Origin IGS: tgataacggtaaagtagagcgcaacagtcggaaaaggagatgaagtgtcattcatatcgactgcatcgataagtacgtatcgaacgggcgcataagaagagagggtgtgccggagcgaaaagctccggcacaccctctcttctatttgtgaatccgaaggaagaagttta .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 taaacttcttccttcggattcacaaatagaagagagggtgtgccggagcttttcgctccggcacaccctctcttcttatgcgcccgttcgatacgtacttatcgatgcagtcgatatgaatgacacttcatctccttttccgactgttgcgctctactttaccgttatca Mask Tandem Repeat Region ================================================ tgataacggtaaagtagagcgcaacagtcggaaaaggagatgaagtgtcattcatatcgactgcatcgataagtacgtatcgaacgggcgcataagaagagagggtgtgccggagcgaaaagctccggcacaccctctcttctatttgtgaatccgaaggaagaagttta Find is-nt database================================================ Query_seq: TF0810:TF0811|TF0810:TF0811:possible outer membrane efflux protein:conserved hypothetical protein; posible sugar phosphate isomerase:->->:869757..869926 170 tgataacggtaaagtagagcgcaacagtcggaaaaggagatgaagtgtcattcatatcgactgcatcgataagtacgtatcgaacgggcgcataagaagagagggtgtgccggagcgaaaagctccggcacaccctctcttctatttgtgaatccgaaggaagaagttta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF0810:TF0811|TF0810:TF0811:possible outer membrane efflux protein:conserved hypothetical protein; posible sugar phosphate isomerase:->->:869757..869926 170 tgataacggtaaagtagagcgcaacagtcggaaaaggagatgaagtgtcattcatatcgactgcatcgataagtacgtatcgaacgggcgcataagaagagagggtgtgccggagcgaaaagctccggcacaccctctcttctatttgtgaatccgaaggaagaagttta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF0810:TF0811|TF0810:TF0811:possible outer membrane efflux protein:conserved hypothetical protein; posible sugar phosphate isomerase:->->:869757..869926 170 tgataacggtaaagtagagcgcaacagtcggaaaaggagatgaagtgtcattcatatcgactgcatcgataagtacgtatcgaacgggcgcataagaagagagggtgtgccggagcgaaaagctccggcacaccctctcttctatttgtgaatccgaaggaagaagttta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tgataacggtaaagtagagcgcaacagtcggaaaaggagatgaagtgtcattcatatcgactgcatcgataagtacgtatcgaacgggcgcataagaagagagggtgtgccggagcgaaaagctccggcacaccctctcttctatttgtgaatccgaaggaagaagttta Predict ORF larger than 30AA ================================================ Protein_Len: 33 Strand: + Start: 50 End: 148 ................................................. M H I D C I D K Y V S N G R I R R E G V P E R K A P A H P L F Y L ...................... Protein_Len: 30 Strand: + Start: 79 End: 168 .............................................................................. M E R A H K K R G C A G A K S S G T P S L L F V N P K E E V .. Protein_Len: 48 Strand: - Start: 2 End: 145 . I V T F Y L A V T P F P S S T D N M D V A D I L V Y R V P A Y S S L T H R L S F S R C V R E E M ......................... tgataacggtaaagtagagcgcaacagtcggaaaaggagatgaagtgtcattcatatcgactgcatcgataagtacgtatcgaacgggcgcataagaagagagggtgtgccggagcgaaaagctccggcacaccctctcttctatttgtgaatccgaaggaagaagttta 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================================================ tgataacggtaaagtagagcgcaacagtcggaaaaggagatgaagtgtcattcatatcgactgcatcgataagtacgtatcgaacgggcgcataagaagagagggtgtgccggagcgaaaagctccggcacaccctctcttctatttgtgaatccgaaggaagaagttta Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 100 HP_score: -32.9 Tail_Score: -3.91897 Start: 94 End: 144 Full_Region: ATCGAACGGGCGCAT AAGAAGAGAGGGTGTGCCGGAGC GAAAA GCTCCGGCACACCCTCTCTTCTA TTTGTGAATCCGAAG .............................................................................................AAGAAGAGAGGGTGTGCCGGAGCGAAAAGCTCCGGCACACCCTCTCTTCTA.......................... TransTerm Strand: + Conf: 100 HP_score: -35.5 Tail_Score: -3.5511 Start: 96 End: 142 Full_Region: CGAACGGGCGCATAA GAAGAGAGGGTGTGCCGGAGC GAAAA GCTCCGGCACACCCTCTCTTC TATTTGTGAATCCGA ...............................................................................................GAAGAGAGGGTGTGCCGGAGCGAAAAGCTCCGGCACACCCTCTCTTC............................ TransTerm Strand: - Conf: 100 HP_score: -35.5 Tail_Score: -3.30159 Start: 96 End: 142 Full_Region: tcggattcacaaata gaagagagggtgtgccggagc ttttc gctccggcacaccctctcttc ttatgcgcccgttcg ...............................................................................................gaagagagggtgtgccggagcttttcgctccggcacaccctctcttc............................ TransTerm Strand: - Conf: 100 HP_score: -31.4 Tail_Score: -3.79113 Start: 99 End: 139 Full_Region: gattcacaaatagaa gagagggtgtgccggagc ttttc gctccggcacaccctctc ttcttatgcgcccgt ..................................................................................................gagagggtgtgccggagcttttcgctccggcacaccctctc............................... Find igs database================================================ Query_seq: TF0810:TF0811|TF0810:TF0811:possible outer membrane efflux protein:conserved hypothetical protein; posible sugar phosphate isomerase:->->:869757..869926 170 tgataacggtaaagtagagcgcaacagtcggaaaaggagatgaagtgtcattcatatcgactgcatcgataagtacgtatcgaacgggcgcataagaagagagggtgtgccggagcgaaaagctccggcacaccctctcttctatttgtgaatccgaaggaagaagttta Intra-Species Hit: Count: 1 Min: 1 Max: 170 Len: 170 Subject: tfor_TF0810_TF0811|possible outer membrane efflux protein:conserved hypothetical protein; posible sugar phosphate isomerase|POSITIVE:POSITIVE|[869757,869926]|170 HSP 1 e-value: 7.0E-92 bit: 337.0 Len: 170 Query Start:1 Query End:170 Subject Strand: POSITIVE Subject Start: 1 Subject End: 170 tgataacggtaaagtagagcgcaacagtcggaaaaggagatgaagtgtcattcatatcgactgcatcgataagtacgtatcgaacgggcgcataagaagagagggtgtgccggagcgaaaagctccggcacaccctctcttctatttgtgaatccgaaggaagaagttta tgataacggtaaagtagagcgcaacagtcggaaaaggagatgaagtgtcattcatatcgactgcatcgataagtacgtatcgaacgggcgcataagaagagagggtgtgccggagcgaaaagctccggcacaccctctcttctatttgtgaatccgaaggaagaagttta HSP 2 e-value: 1.0E-7 bit: 58.0 Len: 49 Query Start:95 Query End:143 Subject Strand: NEGATIVE Subject Start: 95 Subject End: 143 ..............................................................................................agaagagagggtgtgccggagcgaaaagctccggcacaccctctcttct........................... ..............................................................................................agaagagagggtgtgccggagcttttcgctccggcacaccctctcttct........................... Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGAUAACGGUAAAGUAGAGCGCAACAGUCGGAAAAGGAGAUGAAGUGUCAUUCAUAUCGACUGCAUCGAUAAGUACGUAUCGAACGGGCGCAUAAGAAGAGAGGGUGUGCCGGAGCGAAAAGCUCCGGCACACCCUCUCUUCUAUUUGUGAAUCCGAAGGAAGAAGUUUA ......(((.........((((..(((((((.....(((.(((....))))))...)))))))..((((((......))))))....))))...((((((((((((((((((((((.....))))))))))))))))))))))..........))).............. (-76.30) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAACUUCUUCCUUCGGAUUCACAAAUAGAAGAGAGGGUGUGCCGGAGCUUUUCGCUCCGGCACACCCUCUCUUCUUAUGCGCCCGUUCGAUACGUACUUAUCGAUGCAGUCGAUAUGAAUGACACUUCAUCUCCUUUUCCGACUGUUGCGCUCUACUUUACCGUUAUCA ..............(((..........((((((((((((((((((((((.....))))))))))))))))))))))...((((....((((((......)))))).(((((((....((((((....)))).))......))))))).)))).........)))