Origin IGS: cacgaacacatccttttctctgcccttaggacaaatcaagtctctttaaacctatcgcttgctaagaaatttccaagaaatctccgacagcagttcatccaaagaacagtattttatcaataagttgatacaagactcattatagcacgttaaaaataaaaatcaatatgttgtggcaaaaaagttattttttctttttatacacaacatattgatttttta .........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 taaaaaatcaatatgttgtgtataaaaagaaaaaataacttttttgccacaacatattgatttttatttttaacgtgctataatgagtcttgtatcaacttattgataaaatactgttctttggatgaactgctgtcggagatttcttggaaatttcttagcaagcgataggtttaaagagacttgatttgtcctaagggcagagaaaaggatgtgttcgtg Mask Tandem Repeat Region ================================================ cacgaacacatccttttctctgcccttaggacaaatcaagtctctttaaacctatcgcttgctaagaaatttccaagaaatctccgacagcagttcatccaaagaacagtattttatcaataagttgatacaagactcattatagcacgttaaaaataaaaatcaatatgttgtggcaaaaaagttattttttctttttatacacaacatattgatttttta Find is-nt database================================================ Query_seq: SSA_2230:SSA_2231|SSA_2230:SSA_2231:Ribonucleotide reductase, class III, anaerobic, putative:Heme/copper-type cytochrome/quinol oxidases, subunit 1, putative:<-<-:2231249..2231470 222 cacgaacacatccttttctctgcccttaggacaaatcaagtctctttaaacctatcgcttgctaagaaatttccaagaaatctccgacagcagttcatccaaagaacagtattttatcaataagttgatacaagactcattatagcacgttaaaaataaaaatcaatatgttgtggcaaaaaagttattttttctttttatacacaacatattgatttttta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_2230:SSA_2231|SSA_2230:SSA_2231:Ribonucleotide reductase, class III, anaerobic, putative:Heme/copper-type cytochrome/quinol oxidases, subunit 1, putative:<-<-:2231249..2231470 222 cacgaacacatccttttctctgcccttaggacaaatcaagtctctttaaacctatcgcttgctaagaaatttccaagaaatctccgacagcagttcatccaaagaacagtattttatcaataagttgatacaagactcattatagcacgttaaaaataaaaatcaatatgttgtggcaaaaaagttattttttctttttatacacaacatattgatttttta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_2230:SSA_2231|SSA_2230:SSA_2231:Ribonucleotide reductase, class III, anaerobic, putative:Heme/copper-type cytochrome/quinol oxidases, subunit 1, putative:<-<-:2231249..2231470 222 cacgaacacatccttttctctgcccttaggacaaatcaagtctctttaaacctatcgcttgctaagaaatttccaagaaatctccgacagcagttcatccaaagaacagtattttatcaataagttgatacaagactcattatagcacgttaaaaataaaaatcaatatgttgtggcaaaaaagttattttttctttttatacacaacatattgatttttta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 cacgaacacatccttttctctgcccttaggacaaatcaagtctctttaaacctatcgcttgctaagaaatttccaagaaatctccgacagcagttcatccaaagaacagtattttatcaataagttgatacaagactcattatagcacgttaaaaataaaaatcaatatgttgtggcaaaaaagttattttttctttttatacacaacatattgatttttta Predict ORF larger than 30AA ================================================ Protein_Len: 37 Strand: + Start: 10 End: 120 ......... M L F S A L R T N Q V S L N L S L A K K F P R N L R Q Q F I Q R T V F Y Q ...................................................................................................... cacgaacacatccttttctctgcccttaggacaaatcaagtctctttaaacctatcgcttgctaagaaatttccaagaaatctccgacagcagttcatccaaagaacagtattttatcaataagttgatacaagactcattatagcacgttaaaaataaaaatcaatatgttgtggcaaaaaagttattttttctttttatacacaacatattgatttttta Predict Promoter with matrix: RpoD-15 score > 80================================================ Predict Promoter with matrix: RpoD-16 score > 80================================================ Predict Promoter with matrix: RpoD-17 score > 80================================================ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ cacgaacacatccttttctctgcccttaggacaaatcaagtctctttaaacctatcgcttgctaagaaatttccaagaaatctccgacagcagttcatccaaagaacagtattttatcaataagttgatacaagactcattatagcacgttaaaaataaaaatcaatatgttgtggcaaaaaagttattttttctttttatacacaacatattgatttttta Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 