Origin IGS: ttgcatactccttatatcatatatattaacctaagttaaatccacttacacctttaattgtacactatgtttatcaaaatagcaagttttaatttgataactttagaattttttctataaagtgt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 acactttatagaaaaaattctaaagttatcaaattaaaacttgctattttgataaacatagtgtacaattaaaggtgtaagtggatttaacttaggttaatatatatgatataaggagtatgcaa Mask Tandem Repeat Region ================================================ ttgcatactccttatatcatatatattaacctaagttaaatccacttacacctttaattgtacactatgtttatcaaaatagcaagttttaatttgataactttagaattttttctataaagtgt Find is-nt database================================================ Query_seq: TDE1594:TDE1595|TDE1594:TDE1595:pyridine nucleotide-disulphide oxidoreductase family protein:cobalamin biosynthesis protein CbiD:<-<-:1644913..1645037 125 ttgcatactccttatatcatatatattaacctaagttaaatccacttacacctttaattgtacactatgtttatcaaaatagcaagttttaatttgataactttagaattttttctataaagtgt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE1594:TDE1595|TDE1594:TDE1595:pyridine nucleotide-disulphide oxidoreductase family protein:cobalamin biosynthesis protein CbiD:<-<-:1644913..1645037 125 ttgcatactccttatatcatatatattaacctaagttaaatccacttacacctttaattgtacactatgtttatcaaaatagcaagttttaatttgataactttagaattttttctataaagtgt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE1594:TDE1595|TDE1594:TDE1595:pyridine nucleotide-disulphide oxidoreductase family protein:cobalamin biosynthesis protein CbiD:<-<-:1644913..1645037 125 ttgcatactccttatatcatatatattaacctaagttaaatccacttacacctttaattgtacactatgtttatcaaaatagcaagttttaatttgataactttagaattttttctataaagtgt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ttgcatactccttatatcatatatattaacctaagttaaatccacttacacctttaattgtacactatgtttatcaaaatagcaagttttaatttgataactttagaattttttctataaagtgt Predict ORF larger than 30AA ================================================ ttgcatactccttatatcatatatattaacctaagttaaatccacttacacctttaattgtacactatgtttatcaaaatagcaagttttaatttgataactttagaattttttctataaagtgt 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: 85 Start: 57 End: 86 ........................................................CTTGCTATTTTGATAAACATAGTGTACAAT....................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ ttgcatactccttatatcatatatattaacctaagttaaatccacttacacctttaattgtacactatgtttatcaaaatagcaagttttaatttgataactttagaattttttctataaagtgt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE1594:TDE1595|TDE1594:TDE1595:pyridine nucleotide-disulphide oxidoreductase family protein:cobalamin biosynthesis protein CbiD:<-<-:1644913..1645037 125 ttgcatactccttatatcatatatattaacctaagttaaatccacttacacctttaattgtacactatgtttatcaaaatagcaagttttaatttgataactttagaattttttctataaagtgt Intra-Species Hit: Count: 1 Min: 1 Max: 125 Len: 125 Subject: NC_002967_TDE1594_TDE1595|pyridine nucleotide-disulphide oxidoreductase family protein:cobalamin biosynthesis protein CbiD|NEGATIVE:NEGATIVE|[1644913,1645037]|125 HSP 1 e-value: 4.0E-65 bit: 248.0 Len: 125 Query Start:1 Query End:125 Subject Strand: POSITIVE Subject Start: 1 Subject End: 125 ttgcatactccttatatcatatatattaacctaagttaaatccacttacacctttaattgtacactatgtttatcaaaatagcaagttttaatttgataactttagaattttttctataaagtgt ttgcatactccttatatcatatatattaacctaagttaaatccacttacacctttaattgtacactatgtttatcaaaatagcaagttttaatttgataactttagaattttttctataaagtgt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUGCAUACUCCUUAUAUCAUAUAUAUUAACCUAAGUUAAAUCCACUUACACCUUUAAUUGUACACUAUGUUUAUCAAAAUAGCAAGUUUUAAUUUGAUAACUUUAGAAUUUUUUCUAUAAAGUGU .........................(((((....)))))......................(((((....((((((((.(((......))).))))))))...(((((....)))))...))))) (-12.80) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ ACACUUUAUAGAAAAAAUUCUAAAGUUAUCAAAUUAAAACUUGCUAUUUUGAUAAACAUAGUGUACAAUUAAAGGUGUAAGUGGAUUUAACUUAGGUUAAUAUAUAUGAUAUAAGGAGUAUGCAA ((.(((((((.........((.((((((...((((...((((((..(((((((..((.....))...)))))))..)))))).)))))))))).)).............))))))).))