Origin IGS: caatgtaaaacaaaacccatcggtcataagatagccgatgggttttcatatgcgggacttacaagttcttcttttgccgtgaaagaaggtcctcccgattttcctagtt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aactaggaaaatcgggaggaccttctttcacggcaaaagaagaacttgtaagtcccgcatatgaaaacccatcggctatcttatgaccgatgggttttgttttacattg Mask Tandem Repeat Region ================================================ caatgtaaaacaaaacccatcggtcataagatagccgatgggttttcatatgcgggacttacaagttcttcttttgccgtgaaagaaggtcctcccgattttcctagtt Find is-nt database================================================ Query_seq: SSA_1624:SSA_1625|SSA_1624:SSA_1625:hypothetical protein:Lactoylglutathione lyase, putative:-><-:1626558..1626666 109 caatgtaaaacaaaacccatcggtcataagatagccgatgggttttcatatgcgggacttacaagttcttcttttgccgtgaaagaaggtcctcccgattttcctagtt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_1624:SSA_1625|SSA_1624:SSA_1625:hypothetical protein:Lactoylglutathione lyase, putative:-><-:1626558..1626666 109 caatgtaaaacaaaacccatcggtcataagatagccgatgggttttcatatgcgggacttacaagttcttcttttgccgtgaaagaaggtcctcccgattttcctagtt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_1624:SSA_1625|SSA_1624:SSA_1625:hypothetical protein:Lactoylglutathione lyase, putative:-><-:1626558..1626666 109 caatgtaaaacaaaacccatcggtcataagatagccgatgggttttcatatgcgggacttacaagttcttcttttgccgtgaaagaaggtcctcccgattttcctagtt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 caatgtaaaacaaaacccatcggtcataagatagccgatgggttttcatatgcgggacttacaagttcttcttttgccgtgaaagaaggtcctcccgattttcctagtt Predict ORF larger than 30AA ================================================ Protein_Len: 30 Strand: + Start: 19 End: 108 .................. M G H K I A D G F S Y A G L T S S S F A V K E G P P D F P S . caatgtaaaacaaaacccatcggtcataagatagccgatgggttttcatatgcgggacttacaagttcttcttttgccgtgaaagaaggtcctcccgattttcctagtt 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================================================ caatgtaaaacaaaacccatcggtcataagatagccgatgggttttcatatgcgggacttacaagttcttcttttgccgtgaaagaaggtcctcccgattttcctagtt Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 76 HP_score: -9.3 Tail_Score: -3.66379 Start: 17 End: 41 Full_Region: cccgcatatgaaaac ccatcggctat ctt atgaccgatgg gttttgttttacatt ................ccatcggctatcttatgaccgatgg.................................................................... Find igs database================================================ Query_seq: SSA_1624:SSA_1625|SSA_1624:SSA_1625:hypothetical protein:Lactoylglutathione lyase, putative:-><-:1626558..1626666 109 caatgtaaaacaaaacccatcggtcataagatagccgatgggttttcatatgcgggacttacaagttcttcttttgccgtgaaagaaggtcctcccgattttcctagtt Intra-Species Hit: Count: 1 Min: 1 Max: 109 Len: 109 Subject: NC_009009_SSA_1624_SSA_1625|hypothetical protein:Lactoylglutathione lyase, putative|POSITIVE:NEGATIVE|[1626558,1626666]|109 HSP 1 e-value: 1.0E-55 bit: 216.0 Len: 109 Query Start:1 Query End:109 Subject Strand: POSITIVE Subject Start: 1 Subject End: 109 caatgtaaaacaaaacccatcggtcataagatagccgatgggttttcatatgcgggacttacaagttcttcttttgccgtgaaagaaggtcctcccgattttcctagtt caatgtaaaacaaaacccatcggtcataagatagccgatgggttttcatatgcgggacttacaagttcttcttttgccgtgaaagaaggtcctcccgattttcctagtt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CAAUGUAAAACAAAACCCAUCGGUCAUAAGAUAGCCGAUGGGUUUUCAUAUGCGGGACUUACAAGUUCUUCUUUUGCCGUGAAAGAAGGUCCUCCCGAUUUUCCUAGUU ...........(((((((((((((.........)))))))))))))......(((((.........(((((((((.....)))))))))...)))))............ (-32.50) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AACUAGGAAAAUCGGGAGGACCUUCUUUCACGGCAAAAGAAGAACUUGUAAGUCCCGCAUAUGAAAACCCAUCGGCUAUCUUAUGACCGAUGGGUUUUGUUUUACAUUG ............(((((..(((((((((.......))))))).....))...)))))......(((((((((((((........).))))))))))))