Origin IGS: aatttctccattctactgattttttattcacataagtatctgttttttctattatatcgcaattccctatttttaactagctttaccatgaaagctgtcttatcagtaacaagcctttatctatactataagtggcatagcgggctatttctttctttatacttttcattaatagttatggaaaaagaaccaaggaaatcctcagttcttattttaa .........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 ttaaaataagaactgaggatttccttggttctttttccataactattaatgaaaagtataaagaaagaaatagcccgctatgccacttatagtatagataaaggcttgttactgataagacagctttcatggtaaagctagttaaaaatagggaattgcgatataatagaaaaaacagatacttatgtgaataaaaaatcagtagaatggagaaatt Mask Tandem Repeat Region ================================================ aatttctccattctactgattttttattcacataagtatctgttttttctattatatcgcaattccctatttttaactagctttaccatgaaagctgtcttatcagtaacaagcctttatctatactataagtggcatagcgggctatttctttctttatacttttcattaatagttatggaaaaagaaccaaggaaatcctcagttcttattttaa Find is-nt database================================================ Query_seq: SSA_1497:SSA_1498|SSA_1497:SSA_1498:DCMP deaminase, putative:50S ribosomal protein L20, putative:<-<-:1503626..1503842 217 aatttctccattctactgattttttattcacataagtatctgttttttctattatatcgcaattccctatttttaactagctttaccatgaaagctgtcttatcagtaacaagcctttatctatactataagtggcatagcgggctatttctttctttatacttttcattaatagttatggaaaaagaaccaaggaaatcctcagttcttattttaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_1497:SSA_1498|SSA_1497:SSA_1498:DCMP deaminase, putative:50S ribosomal protein L20, putative:<-<-:1503626..1503842 217 aatttctccattctactgattttttattcacataagtatctgttttttctattatatcgcaattccctatttttaactagctttaccatgaaagctgtcttatcagtaacaagcctttatctatactataagtggcatagcgggctatttctttctttatacttttcattaatagttatggaaaaagaaccaaggaaatcctcagttcttattttaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_1497:SSA_1498|SSA_1497:SSA_1498:DCMP deaminase, putative:50S ribosomal protein L20, putative:<-<-:1503626..1503842 217 aatttctccattctactgattttttattcacataagtatctgttttttctattatatcgcaattccctatttttaactagctttaccatgaaagctgtcttatcagtaacaagcctttatctatactataagtggcatagcgggctatttctttctttatacttttcattaatagttatggaaaaagaaccaaggaaatcctcagttcttattttaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aatttctccattctactgattttttattcacataagtatctgttttttctattatatcgcaattccctatttttaactagctttaccatgaaagctgtcttatcagtaacaagcctttatctatactataagtggcatagcgggctatttctttctttatacttttcattaatagttatggaaaaagaaccaaggaaatcctcagttcttattttaa Predict ORF larger than 30AA ================================================ Protein_Len: 60 Strand: + Start: 10 End: 216 ......... M L L I F Y S H K Y L F F L L Y R N S L F L T S F T M K A V L S V T S L Y L Y Y K W H S G L F L S L Y F S L I V M E K E . aatttctccattctactgattttttattcacataagtatctgttttttctattatatcgcaattccctatttttaactagctttaccatgaaagctgtcttatcagtaacaagcctttatctatactataagtggcatagcgggctatttctttctttatacttttcattaatagttatggaaaaagaaccaaggaaatcctcagttcttattttaa 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: 87 Start: 26 End: 55 .........................ATTCACATAAGTATCTGTTTTTTCTATTAT.................................................................................................................................................................. PromScan Matrix: RpoD-17 Strand: - Score: 81 Start: 51 End: 80 ..................................................CTAGTTAAAAATAGGGAATTGCGATATAAT......................................................................