Origin IGS: tttaatttcctccgaatattttatatatctaaaaatccttatgagcttttaaaagatattatttatcttaaaagcttttcaatttcctcttccttataatattgagcttgggcattccagagctcgttgtatttaccctctttgttttaatgagccttattatacaataaaattaatattttgggagagaatggcatagatggta .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 taccatctatgccattctctcccaaaatattaattttattgtataataaggctcattaaaacaaagagggtaaatacaacgagctctggaatgcccaagctcaatattataaggaagaggaaattgaaaagcttttaagataaataatatcttttaaaagctcataaggatttttagatatataaaatattcggaggaaattaaa Mask Tandem Repeat Region ================================================ tttaatttcctccgaatattttatatatctaaaaatccttatgagcttttaaaagatattatttatcttaaaagcttttcaatttcctcttccttataatattgagcttgggcattccagagctcgttgtatttaccctctttgttttaatgagccttattatacaataaaattaatattttgggagagaatggcatagatggta Find is-nt database================================================ Query_seq: TDE0029:TDE0030|TDE0029:TDE0030:ABC transporter, ATP-binding protein, HlyB family:prolipoprotein diacylglyceryl transferase, putative:<-<-:37813..38017 205 tttaatttcctccgaatattttatatatctaaaaatccttatgagcttttaaaagatattatttatcttaaaagcttttcaatttcctcttccttataatattgagcttgggcattccagagctcgttgtatttaccctctttgttttaatgagccttattatacaataaaattaatattttgggagagaatggcatagatggta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE0029:TDE0030|TDE0029:TDE0030:ABC transporter, ATP-binding protein, HlyB family:prolipoprotein diacylglyceryl transferase, putative:<-<-:37813..38017 205 tttaatttcctccgaatattttatatatctaaaaatccttatgagcttttaaaagatattatttatcttaaaagcttttcaatttcctcttccttataatattgagcttgggcattccagagctcgttgtatttaccctctttgttttaatgagccttattatacaataaaattaatattttgggagagaatggcatagatggta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE0029:TDE0030|TDE0029:TDE0030:ABC transporter, ATP-binding protein, HlyB family:prolipoprotein diacylglyceryl transferase, putative:<-<-:37813..38017 205 tttaatttcctccgaatattttatatatctaaaaatccttatgagcttttaaaagatattatttatcttaaaagcttttcaatttcctcttccttataatattgagcttgggcattccagagctcgttgtatttaccctctttgttttaatgagccttattatacaataaaattaatattttgggagagaatggcatagatggta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tttaatttcctccgaatattttatatatctaaaaatccttatgagcttttaaaagatattatttatcttaaaagcttttcaatttcctcttccttataatattgagcttgggcattccagagctcgttgtatttaccctctttgttttaatgagccttattatacaataaaattaatattttgggagagaatggcatagatggta Predict ORF larger than 30AA ================================================ Protein_Len: 47 Strand: + Start: 56 End: 196 ....................................................... M L F I L K A F Q F P L P Y N I E L G H S R A R C I Y P L C F N E P Y Y T I K L I F W E R M A ......... Protein_Len: 31 Strand: - Start: 71 End: 163 ...................................................................... F S K L K R K R I I N L K P M G S S T T N V R K T K I L R I M .......................................... tttaatttcctccgaatattttatatatctaaaaatccttatgagcttttaaaagatattatttatcttaaaagcttttcaatttcctcttccttataatattgagcttgggcattccagagctcgttgtatttaccctctttgttttaatgagccttattatacaataaaattaatattttgggagagaatggcatagatggta 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: 82 Start: 159 End: 188 ..............................................................................................................................................................TCTCCCAAAATATTAATTTTATTGTATAAT................. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ tttaatttcctccgaatattttatatatctaaaaatccttatgagcttttaaaagatattatttatcttaaaagcttttcaatttcctcttccttataatattgagcttgggcattccagagctcgttgtatttaccctctttgttttaatgagccttattatacaataaaattaatattttgggagagaatggcatagatggta Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE0029:TDE0030|TDE0029:TDE0030:ABC transporter, ATP-binding protein, HlyB family:prolipoprotein diacylglyceryl transferase, putative:<-<-:37813..38017 205 tttaatttcctccgaatattttatatatctaaaaatccttatgagcttttaaaagatattatttatcttaaaagcttttcaatttcctcttccttataatattgagcttgggcattccagagctcgttgtatttaccctctttgttttaatgagccttattatacaataaaattaatattttgggagagaatggcatagatggta Intra-Species Hit: Count: 1 Min: 1 Max: 205 Len: 205 Subject: NC_002967_TDE0029_TDE0030|ABC transporter, ATP-binding protein, HlyB family:prolipoprotein diacylglyceryl transferase, putative|NEGATIVE:NEGATIVE|[37813,38017]|205 HSP 1 e-value: 1.0E-112 bit: 406.0 Len: 205 Query Start:1 Query End:205 Subject Strand: POSITIVE Subject Start: 1 Subject End: 205 tttaatttcctccgaatattttatatatctaaaaatccttatgagcttttaaaagatattatttatcttaaaagcttttcaatttcctcttccttataatattgagcttgggcattccagagctcgttgtatttaccctctttgttttaatgagccttattatacaataaaattaatattttgggagagaatggcatagatggta tttaatttcctccgaatattttatatatctaaaaatccttatgagcttttaaaagatattatttatcttaaaagcttttcaatttcctcttccttataatattgagcttgggcattccagagctcgttgtatttaccctctttgttttaatgagccttattatacaataaaattaatattttgggagagaatggcatagatggta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUAAUUUCCUCCGAAUAUUUUAUAUAUCUAAAAAUCCUUAUGAGCUUUUAAAAGAUAUUAUUUAUCUUAAAAGCUUUUCAAUUUCCUCUUCCUUAUAAUAUUGAGCUUGGGCAUUCCAGAGCUCGUUGUAUUUACCCUCUUUGUUUUAAUGAGCCUUAUUAUACAAUAAAAUUAAUAUUUUGGGAGAGAAUGGCAUAGAUGGUA .........................((((((...........(((((((((..(((((.....)))))))))))))).........(((((((....((((((((((((.((....)).)))))).((((((.....(((...........))).......)))))).......))))))..))))))).......))))))... (-42.00) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UACCAUCUAUGCCAUUCUCUCCCAAAAUAUUAAUUUUAUUGUAUAAUAAGGCUCAUUAAAACAAAGAGGGUAAAUACAACGAGCUCUGGAAUGCCCAAGCUCAAUAUUAUAAGGAAGAGGAAAUUGAAAAGCUUUUAAGAUAAAUAAUAUCUUUUAAAAGCUCAUAAGGAUUUUUAGAUAUAUAAAAUAUUCGGAGGAAAUUAAA ..((.(((...((.((((((.((...............((((((......((((.............))))..)))))).(((((.(((.....))))))))..........)).))))))........(((((((((((((.....)))))..)))))))).....))..(((((......))))).....)))))........ (-38.22) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 906 140 91 231 182 NC_002967:TDE0029|5end_ABC_transporter,_ATP-binding_protein,_HlyB_family_37722..37952_NEGATIVE 753 119 71 217 169 NC_002967:TDE0027|5end_DHH_superfamily_protein,_subfamily_1_33986..34216_NEGATIVE 350 142 102 86 47 NC_002967:TDE1006|5end_flagellar_basal-body_rod_protein_FlgG_1030427..1030657_POSITIVE 289 127 87 145 94 NC_002967:TDE2479|5end_hypothetical_protein_2503290..2503520_NEGATIVE 279 129 82 63 11 NC_002967:TDE2485|5end_hypothetical_protein_2509123..2509353_NEGATIVE 279 137 91 153 100 NC_002967:TDE2119|5end_glycine_reductase_complex_selenoprotein_GrdB2_2152693..2152923_NEGATIVE 277 158 111 150 103 NC_002967:TDE2465|5end_hypothetical_protein_2489651..2489881_NEGATIVE 263 146 106 52 9 NC_002967:TDE1405|5end_phosphoribosylformylglycinamidine_synthetase_I_1448674..1448904_NEGATIVE 