Origin IGS: tgtttctctcctcttttattctgttactattttaccataaaagcgcaggctcttcatgaaaatcatcagaaaagtttgccagtctttaaaaatcaagtgaagactctaaaaattgacgcccatacaaaaatccgatgaagttcatcggactctt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aagagtccgatgaacttcatcggatttttgtatgggcgtcaatttttagagtcttcacttgatttttaaagactggcaaacttttctgatgattttcatgaagagcctgcgcttttatggtaaaatagtaacagaataaaagaggagagaaaca Mask Tandem Repeat Region ================================================ tgtttctctcctcttttattctgttactattttaccataaaagcgcaggctcttcatgaaaatcatcagaaaagtttgccagtctttaaaaatcaagtgaagactctaaaaattgacgcccatacaaaaatccgatgaagttcatcggactctt Find is-nt database================================================ Query_seq: SMT_1148:SMT_1149|SMT_1148:SMT_1149:aspartyl-tRNA synthetase:hypothetical protein:<-<-:1093976..1094129 154 tgtttctctcctcttttattctgttactattttaccataaaagcgcaggctcttcatgaaaatcatcagaaaagtttgccagtctttaaaaatcaagtgaagactctaaaaattgacgcccatacaaaaatccgatgaagttcatcggactctt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_1148:SMT_1149|SMT_1148:SMT_1149:aspartyl-tRNA synthetase:hypothetical protein:<-<-:1093976..1094129 154 tgtttctctcctcttttattctgttactattttaccataaaagcgcaggctcttcatgaaaatcatcagaaaagtttgccagtctttaaaaatcaagtgaagactctaaaaattgacgcccatacaaaaatccgatgaagttcatcggactctt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_1148:SMT_1149|SMT_1148:SMT_1149:aspartyl-tRNA synthetase:hypothetical protein:<-<-:1093976..1094129 154 tgtttctctcctcttttattctgttactattttaccataaaagcgcaggctcttcatgaaaatcatcagaaaagtttgccagtctttaaaaatcaagtgaagactctaaaaattgacgcccatacaaaaatccgatgaagttcatcggactctt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tgtttctctcctcttttattctgttactattttaccataaaagcgcaggctcttcatgaaaatcatcagaaaagtttgccagtctttaaaaatcaagtgaagactctaaaaattgacgcccatacaaaaatccgatgaagttcatcggactctt Predict ORF larger than 30AA ================================================ Protein_Len: 33 Strand: + Start: 37 End: 135 .................................... M K A Q A L H E N H Q K S L P V F K N Q V K T L K I D A H T K I R ................... tgtttctctcctcttttattctgttactattttaccataaaagcgcaggctcttcatgaaaatcatcagaaaagtttgccagtctttaaaaatcaagtgaagactctaaaaattgacgcccatacaaaaatccgatgaagttcatcggactctt 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================================================ tgtttctctcctcttttattctgttactattttaccataaaagcgcaggctcttcatgaaaatcatcagaaaagtttgccagtctttaaaaatcaagtgaagactctaaaaattgacgcccatacaaaaatccgatgaagttcatcggactctt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SMT_1148:SMT_1149|SMT_1148:SMT_1149:aspartyl-tRNA synthetase:hypothetical protein:<-<-:1093976..1094129 154 tgtttctctcctcttttattctgttactattttaccataaaagcgcaggctcttcatgaaaatcatcagaaaagtttgccagtctttaaaaatcaagtgaagactctaaaaattgacgcccatacaaaaatccgatgaagttcatcggactctt Intra-Species Hit: Count: 1 Min: 1 Max: 154 Len: 154 Subject: smit_SMT_1148_SMT_1149|aspartyl-tRNA synthetase:hypothetical protein|NEGATIVE:NEGATIVE|[1093976,1094129]|154 HSP 1 e-value: 2.0E-82 bit: 305.0 Len: 154 Query Start:1 Query End:154 Subject Strand: POSITIVE Subject Start: 1 Subject End: 154 tgtttctctcctcttttattctgttactattttaccataaaagcgcaggctcttcatgaaaatcatcagaaaagtttgccagtctttaaaaatcaagtgaagactctaaaaattgacgcccatacaaaaatccgatgaagttcatcggactctt