Origin IGS: agactaccatttagggtggtgaaaaaggcactccactttcatcaggaatatgtctgtgaaatcatccttgaaactctatccgatgtccaaaaattaccaattattaacatgtgtaaaaatattactacaattcatttgtacacaaatgattactatactaaaatgtccgattttgatagttccctcccatcgtttcacctttaattttgcagcaaaaaaacagacttgtcgcaccttctggcaacggctcatgggtatcttcacaagctgcctattataattaagagacctctgcaaaactctattcaaatgtcgaatctatgggtataacttgttgattataatagtggtgttttgttgtaaaaagacttttgcaaaggtcttaataaggtatgtgaggcaagacgacaatatcattaactctttta .........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 taaaagagttaatgatattgtcgtcttgcctcacataccttattaagacctttgcaaaagtctttttacaacaaaacaccactattataatcaacaagttatacccatagattcgacatttgaatagagttttgcagaggtctcttaattataataggcagcttgtgaagatacccatgagccgttgccagaaggtgcgacaagtctgtttttttgctgcaaaattaaaggtgaaacgatgggagggaactatcaaaatcggacattttagtatagtaatcatttgtgtacaaatgaattgtagtaatatttttacacatgttaataattggtaatttttggacatcggatagagtttcaaggatgatttcacagacatattcctgatgaaagtggagtgcctttttcaccaccctaaatggtagtct Mask Tandem Repeat Region ================================================ agactaccatttagggtggtgaaaaaggcactccactttcatcaggaatatgtctgtgaaatcatccttgaaactctatccgatgtccaaaaattaccaattattaacatgtgtaaaaatattactacaattcatttgtacacaaatgattactatactaaaatgtccgattttgatagttccctcccatcgtttcacctttaattttgcagcaaaaaaacagacttgtcgcaccttctggcaacggctcatgggtatcttcacaagctgcctattataattaagagacctctgcaaaactctattcaaatgtcgaatctatgggtataacttgttgattataatagtggtgttttgttgtaaaaagacttttgcaaaggtcttaataaggtatgtgaggcaagacgacaatatcattaactctttta Find is-nt database================================================ Query_seq: TF2894:TF2895|TF2894:TF2895:conserved hypothetical protein; possible Fic family protein:hypothetical protein:->->:3083648..3084075 428 agactaccatttagggtggtgaaaaaggcactccactttcatcaggaatatgtctgtgaaatcatccttgaaactctatccgatgtccaaaaattaccaattattaacatgtgtaaaaatattactacaattcatttgtacacaaatgattactatactaaaatgtccgattttgatagttccctcccatcgtttcacctttaattttgcagcaaaaaaacagacttgtcgcaccttctggcaacggctcatgggtatcttcacaagctgcctattataattaagagacctctgcaaaactctattcaaatgtcgaatctatgggtataacttgttgattataatagtggtgttttgttgtaaaaagacttttgcaaaggtcttaataaggtatgtgaggcaagacgacaatatcattaactctttta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF2894:TF2895|TF2894:TF2895:conserved hypothetical protein; possible Fic family protein:hypothetical protein:->->:3083648..3084075 428 agactaccatttagggtggtgaaaaaggcactccactttcatcaggaatatgtctgtgaaatcatccttgaaactctatccgatgtccaaaaattaccaattattaacatgtgtaaaaatattactacaattcatttgtacacaaatgattactatactaaaatgtccgattttgatagttccctcccatcgtttcacctttaattttgcagcaaaaaaacagacttgtcgcaccttctggcaacggctcatgggtatcttcacaagctgcctattataattaagagacctctgcaaaactctattcaaatgtcgaatctatgggtataacttgttgattataatagtggtgttttgttgtaaaaagacttttgcaaaggtcttaataaggtatgtgaggcaagacgacaatatcattaactctttta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF2894:TF2895|TF2894:TF2895:conserved hypothetical protein; possible Fic family protein:hypothetical protein:->->:3083648..3084075 428 agactaccatttagggtggtgaaaaaggcactccactttcatcaggaatatgtctgtgaaatcatccttgaaactctatccgatgtccaaaaattaccaattattaacatgtgtaaaaatattactacaattcatttgtacacaaatgattactatactaaaatgtccgattttgatagttccctcccatcgtttcacctttaattttgcagcaaaaaaacagacttgtcgcaccttctggcaacggctcatgggtatcttcacaagctgcctattataattaagagacctctgcaaaactctattcaaatgtcgaatctatgggtataacttgttgattataatagtggtgttttgttgtaaaaagacttttgcaaaggtcttaataaggtatgtgaggcaagacgacaatatcattaactctttta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 