...... (-71.80) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 553 137 101 152 116 tfor:TF1898|5end_RNA_polymerase_ECF-type_sigma_factor_2052115..2052345_POSITIVE 432 129 81 121 67 tfor:TF2477|5end_phosphatase_2654229..2654459_POSITIVE 431 138 97 161 119 tfor:TF0476|5end_conserved_hypothetical_protein_494944..495174_POSITIVE 429 138 95 169 124 tfor:TF2536|5end_subtilisin-like_serine_protease_2719286..2719516_POSITIVE 403 130 81 125 82 tfor:TF3067|5end_conserved_hypothetical_protein_3292432..3292662_POSITIVE 403 140 97 203 157 tfor:TF0662|5end_hypothetical_protein_708316..708546_POSITIVE 402 140 94 166 127 tfor:TF2747|5end_heat_shock_protein,_HSP90_family_2928279..2928509_POSITIVE 399 130 81 87 27 tfor:TF1198|5end_conserved_hypothetical_protein_1281464..1281694_POSITIVE 398 140 98 157 114 tfor:TF1284|5end_glyceraldehyde_3-phosphate_dehydrogenase_1367939..1368169_POSITIVE 397 130 81 201 142 tfor:TF1261|5end_GrpE-related_chaperonin;_HSP-70_cofactor_1346504..1346734_POSITIVE 393 128 81 43 5 tfor:TF0421|5end_alpha-L-fucosidase_436021..436251_POSITIVE 391 114 71 190 136 tfor:TF2713|5end_glycosyltransferase_2886582..2886812_POSITIVE 388 130 81 161 115 tfor:TF2380|5end_hemagglutinin_2545012..2545242_POSITIVE 388 130 81 171 119 tfor:TF1739|5end_possible_sulfatase_1866983..1867213_POSITIVE 387 148 104 146 105 tfor:TF2893|5end_conserved_hypothetical_protein;_possible_phosphoesterase_3080766..3080996_POSITIVE 387 138 98 202 161 tfor:TF2593|5end_amino_acid_transport_protein_2762882..2763112_POSITIVE 387 140 94 227 182 tfor:TF1999|5end_ArgK_protein_with_ATPase_and_kinase_domains_2152769..2152999_POSITIVE 383 138 95 226 183 tfor:TF0184|5end_dihydroneopterin_aldolase_195629..195859_POSITIVE 380 138 93 164 115 tfor:TF0792|5end_pyruvate_ferredoxin;_flavodoxin_oxidoreductase_846454..846684_POSITIVE 378 130 82 68 14 tfor:TF0252|5end_hypothetical_protein_283530..283760_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 553 137 101 64 28 tfor:TF1897|3end_conserved_hypothetical_protein;_possible_aminopeptidase_2052107..2052257_POSITIVE 493 149 101 121 74 tfor:TF2413|3end_hypothetical_protein_2590680..2590830_POSITIVE 493 140 99 60 21 tfor:TF1354|3end_TonB_protein_1435216..1435366_POSITIVE 446 137 91 49 2 tfor:TF2765|3end_subtilisin-like_serine_protease_2951460..2951610_POSITIVE 412 130 84 55 7 tfor:TF0247|3end_conserved_hypothetical_protein_278348..278498_POSITIVE 403 140 97 64 18 tfor:TF0661|3end_hypothetical_protein_708257..708407_POSITIVE 402 140 94 53 14 tfor:TF2746|3end_hypothetical_protein_2928246..2928396_POSITIVE 388 130 81 54 2 tfor:TF1738|3end_outer_membrane_protein_1866946..1867096_POSITIVE 387 138 98 47 6 tfor:TF2592|3end_conserved_hypothetical_protein_2762807..2762957_POSITIVE 387 140 94 64 19 tfor:TF1997|3end_ROK_family_transcriptional_regulator_2152686..2152836_POSITIVE 383 138 95 45 2 tfor:TF0182|3end_DNA-binding_protein,_HU-related_195528..195678_POSITIVE 382 138 95 55 11 tfor:TF1416|3end_outer_membrane_protein_1499413..1499563_POSITIVE 379 129 87 114 77 tfor:TF0239|3end_conserved_hypothetical_protein_270323..270473_POSITIVE 377 129 86 117 65 tfor:TF1498|3end_GTP-binding_protein_1598490..1598640_POSITIVE 377 128 81 78 35 tfor:TF1066|3end_hypothetical_protein_1136858..1137008_POSITIVE 376 118 71 77 22 tfor:TF1337|3end_multidrug_efflux_pump,_BexA_1420915..1421065_POSITIVE 375 137 103 43 3 tfor:TF2883|3end_peptidyl-prolyl_cis-trans_isomerase_3075129..3075279_POSITIVE 368 110 61 142 83 tfor:TF1291|3end_response_regulator_(fimR__protein)_1372647..1372797_POSITIVE 367 128 81 55 6 tfor:TF3113|3end_hypothetical_protein_3349706..3349856_POSITIVE 365 120 76 60 18 tfor:TF2164|3end_hypothetical_protein_2341708..2341858_POSITIVE