Origin IGS: gggaaatttcattgacataggaaaatagaatcgcttcaaagggcgatttttatcttctttagataattgaaaaaaagcgctaaatccgctataataggtaggttgaaaggattgaaatactccgatgtaaaataaaaaacaaatactaagattcaccattatcctaaatgaaagaaagagaagaag .........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 cttcttctctttctttcatttaggataatggtgaatcttagtatttgttttttattttacatcggagtatttcaatcctttcaacctacctattatagcggatttagcgctttttttcaattatctaaagaagataaaaatcgccctttgaagcgattctattttcctatgtcaatgaaatttccc Mask Tandem Repeat Region ================================================ gggaaatttcattgacataggaaaatagaatcgcttcaaagggcgatttttatcttctttagataattgaaaaaaagcgctaaatccgctataataggtaggttgaaaggattgaaatactccgatgtaaaataaaaaacaaatactaagattcaccattatcctaaatgaaagaaagagaagaag Find is-nt database================================================ Query_seq: SSA_0697:SSA_0698|SSA_0697:SSA_0698:hypothetical protein:Peptide chain release factor 3, putative:->->:680337..680522 186 gggaaatttcattgacataggaaaatagaatcgcttcaaagggcgatttttatcttctttagataattgaaaaaaagcgctaaatccgctataataggtaggttgaaaggattgaaatactccgatgtaaaataaaaaacaaatactaagattcaccattatcctaaatgaaagaaagagaagaag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_0697:SSA_0698|SSA_0697:SSA_0698:hypothetical protein:Peptide chain release factor 3, putative:->->:680337..680522 186 gggaaatttcattgacataggaaaatagaatcgcttcaaagggcgatttttatcttctttagataattgaaaaaaagcgctaaatccgctataataggtaggttgaaaggattgaaatactccgatgtaaaataaaaaacaaatactaagattcaccattatcctaaatgaaagaaagagaagaag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_0697:SSA_0698|SSA_0697:SSA_0698:hypothetical protein:Peptide chain release factor 3, putative:->->:680337..680522 186 gggaaatttcattgacataggaaaatagaatcgcttcaaagggcgatttttatcttctttagataattgaaaaaaagcgctaaatccgctataataggtaggttgaaaggattgaaatactccgatgtaaaataaaaaacaaatactaagattcaccattatcctaaatgaaagaaagagaagaag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gggaaatttcattgacataggaaaatagaatcgcttcaaagggcgatttttatcttctttagataattgaaaaaaagcgctaaatccgctataataggtaggttgaaaggattgaaatactccgatgtaaaataaaaaacaaatactaagattcaccattatcctaaatgaaagaaagagaagaag Predict ORF larger than 30AA ================================================ Protein_Len: 38 Strand: - Start: 39 End: 152 ...................................... L A I K I K K L Y N F F L A L D A I I P L N F P N F Y E S T F Y F V F V L M .................................. Protein_Len: 54 Strand: - Start: 1 End: 162 P F K M S M P F Y F R K L P R N K D E K S L Q F F A S F G S Y Y T P Q F S Q F V G I Y F L F C I S L N V M M ........................ gggaaatttcattgacataggaaaatagaatcgcttcaaagggcgatttttatcttctttagataattgaaaaaaagcgctaaatccgctataataggtaggttgaaaggattgaaatactccgatgtaaaataaaaaacaaatactaagattcaccattatcctaaatgaaagaaagagaagaag 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: 91 Start: 66 End: 95 .................................................................ATTGAAAAAAAGCGCTAAATCCGCTATAAT........................