Origin IGS: taaatacaatcaacaagtattcaggaagatataattacgcaacaacttgttgcactattaggagaagtttctgaaacgctgtcggcaatctatcactgtgatatcagtcagatagaggaaatcttcaagcactcagccattgttcgcaccaactgggcaagccat .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 atggcttgcccagttggtgcgaacaatggctgagtgcttgaagatttcctctatctgactgatatcacagtgatagattgccgacagcgtttcagaaacttctcctaatagtgcaacaagttgttgcgtaattatatcttcctgaatacttgttgattgtattta Mask Tandem Repeat Region ================================================ taaatacaatcaacaagtattcaggaagatataattacgcaacaacttgttgcactattaggagaagtttctgaaacgctgtcggcaatctatcactgtgatatcagtcagatagaggaaatcttcaagcactcagccattgttcgcaccaactgggcaagccat Find is-nt database================================================ Query_seq: TF0057:TF0058|TF0057:TF0058:conserved hypothetical protein:conserved hypothetical protein:->->:59808..59972 165 taaatacaatcaacaagtattcaggaagatataattacgcaacaacttgttgcactattaggagaagtttctgaaacgctgtcggcaatctatcactgtgatatcagtcagatagaggaaatcttcaagcactcagccattgttcgcaccaactgggcaagccat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF0057:TF0058|TF0057:TF0058:conserved hypothetical protein:conserved hypothetical protein:->->:59808..59972 165 taaatacaatcaacaagtattcaggaagatataattacgcaacaacttgttgcactattaggagaagtttctgaaacgctgtcggcaatctatcactgtgatatcagtcagatagaggaaatcttcaagcactcagccattgttcgcaccaactgggcaagccat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF0057:TF0058|TF0057:TF0058:conserved hypothetical protein:conserved hypothetical protein:->->:59808..59972 165 taaatacaatcaacaagtattcaggaagatataattacgcaacaacttgttgcactattaggagaagtttctgaaacgctgtcggcaatctatcactgtgatatcagtcagatagaggaaatcttcaagcactcagccattgttcgcaccaactgggcaagccat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 taaatacaatcaacaagtattcaggaagatataattacgcaacaacttgttgcactattaggagaagtttctgaaacgctgtcggcaatctatcactgtgatatcagtcagatagaggaaatcttcaagcactcagccattgttcgcaccaactgggcaagccat Predict ORF larger than 30AA ================================================ Protein_Len: 54 Strand: + Start: 4 End: 165 ... M Q S T S I Q E D I I T Q Q L V A L L G E V S E T L S A I Y H C D I S Q I E E I F K H S A I V R T N W A S H taaatacaatcaacaagtattcaggaagatataattacgcaacaacttgttgcactattaggagaagtttctgaaacgctgtcggcaatctatcactgtgatatcagtcagatagaggaaatcttcaagcactcagccattgttcgcaccaactgggcaagccat 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================================================ taaatacaatcaacaagtattcaggaagatataattacgcaacaacttgttgcactattaggagaagtttctgaaacgctgtcggcaatctatcactgtgatatcagtcagatagaggaaatcttcaagcactcagccattgttcgcaccaactgggcaagccat Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TF0057:TF0058|TF0057:TF0058:conserved hypothetical protein:conserved hypothetical protein:->->:59808..59972 165 taaatacaatcaacaagtattcaggaagatataattacgcaacaacttgttgcactattaggagaagtttctgaaacgctgtcggcaatctatcactgtgatatcagtcagatagaggaaatcttcaagcactcagccattgttcgcaccaactgggcaagccat Intra-Species Hit: Count: 1 Min: 1 Max: 165 Len: 165 Subject: tfor_TF0057_TF0058|conserved hypothetical protein:conserved hypothetical protein|POSITIVE:POSITIVE|[59808,59972]|165 HSP 1 e-value: 7.0E-89 bit: 327.0 Len: 165 Query Start:1 Query End:165 Subject Strand: POSITIVE Subject Start: 1 Subject End: 165 taaatacaatcaacaagtattcaggaagatataattacgcaacaacttgttgcactattaggagaagtttctgaaacgctgtcggcaatctatcactgtgatatcagtcagatagaggaaatcttcaagcactcagccattgttcgcaccaactgggcaagccat taaatacaatcaacaagtattcaggaagatataattacgcaacaacttgttgcactattaggagaagtttctgaaacgctgtcggcaatctatcactgtgatatcagtcagatagaggaaatcttcaagcactcagccattgttcgcaccaactgggcaagccat Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAAUACAAUCAACAAGUAUUCAGGAAGAUAUAAUUACGCAACAACUUGUUGCACUAUUAGGAGAAGUUUCUGAAACGCUGUCGGCAAUCUAUCACUGUGAUAUCAGUCAGAUAGAGGAAAUCUUCAAGCACUCAGCCAUUGUUCGCACCAACUGGGCAAGCCAU ...........(((((...((((((((....((((...(((((.....)))))...)))).......))))))))..((((...((..((((((((((......))))..)))))).((.....))..))...))))..))))).((.((....))))....... (-36.90) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUGGCUUGCCCAGUUGGUGCGAACAAUGGCUGAGUGCUUGAAGAUUUCCUCUAUCUGACUGAUAUCACAGUGAUAGAUUGCCGACAGCGUUUCAGAAACUUCUCCUAAUAGUGCAACAAGUUGUUGCGUAAUUAUAUCUUCCUGAAUACUUGUUGAUUGUAUUUA .