Origin IGS: cgacccctctatgtatcttcctccaacttgagaaaatccttggaacgtgttaaaataaaggataaggatttttaataattcattatatagaacgagtggatttcttt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aaagaaatccactcgttctatataatgaattattaaaaatccttatcctttattttaacacgttccaaggattttctcaagttggaggaagatacatagaggggtcg Mask Tandem Repeat Region ================================================ cgacccctctatgtatcttcctccaacttgagaaaatccttggaacgtgttaaaataaaggataaggatttttaataattcattatatagaacgagtggatttcttt Find is-nt database================================================ Query_seq: SMT_511:SMT_512|SMT_511:SMT_512:hypothetical protein predicted by Glimmer/Critica:hypothetical protein:->->:440083..440189 107 cgacccctctatgtatcttcctccaacttgagaaaatccttggaacgtgttaaaataaaggataaggatttttaataattcattatatagaacgagtggatttcttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_511:SMT_512|SMT_511:SMT_512:hypothetical protein predicted by Glimmer/Critica:hypothetical protein:->->:440083..440189 107 cgacccctctatgtatcttcctccaacttgagaaaatccttggaacgtgttaaaataaaggataaggatttttaataattcattatatagaacgagtggatttcttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_511:SMT_512|SMT_511:SMT_512:hypothetical protein predicted by Glimmer/Critica:hypothetical protein:->->:440083..440189 107 cgacccctctatgtatcttcctccaacttgagaaaatccttggaacgtgttaaaataaaggataaggatttttaataattcattatatagaacgagtggatttcttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 cgacccctctatgtatcttcctccaacttgagaaaatccttggaacgtgttaaaataaaggataaggatttttaataattcattatatagaacgagtggatttcttt Predict ORF larger than 30AA ================================================ cgacccctctatgtatcttcctccaacttgagaaaatccttggaacgtgttaaaataaaggataaggatttttaataattcattatatagaacgagtggatttcttt 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: 88 Start: 27 End: 56 ..........................CTTGAGAAAATCCTTGGAACGTGTTAAAAT................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ cgacccctctatgtatcttcctccaacttgagaaaatccttggaacgtgttaaaataaaggataaggatttttaataattcattatatagaacgagtggatttcttt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SMT_511:SMT_512|SMT_511:SMT_512:hypothetical protein predicted by Glimmer/Critica:hypothetical protein:->->:440083..440189 107 cgacccctctatgtatcttcctccaacttgagaaaatccttggaacgtgttaaaataaaggataaggatttttaataattcattatatagaacgagtggatttcttt Intra-Species Hit: Count: 1 Min: 1 Max: 107 Len: 107 Subject: smit_SMT_511_SMT_512|hypothetical protein predicted by Glimmer/Critica:hypothetical protein|POSITIVE:POSITIVE|[440083,440189]|107 HSP 1 e-value: 2.0E-54 bit: 212.0 Len: 107 Query Start:1 Query End:107 Subject Strand: POSITIVE Subject Start: 1 Subject End: 107 cgacccctctatgtatcttcctccaacttgagaaaatccttggaacgtgttaaaataaaggataaggatttttaataattcattatatagaacgagtggatttcttt cgacccctctatgtatcttcctccaacttgagaaaatccttggaacgtgttaaaataaaggataaggatttttaataattcattatatagaacgagtggatttcttt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CGACCCCUCUAUGUAUCUUCCUCCAACUUGAGAAAAUCCUUGGAACGUGUUAAAAUAAAGGAUAAGGAUUUUUAAUAAUUCAUUAUAUAGAACGAGUGGAUUUCUUU .....................((((.((((.(((((((((((.....(((....))).....))))))))))).....(((........)))))))))))....... (-17.10) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAGAAAUCCACUCGUUCUAUAUAAUGAAUUAUUAAAAAUCCUUAUCCUUUAUUUUAACACGUUCCAAGGAUUUUCUCAAGUUGGAGGAAGAUACAUAGAGGGGUCG ......((((.(((.(((........)))................(((((((...........((....))