Origin IGS: actttttatcctatttaaagttttgtcagttcattatatcataaatccttggaatgtgggcaattcatccgctttttcaagcctgagggcataaaataaggacagaatgtcaactaaaaatccaaactcacccagcctgtccaaactgcgaggccaataagcttgaaaccagacaccttctaaacgtatgagtcaaaacaaaaaacagcccgcaagctgtttatttct .........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 agaaataaacagcttgcgggctgttttttgttttgactcatacgtttagaaggtgtctggtttcaagcttattggcctcgcagtttggacaggctgggtgagtttggatttttagttgacattctgtccttattttatgccctcaggcttgaaaaagcggatgaattgcccacattccaaggatttatgatataatgaactgacaaaactttaaataggataaaaagt Mask Tandem Repeat Region ================================================ actttttatcctatttaaagttttgtcagttcattatatcataaatccttggaatgtgggcaattcatccgctttttcaagcctgagggcataaaataaggacagaatgtcaactaaaaatccaaactcacccagcctgtccaaactgcgaggccaataagcttgaaaccagacaccttctaaacgtatgagtcaaaacaaaaaacagcccgcaagctgtttatttct Find is-nt database================================================ Query_seq: SSA_2073:SSA_2074|SSA_2073:SSA_2074:Undecaprenyl pyrophosphate synthetase, putative:Preprotein translocase subunit YajC, putative:<-<-:2076462..2076689 228 actttttatcctatttaaagttttgtcagttcattatatcataaatccttggaatgtgggcaattcatccgctttttcaagcctgagggcataaaataaggacagaatgtcaactaaaaatccaaactcacccagcctgtccaaactgcgaggccaataagcttgaaaccagacaccttctaaacgtatgagtcaaaacaaaaaacagcccgcaagctgtttatttct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_2073:SSA_2074|SSA_2073:SSA_2074:Undecaprenyl pyrophosphate synthetase, putative:Preprotein translocase subunit YajC, putative:<-<-:2076462..2076689 228 actttttatcctatttaaagttttgtcagttcattatatcataaatccttggaatgtgggcaattcatccgctttttcaagcctgagggcataaaataaggacagaatgtcaactaaaaatccaaactcacccagcctgtccaaactgcgaggccaataagcttgaaaccagacaccttctaaacgtatgagtcaaaacaaaaaacagcccgcaagctgtttatttct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_2073:SSA_2074|SSA_2073:SSA_2074:Undecaprenyl pyrophosphate synthetase, putative:Preprotein translocase subunit YajC, putative:<-<-:2076462..2076689 228 actttttatcctatttaaagttttgtcagttcattatatcataaatccttggaatgtgggcaattcatccgctttttcaagcctgagggcataaaataaggacagaatgtcaactaaaaatccaaactcacccagcctgtccaaactgcgaggccaataagcttgaaaccagacaccttctaaacgtatgagtcaaaacaaaaaacagcccgcaagctgtttatttct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 actttttatcctatttaaagttttgtcagttcattatatcataaatccttggaatgtgggcaattcatccgctttttcaagcctgagggcataaaataaggacagaatgtcaactaaaaatccaaactcacccagcctgtccaaactgcgaggccaataagcttgaaaccagacaccttctaaacgtatgagtcaaaacaaaaaacagcccgcaagctgtttatttct Predict ORF larger than 30AA ================================================ Protein_Len: 31 Strand: + Start: 96 End: 188 ............................................................................................... M R T E C Q L K I Q T H P A C P N C E A N K L E T R H L L N V ........................................ Protein_Len: 51 Strand: - Start: 37 End: 189 .................................... I M F G Q F T P L E D A K E L R L A Y F L S L I D V L F G F E G L R D L S R P W Y A Q F W V G E L R M ....................................... actttttatcctatttaaagttttgtcagttcattatatcataaatccttggaatgtgggcaattcatccgctttttcaagcctgagggcataaaataaggacagaatgtcaactaaaaatccaaactcacccagcctgtccaaactgcgaggccaataagcttgaaaccagacaccttctaaacgtatgagtcaaaacaaaaaacagcccgcaagctgtttatttct 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: 86 Start: 13 End: 42 ............ATTTAAAGTTTTGTCAGTTCATTATATCAT.......................................................................................................................