Origin IGS: tgaatttttaggggatgtgcactataccatcccctaaaactagatatagtcatctatgatgacgtcgtataggcgagttgatgggggagacaaccttttctcccttatcggcgctagcattttacaaaagaggagaaaataaaa .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 ttttattttctcctcttttgtaaaatgctagcgccgataagggagaaaaggttgtctcccccatcaactcgcctatacgacgtcatcatagatgactatatctagttttaggggatggtatagtgcacatcccctaaaaattca Mask Tandem Repeat Region ================================================ tgaatttttaggggatgtgcactataccatcccctaaaactagatatagtcatctatgatgacgtcgtataggcgagttgatgggggagacaaccttttctcccttatcggcgctagcattttacaaaagaggagaaaataaaa Find is-nt database================================================ Query_seq: SMT_188:SMT_189|SMT_188:SMT_189:LSU ribosomal protein L30P:50S ribosomal protein L15:->->:123828..123971 144 tgaatttttaggggatgtgcactataccatcccctaaaactagatatagtcatctatgatgacgtcgtataggcgagttgatgggggagacaaccttttctcccttatcggcgctagcattttacaaaagaggagaaaataaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_188:SMT_189|SMT_188:SMT_189:LSU ribosomal protein L30P:50S ribosomal protein L15:->->:123828..123971 144 tgaatttttaggggatgtgcactataccatcccctaaaactagatatagtcatctatgatgacgtcgtataggcgagttgatgggggagacaaccttttctcccttatcggcgctagcattttacaaaagaggagaaaataaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_188:SMT_189|SMT_188:SMT_189:LSU ribosomal protein L30P:50S ribosomal protein L15:->->:123828..123971 144 tgaatttttaggggatgtgcactataccatcccctaaaactagatatagtcatctatgatgacgtcgtataggcgagttgatgggggagacaaccttttctcccttatcggcgctagcattttacaaaagaggagaaaataaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tgaatttttaggggatgtgcactataccatcccctaaaactagatatagtcatctatgatgacgtcgtataggcgagttgatgggggagacaaccttttctcccttatcggcgctagcattttacaaaagaggagaaaataaaa Predict ORF larger than 30AA ================================================ tgaatttttaggggatgtgcactataccatcccctaaaactagatatagtcatctatgatgacgtcgtataggcgagttgatgggggagacaaccttttctcccttatcggcgctagcattttacaaaagaggagaaaataaaa 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================================================ tgaatttttaggggatgtgcactataccatcccctaaaactagatatagtcatctatgatgacgtcgtataggcgagttgatgggggagacaaccttttctcccttatcggcgctagcattttacaaaagaggagaaaataaaa Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SMT_188:SMT_189|SMT_188:SMT_189:LSU ribosomal protein L30P:50S ribosomal protein L15:->->:123828..123971 144 tgaatttttaggggatgtgcactataccatcccctaaaactagatatagtcatctatgatgacgtcgtataggcgagttgatgggggagacaaccttttctcccttatcggcgctagcattttacaaaagaggagaaaataaaa Intra-Species Hit: Count: 1 Min: 1 Max: 144 Len: 144 Subject: smit_SMT_188_SMT_189|LSU ribosomal protein L30P:50S ribosomal protein L15|POSITIVE:POSITIVE|[123828,123971]|144 HSP 1 e-value: 2.0E-76 bit: 285.0 Len: 144 Query Start:1 Query End:144 Subject Strand: POSITIVE Subject Start: 1 Subject End: 144 tgaatttttaggggatgtgcactataccatcccctaaaactagatatagtcatctatgatgacgtcgtataggcgagttgatgggggagacaaccttttctcccttatcggcgctagcattttacaaaagaggagaaaataaaa tgaatttttaggggatgtgcactataccatcccctaaaactagatatagtcatctatgatgacgtcgtataggcgagttgatgggggagacaaccttttctcccttatcggcgctagcattttacaaaagaggagaaaataaaa Inter-species Hit: Count: 3 Min: 1 Max: 144 