Origin IGS: aggcacctcttttgcgagggtttcttgtttctcggaggtgatgattgtgttttgattttgtttctcatttgttaattttttgataaaaaaaattactttttttgtgatccagttcaaaattttatcccattataactattattacttatagatttccgtagaaaaaataggtattctacccaccgctaacaaatgtataacagatatttaacatatcacatcatttatttagcttcgattttgcttaaatatcatgtgattttaacaaaaccgatcgtaaattatctactcagatacgaatttataactatcaaaaaagaggtcgacaaaacattctttgtcgatgtggggagtattt .........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.........1.........2.........3.........4.........5.........6.........7.........8.........9 aaatactccccacatcgacaaagaatgttttgtcgacctcttttttgatagttataaattcgtatctgagtagataatttacgatcggttttgttaaaatcacatgatatttaagcaaaatcgaagctaaataaatgatgtgatatgttaaatatctgttatacatttgttagcggtgggtagaatacctattttttctacggaaatctataagtaataatagttataatgggataaaattttgaactggatcacaaaaaaagtaattttttttatcaaaaaattaacaaatgagaaacaaaatcaaaacacaatcatcacctccgagaaacaagaaaccctcgcaaaagaggtgcct Mask Tandem Repeat Region ================================================ aggcacctcttttgcgagggtttcttgtttctcggaggtgatgattgtgttttgattttgtttctcatttgttaattttttgataaaaaaaattactttttttgtgatccagttcaaaattttatcccattataactattattacttatagatttccgtagaaaaaataggtattctacccaccgctaacaaatgtataacagatatttaacatatcacatcatttatttagcttcgattttgcttaaatatcatgtgattttaacaaaaccgatcgtaaattatctactcagatacgaatttataactatcaaaaaagaggtcgacaaaacattctttgtcgatgtggggagtattt Find is-nt database================================================ Query_seq: AA02674:AA02675|AA02674:AA02675:formate dehydrogenase-related protein:formate dehydrogenase alpha subunit:->->:1860793..1861150 358 aggcacctcttttgcgagggtttcttgtttctcggaggtgatgattgtgttttgattttgtttctcatttgttaattttttgataaaaaaaattactttttttgtgatccagttcaaaattttatcccattataactattattacttatagatttccgtagaaaaaataggtattctacccaccgctaacaaatgtataacagatatttaacatatcacatcatttatttagcttcgattttgcttaaatatcatgtgattttaacaaaaccgatcgtaaattatctactcagatacgaatttataactatcaaaaaagaggtcgacaaaacattctttgtcgatgtggggagtattt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: AA02674:AA02675|AA02674:AA02675:formate dehydrogenase-related protein:formate dehydrogenase alpha subunit:->->:1860793..1861150 358 aggcacctcttttgcgagggtttcttgtttctcggaggtgatgattgtgttttgattttgtttctcatttgttaattttttgataaaaaaaattactttttttgtgatccagttcaaaattttatcccattataactattattacttatagatttccgtagaaaaaataggtattctacccaccgctaacaaatgtataacagatatttaacatatcacatcatttatttagcttcgattttgcttaaatatcatgtgattttaacaaaaccgatcgtaaattatctactcagatacgaatttataactatcaaaaaagaggtcgacaaaacattctttgtcgatgtggggagtattt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: AA02674:AA02675|AA02674:AA02675:formate dehydrogenase-related protein:formate dehydrogenase alpha subunit:->->:1860793..1861150 358 aggcacctcttttgcgagggtttcttgtttctcggaggtgatgattgtgttttgattttgtttctcatttgttaattttttgataaaaaaaattactttttttgtgatccagttcaaaattttatcccattataactattattacttatagatttccgtagaaaaaataggtattctacccaccgctaacaaatgtataacagatatttaacatatcacatcatttatttagcttcgattttgcttaaatatcatgtgattttaacaaaaccgatcgtaaattatctactcagatacgaatttataactatcaaaaaagaggtcgacaaaacattctttgtcgatgtggggagtattt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aggcacctcttttgcgagggtttcttgtttctcggaggtgatgattgtgttttgattttgtttctcatttgttaattttttgataaaaaaaattactttttttgtgatccagttcaaaattttatcccattataactattattacttatagatttccgtagaaaaaataggtattctacccaccgctaacaaatgtataacagatatttaacatatcacatcatttatttagcttcgattttgcttaaatatcatgtgattttaacaaaaccgatcgtaaattatctactcagatacgaatttataactatcaaaaaagaggtcgacaaaacattctttgtcgatgtggggagtattt Predict ORF larger than 30AA ================================================ Protein_Len: 36 Strand: + Start: 249 End: 356 ........................................................................................................................................................................................................................................................ M S C D F N K T D R K L S T Q I R I Y N Y Q K R G R Q N I L C R C G E Y .. Protein_Len: 55 Strand: + Start: 193 End: 357 ................................................................................................................................................................................................ M Y N R Y L T Y H I I Y L A S I L L K Y H V I L T K P I V N Y L L R Y E F I T I K K E V D K T F F V D V G S I . Protein_Len: 40 Strand: - Start: 1 End: 120 P V E K A L T E Q K E S T I I T N Q N Q K E N T L K K I F F I V K K T I W N L M .............................................................................................................................................................................................................................................. aggcacctcttttgcgagggtttcttgtttctcggaggtgatgattgtgttttgattttgtttctcatttgttaattttttgataaaaaaaattactttttttgtgatccagttcaaaattttatcccattataactattattacttatagatttccgtagaaaaaataggtattctacccaccgctaacaaatgtataacagatatttaacatatcacatcatttatttagcttcgattttgcttaaatatcatgtgattttaacaaaaccgatcgtaaattatctactcagatacgaatttataactatcaaaaaagaggtcgacaaaacattctttgtcgatgtggggagtattt 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: 79 End: 108 ..............................................................................TTTGATAAAAAAAATTACTTTTTTTGTGAT.......................................................................................................................................................................................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ PromScan Matrix: RpoN Strand: + Score: 81 Start: 0 End: 16 aAGGCACCTCTTTTGCG...................................................................................................................................................................................................................................................................................................................................................... aggcacctcttttgcgagggtttcttgtttctcggaggtgatgattgtgttttgattttgtttctcatttgttaattttttgataaaaaaaattactttttttgtgatccagttcaaaattttatcccattataactattattacttatagatttccgtagaaaaaataggtattctacccaccgctaacaaatgtataacagatatttaacatatcacatcatttatttagcttcgattttgcttaaatatcatgtgattttaacaaaaccgatcgtaaattatctactcagatacgaatttataactatcaaaaaagaggtcgacaaaacattctttgtcgatgtggggagtattt Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 61 HP_score: -5.1 Tail_Score: -3.99153 Start: 73 End: 95 Full_Region: TTGTTTCTCATTTGT TAATTTTTT GATAA AAAAAATTA CTTTTTTTGTGATCC ........................................................................TAATTTTTTGATAAAAAAAATTA....................................................................................................................................................................................................................................................................... TransTerm Strand: - Conf: 77 HP_score: -5.0 Tail_Score: -5.24129 Start: 168 End: 182 Full_Region: tacatttgttagcgg tgggta gaa taccta ttttttctacggaaa .......................................................................................................................................................................tgggtagaataccta................................................................................................................................................................................ TransTerm