Origin IGS: aagtctaaagatatggtattaattacataagaaaactaaataaaaattcactgctgcaaacttacaaaaaaatcattggattatacaccagtctaataaaaaagttgagctcacaatcaaatctctacatgagaacaacgtgccatacgcacttatttgttaattatgcgaatccagcgtta .........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 taacgctggattcgcataattaacaaataagtgcgtatggcacgttgttctcatgtagagatttgattgtgagctcaacttttttattagactggtgtataatccaatgatttttttgtaagtttgcagcagtgaatttttatttagttttcttatgtaattaataccatatctttagactt Mask Tandem Repeat Region ================================================ aagtctaaagatatggtattaattacataagaaaactaaataaaaattcactgctgcaaacttacaaaaaaatcattggattatacaccagtctaataaaaaagttgagctcacaatcaaatctctacatgagaacaacgtgccatacgcacttatttgttaattatgcgaatccagcgtta Find is-nt database================================================ Query_seq: TF1751:TF1752|TF1751:TF1752:two-component system response regulator:hypothetical protein:->->:1887814..1887995 182 aagtctaaagatatggtattaattacataagaaaactaaataaaaattcactgctgcaaacttacaaaaaaatcattggattatacaccagtctaataaaaaagttgagctcacaatcaaatctctacatgagaacaacgtgccatacgcacttatttgttaattatgcgaatccagcgtta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF1751:TF1752|TF1751:TF1752:two-component system response regulator:hypothetical protein:->->:1887814..1887995 182 aagtctaaagatatggtattaattacataagaaaactaaataaaaattcactgctgcaaacttacaaaaaaatcattggattatacaccagtctaataaaaaagttgagctcacaatcaaatctctacatgagaacaacgtgccatacgcacttatttgttaattatgcgaatccagcgtta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF1751:TF1752|TF1751:TF1752:two-component system response regulator:hypothetical protein:->->:1887814..1887995 182 aagtctaaagatatggtattaattacataagaaaactaaataaaaattcactgctgcaaacttacaaaaaaatcattggattatacaccagtctaataaaaaagttgagctcacaatcaaatctctacatgagaacaacgtgccatacgcacttatttgttaattatgcgaatccagcgtta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aagtctaaagatatggtattaattacataagaaaactaaataaaaattcactgctgcaaacttacaaaaaaatcattggattatacaccagtctaataaaaaagttgagctcacaatcaaatctctacatgagaacaacgtgccatacgcacttatttgttaattatgcgaatccagcgtta Predict ORF larger than 30AA ================================================ Protein_Len: 55 Strand: + Start: 18 End: 182 ................. M N Y I R K L N K N S L L Q T Y K K I I G L Y T S L I K K L S S Q S N L Y M R T T C H T H L F V N Y A N P A L aagtctaaagatatggtattaattacataagaaaactaaataaaaattcactgctgcaaacttacaaaaaaatcattggattatacaccagtctaataaaaaagttgagctcacaatcaaatctctacatgagaacaacgtgccatacgcacttatttgttaattatgcgaatccagcgtta 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: 81 Start: 80 End: 109 ...............................................................................CTCAACTTTTTTATTAGACTGGTGTATAAT......................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ aagtctaaagatatggtattaattacataagaaaactaaataaaaattcactgctgcaaacttacaaaaaaatcattggattatacaccagtctaataaaaaagttgagctcacaatcaaatctctacatgagaacaacgtgccatacgcacttatttgttaattatgcgaatccagcgtta Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TF1751:TF1752|TF1751:TF1752:two-component system response regulator:hypothetical protein:->->:1887814..1887995 182 aagtctaaagatatggtattaattacataagaaaactaaataaaaattcactgctgcaaacttacaaaaaaatcattggattatacaccagtctaataaaaaagttgagctcacaatcaaatctctacatgagaacaacgtgccatacgcacttatttgttaattatgcgaatccagcgtta Intra-Species Hit: Count: 1 Min: 1 Max: 182 Len: 182 Subject: tfor_TF1751_TF1752|two-component system response regulator:hypothetical protein|POSITIVE:POSITIVE|[1887814,1887995]|182 HSP 1 e-value: 2.0E-86 bit: 319.0 Len: 182 Query Start:1 Query End:182 Subject Strand: POSITIVE Subject Start: 1 Subject End: 182 aagtctaaagatatggtattaattacataagaaaactaaataaaaattcactgctgcaaacttacnnnnnnntcattggattatacaccagtctaataaaaaagttgagctcacaatcaaatctctacatgagaacaacgtgccatacgcacttatttgttaattatgcgaatccagcgtta aagtctaaagatatggtattaattacataagaaaactaaataaaaattcactgctgcaaacttacaaaaaaatcattggattatacaccagtctaataaaaaagttgagctcacaatcaaatctctacatgagaacaacgtgccatacgcacttatttgttaattatgcgaatccagcgtta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAGUCUAAAGAUAUGGUAUUAAUUACAUAAGAAAACUAAAUAAAAAUUCACUGCUGCAAACUUACAAAAAAAUCAUUGGAUUAUACACCAGUCUAAUAAAAAAGUUGAGCUCACAAUCAAAUCUCUACAUGAGAACAACGUGCCAUACGCACUUAUUUGUUAAUUAUGCGAAUCCAGCGUUA ...........((((((((.................................(((...(((((...........(((((........))))).........))))).)))...........((((.....)))).....))))))))(((....