Origin IGS: cgtagactccttttctaaactgcaagattgtctaaaagctgattgggtgtatctgtaatctagcttttgttttttctctttctgatgaccattatagaccgtttaaagccaaaaacaagggtttttcggcaactggtcaggtctcataagtaagtggtaaagttctgaaagtgacttgcgctagctctttctgtttttagtataaaatagagaatccaatctgcaggaaacgttgcatatattcaacgaatttttgagttcaattgttaaaattagtaaatttgagtctattttgcataaaaaaaccactgtccaactcaaaatagctgagcttaaaagtggagatttgca .........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.........1.........2.........3.........4.........5.........6.........7.........8.........9 tgcaaatctccacttttaagctcagctattttgagttggacagtggtttttttatgcaaaatagactcaaatttactaattttaacaattgaactcaaaaattcgttgaatatatgcaacgtttcctgcagattggattctctattttatactaaaaacagaaagagctagcgcaagtcactttcagaactttaccacttacttatgagacctgaccagttgccgaaaaacccttgtttttggctttaaacggtctataatggtcatcagaaagagaaaaaacaaaagctagattacagatacacccaatcagcttttagacaatcttgcagtttagaaaaggagtctacg Mask Tandem Repeat Region ================================================ cgtagactccttttctaaactgcaagattgtctaaaagctgattgggtgtatctgtaatctagcttttgttttttctctttctgatgaccattatagaccgtttaaagccaaaaacaagggtttttcggcaactggtcaggtctcataagtaagtggtaaagttctgaaagtgacttgcgctagctctttctgtttttagtataaaatagagaatccaatctgcaggaaacgttgcatatattcaacgaatttttgagttcaattgttaaaattagtaaatttgagtctattttgcataaaaaaaccactgtccaactcaaaatagctgagcttaaaagtggagatttgca Find is-nt database================================================ Query_seq: SSA_0614:SSA_0615|SSA_0614:SSA_0615:Transporter, putative:RggD, putative:<-<-:608065..608415 351 cgtagactccttttctaaactgcaagattgtctaaaagctgattgggtgtatctgtaatctagcttttgttttttctctttctgatgaccattatagaccgtttaaagccaaaaacaagggtttttcggcaactggtcaggtctcataagtaagtggtaaagttctgaaagtgacttgcgctagctctttctgtttttagtataaaatagagaatccaatctgcaggaaacgttgcatatattcaacgaatttttgagttcaattgttaaaattagtaaatttgagtctattttgcataaaaaaaccactgtccaactcaaaatagctgagcttaaaagtggagatttgca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_0614:SSA_0615|SSA_0614:SSA_0615:Transporter, putative:RggD, putative:<-<-:608065..608415 351 cgtagactccttttctaaactgcaagattgtctaaaagctgattgggtgtatctgtaatctagcttttgttttttctctttctgatgaccattatagaccgtttaaagccaaaaacaagggtttttcggcaactggtcaggtctcataagtaagtggtaaagttctgaaagtgacttgcgctagctctttctgtttttagtataaaatagagaatccaatctgcaggaaacgttgcatatattcaacgaatttttgagttcaattgttaaaattagtaaatttgagtctattttgcataaaaaaaccactgtccaactcaaaatagctgagcttaaaagtggagatttgca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_0614:SSA_0615|SSA_0614:SSA_0615:Transporter, putative:RggD, putative:<-<-:608065..608415 351 cgtagactccttttctaaactgcaagattgtctaaaagctgattgggtgtatctgtaatctagcttttgttttttctctttctgatgaccattatagaccgtttaaagccaaaaacaagggtttttcggcaactggtcaggtctcataagtaagtggtaaagttctgaaagtgacttgcgctagctctttctgtttttagtataaaatagagaatccaatctgcaggaaacgttgcatatattcaacgaatttttgagttcaattgttaaaattagtaaatttgagtctattttgcataaaaaaaccactgtccaactcaaaatagctgagcttaaaagtggagatttgca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 cgtagactccttttctaaactgcaagattgtctaaaagctgattgggtgtatctgtaatctagcttttgttttttctctttctgatgaccattatagaccgtttaaagccaaaaacaagggtttttcggcaactggtcaggtctcataagtaagtggtaaagttctgaaagtgacttgcgctagctctttctgtttttagtataaaatagagaatccaatctgcaggaaacgttgcatatattcaacgaatttttgagttcaattgttaaaattagtaaatttgagtctattttgcataaaaaaaccactgtccaactcaaaatagctgagcttaaaagtggagatttgca