Origin IGS: aattttaatccttttaaaataatacttaacctcacggtcgaaacttaactatacttatatttatgttttgtttgtatttctgttatatatataataaggtgtgatatgttgtcgtttcgccttatatta .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 taatataaggcgaaacgacaacatatcacaccttattatatatataacagaaatacaaacaaaacataaatataagtatagttaagtttcgaccgtgaggttaagtattattttaaaaggattaaaatt Mask Tandem Repeat Region ================================================ aattttaatccttttaaaataatacttaacctcacggtcgaaacttaactatacttatatttatgttttgtttgtatttctgttatatatataataaggtgtgatatgttgtcgtttcgccttatatta Find is-nt database================================================ Query_seq: PI0590:PI0591|PI0590:PI0591:ribosomal large subunit pseudouridine synthase B:adenylosuccinate lyase:->->:538606..538734 129 aattttaatccttttaaaataatacttaacctcacggtcgaaacttaactatacttatatttatgttttgtttgtatttctgttatatatataataaggtgtgatatgttgtcgtttcgccttatatta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI0590:PI0591|PI0590:PI0591:ribosomal large subunit pseudouridine synthase B:adenylosuccinate lyase:->->:538606..538734 129 aattttaatccttttaaaataatacttaacctcacggtcgaaacttaactatacttatatttatgttttgtttgtatttctgttatatatataataaggtgtgatatgttgtcgtttcgccttatatta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI0590:PI0591|PI0590:PI0591:ribosomal large subunit pseudouridine synthase B:adenylosuccinate lyase:->->:538606..538734 129 aattttaatccttttaaaataatacttaacctcacggtcgaaacttaactatacttatatttatgttttgtttgtatttctgttatatatataataaggtgtgatatgttgtcgtttcgccttatatta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aattttaatccttttaaaataatacttaacctcacggtcgaaacttaactatacttatatttatgttttgtttgtatttctgttatatatataataaggtgtgatatgttgtcgtttcgccttatatta Predict ORF larger than 30AA ================================================ aattttaatccttttaaaataatacttaacctcacggtcgaaacttaactatacttatatttatgttttgtttgtatttctgttatatatataataaggtgtgatatgttgtcgtttcgccttatatta 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================================================ aattttaatccttttaaaataatacttaacctcacggtcgaaacttaactatacttatatttatgttttgtttgtatttctgttatatatataataaggtgtgatatgttgtcgtttcgccttatatta Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PI0590:PI0591|PI0590:PI0591:ribosomal large subunit pseudouridine synthase B:adenylosuccinate lyase:->->:538606..538734 129 aattttaatccttttaaaataatacttaacctcacggtcgaaacttaactatacttatatttatgttttgtttgtatttctgttatatatataataaggtgtgatatgttgtcgtttcgccttatatta Intra-Species Hit: Count: 1 Min: 1 Max: 129 Len: 129 Subject: pint_PI0590_PI0591|ribosomal large subunit pseudouridine synthase B:adenylosuccinate lyase|POSITIVE:POSITIVE|[538606,538734]|129 HSP 1 e-value: 2.0E-67 bit: 256.0 Len: 129 Query Start:1 Query End:129 Subject Strand: POSITIVE Subject Start: 1 Subject End: 129 aattttaatccttttaaaataatacttaacctcacggtcgaaacttaactatacttatatttatgttttgtttgtatttctgttatatatataataaggtgtgatatgttgtcgtttcgccttatatta aattttaatccttttaaaataatacttaacctcacggtcgaaacttaactatacttatatttatgttttgtttgtatttctgttatatatataataaggtgtgatatgttgtcgtttcgccttatatta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAUUUUAAUCCUUUUAAAAUAAUACUUAACCUCACGGUCGAAACUUAACUAUACUUAUAUUUAUGUUUUGUUUGUAUUUCUGUUAUAUAUAUAAUAAGGUGUGAUAUGUUGUCGUUUCGCCUUAUAUUA .(((((((.....)))))))...............((.((((((.((((.(((.((((((((.((((.(((.((((.......)))).))).)))))))))))))))))))..))))))))........ (-20.70) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAUAUAAGGCGAAACGACAACAUAUCACACCUUAUUAUAUAUAUAACAGAAAUACAAACAAAACAUAAAUAUAAGUAUAGUUAAGUUUCGACCGUGAGGUUAAGUAUUAUUUUAAAAGGAUUAAAAUU ....((((((.(................).))))))...............(((((.....((((.(((.(((....))).))).)))).((((....))))