Origin IGS: cgtatttctcctttttgcacaagtgactacatttttattttaatgagttgtcacttaaaagaccatcacagtataacatcgtgtggtcactttgtcaaacccaaaagaccgtcagaccggcctttttcggctattataaaaaaggaggatgattttctagaatatttctgaaagccgcaaaaccttgtcagatagcgaatttacctacctattctgttttttgacaaagaaaaaacaagtgctgtt .........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 aacagcacttgttttttctttgtcaaaaaacagaataggtaggtaaattcgctatctgacaaggttttgcggctttcagaaatattctagaaaatcatcctccttttttataatagccgaaaaaggccggtctgacggtcttttgggtttgacaaagtgaccacacgatgttatactgtgatggtcttttaagtgacaactcattaaaataaaaatgtagtcacttgtgcaaaaaggagaaatacg Mask Tandem Repeat Region ================================================ cgtatttctcctttttgcacaagtgactacatttttattttaatgagttgtcacttaaaagaccatcacagtataacatcgtgtggtcactttgtcaaacccaaaagaccgtcagaccggcctttttcggctattataaaaaaggaggatgattttctagaatatttctgaaagccgcaaaaccttgtcagatagcgaatttacctacctattctgttttttgacaaagaaaaaacaagtgctgtt Find is-nt database================================================ Query_seq: SSA_0386:SSA_0387|SSA_0386:SSA_0387:Glycine-betaine ABC transporter, ATPase component, putative:Transcriptional regulator, GntR family, putative:<-<-:381546..381791 246 cgtatttctcctttttgcacaagtgactacatttttattttaatgagttgtcacttaaaagaccatcacagtataacatcgtgtggtcactttgtcaaacccaaaagaccgtcagaccggcctttttcggctattataaaaaaggaggatgattttctagaatatttctgaaagccgcaaaaccttgtcagatagcgaatttacctacctattctgttttttgacaaagaaaaaacaagtgctgtt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_0386:SSA_0387|SSA_0386:SSA_0387:Glycine-betaine ABC transporter, ATPase component, putative:Transcriptional regulator, GntR family, putative:<-<-:381546..381791 246 cgtatttctcctttttgcacaagtgactacatttttattttaatgagttgtcacttaaaagaccatcacagtataacatcgtgtggtcactttgtcaaacccaaaagaccgtcagaccggcctttttcggctattataaaaaaggaggatgattttctagaatatttctgaaagccgcaaaaccttgtcagatagcgaatttacctacctattctgttttttgacaaagaaaaaacaagtgctgtt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_0386:SSA_0387|SSA_0386:SSA_0387:Glycine-betaine ABC transporter, ATPase component, putative:Transcriptional regulator, GntR family, putative:<-<-:381546..381791 246 cgtatttctcctttttgcacaagtgactacatttttattttaatgagttgtcacttaaaagaccatcacagtataacatcgtgtggtcactttgtcaaacccaaaagaccgtcagaccggcctttttcggctattataaaaaaggaggatgattttctagaatatttctgaaagccgcaaaaccttgtcagatagcgaatttacctacctattctgttttttgacaaagaaaaaacaagtgctgtt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 cgtatttctcctttttgcacaagtgactacatttttattttaatgagttgtcacttaaaagaccatcacagtataacatcgtgtggtcactttgtcaaacccaaaagaccgtcagaccggcctttttcggctattataaaaaaggaggatgattttctagaatatttctgaaagccgcaaaaccttgtcagatagcgaatttacctacctattctgttttttgacaaagaaaaaacaagtgctgtt Predict ORF larger than 30AA ================================================ Protein_Len: 34 Strand: + Start: 48 End: 149 ............................................... M S L K R P S Q Y N I V W S L C Q T Q K T V R P A F F G Y Y K K G G ................................................................................................. Protein_Len: 55 Strand: + Start: 4 End: 168 ... M S P F C T S D Y I F I L M S C H L K D H H S I T S C G H F V K P K R P S D R P F S A I I K K E D D F L E Y F .............................................................................. Protein_Len: 37 Strand: - Start: 90 End: 200 ......................................................................................... K T L G L L G D S R G K E A I I F F S S S K R S Y K Q F G C F R T L Y R M .............................................. cgtatttctcctttttgcacaagtgactacatttttattttaatgagttgtcacttaaaagaccatcacagtataacatcgtgtggtcactttgtcaaacccaaaagaccgtcagaccggcctttttcggctattataaaaaaggaggatgattttctagaatatttctgaaagccgcaaaaccttgtcagatagcgaatttacctacctattctgttttttgacaaagaaaaaacaagtgctgtt 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: 88 Start: 70 End: 99 .....................................................................TTTGACAAAGTGACCACACGATGTTATACT................................................................................