Origin IGS: aaggaacagagaagactggttttcagtcttctttttttgtttaaggagagggcaattgctttttttgagaggataatttttaaaaaatgatctgatcaacttaaatagtagaatagtatcagtatgtaacaatattttataagaaaaggtttacataatgagctataatataagtaaatgaacaagcaaataagaaagcgagtagaaat .........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 atttctactcgctttcttatttgcttgttcatttacttatattatagctcattatgtaaaccttttcttataaaatattgttacatactgatactattctactatttaagttgatcagatcattttttaaaaattatcctctcaaaaaaagcaattgccctctccttaaacaaaaaaagaagactgaaaaccagtcttctctgttcctt Mask Tandem Repeat Region ================================================ aaggaacagagaagactggttttcagtcttctttttttgtttaaggagagggcaattgctttttttgagaggataatttttaaaaaatgatctgatcaacttaaatagtagaatagtatcagtatgtaacaatattttataagaaaaggtttacataatgagctataatataagtaaatgaacaagcaaataagaaagcgagtagaaat Find is-nt database================================================ Query_seq: SSA_0394:SSA_0395|SSA_0394:SSA_0395:hypothetical protein:6-phospho-beta-glucosidase, putative:->->:390992..391200 209 aaggaacagagaagactggttttcagtcttctttttttgtttaaggagagggcaattgctttttttgagaggataatttttaaaaaatgatctgatcaacttaaatagtagaatagtatcagtatgtaacaatattttataagaaaaggtttacataatgagctataatataagtaaatgaacaagcaaataagaaagcgagtagaaat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_0394:SSA_0395|SSA_0394:SSA_0395:hypothetical protein:6-phospho-beta-glucosidase, putative:->->:390992..391200 209 aaggaacagagaagactggttttcagtcttctttttttgtttaaggagagggcaattgctttttttgagaggataatttttaaaaaatgatctgatcaacttaaatagtagaatagtatcagtatgtaacaatattttataagaaaaggtttacataatgagctataatataagtaaatgaacaagcaaataagaaagcgagtagaaat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_0394:SSA_0395|SSA_0394:SSA_0395:hypothetical protein:6-phospho-beta-glucosidase, putative:->->:390992..391200 209 aaggaacagagaagactggttttcagtcttctttttttgtttaaggagagggcaattgctttttttgagaggataatttttaaaaaatgatctgatcaacttaaatagtagaatagtatcagtatgtaacaatattttataagaaaaggtttacataatgagctataatataagtaaatgaacaagcaaataagaaagcgagtagaaat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aaggaacagagaagactggttttcagtcttctttttttgtttaaggagagggcaattgctttttttgagaggataatttttaaaaaatgatctgatcaacttaaatagtagaatagtatcagtatgtaacaatattttataagaaaaggtttacataatgagctataatataagtaaatgaacaagcaaataagaaagcgagtagaaat Predict ORF larger than 30AA ================================================ Protein_Len: 37 Strand: - Start: 99 End: 209 .................................................................................................. S L Y Y F L I L I Y C Y K I L F P K C L S S Y Y L Y I F L C I L F R T S M Protein_Len: 45 Strand: - Start: 1 End: 135 L F L S S Q N E T K K K Q K L L P C N S K K L P Y N K F F S R I L K F L L I T D T H L L M .......................................................................... aaggaacagagaagactggttttcagtcttctttttttgtttaaggagagggcaattgctttttttgagaggataatttttaaaaaatgatctgatcaacttaaatagtagaatagtatcagtatgtaacaatattttataagaaaaggtttacataatgagctataatataagtaaatgaacaagcaaataagaaagcgagtagaaat 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================================================ aaggaacagagaagactggttttcagtcttctttttttgtttaaggagagggcaattgctttttttgagaggataatttttaaaaaatgatctgatcaacttaaatagtagaatagtatcagtatgtaacaatattttataagaaaaggtttacataatgagctataatataagtaaatgaacaagcaaataagaaagcgagtagaaat Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_0394:SSA_0395|SSA_0394:SSA_0395:hypothetical