Origin IGS: tttctactatttatttttttgtgcttacttataatgccacaaatatatgaagttttatttatctaatacataatgttattcttttatttttagggtatgtttaaaaataagatgctcttgctacaaactatttattaaaatcatgtttatataaatttgttgagttctcttcatgggcttgtcgggcaaatactttttccgat .........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 atcggaaaaagtatttgcccgacaagcccatgaagagaactcaacaaatttatataaacatgattttaataaatagtttgtagcaagagcatcttatttttaaacataccctaaaaataaaagaataacattatgtattagataaataaaacttcatatatttgtggcattataagtaagcacaaaaaaataaatagtagaaa Mask Tandem Repeat Region ================================================ tttctactatttatttttttgtgcttacttataatgccacaaatatatgaagttttatttatctaatacataatgttattcttttatttttagggtatgtttaaaaataagatgctcttgctacaaactatttattaaaatcatgtttatataaatttgttgagttctcttcatgggcttgtcgggcaaatactttttccgat Find is-nt database================================================ Query_seq: TF2929:TF2930|TF2929:TF2930:conserved hypothetical protein:glutamyl-tRNA synthetase:->->:3132623..3132825 203 tttctactatttatttttttgtgcttacttataatgccacaaatatatgaagttttatttatctaatacataatgttattcttttatttttagggtatgtttaaaaataagatgctcttgctacaaactatttattaaaatcatgtttatataaatttgttgagttctcttcatgggcttgtcgggcaaatactttttccgat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF2929:TF2930|TF2929:TF2930:conserved hypothetical protein:glutamyl-tRNA synthetase:->->:3132623..3132825 203 tttctactatttatttttttgtgcttacttataatgccacaaatatatgaagttttatttatctaatacataatgttattcttttatttttagggtatgtttaaaaataagatgctcttgctacaaactatttattaaaatcatgtttatataaatttgttgagttctcttcatgggcttgtcgggcaaatactttttccgat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF2929:TF2930|TF2929:TF2930:conserved hypothetical protein:glutamyl-tRNA synthetase:->->:3132623..3132825 203 tttctactatttatttttttgtgcttacttataatgccacaaatatatgaagttttatttatctaatacataatgttattcttttatttttagggtatgtttaaaaataagatgctcttgctacaaactatttattaaaatcatgtttatataaatttgttgagttctcttcatgggcttgtcgggcaaatactttttccgat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tttctactatttatttttttgtgcttacttataatgccacaaatatatgaagttttatttatctaatacataatgttattcttttatttttagggtatgtttaaaaataagatgctcttgctacaaactatttattaaaatcatgtttatataaatttgttgagttctcttcatgggcttgtcgggcaaatactttttccgat Predict ORF larger than 30AA ================================================ tttctactatttatttttttgtgcttacttataatgccacaaatatatgaagttttatttatctaatacataatgttattcttttatttttagggtatgtttaaaaataagatgctcttgctacaaactatttattaaaatcatgtttatataaatttgttgagttctcttcatgggcttgtcgggcaaatactttttccgat 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================================================ tttctactatttatttttttgtgcttacttataatgccacaaatatatgaagttttatttatctaatacataatgttattcttttatttttagggtatgtttaaaaataagatgctcttgctacaaactatttattaaaatcatgtttatataaatttgttgagttctcttcatgggcttgtcgggcaaatactttttccgat Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 38 HP_score: -2.1 Tail_Score: -2.77523 Start: 82 End: 112 Full_Region: TACATAATGTTATTC TTTTATTTTTAGG GTATG TTTAAAAATAAGA TGCTCTTGCTACAAA .................................................................................TTTTATTTTTAGGGTATGTTTAAAAATAAGA........................................................................................... Find igs database================================================ Query_seq: TF2929:TF2930|TF2929:TF2930:conserved hypothetical protein:glutamyl-tRNA synthetase:->->:3132623..3132825 203 tttctactatttatttttttgtgcttacttataatgccacaaatatatgaagttttatttatctaatacataatgttattcttttatttttagggtatgtttaaaaataagatgctcttgctacaaactatttattaaaatcatgtttatataaatttgttgagttctcttcatgggcttgtcgggcaaatactttttccgat Intra-Species Hit: Count: 1 Min: 21 Max: 203 Len: 183 Subject: tfor_TF2929_TF2930|conserved hypothetical protein:glutamyl-tRNA synthetase|POSITIVE:POSITIVE|[3132623,3132825]|203 HSP 1 e-value: 2.0E-99 bit: 363.0 Len: 183 Query Start:21 Query End:203 Subject Strand: POSITIVE Subject Start: 21 Subject End: 203 ....................gtgcttacttataatgccacaaatatatgaagttttatttatctaatacataatgttattcttttatttttagggtatgtttaaaaataagatgctcttgctacaaactatttattaaaatcatgtttatataaatttgttgagttctcttcatgggcttgtcgggcaaatactttttccgat ....................gtgcttacttataatgccacaaatatatgaagttttatttatctaatacataatgttattcttttatttttagggtatgtttaaaaataagatgctcttgctacaaactatttattaaaatcatgtttatataaatttgttgagttctcttcatgggcttgtcgggcaaatactttttccgat Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GUGCUUACUUAUAAUGCCACAAAUAUAUGAAGUUUUAUUUAUCUAAUACAUAAUGUUAUUCUUUUAUUUUUAGGGUAUGUUUAAAAAUAAGAUGCUCUUGCUACAAACUAUUUAUUAAAAUCAUGUUUAUAUAAAUUUGUUGAGUUCUCUUCAUGGGCUUGUCGGGCAAAUACUUUUUCCGAU ..............