Origin IGS: agcagcctaatcaatcttcaaacgctcctgaaccgctatttgattacaaggggaatgcttcagcaaaaataataaaatctgataccgtgtcaaactaatcccaagttttttttaaaacaattgcgtactcgcttgctcagacaagcggagttgataaagcagatcttgaatctctatcatttcttcctcctttttattgattgatcaatagttgactaatcaggtataatgcaaagtaaaataaattgcaagaatgttgcttggattattacaagatggtaacttcccattcaaattgacaaagaaaaaacgaacgagactcgcttcctatcatgaaagctagatctcattcgtaaaaattatatgacagagtctggt .........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.........1.........2.........3.........4.........5.........6.........7.........8.........9 accagactctgtcatataatttttacgaatgagatctagctttcatgataggaagcgagtctcgttcgttttttctttgtcaatttgaatgggaagttaccatcttgtaataatccaagcaacattcttgcaatttattttactttgcattatacctgattagtcaactattgatcaatcaataaaaaggaggaagaaatgatagagattcaagatctgctttatcaactccgcttgtctgagcaagcgagtacgcaattgttttaaaaaaaacttgggattagtttgacacggtatcagattttattatttttgctgaagcattccccttgtaatcaaatagcggttcaggagcgtttgaagattgattaggctgct Mask Tandem Repeat Region ================================================ agcagcctaatcaatcttcaaacgctcctgaaccgctatttgattacaaggggaatgcttcagcaaaaataataaaatctgataccgtgtcaaactaatcccaagttttttttaaaacaattgcgtactcgcttgctcagacaagcggagttgataaagcagatcttgaatctctatcatttcttcctcctttttattgattgatcaatagttgactaatcaggtataatgcaaagtaaaataaattgcaagaatgttgcttggattattacaagatggtaacttcccattcaaattgacaaagaaaaaacgaacgagactcgcttcctatcatgaaagctagatctcattcgtaaaaattatatgacagagtctggt Find is-nt database================================================ Query_seq: SMT_1127:SMT_1128|SMT_1127:SMT_1128:transcriptional regulator, MarR family:surface antigen:<-<-:1061647..1062024 378 agcagcctaatcaatcttcaaacgctcctgaaccgctatttgattacaaggggaatgcttcagcaaaaataataaaatctgataccgtgtcaaactaatcccaagttttttttaaaacaattgcgtactcgcttgctcagacaagcggagttgataaagcagatcttgaatctctatcatttcttcctcctttttattgattgatcaatagttgactaatcaggtataatgcaaagtaaaataaattgcaagaatgttgcttggattattacaagatggtaacttcccattcaaattgacaaagaaaaaacgaacgagactcgcttcctatcatgaaagctagatctcattcgtaaaaattatatgacagagtctggt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_1127:SMT_1128|SMT_1127:SMT_1128:transcriptional regulator, MarR family:surface antigen:<-<-:1061647..1062024 378 agcagcctaatcaatcttcaaacgctcctgaaccgctatttgattacaaggggaatgcttcagcaaaaataataaaatctgataccgtgtcaaactaatcccaagttttttttaaaacaattgcgtactcgcttgctcagacaagcggagttgataaagcagatcttgaatctctatcatttcttcctcctttttattgattgatcaatagttgactaatcaggtataatgcaaagtaaaataaattgcaagaatgttgcttggattattacaagatggtaacttcccattcaaattgacaaagaaaaaacgaacgagactcgcttcctatcatgaaagctagatctcattcgtaaaaattatatgacagagtctggt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_1127:SMT_1128|SMT_1127:SMT_1128:transcriptional regulator, MarR family:surface antigen:<-<-:1061647..1062024 378 agcagcctaatcaatcttcaaacgctcctgaaccgctatttgattacaaggggaatgcttcagcaaaaataataaaatctgataccgtgtcaaactaatcccaagttttttttaaaacaattgcgtactcgcttgctcagacaagcggagttgataaagcagatcttgaatctctatcatttcttcctcctttttattgattgatcaatagttgactaatcaggtataatgcaaagtaaaataaattgcaagaatgttgcttggattattacaagatggtaacttcccattcaaattgacaaagaaaaaacgaacgagactcgcttcctatcatgaaagctagatctcattcgtaaaaattatatgacagagtctggt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 4 Min: 1 Max: 180 Len: 180 Subject: UniRef90_Q97NG7 Cluster: Transcriptional regulator, MarR family; n=2; Streptococcus pneumoniae|Rep: Transcriptional regulator, MarR family - Streptococcus pneumoniae HSP 1 e-value: 5.0E-22 bit: 105.0 Len: 180 Query Start:1 Query End:180 Subject Strand: null Subject Start: 1 Subject End: 60 M I E I Q D L L Y Q L R L S E Q A S T Q L F * K K L G I S L T R Y Q I L L F L L K H S P C N Q I A V Q E R L K I D * A A ...................................................................................................................................................................................................... M L E I Q D L L Y Q L R L S E Q A S T Q L F E K R L G I S L T R Y Q I L L F L L E H S P C N Q M A V Q E R L K I D Q A A ...................................................................................................................................................................................................... Subject: UniRef90_Q2ZYK0 Cluster: Regulatory protein, MarR; n=1; Streptococcus suis 89/1591|Rep: Regulatory protein, MarR - Streptococcus suis 89/1591 HSP 1 e-value: 1.0E-10 bit: 67.8 Len: 180 Query Start:1 Query End:180 Subject Strand: null Subject