Origin IGS: atgattttaaagcggctgttgaaaaggtgttgccgttttacaatgtgtctgaaaaaaacaaactgcctcaagcatacgcagcccgaggcagtttattttacctgaaggtca .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tgaccttcaggtaaaataaactgcctcgggctgcgtatgcttgaggcagtttgtttttttcagacacattgtaaaacggcaacaccttttcaacagccgctttaaaatcat Mask Tandem Repeat Region ================================================ atgattttaaagcggctgttgaaaaggtgttgccgttttacaatgtgtctgaaaaaaacaaactgcctcaagcatacgcagcccgaggcagtttattttacctgaaggtca Find is-nt database================================================ Query_seq: TF1464:TF1465|TF1464:TF1465:conserved hypothetical protein:modulator of DNA gyrase:->->:1554177..1554287 111 atgattttaaagcggctgttgaaaaggtgttgccgttttacaatgtgtctgaaaaaaacaaactgcctcaagcatacgcagcccgaggcagtttattttacctgaaggtca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF1464:TF1465|TF1464:TF1465:conserved hypothetical protein:modulator of DNA gyrase:->->:1554177..1554287 111 atgattttaaagcggctgttgaaaaggtgttgccgttttacaatgtgtctgaaaaaaacaaactgcctcaagcatacgcagcccgaggcagtttattttacctgaaggtca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF1464:TF1465|TF1464:TF1465:conserved hypothetical protein:modulator of DNA gyrase:->->:1554177..1554287 111 atgattttaaagcggctgttgaaaaggtgttgccgttttacaatgtgtctgaaaaaaacaaactgcctcaagcatacgcagcccgaggcagtttattttacctgaaggtca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 atgattttaaagcggctgttgaaaaggtgttgccgttttacaatgtgtctgaaaaaaacaaactgcctcaagcatacgcagcccgaggcagtttattttacctgaaggtca Predict ORF larger than 30AA ================================================ Protein_Len: 34 Strand: + Start: 1 End: 102 M I L K R L L K R C C R F T M C L K K T N C L K H T Q P E A V Y F T ......... atgattttaaagcggctgttgaaaaggtgttgccgttttacaatgtgtctgaaaaaaacaaactgcctcaagcatacgcagcccgaggcagtttattttacctgaaggtca 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================================================ atgattttaaagcggctgttgaaaaggtgttgccgttttacaatgtgtctgaaaaaaacaaactgcctcaagcatacgcagcccgaggcagtttattttacctgaaggtca Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 75 HP_score: -5.9 Tail_Score: -4.68908 Start: 63 End: 91 Full_Region: TCTGAAAAAAACAAA CTGCCTCAAGC ATACGCA GCCCGAGGCAG TTTATTTTACCTGAA ..............................................................CTGCCTCAAGCATACGCAGCCCGAGGCAG.................... Find igs database================================================ Query_seq: TF1464:TF1465|TF1464:TF1465:conserved hypothetical protein:modulator of DNA gyrase:->->:1554177..1554287 111 atgattttaaagcggctgttgaaaaggtgttgccgttttacaatgtgtctgaaaaaaacaaactgcctcaagcatacgcagcccgaggcagtttattttacctgaaggtca Intra-Species Hit: Count: 1 Min: 1 Max: 111 Len: 111 Subject: tfor_TF1464_TF1465|conserved hypothetical protein:modulator of DNA gyrase|POSITIVE:POSITIVE|[1554177,1554287]|111 HSP 1 e-value: 2.0E-44 bit: 178.0 Len: 111 Query Start:1 Query End:111 Subject Strand: POSITIVE Subject Start: 1 Subject End: 111 atgattttaaagcggctgttgaaaaggtgttgccgttttacaatgtgtctgnnnnnnncaaactgcctcaagcatacgcagcccgaggcagtttattttacctgaaggtca atgattttaaagcggctgttgaaaaggtgttgccgttttacaatgtgtctgaaaaaaacaaactgcctcaagcatacgcagcccgaggcagtttattttacctgaaggtca Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUGAUUUUAAAGCGGCUGUUGAAAAGGUGUUGCCGUUUUACAAUGUGUCUGAAAAAAACAAACUGCCUCAAGCAUACGCAGCCCGAGGCAGUUUAUUUUACCUGAAGGUCA .(((((((((((((((...............)))))))))..............((((.((((((((((..((.......))..)))))))))).))))......)))))) (-30.76) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGACCUUCAGGUAAAAUAAACUGCCUCGGGCUGCGUAUGCUUGAGGCAGUUUGUUUUUUUCAGACACAUUGUAAAACGGCAACACCUUUUCAACAGCCGCUUUAAAAUCAU ..(((....)))(((((((((((((((((((.......)))))))))))))))))))..............((((.((((...............)))).))))