Origin IGS: tgatctctcttatatttttagttagacttacaccattttaccattttatggaagatgttttcaacacaaaagctaaggaagatgtaaagttcttgtaaggaagaaaggtactttgatgtgccttataaacagccattaaaagactttttcaaaaaatatataaaaattttatatattttgcttgacttttttcctaagaggttgtagactatatatagaaagattatatataaatattttacacaaggaggtggtcct .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aggaccacctccttgtgtaaaatatttatatataatctttctatatatagtctacaacctcttaggaaaaaagtcaagcaaaatatataaaatttttatatattttttgaaaaagtcttttaatggctgtttataaggcacatcaaagtacctttcttccttacaagaactttacatcttccttagcttttgtgttgaaaacatcttccataaaatggtaaaatggtgtaagtctaactaaaaatataagagagatca Mask Tandem Repeat Region ================================================ tgatctctcttatatttttagttagacttacaccattttaccattttatggaagatgttttcaacacaaaagctaaggaagatgtaaagttcttgtaaggaagaaaggtactttgatgtgccttataaacagccattaaaagactttttcaaaaaatatataaaaattttatatattttgcttgacttttttcctaagaggttgtagactatatatagaaagattatatataaatattttacacaaggaggtggtcct Find is-nt database================================================ Query_seq: SSA_2335:SSA_2336|SSA_2335:SSA_2336:D-Ala-teichoic acid biosynthesis protein, putative:Transcriptional regulator, PadR family, putative:<-->:2338249..2338506 258 tgatctctcttatatttttagttagacttacaccattttaccattttatggaagatgttttcaacacaaaagctaaggaagatgtaaagttcttgtaaggaagaaaggtactttgatgtgccttataaacagccattaaaagactttttcaaaaaatatataaaaattttatatattttgcttgacttttttcctaagaggttgtagactatatatagaaagattatatataaatattttacacaaggaggtggtcct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_2335:SSA_2336|SSA_2335:SSA_2336:D-Ala-teichoic acid biosynthesis protein, putative:Transcriptional regulator, PadR family, putative:<-->:2338249..2338506 258 tgatctctcttatatttttagttagacttacaccattttaccattttatggaagatgttttcaacacaaaagctaaggaagatgtaaagttcttgtaaggaagaaaggtactttgatgtgccttataaacagccattaaaagactttttcaaaaaatatataaaaattttatatattttgcttgacttttttcctaagaggttgtagactatatatagaaagattatatataaatattttacacaaggaggtggtcct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_2335:SSA_2336|SSA_2335:SSA_2336:D-Ala-teichoic acid biosynthesis protein, putative:Transcriptional regulator, PadR family, putative:<-->:2338249..2338506 258 tgatctctcttatatttttagttagacttacaccattttaccattttatggaagatgttttcaacacaaaagctaaggaagatgtaaagttcttgtaaggaagaaaggtactttgatgtgccttataaacagccattaaaagactttttcaaaaaatatataaaaattttatatattttgcttgacttttttcctaagaggttgtagactatatatagaaagattatatataaatattttacacaaggaggtggtcct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tgatctctcttatatttttagttagacttacaccattttaccattttatggaagatgttttcaacacaaaagctaaggaagatgtaaagttcttgtaaggaagaaaggtactttgatgtgccttataaacagccattaaaagactttttcaaaaaatatataaaaattttatatattttgcttgacttttttcctaagaggttgtagactatatatagaaagattatatataaatattttacacaaggaggtggtcct Predict ORF larger than 30AA ================================================ Protein_Len: 31 Strand: + Start: 3 End: 95 .. M S L I F L V R L T P F Y H F M E D V F N T K A K E D V K F L ................................................................................................................................................................... Protein_Len: 34 Strand: - Start: 126 End: 227 ............................................................................................................................. L C G N F S K K L F Y I F I K Y I K S S K K G L L N Y V I Y L F I M ............................... Protein_Len: 32 Strand: - Start: 41 End: 136 ........................................ W K I S S T K L V F A L S S T F N K Y P L F T S Q H A K Y V A M .......................................................................................................................... tgatctctcttatatttttagttagacttacaccattttaccattttatggaagatgttttcaacacaaaagctaaggaagatgtaaagttcttgtaaggaagaaaggtactttgatgtgccttataaacagccattaaaagactttttcaaaaaatatataaaaattttatatattttgcttgacttttttcctaagaggttgtagactatatatagaaagattatatataaatattttacacaaggaggtggtcct 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: 83 Start: 181 End: 210 ....................................................................................................................................................................................CTTGACTTTTTTCCTAAGAGGTTGTAGACT................................................ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ tgatctctcttatatttttagttagacttacaccattttaccattttatggaagatgttttcaacacaaaagctaaggaagatgtaaagttcttgtaaggaagaaaggtactttgatgtgccttataaacagccattaaaagactttttcaaaaaatatataaaaattttatatattttgcttgacttttttcctaagaggttgtagactatatatagaaagattatatataaatattttacacaaggaggtggtcct Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 82 HP_score: -6.2 Tail_Score: -5.0133 Start: 157 End: 175 Full_Region: aaaagtcaagcaaaa tatataaa att tttatata ttttttgaaaaagtc ............................................................................................................................................................tatataaaatttttatata................................................................................... Find igs database================================================ Query_seq: SSA_2335:SSA_2336|SSA_2335:SSA_2336:D-Ala-teichoic acid biosynthesis protein, putative:Transcriptional regulator, PadR family, putative:<-->:2338249..2338506 258 tgatctctcttatatttttagttagacttacaccattttaccattttatggaagatgttttcaacacaaaagctaaggaagatgtaaagttcttgtaaggaagaaaggtactttgatgtgccttataaacagccattaaaagactttttcaaaaaatatataaaaattttatatattttgcttgacttttttcctaagaggttgtagactatatatagaaagattatatataaatattttacacaaggaggtggtcct Intra-Species Hit: Count: 1 Min: 1 Max: 258 Len: 258 Subject: NC_009009_SSA_2335_SSA_2336|D-Ala-teichoic acid biosynthesis protein, putative:Transcriptional regulator, PadR family, putative|NEGATIVE:POSITIVE|[2338249,2338506]|258 HSP 1 e-value: 5.0E-72 bit: 272.0 Len: 137 Query Start:1 Query End:137 Subject Strand: POSITIVE Subject Start: 1 Subject End: 137 tgatctctcttatatttttagttagacttacaccattttaccattttatggaagatgttttcaacacaaaagctaaggaagatgtaaagttcttgtaaggaagaaaggtactttgatgtgccttataaacagccatt......................................................................................................................... tgatctctcttatatttttagttagacttacaccattttaccattttatggaagatgttttcaacacaaaagctaaggaagatgtaaagttcttgtaaggaagaaaggtactttgatgtgccttataaacagccatt......................................................................................................................... HSP 2 e-value: 1.0E-29 bit: 131.0 Len: 66 Query Start:193 Query End:258 Subject Strand: POSITIVE Subject Start: 193 Subject End: 258 ................................................................................................................................................................................................cctaagaggttgtagactatatatagaaagattatatataaatattttacacaaggaggtggtcct ................................................................................................................................................................................................cctaagaggttgtagactatatatagaaagattatatataaatattttacacaaggaggtggtcct Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGAUCUCUCUUAUAUUUUUAGUUAGACUUACACCAUUUUACCAUUUUAUGGAAGAUGUUUUCAACACAAAAGCUAAGGAAGAUGUAAAGUUCUUGUAAGGAAGAAAGGUACUUUGAUGUGCCUUAUAAACAGCCAUUAAAAGACUUUUUCAAAAAAUAUAUAAAAAUUUUAUAUAUUUUGCUUGACUUUUUUCCUAAGAGGUUGUAGACUAUAUAUAGAAAGAUUAUAUAUAAAUAUUUUACACAAGGAGGUGGUCCU .((((((((((...(((((((((..........((((((.((((...)))))))))).............)))))))))...((((((((((((.(((((....(((((((......)))))))........)).))).))))............((((((((...(((((((((((((((..((((((((....)))))))))))))..))))))))))...))))))))....))))))))..)))))).)))).. (-53.00) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGGACCACCUCCUUGUGUAAAAUAUUUAUAUAUAAUCUUUCUAUAUAUAGUCUACAACCUCUUAGGAAAAAAGUCAAGCAAAAUAUAUAAAAUUUUUAUAUAUUUUUUGAAAAAGUCUUUUAAUGGCUGUUUAUAAGGCACAUCAAAGUACCUUUCUUCCUUACAAGAACUUUACAUCUUCCUUAGCUUUUGUGUUGAAAACAUCUUCCAUAAAAUGGUAAAAUGGUGUAAGUCUAACUAAAAAUAUAAGAGAGAUCA ((((.....))))(((((((.....)))))))..((((((((((((.((((........(((((((((.((((((((..(((((((((((.....)))))))))))))))....(((((.(((.......))).)))))............)))).)))))...))))..((((((((....(((.((((((((..(((......)))))))))).).)))...))))))))....))))