Origin IGS: acaaagaaaggattgttcagttaaatttctaaactgaacccgccctaaacactgtggcaaaaagataaaattctcttagacgcaaacgtcgtcagagaatttcctgttttggatttgtgttttacgggcttggtatttta .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 taaaataccaagcccgtaaaacacaaatccaaaacaggaaattctctgacgacgtttgcgtctaagagaattttatctttttgccacagtgtttagggcgggttcagtttagaaatttaactgaacaatcctttctttgt Mask Tandem Repeat Region ================================================ acaaagaaaggattgttcagttaaatttctaaactgaacccgccctaaacactgtggcaaaaagataaaattctcttagacgcaaacgtcgtcagagaatttcctgttttggatttgtgttttacgggcttggtatttta Find is-nt database================================================ Query_seq: SSA_0240:SSA_0241|SSA_0240:SSA_0241:Acetyltransferase, GNAT family, putative:Ribosomal protein L11 methyltransferase, putative:->->:234021..234160 140 acaaagaaaggattgttcagttaaatttctaaactgaacccgccctaaacactgtggcaaaaagataaaattctcttagacgcaaacgtcgtcagagaatttcctgttttggatttgtgttttacgggcttggtatttta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_0240:SSA_0241|SSA_0240:SSA_0241:Acetyltransferase, GNAT family, putative:Ribosomal protein L11 methyltransferase, putative:->->:234021..234160 140 acaaagaaaggattgttcagttaaatttctaaactgaacccgccctaaacactgtggcaaaaagataaaattctcttagacgcaaacgtcgtcagagaatttcctgttttggatttgtgttttacgggcttggtatttta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_0240:SSA_0241|SSA_0240:SSA_0241:Acetyltransferase, GNAT family, putative:Ribosomal protein L11 methyltransferase, putative:->->:234021..234160 140 acaaagaaaggattgttcagttaaatttctaaactgaacccgccctaaacactgtggcaaaaagataaaattctcttagacgcaaacgtcgtcagagaatttcctgttttggatttgtgttttacgggcttggtatttta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 acaaagaaaggattgttcagttaaatttctaaactgaacccgccctaaacactgtggcaaaaagataaaattctcttagacgcaaacgtcgtcagagaatttcctgttttggatttgtgttttacgggcttggtatttta Predict ORF larger than 30AA ================================================ acaaagaaaggattgttcagttaaatttctaaactgaacccgccctaaacactgtggcaaaaagataaaattctcttagacgcaaacgtcgtcagagaatttcctgttttggatttgtgttttacgggcttggtatttta 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================================================ acaaagaaaggattgttcagttaaatttctaaactgaacccgccctaaacactgtggcaaaaagataaaattctcttagacgcaaacgtcgtcagagaatttcctgttttggatttgtgttttacgggcttggtatttta Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 78 HP_score: -5.4 Tail_Score: -4.98672 Start: 71 End: 99 Full_Region: atccaaaacaggaaa ttctctgacgacg tttg cgtctaagagaa ttttatctttttgcc ......................................................................ttctctgacgacgtttgcgtctaagagaa......................................... Find igs database================================================ Query_seq: SSA_0240:SSA_0241|SSA_0240:SSA_0241:Acetyltransferase, GNAT family, putative:Ribosomal protein L11 methyltransferase, putative:->->:234021..234160 140 acaaagaaaggattgttcagttaaatttctaaactgaacccgccctaaacactgtggcaaaaagataaaattctcttagacgcaaacgtcgtcagagaatttcctgttttggatttgtgttttacgggcttggtatttta Intra-Species Hit: Count: 1 Min: 1 Max: 140 Len: 140 Subject: NC_009009_SSA_0240_SSA_0241|Acetyltransferase, GNAT family, putative:Ribosomal protein L11 methyltransferase, putative|POSITIVE:POSITIVE|[234021,234160]|140 HSP 1 e-value: 5.0E-74 bit: 278.0 Len: 140 Query Start:1 Query End:140 Subject Strand: POSITIVE Subject Start: 1 Subject End: 140 acaaagaaaggattgttcagttaaatttctaaactgaacccgccctaaacactgtggcaaaaagataaaattctcttagacgcaaacgtcgtcagagaatttcctgttttggatttgtgttttacgggcttggtatttta acaaagaaaggattgttcagttaaatttctaaactgaacccgccctaaacactgtggcaaaaagataaaattctcttagacgcaaacgtcgtcagagaatttcctgttttggatttgtgttttacgggcttggtatttta Inter-species Hit: Count: 4 Min: 7 Max: 137 Len: 131 Subject: NC_008533_SPD_1573_SPD_1574|ribosomal