Origin IGS: atatcacctcacacgtataattatagcatataaatacgtgtaagtccataagtatatattttatatattaacaacagacgatgttaaacctatctatgttagaccggtatttctaacagttgccagaatcttt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aaagattctggcaactgttagaaataccggtctaacatagataggtttaacatcgtctgttgttaatatataaaatatatacttatggacttacacgtatttatatgctataattatacgtgtgaggtgatat Mask Tandem Repeat Region ================================================ atatcacctcacacgtataattatagcatataaatacgtgtaagtccataagtatatattttatatattaacaacagacgatgttaaacctatctatgttagaccggtatttctaacagttgccagaatcttt Find is-nt database================================================ Query_seq: TDE2578:TDE2579|TDE2578:TDE2579:hypothetical protein:ATP-dependent DNA helicase RecG:<-<-:2603245..2603377 133 atatcacctcacacgtataattatagcatataaatacgtgtaagtccataagtatatattttatatattaacaacagacgatgttaaacctatctatgttagaccggtatttctaacagttgccagaatcttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE2578:TDE2579|TDE2578:TDE2579:hypothetical protein:ATP-dependent DNA helicase RecG:<-<-:2603245..2603377 133 atatcacctcacacgtataattatagcatataaatacgtgtaagtccataagtatatattttatatattaacaacagacgatgttaaacctatctatgttagaccggtatttctaacagttgccagaatcttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE2578:TDE2579|TDE2578:TDE2579:hypothetical protein:ATP-dependent DNA helicase RecG:<-<-:2603245..2603377 133 atatcacctcacacgtataattatagcatataaatacgtgtaagtccataagtatatattttatatattaacaacagacgatgttaaacctatctatgttagaccggtatttctaacagttgccagaatcttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 atatcacctcacacgtataattatagcatataaatacgtgtaagtccataagtatatattttatatattaacaacagacgatgttaaacctatctatgttagaccggtatttctaacagttgccagaatcttt Predict ORF larger than 30AA ================================================ atatcacctcacacgtataattatagcatataaatacgtgtaagtccataagtatatattttatatattaacaacagacgatgttaaacctatctatgttagaccggtatttctaacagttgccagaatcttt 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: 85 Start: 20 End: 49 ...................ATGGACTTACACGTATTTATATGCTATAAT.................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ atatcacctcacacgtataattatagcatataaatacgtgtaagtccataagtatatattttatatattaacaacagacgatgttaaacctatctatgttagaccggtatttctaacagttgccagaatcttt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE2578:TDE2579|TDE2578:TDE2579:hypothetical protein:ATP-dependent DNA helicase RecG:<-<-:2603245..2603377 133 atatcacctcacacgtataattatagcatataaatacgtgtaagtccataagtatatattttatatattaacaacagacgatgttaaacctatctatgttagaccggtatttctaacagttgccagaatcttt Intra-Species Hit: Count: 1 Min: 1 Max: 133 Len: 133 Subject: NC_002967_TDE2578_TDE2579|hypothetical protein:ATP-dependent DNA helicase RecG|NEGATIVE:NEGATIVE|[2603245,2603377]|133 HSP 1 e-value: 7.0E-70 bit: 264.0 Len: 133 Query Start:1 Query End:133 Subject Strand: POSITIVE Subject Start: 1 Subject End: 133 atatcacctcacacgtataattatagcatataaatacgtgtaagtccataagtatatattttatatattaacaacagacgatgttaaacctatctatgttagaccggtatttctaacagttgccagaatcttt atatcacctcacacgtataattatagcatataaatacgtgtaagtccataagtatatattttatatattaacaacagacgatgttaaacctatctatgttagaccggtatttctaacagttgccagaatcttt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUAUCACCUCACACGUAUAAUUAUAGCAUAUAAAUACGUGUAAGUCCAUAAGUAUAUAUUUUAUAUAUUAACAACAGACGAUGUUAAACCUAUCUAUGUUAGACCGGUAUUUCUAACAGUUGCCAGAAUCUUU (((((..((.((((((((..(((((...))))))))))))).))......((((((((...))))))))..........)))))............(((((((........)))))))............... (-20.90) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAGAUUCUGGCAACUGUUAGAAAUACCGGUCUAACAUAGAUAGGUUUAACAUCGUCUGUUGUUAAUAUAUAAAAUAUAUACUUAUGGACUUACACGUAUUUAUAUGCUAUAAUUAUACGUGUGAGGUGAUAU .....(((((((....)))))))..(((.(((((...))))).)))((((((........)))))).................(((.(.((((((((((((((((...)))))