Origin IGS: tttctaaatgatattaaactttttcaatgcaaaaccagtcttgattttgttttttcataaactccattaaaacccaaaatagactcgggcgtctattctgagtttgcttgtattatacttcaaatatctctatgttttagtttactataaatgcaccgtgaatactagtctaataacttggtttttagcatttttttaagaaaaatttagtcatgctcttcaaattttaaaccatagacttatttggtatttttcaaagtgtt .........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 aacactttgaaaaataccaaataagtctatggtttaaaatttgaagagcatgactaaatttttcttaaaaaaatgctaaaaaccaagttattagactagtattcacggtgcatttatagtaaactaaaacatagagatatttgaagtataatacaagcaaactcagaatagacgcccgagtctattttgggttttaatggagtttatgaaaaaacaaaatcaagactggttttgcattgaaaaagtttaatatcatttagaaa Mask Tandem Repeat Region ================================================ tttctaaatgatattaaactttttcaatgcaaaaccagtcttgattttgttttttcataaactccattaaaacccaaaatagactcgggcgtctattctgagtttgcttgtattatacttcaaatatctctatgttttagtttactataaatgcaccgtgaatactagtctaataacttggtttttagcatttttttaagaaaaatttagtcatgctcttcaaattttaaaccatagacttatttggtatttttcaaagtgtt Find is-nt database================================================ Query_seq: SSA_2305:SSA_2307|SSA_2305:SSA_2307:hypothetical protein:hypothetical protein:<-<-:2308150..2308412 263 tttctaaatgatattaaactttttcaatgcaaaaccagtcttgattttgttttttcataaactccattaaaacccaaaatagactcgggcgtctattctgagtttgcttgtattatacttcaaatatctctatgttttagtttactataaatgcaccgtgaatactagtctaataacttggtttttagcatttttttaagaaaaatttagtcatgctcttcaaattttaaaccatagacttatttggtatttttcaaagtgtt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_2305:SSA_2307|SSA_2305:SSA_2307:hypothetical protein:hypothetical protein:<-<-:2308150..2308412 263 tttctaaatgatattaaactttttcaatgcaaaaccagtcttgattttgttttttcataaactccattaaaacccaaaatagactcgggcgtctattctgagtttgcttgtattatacttcaaatatctctatgttttagtttactataaatgcaccgtgaatactagtctaataacttggtttttagcatttttttaagaaaaatttagtcatgctcttcaaattttaaaccatagacttatttggtatttttcaaagtgtt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_2305:SSA_2307|SSA_2305:SSA_2307:hypothetical protein:hypothetical protein:<-<-:2308150..2308412 263 tttctaaatgatattaaactttttcaatgcaaaaccagtcttgattttgttttttcataaactccattaaaacccaaaatagactcgggcgtctattctgagtttgcttgtattatacttcaaatatctctatgttttagtttactataaatgcaccgtgaatactagtctaataacttggtttttagcatttttttaagaaaaatttagtcatgctcttcaaattttaaaccatagacttatttggtatttttcaaagtgtt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tttctaaatgatattaaactttttcaatgcaaaaccagtcttgattttgttttttcataaactccattaaaacccaaaatagactcgggcgtctattctgagtttgcttgtattatacttcaaatatctctatgttttagtttactataaatgcaccgtgaatactagtctaataacttggtttttagcatttttttaagaaaaatttagtcatgctcttcaaattttaaaccatagacttatttggtatttttcaaagtgtt Predict ORF larger than 30AA ================================================ Protein_Len: 34 Strand: + Start: 95 End: 196 .............................................................................................. M L S L L V L Y F K Y L Y V L V Y Y K C T V N T S L I T W F L A F F ................................................................... tttctaaatgatattaaactttttcaatgcaaaaccagtcttgattttgttttttcataaactccattaaaacccaaaatagactcgggcgtctattctgagtttgcttgtattatacttcaaatatctctatgttttagtttactataaatgcaccgtgaatactagtctaataacttggtttttagcatttttttaagaaaaatttagtcatgctcttcaaattttaaaccatagacttatttggtatttttcaaagtgtt 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================================================ tttctaaatgatattaaactttttcaatgcaaaaccagtcttgattttgttttttcataaactccattaaaacccaaaatagactcgggcgtctattctgagtttgcttgtattatacttcaaatatctctatgttttagtttactataaatgcaccgtgaatactagtctaataacttggtttttagcatttttttaagaaaaatttagtcatgctcttcaaattttaaaccatagacttatttggtatttttcaaagtgtt Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 57 HP_score: -3.6 Tail_Score: -4.09827 Start: 73 End: 102 Full_Region: TAAACTCCATTAAAA CCCAAAATAGAC TCGGGC GTCTATTCTGAG TTTGCTTGTATTATA ........................................................................CCCAAAATAGACTCGGGCGTCTATTCTGAG................................................................................................................................................................. TransTerm Strand: - Conf: 81 HP_score: -8.0 Tail_Score: -4.29432 Start: 73 End: 102 Full_Region: tataatacaagcaaa ctcagaatagac gcccga gtctattttggg ttttaatggagttta ........................................................................ctcagaatagacgcccgagtctattttggg................................................................................................................................................................. TransTerm Strand: - Conf: 59 HP_score: -3.3 Tail_Score: -4.44277 Start: 80 End: 95 Full_Region: caagcaaactcagaa tagac gcccga gtcta ttttgggttttaatg ...............................................................................tagacgcccgagtcta........................................................................................................................................................................ Find igs database================================================ Query_seq: SSA_2305:SSA_2307|SSA_2305:SSA_2307:hypothetical protein:hypothetical protein:<-<-:2308150..2308412 263 tttctaaatgatattaaactttttcaatgcaaaaccagtcttgattttgttttttcataaactccattaaaacccaaaatagactcgggcgtctattctgagtttgcttgtattatacttcaaatatctctatgttttagtttactataaatgcaccgtgaatactagtctaataacttggtttttagcatttttttaagaaaaatttagtcatgctcttcaaattttaaaccatagacttatttggtatttttcaaagtgtt Intra-Species Hit: Count: 1 Min: 1 Max: 263 Len: 263 Subject: NC_009009_SSA_2305_SSA_2307|hypothetical protein:hypothetical protein|NEGATIVE:NEGATIVE|[2308150,2308412]|263 HSP 1 e-value: 1.0E-134 bit: 480.0 Len: 263 Query Start:1 Query End:263 Subject Strand: POSITIVE Subject Start: 1 Subject End: 263 tttctaaatgatattaaactttttcaatgcaaaaccagtcttgattttgttttttcataaactccattaaaacccaaaatagactcgggcgtctattctgagtttgcttgtattatacttcaaatatctctatgttttagtttactataaatgcaccgtgaatactagtctaataacttggtttttagcannnnnnnaagaaaaatttagtcatgctcttcaaattttaaaccatagacttatttggtatttttcaaagtgtt tttctaaatgatattaaactttttcaatgcaaaaccagtcttgattttgttttttcataaactccattaaaacccaaaatagactcgggcgtctattctgagtttgcttgtattatacttcaaatatctctatgttttagtttactataaatgcaccgtgaatactagtctaataacttggtttttagcatttttttaagaaaaatttagtcatgctcttcaaattttaaaccatagacttatttggtatttttcaaagtgtt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUCUAAAUGAUAUUAAACUUUUUCAAUGCAAAACCAGUCUUGAUUUUGUUUUUUCAUAAACUCCAUUAAAACCCAAAAUAGACUCGGGCGUCUAUUCUGAGUUUGCUUGUAUUAUACUUCAAAUAUCUCUAUGUUUUAGUUUACUAUAAAUGCACCGUGAAUACUAGUCUAAUAACUUGGUUUUUAGCAUUUUUUUAAGAAAAAUUUAGUCAUGCUCUUCAAAUUUUAAACCAUAGACUUAUUUGGUAUUUUUCAAAGUGUU .......((((....((((....((((.((.......)).))))....))))..))))...........((((.((.(((((((......))))))).)).))))..(((((.((.(((..((((((....)))))).))).)).)))))..((((..((((((((((((((......((((((..(((((....(((((.....)))))..)))))...........)))))))))))).....)))))...)))..)))). (-39.92) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AACACUUUGAAAAAUACCAAAUAAGUCUAUGGUUUAAAAUUUGAAGAGCAUGACUAAAUUUUUCUUAAAAAAAUGCUAAAAACCAAGUUAUUAGACUAGUAUUCACGGUGCAUUUAUAGUAAACUAAAACAUAGAGAUAUUUGAAGUAUAAUACAAGCAAACUCAGAAUAGACGCCCGAGUCUAUUUUGGGUUUUAAUGGAGUUUAUGAAAAAACAAAAUCAAGACUGGUUUUGCAUUGAAAAAGUUUAAUAUCAUUUAGAAA ....((.(((...((((((((((..((((((((((((((((((...(((((.....................)))))......)))))).))))))..((((.....))))..................))))))..))))))..)))).....((((..(((((((((((((......)))))))))))))(((((((.......(....)..((((((((....)))))))))))))))...))))....)))...))