Origin IGS: acattttctccttaaagttatcaatttatattgttaatataataacatatattttatagaatcatctattacaagttttaaatcaatctttttgttaggataattctaaaaaaagtaattaatcttggagtttcttttttcataatatctaattattttattaattactttatttattattataaaaattatttagaatttcttcatcatttttttcaatacattcctcattagtaaaagcaaaagttattgttttatcatcttttactttt .........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 aaaagtaaaagatgataaaacaataacttttgcttttactaatgaggaatgtattgaaaaaaatgatgaagaaattctaaataatttttataataataaataaagtaattaataaaataattagatattatgaaaaaagaaactccaagattaattactttttttagaattatcctaacaaaaagattgatttaaaacttgtaatagatgattctataaaatatatgttattatattaacaatataaattgataactttaaggagaaaatgt Mask Tandem Repeat Region ================================================ acattttctccttaaagttatcaatttatattgttaatataataacatatattttatagaatcatctattacaagttttaaatcaatctttttgttaggataattctaaaaaaagtaattaatcttggagtttcttttttcataatatctaattattttattaattactttatttattattataaaaattatttagaatttcttcatcatttttttcaatacattcctcattagtaaaagcaaaagttattgttttatcatcttttactttt Find is-nt database================================================ Query_seq: FN1195:FN1196|FN1195:FN1196:hypothetical protein:hypothetical protein:<-<-:1856330..1856601 272 acattttctccttaaagttatcaatttatattgttaatataataacatatattttatagaatcatctattacaagttttaaatcaatctttttgttaggataattctaaaaaaagtaattaatcttggagtttcttttttcataatatctaattattttattaattactttatttattattataaaaattatttagaatttcttcatcatttttttcaatacattcctcattagtaaaagcaaaagttattgttttatcatcttttactttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: FN1195:FN1196|FN1195:FN1196:hypothetical protein:hypothetical protein:<-<-:1856330..1856601 272 acattttctccttaaagttatcaatttatattgttaatataataacatatattttatagaatcatctattacaagttttaaatcaatctttttgttaggataattctaaaaaaagtaattaatcttggagtttcttttttcataatatctaattattttattaattactttatttattattataaaaattatttagaatttcttcatcatttttttcaatacattcctcattagtaaaagcaaaagttattgttttatcatcttttactttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: FN1195:FN1196|FN1195:FN1196:hypothetical protein:hypothetical protein:<-<-:1856330..1856601 272 acattttctccttaaagttatcaatttatattgttaatataataacatatattttatagaatcatctattacaagttttaaatcaatctttttgttaggataattctaaaaaaagtaattaatcttggagtttcttttttcataatatctaattattttattaattactttatttattattataaaaattatttagaatttcttcatcatttttttcaatacattcctcattagtaaaagcaaaagttattgttttatcatcttttactttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 acattttctccttaaagttatcaatttatattgttaatataataacatatattttatagaatcatctattacaagttttaaatcaatctttttgttaggataattctaaaaaaagtaattaatcttggagtttcttttttcataatatctaattattttattaattactttatttattattataaaaattatttagaatttcttcatcatttttttcaatacattcctcattagtaaaagcaaaagttattgttttatcatcttttactttt Predict ORF larger than 30AA ================================================ Protein_Len: 50 Strand: + Start: 82 End: 231 ................................................................................. M N L F V R I I L K K V I N L G V S F F I I S N Y F I N Y F I Y Y Y K N Y L E F L H H F F Q Y I P H ......................................... acattttctccttaaagttatcaatttatattgttaatataataacatatattttatagaatcatctattacaagttttaaatcaatctttttgttaggataattctaaaaaaagtaattaatcttggagtttcttttttcataatatctaattattttattaattactttatttattattataaaaattatttagaatttcttcatcatttttttcaatacattcctcattagtaaaagcaaaagttattgttttatcatcttttactttt 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: 82 Start: 179 End: 208 ..................................................................................................................................................................................GATGAAGAAATTCTAAATAATTTTTATAAT................................................................ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ acattttctccttaaagttatcaatttatattgttaatataataacatatattttatagaatcatctattacaagttttaaatcaatctttttgttaggataattctaaaaaaagtaattaatcttggagtttcttttttcataatatctaattattttattaattactttatttattattataaaaattatttagaatttcttcatcatttttttcaatacattcctcattagtaaaagcaaaagttattgttttatcatcttttactttt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: FN1195:FN1196|FN1195:FN1196:hypothetical protein:hypothetical protein:<-<-:1856330..1856601 272 acattttctccttaaagttatcaatttatattgttaatataataacatatattttatagaatcatctattacaagttttaaatcaatctttttgttaggataattctaaaaaaagtaattaatcttggagtttcttttttcataatatctaattattttattaattactttatttattattataaaaattatttagaatttcttcatcatttttttcaatacattcctcattagtaaaagcaaaagttattgttttatcatcttttactttt Intra-Species Hit: Count: 1 Min: 1 Max: 272 Len: 272 Subject: NC_003454_FN1195_FN1196|hypothetical protein:hypothetical protein|NEGATIVE:NEGATIVE|[1856330,1856601]|272 HSP 1 e-value: 5.0E-54 bit: 212.0 Len: 107 Query Start:1 Query End:107 Subject Strand: POSITIVE Subject Start: 1 Subject End: 107 acattttctccttaaagttatcaatttatattgttaatataataacatatattttatagaatcatctattacaagttttaaatcaatctttttgttaggataattct..................................................................................................................................................................... acattttctccttaaagttatcaatttatattgttaatataataacatatattttatagaatcatctattacaagttttaaatcaatctttttgttaggataattct..................................................................................................................................................................... HSP 2 e-value: 1.0E-23 bit: 111.0 Len: 56 Query Start:217 Query End:272 Subject Strand: POSITIVE Subject Start: 217 Subject End: 272 ........................................................................................................................................................................................................................caatacattcctcattagtaaaagcaaaagttattgttttatcatcttttactttt ........................................................................................................................................................................................................................caatacattcctcattagtaaaagcaaaagttattgttttatcatcttttactttt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ ACAUUUUCUCCUUAAAGUUAUCAAUUUAUAUUGUUAAUAUAAUAACAUAUAUUUUAUAGAAUCAUCUAUUACAAGUUUUAAAUCAAUCUUUUUGUUAGGAUAAUUCUAAAAAAAGUAAUUAAUCUUGGAGUUUCUUUUUUCAUAAUAUCUAAUUAUUUUAUUAAUUACUUUAUUUAUUAUUAUAAAAAUUAUUUAGAAUUUCUUCAUCAUUUUUUUCAAUACAUUCCUCAUUAGUAAAAGCAAAAGUUAUUGUUUUAUCAUCUUUUACUUUU .............(((((..........(((((....((((((((...........((((((.((((...(((((...............)))))..)))).))))))...((((((((((((..(((((.......))))).((((......))))..)))))))))))).....))))))))...........(((....)))...........)))))...............(((((((......)))))))..........))))). (-28.46) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAAGUAAAAGAUGAUAAAACAAUAACUUUUGCUUUUACUAAUGAGGAAUGUAUUGAAAAAAAUGAUGAAGAAAUUCUAAAUAAUUUUUAUAAUAAUAAAUAAAGUAAUUAAUAAAAUAAUUAGAUAUUAUGAAAAAAGAAACUCCAAGAUUAAUUACUUUUUUUAGAAUUAUCCUAACAAAAAGAUUGAUUUAAAACUUGUAAUAGAUGAUUCUAUAAAAUAUAUGUUAUUAUAUUAACAAUAUAAAUUGAUAACUUUAAGGAGAAAAUGU (((((((((((...((......))..)))))))))))............(((((((...........(((....)))...........((((((((((...((((((((((((...(((((.....)))))..................))))))))))))...((((((((((........(((.((......)).)))......)))))))))).........))))))))))