Origin IGS: tttttctcttttcttttattttattttaaaactaaaacaagaggctgagacaagtctgtatcagtcccttttttatatagcaggactgagaaagctagaactaaatgcactagctttctctcgtctgcaatgatagcagt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 actgctatcattgcagacgagagaaagctagtgcatttagttctagctttctcagtcctgctatataaaaaagggactgatacagacttgtctcagcctcttgttttagttttaaaataaaataaaagaaaagagaaaaa Mask Tandem Repeat Region ================================================ tttttctcttttcttttattttattttaaaactaaaacaagaggctgagacaagtctgtatcagtcccttttttatatagcaggactgagaaagctagaactaaatgcactagctttctctcgtctgcaatgatagcagt Find is-nt database================================================ Query_seq: SSA_1796:SSA_1797|SSA_1796:SSA_1797:Transcription elongation factor GreA, putative:Aminodeoxychorismate lyase, putative:<-<-:1778398..1778537 140 tttttctcttttcttttattttattttaaaactaaaacaagaggctgagacaagtctgtatcagtcccttttttatatagcaggactgagaaagctagaactaaatgcactagctttctctcgtctgcaatgatagcagt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_1796:SSA_1797|SSA_1796:SSA_1797:Transcription elongation factor GreA, putative:Aminodeoxychorismate lyase, putative:<-<-:1778398..1778537 140 tttttctcttttcttttattttattttaaaactaaaacaagaggctgagacaagtctgtatcagtcccttttttatatagcaggactgagaaagctagaactaaatgcactagctttctctcgtctgcaatgatagcagt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_1796:SSA_1797|SSA_1796:SSA_1797:Transcription elongation factor GreA, putative:Aminodeoxychorismate lyase, putative:<-<-:1778398..1778537 140 tttttctcttttcttttattttattttaaaactaaaacaagaggctgagacaagtctgtatcagtcccttttttatatagcaggactgagaaagctagaactaaatgcactagctttctctcgtctgcaatgatagcagt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tttttctcttttcttttattttattttaaaactaaaacaagaggctgagacaagtctgtatcagtcccttttttatatagcaggactgagaaagctagaactaaatgcactagctttctctcgtctgcaatgatagcagt Predict ORF larger than 30AA ================================================ Protein_Len: 36 Strand: + Start: 23 End: 130 ...................... M L K L K Q E A E T S L Y Q S L F Y I A G L R K L E L N A L A F S R L Q .......... Protein_Len: 37 Strand: - Start: 24 End: 134 ....................... K L V L V L P Q S L D T D T G K K Y L L V S F A L V L H V L K R E D A I M ...... tttttctcttttcttttattttattttaaaactaaaacaagaggctgagacaagtctgtatcagtcccttttttatatagcaggactgagaaagctagaactaaatgcactagctttctctcgtctgcaatgatagcagt Predict Promoter with matrix: RpoD-15 score > 80================================================ Predict Promoter with matrix: RpoD-16 score > 80================================================ Predict Promoter with matrix: RpoD-17 score > 80================================================ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ tttttctcttttcttttattttattttaaaactaaaacaagaggctgagacaagtctgtatcagtcccttttttatatagcaggactgagaaagctagaactaaatgcactagctttctctcgtctgcaatgatagcagt Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 82 HP_score: -4.8 Tail_Score: -5.36441 Start: 41 End: 68 Full_Region: TTAAAACTAAAACAA GAGGCTGAGACA AGTC TGTATCAGTCCC TTTTTTATATAGCAG ........................................GAGGCTGAGACAAGTCTGTATCAGTCCC........................................................................ TransTerm Strand: - Conf: 61 HP_score: -6.9 Tail_Score: -2.87132 Start: 80 End: 128 Full_Region: actgctatcatt gcagacgagagaaagctagtgc attta gttctagctttctcagtcctgc tatataaaaaaggga ...............................................................................gcagacgagagaaagctagtgcatttagttctagctttctcagtcctgc............ TransTerm Strand: + Conf: 72 HP_score: -9.2 Tail_Score: -2.63913 Start: 88 End: 120 Full_Region: TTATATAGCAGGACT GAGAAAGCTAGAAC TAAAT GCACTAGCTTTCTC TCGTCTGCAATGATA .......................................................................................GAGAAAGCTAGAACTAAATGCACTAGCTTTCTC.................... Find igs database================================================ Query_seq: SSA_1796:SSA_1797|SSA_1796:SSA_1797:Transcription elongation factor GreA, putative:Aminodeoxychorismate lyase, putative:<-<-:1778398..1778537 140 tttttctcttttcttttattttattttaaaactaaaacaagaggctgagacaagtctgtatcagtcccttttttatatagcaggactgagaaagctagaactaaatgcactagctttctctcgtctgcaatgatagcagt Intra-Species Hit: Count: 1 Min: 28 Max: 140 Len: 113 Subject: NC_009009_SSA_1796_SSA_1797|Transcription elongation factor GreA, putative:Aminodeoxychorismate lyase, putative|NEGATIVE:NEGATIVE|[1778398,1778537]|140 HSP 1 e-value: 6.0E-58 bit: 224.0 Len: 113 Query Start:28 Query End:140 Subject Strand: POSITIVE Subject Start: 28 Subject End: 140 ...........................aaaactaaaacaagaggctgagacaagtctgtatcagtcccttttttatatagcaggactgagaaagctagaactaaatgcactagctttctctcgtctgcaatgatagcagt ...........................aaaactaaaacaagaggctgagacaagtctgtatcagtcccttttttatatagcaggactgagaaagctagaactaaatgcactagctttctctcgtctgcaatgatagcagt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAACUAAAACAAGAGGCUGAGACAAGUCUGUAUCAGUCCCUUUUUUAUAUAGCAGGACUGAGAAAGCUAGAACUAAAUGCACUAGCUUUCUCUCGUCUGCAAUGAUAGCAGU .....(((((.(((.((((((.(((....))).)))))).))))))))....(((((...(((((((((((..(.....)..)))))))))))...)))))............ (-37.10) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ ACUGCUAUCAUUGCAGACGAGAGAAAGCUAGUGCAUUUAGUUCUAGCUUUCUCAGUCCUGCUAUAUAAAAAAGGGACUGAUACAGACUUGUCUCAGCCUCUUGUUUUAGUUUU ...((((.....((((((..(((((((((((.((.....)).))))))))))).)).)))).........(((((.((((.((......)).)))).)))))....))))... (-37.20) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 934 100 51 218 169 NC_009009:SSA_1796|5end_Transcription_elongation_factor_GreA,_putative_1778307..1778537_NEGATIVE 376 60 12 187 138 NC_009009:SSA_0151|5end_hypothetical_protein_145354..145584_POSITIVE 331 49 5 66 22 NC_009009:SSA_0936|5end_FAD_synthase,_putative_945139..945369_POSITIVE 329 99 51 199 151 NC_009009:SSA_1345|5end_Bifunctional_pyrimidine_operon_transcriptional_attenuation_protein/uracil_phosphoribosyltransferase,_putative_1363879..1364109_NEGATIVE 316 55 16 204 163 NC_009009:SSA_0911|5end_hypothetical_protein_922078..922308_POSITIVE 300 109 67 227 183 NC_009009:SSA_0604|5end_hypothetical_protein_592451..592681_POSITIVE 294 90 52 183 151 NC_009009:SSA_2105|5end_hypothetical_protein_2107802..2108032_NEGATIVE 291 100 51 86 30 NC_009009:SSA_2322|5end_Transcriptional_regulator,_TetR/AcrR_family,_putative_2327044..2327274_POSITIVE 283 54 15 171 121 NC_009009:SSA_1402|5end_ABC-type_multidrug_transport_system,_ATPase_and_permease_components,_putative_1416220..1416450_NEGATIVE 281 45 16 47 17 