Origin IGS: agccaaggcctgtagttttgtcaataaatgaccatcctctccttctttaccggattttaatggacgtccaagctcgtttttgataactaaattttcttcattgtagaaaaca .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tgttttctacaatgaagaaaatttagttatcaaaaacgagcttggacgtccattaaaatccggtaaagaaggagaggatggtcatttattgacaaaactacaggccttggct Mask Tandem Repeat Region ================================================ agccaaggcctgtagttttgtcaataaatgaccatcctctccttctttaccggattttaatggacgtccaagctcgtttttgataactaaattttcttcattgtagaaaaca Find is-nt database================================================ Query_seq: SSA_2039:SSA_2040|SSA_2039:SSA_2040:Aminoacid specific permease, putative:ABC transporter ATP-binding protein-multiple sugar transport, putative:<-<-:2044546..2044657 112 agccaaggcctgtagttttgtcaataaatgaccatcctctccttctttaccggattttaatggacgtccaagctcgtttttgataactaaattttcttcattgtagaaaaca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_2039:SSA_2040|SSA_2039:SSA_2040:Aminoacid specific permease, putative:ABC transporter ATP-binding protein-multiple sugar transport, putative:<-<-:2044546..2044657 112 agccaaggcctgtagttttgtcaataaatgaccatcctctccttctttaccggattttaatggacgtccaagctcgtttttgataactaaattttcttcattgtagaaaaca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_2039:SSA_2040|SSA_2039:SSA_2040:Aminoacid specific permease, putative:ABC transporter ATP-binding protein-multiple sugar transport, putative:<-<-:2044546..2044657 112 agccaaggcctgtagttttgtcaataaatgaccatcctctccttctttaccggattttaatggacgtccaagctcgtttttgataactaaattttcttcattgtagaaaaca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 agccaaggcctgtagttttgtcaataaatgaccatcctctccttctttaccggattttaatggacgtccaagctcgtttttgataactaaattttcttcattgtagaaaaca Predict ORF larger than 30AA ================================================ agccaaggcctgtagttttgtcaataaatgaccatcctctccttctttaccggattttaatggacgtccaagctcgtttttgataactaaattttcttcattgtagaaaaca 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================================================ agccaaggcctgtagttttgtcaataaatgaccatcctctccttctttaccggattttaatggacgtccaagctcgtttttgataactaaattttcttcattgtagaaaaca Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_2039:SSA_2040|SSA_2039:SSA_2040:Aminoacid specific permease, putative:ABC transporter ATP-binding protein-multiple sugar transport, putative:<-<-:2044546..2044657 112 agccaaggcctgtagttttgtcaataaatgaccatcctctccttctttaccggattttaatggacgtccaagctcgtttttgataactaaattttcttcattgtagaaaaca Intra-Species Hit: Count: 1 Min: 1 Max: 112 Len: 112 Subject: NC_009009_SSA_2039_SSA_2040|Aminoacid specific permease, putative:ABC transporter ATP-binding protein-multiple sugar transport, putative|NEGATIVE:NEGATIVE|[2044546,2044657]|112 HSP 1 e-value: 2.0E-57 bit: 222.0 Len: 112 Query Start:1 Query End:112 Subject Strand: POSITIVE Subject Start: 1 Subject End: 112 agccaaggcctgtagttttgtcaataaatgaccatcctctccttctttaccggattttaatggacgtccaagctcgtttttgataactaaattttcttcattgtagaaaaca agccaaggcctgtagttttgtcaataaatgaccatcctctccttctttaccggattttaatggacgtccaagctcgtttttgataactaaattttcttcattgtagaaaaca Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGCCAAGGCCUGUAGUUUUGUCAAUAAAUGACCAUCCUCUCCUUCUUUACCGGAUUUUAAUGGACGUCCAAGCUCGUUUUUGAUAACUAAAUUUUCUUCAUUGUAGAAAACA .((....))...((((..((((((.((((((.(......(((.........)))......(((....))).).))))))))))))))))..((((((.......)))))).. (-17.70) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGUUUUCUACAAUGAAGAAAAUUUAGUUAUCAAAAACGAGCUUGGACGUCCAUUAAAAUCCGGUAAAGAAGGAGAGGAUGGUCAUUUAUUGACAAAACUACAGGCCUUGGCU .(((((((.......)))))))..............((((((((..(((((.......(((.........)))..)))))((((.....)))).......)))).))))