agactaccatttagggtggtgaaaaaggcactccactttcatcaggaatatgtctgtgaaatcatccttgaaactctatccgatgtccaaaaattaccaattattaacatgtgtaaaaatattactacaattcatttgtacacaaatgattactatactaaaatgtccgattttgatagttccctcccatcgtttcacctttaattttgcagcaaaaaaacagacttgtcgcaccttctggcaacggctcatgggtatcttcacaagctgcctattataattaagagacctctgcaaaactctattcaaatgtcgaatctatgggtataacttgttgattataatagtggtgttttgttgtaaaaagacttttgcaaaggtcttaataaggtatgtgaggcaagacgacaatatcattaactctttta Predict ORF larger than 30AA ================================================ Protein_Len: 60 Strand: + Start: 16 End: 201 ............... M V K K A L H F H Q E Y V C E I I L E T L S D V Q K L P I I N M C K N I T T I H L Y T N D Y Y T K M S D F D S S L P S F ................................................................................................................................................................................................................................... Protein_Len: 60 Strand: + Start: 41 End: 277 ........................................ M R N M S V K S S L K L Y P M S K N Y Q L L T C V K I L L Q F I C T Q M I T I L K C P I L I V P S H R F T F N F A A K K ....................................................................................................................................................... Protein_Len: 31 Strand: + Start: 189 End: 281 ............................................................................................................................................................................................ M V S P L I L Q Q K N R L V A P S G N G S W V S S Q A A Y Y N ................................................................................................................................................... Protein_Len: 34 Strand: + Start: 226 End: 327 ................................................................................................................................................................................................................................. M S H L L A T A H G Y L H K L P I I I K R P L Q N S I Q M S N L W V ..................................................................................................... Protein_Len: 37 Strand: + Start: 317 End: 427 ............................................................................................................................................................................................................................................................................................................................ M Y G Y N L L I I I V V F C C K K T F A K V L I R Y V R Q D D N I I N S F . Protein_Len: 32 Strand: - Start: 322 End: 417 ................................................................................................................................................................................................................................................................................................................................. P