Origin IGS: atgacttaaacaaaatggctccttataaaataaaccaagtcctatctggcttggttttttaatattttaagatgggaattggctgaagcctcttgattttaaaagcaagatgaggaaacgcagtagtttgagggaatctgtctctataaaaaataagaatttattcgcaaaattgcagatatttgaatccgtttacaaaaaataaagacgcctcaaataaaatatggtataatatgtgaagaatatctatttcaggagggaaaatc .........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 gattttccctcctgaaatagatattcttcacatattataccatattttatttgaggcgtctttattttttgtaaacggattcaaatatctgcaattttgcgaataaattcttattttttatagagacagattccctcaaactactgcgtttcctcatcttgcttttaaaatcaagaggcttcagccaattcccatcttaaaatattaaaaaaccaagccagataggacttggtttattttataaggagccattttgtttaagtcat Mask Tandem Repeat Region ================================================ atgacttaaacaaaatggctccttataaaataaaccaagtcctatctggcttggttttttaatattttaagatgggaattggctgaagcctcttgattttaaaagcaagatgaggaaacgcagtagtttgagggaatctgtctctataaaaaataagaatttattcgcaaaattgcagatatttgaatccgtttacaaaaaataaagacgcctcaaataaaatatggtataatatgtgaagaatatctatttcaggagggaaaatc Find is-nt database================================================ Query_seq: SSA_0383:SSA_0384|SSA_0383:SSA_0384:Beta-glucosidase, putative:hypothetical protein:->->:376114..376379 266 atgacttaaacaaaatggctccttataaaataaaccaagtcctatctggcttggttttttaatattttaagatgggaattggctgaagcctcttgattttaaaagcaagatgaggaaacgcagtagtttgagggaatctgtctctataaaaaataagaatttattcgcaaaattgcagatatttgaatccgtttacaaaaaataaagacgcctcaaataaaatatggtataatatgtgaagaatatctatttcaggagggaaaatc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_0383:SSA_0384|SSA_0383:SSA_0384:Beta-glucosidase, putative:hypothetical protein:->->:376114..376379 266 atgacttaaacaaaatggctccttataaaataaaccaagtcctatctggcttggttttttaatattttaagatgggaattggctgaagcctcttgattttaaaagcaagatgaggaaacgcagtagtttgagggaatctgtctctataaaaaataagaatttattcgcaaaattgcagatatttgaatccgtttacaaaaaataaagacgcctcaaataaaatatggtataatatgtgaagaatatctatttcaggagggaaaatc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_0383:SSA_0384|SSA_0383:SSA_0384:Beta-glucosidase, putative:hypothetical protein:->->:376114..376379 266 atgacttaaacaaaatggctccttataaaataaaccaagtcctatctggcttggttttttaatattttaagatgggaattggctgaagcctcttgattttaaaagcaagatgaggaaacgcagtagtttgagggaatctgtctctataaaaaataagaatttattcgcaaaattgcagatatttgaatccgtttacaaaaaataaagacgcctcaaataaaatatggtataatatgtgaagaatatctatttcaggagggaaaatc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 atgacttaaacaaaatggctccttataaaataaaccaagtcctatctggcttggttttttaatattttaagatgggaattggctgaagcctcttgattttaaaagcaagatgaggaaacgcagtagtttgagggaatctgtctctataaaaaataagaatttattcgcaaaattgcagatatttgaatccgtttacaaaaaataaagacgcctcaaataaaatatggtataatatgtgaagaatatctatttcaggagggaaaatc Predict ORF larger than 30AA ================================================ Protein_Len: 40 Strand: + Start: 83 End: 202 .................................................................................. M K P L D F K S K M R K R S S L R E S V S I K N K N L F A K L Q I F E S V Y K K ................................................................ Protein_Len: 34 Strand: - Start: 164 End: 265 ................................................................................................................................................................... E C F Q L Y K F G N V F F L S A E F L I H Y L I H L I D I E P P F M . Protein_Len: 37 Strand: - Start: 70 End: 180 ..................................................................... S P F Q S F G R S K L L L I L F R L L K L S D T E I F F L F K N A F N C M ...................................................................................... Protein_Len: 33 Strand: - Start: 62 End: 160 ............................................................. Y K L I P I P Q L R K I K F A L H P F A T T Q P F R D R Y F I L M .......................................................................................................... atgacttaaacaaaatggctccttataaaataaaccaagtcctatctggcttggttttttaatattttaagatgggaattggctgaagcctcttgattttaaaagcaagatgaggaaacgcagtagtttgagggaatctgtctctataaaaaataagaatttattcgcaaaattgcagatatttgaatccgtttacaaaaaataaagacgcctcaaataaaatatggtataatatgtgaagaatatctatttcaggagggaaaatc 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================================================ atgacttaaacaaaatggctccttataaaataaaccaagtcctatctggcttggttttttaatattttaagatgggaattggctgaagcctcttgattttaaaagcaagatgaggaaacgcagtagtttgagggaatctgtctctataaaaaataagaatttattcgcaaaattgcagatatttgaatccgtttacaaaaaataaagacgcctcaaataaaatatggtataatatgtgaagaatatctatttcaggagggaaaatc Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 59 HP_score: -4.3 Tail_Score: -4.13945 Start: 24 End: 64 Full_Region: AACAAAATGGCTCCT TATAAAATAAACCAAGTC CTATCT GGCTTGGTTTTTTAATA TTTTAAGATGGGAAT .......................TATAAAATAAACCAAGTCCTATCTGGCTTGGTTTTTTAATA.......................................................................................................................................................................................................... TransTerm Strand: - Conf: 68 HP_score: -4.3 Tail_Score: -4.77173 Start: 35 End: 54 Full_Region: taaaatattaaaaaa ccaagcc agata ggacttgg tttattttataagga ..................................ccaagccagataggacttgg.................................................................................................................................................................................................................... Find igs database================================================ Query_seq: SSA_0383:SSA_0384|SSA_0383:SSA_0384:Beta-glucosidase, putative:hypothetical protein:->->:376114..376379 266 atgacttaaacaaaatggctccttataaaataaaccaagtcctatctggcttggttttttaatattttaagatgggaattggctgaagcctcttgattttaaaagcaagatgaggaaacgcagtagtttgagggaatctgtctctataaaaaataagaatttattcgcaaaattgcagatatttgaatccgtttacaaaaaataaagacgcctcaaataaaatatggtataatatgtgaagaatatctatttcaggagggaaaatc Intra-Species Hit: Count: 1 Min: 1 Max: 266 Len: 266 Subject: NC_009009_SSA_0383_SSA_0384|Beta-glucosidase, putative:hypothetical protein|POSITIVE:POSITIVE|[376114,376379]|266 HSP 1 e-value: 1.0E-149 bit: 527.0 Len: 266 Query Start:1 Query End:266 Subject Strand: POSITIVE Subject Start: 1 Subject End: 266 