Origin IGS: ctgaaacctccctttcttctttttaaaattatatcaaatttcaatgggacattctattttttgcttgactttgatttacagagatgttatcatctagttataaagactagataagaaagtgataaagatttgaacgctcaacaagtttttcccaagtgggacgaattaccagaactggagctatatttggaccaagttctgctctatgtaaacaatgtctgtggctcttccatttcagctgctgacaagggactgaccgcttct .........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 agaagcggtcagtcccttgtcagcagctgaaatggaagagccacagacattgtttacatagagcagaacttggtccaaatatagctccagttctggtaattcgtcccacttgggaaaaacttgttgagcgttcaaatctttatcactttcttatctagtctttataactagatgataacatctctgtaaatcaaagtcaagcaaaaaatagaatgtcccattgaaatttgatataattttaaaaagaagaaagggaggtttcag Mask Tandem Repeat Region ================================================ ctgaaacctccctttcttctttttaaaattatatcaaatttcaatgggacattctattttttgcttgactttgatttacagagatgttatcatctagttataaagactagataagaaagtgataaagatttgaacgctcaacaagtttttcccaagtgggacgaattaccagaactggagctatatttggaccaagttctgctctatgtaaacaatgtctgtggctcttccatttcagctgctgacaagggactgaccgcttct Find is-nt database================================================ Query_seq: SSA_1396:SSA_1397|SSA_1396:SSA_1397:hypothetical protein:hypothetical protein:<-->:1410465..1410728 264 ctgaaacctccctttcttctttttaaaattatatcaaatttcaatgggacattctattttttgcttgactttgatttacagagatgttatcatctagttataaagactagataagaaagtgataaagatttgaacgctcaacaagtttttcccaagtgggacgaattaccagaactggagctatatttggaccaagttctgctctatgtaaacaatgtctgtggctcttccatttcagctgctgacaagggactgaccgcttct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_1396:SSA_1397|SSA_1396:SSA_1397:hypothetical protein:hypothetical protein:<-->:1410465..1410728 264 ctgaaacctccctttcttctttttaaaattatatcaaatttcaatgggacattctattttttgcttgactttgatttacagagatgttatcatctagttataaagactagataagaaagtgataaagatttgaacgctcaacaagtttttcccaagtgggacgaattaccagaactggagctatatttggaccaagttctgctctatgtaaacaatgtctgtggctcttccatttcagctgctgacaagggactgaccgcttct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_1396:SSA_1397|SSA_1396:SSA_1397:hypothetical protein:hypothetical protein:<-->:1410465..1410728 264 ctgaaacctccctttcttctttttaaaattatatcaaatttcaatgggacattctattttttgcttgactttgatttacagagatgttatcatctagttataaagactagataagaaagtgataaagatttgaacgctcaacaagtttttcccaagtgggacgaattaccagaactggagctatatttggaccaagttctgctctatgtaaacaatgtctgtggctcttccatttcagctgctgacaagggactgaccgcttct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 2 Min: 148 Max: 264 Len: 117 Subject: UniRef90_Q97PX5 Cluster: Hypothetical protein; n=3; Streptococcus pneumoniae|Rep: Hypothetical protein - Streptococcus pneumoniae HSP 1 e-value: 3.0E-7 bit: 56.6 Len: 117 Query Start:148 Query End:264 Subject Strand: null Subject Start: 7 Subject End: 45 ................................................................................................................................................... F P K W D E L P E L E L Y L D Q V L L Y V N N V C G S S I S A A D K G L T A S ................................................................................................................................................... Y P K W A E I P N I D L Y L D Q V L L Y V N Q V C A P I S P N K D K G L T A S Subject: UniRef90_Q3DKP8 Cluster: Hypothetical protein; n=8; Streptococcus agalactiae|Rep: Hypothetical protein - Streptococcus agalactiae 515 HSP 1 e-value: 2.0E-6 bit: 53.9 Len: 117 Query Start:148 Query End:264 Subject Strand: null Subject Start: 6 Subject End: 44 ................................................................................................................................................... F P K W D E L P E L E L Y L D Q V L L Y V N N V C G S S I S A A D K G L T A S ................................................................................................................................................... Y P K W E E L P E L D L Y L D Q V L L Y V N Q L I N P K T I T N D K L L T A S ctgaaacctccctttcttctttttaaaattatatcaaatttcaatgggacattctattttttgcttgactttgatttacagagatgttatcatctagttataaagactagataagaaagtgataaagatttgaacgctcaacaagttnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn Predict ORF larger than 30AA ================================================ Protein_Len: 