Origin IGS: gaaatcccatcaagtccagtctgcaatttggctgactaaactttgatacaagaaatacgataagggcggggaagcttatttccccagccctttatctgctgttaataggagtaacac .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 gtgttactcctattaacagcagataaagggctggggaaataagcttccccgcccttatcgtatttcttgtatcaaagtttagtcagccaaattgcagactggacttgatgggatttc Mask Tandem Repeat Region ================================================ gaaatcccatcaagtccagtctgcaatttggctgactaaactttgatacaagaaatacgataagggcggggaagcttatttccccagccctttatctgctgttaataggagtaacac Find is-nt database================================================ Query_seq: SSA_0588:SSA_0589|SSA_0588:SSA_0589:L-cystine ABC transporter, substrate-binding component, putative:Acetylornithine deacetylase/succinyl-diaminopimelate desuccinylase (M20/M25/M40 family peptidase), putative:->->:580768..580884 117 gaaatcccatcaagtccagtctgcaatttggctgactaaactttgatacaagaaatacgataagggcggggaagcttatttccccagccctttatctgctgttaataggagtaacac Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_0588:SSA_0589|SSA_0588:SSA_0589:L-cystine ABC transporter, substrate-binding component, putative:Acetylornithine deacetylase/succinyl-diaminopimelate desuccinylase (M20/M25/M40 family peptidase), putative:->->:580768..580884 117 gaaatcccatcaagtccagtctgcaatttggctgactaaactttgatacaagaaatacgataagggcggggaagcttatttccccagccctttatctgctgttaataggagtaacac Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_0588:SSA_0589|SSA_0588:SSA_0589:L-cystine ABC transporter, substrate-binding component, putative:Acetylornithine deacetylase/succinyl-diaminopimelate desuccinylase (M20/M25/M40 family peptidase), putative:->->:580768..580884 117 gaaatcccatcaagtccagtctgcaatttggctgactaaactttgatacaagaaatacgataagggcggggaagcttatttccccagccctttatctgctgttaataggagtaacac Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gaaatcccatcaagtccagtctgcaatttggctgactaaactttgatacaagaaatacgataagggcggggaagcttatttccccagccctttatctgctgttaataggagtaacac Predict ORF larger than 30AA ================================================ gaaatcccatcaagtccagtctgcaatttggctgactaaactttgatacaagaaatacgataagggcggggaagcttatttccccagccctttatctgctgttaataggagtaacac 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================================================ gaaatcccatcaagtccagtctgcaatttggctgactaaactttgatacaagaaatacgataagggcggggaagcttatttccccagccctttatctgctgttaataggagtaacac Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 86 HP_score: -10.9 Tail_Score: -4.13591 Start: 64 End: 90 Full_Region: CAAGAAATACGATAA GGGCGGGGAAG CTTA TTTCCCCAGCCC TTTATCTGCTGTTAA ...............................................................GGGCGGGGAAGCTTATTTCCCCAGCCC........................... Find igs database================================================ Query_seq: SSA_0588:SSA_0589|SSA_0588:SSA_0589:L-cystine ABC transporter, substrate-binding component, putative:Acetylornithine deacetylase/succinyl-diaminopimelate desuccinylase (M20/M25/M40 family peptidase), putative:->->:580768..580884 117 gaaatcccatcaagtccagtctgcaatttggctgactaaactttgatacaagaaatacgataagggcggggaagcttatttccccagccctttatctgctgttaataggagtaacac Intra-Species Hit: Count: 1 Min: 1 Max: 117 Len: 117 Subject: NC_009009_SSA_0588_SSA_0589|L-cystine ABC transporter, substrate-binding component, putative:Acetylornithine deacetylase/succinyl-diaminopimelate desuccinylase (M20/M25/M40 family peptidase), putative|POSITIVE:POSITIVE|[580768,580884]|117 HSP 1 e-value: 2.0E-60 bit: 232.0 Len: 117 Query Start:1 Query End:117 Subject Strand: POSITIVE Subject Start: 1 Subject End: 117 gaaatcccatcaagtccagtctgcaatttggctgactaaactttgatacaagaaatacgataagggcggggaagcttatttccccagccctttatctgctgttaataggagtaacac gaaatcccatcaagtccagtctgcaatttggctgactaaactttgatacaagaaatacgataagggcggggaagcttatttccccagccctttatctgctgttaataggagtaacac Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAAAUCCCAUCAAGUCCAGUCUGCAAUUUGGCUGACUAAACUUUGAUACAAGAAAUACGAUAAGGGCGGGGAAGCUUAUUUCCCCAGCCCUUUAUCUGCUGUUAAUAGGAGUAACAC ....(((.(((((((..((((.((......)).))))..)).)))))...........((((((((((((((((....))))))).)))).)))))...........)))....... (-35.70) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GUGUUACUCCUAUUAACAGCAGAUAAAGGGCUGGGGAAAUAAGCUUCCCCGCCCUUAUCGUAUUUCUUGUAUCAAAGUUUAGUCAGCCAAAUUGCAGACUGGACUUGAUGGGAUUUC .......((((((((......(((((.((((.((((((......)))))))))))))))................(((((((((.