Origin IGS: ctctggacaggtactctaagtctcatatgggcatattatagcaaaaataggcctgattttcaatttgaatcgggcttagggtgccttaaatgactttgccgaaaatctaatctaaaatcagaaattcctcttctttctggtttagcttcatcaggatttttgttataatagtagcattgactttgaaagaggaagaaaa .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 ttttcttcctctttcaaagtcaatgctactattataacaaaaatcctgatgaagctaaaccagaaagaagaggaatttctgattttagattagattttcggcaaagtcatttaaggcaccctaagcccgattcaaattgaaaatcaggcctatttttgctataatatgcccatatgagacttagagtacctgtccagag Mask Tandem Repeat Region ================================================ ctctggacaggtactctaagtctcatatgggcatattatagcaaaaataggcctgattttcaatttgaatcgggcttagggtgccttaaatgactttgccgaaaatctaatctaaaatcagaaattcctcttctttctggtttagcttcatcaggatttttgttataatagtagcattgactttgaaagaggaagaaaa Find is-nt database================================================ Query_seq: SSA_0851:SSA_0852|SSA_0851:SSA_0852:Cation efflux family protein, putative:ATP-dependent DNA helicase, putative:<-->:838991..839189 199 ctctggacaggtactctaagtctcatatgggcatattatagcaaaaataggcctgattttcaatttgaatcgggcttagggtgccttaaatgactttgccgaaaatctaatctaaaatcagaaattcctcttctttctggtttagcttcatcaggatttttgttataatagtagcattgactttgaaagaggaagaaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_0851:SSA_0852|SSA_0851:SSA_0852:Cation efflux family protein, putative:ATP-dependent DNA helicase, putative:<-->:838991..839189 199 ctctggacaggtactctaagtctcatatgggcatattatagcaaaaataggcctgattttcaatttgaatcgggcttagggtgccttaaatgactttgccgaaaatctaatctaaaatcagaaattcctcttctttctggtttagcttcatcaggatttttgttataatagtagcattgactttgaaagaggaagaaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_0851:SSA_0852|SSA_0851:SSA_0852:Cation efflux family protein, putative:ATP-dependent DNA helicase, putative:<-->:838991..839189 199 ctctggacaggtactctaagtctcatatgggcatattatagcaaaaataggcctgattttcaatttgaatcgggcttagggtgccttaaatgactttgccgaaaatctaatctaaaatcagaaattcctcttctttctggtttagcttcatcaggatttttgttataatagtagcattgactttgaaagaggaagaaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ctctggacaggtactctaagtctcatatgggcatattatagcaaaaataggcctgattttcaatttgaatcgggcttagggtgccttaaatgactttgccgaaaatctaatctaaaatcagaaattcctcttctttctggtttagcttcatcaggatttttgttataatagtagcattgactttgaaagaggaagaaaa Predict ORF larger than 30AA ================================================ ctctggacaggtactctaagtctcatatgggcatattatagcaaaaataggcctgattttcaatttgaatcgggcttagggtgccttaaatgactttgccgaaaatctaatctaaaatcagaaattcctcttctttctggtttagcttcatcaggatttttgttataatagtagcattgactttgaaagaggaagaaaa 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: 92 Start: 35 End: 64 ..................................ATTGAAAATCAGGCCTATTTTTGCTATAAT....................................................................................................................................... PromScan Matrix: RpoD-17 Strand: + Score: 84 Start: 140 End: 169 ...........................................................................................................................................GTTTAGCTTCATCAGGATTTTTGTTATAAT.............................. