Origin IGS: tataactgattgccattggagaacacttaacgagtgttctcttttttactaagtgattagacggagactaaccttccgaacttactcttccgataaaaaccattgtaattttgacaaaagaaaagactcagccctgtattacaagaaaactaagtcctttttagaatgatttatcaactttagcgagctgtttctaa .........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 ttagaaacagctcgctaaagttgataaatcattctaaaaaggacttagttttcttgtaatacagggctgagtcttttcttttgtcaaaattacaatggtttttatcggaagagtaagttcggaaggttagtctccgtctaatcacttagtaaaaaagagaacactcgttaagtgttctccaatggcaatcagttata Mask Tandem Repeat Region ================================================ tataactgattgccattggagaacacttaacgagtgttctcttttttactaagtgattagacggagactaaccttccgaacttactcttccgataaaaaccattgtaattttgacaaaagaaaagactcagccctgtattacaagaaaactaagtcctttttagaatgatttatcaactttagcgagctgtttctaa Find is-nt database================================================ Query_seq: SSA_1828:SSA_1829|SSA_1828:SSA_1829:Glycerol uptake facilitator protein, putative:RNA methyltransferase, putative:-><-:1818852..1819048 197 tataactgattgccattggagaacacttaacgagtgttctcttttttactaagtgattagacggagactaaccttccgaacttactcttccgataaaaaccattgtaattttgacaaaagaaaagactcagccctgtattacaagaaaactaagtcctttttagaatgatttatcaactttagcgagctgtttctaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_1828:SSA_1829|SSA_1828:SSA_1829:Glycerol uptake facilitator protein, putative:RNA methyltransferase, putative:-><-:1818852..1819048 197 tataactgattgccattggagaacacttaacgagtgttctcttttttactaagtgattagacggagactaaccttccgaacttactcttccgataaaaaccattgtaattttgacaaaagaaaagactcagccctgtattacaagaaaactaagtcctttttagaatgatttatcaactttagcgagctgtttctaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_1828:SSA_1829|SSA_1828:SSA_1829:Glycerol uptake facilitator protein, putative:RNA methyltransferase, putative:-><-:1818852..1819048 197 tataactgattgccattggagaacacttaacgagtgttctcttttttactaagtgattagacggagactaaccttccgaacttactcttccgataaaaaccattgtaattttgacaaaagaaaagactcagccctgtattacaagaaaactaagtcctttttagaatgatttatcaactttagcgagctgtttctaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tataactgattgccattggagaacacttaacgagtgttctcttttttactaagtgattagacggagactaaccttccgaacttactcttccgataaaaaccattgtaattttgacaaaagaaaagactcagccctgtattacaagaaaactaagtcctttttagaatgatttatcaactttagcgagctgtttctaa Predict ORF larger than 30AA ================================================ Protein_Len: 38 Strand: + Start: 53 End: 166 .................................................... M I R R R L T F R T Y S S D K N H C N F D K R K D S A L Y Y K K T K S F L E ............................... tataactgattgccattggagaacacttaacgagtgttctcttttttactaagtgattagacggagactaaccttccgaacttactcttccgataaaaaccattgtaattttgacaaaagaaaagactcagccctgtattacaagaaaactaagtcctttttagaatgatttatcaactttagcgagctgtttctaa 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: 82 Start: 138 End: 167 .........................................................................................................................................ATTACAAGAAAACTAAGTCCTTTTTAGAAT.............................. