Origin IGS: atggtatataaaaaaatgactcgctggcagatcttacggtatgccaagcgagtactgttatctttgaagtgcagcaacctgcaactatctttccgcttgcaaaggtaagcatttattttattccggcaaagtaaatggcaagaattttatgcgattcacta .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tagtgaatcgcataaaattcttgccatttactttgccggaataaaataaatgcttacctttgcaagcggaaagatagttgcaggttgctgcacttcaaagataacagtactcgcttggcataccgtaagatctgccagcgagtcatttttttatataccat Mask Tandem Repeat Region ================================================ atggtatataaaaaaatgactcgctggcagatcttacggtatgccaagcgagtactgttatctttgaagtgcagcaacctgcaactatctttccgcttgcaaaggtaagcatttattttattccggcaaagtaaatggcaagaattttatgcgattcacta Find is-nt database================================================ Query_seq: TF2363:TF2364|TF2363:TF2364:conserved hypothetical protein:conserved hypothetical protein; possible DNA binding protein, excisionase family:->->:2530341..2530501 161 atggtatataaaaaaatgactcgctggcagatcttacggtatgccaagcgagtactgttatctttgaagtgcagcaacctgcaactatctttccgcttgcaaaggtaagcatttattttattccggcaaagtaaatggcaagaattttatgcgattcacta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF2363:TF2364|TF2363:TF2364:conserved hypothetical protein:conserved hypothetical protein; possible DNA binding protein, excisionase family:->->:2530341..2530501 161 atggtatataaaaaaatgactcgctggcagatcttacggtatgccaagcgagtactgttatctttgaagtgcagcaacctgcaactatctttccgcttgcaaaggtaagcatttattttattccggcaaagtaaatggcaagaattttatgcgattcacta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF2363:TF2364|TF2363:TF2364:conserved hypothetical protein:conserved hypothetical protein; possible DNA binding protein, excisionase family:->->:2530341..2530501 161 atggtatataaaaaaatgactcgctggcagatcttacggtatgccaagcgagtactgttatctttgaagtgcagcaacctgcaactatctttccgcttgcaaaggtaagcatttattttattccggcaaagtaaatggcaagaattttatgcgattcacta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 atggtatataaaaaaatgactcgctggcagatcttacggtatgccaagcgagtactgttatctttgaagtgcagcaacctgcaactatctttccgcttgcaaaggtaagcatttattttattccggcaaagtaaatggcaagaattttatgcgattcacta Predict ORF larger than 30AA ================================================ Protein_Len: 35 Strand: + Start: 1 End: 105 M V Y K K M T R W Q I L R Y A K R V L L S L K C S N L Q L S F R L Q R ........................................................ Protein_Len: 36 Strand: + Start: 24 End: 131 ....................... M A D L T V C Q A S T V I F E V Q Q P A T I F P L A K V S I Y F I P A K .............................. Protein_Len: 38 Strand: - Start: 3 End: 116 .. T Y L F I V R Q C I K R Y A L R T S N D K F H L L R C S D K R K C L Y A N M ............................................. Protein_Len: 37 Strand: - Start: 2 End: 112 . P I Y F F S E S A S R V T H W A L V T I K S T C C G A V I K G S A F T L M ................................................. atggtatataaaaaaatgactcgctggcagatcttacggtatgccaagcgagtactgttatctttgaagtgcagcaacctgcaactatctttccgcttgcaaaggtaagcatttattttattccggcaaagtaaatggcaagaattttatgcgattcacta 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================================================ atggtatataaaaaaatgactcgctggcagatcttacggtatgccaagcgagtactgttatctttgaagtgcagcaacctgcaactatctttccgcttgcaaaggtaagcatttattttattccggcaaagtaaatggcaagaattttatgcgattcacta Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 85 HP_score: -2.8 Tail_Score: -5.71712 Start: 17 End: 54 Full_Region: cttcaaagataacag tactcgcttggcatacc gtaa gatctgccagcgagtca tttttttatatacca ................tactcgcttggcataccgtaagatctgccagcgagtca........................................................................................................... Find igs database================================================ Query_seq: TF2363:TF2364|TF2363:TF2364:conserved hypothetical protein:conserved hypothetical protein; possible DNA binding protein, excisionase family:->->:2530341..2530501 161 atggtatataaaaaaatgactcgctggcagatcttacggtatgccaagcgagtactgttatctttgaagtgcagcaacctgcaactatctttccgcttgcaaaggtaagcatttattttattccggcaaagtaaatggcaagaattttatgcgattcacta Intra-Species Hit: Count: 1 Min: 17 Max: 161 Len: 145 Subject: tfor_TF2363_TF2364|conserved hypothetical protein:conserved hypothetical protein; possible DNA binding protein, excisionase family|POSITIVE:POSITIVE|[2530341,2530501]|161 HSP 1 e-value: 6.0E-77 bit: 287.0 Len: 145 Query Start:17 Query End:161 Subject Strand: POSITIVE Subject Start: 17 Subject End: 161 ................tgactcgctggcagatcttacggtatgccaagcgagtactgttatctttgaagtgcagcaacctgcaactatctttccgcttgcaaaggtaagcatttattttattccggcaaagtaaatggcaagaattttatgcgattcacta ................tgactcgctggcagatcttacggtatgccaagcgagtactgttatctttgaagtgcagcaacctgcaactatctttccgcttgcaaaggtaagcatttattttattccggcaaagtaaatggcaagaattttatgcgattcacta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGACUCGCUGGCAGAUCUUACGGUAUGCCAAGCGAGUACUGUUAUCUUUGAAGUGCAGCAACCUGCAACUAUCUUUCCGCUUGCAAAGGUAAGCAUUUAUUUUAUUCCGGCAAAGUAAAUGGCAAGAAUUUUAUGCGAUUCACUA ..(((((((((((.(((....))).)))).)))))))..(((((((((((.(((((((....)))).)))........((((((....))))))................)))))...)))))).(((((......))))).... (-41.20) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAGUGAAUCGCAUAAAAUUCUUGCCAUUUACUUUGCCGGAAUAAAAUAAAUGCUUACCUUUGCAAGCGGAAAGAUAGUUGCAGGUUGCUGCACUUCAAAGAUAACAGUACUCGCUUGGCAUACCGUAAGAUCUGCCAGCGAGUCA .......((((.....(((((.((.(......).)).)))))........(((........))).))))...((.(((.((((....)))))))))..........(.(((((((.((((...(....)...)))))))))))). (-36.90) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 339 99 55 58 6 tfor:TF2832|5end_possible_proton/sodium:glutamate_symporter_protein_3022660..3022890_POSITIVE 339 57 13 228 186 tfor:TF2339|5end_hypothetical_protein_2500256..2500486_POSITIVE 338 90 43 164 99 tfor:TF3110|5end_conserved_hypothetical_protein_with_helicase_domain_3342714..3342944_POSITIVE 334 46 6 215 171 tfor:TF1822|5end_outer_membrane_lipoprotein_silC_precursor_1967599..1967829_POSITIVE 332 42 6 73 32 tfor:TF2310|5end_dehydrogenase,_possible_3-oxoacyl-[acyl-carrier-protein]_reductase_2470481..2470711_POSITIVE 330 41 1 227 177 tfor:TF2578|5end_30S_ribosomal_protein_S11_2746698..2746928_POSITIVE 330 50 1 165 116 tfor:TF1909|5end_cobalamin_(5`-phosphate)_synthase_2063207..2063437_POSITIVE 322 58 15 203 162 