Origin IGS: ttaattaannnnnaaatcttctgaaaaagtcagatttagctgctctttttgtgctttttttcaggatttttagtacttgtaacaaagacttaaagattctgaaaatttatcaagaggacacggtgataagggtttttaaaaccatatgacgattagaaaagcctgattgacaaggcttggaacttatttacaaaggagaatcatc .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 gatgattctcctttgtaaataagttccaagccttgtcaatcaggcttttctaatcgtcatatggttttaaaaacccttatcaccgtgtcctcttgataaattttcagaatctttaagtctttgttacaagtactaaaaatcctgaaaaaaagcacaaaaagagcagctaaatctgactttttcagaagatttnnnnnttaattaa Mask Tandem Repeat Region ================================================ ttaattaannnnnaaatcttctgaaaaagtcagatttagctgctctttttgtgctttttttcaggatttttagtacttgtaacaaagacttaaagattctgaaaatttatcaagaggacacggtgataagggtttttaaaaccatatgacgattagaaaagcctgattgacaaggcttggaacttatttacaaaggagaatcatc Find is-nt database================================================ Query_seq: SMT_1491:SMT_1492|SMT_1491:SMT_1492:capsular polysaccharide biosynthesis protein, putative:DNA-directed RNA polymerase beta chain:->->:1472028..1472232 205 ttaattaannnnnaaatcttctgaaaaagtcagatttagctgctctttttgtgctttttttcaggatttttagtacttgtaacaaagacttaaagattctgaaaatttatcaagaggacacggtgataagggtttttaaaaccatatgacgattagaaaagcctgattgacaaggcttggaacttatttacaaaggagaatcatc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_1491:SMT_1492|SMT_1491:SMT_1492:capsular polysaccharide biosynthesis protein, putative:DNA-directed RNA polymerase beta chain:->->:1472028..1472232 205 ttaattaannnnnaaatcttctgaaaaagtcagatttagctgctctttttgtgctttttttcaggatttttagtacttgtaacaaagacttaaagattctgaaaatttatcaagaggacacggtgataagggtttttaaaaccatatgacgattagaaaagcctgattgacaaggcttggaacttatttacaaaggagaatcatc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_1491:SMT_1492|SMT_1491:SMT_1492:capsular polysaccharide biosynthesis protein, putative:DNA-directed RNA polymerase beta chain:->->:1472028..1472232 205 ttaattaannnnnaaatcttctgaaaaagtcagatttagctgctctttttgtgctttttttcaggatttttagtacttgtaacaaagacttaaagattctgaaaatttatcaagaggacacggtgataagggtttttaaaaccatatgacgattagaaaagcctgattgacaaggcttggaacttatttacaaaggagaatcatc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ttaattaannnnnaaatcttctgaaaaagtcagatttagctgctctttttgtgctttttttcaggatttttagtacttgtaacaaagacttaaagattctgaaaatttatcaagaggacacggtgataagggtttttaaaaccatatgacgattagaaaagcctgattgacaaggcttggaacttatttacaaaggagaatcatc Predict ORF larger than 30AA ================================================ Protein_Len: 42 Strand: + Start: 21 End: 146 .................... M K K S D L A A L F V L F F R I F S T C N K D L K I L K I Y Q E D T V I R V F K T I ........................................................... Protein_Len: 33 Strand: - Start: 8 End: 106 ....... X X F R R F F D S K A A R K T S K K L I K L V Q L L S K F I R F M ................................................................................................... ttaattaannnnnaaatcttctgaaaaagtcagatttagctgctctttttgtgctttttttcaggatttttagtacttgtaacaaagacttaaagattctgaaaatttatcaagaggacacggtgataagggtttttaaaaccatatgacgattagaaaagcctgattgacaaggcttggaacttatttacaaaggagaatcatc 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================================================ ttaattaannnnnaaatcttctgaaaaagtcagatttagctgctctttttgtgctttttttcaggatttttagtacttgtaacaaagacttaaagattctgaaaatttatcaagaggacacggtgataagggtttttaaaaccatatgacgattagaaaagcctgattgacaaggcttggaacttatttacaaaggagaatcatc Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SMT_1491:SMT_1492|SMT_1491:SMT_1492:capsular polysaccharide biosynthesis protein, putative:DNA-directed RNA polymerase beta chain:->->:1472028..1472232 205 ttaattaannnnnaaatcttctgaaaaagtcagatttagctgctctttttgtgctttttttcaggatttttagtacttgtaacaaagacttaaagattctgaaaatttatcaagaggacacggtgataagggtttttaaaaccatatgacgattagaaaagcctgattgacaaggcttggaacttatttacaaaggagaatcatc Intra-Species Hit: Count: 1 Min: 14 Max: 205 Len: 192 Subject: smit_SMT_1491_SMT_1492|capsular polysaccharide biosynthesis protein, putative:DNA-directed RNA polymerase beta chain|POSITIVE:POSITIVE|[1472028,1472232]|205 HSP 1 e-value: 2.0E-92 bit: 339.0 Len: 192 Query Start:14 Query End:205 Subject Strand: POSITIVE Subject Start: 14 Subject End: 205 .............aaatcttctgaaaaagtcagatttagctgctctttttgtgcnnnnnnncaggatttttagtacttgtaacaaagacttaaagattctgaaaatttatcaagaggacacggtgataagggtttttaaaaccatatgacgattagaaaagcctgattgacaaggcttggaacttatttacaaaggagaatcatc .............aaatcttctgaaaaagtcagatttagctgctctttttgtgctttttttcaggatttttagtacttgtaacaaagacttaaagattctgaaaatttatcaagaggacacggtgataagggtttttaaaaccatatgacgattagaaaagcctgattgacaaggcttggaacttatttacaaaggagaatcatc Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAUCUUCUGAAAAAGUCAGAUUUAGCUGCUCUUUUUGUGCUUUUUUUCAGGAUUUUUAGUACUUGUAACAAAGACUUAAAGAUUCUGAAAAUUUAUCAAGAGGACACGGUGAUAAGGGUUUUUAAAACCAUAUGACGAUUAGAAAAGCCUGAUUGACAAGGCUUGGAACUUAUUUACAAAGGAGAAUCAUC ...((((((......((((......((((.((((((((......(((((((((((((((((.(((......))))).))))))))))))))).....))))))))..))))......((((.....))))...))))........((((((........))))))...............))))))...... (-48.80) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAUGAUUCUCCUUUGUAAAUAAGUUCCAAGCCUUGUCAAUCAGGCUUUUCUAAUCGUCAUAUGGUUUUAAAAACCCUUAUCACCGUGUCCUCUUGAUAAAUUUUCAGAAUCUUUAAGUCUUUGUUACAAGUACUAAAAAUCCUGAAAAAAAGCACAAAAAGAGCAGCUAAAUCUGACUUUUUCAGAAGAUUU (((((((...(((.......)))....((((((........))))))....))))))).((((((..(((......)))..))))))..(((((......(((((((.((.((((.(((((......))).)))))).)).)))))))..........)))))........(((((.....)))))...... (-31.09) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 291 65 26 175 133 smit:SMT_96|5end_hypothetical_protein_28436..28666_POSITIVE 266 52 17 226 182 smit:SMT_1493|5end_DNA-directed_RNA_polymerase,_beta'_subunit/160_kD_subunit_1475737..1475967_POSITIVE 258 166 127 37 1 smit:SMT_428|5end_ribosomal_small_subunit_pseudouridine_synthase_A_369857..370087_NEGATIVE 256 187 142 216 172 smit:SMT_356|5end_hypothetical_protein_292394..292624_POSITIVE 255 62 22 118 80 smit:SMT_1617|5end_K02015_iron_complex_transport_system_permease_protein_1604500..1604730_NEGATIVE 253 42 8 36 4 smit:SMT_1549|5end_hypothetical_protein_1533645..1533875_POSITIVE 252 60 15 198 147 smit:SMT_1332|5end_hypothetical_protein_1307576..1307806_NEGATIVE 251 140 95 67 9 smit:SMT_662|5end_A/G-specific_adenine_glycosylase_573827..574057_NEGATIVE 243 176 138 54 16 smit:SMT_841|5end_dihydrodipicolinate_reductase_788025..788255_NEGATIVE 241 46 4 135 96 