NC_009009:SSA_2185|5end_Adenylosuccinate_synthetase,_putative_2185290..2185520_NEGATIVE 280 60 12 99 43 NC_009009:SSA_0991|5end_Deoxyribonuclease,_putative_993342..993572_NEGATIVE 277 60 13 197 150 NC_009009:SSA_0492|5end_NADH-dependent_flavin_oxidoreductase,_putative_491588..491818_POSITIVE 276 58 13 222 179 NC_009009:SSA_1658|5end_Cationic_amino_acid_transporter,_putative_1654674..1654904_NEGATIVE 276 48 9 35 1 NC_009009:SSA_0749|5end_Competence_protein,_putative_730668..730898_POSITIVE 273 57 12 155 117 NC_009009:SSA_2082|5end_Carbohydrate_kinase,_FGGY_family,_putative_2086874..2087104_NEGATIVE 272 50 5 150 104 NC_009009:SSA_1784|5end_Glutamate_racemase,_putative_1769897..1770127_NEGATIVE 271 59 36 32 8 NC_009009:SSA_0298|5end_Malate_permease,_putative_291336..291566_POSITIVE 268 100 52 52 3 NC_009009:SSA_0215|5end_Periplasmic_sugar-binding_protein_(ribose_porter),_putative_210891..211121_POSITIVE 266 59 12 106 50 NC_009009:SSA_0574|5end_YdjX_protein,_putative_569427..569657_NEGATIVE 263 110 66 190 148 NC_009009:SSA_2070|5end_Zinc_metalloprotease,_putative_2074574..2074804_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 300 54 12 105 57 NC_009009:SSA_0395|3end_6-phospho-beta-glucosidase,_putative_392580..392730_POSITIVE 294 110 67 51 11 NC_009009:SSA_0057|3end_Phosphotransferase_system_sugar-specific_EII_component,_putative_61246..61396_POSITIVE 290 58 15 146 101 NC_009009:SSA_0815|3end_hypothetical_protein_797411..797561_POSITIVE 277 60 13 142 95 NC_009009:SSA_0491|3end_Alpha-ribazole-5'-phosphate_phosphatase,_putative_491613..491763_POSITIVE 276 58 13 65 22 NC_009009:SSA_1659|3end_ABC-type_antimicrobial_peptide_transport_system,_permease_component,_putative_1654831..1654981_NEGATIVE 273 57 12 79 41 NC_009009:SSA_2083|3end_hypothetical_protein_2086950..2087100_NEGATIVE 272 50 5 51 5 NC_009009:SSA_1786|3end_Conserved_uncharacterized_protein_1769996..1770146_NEGATIVE 272 49 13 86 49 NC_009009:SSA_0304|3end_Bacterial_cell_wall_degradation_(CHAP/LysM_domains),_putative_301888..302038_POSITIVE 271 59 36 27 3 NC_009009:SSA_0297|3end_Malolactic_enzyme,_putative_291411..291561_POSITIVE 266 87 49 75 26 NC_009009:SSA_0826|3end_hypothetical_protein_805516..805666_POSITIVE 262 100 52 81 20 NC_009009:SSA_0379|3end_PTS_system,_beta-glucoside-specific_EII_component,_putative_370833..370983_POSITIVE 261 99 57 107 68 NC_009009:SSA_0966|3end_Uridine_kinase,_putative_975790..975940_POSITIVE 260 59 12 134 59 NC_009009:SSA_1491|3end_Methionine_aminopeptidase_A,_putative_1496780..1496930_NEGATIVE 260 100 52 80 38 NC_009009:SSA_0478|3end_Cobalt_transport_protein_cbiN,_putative_480387..480537_POSITIVE 259 99 51 120 76 NC_009009:SSA_0470|3end_Precorrin-4_methylase,_putative_473732..473882_POSITIVE 257 59 13 53 9 NC_009009:SSA_0266|3end_ORFB,_transposon_ISSsa1_260822..260972_POSITIVE 256 54 12 54 13 NC_009009:SSA_1409|3end_DTDP-glucose-4,6-dehydratase,_putative_1421209..1421359_NEGATIVE 255 110 61 74 4 NC_009009:SSA_0897|3end_Two_component_system_histidine_kinase,_putative_889811..889961_POSITIVE 254 77 37 62 21 NC_009009:SSA_1593|3end_Dipeptidase,_putative_1596390..1596540_NEGATIVE 252 100 52 107 49 NC_009009:SSA_0312|3end_Hydrolase,_metallo-beta-lactamase_superfamily,_putative_306703..306853_NEGATIVE