Origin IGS: gtataacagaatacgataaaagaagaactttgtcaaacccctaaggccggtaaaaatctttacttattatatacttatacaaaaagggaaaaatgccgataagtggggt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 accccacttatcggcatttttccctttttgtataagtatataataagtaaagatttttaccggccttaggggtttgacaaagttcttcttttatcgtattctgttatac Mask Tandem Repeat Region ================================================ gtataacagaatacgataaaagaagaactttgtcaaacccctaaggccggtaaaaatctttacttattatatacttatacaaaaagggaaaaatgccgataagtggggt Find is-nt database================================================ Query_seq: TDE2047:TDE2048|TDE2047:TDE2048:hypothetical protein:hypothetical protein:<-->:2076442..2076550 109 gtataacagaatacgataaaagaagaactttgtcaaacccctaaggccggtaaaaatctttacttattatatacttatacaaaaagggaaaaatgccgataagtggggt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE2047:TDE2048|TDE2047:TDE2048:hypothetical protein:hypothetical protein:<-->:2076442..2076550 109 gtataacagaatacgataaaagaagaactttgtcaaacccctaaggccggtaaaaatctttacttattatatacttatacaaaaagggaaaaatgccgataagtggggt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE2047:TDE2048|TDE2047:TDE2048:hypothetical protein:hypothetical protein:<-->:2076442..2076550 109 gtataacagaatacgataaaagaagaactttgtcaaacccctaaggccggtaaaaatctttacttattatatacttatacaaaaagggaaaaatgccgataagtggggt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gtataacagaatacgataaaagaagaactttgtcaaacccctaaggccggtaaaaatctttacttattatatacttatacaaaaagggaaaaatgccgataagtggggt Predict ORF larger than 30AA ================================================ gtataacagaatacgataaaagaagaactttgtcaaacccctaaggccggtaaaaatctttacttattatatacttatacaaaaagggaaaaatgccgataagtggggt 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: 86 Start: 8 End: 37 .......TTTGACAAAGTTCTTCTTTTATCGTATTCT........................................................................ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ gtataacagaatacgataaaagaagaactttgtcaaacccctaaggccggtaaaaatctttacttattatatacttatacaaaaagggaaaaatgccgataagtggggt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE2047:TDE2048|TDE2047:TDE2048:hypothetical protein:hypothetical protein:<-->:2076442..2076550 109 gtataacagaatacgataaaagaagaactttgtcaaacccctaaggccggtaaaaatctttacttattatatacttatacaaaaagggaaaaatgccgataagtggggt Intra-Species Hit: Count: 1 Min: 1 Max: 109 Len: 109 Subject: NC_002967_TDE2047_TDE2048|hypothetical protein:hypothetical protein|NEGATIVE:POSITIVE|[2076442,2076550]|109 HSP 1 e-value: 1.0E-55 bit: 216.0 Len: 109 Query Start:1 Query End:109 Subject Strand: POSITIVE Subject Start: 1 Subject End: 109 gtataacagaatacgataaaagaagaactttgtcaaacccctaaggccggtaaaaatctttacttattatatacttatacaaaaagggaaaaatgccgataagtggggt gtataacagaatacgataaaagaagaactttgtcaaacccctaaggccggtaaaaatctttacttattatatacttatacaaaaagggaaaaatgccgataagtggggt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GUAUAACAGAAUACGAUAAAAGAAGAACUUUGUCAAACCCCUAAGGCCGGUAAAAAUCUUUACUUAUUAUAUACUUAUACAAAAAGGGAAAAAUGCCGAUAAGUGGGGU ..............((((((........))))))..(((((......(((((....(((((......((((....)))).....)))))....)))))......))))) (-19.20) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ ACCCCACUUAUCGGCAUUUUUCCCUUUUUGUAUAAGUAUAUAAUAAGUAAAGAUUUUUACCGGCCUUAGGGGUUUGACAAAGUUCUUCUUUUAUCGUAUUCUGUUAUAC (((((.....((((...((((..(((.((((((....)))))).)))..))))......)))).....))))).(((((.(((..............))).)))))