Origin IGS: gagcgtcaccctctagtttagcgaaaaacagaggctgggttgcaacctctggatttcttcctatcattacgacgtgaaattttcaaaacaatatttttcgaaaaatttttgatgcggtagctgattggattttaggttcgtctttcagactcccaaaaatcctaatcatcctcgcgggggttcgactacgaactaaaaactttcaatttttagttctgtctcaccgc .........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 gcggtgagacagaactaaaaattgaaagtttttagttcgtagtcgaacccccgcgaggatgattaggatttttgggagtctgaaagacgaacctaaaatccaatcagctaccgcatcaaaaatttttcgaaaaatattgttttgaaaatttcacgtcgtaatgataggaagaaatccagaggttgcaacccagcctctgtttttcgctaaactagagggtgacgctc Mask Tandem Repeat Region ================================================ gagcgtcaccctctagtttagcgaaaaacagaggctgggttgcaacctctggatttcttcctatcattacgacgtgaaattttcaaaacaatatttttcgaaaaatttttgatgcggtagctgattggattttaggttcgtctttcagactcccaaaaatcctaatcatcctcgcgggggttcgactacgaactaaaaactttcaatttttagttctgtctcaccgc Find is-nt database================================================ Query_seq: SSA_2006:SSA_2007|SSA_2006:SSA_2007:4-methyl-5(B-hydroxyethyl)-thiazole monophosphate biosynthesis enzyme, putative:Chaperone protein dnaK/HSP70, putative:<-<-:2007306..2007532 227 gagcgtcaccctctagtttagcgaaaaacagaggctgggttgcaacctctggatttcttcctatcattacgacgtgaaattttcaaaacaatatttttcgaaaaatttttgatgcggtagctgattggattttaggttcgtctttcagactcccaaaaatcctaatcatcctcgcgggggttcgactacgaactaaaaactttcaatttttagttctgtctcaccgc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_2006:SSA_2007|SSA_2006:SSA_2007:4-methyl-5(B-hydroxyethyl)-thiazole monophosphate biosynthesis enzyme, putative:Chaperone protein dnaK/HSP70, putative:<-<-:2007306..2007532 227 gagcgtcaccctctagtttagcgaaaaacagaggctgggttgcaacctctggatttcttcctatcattacgacgtgaaattttcaaaacaatatttttcgaaaaatttttgatgcggtagctgattggattttaggttcgtctttcagactcccaaaaatcctaatcatcctcgcgggggttcgactacgaactaaaaactttcaatttttagttctgtctcaccgc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_2006:SSA_2007|SSA_2006:SSA_2007:4-methyl-5(B-hydroxyethyl)-thiazole monophosphate biosynthesis enzyme, putative:Chaperone protein dnaK/HSP70, putative:<-<-:2007306..2007532 227 gagcgtcaccctctagtttagcgaaaaacagaggctgggttgcaacctctggatttcttcctatcattacgacgtgaaattttcaaaacaatatttttcgaaaaatttttgatgcggtagctgattggattttaggttcgtctttcagactcccaaaaatcctaatcatcctcgcgggggttcgactacgaactaaaaactttcaatttttagttctgtctcaccgc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gagcgtcaccctctagtttagcgaaaaacagaggctgggttgcaacctctggatttcttcctatcattacgacgtgaaattttcaaaacaatatttttcgaaaaatttttgatgcggtagctgattggattttaggttcgtctttcagactcccaaaaatcctaatcatcctcgcgggggttcgactacgaactaaaaactttcaatttttagttctgtctcaccgc Predict ORF larger than 30AA ================================================ Protein_Len: 45 Strand: + Start: 93 End: 227 ............................................................................................ M F R K I F D A V A D W I L G S S F R L P K I L I I L A G V R L R T K N F Q F L V L S H R Protein_Len: 35 Strand: - Start: 21 End: 125 .................... R F V S A P N C G R S K K R D N R R S I K L V I N K S F N K I R Y S M ...................................................................................................... gagcgtcaccctctagtttagcgaaaaacagaggctgggttgcaacctctggatttcttcctatcattacgacgtgaaattttcaaaacaatatttttcgaaaaatttttgatgcggtagctgattggattttaggttcgtctttcagactcccaaaaatcctaatcatcctcgcgggggttcgactacgaactaaaaactttcaatttttagttctgtctcaccgc 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================================================ gagcgtcaccctctagtttagcgaaaaacagaggctgggttgcaacctctggatttcttcctatcattacgacgtgaaattttcaaaacaatatttttcgaaaaatttttgatgcggtagctgattggattttaggttcgtctttcagactcccaaaaatcctaatcatcctcgcgggggttcgactacgaactaaaaactttcaatttttagttctgtctcaccgc Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 