Origin IGS: tatcggatattaattacagtataaataccgattacaatatctcaaccccgattaatattataaaaaatcaacaatttcctataaatcgtaaaaaagaaaaaaatgaaattttctcagtatttaaacaagcaaagacgtctaaagctgaaaataaaaatatattaataacaggtcctttcggtataggaaaaacatatttcttatccgaaatatattttttactattacttgaaaaa .........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 tttttcaagtaatagtaaaaaatatatttcggataagaaatatgtttttcctataccgaaaggacctgttattaatatatttttattttcagctttagacgtctttgcttgtttaaatactgagaaaatttcatttttttcttttttacgatttataggaaattgttgattttttataatattaatcggggttgagatattgtaatcggtatttatactgtaattaatatccgata Mask Tandem Repeat Region ================================================ tatcggatattaattacagtataaataccgattacaatatctcaaccccgattaatattataaaaaatcaacaatttcctataaatcgtaaaaaagaaaaaaatgaaattttctcagtatttaaacaagcaaagacgtctaaagctgaaaataaaaatatattaataacaggtcctttcggtataggaaaaacatatttcttatccgaaatatattttttactattacttgaaaaa Find is-nt database================================================ Query_seq: TDE2581:TDE2582|TDE2581:TDE2582:hypothetical protein:GGDEF domain protein:->->:2611693..2611928 236 tatcggatattaattacagtataaataccgattacaatatctcaaccccgattaatattataaaaaatcaacaatttcctataaatcgtaaaaaagaaaaaaatgaaattttctcagtatttaaacaagcaaagacgtctaaagctgaaaataaaaatatattaataacaggtcctttcggtataggaaaaacatatttcttatccgaaatatattttttactattacttgaaaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE2581:TDE2582|TDE2581:TDE2582:hypothetical protein:GGDEF domain protein:->->:2611693..2611928 236 tatcggatattaattacagtataaataccgattacaatatctcaaccccgattaatattataaaaaatcaacaatttcctataaatcgtaaaaaagaaaaaaatgaaattttctcagtatttaaacaagcaaagacgtctaaagctgaaaataaaaatatattaataacaggtcctttcggtataggaaaaacatatttcttatccgaaatatattttttactattacttgaaaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE2581:TDE2582|TDE2581:TDE2582:hypothetical protein:GGDEF domain protein:->->:2611693..2611928 236 tatcggatattaattacagtataaataccgattacaatatctcaaccccgattaatattataaaaaatcaacaatttcctataaatcgtaaaaaagaaaaaaatgaaattttctcagtatttaaacaagcaaagacgtctaaagctgaaaataaaaatatattaataacaggtcctttcggtataggaaaaacatatttcttatccgaaatatattttttactattacttgaaaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tatcggatattaattacagtataaataccgattacaatatctcaaccccgattaatattataaaaaatcaacaatttcctataaatcgtaaaaaagaaaaaaatgaaattttctcagtatttaaacaagcaaagacgtctaaagctgaaaataaaaatatattaataacaggtcctttcggtataggaaaaacatatttcttatccgaaatatattttttactattacttgaaaaa Predict ORF larger than 30AA ================================================ Protein_Len: 60 Strand: + Start: 9 End: 236 ........ M N Y S I N T D Y N I S T P I N I I K N Q Q F P I N R K K E K N E I F S V F K Q A K T S K A E N K N I L I T G P F G I G Protein_Len: 47 Strand: - Start: 71 End: 211 ...................................................................... C N G I F R L F S F F S I K E T N L C A F V D L A S F L F I N I V P G K P I P F V Y K K D S M ......................... tatcggatattaattacagtataaataccgattacaatatctcaaccccgattaatattataaaaaatcaacaatttcctataaatcgtaaaaaagaaaaaaatgaaattttctcagtatttaaacaagcaaagacgtctaaagctgaaaataaaaatatattaataacaggtcctttcggtataggaaaaacatatttcttatccgaaatatattttttactattacttgaaaaa 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: 83 Start: 57 End: 86 ........................................................ATTTATAGGAAATTGTTGATTTTTTATAAT...................................................................................