Y L K N I I I T T N Q Q L F V K A F T K I L Y T L C S S L I M ........... Protein_Len: 60 Strand: - Start: 97 End: 318 ................................................................................................ V C I I V I S F H G I K I T G E W R K V K L K A A F F C V Q R V K Q C R S M P I K V L Q R N Y N L S R Q L V R N L H R M .............................................................................................................. agactaccatttagggtggtgaaaaaggcactccactttcatcaggaatatgtctgtgaaatcatccttgaaactctatccgatgtccaaaaattaccaattattaacatgtgtaaaaatattactacaattcatttgtacacaaatgattactatactaaaatgtccgattttgatagttccctcccatcgtttcacctttaattttgcagcaaaaaaacagacttgtcgcaccttctggcaacggctcatgggtatcttcacaagctgcctattataattaagagacctctgcaaaactctattcaaatgtcgaatctatgggtataacttgttgattataatagtggtgttttgttgtaaaaagacttttgcaaaggtcttaataaggtatgtgaggcaagacgacaatatcattaactctttta 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: 81 Start: 338 End: 367 .................................................................................................................................................................................................................................................................................................................................................CTTTTTACAACAAAACACCACTATTATAAT............................................................. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ agactaccatttagggtggtgaaaaaggcactccactttcatcaggaatatgtctgtgaaatcatccttgaaactctatccgatgtccaaaaattaccaattattaacatgtgtaaaaatattactacaattcatttgtacacaaatgattactatactaaaatgtccgattttgatagttccctcccatcgtttcacctttaattttgcagcaaaaaaacagacttgtcgcaccttctggcaacggctcatgggtatcttcacaagctgcctattataattaagagacctctgcaaaactctattcaaatgtcgaatctatgggtataacttgttgattataatagtggtgttttgttgtaaaaagacttttgcaaaggtcttaataaggtatgtgaggcaagacgacaatatcattaactctttta Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TF2894:TF2895|TF2894:TF2895:conserved hypothetical protein; possible Fic family protein:hypothetical protein:->->:3083648..3084075 428 agactaccatttagggtggtgaaaaaggcactccactttcatcaggaatatgtctgtgaaatcatccttgaaactctatccgatgtccaaaaattaccaattattaacatgtgtaaaaatattactacaattcatttgtacacaaatgattactatactaaaatgtccgattttgatagttccctcccatcgtttcacctttaattttgcagcaaaaaaacagacttgtcgcaccttctggcaacggctcatgggtatcttcacaagctgcctattataattaagagacctctgcaaaactctattcaaatgtcgaatctatgggtataacttgttgattataatagtggtgttttgttgtaaaaagacttttgcaaaggtcttaataaggtatgtgaggcaagacgacaatatcattaactctttta Intra-Species Hit: Count: 1 Min: 1 Max: 428 Len: 428 Subject: tfor_TF2894_TF2895|conserved hypothetical protein; possible Fic family protein:hypothetical protein|POSITIVE:POSITIVE|[3083648,3084075]|428 HSP 1 e-value: 0.0 bit: 807.0 Len: 428 Query Start:1 Query End:428 Subject Strand: POSITIVE Subject Start: 1 Subject End: 428 agactaccatttagggtggtgaaaaaggcactccactttcatcaggaatatgtctgtgaaatcatccttgaaactctatccgatgtccaaaaattaccaattattaacatgtgtaaaaatattactacaattcatttgtacacaaatgattactatactaaaatgtccgattttgatagttccctcccatcgtttcacctttaattttgcagcnnnnnnncagacttgtcgcaccttctggcaacggctcatgggtatcttcacaagctgcctattataattaagagacctctgcaaaactctattcaaatgtcgaatctatgggtataacttgttgattataatagtggtgttttgttgtaaaaagacttttgcaaaggtcttaataaggtatgtgaggcaagacgacaatatcattaactctttta