Origin IGS: tagtttcctccactcttcattaattgcctcaggatgttttgccgtgaaatctttccggattctttcgtgataaaatcatcttttttgtttttttatcggaaatccatcattcgtatttaaacaattgattatcagctgattgacaagttataaaatgccataagtaatgatttagcgacctatcttctgcaatgacacacaacgctttgcataactcgaataacctattgcaaaggtaatactatctacggagaaagacgaaactttctccgtttttcttttctgacggctctctattcagacagctgattctatttttcatcttaatcgttcattgttgtggcagtcttatttgtgaagactgcctttcatttttttcgctctgtcctctgcg .........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.........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 cgcagaggacagagcgaaaaaaatgaaaggcagtcttcacaaataagactgccacaacaatgaacgattaagatgaaaaatagaatcagctgtctgaatagagagccgtcagaaaagaaaaacggagaaagtttcgtctttctccgtagatagtattacctttgcaataggttattcgagttatgcaaagcgttgtgtgtcattgcagaagataggtcgctaaatcattacttatggcattttataacttgtcaatcagctgataatcaattgtttaaatacgaatgatggatttccgataaaaaaacaaaaaagatgattttatcacgaaagaatccggaaagatttcacggcaaaacatcctgaggcaattaatgaagagtggaggaaacta Mask Tandem Repeat Region ================================================ tagtttcctccactcttcattaattgcctcaggatgttttgccgtgaaatctttccggattctttcgtgataaaatcatcttttttgtttttttatcggaaatccatcattcgtatttaaacaattgattatcagctgattgacaagttataaaatgccataagtaatgatttagcgacctatcttctgcaatgacacacaacgctttgcataactcgaataacctattgcaaaggtaatactatctacggagaaagacgaaactttctccgtttttcttttctgacggctctctattcagacagctgattctatttttcatcttaatcgttcattgttgtggcagtcttatttgtgaagactgcctttcatttttttcgctctgtcctctgcg Find is-nt database================================================ Query_seq: TF3045:TF3046|TF3045:TF3046:two-component system response regulator:hypothetical protein:->->:3274694..3275087 394 tagtttcctccactcttcattaattgcctcaggatgttttgccgtgaaatctttccggattctttcgtgataaaatcatcttttttgtttttttatcggaaatccatcattcgtatttaaacaattgattatcagctgattgacaagttataaaatgccataagtaatgatttagcgacctatcttctgcaatgacacacaacgctttgcataactcgaataacctattgcaaaggtaatactatctacggagaaagacgaaactttctccgtttttcttttctgacggctctctattcagacagctgattctatttttcatcttaatcgttcattgttgtggcagtcttatttgtgaagactgcctttcatttttttcgctctgtcctctgcg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF3045:TF3046|TF3045:TF3046:two-component system response regulator:hypothetical protein:->->:3274694..3275087 394 tagtttcctccactcttcattaattgcctcaggatgttttgccgtgaaatctttccggattctttcgtgataaaatcatcttttttgtttttttatcggaaatccatcattcgtatttaaacaattgattatcagctgattgacaagttataaaatgccataagtaatgatttagcgacctatcttctgcaatgacacacaacgctttgcataactcgaataacctattgcaaaggtaatactatctacggagaaagacgaaactttctccgtttttcttttctgacggctctctattcagacagctgattctatttttcatcttaatcgttcattgttgtggcagtcttatttgtgaagactgcctttcatttttttcgctctgtcctctgcg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF3045:TF3046|TF3045:TF3046:two-component system response regulator:hypothetical protein:->->:3274694..3275087 394 tagtttcctccactcttcattaattgcctcaggatgttttgccgtgaaatctttccggattctttcgtgataaaatcatcttttttgtttttttatcggaaatccatcattcgtatttaaacaattgattatcagctgattgacaagttataaaatgccataagtaatgatttagcgacctatcttctgcaatgacacacaacgctttgcataactcgaataacctattgcaaaggtaatactatctacggagaaagacgaaactttctccgtttttcttttctgacggctctctattcagacagctgattctatttttcatcttaatcgttcattgttgtggcagtcttatttgtgaagactgcctttcatttttttcgctctgtcctctgcg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tagtttcctccactcttcattaattgcctcaggatgttttgccgtgaaatctttccggattctttcgtgataaaatcatcttttttgtttttttatcggaaatccatcattcgtatttaaacaattgattatcagctgattgacaagttataaaatgccataagtaatgatttagcgacctatcttctgcaatgacacacaacgctttgcataactcgaataacctattgcaaaggtaatactatctacggagaaagacgaaactttctccgtttttcttttctgacggctctctattcagacagctgattctatttttcatcttaatcgttcattgttgtggcagtcttatttgtgaagactgcctttcatttttttcgctctgtcctctgcg Predict ORF larger than 30AA ================================================ Protein_Len: 33 Strand: + Start: 19 End: 117 .................. M N C L R M F C R E I F P D S F V I K S S F L F F Y R K S I I R I ..................................................................................................................................................................................................................................................................................... Protein_Len: 32 Strand: + Start: 211 End: 306 .................................................................................................................................................................................................................. M T R I T Y C K G N T I Y G E R R N F L R F S F L T A L Y S D S ........................................................................................ Protein_Len: 41 Strand: - Start: 175 End: 297 .............................................................................................................................................................................. R G I K Q L S V C R K A Y S S Y G I A F T I S D V S F S S V K E T K R K Q R S E M ................................................................................................. Protein_Len: 31 Strand: - Start: 110 End: 202 ............................................................................................................. E Y K F L Q N D A S Q C T I F H W L Y H N L S R D E A I V C M ................................................................................................................................................................................................ tagtttcctccactcttcattaattgcctcaggatgttttgccgtgaaatctttccggattctttcgtgataaaatcatcttttttgtttttttatcggaaatccatcattcgtatttaaacaattgattatcagctgattgacaagttataaaatgccataagtaatgatttagcgacctatcttctgcaatgacacacaacgctttgcataactcgaataacctattgcaaaggtaatactatctacggagaaagacgaaactttctccgtttttcttttctgacggctctctattcagacagctgattctatttttcatcttaatcgttcattgttgtggcagtcttatttgtgaagactgcctttcatttttttcgctctgtcctctgcg 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================================================ tagtttcctccactcttcattaattgcctcaggatgttttgccgtgaaatctttccggattctttcgtgataaaatcatcttttttgtttttttatcggaaatccatcattcgtatttaaacaattgattatcagctgattgacaagttataaaatgccataagtaatgatttagcgacctatcttctgcaatgacacacaacgctttgcataactcgaataacctattgcaaaggtaatactatctacggagaaagacgaaactttctccgtttttcttttctgacggctctctattcagacagctgattctatttttcatcttaatcgttcattgttgtggcagtcttatttgtgaagactgcctttcatttttttcgctctgtcctctgcg Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 100 HP_score: -11.1 Tail_Score: -5.54907 Start: 249 End: 272 Full_Region: AGGTAATACTATCTA CGGAGAAAG ACGAAA CTTTCTCCG TTTTTCTTTTCTGAC ........................................................................................................................................................................................................................................................CGGAGAAAGACGAAACTTTCTCCG.......................................................................................................................... TransTerm Strand: + Conf: 60 HP_score: -2.6 Tail_Score: -4.38154 Start: 253 End: 278 Full_Region: AATACTATCTACGGA GAAAGACGAA ACTTTC TCCGTTTTTC TTTTCTGACGGCTCT ............................................................................................................................................................................................................................................................GAAAGACGAAACTTTCTCCGTTTTTC.................................................................................................................... TransTerm Strand: + Conf: 91 HP_score: -10.1 Tail_Score: -4.5187 Start: 342 End: 366 Full_Region: ATCGTTCATTGTTGT GGCAGTCTT ATTTGTG AAGACTGCC TTTCATTTTTTTCGC .....................................................................................................................................................................................................................................................................................................................................................GGCAGTCTTATTTGTGAAGACTGCC............................ Find igs database================================================ Query_seq: TF3045:TF3046|TF3045:TF3046:two-component system response regulator:hypothetical protein:->->:3274694..3275087 394 tagtttcctccactcttcattaattgcctcaggatgttttgccgtgaaatctttccggattctttcgtgataaaatcatcttttttgtttttttatcggaaatccatcattcgtatttaaacaattgattatcagctgattgacaagttataaaatgccataagtaatgatttagcgacctatcttctgcaatgacacacaacgctttgcataactcgaataacctattgcaaaggtaatactatctacggagaaagacgaaactttctccgtttttcttttctgacggctctctattcagacagctgattctatttttcatcttaatcgttcattgttgtggcagtcttatttgtgaagactgcctttcatttttttcgctctgtcctctgcg Intra-Species Hit: Count: 1 Min: 1 Max: 394 Len: 394 Subject: tfor_TF3045_TF3046|two-component system response regulator:hypothetical protein|POSITIVE:POSITIVE|[3274694,3275087]|394 HSP 1 e-value: 1.0E-156 bit: 553.0 Len: 300 Query Start:95 Query End:394 Subject Strand: POSITIVE Subject Start: 95 Subject End: 394 ..............................................................................................atcggaaatccatcattcgtatttaaacaattgattatcagctgattgacaagttataaaatgccataagtaatgatttagcgacctatcttctgcaatgacacacaacgctttgcataactcgaataacctattgcaaaggtaatactatctacggagaaagacgaaactttctccgtttttcttttctgacggctctctattcagacagctgattctatttttcatcttaatcgttcattgttgtggcagtcttatttgtgaagactgcctttcannnnnnncgctctgtcctctgcg ..............................................................................................atcggaaatccatcattcgtatttaaacaattgattatcagctgattgacaagttataaaatgccataagtaatgatttagcgacctatcttctgcaatgacacacaacgctttgcataactcgaataacctattgcaaaggtaatactatctacggagaaagacgaaactttctccgtttttcttttctgacggctctctattcagacagctgattctatttttcatcttaatcgttcattgttgtggcagtcttatttgtgaagactgcctttcatttttttcgctctgtcctctgcg HSP 2 e-value: 9.0E-38 bit: 159.0 Len: 80 Query Start:1 Query End:80 Subject Strand: POSITIVE Subject Start: 1 Subject End: 80 tagtttcctccactcttcattaattgcctcaggatgttttgccgtgaaatctttccggattctttcgtgataaaatcatc.......................................................................................................................................................................................................................................................................................................................... tagtttcctccactcttcattaattgcctcaggatgttttgccgtgaaatctttccggattctttcgtgataaaatcatc.......................................................................................................................................................................................................................................................................................................................... Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAGUUUCCUCCACUCUUCAUUAAUUGCCUCAGGAUGUUUUGCCGUGAAAUCUUUCCGGAUUCUUUCGUGAUAAAAUCAUCUUUUUUGUUUUUUUAUCGGAAAUCCAUCAUUCGUAUUUAAACAAUUGAUUAUCAGCUGAUUGACAAGUUAUAAAAUGCCAUAAGUAAUGAUUUAGCGACCUAUCUUCUGCAAUGACACACAACGCUUUGCAUAACUCGAAUAACCUAUUGCAAAGGUAAUACUAUCUACGGAGAAAGACGAAACUUUCUCCGUUUUUCUUUUCUGACGGCUCUCUAUUCAGACAGCUGAUUCUAUUUUUCAUCUUAAUCGUUCAUUGUUGUGGCAGUCUUAUUUGUGAAGACUGCCUUUCAUUUUUUUCGCUCUGUCCUCUGCG ..(((...((..((..(.((((((((.....(((((.....(((.(((....))))))....((((.((((((((.((.......))...)))))))))))).....))))).........)))))))).)..))..))..)))...................(((..(((..(((((..........(((((((.((...((.(((((((.................)))))))))..........((((((((((......)))))))))).............(((((.(((....))).))))).....................)))))))))...(((((((((.......)))))))))...........)))))..)))...))). (-82.57) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CGCAGAGGACAGAGCGAAAAAAAUGAAAGGCAGUCUUCACAAAUAAGACUGCCACAACAAUGAACGAUUAAGAUGAAAAAUAGAAUCAGCUGUCUGAAUAGAGAGCCGUCAGAAAAGAAAAACGGAGAAAGUUUCGUCUUUCUCCGUAGAUAGUAUUACCUUUGCAAUAGGUUAUUCGAGUUAUGCAAAGCGUUGUGUGUCAUUGCAGAAGAUAGGUCGCUAAAUCAUUACUUAUGGCAUUUUAUAACUUGUCAAUCAGCUGAUAAUCAAUUGUUUAAAUACGAAUGAUGGAUUUCCGAUAAAAAAACAAAAAAGAUGAUUUUAUCACGAAAGAAUCCGGAAAGAUUUCACGGCAAAACAUCCUGAGGCAAUUAAUGAAGAGUGGAGGAAACUA .((..((((.....((............(((((((((.......))))))))).......(((((((((..(((..........((((((((..(((((((((.(((((.((.((.((...((((((((((......)))))))))).((((.(((.