Origin IGS: agcttgatggggagtttaaataatgaataatggtgggaaaagccaataagtagcgaagttttattgaataaaaaagatgataggcagcgagttaaagtatgcgtatggcaatacttcctgctgcctatcatctttttatatta .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 taatataaaaagatgataggcagcaggaagtattgccatacgcatactttaactcgctgcctatcatcttttttattcaataaaacttcgctacttattggcttttcccaccattattcattatttaaactccccatcaagct Mask Tandem Repeat Region ================================================ agcttgatggggagtttaaataatgaataatggtgggaaaagccaataagtagcgaagttttattgaataaaaaagatgataggcagcgagttaaagtatgcgtatggcaatacttcctgctgcctatcatctttttatatta Find is-nt database================================================ Query_seq: PI0541:PI0543|PI0541:PI0543:GTP-binding protein, GTP1/OBG family:adenylate kinase:->->:495070..495212 143 agcttgatggggagtttaaataatgaataatggtgggaaaagccaataagtagcgaagttttattgaataaaaaagatgataggcagcgagttaaagtatgcgtatggcaatacttcctgctgcctatcatctttttatatta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI0541:PI0543|PI0541:PI0543:GTP-binding protein, GTP1/OBG family:adenylate kinase:->->:495070..495212 143 agcttgatggggagtttaaataatgaataatggtgggaaaagccaataagtagcgaagttttattgaataaaaaagatgataggcagcgagttaaagtatgcgtatggcaatacttcctgctgcctatcatctttttatatta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI0541:PI0543|PI0541:PI0543:GTP-binding protein, GTP1/OBG family:adenylate kinase:->->:495070..495212 143 agcttgatggggagtttaaataatgaataatggtgggaaaagccaataagtagcgaagttttattgaataaaaaagatgataggcagcgagttaaagtatgcgtatggcaatacttcctgctgcctatcatctttttatatta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 agcttgatggggagtttaaataatgaataatggtgggaaaagccaataagtagcgaagttttattgaataaaaaagatgataggcagcgagttaaagtatgcgtatggcaatacttcctgctgcctatcatctttttatatta Predict ORF larger than 30AA ================================================ Protein_Len: 32 Strand: + Start: 46 End: 141 ............................................. M S S E V L L N K K D D R Q R V K V C V W Q Y F L L P I I F L Y .. Protein_Len: 43 Strand: - Start: 3 End: 131 .. K I P L K F L S Y H H S F G I L L S T K N F L F S S L C R T L T H T H C Y K R S G I M ............ agcttgatggggagtttaaataatgaataatggtgggaaaagccaataagtagcgaagttttattgaataaaaaagatgataggcagcgagttaaagtatgcgtatggcaatacttcctgctgcctatcatctttttatatta 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================================================ agcttgatggggagtttaaataatgaataatggtgggaaaagccaataagtagcgaagttttattgaataaaaaagatgataggcagcgagttaaagtatgcgtatggcaatacttcctgctgcctatcatctttttatatta Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 100 HP_score: -7.8 Tail_Score: -5.4833 Start: 76 End: 132 Full_Region: taatataaaaa gatgataggcagcaggaagtattgc catac gcatactttaactcgctgcctatcatc ttttttattcaataa ...........................................................................gatgataggcagcaggaagtattgccatacgcatactttaactcgctgcctatcatc........... Find igs database================================================ Query_seq: PI0541:PI0543|PI0541:PI0543:GTP-binding protein, GTP1/OBG family:adenylate kinase:->->:495070..495212 143 agcttgatggggagtttaaataatgaataatggtgggaaaagccaataagtagcgaagttttattgaataaaaaagatgataggcagcgagttaaagtatgcgtatggcaatacttcctgctgcctatcatctttttatatta Intra-Species Hit: Count: 1 Min: 1 Max: 143 Len: 143 Subject: pint_PI0541_PI0543|GTP-binding protein, GTP1/OBG family:adenylate kinase|POSITIVE:POSITIVE|[495070,495212]|143 HSP 1 e-value: 8.0E-76 bit: 283.0 Len: 143 Query Start:1 Query End:143 Subject Strand: POSITIVE Subject Start: 1 Subject End: 143 agcttgatggggagtttaaataatgaataatggtgggaaaagccaataagtagcgaagttttattgaataaaaaagatgataggcagcgagttaaagtatgcgtatggcaatacttcctgctgcctatcatctttttatatta agcttgatggggagtttaaataatgaataatggtgggaaaagccaataagtagcgaagttttattgaataaaaaagatgataggcagcgagttaaagtatgcgtatggcaatacttcctgctgcctatcatctttttatatta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGCUUGAUGGGGAGUUUAAAUAAUGAAUAAUGGUGGGAAAAGCCAAUAAGUAGCGAAGUUUUAUUGAAUAAAAAAGAUGAUAGGCAGCGAGUUAAAGUAUGCGUAUGGCAAUACUUCCUGCUGCCUAUCAUCUUUUUAUAUUA .(((((.(((....(((..((.((.....)).))..)))...))).)))))...............((((((((((((((((((((((.((...