 146 smit:SMT_219|5end_phosphatidate_cytidylyltransferase_150922..151152_POSITIVE 274 81 41 68 26 smit:SMT_1162|5end_ATP-dependent_DNA_helicase_1108895..1109125_NEGATIVE 273 37 5 131 96 smit:SMT_1689|5end_PTS_enzyme,_maltose-and_glucose-specific,_factor_II_homologue_1671542..1671772_POSITIVE 269 67 22 230 172 smit:SMT_1605|5end_hypothetical_protein_1595406..1595636_POSITIVE 268 162 121 129 92 smit:SMT_908|5end_hypothetical_protein_857230..857460_NEGATIVE 267 63 28 72 39 smit:SMT_1446|5end_pneumococcal_vaccine_antigen_A_1429610..1429840_NEGATIVE 252 173 132 70 23 smit:SMT_2079|5end_single_strand_binding_protein_1980144..1980374_POSITIVE 247 68 21 54 10 smit:SMT_155|5end_hypothetical_protein_102704..102934_NEGATIVE 246 78 31 125 86 smit:SMT_2175|5end_hypothetical_protein_2045727..2045957_NEGATIVE 246 78 31 125 86 smit:SMT_2170|5end_hypothetical_protein_2042242..2042472_NEGATIVE 246 78 31 125 86 smit:SMT_2156|5end_hypothetical_protein_predicted_by_Glimmer/Critica_2030476..2030706_NEGATIVE 246 78 31 146 107 smit:SMT_2151|5end_hypothetical_protein_2025520..2025750_NEGATIVE 246 78 31 146 107 smit:SMT_2148|5end_hypothetical_protein_2023635..2023865_NEGATIVE 246 78 31 146 107 smit:SMT_2147|5end_hypothetical_protein_2022895..2023125_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 279 60 20 91 39 smit:SMT_942|3end_hypothetical_protein_893528..893678_NEGATIVE 273 37 5 112 77 smit:SMT_1688|3end_putative_N-acylglucosamine-6-phosphate_2-epimerase_1671603..1671753_POSITIVE 268 162 121 136 99 smit:SMT_909|3end_type_I_restriction_enzyme_M_protein_857223..857373_NEGATIVE 267 63 28 72 39 smit:SMT_1447|3end_hypothetical_protein_1429610..1429760_NEGATIVE 267 60 13 71 20 smit:SMT_1291|3end_hypothetical_protein_1254296..1254446_POSITIVE 262 166 122 101 49 smit:SMT_1723|3end_hypothetical_protein_1709724..1709874_POSITIVE 246 78 31 79 40 smit:SMT_73|3end_peptidase,_M16_family_-84..66_NEGATIVE 245 60 20 34 4 smit:SMT_1011|3end_xanthine_phosphoribosyltransferase_949234..949384_POSITIVE 245 60 11 145 90 smit:SMT_813|3end_acetyltransferase,_GNAT_family_721867..722017_NEGATIVE 242 69 24 78 13 smit:SMT_960|3end_putative_esterase_906126..906276_NEGATIVE 242 150 101 97 39 smit:SMT_459|3end_hypothetical_protein_397690..397840_POSITIVE 239 67 21 50 13 smit:SMT_265|3end_DNA-binding_protein_203879..204029_NEGATIVE 237 67 28 84 50 smit:SMT_578|3end_lipoprotein_signal_peptidase_496602..496752_POSITIVE 236 89 42 64 11 smit:SMT_387|3end_hypothetical_protein_predicted_by_Glimmer/Critica_321118..321268_POSITIVE 236 64 22 140 113 smit:SMT_269|3end_phospho-N-acetylmuramoyl-pentapeptide-transferas_e_208785..208935_POSITIVE 235 127 90 64 24 smit:SMT_1497|3end_acetyltransferase,_GNAT_family_1482030..1482180_POSITIVE 235 64 21 72 8 smit:SMT_747|3end_transcriptional_regulator,_LytR_family_651343..651493_NEGATIVE 234 59 28 81 44 smit:SMT_1386|3end_phosphoenolpyruvate-protein_phosphotransferase_1364610..1364760_POSITIVE 232 144 103 106 73 smit:SMT_1572|3end_excinuclease_ABC_subunit_B_1566470..1566620_POSITIVE 228 90 42 71 16 smit:SMT_1956|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1889537..1889687_NEGATIVE