Origin IGS: gtcagcttcaaacatgctgagaattactcggctcactctgtttgattttttatctaaaatttagaatgcagattcacttgttttttactaatatatccagtgtaactctcttatttttattttcactaaaatttgagtttacaacaaccttggtttattttatatgaaactttttt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aaaaaagtttcatataaaataaaccaaggttgttgtaaactcaaattttagtgaaaataaaaataagagagttacactggatatattagtaaaaaacaagtgaatctgcattctaaattttagataaaaaatcaaacagagtgagccgagtaattctcagcatgtttgaagctgac Mask Tandem Repeat Region ================================================ gtcagcttcaaacatgctgagaattactcggctcactctgtttgattttttatctaaaatttagaatgcagattcacttgttttttactaatatatccagtgtaactctcttatttttattttcactaaaatttgagtttacaacaaccttggtttattttatatgaaactttttt Find is-nt database================================================ Query_seq: FN1604:FN1605|FN1604:FN1605:hypothetical protein:Adenylosuccinate synthetase:<-<-:113913..114088 176 gtcagcttcaaacatgctgagaattactcggctcactctgtttgattttttatctaaaatttagaatgcagattcacttgttttttactaatatatccagtgtaactctcttatttttattttcactaaaatttgagtttacaacaaccttggtttattttatatgaaactttttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: FN1604:FN1605|FN1604:FN1605:hypothetical protein:Adenylosuccinate synthetase:<-<-:113913..114088 176 gtcagcttcaaacatgctgagaattactcggctcactctgtttgattttttatctaaaatttagaatgcagattcacttgttttttactaatatatccagtgtaactctcttatttttattttcactaaaatttgagtttacaacaaccttggtttattttatatgaaactttttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: FN1604:FN1605|FN1604:FN1605:hypothetical protein:Adenylosuccinate synthetase:<-<-:113913..114088 176 gtcagcttcaaacatgctgagaattactcggctcactctgtttgattttttatctaaaatttagaatgcagattcacttgttttttactaatatatccagtgtaactctcttatttttattttcactaaaatttgagtttacaacaaccttggtttattttatatgaaactttttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gtcagcttcaaacatgctgagaattactcggctcactctgtttgattttttatctaaaatttagaatgcagattcacttgttttttactaatatatccagtgtaactctcttatttttattttcactaaaatttgagtttacaacaaccttggtttattttatatgaaactttttt Predict ORF larger than 30AA ================================================ Protein_Len: 41 Strand: + Start: 42 End: 164 ......................................... M I F Y L K F R M Q I H L F F T N I S S V T L L F L F S L K F E F T T T L V Y F I ............ gtcagcttcaaacatgctgagaattactcggctcactctgtttgattttttatctaaaatttagaatgcagattcacttgttttttactaatatatccagtgtaactctcttatttttattttcactaaaatttgagtttacaacaaccttggtttattttatatgaaactttttt 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================================================ gtcagcttcaaacatgctgagaattactcggctcactctgtttgattttttatctaaaatttagaatgcagattcacttgttttttactaatatatccagtgtaactctcttatttttattttcactaaaatttgagtttacaacaaccttggtttattttatatgaaactttttt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: FN1604:FN1605|FN1604:FN1605:hypothetical protein:Adenylosuccinate synthetase:<-<-:113913..114088 176 gtcagcttcaaacatgctgagaattactcggctcactctgtttgattttttatctaaaatttagaatgcagattcacttgttttttactaatatatccagtgtaactctcttatttttattttcactaaaatttgagtttacaacaaccttggtttattttatatgaaactttttt Intra-Species Hit: Count: 1 Min: 1 Max: 176 Len: 176 Subject: NC_003454_FN1604_FN1605|hypothetical protein:Adenylosuccinate synthetase|NEGATIVE:NEGATIVE|[113913,114088]|176 HSP 1 e-value: 2.0E-95 bit: 349.0 Len: 176 Query Start:1 Query End:176 Subject Strand: POSITIVE Subject Start: 1 Subject End: 176 gtcagcttcaaacatgctgagaattactcggctcactctgtttgattttttatctaaaatttagaatgcagattcacttgttttttactaatatatccagtgtaactctcttatttttattttcactaaaatttgagtttacaacaaccttggtttattttatatgaaactttttt gtcagcttcaaacatgctgagaattactcggctcactctgtttgattttttatctaaaatttagaatgcagattcacttgttttttactaatatatccagtgtaactctcttatttttattttcactaaaatttgagtttacaacaaccttggtttattttatatgaaactttttt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GUCAGCUUCAAACAUGCUGAGAAUUACUCGGCUCACUCUGUUUGAUUUUUUAUCUAAAAUUUAGAAUGCAGAUUCACUUGUUUUUUACUAAUAUAUCCAGUGUAACUCUCUUAUUUUUAUUUUCACUAAAAUUUGAGUUUACAACAACCUUGGUUUAUUUUAUAUGAAACUUUUUU (((.((.(((((((.((((((.....))))))......))))))).......((((.....))))..)).)))......(((((.....((((...(((((((((..(((..(((((..........)))))..))).)))))......))))..))))......)))))...... (-28.70) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAAAAGUUUCAUAUAAAAUAAACCAAGGUUGUUGUAAACUCAAAUUUUAGUGAAAAUAAAAAUAAGAGAGUUACACUGGAUAUAUUAGUAAAAAACAAGUGAAUCUGCAUUCUAAAUUUUAGAUAAAAAAUCAAACAGAGUGAGCCGAGUAAUUCUCAGCAUGUUUGAAGCUGAC .....