Origin IGS: aggttatctgtcaagtgatattaataaaaaagtttagacttataactcatgtaattaagagaatttttgagaattaaacgacctaaaaattctcttattttttataacaaaaaattttaaaaacttgccaatttaaaaaaactataatataatttaccataggagatttatgtaaaagaagcgccagaactctttttagagttgacgaggattggaattatcgaagttttcggcggatgttccaaaggtggttacaaccattatcaacaaaaacacagagcaatttgtgtaacaaagagataatagtaacaatctcctattttataatgaaaatttgtaggaggtttttta .........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 taaaaaacctcctacaaattttcattataaaataggagattgttactattatctctttgttacacaaattgctctgtgtttttgttgataatggttgtaaccacctttggaacatccgccgaaaacttcgataattccaatcctcgtcaactctaaaaagagttctggcgcttcttttacataaatctcctatggtaaattatattatagtttttttaaattggcaagtttttaaaattttttgttataaaaaataagagaatttttaggtcgtttaattctcaaaaattctcttaattacatgagttataagtctaaacttttttattaatatcacttgacagataacct Mask Tandem Repeat Region ================================================ aggttatctgtcaagtgatattaataaaaaagtttagacttataactcatgtaattaagagaatttttgagaattaaacgacctaaaaattctcttattttttataacaaaaaattttaaaaacttgccaatttaaaaaaactataatataatttaccataggagatttatgtaaaagaagcgccagaactctttttagagttgacgaggattggaattatcgaagttttcggcggatgttccaaaggtggttacaaccattatcaacaaaaacacagagcaatttgtgtaacaaagagataatagtaacaatctcctattttataatgaaaatttgtaggaggtttttta Find is-nt database================================================ Query_seq: FN0451:FN0452|FN0451:FN0452:hypothetical protein:Glucosamine--fructose-6-phosphate aminotransferase [isomerizing]:->->:1095488..1095838 351 aggttatctgtcaagtgatattaataaaaaagtttagacttataactcatgtaattaagagaatttttgagaattaaacgacctaaaaattctcttattttttataacaaaaaattttaaaaacttgccaatttaaaaaaactataatataatttaccataggagatttatgtaaaagaagcgccagaactctttttagagttgacgaggattggaattatcgaagttttcggcggatgttccaaaggtggttacaaccattatcaacaaaaacacagagcaatttgtgtaacaaagagataatagtaacaatctcctattttataatgaaaatttgtaggaggtttttta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: FN0451:FN0452|FN0451:FN0452:hypothetical protein:Glucosamine--fructose-6-phosphate aminotransferase [isomerizing]:->->:1095488..1095838 351 aggttatctgtcaagtgatattaataaaaaagtttagacttataactcatgtaattaagagaatttttgagaattaaacgacctaaaaattctcttattttttataacaaaaaattttaaaaacttgccaatttaaaaaaactataatataatttaccataggagatttatgtaaaagaagcgccagaactctttttagagttgacgaggattggaattatcgaagttttcggcggatgttccaaaggtggttacaaccattatcaacaaaaacacagagcaatttgtgtaacaaagagataatagtaacaatctcctattttataatgaaaatttgtaggaggtttttta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: FN0451:FN0452|FN0451:FN0452:hypothetical protein:Glucosamine--fructose-6-phosphate aminotransferase [isomerizing]:->->:1095488..1095838 351 aggttatctgtcaagtgatattaataaaaaagtttagacttataactcatgtaattaagagaatttttgagaattaaacgacctaaaaattctcttattttttataacaaaaaattttaaaaacttgccaatttaaaaaaactataatataatttaccataggagatttatgtaaaagaagcgccagaactctttttagagttgacgaggattggaattatcgaagttttcggcggatgttccaaaggtggttacaaccattatcaacaaaaacacagagcaatttgtgtaacaaagagataatagtaacaatctcctattttataatgaaaatttgtaggaggtttttta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aggttatctgtcaagtgatattaataaaaaagtttagacttataactcatgtaattaagagaatttttgagaattaaacgacctaaaaattctcttattttttataacaaaaaattttaaaaacttgccaatttaaaaaaactataatataatttaccataggagatttatgtaaaagaagcgccagaactctttttagagttgacgaggattggaattatcgaagttttcggcggatgttccaaaggtggttacaaccattatcaacaaaaacacagagcaatttgtgtaacaaagagataatagtaacaatctcctattttataatgaaaatttgtaggaggtttttta Predict ORF larger than 30AA ================================================ Protein_Len: 45 Strand: + Start: 166 End: 300 ..................................................................................................................................................................... M Y V K E A P E L F L E L T R I G I I E V F G G C S K G G Y N H Y Q Q K H R A I C V T K R ................................................... Protein_Len: 60 Strand: + Start: 159 End: 350 .............................................................................................................................................................. M