Origin IGS: gtctctcctattctaaaagccaagaaattggcttatctatattttaaatttatgttactctattgtatcataaagcttttaaatagcaatgattccttgaaataaatcatagatatttggtataatgggaagataacaaggagaatcgaac .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 gttcgattctccttgttatcttcccattataccaaatatctatgatttatttcaaggaatcattgctatttaaaagctttatgatacaatagagtaacataaatttaaaatatagataagccaatttcttggcttttagaataggagagac Mask Tandem Repeat Region ================================================ gtctctcctattctaaaagccaagaaattggcttatctatattttaaatttatgttactctattgtatcataaagcttttaaatagcaatgattccttgaaataaatcatagatatttggtataatgggaagataacaaggagaatcgaac Find is-nt database================================================ Query_seq: SSA_0174:SSA_0134|SSA_0174:SSA_0134:Tyrosyl-tRNA synthetase 1, putative:Membrane carboxypeptidase (penicillin-binding protein), putative:<-->:171979..172129 151 gtctctcctattctaaaagccaagaaattggcttatctatattttaaatttatgttactctattgtatcataaagcttttaaatagcaatgattccttgaaataaatcatagatatttggtataatgggaagataacaaggagaatcgaac Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_0174:SSA_0134|SSA_0174:SSA_0134:Tyrosyl-tRNA synthetase 1, putative:Membrane carboxypeptidase (penicillin-binding protein), putative:<-->:171979..172129 151 gtctctcctattctaaaagccaagaaattggcttatctatattttaaatttatgttactctattgtatcataaagcttttaaatagcaatgattccttgaaataaatcatagatatttggtataatgggaagataacaaggagaatcgaac Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_0174:SSA_0134|SSA_0174:SSA_0134:Tyrosyl-tRNA synthetase 1, putative:Membrane carboxypeptidase (penicillin-binding protein), putative:<-->:171979..172129 151 gtctctcctattctaaaagccaagaaattggcttatctatattttaaatttatgttactctattgtatcataaagcttttaaatagcaatgattccttgaaataaatcatagatatttggtataatgggaagataacaaggagaatcgaac Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gtctctcctattctaaaagccaagaaattggcttatctatattttaaatttatgttactctattgtatcataaagcttttaaatagcaatgattccttgaaataaatcatagatatttggtataatgggaagataacaaggagaatcgaac Predict ORF larger than 30AA ================================================ Protein_Len: 31 Strand: + Start: 10 End: 102 ......... M L K A K K L A Y L Y F K F M L L Y C I I K L L N S N D S L K ................................................. gtctctcctattctaaaagccaagaaattggcttatctatattttaaatttatgttactctattgtatcataaagcttttaaatagcaatgattccttgaaataaatcatagatatttggtataatgggaagataacaaggagaatcgaac 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: 42 End: 71 .........................................TTTTAAATTTATGTTACTCTATTGTATCAT................................................................................ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ gtctctcctattctaaaagccaagaaattggcttatctatattttaaatttatgttactctattgtatcataaagcttttaaatagcaatgattccttgaaataaatcatagatatttggtataatgggaagataacaaggagaatcgaac Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 71 HP_score: -6.7 Tail_Score: -4.13767 Start: 19 End: 32 Full_Region: ttaaaatatagataa gccaa tttc ttggc ttttagaataggaga ..................gccaatttcttggc....................................................................................................................... TransTerm Strand: - Conf: 49 HP_score: -3.4 Tail_Score: -3.64103 Start: 49 End: 74 Full_Region: ttgctatttaaaagc tttatgatac aataga gtaacataaa