Origin IGS: tactcctgagaaaacataaacaataagagattggggcctgggtctcagtctcttttgctatcaaactaccatcttgtctagaaatatgctatagtagagaaagtatgagtgtccaatttttagaaaagcagggtaagcaagc .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 gcttgcttaccctgcttttctaaaaattggacactcatactttctctactatagcatatttctagacaagatggtagtttgatagcaaaagagactgagacccaggccccaatctcttattgtttatgttttctcaggagta Mask Tandem Repeat Region ================================================ tactcctgagaaaacataaacaataagagattggggcctgggtctcagtctcttttgctatcaaactaccatcttgtctagaaatatgctatagtagagaaagtatgagtgtccaatttttagaaaagcagggtaagcaagc Find is-nt database================================================ Query_seq: SSA_0779:SSA_0780|SSA_0779:SSA_0780:Glycogen phosphorylase, putative:Acid phosphatase (PAP2 family), putative:->->:764746..764887 142 tactcctgagaaaacataaacaataagagattggggcctgggtctcagtctcttttgctatcaaactaccatcttgtctagaaatatgctatagtagagaaagtatgagtgtccaatttttagaaaagcagggtaagcaagc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_0779:SSA_0780|SSA_0779:SSA_0780:Glycogen phosphorylase, putative:Acid phosphatase (PAP2 family), putative:->->:764746..764887 142 tactcctgagaaaacataaacaataagagattggggcctgggtctcagtctcttttgctatcaaactaccatcttgtctagaaatatgctatagtagagaaagtatgagtgtccaatttttagaaaagcagggtaagcaagc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_0779:SSA_0780|SSA_0779:SSA_0780:Glycogen phosphorylase, putative:Acid phosphatase (PAP2 family), putative:->->:764746..764887 142 tactcctgagaaaacataaacaataagagattggggcctgggtctcagtctcttttgctatcaaactaccatcttgtctagaaatatgctatagtagagaaagtatgagtgtccaatttttagaaaagcagggtaagcaagc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tactcctgagaaaacataaacaataagagattggggcctgggtctcagtctcttttgctatcaaactaccatcttgtctagaaatatgctatagtagagaaagtatgagtgtccaatttttagaaaagcagggtaagcaagc Predict ORF larger than 30AA ================================================ Protein_Len: 37 Strand: + Start: 30 End: 140 ............................. M G A W V S V S F A I K L P S C L E I C Y S R E S M S V Q F L E K Q G K Q .. tactcctgagaaaacataaacaataagagattggggcctgggtctcagtctcttttgctatcaaactaccatcttgtctagaaatatgctatagtagagaaagtatgagtgtccaatttttagaaaagcagggtaagcaagc 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================================================ tactcctgagaaaacataaacaataagagattggggcctgggtctcagtctcttttgctatcaaactaccatcttgtctagaaatatgctatagtagagaaagtatgagtgtccaatttttagaaaagcagggtaagcaagc Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_0779:SSA_0780|SSA_0779:SSA_0780:Glycogen phosphorylase, putative:Acid phosphatase (PAP2 family), putative:->->:764746..764887 142 tactcctgagaaaacataaacaataagagattggggcctgggtctcagtctcttttgctatcaaactaccatcttgtctagaaatatgctatagtagagaaagtatgagtgtccaatttttagaaaagcagggtaagcaagc Intra-Species Hit: Count: 1 Min: 1 Max: 142 Len: 142 Subject: NC_009009_SSA_0779_SSA_0780|Glycogen phosphorylase, putative:Acid phosphatase (PAP2 family), putative|POSITIVE:POSITIVE|[764746,764887]|142 HSP 1 e-value: 3.0E-75 bit: 281.0 Len: 142 Query Start:1 Query End:142 Subject Strand: POSITIVE Subject Start: 1 Subject End: 142 tactcctgagaaaacataaacaataagagattggggcctgggtctcagtctcttttgctatcaaactaccatcttgtctagaaatatgctatagtagagaaagtatgagtgtccaatttttagaaaagcagggtaagcaagc tactcctgagaaaacataaacaataagagattggggcctgggtctcagtctcttttgctatcaaactaccatcttgtctagaaatatgctatagtagagaaagtatgagtgtccaatttttagaaaagcagggtaagcaagc Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UACUCCUGAGAAAACAUAAACAAUAAGAGAUUGGGGCCUGGGUCUCAGUCUCUUUUGCUAUCAAACUACCAUCUUGUCUAGAAAUAUGCUAUAGUAGAGAAAGUAUGAGUGUCCAAUUUUUAGAAAAGCAGGGUAAGCAAGC ........................(((((((((((((....)))))))))))))(((((.......((((..(((.(((((((((((((((((.(......).))).)))))...))))))))).)))...))))))))).. (-36.21) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GCUUGCUUACCCUGCUUUUCUAAAAAUUGGACACUCAUACUUUCUCUACUAUAGCAUAUUUCUAGACAAGAUGGUAGUUUGAUAGCAAAAGAGACUGAGACCCAGGCCCCAAUCUCUUAUUGUUUAUGUUUUCUCAGGAGUA .......(((((((...........((..(((((.(((.(((..((((..(........)..)))).)))))))).)))..)).((((((((((.((.(.(....).).)).)))))).))))