Origin IGS: taatcggctggagaatgagggtggggcgcgatgcgttaatttgttctttaacgtttacccttgccccataatcttatttattctcatagaacttaagaggatatgccaaaatgtaatgttttgacgcatcctcttttggttgtccggtatcggttagccccctgctttgttaacgtaaaaataacatgatgataacatagcttcag .........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 ctgaagctatgttatcatcatgttatttttacgttaacaaagcagggggctaaccgataccggacaaccaaaagaggatgcgtcaaaacattacattttggcatatcctcttaagttctatgagaataaataagattatggggcaagggtaaacgttaaagaacaaattaacgcatcgcgccccaccctcattctccagccgatta Mask Tandem Repeat Region ================================================ taatcggctggagaatgagggtggggcgcgatgcgttaatttgttctttaacgtttacccttgccccataatcttatttattctcatagaacttaagaggatatgccaaaatgtaatgttttgacgcatcctcttttggttgtccggtatcggttagccccctgctttgttaacgtaaaaataacatgatgataacatagcttcag Find is-nt database================================================ Query_seq: TF2288:TF2289|TF2288:TF2289:hypothetical protein:secretion protein, possible HlyD family:->->:2442659..2442864 206 taatcggctggagaatgagggtggggcgcgatgcgttaatttgttctttaacgtttacccttgccccataatcttatttattctcatagaacttaagaggatatgccaaaatgtaatgttttgacgcatcctcttttggttgtccggtatcggttagccccctgctttgttaacgtaaaaataacatgatgataacatagcttcag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF2288:TF2289|TF2288:TF2289:hypothetical protein:secretion protein, possible HlyD family:->->:2442659..2442864 206 taatcggctggagaatgagggtggggcgcgatgcgttaatttgttctttaacgtttacccttgccccataatcttatttattctcatagaacttaagaggatatgccaaaatgtaatgttttgacgcatcctcttttggttgtccggtatcggttagccccctgctttgttaacgtaaaaataacatgatgataacatagcttcag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF2288:TF2289|TF2288:TF2289:hypothetical protein:secretion protein, possible HlyD family:->->:2442659..2442864 206 taatcggctggagaatgagggtggggcgcgatgcgttaatttgttctttaacgtttacccttgccccataatcttatttattctcatagaacttaagaggatatgccaaaatgtaatgttttgacgcatcctcttttggttgtccggtatcggttagccccctgctttgttaacgtaaaaataacatgatgataacatagcttcag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 taatcggctggagaatgagggtggggcgcgatgcgttaatttgttctttaacgtttacccttgccccataatcttatttattctcatagaacttaagaggatatgccaaaatgtaatgttttgacgcatcctcttttggttgtccggtatcggttagccccctgctttgttaacgtaaaaataacatgatgataacatagcttcag Predict ORF larger than 30AA ================================================ Protein_Len: 38 Strand: + Start: 8 End: 121 ....... M E N E G G A R C V N L F F N V Y P C P I I L F I L I E L K R I C Q N V M F ..................................................................................... Protein_Len: 37 Strand: - Start: 96 End: 206 ............................................................................................... S S I G F H L T K V C G R K T T R Y R N A G Q K T L T F I V H H Y C L K M Protein_Len: 31 Strand: - Start: 58 End: 150 ......................................................... G Q G M I K N I R M S S L L I H W F T I N Q R M R K Q N D P M ........................................................ taatcggctggagaatgagggtggggcgcgatgcgttaatttgttctttaacgtttacccttgccccataatcttatttattctcatagaacttaagaggatatgccaaaatgtaatgttttgacgcatcctcttttggttgtccggtatcggttagccccctgctttgttaacgtaaaaataacatgatgataacatagcttcag 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================================================ taatcggctggagaatgagggtggggcgcgatgcgttaatttgttctttaacgtttacccttgccccataatcttatttattctcatagaacttaagaggatatgccaaaatgtaatgttttgacgcatcctcttttggttgtccggtatcggttagccccctgctttgttaacgtaaaaataacatgatgataacatagcttcag Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 73 HP_score: -5.9 Tail_Score: -4.49389 Start: 97 End: 133 Full_Region: TCTCATAGAACTTAA GAGGATATGCCAAAATG TAA TGTTTTGACGCATCCTC TTTTGGTTGTCCGGT ................................................................................................GAGGATATGCCAAAATGTAATGTTTTGACGCATCCTC......................................................................... TransTerm Strand: - Conf: 61 HP_score: -6.7 Tail_Score: -3.26449 Start: 97 End: 133 Full_Region: accggacaaccaaaa gaggatgcgtcaaaa cattaca ttttggcatatcctc ttaagttctatgaga ................................................................................................gaggatgcgtcaaaacattacattttggcatatcctc......................................................................... Find igs database================================================ Query_seq: TF2288:TF2289|TF2288:TF2289:hypothetical protein:secretion protein, possible HlyD family:->->:2442659..2442864 206 taatcggctggagaatgagggtggggcgcgatgcgttaatttgttctttaacgtttacccttgccccataatcttatttattctcatagaacttaagaggatatgccaaaatgtaatgttttgacgcatcctcttttggttgtccggtatcggttagccccctgctttgttaacgtaaaaataacatgatgataacatagcttcag Intra-Species Hit: Count: 1 Min: 1 Max: 206 Len: 206 Subject: tfor_TF2288_TF2289|hypothetical protein:secretion protein, possible HlyD family|POSITIVE:POSITIVE|[2442659,2442864]|206 HSP 1 e-value: 1.0E-113 bit: 408.0 Len: 206 Query Start:1 Query End:206 Subject Strand: POSITIVE Subject Start: 1 Subject End: 206 taatcggctggagaatgagggtggggcgcgatgcgttaatttgttctttaacgtttacccttgccccataatcttatttattctcatagaacttaagaggatatgccaaaatgtaatgttttgacgcatcctcttttggttgtccggtatcggttagccccctgctttgttaacgtaaaaataacatgatgataacatagcttcag taatcggctggagaatgagggtggggcgcgatgcgttaatttgttctttaacgtttacccttgccccataatcttatttattctcatagaacttaagaggatatgccaaaatgtaatgttttgacgcatcctcttttggttgtccggtatcggttagccccctgctttgttaacgtaaaaataacatgatgataacatagcttcag Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAUCGGCUGGAGAAUGAGGGUGGGGCGCGAUGCGUUAAUUUGUUCUUUAACGUUUACCCUUGCCCCAUAAUCUUAUUUAUUCUCAUAGAACUUAAGAGGAUAUGCCAAAAUGUAAUGUUUUGACGCAUCCUCUUUUGGUUGUCCGGUAUCGGUUAGCCCCCUGCUUUGUUAACGUAAAAAUAACAUGAUGAUAACAUAGCUUCAG ((((((((((((((((((((((((((((.(..(((((((........))))))).....).))))))))..))))))))..........((((.((((((((.((.((((((.....)))))).)).))))))))..)))).))))))..)))))).......(((.(((((.(((............))).))))).)))..... (-61.10) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CUGAAGCUAUGUUAUCAUCAUGUUAUUUUUACGUUAACAAAGCAGGGGGCUAACCGAUACCGGACAACCAAAAGAGGAUGCGUCAAAACAUUACAUUUUGGCAUAUCCUCUUAAGUUCUAUGAGAAUAAAUAAGAUUAUGGGGCAAGGGUAAACGUUAAAGAACAAAUUAACGCAUCGCGCCCCACCCUCAUUCUCCAGCCGAUUA (((..(((.(((((.....((((.......))))))))).)))..(((((...(((....)))...(((..(((((((((.(((((((.......))))))).)))))))))..(((((((((............)))))))))...)))...((((((........))))))......)))))............)))