Origin IGS: ttgctattctcaaagaaaactcttgaaaatcataatgtttccccttgcaaaagcttgaaaatttggtataatagtttttactcaagggagtagctaacggaataaccgttacaaggtcgtcaatacgaaagaaatttccggccttgtatgaaatagcgagacttgttaataaacaggtctcttttttgtttctgactttttggatatgactg .........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 cagtcatatccaaaaagtcagaaacaaaaaagagacctgtttattaacaagtctcgctatttcatacaaggccggaaatttctttcgtattgacgaccttgtaacggttattccgttagctactcccttgagtaaaaactattataccaaattttcaagcttttgcaaggggaaacattatgattttcaagagttttctttgagaatagcaa Mask Tandem Repeat Region ================================================ ttgctattctcaaagaaaactcttgaaaatcataatgtttccccttgcaaaagcttgaaaatttggtataatagtttttactcaagggagtagctaacggaataaccgttacaaggtcgtcaatacgaaagaaatttccggccttgtatgaaatagcgagacttgttaataaacaggtctcttttttgtttctgactttttggatatgactg Find is-nt database================================================ Query_seq: SSA_0865:SSA_0866|SSA_0865:SSA_0866:hypothetical protein:Cation-transporting ATPase, E1-E 2 family, putative:->->:856911..857122 212 ttgctattctcaaagaaaactcttgaaaatcataatgtttccccttgcaaaagcttgaaaatttggtataatagtttttactcaagggagtagctaacggaataaccgttacaaggtcgtcaatacgaaagaaatttccggccttgtatgaaatagcgagacttgttaataaacaggtctcttttttgtttctgactttttggatatgactg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_0865:SSA_0866|SSA_0865:SSA_0866:hypothetical protein:Cation-transporting ATPase, E1-E 2 family, putative:->->:856911..857122 212 ttgctattctcaaagaaaactcttgaaaatcataatgtttccccttgcaaaagcttgaaaatttggtataatagtttttactcaagggagtagctaacggaataaccgttacaaggtcgtcaatacgaaagaaatttccggccttgtatgaaatagcgagacttgttaataaacaggtctcttttttgtttctgactttttggatatgactg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_0865:SSA_0866|SSA_0865:SSA_0866:hypothetical protein:Cation-transporting ATPase, E1-E 2 family, putative:->->:856911..857122 212 ttgctattctcaaagaaaactcttgaaaatcataatgtttccccttgcaaaagcttgaaaatttggtataatagtttttactcaagggagtagctaacggaataaccgttacaaggtcgtcaatacgaaagaaatttccggccttgtatgaaatagcgagacttgttaataaacaggtctcttttttgtttctgactttttggatatgactg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ttgctattctcaaagaaaactcttgaaaatcataatgtttccccttgcaaaagcttgaaaatttggtataatagtttttactcaagggagtagctaacggaataaccgttacaaggtcgtcaatacgaaagaaatttccggccttgtatgaaatagcgagacttgttaataaacaggtctcttttttgtttctgactttttggatatgactg Predict ORF larger than 30AA ================================================ Protein_Len: 30 Strand: + Start: 1 End: 90 M L F S K K T L E N H N V S P C K S L K I W Y N S F Y S R E .......................................................................................................................... Protein_Len: 35 Strand: + Start: 102 End: 206 ..................................................................................................... M T V T R S S I R K K F P A L Y E I A R L V N K Q V S F L F L T F W I ...... Protein_Len: 60 Strand: - Start: 2 End: 205 . F D Y H K G K C F S S F K T Y Y N K S L P T A L P I V T V L D D I R F F N G A K Y S I A L S T L L C T E K K N R V K Q M ....... ttgctattctcaaagaaaactcttgaaaatcataatgtttccccttgcaaaagcttgaaaatttggtataatagtttttactcaagggagtagctaacggaataaccgttacaaggtcgtcaatacgaaagaaatttccggccttgtatgaaatagcgagacttgttaataaacaggtctcttttttgtttctgactttttggatatgactg 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================================================ ttgctattctcaaagaaaactcttgaaaatcataatgtttccccttgcaaaagcttgaaaatttggtataatagtttttactcaagggagtagctaacggaataaccgttacaaggtcgtcaatacgaaagaaatttccggccttgtatgaaatagcgagacttgttaataaacaggtctcttttttgtttctgactttttggatatgactg Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 42 HP_score: -2.1 Tail_Score: -3.03338 Start: 126 End: 140 Full_Region: tatttcatacaaggc cggaa atttc tttcg tattgacgaccttgt .............................................................................................................................cggaaatttctttcg........................................................................ TransTerm Strand: + Conf: 100 HP_score: -10.4 Tail_Score: -5.72622 Start: 158 End: 181 Full_Region: CTTGTATGAAATAGC GAGACTTGTT AATA AACAGGTCTC TTTTTTGTTTCTGAC .............................................................................................................................................................GAGACTTGTTAATAAACAGGTCTC............................... Find igs database================================================ Query_seq: SSA_0865:SSA_0866|SSA_0865:SSA_0866:hypothetical protein:Cation-transporting ATPase, E1-E 2 family, putative:->->:856911..857122 212 ttgctattctcaaagaaaactcttgaaaatcataatgtttccccttgcaaaagcttgaaaatttggtataatagtttttactcaagggagtagctaacggaataaccgttacaaggtcgtcaatacgaaagaaatttccggccttgtatgaaatagcgagacttgttaataaacaggtctcttttttgtttctgactttttggatatgactg Intra-Species Hit: Count: 1 Min: 1 Max: 212 Len: 212 Subject: NC_009009_SSA_0865_SSA_0866|hypothetical protein:Cation-transporting ATPase, E1-E 2 family, putative|POSITIVE:POSITIVE|[856911,857122]|212 HSP 1 e-value: 1.0E-117 bit: 420.0 Len: 212 Query Start:1 Query End:212 Subject Strand: POSITIVE Subject Start: 1 Subject End: 212 ttgctattctcaaagaaaactcttgaaaatcataatgtttccccttgcaaaagcttgaaaatttggtataatagtttttactcaagggagtagctaacggaataaccgttacaaggtcgtcaatacgaaagaaatttccggccttgtatgaaatagcgagacttgttaataaacaggtctcttttttgtttctgactttttggatatgactg ttgctattctcaaagaaaactcttgaaaatcataatgtttccccttgcaaaagcttgaaaatttggtataatagtttttactcaagggagtagctaacggaataaccgttacaaggtcgtcaatacgaaagaaatttccggccttgtatgaaatagcgagacttgttaataaacaggtctcttttttgtttctgactttttggatatgactg Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUGCUAUUCUCAAAGAAAACUCUUGAAAAUCAUAAUGUUUCCCCUUGCAAAAGCUUGAAAAUUUGGUAUAAUAGUUUUUACUCAAGGGAGUAGCUAACGGAAUAACCGUUACAAGGUCGUCAAUACGAAAGAAAUUUCCGGCCUUGUAUGAAAUAGCGAGACUUGUUAAUAAACAGGUCUCUUUUUUGUUUCUGACUUUUUGGAUAUGACUG ..(((((((((...(((((((.(((...((((.....((((..(((....)))...))))...)))).))).)))))))......)))))))))....(..(((.((..((((((((((..(((.(....)..)))..)))))))))).(((((((.((((((((((....))))))))))....))))))).........)).)))..).. (-55.10) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CAGUCAUAUCCAAAAAGUCAGAAACAAAAAAGAGACCUGUUUAUUAACAAGUCUCGCUAUUUCAUACAAGGCCGGAAAUUUCUUUCGUAUUGACGACCUUGUAACGGUUAUUCCGUUAGCUACUCCCUUGAGUAAAAACUAUUAUACCAAAUUUUCAAGCUUUUGCAAGGGGAAACAUUAUGAUUUUCAAGAGUUUUCUUUGAGAAUAGCAA ..(..(((.((.........((((.......(((((.((((....)))).)))))....)))).(((((((.((..(((.........)))..)).)))))))..)).)))..)....(((..((((((..((((((.((.................)).)))))).)))))).........(((((((((.......)))))))))))).. (-43.73) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 359 158 112 61 2 NC_009009:SSA_0408|5end_hypothetical_protein_404684..404914_NEGATIVE 337 121 82 142 105 NC_009009:SSA_1016|5end_Phosphoenolpyruvate_synthase,_putative_1019602..1019832_POSITIVE 304 139 93 97 40 NC_009009:SSA_2217|5end_Cps9H,_putative_2219045..2219275_NEGATIVE 283 159 111 170 118 NC_009009:SSA_0725|5end_hypothetical_protein_710247..710477_POSITIVE 274 169 130 82 42 NC_009009:SSA_1236|5end_Mutator_protein,_putative_1261704..1261934_NEGATIVE 271 160 113 177 133 NC_009009:SSA_0770|5end_Ribonucleoside-diphosphate_reductase,_putative_751411..751641_NEGATIVE 269 203 178 127 101 NC_009009:SSA_2044|5end_Cysteinyl-tRNA_synthetase,_putative_2048409..2048639_NEGATIVE 