Origin IGS: gataaacctcttcttttatataaacttattgcatttattttaccacaattacaggcatttcacaaaagcagaaggacattttcttaagaaaaatggactggttagcccaccagcccatttattcatactcaaaataga .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tctattttgagtatgaataaatgggctggtgggctaaccagtccatttttcttaagaaaatgtccttctgcttttgtgaaatgcctgtaattgtggtaaaataaatgcaataagtttatataaaagaagaggtttatc Mask Tandem Repeat Region ================================================ gataaacctcttcttttatataaacttattgcatttattttaccacaattacaggcatttcacaaaagcagaaggacattttcttaagaaaaatggactggttagcccaccagcccatttattcatactcaaaataga Find is-nt database================================================ Query_seq: SSA_1748:SSA_1749|SSA_1748:SSA_1749:Inorganic pyrophosphatase/exopolyphosphatase, putative:Pyruvate formate-lyase-activating enzyme, putative:<-<-:1734569..1734706 138 gataaacctcttcttttatataaacttattgcatttattttaccacaattacaggcatttcacaaaagcagaaggacattttcttaagaaaaatggactggttagcccaccagcccatttattcatactcaaaataga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_1748:SSA_1749|SSA_1748:SSA_1749:Inorganic pyrophosphatase/exopolyphosphatase, putative:Pyruvate formate-lyase-activating enzyme, putative:<-<-:1734569..1734706 138 gataaacctcttcttttatataaacttattgcatttattttaccacaattacaggcatttcacaaaagcagaaggacattttcttaagaaaaatggactggttagcccaccagcccatttattcatactcaaaataga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_1748:SSA_1749|SSA_1748:SSA_1749:Inorganic pyrophosphatase/exopolyphosphatase, putative:Pyruvate formate-lyase-activating enzyme, putative:<-<-:1734569..1734706 138 gataaacctcttcttttatataaacttattgcatttattttaccacaattacaggcatttcacaaaagcagaaggacattttcttaagaaaaatggactggttagcccaccagcccatttattcatactcaaaataga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gataaacctcttcttttatataaacttattgcatttattttaccacaattacaggcatttcacaaaagcagaaggacattttcttaagaaaaatggactggttagcccaccagcccatttattcatactcaaaataga Predict ORF larger than 30AA ================================================ Protein_Len: 45 Strand: + Start: 2 End: 136 . M N L F F Y I N L L H L F Y H N Y R H F T K A E G H F L K K N G L V S P P A H L F I L K I .. Protein_Len: 35 Strand: + Start: 33 End: 134 ................................ M Y F T T I T G I S Q K Q K D I F L R K M D W L A H Q P I Y S Y S K * .... gataaacctcttcttttatataaacttattgcatttattttaccacaattacaggcatttcacaaaagcagaaggacattttcttaagaaaaatggactggttagcccaccagcccatttattcatactcaaaataga 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: 86 Start: 37 End: 66 ....................................TTTGTGAAATGCCTGTAATTGTGGTAAAAT........................................................................ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ gataaacctcttcttttatataaacttattgcatttattttaccacaattacaggcatttcacaaaagcagaaggacattttcttaagaaaaatggactggttagcccaccagcccatttattcatactcaaaataga Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 74 HP_score: -6.7 Tail_Score: -4.2704 Start: 94 End: 117 Full_Region: TTTTCTTAAGAAAAA TGGACTGGT TAGCCC ACCAGCCCA TTTATTCATACTCAA .............................................................................................TGGACTGGTTAGCCCACCAGCCCA..................... Find