Origin IGS: ttcctaatctcccttaaaatccctaattcgagtatagcacaaaataaaggacggaagatttttataagtgtaaaaacacagcaattgaacaatagattagaatatgtctaaaaatagaaagctatcctttaaaaacttattttccaaaaacacctcacaaacctaaaaaatcatgtataataaaaagacaggaaaagaataggagttatc .........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 gataactcctattcttttcctgtctttttattatacatgattttttaggtttgtgaggtgtttttggaaaataagtttttaaaggatagctttctatttttagacatattctaatctattgttcaattgctgtgtttttacacttataaaaatcttccgtcctttattttgtgctatactcgaattagggattttaagggagattaggaa Mask Tandem Repeat Region ================================================ ttcctaatctcccttaaaatccctaattcgagtatagcacaaaataaaggacggaagatttttataagtgtaaaaacacagcaattgaacaatagattagaatatgtctaaaaatagaaagctatcctttaaaaacttattttccaaaaacacctcacaaacctaaaaaatcatgtataataaaaagacaggaaaagaataggagttatc Find is-nt database================================================ Query_seq: SSA_0274:SSA_0276|SSA_0274:SSA_0276:hypothetical protein:Glycosyltransferase, family 2/glycosyltransferase family 8, putative:<-->:269648..269857 210 ttcctaatctcccttaaaatccctaattcgagtatagcacaaaataaaggacggaagatttttataagtgtaaaaacacagcaattgaacaatagattagaatatgtctaaaaatagaaagctatcctttaaaaacttattttccaaaaacacctcacaaacctaaaaaatcatgtataataaaaagacaggaaaagaataggagttatc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_0274:SSA_0276|SSA_0274:SSA_0276:hypothetical protein:Glycosyltransferase, family 2/glycosyltransferase family 8, putative:<-->:269648..269857 210 ttcctaatctcccttaaaatccctaattcgagtatagcacaaaataaaggacggaagatttttataagtgtaaaaacacagcaattgaacaatagattagaatatgtctaaaaatagaaagctatcctttaaaaacttattttccaaaaacacctcacaaacctaaaaaatcatgtataataaaaagacaggaaaagaataggagttatc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_0274:SSA_0276|SSA_0274:SSA_0276:hypothetical protein:Glycosyltransferase, family 2/glycosyltransferase family 8, putative:<-->:269648..269857 210 ttcctaatctcccttaaaatccctaattcgagtatagcacaaaataaaggacggaagatttttataagtgtaaaaacacagcaattgaacaatagattagaatatgtctaaaaatagaaagctatcctttaaaaacttattttccaaaaacacctcacaaacctaaaaaatcatgtataataaaaagacaggaaaagaataggagttatc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ttcctaatctcccttaaaatccctaattcgagtatagcacaaaataaaggacggaagatttttataagtgtaaaaacacagcaattgaacaatagattagaatatgtctaaaaatagaaagctatcctttaaaaacttattttccaaaaacacctcacaaacctaaaaaatcatgtataataaaaagacaggaaaagaataggagttatc Predict ORF larger than 30AA ================================================ Protein_Len: 34 Strand: + Start: 7 End: 108 ...... M S L K I P N S S I A Q N K G R K I F I S V K T Q Q L N N R L E Y V ...................................................................................................... Protein_Len: 38 Strand: + Start: 96 End: 209 ............................................................................................... M R I C L K I E S Y P L K T Y F P K T P H K P K K S C I I K R Q E K N R S Y . Protein_Len: 30 Strand: - Start: 3 End: 92 .. R I E R L I G L E L I A C F L P R F I K I L T F V C C N F M ...................................................................................................................... ttcctaatctcccttaaaatccctaattcgagtatagcacaaaataaaggacggaagatttttataagtgtaaaaacacagcaattgaacaatagattagaatatgtctaaaaatagaaagctatcctttaaaaacttattttccaaaaacacctcacaaacctaaaaaatcatgtataataaaaagacaggaaaagaataggagttatc 