Origin IGS: aaagaacaaaagtaatcaaaaacagtcaaattcttgactgttttttgtttaatataacttgacatatcaagacatatacctgaaaaattctttattttatagaattgtatgtaattgtttttcaataaaaaattttcagataattattgaaatttcactgcttttatgttacaatgaagctaataaatatgaggtaaaaat .........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 atttttacctcatatttattagcttcattgtaacataaaagcagtgaaatttcaataattatctgaaaattttttattgaaaaacaattacatacaattctataaaataaagaatttttcaggtatatgtcttgatatgtcaagttatattaaacaaaaaacagtcaagaatttgactgtttttgattacttttgttcttt Mask Tandem Repeat Region ================================================ aaagaacaaaagtaatcaaaaacagtcaaattcttgactgttttttgtttaatataacttgacatatcaagacatatacctgaaaaattctttattttatagaattgtatgtaattgtttttcaataaaaaattttcagataattattgaaatttcactgcttttatgttacaatgaagctaataaatatgaggtaaaaat Find is-nt database================================================ Query_seq: SSA_0565:SSA_0566|SSA_0565:SSA_0566:hypothetical protein:GTP-sensing transcriptional pleiotropic repressor, putative:->->:559956..560156 201 aaagaacaaaagtaatcaaaaacagtcaaattcttgactgttttttgtttaatataacttgacatatcaagacatatacctgaaaaattctttattttatagaattgtatgtaattgtttttcaataaaaaattttcagataattattgaaatttcactgcttttatgttacaatgaagctaataaatatgaggtaaaaat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_0565:SSA_0566|SSA_0565:SSA_0566:hypothetical protein:GTP-sensing transcriptional pleiotropic repressor, putative:->->:559956..560156 201 aaagaacaaaagtaatcaaaaacagtcaaattcttgactgttttttgtttaatataacttgacatatcaagacatatacctgaaaaattctttattttatagaattgtatgtaattgtttttcaataaaaaattttcagataattattgaaatttcactgcttttatgttacaatgaagctaataaatatgaggtaaaaat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_0565:SSA_0566|SSA_0565:SSA_0566:hypothetical protein:GTP-sensing transcriptional pleiotropic repressor, putative:->->:559956..560156 201 aaagaacaaaagtaatcaaaaacagtcaaattcttgactgttttttgtttaatataacttgacatatcaagacatatacctgaaaaattctttattttatagaattgtatgtaattgtttttcaataaaaaattttcagataattattgaaatttcactgcttttatgttacaatgaagctaataaatatgaggtaaaaat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aaagaacaaaagtaatcaaaaacagtcaaattcttgactgttttttgtttaatataacttgacatatcaagacatatacctgaaaaattctttattttatagaattgtatgtaattgtttttcaataaaaaattttcagataattattgaaatttcactgcttttatgttacaatgaagctaataaatatgaggtaaaaat Predict ORF larger than 30AA ================================================ Protein_Len: 47 Strand: + Start: 59 End: 199 .......................................................... M T Y Q D I Y L K N S L F Y R I V C N C F S I K N F Q I I I E I S L L L C Y N E A N K Y E V K .. Protein_Len: 41 Strand: - Start: 3 End: 125 .. S C F Y D F V T L N K V T K Q K I Y S S M D L C I G S F N K I K Y F Q I Y N N K M ............................................................................ aaagaacaaaagtaatcaaaaacagtcaaattcttgactgttttttgtttaatataacttgacatatcaagacatatacctgaaaaattctttattttatagaattgtatgtaattgtttttcaataaaaaattttcagataattattgaaatttcactgcttttatgttacaatgaagctaataaatatgaggtaaaaat 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: 90 Start: 146 End: 175 .................................................................................................................................................ATTGAAATTTCACTGCTTTTATGTTACAAT.......................