Origin IGS: ttctacaagtatgcttcatttgttctcctgcagaaaggtctgtaggagaatttttatggaaaatttgctatactagaaaaagctcactgaacgaaggagaaatc .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 gatttctccttcgttcagtgagctttttctagtatagcaaattttccataaaaattctcctacagacctttctgcaggagaacaaatgaagcatacttgtagaa Mask Tandem Repeat Region ================================================ ttctacaagtatgcttcatttgttctcctgcagaaaggtctgtaggagaatttttatggaaaatttgctatactagaaaaagctcactgaacgaaggagaaatc Find is-nt database================================================ Query_seq: SSA_1090:SSA_1091|SSA_1090:SSA_1091:Glucokinase, putative:Thymidylate synthase, putative:->->:1108671..1108774 104 ttctacaagtatgcttcatttgttctcctgcagaaaggtctgtaggagaatttttatggaaaatttgctatactagaaaaagctcactgaacgaaggagaaatc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_1090:SSA_1091|SSA_1090:SSA_1091:Glucokinase, putative:Thymidylate synthase, putative:->->:1108671..1108774 104 ttctacaagtatgcttcatttgttctcctgcagaaaggtctgtaggagaatttttatggaaaatttgctatactagaaaaagctcactgaacgaaggagaaatc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_1090:SSA_1091|SSA_1090:SSA_1091:Glucokinase, putative:Thymidylate synthase, putative:->->:1108671..1108774 104 ttctacaagtatgcttcatttgttctcctgcagaaaggtctgtaggagaatttttatggaaaatttgctatactagaaaaagctcactgaacgaaggagaaatc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ttctacaagtatgcttcatttgttctcctgcagaaaggtctgtaggagaatttttatggaaaatttgctatactagaaaaagctcactgaacgaaggagaaatc Predict ORF larger than 30AA ================================================ ttctacaagtatgcttcatttgttctcctgcagaaaggtctgtaggagaatttttatggaaaatttgctatactagaaaaagctcactgaacgaaggagaaatc 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================================================ ttctacaagtatgcttcatttgttctcctgcagaaaggtctgtaggagaatttttatggaaaatttgctatactagaaaaagctcactgaacgaaggagaaatc Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_1090:SSA_1091|SSA_1090:SSA_1091:Glucokinase, putative:Thymidylate synthase, putative:->->:1108671..1108774 104 ttctacaagtatgcttcatttgttctcctgcagaaaggtctgtaggagaatttttatggaaaatttgctatactagaaaaagctcactgaacgaaggagaaatc Intra-Species Hit: Count: 1 Min: 1 Max: 104 Len: 104 Subject: NC_009009_SSA_1090_SSA_1091|Glucokinase, putative:Thymidylate synthase, putative|POSITIVE:POSITIVE|[1108671,1108774]|104 HSP 1 e-value: 1.0E-52 bit: 206.0 Len: 104 Query Start:1 Query End:104 Subject Strand: POSITIVE Subject Start: 1 Subject End: 104 ttctacaagtatgcttcatttgttctcctgcagaaaggtctgtaggagaatttttatggaaaatttgctatactagaaaaagctcactgaacgaaggagaaatc ttctacaagtatgcttcatttgttctcctgcagaaaggtctgtaggagaatttttatggaaaatttgctatactagaaaaagctcactgaacgaaggagaaatc Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUCUACAAGUAUGCUUCAUUUGUUCUCCUGCAGAAAGGUCUGUAGGAGAAUUUUUAUGGAAAAUUUGCUAUACUAGAAAAAGCUCACUGAACGAAGGAGAAAUC ((((...((((((((((((..(((((((((((((....)))))))))))))....)))))......)).)))))))))....(((.((......)))))..... (-30.80) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAUUUCUCCUUCGUUCAGUGAGCUUUUUCUAGUAUAGCAAAUUUUCCAUAAAAAUUCUCCUACAGACCUUUCUGCAGGAGAACAAAUGAAGCAUACUUGUAGAA ........(((((((..((..(((......)))...))................(((((((.((((....)))).)))))))..)))))))