Origin IGS: tctattgctccttataaaataatccagacagattactgtttggatttttacaaaaaatctatctataaaattagtaaaattttactaaatttattgaagttttactcggaaacagttataataaatataagaaaacgattacaatgtcgatcattcattttaaaggagtttagctt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aagctaaactcctttaaaatgaatgatcgacattgtaatcgttttcttatatttattataactgtttccgagtaaaacttcaataaatttagtaaaattttactaattttatagatagattttttgtaaaaatccaaacagtaatctgtctggattattttataaggagcaataga Mask Tandem Repeat Region ================================================ tctattgctccttataaaataatccagacagattactgtttggatttttacaaaaaatctatctataaaattagtaaaattttactaaatttattgaagttttactcggaaacagttataataaatataagaaaacgattacaatgtcgatcattcattttaaaggagtttagctt Find is-nt database================================================ Query_seq: SSA_1007:SSA_1008|SSA_1007:SSA_1008:ABC transporter ATP-binding protein-multiple sugar transport, putative:Galactokinase, putative:->->:1009820..1009995 176 tctattgctccttataaaataatccagacagattactgtttggatttttacaaaaaatctatctataaaattagtaaaattttactaaatttattgaagttttactcggaaacagttataataaatataagaaaacgattacaatgtcgatcattcattttaaaggagtttagctt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_1007:SSA_1008|SSA_1007:SSA_1008:ABC transporter ATP-binding protein-multiple sugar transport, putative:Galactokinase, putative:->->:1009820..1009995 176 tctattgctccttataaaataatccagacagattactgtttggatttttacaaaaaatctatctataaaattagtaaaattttactaaatttattgaagttttactcggaaacagttataataaatataagaaaacgattacaatgtcgatcattcattttaaaggagtttagctt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_1007:SSA_1008|SSA_1007:SSA_1008:ABC transporter ATP-binding protein-multiple sugar transport, putative:Galactokinase, putative:->->:1009820..1009995 176 tctattgctccttataaaataatccagacagattactgtttggatttttacaaaaaatctatctataaaattagtaaaattttactaaatttattgaagttttactcggaaacagttataataaatataagaaaacgattacaatgtcgatcattcattttaaaggagtttagctt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tctattgctccttataaaataatccagacagattactgtttggatttttacaaaaaatctatctataaaattagtaaaattttactaaatttattgaagttttactcggaaacagttataataaatataagaaaacgattacaatgtcgatcattcattttaaaggagtttagctt Predict ORF larger than 30AA ================================================ Protein_Len: 57 Strand: + Start: 4 End: 174 ... M A P Y K I I Q T D Y C L D F Y K K S I Y K I S K I L L N L L K F Y S E T V I I N I R K R L Q C R S F I L K E F S .. tctattgctccttataaaataatccagacagattactgtttggatttttacaaaaaatctatctataaaattagtaaaattttactaaatttattgaagttttactcggaaacagttataataaatataagaaaacgattacaatgtcgatcattcattttaaaggagtttagctt 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: 88 Start: 93 End: 122 ............................................................................................ATTGAAGTTTTACTCGGAAACAGTTATAAT...................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ tctattgctccttataaaataatccagacagattactgtttggatttttacaaaaaatctatctataaaattagtaaaattttactaaatttattgaagttttactcggaaacagttataataaatataagaaaacgattacaatgtcgatcattcattttaaaggagtttagctt Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 76 HP_score: -7.3 Tail_Score: -4.30995 Start: 23 End: 44 Full_Region: gattttttgtaaaaa tccaaacag taat ctgtctgga ttattttataaggag ......................tccaaacagtaatctgtctgga.................................................................................................................................... Find