Origin IGS: atactagtctcctattaaaattatagcactttgaaaatatgatatcatgtaacaaaacagatatgttttattaagatgtcggaaaagtaatagttcttaaaattaaaaaactgaaaaattgataaacctagtccaaaaagttatattaagggaattctttatggtgtaaaataatcgtagaaaatcagatgggaggaaaaac .........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 gtttttcctcccatctgattttctacgattattttacaccataaagaattcccttaatataactttttggactaggtttatcaatttttcagttttttaattttaagaactattacttttccgacatcttaataaaacatatctgttttgttacatgatatcatattttcaaagtgctataattttaataggagactagtat Mask Tandem Repeat Region ================================================ atactagtctcctattaaaattatagcactttgaaaatatgatatcatgtaacaaaacagatatgttttattaagatgtcggaaaagtaatagttcttaaaattaaaaaactgaaaaattgataaacctagtccaaaaagttatattaagggaattctttatggtgtaaaataatcgtagaaaatcagatgggaggaaaaac Find is-nt database================================================ Query_seq: SMT_253:SMT_254|SMT_253:SMT_254:sensor histidine kinase:K02025 multiple sugar transport system permease protein:<-->:190734..190935 202 atactagtctcctattaaaattatagcactttgaaaatatgatatcatgtaacaaaacagatatgttttattaagatgtcggaaaagtaatagttcttaaaattaaaaaactgaaaaattgataaacctagtccaaaaagttatattaagggaattctttatggtgtaaaataatcgtagaaaatcagatgggaggaaaaac Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_253:SMT_254|SMT_253:SMT_254:sensor histidine kinase:K02025 multiple sugar transport system permease protein:<-->:190734..190935 202 atactagtctcctattaaaattatagcactttgaaaatatgatatcatgtaacaaaacagatatgttttattaagatgtcggaaaagtaatagttcttaaaattaaaaaactgaaaaattgataaacctagtccaaaaagttatattaagggaattctttatggtgtaaaataatcgtagaaaatcagatgggaggaaaaac Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_253:SMT_254|SMT_253:SMT_254:sensor histidine kinase:K02025 multiple sugar transport system permease protein:<-->:190734..190935 202 atactagtctcctattaaaattatagcactttgaaaatatgatatcatgtaacaaaacagatatgttttattaagatgtcggaaaagtaatagttcttaaaattaaaaaactgaaaaattgataaacctagtccaaaaagttatattaagggaattctttatggtgtaaaataatcgtagaaaatcagatgggaggaaaaac Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 atactagtctcctattaaaattatagcactttgaaaatatgatatcatgtaacaaaacagatatgttttattaagatgtcggaaaagtaatagttcttaaaattaaaaaactgaaaaattgataaacctagtccaaaaagttatattaagggaattctttatggtgtaaaataatcgtagaaaatcagatgggaggaaaaac Predict ORF larger than 30AA ================================================ atactagtctcctattaaaattatagcactttgaaaatatgatatcatgtaacaaaacagatatgttttattaagatgtcggaaaagtaatagttcttaaaattaaaaaactgaaaaattgataaacctagtccaaaaagttatattaagggaattctttatggtgtaaaataatcgtagaaaatcagatgggaggaaaaac 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: 84 Start: 118 End: 147 .....................................................................................................................ATTGATAAACCTAGTCCAAAAAGTTATATT....................................................... PromScan Matrix: RpoD-17 Strand: - Score: 82 Start: 20 End: 49 ...................CATGATATCATATTTTCAAAGTGCTATAAT......................................................................................