Origin IGS: aagaaaaggcaaattgctatgacccgcaccccaaaagttagacagaaaatctaacttttggggtgtttttaatctgaaattaagttatacaaataaactaggtgtataacctaaaaagaatggtgcttctcgggttcagattgacctcaaatataatatagctgtctcaaatctttagtgttatttgcttgacttaaagcaataaataattgagaagattctagtagatggccaactccatataataagctcccagactgagtttgggagc .........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.........1.........2.........3.........4.........5.........6.........7.........8.........9 gctcccaaactcagtctgggagcttattatatggagttggccatctactagaatcttctcaattatttattgctttaagtcaagcaaataacactaaagatttgagacagctatattatatttgaggtcaatctgaacccgagaagcaccattctttttaggttatacacctagtttatttgtataacttaatttcagattaaaaacaccccaaaagttagattttctgtctaacttttggggtgcgggtcatagcaatttgccttttctt Mask Tandem Repeat Region ================================================ aagaaaaggcaaattgctatgacccgcaccccaaaagttagacagaaaatctaacttttggggtgtttttaatctgaaattaagttatacaaataaactaggtgtataacctaaaaagaatggtgcttctcgggttcagattgacctcaaatataatatagctgtctcaaatctttagtgttatttgcttgacttaaagcaataaataattgagaagattctagtagatggccaactccatataataagctcccagactgagtttgggagc Find is-nt database================================================ Query_seq: SSA_0617:SSA_0618|SSA_0617:SSA_0618:Membrane protease subunits, stomatin/prohibitin-like protein (SPFH domain/band 7 family), putative:hypothetical protein:-><-:611499..611769 271 aagaaaaggcaaattgctatgacccgcaccccaaaagttagacagaaaatctaacttttggggtgtttttaatctgaaattaagttatacaaataaactaggtgtataacctaaaaagaatggtgcttctcgggttcagattgacctcaaatataatatagctgtctcaaatctttagtgttatttgcttgacttaaagcaataaataattgagaagattctagtagatggccaactccatataataagctcccagactgagtttgggagc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_0617:SSA_0618|SSA_0617:SSA_0618:Membrane protease subunits, stomatin/prohibitin-like protein (SPFH domain/band 7 family), putative:hypothetical protein:-><-:611499..611769 271 aagaaaaggcaaattgctatgacccgcaccccaaaagttagacagaaaatctaacttttggggtgtttttaatctgaaattaagttatacaaataaactaggtgtataacctaaaaagaatggtgcttctcgggttcagattgacctcaaatataatatagctgtctcaaatctttagtgttatttgcttgacttaaagcaataaataattgagaagattctagtagatggccaactccatataataagctcccagactgagtttgggagc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_0617:SSA_0618|SSA_0617:SSA_0618:Membrane protease subunits, stomatin/prohibitin-like protein (SPFH domain/band 7 family), putative:hypothetical protein:-><-:611499..611769 271 aagaaaaggcaaattgctatgacccgcaccccaaaagttagacagaaaatctaacttttggggtgtttttaatctgaaattaagttatacaaataaactaggtgtataacctaaaaagaatggtgcttctcgggttcagattgacctcaaatataatatagctgtctcaaatctttagtgttatttgcttgacttaaagcaataaataattgagaagattctagtagatggccaactccatataataagctcccagactgagtttgggagc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aagaaaaggcaaattgctatgacccgcaccccaaaagttagacagaaaatctaacttttggggtgtttttaatctgaaattaagttatacaaataaactaggtgtataacctaaaaagaatggtgcttctcgggttcagattgacctcaaatataatatagctgtctcaaatctttagtgttatttgcttgacttaaagcaataaataattgagaagattctagtagatggccaactccatataataagctcccagactgagtttgggagc Predict ORF larger than 30AA ================================================ aagaaaaggcaaattgctatgacccgcaccccaaaagttagacagaaaatctaacttttggggtgtttttaatctgaaattaagttatacaaataaactaggtgtataacctaaaaagaatggtgcttctcgggttcagattgacctcaaatataatatagctgtctcaaatctttagtgttatttgcttgacttaaagcaataaataattgagaagattctagtagatggccaactccatataataagctcccagactgagtttgggagc 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================================================ aagaaaaggcaaattgctatgacccgcaccccaaaagttagacagaaaatctaacttttggggtgtttttaatctgaaattaagttatacaaataaactaggtgtataacctaaaaagaatggtgcttctcgggttcagattgacctcaaatataatatagctgtctcaaatctttagtgttatttgcttgacttaaagcaataaataattgagaagattctagtagatggccaactccatataataagctcccagactgagtttgggagc Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 100 HP_score: -19.2 Tail_Score: -4.80882 Start: 27 End: 65 Full_Region: AATTGCTATGACCCG CACCCCAAAAGTTAGA CAGAAAA