Origin IGS: caaggcacccctttctctaatttcctatcattttatcatatctagcagataaagcctagagaaaactagctagttaaggaaacgtaagaatgttgttgatttgaaatatatcgtttacacgaaaaaccaaactcttcgagagcttggttttctttatgtcatatt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aatatgacataaagaaaaccaagctctcgaagagtttggtttttcgtgtaaacgatatatttcaaatcaacaacattcttacgtttccttaactagctagttttctctaggctttatctgctagatatgataaaatgataggaaattagagaaaggggtgccttg Mask Tandem Repeat Region ================================================ caaggcacccctttctctaatttcctatcattttatcatatctagcagataaagcctagagaaaactagctagttaaggaaacgtaagaatgttgttgatttgaaatatatcgtttacacgaaaaaccaaactcttcgagagcttggttttctttatgtcatatt Find is-nt database================================================ Query_seq: SSA_1172:SSA_1173|SSA_1172:SSA_1173:hypothetical protein:Lipoate protein ligase A, putative:<-<-:1200017..1200181 165 caaggcacccctttctctaatttcctatcattttatcatatctagcagataaagcctagagaaaactagctagttaaggaaacgtaagaatgttgttgatttgaaatatatcgtttacacgaaaaaccaaactcttcgagagcttggttttctttatgtcatatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_1172:SSA_1173|SSA_1172:SSA_1173:hypothetical protein:Lipoate protein ligase A, putative:<-<-:1200017..1200181 165 caaggcacccctttctctaatttcctatcattttatcatatctagcagataaagcctagagaaaactagctagttaaggaaacgtaagaatgttgttgatttgaaatatatcgtttacacgaaaaaccaaactcttcgagagcttggttttctttatgtcatatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_1172:SSA_1173|SSA_1172:SSA_1173:hypothetical protein:Lipoate protein ligase A, putative:<-<-:1200017..1200181 165 caaggcacccctttctctaatttcctatcattttatcatatctagcagataaagcctagagaaaactagctagttaaggaaacgtaagaatgttgttgatttgaaatatatcgtttacacgaaaaaccaaactcttcgagagcttggttttctttatgtcatatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 caaggcacccctttctctaatttcctatcattttatcatatctagcagataaagcctagagaaaactagctagttaaggaaacgtaagaatgttgttgatttgaaatatatcgtttacacgaaaaaccaaactcttcgagagcttggttttctttatgtcatatt Predict ORF larger than 30AA ================================================ caaggcacccctttctctaatttcctatcattttatcatatctagcagataaagcctagagaaaactagctagttaaggaaacgtaagaatgttgttgatttgaaatatatcgtttacacgaaaaaccaaactcttcgagagcttggttttctttatgtcatatt 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================================================ caaggcacccctttctctaatttcctatcattttatcatatctagcagataaagcctagagaaaactagctagttaaggaaacgtaagaatgttgttgatttgaaatatatcgtttacacgaaaaaccaaactcttcgagagcttggttttctttatgtcatatt Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 90 HP_score: -8.3 Tail_Score: -5.06016 Start: 127 End: 147 Full_Region: CGTTTACACGAAAAA CCAAACTCT TCG AGAGCTTGG TTTTCTTTATGTCAT ..............................................................................................................................CCAAACTCTTCGAGAGCTTGG.................. Find igs database================================================ Query_seq: SSA_1172:SSA_1173|SSA_1172:SSA_1173:hypothetical protein:Lipoate protein ligase A, putative:<-<-:1200017..1200181 165 