Origin IGS: taagctaaaagtttgcgtccgtcttttacaaaacgatgttcttagttatcatctgaaataagcgcagtgtacttccttttattctctaattccgaagttcgagagaaagaagtgctatgcgcttcttttttgtgaaaattttctttatatcaagaaaacttctggaaaatatgatataatagttgcgtataaaatatgaaaaggagtttttgtaac .........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 gttacaaaaactccttttcatattttatacgcaactattatatcatattttccagaagttttcttgatataaagaaaattttcacaaaaaagaagcgcatagcacttctttctctcgaacttcggaattagagaataaaaggaagtacactgcgcttatttcagatgataactaagaacatcgttttgtaaaagacggacgcaaacttttagctta Mask Tandem Repeat Region ================================================ taagctaaaagtttgcgtccgtcttttacaaaacgatgttcttagttatcatctgaaataagcgcagtgtacttccttttattctctaattccgaagttcgagagaaagaagtgctatgcgcttcttttttgtgaaaattttctttatatcaagaaaacttctggaaaatatgatataatagttgcgtataaaatatgaaaaggagtttttgtaac Find is-nt database================================================ Query_seq: SSA_0301:SSA_0302|SSA_0301:SSA_0302:hypothetical protein:Phosphoglycerate kinase, putative:->->:294814..295029 216 taagctaaaagtttgcgtccgtcttttacaaaacgatgttcttagttatcatctgaaataagcgcagtgtacttccttttattctctaattccgaagttcgagagaaagaagtgctatgcgcttcttttttgtgaaaattttctttatatcaagaaaacttctggaaaatatgatataatagttgcgtataaaatatgaaaaggagtttttgtaac Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_0301:SSA_0302|SSA_0301:SSA_0302:hypothetical protein:Phosphoglycerate kinase, putative:->->:294814..295029 216 taagctaaaagtttgcgtccgtcttttacaaaacgatgttcttagttatcatctgaaataagcgcagtgtacttccttttattctctaattccgaagttcgagagaaagaagtgctatgcgcttcttttttgtgaaaattttctttatatcaagaaaacttctggaaaatatgatataatagttgcgtataaaatatgaaaaggagtttttgtaac Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_0301:SSA_0302|SSA_0301:SSA_0302:hypothetical protein:Phosphoglycerate kinase, putative:->->:294814..295029 216 taagctaaaagtttgcgtccgtcttttacaaaacgatgttcttagttatcatctgaaataagcgcagtgtacttccttttattctctaattccgaagttcgagagaaagaagtgctatgcgcttcttttttgtgaaaattttctttatatcaagaaaacttctggaaaatatgatataatagttgcgtataaaatatgaaaaggagtttttgtaac Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 taagctaaaagtttgcgtccgtcttttacaaaacgatgttcttagttatcatctgaaataagcgcagtgtacttccttttattctctaattccgaagttcgagagaaagaagtgctatgcgcttcttttttgtgaaaattttctttatatcaagaaaacttctggaaaatatgatataatagttgcgtataaaatatgaaaaggagtttttgtaac Predict ORF larger than 30AA ================================================ Protein_Len: 36 Strand: + Start: 89 End: 196 ........................................................................................ M P K F E R K K C Y A L L F C E N F L Y I K K T S G K Y D I I V A Y K I .................... Protein_Len: 34 Strand: - Start: 89 End: 190 ........................................................................................ N R L E L S L L A I R K K K T F I K K I D L F S R S F I I Y Y N R M .......................... taagctaaaagtttgcgtccgtcttttacaaaacgatgttcttagttatcatctgaaataagcgcagtgtacttccttttattctctaattccgaagttcgagagaaagaagtgctatgcgcttcttttttgtgaaaattttctttatatcaagaaaacttctggaaaatatgatataatagttgcgtataaaatatgaaaaggagtttttgtaac 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================================================ taagctaaaagtttgcgtccgtcttttacaaaacgatgttcttagttatcatctgaaataagcgcagtgtacttccttttattctctaattccgaagttcgagagaaagaagtgctatgcgcttcttttttgtgaaaattttctttatatcaagaaaacttctggaaaatatgatataatagttgcgtataaaatatgaaaaggagtttttgtaac Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 72 HP_score: -9.0 Tail_Score: -2.76105 Start: 98 End: 136 Full_Region: TCTCTAATTCCGAAG TTCGAGAGAAAGAAGTGC TAT GCGCTTCTTTTTTGTGAA AATTTTCTTTATATC .................................................................................................TTCGAGAGAAAGAAGTGCTATGCGCTTCTTTTTTGTGAA................................................................................ TransTerm Strand: + Conf: 95 HP_score: -8.7 Tail_Score: -5.25803 Start: 109 End: 125 Full_Region: GAAGTTCGAGAGAAA GAAGTGC TAT GCGCTTC TTTTTTGTGAAAATT ............................................................................................................GAAGTGCTATGCGCTTC........................................................................................... Find igs database================================================ Query_seq: SSA_0301:SSA_0302|SSA_0301:SSA_0302:hypothetical protein:Phosphoglycerate kinase, putative:->->:294814..295029 216 taagctaaaagtttgcgtccgtcttttacaaaacgatgttcttagttatcatctgaaataagcgcagtgtacttccttttattctctaattccgaagttcgagagaaagaagtgctatgcgcttcttttttgtgaaaattttctttatatcaagaaaacttctggaaaatatgatataatagttgcgtataaaatatgaaaaggagtttttgtaac Intra-Species Hit: Count: 1 Min: 1 Max: 216 Len: 216 Subject: NC_009009_SSA_0301_SSA_0302|hypothetical protein:Phosphoglycerate kinase, putative|POSITIVE:POSITIVE|[294814,295029]|216 HSP 1 e-value: 1.0E-119 bit: 428.0 Len: 216 Query Start:1 Query End:216 Subject Strand: POSITIVE Subject Start: 1 Subject End: 216 taagctaaaagtttgcgtccgtcttttacaaaacgatgttcttagttatcatctgaaataagcgcagtgtacttccttttattctctaattccgaagttcgagagaaagaagtgctatgcgcttcttttttgtgaaaattttctttatatcaagaaaacttctggaaaatatgatataatagttgcgtataaaatatgaaaaggagtttttgtaac taagctaaaagtttgcgtccgtcttttacaaaacgatgttcttagttatcatctgaaataagcgcagtgtacttccttttattctctaattccgaagttcgagagaaagaagtgctatgcgcttcttttttgtgaaaattttctttatatcaagaaaacttctggaaaatatgatataatagttgcgtataaaatatgaaaaggagtttttgtaac Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAGCUAAAAGUUUGCGUCCGUCUUUUACAAAACGAUGUUCUUAGUUAUCAUCUGAAAUAAGCGCAGUGUACUUCCUUUUAUUCUCUAAUUCCGAAGUUCGAGAGAAAGAAGUGCUAUGCGCUUCUUUUUUGUGAAAAUUUUCUUUAUAUCAAGAAAACUUCUGGAAAAUAUGAUAUAAUAGUUGCGUAUAAAAUAUGAAAAGGAGUUUUUGUAAC (((((.....)))))..........((((.....(((((....((((.((((..((((.(((((((..(((((((.((((..((((.(((......))).)))))))))))))))..))))))).))))..)))).))))......)))))..((((((((((.....((((..((((.........))))..))))....)))))))))))))). (-48.90) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GUUACAAAAACUCCUUUUCAUAUUUUAUACGCAACUAUUAUAUCAUAUUUUCCAGAAGUUUUCUUGAUAUAAAGAAAAUUUUCACAAAAAAGAAGCGCAUAGCACUUCUUUCUCUCGAACUUCGGAAUUAGAGAAUAAAAGGAAGUACACUGCGCUUAUUUCAGAUGAUAACUAAGAACAUCGUUUUGUAAAAGACGGACGCAAACUUUUAGCUUA ..............................((........((((((........(((((((((((......)))))))))))..........(((((((..(.((((((((((((....(....)....)))))).....)))))).)..))))))).......))))))..........(((((((....)))))))..)).............. (-43.20) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 293 107 61 142 98 NC_009009:SSA_2197|5end_hypothetical_protein_2197784..2198014_NEGATIVE 282 135 93 162 114 NC_009009:SSA_1185|5end_DNA_processing_Smf_protein,_putative_1214532..1214762_NEGATIVE 280 68 21 43 1 NC_009009:SSA_0264|5end_PEP_phosphonomutase-like_protein,_putative_258400..258630_POSITIVE 278 135 91 183 138 NC_009009:SSA_0980|5end_3-isopropylmalate_dehydratase_large_subunit,_putative_984004..984234_POSITIVE 274 128 89 130 86 NC_009009:SSA_0393|5end_Bacteriocin_ABC-type_exporter,_ATP_binding/permease_protein,_putative_388766..388996_POSITIVE 269 110 68 184 142 NC_009009:SSA_1778|5end_Segregation_and_condensation_protein_B,_putative_1765711..1765941_NEGATIVE 268 124 81 130 75 NC_009009:SSA_0920|5end_hypothetical_protein_930896..931126_POSITIVE 260 107 63 138 93 