Origin IGS: aatatttatctcctggatttcctaatcctacaagtaatttggtcatttatttttcctttcaaagccaaaagggnnnnnttaattaattaannnnngatttttttcaattgtctttcattttcagtcaaaattggtgggcaaggtaactgagcaaatgactagtaaaactaagcaaagaacttcagttggctcccaattttcaaaagaaaaacataaataaatagttgaaaaaattcacagcattcaccattattttcaaggagaaaaaca .........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.........1.........2.........3.........4.........5.........6.........7.........8.........9 tgtttttctccttgaaaataatggtgaatgctgtgaattttttcaactatttatttatgtttttcttttgaaaattgggagccaactgaagttctttgcttagttttactagtcatttgctcagttaccttgcccaccaattttgactgaaaatgaaagacaattgaaaaaaatcnnnnnttaattaattaannnnncccttttggctttgaaaggaaaaataaatgaccaaattacttgtaggattaggaaatccaggagataaatatt Mask Tandem Repeat Region ================================================ aatatttatctcctggatttcctaatcctacaagtaatttggtcatttatttttcctttcaaagccaaaagggnnnnnttaattaattaannnnngatttttttcaattgtctttcattttcagtcaaaattggtgggcaaggtaactgagcaaatgactagtaaaactaagcaaagaacttcagttggctcccaattttcaaaagaaaaacataaataaatagttgaaaaaattcacagcattcaccattattttcaaggagaaaaaca Find is-nt database================================================ Query_seq: SMT_1906:SMT_1907|SMT_1906:SMT_1907:peptidyl-tRNA hydrolase:phosphate-binding protein:<-->:1853975..1854244 270 aatatttatctcctggatttcctaatcctacaagtaatttggtcatttatttttcctttcaaagccaaaagggnnnnnttaattaattaannnnngatttttttcaattgtctttcattttcagtcaaaattggtgggcaaggtaactgagcaaatgactagtaaaactaagcaaagaacttcagttggctcccaattttcaaaagaaaaacataaataaatagttgaaaaaattcacagcattcaccattattttcaaggagaaaaaca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_1906:SMT_1907|SMT_1906:SMT_1907:peptidyl-tRNA hydrolase:phosphate-binding protein:<-->:1853975..1854244 270 aatatttatctcctggatttcctaatcctacaagtaatttggtcatttatttttcctttcaaagccaaaagggnnnnnttaattaattaannnnngatttttttcaattgtctttcattttcagtcaaaattggtgggcaaggtaactgagcaaatgactagtaaaactaagcaaagaacttcagttggctcccaattttcaaaagaaaaacataaataaatagttgaaaaaattcacagcattcaccattattttcaaggagaaaaaca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_1906:SMT_1907|SMT_1906:SMT_1907:peptidyl-tRNA hydrolase:phosphate-binding protein:<-->:1853975..1854244 270 aatatttatctcctggatttcctaatcctacaagtaatttggtcatttatttttcctttcaaagccaaaagggnnnnnttaattaattaannnnngatttttttcaattgtctttcattttcagtcaaaattggtgggcaaggtaactgagcaaatgactagtaaaactaagcaaagaacttcagttggctcccaattttcaaaagaaaaacataaataaatagttgaaaaaattcacagcattcaccattattttcaaggagaaaaaca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aatatttatctcctggatttcctaatcctacaagtaatttggtcatttatttttcctttcaaagccaaaagggnnnnnttaattaattaannnnngatttttttcaattgtctttcattttcagtcaaaattggtgggcaaggtaactgagcaaatgactagtaaaactaagcaaagaacttcagttggctcccaattttcaaaagaaaaacataaataaatagttgaaaaaattcacagcattcaccattattttcaaggagaaaaaca Predict ORF larger than 30AA ================================================ Protein_Len: 44 Strand: + Start: 86 End: 217 ..................................................................................... M X X X F F S I V F H F Q S K L V G K V T E Q M T S K T K Q R T S V G S Q F S K E K H K ..................................................... Protein_Len: 37 Strand: - Start: 124 End: 234 ........................................................................................................................... D F N T P L T V S C I V L L V L C L V E T P E W N E F S F C L Y I T S F M .................................... aatatttatctcctggatttcctaatcctacaagtaatttggtcatttatttttcctttcaaagccaaaagggnnnnnttaattaattaannnnngatttttttcaattgtctttcattttcagtcaaaattggtgggcaaggtaactgagcaaatgactagtaaaactaagcaaagaacttcagttggctcccaattttcaaaagaaaaacataaataaatagttgaaaaaattcacagcattcaccattattttcaaggagaaaaaca 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: 224 End: 253 ...............................................................................................................................................................................................................................GTTGAAAAAATTCACAGCATTCACCATTAT................. