Origin IGS: attcgtattgatattttgttacgtttgttttgtttacgtttgcaaagatagagagtttccttgttccgtgcaatacctaaaaataggggttcttgcaaaatacctacttttaagtagtggtttgttagctttaatgcagcgttttctacaagaaaagaagttacaaacggactttaatatttttattttacattcattaaagaaatcgcagcaaaacacctaaacaaagttagtaaaacgcaaaaaagatggtagcgcaaaatgtttccacattctacgctaccatcttctatcattagaaattgccatttgtacaatttccgaatacctattatatgtta .........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 taacatataataggtattcggaaattgtacaaatggcaatttctaatgatagaagatggtagcgtagaatgtggaaacattttgcgctaccatcttttttgcgttttactaactttgtttaggtgttttgctgcgatttctttaatgaatgtaaaataaaaatattaaagtccgtttgtaacttcttttcttgtagaaaacgctgcattaaagctaacaaaccactacttaaaagtaggtattttgcaagaacccctatttttaggtattgcacggaacaaggaaactctctatctttgcaaacgtaaacaaaacaaacgtaacaaaatatcaatacgaat Mask Tandem Repeat Region ================================================ attcgtattgatattttgttacgtttgttttgtttacgtttgcaaagatagagagtttccttgttccgtgcaatacctaaaaataggggttcttgcaaaatacctacttttaagtagtggtttgttagctttaatgcagcgttttctacaagaaaagaagttacaaacggactttaatatttttattttacattcattaaagaaatcgcagcaaaacacctaaacaaagttagtaaaacgcaaaaaagatggtagcgcaaaatgtttccacattctacgctaccatcttctatcattagaaattgccatttgtacaatttccgaatacctattatatgtta Find is-nt database================================================ Query_seq: PI1426:PI1427|PI1426:PI1427:flavodoxin:nicotinate-nucleotide pyrophosphorylase:->->:1345507..1345847 341 attcgtattgatattttgttacgtttgttttgtttacgtttgcaaagatagagagtttccttgttccgtgcaatacctaaaaataggggttcttgcaaaatacctacttttaagtagtggtttgttagctttaatgcagcgttttctacaagaaaagaagttacaaacggactttaatatttttattttacattcattaaagaaatcgcagcaaaacacctaaacaaagttagtaaaacgcaaaaaagatggtagcgcaaaatgtttccacattctacgctaccatcttctatcattagaaattgccatttgtacaatttccgaatacctattatatgtta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI1426:PI1427|PI1426:PI1427:flavodoxin:nicotinate-nucleotide pyrophosphorylase:->->:1345507..1345847 341 attcgtattgatattttgttacgtttgttttgtttacgtttgcaaagatagagagtttccttgttccgtgcaatacctaaaaataggggttcttgcaaaatacctacttttaagtagtggtttgttagctttaatgcagcgttttctacaagaaaagaagttacaaacggactttaatatttttattttacattcattaaagaaatcgcagcaaaacacctaaacaaagttagtaaaacgcaaaaaagatggtagcgcaaaatgtttccacattctacgctaccatcttctatcattagaaattgccatttgtacaatttccgaatacctattatatgtta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI1426:PI1427|PI1426:PI1427:flavodoxin:nicotinate-nucleotide pyrophosphorylase:->->:1345507..1345847 341 attcgtattgatattttgttacgtttgttttgtttacgtttgcaaagatagagagtttccttgttccgtgcaatacctaaaaataggggttcttgcaaaatacctacttttaagtagtggtttgttagctttaatgcagcgttttctacaagaaaagaagttacaaacggactttaatatttttattttacattcattaaagaaatcgcagcaaaacacctaaacaaagttagtaaaacgcaaaaaagatggtagcgcaaaatgtttccacattctacgctaccatcttctatcattagaaattgccatttgtacaatttccgaatacctattatatgtta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 attcgtattgatattttgttacgtttgttttgtttacgtttgcaaagatagagagtttccttgttccgtgcaatacctaaaaataggggttcttgcaaaatacctacttttaagtagtggtttgttagctttaatgcagcgttttctacaagaaaagaagttacaaacggactttaatatttttattttacattcattaaagaaatcgcagcaaaacacctaaacaaagttagtaaaacgcaaaaaagatggtagcgcaaaatgtttccacattctacgctaccatcttctatcattagaaattgccatttgtacaatttccgaatacctattatatgtta