Origin IGS: atagcttaaatacagaccaactgtgcaaaagttgagtttaccaactcagctttttaatttttaatattcctggtaggatgatatcaaaggatagccaaggaggacgat .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 atcgtcctccttggctatcctttgatatcatcctaccaggaatattaaaaattaaaaagctgagttggtaaactcaacttttgcacagttggtctgtatttaagctat Mask Tandem Repeat Region ================================================ atagcttaaatacagaccaactgtgcaaaagttgagtttaccaactcagctttttaatttttaatattcctggtaggatgatatcaaaggatagccaaggaggacgat Find is-nt database================================================ Query_seq: SSA_1569:SSA_1570|SSA_1569:SSA_1570:ABC transporter membrane-spanning permease, arginine/histidine transport, putative:hypothetical protein:->->:1572691..1572798 108 atagcttaaatacagaccaactgtgcaaaagttgagtttaccaactcagctttttaatttttaatattcctggtaggatgatatcaaaggatagccaaggaggacgat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_1569:SSA_1570|SSA_1569:SSA_1570:ABC transporter membrane-spanning permease, arginine/histidine transport, putative:hypothetical protein:->->:1572691..1572798 108 atagcttaaatacagaccaactgtgcaaaagttgagtttaccaactcagctttttaatttttaatattcctggtaggatgatatcaaaggatagccaaggaggacgat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_1569:SSA_1570|SSA_1569:SSA_1570:ABC transporter membrane-spanning permease, arginine/histidine transport, putative:hypothetical protein:->->:1572691..1572798 108 atagcttaaatacagaccaactgtgcaaaagttgagtttaccaactcagctttttaatttttaatattcctggtaggatgatatcaaaggatagccaaggaggacgat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 atagcttaaatacagaccaactgtgcaaaagttgagtttaccaactcagctttttaatttttaatattcctggtaggatgatatcaaaggatagccaaggaggacgat Predict ORF larger than 30AA ================================================ atagcttaaatacagaccaactgtgcaaaagttgagtttaccaactcagctttttaatttttaatattcctggtaggatgatatcaaaggatagccaaggaggacgat 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================================================ atagcttaaatacagaccaactgtgcaaaagttgagtttaccaactcagctttttaatttttaatattcctggtaggatgatatcaaaggatagccaaggaggacgat Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_1569:SSA_1570|SSA_1569:SSA_1570:ABC transporter membrane-spanning permease, arginine/histidine transport, putative:hypothetical protein:->->:1572691..1572798 108 atagcttaaatacagaccaactgtgcaaaagttgagtttaccaactcagctttttaatttttaatattcctggtaggatgatatcaaaggatagccaaggaggacgat Intra-Species Hit: Count: 1 Min: 1 Max: 108 Len: 108 Subject: NC_009009_SSA_1569_SSA_1570|ABC transporter membrane-spanning permease, arginine/histidine transport, putative:hypothetical protein|POSITIVE:POSITIVE|[1572691,1572798]|108 HSP 1 e-value: 4.0E-55 bit: 214.0 Len: 108 Query Start:1 Query End:108 Subject Strand: POSITIVE Subject Start: 1 Subject End: 108 atagcttaaatacagaccaactgtgcaaaagttgagtttaccaactcagctttttaatttttaatattcctggtaggatgatatcaaaggatagccaaggaggacgat atagcttaaatacagaccaactgtgcaaaagttgagtttaccaactcagctttttaatttttaatattcctggtaggatgatatcaaaggatagccaaggaggacgat Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUAGCUUAAAUACAGACCAACUGUGCAAAAGUUGAGUUUACCAACUCAGCUUUUUAAUUUUUAAUAUUCCUGGUAGGAUGAUAUCAAAGGAUAGCCAAGGAGGACGAU ..........(((((.....))))).((((((((((((....))))))))))))............(((((....((....((((....)))).)).)))))...... (-23.10) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUCGUCCUCCUUGGCUAUCCUUUGAUAUCAUCCUACCAGGAAUAUUAAAAAUUAAAAAGCUGAGUUGGUAAACUCAACUUUUGCACAGUUGGUCUGUAUUUAAGCUAU ...........(((((....((((((((..(((.....))))))))))).....(((((.((((((....)))))).)))))..