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ cgtatttctcctttttgcacaagtgactacatttttattttaatgagttgtcacttaaaagaccatcacagtataacatcgtgtggtcactttgtcaaacccaaaagaccgtcagaccggcctttttcggctattataaaaaaggaggatgattttctagaatatttctgaaagccgcaaaaccttgtcagatagcgaatttacctacctattctgttttttgacaaagaaaaaacaagtgctgtt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_0386:SSA_0387|SSA_0386:SSA_0387:Glycine-betaine ABC transporter, ATPase component, putative:Transcriptional regulator, GntR family, putative:<-<-:381546..381791 246 cgtatttctcctttttgcacaagtgactacatttttattttaatgagttgtcacttaaaagaccatcacagtataacatcgtgtggtcactttgtcaaacccaaaagaccgtcagaccggcctttttcggctattataaaaaaggaggatgattttctagaatatttctgaaagccgcaaaaccttgtcagatagcgaatttacctacctattctgttttttgacaaagaaaaaacaagtgctgtt Intra-Species Hit: Count: 1 Min: 1 Max: 246 Len: 246 Subject: NC_009009_SSA_0386_SSA_0387|Glycine-betaine ABC transporter, ATPase component, putative:Transcriptional regulator, GntR family, putative|NEGATIVE:NEGATIVE|[381546,381791]|246 HSP 1 e-value: 1.0E-137 bit: 488.0 Len: 246 Query Start:1 Query End:246 Subject Strand: POSITIVE Subject Start: 1 Subject End: 246 cgtatttctcctttttgcacaagtgactacatttttattttaatgagttgtcacttaaaagaccatcacagtataacatcgtgtggtcactttgtcaaacccaaaagaccgtcagaccggcctttttcggctattataaaaaaggaggatgattttctagaatatttctgaaagccgcaaaaccttgtcagatagcgaatttacctacctattctgttttttgacaaagaaaaaacaagtgctgtt cgtatttctcctttttgcacaagtgactacatttttattttaatgagttgtcacttaaaagaccatcacagtataacatcgtgtggtcactttgtcaaacccaaaagaccgtcagaccggcctttttcggctattataaaaaaggaggatgattttctagaatatttctgaaagccgcaaaaccttgtcagatagcgaatttacctacctattctgttttttgacaaagaaaaaacaagtgctgtt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CGUAUUUCUCCUUUUUGCACAAGUGACUACAUUUUUAUUUUAAUGAGUUGUCACUUAAAAGACCAUCACAGUAUAACAUCGUGUGGUCACUUUGUCAAACCCAAAAGACCGUCAGACCGGCCUUUUUCGGCUAUUAUAAAAAAGGAGGAUGAUUUUCUAGAAUAUUUCUGAAAGCCGCAAAACCUUGUCAGAUAGCGAAUUUACCUACCUAUUCUGUUUUUUGACAAAGAAAAAACAAGUGCUGUU .((((((((((((((((((.((((((((((((..((((.....(((...(((........)))..)))....))))....)))))))))))))))....((.(((((.(((......))).)))))..))........))))))))))).(..((((.(((.....)))))))..)......(.((((((((.(((((((..........)))).))).)))))))).).........)))).... (-54.40) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AACAGCACUUGUUUUUUCUUUGUCAAAAAACAGAAUAGGUAGGUAAAUUCGCUAUCUGACAAGGUUUUGCGGCUUUCAGAAAUAUUCUAGAAAAUCAUCCUCCUUUUUUAUAAUAGCCGAAAAAGGCCGGUCUGACGGUCUUUUGGGUUUGACAAAGUGACCACACGAUGUUAUACUGUGAUGGUCUUUUAAGUGACAACUCAUUAAAAUAAAAAUGUAGUCACUUGUGCAAAAAGGAGAAAUACG ....((((.........(((((((((.....((((.(((.(((.....((((.((((....))))...)))).(((((((.....))).)))).....)))))).))))......(((..(((((((((......))))))))).)))))))))))).(((((((((.........)))).)))))....(((((((....((((........))))..)))))))))))................ (-64.60) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 982 130 81 221 172 NC_009009:SSA_0386|5end_Glycine-betaine_ABC_transporter,_ATPase_component,_putative_381455..381685_NEGATIVE 327 149 101 68 19 NC_009009:SSA_0434|5end_Glutamate_formiminotransferase,_putative_436568..436798_NEGATIVE 318 133 111 30 6 NC_009009:SSA_2124|5end_Dehydrogenase,_eukaryotic-like,_putative_2129411..2129641_NEGATIVE 301 130 82 61 1 NC_009009:SSA_0468|5end_Precorrin-6y_C5,15-methyltransferase-like,_putative_471706..471936_POSITIVE 296 130 82 50 1 NC_009009:SSA_1913|5end_Xanthine/uracil_permease_family_protein,_putative_1904666..1904896_NEGATIVE 295 121 85 74 41 NC_009009:SSA_1634|5end_Heme_utilization/adhesion_exoprotein,_putative_1637062..1637292_NEGATIVE 289 120 78 