Origin IGS: taaaaaatttaaattaagtataaagcatttagtaaaaagctaagtgctttttattttaaaaaataatttagaacaaaaaaatcttttttaaatcaagaaaaaatgttacaatatcttaatagagtatgaaaggagaattagtgataaatatgaaaaacacaaaaaaatttactatattactacttatcttagctagtttgtttttaatagcttgtaggaaagatgaaaaaaaagatgatacagaaaataaaacaggagataaagtagaagcaaatgtttccactaatctttcagaagaagagttacaaatagcaaaaggtgtgaatggtgacttaccagatcctgtttatacttatgaagcaatagttgatgaagcaggaggattataccaatcacctcaaccaaatgaagataattatgtaaaaaaacatgatatatggacagaagatgttcaaaaagagttaaaaacaataaaaccagcattagatgaaaatgcttctgaggaggaaattcaacatttatttaatcaatttttatatattgtaggttatgactatacaccatttgaaacaatagatagattttcttatgtaatttttaagaatgat .........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.........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 atcattcttaaaaattacataagaaaatctatctattgtttcaaatggtgtatagtcataacctacaatatataaaaattgattaaataaatgttgaatttcctcctcagaagcattttcatctaatgctggttttattgtttttaactctttttgaacatcttctgtccatatatcatgtttttttacataattatcttcatttggttgaggtgattggtataatcctcctgcttcatcaactattgcttcataagtataaacaggatctggtaagtcaccattcacaccttttgctatttgtaactcttcttctgaaagattagtggaaacatttgcttctactttatctcctgttttattttctgtatcatcttttttttcatctttcctacaagctattaaaaacaaactagctaagataagtagtaatatagtaaatttttttgtgtttttcatatttatcactaattctcctttcatactctattaagatattgtaacattttttcttgatttaaaaaagatttttttgttctaaattattttttaaaataaaaagcacttagctttttactaaatgctttatacttaatttaaatttttta Mask Tandem Repeat Region ================================================ taaaaaatttaaattaagtataaagcatttagtaaaaagctaagtgctttttattttaaaaaataatttagaacaaaaaaatcttttttaaatcaagaaaaaatgttacaatatcttaatagagtatgaaaggagaattagtgataaatatgaaaaacacaaaaaaatttactatattactacttatcttagctagtttgtttttaatagcttgtaggaaagatgaaaaaaaagatgatacagaaaataaaacaggagataaagtagaagcaaatgtttccactaatctttcagaagaagagttacaaatagcaaaaggtgtgaatggtgacttaccagatcctgtttatacttatgaagcaatagttgatgaagcaggaggattataccaatcacctcaaccaaatgaagataattatgtaaaaaaacatgatatatggacagaagatgttcaaaaagagttaaaaacaataaaaccagcattagatgaaaatgcttctgaggaggaaattcaacatttatttaatcaatttttatatattgtaggttatgactatacaccatttgaaacaatagatagattttcttatgtaatttttaagaatgat Find is-nt database================================================ Query_seq: FN0575:FN0576|FN0575:FN0576:hypothetical protein:D-amino acid dehydrogenase large subunit:->->:1225645..1226252 608 taaaaaatttaaattaagtataaagcatttagtaaaaagctaagtgctttttattttaaaaaataatttagaacaaaaaaatcttttttaaatcaagaaaaaatgttacaatatcttaatagagtatgaaaggagaattagtgataaatatgaaaaacacaaaaaaatttactatattactacttatcttagctagtttgtttttaatagcttgtaggaaagatgaaaaaaaagatgatacagaaaataaaacaggagataaagtagaagcaaatgtttccactaatctttcagaagaagagttacaaatagcaaaaggtgtgaatggtgacttaccagatcctgtttatacttatgaagcaatagttgatgaagcaggaggattataccaatcacctcaaccaaatgaagataattatgtaaaaaaacatgatatatggacagaagatgttcaaaaagagttaaaaacaataaaaccagcattagatgaaaatgcttctgaggaggaaattcaacatttatttaatcaatttttatatattgtaggttatgactatacaccatttgaaacaatagatagattttcttatgtaatttttaagaatgat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: FN0575:FN0576|FN0575:FN0576:hypothetical protein:D-amino acid dehydrogenase large subunit:->->:1225645..1226252 608 