Origin IGS: tcagacctccttatattttttgcaaaccactcctttttgtgaaatcgtttgcatgtcgatacatctattatagcacgattttttattttgtaaaggcttttataaaaaaattttctctttttttgcacctaaaatactgcattttctcttcaagagttatatttttgccatattccaacgaaaacgattgcatgaaataaccacaaagtccgcattatttctcctatcaatactgtaacaagcgcaaaaaaactccgtctctcaaggagaacagagttttgaatttt .........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 aaaattcaaaactctgttctccttgagagacggagtttttttgcgcttgttacagtattgataggagaaataatgcggactttgtggttatttcatgcaatcgttttcgttggaatatggcaaaaatataactcttgaagagaaaatgcagtattttaggtgcaaaaaaagagaaaatttttttataaaagcctttacaaaataaaaaatcgtgctataatagatgtatcgacatgcaaacgatttcacaaaaaggagtggtttgcaaaaaatataaggaggtctga Mask Tandem Repeat Region ================================================ tcagacctccttatattttttgcaaaccactcctttttgtgaaatcgtttgcatgtcgatacatctattatagcacgattttttattttgtaaaggcttttataaaaaaattttctctttttttgcacctaaaatactgcattttctcttcaagagttatatttttgccatattccaacgaaaacgattgcatgaaataaccacaaagtccgcattatttctcctatcaatactgtaacaagcgcaaaaaaactccgtctctcaaggagaacagagttttgaatttt Find is-nt database================================================ Query_seq: SSA_1809:SSA_1810|SSA_1809:SSA_1810:PTS system glucose-specific EIIC BA component (EIICBA-Glc) (EII- Glc/EIII-Glc), putative:Two-component response transcriptional regulator (CheY-like receiver and winged-helix DNA-binding domains), putative:<-<-:1794510..1794796 287 tcagacctccttatattttttgcaaaccactcctttttgtgaaatcgtttgcatgtcgatacatctattatagcacgattttttattttgtaaaggcttttataaaaaaattttctctttttttgcacctaaaatactgcattttctcttcaagagttatatttttgccatattccaacgaaaacgattgcatgaaataaccacaaagtccgcattatttctcctatcaatactgtaacaagcgcaaaaaaactccgtctctcaaggagaacagagttttgaatttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_1809:SSA_1810|SSA_1809:SSA_1810:PTS system glucose-specific EIIC BA component (EIICBA-Glc) (EII- Glc/EIII-Glc), putative:Two-component response transcriptional regulator (CheY-like receiver and winged-helix DNA-binding domains), putative:<-<-:1794510..1794796 287 tcagacctccttatattttttgcaaaccactcctttttgtgaaatcgtttgcatgtcgatacatctattatagcacgattttttattttgtaaaggcttttataaaaaaattttctctttttttgcacctaaaatactgcattttctcttcaagagttatatttttgccatattccaacgaaaacgattgcatgaaataaccacaaagtccgcattatttctcctatcaatactgtaacaagcgcaaaaaaactccgtctctcaaggagaacagagttttgaatttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_1809:SSA_1810|SSA_1809:SSA_1810:PTS system glucose-specific EIIC BA component (EIICBA-Glc) (EII- Glc/EIII-Glc), putative:Two-component response transcriptional regulator (CheY-like receiver and winged-helix DNA-binding domains), putative:<-<-:1794510..1794796 287 tcagacctccttatattttttgcaaaccactcctttttgtgaaatcgtttgcatgtcgatacatctattatagcacgattttttattttgtaaaggcttttataaaaaaattttctctttttttgcacctaaaatactgcattttctcttcaagagttatatttttgccatattccaacgaaaacgattgcatgaaataaccacaaagtccgcattatttctcctatcaatactgtaacaagcgcaaaaaaactccgtctctcaaggagaacagagttttgaatttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tcagacctccttatattttttgcaaaccactcctttttgtgaaatcgtttgcatgtcgatacatctattatagcacgattttttattttgtaaaggcttttataaaaaaattttctctttttttgcacctaaaatactgcattttctcttcaagagttatatttttgccatattccaacgaaaacgattgcatgaaataaccacaaagtccgcattatttctcctatcaatactgtaacaagcgcaaaaaaactccgtctctcaaggagaacagagttttgaatttt Predict ORF larger than 30AA ================================================ Protein_Len: 60 Strand: + Start: 15 End: 197 .............. M F C K P L L F V K S F A C R Y I Y Y S T