Origin IGS: atgctgactttttgaaactatcttcggtaatgcattgctctagtcaagtatgtctttctgatttgctaatgtgtttcattgaggaaaaatcgtaaatagaaaaagctgaggcaatgttgtctcagctt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aagctgagacaacattgcctcagctttttctatttacgatttttcctcaatgaaacacattagcaaatcagaaagacatacttgactagagcaatgcattaccgaagatagtttcaaaaagtcagcat Mask Tandem Repeat Region ================================================ atgctgactttttgaaactatcttcggtaatgcattgctctagtcaagtatgtctttctgatttgctaatgtgtttcattgaggaaaaatcgtaaatagaaaaagctgaggcaatgttgtctcagctt Find is-nt database================================================ Query_seq: SSA_0741:SSA_0743|SSA_0741:SSA_0743:Acetylornithine deacetylase/Succinyl-diaminopimelate desuccinylase, putative:Transcriptional repressor (arginine synthesis), putative:-><-:725251..725378 128 atgctgactttttgaaactatcttcggtaatgcattgctctagtcaagtatgtctttctgatttgctaatgtgtttcattgaggaaaaatcgtaaatagaaaaagctgaggcaatgttgtctcagctt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_0741:SSA_0743|SSA_0741:SSA_0743:Acetylornithine deacetylase/Succinyl-diaminopimelate desuccinylase, putative:Transcriptional repressor (arginine synthesis), putative:-><-:725251..725378 128 atgctgactttttgaaactatcttcggtaatgcattgctctagtcaagtatgtctttctgatttgctaatgtgtttcattgaggaaaaatcgtaaatagaaaaagctgaggcaatgttgtctcagctt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_0741:SSA_0743|SSA_0741:SSA_0743:Acetylornithine deacetylase/Succinyl-diaminopimelate desuccinylase, putative:Transcriptional repressor (arginine synthesis), putative:-><-:725251..725378 128 atgctgactttttgaaactatcttcggtaatgcattgctctagtcaagtatgtctttctgatttgctaatgtgtttcattgaggaaaaatcgtaaatagaaaaagctgaggcaatgttgtctcagctt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 atgctgactttttgaaactatcttcggtaatgcattgctctagtcaagtatgtctttctgatttgctaatgtgtttcattgaggaaaaatcgtaaatagaaaaagctgaggcaatgttgtctcagctt Predict ORF larger than 30AA ================================================ atgctgactttttgaaactatcttcggtaatgcattgctctagtcaagtatgtctttctgatttgctaatgtgtttcattgaggaaaaatcgtaaatagaaaaagctgaggcaatgttgtctcagctt 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================================================ atgctgactttttgaaactatcttcggtaatgcattgctctagtcaagtatgtctttctgatttgctaatgtgtttcattgaggaaaaatcgtaaatagaaaaagctgaggcaatgttgtctcagctt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_0741:SSA_0743|SSA_0741:SSA_0743:Acetylornithine deacetylase/Succinyl-diaminopimelate desuccinylase, putative:Transcriptional repressor (arginine synthesis), putative:-><-:725251..725378 128 atgctgactttttgaaactatcttcggtaatgcattgctctagtcaagtatgtctttctgatttgctaatgtgtttcattgaggaaaaatcgtaaatagaaaaagctgaggcaatgttgtctcagctt Intra-Species Hit: Count: 1 Min: 1 Max: 128 Len: 128 Subject: NC_009009_SSA_0741_SSA_0743|Acetylornithine deacetylase/Succinyl-diaminopimelate desuccinylase, putative:Transcriptional repressor (arginine synthesis), putative|POSITIVE:NEGATIVE|[725251,725378]|128 HSP 1 e-value: 6.0E-67 bit: 254.0 Len: 128 Query Start:1 Query End:128 Subject Strand: POSITIVE Subject Start: 1 Subject End: 128 atgctgactttttgaaactatcttcggtaatgcattgctctagtcaagtatgtctttctgatttgctaatgtgtttcattgaggaaaaatcgtaaatagaaaaagctgaggcaatgttgtctcagctt atgctgactttttgaaactatcttcggtaatgcattgctctagtcaagtatgtctttctgatttgctaatgtgtttcattgaggaaaaatcgtaaatagaaaaagctgaggcaatgttgtctcagctt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUGCUGACUUUUUGAAACUAUCUUCGGUAAUGCAUUGCUCUAGUCAAGUAUGUCUUUCUGAUUUGCUAAUGUGUUUCAUUGAGGAAAAAUCGUAAAUAGAAAAAGCUGAGGCAAUGUUGUCUCAGCUU .......((.((((......((((((((((((((((((...(((((............))))).)).))))))))..)))))))).......)))).))...(((((((((((....))))))))))) (-32.72) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAGCUGAGACAACAUUGCCUCAGCUUUUUCUAUUUACGAUUUUUCCUCAAUGAAACACAUUAGCAAAUCAGAAAGACAUACUUGACUAGAGCAAUGCAUUACCGAAGAUAGUUUCAAAAAGUCAGCAU ((((((((.((....)).))))))))...........(((((((......((((((......(((..((((.(((.....)))..)).))....)))....(....)...)))))))))))))