Origin IGS: ttttacctcattattgaatatttagaagctgcattcatgaagaatactccatccgatcaaagactgcttctccatcaatctaggcaaagatttgcaggaatactgagaataaataaaaaactttaaccaagagtgacagggaaggaagcatttagatggaaaactcatctataaatacaggttcttatccctcttattatatcagaaaaattcctattagcccaaaaattattcccaaaaaaattgaagattccttgaaaaatgtgataaaataataacaaaagacacaaaggagcaaat .........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.........1.........2.........3.........4.........5.........6.........7.........8.........9 atttgctcctttgtgtcttttgttattattttatcacatttttcaaggaatcttcaatttttttgggaataatttttgggctaataggaatttttctgatataataagagggataagaacctgtatttatagatgagttttccatctaaatgcttccttccctgtcactcttggttaaagttttttatttattctcagtattcctgcaaatctttgcctagattgatggagaagcagtctttgatcggatggagtattcttcatgaatgcagcttctaaatattcaataatgaggtaaaa Mask Tandem Repeat Region ================================================ ttttacctcattattgaatatttagaagctgcattcatgaagaatactccatccgatcaaagactgcttctccatcaatctaggcaaagatttgcaggaatactgagaataaataaaaaactttaaccaagagtgacagggaaggaagcatttagatggaaaactcatctataaatacaggttcttatccctcttattatatcagaaaaattcctattagcccaaaaattattcccaaaaaaattgaagattccttgaaaaatgtgataaaataataacaaaagacacaaaggagcaaat Find is-nt database================================================ Query_seq: SSA_2261:SSA_2262|SSA_2261:SSA_2262:Transcriptional repressor (arginine synthesis), putative:Arginyl-tRNA synthetase, putative:<-->:2258757..2259056 300 ttttacctcattattgaatatttagaagctgcattcatgaagaatactccatccgatcaaagactgcttctccatcaatctaggcaaagatttgcaggaatactgagaataaataaaaaactttaaccaagagtgacagggaaggaagcatttagatggaaaactcatctataaatacaggttcttatccctcttattatatcagaaaaattcctattagcccaaaaattattcccaaaaaaattgaagattccttgaaaaatgtgataaaataataacaaaagacacaaaggagcaaat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_2261:SSA_2262|SSA_2261:SSA_2262:Transcriptional repressor (arginine synthesis), putative:Arginyl-tRNA synthetase, putative:<-->:2258757..2259056 300 ttttacctcattattgaatatttagaagctgcattcatgaagaatactccatccgatcaaagactgcttctccatcaatctaggcaaagatttgcaggaatactgagaataaataaaaaactttaaccaagagtgacagggaaggaagcatttagatggaaaactcatctataaatacaggttcttatccctcttattatatcagaaaaattcctattagcccaaaaattattcccaaaaaaattgaagattccttgaaaaatgtgataaaataataacaaaagacacaaaggagcaaat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_2261:SSA_2262|SSA_2261:SSA_2262:Transcriptional repressor (arginine synthesis), putative:Arginyl-tRNA synthetase, putative:<-->:2258757..2259056 300 ttttacctcattattgaatatttagaagctgcattcatgaagaatactccatccgatcaaagactgcttctccatcaatctaggcaaagatttgcaggaatactgagaataaataaaaaactttaaccaagagtgacagggaaggaagcatttagatggaaaactcatctataaatacaggttcttatccctcttattatatcagaaaaattcctattagcccaaaaattattcccaaaaaaattgaagattccttgaaaaatgtgataaaataataacaaaagacacaaaggagcaaat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ttttacctcattattgaatatttagaagctgcattcatgaagaatactccatccgatcaaagactgcttctccatcaatctaggcaaagatttgcaggaatactgagaataaataaaaaactttaaccaagagtgacagggaaggaagcatttagatggaaaactcatctataaatacaggttcttatccctcttattatatcagaaaaattcctattagcccaaaaattattcccaaaaaaattgaagattccttgaaaaatgtgataaaataataacaaaagacacaaaggagcaaat Predict ORF larger than 30AA ================================================ Protein_Len: 38 Strand: + Start: 10 End: 