igs database================================================ Query_seq: SSA_1007:SSA_1008|SSA_1007:SSA_1008:ABC transporter ATP-binding protein-multiple sugar transport, putative:Galactokinase, putative:->->:1009820..1009995 176 tctattgctccttataaaataatccagacagattactgtttggatttttacaaaaaatctatctataaaattagtaaaattttactaaatttattgaagttttactcggaaacagttataataaatataagaaaacgattacaatgtcgatcattcattttaaaggagtttagctt Intra-Species Hit: Count: 1 Min: 1 Max: 176 Len: 176 Subject: NC_009009_SSA_1007_SSA_1008|ABC transporter ATP-binding protein-multiple sugar transport, putative:Galactokinase, putative|POSITIVE:POSITIVE|[1009820,1009995]|176 HSP 1 e-value: 2.0E-95 bit: 349.0 Len: 176 Query Start:1 Query End:176 Subject Strand: POSITIVE Subject Start: 1 Subject End: 176 tctattgctccttataaaataatccagacagattactgtttggatttttacaaaaaatctatctataaaattagtaaaattttactaaatttattgaagttttactcggaaacagttataataaatataagaaaacgattacaatgtcgatcattcattttaaaggagtttagctt tctattgctccttataaaataatccagacagattactgtttggatttttacaaaaaatctatctataaaattagtaaaattttactaaatttattgaagttttactcggaaacagttataataaatataagaaaacgattacaatgtcgatcattcattttaaaggagtttagctt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UCUAUUGCUCCUUAUAAAAUAAUCCAGACAGAUUACUGUUUGGAUUUUUACAAAAAAUCUAUCUAUAAAAUUAGUAAAAUUUUACUAAAUUUAUUGAAGUUUUACUCGGAAACAGUUAUAAUAAAUAUAAGAAAACGAUUACAAUGUCGAUCAUUCAUUUUAAAGGAGUUUAGCUU .(((..(((((((.(((((((((((((((((....)))))))))))...........(((.((.(((((.(((((((....))))))).))))).)).(((..(((.(....))))...))).......)))...((((......)))).......))))))))))))).)))... (-39.00) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAGCUAAACUCCUUUAAAAUGAAUGAUCGACAUUGUAAUCGUUUUCUUAUAUUUAUUAUAACUGUUUCCGAGUAAAACUUCAAUAAAUUUAGUAAAAUUUUACUAAUUUUAUAGAUAGAUUUUUUGUAAAAAUCCAAACAGUAAUCUGUCUGGAUUAUUUUAUAAGGAGCAAUAGA ...(((..((((((((((((((.......(((....((((......(((((.....)))))..................((.(((((.(((((((....))))))).))))).))..))))...))).....((((.((((....)))).)))))))))))).))))))...))). (-33.00) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 252 50 6 149 95 NC_009009:SSA_1994|5end_CTP_synthase,_putative_1992474..1992704_NEGATIVE 221 44 1 212 183 NC_009009:SSA_0116|5end_30S_ribosomal_protein_S17,_putative_112632..112862_POSITIVE 219 49 2 159 108 NC_009009:SSA_0834|5end_Accessory_secretory_protein_Asp2,_putative_819510..819740_POSITIVE 218 39 7 231 194 NC_009009:SSA_0758|5end_Ornithine_acetyltransferase_/_amino-acid_acetyltransferase,_putative_740636..740866_POSITIVE 214 49 2 194 142 NC_009009:SSA_2032|5end_Integrase/recombinase,_phage_integrase_family,_putative_2038006..2038236_POSITIVE 200 49 1 205 149 NC_009009:SSA_0785|5end_Proton-translocating_ATPase,_F1_sector,_delta_subunit,_putative_768044..768274_POSITIVE 197 67 24 57 1 NC_009009:SSA_0756|5end_Alanyl-tRNA_synthetase,_putative_736736..736966_POSITIVE 192 40 1 114 75 NC_009009:SSA_2371|5end_Zn-dependent_peptidase,_putative_2373681..2373911_NEGATIVE 190 43 2 227 183 NC_009009:SSA_0065|5end_Low_molecular_weight_phosphotyrosine_protein_phosphatase,_putative_67175..67405_POSITIVE 189 155 127 190 162 NC_009009:SSA_1370|5end_CAAX_amino_terminal_protease_family,_putative_1386968..1387198_NEGATIVE 187 68 28 223 178 