Origin IGS: tgtattctcctttgtcttttacataggactactatatcaaatttcagctacttttacaagattgtacctgcttttctagtaagaaaaaccagagcttacgctctgattcttagga .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tcctaagaatcagagcgtaagctctggtttttcttactagaaaagcaggtacaatcttgtaaaagtagctgaaatttgatatagtagtcctatgtaaaagacaaaggagaataca Mask Tandem Repeat Region ================================================ tgtattctcctttgtcttttacataggactactatatcaaatttcagctacttttacaagattgtacctgcttttctagtaagaaaaaccagagcttacgctctgattcttagga Find is-nt database================================================ Query_seq: SMT_1101:SMT_1102|SMT_1101:SMT_1102:K03210 preprotein translocase YajC subunit:transketolase:<-<-:1043004..1043118 115 tgtattctcctttgtcttttacataggactactatatcaaatttcagctacttttacaagattgtacctgcttttctagtaagaaaaaccagagcttacgctctgattcttagga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_1101:SMT_1102|SMT_1101:SMT_1102:K03210 preprotein translocase YajC subunit:transketolase:<-<-:1043004..1043118 115 tgtattctcctttgtcttttacataggactactatatcaaatttcagctacttttacaagattgtacctgcttttctagtaagaaaaaccagagcttacgctctgattcttagga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_1101:SMT_1102|SMT_1101:SMT_1102:K03210 preprotein translocase YajC subunit:transketolase:<-<-:1043004..1043118 115 tgtattctcctttgtcttttacataggactactatatcaaatttcagctacttttacaagattgtacctgcttttctagtaagaaaaaccagagcttacgctctgattcttagga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tgtattctcctttgtcttttacataggactactatatcaaatttcagctacttttacaagattgtacctgcttttctagtaagaaaaaccagagcttacgctctgattcttagga Predict ORF larger than 30AA ================================================ Protein_Len: 37 Strand: + Start: 4 End: 114 ... M L L C L L H R T T I S N F S Y F Y K I V P A F L V R K T R A Y A L I L R . tgtattctcctttgtcttttacataggactactatatcaaatttcagctacttttacaagattgtacctgcttttctagtaagaaaaaccagagcttacgctctgattcttagga 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: 82 Start: 31 End: 60 ..............................CTTGTAAAAGTAGCTGAAATTTGATATAGT....................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ tgtattctcctttgtcttttacataggactactatatcaaatttcagctacttttacaagattgtacctgcttttctagtaagaaaaaccagagcttacgctctgattcttagga Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SMT_1101:SMT_1102|SMT_1101:SMT_1102:K03210 preprotein translocase YajC subunit:transketolase:<-<-:1043004..1043118 115 tgtattctcctttgtcttttacataggactactatatcaaatttcagctacttttacaagattgtacctgcttttctagtaagaaaaaccagagcttacgctctgattcttagga Intra-Species Hit: Count: 1 Min: 1 Max: 115 Len: 115 Subject: smit_SMT_1101_SMT_1102|K03210 preprotein translocase YajC subunit:transketolase|NEGATIVE:NEGATIVE|[1043004, 1043118]|115 HSP 1 e-value: 3.0E-59 bit: 228.0 Len: 115 Query Start:1 Query End:115 Subject Strand: POSITIVE Subject Start: 1 Subject End: 115 tgtattctcctttgtcttttacataggactactatatcaaatttcagctacttttacaagattgtacctgcttttctagtaagaaaaaccagagcttacgctctgattcttagga tgtattctcctttgtcttttacataggactactatatcaaatttcagctacttttacaagattgtacctgcttttctagtaagaaaaaccagagcttacgctctgattcttagga