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ aatatttatctcctggatttcctaatcctacaagtaatttggtcatttatttttcctttcaaagccaaaagggnnnnnttaattaattaannnnngatttttttcaattgtctttcattttcagtcaaaattggtgggcaaggtaactgagcaaatgactagtaaaactaagcaaagaacttcagttggctcccaattttcaaaagaaaaacataaataaatagttgaaaaaattcacagcattcaccattattttcaaggagaaaaaca Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SMT_1906:SMT_1907|SMT_1906:SMT_1907:peptidyl-tRNA hydrolase:phosphate-binding protein:<-->:1853975..1854244 270 aatatttatctcctggatttcctaatcctacaagtaatttggtcatttatttttcctttcaaagccaaaagggnnnnnttaattaattaannnnngatttttttcaattgtctttcattttcagtcaaaattggtgggcaaggtaactgagcaaatgactagtaaaactaagcaaagaacttcagttggctcccaattttcaaaagaaaaacataaataaatagttgaaaaaattcacagcattcaccattattttcaaggagaaaaaca Intra-Species Hit: Count: 1 Min: 1 Max: 270 Len: 270 Subject: smit_SMT_1906_SMT_1907|peptidyl-tRNA hydrolase:phosphate-binding protein|NEGATIVE:POSITIVE|[1853975,1854244]|270 HSP 1 e-value: 4.0E-48 bit: 192.0 Len: 97 Query Start:105 Query End:201 Subject Strand: POSITIVE Subject Start: 105 Subject End: 201 ........................................................................................................caattgtctttcattttcagtcaaaattggtgggcaaggtaactgagcaaatgactagtaaaactaagcaaagaacttcagttggctcccaattttc..................................................................... ........................................................................................................caattgtctttcattttcagtcaaaattggtgggcaaggtaactgagcaaatgactagtaaaactaagcaaagaacttcagttggctcccaattttc..................................................................... HSP 2 e-value: 6.0E-32 bit: 139.0 Len: 70 Query Start:1 Query End:70 Subject Strand: POSITIVE Subject Start: 1 Subject End: 70 aatatttatctcctggatttcctaatcctacaagtaatttggtcatttatttttcctttcaaagccaaaa........................................................................................................................................................................................................ aatatttatctcctggatttcctaatcctacaagtaatttggtcatttatttttcctttcaaagccaaaa........................................................................................................................................................................................................ HSP 3 e-value: 3.0E-12 bit: 73.8 Len: 37 Query Start:234 Query End:270 Subject Strand: POSITIVE Subject Start: 234 Subject End: 270 .........................................................................................................................................................................................................................................ttcacagcattcaccattattttcaaggagaaaaaca .........................................................................................................................................................................................................................................ttcacagcattcaccattattttcaaggagaaaaaca Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAUAUUUAUCUCCUGGAUUUCCUAAUCCUACAAGUAAUUUGGUCAUUUAUUUUUCCUUUCAAAGCCAAAAGGGNNNNNUUAAUUAAUUAANNNNNGAUUUUUUUCAAUUGUCUUUCAUUUUCAGUCAAAAUUGGUGGGCAAGGUAACUGAGCAAAUGACUAGUAAAACUAAGCAAAGAACUUCAGUUGGCUCCCAAUUUUCAAAAGAAAAACAUAAAUAAAUAGUUGAAAAAAUUCACAGCAUUCACCAUUAUUUUCAAGGAGAAAAACA ........(((((((((((....)))))...((((((..((((...........(((((........))))).......................((.(((((((((((((......(((((..(.((((((((.((((....((((((((....((..(((.....)))..))......)))))))))))))))))))).)...)))))..........))))))))))))).)).........))))))))))...))))))...... (-51.89) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGUUUUUCUCCUUGAAAAUAAUGGUGAAUGCUGUGAAUUUUUUCAACUAUUUAUUUAUGUUUUUCUUUUGAAAAUUGGGAGCCAACUGAAGUUCUUUGCUUAGUUUUACUAGUCAUUUGCUCAGUUACCUUGCCCACCAAUUUUGACUGAAAAUGAAAGACAAUUGAAAAAAAUCNNNNNUUAAUUAAUUAANNNNNCCCUUUUGGCUUUGAAAGGAAAAAUAAAUGACCAAAUUACUUGUAGGAUUAGGAAAUCCAGGAGAUAAAUAUU (((((.(((((.((((((..(((((....))))).....))))))..(((((((((.((((((((((((.(((((((((.((.((((((.((....((.((((.....)))).))...)))))))).....)).).)))))))....).)))).))))))))....................................