I F Y F V K A F I K K F S L F L H L K Y C I F S S R V I F L P Y S N E N D C M .......................................................................................... Protein_Len: 42 Strand: + Start: 110 End: 235 ............................................................................................................. M F S F F A P K I L H F L F K S Y I F A I F Q R K R L H E I T T K S A L F L L S I L .................................................... Protein_Len: 44 Strand: - Start: 153 End: 284 ........................................................................................................................................................ S N Y K Q W I G V F V I A H F L W L T R M I E G I L V T V L A F F S R R E L L V S N Q M ... Protein_Len: 36 Strand: - Start: 86 End: 193 ..................................................................................... K T F A K I F F N E R K K C R F Y Q M K E E L T I N K G Y E L S F S Q M .............................................................................................. Protein_Len: 42 Strand: - Start: 3 End: 128 .. S R R I N K A F W E K K H F R K C T S V D I I A R N K I K Y L S K Y F F K R K K Q M ............................................................................................................................................................... tcagacctccttatattttttgcaaaccactcctttttgtgaaatcgtttgcatgtcgatacatctattatagcacgattttttattttgtaaaggcttttataaaaaaattttctctttttttgcacctaaaatactgcattttctcttcaagagttatatttttgccatattccaacgaaaacgattgcatgaaataaccacaaagtccgcattatttctcctatcaatactgtaacaagcgcaaaaaaactccgtctctcaaggagaacagagttttgaatttt 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================================================ tcagacctccttatattttttgcaaaccactcctttttgtgaaatcgtttgcatgtcgatacatctattatagcacgattttttattttgtaaaggcttttataaaaaaattttctctttttttgcacctaaaatactgcattttctcttcaagagttatatttttgccatattccaacgaaaacgattgcatgaaataaccacaaagtccgcattatttctcctatcaatactgtaacaagcgcaaaaaaactccgtctctcaaggagaacagagttttgaatttt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_1809:SSA_1810|SSA_1809:SSA_1810:PTS system glucose-specific EIIC BA component (EIICBA-Glc) (EII- Glc/EIII-Glc), putative:Two-component response transcriptional regulator (CheY-like receiver and winged-helix DNA-binding domains), putative:<-<-:1794510..1794796 287 tcagacctccttatattttttgcaaaccactcctttttgtgaaatcgtttgcatgtcgatacatctattatagcacgattttttattttgtaaaggcttttataaaaaaattttctctttttttgcacctaaaatactgcattttctcttcaagagttatatttttgccatattccaacgaaaacgattgcatgaaataaccacaaagtccgcattatttctcctatcaatactgtaacaagcgcaaaaaaactccgtctctcaaggagaacagagttttgaatttt Intra-Species Hit: Count: 1 Min: 1 Max: 287 Len: 287 Subject: NC_009009_SSA_1809_SSA_1810|PTS system glucose-specific EIIC BA component (EIICBA-Glc) (EII- Glc/EIII-Glc), putative:Two-component response transcriptional regulator (CheY-like receiver and winged-helix DNA-binding domains), putative|NEGATIVE:NEGATIVE|[1794510,1794796]|287 HSP 1 e-value: 6.0E-75 bit: 281.0 Len: 163 Query Start:125 Query End:287 Subject Strand: POSITIVE Subject Start: 125 Subject End: 287 ............................................................................................................................gcacctaaaatactgcattttctcttcaagagttatatttttgccatattccaacgaaaacgattgcatgaaataaccacaaagtccgcattatttctcctatcaatactgtaacaagcgcnnnnnnnctccgtctctcaaggagaacagagttttgaatttt ............................................................................................................................gcacctaaaatactgcattttctcttcaagagttatatttttgccatattccaacgaaaacgattgcatgaaataaccacaaagtccgcattatttctcctatcaatactgtaacaagcgcaaaaaaactccgtctctcaaggagaacagagttttgaatttt HSP 2 e-value: 1.0E-36 bit: 155.0 Len: 78 Query Start:1 Query End:78 Subject Strand: POSITIVE Subject Start: 1 Subject End: 78 tcagacctccttatattttttgcaaaccactcctttttgtgaaatcgtttgcatgtcgatacatctattatagcacga................................................................................................................................................................................................................. tcagacctccttatattttttgcaaaccactcctttttgtgaaatcgtttgcatgtcgatacatctattatagcacga................................................................................................................................................................................................................. Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UCAGACCUCCUUAUAUUUUUUGCAAACCACUCCUUUUUGUGAAAUCGUUUGCAUGUCGAUACAUCUAUUAUAGCACGAUUUUUUAUUUUGUAAAGGCUUUUAUAAAAAAAUUUUCUCUUUUUUUGCACCUAAAAUACUGCAUUUUCUCUUCAAGAGUUAUAUUUUUGCCAUAUUCCAACGAAAACGAUUGCAUGAAAUAACCACAAAGUCCGCAUUAUUUCUCCUAUCAAUACUGUAACAAGCGCAAAAAAACUCCGUCUCUCAAGGAGAACAGAGUUUUGAAUUUU (((((.(((....((((((.((((((..............((((((((..((.(((.((((....)))))))))))))))))...(((((((((....)))))))))..............))))))...)))))).......(((((((..((((.....((((((((...(((....)))...(((.....(((((((..............)))))))....))).............).)))))))........))))..)))))))..))).)))))..... (-44.06) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAAUUCAAAACUCUGUUCUCCUUGAGAGACGGAGUUUUUUUGCGCUUGUUACAGUAUUGAUAGGAGAAAUAAUGCGGACUUUGUGGUUAUUUCAUGCAAUCGUUUUCGUUGGAAUAUGGCAAAAAUAUAACUCUUGAAGAGAAAAUGCAGUAUUUUAGGUGCAAAAAAAGAGAAAAUUUUUUUAUAAAAGCCUUUACAAAAUAAAAAAUCGUGCUAUAAUAGAUGUAUCGACAUGCAAACGAUUUCACAAAAAGGAGUGGUUUGCAAAAAAUAUAAGGAGGUCUGA .......((((((((((.(((.....)))))))))))))....(.(((((((......))))))).)........((((((((.(...(((((.......(((....((((....(((((((.........(((.....)))........(((....((((....(((((((.....)))))))......)))).)))..............)))))))...))))...)))..(((((((.(((((.......))))).)))))))..)))))..).)))))))). (-63.30) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 829 70 21 161 112 NC_009009:SSA_1809|5end_PTS_system_glucose-specific_EIIC_BA_component_(EIICBA-Glc)_(EII-_Glc/EIII-Glc),_putative_1794419..1794649_NEGATIVE 301 257 211 137 87 NC_009009:SSA_2308|5end_hypothetical_protein_2310474..2310704_NEGATIVE 293 50 5 145 98 NC_009009:SSA_0113|5end_30S_ribosomal_protein_S3,_putative_111322..111552_POSITIVE 290 66 22 200 141 NC_009009:SSA_1614|5end_Acetyltransferase,_GNAT_family,_putative_1618045..1618275_NEGATIVE 277 75 35 223 183 NC_009009:SSA_2146|5end_Metallo-beta-lactamase,_putative_2148399..2148629_NEGATIVE 267 246 201 57 3 NC_009009:SSA_1176|5end_Acetoin_dehydrogenase,_E1_component,_beta_subunit,_putative_1205405..1205635_NEGATIVE 265 61 22 62 28 NC_009009:SSA_0087|5end_V-type_sodium_ATPase,_subunit_E,_putative_88329..88559_POSITIVE 259 260 211 71 17 NC_009009:SSA_0791|5end_UDP-N-acetylglucosamine-like_protein,_putative_773345..773575_POSITIVE 255 230 200 49 21 NC_009009:SSA_1303|5end_RimM_protein,_required_for_16S_rRNA_processing,_putative_1322992..1323222_NEGATIVE 252 267 221 151 99 