93 HP_score: -9.9 Tail_Score: -4.66609 Start: 29 End: 51 Full_Region: tgataggaagaaatc cagaggttg caacc cagcctctg tttttcgctaaacta ............................cagaggttgcaacccagcctctg................................................................................................................................................................................ Find igs database================================================ Query_seq: SSA_2006:SSA_2007|SSA_2006:SSA_2007:4-methyl-5(B-hydroxyethyl)-thiazole monophosphate biosynthesis enzyme, putative:Chaperone protein dnaK/HSP70, putative:<-<-:2007306..2007532 227 gagcgtcaccctctagtttagcgaaaaacagaggctgggttgcaacctctggatttcttcctatcattacgacgtgaaattttcaaaacaatatttttcgaaaaatttttgatgcggtagctgattggattttaggttcgtctttcagactcccaaaaatcctaatcatcctcgcgggggttcgactacgaactaaaaactttcaatttttagttctgtctcaccgc Intra-Species Hit: Count: 1 Min: 1 Max: 227 Len: 227 Subject: NC_009009_SSA_2006_SSA_2007|4-methyl-5(B-hydroxyethyl)-thiazole monophosphate biosynthesis enzyme, putative:Chaperone protein dnaK/HSP70, putative|NEGATIVE:NEGATIVE|[2007306,2007532]|227 HSP 1 e-value: 1.0E-126 bit: 450.0 Len: 227 Query Start:1 Query End:227 Subject Strand: POSITIVE Subject Start: 1 Subject End: 227 gagcgtcaccctctagtttagcgaaaaacagaggctgggttgcaacctctggatttcttcctatcattacgacgtgaaattttcaaaacaatatttttcgaaaaatttttgatgcggtagctgattggattttaggttcgtctttcagactcccaaaaatcctaatcatcctcgcgggggttcgactacgaactaaaaactttcaatttttagttctgtctcaccgc gagcgtcaccctctagtttagcgaaaaacagaggctgggttgcaacctctggatttcttcctatcattacgacgtgaaattttcaaaacaatatttttcgaaaaatttttgatgcggtagctgattggattttaggttcgtctttcagactcccaaaaatcctaatcatcctcgcgggggttcgactacgaactaaaaactttcaatttttagttctgtctcaccgc Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAGCGUCACCCUCUAGUUUAGCGAAAAACAGAGGCUGGGUUGCAACCUCUGGAUUUCUUCCUAUCAUUACGACGUGAAAUUUUCAAAACAAUAUUUUUCGAAAAAUUUUUGAUGCGGUAGCUGAUUGGAUUUUAGGUUCGUCUUUCAGACUCCCAAAAAUCCUAAUCAUCCUCGCGGGGGUUCGACUACGAACUAAAAACUUUCAAUUUUUAGUUCUGUCUCACCGC ..(((..((((((..((((...((((..((((((.((.....)).))))))..))))......((((......))))........))))........(((((.....))))).((((....((((((((((((.((...(((.....)))..)).))))))).)))))...))))))))))..(((...((((((((((.......)))))))))).)))....))) (-58.10) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GCGGUGAGACAGAACUAAAAAUUGAAAGUUUUUAGUUCGUAGUCGAACCCCCGCGAGGAUGAUUAGGAUUUUUGGGAGUCUGAAAGACGAACCUAAAAUCCAAUCAGCUACCGCAUCAAAAAUUUUUCGAAAAAUAUUGUUUUGAAAAUUUCACGUCGUAAUGAUAGGAAGAAAUCCAGAGGUUGCAACCCAGCCUCUGUUUUUCGCUAAACUAGAGGGUGACGCUC ((((((.(((.(((((((((((.....)))))))))))...)))......((....)).(((((.(((((((.((..(((.....)))...)).))))))))))))..)))))).........(((((((((.......))))))))).....(((((...(..(((...((((..(((((((((.....)))))))))..))))......)))..)..)))))... (-73.10) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 1011 50 1 141 92 NC_009009:SSA_2006|5end_4-methyl-5(B-hydroxyethyl)-thiazole_monophosphate_biosynthesis_enzyme,_putative_2007215..2007445_NEGATIVE 350 77 31 93 29 NC_009009:SSA_0441|5end_hypothetical_protein_441481..441711_POSITIVE 325 43 10 149 116 NC_009009:SSA_2269|5end_hypothetical_protein_2270327..2270557_NEGATIVE 322 79 35 65 17 NC_009009:SSA_2049|5end_Polyribonucleotide_nucleotidyltransferase,_putative_2052894..2053124_NEGATIVE 319 50 11 168 123 NC_009009:SSA_1967|5end_Threonine_desaminase,_putative_1963559..1963789_NEGATIVE 315 190 141 155 97 NC_009009:SSA_0789|5end_Proton-translocating_ATPase,_F1_sector,_epsilon_subunit,_putative_772451..772681_POSITIVE 