((((((......))))))..)))))))))...............(((((....))))).))))).))))).. (-52.00) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 773 60 11 151 102 smit:SMT_1906|5end_peptidyl-tRNA_hydrolase_1853884..1854114_NEGATIVE 773 60 11 105 56 smit:SMT_93|5end_peptidyl-tRNA_hydrolase_24046..24276_POSITIVE 634 60 11 175 127 smit:SMT_2113|5end_peptidyl-tRNA_hydrolase_2001191..2001421_NEGATIVE 324 25 1 231 207 smit:SMT_1905|5end_peptidyl-tRNA_hydrolase_1853769..1853999_NEGATIVE 308 60 11 104 46 smit:SMT_1668|5end_K+_transport_system,_NAD-binding_component_1658288..1658518_NEGATIVE 308 60 11 187 129 smit:SMT_1167|5end_aminopeptidase_N_1115076..1115306_NEGATIVE 287 60 13 102 52 smit:SMT_139|5end_hypothetical_protein_90523..90753_POSITIVE 284 63 21 50 4 smit:SMT_1514|5end_methylenetetrahydrofolate_dehydrogenase_(NADP+)_/_methenyltetrahydrofolate_cyclohydrolase_1496640..1496870_NEGATIVE 278 267 235 148 108 smit:SMT_838|5end_cation_efflux_family_protein_782924..783154_POSITIVE 276 156 116 181 143 smit:SMT_514|5end_tRNA_(guanine-N(1)-)-methyltransferase_441377..441607_POSITIVE 265 148 101 166 119 smit:SMT_2126|5end_indole-3-glycerol_phosphate_synthase_2009107..2009337_POSITIVE 265 148 101 166 119 smit:SMT_1751|5end_indole-3-glycerol_phosphate_synthase_1729012..1729242_POSITIVE 259 45 2 143 90 smit:SMT_465|5end_oxidoreductase,_short_chain_dehydrogenase/reductase_family_protein_403244..403474_POSITIVE 259 45 2 143 90 smit:SMT_417|5end_short_chain_dehydrogenase_360373..360603_POSITIVE 259 194 151 55 14 smit:SMT_236|5end_ribosomal_small_subunit_pseudouridine_synthase_A_174625..174855_POSITIVE 247 179 131 223 165 smit:SMT_2109|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1999099..1999329_NEGATIVE 247 150 101 76 31 smit:SMT_1770|5end_hypothetical_protein_1746505..1746735_NEGATIVE 245 201 162 67 31 smit:SMT_1380|5end_pyrroline-5-carboxylate_reductase_1358464..1358694_NEGATIVE 244 145 111 228 189 smit:SMT_1791|5end_hypothetical_protein_1765907..1766137_POSITIVE 244 143 105 218 174 smit:SMT_1606|5end_glutamate_racemase_1595857..1596087_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 604 73 31 45 2 smit:SMT_92|3end_GTP-binding_protein,_probable_translation_factor_24052..24202_POSITIVE 308 60 11 90 32 smit:SMT_1669|3end_potassium_uptake_protein_KtrB_1658302..1658452_NEGATIVE 308 60 11 90 32 smit:SMT_1168|3end_potassium_uptake_protein_KtrB_1115173..1115323_NEGATIVE 275 149 101 141 98 smit:SMT_1376|3end_tetrapyrrole_(corrin/porphyrin)_methylase_family_protein_1354675..1354825_NEGATIVE 266 265 223 44 7 smit:SMT_1328|3end_hypothetical_protein_1304310..1304460_NEGATIVE 265 148 101 77 30 smit:SMT_2125|3end_3-phosphoshikimate_1-carboxyvinyltransferase_2009098..2009248_POSITIVE 265 160 111 136 87 smit:SMT_1448|3end_serine_hydroxymethyltransferase_1430703..1430853_NEGATIVE 259 45 2 122 69 smit:SMT_464|3end_ribonuclease_Z_403303..403453_POSITIVE 259 45 2 122 69 smit:SMT_416|3end_ribonuclease_Z_360432..360582_POSITIVE 254 200 151 67 22 smit:SMT_742|3end_hypothetical_protein_645784..645934_NEGATIVE 249 155 119 46 2 smit:SMT_518|3end_biotin_synthase_443215..443365_NEGATIVE 245 201 162 63 27 smit:SMT_1381|3end_gamma-glutamyl_phosphate_reductase_1358468..1358618_NEGATIVE 243 73 32 70 27 smit:SMT_1483|3end_GTP-binding_protein_1463140..1463290_NEGATIVE 243 73 32 149 106 smit:SMT_1482|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1463061..1463211_NEGATIVE 242 178 131 122 78 smit:SMT_389|3end_PTS_system,_galactitol-specific_IIA_component,_putative_322335..322485_POSITIVE 238 198 163 79 46 smit:SMT_992|3end_hypothetical_protein_934529..934679_NEGATIVE 237 73 38 88 55 smit:SMT_554|3end_K09013_Fe-S_cluster_assembly_ATP-binding_protein_472323..472473_POSITIVE 230 201 167 77 39 smit:SMT_213|3end_leucyl-tRNA_synthetase_146167..146317_POSITIVE 229 140 100 109 69 smit:SMT_1596|3end_oligopeptide_transport_ATP-binding_protein_OppD_1587050..1587200_POSITIVE 228 55 12 60 11 smit:SMT_1266|3end_predicted_transcriptional_regulator_1231774..1231924_POSITIVE