Origin IGS: tagacatttcgtaaaagtaaaaacccatgttctgaaatttaagaacataggttttttaatatgcaagctatgttttcttatgggggtattgtacctttttcttatgtataactaataaatctgcaagcaaaaatatgtaaatatttttctgttcaggttgtttgccataacattcttgttatcaatgtattagaaaacctattgttttgcattccaaaagcggctattttgcaacgcaaaaccta .........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 taggttttgcgttgcaaaatagccgcttttggaatgcaaaacaataggttttctaatacattgataacaagaatgttatggcaaacaacctgaacagaaaaatatttacatatttttgcttgcagatttattagttatacataagaaaaaggtacaatacccccataagaaaacatagcttgcatattaaaaaacctatgttcttaaatttcagaacatgggtttttacttttacgaaatgtcta Mask Tandem Repeat Region ================================================ tagacatttcgtaaaagtaaaaacccatgttctgaaatttaagaacataggttttttaatatgcaagctatgttttcttatgggggtattgtacctttttcttatgtataactaataaatctgcaagcaaaaatatgtaaatatttttctgttcaggttgtttgccataacattcttgttatcaatgtattagaaaacctattgttttgcattccaaaagcggctattttgcaacgcaaaaccta Find is-nt database================================================ Query_seq: PI0977:PI0978|PI0977:PI0978:riboflavin synthase, alpha subunit:hypothetical protein:->->:904762..905006 245 tagacatttcgtaaaagtaaaaacccatgttctgaaatttaagaacataggttttttaatatgcaagctatgttttcttatgggggtattgtacctttttcttatgtataactaataaatctgcaagcaaaaatatgtaaatatttttctgttcaggttgtttgccataacattcttgttatcaatgtattagaaaacctattgttttgcattccaaaagcggctattttgcaacgcaaaaccta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI0977:PI0978|PI0977:PI0978:riboflavin synthase, alpha subunit:hypothetical protein:->->:904762..905006 245 tagacatttcgtaaaagtaaaaacccatgttctgaaatttaagaacataggttttttaatatgcaagctatgttttcttatgggggtattgtacctttttcttatgtataactaataaatctgcaagcaaaaatatgtaaatatttttctgttcaggttgtttgccataacattcttgttatcaatgtattagaaaacctattgttttgcattccaaaagcggctattttgcaacgcaaaaccta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI0977:PI0978|PI0977:PI0978:riboflavin synthase, alpha subunit:hypothetical protein:->->:904762..905006 245 tagacatttcgtaaaagtaaaaacccatgttctgaaatttaagaacataggttttttaatatgcaagctatgttttcttatgggggtattgtacctttttcttatgtataactaataaatctgcaagcaaaaatatgtaaatatttttctgttcaggttgtttgccataacattcttgttatcaatgtattagaaaacctattgttttgcattccaaaagcggctattttgcaacgcaaaaccta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tagacatttcgtaaaagtaaaaacccatgttctgaaatttaagaacataggttttttaatatgcaagctatgttttcttatgggggtattgtacctttttcttatgtataactaataaatctgcaagcaaaaatatgtaaatatttttctgttcaggttgtttgccataacattcttgttatcaatgtattagaaaacctattgttttgcattccaaaagcggctattttgcaacgcaaaaccta Predict ORF larger than 30AA ================================================ Protein_Len: 43 Strand: + Start: 115 End: 243 .................................................................................................................. M N L Q A K I C K Y F S V Q V V C H N I L V I N V L E N L L F C I P K A A I L Q R K T .. Protein_Len: 35 Strand: - Start: 1 End: 105 L C K T F T F V W T R F N L F M P K K I H L S H K R I P T N Y R K R M ............................................................................................................................................ tagacatttcgtaaaagtaaaaacccatgttctgaaatttaagaacataggttttttaatatgcaagctatgttttcttatgggggtattgtacctttttcttatgtataactaataaatctgcaagcaaaaatatgtaaatatttttctgttcaggttgtttgccataacattcttgttatcaatgtattagaaaacctattgttttgcattccaaaagcggctattttgcaacgcaaaaccta 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================================================ tagacatttcgtaaaagtaaaaacccatgttctgaaatttaagaacataggttttttaatatgcaagctatgttttcttatgggggtattgtacctttttcttatgtataactaataaatctgcaagcaaaaatatgtaaatatttttctgttcaggttgtttgccataacattcttgttatcaatgtattagaaaacctattgttttgcattccaaaagcggctattttgcaacgcaaaaccta Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 89 HP_score: -7.8 Tail_Score: -5.0925 Start: 24 End: 51 Full_Region: ttgcatattaaaaaa cctatgttctta aatt tcagaacatggg tttttacttttacga .......................cctatgttcttaaatttcagaacatggg.................................................................................................................................................................................................. TransTerm Strand: + Conf: 80 HP_score: -5.4 Tail_Score: -5.27206 Start: 85 End: 95 Full_Region: ATGTTTTCTTATGGG GGTA TTG TACC TTTTTCTTATGTATA ....................................................................................GGTATTGTACC...................................................................................................................................................... Find igs database================================================ Query_seq: PI0977:PI0978|PI0977:PI0978:riboflavin synthase, alpha subunit:hypothetical protein:->->:904762..905006 245 tagacatttcgtaaaagtaaaaacccatgttctgaaatttaagaacataggttttttaatatgcaagctatgttttcttatgggggtattgtacctttttcttatgtataactaataaatctgcaagcaaaaatatgtaaatatttttctgttcaggttgtttgccataacattcttgttatcaatgtattagaaaacctattgttttgcattccaaaagcggctattttgcaacgcaaaaccta Intra-Species Hit: Count: 1 Min: 1 Max: 245 Len: 245 Subject: pint_PI0977_PI0978|riboflavin synthase, alpha subunit:hypothetical protein|POSITIVE:POSITIVE|[904762,905006]|245 HSP 1 e-value: 1.0E-136 bit: 486.0 Len: 245 Query Start:1 Query End:245 Subject Strand: POSITIVE Subject Start: 1 Subject End: 245 tagacatttcgtaaaagtaaaaacccatgttctgaaatttaagaacataggttttttaatatgcaagctatgttttcttatgggggtattgtacctttttcttatgtataactaataaatctgcaagcaaaaatatgtaaatatttttctgttcaggttgtttgccataacattcttgttatcaatgtattagaaaacctattgttttgcattccaaaagcggctattttgcaacgcaaaaccta tagacatttcgtaaaagtaaaaacccatgttctgaaatttaagaacataggttttttaatatgcaagctatgttttcttatgggggtattgtacctttttcttatgtataactaataaatctgcaagcaaaaatatgtaaatatttttctgttcaggttgtttgccataacattcttgttatcaatgtattagaaaacctattgttttgcattccaaaagcggctattttgcaacgcaaaaccta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAGACAUUUCGUAAAAGUAAAAACCCAUGUUCUGAAAUUUAAGAACAUAGGUUUUUUAAUAUGCAAGCUAUGUUUUCUUAUGGGGGUAUUGUACCUUUUUCUUAUGUAUAACUAAUAAAUCUGCAAGCAAAAAUAUGUAAAUAUUUUUCUGUUCAGGUUGUUUGCCAUAACAUUCUUGUUAUCAAUGUAUUAGAAAACCUAUUGUUUUGCAUUCCAAAAGCGGCUAUUUUGCAACGCAAAACCUA ...........................((((((........))))))(((((((((((((((((((((...(((....((((((((((...)))).....))))))...))).....((((((..((.((((((((....))))))))))...)))))))))))).((((((....))))))....)))))))))))))))..(((((((.((.(((((.......))))).)).)))))))... (-52.90) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAGGUUUUGCGUUGCAAAAUAGCCGCUUUUGGAAUGCAAAACAAUAGGUUUUCUAAUACAUUGAUAACAAGAAUGUUAUGGCAAACAACCUGAACAGAAAAAUAUUUACAUAUUUUUGCUUGCAGAUUUAUUAGUUAUACAUAAGAAAAAGGUACAAUACCCCCAUAAGAAAACAUAGCUUGCAUAUUAAAAAACCUAUGUUCUUAAAUUUCAGAACAUGGGUUUUUACUUUUACGAAAUGUCUA ...((((((((((.(((((.......))))).)))))))))).....(((((((.......(((((((.....((((......))))..(((...((((((((((....)))))))).))..)))........))))).)).........((((...))))......)))))))...............