NC_009009:SSA_0523|5end_Aldehyde_dehydrogenase,_putative_521637..521867_POSITIVE 257 78 32 105 53 NC_009009:SSA_0379|5end_PTS_system,_beta-glucoside-specific_EII_component,_putative_368822..369052_POSITIVE 256 130 84 106 57 NC_009009:SSA_0597|5end_hypothetical_protein_587566..587796_POSITIVE 256 110 65 156 117 NC_009009:SSA_0367|5end_hypothetical_protein_358309..358539_POSITIVE 255 89 42 196 145 NC_009009:SSA_2177|5end_hypothetical_protein_2176215..2176445_NEGATIVE 255 130 81 228 187 NC_009009:SSA_1189|5end_GTP-binding_protein,_putative_1217657..1217887_NEGATIVE 255 55 15 165 126 NC_009009:SSA_0638|5end_Tryptophan_synthase_alpha_chain,_putative_626935..627165_POSITIVE 249 136 91 151 100 NC_009009:SSA_2082|5end_Carbohydrate_kinase,_FGGY_family,_putative_2086874..2087104_NEGATIVE 242 130 81 220 169 NC_009009:SSA_2009|5end_Heat_shock_transcription_repressor_HrcA,_putative_2011132..2011362_NEGATIVE 242 86 41 68 20 NC_009009:SSA_1131|5end_High-affinity_Fe_2+/Pb2+_permease,_putative_1157183..1157413_POSITIVE 237 126 82 144 106 NC_009009:SSA_2048|5end_Serine_acetyltransferase,_putative_2050601..2050831_NEGATIVE 237 130 103 219 192 NC_009009:SSA_1666|5end_Collagen-binding_surface_protein,_putative_1667312..1667542_NEGATIVE 236 69 30 231 193 NC_009009:SSA_1662|5end_NADH-dependent_oxidoreductase,_putative_1659422..1659652_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 293 107 61 84 40 NC_009009:SSA_2198|3end_hypothetical_protein_2197842..2197992_NEGATIVE 278 131 91 92 53 NC_009009:SSA_1930|3end_Acetyl-CoA_carboxylase_alpha_subunit,_putative_1917777..1917927_NEGATIVE 268 124 81 99 44 NC_009009:SSA_0918|3end_Conserved_uncharacterized_protein_930945..931095_POSITIVE 260 107 63 131 86 NC_009009:SSA_0522|3end_Ethanolamine_utilization_protein,_putative_521710..521860_POSITIVE 255 89 42 123 72 NC_009009:SSA_2178|3end_hypothetical_protein_2176288..2176438_NEGATIVE 255 130 81 86 45 NC_009009:SSA_1190|3end_Conserved_uncharacterized_protein_1217799..1217949_NEGATIVE 252 70 30 68 29 NC_009009:SSA_1663|3end_Collagen-binding_protein_A_1659586..1659736_NEGATIVE 249 136 91 75 24 NC_009009:SSA_2083|3end_hypothetical_protein_2086950..2087100_NEGATIVE 242 130 81 56 5 NC_009009:SSA_2010|3end_ABC-type_multidrug_transport_system,_permease_component,_putative_2011296..2011446_NEGATIVE 238 110 61 104 57 NC_009009:SSA_0731|3end_Integral_membrane_protein,_putative_715654..715804_POSITIVE 237 126 82 52 14 NC_009009:SSA_2049|3end_Polyribonucleotide_nucleotidyltransferase,_putative_2050693..2050843_NEGATIVE 234 79 35 129 78 NC_009009:SSA_1084|3end_Conserved_uncharacterized_protein_1102603..1102753_POSITIVE 234 50 3 60 4 NC_009009:SSA_0624|3end_hypothetical_protein_615698..615848_POSITIVE 231 175 134 75 34 NC_009009:SSA_0436|3end_Imidazolonepropionase,_putative_440214..440364_POSITIVE 229 120 72 134 84 NC_009009:SSA_0724|3end_ABC-type_multidrug/protein/lipid_transport_system_(pediocin_PA-1_exporter),_ATPase_and_permease_components,_putative_710312..710462_POSITIVE 227 87 41 74 25 NC_009009:SSA_0533|3end_Glycerol_dehydratase_large_subunit_pduC,_putative_530711..530861_POSITIVE 226 130 84 105 49 NC_009009:SSA_2296|3end_Transcriptional_regulator,_XRE_family,_putative_2298549..2298699_NEGATIVE 225 38 3 123 97 NC_009009:SSA_2136|3end_50S_ribosomal_protein_L34,_putative_2137507..2137657_NEGATIVE 223 129 92 45 8 NC_009009:SSA_0260|3end_Manganese/Zinc_ABC_transporter_substrate-binding_lipoprotein_precursor,_putative_253656..253806_NEGATIVE 222 110 61 120 74 NC_009009:SSA_2158|3end_Methyltransferase,_putative_2158421..2158571_NEGATIVE