Origin IGS: gagtcttcctcctttatcttcttaatcagccagccccctcaagaggtcacatttttctgactgacctttttgtgttataataatagtaacgaaaaaatgggaatttttcaaggaaaaaag .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 cttttttccttgaaaaattcccattttttcgttactattattataacacaaaaaggtcagtcagaaaaatgtgacctcttgagggggctggctgattaagaagataaaggaggaagactc Mask Tandem Repeat Region ================================================ gagtcttcctcctttatcttcttaatcagccagccccctcaagaggtcacatttttctgactgacctttttgtgttataataatagtaacgaaaaaatgggaatttttcaaggaaaaaag Find is-nt database================================================ Query_seq: SMT_412:SMT_413|SMT_412:SMT_413:hypothetical protein predicted by Glimmer/Critica:tRNA delta(2)-isopentenylpyrophosphate transferase:<-->:356697..356816 120 gagtcttcctcctttatcttcttaatcagccagccccctcaagaggtcacatttttctgactgacctttttgtgttataataatagtaacgaaaaaatgggaatttttcaaggaaaaaag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_412:SMT_413|SMT_412:SMT_413:hypothetical protein predicted by Glimmer/Critica:tRNA delta(2)-isopentenylpyrophosphate transferase:<-->:356697..356816 120 gagtcttcctcctttatcttcttaatcagccagccccctcaagaggtcacatttttctgactgacctttttgtgttataataatagtaacgaaaaaatgggaatttttcaaggaaaaaag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_412:SMT_413|SMT_412:SMT_413:hypothetical protein predicted by Glimmer/Critica:tRNA delta(2)-isopentenylpyrophosphate transferase:<-->:356697..356816 120 gagtcttcctcctttatcttcttaatcagccagccccctcaagaggtcacatttttctgactgacctttttgtgttataataatagtaacgaaaaaatgggaatttttcaaggaaaaaag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gagtcttcctcctttatcttcttaatcagccagccccctcaagaggtcacatttttctgactgacctttttgtgttataataatagtaacgaaaaaatgggaatttttcaaggaaaaaag Predict ORF larger than 30AA ================================================ gagtcttcctcctttatcttcttaatcagccagccccctcaagaggtcacatttttctgactgacctttttgtgttataataatagtaacgaaaaaatgggaatttttcaaggaaaaaag 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: 88 Start: 83 End: 112 ..................................................................................CTTGAAAAATTCCCATTTTTTCGTTACTAT........ PromScan Matrix: RpoD-17 Strand: + Score: 85 Start: 52 End: 81 ...................................................TTTTTCTGACTGACCTTTTTGTGTTATAAT....................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ gagtcttcctcctttatcttcttaatcagccagccccctcaagaggtcacatttttctgactgacctttttgtgttataataatagtaacgaaaaaatgggaatttttcaaggaaaaaag Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SMT_412:SMT_413|SMT_412:SMT_413:hypothetical protein predicted by Glimmer/Critica:tRNA delta(2)-isopentenylpyrophosphate transferase:<-->:356697..356816 120 gagtcttcctcctttatcttcttaatcagccagccccctcaagaggtcacatttttctgactgacctttttgtgttataataatagtaacgaaaaaatgggaatttttcaaggaaaaaag Intra-Species Hit: Count: 1 Min: 1 Max: 120 Len: 120 Subject: smit_SMT_412_SMT_413|hypothetical protein predicted by Glimmer/Critica:tRNA delta(2)-isopentenylpyrophosphate