Origin IGS: aaaaacctctaacattgatattttttatctataattttaaatacaccgatcccataataacacaaaaatataaaaataacaatatagccgcatttaatgccgcatttaatgcttgcatttaaagcctcttacatagtataatcctttcccgaacggaggtcatttt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aaaatgacctccgttcgggaaaggattatactatgtaagaggctttaaatgcaagcattaaatgcggcattaaatgcggctatattgttatttttatatttttgtgttattatgggatcggtgtatttaaaattatagataaaaaatatcaatgttagaggttttt Mask Tandem Repeat Region ================================================ aaaaacctctaacattgatattttttatctataattttaaatacaccgatcccataataacacaaaaatataaaaataacaatatannnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnagcctcttacatagtataatcctttcccgaacggaggtcatttt Find is-nt database================================================ Query_seq: TDE1636:TDE1637|TDE1636:TDE1637:surface antigen, putative:DNA polymerase I:<-->:1686046..1686211 166 aaaaacctctaacattgatattttttatctataattttaaatacaccgatcccataataacacaaaaatataaaaataacaatatagccgcatttaatgccgcatttaatgcttgcatttaaagcctcttacatagtataatcctttcccgaacggaggtcatttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE1636:TDE1637|TDE1636:TDE1637:surface antigen, putative:DNA polymerase I:<-->:1686046..1686211 166 aaaaacctctaacattgatattttttatctataattttaaatacaccgatcccataataacacaaaaatataaaaataacaatatagccgcatttaatgccgcatttaatgcttgcatttaaagcctcttacatagtataatcctttcccgaacggaggtcatttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE1636:TDE1637|TDE1636:TDE1637:surface antigen, putative:DNA polymerase I:<-->:1686046..1686211 166 aaaaacctctaacattgatattttttatctataattttaaatacaccgatcccataataacacaaaaatataaaaataacaatatagccgcatttaatgccgcatttaatgcttgcatttaaagcctcttacatagtataatcctttcccgaacggaggtcatttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aaaaacctctaacattgatattttttatctataattttaaatacaccgatcccataataacacaaaaatataaaaataacaatatagccgcatttaatgccgcatttaatgcttgcatttaaagcctcttacatagtataatcctttcccgaacggaggtcatttt Predict ORF larger than 30AA ================================================ Protein_Len: 35 Strand: + Start: 15 End: 119 .............. M I F F I Y N F K Y T D P I I T Q K Y K N N N I A A F N A A F N A C I ............................................... Protein_Len: 33 Strand: - Start: 12 End: 110 ........... C Q Y K K D I I K F V G I G Y Y C L F I F I V I Y G C K I G C K M ........................................................ aaaaacctctaacattgatattttttatctataattttaaatacaccgatcccataataacacaaaaatataaaaataacaatatagccgcatttaatgccgcatttaatgcttgcatttaaagcctcttacatagtataatcctttcccgaacggaggtcatttt 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: 54 End: 83 .....................................................ATTGTTATTTTTATATTTTTGTGTTATTAT................