Predict ORF larger than 30AA ================================================ Protein_Len: 36 Strand: + Start: 39 End: 146 ...................................... M I G C I C N L A F V F S L S D D H Y R P F K A K N K G F S A T G Q V S ............................................................................................................................................................................................................. Protein_Len: 43 Strand: + Start: 221 End: 349 ............................................................................................................................................................................................................................ M Q E T L H I F N E F L S S I V K I S K F E S I L H K K T T V Q L K I A E L K S G D L .. Protein_Len: 47 Strand: - Start: 184 End: 324 ....................................................................................................................................................................................... S K R N K T Y F L S D L R C S V N C I N L S N K L E I T L I L L N S D I K C L F V V T W S L M ........................... Protein_Len: 32 Strand: - Start: 147 End: 242 .................................................................................................................................................. L Y T T F N Q F H S A S A R E T K L I F Y L I W D A P F T A Y M ............................................................................................................. cgtagactccttttctaaactgcaagattgtctaaaagctgattgggtgtatctgtaatctagcttttgttttttctctttctgatgaccattatagaccgtttaaagccaaaaacaagggtttttcggcaactggtcaggtctcataagtaagtggtaaagttctgaaagtgacttgcgctagctctttctgtttttagtataaaatagagaatccaatctgcaggaaacgttgcatatattcaacgaatttttgagttcaattgttaaaattagtaaatttgagtctattttgcataaaaaaaccactgtccaactcaaaatagctgagcttaaaagtggagatttgca 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================================================ cgtagactccttttctaaactgcaagattgtctaaaagctgattgggtgtatctgtaatctagcttttgttttttctctttctgatgaccattatagaccgtttaaagccaaaaacaagggtttttcggcaactggtcaggtctcataagtaagtggtaaagttctgaaagtgacttgcgctagctctttctgtttttagtataaaatagagaatccaatctgcaggaaacgttgcatatattcaacgaatttttgagttcaattgttaaaattagtaaatttgagtctattttgcataaaaaaaccactgtccaactcaaaatagctgagcttaaaagtggagatttgca Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_0614:SSA_0615|SSA_0614:SSA_0615:Transporter, putative:RggD, putative:<-<-:608065..608415 351 cgtagactccttttctaaactgcaagattgtctaaaagctgattgggtgtatctgtaatctagcttttgttttttctctttctgatgaccattatagaccgtttaaagccaaaaacaagggtttttcggcaactggtcaggtctcataagtaagtggtaaagttctgaaagtgacttgcgctagctctttctgtttttagtataaaatagagaatccaatctgcaggaaacgttgcatatattcaacgaatttttgagttcaattgttaaaattagtaaatttgagtctattttgcataaaaaaaccactgtccaactcaaaatagctgagcttaaaagtggagatttgca Intra-Species Hit: Count: 1 Min: 1 Max: 351 Len: 351 Subject: NC_009009_SSA_0614_SSA_0615|Transporter, putative:RggD, putative|NEGATIVE:NEGATIVE|[608065,608415]|351 HSP 1 e-value: 0.0 bit: 654.0 Len: 351 Query Start:1 Query End:351 Subject Strand: POSITIVE Subject Start: 1 Subject End: 351 