123 ......... M I E Y L E A A F M K N T P S D Q R L L L H Q S R Q R F A G I L R I N K K L ................................................................................................................................................................................. Protein_Len: 39 Strand: + Start: 156 End: 272 ........................................................................................................................................................... M E N S S I N T G S Y P S Y Y I R K I P I S P K I I P K K I E D S L K N V I K ............................ Protein_Len: 33 Strand: - Start: 200 End: 298 ....................................................................................................................................................................................................... I L F I G I L G F I I G L F I S S E K F F T I F Y Y C F V C L L M .. Protein_Len: 41 Strand: - Start: 168 End: 290 ....................................................................................................................................................................... R Y I C T R I G R I I D S F N R N A W F N N G F F N F I G Q F I H Y F L L L L C M .......... Protein_Len: 48 Strand: - Start: 25 End: 168 ........................ F S C E H L I S W G I L S Q K E M L R P L S K C S Y Q S Y I F F K L W S H C P L F C K S P F S M .................................................................................................................................... ttttacctcattattgaatatttagaagctgcattcatgaagaatactccatccgatcaaagactgcttctccatcaatctaggcaaagatttgcaggaatactgagaataaataaaaaactttaaccaagagtgacagggaaggaagcatttagatggaaaactcatctataaatacaggttcttatccctcttattatatcagaaaaattcctattagcccaaaaattattcccaaaaaaattgaagattccttgaaaaatgtgataaaataataacaaaagacacaaaggagcaaat 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: 196 End: 225 ...................................................................................................................................................................................................TTGGGCTAATAGGAATTTTTCTGATATAAT........................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ ttttacctcattattgaatatttagaagctgcattcatgaagaatactccatccgatcaaagactgcttctccatcaatctaggcaaagatttgcaggaatactgagaataaataaaaaactttaaccaagagtgacagggaaggaagcatttagatggaaaactcatctataaatacaggttcttatccctcttattatatcagaaaaattcctattagcccaaaaattattcccaaaaaaattgaagattccttgaaaaatgtgataaaataataacaaaagacacaaaggagcaaat Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_2261:SSA_2262|SSA_2261:SSA_2262:Transcriptional repressor (arginine synthesis), putative:Arginyl-tRNA synthetase, putative:<-->:2258757..2259056 300 ttttacctcattattgaatatttagaagctgcattcatgaagaatactccatccgatcaaagactgcttctccatcaatctaggcaaagatttgcaggaatactgagaataaataaaaaactttaaccaagagtgacagggaaggaagcatttagatggaaaactcatctataaatacaggttcttatccctcttattatatcagaaaaattcctattagcccaaaaattattcccaaaaaaattgaagattccttgaaaaatgtgataaaataataacaaaagacacaaaggagcaaat Intra-Species Hit: Count: 1 Min: 1 Max: 300 Len: 300 Subject: NC_009009_SSA_2261_SSA_2262|Transcriptional repressor (arginine synthesis), putative:Arginyl-tRNA