Origin IGS: atatctatagtataaaacttttttgacttttgcaataggaatcaagaaaaatattcaaacttcaatctaagcccaaaagcgggaataagtataagtcctcctcttgaaacaaaatagaaaaaaagatataatccgctctgtagta .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tactacagagcggattatatctttttttctattttgtttcaagaggaggacttatacttattcccgcttttgggcttagattgaagtttgaatatttttcttgattcctattgcaaaagtcaaaaaagttttatactatagatat Mask Tandem Repeat Region ================================================ atatctatagtataaaacttttttgacttttgcaataggaatcaagaaaaatattcaaacttcaatctaagcccaaaagcgggaataagtataagtcctcctcttgaaacaaaatagaaaaaaagatataatccgctctgtagta Find is-nt database================================================ Query_seq: TDE1038:TDE1039|TDE1038:TDE1039:hypothetical protein:riboflavin biosynthesis protein, putative:<-->:1067067..1067211 145 atatctatagtataaaacttttttgacttttgcaataggaatcaagaaaaatattcaaacttcaatctaagcccaaaagcgggaataagtataagtcctcctcttgaaacaaaatagaaaaaaagatataatccgctctgtagta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE1038:TDE1039|TDE1038:TDE1039:hypothetical protein:riboflavin biosynthesis protein, putative:<-->:1067067..1067211 145 atatctatagtataaaacttttttgacttttgcaataggaatcaagaaaaatattcaaacttcaatctaagcccaaaagcgggaataagtataagtcctcctcttgaaacaaaatagaaaaaaagatataatccgctctgtagta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE1038:TDE1039|TDE1038:TDE1039:hypothetical protein:riboflavin biosynthesis protein, putative:<-->:1067067..1067211 145 atatctatagtataaaacttttttgacttttgcaataggaatcaagaaaaatattcaaacttcaatctaagcccaaaagcgggaataagtataagtcctcctcttgaaacaaaatagaaaaaaagatataatccgctctgtagta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 atatctatagtataaaacttttttgacttttgcaataggaatcaagaaaaatattcaaacttcaatctaagcccaaaagcgggaataagtataagtcctcctcttgaaacaaaatagaaaaaaagatataatccgctctgtagta Predict ORF larger than 30AA ================================================ atatctatagtataaaacttttttgacttttgcaataggaatcaagaaaaatattcaaacttcaatctaagcccaaaagcgggaataagtataagtcctcctcttgaaacaaaatagaaaaaaagatataatccgctctgtagta 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: 88 Start: 103 End: 132 ......................................................................................................CTTGAAACAAAATAGAAAAAAAGATATAAT............. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ atatctatagtataaaacttttttgacttttgcaataggaatcaagaaaaatattcaaacttcaatctaagcccaaaagcgggaataagtataagtcctcctcttgaaacaaaatagaaaaaaagatataatccgctctgtagta Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE1038:TDE1039|TDE1038:TDE1039:hypothetical protein:riboflavin biosynthesis protein, putative:<-->:1067067..1067211 145 atatctatagtataaaacttttttgacttttgcaataggaatcaagaaaaatattcaaacttcaatctaagcccaaaagcgggaataagtataagtcctcctcttgaaacaaaatagaaaaaaagatataatccgctctgtagta Intra-Species Hit: Count: 1 Min: 1 Max: 145 Len: 145 Subject: NC_002967_TDE1038_TDE1039|hypothetical protein:riboflavin biosynthesis protein, putative|NEGATIVE:POSITIVE|[1067067,1067211]|145 HSP 1 e-value: 2.0E-64 bit: 246.0 Len: 145 Query Start:1 Query End:145 Subject Strand: POSITIVE Subject Start: 1 Subject End: 145 atatctatagtataaaacttttttgacttttgcaataggaatcaagaaaaatattcaaacttcaatctaagcccaaaagcgggaataagtataagtcctcctcttgaaacaaaatagnnnnnnngatataatccgctctgtagta atatctatagtataaaacttttttgacttttgcaataggaatcaagaaaaatattcaaacttcaatctaagcccaaaagcgggaataagtataagtcctcctcttgaaacaaaatagaaaaaaagatataatccgctctgtagta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUAUCUAUAGUAUAAAACUUUUUUGACUUUUGCAAUAGGAAUCAAGAAAAAUAUUCAAACUUCAAUCUAAGCCCAAAAGCGGGAAUAAGUAUAAGUCCUCCUCUUGAAACAAAAUAGAAAAAAAGAUAUAAUCCGCUCUGUAGUA ....((((((((((...(((((((...((((((((.((((.....(((.....)))..((((..(..((..(((......)))..))..)..))))..)))).)))...)))))....))))))).)))).......)))))).. (-18.91) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UACUACAGAGCGGAUUAUAUCUUUUUUUCUAUUUUGUUUCAAGAGGAGGACUUAUACUUAUUCCCGCUUUUGGGCUUAGAUUGAAGUUUGAAUAUUUUUCUUGAUUCCUAUUGCAAAAGUCAAAAAAGUUUUAUACUAUAGAUAU ..(((.((.......((((.(((((((....((((((.((((((((((...(((.((((..((..(((....)))...))...)))).)))...))))))))))........))))))...)))))))