Origin IGS: cctttctaattattttttagactgaagaggcaagatatctatcccactattgttcctcagataatagcatttcgcttatgtccaacctctataatacacgcttgattcagagaatattttgctacataacatacatatgcgcttttcacataaactcctcatt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aatgaggagtttatgtgaaaagcgcatatgtatgttatgtagcaaaatattctctgaatcaagcgtgtattatagaggttggacataagcgaaatgctattatctgaggaacaatagtgggatagatatcttgcctcttcagtctaaaaaataattagaaagg Mask Tandem Repeat Region ================================================ cctttctaattattttttagactgaagaggcaagatatctatcccactattgttcctcagataatagcatttcgcttatgtccaacctctataatacacgcttgattcagagaatattttgctacataacatacatatgcgcttttcacataaactcctcatt Find is-nt database================================================ Query_seq: SSA_1496:SSA_1497|SSA_1496:SSA_1497:hypothetical protein:DCMP deaminase, putative:<-<-:1502995..1503157 163 cctttctaattattttttagactgaagaggcaagatatctatcccactattgttcctcagataatagcatttcgcttatgtccaacctctataatacacgcttgattcagagaatattttgctacataacatacatatgcgcttttcacataaactcctcatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_1496:SSA_1497|SSA_1496:SSA_1497:hypothetical protein:DCMP deaminase, putative:<-<-:1502995..1503157 163 cctttctaattattttttagactgaagaggcaagatatctatcccactattgttcctcagataatagcatttcgcttatgtccaacctctataatacacgcttgattcagagaatattttgctacataacatacatatgcgcttttcacataaactcctcatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_1496:SSA_1497|SSA_1496:SSA_1497:hypothetical protein:DCMP deaminase, putative:<-<-:1502995..1503157 163 cctttctaattattttttagactgaagaggcaagatatctatcccactattgttcctcagataatagcatttcgcttatgtccaacctctataatacacgcttgattcagagaatattttgctacataacatacatatgcgcttttcacataaactcctcatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 cctttctaattattttttagactgaagaggcaagatatctatcccactattgttcctcagataatagcatttcgcttatgtccaacctctataatacacgcttgattcagagaatattttgctacataacatacatatgcgcttttcacataaactcctcatt Predict ORF larger than 30AA ================================================ Protein_Len: 31 Strand: + Start: 69 End: 161 .................................................................... M S L M S N L Y N T R L I Q R I F C Y I T Y I C A F H I N S S .. Protein_Len: 30 Strand: - Start: 60 End: 149 ........................................................... I I A N R K H G V E I I C A Q N L S Y K A V Y C V Y A S K M .............. cctttctaattattttttagactgaagaggcaagatatctatcccactattgttcctcagataatagcatttcgcttatgtccaacctctataatacacgcttgattcagagaatattttgctacataacatacatatgcgcttttcacataaactcctcatt 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================================================ cctttctaattattttttagactgaagaggcaagatatctatcccactattgttcctcagataatagcatttcgcttatgtccaacctctataatacacgcttgattcagagaatattttgctacataacatacatatgcgcttttcacataaactcctcatt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_1496:SSA_1497|SSA_1496:SSA_1497:hypothetical protein:DCMP deaminase, putative:<-<-:1502995..1503157 163 cctttctaattattttttagactgaagaggcaagatatctatcccactattgttcctcagataatagcatttcgcttatgtccaacctctataatacacgcttgattcagagaatattttgctacataacatacatatgcgcttttcacataaactcctcatt