Origin IGS: aaaaagttttagctcataattaaaataatttagagaatttttttaagaataaaactcttaaaaagattctctttttatatgatttaaaattttcttgctaaaaatataaatttcaaaggtagactattttagttcaatttgttataatgtattaggtttaatataaatatttgaaaggagaggaaca .........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 tgttcctctcctttcaaatatttatattaaacctaatacattataacaaattgaactaaaatagtctacctttgaaatttatatttttagcaagaaaattttaaatcatataaaaagagaatctttttaagagttttattcttaaaaaaattctctaaattattttaattatgagctaaaacttttt Mask Tandem Repeat Region ================================================ aaaaagttttagctcataattaaaataatttagagaatttttttaagaataaaactcttaaaaagattctctttttatatgatttaaaattttcttgctaaaaatataaatttcaaaggtagactattttagttcaatttgttataatgtattaggtttaatataaatatttgaaaggagaggaaca Find is-nt database================================================ Query_seq: FN1161:FN1162|FN1161:FN1162:Glutamate racemase:Hydroxyacylglutathione hydrolase:->->:1820114..1820300 187 aaaaagttttagctcataattaaaataatttagagaatttttttaagaataaaactcttaaaaagattctctttttatatgatttaaaattttcttgctaaaaatataaatttcaaaggtagactattttagttcaatttgttataatgtattaggtttaatataaatatttgaaaggagaggaaca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: FN1161:FN1162|FN1161:FN1162:Glutamate racemase:Hydroxyacylglutathione hydrolase:->->:1820114..1820300 187 aaaaagttttagctcataattaaaataatttagagaatttttttaagaataaaactcttaaaaagattctctttttatatgatttaaaattttcttgctaaaaatataaatttcaaaggtagactattttagttcaatttgttataatgtattaggtttaatataaatatttgaaaggagaggaaca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: FN1161:FN1162|FN1161:FN1162:Glutamate racemase:Hydroxyacylglutathione hydrolase:->->:1820114..1820300 187 aaaaagttttagctcataattaaaataatttagagaatttttttaagaataaaactcttaaaaagattctctttttatatgatttaaaattttcttgctaaaaatataaatttcaaaggtagactattttagttcaatttgttataatgtattaggtttaatataaatatttgaaaggagaggaaca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aaaaagttttagctcataattaaaataatttagagaatttttttaagaataaaactcttaaaaagattctctttttatatgatttaaaattttcttgctaaaaatataaatttcaaaggtagactattttagttcaatttgttataatgtattaggtttaatataaatatttgaaaggagaggaaca Predict ORF larger than 30AA ================================================ aaaaagttttagctcataattaaaataatttagagaatttttttaagaataaaactcttaaaaagattctctttttatatgatttaaaattttcttgctaaaaatataaatttcaaaggtagactattttagttcaatttgttataatgtattaggtttaatataaatatttgaaaggagaggaaca 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: 86 Start: 119 End: 148 ......................................................................................................................GTAGACTATTTTAGTTCAATTTGTTATAAT....................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ aaaaagttttagctcataattaaaataatttagagaatttttttaagaataaaactcttaaaaagattctctttttatatgatttaaaattttcttgctaaaaatataaatttcaaaggtagactattttagttcaatttgttataatgtattaggtttaatataaatatttgaaaggagaggaaca Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 39 HP_score: -2.5 Tail_Score: -3.32963 Start: 20 End: 46 Full_Region: ttaagagttttattc ttaaaaaaatt ctcta aattattttaa ttatgagctaaaact ...................ttaaaaaaattctctaaattattttaa............................................................................................................................................. TransTerm Strand: + Conf: 100 HP_score: -12.8 Tail_Score: -5.06585 Start: 33 End: 71 Full_Region: AATTAAAATAATTTA GAGAATTTTTTTAAGAAT AAA ACTCTTAAAAAGATTCTC TTTTTATATGATTTA ................................GAGAATTTTTTTAAGAATAAAACTCTTAAAAAGATTCTC.................................................................................................................... TransTerm Strand: - Conf: 91 HP_score: -12.8 Tail_Score: -2.77539 Start: 33 End: 71 Full_Region: taaatcatataaaaa gagaatctttttaagagt ttt attcttaaaaaaattctc taaattattttaatt ................................gagaatctttttaagagttttattcttaaaaaaattctc.................................................................................................................... Find igs database================================================ Query_seq: FN1161:FN1162|FN1161:FN1162:Glutamate racemase:Hydroxyacylglutathione hydrolase:->->:1820114..1820300 187 aaaaagttttagctcataattaaaataatttagagaatttttttaagaataaaactcttaaaaagattctctttttatatgatttaaaattttcttgctaaaaatataaatttcaaaggtagactattttagttcaatttgttataatgtattaggtttaatataaatatttgaaaggagaggaaca Intra-Species Hit: Count: 1 Min: 1 Max: 187 Len: 187 Subject: NC_003454_FN1161_FN1162|Glutamate racemase:Hydroxyacylglutathione hydrolase|POSITIVE:POSITIVE|[1820114,1820300]|187 HSP 1 e-value: 2.0E-89 bit: 329.0 Len: 187 Query Start:1 Query End:187 Subject Strand: POSITIVE Subject Start: 1 Subject End: 187 aaaaagttttagctcataattaaaataatttagagaannnnnnnaagaataaaactcttaaaaagattctctttttatatgatttaaaattttcttgctaaaaatataaatttcaaaggtagactattttagttcaatttgttataatgtattaggtttaatataaatatttgaaaggagaggaaca aaaaagttttagctcataattaaaataatttagagaatttttttaagaataaaactcttaaaaagattctctttttatatgatttaaaattttcttgctaaaaatataaatttcaaaggtagactattttagttcaatttgttataatgtattaggtttaatataaatatttgaaaggagaggaaca Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAAAGUUUUAGCUCAUAAUUAAAAUAAUUUAGAGAAUUUUUUUAAGAAUAAAACUCUUAAAAAGAUUCUCUUUUUAUAUGAUUUAAAAUUUUCUUGCUAAAAAUAUAAAUUUCAAAGGUAGACUAUUUUAGUUCAAUUUGUUAUAAUGUAUUAGGUUUAAUAUAAAUAUUUGAAAGGAGAGGAACA ..((((((((((.(((((..(((((......(((((((((((((((((.......))))))))))))))))))))))))))).))))))))))(((.((..((((((..((..((((....(((((...)))))...))))..))..(((((((....))))))).))))))...))..)))..... (-34.20) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGUUCCUCUCCUUUCAAAUAUUUAUAUUAAACCUAAUACAUUAUAACAAAUUGAACUAAAAUAGUCUACCUUUGAAAUUUAUAUUUUUAGCAAGAAAAUUUUAAAUCAUAUAAAAAGAGAAUCUUUUUAAGAGUUUUAUUCUUAAAAAAAUUCUCUAAAUUAUUUUAAUUAUGAGCUAAAACUUUUU .((((.......(((((....(((((...............)))))....))))).(((((((((.....((((((((((...............))))))))))..........(((((((.(((((((((((...))))))))))).)))))))..))))))))).....))))........... (-26.92) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 241 70 32 195 161 NC_003454:FN1075|5end_hypothetical_protein_1722042..1722272_POSITIVE 231 76 32 73 33 NC_003454:FN1678|5end_hypothetical_protein_174287..174517_POSITIVE 230 69 32 231 195 NC_003454:FN0657|5end_Acetyltransferase_1314266..1314496_POSITIVE 195 160 113 99 46 NC_003454:FN1734|5end_V-type_ATP_synthase_subunit_B_234258..234488_NEGATIVE 190 97 55 222 177 NC_003454:FN0182|5end_Sarcosine_oxidase_alpha_subunit_807066..807296_NEGATIVE 181 100 55 116 67 NC_003454:FN0451|5end_hypothetical_protein_1094853..1095083_POSITIVE 181 99 51 206 140 