G D L C K R S A R T L F R V D E D W N Y R S F R R M F Q R W L Q P L S T K T Q S N L C N K E I I V T I S Y F I M K I C . Protein_Len: 31 Strand: - Start: 221 End: 313 ............................................................................................................................................................................................................................ R L K R R I N W L H N C G N D V F V C L L K H L L S I I T V M ...................................... Protein_Len: 38 Strand: - Start: 199 End: 312 ...................................................................................................................................................................................................... L Q R P N S N D F N E A S T G F T T V V M I L L F V S C N T Y C L S L L L M ....................................... Protein_Len: 30 Strand: - Start: 98 End: 187 ................................................................................................. K K Y C F I K F V Q W N L F V I I Y N V M P S K H L L L A M .................................................................................................................................................................... aggttatctgtcaagtgatattaataaaaaagtttagacttataactcatgtaattaagagaatttttgagaattaaacgacctaaaaattctcttattttttataacaaaaaattttaaaaacttgccaatttaaaaaaactataatataatttaccataggagatttatgtaaaagaagcgccagaactctttttagagttgacgaggattggaattatcgaagttttcggcggatgttccaaaggtggttacaaccattatcaacaaaaacacagagcaatttgtgtaacaaagagataatagtaacaatctcctattttataatgaaaatttgtaggaggtttttta 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: 90 Start: 124 End: 153 ...........................................................................................................................CTTGCCAATTTAAAAAAACTATAATATAAT...................................................................................................................................................................................................... PromScan Matrix: RpoD-17 Strand: + Score: 81 Start: 131 End: 160 ..................................................................................................................................ATTTAAAAAAACTATAATATAATTTACCAT............................................................................................................................................................................................... PromScan Matrix: RpoD-17 Strand: - Score: 81 Start: 217 End: 246 ........................................................................................................................................................................................................................TTTGGAACATCCGCCGAAAACTTCGATAAT......................................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ aggttatctgtcaagtgatattaataaaaaagtttagacttataactcatgtaattaagagaatttttgagaattaaacgacctaaaaattctcttattttttataacaaaaaattttaaaaacttgccaatttaaaaaaactataatataatttaccataggagatttatgtaaaagaagcgccagaactctttttagagttgacgaggattggaattatcgaagttttcggcggatgttccaaaggtggttacaaccattatcaacaaaaacacagagcaatttgtgtaacaaagagataatagtaacaatctcctattttataatgaaaatttgtaggaggtttttta Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 74 HP_score: -4.0 Tail_Score: -5.24129 Start: 56 End: 97 Full_Region: TATAACTCATGTAAT TAAGAGAATTTTTGAG AATTAAACGA CCTAAAAATTCTCTTA TTTTTTATAACAAAA .......................................................TAAGAGAATTTTTGAGAATTAAACGACCTAAAAATTCTCTTA.............................................................................................................................................................................................................................................................. Find igs database================================================ Query_seq: FN0451:FN0452|FN0451:FN0452:hypothetical