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ actttttatcctatttaaagttttgtcagttcattatatcataaatccttggaatgtgggcaattcatccgctttttcaagcctgagggcataaaataaggacagaatgtcaactaaaaatccaaactcacccagcctgtccaaactgcgaggccaataagcttgaaaccagacaccttctaaacgtatgagtcaaaacaaaaaacagcccgcaagctgtttatttct Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_2073:SSA_2074|SSA_2073:SSA_2074:Undecaprenyl pyrophosphate synthetase, putative:Preprotein translocase subunit YajC, putative:<-<-:2076462..2076689 228 actttttatcctatttaaagttttgtcagttcattatatcataaatccttggaatgtgggcaattcatccgctttttcaagcctgagggcataaaataaggacagaatgtcaactaaaaatccaaactcacccagcctgtccaaactgcgaggccaataagcttgaaaccagacaccttctaaacgtatgagtcaaaacaaaaaacagcccgcaagctgtttatttct Intra-Species Hit: Count: 1 Min: 1 Max: 228 Len: 228 Subject: NC_009009_SSA_2073_SSA_2074|Undecaprenyl pyrophosphate synthetase, putative:Preprotein translocase subunit YajC, putative|NEGATIVE:NEGATIVE|[2076462,2076689]|228 HSP 1 e-value: 1.0E-126 bit: 452.0 Len: 228 Query Start:1 Query End:228 Subject Strand: POSITIVE Subject Start: 1 Subject End: 228 actttttatcctatttaaagttttgtcagttcattatatcataaatccttggaatgtgggcaattcatccgctttttcaagcctgagggcataaaataaggacagaatgtcaactaaaaatccaaactcacccagcctgtccaaactgcgaggccaataagcttgaaaccagacaccttctaaacgtatgagtcaaaacaaaaaacagcccgcaagctgtttatttct actttttatcctatttaaagttttgtcagttcattatatcataaatccttggaatgtgggcaattcatccgctttttcaagcctgagggcataaaataaggacagaatgtcaactaaaaatccaaactcacccagcctgtccaaactgcgaggccaataagcttgaaaccagacaccttctaaacgtatgagtcaaaacaaaaaacagcccgcaagctgtttatttct Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ ACUUUUUAUCCUAUUUAAAGUUUUGUCAGUUCAUUAUAUCAUAAAUCCUUGGAAUGUGGGCAAUUCAUCCGCUUUUUCAAGCCUGAGGGCAUAAAAUAAGGACAGAAUGUCAACUAAAAAUCCAAACUCACCCAGCCUGUCCAAACUGCGAGGCCAAUAAGCUUGAAACCAGACACCUUCUAAACGUAUGAGUCAAAACAAAAAACAGCCCGCAAGCUGUUUAUUUCU ...................((((((.(...........(((((.....((((((.(((.((.........))..((((((((.((..(((.........((((((..((.......................))..))))))..........)))..)).)))))))).....))).))))))...)))))).))))))...(((((((......)))))))...... (-45.61) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGAAAUAAACAGCUUGCGGGCUGUUUUUUGUUUUGACUCAUACGUUUAGAAGGUGUCUGGUUUCAAGCUUAUUGGCCUCGCAGUUUGGACAGGCUGGGUGAGUUUGGAUUUUUAGUUGACAUUCUGUCCUUAUUUUAUGCCCUCAGGCUUGAAAAAGCGGAUGAAUUGCCCACAUUCCAAGGAUUUAUGAUAUAAUGAACUGACAAAACUUUAAAUAGGAUAAAAAGU .(((((((((((((....))))))...))))))).........(((((((.(.((((.((((((((((((((..((((..(......)..))))..).)))))))).............(((...((((((.(((((.(((....))).)))))....(((((.........))))).))))))..))).......)))))))))...))))))))............ (-50.90) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 943 90 41 181 132 NC_009009:SSA_2073|5end_Undecaprenyl_pyrophosphate_synthetase,_putative_2076371..2076601_NEGATIVE 382 90 46 212 163 NC_009009:SSA_1897|5end_Ribosomal_protein_HS6-type_(S12/L30/L7a),_putative_1894450..1894680_NEGATIVE 352 168 121 69 20 NC_009009:SSA_0375|5end_D-methionine-binding_lipoprotein_(ABC-type_transporter),_putative_364257..364487_POSITIVE 343 90 46 221 181 NC_009009:SSA_0704|5end_Isocitrate_dehydrogenase_[NADP],_putative_689274..689504_POSITIVE 340 177 132 67 22 NC_009009:SSA_1891|5end_Oxidoreductase,_aldo/keto_reductase_family,_putative_1888991..1889221_NEGATIVE 337 90 48 218 169 NC_009009:SSA_1379|5end_hypothetical_protein_1398528..1398758_NEGATIVE 328 153 119 197 160 NC_009009:SSA_0659|5end_hypothetical_protein_643003..643233_POSITIVE 322 96 51 60 