Origin IGS: ggttgaagaagtttcaaccttattttttatattttcgactacgacaaaagctgtttgtaacaccaaaatggagctagcagcaaaaattggaaagtgaaacaatctgagaatgcactatttcagctccttgaaatgatgggatgaagtaagctgatattatcaatgcaagaccgcatcattagattt .........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 aaatctaatgatgcggtcttgcattgataatatcagcttacttcatcccatcatttcaaggagctgaaatagtgcattctcagattgtttcactttccaatttttgctgctagctccattttggtgttacaaacagcttttgtcgtagtcgaaaatataaaaaataaggttgaaacttcttcaacc Mask Tandem Repeat Region ================================================ ggttgaagaagtttcaaccttattttttatattttcgactacgacaaaagctgtttgtaacaccaaaatggagctagcagcaaaaattggaaagtgaaacaatctgagaatgcactatttcagctccttgaaatgatgggatgaagtaagctgatattatcaatgcaagaccgcatcattagattt Find is-nt database================================================ Query_seq: SSA_1921:SSA_1922|SSA_1921:SSA_1922:hypothetical protein:hypothetical protein:-><-:1911378..1911563 186 ggttgaagaagtttcaaccttattttttatattttcgactacgacaaaagctgtttgtaacaccaaaatggagctagcagcaaaaattggaaagtgaaacaatctgagaatgcactatttcagctccttgaaatgatgggatgaagtaagctgatattatcaatgcaagaccgcatcattagattt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_1921:SSA_1922|SSA_1921:SSA_1922:hypothetical protein:hypothetical protein:-><-:1911378..1911563 186 ggttgaagaagtttcaaccttattttttatattttcgactacgacaaaagctgtttgtaacaccaaaatggagctagcagcaaaaattggaaagtgaaacaatctgagaatgcactatttcagctccttgaaatgatgggatgaagtaagctgatattatcaatgcaagaccgcatcattagattt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_1921:SSA_1922|SSA_1921:SSA_1922:hypothetical protein:hypothetical protein:-><-:1911378..1911563 186 ggttgaagaagtttcaaccttattttttatattttcgactacgacaaaagctgtttgtaacaccaaaatggagctagcagcaaaaattggaaagtgaaacaatctgagaatgcactatttcagctccttgaaatgatgggatgaagtaagctgatattatcaatgcaagaccgcatcattagattt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ggttgaagaagtttcaaccttattttttatattttcgactacgacaaaagctgtttgtaacaccaaaatggagctagcagcaaaaattggaaagtgaaacaatctgagaatgcactatttcagctccttgaaatgatgggatgaagtaagctgatattatcaatgcaagaccgcatcattagattt Predict ORF larger than 30AA ================================================ Protein_Len: 37 Strand: - Start: 1 End: 111 T S S T E V K N K I N E V V V F A T Q L V L I S S A A F I P F H F L R L M ........................................................................... ggttgaagaagtttcaaccttattttttatattttcgactacgacaaaagctgtttgtaacaccaaaatggagctagcagcaaaaattggaaagtgaaacaatctgagaatgcactatttcagctccttgaaatgatgggatgaagtaagctgatattatcaatgcaagaccgcatcattagattt 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================================================ ggttgaagaagtttcaaccttattttttatattttcgactacgacaaaagctgtttgtaacaccaaaatggagctagcagcaaaaattggaaagtgaaacaatctgagaatgcactatttcagctccttgaaatgatgggatgaagtaagctgatattatcaatgcaagaccgcatcattagattt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_1921:SSA_1922|SSA_1921:SSA_1922:hypothetical protein:hypothetical protein:-><-:1911378..1911563 186 ggttgaagaagtttcaaccttattttttatattttcgactacgacaaaagctgtttgtaacaccaaaatggagctagcagcaaaaattggaaagtgaaacaatctgagaatgcactatttcagctccttgaaatgatgggatgaagtaagctgatattatcaatgcaagaccgcatcattagattt