Origin IGS: aaataggctgggattcataatgtttcccagcttttttgaacccttatgactctttgccgtcctctatatggaacgggtttagagctgttgagaaggatgaaagtatcatccatttttaaattttggattctttgagatattttgtttagaaaaaggcttgaaaaaagtcggaaaagtgctggattcgggcaaatattagcccctttttcatgaaaattatggtata .........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 tataccataattttcatgaaaaaggggctaatatttgcccgaatccagcacttttccgacttttttcaagcctttttctaaacaaaatatctcaaagaatccaaaatttaaaaatggatgatactttcatccttctcaacagctctaaacccgttccatatagaggacggcaaagagtcataagggttcaaaaaagctgggaaacattatgaatcccagcctattt Mask Tandem Repeat Region ================================================ aaataggctgggattcataatgtttcccagcttttttgaacccttatgactctttgccgtcctctatatggaacgggtttagagctgttgagaaggatgaaagtatcatccatttttaaattttggattctttgagatattttgtttagaaaaaggcttgaaaaaagtcggaaaagtgctggattcgggcaaatattagcccctttttcatgaaaattatggtata Find is-nt database================================================ Query_seq: SSA_0876:SSA_0877|SSA_0876:SSA_0877:4-methyl-5(B-hydroxyethyl)-thiazole monophosphate biosynthesis protein, putative:Phosphoglycolate phosphatase, putative:->->:870922..871147 226 aaataggctgggattcataatgtttcccagcttttttgaacccttatgactctttgccgtcctctatatggaacgggtttagagctgttgagaaggatgaaagtatcatccatttttaaattttggattctttgagatattttgtttagaaaaaggcttgaaaaaagtcggaaaagtgctggattcgggcaaatattagcccctttttcatgaaaattatggtata Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_0876:SSA_0877|SSA_0876:SSA_0877:4-methyl-5(B-hydroxyethyl)-thiazole monophosphate biosynthesis protein, putative:Phosphoglycolate phosphatase, putative:->->:870922..871147 226 aaataggctgggattcataatgtttcccagcttttttgaacccttatgactctttgccgtcctctatatggaacgggtttagagctgttgagaaggatgaaagtatcatccatttttaaattttggattctttgagatattttgtttagaaaaaggcttgaaaaaagtcggaaaagtgctggattcgggcaaatattagcccctttttcatgaaaattatggtata Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_0876:SSA_0877|SSA_0876:SSA_0877:4-methyl-5(B-hydroxyethyl)-thiazole monophosphate biosynthesis protein, putative:Phosphoglycolate phosphatase, putative:->->:870922..871147 226 aaataggctgggattcataatgtttcccagcttttttgaacccttatgactctttgccgtcctctatatggaacgggtttagagctgttgagaaggatgaaagtatcatccatttttaaattttggattctttgagatattttgtttagaaaaaggcttgaaaaaagtcggaaaagtgctggattcgggcaaatattagcccctttttcatgaaaattatggtata Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aaataggctgggattcataatgtttcccagcttttttgaacccttatgactctttgccgtcctctatatggaacgggtttagagctgttgagaaggatgaaagtatcatccatttttaaattttggattctttgagatattttgtttagaaaaaggcttgaaaaaagtcggaaaagtgctggattcgggcaaatattagcccctttttcatgaaaattatggtata Predict ORF larger than 30AA ================================================ Protein_Len: 59 Strand: - Start: 18 End: 194 ................. L T E W S K Q V R I V R Q R G R Y P V P K S S N L L I F T D D M K L N Q I R Q S I K N L F L S S F L R F L A P N P C M ................................ aaataggctgggattcataatgtttcccagcttttttgaacccttatgactctttgccgtcctctatatggaacgggtttagagctgttgagaaggatgaaagtatcatccatttttaaattttggattctttgagatattttgtttagaaaaaggcttgaaaaaagtcggaaaagtgctggattcgggcaaatattagcccctttttcatgaaaattatggtata 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================================================ aaataggctgggattcataatgtttcccagcttttttgaacccttatgactctttgccgtcctctatatggaacgggtttagagctgttgagaaggatgaaagtatcatccatttttaaattttggattctttgagatattttgtttagaaaaaggcttgaaaaaagtcggaaaagtgctggattcgggcaaatattagcccctttttcatgaaaattatggtata Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 67 HP_score: -3.1 Tail_Score: -4.87318 Start: 94 End: 112 Full_Region: TTAGAGCTGTTGAGA AGGATGA AAGTA TCATCCA TTTTTAAATTTTGGA .............................................................................................AGGATGAAAGTATCATCCA.................................................................................................................. TransTerm