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ tataactgattgccattggagaacacttaacgagtgttctcttttttactaagtgattagacggagactaaccttccgaacttactcttccgataaaaaccattgtaattttgacaaaagaaaagactcagccctgtattacaagaaaactaagtcctttttagaatgatttatcaactttagcgagctgtttctaa Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_1828:SSA_1829|SSA_1828:SSA_1829:Glycerol uptake facilitator protein, putative:RNA methyltransferase, putative:-><-:1818852..1819048 197 tataactgattgccattggagaacacttaacgagtgttctcttttttactaagtgattagacggagactaaccttccgaacttactcttccgataaaaaccattgtaattttgacaaaagaaaagactcagccctgtattacaagaaaactaagtcctttttagaatgatttatcaactttagcgagctgtttctaa Intra-Species Hit: Count: 1 Min: 1 Max: 197 Len: 197 Subject: NC_009009_SSA_1828_SSA_1829|Glycerol uptake facilitator protein, putative:RNA methyltransferase, putative|POSITIVE:NEGATIVE|[1818852,1819048]|197 HSP 1 e-value: 1.0E-108 bit: 391.0 Len: 197 Query Start:1 Query End:197 Subject Strand: POSITIVE Subject Start: 1 Subject End: 197 tataactgattgccattggagaacacttaacgagtgttctcttttttactaagtgattagacggagactaaccttccgaacttactcttccgataaaaaccattgtaattttgacaaaagaaaagactcagccctgtattacaagaaaactaagtcctttttagaatgatttatcaactttagcgagctgtttctaa tataactgattgccattggagaacacttaacgagtgttctcttttttactaagtgattagacggagactaaccttccgaacttactcttccgataaaaaccattgtaattttgacaaaagaaaagactcagccctgtattacaagaaaactaagtcctttttagaatgatttatcaactttagcgagctgtttctaa Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAUAACUGAUUGCCAUUGGAGAACACUUAACGAGUGUUCUCUUUUUUACUAAGUGAUUAGACGGAGACUAACCUUCCGAACUUACUCUUCCGAUAAAAACCAUUGUAAUUUUGACAAAAGAAAAGACUCAGCCCUGUAUUACAAGAAAACUAAGUCCUUUUUAGAAUGAUUUAUCAACUUUAGCGAGCUGUUUCUAA .....(((((..(....(((((((((((...)))))))))))..........)..))))).(((((.......)))))........................((((.......))))......(((..((((((((.............(((((.....)))))..(((....)))....))).).))))..))).. (-35.04) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUAGAAACAGCUCGCUAAAGUUGAUAAAUCAUUCUAAAAAGGACUUAGUUUUCUUGUAAUACAGGGCUGAGUCUUUUCUUUUGUCAAAAUUACAAUGGUUUUUAUCGGAAGAGUAAGUUCGGAAGGUUAGUCUCCGUCUAAUCACUUAGUAAAAAAGAGAACACUCGUUAAGUGUUCUCCAAUGGCAAUCAGUUAUA .......(((((......)))))..............((((((((((((...((((.....))))))))))))))))...((((((...((((...(((..(((.((((.((.(((..((....))))).))))))..)))..)))..))))....(((((((((.....)))))))))...))))))......... (-50.20) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 289 79 31 66 8 NC_009009:SSA_2143|5end_Conserved_uncharacterized_protein_2144225..2144455_NEGATIVE 265 150 101 45 7 NC_009009:SSA_0384|5end_hypothetical_protein_376240..376470_POSITIVE 263 95 54 197 162 NC_009009:SSA_0212|5end_Phenylalanyl-tRNA_synthetase,_beta_subunit,_putative_208373..208603_POSITIVE 249 162 122 88 42 NC_009009:SSA_0565|5end_hypothetical_protein_557230..557460_POSITIVE 247 77 33 139 92 NC_009009:SSA_1299|5end_Maltose/maltodextrin_ABC_transport_system,_putative_1316629..1316859_POSITIVE 242 36 6 181 150 NC_009009:SSA_1203|5end_hypothetical_protein_1226985..1227215_POSITIVE 229 170 130 59 19 NC_009009:SSA_1252|5end_hypothetical_protein_1277505..1277735_NEGATIVE 227 153 122 73 41 NC_009009:SSA_2271|5end_hypothetical_protein_2272450..2272680_NEGATIVE 227 91 51 228 185 NC_009009:SSA_2073|5end_Undecaprenyl_pyrophosphate_synthetase,_putative_2076371..2076601_NEGATIVE 227 92 58 87 42 NC_009009:SSA_2024|5end_hypothetical_protein_2029272..2029502_NEGATIVE 226 139 99 70 28 NC_009009:SSA_0574|5end_YdjX_protein,_putative_569427..569657_NEGATIVE 225 102 64 187 154 NC_009009:SSA_0348|5end_CAAX_amino_terminal_protease_family,_putative_340288..340518_POSITIVE 