Origin IGS: tgttttttactgagaatctgaaattagggcacaaaggtaactattttttgcagaatctttaatttccttccttcaaaaaaattcttttatgcccgattttaccgtatatctttctttattggcaagaagcaagtcttttattgcacacgccttaagccaacaccaacttaaaatatccactaattacttcaattttcatacgctaaaccgtggcttcatctatgtcttggattgtggatacacgatgcttcataaagcgtgatcgattttagtacggatttcatgcacatccgtatgcacataaacttccggctgtatatgaacattacataaagtaagtattcaataaatgaatgtccgtatatccatctaaaaatgattcgctcggttagaatcctacacaaaagaatatgaatctgtttcgtgaatca .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tgattcacgaaacagattcatattcttttgtgtaggattctaaccgagcgaatcatttttagatggatatacggacattcatttattgaatacttactttatgtaatgttcatatacagccggaagtttatgtgcatacggatgtgcatgaaatccgtactaaaatcgatcacgctttatgaagcatcgtgtatccacaatccaagacatagatgaagccacggtttagcgtatgaaaattgaagtaattagtggatattttaagttggtgttggcttaaggcgtgtgcaataaaagacttgcttcttgccaataaagaaagatatacggtaaaatcgggcataaaagaatttttttgaaggaaggaaattaaagattctgcaaaaaatagttacctttgtgccctaatttcagattctcagtaaaaaaca Mask Tandem Repeat Region ================================================ tgttttttactgagaatctgaaattagggcacaaaggtaactattttttgcagaatctttaatttccttccttcaaaaaaattcttttatgcccgattttaccgtatatctttctttattggcaagaagcaagtcttttattgcacacgccttaagccaacaccaacttaaaatatccactaattacttcaattttcatacgctaaaccgtggcttcatctatgtcttggattgtggatacacgatgcttcataaagcgtgatcgattttagtacggatttcatgcacatccgtatgcacataaacttccggctgtatatgaacattacataaagtaagtattcaataaatgaatgtccgtatatccatctaaaaatgattcgctcggttagaatcctacacaaaagaatatgaatctgtttcgtgaatca Find is-nt database================================================ Query_seq: TF0219:TF0220|TF0219:TF0220:threonyl-tRNA synthetase:conserved hypothetical protein:->->:245939..246369 431 tgttttttactgagaatctgaaattagggcacaaaggtaactattttttgcagaatctttaatttccttccttcaaaaaaattcttttatgcccgattttaccgtatatctttctttattggcaagaagcaagtcttttattgcacacgccttaagccaacaccaacttaaaatatccactaattacttcaattttcatacgctaaaccgtggcttcatctatgtcttggattgtggatacacgatgcttcataaagcgtgatcgattttagtacggatttcatgcacatccgtatgcacataaacttccggctgtatatgaacattacataaagtaagtattcaataaatgaatgtccgtatatccatctaaaaatgattcgctcggttagaatcctacacaaaagaatatgaatctgtttcgtgaatca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF0219:TF0220|TF0219:TF0220:threonyl-tRNA synthetase:conserved hypothetical protein:->->:245939..246369 431 tgttttttactgagaatctgaaattagggcacaaaggtaactattttttgcagaatctttaatttccttccttcaaaaaaattcttttatgcccgattttaccgtatatctttctttattggcaagaagcaagtcttttattgcacacgccttaagccaacaccaacttaaaatatccactaattacttcaattttcatacgctaaaccgtggcttcatctatgtcttggattgtggatacacgatgcttcataaagcgtgatcgattttagtacggatttcatgcacatccgtatgcacataaacttccggctgtatatgaacattacataaagtaagtattcaataaatgaatgtccgtatatccatctaaaaatgattcgctcggttagaatcctacacaaaagaatatgaatctgtttcgtgaatca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF0219:TF0220|TF0219:TF0220:threonyl-tRNA synthetase:conserved hypothetical protein:->->:245939..246369 431 tgttttttactgagaatctgaaattagggcacaaaggtaactattttttgcagaatctttaatttccttccttcaaaaaaattcttttatgcccgattttaccgtatatctttctttattggcaagaagcaagtcttttattgcacacgccttaagccaacaccaacttaaaatatccactaattacttcaattttcatacgctaaaccgtggcttcatctatgtcttggattgtggatacacgatgcttcataaagcgtgatcgattttagtacggatttcatgcacatccgtatgcacataaacttccggctgtatatgaacattacataaagtaagtattcaataaatgaatgtccgtatatccatctaaaaatgattcgctcggttagaatcctacacaaaagaatatgaatctgtttcgtgaatca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tgttttttactgagaatctgaaattagggcacaaaggtaactattttttgcagaatctttaatttccttccttcaaaaaaattcttttatgcccgattttaccgtatatctttctttattggcaagaagcaagtcttttattgcacacgccttaagccaacaccaacttaaaatatccactaattacttcaattttcatacgctaaaccgtggcttcatctatgtcttggattgtggatacacgatgcttcataaagcgtgatcgattttagtacggatttcatgcacatccgtatgcacataaacttccggctgtatatgaacattacataaagtaagtattcaataaatgaatgtccgtatatccatctaaaaatgattcgctcggttagaatcctacacaaaagaatatgaatctgtttcgtgaatca