Origin IGS: tatttttgatggatttcggcaaaggtccgttatgacaggcctgctagtttcaggaaatagaatgtacggtccagttgctcttttagcgactggattttttatggaatagaaataggtgtaaagttaaagaaaccaagctggttcttctaaaagctatcattttttcttagtgatttttatgattccctgtgttataataagaaagattaaaaatgtaatttatcaaaaggagaatctcca .........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 tggagattctccttttgataaattacatttttaatctttcttattataacacagggaatcataaaaatcactaagaaaaaatgatagcttttagaagaaccagcttggtttctttaactttacacctatttctattccataaaaaatccagtcgctaaaagagcaactggaccgtacattctatttcctgaaactagcaggcctgtcataacggacctttgccgaaatccatcaaaaata Mask Tandem Repeat Region ================================================ tatttttgatggatttcggcaaaggtccgttatgacaggcctgctagtttcaggaaatagaatgtacggtccagttgctcttttagcgactggattttttatggaatagaaataggtgtaaagttaaagaaaccaagctggttcttctaaaagctatcattttttcttagtgatttttatgattccctgtgttataataagaaagattaaaaatgtaatttatcaaaaggagaatctcca Find is-nt database================================================ Query_seq: SSA_0585:SSA_0586|SSA_0585:SSA_0586:hypothetical protein:Conserved uncharacterized protein:->->:577347..577586 240 tatttttgatggatttcggcaaaggtccgttatgacaggcctgctagtttcaggaaatagaatgtacggtccagttgctcttttagcgactggattttttatggaatagaaataggtgtaaagttaaagaaaccaagctggttcttctaaaagctatcattttttcttagtgatttttatgattccctgtgttataataagaaagattaaaaatgtaatttatcaaaaggagaatctcca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_0585:SSA_0586|SSA_0585:SSA_0586:hypothetical protein:Conserved uncharacterized protein:->->:577347..577586 240 tatttttgatggatttcggcaaaggtccgttatgacaggcctgctagtttcaggaaatagaatgtacggtccagttgctcttttagcgactggattttttatggaatagaaataggtgtaaagttaaagaaaccaagctggttcttctaaaagctatcattttttcttagtgatttttatgattccctgtgttataataagaaagattaaaaatgtaatttatcaaaaggagaatctcca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_0585:SSA_0586|SSA_0585:SSA_0586:hypothetical protein:Conserved uncharacterized protein:->->:577347..577586 240 tatttttgatggatttcggcaaaggtccgttatgacaggcctgctagtttcaggaaatagaatgtacggtccagttgctcttttagcgactggattttttatggaatagaaataggtgtaaagttaaagaaaccaagctggttcttctaaaagctatcattttttcttagtgatttttatgattccctgtgttataataagaaagattaaaaatgtaatttatcaaaaggagaatctcca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tatttttgatggatttcggcaaaggtccgttatgacaggcctgctagtttcaggaaatagaatgtacggtccagttgctcttttagcgactggattttttatggaatagaaataggtgtaaagttaaagaaaccaagctggttcttctaaaagctatcattttttcttagtgatttttatgattccctgtgttataataagaaagattaaaaatgtaatttatcaaaaggagaatctcca Predict ORF larger than 30AA ================================================ Protein_Len: 35 Strand: + Start: 2 End: 106 . M F D G F R Q R S V M T G L L V S G N R M Y G P V A L L A T G F F M E ...................................................................................................................................... Protein_Len: 34 Strand: - Start: 1 End: 102 I K S P N R C L D T I V P R S T E P F L I Y P G T A R K A V P N K M .......................................................................................................................................... tatttttgatggatttcggcaaaggtccgttatgacaggcctgctagtttcaggaaatagaatgtacggtccagttgctcttttagcgactggattttttatggaatagaaataggtgtaaagttaaagaaaccaagctggttcttctaaaagctatcattttttcttagtgatttttatgattccctgtgttataataagaaagattaaaaatgtaatttatcaaaaggagaatctcca 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: 82 Start: 169 End: 198 ........................................................................................................................................................................AGTGATTTTTATGATTCCCTGTGTTATAAT.......................