163 105 NC_009009:SSA_0925|5end_ABC-type_antimicrobial_peptide_transport_system,_ATPase_component,_putative_934749..934979_POSITIVE 288 130 84 223 171 NC_009009:SSA_1707|5end_Conserved_uncharacterized_protein_1697782..1698012_POSITIVE 288 120 71 203 151 NC_009009:SSA_0025|5end_DNA_repair_protein_recO,_putative_29694..29924_POSITIVE 287 129 86 218 163 NC_009009:SSA_1187|5end_Transcriptional_antiterminator,_BglG_family,_putative_1216037..1216267_NEGATIVE 284 50 1 157 97 NC_009009:SSA_1013|5end_Phosphatidylserine_synthase,_putative_1017221..1017451_POSITIVE 281 129 83 192 135 NC_009009:SSA_0102|5end_Kinase,_putative_104035..104265_POSITIVE 280 93 54 141 93 NC_009009:SSA_1254|5end_hypothetical_protein_1281484..1281714_NEGATIVE 278 130 86 213 151 NC_009009:SSA_2243|5end_Conserved_uncharacterized_protein_2239341..2239571_NEGATIVE 276 128 90 178 139 NC_009009:SSA_1771|5end_Conserved_DNA_methyltransferase_protein,_putative_1758799..1759029_NEGATIVE 276 206 165 75 13 NC_009009:SSA_0573|5end_hypothetical_protein_568732..568962_NEGATIVE 270 128 84 144 81 NC_009009:SSA_1242|5end_Dihydroorotate_dehydrogenase_B,_putative_1267386..1267616_NEGATIVE 270 124 81 55 17 NC_009009:SSA_0807|5end_GTP-binding_protein,_putative_789449..789679_POSITIVE 270 123 84 65 16 NC_009009:SSA_0540|5end_Glycerol_uptake_facilitator_protein,_putative_534955..535185_POSITIVE 269 146 101 53 7 NC_009009:SSA_1938|5end_Enoyl-acyl_carrier_protein(ACP)_reductase,_putative_1925738..1925968_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 324 127 81 75 17 NC_009009:SSA_1909|3end_Transcriptional_attenuator_LytR,_putative_1900904..1901054_NEGATIVE 278 130 86 77 15 NC_009009:SSA_2244|3end_Arsenate_reductase,_putative_2239477..2239627_NEGATIVE 276 128 90 82 43 NC_009009:SSA_1772|3end_hypothetical_protein_1758895..1759045_NEGATIVE 274 158 114 77 43 NC_009009:SSA_1379|3end_hypothetical_protein_1398178..1398328_NEGATIVE 274 127 98 29 3 NC_009009:SSA_0992|3end_hypothetical_protein_994147..994297_POSITIVE 273 119 80 133 103 NC_009009:SSA_0923|3end_Transcriptional_regulator,_TetR/AcrR_family,_putative_933698..933848_POSITIVE 270 128 84 132 69 NC_009009:SSA_1243|3end_Dihydroorotate_dehydrogenase_electron_transfer_subunit,_putative_1267398..1267548_NEGATIVE 262 148 106 45 10 NC_009009:SSA_1568|3end_ABC_transporter_membrane-spanning_permease,_arginine/histidine_transport,_putative_1571960..1572110_POSITIVE 262 133 100 74 42 NC_009009:SSA_0467|3end_Cobalt-precorrin-6A_synthase_[deacetylating],_putative_471795..471945_POSITIVE 259 130 81 75 37 NC_009009:SSA_2072|3end_Phosphatidate_cytidylyltransferase,_putative_2074800..2074950_NEGATIVE 254 133 116 18 1 NC_009009:SSA_2125|3end_Small_primase-like_protein_(Toprim_domain),_putative_2129423..2129573_NEGATIVE 254 130 84 80 38 NC_009009:SSA_0486|3end_Uroporphyrinogen-III_synthase,_putative_487442..487592_POSITIVE 252 157 113 74 37 NC_009009:SSA_1140|3end_Dihydrolipoamide_acetyl_transferase,_E2_component,_putative_1169207..1169357_POSITIVE 252 132 106 46 18 NC_009009:SSA_0757|3end_N-acetyl-gamma-glutamyl-phosphate_reductase,_putative_740698..740848_POSITIVE 250 195 151 121 74 NC_009009:SSA_1059|3end_hypothetical_protein_1076754..1076904_POSITIVE 250 197 163 120 84 NC_009009:SSA_0320|3end_hypothetical_protein_313824..313974_POSITIVE 249 130 83 66 16 NC_009009:SSA_2378|3end_Two-component_system_transcriptional_regulator,_LytR/AlgR_family,_putative_2383129..2383279_NEGATIVE 249 196 152 137 80 NC_009009:SSA_2335|3end_D-Ala-teichoic_acid_biosynthesis_protein,_putative_2338027..2338177_NEGATIVE 246 130 82 86 23 NC_009009:SSA_2227|3end_Acetyl_transferase,_putative_2227716..2227866_NEGATIVE 245 133 94 57 21 NC_009009:SSA_1651|3end_hypothetical_protein_1649587..1649737_NEGATIVE