Origin IGS: tcgttaaactctcgtaatgcaagcgccaagcctgtttattcgtttgtcgattgcctcatacctccgatcaatctgttcgatattgccggtacggcacaaatcacttgcaaagttttatccttcgcaccttgaggtgttgtatcgtcttgtgatttttgtcctctctctatgataaacgaactca .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tgagttcgtttatcatagagagaggacaaaaatcacaagacgatacaacacctcaaggtgcgaaggataaaactttgcaagtgatttgtgccgtaccggcaatatcgaacagattgatcggaggtatgaggcaatcgacaaacgaataaacaggcttggcgcttgcattacgagagtttaacga Mask Tandem Repeat Region ================================================ tcgttaaactctcgtaatgcaagcgccaagcctgtttattcgtttgtcgattgcctcatacctccgatcaatctgttcgatattgccggtacggcacaaatcacttgcaaagttttatccttcgcaccttgaggtgttgtatcgtcttgtgatttttgtcctctctctatgataaacgaactca Find is-nt database================================================ Query_seq: TF3030:TF3031|TF3030:TF3031:16S rRNA processing protein:conserved hypothetical protein:->->:3254357..3254540 184 tcgttaaactctcgtaatgcaagcgccaagcctgtttattcgtttgtcgattgcctcatacctccgatcaatctgttcgatattgccggtacggcacaaatcacttgcaaagttttatccttcgcaccttgaggtgttgtatcgtcttgtgatttttgtcctctctctatgataaacgaactca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF3030:TF3031|TF3030:TF3031:16S rRNA processing protein:conserved hypothetical protein:->->:3254357..3254540 184 tcgttaaactctcgtaatgcaagcgccaagcctgtttattcgtttgtcgattgcctcatacctccgatcaatctgttcgatattgccggtacggcacaaatcacttgcaaagttttatccttcgcaccttgaggtgttgtatcgtcttgtgatttttgtcctctctctatgataaacgaactca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF3030:TF3031|TF3030:TF3031:16S rRNA processing protein:conserved hypothetical protein:->->:3254357..3254540 184 tcgttaaactctcgtaatgcaagcgccaagcctgtttattcgtttgtcgattgcctcatacctccgatcaatctgttcgatattgccggtacggcacaaatcacttgcaaagttttatccttcgcaccttgaggtgttgtatcgtcttgtgatttttgtcctctctctatgataaacgaactca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tcgttaaactctcgtaatgcaagcgccaagcctgtttattcgtttgtcgattgcctcatacctccgatcaatctgttcgatattgccggtacggcacaaatcacttgcaaagttttatccttcgcaccttgaggtgttgtatcgtcttgtgatttttgtcctctctctatgataaacgaactca Predict ORF larger than 30AA ================================================ Protein_Len: 33 Strand: + Start: 51 End: 149 .................................................. M P H T S D Q S V R Y C R Y G T N H L Q S F I L R T L R C C I V L ................................... Protein_Len: 51 Strand: + Start: 17 End: 169 ................ M Q A P S L F I R L S I A S Y L R S I C S I L P V R H K S L A K F Y P S H L E V L Y R L V I F V L S L ............... Protein_Len: 45 Strand: - Start: 39 End: 173 ...................................... E N T S Q R M G G I L R N S I A P V A C I V Q L T K D K A G Q P T T D D Q S K Q G R E I M ........... Protein_Len: 31 Strand: - Start: 7 End: 99 ...... V R T I C A G L R N I R K D I A E Y R R D I Q E I N G T R C M ..................................................................................... tcgttaaactctcgtaatgcaagcgccaagcctgtttattcgtttgtcgattgcctcatacctccgatcaatctgttcgatattgccggtacggcacaaatcacttgcaaagttttatccttcgcaccttgaggtgttgtatcgtcttgtgatttttgtcctctctctatgataaacgaactca 