Origin IGS: attcttccctctttttcttatttttattaaaaatgacctttacattatccattatacttgataaaatagactttgtctaaaaaatatttaaggagtatcactaa .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 ttagtgatactccttaaatattttttagacaaagtctattttatcaagtataatggataatgtaaaggtcatttttaataaaaataagaaaaagagggaagaat Mask Tandem Repeat Region ================================================ attcttccctctttttcttatttttattaaaaatgacctttacattatccattatacttgataaaatagactttgtctaaaaaatatttaaggagtatcactaa Find is-nt database================================================ Query_seq: SSA_0328:SSA_0329|SSA_0328:SSA_0329:Xaa-Pro dipeptidyl-peptidase, putative:Glycerol uptake facilitator/aquaporin protein, putative:<-->:322866..322969 104 attcttccctctttttcttatttttattaaaaatgacctttacattatccattatacttgataaaatagactttgtctaaaaaatatttaaggagtatcactaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_0328:SSA_0329|SSA_0328:SSA_0329:Xaa-Pro dipeptidyl-peptidase, putative:Glycerol uptake facilitator/aquaporin protein, putative:<-->:322866..322969 104 attcttccctctttttcttatttttattaaaaatgacctttacattatccattatacttgataaaatagactttgtctaaaaaatatttaaggagtatcactaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_0328:SSA_0329|SSA_0328:SSA_0329:Xaa-Pro dipeptidyl-peptidase, putative:Glycerol uptake facilitator/aquaporin protein, putative:<-->:322866..322969 104 attcttccctctttttcttatttttattaaaaatgacctttacattatccattatacttgataaaatagactttgtctaaaaaatatttaaggagtatcactaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 attcttccctctttttcttatttttattaaaaatgacctttacattatccattatacttgataaaatagactttgtctaaaaaatatttaaggagtatcactaa Predict ORF larger than 30AA ================================================ attcttccctctttttcttatttttattaaaaatgacctttacattatccattatacttgataaaatagactttgtctaaaaaatatttaaggagtatcactaa 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: 87 Start: 38 End: 67 .....................................CTTTACATTATCCATTATACTTGATAAAAT..................................... PromScan Matrix: RpoD-17 Strand: - Score: 86 Start: 51 End: 80 ..................................................TTAGACAAAGTCTATTTTATCAAGTATAAT........................ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ attcttccctctttttcttatttttattaaaaatgacctttacattatccattatacttgataaaatagactttgtctaaaaaatatttaaggagtatcactaa Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_0328:SSA_0329|SSA_0328:SSA_0329:Xaa-Pro dipeptidyl-peptidase, putative:Glycerol uptake facilitator/aquaporin protein, putative:<-->:322866..322969 104 attcttccctctttttcttatttttattaaaaatgacctttacattatccattatacttgataaaatagactttgtctaaaaaatatttaaggagtatcactaa Intra-Species Hit: Count: 1 Min: 1 Max: 104 Len: 104 Subject: NC_009009_SSA_0328_SSA_0329|Xaa-Pro dipeptidyl-peptidase, putative:Glycerol uptake facilitator/aquaporin protein, putative|NEGATIVE:POSITIVE|[322866,322969]|104 HSP 1 e-value: 1.0E-52 bit: 206.0 Len: 104 Query Start:1 Query End:104 Subject Strand: POSITIVE Subject Start: 1 Subject End: 104 attcttccctctttttcttatttttattaaaaatgacctttacattatccattatacttgataaaatagactttgtctaaaaaatatttaaggagtatcactaa attcttccctctttttcttatttttattaaaaatgacctttacattatccattatacttgataaaatagactttgtctaaaaaatatttaaggagtatcactaa Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUUCUUCCCUCUUUUUCUUAUUUUUAUUAAAAAUGACCUUUACAUUAUCCAUUAUACUUGAUAAAAUAGACUUUGUCUAAAAAAUAUUUAAGGAGUAUCACUAA ........((((((....(((((((......((((.......)))).............((((((......))))))..)))))))...))))))......... (-10.90) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUAGUGAUACUCCUUAAAUAUUUUUUAGACAAAGUCUAUUUUAUCAAGUAUAAUGGAUAAUGUAAAGGUCAUUUUUAAUAAAAAUAAGAAAAAGAGGGAAGAAU ..........(((((.....((((((..(((..(((((((.(((...))).)))))))..))).......(((((.....)))))..)))))).)))))