agactaccatttagggtggtgaaaaaggcactccactttcatcaggaatatgtctgtgaaatcatccttgaaactctatccgatgtccaaaaattaccaattattaacatgtgtaaaaatattactacaattcatttgtacacaaatgattactatactaaaatgtccgattttgatagttccctcccatcgtttcacctttaattttgcagcaaaaaaacagacttgtcgcaccttctggcaacggctcatgggtatcttcacaagctgcctattataattaagagacctctgcaaaactctattcaaatgtcgaatctatgggtataacttgttgattataatagtggtgttttgttgtaaaaagacttttgcaaaggtcttaataaggtatgtgaggcaagacgacaatatcattaactctttta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGACUACCAUUUAGGGUGGUGAAAAAGGCACUCCACUUUCAUCAGGAAUAUGUCUGUGAAAUCAUCCUUGAAACUCUAUCCGAUGUCCAAAAAUUACCAAUUAUUAACAUGUGUAAAAAUAUUACUACAAUUCAUUUGUACACAAAUGAUUACUAUACUAAAAUGUCCGAUUUUGAUAGUUCCCUCCCAUCGUUUCACCUUUAAUUUUGCAGCAAAAAAACAGACUUGUCGCACCUUCUGGCAACGGCUCAUGGGUAUCUUCACAAGCUGCCUAUUAUAAUUAAGAGACCUCUGCAAAACUCUAUUCAAAUGUCGAAUCUAUGGGUAUAACUUGUUGAUUAUAAUAGUGGUGUUUUGUUGUAAAAAGACUUUUGCAAAGGUCUUAAUAAGGUAUGUGAGGCAAGACGACAAUAUCAUUAACUCUUUUA ..((((((......))))))..((((((...(((..........)))...((.(((..((((......((((((.......((((......(((((.(((......((((((((((.....)))).))...(((((((....))))))).............))))......))).)))))......))))))))))......))))..)))))........((.((((((.((((.(((....))).....))))..(((((((...(((((((((........((((((.(((((((.(((............((((.(..((.....))..).))))...((((..(....)..))))....))).))))))).)))))))))).)))))))))))).....))))))..))......)))))). (-87.11) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAAAGAGUUAAUGAUAUUGUCGUCUUGCCUCACAUACCUUAUUAAGACCUUUGCAAAAGUCUUUUUACAACAAAACACCACUAUUAUAAUCAACAAGUUAUACCCAUAGAUUCGACAUUUGAAUAGAGUUUUGCAGAGGUCUCUUAAUUAUAAUAGGCAGCUUGUGAAGAUACCCAUGAGCCGUUGCCAGAAGGUGCGACAAGUCUGUUUUUUUGCUGCAAAAUUAAAGGUGAAACGAUGGGAGGGAACUAUCAAAAUCGGACAUUUUAGUAUAGUAAUCAUUUGUGUACAAAUGAAUUGUAGUAAUAUUUUUACACAUGUUAAUAAUUGGUAAUUUUUGGACAUCGGAUAGAGUUUCAAGGAUGAUUUCACAGACAUAUUCCUGAUGAAAGUGGAGUGCCUUUUUCACCACCCUAAAUGGUAGUCU ..((((((.....(((.(((((((...(((((.............((((((((((((((.(((..................((((((((((......))))))...)))).(((((...))))).))).)))))))))))))).............(((((((..((........))..)))...)))).).))))))))))))))...))))))(((((.........((((((.(((((...(((((.((((((.....(((((.....((((((..(((((((....)))))))))))))((((.....))))..))))).....)))))).)))))...)))))...........((((...(((((((...(((.......)))...))))))).)))).))))))..........))))).. (-100.11) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 362 269 222 54 3 tfor:TF1951|5end_xanthosine_triphosphate_pyrophosphatase,_Ham1-like_protein_2100792..2101022_POSITIVE 348 272 231 211 178 tfor:TF2775|5end_conserved_hypothetical_protein;_possible_mucoidy_inhibitor-related_protein_2959668..2959898_POSITIVE 327 263 221 66 13 tfor:TF0298|5end_dipeptidase_323127..323357_POSITIVE 326 272 232 176 141 tfor:TF2261|5end_transfer_region-related_protein,_TraM_2430496..2430726_POSITIVE 320 270 225 51 2 tfor:TF0944|5end_TonB-dependent_receptor_986340..986570_POSITIVE 319 272 234 223 178 tfor:TF1191|5end_possible_transcriptional_regulator_1273615..1273845_POSITIVE 316 267 226 230 197 tfor:TF2822|5end_arginine_repressor_3011793..3012023_POSITIVE 