Origin IGS: aagaactccttcagataactatgttacctttatttaaagataacatagttatctttttctgtcaagatttttcctatcctgggatttacattttcccgaaaatcctgtataatagtcgaaacggataagtactattgggcacttttcagaaagtctgcggtggctgtgagcagataaggagaaaataggaaattctaccgttagtttaaaaatgaataattaagcaagtgcacttttgtgaagttggatggaaccgcggctatgccgctccaacagtttcataaagtgcttttatttttggaggtacct .........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.........1.........2.........3.........4.........5.........6.........7.........8.........9 aggtacctccaaaaataaaagcactttatgaaactgttggagcggcatagccgcggttccatccaacttcacaaaagtgcacttgcttaattattcatttttaaactaacggtagaatttcctattttctccttatctgctcacagccaccgcagactttctgaaaagtgcccaatagtacttatccgtttcgactattatacaggattttcgggaaaatgtaaatcccaggataggaaaaatcttgacagaaaaagataactatgttatctttaaataaaggtaacatagttatctgaaggagttctt Mask Tandem Repeat Region ================================================ aagaactccttcagataactatgttacctttatttaaagataacatagttatctttttctgtcaagatttttcctatcctgggatttacattttcccgaaaatcctgtataatagtcgaaacggataagtactattgggcacttttcagaaagtctgcggtggctgtgagcagataaggagaaaataggaaattctaccgttagtttaaaaatgaataattaagcaagtgcacttttgtgaagttggatggaaccgcggctatgccgctccaacagtttcataaagtgcttttatttttggaggtacct Find is-nt database================================================ Query_seq: SSA_1924:SSA_1925|SSA_1924:SSA_1925:Transcriptional regulator, TetR/AcrR family, putative:Seryl-tRNA synthetase, putative:<-->:1913339..1913647 309 aagaactccttcagataactatgttacctttatttaaagataacatagttatctttttctgtcaagatttttcctatcctgggatttacattttcccgaaaatcctgtataatagtcgaaacggataagtactattgggcacttttcagaaagtctgcggtggctgtgagcagataaggagaaaataggaaattctaccgttagtttaaaaatgaataattaagcaagtgcacttttgtgaagttggatggaaccgcggctatgccgctccaacagtttcataaagtgcttttatttttggaggtacct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_1924:SSA_1925|SSA_1924:SSA_1925:Transcriptional regulator, TetR/AcrR family, putative:Seryl-tRNA synthetase, putative:<-->:1913339..1913647 309 aagaactccttcagataactatgttacctttatttaaagataacatagttatctttttctgtcaagatttttcctatcctgggatttacattttcccgaaaatcctgtataatagtcgaaacggataagtactattgggcacttttcagaaagtctgcggtggctgtgagcagataaggagaaaataggaaattctaccgttagtttaaaaatgaataattaagcaagtgcacttttgtgaagttggatggaaccgcggctatgccgctccaacagtttcataaagtgcttttatttttggaggtacct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_1924:SSA_1925|SSA_1924:SSA_1925:Transcriptional regulator, TetR/AcrR family, putative:Seryl-tRNA synthetase, putative:<-->:1913339..1913647 309 aagaactccttcagataactatgttacctttatttaaagataacatagttatctttttctgtcaagatttttcctatcctgggatttacattttcccgaaaatcctgtataatagtcgaaacggataagtactattgggcacttttcagaaagtctgcggtggctgtgagcagataaggagaaaataggaaattctaccgttagtttaaaaatgaataattaagcaagtgcacttttgtgaagttggatggaaccgcggctatgccgctccaacagtttcataaagtgcttttatttttggaggtacct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aagaactccttcagataactatgttacctttatttaaagataacatagttatctttttctgtcaagatttttcctatcctgggatttacattttcccgaaaatcctgtataatagtcgaaacggataagtactattgggcacttttcagaaagtctgcggtggctgtgagcagataaggagaaaataggaaattctaccgttagtttaaaaatgaataattaagcaagtgcacttttgtgaagttggatggaaccgcggctatgccgctccaacagtttcataaagtgcttttatttttggaggtacct Predict ORF larger than 30AA ================================================ Protein_Len: 37 Strand: + Start: 15 End: 125 .............. M T M L P L F K D N I V I F F C Q D F S Y P G I Y I F P K I L Y N S R N G ........................................................................................................................................................................................ Protein_Len: 36 Strand: + Start: 67 End: 174 .................................................................. M F P I L G F T F S R K S C I I V E T D K Y Y W A L F R K S A V A V S R ....................................................................................................................................... Protein_Len: 54 Strand: - Start: 52 End: 213 ................................................... R K R D L N K R D Q S K C K G S F G T Y Y D F R I L V I P C K E S L R R H S H A S L S F I P F E V T L K F M ................................................................................................ aagaactccttcagataactatgttacctttatttaaagataacatagttatctttttctgtcaagatttttcctatcctgggatttacattttcccgaaaatcctgtataatagtcgaaacggataagtactattgggcacttttcagaaagtctgcggtggctgtgagcagataaggagaaaataggaaattctaccgttagtttaaaaatgaataattaagcaagtgcacttttgtgaagttggatggaaccgcggctatgccgctccaacagtttcataaagtgcttttatttttggaggtacct 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: 91 Start: 84 End: 113 ...................................................................................ATTTACATTTTCCCGAAAATCCTGTATAAT.................................................................................................................................................................................................... PromScan Matrix: RpoD-17 Strand: - Score: 85 Start: 37 End: 66 ....................................CTTGACAGAAAAAGATAACTATGTTATCTT................................................................................................................................................................................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ aagaactccttcagataactatgttacctttatttaaagataacatagttatctttttctgtcaagatttttcctatcctgggatttacattttcccgaaaatcctgtataatagtcgaaacggataagtactattgggcacttttcagaaagtctgcggtggctgtgagcagataaggagaaaataggaaattctaccgttagtttaaaaatgaataattaagcaagtgcacttttgtgaagttggatggaaccgcggctatgccgctccaacagtttcataaagtgcttttatttttggaggtacct Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 87 HP_score: -11.7 Tail_Score: -3.48772 Start: 19 End: 48 Full_Region: gacagaaaaagataa ctatgttatcttt aaat aaaggtaacatag ttatctgaaggagtt ..................ctatgttatctttaaataaaggtaacatag..................................................................................................................................................................................................................................................................... Find igs database================================================ Query_seq: SSA_1924:SSA_1925|SSA_1924:SSA_1925:Transcriptional regulator, TetR/AcrR family, putative:Seryl-tRNA synthetase, putative:<-->:1913339..1913647 309 aagaactccttcagataactatgttacctttatttaaagataacatagttatctttttctgtcaagatttttcctatcctgggatttacattttcccgaaaatcctgtataatagtcgaaacggataagtactattgggcacttttcagaaagtctgcggtggctgtgagcagataaggagaaaataggaaattctaccgttagtttaaaaatgaataattaagcaagtgcacttttgtgaagttggatggaaccgcggctatgccgctccaacagtttcataaagtgcttttatttttggaggtacct Intra-Species Hit: Count: 1 Min: 1 Max: 309 Len: 309 Subject: NC_009009_SSA_1924_SSA_1925|Transcriptional regulator, TetR/AcrR family, putative:Seryl-tRNA synthetase, putative|NEGATIVE:POSITIVE|[1913339,1913647]|309 