Origin IGS: taaataaaggaggagcaccacaacagaagttgagcgtaataactagatacaatgcattattgtatagaagatttgtggtaagtccaatgtaattctttgtttttttatgaattacaaattagtgcaaagttgattttcgtttttacaaaaaatgctatggcgaagtttgggttaataaggacccattgccttaaaataggatgaagttttacgtcttgtccggttgaaatccgggggatgagcagcggttagtcgttcggaaattgggaaattcaaaattatcgtgtagctttgtcct .........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 aggacaaagctacacgataattttgaatttcccaatttccgaacgactaaccgctgctcatcccccggatttcaaccggacaagacgtaaaacttcatcctattttaaggcaatgggtccttattaacccaaacttcgccatagcattttttgtaaaaacgaaaatcaactttgcactaatttgtaattcataaaaaaacaaagaattacattggacttaccacaaatcttctatacaataatgcattgtatctagttattacgctcaacttctgttgtggtgctcctcctttattta Mask Tandem Repeat Region ================================================ taaataaaggaggagcaccacaacagaagttgagcgtaataactagatacaatgcattattgtatagaagatttgtggtaagtccaatgtaattctttgtttttttatgaattacaaattagtgcaaagttgattttcgtttttacaaaaaatgctatggcgaagtttgggttaataaggacccattgccttaaaataggatgaagttttacgtcttgtccggttgaaatccgggggatgagcagcggttagtcgttcggaaattgggaaattcaaaattatcgtgtagctttgtcct Find is-nt database================================================ Query_seq: TF3017:TF3018|TF3017:TF3018:hypothetical protein:polyphosphate kinase:->->:3239964..3240261 298 taaataaaggaggagcaccacaacagaagttgagcgtaataactagatacaatgcattattgtatagaagatttgtggtaagtccaatgtaattctttgtttttttatgaattacaaattagtgcaaagttgattttcgtttttacaaaaaatgctatggcgaagtttgggttaataaggacccattgccttaaaataggatgaagttttacgtcttgtccggttgaaatccgggggatgagcagcggttagtcgttcggaaattgggaaattcaaaattatcgtgtagctttgtcct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF3017:TF3018|TF3017:TF3018:hypothetical protein:polyphosphate kinase:->->:3239964..3240261 298 taaataaaggaggagcaccacaacagaagttgagcgtaataactagatacaatgcattattgtatagaagatttgtggtaagtccaatgtaattctttgtttttttatgaattacaaattagtgcaaagttgattttcgtttttacaaaaaatgctatggcgaagtttgggttaataaggacccattgccttaaaataggatgaagttttacgtcttgtccggttgaaatccgggggatgagcagcggttagtcgttcggaaattgggaaattcaaaattatcgtgtagctttgtcct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF3017:TF3018|TF3017:TF3018:hypothetical protein:polyphosphate kinase:->->:3239964..3240261 298 taaataaaggaggagcaccacaacagaagttgagcgtaataactagatacaatgcattattgtatagaagatttgtggtaagtccaatgtaattctttgtttttttatgaattacaaattagtgcaaagttgattttcgtttttacaaaaaatgctatggcgaagtttgggttaataaggacccattgccttaaaataggatgaagttttacgtcttgtccggttgaaatccgggggatgagcagcggttagtcgttcggaaattgggaaattcaaaattatcgtgtagctttgtcct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 taaataaaggaggagcaccacaacagaagttgagcgtaataactagatacaatgcattattgtatagaagatttgtggtaagtccaatgtaattctttgtttttttatgaattacaaattagtgcaaagttgattttcgtttttacaaaaaatgctatggcgaagtttgggttaataaggacccattgccttaaaataggatgaagttttacgtcttgtccggttgaaatccgggggatgagcagcggttagtcgttcggaaattgggaaattcaaaattatcgtgtagctttgtcct Predict ORF larger than 30AA ================================================ Protein_Len: 35 Strand: + Start: 97 End: 201 ................................................................................................ M F F Y E L Q I S A K L I F V F T K N A M A K F G L I R T H C L K I G ................................................................................................. Protein_Len: 36 Strand: - Start: 175 End: 282 .............................................................................................................................................................................. Y P G M A K F Y S S T K R R T R N F D P P H A A T L R E S I P F N L I M ................ Protein_Len: 46 Strand: - Start: 108 End: 245 ........................................................................................................... S N C I L A F N I K T K V F F A I A F N P N I L V W Q R L I P H L K V D Q G T S I R P I L M ..................................................... Protein_Len: 37 Strand: - Start: 2 End: 112 . F L P P A G C C F N L T I V L Y L A N N Y L L N T T L G I Y N K T K K H M .......................................................................................................................................................................................... taaataaaggaggagcaccacaacagaagttgagcgtaataactagatacaatgcattattgtatagaagatttgtggtaagtccaatgtaattctttgtttttttatgaattacaaattagtgcaaagttgattttcgtttttacaaaaaatgctatggcgaagtttgggttaataaggacccattgccttaaaataggatgaagttttacgtcttgtccggttgaaatccgggggatgagcagcggttagtcgttcggaaattgggaaattcaaaattatcgtgtagctttgtcct 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================================================ taaataaaggaggagcaccacaacagaagttgagcgtaataactagatacaatgcattattgtatagaagatttgtggtaagtccaatgtaattctttgtttttttatgaattacaaattagtgcaaagttgattttcgtttttacaaaaaatgctatggcgaagtttgggttaataaggacccattgccttaaaataggatgaagttttacgtcttgtccggttgaaatccgggggatgagcagcggttagtcgttcggaaattgggaaattcaaaattatcgtgtagctttgtcct Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 47 HP_score: -3.8 Tail_Score: -3.02013 Start: 48 End: 64 Full_Region: accacaaatcttcta tacaat aatgc attgta tctagttattacgct ...............................................tacaataatgcattgta.......................................................................................................................................................................................................................................... Find igs database================================================ Query_seq: TF3017:TF3018|TF3017:TF3018:hypothetical protein:polyphosphate kinase:->->:3239964..3240261 298 taaataaaggaggagcaccacaacagaagttgagcgtaataactagatacaatgcattattgtatagaagatttgtggtaagtccaatgtaattctttgtttttttatgaattacaaattagtgcaaagttgattttcgtttttacaaaaaatgctatggcgaagtttgggttaataaggacccattgccttaaaataggatgaagttttacgtcttgtccggttgaaatccgggggatgagcagcggttagtcgttcggaaattgggaaattcaaaattatcgtgtagctttgtcct Intra-Species Hit: Count: 1 Min: 1 Max: 298 Len: 298 Subject: tfor_TF3017_TF3018|hypothetical protein:polyphosphate kinase|POSITIVE:POSITIVE|[3239964,3240261]|298 HSP 1 e-value: 1.0E-155 bit: 549.0 Len: 298 Query Start:1 Query End:298 Subject Strand: POSITIVE Subject Start: 1 Subject End: 298 taaataaaggaggagcaccacaacagaagttgagcgtaataactagatacaatgcattattgtatagaagatttgtggtaagtccaatgtaattctttgnnnnnnnatgaattacaaattagtgcaaagttgattttcgtttttacaaaaaatgctatggcgaagtttgggttaataaggacccattgccttaaaataggatgaagttttacgtcttgtccggttgaaatccgggggatgagcagcggttagtcgttcggaaattgggaaattcaaaattatcgtgtagctttgtcct taaataaaggaggagcaccacaacagaagttgagcgtaataactagatacaatgcattattgtatagaagatttgtggtaagtccaatgtaattctttgtttttttatgaattacaaattagtgcaaagttgattttcgtttttacaaaaaatgctatggcgaagtttgggttaataaggacccattgccttaaaataggatgaagttttacgtcttgtccggttgaaatccgggggatgagcagcggttagtcgttcggaaattgggaaattcaaaattatcgtgtagctttgtcct Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAAUAAAGGAGGAGCACCACAACAGAAGUUGAGCGUAAUAACUAGAUACAAUGCAUUAUUGUAUAGAAGAUUUGUGGUAAGUCCAAUGUAAUUCUUUGUUUUUUUAUGAAUUACAAAUUAGUGCAAAGUUGAUUUUCGUUUUUACAAAAAAUGCUAUGGCGAAGUUUGGGUUAAUAAGGACCCAUUGCCUUAAAAUAGGAUGAAGUUUUACGUCUUGUCCGGUUGAAAUCCGGGGGAUGAGCAGCGGUUAGUCGUUCGGAAAUUGGGAAAUUCAAAAUUAUCGUGUAGCUUUGUCCU .............((((...((((....))))...((((.(((.((((.((((((((((................(((.....))).((((((((.............))))))))...)))))))...)))))))..))).))))......))))..(((((....((((((......))))))))))).......((((..(((((.((((.....(((((((....((((((.(((.(((....))).))).)))))))))))))..............)))).)))))..)))) (-72.13) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGGACAAAGCUACACGAUAAUUUUGAAUUUCCCAAUUUCCGAACGACUAACCGCUGCUCAUCCCCCGGAUUUCAACCGGACAAGACGUAAAACUUCAUCCUAUUUUAAGGCAAUGGGUCCUUAUUAACCCAAACUUCGCCAUAGCAUUUUUUGUAAAAACGAAAAUCAACUUUGCACUAAUUUGUAAUUCAUAAAAAAACAAAGAAUUACAUUGGACUUACCACAAAUCUUCUAUACAAUAAUGCAUUGUAUCUAGUUAUUACGCUCAACUUCUGUUGUGGUGCUCCUCCUUUAUUUA ((((...(((..(((((((.............................................((((.......))))....(((((((((((..............((((((((((........)))))...)).)))...(((((..(((((...........................((((((((.............)))))))).(((.....)))...........))))).))))).........)))).))))).))......)))))))..)))..))))