Origin IGS: tattgtttgttttgtgtcagatgcttttctatgaacagaatgcttccggtacagccgcgattgctatgtgagagattgatagtttataggcaatccatacaccgaaagaattcggatcccataaaatagagcgtccgaaatgttagaagatcttctctc .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 gagagaagatcttctaacatttcggacgctctattttatgggatccgaattctttcggtgtatggattgcctataaactatcaatctctcacatagcaatcgcggctgtaccggaagcattctgttcatagaaaagcatctgacacaaaacaaacaata Mask Tandem Repeat Region ================================================ tattgtttgttttgtgtcagatgcttttctatgaacagaatgcttccggtacagccgcgattgctatgtgagagattgatagtttataggcaatccatacaccgaaagaattcggatcccataaaatagagcgtccgaaatgttagaagatcttctctc Find is-nt database================================================ Query_seq: PG1912:PG1913|PG1912:PG1913:30S ribosomal protein S4:30S ribosomal protein S11:<-<-:2012471..2012629 159 tattgtttgttttgtgtcagatgcttttctatgaacagaatgcttccggtacagccgcgattgctatgtgagagattgatagtttataggcaatccatacaccgaaagaattcggatcccataaaatagagcgtccgaaatgttagaagatcttctctc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG1912:PG1913|PG1912:PG1913:30S ribosomal protein S4:30S ribosomal protein S11:<-<-:2012471..2012629 159 tattgtttgttttgtgtcagatgcttttctatgaacagaatgcttccggtacagccgcgattgctatgtgagagattgatagtttataggcaatccatacaccgaaagaattcggatcccataaaatagagcgtccgaaatgttagaagatcttctctc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG1912:PG1913|PG1912:PG1913:30S ribosomal protein S4:30S ribosomal protein S11:<-<-:2012471..2012629 159 tattgtttgttttgtgtcagatgcttttctatgaacagaatgcttccggtacagccgcgattgctatgtgagagattgatagtttataggcaatccatacaccgaaagaattcggatcccataaaatagagcgtccgaaatgttagaagatcttctctc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tattgtttgttttgtgtcagatgcttttctatgaacagaatgcttccggtacagccgcgattgctatgtgagagattgatagtttataggcaatccatacaccgaaagaattcggatcccataaaatagagcgtccgaaatgttagaagatcttctctc Predict ORF larger than 30AA ================================================ Protein_Len: 40 Strand: + Start: 7 End: 126 ...... M F C V R C F S M N R M L P V Q P R L L C E R L I V Y R Q S I H R K N S D P I K ................................. Protein_Len: 32 Strand: - Start: 32 End: 127 ............................... S C F A E P V A A I A I H S I S L K Y A I W V G F S N P D W L M ................................ tattgtttgttttgtgtcagatgcttttctatgaacagaatgcttccggtacagccgcgattgctatgtgagagattgatagtttataggcaatccatacaccgaaagaattcggatcccataaaatagagcgtccgaaatgttagaagatcttctctc 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================================================ tattgtttgttttgtgtcagatgcttttctatgaacagaatgcttccggtacagccgcgattgctatgtgagagattgatagtttataggcaatccatacaccgaaagaattcggatcccataaaatagagcgtccgaaatgttagaagatcttctctc Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PG1912:PG1913|PG1912:PG1913:30S ribosomal protein S4:30S ribosomal protein S11:<-<-:2012471..2012629 159 tattgtttgttttgtgtcagatgcttttctatgaacagaatgcttccggtacagccgcgattgctatgtgagagattgatagtttataggcaatccatacaccgaaagaattcggatcccataaaatagagcgtccgaaatgttagaagatcttctctc Intra-Species Hit: Count: 1 Min: 1 Max: 159 Len: 159 Subject: NC_002950_PG1912_PG1913|30S ribosomal protein S4:30S ribosomal protein S11|NEGATIVE:NEGATIVE|[2012471,2012629]|159 HSP 1 e-value: 2.0E-85 bit: 315.0 Len: 159 Query Start:1 Query End:159 Subject Strand: POSITIVE Subject Start: 1 Subject End: 159 tattgtttgttttgtgtcagatgcttttctatgaacagaatgcttccggtacagccgcgattgctatgtgagagattgatagtttataggcaatccatacaccgaaagaattcggatcccataaaatagagcgtccgaaatgttagaagatcttctctc tattgtttgttttgtgtcagatgcttttctatgaacagaatgcttccggtacagccgcgattgctatgtgagagattgatagtttataggcaatccatacaccgaaagaattcggatcccataaaatagagcgtccgaaatgttagaagatcttctctc Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAUUGUUUGUUUUGUGUCAGAUGCUUUUCUAUGAACAGAAUGCUUCCGGUACAGCCGCGAUUGCUAUGUGAGAGAUUGAUAGUUUAUAGGCAAUCCAUACACCGAAAGAAUUCGGAUCCCAUAAAAUAGAGCGUCCGAAAUGUUAGAAGAUCUUCUCUC ........(((((((...(((......)))....)))))))((.(((((.....))).))..)).....((((((..(((..((((...(((..........(....)..(((((((.((........).).))))))).)))))))