Origin IGS: ctttcttgcgatacgaggcacctgtttaggtgccttttggtgaataatgaagataggtttggtcatcttgagacaagtgcaggatgaagttggtctaggagaatatc .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 gatattctcctagaccaacttcatcctgcacttgtctcaagatgaccaaacctatcttcattattcaccaaaaggcacctaaacaggtgcctcgtatcgcaagaaag Mask Tandem Repeat Region ================================================ ctttcttgcgatacgaggcacctgtttaggtgccttttggtgaataatgaagataggtttggtcatcttgagacaagtgcaggatgaagttggtctaggagaatatc Find is-nt database================================================ Query_seq: SSA_0672:SSA_0673|SSA_0672:SSA_0673:hypothetical protein:hypothetical protein:->->:656105..656211 107 ctttcttgcgatacgaggcacctgtttaggtgccttttggtgaataatgaagataggtttggtcatcttgagacaagtgcaggatgaagttggtctaggagaatatc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_0672:SSA_0673|SSA_0672:SSA_0673:hypothetical protein:hypothetical protein:->->:656105..656211 107 ctttcttgcgatacgaggcacctgtttaggtgccttttggtgaataatgaagataggtttggtcatcttgagacaagtgcaggatgaagttggtctaggagaatatc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_0672:SSA_0673|SSA_0672:SSA_0673:hypothetical protein:hypothetical protein:->->:656105..656211 107 ctttcttgcgatacgaggcacctgtttaggtgccttttggtgaataatgaagataggtttggtcatcttgagacaagtgcaggatgaagttggtctaggagaatatc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ctttcttgcgatacgaggcacctgtttaggtgccttttggtgaataatgaagataggtttggtcatcttgagacaagtgcaggatgaagttggtctaggagaatatc Predict ORF larger than 30AA ================================================ ctttcttgcgatacgaggcacctgtttaggtgccttttggtgaataatgaagataggtttggtcatcttgagacaagtgcaggatgaagttggtctaggagaatatc 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================================================ ctttcttgcgatacgaggcacctgtttaggtgccttttggtgaataatgaagataggtttggtcatcttgagacaagtgcaggatgaagttggtctaggagaatatc Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 77 HP_score: -11.3 Tail_Score: -2.62184 Start: 17 End: 34 Full_Region: cattattcaccaaaa ggcacct aaac aggtgcc tcgtatcgcaagaaa ................ggcacctaaacaggtgcc......................................................................... Find igs database================================================ Query_seq: SSA_0672:SSA_0673|SSA_0672:SSA_0673:hypothetical protein:hypothetical protein:->->:656105..656211 107 ctttcttgcgatacgaggcacctgtttaggtgccttttggtgaataatgaagataggtttggtcatcttgagacaagtgcaggatgaagttggtctaggagaatatc Intra-Species Hit: Count: 1 Min: 1 Max: 107 Len: 107 Subject: NC_009009_SSA_0672_SSA_0673|hypothetical protein:hypothetical protein|POSITIVE:POSITIVE|[656105,656211]|107 HSP 1 e-value: 2.0E-54 bit: 212.0 Len: 107 Query Start:1 Query End:107 Subject Strand: POSITIVE Subject Start: 1 Subject End: 107 ctttcttgcgatacgaggcacctgtttaggtgccttttggtgaataatgaagataggtttggtcatcttgagacaagtgcaggatgaagttggtctaggagaatatc ctttcttgcgatacgaggcacctgtttaggtgccttttggtgaataatgaagataggtttggtcatcttgagacaagtgcaggatgaagttggtctaggagaatatc Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CUUUCUUGCGAUACGAGGCACCUGUUUAGGUGCCUUUUGGUGAAUAAUGAAGAUAGGUUUGGUCAUCUUGAGACAAGUGCAGGAUGAAGUUGGUCUAGGAGAAUAUC .(((((((.(((..(((((((((....)))))))))..........................((((((((.........)))))))).....))))))))))..... (-29.00) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAUAUUCUCCUAGACCAACUUCAUCCUGCACUUGUCUCAAGAUGACCAAACCUAUCUUCAUUAUUCACCAAAAGGCACCUAAACAGGUGCCUCGUAUCGCAAGAAAG .......................((.(((.........((((((........))))))..............((((((((....))))))))......))).))