Origin IGS: aaagaaagaagtctgttgtttgacaggcttctttttcttgatagtctcttcttgtaaaacctttctcgcagttgtataatagaattagctcaagtgaatgagaagagcaaatgaagtgcagtttgctccagtagattttacgaagagatagaagcggaaagggagttagtcaagaaaga .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tctttcttgactaactccctttccgcttctatctcttcgtaaaatctactggagcaaactgcacttcatttgctcttctcattcacttgagctaattctattatacaactgcgagaaaggttttacaagaagagactatcaagaaaaagaagcctgtcaaacaacagacttctttcttt Mask Tandem Repeat Region ================================================ aaagaaagaagtctgttgtttgacaggcttctttttcttgatagtctcttcttgtaaaacctttctcgcagttgtataatagaattagctcaagtgaatgagaagagcaaatgaagtgcagtttgctccagtagattttacgaagagatagaagcggaaagggagttagtcaagaaaga Find is-nt database================================================ Query_seq: SSA_0908:SSA_0909|SSA_0908:SSA_0909:ABC-type uncharacterized transport system, periplasmic component, putative:Transcriptional regulator, AbrB family (stationary/sporulation gene expression), putative:->->:920848..921026 179 aaagaaagaagtctgttgtttgacaggcttctttttcttgatagtctcttcttgtaaaacctttctcgcagttgtataatagaattagctcaagtgaatgagaagagcaaatgaagtgcagtttgctccagtagattttacgaagagatagaagcggaaagggagttagtcaagaaaga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_0908:SSA_0909|SSA_0908:SSA_0909:ABC-type uncharacterized transport system, periplasmic component, putative:Transcriptional regulator, AbrB family (stationary/sporulation gene expression), putative:->->:920848..921026 179 aaagaaagaagtctgttgtttgacaggcttctttttcttgatagtctcttcttgtaaaacctttctcgcagttgtataatagaattagctcaagtgaatgagaagagcaaatgaagtgcagtttgctccagtagattttacgaagagatagaagcggaaagggagttagtcaagaaaga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_0908:SSA_0909|SSA_0908:SSA_0909:ABC-type uncharacterized transport system, periplasmic component, putative:Transcriptional regulator, AbrB family (stationary/sporulation gene expression), putative:->->:920848..921026 179 aaagaaagaagtctgttgtttgacaggcttctttttcttgatagtctcttcttgtaaaacctttctcgcagttgtataatagaattagctcaagtgaatgagaagagcaaatgaagtgcagtttgctccagtagattttacgaagagatagaagcggaaagggagttagtcaagaaaga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aaagaaagaagtctgttgtttgacaggcttctttttcttgatagtctcttcttgtaaaacctttctcgcagttgtataatagaattagctcaagtgaatgagaagagcaaatgaagtgcagtttgctccagtagattttacgaagagatagaagcggaaagggagttagtcaagaaaga Predict ORF larger than 30AA ================================================ Protein_Len: 45 Strand: - Start: 2 End: 136 . L F F D T T Q C A E K E Q Y D R R T F G K E C N Y L L I L E L S H S S C I F H L K S W Y M ........................................... aaagaaagaagtctgttgtttgacaggcttctttttcttgatagtctcttcttgtaaaacctttctcgcagttgtataatagaattagctcaagtgaatgagaagagcaaatgaagtgcagtttgctccagtagattttacgaagagatagaagcggaaagggagttagtcaagaaaga 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: 85 Start: 51 End: 80 ..................................................CTTGTAAAACCTTTCTCGCAGTTGTATAAT................................................................................................... PromScan Matrix: RpoD-17 Strand: - Score: 83 Start: 76 End: 105 ...........................................................................CTTCTCATTCACTTGAGCTAATTCTATTAT.......................