Origin IGS: gtgcctatttatatcggcaaatatactccaaataaatgaaaatattttttgcgataggatttattaaaagataaattccgatttgtcaatccgataatctttatttcgatatatatagttatcttattttgtttatgataaccccaataaataaagatatgcttttaaccgttttatttctatttcattta .........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 taaatgaaatagaaataaaacggttaaaagcatatctttatttattggggttatcataaacaaaataagataactatatatatcgaaataaagattatcggattgacaaatcggaatttatcttttaataaatcctatcgcaaaaaatattttcatttatttggagtatatttgccgatataaataggcac Mask Tandem Repeat Region ================================================ gtgcctatttatatcggcaaatatactccaaataaatgaaaatattttttgcgataggatttattaaaagataaattccgatttgtcaatccgataatctttatttcgatatatatagttatcttattttgtttatgataaccccaataaataaagatatgcttttaaccgttttatttctatttcattta Find is-nt database================================================ Query_seq: TF0869:TF0870|TF0869:TF0870:conserved hypothetical protein; possible transcriptional regulator:conserved hypothetical protein:->->:922075..922265 191 gtgcctatttatatcggcaaatatactccaaataaatgaaaatattttttgcgataggatttattaaaagataaattccgatttgtcaatccgataatctttatttcgatatatatagttatcttattttgtttatgataaccccaataaataaagatatgcttttaaccgttttatttctatttcattta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF0869:TF0870|TF0869:TF0870:conserved hypothetical protein; possible transcriptional regulator:conserved hypothetical protein:->->:922075..922265 191 gtgcctatttatatcggcaaatatactccaaataaatgaaaatattttttgcgataggatttattaaaagataaattccgatttgtcaatccgataatctttatttcgatatatatagttatcttattttgtttatgataaccccaataaataaagatatgcttttaaccgttttatttctatttcattta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF0869:TF0870|TF0869:TF0870:conserved hypothetical protein; possible transcriptional regulator:conserved hypothetical protein:->->:922075..922265 191 gtgcctatttatatcggcaaatatactccaaataaatgaaaatattttttgcgataggatttattaaaagataaattccgatttgtcaatccgataatctttatttcgatatatatagttatcttattttgtttatgataaccccaataaataaagatatgcttttaaccgttttatttctatttcattta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gtgcctatttatatcggcaaatatactccaaataaatgaaaatattttttgcgataggatttattaaaagataaattccgatttgtcaatccgataatctttatttcgatatatatagttatcttattttgtttatgataaccccaataaataaagatatgcttttaaccgttttatttctatttcattta Predict ORF larger than 30AA ================================================ Protein_Len: 39 Strand: + Start: 75 End: 191 .......................................................................... M P I C Q S D N L Y F D I Y S Y L I L F M I T P I N K D M L L T V L F L F H L Protein_Len: 49 Strand: - Start: 12 End: 158 ........... I P L Y V G F L H F Y K K R Y S K N F S L N R N T L G I I K I E I Y I T I K N Q K H Y G W Y I F M ................................. gtgcctatttatatcggcaaatatactccaaataaatgaaaatattttttgcgataggatttattaaaagataaattccgatttgtcaatccgataatctttatttcgatatatatagttatcttattttgtttatgataaccccaataaataaagatatgcttttaaccgttttatttctatttcattta 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: 61 End: 90 ............................................................ATTGACAAATCGGAATTTATCTTTTAATAA..................................