Origin IGS: tcagtcctcactctagaaggaagtcacttagtggcttccttttgtctttagaaaacacctctaagtatggtaaaatagtaggagaataatgtgaggaaaatga .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tcattttcctcacattattctcctactattttaccatacttagaggtgttttctaaagacaaaaggaagccactaagtgacttccttctagagtgaggactga Mask Tandem Repeat Region ================================================ tcagtcctcactctagaaggaagtcacttagtggcttccttttgtctttagaaaacacctctaagtatggtaaaatagtaggagaataatgtgaggaaaatga Find is-nt database================================================ Query_seq: SMT_231:SMT_232|SMT_231:SMT_232:translation elongation factor G:DNA polymerase III, alpha subunit, Gram-positive type:->->:168283..168385 103 tcagtcctcactctagaaggaagtcacttagtggcttccttttgtctttagaaaacacctctaagtatggtaaaatagtaggagaataatgtgaggaaaatga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_231:SMT_232|SMT_231:SMT_232:translation elongation factor G:DNA polymerase III, alpha subunit, Gram-positive type:->->:168283..168385 103 tcagtcctcactctagaaggaagtcacttagtggcttccttttgtctttagaaaacacctctaagtatggtaaaatagtaggagaataatgtgaggaaaatga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_231:SMT_232|SMT_231:SMT_232:translation elongation factor G:DNA polymerase III, alpha subunit, Gram-positive type:->->:168283..168385 103 tcagtcctcactctagaaggaagtcacttagtggcttccttttgtctttagaaaacacctctaagtatggtaaaatagtaggagaataatgtgaggaaaatga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tcagtcctcactctagaaggaagtcacttagtggcttccttttgtctttagaaaacacctctaagtatggtaaaatagtaggagaataatgtgaggaaaatga Predict ORF larger than 30AA ================================================ tcagtcctcactctagaaggaagtcacttagtggcttccttttgtctttagaaaacacctctaagtatggtaaaatagtaggagaataatgtgaggaaaatga 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================================================ tcagtcctcactctagaaggaagtcacttagtggcttccttttgtctttagaaaacacctctaagtatggtaaaatagtaggagaataatgtgaggaaaatga Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 78 HP_score: -9.7 Tail_Score: -3.32844 Start: 19 End: 39 Full_Region: tttctaaagacaaaa ggaagccac taa gtgacttcc ttctagagtgaggac ..................ggaagccactaagtgacttcc................................................................ Find igs database================================================ Query_seq: SMT_231:SMT_232|SMT_231:SMT_232:translation elongation factor G:DNA polymerase III, alpha subunit, Gram-positive type:->->:168283..168385 103 tcagtcctcactctagaaggaagtcacttagtggcttccttttgtctttagaaaacacctctaagtatggtaaaatagtaggagaataatgtgaggaaaatga Intra-Species Hit: Count: 1 Min: 1 Max: 103 Len: 103 Subject: smit_SMT_231_SMT_232|translation elongation factor G:DNA polymerase III, alpha subunit, Gram-positive type|POSITIVE:POSITIVE|[168283,168385]|103 HSP 1 e-value: 4.0E-52 bit: 204.0 Len: 103 Query Start:1 Query End:103 Subject Strand: POSITIVE Subject Start: 1 Subject End: 103 tcagtcctcactctagaaggaagtcacttagtggcttccttttgtctttagaaaacacctctaagtatggtaaaatagtaggagaataatgtgaggaaaatga