Origin IGS: attagctccaatctcaaagaatgtactaagataagtatagcacagttaggaagaataagctgaaaagcgaaatagttctagaaagaagaagatggtttggataaaaaataagcctcgagttagttcgaggcttaaactgtt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aacagtttaagcctcgaactaactcgaggcttattttttatccaaaccatcttcttctttctagaactatttcgcttttcagcttattcttcctaactgtgctatacttatcttagtacattctttgagattggagctaat Mask Tandem Repeat Region ================================================ attagctccaatctcaaagaatgtactaagataagtatagcacagttaggaagaataagctgaaaagcgaaatagttctagaaagaagaagatggtttggataaaaaataagcctcgagttagttcgaggcttaaactgtt Find is-nt database================================================ Query_seq: SMT_1467:SMT_1468|SMT_1467:SMT_1468:hydroxyacylglutathione hydrolase:pneumococcal surface protein, putative:<-<-:1448724..1448864 141 attagctccaatctcaaagaatgtactaagataagtatagcacagttaggaagaataagctgaaaagcgaaatagttctagaaagaagaagatggtttggataaaaaataagcctcgagttagttcgaggcttaaactgtt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_1467:SMT_1468|SMT_1467:SMT_1468:hydroxyacylglutathione hydrolase:pneumococcal surface protein, putative:<-<-:1448724..1448864 141 attagctccaatctcaaagaatgtactaagataagtatagcacagttaggaagaataagctgaaaagcgaaatagttctagaaagaagaagatggtttggataaaaaataagcctcgagttagttcgaggcttaaactgtt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_1467:SMT_1468|SMT_1467:SMT_1468:hydroxyacylglutathione hydrolase:pneumococcal surface protein, putative:<-<-:1448724..1448864 141 attagctccaatctcaaagaatgtactaagataagtatagcacagttaggaagaataagctgaaaagcgaaatagttctagaaagaagaagatggtttggataaaaaataagcctcgagttagttcgaggcttaaactgtt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 attagctccaatctcaaagaatgtactaagataagtatagcacagttaggaagaataagctgaaaagcgaaatagttctagaaagaagaagatggtttggataaaaaataagcctcgagttagttcgaggcttaaactgtt Predict ORF larger than 30AA ================================================ attagctccaatctcaaagaatgtactaagataagtatagcacagttaggaagaataagctgaaaagcgaaatagttctagaaagaagaagatggtttggataaaaaataagcctcgagttagttcgaggcttaaactgtt 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================================================ attagctccaatctcaaagaatgtactaagataagtatagcacagttaggaagaataagctgaaaagcgaaatagttctagaaagaagaagatggtttggataaaaaataagcctcgagttagttcgaggcttaaactgtt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SMT_1467:SMT_1468|SMT_1467:SMT_1468:hydroxyacylglutathione hydrolase:pneumococcal surface protein, putative:<-<-:1448724..1448864 141 attagctccaatctcaaagaatgtactaagataagtatagcacagttaggaagaataagctgaaaagcgaaatagttctagaaagaagaagatggtttggataaaaaataagcctcgagttagttcgaggcttaaactgtt Intra-Species Hit: Count: 1 Min: 1 Max: 141 Len: 141 Subject: smit_SMT_1467_SMT_1468|hydroxyacylglutathione hydrolase:pneumococcal surface protein, putative|NEGATIVE:NEGATIVE|[1448724,1448864]|141 HSP 1 e-value: 1.0E-74 bit: 280.0 Len: 141 Query Start:1 Query End:141 Subject Strand: POSITIVE Subject Start: 1 Subject End: 141 attagctccaatctcaaagaatgtactaagataagtatagcacagttaggaagaataagctgaaaagcgaaatagttctagaaagaagaagatggtttggataaaaaataagcctcgagttagttcgaggcttaaactgtt attagctccaatctcaaagaatgtactaagataagtatagcacagttaggaagaataagctgaaaagcgaaatagttctagaaagaagaagatggtttggataaaaaataagcctcgagttagttcgaggcttaaactgtt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUUAGCUCCAAUCUCAAAGAAUGUACUAAGAUAAGUAUAGCACAGUUAGGAAGAAUAAGCUGAAAAGCGAAAUAGUUCUAGAAAGAAGAAGAUGGUUUGGAUAAAAAAUAAGCCUCGAGUUAGUUCGAGGCUUAAACUGUU ......(((((((((......((((((......))))))......((((((.......(((....))).......)))))).........)).)).))))).......(((((((((((....)))))))))))....... (-34.74) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AACAGUUUAAGCCUCGAACUAACUCGAGGCUUAUUUUUUAUCCAAACCAUCUUCUUCUUUCUAGAACUAUUUCGCUUUUCAGCUUAUUCUUCCUAACUGUGCUAUACUUAUCUUAGUACAUUCUUUGAGAUUGGAGCUAAU .......((((((((((......)))))))))).....................((((....))))..............(((((..((((......(((((((.........)))))))......))))...)))))