Origin IGS: taattctttctgaaacagaagaaacaataaaatatacaagagcggaactcttttaaagggttccgctctttttttcattctttccgaatacacatctttccgtgcataaagaggcttttcgcccctattttatttcatcttcacatctctttatataggagaaaataaagcaagaatgttgtaaacatttttcacaaagacatgtttcatctaaccacctctctatcaatgcattaccaaaccta .........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 taggtttggtaatgcattgatagagaggtggttagatgaaacatgtctttgtgaaaaatgtttacaacattcttgctttattttctcctatataaagagatgtgaagatgaaataaaataggggcgaaaagcctctttatgcacggaaagatgtgtattcggaaagaatgaaaaaaagagcggaaccctttaaaagagttccgctcttgtatattttattgtttcttctgtttcagaaagaatta Mask Tandem Repeat Region ================================================ taattctttctgaaacagaagaaacaataaaatatacaagagcggaactcttttaaagggttccgctctttttttcattctttccgaatacacatctttccgtgcataaagaggcttttcgcccctattttatttcatcttcacatctctttatataggagaaaataaagcaagaatgttgtaaacatttttcacaaagacatgtttcatctaaccacctctctatcaatgcattaccaaaccta Find is-nt database================================================ Query_seq: PI1828:PI1829|PI1828:PI1829:peptidase, M23/M37 family, C-terminal:hypothetical protein:->->:1769150..1769394 245 taattctttctgaaacagaagaaacaataaaatatacaagagcggaactcttttaaagggttccgctctttttttcattctttccgaatacacatctttccgtgcataaagaggcttttcgcccctattttatttcatcttcacatctctttatataggagaaaataaagcaagaatgttgtaaacatttttcacaaagacatgtttcatctaaccacctctctatcaatgcattaccaaaccta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI1828:PI1829|PI1828:PI1829:peptidase, M23/M37 family, C-terminal:hypothetical protein:->->:1769150..1769394 245 taattctttctgaaacagaagaaacaataaaatatacaagagcggaactcttttaaagggttccgctctttttttcattctttccgaatacacatctttccgtgcataaagaggcttttcgcccctattttatttcatcttcacatctctttatataggagaaaataaagcaagaatgttgtaaacatttttcacaaagacatgtttcatctaaccacctctctatcaatgcattaccaaaccta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI1828:PI1829|PI1828:PI1829:peptidase, M23/M37 family, C-terminal:hypothetical protein:->->:1769150..1769394 245 taattctttctgaaacagaagaaacaataaaatatacaagagcggaactcttttaaagggttccgctctttttttcattctttccgaatacacatctttccgtgcataaagaggcttttcgcccctattttatttcatcttcacatctctttatataggagaaaataaagcaagaatgttgtaaacatttttcacaaagacatgtttcatctaaccacctctctatcaatgcattaccaaaccta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 taattctttctgaaacagaagaaacaataaaatatacaagagcggaactcttttaaagggttccgctctttttttcattctttccgaatacacatctttccgtgcataaagaggcttttcgcccctattttatttcatcttcacatctctttatataggagaaaataaagcaagaatgttgtaaacatttttcacaaagacatgtttcatctaaccacctctctatcaatgcattaccaaaccta Predict ORF larger than 30AA ================================================ Protein_Len: 44 Strand: + Start: 34 End: 165 ................................. M Q E R N S F K G F R S F F H S F R I H I F P C I K R L F A P I L F H L H I S L Y R R K ................................................................................ Protein_Len: 34 Strand: - Start: 128 End: 229 ............................................................................................................................... K I E D E C R K I Y S F I F C S H Q L C K E C L C T E D L W R E I M ................ Protein_Len: 31 Strand: - Start: 1 End: 93 L E K Q F L L F L L I Y L L P V R K F P E A R K K M R E S Y M ........................................................................................................................................................ taattctttctgaaacagaagaaacaataaaatatacaagagcggaactcttttaaagggttccgctctttttttcattctttccgaatacacatctttccgtgcataaagaggcttttcgcccctattttatttcatcttcacatctctttatataggagaaaataaagcaagaatgttgtaaacatttttcacaaagacatgtttcatctaaccacctctctatcaatgcattaccaaaccta 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================================================ taattctttctgaaacagaagaaacaataaaatatacaagagcggaactcttttaaagggttccgctctttttttcattctttccgaatacacatctttccgtgcataaagaggcttttcgcccctattttatttcatcttcacatctctttatataggagaaaataaagcaagaatgttgtaaacatttttcacaaagacatgtttcatctaaccacctctctatcaatgcattaccaaaccta Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 