Origin IGS: aaacagccgcgaatcatttgattcgcggctgttttgtatgttttctaaatgttggactaggactagcaaacatcttctaatattaactcgcaatgcggttcttcaagcagtaatttaaagtttcgcttagacaaagct .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 agctttgtctaagcgaaactttaaattactgcttgaagaaccgcattgcgagttaatattagaagatgtttgctagtcctagtccaacatttagaaaacatacaaaacagccgcgaatcaaatgattcgcggctgttt Mask Tandem Repeat Region ================================================ aaacagccgcgaatcatttgattcgcggctgttttgtatgttttctaaatgttggactaggactagcaaacatcttctaatattaactcgcaatgcggttcttcaagcagtaatttaaagtttcgcttagacaaagct Find is-nt database================================================ Query_seq: SSA_1951:SSA_1952|SSA_1951:SSA_1952:Penicillin-binding protein 3, putative:ABC-type Fe-S cluster assembly transporter, permease component, putative:-><-:1948164..1948301 138 aaacagccgcgaatcatttgattcgcggctgttttgtatgttttctaaatgttggactaggactagcaaacatcttctaatattaactcgcaatgcggttcttcaagcagtaatttaaagtttcgcttagacaaagct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_1951:SSA_1952|SSA_1951:SSA_1952:Penicillin-binding protein 3, putative:ABC-type Fe-S cluster assembly transporter, permease component, putative:-><-:1948164..1948301 138 aaacagccgcgaatcatttgattcgcggctgttttgtatgttttctaaatgttggactaggactagcaaacatcttctaatattaactcgcaatgcggttcttcaagcagtaatttaaagtttcgcttagacaaagct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_1951:SSA_1952|SSA_1951:SSA_1952:Penicillin-binding protein 3, putative:ABC-type Fe-S cluster assembly transporter, permease component, putative:-><-:1948164..1948301 138 aaacagccgcgaatcatttgattcgcggctgttttgtatgttttctaaatgttggactaggactagcaaacatcttctaatattaactcgcaatgcggttcttcaagcagtaatttaaagtttcgcttagacaaagct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aaacagccgcgaatcatttgattcgcggctgttttgtatgttttctaaatgttggactaggactagcaaacatcttctaatattaactcgcaatgcggttcttcaagcagtaatttaaagtttcgcttagacaaagct Predict ORF larger than 30AA ================================================ Protein_Len: 31 Strand: - Start: 1 End: 93 F L R S D N S E R S N Q I N E L H Q V L V L L C R R I N V R M ............................................. aaacagccgcgaatcatttgattcgcggctgttttgtatgttttctaaatgttggactaggactagcaaacatcttctaatattaactcgcaatgcggttcttcaagcagtaatttaaagtttcgcttagacaaagct 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================================================ aaacagccgcgaatcatttgattcgcggctgttttgtatgttttctaaatgttggactaggactagcaaacatcttctaatattaactcgcaatgcggttcttcaagcagtaatttaaagtttcgcttagacaaagct Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_1951:SSA_1952|SSA_1951:SSA_1952:Penicillin-binding protein 3, putative:ABC-type Fe-S cluster assembly transporter, permease component, putative:-><-:1948164..1948301 138 aaacagccgcgaatcatttgattcgcggctgttttgtatgttttctaaatgttggactaggactagcaaacatcttctaatattaactcgcaatgcggttcttcaagcagtaatttaaagtttcgcttagacaaagct Intra-Species Hit: Count: 1 Min: 1 Max: 138 Len: 138 Subject: NC_009009_SSA_1951_SSA_1952|Penicillin-binding protein 