igs database================================================ Query_seq: SSA_1748:SSA_1749|SSA_1748:SSA_1749:Inorganic pyrophosphatase/exopolyphosphatase, putative:Pyruvate formate-lyase-activating enzyme, putative:<-<-:1734569..1734706 138 gataaacctcttcttttatataaacttattgcatttattttaccacaattacaggcatttcacaaaagcagaaggacattttcttaagaaaaatggactggttagcccaccagcccatttattcatactcaaaataga Intra-Species Hit: Count: 1 Min: 1 Max: 138 Len: 138 Subject: NC_009009_SSA_1748_SSA_1749|Inorganic pyrophosphatase/exopolyphosphatase, putative:Pyruvate formate-lyase-activating enzyme, putative|NEGATIVE:NEGATIVE|[1734569,1734706]|138 HSP 1 e-value: 7.0E-73 bit: 274.0 Len: 138 Query Start:1 Query End:138 Subject Strand: POSITIVE Subject Start: 1 Subject End: 138 gataaacctcttcttttatataaacttattgcatttattttaccacaattacaggcatttcacaaaagcagaaggacattttcttaagaaaaatggactggttagcccaccagcccatttattcatactcaaaataga gataaacctcttcttttatataaacttattgcatttattttaccacaattacaggcatttcacaaaagcagaaggacattttcttaagaaaaatggactggttagcccaccagcccatttattcatactcaaaataga Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAUAAACCUCUUCUUUUAUAUAAACUUAUUGCAUUUAUUUUACCACAAUUACAGGCAUUUCACAAAAGCAGAAGGACAUUUUCUUAAGAAAAAUGGACUGGUUAGCCCACCAGCCCAUUUAUUCAUACUCAAAAUAGA ......(((((.(((((.......((.((((..............))))...)).........))))).)).)))............(((((((((.(((((......))))).)))))).))).............. (-19.43) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UCUAUUUUGAGUAUGAAUAAAUGGGCUGGUGGGCUAACCAGUCCAUUUUUCUUAAGAAAAUGUCCUUCUGCUUUUGUGAAAUGCCUGUAAUUGUGGUAAAAUAAAUGCAAUAAGUUUAUAUAAAAGAAGAGGUUUAUC ....(((((((.......((((((((((((......))))))))))))..)))))))..(((..(((((.((((((((((((...((((.((((......)))).))))....)))).)))))))).)))))..))). (-39.00) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 888 120 71 211 162 NC_009009:SSA_1748|5end_Inorganic_pyrophosphatase/exopolyphosphatase,_putative_1734478..1734708_NEGATIVE 276 107 62 221 166 NC_009009:SSA_1595|5end_Tellurite_resistance,_putative_1601814..1602044_NEGATIVE 275 120 71 182 127 NC_009009:SSA_1771|5end_Conserved_DNA_methyltransferase_protein,_putative_1758799..1759029_NEGATIVE 273 117 74 63 14 NC_009009:SSA_1897|5end_Ribosomal_protein_HS6-type_(S12/L30/L7a),_putative_1894450..1894680_NEGATIVE 269 120 72 143 92 NC_009009:SSA_1784|5end_Glutamate_racemase,_putative_1769897..1770127_NEGATIVE 263 114 71 208 150 NC_009009:SSA_2376|5end_ABC_transporter_with_duplicated_ATPase_domains,_putative_2378744..2378974_POSITIVE 259 125 94 163 126 NC_009009:SSA_2278|5end_Ukp_protein,_putative_2281669..2281899_NEGATIVE 256 118 74 91 46 NC_009009:SSA_2048|5end_Serine_acetyltransferase,_putative_2050601..2050831_NEGATIVE 256 119 99 231 208 NC_009009:SSA_1557|5end_SRPR,_signal_recognition_particle-docking_protein,_putative_1560040..1560270_NEGATIVE 249 118 72 217 159 NC_009009:SSA_1443|5end_1-(5-phosphoribosyl)-5-[(5-_phosphoribosylamino)methylideneamino]_imidazole-4-carboxamide_isomerase,_putative_1446672..1446902_NEGATIVE 247 115 92 176 147 NC_009009:SSA_1574|5end_Glycosyl_transferase,_family_1,_putative_1577930..1578160_NEGATIVE 