Len: 144 Subject: NC_008533_SPD_0211_SPD_0212|ribosomal protein L30:ribosomal protein L15|POSITIVE:POSITIVE|[205012,205155]|144 HSP 1 e-value: 3.0E-69 bit: 262.0 Len: 144 Query Start:1 Query End:144 Subject Strand: POSITIVE Subject Start: 1 Subject End: 144 tgaatttttaggggatgtgcactataccatcccctaaaactagatatagtcatctatgatgacgtcgtataggcgagttgatgggggagacaaccttttctcccttatcggcgctagcattttacaaaagaggagaaaataaaa tgaagttttaggggatgtgcactgtaccatcccctaaaactagatatagtcatctatgatgacatcgtataggcgagttgatgggggagacaaccttttctcccttatcggcgctagcattttacaaaagaggagaaaataaaa Subject: NC_003098_spr0207_spr0208|50S ribosomal protein L30:50S ribosomal protein L15|POSITIVE:POSITIVE|[205012,205155]|144 HSP 1 e-value: 3.0E-69 bit: 262.0 Len: 144 Query Start:1 Query End:144 Subject Strand: POSITIVE Subject Start: 1 Subject End: 144 tgaatttttaggggatgtgcactataccatcccctaaaactagatatagtcatctatgatgacgtcgtataggcgagttgatgggggagacaaccttttctcccttatcggcgctagcattttacaaaagaggagaaaataaaa tgaagttttaggggatgtgcactgtaccatcccctaaaactagatatagtcatctatgatgacatcgtataggcgagttgatgggggagacaaccttttctcccttatcggcgctagcattttacaaaagaggagaaaataaaa Subject: NC_003028_SP_0228_SP_0229|50S ribosomal protein L30:50S ribosomal protein L15|POSITIVE:POSITIVE|[202503,202646]|144 HSP 1 e-value: 3.0E-69 bit: 262.0 Len: 144 Query Start:1 Query End:144 Subject Strand: POSITIVE Subject Start: 1 Subject End: 144 tgaatttttaggggatgtgcactataccatcccctaaaactagatatagtcatctatgatgacgtcgtataggcgagttgatgggggagacaaccttttctcccttatcggcgctagcattttacaaaagaggagaaaataaaa tgaagttttaggggatgtgcactgtaccatcccctaaaactagatatagtcatctatgatgacatcgtataggcgagttgatgggggagacaaccttttctcccttatcggcgctagcattttacaaaagaggagaaaataaaa Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGAAUUUUUAGGGGAUGUGCACUAUACCAUCCCCUAAAACUAGAUAUAGUCAUCUAUGAUGACGUCGUAUAGGCGAGUUGAUGGGGGAGACAACCUUUUCUCCCUUAUCGGCGCUAGCAUUUUACAAAAGAGGAGAAAAUAAAA .....((((((((((((.(.......))))))))))))).........((((((...))))))...(((...((..((((((((((((((........))))))))))))))....))....)))................... (-49.00) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUUAUUUUCUCCUCUUUUGUAAAAUGCUAGCGCCGAUAAGGGAGAAAAGGUUGUCUCCCCCAUCAACUCGCCUAUACGACGUCAUCAUAGAUGACUAUAUCUAGUUUUAGGGGAUGGUAUAGUGCACAUCCCCUAAAAAUUCA ..........................(((((....(((..((((((........))))))..)))................((((((...)))))).....)))))(((((((((((((.....)).)))))))))))...... (-39.30) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 347 119 71 199 142 smit:SMT_821|5end_UDP-N-acetylmuramoylalanyl-D-glutamate--2,6-_diaminopimelate_ligase_732775..733005_POSITIVE 339 113 73 80 24 smit:SMT_1050|5end_transcriptional_regulator_PlcR,_putative_990380..990610_NEGATIVE 315 120 75 102 54 smit:SMT_1915|5end_pyridoxine_biosynthesis_protein_1860329..1860559_POSITIVE 308 88 49 54 9 smit:SMT_265|5end_DNA-binding_protein_204073..204303_NEGATIVE 297 89 46 211 159 smit:SMT_106|5end_hypothetical_protein_51441..51671_POSITIVE 294 102 64 231 189 smit:SMT_1611|5end_K05896_segregation_and_condensation_protein_A_1599305..1599535_POSITIVE 293 118 71 200 158 smit:SMT_1343|5end_O-methyltransferase_1320994..1321224_NEGATIVE 293 105 63 215 176 