Origin IGS: aaagagagctttggctctctttttgtttgttagaatgctgaatctgagcattttcgtttagaattatttccataaaaatggtaaaatagtaagagtagaaatggagttcgagac .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 gtctcgaactccatttctactcttactattttaccatttttatggaaataattctaaacgaaaatgctcagattcagcattctaacaaacaaaaagagagccaaagctctcttt Mask Tandem Repeat Region ================================================ aaagagagctttggctctctttttgtttgttagaatgctgaatctgagcattttcgtttagaattatttccataaaaatggtaaaatagtaagagtagaaatggagttcgagac Find is-nt database================================================ Query_seq: SMT_430:SMT_431|SMT_430:SMT_431:hypothetical protein:UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase:->->:372225..372338 114 aaagagagctttggctctctttttgtttgttagaatgctgaatctgagcattttcgtttagaattatttccataaaaatggtaaaatagtaagagtagaaatggagttcgagac Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_430:SMT_431|SMT_430:SMT_431:hypothetical protein:UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase:->->:372225..372338 114 aaagagagctttggctctctttttgtttgttagaatgctgaatctgagcattttcgtttagaattatttccataaaaatggtaaaatagtaagagtagaaatggagttcgagac Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_430:SMT_431|SMT_430:SMT_431:hypothetical protein:UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase:->->:372225..372338 114 aaagagagctttggctctctttttgtttgttagaatgctgaatctgagcattttcgtttagaattatttccataaaaatggtaaaatagtaagagtagaaatggagttcgagac Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aaagagagctttggctctctttttgtttgttagaatgctgaatctgagcattttcgtttagaattatttccataaaaatggtaaaatagtaagagtagaaatggagttcgagac Predict ORF larger than 30AA ================================================ aaagagagctttggctctctttttgtttgttagaatgctgaatctgagcattttcgtttagaattatttccataaaaatggtaaaatagtaagagtagaaatggagttcgagac 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================================================ aaagagagctttggctctctttttgtttgttagaatgctgaatctgagcattttcgtttagaattatttccataaaaatggtaaaatagtaagagtagaaatggagttcgagac Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SMT_430:SMT_431|SMT_430:SMT_431:hypothetical protein:UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase:->->:372225..372338 114 aaagagagctttggctctctttttgtttgttagaatgctgaatctgagcattttcgtttagaattatttccataaaaatggtaaaatagtaagagtagaaatggagttcgagac Intra-Species Hit: Count: 1 Min: 1 Max: 114 Len: 114 Subject: smit_SMT_430_SMT_431|hypothetical protein:UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase|POSITIVE:POSITIVE|[372225,372338]|114 HSP 1 e-value: 1.0E-58 bit: 226.0 Len: 114 Query Start:1 Query End:114 Subject Strand: POSITIVE Subject Start: 1 Subject End: 114 aaagagagctttggctctctttttgtttgttagaatgctgaatctgagcattttcgtttagaattatttccataaaaatggtaaaatagtaagagtagaaatggagttcgagac aaagagagctttggctctctttttgtttgttagaatgctgaatctgagcattttcgtttagaattatttccataaaaatggtaaaatagtaagagtagaaatggagttcgagac Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAGAGAGCUUUGGCUCUCUUUUUGUUUGUUAGAAUGCUGAAUCUGAGCAUUUUCGUUUAGAAUUAUUUCCAUAAAAAUGGUAAAAUAGUAAGAGUAGAAAUGGAGUUCGAGAC .....(((((..(.(((((((.((((((..........(((.(((((((......))))))).)))...((((....))))..)))))).))))).))...)..)))))..... (-26.00) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GUCUCGAACUCCAUUUCUACUCUUACUAUUUUACCAUUUUUAUGGAAAUAAUUCUAAACGAAAAUGCUCAGAUUCAGCAUUCUAACAAACAAAAAGAGAGCCAAAGCUCUCUUU .................................((((....)))).................((((((.......))))))...........