Origin IGS: ttttatttttaccccaatatttaaaatagaatcaatttagtatattatatcatattttatagaaacaaaaaaacagaggctataattttaacctctgtttgtattt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aaatacaaacagaggttaaaattatagcctctgtttttttgtttctataaaatatgatataatatactaaattgattctattttaaatattggggtaaaaataaaa Mask Tandem Repeat Region ================================================ ttttatttttaccccaatatttaaaatagaatcaatttagtatattatatcatattttatagaaacaaaaaaacagaggctataattttaacctctgtttgtattt Find is-nt database================================================ Query_seq: FN0871:FN0872|FN0871:FN0872:3-dehydroquinate synthase:hypothetical protein:<-<-:1531858..1531963 106 ttttatttttaccccaatatttaaaatagaatcaatttagtatattatatcatattttatagaaacaaaaaaacagaggctataattttaacctctgtttgtattt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: FN0871:FN0872|FN0871:FN0872:3-dehydroquinate synthase:hypothetical protein:<-<-:1531858..1531963 106 ttttatttttaccccaatatttaaaatagaatcaatttagtatattatatcatattttatagaaacaaaaaaacagaggctataattttaacctctgtttgtattt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: FN0871:FN0872|FN0871:FN0872:3-dehydroquinate synthase:hypothetical protein:<-<-:1531858..1531963 106 ttttatttttaccccaatatttaaaatagaatcaatttagtatattatatcatattttatagaaacaaaaaaacagaggctataattttaacctctgtttgtattt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ttttatttttaccccaatatttaaaatagaatcaatttagtatattatatcatattttatagaaacaaaaaaacagaggctataattttaacctctgtttgtattt Predict ORF larger than 30AA ================================================ ttttatttttaccccaatatttaaaatagaatcaatttagtatattatatcatattttatagaaacaaaaaaacagaggctataattttaacctctgtttgtattt 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: 83 Start: 19 End: 48 ..................ATTTAAAATAGAATCAATTTAGTATATTAT.......................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ ttttatttttaccccaatatttaaaatagaatcaatttagtatattatatcatattttatagaaacaaaaaaacagaggctataattttaacctctgtttgtattt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: FN0871:FN0872|FN0871:FN0872:3-dehydroquinate synthase:hypothetical protein:<-<-:1531858..1531963 106 ttttatttttaccccaatatttaaaatagaatcaatttagtatattatatcatattttatagaaacaaaaaaacagaggctataattttaacctctgtttgtattt Intra-Species Hit: Count: 1 Min: 1 Max: 106 Len: 106 Subject: NC_003454_FN0871_FN0872|3-dehydroquinate synthase:hypothetical protein|NEGATIVE:NEGATIVE|[1531858,1531963]|106 HSP 1 e-value: 2.0E-41 bit: 168.0 Len: 106 Query Start:1 Query End:106 Subject Strand: POSITIVE Subject Start: 1 Subject End: 106 ttttatttttaccccaatatttaaaatagaatcaatttagtatattatatcatattttatagaaacnnnnnnncagaggctataattttaacctctgtttgtattt ttttatttttaccccaatatttaaaatagaatcaatttagtatattatatcatattttatagaaacaaaaaaacagaggctataattttaacctctgtttgtattt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUUAUUUUUACCCCAAUAUUUAAAAUAGAAUCAAUUUAGUAUAUUAUAUCAUAUUUUAUAGAAACAAAAAAACAGAGGCUAUAAUUUUAACCUCUGUUUGUAUUU (((((((((.............))))))))).............(((((........)))))........(((((((((.((......)).)))))))))...... (-14.82) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAUACAAACAGAGGUUAAAAUUAUAGCCUCUGUUUUUUUGUUUCUAUAAAAUAUGAUAUAAUAUACUAAAUUGAUUCUAUUUUAAAUAUUGGGGUAAAAAUAAAA ......((((((((((((......)))))))))))).(((((((.(((..(((((.....((((..............))))....)))))