Origin IGS: taagcaacaaaagaaaagtattgctactttcctactaaagcgaaccgatggttaagagaagtttaaacataaaaaagaggttggtgcaggaagctaccaacctcgagaaaaatgatttagaaaatctctaaatccataaaaacacgtagcaaatatacgtttattaaataagaaaaccaaataataggcgattataaaacatttattaacacttcctataaaataaaatcaaaattcagataaaacaaaaatcccttacctaaagaatggcaagggatttttattattaattgaaagagaagatta .........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 taatcttctctttcaattaataataaaaatcccttgccattctttaggtaagggatttttgttttatctgaattttgattttattttataggaagtgttaataaatgttttataatcgcctattatttggttttcttatttaataaacgtatatttgctacgtgtttttatggatttagagattttctaaatcatttttctcgaggttggtagcttcctgcaccaacctcttttttatgtttaaacttctcttaaccatcggttcgctttagtaggaaagtagcaatacttttcttttgttgctta Mask Tandem Repeat Region ================================================ taagcaacaaaagaaaagtattgctactttcctactaaagcgaaccgatggttaagagaagtttaaacataaaaaagaggttggtgcaggaagctaccaacctcgagaaaaatgatttagaaaatctctaaatccataaaaacacgtagcaaatatacgtttattaaataagaaaaccaaataataggcgattataaaacatttattaacacttcctataaaataaaatcaaaattcagataaaacaaaaatcccttacctaaagaatggcaagggatttttattattaattgaaagagaagatta Find is-nt database================================================ Query_seq: PI1281:PI1282|PI1281:PI1282:hypothetical protein:ATP synthase, gamma subunit (F0F1-ATPase, gamma subunit):->->:1197052..1197357 306 taagcaacaaaagaaaagtattgctactttcctactaaagcgaaccgatggttaagagaagtttaaacataaaaaagaggttggtgcaggaagctaccaacctcgagaaaaatgatttagaaaatctctaaatccataaaaacacgtagcaaatatacgtttattaaataagaaaaccaaataataggcgattataaaacatttattaacacttcctataaaataaaatcaaaattcagataaaacaaaaatcccttacctaaagaatggcaagggatttttattattaattgaaagagaagatta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI1281:PI1282|PI1281:PI1282:hypothetical protein:ATP synthase, gamma subunit (F0F1-ATPase, gamma subunit):->->:1197052..1197357 306 taagcaacaaaagaaaagtattgctactttcctactaaagcgaaccgatggttaagagaagtttaaacataaaaaagaggttggtgcaggaagctaccaacctcgagaaaaatgatttagaaaatctctaaatccataaaaacacgtagcaaatatacgtttattaaataagaaaaccaaataataggcgattataaaacatttattaacacttcctataaaataaaatcaaaattcagataaaacaaaaatcccttacctaaagaatggcaagggatttttattattaattgaaagagaagatta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI1281:PI1282|PI1281:PI1282:hypothetical protein:ATP synthase, gamma subunit (F0F1-ATPase, gamma subunit):->->:1197052..1197357 306 taagcaacaaaagaaaagtattgctactttcctactaaagcgaaccgatggttaagagaagtttaaacataaaaaagaggttggtgcaggaagctaccaacctcgagaaaaatgatttagaaaatctctaaatccataaaaacacgtagcaaatatacgtttattaaataagaaaaccaaataataggcgattataaaacatttattaacacttcctataaaataaaatcaaaattcagataaaacaaaaatcccttacctaaagaatggcaagggatttttattattaattgaaagagaagatta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 taagcaacaaaagaaaagtattgctactttcctactaaagcgaaccgatggttaagagaagtttaaacataaaaaagaggttggtgcaggaagctaccaacctcgagaaaaatgatttagaaaatctctaaatccataaaaacacgtagcaaatatacgtttattaaataagaaaaccaaataataggcgattataaaacatttattaacacttcctataaaataaaatcaaaattcagataaaacaaaaatcccttacctaaagaatggcaagggatttttattattaattgaaagagaagatta Predict ORF larger than 30AA ================================================ Protein_Len: 41 Strand: - Start: 97 End: 219 ................................................................................................ W G R S F H N L F D R F G Y F C T A F I R K N F L F V L Y Y A I I F C K N V S G M ....................................................................................... taagcaacaaaagaaaagtattgctactttcctactaaagcgaaccgatggttaagagaagtttaaacataaaaaagaggttggtgcaggaagctaccaacctcgagaaaaatgatttagaaaatctctaaatccataaaaacacgtagcaaatatacgtttattaaataagaaaaccaaataataggcgattataaaacatttattaacacttcctataaaataaaatcaaaattcagataaaacaaaaatcccttacctaaagaatggcaagggatttttattattaattgaaagagaagatta 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: 82 Start: 181 End: 210 ....................................................................................................................................................................................GTTAATAAATGTTTTATAATCGCCTATTAT................................................................................................ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ taagcaacaaaagaaaagtattgctactttcctactaaagcgaaccgatggttaagagaagtttaaacataaaaaagaggttggtgcaggaagctaccaacctcgagaaaaatgatttagaaaatctctaaatccataaaaacacgtagcaaatatacgtttattaaataagaaaaccaaataataggcgattataaaacatttattaacacttcctataaaataaaatcaaaattcagataaaacaaaaatcccttacctaaagaatggcaagggatttttattattaattgaaagagaagatta Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 100 HP_score: -10.7 Tail_Score: -5.56264 Start: 77 End: 104 Full_Region: taaatcatttttctc gaggttggtagc ttcct gcaccaacctc ttttttatgtttaaa ............................................................................gaggttggtagcttcctgcaccaacctc.......................................................................................................................................................................................................... TransTerm Strand: - Conf: 70 HP_score: -4.2 Tail_Score: -4.8543 Start: 113 End: 135 Full_Region: gctacgtgtttttat ggatttagag att ttctaaatca tttttctcgaggttg ................................................................................................................ggatttagagattttctaaatca........................................................................................................................................................................... TransTerm Strand: - Conf: 71 HP_score: -7.7 Tail_Score: -3.50535 Start: 114 End: 134 Full_Region: ctacgtgtttttatg gatttagag att ttctaaatc atttttctcgaggtt .................................................................................................................gatttagagattttctaaatc............................................................................................................................................................................ TransTerm Strand: - Conf: 60 HP_score: -5.7 Tail_Score: -3.46546 Start: 236 End: 294 Full_Region: taatcttctctt tcaattaataataaaaatcccttgcc attcttta ggtaagggatttttgttttatctga attttgattttattt ...........................................................................................................................................................................................................................................tcaattaataataaaaatcccttgccattctttaggtaagggatttttgttttatctga............ TransTerm Strand: + Conf: 77 HP_score: -4.7 Tail_Score: -5.3321 Start: 252 End: 277 Full_Region: CAGATAAAACAAAAA TCCCTTACC TAAAGAAT GGCAAGGGA TTTTTATTATTAATT ...........................................................................................................................................................................................................................................................TCCCTTACCTAAAGAATGGCAAGGGA............................. Find igs database================================================ Query_seq: PI1281:PI1282|PI1281:PI1282:hypothetical protein:ATP synthase, gamma subunit (F0F1-ATPase, gamma subunit):->->:1197052..1197357 306 