Origin IGS: ttaacacataatcaaaatttctttttaatgattttttattatataatatttttttattttttacaaattttatcaggtatactttttaaaaatttgtgatataattggagtgtatttaagaaaaagagaggtattatattatggttaataaaggtattgttactaaaattaatggcgatacagtcgctgtaaaattatataaaagttcttcttgttcacattgtagctgttgtagtgaaactaataaa .........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 tttattagtttcactacaacagctacaatgtgaacaagaagaacttttatataattttacagcgactgtatcgccattaattttagtaacaatacctttattaaccataatataatacctctctttttcttaaatacactccaattatatcacaaatttttaaaaagtatacctgataaaatttgtaaaaaataaaaaaatattatataataaaaaatcattaaaaagaaattttgattatgtgttaa Mask Tandem Repeat Region ================================================ ttaacacataatcaaaatttctttttaatgattttttattatataatatttttttattttttacaaattttatcaggtatactttttaaaaatttgtgatataattggagtgtatttaagaaaaagagaggtattatattatggttaataaaggtattgttactaaaattaatggcgatacagtcgctgtaaaattatataaaagttcttcttgttcacattgtagctgttgtagtgaaactaataaa Find is-nt database================================================ Query_seq: FN0337:FN0338|FN0337:FN0338:hypothetical protein:hypothetical protein:<-->:971565..971812 248 ttaacacataatcaaaatttctttttaatgattttttattatataatatttttttattttttacaaattttatcaggtatactttttaaaaatttgtgatataattggagtgtatttaagaaaaagagaggtattatattatggttaataaaggtattgttactaaaattaatggcgatacagtcgctgtaaaattatataaaagttcttcttgttcacattgtagctgttgtagtgaaactaataaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: FN0337:FN0338|FN0337:FN0338:hypothetical protein:hypothetical protein:<-->:971565..971812 248 ttaacacataatcaaaatttctttttaatgattttttattatataatatttttttattttttacaaattttatcaggtatactttttaaaaatttgtgatataattggagtgtatttaagaaaaagagaggtattatattatggttaataaaggtattgttactaaaattaatggcgatacagtcgctgtaaaattatataaaagttcttcttgttcacattgtagctgttgtagtgaaactaataaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: FN0337:FN0338|FN0337:FN0338:hypothetical protein:hypothetical protein:<-->:971565..971812 248 ttaacacataatcaaaatttctttttaatgattttttattatataatatttttttattttttacaaattttatcaggtatactttttaaaaatttgtgatataattggagtgtatttaagaaaaagagaggtattatattatggttaataaaggtattgttactaaaattaatggcgatacagtcgctgtaaaattatataaaagttcttcttgttcacattgtagctgttgtagtgaaactaataaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ttaacacataatcaaaatttctttttaatgattttttattatataatatttttttattttttacaaattttatcaggtatactttttaaaaatttgtgatataattggagtgtatttaagaaaaagagaggtattatattatggttaataaaggtattgttactaaaattaatggcgatacagtcgctgtaaaattatataaaagttcttcttgttcacattgtagctgttgtagtgaaactaataaa Predict ORF larger than 30AA ================================================ Protein_Len: 30 Strand: + Start: 56 End: 145 ....................................................... M F Y K F Y Q V Y F L K I C D I I G V Y L R K R E V L Y Y G ....................................................................................................... Protein_Len: 37 Strand: + Start: 138 End: 248 ......................................................................................................................................... M M V N K G I V T K I N G D T V A V K L Y K S S S C S H C S C C S E T N K Protein_Len: 41 Strand: - Start: 57 End: 179 ........................................................ K K C I K D P I S K L F K H Y L Q L T N L F F L P I I N H N I F T N N S F N I A M ..................................................................... ttaacacataatcaaaatttctttttaatgattttttattatataatatttttttattttttacaaattttatcaggtatactttttaaaaatttgtgatataattggagtgtatttaagaaaaagagaggtattatattatggttaataaaggtattgttactaaaattaatggcgatacagtcgctgtaaaattatataaaagttcttcttgttcacattgtagctgttgtagtgaaactaataaa 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: 84 Start: 0 End: 29 gTTAACACATAATCAAAATTTCTTTTTAAT........................................................................................................................................................................................................................... PromScan Matrix: RpoD-17 Strand: - Score: 84 Start: 38 End: 67 .....................................TTTGTAAAAAATAAAAAAATATTATATAAT..................................................................................................................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ ttaacacataatcaaaatttctttttaatgattttttattatataatatttttttattttttacaaattttatcaggtatactttttaaaaatttgtgatataattggagtgtatttaagaaaaagagaggtattatattatggttaataaaggtattgttactaaaattaatggcgatacagtcgctgtaaaattatataaaagttcttcttgttcacattgtagctgttgtagtgaaactaataaa Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: FN0337:FN0338|FN0337:FN0338:hypothetical protein:hypothetical protein:<-->:971565..971812 248 ttaacacataatcaaaatttctttttaatgattttttattatataatatttttttattttttacaaattttatcaggtatactttttaaaaatttgtgatataattggagtgtatttaagaaaaagagaggtattatattatggttaataaaggtattgttactaaaattaatggcgatacagtcgctgtaaaattatataaaagttcttcttgttcacattgtagctgttgtagtgaaactaataaa Intra-Species Hit: Count: 1 Min: 96 Max: 248 Len: 153 Subject: NC_003454_FN0337_FN0338|hypothetical protein:hypothetical protein|NEGATIVE:POSITIVE|[971565,971812]|248 HSP 1 e-value: 1.0E-81 bit: 303.0 Len: 153 Query Start:96 Query End:248 Subject Strand: POSITIVE Subject Start: 96 Subject End: 248 ...............................................................................................gtgatataattggagtgtatttaagaaaaagagaggtattatattatggttaataaaggtattgttactaaaattaatggcgatacagtcgctgtaaaattatataaaagttcttcttgttcacattgtagctgttgtagtgaaactaataaa ...............................................................................................gtgatataattggagtgtatttaagaaaaagagaggtattatattatggttaataaaggtattgttactaaaattaatggcgatacagtcgctgtaaaattatataaaagttcttcttgttcacattgtagctgttgtagtgaaactaataaa Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GUGAUAUAAUUGGAGUGUAUUUAAGAAAAAGAGAGGUAUUAUAUUAUGGUUAAUAAAGGUAUUGUUACUAAAAUUAAUGGCGAUACAGUCGCUGUAAAAUUAUAUAAAAGUUCUUCUUGUUCACAUUGUAGCUGUUGUAGUGAAACUAAUAAA ....((((((((.(((((......(((...((((((.(((....(((((((......((((....)))).......((((((((...))))))))..)))))))....))).)))))).)))))))).))...)))))).............. (-23.80) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUAUUAGUUUCACUACAACAGCUACAAUGUGAACAAGAAGAACUUUUAUAUAAUUUUACAGCGACUGUAUCGCCAUUAAUUUUAGUAACAAUACCUUUAUUAACCAUAAUAUAAUACCUCUCUUUUUCUUAAAUACACUCCAAUUAUAUCAC .........(((((...............))))).(((((((....((((((.........((((.....))))........(((((((........))))))).....))))))......)))))))