taaaaaatttaaattaagtataaagcatttagtaaaaagctaagtgctttttattttaaaaaataatttagaacaaaaaaatcttttttaaatcaagaaaaaatgttacaatatcttaatagagtatgaaaggagaattagtgataaatatgaaaaacacaaaaaaatttactatattactacttatcttagctagtttgtttttaatagcttgtaggaaagatgaaaaaaaagatgatacagaaaataaaacaggagataaagtagaagcaaatgtttccactaatctttcagaagaagagttacaaatagcaaaaggtgtgaatggtgacttaccagatcctgtttatacttatgaagcaatagttgatgaagcaggaggattataccaatcacctcaaccaaatgaagataattatgtaaaaaaacatgatatatggacagaagatgttcaaaaagagttaaaaacaataaaaccagcattagatgaaaatgcttctgaggaggaaattcaacatttatttaatcaatttttatatattgtaggttatgactatacaccatttgaaacaatagatagattttcttatgtaatttttaagaatgat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: FN0575:FN0576|FN0575:FN0576:hypothetical protein:D-amino acid dehydrogenase large subunit:->->:1225645..1226252 608 taaaaaatttaaattaagtataaagcatttagtaaaaagctaagtgctttttattttaaaaaataatttagaacaaaaaaatcttttttaaatcaagaaaaaatgttacaatatcttaatagagtatgaaaggagaattagtgataaatatgaaaaacacaaaaaaatttactatattactacttatcttagctagtttgtttttaatagcttgtaggaaagatgaaaaaaaagatgatacagaaaataaaacaggagataaagtagaagcaaatgtttccactaatctttcagaagaagagttacaaatagcaaaaggtgtgaatggtgacttaccagatcctgtttatacttatgaagcaatagttgatgaagcaggaggattataccaatcacctcaaccaaatgaagataattatgtaaaaaaacatgatatatggacagaagatgttcaaaaagagttaaaaacaataaaaccagcattagatgaaaatgcttctgaggaggaaattcaacatttatttaatcaatttttatatattgtaggttatgactatacaccatttgaaacaatagatagattttcttatgtaatttttaagaatgat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 taaaaaatttaaattaagtataaagcatttagtaaaaagctaagtgctttttattttaaaaaataatttagaacaaaaaaatcttttttaaatcaagaaaaaatgttacaatatcttaatagagtatgaaaggagaattagtgataaatatgaaaaacacaaaaaaatttactatattactacttatcttagctagtttgtttttaatagcttgtaggaaagatgaaaaaaaagatgatacagaaaataaaacaggagataaagtagaagcaaatgtttccactaatctttcagaagaagagttacaaatagcaaaaggtgtgaatggtgacttaccagatcctgtttatacttatgaagcaatagttgatgaagcaggaggattataccaatcacctcaaccaaatgaagataattatgtaaaaaaacatgatatatggacagaagatgttcaaaaagagttaaaaacaataaaaccagcattagatgaaaatgcttctgaggaggaaattcaacatttatttaatcaatttttatatattgtaggttatgactatacaccatttgaaacaatagatagattttcttatgtaatttttaagaatgat Predict ORF larger than 30AA ================================================ Protein_Len: 34 Strand: + Start: 92 End: 193 ........................................................................................... M K K K C Y N I L I E Y E R R I S D K Y E K H K K I Y Y I T T Y L S ............................................................................................................................................................................................................................................................................................................................................................................................................................... Protein_Len: 60 Strand: + Start: 126 End: 608 ............................................................................................................................. M K G E L V I N M K N T K K F T I L L L I L A S L F L I A C R K D E K K D D T E N K T G D K V E A N V S T