Origin IGS: cttgtatcactactcccgaattttaaaaaaatataaaacatataccaaaaaccatctactattttaccatatataataaagattgtgaataattttttatatttcttattaataaaaaagctattgagtttaaaatacttttttatattcaatagctttaaaaata .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tatttttaaagctattgaatataaaaaagtattttaaactcaatagcttttttattaataagaaatataaaaaattattcacaatctttattatatatggtaaaatagtagatggtttttggtatatgttttatatttttttaaaattcgggagtagtgatacaag Mask Tandem Repeat Region ================================================ cttgtatcactactcccgaattttaaaaaaatataaaacatataccaaaaaccatctactattttaccatatataataaagattgtgaataattttttatatttcttattaataaaaaagctattgagtttaaaatacttttttatattcaatagctttaaaaata Find is-nt database================================================ Query_seq: FN1121:FN1122|FN1121:FN1122:ATP-dependent Zn protease:Long-chain-fatty-acid--CoA ligase:<-<-:1764731..1764896 166 cttgtatcactactcccgaattttaaaaaaatataaaacatataccaaaaaccatctactattttaccatatataataaagattgtgaataattttttatatttcttattaataaaaaagctattgagtttaaaatacttttttatattcaatagctttaaaaata Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: FN1121:FN1122|FN1121:FN1122:ATP-dependent Zn protease:Long-chain-fatty-acid--CoA ligase:<-<-:1764731..1764896 166 cttgtatcactactcccgaattttaaaaaaatataaaacatataccaaaaaccatctactattttaccatatataataaagattgtgaataattttttatatttcttattaataaaaaagctattgagtttaaaatacttttttatattcaatagctttaaaaata Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: FN1121:FN1122|FN1121:FN1122:ATP-dependent Zn protease:Long-chain-fatty-acid--CoA ligase:<-<-:1764731..1764896 166 cttgtatcactactcccgaattttaaaaaaatataaaacatataccaaaaaccatctactattttaccatatataataaagattgtgaataattttttatatttcttattaataaaaaagctattgagtttaaaatacttttttatattcaatagctttaaaaata Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 cttgtatcactactcccgaattttaaaaaaatataaaacatataccaaaaaccatctactattttaccatatataataaagattgtgaataattttttatatttcttattaataaaaaagctattgagtttaaaatacttttttatattcaatagctttaaaaata Predict ORF larger than 30AA ================================================ Protein_Len: 42 Strand: + Start: 40 End: 165 ....................................... M Y Q K P S T I L P Y I I K I V N N F L Y F L L I K K L L S L K Y F F I F N S F K N . Protein_Len: 50 Strand: - Start: 3 End: 152 .. T D S S G F K L F I Y F M Y W F G D V I K G Y I I F I T F L K K Y K K N I F F S N L K F Y K K I N M .............. cttgtatcactactcccgaattttaaaaaaatataaaacatataccaaaaaccatctactattttaccatatataataaagattgtgaataattttttatatttcttattaataaaaaagctattgagtttaaaatacttttttatattcaatagctttaaaaata 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: 87 Start: 61 End: 90 ............................................................ATTCACAATCTTTATTATATATGGTAAAAT............................................................................ PromScan Matrix: RpoD-17 Strand: - Score: 85 Start: 20 End: 49 ...................TTTGGTATATGTTTTATATTTTTTTAAAAT..................................................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ cttgtatcactactcccgaattttaaaaaaatataaaacatataccaaaaaccatctactattttaccatatataataaagattgtgaataattttttatatttcttattaataaaaaagctattgagtttaaaatacttttttatattcaatagctttaaaaata Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: FN1121:FN1122|FN1121:FN1122:ATP-dependent Zn protease:Long-chain-fatty-acid--CoA ligase:<-<-:1764731..1764896 166 cttgtatcactactcccgaattttaaaaaaatataaaacatataccaaaaaccatctactattttaccatatataataaagattgtgaataattttttatatttcttattaataaaaaagctattgagtttaaaatacttttttatattcaatagctttaaaaata Intra-Species Hit: Count: 1 Min: 1 Max: 166 Len: 166 Subject: NC_003454_FN1121_FN1122|ATP-dependent Zn protease:Long-chain-fatty-acid--CoA ligase|NEGATIVE:NEGATIVE|[1764731,1764896]|166 HSP 1 e-value: 6.0E-77 bit: 287.0 Len: 166 Query Start:1 Query End:166 Subject Strand: POSITIVE Subject Start: 1 Subject End: 166 cttgtatcactactcccgaattttnnnnnnntataaaacatataccaaaaaccatctactattttaccatatataataaagattgtgaataattttttatatttcttattaataaaaaagctattgagtttaaaatacttttttatattcaatagctttaaaaata cttgtatcactactcccgaattttaaaaaaatataaaacatataccaaaaaccatctactattttaccatatataataaagattgtgaataattttttatatttcttattaataaaaaagctattgagtttaaaatacttttttatattcaatagctttaaaaata Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CUUGUAUCACUACUCCCGAAUUUUAAAAAAAUAUAAAACAUAUACCAAAAACCAUCUACUAUUUUACCAUAUAUAAUAAAGAUUGUGAAUAAUUUUUUAUAUUUCUUAUUAAUAAAAAAGCUAUUGAGUUUAAAAUACUUUUUUAUAUUCAAUAGCUUUAAAAAUA ...........................................................((((((........((((((..(.