Origin IGS: aagaacctcctttttatcattataacacattttattctttttgaataaaaaagcttgacaaaaattcaaaaaggatatataattcaaaatgaataacaaattaaatggtttcggagcttatttaatttagaaatgaggtgtgaattt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aaattcacacctcatttctaaattaaataagctccgaaaccatttaatttgttattcattttgaattatatatcctttttgaatttttgtcaagcttttttattcaaaaagaataaaatgtgttataatgataaaaaggaggttctt Mask Tandem Repeat Region ================================================ aagaacctcctttttatcattataacacattttattctttttgaataaaaaagcttgacaaaaattcaaaaaggatatataattcaaaatgaataacaaattaaatggtttcggagcttatttaatttagaaatgaggtgtgaattt Find is-nt database================================================ Query_seq: SMT_1228:SMT_1229|SMT_1228:SMT_1229:DNA-binding protein:hypothetical protein:<-->:1191126..1191272 147 aagaacctcctttttatcattataacacattttattctttttgaataaaaaagcttgacaaaaattcaaaaaggatatataattcaaaatgaataacaaattaaatggtttcggagcttatttaatttagaaatgaggtgtgaattt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_1228:SMT_1229|SMT_1228:SMT_1229:DNA-binding protein:hypothetical protein:<-->:1191126..1191272 147 aagaacctcctttttatcattataacacattttattctttttgaataaaaaagcttgacaaaaattcaaaaaggatatataattcaaaatgaataacaaattaaatggtttcggagcttatttaatttagaaatgaggtgtgaattt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_1228:SMT_1229|SMT_1228:SMT_1229:DNA-binding protein:hypothetical protein:<-->:1191126..1191272 147 aagaacctcctttttatcattataacacattttattctttttgaataaaaaagcttgacaaaaattcaaaaaggatatataattcaaaatgaataacaaattaaatggtttcggagcttatttaatttagaaatgaggtgtgaattt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aagaacctcctttttatcattataacacattttattctttttgaataaaaaagcttgacaaaaattcaaaaaggatatataattcaaaatgaataacaaattaaatggtttcggagcttatttaatttagaaatgaggtgtgaattt Predict ORF larger than 30AA ================================================ Protein_Len: 33 Strand: - Start: 1 End: 99 L V E K K D N Y C M K N K K F L F A Q C F N L F S I Y N L I F L M ................................................ aagaacctcctttttatcattataacacattttattctttttgaataaaaaagcttgacaaaaattcaaaaaggatatataattcaaaatgaataacaaattaaatggtttcggagcttatttaatttagaaatgaggtgtgaattt 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: 54 End: 83 .....................................................CTTGACAAAAATTCAAAAAGGATATATAAT................................................................ PromScan Matrix: RpoD-17 Strand: - Score: 81 Start: 19 End: 48 ..................TTATTCAAAAAGAATAAAATGTGTTATAAT................................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ aagaacctcctttttatcattataacacattttattctttttgaataaaaaagcttgacaaaaattcaaaaaggatatataattcaaaatgaataacaaattaaatggtttcggagcttatttaatttagaaatgaggtgtgaattt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SMT_1228:SMT_1229|SMT_1228:SMT_1229:DNA-binding protein:hypothetical protein:<-->:1191126..1191272 147 aagaacctcctttttatcattataacacattttattctttttgaataaaaaagcttgacaaaaattcaaaaaggatatataattcaaaatgaataacaaattaaatggtttcggagcttatttaatttagaaatgaggtgtgaattt Intra-Species Hit: Count: 1 Min: 1 Max: 147 Len: 147 Subject: smit_SMT_1228_SMT_1229|DNA-binding protein:hypothetical protein|NEGATIVE:POSITIVE|[1191126,1191272]|147 HSP 1 e-value: 4.0E-16 bit: 85.7 Len: 43 Query Start:1 Query End:43 Subject Strand: POSITIVE Subject Start: 1 Subject End: 43 aagaacctcctttttatcattataacacattttattctttttg........................................................................................................ aagaacctcctttttatcattataacacattttattctttttg........................................................................................................ HSP 2 e-value: 6.0E-15 bit: 81.8 Len: 41 Query Start:107 Query End:147 Subject Strand: POSITIVE Subject Start: 107 Subject End: 147 ..........................................................................................................ggtttcggagcttatttaatttagaaatgaggtgtgaattt ..........................................................................................................ggtttcggagcttatttaatttagaaatgaggtgtgaattt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAGAACCUCCUUUUUAUCAUUAUAACACAUUUUAUUCUUUUUGAAUAAAAAAGCUUGACAAAAAUUCAAAAAGGAUAUAUAAUUCAAAAUGAAUAACAAAUUAAAUGGUUUCGGAGCUUAUUUAAUUUAGAAAUGAGGUGUGAAUUU ....(((((.(((((.(((((...........((((((((((((((.................))))))))))))))..........))))).....(((((((((((((....))).))))))))))))))).)))))