Origin IGS: ttccttaatggagacgtcgttgaagcgactgcttcttaggctcgattcttcaataaccaagacattattgaaaatagacgttaagtaatcatttactaactgaaaattcaaaaccaaccctccttaagaaaatactttgacaatcaaattttatcagatagaaaagtaatttgcaagcttttttgaaaattaatttgattttcaaatatttttgtaaacaacttgcaaaataagcaaccttgaaccgataca .........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 tgtatcggttcaaggttgcttattttgcaagttgtttacaaaaatatttgaaaatcaaattaattttcaaaaaagcttgcaaattacttttctatctgataaaatttgattgtcaaagtattttcttaaggagggttggttttgaattttcagttagtaaatgattacttaacgtctattttcaataatgtcttggttattgaagaatcgagcctaagaagcagtcgcttcaacgacgtctccattaaggaa Mask Tandem Repeat Region ================================================ ttccttaatggagacgtcgttgaagcgactgcttcttaggctcgattcttcaataaccaagacattattgaaaatagacgttaagtaatcatttactaactgaaaattcaaaaccaaccctccttaagaaaatactttgacaatcaaattttatcagatagaaaagtaatttgcaagcttttttgaaaattaatttgattttcaaatatttttgtaaacaacttgcaaaataagcaaccttgaaccgataca Find is-nt database================================================ Query_seq: SSA_1941:SSA_1942|SSA_1941:SSA_1942:hypothetical protein:Enoyl-CoA hydratase/carnithine racemase, putative:<-<-:1927543..1927794 252 ttccttaatggagacgtcgttgaagcgactgcttcttaggctcgattcttcaataaccaagacattattgaaaatagacgttaagtaatcatttactaactgaaaattcaaaaccaaccctccttaagaaaatactttgacaatcaaattttatcagatagaaaagtaatttgcaagcttttttgaaaattaatttgattttcaaatatttttgtaaacaacttgcaaaataagcaaccttgaaccgataca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_1941:SSA_1942|SSA_1941:SSA_1942:hypothetical protein:Enoyl-CoA hydratase/carnithine racemase, putative:<-<-:1927543..1927794 252 ttccttaatggagacgtcgttgaagcgactgcttcttaggctcgattcttcaataaccaagacattattgaaaatagacgttaagtaatcatttactaactgaaaattcaaaaccaaccctccttaagaaaatactttgacaatcaaattttatcagatagaaaagtaatttgcaagcttttttgaaaattaatttgattttcaaatatttttgtaaacaacttgcaaaataagcaaccttgaaccgataca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_1941:SSA_1942|SSA_1941:SSA_1942:hypothetical protein:Enoyl-CoA hydratase/carnithine racemase, putative:<-<-:1927543..1927794 252 ttccttaatggagacgtcgttgaagcgactgcttcttaggctcgattcttcaataaccaagacattattgaaaatagacgttaagtaatcatttactaactgaaaattcaaaaccaaccctccttaagaaaatactttgacaatcaaattttatcagatagaaaagtaatttgcaagcttttttgaaaattaatttgattttcaaatatttttgtaaacaacttgcaaaataagcaaccttgaaccgataca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 3 Min: 1 Max: 147 Len: 147 Subject: UniRef90_Q1J581 Cluster: Transcriptional regulator, MarR family; n=11; Streptococcus pyogenes|Rep: Transcriptional regulator, MarR family - Streptococcus pyogenes serotype M4 (strain MGAS10750) HSP 1 e-value: 9.0E-8 bit: 58.2 Len: 147 Query Start:1 Query End:147 Subject Strand: null Subject Start: 1 Subject End: 49 L I V K V F S * G G L V L N F Q L V N D Y L T S I F N N V L V I E E S S L R S S R F N D V S I K E ......................................................................................................... M T V K V L L L G G I C L E Y D K I N H Y L V D I F N R I L V I E E M S L K T S Q F N D V S L K E ......................................................................................................... Subject: UniRef90_Q97SF5 Cluster: Transcriptional regulator, MarR family; n=3; Streptococcus pneumoniae|Rep: Transcriptional regulator, MarR family - Streptococcus pneumoniae HSP 1 e-value: 1.0E-7 bit: 57.8 Len: 111 Query Start:1 Query End:111 Subject Strand: null Subject Start: 1 Subject End: 37 L N F Q L V N D Y L T S I F N N V L V I E E S S L R S S R F N D V S I K E ............................................................................................................................................. M D Y Q R I N E Y L T S I F N N V L V I E E V N L R G S R F K D I S I K E ............................................................................................................................................. Subject: UniRef90_Q03M56 Cluster: Transcriptional regulator; n=3; Streptococcus thermophilus|Rep: Transcriptional regulator - Streptococcus thermophilus (strain ATCC BAA-491 / LMD-9) HSP 1 e-value: 8.0E-6 bit: 51.6 Len: 111 Query Start:1 Query End:111 Subject Strand: null Subject Start: 1 Subject End: 37 L N F Q L V N D Y L T S I F N N V L V I E E S S L R S S R F N D V S I K E ............................................................................................................................................. M D Y D K I N G