taagcaacaaaagaaaagtattgctactttcctactaaagcgaaccgatggttaagagaagtttaaacataaaaaagaggttggtgcaggaagctaccaacctcgagaaaaatgatttagaaaatctctaaatccataaaaacacgtagcaaatatacgtttattaaataagaaaaccaaataataggcgattataaaacatttattaacacttcctataaaataaaatcaaaattcagataaaacaaaaatcccttacctaaagaatggcaagggatttttattattaattgaaagagaagatta Intra-Species Hit: Count: 1 Min: 1 Max: 306 Len: 306 Subject: pint_PI1281_PI1282|hypothetical protein:ATP synthase, gamma subunit (F0F1-ATPase, gamma subunit)|POSITIVE:POSITIVE|[1197052,1197357]|306 HSP 1 e-value: 1.0E-121 bit: 434.0 Len: 219 Query Start:1 Query End:219 Subject Strand: POSITIVE Subject Start: 1 Subject End: 219 taagcaacaaaagaaaagtattgctactttcctactaaagcgaaccgatggttaagagaagtttaaacataaaaaagaggttggtgcaggaagctaccaacctcgagaaaaatgatttagaaaatctctaaatccataaaaacacgtagcaaatatacgtttattaaataagaaaaccaaataataggcgattataaaacatttattaacacttcctat....................................................................................... taagcaacaaaagaaaagtattgctactttcctactaaagcgaaccgatggttaagagaagtttaaacataaaaaagaggttggtgcaggaagctaccaacctcgagaaaaatgatttagaaaatctctaaatccataaaaacacgtagcaaatatacgtttattaaataagaaaaccaaataataggcgattataaaacatttattaacacttcctat....................................................................................... HSP 2 e-value: 2.0E-22 bit: 107.0 Len: 54 Query Start:253 Query End:306 Subject Strand: POSITIVE Subject Start: 253 Subject End: 306 ............................................................................................................................................................................................................................................................cccttacctaaagaatggcaagggatttttattattaattgaaagagaagatta ............................................................................................................................................................................................................................................................cccttacctaaagaatggcaagggatttttattattaattgaaagagaagatta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAGCAACAAAAGAAAAGUAUUGCUACUUUCCUACUAAAGCGAACCGAUGGUUAAGAGAAGUUUAAACAUAAAAAAGAGGUUGGUGCAGGAAGCUACCAACCUCGAGAAAAAUGAUUUAGAAAAUCUCUAAAUCCAUAAAAACACGUAGCAAAUAUACGUUUAUUAAAUAAGAAAACCAAAUAAUAGGCGAUUAUAAAACAUUUAUUAACACUUCCUAUAAAAUAAAAUCAAAAUUCAGAUAAAACAAAAAUCCCUUACCUAAAGAAUGGCAAGGGAUUUUUAUUAUUAAUUGAAAGAGAAGAUUA ....................(((((((.(((((.....)).)))...((((((.(((((..(((((((((......(((((((((((.....)).))))))))).......))).))))))...))))).)).))))........))))))).....(((((((((...............))))))))).....................((((((.................(((((.(((((.(((((((((((.((........)).))))))))))).)).))).))))))).)))).... (-66.00) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAUCUUCUCUUUCAAUUAAUAAUAAAAAUCCCUUGCCAUUCUUUAGGUAAGGGAUUUUUGUUUUAUCUGAAUUUUGAUUUUAUUUUAUAGGAAGUGUUAAUAAAUGUUUUAUAAUCGCCUAUUAUUUGGUUUUCUUAUUUAAUAAACGUAUAUUUGCUACGUGUUUUUAUGGAUUUAGAGAUUUUCUAAAUCAUUUUUCUCGAGGUUGGUAGCUUCCUGCACCAACCUCUUUUUUAUGUUUAAACUUCUCUUAACCAUCGGUUCGCUUUAGUAGGAAAGUAGCAAUACUUUUCUUUUGUUGCUUA .((((......((((..(((.(((((((((((((((((........))))))))))))))))))))..))))....)))).....(((..((((((((.((((.((((((.((((..(((........)))....)))).....)))))).)))).)).(((((........(((((((((...))))))))).........(((((((((.((.....))))))))))).....)))))....))))))..)))..........((..(((.(((((((((....))))))))).)))..))