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ atactagtctcctattaaaattatagcactttgaaaatatgatatcatgtaacaaaacagatatgttttattaagatgtcggaaaagtaatagttcttaaaattaaaaaactgaaaaattgataaacctagtccaaaaagttatattaagggaattctttatggtgtaaaataatcgtagaaaatcagatgggaggaaaaac Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SMT_253:SMT_254|SMT_253:SMT_254:sensor histidine kinase:K02025 multiple sugar transport system permease protein:<-->:190734..190935 202 atactagtctcctattaaaattatagcactttgaaaatatgatatcatgtaacaaaacagatatgttttattaagatgtcggaaaagtaatagttcttaaaattaaaaaactgaaaaattgataaacctagtccaaaaagttatattaagggaattctttatggtgtaaaataatcgtagaaaatcagatgggaggaaaaac Intra-Species Hit: Count: 1 Min: 1 Max: 202 Len: 202 Subject: smit_SMT_253_SMT_254|sensor histidine kinase:K02025 multiple sugar transport system permease protein|NEGATIVE:POSITIVE|[190734,190935]|202 HSP 1 e-value: 3.0E-39 bit: 163.0 Len: 82 Query Start:1 Query End:82 Subject Strand: POSITIVE Subject Start: 1 Subject End: 82 atactagtctcctattaaaattatagcactttgaaaatatgatatcatgtaacaaaacagatatgttttattaagatgtcgg........................................................................................................................ atactagtctcctattaaaattatagcactttgaaaatatgatatcatgtaacaaaacagatatgttttattaagatgtcgg........................................................................................................................ HSP 2 e-value: 6.0E-28 bit: 125.0 Len: 63 Query Start:140 Query End:202 Subject Strand: POSITIVE Subject Start: 140 Subject End: 202 ...........................................................................................................................................gttatattaagggaattctttatggtgtaaaataatcgtagaaaatcagatgggaggaaaaac ...........................................................................................................................................gttatattaagggaattctttatggtgtaaaataatcgtagaaaatcagatgggaggaaaaac Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUACUAGUCUCCUAUUAAAAUUAUAGCACUUUGAAAAUAUGAUAUCAUGUAACAAAACAGAUAUGUUUUAUUAAGAUGUCGGAAAAGUAAUAGUUCUUAAAAUUAAAAAACUGAAAAAUUGAUAAACCUAGUCCAAAAAGUUAUAUUAAGGGAAUUCUUUAUGGUGUAAAAUAAUCGUAGAAAAUCAGAUGGGAGGAAAAAC .......(((((((((.....((((((..((((......(((((((...(((.((((((....)))))).))).))))))).........(((((.((.......)).)))))....................))))..))))))............((((((((........))))))))......)))))))))...... (-33.80) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GUUUUUCCUCCCAUCUGAUUUUCUACGAUUAUUUUACACCAUAAAGAAUUCCCUUAAUAUAACUUUUUGGACUAGGUUUAUCAAUUUUUCAGUUUUUUAAUUUUAAGAACUAUUACUUUUCCGACAUCUUAAUAAAACAUAUCUGUUUUGUUACAUGAUAUCAUAUUUUCAAAGUGCUAUAAUUUUAAUAGGAGACUAGUAU ..............(((.(((((((.((((((..(((.(((.((((................)))).)))........(((((.......(((((((.......)))))))..................((((((((((....))))))))))..))))).............)))..))))))....))))))).)))... (-26.19) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 713 50 1 141 92 smit:SMT_253|5end_sensor_histidine_kinase_190643..190873_NEGATIVE 223 200 162 208 169 smit:SMT_810|5end_oxidoreductase_720015..720245_POSITIVE 215 199 160 203 164 smit:SMT_1958|5end_tryptophan_synthase,_beta_subunit_1890980..1891210_POSITIVE 215 199 160 160 121 smit:SMT_466|5end_UDP-N-acetylmuramoylalanine--D-glutamate_ligase_403645..403875_POSITIVE 205 180 132 146 101 smit:SMT_1653|5end_hydrolase_1641328..1641558_POSITIVE 204 167 121 155 98 smit:SMT_1262|5end_ribosomal_protein_L11_methyltransferase_1227152..1227382_POSITIVE 204 98 59 155 117 smit:SMT_649|5end_NADP-dependent_glyceraldehyde-3-phosphate_dehydrogenase_557351..557581_NEGATIVE 