tttaaaatatagata ................................................tttatgatacaatagagtaacataaa............................................................................. Find igs database================================================ Query_seq: SSA_0174:SSA_0134|SSA_0174:SSA_0134:Tyrosyl-tRNA synthetase 1, putative:Membrane carboxypeptidase (penicillin-binding protein), putative:<-->:171979..172129 151 gtctctcctattctaaaagccaagaaattggcttatctatattttaaatttatgttactctattgtatcataaagcttttaaatagcaatgattccttgaaataaatcatagatatttggtataatgggaagataacaaggagaatcgaac Intra-Species Hit: Count: 1 Min: 1 Max: 151 Len: 151 Subject: NC_009009_SSA_0174_SSA_0134|Tyrosyl-tRNA synthetase 1, putative:Membrane carboxypeptidase (penicillin-binding protein), putative|NEGATIVE:POSITIVE|[171979,172129]|151 HSP 1 e-value: 1.0E-80 bit: 299.0 Len: 151 Query Start:1 Query End:151 Subject Strand: POSITIVE Subject Start: 1 Subject End: 151 gtctctcctattctaaaagccaagaaattggcttatctatattttaaatttatgttactctattgtatcataaagcttttaaatagcaatgattccttgaaataaatcatagatatttggtataatgggaagataacaaggagaatcgaac gtctctcctattctaaaagccaagaaattggcttatctatattttaaatttatgttactctattgtatcataaagcttttaaatagcaatgattccttgaaataaatcatagatatttggtataatgggaagataacaaggagaatcgaac Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GUCUCUCCUAUUCUAAAAGCCAAGAAAUUGGCUUAUCUAUAUUUUAAAUUUAUGUUACUCUAUUGUAUCAUAAAGCUUUUAAAUAGCAAUGAUUCCUUGAAAUAAAUCAUAGAUAUUUGGUAUAAUGGGAAGAUAACAAGGAGAAUCGAAC (..((((((.......(((((((....)))))))..................((((((((((((((((((....(((.......))).((((((..........)))))).......)))))))))))..)).)))))))))))..).... (-36.10) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GUUCGAUUCUCCUUGUUAUCUUCCCAUUAUACCAAAUAUCUAUGAUUUAUUUCAAGGAAUCAUUGCUAUUUAAAAGCUUUAUGAUACAAUAGAGUAACAUAAAUUUAAAAUAUAGAUAAGCCAAUUUCUUGGCUUUUAGAAUAGGAGAGAC ......(((((((..((((((............(((((.(.(((((((........))))))).).)))))....(((((((......)))))))..................))))))(((((....))))).........))))))).. (-28.80) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 742 50 1 141 92 NC_009009:SSA_0174|5end_Tyrosyl-tRNA_synthetase_1,_putative_171888..172118_NEGATIVE 258 150 103 195 147 NC_009009:SSA_1589|5end_ABC-type_antimicrobial_peptide_transport_system,_ATPase_component,_putative_1592608..1592838_NEGATIVE 254 33 1 126 100 NC_009009:SSA_0844|5end_hypothetical_protein_829324..829554_NEGATIVE 231 87 48 130 86 NC_009009:SSA_0996|5end_cGMP-specific_phosphodiesterase,_putative_996282..996512_POSITIVE 227 100 60 105 52 NC_009009:SSA_1043|5end_Homoserine_dehydrogenase,_putative_1058565..1058795_POSITIVE 224 40 6 231 198 NC_009009:SSA_0809|5end_Translation_initiation_inhibitor,_yjgF_family_/_endoribonuclease_L-PSP,_putative_791146..791376_POSITIVE 213 98 52 103 54 NC_009009:SSA_1603|5end_hypothetical_protein_1610034..1610264_NEGATIVE 213 90 42 164 106 NC_009009:SSA_0450|5end_Elongation_factor_P,_putative_450587..450817_POSITIVE 212 130 87 69 22 NC_009009:SSA_0387|5end_Transcriptional_regulator,_GntR_family,_putative_382343..382573_NEGATIVE 209 35 2 134 92 NC_009009:SSA_0319|5end_Branched-chain_amino_acid_permease_(L-methionine,_L-isoleucine,_leucine_and_valine),_putative_312721..312951_POSITIVE 208 149 109 49 8 