Intra-Species Hit: Count: 1 Min: 1 Max: 163 Len: 163 Subject: NC_009009_SSA_1496_SSA_1497|hypothetical protein:DCMP deaminase, putative|NEGATIVE:NEGATIVE|[1502995,1503157]|163 HSP 1 e-value: 1.0E-87 bit: 323.0 Len: 163 Query Start:1 Query End:163 Subject Strand: POSITIVE Subject Start: 1 Subject End: 163 cctttctaattattttttagactgaagaggcaagatatctatcccactattgttcctcagataatagcatttcgcttatgtccaacctctataatacacgcttgattcagagaatattttgctacataacatacatatgcgcttttcacataaactcctcatt cctttctaattattttttagactgaagaggcaagatatctatcccactattgttcctcagataatagcatttcgcttatgtccaacctctataatacacgcttgattcagagaatattttgctacataacatacatatgcgcttttcacataaactcctcatt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CCUUUCUAAUUAUUUUUUAGACUGAAGAGGCAAGAUAUCUAUCCCACUAUUGUUCCUCAGAUAAUAGCAUUUCGCUUAUGUCCAACCUCUAUAAUACACGCUUGAUUCAGAGAAUAUUUUGCUACAUAACAUACAUAUGCGCUUUUCACAUAAACUCCUCAUU ....(((((.......))))).((((((((((((((((........((((((((.....))))))))...................((((..(((.((....))))).)))).)))))))))..((((.......))))..)))))))............... (-21.10) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAUGAGGAGUUUAUGUGAAAAGCGCAUAUGUAUGUUAUGUAGCAAAAUAUUCUCUGAAUCAAGCGUGUAUUAUAGAGGUUGGACAUAAGCGAAAUGCUAUUAUCUGAGGAACAAUAGUGGGAUAGAUAUCUUGCCUCUUCAGUCUAAAAAAUAAUUAGAAAGG ........((((((((.....(((((((.......))))).)).......(((((((((((....)).))).))))))....)))))))).............(((((((......(..((((....))))..).)))))))(((((.......))))).... (-30.20) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 891 90 41 181 132 NC_009009:SSA_1496|5end_hypothetical_protein_1502904..1503134_NEGATIVE 345 67 27 78 31 NC_009009:SSA_0502|5end_Peptide_ABC_transporter,_permease_protein,_putative_501554..501784_POSITIVE 273 64 22 59 18 NC_009009:SSA_1678|5end_ABC-type_multidrug_transport_system,_permease_component,_putative_1672181..1672411_NEGATIVE 269 91 51 45 8 NC_009009:SSA_1055|5end_Conserved_uncharacterized_protein_1070899..1071129_POSITIVE 262 59 13 57 6 NC_009009:SSA_1491|5end_Methionine_aminopeptidase_A,_putative_1497637..1497867_NEGATIVE 261 77 33 229 184 NC_009009:SSA_0088|5end_V-type_sodium_ATPase,_subunit_C,_putative_88930..89160_POSITIVE 250 89 41 78 27 NC_009009:SSA_1669|5end_hypothetical_protein_1668442..1668672_NEGATIVE 250 95 53 150 111 NC_009009:SSA_1352|5end_hypothetical_protein_1367941..1368171_NEGATIVE 249 87 44 106 46 NC_009009:SSA_0786|5end_Proton-translocating_ATPase,_F1_sector,_alpha_subunit,_putative_768737..768967_POSITIVE 248 93 52 126 78 NC_009009:SSA_2047|5end_hypothetical_protein_2049953..2050183_NEGATIVE 247 68 42 152 126 NC_009009:SSA_0980|5end_3-isopropylmalate_dehydratase_large_subunit,_putative_984004..984234_POSITIVE 246 83 47 228 194 NC_009009:SSA_1532|5end_Membrane-fusion_protein_/_periplasmic_component_of_efflux_system,_putative_1540623..1540853_NEGATIVE 240 90 42 57 14 NC_009009:SSA_2300|5end_hypothetical_protein_2302508..2302738_NEGATIVE 238 105 68 130 89 NC_009009:SSA_1344|5end_Xanthine/uracil_permeases,_putative_1363352..1363582_NEGATIVE 