Origin IGS: tttctaccctcctgttgcaaatattataataagctttttatctctagttaaattttacaccttttttcgcttttttacaacaataaaaaaagagactgctctaaaagtagtctcttaatcagttaattaa .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 ttaattaactgattaagagactacttttagagcagtctctttttttattgttgtaaaaaagcgaaaaaaggtgtaaaatttaactagagataaaaagcttattataatatttgcaacaggagggtagaaa Mask Tandem Repeat Region ================================================ tttctaccctcctgttgcaaatattataataagctttttatctctagttaaattttacaccttttttcgcttttttacaacaataaaaaaagagactgctctaaaagtagtctcttaatcagttaattaa Find is-nt database================================================ Query_seq: FN1763:FN1764|FN1763:FN1764:Hypothetical cytosolic protein:Enolase:<-<-:256653..256782 130 tttctaccctcctgttgcaaatattataataagctttttatctctagttaaattttacaccttttttcgcttttttacaacaataaaaaaagagactgctctaaaagtagtctcttaatcagttaattaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: FN1763:FN1764|FN1763:FN1764:Hypothetical cytosolic protein:Enolase:<-<-:256653..256782 130 tttctaccctcctgttgcaaatattataataagctttttatctctagttaaattttacaccttttttcgcttttttacaacaataaaaaaagagactgctctaaaagtagtctcttaatcagttaattaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: FN1763:FN1764|FN1763:FN1764:Hypothetical cytosolic protein:Enolase:<-<-:256653..256782 130 tttctaccctcctgttgcaaatattataataagctttttatctctagttaaattttacaccttttttcgcttttttacaacaataaaaaaagagactgctctaaaagtagtctcttaatcagttaattaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tttctaccctcctgttgcaaatattataataagctttttatctctagttaaattttacaccttttttcgcttttttacaacaataaaaaaagagactgctctaaaagtagtctcttaatcagttaattaa Predict ORF larger than 30AA ================================================ Protein_Len: 31 Strand: + Start: 23 End: 115 ...................... M I I S F L S L V K F Y T F F R F F T T I K K E T A L K V V S ............... tttctaccctcctgttgcaaatattataataagctttttatctctagttaaattttacaccttttttcgcttttttacaacaataaaaaaagagactgctctaaaagtagtctcttaatcagttaattaa 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: 52 End: 81 ...................................................GTTGTAAAAAAGCGAAAAAAGGTGTAAAAT................................................. PromScan Matrix: RpoD-17 Strand: - Score: 83 Start: 23 End: 52 ......................TTTAACTAGAGATAAAAAGCTTATTATAAT.............................................................................. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ tttctaccctcctgttgcaaatattataataagctttttatctctagttaaattttacaccttttttcgcttttttacaacaataaaaaaagagactgctctaaaagtagtctcttaatcagttaattaa Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 73 HP_score: -8.5 Tail_Score: -3.23598 Start: 92 End: 114 Full_Region: ACAACAATAAAAAAA GAGACTGCT CTAAA AGTAGTCTC TTAATCAGTTAATTA ...........................................................................................GAGACTGCTCTAAAAGTAGTCTC................ Find igs database================================================ Query_seq: FN1763:FN1764|FN1763:FN1764:Hypothetical cytosolic protein:Enolase:<-<-:256653..256782 130 tttctaccctcctgttgcaaatattataataagctttttatctctagttaaattttacaccttttttcgcttttttacaacaataaaaaaagagactgctctaaaagtagtctcttaatcagttaattaa Intra-Species Hit: Count: 1 Min: 1 Max: 130 Len: 130 Subject: NC_003454_FN1763_FN1764|Hypothetical cytosolic protein:Enolase|NEGATIVE:NEGATIVE|[256653,256782]|130 HSP 1 e-value: 6.0E-27 bit: 121.0 Len: 61 Query Start:1 Query End:61 Subject Strand: POSITIVE Subject Start: 1 Subject End: 61 tttctaccctcctgttgcaaatattataataagctttttatctctagttaaattttacacc..................................................................... tttctaccctcctgttgcaaatattataataagctttttatctctagttaaattttacacc..................................................................... HSP 2 e-value: 8.0E-14 bit: 77.8 Len: 39 Query Start:92 Query End:130 Subject Strand: POSITIVE Subject Start: 92 Subject End: 130 ...........................................................................................gagactgctctaaaagtagtctcttaatcagttaattaa ...........................................................................................gagactgctctaaaagtagtctcttaatcagttaattaa Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUCUACCCUCCUGUUGCAAAUAUUAUAAUAAGCUUUUUAUCUCUAGUUAAAUUUUACACCUUUUUUCGCUUUUUUACAACAAUAAAAAAAGAGACUGCUCUAAAAGUAGUCUCUUAAUCAGUUAAUUAA ............(((((.(((.........((((..................................)))).))).))))).......