Origin IGS: taagatagccttataccatacaaaccaaatcgagtaggaggaaaacgtcttcctactcgatttactataaaacatatcaaaccaaattgtttgctgttttggaatgaagagactttctctatattaacaaatccagtaatgaaacaacgcattgatttaagatgatctttctcagcggtattccattatgaatcgcgttttattctaccatcctttccaaacgattacgggctgttctttgggcgctttttctc .........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 gagaaaaagcgcccaaagaacagcccgtaatcgtttggaaaggatggtagaataaaacgcgattcataatggaataccgctgagaaagatcatcttaaatcaatgcgttgtttcattactggatttgttaatatagagaaagtctcttcattccaaaacagcaaacaatttggtttgatatgttttatagtaaatcgagtaggaagacgttttcctcctactcgatttggtttgtatggtataaggctatctta Mask Tandem Repeat Region ================================================ taagatagccttataccatacaaaccaaatcgagtaggaggaaaacgtcttcctactcgatttactataaaacatatcaaaccaaattgtttgctgttttggaatgaagagactttctctatattaacaaatccagtaatgaaacaacgcattgatttaagatgatctttctcagcggtattccattatgaatcgcgttttattctaccatcctttccaaacgattacgggctgttctttgggcgctttttctc Find is-nt database================================================ Query_seq: TF2295:TF2296|TF2295:TF2296:hypothetical protein:hypothetical protein:->->:2448778..2449031 254 taagatagccttataccatacaaaccaaatcgagtaggaggaaaacgtcttcctactcgatttactataaaacatatcaaaccaaattgtttgctgttttggaatgaagagactttctctatattaacaaatccagtaatgaaacaacgcattgatttaagatgatctttctcagcggtattccattatgaatcgcgttttattctaccatcctttccaaacgattacgggctgttctttgggcgctttttctc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF2295:TF2296|TF2295:TF2296:hypothetical protein:hypothetical protein:->->:2448778..2449031 254 taagatagccttataccatacaaaccaaatcgagtaggaggaaaacgtcttcctactcgatttactataaaacatatcaaaccaaattgtttgctgttttggaatgaagagactttctctatattaacaaatccagtaatgaaacaacgcattgatttaagatgatctttctcagcggtattccattatgaatcgcgttttattctaccatcctttccaaacgattacgggctgttctttgggcgctttttctc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF2295:TF2296|TF2295:TF2296:hypothetical protein:hypothetical protein:->->:2448778..2449031 254 taagatagccttataccatacaaaccaaatcgagtaggaggaaaacgtcttcctactcgatttactataaaacatatcaaaccaaattgtttgctgttttggaatgaagagactttctctatattaacaaatccagtaatgaaacaacgcattgatttaagatgatctttctcagcggtattccattatgaatcgcgttttattctaccatcctttccaaacgattacgggctgttctttgggcgctttttctc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 taagatagccttataccatacaaaccaaatcgagtaggaggaaaacgtcttcctactcgatttactataaaacatatcaaaccaaattgtttgctgttttggaatgaagagactttctctatattaacaaatccagtaatgaaacaacgcattgatttaagatgatctttctcagcggtattccattatgaatcgcgttttattctaccatcctttccaaacgattacgggctgttctttgggcgctttttctc Predict ORF larger than 30AA ================================================ Protein_Len: 50 Strand: + Start: 13 End: 162 ............ M P Y K P N R V G G K R L P T R F T I K H I K P N C L L F W N E E T F S I L T N P V M K Q R I D L R ............................................................................................ Protein_Len: 50 Strand: - Start: 3 End: 152 .. S L R I G Y L G F R T P P F R R G V R N V I F C I L G F Q K S N Q F S S V K E I N V F G T I F C R M ...................................................................................................... Protein_Len: 35 Strand: - Start: 1 End: 105 L I A K Y W V F W I S Y S S F T K R S S K S Y F M D F W I T Q Q K P M ..................................................................................................................................................... taagatagccttataccatacaaaccaaatcgagtaggaggaaaacgtcttcctactcgatttactataaaacatatcaaaccaaattgtttgctgttttggaatgaagagactttctctatattaacaaatccagtaatgaaacaacgcattgatttaagatgatctttctcagcggtattccattatgaatcgcgttttattctaccatcctttccaaacgattacgggctgttctttgggcgctttttctc 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================================================ taagatagccttataccatacaaaccaaatcgagtaggaggaaaacgtcttcctactcgatttactataaaacatatcaaaccaaattgtttgctgttttggaatgaagagactttctctatattaacaaatccagtaatgaaacaacgcattgatttaagatgatctttctcagcggtattccattatgaatcgcgttttattctaccatcctttccaaacgattacgggctgttctttgggcgctttttctc Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 93 HP_score: -14.1 Tail_Score: -3.0636 Start: 26 End: 64 Full_Region: tgatatgttttatag taaatcgagtaggaaga cgttt tcctcctactcgatttg gtttgtatggtataa .........................taaatcgagtaggaagacgttttcctcctactcgatttg.............................................................................................................................................................................................. TransTerm Strand: + Conf: 100 HP_score: -14.9 Tail_Score: -3.83205 Start: 30 End: 60 Full_Region: ACCATACAAACCAAA TCGAGTAGGAGGA AAACG TCTTCCTACTCGA TTTACTATAAAACAT .............................TCGAGTAGGAGGAAAACGTCTTCCTACTCGA.................................................................................................................................................................................................. TransTerm Strand: - Conf: 100 HP_score: -12.7 Tail_Score: -4.18644 Start: 30 End: 60 Full_Region: atgttttatagtaaa tcgagtaggaaga cgttt tcctcctactcga tttggtttgtatggt .............................tcgagtaggaagacgttttcctcctactcga.................................................................................................................................................................................................. Find igs database================================================ Query_seq: TF2295:TF2296|TF2295:TF2296:hypothetical protein:hypothetical protein:->->:2448778..2449031 254 taagatagccttataccatacaaaccaaatcgagtaggaggaaaacgtcttcctactcgatttactataaaacatatcaaaccaaattgtttgctgttttggaatgaagagactttctctatattaacaaatccagtaatgaaacaacgcattgatttaagatgatctttctcagcggtattccattatgaatcgcgttttattctaccatcctttccaaacgattacgggctgttctttgggcgctttttctc Intra-Species Hit: Count: 1 Min: 1 Max: 254 Len: 254 Subject: tfor_TF2295_TF2296|hypothetical protein:hypothetical protein|POSITIVE:POSITIVE|[2448778,2449031]|254 HSP 1 e-value: 1.0E-142 bit: 504.0 Len: 254 Query Start:1 Query End:254 Subject Strand: POSITIVE Subject Start: 1 Subject End: 254 taagatagccttataccatacaaaccaaatcgagtaggaggaaaacgtcttcctactcgatttactataaaacatatcaaaccaaattgtttgctgttttggaatgaagagactttctctatattaacaaatccagtaatgaaacaacgcattgatttaagatgatctttctcagcggtattccattatgaatcgcgttttattctaccatcctttccaaacgattacgggctgttctttgggcgctttttctc taagatagccttataccatacaaaccaaatcgagtaggaggaaaacgtcttcctactcgatttactataaaacatatcaaaccaaattgtttgctgttttggaatgaagagactttctctatattaacaaatccagtaatgaaacaacgcattgatttaagatgatctttctcagcggtattccattatgaatcgcgttttattctaccatcctttccaaacgattacgggctgttctttgggcgctttttctc Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAGAUAGCCUUAUACCAUACAAACCAAAUCGAGUAGGAGGAAAACGUCUUCCUACUCGAUUUACUAUAAAACAUAUCAAACCAAAUUGUUUGCUGUUUUGGAAUGAAGAGACUUUCUCUAUAUUAACAAAUCCAGUAAUGAAACAACGCAUUGAUUUAAGAUGAUCUUUCUCAGCGGUAUUCCAUUAUGAAUCGCGUUUUAUUCUACCAUCCUUUCCAAACGAUUACGGGCUGUUCUUUGGGCGCUUUUUCUC .(((...((((........(((..((.(((((((((((((((.....)))))))))))))))......................((((((((((((.((((.((((.((((.....)))).))))..))))..)))....(((..(((((...((((((.((((.....((.....)).....)))).)))))))))))...)))............)))))))))..))..))).....)))).)))...... (-59.72) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAGAAAAAGCGCCCAAAGAACAGCCCGUAAUCGUUUGGAAAGGAUGGUAGAAUAAAACGCGAUUCAUAAUGGAAUACCGCUGAGAAAGAUCAUCUUAAAUCAAUGCGUUGUUUCAUUACUGGAUUUGUUAAUAUAGAGAAAGUCUCUUCAUUCCAAAACAGCAAACAAUUUGGUUUGAUAUGUUUUAUAGUAAAUCGAGUAGGAAGACGUUUUCCUCCUACUCGAUUUGGUUUGUAUGGUAUAAGGCUAUCUUA ...............((((..((((....(((((.(..(..((((((........((((.((((((((((((((((.((((((..(((.....)))...)))..))).)))))))))).)))))))))).....((((.....)))))))))).((((((.(((((......)))))...))))))....((((((((((((((.