Origin IGS: taaataactcctctggattaccttgtagaactcttggaattctctgggcaaagtatttctattttccaaggggctttaactaattcagaattgaaatataaatagctaaggagtattttattatgttacatactccaactgttttatactccaactgtttttgtaaagaaatttctccgtttcactcatttgcccaaagggg .........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 cccctttgggcaaatgagtgaaacggagaaatttctttacaaaaacagttggagtataaaacagttggagtatgtaacataataaaatactccttagctatttatatttcaattctgaattagttaaagccccttggaaaatagaaatactttgcccagagaattccaagagttctacaaggtaatccagaggagttattta Mask Tandem Repeat Region ================================================ taaataactcctctggattaccttgtagaactcttggaattctctgggcaaagtatttctattttccaaggggctttaactaattcagaattgaaatataaatagctaaggagtattttattatgttacnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnntgtaaagaaatttctccgtttcactcatttgcccaaagggg Find is-nt database================================================ Query_seq: TF0254:TF0255|TF0254:TF0255:hypothetical protein:conserved hypothetical protein:->->:285745..285946 202 taaataactcctctggattaccttgtagaactcttggaattctctgggcaaagtatttctattttccaaggggctttaactaattcagaattgaaatataaatagctaaggagtattttattatgttacatactccaactgttttatactccaactgtttttgtaaagaaatttctccgtttcactcatttgcccaaagggg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF0254:TF0255|TF0254:TF0255:hypothetical protein:conserved hypothetical protein:->->:285745..285946 202 taaataactcctctggattaccttgtagaactcttggaattctctgggcaaagtatttctattttccaaggggctttaactaattcagaattgaaatataaatagctaaggagtattttattatgttacatactccaactgttttatactccaactgtttttgtaaagaaatttctccgtttcactcatttgcccaaagggg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF0254:TF0255|TF0254:TF0255:hypothetical protein:conserved hypothetical protein:->->:285745..285946 202 taaataactcctctggattaccttgtagaactcttggaattctctgggcaaagtatttctattttccaaggggctttaactaattcagaattgaaatataaatagctaaggagtattttattatgttacatactccaactgttttatactccaactgtttttgtaaagaaatttctccgtttcactcatttgcccaaagggg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 taaataactcctctggattaccttgtagaactcttggaattctctgggcaaagtatttctattttccaaggggctttaactaattcagaattgaaatataaatagctaaggagtattttattatgttacatactccaactgttttatactccaactgtttttgtaaagaaatttctccgtttcactcatttgcccaaagggg Predict ORF larger than 30AA ================================================ Protein_Len: 33 Strand: + Start: 4 End: 102 ... M T P L D Y L V E L L E F S G Q S I S I F Q G A L T N S E L K Y K .................................................................................................... Protein_Len: 33 Strand: + Start: 102 End: 200 ..................................................................................................... M A K E Y F I M L H T P T V L Y S N C F C K E I S P F H S F A Q R .. Protein_Len: 30 Strand: - Start: 83 End: 172 .................................................................................. N L I S I Y I A L S Y K I I N C V G V T K Y E L Q K Q L S M .............................. Protein_Len: 32 Strand: - Start: 21 End: 116 .................... R T S S K S N E P C L I E I K W P A K V L E S N F Y L Y S L L M ...................................................................................... taaataactcctctggattaccttgtagaactcttggaattctctgggcaaagtatttctattttccaaggggctttaactaattcagaattgaaatataaatagctaaggagtattttattatgttacatactccaactgttttatactccaactgtttttgtaaagaaatttctccgtttcactcatttgcccaaagggg Predict Promoter with matrix: RpoD-15 score > 80================================================ Predict Promoter with matrix: RpoD-16 score > 80================================================ Predict Promoter with matrix: RpoD-17 score > 80================================================ PromScan Matrix: RpoD-17 Strand: + Score: 82 Start: 90 End: 119 .........................................................................................ATTGAAATATAAATAGCTAAGGAGTATTTT................