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ gtgcctatttatatcggcaaatatactccaaataaatgaaaatattttttgcgataggatttattaaaagataaattccgatttgtcaatccgataatctttatttcgatatatatagttatcttattttgtttatgataaccccaataaataaagatatgcttttaaccgttttatttctatttcattta Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TF0869:TF0870|TF0869:TF0870:conserved hypothetical protein; possible transcriptional regulator:conserved hypothetical protein:->->:922075..922265 191 gtgcctatttatatcggcaaatatactccaaataaatgaaaatattttttgcgataggatttattaaaagataaattccgatttgtcaatccgataatctttatttcgatatatatagttatcttattttgtttatgataaccccaataaataaagatatgcttttaaccgttttatttctatttcattta Intra-Species Hit: Count: 1 Min: 1 Max: 191 Len: 191 Subject: tfor_TF0869_TF0870|conserved hypothetical protein; possible transcriptional regulator:conserved hypothetical protein|POSITIVE:POSITIVE|[922075,922265]|191 HSP 1 e-value: 1.0E-104 bit: 379.0 Len: 191 Query Start:1 Query End:191 Subject Strand: POSITIVE Subject Start: 1 Subject End: 191 gtgcctatttatatcggcaaatatactccaaataaatgaaaatattttttgcgataggatttattaaaagataaattccgatttgtcaatccgataatctttatttcgatatatatagttatcttattttgtttatgataaccccaataaataaagatatgcttttaaccgttttatttctatttcattta gtgcctatttatatcggcaaatatactccaaataaatgaaaatattttttgcgataggatttattaaaagataaattccgatttgtcaatccgataatctttatttcgatatatatagttatcttattttgtttatgataaccccaataaataaagatatgcttttaaccgttttatttctatttcattta Inter-species Hit: Count: 1 Min: 1 Max: 188 Len: 188 Subject: NC_002950_PG1526_PG1527|hypothetical protein:hypothetical protein|NEGATIVE:NEGATIVE|[1605462,1605656]|195 HSP 1 e-value: 1.0E-56 bit: 220.0 Len: 188 Query Start:1 Query End:188 Subject Strand: POSITIVE Subject Start: 1 Subject End: 195 gtgcctatttatatcggcaaatatactccaaataaatgaaaatattttttgcgataggatttattaaaagataaattccgatttgtcaatccgataatctttatttcgatatata--------tagttatcttattttgtttatgataaccccaataaataaagatatgcttttaaccgttttatttctatttcat... gtgcctatttatatcggcaaatatactccaaataaatgaaaatattttttgcgataggatttattataatataaattccgatttgtcaatccgataatctttatttcgatagatatatatctataattttcttattt-gtgtacgataatccaaataaacaaagatgtgcttttaaccgttttgtttctatttcat... Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GUGCCUAUUUAUAUCGGCAAAUAUACUCCAAAUAAAUGAAAAUAUUUUUUGCGAUAGGAUUUAUUAAAAGAUAAAUUCCGAUUUGUCAAUCCGAUAAUCUUUAUUUCGAUAUAUAUAGUUAUCUUAUUUUGUUUAUGAUAACCCCAAUAAAUAAAGAUAUGCUUUUAACCGUUUUAUUUCUAUUUCAU .((((.((....)).))))..............((((((((.........(((...(((((........(((((((....))))))))))))....((((((((((...........((((((.((.......)).))))))......)))))))))).))).........))))))))......... (-25.90) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUGAAAUAGAAAUAAAACGGUUAAAAGCAUAUCUUUAUUUAUUGGGGUUAUCAUAAACAAAAUAAGAUAACUAUAUAUAUCGAAAUAAAGAUUAUCGGAUUGACAAAUCGGAAUUUAUCUUUUAAUAAAUCCUAUCGCAAAAAAUAUUUUCAUUUAUUUGGAGUAUAUUUGCCGAUAUAAAUAGGCAC .((..((((..........((((((((...((((((((((..((.(((((((.............))))))).....))...))))))))))..((.((((....)))).))......)))))))).....))))..))..(((((((((((......))))).))))))(((..........))).. (-30.68) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 259 114 76 93 50 tfor:TF2153|5end_6-phosphofructokinase_2328112..2328342_POSITIVE 245 60 14 202 151 tfor:TF1728|5end_cell_division_ABC_transporter,_ATP-binding_protein_FtsE_1852537..1852767_POSITIVE 222 140 91 230 183 tfor:TF1325|5end_L-fucose_isomerase_1404000..1404230_POSITIVE 222 140 91 74 27 tfor:TF1326|5end_hypothetical_protein_1403844..1404074_POSITIVE 221 125 93 183 152 tfor:TF1077|5end_conserved_hypothetical_protein_1146382..1146612_POSITIVE 219 98 51 214 168 