Origin IGS: taaaaactggtgagaatgttctgcactaatcccaaaagttaaacacaaaaaatctaacttttagggtgcagttcagttcctcgaccagttttttcaattgctttaaaatattttcccta .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tagggaaaatattttaaagcaattgaaaaaactggtcgaggaactgaactgcaccctaaaagttagattttttgtgtttaacttttgggattagtgcagaacattctcaccagttttta Mask Tandem Repeat Region ================================================ taaaaactggtgagaatgttctgcactaatcccaaaagttaaacacaaaaaatctaacttttagggtgcagttcagttcctcgaccagttttttcaattgctttaaaatattttcccta Find is-nt database================================================ Query_seq: SSA_0322:SSA_0323|SSA_0322:SSA_0323:Transcriptional activator, TipA family, putative:Flavoprotein, putative:-><-:315595..315713 119 taaaaactggtgagaatgttctgcactaatcccaaaagttaaacacaaaaaatctaacttttagggtgcagttcagttcctcgaccagttttttcaattgctttaaaatattttcccta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_0322:SSA_0323|SSA_0322:SSA_0323:Transcriptional activator, TipA family, putative:Flavoprotein, putative:-><-:315595..315713 119 taaaaactggtgagaatgttctgcactaatcccaaaagttaaacacaaaaaatctaacttttagggtgcagttcagttcctcgaccagttttttcaattgctttaaaatattttcccta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_0322:SSA_0323|SSA_0322:SSA_0323:Transcriptional activator, TipA family, putative:Flavoprotein, putative:-><-:315595..315713 119 taaaaactggtgagaatgttctgcactaatcccaaaagttaaacacaaaaaatctaacttttagggtgcagttcagttcctcgaccagttttttcaattgctttaaaatattttcccta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 taaaaactggtgagaatgttctgcactaatcccaaaagttaaacacaaaaaatctaacttttagggtgcagttcagttcctcgaccagttttttcaattgctttaaaatattttcccta Predict ORF larger than 30AA ================================================ taaaaactggtgagaatgttctgcactaatcccaaaagttaaacacaaaaaatctaacttttagggtgcagttcagttcctcgaccagttttttcaattgctttaaaatattttcccta 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: 82 Start: 80 End: 109 ...............................................................................CTCGACCAGTTTTTTCAATTGCTTTAAAAT.......... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ taaaaactggtgagaatgttctgcactaatcccaaaagttaaacacaaaaaatctaacttttagggtgcagttcagttcctcgaccagttttttcaattgctttaaaatattttcccta Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_0322:SSA_0323|SSA_0322:SSA_0323:Transcriptional activator, TipA family, putative:Flavoprotein, putative:-><-:315595..315713 119 taaaaactggtgagaatgttctgcactaatcccaaaagttaaacacaaaaaatctaacttttagggtgcagttcagttcctcgaccagttttttcaattgctttaaaatattttcccta Intra-Species Hit: Count: 1 Min: 1 Max: 119 Len: 119 Subject: NC_009009_SSA_0322_SSA_0323|Transcriptional activator, TipA family, putative:Flavoprotein, putative|POSITIVE:NEGATIVE|[315595,315713]|119 HSP 1 e-value: 1.0E-61 bit: 236.0 Len: 119 Query Start:1 Query End:119 Subject Strand: POSITIVE Subject Start: 1 Subject End: 119 taaaaactggtgagaatgttctgcactaatcccaaaagttaaacacaaaaaatctaacttttagggtgcagttcagttcctcgaccagttttttcaattgctttaaaatattttcccta taaaaactggtgagaatgttctgcactaatcccaaaagttaaacacaaaaaatctaacttttagggtgcagttcagttcctcgaccagttttttcaattgctttaaaatattttcccta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAAAACUGGUGAGAAUGUUCUGCACUAAUCCCAAAAGUUAAACACAAAAAAUCUAACUUUUAGGGUGCAGUUCAGUUCCUCGACCAGUUUUUUCAAUUGCUUUAAAAUAUUUUCCCUA .(((((((((((((..((..((((((....((.((((((((.............)))))))).))))))))..))....))).)))))))))).......................... (-31.52) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAGGGAAAAUAUUUUAAAGCAAUUGAAAAAACUGGUCGAGGAACUGAACUGCACCCUAAAAGUUAGAUUUUUUGUGUUUAACUUUUGGGAUUAGUGCAGAACAUUCUCACCAGUUUUUA ..........................((((((((((.(((((..((..((((((((((((((((((((.......))))))))))))))....))))))