Origin IGS: cttatttgaagttatttttccaataattttagctttcttgctatttttctcactttgtaacataaaaattgtagtattattttctttttttattgataaatcatagctttcagcaagaaattgtaaaattgaatttacatcttctcccttgttgaaatatgtatctattacaatatctttggcttcttaattttttcctgtttccttagataaaactgctaaaacttcgtgcaaaggcatatctataatatctatatcacgatttaaagcagctggaaatataaaggtattaaaaattaaaaatatgattaaagtaaattttt .........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 aaaaatttactttaatcatatttttaatttttaatacctttatatttccagctgctttaaatcgtgatatagatattatagatatgcctttgcacgaagttttagcagttttatctaaggaaacaggaaaaaattaagaagccaaagatattgtaatagatacatatttcaacaagggagaagatgtaaattcaattttacaatttcttgctgaaagctatgatttatcaataaaaaaagaaaataatactacaatttttatgttacaaagtgagaaaaatagcaagaaagctaaaattattggaaaaataacttcaaataag Mask Tandem Repeat Region ================================================ cttatttgaagttatttttccaataattttagctttcttgctatttttctcactttgtaacataaaaattgtagtattattttctttttttattgataaatcatagctttcagcaagaaattgtaaaattgaatttacatcttctcccttgttgaaatatgtatctattacaatatctttggcttcttaattttttcctgtttccttagataaaactgctaaaacttcgtgcaaaggcatatctataatatctatatcacgatttaaagcagctggaaatataaaggtattaaaaattaaaaatatgattaaagtaaattttt Find is-nt database================================================ Query_seq: FN2086:FN2087|FN2086:FN2087:General secretion pathway protein D:hypothetical protein:<-<-:598806..599128 323 cttatttgaagttatttttccaataattttagctttcttgctatttttctcactttgtaacataaaaattgtagtattattttctttttttattgataaatcatagctttcagcaagaaattgtaaaattgaatttacatcttctcccttgttgaaatatgtatctattacaatatctttggcttcttaattttttcctgtttccttagataaaactgctaaaacttcgtgcaaaggcatatctataatatctatatcacgatttaaagcagctggaaatataaaggtattaaaaattaaaaatatgattaaagtaaattttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: FN2086:FN2087|FN2086:FN2087:General secretion pathway protein D:hypothetical protein:<-<-:598806..599128 323 cttatttgaagttatttttccaataattttagctttcttgctatttttctcactttgtaacataaaaattgtagtattattttctttttttattgataaatcatagctttcagcaagaaattgtaaaattgaatttacatcttctcccttgttgaaatatgtatctattacaatatctttggcttcttaattttttcctgtttccttagataaaactgctaaaacttcgtgcaaaggcatatctataatatctatatcacgatttaaagcagctggaaatataaaggtattaaaaattaaaaatatgattaaagtaaattttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: FN2086:FN2087|FN2086:FN2087:General secretion pathway protein D:hypothetical protein:<-<-:598806..599128 323 cttatttgaagttatttttccaataattttagctttcttgctatttttctcactttgtaacataaaaattgtagtattattttctttttttattgataaatcatagctttcagcaagaaattgtaaaattgaatttacatcttctcccttgttgaaatatgtatctattacaatatctttggcttcttaattttttcctgtttccttagataaaactgctaaaacttcgtgcaaaggcatatctataatatctatatcacgatttaaagcagctggaaatataaaggtattaaaaattaaaaatatgattaaagtaaattttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 cttatttgaagttatttttccaataattttagctttcttgctatttttctcactttgtaacataaaaattgtagtattattttctttttttattgataaatcatagctttcagcaagaaattgtaaaattgaatttacatcttctcccttgttgaaatatgtatctattacaatatctttggcttcttaattttttcctgtttccttagataaaactgctaaaacttcgtgcaaaggcatatctataatatctatatcacgatttaaagcagctggaaatataaaggtattaaaaattaaaaatatgattaaagtaaattttt Predict ORF larger than 30AA ================================================ Protein_Len: 30 Strand: + Start: 14 End: 103 ............. M F P I I L A F L L F F S L C N I K I V V L