(((((((((((.....))))))))))).............. (-17.78) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUAAUUAACUGAUUAAGAGACUACUUUUAGAGCAGUCUCUUUUUUUAUUGUUGUAAAAAAGCGAAAAAAGGUGUAAAAUUUAACUAGAGAUAAAAAGCUUAUUAUAAUAUUUGCAACAGGAGGGUAGAAA .......(((....((((((((.(((...))).))))))))......((((((((((............(((..........)))...(((((.....)))))......))))))))))...)))..... (-20.40) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 750 50 1 141 92 NC_003454:FN1763|5end_Hypothetical_cytosolic_protein_256562..256792_NEGATIVE 292 48 1 211 156 NC_003454:FN1598|5end_hypothetical_protein_108152..108382_NEGATIVE 242 47 1 104 54 NC_003454:FN0597|5end_Lipid-A-disaccharide_synthase_1250814..1251044_POSITIVE 231 49 1 107 45 NC_003454:FN1607|5end_Cytidylate_kinase_117893..118123_NEGATIVE 218 66 32 109 74 NC_003454:FN1557|5end_30S_ribosomal_protein_S7_80122..80352_NEGATIVE 213 83 41 70 21 NC_003454:FN0288|5end_Hypoxanthine-guanine_phosphoribosyltransferase_915765..915995_NEGATIVE 210 43 8 138 101 NC_003454:FN1020|5end_3-hydroxybutyryl-CoA_dehydratase_1674576..1674806_NEGATIVE 210 49 12 156 118 NC_003454:FN1660|5end_ATP-dependent_DNA_helicase_recG_157908..158138_NEGATIVE 210 76 31 64 20 NC_003454:FN1616|5end_transcription_antitermination_protein_NusB_126437..126667_NEGATIVE 205 76 34 147 101 NC_003454:FN0606|5end_Translation_initiation_inhibitor_1261014..1261244_POSITIVE 203 81 49 84 54 NC_003454:FN1884|5end_hypothetical_protein_370507..370737_NEGATIVE 202 43 1 81 37 NC_003454:FN0855|5end_glucose-1-phosphate_adenylyltransferase_1514662..1514892_NEGATIVE 201 43 12 148 119 NC_003454:FN1160|5end_SWF/SNF_family_helicase_1815836..1816066_POSITIVE 200 130 88 144 100 NC_003454:FN0626|5end_Hypothetical_cytosolic_protein_1286092..1286322_NEGATIVE 197 21 2 205 186 NC_003454:FN1381|5end_hypothetical_protein_2032434..2032664_NEGATIVE 197 35 9 29 1 NC_003454:FN0815|5end_Propionate_permease_1474390..1474620_POSITIVE 197 56 11 208 168 NC_003454:FN0681|5end_Transcriptional_regulator,_MarR_family_1336115..1336345_POSITIVE 195 70 21 218 155 NC_003454:FN1279|5end_Zinc_metallohydrolase,_glyoxalase_II_family_1938270..1938500_NEGATIVE 195 39 9 164 138 NC_003454:FN0955|5end_hypothetical_protein_1612455..1612685_NEGATIVE 194 45 13 230 189 NC_003454:FN0236|5end_ABC_transporter_substrate-binding_protein_861416..861646_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 292 48 1 86 31 NC_003454:FN1599|3end_hypothetical_protein_108277..108427_NEGATIVE 242 47 1 94 44 NC_003454:FN0596|3end_hypothetical_protein_1250884..1251034_POSITIVE 231 49 1 91 29 NC_003454:FN1608|3end_Ribosomal_protein_L11_methyltransferase_117909..118059_NEGATIVE 226 56 12 97 40 NC_003454:FN0031|3end_hypothetical_protein_667899..668049_NEGATIVE 218 66 32 81 46 NC_003454:FN1558|3end_30S_ribosomal_protein_S12_80150..80300_NEGATIVE 215 77 33 124 62 NC_003454:FN1085|3end_4-methyl-5(B-hydroxyethyl)-thiazole_monophosphate_biosynthesis_enzyme_1729562..1729712_POSITIVE 210 49 12 101 63 NC_003454:FN1661|3end_Hypothetical_cytosolic_protein_157963..158113_NEGATIVE 210 76 31 59 15 NC_003454:FN1617|3end_Prolipoprotein_diacylglyceryltransferase_126442..126592_NEGATIVE 205 76 34 150 104 NC_003454:FN0605|3end_aspartate_aminotransferase_1261097..1261247_POSITIVE 202 43 1 54 10 NC_003454:FN0856|3end_glycogen_branching_enzyme_1514689..1514839_NEGATIVE 201 43 12 83 54 NC_003454:FN1159|3end_fructose_1,6-bisphosphatase_II_1815851..1816001_POSITIVE 200 130 88 81 37 NC_003454:FN0627|3end_Glucosamine--fructose-6-phosphate_aminotransferase_[isomerizing]_1286155..1286305_NEGATIVE 198 36 12 48 25 NC_003454:FN1984|3end_Glutaredoxin-like_protein_487204..487354_POSITIVE 193 64 29 73 31 NC_003454:FN1759|3end_Hydroxymethylpyrimidine_kinase_253896..254046_NEGATIVE 189 46 2 104 58 NC_003454:FN1473|3end_N-acetylneuraminate_transporter_large_subunit_2156965..2157115_POSITIVE 188 46 1 142 106 NC_003454:FN0521|3end_DNA_integration/recombination/invertion_protein_1172288..1172438_NEGATIVE 188 77 32 118 53 NC_003454:FN0107|3end_Sodium/proline_symporter_743240..743390_POSITIVE 186 68 32 71 26 NC_003454:FN1868|3end_Hypothetical_cytosolic_protein_359615..359765_NEGATIVE 185 77 32 124 79 NC_003454:FN0039|3end_DNA_primase_(bacterial_type)_and_small_primase-like_proteins_678661..678811_NEGATIVE 185 85 54 51 16 NC_003454:FN1505|3end_6,7-dimethyl-8-ribityllumazine_synthase_10949..11099_POSITIVE