Origin IGS: tatttaaaagaatctcgcttgtcagtgagattcttttttgtgttttccggcctgcaaattttagcatggaaacttcgctcgatatatggtataatgggcctatcgcatatttttaggagaataaaa .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 ttttattctcctaaaaatatgcgataggcccattataccatatatcgagcgaagtttccatgctaaaatttgcaggccggaaaacacaaaaaagaatctcactgacaagcgagattcttttaaata Mask Tandem Repeat Region ================================================ tatttaaaagaatctcgcttgtcagtgagattcttttttgtgttttccggcctgcaaattttagcatggaaacttcgctcgatatatggtataatgggcctatcgcatatttttaggagaataaaa Find is-nt database================================================ Query_seq: SSA_1082:SSA_1083|SSA_1082:SSA_1083:PTS system, fructose specific II ABC components, putative:Conserved uncharacterized protein:->->:1101312..1101437 126 tatttaaaagaatctcgcttgtcagtgagattcttttttgtgttttccggcctgcaaattttagcatggaaacttcgctcgatatatggtataatgggcctatcgcatatttttaggagaataaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_1082:SSA_1083|SSA_1082:SSA_1083:PTS system, fructose specific II ABC components, putative:Conserved uncharacterized protein:->->:1101312..1101437 126 tatttaaaagaatctcgcttgtcagtgagattcttttttgtgttttccggcctgcaaattttagcatggaaacttcgctcgatatatggtataatgggcctatcgcatatttttaggagaataaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_1082:SSA_1083|SSA_1082:SSA_1083:PTS system, fructose specific II ABC components, putative:Conserved uncharacterized protein:->->:1101312..1101437 126 tatttaaaagaatctcgcttgtcagtgagattcttttttgtgttttccggcctgcaaattttagcatggaaacttcgctcgatatatggtataatgggcctatcgcatatttttaggagaataaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tatttaaaagaatctcgcttgtcagtgagattcttttttgtgttttccggcctgcaaattttagcatggaaacttcgctcgatatatggtataatgggcctatcgcatatttttaggagaataaaa Predict ORF larger than 30AA ================================================ Protein_Len: 34 Strand: + Start: 12 End: 113 ........... M S L V S E I L F C V F R P A N F S M E T S L D I W Y N G P I A Y F ............. Protein_Len: 36 Strand: + Start: 19 End: 126 .................. M S V R F F F V F S G L Q I L A W K L R S I Y G I M G L S H I F R R I K Protein_Len: 40 Strand: - Start: 3 End: 122 .. K F S D R K D T L N K K T N E P R C I K A H F S R E I Y P I I P R D C I K L L M .... Protein_Len: 34 Strand: - Start: 2 End: 103 . N L L I E S T L S I R K Q T K R G A F K L M S V E S S I H Y L P G M ....................... tatttaaaagaatctcgcttgtcagtgagattcttttttgtgttttccggcctgcaaattttagcatggaaacttcgctcgatatatggtataatgggcctatcgcatatttttaggagaataaaa 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: 85 Start: 66 End: 95 .................................................................ATGGAAACTTCGCTCGATATATGGTATAAT............................