Origin IGS: taaatcgaattgaatcgttcacgtaatccgtaaaaagagggtgtgccaaaatacaatatttgggcacaccttttttctctcacaggtatccgataagctattgaaacatttgaaaaagcgatcagccgttttcagccgttagaaacaatccaacgcccgaaggccaaaatcagaccttcaaagttcgtccgcgaacaagaaaagtaatca .........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 tgattacttttcttgttcgcggacgaactttgaaggtctgattttggccttcgggcgttggattgtttctaacggctgaaaacggctgatcgctttttcaaatgtttcaatagcttatcggatacctgtgagagaaaaaaggtgtgcccaaatattgtattttggcacaccctctttttacggattacgtgaacgattcaattcgattta Mask Tandem Repeat Region ================================================ taaatcgaattgaatcgttcacgtaatccgtaaaaagagggtgtgccaaaatacaatatttgggcacaccttttttctctcacaggtatccgataagctattgaaacatttgaaaaagcgatcagccgttttcagccgttagaaacaatccaacgcccgaaggccaaaatcagaccttcaaagttcgtccgcgaacaagaaaagtaatca Find is-nt database================================================ Query_seq: TF1416:TF1417|TF1416:TF1417:outer membrane protein:conserved hypothetical protein:->->:1499474..1499683 210 taaatcgaattgaatcgttcacgtaatccgtaaaaagagggtgtgccaaaatacaatatttgggcacaccttttttctctcacaggtatccgataagctattgaaacatttgaaaaagcgatcagccgttttcagccgttagaaacaatccaacgcccgaaggccaaaatcagaccttcaaagttcgtccgcgaacaagaaaagtaatca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF1416:TF1417|TF1416:TF1417:outer membrane protein:conserved hypothetical protein:->->:1499474..1499683 210 taaatcgaattgaatcgttcacgtaatccgtaaaaagagggtgtgccaaaatacaatatttgggcacaccttttttctctcacaggtatccgataagctattgaaacatttgaaaaagcgatcagccgttttcagccgttagaaacaatccaacgcccgaaggccaaaatcagaccttcaaagttcgtccgcgaacaagaaaagtaatca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF1416:TF1417|TF1416:TF1417:outer membrane protein:conserved hypothetical protein:->->:1499474..1499683 210 taaatcgaattgaatcgttcacgtaatccgtaaaaagagggtgtgccaaaatacaatatttgggcacaccttttttctctcacaggtatccgataagctattgaaacatttgaaaaagcgatcagccgttttcagccgttagaaacaatccaacgcccgaaggccaaaatcagaccttcaaagttcgtccgcgaacaagaaaagtaatca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 taaatcgaattgaatcgttcacgtaatccgtaaaaagagggtgtgccaaaatacaatatttgggcacaccttttttctctcacaggtatccgataagctattgaaacatttgaaaaagcgatcagccgttttcagccgttagaaacaatccaacgcccgaaggccaaaatcagaccttcaaagttcgtccgcgaacaagaaaagtaatca Predict ORF larger than 30AA ================================================ Protein_Len: 42 Strand: + Start: 14 End: 139 ............. M V H V I R K K R V C Q N T I F G H T F F L S Q V S D K L L K H L K K R S A V F S R ....................................................................... Protein_Len: 35 Strand: + Start: 100 End: 204 ................................................................................................... M E T F E K A I S R F Q P L E T I Q R P K A K I R P S K F V R E Q E K ...... Protein_Len: 38 Strand: - Start: 22 End: 135 ..................... T I R L F L T H W F V I N P C V K K R E C T D S L S N F C K F F R D A T K M ........................................................................... Protein_Len: 41 Strand: - Start: 3 End: 125 .. I S N F R E R L G Y F S P T G F Y L I Q A C R K E R V P I R Y A I S V N S F A I M ..................................................................................... taaatcgaattgaatcgttcacgtaatccgtaaaaagagggtgtgccaaaatacaatatttgggcacaccttttttctctcacaggtatccgataagctattgaaacatttgaaaaagcgatcagccgttttcagccgttagaaacaatccaacgcccgaaggccaaaatcagaccttcaaagttcgtccgcgaacaagaaaagtaatca 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================================================ taaatcgaattgaatcgttcacgtaatccgtaaaaagagggtgtgccaaaatacaatatttgggcacaccttttttctctcacaggtatccgataagctattgaaacatttgaaaaagcgatcagccgttttcagccgttagaaacaatccaacgcccgaaggccaaaatcagaccttcaaagttcgtccgcgaacaagaaaagtaatca Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 100 HP_score: -15.6 Tail_Score: -5.36441 Start: 40 End: 70 Full_Region: AATCCGTAAAAAGAG GGTGTGCCAAAATA CAA TATTTGGGCACACC TTTTTTCTCTCACAG .......................................GGTGTGCCAAAATACAATATTTGGGCACACC............................................................................................................................................ TransTerm Strand: - Conf: 100 HP_score: -15.6 Tail_Score: -2.94823 Start: 40 End: 70 Full_Region: ctgtgagagaaaaaa ggtgtgcccaaata ttg tattttggcacacc ctctttttacggatt .......................................ggtgtgcccaaatattgtattttggcacacc............................................................................................................................................ Find igs database================================================ Query_seq: TF1416:TF1417|TF1416:TF1417:outer membrane protein:conserved hypothetical protein:->->:1499474..1499683 210 taaatcgaattgaatcgttcacgtaatccgtaaaaagagggtgtgccaaaatacaatatttgggcacaccttttttctctcacaggtatccgataagctattgaaacatttgaaaaagcgatcagccgttttcagccgttagaaacaatccaacgcccgaaggccaaaatcagaccttcaaagttcgtccgcgaacaagaaaagtaatca Intra-Species Hit: Count: 1 Min: 1 Max: 210 Len: 210 Subject: tfor_TF1416_TF1417|outer membrane protein:conserved hypothetical protein|POSITIVE:POSITIVE|[1499474,1499683]|210 HSP 1 e-value: 1.0E-115 bit: 416.0 Len: 210 Query Start:1 Query End:210 Subject Strand: POSITIVE Subject Start: 1 Subject End: 210 taaatcgaattgaatcgttcacgtaatccgtaaaaagagggtgtgccaaaatacaatatttgggcacaccttttttctctcacaggtatccgataagctattgaaacatttgaaaaagcgatcagccgttttcagccgttagaaacaatccaacgcccgaaggccaaaatcagaccttcaaagttcgtccgcgaacaagaaaagtaatca taaatcgaattgaatcgttcacgtaatccgtaaaaagagggtgtgccaaaatacaatatttgggcacaccttttttctctcacaggtatccgataagctattgaaacatttgaaaaagcgatcagccgttttcagccgttagaaacaatccaacgcccgaaggccaaaatcagaccttcaaagttcgtccgcgaacaagaaaagtaatca Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAAUCGAAUUGAAUCGUUCACGUAAUCCGUAAAAAGAGGGUGUGCCAAAAUACAAUAUUUGGGCACACCUUUUUUCUCUCACAGGUAUCCGAUAAGCUAUUGAAACAUUUGAAAAAGCGAUCAGCCGUUUUCAGCCGUUAGAAACAAUCCAACGCCCGAAGGCCAAAAUCAGACCUUCAAAGUUCGUCCGCGAACAAGAAAAGUAAUCA ................((((.((..(((.((..((((((((((((((.(((((...))))).)))))))))))))).....)).)))....((..((((.(((((...(((((....((.....)).((((((.(.((((.((.....)).)))).).)))))).....)))))..)))))))))..)))).)))).............. (-47.80) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGAUUACUUUUCUUGUUCGCGGACGAACUUUGAAGGUCUGAUUUUGGCCUUCGGGCGUUGGAUUGUUUCUAACGGCUGAAAACGGCUGAUCGCUUUUUCAAAUGUUUCAAUAGCUUAUCGGAUACCUGUGAGAGAAAAAAGGUGUGCCCAAAUAUUGUAUUUUGGCACACCCUCUUUUUACGGAUUACGUGAACGAUUCAAUUCGAUUUA ............(((((((((...((((((((((((..(((((..(((((((((.(((((((.....))))))).)))))...)))))))))..)))))))).))))..................(((((((((......((((((((.(((((...))))).))))))))...)))))))))