Origin IGS: aatatcctcgattctatctatcctatcaattataccatattttattccatttcagtagtctcacttatttaggctatttctagtagcttctctagtaaaaaaggctggaatttgtgaatcccaacctcttttcagtca .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tgactgaaaagaggttgggattcacaaattccagccttttttactagagaagctactagaaatagcctaaataagtgagactactgaaatggaataaaatatggtataattgataggatagatagaatcgaggatatt Mask Tandem Repeat Region ================================================ aatatcctcgattctatctatcctatcaattataccatattttattccatttcagtagtctcacttatttaggctatttctagtagcttctctagtaaaaaaggctggaatttgtgaatcccaacctcttttcagtca Find is-nt database================================================ Query_seq: SMT_1778:SMT_1779|SMT_1778:SMT_1779:ATP-dependent RNA helicase:hypothetical protein:<-<-:1755045..1755182 138 aatatcctcgattctatctatcctatcaattataccatattttattccatttcagtagtctcacttatttaggctatttctagtagcttctctagtaaaaaaggctggaatttgtgaatcccaacctcttttcagtca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_1778:SMT_1779|SMT_1778:SMT_1779:ATP-dependent RNA helicase:hypothetical protein:<-<-:1755045..1755182 138 aatatcctcgattctatctatcctatcaattataccatattttattccatttcagtagtctcacttatttaggctatttctagtagcttctctagtaaaaaaggctggaatttgtgaatcccaacctcttttcagtca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_1778:SMT_1779|SMT_1778:SMT_1779:ATP-dependent RNA helicase:hypothetical protein:<-<-:1755045..1755182 138 aatatcctcgattctatctatcctatcaattataccatattttattccatttcagtagtctcacttatttaggctatttctagtagcttctctagtaaaaaaggctggaatttgtgaatcccaacctcttttcagtca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aatatcctcgattctatctatcctatcaattataccatattttattccatttcagtagtctcacttatttaggctatttctagtagcttctctagtaaaaaaggctggaatttgtgaatcccaacctcttttcagtca Predict ORF larger than 30AA ================================================ aatatcctcgattctatctatcctatcaattataccatattttattccatttcagtagtctcacttatttaggctatttctagtagcttctctagtaaaaaaggctggaatttgtgaatcccaacctcttttcagtca Predict Promoter with matrix: RpoD-15 score > 80================================================ Predict Promoter with matrix: RpoD-16 score > 80================================================ Predict Promoter with matrix: RpoD-17 score > 80================================================ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ aatatcctcgattctatctatcctatcaattataccatattttattccatttcagtagtctcacttatttaggctatttctagtagcttctctagtaaaaaaggctggaatttgtgaatcccaacctcttttcagtca Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SMT_1778:SMT_1779|SMT_1778:SMT_1779:ATP-dependent RNA helicase:hypothetical protein:<-<-:1755045..1755182 138 aatatcctcgattctatctatcctatcaattataccatattttattccatttcagtagtctcacttatttaggctatttctagtagcttctctagtaaaaaaggctggaatttgtgaatcccaacctcttttcagtca Intra-Species Hit: Count: 1 Min: 1 Max: 138 Len: 138 Subject: smit_SMT_1778_SMT_1779|ATP-dependent RNA helicase:hypothetical protein|NEGATIVE:NEGATIVE|[1755045,1755182]|138 HSP 1 e-value: 7.0E-73 bit: 274.0 Len: 138 Query Start:1 Query End:138 Subject Strand: POSITIVE Subject Start: 1 Subject End: 138 aatatcctcgattctatctatcctatcaattataccatattttattccatttcagtagtctcacttatttaggctatttctagtagcttctctagtaaaaaaggctggaatttgtgaatcccaacctcttttcagtca aatatcctcgattctatctatcctatcaattataccatattttattccatttcagtagtctcacttatttaggctatttctagtagcttctctagtaaaaaaggctggaatttgtgaatcccaacctcttttcagtca