Origin IGS: gagatttcctttctaatttttctcttctgcaatataagctaggctaggcctagcttatattttagttttaatgaatgaaattcgatctaaaccctttgtgaaaaagatgtgggactaaaaatattgacttccaccaaatatgattttcactgcgagttttcaacctacttcttatc .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 gataagaagtaggttgaaaactcgcagtgaaaatcatatttggtggaagtcaatatttttagtcccacatctttttcacaaagggtttagatcgaatttcattcattaaaactaaaatataagctaggcctagcctagcttatattgcagaagagaaaaattagaaaggaaatctc Mask Tandem Repeat Region ================================================ gagatttcctttctaatttttctcttctgcaatataagctaggctaggcctagcttatattttagttttaatgaatgaaattcgatctaaaccctttgtgaaaaagatgtgggactaaaaatattgacttccaccaaatatgattttcactgcgagttttcaacctacttcttatc Find is-nt database================================================ Query_seq: SSA_1895:SSA_1896|SSA_1895:SSA_1896:Ribosome-binding factor A, putative:Translation initiation factor IF-2, putative:<-<-:1891256..1891431 176 gagatttcctttctaatttttctcttctgcaatataagctaggctaggcctagcttatattttagttttaatgaatgaaattcgatctaaaccctttgtgaaaaagatgtgggactaaaaatattgacttccaccaaatatgattttcactgcgagttttcaacctacttcttatc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_1895:SSA_1896|SSA_1895:SSA_1896:Ribosome-binding factor A, putative:Translation initiation factor IF-2, putative:<-<-:1891256..1891431 176 gagatttcctttctaatttttctcttctgcaatataagctaggctaggcctagcttatattttagttttaatgaatgaaattcgatctaaaccctttgtgaaaaagatgtgggactaaaaatattgacttccaccaaatatgattttcactgcgagttttcaacctacttcttatc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_1895:SSA_1896|SSA_1895:SSA_1896:Ribosome-binding factor A, putative:Translation initiation factor IF-2, putative:<-<-:1891256..1891431 176 gagatttcctttctaatttttctcttctgcaatataagctaggctaggcctagcttatattttagttttaatgaatgaaattcgatctaaaccctttgtgaaaaagatgtgggactaaaaatattgacttccaccaaatatgattttcactgcgagttttcaacctacttcttatc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gagatttcctttctaatttttctcttctgcaatataagctaggctaggcctagcttatattttagttttaatgaatgaaattcgatctaaaccctttgtgaaaaagatgtgggactaaaaatattgacttccaccaaatatgattttcactgcgagttttcaacctacttcttatc Predict ORF larger than 30AA ================================================ Protein_Len: 35 Strand: - Start: 71 End: 175 ...................................................................... H I F N S R F G K H F L H P V L F I S K W W I H N E S R T K L R S R M . gagatttcctttctaatttttctcttctgcaatataagctaggctaggcctagcttatattttagttttaatgaatgaaattcgatctaaaccctttgtgaaaaagatgtgggactaaaaatattgacttccaccaaatatgattttcactgcgagttttcaacctacttcttatc 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================================================ gagatttcctttctaatttttctcttctgcaatataagctaggctaggcctagcttatattttagttttaatgaatgaaattcgatctaaaccctttgtgaaaaagatgtgggactaaaaatattgacttccaccaaatatgattttcactgcgagttttcaacctacttcttatc Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 100 HP_score: -17.0 Tail_Score: -4.2828 Start: 27 End: 65 Full_Region: TCTAATTTTTCTCTT CTGCAATATAAGCTAGGC TAG GCCTAGCTTATATTTTAG TTTTAATGAATGAAA ..........................CTGCAATATAAGCTAGGCTAGGCCTAGCTTATATTTTAG............................................................................................................... TransTerm Strand: - Conf: 100 HP_score: -15.0 Tail_Score: -3.01712 Start: 35 End: 57 Full_Region: attaaaactaaaata taagctaggc cta gcctagctta tattgcagaagagaa ..................................taagctaggcctagcctagctta....................................................................................................................... TransTerm Strand: - Conf: 95 HP_score: -12.3 Tail_Score: -3.65812 Start: 38 End: 54 Full_Region: aaaactaaaatataa gctaggc cta gcctagc ttatattgcagaaga .....................................gctaggcctagcctagc.......................................................................................................................... Find igs database================================================ Query_seq: SSA_1895:SSA_1896|SSA_1895:SSA_1896:Ribosome-binding factor A, putative:Translation initiation factor IF-2, putative:<-<-:1891256..1891431 176 gagatttcctttctaatttttctcttctgcaatataagctaggctaggcctagcttatattttagttttaatgaatgaaattcgatctaaaccctttgtgaaaaagatgtgggactaaaaatattgacttccaccaaatatgattttcactgcgagttttcaacctacttcttatc Intra-Species Hit: Count: 1 Min: 1 Max: 176 Len: 176 Subject: NC_009009_SSA_1895_SSA_1896|Ribosome-binding factor A, putative:Translation initiation factor IF-2, putative|NEGATIVE:NEGATIVE|[1891256,1891431]|176 HSP 1 e-value: 2.0E-95 bit: 349.0 Len: 176 Query Start:1 Query End:176 Subject Strand: POSITIVE Subject Start: 1 Subject End: 176 gagatttcctttctaatttttctcttctgcaatataagctaggctaggcctagcttatattttagttttaatgaatgaaattcgatctaaaccctttgtgaaaaagatgtgggactaaaaatattgacttccaccaaatatgattttcactgcgagttttcaacctacttcttatc gagatttcctttctaatttttctcttctgcaatataagctaggctaggcctagcttatattttagttttaatgaatgaaattcgatctaaaccctttgtgaaaaagatgtgggactaaaaatattgacttccaccaaatatgattttcactgcgagttttcaacctacttcttatc Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAGAUUUCCUUUCUAAUUUUUCUCUUCUGCAAUAUAAGCUAGGCUAGGCCUAGCUUAUAUUUUAGUUUUAAUGAAUGAAAUUCGAUCUAAACCCUUUGUGAAAAAGAUGUGGGACUAAAAAUAUUGACUUCCACCAAAUAUGAUUUUCACUGCGAGUUUUCAACCUACUUCUUAUC .(((((...((((..((((.......(((.((((((((((((((...)))))))))))))).))).......))))))))...)))))...............((((.(((((..........(((........)))...(((..(((.....)))...))).))))).))))... (-37.24) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAUAAGAAGUAGGUUGAAAACUCGCAGUGAAAAUCAUAUUUGGUGGAAGUCAAUAUUUUUAGUCCCACAUCUUUUUCACAAAGGGUUUAGAUCGAAUUUCAUUCAUUAAAACUAAAAUAUAAGCUAGGCCUAGCCUAGCUUAUAUUGCAGAAGAGAAAAAUUAGAAAGGAAAUCUC (((..(((((.((((..((((((...(((((((.........((((..................))))....)))))))...)))))).))))..)))))...........((..((((((((((((((...))))))))))))))..)).....................))).. (-42.19) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 856 50 1 141 92 NC_009009:SSA_1895|5end_Ribosome-binding_factor_A,_putative_1891165..1891395_NEGATIVE 296 56 11 142 87 NC_009009:SSA_2082|5end_Carbohydrate_kinase,_FGGY_family,_putative_2086874..2087104_NEGATIVE 291 166 124 212 176 NC_009009:SSA_0226|5end_60_kDa_chaperonin_218947..219177_POSITIVE 290 50 4 217 165 NC_009009:SSA_0988|5end_TfoX_N-terminal_domain_family_protein,_putative_990662..990892_POSITIVE 287 56 11 131 84 NC_009009:SSA_1490|5end_Ribonuclease_BN,_putative_1496732..1496962_NEGATIVE 277 69 29 194 152 NC_009009:SSA_2105|5end_hypothetical_protein_2107802..2108032_NEGATIVE 277 170 121 153 90 NC_009009:SSA_0893|5end_ATP-binding_cassette_transporter-like_protein,_putative_884527..884757_POSITIVE 276 117 71 98 51 NC_009009:SSA_2336|5end_Transcriptional_regulator,_PadR_family,_putative_2338367..2338597_POSITIVE 275 56 11 138 94 NC_009009:SSA_1451|5end_Exonuclease_RexA,_putative_1456418..1456648_NEGATIVE 275 56 17 140 106 