cgtagactccttttctaaactgcaagattgtctaaaagctgattgggtgtatctgtaatctagcttttgttttttctctttctgatgaccattatagaccgtttaaagccaaaaacaagggtttttcggcaactggtcaggtctcataagtaagtggtaaagttctgaaagtgacttgcgctagctctttctgtttttagtataaaatagagaatccaatctgcaggaaacgttgcatatattcaacgaatttttgagttcaattgttaaaattagtaaatttgagtctattttgcatnnnnnnnccactgtccaactcaaaatagctgagcttaaaagtggagatttgca cgtagactccttttctaaactgcaagattgtctaaaagctgattgggtgtatctgtaatctagcttttgttttttctctttctgatgaccattatagaccgtttaaagccaaaaacaagggtttttcggcaactggtcaggtctcataagtaagtggtaaagttctgaaagtgacttgcgctagctctttctgtttttagtataaaatagagaatccaatctgcaggaaacgttgcatatattcaacgaatttttgagttcaattgttaaaattagtaaatttgagtctattttgcataaaaaaaccactgtccaactcaaaatagctgagcttaaaagtggagatttgca Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CGUAGACUCCUUUUCUAAACUGCAAGAUUGUCUAAAAGCUGAUUGGGUGUAUCUGUAAUCUAGCUUUUGUUUUUUCUCUUUCUGAUGACCAUUAUAGACCGUUUAAAGCCAAAAACAAGGGUUUUUCGGCAACUGGUCAGGUCUCAUAAGUAAGUGGUAAAGUUCUGAAAGUGACUUGCGCUAGCUCUUUCUGUUUUUAGUAUAAAAUAGAGAAUCCAAUCUGCAGGAAACGUUGCAUAUAUUCAACGAAUUUUUGAGUUCAAUUGUUAAAAUUAGUAAAUUUGAGUCUAUUUUGCAUAAAAAAACCACUGUCCAACUCAAAAUAGCUGAGCUUAAAAGUGGAGAUUUGCA .(((((((((.........(((((.(((((..(((((((((((((.(......).))))).)))))))).....((.(((((.((..(((((((((((((..(((..(((((((((....)))))).)))...)))...))))).))).....))))).....)).))))).))...((....))..((((((((((......))))))))))...))))))))))....(((((........))))).(((((((((((((.(((((.............((((((............................))))))))))).))))))))))))))))).))))). (-84.90) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGCAAAUCUCCACUUUUAAGCUCAGCUAUUUUGAGUUGGACAGUGGUUUUUUUAUGCAAAAUAGACUCAAAUUUACUAAUUUUAACAAUUGAACUCAAAAAUUCGUUGAAUAUAUGCAACGUUUCCUGCAGAUUGGAUUCUCUAUUUUAUACUAAAAACAGAAAGAGCUAGCGCAAGUCACUUUCAGAACUUUACCACUUACUUAUGAGACCUGACCAGUUGCCGAAAAACCCUUGUUUUUGGCUUUAAACGGUCUAUAAUGGUCAUCAGAAAGAGAAAAAACAAAAGCUAGAUUACAGAUACACCCAAUCAGCUUUUAGACAAUCUUGCAGUUUAGAAAAGGAGUCUACG ((((.....(((((.((.(((((((.....))))))).)).)))))........))))...(((((((...(((.((((........................(((((........)))))....((((((((((..((((((.................(((((.(...((....))).)))))....................(((((((.((((.(((((((((((.......))))))))....)))))))......)))).)))...)))))).....(((((((.((((............)))))))))))...))))).))))).)))).))).))))))).. (-84.52) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 872 50 1 141 92 NC_009009:SSA_0614|5end_Transporter,_putative_607974..608204_NEGATIVE 348 129 83 160 114 NC_009009:SSA_1662|5end_NADH-dependent_oxidoreductase,_putative_1659422..1659652_NEGATIVE 316 79 31 51 3 NC_009009:SSA_0576|5end_Conserved_GTPase,_putative_570039..570269_POSITIVE 315 130 88 224 176 NC_009009:SSA_2194|5end_Nicotinamide_mononucleotide_transporter,_putative_2195663..2195893_NEGATIVE 310 69 22 204 155 NC_009009:SSA_0714|5end_hypothetical_protein_700042..700272_POSITIVE 307 130 81 169 109 NC_009009:SSA_1664|5end_Phosphatidylethanolamine_N-methyltransferase,_putative_1665189..1665419_NEGATIVE 293 130 81 95 55 NC_009009:SSA_1362|5end_ORFB,_transposon_ISSsa2_1377911..1378141_POSITIVE 293 130 81 95 55 NC_009009:SSA_0266|5end_ORFB,_transposon_ISSsa1_260134..260364_POSITIVE 290 195 153 220 170 NC_009009:SSA_1871|5end_Penicillin-binding_protein_2X,_putative_1868873..1869103_NEGATIVE 288 130 84 186 147 NC_009009:SSA_1879|5end_Glycyl-tRNA_synthetase_beta_chain,_putative_1874262..1874492_NEGATIVE 286 65 31 48 15 