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ tatttaaaagaatctcgcttgtcagtgagattcttttttgtgttttccggcctgcaaattttagcatggaaacttcgctcgatatatggtataatgggcctatcgcatatttttaggagaataaaa Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_1082:SSA_1083|SSA_1082:SSA_1083:PTS system, fructose specific II ABC components, putative:Conserved uncharacterized protein:->->:1101312..1101437 126 tatttaaaagaatctcgcttgtcagtgagattcttttttgtgttttccggcctgcaaattttagcatggaaacttcgctcgatatatggtataatgggcctatcgcatatttttaggagaataaaa Intra-Species Hit: Count: 1 Min: 1 Max: 126 Len: 126 Subject: NC_009009_SSA_1082_SSA_1083|PTS system, fructose specific II ABC components, putative:Conserved uncharacterized protein|POSITIVE:POSITIVE|[1101312,1101437]|126 HSP 1 e-value: 9.0E-66 bit: 250.0 Len: 126 Query Start:1 Query End:126 Subject Strand: POSITIVE Subject Start: 1 Subject End: 126 tatttaaaagaatctcgcttgtcagtgagattcttttttgtgttttccggcctgcaaattttagcatggaaacttcgctcgatatatggtataatgggcctatcgcatatttttaggagaataaaa tatttaaaagaatctcgcttgtcagtgagattcttttttgtgttttccggcctgcaaattttagcatggaaacttcgctcgatatatggtataatgggcctatcgcatatttttaggagaataaaa Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAUUUAAAAGAAUCUCGCUUGUCAGUGAGAUUCUUUUUUGUGUUUUCCGGCCUGCAAAUUUUAGCAUGGAAACUUCGCUCGAUAUAUGGUAUAAUGGGCCUAUCGCAUAUUUUUAGGAGAAUAAAA .....((((((((((((((....))))))))))))))...((((((((..(((((........))).)).......(((((.((((...)))).)))))................))))))))... (-34.70) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUUAUUCUCCUAAAAAUAUGCGAUAGGCCCAUUAUACCAUAUAUCGAGCGAAGUUUCCAUGCUAAAAUUUGCAGGCCGGAAAACACAAAAAAGAAUCUCACUGACAAGCGAGAUUCUUUUAAAUA ........((((....(((((..((((.....))))..)))))....)).))..(((((.(((........)))....)))))......(((((((((((.((....)).)))))))))))..... (-25.80) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 336 56 13 122 76 NC_009009:SSA_0676|5end_Farnesyl_diphosphate_synthase,_putative_658598..658828_POSITIVE 328 100 52 68 29 NC_009009:SSA_1493|5end_hypothetical_protein_1499480..1499710_NEGATIVE 324 55 17 205 163 NC_009009:SSA_2239|5end_Conserved_uncharacterized_cytosolic_protein_2237233..2237463_NEGATIVE 315 56 13 45 1 NC_009009:SSA_2277|5end_DNA_segregation_ATPase_FtsK/SpoIIIE_family_protein,_putative_2280407..2280637_NEGATIVE 310 53 15 47 10 NC_009009:SSA_1763|5end_ABC-type_molybdenum_transport_system,_ATPase_component,_putative_1750077..1750307_POSITIVE 304 83 41 49 4 NC_009009:SSA_2019|5end_hypothetical_protein_2019078..2019308_NEGATIVE 299 105 62 144 86 NC_009009:SSA_0152|5end_hypothetical_protein_145799..146029_POSITIVE 298 100 59 46 1 NC_009009:SSA_1341|5end_Carbamoyl-phosphate_synthase_large_chain,_putative_1359827..1360057_NEGATIVE 292 107 64 215 171 NC_009009:SSA_0517|5end_Sensor_histidine_kinase,_putative_515060..515290_POSITIVE 285 56 13 117 82 NC_009009:SSA_0140|5end_Copper-translocating_P-type_ATPase,_putative_134626..134856_POSITIVE 280 89 42 154 105 NC_009009:SSA_0620|5end_hypothetical_protein_612325..612555_NEGATIVE 275 108 64 219 181 NC_009009:SSA_0238|5end_hypothetical_protein_232481..232711_POSITIVE 273 80 31 149 105 NC_009009:SSA_2219|5end_UDP-glucose_4-epimerase,_putative_2220827..2221057_NEGATIVE 273 52 16 46 9 NC_009009:SSA_1550|5end_hypothetical_protein_1552665..1552895_NEGATIVE 273 100 52 