((((.....)))).....))))). (-22.90) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 282 70 21 212 160 NC_009009:SSA_1006|5end_Dextransucrase,_putative_1007076..1007306_POSITIVE 270 70 27 149 108 NC_009009:SSA_1490|5end_Ribonuclease_BN,_putative_1496732..1496962_NEGATIVE 241 80 34 168 121 NC_009009:SSA_1726|5end_ABC_transporter_ATP-binding_protein-branched_chain_amino_acid_transport,_putative_1712467..1712697_NEGATIVE 240 99 52 228 167 NC_009009:SSA_2340|5end_hypothetical_protein_2342843..2343073_NEGATIVE 232 76 33 130 91 NC_009009:SSA_0929|5end_ABC-type_multidrug_transporter,_ATPase_and_permease_components,_putative_938438..938668_POSITIVE 228 96 67 226 197 NC_009009:SSA_0513|5end_ATP:cob(I)alamin_adenosyltransferase,_putative_511558..511788_POSITIVE 228 88 41 97 51 NC_009009:SSA_0062|5end_Aldose_1-epimerase,_putative_63732..63962_POSITIVE 227 57 15 200 158 NC_009009:SSA_0102|5end_Kinase,_putative_104035..104265_POSITIVE 226 49 2 150 104 NC_009009:SSA_2289|5end_Cadmium_efflux_system_transcriptional_regulator_(ArsR-like),_putative_2291087..2291317_POSITIVE 226 49 2 150 104 NC_009009:SSA_2389|5end_Arsenical_resistance_operon_transcription_repressor,_putative_2032183..2032413_NEGATIVE 226 49 2 120 74 NC_009009:SSA_2387|5end_Arsenical_resistance_operon_transcription_repressor,_putative_2032213..2032443_NEGATIVE 226 49 13 170 130 NC_009009:SSA_1904|5end_ABC-type_multidrug_transport_system,_permease_component,_putative_1899279..1899509_NEGATIVE 225 52 14 171 120 NC_009009:SSA_0802|5end_hypothetical_protein_784300..784530_POSITIVE 220 96 66 219 182 NC_009009:SSA_0220|5end_PTS_system,_mannose-specific_IIB_component,_putative_215848..216078_POSITIVE 218 49 15 177 141 NC_009009:SSA_1945|5end_Oligopeptide_transport_ATP-binding_protein,_putative_1937689..1937919_NEGATIVE 218 43 13 90 55 NC_009009:SSA_0688|5end_2,3-bisphosphoglycerate-dependent_phosphoglycerate_mutase,_putative_671360..671590_POSITIVE 218 97 70 63 33 NC_009009:SSA_0274|5end_hypothetical_protein_269557..269787_NEGATIVE 216 99 70 190 157 NC_009009:SSA_0481|5end_Cobyric_acid_synthase,_putative_481962..482192_POSITIVE 215 52 21 44 12 NC_009009:SSA_0539|5end_PduO_protein,_putative_534233..534463_POSITIVE 215 50 4 110 53 NC_009009:SSA_0188|5end_hypothetical_protein_190798..191028_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 270 70 27 101 60 NC_009009:SSA_1491|3end_Methionine_aminopeptidase_A,_putative_1496780..1496930_NEGATIVE 259 50 3 138 88 NC_009009:SSA_0272|3end_Oxidoreductase,_aldo/keto_reductase_family,_putative_267032..267182_POSITIVE 233 55 16 65 9 NC_009009:SSA_0234|3end_hypothetical_protein_228423..228573_NEGATIVE 232 76 33 137 98 NC_009009:SSA_0928|3end_ABC-type_multidrug_transporter,_ATPase_and_permease_components,_putative_938525..938675_POSITIVE 228 88 41 72 26 NC_009009:SSA_0061|3end_Tagatose_1,6-diphosphate_aldolase,_putative_63787..63937_POSITIVE 226 49 2 138 92 NC_009009:SSA_2288|3end_Cadmium_resistance_transporter,_putative_2291155..2291305_POSITIVE 226 49 2 138 92 NC_009009:SSA_2026|3end_Cadmium_resistance_transporter,_putative_2032195..2032345_NEGATIVE 215 50 4 84 27 NC_009009:SSA_0187|3end_Competence_protein_ComYD,_putative_190852..191002_POSITIVE 214 54 27 64 37 NC_009009:SSA_1569|3end_ABC_transporter_membrane-spanning_permease,_arginine/histidine_transport,_putative_1572630..1572780_POSITIVE 205 61 25 51 16 NC_009009:SSA_1374|3end_Multidrug_ABC_transporter,_ATPase_and_permease_components,_putative_1391359..1391509_NEGATIVE 204 50 1 72 10 NC_009009:SSA_1899|3end_hypothetical_protein_1894443..1894593_NEGATIVE 203 48 1 54 19 NC_009009:SSA_1577|3end_Proline_dipeptidase,_putative_1581456..1581606_POSITIVE 201 97 54 143 91 NC_009009:SSA_2300|3end_hypothetical_protein_2301594..2301744_NEGATIVE 200 54 11 99 54 NC_009009:SSA_0667|3end_Transcriptional_regulator,_putative_650757..650907_POSITIVE 200 54 13 81 42 NC_009009:SSA_0567|3end_Isochorismitase_family_protein,_putative_561442..561592_POSITIVE 200 52 13 75 26 NC_009009:SSA_0488|3end_Glutamate-1-semialdehyde_2,1-aminotransferase,_putative_489742..489892_POSITIVE 199 77 31 126 67 NC_009009:SSA_1373|3end_ATPase_components_of_ABC_transporters_with_duplicated_ATPase_domains,_multidrug_transport_system,_putative_1391313..1391463_POSITIVE 199 39 14 82 55 NC_009009:SSA_0819|3end_hypothetical_protein_801181..801331_POSITIVE 199 100 67 39 5 NC_009009:SSA_0217|3end_Two-component_system_transcriptional_regulator_(CheY_domain_and_HTH-like_DNA-binding_domain),_putative_213946..214096_POSITIVE 197 50 1 62 5 NC_009009:SSA_1973|3end_Histidine_kinase,_putative_1968407..1968557_NEGATIVE