N L S E E E L Protein_Len: 60 Strand: - Start: 286 End: 522 ............................................................................................................................................................................................................................................................................................. Q K Y K H L L L Q H L L L I I G I V E V L H L Y N H L F V H Y I S L L H E F L T L F L L V L M L H F H K Q P P F E V N M ...................................................................................... Protein_Len: 60 Strand: - Start: 119 End: 310 ...................................................................................................................... P S N T I F I F F V F F N V I N S S I K A L K N K I A Q L F S S F F S S V S F L V P S L T S A F T E V L R E S S S N C M .......................................................................................................................................................................................................................................................................................................... taaaaaatttaaattaagtataaagcatttagtaaaaagctaagtgctttttattttaaaaaataatttagaacaaaaaaatcttttttaaatcaagaaaaaatgttacaatatcttaatagagtatgaaaggagaattagtgataaatatgaaaaacacaaaaaaatttactatattactacttatcttagctagtttgtttttaatagcttgtaggaaagatgaaaaaaaagatgatacagaaaataaaacaggagataaagtagaagcaaatgtttccactaatctttcagaagaagagttacaaatagcaaaaggtgtgaatggtgacttaccagatcctgtttatacttatgaagcaatagttgatgaagcaggaggattataccaatcacctcaaccaaatgaagataattatgtaaaaaaacatgatatatggacagaagatgttcaaaaagagttaaaaacaataaaaccagcattagatgaaaatgcttctgaggaggaaattcaacatttatttaatcaatttttatatattgtaggttatgactatacaccatttgaaacaatagatagattttcttatgtaatttttaagaatgat 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: 235 End: 264 ..........................................................................................................................................................................................................................................CTTTATCTCCTGTTTTATTTTCTGTATCAT........................................................................................................................................................................................................................................................................................................................................................ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ taaaaaatttaaattaagtataaagcatttagtaaaaagctaagtgctttttattttaaaaaataatttagaacaaaaaaatcttttttaaatcaagaaaaaatgttacaatatcttaatagagtatgaaaggagaattagtgataaatatgaaaaacacaaaaaaatttactatattactacttatcttagctagtttgtttttaatagcttgtaggaaagatgaaaaaaaagatgatacagaaaataaaacaggagataaagtagaagcaaatgtttccactaatctttcagaagaagagttacaaatagcaaaaggtgtgaatggtgacttaccagatcctgtttatacttatgaagcaatagttgatgaagcaggaggattataccaatcacctcaaccaaatgaagataattatgtaaaaaaacatgatatatggacagaagatgttcaaaaagagttaaaaacaataaaaccagcattagatgaaaatgcttctgaggaggaaattcaacatttatttaatcaatttttatatattgtaggttatgactatacaccatttgaaacaatagatagattttcttatgtaatttttaagaatgat Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 42 HP_score: -3.0 Tail_Score: -2.75455 Start: 19 End: 53 Full_Region: aattattttttaaaa taaaaagcacttag cttttta ctaaatgctttata cttaatttaaatttt ..................taaaaagcacttagctttttactaaatgctttata........................