Predict ORF larger than 30AA ================================================ Protein_Len: 60 Strand: + Start: 8 End: 220 ....... M I F C Y V C F V Y V C K D R E F P C S V Q Y L K I G V L A K Y L L L S S G L L A L M Q R F L Q E K K L Q T D F N I F I ......................................................................................................................... Protein_Len: 50 Strand: - Start: 186 End: 335 ......................................................................................................................................................................................... K V N M L S I A A F C R F L T L L V C F L H Y R L I N G C E V S G D E I M L F Q W K Y L K R I G I M ...... Protein_Len: 60 Strand: - Start: 37 End: 219 .................................... Q L S L S N G Q E T C Y R F I P T R A F Y R S K L L P K N A K I C R K R C S F F N C V S K L I K I K C E N F F D C C F M .......................................................................................................................... Protein_Len: 33 Strand: - Start: 3 End: 101 .. R I S I K N R K N Q K R K C L Y L T E K N R A I G L F L P E Q L M ................................................................................................................................................................................................................................................ attcgtattgatattttgttacgtttgttttgtttacgtttgcaaagatagagagtttccttgttccgtgcaatacctaaaaataggggttcttgcaaaatacctacttttaagtagtggtttgttagctttaatgcagcgttttctacaagaaaagaagttacaaacggactttaatatttttattttacattcattaaagaaatcgcagcaaaacacctaaacaaagttagtaaaacgcaaaaaagatggtagcgcaaaatgtttccacattctacgctaccatcttctatcattagaaattgccatttgtacaatttccgaatacctattatatgtta 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================================================ attcgtattgatattttgttacgtttgttttgtttacgtttgcaaagatagagagtttccttgttccgtgcaatacctaaaaataggggttcttgcaaaatacctacttttaagtagtggtttgttagctttaatgcagcgttttctacaagaaaagaagttacaaacggactttaatatttttattttacattcattaaagaaatcgcagcaaaacacctaaacaaagttagtaaaacgcaaaaaagatggtagcgcaaaatgtttccacattctacgctaccatcttctatcattagaaattgccatttgtacaatttccgaatacctattatatgtta Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 100 HP_score: -19.6 Tail_Score: -5.2696 Start: 248 End: 287 Full_Region: tttctaatgatagaa gatggtagcgtagaatgt ggaa acattttgcgctaccatc ttttttgcgttttac .......................................................................................................................................................................................................................................................gatggtagcgtagaatgtggaaacattttgcgctaccatc...................................................... Find igs database================================================ Query_seq: PI1426:PI1427|PI1426:PI1427:flavodoxin:nicotinate-nucleotide pyrophosphorylase:->->:1345507..1345847 341 