tgtttctctcctcttttattctgttactattttaccataaaagcgcaggctcttcatgaaaatcatcagaaaagtttgccagtctttaaaaatcaagtgaagactctaaaaattgacgcccatacaaaaatccgatgaagttcatcggactctt Inter-species Hit: Count: 3 Min: 3 Max: 114 Len: 112 Subject: NC_008533_SPD_1941_SPD_1942|aspartyl-tRNA synthetase:hypothetical protein|NEGATIVE:NEGATIVE|[1916161,1916278]|118 HSP 1 e-value: 2.0E-45 bit: 182.0 Len: 112 Query Start:3 Query End:114 Subject Strand: POSITIVE Subject Start: 3 Subject End: 114 ..tttctctcctcttttattctgttactattttaccataaaagcgcaggctcttcatgaaaatcatcagaaaagtttgccagtctttaaaaatcaagtgaagactctaaaaatt........................................ ..tttctctcctcttttattctgttactattttaccataaaagcgcaggctcttcatgaaaatcatcagaaaagtttgccagtctttaaaagtcaggtgaaagccctaaaaatt........................................ Subject: NC_003098_spr1924_spr1925|aspartyl-tRNA synthetase:hypothetical protein|NEGATIVE:NEGATIVE|[1908629,1908979]|351 HSP 1 e-value: 2.0E-45 bit: 182.0 Len: 112 Query Start:3 Query End:114 Subject Strand: POSITIVE Subject Start: 3 Subject End: 114 ..tttctctcctcttttattctgttactattttaccataaaagcgcaggctcttcatgaaaatcatcagaaaagtttgccagtctttaaaaatcaagtgaagactctaaaaatt........................................ ..tttctctcctcttttattctgttactattttaccataaaagcgcaggctcttcatgaaaatcatcagaaaagtttgccagtctttaaaagtcaggtgaaagccctaaaaatt........................................ Subject: NC_003028_SP_2114_SP_2115|aspartyl-tRNA synthetase:hypothetical protein|NEGATIVE:NEGATIVE|[2029292,2029642]|351 HSP 1 e-value: 2.0E-45 bit: 182.0 Len: 112 Query Start:3 Query End:114 Subject Strand: POSITIVE Subject Start: 3 Subject End: 114 ..tttctctcctcttttattctgttactattttaccataaaagcgcaggctcttcatgaaaatcatcagaaaagtttgccagtctttaaaaatcaagtgaagactctaaaaatt........................................ ..tttctctcctcttttattctgttactattttaccataaaagcgcaggctcttcatgaaaatcatcagaaaagtttgccagtctttaaaagtcaggtgaaagccctaaaaatt........................................ Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUCUCUCCUCUUUUAUUCUGUUACUAUUUUACCAUAAAAGCGCAGGCUCUUCAUGAAAAUCAUCAGAAAAGUUUGCCAGUCUUUAAAAAUCAAGUGAAGACUCUAAAAAUU ..........(((((((..((.........))..))))))).(((((((.(((.(((......)))))).))))))).((((((((.........))))))))......... (-17.70) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAUUUUUAGAGUCUUCACUUGAUUUUUAAAGACUGGCAAACUUUUCUGAUGAUUUUCAUGAAGAGCCUGCGCUUUUAUGGUAAAAUAGUAACAGAAUAAAAGAGGAGAGAAA ...........(((((...................(((..(((((((((......))).))))))..))).(((((((.((.........))...))))))).))))).... (-19.60) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 876 80 31 173 124 smit:SMT_1148|5end_aspartyl-tRNA_synthetase_1093885..1094115_NEGATIVE 295 57 11 131 81 smit:SMT_651|5end_DNA_ligase_561944..562174_NEGATIVE 288 47 9 139 99 smit:SMT_1517|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1498313..1498543_POSITIVE 280 50 5 122 83 smit:SMT_378|5end_hypothetical_protein_predicted_by_Glimmer/Critica_315884..316114_POSITIVE 261 50 4 143 96 smit:SMT_91|5end_hypothetical_protein_22578..22808_POSITIVE 259 58 33 79 54 smit:SMT_1142|5end_K02027_multiple_sugar_transport_system_substrate-binding_protein_1085546..1085776_POSITIVE 257 84 42 163 120 smit:SMT_954|5end_cation-transporting_ATPase,_E1-E2_family_904025..904255_NEGATIVE 