Origin IGS: ttttaaatcctcctttgtggttttggcggtaattagagatttttacctcccacaagtatgctttacacatactcatctattatacactatttatctataattgcaagagaaaagtttattttttatactca .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tgagtataaaaaataaacttttctcttgcaattatagataaatagtgtataatagatgagtatgtgtaaagcatacttgtgggaggtaaaaatctctaattaccgccaaaaccacaaaggaggatttaaaa Mask Tandem Repeat Region ================================================ ttttaaatcctcctttgtggttttggcggtaattagagatttttacctcccacaagtatgctttacacatactcatctattatacactatttatctataattgcaagagaaaagtttattttttatactca Find is-nt database================================================ Query_seq: SMT_866:SMT_867|SMT_866:SMT_867:50S ribosomal protein L11:hypothetical protein:<-->:816325..816455 131 ttttaaatcctcctttgtggttttggcggtaattagagatttttacctcccacaagtatgctttacacatactcatctattatacactatttatctataattgcaagagaaaagtttattttttatactca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_866:SMT_867|SMT_866:SMT_867:50S ribosomal protein L11:hypothetical protein:<-->:816325..816455 131 ttttaaatcctcctttgtggttttggcggtaattagagatttttacctcccacaagtatgctttacacatactcatctattatacactatttatctataattgcaagagaaaagtttattttttatactca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_866:SMT_867|SMT_866:SMT_867:50S ribosomal protein L11:hypothetical protein:<-->:816325..816455 131 ttttaaatcctcctttgtggttttggcggtaattagagatttttacctcccacaagtatgctttacacatactcatctattatacactatttatctataattgcaagagaaaagtttattttttatactca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ttttaaatcctcctttgtggttttggcggtaattagagatttttacctcccacaagtatgctttacacatactcatctattatacactatttatctataattgcaagagaaaagtttattttttatactca Predict ORF larger than 30AA ================================================ Protein_Len: 31 Strand: + Start: 39 End: 131 ...................................... M F T S H K Y A L H I L I Y Y T L F I Y N C K R K V Y F L Y S ttttaaatcctcctttgtggttttggcggtaattagagatttttacctcccacaagtatgctttacacatactcatctattatacactatttatctataattgcaagagaaaagtttattttttatactca 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: 100 End: 129 ...................................................................................................ATTGCAAGAGAAAAGTTTATTTTTTATACT.. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ ttttaaatcctcctttgtggttttggcggtaattagagatttttacctcccacaagtatgctttacacatactcatctattatacactatttatctataattgcaagagaaaagtttattttttatactca Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SMT_866:SMT_867|SMT_866:SMT_867:50S ribosomal protein L11:hypothetical protein:<-->:816325..816455 131 ttttaaatcctcctttgtggttttggcggtaattagagatttttacctcccacaagtatgctttacacatactcatctattatacactatttatctataattgcaagagaaaagtttattttttatactca Intra-Species Hit: Count: 1 Min: 1 Max: 131 Len: 131 Subject: smit_SMT_866_SMT_867|50S ribosomal protein L11:hypothetical protein|NEGATIVE:POSITIVE|[816325,816455]|131 HSP 1 e-value: 1.0E-68 bit: 260.0 Len: 131 Query Start:1 Query End:131 Subject Strand: POSITIVE Subject Start: 1 Subject End: 131 ttttaaatcctcctttgtggttttggcggtaattagagatttttacctcccacaagtatgctttacacatactcatctattatacactatttatctataattgcaagagaaaagtttattttttatactca