Origin IGS: aatagagtcattctgtataaaaaggagcttgaaatcaatagatagctccttttttgaatgaaaaaaatatttttaagataaaaattcaaaaaaacacttgacaagcaacttggatagagttataattatacaaaattaacagagaggtcgtttattt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aaataaacgacctctctgttaattttgtataattataactctatccaagttgcttgtcaagtgtttttttgaatttttatcttaaaaatatttttttcattcaaaaaaggagctatctattgatttcaagctcctttttatacagaatgactctatt Mask Tandem Repeat Region ================================================ aatagagtcattctgtataaaaaggagcttgaaatcaatagatagctccttttttgaatgaaaaaaatatttttaagataaaaattcaaaaaaacacttgacaagcaacttggatagagttataattatacaaaattaacagagaggtcgtttattt Find is-nt database================================================ Query_seq: SMT_1463:SMT_1464|SMT_1463:SMT_1464:phosphate transport system protein PhoU:K02030 polar amino acid transport system substrate-binding protein:->->:1444704..1444860 157 aatagagtcattctgtataaaaaggagcttgaaatcaatagatagctccttttttgaatgaaaaaaatatttttaagataaaaattcaaaaaaacacttgacaagcaacttggatagagttataattatacaaaattaacagagaggtcgtttattt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_1463:SMT_1464|SMT_1463:SMT_1464:phosphate transport system protein PhoU:K02030 polar amino acid transport system substrate-binding protein:->->:1444704..1444860 157 aatagagtcattctgtataaaaaggagcttgaaatcaatagatagctccttttttgaatgaaaaaaatatttttaagataaaaattcaaaaaaacacttgacaagcaacttggatagagttataattatacaaaattaacagagaggtcgtttattt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_1463:SMT_1464|SMT_1463:SMT_1464:phosphate transport system protein PhoU:K02030 polar amino acid transport system substrate-binding protein:->->:1444704..1444860 157 aatagagtcattctgtataaaaaggagcttgaaatcaatagatagctccttttttgaatgaaaaaaatatttttaagataaaaattcaaaaaaacacttgacaagcaacttggatagagttataattatacaaaattaacagagaggtcgtttattt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aatagagtcattctgtataaaaaggagcttgaaatcaatagatagctccttttttgaatgaaaaaaatatttttaagataaaaattcaaaaaaacacttgacaagcaacttggatagagttataattatacaaaattaacagagaggtcgtttattt Predict ORF larger than 30AA ================================================ Protein_Len: 34 Strand: - Start: 3 End: 104 .. L T M R Y L F S S S I L L Y S R K Q I F F I N K L Y F N L F V S S M ..................................................... aatagagtcattctgtataaaaaggagcttgaaatcaatagatagctccttttttgaatgaaaaaaatatttttaagataaaaattcaaaaaaacacttgacaagcaacttggatagagttataattatacaaaattaacagagaggtcgtttattt 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: 92 Start: 97 End: 126 ................................................................................................CTTGACAAGCAACTTGGATAGAGTTATAAT............................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ aatagagtcattctgtataaaaaggagcttgaaatcaatagatagctccttttttgaatgaaaaaaatatttttaagataaaaattcaaaaaaacacttgacaagcaacttggatagagttataattatacaaaattaacagagaggtcgtttattt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SMT_1463:SMT_1464|SMT_1463:SMT_1464:phosphate transport system protein PhoU:K02030 polar amino acid transport system substrate-binding protein:->->:1444704..1444860 157 aatagagtcattctgtataaaaaggagcttgaaatcaatagatagctccttttttgaatgaaaaaaatatttttaagataaaaattcaaaaaaacacttgacaagcaacttggatagagttataattatacaaaattaacagagaggtcgtttattt Intra-Species Hit: Count: 1 Min: 1 Max: 157 Len: 157 Subject: smit_SMT_1463_SMT_1464|phosphate transport system protein PhoU:K02030 polar amino acid transport system substrate-binding protein|POSITIVE:POSITIVE|[1444704,1444860]|157 HSP 1 e-value: 5.0E-28 bit: 125.0 Len: 63 Query Start:95 Query End:157 Subject Strand: POSITIVE Subject Start: 95 Subject End: 157 ..............................................................................................cacttgacaagcaacttggatagagttataattatacaaaattaacagagaggtcgtttattt ..............................................................................................cacttgacaagcaacttggatagagttataattatacaaaattaacagagaggtcgtttattt HSP 2 e-value: 3.0E-26 bit: 119.0 Len: 60 Query Start:1 Query End:60 Subject Strand: POSITIVE Subject Start: 1 Subject End: 60 