Origin IGS: aagcatactcctataaaaacttctaataattttataataaaattatacaccagtacaagaaaaattacaagtttttttggaaatactagtataatgtcatccaaaataaaactaagacggccgctccaatataaaaataacagccctattctcgaattgtgtagaaaaacctgccgttccccttattttgggaaacggcagtaaagtttaaacctatatatttttcctt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aaggaaaaatatataggtttaaactttactgccgtttcccaaaataaggggaacggcaggtttttctacacaattcgagaatagggctgttatttttatattggagcggccgtcttagttttattttggatgacattatactagtatttccaaaaaaacttgtaatttttcttgtactggtgtataattttattataaaattattagaagtttttataggagtatgctt Mask Tandem Repeat Region ================================================ aagcatactcctataaaaacttctaataattttataataaaattatacaccagtacaagaaaaattacaagtttttttggaaatactagtataatgtcatccaaaataaaactaagacggccgctccaatataaaaataacagccctattctcgaattgtgtagaaaaacctgccgttccccttattttgggaaacggcagtaaagtttaaacctatatatttttcctt Find is-nt database================================================ Query_seq: TDE2257:TDE2258|TDE2257:TDE2258:5'-nucleotidase family protein:surface antigen BspA, putative:<-<-:2295195..2295423 229 aagcatactcctataaaaacttctaataattttataataaaattatacaccagtacaagaaaaattacaagtttttttggaaatactagtataatgtcatccaaaataaaactaagacggccgctccaatataaaaataacagccctattctcgaattgtgtagaaaaacctgccgttccccttattttgggaaacggcagtaaagtttaaacctatatatttttcctt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE2257:TDE2258|TDE2257:TDE2258:5'-nucleotidase family protein:surface antigen BspA, putative:<-<-:2295195..2295423 229 aagcatactcctataaaaacttctaataattttataataaaattatacaccagtacaagaaaaattacaagtttttttggaaatactagtataatgtcatccaaaataaaactaagacggccgctccaatataaaaataacagccctattctcgaattgtgtagaaaaacctgccgttccccttattttgggaaacggcagtaaagtttaaacctatatatttttcctt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE2257:TDE2258|TDE2257:TDE2258:5'-nucleotidase family protein:surface antigen BspA, putative:<-<-:2295195..2295423 229 aagcatactcctataaaaacttctaataattttataataaaattatacaccagtacaagaaaaattacaagtttttttggaaatactagtataatgtcatccaaaataaaactaagacggccgctccaatataaaaataacagccctattctcgaattgtgtagaaaaacctgccgttccccttattttgggaaacggcagtaaagtttaaacctatatatttttcctt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aagcatactcctataaaaacttctaataattttataataaaattatacaccagtacaagaaaaattacaagtttttttggaaatactagtataatgtcatccaaaataaaactaagacggccgctccaatataaaaataacagccctattctcgaattgtgtagaaaaacctgccgttccccttattttgggaaacggcagtaaagtttaaacctatatatttttcctt Predict ORF larger than 30AA ================================================ Protein_Len: 60 Strand: + Start: 13 End: 201 ............ M K T S N N F I I K L Y T S T R K I T S F F G N T S I M S S K I K L R R P L Q Y K N N S P I L E L C R K T C R S P Y F G ............................ Protein_Len: 49 Strand: - Start: 3 End: 149 .. C V G I F V E L L K I I F N Y V L V L F I V L K K P F V L I I D D L I F S L R G S W Y L F L L G M ................................................................................ aagcatactcctataaaaacttctaataattttataataaaattatacaccagtacaagaaaaattacaagtttttttggaaatactagtataatgtcatccaaaataaaactaagacggccgctccaatataaaaataacagccctattctcgaattgtgtagaaaaacctgccgttccccttattttgggaaacggcagtaaagtttaaacctatatatttttcctt 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: 87 Start: 42 End: 71 .........................................CTTGTAATTTTTCTTGTACTGGTGTATAAT.............................................................................................................................................................. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ aagcatactcctataaaaacttctaataattttataataaaattatacaccagtacaagaaaaattacaagtttttttggaaatactagtataatgtcatccaaaataaaactaagacggccgctccaatataaaaataacagccctattctcgaattgtgtagaaaaacctgccgttccccttattttgggaaacggcagtaaagtttaaacctatatatttttcctt Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 100 HP_score: -11.3 Tail_Score: -4.84017 Start: 170 End: 202 Full_Region: ataggtttaaacttt actgccgtttccc aaaataa ggggaacggcagg tttttctacacaatt .........................................................................................................................................................................actgccgtttcccaaaataaggggaacggcagg........................... Find igs database================================================ Query_seq: TDE2257:TDE2258|TDE2257:TDE2258:5'-nucleotidase family protein:surface antigen BspA, putative:<-<-:2295195..2295423 229 aagcatactcctataaaaacttctaataattttataataaaattatacaccagtacaagaaaaattacaagtttttttggaaatactagtataatgtcatccaaaataaaactaagacggccgctccaatataaaaataacagccctattctcgaattgtgtagaaaaacctgccgttccccttattttgggaaacggcagtaaagtttaaacctatatatttttcctt Intra-Species Hit: Count: 1 Min: 1 Max: 229 Len: 229 Subject: NC_002967_TDE2257_TDE2258|5'-nucleotidase family protein:surface antigen BspA, putative|NEGATIVE:NEGATIVE|[2295195,2295423]|229 HSP 1 e-value: 1.0E-114 bit: 412.0 Len: 229 Query Start:1 Query End:229 Subject Strand: POSITIVE Subject Start: 1 Subject End: 229 aagcatactcctataaaaacttctaataattttataataaaattatacaccagtacaagaaaaattacaagnnnnnnnggaaatactagtataatgtcatccaaaataaaactaagacggccgctccaatataaaaataacagccctattctcgaattgtgtagaaaaacctgccgttccccttattttgggaaacggcagtaaagtttaaacctatatatttttcctt aagcatactcctataaaaacttctaataattttataataaaattatacaccagtacaagaaaaattacaagtttttttggaaatactagtataatgtcatccaaaataaaactaagacggccgctccaatataaaaataacagccctattctcgaattgtgtagaaaaacctgccgttccccttattttgggaaacggcagtaaagtttaaacctatatatttttcctt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAGCAUACUCCUAUAAAAACUUCUAAUAAUUUUAUAAUAAAAUUAUACACCAGUACAAGAAAAAUUACAAGUUUUUUUGGAAAUACUAGUAUAAUGUCAUCCAAAAUAAAACUAAGACGGCCGCUCCAAUAUAAAAAUAACAGCCCUAUUCUCGAAUUGUGUAGAAAAACCUGCCGUUCCCCUUAUUUUGGGAAACGGCAGUAAAGUUUAAACCUAUAUAUUUUUCCUU ................((((((....((((((((...))))))))(((((.(((.(.((((........((((((((((((...((.........))..))))))..)))))).....(((.....................)))...)))).).)))))))).......((((((((.(((.......))).))))))))..)))))).................... (-38.70) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAGGAAAAAUAUAUAGGUUUAAACUUUACUGCCGUUUCCCAAAAUAAGGGGAACGGCAGGUUUUUCUACACAAUUCGAGAAUAGGGCUGUUAUUUUUAUAUUGGAGCGGCCGUCUUAGUUUUAUUUUGGAUGACAUUAUACUAGUAUUUCCAAAAAAACUUGUAAUUUUUCUUGUACUGGUGUAUAAUUUUAUUAUAAAAUUAUUAGAAGUUUUUAUAGGAGUAUGCUU .(((((((((.(((((((((........((((((((((((.......)))))))))))).................((((....(((((((.............))))))).)))).......(((((((..((.........))...)))))))))))))))))))))))))........(((((.((((((...