protein L11 methyltransferase:MutT/nudix family protein|NEGATIVE:NEGATIVE|[1592462,1592598]|137 HSP 1 e-value: 5.0E-49 bit: 194.0 Len: 130 Query Start:7 Query End:136 Subject Strand: NEGATIVE Subject Start: 8 Subject End: 137 ......aaaggattgttcagttaaatttctaaactgaacccgccctaaacactgtggcaaaaagataaaattctcttagacgcaaacgtcgtcagagaatttcctgttttggatttgtgttttacgggcttggtat.... ......aaaggatggttcagttaaatttctaaactgaacccgccctaaacactgtgccaaaaagataaacttctcttagacacaagcgtcttcagagaatttcctattttggttttgtgttttacgggcttggtat.... Subject: NC_003028_SP_1782_SP_1783|ribosomal protein L11 methyltransferase:MutT/nudix family protein|NEGATIVE:NEGATIVE|[1701271,1701405]|135 HSP 1 e-value: 3.0E-47 bit: 188.0 Len: 131 Query Start:7 Query End:137 Subject Strand: NEGATIVE Subject Start: 5 Subject End: 135 ......aaaggattgttcagttaaatttctaaactgaacccgccctaaacactgtggcaaaaagataaaattctcttagacgcaaacgtcgtcagagaatttcctgttttggatttgtgttttacgggcttggtatt... ......aaaggatggttcagttacatttctaaactgaacccgccctaaacactgtgccaaaaagataaacttctcttagacacaagcgtcttcagagaatttcctattttggttttgtgttttacgggcttggtatt... Subject: smit_SMT_1261_SMT_1262|MutT/NUDIX family protein:ribosomal protein L11 methyltransferase|POSITIVE:POSITIVE|[1227155, 1227291]|137 HSP 1 e-value: 1.0E-46 bit: 186.0 Len: 130 Query Start:7 Query End:136 Subject Strand: POSITIVE Subject Start: 1 Subject End: 130 ......aaaggattgttcagttaaatttctaaactgaacccgccctaaacactgtggcaaaaagataaaattctcttagacgcaaacgtcgtcagagaatttcctgttttggatttgtgttttacgggcttggtat.... ......aaaggatggttcggttaaatttctaaactgaacccgccctaaacactgtgccaaaaagataaacttctcttagacacaagcgtcttcagagaatttcctattttggctttgtgttttacgggcttggtat.... Subject: NC_003098_spr1608_spr1609|ribosomal protein L11 methyltransferase:7, 8-dihydro-8-oxoguanine- triphosphatase|NEGATIVE:NEGATIVE|[1584958,1585067]|110 HSP 1 e-value: 5.0E-37 bit: 155.0 Len: 106 Query Start:7 Query End:112 Subject Strand: NEGATIVE Subject Start: 5 Subject End: 110 ......aaaggattgttcagttaaatttctaaactgaacccgccctaaacactgtggcaaaaagataaaattctcttagacgcaaacgtcgtcagagaatttcctgttttgg............................ ......aaaggatggttcagttaaatttctaaactgaacccgccctaaacactgtgccaaaaagataaacttctcttagacacaagcgtcttcagagaatttcctattttgg............................ Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAGGAUUGUUCAGUUAAAUUUCUAAACUGAACCCGCCCUAAACACUGUGGCAAAAAGAUAAAAUUCUCUUAGACGCAAACGUCGUCAGAGAAUUUCCUGUUUUGGAUUUGUGUUUUACGGGCUUGGUAUU ........((((((((.........))))))))..((((.((((((.....(((((.....(((((((((..((((....))))...)))))))))....))))).....))))))...))))........ (-38.00) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAUACCAAGCCCGUAAAACACAAAUCCAAAACAGGAAAUUCUCUGACGACGUUUGCGUCUAAGAGAAUUUUAUCUUUUUGCCACAGUGUUUAGGGCGGGUUCAGUUUAGAAAUUUAACUGAACAAUCCUUU ........((((...((((((.....(((((...((((((((((...((((....))))..))))))))))....))))).....)))))).))))..((((((((.(....)..))))))))........ (-42.30) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 299 39 3 138 113 NC_009009:SSA_2322|5end_Transcriptional_regulator,_TetR/AcrR_family,_putative_2327044..2327274_POSITIVE 295 59 20 189 129 NC_009009:SSA_1987|5end_hypothetical_protein_1983368..1983598_NEGATIVE 286 127 82 185 149 NC_009009:SSA_1439|5end_hypothetical_protein_1444373..1444603_NEGATIVE 283 130 87 66 17 NC_009009:SSA_0703|5end_Citrate_synthase,_putative_688154..688384_POSITIVE 272 120 72 97 40 NC_009009:SSA_0588|5end_L-cystine_ABC_transporter,_substrate-binding_component,_putative_579800..580030_POSITIVE 266 91 64 162 134 NC_009009:SSA_2007|5end_Chaperone_protein_dnaK/HSP70,_putative_2009272..2009502_NEGATIVE 266 93 55 216 180 NC_009009:SSA_1832|5end_hypothetical_protein_1822001..1822231_POSITIVE 262 107 75 45 1 