... (-21.10) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 918 80 31 171 122 NC_009009:SSA_2039|5end_Aminoacid_specific_permease,_putative_2044455..2044685_NEGATIVE 321 75 32 142 88 NC_009009:SSA_0981|5end_3-isopropylmalate_dehydratase_small_subunit,_putative_985396..985626_POSITIVE 296 47 2 69 17 NC_009009:SSA_1406|5end_Histone_acetyltransferase_HPA2,_putative_1420315..1420545_NEGATIVE 293 44 2 164 126 NC_009009:SSA_0486|5end_Uroporphyrinogen-III_synthase,_putative_486637..486867_POSITIVE 286 78 31 145 87 NC_009009:SSA_0752|5end_hypothetical_protein_734171..734401_POSITIVE 282 54 11 109 74 NC_009009:SSA_2105|5end_hypothetical_protein_2107802..2108032_NEGATIVE 282 42 3 152 104 NC_009009:SSA_1736|5end_L-cysteine_desulfhydrase,_putative_1722619..1722849_NEGATIVE 281 53 16 115 72 NC_009009:SSA_0135|5end_Multiple_antibiotic_resistance_operon_transcriptional_repressor_(MarR),_putative_130574..130804_POSITIVE 279 79 31 79 23 NC_009009:SSA_2141|5end_Argininosuccinate_lyase,_putative_2142201..2142431_NEGATIVE 279 45 1 40 5 NC_009009:SSA_1459|5end_RNA_methyltransferase,_putative_1467481..1467711_NEGATIVE 278 46 6 175 127 NC_009009:SSA_1779|5end_Segregation_and_condensation_protein_A,_putative_1766414..1766644_NEGATIVE 278 43 2 60 16 NC_009009:SSA_1092|5end_Dihydrofolate_reductase,_putative_1109599..1109829_POSITIVE 277 86 41 166 122 NC_009009:SSA_2356|5end_Replicative_DNA_helicase,_putative_2357958..2358188_NEGATIVE 277 47 1 169 119 NC_009009:SSA_1451|5end_Exonuclease_RexA,_putative_1456418..1456648_NEGATIVE 277 80 35 72 32 NC_009009:SSA_0539|5end_PduO_protein,_putative_534233..534463_POSITIVE 271 49 2 112 63 NC_009009:SSA_1045|5end_hypothetical_protein_1060841..1061071_POSITIVE 266 49 2 108 57 NC_009009:SSA_0529|5end_Ethanolamine_utilization_protein,_putative_525945..526175_POSITIVE 261 80 32 51 1 NC_009009:SSA_0986|5end_Choline_transporter,_putative_988273..988503_POSITIVE 260 70 27 49 14 NC_009009:SSA_1809|5end_PTS_system_glucose-specific_EIIC_BA_component_(EIICBA-Glc)_(EII-_Glc/EIII-Glc),_putative_1794419..1794649_NEGATIVE 260 49 9 121 79 NC_009009:SSA_1327|5end_hypothetical_protein_1344301..1344531_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 321 75 32 132 78 NC_009009:SSA_0980|3end_3-isopropylmalate_dehydratase_large_subunit,_putative_985466..985616_POSITIVE 286 78 31 143 85 NC_009009:SSA_0751|3end_Oligoendopeptidase_F,_putative_734249..734399_POSITIVE 282 42 3 150 102 NC_009009:SSA_1737|3end_Cystathionine_gamma-synthase,_putative_1722621..1722771_NEGATIVE 279 79 31 64 8 NC_009009:SSA_2142|3end_Argininosuccinate_synthase,_putative_2142216..2142366_NEGATIVE 277 86 41 139 95 NC_009009:SSA_2357|3end_50S_ribosomal_protein_L9,_putative_2357985..2358135_NEGATIVE 276 82 41 151 107 NC_009009:SSA_0987|3end_ABC-type_choline_transporter,_membrane-spanning_permease,_putative_990594..990744_POSITIVE 266 49 2 93 42 NC_009009:SSA_0528|3end_Conserved_uncharacterized_protein_526010..526160_POSITIVE 264 88 43 139 98 NC_009009:SSA_0626|3end_hypothetical_protein_617212..617362_POSITIVE 260 49 9 80 38 NC_009009:SSA_1328|3end_hypothetical_protein_1344342..1344492_NEGATIVE 259 47 1 67 19 NC_009009:SSA_1448|3end_ATP_phosphoribosyltransferase_regulatory_subunit,_putative_1449828..1449978_NEGATIVE 258 78 40 79 39 NC_009009:SSA_0172|3end_Transcriptional_regulator,_XRE_family,_putative_169672..169822_POSITIVE 254 69 33 125 82 NC_009009:SSA_2219|3end_UDP-glucose_4-epimerase,_putative_2219967..2220117_NEGATIVE 252 73 32 70 13 NC_009009:SSA_1864|3end_Nicotinate_phosphoribosyltransferase_(NAPRTase),_subgroup_A,_putative_1859410..1859560_NEGATIVE 250 78 39 58 27 NC_009009:SSA_1899|3end_hypothetical_protein_1894443..1894593_NEGATIVE 250 58 11 104 57 NC_009009:SSA_1257|3end_hypothetical_protein_1283106..1283256_NEGATIVE 249 75 35 144 84 NC_009009:SSA_1374|3end_Multidrug_ABC_transporter,_ATPase_and_permease_components,_putative_1391359..1391509_NEGATIVE 247 45 3 135 79 NC_009009:SSA_0963|3end_Peptidoglycan_N-acetylglucosamine_deacetylase_A,_putative_972890..973040_POSITIVE 246 49 1 87 21 NC_009009:SSA_1414|3end_hypothetical_protein_1424942..1425092_NEGATIVE 245 78 32 133 84 NC_009009:SSA_1558|3end_Hydrolase,_HAD_superfamily_1560044..1560194_NEGATIVE 243 74 33 113 79 NC_009009:SSA_2082|3end_Carbohydrate_kinase,_FGGY_family,_putative_2085351..2085501_NEGATIVE