Origin IGS: cttctagtcgctttggaaactgtaaggaaattttaaaaatttctaaaaaacttgaccctccccttaggtcatggtatatactagttaggtaaggaggtctatc .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 gatagacctccttacctaactagtatataccatgacctaaggggagggtcaagttttttagaaatttttaaaatttccttacagtttccaaagcgactagaag Mask Tandem Repeat Region ================================================ cttctagtcgctttggaaactgtaaggaaattttaaaaatttctaaaaaacttgaccctccccttaggtcatggtatatactagttaggtaaggaggtctatc Find is-nt database================================================ Query_seq: SSA_0321:SSA_0322|SSA_0321:SSA_0322:Methylase, putative:Transcriptional activator, TipA family, putative:->->:314754..314856 103 cttctagtcgctttggaaactgtaaggaaattttaaaaatttctaaaaaacttgaccctccccttaggtcatggtatatactagttaggtaaggaggtctatc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_0321:SSA_0322|SSA_0321:SSA_0322:Methylase, putative:Transcriptional activator, TipA family, putative:->->:314754..314856 103 cttctagtcgctttggaaactgtaaggaaattttaaaaatttctaaaaaacttgaccctccccttaggtcatggtatatactagttaggtaaggaggtctatc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_0321:SSA_0322|SSA_0321:SSA_0322:Methylase, putative:Transcriptional activator, TipA family, putative:->->:314754..314856 103 cttctagtcgctttggaaactgtaaggaaattttaaaaatttctaaaaaacttgaccctccccttaggtcatggtatatactagttaggtaaggaggtctatc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 cttctagtcgctttggaaactgtaaggaaattttaaaaatttctaaaaaacttgaccctccccttaggtcatggtatatactagttaggtaaggaggtctatc Predict ORF larger than 30AA ================================================ cttctagtcgctttggaaactgtaaggaaattttaaaaatttctaaaaaacttgaccctccccttaggtcatggtatatactagttaggtaaggaggtctatc 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================================================ cttctagtcgctttggaaactgtaaggaaattttaaaaatttctaaaaaacttgaccctccccttaggtcatggtatatactagttaggtaaggaggtctatc Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_0321:SSA_0322|SSA_0321:SSA_0322:Methylase, putative:Transcriptional activator, TipA family, putative:->->:314754..314856 103 cttctagtcgctttggaaactgtaaggaaattttaaaaatttctaaaaaacttgaccctccccttaggtcatggtatatactagttaggtaaggaggtctatc Intra-Species Hit: Count: 1 Min: 1 Max: 103 Len: 103 Subject: NC_009009_SSA_0321_SSA_0322|Methylase, putative:Transcriptional activator, TipA family, putative|POSITIVE:POSITIVE|[314754,314856]|103 HSP 1 e-value: 4.0E-52 bit: 204.0 Len: 103 Query Start:1 Query End:103 Subject Strand: POSITIVE Subject Start: 1 Subject End: 103 cttctagtcgctttggaaactgtaaggaaattttaaaaatttctaaaaaacttgaccctccccttaggtcatggtatatactagttaggtaaggaggtctatc cttctagtcgctttggaaactgtaaggaaattttaaaaatttctaaaaaacttgaccctccccttaggtcatggtatatactagttaggtaaggaggtctatc Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CUUCUAGUCGCUUUGGAAACUGUAAGGAAAUUUUAAAAAUUUCUAAAAAACUUGACCCUCCCCUUAGGUCAUGGUAUAUACUAGUUAGGUAAGGAGGUCUAUC (((((..((...((((.........(((((((.....))))))).....((((((((.........))))).))).....))))...))..)))))....... (-18.00) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAUAGACCUCCUUACCUAACUAGUAUAUACCAUGACCUAAGGGGAGGGUCAAGUUUUUUAGAAAUUUUUAAAAUUUCCUUACAGUUUCCAAAGCGACUAGAAG ...................(((((........((((((.......)))))).(((((...((((((..(((.......))).)))))).))))).)))))