Origin IGS: cgtcaggagtcgaataaataacggaaagaaggggaagaggaaaagagtggtaacgagagagccgaaggccgagaagaggagtaagctttgatgacaaatacgcttttatttcgcgctaagcagtttccctctgatctcgatctccggctcttagagaacattaa .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 ttaatgttctctaagagccggagatcgagatcagagggaaactgcttagcgcgaaataaaagcgtatttgtcatcaaagcttactcctcttctcggccttcggctctctcgttaccactcttttcctcttccccttctttccgttatttattcgactcctgacg Mask Tandem Repeat Region ================================================ cgtcaggagtcgaataaataacggaaagaaggggaagaggaaaagagtggtaacgagagagccgaaggccgagaagaggagtaagctttgatgacaaatacgcttttatttcgcgctaagcagtttccctctgatctcgatctccggctcttagagaacattaa Find is-nt database================================================ Query_seq: PG1857:PG1858|PG1857:PG1858:hypothetical protein:flavodoxin:<-<-:1956464..1956627 164 cgtcaggagtcgaataaataacggaaagaaggggaagaggaaaagagtggtaacgagagagccgaaggccgagaagaggagtaagctttgatgacaaatacgcttttatttcgcgctaagcagtttccctctgatctcgatctccggctcttagagaacattaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG1857:PG1858|PG1857:PG1858:hypothetical protein:flavodoxin:<-<-:1956464..1956627 164 cgtcaggagtcgaataaataacggaaagaaggggaagaggaaaagagtggtaacgagagagccgaaggccgagaagaggagtaagctttgatgacaaatacgcttttatttcgcgctaagcagtttccctctgatctcgatctccggctcttagagaacattaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG1857:PG1858|PG1857:PG1858:hypothetical protein:flavodoxin:<-<-:1956464..1956627 164 cgtcaggagtcgaataaataacggaaagaaggggaagaggaaaagagtggtaacgagagagccgaaggccgagaagaggagtaagctttgatgacaaatacgcttttatttcgcgctaagcagtttccctctgatctcgatctccggctcttagagaacattaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 cgtcaggagtcgaataaataacggaaagaaggggaagaggaaaagagtggtaacgagagagccgaaggccgagaagaggagtaagctttgatgacaaatacgcttttatttcgcgctaagcagtttccctctgatctcgatctccggctcttagagaacattaa Predict ORF larger than 30AA ================================================ Protein_Len: 53 Strand: - Start: 6 End: 161 ..... * S D F L Y R F S P S S S F L P L S L A S P R S S S Y A K I V F V S K N R A L C N G E S R S R R S K S F M ... Protein_Len: 36 Strand: - Start: 2 End: 109 . D P T S Y I V S L L P L P F S H Y R S L R L G L L P T L K S S L Y A K M ....................................................... Protein_Len: 33 Strand: - Start: 1 End: 99 T L L R I F L P F F P F L F L T T V L S G F A S F L L L S Q H C M ................................................................. cgtcaggagtcgaataaataacggaaagaaggggaagaggaaaagagtggtaacgagagagccgaaggccgagaagaggagtaagctttgatgacaaatacgcttttatttcgcgctaagcagtttccctctgatctcgatctccggctcttagagaacattaa 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================================================ cgtcaggagtcgaataaataacggaaagaaggggaagaggaaaagagtggtaacgagagagccgaaggccgagaagaggagtaagctttgatgacaaatacgcttttatttcgcgctaagcagtttccctctgatctcgatctccggctcttagagaacattaa Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PG1857:PG1858|PG1857:PG1858:hypothetical protein:flavodoxin:<-<-:1956464..1956627 164 cgtcaggagtcgaataaataacggaaagaaggggaagaggaaaagagtggtaacgagagagccgaaggccgagaagaggagtaagctttgatgacaaatacgcttttatttcgcgctaagcagtttccctctgatctcgatctccggctcttagagaacattaa Intra-Species Hit: Count: 1 Min: 1 Max: 164 Len: 164 Subject: NC_002950_PG1857_PG1858|hypothetical protein:flavodoxin|NEGATIVE:NEGATIVE|[1956464, 1956627]|164 HSP 1 e-value: 3.0E-88 bit: 325.0 Len: 164 Query Start:1 Query End:164 Subject Strand: POSITIVE Subject Start: 1 Subject End: 164 cgtcaggagtcgaataaataacggaaagaaggggaagaggaaaagagtggtaacgagagagccgaaggccgagaagaggagtaagctttgatgacaaatacgcttttatttcgcgctaagcagtttccctctgatctcgatctccggctcttagagaacattaa cgtcaggagtcgaataaataacggaaagaaggggaagaggaaaagagtggtaacgagagagccgaaggccgagaagaggagtaagctttgatgacaaatacgcttttatttcgcgctaagcagtttccctctgatctcgatctccggctcttagagaacattaa Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CGUCAGGAGUCGAAUAAAUAACGGAAAGAAGGGGAAGAGGAAAAGAGUGGUAACGAGAGAGCCGAAGGCCGAGAAGAGGAGUAAGCUUUGAUGACAAAUACGCUUUUAUUUCGCGCUAAGCAGUUUCCCUCUGAUCUCGAUCUCCGGCUCUUAGAGAACAUUAA ..(((((((((..........(.....)..(((((.((((...((((.((.(((.....((((((((....(((((....(((...((((....))))))).))))).))))).))).....))).))))))..))))..)))))))))))).))