attcgtattgatattttgttacgtttgttttgtttacgtttgcaaagatagagagtttccttgttccgtgcaatacctaaaaataggggttcttgcaaaatacctacttttaagtagtggtttgttagctttaatgcagcgttttctacaagaaaagaagttacaaacggactttaatatttttattttacattcattaaagaaatcgcagcaaaacacctaaacaaagttagtaaaacgcaaaaaagatggtagcgcaaaatgtttccacattctacgctaccatcttctatcattagaaattgccatttgtacaatttccgaatacctattatatgtta Intra-Species Hit: Count: 1 Min: 1 Max: 341 Len: 341 Subject: pint_PI1426_PI1427|flavodoxin:nicotinate-nucleotide pyrophosphorylase|POSITIVE:POSITIVE|[1345507, 1345847]|341 HSP 1 e-value: 0.0 bit: 676.0 Len: 341 Query Start:1 Query End:341 Subject Strand: POSITIVE Subject Start: 1 Subject End: 341 attcgtattgatattttgttacgtttgttttgtttacgtttgcaaagatagagagtttccttgttccgtgcaatacctaaaaataggggttcttgcaaaatacctacttttaagtagtggtttgttagctttaatgcagcgttttctacaagaaaagaagttacaaacggactttaatatttttattttacattcattaaagaaatcgcagcaaaacacctaaacaaagttagtaaaacgcaaaaaagatggtagcgcaaaatgtttccacattctacgctaccatcttctatcattagaaattgccatttgtacaatttccgaatacctattatatgtta attcgtattgatattttgttacgtttgttttgtttacgtttgcaaagatagagagtttccttgttccgtgcaatacctaaaaataggggttcttgcaaaatacctacttttaagtagtggtttgttagctttaatgcagcgttttctacaagaaaagaagttacaaacggactttaatatttttattttacattcattaaagaaatcgcagcaaaacacctaaacaaagttagtaaaacgcaaaaaagatggtagcgcaaaatgtttccacattctacgctaccatcttctatcattagaaattgccatttgtacaatttccgaatacctattatatgtta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUUCGUAUUGAUAUUUUGUUACGUUUGUUUUGUUUACGUUUGCAAAGAUAGAGAGUUUCCUUGUUCCGUGCAAUACCUAAAAAUAGGGGUUCUUGCAAAAUACCUACUUUUAAGUAGUGGUUUGUUAGCUUUAAUGCAGCGUUUUCUACAAGAAAAGAAGUUACAAACGGACUUUAAUAUUUUUAUUUUACAUUCAUUAAAGAAAUCGCAGCAAAACACCUAAACAAAGUUAGUAAAACGCAAAAAAGAUGGUAGCGCAAAAUGUUUCCACAUUCUACGCUACCAUCUUCUAUCAUUAGAAAUUGCCAUUUGUACAAUUUCCGAAUACCUAUUAUAUGUUA (((((.((((..((((((((.....((((((((.......(((.((((((((((........((.((((((((.((((........))))..)))).......((.(((((..((((.....((((.((......))))))....))))...))))).))......)))))).......))))))))))...(((......)))...)))))))))))....)))))))).........((((...(((((((((((...(((((....)))))...)))))))))))((((....))))..))))........))))...)))))............... (-73.47) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAACAUAUAAUAGGUAUUCGGAAAUUGUACAAAUGGCAAUUUCUAAUGAUAGAAGAUGGUAGCGUAGAAUGUGGAAACAUUUUGCGCUACCAUCUUUUUUGCGUUUUACUAACUUUGUUUAGGUGUUUUGCUGCGAUUUCUUUAAUGAAUGUAAAAUAAAAAUAUUAAAGUCCGUUUGUAACUUCUUUUCUUGUAGAAAACGCUGCAUUAAAGCUAACAAACCACUACUUAAAAGUAGGUAUUUUGCAAGAACCCCUAUUUUUAGGUAUUGCACGGAACAAGGAAACUCUCUAUCUUUGCAAACGUAAACAAAACAAACGUAACAAAAUAUCAAUACGAAU ............((((...(((((((((.......)))))))))((((..((((((((((((((((((((((....))))))))))))))))))))))...)))).))))...(((((...(((((((((.((((....((((((((...............))))))))..(((((((((...((((...(((((......)))))..)))).........((.((((((((((((((..(((.....)))..)))))))))))))).))...(((...((....)).)))....))))))))).............)))).)))))))))