Origin IGS: agaaagctcacttttttcttgtccagcaaatacttctaattccaaggcttttctccttttttgtctttccttactattttacgctaatttccaaaaatagtcaaagggttaccatttatattttaagttaaaatttt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aaaattttaacttaaaatataaatggtaaccctttgactatttttggaaattagcgtaaaatagtaaggaaagacaaaaaaggagaaaagccttggaattagaagtatttgctggacaagaaaaaagtgagctttct Mask Tandem Repeat Region ================================================ agaaagctcacttttttcttgtccagcaaatacttctaattccaaggcttttctccttttttgtctttccttactattttacgctaatttccaaaaatagtcaaagggttaccatttatattttaagttaaaatttt Find is-nt database================================================ Query_seq: SSA_1996:SSA_1997|SSA_1996:SSA_1997:DNA-directed RNA polymerase delta subunit, putative:Membrane spanning protein, putative:<-<-:1994115..1994251 137 agaaagctcacttttttcttgtccagcaaatacttctaattccaaggcttttctccttttttgtctttccttactattttacgctaatttccaaaaatagtcaaagggttaccatttatattttaagttaaaatttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_1996:SSA_1997|SSA_1996:SSA_1997:DNA-directed RNA polymerase delta subunit, putative:Membrane spanning protein, putative:<-<-:1994115..1994251 137 agaaagctcacttttttcttgtccagcaaatacttctaattccaaggcttttctccttttttgtctttccttactattttacgctaatttccaaaaatagtcaaagggttaccatttatattttaagttaaaatttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_1996:SSA_1997|SSA_1996:SSA_1997:DNA-directed RNA polymerase delta subunit, putative:Membrane spanning protein, putative:<-<-:1994115..1994251 137 agaaagctcacttttttcttgtccagcaaatacttctaattccaaggcttttctccttttttgtctttccttactattttacgctaatttccaaaaatagtcaaagggttaccatttatattttaagttaaaatttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 agaaagctcacttttttcttgtccagcaaatacttctaattccaaggcttttctccttttttgtctttccttactattttacgctaatttccaaaaatagtcaaagggttaccatttatattttaagttaaaatttt Predict ORF larger than 30AA ================================================ Protein_Len: 33 Strand: + Start: 30 End: 128 ............................. M L L I P R L F S F F V F P Y Y F T L I S K N S Q R V T I Y I L S ......... agaaagctcacttttttcttgtccagcaaatacttctaattccaaggcttttctccttttttgtctttccttactattttacgctaatttccaaaaatagtcaaagggttaccatttatattttaagttaaaatttt 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: 90 Start: 76 End: 105 ...........................................................................TTTGACTATTTTTGGAAATTAGCGTAAAAT................................ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ agaaagctcacttttttcttgtccagcaaatacttctaattccaaggcttttctccttttttgtctttccttactattttacgctaatttccaaaaatagtcaaagggttaccatttatattttaagttaaaatttt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_1996:SSA_1997|SSA_1996:SSA_1997:DNA-directed RNA polymerase delta subunit, putative:Membrane spanning protein, putative:<-<-:1994115..1994251 137 agaaagctcacttttttcttgtccagcaaatacttctaattccaaggcttttctccttttttgtctttccttactattttacgctaatttccaaaaatagtcaaagggttaccatttatattttaagttaaaatttt Intra-Species Hit: Count: 1 Min: 1 Max: 137 Len: 137 Subject: NC_009009_SSA_1996_SSA_1997|DNA-directed RNA polymerase delta subunit, putative:Membrane spanning protein, putative|NEGATIVE:NEGATIVE|[1994115,1994251]|137 HSP 1 e-value: 3.0E-72 bit: 272.0 Len: 137 Query Start:1 Query End:137 Subject Strand: POSITIVE Subject Start: 1 Subject End: 137 agaaagctcacttttttcttgtccagcaaatacttctaattccaaggcttttctccttttttgtctttccttactattttacgctaatttccaaaaatagtcaaagggttaccatttatattttaagttaaaatttt agaaagctcacttttttcttgtccagcaaatacttctaattccaaggcttttctccttttttgtctttccttactattttacgctaatttccaaaaatagtcaaagggttaccatttatattttaagttaaaatttt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGAAAGCUCACUUUUUUCUUGUCCAGCAAAUACUUCUAAUUCCAAGGCUUUUCUCCUUUUUUGUCUUUCCUUACUAUUUUACGCUAAUUUCCAAAAAUAGUCAAAGGGUUACCAUUUAUAUUUUAAGUUAAAAUUUU ...........((((..((((......................(((((..............)))))(((((((((((((.............))))))))..)))))...............))))..)))).... (-11.46) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAAUUUUAACUUAAAAUAUAAAUGGUAACCCUUUGACUAUUUUUGGAAAUUAGCGUAAAAUAGUAAGGAAAGACAAAAAAGGAGAAAAGCCUUGGAAUUAGAAGUAUUUGCUGGACAAGAAAAAAGUGAGCUUUCU ..........((..((((((...((((...((((..((((((((((........)).))))))))))))..........((((.......))))...))))...))))))...))........