Origin IGS: tgtatacaaaaatatacagcaattattaaatatttgcttttccgatttaaaatctttataaaattgtaataactccattatttacgactaaaaagctgcttatcttagcacactttttgcttattaacttatgaggtaataaatt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aatttattacctcataagttaataagcaaaaagtgtgctaagataagcagctttttagtcgtaaataatggagttattacaattttataaagattttaaatcggaaaagcaaatatttaataattgctgtatatttttgtataca Mask Tandem Repeat Region ================================================ tgtatacaaaaatatacagcaattattaaatatttgcttttccgatttaaaatctttataaaattgtaataactccattatttacgactaaaaagctgcttatcttagcacactttttgcttattaacttatgaggtaataaatt Find is-nt database================================================ Query_seq: TDE0069:TDE0070|TDE0069:TDE0070:conserved hypothetical protein TIGR00238:RNA polymerase sigma-70 factor, region 2 family:->->:77708..77852 145 tgtatacaaaaatatacagcaattattaaatatttgcttttccgatttaaaatctttataaaattgtaataactccattatttacgactaaaaagctgcttatcttagcacactttttgcttattaacttatgaggtaataaatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE0069:TDE0070|TDE0069:TDE0070:conserved hypothetical protein TIGR00238:RNA polymerase sigma-70 factor, region 2 family:->->:77708..77852 145 tgtatacaaaaatatacagcaattattaaatatttgcttttccgatttaaaatctttataaaattgtaataactccattatttacgactaaaaagctgcttatcttagcacactttttgcttattaacttatgaggtaataaatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE0069:TDE0070|TDE0069:TDE0070:conserved hypothetical protein TIGR00238:RNA polymerase sigma-70 factor, region 2 family:->->:77708..77852 145 tgtatacaaaaatatacagcaattattaaatatttgcttttccgatttaaaatctttataaaattgtaataactccattatttacgactaaaaagctgcttatcttagcacactttttgcttattaacttatgaggtaataaatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tgtatacaaaaatatacagcaattattaaatatttgcttttccgatttaaaatctttataaaattgtaataactccattatttacgactaaaaagctgcttatcttagcacactttttgcttattaacttatgaggtaataaatt Predict ORF larger than 30AA ================================================ tgtatacaaaaatatacagcaattattaaatatttgcttttccgatttaaaatctttataaaattgtaataactccattatttacgactaaaaagctgcttatcttagcacactttttgcttattaacttatgaggtaataaatt 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================================================ PromScan Matrix: RpoN Strand: + Score: 82 Start: 105 End: 121 ........................................................................................................TTAGCACACTTTTTGCT........................ tgtatacaaaaatatacagcaattattaaatatttgcttttccgatttaaaatctttataaaattgtaataactccattatttacgactaaaaagctgcttatcttagcacactttttgcttattaacttatgaggtaataaatt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE0069:TDE0070|TDE0069:TDE0070:conserved hypothetical protein TIGR00238:RNA polymerase sigma-70 factor, region 2 family:->->:77708..77852 145 tgtatacaaaaatatacagcaattattaaatatttgcttttccgatttaaaatctttataaaattgtaataactccattatttacgactaaaaagctgcttatcttagcacactttttgcttattaacttatgaggtaataaatt Intra-Species Hit: Count: 1 Min: 1 Max: 145 Len: 145 Subject: NC_002967_TDE0069_TDE0070|conserved hypothetical protein TIGR00238:RNA polymerase sigma-70 factor, region 2 family|POSITIVE:POSITIVE|[77708,77852]|145 HSP 1 e-value: 5.0E-77 bit: 287.0 Len: 145 Query Start:1 Query End:145 Subject Strand: POSITIVE Subject Start: 1 Subject End: 145 tgtatacaaaaatatacagcaattattaaatatttgcttttccgatttaaaatctttataaaattgtaataactccattatttacgactaaaaagctgcttatcttagcacactttttgcttattaacttatgaggtaataaatt tgtatacaaaaatatacagcaattattaaatatttgcttttccgatttaaaatctttataaaattgtaataactccattatttacgactaaaaagctgcttatcttagcacactttttgcttattaacttatgaggtaataaatt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGUAUACAAAAAUAUACAGCAAUUAUUAAAUAUUUGCUUUUCCGAUUUAAAAUCUUUAUAAAAUUGUAAUAACUCCAUUAUUUACGACUAAAAAGCUGCUUAUCUUAGCACACUUUUUGCUUAUUAACUUAUGAGGUAAUAAAUU .(((((......))))).((((.(((...))).))))......((((((....((((((((..((((((............)))))).(((((((.((((......))))..))))))).........))))))))...)))))) (-20.10) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAUUUAUUACCUCAUAAGUUAAUAAGCAAAAAGUGUGCUAAGAUAAGCAGCUUUUUAGUCGUAAAUAAUGGAGUUAUUACAAUUUUAUAAAGAUUUUAAAUCGGAAAAGCAAAUAUUUAAUAAUUGCUGUAUAUUUUUGUAUACA ..(((((((.((....)).)))))))......((((((.((((((.(((((...