Origin IGS: agtttacttagaaggcctaaaatcagctggatatctggctgattttttcttaggatgtccaatgaaagaaagtgaagtagctgatgcttaaaaggaagaattttctct .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 agagaaaattcttccttttaagcatcagctacttcactttctttcattggacatcctaagaaaaaatcagccagatatccagctgattttaggccttctaagtaaact Mask Tandem Repeat Region ================================================ agtttacttagaaggcctaaaatcagctggatatctggctgattttttcttaggatgtccaatgaaagaaagtgaagtagctgatgcttaaaaggaagaattttctct Find is-nt database================================================ Query_seq: SSA_0095:SSA_0097|SSA_0095:SSA_0097:Threonine synthase, putative:Multi antimicrobial extrusion (MATE) family transporter, putative:->->:98180..98287 108 agtttacttagaaggcctaaaatcagctggatatctggctgattttttcttaggatgtccaatgaaagaaagtgaagtagctgatgcttaaaaggaagaattttctct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_0095:SSA_0097|SSA_0095:SSA_0097:Threonine synthase, putative:Multi antimicrobial extrusion (MATE) family transporter, putative:->->:98180..98287 108 agtttacttagaaggcctaaaatcagctggatatctggctgattttttcttaggatgtccaatgaaagaaagtgaagtagctgatgcttaaaaggaagaattttctct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_0095:SSA_0097|SSA_0095:SSA_0097:Threonine synthase, putative:Multi antimicrobial extrusion (MATE) family transporter, putative:->->:98180..98287 108 agtttacttagaaggcctaaaatcagctggatatctggctgattttttcttaggatgtccaatgaaagaaagtgaagtagctgatgcttaaaaggaagaattttctct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 agtttacttagaaggcctaaaatcagctggatatctggctgattttttcttaggatgtccaatgaaagaaagtgaagtagctgatgcttaaaaggaagaattttctct Predict ORF larger than 30AA ================================================ Protein_Len: 33 Strand: - Start: 3 End: 101 .. K S L L G L I L Q I D P Q N K R L I D L S L F H L L Q H K F P L M ....... agtttacttagaaggcctaaaatcagctggatatctggctgattttttcttaggatgtccaatgaaagaaagtgaagtagctgatgcttaaaaggaagaattttctct 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================================================ agtttacttagaaggcctaaaatcagctggatatctggctgattttttcttaggatgtccaatgaaagaaagtgaagtagctgatgcttaaaaggaagaattttctct Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_0095:SSA_0097|SSA_0095:SSA_0097:Threonine synthase, putative:Multi antimicrobial extrusion (MATE) family transporter, putative:->->:98180..98287 108 agtttacttagaaggcctaaaatcagctggatatctggctgattttttcttaggatgtccaatgaaagaaagtgaagtagctgatgcttaaaaggaagaattttctct Intra-Species Hit: Count: 1 Min: 1 Max: 108 Len: 108 Subject: NC_009009_SSA_0095_SSA_0097|Threonine synthase, putative:Multi antimicrobial extrusion (MATE) family transporter, putative|POSITIVE:POSITIVE|[98180,98287]|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 agtttacttagaaggcctaaaatcagctggatatctggctgattttttcttaggatgtccaatgaaagaaagtgaagtagctgatgcttaaaaggaagaattttctct agtttacttagaaggcctaaaatcagctggatatctggctgattttttcttaggatgtccaatgaaagaaagtgaagtagctgatgcttaaaaggaagaattttctct Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGUUUACUUAGAAGGCCUAAAAUCAGCUGGAUAUCUGGCUGAUUUUUUCUUAGGAUGUCCAAUGAAAGAAAGUGAAGUAGCUGAUGCUUAAAAGGAAGAAUUUUCUCU ..(((((((..((((...(((((((((..(....)..))))))))).)))).((....)).........)))))))..(((....))).................... (-24.20) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGAGAAAAUUCUUCCUUUUAAGCAUCAGCUACUUCACUUUCUUUCAUUGGACAUCCUAAGAAAAAAUCAGCCAGAUAUCCAGCUGAUUUUAGGCCUUCUAAGUAAACU .((((....)))).......(((....)))................(((((...(((((.....(((((((..(....)..))))))))))))...)))))