Origin IGS: agttcaggtcaaagattcaaacatccgtacgggagaagaaagaagttgtttttcacttatttctcccttacgaatacctgtttgccgatctcattgtacgaaaagaaatgggcgtattacatcggagaggagcgcttcctgcctcctctctctcggccgttca .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tgaacggccgagagagaggaggcaggaagcgctcctctccgatgtaatacgcccatttcttttcgtacaatgagatcggcaaacaggtattcgtaagggagaaataagtgaaaaacaacttctttcttctcccgtacggatgtttgaatctttgacctgaact Mask Tandem Repeat Region ================================================ agttcaggtcaaagattcaaacatccgtacgggagaagaaagaagttgtttttcacttatttctcccttacgaatacctgtttgccgatctcattgtacgaaaagaaatgggcgtattacatcggagaggagcgcttcctgcctcctctctctcggccgttca Find is-nt database================================================ Query_seq: TF1239:TF1240|TF1239:TF1240:RNA polymerase ECF-type sigma factor:conserved hypothetical protein:->->:1324281..1324443 163 agttcaggtcaaagattcaaacatccgtacgggagaagaaagaagttgtttttcacttatttctcccttacgaatacctgtttgccgatctcattgtacgaaaagaaatgggcgtattacatcggagaggagcgcttcctgcctcctctctctcggccgttca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF1239:TF1240|TF1239:TF1240:RNA polymerase ECF-type sigma factor:conserved hypothetical protein:->->:1324281..1324443 163 agttcaggtcaaagattcaaacatccgtacgggagaagaaagaagttgtttttcacttatttctcccttacgaatacctgtttgccgatctcattgtacgaaaagaaatgggcgtattacatcggagaggagcgcttcctgcctcctctctctcggccgttca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF1239:TF1240|TF1239:TF1240:RNA polymerase ECF-type sigma factor:conserved hypothetical protein:->->:1324281..1324443 163 agttcaggtcaaagattcaaacatccgtacgggagaagaaagaagttgtttttcacttatttctcccttacgaatacctgtttgccgatctcattgtacgaaaagaaatgggcgtattacatcggagaggagcgcttcctgcctcctctctctcggccgttca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 agttcaggtcaaagattcaaacatccgtacgggagaagaaagaagttgtttttcacttatttctcccttacgaatacctgtttgccgatctcattgtacgaaaagaaatgggcgtattacatcggagaggagcgcttcctgcctcctctctctcggccgttca Predict ORF larger than 30AA ================================================ Protein_Len: 49 Strand: + Start: 15 End: 161 .............. M Q T S V R E K K E V V F H L F L P Y E Y L F A D L I V R K E M G V L H R R G A L P A S S L S A V .. Protein_Len: 39 Strand: + Start: 46 End: 162 ............................................. M F F T Y F S L T N T C L P I S L Y E K K W A Y Y I G E E R F L P P L S R P F . Protein_Len: 47 Strand: + Start: 23 End: 163 ...................... M R T G E E R S C F S L I S P L R I P V C R S H C T K R N G R I T S E R S A S C L L S L G R S agttcaggtcaaagattcaaacatccgtacgggagaagaaagaagttgtttttcacttatttctcccttacgaatacctgtttgccgatctcattgtacgaaaagaaatgggcgtattacatcggagaggagcgcttcctgcctcctctctctcggccgttca 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================================================ agttcaggtcaaagattcaaacatccgtacgggagaagaaagaagttgtttttcacttatttctcccttacgaatacctgtttgccgatctcattgtacgaaaagaaatgggcgtattacatcggagaggagcgcttcctgcctcctctctctcggccgttca Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TF1239:TF1240|TF1239:TF1240:RNA polymerase ECF-type sigma factor:conserved hypothetical protein:->->:1324281..1324443 163 agttcaggtcaaagattcaaacatccgtacgggagaagaaagaagttgtttttcacttatttctcccttacgaatacctgtttgccgatctcattgtacgaaaagaaatgggcgtattacatcggagaggagcgcttcctgcctcctctctctcggccgttca Intra-Species Hit: Count: 1 Min: 1 Max: 163 Len: 163 Subject: tfor_TF1239_TF1240|RNA polymerase ECF-type sigma factor:conserved hypothetical protein|POSITIVE:POSITIVE|[1324281,1324443]|163 HSP 1 e-value: 1.0E-87 bit: 323.0 Len: 163 Query Start:1 Query End:163 Subject Strand: POSITIVE Subject Start: 1 Subject End: 163 agttcaggtcaaagattcaaacatccgtacgggagaagaaagaagttgtttttcacttatttctcccttacgaatacctgtttgccgatctcattgtacgaaaagaaatgggcgtattacatcggagaggagcgcttcctgcctcctctctctcggccgttca agttcaggtcaaagattcaaacatccgtacgggagaagaaagaagttgtttttcacttatttctcccttacgaatacctgtttgccgatctcattgtacgaaaagaaatgggcgtattacatcggagaggagcgcttcctgcctcctctctctcggccgttca Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGUUCAGGUCAAAGAUUCAAACAUCCGUACGGGAGAAGAAAGAAGUUGUUUUUCACUUAUUUCUCCCUUACGAAUACCUGUUUGCCGAUCUCAUUGUACGAAAAGAAAUGGGCGUAUUACAUCGGAGAGGAGCGCUUCCUGCCUCCUCUCUCUCGGCCGUUCA ....(((((....(((......)))((((.((((((((....((((........)))).)))))))).))))...)))))...(((((.......(((((...(....)...)))))......(((((((((.((.....))))))))))).)))))