... (-50.10) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 894 110 61 201 152 NC_009009:SSA_2305|5end_hypothetical_protein_2308059..2308289_NEGATIVE 298 100 57 182 138 NC_009009:SSA_0128|5end_Adenylate_kinase,_putative_119201..119431_POSITIVE 274 95 51 132 84 NC_009009:SSA_0981|5end_3-isopropylmalate_dehydratase_small_subunit,_putative_985396..985626_POSITIVE 271 129 81 95 53 NC_009009:SSA_1488|5end_Multiple_antibiotic_resistance_operon_transcription_repressor_(MarR),_putative_1494657..1494887_NEGATIVE 267 101 70 60 30 NC_009009:SSA_0697|5end_hypothetical_protein_680083..680313_POSITIVE 267 108 62 209 164 NC_009009:SSA_0239|5end_7,8-dihydro-8-oxoguanine-triphosphatase,_putative_232961..233191_POSITIVE 259 108 63 207 158 NC_009009:SSA_0250|5end_GTP_pyrophosphokinase,_putative_242167..242397_POSITIVE 254 78 32 189 137 NC_009009:SSA_0182|5end_Endoglucanase,_putative_186299..186529_POSITIVE 251 65 25 159 119 NC_009009:SSA_1490|5end_Ribonuclease_BN,_putative_1496732..1496962_NEGATIVE 248 127 81 77 32 NC_009009:SSA_2053|5end_hypothetical_protein_2057747..2057977_NEGATIVE 246 57 11 107 65 NC_009009:SSA_1575|5end_Glycosyl_transferase,_putative_1579110..1579340_NEGATIVE 242 110 62 146 98 NC_009009:SSA_0748|5end_Sugar:H+_symporter,_permease_of_the_major_facilitator_superfamily,_putative_729386..729616_POSITIVE 242 130 84 113 62 NC_009009:SSA_0240|5end_Acetyltransferase,_GNAT_family,_putative_233410..233640_POSITIVE 241 115 74 100 62 NC_009009:SSA_1600|5end_hypothetical_protein_1606595..1606825_NEGATIVE 238 120 79 177 141 NC_009009:SSA_1318|5end_GTP-binding_protein_lepA,_putative_1335821..1336051_NEGATIVE 236 109 81 167 137 NC_009009:SSA_1571|5end_Threonyl-tRNA_synthetase,_putative_1575154..1575384_NEGATIVE 236 107 65 190 149 NC_009009:SSA_0310|5end_hypothetical_protein_305306..305536_POSITIVE 235 129 85 110 60 NC_009009:SSA_1639|5end_5'-methylthioadenosine/S-adenosylhomocysteine_nucleosidase,_putative_1642031..1642261_NEGATIVE 233 128 84 140 93 NC_009009:SSA_0095|5end_Threonine_synthase,_putative_96555..96785_POSITIVE 232 88 41 127 65 NC_009009:SSA_2065|5end_hypothetical_protein_2065743..2065973_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 274 95 51 122 74 NC_009009:SSA_0980|3end_3-isopropylmalate_dehydratase_large_subunit,_putative_985466..985616_POSITIVE 272 110 83 126 101 NC_009009:SSA_1044|3end_Homoserine_kinase,_putative_1060799..1060949_POSITIVE 259 89 41 62 3 NC_009009:SSA_0773|3end_PTS_enzyme_I,_putative_754416..754566_POSITIVE 259 108 63 75 26 NC_009009:SSA_0249|3end_hypothetical_protein_242115..242265_POSITIVE 254 78 32 102 50 NC_009009:SSA_0181|3end_Glycosyltransferase_(vectorial_glycosyl_polymerization_(VGP)_family),_putative_186292..186442_POSITIVE 251 120 73 68 19 NC_009009:SSA_2176|3end_hypothetical_protein_2174269..2174419_NEGATIVE 251 65 25 111 71 NC_009009:SSA_1491|3end_Methionine_aminopeptidase_A,_putative_1496780..1496930_NEGATIVE 245 120 85 114 78 NC_009009:SSA_1944|3end_Oligopeptide_transport_ATP-binding_protein,_putative_1935685..1935835_NEGATIVE 243 114 71 120 65 NC_009009:SSA_1269|3end_hypothetical_protein_1291970..1292120_NEGATIVE 242 110 62 51 3 NC_009009:SSA_0747|3end_DD-carboxypeptidase,_putative_729371..729521_POSITIVE 242 130 84 116 65 NC_009009:SSA_0239|3end_7,8-dihydro-8-oxoguanine-triphosphatase,_putative_233493..233643_POSITIVE 241 115 74 103 65 NC_009009:SSA_1601|3end_VacB-like_protein,_putative_1606592..1606742_NEGATIVE 238 57 17 40 5 NC_009009:SSA_1576|3end_Catabolite_control_protein_A,_putative_1579177..1579327_NEGATIVE 232 88 41 121 59 NC_009009:SSA_2066|3end_DNA_polymerase_III_polC-type,_putative_2065749..2065899_NEGATIVE 232 247 210 40 8 NC_009009:SSA_0042|3end_Amino_acid_recemase,_putative_48671..48821_POSITIVE 230 197 151 50 7 NC_009009:SSA_0892|3end_ATP-binding_cassette_lipoprotein,_putative_884578..884728_POSITIVE 227 130 84 55 11 NC_009009:SSA_1822|3end_hypothetical_protein_1810871..1811021_NEGATIVE 226 76 33 63 18 NC_009009:SSA_1949|3end_AliA_protein,_putative_1942403..1942553_NEGATIVE 225 112 73 149 101 NC_009009:SSA_1155|3end_Serine_hydroxymethyltransferase,_putative_1184640..1184790_POSITIVE 225 108 74 43 11 NC_009009:SSA_0086|3end_V-type_sodium_ATPase,_subunit_K,_putative_88398..88548_POSITIVE