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ ctctggacaggtactctaagtctcatatgggcatattatagcaaaaataggcctgattttcaatttgaatcgggcttagggtgccttaaatgactttgccgaaaatctaatctaaaatcagaaattcctcttctttctggtttagcttcatcaggatttttgttataatagtagcattgactttgaaagaggaagaaaa Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_0851:SSA_0852|SSA_0851:SSA_0852:Cation efflux family protein, putative:ATP-dependent DNA helicase, putative:<-->:838991..839189 199 ctctggacaggtactctaagtctcatatgggcatattatagcaaaaataggcctgattttcaatttgaatcgggcttagggtgccttaaatgactttgccgaaaatctaatctaaaatcagaaattcctcttctttctggtttagcttcatcaggatttttgttataatagtagcattgactttgaaagaggaagaaaa Intra-Species Hit: Count: 1 Min: 1 Max: 199 Len: 199 Subject: NC_009009_SSA_0851_SSA_0852|Cation efflux family protein, putative:ATP-dependent DNA helicase, putative|NEGATIVE:POSITIVE|[838991,839189]|199 HSP 1 e-value: 1.0E-109 bit: 394.0 Len: 199 Query Start:1 Query End:199 Subject Strand: POSITIVE Subject Start: 1 Subject End: 199 ctctggacaggtactctaagtctcatatgggcatattatagcaaaaataggcctgattttcaatttgaatcgggcttagggtgccttaaatgactttgccgaaaatctaatctaaaatcagaaattcctcttctttctggtttagcttcatcaggatttttgttataatagtagcattgactttgaaagaggaagaaaa ctctggacaggtactctaagtctcatatgggcatattatagcaaaaataggcctgattttcaatttgaatcgggcttagggtgccttaaatgactttgccgaaaatctaatctaaaatcagaaattcctcttctttctggtttagcttcatcaggatttttgttataatagtagcattgactttgaaagaggaagaaaa Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CUCUGGACAGGUACUCUAAGUCUCAUAUGGGCAUAUUAUAGCAAAAAUAGGCCUGAUUUUCAAUUUGAAUCGGGCUUAGGGUGCCUUAAAUGACUUUGCCGAAAAUCUAAUCUAAAAUCAGAAAUUCCUCUUCUUUCUGGUUUAGCUUCAUCAGGAUUUUUGUUAUAAUAGUAGCAUUGACUUUGAAAGAGGAAGAAAA .(((((..((((((((((((((......((((.((((........)))).))))(((((.......))))).)))))))))))))).....((.(((....))).))..........)))))..(((.(((((((((.((((..(((.......(((....)))........)))...))))..))))))))).))).. (-51.06) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUUCUUCCUCUUUCAAAGUCAAUGCUACUAUUAUAACAAAAAUCCUGAUGAAGCUAAACCAGAAAGAAGAGGAAUUUCUGAUUUUAGAUUAGAUUUUCGGCAAAGUCAUUUAAGGCACCCUAAGCCCGAUUCAAAUUGAAAAUCAGGCCUAUUUUUGCUAUAAUAUGCCCAUAUGAGACUUAGAGUACCUGUCCAGAG ........(((((((.(((((.(((....(((((((.(((((((((((((....(((((.((((((.........))))))..)))))....((((((....))))))......(((.......)))...............))))))...))))))).)))))))....)))....))))).))).........)))) (-34.80) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 909 100 51 191 142 NC_009009:SSA_0851|5end_Cation_efflux_family_protein,_putative_838900..839130_NEGATIVE 321 149 101 196 152 NC_009009:SSA_0316|5end_hypothetical_protein_310576..310806_POSITIVE 304 38 2 202 168 NC_009009:SSA_0760|5end_Acetylornithine_aminotransferase,_putative_742581..742811_POSITIVE 297 75 31 68 25 NC_009009:SSA_1016|5end_Phosphoenolpyruvate_synthase,_putative_1019602..1019832_POSITIVE 292 100 52 223 171 NC_009009:SSA_1242|5end_Dihydroorotate_dehydrogenase_B,_putative_1267386..1267616_NEGATIVE 287 159 111 98 45 NC_009009:SSA_2228|5end_Acetyltransferase_(GNAT)_family,_putative_2228768..2228998_NEGATIVE 286 157 117 130 90 NC_009009:SSA_1027|5end_hypothetical_protein_1043527..1043757_POSITIVE 279 99 57 148 108 NC_009009:SSA_1445|5end_Imidazole_glycerol-phosphate_dehydratase,_putative_1447886..1448116_NEGATIVE 274 180 136 212 163 NC_009009:SSA_1499|5end_50S_ribosomal_protein_L35,_putative_1504357..1504587_NEGATIVE 274 178 136 153 110 NC_009009:SSA_0497|5end_Nickel_ABC_transporter,_putative_496922..497152_POSITIVE 272 89 49 57 16 