....))))))))).............. (-67.10) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 435 76 35 163 119 tfor:TF0476|5end_conserved_hypothetical_protein_494944..495174_POSITIVE 410 76 37 171 132 tfor:TF2536|5end_subtilisin-like_serine_protease_2719286..2719516_POSITIVE 404 79 37 204 160 tfor:TF0662|5end_hypothetical_protein_708316..708546_POSITIVE 401 80 34 210 161 tfor:TF2593|5end_amino_acid_transport_protein_2762882..2763112_POSITIVE 388 80 35 218 173 tfor:TF1505|5end_conserved_hypothetical_protein_1610773..1611003_POSITIVE 382 80 36 167 124 tfor:TF0811|5end_conserved_hypothetical_protein;_posible_sugar_phosphate_isomerase_869787..870017_POSITIVE 379 76 33 157 114 tfor:TF1024|5end_50S_ribosomal_protein_L19_1081948..1082178_POSITIVE 379 76 33 165 122 tfor:TF0702|5end_possible_peptidyl-prolyl_isomerase_744977..745207_POSITIVE 374 69 37 231 199 tfor:TF2414|5end_hypothetical_protein_2590725..2590955_POSITIVE 361 190 145 87 36 tfor:TF2385|5end_conserved_hypothetical_protein;_possible_MazG_family_protein_2550676..2550906_POSITIVE 351 197 151 161 118 tfor:TF3110|5end_conserved_hypothetical_protein_with_helicase_domain_3342714..3342944_POSITIVE 342 165 121 64 26 tfor:TF2833|5end_lipid_A_disaccharide_synthase_3023973..3024203_POSITIVE 342 78 33 210 161 tfor:TF2289|5end_secretion_protein,_possible_HlyD_family_2442725..2442955_POSITIVE 342 76 32 229 185 tfor:TF1999|5end_ArgK_protein_with_ATPase_and_kinase_domains_2152769..2152999_POSITIVE 341 190 142 170 123 tfor:TF2581|5end_50S_ribosomal_protein_L17_2748814..2749044_POSITIVE 339 197 151 87 46 tfor:TF2017|5end_conserved_hypothetical_protein_2173504..2173734_POSITIVE 337 163 122 157 116 tfor:TF1818|5end_conserved_hypothetical_protein_1957967..1958197_POSITIVE 335 165 121 162 111 tfor:TF1925|5end_hypothetical_protein_2074458..2074688_POSITIVE 335 165 121 119 68 tfor:TF1926|5end_hypothetical_protein_2074415..2074645_POSITIVE 331 166 124 188 138 tfor:TF0810|5end_possible_outer_membrane_efflux_protein_868438..868668_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 467 76 37 113 74 tfor:TF2413|3end_hypothetical_protein_2590680..2590830_POSITIVE 446 160 117 51 2 tfor:TF1715|3end_thermolysin;_zinc_metalloprotease_1837202..1837352_POSITIVE 413 76 34 57 15 tfor:TF1416|3end_outer_membrane_protein_1499413..1499563_POSITIVE 404 79 37 65 21 tfor:TF0661|3end_hypothetical_protein_708257..708407_POSITIVE 401 80 34 55 6 tfor:TF2592|3end_conserved_hypothetical_protein_2762807..2762957_POSITIVE 390 79 33 58 9 tfor:TF2765|3end_subtilisin-like_serine_protease_2951460..2951610_POSITIVE 362 198 151 136 94 tfor:TF2651|3end_hypothetical_protein_2822014..2822164_POSITIVE 361 190 145 87 36 tfor:TF2384|3end_thiol:disulfide_interchange_protein_2550756..2550906_POSITIVE 348 75 36 60 22 tfor:TF1354|3end_TonB_protein_1435216..1435366_POSITIVE 342 76 32 66 22 tfor:TF1997|3end_ROK_family_transcriptional_regulator_2152686..2152836_POSITIVE 337 163 122 84 43 tfor:TF1816|3end_hypothetical_protein_1957974..1958124_POSITIVE 337 163 122 101 60 tfor:TF1817|3end_hypothetical_protein_1957991..1958141_POSITIVE 335 165 121 141 90 tfor:TF1915|3end_NAD-dependent_protein_deacetylase,_SIR2_family_2068489..2068639_POSITIVE 325 159 119 33 2 tfor:TF2127|3end_hypothetical_protein_2304306..2304456_POSITIVE 325 48 4 71 14 tfor:TF0694|3end_possible_hemolysin,_acyltransferase_family_739101..739251_POSITIVE 317 76 33 47 4 tfor:TF0182|3end_DNA-binding_protein,_HU-related_195528..195678_POSITIVE 313 166 121 145 102 tfor:TF2677|3end_aspartate_transaminase_2852079..2852229_POSITIVE 309 78 34 65 22 tfor:TF1045|3end_conserved_hypothetical_protein_1108245..1108395_POSITIVE 309 198 154 72 29 tfor:TF0023|3end_possible_response_element_in_two_component_regulation_20233..20383_POSITIVE 297 164 123 58 1 tfor:TF1291|3end_response_regulator_(fimR__protein)_1372647..1372797_POSITIVE