100 HP_score: -6.6 Tail_Score: -5.61881 Start: 163 End: 215 Full_Region: taaaaaa tcaatatgttgtgtataaaaag aaaaaataa cttttttgccacaacatattga tttttatttttaacg ..................................................................................................................................................................tcaatatgttgtgtataaaaagaaaaaataacttttttgccacaacatattga....... Find igs database================================================ Query_seq: SSA_2230:SSA_2231|SSA_2230:SSA_2231:Ribonucleotide reductase, class III, anaerobic, putative:Heme/copper-type cytochrome/quinol oxidases, subunit 1, putative:<-<-:2231249..2231470 222 cacgaacacatccttttctctgcccttaggacaaatcaagtctctttaaacctatcgcttgctaagaaatttccaagaaatctccgacagcagttcatccaaagaacagtattttatcaataagttgatacaagactcattatagcacgttaaaaataaaaatcaatatgttgtggcaaaaaagttattttttctttttatacacaacatattgatttttta Intra-Species Hit: Count: 1 Min: 1 Max: 187 Len: 187 Subject: NC_009009_SSA_2230_SSA_2231|Ribonucleotide reductase, class III, anaerobic, putative:Heme/copper-type cytochrome/quinol oxidases, subunit 1, putative|NEGATIVE:NEGATIVE|[2231249,2231470]|222 HSP 1 e-value: 1.0E-102 bit: 371.0 Len: 187 Query Start:1 Query End:187 Subject Strand: POSITIVE Subject Start: 1 Subject End: 187 cacgaacacatccttttctctgcccttaggacaaatcaagtctctttaaacctatcgcttgctaagaaatttccaagaaatctccgacagcagttcatccaaagaacagtattttatcaataagttgatacaagactcattatagcacgttaaaaataaaaatcaatatgttgtggcaaaaaagtta................................... cacgaacacatccttttctctgcccttaggacaaatcaagtctctttaaacctatcgcttgctaagaaatttccaagaaatctccgacagcagttcatccaaagaacagtattttatcaataagttgatacaagactcattatagcacgttaaaaataaaaatcaatatgttgtggcaaaaaagtta................................... Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CACGAACACAUCCUUUUCUCUGCCCUUAGGACAAAUCAAGUCUCUUUAAACCUAUCGCUUGCUAAGAAAUUUCCAAGAAAUCUCCGACAGCAGUUCAUCCAAAGAACAGUAUUUUAUCAAUAAGUUGAUACAAGACUCAUUAUAGCACGUUAAAAAUAAAAAUCAAUAUGUUGUGGCAAAAAAGUUA ............(((((...((((....((((.......))))..............((((..((....))..)))).........((((((((((.......)))).((.((.((((((....)))))).)).))................................)))))))))).)))))... (-23.30) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAACUUUUUUGCCACAACAUAUUGAUUUUUAUUUUUAACGUGCUAUAAUGAGUCUUGUAUCAACUUAUUGAUAAAAUACUGUUCUUUGGAUGAACUGCUGUCGGAGAUUUCUUGGAAAUUUCUUAGCAAGCGAUAGGUUUAAAGAGACUUGAUUUGUCCUAAGGGCAGAGAAAAGGAUGUGUUCGUG ............(((((((((((...(((((((..(((..((.(((((......))))).))..)))..)))))))..((((((((.(((..((.(((((..(((((((((...)))))))))))))).....(((((((....))))))).))..))).)))))))).......)))))))).))) (-46.50) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 917 100 51 191 142 NC_009009:SSA_2230|5end_Ribonucleotide_reductase,_class_III,_anaerobic,_putative_2231158..2231388_NEGATIVE 336 57 11 142 92 NC_009009:SSA_0911|5end_hypothetical_protein_922078..922308_POSITIVE 300 99 51 167 109 NC_009009:SSA_0030|5end_Phosphoribosylformylglycinamidine_synthase,_putative_32610..32840_POSITIVE 294 44 1 132 83 NC_009009:SSA_0874|5end_hypothetical_protein_867935..868165_POSITIVE 288 60 15 188 134 NC_009009:SSA_1989|5end_ABC-type_transport_system_(uncharacterized),_ATPase_component,_putative_1985182..1985412_NEGATIVE 283 53 15 103 61 NC_009009:SSA_0561|5end_RNA:NAD_2'-phosphotransferase,_putative_553630..553860_POSITIVE 282 99 55 155 105 NC_009009:SSA_1575|5end_Glycosyl_transferase,_putative_1579110..1579340_NEGATIVE 280 100 55 202 157 NC_009009:SSA_0492|5end_NADH-dependent_flavin_oxidoreductase,_putative_491588..491818_POSITIVE 