95 HP_score: -9.2 Tail_Score: -5.08731 Start: 33 End: 75 Full_Region: tattcggaaagaatg aaaaaaagagcggaaccctt taa aagagttccgctcttgtata ttttattgtttcttc ................................aaaaaaagagcggaaccctttaaaagagttccgctcttgtata.......................................................................................................................................................................... TransTerm Strand: - Conf: 100 HP_score: -11.8 Tail_Score: -4.12859 Start: 35 End: 73 Full_Region: ttcggaaagaatgaa aaaaagagcggaaccctt taa aagagttccgctcttgta tattttattgtttct ..................................aaaaagagcggaaccctttaaaagagttccgctcttgta............................................................................................................................................................................ TransTerm Strand: + Conf: 100 HP_score: -18.3 Tail_Score: -5.73672 Start: 40 End: 68 Full_Region: CAATAAAATATACAA GAGCGGAACTCTT TTA AAGGGTTCCGCTC TTTTTTTCATTCTTT .......................................GAGCGGAACTCTTTTAAAGGGTTCCGCTC................................................................................................................................................................................. TransTerm Strand: - Conf: 100 HP_score: -16.1 Tail_Score: -3.89068 Start: 40 End: 68 Full_Region: aaagaatgaaaaaaa gagcggaaccctt taa aagagttccgctc ttgtatattttattg .......................................gagcggaaccctttaaaagagttccgctc................................................................................................................................................................................. Find igs database================================================ Query_seq: PI1828:PI1829|PI1828:PI1829:peptidase, M23/M37 family, C-terminal:hypothetical protein:->->:1769150..1769394 245 taattctttctgaaacagaagaaacaataaaatatacaagagcggaactcttttaaagggttccgctctttttttcattctttccgaatacacatctttccgtgcataaagaggcttttcgcccctattttatttcatcttcacatctctttatataggagaaaataaagcaagaatgttgtaaacatttttcacaaagacatgtttcatctaaccacctctctatcaatgcattaccaaaccta Intra-Species Hit: Count: 1 Min: 1 Max: 245 Len: 245 Subject: pint_PI1828_PI1829|peptidase, M23/M37 family, C-terminal:hypothetical protein|POSITIVE:POSITIVE|[1769150,1769394]|245 HSP 1 e-value: 1.0E-124 bit: 444.0 Len: 245 Query Start:1 Query End:245 Subject Strand: POSITIVE Subject Start: 1 Subject End: 245 taattctttctgaaacagaagaaacaataaaatatacaagagcggaactcttttaaagggttccgctcnnnnnnncattctttccgaatacacatctttccgtgcataaagaggcttttcgcccctattttatttcatcttcacatctctttatataggagaaaataaagcaagaatgttgtaaacatttttcacaaagacatgtttcatctaaccacctctctatcaatgcattaccaaaccta taattctttctgaaacagaagaaacaataaaatatacaagagcggaactcttttaaagggttccgctctttttttcattctttccgaatacacatctttccgtgcataaagaggcttttcgcccctattttatttcatcttcacatctctttatataggagaaaataaagcaagaatgttgtaaacatttttcacaaagacatgtttcatctaaccacctctctatcaatgcattaccaaaccta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAUUCUUUCUGAAACAGAAGAAACAAUAAAAUAUACAAGAGCGGAACUCUUUUAAAGGGUUCCGCUCUUUUUUUCAUUCUUUCCGAAUACACAUCUUUCCGUGCAUAAAGAGGCUUUUCGCCCCUAUUUUAUUUCAUCUUCACAUCUCUUUAUAUAGGAGAAAAUAAAGCAAGAAUGUUGUAAACAUUUUUCACAAAGACAUGUUUCAUCUAACCACCUCUCUAUCAAUGCAUUACCAAACCUA ..........((((((((((((...(((((((((...((((((((((((((.....))))))))))))))........(((((....((.(((........))).)))))))(((.....)))..)))))))))...)))))...((((((.....)))))).......(.((((((((.....))))))))).........))))))).................................... (-52.30) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAGGUUUGGUAAUGCAUUGAUAGAGAGGUGGUUAGAUGAAACAUGUCUUUGUGAAAAAUGUUUACAACAUUCUUGCUUUAUUUUCUCCUAUAUAAAGAGAUGUGAAGAUGAAAUAAAAUAGGGGCGAAAAGCCUCUUUAUGCACGGAAAGAUGUGUAUUCGGAAAGAAUGAAAAAAAGAGCGGAACCCUUUAAAAGAGUUCCGCUCUUGUAUAUUUUAUUGUUUCUUCUGUUUCAGAAAGAAUUA ........((((.