Origin IGS: agcaaatcctttctatgcaactgttagtataagattaacgaatctcatttttaacagttaggttatgttatttctataaaattatacctctgtaacatttctataatattgtaatactatttcatttttatagagattatattactaattggtgataaaaacaaacaattattatataatatgtaaacgtttacaaacatcgttttttgtgctattattatagggatgaaaggagaatgcct .........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 aggcattctcctttcatccctataataatagcacaaaaaacgatgtttgtaaacgtttacatattatataataattgtttgtttttatcaccaattagtaatataatctctataaaaatgaaatagtattacaatattatagaaatgttacagaggtataattttatagaaataacataacctaactgttaaaaatgagattcgttaatcttatactaacagttgcatagaaaggatttgct Mask Tandem Repeat Region ================================================ agcaaatcctttctatgcaactgttagtataagattaacgaatctcatttttaacagttaggttatgttatttctataaaattatacctctgtaacatttctataatattgtaatactatttcatttttatagagattatattactaattggtgataaaaacaaacaattattatataatatgtaaacgtttacaaacatcgttttttgtgctattattatagggatgaaaggagaatgcct Find is-nt database================================================ Query_seq: SSA_1064:SSA_1065|SSA_1064:SSA_1065:hypothetical protein:Beta-hexosamidase A, putative:<-->:1081156..1081397 242 agcaaatcctttctatgcaactgttagtataagattaacgaatctcatttttaacagttaggttatgttatttctataaaattatacctctgtaacatttctataatattgtaatactatttcatttttatagagattatattactaattggtgataaaaacaaacaattattatataatatgtaaacgtttacaaacatcgttttttgtgctattattatagggatgaaaggagaatgcct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_1064:SSA_1065|SSA_1064:SSA_1065:hypothetical protein:Beta-hexosamidase A, putative:<-->:1081156..1081397 242 agcaaatcctttctatgcaactgttagtataagattaacgaatctcatttttaacagttaggttatgttatttctataaaattatacctctgtaacatttctataatattgtaatactatttcatttttatagagattatattactaattggtgataaaaacaaacaattattatataatatgtaaacgtttacaaacatcgttttttgtgctattattatagggatgaaaggagaatgcct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_1064:SSA_1065|SSA_1064:SSA_1065:hypothetical protein:Beta-hexosamidase A, putative:<-->:1081156..1081397 242 agcaaatcctttctatgcaactgttagtataagattaacgaatctcatttttaacagttaggttatgttatttctataaaattatacctctgtaacatttctataatattgtaatactatttcatttttatagagattatattactaattggtgataaaaacaaacaattattatataatatgtaaacgtttacaaacatcgttttttgtgctattattatagggatgaaaggagaatgcct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 agcaaatcctttctatgcaactgttagtataagattaacgaatctcatttttaacagttaggttatgttatttctataaaattatacctctgtaacatttctataatattgtaatactatttcatttttatagagattatattactaattggtgataaaaacaaacaattattatataatatgtaaacgtttacaaacatcgttttttgtgctattattatagggatgaaaggagaatgcct Predict ORF larger than 30AA ================================================ Protein_Len: 36 Strand: - Start: 120 End: 227 ....................................................................................................................... K M K I S I I N S I P S L F L C N N Y L I Y V N V F M T K Q A I I I P M ............... agcaaatcctttctatgcaactgttagtataagattaacgaatctcatttttaacagttaggttatgttatttctataaaattatacctctgtaacatttctataatattgtaatactatttcatttttatagagattatattactaattggtgataaaaacaaacaattattatataatatgtaaacgtttacaaacatcgttttttgtgctattattatagggatgaaaggagaatgcct 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: 88 Start: 189 End: 218 ............................................................................................................................................................................................GTTTACAAACATCGTTTTTTGTGCTATTAT........................ PromScan Matrix: RpoD-17 Strand: - Score: 85 Start: 136 End: 165 .......................................................................................................................................TTTGTTTTTATCACCAATTAGTAATATAAT............................................................................. PromScan Matrix: RpoD-17 Strand: - Score: 82 Start: 26 End: 55 .........................GTTAAAAATGAGATTCGTTAATCTTATACT........................................................................................................................................................................................... PromScan Matrix: RpoD-17 Strand: + Score: 82 Start: 151 End: 180 ......................................................................................................................................................GGTGATAAAAACAAACAATTATTATATAAT.............................................................. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ agcaaatcctttctatgcaactgttagtataagattaacgaatctcatttttaacagttaggttatgttatttctataaaattatacctctgtaacatttctataatattgtaatactatttcatttttatagagattatattactaattggtgataaaaacaaacaattattatataatatgtaaacgtttacaaacatcgttttttgtgctattattatagggatgaaaggagaatgcct Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_1064:SSA_1065|SSA_1064:SSA_1065:hypothetical protein:Beta-hexosamidase A, putative:<-->:1081156..1081397 242 agcaaatcctttctatgcaactgttagtataagattaacgaatctcatttttaacagttaggttatgttatttctataaaattatacctctgtaacatttctataatattgtaatactatttcatttttatagagattatattactaattggtgataaaaacaaacaattattatataatatgtaaacgtttacaaacatcgttttttgtgctattattatagggatgaaaggagaatgcct Intra-Species Hit: Count: 1 Min: 1 Max: 242 Len: 242 Subject: NC_009009_SSA_1064_SSA_1065|hypothetical protein:Beta-hexosamidase A, putative|NEGATIVE:POSITIVE|[1081156,1081397]|242 HSP 1 e-value: 1.0E-134 bit: 480.0 Len: 242 Query Start:1 Query End:242 Subject Strand: POSITIVE Subject Start: 1 Subject End: 242 agcaaatcctttctatgcaactgttagtataagattaacgaatctcatttttaacagttaggttatgttatttctataaaattatacctctgtaacatttctataatattgtaatactatttcatttttatagagattatattactaattggtgataaaaacaaacaattattatataatatgtaaacgtttacaaacatcgttttttgtgctattattatagggatgaaaggagaatgcct agcaaatcctttctatgcaactgttagtataagattaacgaatctcatttttaacagttaggttatgttatttctataaaattatacctctgtaacatttctataatattgtaatactatttcatttttatagagattatattactaattggtgataaaaacaaacaattattatataatatgtaaacgtttacaaacatcgttttttgtgctattattatagggatgaaaggagaatgcct Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGCAAAUCCUUUCUAUGCAACUGUUAGUAUAAGAUUAACGAAUCUCAUUUUUAACAGUUAGGUUAUGUUAUUUCUAUAAAAUUAUACCUCUGUAACAUUUCUAUAAUAUUGUAAUACUAUUUCAUUUUUAUAGAGAUUAUAUUACUAAUUGGUGAUAAAAACAAACAAUUAUUAUAUAAUAUGUAAACGUUUACAAACAUCGUUUUUUGUGCUAUUAUUAUAGGGAUGAAAGGAGAAUGCCU .(((..(((((((..(((.((((((((.((.(((((....))))).))..)))))))).((((....((((....))))......))))..)))..((..((((((((..((((((..(((((.........)))))..))))))....((((...((((((.....(((((...))))).(((((....)))))......))))))...)))).))))))))..)))))))))...))).. (-48.00) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGGCAUUCUCCUUUCAUCCCUAUAAUAAUAGCACAAAAAACGAUGUUUGUAAACGUUUACAUAUUAUAUAAUAAUUGUUUGUUUUUAUCACCAAUUAGUAAUAUAAUCUCUAUAAAAAUGAAAUAGUAUUACAAUAUUAUAGAAAUGUUACAGAGGUAUAAUUUUAUAGAAAUAACAUAACCUAACUGUUAAAAAUGAGAUUCGUUAAUCUUAUACUAACAGUUGCAUAGAAAGGAUUUGCU .((((...(((((((....((((((.................((.(((((((.(((((..(((.(((.(((((....((..(((((((.....((((......))))....)))))))..))....)))))..))).)))..)))))))))))).))......)))))).............(((((((((...((((((((....))))))))..)))))))))....)))))))..)))) (-47.90) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 772 50 1 141 92 NC_009009:SSA_1064|5end_hypothetical_protein_1081065..1081295_NEGATIVE 224 236 199 74 34 NC_009009:SSA_1468|5end_3-dehydroquinate_synthase,_putative_1475452..1475682_NEGATIVE 219 42 3 125 93 NC_009009:SSA_0306|5end_Transcription_regulator_(glutamine_synthetase_repressor),_putative_302590..302820_POSITIVE 217 103 61 182 130 NC_009009:SSA_1758|5end_hypothetical_protein_1746619..1746849_NEGATIVE 211 47 4 170 129 NC_009009:SSA_0572|5end_Dehydrogenase,_putative_567426..567656_POSITIVE 208 240 195 56 1 NC_009009:SSA_2166|5end_ABC-type_multidrug_transporter,_ATPase_and_permease_components,_putative_2165642..2165872_NEGATIVE 