caaggcacccctttctctaatttcctatcattttatcatatctagcagataaagcctagagaaaactagctagttaaggaaacgtaagaatgttgttgatttgaaatatatcgtttacacgaaaaaccaaactcttcgagagcttggttttctttatgtcatatt Intra-Species Hit: Count: 1 Min: 1 Max: 165 Len: 165 Subject: NC_009009_SSA_1172_SSA_1173|hypothetical protein:Lipoate protein ligase A, putative|NEGATIVE:NEGATIVE|[1200017,1200181]|165 HSP 1 e-value: 7.0E-89 bit: 327.0 Len: 165 Query Start:1 Query End:165 Subject Strand: POSITIVE Subject Start: 1 Subject End: 165 caaggcacccctttctctaatttcctatcattttatcatatctagcagataaagcctagagaaaactagctagttaaggaaacgtaagaatgttgttgatttgaaatatatcgtttacacgaaaaaccaaactcttcgagagcttggttttctttatgtcatatt caaggcacccctttctctaatttcctatcattttatcatatctagcagataaagcctagagaaaactagctagttaaggaaacgtaagaatgttgttgatttgaaatatatcgtttacacgaaaaaccaaactcttcgagagcttggttttctttatgtcatatt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CAAGGCACCCCUUUCUCUAAUUUCCUAUCAUUUUAUCAUAUCUAGCAGAUAAAGCCUAGAGAAAACUAGCUAGUUAAGGAAACGUAAGAAUGUUGUUGAUUUGAAAUAUAUCGUUUACACGAAAAACCAAACUCUUCGAGAGCUUGGUUUUCUUUAUGUCAUAUU ...(((.....((((((((...........(((((((..........)))))))..))))))))..........((((((..(((..(((((.((((.......))))...)))))..)))..(((((((.(((.....))).))))))))))))).)))..... (-28.62) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAUAUGACAUAAAGAAAACCAAGCUCUCGAAGAGUUUGGUUUUUCGUGUAAACGAUAUAUUUCAAAUCAACAACAUUCUUACGUUUCCUUAACUAGCUAGUUUUCUCUAGGCUUUAUCUGCUAGAUAUGAUAAAAUGAUAGGAAAUUAGAGAAAGGGGUGCCUUG ....(((.(((...((((((((((((.....))))))))))))((((....))))..))).))).....((..(.(((((..(((((((...(((((.(((((.....)))))......))))).(((......)))..)))))))..))))).)..))...... (-38.00) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 843 50 1 141 92 NC_009009:SSA_1172|5end_hypothetical_protein_1199926..1200156_NEGATIVE 291 60 12 151 96 NC_009009:SSA_0250|5end_GTP_pyrophosphokinase,_putative_242167..242397_POSITIVE 282 99 54 70 28 NC_009009:SSA_2056|5end_Cinnamoyl_ester_hydrolase,_putative_2058587..2058817_POSITIVE 271 50 2 124 72 NC_009009:SSA_0596|5end_hypothetical_protein_586913..587143_POSITIVE 257 158 112 178 121 NC_009009:SSA_1362|5end_ORFB,_transposon_ISSsa2_1377911..1378141_POSITIVE 254 158 130 178 149 NC_009009:SSA_0266|5end_ORFB,_transposon_ISSsa1_260134..260364_POSITIVE 253 58 12 133 92 NC_009009:SSA_2222|5end_Tyrosine-protein_kinase_Wze,_putative_2223997..2224227_NEGATIVE 253 59 19 134 94 NC_009009:SSA_0928|5end_ABC-type_multidrug_transporter,_ATPase_and_permease_components,_putative_936679..936909_POSITIVE 247 90 44 54 16 NC_009009:SSA_0639|5end_hypothetical_protein_627906..628136_NEGATIVE 242 75 43 48 10 NC_009009:SSA_1672|5end_hypothetical_protein_1670389..1670619_NEGATIVE 238 80 39 223 167 NC_009009:SSA_0591|5end_Conserved_uncharacterized_protein_582769..582999_POSITIVE 237 153 128 176 142 NC_009009:SSA_0232|5end_hypothetical_protein_227012..227242_POSITIVE 237 70 21 140 97 NC_009009:SSA_0098|5end_Hydrolase,_haloacid_dehalogenase-like_family,_putative_99422..99652_POSITIVE 234 71 36 190 152 NC_009009:SSA_1869|5end_ATP-dependent_RNA_helicase,_putative_1865495..1865725_NEGATIVE 