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ gggaaatttcattgacataggaaaatagaatcgcttcaaagggcgatttttatcttctttagataattgaaaaaaagcgctaaatccgctataataggtaggttgaaaggattgaaatactccgatgtaaaataaaaaacaaatactaagattcaccattatcctaaatgaaagaaagagaagaag Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_0697:SSA_0698|SSA_0697:SSA_0698:hypothetical protein:Peptide chain release factor 3, putative:->->:680337..680522 186 gggaaatttcattgacataggaaaatagaatcgcttcaaagggcgatttttatcttctttagataattgaaaaaaagcgctaaatccgctataataggtaggttgaaaggattgaaatactccgatgtaaaataaaaaacaaatactaagattcaccattatcctaaatgaaagaaagagaagaag Intra-Species Hit: Count: 1 Min: 1 Max: 186 Len: 186 Subject: NC_009009_SSA_0697_SSA_0698|hypothetical protein:Peptide chain release factor 3, putative|POSITIVE:POSITIVE|[680337,680522]|186 HSP 1 e-value: 8.0E-89 bit: 327.0 Len: 186 Query Start:1 Query End:186 Subject Strand: POSITIVE Subject Start: 1 Subject End: 186 gggaaatttcattgacataggaaaatagaatcgcttcaaagggcgatttttatcttctttagataattgnnnnnnngcgctaaatccgctataataggtaggttgaaaggattgaaatactccgatgtaaaataaaaaacaaatactaagattcaccattatcctaaatgaaagaaagagaagaag gggaaatttcattgacataggaaaatagaatcgcttcaaagggcgatttttatcttctttagataattgaaaaaaagcgctaaatccgctataataggtaggttgaaaggattgaaatactccgatgtaaaataaaaaacaaatactaagattcaccattatcctaaatgaaagaaagagaagaag Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GGGAAAUUUCAUUGACAUAGGAAAAUAGAAUCGCUUCAAAGGGCGAUUUUUAUCUUCUUUAGAUAAUUGAAAAAAAGCGCUAAAUCCGCUAUAAUAGGUAGGUUGAAAGGAUUGAAAUACUCCGAUGUAAAAUAAAAAACAAAUACUAAGAUUCACCAUUAUCCUAAAUGAAAGAAAGAGAAGAAG ......(((((((....(((((.....((((((((......))))))))((((((.....)))))).........((((.......))))......(((..(((....(((.........)))..(((..........)))........)))..)))....))))))))))))............. (-29.90) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CUUCUUCUCUUUCUUUCAUUUAGGAUAAUGGUGAAUCUUAGUAUUUGUUUUUUAUUUUACAUCGGAGUAUUUCAAUCCUUUCAACCUACCUAUUAUAGCGGAUUUAGCGCUUUUUUUCAAUUAUCUAAAGAAGAUAAAAAUCGCCCUUUGAAGCGAUUCUAUUUUCCUAUGUCAAUGAAAUUUCCC .............((((((((((((.(((((............((((((((((..........(((.........)))..................((((.......)))).................))))))))))((((((........))))))))))).)))))....)))))))...... (-27.40) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 285 117 80 84 43 NC_009009:SSA_1518|5end_Glycosyl_transferase,_putative_1524787..1525017_NEGATIVE 258 69 24 48 2 NC_009009:SSA_1086|5end_TRNA_nucleotidyltransferase,_putative_1103328..1103558_POSITIVE 249 55 11 213 180 NC_009009:SSA_1268|5end_Chorismate_mutase/prephenate_dehydratase,_putative_1291610..1291840_NEGATIVE 244 127 93 47 8 NC_009009:SSA_0842|5end_Effector_of_murein_hydrolase_LrgA/holin-like_protein,_putative_827330..827560_POSITIVE 242 90 53 134 98 NC_009009:SSA_2012|5end_hypothetical_protein_2013470..2013700_NEGATIVE 240 110 66 48 17 NC_009009:SSA_0736|5end_Catabolite_gene_activator_and_regulatory_subunit_of_cAMP-dependent_protein_kinases,_putative_717648..717878_POSITIVE 240 69 25 59 8 NC_009009:SSA_0674|5end_Exodeoxyribonuclease_VII_large_subunit,_putative_657071..657301_POSITIVE 239 127 85 80 33 NC_009009:SSA_0537|5end_Propanediol_utilization:dioldehydratase_reactivation,_putative_531957..532187_POSITIVE 239 45 1 203 167 NC_009009:SSA_0051|5end_Dihydroxyacetone_kinase_phosphotransfer_protein,_putative_55190..55420_POSITIVE 