..))))).................... (-13.69) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 247 118 76 218 155 pint:PI0798|5end_malonyl_CoA-acyl_carrier_protein_transacylase_736011..736241_POSITIVE 246 119 71 152 98 pint:PI0566|5end_enoyl-[acyl-carrier-protein]_reductase_511832..512062_POSITIVE 233 120 71 217 175 pint:PI0975|5end_glycine_dehydrogenase_[decarboxylating]_subunit_2_900798..901028_POSITIVE 230 120 71 145 95 pint:PI1672|5end_conserved_hypothetical_protein;_possible_DNA-binding_protein,_histone-like_family_1587027..1587257_POSITIVE 229 120 74 60 12 pint:PI0221|5end_DNA_methylase,_site-specific_DNA-methyltransferase_(adenine-specific)_212356..212586_POSITIVE 228 120 80 156 110 pint:PI0753|5end_hypothetical_protein_683391..683621_POSITIVE 222 104 69 136 102 pint:PI0067|5end_hypothetical_protein_66273..66503_POSITIVE 220 60 15 152 106 pint:PI0076|5end_conserved_hypothetical_protein_75645..75875_POSITIVE 215 119 92 194 164 pint:PI0776|5end_predicted_TPR-repeat-containing_protein_712077..712307_POSITIVE 198 41 30 13 2 pint:PI1651|5end_hypothetical_protein_1563845..1564075_POSITIVE 196 98 57 149 110 pint:PI1057|5end_hypothetical_protein_977286..977516_POSITIVE 195 120 76 157 105 pint:PI0033|5end_peptidylprolyl_isomerase_36215..36445_POSITIVE 194 46 10 139 102 pint:PI1913|5end_conserved_hypothetical_protein_1857104..1857334_POSITIVE 194 120 72 161 112 pint:PI1340|5end_hypothetical_protein_1256568..1256798_POSITIVE 194 84 41 149 113 pint:PI0777|5end_predicted_TPR-repeat-containing_protein_713285..713515_POSITIVE 191 120 86 193 160 pint:PI1385|5end_3-deoxy-d-manno-octulosonic_acid_8-phosphate_synthase_(DAHP_synthase,_Class_I)_1306224..1306454_POSITIVE 191 75 35 41 1 pint:PI0040|5end_conserved_hypothetical_protein_(possible_integral_membrane_protein)_41010..41240_POSITIVE 189 79 36 76 29 pint:PI1234|5end_valyl-tRNA_synthetase_(valine--tRNA_ligase)_1154359..1154589_POSITIVE 189 120 100 113 92 pint:PI0179|5end_hypothetical_protein_171757..171987_POSITIVE 188 72 37 40 2 pint:PI2032|5end_RNA_polymerase_sigma_factor,_ECF_subfamily_1986544..1986774_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 272 118 77 102 55 pint:PI0658|3end_conserved_hypothetical_protein_603043..603193_POSITIVE 230 120 71 64 14 pint:PI1670|3end_hypothetical_protein_1587026..1587176_POSITIVE 227 119 80 100 64 pint:PI1693|3end_possible_RmuC_domain_protein_1609558..1609708_POSITIVE 214 43 7 96 65 pint:PI0082|3end_conserved_hypothetical_protein_(possible_phosphoglycerol_transferase)_82711..82861_POSITIVE 212 120 80 146 106 pint:PI0752|3end_conserved_hypothetical_protein_683467..683617_POSITIVE 206 75 34 95 47 pint:PI0601|3end_hypothetical_protein_549020..549170_POSITIVE 204 110 65 68 28 pint:PI1930|3end_conserved_hypothetical_protein;_possible_ankyrin_repeat_protein_(eukaryotic-like)_1875054..1875204_POSITIVE 195 120 76 116 64 pint:PI0032|3end_hypothetical_protein_36254..36404_POSITIVE 194 46 10 121 84 pint:PI1912|3end_possible_DNA_repair_protein_1857166..1857316_POSITIVE 194 120 72 107 58 pint:PI1338|3end_phosphoserine_phosphatase_1256594..1256744_POSITIVE 194 84 41 107 71 pint:PI0776|3end_predicted_TPR-repeat-containing_protein_713323..713473_POSITIVE 194 70 22 98 49 pint:PI0292|3end_ISPg-3_transposase_fragment_275904..276054_POSITIVE 192 120 81 139 105 pint:PI1392|3end_hypothetical_protein_1312748..1312898_POSITIVE 191 120 86 63 30 pint:PI1384|3end_conserved_hypothetical_protein_1306174..1306324_POSITIVE 190 120 80 150 116 pint:PI0023|3end_internalin-related_protein_28070..28220_POSITIVE 188 120 79 46 5 pint:PI0084|3end_conserved_hypothetical_protein_84520..84670_POSITIVE 185 120 98 150 127 pint:PI1927|3end_hypothetical_protein_1872046..1872196_POSITIVE 185 108 61 54 2 pint:PI0971|3end_glycine_cleavage_system_T_protein_(aminomethyltransferase)_898931..899081_POSITIVE 185 69 25 75 30 pint:PI0507|3end_transcriptional_regulator_466547..466697_POSITIVE 183 103 66 101 67 pint:PI1946|3end_hypothetical_protein_1903020..1903170_POSITIVE