HSP 1 e-value: 1.0E-174 bit: 613.0 Len: 309 Query Start:1 Query End:309 Subject Strand: POSITIVE Subject Start: 1 Subject End: 309 aagaactccttcagataactatgttacctttatttaaagataacatagttatctttttctgtcaagatttttcctatcctgggatttacattttcccgaaaatcctgtataatagtcgaaacggataagtactattgggcacttttcagaaagtctgcggtggctgtgagcagataaggagaaaataggaaattctaccgttagtttaaaaatgaataattaagcaagtgcacttttgtgaagttggatggaaccgcggctatgccgctccaacagtttcataaagtgcttttatttttggaggtacct aagaactccttcagataactatgttacctttatttaaagataacatagttatctttttctgtcaagatttttcctatcctgggatttacattttcccgaaaatcctgtataatagtcgaaacggataagtactattgggcacttttcagaaagtctgcggtggctgtgagcagataaggagaaaataggaaattctaccgttagtttaaaaatgaataattaagcaagtgcacttttgtgaagttggatggaaccgcggctatgccgctccaacagtttcataaagtgcttttatttttggaggtacct Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAGAACUCCUUCAGAUAACUAUGUUACCUUUAUUUAAAGAUAACAUAGUUAUCUUUUUCUGUCAAGAUUUUUCCUAUCCUGGGAUUUACAUUUUCCCGAAAAUCCUGUAUAAUAGUCGAAACGGAUAAGUACUAUUGGGCACUUUUCAGAAAGUCUGCGGUGGCUGUGAGCAGAUAAGGAGAAAAUAGGAAAUUCUACCGUUAGUUUAAAAAUGAAUAAUUAAGCAAGUGCACUUUUGUGAAGUUGGAUGGAACCGCGGCUAUGCCGCUCCAACAGUUUCAUAAAGUGCUUUUAUUUUUGGAGGUACCU .....((((...((((((((((((((.((((....)))).))))))))))))))((((((((.....((((((((....(((((.........)))))......((((...(((((((...(((((((((.((....)).))))........)))))...)))))))..))))...))))))))))))))))...........((((((..........))))))....(((((((.(((((..((..((((...(((((...))))))))).))..))))))))))))..........))))...... (-87.60) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGGUACCUCCAAAAAUAAAAGCACUUUAUGAAACUGUUGGAGCGGCAUAGCCGCGGUUCCAUCCAACUUCACAAAAGUGCACUUGCUUAAUUAUUCAUUUUUAAACUAACGGUAGAAUUUCCUAUUUUCUCCUUAUCUGCUCACAGCCACCGCAGACUUUCUGAAAAGUGCCCAAUAGUACUUAUCCGUUUCGACUAUUAUACAGGAUUUUCGGGAAAAUGUAAAUCCCAGGAUAGGAAAAAUCUUGACAGAAAAAGAUAACUAUGUUAUCUUUAAAUAAAGGUAACAUAGUUAUCUGAAGGAGUUCUU ......((((..........(((((((.((((...(((((((((((...))))).......))))))))))..))))))).............(((.........(((....)))..((((((((((..((((..(((((...........)))))......((.((((((......)))))).)).................)))).....((((.........)))).))))))))))..........)))..(((((((((((((((((((....)))))))))))))))))))...))))..... (-82.41) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 848 140 91 231 182 NC_009009:SSA_1924|5end_Transcriptional_regulator,_TetR/AcrR_family,_putative_1913248..1913478_NEGATIVE 336 280 232 53 10 NC_009009:SSA_0063|5end_Holliday_junction_DNA_helicase_ruvB,_putative_65335..65565_POSITIVE 324 270 223 227 181 NC_009009:SSA_0069|5end_Hypothetical_protein,_possibly_membrane-associated_73037..73267_POSITIVE 322 299 255 95 46 NC_009009:SSA_2146|5end_Metallo-beta-lactamase,_putative_2148399..2148629_NEGATIVE 320 159 115 178 127 NC_009009:SSA_1078|5end_hypothetical_protein_1095742..1095972_POSITIVE 314 290 253 225 188 NC_009009:SSA_2239|5end_Conserved_uncharacterized_cytosolic_protein_2237233..2237463_NEGATIVE 314 178 136 215 169 NC_009009:SSA_1722|5end_Thymidylate_kinase,_putative_1708663..1708893_NEGATIVE 313 267 223 68 23 NC_009009:SSA_1430|5end_Ribonuclease_Z,_putative_1438036..1438266_NEGATIVE 309 268 222 180 138 NC_009009:SSA_2050|5end_Arabinose_efflux_permease,_putative_2053255..2053485_POSITIVE 305 290 243 76 30 NC_009009:SSA_1274|5end_hypothetical_protein_1297454..1297684_NEGATIVE 304 268 223 65 19 NC_009009:SSA_0421|5end_Phosphoglycerate_mutase_family_protein,_putative_419564..419794_POSITIVE 297 290 255 62 22 