aatagagtcattctgtataaaaaggagcttgaaatcaatagatagctccttttttgaatg................................................................................................. aatagagtcattctgtataaaaaggagcttgaaatcaatagatagctccttttttgaatg................................................................................................. Inter-species Hit: Count: 3 Min: 10 Max: 157 Len: 148 Subject: NC_008533_SPD_1226_SPD_1227|amino acid ABC transporter, amino acid-binding protein:phosphate transport system regulatory protein PhoU, putative|NEGATIVE:NEGATIVE|[1258962,1259117]|156 HSP 1 e-value: 2.0E-18 bit: 93.7 Len: 63 Query Start:95 Query End:157 Subject Strand: NEGATIVE Subject Start: 1 Subject End: 63 ..............................................................................................cacttgacaagcaacttggatagagttataattatacaaaattaacagagaggtcgtttattt ..............................................................................................cacttgacaagtaacttggatatcgttataattatacaaaattaacagagaggttgtttattt HSP 2 e-value: 9.0E-11 bit: 67.9 Len: 46 Query Start:10 Query End:55 Subject Strand: NEGATIVE Subject Start: 102 Subject End: 147 .........attctgtataaaaaggagcttgaaatcaatagatagctcctttttt...................................................................................................... .........attctgtataaaaaggagcttgaaatcaactgatggctcctttttt...................................................................................................... Subject: NC_003098_spr1251_spr1252|ABC transporter substrate-binding protein - glutamine-binding protein:Phosphate transport system regulatory protein|NEGATIVE:NEGATIVE|[1251431,1251586]|156 HSP 1 e-value: 2.0E-18 bit: 93.7 Len: 63 Query Start:95 Query End:157 Subject Strand: NEGATIVE Subject Start: 1 Subject End: 63 ..............................................................................................cacttgacaagcaacttggatagagttataattatacaaaattaacagagaggtcgtttattt ..............................................................................................cacttgacaagtaacttggatatcgttataattatacaaaattaacagagaggttgtttattt HSP 2 e-value: 9.0E-11 bit: 67.9 Len: 46 Query Start:10 Query End:55 Subject Strand: NEGATIVE Subject Start: 102 Subject End: 147 .........attctgtataaaaaggagcttgaaatcaatagatagctcctttttt...................................................................................................... .........attctgtataaaaaggagcttgaaatcaactgatggctcctttttt...................................................................................................... Subject: NC_003028_SP_1394_SP_1395|amino acid ABC transporter, amino acid-binding protein:phosphate transport system regulatory protein PhoU, putative|NEGATIVE:NEGATIVE|[1318863,1319018]|156 HSP 1 e-value: 2.0E-18 bit: 93.7 Len: 63 Query Start:95 Query End:157 Subject Strand: NEGATIVE Subject Start: 1 Subject End: 63 ..............................................................................................cacttgacaagcaacttggatagagttataattatacaaaattaacagagaggtcgtttattt ..............................................................................................cacttgacaagtaacttggatatcgttataattatacaaaattaacagagaggttgtttattt HSP 2 e-value: 2.0E-8 bit: 60.0 Len: 46 Query Start:10 Query End:55 Subject Strand: NEGATIVE Subject Start: 102 Subject End: 147 .........attctgtataaaaaggagcttgaaatcaatagatagctcctttttt...................................................................................................... .........attctgtataaaagggagcttgaaatcaactgatggctcctttttt...................................................................................................... Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUUCUGUAUAAAAAGGAGCUUGAAAUCAAUAGAUAGCUCCUUUUUUGAAUGAAAAAAAUAUUUUUAAGAUAAAAAUUCAAAAAAACACUUGACAAGCAACUUGGAUAGAGUUAUAAUUAUACAAAAUUAACAGAGAGGUCGUUUAUUU .((((((....(((((((((....(((....))))))))))))(((((((........................)))))))..(((.((...((((...))))...)).))).................))))))