231 181 NC_009009:SSA_1307|5end_Trk_transporter_membrane-spanning_protein-K+_transport,_putative_1326270..1326500_NEGATIVE 272 90 43 66 17 NC_009009:SSA_0114|5end_50S_ribosomal_protein_L16,_putative_111979..112209_POSITIVE 271 54 14 120 77 NC_009009:SSA_2337|5end_hypothetical_protein_2338680..2338910_POSITIVE 271 90 52 118 73 NC_009009:SSA_1969|5end_Acetolactate_synthase_small_subunit,_putative_1965222..1965452_NEGATIVE 268 58 15 65 12 NC_009009:SSA_1167|5end_SRP54,_signal_recognition_particle_GTPase_protein,_putative_1192517..1192747_POSITIVE 266 90 43 149 104 NC_009009:SSA_0467|5end_Cobalt-precorrin-6A_synthase_[deacetylating],_putative_470588..470818_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 338 79 32 46 1 NC_009009:SSA_2230|3end_Ribonucleotide_reductase,_class_III,_anaerobic,_putative_2228963..2229113_NEGATIVE 336 56 13 125 79 NC_009009:SSA_0675|3end_Exodeoxyribonuclease_VII_small_subunit,_putative_658681..658831_POSITIVE 310 37 6 85 54 NC_009009:SSA_1082|3end_PTS_system,_fructose_specific_II_ABC_components,_putative_1101251..1101401_POSITIVE 299 105 62 136 78 NC_009009:SSA_0151|3end_hypothetical_protein_145871..146021_POSITIVE 285 79 40 151 111 NC_009009:SSA_1140|3end_Dihydrolipoamide_acetyl_transferase,_E2_component,_putative_1169207..1169357_POSITIVE 285 56 13 117 82 NC_009009:SSA_0139|3end_Copper_transport_operon_or_penicillinase_transcriptional_repressor,_putative_134706..134856_POSITIVE 273 80 31 142 98 NC_009009:SSA_2220|3end_Galactosyltransferase,_putative_2220834..2220984_NEGATIVE 273 52 16 59 22 NC_009009:SSA_1551|3end_Transcriptional_accessory_ribonuclease_(YqgFc,_S1),_putative_1552652..1552802_NEGATIVE 272 90 43 62 13 NC_009009:SSA_0113|3end_30S_ribosomal_protein_S3,_putative_112055..112205_POSITIVE 271 54 14 145 102 NC_009009:SSA_2336|3end_Transcriptional_regulator,_PadR_family,_putative_2338785..2338935_POSITIVE 271 90 52 125 80 NC_009009:SSA_1970|3end_Acetolactate_synthase,_large_subunit,_biosynthetic_type,_putative_1965215..1965365_NEGATIVE 270 106 63 36 4 NC_009009:SSA_1494|3end_Conserved_uncharacterized_protein_1499514..1499664_NEGATIVE 266 90 43 149 104 NC_009009:SSA_0466|3end_Precorrin-8X_methylmutase_/_precorrin_isomerase,_putative_470668..470818_POSITIVE 263 56 15 137 96 NC_009009:SSA_1341|3end_Carbamoyl-phosphate_synthase_large_chain,_putative_1356648..1356798_NEGATIVE 262 104 62 66 16 NC_009009:SSA_2113|3end_hypothetical_protein_2116228..2116378_NEGATIVE 262 70 21 59 1 NC_009009:SSA_0338|3end_Hydroxymethylglutaryl-CoA_synthase,_putative_332160..332310_NEGATIVE 260 55 13 56 22 NC_009009:SSA_0470|3end_Precorrin-4_methylase,_putative_473732..473882_POSITIVE 256 68 29 80 39 NC_009009:SSA_1778|3end_Segregation_and_condensation_protein_B,_putative_1765142..1765292_NEGATIVE 254 56 16 42 1 NC_009009:SSA_2278|3end_Ukp_protein,_putative_2280410..2280560_NEGATIVE 253 60 15 134 76 NC_009009:SSA_0704|3end_Isocitrate_dehydrogenase_[NADP],_putative_690550..690700_POSITIVE