NC_009009:SSA_0199|5end_GTP_cyclohydrolase_I,_putative_198276..198506_POSITIVE 296 268 221 211 160 NC_009009:SSA_0664|5end_Conserved_uncharacterized_protein_649086..649316_NEGATIVE 295 265 223 69 26 NC_009009:SSA_1469|5end_Shikimate_dehydrogenase,_putative_1476317..1476547_NEGATIVE 295 178 132 144 88 NC_009009:SSA_0987|5end_ABC-type_choline_transporter,_membrane-spanning_permease,_putative_988994..989224_POSITIVE 294 289 242 183 138 NC_009009:SSA_1821|5end_Acetyltransferase_(N-acetylase_of_ribosomal_proteins),_putative_1810610..1810840_NEGATIVE 294 170 122 195 136 NC_009009:SSA_0928|5end_ABC-type_multidrug_transporter,_ATPase_and_permease_components,_putative_936679..936909_POSITIVE 291 169 123 66 25 NC_009009:SSA_1961|5end_Amino_acid_ABC_transporter,_amino_acid-binding_protein/permease_protein,_putative_1958548..1958778_POSITIVE 291 271 235 186 152 NC_009009:SSA_1082|5end_PTS_system,_fructose_specific_II_ABC_components,_putative_1099186..1099416_POSITIVE 290 266 222 80 43 NC_009009:SSA_0233|5end_Permease,_putative_227203..227433_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 356 174 135 118 84 NC_009009:SSA_2212|3end_Possible_polysaccharide_transport_protein,_putative_2212627..2212777_NEGATIVE 340 189 152 149 103 NC_009009:SSA_1680|3end_ABC-type_bacitracin_resistance_protein_A,_permease_component,_putative_1673200..1673350_NEGATIVE 318 182 141 60 6 NC_009009:SSA_0184|3end_Competence_protein_ComYA,_putative_189177..189327_POSITIVE 313 267 223 57 12 NC_009009:SSA_1431|3end_hypothetical_protein_1438047..1438197_NEGATIVE 304 268 223 53 7 NC_009009:SSA_0420|3end_Hydrolase,_HAD_superfamily,_putative_419632..419782_POSITIVE 297 290 255 81 41 NC_009009:SSA_0198|3end_Dihydrofolate_synthetase,_putative_198375..198525_POSITIVE 296 268 221 143 92 NC_009009:SSA_0665|3end_NTP_pyrophosphohydrolases_including_oxidative_damage_repair_enzymes_(MutT/NUDIX_family)_649154..649304_NEGATIVE 295 265 223 79 36 NC_009009:SSA_1470|3end_3-dehydroquinate_dehydratase,_putative_1476307..1476457_NEGATIVE 295 178 132 151 95 NC_009009:SSA_0986|3end_Choline_transporter,_putative_989081..989231_POSITIVE 294 200 156 142 108 NC_009009:SSA_1659|3end_ABC-type_antimicrobial_peptide_transport_system,_permease_component,_putative_1654831..1654981_NEGATIVE 294 290 241 71 20 NC_009009:SSA_1077|3end_N-acetyl-glucosamine_matabolism,_putative_1095829..1095979_POSITIVE 291 167 124 39 2 NC_009009:SSA_0281|3end_hypothetical_protein_273963..274113_POSITIVE 290 266 222 74 37 NC_009009:SSA_0232|3end_hypothetical_protein_227277..227427_POSITIVE 288 299 255 72 22 NC_009009:SSA_0468|3end_Precorrin-6y_C5,15-methyltransferase-like,_putative_472418..472568_POSITIVE 286 269 222 127 76 NC_009009:SSA_1738|3end_Polysaccharide_biosynthesis_protein,_putative_1723875..1724025_NEGATIVE 286 299 255 71 13 NC_009009:SSA_1181|3end_Hydrolase,_alpha/beta_superfamily,_putative_1208592..1208742_NEGATIVE 281 277 233 77 13 NC_009009:SSA_2037|3end_tRNA_(Guanosine-2'-O-)-methyltransferase,_TrmH_family,_putative_2040796..2040946_NEGATIVE 281 265 222 145 105 NC_009009:SSA_1194|3end_Aspartate-semialdehyde_dehydrogenase,_putative_1220113..1220263_NEGATIVE 281 87 43 134 77 NC_009009:SSA_0892|3end_ATP-binding_cassette_lipoprotein,_putative_884578..884728_POSITIVE 281 293 253 61 24 NC_009009:SSA_0676|3end_Farnesyl_diphosphate_synthase,_putative_659553..659703_POSITIVE