transferase|NEGATIVE:POSITIVE|[356697,356816]|120 HSP 1 e-value: 3.0E-62 bit: 238.0 Len: 120 Query Start:1 Query End:120 Subject Strand: POSITIVE Subject Start: 1 Subject End: 120 gagtcttcctcctttatcttcttaatcagccagccccctcaagaggtcacatttttctgactgacctttttgtgttataataatagtaacgaaaaaatgggaatttttcaaggaaaaaag gagtcttcctcctttatcttcttaatcagccagccccctcaagaggtcacatttttctgactgacctttttgtgttataataatagtaacgaaaaaatgggaatttttcaaggaaaaaag Inter-species Hit: Count: 2 Min: 1 Max: 120 Len: 120 Subject: NC_008533_SPD_0582_SPD_0583|hypothetical protein:tRNA delta(2)-isopentenylpyrophosphate transferase|NEGATIVE:POSITIVE|[609796,609915]|120 HSP 1 e-value: 5.0E-55 bit: 214.0 Len: 120 Query Start:1 Query End:120 Subject Strand: POSITIVE Subject Start: 1 Subject End: 120 gagtcttcctcctttatcttcttaatcagccagccccctcaagaggtcacatttttctgactgacctttttgtgttataataatagtaacgaaaaaatgggaatttttcaaggaaaaaag gagtcttcctcctttatattctcaatcagccagcctcctcaagaggtcacatttttctgactgacctttttgtgttataataatagtaacgaaaaaatgggaatttttcaaggaaaaaag Subject: NC_003028_SP_0670_SP_0671|hypothetical protein:tRNA delta(2)-isopentenylpyrophosphate transferase|NEGATIVE:POSITIVE|[646190,646309]|120 HSP 1 e-value: 5.0E-55 bit: 214.0 Len: 120 Query Start:1 Query End:120 Subject Strand: POSITIVE Subject Start: 1 Subject End: 120 gagtcttcctcctttatcttcttaatcagccagccccctcaagaggtcacatttttctgactgacctttttgtgttataataatagtaacgaaaaaatgggaatttttcaaggaaaaaag gagtcttcctcctttatattctcaatcagccagcctcctcaagaggtcacatttttctgactgacctttttgtgttataataatagtaacgaaaaaatgggaatttttcaaggaaaaaag Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAGUCUUCCUCCUUUAUCUUCUUAAUCAGCCAGCCCCCUCAAGAGGUCACAUUUUUCUGACUGACCUUUUUGUGUUAUAAUAAUAGUAACGAAAAAAUGGGAAUUUUUCAAGGAAAAAAG .........(((((.(..((((((................(((((((((((......))..)))))))))..((((((.......))))))......))))))..)...)))))...... (-18.00) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CUUUUUUCCUUGAAAAAUUCCCAUUUUUUCGUUACUAUUAUUAUAACACAAAAAGGUCAGUCAGAAAAAUGUGACCUCUUGAGGGGGCUGGCUGAUUAAGAAGAUAAAGGAGGAAGACUC .((((((((((((((((.......))))))........................((((((((((..........((((....)))).)))))))))).........)))))))))).... (-27.90) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 986 50 1 141 92 smit:SMT_412|5end_hypothetical_protein_predicted_by_Glimmer/Critica_356606..356836_NEGATIVE 332 50 1 188 128 smit:SMT_1645|5end_hypothetical_protein_1631738..1631968_POSITIVE 297 32 2 150 121 smit:SMT_553|5end_hypothetical_protein_471128..471358_POSITIVE 288 46 4 157 114 smit:SMT_495|5end_bacterial_peptide_chain_release_factor_2_(RF-2)_429038..429268_POSITIVE 281 49 1 90 46 smit:SMT_191|5end_adenylate_kinase_125745..125975_POSITIVE 275 49 1 219 155 smit:SMT_1113|5end_hypothetical_protein_1052071..1052301_NEGATIVE 269 49 1 218 157 smit:SMT_832|5end_hypothetical_protein_775104..775334_NEGATIVE 269 52 16 61 24 smit:SMT_745|5end_glycosyl_transferase,_group_1_family_protein_650387..650617_NEGATIVE 267 49 8 136 102 