atgacttaaacaaaatggctccttataaaataaaccaagtcctatctggcttggttttttaatattttaagatgggaattggctgaagcctcttgattttaaaagcaagatgaggaaacgcagtagtttgagggaatctgtctctataaaaaataagaatttattcgcaaaattgcagatatttgaatccgtttacaaaaaataaagacgcctcaaataaaatatggtataatatgtgaagaatatctatttcaggagggaaaatc atgacttaaacaaaatggctccttataaaataaaccaagtcctatctggcttggttttttaatattttaagatgggaattggctgaagcctcttgattttaaaagcaagatgaggaaacgcagtagtttgagggaatctgtctctataaaaaataagaatttattcgcaaaattgcagatatttgaatccgtttacaaaaaataaagacgcctcaaataaaatatggtataatatgtgaagaatatctatttcaggagggaaaatc Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUGACUUAAACAAAAUGGCUCCUUAUAAAAUAAACCAAGUCCUAUCUGGCUUGGUUUUUUAAUAUUUUAAGAUGGGAAUUGGCUGAAGCCUCUUGAUUUUAAAAGCAAGAUGAGGAAACGCAGUAGUUUGAGGGAAUCUGUCUCUAUAAAAAAUAAGAAUUUAUUCGCAAAAUUGCAGAUAUUUGAAUCCGUUUACAAAAAAUAAAGACGCCUCAAAUAAAAUAUGGUAUAAUAUGUGAAGAAUAUCUAUUUCAGGAGGGAAAAUC ....(((((((....((..(((((((..((.((((((((((......)))))))))).))....(((((((((((((...(((....))))))).))))))))).....)))))))..)).....)))))))........(((((.....(((((.((((((.((((((....(((...(((((((...(((((...........)))))..))))))).......))).....)))))))))).)))))))....)))))..... (-55.40) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAUUUUCCCUCCUGAAAUAGAUAUUCUUCACAUAUUAUACCAUAUUUUAUUUGAGGCGUCUUUAUUUUUUGUAAACGGAUUCAAAUAUCUGCAAUUUUGCGAAUAAAUUCUUAUUUUUUAUAGAGACAGAUUCCCUCAAACUACUGCGUUUCCUCAUCUUGCUUUUAAAAUCAAGAGGCUUCAGCCAAUUCCCAUCUUAAAAUAUUAAAAAACCAAGCCAGAUAGGACUUGGUUUAUUUUAUAAGGAGCCAUUUUGUUUAAGUCAU (((((...(((((...(((((....................((((((((..(((((.((((((((..(((((((((((((......)))))....))))))))................))))))))..........((((......)))))))))(((((.((....)).)))))(((....)))...........))))))))....((((((((((.....)).))))))))..))))).)))))...........))))).. (-47.41) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 304 115 71 161 123 NC_009009:SSA_2048|5end_Serine_acetyltransferase,_putative_2050601..2050831_NEGATIVE 291 149 101 186 118 NC_009009:SSA_1800|5end_UDP-N-acetylmuramate--L-alanine_ligase,_putative_1782371..1782601_NEGATIVE 285 125 81 136 92 NC_009009:SSA_1641|5end_MutT/nudix_family_protein,_putative_1643094..1643324_NEGATIVE 282 55 16 140 95 NC_009009:SSA_0838|5end_GtfB,_putative_825406..825636_POSITIVE 273 90 41 171 116 NC_009009:SSA_0710|5end_Exopolysaccharide_biosynthesis_protein,_acetyltransferase,_putative_695639..695869_NEGATIVE 272 85 41 230 192 NC_009009:SSA_2132|5end_Ure_cluster_protein,_putative_2134170..2134400_POSITIVE 268 84 41 146 101 NC_009009:SSA_0088|5end_V-type_sodium_ATPase,_subunit_C,_putative_88930..89160_POSITIVE 264 121 81 193 142 NC_009009:SSA_1921|5end_hypothetical_protein_1910875..1911105_POSITIVE 264 139 104 85 39 NC_009009:SSA_0227|5end_Collagen-binding_surface_protein,_putative_221037..221267_POSITIVE 258 162 131 176 147 NC_009009:SSA_2129|5end_Arsenical_resistance_operon_transcription_repressor_(ArsR),_putative_2133308..2133538_NEGATIVE 258 116 72 174 131 NC_009009:SSA_2015|5end_Phosphoglycerate_mutase,_putative_2015492..2015722_NEGATIVE 257 89 49 177 139 NC_009009:SSA_1303|5end_RimM_protein,_required_for_16S_rRNA_processing,_putative_1322992..1323222_NEGATIVE 246 100 52 146 99 NC_009009:SSA_0334|5end_Diphosphomevalonate_decarboxylase,_putative_327855..328085_POSITIVE 