protein:Glucosamine--fructose-6-phosphate aminotransferase [isomerizing]:->->:1095488..1095838 351 aggttatctgtcaagtgatattaataaaaaagtttagacttataactcatgtaattaagagaatttttgagaattaaacgacctaaaaattctcttattttttataacaaaaaattttaaaaacttgccaatttaaaaaaactataatataatttaccataggagatttatgtaaaagaagcgccagaactctttttagagttgacgaggattggaattatcgaagttttcggcggatgttccaaaggtggttacaaccattatcaacaaaaacacagagcaatttgtgtaacaaagagataatagtaacaatctcctattttataatgaaaatttgtaggaggtttttta Intra-Species Hit: Count: 1 Min: 1 Max: 351 Len: 351 Subject: NC_003454_FN0451_FN0452|hypothetical protein:Glucosamine--fructose-6-phosphate aminotransferase [isomerizing]|POSITIVE:POSITIVE|[1095488,1095838]|351 HSP 1 e-value: 1.0E-115 bit: 416.0 Len: 210 Query Start:142 Query End:351 Subject Strand: POSITIVE Subject Start: 142 Subject End: 351 .............................................................................................................................................ctataatataatttaccataggagatttatgtaaaagaagcgccagaactctttttagagttgacgaggattggaattatcgaagttttcggcggatgttccaaaggtggttacaaccattatcaacaaaaacacagagcaatttgtgtaacaaagagataatagtaacaatctcctattttataatgaaaatttgtaggaggtttttta .............................................................................................................................................ctataatataatttaccataggagatttatgtaaaagaagcgccagaactctttttagagttgacgaggattggaattatcgaagttttcggcggatgttccaaaggtggttacaaccattatcaacaaaaacacagagcaatttgtgtaacaaagagataatagtaacaatctcctattttataatgaaaatttgtaggaggtttttta HSP 2 e-value: 2.0E-26 bit: 121.0 Len: 61 Query Start:1 Query End:61 Subject Strand: POSITIVE Subject Start: 1 Subject End: 61 aggttatctgtcaagtgatattaataaaaaagtttagacttataactcatgtaattaagag.................................................................................................................................................................................................................................................................................................. aggttatctgtcaagtgatattaataaaaaagtttagacttataactcatgtaattaagag.................................................................................................................................................................................................................................................................................................. Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGGUUAUCUGUCAAGUGAUAUUAAUAAAAAAGUUUAGACUUAUAACUCAUGUAAUUAAGAGAAUUUUUGAGAAUUAAACGACCUAAAAAUUCUCUUAUUUUUUAUAACAAAAAAUUUUAAAAACUUGCCAAUUUAAAAAAACUAUAAUAUAAUUUACCAUAGGAGAUUUAUGUAAAAGAAGCGCCAGAACUCUUUUUAGAGUUGACGAGGAUUGGAAUUAUCGAAGUUUUCGGCGGAUGUUCCAAAGGUGGUUACAACCAUUAUCAACAAAAACACAGAGCAAUUUGUGUAACAAAGAGAUAAUAGUAACAAUCUCCUAUUUUAUAAUGAAAAUUUGUAGGAGGUUUUUUA .((((((..(((........................)))..))))))..(((((.((((((((((((((..............))))))))))))))....)))))............((((((((.((.............................((((((((((..........((.((((..((((((....))))))........(((((((..(((..(....)..)))..))))))).)))).))...((.((((((.......(((((((....)))))))........)))))).))...))))))))))..(((((.......))))))))))))))).. (-70.36) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAAAAACCUCCUACAAAUUUUCAUUAUAAAAUAGGAGAUUGUUACUAUUAUCUCUUUGUUACACAAAUUGCUCUGUGUUUUUGUUGAUAAUGGUUGUAACCACCUUUGGAACAUCCGCCGAAAACUUCGAUAAUUCCAAUCCUCGUCAACUCUAAAAAGAGUUCUGGCGCUUCUUUUACAUAAAUCUCCUAUGGUAAAUUAUAUUAUAGUUUUUUUAAAUUGGCAAGUUUUUAAAAUUUUUUGUUAUAAAAAAUAAGAGAAUUUUUAGGUCGUUUAAUUCUCAAAAAUUCUCUUAAUUACAUGAGUUAUAAGUCUAAACUUUUUUAUUAAUAUCACUUGACAGAUAACCU ....((((..((((.((((((((.((((...((((((((((...(((((((((........(((((........))))).......)))))))))(((((......((((((.......(((.....)))....))))))....((((((((((....)))))..)))))......)))))..)))))))))).))))...........(((((((.....(((((((............))))))).)))))))..)))))))).))))..)))).............................(((((..(((........................)))