Intra-Species Hit: Count: 1 Min: 1 Max: 186 Len: 186 Subject: NC_009009_SSA_1921_SSA_1922|hypothetical protein:hypothetical protein|POSITIVE:NEGATIVE|[1911378,1911563]|186 HSP 1 e-value: 1.0E-101 bit: 369.0 Len: 186 Query Start:1 Query End:186 Subject Strand: POSITIVE Subject Start: 1 Subject End: 186 ggttgaagaagtttcaaccttattttttatattttcgactacgacaaaagctgtttgtaacaccaaaatggagctagcagcaaaaattggaaagtgaaacaatctgagaatgcactatttcagctccttgaaatgatgggatgaagtaagctgatattatcaatgcaagaccgcatcattagattt ggttgaagaagtttcaaccttattttttatattttcgactacgacaaaagctgtttgtaacaccaaaatggagctagcagcaaaaattggaaagtgaaacaatctgagaatgcactatttcagctccttgaaatgatgggatgaagtaagctgatattatcaatgcaagaccgcatcattagattt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GGUUGAAGAAGUUUCAACCUUAUUUUUUAUAUUUUCGACUACGACAAAAGCUGUUUGUAACACCAAAAUGGAGCUAGCAGCAAAAAUUGGAAAGUGAAACAAUCUGAGAAUGCACUAUUUCAGCUCCUUGAAAUGAUGGGAUGAAGUAAGCUGAUAUUAUCAAUGCAAGACCGCAUCAUUAGAUUU ((((((((...))))))))((((((((((.....(((....))).....((((((.((..((......))..)).))))))......))))))))))...(((((((..((((..(((((((..((((.........))))))))))).((((((...))))..))......))))..))))))). (-42.60) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAUCUAAUGAUGCGGUCUUGCAUUGAUAAUAUCAGCUUACUUCAUCCCAUCAUUUCAAGGAGCUGAAAUAGUGCAUUCUCAGAUUGUUUCACUUUCCAAUUUUUGCUGCUAGCUCCAUUUUGGUGUUACAAACAGCUUUUGUCGUAGUCGAAAAUAUAAAAAAUAAGGUUGAAACUUCUUCAACC ........(((.((((((((((((((......(((((((.(((..............))))))))))..))))))).....))))))).))).......(((((((((((.(((.((.....)).)))(((((.....))))).)))).)))))))...........(((((((.....))))))) (-39.24) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 305 130 87 191 138 NC_009009:SSA_2191|5end_Conserved_uncharacterized_protein_2192049..2192279_POSITIVE 287 110 63 45 1 NC_009009:SSA_0963|5end_Peptidoglycan_N-acetylglucosamine_deacetylase_A,_putative_971413..971643_POSITIVE 286 90 49 211 178 NC_009009:SSA_0116|5end_30S_ribosomal_protein_S17,_putative_112632..112862_POSITIVE 274 43 1 198 153 NC_009009:SSA_0325|5end_Membrane-anchored_glycerophosphoryl_diester_phosphodiesterase,_putative_317603..317833_POSITIVE 273 81 46 197 164 NC_009009:SSA_1876|5end_hypothetical_protein_1871120..1871350_POSITIVE 269 155 116 140 91 NC_009009:SSA_0607|5end_ABC_transporter,_permease_component,_putative_596926..597156_NEGATIVE 268 131 100 45 16 NC_009009:SSA_1713|5end_D-3-phosphoglycerate_dehydrogenase,_putative_1701384..1701614_NEGATIVE 267 169 121 76 17 NC_009009:SSA_1897|5end_Ribosomal_protein_HS6-type_(S12/L30/L7a),_putative_1894450..1894680_NEGATIVE 267 139 95 214 171 NC_009009:SSA_1498|5end_50S_ribosomal_protein_L20,_putative_1504112..1504342_NEGATIVE 260 143 101 72 20 NC_009009:SSA_0287|5end_Glycerol_dehydrogenase,_NAD+_dependent,_putative_279528..279758_POSITIVE 258 90 42 120 77 NC_009009:SSA_0188|5end_hypothetical_protein_190798..191028_POSITIVE 253 168 121 143 93 NC_009009:SSA_1051|5end_Spermidine/putrescine_ABC_transporter,_spermidine/putrescine-binding_protein,_putative_1065658..1065888_POSITIVE 252 177 134 64 4 NC_009009:SSA_1182|5end_Gid-like_protein,_putative_1210866..1211096_NEGATIVE 