protein:6-phospho-beta-glucosidase, putative:->->:390992..391200 209 aaggaacagagaagactggttttcagtcttctttttttgtttaaggagagggcaattgctttttttgagaggataatttttaaaaaatgatctgatcaacttaaatagtagaatagtatcagtatgtaacaatattttataagaaaaggtttacataatgagctataatataagtaaatgaacaagcaaataagaaagcgagtagaaat Intra-Species Hit: Count: 1 Min: 1 Max: 209 Len: 209 Subject: NC_009009_SSA_0394_SSA_0395|hypothetical protein:6-phospho-beta-glucosidase, putative|POSITIVE:POSITIVE|[390992,391200]|209 HSP 1 e-value: 5.0E-90 bit: 331.0 Len: 209 Query Start:1 Query End:209 Subject Strand: POSITIVE Subject Start: 1 Subject End: 209 aaggaacagagaagactggttttcagtcttcnnnnnnngtttaaggagagggcaattgcnnnnnnngagaggataatttttaaaaaatgatctgatcaacttaaatagtagaatagtatcagtatgtaacaatattttataagaaaaggtttacataatgagctataatataagtaaatgaacaagcaaataagaaagcgagtagaaat aaggaacagagaagactggttttcagtcttctttttttgtttaaggagagggcaattgctttttttgagaggataatttttaaaaaatgatctgatcaacttaaatagtagaatagtatcagtatgtaacaatattttataagaaaaggtttacataatgagctataatataagtaaatgaacaagcaaataagaaagcgagtagaaat Inter-species Hit: Count: 1 Min: 68 Max: 206 Len: 139 Subject: smit_SMT_459_SMT_460|hypothetical protein:6-phospho-beta- glucosidase|POSITIVE:POSITIVE|[397751,397958]|208 HSP 1 e-value: 1.0E-47 bit: 190.0 Len: 139 Query Start:68 Query End:206 Subject Strand: POSITIVE Subject Start: 66 Subject End: 205 ...................................................................agaggataatttt-taaaaaatgatctgatcaacttaaatagtagaatagtatcagtatgtaacaatattttataagaaaaggtttacataatgagctataatataagtaaatgaacaagcaaataagaaagcgagtaga... ...................................................................agaggataattttttaaaaaacaatctgataaacttaaatagtagaatagtatcagtatgtcacagtattttataagaaaaggtttacagaataagttataatataagtaaatgaacaagcaaataagaaagtgagtaga... Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGAGGAUAAUUUUUAAAAAAUGAUCUGAUCAACUUAAAUAGUAGAAUAGUAUCAGUAUGUAACAAUAUUUUAUAAGAAAAGGUUUACAUAAUGAGCUAUAAUAUAAGUAAAUGAACAAGCAAAUAAGAAAGCGAGUAGA ...((((.((((.....)))).))))..((.((((.....(((..(((((.(((.((((((((....((((.....)))).).))))))).))))))))..)))..((......))................)))).)) (-15.30) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UCUACUCGCUUUCUUAUUUGCUUGUUCAUUUACUUAUAUUAUAGCUCAUUAUGUAAACCUUUUCUUAUAAAAUAUUGUUACAUACUGAUACUAUUCUACUAUUUAAGUUGAUCAGAUCAUUUUUUAAAAAUUAUCCUCU .....................(((.(((((((..((((..((((.(((.(((((((....(((......))).....))))))).)))..))))..)).))..)))).))).)))........................ (-10.90) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 191 59 16 44 8 NC_009009:SSA_1203|5end_hypothetical_protein_1226985..1227215_POSITIVE 191 73 40 104 71 NC_009009:SSA_0397|5end_hypothetical_protein_394657..394887_NEGATIVE 182 60 25 32 1 NC_009009:SSA_2032|5end_Integrase/recombinase,_phage_integrase_family,_putative_2038006..2038236_POSITIVE 177 59 21 214 174 NC_009009:SSA_1390|5end_hypothetical_protein_1406118..1406348_NEGATIVE 169 86 48 121 74 NC_009009:SSA_1201|5end_hypothetical_protein_1225755..1225985_POSITIVE 169 100 51 159 112 NC_009009:SSA_1070|5end_Ribosomal_large_subunit_pseudouridine_synthase_D,_putative_1088742..1088972_POSITIVE 169 53 24 49 13 NC_009009:SSA_0089|5end_V-type_sodium_ATPase,_subunit_F,_putative_89930..90160_POSITIVE 167 106 64 188 150 NC_009009:SSA_0824|5end_DNA_primase_(bacterial_type),_putative_802053..802283_POSITIVE 166 80 39 219 180 