Strand: - Conf: 46 HP_score: -2.9 Tail_Score: -3.32471 Start: 203 End: 217 Full_Region: ctaaataaatgatgt gatat gttaa atatc tgttatacatttgtt ..........................................................................................................................................................................................................gatatgttaaatatc............................................................................................................................................. Find igs database================================================ Query_seq: AA02674:AA02675|AA02674:AA02675:formate dehydrogenase-related protein:formate dehydrogenase alpha subunit:->->:1860793..1861150 358 aggcacctcttttgcgagggtttcttgtttctcggaggtgatgattgtgttttgattttgtttctcatttgttaattttttgataaaaaaaattactttttttgtgatccagttcaaaattttatcccattataactattattacttatagatttccgtagaaaaaataggtattctacccaccgctaacaaatgtataacagatatttaacatatcacatcatttatttagcttcgattttgcttaaatatcatgtgattttaacaaaaccgatcgtaaattatctactcagatacgaatttataactatcaaaaaagaggtcgacaaaacattctttgtcgatgtggggagtattt Intra-Species Hit: Count: 1 Min: 104 Max: 358 Len: 255 Subject: aact_AA02674_AA02675|formate dehydrogenase-related protein:formate dehydrogenase alpha subunit|POSITIVE:POSITIVE|[1860793,1861150]|358 HSP 1 e-value: 1.0E-142 bit: 505.0 Len: 255 Query Start:104 Query End:358 Subject Strand: POSITIVE Subject Start: 104 Subject End: 358 .......................................................................................................gtgatccagttcaaaattttatcccattataactattattacttatagatttccgtagaaaaaataggtattctacccaccgctaacaaatgtataacagatatttaacatatcacatcatttatttagcttcgattttgcttaaatatcatgtgattttaacaaaaccgatcgtaaattatctactcagatacgaatttataactatcaaaaaagaggtcgacaaaacattctttgtcgatgtggggagtattt .......................................................................................................gtgatccagttcaaaattttatcccattataactattattacttatagatttccgtagaaaaaataggtattctacccaccgctaacaaatgtataacagatatttaacatatcacatcatttatttagcttcgattttgcttaaatatcatgtgattttaacaaaaccgatcgtaaattatctactcagatacgaatttataactatcaaaaaagaggtcgacaaaacattctttgtcgatgtggggagtattt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GUGAUCCAGUUCAAAAUUUUAUCCCAUUAUAACUAUUAUUACUUAUAGAUUUCCGUAGAAAAAAUAGGUAUUCUACCCACCGCUAACAAAUGUAUAACAGAUAUUUAACAUAUCACAUCAUUUAUUUAGCUUCGAUUUUGCUUAAAUAUCAUGUGAUUUUAACAAAACCGAUCGUAAAUUAUCUACUCAGAUACGAAUUUAUAACUAUCAAAAAAGAGGUCGACAAAACAUUCUUUGUCGAUGUGGGGAGUAUUU .(((......)))........((((.................(((((((((..((((.......((((((...(((.....(((((.(((((.......(((((.....)))))....)))))..))))).(((.(((((.(((((.(((....))))))))))))).)))..)))...))))))......)))))))))))))............(.(((((((((......))))))))).).))))...... (-46.02) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAUACUCCCCACAUCGACAAAGAAUGUUUUGUCGACCUCUUUUUUGAUAGUUAUAAAUUCGUAUCUGAGUAGAUAAUUUACGAUCGGUUUUGUUAAAAUCACAUGAUAUUUAAGCAAAAUCGAAGCUAAAUAAAUGAUGUGAUAUGUUAAAUAUCUGUUAUACAUUUGUUAGCGGUGGGUAGAAUACCUAUUUUUUCUACGGAAAUCUAUAAGUAAUAAUAGUUAUAAUGGGAUAAAAUUUUGAACUGGAUCAC .....((.(((((.(((((((((....))))))))).............((((((..(((((....)))))..)))))).....(((((((((((((((((....))).))).))))))))))).(((((.(((((((((.(((((.....)))))...))).))))))))))).))))).))....((((((.((((....)))).((((.(....).))))....))))))