..))).)))))) (-32.60) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAGAGAAGAUCUUCUAACAUUUCGGACGCUCUAUUUUAUGGGAUCCGAAUUCUUUCGGUGUAUGGAUUGCCUAUAAACUAUCAAUCUCUCACAUAGCAAUCGCGGCUGUACCGGAAGCAUUCUGUUCAUAGAAAAGCAUCUGACACAAAACAAACAAUA ...((((....))))......(((((.(((...(((((((((....((((.(((((((((..((((((((.(((..................))))))))).))....))))))))).))))..))))))))).))).)))))................ (-36.47) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 962 80 31 171 122 NC_002950:PG1912|5end_30S_ribosomal_protein_S4_2012380..2012610_NEGATIVE 336 48 9 222 181 NC_002950:PG1388|5end_hypothetical_protein_1470889..1471119_NEGATIVE 331 49 1 151 106 NC_002950:PG1199|5end_hypothetical_protein_1276893..1277123_POSITIVE 324 69 22 79 26 NC_002950:PG1119|5end_flavodoxin,_putative_1194843..1195073_POSITIVE 321 50 1 163 113 NC_002950:PG1706|5end_hypothetical_protein_1794211..1794441_NEGATIVE 316 60 15 93 46 NC_002950:PG1884|5end_alpha-L-fucosidase_precursor,_putative_1980992..1981222_NEGATIVE 313 68 22 165 123 NC_002950:PG1132|5end_valyl-tRNA_synthetase_1210912..1211142_POSITIVE 310 59 11 68 2 NC_002950:PG1862|5end_hypothetical_protein_1960363..1960593_NEGATIVE 309 84 42 68 16 NC_002950:PG0909|5end_hypothetical_protein_973039..973269_NEGATIVE 309 58 15 121 74 NC_002950:PG0703|5end_cobalamin_(5'-phosphate)_synthase,_putative_758144..758374_POSITIVE 308 70 21 215 145 NC_002950:PG1655|5end_hypothetical_protein_1737095..1737325_POSITIVE 307 60 11 63 14 NC_002950:PG1917|5end_methionine_aminopeptidase,_type_I_2014490..2014720_NEGATIVE 306 63 23 224 184 NC_002950:PG0987|5end_hypothetical_protein_1048002..1048232_POSITIVE 302 78 31 66 18 NC_002950:PG0671|5end_iron_compound_ABC_transporter,_permease_protein_721888..722118_POSITIVE 299 90 41 155 103 NC_002950:PG1735|5end_MutT/nudix_family_protein_1823082..1823312_NEGATIVE 298 69 23 69 19 NC_002950:PG2185|5end_transporter,_putative_2293249..2293479_NEGATIVE 298 68 21 74 21 NC_002950:PG0223|5end_exonuclease_257610..257840_NEGATIVE 297 57 15 67 30 NC_002950:PG1037|5end_hypothetical_protein_1101365..1101595_POSITIVE 297 84 46 226 185 NC_002950:PG0709|5end_peptidyl-prolyl_cis-trans_isomerase_FkpA,_FKBP-type_765417..765647_NEGATIVE 296 65 22 214 171 NC_002950:PG1640|5end_DNA-damage-inducible_protein_F_1721245..1721475_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 331 49 1 147 102 NC_002950:PG1198|3end_hypothetical_protein_1276969..1277119_POSITIVE 323 80 35 52 12 NC_002950:PG0354|3end_hypothetical_protein_389131..389281_NEGATIVE 321 50 1 142 92 NC_002950:PG1707|3end_hypothetical_protein_1794232..1794382_NEGATIVE 319 69 22 149 98 NC_002950:PG1030|3end_hypothetical_protein_1092820..1092970_POSITIVE 310 59 11 67 1 NC_002950:PG1863|3end_hypothetical_protein_1960364..1960514_NEGATIVE 309 58 15 114 67 NC_002950:PG0702|3end_nicotinate-nucleotide--dimethylbenzimidazole_phosphoribosyltransferase,_putative_758217..758367_POSITIVE 308 66 29 122 91 NC_002950:PG1943|3end_hypothetical_protein_2028974..2029124_NEGATIVE 307 60 11 63 14 NC_002950:PG1918|3end_preprotein_translocase_SecY_2014490..2014640_NEGATIVE 304 74 35 149 101 NC_002950:PG1414|3end_hypothetical_protein_1499704..1499854_POSITIVE 302 95 52 129 78 NC_002950:PG1118|3end_clpB_protein_1192083..1192233_NEGATIVE 302 78 31 69 21 NC_002950:PG0670|3end_lipoprotein,_putative_721971..722121_POSITIVE 298 68 21 70 17 NC_002950:PG0224|3end_hypothetical_protein_257614..257764_NEGATIVE 297 57 15 41 4 NC_002950:PG1036|3end_excinuclease_ABC,_A_subunit_1101419..1101569_POSITIVE 296 84 46 71 31 NC_002950:PG1639|3end_hypothetical_protein_1719776..1719926_NEGATIVE 295 64 29 104 63 NC_002950:PG0619|3end_alkyl_hydroperoxide_reductase,_F_subunit_672731..672881_POSITIVE 292 69 23 149 105 NC_002950:PG2102|3end_immunoreactive_61_kDa_antigen_PG91_2211424..2211574_NEGATIVE 289 78 36 75 31 NC_002950:PG1953|3end_YitT_family_protein_2044589..2044739_POSITIVE 287 75 32 62 11 NC_002950:PG1599|3end_hypothetical_protein_1679955..1680105_POSITIVE 287 89 44 96 49 NC_002950:PG0443|3end_hemagglutinin-related_protein_483147..483297_POSITIVE 286 100 51 107 42 NC_002950:PG0660|3end_nitroreductase_family_protein_709141..709291_NEGATIVE