smit:SMT_573|5end_1-phosphofructokinase_490976..491206_POSITIVE 266 57 18 231 194 smit:SMT_533|5end_RNA_binding_protein_453218..453448_POSITIVE 266 57 18 89 52 smit:SMT_532|5end_30S_ribosomal_protein_S16_453076..453306_POSITIVE 266 57 18 231 194 smit:SMT_526|5end_RNA_binding_protein_451149..451379_POSITIVE 266 57 18 231 194 smit:SMT_510|5end_hypothetical_protein_439038..439268_POSITIVE 266 74 31 151 99 smit:SMT_478|5end_hypothetical_protein_predicted_by_Glimmer/Critica_414644..414874_POSITIVE 258 50 3 198 149 smit:SMT_102|5end_competence-specific_global_transcription_modulator_34108..34338_POSITIVE 254 64 24 63 22 smit:SMT_1523|5end_ferrochelatase_1504460..1504690_NEGATIVE 254 46 19 212 187 smit:SMT_1176|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1128993..1129223_NEGATIVE 250 50 4 133 95 smit:SMT_1451|5end_K02057_simple_sugar_transport_system_permease_protein_1434683..1434913_NEGATIVE 250 65 26 195 139 smit:SMT_772|5end_spermidine/putrescine_ABC_transporter,_ATP-binding_protein_683300..683530_NEGATIVE 250 56 12 124 82 smit:SMT_384|5end_hypothetical_protein_319406..319636_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 297 32 2 122 93 smit:SMT_552|3end_DNA_polymerase_III,_gamma_and_tau_subunits_471180..471330_POSITIVE 269 49 1 139 78 smit:SMT_833|3end_hypothetical_protein_predicted_by_Glimmer/Critica_775183..775333_NEGATIVE 269 52 16 71 34 smit:SMT_746|3end_LPS_biosynthesis_protein_650377..650527_NEGATIVE 267 49 8 139 105 smit:SMT_572|3end_fructose_repressor_491059..491209_POSITIVE 264 68 28 63 24 smit:SMT_1941|3end_hypothetical_protein_1877663..1877813_POSITIVE 258 50 3 77 28 smit:SMT_101|3end_cell_division_protein_34067..34217_POSITIVE 253 68 21 61 2 smit:SMT_665|3end_NAD+_kinase_575927..576077_NEGATIVE 251 47 6 147 94 smit:SMT_903|3end_hypothetical_protein_851945..852095_NEGATIVE 250 50 4 140 102 smit:SMT_1452|3end_ABC-type_uncharacterized_transport_system,_ATPase_component_1434676..1434826_NEGATIVE 250 56 12 45 3 smit:SMT_383|3end_cysteinyl-tRNA_synthetase_319407..319557_POSITIVE 248 50 1 79 35 smit:SMT_1181|3end_phosphotransferase_system,_mannose/fructose-specific_component_IIA_1139413..1139563_NEGATIVE 247 67 21 59 1 smit:SMT_677|3end_DNA_topoisomerase_I_585303..585453_NEGATIVE 246 41 1 127 74 smit:SMT_1218|3end_DNA_polymerase_I_1176688..1176838_NEGATIVE 243 47 5 143 110 smit:SMT_794|3end_hypothetical_protein_703245..703395_NEGATIVE 239 60 11 149 104 smit:SMT_1061|3end_hypothetical_protein_999915..1000065_POSITIVE 237 47 5 138 95 smit:SMT_1663|3end_DNA-binding_response_regulator_1652357..1652507_NEGATIVE 236 47 1 134 98 smit:SMT_1994|3end_phosphoglycerate_mutase_1920058..1920208_NEGATIVE 236 47 1 134 98 smit:SMT_201|3end_phosphoglycerate_mutase_132101..132251_POSITIVE 235 80 37 48 1 smit:SMT_1574|3end_K02529_LacI_family_transcriptional_regulator_1568144..1568294_POSITIVE 232 72 35 48 1 smit:SMT_1177|3end_immunoglobulin_A1_protease_1129193..1129343_NEGATIVE