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================================================ ttcctaatctcccttaaaatccctaattcgagtatagcacaaaataaaggacggaagatttttataagtgtaaaaacacagcaattgaacaatagattagaatatgtctaaaaatagaaagctatcctttaaaaacttattttccaaaaacacctcacaaacctaaaaaatcatgtataataaaaagacaggaaaagaataggagttatc Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 46 HP_score: -2.9 Tail_Score: -3.28973 Start: 97 End: 111 Full_Region: gatagctttctattt ttaga catat tctaa tctattgttcaattg ................................................................................................ttagacatattctaa................................................................................................... Find igs database================================================ Query_seq: SSA_0274:SSA_0276|SSA_0274:SSA_0276:hypothetical protein:Glycosyltransferase, family 2/glycosyltransferase family 8, putative:<-->:269648..269857 210 ttcctaatctcccttaaaatccctaattcgagtatagcacaaaataaaggacggaagatttttataagtgtaaaaacacagcaattgaacaatagattagaatatgtctaaaaatagaaagctatcctttaaaaacttattttccaaaaacacctcacaaacctaaaaaatcatgtataataaaaagacaggaaaagaataggagttatc Intra-Species Hit: Count: 1 Min: 1 Max: 109 Len: 109 Subject: NC_009009_SSA_0274_SSA_0276|hypothetical protein:Glycosyltransferase, family 2/glycosyltransferase family 8, putative|NEGATIVE:POSITIVE|[269648,269857]|210 HSP 1 e-value: 2.0E-55 bit: 216.0 Len: 109 Query Start:1 Query End:109 Subject Strand: POSITIVE Subject Start: 1 Subject End: 109 ttcctaatctcccttaaaatccctaattcgagtatagcacaaaataaaggacggaagatttttataagtgtaaaaacacagcaattgaacaatagattagaatatgtct..................................................................................................... ttcctaatctcccttaaaatccctaattcgagtatagcacaaaataaaggacggaagatttttataagtgtaaaaacacagcaattgaacaatagattagaatatgtct..................................................................................................... Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUCCUAAUCUCCCUUAAAAUCCCUAAUUCGAGUAUAGCACAAAAUAAAGGACGGAAGAUUUUUAUAAGUGUAAAAACACAGCAAUUGAACAAUAGAUUAGAAUAUGUCU ...(((((((..((..((........))..))....((.....(((((((.(....).)))))))..((((....)))).))...........)))))))......... (-15.60) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGACAUAUUCUAAUCUAUUGUUCAAUUGCUGUGUUUUUACACUUAUAAAAAUCUUCCGUCCUUUAUUUUGUGCUAUACUCGAAUUAGGGAUUUUAAGGGAGAUUAGGAA .......(((((((((..............((((....)))).........((((..((((((...((((.(.....).))))..))))))...)))).))))))))). (-20.10) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 827 60 11 151 102 NC_009009:SSA_0274|5end_hypothetical_protein_269557..269787_NEGATIVE 263 56 12 155 116 NC_009009:SSA_0587|5end_Metal-dependent_amidase/aminoacylase/carboxypeptidase,_putative_578539..578769_POSITIVE 237 38 1 132 96 NC_009009:SSA_0486|5end_Uroporphyrinogen-III_synthase,_putative_486637..486867_POSITIVE 236 65 27 217 188 NC_009009:SSA_1979|5end_Alkaline-shock_protein,_putative_1974301..1974531_NEGATIVE 230 38 3 137 94 NC_009009:SSA_2017|5end_Hypothetical_protein_(possibly_membrane-associated)_2017331..2017561_NEGATIVE 219 50 1 142 91 NC_009009:SSA_1128|5end_Voltage_gated_chloride_channel_EriC,_putative_1153250..1153480_POSITIVE 216 59 11 174 141 NC_009009:SSA_1726|5end_ABC_transporter_ATP-binding_protein-branched_chain_amino_acid_transport,_putative_1712467..1712697_NEGATIVE 214 41 3 198 160 