smit:SMT_1134|5end_glutamyl-tRNA_synthetase_1076464..1076694_NEGATIVE 241 48 5 212 162 smit:SMT_331|5end_endo-beta-N-acetylglucosaminidase_266416..266646_POSITIVE 239 53 15 53 14 smit:SMT_1678|5end_inorganic_pyrophosphatase_1662126..1662356_POSITIVE 237 42 4 116 66 smit:SMT_1069|5end_acetyl_xylan_esterase,_putative_1009330..1009560_POSITIVE 236 142 102 90 44 smit:SMT_313|5end_3R-hydroxymyristoyl_ACP_dehydrase_253843..254073_POSITIVE 235 165 132 170 144 smit:SMT_554|5end_K09013_Fe-S_cluster_assembly_ATP-binding_protein_471425..471655_POSITIVE 234 150 101 52 9 smit:SMT_1856|5end_polypeptide_deformylase_1820650..1820880_POSITIVE 234 187 141 206 159 smit:SMT_1015|5end_galactose_operon_repressor_951938..952168_POSITIVE 233 54 14 52 14 smit:SMT_1991|5end_K03706_transcriptional_pleiotropic_repressor_1918264..1918494_NEGATIVE 232 159 111 104 53 smit:SMT_2164|5end_K06147_ATP-binding_cassette,_subfamily_B,_bacterial_2037861..2038091_POSITIVE 232 166 134 28 3 smit:SMT_1170|5end_acetyltransferase,_CysE/LacA/LpxA/NodL_family_1118126..1118356_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 295 67 22 126 66 smit:SMT_1525|3end_pneumococcal_histidine_triad_protein_A_precursor_1505873..1506023_NEGATIVE 267 58 14 115 65 smit:SMT_1370|3end_K06217_phosphate_starvation-inducible_protein_PhoH_and_related_proteins_1349499..1349649_NEGATIVE 262 64 25 123 79 smit:SMT_141|3end_K03495_glucose_inhibited_division_protein_A_93401..93551_POSITIVE 256 187 142 55 11 smit:SMT_355|3end_hypothetical_protein_292313..292463_POSITIVE 255 62 22 128 90 smit:SMT_1618|3end_K02015_iron_complex_transport_system_permease_protein_1604490..1604640_NEGATIVE 244 159 111 63 21 smit:SMT_316|3end_acetyl-CoA_carboxylase_carboxyl_transferase_subunit_alpha_257391..257541_POSITIVE 238 130 83 76 37 smit:SMT_317|3end_K03625_N_utilization_substance_protein_B_257475..257625_NEGATIVE 236 142 102 93 47 smit:SMT_312|3end_acetyl-CoA_carboxylase,_biotin_carboxyl_carrier_protein_253926..254076_POSITIVE 235 165 132 67 41 smit:SMT_553|3end_hypothetical_protein_471402..471552_POSITIVE 233 167 121 81 35 smit:SMT_1186|3end_hypothetical_protein_1144886..1145036_POSITIVE 232 159 111 80 29 smit:SMT_2163|3end_cell_division_protein_FtsA_2037917..2038067_POSITIVE 226 169 125 79 42 smit:SMT_1291|3end_hypothetical_protein_1254296..1254446_POSITIVE 226 78 31 149 95 smit:SMT_968|3end_K01990_ABC-2_type_transport_system_ATP-binding_protein_913299..913449_NEGATIVE 224 70 30 61 22 smit:SMT_1571|3end_CAAX_amino_terminal_protease_family_protein_1564405..1564555_POSITIVE 222 164 125 43 6 smit:SMT_230|3end_hypothetical_protein_predicted_by_Glimmer/Critica_165666..165816_NEGATIVE 221 119 80 151 120 smit:SMT_1163|3end_hypothetical_protein_1109096..1109246_NEGATIVE 220 58 28 140 106 smit:SMT_297|3end_ABC_transporter_substrate-binding_protein_-_oligopeptide_transport_240606..240756_POSITIVE 219 70 27 112 59 smit:SMT_1750|3end_anthranilate_phosphoribosyltransferase_1729095..1729245_POSITIVE 219 183 142 75 34 smit:SMT_605|3end_DNA-binding_protein_HU_519257..519407_POSITIVE 218 171 132 73 35 smit:SMT_1990|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1917677..1917827_POSITIVE