188 165 129 182 139 smit:SMT_1050|5end_transcriptional_regulator_PlcR,_putative_990380..990610_NEGATIVE 183 197 157 69 30 smit:SMT_430|5end_hypothetical_protein_371830..372060_POSITIVE 181 166 128 230 186 smit:SMT_447|5end_ABC-type_cobalt_transport_system,_permease_component_CbiQ_related_transporter_386257..386487_POSITIVE 180 167 130 80 43 smit:SMT_1264|5end_oligoendopeptidase_F_1228858..1229088_POSITIVE 179 200 151 152 92 smit:SMT_871|5end_K03311_branched-chain_amino_acid:cation_transporter,_LIVCS_family_820160..820390_NEGATIVE 179 200 163 111 76 smit:SMT_535|5end_hypothetical_protein_454215..454445_POSITIVE 179 200 151 152 92 smit:SMT_386|5end_branched-chain_amino_acid_transport_system_II_carrier_protein_320353..320583_POSITIVE 178 153 111 66 25 smit:SMT_1300|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1262844..1263074_NEGATIVE 178 199 155 207 155 smit:SMT_205|5end_K02012_iron(III)_transport_system_substrate-binding_protein_137174..137404_NEGATIVE 177 194 163 78 45 smit:SMT_862|5end_hypothetical_protein_predicted_by_Glimmer/Critica_808587..808817_POSITIVE 175 195 160 230 195 smit:SMT_1154|5end_tryptophanyl-tRNA_synthetase_1098921..1099151_NEGATIVE 172 197 157 117 70 smit:SMT_1045|5end_cochaperonin_GroES_987582..987812_NEGATIVE 169 88 48 188 146 smit:SMT_1445|5end_hypothetical_protein_1428922..1429152_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 215 199 160 151 112 smit:SMT_2008|3end_K07485_transposase_1928165..1928315_NEGATIVE 215 199 160 142 103 smit:SMT_465|3end_oxidoreductase,_short_chain_dehydrogenase/reductase_family_protein_403707..403857_POSITIVE 205 180 132 146 101 smit:SMT_1652|3end_Cof_family_protein_1641408..1641558_POSITIVE 201 200 151 59 13 smit:SMT_831|3end_transcriptional_activator,_putative_774355..774505_POSITIVE 186 168 140 50 15 smit:SMT_638|3end_hypothetical_protein_543180..543330_NEGATIVE 183 85 41 70 30 smit:SMT_1864|3end_integral_membrane_protein_1827172..1827322_POSITIVE 183 197 157 49 10 smit:SMT_429|3end_K06207_GTP-binding_protein_371890..372040_POSITIVE 181 86 41 134 83 smit:SMT_1857|3end_hypothetical_protein_1821145..1821295_POSITIVE 180 167 130 69 32 smit:SMT_1263|3end_hypothetical_protein_1228927..1229077_POSITIVE 180 199 154 54 9 smit:SMT_1163|3end_hypothetical_protein_1109096..1109246_NEGATIVE 179 167 126 90 55 smit:SMT_872|3end_hypothetical_protein_820331..820481_NEGATIVE 179 167 126 90 55 smit:SMT_385|3end_hypothetical_protein_320262..320412_POSITIVE 178 98 57 48 6 smit:SMT_2086|3end_hypothetical_protein_1983331..1983481_NEGATIVE 178 196 151 102 67 smit:SMT_1528|3end_K03310_alanine_or_glycine:cation_symporter,_AGCS_family_1511324..1511474_NEGATIVE 173 165 126 142 104 smit:SMT_1866|3end_extramembranal_protein_1827939..1828089_POSITIVE 172 197 157 61 14 smit:SMT_1046|3end_chaperonin_GroEL_987638..987788_NEGATIVE 171 188 145 55 15 smit:SMT_436|3end_amidase_related_to_nicotinamidase_377575..377725_NEGATIVE 169 88 48 114 72 smit:SMT_1446|3end_pneumococcal_vaccine_antigen_A_1428996..1429146_NEGATIVE 167 97 61 151 116 smit:SMT_987|3end_N-acetylmannosamine_kinase_/_transcriptional_regulator_931655..931805_NEGATIVE 166 83 41 137 87 smit:SMT_957|3end_UDP-glucose_4-epimerase_904776..904926_NEGATIVE