Origin IGS: ctttgcgataccttcgccgggtactttcctgtcttttcgccacgttgcaactacttatcgtcggatcatttttcttcttaaccccacattccggcataaattgttgcaagaatgctaacaaccattaacaattgacggttatacacaggcgttttccgatgtttacgcg .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 cgcgtaaacatcggaaaacgcctgtgtataaccgtcaattgttaatggttgttagcattcttgcaacaatttatgccggaatgtggggttaagaagaaaaatgatccgacgataagtagttgcaacgtggcgaaaagacaggaaagtacccggcgaaggtatcgcaaag Mask Tandem Repeat Region ================================================ ctttgcgataccttcgccgggtactttcctgtcttttcgccacgttgcaactacttatcgtcggatcatttttcttcttaaccccacattccggcataaattgttgcaagaatgctaacaaccattaacaattgacggttatacacaggcgttttccgatgtttacgcg Find is-nt database================================================ Query_seq: TF3141:TF3142|TF3141:TF3142:NADH: ubiquinone oxidoreductase, subunit A:conserved hypothetical protein:->->:3376328..3376496 169 ctttgcgataccttcgccgggtactttcctgtcttttcgccacgttgcaactacttatcgtcggatcatttttcttcttaaccccacattccggcataaattgttgcaagaatgctaacaaccattaacaattgacggttatacacaggcgttttccgatgtttacgcg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF3141:TF3142|TF3141:TF3142:NADH: ubiquinone oxidoreductase, subunit A:conserved hypothetical protein:->->:3376328..3376496 169 ctttgcgataccttcgccgggtactttcctgtcttttcgccacgttgcaactacttatcgtcggatcatttttcttcttaaccccacattccggcataaattgttgcaagaatgctaacaaccattaacaattgacggttatacacaggcgttttccgatgtttacgcg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF3141:TF3142|TF3141:TF3142:NADH: ubiquinone oxidoreductase, subunit A:conserved hypothetical protein:->->:3376328..3376496 169 ctttgcgataccttcgccgggtactttcctgtcttttcgccacgttgcaactacttatcgtcggatcatttttcttcttaaccccacattccggcataaattgttgcaagaatgctaacaaccattaacaattgacggttatacacaggcgttttccgatgtttacgcg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ctttgcgataccttcgccgggtactttcctgtcttttcgccacgttgcaactacttatcgtcggatcatttttcttcttaaccccacattccggcataaattgttgcaagaatgctaacaaccattaacaattgacggttatacacaggcgttttccgatgtttacgcg Predict ORF larger than 30AA ================================================ Protein_Len: 36 Strand: + Start: 8 End: 115 ....... M P S P G T F L S F R H V A T T Y R R I I F L L N P T F R H K L L Q E C ...................................................... Protein_Len: 41 Strand: + Start: 3 End: 125 .. M R Y L R R V L S C L F A T L Q L L I V G S F F F L T P H S G I N C C K N A N N H ............................................ Protein_Len: 40 Strand: - Start: 2 End: 121 . K R Y R R R T S E Q R K A V N C S S I T P D N K K K V G C E P M F Q Q L F A L M ................................................ ctttgcgataccttcgccgggtactttcctgtcttttcgccacgttgcaactacttatcgtcggatcatttttcttcttaaccccacattccggcataaattgttgcaagaatgctaacaaccattaacaattgacggttatacacaggcgttttccgatgtttacgcg 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================================================ ctttgcgataccttcgccgggtactttcctgtcttttcgccacgttgcaactacttatcgtcggatcatttttcttcttaaccccacattccggcataaattgttgcaagaatgctaacaaccattaacaattgacggttatacacaggcgttttccgatgtttacgcg Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TF3141:TF3142|TF3141:TF3142:NADH: ubiquinone oxidoreductase, subunit A:conserved hypothetical protein:->->:3376328..3376496 169 ctttgcgataccttcgccgggtactttcctgtcttttcgccacgttgcaactacttatcgtcggatcatttttcttcttaaccccacattccggcataaattgttgcaagaatgctaacaaccattaacaattgacggttatacacaggcgttttccgatgtttacgcg Intra-Species Hit: Count: 1 Min: 1 Max: 169 Len: 169 Subject: tfor_TF3141_TF3142|NADH: ubiquinone oxidoreductase, subunit A:conserved hypothetical protein|POSITIVE:POSITIVE|[3376328,3376496]|169 HSP 1 e-value: 3.0E-91 bit: 335.0 Len: 169 Query Start:1 Query End:169 Subject Strand: POSITIVE Subject Start: 1 Subject End: 169 ctttgcgataccttcgccgggtactttcctgtcttttcgccacgttgcaactacttatcgtcggatcatttttcttcttaaccccacattccggcataaattgttgcaagaatgctaacaaccattaacaattgacggttatacacaggcgttttccgatgtttacgcg ctttgcgataccttcgccgggtactttcctgtcttttcgccacgttgcaactacttatcgtcggatcatttttcttcttaaccccacattccggcataaattgttgcaagaatgctaacaaccattaacaattgacggttatacacaggcgttttccgatgtttacgcg Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CUUUGCGAUACCUUCGCCGGGUACUUUCCUGUCUUUUCGCCACGUUGCAACUACUUAUCGUCGGAUCAUUUUUCUUCUUAACCCCACAUUCCGGCAUAAAUUGUUGCAAGAAUGCUAACAACCAUUAACAAUUGACGGUUAUACACAGGCGUUUUCCGAUGUUUACGCG ....