Origin IGS: tcactactttgatgttaattaaaaaaccagcaggaacagaaacctgctggtttttttaacttttctatttaatattttaaagcccggctgattatacagctgcaaaaccaaccat .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 atggttggttttgcagctgtataatcagccgggctttaaaatattaaatagaaaagttaaaaaaaccagcaggtttctgttcctgctggttttttaattaacatcaaagtagtga Mask Tandem Repeat Region ================================================ tcactactttgatgttaattaaaaaaccagcaggaacagaaacctgctggtttttttaacttttctatttaatattttaaagcccggctgattatacagctgcaaaaccaaccat Find is-nt database================================================ Query_seq: SSA_2165:SSA_2166|SSA_2165:SSA_2166:ABC-type oligopeptide transporter, periplasmic component, putative:ABC-type multidrug transporter, ATPase and permease components, putative:-><-:2163848..2163962 115 tcactactttgatgttaattaaaaaaccagcaggaacagaaacctgctggtttttttaacttttctatttaatattttaaagcccggctgattatacagctgcaaaaccaaccat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_2165:SSA_2166|SSA_2165:SSA_2166:ABC-type oligopeptide transporter, periplasmic component, putative:ABC-type multidrug transporter, ATPase and permease components, putative:-><-:2163848..2163962 115 tcactactttgatgttaattaaaaaaccagcaggaacagaaacctgctggtttttttaacttttctatttaatattttaaagcccggctgattatacagctgcaaaaccaaccat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_2165:SSA_2166|SSA_2165:SSA_2166:ABC-type oligopeptide transporter, periplasmic component, putative:ABC-type multidrug transporter, ATPase and permease components, putative:-><-:2163848..2163962 115 tcactactttgatgttaattaaaaaaccagcaggaacagaaacctgctggtttttttaacttttctatttaatattttaaagcccggctgattatacagctgcaaaaccaaccat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tcactactttgatgttaattaaaaaaccagcaggaacagaaacctgctggtttttttaacttttctatttaatattttaaagcccggctgattatacagctgcaaaaccaaccat Predict ORF larger than 30AA ================================================ Protein_Len: 30 Strand: - Start: 22 End: 111 ..................... F V L L F L F R S T K K V K R N L I K F G P Q N Y L Q L V M .... tcactactttgatgttaattaaaaaaccagcaggaacagaaacctgctggtttttttaacttttctatttaatattttaaagcccggctgattatacagctgcaaaaccaaccat 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================================================ tcactactttgatgttaattaaaaaaccagcaggaacagaaacctgctggtttttttaacttttctatttaatattttaaagcccggctgattatacagctgcaaaaccaaccat Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 86 HP_score: -7.3 Tail_Score: -4.83032 Start: 18 End: 60 Full_Region: ACTACTTTGATGTTA ATTAAAAAACCAGCAGG AACAGAAA CCTGCTGGTTTTTTTAAC TTTTCTATTTAATAT .................ATTAAAAAACCAGCAGGAACAGAAACCTGCTGGTTTTTTTAAC....................................................... TransTerm Strand: - Conf: 100 HP_score: -9.6 Tail_Score: -5.27477 Start: 27 End: 50 Full_Region: gaaaagttaaaaaaa ccagcagg tttctgtt cctgctgg ttttttaattaacat ..........................ccagcaggtttctgttcctgctgg................................................................. Find igs database================================================ Query_seq: SSA_2165:SSA_2166|SSA_2165:SSA_2166:ABC-type oligopeptide transporter, periplasmic component, putative:ABC-type multidrug transporter, ATPase and permease components, putative:-><-:2163848..2163962 115 tcactactttgatgttaattaaaaaaccagcaggaacagaaacctgctggtttttttaacttttctatttaatattttaaagcccggctgattatacagctgcaaaaccaaccat Intra-Species Hit: Count: 1 Min: 1 Max: 115 Len: 115 Subject: NC_009009_SSA_2165_SSA_2166|ABC-type oligopeptide transporter, periplasmic component, putative:ABC-type multidrug transporter, ATPase and permease components, putative|POSITIVE:NEGATIVE|[2163848,2163962]|115 HSP 1 e-value: 1.0E-46 bit: 186.0 Len: 115 Query Start:1 Query End:115 Subject Strand: POSITIVE Subject Start: 1 Subject End: 115 tcactactttgatgttaattaaaaaaccagcaggaacagaaacctgctggnnnnnnnaacttttctatttaatattttaaagcccggctgattatacagctgcaaaaccaaccat tcactactttgatgttaattaaaaaaccagcaggaacagaaacctgctggtttttttaacttttctatttaatattttaaagcccggctgattatacagctgcaaaaccaaccat Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UCACUACUUUGAUGUUAAUUAAAAAACCAGCAGGAACAGAAACCUGCUGGUUUUUUUAACUUUUCUAUUUAAUAUUUUAAAGCCCGGCUGAUUAUACAGCUGCAAAACCAACCAU ......((((((((((((..((((((((((((((........))))))))))))))............))))))))..))))..((((((......))))))............. (-31.14) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUGGUUGGUUUUGCAGCUGUAUAAUCAGCCGGGCUUUAAAAUAUUAAAUAGAAAAGUUAAAAAAACCAGCAGGUUUCUGUUCCUGCUGGUUUUUUAAUUAACAUCAAAGUAGUGA .