Origin IGS: cagcttgtgatgattccgagttgaattcgttatttttctcgtttttcttgcatgttacctatcggtaacgtaactttgcggttacttatcggtaacattacaattgagaaggagac .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 gtctccttctcaattgtaatgttaccgataagtaaccgcaaagttacgttaccgataggtaacatgcaagaaaaacgagaaaaataacgaattcaactcggaatcatcacaagctg Mask Tandem Repeat Region ================================================ cagcttgtgatgattccgagttgaattcgttatttttctcgtttttcttgcatgttacctatcggtaacgtaactttgcggttacttatcggtaacattacaattgagaaggagac Find is-nt database================================================ Query_seq: TF1911:TF1912|TF1911:TF1912:conserved hypothetical protein:transcriptional regulator, TetR family:->->:2065994..2066109 116 cagcttgtgatgattccgagttgaattcgttatttttctcgtttttcttgcatgttacctatcggtaacgtaactttgcggttacttatcggtaacattacaattgagaaggagac Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF1911:TF1912|TF1911:TF1912:conserved hypothetical protein:transcriptional regulator, TetR family:->->:2065994..2066109 116 cagcttgtgatgattccgagttgaattcgttatttttctcgtttttcttgcatgttacctatcggtaacgtaactttgcggttacttatcggtaacattacaattgagaaggagac Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF1911:TF1912|TF1911:TF1912:conserved hypothetical protein:transcriptional regulator, TetR family:->->:2065994..2066109 116 cagcttgtgatgattccgagttgaattcgttatttttctcgtttttcttgcatgttacctatcggtaacgtaactttgcggttacttatcggtaacattacaattgagaaggagac Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 cagcttgtgatgattccgagttgaattcgttatttttctcgtttttcttgcatgttacctatcggtaacgtaactttgcggttacttatcggtaacattacaattgagaaggagac Predict ORF larger than 30AA ================================================ Protein_Len: 30 Strand: + Start: 25 End: 114 ........................ M R Y F S R F S C M L P I G N V T L R L L I G N I T I E K E .. cagcttgtgatgattccgagttgaattcgttatttttctcgtttttcttgcatgttacctatcggtaacgtaactttgcggttacttatcggtaacattacaattgagaaggagac 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================================================ cagcttgtgatgattccgagttgaattcgttatttttctcgtttttcttgcatgttacctatcggtaacgtaactttgcggttacttatcggtaacattacaattgagaaggagac Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TF1911:TF1912|TF1911:TF1912:conserved hypothetical protein:transcriptional regulator, TetR family:->->:2065994..2066109 116 cagcttgtgatgattccgagttgaattcgttatttttctcgtttttcttgcatgttacctatcggtaacgtaactttgcggttacttatcggtaacattacaattgagaaggagac Intra-Species Hit: Count: 1 Min: 1 Max: 116 Len: 116 Subject: tfor_TF1911_TF1912|conserved hypothetical protein:transcriptional regulator, TetR family|POSITIVE:POSITIVE|[2065994,2066109]|116 HSP 1 e-value: 8.0E-60 bit: 230.0 Len: 116 Query Start:1 Query End:116 Subject Strand: POSITIVE Subject Start: 1 Subject End: 116 cagcttgtgatgattccgagttgaattcgttatttttctcgtttttcttgcatgttacctatcggtaacgtaactttgcggttacttatcggtaacattacaattgagaaggagac cagcttgtgatgattccgagttgaattcgttatttttctcgtttttcttgcatgttacctatcggtaacgtaactttgcggttacttatcggtaacattacaattgagaaggagac Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CAGCUUGUGAUGAUUCCGAGUUGAAUUCGUUAUUUUUCUCGUUUUUCUUGCAUGUUACCUAUCGGUAACGUAACUUUGCGGUUACUUAUCGGUAACAUUACAAUUGAGAAGGAGAC (((((((.((....))))))))).............((((.(((((.(((.((((((((.((.(((((((((....))).)))))).)).))))))))..)))..))))).)))). (-33.60) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GUCUCCUUCUCAAUUGUAAUGUUACCGAUAAGUAACCGCAAAGUUACGUUACCGAUAGGUAACAUGCAAGAAAAACGAGAAAAAUAACGAAUUCAACUCGGAAUCAUCACAAGCUG .((((........(((((.(((((((.((..(((((...........)))))..)).)))))))))))).......))))........((.(((.....))).))