..... (-11.40) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 699 80 31 171 122 NC_009009:SSA_0328|5end_Xaa-Pro_dipeptidyl-peptidase,_putative_322775..323005_NEGATIVE 242 50 2 141 92 NC_009009:SSA_0135|5end_Multiple_antibiotic_resistance_operon_transcriptional_repressor_(MarR),_putative_130574..130804_POSITIVE 214 72 37 188 154 NC_009009:SSA_0227|5end_Collagen-binding_surface_protein,_putative_221037..221267_POSITIVE 212 50 1 84 26 NC_009009:SSA_1797|5end_Aminodeoxychorismate_lyase,_putative_1779947..1780177_NEGATIVE 209 42 2 131 93 NC_009009:SSA_1993|5end_Conserved_uncharacterized_protein_1990790..1991020_NEGATIVE 209 85 42 172 127 NC_009009:SSA_0830|5end_Glycosyltransferase,_putative_812430..812660_POSITIVE 206 49 2 121 66 NC_009009:SSA_0689|5end_Penicillin-binding_protein_2B,_putative_672262..672492_POSITIVE 205 47 3 143 98 NC_009009:SSA_2113|5end_hypothetical_protein_2116692..2116922_NEGATIVE 204 30 2 122 96 NC_009009:SSA_0076|5end_ABC_sugar_transporter,_permease_protein,_putative_79847..80077_POSITIVE 201 36 1 126 90 NC_009009:SSA_1007|5end_ABC_transporter_ATP-binding_protein-multiple_sugar_transport,_putative_1008543..1008773_POSITIVE 192 47 12 131 96 NC_009009:SSA_2075|5end_Transketolase,_putative_2079089..2079319_NEGATIVE 192 60 11 140 92 NC_009009:SSA_0263|5end_Zinc_metalloproteinase_in_scaA_5'region,_putative_256274..256504_POSITIVE 189 29 4 118 94 NC_009009:SSA_0258|5end_hypothetical_protein_251845..252075_POSITIVE 187 35 2 138 95 NC_009009:SSA_1586|5end_hypothetical_protein_1588182..1588412_NEGATIVE 183 21 5 113 97 NC_009009:SSA_1724|5end_CBS_domain_protein,_putative_1710553..1710783_NEGATIVE 183 32 1 129 92 NC_009009:SSA_0749|5end_Competence_protein,_putative_730668..730898_POSITIVE 181 77 34 224 182 NC_009009:SSA_0410|5end_hypothetical_protein_406442..406672_NEGATIVE 180 29 2 93 66 NC_009009:SSA_1901|5end_Conserved_uncharacterized_protein_1896599..1896829_NEGATIVE 179 49 1 80 23 NC_009009:SSA_0866|5end_Cation-transporting_ATPase,_E1-E_2_family,_putative_856983..857213_POSITIVE 178 18 4 108 94 NC_009009:SSA_0001|5end_Chromosomal_replication_initiator_protein_dnaA,_putative_74..304_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 216 63 30 105 63 NC_009009:SSA_1617|3end_hypothetical_protein_1620436..1620586_NEGATIVE 209 42 2 60 22 NC_009009:SSA_1994|3end_CTP_synthase,_putative_1990861..1991011_NEGATIVE 205 47 3 121 76 NC_009009:SSA_2114|3end_Transcriptional_repressor_of_purine_operon,_putative_2116714..2116864_NEGATIVE 204 30 2 122 96 NC_009009:SSA_0075|3end_ABC_sugar_transporter,_permease_protein,_putative_79927..80077_POSITIVE 201 36 1 104 68 NC_009009:SSA_1006|3end_Dextransucrase,_putative_1008601..1008751_POSITIVE 198 79 37 49 5 NC_009009:SSA_1432|3end_HflX_GTPase,_putative_1438663..1438813_NEGATIVE 196 95 55 56 22 NC_009009:SSA_2096|3end_ATP-dependent_protease,_ATP-binding_subunit,_putative_2099557..2099707_NEGATIVE 189 29 4 33 9 NC_009009:SSA_0257|3end_N-acetylmuramidase/lysin,_putative_251840..251990_POSITIVE 187 35 2 82 39 NC_009009:SSA_1587|3end_hypothetical_protein_1588238..1588388_NEGATIVE 177 39 4 43 2 NC_009009:SSA_2128|3end_hypothetical_protein_2130851..2131001_NEGATIVE 177 39 4 142 101 NC_009009:SSA_2127|3end_hypothetical_protein_2130752..2130902_NEGATIVE 172 40 3 76 32 NC_009009:SSA_0375|3end_D-methionine-binding_lipoprotein_(ABC-type_transporter),_putative_365209..365359_POSITIVE 168 38 2 107 68 NC_009009:SSA_2394|3end_Competence_stimulating_peptide_2385261..2385411_NEGATIVE 167 50 8 127 81 NC_009009:SSA_1707|3end_Conserved_uncharacterized_protein_1698248..1698398_POSITIVE 165 44 3 130 94 NC_009009:SSA_0994|3end_Peptidase_E,_putative_995390..995540_POSITIVE 164 41 2 89 49 NC_009009:SSA_0205|3end_NisK_(sensor-receptor_histidine_kinase_domain),_putative_203839..203989_POSITIVE 164 59 19 58 23 NC_009009:SSA_0176|3end_DNA-directed_RNA_polymerase_I,_beta_chain_(140_kDa_subunit),_putative_178444..178594_POSITIVE 163 76 34 119 87 NC_009009:SSA_0687|3end_hypothetical_protein_671290..671440_POSITIVE 159 36 3 45 5 NC_009009:SSA_0552|3end_Cof_family_protein,_putative_548901..549051_POSITIVE 156 37 1 144 108 NC_009009:SSA_1256|3end_NAD-dependent_deacetylase,_putative_1282357..1282507_NEGATIVE