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================================================ tcgttaaactctcgtaatgcaagcgccaagcctgtttattcgtttgtcgattgcctcatacctccgatcaatctgttcgatattgccggtacggcacaaatcacttgcaaagttttatccttcgcaccttgaggtgttgtatcgtcttgtgatttttgtcctctctctatgataaacgaactca Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TF3030:TF3031|TF3030:TF3031:16S rRNA processing protein:conserved hypothetical protein:->->:3254357..3254540 184 tcgttaaactctcgtaatgcaagcgccaagcctgtttattcgtttgtcgattgcctcatacctccgatcaatctgttcgatattgccggtacggcacaaatcacttgcaaagttttatccttcgcaccttgaggtgttgtatcgtcttgtgatttttgtcctctctctatgataaacgaactca Intra-Species Hit: Count: 1 Min: 1 Max: 184 Len: 184 Subject: tfor_TF3030_TF3031|16S rRNA processing protein:conserved hypothetical protein|POSITIVE:POSITIVE|[3254357,3254540]|184 HSP 1 e-value: 1.0E-100 bit: 365.0 Len: 184 Query Start:1 Query End:184 Subject Strand: POSITIVE Subject Start: 1 Subject End: 184 tcgttaaactctcgtaatgcaagcgccaagcctgtttattcgtttgtcgattgcctcatacctccgatcaatctgttcgatattgccggtacggcacaaatcacttgcaaagttttatccttcgcaccttgaggtgttgtatcgtcttgtgatttttgtcctctctctatgataaacgaactca tcgttaaactctcgtaatgcaagcgccaagcctgtttattcgtttgtcgattgcctcatacctccgatcaatctgttcgatattgccggtacggcacaaatcacttgcaaagttttatccttcgcaccttgaggtgttgtatcgtcttgtgatttttgtcctctctctatgataaacgaactca Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UCGUUAAACUCUCGUAAUGCAAGCGCCAAGCCUGUUUAUUCGUUUGUCGAUUGCCUCAUACCUCCGAUCAAUCUGUUCGAUAUUGCCGGUACGGCACAAAUCACUUGCAAAGUUUUAUCCUUCGCACCUUGAGGUGUUGUAUCGUCUUGUGAUUUUUGUCCUCUCUCUAUGAUAAACGAACUCA ..................(((.((.....)).)))...(((((((((((((((..((........)).))))).(..(((.((..((((((((((((...(((..(((.(((.......))).)))...))).)))))))))))....)..))..)))..).........)))))))))).... (-39.40) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGAGUUCGUUUAUCAUAGAGAGAGGACAAAAAUCACAAGACGAUACAACACCUCAAGGUGCGAAGGAUAAAACUUUGCAAGUGAUUUGUGCCGUACCGGCAAUAUCGAACAGAUUGAUCGGAGGUAUGAGGCAAUCGACAAACGAAUAAACAGGCUUGGCGCUUGCAUUACGAGAGUUUAACGA ...((((((((.((...............(((((((.............(((....)))((((((.......))))))..))))))).(((((((((..(...(((((.....)))))..).)))))..))))...)).))))))))...(((((.....)))))....((....))....... (-43.90) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 402 94 58 186 145 tfor:TF0946|5end_iron(III)_ABC_transporter,_periplasmic_iron-binding_protein_989482..989712_POSITIVE 398 98 53 157 109 tfor:TF2674|5end_conserved_hypothetical_protein;_possible_phosphoesterase_2848176..2848406_POSITIVE 374 98 54 53 10 tfor:TF2797|5end_cytochrome_d_oxidase,_subunit_I_2982450..2982680_POSITIVE 349 96 51 204 152 tfor:TF1011|5end_cell_division_protein;_rod_shape-determining_protein_1066647..1066877_POSITIVE 347 80 31 195 143 tfor:TF2314|5end_conserved_hypothetical_protein_2473530..2473760_POSITIVE 342 98 53 57 5 tfor:TF1455|5end_conserved_hypothetical_protein_1540688..1540918_POSITIVE 341 89 46 56 8 tfor:TF2511|5end_RNA_binding_protein_2689910..2690140_POSITIVE 341 160 118 61 10 