Origin IGS: cgattttgataagtgtatgcgaaaacgtccaacctctgcaaaagttctgcttgaatcatactttaaacatgcctttttacagcaaatttgatagaatagagttactaatacaaaggataaaagg .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 ccttttatcctttgtattagtaactctattctatcaaatttgctgtaaaaaggcatgtttaaagtatgattcaagcagaacttttgcagaggttggacgttttcgcatacacttatcaaaatcg Mask Tandem Repeat Region ================================================ cgattttgataagtgtatgcgaaaacgtccaacctctgcaaaagttctgcttgaatcatactttaaacatgcctttttacagcaaatttgatagaatagagttactaatacaaaggataaaagg Find is-nt database================================================ Query_seq: SSA_1091:SSA_1092|SSA_1091:SSA_1092:Thymidylate synthase, putative:Dihydrofolate reductase, putative:->->:1109615..1109738 124 cgattttgataagtgtatgcgaaaacgtccaacctctgcaaaagttctgcttgaatcatactttaaacatgcctttttacagcaaatttgatagaatagagttactaatacaaaggataaaagg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_1091:SSA_1092|SSA_1091:SSA_1092:Thymidylate synthase, putative:Dihydrofolate reductase, putative:->->:1109615..1109738 124 cgattttgataagtgtatgcgaaaacgtccaacctctgcaaaagttctgcttgaatcatactttaaacatgcctttttacagcaaatttgatagaatagagttactaatacaaaggataaaagg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_1091:SSA_1092|SSA_1091:SSA_1092:Thymidylate synthase, putative:Dihydrofolate reductase, putative:->->:1109615..1109738 124 cgattttgataagtgtatgcgaaaacgtccaacctctgcaaaagttctgcttgaatcatactttaaacatgcctttttacagcaaatttgatagaatagagttactaatacaaaggataaaagg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 cgattttgataagtgtatgcgaaaacgtccaacctctgcaaaagttctgcttgaatcatactttaaacatgcctttttacagcaaatttgatagaatagagttactaatacaaaggataaaagg Predict ORF larger than 30AA ================================================ Protein_Len: 40 Strand: + Start: 3 End: 122 .. M L I S V C E N V Q P L Q K F C L N H T L N M P F Y S K F D R I E L L I Q R I K .. cgattttgataagtgtatgcgaaaacgtccaacctctgcaaaagttctgcttgaatcatactttaaacatgcctttttacagcaaatttgatagaatagagttactaatacaaaggataaaagg 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================================================ cgattttgataagtgtatgcgaaaacgtccaacctctgcaaaagttctgcttgaatcatactttaaacatgcctttttacagcaaatttgatagaatagagttactaatacaaaggataaaagg Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_1091:SSA_1092|SSA_1091:SSA_1092:Thymidylate synthase, putative:Dihydrofolate reductase, putative:->->:1109615..1109738 124 cgattttgataagtgtatgcgaaaacgtccaacctctgcaaaagttctgcttgaatcatactttaaacatgcctttttacagcaaatttgatagaatagagttactaatacaaaggataaaagg Intra-Species Hit: Count: 1 Min: 1 Max: 124 Len: 124 Subject: NC_009009_SSA_1091_SSA_1092|Thymidylate synthase, putative:Dihydrofolate reductase, putative|POSITIVE:POSITIVE|[1109615,1109738]|124 HSP 1 e-value: 1.0E-64 bit: 246.0 Len: 124 Query Start:1 Query End:124 Subject Strand: POSITIVE Subject Start: 1 Subject End: 124 cgattttgataagtgtatgcgaaaacgtccaacctctgcaaaagttctgcttgaatcatactttaaacatgcctttttacagcaaatttgatagaatagagttactaatacaaaggataaaagg cgattttgataagtgtatgcgaaaacgtccaacctctgcaaaagttctgcttgaatcatactttaaacatgcctttttacagcaaatttgatagaatagagttactaatacaaaggataaaagg Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CGAUUUUGAUAAGUGUAUGCGAAAACGUCCAACCUCUGCAAAAGUUCUGCUUGAAUCAUACUUUAAACAUGCCUUUUUACAGCAAAUUUGAUAGAAUAGAGUUACUAAUACAAAGGAUAAAAGG ((.((((((((....))).))))).)).....(((.((....(((...((((...((.....(((((..(((.........)))..)))))..))...)))).)))....)).)))........ (-12.10) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CCUUUUAUCCUUUGUAUUAGUAACUCUAUUCUAUCAAAUUUGCUGUAAAAAGGCAUGUUUAAAGUAUGAUUCAAGCAGAACUUUUGCAGAGGUUGGACGUUUUCGCAUACACUUAUCAAAAUCG ...((((.((((((((..(((...(((.((..((((.(((((((((......))).))...)))).))))..))..))))))..)))))))).))))