...))))). (-97.16) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 293 285 247 203 153 pint:PI0125|5end_undecaprenyl_pyrophosphate_synthase_117106..117336_POSITIVE 288 63 21 226 179 pint:PI0110|5end_ABC_transport_system,_ATP-binding_protein_107136..107366_POSITIVE 282 307 270 183 150 pint:PI0844|5end_cytidine/deoxycytidylate_deaminase_(dCMP_deaminase)_777793..778023_POSITIVE 277 79 37 78 32 pint:PI2128|5end_hypothetical_protein_2076512..2076742_POSITIVE 277 65 23 44 1 pint:PI0284|5end_flavoprotein_A_268848..269078_POSITIVE 268 79 32 42 1 pint:PI2131|5end_hypothetical_protein_2080678..2080908_POSITIVE 268 69 22 49 4 pint:PI0051|5end_hypothetical_protein_52607..52837_POSITIVE 264 281 246 155 127 pint:PI0380|5end_conserved_hypothetical_protein_350162..350392_POSITIVE 262 79 31 207 165 pint:PI0159|5end_hypothetical_protein_151273..151503_POSITIVE 262 79 31 119 77 pint:PI0157|5end_hypothetical_protein_151185..151415_POSITIVE 261 281 246 132 94 pint:PI0938|5end_hypothetical_protein_869345..869575_POSITIVE 260 79 39 42 3 pint:PI1733|5end_hypothetical_protein_1652160..1652390_POSITIVE 260 79 39 42 3 pint:PI0182|5end_hypothetical_protein_174093..174323_POSITIVE 259 89 41 61 10 pint:PI0590|5end_ribosomal_large_subunit_pseudouridine_synthase_B_536963..537193_POSITIVE 259 286 250 57 6 pint:PI0545|5end_sugar_kinase_496411..496641_POSITIVE 257 73 39 59 25 pint:PI0632|5end_NusB_family_protein_(N_utilization_substance_protein_B)_578476..578706_POSITIVE 255 149 101 52 7 pint:PI0064|5end_hypothetical_protein_63622..63852_POSITIVE 251 289 249 153 113 pint:PI0667|5end_hypothetical_protein_610113..610343_POSITIVE 250 120 73 201 152 pint:PI2149|5end_3-oxoacyl-acyl-carrier-protein_synthase_2095454..2095684_POSITIVE 250 56 15 164 120 pint:PI2019|5end_elongation_factor_P_1976131..1976361_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 276 79 31 146 104 pint:PI0182|3end_hypothetical_protein_174277..174427_POSITIVE 271 78 32 151 111 pint:PI0551|3end_hypothetical_protein_502683..502833_POSITIVE 268 69 22 77 32 pint:PI0052|3end_hypothetical_protein_52715..52865_POSITIVE 257 78 32 151 111 pint:PI2131|3end_hypothetical_protein_2080868..2081018_POSITIVE 255 280 246 149 124 pint:PI0379|3end_conserved_hypothetical_protein_350239..350389_POSITIVE 251 289 249 131 91 pint:PI0666|3end_chorismate_synthase_610171..610321_POSITIVE 251 78 31 151 110 pint:PI0158|3end_hypothetical_protein_151298..151448_POSITIVE 250 113 83 91 59 pint:PI1379|3end_hypothetical_protein_1302292..1302442_POSITIVE 247 89 41 103 52 pint:PI1065|3end_hypothetical_protein_983650..983800_POSITIVE 245 96 59 53 11 pint:PI2090|3end_thioesterase_family_protein_2048066..2048216_POSITIVE 245 280 240 116 81 pint:PI1087|3end_conserved_hypothetical_protein_1011557..1011707_POSITIVE 243 280 238 117 74 pint:PI0669|3end_hypothetical_protein_611147..611297_POSITIVE 242 78 36 151 118 pint:PI2011|3end_hypothetical_protein_1970730..1970880_POSITIVE 242 97 57 73 31 pint:PI1569|3end_hypothetical_protein_1493267..1493417_POSITIVE 239 130 93 135 102 pint:PI0933|3end_hypothetical_protein_865884..866034_POSITIVE 239 110 61 76 33 pint:PI0641|3end_conserved_hypothetical_protein_584560..584710_POSITIVE 238 142 101 106 59 pint:PI0201|3end_hypothetical_protein_195398..195548_POSITIVE 237 89 46 49 5 pint:PI1879|3end_uracil_phosphoribosyltransferase_1821245..1821395_POSITIVE 235 307 261 126 82 pint:PI1574|3end_conserved_hypothetical_protein_1501226..1501376_POSITIVE 233 323 284 48 6 pint:PI1135|3end_hypothetical_protein_1062203..1062353_POSITIVE