TCTAACTTTTGGGGTG TTTTTAATCTGAAAT ..........................CACCCCAAAAGTTAGACAGAAAATCTAACTTTTGGGGTG.............................................................................................................................................................................................................. TransTerm Strand: - Conf: 58 HP_score: -3.9 Tail_Score: -4.13945 Start: 37 End: 55 Full_Region: aaaaacaccccaaaa gttagat tttct gtctaac ttttggggtgcgggt ....................................gttagattttctgtctaac........................................................................................................................................................................................................................ Find igs database================================================ Query_seq: SSA_0617:SSA_0618|SSA_0617:SSA_0618:Membrane protease subunits, stomatin/prohibitin-like protein (SPFH domain/band 7 family), putative:hypothetical protein:-><-:611499..611769 271 aagaaaaggcaaattgctatgacccgcaccccaaaagttagacagaaaatctaacttttggggtgtttttaatctgaaattaagttatacaaataaactaggtgtataacctaaaaagaatggtgcttctcgggttcagattgacctcaaatataatatagctgtctcaaatctttagtgttatttgcttgacttaaagcaataaataattgagaagattctagtagatggccaactccatataataagctcccagactgagtttgggagc Intra-Species Hit: Count: 1 Min: 1 Max: 271 Len: 271 Subject: NC_009009_SSA_0617_SSA_0618|Membrane protease subunits, stomatin/prohibitin-like protein (SPFH domain/band 7 family), putative:hypothetical protein|POSITIVE:NEGATIVE|[611499,611769]|271 HSP 1 e-value: 1.0E-152 bit: 537.0 Len: 271 Query Start:1 Query End:271 Subject Strand: POSITIVE Subject Start: 1 Subject End: 271 aagaaaaggcaaattgctatgacccgcaccccaaaagttagacagaaaatctaacttttggggtgtttttaatctgaaattaagttatacaaataaactaggtgtataacctaaaaagaatggtgcttctcgggttcagattgacctcaaatataatatagctgtctcaaatctttagtgttatttgcttgacttaaagcaataaataattgagaagattctagtagatggccaactccatataataagctcccagactgagtttgggagc aagaaaaggcaaattgctatgacccgcaccccaaaagttagacagaaaatctaacttttggggtgtttttaatctgaaattaagttatacaaataaactaggtgtataacctaaaaagaatggtgcttctcgggttcagattgacctcaaatataatatagctgtctcaaatctttagtgttatttgcttgacttaaagcaataaataattgagaagattctagtagatggccaactccatataataagctcccagactgagtttgggagc Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAGAAAAGGCAAAUUGCUAUGACCCGCACCCCAAAAGUUAGACAGAAAAUCUAACUUUUGGGGUGUUUUUAAUCUGAAAUUAAGUUAUACAAAUAAACUAGGUGUAUAACCUAAAAAGAAUGGUGCUUCUCGGGUUCAGAUUGACCUCAAAUAUAAUAUAGCUGUCUCAAAUCUUUAGUGUUAUUUGCUUGACUUAAAGCAAUAAAUAAUUGAGAAGAUUCUAGUAGAUGGCCAACUCCAUAUAAUAAGCUCCCAGACUGAGUUUGGGAGC .......(((.....((((((....(((((((((((((((((.......)))))))))))))))))..((((((((((.(..((...(((........(((((.....))))).........)))...))..).))))))))))............)))))).(((((.(((((((...(((((((((((......)))))...))))))...)))))))...).)))).)))...............((((((((((...)))))))))) (-84.83) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GCUCCCAAACUCAGUCUGGGAGCUUAUUAUAUGGAGUUGGCCAUCUACUAGAAUCUUCUCAAUUAUUUAUUGCUUUAAGUCAAGCAAAUAACACUAAAGAUUUGAGACAGCUAUAUUAUAUUUGAGGUCAAUCUGAACCCGAGAAGCACCAUUCUUUUUAGGUUAUACACCUAGUUUAUUUGUAUAACUUAAUUUCAGAUUAAAAACACCCCAAAAGUUAGAUUUUCUGUCUAACUUUUGGGGUGCGGGUCAUAGCAAUUUGCCUUUUCUU (((((((.((...)).))))))).........((((..(((..(((....(((((((.....(((((...(((((......)))))))))).....))))))).)))..(((((...............((((((((...(((((......))))).((((((((((((...........)))))))))))).)))))))).....(((((((((((((((((.....)))))))))))))))))......))))).....)))