264 75 42 182 152 NC_009009:SSA_0448|5end_Excinuclease_ATPase_subunit_A,_putative_446480..446710_POSITIVE 257 148 106 44 6 NC_009009:SSA_0086|5end_V-type_sodium_ATPase,_subunit_K,_putative_87839..88069_POSITIVE 255 128 83 222 178 NC_009009:SSA_0516|5end_AmiR_two-component_response_regulator_with_transcriptional_antiterminator_output_domain,_putative_514485..514715_POSITIVE 254 198 154 222 176 NC_009009:SSA_2223|5end_Capsular_polysaccharide_biosynthesis_protein_Wzd_(chain_length_regulator),_putative_2224703..2224933_NEGATIVE 251 127 81 60 6 NC_009009:SSA_0318|5end_Secreted_metalloendopeptidase_Gcp_311701..311931_POSITIVE 248 210 175 69 34 NC_009009:SSA_0706|5end_RNA_helicase,_putative_691363..691593_POSITIVE 247 100 53 184 131 NC_009009:SSA_1280|5end_hypothetical_protein_1301596..1301826_NEGATIVE 247 119 75 139 98 NC_009009:SSA_0981|5end_3-isopropylmalate_dehydratase_small_subunit,_putative_985396..985626_POSITIVE 246 128 81 81 32 NC_009009:SSA_1044|5end_Homoserine_kinase,_putative_1059853..1060083_POSITIVE 245 66 31 129 89 NC_009009:SSA_0105|5end_Uridine_kinase,_putative_106761..106991_POSITIVE 244 117 75 46 3 NC_009009:SSA_2206|5end_hypothetical_protein_2206839..2207069_POSITIVE 244 157 113 162 119 NC_009009:SSA_1156|5end_hypothetical_protein_1184562..1184792_POSITIVE 241 179 139 51 7 NC_009009:SSA_2361|5end_L-serine_dehydratase_beta_subunit_2364028..2364258_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 337 121 82 142 105 NC_009009:SSA_1015|3end_4-hydroxybenzoate_octaprenyltransferase,_putative_1019682..1019832_POSITIVE 299 120 72 146 92 NC_009009:SSA_2202|3end_Elongation_factor_Ts,_putative_2202307..2202457_NEGATIVE 274 169 130 73 33 NC_009009:SSA_1237|3end_Uracil-DNA_glycosylase,_putative_1261713..1261863_NEGATIVE 269 203 178 109 83 NC_009009:SSA_2045|3end_Reductase,_putative_2048427..2048577_NEGATIVE 251 147 114 81 37 NC_009009:SSA_2374|3end_Inosine-5'-monophosphate_dehydrogenase,_putative_2375534..2375684_NEGATIVE 251 127 81 70 16 NC_009009:SSA_0317|3end_Ribosomal_protein_alanine_acetyl_transferase,_putative_311791..311941_POSITIVE 249 128 81 151 104 NC_009009:SSA_2058|3end_30S_ribosomal_protein_S15,_putative_2060058..2060208_NEGATIVE 247 119 75 129 88 NC_009009:SSA_0980|3end_3-isopropylmalate_dehydratase_large_subunit,_putative_985466..985616_POSITIVE 246 128 81 79 30 NC_009009:SSA_1043|3end_Homoserine_dehydrogenase,_putative_1059931..1060081_POSITIVE 245 66 31 103 63 NC_009009:SSA_0104|3end_Queuine_tRNA-ribosyltransferase,_putative_106815..106965_POSITIVE 244 148 115 135 108 NC_009009:SSA_0436|3end_Imidazolonepropionase,_putative_440214..440364_POSITIVE 238 127 81 99 54 NC_009009:SSA_2044|3end_Cysteinyl-tRNA_synthetase,_putative_2047066..2047216_NEGATIVE 237 199 151 58 7 NC_009009:SSA_0183|3end_hypothetical_protein_188106..188256_POSITIVE 236 148 105 41 5 NC_009009:SSA_1067|3end_hypothetical_protein_1087345..1087495_POSITIVE 232 121 85 81 45 NC_009009:SSA_0293|3end_hypothetical_protein_287356..287506_NEGATIVE 232 107 70 145 108 NC_009009:SSA_0239|3end_7,8-dihydro-8-oxoguanine-triphosphatase,_putative_233493..233643_POSITIVE 231 140 92 47 14 NC_009009:SSA_0870|3end_Cell_division_protein_FtsE,_putative_863708..863858_POSITIVE 230 194 159 151 112 NC_009009:SSA_0807|3end_GTP-binding_protein,_putative_790839..790989_POSITIVE 230 120 71 66 10 NC_009009:SSA_0461|3end_ABC-type_multidrug_transport_system,_ATPase_and_permease_components,_putative_464905..465055_POSITIVE 227 143 102 145 113 NC_009009:SSA_0576|3end_Conserved_GTPase,_putative_571225..571375_POSITIVE