Origin IGS: aatatcaactcctttacttggttttattatagcgaattaaatcgaaaaagtaaaggattaggtcaattatttgagcctaatcctttactttttagatactgta .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tacagtatctaaaaagtaaaggattaggctcaaataattgacctaatcctttactttttcgatttaattcgctataataaaaccaagtaaaggagttgatatt Mask Tandem Repeat Region ================================================ aatatcaactcctttacttggttttattatagcgaattaaatcgaaaaagtaaaggattaggtcaattatttgagcctaatcctttactttttagatactgta Find is-nt database================================================ Query_seq: SSA_1028:SSA_1029|SSA_1028:SSA_1029:Transcriptional repressor, XRE family, putative:hypothetical protein:<-<-:1046154..1046256 103 aatatcaactcctttacttggttttattatagcgaattaaatcgaaaaagtaaaggattaggtcaattatttgagcctaatcctttactttttagatactgta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_1028:SSA_1029|SSA_1028:SSA_1029:Transcriptional repressor, XRE family, putative:hypothetical protein:<-<-:1046154..1046256 103 aatatcaactcctttacttggttttattatagcgaattaaatcgaaaaagtaaaggattaggtcaattatttgagcctaatcctttactttttagatactgta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_1028:SSA_1029|SSA_1028:SSA_1029:Transcriptional repressor, XRE family, putative:hypothetical protein:<-<-:1046154..1046256 103 aatatcaactcctttacttggttttattatagcgaattaaatcgaaaaagtaaaggattaggtcaattatttgagcctaatcctttactttttagatactgta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aatatcaactcctttacttggttttattatagcgaattaaatcgaaaaagtaaaggattaggtcaattatttgagcctaatcctttactttttagatactgta Predict ORF larger than 30AA ================================================ Protein_Len: 33 Strand: + Start: 4 End: 102 ... M N S F T W F Y Y S E L N R K S K G L G Q L F E P N P L L F R Y C . aatatcaactcctttacttggttttattatagcgaattaaatcgaaaaagtaaaggattaggtcaattatttgagcctaatcctttactttttagatactgta 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: 87 Start: 26 End: 55 .........................CTTTACTTTTTCGATTTAATTCGCTATAAT................................................ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ aatatcaactcctttacttggttttattatagcgaattaaatcgaaaaagtaaaggattaggtcaattatttgagcctaatcctttactttttagatactgta Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 100 HP_score: -13.4 Tail_Score: -3.41075 Start: 51 End: 87 Full_Region: ATTAAATCGAAAAAG TAAAGGATTAGGTCAA TTAT TTGAGCCTAATCCTTTA CTTTTTAGATACTGT ..................................................TAAAGGATTAGGTCAATTATTTGAGCCTAATCCTTTA................ TransTerm Strand: + Conf: 91 HP_score: -9.8 Tail_Score: -4.33653 Start: 55 End: 83 Full_Region: AATCGAAAAAGTAAA GGATTAGGTCAA TTAT TTGAGCCTAATCC TTTACTTTTTAGATA ......................................................GGATTAGGTCAATTATTTGAGCCTAATCC.................... Find igs database================================================ Query_seq: SSA_1028:SSA_1029|SSA_1028:SSA_1029:Transcriptional repressor, XRE family, putative:hypothetical protein:<-<-:1046154..1046256 103 aatatcaactcctttacttggttttattatagcgaattaaatcgaaaaagtaaaggattaggtcaattatttgagcctaatcctttactttttagatactgta Intra-Species Hit: Count: 1 Min: 1 Max: 103 Len: 103 Subject: NC_009009_SSA_1028_SSA_1029|Transcriptional repressor, XRE family, putative:hypothetical protein|NEGATIVE:NEGATIVE|[1046154,1046256]|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 aatatcaactcctttacttggttttattatagcgaattaaatcgaaaaagtaaaggattaggtcaattatttgagcctaatcctttactttttagatactgta aatatcaactcctttacttggttttattatagcgaattaaatcgaaaaagtaaaggattaggtcaattatttgagcctaatcctttactttttagatactgta HSP 2 e-value: 3.0E-6 bit: 52.0 Len: 49 Query Start:45 Query End:93 Subject Strand: NEGATIVE Subject Start: 45 Subject End: 93 ............................................aaaaagtaaaggattagg-tcaattatttgagcctaatcctttacttttt.......... ............................................aaaaagtaaaggattaggctcaaataattga-cctaatcctttacttttt.......... Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAUAUCAACUCCUUUACUUGGUUUUAUUAUAGCGAAUUAAAUCGAAAAAGUAAAGGAUUAGGUCAAUUAUUUGAGCCUAAUCCUUUACUUUUUAGAUACUGUA ..((((......((((.((.(((.......))).)).))))...((((((((((((((((((((((....)))).)))))))))))))))))).))))..... (-31.10) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UACAGUAUCUAAAAAGUAAAGGAUUAGGCUCAAAUAAUUGACCUAAUCCUUUACUUUUUCGAUUUAAUUCGCUAUAAUAAAACCAAGUAAAGGAGUUGAUAUU ......(((.((((((((((((((((((.((((....)))))))))))))))))))))).)))(((((((.