Origin IGS: atagagtgaggaaaattgatttctcgctcttttttatataatgattgacttttttgttagacaagtgtagaataaaaatagaaatagcattaatttagaaagcgcgtggaacg .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 cgttccacgcgctttctaaattaatgctatttctatttttattctacacttgtctaacaaaaaagtcaatcattatataaaaaagagcgagaaatcaattttcctcactctat Mask Tandem Repeat Region ================================================ atagagtgaggaaaattgatttctcgctcttttttatataatgattgacttttttgttagacaagtgtagaataaaaatagaaatagcattaatttagaaagcgcgtggaacg Find is-nt database================================================ Query_seq: SSA_0815:SSA_0816|SSA_0815:SSA_0816:hypothetical protein:Copper transport operon or penicillinase transcription repressor, putative:->->:797472..797584 113 atagagtgaggaaaattgatttctcgctcttttttatataatgattgacttttttgttagacaagtgtagaataaaaatagaaatagcattaatttagaaagcgcgtggaacg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_0815:SSA_0816|SSA_0815:SSA_0816:hypothetical protein:Copper transport operon or penicillinase transcription repressor, putative:->->:797472..797584 113 atagagtgaggaaaattgatttctcgctcttttttatataatgattgacttttttgttagacaagtgtagaataaaaatagaaatagcattaatttagaaagcgcgtggaacg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_0815:SSA_0816|SSA_0815:SSA_0816:hypothetical protein:Copper transport operon or penicillinase transcription repressor, putative:->->:797472..797584 113 atagagtgaggaaaattgatttctcgctcttttttatataatgattgacttttttgttagacaagtgtagaataaaaatagaaatagcattaatttagaaagcgcgtggaacg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 atagagtgaggaaaattgatttctcgctcttttttatataatgattgacttttttgttagacaagtgtagaataaaaatagaaatagcattaatttagaaagcgcgtggaacg Predict ORF larger than 30AA ================================================ Protein_Len: 31 Strand: - Start: 2 End: 94 . L T L F I S K E S K K I Y H N V K K N S L H L I F I S I A N M ................... atagagtgaggaaaattgatttctcgctcttttttatataatgattgacttttttgttagacaagtgtagaataaaaatagaaatagcattaatttagaaagcgcgtggaacg 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: 89 Start: 44 End: 73 ...........................................ATTGACTTTTTTGTTAGACAAGTGTAGAAT........................................ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ atagagtgaggaaaattgatttctcgctcttttttatataatgattgacttttttgttagacaagtgtagaataaaaatagaaatagcattaatttagaaagcgcgtggaacg Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_0815:SSA_0816|SSA_0815:SSA_0816:hypothetical protein:Copper transport operon or penicillinase transcription repressor, putative:->->:797472..797584 113 atagagtgaggaaaattgatttctcgctcttttttatataatgattgacttttttgttagacaagtgtagaataaaaatagaaatagcattaatttagaaagcgcgtggaacg Intra-Species Hit: Count: 1 Min: 1 Max: 113 Len: 113 Subject: NC_009009_SSA_0815_SSA_0816|hypothetical protein:Copper transport operon or penicillinase transcription repressor, putative|POSITIVE:POSITIVE|[797472,797584]|113 HSP 1 e-value: 5.0E-58 bit: 224.0 Len: 113 Query Start:1 Query End:113 Subject Strand: POSITIVE Subject Start: 1 Subject End: 113 atagagtgaggaaaattgatttctcgctcttttttatataatgattgacttttttgttagacaagtgtagaataaaaatagaaatagcattaatttagaaagcgcgtggaacg atagagtgaggaaaattgatttctcgctcttttttatataatgattgacttttttgttagacaagtgtagaataaaaatagaaatagcattaatttagaaagcgcgtggaacg Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUAGAGUGAGGAAAAUUGAUUUCUCGCUCUUUUUUAUAUAAUGAUUGACUUUUUUGUUAGACAAGUGUAGAAUAAAAAUAGAAAUAGCAUUAAUUUAGAAAGCGCGUGGAACG ..(((((((((((......)))))))))))((((((..(((((.....((((((((((..((....))..)))))))).))......)))))...))))))............ (-22.80) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CGUUCCACGCGCUUUCUAAAUUAAUGCUAUUUCUAUUUUUAUUCUACACUUGUCUAACAAAAAAGUCAAUCAUUAUAUAAAAAAGAGCGAGAAAUCAAUUUUCCUCACUCUAU ..........((.............))........(((((((.......(((.((........)).))).......)))))))((((.