Inter-species Hit: Count: 3 Min: 5 Max: 115 Len: 111 Subject: NC_008533_SPD_1838_SPD_1839|preprotein translocase, YajC subunit:transketolase|NEGATIVE:NEGATIVE|[1823367, 1823482]|116 HSP 1 e-value: 4.0E-43 bit: 174.0 Len: 111 Query Start:5 Query End:115 Subject Strand: POSITIVE Subject Start: 5 Subject End: 116 ....ttctcctttgtcttttacataggactactatatcaaatttcagctacttttacaagattgtacc-tgcttttctagtaagaaaaaccagagcttacgctctgattcttagga ....ttctcctttgtcttttacataggactactatatcaaatttcagctacttttacaagattgtaccttacttttctggtaagaaaaaccagagcttacgccctgatttttagga Subject: NC_003098_spr1840_spr1841|preprotein translocase subunit YajC:transketolase|NEGATIVE:NEGATIVE|[1815835, 1815950]|116 HSP 1 e-value: 4.0E-43 bit: 174.0 Len: 111 Query Start:5 Query End:115 Subject Strand: POSITIVE Subject Start: 5 Subject End: 116 ....ttctcctttgtcttttacataggactactatatcaaatttcagctacttttacaagattgtacc-tgcttttctagtaagaaaaaccagagcttacgctctgattcttagga ....ttctcctttgtcttttacataggactactatatcaaatttcagctacttttacaagattgtaccttacttttctggtaagaaaaaccagagcttacgccctgatttttagga Subject: NC_003028_SP_2029_SP_2030|preprotein translocase subunit YajC:transketolase|NEGATIVE:NEGATIVE|[1934912, 1935027]|116 HSP 1 e-value: 4.0E-43 bit: 174.0 Len: 111 Query Start:5 Query End:115 Subject Strand: POSITIVE Subject Start: 5 Subject End: 116 ....ttctcctttgtcttttacataggactactatatcaaatttcagctacttttacaagattgtacc-tgcttttctagtaagaaaaaccagagcttacgctctgattcttagga ....ttctcctttgtcttttacataggactactatatcaaatttcagctacttttacaagattgtaccttacttttctggtaagaaaaaccagagcttacgccctgatttttagga Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUCUCCUUUGUCUUUUACAUAGGACUACUAUAUCAAAUUUCAGCUACUUUUACAAGAUUGUACCUGCUUUUCUAGUAAGAAAAACCAGAGCUUACGCUCUGAUUCUUAGGA ...((((..(((((......)))))......................((((((.(((..((....))...))).)))))).....((((((....))))))......)))) (-21.30) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UCCUAAGAAUCAGAGCGUAAGCUCUGGUUUUUCUUACUAGAAAAGCAGGUACAAUCUUGUAAAAGUAGCUGAAAUUUGAUAUAGUAGUCCUAUGUAAAAGACAAAGGAGAA ....((((((((((((....))))))))))))..(((((..(((.(((.(((............))).)))...)))....))))).((((.(((.....))).))))... (-32.10) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 879 110 61 205 156 smit:SMT_1101|5end_K03210_preprotein_translocase_YajC_subunit_1042913..1043143_NEGATIVE 281 88 42 75 25 smit:SMT_1760|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1735910..1736140_NEGATIVE 281 88 42 212 162 smit:SMT_1759|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1735773..1736003_NEGATIVE 270 101 61 139 99 smit:SMT_869|5end_hypothetical_protein_817698..817928_NEGATIVE 270 44 1 140 93 smit:SMT_745|5end_glycosyl_transferase,_group_1_family_protein_650387..650617_NEGATIVE 267 98 54 58 5 smit:SMT_304|5end_hypothetical_protein_246580..246810_POSITIVE 262 78 36 230 175 smit:SMT_629|5end_glycogen_synthase_533967..534197_POSITIVE 257 68 29 113 84 smit:SMT_1223|5end_pneumococcal_surface_protein_A_1187780..1188010_NEGATIVE 255 106 63 163 115 smit:SMT_1189|5end_phosphoribosylaminoimidazole_carboxylase_ATPase_subunit_1147754..1147984_NEGATIVE 