....... (-16.60) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 304 46 1 160 121 NC_009009:SSA_2274|5end_hypothetical_protein_2275232..2275462_NEGATIVE 300 67 21 85 35 NC_009009:SSA_0487|5end_Delta-aminolevulinic_acid_dehydratase,_putative_487349..487579_POSITIVE 288 55 13 202 161 NC_009009:SSA_1661|5end_hypothetical_protein_1658004..1658234_NEGATIVE 286 57 14 49 1 NC_009009:SSA_2334|5end_D-alanine--D-alanyl_carrier_protein_ligase,_putative_2338007..2338237_NEGATIVE 283 60 14 59 20 NC_009009:SSA_0452|5end_Nitrogen_utilization_substance_protein_B,_putative_451534..451764_POSITIVE 282 61 23 158 120 NC_009009:SSA_2065|5end_hypothetical_protein_2065743..2065973_NEGATIVE 281 60 14 117 67 NC_009009:SSA_0710|5end_Exopolysaccharide_biosynthesis_protein,_acetyltransferase,_putative_695639..695869_NEGATIVE 275 60 16 179 130 NC_009009:SSA_0216|5end_Histidine_kinase,_putative_211877..212107_POSITIVE 270 51 11 146 103 NC_009009:SSA_0547|5end_Acyl_carrier_protein_synthase,_putative_541991..542221_POSITIVE 270 49 14 62 32 NC_009009:SSA_0272|5end_Oxidoreductase,_aldo/keto_reductase_family,_putative_266023..266253_POSITIVE 266 41 10 69 36 NC_009009:SSA_1553|5end_Permease,_putative_1555047..1555277_POSITIVE 266 49 10 110 68 NC_009009:SSA_1169|5end_Conserved_hypothetical_protein_with_an_alpha/beta_hydrolase_fold,_putative_1195951..1196181_POSITIVE 265 44 10 64 19 NC_009009:SSA_2066|5end_DNA_polymerase_III_polC-type,_putative_2070137..2070367_NEGATIVE 263 60 23 113 79 NC_009009:SSA_2347|5end_Coenzyme_F390_synthetase,_putative_2349939..2350169_NEGATIVE 263 40 2 37 1 NC_009009:SSA_1077|5end_N-acetyl-glucosamine_matabolism,_putative_1094979..1095209_POSITIVE 263 60 12 197 144 NC_009009:SSA_0389|5end_hypothetical_protein_384172..384402_POSITIVE 262 59 12 61 15 NC_009009:SSA_0546|5end_Phospho-2-dehydro-3-deoxyheptonate_aldolase_(DAHP_synthatase),_possibly_tyr-sensitive,_putative_540852..541082_POSITIVE 262 60 16 148 99 NC_009009:SSA_0422|5end_Phosphoglycerate_mutase_family_protein,_putative_420157..420387_POSITIVE 260 42 10 164 132 NC_009009:SSA_0531|5end_Ethanolamine_utilization_protein_eutQ_(cobalamin-dependent_degradation_of_ethanolamine),_putative_527355..527585_POSITIVE 257 60 14 201 164 NC_009009:SSA_1322|5end_Glycosyl_transferase,_putative_1339819..1340049_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 343 60 14 77 31 NC_009009:SSA_0095|3end_Threonine_synthase,_putative_98119..98269_POSITIVE 300 67 21 98 48 NC_009009:SSA_0486|3end_Uroporphyrinogen-III_synthase,_putative_487442..487592_POSITIVE 288 64 33 130 101 NC_009009:SSA_2074|3end_Preprotein_translocase_subunit_YajC,_putative_2076600..2076750_NEGATIVE 283 60 14 81 42 NC_009009:SSA_0451|3end_Conserved_uncharacterized_protein_451636..451786_POSITIVE 281 62 21 102 62 NC_009009:SSA_1745|3end_General_stress_response_protein_CsbD,_putative_1731997..1732147_NEGATIVE 281 60 14 124 74 NC_009009:SSA_0709|3end_hypothetical_protein_695632..695782_NEGATIVE 278 60 13 151 110 NC_009009:SSA_2066|3end_DNA_polymerase_III_polC-type,_putative_2065749..2065899_NEGATIVE 270 49 14 52 22 NC_009009:SSA_0271|3end_Glycosylhydrolase,_family_35,_putative_266093..266243_POSITIVE 269 60 13 45 1 NC_009009:SSA_1076|3end_hypothetical_protein_1095047..1095197_POSITIVE 269 48 1 85 39 NC_009009:SSA_0243|3end_Cyclo-nucleotide_phosphodiesterase,_putative_235824..235974_NEGATIVE 267 58 13 60 15 NC_009009:SSA_0573|3end_hypothetical_protein_568616..568766_NEGATIVE 266 41 10 72 39 NC_009009:SSA_1552|3end_hypothetical_protein_1555130..1555280_POSITIVE 265 59 12 81 33 NC_009009:SSA_1867|3end_ABC-type_polar_amino_acid_transport_system,_ATPase_component,_putative_1862353..1862503_NEGATIVE 263 64 24 106 70 NC_009009:SSA_2004|3end_Zinc_metalloprotease_zmpB_precursor,_putative_1999216..1999366_NEGATIVE 262 59 12 59 13 NC_009009:SSA_0544|3end_Phospho-2-dehydro-3-deoxyheptonate_aldolase,_putative_540930..541080_POSITIVE 262 60 16 151 102 NC_009009:SSA_0421|3end_Phosphoglycerate_mutase_family_protein,_putative_420240..420390_POSITIVE 260 42 10 146 114 NC_009009:SSA_0530|3end_Ethanolamine_utilization_protein_(transporter),_putative_527417..527567_POSITIVE 259 40 1 150 117 NC_009009:SSA_1615|3end_Alanine_dehydrogenase,_putative_1619318..1619468_POSITIVE 256 56 14 115 77 NC_009009:SSA_2366|3end_ABC-type_cobalt_transport_system,_ATPase_component,_putative_2368030..2368180_NEGATIVE 255 59 11 130 78 NC_009009:SSA_0879|3end_Cell_division_regulator,_negative_regulator_of_FtsZ_septation_ring_formation,_putative_875436..875586_POSITIVE