Origin IGS: ttttctgtctccttcttatttcttgcctctatgataataaaaaagaaaggccggtaccataacctaacctttcatttgctagttttattcttacaattttgtcacttttaaaaatcatgcaggagcattcgtaaaaataggacaaaac .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 gttttgtcctatttttacgaatgctcctgcatgatttttaaaagtgacaaaattgtaagaataaaactagcaaatgaaaggttaggttatggtaccggcctttcttttttattatcatagaggcaagaaataagaaggagacagaaaa Mask Tandem Repeat Region ================================================ ttttctgtctccttcttatttcttgcctctatgataataaaaaagaaaggccggtaccataacctaacctttcatttgctagttttattcttacaattttgtcacttttaaaaatcatgcaggagcattcgtaaaaataggacaaaac Find is-nt database================================================ Query_seq: SSA_1682:SSA_1683|SSA_1682:SSA_1683:hypothetical protein:NrdI protein, putative:<-<-:1676976..1677123 148 ttttctgtctccttcttatttcttgcctctatgataataaaaaagaaaggccggtaccataacctaacctttcatttgctagttttattcttacaattttgtcacttttaaaaatcatgcaggagcattcgtaaaaataggacaaaac Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_1682:SSA_1683|SSA_1682:SSA_1683:hypothetical protein:NrdI protein, putative:<-<-:1676976..1677123 148 ttttctgtctccttcttatttcttgcctctatgataataaaaaagaaaggccggtaccataacctaacctttcatttgctagttttattcttacaattttgtcacttttaaaaatcatgcaggagcattcgtaaaaataggacaaaac Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_1682:SSA_1683|SSA_1682:SSA_1683:hypothetical protein:NrdI protein, putative:<-<-:1676976..1677123 148 ttttctgtctccttcttatttcttgcctctatgataataaaaaagaaaggccggtaccataacctaacctttcatttgctagttttattcttacaattttgtcacttttaaaaatcatgcaggagcattcgtaaaaataggacaaaac Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ttttctgtctccttcttatttcttgcctctatgataataaaaaagaaaggccggtaccataacctaacctttcatttgctagttttattcttacaattttgtcacttttaaaaatcatgcaggagcattcgtaaaaataggacaaaac Predict ORF larger than 30AA ================================================ Protein_Len: 38 Strand: - Start: 32 End: 145 ............................... S L L F S L G T G Y G L R E N A L K I R V I K D S K F I M C S C E Y F Y S M ... ttttctgtctccttcttatttcttgcctctatgataataaaaaagaaaggccggtaccataacctaacctttcatttgctagttttattcttacaattttgtcacttttaaaaatcatgcaggagcattcgtaaaaataggacaaaac 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================================================ ttttctgtctccttcttatttcttgcctctatgataataaaaaagaaaggccggtaccataacctaacctttcatttgctagttttattcttacaattttgtcacttttaaaaatcatgcaggagcattcgtaaaaataggacaaaac Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 75 HP_score: -2.5 Tail_Score: -5.58179 Start: 45 End: 73 Full_Region: ataaaactagcaaat gaaaggttaggt tatggt accggcctttc ttttttattatcata ............................................gaaaggttaggttatggtaccggcctttc........................................................................... Find igs database================================================ Query_seq: SSA_1682:SSA_1683|SSA_1682:SSA_1683:hypothetical protein:NrdI protein, putative:<-<-:1676976..1677123 148 ttttctgtctccttcttatttcttgcctctatgataataaaaaagaaaggccggtaccataacctaacctttcatttgctagttttattcttacaattttgtcacttttaaaaatcatgcaggagcattcgtaaaaataggacaaaac Intra-Species Hit: Count: 1 Min: 1 Max: 148 Len: 148 Subject: NC_009009_SSA_1682_SSA_1683|hypothetical protein:NrdI protein, putative|NEGATIVE:NEGATIVE|[1676976,1677123]|148 HSP 1 e-value: 8.0E-79 bit: 293.0 Len: 148 Query Start:1 Query End:148 Subject Strand: POSITIVE Subject Start: 1 Subject End: 148 ttttctgtctccttcttatttcttgcctctatgataataaaaaagaaaggccggtaccataacctaacctttcatttgctagttttattcttacaattttgtcacttttaaaaatcatgcaggagcattcgtaaaaataggacaaaac ttttctgtctccttcttatttcttgcctctatgataataaaaaagaaaggccggtaccataacctaacctttcatttgctagttttattcttacaattttgtcacttttaaaaatcatgcaggagcattcgtaaaaataggacaaaac Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUUCUGUCUCCUUCUUAUUUCUUGCCUCUAUGAUAAUAAAAAAGAAAGGCCGGUACCAUAACCUAACCUUUCAUUUGCUAGUUUUAUUCUUACAAUUUUGUCACUUUUAAAAAUCAUGCAGGAGCAUUCGUAAAAAUAGGACAAAAC .....(((((..((.(((((((((((....(((((..(((((..((((((..(((......)))...))))))..(((..((.......))..))).........)))))...)))))))))))).....)))).))..))))).... (-24.70) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GUUUUGUCCUAUUUUUACGAAUGCUCCUGCAUGAUUUUUAAAAGUGACAAAAUUGUAAGAAUAAAACUAGCAAAUGAAAGGUUAGGUUAUGGUACCGGCCUUUCUUUUUUAUUAUCAUAGAGGCAAGAAAUAAGAAGGAGACAGAAAA .(((((((((.((((......(((..((..(((((...((((((........