Origin IGS: taaatcctcatattaaagcaaaagggggacaccgaattgttccgtgtctccctttttacatcgttttctgcaaccaatagtcgcagaatttgttcttatactttgcttgtta .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 taacaagcaaagtataagaacaaattctgcgactattggttgcagaaaacgatgtaaaaagggagacacggaacaattcggtgtcccccttttgctttaatatgaggattta Mask Tandem Repeat Region ================================================ taaatcctcatattaaagcaaaagggggacaccgaattgttccgtgtctccctttttacatcgttttctgcaaccaatagtcgcagaatttgttcttatactttgcttgtta Find is-nt database================================================ Query_seq: TF1302:TF1303|TF1302:TF1303:conserved hypothetical protein; possible tetracycline resistance element:conserved hypothetical protein:->->:1383897..1384008 112 taaatcctcatattaaagcaaaagggggacaccgaattgttccgtgtctccctttttacatcgttttctgcaaccaatagtcgcagaatttgttcttatactttgcttgtta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF1302:TF1303|TF1302:TF1303:conserved hypothetical protein; possible tetracycline resistance element:conserved hypothetical protein:->->:1383897..1384008 112 taaatcctcatattaaagcaaaagggggacaccgaattgttccgtgtctccctttttacatcgttttctgcaaccaatagtcgcagaatttgttcttatactttgcttgtta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF1302:TF1303|TF1302:TF1303:conserved hypothetical protein; possible tetracycline resistance element:conserved hypothetical protein:->->:1383897..1384008 112 taaatcctcatattaaagcaaaagggggacaccgaattgttccgtgtctccctttttacatcgttttctgcaaccaatagtcgcagaatttgttcttatactttgcttgtta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 taaatcctcatattaaagcaaaagggggacaccgaattgttccgtgtctccctttttacatcgttttctgcaaccaatagtcgcagaatttgttcttatactttgcttgtta Predict ORF larger than 30AA ================================================ Protein_Len: 36 Strand: + Start: 4 End: 111 ... M L I L K Q K G D T E L F R V S L F T S F S A T N S R R I C S Y T L L V . taaatcctcatattaaagcaaaagggggacaccgaattgttccgtgtctccctttttacatcgttttctgcaaccaatagtcgcagaatttgttcttatactttgcttgtta 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================================================ taaatcctcatattaaagcaaaagggggacaccgaattgttccgtgtctccctttttacatcgttttctgcaaccaatagtcgcagaatttgttcttatactttgcttgtta Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 83 HP_score: -11.8 Tail_Score: -2.8978 Start: 19 End: 57 Full_Region: tgcagaaaacgatgt aaaaagggagacacggaa caa ttcggtgtcccccttttg ctttaatatgaggat ..................aaaaagggagacacggaacaattcggtgtcccccttttg....................................................... TransTerm Strand: - Conf: 100 HP_score: -11.7 Tail_Score: -4.6038 Start: 24 End: 52 Full_Region: aaaacgatgtaaaaa gggagacacggaa caa ttcggtgtccccc ttttgctttaatatg .......................gggagacacggaacaattcggtgtccccc............................................................ TransTerm Strand: + Conf: 74 HP_score: -6.3 Tail_Score: -4.54323 Start: 66 End: 88 Full_Region: CCTTTTTACATCGTT TTCTGCAAC CAATA GTCGCAGAA TTTGTTCTTATACTT .................................................................TTCTGCAACCAATAGTCGCAGAA........................ Find igs database================================================ Query_seq: TF1302:TF1303|TF1302:TF1303:conserved hypothetical protein; possible tetracycline resistance element:conserved hypothetical protein:->->:1383897..1384008 112 taaatcctcatattaaagcaaaagggggacaccgaattgttccgtgtctccctttttacatcgttttctgcaaccaatagtcgcagaatttgttcttatactttgcttgtta Intra-Species Hit: Count: 1 Min: 1 Max: 112 Len: 112 Subject: tfor_TF1302_TF1303|conserved hypothetical protein; possible tetracycline resistance element:conserved hypothetical protein|POSITIVE:POSITIVE|[1383897,1384008]|112 HSP 1 e-value: 2.0E-57 bit: 222.0 Len: 112 Query Start:1 Query End:112 Subject Strand: POSITIVE Subject Start: 1 Subject End: 112 taaatcctcatattaaagcaaaagggggacaccgaattgttccgtgtctccctttttacatcgttttctgcaaccaatagtcgcagaatttgttcttatactttgcttgtta taaatcctcatattaaagcaaaagggggacaccgaattgttccgtgtctccctttttacatcgttttctgcaaccaatagtcgcagaatttgttcttatactttgcttgtta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAAUCCUCAUAUUAAAGCAAAAGGGGGACACCGAAUUGUUCCGUGUCUCCCUUUUUACAUCGUUUUCUGCAACCAAUAGUCGCAGAAUUUGUUCUUAUACUUUGCUUGUUA ...............