249 98 57 214 173 smit:SMT_1626|5end_undecaprenyl-diphosphatase_1616028..1616258_NEGATIVE 245 110 64 74 22 smit:SMT_1361|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1341402..1341632_NEGATIVE 244 99 53 67 19 smit:SMT_414|5end_K03665_GTP-binding_protein_HflX_357554..357784_POSITIVE 238 100 53 222 185 smit:SMT_1605|5end_hypothetical_protein_1595406..1595636_POSITIVE 238 98 53 64 19 smit:SMT_145|5end_hypothetical_protein_95873..96103_POSITIVE 233 100 56 50 2 smit:SMT_1704|5end_D-alanine-D-alanine_ligase_1687431..1687661_POSITIVE 233 93 53 55 13 smit:SMT_757|5end_K06969_putative_SAM-dependent_methyltransferase_661744..661974_NEGATIVE 227 68 23 216 174 smit:SMT_577|5end_transcriptional_regulator,_LysR_family_495324..495554_POSITIVE 227 68 23 49 7 smit:SMT_576|5end_transcriptional_regulator,_LysR_family_495157..495387_POSITIVE 225 110 64 55 10 smit:SMT_1849|5end_hypothetical_protein_1813074..1813304_POSITIVE 224 109 64 88 34 smit:SMT_607|5end_K03294_basic_amino_acid/polyamine_antiporter,_APA_family_520119..520349_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 270 101 61 137 97 smit:SMT_870|3end_hypothetical_protein_817700..817850_NEGATIVE 270 44 1 150 103 smit:SMT_746|3end_LPS_biosynthesis_protein_650377..650527_NEGATIVE 269 92 57 52 19 smit:SMT_1591|3end_DNA-entry_nuclease_1579468..1579618_POSITIVE 257 90 42 49 5 smit:SMT_1026|3end_sucrose_phosphorylase_960873..961023_NEGATIVE 245 110 64 62 10 smit:SMT_1362|3end_chaperone_protein_hscC_1341414..1341564_NEGATIVE 244 99 53 74 26 smit:SMT_413|3end_tRNA_delta(2)-isopentenylpyrophosphate_transferase_357641..357791_POSITIVE 228 101 64 60 30 smit:SMT_1958|3end_tryptophan_synthase,_beta_subunit_1892052..1892202_POSITIVE 224 107 65 88 49 smit:SMT_695|3end_heat_shock_protein_HtpX_605984..606134_NEGATIVE 220 67 22 81 40 smit:SMT_230|3end_hypothetical_protein_predicted_by_Glimmer/Critica_165666..165816_NEGATIVE 218 107 69 82 43 smit:SMT_546|3end_DNA_topoisomerase_IV_subunit_A_463892..464042_POSITIVE 218 76 40 136 87 smit:SMT_229|3end_mechanosensitive_ion_channel_165429..165579_NEGATIVE 217 88 41 137 85 smit:SMT_359|3end_transcription_termination-antitermination_factor_295686..295836_POSITIVE 215 90 41 142 84 smit:SMT_773|3end_UDP-N-acetylenolpyruvoylglucosamine_reductase_683460..683610_NEGATIVE 215 104 61 96 53 smit:SMT_154|3end_K03647_protein_involved_in_ribonucleotide_reduction_102474..102624_POSITIVE 211 100 57 146 93 smit:SMT_1617|3end_K02015_iron_complex_transport_system_permease_protein_1603544..1603694_NEGATIVE 211 107 65 128 89 smit:SMT_309|3end_acyl-carrier-protein_S-malonyltransferase_251406..251556_POSITIVE 209 96 59 42 7 smit:SMT_2067|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1974216..1974366_POSITIVE 209 107 82 137 103 smit:SMT_1494|3end_nucleoside_diphosphate_kinase_1480221..1480371_POSITIVE 208 56 16 95 56 smit:SMT_1826|3end_ATP_synthase_beta_chain_1797622..1797772_POSITIVE 208 48 1 121 80 smit:SMT_1282|3end_hypothetical_protein_1245025..1245175_NEGATIVE