F S F F I D K S ............................................................................................................................................................................................................................ Protein_Len: 40 Strand: - Start: 190 End: 309 ............................................................................................................................................................................................. N K G T E K S L V A L V E H L P M D I I D I D R N L A A P F I F T N F I L F I M .............. Protein_Len: 58 Strand: - Start: 1 End: 174 K N S T I K G I I K A K K S N K E S Q L M F I T T N N E K K I S L D Y S E A L F Q L I S N V D E G K N F Y T D I V M ..................................................................................................................................................... cttatttgaagttatttttccaataattttagctttcttgctatttttctcactttgtaacataaaaattgtagtattattttctttttttattgataaatcatagctttcagcaagaaattgtaaaattgaatttacatcttctcccttgttgaaatatgtatctattacaatatctttggcttcttaattttttcctgtttccttagataaaactgctaaaacttcgtgcaaaggcatatctataatatctatatcacgatttaaagcagctggaaatataaaggtattaaaaattaaaaatatgattaaagtaaattttt 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================================================ cttatttgaagttatttttccaataattttagctttcttgctatttttctcactttgtaacataaaaattgtagtattattttctttttttattgataaatcatagctttcagcaagaaattgtaaaattgaatttacatcttctcccttgttgaaatatgtatctattacaatatctttggcttcttaattttttcctgtttccttagataaaactgctaaaacttcgtgcaaaggcatatctataatatctatatcacgatttaaagcagctggaaatataaaggtattaaaaattaaaaatatgattaaagtaaattttt Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 44 HP_score: -2.8 Tail_Score: -3.30629 Start: 122 End: 139 Full_Region: CTTTCAGCAAGAAAT TGTAAA ATTGAA TTTACA TCTTCTCCCTTGTTG .........................................................................................................................TGTAAAATTGAATTTACA........................................................................................................................................................................................ TransTerm Strand: - Conf: 42 HP_score: -2.8 Tail_Score: -3.14284 Start: 122 End: 139 Full_Region: caacaagggagaaga tgtaaa ttcaat tttaca atttcttgctgaaag .........................................................................................................................tgtaaattcaattttaca........................................................................................................................................................................................ Find igs database================================================ Query_seq: FN2086:FN2087|FN2086:FN2087:General secretion pathway protein D:hypothetical protein:<-<-:598806..599128 323 cttatttgaagttatttttccaataattttagctttcttgctatttttctcactttgtaacataaaaattgtagtattattttctttttttattgataaatcatagctttcagcaagaaattgtaaaattgaatttacatcttctcccttgttgaaatatgtatctattacaatatctttggcttcttaattttttcctgtttccttagataaaactgctaaaacttcgtgcaaaggcatatctataatatctatatcacgatttaaagcagctggaaatataaaggtattaaaaattaaaaatatgattaaagtaaattttt Intra-Species Hit: Count: 1 Min: 1 Max: 323 Len: 