Origin IGS: tgatccaaatagaagcaatctttaaaagatgcctaagccttgtaaggcaaggaagaagccaatcaaaacccctgggataacagtatctcaggggttttctatgctt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aagcatagaaaacccctgagatactgttatcccaggggttttgattggcttcttccttgccttacaaggcttaggcatcttttaaagattgcttctatttggatca Mask Tandem Repeat Region ================================================ tgatccaaatagaagcaatctttaaaagatgcctaagccttgtaaggcaaggaagaagccaatcaaaacccctgggataacagtatctcaggggttttctatgctt Find is-nt database================================================ Query_seq: SSA_0384:SSA_0385|SSA_0384:SSA_0385:hypothetical protein:ABC transporter, glycine-betaine/proline permease protein, putative:-><-:378510..378615 106 tgatccaaatagaagcaatctttaaaagatgcctaagccttgtaaggcaaggaagaagccaatcaaaacccctgggataacagtatctcaggggttttctatgctt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_0384:SSA_0385|SSA_0384:SSA_0385:hypothetical protein:ABC transporter, glycine-betaine/proline permease protein, putative:-><-:378510..378615 106 tgatccaaatagaagcaatctttaaaagatgcctaagccttgtaaggcaaggaagaagccaatcaaaacccctgggataacagtatctcaggggttttctatgctt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_0384:SSA_0385|SSA_0384:SSA_0385:hypothetical protein:ABC transporter, glycine-betaine/proline permease protein, putative:-><-:378510..378615 106 tgatccaaatagaagcaatctttaaaagatgcctaagccttgtaaggcaaggaagaagccaatcaaaacccctgggataacagtatctcaggggttttctatgctt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tgatccaaatagaagcaatctttaaaagatgcctaagccttgtaaggcaaggaagaagccaatcaaaacccctgggataacagtatctcaggggttttctatgctt Predict ORF larger than 30AA ================================================ Protein_Len: 30 Strand: - Start: 2 End: 91 . I W I S A I K L L H R L R T L C P L L W D F G R P Y C Y R M ............... tgatccaaatagaagcaatctttaaaagatgcctaagccttgtaaggcaaggaagaagccaatcaaaacccctgggataacagtatctcaggggttttctatgctt 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================================================ tgatccaaatagaagcaatctttaaaagatgcctaagccttgtaaggcaaggaagaagccaatcaaaacccctgggataacagtatctcaggggttttctatgctt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_0384:SSA_0385|SSA_0384:SSA_0385:hypothetical protein:ABC transporter, glycine-betaine/proline permease protein, putative:-><-:378510..378615 106 tgatccaaatagaagcaatctttaaaagatgcctaagccttgtaaggcaaggaagaagccaatcaaaacccctgggataacagtatctcaggggttttctatgctt Intra-Species Hit: Count: 1 Min: 1 Max: 106 Len: 106 Subject: NC_009009_SSA_0384_SSA_0385|hypothetical protein:ABC transporter, glycine-betaine/proline permease protein, putative|POSITIVE:NEGATIVE|[378510,378615]|106 HSP 1 e-value: 6.0E-54 bit: 210.0 Len: 106 Query Start:1 Query End:106 Subject Strand: POSITIVE Subject Start: 1 Subject End: 106 tgatccaaatagaagcaatctttaaaagatgcctaagccttgtaaggcaaggaagaagccaatcaaaacccctgggataacagtatctcaggggttttctatgctt tgatccaaatagaagcaatctttaaaagatgcctaagccttgtaaggcaaggaagaagccaatcaaaacccctgggataacagtatctcaggggttttctatgctt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGAUCCAAAUAGAAGCAAUCUUUAAAAGAUGCCUAAGCCUUGUAAGGCAAGGAAGAAGCCAAUCAAAACCCCUGGGAUAACAGUAUCUCAGGGGUUUUCUAUGCUU ...(((........(((.(((.....))))))....((((....))))..)))..((((.....(((((((((((((((....)))))))))))))))....)))) (-36.80) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAGCAUAGAAAACCCCUGAGAUACUGUUAUCCCAGGGGUUUUGAUUGGCUUCUUCCUUGCCUUACAAGGCUUAGGCAUCUUUUAAAGAUUGCUUCUAUUUGGAUCA ((((....((((((((((.((((....)))).)))))))))).....))))..(((..((((....))))..((((((((.....))).)))))......)))