Origin IGS: tttattatatcataaatgcattatgatacactaaaatatttaaaaatattttagttttttccaaaatttgttgacaaaaaaggacagtctgtattaattttcggtaaattctttcttccttctcgaaaaaccaatattttatactgtttttgacaacagaaaaagaggtaaaacctcttttatatcagtattttacttggttt .........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 aaaccaagtaaaatactgatataaaagaggttttacctctttttctgttgtcaaaaacagtataaaatattggtttttcgagaaggaagaaagaatttaccgaaaattaatacagactgtccttttttgtcaacaaattttggaaaaaactaaaatatttttaaatattttagtgtatcataatgcatttatgatataataaa Mask Tandem Repeat Region ================================================ tttattatatcataaatgcattatgatacactaaaatatttaaaaatattttagttttttccaaaatttgttgacaaaaaaggacagtctgtattaattttcggtaaattctttcttccttctcgaaaaaccaatattttatactgtttttgacaacagaaaaagaggtaaaacctcttttatatcagtattttacttggttt Find is-nt database================================================ Query_seq: SSA_2225:SSA_2226|SSA_2225:SSA_2226:Transcriptional attenuator LytR, putative:Organic radical activating chaperone, putative:<-<-:2227038..2227240 203 tttattatatcataaatgcattatgatacactaaaatatttaaaaatattttagttttttccaaaatttgttgacaaaaaaggacagtctgtattaattttcggtaaattctttcttccttctcgaaaaaccaatattttatactgtttttgacaacagaaaaagaggtaaaacctcttttatatcagtattttacttggttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_2225:SSA_2226|SSA_2225:SSA_2226:Transcriptional attenuator LytR, putative:Organic radical activating chaperone, putative:<-<-:2227038..2227240 203 tttattatatcataaatgcattatgatacactaaaatatttaaaaatattttagttttttccaaaatttgttgacaaaaaaggacagtctgtattaattttcggtaaattctttcttccttctcgaaaaaccaatattttatactgtttttgacaacagaaaaagaggtaaaacctcttttatatcagtattttacttggttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_2225:SSA_2226|SSA_2225:SSA_2226:Transcriptional attenuator LytR, putative:Organic radical activating chaperone, putative:<-<-:2227038..2227240 203 tttattatatcataaatgcattatgatacactaaaatatttaaaaatattttagttttttccaaaatttgttgacaaaaaaggacagtctgtattaattttcggtaaattctttcttccttctcgaaaaaccaatattttatactgtttttgacaacagaaaaagaggtaaaacctcttttatatcagtattttacttggttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tttattatatcataaatgcattatgatacactaaaatatttaaaaatattttagttttttccaaaatttgttgacaaaaaaggacagtctgtattaattttcggtaaattctttcttccttctcgaaaaaccaatattttatactgtttttgacaacagaaaaagaggtaaaacctcttttatatcagtattttacttggttt Predict ORF larger than 30AA ================================================ Protein_Len: 32 Strand: + Start: 108 End: 203 ........................................................................................................... M L S S F S K N Q Y F I L F L T T E K E V K P L L Y Q Y F T W F Protein_Len: 45 Strand: - Start: 8 End: 142 ....... I M F A N H Y V L I N L F I K T K E L I Q Q C F L V T Q I L K R Y I R E E K E F F W Y K M ............................................................. tttattatatcataaatgcattatgatacactaaaatatttaaaaatattttagttttttccaaaatttgttgacaaaaaaggacagtctgtattaattttcggtaaattctttcttccttctcgaaaaaccaatattttatactgtttttgacaacagaaaaagaggtaaaacctcttttatatcagtattttacttggttt 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: 38 End: 67 .....................................ATTTAAAAATATTTTAGTTTTTTCCAAAAT........................................................................................................................................ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ tttattatatcataaatgcattatgatacactaaaatatttaaaaatattttagttttttccaaaatttgttgacaaaaaaggacagtctgtattaattttcggtaaattctttcttccttctcgaaaaaccaatattttatactgtttttgacaacagaaaaagaggtaaaacctcttttatatcagtattttacttggttt Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 71 HP_score: -8.4 Tail_Score: -2.96395 Start: 31 End: 54 Full_Region: aaattttggaaaaaa ctaaaatatt ttta aatattttag tgtatcataatgcat ..............................ctaaaatatttttaaatattttag..................................................................................................................................................... TransTerm Strand: + Conf: 83 HP_score: -7.7 Tail_Score: -4.56961 Start: 165 End: 177 Full_Region: TTGACAACAGAAAAA GAGGT AAA ACCTC TTTTATATCAGTATT ....................................................................................................................................................................GAGGTAAAACCTC.......................... Find igs database================================================ Query_seq: SSA_2225:SSA_2226|SSA_2225:SSA_2226:Transcriptional attenuator LytR, putative:Organic radical activating chaperone, putative:<-<-:2227038..2227240 203 tttattatatcataaatgcattatgatacactaaaatatttaaaaatattttagttttttccaaaatttgttgacaaaaaaggacagtctgtattaattttcggtaaattctttcttccttctcgaaaaaccaatattttatactgtttttgacaacagaaaaagaggtaaaacctcttttatatcagtattttacttggttt Intra-Species Hit: Count: 1 Min: 1 Max: 203 Len: 203 Subject: NC_009009_SSA_2225_SSA_2226|Transcriptional attenuator LytR, putative:Organic radical activating chaperone, putative|NEGATIVE:NEGATIVE|[2227038,2227240]|203 HSP 1 e-value: 4.0E-63 bit: 242.0 Len: 122 Query Start:82 Query End:203 Subject Strand: POSITIVE Subject Start: 82 Subject End: 203 .................................................................................ggacagtctgtattaattttcggtaaattctttcttccttctcgaaaaaccaatattttatactgtttttgacaacagaaaaagaggtaaaacctcttttatatcagtattttacttggttt .................................................................................ggacagtctgtattaattttcggtaaattctttcttccttctcgaaaaaccaatattttatactgtttttgacaacagaaaaagaggtaaaacctcttttatatcagtattttacttggttt HSP 2 e-value: 2.0E-9 bit: 63.9 Len: 32 Query Start:1 Query End:32 Subject Strand: POSITIVE Subject Start: 1 Subject End: 32 tttattatatcataaatgcattatgatacact........................................................................................................................................................................... tttattatatcataaatgcattatgatacact........................................................................................................................................................................... Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUAUUAUAUCAUAAAUGCAUUAUGAUACACUAAAAUAUUUAAAAAUAUUUUAGUUUUUUCCAAAAUUUGUUGACAAAAAAGGACAGUCUGUAUUAAUUUUCGGUAAAUUCUUUCUUCCUUCUCGAAAAACCAAUAUUUUAUACUGUUUUUGACAACAGAAAAAGAGGUAAAACCUCUUUUAUAUCAGUAUUUUACUUGGUUU .......((((((((.....)))))))).(((((((((((....))))))))))).....((((..(((((((.((((....((((((..(((((..(((((((..................)))))))...))))).....)))))))))).)))))))((((((((.....))))))))...............))))... (-40.27) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAACCAAGUAAAAUACUGAUAUAAAAGAGGUUUUACCUCUUUUUCUGUUGUCAAAAACAGUAUAAAAUAUUGGUUUUUCGAGAAGGAAGAAAGAAUUUACCGAAAAUUAAUACAGACUGUCCUUUUUUGUCAACAAAUUUUGGAAAAAACUAAAAUAUUUUUAAAUAUUUUAGUGUAUCAUAAUGCAUUUAUGAUAUAAUAAA ...(((((..............((((((((.....))))))))..(((((.((((((((((......((((((((((.((..(((..........)))..))))))))))))...)))))....))))).)))))...))))).....(((((((((((....)))))))))))(((((((((.....)))))))))...... (-45.40) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 776 130 81 221 172 NC_009009:SSA_2225|5end_Transcriptional_attenuator_LytR,_putative_2226947..2227177_NEGATIVE 255 125 81 220 178 NC_009009:SSA_0041|5end_hypothetical_protein_47662..47892_POSITIVE 254 127 95 108 66 NC_009009:SSA_0568|5end_Aspartyl-tRNA_synthetase_1,_putative_561674..561904_POSITIVE 252 127 81 115 65 NC_009009:SSA_1017|5end_hypothetical_protein_1022072..1022302_POSITIVE 247 126 83 127 69 NC_009009:SSA_1392|5end_hypothetical_protein_1408423..1408653_NEGATIVE 244 127 82 109 50 NC_009009:SSA_1794|5end_Two-component_response_transcriptional_regulator_(CheY-like_receiver_and_winged-helix_DNA-binding_domains),_putative_1777049..1777279_NEGATIVE 