....... (-54.60) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 492 165 121 219 169 tfor:TF2824|5end_nucleoside-transporting_protein_nupG_3014701..3014931_POSITIVE 443 139 95 155 109 tfor:TF2947|5end_isochorismate_synthase_3153633..3153863_POSITIVE 432 46 4 221 178 tfor:TF2016|5end_hypothetical_protein_2172948..2173178_POSITIVE 422 137 91 215 168 tfor:TF1505|5end_conserved_hypothetical_protein_1610773..1611003_POSITIVE 405 137 91 201 153 tfor:TF0662|5end_hypothetical_protein_708316..708546_POSITIVE 398 49 5 127 82 tfor:TF3158|5end_inner_membrane_protein_3393729..3393959_POSITIVE 393 136 95 228 187 tfor:TF0184|5end_dihydroneopterin_aldolase_195629..195859_POSITIVE 387 175 132 218 159 tfor:TF2255|5end_transfer_region-related_protein,_TraH_2427504..2427734_POSITIVE 387 140 94 167 118 tfor:TF0476|5end_conserved_hypothetical_protein_494944..495174_POSITIVE 367 49 3 134 82 tfor:TF0690|5end_preprotein_translocase_subunit_735243..735473_POSITIVE 365 34 5 161 119 tfor:TF1919|5end_hypothetical_protein_2070037..2070267_POSITIVE 365 34 5 121 79 tfor:TF1917|5end_hypothetical_protein_2069997..2070227_POSITIVE 361 165 140 37 5 tfor:TF2893|5end_conserved_hypothetical_protein;_possible_phosphoesterase_3080766..3080996_POSITIVE 360 140 95 81 36 tfor:TF1046|5end_hypothetical_protein_1108178..1108408_POSITIVE 358 170 126 82 31 tfor:TF0816|5end_hypothetical_protein_874217..874447_POSITIVE 354 69 21 62 11 tfor:TF2533|5end_adenylosuccinate_synthetase_2715666..2715896_POSITIVE 354 43 4 99 63 tfor:TF0886|5end_conjugative_transposon_protein_fragment_937914..938144_POSITIVE 349 164 121 210 148 tfor:TF0537|5end_conserved_hypothetical_protein_563145..563375_POSITIVE 348 148 102 108 53 tfor:TF0002|5end_hypothetical_protein_316..546_POSITIVE 339 49 5 169 117 tfor:TF1543|5end_conserved_hypothetical_protein_1649429..1649659_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 405 137 91 62 14 tfor:TF0661|3end_hypothetical_protein_708257..708407_POSITIVE 398 49 5 105 60 tfor:TF3157|3end_sodium/solute_symporter_3393787..3393937_POSITIVE 393 136 95 47 6 tfor:TF0182|3end_DNA-binding_protein,_HU-related_195528..195678_POSITIVE 371 149 116 34 2 tfor:TF0178|3end_ferritin_188223..188373_POSITIVE 365 34 5 149 107 tfor:TF1918|3end_hypothetical_protein_2070105..2070255_POSITIVE 360 140 95 68 23 tfor:TF1045|3end_conserved_hypothetical_protein_1108245..1108395_POSITIVE 353 133 95 49 11 tfor:TF2765|3end_subtilisin-like_serine_protease_2951460..2951610_POSITIVE 344 165 125 97 56 tfor:TF1182|3end_hypothetical_protein_1268938..1269088_POSITIVE 337 166 121 148 92 tfor:TF0536|3end_conserved_hypothetical_protein_563169..563319_POSITIVE 336 170 121 73 31 tfor:TF2260|3end_transfer_region-related_protein,_TraL_2430592..2430742_POSITIVE 336 48 6 141 89 tfor:TF1433|3end_ribose_5-phosphate_isomerase_1517551..1517701_POSITIVE 335 43 4 139 105 tfor:TF0710|3end_two_component_system_histidine_kinase_761385..761535_POSITIVE 334 36 4 134 95 tfor:TF2895|3end_hypothetical_protein_3084192..3084342_POSITIVE 334 139 95 63 17 tfor:TF1416|3end_outer_membrane_protein_1499413..1499563_POSITIVE 332 30 4 146 124 tfor:TF0885|3end_conjugative_transposon_protein_fragment_938055..938205_POSITIVE 330 60 16 77 42 tfor:TF1597|3end_TatD_family_protein_1713418..1713568_POSITIVE 330 36 6 130 97 tfor:TF1204|3end_possible_metal-dependent_membrane_protease_1287461..1287611_POSITIVE 327 39 4 91 50 tfor:TF1336|3end_hypothetical_protein_1419575..1419725_POSITIVE 325 170 126 61 10 tfor:TF2874|3end_conserved_hypothetical_protein_3065224..3065374_POSITIVE 323 36 3 54 22 tfor:TF1680|3end_peptide_chain_release_factor_3_1794969..1795119_POSITIVE