Origin IGS: actctctatttgtatgacgaattagttggggtagaagttacaagaacaagtgtaaaaagaccgcattttaaccttcattaagaacctgaatactctttcctgccgaaagaaacaatagttggcaccttgcgccaatgcacctatgttggagttttta .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 taaaaactccaacataggtgcattggcgcaaggtgccaactattgtttctttcggcaggaaagagtattcaggttcttaatgaaggttaaaatgcggtctttttacacttgttcttgtaacttctaccccaactaattcgtcatacaaatagagagt Mask Tandem Repeat Region ================================================ actctctatttgtatgacgaattagttggggtagaagttacaagaacaagtgtaaaaagaccgcattttaaccttcattaagaacctgaatactctttcctgccgaaagaaacaatagttggcaccttgcgccaatgcacctatgttggagttttta Find is-nt database================================================ Query_seq: PI2026:PI2027|PI2026:PI2027:RNA polymerase sigma-70 factor, ECF subfamily:arginine decarboxylase:->->:1980144..1980300 157 actctctatttgtatgacgaattagttggggtagaagttacaagaacaagtgtaaaaagaccgcattttaaccttcattaagaacctgaatactctttcctgccgaaagaaacaatagttggcaccttgcgccaatgcacctatgttggagttttta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI2026:PI2027|PI2026:PI2027:RNA polymerase sigma-70 factor, ECF subfamily:arginine decarboxylase:->->:1980144..1980300 157 actctctatttgtatgacgaattagttggggtagaagttacaagaacaagtgtaaaaagaccgcattttaaccttcattaagaacctgaatactctttcctgccgaaagaaacaatagttggcaccttgcgccaatgcacctatgttggagttttta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI2026:PI2027|PI2026:PI2027:RNA polymerase sigma-70 factor, ECF subfamily:arginine decarboxylase:->->:1980144..1980300 157 actctctatttgtatgacgaattagttggggtagaagttacaagaacaagtgtaaaaagaccgcattttaaccttcattaagaacctgaatactctttcctgccgaaagaaacaatagttggcaccttgcgccaatgcacctatgttggagttttta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 actctctatttgtatgacgaattagttggggtagaagttacaagaacaagtgtaaaaagaccgcattttaaccttcattaagaacctgaatactctttcctgccgaaagaaacaatagttggcaccttgcgccaatgcacctatgttggagttttta Predict ORF larger than 30AA ================================================ Protein_Len: 40 Strand: - Start: 25 End: 144 ........................ N P Y F N C S C T Y F S R M K V K M L F R F V R E Q R F F C Y N A G Q A L A G M ............. actctctatttgtatgacgaattagttggggtagaagttacaagaacaagtgtaaaaagaccgcattttaaccttcattaagaacctgaatactctttcctgccgaaagaaacaatagttggcaccttgcgccaatgcacctatgttggagttttta 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================================================ actctctatttgtatgacgaattagttggggtagaagttacaagaacaagtgtaaaaagaccgcattttaaccttcattaagaacctgaatactctttcctgccgaaagaaacaatagttggcaccttgcgccaatgcacctatgttggagttttta Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PI2026:PI2027|PI2026:PI2027:RNA polymerase sigma-70 factor, ECF subfamily:arginine decarboxylase:->->:1980144..1980300 157 actctctatttgtatgacgaattagttggggtagaagttacaagaacaagtgtaaaaagaccgcattttaaccttcattaagaacctgaatactctttcctgccgaaagaaacaatagttggcaccttgcgccaatgcacctatgttggagttttta Intra-Species Hit: Count: 1 Min: 1 Max: 157 Len: 157 Subject: pint_PI2026_PI2027|RNA polymerase sigma-70 factor, ECF subfamily:arginine decarboxylase|POSITIVE:POSITIVE|[1980144,1980300]|157 HSP 1 e-value: 4.0E-84 bit: 311.0 Len: 157 Query Start:1 Query End:157 Subject Strand: POSITIVE Subject Start: 1 Subject End: 157 actctctatttgtatgacgaattagttggggtagaagttacaagaacaagtgtaaaaagaccgcattttaaccttcattaagaacctgaatactctttcctgccgaaagaaacaatagttggcaccttgcgccaatgcacctatgttggagttttta actctctatttgtatgacgaattagttggggtagaagttacaagaacaagtgtaaaaagaccgcattttaaccttcattaagaacctgaatactctttcctgccgaaagaaacaatagttggcaccttgcgccaatgcacctatgttggagttttta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ ACUCUCUAUUUGUAUGACGAAUUAGUUGGGGUAGAAGUUACAAGAACAAGUGUAAAAAGACCGCAUUUUAACCUUCAUUAAGAACCUGAAUACUCUUUCCUGCCGAAAGAAACAAUAGUUGGCACCUUGCGCCAAUGCACCUAUGUUGGAGUUUUUA ..................(((((((.((.(((.....(((((........)))))....))).))..))))..)))..((((((((..(....((((((.....)))))).......((((((.......)))))).........)..).))))))) (-27.40) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAAAACUCCAACAUAGGUGCAUUGGCGCAAGGUGCCAACUAUUGUUUCUUUCGGCAGGAAAGAGUAUUCAGGUUCUUAAUGAAGGUUAAAAUGCGGUCUUUUUACACUUGUUCUUGUAACUUCUACCCCAACUAAUUCGUCAUACAAAUAGAGAGU .....