...)))).)))))))).. (-45.60) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 826 120 71 211 162 NC_009009:SSA_2335|5end_D-Ala-teichoic_acid_biosynthesis_protein,_putative_2338158..2338388_NEGATIVE 266 150 105 105 50 NC_009009:SSA_2054|5end_hypothetical_protein_2057899..2058129_NEGATIVE 256 45 12 228 187 NC_009009:SSA_1698|5end_Galactose-6-phosphate_isomerase,_LacB_subunit,_putative_1690648..1690878_NEGATIVE 254 150 106 175 121 NC_009009:SSA_0570|5end_Glutamyl-tRNA(Gln)_amidotransferase_subunit_A,_putative_563915..564145_POSITIVE 247 226 181 84 32 NC_009009:SSA_0643|5end_hypothetical_protein_630194..630424_NEGATIVE 247 226 181 225 173 NC_009009:SSA_0642|5end_Type_4_prepilin_peptidase,_putative_630053..630283_NEGATIVE 238 150 106 100 62 NC_009009:SSA_1133|5end_TatA,_sec-independent_protein_secretion_pathway_component,_putative_1159397..1159627_POSITIVE 235 124 86 59 27 NC_009009:SSA_0346|5end_hypothetical_protein_339448..339678_POSITIVE 233 150 102 94 42 NC_009009:SSA_1208|5end_23S_rRNA_pseudouridine_synthase,_putative_1233185..1233415_NEGATIVE 230 47 3 152 100 NC_009009:SSA_1221|5end_L-lactate_dehydrogenase,_putative_1243956..1244186_POSITIVE 226 219 179 130 91 NC_009009:SSA_1997|5end_Membrane_spanning_protein,_putative_1994911..1995141_NEGATIVE 226 134 96 207 173 NC_009009:SSA_1856|5end_hypothetical_protein_1852208..1852438_NEGATIVE 226 108 63 171 137 NC_009009:SSA_0238|5end_hypothetical_protein_232481..232711_POSITIVE 225 134 91 58 3 NC_009009:SSA_0597|5end_hypothetical_protein_587566..587796_POSITIVE 218 90 49 227 178 NC_009009:SSA_0745|5end_hypothetical_protein_727035..727265_NEGATIVE 216 110 63 128 72 NC_009009:SSA_0175|5end_Penicillin-binding_protein_1B,_putative_172152..172382_POSITIVE 215 120 76 220 174 NC_009009:SSA_1971|5end_hypothetical_protein_1967167..1967397_POSITIVE 215 120 71 94 41 NC_009009:SSA_1948|5end_Oligopeptide-binding_lipoprotein_precursor,_putative_1942170..1942400_NEGATIVE 215 47 4 105 73 NC_009009:SSA_0539|5end_PduO_protein,_putative_534233..534463_POSITIVE 211 134 94 229 175 NC_009009:SSA_2002|5end_tRNA_pseudouridine_synthase_A,_putative_1998959..1999189_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 266 150 105 68 13 NC_009009:SSA_2055|3end_hypothetical_protein_2057936..2058086_NEGATIVE 241 122 91 138 110 NC_009009:SSA_0569|3end_Aspartyl/glutamyl-tRNA(Asn/Gln)_amidotransferase_subunit_C,_putative_563995..564145_POSITIVE 238 150 106 100 62 NC_009009:SSA_1132|3end_TatC,_sec-independent_protein_translocase,_putative_1159477..1159627_POSITIVE 236 114 72 91 55 NC_009009:SSA_1877|3end_hypothetical_protein_1871915..1872065_POSITIVE 233 150 102 97 45 NC_009009:SSA_1209|3end_Inorganic_polyphosphate/ATP-NAD_kinase,_putative_1233182..1233332_NEGATIVE 215 47 4 46 14 NC_009009:SSA_0538|3end_PduH_protein,_putative_534254..534404_POSITIVE 209 62 25 43 11 NC_009009:SSA_0938|3end_hypothetical_protein_946945..947095_POSITIVE 207 220 182 143 107 NC_009009:SSA_0734|3end_Arsenical_resistance_operon_transcription_repressor_(ArsR),_putative_717196..717346_POSITIVE 206 134 91 44 5 NC_009009:SSA_1724|3end_CBS_domain_protein,_putative_1709897..1710047_NEGATIVE 206 137 92 58 5 NC_009009:SSA_0986|3end_Choline_transporter,_putative_989081..989231_POSITIVE 206 209 179 151 114 NC_009009:SSA_0313|3end_Conserved_uncharacterized_protein_308389..308539_NEGATIVE 204 79 39 74 22 NC_009009:SSA_2016|3end_Phosphoglycerate_mutase,_putative_2015592..2015742_NEGATIVE 203 205 176 37 12 NC_009009:SSA_0784|3end_Proton-translocating_ATPase,_F0_sector,_subunit_b,_putative_768124..768274_POSITIVE 202 122 88 134 101 NC_009009:SSA_1180|3end_hypothetical_protein_1207819..1207969_NEGATIVE 201 218 174 110 70 NC_009009:SSA_0567|3end_Isochorismitase_family_protein,_putative_561442..561592_POSITIVE 200 150 107 61 14 NC_009009:SSA_1075|3end_Coproporphyrinogen_III_oxidase,_putative_1094303..1094453_POSITIVE 200 127 93 77 37 NC_009009:SSA_0033|3end_Phosphoribosylglycinamide_(GAR)_formyltransferase,_putative_39600..39750_POSITIVE 198 122 92 34 2 NC_009009:SSA_0885|3end_hypothetical_protein_879065..879215_NEGATIVE 198 78 32 104 52 NC_009009:SSA_0195|3end_hypothetical_protein_195831..195981_POSITIVE 197 119 71 89 37 NC_009009:SSA_2207|3end_hypothetical_protein_2206868..2207018_NEGATIVE