((((....)))).. (-14.50) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 833 70 21 161 112 NC_009009:SSA_1996|5end_DNA-directed_RNA_polymerase_delta_subunit,_putative_1994024..1994254_NEGATIVE 320 60 11 105 53 NC_009009:SSA_2393|5end_Transcriptional_regulator,_XRE_family,_putative_204056..204286_POSITIVE 307 60 11 194 139 NC_009009:SSA_0676|5end_Farnesyl_diphosphate_synthase,_putative_658598..658828_POSITIVE 301 53 17 177 142 NC_009009:SSA_1733|5end_hypothetical_protein_1717494..1717724_POSITIVE 292 38 4 57 23 NC_009009:SSA_2126|5end_hypothetical_protein_2130755..2130985_NEGATIVE 291 70 25 65 18 NC_009009:SSA_1722|5end_Thymidylate_kinase,_putative_1708663..1708893_NEGATIVE 287 60 11 131 81 NC_009009:SSA_1103|5end_hypothetical_protein_1123833..1124063_POSITIVE 285 79 35 130 77 NC_009009:SSA_0487|5end_Delta-aminolevulinic_acid_dehydratase,_putative_487349..487579_POSITIVE 283 100 54 144 96 NC_009009:SSA_1523|5end_Glutathione_peroxidase,_putative_1532067..1532297_POSITIVE 281 50 6 210 172 NC_009009:SSA_1720|5end_Initiation-control_protein,_putative_1707113..1707343_NEGATIVE 278 49 8 141 96 NC_009009:SSA_1139|5end_Pyruvate_dehydrogenase_E1_component_beta_subunit,_putative_1166823..1167053_POSITIVE 276 56 17 215 173 NC_009009:SSA_2122|5end_hypothetical_protein_2127607..2127837_NEGATIVE 274 56 17 135 91 NC_009009:SSA_0752|5end_hypothetical_protein_734171..734401_POSITIVE 269 60 11 67 22 NC_009009:SSA_2309|5end_Fimbrial_assembly_protein,_putative_2311886..2312116_NEGATIVE 267 58 18 103 73 NC_009009:SSA_2175|5end_hypothetical_protein_2174042..2174272_NEGATIVE 267 57 18 209 171 NC_009009:SSA_1487|5end_Conserved_uncharacterized_protein_1494190..1494420_NEGATIVE 266 73 33 141 100 NC_009009:SSA_2218|5end_Glycosyltransferase_(cell_wall_biogenesis)_Cps9G,_putative_2219941..2220171_NEGATIVE 266 64 32 42 7 NC_009009:SSA_1366|5end_Alkaline_D-stereospecific_endopeptidase_precursor,_putative_1383663..1383893_NEGATIVE 265 65 21 110 56 NC_009009:SSA_1029|5end_hypothetical_protein_1047009..1047239_NEGATIVE 258 101 61 115 79 NC_009009:SSA_1113|5end_Two-component_response_transcriptional_regulator_(CheY-like_receiver_domain_and_a_winged-helix_DNA-binding_domains),_putative_1139742..1139972_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 318 47 3 84 29 NC_009009:SSA_0963|3end_Peptidoglycan_N-acetylglucosamine_deacetylase_A,_putative_972890..973040_POSITIVE 295 56 12 44 5 NC_009009:SSA_0820|3end_Ribosomal_protein_S21,_putative_801505..801655_POSITIVE 292 38 4 60 26 NC_009009:SSA_2127|3end_hypothetical_protein_2130752..2130902_NEGATIVE 285 79 35 143 90 NC_009009:SSA_0486|3end_Uroporphyrinogen-III_synthase,_putative_487442..487592_POSITIVE 278 49 8 122 77 NC_009009:SSA_1138|3end_Pyruvate_dehydrogenase,_TPP-dependent_E1_component_alpha-subunit,_putative_1166884..1167034_POSITIVE 274 56 17 133 89 NC_009009:SSA_0751|3end_Oligoendopeptidase_F,_putative_734249..734399_POSITIVE 268 38 5 72 43 NC_009009:SSA_1047|3end_UDP-N-acetylenolpyruvoylglucosamine_reductase,_putative_1062845..1062995_POSITIVE 266 73 33 115 74 NC_009009:SSA_2219|3end_UDP-glucose_4-epimerase,_putative_2219967..2220117_NEGATIVE 259 38 1 137 97 NC_009009:SSA_0968|3end_hypothetical_protein_977141..977291_POSITIVE 253 58 12 108 49 NC_009009:SSA_1782|3end_hypothetical_protein_1767602..1767752_NEGATIVE 252 75 33 139 90 NC_009009:SSA_1260|3end_Phosphopentomutase,_putative_1285752..1285902_NEGATIVE 251 43 18 151 127 NC_009009:SSA_0022|3end_Surface_protein_cell_wall_anchor,_sortase_B_family,_putative_28428..28578_POSITIVE 248 55 11 150 102 NC_009009:SSA_0791|3end_UDP-N-acetylglucosamine-like_protein,_putative_774705..774855_POSITIVE 246 86 42 117 71 NC_009009:SSA_1772|3end_hypothetical_protein_1758895..1759045_NEGATIVE 246 78 47 68 32 NC_009009:SSA_1587|3end_hypothetical_protein_1588238..1588388_NEGATIVE 246 70 22 96 56 NC_009009:SSA_2392|3end_50S_ribosomal_protein_L36,_putative_120394..120544_POSITIVE 242 60 11 148 83 NC_009009:SSA_1739|3end_UDP-N-acetylmuramoylalanyl-D-glutamate--2,_6-diaminopimelate_ligase,_putative_1727065..1727215_POSITIVE 241 37 2 118 79 NC_009009:SSA_2142|3end_Argininosuccinate_synthase,_putative_2142216..2142366_NEGATIVE 241 57 16 51 6 NC_009009:SSA_0554|3end_hypothetical_protein_549692..549842_POSITIVE 240 47 3 139 98 NC_009009:SSA_1239|3end_hypothetical_protein_1263151..1263301_NEGATIVE