Inter-species Hit: Count: 3 Min: 4 Max: 136 Len: 133 Subject: NC_008533_SPD_0662_SPD_0663|endonuclease/exonuclease/phosphatase family protein:ATP-dependent RNA helicase, DEAD/DEAH box family protein|POSITIVE:POSITIVE|[681953,682091]|139 HSP 1 e-value: 1.0E-46 bit: 186.0 Len: 133 Query Start:4 Query End:136 Subject Strand: NEGATIVE Subject Start: 3 Subject End: 136 ...atcctcgattctatctatcctatcaattataccatattttattccatttcagtagtctcacttatttaggctatttctagtagcttctctagtaa-aaaaggctggaatttgtgaatcccaacctcttttcagt.. ...atcctcgattctatctatcttatcaattataccatattttattccattacagtagtctcacttatttaggctatttccagtagcttctctagtaagaaaaggctggaattttatagttccaacctcttttcagt.. Subject: NC_003098_spr0669_spr0670|hypothetical protein:ATP-dependent RNA helicase|POSITIVE:POSITIVE|[674422,674560]|139 HSP 1 e-value: 1.0E-46 bit: 186.0 Len: 133 Query Start:4 Query End:136 Subject Strand: NEGATIVE Subject Start: 3 Subject End: 136 ...atcctcgattctatctatcctatcaattataccatattttattccatttcagtagtctcacttatttaggctatttctagtagcttctctagtaa-aaaaggctggaatttgtgaatcccaacctcttttcagt.. ...atcctcgattctatctatcttatcaattataccatattttattccattacagtagtctcacttatttaggctatttccagtagcttctctagtaagaaaaggctggaattttatagttccaacctcttttcagt.. Subject: NC_003028_SP_0760_SP_0761|hypothetical protein:ATP-dependent RNA helicase, DEAD/DEAH box family|POSITIVE:POSITIVE|[719761,719899]|139 HSP 1 e-value: 3.0E-44 bit: 178.0 Len: 133 Query Start:4 Query End:136 Subject Strand: NEGATIVE Subject Start: 3 Subject End: 136 ...atcctcgattctatctatcctatcaattataccatattttattccatttcagtagtctcacttatttaggctatttctagtagcttctctagtaa-aaaaggctggaatttgtgaatcccaacctcttttcagt.. ...atcctcgattctatctaccttatcaattataccatattttattccattacagtagtctcacttatttaggctatttccagtagcttctctagtaagaaaaggctggaattttatagttccaacctcttttcagt.. Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUCCUCGAUUCUAUCUAUCCUAUCAAUUAUACCAUAUUUUAUUCCAUUUCAGUAGUCUCACUUAUUUAGGCUAUUUCUAGUAGCUUCUCUAGUAAAAAAGGCUGGAAUUUGUGAAUCCCAACCUCUUUUCAGU .....................................(((((...((((((((......(((.....(((((((.....)))))))....))).......))))))))..))))).................. (-16.42) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ ACUGAAAAGAGGUUGGGAUUCACAAAUUCCAGCCUUUUUUACUAGAGAAGCUACUAGAAAUAGCCUAAAUAAGUGAGACUACUGAAAUGGAAUAAAAUAUGGUAUAAUUGAUAGGAUAGAUAGAAUCGAGGAU ....((((((((((((((((....)))))))))))))))).((...((..((((((.......((((....(((...((((..................))))...)))..)))).))).)))..)).))... (-26.27) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 845 130 81 224 175 smit:SMT_1778|5end_ATP-dependent_RNA_helicase_1754954..1755184_NEGATIVE 302 85 44 197 151 smit:SMT_1068|5end_ATP-dependent_DNA_helicase_RecG_1006891..1007121_POSITIVE 295 109 70 123 77 smit:SMT_1679|5end_hypothetical_protein_1662998..1663228_POSITIVE 294 112 71 206 149 smit:SMT_788|5end_hypothetical_protein_700319..700549_NEGATIVE 282 90 41 215 145 smit:SMT_1250|5end_hypothetical_protein_1211345..1211575_NEGATIVE 279 124 84 144 99 smit:SMT_1700|5end_diaminopimelate_decarboxylase_1682032..1682262_POSITIVE 277 46 1 146 97 smit:SMT_576|5end_transcriptional_regulator,_LysR_family_495157..495387_POSITIVE 259 127 89 182 144 smit:SMT_160|5end_folylpolyglutamate_synthase_104741..104971_POSITIVE 253 40 4 135 