Origin IGS: cattttatgaagaggtgacaatcagactttgcagtctctccgccttgtgctataataagtgtcaatgaaagaaagtataaaaaataagaaagaataggtaaaacaatcc .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 ggattgttttacctattctttcttattttttatactttctttcattgacacttattatagcacaaggcggagagactgcaaagtctgattgtcacctcttcataaaatg Mask Tandem Repeat Region ================================================ cattttatgaagaggtgacaatcagactttgcagtctctccgccttgtgctataataagtgtcaatgaaagaaagtataaaaaataagaaagaataggtaaaacaatcc Find is-nt database================================================ Query_seq: SSA_0403:SSA_0405|SSA_0403:SSA_0405:CAAX amino terminal protease family, putative:Transcriptional regulator, XRE family, putative:->->:401449..401557 109 cattttatgaagaggtgacaatcagactttgcagtctctccgccttgtgctataataagtgtcaatgaaagaaagtataaaaaataagaaagaataggtaaaacaatcc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_0403:SSA_0405|SSA_0403:SSA_0405:CAAX amino terminal protease family, putative:Transcriptional regulator, XRE family, putative:->->:401449..401557 109 cattttatgaagaggtgacaatcagactttgcagtctctccgccttgtgctataataagtgtcaatgaaagaaagtataaaaaataagaaagaataggtaaaacaatcc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_0403:SSA_0405|SSA_0403:SSA_0405:CAAX amino terminal protease family, putative:Transcriptional regulator, XRE family, putative:->->:401449..401557 109 cattttatgaagaggtgacaatcagactttgcagtctctccgccttgtgctataataagtgtcaatgaaagaaagtataaaaaataagaaagaataggtaaaacaatcc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 cattttatgaagaggtgacaatcagactttgcagtctctccgccttgtgctataataagtgtcaatgaaagaaagtataaaaaataagaaagaataggtaaaacaatcc Predict ORF larger than 30AA ================================================ Protein_Len: 35 Strand: - Start: 3 End: 107 .. K I F L H C D S K A T E G G Q A I I L T L S L F Y L F Y S L I P L V M .. cattttatgaagaggtgacaatcagactttgcagtctctccgccttgtgctataataagtgtcaatgaaagaaagtataaaaaataagaaagaataggtaaaacaatcc 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: 27 End: 56 ..........................CTTTGCAGTCTCTCCGCCTTGTGCTATAAT..................................................... PromScan Matrix: RpoD-17 Strand: - Score: 84 Start: 74 End: 103 .........................................................................TTTTACCTATTCTTTCTTATTTTTTATACT...... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ cattttatgaagaggtgacaatcagactttgcagtctctccgccttgtgctataataagtgtcaatgaaagaaagtataaaaaataagaaagaataggtaaaacaatcc Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_0403:SSA_0405|SSA_0403:SSA_0405:CAAX amino terminal protease family, putative:Transcriptional regulator, XRE family, putative:->->:401449..401557 109 cattttatgaagaggtgacaatcagactttgcagtctctccgccttgtgctataataagtgtcaatgaaagaaagtataaaaaataagaaagaataggtaaaacaatcc Intra-Species Hit: Count: 1 Min: 1 Max: 109 Len: 109 Subject: NC_009009_SSA_0403_SSA_0405|CAAX amino terminal protease family, putative:Transcriptional regulator, XRE family, putative|POSITIVE:POSITIVE|[401449,401557]|109 HSP 1 e-value: 1.0E-55 bit: 216.0 Len: 109 Query Start:1 Query End:109 Subject Strand: POSITIVE Subject Start: 1 Subject End: 109 cattttatgaagaggtgacaatcagactttgcagtctctccgccttgtgctataataagtgtcaatgaaagaaagtataaaaaataagaaagaataggtaaaacaatcc cattttatgaagaggtgacaatcagactttgcagtctctccgccttgtgctataataagtgtcaatgaaagaaagtataaaaaataagaaagaataggtaaaacaatcc Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CAUUUUAUGAAGAGGUGACAAUCAGACUUUGCAGUCUCUCCGCCUUGUGCUAUAAUAAGUGUCAAUGAAAGAAAGUAUAAAAAAUAAGAAAGAAUAGGUAAAACAAUCC ..(((((((..((((((......(((((....)))))...))))))..(((......)))...............)))))))........................... (-12.50) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GGAUUGUUUUACCUAUUCUUUCUUAUUUUUUAUACUUUCUUUCAUUGACACUUAUUAUAGCACAAGGCGGAGAGACUGCAAAGUCUGAUUGUCACCUCUUCAUAAAAUG .............................................(((((.........((.....))....(((((....)))))...)))))