Strand: + Conf: 64 HP_score: -6.6 Tail_Score: -3.51307 Start: 95 End: 111 Full_Region: TAGAGCTGTTGAGAA GGATGA AAGTA TCATCC ATTTTTAAATTTTGG ..............................................................................................GGATGAAAGTATCATCC................................................................................................................... TransTerm Strand: - Conf: 62 HP_score: -6.6 Tail_Score: -3.29829 Start: 95 End: 111 Full_Region: ccaaaatttaaaaat ggatga tactt tcatcc ttctcaacagctcta ..............................................................................................ggatgatactttcatcc................................................................................................................... Find igs database================================================ Query_seq: SSA_0876:SSA_0877|SSA_0876:SSA_0877:4-methyl-5(B-hydroxyethyl)-thiazole monophosphate biosynthesis protein, putative:Phosphoglycolate phosphatase, putative:->->:870922..871147 226 aaataggctgggattcataatgtttcccagcttttttgaacccttatgactctttgccgtcctctatatggaacgggtttagagctgttgagaaggatgaaagtatcatccatttttaaattttggattctttgagatattttgtttagaaaaaggcttgaaaaaagtcggaaaagtgctggattcgggcaaatattagcccctttttcatgaaaattatggtata Intra-Species Hit: Count: 1 Min: 1 Max: 226 Len: 226 Subject: NC_009009_SSA_0876_SSA_0877|4-methyl-5(B-hydroxyethyl)-thiazole monophosphate biosynthesis protein, putative:Phosphoglycolate phosphatase, putative|POSITIVE:POSITIVE|[870922,871147]|226 HSP 1 e-value: 1.0E-125 bit: 448.0 Len: 226 Query Start:1 Query End:226 Subject Strand: POSITIVE Subject Start: 1 Subject End: 226 aaataggctgggattcataatgtttcccagcttttttgaacccttatgactctttgccgtcctctatatggaacgggtttagagctgttgagaaggatgaaagtatcatccatttttaaattttggattctttgagatattttgtttagaaaaaggcttgaaaaaagtcggaaaagtgctggattcgggcaaatattagcccctttttcatgaaaattatggtata aaataggctgggattcataatgtttcccagcttttttgaacccttatgactctttgccgtcctctatatggaacgggtttagagctgttgagaaggatgaaagtatcatccatttttaaattttggattctttgagatattttgtttagaaaaaggcttgaaaaaagtcggaaaagtgctggattcgggcaaatattagcccctttttcatgaaaattatggtata Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAUAGGCUGGGAUUCAUAAUGUUUCCCAGCUUUUUUGAACCCUUAUGACUCUUUGCCGUCCUCUAUAUGGAACGGGUUUAGAGCUGUUGAGAAGGAUGAAAGUAUCAUCCAUUUUUAAAUUUUGGAUUCUUUGAGAUAUUUUGUUUAGAAAAAGGCUUGAAAAAAGUCGGAAAAGUGCUGGAUUCGGGCAAAUAUUAGCCCCUUUUUCAUGAAAAUUAUGGUAUA (((.(((((((((..(.....)..))))))))).)))..(((.......((((..(((.(((.......)))...)))..))))...(((((((((((((.....)))))).)))))))........(((..(((((......((((((.....(((((.....))))).........))))))..((((........))))...))))).)))......)))... (-57.54) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAUACCAUAAUUUUCAUGAAAAAGGGGCUAAUAUUUGCCCGAAUCCAGCACUUUUCCGACUUUUUUCAAGCCUUUUUCUAAACAAAAUAUCUCAAAGAAUCCAAAAUUUAAAAAUGGAUGAUACUUUCAUCCUUCUCAACAGCUCUAAACCCGUUCCAUAUAGAGGACGGCAAAGAGUCAUAAGGGUUCAAAAAAGCUGGGAAACAUUAUGAAUCCCAGCCUAUUU .................(((((((((((........)))).................((......))....)))))))..................((((((.............((((((.....)))))).........(((((....((((((........))))))...))))).....))))))......(((((((..(.....)..)))))))...... (-52.40) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 371 80 36 121 64 NC_009009:SSA_1902|5end_tRNA_(guanine-N(7)-)-methyltransferase,_putative_1897391..1897621_NEGATIVE 368 210 178 35 6 NC_009009:SSA_0749|5end_Competence_protein,_putative_730668..730898_POSITIVE 328 98 51 149 91 NC_009009:SSA_0694|5end_Mutator_protein,_putative_677730..677960_POSITIVE 317 65 21 85 37 NC_009009:SSA_2175|5end_hypothetical_protein_2174042..2174272_NEGATIVE 317 100 56 161 114 NC_009009:SSA_0913|5end_Acetyltransferase,_putative_924195..924425_POSITIVE 309 97 51 139 98 NC_009009:SSA_2354|5end_hypothetical_protein_2356237..2356467_NEGATIVE 308 75 31 85 