Origin IGS: aggaattgctttcagcagatagtagacaaagtgcctatgctatattataatgaaagcagtaacaaccgtttcgacaccaaggggtattccttgctggatgtaaaaaatatttaaggagtctact .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 agtagactccttaaatattttttacatccagcaaggaataccccttggtgtcgaaacggttgttactgctttcattataatatagcataggcactttgtctactatctgctgaaagcaattcct Mask Tandem Repeat Region ================================================ aggaattgctttcagcagatagtagacaaagtgcctatgctatattataatgaaagcagtaacaaccgtttcgacaccaaggggtattccttgctggatgtaaaaaatatttaaggagtctact Find is-nt database================================================ Query_seq: SSA_0780:SSA_0781|SSA_0780:SSA_0781:Acid phosphatase (PAP2 family), putative:Mannose-6-phosphate isomerase, putative:->->:765389..765512 124 aggaattgctttcagcagatagtagacaaagtgcctatgctatattataatgaaagcagtaacaaccgtttcgacaccaaggggtattccttgctggatgtaaaaaatatttaaggagtctact Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_0780:SSA_0781|SSA_0780:SSA_0781:Acid phosphatase (PAP2 family), putative:Mannose-6-phosphate isomerase, putative:->->:765389..765512 124 aggaattgctttcagcagatagtagacaaagtgcctatgctatattataatgaaagcagtaacaaccgtttcgacaccaaggggtattccttgctggatgtaaaaaatatttaaggagtctact Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_0780:SSA_0781|SSA_0780:SSA_0781:Acid phosphatase (PAP2 family), putative:Mannose-6-phosphate isomerase, putative:->->:765389..765512 124 aggaattgctttcagcagatagtagacaaagtgcctatgctatattataatgaaagcagtaacaaccgtttcgacaccaaggggtattccttgctggatgtaaaaaatatttaaggagtctact Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aggaattgctttcagcagatagtagacaaagtgcctatgctatattataatgaaagcagtaacaaccgtttcgacaccaaggggtattccttgctggatgtaaaaaatatttaaggagtctact Predict ORF larger than 30AA ================================================ Protein_Len: 31 Strand: + Start: 19 End: 111 .................. M V D K V P M L Y Y N E S S N N R F D T K G Y S L L D V K N I ............. aggaattgctttcagcagatagtagacaaagtgcctatgctatattataatgaaagcagtaacaaccgtttcgacaccaaggggtattccttgctggatgtaaaaaatatttaaggagtctact 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: 22 End: 51 .....................GTAGACAAAGTGCCTATGCTATATTATAAT......................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ aggaattgctttcagcagatagtagacaaagtgcctatgctatattataatgaaagcagtaacaaccgtttcgacaccaaggggtattccttgctggatgtaaaaaatatttaaggagtctact Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_0780:SSA_0781|SSA_0780:SSA_0781:Acid phosphatase (PAP2 family), putative:Mannose-6-phosphate isomerase, putative:->->:765389..765512 124 aggaattgctttcagcagatagtagacaaagtgcctatgctatattataatgaaagcagtaacaaccgtttcgacaccaaggggtattccttgctggatgtaaaaaatatttaaggagtctact Intra-Species Hit: Count: 1 Min: 1 Max: 124 Len: 124 Subject: NC_009009_SSA_0780_SSA_0781|Acid phosphatase (PAP2 family), putative:Mannose-6-phosphate isomerase, putative|POSITIVE:POSITIVE|[765389,765512]|124 HSP 1 e-value: 1.0E-64 bit: 246.0 Len: 124 Query Start:1 Query End:124 Subject Strand: POSITIVE Subject Start: 1 Subject End: 124 aggaattgctttcagcagatagtagacaaagtgcctatgctatattataatgaaagcagtaacaaccgtttcgacaccaaggggtattccttgctggatgtaaaaaatatttaaggagtctact aggaattgctttcagcagatagtagacaaagtgcctatgctatattataatgaaagcagtaacaaccgtttcgacaccaaggggtattccttgctggatgtaaaaaatatttaaggagtctact Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGGAAUUGCUUUCAGCAGAUAGUAGACAAAGUGCCUAUGCUAUAUUAUAAUGAAAGCAGUAACAACCGUUUCGACACCAAGGGGUAUUCCUUGCUGGAUGUAAAAAAUAUUUAAGGAGUCUACU .(..((((((((((....((((((.....(((......))).))))))..))))))))))..).........(((.((...(((((((..((((.....))))..)))))))..)).))).... (-28.20) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGUAGACUCCUUAAAUAUUUUUUACAUCCAGCAAGGAAUACCCCUUGGUGUCGAAACGGUUGUUACUGCUUUCAUUAUAAUAUAGCAUAGGCACUUUGUCUACUAUCUGCUGAAAGCAAUUCCU (((((((.......(((((.........((.(((((......))))).))..((((((((....)))).)))).....))))).((....)).....)))))))...(((.....)))