Origin IGS: ttcaggaaataaaaagagctgtcaagttccttgacaaacttgtcaacatgctgtggaaaacttttaagaatgactggtgttatgcagaataactagattgttagggaaatgctattggcaaatggtttcattatttttataataaagatgaaaaaagaaaatcatctaaataattttatttgaagaaaggagatcatc .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 gatgatctcctttcttcaaataaaattatttagatgattttcttttttcatctttattataaaaataatgaaaccatttgccaatagcatttccctaacaatctagttattctgcataacaccagtcattcttaaaagttttccacagcatgttgacaagtttgtcaaggaacttgacagctctttttatttcctgaa Mask Tandem Repeat Region ================================================ ttcaggaaataaaaagagctgtcaagttccttgacaaacttgtcaacatgctgtggaaaacttttaagaatgactggtgttatgcagaataactagattgttagggaaatgctattggcaaatggtttcattatttttataataaagatgaaaaaagaaaatcatctaaataattttatttgaagaaaggagatcatc Find is-nt database================================================ Query_seq: SSA_2246:SSA_2247|SSA_2246:SSA_2247:Competence-damage protein, putative:hypothetical protein:<-->:2242587..2242784 198 ttcaggaaataaaaagagctgtcaagttccttgacaaacttgtcaacatgctgtggaaaacttttaagaatgactggtgttatgcagaataactagattgttagggaaatgctattggcaaatggtttcattatttttataataaagatgaaaaaagaaaatcatctaaataattttatttgaagaaaggagatcatc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_2246:SSA_2247|SSA_2246:SSA_2247:Competence-damage protein, putative:hypothetical protein:<-->:2242587..2242784 198 ttcaggaaataaaaagagctgtcaagttccttgacaaacttgtcaacatgctgtggaaaacttttaagaatgactggtgttatgcagaataactagattgttagggaaatgctattggcaaatggtttcattatttttataataaagatgaaaaaagaaaatcatctaaataattttatttgaagaaaggagatcatc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_2246:SSA_2247|SSA_2246:SSA_2247:Competence-damage protein, putative:hypothetical protein:<-->:2242587..2242784 198 ttcaggaaataaaaagagctgtcaagttccttgacaaacttgtcaacatgctgtggaaaacttttaagaatgactggtgttatgcagaataactagattgttagggaaatgctattggcaaatggtttcattatttttataataaagatgaaaaaagaaaatcatctaaataattttatttgaagaaaggagatcatc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ttcaggaaataaaaagagctgtcaagttccttgacaaacttgtcaacatgctgtggaaaacttttaagaatgactggtgttatgcagaataactagattgttagggaaatgctattggcaaatggtttcattatttttataataaagatgaaaaaagaaaatcatctaaataattttatttgaagaaaggagatcatc Predict ORF larger than 30AA ================================================ ttcaggaaataaaaagagctgtcaagttccttgacaaacttgtcaacatgctgtggaaaacttttaagaatgactggtgttatgcagaataactagattgttagggaaatgctattggcaaatggtttcattatttttataataaagatgaaaaaagaaaatcatctaaataattttatttgaagaaaggagatcatc 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: 92 Start: 114 End: 143 .................................................................................................................ATTGGCAAATGGTTTCATTATTTTTATAAT....................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ ttcaggaaataaaaagagctgtcaagttccttgacaaacttgtcaacatgctgtggaaaacttttaagaatgactggtgttatgcagaataactagattgttagggaaatgctattggcaaatggtttcattatttttataataaagatgaaaaaagaaaatcatctaaataattttatttgaagaaaggagatcatc Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 70 HP_score: -8.2 Tail_Score: -3.16035 Start: 19 End: 37 Full_Region: agcatgttgacaagt ttgtcaag gaa cttgacag ctctttttatttcct ..................ttgtcaaggaacttgacag................................................................................................................................................................. Find igs database================================================ Query_seq: SSA_2246:SSA_2247|SSA_2246:SSA_2247:Competence-damage protein, putative:hypothetical protein:<-->:2242587..2242784 198 ttcaggaaataaaaagagctgtcaagttccttgacaaacttgtcaacatgctgtggaaaacttttaagaatgactggtgttatgcagaataactagattgttagggaaatgctattggcaaatggtttcattatttttataataaagatgaaaaaagaaaatcatctaaataattttatttgaagaaaggagatcatc Intra-Species Hit: Count: 1 Min: 1 Max: 198 Len: 198 Subject: NC_009009_SSA_2246_SSA_2247|Competence-damage protein, putative:hypothetical protein|NEGATIVE:POSITIVE|[2242587,2242784]|198 HSP 1 e-value: 1.0E-108 bit: 392.0 Len: 198 Query Start:1 Query End:198 Subject Strand: POSITIVE Subject Start: 1 Subject End: 198 ttcaggaaataaaaagagctgtcaagttccttgacaaacttgtcaacatgctgtggaaaacttttaagaatgactggtgttatgcagaataactagattgttagggaaatgctattggcaaatggtttcattatttttataataaagatgaaaaaagaaaatcatctaaataattttatttgaagaaaggagatcatc ttcaggaaataaaaagagctgtcaagttccttgacaaacttgtcaacatgctgtggaaaacttttaagaatgactggtgttatgcagaataactagattgttagggaaatgctattggcaaatggtttcattatttttataataaagatgaaaaaagaaaatcatctaaataattttatttgaagaaaggagatcatc Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUCAGGAAAUAAAAAGAGCUGUCAAGUUCCUUGACAAACUUGUCAACAUGCUGUGGAAAACUUUUAAGAAUGACUGGUGUUAUGCAGAAUAACUAGAUUGUUAGGGAAAUGCUAUUGGCAAAUGGUUUCAUUAUUUUUAUAAUAAAGAUGAAAAAAGAAAAUCAUCUAAAUAAUUUUAUUUGAAGAAAGGAGAUCAUC ...................((((((.(((((((((((.((.((.....(((.((.....))........(((((....)))))))).....)).)).)))))))))))......)))))).((((((((....((((((.(((((((((((..........))))))........)))))))))))...)))))))). (-37.10) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAUGAUCUCCUUUCUUCAAAUAAAAUUAUUUAGAUGAUUUUCUUUUUUCAUCUUUAUUAUAAAAAUAAUGAAACCAUUUGCCAAUAGCAUUUCCCUAACAAUCUAGUUAUUCUGCAUAACACCAGUCAUUCUUAAAAGUUUUCCACAGCAUGUUGACAAGUUUGUCAAGGAACUUGACAGCUCUUUUUAUUUCCUGAA ...........(((...((((((((......((((((..........))))))(((((((....)))))))....(((((.(((((((.......((((......))))..(((........)))......................)).))))).)))))((((((((...))))))))....))))))))...))) (-25.30) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 865 120 71 211 162 NC_009009:SSA_2246|5end_Competence-damage_protein,_putative_2242496..2242726_NEGATIVE 340 56 17 225 183 NC_009009:SSA_0411|5end_hypothetical_protein_407238..407468_NEGATIVE 327 120 73 144 93 NC_009009:SSA_1901|5end_Conserved_uncharacterized_protein_1896599..1896829_NEGATIVE 298 139 93 110 59 NC_009009:SSA_1292|5end_hypothetical_protein_1311578..1311808_NEGATIVE 282 42 1 174 132 NC_009009:SSA_1683|5end_NrdI_protein,_putative_1677405..1677635_NEGATIVE 279 126 83 64 17 NC_009009:SSA_1671|5end_hypothetical_protein_1669304..1669534_POSITIVE 277 119 71 164 116 NC_009009:SSA_0216|5end_Histidine_kinase,_putative_211877..212107_POSITIVE 273 57 18 63 15 NC_009009:SSA_2270|5end_Aspartyl-tRNA_synthetase,_putative_2272068..2272298_NEGATIVE 264 77 37 163 116 NC_009009:SSA_0240|5end_Acetyltransferase,_GNAT_family,_putative_233410..233640_POSITIVE 255 138 91 200 160 NC_009009:SSA_1332|5end_hypothetical_protein_1347645..1347875_NEGATIVE 255 140 94 91 35 