Origin IGS: ataagaagtataaacctcccttaatttttcttttttagggagccaaggtacgtcttcagacaacatattttgttaaaatcatttttacacagggacatcaaacaaaagcggccgagcagtctcgaccgctttatcattttttagaac .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 gttctaaaaaatgataaagcggtcgagactgctcggccgcttttgtttgatgtccctgtgtaaaaatgattttaacaaaatatgttgtctgaagacgtaccttggctccctaaaaaagaaaaattaagggaggtttatacttcttat Mask Tandem Repeat Region ================================================ ataagaagtataaacctcccttaatttttcttttttagggagccaaggtacgtcttcagacaacatattttgttaaaatcatttttacacagggacatcaaacaaaagcggccgagcagtctcgaccgctttatcattttttagaac Find is-nt database================================================ Query_seq: TDE1711:TDE1712|TDE1711:TDE1712:RelA/SpoT domain protein:flagellar filament outer layer protein:<-<-:1766809..1766955 147 ataagaagtataaacctcccttaatttttcttttttagggagccaaggtacgtcttcagacaacatattttgttaaaatcatttttacacagggacatcaaacaaaagcggccgagcagtctcgaccgctttatcattttttagaac Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE1711:TDE1712|TDE1711:TDE1712:RelA/SpoT domain protein:flagellar filament outer layer protein:<-<-:1766809..1766955 147 ataagaagtataaacctcccttaatttttcttttttagggagccaaggtacgtcttcagacaacatattttgttaaaatcatttttacacagggacatcaaacaaaagcggccgagcagtctcgaccgctttatcattttttagaac Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE1711:TDE1712|TDE1711:TDE1712:RelA/SpoT domain protein:flagellar filament outer layer protein:<-<-:1766809..1766955 147 ataagaagtataaacctcccttaatttttcttttttagggagccaaggtacgtcttcagacaacatattttgttaaaatcatttttacacagggacatcaaacaaaagcggccgagcagtctcgaccgctttatcattttttagaac Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ataagaagtataaacctcccttaatttttcttttttagggagccaaggtacgtcttcagacaacatattttgttaaaatcatttttacacagggacatcaaacaaaagcggccgagcagtctcgaccgctttatcattttttagaac Predict ORF larger than 30AA ================================================ Protein_Len: 38 Strand: - Start: 24 End: 137 ....................... N K K K L S G L Y T K L C C I K N F D N K C L S M L C F R G L L R S R K I M .......... ataagaagtataaacctcccttaatttttcttttttagggagccaaggtacgtcttcagacaacatattttgttaaaatcatttttacacagggacatcaaacaaaagcggccgagcagtctcgaccgctttatcattttttagaac 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================================================ ataagaagtataaacctcccttaatttttcttttttagggagccaaggtacgtcttcagacaacatattttgttaaaatcatttttacacagggacatcaaacaaaagcggccgagcagtctcgaccgctttatcattttttagaac Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 91 HP_score: -11.5 Tail_Score: -4.3179 Start: 108 End: 129 Full_Region: GGACATCAAACAAAA GCGGCCGAG CAGT CTCGACCGC TTTATCATTTTTTAG ...........................................................................................................GCGGCCGAGCAGTCTCGACCGC.................. Find igs database================================================ Query_seq: TDE1711:TDE1712|TDE1711:TDE1712:RelA/SpoT domain protein:flagellar filament outer layer protein:<-<-:1766809..1766955 147 ataagaagtataaacctcccttaatttttcttttttagggagccaaggtacgtcttcagacaacatattttgttaaaatcatttttacacagggacatcaaacaaaagcggccgagcagtctcgaccgctttatcattttttagaac Intra-Species Hit: Count: 1 Min: 37 Max: 147 Len: 111 Subject: NC_002967_TDE1711_TDE1712|RelA/SpoT domain protein:flagellar filament outer layer protein|NEGATIVE:NEGATIVE|[1766809,1766955]|147 HSP 1 e-value: 1.0E-56 bit: 220.0 Len: 111 Query Start:37 Query End:147 Subject Strand: POSITIVE Subject Start: 37 Subject End: 147 ....................................agggagccaaggtacgtcttcagacaacatattttgttaaaatcatttttacacagggacatcaaacaaaagcggccgagcagtctcgaccgctttatcattttttagaac ....................................agggagccaaggtacgtcttcagacaacatattttgttaaaatcatttttacacagggacatcaaacaaaagcggccgagcagtctcgaccgctttatcattttttagaac Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGGGAGCCAAGGUACGUCUUCAGACAACAUAUUUUGUUAAAAUCAUUUUUACACAGGGACAUCAAACAAAAGCGGCCGAGCAGUCUCGACCGCUUUAUCAUUUUUUAGAAC ...((.((.......(((....))).........((((((((....))))).))).))...)).....(((((((.((((....)))).)))))))............... (-22.30) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GUUCUAAAAAAUGAUAAAGCGGUCGAGACUGCUCGGCCGCUUUUGUUUGAUGUCCCUGUGUAAAAAUGAUUUUAACAAAAUAUGUUGUCUGAAGACGUACCUUGGCUCCCU ........