....... (-51.62) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 498 268 221 166 109 tfor:TF0995|5end_conserved_hypothetical_protein_1049695..1049925_POSITIVE 433 260 212 216 167 tfor:TF2314|5end_conserved_hypothetical_protein_2473530..2473760_POSITIVE 431 258 214 117 67 tfor:TF0826|5end_primosomal_protein_N'_883751..883981_POSITIVE 421 255 213 195 143 tfor:TF2154|5end_conserved_hypothetical_protein_2329153..2329383_POSITIVE 398 247 206 231 188 tfor:TF0304|5end_peptidyl-prolyl_cis-trans_isomerase_329567..329797_POSITIVE 394 258 212 219 162 tfor:TF0971|5end_conserved_hypothetical_protein_1021355..1021585_POSITIVE 393 260 213 209 153 tfor:TF1346|5end_hypothetical_protein_1425880..1426110_POSITIVE 391 260 212 207 150 tfor:TF2835|5end_stationary-phase_survival_protein_SurE_3025113..3025343_POSITIVE 390 260 212 66 10 tfor:TF1910|5end_nicotinate-nucleotide--dimethylbenzimidazole_phosphoribosyltransferase_2064001..2064231_POSITIVE 389 260 211 185 140 tfor:TF0249|5end_3-hydroxymyristoyl/3-hydroxydecanoyl-(acyl_carrier_protein)_dehydratase_278808..279038_POSITIVE 388 261 221 192 148 tfor:TF1980|5end_conserved_hypothetical_protein_2129869..2130099_POSITIVE 385 268 230 199 149 tfor:TF1430|5end_hypothetical_protein_1514867..1515097_POSITIVE 385 260 211 61 1 tfor:TF0250|5end_glycosyltransferase_Family_2_protein_279176..279406_POSITIVE 379 269 222 207 157 tfor:TF1669|5end_ATP_synthase,_gamma_subunit_1783566..1783796_POSITIVE 379 260 212 181 130 tfor:TF1179|5end_two-component_sensor_histidine_kinase_1266057..1266287_POSITIVE 374 260 212 81 25 tfor:TF2974|5end_conserved_hypothetical_protein;_possible_hydrolase_3181418..3181648_POSITIVE 372 260 212 64 8 tfor:TF0425|5end_outer_membrane_protein_443069..443299_POSITIVE 367 260 212 199 141 tfor:TF2779|5end_fucose_permease_2964566..2964796_POSITIVE 364 248 210 42 2 tfor:TF1530|5end_1-deoxyxylulose-5-phosphate_synthase_1634609..1634839_POSITIVE 361 260 211 139 92 tfor:TF1815|5end_conserved_hypothetical_protein_1956604..1956834_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 431 258 214 136 86 tfor:TF0825|3end_hypothetical_protein_883850..884000_POSITIVE 421 255 213 134 82 tfor:TF2153|3end_6-phosphofructokinase_2329172..2329322_POSITIVE 414 253 212 62 14 tfor:TF1298|3end_possible_membrane_protein_1381197..1381347_POSITIVE 390 260 212 60 4 tfor:TF1909|3end_cobalamin_(5`-phosphate)_synthase_2064075..2064225_POSITIVE 386 248 202 146 99 tfor:TF0994|3end_maltose_O-acetyltransferase_1049782..1049932_POSITIVE 385 260 211 61 1 tfor:TF0249|3end_3-hydroxymyristoyl/3-hydroxydecanoyl-(acyl_carrier_protein)_dehydratase_279256..279406_POSITIVE 382 260 211 64 23 tfor:TF2911|3end_hypothetical_protein_3106640..3106790_POSITIVE 361 260 211 125 78 tfor:TF1814|3end_conserved_hypothetical_protein;_possible_biotin_synthase_related_domain_containing_protein_1956670..1956820_POSITIVE 358 258 217 133 96 tfor:TF1160|3end_MutT/nudix_family_protein_1241008..1241158_POSITIVE 351 260 211 141 74 tfor:TF1775|3end_oxidoreductase,_Gfo/Idh/MocA_family_1914618..1914768_POSITIVE 350 269 221 147 102 tfor:TF0710|3end_two_component_system_histidine_kinase_761385..761535_POSITIVE 350 260 216 107 65 tfor:TF0470|3end_hypothetical_protein_487518..487668_POSITIVE 347 259 219 148 112 tfor:TF2887|3end_phosphomannomutase/phosphoglucomutase_3077792..3077942_POSITIVE 346 268 222 115 63 tfor:TF0708|3end_possible_alkaline_phosphatase_753836..753986_POSITIVE 344 249 216 68 36 tfor:TF2483|3end_hypothetical_protein_2660022..2660172_POSITIVE 342 259 211 116 68 tfor:TF2774|3end_2-amino-4-hydroxy-6-hydroxymethyldihydropteridine_pyrophosphokinase_2959719..2959869_POSITIVE 341 259 211 147 106 tfor:TF0717|3end_signal_recognition_particle_769059..769209_POSITIVE 340 261 222 103 60 tfor:TF0828|3end_hypothetical_protein_887508..887658_POSITIVE 333 260 212 150 84 tfor:TF2892|3end_seryl-tRNA_synthetase_3080726..3080876_POSITIVE 332 260 212 110 57 tfor:TF0982|3end_conserved_hypothetical_protein_1039474..1039624_POSITIVE