224 160 116 175 116 NC_009009:SSA_1193|5end_Dihydrodipicolinate_synthase,_putative_1220030..1220260_NEGATIVE 223 69 26 223 179 NC_009009:SSA_1574|5end_Glycosyl_transferase,_family_1,_putative_1577930..1578160_NEGATIVE 222 139 92 186 140 NC_009009:SSA_2353|5end_ABC-type_nitrate/sulfonate/bicarbonate_transport_system,_permease_component,_putative_2355302..2355532_NEGATIVE 222 190 143 196 130 NC_009009:SSA_0924|5end_ABC-type_antimicrobial_peptide_transport_system,_permease_component,_putative_933738..933968_POSITIVE 222 185 141 226 170 NC_009009:SSA_0123|5end_50S_ribosomal_protein_L18P,_putative_116048..116278_POSITIVE 221 50 4 215 179 NC_009009:SSA_1230|5end_Conserved_uncharacterized_protein_1253358..1253588_NEGATIVE 218 87 41 141 98 NC_009009:SSA_1793|5end_Histidine_kinase_(sensor_protein),_putative_1776361..1776591_NEGATIVE 216 103 63 129 94 NC_009009:SSA_0977|5end_3-isopropylmalate_dehydrogenase,_putative_982771..983001_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 293 160 120 41 1 NC_009009:SSA_0611|3end_HtpX_protease,_putative_600515..600665_POSITIVE 278 189 149 112 62 NC_009009:SSA_0999|3end_Biotin--[acetyl-CoA-carboxylase]_ligase,_putative_998781..998931_NEGATIVE 253 70 21 110 52 NC_009009:SSA_1828|3end_Glycerol_uptake_facilitator_protein,_putative_1818791..1818941_POSITIVE 247 77 33 57 10 NC_009009:SSA_1298|3end_Maltose/maltodextrin_ABC_transporter,_sugar-binding_protein_MalX,_putative_1316627..1316777_POSITIVE 227 159 127 47 13 NC_009009:SSA_0470|3end_Precorrin-4_methylase,_putative_473732..473882_POSITIVE 226 90 43 123 77 NC_009009:SSA_0593|3end_Rhodanese-like_sulfurtransferase,_putative_585551..585701_POSITIVE 225 102 64 141 108 NC_009009:SSA_0346|3end_hypothetical_protein_340322..340472_POSITIVE 224 160 116 92 33 NC_009009:SSA_1194|3end_Aspartate-semialdehyde_dehydrogenase,_putative_1220113..1220263_NEGATIVE 223 95 57 141 104 NC_009009:SSA_0403|3end_CAAX_amino_terminal_protease_family,_putative_401388..401538_POSITIVE 222 190 143 76 10 NC_009009:SSA_0923|3end_Transcriptional_regulator,_TetR/AcrR_family,_putative_933698..933848_POSITIVE 222 185 141 141 85 NC_009009:SSA_0122|3end_50S_ribosomal_protein_L6,_putative_116043..116193_POSITIVE 221 79 34 117 79 NC_009009:SSA_2185|3end_Adenylosuccinate_synthetase,_putative_2183998..2184148_NEGATIVE 220 129 88 59 15 NC_009009:SSA_1302|3end_tRNA_(Guanine-N(1)-)-methyltransferase,_putative_1321762..1321912_NEGATIVE 218 48 7 149 105 NC_009009:SSA_0133|3end_50S_ribosomal_protein_L17,_putative_122562..122712_POSITIVE 216 103 63 47 12 NC_009009:SSA_0975|3end_2-isopropylmalate_synthase,_putative_982769..982919_POSITIVE 213 89 44 91 44 NC_009009:SSA_2189|3end_hypothetical_protein_2190279..2190429_NEGATIVE 213 46 6 139 112 NC_009009:SSA_0379|3end_PTS_system,_beta-glucoside-specific_EII_component,_putative_370833..370983_POSITIVE 211 67 24 85 41 NC_009009:SSA_1175|3end_Acetoin_dehydrogenase_complex,_E2_component,_dihydrolipoamide_acetyltransferase,_putative_1202933..1203083_NEGATIVE 210 92 59 69 45 NC_009009:SSA_1413|3end_GufA-like_protein,_putative_1424095..1424245_NEGATIVE 210 46 11 146 105 NC_009009:SSA_0708|3end_hypothetical_protein_694757..694907_POSITIVE