246 119 98 50 23 NC_009009:SSA_0377|5end_ABC-type_methionine_transporter,_permease_component,_putative_366446..366676_POSITIVE 244 107 66 52 15 NC_009009:SSA_1636|5end_ABC-type_antibiotic_exporter,_ATPase_component,_putative_1640905..1641135_NEGATIVE 240 99 52 183 134 NC_009009:SSA_0023|5end_Aspartate_aminotransferase,_putative_28529..28759_POSITIVE 239 119 75 231 180 NC_009009:SSA_0185|5end_Competence_protein_ComYB,_putative_189057..189287_POSITIVE 238 110 63 55 4 NC_009009:SSA_2308|5end_hypothetical_protein_2310474..2310704_NEGATIVE 238 130 93 60 10 NC_009009:SSA_1066|5end_ABC-type_oligopeptide_transport_system,_putative_1084335..1084565_POSITIVE 237 86 41 176 133 NC_009009:SSA_0207|5end_hypothetical_protein_204430..204660_POSITIVE 236 124 94 57 26 NC_009009:SSA_0647|5end_hypothetical_protein_630998..631228_POSITIVE 234 119 71 221 144 NC_009009:SSA_0762|5end_hypothetical_protein_744187..744417_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 334 116 77 129 83 NC_009009:SSA_0815|3end_hypothetical_protein_797411..797561_POSITIVE 315 115 74 51 11 NC_009009:SSA_1602|3end_Exoribonuclease,_VacB/Rnb_family,_putative_1607022..1607172_NEGATIVE 275 120 71 86 31 NC_009009:SSA_1772|3end_hypothetical_protein_1758895..1759045_NEGATIVE 273 117 74 70 21 NC_009009:SSA_1899|3end_hypothetical_protein_1894443..1894593_NEGATIVE 260 100 54 96 45 NC_009009:SSA_0673|3end_hypothetical_protein_656994..657144_POSITIVE 248 127 82 58 9 NC_009009:SSA_1530|3end_ABC-type_antimicrobial_peptide_transport_system,_permease_component,_putative_1537510..1537660_NEGATIVE 248 124 93 40 5 NC_009009:SSA_0844|3end_hypothetical_protein_828491..828641_NEGATIVE 246 119 98 50 23 NC_009009:SSA_0376|3end_ABC-type_methionine_transporter,_ATPase_component,_putative_366526..366676_POSITIVE 238 110 63 55 4 NC_009009:SSA_2309|3end_Fimbrial_assembly_protein,_putative_2310474..2310624_NEGATIVE 236 115 87 81 48 NC_009009:SSA_1729|3end_ABC_transporter_substrate-binding_protein-branched_chain_amino_acid_transport,_putative_1714539..1714689_NEGATIVE 236 124 94 55 24 NC_009009:SSA_0646|3end_hypothetical_protein_631076..631226_POSITIVE 234 119 71 123 46 NC_009009:SSA_0761|3end_Transcriptional_regulator,_XRE_family,_putative_744169..744319_POSITIVE 233 119 78 48 1 NC_009009:SSA_0921|3end_Zn-dependeant_threonine_dehydrogenase,_putative_932164..932314_POSITIVE 233 71 31 114 63 NC_009009:SSA_0568|3end_Aspartyl-tRNA_synthetase_1,_putative_563490..563640_POSITIVE 231 127 94 118 82 NC_009009:SSA_1269|3end_hypothetical_protein_1291970..1292120_NEGATIVE 230 125 99 115 94 NC_009009:SSA_0621|3end_SOS_responce_UmuC_protein,_putative_612322..612472_NEGATIVE 229 109 67 47 3 NC_009009:SSA_1014|3end_Phosphatidylserine_decarboxylase_proenzyme_2,_putative_1018798..1018948_POSITIVE 229 117 72 106 56 NC_009009:SSA_0151|3end_hypothetical_protein_145871..146021_POSITIVE 228 107 66 60 16 NC_009009:SSA_1627|3end_hypothetical_protein_1629508..1629658_NEGATIVE 225 115 71 129 83 NC_009009:SSA_1771|3end_Conserved_DNA_methyltransferase_protein,_putative_1758491..1758641_NEGATIVE