((((...((((((((((((....)))))))))))).))))...........................(((..((((((.......))))))..)))....... (-24.80) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 1016 100 51 227 178 NC_002967:TDE1711|5end_RelA/SpoT_domain_protein_1766718..1766948_NEGATIVE 309 93 55 229 180 NC_002967:TDE2418|5end_hypothetical_protein_2443833..2444063_NEGATIVE 305 94 51 189 139 NC_002967:TDE1391|5end_NQR2/RnfD/RnfE_family_protein_1430975..1431205_POSITIVE 295 96 73 209 182 NC_002967:TDE1734|5end_exodeoxyribonuclease_III_1788613..1788843_POSITIVE 292 88 55 199 165 NC_002967:TDE0884|5end_tRNA_(guanine-N(1)-)-methyltransferase_902221..902451_POSITIVE 292 88 54 62 26 NC_002967:TDE0389|5end_(R)-2-hydroxyglutaryl-CoA_dehydratase,_beta_subunit,_putative_440008..440238_POSITIVE 288 99 53 119 67 NC_002967:TDE1926|5end_hypothetical_protein_1942495..1942725_POSITIVE 287 98 53 178 110 NC_002967:TDE0073|5end_riboflavin_biosynthesis_protein_RibF,_putative_84082..84312_NEGATIVE 285 93 55 165 114 NC_002967:TDE0780|5end_ribosomal_protein_S14_812364..812594_POSITIVE 284 93 60 202 158 NC_002967:TDE2130|5end_hypothetical_protein_2162059..2162289_NEGATIVE 274 96 55 151 107 NC_002967:TDE0135|5end_pyridine_nucleotide-disulphide_oxidoreductase_family_protein_154927..155157_POSITIVE 270 95 56 209 168 NC_002967:TDE1313|5end_signal_peptidase_I_1350650..1350880_POSITIVE 270 93 51 142 91 NC_002967:TDE1233|5end_hypothetical_protein_1267203..1267433_POSITIVE 263 95 55 192 148 NC_002967:TDE2605|5end_phosphoglycerate_mutase_family_protein_2645818..2646048_POSITIVE 263 91 51 183 145 NC_002967:TDE2210|5end_hypothetical_protein_2250701..2250931_NEGATIVE 262 93 71 225 202 NC_002967:TDE2056|5end_outer_membrane_hemin-binding_protein_A_2085070..2085300_NEGATIVE 262 100 57 75 32 NC_002967:TDE0355|5end_hypothetical_protein_399005..399235_POSITIVE 259 100 55 173 115 NC_002967:TDE2428|5end_ribosomal_protein_L33_2456292..2456522_NEGATIVE 259 96 72 185 160 NC_002967:TDE2399|5end_ribonuclease_P_protein_component_2426160..2426390_NEGATIVE 259 104 68 205 159 NC_002967:TDE2256|5end_hypothetical_protein_2293387..2293617_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 290 105 61 151 95 NC_002967:TDE1054|3end_methyl-accepting_chemotaxis_protein_1082998..1083148_POSITIVE 288 99 53 149 97 NC_002967:TDE1925|3end_peptidyl-prolyl_cis-trans_isomerase,_FKBP-type_1942605..1942755_POSITIVE 287 98 53 104 36 NC_002967:TDE0074|3end_amino_acid_permease_family_protein_84156..84306_NEGATIVE 282 88 41 151 82 NC_002967:TDE0779|3end_ribosomal_protein_L5_812432..812582_POSITIVE 281 97 53 78 34 NC_002967:TDE2260|3end_hypothetical_protein_2297573..2297723_POSITIVE 277 99 56 61 23 NC_002967:TDE0763|3end_hypothetical_protein_804234..804384_NEGATIVE 273 99 70 37 1 NC_002967:TDE0017|3end_hypothetical_protein_21908..22058_NEGATIVE 272 94 52 92 60 NC_002967:TDE2622|3end_ABC_transporter,_ATP-binding_protein_2662178..2662328_NEGATIVE 270 99 73 148 112 NC_002967:TDE0354|3end_general_stress_protein_14_399001..399151_POSITIVE 265 100 55 58 15 NC_002967:TDE2436|3end_hypothetical_protein_2467446..2467596_POSITIVE 263 98 52 52 6 NC_002967:TDE2209|3end_CarB_family_protein_2249300..2249450_POSITIVE 262 93 71 137 114 NC_002967:TDE2057|3end_hypothetical_protein_2085158..2085308_NEGATIVE 262 110 68 75 33 NC_002967:TDE0296|3end_formiminotransferase,_putative_326842..326992_NEGATIVE 259 104 68 89 43 NC_002967:TDE2257|3end_5'-nucleotidase_family_protein_2293503..2293653_NEGATIVE 257 93 66 39 1 NC_002967:TDE2419|3end_hypothetical_protein_2444023..2444173_NEGATIVE 251 94 52 45 1 NC_002967:TDE1803|3end_hypothetical_protein_1838395..1838545_NEGATIVE 251 92 68 84 59 NC_002967:TDE1530|3end_hypothetical_protein_1575096..1575246_NEGATIVE 250 86 42 91 49 NC_002967:TDE2529|3end_hypothetical_protein_2556978..2557128_NEGATIVE 250 97 72 67 43 NC_002967:TDE2275|3end_tRNA_pseudouridine_synthase_A_2311962..2312112_POSITIVE 250 98 55 83 35 NC_002967:TDE0362|3end_bacterial_Ig-like_domain_protein_407501..407651_NEGATIVE