257 47 7 147 99 smit:SMT_145|5end_hypothetical_protein_95873..96103_POSITIVE 256 47 7 204 170 smit:SMT_878|5end_excinuclease_ABC,_subunit_C_826249..826479_NEGATIVE 253 36 1 128 86 smit:SMT_431|5end_UDP-N-acetylmuramoyl-L-alanyl-D-glutamate_synthetase_372199..372429_POSITIVE 253 47 7 137 98 smit:SMT_232|5end_DNA_polymerase_III,_alpha_subunit,_Gram-positive_type_168246..168476_POSITIVE 252 48 4 140 81 smit:SMT_966|5end_transcriptional_regulator,_TetR_family_912191..912421_NEGATIVE 252 54 15 135 91 smit:SMT_266|5end_S-adenosyl-methyltransferase_204190..204420_POSITIVE 251 87 44 99 52 smit:SMT_1794|5end_SOS_responce_UmuC_protein_1769074..1769304_NEGATIVE 243 50 2 140 99 smit:SMT_1540|5end_hypothetical_protein_1525005..1525235_NEGATIVE 242 49 1 76 18 smit:SMT_1667|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1657567..1657797_NEGATIVE 242 49 1 176 118 smit:SMT_1666|5end_hypothetical_protein_1657467..1657697_NEGATIVE 241 79 31 59 10 smit:SMT_1876|5end_transcriptional_regulator,_MarR_family_1833594..1833824_POSITIVE 240 77 39 171 126 smit:SMT_1698|5end_CMP-binding_factor_1680092..1680322_POSITIVE 240 46 4 211 162 smit:SMT_1494|5end_nucleoside_diphosphate_kinase_1479500..1479730_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 305 43 2 62 22 smit:SMT_1545|3end_choline-binding_protein_1529160..1529310_NEGATIVE 261 50 4 78 31 smit:SMT_90|3end_DNA_polymerase_III_beta_subunit_22593..22743_POSITIVE 252 48 4 116 57 smit:SMT_967|3end_K01992_ABC-2_type_transport_system_permease_protein_912215..912365_NEGATIVE 249 57 20 67 29 smit:SMT_1106|3end_ribonuclease_P_protein_component_1047601..1047751_NEGATIVE 243 50 2 62 21 smit:SMT_1541|3end_isopentenyl-diphosphate_delta-isomerase_1525083..1525233_NEGATIVE 240 46 4 125 76 smit:SMT_1493|3end_DNA-directed_RNA_polymerase,_beta'_subunit/160_kD_subunit_1479494..1479644_POSITIVE 239 38 4 46 13 smit:SMT_1375|3end_putative_glucose-inhibited_division_protein_1353104..1353254_NEGATIVE 238 80 31 77 19 smit:SMT_777|3end_hypothetical_protein_686618..686768_NEGATIVE 233 46 5 149 104 smit:SMT_746|3end_LPS_biosynthesis_protein_650377..650527_NEGATIVE 231 57 24 38 2 smit:SMT_652|3end_transporter,_putative_562037..562187_NEGATIVE 230 76 31 70 15 smit:SMT_1431|3end_K08986_putative_membrane_protein_1416654..1416804_POSITIVE 230 43 3 144 101 smit:SMT_282|3end_hypothetical_protein_225446..225596_POSITIVE 224 56 24 147 115 smit:SMT_1366|3end_K02238_competence_protein_ComEC_1344648..1344798_NEGATIVE 221 105 61 57 12 smit:SMT_315|3end_acetyl-coenzyme_A_carboxylase_carboxyl_transferase_subunit_beta_256627..256777_POSITIVE 219 43 2 112 78 smit:SMT_1200|3end_K06148_ATP-binding_cassette,_subfamily_C,_bacterial_1161076..1161226_NEGATIVE 218 50 7 52 7 smit:SMT_1486|3end_hypothetical_protein_1466444..1466594_POSITIVE 218 79 33 151 113 smit:SMT_278|3end_tyrosine-protein_kinase_221048..221198_POSITIVE 215 50 7 92 49 smit:SMT_1251|3end_hypothetical_protein_1211329..1211479_NEGATIVE 213 56 13 95 38 smit:SMT_1786|3end_phenylalanyl-tRNA_synthetase_beta_chain_1763235..1763385_NEGATIVE 213 90 41 82 32 smit:SMT_345|3end_K01990_ABC-2_type_transport_system_ATP-binding_protein_284803..284953_POSITIVE