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ aatttctccattctactgattttttattcacataagtatctgttttttctattatatcgcaattccctatttttaactagctttaccatgaaagctgtcttatcagtaacaagcctttatctatactataagtggcatagcgggctatttctttctttatacttttcattaatagttatggaaaaagaaccaaggaaatcctcagttcttattttaa Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_1497:SSA_1498|SSA_1497:SSA_1498:DCMP deaminase, putative:50S ribosomal protein L20, putative:<-<-:1503626..1503842 217 aatttctccattctactgattttttattcacataagtatctgttttttctattatatcgcaattccctatttttaactagctttaccatgaaagctgtcttatcagtaacaagcctttatctatactataagtggcatagcgggctatttctttctttatacttttcattaatagttatggaaaaagaaccaaggaaatcctcagttcttattttaa Intra-Species Hit: Count: 1 Min: 1 Max: 217 Len: 217 Subject: NC_009009_SSA_1497_SSA_1498|DCMP deaminase, putative:50S ribosomal protein L20, putative|NEGATIVE:NEGATIVE|[1503626,1503842]|217 HSP 1 e-value: 1.0E-120 bit: 430.0 Len: 217 Query Start:1 Query End:217 Subject Strand: POSITIVE Subject Start: 1 Subject End: 217 aatttctccattctactgattttttattcacataagtatctgttttttctattatatcgcaattccctatttttaactagctttaccatgaaagctgtcttatcagtaacaagcctttatctatactataagtggcatagcgggctatttctttctttatacttttcattaatagttatggaaaaagaaccaaggaaatcctcagttcttattttaa aatttctccattctactgattttttattcacataagtatctgttttttctattatatcgcaattccctatttttaactagctttaccatgaaagctgtcttatcagtaacaagcctttatctatactataagtggcatagcgggctatttctttctttatacttttcattaatagttatggaaaaagaaccaaggaaatcctcagttcttattttaa Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAUUUCUCCAUUCUACUGAUUUUUUAUUCACAUAAGUAUCUGUUUUUUCUAUUAUAUCGCAAUUCCCUAUUUUUAACUAGCUUUACCAUGAAAGCUGUCUUAUCAGUAACAAGCCUUUAUCUAUACUAUAAGUGGCAUAGCGGGCUAUUUCUUUCUUUAUACUUUUCAUUAAUAGUUAUGGAAAAAGAACCAAGGAAAUCCUCAGUUCUUAUUUUAA ......(((((..(((((((.........(((........)))..................................(((((((......)))))))....)))))))...(((((....((((.(((....))).)))).)))))...............................)))))..((((((..(((....)))..))))))....... (-34.30) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUAAAAUAAGAACUGAGGAUUUCCUUGGUUCUUUUUCCAUAACUAUUAAUGAAAAGUAUAAAGAAAGAAAUAGCCCGCUAUGCCACUUAUAGUAUAGAUAAAGGCUUGUUACUGAUAAGACAGCUUUCAUGGUAAAGCUAGUUAAAAAUAGGGAAUUGCGAUAUAAUAGAAAAAACAGAUACUUAUGUGAAUAAAAAAUCAGUAGAAUGGAGAAAUU ........(((((..(((....)))..)))))((((((((...............................((((..((((((........)))))).....))))..((((((((..(((((((((......)))))).)))....(((((...(((.................)))...)))))...........)))))))).))))))))... (-45.03) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 824 140 91 231 182 NC_009009:SSA_1497|5end_DCMP_deaminase,_putative_1503535..1503765_NEGATIVE 282 150 105 70 14 NC_009009:SSA_1112|5end_Cell_wall_surface_anchor_family_protein,_putative_1138081..1138311_POSITIVE 277 118 81 79 32 NC_009009:SSA_0882|5end_Phosphoserine_phosphatase,_putative_876903..877133_POSITIVE 275 120 73 166 121 NC_009009:SSA_0019|5end_Secreted_antigen_GbpB/SagA;_peptidoglycan_hydrolase;_PcsB_protein_precursor,_putative_24225..24455_POSITIVE 274 130 87 50 5 NC_009009:SSA_1648|5end_hypothetical_protein_1647909..1648139_NEGATIVE 271 158 111 165 111 NC_009009:SSA_2345|5end_hypothetical_protein_2346919..2347149_POSITIVE 271 168 126 102 56 NC_009009:SSA_0843|5end_hypothetical_protein_827682..827912_POSITIVE 271 153 111 214 170 NC_009009:SSA_0179|5end_hypothetical_protein_183966..184196_POSITIVE 268 166 130 170 136 NC_009009:SSA_0356|5end_Dipeptidase,_putative_349259..349489_POSITIVE 265 123 81 208 167 NC_009009:SSA_0469|5end_Precorrin-6B_methylase_2,putative_472310..472540_POSITIVE 