Origin IGS: aatttgtacctcaaaagtattttatagtttattctaccatattttatacagggtgtaaaagaggaagggtctaaatcaactgtctaggcggaaatttccaagcaaaaaaggacggaaaatttccatcctttttaaataaaga .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tctttatttaaaaaggatggaaattttccgtccttttttgcttggaaatttccgcctagacagttgatttagacccttcctcttttacaccctgtataaaatatggtagaataaactataaaatacttttgaggtacaaatt Mask Tandem Repeat Region ================================================ aatttgtacctcaaaagtattttatagtttattctaccatattttatacagggtgtaaaagaggaagggtctaaatcaactgtctaggcggaaatttccaagcaaaaaaggacggaaaatttccatcctttttaaataaaga Find is-nt database================================================ Query_seq: SSA_1979:SSA_1980|SSA_1979:SSA_1980:Alkaline-shock protein, putative:50S ribosomal protein L28, putative:<-<-:1974392..1974533 142 aatttgtacctcaaaagtattttatagtttattctaccatattttatacagggtgtaaaagaggaagggtctaaatcaactgtctaggcggaaatttccaagcaaaaaaggacggaaaatttccatcctttttaaataaaga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_1979:SSA_1980|SSA_1979:SSA_1980:Alkaline-shock protein, putative:50S ribosomal protein L28, putative:<-<-:1974392..1974533 142 aatttgtacctcaaaagtattttatagtttattctaccatattttatacagggtgtaaaagaggaagggtctaaatcaactgtctaggcggaaatttccaagcaaaaaaggacggaaaatttccatcctttttaaataaaga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_1979:SSA_1980|SSA_1979:SSA_1980:Alkaline-shock protein, putative:50S ribosomal protein L28, putative:<-<-:1974392..1974533 142 aatttgtacctcaaaagtattttatagtttattctaccatattttatacagggtgtaaaagaggaagggtctaaatcaactgtctaggcggaaatttccaagcaaaaaaggacggaaaatttccatcctttttaaataaaga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aatttgtacctcaaaagtattttatagtttattctaccatattttatacagggtgtaaaagaggaagggtctaaatcaactgtctaggcggaaatttccaagcaaaaaaggacggaaaatttccatcctttttaaataaaga Predict ORF larger than 30AA ================================================ aatttgtacctcaaaagtattttatagtttattctaccatattttatacagggtgtaaaagaggaagggtctaaatcaactgtctaggcggaaatttccaagcaaaaaaggacggaaaatttccatcctttttaaataaaga Predict Promoter with matrix: RpoD-15 score > 80================================================ Predict Promoter with matrix: RpoD-16 score > 80================================================ Predict Promoter with matrix: RpoD-17 score > 80================================================ PromScan Matrix: RpoD-17 Strand: - Score: 85 Start: 31 End: 60 ..............................TTTTACACCCTGTATAAAATATGGTAGAAT.................................................................................. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ aatttgtacctcaaaagtattttatagtttattctaccatattttatacagggtgtaaaagaggaagggtctaaatcaactgtctaggcggaaatttccaagcaaaaaaggacggaaaatttccatcctttttaaataaaga Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_1979:SSA_1980|SSA_1979:SSA_1980:Alkaline-shock protein, putative:50S ribosomal protein L28, putative:<-<-:1974392..1974533 142 aatttgtacctcaaaagtattttatagtttattctaccatattttatacagggtgtaaaagaggaagggtctaaatcaactgtctaggcggaaatttccaagcaaaaaaggacggaaaatttccatcctttttaaataaaga