(((((((((.(((....))).)))))))))..........(((((....((...((((((((((((((((((........)))))))))))))...))))).))....))))). (-35.70) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 329 66 26 82 44 NC_009009:SSA_1541|5end_Peptidase,_U32_family,_putative_1546600..1546830_NEGATIVE 288 109 75 65 37 NC_009009:SSA_2219|5end_UDP-glucose_4-epimerase,_putative_2220827..2221057_NEGATIVE 276 49 1 177 124 NC_009009:SSA_0441|5end_hypothetical_protein_441481..441711_POSITIVE 269 68 28 91 52 NC_009009:SSA_1261|5end_Ribose-5-phosphate_isomerase_A,_putative_1287654..1287884_NEGATIVE 266 110 61 154 105 NC_009009:SSA_2044|5end_Cysteinyl-tRNA_synthetase,_putative_2048409..2048639_NEGATIVE 266 60 13 52 1 NC_009009:SSA_0143|5end_Conserved_uncharacterized_protein_137465..137695_POSITIVE 258 49 4 42 1 NC_009009:SSA_1408|5end_hypothetical_protein_1421005..1421235_NEGATIVE 250 69 27 152 106 NC_009009:SSA_0188|5end_hypothetical_protein_190798..191028_POSITIVE 249 53 27 165 139 NC_009009:SSA_0389|5end_hypothetical_protein_384172..384402_POSITIVE 248 102 61 138 103 NC_009009:SSA_0350|5end_Helicase,_putative_344218..344448_NEGATIVE 245 90 44 160 115 NC_009009:SSA_0488|5end_Glutamate-1-semialdehyde_2,1-aminotransferase,_putative_488364..488594_POSITIVE 244 64 24 150 100 NC_009009:SSA_1068|5end_Transcriptional_regulator,_LysR_family_(capsular_polysaccharide_biosynthesis_regulation),_putative_1087355..1087585_POSITIVE 244 110 73 56 8 NC_009009:SSA_0069|5end_Hypothetical_protein,_possibly_membrane-associated_73037..73267_POSITIVE 243 66 27 67 4 NC_009009:SSA_2303|5end_hypothetical_protein_2305177..2305407_NEGATIVE 242 110 62 66 26 NC_009009:SSA_1413|5end_GufA-like_protein,_putative_1424919..1425149_NEGATIVE 242 69 26 107 50 NC_009009:SSA_0005|5end_GTP-binding_protein,_putative_3821..4051_POSITIVE 239 102 61 147 97 NC_009009:SSA_2253|5end_3-Methyladenine_DNA_glycosylase_I,_constitutive,_putative_2249424..2249654_NEGATIVE 239 70 28 45 4 NC_009009:SSA_0827|5end_Conserved_uncharacterized_cytosolic_protein,_putative_806033..806263_POSITIVE 238 110 61 218 162 NC_009009:SSA_0591|5end_Conserved_uncharacterized_protein_582769..582999_POSITIVE 233 110 83 65 26 NC_009009:SSA_0373|5end_Dihydroorotate_dehydrogenase,_putative_362062..362292_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 372 60 14 77 31 NC_009009:SSA_2165|3end_ABC-type_oligopeptide_transporter,_periplasmic_component,_putative_2163787..2163937_POSITIVE 342 57 11 80 36 NC_009009:SSA_2135|3end_Transcriptional_repressor,_DeoR_family_(possibly_truncated),_putative_2137474..2137624_POSITIVE 288 109 75 58 30 NC_009009:SSA_2220|3end_Galactosyltransferase,_putative_2220834..2220984_NEGATIVE 281 56 21 75 40 NC_009009:SSA_2136|3end_50S_ribosomal_protein_L34,_putative_2137507..2137657_NEGATIVE 276 49 1 81 28 NC_009009:SSA_0440|3end_30S_ribosomal_protein_S18,_putative_441465..441615_POSITIVE 267 67 22 93 44 NC_009009:SSA_0415|3end_Permease,_putative_411730..411880_POSITIVE 266 110 61 136 87 NC_009009:SSA_2045|3end_Reductase,_putative_2048427..2048577_NEGATIVE 252 90 43 145 86 NC_009009:SSA_0705|3end_hypothetical_protein_690552..690702_NEGATIVE 250 69 27 126 80 NC_009009:SSA_0187|3end_Competence_protein_ComYD,_putative_190852..191002_POSITIVE 248 102 61 78 43 NC_009009:SSA_0351|3end_Signal_peptidase_I,_putative_344278..344428_NEGATIVE 245 90 44 116 71 NC_009009:SSA_0487|3end_Delta-aminolevulinic_acid_dehydratase,_putative_488400..488550_POSITIVE 244 64 24 60 10 NC_009009:SSA_1067|3end_hypothetical_protein_1087345..1087495_POSITIVE 243 110 61 140 81 NC_009009:SSA_2346|3end_3-oxoacyl-[acyl-carrier-protein]_synthase_III,_putative_2347602..2347752_NEGATIVE 242 110 62 43 3 NC_009009:SSA_1414|3end_hypothetical_protein_1424942..1425092_NEGATIVE 240 90 46 115 66 NC_009009:SSA_0827|3end_Conserved_uncharacterized_cytosolic_protein,_putative_806952..807102_POSITIVE 239 102 61 137 87 NC_009009:SSA_2254|3end_Holliday_junction_DNA_helicase_ruvA,_putative_2249434..2249584_NEGATIVE 238 64 21 100 65 NC_009009:SSA_0861|3end_hypothetical_protein_851742..851892_NEGATIVE 236 68 30 74 31 NC_009009:SSA_1501|3end_Cytidylate_kinase,_putative_1505095..1505245_NEGATIVE 232 110 80 148 116 NC_009009:SSA_0956|3end_surface_protein_D_965418..965568_POSITIVE 230 70 26 101 52 NC_009009:SSA_1190|3end_Conserved_uncharacterized_protein_1217799..1217949_NEGATIVE