............. (-20.50) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 321 46 12 201 166 NC_009009:SSA_0954|5end_hypothetical_protein_958024..958254_POSITIVE 314 49 7 67 22 NC_009009:SSA_2194|5end_Nicotinamide_mononucleotide_transporter,_putative_2195663..2195893_NEGATIVE 282 49 1 228 185 NC_009009:SSA_1487|5end_Conserved_uncharacterized_protein_1494190..1494420_NEGATIVE 278 60 11 130 83 NC_009009:SSA_1374|5end_Multidrug_ABC_transporter,_ATPase_and_permease_components,_putative_1393095..1393325_NEGATIVE 269 69 28 208 155 NC_009009:SSA_0351|5end_Signal_peptidase_I,_putative_344907..345137_NEGATIVE 265 47 3 216 163 NC_009009:SSA_0528|5end_Conserved_uncharacterized_protein_525283..525513_POSITIVE 256 49 13 228 191 NC_009009:SSA_1431|5end_hypothetical_protein_1438730..1438960_NEGATIVE 252 63 22 195 134 NC_009009:SSA_2207|5end_hypothetical_protein_2207221..2207451_NEGATIVE 251 46 4 63 14 NC_009009:SSA_0677|5end_rRNA_methylase,_putative_659466..659696_POSITIVE 246 49 4 53 9 NC_009009:SSA_1862|5end_hypothetical_protein_1858541..1858771_NEGATIVE 246 70 26 142 100 NC_009009:SSA_1289|5end_hypothetical_protein_1308385..1308615_NEGATIVE 246 59 12 145 97 NC_009009:SSA_0072|5end_ABC_sugar_transporter,_MsmK-like_protein,_putative_75922..76152_POSITIVE 243 47 1 223 176 NC_009009:SSA_0978|5end_hypothetical_protein_983736..983966_POSITIVE 242 60 11 148 108 NC_009009:SSA_0792|5end_hypothetical_protein_774618..774848_POSITIVE 242 47 9 75 36 NC_009009:SSA_0781|5end_Mannose-6-phosphate_isomerase,_putative_765373..765603_POSITIVE 242 60 11 162 122 NC_009009:SSA_0026|5end_Fatty_acid/phospholipid_synthesis_protein_plsX,_putative_30473..30703_POSITIVE 241 45 2 140 103 NC_009009:SSA_1460|5end_Transcriptional_attenuator_LytR,_putative_1468915..1469145_NEGATIVE 241 58 11 68 12 NC_009009:SSA_0537|5end_Propanediol_utilization:dioldehydratase_reactivation,_putative_531957..532187_POSITIVE 240 50 1 187 128 NC_009009:SSA_0806|5end_hypothetical_protein_789270..789500_POSITIVE 239 59 12 225 164 NC_009009:SSA_0085|5end_V-type_sodium_ATPase,_subunit_I,_putative_85750..85980_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 372 50 1 68 13 NC_009009:SSA_1090|3end_Glucokinase,_putative_1108610..1108760_POSITIVE 309 70 21 65 14 NC_009009:SSA_2195|3end_ATPase/kinase,_putative_2195685..2195835_NEGATIVE 278 60 11 140 93 NC_009009:SSA_1375|3end_Multidrug_ABC_transporter,_ATPase_and_permease_components,_putative_1393085..1393235_NEGATIVE 273 49 2 146 100 NC_009009:SSA_0611|3end_HtpX_protease,_putative_600515..600665_POSITIVE 262 79 32 63 15 NC_009009:SSA_0369|3end_NADP-specific_glutamate_dehydrogenase,_putative_359723..359873_NEGATIVE 251 46 4 70 21 NC_009009:SSA_0676|3end_Farnesyl_diphosphate_synthase,_putative_659553..659703_POSITIVE 246 59 12 131 83 NC_009009:SSA_0071|3end_N-acetylmannosamine-6-p_hosphate_2-epimerase_1,_putative_75988..76138_POSITIVE 243 49 1 66 6 NC_009009:SSA_0451|3end_Conserved_uncharacterized_protein_451636..451786_POSITIVE 241 45 2 121 84 NC_009009:SSA_1462|3end_Prephenate_dehydratase,_putative_1468934..1469084_NEGATIVE 240 50 1 69 10 NC_009009:SSA_0805|3end_Collagen-binding_surface_protein,_putative_789232..789382_POSITIVE 237 48 1 133 70 NC_009009:SSA_0202|3end_hypothetical_protein_201402..201552_POSITIVE 235 50 1 68 31 NC_009009:SSA_0348|3end_CAAX_amino_terminal_protease_family,_putative_341114..341264_POSITIVE 231 60 12 73 15 NC_009009:SSA_0768|3end_Ribonucleoside-diphosphate_reductase_2,_beta_subunit,_putative_748136..748286_NEGATIVE 230 69 21 121 73 NC_009009:SSA_1257|3end_hypothetical_protein_1283106..1283256_NEGATIVE 229 60 26 56 15 NC_009009:SSA_0407|3end_ABC-type_multidrug_transport_system_(3-component_subtilin_immunity_exporter),_ATPase_component,_putative_402911..403061_NEGATIVE 229 52 13 47 6 NC_009009:SSA_0186|3end_Competence_protein_ComYC,_putative_190458..190608_POSITIVE 229 47 1 140 97 NC_009009:SSA_0095|3end_Threonine_synthase,_putative_98119..98269_POSITIVE 228 58 12 105 68 NC_009009:SSA_0486|3end_Uroporphyrinogen-III_synthase,_putative_487442..487592_POSITIVE 225 60 18 147 103 NC_009009:SSA_1592|3end_hypothetical_protein_1595576..1595726_NEGATIVE 223 44 12 62 23 NC_009009:SSA_0566|3end_GTP-sensing_transcriptional_pleiotropic_repressor,_putative_560885..561035_POSITIVE