245 50 19 130 98 NC_009009:SSA_2175|5end_hypothetical_protein_2174042..2174272_NEGATIVE 242 137 104 59 15 NC_009009:SSA_0497|5end_Nickel_ABC_transporter,_putative_496922..497152_POSITIVE 241 90 42 176 128 NC_009009:SSA_1746|5end_hypothetical_protein_1732945..1733175_NEGATIVE 241 58 11 61 4 NC_009009:SSA_0695|5end_hypothetical_protein_678449..678679_POSITIVE 240 145 101 181 128 NC_009009:SSA_1957|5end_Glycosyl_transferase_N-acetylglucosaminyltransferase,_putative_1954670..1954900_NEGATIVE 240 88 42 149 100 NC_009009:SSA_1860|5end_Penicillin-binding_protein_1A,_putative_1854299..1854529_POSITIVE 240 141 103 66 32 NC_009009:SSA_1578|5end_ABC-type_Fe3+-siderophore_transport_system,_permease_component,_putative_1581803..1582033_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 304 115 71 69 31 NC_009009:SSA_2049|3end_Polyribonucleotide_nucleotidyltransferase,_putative_2050693..2050843_NEGATIVE 285 125 81 127 83 NC_009009:SSA_1642|3end_N-acetylglucosamine-1-phosphate_uridyltransferase,_putative_1643103..1643253_NEGATIVE 275 130 81 81 25 NC_009009:SSA_0605|3end_Methyltransferase_gidB,_putative_592994..593144_NEGATIVE 268 84 41 135 90 NC_009009:SSA_0087|3end_V-type_sodium_ATPase,_subunit_E,_putative_88999..89149_POSITIVE 266 116 75 149 100 NC_009009:SSA_1479|3end_Transposase,_putative_1483889..1484039_POSITIVE 265 90 44 79 36 NC_009009:SSA_1659|3end_ABC-type_antimicrobial_peptide_transport_system,_permease_component,_putative_1654831..1654981_NEGATIVE 264 121 81 122 71 NC_009009:SSA_1920|3end_Phosphotransferase_system,_mannose-specific_EIID,_putative_1910884..1911034_POSITIVE 258 116 72 74 31 NC_009009:SSA_2016|3end_Phosphoglycerate_mutase,_putative_2015592..2015742_NEGATIVE 257 89 49 82 44 NC_009009:SSA_1304|3end_hypothetical_protein_1323087..1323237_NEGATIVE 252 94 52 138 88 NC_009009:SSA_1708|3end_hypothetical_protein_1698194..1698344_NEGATIVE 247 60 13 122 79 NC_009009:SSA_1497|3end_DCMP_deaminase,_putative_1503068..1503218_NEGATIVE 247 128 81 44 5 NC_009009:SSA_1051|3end_Spermidine/putrescine_ABC_transporter,_spermidine/putrescine-binding_protein,_putative_1066808..1066958_POSITIVE 243 129 81 85 39 NC_009009:SSA_1777|3end_Ribosomal_large_subunit_pseudouridine_synthase_B,_putative_1764427..1764577_NEGATIVE 243 114 71 108 50 NC_009009:SSA_1523|3end_Glutathione_peroxidase,_putative_1532620..1532770_POSITIVE 243 80 32 87 45 NC_009009:SSA_1105|3end_50S_ribosomal_protein_L7/_L12,_putative_1125765..1125915_POSITIVE 243 60 16 85 28 NC_009009:SSA_0819|3end_hypothetical_protein_801181..801331_POSITIVE 242 137 104 66 22 NC_009009:SSA_0496|3end_Succinylglutamate_desuccinylase_/_Aspartoacylase_family,_putative_497009..497159_POSITIVE 241 143 104 145 105 NC_009009:SSA_1164|3end_hypothetical_protein_1191007..1191157_NEGATIVE 239 89 42 110 66 NC_009009:SSA_1476|3end_Phosphoglycerol_transferase,_alkaline_phosphatase_superfamily,_putative_1482448..1482598_POSITIVE 238 144 105 57 6 NC_009009:SSA_0980|3end_3-isopropylmalate_dehydratase_large_subunit,_putative_985466..985616_POSITIVE