... (-33.40) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 314 80 31 70 17 NC_009009:SSA_1792|5end_Preprotein_translocase_subunit_YidC,_putative_1774036..1774266_POSITIVE 307 60 11 61 11 NC_009009:SSA_0375|5end_D-methionine-binding_lipoprotein_(ABC-type_transporter),_putative_364257..364487_POSITIVE 297 79 31 71 22 NC_009009:SSA_1466|5end_Prephenate_dehydrogenase,_putative_1473111..1473341_NEGATIVE 296 76 33 52 7 NC_009009:SSA_0085|5end_V-type_sodium_ATPase,_subunit_I,_putative_85750..85980_POSITIVE 292 59 11 70 17 NC_009009:SSA_1057|5end_Aminotransferase,_class-V,_putative_1073771..1074001_POSITIVE 284 63 29 67 30 NC_009009:SSA_0642|5end_Type_4_prepilin_peptidase,_putative_630053..630283_NEGATIVE 280 79 35 47 6 NC_009009:SSA_1357|5end_hypothetical_protein_1373024..1373254_NEGATIVE 274 77 32 68 22 NC_009009:SSA_1149|5end_Glycosyl_hydrolase,_family_1,_putative_1178399..1178629_POSITIVE 273 58 11 201 152 NC_009009:SSA_0659|5end_hypothetical_protein_643003..643233_POSITIVE 268 87 42 52 9 NC_009009:SSA_0153|5end_hypothetical_protein_148677..148907_POSITIVE 266 100 55 88 41 NC_009009:SSA_1891|5end_Oxidoreductase,_aldo/keto_reductase_family,_putative_1888991..1889221_NEGATIVE 266 76 31 60 12 NC_009009:SSA_0878|5end_DNA_gyrase,_putative_871596..871826_POSITIVE 264 47 6 55 16 NC_009009:SSA_2118|5end_Thiamine_pyrophosphokinase,_putative_2120500..2120730_NEGATIVE 263 79 36 65 23 NC_009009:SSA_1593|5end_Dipeptidase,_putative_1598054..1598284_NEGATIVE 260 76 31 174 131 NC_009009:SSA_1323|5end_hypothetical_protein_1340450..1340680_NEGATIVE 258 60 11 191 142 NC_009009:SSA_0516|5end_AmiR_two-component_response_regulator_with_transcriptional_antiterminator_output_domain,_putative_514485..514715_POSITIVE 257 64 26 61 12 NC_009009:SSA_2050|5end_Arabinose_efflux_permease,_putative_2053255..2053485_POSITIVE 257 75 31 139 96 NC_009009:SSA_0838|5end_GtfB,_putative_825406..825636_POSITIVE 254 80 37 212 166 NC_009009:SSA_0490|5end_Cobalamin_5'-phosphate_synthase,_putative_490236..490466_POSITIVE 253 60 16 52 1 NC_009009:SSA_0590|5end_hypothetical_protein_582144..582374_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 362 98 66 128 97 NC_009009:SSA_2209|3end_Penicillin-binding_protein_2A,_putative_2208144..2208294_NEGATIVE 308 96 56 85 45 NC_009009:SSA_1889|3end_Conserved_uncharacterized_protein_1886283..1886433_NEGATIVE 297 79 31 55 6 NC_009009:SSA_1467|3end_Chorismate_synthase,_putative_1473127..1473277_NEGATIVE 296 76 33 62 17 NC_009009:SSA_0083|3end_hypothetical_protein_85840..85990_POSITIVE 284 63 29 48 11 NC_009009:SSA_0643|3end_hypothetical_protein_630072..630222_NEGATIVE 282 100 53 100 45 NC_009009:SSA_0506|3end_Iron-sulfur_cluster-binding_protein,_putative_504430..504580_NEGATIVE 274 77 32 62 16 NC_009009:SSA_1148|3end_Beta-glucosides_PTS,_EIIC,_putative_1178473..1178623_POSITIVE 269 100 66 90 57 NC_009009:SSA_0505|3end_Conserved_protein/domain_typically_associated_with_flavoprotein_oxygenases,_DIM6/NTAB_family,_putative_504427..504577_POSITIVE 264 47 6 116 77 NC_009009:SSA_2119|3end_Pentose-5-phosphate-3-epimerase,_putative_2120439..2120589_NEGATIVE 260 100 51 91 39 NC_009009:SSA_1680|3end_ABC-type_bacitracin_resistance_protein_A,_permease_component,_putative_1673200..1673350_NEGATIVE 250 61 26 47 4 NC_009009:SSA_1003|3end_ABC_transporter_substrate-binding_protein-multiple_sugars,_putative_1005214..1005364_POSITIVE 250 76 33 47 3 NC_009009:SSA_0877|3end_Phosphoglycolate_phosphatase,_putative_871663..871813_POSITIVE 249 77 35 43 11 NC_009009:SSA_1131|3end_High-affinity_Fe_2+/Pb2+_permease,_putative_1158768..1158918_POSITIVE 249 55 18 90 50 NC_009009:SSA_0672|3end_hypothetical_protein_656044..656194_POSITIVE 246 95 57 98 55 NC_009009:SSA_1365|3end_FmtA-like_protein,_putative_1381352..1381502_NEGATIVE 242 90 41 40 1 NC_009009:SSA_1982|3end_Transcriptional_regulator,_LytR/AlgR_family,_putative_1975427..1975577_NEGATIVE 242 72 31 82 30 NC_009009:SSA_1309|3end_RNA-binding_protein_(KH_domain),_putative_1327079..1327229_NEGATIVE 241 98 73 26 1 NC_009009:SSA_0384|3end_hypothetical_protein_378449..378599_POSITIVE 240 53 14 124 83 NC_009009:SSA_2091|3end_Phosphotransferase_system_sugar-specific_EII_component,_putative_2095062..2095212_NEGATIVE 237 60 14 150 115 NC_009009:SSA_1007|3end_ABC_transporter_ATP-binding_protein-multiple_sugar_transport,_putative_1009759..1009909_POSITIVE