Predict ORF larger than 30AA ================================================ Protein_Len: 42 Strand: + Start: 43 End: 168 .......................................... M F C R I F N F L P S K K F F Y A R F Y R I S F F I G K K Q V F Y C T R L K P T P T ....................................................................................................................................................................................................................................................................... Protein_Len: 60 Strand: + Start: 62 End: 259 ............................................................. M S F L Q K N S F M P D F T V Y L S L L A R S K S F I A H A L S Q H Q L K I S T N Y F N F H T L N R G F I Y V L D C G Y ............................................................................................................................................................................ Protein_Len: 30 Strand: - Start: 253 End: 342 ............................................................................................................................................................................................................................................................ L A H D I K T R I E H V D T H V Y V E P Q I H V N C L T L M ......................................................................................... Protein_Len: 60 Strand: - Start: 219 End: 416 .......................................................................................................................................................................................................................... I C S A E Y L T I S K L V S K M C M R I C M F K R S Y I F M V Y L L Y E I F S H G Y I W R F I I R E T L I R C L L I H M ............... Protein_Len: 35 Strand: - Start: 76 End: 180 ........................................................................... F F E K I G S K V T Y R E K N A L L L D K I A C A K L W C W S L I D M ........................................................................................................................................................................................................................................................... tgttttttactgagaatctgaaattagggcacaaaggtaactattttttgcagaatctttaatttccttccttcaaaaaaattcttttatgcccgattttaccgtatatctttctttattggcaagaagcaagtcttttattgcacacgccttaagccaacaccaacttaaaatatccactaattacttcaattttcatacgctaaaccgtggcttcatctatgtcttggattgtggatacacgatgcttcataaagcgtgatcgattttagtacggatttcatgcacatccgtatgcacataaacttccggctgtatatgaacattacataaagtaagtattcaataaatgaatgtccgtatatccatctaaaaatgattcgctcggttagaatcctacacaaaagaatatgaatctgtttcgtgaatca 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================================================ tgttttttactgagaatctgaaattagggcacaaaggtaactattttttgcagaatctttaatttccttccttcaaaaaaattcttttatgcccgattttaccgtatatctttctttattggcaagaagcaagtcttttattgcacacgccttaagccaacaccaacttaaaatatccactaattacttcaattttcatacgctaaaccgtggcttcatctatgtcttggattgtggatacacgatgcttcataaagcgtgatcgattttagtacggatttcatgcacatccgtatgcacataaacttccggctgtatatgaacattacataaagtaagtattcaataaatgaatgtccgtatatccatctaaaaatgattcgctcggttagaatcctacacaaaagaatatgaatctgtttcgtgaatca Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TF0219:TF0220|TF0219:TF0220:threonyl-tRNA synthetase:conserved hypothetical protein:->->:245939..246369 431 