271 90 47 224 186 NC_009009:SSA_2289|5end_Cadmium_efflux_system_transcriptional_regulator_(ArsR-like),_putative_2291087..2291317_POSITIVE 271 90 47 224 186 NC_009009:SSA_2389|5end_Arsenical_resistance_operon_transcription_repressor,_putative_2032183..2032413_NEGATIVE 271 90 47 194 156 NC_009009:SSA_2387|5end_Arsenical_resistance_operon_transcription_repressor,_putative_2032213..2032443_NEGATIVE 262 100 54 62 20 NC_009009:SSA_2235|5end_Conserved_uncharacterized_protein_2235450..2235680_NEGATIVE 260 50 2 55 8 NC_009009:SSA_1651|5end_hypothetical_protein_1649853..1650083_NEGATIVE 258 40 10 176 142 NC_009009:SSA_2148|5end_Alkaline_shock_stress_response_protein,_putative_2150039..2150269_NEGATIVE 253 130 88 222 177 NC_009009:SSA_0469|5end_Precorrin-6B_methylase_2,putative_472310..472540_POSITIVE 252 60 14 103 48 NC_009009:SSA_1447|5end_ATP_phosphoribosyltransferase,_putative_1449831..1450061_NEGATIVE 252 59 11 137 96 NC_009009:SSA_0690|5end_Recombinational_DNA_repair_protein_(RecF_pathway),_putative_674432..674662_POSITIVE 251 56 13 116 72 NC_009009:SSA_0172|5end_Transcriptional_regulator,_XRE_family,_putative_169140..169370_POSITIVE 250 65 25 48 6 NC_009009:SSA_0794|5end_Zn-dependent_protease,_putative_775896..776126_POSITIVE 249 60 11 137 87 NC_009009:SSA_2227|5end_Acetyl_transferase,_putative_2228261..2228491_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 336 57 11 145 95 NC_009009:SSA_0910|3end_ABC-type_multidrug_transporter,_ATPase_component,_putative_922161..922311_POSITIVE 300 99 51 147 89 NC_009009:SSA_0028|3end_Phosphoribosylaminoimidazole-succinocarboxamide_synthase,_putative_32670..32820_POSITIVE 283 53 15 110 68 NC_009009:SSA_0560|3end_hypothetical_protein_553717..553867_POSITIVE 282 99 55 88 38 NC_009009:SSA_1576|3end_Catabolite_control_protein_A,_putative_1579177..1579327_NEGATIVE 281 42 8 44 4 NC_009009:SSA_1593|3end_Dipeptidase,_putative_1596390..1596540_NEGATIVE 280 100 55 147 102 NC_009009:SSA_0491|3end_Alpha-ribazole-5'-phosphate_phosphatase,_putative_491613..491763_POSITIVE 261 99 51 53 1 NC_009009:SSA_0211|3end_hypothetical_protein_208456..208606_POSITIVE 252 60 14 106 51 NC_009009:SSA_1448|3end_ATP_phosphoribosyltransferase_regulatory_subunit,_putative_1449828..1449978_NEGATIVE 251 108 70 148 95 NC_009009:SSA_1848|3end_Methionyl-tRNA_formyltransferase,_putative_1842243..1842393_NEGATIVE 250 100 51 81 27 NC_009009:SSA_1255|3end_hypothetical_protein_1281456..1281606_NEGATIVE 249 60 11 127 77 NC_009009:SSA_2228|3end_Acetyltransferase_(GNAT)_family,_putative_2228271..2228421_NEGATIVE 244 58 11 131 83 NC_009009:SSA_0060|3end_Tagatose-6-phosphate_ketose/aldose_isomerase,_putative_62735..62885_POSITIVE 243 119 72 149 94 NC_009009:SSA_1121|3end_Cytochrome_C-type_biogenesis_protein,_putative_1147936..1148086_POSITIVE 242 76 38 138 105 NC_009009:SSA_1757|3end_hypothetical_protein_1745282..1745432_NEGATIVE 238 45 3 113 61 NC_009009:SSA_2091|3end_Phosphotransferase_system_sugar-specific_EII_component,_putative_2095062..2095212_NEGATIVE 238 40 6 138 106 NC_009009:SSA_1026|3end_ABC-type_multidrug_transporter,_ATPase_component,_putative_1043617..1043767_POSITIVE 238 96 52 113 71 NC_009009:SSA_0826|3end_hypothetical_protein_805516..805666_POSITIVE 236 94 55 123 82 NC_009009:SSA_0126|3end_50S_ribosomal_protein_L15,_putative_117787..117937_POSITIVE 234 103 61 136 98 NC_009009:SSA_0593|3end_Rhodanese-like_sulfurtransferase,_putative_585551..585701_POSITIVE 234 95 54 134 90 NC_009009:SSA_0239|3end_7,8-dihydro-8-oxoguanine-triphosphatase,_putative_233493..233643_POSITIVE