314 256 212 69 16 tfor:TF0923|5end_tetracycline_resistance_element_mobilization_regulatory_protein_961256..961486_POSITIVE 314 270 222 98 31 tfor:TF0310|5end_conserved_hypothetical_protein_334685..334915_POSITIVE 313 270 222 182 124 tfor:TF0352|5end_transposase_element_371223..371453_POSITIVE 304 270 226 192 148 tfor:TF2357|5end_collagenase_2522561..2522791_POSITIVE 304 270 221 212 162 tfor:TF0265|5end_conserved_hypothetical_protein,_Rhs_family_293279..293509_POSITIVE 303 250 207 216 158 tfor:TF3149|5end_conserved_hypothetical_protein_3384424..3384654_POSITIVE 303 262 225 165 122 tfor:TF2256|5end_transfer_region-related_protein,_TraI_2427908..2428138_POSITIVE 303 270 224 156 81 tfor:TF2043|5end_fructokinase_2202267..2202497_POSITIVE 303 270 222 215 167 tfor:TF1447|5end_D-ribulose-phosphate-3_epimerase_1530977..1531207_POSITIVE 302 269 221 204 127 tfor:TF1610|5end_peptide_chain_release_factor_RF-2_1728635..1728865_POSITIVE 302 269 221 138 61 tfor:TF1612|5end_conserved_hypothetical_protein_1728569..1728799_POSITIVE 300 270 225 231 174 tfor:TF1793|5end_polyphosphate-selective_porin_O_1933256..1933486_POSITIVE 300 262 226 188 149 tfor:TF1768|5end_conserved_hypothetical_protein;_possible_transposase_1906526..1906756_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 327 269 230 46 8 tfor:TF0095|3end_methyltransferase_106845..106995_POSITIVE 319 270 222 148 103 tfor:TF2913|3end_conserved_hypothetical_protein_3109117..3109267_POSITIVE 314 270 222 108 41 tfor:TF0309|3end_conserved_hypothetical_protein_334775..334925_POSITIVE 313 270 222 105 47 tfor:TF0351|3end_hypothetical_protein_371226..371376_POSITIVE 303 262 225 138 95 tfor:TF2255|3end_transfer_region-related_protein,_TraH_2427961..2428111_POSITIVE 303 278 239 87 52 tfor:TF0242|3end_conserved_hypothetical_protein_274069..274219_POSITIVE 302 269 221 109 32 tfor:TF1609|3end_hypothetical_protein_1728620..1728770_POSITIVE 298 271 234 77 34 tfor:TF0535|3end_surface_antigen_BspA_561701..561851_POSITIVE 293 267 230 132 91 tfor:TF2609|3end_dipeptidase,_pathogenicity_island-encoded_protein_D_2786264..2786414_POSITIVE 293 270 229 139 95 tfor:TF2386|3end_beta-galactosidase_2554449..2554599_POSITIVE 293 270 230 124 83 tfor:TF2204|3end_conserved_hypothetical_protein_2379122..2379272_POSITIVE 288 213 172 72 29 tfor:TF2575|3end_methionine_aminopeptidase_2745985..2746135_POSITIVE 284 277 231 50 12 tfor:TF1113|3end_possible_transposase_1185007..1185157_POSITIVE 283 255 212 73 24 tfor:TF2847|3end_hypothetical_protein_3034985..3035135_POSITIVE 283 256 212 92 42 tfor:TF1449|3end_RNA_polymerase_sigma_factor,_RpoD_1534061..1534211_POSITIVE 283 198 156 135 94 tfor:TF0117|3end_2-dehydro-3-deoxygluconokinase_129808..129958_POSITIVE 282 277 231 56 8 tfor:TF3071|3end_integral_membrane_protein,_possible_MotA/TolQ/ExbB_proton_channel_family_3295382..3295532_POSITIVE 282 270 226 75 36 tfor:TF2188|3end_conserved_hypothetical_protein_2363535..2363685_POSITIVE 281 272 231 144 95 tfor:TF3120|3end_HD_superfamily_hydrolase_3354775..3354925_POSITIVE 280 248 208 141 92 tfor:TF2928|3end_predicted_DNA_repair__protein_3131439..3131589_POSITIVE