........... (-21.56) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 308 54 11 42 1 tfor:TF0683|5end_conserved_hypothetical_protein_727506..727736_POSITIVE 300 96 53 201 152 tfor:TF2820|5end_argininosuccinate_synthetase_3009876..3010106_POSITIVE 299 60 12 180 132 tfor:TF2621|5end_conserved_hypothetical_protein;_possible_SAM-dependent_methyltransferase_2796760..2796990_POSITIVE 282 82 41 209 169 tfor:TF3138|5end_Na+-translocating_quinone_reductase,_subunit_D_3371948..3372178_POSITIVE 280 64 27 129 94 tfor:TF1115|5end_lantibiotic_biosynthesis_protein_1185277..1185507_POSITIVE 271 47 3 204 153 tfor:TF2892|5end_seryl-tRNA_synthetase_3079309..3079539_POSITIVE 270 50 1 65 11 tfor:TF2226|5end_CTn_excision_protein_2395529..2395759_POSITIVE 268 79 31 211 170 tfor:TF0543|5end_glycine_cleavage_system_p-protein_572251..572481_POSITIVE 267 94 51 219 173 tfor:TF0559|5end_methanol_dehydrogenase_regulator,_MoxR-like;_magnesium_chelatase,_subunit_I_591015..591245_POSITIVE 261 48 1 97 55 tfor:TF1995|5end_exonuclease_2147148..2147378_POSITIVE 260 90 43 54 20 tfor:TF0722|5end_pyruvate_dehydrogenase_E3_component(dihydrolipoamide_dehydrogenase)_772873..773103_POSITIVE 259 81 48 147 114 tfor:TF0236|5end_multidrug_resistance_protein_261779..262009_POSITIVE 258 85 41 43 2 tfor:TF1369|5end_hypothetical_protein_1447192..1447422_POSITIVE 258 87 41 51 7 tfor:TF0242|5end_conserved_hypothetical_protein_272439..272669_POSITIVE 257 42 2 58 7 tfor:TF1804|5end_hypothetical_protein_1947101..1947331_POSITIVE 257 90 46 110 54 tfor:TF1109|5end_lipoprotein_1178784..1179014_POSITIVE 257 70 21 54 12 tfor:TF1065|5end_conserved_hypothetical_protein_1135313..1135543_POSITIVE 257 60 11 97 42 tfor:TF0660|5end_conserved_hypothetical_protein_706009..706239_POSITIVE 257 50 2 180 127 tfor:TF0310|5end_conserved_hypothetical_protein_334685..334915_POSITIVE 256 49 2 197 156 tfor:TF3021|5end_FKBP-type_peptidyl-prolyl_cis-trans_isomerase_3245437..3245667_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 299 60 12 146 98 tfor:TF2620|3end_conserved_hypothetical_protein_2796806..2796956_POSITIVE 286 77 33 74 25 tfor:TF2840|3end_hypothetical_protein_3031289..3031439_POSITIVE 282 102 61 131 90 tfor:TF0145|3end_glutamine_synthetase_154718..154868_POSITIVE 280 64 27 93 58 tfor:TF1114|3end_hypothetical_protein_1185321..1185471_POSITIVE 274 90 41 47 2 tfor:TF1382|3end_hypothetical_protein_1457777..1457927_POSITIVE 271 90 47 70 25 tfor:TF2165|3end_hypothetical_protein_2341922..2342072_POSITIVE 270 50 1 58 4 tfor:TF2225|3end_CTn_excision_protein_2395602..2395752_POSITIVE 268 80 33 88 49 tfor:TF1164|3end_two-component_system_sensor_histidine_kinase_1244778..1244928_POSITIVE 261 48 1 97 55 tfor:TF1994|3end_acyl-CoA_synthetase_2147228..2147378_POSITIVE 259 81 48 137 104 tfor:TF0235|3end_hypothetical_protein_261849..261999_POSITIVE 258 85 41 43 2 tfor:TF1367|3end_hypothetical_protein_1447272..1447422_POSITIVE 257 90 46 97 41 tfor:TF1108|3end_conserved_hypothetical_protein;_possible_lipoprotein_1178851..1179001_POSITIVE 257 70 21 43 1 tfor:TF1064|3end_ampG_permease_1135382..1135532_POSITIVE 257 60 11 73 18 tfor:TF0659|3end_RNA_polymerase,_ECF-type_sigma_factor_706065..706215_POSITIVE 256 49 2 139 98 tfor:TF3020|3end_possible_sulfatase_3245459..3245609_POSITIVE 256 47 4 65 20 tfor:TF1329|3end_glucose-1-phosphate_thymidyltransferase_1409545..1409695_POSITIVE 256 49 3 136 97 tfor:TF1168|3end_hypothetical_protein_1249092..1249242_POSITIVE 253 46 1 59 7 tfor:TF2123|3end_conserved_hypothetical_protein;_TPR-repeat_protein_2300344..2300494_POSITIVE 252 92 60 134 98 tfor:TF2533|3end_adenylosuccinate_synthetase_2717014..2717164_POSITIVE 251 81 42 139 93 tfor:TF0439|3end_Na+-transporting_NADH:ubiquinone_oxidoreductase,_subunit_1_463689..463839_POSITIVE