Intra-Species Hit: Count: 1 Min: 1 Max: 142 Len: 142 Subject: NC_009009_SSA_1979_SSA_1980|Alkaline-shock protein, putative:50S ribosomal protein L28, putative|NEGATIVE:NEGATIVE|[1974392,1974533]|142 HSP 1 e-value: 3.0E-75 bit: 281.0 Len: 142 Query Start:1 Query End:142 Subject Strand: POSITIVE Subject Start: 1 Subject End: 142 aatttgtacctcaaaagtattttatagtttattctaccatattttatacagggtgtaaaagaggaagggtctaaatcaactgtctaggcggaaatttccaagcaaaaaaggacggaaaatttccatcctttttaaataaaga aatttgtacctcaaaagtattttatagtttattctaccatattttatacagggtgtaaaagaggaagggtctaaatcaactgtctaggcggaaatttccaagcaaaaaaggacggaaaatttccatcctttttaaataaaga Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAUUUGUACCUCAAAAGUAUUUUAUAGUUUAUUCUACCAUAUUUUAUACAGGGUGUAAAAGAGGAAGGGUCUAAAUCAACUGUCUAGGCGGAAAUUUCCAAGCAAAAAAGGACGGAAAAUUUCCAUCCUUUUUAAAUAAAGA ..((((.....))))....((((((.(((((((((.((...((((((((...))))))))..)).))))).........((((....))))........)))).((((((((.(((.....))).))))))))..)))))). (-25.50) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UCUUUAUUUAAAAAGGAUGGAAAUUUUCCGUCCUUUUUUGCUUGGAAAUUUCCGCCUAGACAGUUGAUUUAGACCCUUCCUCUUUUACACCCUGUAUAAAAUAUGGUAGAAUAAACUAUAAAAUACUUUUGAGGUACAAAUU (((......((((((((((((.....)))))))))))).....))).......((((..((((.((....(((.......)))....))..))))......((((((.......))))))...........))))....... (-26.20) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 911 100 51 191 142 NC_009009:SSA_1979|5end_Alkaline-shock_protein,_putative_1974301..1974531_NEGATIVE 296 100 51 154 104 NC_009009:SSA_1132|5end_TatC,_sec-independent_protein_translocase,_putative_1158645..1158875_POSITIVE 286 103 61 63 19 NC_009009:SSA_1306|5end_Trk_transporter_NAD+_binding_protein-K+_transport,_putative_1324910..1325140_NEGATIVE 281 88 50 56 14 NC_009009:SSA_1396|5end_hypothetical_protein_1410374..1410604_NEGATIVE 278 100 52 106 62 NC_009009:SSA_0578|5end_Nicotinate-nucleotide_adenylyltransferase,_putative_571591..571821_POSITIVE 272 128 87 197 163 NC_009009:SSA_1844|5end_hypothetical_protein_1838183..1838413_NEGATIVE 271 110 61 168 118 NC_009009:SSA_1735|5end_UreX,_putative_1721072..1721302_NEGATIVE 266 87 46 55 21 NC_009009:SSA_1115|5end_Cytochrome_C-type_biogenesis_protein,_putative_1141614..1141844_POSITIVE 264 133 95 225 183 NC_009009:SSA_0460|5end_Multiple_antibiotic_resistance_operon_transcription_repressor_(MarR),_putative_462608..462838_POSITIVE 262 110 63 196 141 NC_009009:SSA_0098|5end_Hydrolase,_haloacid_dehalogenase-like_family,_putative_99422..99652_POSITIVE 258 130 81 164 110 NC_009009:SSA_1415|5end_Oxidoreductase,_putative_1426508..1426738_NEGATIVE 255 77 33 73 18 NC_009009:SSA_1779|5end_Segregation_and_condensation_protein_A,_putative_1766414..1766644_NEGATIVE 255 130 82 87 34 NC_009009:SSA_1118|5end_Peptide_methionine_sulfoxide_reductase,_putative_1143322..1143552_POSITIVE 255 129 83 170 120 NC_009009:SSA_0997|5end_DNA-directed_DNA_polymerase_III_chain,_putative_996779..997009_POSITIVE 251 130 82 169 