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ tatcggatattaattacagtataaataccgattacaatatctcaaccccgattaatattataaaaaatcaacaatttcctataaatcgtaaaaaagaaaaaaatgaaattttctcagtatttaaacaagcaaagacgtctaaagctgaaaataaaaatatattaataacaggtcctttcggtataggaaaaacatatttcttatccgaaatatattttttactattacttgaaaaa Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 82 HP_score: -2.7 Tail_Score: -6.28401 Start: 104 End: 116 Full_Region: tgcttgtttaaatac tgaga aaa tttca tttttttctttttta .......................................................................................................tgagaaaatttca........................................................................................................................ TransTerm Strand: + Conf: 65 HP_score: -6.0 Tail_Score: -3.7035 Start: 176 End: 210 Full_Region: ATTAATAACAGGTCC TTTCGGTATAGGAAA AACATA TTTCTTATCCGAAA TATATTTTTTACTAT ...............................................................................................................................................................................TTTCGGTATAGGAAAAACATATTTCTTATCCGAAA.......................... Find igs database================================================ Query_seq: TDE2581:TDE2582|TDE2581:TDE2582:hypothetical protein:GGDEF domain protein:->->:2611693..2611928 236 tatcggatattaattacagtataaataccgattacaatatctcaaccccgattaatattataaaaaatcaacaatttcctataaatcgtaaaaaagaaaaaaatgaaattttctcagtatttaaacaagcaaagacgtctaaagctgaaaataaaaatatattaataacaggtcctttcggtataggaaaaacatatttcttatccgaaatatattttttactattacttgaaaaa Intra-Species Hit: Count: 1 Min: 1 Max: 236 Len: 236 Subject: NC_002967_TDE2581_TDE2582|hypothetical protein:GGDEF domain protein|POSITIVE:POSITIVE|[2611693,2611928]|236 HSP 1 e-value: 1.0E-69 bit: 264.0 Len: 133 Query Start:104 Query End:236 Subject Strand: POSITIVE Subject Start: 104 Subject End: 236 .......................................................................................................tgaaattttctcagtatttaaacaagcaaagacgtctaaagctgaaaataaaaatatattaataacaggtcctttcggtataggaaaaacatatttcttatccgaaatatattttttactattacttgaaaaa .......................................................................................................tgaaattttctcagtatttaaacaagcaaagacgtctaaagctgaaaataaaaatatattaataacaggtcctttcggtataggaaaaacatatttcttatccgaaatatattttttactattacttgaaaaa HSP 2 e-value: 2.0E-43 bit: 176.0 Len: 89 Query Start:1 Query End:89 Subject Strand: POSITIVE Subject Start: 1 Subject End: 89 tatcggatattaattacagtataaataccgattacaatatctcaaccccgattaatattataaaaaatcaacaatttcctataaatcgt................................................................................................................................................... tatcggatattaattacagtataaataccgattacaatatctcaaccccgattaatattataaaaaatcaacaatttcctataaatcgt................................................................................................................................................... Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAUCGGAUAUUAAUUACAGUAUAAAUACCGAUUACAAUAUCUCAACCCCGAUUAAUAUUAUAAAAAAUCAACAAUUUCCUAUAAAUCGUAAAAAAGAAAAAAAUGAAAUUUUCUCAGUAUUUAAACAAGCAAAGACGUCUAAAGCUGAAAAUAAAAAUAUAUUAAUAACAGGUCCUUUCGGUAUAGGAAAAACAUAUUUCUUAUCCGAAAUAUAUUUUUUACUAUUACUUGAAAAA .(((((.((((.((......)).))))))))).........((((..((.((((((((..............((((((.......((........)).......))))))...(((((.((((.((..........)).)))))))))..........))))))))....))...((((((.((((((((......))))))))))))))..................)))).... (-31.44) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUUUCAAGUAAUAGUAAAAAAUAUAUUUCGGAUAAGAAAUAUGUUUUUCCUAUACCGAAAGGACCUGUUAUUAAUAUAUUUUUAUUUUCAGCUUUAGACGUCUUUGCUUGUUUAAAUACUGAGAAAAUUUCAUUUUUUUCUUUUUUACGAUUUAUAGGAAAUUGUUGAUUUUUUAUAAUAUUAAUCGGGGUUGAGAUAUUGUAAUCGGUAUUUAUACUGUAAUUAAUAUCCGAUA .......((((((((..(((((((((((((......)))))))))))))......((....))..))))))))............(((((((.((((((((........))))))))..)))))))......................((((((((((((((((...))))))))))).....)))))..((((.(((((((....(((((....)))))