Origin IGS: ggtatattctcgctttcctaggtttgattttagtatacaagctagatttcaaatatttctcaagaaattctaaaatatttctaaagaaatgcagaatcaatccaaaagcaataaaaaagcagccaaagggctgactgcttaaat .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 atttaagcagtcagccctttggctgcttttttattgcttttggattgattctgcatttctttagaaatattttagaatttcttgagaaatatttgaaatctagcttgtatactaaaatcaaacctaggaaagcgagaatatacc Mask Tandem Repeat Region ================================================ ggtatattctcgctttcctaggtttgattttagtatacaagctagatttcaaatatttctcaagaaattctaaaatatttctaaagaaatgcagaatcaatccaaaagcaataaaaaagcagccaaagggctgactgcttaaat Find is-nt database================================================ Query_seq: SSA_0409:SSA_0410|SSA_0409:SSA_0410:ABC-type multidrug transport system, ATPase component, putative:hypothetical protein:<-<-:405696..405839 144 ggtatattctcgctttcctaggtttgattttagtatacaagctagatttcaaatatttctcaagaaattctaaaatatttctaaagaaatgcagaatcaatccaaaagcaataaaaaagcagccaaagggctgactgcttaaat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_0409:SSA_0410|SSA_0409:SSA_0410:ABC-type multidrug transport system, ATPase component, putative:hypothetical protein:<-<-:405696..405839 144 ggtatattctcgctttcctaggtttgattttagtatacaagctagatttcaaatatttctcaagaaattctaaaatatttctaaagaaatgcagaatcaatccaaaagcaataaaaaagcagccaaagggctgactgcttaaat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_0409:SSA_0410|SSA_0409:SSA_0410:ABC-type multidrug transport system, ATPase component, putative:hypothetical protein:<-<-:405696..405839 144 ggtatattctcgctttcctaggtttgattttagtatacaagctagatttcaaatatttctcaagaaattctaaaatatttctaaagaaatgcagaatcaatccaaaagcaataaaaaagcagccaaagggctgactgcttaaat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ggtatattctcgctttcctaggtttgattttagtatacaagctagatttcaaatatttctcaagaaattctaaaatatttctaaagaaatgcagaatcaatccaaaagcaataaaaaagcagccaaagggctgactgcttaaat Predict ORF larger than 30AA ================================================ Protein_Len: 42 Strand: + Start: 6 End: 131 ..... M L A F L G L I L V Y K L D F K Y F S R N S K I F L K K C R I N P K A I K K Q P K G ............. Protein_Len: 37 Strand: - Start: 2 End: 112 . Y I R A K R P K I K T Y L S S K L Y K E L F E L I N R F F H L I L G F A M ................................ ggtatattctcgctttcctaggtttgattttagtatacaagctagatttcaaatatttctcaagaaattctaaaatatttctaaagaaatgcagaatcaatccaaaagcaataaaaaagcagccaaagggctgactgcttaaat 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: 83 Start: 47 End: 76 ..............................................TTTCAAATATTTCTCAAGAAATTCTAAAAT.................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ ggtatattctcgctttcctaggtttgattttagtatacaagctagatttcaaatatttctcaagaaattctaaaatatttctaaagaaatgcagaatcaatccaaaagcaataaaaaagcagccaaagggctgactgcttaaat Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_0409:SSA_0410|SSA_0409:SSA_0410:ABC-type multidrug transport system, ATPase component, putative:hypothetical protein:<-<-:405696..405839 144 