Origin IGS: aaactatcaatttgccgctgcaaaattacggtttaaatcttatacagcaaattggttgcgttgcaattacttgtaaaaataataaacaaaagtaaacaggcaacgcacta .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tagtgcgttgcctgtttacttttgtttattatttttacaagtaattgcaacgcaaccaatttgctgtataagatttaaaccgtaattttgcagcggcaaattgatagttt Mask Tandem Repeat Region ================================================ aaactatcaatttgccgctgcaaaattacggtttaaatcttatacagcaaattggttgcgttgcaattacttgtaaaaataataaacaaaagtaaacaggcaacgcacta Find is-nt database================================================ Query_seq: PI2084:PI2085|PI2084:PI2085:hypothetical protein:conserved hypothetical protein:->->:2041130..2041239 110 aaactatcaatttgccgctgcaaaattacggtttaaatcttatacagcaaattggttgcgttgcaattacttgtaaaaataataaacaaaagtaaacaggcaacgcacta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI2084:PI2085|PI2084:PI2085:hypothetical protein:conserved hypothetical protein:->->:2041130..2041239 110 aaactatcaatttgccgctgcaaaattacggtttaaatcttatacagcaaattggttgcgttgcaattacttgtaaaaataataaacaaaagtaaacaggcaacgcacta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI2084:PI2085|PI2084:PI2085:hypothetical protein:conserved hypothetical protein:->->:2041130..2041239 110 aaactatcaatttgccgctgcaaaattacggtttaaatcttatacagcaaattggttgcgttgcaattacttgtaaaaataataaacaaaagtaaacaggcaacgcacta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aaactatcaatttgccgctgcaaaattacggtttaaatcttatacagcaaattggttgcgttgcaattacttgtaaaaataataaacaaaagtaaacaggcaacgcacta Predict ORF larger than 30AA ================================================ aaactatcaatttgccgctgcaaaattacggtttaaatcttatacagcaaattggttgcgttgcaattacttgtaaaaataataaacaaaagtaaacaggcaacgcacta 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================================================ aaactatcaatttgccgctgcaaaattacggtttaaatcttatacagcaaattggttgcgttgcaattacttgtaaaaataataaacaaaagtaaacaggcaacgcacta Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 44 HP_score: -3.4 Tail_Score: -2.9348 Start: 47 End: 59 Full_Region: acaagtaattgcaac gcaa ccaat ttgc tgtataagatttaaa ..............................................gcaaccaatttgc................................................... Find igs database================================================ Query_seq: PI2084:PI2085|PI2084:PI2085:hypothetical protein:conserved hypothetical protein:->->:2041130..2041239 110 aaactatcaatttgccgctgcaaaattacggtttaaatcttatacagcaaattggttgcgttgcaattacttgtaaaaataataaacaaaagtaaacaggcaacgcacta Intra-Species Hit: Count: 1 Min: 1 Max: 110 Len: 110 Subject: pint_PI2084_PI2085|hypothetical protein:conserved hypothetical protein|POSITIVE:POSITIVE|[2041130,2041239]|110 HSP 1 e-value: 3.0E-56 bit: 218.0 Len: 110 Query Start:1 Query End:110 Subject Strand: POSITIVE Subject Start: 1 Subject End: 110 aaactatcaatttgccgctgcaaaattacggtttaaatcttatacagcaaattggttgcgttgcaattacttgtaaaaataataaacaaaagtaaacaggcaacgcacta aaactatcaatttgccgctgcaaaattacggtttaaatcttatacagcaaattggttgcgttgcaattacttgtaaaaataataaacaaaagtaaacaggcaacgcacta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAACUAUCAAUUUGCCGCUGCAAAAUUACGGUUUAAAUCUUAUACAGCAAAUUGGUUGCGUUGCAAUUACUUGUAAAAAUAAUAAACAAAAGUAAACAGGCAACGCACUA .....((((((((((.((((........))))..............))))))))))((((((((..((((((.................))))))....))))))))... (-24.49) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAGUGCGUUGCCUGUUUACUUUUGUUUAUUAUUUUUACAAGUAAUUGCAACGCAACCAAUUUGCUGUAUAAGAUUUAAACCGUAAUUUUGCAGCGGCAAAUUGAUAGUUU ...((((((((....(((((..(((..(.....)..))))))))..))))))))..(((((((((((.(((((((........)))))))..)))))))))))