synthetase, putative|NEGATIVE:POSITIVE|[2258757,2259056]|300 HSP 1 e-value: 1.0E-156 bit: 553.0 Len: 300 Query Start:1 Query End:300 Subject Strand: POSITIVE Subject Start: 1 Subject End: 300 ttttacctcattattgaatatttagaagctgcattcatgaagaatactccatccgatcaaagactgcttctccatcaatctaggcaaagatttgcaggaatactgagaataaataaaaaactttaaccaagagtgacagggaaggaagcatttagatggaaaactcatctataaatacaggttcttatccctcttattatatcagaaaaattcctattagcccaaaaattattcccnnnnnnnttgaagattccttgaaaaatgtgataaaataataacaaaagacacaaaggagcaaat ttttacctcattattgaatatttagaagctgcattcatgaagaatactccatccgatcaaagactgcttctccatcaatctaggcaaagatttgcaggaatactgagaataaataaaaaactttaaccaagagtgacagggaaggaagcatttagatggaaaactcatctataaatacaggttcttatccctcttattatatcagaaaaattcctattagcccaaaaattattcccaaaaaaattgaagattccttgaaaaatgtgataaaataataacaaaagacacaaaggagcaaat Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUUACCUCAUUAUUGAAUAUUUAGAAGCUGCAUUCAUGAAGAAUACUCCAUCCGAUCAAAGACUGCUUCUCCAUCAAUCUAGGCAAAGAUUUGCAGGAAUACUGAGAAUAAAUAAAAAACUUUAACCAAGAGUGACAGGGAAGGAAGCAUUUAGAUGGAAAACUCAUCUAUAAAUACAGGUUCUUAUCCCUCUUAUUAUAUCAGAAAAAUUCCUAUUAGCCCAAAAAUUAUUCCCAAAAAAAUUGAAGAUUCCUUGAAAAAUGUGAUAAAAUAAUAACAAAAGACACAAAGGAGCAAAU .......(((....)))...(((((((......))).)))).....((((......((((.((...((((......(((((......)))))...((((((.((((.(((((.......(((((.....)))))...((((((((((.(...(((((((.....)))))))........).))))).))))).)))))...))))....))))))..............................))))..)).))))....((((...................))))..))))..... (-45.21) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUUUGCUCCUUUGUGUCUUUUGUUAUUAUUUUAUCACAUUUUUCAAGGAAUCUUCAAUUUUUUUGGGAAUAAUUUUUGGGCUAAUAGGAAUUUUUCUGAUAUAAUAAGAGGGAUAAGAACCUGUAUUUAUAGAUGAGUUUUCCAUCUAAAUGCUUCCUUCCCUGUCACUCUUGGUUAAAGUUUUUUAUUUAUUCUCAGUAUUCCUGCAAAUCUUUGCCUAGAUUGAUGGAGAAGCAGUCUUUGAUCGGAUGGAGUAUUCUUCAUGAAUGCAGCUUCUAAAUAUUCAAUAAUGAGGUAAAA .(((((..(..(((.((((((((((......(((((...((..(((((((........)))))))..)).((((((((......))))))))....))))))))))))))).)))((((.((((((((((.((.((((.(((((((((((.(((..((((.((((((.(((.(((.((((..........(((..(((.....)))..)))))))))).))).)))))).)))).))).)))....)))))))).)))).)))))))))))).))))..............)..))))). (-69.90) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 913 90 41 181 132 NC_009009:SSA_2261|5end_Transcriptional_repressor_(arginine_synthesis),_putative_2258666..2258896_NEGATIVE 314 90 41 135 92 NC_009009:SSA_0299|5end_hypothetical_protein_292759..292989_POSITIVE 303 86 47 173 138 NC_009009:SSA_2275|5end_hypothetical_protein_2275590..2275820_NEGATIVE 299 99 64 63 25 NC_009009:SSA_1008|5end_Galactokinase,_putative_1009856..1010086_POSITIVE 297 99 52 72 23 NC_009009:SSA_0591|5end_Conserved_uncharacterized_protein_582769..582999_POSITIVE 289 68 27 59 2 NC_009009:SSA_0179|5end_hypothetical_protein_183966..184196_POSITIVE 280 80 34 70 26 NC_009009:SSA_1275|5end_hypothetical_protein_1297606..1297836_NEGATIVE 280 80 34 222 178 NC_009009:SSA_1274|5end_hypothetical_protein_1297454..1297684_NEGATIVE 276 44 1 139 93 NC_009009:SSA_1742|5end_Ferrichrome-binding_protein,_putative_1728872..1729102_POSITIVE 275 90 47 72 35 NC_009009:SSA_1937|5end_Malonyl-CoA:ACP_transacylase,_putative_1924771..1925001_NEGATIVE 275 109 61 185 127 