NC_009009:SSA_0758|5end_Ornithine_acetyltransferase_/_amino-acid_acetyltransferase,_putative_740636..740866_POSITIVE 255 59 16 214 177 NC_009009:SSA_0116|5end_30S_ribosomal_protein_S17,_putative_112632..112862_POSITIVE 252 59 16 194 150 NC_009009:SSA_0579|5end_Hydrolase,_HAD_superfamily,_putative_572220..572450_POSITIVE 252 51 17 40 8 NC_009009:SSA_0212|5end_Phenylalanyl-tRNA_synthetase,_beta_subunit,_putative_208373..208603_POSITIVE 248 138 100 105 67 NC_009009:SSA_1372|5end_hypothetical_protein_1389137..1389367_NEGATIVE 247 52 15 78 39 NC_009009:SSA_0900|5end_Tetratricopeptide_repeat_(TPR)_family_protein_891068..891298_POSITIVE 246 120 71 90 34 NC_009009:SSA_2166|5end_ABC-type_multidrug_transporter,_ATPase_and_permease_components,_putative_2165642..2165872_NEGATIVE 246 56 19 53 13 NC_009009:SSA_0065|5end_Low_molecular_weight_phosphotyrosine_protein_phosphatase,_putative_67175..67405_POSITIVE 239 59 15 66 15 NC_009009:SSA_0463|5end_Cobyrinic_acid_A,C-diamide_synthase,_putative_466865..467095_POSITIVE 237 57 14 231 180 NC_009009:SSA_0122|5end_50S_ribosomal_protein_L6,_putative_115427..115657_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 298 139 93 134 83 NC_009009:SSA_1293|3end_hypothetical_protein_1311554..1311704_NEGATIVE 257 55 19 129 88 NC_009009:SSA_1550|3end_hypothetical_protein_1552228..1552378_NEGATIVE 255 140 94 73 17 NC_009009:SSA_0757|3end_N-acetyl-gamma-glutamyl-phosphate_reductase,_putative_740698..740848_POSITIVE 252 130 85 146 108 NC_009009:SSA_1333|3end_hypothetical_protein_1347693..1347843_NEGATIVE 252 51 17 43 11 NC_009009:SSA_0211|3end_hypothetical_protein_208456..208606_POSITIVE 249 102 61 131 85 NC_009009:SSA_0328|3end_Xaa-Pro_dipeptidyl-peptidase,_putative_320487..320637_NEGATIVE 247 52 15 91 52 NC_009009:SSA_0899|3end_Conserved_permease,_putative_891161..891311_POSITIVE 246 120 71 88 32 NC_009009:SSA_2167|3end_ABC-type_multidrug_transporter,_ATPase_and_permease_components,_putative_2165644..2165794_NEGATIVE 246 40 1 151 111 NC_009009:SSA_1684|3end_Histidine_kinase,_putative_1677426..1677576_NEGATIVE 240 126 82 43 1 NC_009009:SSA_0066|3end_hypothetical_protein_68095..68245_POSITIVE 233 100 51 130 85 NC_009009:SSA_1901|3end_Conserved_uncharacterized_protein_1896066..1896216_NEGATIVE 232 55 18 47 12 NC_009009:SSA_0566|3end_GTP-sensing_transcriptional_pleiotropic_repressor,_putative_560885..561035_POSITIVE 232 65 37 148 119 NC_009009:SSA_0239|3end_7,8-dihydro-8-oxoguanine-triphosphatase,_putative_233493..233643_POSITIVE 230 43 2 82 39 NC_009009:SSA_1663|3end_Collagen-binding_protein_A_1659586..1659736_NEGATIVE 230 44 1 119 62 NC_009009:SSA_0801|3end_Mur_ligase_family_protein,_putative_782774..782924_NEGATIVE 226 51 15 145 115 NC_009009:SSA_1611|3end_Era-like_GTP-binding_protein,_putative_1615133..1615283_NEGATIVE 224 53 17 52 15 NC_009009:SSA_1238|3end_hypothetical_protein_1262402..1262552_NEGATIVE 224 79 31 65 19 NC_009009:SSA_0882|3end_Phosphoserine_phosphatase,_putative_877630..877780_POSITIVE 220 60 11 110 69 NC_009009:SSA_2143|3end_Conserved_uncharacterized_protein_2143590..2143740_NEGATIVE 220 90 47 123 71 NC_009009:SSA_1538|3end_hypothetical_protein_1544918..1545068_POSITIVE