Origin IGS: atttttatctcctttttccgaaccggaatttgttattataatagcagcagcagttcccgcaactaaaatcataaacgcaattgcaataatcataatccataattttttcattttatctttcc .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 ggaaagataaaatgaaaaaattatggattatgattattgcaattgcgtttatgattttagttgcgggaactgctgctgctattataataacaaattccggttcggaaaaaggagataaaaat Mask Tandem Repeat Region ================================================ atttttatctcctttttccgaaccggaatttgttattataatagcagcagcagttcccgcaactaaaatcataaacgcaattgcaataatcataatccataattttttcattttatctttcc Find is-nt database================================================ Query_seq: TDE2391:TDE2392|TDE2391:TDE2392:peptidyl-prolyl cis-trans isomerase:hypothetical protein:<-<-:2421641..2421762 122 atttttatctcctttttccgaaccggaatttgttattataatagcagcagcagttcccgcaactaaaatcataaacgcaattgcaataatcataatccataattttttcattttatctttcc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE2391:TDE2392|TDE2391:TDE2392:peptidyl-prolyl cis-trans isomerase:hypothetical protein:<-<-:2421641..2421762 122 atttttatctcctttttccgaaccggaatttgttattataatagcagcagcagttcccgcaactaaaatcataaacgcaattgcaataatcataatccataattttttcattttatctttcc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE2391:TDE2392|TDE2391:TDE2392:peptidyl-prolyl cis-trans isomerase:hypothetical protein:<-<-:2421641..2421762 122 atttttatctcctttttccgaaccggaatttgttattataatagcagcagcagttcccgcaactaaaatcataaacgcaattgcaataatcataatccataattttttcattttatctttcc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 atttttatctcctttttccgaaccggaatttgttattataatagcagcagcagttcccgcaactaaaatcataaacgcaattgcaataatcataatccataattttttcattttatctttcc Predict ORF larger than 30AA ================================================ Protein_Len: 32 Strand: - Start: 8 End: 103 ....... R R K G F R F K N N Y Y C C C N G C S F D Y V C N C Y D Y D M M ................... Protein_Len: 37 Strand: - Start: 1 End: 111 N K D G K E S G S N T I I I A A A T G A V L I M F A I A I I M I W L K K M ........... atttttatctcctttttccgaaccggaatttgttattataatagcagcagcagttcccgcaactaaaatcataaacgcaattgcaataatcataatccataattttttcattttatctttcc 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: 83 Start: 13 End: 42 ............TTTTTCCGAACCGGAATTTGTTATTATAAT................................................................................ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ atttttatctcctttttccgaaccggaatttgttattataatagcagcagcagttcccgcaactaaaatcataaacgcaattgcaataatcataatccataattttttcattttatctttcc Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE2391:TDE2392|TDE2391:TDE2392:peptidyl-prolyl cis-trans isomerase:hypothetical protein:<-<-:2421641..2421762 122 atttttatctcctttttccgaaccggaatttgttattataatagcagcagcagttcccgcaactaaaatcataaacgcaattgcaataatcataatccataattttttcattttatctttcc Intra-Species Hit: Count: 1 Min: 1 Max: 122 Len: 122 Subject: NC_002967_TDE2391_TDE2392|peptidyl-prolyl cis-trans isomerase:hypothetical protein|NEGATIVE:NEGATIVE|[2421641,2421762]|122 HSP 1 e-value: 2.0E-63 bit: 242.0 Len: 122 Query Start:1 Query End:122 Subject Strand: POSITIVE Subject Start: 1 Subject End: 122 atttttatctcctttttccgaaccggaatttgttattataatagcagcagcagttcccgcaactaaaatcataaacgcaattgcaataatcataatccataattttttcattttatctttcc atttttatctcctttttccgaaccggaatttgttattataatagcagcagcagttcccgcaactaaaatcataaacgcaattgcaataatcataatccataattttttcattttatctttcc Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUUUUUAUCUCCUUUUUCCGAACCGGAAUUUGUUAUUAUAAUAGCAGCAGCAGUUCCCGCAACUAAAAUCAUAAACGCAAUUGCAAUAAUCAUAAUCCAUAAUUUUUUCAUUUUAUCUUUCC ........................(((..(((((((....)))))))..((((((...((................))))))))...........)))........................ (-11.29) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GGAAAGAUAAAAUGAAAAAAUUAUGGAUUAUGAUUAUUGCAAUUGCGUUUAUGAUUUUAGUUGCGGGAACUGCUGCUGCUAUUAUAAUAACAAAUUCCGGUUCGGAAAAAGGAGAUAAAAAU ((((....................(((((((((....(((....))).)))))))))((((.((((......)))).)))).............))))