smit:SMT_840|5end_tRNA_nucleotidyltransferase_(CCA-adding_enzyme)_787261..787491_NEGATIVE 292 119 72 110 51 smit:SMT_562|5end_ATP-dependent_RNA_helicase,_DEAD/DEAH_box_family_480928..481158_NEGATIVE 286 86 54 38 7 smit:SMT_647|5end_DNA_gyrase,_A_subunit_554170..554400_NEGATIVE 285 119 71 68 5 smit:SMT_1872|5end_K03217_preprotein_translocase_YidC_subunit_1831764..1831994_NEGATIVE 285 112 72 55 16 smit:SMT_1508|5end_hypothetical_protein_1491568..1491798_NEGATIVE 285 120 71 58 13 smit:SMT_555|5end_K09015_Fe-S_cluster_assembly_protein_SufD_472271..472501_POSITIVE 283 119 71 170 113 smit:SMT_1897|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1848858..1849088_NEGATIVE 282 118 76 58 8 smit:SMT_1220|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1183775..1184005_NEGATIVE 281 112 71 76 36 smit:SMT_1622|5end_K03499_trk_system_potassium_uptake_protein_TrkA_1608243..1608473_POSITIVE 280 118 74 61 23 smit:SMT_1262|5end_ribosomal_protein_L11_methyltransferase_1227152..1227382_POSITIVE 280 118 72 55 14 smit:SMT_181|5end_50S_ribosomal_protein_L24_120125..120355_POSITIVE 278 89 44 170 122 smit:SMT_2034|5end_hydrolase,_haloacid_dehalogenase-like_family_1946671..1946901_POSITIVE 274 115 72 69 9 smit:SMT_929|5end_hypothetical_protein_883342..883572_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 328 39 6 85 52 smit:SMT_188|3end_LSU_ribosomal_protein_L30P_123767..123917_POSITIVE 307 110 63 90 41 smit:SMT_640|3end_PTS_system,_lactose-specific_IIBC_component_545099..545249_NEGATIVE 305 90 41 78 14 smit:SMT_1216|3end_hypothetical_protein_1175969..1176119_POSITIVE 289 105 81 142 111 smit:SMT_1998|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1922640..1922790_POSITIVE 285 112 72 53 14 smit:SMT_1509|3end_phosphopentomutase_1491570..1491720_NEGATIVE 285 90 48 69 22 smit:SMT_124|3end_hypothetical_protein_75590..75740_NEGATIVE 283 119 71 151 94 smit:SMT_1898|3end_aminotransferase_(class_V),_putative_1848877..1849027_NEGATIVE 281 90 48 77 28 smit:SMT_1471|3end_hypothetical_protein_1453442..1453592_NEGATIVE 278 120 71 149 94 smit:SMT_1945|3end_putative_dihydrolipoamide_S-acetyltransferase_1880646..1880796_POSITIVE 276 88 48 64 5 smit:SMT_1562|3end_hypothetical_protein_1554819..1554969_NEGATIVE 274 90 48 70 24 smit:SMT_1569|3end_dihydroxy-acid_dehydratase_1563068..1563218_POSITIVE 271 112 82 95 57 smit:SMT_1726|3end_tRNA_pseudouridine_synthase_B_1712453..1712603_POSITIVE 263 90 47 70 18 smit:SMT_1536|3end_trigger_factor_1520636..1520786_NEGATIVE 263 77 31 132 87 smit:SMT_218|3end_undecaprenyl_pyrophosphate_synthetase_150993..151143_POSITIVE 260 100 57 82 40 smit:SMT_915|3end_sucrose_operon_repressor_868619..868769_POSITIVE 260 80 31 134 84 smit:SMT_243|3end_PTS_system,_mannose-specific_IIC_component_180089..180239_NEGATIVE 259 100 57 82 40 smit:SMT_834|3end_hypothetical_protein_775517..775667_NEGATIVE 258 90 48 49 2 smit:SMT_1815|3end_K02035_peptide/nickel_transport_system_substrate-binding_protein_1788899..1789049_NEGATIVE 255 114 76 140 99 smit:SMT_1341|3end_putative_cell_division_protein_1317892..1318042_NEGATIVE 253 120 71 143 100 smit:SMT_1643|3end_2-isopropylmalate_synthase_1630772..1630922_POSITIVE