237 68 22 203 157 NC_009009:SSA_2153|5end_ABC-type_transporter_(uncharacterized),_permease_component,_putative_2154664..2154894_NEGATIVE 236 60 13 167 120 NC_009009:SSA_2098|5end_ABC-type_arginine/histidine_transporter,_permease_protein,_putative_2103617..2103847_NEGATIVE 236 46 2 144 100 NC_009009:SSA_1559|5end_Conserved_uncharacterized_protein_1561656..1561886_NEGATIVE 232 50 1 193 144 NC_009009:SSA_2016|5end_Phosphoglycerate_mutase,_putative_2016293..2016523_NEGATIVE 232 67 24 189 140 NC_009009:SSA_1368|5end_hypothetical_protein_1384077..1384307_NEGATIVE 230 43 1 150 98 NC_009009:SSA_2062|5end_hypothetical_protein_2063521..2063751_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 307 62 24 91 50 NC_009009:SSA_0020|3end_Ribose-phosphate_pyrophosphokinase_1,_putative_26609..26759_POSITIVE 273 64 22 57 16 NC_009009:SSA_1679|3end_ABC-type_multidrug_transport_system,_ATPase_component,_putative_1672183..1672333_NEGATIVE 269 91 51 39 2 NC_009009:SSA_1054|3end_CBS_domain_protein,_putative_1070973..1071123_POSITIVE 254 59 12 98 60 NC_009009:SSA_1306|3end_Trk_transporter_NAD+_binding_protein-K+_transport,_putative_1324245..1324395_NEGATIVE 250 95 53 117 78 NC_009009:SSA_1353|3end_hypothetical_protein_1367974..1368124_NEGATIVE 248 93 52 95 47 NC_009009:SSA_2048|3end_Serine_acetyltransferase,_putative_2049984..2050134_NEGATIVE 247 68 42 150 124 NC_009009:SSA_0978|3end_hypothetical_protein_984082..984232_POSITIVE 246 61 28 146 116 NC_009009:SSA_1870|3end_Phospho-N-acetylmuramoyl-pentapeptide-_transferase,_putative_1865600..1865750_NEGATIVE 238 105 68 121 80 NC_009009:SSA_1345|3end_Bifunctional_pyrimidine_operon_transcriptional_attenuation_protein/uracil_phosphoribosyltransferase,_putative_1363361..1363511_NEGATIVE 237 68 22 105 59 NC_009009:SSA_2154|3end_Conserved_uncharacterized_protein_2154762..2154912_NEGATIVE 236 46 2 142 98 NC_009009:SSA_1560|3end_Structural_maintenance_of_chromosome_protein_(chromosome_segregation_ATPase),_putative_1561658..1561808_NEGATIVE 234 57 12 128 86 NC_009009:SSA_2242|3end_hypothetical_protein_2238121..2238271_NEGATIVE 232 50 1 51 2 NC_009009:SSA_2017|3end_Hypothetical_protein_(possibly_membrane-associated)_2016435..2016585_NEGATIVE 232 67 24 124 75 NC_009009:SSA_1369|3end_FmtA-like_protein,_putative_1384142..1384292_NEGATIVE 232 60 15 58 12 NC_009009:SSA_1031|3end_DNA_topology_modulation_protein_FlaR,_putative_1047734..1047884_NEGATIVE 231 120 71 119 72 NC_009009:SSA_0087|3end_V-type_sodium_ATPase,_subunit_E,_putative_88999..89149_POSITIVE 230 43 1 55 3 NC_009009:SSA_2063|3end_Aminopeptidase_PepS,_putative_2063616..2063766_NEGATIVE 230 159 119 127 79 NC_009009:SSA_0842|3end_Effector_of_murein_hydrolase_LrgA/holin-like_protein,_putative_827790..827940_POSITIVE 230 98 51 59 17 NC_009009:SSA_0376|3end_ABC-type_methionine_transporter,_ATPase_component,_putative_366526..366676_POSITIVE 227 89 41 123 69 NC_009009:SSA_1439|3end_hypothetical_protein_1443624..1443774_NEGATIVE