....))))))).......................... (-38.34) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 661 130 81 221 172 NC_003454:FN1195|5end_hypothetical_protein_1856239..1856469_NEGATIVE 289 242 201 77 27 NC_003454:FN1495|5end_hypothetical_protein_2174410..2174640_NEGATIVE 289 242 201 101 51 NC_003454:FN1494|5end_Rod_shape-determining_protein_mreC_2174386..2174616_NEGATIVE 255 229 187 108 68 NC_003454:FN2123|5end_Phenylalanyl-tRNA_synthetase_alpha_chain_633224..633454_NEGATIVE 228 228 191 176 140 NC_003454:FN2047|5end_Fusobacterium_outer_membrane_protein_family_556383..556613_NEGATIVE 212 48 3 135 95 NC_003454:FN1732|5end_hypothetical_protein_232078..232308_NEGATIVE 209 237 201 110 72 NC_003454:FN1289|5end_hypothetical_protein_1946447..1946677_NEGATIVE 207 270 224 69 20 NC_003454:FN2098|5end_MRP-family_nucleotide-binding_protein_608146..608376_NEGATIVE 207 250 206 216 175 NC_003454:FN1787|5end_Tetratricopeptide_repeat_family_protein_267762..267992_POSITIVE 202 270 223 111 66 NC_003454:FN0206|5end_Activator_of_(R)-2-hydroxyglutaryl-CoA_dehydratase_832758..832988_POSITIVE 201 162 129 112 77 NC_003454:FN1070|5end_glucose-inhibited_division_protein_A_1717121..1717351_POSITIVE 200 96 52 109 68 NC_003454:FN1612|5end_coproporphyrinogen_III_oxidase_122533..122763_NEGATIVE 199 268 223 43 6 NC_003454:FN0399|5end_Dipeptide_transport_ATP-binding_protein_dppD_1037646..1037876_POSITIVE 198 269 223 211 167 NC_003454:FN1164|5end_Glucokinase_1821754..1821984_POSITIVE 194 263 231 187 149 NC_003454:FN1014|5end_Dihydrofolate_synthase_1669601..1669831_NEGATIVE 193 236 195 117 72 NC_003454:FN1179|5end_ATP-dependent_RNA_helicase_1841768..1841998_NEGATIVE 193 86 45 174 137 NC_003454:FN0818|5end_DNA-binding_protein_HU_1477034..1477264_NEGATIVE 191 266 224 62 24 NC_003454:FN1205|5end_Protease_1865162..1865392_NEGATIVE 190 152 121 181 152 NC_003454:FN0545|5end_Lipopolysaccharide_core_biosynthesis_protein_rfaY_1198041..1198271_POSITIVE 190 123 81 177 137 NC_003454:FN0109|5end_hypothetical_protein_744809..745039_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 289 242 201 76 26 NC_003454:FN1495|3end_hypothetical_protein_-89..61_NEGATIVE 255 229 187 81 41 NC_003454:FN2124|3end_Hypothetical_protein_with_Metallo-phosphoesterase_motif_633251..633401_NEGATIVE 209 237 201 113 75 NC_003454:FN1290|3end_hypothetical_protein_1946444..1946594_NEGATIVE 202 270 223 81 36 NC_003454:FN0205|3end_Sodium/glutamate_symport_carrier_protein_832808..832958_POSITIVE 200 96 52 106 65 NC_003454:FN1613|3end_hypothetical_protein_122536..122686_NEGATIVE 190 268 249 24 5 NC_003454:FN0398|3end_Dipeptide_transport_system_permease_protein_dppC_1037707..1037857_POSITIVE 189 37 4 107 77 NC_003454:FN0593|3end_UDP-3-O-[3-hydroxymyristoyl]_N-acetylglucosamine_deacetylase_1248843..1248993_POSITIVE 186 233 191 136 97 NC_003454:FN0773|3end_hypothetical_protein_1429635..1429785_POSITIVE 186 85 47 46 5 NC_003454:FN1759|3end_Hydroxymethylpyrimidine_kinase_253896..254046_NEGATIVE 185 236 197 81 42 NC_003454:FN1209|3end_Hypothetical_RNA_binding_protein_1868615..1868765_NEGATIVE 184 237 192 80 41 NC_003454:FN0560|3end_Oxygen-independent_coproporphyrinogen_III_oxidase_1214219..1214369_POSITIVE 184 218 188 44 11 NC_003454:FN1551|3end_hypothetical_protein_65654..65804_NEGATIVE 182 166 122 57 20 NC_003454:FN1712|3end_hypothetical_protein_207608..207758_POSITIVE 178 232 192 50 13 NC_003454:FN1717|3end_NAD-dependent_DNA_ligase_215320..215470_POSITIVE 177 97 51 128 88 NC_003454:FN1224|3end_2-dehydro-3-deoxyphosphooctonate_aldolase_1882540..1882690_NEGATIVE 176 270 224 85 44 NC_003454:FN1166|3end_Galactoside_transport_ATP-binding_protein_mglA_1825595..1825745_POSITIVE 176 254 211 129 80 NC_003454:FN0956|3end_hypothetical_protein_1612458..1612608_NEGATIVE 176 164 124 111 70 NC_003454:FN1894|3end_BAX_protein_381731..381881_NEGATIVE 175 228 185 127 87 NC_003454:FN1283|3end_DNA-directed_RNA_polymerase_alpha_subunit_1941647..1941797_NEGATIVE 175 150 120 44 16 NC_003454:FN0971|3end_Huntington_interacting_Protein_HYPE_1623281..1623431_NEGATIVE