NC_009009:SSA_1377|5end_Asparaginyl-tRNA_synthetase,_putative_1397614..1397844_NEGATIVE 272 98 56 60 14 NC_009009:SSA_0495|5end_ABC-type_oligopeptide/nickel_transport_system,_ATPase_component,_putative_495186..495416_POSITIVE 271 90 48 172 114 NC_009009:SSA_2159|5end_hypothetical_protein_2159621..2159851_NEGATIVE 269 109 65 122 75 NC_009009:SSA_2212|5end_Possible_polysaccharide_transport_protein,_putative_2213928..2214158_NEGATIVE 267 90 48 180 140 NC_009009:SSA_2243|5end_Conserved_uncharacterized_protein_2239341..2239571_NEGATIVE 267 87 52 63 28 NC_009009:SSA_2018|5end_hypothetical_protein_2018801..2019031_NEGATIVE 266 236 203 187 154 NC_009009:SSA_1829|5end_RNA_methyltransferase,_putative_1820329..1820559_NEGATIVE 264 86 47 56 1 NC_009009:SSA_2285|5end_hypothetical_protein_2287404..2287634_POSITIVE 261 107 64 209 162 NC_009009:SSA_0954|5end_hypothetical_protein_958024..958254_POSITIVE 258 170 127 94 52 NC_009009:SSA_1242|5end_Dihydroorotate_dehydrogenase_B,_putative_1267386..1267616_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 326 88 49 82 48 NC_009009:SSA_0789|3end_Proton-translocating_ATPase,_F1_sector,_epsilon_subunit,_putative_772953..773103_POSITIVE 289 68 27 66 9 NC_009009:SSA_0178|3end_UDP-N-acetylglucosamine_2-epimerase,_putative_184053..184203_POSITIVE 276 44 1 59 13 NC_009009:SSA_1741|3end_ABC-type_Fe3+-siderophores_transporter,_ATPase_component,_putative_1728872..1729022_POSITIVE 275 90 47 79 42 NC_009009:SSA_1938|3end_Enoyl-acyl_carrier_protein(ACP)_reductase,_putative_1924764..1924914_NEGATIVE 272 98 56 63 17 NC_009009:SSA_0494|3end_ABC-type_dipeptide/oligopeptide/nickel_transport_system,_ATPase_component,_putative_495269..495419_POSITIVE 267 90 48 44 4 NC_009009:SSA_2244|3end_Arsenate_reductase,_putative_2239477..2239627_NEGATIVE 267 87 52 52 17 NC_009009:SSA_2019|3end_hypothetical_protein_2018812..2018962_NEGATIVE 266 99 66 50 18 NC_009009:SSA_1610|3end_hypothetical_protein_1614004..1614154_NEGATIVE 266 110 65 144 101 NC_009009:SSA_0713|3end_1-acyl-sn-glycerol-3-phosphate_acyltransferase,_putative_700028..700178_POSITIVE 258 96 61 151 105 NC_009009:SSA_1378|3end_hypothetical_protein_1397636..1397786_NEGATIVE 258 170 127 82 40 NC_009009:SSA_1243|3end_Dihydroorotate_dehydrogenase_electron_transfer_subunit,_putative_1267398..1267548_NEGATIVE 257 60 24 128 77 NC_009009:SSA_0279|3end_Sugar-binding_transcriptional_repressor_(DeoR),_putative_273370..273520_POSITIVE 256 85 42 147 96 NC_009009:SSA_0826|3end_hypothetical_protein_805516..805666_POSITIVE 253 88 41 95 41 NC_009009:SSA_1255|3end_hypothetical_protein_1281456..1281606_NEGATIVE 249 99 64 128 91 NC_009009:SSA_1776|3end_Potassium_uptake_protein,_Trk_family,_putative_1764158..1764308_POSITIVE 249 85 42 70 25 NC_009009:SSA_1510|3end_Rhamnosyltransferase,_putative_1514188..1514338_NEGATIVE 247 77 31 51 3 NC_009009:SSA_1649|3end_hypothetical_protein_1647906..1648056_NEGATIVE 243 98 51 150 97 NC_009009:SSA_1994|3end_CTP_synthase,_putative_1990861..1991011_NEGATIVE 243 95 51 133 94 NC_009009:SSA_0865|3end_hypothetical_protein_856850..857000_POSITIVE 242 86 48 151 112 NC_009009:SSA_2160|3end_Deoxyuridinetriphosphatase,_putative_2159623..2159773_NEGATIVE