37 Strand: + Start: 1 End: 111 M K P P F L L F K I I S N F N G T F Y F L L D F D L Q R C Y H L V I K T R ......................................................................................................................................................... Protein_Len: 45 Strand: + Start: 130 End: 264 ................................................................................................................................. M N A Q Q V F P K W D E L P E L E L Y L D Q V L L Y V N N V C G S S I S A A D K G L T A S Protein_Len: 43 Strand: - Start: 110 End: 238 ............................................................................................................. I L F H Y L N S R E V L K E W T P R I V L V P A I N P G L E A R H L C H R H S K W K M .......................... ctgaaacctccctttcttctttttaaaattatatcaaatttcaatgggacattctattttttgcttgactttgatttacagagatgttatcatctagttataaagactagataagaaagtgataaagatttgaacgctcaacaagttnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn 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: 86 Start: 64 End: 93 ...............................................................CTTGACTTTGATTTACAGAGATGTTATCAT........................................................................................................................................................................... PromScan Matrix: RpoD-17 Strand: + Score: 83 Start: 0 End: 29 tCTGAAACCTCCCTTTCTTCTTTTTAAAAT........................................................................................................................................................................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ ctgaaacctccctttcttctttttaaaattatatcaaatttcaatgggacattctattttttgcttgactttgatttacagagatgttatcatctagttataaagactagataagaaagtgataaagatttgaacgctcaacaagttnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_1396:SSA_1397|SSA_1396:SSA_1397:hypothetical protein:hypothetical protein:<-->:1410465..1410728 264 ctgaaacctccctttcttctttttaaaattatatcaaatttcaatgggacattctattttttgcttgactttgatttacagagatgttatcatctagttataaagactagataagaaagtgataaagatttgaacgctcaacaagttnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn Intra-Species Hit: Count: 1 Min: 1 Max: 147 Len: 147 Subject: NC_009009_SSA_1396_SSA_1397|hypothetical protein:hypothetical protein|NEGATIVE:POSITIVE|[1410465,1410728]|264 HSP 1 e-value: 6.0E-78 bit: 291.0 Len: 147 Query Start:1 Query End:147 Subject Strand: POSITIVE Subject Start: 1 Subject End: 147 ctgaaacctccctttcttctttttaaaattatatcaaatttcaatgggacattctattttttgcttgactttgatttacagagatgttatcatctagttataaagactagataagaaagtgataaagatttgaacgctcaacaagtt..................................................................................................................... ctgaaacctccctttcttctttttaaaattatatcaaatttcaatgggacattctattttttgcttgactttgatttacagagatgttatcatctagttataaagactagataagaaagtgataaagatttgaacgctcaacaagtt..................................................................................................................... Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CUGAAACCUCCCUUUCUUCUUUUUAAAAUUAUAUCAAAUUUCAAUGGGACAUUCUAUUUUUUGCUUGACUUUGAUUUACAGAGAUGUUAUCAUCUAGUUAUAAAGACUAGAUAAGAAAGUGAUAAAGAUUUGAACGCUCAACAAGUU ........((.(((((((((((...((((((..((((.....((((((....))))))......))))...))))))..))))).......((((((((.....)))))))).)))))).))....((((((.........)))))) (-21.30) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AACUUGUUGAGCGUUCAAAUCUUUAUCACUUUCUUAUCUAGUCUUUAUAACUAGAUGAUAACAUCUCUGUAAAUCAAAGUCAAGCAAAAAAUAGAAUGUCCCAUUGAAAUUUGAUAUAAUUUUAAAAAGAAGAAAGGGAGGUUUCAG .......(((((.(((...(((((.........(((((((((.......)))))))))..((((.(((((....................)))))))))....((((((((......))))))))...)))))