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................... Find igs database================================================ Query_seq: FN0575:FN0576|FN0575:FN0576:hypothetical protein:D-amino acid dehydrogenase large subunit:->->:1225645..1226252 608 taaaaaatttaaattaagtataaagcatttagtaaaaagctaagtgctttttattttaaaaaataatttagaacaaaaaaatcttttttaaatcaagaaaaaatgttacaatatcttaatagagtatgaaaggagaattagtgataaatatgaaaaacacaaaaaaatttactatattactacttatcttagctagtttgtttttaatagcttgtaggaaagatgaaaaaaaagatgatacagaaaataaaacaggagataaagtagaagcaaatgtttccactaatctttcagaagaagagttacaaatagcaaaaggtgtgaatggtgacttaccagatcctgtttatacttatgaagcaatagttgatgaagcaggaggattataccaatcacctcaaccaaatgaagataattatgtaaaaaaacatgatatatggacagaagatgttcaaaaagagttaaaaacaataaaaccagcattagatgaaaatgcttctgaggaggaaattcaacatttatttaatcaatttttatatattgtaggttatgactatacaccatttgaaacaatagatagattttcttatgtaatttttaagaatgat Intra-Species Hit: Count: 1 Min: 105 Max: 608 Len: 504 Subject: NC_003454_FN0575_FN0576|hypothetical protein:D-amino acid dehydrogenase large subunit|POSITIVE:POSITIVE|[1225645,1226252]|608 HSP 1 e-value: 0.0 bit: 868.0 Len: 504 Query Start:105 Query End:608 Subject Strand: POSITIVE Subject Start: 105 Subject End: 608 ........................................................................................................gttacaatatcttaatagagtatgaaaggagaattagtgataaatatgaaaaacacnnnnnnntttactatattactacttatcttagctagtttgtttttaatagcttgtaggaaagatgnnnnnnnngatgatacagaaaataaaacaggagataaagtagaagcaaatgtttccactaatctttcagaagaagagttacaaatagcaaaaggtgtgaatggtgacttaccagatcctgtttatacttatgaagcaatagttgatgaagcaggaggattataccaatcacctcaaccaaatgaagataattatgtnnnnnnncatgatatatggacagaagatgttcaaaaagagttaaaaacaataaaaccagcattagatgaaaatgcttctgaggaggaaattcaacatttatttaatcaatttttatatattgtaggttatgactatacaccatttgaaacaatagatagattttcttatgtaatttttaagaatgat ........................................................................................................gttacaatatcttaatagagtatgaaaggagaattagtgataaatatgaaaaacacaaaaaaatttactatattactacttatcttagctagtttgtttttaatagcttgtaggaaagatgaaaaaaaagatgatacagaaaataaaacaggagataaagtagaagcaaatgtttccactaatctttcagaagaagagttacaaatagcaaaaggtgtgaatggtgacttaccagatcctgtttatacttatgaagcaatagttgatgaagcaggaggattataccaatcacctcaaccaaatgaagataattatgtaaaaaaacatgatatatggacagaagatgttcaaaaagagttaaaaacaataaaaccagcattagatgaaaatgcttctgaggaggaaattcaacatttatttaatcaatttttatatattgtaggttatgactatacaccatttgaaacaatagatagattttcttatgtaatttttaagaatgat Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GUUACAAUAUCUUAAUAGAGUAUGAAAGGAGAAUUAGUGAUAAAUAUGAAAAACACAAAAAAAUUUACUAUAUUACUACUUAUCUUAGCUAGUUUGUUUUUAAUAGCUUGUAGGAAAGAUGAAAAAAAAGAUGAUACAGAAAAUAAAACAGGAGAUAAAGUAGAAGCAAAUGUUUCCACUAAUCUUUCAGAAGAAGAGUUACAAAUAGCAAAAGGUGUGAAUGGUGACUUACCAGAUCCUGUUUAUACUUAUGAAGCAAUAGUUGAUGAAGCAGGAGGAUUAUACCAAUCACCUCAACCAAAUGAAGAUAAUUAUGUAAAAAAACAUGAUAUAUGGACAGAAGAUGUUCAAAAAGAGUUAAAAACAAUAAAACCAGCAUUAGAUGAAAAUGCUUCUGAGGAGGAAAUUCAACAUUUAUUUAAUCAAUUUUUAUAUAUUGUAGGUUAUGACUAUACACCAUUUGAAACAAUAGAUAGAUUUUCUUAUGUAAUUUUUAAGAAUGAU .........