(((((.(((((((.(((...........))).)))))))....)))))))))...((((((.((((((..((((.........)))).)))))).(((((((....((((((.....))))))..(((((((......)))))))..(((((.(((((((..(((((((((((.((.....)).))))))))))).....))))))).)))))..)))))))..)))))).. (-70.30) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 369 140 95 154 109 pint:PI0886|5end_hypothetical_protein_817640..817870_POSITIVE 369 140 95 50 5 pint:PI0887|5end_hypothetical_protein_817536..817766_POSITIVE 354 90 43 72 31 pint:PI0263|5end_conjugative_transposon_protein,_TraM_255256..255486_POSITIVE 331 77 37 131 94 pint:PI1845|5end_hypothetical_protein_1791457..1791687_POSITIVE 302 86 42 166 126 pint:PI0516|5end_ferredoxin,_4Fe-4S_475864..476094_POSITIVE 300 217 171 115 61 pint:PI0991|5end_conserved_hypothetical_protein_915309..915539_POSITIVE 299 197 151 107 61 pint:PI0653|5end_hypothetical_protein_596046..596276_POSITIVE 299 87 42 230 182 pint:PI0548|5end_possible_acetylxylan_esterase_499532..499762_POSITIVE 297 87 41 75 21 pint:PI1653|5end_hypothetical_protein_1565158..1565388_POSITIVE 290 173 138 46 11 pint:PI0253|5end_conjugative_transposon_protein,_TraD_248294..248524_POSITIVE 286 88 42 73 28 pint:PI0404|5end_integrase_371295..371525_POSITIVE 279 100 51 200 135 pint:PI2058|5end_riboflavin_biosynthesis_protein_2015800..2016030_POSITIVE 278 86 41 134 71 pint:PI1839|5end_hypothetical_protein_1782178..1782408_POSITIVE 278 128 84 211 171 pint:PI1660|5end_hypothetical_protein_1574659..1574889_POSITIVE 272 67 37 57 23 pint:PI1666|5end_conserved_hypothetical_protein_1579231..1579461_POSITIVE 269 126 88 168 122 pint:PI2124|5end_excinuclease_ABC,_subunit_C_2072584..2072814_POSITIVE 269 237 203 109 77 pint:PI0211|5end_hypothetical_protein_204067..204297_POSITIVE 269 129 94 163 125 pint:PI0086|5end_possible_uroporphyrinogen-III_synthase_84944..85174_POSITIVE 265 129 82 222 175 pint:PI0706|5end_pyridoxal_phosphate_biosynthetic_protein_(4-hydroxythreonine-4-phosphate_dehydrogenase)_642226..642456_POSITIVE 264 123 82 217 171 pint:PI0233|5end_membrane_protein,_possible_exporter_231844..232074_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 495 70 38 53 21 pint:PI1828|3end_peptidase,_M23/M37_family,_C-terminal_1769089..1769239_POSITIVE 369 140 95 103 58 pint:PI0884|3end_hypothetical_protein_817669..817819_POSITIVE 307 125 84 115 74 pint:PI1065|3end_hypothetical_protein_983650..983800_POSITIVE 299 87 42 84 36 pint:PI0547|3end_fructose-bisphosphate_aldolase_499466..499616_POSITIVE 297 87 41 72 18 pint:PI1652|3end_hypothetical_protein_1565235..1565385_POSITIVE 294 237 212 121 96 pint:PI0069|3end_hypothetical_protein_67379..67529_POSITIVE 290 105 61 147 111 pint:PI2122|3end_conserved_hypothetical_protein_2070480..2070630_POSITIVE 290 173 138 55 20 pint:PI0252|3end_conserved_hypothetical_protein_248383..248533_POSITIVE 285 230 181 87 38 pint:PI0866|3end_hypothetical_protein_803993..804143_POSITIVE 269 129 94 99 61 pint:PI0085|3end_RNase_P_protein_component_84960..85110_POSITIVE 263 151 111 84 35 pint:PI0358|3end_hypothetical_protein_328105..328255_POSITIVE 255 122 82 147 106 pint:PI1153|3end_histidine_kinase_sensor_protein_1078638..1078788_POSITIVE 255 126 93 130 100 pint:PI0035|3end_NAD-dependent_protein_deacetylase,_SIR2_family_38642..38792_POSITIVE 254 80 42 69 35 pint:PI0261|3end_conjugative_transposon_protein,_TraK_254765..254915_POSITIVE 253 52 11 125 83 pint:PI1422|3end_hypothetical_protein_1341942..1342092_POSITIVE 244 65 22 50 5 pint:PI0723|3end_conserved_hypothetical_protein_657379..657529_POSITIVE 244 149 101 117 76 pint:PI0639|3end_small_heat_shock_protein_583165..583315_POSITIVE 239 76 37 124 78 pint:PI0522|3end_50S_ribosomal_protein_L19_479449..479599_POSITIVE 238 230 181 92 43 pint:PI0659|3end_hypothetical_protein_603396..603546_POSITIVE 237 237 191 121 75 pint:PI0826|3end_hypothetical_protein_764045..764195_POSITIVE