Y L V D I F N N V V I I E E A S L K N S K F N D I S L K E ............................................................................................................................................. nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnattttatcagatagaaaagtaatttgcaagcttttttgaaaattaatttgattttcaaatatttttgtaaacaacttgcaaaataagcaaccttgaaccgataca Predict ORF larger than 30AA ================================================ Protein_Len: 38 Strand: - Start: 92 End: 205 ........................................................................................... K S V S F E F G V R R L F I S Q C D F K I L Y F L L K C A K K F I L K I K M ............................................... Protein_Len: 39 Strand: - Start: 1 End: 117 E K I S V D N F R S S R L S S E E I V L V N N F I S T L Y D N V L Q F N L V M ....................................................................................................................................... nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnattttatcagatagaaaagtaatttgcaagcttttttgaaaattaatttgattttcaaatatttttgtaaacaacttgcaaaataagcaaccttgaaccgataca Predict Promoter with matrix: RpoD-15 score > 80================================================ Predict Promoter with matrix: RpoD-16 score > 80================================================ Predict Promoter with matrix: RpoD-17 score > 80================================================ PromScan Matrix: RpoD-17 Strand: - Score: 88 Start: 148 End: 177 ...................................................................................................................................................CTTGCAAATTACTTTTCTATCTGATAAAAT........................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnattttatcagatagaaaagtaatttgcaagcttttttgaaaattaatttgattttcaaatatttttgtaaacaacttgcaaaataagcaaccttgaaccgataca Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 75 HP_score: -5.5 Tail_Score: -4.83169 Start: 180 End: 208 Full_Region: AGTAATTTGCAAGCT TTTTTGAAAATTA ATT TGATTTTCAAATA TTTTTGTAAACAACT ...................................................................................................................................................................................TTTTTGAAAATTAATTTGATTTTCAAATA............................................ TransTerm Strand: + Conf: 81 HP_score: -8.1 Tail_Score: -4.03995 Start: 182 End: 206 Full_Region: TAATTTGCAAGCTTT TTTGAAAATTA ATT TGATTTTCAAA TATTTTTGTAAACAA .....................................................................................................................................................................................TTTGAAAATTAATTTGATTTTCAAA.............................................. Find igs database================================================ Query_seq: SSA_1941:SSA_1942|SSA_1941:SSA_1942:hypothetical protein:Enoyl-CoA hydratase/carnithine racemase, putative:<-<-:1927543..1927794 252 nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnattttatcagatagaaaagtaatttgcaagcttttttgaaaattaatttgattttcaaatatttttgtaaacaacttgcaaaataagcaaccttgaaccgataca Intra-Species Hit: Count: 1 Min: 148 Max: 252 Len: 105 Subject: NC_009009_SSA_1941_SSA_1942|hypothetical protein:Enoyl-CoA hydratase/carnithine racemase, putative|NEGATIVE:NEGATIVE|[1927543,1927794]|252 HSP 1 e-value: 7.0E-53 bit: 208.0 Len: 105 Query Start:148 Query End:252 Subject Strand: POSITIVE Subject Start: 148 Subject End: 252 ...................................................................................................................................................attttatcagatagaaaagtaatttgcaagcttttttgaaaattaatttgattttcaaatatttttgtaaacaacttgcaaaataagcaaccttgaaccgataca ...................................................................................................................................................attttatcagatagaaaagtaatttgcaagcttttttgaaaattaatttgattttcaaatatttttgtaaacaacttgcaaaataagcaaccttgaaccgataca Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUUUUAUCAGAUAGAAAAGUAAUUUGCAAGCUUUUUUGAAAAUUAAUUUGAUUUUCAAAUAUUUUUGUAAACAACUUGCAAAAUAAGCAACCUUGAACCGAUACA ....((((........((((..((((((((..(.((((((((((.....)))))))))).)..))))))))..))))((.......))...........)))).. (-17.90) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGUAUCGGUUCAAGGUUGCUUAUUUUGCAAGUUGUUUACAAAAAUAUUUGAAAAUCAAAUUAAUUUUCAAAAAAGCUUGCAAAUUACUUUUCUAUCUGAUAAAAU ..