...........))))))).........))))))).. (-14.75) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 335 49 4 195 143 smit:SMT_382|5end_valyl-tRNA_synthetase_317706..317936_POSITIVE 239 50 5 93 51 smit:SMT_1379|5end_thymidylate_kinase_1357438..1357668_NEGATIVE 237 69 21 119 56 smit:SMT_1609|5end_hypothetical_protein_1598113..1598343_POSITIVE 237 32 13 230 212 smit:SMT_854|5end_hypothetical_protein_799492..799722_NEGATIVE 235 42 1 176 124 smit:SMT_261|5end_ImpB/MucB/SamB_family_protein_200160..200390_POSITIVE 232 48 1 133 85 smit:SMT_1993|5end_hypothetical_protein_1919800..1920030_NEGATIVE 230 48 2 153 118 smit:SMT_2017|5end_exonuclease_RexA_1936785..1937015_NEGATIVE 230 48 2 153 118 smit:SMT_1798|5end_exonuclease_RexA_1773441..1773671_NEGATIVE 226 67 22 86 39 smit:SMT_1210|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1171051..1171281_NEGATIVE 226 67 22 165 118 smit:SMT_1209|5end_choline_binding_protein_PcpA_1170972..1171202_NEGATIVE 224 45 4 130 86 smit:SMT_1303|5end_tRNA-dihydrouridine_synthase_1265731..1265961_NEGATIVE 224 50 6 218 181 smit:SMT_455|5end_cation_transport_ATPase_391670..391900_POSITIVE 218 53 16 197 147 smit:SMT_1116|5end_K02244_competence_protein_ComGB_1053841..1054071_NEGATIVE 217 43 5 99 54 smit:SMT_1673|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1659831..1660061_POSITIVE 217 51 15 72 33 smit:SMT_1474|5end_K02003_1455170..1455400_POSITIVE 215 43 2 49 13 smit:SMT_952|5end_hypothetical_protein_900912..901142_NEGATIVE 213 50 6 57 6 smit:SMT_778|5end_S-adenosylmethionine:tRNA_ribosyltransferase-isomerase_686870..687100_POSITIVE 212 34 1 37 4 smit:SMT_376|5end_DNA_(cytosine-5-)-methyltransferase_312900..313130_POSITIVE 210 50 5 61 8 smit:SMT_588|5end_hypothetical_protein_505477..505707_NEGATIVE 207 56 14 180 136 smit:SMT_700|5end_putative_signal_recognition_particle_-inhibited_division_protein_611511..611741_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 252 50 8 136 87 smit:SMT_1124|3end_pyrrolidone-carboxylate_peptidase_1060225..1060375_NEGATIVE 237 69 21 122 59 smit:SMT_1608|3end_hypothetical_protein_1598196..1598346_POSITIVE 230 48 2 54 19 smit:SMT_1800|3end_exonuclease_RexA_1773540..1773690_NEGATIVE 215 43 2 62 26 smit:SMT_953|3end_hypothetical_protein_900899..901049_NEGATIVE 209 34 1 71 34 smit:SMT_932|3end_tellurite_resistance_protein_885402..885552_POSITIVE 205 50 6 89 39 smit:SMT_943|3end_hypothetical_protein_894136..894286_NEGATIVE 200 43 12 122 85 smit:SMT_1262|3end_ribosomal_protein_L11_methyltransferase_1228182..1228332_POSITIVE 200 57 15 87 45 smit:SMT_940|3end_tRNA_pseudouridine_synthase_A_892015..892165_NEGATIVE 197 28 4 109 85 smit:SMT_445|3end_hypothetical_protein_384949..385099_POSITIVE 196 39 1 133 83 smit:SMT_1635|3end_putative_N-acetyldiaminopimelate_deacetylase_1622636..1622786_POSITIVE 193 69 38 61 21 smit:SMT_518|3end_biotin_synthase_443215..443365_NEGATIVE 192 49 1 123 68 smit:SMT_356|3end_hypothetical_protein_293268..293418_POSITIVE 190 47 7 132 96 smit:SMT_1351|3end_dephospho-CoA_kinase_1329212..1329362_NEGATIVE 190 32 8 84 55 smit:SMT_1163|3end_hypothetical_protein_1109096..1109246_NEGATIVE 188 40 1 87 43 smit:SMT_1750|3end_anthranilate_phosphoribosyltransferase_1729095..1729245_POSITIVE 187 50 25 70 43 smit:SMT_1394|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1371157..1371307_POSITIVE 186 39 7 57 22 smit:SMT_921|3end_putative_PP2C_protein_phosphatase_874498..874648_NEGATIVE 185 29 4 118 95 smit:SMT_963|3end_K02015_iron_complex_transport_system_permease_protein_908586..908736_NEGATIVE 184 67 26 62 26 smit:SMT_1249|3end_hypothetical_protein_1210541..1210691_NEGATIVE 184 50 2 137 99 smit:SMT_315|3end_acetyl-coenzyme_A_carboxylase_carboxyl_transferase_subunit_beta_256627..256777_POSITIVE