............... (-10.90) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 331 57 11 212 165 NC_009009:SSA_2037|5end_tRNA_(Guanosine-2'-O-)-methyltransferase,_TrmH_family,_putative_2041524..2041754_NEGATIVE 299 64 24 60 26 NC_009009:SSA_0269|5end_Phosphotransferase_system_(PTS)_cellobiose-specific_component_IIA,_putative_262550..262780_POSITIVE 286 52 13 101 62 NC_009009:SSA_2055|5end_hypothetical_protein_2058160..2058390_NEGATIVE 283 44 8 162 117 NC_009009:SSA_1726|5end_ABC_transporter_ATP-binding_protein-branched_chain_amino_acid_transport,_putative_1712467..1712697_NEGATIVE 282 51 11 53 11 NC_009009:SSA_0163|5end_hypothetical_protein_162127..162357_POSITIVE 278 59 12 61 2 NC_009009:SSA_1367|5end_hypothetical_protein_1383593..1383823_POSITIVE 276 70 21 84 35 NC_009009:SSA_0656|5end_Cell_division_protein_FtsZ,_putative_640159..640389_POSITIVE 266 59 13 70 15 NC_009009:SSA_2131|5end_DNA-binding_protein,_putative_2133949..2134179_POSITIVE 265 51 22 120 84 NC_009009:SSA_1910|5end_hypothetical_protein_1902672..1902902_NEGATIVE 263 70 25 162 122 NC_009009:SSA_0696|5end_hypothetical_protein_679154..679384_POSITIVE 262 51 13 57 21 NC_009009:SSA_1070|5end_Ribosomal_large_subunit_pseudouridine_synthase_D,_putative_1088742..1088972_POSITIVE 260 51 19 54 16 NC_009009:SSA_0241|5end_Ribosomal_protein_L11_methyltransferase,_putative_234021..234251_POSITIVE 259 39 2 153 109 NC_009009:SSA_2302|5end_Type_IV_fimbrial_biogenesis_protein,_prepilin_cysteine_protease_(C20)_PilD,_putative_2304044..2304274_NEGATIVE 256 48 10 87 51 NC_009009:SSA_1901|5end_Conserved_uncharacterized_protein_1896599..1896829_NEGATIVE 251 45 16 103 78 NC_009009:SSA_0561|5end_RNA:NAD_2'-phosphotransferase,_putative_553630..553860_POSITIVE 248 78 36 227 177 NC_009009:SSA_1325|5end_Ketoacyl_reductase_hetN,_putative_1342343..1342573_NEGATIVE 248 51 12 170 125 NC_009009:SSA_0364|5end_Serine/threonine:Na+_symporter,_putative_356348..356578_NEGATIVE 246 45 6 138 104 NC_009009:SSA_2228|5end_Acetyltransferase_(GNAT)_family,_putative_2228768..2228998_NEGATIVE 246 75 31 67 31 NC_009009:SSA_2001|5end_Hydroxymethylpyrimidine/phosphomethylpyrimidine_kinase,_putative_1998220..1998450_NEGATIVE 246 50 10 70 23 NC_009009:SSA_1045|5end_hypothetical_protein_1060841..1061071_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 307 51 11 107 67 NC_009009:SSA_0686|3end_Fe2+/Zn2+_uptake_regulation_protein,_putative_670079..670229_POSITIVE 299 64 24 51 17 NC_009009:SSA_0268|3end_Phosphotransferase_system_(PTS)_cellobiose-specific_component_IIB,_putative_262621..262771_POSITIVE 276 70 21 67 18 NC_009009:SSA_0655|3end_Cell_division_protein_FtsA,_putative_640222..640372_POSITIVE 266 59 13 61 6 NC_009009:SSA_2130|3end_hypothetical_protein_2134020..2134170_POSITIVE 265 51 22 127 91 NC_009009:SSA_1911|3end_Conserved_uncharacterized_protein_1902665..1902815_NEGATIVE 263 70 25 143 103 NC_009009:SSA_0695|3end_hypothetical_protein_679215..679365_POSITIVE 262 50 12 122 78 NC_009009:SSA_1960|3end_hypothetical_protein_1956571..1956721_NEGATIVE 262 51 13 73 37 NC_009009:SSA_1069|3end_Lipoprotein_signal_peptidase,_putative_1088838..1088988_POSITIVE 259 39 2 84 40 NC_009009:SSA_2303|3end_hypothetical_protein_2304113..2304263_NEGATIVE 251 45 16 110 85 NC_009009:SSA_0560|3end_hypothetical_protein_553717..553867_POSITIVE 249 52 21 136 100 NC_009009:SSA_2340|3end_hypothetical_protein_2341539..2341689_NEGATIVE 247 50 8 138 99 NC_009009:SSA_2018|3end_hypothetical_protein_2017464..2017614_NEGATIVE 246 45 6 85 51 NC_009009:SSA_2229|3end_hypothetical_protein_2228821..2228971_NEGATIVE 246 75 31 77 41 NC_009009:SSA_2002|3end_tRNA_pseudouridine_synthase_A,_putative_1998210..1998360_NEGATIVE 246 63 24 147 111 NC_009009:SSA_0322|3end_Transcriptional_activator,_TipA_family,_putative_315534..315684_POSITIVE 245 48 2 94 52 NC_009009:SSA_1576|3end_Catabolite_control_protein_A,_putative_1579177..1579327_NEGATIVE 242 62 24 104 64 NC_009009:SSA_0407|3end_ABC-type_multidrug_transport_system_(3-component_subtilin_immunity_exporter),_ATPase_component,_putative_402911..403061_NEGATIVE 241 50 7 151 104 NC_009009:SSA_0738|3end_Ornithine_carbamoyltransferase,_catabolic,_putative_721000..721150_POSITIVE 240 68 24 128 79 NC_009009:SSA_0522|3end_Ethanolamine_utilization_protein,_putative_521710..521860_POSITIVE 237 45 7 92 54 NC_009009:SSA_0882|3end_Phosphoserine_phosphatase,_putative_877630..877780_POSITIVE