ggtatattctcgctttcctaggtttgattttagtatacaagctagatttcaaatatttctcaagaaattctaaaatatttctaaagaaatgcagaatcaatccaaaagcaataaaaaagcagccaaagggctgactgcttaaat Intra-Species Hit: Count: 1 Min: 1 Max: 144 Len: 144 Subject: NC_009009_SSA_0409_SSA_0410|ABC-type multidrug transport system, ATPase component, putative:hypothetical protein|NEGATIVE:NEGATIVE|[405696,405839]|144 HSP 1 e-value: 2.0E-76 bit: 285.0 Len: 144 Query Start:1 Query End:144 Subject Strand: POSITIVE Subject Start: 1 Subject End: 144 ggtatattctcgctttcctaggtttgattttagtatacaagctagatttcaaatatttctcaagaaattctaaaatatttctaaagaaatgcagaatcaatccaaaagcaataaaaaagcagccaaagggctgactgcttaaat ggtatattctcgctttcctaggtttgattttagtatacaagctagatttcaaatatttctcaagaaattctaaaatatttctaaagaaatgcagaatcaatccaaaagcaataaaaaagcagccaaagggctgactgcttaaat Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GGUAUAUUCUCGCUUUCCUAGGUUUGAUUUUAGUAUACAAGCUAGAUUUCAAAUAUUUCUCAAGAAAUUCUAAAAUAUUUCUAAAGAAAUGCAGAAUCAAUCCAAAAGCAAUAAAAAAGCAGCCAAAGGGCUGACUGCUUAAAU ((...(((((.((........((((((.((((((......))))))..)))))).(((((..((((((........))))))..))))).)))))))....))..(((((.........(((((....)))))..))))).... (-32.80) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUUUAAGCAGUCAGCCCUUUGGCUGCUUUUUUAUUGCUUUUGGAUUGAUUCUGCAUUUCUUUAGAAAUAUUUUAGAAUUUCUUGAGAAAUAUUUGAAAUCUAGCUUGUAUACUAAAAUCAAACCUAGGAAAGCGAGAAUAUACC ....((((((((((....)))))))))).....((((((((((.((((((....(((((((.((((((........)))))).)))))))..........(((........))).)))))).))...))))))))......... (-33.60) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 898 140 91 231 182 NC_009009:SSA_0409|5end_ABC-type_multidrug_transport_system,_ATPase_component,_putative_405605..405835_NEGATIVE 599 80 31 175 126 NC_009009:SSA_0407|5end_ABC-type_multidrug_transport_system_(3-component_subtilin_immunity_exporter),_ATPase_component,_putative_403843..404073_NEGATIVE 315 42 1 151 94 NC_009009:SSA_0378|5end_TRZ/ATZ_family_hydrolase,_putative_367276..367506_POSITIVE 303 140 91 189 143 NC_009009:SSA_0875|5end_Rod_shape_determining_protein_(cell-cycle_protein),_putative_868928..869158_POSITIVE 301 86 41 200 154 NC_009009:SSA_0412|5end_ABC-type_multidrug_transport_system_(3-component_subtilin_immunity_exporter),_ATPase_component,_putative_408163..408393_NEGATIVE 291 139 119 47 27 NC_009009:SSA_0918|5end_Conserved_uncharacterized_protein_930398..930628_POSITIVE 280 140 102 229 183 NC_009009:SSA_1739|5end_UDP-N-acetylmuramoylalanyl-D-glutamate--2,_6-diaminopimelate_ligase,_putative_1725540..1725770_POSITIVE 274 140 91 49 4 NC_009009:SSA_0215|5end_Periplasmic_sugar-binding_protein_(ribose_porter),_putative_210891..211121_POSITIVE 271 140 92 167 105 NC_009009:SSA_1014|5end_Phosphatidylserine_decarboxylase_proenzyme_2,_putative_1017846..1018076_POSITIVE 265 139 97 176 138 NC_009009:SSA_0441|5end_hypothetical_protein_441481..441711_POSITIVE 265 138 91 55 11 NC_009009:SSA_0319|5end_Branched-chain_amino_acid_permease_(L-methionine,_L-isoleucine,_leucine_and_valine),_putative_312721..312951_POSITIVE 262 139 104 168 135 NC_009009:SSA_0154|5end_hypothetical_protein_149836..150066_POSITIVE 