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ taaataactcctctggattaccttgtagaactcttggaattctctgggcaaagtatttctattttccaaggggctttaactaattcagaattgaaatataaatagctaaggagtattttattatgttacatactccaactgttttatactccaactgtttttgtaaagaaatttctccgtttcactcatttgcccaaagggg Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 44 HP_score: -2.3 Tail_Score: -3.28393 Start: 110 End: 136 Full_Region: gagtataaaacagtt ggagtatgtaa cataa taaaatactcc ttagctatttatatt .............................................................................................................ggagtatgtaacataataaaatactcc.................................................................. Find igs database================================================ Query_seq: TF0254:TF0255|TF0254:TF0255:hypothetical protein:conserved hypothetical protein:->->:285745..285946 202 taaataactcctctggattaccttgtagaactcttggaattctctgggcaaagtatttctattttccaaggggctttaactaattcagaattgaaatataaatagctaaggagtattttattatgttacatactccaactgttttatactccaactgtttttgtaaagaaatttctccgtttcactcatttgcccaaagggg Intra-Species Hit: Count: 1 Min: 1 Max: 202 Len: 202 Subject: tfor_TF0254_TF0255|hypothetical protein:conserved hypothetical protein|POSITIVE:POSITIVE|[285745,285946]|202 HSP 1 e-value: 1.0E-111 bit: 400.0 Len: 202 Query Start:1 Query End:202 Subject Strand: POSITIVE Subject Start: 1 Subject End: 202 taaataactcctctggattaccttgtagaactcttggaattctctgggcaaagtatttctattttccaaggggctttaactaattcagaattgaaatataaatagctaaggagtattttattatgttacatactccaactgttttatactccaactgtttttgtaaagaaatttctccgtttcactcatttgcccaaagggg taaataactcctctggattaccttgtagaactcttggaattctctgggcaaagtatttctattttccaaggggctttaactaattcagaattgaaatataaatagctaaggagtattttattatgttacatactccaactgttttatactccaactgtttttgtaaagaaatttctccgtttcactcatttgcccaaagggg Inter-species Hit: Count: 1 Min: 1 Max: 181 Len: 181 Subject: NC_002967_TDE2330_TDE2332|hypothetical protein:hypothetical protein|POSITIVE:NEGATIVE|[2366759,2367627]|869 HSP 1 e-value: 2.0E-74 bit: 280.0 Len: 145 Query Start:1 Query End:145 Subject Strand: NEGATIVE Subject Start: 21 Subject End: 165 taaataactcctctggattaccttgtagaactcttggaattctctgggcaaagtatttctattttccaaggggctttaactaattcagaattgaaatataaatagctaaggagtattttattatgttacatactccaactgtttt......................................................... taaataactcctctggattaccttgtagaactcttggaattctctgggcaaagtatttctattttccaaggggctttaactaattcaggattgaaatataaatagctaaggagtattttattatgttacatactccaactgtttt......................................................... HSP 2 e-value: 8.0E-12 bit: 71.9 Len: 36 Query Start:146 Query End:181 Subject Strand: NEGATIVE Subject Start: 1 Subject End: 36 .................................................................................................................................................atactccaactgtttttgtaaagaaatttctccgtt..................... .................................................................................................................................................atactccaactgtttttgtaaagaaatttctccgtt..................... Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAAUAACUCCUCUGGAUUACCUUGUAGAACUCUUGGAAUUCUCUGGGCAAAGUAUUUCUAUUUUCCAAGGGGCUUUAACUAAUUCAGAAUUGAAAUAUAAAUAGCUAAGGAGUAUUUUAUUAUGUUACAUACUCCAACUGUUUUAUACUCCAACUGUUUUUGUAAAGAAAUUUCUCCGUU ...........(((((((((.....((((.(((((((((.....((((.........))))..)))))))))..))))..)))))))))......(((.((((((....(((((((...((...(((.........))).))...)))))))..)))))).)))................. (-31.70) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AACGGAGAAAUUUCUUUACAAAAACAGUUGGAGUAUAAAACAGUUGGAGUAUGUAACAUAAUAAAAUACUCCUUAGCUAUUUAUAUUUCAAUUCUGAAUUAGUUAAAGCCCCUUGGAAAAUAGAAAUACUUUGCCCAGAGAAUUCCAAGAGUUCUACAAGGUAAUCCAGAGGAGUUAUUUA ...(((((....))))).......(((((((((((((((..(((((((((((.............)))))))..)))).))))))))))))..)))..........(((((.(((((...((....))..(((((...(((((((...)))))))....)))))))))).)).)))