tgttttttactgagaatctgaaattagggcacaaaggtaactattttttgcagaatctttaatttccttccttcaaaaaaattcttttatgcccgattttaccgtatatctttctttattggcaagaagcaagtcttttattgcacacgccttaagccaacaccaacttaaaatatccactaattacttcaattttcatacgctaaaccgtggcttcatctatgtcttggattgtggatacacgatgcttcataaagcgtgatcgattttagtacggatttcatgcacatccgtatgcacataaacttccggctgtatatgaacattacataaagtaagtattcaataaatgaatgtccgtatatccatctaaaaatgattcgctcggttagaatcctacacaaaagaatatgaatctgtttcgtgaatca Intra-Species Hit: Count: 1 Min: 1 Max: 431 Len: 431 Subject: tfor_TF0219_TF0220|threonyl-tRNA synthetase:conserved hypothetical protein|POSITIVE:POSITIVE|[245939,246369]|431 HSP 1 e-value: 0.0 bit: 813.0 Len: 431 Query Start:1 Query End:431 Subject Strand: POSITIVE Subject Start: 1 Subject End: 431 tgttttttactgagaatctgaaattagggcacaaaggtaactattttttgcagaatctttaatttccttccttcnnnnnnnttcttttatgcccgattttaccgtatatctttctttattggcaagaagcaagtcttttattgcacacgccttaagccaacaccaacttaaaatatccactaattacttcaattttcatacgctaaaccgtggcttcatctatgtcttggattgtggatacacgatgcttcataaagcgtgatcgattttagtacggatttcatgcacatccgtatgcacataaacttccggctgtatatgaacattacataaagtaagtattcaataaatgaatgtccgtatatccatctaaaaatgattcgctcggttagaatcctacacaaaagaatatgaatctgtttcgtgaatca tgttttttactgagaatctgaaattagggcacaaaggtaactattttttgcagaatctttaatttccttccttcaaaaaaattcttttatgcccgattttaccgtatatctttctttattggcaagaagcaagtcttttattgcacacgccttaagccaacaccaacttaaaatatccactaattacttcaattttcatacgctaaaccgtggcttcatctatgtcttggattgtggatacacgatgcttcataaagcgtgatcgattttagtacggatttcatgcacatccgtatgcacataaacttccggctgtatatgaacattacataaagtaagtattcaataaatgaatgtccgtatatccatctaaaaatgattcgctcggttagaatcctacacaaaagaatatgaatctgtttcgtgaatca Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGUUUUUUACUGAGAAUCUGAAAUUAGGGCACAAAGGUAACUAUUUUUUGCAGAAUCUUUAAUUUCCUUCCUUCAAAAAAAUUCUUUUAUGCCCGAUUUUACCGUAUAUCUUUCUUUAUUGGCAAGAAGCAAGUCUUUUAUUGCACACGCCUUAAGCCAACACCAACUUAAAAUAUCCACUAAUUACUUCAAUUUUCAUACGCUAAACCGUGGCUUCAUCUAUGUCUUGGAUUGUGGAUACACGAUGCUUCAUAAAGCGUGAUCGAUUUUAGUACGGAUUUCAUGCACAUCCGUAUGCACAUAAACUUCCGGCUGUAUAUGAACAUUACAUAAAGUAAGUAUUCAAUAAAUGAAUGUCCGUAUAUCCAUCUAAAAAUGAUUCGCUCGGUUAGAAUCCUACACAAAAGAAUAUGAAUCUGUUUCGUGAAUCA .....(((((.((((....((((((((((.......((((.......)))).....))))))))))..............((((((((.((...((((((((((.....................((((((.....((((..((....))..)))).................(((((((.....................((((.....))))...(((((.....))))).))))))).....))))))....((((.(((((.((((((((((((((((((..(((.(((...(........)...))).)))...((((..((((.....))))...))))....))))).))))))).......)))))).)))))))))))).)))))))...)).)))))))).........)))))))))... (-82.41) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGAUUCACGAAACAGAUUCAUAUUCUUUUGUGUAGGAUUCUAACCGAGCGAAUCAUUUUUAGAUGGAUAUACGGACAUUCAUUUAUUGAAUACUUACUUUAUGUAAUGUUCAUAUACAGCCGGAAGUUUAUGUGCAUACGGAUGUGCAUGAAAUCCGUACUAAAAUCGAUCACGCUUUAUGAAGCAUCGUGUAUCCACAAUCCAAGACAUAGAUGAAGCCACGGUUUAGCGUAUGAAAAUUGAAGUAAUUAGUGGAUAUUUUAAGUUGGUGUUGGCUUAAGGCGUGUGCAAUAAAAGACUUGCUUCUUGCCAAUAAAGAAAGAUAUACGGUAAAAUCGGGCAUAAAAGAAUUUUUUUGAAGGAAGGAAAUUAAAGAUUCUGCAAAAAAUAGUUACCUUUGUGCCCUAAUUUCAGAUUCUCAGUAAAAAACA (((.((........)).))).((((((((((((..((((...((((.((((.((..((((((((((((...(((............((((((.((((.....)))))))))).......)))....((((((..(((....)))..)))))))))))).))))))..(..(((((((((.(.(((((((.((((((((.........(((((...((((....))))..).)))).......((....)).)))))))).......)))))))..).)))))))))..).......)).)))).((((.......))))........))))..))))..))))))))))))...(((((((..(((....(((((...(((.......)))....)))))...)))..)))))))................ (-99.01) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 345 380 351 175 146 tfor:TF2703|5end_conserved_hypothetical_protein_2876067..2876297_POSITIVE 313 296 256 200 159 tfor:TF1639|5end_conserved_hypothetical_protein_1747652..1747882_POSITIVE 306 248 201 230 188 tfor:TF1185|5end_hypothetical_protein_1269238..1269468_POSITIVE 305 315 271 74 39 tfor:TF0024|5end_conserved_hypothetical_protein;_possible_ATPase_20191..20421_POSITIVE 303 313 272 229 183 tfor:TF1815|5end_conserved_hypothetical_protein_1956604..1956834_POSITIVE 301 224 186 68 33 tfor:TF2477|5end_phosphatase_2654229..2654459_POSITIVE 297 313 275 129 81 tfor:TF2831|5end_ABC_transporter,_permease_component_3021317..3021547_POSITIVE 296 250 202 214 159 tfor:TF2687|5end_iron-regulated_ABC-type_transporter_membrane_component_2863509..2863739_POSITIVE 294 385 344 140 97 tfor:TF2305|5end_S-adenosylmethionine:tRNA_ribosyltransferase-isomerase_2461348..2461578_POSITIVE 289 149 102 182 127 tfor:TF2852|5end_conserved_hypothetical_protein_3038966..3039196_POSITIVE 289 240 202 151 114 tfor:TF2383|5end_hypothetical_protein_2548300..2548530_POSITIVE 288 299 257 213 178 tfor:TF1234|5end_rhamnulose-1-phosphate_aldolase_1318875..1319105_POSITIVE 288 246 206 64 25 tfor:TF1173|5end_ABC_transporter,_permease_component_1255444..1255674_POSITIVE 288 287 241 49 1 tfor:TF0279|5end_conserved_hypothetical_protein_307142..307372_POSITIVE 282 117 74 70 23 tfor:TF1994|5end_acyl-CoA_synthetase_2144980..2145210_POSITIVE 282 149 101 56 15 tfor:TF1294|5end_conserved_hypothetical_protein_1377142..1377372_POSITIVE 281 249 202 188 146 tfor:TF1018|5end_50S_ribosomal_protein_L9_1074815..1075045_POSITIVE 281 238 192 64 25 tfor:TF0800|5end_conserved_hypothetical_protein_855864..856094_POSITIVE 280 286 243 228 178 tfor:TF2601|5end_conserved_hypothetical_protein_2774721..2774951_POSITIVE 280 267 229 226 189 tfor:TF1804|5end_hypothetical_protein_1947101..1947331_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 305 315 271 36 1 tfor:TF0023|3end_possible_response_element_in_two_component_regulation_20233..20383_POSITIVE 297 313 275 151 103 tfor:TF2830|3end_ABC_transporter,_ATP-binding_protein_3021419..3021569_POSITIVE 294 385 344 127 84 tfor:TF2304|3end_OmpA_family_protein_2461415..2461565_POSITIVE 290 297 251 142 99 tfor:TF2600|3end_ribose-phosphate_pyrophosphokinase_2774709..2774859_POSITIVE 288 299 257 113 78 tfor:TF1233|3end_dihydrodipicolinate_synthase_1318855..1319005_POSITIVE 282 149 101 90 49 tfor:TF1295|3end_conserved_hypothetical_protein_1377256..1377406_POSITIVE 281 249 201 137 79 tfor:TF2647|3end_transcriptional_regulator,_possible_arylsulfatase_regulator_2818135..2818285_POSITIVE 278 317 272 129 85 tfor:TF1744|3end_phenylacetate-CoA_ligase_1879218..1879368_POSITIVE 275 317 271 107 56 tfor:TF3039|3end_ABC_transporter,_ATP-binding_protein_3267697..3267847_POSITIVE 274 420 376 91 34 tfor:TF2457|3end_ABC_transporter,_permease_component,_zinc-binding_protein_2635302..2635452_POSITIVE 272 248 201 140 98 tfor:TF1186|3end_hypothetical_protein_1269815..1269965_POSITIVE 271 238 193 145 92 tfor:TF2572|3end_50S_ribosomal_protein_L30_2743334..2743484_POSITIVE 269 318 271 84 34 tfor:TF2789|3end_enoyl-[acyl-carrier-protein]_reductase_2973365..2973515_POSITIVE 269 125 88 148 103 tfor:TF1749|3end_outer_membrane_protein,_TonB_dependent_receptor_1885799..1885949_POSITIVE 266 320 274 74 33 tfor:TF2628|3end_conserved_hypothetical_protein_2801376..2801526_POSITIVE 265 299 251 133 81 tfor:TF2523|3end_NAD(P)H-flavin_oxidoreductase_2702916..2703066_POSITIVE 265 190 141 77 23 tfor:TF2366|3end_conserved_hypothetical_protein_2531892..2532042_POSITIVE 265 318 274 131 82 tfor:TF2204|3end_conserved_hypothetical_protein_2379122..2379272_POSITIVE 264 250 202 142 97 tfor:TF0021|3end_outer_membrane_phospholipase_A_16919..17069_POSITIVE 263 300 252 111 62 tfor:TF2339|3end_hypothetical_protein_2505783..2505933_POSITIVE