Origin IGS: tgaaaccgaagagcgagccgctataagaagaaaatgcctgtaataacggtggataaaaggaagtaacatatttgatttatttttacccgaaagcaataaaaaagaaaaaggaaaagtactatcctttcctttctctttttttatgattgacgatgccatccttaagatcacaacatcagttgataatacaacgaattaggtcactta .........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 taagtgacctaattcgttgtattatcaactgatgttgtgatcttaaggatggcatcgtcaatcataaaaaaagagaaaggaaaggatagtacttttcctttttcttttttattgctttcgggtaaaaataaatcaaatatgttacttccttttatccaccgttattacaggcattttcttcttatagcggctcgctcttcggtttca Mask Tandem Repeat Region ================================================ tgaaaccgaagagcgagccgctataagaagaaaatgcctgtaataacggtggataaaaggaagtaacatatttgatttatttttacccgaaagcaataaaaaagaaaaaggaaaagtactatcctttcctttctctttttttatgattgacgatgccatccttaagatcacaacatcagttgataatacaacgaattaggtcactta Find is-nt database================================================ Query_seq: TF2189:TF2190|TF2189:TF2190:conserved hypothetical protein:conserved hypothetical protein:->->:2364945..2365151 207 tgaaaccgaagagcgagccgctataagaagaaaatgcctgtaataacggtggataaaaggaagtaacatatttgatttatttttacccgaaagcaataaaaaagaaaaaggaaaagtactatcctttcctttctctttttttatgattgacgatgccatccttaagatcacaacatcagttgataatacaacgaattaggtcactta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF2189:TF2190|TF2189:TF2190:conserved hypothetical protein:conserved hypothetical protein:->->:2364945..2365151 207 tgaaaccgaagagcgagccgctataagaagaaaatgcctgtaataacggtggataaaaggaagtaacatatttgatttatttttacccgaaagcaataaaaaagaaaaaggaaaagtactatcctttcctttctctttttttatgattgacgatgccatccttaagatcacaacatcagttgataatacaacgaattaggtcactta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF2189:TF2190|TF2189:TF2190:conserved hypothetical protein:conserved hypothetical protein:->->:2364945..2365151 207 tgaaaccgaagagcgagccgctataagaagaaaatgcctgtaataacggtggataaaaggaagtaacatatttgatttatttttacccgaaagcaataaaaaagaaaaaggaaaagtactatcctttcctttctctttttttatgattgacgatgccatccttaagatcacaacatcagttgataatacaacgaattaggtcactta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tgaaaccgaagagcgagccgctataagaagaaaatgcctgtaataacggtggataaaaggaagtaacatatttgatttatttttacccgaaagcaataaaaaagaaaaaggaaaagtactatcctttcctttctctttttttatgattgacgatgccatccttaagatcacaacatcagttgataatacaacgaattaggtcactta Predict ORF larger than 30AA ================================================ Protein_Len: 48 Strand: + Start: 53 End: 196 .................................................... M K G S N I F D L F L P E S N K K E K G K V L S F P F S F F M I D D A I L K I T T S V D N T T N ........... Protein_Len: 33 Strand: - Start: 24 End: 122 ....................... L F F I G T I V T S L L F Y C I Q N I K V R F C Y F L F L F L V M ..................................................................................... Protein_Len: 57 Strand: - Start: 1 End: 171 S V S S R A A I L L F H R Y Y R H I F P L L M N S K N K G S L L L F S F P F T S D K G K E K K I I S S A M R L I M .................................... tgaaaccgaagagcgagccgctataagaagaaaatgcctgtaataacggtggataaaaggaagtaacatatttgatttatttttacccgaaagcaataaaaaagaaaaaggaaaagtactatcctttcctttctctttttttatgattgacgatgccatccttaagatcacaacatcagttgataatacaacgaattaggtcactta 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================================================ tgaaaccgaagagcgagccgctataagaagaaaatgcctgtaataacggtggataaaaggaagtaacatatttgatttatttttacccgaaagcaataaaaaagaaaaaggaaaagtactatcctttcctttctctttttttatgattgacgatgccatccttaagatcacaacatcagttgataatacaacgaattaggtcactta Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 85 HP_score: -4.5 Tail_Score: -5.71983 Start: 104 End: 135 Full_Region: GAAAGCAATAAAAAA GAAAAAGGAAAAG TACTAT CCTTTCCTTTCTC TTTTTTTATGATTGA .......................................................................................................GAAAAAGGAAAAGTACTATCCTTTCCTTTCTC........................................................................ TransTerm Strand: - Conf: 95 HP_score: -8.9 Tail_Score: -5.59655 Start: 104 End: 135 Full_Region: tcaatcataaaaaaa gagaaaggaaagg atagta cttttcctttttc ttttttattgctttc .......................................................................................................gagaaaggaaaggatagtacttttcctttttc........................................................................ TransTerm Strand: - Conf: 91 HP_score: -4.3 Tail_Score: -5.84011 Start: 110 End: 129 Full_Region: ataaaaaaagagaaa ggaaagg atagta cttttcc tttttcttttttatt .............................................................................................................ggaaaggatagtacttttcc.............................................................................. Find igs database================================================ Query_seq: TF2189:TF2190|TF2189:TF2190:conserved hypothetical protein:conserved hypothetical protein:->->:2364945..2365151 207 tgaaaccgaagagcgagccgctataagaagaaaatgcctgtaataacggtggataaaaggaagtaacatatttgatttatttttacccgaaagcaataaaaaagaaaaaggaaaagtactatcctttcctttctctttttttatgattgacgatgccatccttaagatcacaacatcagttgataatacaacgaattaggtcactta Intra-Species Hit: Count: 1 Min: 1 Max: 207 Len: 207 Subject: tfor_TF2189_TF2190|conserved hypothetical protein:conserved hypothetical protein|POSITIVE:POSITIVE|[2364945,2365151]|207 HSP 1 e-value: 3.0E-48 bit: 192.0 Len: 97 Query Start:1 Query End:97 Subject Strand: POSITIVE Subject Start: 1 Subject End: 97 tgaaaccgaagagcgagccgctataagaagaaaatgcctgtaataacggtggataaaaggaagtaacatatttgatttatttttacccgaaagcaat.............................................................................................................. tgaaaccgaagagcgagccgctataagaagaaaatgcctgtaataacggtggataaaaggaagtaacatatttgatttatttttacccgaaagcaat.............................................................................................................. HSP 2 e-value: 1.0E-32 bit: 141.0 Len: 92 Query Start:116 Query End:207 Subject Strand: POSITIVE Subject Start: 116 Subject End: 207 ...................................................................................................................gtactatcctttcctttctcnnnnnnnatgattgacgatgccatccttaagatcacaacatcagttgataatacaacgaattaggtcactta ...................................................................................................................gtactatcctttcctttctctttttttatgattgacgatgccatccttaagatcacaacatcagttgataatacaacgaattaggtcactta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGAAACCGAAGAGCGAGCCGCUAUAAGAAGAAAAUGCCUGUAAUAACGGUGGAUAAAAGGAAGUAACAUAUUUGAUUUAUUUUUACCCGAAAGCAAUAAAAAAGAAAAAGGAAAAGUACUAUCCUUUCCUUUCUCUUUUUUUAUGAUUGACGAUGCCAUCCUUAAGAUCACAACAUCAGUUGAUAAUACAACGAAUUAGGUCACUUA ...........((((...)))).............(((((.......(((((((..(((((.(...(((..(..(((..........(....)....((((((((.((((((((.(......).)))))))).))))))))...)))..)..))).).)))))...)))....)))).((((......))))....)))))...... (-34.10) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAGUGACCUAAUUCGUUGUAUUAUCAACUGAUGUUGUGAUCUUAAGGAUGGCAUCGUCAAUCAUAAAAAAAGAGAAAGGAAAGGAUAGUACUUUUCCUUUUUCUUUUUUAUUGCUUUCGGGUAAAAAUAAAUCAAAUAUGUUACUUCCUUUUAUCCACCGUUAUUACAGGCAUUUUCUUCUUAUAGCGGCUCGCUCUUCGGUUUCA ...(.((((......((((......)))).((((.(((.(((.....))).))).)))).......(((((((((((((((((((......)))))))))))))))))))...((....((((((((......................)))))))).(((((((...(((......)))...)))))))