(((((....((((.((.(((((((...))))))).......(((((((.....))))))).......)).))))((((.(((((...((.(((....(((((........))))).....))).))..)))))..)))).......).)))) (-26.10) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 350 138 93 188 138 pint:PI0815|5end_hypothetical_protein_754475..754705_POSITIVE 345 138 91 51 2 pint:PI1687|5end_ribosome_recycling_factor_1602307..1602537_POSITIVE 334 150 101 224 179 pint:PI1072|5end_hypothetical_protein_990220..990450_POSITIVE 330 148 101 190 142 pint:PI0609|5end_conserved_hypothetical_protein_556519..556749_POSITIVE 316 150 101 164 108 pint:PI1448|5end_hypothetical_protein_1371579..1371809_POSITIVE 312 149 105 68 16 pint:PI1741|5end_lipid-A-disaccharide_synthase_1662754..1662984_POSITIVE 306 148 101 53 10 pint:PI0531|5end_ABC_transporter,_ATP-binding_protein;_possible_gliding_motility_related_484696..484926_POSITIVE 293 140 95 228 187 pint:PI0092|5end_regulatory_protein_RecX_89080..89310_POSITIVE 292 148 101 67 20 pint:PI0550|5end_possible_glycosyl_hydrolase_500650..500880_POSITIVE 288 150 103 85 39 pint:PI1066|5end_dihydrofolate_reductase_983427..983657_POSITIVE 286 150 103 50 6 pint:PI1313|5end_possible_POT_family_(proton-dependent_oligopeptide_transport_family)_1229710..1229940_POSITIVE 284 139 94 178 137 pint:PI0981|5end_outer_membrane_protein,_TonB_dependent_receptor_906968..907198_POSITIVE 277 148 101 138 86 pint:PI1611|5end_aspartate-semialdehyde_dehydrogenase_1538156..1538386_POSITIVE 276 67 24 90 54 pint:PI1858|5end_conserved_hypothetical_protein_1804400..1804630_POSITIVE 275 129 85 91 46 pint:PI1637|5end_hypothetical_protein_1554500..1554730_POSITIVE 273 137 95 169 125 pint:PI1769|5end_hypothetical_protein_1696507..1696737_POSITIVE 273 149 105 166 114 pint:PI1640|5end_hypothetical_protein_1558062..1558292_POSITIVE 273 138 93 141 77 pint:PI0301|5end_probable_transposase_285672..285902_POSITIVE 270 150 101 124 79 pint:PI0932|5end_conserved_hypothetical_protein;_possible_hemin_receptor_863854..864084_POSITIVE 270 137 92 50 2 pint:PI0676|5end_hypothetical_protein_614576..614806_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 350 138 93 59 9 pint:PI0814|3end_conserved_hypothetical_protein_754426..754576_POSITIVE 334 150 101 150 105 pint:PI1071|3end_DNA_topoisomerase_III_990226..990376_POSITIVE 284 139 94 151 110 pint:PI0980|3end_conserved_hypothetical_protein_907021..907171_POSITIVE 279 149 101 134 77 pint:PI0537|3end_alanyl-tRNA_synthetase_(alanine--tRNA_ligase)_492412..492562_POSITIVE 276 133 101 147 118 pint:PI1370|3end_alkyl_hydroperoxide_reductase,_subunit_F_1292176..1292326_POSITIVE 273 138 93 150 86 pint:PI0300|3end_transposase_285761..285911_POSITIVE 268 139 97 119 71 pint:PI0857|3end_hypothetical_protein_790986..791136_POSITIVE 260 138 98 107 60 pint:PI1013|3end_probable_transcriptional_regulator_934368..934518_POSITIVE 256 147 101 94 58 pint:PI1141|3end_hypothetical_protein_1069713..1069863_POSITIVE 251 128 82 150 110 pint:PI0083|3end_tyrosyl-tRNA_synthetase_84115..84265_POSITIVE 250 148 117 34 3 pint:PI0530|3end_possible_membrane-fusion_protein_484757..484907_POSITIVE 249 130 83 62 18 pint:PI1608|3end_possible_Na+/H+_anti-porter_1536300..1536450_POSITIVE 245 135 91 132 79 pint:PI1660|3end_hypothetical_protein_1575005..1575155_POSITIVE 245 150 102 149 79 pint:PI0768|3end_conserved_hypothetical_protein;_possible_acetyltransferase_704661..704811_POSITIVE 245 150 115 99 61 pint:PI0057|3end_conserved_hypothetical_protein_56512..56662_POSITIVE 244 140 100 58 1 pint:PI2166|3end_hypothetical_protein_2112073..2112223_POSITIVE 242 107 63 124 64 pint:PI1745|3end_conserved_hypothetical_protein_1667417..1667567_POSITIVE 241 142 107 146 100 pint:PI0092|3end_regulatory_protein_RecX_89651..89801_POSITIVE 239 138 94 148 89 pint:PI1712|3end_hypothetical_protein_1627774..1627924_POSITIVE 237 149 101 80 30 pint:PI1466|3end_GTP-binding_protein,_possible_GTP1/OBG_family_1393133..1393283_POSITIVE