((((((.....((((.(((((((..((((((((............................)))))))).((((((..((((.(((((.......(((((.(..(((((((.........(......).............(((((((..((....))...)))))))....)))))))..)....))))))))))))))....((((((..(.(((((((((....((((((((..(((.((......))))).....)))))))).(((((.........(((((......((......(((((((......)))))))...((((((.....))))))..............))........((((((.......))))))..)))))..(.....)..........)))))..............))))))))).)...))))))............)))))).))))))).))))....))))))..... (-86.00) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUCAUUCUUAAAAAUUACAUAAGAAAAUCUAUCUAUUGUUUCAAAUGGUGUAUAGUCAUAACCUACAAUAUAUAAAAAUUGAUUAAAUAAAUGUUGAAUUUCCUCCUCAGAAGCAUUUUCAUCUAAUGCUGGUUUUAUUGUUUUUAACUCUUUUUGAACAUCUUCUGUCCAUAUAUCAUGUUUUUUUACAUAAUUAUCUUCAUUUGGUUGAGGUGAUUGGUAUAAUCCUCCUGCUUCAUCAACUAUUGCUUCAUAAGUAUAAACAGGAUCUGGUAAGUCACCAUUCACACCUUUUGCUAUUUGUAACUCUUCUUCUGAAAGAUUAGUGGAAACAUUUGCUUCUACUUUAUCUCCUGUUUUAUUUUCUGUAUCAUCUUUUUUUUCAUCUUUCCUACAAGCUAUUAAAAACAAACUAGCUAAGAUAAGUAGUAAUAUAGUAAAUUUUUUUGUGUUUUUCAUAUUUAUCACUAAUUCUCCUUUCAUACUCUAUUAAGAUAUUGUAAC ....((((((.........))))))...................(((((((((.(.((.......((((........)))).(((((.....((((((.............((((((.......))))))............))))))....)))))........)).).)))))))))......(((((....((((((.((..(((.((((.(((((((((((.....((((((.(((......(((.....(((((.(((((((...((((.....))))..........((((.....)))).............((((.(((((((.(....).)))))))..))))))))))))))))...)))..........................(((((............)))))..))))))))).(((((((.........)))))))........)))).)))))))..))))....)))..)).)))))).))))). (-74.01) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 279 107 64 132 80 NC_003454:FN1209|5end_Hypothetical_RNA_binding_protein_1868914..1869144_NEGATIVE 243 189 149 102 58 NC_003454:FN0563|5end_tRNA_(5-methylaminomethyl-2-thiouridylate)_-methyltransferase_1215286..1215516_POSITIVE 240 249 206 197 152 NC_003454:FN0312|5end_Anaerobic_ribonucleoside-triphosphate_reductase_activating_protein_949316..949546_POSITIVE 237 300 256 56 18 NC_003454:FN1457|5end_UDP-N-acetylglucosamine-N-acetylmuramyl-_Pentapeptide_pyrophosphoryl-undecaprenol_N-acetylglucosamine_transferase_2138976..2139206_NEGATIVE 233 350 305 83 41 NC_003454:FN1238|5end_hypothetical_protein_1896291..1896521_NEGATIVE 229 284 253 159 120 NC_003454:FN0246|5end_hypothetical_protein_870797..871027_NEGATIVE 221 207 171 180 138 NC_003454:FN0551|5end_Bacterial_regulatory_proteins,_crp_family_1203276..1203506_POSITIVE 217 299 251 49 5 NC_003454:FN1451|5end_cell_division_protein_FtsZ_2132710..2132940_NEGATIVE 215 403 361 221 175 NC_003454:FN0687|5end_hypothetical_protein_1342563..1342793_POSITIVE 215 300 252 167 116 NC_003454:FN1750|5end_Pyruvate-flavodoxin_oxidoreductase_247811..248041_POSITIVE 