......... (-40.50) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUAAUGUUCUCUAAGAGCCGGAGAUCGAGAUCAGAGGGAAACUGCUUAGCGCGAAAUAAAAGCGUAUUUGUCAUCAAAGCUUACUCCUCUUCUCGGCCUUCGGCUCUCUCGUUACCACUCUUUUCCUCUUCCCCUUCUUUCCGUUAUUUAUUCGACUCCUGACG .(((((.......((((((((((..(((((..((((((.....((((.((((.........))))...((....))))))....)))))))))))..))))))))))..)))))...........................(((((.............))))) (-41.22) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 1055 80 31 171 122 NC_002950:PG1857|5end_hypothetical_protein_1956373..1956603_NEGATIVE 412 79 32 82 23 NC_002950:PG0662|5end_hypothetical_protein_709867..710097_POSITIVE 402 80 31 69 21 NC_002950:PG1967|5end_TPR_domain_protein_2057168..2057398_POSITIVE 377 66 23 224 168 NC_002950:PG0583|5end_cell_division_protein_FtsA_640425..640655_POSITIVE 377 79 37 167 116 NC_002950:PG0084|5end_L-serine_dehydratase,_iron-sulfur-dependent,_single_chain_form_97832..98062_POSITIVE 359 147 111 193 161 NC_002950:PG2075|5end_hypothetical_protein_2176466..2176696_NEGATIVE 359 69 21 176 122 NC_002950:PG1481|5end_conjugative_transposon_protein_TraG_1558447..1558677_NEGATIVE 357 86 48 38 1 NC_002950:PG1792|5end_sodium/hydrogen_antiporter_1881622..1881852_POSITIVE 357 65 23 55 23 NC_002950:PG0788|5end_hypothetical_protein_840676..840906_NEGATIVE 354 78 32 138 100 NC_002950:PG1402|5end_AP_endonuclease_domain_protein_1485963..1486193_NEGATIVE 350 79 31 189 119 NC_002950:PG1794|5end_DNA_polymerase_type_I_1885978..1886208_POSITIVE 350 78 32 46 8 NC_002950:PG0327|5end_hypothetical_protein_362061..362291_NEGATIVE 345 69 21 157 108 NC_002950:PG0680|5end_efflux_transporter,_MFP_component,_RND_family_730968..731198_POSITIVE 345 80 31 150 92 NC_002950:PG0240|5end_hydrolase,_haloacid_dehalogenase-like_family_277093..277323_NEGATIVE 344 79 31 230 178 NC_002950:PG0222|5end_DNA-binding_protein,_histone-like_family_256380..256610_NEGATIVE 343 90 45 68 17 NC_002950:PG0676|5end_oxidoreductase,_short_chain_dehydrogenase/reductase_family_727275..727505_NEGATIVE 342 148 102 180 118 NC_002950:PG1709|5end_ISPg5,_transposase_Orf1_1794914..1795144_POSITIVE 341 87 42 78 27 NC_002950:PG1225|5end_ABC_transporter,_ATP-binding_protein_1301385..1301615_POSITIVE 341 68 21 179 129 NC_002950:PG0355|5end_hypothetical_protein_389644..389874_POSITIVE 340 78 39 46 2 NC_002950:PG1639|5end_hypothetical_protein_1719919..1720149_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 378 81 43 150 112 NC_002950:PG0932|3end_DNA_polymerase_III,_delta_prime_subunit,_putative_989833..989983_POSITIVE 377 79 37 72 21 NC_002950:PG0083|3end_hypothetical_protein_97817..97967_POSITIVE 360 157 111 67 12 NC_002950:PG1676|3end_phosphoenolpyruvate_carboxykinase_1760489..1760639_NEGATIVE 350 79 31 139 69 NC_002950:PG1793|3end_1,4-alpha-glucan_branching_enzyme_1886008..1886158_POSITIVE 349 147 101 83 38 NC_002950:PG2032|3end_primosomal_protein_N'_2130868..2131018_NEGATIVE 345 69 21 117 68 NC_002950:PG0679|3end_outer_membrane_efflux_protein_731008..731158_POSITIVE 343 69 22 130 75 NC_002950:PG0164|3end_hypothetical_protein_187081..187231_NEGATIVE 342 80 31 53 2 NC_002950:PG0028|3end_2C-methyl-D-erythritol_2,4-cyclodiphosphate_synthase_34431..34581_POSITIVE 338 72 31 120 79 NC_002950:PG0363|3end_hypothetical_protein_398377..398527_POSITIVE 337 52 23 151 119 NC_002950:PG0582|3end_cell_division_protein_FtsQ,_putative_640456..640606_POSITIVE 336 69 21 56 6 NC_002950:PG1179|3end_hypothetical_protein_1260341..1260491_NEGATIVE 336 147 101 68 10 NC_002950:PG0032|3end_beta-mannosidase,_putative_37627..37777_NEGATIVE 334 152 112 134 95 NC_002950:PG0141|3end_spoOJ_protein_163878..164028_NEGATIVE 332 146 102 62 15 NC_002950:PG1694|3end_hypothetical_protein_1777916..1778066_NEGATIVE 330 69 23 139 88 NC_002950:PG1359|3end_hypothetical_protein_1437644..1437794_NEGATIVE 330 78 32 88 49 NC_002950:PG1034|3end_ABC_transporter,_ATP-binding_protein_1096977..1097127_POSITIVE 329 67 22 54 11 NC_002950:PG1713|3end_lipoprotein,_putative_1801407..1801557_NEGATIVE 328 79 33 83 34 NC_002950:PG1603|3end_HAM1_protein_1682829..1682979_POSITIVE 326 89 47 92 43 NC_002950:PG2046|3end_hypothetical_protein_2145793..2145943_POSITIVE 326 150 101 74 23 NC_002950:PG0431|3end_hypothetical_protein_469174..469324_POSITIVE