Origin IGS: aaattacacctccatgagtaaaaaaggactgttacacaataagctgtaacagtccaagtattataagtttatttgtgtaaaataatcaatgtaaataattattt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aaataattatttacattgattattttacacaaataaacttataatacttggactgttacagcttattgtgtaacagtccttttttactcatggaggtgtaattt Mask Tandem Repeat Region ================================================ aaattacacctccatgagtaaaaaaggactgttacacaataagctgtaacagtccaagtattataagtttatttgtgtaaaataatcaatgtaaataattattt Find is-nt database================================================ Query_seq: FN0340:FN0341|FN0340:FN0341:Hypothetical membrane-spanning Protein:transport protein:<-<-:974039..974142 104 aaattacacctccatgagtaaaaaaggactgttacacaataagctgtaacagtccaagtattataagtttatttgtgtaaaataatcaatgtaaataattattt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: FN0340:FN0341|FN0340:FN0341:Hypothetical membrane-spanning Protein:transport protein:<-<-:974039..974142 104 aaattacacctccatgagtaaaaaaggactgttacacaataagctgtaacagtccaagtattataagtttatttgtgtaaaataatcaatgtaaataattattt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: FN0340:FN0341|FN0340:FN0341:Hypothetical membrane-spanning Protein:transport protein:<-<-:974039..974142 104 aaattacacctccatgagtaaaaaaggactgttacacaataagctgtaacagtccaagtattataagtttatttgtgtaaaataatcaatgtaaataattattt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aaattacacctccatgagtaaaaaaggactgttacacaataagctgtaacagtccaagtattataagtttatttgtgtaaaataatcaatgtaaataattattt Predict ORF larger than 30AA ================================================ aaattacacctccatgagtaaaaaaggactgttacacaataagctgtaacagtccaagtattataagtttatttgtgtaaaataatcaatgtaaataattattt 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================================================ aaattacacctccatgagtaaaaaaggactgttacacaataagctgtaacagtccaagtattataagtttatttgtgtaaaataatcaatgtaaataattattt Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 100 HP_score: -10.9 Tail_Score: -5.1861 Start: 26 End: 55 Full_Region: aaacttataatactt ggactgttaca gcttattg tgtaacagtcc ttttttactcatgga .........................ggactgttacagcttattgtgtaacagtcc................................................. Find igs database================================================ Query_seq: FN0340:FN0341|FN0340:FN0341:Hypothetical membrane-spanning Protein:transport protein:<-<-:974039..974142 104 aaattacacctccatgagtaaaaaaggactgttacacaataagctgtaacagtccaagtattataagtttatttgtgtaaaataatcaatgtaaataattattt Intra-Species Hit: Count: 1 Min: 1 Max: 104 Len: 104 Subject: NC_003454_FN0340_FN0341|Hypothetical membrane-spanning Protein:transport protein|NEGATIVE:NEGATIVE|[974039,974142]|104 HSP 1 e-value: 1.0E-52 bit: 206.0 Len: 104 Query Start:1 Query End:104 Subject Strand: POSITIVE Subject Start: 1 Subject End: 104 aaattacacctccatgagtaaaaaaggactgttacacaataagctgtaacagtccaagtattataagtttatttgtgtaaaataatcaatgtaaataattattt aaattacacctccatgagtaaaaaaggactgttacacaataagctgtaacagtccaagtattataagtttatttgtgtaaaataatcaatgtaaataattattt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAUUACACCUCCAUGAGUAAAAAAGGACUGUUACACAAUAAGCUGUAACAGUCCAAGUAUUAUAAGUUUAUUUGUGUAAAAUAAUCAAUGUAAAUAAUUAUUU ...(((((.................(((((((((((........)))))))))))...........(.((((((.....)))))).)..))))).......... (-21.90) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAUAAUUAUUUACAUUGAUUAUUUUACACAAAUAAACUUAUAAUACUUGGACUGUUACAGCUUAUUGUGUAACAGUCCUUUUUUACUCAUGGAGGUGUAAUUU .((((((((.......))))))))((((((...................(((((((((((.(.....)))))))))))).......(((...)))))))))