Origin IGS: ttagttactccattgattaattctgaaaatttccaaacttggctgatttttcagcctgatagaacatatttgtcggaatgtaaaatcatatcaaagaagacttctcaaaagatatttttatccgacttt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aaagtcggataaaaatatcttttgagaagtcttctttgatatgattttacattccgacaaatatgttctatcaggctgaaaaatcagccaagtttggaaattttcagaattaatcaatggagtaactaa Mask Tandem Repeat Region ================================================ ttagttactccattgattaattctgaaaatttccaaacttggctgatttttcagcctgatagaacatatttgtcggaatgtaaaatcatatcaaagaagacttctcaaaagatatttttatccgacttt Find is-nt database================================================ Query_seq: SSA_1328:SSA_1329|SSA_1328:SSA_1329:hypothetical protein:Conserved uncharacterized protein:<-<-:1344987..1345115 129 ttagttactccattgattaattctgaaaatttccaaacttggctgatttttcagcctgatagaacatatttgtcggaatgtaaaatcatatcaaagaagacttctcaaaagatatttttatccgacttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_1328:SSA_1329|SSA_1328:SSA_1329:hypothetical protein:Conserved uncharacterized protein:<-<-:1344987..1345115 129 ttagttactccattgattaattctgaaaatttccaaacttggctgatttttcagcctgatagaacatatttgtcggaatgtaaaatcatatcaaagaagacttctcaaaagatatttttatccgacttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_1328:SSA_1329|SSA_1328:SSA_1329:hypothetical protein:Conserved uncharacterized protein:<-<-:1344987..1345115 129 ttagttactccattgattaattctgaaaatttccaaacttggctgatttttcagcctgatagaacatatttgtcggaatgtaaaatcatatcaaagaagacttctcaaaagatatttttatccgacttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ttagttactccattgattaattctgaaaatttccaaacttggctgatttttcagcctgatagaacatatttgtcggaatgtaaaatcatatcaaagaagacttctcaaaagatatttttatccgacttt Predict ORF larger than 30AA ================================================ Protein_Len: 39 Strand: + Start: 13 End: 129 ............ M I N S E N F Q T W L I F Q P D R T Y L S E C K I I S K K T S Q K I F L S D F ttagttactccattgattaattctgaaaatttccaaacttggctgatttttcagcctgatagaacatatttgtcggaatgtaaaatcatatcaaagaagacttctcaaaagatatttttatccgacttt 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================================================ ttagttactccattgattaattctgaaaatttccaaacttggctgatttttcagcctgatagaacatatttgtcggaatgtaaaatcatatcaaagaagacttctcaaaagatatttttatccgacttt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_1328:SSA_1329|SSA_1328:SSA_1329:hypothetical protein:Conserved uncharacterized protein:<-<-:1344987..1345115 129 ttagttactccattgattaattctgaaaatttccaaacttggctgatttttcagcctgatagaacatatttgtcggaatgtaaaatcatatcaaagaagacttctcaaaagatatttttatccgacttt Intra-Species Hit: Count: 1 Min: 1 Max: 129 Len: 129 Subject: NC_009009_SSA_1328_SSA_1329|hypothetical protein:Conserved uncharacterized protein|NEGATIVE:NEGATIVE|[1344987,1345115]|129 HSP 1 e-value: 2.0E-67 bit: 256.0 Len: 129 Query Start:1 Query End:129 Subject Strand: POSITIVE Subject Start: 1 Subject End: 129 ttagttactccattgattaattctgaaaatttccaaacttggctgatttttcagcctgatagaacatatttgtcggaatgtaaaatcatatcaaagaagacttctcaaaagatatttttatccgacttt ttagttactccattgattaattctgaaaatttccaaacttggctgatttttcagcctgatagaacatatttgtcggaatgtaaaatcatatcaaagaagacttctcaaaagatatttttatccgacttt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUAGUUACUCCAUUGAUUAAUUCUGAAAAUUUCCAAACUUGGCUGAUUUUUCAGCCUGAUAGAACAUAUUUGUCGGAAUGUAAAAUCAUAUCAAAGAAGACUUCUCAAAAGAUAUUUUUAUCCGACUUU ..((((.......(((((.(((((((((((..........((((((....))))))...........)))).)))))))....))))).......(((((..(((....)))..)))))....)))).. (-22.80) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAGUCGGAUAAAAAUAUCUUUUGAGAAGUCUUCUUUGAUAUGAUUUUACAUUCCGACAAAUAUGUUCUAUCAGGCUGAAAAAUCAGCCAAGUUUGGAAAUUUUCAGAAUUAAUCAAUGGAGUAACUAA ...((((((((((((((((....((((.....)))).)))))..)))))...)))))).......((((((..((((((....))))))...((((((....))))))........))))))