Origin IGS: taatcctgtctcgaacagataatatatcaggccgattctgccgcaagacagagcttactggaaaccggtaagcctgttttgcggcagataaatccgaaattctcccaacggcgcagagcgtcagtgatgacttcttcctaccgaagaaaagatgcgatttatttcttatatttgtgtgcaaaacaaaactaatcgaacaaa .........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 tttgttcgattagttttgttttgcacacaaatataagaaataaatcgcatcttttcttcggtaggaagaagtcatcactgacgctctgcgccgttgggagaatttcggatttatctgccgcaaaacaggcttaccggtttccagtaagctctgtcttgcggcagaatcggcctgatatattatctgttcgagacaggatta Mask Tandem Repeat Region ================================================ taatcctgtctcgaacagataatatatcaggccgattctgccgcaagacagagcttactggaaaccggtaagcctgttttgcggcagataaatccgaaattctcccaacggcgcagagcgtcagtgatgacttcttcctaccgaagaaaagatgcgatttatttcttatatttgtgtgcaaaacaaaactaatcgaacaaa Find is-nt database================================================ Query_seq: TF0112:TF0113|TF0112:TF0113:outer membrane protein:4-deoxy-L-threo-5-hexosulose-uronate ketol-isomerase:->->:123088..123288 201 taatcctgtctcgaacagataatatatcaggccgattctgccgcaagacagagcttactggaaaccggtaagcctgttttgcggcagataaatccgaaattctcccaacggcgcagagcgtcagtgatgacttcttcctaccgaagaaaagatgcgatttatttcttatatttgtgtgcaaaacaaaactaatcgaacaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF0112:TF0113|TF0112:TF0113:outer membrane protein:4-deoxy-L-threo-5-hexosulose-uronate ketol-isomerase:->->:123088..123288 201 taatcctgtctcgaacagataatatatcaggccgattctgccgcaagacagagcttactggaaaccggtaagcctgttttgcggcagataaatccgaaattctcccaacggcgcagagcgtcagtgatgacttcttcctaccgaagaaaagatgcgatttatttcttatatttgtgtgcaaaacaaaactaatcgaacaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF0112:TF0113|TF0112:TF0113:outer membrane protein:4-deoxy-L-threo-5-hexosulose-uronate ketol-isomerase:->->:123088..123288 201 taatcctgtctcgaacagataatatatcaggccgattctgccgcaagacagagcttactggaaaccggtaagcctgttttgcggcagataaatccgaaattctcccaacggcgcagagcgtcagtgatgacttcttcctaccgaagaaaagatgcgatttatttcttatatttgtgtgcaaaacaaaactaatcgaacaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 taatcctgtctcgaacagataatatatcaggccgattctgccgcaagacagagcttactggaaaccggtaagcctgttttgcggcagataaatccgaaattctcccaacggcgcagagcgtcagtgatgacttcttcctaccgaagaaaagatgcgatttatttcttatatttgtgtgcaaaacaaaactaatcgaacaaa Predict ORF larger than 30AA ================================================ Protein_Len: 57 Strand: + Start: 19 End: 189 .................. M I Y Q A D S A A R Q S L L E T G K P V L R Q I N P K F S Q R R R A S V M T S S Y R R K D A I Y F L Y L C A K Q N ............ Protein_Len: 34 Strand: + Start: 99 End: 200 .................................................................................................. M L P T A Q S V S D D F F L P K K R C D L F L I F V C K T K L I E Q . Protein_Len: 33 Strand: - Start: 30 End: 128 ............................. A S E A A L C L K S S V P L G T K R C I F G F N E W R R L A D T M ......................................................................... Protein_Len: 60 Strand: - Start: 2 End: 193 . V S L I D P R N Q R L V S S V P F R Y A Q K A A S L D S I R G V A C L T L S S K K R G F F L H S K N R I N T H L V F S M ........ taatcctgtctcgaacagataatatatcaggccgattctgccgcaagacagagcttactggaaaccggtaagcctgttttgcggcagataaatccgaaattctcccaacggcgcagagcgtcagtgatgacttcttcctaccgaagaaaagatgcgatttatttcttatatttgtgtgcaaaacaaaactaatcgaacaaa 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================================================ taatcctgtctcgaacagataatatatcaggccgattctgccgcaagacagagcttactggaaaccggtaagcctgttttgcggcagataaatccgaaattctcccaacggcgcagagcgtcagtgatgacttcttcctaccgaagaaaagatgcgatttatttcttatatttgtgtgcaaaacaaaactaatcgaacaaa Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 91 HP_score: -11.4 Tail_Score: -4.08216 Start: 49 End: 76 Full_Region: GATTCTGCCGCAAGA CAGAGCTTACTGG AAA CCGGTAAGCCTG TTTTGCGGCAGATAA ................................................CAGAGCTTACTGGAAACCGGTAAGCCTG............................................................................................................................. TransTerm Strand: + Conf: 79 HP_score: -11.9 Tail_Score: -2.78032 Start: 53 End: 73 Full_Region: CTGCCGCAAGACAGA GCTTACTGG AAA CCGGTAAGC CTGTTTTGCGGCAGA ....................................................GCTTACTGGAAACCGGTAAGC................................................................................................................................ TransTerm Strand: - Conf: 71 HP_score: -9.7 Tail_Score: -3.09273 Start: 53 End: 73 Full_Region: tctgccgcaaaacag gcttaccgg ttt ccagtaagc tctgtcttgcggcag ....................................................gcttaccggtttccagtaagc................................................................................................................................ Find igs database================================================ Query_seq: TF0112:TF0113|TF0112:TF0113:outer membrane protein:4-deoxy-L-threo-5-hexosulose-uronate ketol-isomerase:->->:123088..123288 201 taatcctgtctcgaacagataatatatcaggccgattctgccgcaagacagagcttactggaaaccggtaagcctgttttgcggcagataaatccgaaattctcccaacggcgcagagcgtcagtgatgacttcttcctaccgaagaaaagatgcgatttatttcttatatttgtgtgcaaaacaaaactaatcgaacaaa Intra-Species Hit: Count: 1 Min: 1 Max: 201 Len: 201 Subject: tfor_TF0112_TF0113|outer membrane protein:4-deoxy-L-threo-5-hexosulose-uronate ketol-isomerase|POSITIVE:POSITIVE|[123088,123288]|201 HSP 1 e-value: 1.0E-110 bit: 398.0 Len: 201 Query Start:1 Query End:201 Subject Strand: POSITIVE Subject Start: 1 Subject End: 201 taatcctgtctcgaacagataatatatcaggccgattctgccgcaagacagagcttactggaaaccggtaagcctgttttgcggcagataaatccgaaattctcccaacggcgcagagcgtcagtgatgacttcttcctaccgaagaaaagatgcgatttatttcttatatttgtgtgcaaaacaaaactaatcgaacaaa taatcctgtctcgaacagataatatatcaggccgattctgccgcaagacagagcttactggaaaccggtaagcctgttttgcggcagataaatccgaaattctcccaacggcgcagagcgtcagtgatgacttcttcctaccgaagaaaagatgcgatttatttcttatatttgtgtgcaaaacaaaactaatcgaacaaa Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAUCCUGUCUCGAACAGAUAAUAUAUCAGGCCGAUUCUGCCGCAAGACAGAGCUUACUGGAAACCGGUAAGCCUGUUUUGCGGCAGAUAAAUCCGAAAUUCUCCCAACGGCGCAGAGCGUCAGUGAUGACUUCUUCCUACCGAAGAAAAGAUGCGAUUUAUUUCUUAUAUUUGUGUGCAAAACAAAACUAAUCGAACAAA ......(((.((((..(((.((((.(((..((((..(((((((((((((((.(((((((((...)))))))))))))))))))))))).......((.....))....)))).......((((....)))).(((((.....)))))........))).)))))))....(((((.......))))).....))))))).. (-67.00) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUGUUCGAUUAGUUUUGUUUUGCACACAAAUAUAAGAAAUAAAUCGCAUCUUUUCUUCGGUAGGAAGAAGUCAUCACUGACGCUCUGCGCCGUUGGGAGAAUUUCGGAUUUAUCUGCCGCAAAACAGGCUUACCGGUUUCCAGUAAGCUCUGUCUUGCGGCAGAAUCGGCCUGAUAUAUUAUCUGUUCGAGACAGGAUUA ..........(((((((((((((.(((..((((((.....((((((...((((..(....).)))).(((((..((.(..((((.....).)))..)))..))))).))))))((((((((((.((((((((((.((...)).)))))).)))).))))))))))..........))))))