........................ (-18.10) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 913 60 11 151 102 NC_002967:TDE2391|5end_peptidyl-prolyl_cis-trans_isomerase_2421550..2421780_NEGATIVE 304 60 16 136 98 NC_002967:TDE2102|5end_hypothetical_protein_2127347..2127577_NEGATIVE 292 56 15 66 21 NC_002967:TDE2408|5end_hypothetical_protein_2435387..2435617_NEGATIVE 290 96 51 183 138 NC_002967:TDE0395|5end_oligopeptide/dipeptide_ABC_transporter,_permease_protein_444955..445185_POSITIVE 284 60 11 72 20 NC_002967:TDE2162|5end_NOL1/NOP2/sun_family_protein_2194689..2194919_POSITIVE 281 59 11 76 26 NC_002967:TDE2435|5end_hypothetical_protein_2466462..2466692_NEGATIVE 271 69 22 76 20 NC_002967:TDE2542|5end_antigen,_putative_2570826..2571056_NEGATIVE 263 78 40 81 42 NC_002967:TDE1408|5end_flagellar_filament_outer_layer_protein_FlaA,_putative_1450829..1451059_POSITIVE 262 60 12 61 9 NC_002967:TDE2240|5end_hypothetical_protein_2278422..2278652_NEGATIVE 262 70 22 68 18 NC_002967:TDE2163|5end_hypothetical_protein_2196213..2196443_NEGATIVE 262 78 43 76 32 NC_002967:TDE0405|5end_major_outer_sheath_protein_455470..455700_POSITIVE 261 95 57 66 24 NC_002967:TDE0139|5end_hypothetical_protein_162583..162813_NEGATIVE 256 60 13 198 139 NC_002967:TDE0987|5end_oligopeptide/dipeptide_ABC_transporter,_ATP-binding_protein_1014041..1014271_POSITIVE 255 59 11 77 19 NC_002967:TDE1917|5end_cytidylyltransferase_domain_protein_1937394..1937624_NEGATIVE 255 60 11 224 165 NC_002967:TDE0900|5end_ABC_transporter,_ATP-binding_protein_917188..917418_POSITIVE 254 86 41 229 179 NC_002967:TDE0249|5end_flavoredoxin,_putative_282539..282769_POSITIVE 253 60 12 154 95 NC_002967:TDE0143|5end_thiamine_ABC_transporter,_thiamine-binding_protein_164013..164243_POSITIVE 244 100 62 125 81 NC_002967:TDE0280|5end_PIN_domain_protein_310296..310526_NEGATIVE 242 73 44 92 60 NC_002967:TDE1679|5end_ATP_synthase_subunit_K_1731049..1731279_NEGATIVE 242 60 13 178 133 NC_002967:TDE0283|5end_transporter,_putative_312825..313055_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 291 87 43 144 106 NC_002967:TDE0031|3end_hypothetical_protein_38835..38985_NEGATIVE 271 69 22 149 93 NC_002967:TDE2543|3end_hypothetical_protein_2570753..2570903_NEGATIVE 267 58 15 65 21 NC_002967:TDE1347|3end_hypothetical_protein_1388032..1388182_POSITIVE 261 60 11 81 27 NC_002967:TDE1692|3end_hypothetical_protein_1748471..1748621_POSITIVE 257 88 41 53 5 NC_002967:TDE2164|3end_hypothetical_protein_2196248..2196398_NEGATIVE 255 59 11 80 22 NC_002967:TDE1918|3end_hypothetical_protein_1937391..1937541_NEGATIVE 254 86 41 126 76 NC_002967:TDE0248|3end_hypothetical_protein_282516..282666_POSITIVE 253 60 12 126 67 NC_002967:TDE0141|3end_hypothetical_protein_164065..164215_POSITIVE 250 60 12 56 17 NC_002967:TDE0099|3end_adenine-specific_DNA_modification_methyltransferase_117014..117164_POSITIVE 247 60 17 75 24 NC_002967:TDE2715|3end_hypothetical_protein_2772936..2773086_POSITIVE 244 100 62 128 84 NC_002967:TDE0281|3end_hypothetical_protein_310293..310443_NEGATIVE 240 60 12 115 60 NC_002967:TDE2674|3end_hypothetical_protein_2712465..2712615_NEGATIVE 235 48 2 126 88 NC_002967:TDE2761|3end_hypothetical_protein_2815878..2816028_NEGATIVE 233 85 47 138 110 NC_002967:TDE2057|3end_hypothetical_protein_2085158..2085308_NEGATIVE 231 46 1 85 39 NC_002967:TDE0612|3end_hypothetical_protein_647367..647517_NEGATIVE 230 60 19 149 110 NC_002967:TDE0571|3end_hypothetical_protein_603497..603647_POSITIVE 227 60 11 64 7 NC_002967:TDE2365|3end_high-affinity_branched-chain_amino_acid_ABC_transporter,_permease_protein_2398930..2399080_NEGATIVE 226 59 21 64 37 NC_002967:TDE0266|3end_hypothetical_protein_297767..297917_NEGATIVE 225 89 45 57 8 NC_002967:TDE1990|3end_ATP-dependent_helicase,_DinG_family_2006367..2006517_NEGATIVE 223 84 41 61 21 NC_002967:TDE0405|3end_major_outer_sheath_protein_457181..457331_POSITIVE