..... (-40.22) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 306 49 8 118 80 tfor:TF1814|5end_conserved_hypothetical_protein;_possible_biotin_synthase_related_domain_containing_protein_1955325..1955555_POSITIVE 292 51 14 211 172 tfor:TF1760|5end_guanosine-3',5'-bis(diphosphate)_3'-pyrophosphohydrolase_1897081..1897311_POSITIVE 284 59 13 57 17 tfor:TF2114|5end_1-hydroxy-2-methyl-2-(E)-butenyl_4-diphosphate_synthase,_GcpE_2283006..2283236_POSITIVE 280 76 31 87 39 tfor:TF1710|5end_possible_cell_filamentation_protein_1829679..1829909_POSITIVE 280 74 36 158 125 tfor:TF0451|5end_rhomboid_family_membrane_protein_470085..470315_POSITIVE 279 46 10 93 55 tfor:TF2793|5end_possible_L-lysine_2,3-aminomutase_2977661..2977891_POSITIVE 277 68 21 90 24 tfor:TF1523|5end_hypothetical_protein_1630273..1630503_POSITIVE 267 50 13 221 166 tfor:TF0587|5end_outer_membrane_protein_618319..618549_POSITIVE 263 49 10 169 123 tfor:TF0414|5end_N-ethylammeline_chlorohydrolase_431789..432019_POSITIVE 260 180 145 86 46 tfor:TF2236|5end_two-component_system_histidine_kinase_involved_in_CTn_2410183..2410413_POSITIVE 258 42 11 160 125 tfor:TF1531|5end_potassium_uptake_protein_1636534..1636764_POSITIVE 257 59 11 230 182 tfor:TF3055|5end_hypothetical_protein_3278775..3279005_POSITIVE 255 179 138 55 12 tfor:TF2511|5end_RNA_binding_protein_2689910..2690140_POSITIVE 254 59 11 56 11 tfor:TF1618|5end_conserved_hypothetical_protein_1733435..1733665_POSITIVE 252 60 13 207 158 tfor:TF2450|5end_outer_membrane_protein_2626471..2626701_POSITIVE 252 70 24 166 112 tfor:TF0927|5end_conserved_hypothetical_protein;_possible_ATPase_of_the_AAA_superfamily_963456..963686_POSITIVE 249 97 53 92 30 tfor:TF1790|5end_conserved_hypothetical_protein_1931227..1931457_POSITIVE 248 50 6 211 160 tfor:TF1793|5end_polyphosphate-selective_porin_O_1933256..1933486_POSITIVE 246 77 36 126 83 tfor:TF2469|5end_oxidoreductase,_possible_Gfo/Idh/MocA_family_2646505..2646735_POSITIVE 245 50 4 229 185 tfor:TF2729|5end_possible_outer_membrane_protein_2908216..2908446_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 284 59 13 57 17 tfor:TF2113|3end_phosphoribosylaminoimidazole_carboxylase_2283086..2283236_POSITIVE 275 68 28 55 2 tfor:TF1522|3end_hypothetical_protein_1630318..1630468_POSITIVE 260 180 145 83 43 tfor:TF2235|3end_tetracycline_resistance_protein_related_to_CtnDOT_tetQ_2410260..2410410_POSITIVE 251 59 27 31 1 tfor:TF1617|3end_conserved_hypothetical_protein;_possible_methyltransferase_1733490..1733640_POSITIVE 246 77 36 123 80 tfor:TF2468|3end_hypothetical_protein_2646582..2646732_POSITIVE 244 76 31 103 67 tfor:TF0911|3end_transposase_954297..954447_POSITIVE 240 45 6 53 12 tfor:TF3120|3end_HD_superfamily_hydrolase_3354775..3354925_POSITIVE 240 66 30 82 44 tfor:TF2765|3end_subtilisin-like_serine_protease_2951460..2951610_POSITIVE 239 73 31 138 92 tfor:TF2816|3end_hypothetical_protein_3007184..3007334_POSITIVE 237 60 11 68 15 tfor:TF1367|3end_hypothetical_protein_1447272..1447422_POSITIVE 237 60 11 64 11 tfor:TF1368|3end_hypothetical_protein_1447268..1447418_POSITIVE 235 28 2 76 46 tfor:TF3087|3end_conserved_hypothetical_protein_3322582..3322732_POSITIVE 232 60 14 58 15 tfor:TF0522|3end_hypothetical_protein_547873..548023_POSITIVE 232 60 14 80 37 tfor:TF0521|3end_hypothetical_protein_547895..548045_POSITIVE 231 60 11 68 15 tfor:TF1382|3end_hypothetical_protein_1457777..1457927_POSITIVE 231 60 11 64 11 tfor:TF1383|3end_hypothetical_protein_1457773..1457923_POSITIVE 230 49 10 52 13 tfor:TF1680|3end_peptide_chain_release_factor_3_1794969..1795119_POSITIVE 227 49 4 149 77 tfor:TF1108|3end_conserved_hypothetical_protein;_possible_lipoprotein_1178851..1179001_POSITIVE 227 88 45 133 92 tfor:TF0515|3end_conserved_hypothetical_protein_539575..539725_POSITIVE 224 74 48 104 78 tfor:TF0861|3end_HAD-superfamily_hydrolase,_subfamily_IA,_variant_1_family_protein_914122..914272_POSITIVE