(((((((.(((((((((.((.....)).))))))))).........((..((((((.((.....)).))))))..)).........))))))).... (-32.50) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAACAAGCAAAGUAUAAGAACAAAUUCUGCGACUAUUGGUUGCAGAAAACGAUGUAAAAAGGGAGACACGGAACAAUUCGGUGUCCCCCUUUUGCUUUAAUAUGAGGAUUUA ....((((................(((((((((.....))))))))).........(((((((.(((((.((.....)).))))).)))))))))))............... (-34.30) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 342 89 41 146 95 tfor:TF1009|5end_conserved_hypothetical_protein;_posible_rod-shape_determining_protein,_MreD_1064290..1064520_POSITIVE 339 70 23 66 17 tfor:TF0605|5end_conserved_hypothetical_protein_636051..636281_POSITIVE 338 80 32 52 9 tfor:TF2450|5end_outer_membrane_protein_2626471..2626701_POSITIVE 330 46 23 208 184 tfor:TF0712|5end_TPR-repeat-containing_protein_761348..761578_POSITIVE 325 88 43 222 171 tfor:TF0180|5end_carboxynorspermidine_decarboxylase_191267..191497_POSITIVE 307 56 24 178 141 tfor:TF1840|5end_transposase_1990221..1990451_POSITIVE 303 75 32 199 154 tfor:TF3043|5end_conserved_hypothetical_protein_3271925..3272155_POSITIVE 294 68 22 206 154 tfor:TF3108|5end_glutamine-hydrolyzing_carbamoyl-phosphate_synthase,_large_subunit_3338732..3338962_POSITIVE 294 57 17 141 97 tfor:TF1141|5end_conserved_hypothetical_protein_1217972..1218202_POSITIVE 292 69 21 199 145 tfor:TF2564|5end_50S_ribosomal_protein_L14_2739604..2739834_POSITIVE 290 71 32 169 141 tfor:TF0480|5end_ornithine_carbamoyltransferase_498550..498780_POSITIVE 284 95 56 172 130 tfor:TF2932|5end_capsule_biosynthesis_protein_3135514..3135744_POSITIVE 283 75 33 70 25 tfor:TF0239|5end_conserved_hypothetical_protein_268894..269124_POSITIVE 280 78 33 214 167 tfor:TF2295|5end_hypothetical_protein_2448164..2448394_POSITIVE 280 78 33 62 15 tfor:TF2294|5end_hypothetical_protein_2448012..2448242_POSITIVE 279 65 23 225 183 tfor:TF1534|5end_conserved_hypothetical_protein_1639485..1639715_POSITIVE 279 51 18 231 186 tfor:TF1191|5end_possible_transcriptional_regulator_1273615..1273845_POSITIVE 277 88 41 62 2 tfor:TF2317|5end_3-oxoacyl-[acyl-carrier-protein]_synthase_II_2474418..2474648_POSITIVE 276 59 21 102 67 tfor:TF2681|5end_conserved_hypothetical_protein_2855796..2856026_POSITIVE 273 60 11 162 120 tfor:TF2742|5end_single-strand_DNA-specific_exonuclease_2923802..2924032_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 379 56 20 71 35 tfor:TF1302|3end_conserved_hypothetical_protein;_possible_tetracycline_resistance_element_1383836..1383986_POSITIVE 342 89 41 150 99 tfor:TF1008|3end_rod_shape-determining_protein_MreC_1064374..1064524_POSITIVE 339 70 23 131 82 tfor:TF0604|3end_hypothetical_protein_636196..636346_POSITIVE 310 69 24 106 46 tfor:TF1969|3end_transcriptional_regulator,_AsnC_family_2116634..2116784_POSITIVE 307 84 42 45 12 tfor:TF2449|3end_undecaprenyl_diphosphate_synthase_2626541..2626691_POSITIVE 303 75 32 143 98 tfor:TF3042|3end_ferrous_iron_transport_protein_B_3271949..3272099_POSITIVE 294 68 22 130 78 tfor:TF3107|3end_hypothetical_protein_3338736..3338886_POSITIVE 283 75 33 53 8 tfor:TF0238|3end_outer_membrane_protein_268957..269107_POSITIVE 280 78 33 53 6 tfor:TF2293|3end_hypothetical_protein_2448083..2448233_POSITIVE 279 65 23 75 33 tfor:TF1532|3end_potassium_uptake_system_protein_1639415..1639565_POSITIVE 278 45 5 145 104 tfor:TF0242|3end_conserved_hypothetical_protein_274069..274219_POSITIVE 277 88 41 62 2 tfor:TF2315|3end_thioesterase_2474498..2474648_POSITIVE 276 46 23 97 72 tfor:TF2730|3end_thiol:disulfide_interchange_protein_2910946..2911096_POSITIVE 273 110 68 49 7 tfor:TF2566|3end_50S_ribosomal_protein_L5_2740940..2741090_POSITIVE 273 105 62 62 8 tfor:TF0378|3end_aspartyl-tRNA_synthetase_399520..399670_POSITIVE 269 57 15 66 18 tfor:TF1997|3end_ROK_family_transcriptional_regulator_2152686..2152836_POSITIVE 268 57 17 66 23 tfor:TF2651|3end_hypothetical_protein_2822014..2822164_POSITIVE 266 86 41 126 80 tfor:TF2225|3end_CTn_excision_protein_2395602..2395752_POSITIVE 264 52 18 71 28 tfor:TF1603|3end_RNA_polymerase_ECF-type_sigma_factor_1717846..1717996_POSITIVE 262 67 22 63 16 tfor:TF2418|3end_GTP-binding_protein_2598384..2598534_POSITIVE