............. (-23.66) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAUAAACGACCUCUCUGUUAAUUUUGUAUAAUUAUAACUCUAUCCAAGUUGCUUGUCAAGUGUUUUUUUGAAUUUUUAUCUUAAAAAUAUUUUUUUCAUUCAAAAAAGGAGCUAUCUAUUGAUUUCAAGCUCCUUUUUAUACAGAAU .....................(((((((((((.................(((..((..((((((((((..((.......))..))))))))))....))..))).((((((((((((....)))....)))))))))))))))))))) (-27.30) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 270 53 11 231 198 smit:SMT_494|5end_K04767_acetoin_utilization_protein_AcuB_428155..428385_POSITIVE 227 51 13 72 34 smit:SMT_1909|5end_zinc_metalloprotease_ZmpB,_truncated_1856749..1856979_NEGATIVE 202 48 2 98 53 smit:SMT_1267|5end_hypothetical_protein_1231658..1231888_POSITIVE 197 52 15 190 154 smit:SMT_1924|5end_isoleucyl-tRNA_synthetase_1866188..1866418_POSITIVE 197 139 95 187 145 smit:SMT_1848|5end_K03458_nucleobase:cation_symporter-2,_NCS2_family_1813014..1813244_NEGATIVE 195 46 9 213 174 smit:SMT_1809|5end_MutT/NUDIX_family_protein_1784602..1784832_POSITIVE 194 45 14 114 76 smit:SMT_1901|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1850537..1850767_POSITIVE 194 46 4 177 148 smit:SMT_1217|5end_hypothetical_protein_1176603..1176833_NEGATIVE 194 96 64 219 180 smit:SMT_338|5end_heat-inducible_transcription_repressor_HrcA_276825..277055_POSITIVE 192 40 14 225 196 smit:SMT_2051|5end_enoyl-CoA_hydratase_1960639..1960869_NEGATIVE 191 46 3 155 108 smit:SMT_1803|5end_K03693_penicillin_binding_protein_1776804..1777034_POSITIVE 191 49 1 206 160 smit:SMT_940|5end_tRNA_pseudouridine_synthase_A_892764..892994_NEGATIVE 190 53 13 148 102 smit:SMT_942|5end_hypothetical_protein_894067..894297_NEGATIVE 189 110 86 28 5 smit:SMT_882|5end_acetyl_esterase_830441..830671_NEGATIVE 189 42 2 158 116 smit:SMT_690|5end_pyrimidine_regulatory_protein_602168..602398_NEGATIVE 187 62 27 36 3 smit:SMT_2048|5end_competence-specific_global_transcription_modulator_1958278..1958508_NEGATIVE 187 47 5 109 44 smit:SMT_1782|5end_hypothetical_protein_1759520..1759750_POSITIVE 185 71 32 207 155 smit:SMT_1341|5end_putative_cell_division_protein_1319115..1319345_NEGATIVE 185 52 14 199 154 smit:SMT_962|5end_putative_hemin_transport_system_ATP-binding_protein_fecE_908584..908814_NEGATIVE 185 52 16 151 116 smit:SMT_523|5end_K02004_447422..447652_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 269 52 11 83 38 smit:SMT_1463|3end_phosphate_transport_system_protein_PhoU_1444643..1444793_POSITIVE 266 42 4 60 19 smit:SMT_2087|3end_cadmium_efflux_system_accessory_protein_1984108..1984258_POSITIVE 266 42 4 60 19 smit:SMT_1234|3end_cadmium_efflux_system_accessory_protein_1195350..1195500_POSITIVE 222 45 3 72 29 smit:SMT_1801|3end_heavy_metal_translocating_P-type_ATPase_1775408..1775558_POSITIVE 210 48 1 90 37 smit:SMT_317|3end_K03625_N_utilization_substance_protein_B_257475..257625_NEGATIVE 206 58 14 117 60 smit:SMT_603|3end_hypothetical_protein_518532..518682_POSITIVE 202 48 2 134 89 smit:SMT_1266|3end_predicted_transcriptional_regulator_1231774..1231924_POSITIVE 201 40 4 119 76 smit:SMT_1152|3end_hypothetical_protein_1096400..1096550_NEGATIVE 195 46 9 83 44 smit:SMT_1808|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1784552..1784702_POSITIVE 194 45 14 117 79 smit:SMT_1900|3end_K03710_GntR_family_transcriptional_regulator_1850620..1850770_POSITIVE 194 46 4 92 63 smit:SMT_1218|3end_DNA_polymerase_I_1176688..1176838_NEGATIVE 191 49 1 107 61 smit:SMT_941|3end_hypothetical_protein_892863..893013_NEGATIVE 190 53 13 79 33 smit:SMT_943|3end_hypothetical_protein_894136..894286_NEGATIVE 187 140 97 70 23 smit:SMT_239|3end_hypothetical_protein_177788..177938_POSITIVE 185 52 16 149 114 smit:SMT_522|3end_K02003_447500..447650_POSITIVE 181 55 12 98 50 smit:SMT_1307|3end_glycerol_uptake_facilitator_protein_1272448..1272598_POSITIVE 181 48 1 151 102 smit:SMT_678|3end_K04096_DNA_processing_protein_587447..587597_NEGATIVE 181 38 2 63 23 smit:SMT_605|3end_DNA-binding_protein_HU_519257..519407_POSITIVE 178 140 93 64 19 smit:SMT_160|3end_folylpolyglutamate_synthase_105342..105492_POSITIVE 175 43 3 61 9 smit:SMT_2038|3end_zinc_metalloprotease_ZmpB,_truncated_1949615..1949765_POSITIVE