Start: 1 Subject End: 60 M I E I Q D L L Y Q L R L S E Q A S T Q L F * K K L G I S L T R Y Q I L L F L L K H S P C N Q I A V Q E R L K I D * A A ...................................................................................................................................................................................................... M Q E M E D L L Y R L K V A D E T I S N L F E K Q L G I S L T R Y S I L Q T L L K D A P L H Q L A L Q E R L Q I D R A A ...................................................................................................................................................................................................... Subject: UniRef90_Q838N6 Cluster: Transcriptional regulator, MarR family; n=1; Enterococcus faecalis|Rep: Transcriptional regulator, MarR family - Enterococcus faecalis (Streptococcus faecalis) HSP 1 e-value: 3.0E-7 bit: 56.2 Len: 165 Query Start:10 Query End:174 Subject Strand: null Subject Start: 7 Subject End: 61 ......... E I Q D L L Y Q L R L S E Q A S T Q L F * K K L G I S L T R Y Q I L L F L L K H S P C N Q I A V Q E R L K I D ............................................................................................................................................................................................................ ......... E V S Q L L C Q L K V L D Q K I T K V F E E Q V G L S L T R Y E L L M I L K E R Q P C L Q T E I Q E H L K I D ............................................................................................................................................................................................................ Subject: UniRef90_Q3Y147 Cluster: Regulatory protein, MarR; n=1; Enterococcus faecium DO|Rep: Regulatory protein, MarR - Enterococcus faecium DO HSP 1 e-value: 3.0E-7 bit: 56.2 Len: 165 Query Start:10 Query End:174 Subject Strand: null Subject Start: 5 Subject End: 59 ......... E I Q D L L Y Q L R L S E Q A S T Q L F * K K L G I S L T R Y Q I L L F L L K H S P C N Q I A V Q E R L K I D ............................................................................................................................................................................................................ ......... E I S H L L Y Q I K L A D Q K I V Q I F E E N I G I S L T R Y E I M M R L K E E N P L L Q S S L Q E K L Q I D ............................................................................................................................................................................................................ nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnttcttcctcctttttattgattgatcaatagttgactaatcaggtataatgcaaagtaaaataaattgcaagaatgttgcttggattattacaagatggtaacttcccattcaaattgacaaagaaaaaacgaacgagactcgcttcctatcatgaaagctagatctcattcgtaaaaattatatgacagagtctggt Predict ORF larger than 30AA ================================================ Protein_Len: 41 Strand: + Start: 79 End: 201 .............................................................................. M I P C Q T N P K F F L K Q L R T R L L R Q A E L I K Q I L N L Y H F F L L F I D ................................................................................................................................................................................. Protein_Len: 32 Strand: + Start: 245 End: 340 .................................................................................................................................................................................................................................................... M A R M L L G L L Q D G N F P F K L T K K K R T R L A S Y H E S ...................................... Protein_Len: 30 Strand: - Start: 10 End: 99 ......... D I K L R E Q V A I Q N C P S H K L L F L L I Q Y R T L S M ....................................................................................................................................................................................................................................................................................... nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnttcttcctcctttttattgattgatcaatagttgactaatcaggtataatgcaaagtaaaataaattgcaagaatgttgcttggattattacaagatggtaacttcccattcaaattgacaaagaaaaaacgaacgagactcgcttcctatcatgaaagctagatctcattcgtaaaaattatatgacagagtctggt 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: 81 Start: 223 End: 252 ..............................................................................................................................................................................................................................CTTGCAATTTATTTTACTTTGCATTATACC.............................................................................................................................. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnttcttcctcctttttattgattgatcaatagttgactaatcaggtataatgcaaagtaaaataaattgcaagaatgttgcttggattattacaagatggtaacttcccattcaaattgacaaagaaaaaacgaacgagactcgcttcctatcatgaaagctagatctcattcgtaaaaattatatgacagagtctggt Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 47 HP_score: -3.4 Tail_Score: -3.28745 Start: 248 End: 260 Full_Region: AAAGTAAAATAAATT GCAA GAATG TTGC TTGGATTATTACAAG .......................................................................................................................................................................................................................................................GCAAGAATGTTGC...................................................................................................................... TransTerm Strand: - Conf: 43 HP_score: -3.4 Tail_Score: -2.67276 Start: 248 End: 260 Full_Region: cttgtaataatccaa gcaa cattc ttgc aatttattttacttt .......................................................................................................................................................................................................................................................gcaacattcttgc...................................................................................................................... TransTerm Strand: - Conf: 100 HP_score: -8.6 Tail_Score: -5.72622 Start: 311 End: 353 Full_Region: gtcatataattttta cgaatgagatctagctttc atgata ggaagcgagtctcgttcg ttttttctttgtcaa ......................................................................................................................................................................................................................................................................................................................cgaatgagatctagctttcatgataggaagcgagtctcgttcg......................... Find igs database================================================ Query_seq: SMT_1127:SMT_1128|SMT_1127:SMT_1128:transcriptional regulator, MarR family:surface antigen:<-<-:1061647..1062024 378 nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnttcttcctcctttttattgattgatcaatagttgactaatcaggtataatgcaaagtaaaataaattgcaagaatgttgcttggattattacaagatggtaacttcccattcaaattgacaaagaaaaaacgaacgagactcgcttcctatcatgaaagctagatctcattcgtaaaaattatatgacagagtctggt Intra-Species Hit: Count: 1 Min: 181 Max: 378 Len: 198 Subject: smit_SMT_1127_SMT_1128|transcriptional regulator, MarR family:surface antigen|NEGATIVE:NEGATIVE|[1061647,1062024]|378 HSP 1 e-value: 1.0E-108 bit: 392.0 Len: 198 Query Start:181 Query End:378 Subject Strand: POSITIVE Subject Start: 181 Subject End: 378 ....................................................................................................................................................................................ttcttcctcctttttattgattgatcaatagttgactaatcaggtataatgcaaagtaaaataaattgcaagaatgttgcttggattattacaagatggtaacttcccattcaaattgacaaagaaaaaacgaacgagactcgcttcctatcatgaaagctagatctcattcgtaaaaattatatgacagagtctggt ....................................................................................................................................................................................ttcttcctcctttttattgattgatcaatagttgactaatcaggtataatgcaaagtaaaataaattgcaagaatgttgcttggattattacaagatggtaacttcccattcaaattgacaaagaaaaaacgaacgagactcgcttcctatcatgaaagctagatctcattcgtaaaaattatatgacagagtctggt Inter-species Hit: Count: 2 Min: 181 Max: 360 Len: 180 Subject: NC_003098_spr1874_spr1875|Transcriptional regulator - MarR family:hypothetical protein|NEGATIVE:NEGATIVE|[1844120,1844524]|405 HSP 1 e-value: 4.0E-21 bit: 103.0 Len: 64 Query Start:297 Query End:360 Subject Strand: POSITIVE Subject Start: 324 Subject End: 387 ........................................................................................................................................................................................................................................................................................................tgacaaagaaaaaacgaacgagactcgcttcctatcatgaaagctagatctcattcgtaaaaat.................. ........................................................................................................................................................................................................................................................................................................tgacaaagaaaaaacgaacgagaatcgcttcctatcacgaaagctagatctcattcgtcaaaat.................. HSP 2 e-value: 4.0E-18 bit: 93.7 Len: 111 Query Start:181 Query End:291 Subject Strand: POSITIVE Subject Start: 87 Subject End: 197 ....................................................................................................................................................................................ttcttcctcctttttattgattgatcaatagttgactaatcaggtataatgcaaagtaaaataaattgcaagaatgttgcttggattattacaagatggtaacttcccatt....................................................................................... ....................................................................................................................................................................................ttcttcctcctatccattgacttatcaatagttgaccaatcaattgtgatataaagtaaaatagattgcaagaatgttgcttggattattacaagataataactttccatt....................................................................................... Subject: NC_003028_SP_2062_SP_2063|transcriptional regulator, MarR family:LysM domain-containing protein|NEGATIVE:NEGATIVE|[1963312,1963633]|322 HSP 1 e-value: 3.0E-16 bit: 87.7 Len: 64 Query Start:297 Query End:360 Subject Strand: POSITIVE Subject Start: 241 Subject End: 304 ........................................................................................................................................................................................................................................................................................................tgacaaagaaaaaacgaacgagactcgcttcctatcatgaaagctagatctcattcgtaaaaat.................. ........................................................................................................................................................................................................................................................................................................tgacaaagaaaaaacgaacgagaatcgctttccatcacgaaagctagatctcattcgtcaaaat.................. HSP 2 e-value: 1.0E-12 bit: 75.8 Len: 102 Query Start:190 Query End:291 Subject Strand: POSITIVE Subject Start: 13 Subject End: 114 .............................................................................................................................................................................................ctttttattgattgatcaatagttgactaatcaggtataatgcaaagtaaaataaattgcaagaatgttgcttggattattacaagatggtaacttcccatt....................................................................................... .............................................................................................................................................................................................ctttttattgatttatcaatatttgactaattaattgtgatataaagtaaaatagattgcaagaatgttgcttaactcattacaagatgataactttccatt....................................................................................... Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUCUUCCUCCUUUUUAUUGAUUGAUCAAUAGUUGACUAAUCAGGUAUAAUGCAAAGUAAAAUAAAUUGCAAGAAUGUUGCUUGGAUUAUUACAAGAUGGUAACUUCCCAUUCAAAUUGACAAAGAAAAAACGAACGAGACUCGCUUCCUAUCAUGAAAGCUAGAUCUCAUUCGUAAAAAU (((((..((.......(((((((.(((.....))).)))))))......(((((...........))))).(((((......(((...((((......))))..)))))))).....))..)))))...(((((.((((((.((((.(......).)))).)).)))).)))))...... (-34.20) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUUUUUACGAAUGAGAUCUAGCUUUCAUGAUAGGAAGCGAGUCUCGUUCGUUUUUUCUUUGUCAAUUUGAAUGGGAAGUUACCAUCUUGUAAUAAUCCAAGCAACAUUCUUGCAAUUUAUUUUACUUUGCAUUAUACCUGAUUAGUCAACUAUUGAUCAAUCAAUAAAAAGGAGGAAGAA ......(((((((((((...((((((......))))))..)))))))))))...((((((.((...(((..((((..(((((......)))))..))))..)))......(((((...........))))).......(((((.((((.....)))).)))))