....... (-29.10) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 848 80 31 171 122 NC_009009:SSA_1328|5end_hypothetical_protein_1344896..1345126_NEGATIVE 341 84 41 88 42 NC_009009:SSA_0479|5end_CbiQ_protein,_putative_480425..480655_POSITIVE 320 80 38 76 28 NC_009009:SSA_1925|5end_Seryl-tRNA_synthetase,_putative_1913508..1913738_POSITIVE 310 95 52 70 25 NC_009009:SSA_1227|5end_Aminoglycoside_adenylyltransferase,_putative_1252297..1252527_NEGATIVE 309 76 31 217 166 NC_009009:SSA_0657|5end_PyridoxaL_5'-phosphate_Dependent_Enzymes_class_III,_putative_641445..641675_POSITIVE 297 67 22 219 169 NC_009009:SSA_0713|5end_1-acyl-sn-glycerol-3-phosphate_acyltransferase,_putative_699208..699438_POSITIVE 295 76 32 161 108 NC_009009:SSA_0030|5end_Phosphoribosylformylglycinamidine_synthase,_putative_32610..32840_POSITIVE 291 99 51 165 125 NC_009009:SSA_2105|5end_hypothetical_protein_2107802..2108032_NEGATIVE 275 63 30 205 174 NC_009009:SSA_2346|5end_3-oxoacyl-[acyl-carrier-protein]_synthase_III,_putative_2348546..2348776_NEGATIVE 265 74 31 98 53 NC_009009:SSA_1378|5end_hypothetical_protein_1397998..1398228_NEGATIVE 261 70 21 221 167 NC_009009:SSA_1010|5end_UDP-glucose_4-epimerase,_putative_1012739..1012969_POSITIVE 257 57 14 101 58 NC_009009:SSA_0990|5end_hypothetical_protein_991733..991963_POSITIVE 254 60 13 193 146 NC_009009:SSA_2166|5end_ABC-type_multidrug_transporter,_ATPase_and_permease_components,_putative_2165642..2165872_NEGATIVE 253 63 21 81 41 NC_009009:SSA_1014|5end_Phosphatidylserine_decarboxylase_proenzyme_2,_putative_1017846..1018076_POSITIVE 250 75 33 68 18 NC_009009:SSA_2124|5end_Dehydrogenase,_eukaryotic-like,_putative_2129411..2129641_NEGATIVE 249 49 4 129 93 NC_009009:SSA_0027|5end_Acyl_carrier_protein,_putative_31474..31704_POSITIVE 240 80 41 74 35 NC_009009:SSA_1400|5end_Pyridoxal_kinase,_putative_1413072..1413302_NEGATIVE 237 74 31 198 151 NC_009009:SSA_1660|5end_ABC-type_antimicrobial_peptide_transport_system,_ATPase_component,_putative_1657580..1657810_NEGATIVE 237 87 41 217 155 NC_009009:SSA_0431|5end_hypothetical_protein_433275..433505_NEGATIVE 236 80 33 202 161 NC_009009:SSA_0204|5end_Nisin_biosynthesis_two-component_response_transcriptional_regulator_nisR,_putative_202057..202287_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 310 95 52 53 8 NC_009009:SSA_1229|3end_hypothetical_protein_1252314..1252464_NEGATIVE 295 76 32 141 88 NC_009009:SSA_0028|3end_Phosphoribosylaminoimidazole-succinocarboxamide_synthase,_putative_32670..32820_POSITIVE 275 63 30 104 73 NC_009009:SSA_2347|3end_Coenzyme_F390_synthetase,_putative_2348647..2348797_NEGATIVE 257 57 14 104 61 NC_009009:SSA_0989|3end_Conserved_protein,_possible_transcriptional_regulator_(sigma-70,_region_4),_putative_991816..991966_POSITIVE 253 63 21 88 48 NC_009009:SSA_1013|3end_Phosphatidylserine_synthase,_putative_1017933..1018083_POSITIVE 250 75 33 56 6 NC_009009:SSA_2125|3end_Small_primase-like_protein_(Toprim_domain),_putative_2129423..2129573_NEGATIVE 249 49 4 126 90 NC_009009:SSA_0026|3end_Fatty_acid/phospholipid_synthesis_protein_plsX,_putative_31551..31701_POSITIVE 240 68 21 87 44 NC_009009:SSA_0897|3end_Two_component_system_histidine_kinase,_putative_889811..889961_POSITIVE 225 76 33 60 5 NC_009009:SSA_1778|3end_Segregation_and_condensation_protein_B,_putative_1765142..1765292_NEGATIVE 221 64 22 51 4 NC_009009:SSA_2030|3end_hypothetical_protein_2036514..2036664_NEGATIVE 221 76 33 150 106 NC_009009:SSA_0100|3end_DNA_polymerase_I_-_3'-5'_exonuclease_and_polymerase_domains,_putative_103402..103552_POSITIVE 220 73 41 136 104 NC_009009:SSA_0507|3end_hypothetical_protein_506442..506592_POSITIVE 219 82 45 59 21 NC_009009:SSA_2078|3end_hypothetical_protein_2082176..2082326_NEGATIVE 218 77 33 100 64 NC_009009:SSA_1941|3end_hypothetical_protein_1927129..1927279_NEGATIVE 218 57 22 36 6 NC_009009:SSA_1665|3end_hypothetical_protein_1665222..1665372_NEGATIVE 218 55 33 132 102 NC_009009:SSA_1261|3end_Ribose-5-phosphate_isomerase_A,_putative_1286977..1287127_NEGATIVE 217 90 41 74 17 NC_009009:SSA_1610|3end_hypothetical_protein_1614004..1614154_NEGATIVE 217 77 32 88 49 NC_009009:SSA_0468|3end_Precorrin-6y_C5,15-methyltransferase-like,_putative_472418..472568_POSITIVE 215 70 31 113 82 NC_009009:SSA_1558|3end_Hydrolase,_HAD_superfamily_1560044..1560194_NEGATIVE 215 80 33 89 37 NC_009009:SSA_1443|3end_1-(5-phosphoribosyl)-5-[(5-_phosphoribosylamino)methylideneamino]_imidazole-4-carboxamide_isomerase,_putative_1445944..1446094_NEGATIVE