NC_009009:SSA_1817|5end_Conserved_uncharacterized_protein_1805595..1805825_NEGATIVE 214 60 18 82 44 NC_009009:SSA_1115|5end_Cytochrome_C-type_biogenesis_protein,_putative_1141614..1141844_POSITIVE 209 100 52 143 92 NC_009009:SSA_0175|5end_Penicillin-binding_protein_1B,_putative_172152..172382_POSITIVE 204 69 21 131 74 NC_009009:SSA_2358|5end_hypothetical_protein_2360497..2360727_NEGATIVE 203 29 1 121 93 NC_009009:SSA_2221|5end_Cps9E,_putative_2223257..2223487_NEGATIVE 202 26 1 120 94 NC_009009:SSA_2309|5end_Fimbrial_assembly_protein,_putative_2311886..2312116_NEGATIVE 202 37 1 41 12 NC_009009:SSA_1921|5end_hypothetical_protein_1910875..1911105_POSITIVE 202 83 49 86 45 NC_009009:SSA_0436|5end_Imidazolonepropionase,_putative_438869..439099_POSITIVE 197 66 29 221 189 NC_009009:SSA_2019|5end_hypothetical_protein_2019078..2019308_NEGATIVE 192 36 1 123 87 NC_009009:SSA_2304|5end_Conserved_uncharacterized_protein_2306270..2306500_NEGATIVE 192 41 6 55 22 NC_009009:SSA_0703|5end_Citrate_synthase,_putative_688154..688384_POSITIVE 191 32 3 200 177 NC_009009:SSA_2091|5end_Phosphotransferase_system_sugar-specific_EII_component,_putative_2095562..2095792_NEGATIVE 191 44 8 129 98 NC_009009:SSA_1065|5end_Beta-hexosamidase_A,_putative_1081258..1081488_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 239 59 11 75 24 NC_009009:SSA_0027|3end_Acyl_carrier_protein,_putative_31802..31952_POSITIVE 237 38 1 147 111 NC_009009:SSA_0485|3end_Porphobilinogen_deaminase,_putative_486732..486882_POSITIVE 236 65 27 74 45 NC_009009:SSA_1980|3end_50S_ribosomal_protein_L28,_putative_1974444..1974594_NEGATIVE 217 38 7 122 83 NC_009009:SSA_0826|3end_hypothetical_protein_805516..805666_POSITIVE 214 41 3 138 100 NC_009009:SSA_1818|3end_Very_short_patch_repair_endonuclease,_putative_1805655..1805805_NEGATIVE 203 29 1 79 51 NC_009009:SSA_2222|3end_Tyrosine-protein_kinase_Wze,_putative_2223299..2223449_NEGATIVE 202 26 1 75 49 NC_009009:SSA_2310|3end_hypothetical_protein_2311931..2312081_NEGATIVE 196 57 11 59 23 NC_009009:SSA_1234|3end_5'-nucleotidase,_putative_1257636..1257786_NEGATIVE 192 36 1 67 31 NC_009009:SSA_2305|3end_hypothetical_protein_2306326..2306476_NEGATIVE 192 41 6 52 19 NC_009009:SSA_0702|3end_Aconitase_A,_putative_688231..688381_POSITIVE 191 32 3 65 42 NC_009009:SSA_2092|3end_Phosphotransferase_system_sugar-specific_EII_component,_putative_2095697..2095847_NEGATIVE 188 42 10 137 106 NC_009009:SSA_1286|3end_hypothetical_protein_1305759..1305909_NEGATIVE 188 75 31 87 37 NC_009009:SSA_0186|3end_Competence_protein_ComYC,_putative_190458..190608_POSITIVE 186 60 11 127 88 NC_009009:SSA_0697|3end_hypothetical_protein_680276..680426_POSITIVE 185 50 2 122 82 NC_009009:SSA_0212|3end_Phenylalanyl-tRNA_synthetase,_beta_subunit,_putative_209079..209229_POSITIVE 183 60 33 58 37 NC_009009:SSA_0403|3end_CAAX_amino_terminal_protease_family,_putative_401388..401538_POSITIVE 180 63 26 67 14 NC_009009:SSA_0349|3end_Transcriptional_regulator,_TetR/AcrR_family,_putative_341828..341978_POSITIVE 179 56 14 131 91 NC_009009:SSA_1015|3end_4-hydroxybenzoate_octaprenyltransferase,_putative_1019682..1019832_POSITIVE 176 41 8 44 1 NC_009009:SSA_1021|3end_Conserved_uncharacterized_protein_1037270..1037420_POSITIVE 176 55 11 76 32 NC_009009:SSA_0193|3end_CAAX_amino_terminal_protease_family_protein,_putative_195075..195225_POSITIVE