(((((((((.(((.((....)).)))))))))).)).))))))).......................)).)).)).))))).))))))......)))..)))))))).))))))))))))....))..(((....((((((................((((....)))).(....)....))))))....)))..........))))...))................((....)). (-94.20) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 331 305 264 138 96 tfor:TF2043|5end_fructokinase_2202267..2202497_POSITIVE 330 390 342 222 158 tfor:TF2891|5end_lipoprotein_3078762..3078992_POSITIVE 320 309 265 63 5 tfor:TF1793|5end_polyphosphate-selective_porin_O_1933256..1933486_POSITIVE 315 308 264 206 156 tfor:TF2484|5end_hypothetical_protein_2660005..2660235_POSITIVE 315 300 258 35 1 tfor:TF2394|5end_integrase/recombinase_XerD_2565608..2565838_POSITIVE 309 68 25 145 99 tfor:TF1609|5end_hypothetical_protein_1728340..1728570_POSITIVE 307 70 24 69 13 tfor:TF0693|5end_sigma-54_dependent_transcriptional_regulator_736902..737132_POSITIVE 305 68 23 162 109 tfor:TF2952|5end_transposase_3159572..3159802_POSITIVE 305 290 248 173 130 tfor:TF2847|5end_hypothetical_protein_3034744..3034974_POSITIVE 305 289 248 172 131 tfor:TF1429|5end_S-adenosyl-methyltransferase_1513927..1514157_POSITIVE 304 72 32 186 144 tfor:TF1909|5end_cobalamin_(5`-phosphate)_synthase_2063207..2063437_POSITIVE 303 70 27 94 47 tfor:TF0324|5end_conserved_hypothetical_protein_351228..351458_POSITIVE 301 309 269 48 6 tfor:TF2267|5end_lysozyme-related_protein_2434869..2435099_POSITIVE 301 45 1 212 167 tfor:TF2259|5end_transfer_region-related_protein,_TraK_2429577..2429807_POSITIVE 294 78 32 50 2 tfor:TF1661|5end_conserved_hypothetical_protein_1776065..1776295_POSITIVE 293 348 306 186 148 tfor:TF2879|5end_tRNA_(guanine-N-1)-methyltransferase_3068254..3068484_POSITIVE 293 47 15 114 86 tfor:TF0819|5end_phosphoglycerate_mutase_878447..878677_POSITIVE 290 290 245 166 126 tfor:TF1767|5end_3-dehydroquinate_synthase_1905492..1905722_POSITIVE 289 290 256 182 146 tfor:TF2789|5end_enoyl-[acyl-carrier-protein]_reductase_2972431..2972661_POSITIVE 287 68 23 126 77 tfor:TF2892|5end_seryl-tRNA_synthetase_3079309..3079539_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 331 305 264 147 105 tfor:TF2042|3end_sugar_phosphate_isomerase,_polysialic_acid_capsule_expression_protein_2202356..2202506_POSITIVE 330 390 342 68 4 tfor:TF2889|3end_50S_ribosomal_protein_L27_3078688..3078838_POSITIVE 315 308 264 143 93 tfor:TF2483|3end_hypothetical_protein_2660022..2660172_POSITIVE 314 295 251 62 20 tfor:TF2349|3end_conserved_hypothetical_protein_2514921..2515071_POSITIVE 307 70 24 79 23 tfor:TF0692|3end_conserved_hypothetical_protein_736992..737142_POSITIVE 305 68 23 132 79 tfor:TF2951|3end_O-succinylbenzoic_acid--CoA_ligase_3159622..3159772_POSITIVE 305 290 248 106 63 tfor:TF2845|3end_hypothetical_protein_3034757..3034907_POSITIVE 301 309 269 48 6 tfor:TF2266|3end_transfer_region-related_protein,_TraQ_2434949..2435099_POSITIVE 293 348 306 135 97 tfor:TF2878|3end_conserved_hypothetical_protein;_possible_CAAX_amino_terminal_protease_family_3068283..3068433_POSITIVE 293 47 15 104 76 tfor:TF0818|3end_bifunctional_protein:__aspartokinase_I;_homoserine_dehydrogenase_878517..878667_POSITIVE 292 339 292 133 86 tfor:TF2795|3end_hypothetical_protein_2980909..2981059_POSITIVE 287 68 23 118 69 tfor:TF2891|3end_lipoprotein_3079381..3079531_POSITIVE 287 309 264 76 22 tfor:TF2188|3end_conserved_hypothetical_protein_2363535..2363685_POSITIVE 286 62 25 59 21 tfor:TF2439|3end_conserved_hypothetical_protein_2616930..2617080_POSITIVE 283 347 301 79 18 tfor:TF2225|3end_CTn_excision_protein_2395602..2395752_POSITIVE 280 388 342 41 3 tfor:TF0930|3end_conserved_hypothetical_protein;_possible_prophage_protein_969965..970115_POSITIVE 278 42 1 85 30 tfor:TF0874|3end_transposase_926652..926802_POSITIVE 277 387 342 59 25 tfor:TF0095|3end_methyltransferase_106845..106995_POSITIVE 276 80 31 148 102 tfor:TF2081|3end_phosphopantetheine_adenylyltransferase_2249031..2249181_POSITIVE 273 69 22 56 5 tfor:TF2836|3end_methyltransferase_3028028..3028178_POSITIVE