..)))). (-83.70) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 384 65 22 139 94 NC_009009:SSA_1361|5end_ORFA,_transposon_ISSsa2_1377168..1377398_POSITIVE 384 65 22 139 94 NC_009009:SSA_0573|5end_hypothetical_protein_568732..568962_NEGATIVE 384 65 22 139 94 NC_009009:SSA_0265|5end_ORFA,_transposon_ISSsa1_259391..259621_POSITIVE 375 75 31 206 158 NC_009009:SSA_1218|5end_DNA_repair_protein_radC,_putative_1240459..1240689_NEGATIVE 328 48 2 133 92 NC_009009:SSA_0299|5end_hypothetical_protein_292759..292989_POSITIVE 318 270 221 174 132 NC_009009:SSA_1388|5end_hypothetical_protein_1404373..1404603_NEGATIVE 306 169 122 59 13 NC_009009:SSA_0579|5end_Hydrolase,_HAD_superfamily,_putative_572220..572450_POSITIVE 283 60 19 51 1 NC_009009:SSA_0357|5end_Thioredoxin,_putative_350763..350993_POSITIVE 280 46 1 78 18 NC_009009:SSA_2331|5end_D-alanine_transfer_protein,_putative_2334964..2335194_NEGATIVE 270 270 230 73 17 NC_009009:SSA_0591|5end_Conserved_uncharacterized_protein_582769..582999_POSITIVE 267 256 216 174 131 NC_009009:SSA_0231|5end_Conserved_uncharacterized_protein_225713..225943_POSITIVE 262 148 104 176 138 NC_009009:SSA_1476|5end_Phosphoglycerol_transferase,_alkaline_phosphatase_superfamily,_putative_1480173..1480403_POSITIVE 259 269 221 211 165 NC_009009:SSA_0212|5end_Phenylalanyl-tRNA_synthetase,_beta_subunit,_putative_208373..208603_POSITIVE 256 154 116 185 144 NC_009009:SSA_1969|5end_Acetolactate_synthase_small_subunit,_putative_1965222..1965452_NEGATIVE 256 64 21 163 122 NC_009009:SSA_1854|5end_Conserved_uncharacterized_protein_1850884..1851114_NEGATIVE 254 270 239 123 89 NC_009009:SSA_0607|5end_ABC_transporter,_permease_component,_putative_596926..597156_NEGATIVE 253 265 225 200 160 NC_009009:SSA_2315|5end_Conserved_uncharacterized_protein_2316945..2317175_NEGATIVE 252 179 132 52 5 NC_009009:SSA_0262|5end_ABC-type_Mn/Zn_transporter,_ATP-ase_component,_putative_256204..256434_NEGATIVE 251 162 122 188 142 NC_009009:SSA_1383|5end_Aspartate_aminotransferase,_putative_1401718..1401948_NEGATIVE 251 45 9 147 105 NC_009009:SSA_1363|5end_FmtA-like_protein,_putative_1380417..1380647_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 447 65 30 39 2 NC_009009:SSA_0323|3end_Flavoprotein,_putative_315624..315774_NEGATIVE 394 65 22 64 21 NC_009009:SSA_0617|3end_Membrane_protease_subunits,_stomatin/prohibitin-like_protein_(SPFH_domain/band_7_family),_putative_611438..611588_POSITIVE 384 65 22 61 16 NC_009009:SSA_1360|3end_Arginine/histidine_ABC_transporter,_ATPase_component,_putative_1377170..1377320_POSITIVE 384 65 22 70 25 NC_009009:SSA_0574|3end_YdjX_protein,_putative_568801..568951_NEGATIVE 377 65 25 44 4 NC_009009:SSA_0264|3end_PEP_phosphonomutase-like_protein,_putative_259376..259526_POSITIVE 375 75 31 83 35 NC_009009:SSA_1219|3end_Sortase,_putative_1240582..1240732_NEGATIVE 362 66 34 35 1 NC_009009:SSA_1274|3end_hypothetical_protein_1295517..1295667_NEGATIVE 306 169 122 62 16 NC_009009:SSA_0578|3end_Nicotinate-nucleotide_adenylyltransferase,_putative_572303..572453_POSITIVE 280 46 1 85 25 NC_009009:SSA_2332|3end_D-alanyl_carrier_protein,_putative_2334957..2335107_NEGATIVE 279 46 1 87 39 NC_009009:SSA_1362|3end_ORFB,_transposon_ISSsa2_1378599..1378749_POSITIVE 269 150 121 114 87 NC_009009:SSA_2210|3end_Ribosomal_large_subunit_pseudouridine_synthase_D,_putative_2211454..2211604_POSITIVE 264 259 212 134 83 NC_009009:SSA_2242|3end_hypothetical_protein_2238121..2238271_NEGATIVE 261 64 26 62 22 NC_009009:SSA_0322|3end_Transcriptional_activator,_TipA_family,_putative_315534..315684_POSITIVE 256 64 21 150 109 NC_009009:SSA_1855|3end_hypothetical_protein_1850897..1851047_NEGATIVE 255 269 221 125 72 NC_009009:SSA_0149|3end_hypothetical_protein_143833..143983_POSITIVE 254 270 239 148 114 NC_009009:SSA_0608|3end_Macrolide-efflux_protein,_putative_596901..597051_NEGATIVE 253 269 221 149 106 NC_009009:SSA_2062|3end_hypothetical_protein_2063291..2063441_NEGATIVE 251 45 9 82 40 NC_009009:SSA_1364|3end_hypothetical_protein_1380482..1380632_NEGATIVE 250 47 16 55 19 NC_009009:SSA_1039|3end_Sugar_ABC_transporter,_ATP-binding_protein,_putative_1055389..1055539_POSITIVE 249 270 221 46 1 NC_009009:SSA_2357|3end_50S_ribosomal_protein_L9,_putative_2357985..2358135_NEGATIVE