261 137 91 60 7 NC_009009:SSA_0626|5end_hypothetical_protein_616089..616319_POSITIVE 257 88 41 179 132 NC_009009:SSA_0253|5end_CAAX_amino_terminal_protease_family_protein,_putative_246289..246519_POSITIVE 252 139 106 206 173 NC_009009:SSA_0962|5end_Lactoylglutathione_lyase,_putative_970965..971195_POSITIVE 245 138 92 193 151 NC_009009:SSA_0659|5end_hypothetical_protein_643003..643233_POSITIVE 245 138 95 51 5 NC_009009:SSA_0330|5end_hypothetical_protein_323799..324029_POSITIVE 243 139 93 189 137 NC_009009:SSA_2087|5end_Conserved_uncharacterized_protein_2092657..2092887_NEGATIVE 241 137 92 57 2 NC_009009:SSA_1840|5end_RNA_binding_protein,_putative_1834422..1834652_NEGATIVE 237 140 97 135 96 NC_009009:SSA_2205|5end_Transcription_antitermination_factor_NusG,_putative_2206100..2206330_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 449 97 52 46 1 NC_009009:SSA_0408|3end_hypothetical_protein_403989..404139_NEGATIVE 320 133 100 137 98 NC_009009:SSA_1682|3end_hypothetical_protein_1676130..1676280_NEGATIVE 301 86 41 48 2 NC_009009:SSA_0413|3end_Anthranilate/para-aminobenzoate_synthases_component_I/_Chorismate_binding_enzyme,_putative_408315..408465_NEGATIVE 265 139 97 80 42 NC_009009:SSA_0440|3end_30S_ribosomal_protein_S18,_putative_441465..441615_POSITIVE 265 138 91 45 1 NC_009009:SSA_0318|3end_Secreted_metalloendopeptidase_Gcp_312791..312941_POSITIVE 261 137 91 73 20 NC_009009:SSA_0625|3end_Phosphopantetheine_adenylyltransferase_616182..616332_POSITIVE 258 140 91 89 9 NC_009009:SSA_0242|3end_hypothetical_protein_235810..235960_POSITIVE 252 139 106 92 59 NC_009009:SSA_0961|3end_Possible_ketopantoate_reductase_PanE/ApbA,_putative_970931..971081_POSITIVE 251 140 91 56 8 NC_009009:SSA_0273|3end_hypothetical_protein_268566..268716_POSITIVE 243 139 93 80 28 NC_009009:SSA_2088|3end_Carbohydrate_isomerase,_AraD/FucA_family,_putative_2092766..2092916_NEGATIVE 241 137 92 57 2 NC_009009:SSA_1841|3end_Cof_family_protein/peptidyl-prolyl_cis-trans_isomerase,_cyclophilin_type,_putative_1834422..1834572_NEGATIVE 239 139 100 67 20 NC_009009:SSA_0099|3end_hypothetical_protein_100134..100284_NEGATIVE 236 137 115 56 29 NC_009009:SSA_0581|3end_Conserved_uncharacterized_protein_573774..573924_POSITIVE 233 139 108 76 38 NC_009009:SSA_0868|3end_hypothetical_protein_860675..860825_NEGATIVE 231 139 92 81 22 NC_009009:SSA_0812|3end_hypothetical_protein_794434..794584_POSITIVE 230 138 118 63 42 NC_009009:SSA_0996|3end_cGMP-specific_phosphodiesterase,_putative_996859..997009_POSITIVE 228 139 96 84 39 NC_009009:SSA_0931|3end_hypothetical_protein_941335..941485_POSITIVE 227 134 91 63 6 NC_009009:SSA_1982|3end_Transcriptional_regulator,_LytR/AlgR_family,_putative_1975427..1975577_NEGATIVE 225 46 9 61 16 NC_009009:SSA_0274|3end_hypothetical_protein_268580..268730_NEGATIVE 224 140 92 56 13 NC_009009:SSA_2200|3end_Firmicutes_transcriptional_repressor_of_class_III_stress_genes_(CtsR),_putative_2201109..2201259_NEGATIVE