214 279 241 182 136 NC_003454:FN1904|5end_Transcriptional_regulator,_MarR_family_393107..393337_POSITIVE 213 200 151 65 6 NC_003454:FN1909|5end_UDP-3-O-[3-hydroxymyristoyl]_glucosamine_N-acyltransferase_402710..402940_NEGATIVE 213 210 161 223 168 NC_003454:FN1787|5end_Tetratricopeptide_repeat_family_protein_267762..267992_POSITIVE 210 290 241 87 31 NC_003454:FN1952|5end_Na(+)-linked_D-alanine_glycine_permease_459050..459280_NEGATIVE 210 290 241 210 154 NC_003454:FN1951|5end_ATPase_associated_with_chromosome_architecture/replication_458927..459157_NEGATIVE 207 279 254 26 2 NC_003454:FN1924|5end_Arsenical_pump_membrane_protein_422993..423223_NEGATIVE 206 431 392 173 139 NC_003454:FN1105|5end_hypothetical_protein_1750041..1750271_POSITIVE 205 244 211 184 149 NC_003454:FN0781|5end_Integral_membrane_protein_1438281..1438511_NEGATIVE 204 489 441 222 172 NC_003454:FN1348|5end_ABC_transporter_ATP-binding_protein_2001141..2001371_NEGATIVE 204 243 213 74 45 NC_003454:FN0597|5end_Lipid-A-disaccharide_synthase_1250814..1251044_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 279 107 64 106 54 NC_003454:FN1210|3end_Metal_dependent_hydrolase_1868940..1869090_NEGATIVE 243 189 149 115 71 NC_003454:FN0562|3end_Hypothetical_cytosolic_protein_1215379..1215529_POSITIVE 237 300 256 55 17 NC_003454:FN1458|3end_UDP-N-acetylmuramoylalanine--D-glutamate_ligase_2138977..2139127_NEGATIVE 215 250 207 52 15 NC_003454:FN1941|3end_ClpB_protein_443953..444103_POSITIVE 204 243 213 64 35 NC_003454:FN0596|3end_hypothetical_protein_1250884..1251034_POSITIVE 204 294 251 151 112 NC_003454:FN1723|3end_glucose-inhibited_division_protein_A_220744..220894_NEGATIVE 203 279 236 76 27 NC_003454:FN0265|3end_Cell_division_protein_ftsX_892410..892560_POSITIVE 200 198 159 58 15 NC_003454:FN2065|3end_Transcriptional_repressor_576397..576547_POSITIVE 200 429 388 86 42 NC_003454:FN1867|3end_Zn-dependent_alcohol_dehydrogenase_and_related_dehydrogenase_358560..358710_NEGATIVE 199 210 165 48 9 NC_003454:FN0491|3end_Alanine_racemase_1136239..1136389_NEGATIVE 198 189 150 65 30 NC_003454:FN1921|3end_Biotin_operon_repressor_416910..417060_NEGATIVE 198 187 149 144 105 NC_003454:FN1555|3end_Protein_Translation_Elongation_Factor_Tu_76252..76402_NEGATIVE 197 416 381 145 112 NC_003454:FN0777|3end_GTP-binding_protein_LepA_1433018..1433168_NEGATIVE 197 246 204 41 3 NC_003454:FN0077|3end_Ethanolamine_two-component_sensor_kinase_716172..716322_POSITIVE 196 222 181 140 95 NC_003454:FN0209|3end_Hypothetical_cytosolic_protein_836800..836950_POSITIVE 194 296 251 89 34 NC_003454:FN0480|3end_hypothetical_protein_1127839..1127989_POSITIVE 194 492 459 84 50 NC_003454:FN0093|3end_Thioredoxin_729560..729710_POSITIVE 194 210 173 33 1 NC_003454:FN0072|3end_2-amino-4-hydroxy-6-_hydroxymethyldihydropteridine_pyrophosphokinase_712619..712769_POSITIVE 192 210 162 57 16 NC_003454:FN1336|3end_hypothetical_protein_1989936..1990086_NEGATIVE 192 272 231 38 3 NC_003454:FN0505|3end_Anthranilate_synthase_component_II_1155044..1155194_NEGATIVE