3, putative:ABC-type Fe-S cluster assembly transporter, permease component, putative|POSITIVE:NEGATIVE|[1948164,1948301]|138 HSP 1 e-value: 7.0E-73 bit: 274.0 Len: 138 Query Start:1 Query End:138 Subject Strand: POSITIVE Subject Start: 1 Subject End: 138 aaacagccgcgaatcatttgattcgcggctgttttgtatgttttctaaatgttggactaggactagcaaacatcttctaatattaactcgcaatgcggttcttcaagcagtaatttaaagtttcgcttagacaaagct aaacagccgcgaatcatttgattcgcggctgttttgtatgttttctaaatgttggactaggactagcaaacatcttctaatattaactcgcaatgcggttcttcaagcagtaatttaaagtttcgcttagacaaagct HSP 2 e-value: 5.0E-6 bit: 52.0 Len: 34 Query Start:1 Query End:34 Subject Strand: NEGATIVE Subject Start: 1 Subject End: 34 aaacagccgcgaatcatttgattcgcggctgttt........................................................................................................ aaacagccgcgaatcaaatgattcgcggctgttt........................................................................................................ Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAACAGCCGCGAAUCAUUUGAUUCGCGGCUGUUUUGUAUGUUUUCUAAAUGUUGGACUAGGACUAGCAAACAUCUUCUAAUAUUAACUCGCAAUGCGGUUCUUCAAGCAGUAAUUUAAAGUUUCGCUUAGACAAAGCU (((((((((((((((....)))))))))))))))....(((((....(((((((((...(((..........))))))))))))..........((((..(((.(((......))).)))..))))..)))))..... (-38.90) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGCUUUGUCUAAGCGAAACUUUAAAUUACUGCUUGAAGAACCGCAUUGCGAGUUAAUAUUAGAAGAUGUUUGCUAGUCCUAGUCCAACAUUUAGAAAACAUACAAAACAGCCGCGAAUCAAAUGAUUCGCGGCUGUUU .(((..(.(((.(((((.((((.(((....(((((((........)).)))))....))).))))...)))))))).)..))).....................(((((((((((((((....))))))))))))))) (-40.90) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 322 60 16 207 156 NC_009009:SSA_2263|5end_Ribonucleotide_reductase_(NrdI_family_protein),_putative_2261176..2261406_NEGATIVE 290 34 3 205 180 NC_009009:SSA_1932|5end_Biotin_carboxylase,_putative_1920874..1921104_NEGATIVE 290 128 94 125 94 NC_009009:SSA_1910|5end_hypothetical_protein_1902672..1902902_NEGATIVE 288 45 1 164 112 NC_009009:SSA_2072|5end_Phosphatidate_cytidylyltransferase,_putative_2075603..2075833_NEGATIVE 280 45 2 170 117 NC_009009:SSA_0090|5end_Acetyltransferase,_GNAT_family,_putative_90258..90488_POSITIVE 276 56 11 82 36 NC_009009:SSA_0471|5end_CbiG_protein,_putative_473600..473830_POSITIVE 271 130 88 182 144 NC_009009:SSA_2035|5end_Conserved_uncharacterized_protein_2040288..2040518_NEGATIVE 270 40 3 202 155 NC_009009:SSA_1307|5end_Trk_transporter_membrane-spanning_protein-K+_transport,_putative_1326270..1326500_NEGATIVE 270 78 31 155 111 NC_009009:SSA_1264|5end_hypothetical_protein_1290042..1290272_NEGATIVE 269 108 66 69 21 NC_009009:SSA_0219|5end_PTS_system,_sugar-specific_enzyme_IIA_component,_putative_215367..215597_POSITIVE 267 45 1 188 140 NC_009009:SSA_2226|5end_Organic_radical_activating_chaperone,_putative_2227756..2227986_NEGATIVE 267 47 4 213 166 NC_009009:SSA_1511|5end_Glycosyltransferase,_putative_1516697..1516927_NEGATIVE 266 68 25 129 73 