((((((......)))))).)))))).))))).. (-59.72) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 816 130 81 221 172 NC_002967:TDE2257|5end_5'-nucleotidase_family_protein_2295104..2295334_NEGATIVE 340 210 161 125 67 NC_002967:TDE2149|5end_transglycosylase,_SLT_family_2187293..2187523_NEGATIVE 282 200 151 119 72 NC_002967:TDE0873|5end_hypothetical_protein_896143..896373_POSITIVE 274 189 141 186 143 NC_002967:TDE1304|5end_hypothetical_protein_1339716..1339946_POSITIVE 265 209 165 180 143 NC_002967:TDE0400|5end_transcriptional_regulator,_LysR_family_451803..452033_NEGATIVE 264 204 172 228 191 NC_002967:TDE2522|5end_ABC_transporter,_ATP-binding_protein_2548098..2548328_POSITIVE 262 144 118 79 56 NC_002967:TDE0163|5end_flavodoxin_193383..193613_NEGATIVE 259 197 153 44 1 NC_002967:TDE0679|5end_aminotransferase,_class_V_716345..716575_POSITIVE 258 188 142 54 12 NC_002967:TDE0506|5end_DNA-damage-inducible_protein_J,_putative_558717..558947_NEGATIVE 257 197 160 197 167 NC_002967:TDE2250|5end_hypothetical_protein_2288568..2288798_POSITIVE 255 199 156 202 160 NC_002967:TDE0945|5end_hypothetical_protein_967128..967358_POSITIVE 254 210 169 189 152 NC_002967:TDE2714|5end_hypothetical_protein_2772618..2772848_NEGATIVE 254 125 88 68 38 NC_002967:TDE0209|5end_arsenical_pump_membrane_protein,_putative_244195..244425_POSITIVE 251 206 171 75 35 NC_002967:TDE2521|5end_hypothetical_protein_2548074..2548304_NEGATIVE 251 181 141 164 120 NC_002967:TDE1671|5end_trigger_factor_1724912..1725142_POSITIVE 250 155 111 126 80 NC_002967:TDE0689|5end_5-methylthioribose_kinase_725690..725920_POSITIVE 249 151 118 98 65 NC_002967:TDE0614|5end_precorrin-4_C11-methyltransferase_647987..648217_POSITIVE 247 207 171 161 122 NC_002967:TDE1104|5end_tRNA_pseudouridine_synthase_B_1137786..1138016_NEGATIVE 247 202 169 181 148 NC_002967:TDE0590|5end_acetyl-CoA_carboxylase,_carboxyl_transferase,_beta_subunit_629856..630086_NEGATIVE 246 181 143 220 181 NC_002967:TDE0190|5end_hypothetical_protein_227366..227596_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 295 197 151 57 12 NC_002967:TDE0678|3end_hypothetical_protein_716438..716588_POSITIVE 290 193 161 148 106 NC_002967:TDE2150|3end_hypothetical_protein_2187254..2187404_NEGATIVE 282 200 151 61 14 NC_002967:TDE0872|3end_recA_protein_896165..896315_POSITIVE 275 170 121 50 7 NC_002967:TDE2604|3end_hypothetical_protein_2644224..2644374_NEGATIVE 265 209 165 146 109 NC_002967:TDE0401|3end_adenylate/guanylate_cyclase_catalytic_domain_protein_451837..451987_NEGATIVE 264 188 146 142 91 NC_002967:TDE2441|3end_hypothetical_protein_2472356..2472506_NEGATIVE 262 144 118 45 22 NC_002967:TDE0164|3end_hypothetical_protein_193417..193567_NEGATIVE 258 210 172 69 24 NC_002967:TDE1386|3end_methyl-accepting_chemotaxis_protein_1426856..1427006_POSITIVE 258 185 141 57 2 NC_002967:TDE0976|3end_hypothetical_protein_1000498..1000648_POSITIVE 255 198 151 59 12 NC_002967:TDE0210|3end_cob(I)yrinic_acid_a,c-diamide_adenosyltransferase_246146..246296_POSITIVE 250 155 111 113 67 NC_002967:TDE0688|3end_hypothetical_protein_725757..725907_POSITIVE 249 182 142 59 15 NC_002967:TDE0870|3end_phosphatase/nucleotidase_894676..894826_POSITIVE 247 207 171 146 107 NC_002967:TDE1105|3end_ribosome-binding_factor_A_1137801..1137951_NEGATIVE 246 158 115 52 12 NC_002967:TDE2666|3end_hydrolase,_carbon-nitrogen_family_2703663..2703813_NEGATIVE 244 199 157 42 1 NC_002967:TDE2693|3end_ankyrin_repeat_protein_2734014..2734164_POSITIVE 241 216 171 73 42 NC_002967:TDE2214|3end_hypothetical_protein_2253465..2253615_POSITIVE 239 209 164 63 5 NC_002967:TDE0435|3end_ATP-dependent_DNA_helicase,_RecQ_family_489558..489708_NEGATIVE 238 212 178 55 10 NC_002967:TDE2712|3end_hypothetical_protein_2769615..2769765_POSITIVE 238 181 144 79 46 NC_002967:TDE0569|3end_hypothetical_protein_600162..600312_POSITIVE 237 203 169 43 11 NC_002967:TDE2402|3end_radical_SAM_domain_protein_2428664..2428814_POSITIVE