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ aaagaaagaagtctgttgtttgacaggcttctttttcttgatagtctcttcttgtaaaacctttctcgcagttgtataatagaattagctcaagtgaatgagaagagcaaatgaagtgcagtttgctccagtagattttacgaagagatagaagcggaaagggagttagtcaagaaaga Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 57 HP_score: -4.7 Tail_Score: -3.54109 Start: 105 End: 128 Full_Region: tcgtaaaatctactg gagcaaactg cactt catttgctc ttctcattcacttga ........................................................................................................gagcaaactgcacttcatttgctc................................................... Find igs database================================================ Query_seq: SSA_0908:SSA_0909|SSA_0908:SSA_0909:ABC-type uncharacterized transport system, periplasmic component, putative:Transcriptional regulator, AbrB family (stationary/sporulation gene expression), putative:->->:920848..921026 179 aaagaaagaagtctgttgtttgacaggcttctttttcttgatagtctcttcttgtaaaacctttctcgcagttgtataatagaattagctcaagtgaatgagaagagcaaatgaagtgcagtttgctccagtagattttacgaagagatagaagcggaaagggagttagtcaagaaaga Intra-Species Hit: Count: 1 Min: 1 Max: 179 Len: 179 Subject: NC_009009_SSA_0908_SSA_0909|ABC-type uncharacterized transport system, periplasmic component, putative:Transcriptional regulator, AbrB family (stationary/sporulation gene expression), putative|POSITIVE:POSITIVE|[920848,921026]|179 HSP 1 e-value: 3.0E-97 bit: 355.0 Len: 179 Query Start:1 Query End:179 Subject Strand: POSITIVE Subject Start: 1 Subject End: 179 aaagaaagaagtctgttgtttgacaggcttctttttcttgatagtctcttcttgtaaaacctttctcgcagttgtataatagaattagctcaagtgaatgagaagagcaaatgaagtgcagtttgctccagtagattttacgaagagatagaagcggaaagggagttagtcaagaaaga aaagaaagaagtctgttgtttgacaggcttctttttcttgatagtctcttcttgtaaaacctttctcgcagttgtataatagaattagctcaagtgaatgagaagagcaaatgaagtgcagtttgctccagtagattttacgaagagatagaagcggaaagggagttagtcaagaaaga Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAGAAAGAAGUCUGUUGUUUGACAGGCUUCUUUUUCUUGAUAGUCUCUUCUUGUAAAACCUUUCUCGCAGUUGUAUAAUAGAAUUAGCUCAAGUGAAUGAGAAGAGCAAAUGAAGUGCAGUUUGCUCCAGUAGAUUUUACGAAGAGAUAGAAGCGGAAAGGGAGUUAGUCAAGAAAGA ...((((((((((((((....))))))))))))))((((((((.((((((..(((.....((.((((....(((((.(((........((((......))))..((((((((........))))))))......))).))))).)))).))..)))..)))))).)..))))))).... (-53.60) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UCUUUCUUGACUAACUCCCUUUCCGCUUCUAUCUCUUCGUAAAAUCUACUGGAGCAAACUGCACUUCAUUUGCUCUUCUCAUUCACUUGAGCUAAUUCUAUUAUACAACUGCGAGAAAGGUUUUACAAGAAGAGACUAUCAAGAAAAAGAAGCCUGUCAAACAACAGACUUCUUUCUUU ...(((((((........(.....)......((((((((((((((((...((((((((.((.....)))))))))).((((......))))..........................)))))))))..)))))))...)))))))(((((((.((((......)))).))))))).... (-40.00) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 330 129 81 227 181 NC_009009:SSA_2000|5end_hypothetical_protein_1997469..1997699_NEGATIVE 325 69 26 136 96 NC_009009:SSA_1601|5end_VacB-like_protein,_putative_1607059..1607289_NEGATIVE 312 169 123 56 13 NC_009009:SSA_1657|5end_hypothetical_protein_1653231..1653461_NEGATIVE 290 129 87 149 109 NC_009009:SSA_2237|5end_Dihydrofolate:folylpolyglutamate_synthetase,_putative_2236740..2236970_NEGATIVE 290 168 124 63 24 NC_009009:SSA_1020|5end_hypothetical_protein_1035557..1035787_POSITIVE 276 157 112 43 7 NC_009009:SSA_1143|5end_Na+-driven_multidrug_efflux_pump,_putative_1173497..1173727_NEGATIVE 274 158 112 113 72 NC_009009:SSA_0364|5end_Serine/threonine:Na+_symporter,_putative_356348..356578_NEGATIVE 273 49 10 179 142 NC_009009:SSA_1376|5end_Transport_protein,_putative_1396111..1396341_NEGATIVE 271 147 105 161 122 NC_009009:SSA_0817|5end_Antirepressor_regulating_drug_resistance_(membrane-bound),_putative_797838..798068_POSITIVE 271 159 111 197 142 