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ aaagaacaaaagtaatcaaaaacagtcaaattcttgactgttttttgtttaatataacttgacatatcaagacatatacctgaaaaattctttattttatagaattgtatgtaattgtttttcaataaaaaattttcagataattattgaaatttcactgcttttatgttacaatgaagctaataaatatgaggtaaaaat Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 76 HP_score: -9.5 Tail_Score: -2.91144 Start: 17 End: 46 Full_Region: caagttatattaaac aaaaaacagtcaa gaat ttgactgtttttg attacttttgttctt ................aaaaaacagtcaagaatttgactgtttttg........................................................................................................................................................... TransTerm Strand: - Conf: 93 HP_score: -8.5 Tail_Score: -4.97312 Start: 23 End: 40 Full_Region: atattaaacaaaaaa cagtcaa gaat ttgactg tttttgattactttt ......................cagtcaagaatttgactg................................................................................................................................................................. Find igs database================================================ Query_seq: SSA_0565:SSA_0566|SSA_0565:SSA_0566:hypothetical protein:GTP-sensing transcriptional pleiotropic repressor, putative:->->:559956..560156 201 aaagaacaaaagtaatcaaaaacagtcaaattcttgactgttttttgtttaatataacttgacatatcaagacatatacctgaaaaattctttattttatagaattgtatgtaattgtttttcaataaaaaattttcagataattattgaaatttcactgcttttatgttacaatgaagctaataaatatgaggtaaaaat Intra-Species Hit: Count: 1 Min: 1 Max: 201 Len: 201 Subject: NC_009009_SSA_0565_SSA_0566|hypothetical protein:GTP-sensing transcriptional pleiotropic repressor, putative|POSITIVE:POSITIVE|[559956,560156]|201 HSP 1 e-value: 1.0E-110 bit: 398.0 Len: 201 Query Start:1 Query End:201 Subject Strand: POSITIVE Subject Start: 1 Subject End: 201 aaagaacaaaagtaatcaaaaacagtcaaattcttgactgttttttgtttaatataacttgacatatcaagacatatacctgaaaaattctttattttatagaattgtatgtaattgtttttcaataaaaaattttcagataattattgaaatttcactgcttttatgttacaatgaagctaataaatatgaggtaaaaat aaagaacaaaagtaatcaaaaacagtcaaattcttgactgttttttgtttaatataacttgacatatcaagacatatacctgaaaaattctttattttatagaattgtatgtaattgtttttcaataaaaaattttcagataattattgaaatttcactgcttttatgttacaatgaagctaataaatatgaggtaaaaat Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAGAACAAAAGUAAUCAAAAACAGUCAAAUUCUUGACUGUUUUUUGUUUAAUAUAACUUGACAUAUCAAGACAUAUACCUGAAAAAUUCUUUAUUUUAUAGAAUUGUAUGUAAUUGUUUUUCAAUAAAAAAUUUUCAGAUAAUUAUUGAAAUUUCACUGCUUUUAUGUUACAAUGAAGCUAAUAAAUAUGAGGUAAAAAU ...((((((((.........(((((((((....))))))))))))))))).......(((((....))))).....(((((.(.........(((((..(((.(((((((((((..((.(((((((((...(((....)))..))))))))).......))..))))).))))))....)))..)))))).)))))..... (-34.10) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUUUUUACCUCAUAUUUAUUAGCUUCAUUGUAACAUAAAAGCAGUGAAAUUUCAAUAAUUAUCUGAAAAUUUUUUAUUGAAAAACAAUUACAUACAAUUCUAUAAAAUAAAGAAUUUUUCAGGUAUAUGUCUUGAUAUGUCAAGUUAUAUUAAACAAAAAACAGUCAAGAAUUUGACUGUUUUUGAUUACUUUUGUUCUUU .......................((((((((.........))))))))...........(((((((((((((((((((.......((((......))))......))))))))).))))))))))((((.(((((....))))).)))).......((((((((((((....))))))))))))................. (-36.32) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 248 43 3 231 184 NC_009009:SSA_0409|5end_ABC-type_multidrug_transport_system,_ATPase_component,_putative_405605..405835_NEGATIVE 234 196 154 68 27 NC_009009:SSA_0490|5end_Cobalamin_5'-phosphate_synthase,_putative_490236..490466_POSITIVE 233 180 147 38 5 NC_009009:SSA_0856|5end_Glycosyltransferase_(vectorial_glycosyl_polymerization_(VGP)_family),_putative_843210..843440_POSITIVE 222 197 158 60 13 NC_009009:SSA_1065|5end_Beta-hexosamidase_A,_putative_1081258..1081488_POSITIVE 208 54 16 193 149 NC_009009:SSA_0089|5end_V-type_sodium_ATPase,_subunit_F,_putative_89930..90160_POSITIVE 203 50 3 197 155 NC_009009:SSA_2087|5end_Conserved_uncharacterized_protein_2092657..2092887_NEGATIVE 196 183 158 84 58 NC_009009:SSA_0360|5end_Conserved_uncharacterized_protein_352704..352934_POSITIVE 