((..((((((....)).)))).)).....(((((((............((((((..((((......))))))))))....((((((.(((((((..........((((..((((((.....))))))..)))).......))))).))))))))...))))))) (-35.73) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 350 158 116 191 133 tfor:TF2673|5end_conserved_hypothetical_protein_2846987..2847217_POSITIVE 341 149 102 144 96 tfor:TF3132|5end_conserved_hypothetical_protein_3365175..3365405_POSITIVE 341 147 105 189 151 tfor:TF0931|5end_superfamily_II_DNA/RNA_helicase,_SNF2_family_970031..970261_POSITIVE 338 109 65 83 30 tfor:TF0994|5end_maltose_O-acetyltransferase_1049127..1049357_POSITIVE 338 108 61 73 25 tfor:TF0923|5end_tetracycline_resistance_element_mobilization_regulatory_protein_961256..961486_POSITIVE 332 158 119 85 32 tfor:TF2198|5end_outer_membrane_protein,_possibly_involved_in_nutrient_binding_2372906..2373136_POSITIVE 329 158 116 51 6 tfor:TF1837|5end_conserved_hypothetical_protein;_possible_outer_membrane_protein_1985480..1985710_POSITIVE 327 100 60 86 39 tfor:TF2224|5end_CTn_excision_protein_2394592..2394822_POSITIVE 327 87 41 56 14 tfor:TF1853|5end_homoserine_O-succinyltransferase_2006470..2006700_POSITIVE 317 160 115 54 10 tfor:TF0423|5end_G:T/U_mismatch-specific_DNA_glycosylase_438620..438850_POSITIVE 314 111 75 114 72 tfor:TF0789|5end_preprotein_translocase,_secDF_family_841293..841523_POSITIVE 310 156 117 212 170 tfor:TF2498|5end_electron_transfer_flavoprotein,_alpha_subunit_2672801..2673031_POSITIVE 308 157 111 143 106 tfor:TF1538|5end_conserved_hypothetical_protein_1643531..1643761_POSITIVE 307 85 42 229 175 tfor:TF2332|5end_signal_peptidase_I_2491694..2491924_POSITIVE 306 109 61 162 105 tfor:TF0184|5end_dihydroneopterin_aldolase_195629..195859_POSITIVE 299 140 96 156 108 tfor:TF1984|5end_conserved_hypothetical_protein_2135278..2135508_POSITIVE 297 150 104 213 159 tfor:TF0375|5end_thioredoxin_reductase_393323..393553_POSITIVE 292 158 126 40 2 tfor:TF2320|5end_hypothetical_protein_2476654..2476884_POSITIVE 292 108 61 156 117 tfor:TF1499|5end_3-oxyacyl-[acyl-carrier_protein]_synthase_1598394..1598624_POSITIVE 292 150 104 208 150 tfor:TF1334|5end_hypothetical_protein_1415996..1416226_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 350 158 116 138 80 tfor:TF2672|3end_lipoic_acid_synthetase_2847014..2847164_POSITIVE 341 149 102 137 89 tfor:TF3131|3end_uracil-DNA_glycosylase_3365248..3365398_POSITIVE 341 147 105 43 5 tfor:TF0930|3end_conserved_hypothetical_protein;_possible_prophage_protein_969965..970115_POSITIVE 327 87 41 52 10 tfor:TF1852|3end_prtQ_protein_2006546..2006696_POSITIVE 321 158 124 45 2 tfor:TF2197|3end_conserved_hypothetical_protein_2372946..2373096_POSITIVE 317 160 115 49 5 tfor:TF0422|3end_proline_dehydrogenase_438695..438845_POSITIVE 316 100 60 46 2 tfor:TF2223|3end_CTn_excision__protein_2394632..2394782_POSITIVE 314 111 75 111 69 tfor:TF0788|3end_protein-export_membrane_protein_841370..841520_POSITIVE 292 150 104 146 88 tfor:TF1333|3end_probable_acylaminoacyl_peptidase;_alanyl_dipeptidyl_peptidase_1416014..1416164_POSITIVE 286 110 61 140 95 tfor:TF0969|3end_oxidoreductase_1020439..1020589_POSITIVE 284 88 49 112 76 tfor:TF2588|3end_coproporphryninogen_III_oxidase_2753432..2753582_POSITIVE 277 159 122 140 104 tfor:TF0146|3end_glutamine-dependent_NAD(+)_synthetase_156863..157013_POSITIVE 277 107 71 141 103 tfor:TF0037|3end_sialic_acid-specific_9-O-acetylesterase_39991..40141_POSITIVE 276 155 114 106 58 tfor:TF2433|3end_possible_UDP-2,3-diacylglucosamine_hydrolase_2614043..2614193_POSITIVE 272 90 44 132 77 tfor:TF1744|3end_phenylacetate-CoA_ligase_1879218..1879368_POSITIVE 272 156 123 144 114 tfor:TF1122|3end_conserved_hypothetical_protein_1197239..1197389_POSITIVE 270 78 31 85 37 tfor:TF3060|3end_conserved_hypothetical_protein_3285130..3285280_POSITIVE 268 100 58 38 2 tfor:TF1575|3end_DNA-binding_response_regulator_1685895..1686045_POSITIVE 268 100 63 151 106 tfor:TF0757|3end_50S_ribosomal_protein_L25;_general_stress_protein_805293..805443_POSITIVE 266 146 110 115 72 tfor:TF0991|3end_probable_NAD(FAD)-dependent_dehydrogenase_1048334..1048484_POSITIVE