((......)).))))))))))))))))).... (-42.20) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 317 109 63 121 76 NC_009009:SSA_0620|5end_hypothetical_protein_612325..612555_NEGATIVE 310 109 63 58 6 NC_009009:SSA_0576|5end_Conserved_GTPase,_putative_570039..570269_POSITIVE 308 101 61 148 105 NC_009009:SSA_2097|5end_Amino_acid_ABC_transporter,_ATP-binding_protein,_putative_2102918..2103148_NEGATIVE 306 102 63 225 191 NC_009009:SSA_1903|5end_hypothetical_protein_1898182..1898412_NEGATIVE 303 98 56 198 138 NC_009009:SSA_0938|5end_hypothetical_protein_946587..946817_POSITIVE 301 80 31 213 155 NC_009009:SSA_2102|5end_Conserved_uncharacterized_protein_2106410..2106640_NEGATIVE 301 100 57 183 137 NC_009009:SSA_1967|5end_Threonine_desaminase,_putative_1963559..1963789_NEGATIVE 300 96 63 231 192 NC_009009:SSA_1620|5end_Uridylate_kinase,_putative_1622981..1623211_NEGATIVE 300 100 64 64 26 NC_009009:SSA_1429|5end_hypothetical_protein_1437110..1437340_NEGATIVE 296 103 62 188 150 NC_009009:SSA_0062|5end_Aldose_1-epimerase,_putative_63732..63962_POSITIVE 293 99 57 145 93 NC_009009:SSA_2207|5end_hypothetical_protein_2207221..2207451_NEGATIVE 290 98 51 198 152 NC_009009:SSA_2091|5end_Phosphotransferase_system_sugar-specific_EII_component,_putative_2095562..2095792_NEGATIVE 289 37 5 130 97 NC_009009:SSA_0582|5end_Methylase,_putative_573769..573999_POSITIVE 285 90 49 40 7 NC_009009:SSA_1111|5end_Branched-chain_amino_acid_transport_system_II_carrier_protein,_putative_1136532..1136762_POSITIVE 282 100 58 47 6 NC_009009:SSA_2359|5end_Glucose_inhibited_division_protein_A,_putative_2362520..2362750_NEGATIVE 281 94 58 30 6 NC_009009:SSA_2270|5end_Aspartyl-tRNA_synthetase,_putative_2272068..2272298_NEGATIVE 281 110 63 229 179 NC_009009:SSA_1507|5end_ABC-type_lipopolysaccharide_transport_system,_ATPase_component,_putative_1512444..1512674_NEGATIVE 280 110 63 63 9 NC_009009:SSA_1981|5end_hypothetical_protein_1975421..1975651_NEGATIVE 280 92 59 57 17 NC_009009:SSA_0261|5end_ABC-type_Mn2+/Zn2+_transport_systems,_permease_component,_putative_255468..255698_NEGATIVE 279 92 62 184 152 NC_009009:SSA_0504|5end_Peptide_ABC_transporter,_ATP-binding_protein,_putative_503009..503239_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 388 92 59 42 10 NC_009009:SSA_0375|3end_D-methionine-binding_lipoprotein_(ABC-type_transporter),_putative_365209..365359_POSITIVE 366 96 64 32 1 NC_009009:SSA_0588|3end_L-cystine_ABC_transporter,_substrate-binding_component,_putative_580707..580857_POSITIVE 338 110 63 51 1 NC_009009:SSA_1621|3end_Amino_acid_transporter,_putative_1623172..1623322_NEGATIVE 317 109 63 124 79 NC_009009:SSA_0621|3end_SOS_responce_UmuC_protein,_putative_612322..612472_NEGATIVE 310 109 63 55 3 NC_009009:SSA_0575|3end_Hydrolase,_HAD_superfamily,_putative_570116..570266_POSITIVE 308 101 61 135 92 NC_009009:SSA_2098|3end_ABC-type_arginine/histidine_transporter,_permease_protein,_putative_2102931..2103081_NEGATIVE 301 80 31 123 65 NC_009009:SSA_2103|3end_hypothetical_protein_2106500..2106650_NEGATIVE 301 100 57 83 37 NC_009009:SSA_1968|3end_Ketol-acid_reductoisomerase,_putative_1963659..1963809_NEGATIVE 301 108 63 72 26 NC_009009:SSA_0738|3end_Ornithine_carbamoyltransferase,_catabolic,_putative_721000..721150_POSITIVE 300 100 64 67 29 NC_009009:SSA_1430|3end_Ribonuclease_Z,_putative_1437107..1437257_NEGATIVE 296 100 51 100 48 NC_009009:SSA_1729|3end_ABC_transporter_substrate-binding_protein-branched_chain_amino_acid_transport,_putative_1714539..1714689_NEGATIVE 296 91 55 73 42 NC_009009:SSA_0562|3end_hypothetical_protein_554859..555009_POSITIVE 290 98 51 63 17 NC_009009:SSA_2092|3end_Phosphotransferase_system_sugar-specific_EII_component,_putative_2095697..2095847_NEGATIVE 289 45 10 124 87 NC_009009:SSA_2205|3end_Transcription_antitermination_factor_NusG,_putative_2205564..2205714_NEGATIVE 289 37 5 55 22 NC_009009:SSA_0581|3end_Conserved_uncharacterized_protein_573774..573924_POSITIVE 280 110 63 57 3 NC_009009:SSA_1982|3end_Transcriptional_regulator,_LytR/AlgR_family,_putative_1975427..1975577_NEGATIVE 280 92 59 70 30 NC_009009:SSA_0262|3end_ABC-type_Mn/Zn_transporter,_ATP-ase_component,_putative_255455..255605_NEGATIVE 272 91 57 72 43 NC_009009:SSA_0556|3end_hypothetical_protein_551922..552072_POSITIVE 266 110 61 146 105 NC_009009:SSA_0815|3end_hypothetical_protein_797411..797561_POSITIVE 264 110 63 114 78 NC_009009:SSA_0910|3end_ABC-type_multidrug_transporter,_ATPase_component,_putative_922161..922311_POSITIVE