Origin IGS: agcctgccttttcctctagaaaatataggaacattataccatttttgccgataattctcatggagaatagtcccaaagcccgattagaactcaacgtccaaatagagctttaataactagcctcgtcatttccataaaaaacgaaaaagccactgcttccagtgacttcctaaggctcttacttctttcaaagtaagggc .........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 gcccttactttgaaagaagtaagagccttaggaagtcactggaagcagtggctttttcgttttttatggaaatgacgaggctagttattaaagctctatttggacgttgagttctaatcgggctttgggactattctccatgagaattatcggcaaaaatggtataatgttcctatattttctagaggaaaaggcaggct Mask Tandem Repeat Region ================================================ agcctgccttttcctctagaaaatataggaacattataccatttttgccgataattctcatggagaatagtcccaaagcccgattagaactcaacgtccaaatagagctttaataactagcctcgtcatttccataaaaaacgaaaaagccactgcttccagtgacttcctaaggctcttacttctttcaaagtaagggc Find is-nt database================================================ Query_seq: SSA_1452:SSA_1453|SSA_1452:SSA_1453:Second subunit of major exonuclease, putative:hypothetical protein:<-<-:1459787..1459986 200 agcctgccttttcctctagaaaatataggaacattataccatttttgccgataattctcatggagaatagtcccaaagcccgattagaactcaacgtccaaatagagctttaataactagcctcgtcatttccataaaaaacgaaaaagccactgcttccagtgacttcctaaggctcttacttctttcaaagtaagggc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_1452:SSA_1453|SSA_1452:SSA_1453:Second subunit of major exonuclease, putative:hypothetical protein:<-<-:1459787..1459986 200 agcctgccttttcctctagaaaatataggaacattataccatttttgccgataattctcatggagaatagtcccaaagcccgattagaactcaacgtccaaatagagctttaataactagcctcgtcatttccataaaaaacgaaaaagccactgcttccagtgacttcctaaggctcttacttctttcaaagtaagggc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_1452:SSA_1453|SSA_1452:SSA_1453:Second subunit of major exonuclease, putative:hypothetical protein:<-<-:1459787..1459986 200 agcctgccttttcctctagaaaatataggaacattataccatttttgccgataattctcatggagaatagtcccaaagcccgattagaactcaacgtccaaatagagctttaataactagcctcgtcatttccataaaaaacgaaaaagccactgcttccagtgacttcctaaggctcttacttctttcaaagtaagggc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 agcctgccttttcctctagaaaatataggaacattataccatttttgccgataattctcatggagaatagtcccaaagcccgattagaactcaacgtccaaatagagctttaataactagcctcgtcatttccataaaaaacgaaaaagccactgcttccagtgacttcctaaggctcttacttctttcaaagtaagggc Predict ORF larger than 30AA ================================================ Protein_Len: 37 Strand: + Start: 83 End: 193 .................................................................................. M R T Q R P N R A L I T S L V I S I K N E K A T A S S D F L R L L L L S K ....... Protein_Len: 34 Strand: - Start: 2 End: 103 . G A K E E L F Y L F M I G N K G I I R M S F L G L A R N S S L T W M ................................................................................................. agcctgccttttcctctagaaaatataggaacattataccatttttgccgataattctcatggagaatagtcccaaagcccgattagaactcaacgtccaaatagagctttaataactagcctcgtcatttccataaaaaacgaaaaagccactgcttccagtgacttcctaaggctcttacttctttcaaagtaagggc 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: 83 Start: 33 End: 62 ................................CATGAGAATTATCGGCAAAAATGGTATAAT.......................................................................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ agcctgccttttcctctagaaaatataggaacattataccatttttgccgataattctcatggagaatagtcccaaagcccgattagaactcaacgtccaaatagagctttaataactagcctcgtcatttccataaaaaacgaaaaagccactgcttccagtgacttcctaaggctcttacttctttcaaagtaagggc Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 50 HP_score: -2.5 Tail_Score: -3.61774 Start: 78 End: 108 Full_Region: aggctagttattaaa gctctatttggac gttga gttctaatcgggc tttgggactattctc .............................................................................gctctatttggacgttgagttctaatcgggc............................................................................................ Find igs database================================================ Query_seq: SSA_1452:SSA_1453|SSA_1452:SSA_1453:Second subunit of major exonuclease, putative:hypothetical protein:<-<-:1459787..1459986 200 agcctgccttttcctctagaaaatataggaacattataccatttttgccgataattctcatggagaatagtcccaaagcccgattagaactcaacgtccaaatagagctttaataactagcctcgtcatttccataaaaaacgaaaaagccactgcttccagtgacttcctaaggctcttacttctttcaaagtaagggc Intra-Species Hit: Count: 1 Min: 1 Max: 200 Len: 200 Subject: NC_009009_SSA_1452_SSA_1453|Second subunit of major exonuclease, putative:hypothetical protein|NEGATIVE:NEGATIVE|[1459787,1459986]|200 HSP 1 e-value: 7.0E-71 bit: 268.0 Len: 135 Query Start:1 Query End:135 Subject Strand: POSITIVE Subject Start: 1 Subject End: 135 agcctgccttttcctctagaaaatataggaacattataccatttttgccgataattctcatggagaatagtcccaaagcccgattagaactcaacgtccaaatagagctttaataactagcctcgtcatttccat................................................................. agcctgccttttcctctagaaaatataggaacattataccatttttgccgataattctcatggagaatagtcccaaagcccgattagaactcaacgtccaaatagagctttaataactagcctcgtcatttccat................................................................. HSP 2 e-value: 2.0E-21 bit: 103.0 Len: 52 Query Start:149 Query End:200 Subject Strand: POSITIVE Subject Start: 149 Subject End: 200 ....................................................................................................................................................gccactgcttccagtgacttcctaaggctcttacttctttcaaagtaagggc ....................................................................................................................................................gccactgcttccagtgacttcctaaggctcttacttctttcaaagtaagggc Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGCCUGCCUUUUCCUCUAGAAAAUAUAGGAACAUUAUACCAUUUUUGCCGAUAAUUCUCAUGGAGAAUAGUCCCAAAGCCCGAUUAGAACUCAACGUCCAAAUAGAGCUUUAAUAACUAGCCUCGUCAUUUCCAUAAAAAACGAAAAAGCCACUGCUUCCAGUGACUUCCUAAGGCUCUUACUUCUUUCAAAGUAAGGGC ..((((..(((((.....)))))..))))....................(((.((((((...)))))).))).....((((......................(((((((((..........((((..(((....)))..))))..(((.(((((....))))).)))..)))))))))(((((......))))).)))) (-39.10) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GCCCUUACUUUGAAAGAAGUAAGAGCCUUAGGAAGUCACUGGAAGCAGUGGCUUUUUCGUUUUUUAUGGAAAUGACGAGGCUAGUUAUUAAAGCUCUAUUUGGACGUUGAGUUCUAAUCGGGCUUUGGGACUAUUCUCCAUGAGAAUUAUCGGCAAAAAUGGUAUAAUGUUCCUAUAUUUUCUAGAGGAAAAGGCAGGCU (((((((((((....)))))))).(((((.(((((((((((....)))))))))))...(((((((.(((((((..(((..(((((.(((((((((.(((.((((.....)))).))).))))))))))))))..))).....(((((((((.......)))))....))))...)))))))))))))).))))).))). (-65.30) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 927 110 61 201 152 NC_009009:SSA_1452|5end_Second_subunit_of_major_exonuclease,_putative_1459696..1459926_NEGATIVE 320 200 159 173 137 NC_009009:SSA_1558|5end_Hydrolase,_HAD_superfamily_1560862..1561092_NEGATIVE 314 188 143 103 40 NC_009009:SSA_0992|5end_hypothetical_protein_993486..993716_POSITIVE 313 159 119 195 150 NC_009009:SSA_1897|5end_Ribosomal_protein_HS6-type_(S12/L30/L7a),_putative_1894450..1894680_NEGATIVE 303 134 95 54 16 NC_009009:SSA_2145|5end_Tributyrin_esterase,_putative_2146658..2146888_NEGATIVE 302 90 41 113 70 NC_009009:SSA_0241|5end_Ribosomal_protein_L11_methyltransferase,_putative_234021..234251_POSITIVE 297 200 151 67 16 NC_009009:SSA_0189|5end_Competence_protein_ComGF,_putative_191015..191245_POSITIVE 296 190 148 