311 195 151 81 40 NC_009009:SSA_2185|5end_Adenylosuccinate_synthetase,_putative_2185290..2185520_NEGATIVE 307 154 116 101 53 NC_009009:SSA_2285|5end_hypothetical_protein_2287404..2287634_POSITIVE 306 156 111 168 128 NC_009009:SSA_0476|5end_Precorrin-2_C20-methyltransferase,_putative_478500..478730_POSITIVE 305 54 11 209 162 NC_009009:SSA_1045|5end_hypothetical_protein_1060841..1061071_POSITIVE 303 178 135 56 11 NC_009009:SSA_1321|5end_Ferrochelatase,_putative_1338343..1338573_NEGATIVE 303 60 11 68 20 NC_009009:SSA_0616|5end_YlbN-like_protein,_putative_609245..609475_POSITIVE 301 178 137 131 87 NC_009009:SSA_2324|5end_hypothetical_protein_2330109..2330339_NEGATIVE 299 43 2 214 166 NC_009009:SSA_0606|5end_ABC-type_antimicrobial_peptide_transport_system,_ATPase_component,_putative_594532..594762_NEGATIVE 298 57 11 59 5 NC_009009:SSA_0452|5end_Nitrogen_utilization_substance_protein_B,_putative_451534..451764_POSITIVE 297 160 113 228 182 NC_009009:SSA_1238|5end_hypothetical_protein_1263154..1263384_NEGATIVE 296 178 138 118 88 NC_009009:SSA_0535|5end_Propanediol_utilization:_dehydratase,_medium_subunit,_putative_530643..530873_POSITIVE 295 59 12 68 21 NC_009009:SSA_1840|5end_RNA_binding_protein,_putative_1834422..1834652_NEGATIVE 290 53 12 210 165 NC_009009:SSA_2085|5end_Glyoxylate_reductase,_NADH-dependent,_putative_2090404..2090634_NEGATIVE 288 69 21 80 34 NC_009009:SSA_1911|5end_Conserved_uncharacterized_protein_1903105..1903335_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 503 177 136 90 48 NC_009009:SSA_0686|3end_Fe2+/Zn2+_uptake_regulation_protein,_putative_670079..670229_POSITIVE 319 50 11 68 23 NC_009009:SSA_1968|3end_Ketol-acid_reductoisomerase,_putative_1963659..1963809_NEGATIVE 318 48 2 148 97 NC_009009:SSA_1631|3end_Sortase-like_protein,_putative_1631651..1631801_NEGATIVE 315 190 141 147 89 NC_009009:SSA_0788|3end_Proton-translocating_ATPase,_F1_sector,_beta_subunit,_putative_772523..772673_POSITIVE 313 60 11 115 56 NC_009009:SSA_1314|3end_Fe-S-cluster_oxidoreductase,_putative_1330746..1330896_NEGATIVE 305 54 11 87 40 NC_009009:SSA_1044|3end_Homoserine_kinase,_putative_1060799..1060949_POSITIVE 301 178 137 127 83 NC_009009:SSA_2325|3end_3-methyladenine_DNA_glycosylase,_putative_2330113..2330263_NEGATIVE 298 57 11 81 27 NC_009009:SSA_0451|3end_Conserved_uncharacterized_protein_451636..451786_POSITIVE 296 178 138 106 76 NC_009009:SSA_0533|3end_Glycerol_dehydratase_large_subunit_pduC,_putative_530711..530861_POSITIVE 295 59 12 68 21 NC_009009:SSA_1841|3end_Cof_family_protein/peptidyl-prolyl_cis-trans_isomerase,_cyclophilin_type,_putative_1834422..1834572_NEGATIVE 288 69 21 72 26 NC_009009:SSA_1912|3end_hypothetical_protein_1903113..1903263_NEGATIVE 288 58 11 92 42 NC_009009:SSA_1562|3end_hypothetical_protein_1566005..1566155_NEGATIVE 285 170 122 66 10 NC_009009:SSA_0949|3end_hypothetical_protein_956395..956545_POSITIVE 281 189 141 141 88 NC_009009:SSA_0320|3end_hypothetical_protein_313824..313974_POSITIVE 278 50 2 62 11 NC_009009:SSA_2244|3end_Arsenate_reductase,_putative_2239477..2239627_NEGATIVE 278 63 30 33 5 NC_009009:SSA_2216|3end_LPS_biosynthesis_protein,_putative_2217157..2217307_NEGATIVE 278 56 19 82 37 NC_009009:SSA_1533|3end_Glutathione_reductase,_putative_1542212..1542362_POSITIVE 275 59 11 81 29 NC_009009:SSA_2275|3end_hypothetical_protein_2275225..2275375_NEGATIVE 274 71 35 136 108 NC_009009:SSA_1249|3end_hypothetical_protein_1273275..1273425_NEGATIVE 273 61 21 101 59 NC_009009:SSA_2206|3end_hypothetical_protein_2207275..2207425_POSITIVE