94 smit:SMT_1106|5end_ribonuclease_P_protein_component_1047972..1048202_NEGATIVE 253 108 69 62 11 smit:SMT_90|5end_DNA_polymerase_III_beta_subunit_21377..21607_POSITIVE 251 93 51 225 176 smit:SMT_83|5end_K07707_two-component_system,_AgrA_family,_response_regulator_AgrA_15295..15525_NEGATIVE 250 129 87 144 109 smit:SMT_236|5end_ribosomal_small_subunit_pseudouridine_synthase_A_174625..174855_POSITIVE 250 126 89 181 144 smit:SMT_161|5end_putative_folyl-polyglutamate_synthetase_105358..105588_POSITIVE 248 41 3 138 99 smit:SMT_1429|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1414725..1414955_POSITIVE 248 81 57 115 87 smit:SMT_467|5end_UDP-N-acetylglucosamine--N-acetylmuramyl-_(pentapeptide)_pyrophosphoryl-undecaprenol_N-acetylglucosamine_transferase_404329..404559_POSITIVE 245 130 82 85 32 smit:SMT_337|5end_hypothetical_protein_275539..275769_POSITIVE 243 126 95 187 160 smit:SMT_1397|5end_mutator_MutT_protein_1372727..1372957_POSITIVE 240 89 41 216 171 smit:SMT_1603|5end_K05832_putative_ABC_transport_system_permease_protein_1593374..1593604_POSITIVE 240 59 13 149 104 smit:SMT_905|5end_hypothetical_protein_predicted_by_Glimmer/Critica_853467..853697_NEGATIVE 240 130 88 105 63 smit:SMT_516|5end_hypothetical_protein_442847..443077_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 279 124 84 77 32 smit:SMT_1699|3end_purine_operon_repressor_1682045..1682195_POSITIVE 254 106 61 110 63 smit:SMT_1267|3end_hypothetical_protein_1232577..1232727_POSITIVE 253 40 4 118 77 smit:SMT_1107|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1047989..1048139_NEGATIVE 250 126 89 85 48 smit:SMT_160|3end_folylpolyglutamate_synthase_105342..105492_POSITIVE 248 81 57 48 20 smit:SMT_466|3end_UDP-N-acetylmuramoylalanine--D-glutamate_ligase_404342..404492_POSITIVE 245 130 82 88 35 smit:SMT_336|3end_hypothetical_protein_275622..275772_POSITIVE 238 38 5 108 72 smit:SMT_731|3end_hypothetical_protein_predicted_by_Glimmer/Critica_638387..638537_NEGATIVE 237 90 42 145 97 smit:SMT_690|3end_pyrimidine_regulatory_protein_601647..601797_NEGATIVE 234 94 54 151 107 smit:SMT_1432|3end_hypothetical_protein_1416752..1416902_NEGATIVE 224 106 61 68 18 smit:SMT_625|3end_50S_ribosomal_protein_L27_530400..530550_POSITIVE 222 129 84 82 26 smit:SMT_1268|3end_acetoin_reductase_1232655..1232805_NEGATIVE 221 130 85 82 31 smit:SMT_1805|3end_2,3,4,5-tetrahydropyridine-2-carboxylate_N-succinyltransferase,_putative_1781241..1781391_POSITIVE 221 130 85 82 31 smit:SMT_1634|3end_2,3,4,5-tetrahydropyridine-2-carboxylate_N-succinyltransferase,_putative_1621438..1621588_POSITIVE 221 112 83 87 58 smit:SMT_1609|3end_hypothetical_protein_1598654..1598804_POSITIVE 219 129 81 87 25 smit:SMT_1620|3end_hypothetical_protein_1606695..1606845_NEGATIVE 219 120 84 65 33 smit:SMT_1330|3end_hypothetical_protein_1305852..1306002_NEGATIVE 218 52 14 76 41 smit:SMT_1739|3end_hypothetical_protein_1721633..1721783_POSITIVE 218 58 12 56 4 smit:SMT_817|3end_aminotransferase_727533..727683_NEGATIVE 218 50 2 126 76 smit:SMT_566|3end_K07282_poly-gamma-glutamate_synthesis_protein_(capsule_biosynthesis_protein)_484903..485053_POSITIVE 216 128 86 69 17 smit:SMT_1738|3end_peptidyl-prolyl_cis-trans_isomerase_1721341..1721491_POSITIVE