((((((.......))))))...)))... (-23.85) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAACGCUGGAUUCGCAUAAUUAACAAAUAAGUGCGUAUGGCACGUUGUUCUCAUGUAGAGAUUUGAUUGUGAGCUCAACUUUUUUAUUAGACUGGUGUAUAAUCCAAUGAUUUUUUUGUAAGUUUGCAGCAGUGAAUUUUUAUUUAGUUUUCUUAUGUAAUUAAUACCAUAUCUUUAGACUU ......((((((.((((((..(((((....((((.....)))).))))).....(((((((((((.(((..((((..((......((((...(((........))).))))......)).))))..)))...))))))))))).........))))))....))).)))............. (-29.20) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 266 150 109 210 159 tfor:TF2245|5end_conserved_hypothetical_protein_2420654..2420884_POSITIVE 256 179 141 201 160 tfor:TF1599|5end_ribonuclease_P_protein_component_1713564..1713794_POSITIVE 248 178 145 226 193 tfor:TF1818|5end_conserved_hypothetical_protein_1957967..1958197_POSITIVE 248 179 134 115 76 tfor:TF0215|5end_tRNA/rRNA_methyltransferase,_TrmH_family_241463..241693_POSITIVE 245 179 131 64 21 tfor:TF1472|5end_acyl-ACP_thioesterase_1565475..1565705_POSITIVE 240 170 122 164 115 tfor:TF2475|5end_GTP_pyrophosphokinase,_(p)ppGpp_synthetase_2651925..2652155_POSITIVE 238 150 103 66 24 tfor:TF1606|5end_outer_membrane_protein_1722352..1722582_POSITIVE 237 150 104 42 7 tfor:TF1459|5end_possible_protease_1548434..1548664_POSITIVE 237 161 123 53 9 tfor:TF0148|5end_conserved_hypothetical_protein_159448..159678_POSITIVE 235 179 132 224 170 tfor:TF2229.1|5end_rteR_regulatory_ortholog_(with_internal_stop)_2399454..2399684_POSITIVE 235 179 139 45 10 tfor:TF0038|5end_conserved_hypothetical_protein_39907..40137_POSITIVE 234 180 131 98 41 tfor:TF2367|5end_delta-1-pyrroline-5-carboxylate_dehydrogenase_2532002..2532232_POSITIVE 232 180 131 90 41 tfor:TF2540|5end_conserved_hypothetical_protein_2723058..2723288_POSITIVE 230 149 123 127 94 tfor:TF0288|5end_conserved_hypothetical_protein_317474..317704_POSITIVE 227 180 142 158 115 tfor:TF3080|5end_conserved_hypothetical_protein_3310480..3310710_POSITIVE 224 179 131 222 178 tfor:TF2976|5end_hypothetical_protein_3183246..3183476_POSITIVE 222 163 123 167 122 tfor:TF0231|5end_conserved_hypothetical_protein_257804..258034_POSITIVE 221 160 115 106 49 tfor:TF3164|5end_hypothetical_protein_3403897..3404127_POSITIVE 221 179 139 200 171 tfor:TF0063|5end_conserved_hypothetical_protein_66110..66340_POSITIVE 220 146 101 212 157 tfor:TF2234|5end_acetyltransferase,_GNAT_family_2407144..2407374_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 248 179 134 143 104 tfor:TF0214|3end_DNA_recombination_and_repair_protein,_RecN_241571..241721_POSITIVE 238 150 103 48 6 tfor:TF1605|3end_outer_membrane_protein,_TonB_dependent_receptor_1722414..1722564_POSITIVE 237 178 133 60 14 tfor:TF0825|3end_hypothetical_protein_883850..884000_POSITIVE 235 179 139 49 14 tfor:TF0037|3end_sialic_acid-specific_9-O-acetylesterase_39991..40141_POSITIVE 232 180 131 68 19 tfor:TF2539|3end_hypothetical_protein_2723116..2723266_POSITIVE 230 149 123 40 7 tfor:TF0287|3end_peptidase,_M23_family_317467..317617_POSITIVE 222 180 139 61 19 tfor:TF1834|3end_3-isopropylmalate_dehydrogenase_1984311..1984461_POSITIVE 222 163 123 145 100 tfor:TF0230|3end_hydrolase,_haloacid_dehalogenase-like_family_257862..258012_POSITIVE 220 179 133 136 93 tfor:TF1824|3end_ABC_transporter,_ATP-binding_protein_1973510..1973660_POSITIVE 219 180 132 72 14 tfor:TF1408|3end_cation_efflux_system_protein_1485546..1485696_POSITIVE 217 154 113 75 24 tfor:TF1323|3end_metallo-beta-lactamase_superfamily_protein_1403533..1403683_POSITIVE 216 170 121 94 54 tfor:TF0462|3end_possible_cobalamin_biosynthesis_precorrin-3_methylase_479095..479245_POSITIVE 214 180 140 145 102 tfor:TF3118|3end_conserved_hypothetical_protein_3352824..3352974_POSITIVE 211 175 145 149 120 tfor:TF1816|3end_hypothetical_protein_1957974..1958124_POSITIVE 210 169 126 103 64 tfor:TF2991|3end_conserved_hypothetical_protein_3209107..3209257_POSITIVE 210 176 131 55 9 tfor:TF2740|3end_conserved_hypothetical_protein_2921972..2922122_POSITIVE 210 179 148 132 96 tfor:TF1104|3end_hypothetical_protein_1172194..1172344_POSITIVE 209 170 122 125 66 tfor:TF1300|3end_conserved_hypothetical_protein_1383149..1383299_POSITIVE 207 179 139 71 32 tfor:TF1022|3end_chromosomal_replication_initiator_ATPase,_DnaA_1079259..1079409_POSITIVE 206 95 52 73 35 tfor:TF0692|3end_conserved_hypothetical_protein_736992..737142_POSITIVE