195 178 134 56 1 NC_009009:SSA_0691|5end_D-ala,D-ala_ligase,_putative_675233..675463_POSITIVE 193 53 12 79 33 NC_009009:SSA_1979|5end_Alkaline-shock_protein,_putative_1974301..1974531_NEGATIVE 192 180 132 126 76 NC_009009:SSA_1630|5end_hypothetical_protein_1631192..1631422_POSITIVE 192 196 156 97 43 NC_009009:SSA_1043|5end_Homoserine_dehydrogenase,_putative_1058565..1058795_POSITIVE 190 60 21 66 26 NC_009009:SSA_1869|5end_ATP-dependent_RNA_helicase,_putative_1865495..1865725_NEGATIVE 189 70 24 72 21 NC_009009:SSA_0476|5end_Precorrin-2_C20-methyltransferase,_putative_478500..478730_POSITIVE 183 196 152 157 109 NC_009009:SSA_0966|5end_Uridine_kinase,_putative_975063..975293_POSITIVE 180 109 68 227 181 NC_009009:SSA_2079|5end_Acetyltransferase,_putative_2083971..2084201_POSITIVE 178 64 31 42 8 NC_009009:SSA_0474|5end_Uroporphyrin-III_C-methyltransferase/uroporphyrinogen-III_synthase,_putative_476270..476500_POSITIVE 177 173 131 136 95 NC_009009:SSA_0905|5end_CshA-like_fibrillar_surface_protein_B_903080..903310_POSITIVE 176 98 55 194 146 NC_009009:SSA_2200|5end_Firmicutes_transcriptional_repressor_of_class_III_stress_genes_(CtsR),_putative_2201573..2201803_NEGATIVE 176 69 21 90 29 NC_009009:SSA_1472|5end_hypothetical_protein_1478655..1478885_NEGATIVE 176 64 21 188 138 NC_009009:SSA_1320|5end_hypothetical_protein_1337194..1337424_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 251 48 3 94 39 NC_009009:SSA_0410|3end_hypothetical_protein_405750..405900_NEGATIVE 234 196 154 71 30 NC_009009:SSA_0489|3end_Adenosylcobinamide_kinase_/_adenosylcobinamide_phosphate_guanyltransferase,_putative_490319..490469_POSITIVE 227 43 20 128 105 NC_009009:SSA_1478|3end_Transposase_ORF1,_putative_1483124..1483274_POSITIVE 217 45 2 72 18 NC_009009:SSA_1672|3end_hypothetical_protein_1670291..1670441_NEGATIVE 216 45 18 73 46 NC_009009:SSA_0565|3end_hypothetical_protein_559895..560045_POSITIVE 214 86 41 150 98 NC_009009:SSA_1832|3end_hypothetical_protein_1822614..1822764_POSITIVE 205 44 12 92 63 NC_009009:SSA_1269|3end_hypothetical_protein_1291970..1292120_NEGATIVE 203 50 3 88 46 NC_009009:SSA_2088|3end_Carbohydrate_isomerase,_AraD/FucA_family,_putative_2092766..2092916_NEGATIVE 192 180 132 90 40 NC_009009:SSA_1629|3end_Peptidyl-prolyl_cis-trans_isomerase,_cyclophilin-type,_putative_1631236..1631386_POSITIVE 191 50 18 91 51 NC_009009:SSA_1663|3end_Collagen-binding_protein_A_1659586..1659736_NEGATIVE 189 70 24 62 11 NC_009009:SSA_0475|3end_CbiK_protein,_putative_478570..478720_POSITIVE 183 80 37 148 93 NC_009009:SSA_1689|3end_hypothetical_protein_1681945..1682095_NEGATIVE 182 47 10 123 82 NC_009009:SSA_0095|3end_Threonine_synthase,_putative_98119..98269_POSITIVE 176 64 21 136 86 NC_009009:SSA_1321|3end_Ferrochelatase,_putative_1337246..1337396_NEGATIVE 176 68 21 99 48 NC_009009:SSA_0460|3end_Multiple_antibiotic_resistance_operon_transcription_repressor_(MarR),_putative_463146..463296_POSITIVE 175 48 1 101 39 NC_009009:SSA_0081|3end_Transcriptional_regulator,_RpiR_family_(phosphosugar-binding),_putative_84220..84370_NEGATIVE 172 49 24 70 45 NC_009009:SSA_0893|3end_ATP-binding_cassette_transporter-like_protein,_putative_885872..886022_POSITIVE 170 57 12 82 35 NC_009009:SSA_1761|3end_Hemolysin_(containing_CBS_domains),_putative_1747437..1747587_NEGATIVE 170 179 132 59 7 NC_009009:SSA_1493|3end_hypothetical_protein_1498929..1499079_NEGATIVE 170 60 11 99 45 NC_009009:SSA_0662|3end_Multiple_antibiotic_resistance_operon_transcription_repressor_(MarR),_putative_647847..647997_NEGATIVE