tfor:TF2544|5end_cytidine_deaminase_2728322..2728552_POSITIVE 215 58 16 42 5 tfor:TF2886|5end_RNA_methylase_SpoU_family_3075651..3075881_POSITIVE 215 95 51 227 183 tfor:TF0451|5end_rhomboid_family_membrane_protein_470085..470315_POSITIVE 208 95 53 191 159 tfor:TF3048|5end_conserved_hypothetical_protein_3276747..3276977_POSITIVE 206 108 77 67 31 tfor:TF2282|5end_hypothetical_protein_2439401..2439631_POSITIVE 205 108 76 51 20 tfor:TF2945|5end_DNA-directed_RNA_polymerase_beta'_subunit_3147448..3147678_POSITIVE 203 93 51 185 150 tfor:TF2846|5end_cobyric_acid_synthase_3034896..3035126_POSITIVE 203 162 134 89 62 tfor:TF0682|5end_outer_membrane_protein,_TonB_dependent_receptor_724450..724680_POSITIVE 203 113 71 76 28 tfor:TF0413|5end_succinyl-diaminopimelate_desuccinylase_430434..430664_POSITIVE 202 98 57 143 95 tfor:TF1214|5end_conserved_hypothetical_protein_1301213..1301443_POSITIVE 202 97 51 42 10 tfor:TF0493|5end_outer_membrane_protein_517537..517767_POSITIVE 202 60 14 61 13 tfor:TF0442|5end_Na+-transporting_NADH:ubiquinone_oxidoreductase,_subunit_4_465270..465500_POSITIVE 201 179 140 199 157 tfor:TF2499|5end_possible_thioesterase_family_protein_2673903..2674133_POSITIVE 198 55 12 48 1 tfor:TF2471|5end_conserved_hypothetical_protein_2649219..2649449_POSITIVE 195 111 79 209 181 tfor:TF2876|5end_cytosine_deaminase_3065144..3065374_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 222 140 91 96 49 tfor:TF1324|3end_conserved_hypothetical_protein_1403946..1404096_POSITIVE 219 98 51 78 32 tfor:TF2543|3end_RNA_polymerase_sigma-70_factor,_ECF_subfamily_2728266..2728416_POSITIVE 215 58 16 59 22 tfor:TF2884|3end_conserved_hypothetical_protein_3075748..3075898_POSITIVE 206 108 77 60 24 tfor:TF2280|3end_hypothetical_protein_2439474..2439624_POSITIVE 205 95 52 43 7 tfor:TF0177|3end_hypothetical_protein_187154..187304_POSITIVE 201 179 140 101 59 tfor:TF2498|3end_electron_transfer_flavoprotein,_alpha_subunit_2673885..2674035_POSITIVE 199 94 57 32 5 tfor:TF2640|3end_hypothetical_protein_2809533..2809683_POSITIVE 193 112 73 151 112 tfor:TF1871|3end_hypothetical_protein_2024551..2024701_POSITIVE 191 95 57 92 51 tfor:TF2833|3end_lipid_A_disaccharide_synthase_3025183..3025333_POSITIVE 189 109 69 131 92 tfor:TF2180|3end_phosphoribosylamine--glycine_ligase_2353931..2354081_POSITIVE 187 80 35 74 20 tfor:TF0444|3end_Na+-translocating_NADH-quinone_oxidoreductase,_subunit_5_466518..466668_POSITIVE 185 138 91 100 57 tfor:TF2357|3end_collagenase_2523900..2524050_POSITIVE 185 59 14 108 67 tfor:TF0472|3end_multidrug_resistance_protein,_AcrB/AcrD/AcrF_family_(cation_efflux_pump)_491057..491207_POSITIVE 184 144 104 109 68 tfor:TF1737|3end_outer_membrane_protein,_TonB_dependent_receptor_1865306..1865456_POSITIVE 182 60 11 116 65 tfor:TF2606|3end_conserved_hypothetical_protein_2783551..2783701_POSITIVE 182 111 80 38 3 tfor:TF1224|3end_hypothetical_protein_1311657..1311807_POSITIVE 182 172 137 85 48 tfor:TF0199|3end_conserved_hypothetical_protein_224064..224214_POSITIVE 181 110 79 47 11 tfor:TF2550|3end_translation_elongation_factor_G_2734492..2734642_POSITIVE 181 114 76 115 81 tfor:TF1301|3end_hypothetical_protein_1383487..1383637_POSITIVE 181 100 68 60 30 tfor:TF1206|3end_conserved_hypothetical_protein_1290136..1290286_POSITIVE