....... (-35.26) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 436 104 63 185 143 tfor:TF1900|5end_conserved_hypothetical_protein_2053867..2054097_POSITIVE 351 94 61 179 143 tfor:TF2752|5end_endonuclease_III_2936781..2937011_POSITIVE 343 89 44 231 177 tfor:TF2697|5end_small_heat_shock_protein_2871678..2871908_POSITIVE 340 107 63 53 7 tfor:TF1236|5end_L-rhamnose_isomerase_1320743..1320973_POSITIVE 332 110 61 151 98 tfor:TF0746|5end_possible_DNA_polymerase_III_792261..792491_POSITIVE 324 108 63 89 44 tfor:TF3014|5end_oxidoreductase,_short-chain_dehydrogenase/reductase_family_3237623..3237853_POSITIVE 322 104 63 69 24 tfor:TF3154|5end_conserved_hypothetical_protein_3389219..3389449_POSITIVE 322 50 10 203 160 tfor:TF2531|5end_possible_dipeptidyl-peptidase_III_2713045..2713275_POSITIVE 320 106 68 63 19 tfor:TF0091|5end_outer_membrane_protein_97701..97931_POSITIVE 306 59 11 66 14 tfor:TF1237|5end_possible_L-fuculose_kinase_1322041..1322271_POSITIVE 305 92 62 67 36 tfor:TF1349|5end_conserved_hypothetical_protein;_possible_prophage_maintanence_or_virulance_related_1429054..1429284_POSITIVE 305 110 64 192 145 tfor:TF0140|5end_exodeoxyribonuclease_VII,_small_subunit_148203..148433_POSITIVE 304 102 65 47 16 tfor:TF2978|5end_conserved_hypothetical_protein_3186076..3186306_POSITIVE 302 52 12 66 22 tfor:TF2829|5end_conserved_hypothetical_protein_3019562..3019792_POSITIVE 300 51 14 57 19 tfor:TF3073|5end_magnesium-protoporphyrin_O-methyltransferase;_cobalamin_biosynthesis_protein_N_3296008..3296238_POSITIVE 298 90 44 185 136 tfor:TF1224|5end_hypothetical_protein_1311203..1311433_POSITIVE 296 51 12 69 35 tfor:TF1670|5end_ATP_synthase,_alpha_subunit_1784455..1784685_POSITIVE 295 109 61 229 188 tfor:TF0073|5end_possible_dTDP-glucose_4,6-dehydratase,_NAD-dependent_epimerase/dehydratase_family_80946..81176_POSITIVE 295 109 61 52 11 tfor:TF0072|5end_hypothetical_protein_80769..80999_POSITIVE 294 90 41 211 153 tfor:TF2583|5end_possible_ABC_transporter,__permease_component_2750206..2750436_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 436 104 63 53 11 tfor:TF1899|3end_anti-sigma_factor_2053815..2053965_POSITIVE 351 94 61 133 97 tfor:TF2751|3end_phenylalanyl-tRNA_synthetase,_alpha_subunit_2936815..2936965_POSITIVE 343 89 44 84 30 tfor:TF2696|3end_oxidoreductase,_short_chain_dehydrogenase/reductase_family_2871611..2871761_POSITIVE 332 110 61 118 65 tfor:TF0744|3end_DNA_polymerase_III_subunit,_gamma/tau_792308..792458_POSITIVE 322 104 63 94 49 tfor:TF3153|3end_conserved_hypothetical_protein_3389324..3389474_POSITIVE 308 53 11 146 97 tfor:TF0789|3end_preprotein_translocase,_secDF_family_843670..843820_POSITIVE 302 52 12 66 22 tfor:TF2827|3end_conserved_hypothetical_protein_3019642..3019792_POSITIVE 300 51 14 52 14 tfor:TF3072|3end_conserved_hypothetical_protein_3296083..3296233_POSITIVE 296 51 12 37 3 tfor:TF1669|3end_ATP_synthase,_gamma_subunit_1784503..1784653_POSITIVE 295 88 41 62 14 tfor:TF2587|3end_hypothetical_protein_2752212..2752362_POSITIVE 295 109 61 74 33 tfor:TF0071|3end_conserved_hypothetical_protein_80871..81021_POSITIVE 288 39 12 47 12 tfor:TF1458|3end_conserved_hypothetical_protein_1548381..1548531_POSITIVE 286 79 34 127 78 tfor:TF0939|3end_ISPg1_transposase,_IS1106-related_transposase_981115..981265_POSITIVE 285 50 5 48 3 tfor:TF0568|3end_indolepyruvate_ferredoxin_oxidoreductase,_alpha_subunit_601798..601948_POSITIVE 284 79 31 146 106 tfor:TF2610|3end_nitroreductase_2787241..2787391_POSITIVE 283 110 61 103 61 tfor:TF1792|3end_acid_phosphatase_1933319..1933469_POSITIVE 280 79 31 79 19 tfor:TF3060|3end_conserved_hypothetical_protein_3285130..3285280_POSITIVE 278 110 70 41 5 tfor:TF2218|3end_two-component_system_response_regulator_2390928..2391078_POSITIVE 276 110 61 139 98 tfor:TF0448|3end_hypothetical_protein_467911..468061_POSITIVE 274 110 68 149 107 tfor:TF3085|3end_hypothetical_protein_3319003..3319153_POSITIVE