Origin IGS: acgtttctcaatatcccatcattcaattcatgttacagatcatttccctacttaactcaggaaaatagaatcttgtctcctcactatactaccacttttacttccaaacgaacataggaaattcaaaaataattatcatattttatcacacactaaaaaacccacctttacgggcaggtttctattttgtagtcttcagctagattaagctttaccttc .........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 gaaggtaaagcttaatctagctgaagactacaaaatagaaacctgcccgtaaaggtgggttttttagtgtgtgataaaatatgataattatttttgaatttcctatgttcgtttggaagtaaaagtggtagtatagtgaggagacaagattctattttcctgagttaagtagggaaatgatctgtaacatgaattgaatgatgggatattgagaaacgt Mask Tandem Repeat Region ================================================ acgtttctcaatatcccatcattcaattcatgttacagatcatttccctacttaactcaggaaaatagaatcttgtctcctcactatactaccacttttacttccaaacgaacataggaaattcaaaaataattatcatattttatcacacactaaaaaacccacctttacgggcaggtttctattttgtagtcttcagctagattaagctttaccttc Find is-nt database================================================ Query_seq: SSA_1989:SSA_1990|SSA_1989:SSA_1990:ABC-type transport system (uncharacterized), ATPase component, putative:Zn-porter lipoprotein, putative:<-<-:1985273..1985491 219 acgtttctcaatatcccatcattcaattcatgttacagatcatttccctacttaactcaggaaaatagaatcttgtctcctcactatactaccacttttacttccaaacgaacataggaaattcaaaaataattatcatattttatcacacactaaaaaacccacctttacgggcaggtttctattttgtagtcttcagctagattaagctttaccttc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_1989:SSA_1990|SSA_1989:SSA_1990:ABC-type transport system (uncharacterized), ATPase component, putative:Zn-porter lipoprotein, putative:<-<-:1985273..1985491 219 acgtttctcaatatcccatcattcaattcatgttacagatcatttccctacttaactcaggaaaatagaatcttgtctcctcactatactaccacttttacttccaaacgaacataggaaattcaaaaataattatcatattttatcacacactaaaaaacccacctttacgggcaggtttctattttgtagtcttcagctagattaagctttaccttc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_1989:SSA_1990|SSA_1989:SSA_1990:ABC-type transport system (uncharacterized), ATPase component, putative:Zn-porter lipoprotein, putative:<-<-:1985273..1985491 219 acgtttctcaatatcccatcattcaattcatgttacagatcatttccctacttaactcaggaaaatagaatcttgtctcctcactatactaccacttttacttccaaacgaacataggaaattcaaaaataattatcatattttatcacacactaaaaaacccacctttacgggcaggtttctattttgtagtcttcagctagattaagctttaccttc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 acgtttctcaatatcccatcattcaattcatgttacagatcatttccctacttaactcaggaaaatagaatcttgtctcctcactatactaccacttttacttccaaacgaacataggaaattcaaaaataattatcatattttatcacacactaaaaaacccacctttacgggcaggtttctattttgtagtcttcagctagattaagctttaccttc Predict ORF larger than 30AA ================================================ Protein_Len: 34 Strand: + Start: 13 End: 114 ............ M P S F N S C Y R S F P Y L T Q E N R I L S P H Y T T T F T S K R T ......................................................................................................... Protein_Len: 47 Strand: + Start: 65 End: 205 ................................................................ M E S C L L T I L P L L L P N E H R K F K N N Y H I L S H T K K P T F T G R F L F C S L Q L D .............. acgtttctcaatatcccatcattcaattcatgttacagatcatttccctacttaactcaggaaaatagaatcttgtctcctcactatactaccacttttacttccaaacgaacataggaaattcaaaaataattatcatattttatcacacactaaaaaacccacctttacgggcaggtttctattttgtagtcttcagctagattaagctttaccttc 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================================================ acgtttctcaatatcccatcattcaattcatgttacagatcatttccctacttaactcaggaaaatagaatcttgtctcctcactatactaccacttttacttccaaacgaacataggaaattcaaaaataattatcatattttatcacacactaaaaaacccacctttacgggcaggtttctattttgtagtcttcagctagattaagctttaccttc Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_1989:SSA_1990|SSA_1989:SSA_1990:ABC-type transport system (uncharacterized), ATPase component, putative:Zn-porter lipoprotein, putative:<-<-:1985273..1985491 219 acgtttctcaatatcccatcattcaattcatgttacagatcatttccctacttaactcaggaaaatagaatcttgtctcctcactatactaccacttttacttccaaacgaacataggaaattcaaaaataattatcatattttatcacacactaaaaaacccacctttacgggcaggtttctattttgtagtcttcagctagattaagctttaccttc Intra-Species Hit: Count: 1 Min: 1 Max: 219 Len: 219 Subject: NC_009009_SSA_1989_SSA_1990|ABC-type transport system (uncharacterized), ATPase component, putative:Zn-porter lipoprotein, putative|NEGATIVE:NEGATIVE|[1985273,1985491]|219 HSP 1 e-value: 1.0E-121 bit: 434.0 Len: 219 Query Start:1 Query End:219 Subject Strand: POSITIVE Subject Start: 1 Subject End: 219 acgtttctcaatatcccatcattcaattcatgttacagatcatttccctacttaactcaggaaaatagaatcttgtctcctcactatactaccacttttacttccaaacgaacataggaaattcaaaaataattatcatattttatcacacactaaaaaacccacctttacgggcaggtttctattttgtagtcttcagctagattaagctttaccttc acgtttctcaatatcccatcattcaattcatgttacagatcatttccctacttaactcaggaaaatagaatcttgtctcctcactatactaccacttttacttccaaacgaacataggaaattcaaaaataattatcatattttatcacacactaaaaaacccacctttacgggcaggtttctattttgtagtcttcagctagattaagctttaccttc Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ ACGUUUCUCAAUAUCCCAUCAUUCAAUUCAUGUUACAGAUCAUUUCCCUACUUAACUCAGGAAAAUAGAAUCUUGUCUCCUCACUAUACUACCACUUUUACUUCCAAACGAACAUAGGAAAUUCAAAAAUAAUUAUCAUAUUUUAUCACACACUAAAAAACCCACCUUUACGGGCAGGUUUCUAUUUUGUAGUCUUCAGCUAGAUUAAGCUUUACCUUC ................................(((((((...(((((............))))).(((((.(((((((.......................((((...........)))).....((((((.......))))))...........................))))))).))))).))))))).....((((......))))........ (-22.80) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAAGGUAAAGCUUAAUCUAGCUGAAGACUACAAAAUAGAAACCUGCCCGUAAAGGUGGGUUUUUUAGUGUGUGAUAAAAUAUGAUAAUUAUUUUUGAAUUUCCUAUGUUCGUUUGGAAGUAAAAGUGGUAGUAUAGUGAGGAGACAAGAUUCUAUUUUCCUGAGUUAAGUAGGGAAAUGAUCUGUAACAUGAAUUGAAUGAUGGGAUAUUGAGAAACGU ...(((..((((......))))....)))(((....(((((((..((......))..)))))))...)))....................(((((.(((.(((((...(((((..(........(((....(((((...(....).......((((((((((.......))))))))))..))))).)))...)..)))))))))).))).)))))... (-45.90) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 853 120 71 211 162 NC_009009:SSA_1989|5end_ABC-type_transport_system_(uncharacterized),_ATPase_component,_putative_1985182..1985412_NEGATIVE 327 210 163 127 82 NC_009009:SSA_0585|5end_hypothetical_protein_576937..577167_POSITIVE 303 180 139 177 137 NC_009009:SSA_0244|5end_hypothetical_protein_238698..238928_POSITIVE 293 100 65 197 168 NC_009009:SSA_1759|5end_hypothetical_protein_1746969..1747199_NEGATIVE 270 200 158 159 113 NC_009009:SSA_1257|5end_hypothetical_protein_1283867..1284097_NEGATIVE 268 210 163 200 152 NC_009009:SSA_0618|5end_hypothetical_protein_611973..612203_NEGATIVE 266 203 161 225 185 NC_009009:SSA_2237|5end_Dihydrofolate:folylpolyglutamate_synthetase,_putative_2236740..2236970_NEGATIVE 266 201 162 153 105 NC_009009:SSA_1783|5end_Xanthosine_triphosphate_pyrophosphatase_(NTPase/HAM1_family),_putative_1769106..1769336_NEGATIVE 253 42 6 116 66 