323 Subject: NC_003454_FN2086_FN2087|General secretion pathway protein D:hypothetical protein|NEGATIVE:NEGATIVE|[598806,599128]|323 HSP 1 e-value: 1.0E-170 bit: 599.0 Len: 323 Query Start:1 Query End:323 Subject Strand: POSITIVE Subject Start: 1 Subject End: 323 cttatttgaagttatttttccaataattttagctttcttgctatttttctcactttgtaacataaaaattgtagtattattttcnnnnnnnattgataaatcatagctttcagcaagaaattgtaaaattgaatttacatcttctcccttgttgaaatatgtatctattacaatatctttggcttcttaattttttcctgtttccttagataaaactgctaaaacttcgtgcaaaggcatatctataatatctatatcacgatttaaagcagctggaaatataaaggtattaaaaattaaaaatatgattaaagtaaattttt cttatttgaagttatttttccaataattttagctttcttgctatttttctcactttgtaacataaaaattgtagtattattttctttttttattgataaatcatagctttcagcaagaaattgtaaaattgaatttacatcttctcccttgttgaaatatgtatctattacaatatctttggcttcttaattttttcctgtttccttagataaaactgctaaaacttcgtgcaaaggcatatctataatatctatatcacgatttaaagcagctggaaatataaaggtattaaaaattaaaaatatgattaaagtaaattttt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CUUAUUUGAAGUUAUUUUUCCAAUAAUUUUAGCUUUCUUGCUAUUUUUCUCACUUUGUAACAUAAAAAUUGUAGUAUUAUUUUCUUUUUUUAUUGAUAAAUCAUAGCUUUCAGCAAGAAAUUGUAAAAUUGAAUUUACAUCUUCUCCCUUGUUGAAAUAUGUAUCUAUUACAAUAUCUUUGGCUUCUUAAUUUUUUCCUGUUUCCUUAGAUAAAACUGCUAAAACUUCGUGCAAAGGCAUAUCUAUAAUAUCUAUAUCACGAUUUAAAGCAGCUGGAAAUAUAAAGGUAUUAAAAAUUAAAAAUAUGAUUAAAGUAAAUUUUU .(((((.((((.....)))).)))))...((((......))))........((((((...((((...(((((((((..................((((...((((..((((((((((((..((((((......))))))..))))....)))))))))))))))))))))))))............(((((((((.(((((((((..........(((((......(((((....((.((((.....))))))....))))).....)))))..))))))....)))....)))))))))...))))..))))))........ (-53.56) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAAAUUUACUUUAAUCAUAUUUUUAAUUUUUAAUACCUUUAUAUUUCCAGCUGCUUUAAAUCGUGAUAUAGAUAUUAUAGAUAUGCCUUUGCACGAAGUUUUAGCAGUUUUAUCUAAGGAAACAGGAAAAAAUUAAGAAGCCAAAGAUAUUGUAAUAGAUACAUAUUUCAACAAGGGAGAAGAUGUAAAUUCAAUUUUACAAUUUCUUGCUGAAAGCUAUGAUUUAUCAAUAAAAAAAGAAAAUAAUACUACAAUUUUUAUGUUACAAAGUGAGAAAAAUAGCAAGAAAGCUAAAAUUAUUGGAAAAAUAACUUCAAAUAAG .....((((((((...((((((((((((((((....(((.....((((((((((((..((.(((((....((.(((.......))).))...)))))..))..)))))))........))))).))).))))))))))))........(((((..((((((.(((((((((.((((..(.....((((((......)))))).)..)))).)))))..)))))))))))))))..........................))))....)))))))).....((((......))))...(((((.(((.......))).))))). (-55.80) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 697 80 31 171 122 NC_003454:FN2086|5end_General_secretion_pathway_protein_D_598715..598945_NEGATIVE 270 50 6 117 76 NC_003454:FN1844|5end_Ketoacyl_reductase_hetN_333593..333823_POSITIVE 257 175 133 201 153 NC_003454:FN0884|5end_Hemin_transport_system_permease_protein_hmuU_1544741..1544971_NEGATIVE 241 188 141 99 49 NC_003454:FN1605|5end_Adenylosuccinate_synthetase_115276..115506_NEGATIVE 240 74 31 141 97 NC_003454:FN0762|5end_hypothetical_protein_1420100..1420330_NEGATIVE 238 52 27 90 64 NC_003454:FN1329|5end_Methyltransferase_1983890..1984120_NEGATIVE 237 188 142 210 141 NC_003454:FN2067|5end_Thiol:disulfide_interchange_protein_tlpA_577378..577608_NEGATIVE 231 55 11 179 129 NC_003454:FN1381|5end_hypothetical_protein_2032434..2032664_NEGATIVE 231 80 34 212 176 