((((((((.....)).)))))).)))))))))))))))))))).)))). (-42.30) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAUAUAAAAAGAUGAUAGGCAGCAGGAAGUAUUGCCAUACGCAUACUUUAACUCGCUGCCUAUCAUCUUUUUUAUUCAAUAAAACUUCGCUACUUAUUGGCUUUUCCCACCAUUAUUCAUUAUUUAAACUCCCCAUCAAGCU .((((.(((((((((((((((((((((((((((.((.....)))))))))..)).))))))))))))))))))))))............((((.....))))......................................... (-38.30) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 326 125 83 80 25 pint:PI1034|5end_conserved_hypothetical_protein;_possible_membrane_protein_952093..952323_POSITIVE 308 137 101 133 83 pint:PI0263|5end_conjugative_transposon_protein,_TraM_255256..255486_POSITIVE 294 135 93 171 119 pint:PI0029|5end_glutamine_amidotransferase_(GMP_synthase_(glutamine-hydrolyzing))_32593..32823_POSITIVE 292 129 83 71 28 pint:PI0342|5end_hypothetical_protein_317556..317786_POSITIVE 290 126 83 126 76 pint:PI0701|5end_hypothetical_protein_638356..638586_POSITIVE 290 125 82 208 169 pint:PI0167|5end_hypothetical_protein_163164..163394_POSITIVE 289 89 49 111 74 pint:PI1440|5end_conserved_hypothetical_protein_1357185..1357415_POSITIVE 287 123 83 230 181 pint:PI0753|5end_hypothetical_protein_683391..683621_POSITIVE 285 128 82 136 81 pint:PI1816|5end_acid_phosphatase_1754646..1754876_POSITIVE 284 127 83 128 78 pint:PI1468|5end_conserved_hypothetical_protein;_probable_TPR_domain_protein_1393900..1394130_POSITIVE 277 130 85 73 19 pint:PI0303|5end_hypothetical_protein_286946..287176_POSITIVE 275 123 83 196 164 pint:PI0720|5end_conserved_hypothetical_protein_653949..654179_POSITIVE 272 123 82 109 57 pint:PI0705|5end_conserved_hypothetical_protein;_possible_lipoprotein_641274..641504_POSITIVE 266 124 82 168 127 pint:PI0897|5end_ferredoxin,_4Fe-4S_828227..828457_POSITIVE 266 114 76 74 35 pint:PI0780|5end_DNA_gyrase,_subunit_A_(DNA_topoisomerase_(ATP-hydrolyzing))_715902..716132_POSITIVE 264 129 83 220 169 pint:PI0251|5end_hypothetical_protein_247551..247781_POSITIVE 262 125 83 210 171 pint:PI1246|5end_conserved_hypothetical_protein;_possible_lipoprotein_1169392..1169622_POSITIVE 262 126 82 83 40 pint:PI1055|5end_aspartokinase_974909..975139_POSITIVE 262 125 82 69 27 pint:PI0316|5end_conserved_hypothetical_protein_298379..298609_POSITIVE 261 130 82 191 143 pint:PI0404|5end_integrase_371295..371525_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 328 129 82 126 78 pint:PI0242|3end_hypothetical_protein_240227..240377_POSITIVE 292 129 83 50 7 pint:PI0341|3end_conserved_hypothetical_protein_317615..317765_POSITIVE 290 126 83 103 53 pint:PI0700|3end_UDP-glucose_4-epimerase_638413..638563_POSITIVE 289 89 49 121 84 pint:PI1438|3end_penicillin_tolerance_protein/steroid_biosynthesis_1357275..1357425_POSITIVE 287 125 82 136 97 pint:PI0028|3end_aminopeptidase_32727..32877_POSITIVE 284 127 83 57 7 pint:PI1467|3end_conserved_hypothetical_protein_1393909..1394059_POSITIVE 282 129 96 41 5 pint:PI1734|3end_possible_carboxyl-terminal_protease-related_protein_1653829..1653979_POSITIVE 277 130 85 66 12 pint:PI0302|3end_hypothetical_protein_287019..287169_POSITIVE 274 130 82 137 92 pint:PI0494|3end_hypothetical_protein_455170..455320_POSITIVE 272 123 82 119 67 pint:PI0704|3end_conserved_hypothetical_protein_641364..641514_POSITIVE 266 124 82 137 96 pint:PI0896|3end_2-oxoglutarate_oxidoreductase,_alpha_subunit_828276..828426_POSITIVE 262 126 82 72 29 pint:PI1054|3end_conserved_hypothetical_protein_974978..975128_POSITIVE 261 127 83 134 93 pint:PI0184|3end_possible_fibronectin_type_III_domain_protein_176516..176666_POSITIVE 258 49 3 108 63 pint:PI2028|3end_shikimate_kinase_1982802..1982952_POSITIVE 258 126 83 134 66 pint:PI0981|3end_outer_membrane_protein,_TonB_dependent_receptor_909390..909540_POSITIVE 258 128 82 146 103 pint:PI0524|3end_meso-diaminopimelate_D-dehydrogenase_480849..480999_POSITIVE 257 134 101 95 56 pint:PI1943|3end_hypothetical_protein_1902206..1902356_POSITIVE 255 135 99 148 110 pint:PI0588|3end_hypothetical_protein_535425..535575_POSITIVE 255 135 99 70 32 pint:PI0587|3end_conserved_hypothetical_protein_535347..535497_POSITIVE 253 43 2 101 55 pint:PI0589|3end_asparaginyl-tRNA_synthetase_(asparagine--tRNA_ligase)_536959..537109_POSITIVE