(((..((..(((.((((......))))......((((...(((((((...((((.((((((........................))))))))))...)))))))..........((((.(((.....))).)))).......)))).....))).))...))). (-37.06) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CGCGUAAACAUCGGAAAACGCCUGUGUAUAACCGUCAAUUGUUAAUGGUUGUUAGCAUUCUUGCAACAAUUUAUGCCGGAAUGUGGGGUUAAGAAGAAAAAUGAUCCGACGAUAAGUAGUUGCAACGUGGCGAAAAGACAGGAAAGUACCCGGCGAAGGUAUCGCAAAG .(((...((.((((...((.(((((.(.....(((((..(((((((....)))))))...(((((((.((((((.......(((.((((((..........)))))).))))))))).)))))))..)))))...).)))))...))..)))).....))..))).... (-41.91) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 377 60 11 223 164 tfor:TF0971|5end_conserved_hypothetical_protein_1021355..1021585_POSITIVE 372 60 12 60 4 tfor:TF1841|5end_hypothetical_protein_1991936..1992166_POSITIVE 367 60 12 208 151 tfor:TF1845|5end_hypothetical_protein_1996620..1996850_POSITIVE 367 60 12 208 151 tfor:TF1185|5end_hypothetical_protein_1269238..1269468_POSITIVE 355 60 13 195 143 tfor:TF0811|5end_conserved_hypothetical_protein;_posible_sugar_phosphate_isomerase_869787..870017_POSITIVE 351 50 4 69 14 tfor:TF1773|5end_hypothetical_protein_1910939..1911169_POSITIVE 346 48 1 220 156 tfor:TF2186|5end_outer_membrane_protein_2360291..2360521_POSITIVE 343 48 4 93 47 tfor:TF1664|5end_conserved_hypothetical_protein_1778761..1778991_POSITIVE 342 53 11 75 27 tfor:TF2804|5end_conserved_hypothetical_protein_2993494..2993724_POSITIVE 340 44 5 212 157 tfor:TF0289|5end_conserved_hypothetical_protein_318015..318245_POSITIVE 339 48 1 224 169 tfor:TF1942|5end_conserved_hypothetical_protein_2090129..2090359_POSITIVE 338 60 12 118 61 tfor:TF1182|5end_hypothetical_protein_1268565..1268795_POSITIVE 337 50 3 67 22 tfor:TF0239|5end_conserved_hypothetical_protein_268894..269124_POSITIVE 334 49 7 49 11 tfor:TF2704|5end_ribonuclease_HII_2876242..2876472_POSITIVE 332 49 1 61 1 tfor:TF0496|5end_conserved_hypothetical_protein_522332..522562_POSITIVE 330 44 5 41 6 tfor:TF0710|5end_two_component_system_histidine_kinase_757250..757480_POSITIVE 325 48 1 83 27 tfor:TF1239|5end_RNA_polymerase_ECF-type_sigma_factor_1323580..1323810_POSITIVE 323 48 4 144 95 tfor:TF2469|5end_oxidoreductase,_possible_Gfo/Idh/MocA_family_2646505..2646735_POSITIVE 322 60 11 213 150 tfor:TF0970|5end_2-keto-3-deoxygluconate_kinase_1020396..1020626_POSITIVE 321 47 2 187 121 tfor:TF2932|5end_capsule_biosynthesis_protein_3135514..3135744_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 354 60 11 54 2 tfor:TF2840|3end_hypothetical_protein_3031289..3031439_POSITIVE 352 49 1 115 67 tfor:TF2547|3end_hypothetical_protein_2730947..2731097_POSITIVE 345 49 5 44 1 tfor:TF2703|3end_conserved_hypothetical_protein_2876317..2876467_POSITIVE 338 60 12 118 61 tfor:TF1186|3end_hypothetical_protein_1269815..1269965_POSITIVE 337 50 3 50 5 tfor:TF0238|3end_outer_membrane_protein_268957..269107_POSITIVE 336 48 7 130 94 tfor:TF3006|3end_response_regulator,_transcriptional_regulator_RprY_3227162..3227312_POSITIVE 330 48 6 142 98 tfor:TF2745|3end_hypothetical_protein_2927947..2928097_POSITIVE 323 48 4 141 92 tfor:TF2468|3end_hypothetical_protein_2646582..2646732_POSITIVE 321 49 2 142 92 tfor:TF2339|3end_hypothetical_protein_2505783..2505933_POSITIVE 321 49 2 142 92 tfor:TF1259|3end_hypothetical_protein_1345204..1345354_POSITIVE 319 48 2 78 22 tfor:TF1173|3end_ABC_transporter,_permease_component_1256651..1256801_POSITIVE 315 59 13 59 8 tfor:TF2574|3end_preprotein_translocase_SecY_2745200..2745350_POSITIVE 310 49 1 83 26 tfor:TF2911|3end_hypothetical_protein_3106640..3106790_POSITIVE 310 45 1 150 115 tfor:TF0240|3end_conserved_hypothetical_protein;_possible_gycosyltransferase_I_family_protein_271407..271557_POSITIVE 309 42 1 57 15 tfor:TF3118|3end_conserved_hypothetical_protein_3352824..3352974_POSITIVE 304 49 5 77 35 tfor:TF1185|3end_hypothetical_protein_1269563..1269713_POSITIVE 302 48 5 110 64 tfor:TF2330|3end_conserved_hypothetical_protein_2491109..2491259_POSITIVE 301 48 2 55 17 tfor:TF0212|3end_DNA/pantothenate_metabolism_flavoprotein_239001..239151_POSITIVE 297 50 1 101 43 tfor:TF2609|3end_dipeptidase,_pathogenicity_island-encoded_protein_D_2786264..2786414_POSITIVE 297 62 28 53 13 tfor:TF2226|3end_CTn_excision_protein_2395956..2396106_POSITIVE