... (-14.70) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 289 99 51 222 167 NC_009009:SSA_0067|5end_Acyltransferase_(yrhL-like_subfamily_of_SGNH-hydrolases),_putative_68005..68235_POSITIVE 279 98 57 194 152 NC_009009:SSA_0434|5end_Glutamate_formiminotransferase,_putative_436568..436798_NEGATIVE 260 100 56 38 1 NC_009009:SSA_1440|5end_Phosphoribosyl-ATP_pyrophosphohydrolase,_putative_1444721..1444951_NEGATIVE 250 98 51 75 26 NC_009009:SSA_0620|5end_hypothetical_protein_612325..612555_NEGATIVE 244 99 51 177 137 NC_009009:SSA_2334|5end_D-alanine--D-alanyl_carrier_protein_ligase,_putative_2338007..2338237_NEGATIVE 244 100 51 117 70 NC_009009:SSA_1311|5end_Hydrolase,_haloacid_dehalogenase-like_family,_putative_1328393..1328623_NEGATIVE 241 100 67 205 178 NC_009009:SSA_0398|5end_hypothetical_protein_396452..396682_NEGATIVE 240 78 40 43 4 NC_009009:SSA_0140|5end_Copper-translocating_P-type_ATPase,_putative_134626..134856_POSITIVE 239 98 57 150 104 NC_009009:SSA_1045|5end_hypothetical_protein_1060841..1061071_POSITIVE 236 75 39 94 65 NC_009009:SSA_0499|5end_ABC-type_dipeptide_transport_system,_periplasmic_component,_putative_498915..499145_POSITIVE 235 100 57 148 98 NC_009009:SSA_2372|5end_hypothetical_protein_2373807..2374037_POSITIVE 234 44 4 202 159 NC_009009:SSA_1900|5end_N_utilization_substance_protein_A,_putative_1896012..1896242_NEGATIVE 231 90 50 141 104 NC_009009:SSA_1074|5end_Pyrroline-5-carboxylate_reductase,_putative_1092151..1092381_POSITIVE 230 100 58 151 100 NC_009009:SSA_2132|5end_Ure_cluster_protein,_putative_2134170..2134400_POSITIVE 228 73 39 171 138 NC_009009:SSA_1758|5end_hypothetical_protein_1746619..1746849_NEGATIVE 227 90 55 45 4 NC_009009:SSA_2346|5end_3-oxoacyl-[acyl-carrier-protein]_synthase_III,_putative_2348546..2348776_NEGATIVE 223 71 51 36 8 NC_009009:SSA_1720|5end_Initiation-control_protein,_putative_1707113..1707343_NEGATIVE 223 100 59 53 17 NC_009009:SSA_0486|5end_Uroporphyrinogen-III_synthase,_putative_486637..486867_POSITIVE 222 99 52 149 94 NC_009009:SSA_1971|5end_hypothetical_protein_1967167..1967397_POSITIVE 222 93 51 43 2 NC_009009:SSA_1728|5end_ABC_transporter_membrane-spanning_permease-branched_chain_amino_acid_transport,_putative_1714293..1714523_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 279 98 57 73 31 NC_009009:SSA_0435|3end_Urocanate_hydratase,_putative_436689..436839_NEGATIVE 261 31 1 132 106 NC_009009:SSA_0819|3end_hypothetical_protein_801181..801331_POSITIVE 250 98 51 78 29 NC_009009:SSA_0621|3end_SOS_responce_UmuC_protein,_putative_612322..612472_NEGATIVE 240 97 60 47 11 NC_009009:SSA_2293|3end_hypothetical_protein_2295955..2296105_POSITIVE 240 78 40 43 4 NC_009009:SSA_0139|3end_Copper_transport_operon_or_penicillinase_transcriptional_repressor,_putative_134706..134856_POSITIVE 234 44 4 148 105 NC_009009:SSA_1901|3end_Conserved_uncharacterized_protein_1896066..1896216_NEGATIVE 233 92 55 133 104 NC_009009:SSA_0548|3end_Alanine_racemase,_putative_543529..543679_POSITIVE 231 90 50 138 101 NC_009009:SSA_1073|3end_Gamma-glutamyl_phosphate_reductase,_putative_1092228..1092378_POSITIVE 230 100 58 148 97 NC_009009:SSA_2131|3end_DNA-binding_protein,_putative_2134247..2134397_POSITIVE 229 100 57 146 96 NC_009009:SSA_0915|3end_hypothetical_protein_928014..928164_POSITIVE 228 73 39 126 93 NC_009009:SSA_1759|3end_hypothetical_protein_1746664..1746814_NEGATIVE 223 100 59 68 32 NC_009009:SSA_0485|3end_Porphobilinogen_deaminase,_putative_486732..486882_POSITIVE 223 74 49 144 116 NC_009009:SSA_0205|3end_NisK_(sensor-receptor_histidine_kinase_domain),_putative_203839..203989_POSITIVE 220 97 52 54 7 NC_009009:SSA_0837|3end_Glucosyltransferase,_putative_825502..825652_POSITIVE 219 100 56 151 98 NC_009009:SSA_1384|3end_hypothetical_protein_1401715..1401865_NEGATIVE 217 100 52 68 20 NC_009009:SSA_0576|3end_Conserved_GTPase,_putative_571225..571375_POSITIVE 216 22 3 122 106 NC_009009:SSA_0416|3end_5-methyltetrahydropteroyltriglutamate--_homocysteine_methyltransferase,_putative_414222..414372_POSITIVE 215 29 2 31 8 NC_009009:SSA_0703|3end_Citrate_synthase,_putative_689352..689502_POSITIVE 213 98 53 68 2 NC_009009:SSA_1593|3end_Dipeptidase,_putative_1596390..1596540_NEGATIVE 208 100 58 69 33 NC_009009:SSA_0070|3end_Acetylxylan_esterase,_putative_74914..75064_POSITIVE