..... (-21.20) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 284 67 23 115 69 NC_009009:SSA_0185|5end_Competence_protein_ComYB,_putative_189057..189287_POSITIVE 275 70 22 64 20 NC_009009:SSA_1583|5end_6-O-methylguanine-DNA_methyltransferase,_putative_1586026..1586256_NEGATIVE 264 49 3 229 174 NC_009009:SSA_0336|5end_Isopentenyl-diphosphate_delta-isomerase,_putative_329792..330022_POSITIVE 255 76 35 214 182 NC_009009:SSA_2054|5end_hypothetical_protein_2057899..2058129_NEGATIVE 255 49 3 79 42 NC_009009:SSA_0558|5end_Conserved_hypothetical_cytosolic_protein,_putative_552335..552565_POSITIVE 255 68 21 53 12 NC_009009:SSA_0489|5end_Adenosylcobinamide_kinase_/_adenosylcobinamide_phosphate_guanyltransferase,_putative_489655..489885_POSITIVE 251 76 43 81 46 NC_009009:SSA_0348|5end_CAAX_amino_terminal_protease_family,_putative_340288..340518_POSITIVE 250 77 35 88 51 NC_009009:SSA_1799|5end_Acetyltransferase,_putative_1781025..1781255_NEGATIVE 250 69 24 112 60 NC_009009:SSA_1743|5end_ABC-type_Fe3+-siderophore_transport_system,_permease_component,_putative_1730170..1730400_POSITIVE 249 67 23 81 24 NC_009009:SSA_0834|5end_Accessory_secretory_protein_Asp2,_putative_819510..819740_POSITIVE 246 67 21 75 22 NC_009009:SSA_2223|5end_Capsular_polysaccharide_biosynthesis_protein_Wzd_(chain_length_regulator),_putative_2224703..2224933_NEGATIVE 246 68 23 90 45 NC_009009:SSA_0704|5end_Isocitrate_dehydrogenase_[NADP],_putative_689274..689504_POSITIVE 241 59 15 60 23 NC_009009:SSA_0043|5end_hypothetical_protein_48801..49031_POSITIVE 241 67 22 201 155 NC_009009:SSA_0031|5end_Glutamine_phosphoribosylpyrophosphate_amidotransferase,_putative_36439..36669_POSITIVE 240 60 11 171 115 NC_009009:SSA_1311|5end_Hydrolase,_haloacid_dehalogenase-like_family,_putative_1328393..1328623_NEGATIVE 239 119 97 204 180 NC_009009:SSA_2000|5end_hypothetical_protein_1997469..1997699_NEGATIVE 239 65 21 61 18 NC_009009:SSA_1753|5end_Transcriptional_regulator,_GntR_family_(repressor_of_trehalose_operon),_putative_1741944..1742174_POSITIVE 237 78 32 137 88 NC_009009:SSA_2331|5end_D-alanine_transfer_protein,_putative_2334964..2335194_NEGATIVE 236 70 21 211 140 NC_009009:SSA_1955|5end_ABC-type_Fe-S_cluster_assembly_transporter,_permease_component,_putative_1952602..1952832_NEGATIVE 236 64 23 203 158 NC_009009:SSA_1704|5end_Conserved_uncharacterized_protein_1696401..1696631_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 279 60 23 146 109 NC_009009:SSA_0184|3end_Competence_protein_ComYA,_putative_189177..189327_POSITIVE 277 66 21 56 20 NC_009009:SSA_0567|3end_Isochorismitase_family_protein,_putative_561442..561592_POSITIVE 263 50 2 132 78 NC_009009:SSA_0548|3end_Alanine_racemase,_putative_543529..543679_POSITIVE 261 67 22 145 102 NC_009009:SSA_0456|3end_Phosphotransferase_system_IIC_components,_glucose/maltose/N-acetylglucosamine-specific,_putative_460585..460735_POSITIVE 255 49 3 57 20 NC_009009:SSA_0557|3end_hypothetical_protein_552393..552543_POSITIVE 255 68 21 60 19 NC_009009:SSA_0488|3end_Glutamate-1-semialdehyde_2,1-aminotransferase,_putative_489742..489892_POSITIVE 250 77 35 76 39 NC_009009:SSA_1800|3end_UDP-N-acetylmuramate--L-alanine_ligase,_putative_1781037..1781187_NEGATIVE 250 117 78 49 13 NC_009009:SSA_0234|3end_hypothetical_protein_228423..228573_NEGATIVE 249 67 23 91 34 NC_009009:SSA_0833|3end_Accessory_secretory_protein_Asp1,_putative_819600..819750_POSITIVE 246 67 21 67 14 NC_009009:SSA_2224|3end_Phosphotyrosine-protein_phosphatase,_putative_2224711..2224861_NEGATIVE 246 68 23 88 43 NC_009009:SSA_0703|3end_Citrate_synthase,_putative_689352..689502_POSITIVE 242 66 23 123 68 NC_009009:SSA_2061|3end_Peptide_deformylase,_putative_2063259..2063409_POSITIVE 242 85 42 147 111 NC_009009:SSA_0778|3end_Glycogen_synthase,_putative_762076..762226_POSITIVE 241 47 2 139 104 NC_009009:SSA_0727|3end_Metal-dependent_membrane_protease,_putative_713639..713789_POSITIVE 241 67 22 106 60 NC_009009:SSA_0030|3end_Phosphoribosylformylglycinamidine_synthase,_putative_36424..36574_POSITIVE 237 78 32 144 95 NC_009009:SSA_2332|3end_D-alanyl_carrier_protein,_putative_2334957..2335107_NEGATIVE 237 66 30 132 93 NC_009009:SSA_1865|3end_Thioredoxin_reductase,_putative_1860978..1861128_NEGATIVE 232 59 11 148 86 NC_009009:SSA_1956|3end_ABC-type_Fe-S_cluster_assembly_transporter,_ATPase_component,_putative_1952644..1952794_NEGATIVE 230 78 39 84 33 NC_009009:SSA_1191|3end_hypothetical_protein_1218222..1218372_NEGATIVE 229 50 11 127 85 NC_009009:SSA_1969|3end_Acetolactate_synthase_small_subunit,_putative_1964746..1964896_NEGATIVE