((((((......)))))).)..)))))).....(((((((((((((.(((((.....))))).))))))))))))).)))))) (-24.40) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAUUUUUAAAGCUAUUGAAUAUAAAAAAGUAUUUUAAACUCAAUAGCUUUUUUAUUAAUAAGAAAUAUAAAAAAUUAUUCACAAUCUUUAUUAUAUAUGGUAAAAUAGUAGAUGGUUUUUGGUAUAUGUUUUAUAUUUUUUUAAAAUUCGGGAGUAGUGAUACAAG .......(((((((((((.(.(((((.....))))).).))))))))))).........(((((((((((((...((((((.((((((((((((..........)))))))).))))..))).)))..)))))))))))))............(((....)))... (-28.20) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 688 60 11 151 102 NC_003454:FN1121|5end_ATP-dependent_Zn_protease_1764640..1764870_NEGATIVE 219 160 111 193 149 NC_003454:FN0313|5end_16S_rRNA_m(5)C_967_methyltransferase_949903..950133_POSITIVE 200 157 115 192 159 NC_003454:FN0504|5end_Arginine_permease_1155009..1155239_NEGATIVE 199 155 122 201 163 NC_003454:FN1143|5end_glucosamine-6-phosphate_deaminase_1792461..1792691_POSITIVE 199 100 51 154 95 NC_003454:FN0217|5end_Catabolite_gene_activator_841002..841232_POSITIVE 188 159 115 222 189 NC_003454:FN0093|5end_Thioredoxin_729169..729399_POSITIVE 186 159 114 183 149 NC_003454:FN0462|5end_DNA_mismatch_repair_protein_mutL_1107184..1107414_POSITIVE 177 135 96 179 138 NC_003454:FN1732|5end_hypothetical_protein_232078..232308_NEGATIVE 176 160 119 119 86 NC_003454:FN0157|5end_DNA_repair_protein_RadA_784898..785128_POSITIVE 176 55 32 170 147 NC_003454:FN1502|5end_Nickel_transport_system_permease_protein_nikC_7522..7752_NEGATIVE 172 80 41 46 8 NC_003454:FN0221|5end_Carbon_starvation_protein_A_845209..845439_POSITIVE 171 156 119 192 157 NC_003454:FN0699|5end_Protein_translocase_subunit_secD_1357051..1357281_POSITIVE 169 157 139 146 128 NC_003454:FN0918|5end_hypothetical_protein_1574237..1574467_NEGATIVE 168 24 5 106 86 NC_003454:FN0679|5end_GTPase_1334596..1334826_POSITIVE 165 157 115 227 194 NC_003454:FN0165|5end_hypothetical_protein_793491..793721_POSITIVE 164 150 103 151 106 NC_003454:FN1264|5end_hypothetical_protein_1920766..1920996_POSITIVE 163 66 41 159 127 NC_003454:FN2040|5end_LSU_ribosomal_protein_L11P_549043..549273_NEGATIVE 162 160 121 135 95 NC_003454:FN1431|5end_Branched-chain_amino_acid_transport_system_permease_protein_livH_2100252..2100482_NEGATIVE 161 134 91 179 137 NC_003454:FN1563|5end_hypothetical_protein_85040..85270_NEGATIVE 159 156 126 168 126 NC_003454:FN1370|5end_Endonuclease_2019349..2019579_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 219 160 111 112 68 NC_003454:FN0312|3end_Anaerobic_ribonucleoside-triphosphate_reductase_activating_protein_949902..950052_POSITIVE 219 69 38 149 118 NC_003454:FN1752|3end_Regulatory_protein_TENI_248591..248741_NEGATIVE 212 106 64 119 71 NC_003454:FN0052|3end_Arsenate_reductase_689291..689441_POSITIVE 199 145 106 77 31 NC_003454:FN1671|3end_ABC_transporter_ATP-binding_protein_168483..168633_NEGATIVE 188 159 115 79 46 NC_003454:FN0092|3end_NADPH-dependent_butanol_dehydrogenase_729106..729256_POSITIVE 186 159 114 66 32 NC_003454:FN0461|3end_Probable_sigma(54)_modulation_protein_1107147..1107297_POSITIVE 185 158 115 100 59 NC_003454:FN0996|3end_Hypothetical_membrane-spanning_protein_1650673..1650823_NEGATIVE 176 160 119 115 82 NC_003454:FN0156|3end_Phosphopantetheine_adenylyltransferase_784974..785124_POSITIVE 170 75 40 138 100 NC_003454:FN0016|3end_hypothetical_protein_654366..654516_POSITIVE 169 157 139 84 66 NC_003454:FN0919|3end_DNA-dependent_DNA_polymerase_III_alpha_chain_1574299..1574449_NEGATIVE 168 24 5 81 61 NC_003454:FN0678|3end_Ser/Thr_protein_kinase_1334651..1334801_POSITIVE 168 160 114 93 60 NC_003454:FN1497|3end_Multidrug_resistance_protein_2_1014..1164_NEGATIVE 167 107 67 101 61 NC_003454:FN1417|3end_L-fuculose_phosphate_aldolase_2079020..2079170_POSITIVE 166 158 114 65 29 NC_003454:FN0662|3end_Formiminoglutamase_1319188..1319338_POSITIVE 165 159 114 84 53 NC_003454:FN2001|3end_hypothetical_protein_501298..501448_NEGATIVE 163 66 41 124 92 NC_003454:FN2041|3end_Transcription_antitermination_protein_nusG_549078..549228_NEGATIVE 163 97 63 82 47 NC_003454:FN1762|3end_Protein_yaaA_255258..255408_NEGATIVE 159 155 117 45 13 NC_003454:FN1241|3end_Hypohetical_Teichoic_Acid_Biosynthesis_Protein_1897781..1897931_NEGATIVE 157 160 111 103 54 NC_003454:FN1279|3end_Zinc_metallohydrolase,_glyoxalase_II_family_1937290..1937440_NEGATIVE 156 157 116 131 86 NC_003454:FN0976|3end_hypothetical_protein_1628146..1628296_NEGATIVE