Origin IGS: tcaatacgattatatcaacgtttcaaagcactcaaaagtttaccttatgggtgcttttttcgtgtttttttgaaaagttcacctcaaagtttaccttattttcacc .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 ggtgaaaataaggtaaactttgaggtgaacttttcaaaaaaacacgaaaaaagcacccataaggtaaacttttgagtgctttgaaacgttgatataatcgtattga Mask Tandem Repeat Region ================================================ tcaatacgattatatcaacgtttcaaagcactcaaaagtttaccttatgggtgcttttttcgtgtttttttgaaaagttcacctcaaagtttaccttattttcacc Find is-nt database================================================ Query_seq: SMT_247:SMT_248|SMT_247:SMT_248:K02996 small subunit ribosomal protein S9:site-specific recombinase, phage integrase family:-><-:183700..183805 106 tcaatacgattatatcaacgtttcaaagcactcaaaagtttaccttatgggtgcttttttcgtgtttttttgaaaagttcacctcaaagtttaccttattttcacc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_247:SMT_248|SMT_247:SMT_248:K02996 small subunit ribosomal protein S9:site-specific recombinase, phage integrase family:-><-:183700..183805 106 tcaatacgattatatcaacgtttcaaagcactcaaaagtttaccttatgggtgcttttttcgtgtttttttgaaaagttcacctcaaagtttaccttattttcacc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_247:SMT_248|SMT_247:SMT_248:K02996 small subunit ribosomal protein S9:site-specific recombinase, phage integrase family:-><-:183700..183805 106 tcaatacgattatatcaacgtttcaaagcactcaaaagtttaccttatgggtgcttttttcgtgtttttttgaaaagttcacctcaaagtttaccttattttcacc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tcaatacgattatatcaacgtttcaaagcactcaaaagtttaccttatgggtgcttttttcgtgtttttttgaaaagttcacctcaaagtttaccttattttcacc Predict ORF larger than 30AA ================================================ Protein_Len: 32 Strand: + Start: 9 End: 104 ........ M I S T F Q S T Q K F T L W V L F S C F F E K F T S K F T L F S .. Protein_Len: 34 Strand: + Start: 4 End: 105 ... M R L Y Q R F K A L K S L P Y G C F F R V F L K S S P Q S L P Y F H . tcaatacgattatatcaacgtttcaaagcactcaaaagtttaccttatgggtgcttttttcgtgtttttttgaaaagttcacctcaaagtttaccttattttcacc 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================================================ tcaatacgattatatcaacgtttcaaagcactcaaaagtttaccttatgggtgcttttttcgtgtttttttgaaaagttcacctcaaagtttaccttattttcacc Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 59 HP_score: -5.1 Tail_Score: -3.58037 Start: 28 End: 54 Full_Region: aaaaacacgaaaaaa gcacccataag gtaaa cttttgagtgc tttgaaacgttgata ...........................gcacccataaggtaaacttttgagtgc.................................................... Find igs database================================================ Query_seq: SMT_247:SMT_248|SMT_247:SMT_248:K02996 small subunit ribosomal protein S9:site-specific recombinase, phage integrase family:-><-:183700..183805 106 tcaatacgattatatcaacgtttcaaagcactcaaaagtttaccttatgggtgcttttttcgtgtttttttgaaaagttcacctcaaagtttaccttattttcacc Intra-Species Hit: Count: 1 Min: 1 Max: 106 Len: 106 Subject: smit_SMT_247_SMT_248|K02996 small subunit ribosomal protein S9:site-specific recombinase, phage integrase family|POSITIVE:NEGATIVE|[183700,183805]|106 HSP 1 e-value: 7.0E-23 bit: 107.0 Len: 54 Query Start:1 Query End:54 Subject Strand: POSITIVE Subject Start: 1 Subject End: 54 tcaatacgattatatcaacgtttcaaagcactcaaaagtttaccttatgggtgc.................................................... tcaatacgattatatcaacgtttcaaagcactcaaaagtttaccttatgggtgc.................................................... HSP 2 e-value: 2.0E-11 bit: 69.9 Len: 35 Query Start:72 Query End:106 Subject Strand: POSITIVE Subject Start: 72 Subject End: 106 .......................................................................gaaaagttcacctcaaagtttaccttattttcacc .......................................................................gaaaagttcacctcaaagtttaccttattttcacc Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UCAAUACGAUUAUAUCAACGUUUCAAAGCACUCAAAAGUUUACCUUAUGGGUGCUUUUUUCGUGUUUUUUUGAAAAGUUCACCUCAAAGUUUACCUUAUUUUCACC .......((..(((...(((....((((((((((.(((.....))).))))))))))...)))....((((((..........)))))).......)))..))