244 125 82 115 58 NC_009009:SSA_1037|5end_Cytidine_deaminase,_putative_1052118..1052348_POSITIVE 233 120 79 85 40 NC_009009:SSA_2301|5end_S-layer_protein/_peptidoglycan_endo-beta-N-acetylglucosaminidase,_putative_2303268..2303498_NEGATIVE 232 118 81 108 59 NC_009009:SSA_2356|5end_Replicative_DNA_helicase,_putative_2357958..2358188_NEGATIVE 231 126 82 109 56 NC_009009:SSA_1147|5end_Beta-glucosides_PTS,_EIIB,_putative_1176782..1177012_POSITIVE 231 126 85 108 70 NC_009009:SSA_0476|5end_Precorrin-2_C20-methyltransferase,_putative_478500..478730_POSITIVE 227 119 79 59 22 NC_009009:SSA_2185|5end_Adenylosuccinate_synthetase,_putative_2185290..2185520_NEGATIVE 227 126 81 94 41 NC_009009:SSA_1816|5end_hypothetical_protein_1802885..1803115_NEGATIVE 225 119 75 55 11 NC_009009:SSA_1016|5end_Phosphoenolpyruvate_synthase,_putative_1019602..1019832_POSITIVE 225 127 82 96 51 NC_009009:SSA_0306|5end_Transcription_regulator_(glutamine_synthetase_repressor),_putative_302590..302820_POSITIVE 224 176 144 214 173 NC_009009:SSA_1700|5end_hypothetical_protein_1691288..1691518_NEGATIVE 220 160 111 66 28 NC_009009:SSA_2129|5end_Arsenical_resistance_operon_transcription_repressor_(ArsR),_putative_2133308..2133538_NEGATIVE 219 104 62 219 172 NC_009009:SSA_1701|5end_Transcriptional_repressor_of_sugar_metabolism,_GlpR/DeoR_family,_putative_1692054..1692284_NEGATIVE 218 199 156 204 147 NC_009009:SSA_2066|5end_DNA_polymerase_III_polC-type,_putative_2070137..2070367_NEGATIVE 218 125 82 110 61 NC_009009:SSA_0603|5end_Cobalt_transporter,_putative_591596..591826_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 265 126 82 61 18 NC_009009:SSA_1459|3end_RNA_methyltransferase,_putative_1466111..1466261_NEGATIVE 254 123 84 120 86 NC_009009:SSA_1754|3end_hypothetical_protein_1743125..1743275_NEGATIVE 252 127 81 128 78 NC_009009:SSA_1016|3end_Phosphoenolpyruvate_synthase,_putative_1022165..1022315_POSITIVE 247 126 83 136 78 NC_009009:SSA_1393|3end_hypothetical_protein_1408414..1408564_NEGATIVE 246 150 102 132 82 NC_009009:SSA_1256|3end_NAD-dependent_deacetylase,_putative_1282357..1282507_NEGATIVE 244 127 82 107 48 NC_009009:SSA_1795|3end_Guanosine_3',5'-bis-pyrophosphate_(ppGpp)_synthetase,_putative_1777051..1777201_NEGATIVE 244 125 82 128 71 NC_009009:SSA_1036|3end_Deoxyribose-phosphate_aldolase,_putative_1052211..1052361_POSITIVE 233 120 79 49 4 NC_009009:SSA_2302|3end_Type_IV_fimbrial_biogenesis_protein,_prepilin_cysteine_protease_(C20)_PilD,_putative_2303304..2303454_NEGATIVE 232 118 81 81 32 NC_009009:SSA_2357|3end_50S_ribosomal_protein_L9,_putative_2357985..2358135_NEGATIVE 231 126 82 112 59 NC_009009:SSA_1146|3end_Phosphotransferase_system_cellobiose-specific_component_IIA,_putative_1176865..1177015_POSITIVE 231 126 85 98 60 NC_009009:SSA_0475|3end_CbiK_protein,_putative_478570..478720_POSITIVE 227 126 81 101 48 NC_009009:SSA_1817|3end_Conserved_uncharacterized_protein_1802878..1803028_NEGATIVE 225 119 75 55 11 NC_009009:SSA_1015|3end_4-hydroxybenzoate_octaprenyltransferase,_putative_1019682..1019832_POSITIVE 223 181 145 81 41 NC_009009:SSA_0446|3end_hypothetical_protein_444764..444914_NEGATIVE 219 104 62 76 29 NC_009009:SSA_1702|3end_hypothetical_protein_1692197..1692347_NEGATIVE 218 125 82 117 68 NC_009009:SSA_0602|3end_ABC-type_cobalt_transport_system,_ATPase_component,_putative_591683..591833_POSITIVE 215 124 86 120 83 NC_009009:SSA_0906|3end_CshA-like_fibrillar_surface_protein_C_917411..917561_POSITIVE 212 124 84 78 44 NC_009009:SSA_0379|3end_PTS_system,_beta-glucoside-specific_EII_component,_putative_370833..370983_POSITIVE 206 121 81 111 60 NC_009009:SSA_2086|3end_hypothetical_protein_2090397..2090547_NEGATIVE 202 123 86 130 97 NC_009009:SSA_1626|3end_DNA_translocase_ftsK,_putative_1627077..1627227_NEGATIVE