ttttaaatcctcctttgtggttttggcggtaattagagatttttacctcccacaagtatgctttacacatactcatctattatacactatttatctataattgcaagagaaaagtttattttttatactca Inter-species Hit: Count: 3 Min: 1 Max: 131 Len: 131 Subject: NC_008533_SPD_0549_SPD_0550|lipoprotein, putative:ribosomal protein L11|POSITIVE:POSITIVE|[561971,562278]|308 HSP 1 e-value: 5.0E-52 bit: 204.0 Len: 131 Query Start:1 Query End:131 Subject Strand: NEGATIVE Subject Start: 178 Subject End: 308 ttttaaatcctcctttgtggttttggcggtaattagagatttttacctcccacaagtatgctttacacatactcatctattatacactatttatctataattgcaagagaaaagtttattttttatactca ttttaaatcctcctttgtggttttggcggtaattagagatttttacctcccacaagtatgtttttcacatacccatccattatacactatttatctggaattgcaagagaaaagtttattttttgtactca Subject: NC_003098_spr0554_spr0555|hypothetical protein:50S ribosomal protein L11|POSITIVE:POSITIVE|[554441,554748]|308 HSP 1 e-value: 5.0E-52 bit: 204.0 Len: 131 Query Start:1 Query End:131 Subject Strand: NEGATIVE Subject Start: 178 Subject End: 308 ttttaaatcctcctttgtggttttggcggtaattagagatttttacctcccacaagtatgctttacacatactcatctattatacactatttatctataattgcaagagaaaagtttattttttatactca ttttaaatcctcctttgtggttttggcggtaattagagatttttacctcccacaagtatgtttttcacatacccatccattatacactatttatctggaattgcaagagaaaagtttattttttgtactca Subject: NC_003028_SP_0629_SP_0630|hypothetical protein:50S ribosomal protein L11|POSITIVE:POSITIVE|[596487,596794]|308 HSP 1 e-value: 1.0E-49 bit: 196.0 Len: 131 Query Start:1 Query End:131 Subject Strand: NEGATIVE Subject Start: 178 Subject End: 308 ttttaaatcctcctttgtggttttggcggtaattagagatttttacctcccacaagtatgctttacacatactcatctattatacactatttatctataattgcaagagaaaagtttattttttatactca ttttaaatcctcctttgtggttttggcggtaattagagatttttacctcccacaagtatgtttttcacatacccatccattatacactatttatctggaattgcaagagaaaagtttactttttgtactca Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUUAAAUCCUCCUUUGUGGUUUUGGCGGUAAUUAGAGAUUUUUACCUCCCACAAGUAUGCUUUACACAUACUCAUCUAUUAUACACUAUUUAUCUAUAAUUGCAAGAGAAAAGUUUAUUUUUUAUACUCA ...(((((..((.((((..(((..((.(((((..(....)..))))).))....((((((.......)))))).........................)))..)))).))...)))))............. (-17.80) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGAGUAUAAAAAAUAAACUUUUCUCUUGCAAUUAUAGAUAAAUAGUGUAUAAUAGAUGAGUAUGUGUAAAGCAUACUUGUGGGAGGUAAAAAUCUCUAAUUACCGCCAAAACCACAAAGGAGGAUUUAAAA ....................(((((((...((((((.((.....)).))))))..(..(((((((.....)))))))..).((.(((((..........))))).))..........)))))))....... (-24.90) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 865 60 11 151 102 smit:SMT_866|5end_50S_ribosomal_protein_L11_816234..816464_NEGATIVE 299 60 14 108 63 smit:SMT_167|5end_acetyltransferase,_GNAT_family_113171..113401_POSITIVE 242 50 6 102 53 smit:SMT_1067|5end_alanine_racemase_1005769..1005999_POSITIVE 240 38 8 163 135 smit:SMT_568|5end_hypothetical_protein_485674..485904_POSITIVE 238 67 24 220 177 smit:SMT_1487|5end_hypothetical_protein_1466361..1466591_POSITIVE 235 63 22 157 119 smit:SMT_723|5end_hypothetical_protein_629475..629705_NEGATIVE 231 80 39 159 95 smit:SMT_807|5end_hypothetical_protein_predicted_by_Glimmer/Critica_716815..717045_NEGATIVE 227 50 8 204 147 smit:SMT_1116|5end_K02244_competence_protein_ComGB_1053841..1054071_NEGATIVE 