NC_003454:FN2120|5end_Hypothetical_exported_24-amino_acid_repeat_protein_628930..629160_NEGATIVE 180 99 67 183 145 NC_003454:FN0690|5end_hypothetical_protein_1345187..1345417_POSITIVE 174 106 64 231 186 NC_003454:FN1456|5end_UDP-N-acetylmuramate--alanine_ligase_2137922..2138152_NEGATIVE 173 155 117 191 148 NC_003454:FN0639|5end_hypothetical_protein_1297427..1297657_NEGATIVE 173 159 117 219 169 NC_003454:FN0542|5end_Beta_1,4_glucosyltransferase_1195223..1195453_POSITIVE 173 100 54 152 100 NC_003454:FN0394|5end_Outer_membrane_protein_1032327..1032557_POSITIVE 171 100 55 221 178 NC_003454:FN1932|5end_Dephospho-CoA_kinase_432999..433229_NEGATIVE 171 160 121 196 158 NC_003454:FN1700|5end_hypothetical_protein_195799..196029_NEGATIVE 169 91 51 127 83 NC_003454:FN0201|5end_Glutaconyl-COA_decarboxylase_beta_subunit_826542..826772_POSITIVE 168 180 153 42 16 NC_003454:FN0955|5end_hypothetical_protein_1612455..1612685_NEGATIVE 168 103 67 84 38 NC_003454:FN0284|5end_16S_rRNA_processing_protein_rimM_913923..914153_NEGATIVE 167 105 65 86 41 NC_003454:FN1805|5end_hypothetical_protein_286453..286683_POSITIVE 165 159 112 54 17 NC_003454:FN1172|5end_Phosphate_acetyltransferase_1834625..1834855_NEGATIVE 165 97 55 208 156 NC_003454:FN1050|5end_Lactoylglutathione_lyase_1699377..1699607_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 342 80 32 96 50 NC_003454:FN0812|3end_Hypothetical_cytosolic_protein_1471397..1471547_POSITIVE 306 78 32 82 34 NC_003454:FN0656|3end_hypothetical_protein_1314185..1314335_POSITIVE 294 72 32 59 19 NC_003454:FN1161|3end_Glutamate_racemase_1820053..1820203_POSITIVE 293 72 32 63 24 NC_003454:FN0470|3end_Putative_efflux_pump_component_MtrF_1116359..1116509_POSITIVE 241 70 32 81 47 NC_003454:FN1074|3end_Signal_recognition_particle_receptor_FtsY_1722008..1722158_POSITIVE 227 72 32 75 35 NC_003454:FN0792|3end_urocanate_hydratase_1450364..1450514_POSITIVE 227 80 32 60 16 NC_003454:FN0599|3end_Transposase_1255199..1255349_POSITIVE 207 75 32 55 17 NC_003454:FN0274|3end_Transposase_900285..900435_NEGATIVE 206 80 46 128 93 NC_003454:FN1893|3end_Fusobacterium_outer_membrane_protein_family_374412..374562_NEGATIVE 198 136 91 118 76 NC_003454:FN0355|3end_S-adenosylmethionine_synthetase_986076..986226_NEGATIVE 195 160 113 106 53 NC_003454:FN1735|3end_V-type_ATP_synthase_subunit_A_234251..234401_NEGATIVE 181 100 55 113 64 NC_003454:FN0450|3end_ABC_transporter_ATP-binding_protein_1094930..1095080_POSITIVE 181 99 51 100 34 NC_003454:FN2121|3end_Hypothetical_exported_24-amino_acid_repeat_protein_629036..629186_NEGATIVE 180 99 67 115 77 NC_003454:FN0689|3end_hypothetical_protein_1345199..1345349_POSITIVE 178 144 110 101 65 NC_003454:FN1680|3end_Transposase_175971..176121_NEGATIVE 176 72 32 79 42 NC_003454:FN1951|3end_ATPase_associated_with_chromosome_architecture/replication_458400..458550_NEGATIVE 175 80 32 60 16 NC_003454:FN1815|3end_Transposase_295626..295776_NEGATIVE 173 148 107 46 6 NC_003454:FN0667|3end_Na+_driven_multidrug_efflux_pump_1322344..1322494_NEGATIVE 173 100 54 149 97 NC_003454:FN0393|3end_Polysaccharide_deacetylase_1032404..1032554_POSITIVE 169 91 51 112 68 NC_003454:FN0200|3end_Biotin_carboxyl_carrier_protein_of_glutaconyl-COA_decarboxylase_826607..826757_POSITIVE