37 NC_009009:SSA_2270|5end_Aspartyl-tRNA_synthetase,_putative_2272068..2272298_NEGATIVE 300 220 177 216 176 NC_009009:SSA_1412|5end_hypothetical_protein_1424095..1424325_NEGATIVE 297 115 74 57 11 NC_009009:SSA_1268|5end_Chorismate_mutase/prephenate_dehydratase,_putative_1291610..1291840_NEGATIVE 297 46 5 218 175 NC_009009:SSA_0221|5end_PTS_system,_mannose-specific_IIC_component,_putative_216370..216600_POSITIVE 293 190 147 172 130 NC_009009:SSA_0503|5end_Peptide_ABC_transporter,_ATP-binding_protein,_putative_502231..502461_POSITIVE 292 90 41 228 161 NC_009009:SSA_0580|5end_Isochorismatase_family_protein,_putative_572816..573046_POSITIVE 290 90 42 61 18 NC_009009:SSA_1794|5end_Two-component_response_transcriptional_regulator_(CheY-like_receiver_and_winged-helix_DNA-binding_domains),_putative_1777049..1777279_NEGATIVE 290 64 23 145 92 NC_009009:SSA_1103|5end_hypothetical_protein_1123833..1124063_POSITIVE 286 110 69 229 184 NC_009009:SSA_1670|5end_Transcriptional_regulator,_TetR/AcrR_family,_putative_1669248..1669478_NEGATIVE 285 69 23 60 7 NC_009009:SSA_2224|5end_Phosphotyrosine-protein_phosphatase,_putative_2225442..2225672_NEGATIVE 280 68 25 205 167 NC_009009:SSA_0390|5end_hypothetical_protein_385002..385232_POSITIVE 279 41 5 152 120 NC_009009:SSA_2082|5end_Carbohydrate_kinase,_FGGY_family,_putative_2086874..2087104_NEGATIVE 278 209 166 225 173 NC_009009:SSA_2044|5end_Cysteinyl-tRNA_synthetase,_putative_2048409..2048639_NEGATIVE 278 49 6 228 179 NC_009009:SSA_0653|5end_UDP-N-acetylglucosamine--N-acetylmuramyl-_(pentapeptide)_pyrophosphoryl-undecaprenol_N-acetylglucosamine_transferase,_putative_636390..636620_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 371 80 36 124 67 NC_009009:SSA_1903|3end_hypothetical_protein_1897388..1897538_NEGATIVE 321 43 5 75 37 NC_009009:SSA_0234|3end_hypothetical_protein_228423..228573_NEGATIVE 317 100 56 115 68 NC_009009:SSA_0912|3end_Phenylalanyl-tRNA_synthetase_alpha_chain,_putative_924229..924379_POSITIVE 309 97 51 51 10 NC_009009:SSA_2355|3end_Conserved_uncharacterized_protein_2356325..2356475_NEGATIVE 302 43 5 99 58 NC_009009:SSA_0876|3end_4-methyl-5(B-hydroxyethyl)-thiazole_monophosphate_biosynthesis_protein,_putative_870861..871011_POSITIVE 290 90 42 59 16 NC_009009:SSA_1795|3end_Guanosine_3',5'-bis-pyrophosphate_(ppGpp)_synthetase,_putative_1777051..1777201_NEGATIVE 290 35 5 42 16 NC_009009:SSA_1409|3end_DTDP-glucose-4,6-dehydratase,_putative_1421209..1421359_NEGATIVE 289 50 5 95 51 NC_009009:SSA_0564|3end_Potential_aminotransferase,_putative_556988..557138_POSITIVE 285 69 23 63 10 NC_009009:SSA_2225|3end_Transcriptional_attenuator_LytR,_putative_2225439..2225589_NEGATIVE 285 46 5 101 53 NC_009009:SSA_0964|3end_DEAD_RNA_helicase,_putative_972954..973104_NEGATIVE 283 45 1 98 58 NC_009009:SSA_2301|3end_S-layer_protein/_peptidoglycan_endo-beta-N-acetylglucosaminidase,_putative_2302669..2302819_NEGATIVE 280 45 5 108 61 NC_009009:SSA_0303|3end_surface_protein_C_301051..301201_POSITIVE 279 41 5 76 44 NC_009009:SSA_2083|3end_hypothetical_protein_2086950..2087100_NEGATIVE 277 206 165 73 26 NC_009009:SSA_1029|3end_hypothetical_protein_1046167..1046317_NEGATIVE 277 110 70 91 57 NC_009009:SSA_0294|3end_hypothetical_protein_287772..287922_NEGATIVE 274 65 27 107 62 NC_009009:SSA_0911|3end_hypothetical_protein_922898..923048_POSITIVE 273 45 5 104 62 NC_009009:SSA_1491|3end_Methionine_aminopeptidase_A,_putative_1496780..1496930_NEGATIVE 271 100 52 145 105 NC_009009:SSA_2136|3end_50S_ribosomal_protein_L34,_putative_2137507..2137657_NEGATIVE 268 44 5 92 60 NC_009009:SSA_0395|3end_6-phospho-beta-glucosidase,_putative_392580..392730_POSITIVE 268 100 53 85 14 NC_009009:SSA_0009|3end_Ribosome-associated_heat_shock_protein_(S4),_putative_9511..9661_POSITIVE