NC_009009:SSA_2035|5end_Conserved_uncharacterized_protein_2040288..2040518_NEGATIVE 250 59 27 96 58 NC_009009:SSA_2213|5end_Nucleotide_sugar_dehydratase,_putative_2215111..2215341_NEGATIVE 250 267 222 154 104 NC_009009:SSA_1844|5end_hypothetical_protein_1838183..1838413_NEGATIVE 248 50 3 106 58 NC_009009:SSA_2013|5end_hypothetical_protein_2013793..2014023_NEGATIVE 248 267 221 202 160 NC_009009:SSA_1655|5end_hypothetical_protein_1651816..1652046_NEGATIVE 247 77 35 103 51 NC_009009:SSA_2344|5end_hypothetical_protein_2346537..2346767_POSITIVE 246 48 6 148 101 NC_009009:SSA_2164|5end_Glutamine_amidotransferase,_putative_2161555..2161785_NEGATIVE 246 50 1 153 97 NC_009009:SSA_1992|5end_Fructose-bisphosphate_aldolase,_putative_1989972..1990202_NEGATIVE 246 59 19 155 116 NC_009009:SSA_1298|5end_Maltose/maltodextrin_ABC_transporter,_sugar-binding_protein_MalX,_putative_1315291..1315521_POSITIVE 246 179 138 130 87 NC_009009:SSA_0513|5end_ATP:cob(I)alamin_adenosyltransferase,_putative_511558..511788_POSITIVE 244 210 177 169 135 NC_009009:SSA_0674|5end_Exodeoxyribonuclease_VII_large_subunit,_putative_657071..657301_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 301 257 211 137 87 NC_009009:SSA_2309|3end_Fimbrial_assembly_protein,_putative_2310474..2310624_NEGATIVE 293 50 5 132 85 NC_009009:SSA_0112|3end_50S_ribosomal_protein_L22,_putative_111389..111539_POSITIVE 265 61 22 51 17 NC_009009:SSA_0086|3end_V-type_sodium_ATPase,_subunit_K,_putative_88398..88548_POSITIVE 254 275 241 64 34 NC_009009:SSA_0756|3end_Alanyl-tRNA_synthetase,_putative_739434..739584_POSITIVE 250 59 27 94 56 NC_009009:SSA_2214|3end_2-C-methyl-D-erythritol_4-phosphate_cytidylyltransferase_2,_putative_2215113..2215263_NEGATIVE 250 275 254 136 115 NC_009009:SSA_0752|3end_hypothetical_protein_734934..735084_POSITIVE 248 267 221 138 96 NC_009009:SSA_1656|3end_Nisin_resistance_protein,_putative_1651880..1652030_NEGATIVE 248 268 221 74 29 NC_009009:SSA_1397|3end_hypothetical_protein_1410995..1411145_POSITIVE 246 179 138 117 74 NC_009009:SSA_0512|3end_Nicotinate-nucleotide--dimethylbenzimidazole_phosphoribosyltransferase,_putative_511625..511775_POSITIVE 244 169 121 50 6 NC_009009:SSA_0554|3end_hypothetical_protein_549692..549842_POSITIVE 244 50 2 107 56 NC_009009:SSA_0030|3end_Phosphoribosylformylglycinamidine_synthase,_putative_36424..36574_POSITIVE 242 279 239 122 73 NC_009009:SSA_2298|3end_Serine_protease_containing_a_PDZ_domain,_putative_2299569..2299719_NEGATIVE 241 180 134 135 86 NC_009009:SSA_1728|3end_ABC_transporter_membrane-spanning_permease-branched_chain_amino_acid_transport,_putative_1713424..1713574_NEGATIVE 241 65 26 77 36 NC_009009:SSA_0421|3end_Phosphoglycerate_mutase_family_protein,_putative_420240..420390_POSITIVE 239 57 11 95 48 NC_009009:SSA_0508|3end_Conserved_uncharacterized_protein,_possible_phosphoserine_phosphatase_508064..508214_POSITIVE 238 70 30 76 30 NC_009009:SSA_1419|3end_hypothetical_protein_1428995..1429145_NEGATIVE 237 246 205 52 15 NC_009009:SSA_0751|3end_Oligoendopeptidase_F,_putative_734249..734399_POSITIVE 237 55 16 127 84 NC_009009:SSA_0675|3end_Exodeoxyribonuclease_VII_small_subunit,_putative_658681..658831_POSITIVE 236 280 240 76 35 NC_009009:SSA_1588|3end_Conserved_ABC-type_antimicrobial_permease-like_protein,_putative_1589182..1589332_NEGATIVE 232 36 7 100 70 NC_009009:SSA_0244|3end_hypothetical_protein_239170..239320_POSITIVE