Origin IGS: tagctgcgctaaagatactaactgatacttttttatcatgtccatttagcttcagttaggaagttatattgatttatttatgcatttgtgataagataatgggtataaaaaaattatagaggagaatttt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aaaattctcctctataatttttttatacccattatcttatcacaaatgcataaataaatcaatataacttcctaactgaagctaaatggacatgataaaaaagtatcagttagtatctttagcgcagcta Mask Tandem Repeat Region ================================================ tagctgcgctaaagatactaactgatacttttttatcatgtccatttagcttcagttaggaagttatattgatttatttatgcatttgtgataagataatgggtataaaaaaattatagaggagaatttt Find is-nt database================================================ Query_seq: SSA_0716:SSA_0718|SSA_0716:SSA_0718:Competence protein, putative:Conserved uncharacterized protein:->->:703771..703900 130 tagctgcgctaaagatactaactgatacttttttatcatgtccatttagcttcagttaggaagttatattgatttatttatgcatttgtgataagataatgggtataaaaaaattatagaggagaatttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_0716:SSA_0718|SSA_0716:SSA_0718:Competence protein, putative:Conserved uncharacterized protein:->->:703771..703900 130 tagctgcgctaaagatactaactgatacttttttatcatgtccatttagcttcagttaggaagttatattgatttatttatgcatttgtgataagataatgggtataaaaaaattatagaggagaatttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_0716:SSA_0718|SSA_0716:SSA_0718:Competence protein, putative:Conserved uncharacterized protein:->->:703771..703900 130 tagctgcgctaaagatactaactgatacttttttatcatgtccatttagcttcagttaggaagttatattgatttatttatgcatttgtgataagataatgggtataaaaaaattatagaggagaatttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tagctgcgctaaagatactaactgatacttttttatcatgtccatttagcttcagttaggaagttatattgatttatttatgcatttgtgataagataatgggtataaaaaaattatagaggagaatttt Predict ORF larger than 30AA ================================================ tagctgcgctaaagatactaactgatacttttttatcatgtccatttagcttcagttaggaagttatattgatttatttatgcatttgtgataagataatgggtataaaaaaattatagaggagaatttt 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: 84 Start: 68 End: 97 ...................................................................ATTGATTTATTTATGCATTTGTGATAAGAT................................. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ tagctgcgctaaagatactaactgatacttttttatcatgtccatttagcttcagttaggaagttatattgatttatttatgcatttgtgataagataatgggtataaaaaaattatagaggagaatttt Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 46 HP_score: -2.9 Tail_Score: -3.46146 Start: 47 End: 66 Full_Region: TTTATCATGTCCATT TAGCTTC AGTTAG GAAGTTA TATTGATTTATTTAT ..............................................TAGCTTCAGTTAGGAAGTTA................................................................ Find igs database================================================ Query_seq: SSA_0716:SSA_0718|SSA_0716:SSA_0718:Competence protein, putative:Conserved uncharacterized protein:->->:703771..703900 130 tagctgcgctaaagatactaactgatacttttttatcatgtccatttagcttcagttaggaagttatattgatttatttatgcatttgtgataagataatgggtataaaaaaattatagaggagaatttt Intra-Species Hit: Count: 1 Min: 1 Max: 130 Len: 130 Subject: NC_009009_SSA_0716_SSA_0718|Competence protein, putative:Conserved uncharacterized protein|POSITIVE:POSITIVE|[703771,703900]|130 HSP 1 e-value: 1.0E-55 bit: 216.0 Len: 130 Query Start:1 Query End:130 Subject Strand: POSITIVE Subject Start: 1 Subject End: 130 tagctgcgctaaagatactaactgatacttttttatcatgtccatttagcttcagttaggaagttatattgatttatttatgcatttgtgataagataatgggtatnnnnnnnttatagaggagaatttt tagctgcgctaaagatactaactgatacttttttatcatgtccatttagcttcagttaggaagttatattgatttatttatgcatttgtgataagataatgggtataaaaaaattatagaggagaatttt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAGCUGCGCUAAAGAUACUAACUGAUACUUUUUUAUCAUGUCCAUUUAGCUUCAGUUAGGAAGUUAUAUUGAUUUAUUUAUGCAUUUGUGAUAAGAUAAUGGGUAUAAAAAAAUUAUAGAGGAGAAUUUU ((((((.((((((...((....(((((......))))).))...))))))..))))))...........((((((.(((((((..((((......))))...))))))).)))))).............. (-22.50) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAAUUCUCCUCUAUAAUUUUUUUAUACCCAUUAUCUUAUCACAAAUGCAUAAAUAAAUCAAUAUAACUUCCUAACUGAAGCUAAAUGGACAUGAUAAAAAAGUAUCAGUUAGUAUCUUUAGCGCAGCUA ................((((((((((..(((((...((((((....)).))))..............((((......))))...))))).....))))))))))....(((((.....)))))