Origin IGS: aagtaactttctaaaattttattttcatcctagtataacaaaaaaatcctaaataaaaccaatttaaaaactggaaattaagggctggtataatactttacttgccaaactgtctctttttgtttatattagttctataaggtttcttggaggcgtttgc .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 gcaaacgcctccaagaaaccttatagaactaatataaacaaaaagagacagtttggcaagtaaagtattataccagcccttaatttccagtttttaaattggttttatttaggatttttttgttatactaggatgaaaataaaattttagaaagttactt Mask Tandem Repeat Region ================================================ aagtaactttctaaaattttattttcatcctagtataacaaaaaaatcctaaataaaaccaatttaaaaactggaaattaagggctggtataatactttacttgccaaactgtctctttttgtttatattagttctataaggtttcttggaggcgtttgc Find is-nt database================================================ Query_seq: SSA_0426:SSA_0427|SSA_0426:SSA_0427:hypothetical protein:DNA-binding transcriptional activator, SARP family, putative:<-->:424477..424636 160 aagtaactttctaaaattttattttcatcctagtataacaaaaaaatcctaaataaaaccaatttaaaaactggaaattaagggctggtataatactttacttgccaaactgtctctttttgtttatattagttctataaggtttcttggaggcgtttgc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_0426:SSA_0427|SSA_0426:SSA_0427:hypothetical protein:DNA-binding transcriptional activator, SARP family, putative:<-->:424477..424636 160 aagtaactttctaaaattttattttcatcctagtataacaaaaaaatcctaaataaaaccaatttaaaaactggaaattaagggctggtataatactttacttgccaaactgtctctttttgtttatattagttctataaggtttcttggaggcgtttgc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_0426:SSA_0427|SSA_0426:SSA_0427:hypothetical protein:DNA-binding transcriptional activator, SARP family, putative:<-->:424477..424636 160 aagtaactttctaaaattttattttcatcctagtataacaaaaaaatcctaaataaaaccaatttaaaaactggaaattaagggctggtataatactttacttgccaaactgtctctttttgtttatattagttctataaggtttcttggaggcgtttgc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aagtaactttctaaaattttattttcatcctagtataacaaaaaaatcctaaataaaaccaatttaaaaactggaaattaagggctggtataatactttacttgccaaactgtctctttttgtttatattagttctataaggtttcttggaggcgtttgc Predict ORF larger than 30AA ================================================ Protein_Len: 30 Strand: + Start: 71 End: 160 ...................................................................... M E I K G W Y N T L L A K L S L F V Y I S S I R F L G G V C aagtaactttctaaaattttattttcatcctagtataacaaaaaaatcctaaataaaaccaatttaaaaactggaaattaagggctggtataatactttacttgccaaactgtctctttttgtttatattagttctataaggtttcttggaggcgtttgc 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: 89 Start: 101 End: 130 ....................................................................................................CTTGCCAAACTGTCTCTTTTTGTTTATATT.............................. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ aagtaactttctaaaattttattttcatcctagtataacaaaaaaatcctaaataaaaccaatttaaaaactggaaattaagggctggtataatactttacttgccaaactgtctctttttgtttatattagttctataaggtttcttggaggcgtttgc Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_0426:SSA_0427|SSA_0426:SSA_0427:hypothetical protein:DNA-binding transcriptional activator, SARP family, putative:<-->:424477..424636 160 aagtaactttctaaaattttattttcatcctagtataacaaaaaaatcctaaataaaaccaatttaaaaactggaaattaagggctggtataatactttacttgccaaactgtctctttttgtttatattagttctataaggtttcttggaggcgtttgc Intra-Species Hit: Count: 1 Min: 1 Max: 160 Len: 160 Subject: NC_009009_SSA_0426_SSA_0427|hypothetical protein:DNA-binding transcriptional activator, SARP family, putative|NEGATIVE:POSITIVE|[424477,424636]|160 HSP 1 e-value: 2.0E-73 bit: 276.0 Len: 160 Query Start:1 Query End:160 Subject Strand: POSITIVE Subject Start: 1 Subject End: 160 aagtaactttctaaaattttattttcatcctagtataacnnnnnnntcctaaataaaaccaatttaaaaactggaaattaagggctggtataatactttacttgccaaactgtctctttttgtttatattagttctataaggtttcttggaggcgtttgc aagtaactttctaaaattttattttcatcctagtataacaaaaaaatcctaaataaaaccaatttaaaaactggaaattaagggctggtataatactttacttgccaaactgtctctttttgtttatattagttctataaggtttcttggaggcgtttgc Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAGUAACUUUCUAAAAUUUUAUUUUCAUCCUAGUAUAACAAAAAAAUCCUAAAUAAAACCAAUUUAAAAACUGGAAAUUAAGGGCUGGUAUAAUACUUUACUUGCCAAACUGUCUCUUUUUGUUUAUAUUAGUUCUAUAAGGUUUCUUGGAGGCGUUUGC ......(((((..(((((((((.......(((((((((((((((..............(((..........)))........(((.((((........)))).)))..........)))))).)))))))))....)))))))))...)))))....... (-26.90) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GCAAACGCCUCCAAGAAACCUUAUAGAACUAAUAUAAACAAAAAGAGACAGUUUGGCAAGUAAAGUAUUAUACCAGCCCUUAAUUUCCAGUUUUUAAAUUGGUUUUAUUUAGGAUUUUUUUGUUAUACUAGGAUGAAAAUAAAAUUUUAGAAAGUUACUU ...(((.....((((((((((.(((((((((((.((((.((...((((......(((..(((........)))..))).....))))...)))))).)))))))))))..)))..))))))).....(((((((.........)))))))...))).... (-25.90) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 827 120 71 211 162 NC_009009:SSA_0426|5end_hypothetical_protein_424386..424616_NEGATIVE 303 123 81 154 114 NC_009009:SSA_1828|5end_Glycerol_uptake_facilitator_protein,_putative_1818007..1818237_POSITIVE 283 120 71 165 108 NC_009009:SSA_1467|5end_Chorismate_synthase,_putative_1474293..1474523_NEGATIVE 274 118 71 60 8 NC_009009:SSA_2182|5end_hypothetical_protein_2181020..2181250_NEGATIVE 274 119 71 79 32 NC_009009:SSA_0441|5end_hypothetical_protein_441481..441711_POSITIVE 267 160 116 227 178 NC_009009:SSA_1398|5end_Membrane_protein,_hemolysin_III-like,_putative_1410881..1411111_POSITIVE 267 140 91 86 32 NC_009009:SSA_1010|5end_UDP-glucose_4-epimerase,_putative_1012739..1012969_POSITIVE 266 125 82 202 150 NC_009009:SSA_0487|5end_Delta-aminolevulinic_acid_dehydratase,_putative_487349..487579_POSITIVE 256 160 113 106 52 NC_009009:SSA_1754|5end_hypothetical_protein_1743478..1743708_NEGATIVE 252 124 81 110 64 NC_009009:SSA_1621|5end_Amino_acid_transporter,_putative_1624623..1624853_NEGATIVE 247 114 71 121 76 NC_009009:SSA_1659|5end_ABC-type_antimicrobial_peptide_transport_system,_permease_component,_putative_1656819..1657049_NEGATIVE 245 160 113 88 34 NC_009009:SSA_2309|5end_Fimbrial_assembly_protein,_putative_2311886..2312116_NEGATIVE 245 154 113 136 96 NC_009009:SSA_2062|5end_hypothetical_protein_2063521..2063751_NEGATIVE 244 121 81 128 85 NC_009009:SSA_1789|5end_Metal-dependent_phosphohydrolase,_HD_superfamily,_putative_1772856..1773086_NEGATIVE 