263 150 109 110 76 NC_002967:TDE0987|5end_oligopeptide/dipeptide_ABC_transporter,_ATP-binding_protein_1014041..1014271_POSITIVE 260 129 86 99 40 NC_002967:TDE2268|5end_hypothetical_protein_2304959..2305189_NEGATIVE 260 141 104 68 24 NC_002967:TDE1892|5end_hypothetical_protein_1912065..1912295_POSITIVE 256 130 83 225 160 NC_002967:TDE1982|5end_hypothetical_protein_1992984..1993214_NEGATIVE 256 129 84 160 114 NC_002967:TDE0356|5end_hypothetical_protein_400088..400318_NEGATIVE 255 143 101 104 63 NC_002967:TDE1271|5end_oligopeptide/dipeptide_ABC_transporter,_ATP-binding_protein_1306000..1306230_NEGATIVE 255 148 102 201 150 NC_002967:TDE0736|5end_hypothetical_protein_775230..775460_NEGATIVE 254 153 112 52 14 NC_002967:TDE2784|5end_hypothetical_protein_2836838..2837068_POSITIVE 253 119 75 152 101 NC_002967:TDE1141|5end_tail_fiber_domain_protein_1171443..1171673_NEGATIVE 253 159 111 68 26 NC_002967:TDE0572|5end_hypothetical_protein_603494..603724_POSITIVE 250 130 87 138 99 NC_002967:TDE2423|5end_ribosomal_protein_L10_2454034..2454264_NEGATIVE 250 148 102 159 115 NC_002967:TDE2375|5end_hypothetical_protein_2406661..2406891_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 753 119 71 147 99 NC_002967:TDE0028|3end_ABC_transporter,_ATP-binding_protein,_HlyB_family_34056..34206_NEGATIVE 350 142 102 74 35 NC_002967:TDE1005|3end_hypothetical_protein_1030495..1030645_POSITIVE 317 159 111 93 41 NC_002967:TDE0833|3end_lipoprotein,_putative_854097..854247_POSITIVE 302 130 86 149 105 NC_002967:TDE0315|3end_ABC_transporter,_ATP-binding/permease_protein,_HlyB_family_348802..348952_POSITIVE 291 127 85 143 104 NC_002967:TDE2524|3end_ABC_transporter,_ATP-binding_protein_2551807..2551957_POSITIVE 289 127 87 69 18 NC_002967:TDE2480|3end_heat_shock_protein_90_2503366..2503516_NEGATIVE 279 137 91 141 88 NC_002967:TDE2120|3end_glycine_reductase_complex_proprotein_GrdE2_2152705..2152855_NEGATIVE 277 158 111 150 103 NC_002967:TDE2466|3end_hypothetical_protein_2489651..2489801_NEGATIVE 270 119 94 132 107 NC_002967:TDE1062|3end_ABC_transporter,_ATP-binding_protein,_HlyB_family_1090387..1090537_POSITIVE 269 147 106 53 2 NC_002967:TDE2682|3end_hypothetical_protein_2721388..2721538_NEGATIVE 263 146 106 49 6 NC_002967:TDE1406|3end_hypothetical_protein_1448677..1448827_NEGATIVE 263 150 109 110 76 NC_002967:TDE0986|3end_oligopeptide/dipeptide_ABC_transporter,_ATP-binding_protein_1014121..1014271_POSITIVE 262 115 74 137 99 NC_002967:TDE0133|3end_transcriptional_regulator,_GntR_family_153202..153352_POSITIVE 260 129 86 127 68 NC_002967:TDE2269|3end_hypothetical_protein_2304931..2305081_NEGATIVE 256 129 84 140 94 NC_002967:TDE0357|3end_hypothetical_protein_400108..400258_NEGATIVE 255 143 101 114 73 NC_002967:TDE1272|3end_oligopeptide/dipeptide_ABC_transporter,_ATP-binding_protein_1305990..1306140_NEGATIVE 253 119 75 127 76 NC_002967:TDE1142|3end_phage_minor_structural_protein,_putative_1171468..1171618_NEGATIVE 250 130 87 135 96 NC_002967:TDE2424|3end_50S_ribosomal_protein_L1_2454037..2454187_NEGATIVE 248 149 102 133 91 NC_002967:TDE1084|3end_folylpolyglutamate_synthetase,_putative_1114934..1115084_NEGATIVE 246 150 102 85 28 NC_002967:TDE1460|3end_hypothetical_protein_1508707..1508857_NEGATIVE