....... (-12.40) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 267 39 2 145 111 NC_009009:SSA_1595|5end_Tellurite_resistance,_putative_1601814..1602044_NEGATIVE 233 127 88 67 26 NC_009009:SSA_1843|5end_Histidine_kinase,_putative_1837491..1837721_NEGATIVE 231 47 15 179 142 NC_009009:SSA_1663|5end_Collagen-binding_protein_A_1664121..1664351_NEGATIVE 229 43 3 67 24 NC_009009:SSA_1836|5end_Superfamily_II_ATP-dependent_DNA/RNA_helicase_required_for_DNA_uptake_(late_competence_protein),_putative_1832236..1832466_NEGATIVE 228 56 16 148 108 NC_009009:SSA_1755|5end_hypothetical_protein_1743768..1743998_NEGATIVE 223 88 42 73 29 NC_009009:SSA_2223|5end_Capsular_polysaccharide_biosynthesis_protein_Wzd_(chain_length_regulator),_putative_2224703..2224933_NEGATIVE 222 43 3 115 64 NC_009009:SSA_1835|5end_Late_competence_protein,_putative_1830941..1831171_NEGATIVE 222 65 22 118 78 NC_009009:SSA_0163|5end_hypothetical_protein_162127..162357_POSITIVE 211 87 49 99 59 NC_009009:SSA_0383|5end_Beta-glucosidase,_putative_374534..374764_POSITIVE 209 48 1 167 123 NC_009009:SSA_2036|5end_Conserved_hypothetical_cytosolic_protein_2040799..2041029_NEGATIVE 209 46 1 92 45 NC_009009:SSA_0468|5end_Precorrin-6y_C5,15-methyltransferase-like,_putative_471706..471936_POSITIVE 207 44 1 138 91 NC_009009:SSA_2118|5end_Thiamine_pyrophosphokinase,_putative_2120500..2120730_NEGATIVE 206 43 2 94 52 NC_009009:SSA_2271|5end_hypothetical_protein_2272450..2272680_NEGATIVE 206 50 1 170 125 NC_009009:SSA_1070|5end_Ribosomal_large_subunit_pseudouridine_synthase_D,_putative_1088742..1088972_POSITIVE 205 51 12 115 68 NC_009009:SSA_1441|5end_Phosphoribosyl-AMP_cyclohydrolase,_putative_1445183..1445413_NEGATIVE 205 50 1 190 137 NC_009009:SSA_0963|5end_Peptidoglycan_N-acetylglucosamine_deacetylase_A,_putative_971413..971643_POSITIVE 205 57 12 195 141 NC_009009:SSA_0514|5end_PduQ_protein,_putative_512877..513107_POSITIVE 204 49 3 87 46 NC_009009:SSA_0594|5end_Transcriptional_regulator,_AraC_family,_putative_585630..585860_POSITIVE 203 50 1 94 58 NC_009009:SSA_2322|5end_Transcriptional_regulator,_TetR/AcrR_family,_putative_2327044..2327274_POSITIVE 201 68 42 38 9 NC_009009:SSA_0762|5end_hypothetical_protein_744187..744417_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 233 127 88 70 29 NC_009009:SSA_1844|3end_hypothetical_protein_1837488..1837638_NEGATIVE 228 56 16 139 99 NC_009009:SSA_1756|3end_Conserved_uncharacterized_protein_1743777..1743927_NEGATIVE 223 88 42 65 21 NC_009009:SSA_2224|3end_Phosphotyrosine-protein_phosphatase,_putative_2224711..2224861_NEGATIVE 222 43 3 118 67 NC_009009:SSA_1836|3end_Superfamily_II_ATP-dependent_DNA/RNA_helicase_required_for_DNA_uptake_(late_competence_protein),_putative_1830938..1831088_NEGATIVE 222 65 22 50 10 NC_009009:SSA_0162|3end_hypothetical_protein_162139..162289_POSITIVE 218 56 23 149 111 NC_009009:SSA_2239|3end_Conserved_uncharacterized_cytosolic_protein_2236922..2237072_NEGATIVE 210 77 36 43 3 NC_009009:SSA_1196|3end_Acetyltransferase,_GNAT_family,_putative_1221528..1221678_NEGATIVE 209 46 1 101 54 NC_009009:SSA_0467|3end_Cobalt-precorrin-6A_synthase_[deacetylating],_putative_471795..471945_POSITIVE 205 50 3 84 37 NC_009009:SSA_1822|3end_hypothetical_protein_1810871..1811021_NEGATIVE 205 51 12 115 68 NC_009009:SSA_1442|3end_Imidazole_glycerol-phosphate_synthase_subunit_hisF,_putative_1445183..1445333_NEGATIVE 205 50 1 128 75 NC_009009:SSA_0962|3end_Lactoylglutathione_lyase,_putative_971431..971581_POSITIVE 200 39 3 42 11 NC_009009:SSA_2324|3end_hypothetical_protein_2328847..2328997_NEGATIVE 200 89 42 111 61 NC_009009:SSA_0586|3end_Conserved_uncharacterized_protein_578243..578393_POSITIVE 199 61 22 137 97 NC_009009:SSA_1976|3end_Conserved_uncharacterized_protein_1971550..1971700_NEGATIVE 198 47 1 57 13 NC_009009:SSA_2302|3end_Type_IV_fimbrial_biogenesis_protein,_prepilin_cysteine_protease_(C20)_PilD,_putative_2303304..2303454_NEGATIVE 196 50 3 110 54 NC_009009:SSA_0595|3end_hypothetical_protein_586983..587133_POSITIVE 196 41 2 81 42 NC_009009:SSA_0478|3end_Cobalt_transport_protein_cbiN,_putative_480387..480537_POSITIVE 195 72 31 145 103 NC_009009:SSA_0332|3end_hypothetical_protein_326924..327074_POSITIVE 195 50 7 84 46 NC_009009:SSA_0203|3end_hypothetical_protein_202124..202274_POSITIVE 194 103 81 144 124 NC_009009:SSA_1928|3end_Acyl-CoA_dehydrogenase,_putative_1915946..1916096_NEGATIVE