........... (-30.50) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 346 56 14 94 39 NC_009009:SSA_0312|5end_Hydrolase,_metallo-beta-lactamase_superfamily,_putative_308385..308615_NEGATIVE 344 98 53 64 10 NC_009009:SSA_2117|5end_DNA_recombination_protein_RmuC,_putative_2119812..2120042_NEGATIVE 301 95 51 101 60 NC_009009:SSA_1601|5end_VacB-like_protein,_putative_1607059..1607289_NEGATIVE 298 70 23 102 51 NC_009009:SSA_1771|5end_Conserved_DNA_methyltransferase_protein,_putative_1758799..1759029_NEGATIVE 294 77 33 218 169 NC_009009:SSA_1176|5end_Acetoin_dehydrogenase,_E1_component,_beta_subunit,_putative_1205405..1205635_NEGATIVE 293 80 36 204 167 NC_009009:SSA_1448|5end_ATP_phosphoribosyltransferase_regulatory_subunit,_putative_1450817..1451047_NEGATIVE 288 79 34 157 107 NC_009009:SSA_1010|5end_UDP-glucose_4-epimerase,_putative_1012739..1012969_POSITIVE 285 70 21 114 53 NC_009009:SSA_1429|5end_hypothetical_protein_1437110..1437340_NEGATIVE 283 79 32 191 128 NC_009009:SSA_0929|5end_ABC-type_multidrug_transporter,_ATPase_and_permease_components,_putative_938438..938668_POSITIVE 283 100 66 108 76 NC_009009:SSA_0751|5end_Oligoendopeptidase_F,_putative_732367..732597_POSITIVE 280 78 36 217 163 NC_009009:SSA_1770|5end_hypothetical_protein_1758431..1758661_NEGATIVE 274 82 41 51 19 NC_009009:SSA_1038|5end_Lipoprotein,_putative_1052579..1052809_POSITIVE 272 80 31 79 19 NC_009009:SSA_0689|5end_Penicillin-binding_protein_2B,_putative_672262..672492_POSITIVE 272 93 52 223 175 NC_009009:SSA_0653|5end_UDP-N-acetylglucosamine--N-acetylmuramyl-_(pentapeptide)_pyrophosphoryl-undecaprenol_N-acetylglucosamine_transferase,_putative_636390..636620_POSITIVE 266 95 53 103 64 NC_009009:SSA_1694|5end_PTS_system,_lactose-specific_IIA_component,_putative_1687128..1687358_NEGATIVE 265 77 31 130 93 NC_009009:SSA_1643|5end_hypothetical_protein_1645269..1645499_NEGATIVE 264 96 51 157 110 NC_009009:SSA_1650|5end_3-Ketoacyl-ACP_reductase,_putative_1649594..1649824_NEGATIVE 264 59 17 78 25 NC_009009:SSA_0306|5end_Transcription_regulator_(glutamine_synthetase_repressor),_putative_302590..302820_POSITIVE 262 60 17 101 51 NC_009009:SSA_2021|5end_hypothetical_protein_2023534..2023764_NEGATIVE 260 67 21 201 164 NC_009009:SSA_1974|5end_ABC-type_multidrug_transport_system,_permease_component,_putative_1970246..1970476_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 346 56 14 90 35 NC_009009:SSA_0313|3end_Conserved_uncharacterized_protein_308389..308539_NEGATIVE 344 98 53 62 8 NC_009009:SSA_2118|3end_Thiamine_pyrophosphokinase,_putative_2119814..2119964_NEGATIVE 343 57 12 98 45 NC_009009:SSA_1624|3end_hypothetical_protein_1626497..1626647_POSITIVE 302 60 15 45 5 NC_009009:SSA_0861|3end_hypothetical_protein_851742..851892_NEGATIVE 301 95 51 138 97 NC_009009:SSA_1602|3end_Exoribonuclease,_VacB/Rnb_family,_putative_1607022..1607172_NEGATIVE 293 80 36 148 111 NC_009009:SSA_1449|3end_Histidinol-phosphate/aromatic_aminotransferase_and_cobyric_acid_decarboxylase,_putative_1450873..1451023_NEGATIVE 285 70 21 117 56 NC_009009:SSA_1430|3end_Ribonuclease_Z,_putative_1437107..1437257_NEGATIVE 278 80 34 116 51 NC_009009:SSA_1306|3end_Trk_transporter_NAD+_binding_protein-K+_transport,_putative_1324245..1324395_NEGATIVE 277 76 34 149 103 NC_009009:SSA_1009|3end_Galactose-1-phosphate-uridylyltransferase,_putative_1012815..1012965_POSITIVE 275 97 54 139 101 NC_009009:SSA_0641|3end_hypothetical_protein_629427..629577_POSITIVE 269 68 21 151 95 NC_009009:SSA_1056|3end_Firmicute_fructose-1,6-bisphosphatase,_putative_1073750..1073900_POSITIVE 266 95 53 54 15 NC_009009:SSA_1695|3end_Transcriptional_antiterminator,_BglG/SacY_family_(induction_of_sugar_metabolism),_putative_1687177..1687327_NEGATIVE 265 76 31 123 79 NC_009009:SSA_1548|3end_NTP_pyrophosphohydrolases_including_oxidative_damage_repair_enzymes,_putative_1551119..1551269_NEGATIVE 253 96 51 127 84 NC_009009:SSA_0273|3end_hypothetical_protein_268566..268716_POSITIVE 252 58 14 51 14 NC_009009:SSA_1795|3end_Guanosine_3',5'-bis-pyrophosphate_(ppGpp)_synthetase,_putative_1777051..1777201_NEGATIVE 252 78 34 60 8 NC_009009:SSA_1779|3end_Segregation_and_condensation_protein_A,_putative_1765704..1765854_NEGATIVE 252 96 67 45 3 NC_009009:SSA_0210|3end_hypothetical_protein_208124..208274_POSITIVE 250 77 33 67 15 NC_009009:SSA_0610|3end_LemA-like_protein,_putative_599617..599767_POSITIVE 250 96 51 49 6 NC_009009:SSA_0473|3end_Precorrin-6x_reductase,_putative_476331..476481_POSITIVE 247 90 50 140 94 NC_009009:SSA_1026|3end_ABC-type_multidrug_transporter,_ATPase_component,_putative_1043617..1043767_POSITIVE