...))).))))))))))))) (-66.90) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 391 139 91 52 3 tfor:TF0145|5end_glutamine_synthetase_152446..152676_POSITIVE 390 119 71 224 176 tfor:TF1889|5end_hypothetical_protein_2041479..2041709_POSITIVE 384 119 71 58 13 tfor:TF1292|5end_sensor_histidine_protein_kinase_1372567..1372797_POSITIVE 380 96 53 65 27 tfor:TF0389|5end_conserved_hypothetical_protein;_possible_integral_membrane_protein_408774..409004_POSITIVE 372 145 101 222 169 tfor:TF0763|5end_chromate_transport_protein_809675..809905_POSITIVE 369 112 72 40 5 tfor:TF0991|5end_probable_NAD(FAD)-dependent_dehydrogenase_1046671..1046901_POSITIVE 367 76 31 49 6 tfor:TF0801|5end_transport_permease_858586..858816_POSITIVE 366 137 95 89 46 tfor:TF3005|5end_histidine_kinase_sensor_protein_3224805..3225035_POSITIVE 364 138 92 59 14 tfor:TF1548|5end_thiophene_and_furan_oxidation_protein_1652501..1652731_POSITIVE 362 120 71 190 138 tfor:TF3141|5end_NADH:_ubiquinone_oxidoreductase,_subunit_A_3374667..3374897_POSITIVE 359 90 41 226 173 tfor:TF0529|5end_transposase_554776..555006_POSITIVE 358 76 31 169 128 tfor:TF2450|5end_outer_membrane_protein_2626471..2626701_POSITIVE 356 139 94 190 152 tfor:TF1768|5end_conserved_hypothetical_protein;_possible_transposase_1906526..1906756_POSITIVE 355 68 28 54 15 tfor:TF2337|5end_conserved_hypothetical_protein_2497997..2498227_POSITIVE 351 80 34 197 142 tfor:TF0776|5end_ABC_transporter,_permease_component_824855..825085_POSITIVE 344 130 83 97 38 tfor:TF2341|5end_hypothetical_protein_2505735..2505965_POSITIVE 343 145 101 64 27 tfor:TF2951|5end_O-succinylbenzoic_acid--CoA_ligase_3158496..3158726_POSITIVE 341 70 21 223 148 tfor:TF2812|5end_hypothetical_protein_3002726..3002956_POSITIVE 341 146 108 214 173 tfor:TF0033|5end_outer_membrane_protein_29191..29421_POSITIVE 340 128 83 149 114 tfor:TF1681|5end_dTDP-4-keto-L-rhamnose_reductase_1794904..1795134_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 745 88 41 54 7 tfor:TF0112|3end_outer_membrane_protein_123027..123177_POSITIVE 384 119 71 58 13 tfor:TF1291|3end_response_regulator_(fimR__protein)_1372647..1372797_POSITIVE 380 96 53 57 19 tfor:TF0388|3end_conserved_hypothetical_protein;_possible_integral_membrane_protein_408846..408996_POSITIVE 368 85 41 72 14 tfor:TF2690|3end_possible_permease_2866562..2866712_POSITIVE 359 90 41 149 96 tfor:TF0528|3end_two-component_system_sensor_histidine_kinase_554779..554929_POSITIVE 355 68 28 136 97 tfor:TF2336|3end_conserved_hypothetical_protein_2498159..2498309_POSITIVE 344 130 83 65 6 tfor:TF2339|3end_hypothetical_protein_2505783..2505933_POSITIVE 343 90 41 135 64 tfor:TF2609|3end_dipeptidase,_pathogenicity_island-encoded_protein_D_2786264..2786414_POSITIVE 342 85 41 150 101 tfor:TF1774|3end_arylsulfatase_precursor_1912939..1913089_POSITIVE 340 128 83 134 99 tfor:TF1680|3end_peptide_chain_release_factor_3_1794969..1795119_POSITIVE 336 119 71 78 11 tfor:TF1653|3end_hypothetical_protein_1766481..1766631_POSITIVE 336 119 71 78 11 tfor:TF0979|3end_hypothetical_protein_1033118..1033268_POSITIVE 327 80 32 98 46 tfor:TF3153|3end_conserved_hypothetical_protein_3389324..3389474_POSITIVE 327 145 102 37 1 tfor:TF2950|3end_chloromuconate_cycloisomerase_3158549..3158699_POSITIVE 322 90 41 120 61 tfor:TF2271|3end_conserved_hypothetical_protein_2436187..2436337_POSITIVE 321 78 31 78 25 tfor:TF2275|3end_conserved_hypothetical_protein_2438300..2438450_POSITIVE 320 88 44 56 1 tfor:TF2900|3end_conserved_hypothetical_protein_3090029..3090179_POSITIVE 319 148 111 65 30 tfor:TF2490|3end_4-hydroxyphenylacetate-3-hydroxylase/4-hydroxybut_yryl_dehydratase_2666755..2666905_POSITIVE 319 123 82 143 104 tfor:TF2397|3end_magnesium_and_cobalt_transport_protein_2569569..2569719_POSITIVE 318 85 41 72 31 tfor:TF1296|3end_possible_DNA-binding_protein,_histone-like_family_1378982..1379132_POSITIVE