..))))).. (-66.92) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 451 78 31 53 6 NC_003454:FN1678|5end_hypothetical_protein_174287..174517_POSITIVE 251 279 231 109 52 NC_003454:FN1043|5end_hypothetical_protein_1694239..1694469_POSITIVE 240 108 77 212 182 NC_003454:FN1039|5end_Branched-chain_amino_acid_transport_protein_azlC_1690997..1691227_POSITIVE 239 250 202 228 181 NC_003454:FN1449|5end_Fusobacterium_outer_membrane_protein_family_2128109..2128339_NEGATIVE 237 317 273 43 11 NC_003454:FN0365|5end_ATP_synthase_protein_I,_sodium_ion_specific_994859..995089_NEGATIVE 231 256 221 90 48 NC_003454:FN0050|5end_Fumarate_reductase_flavoprotein_subunit_687043..687273_POSITIVE 223 230 191 182 131 NC_003454:FN0046|5end_3-dehydroquinate_dehydratase_683742..683972_POSITIVE 217 234 201 87 48 NC_003454:FN1460|5end_Hypothetical_cytosolic_protein_2141429..2141659_POSITIVE 215 203 161 111 66 NC_003454:FN1837|5end_putative_nucleotide-binding_protein_327255..327485_NEGATIVE 212 245 221 66 42 NC_003454:FN0644|5end_UROPORPHYRINOGEN-III_SYNTHASE_1301344..1301574_NEGATIVE 209 288 247 199 150 NC_003454:FN1284|5end_30S_ribosomal_protein_S4_1943243..1943473_NEGATIVE 208 292 262 183 145 NC_003454:FN0702|5end_N-acyl-L-amino_acid_amidohydrolase_1361002..1361232_NEGATIVE 199 252 223 68 45 NC_003454:FN0129|5end_Urease_accessory_protein_ureG_757595..757825_POSITIVE 198 252 225 180 147 NC_003454:FN1032|5end_hypothetical_protein_1686348..1686578_NEGATIVE 198 263 221 193 151 NC_003454:FN2040|5end_LSU_ribosomal_protein_L11P_549043..549273_NEGATIVE 197 204 161 81 38 NC_003454:FN0763|5end_Transporter,_LysE_family_1420169..1420399_POSITIVE 196 260 219 193 156 NC_003454:FN1022|5end_Calcium-transporting_ATPase_1674833..1675063_POSITIVE 195 208 183 121 87 NC_003454:FN1656|5end_SSU_ribosomal_protein_S18P_152760..152990_NEGATIVE 194 276 238 46 2 NC_003454:FN0866|5end_Integral_membrane_protein_1524515..1524745_NEGATIVE 194 242 206 213 167 NC_003454:FN0856|5end_glycogen_branching_enzyme_1516524..1516754_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 353 74 31 67 23 NC_003454:FN0812|3end_Hypothetical_cytosolic_protein_1471397..1471547_POSITIVE 249 96 52 52 5 NC_003454:FN0599|3end_Transposase_1255199..1255349_POSITIVE 249 96 52 53 6 NC_003454:FN0274|3end_Transposase_900285..900435_NEGATIVE 216 238 194 151 97 NC_003454:FN1531|3end_Negative_regulator_of_murein_hydrolase_44236..44386_NEGATIVE 212 245 221 42 18 NC_003454:FN0645|3end_Porphobilinogen_deaminase_1301368..1301518_NEGATIVE 208 292 262 117 79 NC_003454:FN0703|3end_N-acyl-L-amino_acid_amidohydrolase_1361068..1361218_NEGATIVE 208 24 4 111 91 NC_003454:FN1559|3end_cell_volume_regulation_protein_CvrA_82490..82640_POSITIVE 199 264 247 128 110 NC_003454:FN1285|3end_30S_ribosomal_protein_S11_1943283..1943433_NEGATIVE 199 252 223 68 45 NC_003454:FN0128|3end_Spermidine/putrescine-binding_protein_757675..757825_POSITIVE 198 198 151 143 93 NC_003454:FN0139|3end_Transposase_771640..771790_POSITIVE 198 257 213 61 19 NC_003454:FN2109|3end_UDP-glucose_4-epimerase_621917..622067_POSITIVE 195 208 183 76 42 NC_003454:FN1657|3end_SSU_ribosomal_protein_S6P_152805..152955_NEGATIVE 192 243 208 129 93 NC_003454:FN1304|3end_Single-strand_DNA_binding_protein_1960299..1960449_NEGATIVE 192 199 151 144 93 NC_003454:FN1680|3end_Transposase_175971..176121_NEGATIVE 191 324 295 84 52 NC_003454:FN0347|3end_phosphatidylserine_decarboxylase_979254..979404_NEGATIVE 190 97 57 53 15 NC_003454:FN1815|3end_Transposase_295626..295776_NEGATIVE 189 347 301 142 92 NC_003454:FN1073|3end_hypothetical_protein_1720989..1721139_POSITIVE 188 197 161 70 31 NC_003454:FN1059|3end_Branched_chain_amino_acid_transport_system_II_carrier_protein_1707020..1707170_POSITIVE 188 205 166 75 29 NC_003454:FN0899|3end_3-oxoacyl-[acyl-carrier_protein]_reductase_1559253..1559403_POSITIVE 186 48 5 117 75 NC_003454:FN1974|3end_DNA/RNA_helicase_(DEAD/DEAH_BOX_family)_472698..472848_NEGATIVE