234 85 41 180 136 NC_009009:SSA_1414|5end_hypothetical_protein_1425412..1425642_NEGATIVE 234 55 13 139 91 NC_009009:SSA_1128|5end_Voltage_gated_chloride_channel_EriC,_putative_1153250..1153480_POSITIVE 232 50 14 142 103 NC_009009:SSA_2017|5end_Hypothetical_protein_(possibly_membrane-associated)_2017331..2017561_NEGATIVE 232 152 111 61 24 NC_009009:SSA_1152|5end_Protein_chain_release_factor_A,_putative_1180759..1180989_POSITIVE 231 79 40 207 147 NC_009009:SSA_1866|5end_hypothetical_protein_1862182..1862412_NEGATIVE 231 40 12 129 96 NC_009009:SSA_1529|5end_Lysyl-tRNA_synthetase,_putative_1535871..1536101_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 306 89 44 69 20 NC_009009:SSA_0186|3end_Competence_protein_ComYC,_putative_190458..190608_POSITIVE 271 50 2 114 62 NC_009009:SSA_0595|3end_hypothetical_protein_586983..587133_POSITIVE 265 84 44 56 8 NC_009009:SSA_1685|3end_Two-component_response_transcriptional_regulator_(CheY-like_receiver_and_winged-helix_DNA-binding_domains),_putative_1678390..1678540_NEGATIVE 253 58 12 122 81 NC_009009:SSA_2223|3end_Capsular_polysaccharide_biosynthesis_protein_Wzd_(chain_length_regulator),_putative_2224008..2224158_NEGATIVE 253 59 19 115 75 NC_009009:SSA_0927|3end_Transcriptional_regulator,_TetR/AcrR_family,_putative_936740..936890_POSITIVE 246 80 40 34 3 NC_009009:SSA_2076|3end_Conserved_uncharacterized_protein_2079390..2079540_NEGATIVE 242 75 43 146 108 NC_009009:SSA_1672|3end_hypothetical_protein_1670291..1670441_NEGATIVE 237 49 7 126 94 NC_009009:SSA_0865|3end_hypothetical_protein_856850..857000_POSITIVE 237 70 21 143 100 NC_009009:SSA_0097|3end_Multi_antimicrobial_extrusion_(MATE)_family_transporter,_putative_99505..99655_POSITIVE 234 71 36 85 47 NC_009009:SSA_1870|3end_Phospho-N-acetylmuramoyl-pentapeptide-_transferase,_putative_1865600..1865750_NEGATIVE 232 60 14 95 37 NC_009009:SSA_0195|3end_hypothetical_protein_195831..195981_POSITIVE 227 79 36 140 88 NC_009009:SSA_2170|3end_hypothetical_protein_2169557..2169707_NEGATIVE 227 89 42 69 17 NC_009009:SSA_0220|3end_PTS_system,_mannose-specific_IIB_component,_putative_216422..216572_POSITIVE 225 79 44 151 112 NC_009009:SSA_0410|3end_hypothetical_protein_405750..405900_NEGATIVE 224 79 34 71 15 NC_009009:SSA_0690|3end_Recombinational_DNA_repair_protein_(RecF_pathway),_putative_675108..675258_POSITIVE 224 48 2 114 69 NC_009009:SSA_0193|3end_CAAX_amino_terminal_protease_family_protein,_putative_195075..195225_POSITIVE 223 60 11 74 26 NC_009009:SSA_1133|3end_TatA,_sec-independent_protein_secretion_pathway_component,_putative_1159665..1159815_POSITIVE 223 78 34 65 6 NC_009009:SSA_0477|3end_Cobalamin_biosynthesis_protein_CbiM_(ABC-type_cobalt_transporter),_putative_480085..480235_POSITIVE 223 74 43 32 5 NC_009009:SSA_0375|3end_D-methionine-binding_lipoprotein_(ABC-type_transporter),_putative_365209..365359_POSITIVE 221 49 1 102 47 NC_009009:SSA_2217|3end_Cps9H,_putative_2218086..2218236_NEGATIVE