Origin IGS: taggctttaagtagctctgaatatagcgttcaaacagcttgaaaatagcattcaggcagtttgaaagtagcgttcagacagcttgaaaataaaactatcgcctcccta .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tagggaggcgatagttttattttcaagctgtctgaacgctactttcaaactgcctgaatgctattttcaagctgtttgaacgctatattcagagctacttaaagccta Mask Tandem Repeat Region ================================================ taggctttaagtnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnataaaactatcgcctcccta Find is-nt database================================================ Query_seq: PI2137:PI2138|PI2137:PI2138:RNA methylase SpoU family:nicotinate phosphoribosyltransferase:->->:2083868..2083975 108 taggctttaagtagctctgaatatagcgttcaaacagcttgaaaatagcattcaggcagtttgaaagtagcgttcagacagcttgaaaataaaactatcgcctcccta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI2137:PI2138|PI2137:PI2138:RNA methylase SpoU family:nicotinate phosphoribosyltransferase:->->:2083868..2083975 108 taggctttaagtagctctgaatatagcgttcaaacagcttgaaaatagcattcaggcagtttgaaagtagcgttcagacagcttgaaaataaaactatcgcctcccta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI2137:PI2138|PI2137:PI2138:RNA methylase SpoU family:nicotinate phosphoribosyltransferase:->->:2083868..2083975 108 taggctttaagtagctctgaatatagcgttcaaacagcttgaaaatagcattcaggcagtttgaaagtagcgttcagacagcttgaaaataaaactatcgcctcccta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 taggctttaagtagctctgaatatagcgttcaaacagcttgaaaatagcattcaggcagtttgaaagtagcgttcagacagcttgaaaataaaactatcgcctcccta Predict ORF larger than 30AA ================================================ taggctttaagtagctctgaatatagcgttcaaacagcttgaaaatagcattcaggcagtttgaaagtagcgttcagacagcttgaaaataaaactatcgcctcccta 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================================================ taggctttaagtagctctgaatatagcgttcaaacagcttgaaaatagcattcaggcagtttgaaagtagcgttcagacagcttgaaaataaaactatcgcctcccta Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 42 HP_score: -2.0 Tail_Score: -3.07344 Start: 26 End: 68 Full_Region: agctgtctgaacgct actttcaaactgcctgaa tgctatt ttcaagctgtttgaacgc tatattcagagctac .........................actttcaaactgcctgaatgctattttcaagctgtttgaacgc........................................ Find igs database================================================ Query_seq: PI2137:PI2138|PI2137:PI2138:RNA methylase SpoU family:nicotinate phosphoribosyltransferase:->->:2083868..2083975 108 taggctttaagtagctctgaatatagcgttcaaacagcttgaaaatagcattcaggcagtttgaaagtagcgttcagacagcttgaaaataaaactatcgcctcccta Intra-Species Hit: Count: 1 Min: 1 Max: 108 Len: 108 Subject: pint_PI2137_PI2138|RNA methylase SpoU family:nicotinate phosphoribosyltransferase|POSITIVE:POSITIVE|[2083868, 2083975]|108 HSP 1 e-value: 4.0E-55 bit: 214.0 Len: 108 Query Start:1 Query End:108 Subject Strand: POSITIVE Subject Start: 1 Subject End: 108 taggctttaagtagctctgaatatagcgttcaaacagcttgaaaatagcattcaggcagtttgaaagtagcgttcagacagcttgaaaataaaactatcgcctcccta taggctttaagtagctctgaatatagcgttcaaacagcttgaaaatagcattcaggcagtttgaaagtagcgttcagacagcttgaaaataaaactatcgcctcccta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAGGCUUUAAGUAGCUCUGAAUAUAGCGUUCAAACAGCUUGAAAAUAGCAUUCAGGCAGUUUGAAAGUAGCGUUCAGACAGCUUGAAAAUAAAACUAUCGCCUCCCUA .(((((((((((.(.((((((..(.((.(((((((.(((((((.......))))))).))))))).)).)..))))))).)))))))............))))..... (-32.70) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAGGGAGGCGAUAGUUUUAUUUUCAAGCUGUCUGAACGCUACUUUCAAACUGCCUGAAUGCUAUUUUCAAGCUGUUUGAACGCUAUAUUCAGAGCUACUUAAAGCCUA .....((((...(((..........(((..((((((.......(((((((.((.((((.......)))).)).))))))).......))))))))))))