...................... (-56.70) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 301 85 51 46 9 aact:AA00132|5end_conserved_hypothetical_protein_(possible_regulator_protein,_VirR_family)_94938..95168_POSITIVE 254 250 209 164 130 aact:AA01689|5end_conserved_hypothetical_protein_(possible_inner_membrane_protein)_1145500..1145730_POSITIVE 249 250 205 190 143 aact:AA02970|5end_tyrosine_phenol-lyase_2076373..2076603_POSITIVE 247 83 42 54 12 aact:AA01937|5end_sugar_fermentation_stimulation_protein_1308478..1308708_POSITIVE 243 250 214 173 134 aact:AA01311|5end_transcriptional_regulator_888968..889198_POSITIVE 233 102 67 210 172 aact:AA01475|5end_conserved_hypothetical_protein_(possible_cytoplasmic_protein;_DNA_binding_protein)_990364..990594_POSITIVE 233 102 67 105 67 aact:AA01474|5end_hypothetical_protein_990259..990489_POSITIVE 233 176 134 194 145 aact:AA01462|5end_xylose_operon_regulatory_protein_981530..981760_POSITIVE 233 176 134 76 27 aact:AA01460|5end_hypothetical_protein_981412..981642_POSITIVE 231 248 205 171 123 aact:AA00596|5end_uridylate_kinase_407496..407726_POSITIVE 228 248 208 143 100 aact:AA00569|5end_ketol-acid_reductoisomerase_391191..391421_POSITIVE 225 108 67 228 187 aact:AA02723|5end_hypothetical_protein_1906263..1906493_POSITIVE 222 249 202 191 142 aact:AA02134|5end_aminopeptidase_N_1456181..1456411_POSITIVE 215 209 167 152 97 aact:AA01336|5end_hypothetical_protein_904056..904286_POSITIVE 213 248 230 186 167 aact:AA01538|5end_conserved_hypothetical_protein_1031527..1031757_POSITIVE 212 85 42 136 101 aact:AA02196|5end_oxaloacetate_decarboxylase_beta_chain_1496308..1496538_POSITIVE 210 88 47 166 123 aact:AA02156|5end_conserved_hypothetical_protein_1474581..1474811_POSITIVE 209 87 53 185 157 aact:AA01981|5end_4-alpha-glucanotransferase_1337202..1337432_POSITIVE 209 87 53 38 10 aact:AA01978|5end_hypothetical_protein_1337055..1337285_POSITIVE 209 83 46 117 79 aact:AA01078|5end_transcriptional_regulator_(probable_MerR_family)_746873..747103_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 254 250 209 67 33 aact:AA01688|3end_conserved_hypothetical_protein;_possible_membrane_protein_1145483..1145633_POSITIVE 243 250 214 146 107 aact:AA01310|3end_conserved_hypothetical_protein_889021..889171_POSITIVE 233 176 134 76 27 aact:AA01459|3end_Na(+)/H(+)_antiporter_981492..981642_POSITIVE 229 86 54 146 114 aact:AA02930|3end_fructose-1,6-bisphosphatase_2050518..2050668_POSITIVE 228 248 208 148 105 aact:AA00568|3end_hypothetical_protein_391276..391426_POSITIVE 222 249 202 115 66 aact:AA02132|3end_dihydroorotate_dehydrogenase_1456185..1456335_POSITIVE 219 89 57 111 84 aact:AA01113|3end_transcriptional_regulator_(merR_family)_765249..765399_POSITIVE 215 209 167 125 70 aact:AA01335|3end_primosomal_protein_N'_904109..904259_POSITIVE 213 83 54 76 50 aact:AA02865|3end_iron-regulated_outer_membrane_protein_(omp64)_2012542..2012692_POSITIVE 212 85 42 122 87 aact:AA02195|3end_oxaloacetate_decarboxylase_alpha_chain_1496374..1496524_POSITIVE 210 88 47 126 83 aact:AA02154|3end_possible_ATP-binding_protein_of_ABC_transporter_1474621..1474771_POSITIVE 209 170 122 80 29 aact:AA02281|3end_phosphoglycerate_transport_system_activator_protein_1553474..1553624_POSITIVE 209 87 53 35 7 aact:AA01976|3end_colicin_V_production_protein_1337132..1337282_POSITIVE 206 83 47 108 57 aact:AA01128|3end_hypothetical_protein_774202..774352_POSITIVE 205 247 215 113 79 aact:AA01319|3end_transcriptional_regulatory_protein_893401..893551_POSITIVE 202 249 215 146 105 aact:AA02983|3end_formate_acetyltransferase_2087584..2087734_POSITIVE 202 176 131 79 40 aact:AA02443|3end_cytochrome_C_related_protein_1686590..1686740_POSITIVE 202 176 131 124 85 aact:AA02444|3end_hypothetical_protein_1686635..1686785_POSITIVE 200 83 53 141 114 aact:AA01092|3end_hypothetical_protein_756361..756511_POSITIVE 198 247 205 151 107 aact:AA02969|3end_beta_tyrosinase_(tyrosine_phenol-lyase)_2076417..2076567_POSITIVE