Origin IGS: gctcgacctccttcacgagttctatggactagcgacagagccagctttcctttcaactatatactattattatagcagatttacctcttgttttctaaaaaaaggaggcaagaatcatatcttgcctctttcatct .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 agatgaaagaggcaagatatgattcttgcctcctttttttagaaaacaagaggtaaatctgctataataatagtatatagttgaaaggaaagctggctctgtcgctagtccatagaactcgtgaaggaggtcgagc Mask Tandem Repeat Region ================================================ gctcgacctccttcacgagttctatggactagcgacagagccagctttcctttcaactatatactattattatagcagatttacctcttgttttctaaaaaaaggaggcaagaatcatatcttgcctctttcatct Find is-nt database================================================ Query_seq: SSA_1997:SSA_1998|SSA_1997:SSA_1998:Membrane spanning protein, putative:Trigger factor, putative:<-<-:1995002..1995137 136 gctcgacctccttcacgagttctatggactagcgacagagccagctttcctttcaactatatactattattatagcagatttacctcttgttttctaaaaaaaggaggcaagaatcatatcttgcctctttcatct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_1997:SSA_1998|SSA_1997:SSA_1998:Membrane spanning protein, putative:Trigger factor, putative:<-<-:1995002..1995137 136 gctcgacctccttcacgagttctatggactagcgacagagccagctttcctttcaactatatactattattatagcagatttacctcttgttttctaaaaaaaggaggcaagaatcatatcttgcctctttcatct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_1997:SSA_1998|SSA_1997:SSA_1998:Membrane spanning protein, putative:Trigger factor, putative:<-<-:1995002..1995137 136 gctcgacctccttcacgagttctatggactagcgacagagccagctttcctttcaactatatactattattatagcagatttacctcttgttttctaaaaaaaggaggcaagaatcatatcttgcctctttcatct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gctcgacctccttcacgagttctatggactagcgacagagccagctttcctttcaactatatactattattatagcagatttacctcttgttttctaaaaaaaggaggcaagaatcatatcttgcctctttcatct Predict ORF larger than 30AA ================================================ gctcgacctccttcacgagttctatggactagcgacagagccagctttcctttcaactatatactattattatagcagatttacctcttgttttctaaaaaaaggaggcaagaatcatatcttgcctctttcatct 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: 83 Start: 69 End: 98 ....................................................................TTAGAAAACAAGAGGTAAATCTGCTATAAT...................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ gctcgacctccttcacgagttctatggactagcgacagagccagctttcctttcaactatatactattattatagcagatttacctcttgttttctaaaaaaaggaggcaagaatcatatcttgcctctttcatct Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_1997:SSA_1998|SSA_1997:SSA_1998:Membrane spanning protein, putative:Trigger factor, putative:<-<-:1995002..1995137 136 gctcgacctccttcacgagttctatggactagcgacagagccagctttcctttcaactatatactattattatagcagatttacctcttgttttctaaaaaaaggaggcaagaatcatatcttgcctctttcatct Intra-Species Hit: Count: 1 Min: 1 Max: 136 Len: 136 Subject: NC_009009_SSA_1997_SSA_1998|Membrane spanning protein, putative:Trigger factor, putative|NEGATIVE:NEGATIVE|[1995002,1995137]|136 HSP 1 e-value: 4.0E-59 bit: 228.0 Len: 136 Query Start:1 Query End:136 Subject Strand: POSITIVE Subject Start: 1 Subject End: 136 gctcgacctccttcacgagttctatggactagcgacagagccagctttcctttcaactatatactattattatagcagatttacctcttgttttctnnnnnnnggaggcaagaatcatatcttgcctctttcatct gctcgacctccttcacgagttctatggactagcgacagagccagctttcctttcaactatatactattattatagcagatttacctcttgttttctaaaaaaaggaggcaagaatcatatcttgcctctttcatct Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GCUCGACCUCCUUCACGAGUUCUAUGGACUAGCGACAGAGCCAGCUUUCCUUUCAACUAUAUACUAUUAUUAUAGCAGAUUUACCUCUUGUUUUCUAAAAAAAGGAGGCAAGAAUCAUAUCUUGCCUCUUUCAUCU (((....(((..((.(.((((.....)))).).))..)))..))).......((..(((((.........)))))..))......................((((((((((((......))))))))))))..... (-28.50) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGAUGAAAGAGGCAAGAUAUGAUUCUUGCCUCCUUUUUUUAGAAAACAAGAGGUAAAUCUGCUAUAAUAAUAGUAUAUAGUUGAAAGGAAAGCUGGCUCUGUCGCUAGUCCAUAGAACUCGUGAAGGAGGUCGAGC .(((....(((((((((......)))))))))..............((.(((.....((.((((((.........)))))).))..((...((((((......))))))))......))).))