NC_009009:SSA_0334|5end_Diphosphomevalonate_decarboxylase,_putative_327855..328085_POSITIVE 273 50 2 125 75 NC_009009:SSA_0548|5end_Alanine_racemase,_putative_542340..542570_POSITIVE 273 49 2 149 96 NC_009009:SSA_0040|5end_Phosphoribosylaminoimidazole_carboxylase,_ATPase_subunit,_putative_46308..46538_POSITIVE 271 49 6 168 116 NC_009009:SSA_1900|5end_N_utilization_substance_protein_A,_putative_1896012..1896242_NEGATIVE 264 51 17 122 92 NC_009009:SSA_1087|5end_ABC-type_transporter_(antibiotic_resistance_protein),_ATPase_component,_putative_1104524..1104754_POSITIVE 262 170 125 106 62 NC_009009:SSA_1943|5end_Aspartate_kinase,_putative_1928697..1928927_POSITIVE 259 54 22 64 32 NC_009009:SSA_1777|5end_Ribosomal_large_subunit_pseudouridine_synthase_B,_putative_1765155..1765385_NEGATIVE 258 51 17 227 193 NC_009009:SSA_0553|5end_hypothetical_protein_548911..549141_POSITIVE 256 60 11 63 13 NC_009009:SSA_1074|5end_Pyrroline-5-carboxylate_reductase,_putative_1092151..1092381_POSITIVE 256 54 11 136 91 NC_009009:SSA_0319|5end_Branched-chain_amino_acid_permease_(L-methionine,_L-isoleucine,_leucine_and_valine),_putative_312721..312951_POSITIVE 250 50 11 67 19 NC_009009:SSA_1981|5end_hypothetical_protein_1975421..1975651_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 305 54 11 72 19 NC_009009:SSA_0070|3end_Acetylxylan_esterase,_putative_74914..75064_POSITIVE 296 56 11 66 11 NC_009009:SSA_2083|3end_hypothetical_protein_2086950..2087100_NEGATIVE 296 54 22 149 117 NC_009009:SSA_1008|3end_Galactokinase,_putative_1011114..1011264_POSITIVE 290 50 4 69 17 NC_009009:SSA_0987|3end_ABC-type_choline_transporter,_membrane-spanning_permease,_putative_990594..990744_POSITIVE 287 56 11 83 36 NC_009009:SSA_1491|3end_Methionine_aminopeptidase_A,_putative_1496780..1496930_NEGATIVE 280 49 1 144 95 NC_009009:SSA_0727|3end_Metal-dependent_membrane_protease,_putative_713639..713789_POSITIVE 277 49 3 91 48 NC_009009:SSA_0897|3end_Two_component_system_histidine_kinase,_putative_889811..889961_POSITIVE 277 170 121 124 61 NC_009009:SSA_0892|3end_ATP-binding_cassette_lipoprotein,_putative_884578..884728_POSITIVE 275 56 11 141 97 NC_009009:SSA_1452|3end_Second_subunit_of_major_exonuclease,_putative_1456415..1456565_NEGATIVE 273 50 2 138 88 NC_009009:SSA_0547|3end_Acyl_carrier_protein_synthase,_putative_542433..542583_POSITIVE 271 49 6 114 62 NC_009009:SSA_1901|3end_Conserved_uncharacterized_protein_1896066..1896216_NEGATIVE 267 55 16 71 33 NC_009009:SSA_0886|3end_Enolase,_putative_881057..881207_POSITIVE 265 68 21 151 112 NC_009009:SSA_1746|3end_hypothetical_protein_1732292..1732442_NEGATIVE 264 51 17 125 95 NC_009009:SSA_1086|3end_TRNA_nucleotidyltransferase,_putative_1104607..1104757_POSITIVE 262 69 34 98 58 NC_009009:SSA_0312|3end_Hydrolase,_metallo-beta-lactamase_superfamily,_putative_306703..306853_NEGATIVE 259 54 22 77 45 NC_009009:SSA_1778|3end_Segregation_and_condensation_protein_B,_putative_1765142..1765292_NEGATIVE 258 51 17 137 103 NC_009009:SSA_0552|3end_Cof_family_protein,_putative_548901..549051_POSITIVE 256 60 11 60 10 NC_009009:SSA_1073|3end_Gamma-glutamyl_phosphate_reductase,_putative_1092228..1092378_POSITIVE 256 54 11 126 81 NC_009009:SSA_0318|3end_Secreted_metalloendopeptidase_Gcp_312791..312941_POSITIVE 251 50 7 109 47 NC_009009:SSA_0531|3end_Ethanolamine_utilization_protein_eutQ_(cobalamin-dependent_degradation_of_ethanolamine),_putative_527884..528034_POSITIVE