...... (-17.45) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 736 90 41 181 132 NC_002967:TDE1594|5end_pyridine_nucleotide-disulphide_oxidoreductase_family_protein_1644822..1645052_NEGATIVE 226 85 41 150 106 NC_002967:TDE1209|5end_site-specific_recombinase,_phage_integrase_family_1242345..1242575_POSITIVE 221 48 3 135 73 NC_002967:TDE1695|5end_CoA-substrate-specific_enzyme_activase_domain_protein_1754000..1754230_NEGATIVE 203 90 43 62 4 NC_002967:TDE1046|5end_hypothetical_protein_1073646..1073876_POSITIVE 200 107 75 157 129 NC_002967:TDE0233|5end_fic_family_protein_266920..267150_NEGATIVE 199 21 1 110 92 NC_002967:TDE1736|5end_ferredoxin,_2(4Fe-4S)_1789908..1790138_POSITIVE 193 109 68 57 11 NC_002967:TDE1363|5end_nitroreductase_family_protein_1404635..1404865_NEGATIVE 187 83 41 143 100 NC_002967:TDE1621|5end_hypothetical_protein_1670743..1670973_NEGATIVE 185 56 25 90 56 NC_002967:TDE0690|5end_tRNA_(5-methylaminomethyl-2-thiouridylate)-methyltransferase_726898..727128_POSITIVE 185 85 41 140 91 NC_002967:TDE0321|5end_CBS_domain_protein_355094..355324_NEGATIVE 180 50 2 129 76 NC_002967:TDE1512|5end_hypothetical_protein_1559203..1559433_POSITIVE 178 120 71 109 66 NC_002967:TDE1798|5end_hypothetical_protein_1836676..1836906_NEGATIVE 177 90 46 193 137 NC_002967:TDE1668|5end_amino_acid_permease_family_protein_1721218..1721448_POSITIVE 175 43 2 109 68 NC_002967:TDE0472|5end_hypothetical_protein_528376..528606_POSITIVE 174 87 44 167 123 NC_002967:TDE1339|5end_stage_V_sporulation_protein_G_1375807..1376037_POSITIVE 173 115 82 148 112 NC_002967:TDE0575|5end_aspartyl/glutamyl-tRNA_amidotransferase_subunit_B_607733..607963_NEGATIVE 173 50 2 144 91 NC_002967:TDE0241|5end_hypothetical_protein_275303..275533_NEGATIVE 171 83 47 211 186 NC_002967:TDE2678|5end_alpha-amylase_family_protein_2719390..2719620_NEGATIVE 170 83 41 149 98 NC_002967:TDE1767|5end_hypothetical_protein_1813567..1813797_NEGATIVE 169 66 41 113 87 NC_002967:TDE1953|5end_transcriptional_regulator,_TetR_family_1969671..1969901_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 221 48 3 115 53 NC_002967:TDE1696|3end_hypothetical_protein_1754020..1754170_NEGATIVE 204 70 41 145 113 NC_002967:TDE1208|3end_DNA_topoisomerase_I_1242432..1242582_POSITIVE 203 90 43 75 17 NC_002967:TDE1045|3end_hypothetical_protein_1073739..1073889_POSITIVE 199 21 1 120 102 NC_002967:TDE1735|3end_hypothetical_protein_1789998..1790148_POSITIVE 187 83 41 66 23 NC_002967:TDE1622|3end_hypothetical_protein_1670820..1670970_NEGATIVE 185 56 25 84 50 NC_002967:TDE0689|3end_5-methylthioribose_kinase_726972..727122_POSITIVE 185 85 41 128 79 NC_002967:TDE0322|3end_regulatory_protein,_P-II_family_355106..355256_NEGATIVE 178 120 71 96 53 NC_002967:TDE1799|3end_hypothetical_protein_1836689..1836839_NEGATIVE 177 83 58 129 102 NC_002967:TDE1758|3end_hypothetical_protein_1807980..1808130_NEGATIVE 174 87 44 103 59 NC_002967:TDE1338|3end_4-diphosphocytidyl-2C-methyl-D-erythritol_kinase_1375823..1375973_POSITIVE 173 50 2 133 80 NC_002967:TDE0242|3end_hypothetical_protein_275314..275464_NEGATIVE 172 90 41 135 83 NC_002967:TDE1140|3end_hypothetical_protein_1168730..1168880_NEGATIVE 170 20 1 112 94 NC_002967:TDE2542|3end_antigen,_putative_2569441..2569591_NEGATIVE 167 80 40 88 39 NC_002967:TDE1346|3end_RNA_polymerase_sigma_factor_1387158..1387308_POSITIVE 161 118 82 114 86 NC_002967:TDE1451|3end_hypothetical_protein_1497850..1498000_NEGATIVE 158 98 63 117 82 NC_002967:TDE0667|3end_FeS_assembly_protein_SufB_705836..705986_POSITIVE 156 47 1 151 103 NC_002967:TDE1888|3end_hypothetical_protein_1909123..1909273_NEGATIVE 155 47 5 109 53 NC_002967:TDE0234|3end_ABC_transporter,_ATP-binding_protein,_HlyB_family_268944..269094_POSITIVE 153 85 41 79 32 NC_002967:TDE2781|3end_ABC_transporter,_ATP-binding/permease_protein_2830639..2830789_NEGATIVE 152 99 59 51 9 NC_002967:TDE2402|3end_radical_SAM_domain_protein_2428664..2428814_POSITIVE