...))).).)))). (-22.25) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 768 110 61 201 152 NC_009009:SSA_1396|5end_hypothetical_protein_1410374..1410604_NEGATIVE 259 50 7 135 99 NC_009009:SSA_1610|5end_hypothetical_protein_1614909..1615139_NEGATIVE 239 50 2 209 149 NC_009009:SSA_1758|5end_hypothetical_protein_1746619..1746849_NEGATIVE 230 42 7 99 67 NC_009009:SSA_1730|5end_hypothetical_protein_1716057..1716287_NEGATIVE 229 54 11 113 69 NC_009009:SSA_2090|5end_Hexulose-6-phosphate_synthase,_putative_2095038..2095268_NEGATIVE 228 49 8 131 94 NC_009009:SSA_0258|5end_hypothetical_protein_251845..252075_POSITIVE 224 44 3 145 106 NC_009009:SSA_0305|5end_hypothetical_protein_301985..302215_POSITIVE 223 88 60 146 123 NC_009009:SSA_0578|5end_Nicotinate-nucleotide_adenylyltransferase,_putative_571591..571821_POSITIVE 220 140 110 172 143 NC_009009:SSA_0291|5end_Oxidoreductase,_putative_285362..285592_POSITIVE 217 49 8 136 98 NC_009009:SSA_1731|5end_ATP-dependent_Clp_protease,_proteolytic_subunit,_putative_1716808..1717038_NEGATIVE 212 86 45 216 174 NC_009009:SSA_1448|5end_ATP_phosphoribosyltransferase_regulatory_subunit,_putative_1450817..1451047_NEGATIVE 211 119 74 174 128 NC_009009:SSA_1235|5end_Dihydroorotase,_putative_1261227..1261457_NEGATIVE 211 87 46 178 139 NC_009009:SSA_0610|5end_LemA-like_protein,_putative_598968..599198_POSITIVE 210 100 52 151 116 NC_009009:SSA_0995|5end_Antibiotic-resistance_protein,_alpha/beta_superfamily_hydrolase,_putative_995716..995946_POSITIVE 208 134 95 190 145 NC_009009:SSA_0644|5end_DNA_Protection_System,_DNA-binding_ferritin-like_protein_(oxidative_damage_protectant),_putative_630170..630400_POSITIVE 204 140 96 221 177 NC_009009:SSA_0193|5end_CAAX_amino_terminal_protease_family_protein,_putative_194318..194548_POSITIVE 202 42 1 119 77 NC_009009:SSA_2175|5end_hypothetical_protein_2174042..2174272_NEGATIVE 202 25 1 50 25 NC_009009:SSA_0163|5end_hypothetical_protein_162127..162357_POSITIVE 200 125 84 51 17 NC_009009:SSA_0978|5end_hypothetical_protein_983736..983966_POSITIVE 199 107 65 153 109 NC_009009:SSA_2022|5end_Transcriptional_regulator,_MerR_family_(multidrug-efflux_transporter_genes),_putative_2023572..2023802_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 229 54 11 89 45 NC_009009:SSA_2091|3end_Phosphotransferase_system_sugar-specific_EII_component,_putative_2095062..2095212_NEGATIVE 229 80 34 137 91 NC_009009:SSA_1837|3end_hypothetical_protein_1832955..1833105_POSITIVE 228 49 8 46 9 NC_009009:SSA_0257|3end_N-acetylmuramidase/lysin,_putative_251840..251990_POSITIVE 223 88 60 119 96 NC_009009:SSA_0577|3end_Ancient_RNA-binding_IF3-C_fold_(CRS1/YhbY_domain),_putative_571644..571794_POSITIVE 208 101 62 143 97 NC_009009:SSA_2092|3end_Phosphotransferase_system_sugar-specific_EII_component,_putative_2095697..2095847_NEGATIVE 205 48 4 90 49 NC_009009:SSA_1759|3end_hypothetical_protein_1746664..1746814_NEGATIVE 201 100 54 142 88 NC_009009:SSA_1729|3end_ABC_transporter_substrate-binding_protein-branched_chain_amino_acid_transport,_putative_1714539..1714689_NEGATIVE 200 125 84 54 20 NC_009009:SSA_0977|3end_3-isopropylmalate_dehydrogenase,_putative_983819..983969_POSITIVE 197 138 93 136 97 NC_009009:SSA_2158|3end_Methyltransferase,_putative_2158421..2158571_NEGATIVE 197 88 41 64 8 NC_009009:SSA_2053|3end_hypothetical_protein_2057526..2057676_NEGATIVE 196 50 12 138 99 NC_009009:SSA_1517|3end_Cell-wall_biogenesis_glycosyltransferase,_putative_1522842..1522992_NEGATIVE 191 88 45 106 64 NC_009009:SSA_0395|3end_6-phospho-beta-glucosidase,_putative_392580..392730_POSITIVE 190 49 8 64 26 NC_009009:SSA_0901|3end_Alpha-acetolactate_decarboxylase,_putative_893246..893396_POSITIVE 189 95 51 139 93 NC_009009:SSA_1100|3end_Hemolysin_exporter,_ATPase_component,_putative_1122088..1122238_POSITIVE 188 109 79 118 83 NC_009009:SSA_0752|3end_hypothetical_protein_734934..735084_POSITIVE 187 85 41 137 90 NC_009009:SSA_0857|3end_hypothetical_protein_845482..845632_POSITIVE 187 24 1 135 114 NC_009009:SSA_0190|3end_hypothetical_protein_191905..192055_POSITIVE 186 97 62 133 103 NC_009009:SSA_0644|3end_DNA_Protection_System,_DNA-binding_ferritin-like_protein_(oxidative_damage_protectant),_putative_630765..630915_POSITIVE 185 108 71 148 115 NC_009009:SSA_1379|3end_hypothetical_protein_1398178..1398328_NEGATIVE 185 72 36 121 76 NC_009009:SSA_0858|3end_DTDP-L-rhamnose_synthase,_putative_846446..846596_POSITIVE