206 50 3 104 61 NC_009009:SSA_1243|5end_Dihydroorotate_dehydrogenase_electron_transfer_subunit,_putative_1268204..1268434_NEGATIVE 202 237 197 132 95 NC_009009:SSA_1728|5end_ABC_transporter_membrane-spanning_permease-branched_chain_amino_acid_transport,_putative_1714293..1714523_NEGATIVE 201 240 200 150 103 NC_009009:SSA_2294|5end_hypothetical_protein_2296082..2296312_POSITIVE 201 48 6 67 23 NC_009009:SSA_0244|5end_hypothetical_protein_238698..238928_POSITIVE 196 224 194 94 68 NC_009009:SSA_2125|5end_Small_primase-like_protein_(Toprim_domain),_putative_2130019..2130249_NEGATIVE 196 75 32 106 60 NC_009009:SSA_0302|5end_Phosphoglycerate_kinase,_putative_294890..295120_POSITIVE 193 50 10 220 187 NC_009009:SSA_1296|5end_hypothetical_protein_1313013..1313243_NEGATIVE 192 100 62 127 87 NC_009009:SSA_1523|5end_Glutathione_peroxidase,_putative_1532067..1532297_POSITIVE 192 17 2 129 114 NC_009009:SSA_1329|5end_Conserved_uncharacterized_protein_1345904..1346134_NEGATIVE 191 119 71 130 85 NC_009009:SSA_1958|5end_Adapter_protein_mecA,_putative_1955413..1955643_NEGATIVE 189 238 198 64 30 NC_009009:SSA_0288|5end_hypothetical_protein_281303..281533_NEGATIVE 187 240 198 188 145 NC_009009:SSA_0269|5end_Phosphotransferase_system_(PTS)_cellobiose-specific_component_IIA,_putative_262550..262780_POSITIVE 186 23 2 115 93 NC_009009:SSA_1854|5end_Conserved_uncharacterized_protein_1850884..1851114_NEGATIVE 185 229 186 51 17 NC_009009:SSA_0019|5end_Secreted_antigen_GbpB/SagA;_peptidoglycan_hydrolase;_PcsB_protein_precursor,_putative_24225..24455_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 231 226 193 74 43 NC_009009:SSA_0701|3end_Cation_transporter_CorA_family,_putative_685356..685506_POSITIVE 224 236 199 63 23 NC_009009:SSA_1469|3end_Shikimate_dehydrogenase,_putative_1475463..1475613_NEGATIVE 219 42 3 44 12 NC_009009:SSA_0305|3end_hypothetical_protein_302589..302739_POSITIVE 217 103 61 137 85 NC_009009:SSA_1759|3end_hypothetical_protein_1746664..1746814_NEGATIVE 203 75 33 124 75 NC_009009:SSA_1297|3end_Nuclease_subunit_of_the_excinuclease_complex,_subunit_C,_putative_1313141..1313291_NEGATIVE 198 47 1 133 98 NC_009009:SSA_1465|3end_Conserved_uncharacterized_protein_1471648..1471798_NEGATIVE 197 50 1 131 93 NC_009009:SSA_0826|3end_hypothetical_protein_805516..805666_POSITIVE 196 224 194 128 102 NC_009009:SSA_2126|3end_hypothetical_protein_2129985..2130135_NEGATIVE 192 17 2 132 117 NC_009009:SSA_1330|3end_hypothetical_protein_1345901..1346051_NEGATIVE 190 240 197 54 1 NC_009009:SSA_2167|3end_ABC-type_multidrug_transporter,_ATPase_and_permease_components,_putative_2165644..2165794_NEGATIVE 186 23 2 102 80 NC_009009:SSA_1855|3end_hypothetical_protein_1850897..1851047_NEGATIVE 184 129 81 80 21 NC_009009:SSA_0793|3end_DNA-entry_nuclease,_putative_775799..775949_POSITIVE 184 235 196 68 24 NC_009009:SSA_0479|3end_CbiQ_protein,_putative_481179..481329_POSITIVE 181 213 183 133 101 NC_009009:SSA_2007|3end_Chaperone_protein_dnaK/HSP70,_putative_2007443..2007593_NEGATIVE 180 154 117 112 70 NC_009009:SSA_1047|3end_UDP-N-acetylenolpyruvoylglucosamine_reductase,_putative_1062845..1062995_POSITIVE 179 89 55 53 19 NC_009009:SSA_0395|3end_6-phospho-beta-glucosidase,_putative_392580..392730_POSITIVE 178 23 1 136 116 NC_009009:SSA_2354|3end_hypothetical_protein_2355605..2355755_NEGATIVE 178 89 47 81 36 NC_009009:SSA_2011|3end_ABC-type_multidrug_transport_system,_ATPase_component,_putative_2012017..2012167_NEGATIVE 178 240 200 125 81 NC_009009:SSA_1870|3end_Phospho-N-acetylmuramoyl-pentapeptide-_transferase,_putative_1865600..1865750_NEGATIVE 178 240 211 61 36 NC_009009:SSA_1042|3end_Xylanase/chitin_deacetylase,_putative_1057509..1057659_NEGATIVE