... (-31.50) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 846 140 91 231 182 smit:SMT_1467|5end_hydroxyacylglutathione_hydrolase_1448633..1448863_NEGATIVE 293 46 3 141 91 smit:SMT_1431|5end_K08986_putative_membrane_protein_1415759..1415989_POSITIVE 273 97 51 202 151 smit:SMT_1310|5end_D-alanine-activating_enzyme_1274237..1274467_POSITIVE 272 49 3 206 146 smit:SMT_1739|5end_hypothetical_protein_1721263..1721493_POSITIVE 268 97 58 47 1 smit:SMT_1309|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1274082..1274312_POSITIVE 244 85 42 196 149 smit:SMT_970|5end_threonyl-tRNA_synthetase_915772..916002_POSITIVE 239 137 92 102 48 smit:SMT_1457|5end_16S_rRNA_m(2)G_1207_methyltransferase_1440209..1440439_NEGATIVE 238 134 91 140 105 smit:SMT_1351|5end_dephospho-CoA_kinase_1329817..1330047_NEGATIVE 237 90 43 83 29 smit:SMT_1161|5end_K05837_rod_shape_determining_protein_RodA_1106408..1106638_NEGATIVE 236 89 46 217 174 smit:SMT_494|5end_K04767_acetoin_utilization_protein_AcuB_428155..428385_POSITIVE 231 132 91 231 185 smit:SMT_1731|5end_K06442_putative_hemolysin_1715643..1715873_POSITIVE 231 139 94 216 181 smit:SMT_1409|5end_hypothetical_protein_1388514..1388744_NEGATIVE 231 80 31 79 30 smit:SMT_1293|5end_K02051_sulfonate/nitrate/taurine_transport_system_substrate-binding_protein_1254976..1255206_POSITIVE 231 78 34 177 140 smit:SMT_864|5end_K07485_transposase_814322..814552_POSITIVE 228 140 110 169 141 smit:SMT_832|5end_hypothetical_protein_775104..775334_NEGATIVE 226 47 3 107 73 smit:SMT_1482|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1463111..1463341_NEGATIVE 225 130 84 68 16 smit:SMT_1866|5end_extramembranal_protein_1827290..1827520_POSITIVE 225 130 84 68 16 smit:SMT_1313|5end_extramembranal_protein_1277274..1277504_POSITIVE 224 131 112 45 21 smit:SMT_916|5end_3-hydroxy-3-methylglutaryl-CoA_reductase_870004..870234_NEGATIVE 223 133 98 231 196 smit:SMT_1871|5end_modification_methylase,_HemK_family_1830501..1830731_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 293 46 3 144 94 smit:SMT_1430|3end_hypothetical_protein_1415842..1415992_POSITIVE 240 75 36 102 59 smit:SMT_1094|3end_membrane_carboxypeptidase_(penicillin-binding_protein)_1034141..1034291_NEGATIVE 240 133 91 63 18 smit:SMT_225|3end_pullulanase_159666..159816_NEGATIVE 238 134 91 140 105 smit:SMT_1352|3end_formamidopyrimidine-DNA_glycosylase_1329817..1329967_NEGATIVE 228 140 110 90 62 smit:SMT_833|3end_hypothetical_protein_predicted_by_Glimmer/Critica_775183..775333_NEGATIVE 226 47 3 78 44 smit:SMT_1483|3end_GTP-binding_protein_1463140..1463290_NEGATIVE 225 130 84 75 23 smit:SMT_1865|3end_D-alanyl_carrier_protein_1827377..1827527_POSITIVE 225 130 84 75 23 smit:SMT_1312|3end_D-alanyl_carrier_protein_1277361..1277511_POSITIVE 224 131 112 45 21 smit:SMT_917|3end_hydroxymethylglutaryl-CoA_synthase_870004..870154_NEGATIVE 221 50 5 142 99 smit:SMT_770|3end_K02053_spermidine/putrescine_transport_system_permease_protein_680586..680736_NEGATIVE 220 79 37 58 21 smit:SMT_1874|3end_hypothetical_protein_1832623..1832773_NEGATIVE 220 62 23 105 67 smit:SMT_942|3end_hypothetical_protein_893528..893678_NEGATIVE 217 140 107 64 31 smit:SMT_869|3end_hypothetical_protein_817228..817378_NEGATIVE 211 126 93 53 21 smit:SMT_1381|3end_gamma-glutamyl_phosphate_reductase_1358468..1358618_NEGATIVE 211 82 44 109 73 smit:SMT_969|3end_30S_ribosomal_protein_S15_914653..914803_NEGATIVE 211 140 112 34 4 smit:SMT_789|3end_hypothetical_protein_700332..700482_NEGATIVE 204 140 105 44 1 smit:SMT_1433|3end_hypothetical_protein_1417472..1417622_NEGATIVE 203 98 58 118 76 smit:SMT_886|3end_single-stranded-DNA-specific_exonuclease_RecJ_832599..832749_NEGATIVE 200 131 93 106 59 smit:SMT_1244|3end_putative_repressor_protein_1205149..1205299_POSITIVE 200 138 94 97 52 smit:SMT_1055|3end_transcriptional_regulator,_GntR_family_994387..994537_NEGATIVE