....)))). (-25.94) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 289 70 25 222 172 pint:PI1850|5end_prenyltransferase,_UbiA_family_1795967..1796197_POSITIVE 287 77 34 226 169 pint:PI1872|5end_glycosyl_transferase,_group_2_family_protein_1817057..1817287_POSITIVE 286 85 45 78 36 pint:PI2045|5end_hypothetical_protein_1998494..1998724_POSITIVE 283 57 11 159 116 pint:PI2094|5end_hypothetical_protein_2049540..2049770_POSITIVE 266 87 47 85 45 pint:PI0792|5end_conserved_hypothetical_protein_729068..729298_POSITIVE 263 76 31 70 19 pint:PI1474|5end_conserved_hypothetical_protein_1395927..1396157_POSITIVE 253 70 23 220 185 pint:PI1908|5end_transcriptional_regulator,_AraC_family_1852261..1852491_POSITIVE 253 88 48 62 14 pint:PI0072|5end_conserved_hypothetical_protein_70139..70369_POSITIVE 251 68 26 129 80 pint:PI0071|5end_hypothetical_protein_69958..70188_POSITIVE 250 40 2 82 48 pint:PI0110|5end_ABC_transport_system,_ATP-binding_protein_107136..107366_POSITIVE 249 60 13 174 119 pint:PI1806|5end_integral_membrane_transport_protein;_possible_sugar_transport_proteins_1740777..1741007_POSITIVE 249 75 33 37 4 pint:PI1206|5end_ATP-dependent_DNA_helicase,_UvrD/PcrA/Rep_family_1124698..1124928_POSITIVE 244 58 16 57 26 pint:PI0958|5end_G:T/U_mismatch-specific_DNA_glycosylase_889911..890141_POSITIVE 243 73 32 143 102 pint:PI0719|5end_conserved_hypothetical_protein_653043..653273_POSITIVE 243 82 41 160 112 pint:PI0032|5end_hypothetical_protein_36085..36315_POSITIVE 241 78 33 132 67 pint:PI0121|5end_outer_membrane_protein,_ompH_family_112625..112855_POSITIVE 240 81 49 36 1 pint:PI0235|5end_hypothetical_protein_234938..235168_POSITIVE 239 49 1 216 169 pint:PI0058|5end_conserved_hypothetical_protein_56398..56628_POSITIVE 237 39 4 73 44 pint:PI1144|5end_50S_ribosomal_protein_L20_1072138..1072368_POSITIVE 236 87 44 64 21 pint:PI1887|5end_cell_division_protein_1829115..1829345_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 268 50 4 58 1 pint:PI0704|3end_conserved_hypothetical_protein_641364..641514_POSITIVE 266 87 47 143 103 pint:PI0790|3end_hypothetical_protein_729206..729356_POSITIVE 266 87 47 46 6 pint:PI0791|3end_conserved_hypothetical_protein_729109..729259_POSITIVE 262 78 34 100 45 pint:PI0821|3end_conserved_hypothetical_protein_761213..761363_POSITIVE 253 88 48 72 24 pint:PI0071|3end_hypothetical_protein_70229..70379_POSITIVE 250 40 2 49 15 pint:PI0109|3end_hypothetical_protein_107183..107333_POSITIVE 249 59 13 79 27 pint:PI0047|3end_phosphomethylpyrimidine_kinase_46781..46931_POSITIVE 248 78 31 75 28 pint:PI2137|3end_RNA_methylase_SpoU_family_2083807..2083957_POSITIVE 248 73 37 75 22 pint:PI0888|3end_hypothetical_protein_818613..818763_POSITIVE 246 80 53 145 114 pint:PI1907|3end_possible_IS1249-related_transposase_1852027..1852177_POSITIVE 246 80 53 145 114 pint:PI1292|3end_conserved_hypothetical_protein_1207028..1207178_POSITIVE 246 80 53 145 114 pint:PI1268|3end_possible_IS1249-related_transposase_1187983..1188133_POSITIVE 246 80 53 145 114 pint:PI1266|3end_hypothetical_protein_1185937..1186087_POSITIVE 246 80 53 145 114 pint:PI0840|3end_conserved_hypothetical_protein;_possible_transposase_775149..775299_POSITIVE 246 80 53 145 114 pint:PI0709|3end_possible_IS1249-related_transposase_647389..647539_POSITIVE 246 80 53 145 114 pint:PI0153|3end_IS1249-related_transposase_146852..147002_POSITIVE 244 58 16 53 22 pint:PI0957|3end_conserved_hypothetical_protein_889987..890137_POSITIVE 243 73 32 140 99 pint:PI0717|3end_conserved_hypothetical_protein_653120..653270_POSITIVE 243 82 41 126 78 pint:PI0031|3end_peptidylprolyl_isomerase_36131..36281_POSITIVE 241 78 33 124 59 pint:PI0120|3end_glutamate_racemase_112697..112847_POSITIVE