...))).))))))). (-19.74) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 685 100 51 191 142 NC_003454:FN0871|5end_3-dehydroquinate_synthase_1531767..1531997_NEGATIVE 221 69 37 159 122 NC_003454:FN2069|5end_Amino_acid_carrier_protein_alsT_580377..580607_NEGATIVE 209 50 1 169 108 NC_003454:FN1550|5end_hypothetical_protein_65630..65860_NEGATIVE 197 45 1 108 59 NC_003454:FN1759|5end_Hydroxymethylpyrimidine_kinase_254765..254995_NEGATIVE 189 83 46 192 148 NC_003454:FN2010|5end_Transcriptional_regulator,_MarR_family_510302..510532_NEGATIVE 186 81 49 201 172 NC_003454:FN0352|5end_NA+/H+_antiporter_NHAC_983541..983771_POSITIVE 183 57 12 104 60 NC_003454:FN0850|5end_Hypothetical_cytosolic_protein_1508913..1509143_POSITIVE 174 41 1 208 173 NC_003454:FN0518|5end_Hypothetical_exported_24-amino_acid_repeat_protein_1170529..1170759_NEGATIVE 167 65 21 160 115 NC_003454:FN1391|5end_Acetyltransferase_2048784..2049014_POSITIVE 166 54 12 137 97 NC_003454:FN1346|5end_Hypothetical_cytosolic_protein_1999579..1999809_NEGATIVE 159 58 13 96 50 NC_003454:FN0822|5end_Shikimate_kinase_1481828..1482058_POSITIVE 158 99 76 22 3 NC_003454:FN0994|5end_hypothetical_protein_1649223..1649453_POSITIVE 157 99 80 174 155 NC_003454:FN0884|5end_Hemin_transport_system_permease_protein_hmuU_1544741..1544971_NEGATIVE 157 54 18 150 119 NC_003454:FN0837|5end_Integrase/recombinase_1499125..1499355_POSITIVE 157 49 1 124 86 NC_003454:FN0042|5end_Rod_shape-determining_protein_rodA_682129..682359_NEGATIVE 156 60 14 114 66 NC_003454:FN1434|5end_Tetratricopeptide_repeat_family_protein_2104511..2104741_NEGATIVE 155 40 2 143 102 NC_003454:FN1702|5end_undecaprenyl_pyrophosphate_phosphatase_197964..198194_NEGATIVE 154 97 55 188 144 NC_003454:FN1790|5end_Cob(I)alamin_adenosyltransferase_271511..271741_POSITIVE 152 96 53 220 177 NC_003454:FN1448|5end_Hypothetical_cytosolic_protein_2118428..2118658_NEGATIVE 151 91 61 70 42 NC_003454:FN0194|5end_Dipeptide_transport_system_permease_protein_dppC_819839..820069_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 220 45 1 142 89 NC_003454:FN0273|3end_Butyrate-acetoacetate_CoA-transferase_subunit_B_900162..900312_POSITIVE 209 50 1 145 84 NC_003454:FN1551|3end_hypothetical_protein_65654..65804_NEGATIVE 191 96 53 75 33 NC_003454:FN1426|3end_Serine_protease_2092577..2092727_NEGATIVE 190 69 42 32 2 NC_003454:FN2070|3end_Cobyric_acid_synthase_580504..580654_NEGATIVE 189 83 46 61 17 NC_003454:FN2011|3end_Valyl-tRNA_synthetase_510433..510583_NEGATIVE 183 57 12 103 59 NC_003454:FN0849|3end_8-amino-7-oxononanoate_synthase_1508992..1509142_POSITIVE 174 41 1 99 64 NC_003454:FN0519|3end_Hypothetical_exported_24-amino_acid_repeat_protein_1170638..1170788_NEGATIVE 171 53 12 122 79 NC_003454:FN1826|3end_Protease_314654..314804_NEGATIVE 166 54 12 72 32 NC_003454:FN1347|3end_Hypothetical_cytosolic_protein_1999644..1999794_NEGATIVE 166 100 60 146 106 NC_003454:FN0047|3end_Exodeoxyribonuclease_III_685268..685418_POSITIVE 162 59 18 110 65 NC_003454:FN1654|3end_hypothetical_protein_149163..149313_NEGATIVE 157 54 18 123 92 NC_003454:FN0836|3end_hypothetical_protein_1499178..1499328_POSITIVE 155 40 2 113 72 NC_003454:FN1703|3end_ADP-L-glycero-D-manno-heptose-6-epimerase_197994..198144_NEGATIVE 151 100 75 91 70 NC_003454:FN0746|3end_Hypothetical_Metal-Binding_Protein_1405749..1405899_POSITIVE 151 91 61 73 45 NC_003454:FN0193|3end_Dipeptide_transport_system_permease_protein_dppB_819922..820072_POSITIVE 151 59 11 81 38 NC_003454:FN0008|3end_quinolinate_synthetase_648986..649136_POSITIVE 149 97 53 145 100 NC_003454:FN1555|3end_Protein_Translation_Elongation_Factor_Tu_76252..76402_NEGATIVE 148 52 12 66 12 NC_003454:FN0775|3end_putative_aminopeptidase_2_1431937..1432087_POSITIVE 145 48 6 80 26 NC_003454:FN1966|3end_hypothetical_protein_465165..465315_NEGATIVE 142 96 56 79 31 NC_003454:FN1839|3end_glycerol_kinase_329845..329995_POSITIVE