NC_009009:SSA_2093|5end_PTS_system,_membrane_component,_putative_2097462..2097692_NEGATIVE 185 44 4 72 37 NC_009009:SSA_2356|5end_Replicative_DNA_helicase,_putative_2357958..2358188_NEGATIVE 185 39 6 176 146 NC_009009:SSA_1119|5end_Two-component_response_transcriptional_regulator_(CheY-like_receiver_and_AraC-type_DNA-binding_domains),_putative_1144491..1144721_POSITIVE 181 63 40 104 80 NC_009009:SSA_1890|5end_Acetyltransferase,_putative_1888145..1888375_NEGATIVE 180 49 6 75 35 NC_009009:SSA_2113|5end_hypothetical_protein_2116692..2116922_NEGATIVE 180 32 6 123 96 NC_009009:SSA_1368|5end_hypothetical_protein_1384077..1384307_NEGATIVE 179 50 5 127 82 NC_009009:SSA_0331|5end_C3-degrading_proteinase,_putative_325178..325408_POSITIVE 177 38 4 51 21 NC_009009:SSA_1040|5end_Sugar_ABC_transporter,_permease_protein,_putative_1055302..1055532_POSITIVE 177 115 81 37 3 NC_009009:SSA_0736|5end_Catabolite_gene_activator_and_regulatory_subunit_of_cAMP-dependent_protein_kinases,_putative_717648..717878_POSITIVE 176 50 13 226 182 NC_009009:SSA_1701|5end_Transcriptional_repressor_of_sugar_metabolism,_GlpR/DeoR_family,_putative_1692054..1692284_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 248 46 21 70 45 NC_009009:SSA_1007|3end_ABC_transporter_ATP-binding_protein-multiple_sugar_transport,_putative_1009759..1009909_POSITIVE 246 150 106 78 41 NC_009009:SSA_1744|3end_Iron_compound_ABC_transporter,_permease_protein,_putative_1731999..1732149_POSITIVE 224 48 5 149 109 NC_009009:SSA_2067|3end_hypothetical_protein_2070876..2071026_POSITIVE 196 32 8 114 87 NC_009009:SSA_2158|3end_Methyltransferase,_putative_2158421..2158571_NEGATIVE 189 155 127 107 79 NC_009009:SSA_1371|3end_FmtA-like_protein,_putative_1387051..1387201_NEGATIVE 185 44 4 45 10 NC_009009:SSA_2357|3end_50S_ribosomal_protein_L9,_putative_2357985..2358135_NEGATIVE 185 39 6 116 86 NC_009009:SSA_1118|3end_Peptide_methionine_sulfoxide_reductase,_putative_1144511..1144661_POSITIVE 184 47 12 84 51 NC_009009:SSA_2291|3end_hypothetical_protein_2293733..2293883_POSITIVE 181 63 40 103 79 NC_009009:SSA_1891|3end_Oxidoreductase,_aldo/keto_reductase_family,_putative_1888146..1888296_NEGATIVE 180 49 6 53 13 NC_009009:SSA_2114|3end_Transcriptional_repressor_of_purine_operon,_putative_2116714..2116864_NEGATIVE 180 32 6 58 31 NC_009009:SSA_1369|3end_FmtA-like_protein,_putative_1384142..1384292_NEGATIVE 177 38 4 58 28 NC_009009:SSA_1039|3end_Sugar_ABC_transporter,_ATP-binding_protein,_putative_1055389..1055539_POSITIVE 176 50 13 83 39 NC_009009:SSA_1702|3end_hypothetical_protein_1692197..1692347_NEGATIVE 176 50 6 109 59 NC_009009:SSA_1354|3end_hypothetical_protein_1368555..1368705_NEGATIVE 176 50 8 133 87 NC_009009:SSA_0231|3end_Conserved_uncharacterized_protein_227082..227232_POSITIVE 174 48 1 45 1 NC_009009:SSA_1710|3end_Transcriptional_regulator,_XRE_family,_putative_1699011..1699161_POSITIVE 174 74 34 74 39 NC_009009:SSA_0723|3end_hypothetical_protein_708466..708616_POSITIVE 172 41 4 63 24 NC_009009:SSA_1955|3end_ABC-type_Fe-S_cluster_assembly_transporter,_permease_component,_putative_1951340..1951490_NEGATIVE 169 159 130 45 10 NC_009009:SSA_2284|3end_Histidyl-tRNA_synthetase,_putative_2285992..2286142_NEGATIVE 165 60 24 73 40 NC_009009:SSA_0626|3end_hypothetical_protein_617212..617362_POSITIVE