NC_009009:SSA_0812|5end_hypothetical_protein_793443..793673_POSITIVE 270 47 13 120 85 NC_009009:SSA_1756|5end_Conserved_uncharacterized_protein_1745291..1745521_NEGATIVE 270 170 125 193 145 NC_009009:SSA_0727|5end_Metal-dependent_membrane_protease,_putative_712735..712965_POSITIVE 269 49 7 178 121 NC_009009:SSA_0509|5end_Propanediol_utilization_protein,_putative_508024..508254_POSITIVE 268 130 81 43 2 NC_009009:SSA_0365|5end_Small-conductance_mechanosensitive_efflux_channel,_putative_356621..356851_POSITIVE 268 69 21 158 108 NC_009009:SSA_0311|5end_hypothetical_protein_305877..306107_POSITIVE 265 165 121 164 109 NC_009009:SSA_2071|5end_hypothetical_protein_2074766..2074996_NEGATIVE 265 45 1 160 110 NC_009009:SSA_0185|5end_Competence_protein_ComYB,_putative_189057..189287_POSITIVE 264 164 121 178 138 NC_009009:SSA_1176|5end_Acetoin_dehydrogenase,_E1_component,_beta_subunit,_putative_1205405..1205635_NEGATIVE 262 100 52 85 31 NC_009009:SSA_1237|5end_Uracil-DNA_glycosylase,_putative_1262366..1262596_NEGATIVE 259 133 95 209 165 NC_009009:SSA_1903|5end_hypothetical_protein_1898182..1898412_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 340 47 3 104 55 NC_009009:SSA_0908|3end_ABC-type_uncharacterized_transport_system,_periplasmic_component,_putative_920787..920937_POSITIVE 299 69 24 147 102 NC_009009:SSA_1544|3end_Conserved_uncharacterized_protein_1548314..1548464_NEGATIVE 290 159 118 85 51 NC_009009:SSA_0036|3end_Secreted_protein,_possible_function_in_cell-wall_metabolism_(amidase),_putative_42050..42200_NEGATIVE 271 147 105 145 106 NC_009009:SSA_0816|3end_Copper_transport_operon_or_penicillinase_transcription_repressor,_putative_797902..798052_POSITIVE 270 47 13 129 94 NC_009009:SSA_1757|3end_hypothetical_protein_1745282..1745432_NEGATIVE 269 49 7 138 81 NC_009009:SSA_0508|3end_Conserved_uncharacterized_protein,_possible_phosphoserine_phosphatase_508064..508214_POSITIVE 268 54 12 108 62 NC_009009:SSA_0345|3end_hypothetical_protein_339209..339359_POSITIVE 265 165 121 130 75 NC_009009:SSA_2072|3end_Phosphatidate_cytidylyltransferase,_putative_2074800..2074950_NEGATIVE 265 164 123 56 17 NC_009009:SSA_0150|3end_hypothetical_protein_145227..145377_POSITIVE 264 164 121 134 94 NC_009009:SSA_1178|3end_Acetoin_dehydrogenase,_E1_component,_alpha_subunit,_putative_1205449..1205599_NEGATIVE 262 131 93 36 1 NC_009009:SSA_0485|3end_Porphobilinogen_deaminase,_putative_486732..486882_POSITIVE 259 170 121 73 31 NC_009009:SSA_0407|3end_ABC-type_multidrug_transport_system_(3-component_subtilin_immunity_exporter),_ATPase_component,_putative_402911..403061_NEGATIVE 258 102 61 132 83 NC_009009:SSA_0589|3end_Acetylornithine_deacetylase/succinyl-diaminopimelate_desuccinylase_(M20/M25/M40_family_peptidase),_putative_582207..582357_POSITIVE 256 46 7 75 35 NC_009009:SSA_1694|3end_PTS_system,_lactose-specific_IIA_component,_putative_1686811..1686961_NEGATIVE 255 143 105 39 3 NC_009009:SSA_0892|3end_ATP-binding_cassette_lipoprotein,_putative_884578..884728_POSITIVE 254 108 68 75 31 NC_009009:SSA_0868|3end_hypothetical_protein_860675..860825_NEGATIVE 253 131 91 74 14 NC_009009:SSA_2332|3end_D-alanyl_carrier_protein,_putative_2334957..2335107_NEGATIVE 253 144 105 127 86 NC_009009:SSA_2212|3end_Possible_polysaccharide_transport_protein,_putative_2212627..2212777_NEGATIVE 253 66 22 92 28 NC_009009:SSA_1855|3end_hypothetical_protein_1850897..1851047_NEGATIVE 253 119 71 86 32 NC_009009:SSA_0705|3end_hypothetical_protein_690552..690702_NEGATIVE