..))))))))))).).))). (-28.80) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 834 120 71 211 162 NC_002967:TDE2578|5end_hypothetical_protein_2603154..2603384_NEGATIVE 250 129 86 160 121 NC_002967:TDE0016|5end_ATPase,_AAA_family_20457..20687_POSITIVE 235 120 75 202 156 NC_002967:TDE2084|5end_RNA_methyltransferase,_TrmH_family_2113394..2113624_POSITIVE 232 65 29 107 68 NC_002967:TDE1831|5end_hypothetical_protein_1865032..1865262_NEGATIVE 232 65 29 107 68 NC_002967:TDE1797|5end_hypothetical_protein_1836272..1836502_NEGATIVE 231 108 72 67 28 NC_002967:TDE0588|5end_histidine_ammonia-lyase_626450..626680_POSITIVE 219 127 95 201 168 NC_002967:TDE1547|5end_ribonuclease_HII_1591124..1591354_POSITIVE 215 127 101 230 204 NC_002967:TDE2631|5end_peptide_ABC_transporter,_permease_protein,_putative_2671829..2672059_POSITIVE 207 46 6 135 96 NC_002967:TDE1959|5end_hypothetical_protein_1974197..1974427_NEGATIVE 206 124 84 176 131 NC_002967:TDE1550|5end_diphosphate--fructose-6-phosphate_1-phosphotransferase_1592747..1592977_POSITIVE 206 47 1 177 131 NC_002967:TDE0241|5end_hypothetical_protein_275303..275533_NEGATIVE 205 112 80 178 145 NC_002967:TDE1970|5end_sensory_box_histidine_kinase_1985744..1985974_NEGATIVE 202 114 72 58 4 NC_002967:TDE0582|5end_hypothetical_protein_620383..620613_POSITIVE 198 69 25 59 11 NC_002967:TDE2444|5end_hypothetical_protein_2474212..2474442_NEGATIVE 198 120 71 184 135 NC_002967:TDE1833|5end_hypothetical_protein_1866714..1866944_NEGATIVE 198 120 71 184 135 NC_002967:TDE1777|5end_hypothetical_protein_1820393..1820623_NEGATIVE 192 47 7 167 126 NC_002967:TDE0697|5end_hypothetical_protein_734372..734602_NEGATIVE 190 46 4 137 98 NC_002967:TDE2625|5end_ABC_transporter,_ATP-binding/permease_protein_2666664..2666894_NEGATIVE 189 119 75 65 17 NC_002967:TDE1951|5end_ribonuclease_Z_1968329..1968559_NEGATIVE 187 126 91 170 136 NC_002967:TDE0848|5end_hypothetical_protein_871269..871499_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 201 128 87 118 83 NC_002967:TDE2588|3end_integrase_domain_protein_2624778..2624928_POSITIVE 198 120 71 115 66 NC_002967:TDE1834|3end_hypothetical_protein_1866783..1866933_NEGATIVE 198 120 71 115 66 NC_002967:TDE1778|3end_hypothetical_protein_1820462..1820612_NEGATIVE 190 46 4 144 105 NC_002967:TDE2626|3end_ABC_transporter,_ATP-binding/permease_protein_2666657..2666807_NEGATIVE 186 114 78 137 93 NC_002967:TDE2313|3end_hypothetical_protein_2349506..2349656_NEGATIVE 186 108 61 108 48 NC_002967:TDE1599|3end_ABC_transporter,_ATP-binding/permease_protein_1648920..1649070_NEGATIVE 186 130 89 132 85 NC_002967:TDE0053|3end_flagellar_biosynthetic_protein_FliR_62467..62617_POSITIVE 184 124 83 126 78 NC_002967:TDE0938|3end_hypothetical_protein_960963..961113_NEGATIVE 184 80 38 83 39 NC_002967:TDE0891|3end_transcriptional_regulator,_putative_908592..908742_POSITIVE 184 114 79 150 120 NC_002967:TDE0015|3end_lipoprotein,_putative_20544..20694_POSITIVE 183 88 41 52 12 NC_002967:TDE2148|3end_OmpA_family_protein_2184597..2184747_NEGATIVE 183 124 93 141 110 NC_002967:TDE1166|3end_hypothetical_protein_1198394..1198544_NEGATIVE 183 126 82 123 89 NC_002967:TDE0490|3end_hypothetical_protein_546272..546422_NEGATIVE 182 43 1 47 12 NC_002967:TDE2727|3end_GTPase_YjeQ,_putative_2784251..2784401_NEGATIVE 182 125 94 121 94 NC_002967:TDE2051|3end_hypothetical_protein_2079990..2080140_NEGATIVE 182 127 96 61 25 NC_002967:TDE1469|3end_conserved_hypothetical_protein_TIGR00150_1517333..1517483_NEGATIVE 179 130 81 106 58 NC_002967:TDE2517|3end_DNA_repair_protein_RadA_2542454..2542604_NEGATIVE 178 46 4 102 52 NC_002967:TDE2563|3end_hypothetical_protein_2590068..2590218_POSITIVE 178 107 80 80 53 NC_002967:TDE0521|3end_carboxylesterase_family_protein_566756..566906_NEGATIVE 177 125 89 149 103 NC_002967:TDE1306|3end_hypothetical_protein_1340452..1340602_NEGATIVE