NC_009009:SSA_1947|5end_Oligopeptide_transport_system_permease_protein,_putative_1940120..1940350_NEGATIVE 208 31 2 144 108 NC_009009:SSA_1100|5end_Hemolysin_exporter,_ATPase_component,_putative_1119873..1120103_POSITIVE 207 100 53 196 153 NC_009009:SSA_1378|5end_hypothetical_protein_1397998..1398228_NEGATIVE 203 73 34 133 97 NC_009009:SSA_1555|5end_Glucose-6-phosphate_1-dehydrogenase,_putative_1556942..1557172_POSITIVE 202 37 3 230 193 NC_009009:SSA_0102|5end_Kinase,_putative_104035..104265_POSITIVE 201 148 108 210 166 NC_009009:SSA_1727|5end_ABC_transporter_membrane-spanning_permease-branched_chain_amino_acid_transport,_putative_1713420..1713650_NEGATIVE 201 33 4 120 95 NC_009009:SSA_0006|5end_Peptidyl-tRNA_hydrolase,_putative_5009..5239_POSITIVE 199 80 60 145 125 NC_009009:SSA_0341|5end_hypothetical_protein_334731..334961_NEGATIVE 198 60 11 59 14 NC_009009:SSA_0476|5end_Precorrin-2_C20-methyltransferase,_putative_478500..478730_POSITIVE 196 32 5 183 151 NC_009009:SSA_1987|5end_hypothetical_protein_1983368..1983598_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 254 33 1 111 85 NC_009009:SSA_0845|3end_ABC-type_multidrug_transport_system,_ATPase_component,_putative_829339..829489_NEGATIVE 231 87 48 100 56 NC_009009:SSA_0995|3end_Antibiotic-resistance_protein,_alpha/beta_superfamily_hydrolase,_putative_996332..996482_POSITIVE 228 98 57 44 3 NC_009009:SSA_1013|3end_Phosphatidylserine_synthase,_putative_1017933..1018083_POSITIVE 218 99 53 130 78 NC_009009:SSA_1867|3end_ABC-type_polar_amino_acid_transport_system,_ATPase_component,_putative_1862353..1862503_NEGATIVE 216 44 3 136 94 NC_009009:SSA_0245|3end_hypothetical_protein_239608..239758_POSITIVE 213 90 42 102 44 NC_009009:SSA_0449|3end_Aminopeptidase_P;_XAA-pro_aminopeptidase,_putative_450605..450755_POSITIVE 209 35 2 124 82 NC_009009:SSA_0318|3end_Secreted_metalloendopeptidase_Gcp_312791..312941_POSITIVE 208 31 2 65 29 NC_009009:SSA_1099|3end_Calcium_binding_hemolysin-like_protein,_putative_1119874..1120024_POSITIVE 207 44 2 96 46 NC_009009:SSA_0706|3end_RNA_helicase,_putative_692909..693059_POSITIVE 205 37 1 46 8 NC_009009:SSA_0042|3end_Amino_acid_recemase,_putative_48671..48821_POSITIVE 201 33 4 47 22 NC_009009:SSA_0005|3end_GTP-binding_protein,_putative_5016..5166_POSITIVE 198 60 11 49 4 NC_009009:SSA_0475|3end_CbiK_protein,_putative_478570..478720_POSITIVE 194 32 4 26 2 NC_009009:SSA_2140|3end_Ribonuclease_P_protein_component,_putative_2140308..2140458_NEGATIVE 193 60 11 107 44 NC_009009:SSA_0722|3end_hypothetical_protein_708115..708265_POSITIVE 191 44 4 64 29 NC_009009:SSA_1419|3end_hypothetical_protein_1428995..1429145_NEGATIVE 190 33 5 75 47 NC_009009:SSA_1691|3end_Transcriptional_regulator,_XRE_family,_putative_1683570..1683720_POSITIVE 190 33 1 114 78 NC_009009:SSA_1262|3end_tRNA_modification_GTPase,_possibly_iron-binding,_putative_1289235..1289385_POSITIVE 188 38 5 86 48 NC_009009:SSA_2210|3end_Ribosomal_large_subunit_pseudouridine_synthase_D,_putative_2211454..2211604_POSITIVE 188 129 93 76 43 NC_009009:SSA_1466|3end_Prephenate_dehydrogenase,_putative_1472005..1472155_NEGATIVE 186 42 18 137 112 NC_009009:SSA_2107|3end_Glucosamine--fructose-6-phosphate_aminotransferase_[isomerizing],_putative_2109295..2109445_NEGATIVE