196 133 NC_009009:SSA_1721|5end_DNA_polymerase_III,_delta'_subunit,_putative_1708028..1708258_NEGATIVE 289 190 142 90 31 NC_009009:SSA_1948|5end_Oligopeptide-binding_lipoprotein_precursor,_putative_1942170..1942400_NEGATIVE 288 107 62 220 177 NC_009009:SSA_2338|5end_Conserved_uncharacterized_protein_2339272..2339502_POSITIVE 288 65 39 229 202 NC_009009:SSA_1956|5end_ABC-type_Fe-S_cluster_assembly_transporter,_ATPase_component,_putative_1953414..1953644_NEGATIVE 288 199 155 59 10 NC_009009:SSA_0469|5end_Precorrin-6B_methylase_2,putative_472310..472540_POSITIVE 288 79 46 217 174 NC_009009:SSA_0026|5end_Fatty_acid/phospholipid_synthesis_protein_plsX,_putative_30473..30703_POSITIVE 287 107 64 212 158 NC_009009:SSA_1012|5end_Phosphoenolpyruvate_synthase,_putative_1014739..1014969_POSITIVE 286 189 151 153 120 NC_009009:SSA_0311|5end_hypothetical_protein_305877..306107_POSITIVE 285 190 142 215 151 NC_009009:SSA_0251|5end_D-tyrosyl-tRNA(Tyr)_deacylase,_putative_244455..244685_POSITIVE 285 100 59 49 5 NC_009009:SSA_0181|5end_Glycosyltransferase_(vectorial_glycosyl_polymerization_(VGP)_family),_putative_184902..185132_POSITIVE 284 200 151 64 5 NC_009009:SSA_1900|5end_N_utilization_substance_protein_A,_putative_1896012..1896242_NEGATIVE 283 109 69 50 1 NC_009009:SSA_2350|5end_30S_ribosomal_protein_S4,_putative_2352648..2352878_NEGATIVE 280 190 149 41 5 NC_009009:SSA_1557|5end_SRPR,_signal_recognition_particle-docking_protein,_putative_1560040..1560270_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 395 80 33 72 34 NC_009009:SSA_0931|3end_hypothetical_protein_941335..941485_POSITIVE 354 75 39 151 112 NC_009009:SSA_1957|3end_Glycosyl_transferase_N-acetylglucosaminyltransferase,_putative_1953504..1953654_NEGATIVE 313 178 142 141 111 NC_009009:SSA_0273|3end_hypothetical_protein_268566..268716_POSITIVE 297 200 151 83 32 NC_009009:SSA_0188|3end_hypothetical_protein_191111..191261_POSITIVE 293 175 142 136 111 NC_009009:SSA_2260|3end_DNA_mismatch_repair_protein_hexA,_putative_2255601..2255751_NEGATIVE 292 92 56 151 109 NC_009009:SSA_0871|3end_Cell_division_protein_FtsX,_putative_864627..864777_POSITIVE 290 190 141 104 54 NC_009009:SSA_1435|3end_hypothetical_protein_1441751..1441901_NEGATIVE 288 199 155 87 38 NC_009009:SSA_0468|3end_Precorrin-6y_C5,15-methyltransferase-like,_putative_472418..472568_POSITIVE 285 190 142 146 82 NC_009009:SSA_0250|3end_GTP_pyrophosphokinase,_putative_244466..244616_POSITIVE 285 100 59 56 12 NC_009009:SSA_0180|3end_hypothetical_protein_184989..185139_POSITIVE 280 190 149 37 1 NC_009009:SSA_1558|3end_Hydrolase,_HAD_superfamily_1560044..1560194_NEGATIVE 270 127 90 42 5 NC_009009:SSA_1013|3end_Phosphatidylserine_synthase,_putative_1017933..1018083_POSITIVE 266 200 151 144 88 NC_009009:SSA_0333|3end_Mevalonate_kinase,_putative_327953..328103_POSITIVE 261 190 148 69 19 NC_009009:SSA_1668|3end_NrdI_protein,_putative_1667738..1667888_NEGATIVE 261 190 143 106 45 NC_009009:SSA_1306|3end_Trk_transporter_NAD+_binding_protein-K+_transport,_putative_1324245..1324395_NEGATIVE 260 199 159 88 46 NC_009009:SSA_1379|3end_hypothetical_protein_1398178..1398328_NEGATIVE 260 190 148 54 1 NC_009009:SSA_0028|3end_Phosphoribosylaminoimidazole-succinocarboxamide_synthase,_putative_32670..32820_POSITIVE 259 41 1 102 55 NC_009009:SSA_1371|3end_FmtA-like_protein,_putative_1387051..1387201_NEGATIVE 256 198 156 132 87 NC_009009:SSA_0932|3end_hypothetical_protein_942804..942954_POSITIVE 256 82 47 147 116 NC_009009:SSA_0788|3end_Proton-translocating_ATPase,_F1_sector,_beta_subunit,_putative_772523..772673_POSITIVE