...)).....)))).). (-51.85) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 313 47 6 56 10 tfor:TF0441|5end_Na+-transporting_NADH:ubiquinone_oxidoreductase,_subunit_3_464614..464844_POSITIVE 309 42 6 50 7 tfor:TF2482|5end_hypothetical_protein_2658503..2658733_POSITIVE 305 55 13 65 22 tfor:TF3076|5end_outer_membrane_protein,_TonB_dependent_receptor_3302785..3303015_POSITIVE 305 53 14 230 197 tfor:TF0898|5end_hypothetical_protein_945366..945596_POSITIVE 305 53 14 223 190 tfor:TF0897|5end_hypothetical_protein_945359..945589_POSITIVE 301 50 1 67 3 tfor:TF0321|5end_glycosyltransferase_347438..347668_POSITIVE 300 49 2 97 47 tfor:TF1192|5end_alpha-amylase_1274007..1274237_POSITIVE 293 48 5 77 29 tfor:TF2763|5end_pyridine_nucleotide-disulphide_oxidoreductase_family_protein_2946073..2946303_POSITIVE 278 157 113 184 134 tfor:TF0782|5end_ThiJ/PfpI_family_protein_835976..836206_POSITIVE 274 34 5 64 31 tfor:TF0409|5end_conserved_hypothetical_protein_426240..426470_POSITIVE 272 200 151 50 10 tfor:TF0244|5end_DNA_recombination_protein_274683..274913_POSITIVE 272 49 1 155 100 tfor:TF0038|5end_conserved_hypothetical_protein_39907..40137_POSITIVE 271 47 4 74 37 tfor:TF2276|5end_conserved_hypothetical_protein_2438226..2438456_POSITIVE 270 49 1 144 81 tfor:TF0523|5end_protein_protease_IV/endopeptidase_545871..546101_POSITIVE 267 53 11 72 34 tfor:TF1275|5end_transcription-repair_coupling_factor_1357866..1358096_POSITIVE 267 59 11 212 169 tfor:TF0151|5end_hydrolase/beta-alanine_synthase_161117..161347_POSITIVE 264 53 11 107 59 tfor:TF2377|5end_orotidine_5'_phosphate_decarboxylase_2541799..2542029_POSITIVE 262 49 7 202 158 tfor:TF2157|5end_conserved_hypothetical_protein_2332915..2333145_POSITIVE 260 161 125 136 99 tfor:TF2135|5end_conserved_hypothetical_protein_2311316..2311546_POSITIVE 259 49 6 210 165 tfor:TF0175|5end_hypothetical_protein_185585..185815_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 313 47 6 50 4 tfor:TF0440|3end_Na+-transporting_NADH:ubiquinone_oxidoreductase,_subunit_2_464688..464838_POSITIVE 309 42 6 50 7 tfor:TF2481|3end_possible_thiol_protease/hemagglutinin_PrtT_2658583..2658733_POSITIVE 301 50 1 67 3 tfor:TF0320|3end_dihydroorotase_347518..347668_POSITIVE 293 48 5 58 10 tfor:TF2762|3end_conserved_hypothetical_protein_2946134..2946284_POSITIVE 278 157 113 132 82 tfor:TF0781|3end_serine_protease_inhibitor_836004..836154_POSITIVE 274 34 5 68 35 tfor:TF0408|3end_possible_gliding_motility-related_lipoprotein_426324..426474_POSITIVE 272 200 151 45 5 tfor:TF0243|3end_conserved_hypothetical_protein_274758..274908_POSITIVE 271 47 4 68 31 tfor:TF2275|3end_conserved_hypothetical_protein_2438300..2438450_POSITIVE 270 49 1 122 59 tfor:TF0520|3end_tetraacyldisaccharide_4'-kinase_545929..546079_POSITIVE 265 167 122 79 32 tfor:TF2458|3end_ribosome-binding_factor_A_2635645..2635795_POSITIVE 264 53 11 73 25 tfor:TF2375|3end_conserved_hypothetical_protein_2541845..2541995_POSITIVE 264 50 8 135 93 tfor:TF1261|3end_GrpE-related_chaperonin;_HSP-70_cofactor_1347192..1347342_POSITIVE 260 161 125 102 65 tfor:TF2133|3end_aspartate-semialdehyde_dehydrogenase_2311362..2311512_POSITIVE 259 49 6 145 100 tfor:TF0174|3end_hypothetical_protein_185600..185750_POSITIVE 255 54 13 104 62 tfor:TF2917|3end_conserved_hypothetical_protein_3114161..3114311_POSITIVE 255 49 2 83 35 tfor:TF2527|3end_RNA_polymerase_ECF-type_sigma_factor_2710749..2710899_POSITIVE 255 50 6 90 30 tfor:TF0996|3end_ribonuclease_D_1051555..1051705_POSITIVE 252 55 11 64 22 tfor:TF3067|3end_conserved_hypothetical_protein_3292877..3293027_POSITIVE 251 55 11 56 13 tfor:TF1409|3end_outer_membrane_protein_TolC_1487079..1487229_POSITIVE 250 47 7 69 21 tfor:TF0782|3end_ThiJ/PfpI_family_protein_836592..836742_POSITIVE