Origin IGS: gctttgctggtttaacaactttaaattaaaatacgttaggggatgggattttctcagcccctaaaactaaatatatgtataggcgagtttatataggagacaccttttctcctatatgagcgctagcattttacaaaagaggagaaataatata .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tatattatttctcctcttttgtaaaatgctagcgctcatataggagaaaaggtgtctcctatataaactcgcctatacatatatttagttttaggggctgagaaaatcccatcccctaacgtattttaatttaaagttgttaaaccagcaaagc Mask Tandem Repeat Region ================================================ gctttgctggtttaacaactttaaattaaaatacgttaggggatgggattttctcagcccctaaaactaaatatatgtataggcgagtttatataggagacaccttttctcctatatgagcgctagcattttacaaaagaggagaaataatata Find is-nt database================================================ Query_seq: SSA_0125:SSA_0126|SSA_0125:SSA_0126:50S ribosomal protein L30, putative:50S ribosomal protein L15, putative:->->:117253..117406 154 gctttgctggtttaacaactttaaattaaaatacgttaggggatgggattttctcagcccctaaaactaaatatatgtataggcgagtttatataggagacaccttttctcctatatgagcgctagcattttacaaaagaggagaaataatata Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_0125:SSA_0126|SSA_0125:SSA_0126:50S ribosomal protein L30, putative:50S ribosomal protein L15, putative:->->:117253..117406 154 gctttgctggtttaacaactttaaattaaaatacgttaggggatgggattttctcagcccctaaaactaaatatatgtataggcgagtttatataggagacaccttttctcctatatgagcgctagcattttacaaaagaggagaaataatata Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_0125:SSA_0126|SSA_0125:SSA_0126:50S ribosomal protein L30, putative:50S ribosomal protein L15, putative:->->:117253..117406 154 gctttgctggtttaacaactttaaattaaaatacgttaggggatgggattttctcagcccctaaaactaaatatatgtataggcgagtttatataggagacaccttttctcctatatgagcgctagcattttacaaaagaggagaaataatata Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gctttgctggtttaacaactttaaattaaaatacgttaggggatgggattttctcagcccctaaaactaaatatatgtataggcgagtttatataggagacaccttttctcctatatgagcgctagcattttacaaaagaggagaaataatata Predict ORF larger than 30AA ================================================ gctttgctggtttaacaactttaaattaaaatacgttaggggatgggattttctcagcccctaaaactaaatatatgtataggcgagtttatataggagacaccttttctcctatatgagcgctagcattttacaaaagaggagaaataatata 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: 83 Start: 3 End: 32 ..TTTGCTGGTTTAACAACTTTAAATTAAAAT.......................................................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ gctttgctggtttaacaactttaaattaaaatacgttaggggatgggattttctcagcccctaaaactaaatatatgtataggcgagtttatataggagacaccttttctcctatatgagcgctagcattttacaaaagaggagaaataatata Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_0125:SSA_0126|SSA_0125:SSA_0126:50S ribosomal protein L30, putative:50S ribosomal protein L15, putative:->->:117253..117406 154 gctttgctggtttaacaactttaaattaaaatacgttaggggatgggattttctcagcccctaaaactaaatatatgtataggcgagtttatataggagacaccttttctcctatatgagcgctagcattttacaaaagaggagaaataatata Intra-Species Hit: Count: 1 Min: 1 Max: 154 Len: 154 Subject: NC_009009_SSA_0125_SSA_0126|50S ribosomal protein L30, putative:50S ribosomal protein L15, putative|POSITIVE:POSITIVE|[117253,117406]|154 HSP 1 e-value: 2.0E-82 bit: 305.0 Len: 154 Query Start:1 Query End:154 Subject Strand: POSITIVE Subject Start: 1 Subject End: 154 gctttgctggtttaacaactttaaattaaaatacgttaggggatgggattttctcagcccctaaaactaaatatatgtataggcgagtttatataggagacaccttttctcctatatgagcgctagcattttacaaaagaggagaaataatata gctttgctggtttaacaactttaaattaaaatacgttaggggatgggattttctcagcccctaaaactaaatatatgtataggcgagtttatataggagacaccttttctcctatatgagcgctagcattttacaaaagaggagaaataatata Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GCUUUGCUGGUUUAACAACUUUAAAUUAAAAUACGUUAGGGGAUGGGAUUUUCUCAGCCCCUAAAACUAAAUAUAUGUAUAGGCGAGUUUAUAUAGGAGACACCUUUUCUCCUAUAUGAGCGCUAGCAUUUUACAAAAGAGGAGAAAUAAUAUA .(((..((...........................(((((((.((((.....)))).)))))))...........((((...((..((((((((((((((.......))))))))))))))....))....))))..))..))).......... (-42.80) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAUAUUAUUUCUCCUCUUUUGUAAAAUGCUAGCGCUCAUAUAGGAGAAAAGGUGUCUCCUAUAUAAACUCGCCUAUACAUAUAUUUAGUUUUAGGGGCUGAGAAAAUCCCAUCCCCUAACGUAUUUUAAUUUAAAGUUGUUAAACCAGCAAAGC .....................((((((((..(((...((((((((((.......)))))))))).....)))..................(((((((.((.(.....).)).))))))).)))))))).......((((......))))