114 NC_009009:SSA_1901|5end_Conserved_uncharacterized_protein_1896599..1896829_NEGATIVE 244 100 54 66 6 NC_009009:SSA_1722|5end_Thymidylate_kinase,_putative_1708663..1708893_NEGATIVE 243 128 86 46 6 NC_009009:SSA_1550|5end_hypothetical_protein_1552665..1552895_NEGATIVE 243 90 45 171 119 NC_009009:SSA_0201|5end_ABC_multidrug_transporter_(3-component_subtilin_immunity_exporter),_putative_199825..200055_POSITIVE 240 120 71 52 5 NC_009009:SSA_0403|5end_CAAX_amino_terminal_protease_family,_putative_400475..400705_POSITIVE 238 89 47 61 19 NC_009009:SSA_0493|5end_ABC-type_dipeptide/nickel_transport_system,_periplasmic_component,_putative_492868..493098_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 286 103 61 52 8 NC_009009:SSA_1307|3end_Trk_transporter_membrane-spanning_protein-K+_transport,_putative_1324921..1325071_NEGATIVE 278 134 105 64 34 NC_009009:SSA_2023|3end_Fructan_beta-fructosidase_precursor,_putative_2024609..2024759_NEGATIVE 278 100 52 79 35 NC_009009:SSA_0577|3end_Ancient_RNA-binding_IF3-C_fold_(CRS1/YhbY_domain),_putative_571644..571794_POSITIVE 272 128 87 52 18 NC_009009:SSA_1845|3end_Serine/threonine_protein_kinase,_putative_1838328..1838478_NEGATIVE 264 133 95 50 8 NC_009009:SSA_0459|3end_hypothetical_protein_462513..462663_POSITIVE 255 77 33 71 16 NC_009009:SSA_1780|3end_Tyrosine_recombinase_xerD,_putative_1766416..1766566_NEGATIVE 255 130 82 71 18 NC_009009:SSA_1117|3end_hypothetical_protein_1143386..1143536_POSITIVE 249 129 81 151 98 NC_009009:SSA_1416|3end_hypothetical_protein_1426520..1426670_NEGATIVE 247 104 61 70 9 NC_009009:SSA_1048|3end_ABC_transporter_ATP-binding_protein-spermidine/putrescine_transport,_putative_1064184..1064334_POSITIVE 243 128 86 59 19 NC_009009:SSA_1551|3end_Transcriptional_accessory_ribonuclease_(YqgFc,_S1),_putative_1552652..1552802_NEGATIVE 243 90 45 76 24 NC_009009:SSA_0200|3end_Bifunctional_folate_synthesis_protein,_putative_199810..199960_POSITIVE 237 68 28 125 90 NC_009009:SSA_1318|3end_GTP-binding_protein_lepA,_putative_1333989..1334139_NEGATIVE 237 94 58 53 24 NC_009009:SSA_0748|3end_Sugar:H+_symporter,_permease_of_the_major_facilitator_superfamily,_putative_730635..730785_POSITIVE 235 99 57 65 16 NC_009009:SSA_0102|3end_Kinase,_putative_104627..104777_POSITIVE 235 117 75 72 16 NC_009009:SSA_0027|3end_Acyl_carrier_protein,_putative_31802..31952_POSITIVE 234 90 49 106 62 NC_009009:SSA_0842|3end_Effector_of_murein_hydrolase_LrgA/holin-like_protein,_putative_827790..827940_POSITIVE 233 98 56 77 42 NC_009009:SSA_1485|3end_Citrulline_cluster-linked_gene,_putative_1492294..1492444_NEGATIVE 233 85 43 84 47 NC_009009:SSA_0774|3end_NADP-dependent_glyceraldehyde-3-phosphate_dehydrogenase,_putative_756075..756225_POSITIVE 232 100 60 116 80 NC_009009:SSA_1314|3end_Fe-S-cluster_oxidoreductase,_putative_1330746..1330896_NEGATIVE 229 92 62 107 78 NC_009009:SSA_2151|3end_M_protein_trans-acting_positive_transcriptional_regulator_(MGA),_putative_2152921..2153071_POSITIVE