251 150 106 187 145 NC_009009:SSA_1650|5end_3-Ketoacyl-ACP_reductase,_putative_1649594..1649824_NEGATIVE 250 148 103 56 9 NC_009009:SSA_0019|5end_Secreted_antigen_GbpB/SagA;_peptidoglycan_hydrolase;_PcsB_protein_precursor,_putative_24225..24455_POSITIVE 249 155 112 59 5 NC_009009:SSA_1149|5end_Glycosyl_hydrolase,_family_1,_putative_1178399..1178629_POSITIVE 249 160 111 84 27 NC_009009:SSA_0406|5end_hypothetical_protein_402918..403148_NEGATIVE 248 85 42 51 4 NC_009009:SSA_1892|5end_hypothetical_protein_1889262..1889492_NEGATIVE 245 145 108 116 81 NC_009009:SSA_0418|5end_AraC-type_DNA-binding_domain-containing_protein,_putative_415256..415486_POSITIVE 244 147 106 39 1 NC_009009:SSA_1535|5end_hypothetical_protein_1543188..1543418_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 312 168 122 143 97 NC_009009:SSA_1019|3end_Collagen-binding_surface_protein,_putative_1035377..1035527_POSITIVE 274 43 1 108 63 NC_009009:SSA_0324|3end_Conserved_uncharacterized_protein_317593..317743_POSITIVE 268 131 100 32 3 NC_009009:SSA_1715|3end_Phosphoserine_aminotransferase,_putative_1701397..1701547_NEGATIVE 267 169 121 83 24 NC_009009:SSA_1899|3end_hypothetical_protein_1894443..1894593_NEGATIVE 258 90 42 94 51 NC_009009:SSA_0187|3end_Competence_protein_ComYD,_putative_190852..191002_POSITIVE 253 168 121 146 96 NC_009009:SSA_1050|3end_ABC_transporter_membrane-spanning_permease-spermidine/putrescine_transport,_putative_1065741..1065891_POSITIVE 249 160 111 91 34 NC_009009:SSA_0407|3end_ABC-type_multidrug_transport_system_(3-component_subtilin_immunity_exporter),_ATPase_component,_putative_402911..403061_NEGATIVE 248 155 113 53 7 NC_009009:SSA_1148|3end_Beta-glucosides_PTS,_EIIC,_putative_1178473..1178623_POSITIVE 245 178 132 116 63 NC_009009:SSA_2354|3end_hypothetical_protein_2355605..2355755_NEGATIVE 243 106 73 48 11 NC_009009:SSA_0055|3end_PTS_system,_IIC_component,_putative_60019..60169_POSITIVE 238 168 127 136 95 NC_009009:SSA_2252|3end_hypothetical_protein_2248212..2248362_NEGATIVE 238 154 111 53 10 NC_009009:SSA_1954|3end_Aminotransferase,_class-V,_putative_1950066..1950216_NEGATIVE 238 87 49 75 39 NC_009009:SSA_0011|3end_hypothetical_protein_10003..10153_POSITIVE 237 162 121 121 83 NC_009009:SSA_1311|3end_Hydrolase,_haloacid_dehalogenase-like_family,_putative_1327842..1327992_NEGATIVE 236 78 31 76 27 NC_009009:SSA_2367|3end_ABC-type_cobalt_transport_system,_ATPase_component,_putative_2368845..2368995_NEGATIVE 236 126 86 91 54 NC_009009:SSA_1341|3end_Carbamoyl-phosphate_synthase_large_chain,_putative_1356648..1356798_NEGATIVE 234 154 116 138 92 NC_009009:SSA_1299|3end_Maltose/maltodextrin_ABC_transport_system,_putative_1318067..1318217_POSITIVE 233 159 115 136 86 NC_009009:SSA_2118|3end_Thiamine_pyrophosphokinase,_putative_2119814..2119964_NEGATIVE 232 157 112 151 108 NC_009009:SSA_1322|3end_Glycosyl_transferase,_putative_1338536..1338686_NEGATIVE 230 84 47 76 36 NC_009009:SSA_1531|3end_ABC-type_antimicrobial_peptide_transporter,_ATPase_component,_putative_1538778..1538928_NEGATIVE