NC_009009:SSA_0476|5end_Precorrin-2_C20-methyltransferase,_putative_478500..478730_POSITIVE 284 78 37 227 176 NC_009009:SSA_0990|5end_hypothetical_protein_991733..991963_POSITIVE 283 157 118 172 140 NC_009009:SSA_1438|5end_Acetyltransferase,_putative_1443612..1443842_NEGATIVE 283 200 155 87 44 NC_009009:SSA_0539|5end_PduO_protein,_putative_534233..534463_POSITIVE 282 350 304 57 16 NC_009009:SSA_0801|5end_Mur_ligase_family_protein,_putative_784117..784347_NEGATIVE 281 69 21 228 188 NC_009009:SSA_1153|5end_HemK_protein,_putative_1181838..1182068_POSITIVE 281 48 1 127 89 NC_009009:SSA_0495|5end_ABC-type_oligopeptide/nickel_transport_system,_ATPase_component,_putative_495186..495416_POSITIVE 279 179 133 59 15 NC_009009:SSA_1890|5end_Acetyltransferase,_putative_1888145..1888375_NEGATIVE 278 349 306 203 152 NC_009009:SSA_1987|5end_hypothetical_protein_1983368..1983598_NEGATIVE 276 68 22 180 125 NC_009009:SSA_2029|5end_Transposase_and_inactivated_derivatives,_putative_2036028..2036258_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 310 69 22 110 61 NC_009009:SSA_0713|3end_1-acyl-sn-glycerol-3-phosphate_acyltransferase,_putative_700028..700178_POSITIVE 307 130 81 136 76 NC_009009:SSA_1665|3end_hypothetical_protein_1665222..1665372_NEGATIVE 305 79 37 48 5 NC_009009:SSA_0575|3end_Hydrolase,_HAD_superfamily,_putative_570116..570266_POSITIVE 295 159 123 52 7 NC_009009:SSA_0730|3end_Arsenical_resistance_operon_transcription_repressor_(ArsR),_putative_715167..715317_POSITIVE 286 65 31 38 5 NC_009009:SSA_0475|3end_CbiK_protein,_putative_478570..478720_POSITIVE 281 48 1 130 92 NC_009009:SSA_0494|3end_ABC-type_dipeptide/oligopeptide/nickel_transport_system,_ATPase_component,_putative_495269..495419_POSITIVE 279 179 133 58 14 NC_009009:SSA_1891|3end_Oxidoreductase,_aldo/keto_reductase_family,_putative_1888146..1888296_NEGATIVE 276 90 42 138 82 NC_009009:SSA_1391|3end_hypothetical_protein_1406158..1406308_NEGATIVE 267 167 122 149 98 NC_009009:SSA_0487|3end_Delta-aminolevulinic_acid_dehydratase,_putative_488400..488550_POSITIVE 267 90 46 110 56 NC_009009:SSA_0315|3end_Transcriptional_regulator,_MarR_family,_putative_310646..310796_POSITIVE 263 49 2 83 34 NC_009009:SSA_2349|3end_DTDP-4-dehydrorhamnose_3,5-epimerase,_putative_2350677..2350827_NEGATIVE 262 110 61 142 91 NC_009009:SSA_2118|3end_Thiamine_pyrophosphokinase,_putative_2119814..2119964_NEGATIVE 260 85 41 106 68 NC_009009:SSA_0482|3end_ATP:cobalamin_adenosyl_transferase,_putative_484113..484263_POSITIVE 260 130 89 147 102 NC_009009:SSA_0394|3end_hypothetical_protein_390931..391081_POSITIVE 258 199 153 133 77 NC_009009:SSA_1124|3end_Oxidoreductase,_putative_1148547..1148697_NEGATIVE 258 145 126 146 125 NC_009009:SSA_0876|3end_4-methyl-5(B-hydroxyethyl)-thiazole_monophosphate_biosynthesis_protein,_putative_870861..871011_POSITIVE 256 179 131 60 10 NC_009009:SSA_0472|3end_Precorrin-3B_C17-methyltransferase,_putative_475585..475735_POSITIVE 256 120 76 139 101 NC_009009:SSA_0453|3end_Type_II_secretory_pathway,_pullulanase_PulA_glycosidase,_putative_455993..456143_POSITIVE 253 89 53 111 83 NC_009009:SSA_1020|3end_hypothetical_protein_1036104..1036254_POSITIVE 253 159 116 76 22 NC_009009:SSA_0745|3end_hypothetical_protein_726814..726964_NEGATIVE