..... (-34.30) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 315 128 93 212 169 NC_009009:SSA_0185|5end_Competence_protein_ComYB,_putative_189057..189287_POSITIVE 279 127 81 182 135 NC_009009:SSA_2277|5end_DNA_segregation_ATPase_FtsK/SpoIIIE_family_protein,_putative_2280407..2280637_NEGATIVE 266 130 82 92 39 NC_009009:SSA_2088|5end_Carbohydrate_isomerase,_AraD/FucA_family,_putative_2093476..2093706_NEGATIVE 264 64 38 170 140 NC_009009:SSA_1967|5end_Threonine_desaminase,_putative_1963559..1963789_NEGATIVE 264 130 81 225 179 NC_009009:SSA_0836|5end_SecA-like_protein,_putative_821508..821738_POSITIVE 264 149 103 62 6 NC_009009:SSA_0574|5end_YdjX_protein,_putative_569427..569657_NEGATIVE 262 64 37 198 166 NC_009009:SSA_0093|5end_V-type_sodium_ATPase,_subunit_D,_putative_94286..94516_POSITIVE 261 126 81 212 173 NC_009009:SSA_0964|5end_DEAD_RNA_helicase,_putative_974114..974344_NEGATIVE 260 59 16 56 19 NC_009009:SSA_1021|5end_Conserved_uncharacterized_protein_1036144..1036374_POSITIVE 256 130 81 214 164 NC_009009:SSA_2220|5end_Galactosyltransferase,_putative_2221439..2221669_NEGATIVE 255 126 82 183 141 NC_009009:SSA_1779|5end_Segregation_and_condensation_protein_A,_putative_1766414..1766644_NEGATIVE 252 90 41 78 22 NC_009009:SSA_0810|5end_P-loop_ATPase,_putative_791582..791812_POSITIVE 252 128 81 69 27 NC_009009:SSA_0502|5end_Peptide_ABC_transporter,_permease_protein,_putative_501554..501784_POSITIVE 242 127 81 124 73 NC_009009:SSA_0269|5end_Phosphotransferase_system_(PTS)_cellobiose-specific_component_IIA,_putative_262550..262780_POSITIVE 240 144 117 174 143 NC_009009:SSA_1485|5end_Citrulline_cluster-linked_gene,_putative_1492809..1493039_NEGATIVE 239 128 81 166 120 NC_009009:SSA_1800|5end_UDP-N-acetylmuramate--L-alanine_ligase,_putative_1782371..1782601_NEGATIVE 239 127 81 173 120 NC_009009:SSA_0334|5end_Diphosphomevalonate_decarboxylase,_putative_327855..328085_POSITIVE 238 127 81 53 9 NC_009009:SSA_2207|5end_hypothetical_protein_2207221..2207451_NEGATIVE 238 130 84 76 24 NC_009009:SSA_0986|5end_Choline_transporter,_putative_988273..988503_POSITIVE 237 144 101 225 165 NC_009009:SSA_2023|5end_Fructan_beta-fructosidase_precursor,_putative_2028826..2029056_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 271 64 36 55 27 NC_009009:SSA_0125|3end_50S_ribosomal_protein_L30,_putative_117192..117342_POSITIVE 270 59 16 81 37 NC_009009:SSA_1729|3end_ABC_transporter_substrate-binding_protein-branched_chain_amino_acid_transport,_putative_1714539..1714689_NEGATIVE 266 130 82 92 39 NC_009009:SSA_2089|3end_L-xylulose-5-phosphate_3-epimerase,_putative_2093476..2093626_NEGATIVE 264 64 38 70 40 NC_009009:SSA_1968|3end_Ketol-acid_reductoisomerase,_putative_1963659..1963809_NEGATIVE 256 123 81 113 59 NC_009009:SSA_0967|3end_hypothetical_protein_976620..976770_POSITIVE 242 127 81 115 64 NC_009009:SSA_0268|3end_Phosphotransferase_system_(PTS)_cellobiose-specific_component_IIB,_putative_262621..262771_POSITIVE 238 130 84 62 10 NC_009009:SSA_0985|3end_hypothetical_protein_988339..988489_POSITIVE 234 148 105 131 100 NC_009009:SSA_1831|3end_hypothetical_protein_1821994..1822144_POSITIVE 233 61 34 67 37 NC_009009:SSA_1066|3end_ABC-type_oligopeptide_transport_system,_putative_1086376..1086526_POSITIVE 233 144 103 42 5 NC_009009:SSA_0158|3end_hypothetical_protein_155074..155224_POSITIVE 231 128 81 116 66 NC_009009:SSA_1713|3end_D-3-phosphoglycerate_dehydrogenase,_putative_1700209..1700359_NEGATIVE 230 112 81 37 6 NC_009009:SSA_1621|3end_Amino_acid_transporter,_putative_1623172..1623322_NEGATIVE 230 127 81 61 12 NC_009009:SSA_0111|3end_30S_ribosomal_protein_S19,_putative_111033..111183_POSITIVE 225 147 102 64 1 NC_009009:SSA_0356|3end_Dipeptidase,_putative_350757..350907_POSITIVE 223 126 83 132 96 NC_009009:SSA_1026|3end_ABC-type_multidrug_transporter,_ATPase_component,_putative_1043617..1043767_POSITIVE 220 70 40 145 112 NC_009009:SSA_1798|3end_hypothetical_protein_1779998..1780148_NEGATIVE 217 127 81 44 6 NC_009009:SSA_2101|3end_Amino_acid_ABC_transporter,_periplasmic_amino_acid-binding_protein,_putative_2104509..2104659_NEGATIVE 217 136 96 67 21 NC_009009:SSA_1409|3end_DTDP-glucose-4,6-dehydratase,_putative_1421209..1421359_NEGATIVE 215 62 38 73 49 NC_009009:SSA_2203|3end_30S_ribosomal_protein_S2,_putative_2203423..2203573_NEGATIVE 215 128 82 121 71 NC_009009:SSA_1531|3end_ABC-type_antimicrobial_peptide_transporter,_ATPase_component,_putative_1538778..1538928_NEGATIVE