((((.((.......)).))))..((((((((.(((......))))))))))).))))))..)))))))..)))......)))).)).))))))).. (-33.20) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 860 70 21 161 112 NC_009009:SSA_1682|5end_hypothetical_protein_1676885..1677115_NEGATIVE 359 87 45 188 136 NC_009009:SSA_1660|5end_ABC-type_antimicrobial_peptide_transport_system,_ATPase_component,_putative_1657580..1657810_NEGATIVE 324 107 65 122 81 NC_009009:SSA_1661|5end_hypothetical_protein_1658004..1658234_NEGATIVE 293 87 45 56 19 NC_009009:SSA_0807|5end_GTP-binding_protein,_putative_789449..789679_POSITIVE 286 59 13 206 160 NC_009009:SSA_0862|5end_MurM,_putative_854221..854451_NEGATIVE 278 69 25 137 102 NC_009009:SSA_0977|5end_3-isopropylmalate_dehydrogenase,_putative_982771..983001_POSITIVE 277 133 96 47 12 NC_009009:SSA_0538|5end_PduH_protein,_putative_533794..534024_POSITIVE 254 53 11 137 102 NC_009009:SSA_0604|5end_hypothetical_protein_592451..592681_POSITIVE 254 67 21 147 93 NC_009009:SSA_0075|5end_ABC_sugar_transporter,_permease_protein,_putative_78963..79193_POSITIVE 251 94 51 97 57 NC_009009:SSA_1031|5end_DNA_topology_modulation_protein_FlaR,_putative_1048255..1048485_NEGATIVE 246 90 43 187 138 NC_009009:SSA_0419|5end_Alpha-galactosidase,_putative_416213..416443_POSITIVE 245 41 9 123 91 NC_009009:SSA_0874|5end_hypothetical_protein_867935..868165_POSITIVE 245 27 1 126 93 NC_009009:SSA_0219|5end_PTS_system,_sugar-specific_enzyme_IIA_component,_putative_215367..215597_POSITIVE 238 90 48 120 70 NC_009009:SSA_0674|5end_Exodeoxyribonuclease_VII_large_subunit,_putative_657071..657301_POSITIVE 235 37 6 119 95 NC_009009:SSA_1237|5end_Uracil-DNA_glycosylase,_putative_1262366..1262596_NEGATIVE 234 36 4 129 96 NC_009009:SSA_2155|5end_hypothetical_protein_2156102..2156332_NEGATIVE 230 91 51 66 22 NC_009009:SSA_1737|5end_Cystathionine_gamma-synthase,_putative_1723778..1724008_NEGATIVE 230 27 1 118 93 NC_009009:SSA_1664|5end_Phosphatidylethanolamine_N-methyltransferase,_putative_1665189..1665419_NEGATIVE 230 104 63 226 188 NC_009009:SSA_1250|5end_Conserved_uncharacterized_protein,_putative_1274512..1274742_NEGATIVE 229 50 7 224 180 NC_009009:SSA_2078|5end_hypothetical_protein_2083837..2084067_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 327 87 44 64 11 NC_009009:SSA_1409|3end_DTDP-glucose-4,6-dehydratase,_putative_1421209..1421359_NEGATIVE 278 69 25 55 20 NC_009009:SSA_0975|3end_2-isopropylmalate_synthase,_putative_982769..982919_POSITIVE 277 133 96 66 31 NC_009009:SSA_0537|3end_Propanediol_utilization:dioldehydratase_reactivation,_putative_533893..534043_POSITIVE 271 80 33 88 37 NC_009009:SSA_0564|3end_Potential_aminotransferase,_putative_556988..557138_POSITIVE 257 31 1 151 121 NC_009009:SSA_1124|3end_Oxidoreductase,_putative_1148547..1148697_NEGATIVE 256 60 11 138 86 NC_009009:SSA_1374|3end_Multidrug_ABC_transporter,_ATPase_and_permease_components,_putative_1391359..1391509_NEGATIVE 254 53 11 118 83 NC_009009:SSA_0603|3end_Cobalt_transporter,_putative_592512..592662_POSITIVE 254 67 21 79 25 NC_009009:SSA_0074|3end_ABC_transporter_substrate-binding_protein-sugar_transport,_putative_78975..79125_POSITIVE 246 90 43 78 29 NC_009009:SSA_0418|3end_AraC-type_DNA-binding_domain-containing_protein,_putative_416184..416334_POSITIVE 237 106 72 92 55 NC_009009:SSA_1597|3end_hypothetical_protein_1603267..1603417_NEGATIVE 235 37 6 83 59 NC_009009:SSA_1238|3end_hypothetical_protein_1262402..1262552_NEGATIVE 235 26 1 112 84 NC_009009:SSA_0366|3end_hypothetical_protein_358212..358362_POSITIVE 233 35 1 131 94 NC_009009:SSA_1231|3end_hypothetical_protein_1253649..1253799_NEGATIVE 230 27 1 85 60 NC_009009:SSA_1665|3end_hypothetical_protein_1665222..1665372_NEGATIVE 227 76 41 78 44 NC_009009:SSA_1460|3end_Transcriptional_attenuator_LytR,_putative_1467566..1467716_NEGATIVE 227 27 4 120 94 NC_009009:SSA_0992|3end_hypothetical_protein_994147..994297_POSITIVE 222 59 13 76 19 NC_009009:SSA_0070|3end_Acetylxylan_esterase,_putative_74914..75064_POSITIVE 220 126 82 79 34 NC_009009:SSA_0956|3end_surface_protein_D_965418..965568_POSITIVE 220 97 51 105 44 NC_009009:SSA_0703|3end_Citrate_synthase,_putative_689352..689502_POSITIVE 218 77 43 96 67 NC_009009:SSA_1601|3end_VacB-like_protein,_putative_1606592..1606742_NEGATIVE