....... (-31.60) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 310 58 17 201 153 pint:PI0435|5end_30S_ribosomal_protein_S21_406997..407227_POSITIVE 279 60 17 217 178 pint:PI0050|5end_conserved_hypothetical_protein_51539..51769_POSITIVE 258 53 11 101 66 pint:PI2125|5end_D-tyrosyl-tRNA(Tyr)_deacylase_2074450..2074680_POSITIVE 258 69 29 212 167 pint:PI0829|5end_nucleotidyl_transferase_family;_possible_mannose-1-phosphate_guanyltransferase_765665..765895_POSITIVE 244 60 13 184 138 pint:PI0636|5end_hypothetical_protein_582032..582262_POSITIVE 242 33 9 35 9 pint:PI1928|5end_conserved_hypothetical_protein_1871996..1872226_POSITIVE 241 59 16 61 2 pint:PI0113|5end_arginyl-tRNA_synthetase_108371..108601_POSITIVE 233 59 11 188 148 pint:PI1822|5end_ABC_transporter,_ATP-binding_/_permease_1761452..1761682_POSITIVE 229 60 11 88 26 pint:PI1583|5end_phosphoribosylaminoimidazolecarboxamide_formyltransferase_(AICAR)/IMP_cyclohydrolase_(ATIC)_1510530..1510760_POSITIVE 229 64 21 58 14 pint:PI1419|5end_conserved_hypothetical_protein;_membrane_protease_subunits,_stomatin/prohibitin_homologs_1339136..1339366_POSITIVE 227 60 13 180 121 pint:PI0732|5end_conserved_hypothetical_protein_663598..663828_POSITIVE 227 59 12 171 120 pint:PI0088|5end_S-adenosylmethionine_synthetase_86663..86893_POSITIVE 224 59 11 84 31 pint:PI1694|5end_hypothetical_protein_1609717..1609947_POSITIVE 224 50 7 152 116 pint:PI1627|5end_hypothetical_protein_1550445..1550675_POSITIVE 223 60 13 85 19 pint:PI1496|5end_nucleoside_phosphorylase_1417116..1417346_POSITIVE 222 60 13 99 44 pint:PI1619|5end_two-component_system_response_regulator_1543210..1543440_POSITIVE 221 64 30 174 142 pint:PI1386|5end_sugar_phosphate_isomerase_1307004..1307234_POSITIVE 221 59 13 181 140 pint:PI1069|5end_hypothetical_protein_988067..988297_POSITIVE 219 59 13 85 49 pint:PI0729|5end_integrase_661428..661658_POSITIVE 213 58 11 128 72 pint:PI1879|5end_uracil_phosphoribosyltransferase_1820671..1820901_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 280 48 5 131 84 pint:PI1450|3end_hypothetical_protein_1372891..1373041_POSITIVE 261 60 12 103 46 pint:PI0005|3end_hypothetical_protein_7450..7600_POSITIVE 258 53 11 67 32 pint:PI2124|3end_excinuclease_ABC,_subunit_C_2074496..2074646_POSITIVE 251 49 3 44 2 pint:PI0454|3end_hypothetical_protein_426963..427113_POSITIVE 249 60 13 118 62 pint:PI1623|3end_hypothetical_protein_1549261..1549411_POSITIVE 249 60 13 148 92 pint:PI0331|3end_hypothetical_protein_312575..312725_POSITIVE 249 60 13 118 62 pint:PI0330|3end_hypothetical_protein_312545..312695_POSITIVE 243 107 89 58 40 pint:PI0199|3end_phosphate_acetyltransferase_190923..191073_POSITIVE 241 59 16 137 78 pint:PI0114|3end_hypothetical_protein_108527..108677_POSITIVE 229 50 11 128 87 pint:PI0023|3end_internalin-related_protein_28070..28220_POSITIVE 228 60 19 135 89 pint:PI0538|3end_transcriptional_regulator_492925..493075_POSITIVE 224 50 7 149 113 pint:PI1626|3end_hypothetical_protein_1550522..1550672_POSITIVE 223 60 12 139 97 pint:PI0345|3end_conserved_hypothetical_protein_320809..320959_POSITIVE 221 64 30 149 117 pint:PI1385|3end_3-deoxy-d-manno-octulosonic_acid_8-phosphate_synthase_(DAHP_synthase,_Class_I)_1307059..1307209_POSITIVE 221 59 29 147 117 pint:PI0828|3end_GMP_synthase_(glutamine_amidotransferase)_765695..765845_POSITIVE 219 59 13 85 49 pint:PI0728|3end_integrase_661508..661658_POSITIVE 215 60 13 140 92 pint:PI1013|3end_probable_transcriptional_regulator_934368..934518_POSITIVE 214 64 28 43 5 pint:PI1418|3end_UDP-N-acetylglucosamine_2-epimerase_1339201..1339351_POSITIVE 212 59 11 115 73 pint:PI1141|3end_hypothetical_protein_1069713..1069863_POSITIVE 212 59 11 56 14 pint:PI0054|3end_hypothetical_protein_54829..54979_POSITIVE