225 37 8 124 98 smit:SMT_889|5end_K02029_polar_amino_acid_transport_system_permease_protein_836266..836496_POSITIVE 223 43 1 137 96 smit:SMT_1366|5end_K02238_competence_protein_ComEC_1346888..1347118_NEGATIVE 223 50 5 150 101 smit:SMT_1292|5end_K02050_sulfonate/nitrate/taurine_transport_system_permease_protein_1254179..1254409_POSITIVE 222 67 26 120 75 smit:SMT_1021|5end_K05846_osmoprotectant_transport_system_permease_protein_957999..958229_NEGATIVE 220 48 7 175 135 smit:SMT_1984|5end_phosphinothricin_N-acetyltransferase_1914028..1914258_NEGATIVE 220 48 7 175 135 smit:SMT_1869|5end_phosphinothricin_N-acetyltransferase_1829215..1829445_NEGATIVE 218 50 10 103 52 smit:SMT_1774|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1750666..1750896_NEGATIVE 217 42 8 46 12 smit:SMT_301|5end_hypothetical_protein_244086..244316_POSITIVE 216 48 10 202 167 smit:SMT_1289|5end_hypothetical_protein_1252208..1252438_POSITIVE 215 58 17 173 130 smit:SMT_1921|5end_D-alanine-activating_enzyme_1863185..1863415_POSITIVE 214 59 11 91 24 smit:SMT_1085|5end_sensor_histidine_kinase_(homolog_to_HK11_Spn)_1022267..1022497_NEGATIVE 214 50 4 159 95 smit:SMT_993|5end_hypothetical_protein_935476..935706_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 299 60 14 64 19 smit:SMT_166|3end_hypothetical_protein_113207..113357_POSITIVE 242 50 6 112 63 smit:SMT_1066|3end_holo-(acyl_carrier_protein)_synthase_1005859..1006009_POSITIVE 231 41 12 71 45 smit:SMT_325|3end_K02029_polar_amino_acid_transport_system_permease_protein_262247..262397_NEGATIVE 225 37 8 111 85 smit:SMT_888|3end_K02030_polar_amino_acid_transport_system_substrate-binding_protein_836333..836483_POSITIVE 222 67 26 127 82 smit:SMT_1022|3end_glycine_betaine_transport_ATP-binding_protein_957992..958142_NEGATIVE 219 50 10 83 39 smit:SMT_2046|3end_choline_binding_protein_C_1957280..1957430_NEGATIVE 214 60 27 138 105 smit:SMT_2108|3end_adenylosuccinate_lyase_1998744..1998894_NEGATIVE 214 50 14 86 53 smit:SMT_195|3end_30S_ribosomal_protein_S13_127322..127472_POSITIVE 213 56 12 84 31 smit:SMT_1826|3end_ATP_synthase_beta_chain_1797622..1797772_POSITIVE 213 48 5 96 44 smit:SMT_666|3end_GTP_pyrophosphokinase-like_protein_576729..576879_NEGATIVE 210 109 61 131 90 smit:SMT_1043|3end_chaperonin_GroEL_985110..985260_NEGATIVE 207 123 86 127 90 smit:SMT_1303|3end_tRNA-dihydrouridine_synthase_1264676..1264826_NEGATIVE 207 77 35 112 58 smit:SMT_486|3end_hypothetical_protein_421460..421610_NEGATIVE 205 41 1 151 112 smit:SMT_1367|3end_K02237_competence_protein_ComEA_1346872..1347022_NEGATIVE 205 39 4 144 95 smit:SMT_994|3end_nicotinate-nucleotide_adenylyltransferase_935476..935626_NEGATIVE 204 51 13 83 45 smit:SMT_178|3end_50S_ribosomal_protein_L29_119447..119597_POSITIVE 203 34 1 139 103 smit:SMT_1879|3end_K06147_ATP-binding_cassette,_subfamily_B,_bacterial_1836567..1836717_NEGATIVE 202 40 9 126 90 smit:SMT_1963|3end_ribonuclease_BN,_putative_1895911..1896061_NEGATIVE 201 57 15 67 20 smit:SMT_1591|3end_DNA-entry_nuclease_1579468..1579618_POSITIVE 201 50 7 130 93 smit:SMT_1423|3end_hypothetical_protein_1409811..1409961_POSITIVE