NC_009009:SSA_1938|5end_Enoyl-acyl_carrier_protein(ACP)_reductase,_putative_1925738..1925968_NEGATIVE 260 130 81 145 89 NC_009009:SSA_0633|5end_Anthranilate_synthase_component_II,_putative_622813..623043_POSITIVE 259 99 65 221 189 NC_009009:SSA_1956|5end_ABC-type_Fe-S_cluster_assembly_transporter,_ATPase_component,_putative_1953414..1953644_NEGATIVE 254 127 82 210 170 NC_009009:SSA_1843|5end_Histidine_kinase,_putative_1837491..1837721_NEGATIVE 250 60 11 176 127 NC_009009:SSA_1680|5end_ABC-type_bacitracin_resistance_protein_A,_permease_component,_putative_1675200..1675430_NEGATIVE 250 60 11 177 128 NC_009009:SSA_1659|5end_ABC-type_antimicrobial_peptide_transport_system,_permease_component,_putative_1656819..1657049_NEGATIVE 248 68 25 64 13 NC_009009:SSA_0691|5end_D-ala,D-ala_ligase,_putative_675233..675463_POSITIVE 246 100 51 191 135 NC_009009:SSA_0749|5end_Competence_protein,_putative_730668..730898_POSITIVE 245 125 86 159 122 NC_009009:SSA_1575|5end_Glycosyl_transferase,_putative_1579110..1579340_NEGATIVE 244 60 20 47 4 NC_009009:SSA_0140|5end_Copper-translocating_P-type_ATPase,_putative_134626..134856_POSITIVE 243 70 21 88 30 NC_009009:SSA_1891|5end_Oxidoreductase,_aldo/keto_reductase_family,_putative_1888991..1889221_NEGATIVE 243 87 46 40 6 NC_009009:SSA_1753|5end_Transcriptional_regulator,_GntR_family_(repressor_of_trehalose_operon),_putative_1741944..1742174_POSITIVE 239 112 73 58 6 NC_009009:SSA_1913|5end_Xanthine/uracil_permease_family_protein,_putative_1904666..1904896_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 286 127 82 151 115 NC_009009:SSA_1440|3end_Phosphoribosyl-ATP_pyrophosphohydrolase,_putative_1444407..1444557_NEGATIVE 283 130 87 63 14 NC_009009:SSA_0702|3end_Aconitase_A,_putative_688231..688381_POSITIVE 282 128 96 37 7 NC_009009:SSA_0484|3end_Glutamyl-tRNA_reductase,_putative_485825..485975_POSITIVE 266 93 55 129 93 NC_009009:SSA_1831|3end_hypothetical_protein_1821994..1822144_POSITIVE 260 130 81 148 92 NC_009009:SSA_0632|3end_Anthranilate_synthase_component_I,_putative_622896..623046_POSITIVE 259 99 65 131 99 NC_009009:SSA_1957|3end_Glycosyl_transferase_N-acetylglucosaminyltransferase,_putative_1953504..1953654_NEGATIVE 259 128 81 53 3 NC_009009:SSA_0240|3end_Acetyltransferase,_GNAT_family,_putative_233960..234110_POSITIVE 253 106 75 133 104 NC_009009:SSA_1853|3end_S-ribosylhomocysteine_lyase,_putative_1849360..1849510_POSITIVE 253 129 82 143 102 NC_009009:SSA_0149|3end_hypothetical_protein_143833..143983_POSITIVE 248 110 62 109 54 NC_009009:SSA_2256|3end_hypothetical_protein_2251235..2251385_POSITIVE 248 129 81 103 49 NC_009009:SSA_1680|3end_ABC-type_bacitracin_resistance_protein_A,_permease_component,_putative_1673200..1673350_NEGATIVE 246 100 51 78 22 NC_009009:SSA_0748|3end_Sugar:H+_symporter,_permease_of_the_major_facilitator_superfamily,_putative_730635..730785_POSITIVE 245 125 86 92 55 NC_009009:SSA_1576|3end_Catabolite_control_protein_A,_putative_1579177..1579327_NEGATIVE 244 60 20 47 4 NC_009009:SSA_0139|3end_Copper_transport_operon_or_penicillinase_transcriptional_repressor,_putative_134706..134856_POSITIVE 243 123 83 79 23 NC_009009:SSA_2204|3end_hypothetical_protein_2205507..2205657_POSITIVE 243 127 82 67 12 NC_009009:SSA_1778|3end_Segregation_and_condensation_protein_B,_putative_1765142..1765292_NEGATIVE 239 125 86 63 15 NC_009009:SSA_1451|3end_Exonuclease_RexA,_putative_1452744..1452894_NEGATIVE 231 105 65 60 10 NC_009009:SSA_0387|3end_Transcriptional_regulator,_GntR_family,_putative_381702..381852_NEGATIVE 230 129 82 125 75 NC_009009:SSA_0051|3end_Dihydroxyacetone_kinase_phosphotransfer_protein,_putative_55644..55794_POSITIVE 229 123 81 48 1 NC_009009:SSA_1606|3end_Dephospho-CoA_kinase,_putative_1611829..1611979_NEGATIVE