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ aaaaacctctaacattgatattttttatctataattttaaatacaccgatcccataataacacaaaaatataaaaataacaatatagccgcatttaatgccgcatttaatgcttgcatttaaagcctcttacatagtataatcctttcccgaacggaggtcatttt Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 70 HP_score: -7.8 Tail_Score: -3.27704 Start: 90 End: 112 Full_Region: AATAACAATATAGCC GCATTTAATG CCG CATTTAATGC TTGCATTTAAAGCCT .........................................................................................GCATTTAATGCCGCATTTAATGC...................................................... Find igs database================================================ Query_seq: TDE1636:TDE1637|TDE1636:TDE1637:surface antigen, putative:DNA polymerase I:<-->:1686046..1686211 166 aaaaacctctaacattgatattttttatctataattttaaatacaccgatcccataataacacaaaaatataaaaataacaatatagccgcatttaatgccgcatttaatgcttgcatttaaagcctcttacatagtataatcctttcccgaacggaggtcatttt Intra-Species Hit: Count: 1 Min: 1 Max: 166 Len: 166 Subject: NC_002967_TDE1636_TDE1637|surface antigen, putative:DNA polymerase I|NEGATIVE:POSITIVE|[1686046,1686211]|166 HSP 1 e-value: 2.0E-89 bit: 329.0 Len: 166 Query Start:1 Query End:166 Subject Strand: POSITIVE Subject Start: 1 Subject End: 166 aaaaacctctaacattgatattttttatctataattttaaatacaccgatcccataataacacaaaaatataaaaataacaatatagccgcatttaatgccgcatttaatgcttgcatttaaagcctcttacatagtataatcctttcccgaacggaggtcatttt aaaaacctctaacattgatattttttatctataattttaaatacaccgatcccataataacacaaaaatataaaaataacaatatagccgcatttaatgccgcatttaatgcttgcatttaaagcctcttacatagtataatcctttcccgaacggaggtcatttt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAAACCUCUAACAUUGAUAUUUUUUAUCUAUAAUUUUAAAUACACCGAUCCCAUAAUAACACAAAAAUAUAAAAAUAACAAUAUAGCCGCAUUUAAUGCCGCAUUUAAUGCUUGCAUUUAAAGCCUCUUACAUAGUAUAAUCCUUUCCCGAACGGAGGUCAUUUU ....((((((......((((.....))))...........((((..........................................((.((((...)))).)).......((((.......))))..........))))...............))))))...... (-19.80) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAAUGACCUCCGUUCGGGAAAGGAUUAUACUAUGUAAGAGGCUUUAAAUGCAAGCAUUAAAUGCGGCAUUAAAUGCGGCUAUAUUGUUAUUUUUAUAUUUUUGUGUUAUUAUGGGAUCGGUGUAUUUAAAAUUAUAGAUAAAAAAUAUCAAUGUUAGAGGUUUUU .....((((((...((((.....(((.((((.((((((((.((.......)).((((.((...((.((((...)))).))..)).))))..))))))))....)))).)))......))))................((((.....)))).......))))))... (-28.00) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 849 130 81 221 172 NC_002967:TDE1636|5end_surface_antigen,_putative_1685955..1686185_NEGATIVE 328 158 112 178 128 NC_002967:TDE1310|5end_modulator_of_DNA_gyrase_family_protein_1345962..1346192_POSITIVE 293 130 86 55 5 NC_002967:TDE0340|5end_fructose-bisphosphate_aldolase_378639..378869_POSITIVE 283 127 87 229 199 NC_002967:TDE1151|5end_hypothetical_protein_1188534..1188764_NEGATIVE 279 160 112 187 130 NC_002967:TDE1214|5end_flagellar_basal_body_protein_1246307..1246537_POSITIVE 274 152 113 222 175 NC_002967:TDE2440|5end_ABC_transporter,_ATP-binding/permease_protein,_putative_2472043..2472273_NEGATIVE 270 120 85 66 19 NC_002967:TDE1979|5end_hypothetical_protein_1991985..1992215_NEGATIVE 270 128 86 172 132 NC_002967:TDE1820|5end_hypothetical_protein_1854692..1854922_NEGATIVE 269 138 91 195 145 NC_002967:TDE1261|5end_choline/carnitine/betaine_transporter_family_protein_1295593..1295823_POSITIVE 264 135 100 127 85 NC_002967:TDE2478|5end_excinuclease_ABC,_C_subunit_2500873..2501103_POSITIVE 