......))).... (-34.10) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 1059 50 1 141 92 NC_009009:SSA_1997|5end_Membrane_spanning_protein,_putative_1994911..1995141_NEGATIVE 368 50 1 52 6 NC_009009:SSA_1226|5end_ParC,_putative_1251233..1251463_NEGATIVE 339 50 1 146 87 NC_009009:SSA_2338|5end_Conserved_uncharacterized_protein_2339272..2339502_POSITIVE 319 50 1 224 181 NC_009009:SSA_0940|5end_NOL1/NOP2/sun_family_protein,_putative_947626..947856_POSITIVE 318 50 6 145 98 NC_009009:SSA_1016|5end_Phosphoenolpyruvate_synthase,_putative_1019602..1019832_POSITIVE 317 48 1 179 121 NC_009009:SSA_0928|5end_ABC-type_multidrug_transporter,_ATPase_and_permease_components,_putative_936679..936909_POSITIVE 309 50 1 60 3 NC_009009:SSA_1752|5end_Phosphotransferase_system,_trehalose-specific_IIBC_component,_putative_1741875..1742105_NEGATIVE 307 129 84 144 97 NC_009009:SSA_2048|5end_Serine_acetyltransferase,_putative_2050601..2050831_NEGATIVE 305 49 4 231 186 NC_009009:SSA_1276|5end_Conserved_uncharacterized_protein_1298446..1298676_NEGATIVE 304 42 3 126 96 NC_009009:SSA_1805|5end_Primosomal_protein_DnaI,_putative_1789564..1789794_NEGATIVE 304 58 19 153 109 NC_009009:SSA_0706|5end_RNA_helicase,_putative_691363..691593_POSITIVE 304 50 2 111 37 NC_009009:SSA_0620|5end_hypothetical_protein_612325..612555_NEGATIVE 303 50 1 227 160 NC_009009:SSA_2197|5end_hypothetical_protein_2197784..2198014_NEGATIVE 303 45 2 228 182 NC_009009:SSA_0607|5end_ABC_transporter,_permease_component,_putative_596926..597156_NEGATIVE 302 130 83 103 50 NC_009009:SSA_0062|5end_Aldose_1-epimerase,_putative_63732..63962_POSITIVE 301 45 2 155 111 NC_009009:SSA_0752|5end_hypothetical_protein_734171..734401_POSITIVE 298 50 7 222 182 NC_009009:SSA_1444|5end_Imidazole_glycerol-phosphate_synthase_subunit_hisH,_putative_1447267..1447497_NEGATIVE 297 49 5 143 100 NC_009009:SSA_1726|5end_ABC_transporter_ATP-binding_protein-branched_chain_amino_acid_transport,_putative_1712467..1712697_NEGATIVE 297 50 1 146 87 NC_009009:SSA_0213|5end_hypothetical_protein_210135..210365_NEGATIVE 297 50 2 162 111 NC_009009:SSA_0090|5end_Acetyltransferase,_GNAT_family,_putative_90258..90488_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 343 46 8 151 94 NC_009009:SSA_2269|3end_hypothetical_protein_2269392..2269542_NEGATIVE 332 47 7 90 46 NC_009009:SSA_1459|3end_RNA_methyltransferase,_putative_1466111..1466261_NEGATIVE 326 50 1 75 17 NC_009009:SSA_1324|3end_Ceramide_glucosyltransferase,_putative_1340428..1340578_NEGATIVE 322 48 1 150 94 NC_009009:SSA_2337|3end_hypothetical_protein_2339359..2339509_POSITIVE 318 50 6 145 98 NC_009009:SSA_1015|3end_4-hydroxybenzoate_octaprenyltransferase,_putative_1019682..1019832_POSITIVE 307 129 84 52 5 NC_009009:SSA_2049|3end_Polyribonucleotide_nucleotidyltransferase,_putative_2050693..2050843_NEGATIVE 304 42 3 125 95 NC_009009:SSA_1806|3end_Replication_initiation/membrane_attachment_protein_DnaB,_putative_1789565..1789715_NEGATIVE 304 50 2 114 40 NC_009009:SSA_0621|3end_SOS_responce_UmuC_protein,_putative_612322..612472_NEGATIVE 302 130 83 78 25 NC_009009:SSA_0061|3end_Tagatose_1,6-diphosphate_aldolase,_putative_63787..63937_POSITIVE 299 50 2 109 61 NC_009009:SSA_1269|3end_hypothetical_protein_1291970..1292120_NEGATIVE 297 49 5 143 100 NC_009009:SSA_1727|3end_ABC_transporter_membrane-spanning_permease-branched_chain_amino_acid_transport,_putative_1712467..1712617_NEGATIVE 294 47 1 91 47 NC_009009:SSA_1069|3end_Lipoprotein_signal_peptidase,_putative_1088838..1088988_POSITIVE 284 50 8 74 33 NC_009009:SSA_0070|3end_Acetylxylan_esterase,_putative_74914..75064_POSITIVE 282 51 20 46 12 NC_009009:SSA_1375|3end_Multidrug_ABC_transporter,_ATPase_and_permease_components,_putative_1393085..1393235_NEGATIVE 281 50 8 69 33 NC_009009:SSA_1364|3end_hypothetical_protein_1380482..1380632_NEGATIVE 279 46 1 143 100 NC_009009:SSA_0500|3end_Peptide_ABC_transporter,_permease_protein,_putative_501524..501674_POSITIVE 278 56 12 114 62 NC_009009:SSA_1464|3end_3-phosphoshikimate_1-carboxyvinyltransferase,_putative_1470233..1470383_NEGATIVE 276 47 1 70 22 NC_009009:SSA_1248|3end_hypothetical_protein_1272355..1272505_NEGATIVE 276 46 1 41 4 NC_009009:SSA_0234|3end_hypothetical_protein_228423..228573_NEGATIVE 274 50 1 139 97 NC_009009:SSA_1784|3end_Glutamate_racemase,_putative_1769103..1769253_NEGATIVE