(((....((((((((((((((.....))))))))...(((.....)))...........)))))).)))..))))).)))))).)))))). (-25.10) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 257 123 81 202 163 NC_002967:TDE2221|5end_hypothetical_protein_2262684..2262914_POSITIVE 239 123 86 161 128 NC_002967:TDE2491|5end_DNA_polymerase_domain_protein_2515499..2515729_NEGATIVE 239 137 108 196 164 NC_002967:TDE0199|5end_hypothetical_protein_234708..234938_NEGATIVE 233 140 91 199 151 NC_002967:TDE1908|5end_hypothetical_protein_1926058..1926288_NEGATIVE 231 122 93 80 53 NC_002967:TDE2273|5end_hypothetical_protein_2309980..2310210_POSITIVE 223 99 55 122 87 NC_002967:TDE1078|5end_metallo-beta-lactamase_family_protein_1109739..1109969_POSITIVE 220 136 99 141 107 NC_002967:TDE2365|5end_high-affinity_branched-chain_amino_acid_ABC_transporter,_permease_protein_2399949..2400179_NEGATIVE 220 124 84 109 64 NC_002967:TDE1029|5end_Hsp20/alpha_crystallin_family_protein_1058574..1058804_POSITIVE 215 78 34 100 61 NC_002967:TDE2606|5end_urocanate_hydratase_2646447..2646677_POSITIVE 215 121 85 101 64 NC_002967:TDE0904|5end_hypothetical_protein_922406..922636_NEGATIVE 212 109 76 140 111 NC_002967:TDE1706|5end_competence/damage-inducible_protein_CinA_1762753..1762983_NEGATIVE 212 125 81 165 120 NC_002967:TDE0090|5end_hypothetical_protein_109206..109436_NEGATIVE 209 127 83 46 6 NC_002967:TDE2412|5end_acetyltransferase,_GNAT_family_2440262..2440492_NEGATIVE 208 138 94 223 184 NC_002967:TDE0870|5end_phosphatase/nucleotidase_892698..892928_POSITIVE 204 138 92 114 63 NC_002967:TDE1673|5end_ATP-dependent_protease_ATP-binding_subunit_1726878..1727108_POSITIVE 201 138 91 97 42 NC_002967:TDE1592|5end_ABC_transporter,_ATP-binding_protein_1639491..1639721_POSITIVE 201 139 95 169 131 NC_002967:TDE0474|5end_hypothetical_protein_530740..530970_POSITIVE 199 108 64 181 136 NC_002967:TDE2347|5end_30S_ribosomal_protein_S2_2384378..2384608_NEGATIVE 199 120 91 220 196 NC_002967:TDE1709|5end_DNA-binding_protein,_HU_family_1765139..1765369_NEGATIVE 197 118 84 59 25 NC_002967:TDE2148|5end_OmpA_family_protein_2185946..2186176_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 253 136 91 102 42 NC_002967:TDE2778|3end_PspC_domain_protein_2829371..2829521_NEGATIVE 244 109 63 79 28 NC_002967:TDE1958|3end_surface_protein,_putative_1972309..1972459_NEGATIVE 239 123 86 151 118 NC_002967:TDE2492|3end_hypothetical_protein_2515509..2515659_NEGATIVE 226 122 81 122 75 NC_002967:TDE2659|3end_GAF_domain/HD_domain_protein_2697183..2697333_POSITIVE 220 136 99 131 97 NC_002967:TDE2366|3end_high-affinity_branched-chain_amino_acid_ABC_transporter,_permease_protein_2399959..2400109_NEGATIVE 220 124 84 116 71 NC_002967:TDE1028|3end_hypothetical_protein_1058661..1058811_POSITIVE 212 109 76 118 89 NC_002967:TDE1707|3end_hypothetical_protein_1762775..1762925_NEGATIVE 208 138 94 107 68 NC_002967:TDE0869|3end_hypothetical_protein_892662..892812_POSITIVE 208 130 91 119 82 NC_002967:TDE0456|3end_pyridoxine_biosynthesis_protein_512536..512686_NEGATIVE 204 138 92 121 70 NC_002967:TDE1672|3end_ATP-dependent_Clp_protease,_proteolytic_subunit_ClpP_1726965..1727115_POSITIVE 204 138 95 116 82 NC_002967:TDE1534|3end_hypothetical_protein_1578667..1578817_NEGATIVE 201 139 95 149 111 NC_002967:TDE0473|3end_heavy_metal_translocating_P-type_ATPase_530800..530950_POSITIVE 199 120 91 143 119 NC_002967:TDE1710|3end_ribosomal_protein_S20_1765216..1765366_NEGATIVE 199 136 91 60 8 NC_002967:TDE0320|3end_CBS_domain_protein_352480..352630_NEGATIVE 197 118 84 40 6 NC_002967:TDE2149|3end_transglycosylase,_SLT_family_2185965..2186115_NEGATIVE 192 113 74 85 36 NC_002967:TDE1562|3end_hypothetical_protein_1615645..1615795_POSITIVE 190 77 33 108 60 NC_002967:TDE2625|3end_ABC_transporter,_ATP-binding/permease_protein_2664925..2665075_NEGATIVE 189 116 73 81 36 NC_002967:TDE2426|3end_transcription_antitermination_protein_NusG_2455242..2455392_NEGATIVE 189 140 95 107 65 NC_002967:TDE2128|3end_hypothetical_protein_2161558..2161708_POSITIVE 189 119 72 66 12 NC_002967:TDE1114|3end_transcriptional_regulator,_TetR_family_1148234..1148384_NEGATIVE