242 114 82 120 86 NC_009009:SSA_1680|5end_ABC-type_bacitracin_resistance_protein_A,_permease_component,_putative_1675200..1675430_NEGATIVE 238 112 72 152 108 NC_009009:SSA_2338|5end_Conserved_uncharacterized_protein_2339272..2339502_POSITIVE 238 128 82 112 63 NC_009009:SSA_1386|5end_NADPH-dependent_FMN_reductase,_putative_1402800..1403030_POSITIVE 237 119 71 79 13 NC_009009:SSA_1575|5end_Glycosyl_transferase,_putative_1579110..1579340_NEGATIVE 236 123 81 161 118 NC_009009:SSA_0589|5end_Acetylornithine_deacetylase/succinyl-diaminopimelate_desuccinylase_(M20/M25/M40_family_peptidase),_putative_580745..580975_POSITIVE 235 160 115 177 136 NC_009009:SSA_2122|5end_hypothetical_protein_2127607..2127837_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 303 123 81 85 45 NC_009009:SSA_1827|3end_Alpha-glycerophosphate_oxidase,_putative_1818018..1818168_POSITIVE 283 120 71 73 16 NC_009009:SSA_1468|3end_3-dehydroquinate_synthase,_putative_1474385..1474535_NEGATIVE 267 140 91 82 28 NC_009009:SSA_1009|3end_Galactose-1-phosphate-uridylyltransferase,_putative_1012815..1012965_POSITIVE 256 160 113 109 55 NC_009009:SSA_1755|3end_hypothetical_protein_1743475..1743625_NEGATIVE 248 103 66 55 12 NC_009009:SSA_1754|3end_hypothetical_protein_1743125..1743275_NEGATIVE 247 114 71 121 76 NC_009009:SSA_1660|3end_ABC-type_antimicrobial_peptide_transport_system,_ATPase_component,_putative_1656819..1656969_NEGATIVE 245 154 113 41 1 NC_009009:SSA_2063|3end_Aminopeptidase_PepS,_putative_2063616..2063766_NEGATIVE 244 121 81 83 40 NC_009009:SSA_1790|3end_SpoU_rRNA_Methylase_family_protein,_putative_1772901..1773051_NEGATIVE 242 114 82 139 105 NC_009009:SSA_1681|3end_ABC-type_bacitracin_resistance_protein_A,_ATPase_component,_putative_1675181..1675331_NEGATIVE 235 160 115 120 79 NC_009009:SSA_2123|3end_Dimethyladenosine_transferase,_putative_2127664..2127814_NEGATIVE 234 160 112 113 75 NC_009009:SSA_0613|3end_Glucosyltransferase,_putative_606633..606783_POSITIVE 233 150 101 114 68 NC_009009:SSA_1848|3end_Methionyl-tRNA_formyltransferase,_putative_1842243..1842393_NEGATIVE 233 159 111 58 9 NC_009009:SSA_0554|3end_hypothetical_protein_549692..549842_POSITIVE 232 150 110 112 69 NC_009009:SSA_0138|3end_Metal-binding_(Zn)_permease,_putative_134115..134265_POSITIVE 231 118 71 67 26 NC_009009:SSA_1448|3end_ATP_phosphoribosyltransferase_regulatory_subunit,_putative_1449828..1449978_NEGATIVE 225 150 101 148 103 NC_009009:SSA_1375|3end_Multidrug_ABC_transporter,_ATPase_and_permease_components,_putative_1393085..1393235_NEGATIVE 225 114 71 77 21 NC_009009:SSA_1079|3end_hypothetical_protein_1097448..1097598_POSITIVE 224 150 108 104 59 NC_009009:SSA_1752|3end_Phosphotransferase_system,_trehalose-specific_IIBC_component,_putative_1739812..1739962_NEGATIVE 224 148 104 117 77 NC_009009:SSA_0520|3end_Ethanolamine_ammonia-lyase_light_chain,_putative_520462..520612_POSITIVE 223 150 101 124 85 NC_009009:SSA_1070|3end_Ribosomal_large_subunit_pseudouridine_synthase_D,_putative_1089718..1089868_POSITIVE