tcagtcctcactctagaaggaagtcacttagtggcttccttttgtctttagaaaacacctctaagtatggtaaaatagtaggagaataatgtgaggaaaatga Inter-species Hit: Count: 3 Min: 4 Max: 103 Len: 100 Subject: NC_008533_SPD_0253_SPD_0254|translation elongation factor G:DNA polymerase III, alpha subunit, Gram-positive type|POSITIVE:POSITIVE|[250972,251074]|103 HSP 1 e-value: 3.0E-43 bit: 174.0 Len: 100 Query Start:4 Query End:103 Subject Strand: POSITIVE Subject Start: 4 Subject End: 103 ...gtcctcactctagaaggaagtcacttagtggcttccttttgtctttagaaaacacctctaagtatggtaaaatagtaggagaataatgtgaggaaaatga ...gtcctcactctagaaggaagtcacttagtggcttccttttgtctttagaaaatacctctaaatatggtaaaatagtagaagaataatgtgaggaaaatga Subject: NC_003098_spr0250_spr0251|elongation factor EF-2:DNA polymerase III subunit alpha|POSITIVE:POSITIVE|[250971,251073]|103 HSP 1 e-value: 3.0E-43 bit: 174.0 Len: 100 Query Start:4 Query End:103 Subject Strand: POSITIVE Subject Start: 4 Subject End: 103 ...gtcctcactctagaaggaagtcacttagtggcttccttttgtctttagaaaacacctctaagtatggtaaaatagtaggagaataatgtgaggaaaatga ...gtcctcactctagaaggaagtcacttagtggcttccttttgtctttagaaaatacctctaaatatggtaaaatagtagaagaataatgtgaggaaaatga Subject: NC_003028_SP_0273_SP_0274|elongation factor EF-2:DNA polymerase III subunit alpha|POSITIVE:POSITIVE|[250515,250617]|103 HSP 1 e-value: 3.0E-43 bit: 174.0 Len: 100 Query Start:4 Query End:103 Subject Strand: POSITIVE Subject Start: 4 Subject End: 103 ...gtcctcactctagaaggaagtcacttagtggcttccttttgtctttagaaaacacctctaagtatggtaaaatagtaggagaataatgtgaggaaaatga ...gtcctcactctagaaggaagtcacttagtggcttccttttgtctttagaaaatacctctaaatatggtaaaatagtagaagaataatgtgaggaaaatga Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GUCCUCACUCUAGAAGGAAGUCACUUAGUGGCUUCCUUUUGUCUUUAGAAAACACCUCUAAGUAUGGUAAAAUAGUAGGAGAAUAAUGUGAGGAAAAUGA .(((((((..((((((((((((((...))))))))))))))..............((((.(.(((......))).).))))......)))))))...... (-34.10) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UCAUUUUCCUCACAUUAUUCUCCUACUAUUUUACCAUACUUAGAGGUGUUUUCUAAAGACAAAAGGAAGCCACUAAGUGACUUCCUUCUAGAGUGAGGAC ......(((((((......(.(((.(((............)))))).)..............(((((((.(((...))).))))))).....))))))). (-24.60) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 343 47 2 71 18 smit:SMT_1854|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1818375..1818605_POSITIVE 284 46 9 108 63 smit:SMT_516|5end_hypothetical_protein_442847..443077_NEGATIVE 278 48 1 211 153 smit:SMT_407|5end_para-aminobenzoate_synthetase_component_I_/_4-amino-4-deoxychorismate_lyase_351365..351595_POSITIVE 265 50 2 221 179 smit:SMT_1626|5end_undecaprenyl-diphosphatase_1616028..1616258_NEGATIVE 262 80 31 75 16 smit:SMT_1697|5end_hypothetical_protein_1678846..1679076_POSITIVE 252 95 61 176 133 smit:SMT_1545|5end_choline-binding_protein_1530026..1530256_NEGATIVE 249 49 2 53 3 smit:SMT_1069|5end_acetyl_xylan_esterase,_putative_1009330..1009560_POSITIVE 242 94 58 156 112 smit:SMT_703|5end_hypothetical_protein_612345..612575_POSITIVE 236 50 1 154 98 smit:SMT_1617|5end_K02015_iron_complex_transport_system_permease_protein_1604500..1604730_NEGATIVE 235 37 