....))))))))))). (-51.00) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 239 214 173 140 98 NC_002967:TDE2425|5end_50S_ribosomal_protein_L11_2455150..2455380_NEGATIVE 231 160 125 183 142 NC_002967:TDE0937|5end_RNA_polymerase_sigma-70_factor_family_protein_959951..960181_POSITIVE 230 219 172 152 95 NC_002967:TDE0877|5end_hypothetical_protein_898589..898819_POSITIVE 227 208 163 141 94 NC_002967:TDE0388|5end_hypothetical_protein_439173..439403_POSITIVE 221 83 44 193 155 NC_002967:TDE2365|5end_high-affinity_branched-chain_amino_acid_ABC_transporter,_permease_protein_2399949..2400179_NEGATIVE 214 145 109 88 45 NC_002967:TDE0197|5end_PIN_domain_protein_232765..232995_POSITIVE 211 161 127 37 1 NC_002967:TDE0819|5end_ABC_transporter,_ATP-binding/permease_protein_843385..843615_NEGATIVE 209 49 2 163 121 NC_002967:TDE2596|5end_hypothetical_protein_2632039..2632269_NEGATIVE 209 53 12 83 41 NC_002967:TDE1137|5end_hypothetical_protein_1166749..1166979_NEGATIVE 207 210 169 168 114 NC_002967:TDE0292|5end_hypothetical_protein_322014..322244_NEGATIVE 203 44 1 69 31 NC_002967:TDE1049|5end_elongation_factor_EF-2_1075287..1075517_POSITIVE 199 189 141 59 15 NC_002967:TDE1909|5end_conserved_hypothetical_protein_TIGR00159_1926872..1927102_NEGATIVE 197 50 5 59 16 NC_002967:TDE2178|5end_hypothetical_protein_2208758..2208988_NEGATIVE 197 59 37 119 90 NC_002967:TDE1450|5end_MutS2_family_protein_1495320..1495550_POSITIVE 196 148 125 131 104 NC_002967:TDE1353|5end_rod_shape-determining_protein_RodA_1393550..1393780_POSITIVE 194 207 164 204 156 NC_002967:TDE0846|5end_hypothetical_protein_868623..868853_POSITIVE 193 209 173 177 140 NC_002967:TDE1199|5end_cell_division_protein_FtsL,_putative_1231341..1231571_POSITIVE 192 179 136 100 55 NC_002967:TDE0601|5end_malonyl_CoA-acyl_carrier_protein_transacylase,_putative_639811..640041_NEGATIVE 191 210 169 221 171 NC_002967:TDE2155|5end_50S_ribosomal_protein_L35_2190165..2190395_NEGATIVE 190 219 171 221 168 NC_002967:TDE1202|5end_cell_division_protein_FtsQ,_putative_1234183..1234413_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 239 214 173 48 6 NC_002967:TDE2426|3end_transcription_antitermination_protein_NusG_2455242..2455392_NEGATIVE 238 220 171 61 9 NC_002967:TDE1002|3end_hypothetical_protein_1028445..1028595_NEGATIVE 227 208 163 144 97 NC_002967:TDE0387|3end_(R)-hydroxyglutaryl-CoA_dehydratase_activator_439256..439406_POSITIVE 218 48 3 103 60 NC_002967:TDE0820|3end_transcriptional_regulator,_TetR_family_843714..843864_NEGATIVE 214 145 109 88 45 NC_002967:TDE0196|3end_hypothetical_protein_232845..232995_POSITIVE 211 218 176 130 89 NC_002967:TDE2098|3end_hypothetical_protein_2124951..2125101_NEGATIVE 210 168 121 97 41 NC_002967:TDE0427|3end_hypothetical_protein_484479..484629_POSITIVE 199 189 141 55 11 NC_002967:TDE1910|3end_1-deoxy-D-xylulose-5-phosphate_synthase_1926876..1927026_NEGATIVE 197 59 37 98 69 NC_002967:TDE1449|3end_GTPase_YjeQ_1495379..1495529_POSITIVE 196 148 125 134 107 NC_002967:TDE1352|3end_penicillin-binding_protein_1393633..1393783_POSITIVE 194 207 164 50 2 NC_002967:TDE0845|3end_conserved_hypothetical_protein_TIGR00266_868549..868699_POSITIVE 192 179 136 75 30 NC_002967:TDE0602|3end_3-oxoacyl-(acyl-carrier-protein)_synthase_III_639836..639986_NEGATIVE 191 52 17 121 81 NC_002967:TDE1450|3end_MutS2_family_protein_1497856..1498006_POSITIVE 189 147 128 44 25 NC_002967:TDE2062|3end_hypothetical_protein_2087802..2087952_NEGATIVE 189 209 167 146 103 NC_002967:TDE0047|3end_imidazolonepropionase_55920..56070_NEGATIVE 187 146 107 144 104 NC_002967:TDE2063|3end_ferrous_iron_transport_protein_B_2088430..2088580_NEGATIVE 186 206 164 91 48 NC_002967:TDE0624|3end_precorrin-6X_reductase,_putative_657340..657490_POSITIVE 180 206 169 37 1 NC_002967:TDE0558|3end_hypothetical_protein_593516..593666_POSITIVE 178 187 170 17 3 NC_002967:TDE0660|3end_transcriptional_regulator,_putative_696279..696429_NEGATIVE 177 212 171 67 14 NC_002967:TDE2679|3end_hypothetical_protein_2720482..2720632_POSITIVE