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ tatttttgatggatttcggcaaaggtccgttatgacaggcctgctagtttcaggaaatagaatgtacggtccagttgctcttttagcgactggattttttatggaatagaaataggtgtaaagttaaagaaaccaagctggttcttctaaaagctatcattttttcttagtgatttttatgattccctgtgttataataagaaagattaaaaatgtaatttatcaaaaggagaatctcca Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 100 HP_score: -10.8 Tail_Score: -5.26316 Start: 70 End: 94 Full_Region: AAATAGAATGTACGG TCCAGTTGCT CTTTT AGCGACTGGA TTTTTTATGGAATAG .....................................................................TCCAGTTGCTCTTTTAGCGACTGGA.................................................................................................................................................. Find igs database================================================ Query_seq: SSA_0585:SSA_0586|SSA_0585:SSA_0586:hypothetical protein:Conserved uncharacterized protein:->->:577347..577586 240 tatttttgatggatttcggcaaaggtccgttatgacaggcctgctagtttcaggaaatagaatgtacggtccagttgctcttttagcgactggattttttatggaatagaaataggtgtaaagttaaagaaaccaagctggttcttctaaaagctatcattttttcttagtgatttttatgattccctgtgttataataagaaagattaaaaatgtaatttatcaaaaggagaatctcca Intra-Species Hit: Count: 1 Min: 1 Max: 240 Len: 240 Subject: NC_009009_SSA_0585_SSA_0586|hypothetical protein:Conserved uncharacterized protein|POSITIVE:POSITIVE|[577347,577586]|240 HSP 1 e-value: 1.0E-133 bit: 476.0 Len: 240 Query Start:1 Query End:240 Subject Strand: POSITIVE Subject Start: 1 Subject End: 240 tatttttgatggatttcggcaaaggtccgttatgacaggcctgctagtttcaggaaatagaatgtacggtccagttgctcttttagcgactggattttttatggaatagaaataggtgtaaagttaaagaaaccaagctggttcttctaaaagctatcattttttcttagtgatttttatgattccctgtgttataataagaaagattaaaaatgtaatttatcaaaaggagaatctcca tatttttgatggatttcggcaaaggtccgttatgacaggcctgctagtttcaggaaatagaatgtacggtccagttgctcttttagcgactggattttttatggaatagaaataggtgtaaagttaaagaaaccaagctggttcttctaaaagctatcattttttcttagtgatttttatgattccctgtgttataataagaaagattaaaaatgtaatttatcaaaaggagaatctcca Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAUUUUUGAUGGAUUUCGGCAAAGGUCCGUUAUGACAGGCCUGCUAGUUUCAGGAAAUAGAAUGUACGGUCCAGUUGCUCUUUUAGCGACUGGAUUUUUUAUGGAAUAGAAAUAGGUGUAAAGUUAAAGAAACCAAGCUGGUUCUUCUAAAAGCUAUCAUUUUUUCUUAGUGAUUUUUAUGAUUCCCUGUGUUAUAAUAAGAAAGAUUAAAAAUGUAAUUUAUCAAAAGGAGAAUCUCCA ...((((((((((((..((((..((((.((....)).)))))))).....((((..((((((..(((.(((((((((((.....)))))))))))............(((((.(((((...((((..(((((((.....)))..))))...))))..))))))))))..)))..)))))).....))))...........................))))))))))))((((...)))). (-55.00) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGGAGAUUCUCCUUUUGAUAAAUUACAUUUUUAAUCUUUCUUAUUAUAACACAGGGAAUCAUAAAAAUCACUAAGAAAAAAUGAUAGCUUUUAGAAGAACCAGCUUGGUUUCUUUAACUUUACACCUAUUUCUAUUCCAUAAAAAAUCCAGUCGCUAAAAGAGCAACUGGACCGUACAUUCUAUUUCCUGAAACUAGCAGGCCUGUCAUAACGGACCUUUGCCGAAAUCCAUCAAAAAUA .((((...)))).((((((................................((((((((..............(((((............(((((..((((.....))))..)))))...........))))).............((((((.(((.....))).))))))...........))))))))......(((((.((((....)))).))..)))........)))))).... (-42.60) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 359 58 19 177 137 NC_009009:SSA_0940|5end_NOL1/NOP2/sun_family_protein,_putative_947626..947856_POSITIVE 327 90 41 228 186 NC_009009:SSA_0403|5end_CAAX_amino_terminal_protease_family,_putative_400475..400705_POSITIVE 327 49 2 201 146 NC_009009:SSA_0251|5end_D-tyrosyl-tRNA(Tyr)_deacylase,_putative_244455..244685_POSITIVE 307 80 33 222 160 NC_009009:SSA_0618|5end_hypothetical_protein_611973..612203_NEGATIVE 301 54 11 180 141 NC_009009:SSA_1530|5end_ABC-type_antimicrobial_peptide_transport_system,_permease_component,_putative_1538778..1539008_NEGATIVE 301 87 41 228 170 NC_009009:SSA_1501|5end_Cytidylate_kinase,_putative_1505772..1506002_NEGATIVE 299 53 11 182 130 