........................... (-18.80) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 278 58 15 54 15 NC_009009:SSA_2359|5end_Glucose_inhibited_division_protein_A,_putative_2362520..2362750_NEGATIVE 270 65 25 97 59 NC_009009:SSA_2033|5end_30S_ribosomal_protein_S9,_putative_2038779..2039009_NEGATIVE 269 43 2 199 160 NC_009009:SSA_1595|5end_Tellurite_resistance,_putative_1601814..1602044_NEGATIVE 269 90 43 212 166 NC_009009:SSA_0452|5end_Nitrogen_utilization_substance_protein_B,_putative_451534..451764_POSITIVE 263 54 25 48 15 NC_009009:SSA_1845|5end_Serine/threonine_protein_kinase,_putative_1840181..1840411_NEGATIVE 261 50 1 203 144 NC_009009:SSA_0106|5end_30S_ribosomal_protein_S10,_putative_107772..108002_POSITIVE 256 47 1 206 145 NC_009009:SSA_2331|5end_D-alanine_transfer_protein,_putative_2334964..2335194_NEGATIVE 255 55 21 229 194 NC_009009:SSA_1266|5end_crcB-like_protein_1,_putative_1291000..1291230_NEGATIVE 254 50 1 180 124 NC_009009:SSA_0102|5end_Kinase,_putative_104035..104265_POSITIVE 251 79 32 84 31 NC_009009:SSA_0527|5end_Propanediol_utilization_protein_PduL_524625..524855_POSITIVE 250 49 1 196 146 NC_009009:SSA_1187|5end_Transcriptional_antiterminator,_BglG_family,_putative_1216037..1216267_NEGATIVE 242 80 31 186 124 NC_009009:SSA_1760|5end_hypothetical_protein_1747284..1747514_NEGATIVE 241 67 25 127 83 NC_009009:SSA_2089|5end_L-xylulose-5-phosphate_3-epimerase,_putative_2094339..2094569_NEGATIVE 240 75 34 197 156 NC_009009:SSA_2001|5end_Hydroxymethylpyrimidine/phosphomethylpyrimidine_kinase,_putative_1998220..1998450_NEGATIVE 238 55 16 175 137 NC_009009:SSA_0747|5end_DD-carboxypeptidase,_putative_727936..728166_POSITIVE 233 60 20 46 1 NC_009009:SSA_1278|5end_Rhodanese-like_domain_protein,_putative_1299877..1300107_NEGATIVE 233 50 18 193 157 NC_009009:SSA_0659|5end_hypothetical_protein_643003..643233_POSITIVE 232 60 18 207 164 NC_009009:SSA_1307|5end_Trk_transporter_membrane-spanning_protein-K+_transport,_putative_1326270..1326500_NEGATIVE 230 53 12 75 26 NC_009009:SSA_0796|5end_ABC-NBD_transporters_with_duplicated_ATPase_domains,_putative_777085..777315_POSITIVE 229 85 51 161 129 NC_009009:SSA_1332|5end_hypothetical_protein_1347645..1347875_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 270 65 25 78 40 NC_009009:SSA_2034|3end_50S_ribosomal_protein_L13,_putative_2038798..2038948_NEGATIVE 263 54 25 51 18 NC_009009:SSA_1846|3end_Phosphoprotein_phosphatase,_putative_1840178..1840328_NEGATIVE 251 79 32 60 7 NC_009009:SSA_0526|3end_hypothetical_protein_524681..524831_POSITIVE 246 48 2 81 35 NC_009009:SSA_1504|3end_hypothetical_protein_1506459..1506609_NEGATIVE 245 60 18 53 7 NC_009009:SSA_1279|3end_Oxidoreductase,_putative_1299870..1300020_NEGATIVE 241 67 25 123 79 NC_009009:SSA_2090|3end_Hexulose-6-phosphate_synthase,_putative_2094343..2094493_NEGATIVE 229 85 51 113 81 NC_009009:SSA_1333|3end_hypothetical_protein_1347693..1347843_NEGATIVE 229 83 46 65 34 NC_009009:SSA_0635|3end_Indole-3-glycerol_phosphate_synthase,_putative_625235..625385_POSITIVE 225 59 12 52 5 NC_009009:SSA_0787|3end_Proton-translocating_ATPase,_F1_sector,_gamma_subunit,_putative_771078..771228_POSITIVE 223 77 34 60 5 NC_009009:SSA_1956|3end_ABC-type_Fe-S_cluster_assembly_transporter,_ATPase_component,_putative_1952644..1952794_NEGATIVE 223 40 1 142 104 NC_009009:SSA_0690|3end_Recombinational_DNA_repair_protein_(RecF_pathway),_putative_675108..675258_POSITIVE 223 50 1 144 105 NC_009009:SSA_0338|3end_Hydroxymethylglutaryl-CoA_synthase,_putative_332160..332310_NEGATIVE 221 58 12 140 100 NC_009009:SSA_2098|3end_ABC-type_arginine/histidine_transporter,_permease_protein,_putative_2102931..2103081_NEGATIVE 221 90 46 147 104 NC_009009:SSA_1774|3end_RRNA_methylase,_putative_1760489..1760639_NEGATIVE 219 59 12 140 93 NC_009009:SSA_2160|3end_Deoxyuridinetriphosphatase,_putative_2159623..2159773_NEGATIVE 218 59 12 123 76 NC_009009:SSA_1179|3end_Carbamoylphosphate_synthase_large_subunit_/_biotin_carboxylase,_putative_1206640..1206790_NEGATIVE 218 74 33 136 96 NC_009009:SSA_0245|3end_hypothetical_protein_239608..239758_POSITIVE 216 56 26 75 37 NC_009009:SSA_1868|3end_ABC-type_arginine/histidine_transport_system,_permease_component,_putative_1863096..1863246_NEGATIVE 216 83 45 108 66 NC_009009:SSA_1658|3end_Cationic_amino_acid_transporter,_putative_1653274..1653424_NEGATIVE 215 59 14 75 25 NC_009009:SSA_1061|3end_50S_ribosomal_protein_L21,_putative_1077986..1078136_POSITIVE