((((((...(((((.......(((((((((((....))......(((((((((.......)))))))))...)))))))))..))))).....)))))).... (-20.20) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 204 100 52 120 74 NC_009009:SSA_0967|5end_hypothetical_protein_975872..976102_POSITIVE 198 32 2 139 108 NC_009009:SSA_0195|5end_hypothetical_protein_195113..195343_POSITIVE 191 56 17 217 179 NC_009009:SSA_1980|5end_50S_ribosomal_protein_L28,_putative_1974632..1974862_NEGATIVE 186 99 51 162 114 NC_009009:SSA_1778|5end_Segregation_and_condensation_protein_B,_putative_1765711..1765941_NEGATIVE 186 50 1 68 15 NC_009009:SSA_1404|5end_hypothetical_protein_1418723..1418953_NEGATIVE 184 99 58 89 42 NC_009009:SSA_0283|5end_Phosphotransferase_system_(PTS),_cellobiose-specific_IIB_component,_putative_274559..274789_POSITIVE 182 57 17 90 44 NC_009009:SSA_0367|5end_hypothetical_protein_358309..358539_POSITIVE 179 41 6 220 181 NC_009009:SSA_0091|5end_V-type_sodium_ATPase,_subunit_A,_putative_91037..91267_POSITIVE 177 79 32 64 22 NC_009009:SSA_0913|5end_Acetyltransferase,_putative_924195..924425_POSITIVE 175 40 3 119 87 NC_009009:SSA_1856|5end_hypothetical_protein_1852208..1852438_NEGATIVE 174 39 11 215 188 NC_009009:SSA_0483|5end_Siroheme_synthase,_putative_484045..484275_POSITIVE 173 40 6 191 157 NC_009009:SSA_2367|5end_ABC-type_cobalt_transport_system,_ATPase_component,_putative_2369732..2369962_NEGATIVE 173 37 1 57 14 NC_009009:SSA_0465|5end_Precorrin-8X_methylmutase_/_precorrin_isomerase,_putative_469185..469415_POSITIVE 172 39 6 60 23 NC_009009:SSA_1577|5end_Proline_dipeptidase,_putative_1580294..1580524_POSITIVE 172 68 25 97 56 NC_009009:SSA_0735|5end_Integral_membrane_protein,_putative_717103..717333_POSITIVE 171 29 1 108 76 NC_009009:SSA_0299|5end_hypothetical_protein_292759..292989_POSITIVE 169 68 31 165 120 NC_009009:SSA_0526|5end_hypothetical_protein_523960..524190_POSITIVE 168 88 47 201 148 NC_009009:SSA_1230|5end_Conserved_uncharacterized_protein_1253358..1253588_NEGATIVE 168 59 16 167 121 NC_009009:SSA_1136|5end_ATPases_with_chaperone_activity,_ATP-binding_subunit,_putative_1161924..1162154_POSITIVE 166 62 23 198 158 NC_009009:SSA_0078|5end_N-acetylneuraminate_lyase,_putative_81904..82134_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 196 39 2 53 10 NC_009009:SSA_0706|3end_RNA_helicase,_putative_692909..693059_POSITIVE 191 56 17 90 52 NC_009009:SSA_1981|3end_hypothetical_protein_1974759..1974909_NEGATIVE 184 99 58 68 21 NC_009009:SSA_0282|3end_Phosphotransferase_system_(PTS),_cellobiose-specific_IIA_component,_putative_274618..274768_POSITIVE 183 32 5 134 108 NC_009009:SSA_1166|3end_hypothetical_protein_1192350..1192500_POSITIVE 179 41 6 136 97 NC_009009:SSA_0090|3end_Acetyltransferase,_GNAT_family,_putative_91033..91183_POSITIVE 176 32 1 58 27 NC_009009:SSA_0911|3end_hypothetical_protein_922898..923048_POSITIVE 173 37 1 47 4 NC_009009:SSA_0464|3end_Cobalamin_biosynthesis_protein_cobD,_putative_469255..469405_POSITIVE 172 68 25 110 69 NC_009009:SSA_0734|3end_Arsenical_resistance_operon_transcription_repressor_(ArsR),_putative_717196..717346_POSITIVE 167 42 13 47 15 NC_009009:SSA_0369|3end_NADP-specific_glutamate_dehydrogenase,_putative_359723..359873_NEGATIVE 166 62 23 135 95 NC_009009:SSA_0077|3end_Oxidoreductase,_putative_81921..82071_POSITIVE 164 98 60 67 33 NC_009009:SSA_2178|3end_hypothetical_protein_2176288..2176438_NEGATIVE 162 45 1 99 51 NC_009009:SSA_1157|3end_PvaA-like_protein,_putative_1186218..1186368_POSITIVE 162 40 8 77 45 NC_009009:SSA_0767|3end_Diacylglycerol_kinase_catalytic_domain_protein,_putative_748054..748204_POSITIVE 160 100 52 78 37 NC_009009:SSA_2186|3end_Glutathione_biosynthesis_bifunctional_protein_gshAB_(Gamma-GCS-GS)_(GCS-GS),_putative_2187870..2188020_POSITIVE 159 79 31 130 86 NC_009009:SSA_2240|3end_Holliday_junction_resolvase,_putative_2237258..2237408_NEGATIVE 156 36 1 118 85 NC_009009:SSA_2175|3end_hypothetical_protein_2173146..2173296_NEGATIVE 156 70 24 39 2 NC_009009:SSA_0378|3end_TRZ/ATZ_family_hydrolase,_putative_368627..368777_POSITIVE 155 39 9 128 93 NC_009009:SSA_0643|3end_hypothetical_protein_630072..630222_NEGATIVE 155 100 80 56 35 NC_009009:SSA_0288|3end_hypothetical_protein_280740..280890_NEGATIVE 153 57 17 58 20 NC_009009:SSA_1975|3end_ABC-type_multidrug_transport_system,_ATPase_component,_putative_1970257..1970407_NEGATIVE