...........)))).))) (-24.30) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 370 62 25 221 185 NC_009009:SSA_1949|5end_AliA_protein,_putative_1944373..1944603_NEGATIVE 349 73 31 144 103 NC_009009:SSA_2345|5end_hypothetical_protein_2346919..2347149_POSITIVE 334 59 27 140 110 NC_009009:SSA_0680|5end_Serine/threonine_protein_phosphatase,_putative_662425..662655_POSITIVE 311 69 32 199 146 NC_009009:SSA_2029|5end_Transposase_and_inactivated_derivatives,_putative_2036028..2036258_NEGATIVE 304 61 26 158 126 NC_009009:SSA_1856|5end_hypothetical_protein_1852208..1852438_NEGATIVE 301 79 31 223 170 NC_009009:SSA_1412|5end_hypothetical_protein_1424095..1424325_NEGATIVE 297 80 31 194 135 NC_009009:SSA_0778|5end_Glycogen_synthase,_putative_760566..760796_POSITIVE 296 78 32 98 56 NC_009009:SSA_0496|5end_Succinylglutamate_desuccinylase_/_Aspartoacylase_family,_putative_495946..496176_POSITIVE 293 79 37 223 178 NC_009009:SSA_2197|5end_hypothetical_protein_2197784..2198014_NEGATIVE 291 80 37 75 28 NC_009009:SSA_1613|5end_hypothetical_protein_1616975..1617205_NEGATIVE 289 50 1 166 116 NC_009009:SSA_0155|5end_hypothetical_protein_150961..151191_POSITIVE 286 70 27 92 56 NC_009009:SSA_0729|5end_hypothetical_protein_714397..714627_POSITIVE 284 76 31 49 5 NC_009009:SSA_1218|5end_DNA_repair_protein_radC,_putative_1240459..1240689_NEGATIVE 284 80 32 169 128 NC_009009:SSA_0520|5end_Ethanolamine_ammonia-lyase_light_chain,_putative_519462..519692_POSITIVE 280 55 24 230 187 NC_009009:SSA_2206|5end_hypothetical_protein_2206839..2207069_POSITIVE 280 78 31 120 67 NC_009009:SSA_1447|5end_ATP_phosphoribosyltransferase,_putative_1449831..1450061_NEGATIVE 277 80 35 66 28 NC_009009:SSA_1683|5end_NrdI_protein,_putative_1677405..1677635_NEGATIVE 273 79 33 119 61 NC_009009:SSA_0218|5end_Sugar-binding_periplasmic_protein,_putative_213863..214093_POSITIVE 272 79 34 93 37 NC_009009:SSA_0485|5end_Porphobilinogen_deaminase,_putative_485732..485962_POSITIVE 267 56 11 163 119 NC_009009:SSA_1796|5end_Transcription_elongation_factor_GreA,_putative_1778307..1778537_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 435 57 21 70 34 NC_009009:SSA_0779|3end_Glycogen_phosphorylase,_putative_764685..764835_POSITIVE 334 59 27 87 57 NC_009009:SSA_0679|3end_DNA_repair_and_genetic_recombination,_putative_662452..662602_POSITIVE 317 56 15 76 35 NC_009009:SSA_1909|3end_Transcriptional_attenuator_LytR,_putative_1900904..1901054_NEGATIVE 296 78 32 108 66 NC_009009:SSA_0495|3end_ABC-type_oligopeptide/nickel_transport_system,_ATPase_component,_putative_496036..496186_POSITIVE 289 50 1 75 25 NC_009009:SSA_0154|3end_hypothetical_protein_150950..151100_POSITIVE 286 70 27 138 102 NC_009009:SSA_0728|3end_Protease,_putative_714523..714673_POSITIVE 281 63 25 53 15 NC_009009:SSA_0956|3end_surface_protein_D_965418..965568_POSITIVE 280 78 31 123 70 NC_009009:SSA_1448|3end_ATP_phosphoribosyltransferase_regulatory_subunit,_putative_1449828..1449978_NEGATIVE 277 80 35 45 7 NC_009009:SSA_1684|3end_Histidine_kinase,_putative_1677426..1677576_NEGATIVE 277 75 32 149 111 NC_009009:SSA_0519|3end_Ethanolamine_ammonia-lyase_large_subunit,_putative_519525..519675_POSITIVE 273 79 33 122 64 NC_009009:SSA_0217|3end_Two-component_system_transcriptional_regulator_(CheY_domain_and_HTH-like_DNA-binding_domain),_putative_213946..214096_POSITIVE 272 79 34 106 50 NC_009009:SSA_0484|3end_Glutamyl-tRNA_reductase,_putative_485825..485975_POSITIVE 267 59 21 35 2 NC_009009:SSA_0326|3end_Conserved_uncharacterized_BCR,_YbaB_family_319524..319674_NEGATIVE 264 68 21 112 60 NC_009009:SSA_0680|3end_Serine/threonine_protein_phosphatase,_putative_663233..663383_POSITIVE 263 59 25 88 46 NC_009009:SSA_1349|3end_Transcriptional_regulator,_biotin_repressor_family,_putative_1366513..1366663_POSITIVE 263 79 31 48 5 NC_009009:SSA_0971|3end_Conserved_uncharacterized_protein_980069..980219_POSITIVE 263 82 43 148 102 NC_009009:SSA_0833|3end_Accessory_secretory_protein_Asp1,_putative_819600..819750_POSITIVE 261 59 18 100 51 NC_009009:SSA_1729|3end_ABC_transporter_substrate-binding_protein-branched_chain_amino_acid_transport,_putative_1714539..1714689_NEGATIVE 260 61 26 88 48 NC_009009:SSA_2174|3end_2,3,4,5-tetrahydropyridine-2-carboxylate_N-succinyltransferase,_putative_2171991..2172141_NEGATIVE 259 62 37 33 9 NC_009009:SSA_0657|3end_PyridoxaL_5'-phosphate_Dependent_Enzymes_class_III,_putative_642196..642346_POSITIVE