260 197 174 151 127 NC_009009:SSA_1503|5end_Ferredoxin,_putative_1506209..1506439_POSITIVE 257 147 101 42 4 NC_009009:SSA_0221|5end_PTS_system,_mannose-specific_IIC_component,_putative_216370..216600_POSITIVE 256 119 77 172 104 NC_009009:SSA_1793|5end_Histidine_kinase_(sensor_protein),_putative_1776361..1776591_NEGATIVE 255 155 114 145 101 NC_009009:SSA_1997|5end_Membrane_spanning_protein,_putative_1994911..1995141_NEGATIVE 255 120 80 207 161 NC_009009:SSA_0200|5end_Bifunctional_folate_synthesis_protein,_putative_198918..199148_POSITIVE 254 149 103 155 108 NC_009009:SSA_0023|5end_Aspartate_aminotransferase,_putative_28529..28759_POSITIVE 252 80 31 58 8 NC_009009:SSA_1119|5end_Two-component_response_transcriptional_regulator_(CheY-like_receiver_and_AraC-type_DNA-binding_domains),_putative_1144491..1144721_POSITIVE 248 145 105 207 165 NC_009009:SSA_1242|5end_Dihydroorotate_dehydrogenase_B,_putative_1267386..1267616_NEGATIVE 248 140 96 44 2 NC_009009:SSA_0457|5end_Fructokinase,_putative_460663..460893_POSITIVE 246 158 113 113 63 NC_009009:SSA_0943|5end_ABC_transporter_membrane-spanning_permease-phosphate_transport,_putative_950846..951076_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 275 120 73 69 24 NC_009009:SSA_0018|3end_Cell-shape_determining_protein_MreD,_putative_24208..24358_POSITIVE 274 130 87 53 8 NC_009009:SSA_1649|3end_hypothetical_protein_1647906..1648056_NEGATIVE 272 50 3 95 44 NC_009009:SSA_1459|3end_RNA_methyltransferase,_putative_1466111..1466261_NEGATIVE 271 168 126 130 84 NC_009009:SSA_0842|3end_Effector_of_murein_hydrolase_LrgA/holin-like_protein,_putative_827790..827940_POSITIVE 268 166 130 91 57 NC_009009:SSA_0355|3end_DNA_mismatch_repair_protein,_putative_349260..349410_POSITIVE 255 118 86 45 3 NC_009009:SSA_0881|3end_Lipoprotein,_putative_876949..877099_POSITIVE 255 120 80 119 73 NC_009009:SSA_0199|3end_GTP_cyclohydrolase_I,_putative_198910..199060_POSITIVE 247 150 108 140 101 NC_009009:SSA_0889|3end_Isoleucyl-tRNA_synthetase,_putative_882763..882913_NEGATIVE 246 158 113 123 73 NC_009009:SSA_0942|3end_ABC_transporter_membrane-spanning_permease-phosphate_transport,_putative_950936..951086_POSITIVE 246 146 101 137 89 NC_009009:SSA_0463|3end_Cobyrinic_acid_A,C-diamide_synthase,_putative_468303..468453_POSITIVE 242 166 136 105 71 NC_009009:SSA_2045|3end_Reductase,_putative_2048427..2048577_NEGATIVE 241 45 3 140 97 NC_009009:SSA_0994|3end_Peptidase_E,_putative_995390..995540_POSITIVE 240 89 41 103 49 NC_009009:SSA_0978|3end_hypothetical_protein_984082..984232_POSITIVE 238 144 102 52 10 NC_009009:SSA_2253|3end_3-Methyladenine_DNA_glycosylase_I,_constitutive,_putative_2248870..2249020_NEGATIVE 238 146 103 137 98 NC_009009:SSA_2047|3end_hypothetical_protein_2049735..2049885_NEGATIVE 238 209 162 78 34 NC_009009:SSA_0329|3end_Glycerol_uptake_facilitator/aquaporin_protein,_putative_323815..323965_POSITIVE 237 146 103 60 6 NC_009009:SSA_0268|3end_Phosphotransferase_system_(PTS)_cellobiose-specific_component_IIB,_putative_262621..262771_POSITIVE 235 155 112 129 78 NC_009009:SSA_0757|3end_N-acetyl-gamma-glutamyl-phosphate_reductase,_putative_740698..740848_POSITIVE 235 177 134 79 45 NC_009009:SSA_0584|3end_hypothetical_protein_576689..576839_POSITIVE 233 168 138 106 74 NC_009009:SSA_1190|3end_Conserved_uncharacterized_protein_1217799..1217949_NEGATIVE