... (-24.60) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 829 60 11 151 102 NC_003454:FN0340|5end_Hypothetical_membrane-spanning_Protein_973948..974178_NEGATIVE 229 61 21 39 5 NC_003454:FN1542|5end_1,4-dihydroxy-2-naphthoate_octaprenyltransferase_56192..56422_POSITIVE 226 54 12 134 96 NC_003454:FN0626|5end_Hypothetical_cytosolic_protein_1286092..1286322_NEGATIVE 219 55 11 135 81 NC_003454:FN1269|5end_Hypothetical_lipoprotein_1926242..1926472_NEGATIVE 216 60 11 111 68 NC_003454:FN0050|5end_Fumarate_reductase_flavoprotein_subunit_687043..687273_POSITIVE 211 50 7 76 43 NC_003454:FN0535|5end_hypothetical_protein_1189351..1189581_POSITIVE 207 41 3 93 38 NC_003454:FN0327|5end_Bacterial_Protein_Translation_Initiation_Factor_3_(IF-3)_962149..962379_NEGATIVE 197 47 1 152 103 NC_003454:FN1111|5end_Dipeptide-binding_protein_1756181..1756411_NEGATIVE 194 43 12 205 168 NC_003454:FN0300|5end_Iron(III)_dicitrate-binding_protein_934679..934909_POSITIVE 192 33 6 132 96 NC_003454:FN1136|5end_Phosphonates_transport_ATP-binding_protein_phnC_1783057..1783287_POSITIVE 189 54 11 140 98 NC_003454:FN1160|5end_SWF/SNF_family_helicase_1815836..1816066_POSITIVE 188 76 44 52 18 NC_003454:FN0030|5end_5-nitroimidazole_antibiotic_resistance_protein_667120..667350_POSITIVE 187 60 25 49 2 NC_003454:FN0489|5end_Prolipoprotein_diacylglyceryl_transferase_1135425..1135655_NEGATIVE 186 46 9 141 112 NC_003454:FN1146|5end_Hypothetical_exported_24-amino_acid_repeat_protein_1796466..1796696_NEGATIVE 184 60 18 168 129 NC_003454:FN0173|5end_hypothetical_protein_797839..798069_POSITIVE 182 76 41 109 76 NC_003454:FN1893|5end_Fusobacterium_outer_membrane_protein_family_378497..378727_NEGATIVE 181 47 25 43 14 NC_003454:FN1716|5end_hypothetical_protein_212476..212706_POSITIVE 180 50 7 148 99 NC_003454:FN2078|5end_Transcriptional_regulator,_DeoR_family_590266..590496_NEGATIVE 180 64 43 149 123 NC_003454:FN1711|5end_Methyltransferase_206325..206555_POSITIVE 179 62 24 60 21 NC_003454:FN0789|5end_Transporter_1445278..1445508_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 249 55 14 81 46 NC_003454:FN0316|3end_hypothetical_protein_953234..953384_NEGATIVE 229 61 21 42 8 NC_003454:FN1541|3end_Heptaprenyl_diphosphate_synthase_component_II_56275..56425_POSITIVE 226 54 12 71 33 NC_003454:FN0627|3end_Glucosamine--fructose-6-phosphate_aminotransferase_[isomerizing]_1286155..1286305_NEGATIVE 223 56 18 81 30 NC_003454:FN1141|3end_Formate_transporter_1790493..1790643_NEGATIVE 217 53 17 79 35 NC_003454:FN0390|3end_hypothetical_protein_1028067..1028217_NEGATIVE 210 54 13 81 40 NC_003454:FN1081|3end_hypothetical_protein_1727325..1727475_NEGATIVE 209 53 14 82 33 NC_003454:FN0017|3end_hypothetical_protein_655957..656107_POSITIVE 205 55 14 73 35 NC_003454:FN0658|3end_ABC_transporter_substrate-binding_protein_1314890..1315040_NEGATIVE 200 70 23 106 51 NC_003454:FN1276|3end_hypothetical_protein_1935280..1935430_POSITIVE 194 60 39 132 106 NC_003454:FN0320|3end_Hypothetical_cytosolic_protein_957562..957712_POSITIVE 194 48 14 36 2 NC_003454:FN1989|3end_Sodium-dependent_tyrosine_transporter_493827..493977_POSITIVE 192 33 6 54 18 NC_003454:FN1135|3end_Phosphonates-binding_protein_1783059..1783209_POSITIVE 189 54 11 75 33 NC_003454:FN1159|3end_fructose_1,6-bisphosphatase_II_1815851..1816001_POSITIVE 188 55 20 84 34 NC_003454:FN1340|3end_Glutamyl-tRNA_synthetase_1993353..1993503_NEGATIVE 188 55 21 72 37 NC_003454:FN1784|3end_hypothetical_protein_265735..265885_NEGATIVE 187 55 11 63 7 NC_003454:FN1908|3end_Glycerophosphoryl_diester_phosphodiesterase_400596..400746_NEGATIVE 184 60 18 54 15 NC_003454:FN0172|3end_RNA_binding_protein_797805..797955_POSITIVE 183 57 14 85 39 NC_003454:FN0144|3end_hypothetical_protein_774165..774315_NEGATIVE 183 65 31 59 24 NC_003454:FN0031|3end_hypothetical_protein_667899..668049_NEGATIVE 180 50 7 72 23 NC_003454:FN2079|3end_ABC_transporter_ATP-binding_protein_590342..590492_NEGATIVE