...)))))).))).... (-22.81) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 872 110 61 201 152 NC_002967:TDE1038|5end_hypothetical_protein_1066976..1067206_NEGATIVE 290 47 5 198 148 NC_002967:TDE0050|5end_RNA_methyltransferase,_TrmH_family_60071..60301_NEGATIVE 257 106 61 131 87 NC_002967:TDE1310|5end_modulator_of_DNA_gyrase_family_protein_1345962..1346192_POSITIVE 252 43 1 59 21 NC_002967:TDE0414|5end_hypothetical_protein_467260..467490_POSITIVE 244 135 92 56 20 NC_002967:TDE0194|5end_hypothetical_protein_231881..232111_NEGATIVE 244 99 58 167 131 NC_002967:TDE0134|5end_oxidoreductase,_FAD-dependent_153404..153634_POSITIVE 243 112 71 81 21 NC_002967:TDE1974|5end_UDP-N-acetylglucosamine--N-acetylmuramyl-_(pentapeptide)_pyrophosphoryl-undecaprenol_N-acetylglucosamine_transferase_1988910..1989140_NEGATIVE 237 116 71 116 69 NC_002967:TDE2209|5end_CarB_family_protein_2247589..2247819_POSITIVE 230 50 5 151 109 NC_002967:TDE0040|5end_AMP-binding_protein_47428..47658_NEGATIVE 225 101 70 80 41 NC_002967:TDE2403|5end_metallo-beta-lactamase_family_protein_2429282..2429512_NEGATIVE 225 110 64 70 16 NC_002967:TDE1896|5end_phosphoribosylaminoimidazolecarboxamide_formyltransferase/IMP_cyclohydrolase_1917505..1917735_NEGATIVE 223 118 73 116 75 NC_002967:TDE2131|5end_cobalamin_biosynthesis_protein_CbiM,_putative_2162683..2162913_NEGATIVE 221 46 15 64 36 NC_002967:TDE1582|5end_glycogen_synthase_1631759..1631989_NEGATIVE 218 110 64 73 28 NC_002967:TDE1753|5end_UDP-glucose_4-epimerase_1806540..1806770_NEGATIVE 216 105 66 177 142 NC_002967:TDE2539|5end_hypothetical_protein_2565158..2565388_NEGATIVE 216 103 66 105 63 NC_002967:TDE2181|5end_PAP2_family_protein_2213035..2213265_NEGATIVE 213 110 68 200 169 NC_002967:TDE0144|5end_thiamine_ABC_transporter,_permease_protein_165007..165237_POSITIVE 212 109 69 230 191 NC_002967:TDE2260|5end_hypothetical_protein_2297338..2297568_POSITIVE 209 118 72 181 133 NC_002967:TDE2736|5end_hypothetical_protein_2791812..2792042_NEGATIVE 209 98 60 222 191 NC_002967:TDE1214|5end_flagellar_basal_body_protein_1246307..1246537_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 257 106 61 131 87 NC_002967:TDE1309|3end_modulator_of_DNA_gyrase_family_protein_1346042..1346192_POSITIVE 252 43 1 87 49 NC_002967:TDE0413|3end_lipoprotein,_putative_467368..467518_POSITIVE 242 107 62 60 11 NC_002967:TDE0099|3end_adenine-specific_DNA_modification_methyltransferase_117014..117164_POSITIVE 228 107 67 151 98 NC_002967:TDE0435|3end_ATP-dependent_DNA_helicase,_RecQ_family_489558..489708_NEGATIVE 225 101 70 49 10 NC_002967:TDE2404|3end_RNA_polymerase_sigma-54_factor,_putative_2429313..2429463_NEGATIVE 225 101 67 131 100 NC_002967:TDE1056|3end_hypothetical_protein_1085895..1086045_POSITIVE 223 118 73 43 2 NC_002967:TDE2132|3end_cobalt_ABC_transporter,_ATP-binding_protein,_putative_2162756..2162906_NEGATIVE 216 105 66 140 105 NC_002967:TDE2540|3end_lipoprotein,_putative_2565195..2565345_NEGATIVE 216 103 66 105 63 NC_002967:TDE2182|3end_hypothetical_protein_2213035..2213185_NEGATIVE 215 113 71 60 7 NC_002967:TDE2763|3end_flagellar_motor_switch_protein_2817737..2817887_NEGATIVE 211 103 79 136 114 NC_002967:TDE2047|3end_hypothetical_protein_2076058..2076208_NEGATIVE 210 105 65 137 93 NC_002967:TDE2474|3end_acetyltransferase,_GNAT_family_2496602..2496752_NEGATIVE 210 107 61 86 42 NC_002967:TDE1893|3end_GTP-binding_protein_LepA_1912212..1912362_NEGATIVE 209 100 54 46 1 NC_002967:TDE0239|3end_glycine_reductase_complex_protein_GrdD_271828..271978_NEGATIVE 207 104 71 52 13 NC_002967:TDE2785|3end_hypothetical_protein_2838601..2838751_NEGATIVE 207 94 58 44 7 NC_002967:TDE1325|3end_hypothetical_protein_1361620..1361770_NEGATIVE 207 105 80 123 97 NC_002967:TDE0580|3end_hypothetical_protein_616716..616866_POSITIVE 204 85 61 85 60 NC_002967:TDE2593|3end_sigma-54-binding_protein_2628963..2629113_POSITIVE 204 100 59 69 31 NC_002967:TDE1540|3end_hypothetical_protein_1584948..1585098_POSITIVE 201 103 78 37 6 NC_002967:TDE1669|3end_hemolysin_1723878..1724028_POSITIVE