... (-20.20) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 313 41 6 124 85 NC_009009:SSA_1332|5end_hypothetical_protein_1347645..1347875_NEGATIVE 306 34 3 165 131 NC_009009:SSA_1037|5end_Cytidine_deaminase,_putative_1052118..1052348_POSITIVE 284 75 31 54 12 NC_009009:SSA_1874|5end_YorfE_protein,_putative_1870295..1870525_POSITIVE 274 44 2 73 34 NC_009009:SSA_0486|5end_Uroporphyrinogen-III_synthase,_putative_486637..486867_POSITIVE 273 40 3 156 110 NC_009009:SSA_0585|5end_hypothetical_protein_576937..577167_POSITIVE 270 80 31 214 154 NC_009009:SSA_0057|5end_Phosphotransferase_system_sugar-specific_EII_component,_putative_60762..60992_POSITIVE 268 100 51 58 8 NC_009009:SSA_0668|5end_hypothetical_protein_650737..650967_POSITIVE 268 86 45 151 105 NC_009009:SSA_0482|5end_ATP:cobalamin_adenosyl_transferase,_putative_483458..483688_POSITIVE 267 99 52 49 4 NC_009009:SSA_1891|5end_Oxidoreductase,_aldo/keto_reductase_family,_putative_1888991..1889221_NEGATIVE 264 100 67 29 1 NC_009009:SSA_1623|5end_50S_ribosomal_protein_L11,_putative_1625968..1626198_NEGATIVE 262 100 56 50 9 NC_009009:SSA_1948|5end_Oligopeptide-binding_lipoprotein_precursor,_putative_1942170..1942400_NEGATIVE 260 70 21 68 7 NC_009009:SSA_1876|5end_hypothetical_protein_1871120..1871350_POSITIVE 260 70 21 68 7 NC_009009:SSA_1875|5end_hypothetical_protein_1870558..1870788_POSITIVE 258 50 4 86 48 NC_009009:SSA_2110|5end_30S_ribosomal_protein_S7,_putative_2115579..2115809_NEGATIVE 258 42 5 195 147 NC_009009:SSA_1788|5end_Integral_membrane_protein,_possible_receptor,_putative_1772339..1772569_NEGATIVE 258 78 31 226 186 NC_009009:SSA_1155|5end_Serine_hydroxymethyltransferase,_putative_1183298..1183528_POSITIVE 257 89 41 193 135 NC_009009:SSA_0945|5end_Phosphate_import_ATP-binding_protein_pstB_1,_putative_952605..952835_POSITIVE 257 45 8 77 42 NC_009009:SSA_0319|5end_Branched-chain_amino_acid_permease_(L-methionine,_L-isoleucine,_leucine_and_valine),_putative_312721..312951_POSITIVE 255 41 1 220 187 NC_009009:SSA_1713|5end_D-3-phosphoglycerate_dehydrogenase,_putative_1701384..1701614_NEGATIVE 254 70 21 102 49 NC_009009:SSA_0127|5end_Multispanning_membrane_protein,_translocator_of_proteins,_putative_117720..117950_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 353 80 32 101 45 NC_009009:SSA_2175|3end_hypothetical_protein_2173146..2173296_NEGATIVE 313 41 6 76 37 NC_009009:SSA_1333|3end_hypothetical_protein_1347693..1347843_NEGATIVE 283 100 51 151 116 NC_009009:SSA_1079|3end_hypothetical_protein_1097448..1097598_POSITIVE 274 67 33 144 113 NC_009009:SSA_1457|3end_Neopullulanase,_putative_1462485..1462635_NEGATIVE 274 44 2 88 49 NC_009009:SSA_0485|3end_Porphobilinogen_deaminase,_putative_486732..486882_POSITIVE 263 95 58 133 97 NC_009009:SSA_1203|3end_hypothetical_protein_1227628..1227778_POSITIVE 259 42 6 147 101 NC_009009:SSA_2324|3end_hypothetical_protein_2328847..2328997_NEGATIVE 258 50 4 66 28 NC_009009:SSA_2111|3end_30S_ribosomal_protein_S12,_putative_2115599..2115749_NEGATIVE 257 89 41 132 74 NC_009009:SSA_0944|3end_Phosphate_import_ATP-binding_protein_pstB_2,_putative_952624..952774_POSITIVE 257 45 8 67 32 NC_009009:SSA_0318|3end_Secreted_metalloendopeptidase_Gcp_312791..312941_POSITIVE 256 100 57 41 6 NC_009009:SSA_2081|3end_hypothetical_protein_2085490..2085640_POSITIVE 254 70 21 89 36 NC_009009:SSA_0126|3end_50S_ribosomal_protein_L15,_putative_117787..117937_POSITIVE 253 98 52 62 22 NC_009009:SSA_0500|3end_Peptide_ABC_transporter,_permease_protein,_putative_501524..501674_POSITIVE 249 38 1 67 36 NC_009009:SSA_0384|3end_hypothetical_protein_378449..378599_POSITIVE 246 43 5 64 31 NC_009009:SSA_1429|3end_hypothetical_protein_1436355..1436505_NEGATIVE 246 99 51 141 84 NC_009009:SSA_0986|3end_Choline_transporter,_putative_989081..989231_POSITIVE 244 43 1 119 62 NC_009009:SSA_1424|3end_Hydrolase,_putative_1433889..1434039_NEGATIVE 244 93 52 119 69 NC_009009:SSA_0874|3end_hypothetical_protein_868995..869145_POSITIVE 244 78 41 148 111 NC_009009:SSA_0243|3end_Cyclo-nucleotide_phosphodiesterase,_putative_235824..235974_NEGATIVE 243 37 3 51 8 NC_009009:SSA_0512|3end_Nicotinate-nucleotide--dimethylbenzimidazole_phosphoribosyltransferase,_putative_511625..511775_POSITIVE