262 150 109 164 119 NC_002967:TDE1543|5end_conserved_hypothetical_protein_TIGR00247_1586068..1586298_POSITIVE 260 127 81 72 28 NC_002967:TDE0449|5end_ferritin,_putative_507031..507261_NEGATIVE 257 128 86 100 62 NC_002967:TDE2770|5end_flagellar_hook-length_control_protein_FliK_2824417..2824647_NEGATIVE 256 128 86 199 148 NC_002967:TDE1300|5end_hypothetical_protein_1337419..1337649_NEGATIVE 253 152 111 231 201 NC_002967:TDE2644|5end_pyridine_nucleotide-disulphide_oxidoreductase_family_protein_2683651..2683881_POSITIVE 253 125 90 49 21 NC_002967:TDE1849|5end_hypothetical_protein_1878123..1878353_NEGATIVE 250 108 63 129 89 NC_002967:TDE2628|5end_hypothetical_protein_2669068..2669298_POSITIVE 248 158 111 60 6 NC_002967:TDE2265|5end_hypothetical_protein_2302165..2302395_POSITIVE 248 130 88 130 86 NC_002967:TDE1973|5end_CvpA_family_protein_1987706..1987936_NEGATIVE 247 130 91 142 109 NC_002967:TDE1795|5end_funZ_protein,_putative_1834673..1834903_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 270 120 85 91 44 NC_002967:TDE1980|3end_hypothetical_protein_1991960..1992110_NEGATIVE 270 128 86 49 9 NC_002967:TDE1821|3end_hypothetical_protein_1854815..1854965_NEGATIVE 265 159 113 60 25 NC_002967:TDE2702|3end_hypothetical_protein_2745832..2745982_NEGATIVE 264 135 100 123 81 NC_002967:TDE2477|3end_selenocysteine_synthase_2500949..2501099_POSITIVE 263 159 112 151 95 NC_002967:TDE1213|3end_flagellar_basal_body_rod_protein_1246352..1246502_POSITIVE 262 150 109 144 99 NC_002967:TDE1542|3end_hypothetical_protein_1586128..1586278_POSITIVE 259 116 79 57 24 NC_002967:TDE1529|3end_hypothetical_protein_1575067..1575217_POSITIVE 248 130 88 101 57 NC_002967:TDE1974|3end_UDP-N-acetylglucosamine--N-acetylmuramyl-_(pentapeptide)_pyrophosphoryl-undecaprenol_N-acetylglucosamine_transferase_1987735..1987885_NEGATIVE 247 130 91 49 16 NC_002967:TDE1796|3end_hypothetical_protein_1834766..1834916_NEGATIVE 240 129 85 139 92 NC_002967:TDE2155|3end_50S_ribosomal_protein_L35_2189965..2190115_NEGATIVE 240 123 87 54 17 NC_002967:TDE0610|3end_3-hydroxyacyl-CoA_dehydrogenase,_putative_646357..646507_NEGATIVE 239 159 111 114 50 NC_002967:TDE1005|3end_hypothetical_protein_1030495..1030645_POSITIVE 237 150 101 128 87 NC_002967:TDE0915|3end_hypothetical_protein_933147..933297_NEGATIVE 233 157 122 78 30 NC_002967:TDE1857|3end_hypothetical_protein_1883929..1884079_NEGATIVE 233 160 112 112 72 NC_002967:TDE0702|3end_ABC_transporter,_ATP-binding_protein_737244..737394_NEGATIVE 233 156 143 30 17 NC_002967:TDE0099|3end_adenine-specific_DNA_modification_methyltransferase_117014..117164_POSITIVE 231 132 99 42 11 NC_002967:TDE0829|3end_putative_aminopeptidase_2_850185..850335_NEGATIVE 231 160 119 78 28 NC_002967:TDE0018|3end_LysM_domain_protein_23073..23223_NEGATIVE 227 156 111 69 28 NC_002967:TDE1145|3end_hypothetical_protein_1182868..1183018_NEGATIVE 226 118 84 82 49 NC_002967:TDE2365|3end_high-affinity_branched-chain_amino_acid_ABC_transporter,_permease_protein_2398930..2399080_NEGATIVE