... (-19.30) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GGUGAAAAUAAGGUAAACUUUGAGGUGAACUUUUCAAAAAAACACGAAAAAAGCACCCAUAAGGUAAACUUUUGAGUGCUUUGAAACGUUGAUAUAAUCGUAUUGA ......((((.(((....(((((((......))))))).....(((...(((((((.((.(((.....))).)).)))))))....))).......))).)))).. (-18.90) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 297 73 36 195 156 smit:SMT_1878|5end_K06147_ATP-binding_cassette,_subfamily_B,_bacterial_1836577..1836807_NEGATIVE 291 90 42 162 121 smit:SMT_989|5end_hypothetical_protein_933548..933778_NEGATIVE 240 87 43 133 81 smit:SMT_412|5end_hypothetical_protein_predicted_by_Glimmer/Critica_356606..356836_NEGATIVE 234 63 23 108 67 smit:SMT_903|5end_hypothetical_protein_852310..852540_NEGATIVE 232 78 32 66 12 smit:SMT_907|5end_hypothetical_protein_856054..856284_NEGATIVE 231 69 27 168 124 smit:SMT_196|5end_30S_ribosomal_protein_S11_127260..127490_POSITIVE 230 61 23 108 70 smit:SMT_999|5end_hypothetical_protein_predicted_by_Glimmer/Critica_941642..941872_NEGATIVE 228 98 51 80 22 smit:SMT_1986|5end_mercuric_reductase_1914843..1915073_POSITIVE 228 65 27 201 158 smit:SMT_177|5end_K02878_large_subunit_ribosomal_protein_L16_118738..118968_POSITIVE 224 88 43 52 4 smit:SMT_1925|5end_K03697_ATP-dependent_Clp_protease_ATP-binding_subunit_ClpE_1867262..1867492_POSITIVE 219 83 43 231 185 smit:SMT_574|5end_PTS_system,_fructose_specific_IIABC_components_491884..492114_POSITIVE 218 80 33 199 149 smit:SMT_1855|5end_K03650_tRNA_modification_GTPase_1819711..1819941_POSITIVE 217 85 48 97 53 smit:SMT_2071|5end_phosphoenolpyruvate_carboxylase_1975887..1976117_NEGATIVE 217 98 51 80 22 smit:SMT_1236|5end_mercuric_reductase_1195960..1196190_POSITIVE 212 99 53 203 147 smit:SMT_1518|5end_sensor_histidine_kinase_1499009..1499239_NEGATIVE 210 56 16 157 115 smit:SMT_1915|5end_pyridoxine_biosynthesis_protein_1860329..1860559_POSITIVE 209 65 26 194 155 smit:SMT_382|5end_valyl-tRNA_synthetase_317706..317936_POSITIVE 208 90 47 57 23 smit:SMT_1966|5end_DNA_polymerase_III_alpha_subunit_1897934..1898164_POSITIVE 208 83 50 184 148 smit:SMT_1432|5end_hypothetical_protein_1417468..1417698_NEGATIVE 207 70 29 85 50 smit:SMT_1427|5end_S1_RNA_binding_domain_protein_1413429..1413659_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 788 90 41 74 25 smit:SMT_1239|3end_site-specific_recombinase,_phage_integrase_family_1199639..1199789_NEGATIVE 275 89 42 151 111 smit:SMT_990|3end_hypothetical_protein_933558..933708_NEGATIVE 251 57 18 66 28 smit:SMT_247|3end_K02996_small_subunit_ribosomal_protein_S9_183639..183789_POSITIVE 234 63 23 124 83 smit:SMT_904|3end_hypothetical_protein_852294..852444_NEGATIVE 231 69 27 150 106 smit:SMT_195|3end_30S_ribosomal_protein_S13_127322..127472_POSITIVE 218 84 49 43 1 smit:SMT_2046|3end_choline_binding_protein_C_1957280..1957430_NEGATIVE 210 56 16 72 30 smit:SMT_1914|3end_K03696_ATP-dependent_Clp_protease_ATP-binding_subunit_ClpC_1860324..1860474_POSITIVE 209 83 43 77 39 smit:SMT_478|3end_hypothetical_protein_predicted_by_Glimmer/Critica_415257..415407_POSITIVE 204 96 61 104 64 smit:SMT_665|3end_NAD+_kinase_575927..576077_NEGATIVE 204 53 19 44 13 smit:SMT_304|3end_hypothetical_protein_247583..247733_POSITIVE 203 79 47 145 109 smit:SMT_412|3end_hypothetical_protein_predicted_by_Glimmer/Critica_356436..356586_NEGATIVE 202 96 51 110 63 smit:SMT_1972|3end_uncharacterized_conserved_phage_related_protein_1904440..1904590_POSITIVE 199 60 21 65 30 smit:SMT_1317|3end_glycosyltransferase_1283587..1283737_POSITIVE 198 97 51 50 10 smit:SMT_177|3end_K02878_large_subunit_ribosomal_protein_L16_119231..119381_POSITIVE 196 80 31 102 51 smit:SMT_1511|3end_hypothetical_protein_1493902..1494052_POSITIVE 195 81 48 151 121 smit:SMT_2042|3end_K04077_chaperonin_GroEL_(Hsp60)_1952960..1953110_NEGATIVE 195 73 43 50 12 smit:SMT_2025|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1940995..1941145_NEGATIVE 195 97 51 69 15 smit:SMT_558|3end_K09014_Fe-S_cluster_assembly_protein_SufB_476747..476897_POSITIVE 191 55 18 109 77 smit:SMT_1853|3end_1,4-alpha-glucan_branching_enzyme_1817687..1817837_NEGATIVE 191 68 27 87 35 smit:SMT_630|3end_phosphoserine_phosphatase_536183..536333_POSITIVE