NC_009009:SSA_0546|5end_Phospho-2-dehydro-3-deoxyheptonate_aldolase_(DAHP_synthatase),_possibly_tyr-sensitive,_putative_540852..541082_POSITIVE 268 156 116 120 86 NC_009009:SSA_2090|5end_Hexulose-6-phosphate_synthase,_putative_2095038..2095268_NEGATIVE 268 87 51 196 167 NC_009009:SSA_1258|5end_Purine_nucleoside_phosphorylase,_family_1,_putative_1284652..1284882_NEGATIVE 268 62 27 65 26 NC_009009:SSA_0800|5end_Glutamine_amidotransferase,_putative_782774..783004_NEGATIVE 264 85 49 202 171 NC_009009:SSA_1446|5end_Histidinol_dehydrogenase,_putative_1449190..1449420_NEGATIVE 264 32 4 195 171 NC_009009:SSA_1364|5end_hypothetical_protein_1381297..1381527_NEGATIVE 257 99 51 61 15 NC_009009:SSA_2049|5end_Polyribonucleotide_nucleotidyltransferase,_putative_2052894..2053124_NEGATIVE 257 167 131 141 97 NC_009009:SSA_1741|5end_ABC-type_Fe3+-siderophores_transporter,_ATPase_component,_putative_1728007..1728237_POSITIVE 256 75 32 231 193 NC_009009:SSA_1835|5end_Late_competence_protein,_putative_1830941..1831171_NEGATIVE 256 100 51 169 131 NC_009009:SSA_0978|5end_hypothetical_protein_983736..983966_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 297 75 31 68 25 NC_009009:SSA_1015|3end_4-hydroxybenzoate_octaprenyltransferase,_putative_1019682..1019832_POSITIVE 286 157 117 140 100 NC_009009:SSA_1026|3end_ABC-type_multidrug_transporter,_ATPase_component,_putative_1043617..1043767_POSITIVE 279 99 57 136 96 NC_009009:SSA_1446|3end_Histidinol_dehydrogenase,_putative_1447898..1448048_NEGATIVE 272 89 49 55 14 NC_009009:SSA_0544|3end_Phospho-2-dehydro-3-deoxyheptonate_aldolase,_putative_540930..541080_POSITIVE 268 156 116 96 62 NC_009009:SSA_2091|3end_Phosphotransferase_system_sugar-specific_EII_component,_putative_2095062..2095212_NEGATIVE 268 62 27 65 26 NC_009009:SSA_0801|3end_Mur_ligase_family_protein,_putative_782774..782924_NEGATIVE 264 32 4 140 116 NC_009009:SSA_1365|3end_FmtA-like_protein,_putative_1381352..1381502_NEGATIVE 263 162 125 49 3 NC_009009:SSA_2229|3end_hypothetical_protein_2228821..2228971_NEGATIVE 256 93 53 75 32 NC_009009:SSA_0339|3end_hypothetical_protein_333483..333633_NEGATIVE 254 101 61 61 21 NC_009009:SSA_1236|3end_Mutator_protein,_putative_1261240..1261390_NEGATIVE 254 149 111 120 76 NC_009009:SSA_0808|3end_hypothetical_protein_791012..791162_POSITIVE 250 84 42 99 44 NC_009009:SSA_1434|3end_Conserved_uncharacterized_Firmicutes_protein_1441100..1441250_POSITIVE 250 76 36 114 60 NC_009009:SSA_1249|3end_hypothetical_protein_1273275..1273425_NEGATIVE 248 41 5 139 107 NC_009009:SSA_0703|3end_Citrate_synthase,_putative_689352..689502_POSITIVE 246 100 53 121 84 NC_009009:SSA_1264|3end_hypothetical_protein_1289305..1289455_NEGATIVE 246 164 125 141 104 NC_009009:SSA_0496|3end_Succinylglutamate_desuccinylase_/_Aspartoacylase_family,_putative_497009..497159_POSITIVE 246 156 111 128 84 NC_009009:SSA_0050|3end_Dihydroxyacetone_kinase,_phosphatase_domain_(Dak2),_putative_55270..55420_POSITIVE 243 110 64 63 8 NC_009009:SSA_2317|3end_Tfp_pilus_assembly_protein,_pilus_retraction_ATPase_PilT,_putative_2318346..2318496_NEGATIVE 243 155 119 86 48 NC_009009:SSA_1759|3end_hypothetical_protein_1746664..1746814_NEGATIVE 243 107 69 45 3 NC_009009:SSA_1307|3end_Trk_transporter_membrane-spanning_protein-K+_transport,_putative_1324921..1325071_NEGATIVE