(((((((.(((...........((((......))))...(((((.((....)).)))))..(((((((((...((((.((((.((.....)).)))).)))).((((((..(((((......))))).....))))))......)))))))))....))).)))))))... (-29.30) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 872 50 1 141 92 NC_003454:FN1604|5end_hypothetical_protein_113822..114052_NEGATIVE 576 50 4 105 59 NC_003454:FN1460|5end_Hypothetical_cytosolic_protein_2141429..2141659_POSITIVE 425 60 11 149 100 NC_003454:FN1507|5end_riboflavin_synthase_subunit_alpha_12073..12303_POSITIVE 278 34 2 231 196 NC_003454:FN1651|5end_Oligopeptide_transport_system_permease_protein_oppB_145799..146029_NEGATIVE 251 87 47 231 191 NC_003454:FN1615|5end_Integral_membrane_protein_125125..125355_POSITIVE 245 55 14 154 114 NC_003454:FN0080|5end_ethanolamine_ammonia-lyase_small_subunit_719041..719271_POSITIVE 242 130 81 106 60 NC_003454:FN0325|5end_50S_ribosomal_protein_L20_961274..961504_NEGATIVE 239 86 56 180 151 NC_003454:FN0081|5end_Ethanolamine_utilization_protein_eutL_720035..720265_POSITIVE 228 126 86 99 47 NC_003454:FN1875|5end_Peptidyl-prolyl_cis-trans_isomerase_364400..364630_NEGATIVE 227 57 18 115 73 NC_003454:FN0350|5end_hypothetical_protein_982372..982602_POSITIVE 220 41 11 73 38 NC_003454:FN0378|5end_UDP-glucose_4-epimerase_1010196..1010426_NEGATIVE 217 158 115 202 158 NC_003454:FN0680|5end_Ribulose-phosphate_3-epimerase_1335455..1335685_POSITIVE 213 50 6 231 193 NC_003454:FN0120|5end_hypothetical_protein_752891..753121_NEGATIVE 211 151 134 204 187 NC_003454:FN1420|5end_NA+/H+_antiporter_NHAC_2081899..2082129_POSITIVE 210 53 11 75 36 NC_003454:FN0398|5end_Dipeptide_transport_system_permease_protein_dppC_1036758..1036988_POSITIVE 209 119 99 161 141 NC_003454:FN1440|5end_1-phosphofructokinase_2107238..2107468_POSITIVE 203 87 47 84 45 NC_003454:FN0757|5end_Hypothetical_cytosolic_protein_1416201..1416431_NEGATIVE 203 138 96 222 186 NC_003454:FN0222|5end_Melibiose_carrier_protein_846812..847042_POSITIVE 202 117 73 112 66 NC_003454:FN0334|5end_Aspartate/aromatic_aminotransferase_969066..969296_NEGATIVE 201 97 59 61 22 NC_003454:FN1118|5end_hypothetical_protein_1760559..1760789_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 539 79 31 51 3 NC_003454:FN0796|3end_pyruvate_phosphate_dikinase_1455643..1455793_POSITIVE 425 60 11 56 7 NC_003454:FN1506|3end_5-amino-6-(5-phosphoribosylamino)uracil_reductase_12060..12210_POSITIVE 289 68 27 60 19 NC_003454:FN0713|3end_Chromate_transport_protein_1371943..1372093_POSITIVE 245 55 14 142 102 NC_003454:FN0079|3end_Ethanolamine_ammonia-lyase_heavy_chain_719109..719259_POSITIVE 242 130 81 81 35 NC_003454:FN0326|3end_LSU_ribosomal_protein_L35P_961299..961449_NEGATIVE 239 86 56 73 44 NC_003454:FN0080|3end_ethanolamine_ammonia-lyase_small_subunit_720008..720158_POSITIVE 227 150 101 76 22 NC_003454:FN1652|3end_Oligopeptide-binding_protein_oppA_146041..146191_NEGATIVE 211 151 134 57 40 NC_003454:FN1419|3end_methionine_gamma-lyase_2081832..2081982_POSITIVE 210 53 11 65 26 NC_003454:FN0397|3end_Dipeptide_transport_system_permease_protein_dppB_1036828..1036978_POSITIVE 209 119 99 88 68 NC_003454:FN1439|3end_Transcriptional_regulator,_DeoR_family_2107245..2107395_POSITIVE 203 87 47 71 32 NC_003454:FN0758|3end_Rod_shape-determining_protein_mreB_1416214..1416364_NEGATIVE 203 138 96 43 7 NC_003454:FN0221|3end_Carbon_starvation_protein_A_846713..846863_POSITIVE 201 97 59 58 19 NC_003454:FN1117|3end_LSU_ribosomal_protein_L21P_1760636..1760786_POSITIVE 201 121 99 95 73 NC_003454:FN0109|3end_hypothetical_protein_744333..744483_NEGATIVE 196 101 67 72 38 NC_003454:FN1864|3end_DNA_mismatch_repair_protein_mutS_354678..354828_NEGATIVE 195 113 81 83 48 NC_003454:FN1342|3end_Holo-[acyl-carrier_protein]_synthase_1996091..1996241_NEGATIVE 189 47 6 56 11 NC_003454:FN0930|3end_Glycerol-3-phosphate_cytidylyltransferase_1583482..1583632_NEGATIVE 188 114 72 140 93 NC_003454:FN1170|3end_Pyruvate-flavodoxin_oxidoreductase_1828707..1828857_NEGATIVE 188 133 93 115 68 NC_003454:FN1106|3end_L-serine_dehydratase_1751873..1752023_POSITIVE 187 125 88 143 105 NC_003454:FN0721|3end_hypothetical_protein_1377633..1377783_NEGATIVE