NC_009009:SSA_0548|5end_Alanine_racemase,_putative_542340..542570_POSITIVE 264 67 21 202 153 NC_009009:SSA_1600|5end_hypothetical_protein_1606595..1606825_NEGATIVE 264 64 21 183 143 NC_009009:SSA_1448|5end_ATP_phosphoribosyltransferase_regulatory_subunit,_putative_1450817..1451047_NEGATIVE 262 41 4 35 1 NC_009009:SSA_2243|5end_Conserved_uncharacterized_protein_2239341..2239571_NEGATIVE 262 38 4 177 135 NC_009009:SSA_1082|5end_PTS_system,_fructose_specific_II_ABC_components,_putative_1099186..1099416_POSITIVE 262 67 22 51 5 NC_009009:SSA_0102|5end_Kinase,_putative_104035..104265_POSITIVE 259 56 19 224 182 NC_009009:SSA_2278|5end_Ukp_protein,_putative_2281669..2281899_NEGATIVE 259 58 14 231 189 NC_009009:SSA_2188|5end_Conserved_uncharacterized_protein_2188896..2189126_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 587 46 1 101 57 NC_009009:SSA_1951|3end_Penicillin-binding_protein_3,_putative_1948103..1948253_POSITIVE 322 60 16 144 93 NC_009009:SSA_2264|3end_hypothetical_protein_2261239..2261389_NEGATIVE 290 128 94 132 101 NC_009009:SSA_1911|3end_Conserved_uncharacterized_protein_1902665..1902815_NEGATIVE 288 45 1 145 93 NC_009009:SSA_2073|3end_Undecaprenyl_pyrophosphate_synthetase,_putative_2075622..2075772_NEGATIVE 276 56 11 134 88 NC_009009:SSA_0470|3end_Precorrin-4_methylase,_putative_473732..473882_POSITIVE 275 40 1 61 11 NC_009009:SSA_0922|3end_hypothetical_protein_932225..932375_NEGATIVE 266 68 25 142 86 NC_009009:SSA_0547|3end_Acyl_carrier_protein_synthase,_putative_542433..542583_POSITIVE 264 64 21 127 87 NC_009009:SSA_1449|3end_Histidinol-phosphate/aromatic_aminotransferase_and_cobyric_acid_decarboxylase,_putative_1450873..1451023_NEGATIVE 263 67 21 66 1 NC_009009:SSA_1061|3end_50S_ribosomal_protein_L21,_putative_1077986..1078136_POSITIVE 262 67 22 49 3 NC_009009:SSA_0101|3end_Conserved_uncharacterized_protein_104113..104263_POSITIVE 258 47 1 87 37 NC_009009:SSA_0921|3end_Zn-dependeant_threonine_dehydrogenase,_putative_932164..932314_POSITIVE 257 50 1 103 43 NC_009009:SSA_0276|3end_Glycosyltransferase,_family_2/glycosyltransferase_family_8,_putative_270667..270817_POSITIVE 257 43 4 75 30 NC_009009:SSA_0113|3end_30S_ribosomal_protein_S3,_putative_112055..112205_POSITIVE 252 97 51 106 62 NC_009009:SSA_0161|3end_hypothetical_protein_161462..161612_POSITIVE 250 47 5 50 11 NC_009009:SSA_0895|3end_ATP-binding_cassette_transporter-like_protein,_putative_887763..887913_POSITIVE 249 109 63 151 96 NC_009009:SSA_1138|3end_Pyruvate_dehydrogenase,_TPP-dependent_E1_component_alpha-subunit,_putative_1166884..1167034_POSITIVE 245 46 1 90 50 NC_009009:SSA_0320|3end_hypothetical_protein_313824..313974_POSITIVE 236 129 87 137 85 NC_009009:SSA_0685|3end_hypothetical_protein_669432..669582_POSITIVE 231 40 4 124 92 NC_009009:SSA_1442|3end_Imidazole_glycerol-phosphate_synthase_subunit_hisF,_putative_1445183..1445333_NEGATIVE 231 37 1 64 25 NC_009009:SSA_1069|3end_Lipoprotein_signal_peptidase,_putative_1088838..1088988_POSITIVE