(((((((((....))))))))) (-18.50) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 295 49 4 55 8 smit:SMT_893|5end_leucine_rich_protein_841311..841541_NEGATIVE 274 48 5 188 138 smit:SMT_108|5end_hypothetical_protein_53488..53718_POSITIVE 272 50 8 147 94 smit:SMT_1337|5end_K05833_putative_ABC_transport_system_ATP-binding_protein_1312812..1313042_NEGATIVE 266 58 16 147 100 smit:SMT_742|5end_hypothetical_protein_646818..647048_NEGATIVE 265 47 1 70 15 smit:SMT_1929|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1869785..1870015_NEGATIVE 265 47 1 203 148 smit:SMT_1928|5end_O-methyltransferase_family_protein_1869652..1869882_NEGATIVE 263 50 3 181 123 smit:SMT_695|5end_heat_shock_protein_HtpX_606883..607113_NEGATIVE 253 48 7 64 24 smit:SMT_1900|5end_K03710_GntR_family_transcriptional_regulator_1850208..1850438_POSITIVE 253 49 3 184 122 smit:SMT_1347|5end_SsrA-binding_protein_1325185..1325415_NEGATIVE 247 50 4 181 117 smit:SMT_167|5end_acetyltransferase,_GNAT_family_113171..113401_POSITIVE 246 49 5 182 140 smit:SMT_1979|5end_possible_cell_surface_protein_1911052..1911282_NEGATIVE 246 49 6 179 126 smit:SMT_1591|5end_DNA-entry_nuclease_1578873..1579103_POSITIVE 240 59 11 53 3 smit:SMT_140|5end_NUDIX_family_hydrolase_90990..91220_POSITIVE 237 50 4 201 149 smit:SMT_1159|5end_hypothetical_protein_1104544..1104774_NEGATIVE 237 59 14 126 86 smit:SMT_1114|5end_competence_protein_1052555..1052785_NEGATIVE 237 50 3 90 32 smit:SMT_714|5end_hypothetical_protein_predicted_by_Glimmer/Critica_620979..621209_NEGATIVE 237 50 3 181 123 smit:SMT_713|5end_heat_shock_protein_HtpX_620888..621118_NEGATIVE 232 45 11 47 15 smit:SMT_1549|5end_hypothetical_protein_1533645..1533875_POSITIVE 231 72 31 62 12 smit:SMT_939|5end_phosphomethylpyrimidine_kinase_892025..892255_NEGATIVE 230 41 1 190 151 smit:SMT_554|5end_K09013_Fe-S_cluster_assembly_ATP-binding_protein_471425..471655_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 318 49 1 116 64 smit:SMT_1342|3end_protease_maturation_protein,_putative_1319276..1319426_NEGATIVE 315 50 1 119 69 smit:SMT_430|3end_hypothetical_protein_372164..372314_POSITIVE 295 49 4 51 4 smit:SMT_894|3end_hypothetical_protein_841315..841465_NEGATIVE 274 48 5 70 20 smit:SMT_107|3end_ribose-phosphate_pyrophosphokinase_53450..53600_POSITIVE 272 50 8 150 97 smit:SMT_1338|3end_K05832_putative_ABC_transport_system_permease_protein_1312809..1312959_NEGATIVE 265 47 1 70 15 smit:SMT_1930|3end_peptide_chain_release_factor_1_1869785..1869935_NEGATIVE 257 49 1 120 59 smit:SMT_1279|3end_translation_elongation_factor_Ts_1243451..1243601_POSITIVE 253 48 7 113 73 smit:SMT_1899|3end_hypothetical_protein_1850337..1850487_POSITIVE 249 45 1 116 63 smit:SMT_2078|3end_acetyl_xylan_esterase,_putative_1979839..1979989_POSITIVE 248 48 4 126 81 smit:SMT_225|3end_pullulanase_159666..159816_NEGATIVE 247 50 4 137 73 smit:SMT_166|3end_hypothetical_protein_113207..113357_POSITIVE 242 50 1 116 49 smit:SMT_1419|3end_hypothetical_protein_1404582..1404732_POSITIVE 241 32 1 146 110 smit:SMT_1929|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1869690..1869840_NEGATIVE 241 48 1 116 65 smit:SMT_494|3end_K04767_acetoin_utilization_protein_AcuB_428891..429041_POSITIVE 237 50 4 125 73 smit:SMT_1160|3end_K03152_4-methyl-5(b-hydroxyethyl)-thiazole_monophosphate_biosynthesis_1104620..1104770_NEGATIVE 232 45 11 42 10 smit:SMT_1548|3end_cell_division_protein_FtsZ_1533720..1533870_POSITIVE 231 72 31 72 22 smit:SMT_940|3end_tRNA_pseudouridine_synthase_A_892015..892165_NEGATIVE 230 41 1 87 48 smit:SMT_553|3end_hypothetical_protein_471402..471552_POSITIVE 227 50 8 63 12 smit:SMT_1768|3end_hydrolase,_alpha/beta_fold_family_1744123..1744273_NEGATIVE 227 59 17 41 1 smit:SMT_139|3end_hypothetical_protein_91058..91208_POSITIVE