tfor:TF1439|5end_outer_membrane_protein,_TonB_dependent_receptor_1522479..1522709_POSITIVE 319 50 6 76 32 tfor:TF2728|5end_outer_membrane_protein,_TonB_dependent_receptor_2904608..2904838_POSITIVE 315 80 31 228 168 tfor:TF2224|5end_CTn_excision_protein_2394592..2394822_POSITIVE 313 73 32 200 150 tfor:TF2332|5end_signal_peptidase_I_2491694..2491924_POSITIVE 305 45 3 210 156 tfor:TF1771|5end_prolipoprotein_diacylglyceryl_transferase_1909562..1909792_POSITIVE 305 42 4 51 8 tfor:TF1589|5end_surface_antigen_BspA_1703189..1703419_POSITIVE 303 86 47 91 53 tfor:TF2997|5end_hypothetical_protein_3211408..3211638_POSITIVE 303 48 4 208 158 tfor:TF2655|5end_DNA_topoisomerase_I_2824543..2824773_POSITIVE 301 94 51 229 180 tfor:TF2157|5end_conserved_hypothetical_protein_2332915..2333145_POSITIVE 300 75 32 52 12 tfor:TF0840|5end_hypothetical_protein_891561..891791_POSITIVE 299 94 62 46 1 tfor:TF1259|5end_hypothetical_protein_1338549..1338779_POSITIVE 298 44 4 225 183 tfor:TF2160|5end_magnesium_chelatase,_subunit_I_2335974..2336204_POSITIVE 298 42 8 92 50 tfor:TF1281|5end_2-dehydro-3-deoxyphosphooctonate_aldolase_(3-deoxy-D-manno-2-octulosonate-8-phosphate_synthase)_(KDO-8-phosphate_synthetase)_(KDO_8-P_synthase)_1365604..1365834_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 361 47 1 89 33 tfor:TF2340|3end_hypothetical_protein_2500915..2501065_POSITIVE 337 66 21 119 68 tfor:TF3143|3end_conserved_hypothetical_protein;_possible_membrane_protein_3379227..3379377_POSITIVE 336 37 3 72 38 tfor:TF2363|3end_conserved_hypothetical_protein_2530280..2530430_POSITIVE 305 48 4 144 99 tfor:TF0757|3end_50S_ribosomal_protein_L25;_general_stress_protein_805293..805443_POSITIVE 304 94 51 70 31 tfor:TF2515|3end_outer_membrane_protein,_TonB_dependent_receptor_2694865..2695015_POSITIVE 303 48 4 144 94 tfor:TF2654|3end_arginyl-tRNA_synthetase_2824559..2824709_POSITIVE 296 66 21 61 15 tfor:TF2154|3end_conserved_hypothetical_protein_2329529..2329679_POSITIVE 295 43 1 62 24 tfor:TF3140|3end_Na+-translocating_NADH-quinone_reductase,_subunit_B_3374573..3374723_POSITIVE 295 46 1 57 19 tfor:TF0994|3end_maltose_O-acetyltransferase_1049782..1049932_POSITIVE 294 58 17 74 34 tfor:TF3060|3end_conserved_hypothetical_protein_3285130..3285280_POSITIVE 294 80 32 56 14 tfor:TF0365|3end_hypothetical_protein_383152..383302_POSITIVE 292 68 21 61 12 tfor:TF2883|3end_peptidyl-prolyl_cis-trans_isomerase_3075129..3075279_POSITIVE 290 65 21 46 4 tfor:TF2582|3end_ABC_transporter,_ATP-binding_protein_2750283..2750433_POSITIVE 289 50 5 112 58 tfor:TF2456|3end_ABC_transporter,_ATP-binding_protein_2633208..2633358_POSITIVE 289 46 1 77 39 tfor:TF0809|3end_cation_efflux_protein_868518..868668_POSITIVE 285 94 57 78 35 tfor:TF2839|3end_ATP-dependent_exodeoxyribonuclease_3031035..3031185_POSITIVE 283 69 21 73 27 tfor:TF2275|3end_conserved_hypothetical_protein_2438300..2438450_POSITIVE 281 115 71 45 3 tfor:TF1639|3end_conserved_hypothetical_protein_1748022..1748172_POSITIVE 281 70 21 43 1 tfor:TF0360|3end_hypothetical_protein_379538..379688_POSITIVE 281 48 8 55 9 tfor:TF0298|3end_dipeptidase_324868..325018_POSITIVE