((.....)).)))))))))))))).)..).)))))....)))).)))). (-65.30) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 371 248 203 42 2 tfor:TF2876|5end_cytosine_deaminase_3065144..3065374_POSITIVE 358 245 209 44 1 tfor:TF1591|5end_surface_antigen_BspA_1706387..1706617_POSITIVE 332 245 209 44 1 tfor:TF1589|5end_surface_antigen_BspA_1703189..1703419_POSITIVE 332 246 205 193 154 tfor:TF0676|5end_methyltransferase_719027..719257_POSITIVE 332 57 28 174 132 tfor:TF0200|5end_2-nitropropane_dioxygenase_225061..225291_POSITIVE 326 247 203 187 145 tfor:TF0534|5end_hypothetical_protein_559509..559739_POSITIVE 317 250 201 138 85 tfor:TF2831|5end_ABC_transporter,_permease_component_3021317..3021547_POSITIVE 304 249 203 164 124 tfor:TF1948|5end_conserved_hypothetical_protein_2095942..2096172_POSITIVE 297 248 201 197 143 tfor:TF0595|5end_hypothetical_protein_627820..628050_POSITIVE 297 246 219 132 102 tfor:TF0457|5end_beta-glucanase_precursor_474099..474329_POSITIVE 292 247 212 69 19 tfor:TF1710|5end_possible_cell_filamentation_protein_1829679..1829909_POSITIVE 292 248 203 221 157 tfor:TF0988|5end_conserved_hypothetical_protein;_possible_nucleotidyltransferase_1044463..1044693_POSITIVE 291 218 175 208 171 tfor:TF2561|5end_50S_ribosomal_protein_L16_2738693..2738923_POSITIVE 291 240 194 154 109 tfor:TF1735|5end_dehydrogenase,_possible_NADH-dependent_dehydrogenase_1860127..1860357_POSITIVE 290 246 202 46 2 tfor:TF0544|5end_metallo-beta_lactamase_family_protein_575121..575351_POSITIVE 282 248 213 140 95 tfor:TF0637|5end_TPR-repeat-containing_protein_673195..673425_POSITIVE 281 249 213 191 152 tfor:TF2682|5end_N_utilization_substance_protein_A_2856308..2856538_POSITIVE 281 248 211 50 15 tfor:TF1461|5end_DNA-damage-inducible_protein_F_1550845..1551075_POSITIVE 280 250 210 50 1 tfor:TF1145|5end_anaerobic_C4-dicarboxylate_membrane_transporter_1225799..1226029_POSITIVE 279 250 201 204 150 tfor:TF2512|5end_possible_abortive_infection_protein_2690247..2690477_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 460 63 27 64 28 tfor:TF2295|3end_hypothetical_protein_2448717..2448867_POSITIVE 371 248 203 42 2 tfor:TF2874|3end_conserved_hypothetical_protein_3065224..3065374_POSITIVE 332 246 205 105 66 tfor:TF0675|3end_conserved_hypothetical_protein_719019..719169_POSITIVE 326 247 203 117 75 tfor:TF0533|3end_hypothetical_protein_559519..559669_POSITIVE 297 246 219 125 95 tfor:TF0456|3end_conserved_hypothetical_protein_474172..474322_POSITIVE 293 227 188 90 55 tfor:TF2288|3end_hypothetical_protein_2442598..2442748_POSITIVE 291 240 194 65 20 tfor:TF1734|3end_conserved_hypothetical_protein_1860118..1860268_POSITIVE 282 248 213 149 104 tfor:TF0636|3end_beta-galactosidase_673284..673434_POSITIVE 279 250 201 109 55 tfor:TF2511|3end_RNA_binding_protein_2690232..2690382_POSITIVE 270 250 205 53 1 tfor:TF2888|3end_50S_ribosomal_protein_L21_3078389..3078539_POSITIVE 269 244 201 151 107 tfor:TF2830|3end_ABC_transporter,_ATP-binding_protein_3021419..3021569_POSITIVE 267 250 206 82 26 tfor:TF2189|3end_conserved_hypothetical_protein_2364884..2365034_POSITIVE 267 245 209 75 34 tfor:TF0939|3end_ISPg1_transposase,_IS1106-related_transposase_981115..981265_POSITIVE 266 198 168 126 96 tfor:TF2349|3end_conserved_hypothetical_protein_2514921..2515071_POSITIVE 265 79 31 75 25 tfor:TF2217|3end_hypothetical_protein_2390165..2390315_POSITIVE 264 246 203 76 12 tfor:TF2171|3end_hypothetical_protein_2345792..2345942_POSITIVE 264 65 24 64 12 tfor:TF0133|3end_transposase_element_145556..145706_POSITIVE 263 250 208 48 3 tfor:TF3003|3end_hypothetical_protein_3220629..3220779_POSITIVE 263 245 210 128 91 tfor:TF1154|3end_RNA_pseudouridylate_synthetase_1236822..1236972_POSITIVE 259 219 174 122 83 tfor:TF1780|3end_formiminotransferase-cyclodeaminases_1922087..1922237_POSITIVE