...... (-26.10) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 295 44 3 219 186 NC_009009:SSA_1242|5end_Dihydroorotate_dehydrogenase_B,_putative_1267386..1267616_NEGATIVE 295 41 8 200 166 NC_009009:SSA_0197|5end_Dihydropteroate_synthase,_putative_195946..196176_POSITIVE 280 95 55 47 11 NC_009009:SSA_2359|5end_Glucose_inhibited_division_protein_A,_putative_2362520..2362750_NEGATIVE 274 78 52 40 10 NC_009009:SSA_0118|5end_50S_ribosomal_protein_L24,_putative_113363..113593_POSITIVE 260 99 54 150 112 NC_009009:SSA_1251|5end_Hydrolase,_HD_superfamily,_putative_1276790..1277020_NEGATIVE 257 98 54 45 1 NC_009009:SSA_1261|5end_Ribose-5-phosphate_isomerase_A,_putative_1287654..1287884_NEGATIVE 253 100 56 177 122 NC_009009:SSA_0580|5end_Isochorismatase_family_protein,_putative_572816..573046_POSITIVE 252 42 1 75 32 NC_009009:SSA_2067|5end_hypothetical_protein_2070254..2070484_POSITIVE 252 99 51 191 135 NC_009009:SSA_0537|5end_Propanediol_utilization:dioldehydratase_reactivation,_putative_531957..532187_POSITIVE 250 100 52 156 84 NC_009009:SSA_2207|5end_hypothetical_protein_2207221..2207451_NEGATIVE 250 100 57 155 115 NC_009009:SSA_1076|5end_hypothetical_protein_1094227..1094457_POSITIVE 247 110 65 78 11 NC_009009:SSA_0297|5end_Malolactic_enzyme,_putative_289706..289936_POSITIVE 242 37 1 168 136 NC_009009:SSA_2354|5end_hypothetical_protein_2356237..2356467_NEGATIVE 241 102 61 217 178 NC_009009:SSA_2219|5end_UDP-glucose_4-epimerase,_putative_2220827..2221057_NEGATIVE 240 94 55 217 171 NC_009009:SSA_1700|5end_hypothetical_protein_1691288..1691518_NEGATIVE 240 98 55 189 137 NC_009009:SSA_0579|5end_Hydrolase,_HAD_superfamily,_putative_572220..572450_POSITIVE 239 40 1 49 8 NC_009009:SSA_0004|5end_Lipoprotein,_putative_3704..3934_NEGATIVE 237 99 55 176 117 NC_009009:SSA_2347|5end_Coenzyme_F390_synthetase,_putative_2349939..2350169_NEGATIVE 237 94 57 207 179 NC_009009:SSA_1797|5end_Aminodeoxychorismate_lyase,_putative_1779947..1780177_NEGATIVE 237 41 5 65 29 NC_009009:SSA_0457|5end_Fructokinase,_putative_460663..460893_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 317 99 53 146 104 NC_009009:SSA_0205|3end_NisK_(sensor-receptor_histidine_kinase_domain),_putative_203839..203989_POSITIVE 299 100 56 84 36 NC_009009:SSA_1540|3end_hypothetical_protein_1544915..1545065_NEGATIVE 291 67 21 151 101 NC_009009:SSA_0222|3end_PTS_system,_mannose-specific_IID_component,_putative_218133..218283_POSITIVE 286 98 54 141 109 NC_009009:SSA_0752|3end_hypothetical_protein_734934..735084_POSITIVE 283 40 1 50 14 NC_009009:SSA_0715|3end_DNA_uptake_protein,_putative_701486..701636_POSITIVE 265 45 12 107 74 NC_009009:SSA_2101|3end_Amino_acid_ABC_transporter,_periplasmic_amino_acid-binding_protein,_putative_2104509..2104659_NEGATIVE 255 97 55 143 100 NC_009009:SSA_0576|3end_Conserved_GTPase,_putative_571225..571375_POSITIVE 252 99 51 91 35 NC_009009:SSA_0536|3end_B12-dependent_diol_dehydratase_small_subunit,_putative_531937..532087_POSITIVE 250 99 51 60 16 NC_009009:SSA_1280|3end_hypothetical_protein_1301108..1301258_NEGATIVE 250 100 57 151 111 NC_009009:SSA_1075|3end_Coproporphyrinogen_III_oxidase,_putative_1094303..1094453_POSITIVE 242 37 1 80 48 NC_009009:SSA_2355|3end_Conserved_uncharacterized_protein_2356325..2356475_NEGATIVE 239 97 55 49 7 NC_009009:SSA_1464|3end_3-phosphoshikimate_1-carboxyvinyltransferase,_putative_1470233..1470383_NEGATIVE 235 99 56 80 49 NC_009009:SSA_2186|3end_Glutathione_biosynthesis_bifunctional_protein_gshAB_(Gamma-GCS-GS)_(GCS-GS),_putative_2187870..2188020_POSITIVE 232 76 31 139 101 NC_009009:SSA_1459|3end_RNA_methyltransferase,_putative_1466111..1466261_NEGATIVE 228 47 1 100 55 NC_009009:SSA_0606|3end_ABC-type_antimicrobial_peptide_transport_system,_ATPase_component,_putative_593789..593939_NEGATIVE 226 98 52 129 94 NC_009009:SSA_1960|3end_hypothetical_protein_1956571..1956721_NEGATIVE 222 95 66 61 32 NC_009009:SSA_1795|3end_Guanosine_3',5'-bis-pyrophosphate_(ppGpp)_synthetase,_putative_1777051..1777201_NEGATIVE 222 85 56 80 50 NC_009009:SSA_1153|3end_HemK_protein,_putative_1182748..1182898_POSITIVE 219 44 2 151 101 NC_009009:SSA_1627|3end_hypothetical_protein_1629508..1629658_NEGATIVE 218 89 49 150 111 NC_009009:SSA_1181|3end_Hydrolase,_alpha/beta_superfamily,_putative_1208592..1208742_NEGATIVE