......................... (-12.96) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 621 45 1 231 187 NC_003454:FN0337|5end_hypothetical_protein_971474..971704_NEGATIVE 259 148 107 63 24 NC_003454:FN1147|5end_hypothetical_protein_1797829..1798059_NEGATIVE 259 147 116 41 6 NC_003454:FN1547|5end_PTS_permease_for_N-acetylglucosamine_and_glucose_63270..63500_NEGATIVE 258 144 106 183 146 NC_003454:FN1860|5end_NA+/H+_antiporter_NHAC_351477..351707_NEGATIVE 219 98 54 77 17 NC_003454:FN1507|5end_riboflavin_synthase_subunit_alpha_12073..12303_POSITIVE 217 50 12 37 7 NC_003454:FN0667|5end_Na+_driven_multidrug_efflux_pump_1323624..1323854_NEGATIVE 211 106 68 37 6 NC_003454:FN0866|5end_Integral_membrane_protein_1524515..1524745_NEGATIVE 209 140 91 196 136 NC_003454:FN0090|5end_Ethanolamine_utilization_protein_eutQ_726315..726545_POSITIVE 207 137 91 110 59 NC_003454:FN1458|5end_UDP-N-acetylmuramoylalanine--D-glutamate_ligase_2140341..2140571_NEGATIVE 204 143 109 217 176 NC_003454:FN2091|5end_hypothetical_protein_602481..602711_NEGATIVE 199 118 72 102 62 NC_003454:FN0725|5end_Molybdopterin_biosynthesis_MoeB_protein_1384885..1385115_NEGATIVE 198 98 54 58 11 NC_003454:FN2003|5end_bioY_protein_503745..503975_POSITIVE 194 137 100 178 143 NC_003454:FN1868|5end_Hypothetical_cytosolic_protein_360433..360663_NEGATIVE 193 143 114 72 25 NC_003454:FN0053|5end_Branched-chain_amino_acid_transport_system_carrier_protein_689340..689570_POSITIVE 193 40 7 38 11 NC_003454:FN2036|5end_DNA-directed_RNA_polymerase_beta_chain_546371..546601_NEGATIVE 192 38 5 191 151 NC_003454:FN1435|5end_Export_ABC_transporter_2105034..2105264_POSITIVE 192 133 100 49 15 NC_003454:FN1295|5end_Acetyltransferase_1953565..1953795_NEGATIVE 188 139 109 183 147 NC_003454:FN2037|5end_LSU_ribosomal_protein_L12P_(L7/L12)_547137..547367_NEGATIVE 188 97 61 70 23 NC_003454:FN1604|5end_hypothetical_protein_113822..114052_NEGATIVE 188 97 61 231 184 NC_003454:FN1603|5end_2',3'-cyclic_nucleotide_3'-phosphodiesterase_113661..113891_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 246 87 41 148 98 NC_003454:FN1989|3end_Sodium-dependent_tyrosine_transporter_493827..493977_POSITIVE 218 94 57 140 106 NC_003454:FN0934|3end_chorismate_synthase_1587593..1587743_POSITIVE 204 143 109 84 43 NC_003454:FN2092|3end_Integral_membrane_protein_602614..602764_NEGATIVE 195 138 91 123 65 NC_003454:FN1487|3end_hypothetical_protein_2169559..2169709_NEGATIVE 192 95 51 86 50 NC_003454:FN0721|3end_hypothetical_protein_1377633..1377783_NEGATIVE 188 44 20 29 4 NC_003454:FN1219|3end_hypothetical_protein_1879101..1879251_POSITIVE 188 139 109 136 100 NC_003454:FN2038|3end_LSU_ribosomal_protein_L10P_547184..547334_NEGATIVE 186 136 93 80 40 NC_003454:FN1401|3end_urocanate_hydratase_2060426..2060576_POSITIVE 186 138 103 138 106 NC_003454:FN1215|3end_Hypothetical_cytosolic_protein_1875460..1875610_NEGATIVE 185 137 93 122 77 NC_003454:FN1379|3end_Citrate_lyase_beta_chain_2027325..2027475_POSITIVE 184 149 109 116 80 NC_003454:FN0923|3end_Cardiolipin_synthetase_1577538..1577688_NEGATIVE 181 135 103 102 68 NC_003454:FN0595|3end_UDP-N-acetylglucosamine_acyltransferase_1250081..1250231_POSITIVE 180 141 103 49 7 NC_003454:FN0031|3end_hypothetical_protein_667899..668049_NEGATIVE 174 136 91 113 64 NC_003454:FN1709|3end_CDP-diacylglycerol--glycerol-3-phosphate_3-phosphatidyltransferase_206058..206208_POSITIVE 173 139 91 46 3 NC_003454:FN1495|3end_hypothetical_protein_-89..61_NEGATIVE 173 145 106 139 95 NC_003454:FN0737|3end_hypothetical_protein_1395415..1395565_NEGATIVE 173 147 111 120 77 NC_003454:FN0594|3end_(3R)-hydroxymyristoyl-[acyl_carrier_protein]_dehydratase_1249290..1249440_POSITIVE 170 50 9 42 2 NC_003454:FN1193|3end_hypothetical_protein_1855401..1855551_POSITIVE 170 43 9 47 7 NC_003454:FN0225|3end_Gluconate_permease_851715..851865_NEGATIVE 169 125 87 70 38 NC_003454:FN1485|3end_Transporter_2167351..2167501_NEGATIVE