...... (-51.00) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGAACGGCCGAGAGAGAGGAGGCAGGAAGCGCUCCUCUCCGAUGUAAUACGCCCAUUUCUUUUCGUACAAUGAGAUCGGCAAACAGGUAUUCGUAAGGGAGAAAUAAGUGAAAAACAACUUCUUUCUUCUCCCGUACGGAUGUUUGAAUCUUUGACCUGAACU .....(((.((((((((((((((.....)).))))))))...........(((.(((((............))))).)))...((..((((((((.(((((((..(((.............)))..))))))).))))))))..))..)))).).))...... (-53.42) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 417 158 111 182 134 tfor:TF0310|5end_conserved_hypothetical_protein_334685..334915_POSITIVE 410 160 112 72 8 tfor:TF2159|5end_conserved_hypothetical_protein_2334446..2334676_POSITIVE 394 159 122 66 15 tfor:TF1720|5end_conserved_hypothetical_protein_1843679..1843909_POSITIVE 384 159 111 221 151 tfor:TF2677|5end_aspartate_transaminase_2850809..2851039_POSITIVE 375 157 112 43 3 tfor:TF2446|5end_riboflavin-specific_deaminase_2622370..2622600_POSITIVE 373 160 113 57 3 tfor:TF2724|5end_anti-sigma_factor_2898193..2898423_POSITIVE 370 157 112 73 36 tfor:TF2759|5end_xylose_repressor,_ROK_family_2943568..2943798_POSITIVE 368 144 107 49 8 tfor:TF0680|5end_tail-specific_protease_721393..721623_POSITIVE 363 160 111 142 77 tfor:TF1253|5end_hypothetical_protein_1335982..1336212_POSITIVE 361 159 120 55 2 tfor:TF0414|5end_N-ethylammeline_chlorohydrolase_431789..432019_POSITIVE 359 160 121 54 3 tfor:TF2422|5end_hypothetical_protein_2601298..2601528_POSITIVE 359 158 119 64 12 tfor:TF0324|5end_conserved_hypothetical_protein_351228..351458_POSITIVE 358 160 111 171 123 tfor:TF2161|5end_conserved_hypothetical_protein_2336972..2337202_POSITIVE 357 158 121 158 118 tfor:TF0352|5end_transposase_element_371223..371453_POSITIVE 353 158 111 190 126 tfor:TF0594|5end_conserved_hypothetical_protein;_possible_PAP2_superfamily_protein_626971..627201_POSITIVE 350 158 111 104 43 tfor:TF3123|5end_dTDP-4-dehydrorhamnose_3,5-epimerase_3357775..3358005_POSITIVE 350 158 112 122 80 tfor:TF2477|5end_phosphatase_2654229..2654459_POSITIVE 350 159 117 165 111 tfor:TF2357|5end_collagenase_2522561..2522791_POSITIVE 350 150 107 64 8 tfor:TF1856|5end_conserved_hypothetical_protein_2009969..2010199_POSITIVE 349 157 112 147 98 tfor:TF0962|5end_possible_amidohydrolase_1011593..1011823_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 428 155 112 151 107 tfor:TF0242|3end_conserved_hypothetical_protein_274069..274219_POSITIVE 410 160 112 130 66 tfor:TF2158|3end_conserved_hypothetical_protein_2334584..2334734_POSITIVE 368 144 107 65 24 tfor:TF0679|3end_hypothetical_protein_721489..721639_POSITIVE 361 159 120 55 2 tfor:TF0413|3end_succinyl-diaminopimelate_desuccinylase_431869..432019_POSITIVE 357 158 121 81 41 tfor:TF0351|3end_hypothetical_protein_371226..371376_POSITIVE 349 157 112 147 98 tfor:TF0961|3end_translation_initiation_inhibitor,_endoribonuclease_activity_1011673..1011823_POSITIVE 341 143 110 57 20 tfor:TF1381|3end_hypothetical_protein_1456814..1456964_POSITIVE 334 159 111 64 1 tfor:TF1422|3end_GLCNAC_transferase_(UDP-N-acetylglucosamine-N-acetylmuramyl-(pentapeptide)-pyr_ophosphoryl-undecaprenol_N-acetylglucosamine_transferase)_1505823..1505973_POSITIVE 333 159 112 55 2 tfor:TF2563|3end_30S_ribosomal_protein_S17_2739679..2739829_POSITIVE 328 159 113 122 67 tfor:TF2654|3end_arginyl-tRNA_synthetase_2824559..2824709_POSITIVE 324 117 75 35 3 tfor:TF2593|3end_amino_acid_transport_protein_2764242..2764392_POSITIVE 322 159 124 147 93 tfor:TF1292|3end_sensor_histidine_protein_kinase_1374554..1374704_POSITIVE 321 159 121 75 36 tfor:TF1897|3end_conserved_hypothetical_protein;_possible_aminopeptidase_2052107..2052257_POSITIVE 320 160 120 70 15 tfor:TF1160|3end_MutT/nudix_family_protein_1241008..1241158_POSITIVE 318 157 124 62 36 tfor:TF1762|3end_hypothetical_protein_1899648..1899798_POSITIVE 315 129 82 61 11 tfor:TF1931|3end_ATPase/GTPase_2078622..2078772_POSITIVE 314 158 125 34 5 tfor:TF2475|3end_GTP_pyrophosphokinase,_(p)ppGpp_synthetase_2654221..2654371_POSITIVE 310 141 108 70 33 tfor:TF1472|3end_acyl-ACP_thioesterase_1566337..1566487_POSITIVE 310 160 111 132 65 tfor:TF1009|3end_conserved_hypothetical_protein;_posible_rod-shape_determining_protein,_MreD_1064885..1065035_POSITIVE 310 157 112 59 12 tfor:TF0073|3end_possible_dTDP-glucose_4,6-dehydratase,_NAD-dependent_epimerase/dehydratase_family_82051..82201_POSITIVE