((((((((...(((((((.......................................(((((((.((.......)).))))))).(((.(((...((((((((((......)))).))))))...))))))...)))))))...))))..))))............... (-25.70) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUCGGAAAAAGUAUUUGCCCGACAAGCCCAUGAAGAGAACUCAACAAAUUUAUAUAAACAUGAUUUUAAUAAAUAGUUUGUAGCAAGAGCAUCUUAUUUUUAAACAUACCCUAAAAAUAAAAGAAUAACAUUAUGUAUUAGAUAAAUAAAACUUCAUAUAUUUGUGGCAUUAUAAGUAAGCAC ..........(((..((((..(((((...((((((.(....).....((((((.((((((((((.(((..............((....))...(((((((((.........))))))))).....))).))))))).))).))))))....))))))...))))))))).))).......... (-24.80) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 274 170 121 160 103 tfor:TF3148|5end_hypoxanthine-guanine_phosphoribosyltransferase_3383652..3383882_POSITIVE 268 174 146 229 192 tfor:TF1586|5end_hypothetical_protein_1690971..1691201_POSITIVE 260 176 142 190 146 tfor:TF1887|5end_hypothetical_protein_2040301..2040531_POSITIVE 255 180 134 231 178 tfor:TF3053|5end_conserved_hypothetical_protein_3278564..3278794_POSITIVE 255 170 136 52 18 tfor:TF2786|5end_hypothetical_protein_2969851..2970081_POSITIVE 253 164 121 161 120 tfor:TF0665|5end_conserved_hypothetical_protein_709497..709727_POSITIVE 252 180 140 181 146 tfor:TF2570|5end_50S_ribosomal_protein_L18_2742198..2742428_POSITIVE 249 168 139 212 181 tfor:TF0147|5end_patatin-like_phospholipase_156798..157028_POSITIVE 248 176 142 171 144 tfor:TF2130|5end_conserved_hypothetical_protein;_possible_permease_2306486..2306716_POSITIVE 248 167 138 49 11 tfor:TF1840|5end_transposase_1990221..1990451_POSITIVE 246 173 137 205 164 tfor:TF0115|5end_sulfatase_125144..125374_POSITIVE 245 165 122 216 169 tfor:TF1754|5end_conserved_hypothetical_protein_1890937..1891167_POSITIVE 244 169 144 135 111 tfor:TF0303|5end_conserved_hypothetical_protein_328331..328561_POSITIVE 243 170 144 146 121 tfor:TF2320|5end_hypothetical_protein_2476654..2476884_POSITIVE 242 176 146 36 10 tfor:TF1598|5end_conserved_hypothetical_protein_1713358..1713588_POSITIVE 242 167 124 121 72 tfor:TF0454|5end_xanthine/uracil_permease_family_protein_472087..472317_POSITIVE 242 167 147 210 179 tfor:TF0294|5end_possible_translation_factor_321211..321441_POSITIVE 241 170 121 88 30 tfor:TF3137|5end_Na+-translocating_NADH-quinone_reductase,_subunit_E_3371307..3371537_POSITIVE 241 172 140 82 51 tfor:TF0023|5end_possible_response_element_in_two_component_regulation_19446..19676_POSITIVE 239 168 136 44 5 tfor:TF1464|5end_conserved_hypothetical_protein_1553467..1553697_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 274 170 121 132 75 tfor:TF3147|3end_adenylate_kinase_3383704..3383854_POSITIVE 262 167 136 89 63 tfor:TF2921|3end_hypothetical_protein_3118790..3118940_POSITIVE 262 167 136 89 63 tfor:TF2438|3end_hypothetical_protein_2616157..2616307_POSITIVE 260 176 142 150 106 tfor:TF1886|3end_auxin-regulated_protein_2040341..2040491_POSITIVE 255 170 136 38 4 tfor:TF2785|3end_RNA_polymerase_sigma_factor,_ECF_subfamily_(sigma-70)_2969917..2970067_POSITIVE 243 170 121 130 75 tfor:TF0135|3end_hypothetical_protein_146554..146704_POSITIVE 242 167 124 97 48 tfor:TF0452|3end_conserved_hypothetical_protein,_endonuclease/exonuclease/phosphatase_family_472143..472293_POSITIVE 242 167 147 143 112 tfor:TF0293|3end_GTP_cyclohydrolase_I_321224..321374_POSITIVE 241 172 140 78 47 tfor:TF0022|3end_two-component_system_sensor_histidine_kinase_19522..19672_POSITIVE 236 167 136 140 114 tfor:TF2653|3end_hypothetical_protein_2822460..2822610_POSITIVE 235 168 136 149 117 tfor:TF1995|3end_exonuclease_2148433..2148583_POSITIVE 235 176 136 132 82 tfor:TF1621|3end_DNA_replication_and_repair_protein_RecF_1736473..1736623_POSITIVE 235 168 136 66 24 tfor:TF1156|3end_oxidoreductase,_FAD-binding_1238092..1238242_POSITIVE 231 168 144 39 9 tfor:TF2266|3end_transfer_region-related_protein,_TraQ_2434949..2435099_POSITIVE 230 167 144 129 109 tfor:TF0469|3end_hypothetical_protein_487228..487378_POSITIVE 230 167 144 89 69 tfor:TF0468|3end_hypothetical_protein_487188..487338_POSITIVE 228 179 136 60 17 tfor:TF1664|3end_conserved_hypothetical_protein_1779206..1779356_POSITIVE 228 167 134 59 23 tfor:TF0385|3end_conserved_hypothetical_protein_406980..407130_POSITIVE 227 168 138 80 49 tfor:TF0010|3end_conserved_hypothetical_protein_4790..4940_POSITIVE 226 176 135 89 40 tfor:TF0075|3end_transcriptional_regulator_83118..83268_POSITIVE