NC_009009:SSA_1060|5end_hypothetical_protein_1076765..1076995_POSITIVE 253 200 166 185 145 NC_009009:SSA_0487|5end_Delta-aminolevulinic_acid_dehydratase,_putative_487349..487579_POSITIVE 251 210 161 53 4 NC_009009:SSA_1153|5end_HemK_protein,_putative_1181838..1182068_POSITIVE 250 201 163 174 141 NC_009009:SSA_2340|5end_hypothetical_protein_2342843..2343073_NEGATIVE 247 210 161 211 155 NC_009009:SSA_0672|5end_hypothetical_protein_655191..655421_POSITIVE 246 49 2 136 80 NC_009009:SSA_0469|5end_Precorrin-6B_methylase_2,putative_472310..472540_POSITIVE 245 205 164 199 159 NC_009009:SSA_0963|5end_Peptidoglycan_N-acetylglucosamine_deacetylase_A,_putative_971413..971643_POSITIVE 244 196 161 82 40 NC_009009:SSA_0793|5end_DNA-entry_nuclease,_putative_774859..775089_POSITIVE 243 200 153 209 158 NC_009009:SSA_0998|5end_hypothetical_protein_998487..998717_POSITIVE 242 210 171 55 9 NC_009009:SSA_0214|5end_Single-strand_DNA-binding_protein_(conjugal_DNA-protein_transfer_system),_putative_210215..210445_POSITIVE 241 210 171 62 27 NC_009009:SSA_1367|5end_hypothetical_protein_1383593..1383823_POSITIVE 240 201 171 231 198 NC_009009:SSA_0739|5end_Carbamate_kinase,_putative_721087..721317_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 321 118 71 116 56 NC_009009:SSA_0541|3end_Acetate_kinase,_putative_537082..537232_POSITIVE 305 210 162 118 61 NC_009009:SSA_0571|3end_Aspartyl/glutamyl-tRNA(Asn/Gln)_amidotransferase_subunit_B,_putative_566894..567044_POSITIVE 297 210 161 121 69 NC_009009:SSA_1459|3end_RNA_methyltransferase,_putative_1466111..1466261_NEGATIVE 293 100 65 40 11 NC_009009:SSA_1760|3end_hypothetical_protein_1747126..1747276_NEGATIVE 266 203 161 43 3 NC_009009:SSA_2239|3end_Conserved_uncharacterized_cytosolic_protein_2236922..2237072_NEGATIVE 264 110 62 138 87 NC_009009:SSA_0793|3end_DNA-entry_nuclease,_putative_775799..775949_POSITIVE 256 199 153 146 95 NC_009009:SSA_2307|3end_hypothetical_protein_2308323..2308473_NEGATIVE 254 204 161 95 36 NC_009009:SSA_0429|3end_Histidine_ammonia-lyase,_putative_429701..429851_NEGATIVE 253 201 163 143 97 NC_009009:SSA_0093|3end_V-type_sodium_ATPase,_subunit_D,_putative_94989..95139_POSITIVE 252 207 163 149 85 NC_009009:SSA_1186|3end_Acetyltransferase,_CysE/LacA/Lpx_A/NodL_family,_putative_1214656..1214806_NEGATIVE 251 210 161 53 4 NC_009009:SSA_1152|3end_Protein_chain_release_factor_A,_putative_1181918..1182068_POSITIVE 249 206 166 134 86 NC_009009:SSA_0704|3end_Isocitrate_dehydrogenase_[NADP],_putative_690550..690700_POSITIVE 245 205 164 137 97 NC_009009:SSA_0962|3end_Lactoylglutathione_lyase,_putative_971431..971581_POSITIVE 242 188 142 85 28 NC_009009:SSA_1444|3end_Imidazole_glycerol-phosphate_synthase_subunit_hisH,_putative_1446644..1446794_NEGATIVE 240 201 171 64 31 NC_009009:SSA_0738|3end_Ornithine_carbamoyltransferase,_catabolic,_putative_721000..721150_POSITIVE 239 104 70 50 18 NC_009009:SSA_0482|3end_ATP:cobalamin_adenosyl_transferase,_putative_484113..484263_POSITIVE 236 96 51 107 65 NC_009009:SSA_1364|3end_hypothetical_protein_1380482..1380632_NEGATIVE 233 201 173 71 44 NC_009009:SSA_0239|3end_7,8-dihydro-8-oxoguanine-triphosphatase,_putative_233493..233643_POSITIVE 233 206 162 143 110 NC_009009:SSA_0126|3end_50S_ribosomal_protein_L15,_putative_117787..117937_POSITIVE 232 178 150 55 22 NC_009009:SSA_0249|3end_hypothetical_protein_242115..242265_POSITIVE