NC_009009:SSA_1620|5end_Uridylate_kinase,_putative_1622981..1623211_NEGATIVE 157 71 32 142 99 NC_009009:SSA_2271|5end_hypothetical_protein_2272450..2272680_NEGATIVE 156 82 41 210 170 NC_009009:SSA_0448|5end_Excinuclease_ATPase_subunit_A,_putative_446480..446710_POSITIVE 155 50 1 229 188 NC_009009:SSA_0923|5end_Transcriptional_regulator,_TetR/AcrR_family,_putative_933010..933240_POSITIVE 155 81 41 57 12 NC_009009:SSA_0017|5end_Cell_shape_determining_protein_MreC,_putative_22811..23041_POSITIVE 154 97 51 87 44 NC_009009:SSA_0966|5end_Uridine_kinase,_putative_975063..975293_POSITIVE 151 80 38 152 111 NC_009009:SSA_1171|5end_Tyrosine_recombinase_xerC_1198088..1198318_POSITIVE 149 50 4 184 142 NC_009009:SSA_0945|5end_Phosphate_import_ATP-binding_protein_pstB_1,_putative_952605..952835_POSITIVE 147 60 21 84 55 NC_009009:SSA_1656|5end_Nisin_resistance_protein,_putative_1652890..1653120_NEGATIVE 147 57 21 62 19 NC_009009:SSA_0128|5end_Adenylate_kinase,_putative_119201..119431_POSITIVE 146 44 2 87 52 NC_009009:SSA_1893|5end_N-acetylglucosamine-6-phosphate_deacetylase,_putative_1890572..1890802_NEGATIVE 144 70 48 63 41 NC_009009:SSA_1541|5end_Peptidase,_U32_family,_putative_1546600..1546830_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 191 59 16 60 24 NC_009009:SSA_1202|3end_Dfp-like_protein,_putative_1227081..1227231_POSITIVE 191 73 40 87 54 NC_009009:SSA_0398|3end_hypothetical_protein_394674..394824_NEGATIVE 183 76 32 129 76 NC_009009:SSA_2365|3end_Cobalt_transport_protein_cbiQ,_putative_2367243..2367393_NEGATIVE 170 34 18 133 117 NC_009009:SSA_2051|3end_Oligoendopeptidase,_putative_2056607..2056757_POSITIVE 169 53 24 62 26 NC_009009:SSA_0088|3end_V-type_sodium_ATPase,_subunit_C,_putative_90023..90173_POSITIVE 158 43 8 133 94 NC_009009:SSA_1997|3end_Membrane_spanning_protein,_putative_1994162..1994312_NEGATIVE 149 50 4 123 81 NC_009009:SSA_0944|3end_Phosphate_import_ATP-binding_protein_pstB_2,_putative_952624..952774_POSITIVE 148 52 23 107 81 NC_009009:SSA_2017|3end_Hypothetical_protein_(possibly_membrane-associated)_2016435..2016585_NEGATIVE 143 57 16 44 2 NC_009009:SSA_1852|3end_Metal_dependent_phosphohydrolase_(HD_motif),_putative_1846869..1847019_NEGATIVE 139 28 1 58 27 NC_009009:SSA_1240|3end_Orotate_phosphoribosyltransferase,_putative_1264801..1264951_NEGATIVE 136 58 24 36 1 NC_009009:SSA_2211|3end_Transmembrane_protein,_putative_2211499..2211649_NEGATIVE 135 55 21 94 59 NC_009009:SSA_0916|3end_2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoate_hydrolase,_putative_928992..929142_POSITIVE 134 54 13 93 36 NC_009009:SSA_1927|3end_Exfoliative_toxin,_putative_1914956..1915106_NEGATIVE 133 97 51 69 27 NC_009009:SSA_0998|3end_hypothetical_protein_998758..998908_POSITIVE 133 128 87 71 21 NC_009009:SSA_0844|3end_hypothetical_protein_828491..828641_NEGATIVE 132 121 81 145 115 NC_009009:SSA_0232|3end_hypothetical_protein_227277..227427_POSITIVE 131 61 32 71 39 NC_009009:SSA_2123|3end_Dimethyladenosine_transferase,_putative_2127664..2127814_NEGATIVE 131 101 61 110 71 NC_009009:SSA_1457|3end_Neopullulanase,_putative_1462485..1462635_NEGATIVE 131 96 52 59 18 NC_009009:SSA_1050|3end_ABC_transporter_membrane-spanning_permease-spermidine/putrescine_transport,_putative_1065741..1065891_POSITIVE 131 56 20 150 107 NC_009009:SSA_0648|3end_hypothetical_protein_631775..631925_POSITIVE