NC_003454:FN1197|5end_hypothetical_protein_1857676..1857906_NEGATIVE 230 210 180 34 1 NC_003454:FN1145|5end_Oligoendopeptidase_F_1795931..1796161_NEGATIVE 229 50 1 196 131 NC_003454:FN0307|5end_Iron(III)_dicitrate_transport_ATP-binding_protein_fecE_942095..942325_POSITIVE 227 210 163 161 115 NC_003454:FN1595|5end_Na(+)-translocating_NADH-quinone_reductase_subunit_B_105827..106057_NEGATIVE 226 163 133 154 120 NC_003454:FN0350|5end_hypothetical_protein_982372..982602_POSITIVE 223 234 193 159 125 NC_003454:FN1464|5end_1-deoxy-D-xylulose-5-phosphate_synthase_2147705..2147935_NEGATIVE 223 39 5 60 23 NC_003454:FN1041|5end_Acetyltransferase_1692081..1692311_POSITIVE 223 219 172 67 14 NC_003454:FN0661|5end_hypothetical_protein_1317729..1317959_POSITIVE 221 49 6 155 114 NC_003454:FN0766|5end_Large-conductance_mechanosensitive_channel_1421910..1422140_POSITIVE 220 198 151 153 111 NC_003454:FN1683|5end_Acetyltransferase_179082..179312_NEGATIVE 219 207 163 157 111 NC_003454:FN0120|5end_hypothetical_protein_752891..753121_NEGATIVE 218 60 15 63 8 NC_003454:FN2032|5end_DNA-directed_RNA_polymerase_omega_chain_537315..537545_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 264 46 7 121 87 NC_003454:FN0222|3end_Melibiose_carrier_protein_848238..848388_POSITIVE 241 188 141 89 39 NC_003454:FN1606|3end_3-deoxy-D-manno-octulosonic-acid_transferase_115286..115436_NEGATIVE 238 52 27 77 51 NC_003454:FN1330|3end_S-adenosylmethionine:tRNA_ribosyltransferase-isomerase_1983903..1984053_NEGATIVE 237 188 142 143 74 NC_003454:FN2068|3end_dGTP_triphosphohydrolase_577445..577595_NEGATIVE 227 210 163 135 89 NC_003454:FN1596|3end_Nitrogen_fixation_iron-sulphur_protein_RNFC_105853..106003_NEGATIVE 226 163 133 38 4 NC_003454:FN0349|3end_D-tyrosyl-tRNA_deacylase_982336..982486_POSITIVE 223 39 5 48 11 NC_003454:FN1040|3end_Branched-chain_amino_acid_transport_protein_azlD_1692149..1692299_POSITIVE 221 49 6 125 84 NC_003454:FN0765|3end_tRNA_(5-methylaminomethyl-2-thiouridylate)_-methyltransferase_1421960..1422110_POSITIVE 219 207 163 140 94 NC_003454:FN0121|3end_hypothetical_protein_752908..753058_NEGATIVE 219 180 134 139 95 NC_003454:FN1684|3end_N-acetylneuraminate_synthase_179083..179233_NEGATIVE 217 42 2 103 64 NC_003454:FN1366|3end_Triosephosphate_isomerase_2016763..2016913_NEGATIVE 213 188 143 51 14 NC_003454:FN0057|3end_Endonuclease_III_693900..694050_POSITIVE 210 115 72 136 83 NC_003454:FN0597|3end_Lipid-A-disaccharide_synthase_1251964..1252114_POSITIVE 208 64 24 98 55 NC_003454:FN1489|3end_Methionyl-tRNA_formyltransferase_2170880..2171030_NEGATIVE 208 58 18 54 13 NC_003454:FN1472|3end_N-acetylneuraminate-binding_protein_2155088..2155238_POSITIVE 208 294 265 120 94 NC_003454:FN1838|3end_Glycerol_uptake_facilitator_protein_328333..328483_POSITIVE 208 80 34 53 17 NC_003454:FN1575|3end_Hypothetical_cytosolic_protein_86193..86343_NEGATIVE 207 235 191 140 81 NC_003454:FN0423|3end_Dihydroorotate_dehydrogenase_electron_transfer_subunit_1067187..1067337_POSITIVE 207 164 129 103 64 NC_003454:FN0292|3end_Hemolysin_activator_protein_precursor_925011..925161_NEGATIVE 206 188 142 116 63 NC_003454:FN0622|3end_N-glycosylase/DNA_lyase_1282011..1282161_POSITIVE