((((((.....))).))).)))).. (-10.66) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 230 35 3 226 197 NC_009009:SSA_0460|5end_Multiple_antibiotic_resistance_operon_transcription_repressor_(MarR),_putative_462608..462838_POSITIVE 216 35 4 48 19 NC_009009:SSA_0184|5end_Competence_protein_ComYA,_putative_188156..188386_POSITIVE 213 68 21 142 94 NC_009009:SSA_1702|5end_hypothetical_protein_1693462..1693692_NEGATIVE 213 63 24 147 94 NC_009009:SSA_0173|5end_23S_rRNA_m1G745_methyltransferase,_putative_170535..170765_NEGATIVE 210 46 4 111 65 NC_009009:SSA_1645|5end_hypothetical_protein_1646227..1646457_NEGATIVE 208 52 14 49 15 NC_009009:SSA_2082|5end_Carbohydrate_kinase,_FGGY_family,_putative_2086874..2087104_NEGATIVE 207 37 2 176 136 NC_009009:SSA_1598|5end_hypothetical_protein_1605238..1605468_NEGATIVE 201 35 1 223 186 NC_009009:SSA_1320|5end_hypothetical_protein_1337194..1337424_NEGATIVE 200 49 3 73 27 NC_009009:SSA_1716|5end_Restriction_endonuclease_SsuRB,_putative_1703616..1703846_NEGATIVE 200 36 3 149 123 NC_009009:SSA_0810|5end_P-loop_ATPase,_putative_791582..791812_POSITIVE 199 28 3 92 63 NC_009009:SSA_1843|5end_Histidine_kinase,_putative_1837491..1837721_NEGATIVE 198 109 64 227 182 NC_009009:SSA_0314|5end_Nucleoside-diphosphate-sugar_epimerase,_putative_310019..310249_NEGATIVE 197 29 1 128 100 NC_009009:SSA_1550|5end_hypothetical_protein_1552665..1552895_NEGATIVE 196 68 21 148 98 NC_009009:SSA_1896|5end_Translation_initiation_factor_IF-2,_putative_1894134..1894364_NEGATIVE 195 68 23 222 165 NC_009009:SSA_2354|5end_hypothetical_protein_2356237..2356467_NEGATIVE 194 70 22 156 109 NC_009009:SSA_1492|5end_hypothetical_protein_1498954..1499184_NEGATIVE 191 67 25 142 102 NC_009009:SSA_0019|5end_Secreted_antigen_GbpB/SagA;_peptidoglycan_hydrolase;_PcsB_protein_precursor,_putative_24225..24455_POSITIVE 190 51 16 221 182 NC_009009:SSA_0421|5end_Phosphoglycerate_mutase_family_protein,_putative_419564..419794_POSITIVE 188 28 1 61 33 NC_009009:SSA_1201|5end_hypothetical_protein_1225755..1225985_POSITIVE 187 34 3 81 52 NC_009009:SSA_1901|5end_Conserved_uncharacterized_protein_1896599..1896829_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 258 59 15 93 43 NC_009009:SSA_0205|3end_NisK_(sensor-receptor_histidine_kinase_domain),_putative_203839..203989_POSITIVE 257 42 3 65 17 NC_009009:SSA_1171|3end_Tyrosine_recombinase_xerC_1199238..1199388_POSITIVE 249 30 3 88 61 NC_009009:SSA_0815|3end_hypothetical_protein_797411..797561_POSITIVE 243 49 3 61 22 NC_009009:SSA_0459|3end_hypothetical_protein_462513..462663_POSITIVE 238 69 23 115 78 NC_009009:SSA_1739|3end_UDP-N-acetylmuramoylalanyl-D-glutamate--2,_6-diaminopimelate_ligase,_putative_1727065..1727215_POSITIVE 228 110 69 39 1 NC_009009:SSA_2366|3end_ABC-type_cobalt_transport_system,_ATPase_component,_putative_2368030..2368180_NEGATIVE 207 41 3 96 54 NC_009009:SSA_1172|3end_hypothetical_protein_1199288..1199438_NEGATIVE 206 70 22 101 63 NC_009009:SSA_1909|3end_Transcriptional_attenuator_LytR,_putative_1900904..1901054_NEGATIVE 205 69 33 132 95 NC_009009:SSA_1098|3end_Formate-nitrate_transporter,_putative_1115011..1115161_POSITIVE 200 36 3 93 67 NC_009009:SSA_0809|3end_Translation_initiation_inhibitor,_yjgF_family_/_endoribonuclease_L-PSP,_putative_791606..791756_POSITIVE 199 28 3 95 66 NC_009009:SSA_1844|3end_hypothetical_protein_1837488..1837638_NEGATIVE 199 35 3 62 34 NC_009009:SSA_0233|3end_Permease,_putative_228179..228329_POSITIVE 197 29 1 141 113 NC_009009:SSA_1551|3end_Transcriptional_accessory_ribonuclease_(YqgFc,_S1),_putative_1552652..1552802_NEGATIVE 197 63 25 53 1 NC_009009:SSA_0174|3end_Tyrosyl-tRNA_synthetase_1,_putative_170629..170779_NEGATIVE 196 68 21 128 78 NC_009009:SSA_1897|3end_Ribosomal_protein_HS6-type_(S12/L30/L7a),_putative_1894154..1894304_NEGATIVE 195 68 23 134 77 NC_009009:SSA_2355|3end_Conserved_uncharacterized_protein_2356325..2356475_NEGATIVE 191 67 25 45 5 NC_009009:SSA_0018|3end_Cell-shape_determining_protein_MreD,_putative_24208..24358_POSITIVE 186 89 44 66 30 NC_009009:SSA_0440|3end_30S_ribosomal_protein_S18,_putative_441465..441615_POSITIVE 185 50 3 121 64 NC_009009:SSA_2118|3end_Thiamine_pyrophosphokinase,_putative_2119814..2119964_NEGATIVE 183 107 66 76 26 NC_009009:SSA_0207|3end_hypothetical_protein_204944..205094_POSITIVE