((.................))))))))).... (-30.83) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 764 90 41 181 132 NC_009009:SSA_1028|5end_Transcriptional_repressor,_XRE_family,_putative_1046063..1046293_NEGATIVE 307 47 5 145 97 NC_009009:SSA_1119|5end_Two-component_response_transcriptional_regulator_(CheY-like_receiver_and_AraC-type_DNA-binding_domains),_putative_1144491..1144721_POSITIVE 242 96 67 103 76 NC_009009:SSA_0789|5end_Proton-translocating_ATPase,_F1_sector,_epsilon_subunit,_putative_772451..772681_POSITIVE 220 98 55 108 59 NC_009009:SSA_2018|5end_hypothetical_protein_2018801..2019031_NEGATIVE 212 50 2 133 92 NC_009009:SSA_0184|5end_Competence_protein_ComYA,_putative_188156..188386_POSITIVE 202 90 42 78 38 NC_009009:SSA_1730|5end_hypothetical_protein_1716057..1716287_NEGATIVE 200 97 56 112 79 NC_009009:SSA_1935|5end_Beta-ketoacyl-ACP_synthase_II_(3-oxoacyl-(Acyl-carrier-protein)_synthase_II),_putative_1923039..1923269_NEGATIVE 200 36 7 125 96 NC_009009:SSA_0879|5end_Cell_division_regulator,_negative_regulator_of_FtsZ_septation_ring_formation,_putative_873632..873862_POSITIVE 195 97 51 100 53 NC_009009:SSA_2305|5end_hypothetical_protein_2308059..2308289_NEGATIVE 194 97 63 69 31 NC_009009:SSA_2071|5end_hypothetical_protein_2074766..2074996_NEGATIVE 194 95 54 113 74 NC_009009:SSA_1238|5end_hypothetical_protein_1263154..1263384_NEGATIVE 191 50 9 147 98 NC_009009:SSA_1547|5end_HPr_kinase/phosphorylase,_putative_1550980..1551210_NEGATIVE 191 97 60 145 110 NC_009009:SSA_0716|5end_Competence_protein,_putative_701390..701620_POSITIVE 191 36 2 129 93 NC_009009:SSA_0641|5end_hypothetical_protein_628898..629128_POSITIVE 190 44 9 195 156 NC_009009:SSA_2046|5end_Uridine_phosphorylase,_putative_2049721..2049951_NEGATIVE 190 89 45 231 196 NC_009009:SSA_1595|5end_Tellurite_resistance,_putative_1601814..1602044_NEGATIVE 188 86 53 231 195 NC_009009:SSA_2051|5end_Oligoendopeptidase,_putative_2054731..2054961_POSITIVE 188 97 58 201 152 NC_009009:SSA_0520|5end_Ethanolamine_ammonia-lyase_light_chain,_putative_519462..519692_POSITIVE 187 93 62 109 81 NC_009009:SSA_1610|5end_hypothetical_protein_1614909..1615139_NEGATIVE 187 35 9 59 28 NC_009009:SSA_0791|5end_UDP-N-acetylglucosamine-like_protein,_putative_773345..773575_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 307 47 5 85 37 NC_009009:SSA_1118|3end_Peptide_methionine_sulfoxide_reductase,_putative_1144511..1144661_POSITIVE 242 96 67 95 68 NC_009009:SSA_0788|3end_Proton-translocating_ATPase,_F1_sector,_beta_subunit,_putative_772523..772673_POSITIVE 221 78 42 86 49 NC_009009:SSA_2081|3end_hypothetical_protein_2085490..2085640_POSITIVE 220 98 55 97 48 NC_009009:SSA_2019|3end_hypothetical_protein_2018812..2018962_NEGATIVE 213 86 41 76 43 NC_009009:SSA_0886|3end_Enolase,_putative_881057..881207_POSITIVE 211 24 2 114 88 NC_009009:SSA_0948|3end_hypothetical_protein_955628..955778_POSITIVE 200 97 56 47 14 NC_009009:SSA_1936|3end_3-oxoacyl-[acyl-carrier_protein]_reductase,_putative_1923104..1923254_NEGATIVE 200 36 7 38 9 NC_009009:SSA_0878|3end_DNA_gyrase,_putative_873625..873775_POSITIVE 194 95 54 116 77 NC_009009:SSA_1239|3end_hypothetical_protein_1263151..1263301_NEGATIVE 194 77 31 116 70 NC_009009:SSA_0916|3end_2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoate_hydrolase,_putative_928992..929142_POSITIVE 188 86 53 116 80 NC_009009:SSA_2050|3end_Arabinose_efflux_permease,_putative_2054696..2054846_POSITIVE 188 76 31 111 62 NC_009009:SSA_1317|3end_hypothetical_protein_1333398..1333548_NEGATIVE 186 95 54 116 79 NC_009009:SSA_0621|3end_SOS_responce_UmuC_protein,_putative_612322..612472_NEGATIVE 184 84 41 110 67 NC_009009:SSA_1074|3end_Pyrroline-5-carboxylate_reductase,_putative_1093034..1093184_POSITIVE 183 96 51 80 32 NC_009009:SSA_1750|3end_Extracellular_nuclease,_putative_1735673..1735823_NEGATIVE 180 90 53 91 62 NC_009009:SSA_0595|3end_hypothetical_protein_586983..587133_POSITIVE 178 90 41 96 39 NC_009009:SSA_2227|3end_Acetyl_transferase,_putative_2227716..2227866_NEGATIVE 176 97 69 35 3 NC_009009:SSA_2072|3end_Phosphatidate_cytidylyltransferase,_putative_2074800..2074950_NEGATIVE 176 98 54 111 64 NC_009009:SSA_1726|3end_ABC_transporter_ATP-binding_protein-branched_chain_amino_acid_transport,_putative_1711703..1711853_NEGATIVE 176 57 12 79 39 NC_009009:SSA_1348|3end_hypothetical_protein_1365959..1366109_POSITIVE