tfor:TF2231|5end_DNA_methylase,_site-specific_DNA-methyltransferase_(adenine-specific)_2400307..2400537_POSITIVE 340 98 53 213 157 tfor:TF0446|5end_hypothetical_protein_466473..466703_POSITIVE 339 88 41 213 161 tfor:TF2611|5end_conserved_hypothetical_protein_2787204..2787434_POSITIVE 338 88 41 175 119 tfor:TF0992|5end_hypothetical_protein_1048251..1048481_POSITIVE 337 58 12 225 169 tfor:TF0152|5end_RNA_polymerase_ECF-type_sigma_factor_162021..162251_POSITIVE 332 95 53 73 30 tfor:TF0143|5end_aspartate--ammonia_ligase_151390..151620_POSITIVE 331 98 51 129 82 tfor:TF2189|5end_conserved_hypothetical_protein_2363455..2363685_POSITIVE 330 107 63 218 167 tfor:TF2247|5end_transfer_region-related_protein,_TraA_2421463..2421693_POSITIVE 329 90 41 191 128 tfor:TF1925|5end_hypothetical_protein_2074458..2074688_POSITIVE 329 90 41 148 85 tfor:TF1926|5end_hypothetical_protein_2074415..2074645_POSITIVE 326 54 14 130 88 tfor:TF1856|5end_conserved_hypothetical_protein_2009969..2010199_POSITIVE 325 70 23 59 9 tfor:TF2443|5end_amidophosphoribosyl-transferase_2620287..2620517_POSITIVE 325 97 52 186 132 tfor:TF0971|5end_conserved_hypothetical_protein_1021355..1021585_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 341 160 118 68 17 tfor:TF2230|3end_CTn_excision_protein_2400394..2400544_POSITIVE 333 107 61 70 13 tfor:TF0804|3end_possible_phosphatidylglycerophosphate_synthase_862899..863049_POSITIVE 332 61 23 91 50 tfor:TF0815|3end_conserved_hypothetical_protein_873974..874124_POSITIVE 332 95 53 86 43 tfor:TF0144|3end_hypothetical_protein_151483..151633_POSITIVE 331 98 51 129 82 tfor:TF2188|3end_conserved_hypothetical_protein_2363535..2363685_POSITIVE 328 90 42 150 108 tfor:TF0179|3end_pyrophosphate-energized_proton_pump_190691..190841_POSITIVE 322 86 41 69 27 tfor:TF2575|3end_methionine_aminopeptidase_2745985..2746135_POSITIVE 322 89 41 146 82 tfor:TF2501|3end_DNA_mismatch_repair_protein_2678183..2678333_POSITIVE 317 69 23 76 31 tfor:TF1326|3end_hypothetical_protein_1404100..1404250_POSITIVE 317 89 41 56 17 tfor:TF0413|3end_succinyl-diaminopimelate_desuccinylase_431869..432019_POSITIVE 316 80 31 119 61 tfor:TF3144|3end_phosphomannomutase/phosphoglucomutase_3381184..3381334_POSITIVE 312 88 41 127 73 tfor:TF1690|3end_chaperone_protein_dnaK_1808721..1808871_POSITIVE 312 98 65 54 26 tfor:TF0699|3end_pyridoxal_phosphate_biosynthetic_protein_742745..742895_POSITIVE 311 90 41 114 68 tfor:TF3053|3end_conserved_hypothetical_protein_3278889..3279039_POSITIVE 311 107 61 59 16 tfor:TF1847|3end_hypothetical_protein_1997666..1997816_POSITIVE 308 95 51 117 74 tfor:TF2347|3end_outer_membrane_protein,_TonB_dependent_receptor_2511092..2511242_POSITIVE 308 120 75 47 6 tfor:TF0323|3end_NAD-dependent_epimerase/dehydratase_family_protein_351053..351203_POSITIVE 307 94 51 66 22 tfor:TF2012|3end_conserved_hypothetical_protein_2168720..2168870_POSITIVE 307 95 53 43 6 tfor:TF1474|3end_6-phosphogluconolactonase_1568123..1568273_POSITIVE 305 79 39 148 116 tfor:TF2673|3end_conserved_hypothetical_protein_2848272..2848422_POSITIVE