..))))))))))))))))). (-40.50) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 290 103 61 69 18 NC_009009:SSA_1152|5end_Protein_chain_release_factor_A,_putative_1180759..1180989_POSITIVE 275 89 46 77 22 NC_009009:SSA_0219|5end_PTS_system,_sugar-specific_enzyme_IIA_component,_putative_215367..215597_POSITIVE 268 81 58 131 109 NC_009009:SSA_1258|5end_Purine_nucleoside_phosphorylase,_family_1,_putative_1284652..1284882_NEGATIVE 266 95 53 164 124 NC_009009:SSA_0265|5end_ORFA,_transposon_ISSsa1_259391..259621_POSITIVE 259 104 74 126 96 NC_009009:SSA_1910|5end_hypothetical_protein_1902672..1902902_NEGATIVE 256 100 53 163 104 NC_009009:SSA_1783|5end_Xanthosine_triphosphate_pyrophosphatase_(NTPase/HAM1_family),_putative_1769106..1769336_NEGATIVE 256 75 31 146 102 NC_009009:SSA_1361|5end_ORFA,_transposon_ISSsa2_1377168..1377398_POSITIVE 255 102 62 57 20 NC_009009:SSA_1070|5end_Ribosomal_large_subunit_pseudouridine_synthase_D,_putative_1088742..1088972_POSITIVE 254 105 63 51 7 NC_009009:SSA_1989|5end_ABC-type_transport_system_(uncharacterized),_ATPase_component,_putative_1985182..1985412_NEGATIVE 254 102 67 61 18 NC_009009:SSA_0539|5end_PduO_protein,_putative_534233..534463_POSITIVE 253 78 31 154 102 NC_009009:SSA_0573|5end_hypothetical_protein_568732..568962_NEGATIVE 247 93 62 73 38 NC_009009:SSA_0592|5end_hypothetical_protein_583626..583856_POSITIVE 246 100 51 218 149 NC_009009:SSA_0034|5end_hypothetical_protein_39547..39777_POSITIVE 244 103 63 149 106 NC_009009:SSA_2322|5end_Transcriptional_regulator,_TetR/AcrR_family,_putative_2327044..2327274_POSITIVE 242 105 61 98 43 NC_009009:SSA_0973|5end_hypothetical_protein_980296..980526_POSITIVE 242 102 65 118 79 NC_009009:SSA_0549|5end_ATP-dependent_DNA_helicase_recG,_transcription-repair_coupling_factor,_putative_543556..543786_POSITIVE 241 101 61 164 126 NC_009009:SSA_1404|5end_hypothetical_protein_1418723..1418953_NEGATIVE 240 41 6 48 14 NC_009009:SSA_0540|5end_Glycerol_uptake_facilitator_protein,_putative_534955..535185_POSITIVE 238 103 64 210 165 NC_009009:SSA_2101|5end_Amino_acid_ABC_transporter,_periplasmic_amino_acid-binding_protein,_putative_2105393..2105623_NEGATIVE 237 100 60 199 147 NC_009009:SSA_2188|5end_Conserved_uncharacterized_protein_2188896..2189126_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 266 95 53 69 29 NC_009009:SSA_0264|3end_PEP_phosphonomutase-like_protein,_putative_259376..259526_POSITIVE 265 102 63 151 117 NC_009009:SSA_2020|3end_hypothetical_protein_2022471..2022621_POSITIVE 261 69 29 65 27 NC_009009:SSA_0617|3end_Membrane_protease_subunits,_stomatin/prohibitin-like_protein_(SPFH_domain/band_7_family),_putative_611438..611588_POSITIVE 259 104 74 133 103 NC_009009:SSA_1911|3end_Conserved_uncharacterized_protein_1902665..1902815_NEGATIVE 256 75 31 68 24 NC_009009:SSA_1360|3end_Arginine/histidine_ABC_transporter,_ATPase_component,_putative_1377170..1377320_POSITIVE 255 102 62 73 36 NC_009009:SSA_1069|3end_Lipoprotein_signal_peptidase,_putative_1088838..1088988_POSITIVE 253 78 31 85 33 NC_009009:SSA_0574|3end_YdjX_protein,_putative_568801..568951_NEGATIVE 251 93 55 89 50 NC_009009:SSA_0322|3end_Transcriptional_activator,_TipA_family,_putative_315534..315684_POSITIVE 247 93 62 61 26 NC_009009:SSA_0591|3end_Conserved_uncharacterized_protein_583694..583844_POSITIVE 243 88 41 89 31 NC_009009:SSA_2010|3end_ABC-type_multidrug_transport_system,_permease_component,_putative_2011296..2011446_NEGATIVE 242 105 61 86 31 NC_009009:SSA_0972|3end_hypothetical_protein_980364..980514_POSITIVE 241 101 61 129 91 NC_009009:SSA_1405|3end_Copper_homeostasis_protein_CutC,_putative_1418758..1418908_NEGATIVE 237 106 67 70 31 NC_009009:SSA_0198|3end_Dihydrofolate_synthetase,_putative_198375..198525_POSITIVE 229 99 57 146 107 NC_009009:SSA_1837|3end_hypothetical_protein_1832955..1833105_POSITIVE 226 95 61 47 10 NC_009009:SSA_1904|3end_ABC-type_multidrug_transport_system,_permease_component,_putative_1898233..1898383_NEGATIVE 226 88 52 139 100 NC_009009:SSA_1649|3end_hypothetical_protein_1647906..1648056_NEGATIVE 226 88 57 79 42 NC_009009:SSA_0472|3end_Precorrin-3B_C17-methyltransferase,_putative_475585..475735_POSITIVE 224 47 3 118 77 NC_009009:SSA_1668|3end_NrdI_protein,_putative_1667738..1667888_NEGATIVE 222 84 53 141 97 NC_009009:SSA_1848|3end_Methionyl-tRNA_formyltransferase,_putative_1842243..1842393_NEGATIVE 222 91 53 146 107 NC_009009:SSA_1784|3end_Glutamate_racemase,_putative_1769103..1769253_NEGATIVE