... (-17.34) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 861 50 1 141 92 NC_002967:TDE2047|5end_hypothetical_protein_2076351..2076581_NEGATIVE 321 57 26 148 113 NC_002967:TDE1699|5end_hypothetical_protein_1757920..1758150_NEGATIVE 247 52 17 71 25 NC_002967:TDE0760|5end_hypothetical_protein_799436..799666_POSITIVE 242 98 71 182 156 NC_002967:TDE1393|5end_hypothetical_protein_1432494..1432724_POSITIVE 241 75 32 227 174 NC_002967:TDE1678|5end_ribosomal_protein_S6_1730483..1730713_NEGATIVE 241 59 13 186 137 NC_002967:TDE1651|5end_BioY_family_protein_1698732..1698962_NEGATIVE 234 50 8 43 7 NC_002967:TDE2736|5end_hypothetical_protein_2791812..2792042_NEGATIVE 229 58 25 189 151 NC_002967:TDE1335|5end_alginate_O-acetylation_protein,_putative_1370816..1371046_POSITIVE 229 48 24 222 199 NC_002967:TDE0092|5end_cysteinyl-tRNA_synthetase_111255..111485_NEGATIVE 222 48 14 204 176 NC_002967:TDE2737|5end_hypothetical_protein_2791870..2792100_POSITIVE 220 49 9 66 27 NC_002967:TDE1110|5end_lipoprotein,_putative_1144272..1144502_POSITIVE 220 35 7 153 125 NC_002967:TDE0729|5end_hypothetical_protein_769124..769354_NEGATIVE 217 67 21 78 20 NC_002967:TDE0138|5end_alkyldihydroxyacetonephosphate_synthase,_putative_158221..158451_POSITIVE 214 63 22 173 134 NC_002967:TDE1580|5end_hypothetical_protein_1629726..1629956_NEGATIVE 214 53 28 144 114 NC_002967:TDE0388|5end_hypothetical_protein_439173..439403_POSITIVE 213 57 28 171 140 NC_002967:TDE1037|5end_hypothetical_protein_1064470..1064700_POSITIVE 212 67 27 217 173 NC_002967:TDE0294|5end_TrkA_domain_protein_324210..324440_NEGATIVE 211 65 24 50 8 NC_002967:TDE1079|5end_DNA-binding_protein/PTS_system,_IIA_component_1111120..1111350_POSITIVE 210 60 13 211 166 NC_002967:TDE1343|5end_trypsin_domain/PDZ_domain_protein_1380546..1380776_POSITIVE 210 53 21 167 129 NC_002967:TDE1030|5end_hypothetical_protein_1059114..1059344_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 241 75 32 83 30 NC_002967:TDE1679|3end_ATP_synthase_subunit_K_1730627..1730777_NEGATIVE 241 59 13 61 12 NC_002967:TDE1652|3end_ABC_transporter,_ATP-binding/permease_protein_1698857..1699007_NEGATIVE 233 47 28 126 103 NC_002967:TDE0670|3end_ATP-dependent_protease_La_710393..710543_POSITIVE 230 50 18 72 37 NC_002967:TDE0870|3end_phosphatase/nucleotidase_894676..894826_POSITIVE 228 50 17 80 45 NC_002967:TDE2593|3end_sigma-54-binding_protein_2628963..2629113_POSITIVE 220 49 9 43 4 NC_002967:TDE1109|3end_decarboxylase,_pyridoxal-dependent_family_1144329..1144479_POSITIVE 220 35 7 81 53 NC_002967:TDE0730|3end_hypothetical_protein_769196..769346_NEGATIVE 214 53 28 147 117 NC_002967:TDE0387|3end_(R)-hydroxyglutaryl-CoA_dehydratase_activator_439256..439406_POSITIVE 213 53 11 39 1 NC_002967:TDE2086|3end_DnaJ_domain_protein_2115475..2115625_POSITIVE 211 67 39 56 27 NC_002967:TDE0137|3end_carbohydrate_kinase,_FGGY_family_158279..158429_POSITIVE 210 60 13 146 101 NC_002967:TDE1342|3end_hypothetical_protein_1380561..1380711_POSITIVE 210 53 21 67 29 NC_002967:TDE1029|3end_Hsp20/alpha_crystallin_family_protein_1059094..1059244_POSITIVE 204 78 31 69 23 NC_002967:TDE0685|3end_oxidoreductase,_short_chain_dehydrogenase/reductase_family_721823..721973_NEGATIVE 202 61 24 66 31 NC_002967:TDE1404|3end_lipoprotein,_putative_1446508..1446658_NEGATIVE 200 51 35 144 128 NC_002967:TDE0015|3end_lipoprotein,_putative_20544..20694_POSITIVE 197 81 43 70 37 NC_002967:TDE1749|3end_50S_ribosomal_protein_L27_1803158..1803308_NEGATIVE 195 71 43 61 36 NC_002967:TDE1998|3end_phosphohexose_mutase_family_protein_2017143..2017293_POSITIVE 195 99 54 90 49 NC_002967:TDE1473|3end_flagellin_FlaG,_putative_1520760..1520910_NEGATIVE 194 42 14 140 112 NC_002967:TDE2439|3end_hypothetical_protein_2469270..2469420_NEGATIVE 194 63 24 102 55 NC_002967:TDE1286|3end_TPR_domain_protein_1322817..1322967_POSITIVE