(((((((((((((((........))))))))))))))).................. (-53.30) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 649 236 194 82 41 pint:PI0119|5end_hypothetical_protein_111506..111736_POSITIVE 634 225 181 179 135 pint:PI0827|5end_hypothetical_protein_763991..764221_POSITIVE 622 225 181 165 121 pint:PI0024|5end_hypothetical_protein_28378..28608_POSITIVE 610 225 182 192 149 pint:PI1333|5end_conserved_hypothetical_protein_1250777..1251007_POSITIVE 596 236 194 175 134 pint:PI2046|5end_hypothetical_protein_1999030..1999260_POSITIVE 596 236 194 189 148 pint:PI0887|5end_hypothetical_protein_817536..817766_POSITIVE 596 236 194 82 41 pint:PI0867|5end_hypothetical_protein_803859..804089_POSITIVE 596 236 194 230 189 pint:PI0695|5end_xanthine/uracil_permease_family_protein_631413..631643_POSITIVE 575 220 175 136 91 pint:PI0211|5end_hypothetical_protein_204067..204297_POSITIVE 562 225 181 205 161 pint:PI2024|5end_hypothetical_protein_1978804..1979034_POSITIVE 559 225 181 179 135 pint:PI0575|5end_hypothetical_protein_519561..519791_POSITIVE 553 236 198 38 1 pint:PI1204|5end_hypothetical_protein_1124430..1124660_POSITIVE 542 240 194 194 148 pint:PI0653|5end_hypothetical_protein_596046..596276_POSITIVE 540 236 194 42 1 pint:PI2022|5end_hypothetical_protein_1978631..1978861_POSITIVE 540 236 194 169 128 pint:PI0991|5end_conserved_hypothetical_protein_915309..915539_POSITIVE 539 220 173 224 177 pint:PI1982|5end_conserved_hypothetical_protein_1938439..1938669_POSITIVE 539 220 173 224 177 pint:PI1959|5end_hypothetical_protein_1917708..1917938_POSITIVE 523 225 181 229 185 pint:PI0096|5end_glycerol-3-phosphate_cytidylyltransferase_91885..92115_POSITIVE 517 225 181 230 186 pint:PI0090|5end_amidophosphoribosyltransferase_88379..88609_POSITIVE 503 220 171 155 107 pint:PI0196|5end_hypothetical_protein_188435..188665_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 649 236 194 136 95 pint:PI0118|3end_hypothetical_protein_111640..111790_POSITIVE 596 236 194 136 95 pint:PI1797|3end_hypothetical_protein_1731559..1731709_POSITIVE 596 236 194 136 95 pint:PI0885|3end_hypothetical_protein_817563..817713_POSITIVE 596 236 194 136 95 pint:PI0866|3end_hypothetical_protein_803993..804143_POSITIVE 596 236 194 136 95 pint:PI0820|3end_hypothetical_protein_759980..760130_POSITIVE 596 236 194 75 34 pint:PI0819|3end_hypothetical_protein_759919..760069_POSITIVE 596 236 194 124 83 pint:PI0815|3end_hypothetical_protein_754677..754827_POSITIVE 596 236 194 124 83 pint:PI0095|3end_hypothetical_protein_91850..92000_POSITIVE 596 236 194 136 95 pint:PI0089|3end_hypothetical_protein_88355..88505_POSITIVE 596 236 194 124 83 pint:PI0081|3end_hypothetical_protein_80700..80850_POSITIVE 587 234 194 135 95 pint:PI1005|3end_hypothetical_protein_926481..926631_POSITIVE 581 223 181 151 109 pint:PI0826|3end_hypothetical_protein_764045..764195_POSITIVE 570 240 194 141 95 pint:PI1041|3end_hypothetical_protein_960675..960825_POSITIVE 570 240 194 129 83 pint:PI0638|3end_hypothetical_protein_582402..582552_POSITIVE 570 240 194 124 78 pint:PI0637|3end_hypothetical_protein_582397..582547_POSITIVE 553 220 175 82 37 pint:PI0905|3end_hypothetical_protein_834697..834847_POSITIVE 540 236 194 124 83 pint:PI0568|3end_hypothetical_protein_513131..513281_POSITIVE 540 236 194 48 7 pint:PI0567|3end_hypothetical_protein_513055..513205_POSITIVE 522 223 181 151 109 pint:PI0069|3end_hypothetical_protein_67379..67529_POSITIVE 520 236 194 124 83 pint:PI1252|3end_hypothetical_protein_1175440..1175590_POSITIVE