Origin IGS: gaacttagcttctaaccgctaaatcaaaataggaaagattcgtttatggatctttcctatttttgttaaaaatagactgttttcaacaaagtgtctaattataatgttagtttcttacaattatagttatatatatggataactaaaatagaatagtgtataataaaagctgcaatttaaatgattatttaggagattatt .........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 aataatctcctaaataatcatttaaattgcagcttttattatacactattctattttagttatccatatatataactataattgtaagaaactaacattataattagacactttgttgaaaacagtctatttttaacaaaaataggaaagatccataaacgaatctttcctattttgatttagcggttagaagctaagttc Mask Tandem Repeat Region ================================================ gaacttagcttctaaccgctaaatcaaaataggaaagattcgtttatggatctttcctatttttgttaaaaatagactgttttcaacaaagtgtctaattataatgttagtttcttacaattatagttatatatatggataactaaaatagaatagtgtataataaaagctgcaatttaaatgattatttaggagattatt Find is-nt database================================================ Query_seq: SSA_0904:SSA_0905|SSA_0904:SSA_0905:CshA-like fibrillar surface protein A:CshA-like fibrillar surface protein B:->->:903019..903219 201 gaacttagcttctaaccgctaaatcaaaataggaaagattcgtttatggatctttcctatttttgttaaaaatagactgttttcaacaaagtgtctaattataatgttagtttcttacaattatagttatatatatggataactaaaatagaatagtgtataataaaagctgcaatttaaatgattatttaggagattatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_0904:SSA_0905|SSA_0904:SSA_0905:CshA-like fibrillar surface protein A:CshA-like fibrillar surface protein B:->->:903019..903219 201 gaacttagcttctaaccgctaaatcaaaataggaaagattcgtttatggatctttcctatttttgttaaaaatagactgttttcaacaaagtgtctaattataatgttagtttcttacaattatagttatatatatggataactaaaatagaatagtgtataataaaagctgcaatttaaatgattatttaggagattatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_0904:SSA_0905|SSA_0904:SSA_0905:CshA-like fibrillar surface protein A:CshA-like fibrillar surface protein B:->->:903019..903219 201 gaacttagcttctaaccgctaaatcaaaataggaaagattcgtttatggatctttcctatttttgttaaaaatagactgttttcaacaaagtgtctaattataatgttagtttcttacaattatagttatatatatggataactaaaatagaatagtgtataataaaagctgcaatttaaatgattatttaggagattatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gaacttagcttctaaccgctaaatcaaaataggaaagattcgtttatggatctttcctatttttgttaaaaatagactgttttcaacaaagtgtctaattataatgttagtttcttacaattatagttatatatatggataactaaaatagaatagtgtataataaaagctgcaatttaaatgattatttaggagattatt Predict ORF larger than 30AA ================================================ Protein_Len: 39 Strand: + Start: 23 End: 139 ...................... M K I G K I R L W I F P I F V K N R L F S T K C L I I M L V S Y N Y S Y I Y G .............................................................. gaacttagcttctaaccgctaaatcaaaataggaaagattcgtttatggatctttcctatttttgttaaaaatagactgttttcaacaaagtgtctaattataatgttagtttcttacaattatagttatatatatggataactaaaatagaatagtgtataataaaagctgcaatttaaatgattatttaggagattatt 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: 135 End: 164 ......................................................................................................................................ATGGATAACTAAAATAGAATAGTGTATAAT..................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ gaacttagcttctaaccgctaaatcaaaataggaaagattcgtttatggatctttcctatttttgttaaaaatagactgttttcaacaaagtgtctaattataatgttagtttcttacaattatagttatatatatggataactaaaatagaatagtgtataataaaagctgcaatttaaatgattatttaggagattatt Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 68 HP_score: -8.1 Tail_Score: -2.76261 Start: 25 End: 64 Full_Region: cagtctatttttaac aaaaataggaaagatcc ataaac gaatctttcctattttg atttagcggttagaa ........................aaaaataggaaagatccataaacgaatctttcctattttg......................................................................................................................................... TransTerm Strand: - Conf: 83 HP_score: -8.0 Tail_Score: -4.55128 Start: 30 End: 59 Full_Region: tatttttaacaaaaa taggaaagatcc ataaac gaatctttccta ttttgatttagcggt .............................taggaaagatccataaacgaatctttccta.............................................................................................................................................. Find igs database================================================ Query_seq: SSA_0904:SSA_0905|SSA_0904:SSA_0905:CshA-like fibrillar surface protein A:CshA-like fibrillar surface protein B:->->:903019..903219 201 gaacttagcttctaaccgctaaatcaaaataggaaagattcgtttatggatctttcctatttttgttaaaaatagactgttttcaacaaagtgtctaattataatgttagtttcttacaattatagttatatatatggataactaaaatagaatagtgtataataaaagctgcaatttaaatgattatttaggagattatt Intra-Species Hit: Count: 1 Min: 1 Max: 201 Len: 201 Subject: NC_009009_SSA_0904_SSA_0905|CshA-like fibrillar surface protein A:CshA-like fibrillar surface protein B|POSITIVE:POSITIVE|[903019,903219]|201 HSP 1 e-value: 1.0E-110 bit: 398.0 Len: 201 Query Start:1 Query End:201 Subject Strand: POSITIVE Subject Start: 1 Subject End: 201 gaacttagcttctaaccgctaaatcaaaataggaaagattcgtttatggatctttcctatttttgttaaaaatagactgttttcaacaaagtgtctaattataatgttagtttcttacaattatagttatatatatggataactaaaatagaatagtgtataataaaagctgcaatttaaatgattatttaggagattatt gaacttagcttctaaccgctaaatcaaaataggaaagattcgtttatggatctttcctatttttgttaaaaatagactgttttcaacaaagtgtctaattataatgttagtttcttacaattatagttatatatatggataactaaaatagaatagtgtataataaaagctgcaatttaaatgattatttaggagattatt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAACUUAGCUUCUAACCGCUAAAUCAAAAUAGGAAAGAUUCGUUUAUGGAUCUUUCCUAUUUUUGUUAAAAAUAGACUGUUUUCAACAAAGUGUCUAAUUAUAAUGUUAGUUUCUUACAAUUAUAGUUAUAUAUAUGGAUAACUAAAAUAGAAUAGUGUAUAAUAAAAGCUGCAAUUUAAAUGAUUAUUUAGGAGAUUAUU ........(((((((..(((.(((.(((((((((((((((((....))))))))))))))))).)))....(((.((((((((.....(((...(((((......)))))...))).......(((((((........)))))))....)))))))).)))......)))...((((.....))))..)))))))...... (-44.50) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAUAAUCUCCUAAAUAAUCAUUUAAAUUGCAGCUUUUAUUAUACACUAUUCUAUUUUAGUUAUCCAUAUAUAUAACUAUAAUUGUAAGAAACUAACAUUAUAAUUAGACACUUUGUUGAAAACAGUCUAUUUUUAACAAAAAUAGGAAAGAUCCAUAAACGAAUCUUUCCUAUUUUGAUUUAGCGGUUAGAAGCUAAGUUC ........................((((..((((..............(((((((.(((((((........))))))).)))....)))).(((((.....(((((((...(((((((((((.......))))))))))).(((((((((((.(......).)))))))))))))))))).....))))).)))).)))). (-35.00) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 285 50 4 192 145 NC_009009:SSA_0317|5end_Ribosomal_protein_alanine_acetyl_transferase,_putative_311259..311489_POSITIVE 273 46 7 71 32 NC_009009:SSA_0206|5end_hypothetical_protein_204256..204486_POSITIVE 251 41 5 73 34 NC_009009:SSA_1210|5end_GTP_pyrophosphokinase,_putative_1234655..1234885_NEGATIVE 235 50 6 175 126 NC_009009:SSA_0281|5end_hypothetical_protein_273404..273634_POSITIVE 234 58 11 231 177 NC_009009:SSA_0072|5end_ABC_sugar_transporter,_MsmK-like_protein,_putative_75922..76152_POSITIVE 233 89 41 75 25 NC_009009:SSA_0342|5end_Pyruvate_formate-lyase,_putative_337206..337436_NEGATIVE 226 195 162 43 5 NC_009009:SSA_0877|5end_Phosphoglycolate_phosphatase,_putative_871008..871238_POSITIVE 226 60 15 180 135 NC_009009:SSA_0794|5end_Zn-dependent_protease,_putative_775896..776126_POSITIVE 226 96 56 212 172 