13 NC_009009:SSA_0320|5end_hypothetical_protein_313406..313636_POSITIVE 316 176 133 75 16 NC_009009:SSA_0565|5end_hypothetical_protein_557230..557460_POSITIVE 315 90 46 49 1 NC_009009:SSA_1232|5end_Topoisomerase_IV_subunit_B,_putative_1256755..1256985_NEGATIVE 314 174 133 139 95 NC_009009:SSA_0834|5end_Accessory_secretory_protein_Asp2,_putative_819510..819740_POSITIVE 312 178 133 187 131 NC_009009:SSA_0583|5end_Nucleotidyltransferase,_putative_574505..574735_POSITIVE 311 111 73 58 21 NC_009009:SSA_2223|5end_Capsular_polysaccharide_biosynthesis_protein_Wzd_(chain_length_regulator),_putative_2224703..2224933_NEGATIVE 310 165 124 56 9 NC_009009:SSA_0715|5end_DNA_uptake_protein,_putative_700726..700956_POSITIVE 307 175 131 202 161 NC_009009:SSA_0470|5end_Precorrin-4_methylase,_putative_472879..473109_POSITIVE 306 180 131 105 42 NC_009009:SSA_0508|5end_Conserved_uncharacterized_protein,_possible_phosphoserine_phosphatase_506668..506898_POSITIVE 304 167 121 157 95 NC_009009:SSA_2042|5end_hypothetical_protein_2047073..2047303_NEGATIVE 303 175 131 74 26 NC_009009:SSA_2062|5end_hypothetical_protein_2063521..2063751_NEGATIVE 303 173 132 229 179 NC_009009:SSA_1835|5end_Late_competence_protein,_putative_1830941..1831171_NEGATIVE 302 172 133 126 95 NC_009009:SSA_1644|5end_hypothetical_protein_1645617..1645847_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 322 96 51 70 23 NC_009009:SSA_0319|3end_Branched-chain_amino_acid_permease_(L-methionine,_L-isoleucine,_leucine_and_valine),_putative_313496..313646_POSITIVE 314 174 133 149 105 NC_009009:SSA_0833|3end_Accessory_secretory_protein_Asp1,_putative_819600..819750_POSITIVE 311 111 73 50 13 NC_009009:SSA_2224|3end_Phosphotyrosine-protein_phosphatase,_putative_2224711..2224861_NEGATIVE 302 172 133 142 111 NC_009009:SSA_1645|3end_hypothetical_protein_1645601..1645751_NEGATIVE 293 165 127 62 22 NC_009009:SSA_0376|3end_ABC-type_methionine_transporter,_ATPase_component,_putative_366526..366676_POSITIVE 291 178 132 142 101 NC_009009:SSA_1960|3end_hypothetical_protein_1956571..1956721_NEGATIVE 286 90 46 80 34 NC_009009:SSA_1364|3end_hypothetical_protein_1380482..1380632_NEGATIVE 285 156 118 55 20 NC_009009:SSA_0388|3end_Mismatch_repair_ATPase_(MutS_family),_putative_384248..384398_POSITIVE 285 120 71 64 10 NC_009009:SSA_0350|3end_Helicase,_putative_341852..342002_NEGATIVE 283 157 122 45 9 NC_009009:SSA_2142|3end_Argininosuccinate_synthase,_putative_2142216..2142366_NEGATIVE 283 180 136 64 4 NC_009009:SSA_1384|3end_hypothetical_protein_1401715..1401865_NEGATIVE 282 177 131 135 85 NC_009009:SSA_1959|3end_Undecaprenyl-diphosphatase,_putative_1955589..1955739_NEGATIVE 282 97 51 91 48 NC_009009:SSA_0581|3end_Conserved_uncharacterized_protein_573774..573924_POSITIVE 278 178 134 145 94 NC_009009:SSA_1627|3end_hypothetical_protein_1629508..1629658_NEGATIVE 278 218 176 81 30 NC_009009:SSA_0812|3end_hypothetical_protein_794434..794584_POSITIVE 278 162 129 39 7 NC_009009:SSA_0604|3end_hypothetical_protein_592992..593142_POSITIVE 276 92 54 110 56 NC_009009:SSA_1342|3end_Carbamoyl-phosphate_synthase_small_chain,_putative_1359851..1360001_NEGATIVE 274 90 41 126 64 NC_009009:SSA_2090|3end_Hexulose-6-phosphate_synthase,_putative_2094343..2094493_NEGATIVE 274 165 127 139 101 NC_009009:SSA_0621|3end_SOS_responce_UmuC_protein,_putative_612322..612472_NEGATIVE 273 90 50 68 35 NC_009009:SSA_2044|3end_Cysteinyl-tRNA_synthetase,_putative_2047066..2047216_NEGATIVE