... (-81.50) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 362 103 62 184 141 pint:PI0831|5end_hypothetical_protein_768129..768359_POSITIVE 357 108 67 80 42 pint:PI1822|5end_ABC_transporter,_ATP-binding_/_permease_1761452..1761682_POSITIVE 267 65 31 195 159 pint:PI0093|5end_riboflavin_biosynthesis_protein_90489..90719_POSITIVE 264 97 55 142 101 pint:PI0776|5end_predicted_TPR-repeat-containing_protein_712077..712307_POSITIVE 264 110 76 107 69 pint:PI0735|5end_ABC_transporter,_ATP-binding_/_permease_668793..669023_POSITIVE 263 60 12 62 17 pint:PI1043|5end_conserved_hypothetical_protein_960855..961085_POSITIVE 263 109 75 68 32 pint:PI0723|5end_conserved_hypothetical_protein_656043..656273_POSITIVE 259 290 242 171 121 pint:PI0640|5end_conserved_hypothetical_protein_583289..583519_POSITIVE 255 104 76 47 19 pint:PI0034|5end_FKBP-type_peptidyl-prolyl_cis-trans_isomerase_37151..37381_POSITIVE 254 108 83 29 4 pint:PI0854|5end_MiaB-like_tRNA_modifying_enzyme_786513..786743_POSITIVE 246 93 77 173 156 pint:PI1904|5end_glutamine_synthetase_1845168..1845398_POSITIVE 246 109 75 56 18 pint:PI1729|5end_FKBP-type_peptidyl-prolyl_cis-trans_isomerase,_trigger_factor_1648416..1648646_POSITIVE 246 90 45 220 178 pint:PI1070|5end_peptidoglycan-associated_lipoprotein_986110..986340_POSITIVE 244 109 77 72 33 pint:PI1576|5end_serine_protease_precursor_1502172..1502402_POSITIVE 241 107 78 67 34 pint:PI1492|5end_triosephosphate_isomerase_1410155..1410385_POSITIVE 240 60 19 148 106 pint:PI0028|5end_aminopeptidase_31559..31789_POSITIVE 238 109 77 175 144 pint:PI1298|5end_glycosyltransferase_1211184..1211414_POSITIVE 238 106 81 157 132 pint:PI0732|5end_conserved_hypothetical_protein_663598..663828_POSITIVE 234 88 41 194 156 pint:PI1508|5end_undecaprenol_kinase_1427288..1427518_POSITIVE 231 100 57 115 73 pint:PI0896|5end_2-oxoglutarate_oxidoreductase,_alpha_subunit_827138..827368_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 357 108 67 65 27 pint:PI1821|3end_possible_thioredoxin_family_protein_1761517..1761667_POSITIVE 273 122 83 80 26 pint:PI0041|3end_hypothetical_protein_42023..42173_POSITIVE 267 65 31 137 101 pint:PI0094|3end_protoporphyrinogen_oxidase_90511..90661_POSITIVE 254 108 83 29 4 pint:PI0853|3end_glycosyl_transferase,_group_2_family_protein_786593..786743_POSITIVE 248 114 75 90 50 pint:PI1749|3end_conserved_hypothetical_protein_1671637..1671787_POSITIVE 246 93 77 100 83 pint:PI1902|3end_hypothetical_protein_1845175..1845325_POSITIVE 245 108 65 128 80 pint:PI2174|3end_hypothetical_protein_2114969..2115119_POSITIVE 241 120 79 68 19 pint:PI2159|3end_immunoreactive_84_kDa_antigen_PG93_2107371..2107521_POSITIVE 238 96 55 151 111 pint:PI0775|3end_ATP-independent_RNA_helicase_712167..712317_POSITIVE 238 110 74 69 39 pint:PI0006|3end_hypothetical_protein_8268..8418_POSITIVE 234 90 41 100 33 pint:PI1408|3end_glucose-1-phosphate_thymidylyltransferase_1329761..1329911_POSITIVE 234 99 55 98 48 pint:PI0286|3end_ISPg3-related_transposase_272065..272215_POSITIVE 233 109 72 135 102 pint:PI2006|3end_potassium_uptake_system_protein_1965846..1965996_POSITIVE 231 100 57 91 49 pint:PI0895|3end_2-oxoglutarate_oxidoreductase,_beta_subunit,_possible_ketoisovalerate_oxidoreductase,__vorA_827194..827344_POSITIVE 224 103 61 51 5 pint:PI1142|3end_S1_RNA_binding_domain_protein,_S1_ribosomal_protein_1072122..1072272_POSITIVE 224 70 24 50 2 pint:PI0659|3end_hypothetical_protein_603396..603546_POSITIVE 222 105 81 151 127 pint:PI0731|3end_conserved_hypothetical_protein_663673..663823_POSITIVE 221 59 17 144 96 pint:PI2085|3end_conserved_hypothetical_protein_2041803..2041953_POSITIVE 221 50 4 118 69 pint:PI1758|3end_hypothetical_protein_1684057..1684207_POSITIVE 221 53 19 139 105 pint:PI1136|3end_conserved_hypothetical_protein_1062541..1062691_POSITIVE