NC_009009:SSA_2103|5end_hypothetical_protein_2106700..2106930_NEGATIVE 299 100 51 87 23 NC_009009:SSA_1172|5end_hypothetical_protein_1199926..1200156_NEGATIVE 296 80 38 56 16 NC_009009:SSA_1792|5end_Preprotein_translocase_subunit_YidC,_putative_1774036..1774266_POSITIVE 296 54 11 208 164 NC_009009:SSA_0464|5end_Cobalamin_biosynthesis_protein_cobD,_putative_468225..468455_POSITIVE 295 52 16 44 6 NC_009009:SSA_1873|5end_S-adenosyl-methyltransferase_mraW,_putative_1870144..1870374_NEGATIVE 295 77 31 76 20 NC_009009:SSA_1632|5end_Surface_protein,_putative_1634045..1634275_NEGATIVE 289 48 2 158 123 NC_009009:SSA_0634|5end_Anthranilate_phosphoribosyltransferase,_putative_623387..623617_POSITIVE 287 94 51 179 131 NC_009009:SSA_0872|5end_Zn-dependent_hydrolases,_including_glyoxylases,_putative_865305..865535_NEGATIVE 286 47 10 31 4 NC_009009:SSA_2352|5end_ABC-type_nitrate/sulfonate/bicarbonate_transporter,_periplasmic_component,_putative_2354508..2354738_NEGATIVE 284 57 17 43 1 NC_009009:SSA_0488|5end_Glutamate-1-semialdehyde_2,1-aminotransferase,_putative_488364..488594_POSITIVE 280 90 41 46 1 NC_009009:SSA_1848|5end_Methionyl-tRNA_formyltransferase,_putative_1843178..1843408_NEGATIVE 277 50 6 56 6 NC_009009:SSA_0491|5end_Alpha-ribazole-5'-phosphate_phosphatase,_putative_490961..491191_POSITIVE 277 44 5 45 7 NC_009009:SSA_0306|5end_Transcription_regulator_(glutamine_synthetase_repressor),_putative_302590..302820_POSITIVE 277 55 14 131 85 NC_009009:SSA_0269|5end_Phosphotransferase_system_(PTS)_cellobiose-specific_component_IIA,_putative_262550..262780_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 327 49 2 132 77 NC_009009:SSA_0250|3end_GTP_pyrophosphokinase,_putative_244466..244616_POSITIVE 308 41 3 150 107 NC_009009:SSA_0243|3end_Cyclo-nucleotide_phosphodiesterase,_putative_235824..235974_NEGATIVE 299 53 11 126 74 NC_009009:SSA_2105|3end_hypothetical_protein_2106756..2106906_NEGATIVE 296 48 10 136 87 NC_009009:SSA_2136|3end_50S_ribosomal_protein_L34,_putative_2137507..2137657_NEGATIVE 292 56 13 137 99 NC_009009:SSA_0390|3end_hypothetical_protein_385714..385864_POSITIVE 289 48 2 147 112 NC_009009:SSA_0633|3end_Anthranilate_synthase_component_II,_putative_623456..623606_POSITIVE 283 55 12 151 103 NC_009009:SSA_1079|3end_hypothetical_protein_1097448..1097598_POSITIVE 277 50 6 59 9 NC_009009:SSA_0490|3end_Cobalamin_5'-phosphate_synthase,_putative_491044..491194_POSITIVE 277 55 14 122 76 NC_009009:SSA_0268|3end_Phosphotransferase_system_(PTS)_cellobiose-specific_component_IIB,_putative_262621..262771_POSITIVE 275 70 21 95 48 NC_009009:SSA_0451|3end_Conserved_uncharacterized_protein_451636..451786_POSITIVE 275 67 28 88 46 NC_009009:SSA_0153|3end_hypothetical_protein_149503..149653_POSITIVE 274 94 52 142 113 NC_009009:SSA_2020|3end_hypothetical_protein_2022471..2022621_POSITIVE 274 80 33 80 25 NC_009009:SSA_1038|3end_Lipoprotein,_putative_1053714..1053864_POSITIVE 268 47 15 151 122 NC_009009:SSA_1448|3end_ATP_phosphoribosyltransferase_regulatory_subunit,_putative_1449828..1449978_NEGATIVE 268 97 67 56 22 NC_009009:SSA_0488|3end_Glutamate-1-semialdehyde_2,1-aminotransferase,_putative_489742..489892_POSITIVE 267 69 22 62 10 NC_009009:SSA_1417|3end_SAM-dependent_methyltransferase,_putative_1427304..1427454_NEGATIVE 266 100 51 91 39 NC_009009:SSA_1189|3end_GTP-binding_protein,_putative_1216806..1216956_NEGATIVE 266 54 11 79 34 NC_009009:SSA_0434|3end_Glutamate_formiminotransferase,_putative_435669..435819_NEGATIVE 264 57 12 48 4 NC_009009:SSA_0826|3end_hypothetical_protein_805516..805666_POSITIVE 263 58 11 87 45 NC_009009:SSA_2334|3end_D-alanine--D-alanyl_carrier_protein_ligase,_putative_2336457..2336607_NEGATIVE