........ (-26.93) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAUUCACACCUCAUUUCUAAAUUAAAUAAGCUCCGAAACCAUUUAAUUUGUUAUUCAUUUUGAAUUAUAUAUCCUUUUUGAAUUUUUGUCAAGCUUUUUUAUUCAAAAAGAAUAAAAUGUGUUAUAAUGAUAAAAAGGAGGUUCUU ........(((((.....((((((((((.............))))))))))................................((((((((((((..((((((((.....))))))))...)))....))))))))).))))).... (-22.02) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 723 140 91 231 182 smit:SMT_1228|5end_DNA-binding_protein_1191035..1191265_NEGATIVE 285 139 109 142 111 smit:SMT_1227|5end_site-specific_recombinase,_phage_integrase_family_1190465..1190695_NEGATIVE 231 93 52 53 11 smit:SMT_1761|5end_transcriptional_activator,_putative_1736458..1736688_POSITIVE 222 137 106 198 159 smit:SMT_1076|5end_2-amino-4-hydroxy-6-_hydroxymethyldihydropteridine_pyrophosphokinase_/_dihydroneopterin_aldolase_1014813..1015043_NEGATIVE 203 139 96 216 178 smit:SMT_409|5end_pneumococcal_surface_protein,_putative_353754..353984_POSITIVE 198 48 7 140 97 smit:SMT_1876|5end_transcriptional_regulator,_MarR_family_1833594..1833824_POSITIVE 195 64 23 221 181 smit:SMT_1150|5end_hypothetical_protein_1094803..1095033_NEGATIVE 191 140 105 79 47 smit:SMT_535|5end_hypothetical_protein_454215..454445_POSITIVE 186 32 5 127 98 smit:SMT_2141|5end_hypothetical_protein_2019976..2020206_NEGATIVE 186 32 5 127 98 smit:SMT_870|5end_hypothetical_protein_818737..818967_NEGATIVE 180 56 13 138 101 smit:SMT_833|5end_hypothetical_protein_predicted_by_Glimmer/Critica_775362..775592_NEGATIVE 177 30 4 126 97 smit:SMT_1600|5end_malolactic_enzyme_1589941..1590171_POSITIVE 177 140 102 158 123 smit:SMT_1369|5end_alanine_dehydrogenase_1348280..1348510_POSITIVE 176 77 34 228 187 smit:SMT_184|5end_30S_ribosomal_protein_S8_121413..121643_POSITIVE 175 69 29 159 113 smit:SMT_1810|5end_hypothetical_protein_1785219..1785449_POSITIVE 172 75 45 189 161 smit:SMT_1556|5end_phosphoglycerate_mutase_1541194..1541424_POSITIVE 172 35 2 125 95 smit:SMT_981|5end_hypothetical_protein_928709..928939_POSITIVE 170 45 7 125 97 smit:SMT_944|5end_PhnA_protein_895106..895336_NEGATIVE 170 48 1 158 101 smit:SMT_393|5end_hypothetical_protein_predicted_by_Glimmer/Critica_323973..324203_POSITIVE 169 97 65 180 142 smit:SMT_1234|5end_cadmium_efflux_system_accessory_protein_1194932..1195162_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 285 139 109 90 59 smit:SMT_1228|3end_DNA-binding_protein_1190517..1190667_NEGATIVE 203 131 106 144 116 smit:SMT_1077|3end_GTP_cyclohydrolase_I_1014856..1015006_NEGATIVE 189 139 106 66 31 smit:SMT_1525|3end_pneumococcal_histidine_triad_protein_A_precursor_1505873..1506023_NEGATIVE 170 32 6 29 1 smit:SMT_871|3end_K03311_branched-chain_amino_acid:cation_transporter,_LIVCS_family_818835..818985_NEGATIVE 170 48 1 112 55 smit:SMT_392|3end_acetyltransferase,_GNAT_family_324007..324157_POSITIVE 169 44 3 121 76 smit:SMT_274|3end_ABC_transporter_substrate-binding_protein_-_oligopeptide_transport_217259..217409_POSITIVE 165 16 2 46 32 smit:SMT_125|3end_hypothetical_protein_76717..76867_NEGATIVE 164 27 6 65 43 smit:SMT_1094|3end_membrane_carboxypeptidase_(penicillin-binding_protein)_1034141..1034291_NEGATIVE 164 138 97 45 8 smit:SMT_502|3end_peptidyl-prolyl_cis-trans_isomerase,_cyclophilin-type_434872..435022_NEGATIVE 164 28 1 67 47 smit:SMT_198|3end_50S_ribosomal_protein_L17_129281..129431_POSITIVE 163 140 107 84 46 smit:SMT_1095|3end_ribosomal_large_subunit_pseudouridine_synthase,_RluD_subfamily_1037328..1037478_POSITIVE 162 119 82 134 93 smit:SMT_523|3end_K02004_448761..448911_POSITIVE 161 45 9 41 6 smit:SMT_761|3end_prephenate_dehydrogenase_666482..666632_NEGATIVE 160 45 6 140 105 smit:SMT_1024|3end_transcriptional_regulator,_MarR_family_958961..959111_NEGATIVE 158 32 2 92 66 smit:SMT_1081|3end_K06901_putative_MFS_transporter,_AGZA_family,_xanthine/uracil_permease_1018595..1018745_NEGATIVE 158 29 3 52 26 smit:SMT_422|3end_K02004_365876..366026_POSITIVE 157 139 107 136 100 smit:SMT_1007|3end_radical_SAM_domain_protein_947549..947699_POSITIVE 156 44 8 130 95 smit:SMT_1871|3end_modification_methylase,_HemK_family_1829803..1829953_NEGATIVE 156 34 7 49 25 smit:SMT_1541|3end_isopentenyl-diphosphate_delta-isomerase_1525083..1525233_NEGATIVE 154 33 2 41 7 smit:SMT_1218|3end_DNA_polymerase_I_1176688..1176838_NEGATIVE