1 55 22 smit:SMT_1080|5end_CAAX_amino_terminal_protease_family_protein_1018490..1018720_NEGATIVE 233 50 2 200 134 smit:SMT_1378|5end_DNA_polymerase_III,_delta'_subunit_1356803..1357033_NEGATIVE 231 44 9 210 170 smit:SMT_2096|5end_ATP-dependent_exonuclease_RexB_1990380..1990610_NEGATIVE 229 50 1 221 168 smit:SMT_1068|5end_ATP-dependent_DNA_helicase_RecG_1006891..1007121_POSITIVE 229 46 3 43 4 smit:SMT_408|5end_hypothetical_protein_353087..353317_POSITIVE 228 47 3 77 25 smit:SMT_1747|5end_anthranilate_synthase_component_I_1726279..1726509_POSITIVE 226 79 32 165 103 smit:SMT_1540|5end_hypothetical_protein_1525005..1525235_NEGATIVE 224 36 3 141 100 smit:SMT_1350|5end_multidrug_resistance_efflux_pump_1329225..1329455_NEGATIVE 224 97 53 84 25 smit:SMT_809|5end_sensor_histidine_kinase_(homolog_to_BlpH_Spn)_719745..719975_NEGATIVE 221 36 2 166 136 smit:SMT_141|5end_K03495_glucose_inhibited_division_protein_A_91408..91638_POSITIVE 218 37 2 69 21 smit:SMT_2041|5end_transcription-repair_coupling_factor_1952518..1952748_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 389 57 12 103 44 smit:SMT_231|3end_translation_elongation_factor_G_168222..168372_POSITIVE 298 45 9 92 56 smit:SMT_699|3end_K03106_signal_recognition_particle,_subunit_SRP54_609941..610091_NEGATIVE 262 80 31 73 14 smit:SMT_1696|3end_hypothetical_protein_1678924..1679074_POSITIVE 261 36 2 150 118 smit:SMT_1627|3end_hypothetical_protein_1616089..1616239_NEGATIVE 247 44 2 69 21 smit:SMT_1628|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1616610..1616760_NEGATIVE 247 50 9 125 70 smit:SMT_1504|3end_topology_modulation_protein_1487808..1487958_POSITIVE 237 50 1 101 39 smit:SMT_419|3end_hypothetical_protein_predicted_by_Glimmer/Critica_362510..362660_POSITIVE 236 50 5 96 51 smit:SMT_1036|3end_alpha-galactosidase_978160..978310_NEGATIVE 232 35 1 138 109 smit:SMT_1569|3end_dihydroxy-acid_dehydratase_1563068..1563218_POSITIVE 231 44 9 115 75 smit:SMT_2097|3end_type_I_restriction_enzyme_M_protein_1990475..1990625_NEGATIVE 230 48 12 94 60 smit:SMT_1279|3end_translation_elongation_factor_Ts_1243451..1243601_POSITIVE 229 46 3 42 3 smit:SMT_407|3end_para-aminobenzoate_synthetase_component_I_/_4-amino-4-deoxychorismate_lyase_353166..353316_POSITIVE 226 79 32 87 25 smit:SMT_1541|3end_isopentenyl-diphosphate_delta-isomerase_1525083..1525233_NEGATIVE 225 45 6 92 60 smit:SMT_494|3end_K04767_acetoin_utilization_protein_AcuB_428891..429041_POSITIVE 221 67 29 131 92 smit:SMT_235|3end_hypothetical_protein_174391..174541_POSITIVE 219 49 12 85 41 smit:SMT_1505|3end_purine-nucleoside_phosphorylase_1487805..1487955_NEGATIVE 218 46 5 48 2 smit:SMT_1189|3end_phosphoribosylaminoimidazole_carboxylase_ATPase_subunit_1146663..1146813_NEGATIVE 217 45 7 49 6 smit:SMT_1388|3end_hypothetical_protein_1365833..1365983_POSITIVE 217 44 10 85 42 smit:SMT_832|3end_hypothetical_protein_774376..774526_NEGATIVE 215 65 21 131 88 smit:SMT_1458|3end_K02040_phosphate_transport_system_substrate-binding_protein_1440602..1440752_POSITIVE