238 64 26 66 10 NC_009009:SSA_0286|5end_Transaldolase-like_protein,_putative_278814..279044_POSITIVE 237 113 76 214 172 NC_009009:SSA_1877|5end_hypothetical_protein_1871659..1871889_POSITIVE 234 59 27 33 5 NC_009009:SSA_0078|5end_N-acetylneuraminate_lyase,_putative_81904..82134_POSITIVE 233 90 41 137 80 NC_009009:SSA_0838|5end_GtfB,_putative_825406..825636_POSITIVE 230 58 12 187 132 NC_009009:SSA_1990|5end_Zn-porter_lipoprotein,_putative_1986319..1986549_NEGATIVE 230 114 75 38 3 NC_009009:SSA_0198|5end_Dihydrofolate_synthetase,_putative_196901..197131_POSITIVE 227 124 85 51 11 NC_009009:SSA_1026|5end_ABC-type_multidrug_transporter,_ATPase_component,_putative_1042794..1043024_POSITIVE 226 90 47 61 18 NC_009009:SSA_1412|5end_hypothetical_protein_1424095..1424325_NEGATIVE 226 90 47 196 153 NC_009009:SSA_1411|5end_Glucose-1-phosphate_thymidylytransferase,_putative_1423960..1424190_NEGATIVE 224 128 86 87 49 NC_009009:SSA_1274|5end_hypothetical_protein_1297454..1297684_NEGATIVE 223 60 12 190 140 NC_009009:SSA_0624|5end_hypothetical_protein_615079..615309_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 288 58 16 79 36 NC_009009:SSA_0756|3end_Alanyl-tRNA_synthetase,_putative_739434..739584_POSITIVE 285 117 80 76 35 NC_009009:SSA_1519|3end_Polysaccharide/teichoic_acid_transporter,_putative_1524795..1524945_NEGATIVE 274 110 75 132 104 NC_009009:SSA_0611|3end_HtpX_protease,_putative_600515..600665_POSITIVE 265 47 1 69 21 NC_009009:SSA_1367|3end_hypothetical_protein_1383828..1383978_POSITIVE 258 69 24 51 5 NC_009009:SSA_1085|3end_Dihydrodipicolinate_reductase,_putative_1103411..1103561_POSITIVE 247 60 12 89 37 NC_009009:SSA_0888|3end_Magnesium/cobalt_transporter,_putative_882749..882899_POSITIVE 242 90 53 134 98 NC_009009:SSA_2013|3end_hypothetical_protein_2013470..2013620_NEGATIVE 239 104 67 73 32 NC_009009:SSA_2286|3end_Dihydroxy-acid_dehydratase,_putative_2287878..2288028_NEGATIVE 239 80 33 98 50 NC_009009:SSA_1980|3end_50S_ribosomal_protein_L28,_putative_1974444..1974594_NEGATIVE 230 114 75 36 1 NC_009009:SSA_0197|3end_Dihydropteroate_synthase,_putative_196979..197129_POSITIVE 228 103 68 113 78 NC_009009:SSA_0884|3end_hypothetical_protein_878725..878875_NEGATIVE 228 71 33 108 71 NC_009009:SSA_0070|3end_Acetylxylan_esterase,_putative_74914..75064_POSITIVE 227 116 76 49 9 NC_009009:SSA_1036|3end_Deoxyribose-phosphate_aldolase,_putative_1052211..1052361_POSITIVE 227 88 41 150 96 NC_009009:SSA_0837|3end_Glucosyltransferase,_putative_825502..825652_POSITIVE 226 90 47 61 18 NC_009009:SSA_1413|3end_GufA-like_protein,_putative_1424095..1424245_NEGATIVE 223 60 12 111 61 NC_009009:SSA_0623|3end_hypothetical_protein_615080..615230_POSITIVE 223 158 111 101 56 NC_009009:SSA_0289|3end_Leucyl-tRNA_synthetase,_putative_283999..284149_POSITIVE 219 130 88 148 85 NC_009009:SSA_0725|3end_hypothetical_protein_710812..710962_POSITIVE 217 58 29 35 4 NC_009009:SSA_1816|3end_hypothetical_protein_1800927..1801077_NEGATIVE 215 118 76 127 78 NC_009009:SSA_0735|3end_Integral_membrane_protein,_putative_717680..717830_POSITIVE