NC_009009:SSA_0688|5end_2,3-bisphosphoglycerate-dependent_phosphoglycerate_mutase,_putative_671360..671590_POSITIVE 224 42 4 215 180 NC_009009:SSA_1759|5end_hypothetical_protein_1746969..1747199_NEGATIVE 221 99 53 64 19 NC_009009:SSA_0678|5end_Transcriptional_regulator,_ArgR_family,_putative_660274..660504_POSITIVE 213 82 41 84 45 NC_009009:SSA_0321|5end_Methylase,_putative_313867..314097_POSITIVE 212 97 60 221 181 NC_009009:SSA_1587|5end_hypothetical_protein_1589086..1589316_NEGATIVE 212 60 11 182 129 NC_009009:SSA_0270|5end_Phosphotransferase_system_(PTS)_cellobiose-specific,_IIC_component,_putative_262873..263103_POSITIVE 210 195 154 224 189 NC_009009:SSA_0663|5end_Acetyltransferase,_putative_648352..648582_POSITIVE 210 80 41 48 12 NC_009009:SSA_0200|5end_Bifunctional_folate_synthesis_protein,_putative_198918..199148_POSITIVE 209 97 51 153 100 NC_009009:SSA_1287|5end_hypothetical_protein_1306737..1306967_NEGATIVE 208 84 41 171 120 NC_009009:SSA_1989|5end_ABC-type_transport_system_(uncharacterized),_ATPase_component,_putative_1985182..1985412_NEGATIVE 208 50 6 140 96 NC_009009:SSA_1246|5end_hypothetical_protein_1271225..1271455_NEGATIVE 207 79 39 176 130 NC_009009:SSA_2218|5end_Glycosyltransferase_(cell_wall_biogenesis)_Cps9G,_putative_2219941..2220171_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 408 63 26 65 28 NC_009009:SSA_0904|3end_CshA-like_fibrillar_surface_protein_A_902958..903108_POSITIVE 273 46 7 74 35 NC_009009:SSA_2393|3end_Transcriptional_regulator,_XRE_family,_putative_204339..204489_POSITIVE 243 199 169 52 20 NC_009009:SSA_2135|3end_Transcriptional_repressor,_DeoR_family_(possibly_truncated),_putative_2137474..2137624_POSITIVE 235 50 6 61 12 NC_009009:SSA_0279|3end_Sugar-binding_transcriptional_repressor_(DeoR),_putative_273370..273520_POSITIVE 226 96 56 62 22 NC_009009:SSA_0687|3end_hypothetical_protein_671290..671440_POSITIVE 224 42 4 58 23 NC_009009:SSA_1760|3end_hypothetical_protein_1747126..1747276_NEGATIVE 221 99 53 71 26 NC_009009:SSA_0677|3end_rRNA_methylase,_putative_660361..660511_POSITIVE 212 97 60 125 85 NC_009009:SSA_1588|3end_Conserved_ABC-type_antimicrobial_permease-like_protein,_putative_1589182..1589332_NEGATIVE 208 50 6 143 99 NC_009009:SSA_1247|3end_hypothetical_protein_1271222..1271372_NEGATIVE 207 79 39 150 104 NC_009009:SSA_2219|3end_UDP-glucose_4-epimerase,_putative_2219967..2220117_NEGATIVE 207 56 15 53 4 NC_009009:SSA_0381|3end_hypothetical_protein_373514..373664_POSITIVE 205 80 32 111 64 NC_009009:SSA_0876|3end_4-methyl-5(B-hydroxyethyl)-thiazole_monophosphate_biosynthesis_protein,_putative_870861..871011_POSITIVE 204 75 31 102 53 NC_009009:SSA_0927|3end_Transcriptional_regulator,_TetR/AcrR_family,_putative_936740..936890_POSITIVE 203 68 29 83 37 NC_009009:SSA_0756|3end_Alanyl-tRNA_synthetase,_putative_739434..739584_POSITIVE 202 89 41 110 57 NC_009009:SSA_0585|3end_hypothetical_protein_577286..577436_POSITIVE 200 64 25 92 54 NC_009009:SSA_0903|3end_NAD(P)H_dehydrogenase_(quinone),_putative_893813..893963_POSITIVE 197 109 61 121 74 NC_009009:SSA_1456|3end_hypothetical_protein_1462113..1462263_NEGATIVE 197 84 42 74 32 NC_009009:SSA_0576|3end_Conserved_GTPase,_putative_571225..571375_POSITIVE 196 57 15 88 48 NC_009009:SSA_1639|3end_5'-methylthioadenosine/S-adenosylhomocysteine_nucleosidase,_putative_1641339..1641489_NEGATIVE 196 98 51 123 79 NC_009009:SSA_0724|3end_ABC-type_multidrug/protein/lipid_transport_system_(pediocin_PA-1_exporter),_ATPase_and_permease_components,_putative_710312..710462_POSITIVE