........)).)))))) (-45.90) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 281 171 137 161 120 smit:SMT_1634|5end_2,3,4,5-tetrahydropyridine-2-carboxylate_N-succinyltransferase,_putative_1621074..1621304_POSITIVE 259 163 143 55 35 smit:SMT_774|5end_hypothetical_protein_685231..685461_NEGATIVE 257 170 142 28 3 smit:SMT_356|5end_hypothetical_protein_292394..292624_POSITIVE 249 168 127 109 65 smit:SMT_1849|5end_hypothetical_protein_1813074..1813304_POSITIVE 248 168 134 101 65 smit:SMT_275|5end_transcriptional_activator-exopolysaccharide_biosynthesis_217369..217599_POSITIVE 241 31 1 209 163 smit:SMT_1894|5end_K02025_multiple_sugar_transport_system_permease_protein_1846508..1846738_POSITIVE 241 31 1 209 163 smit:SMT_1764|5end_K02025_multiple_sugar_transport_system_permease_protein_1739943..1740173_POSITIVE 240 140 91 221 164 smit:SMT_1734|5end_serine/threonine_protein_phosphatase_1718558..1718788_POSITIVE 239 170 135 43 4 smit:SMT_2058|5end_hypoxanthine-guanine_phosphoribosyltransferase_1967697..1967927_NEGATIVE 233 178 142 93 58 smit:SMT_607|5end_K03294_basic_amino_acid/polyamine_antiporter,_APA_family_520119..520349_POSITIVE 230 175 131 65 14 smit:SMT_567|5end_conserved_hypothetical_protein_484845..485075_POSITIVE 223 44 6 145 98 smit:SMT_1169|5end_phosphorylase,_Pnp/UDP_family_1117350..1117580_NEGATIVE 223 146 107 217 180 smit:SMT_414|5end_K03665_GTP-binding_protein_HflX_357554..357784_POSITIVE 219 167 129 47 9 smit:SMT_431|5end_UDP-N-acetylmuramoyl-L-alanyl-D-glutamate_synthetase_372199..372429_POSITIVE 218 42 8 180 146 smit:SMT_1583|5end_polysaccharide_transporter,_PST_family_1573963..1574193_POSITIVE 218 42 8 180 146 smit:SMT_286|5end_polysaccharide_transporter,_PST_family_228655..228885_POSITIVE 217 174 131 227 180 smit:SMT_493|5end_K01996_branched-chain_amino_acid_transport_system_ATP-binding_protein_427137..427367_POSITIVE 216 175 137 200 163 smit:SMT_1719|5end_DNA_mismatch_repair_protein_1706842..1707072_NEGATIVE 216 144 102 61 14 smit:SMT_427|5end_hypothetical_protein_predicted_by_Glimmer/Critica_368812..369042_POSITIVE 215 170 130 91 54 smit:SMT_1612|5end_K06024_segregation_and_condensation_protein_B_1600052..1600282_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 259 163 143 45 25 smit:SMT_775|3end_alpha-acetolactate_decarboxylase_685241..685391_NEGATIVE 241 31 1 113 67 smit:SMT_1893|3end_ABC_transporter_substrate-binding_protein_-_sugar_transport_1846492..1846642_POSITIVE 241 31 1 113 67 smit:SMT_1763|3end_K02027_multiple_sugar_transport_system_substrate-binding_protein_1739927..1740077_POSITIVE 236 174 131 91 53 smit:SMT_1453|3end_K07335_basic_membrane_protein_A_and_related_proteins_1436355..1436505_NEGATIVE 233 178 142 41 6 smit:SMT_606|3end_cytochrome_c-type_biogenesis_protein_CcdA_520147..520297_POSITIVE 226 120 80 68 25 smit:SMT_493|3end_K01996_branched-chain_amino_acid_transport_system_ATP-binding_protein_427927..428077_POSITIVE 226 168 137 58 30 smit:SMT_256|3end_K02027_multiple_sugar_transport_system_substrate-binding_protein_194282..194432_POSITIVE 225 146 103 73 16 smit:SMT_865|3end_50S_ribosomal_protein_L1_815022..815172_NEGATIVE 218 42 8 137 103 smit:SMT_1582|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1574000..1574150_POSITIVE 218 42 8 137 103 smit:SMT_285|3end_polysaccharide_polymerase_228692..228842_POSITIVE 215 170 130 72 35 smit:SMT_1611|3end_K05896_segregation_and_condensation_protein_A_1600113..1600263_POSITIVE 215 107 66 150 107 smit:SMT_1319|3end_muscus_binding_protein_1289974..1290124_POSITIVE 212 100 51 70 22 smit:SMT_2011|3end_lysyl-tRNA_synthetase_1929759..1929909_NEGATIVE 212 149 103 82 33 smit:SMT_1279|3end_translation_elongation_factor_Ts_1243451..1243601_POSITIVE 211 168 131 67 26 smit:SMT_1736|3end_acetyltransferase,_GNAT_family_1719862..1720012_POSITIVE 209 175 135 43 6 smit:SMT_566|3end_K07282_poly-gamma-glutamate_synthesis_protein_(capsule_biosynthesis_protein)_484903..485053_POSITIVE 208 172 131 96 47 smit:SMT_626|3end_1,4-alpha-glucan_branching_enzyme_531789..531939_POSITIVE 207 110 65 115 71 smit:SMT_1607|3end_K03341_putative_deoxyribonucleotide_triphosphate_pyrophosphatase_1597699..1597849_POSITIVE 204 110 68 146 108 smit:SMT_2153|3end_putative_cell_division_protein_2027512..2027662_POSITIVE 203 176 132 81 37 smit:SMT_2065|3end_transcriptional_regulator,_MarR_family_1973185..1973335_POSITIVE