Origin IGS: atttagagttcctttcaaatgttattttaaaaactatttataattgatttttattgaatgtacattaagatttggcagacgcgattgtacactaatttttgtatttttactagatgtttatgtaataaataaatgaaaaatattataatggagaaaacttataaaatagaaatttaatgccgatgtttt .........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 aaaacatcggcattaaatttctattttataagttttctccattataatatttttcatttatttattacataaacatctagtaaaaatacaaaaattagtgtacaatcgcgtctgccaaatcttaatgtacattcaataaaaatcaattataaatagtttttaaaataacatttgaaaggaactctaaat Mask Tandem Repeat Region ================================================ atttagagttcctttcaaatgttattttaaaaactatttataattgatttttattgaatgtacattaagatttggcagacgcgattgtacactaatttttgtatttttactagatgtttatgtaataaataaatgaaaaatattataatggagaaaacttataaaatagaaatttaatgccgatgtttt Find is-nt database================================================ Query_seq: TDE0484:TDE0485|TDE0484:TDE0485:methyl-accepting chemotaxis protein:hypothetical protein:<-<-:541907..542095 189 atttagagttcctttcaaatgttattttaaaaactatttataattgatttttattgaatgtacattaagatttggcagacgcgattgtacactaatttttgtatttttactagatgtttatgtaataaataaatgaaaaatattataatggagaaaacttataaaatagaaatttaatgccgatgtttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE0484:TDE0485|TDE0484:TDE0485:methyl-accepting chemotaxis protein:hypothetical protein:<-<-:541907..542095 189 atttagagttcctttcaaatgttattttaaaaactatttataattgatttttattgaatgtacattaagatttggcagacgcgattgtacactaatttttgtatttttactagatgtttatgtaataaataaatgaaaaatattataatggagaaaacttataaaatagaaatttaatgccgatgtttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE0484:TDE0485|TDE0484:TDE0485:methyl-accepting chemotaxis protein:hypothetical protein:<-<-:541907..542095 189 atttagagttcctttcaaatgttattttaaaaactatttataattgatttttattgaatgtacattaagatttggcagacgcgattgtacactaatttttgtatttttactagatgtttatgtaataaataaatgaaaaatattataatggagaaaacttataaaatagaaatttaatgccgatgtttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 atttagagttcctttcaaatgttattttaaaaactatttataattgatttttattgaatgtacattaagatttggcagacgcgattgtacactaatttttgtatttttactagatgtttatgtaataaataaatgaaaaatattataatggagaaaacttataaaatagaaatttaatgccgatgtttt Predict ORF larger than 30AA ================================================ Protein_Len: 30 Strand: + Start: 44 End: 133 ........................................... M I F I E C T L R F G R R D C T L I F V F L L D V Y V I N K ........................................................ Protein_Len: 32 Strand: - Start: 54 End: 149 ..................................................... Q I Y M L I Q C V R N Y V L K Q I K V L H K H L L Y I F F I I M ........................................ atttagagttcctttcaaatgttattttaaaaactatttataattgatttttattgaatgtacattaagatttggcagacgcgattgtacactaatttttgtatttttactagatgtttatgtaataaataaatgaaaaatattataatggagaaaacttataaaatagaaatttaatgccgatgtttt 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================================================ atttagagttcctttcaaatgttattttaaaaactatttataattgatttttattgaatgtacattaagatttggcagacgcgattgtacactaatttttgtatttttactagatgtttatgtaataaataaatgaaaaatattataatggagaaaacttataaaatagaaatttaatgccgatgtttt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE0484:TDE0485|TDE0484:TDE0485:methyl-accepting chemotaxis protein:hypothetical protein:<-<-:541907..542095 189 atttagagttcctttcaaatgttattttaaaaactatttataattgatttttattgaatgtacattaagatttggcagacgcgattgtacactaatttttgtatttttactagatgtttatgtaataaataaatgaaaaatattataatggagaaaacttataaaatagaaatttaatgccgatgtttt Intra-Species Hit: Count: 1 Min: 1 Max: 122 Len: 122 Subject: NC_002967_TDE0484_TDE0485|methyl-accepting chemotaxis protein:hypothetical protein|NEGATIVE:NEGATIVE|[541907,542095]|189 HSP 1 e-value: 4.0E-63 bit: 242.0 Len: 122 Query Start:1 Query End:122 Subject Strand: POSITIVE Subject Start: 1 Subject End: 122 atttagagttcctttcaaatgttattttaaaaactatttataattgatttttattgaatgtacattaagatttggcagacgcgattgtacactaatttttgtatttttactagatgtttatg................................................................... atttagagttcctttcaaatgttattttaaaaactatttataattgatttttattgaatgtacattaagatttggcagacgcgattgtacactaatttttgtatttttactagatgtttatg................................................................... Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUUUAGAGUUCCUUUCAAAUGUUAUUUUAAAAACUAUUUAUAAUUGAUUUUUAUUGAAUGUACAUUAAGAUUUGGCAGACGCGAUUGUACACUAAUUUUUGUAUUUUUACUAGAUGUUUAUG ((((((.(((((..((.((((((((((((((((.((........)).))))))..))))).)))))..))...))..)))..((..(((((........)))))..)).))))))....... (-12.50) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CAUAAACAUCUAGUAAAAAUACAAAAAUUAGUGUACAAUCGCGUCUGCCAAAUCUUAAUGUACAUUCAAUAAAAAUCAAUUAUAAAUAGUUUUUAAAAUAACAUUUGAAAGGAACUCUAAAU ........(((...............(((((((((((.....................)))))))).)))............(((((.(((........))))))))...)))......... ( -7.00) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 763 100 51 191 142 NC_002967:TDE0484|5end_methyl-accepting_chemotaxis_protein_541816..542046_NEGATIVE 243 79 31 222 170 NC_002967:TDE1971|5end_DNA_polymerase_III_domain_protein_1987030..1987260_NEGATIVE 228 94 71 125 104 NC_002967:TDE2260|5end_hypothetical_protein_2297338..2297568_POSITIVE 221 100 54 176 126 NC_002967:TDE2766|5end_motility_protein_A_2820874..2821104_NEGATIVE 221 119 75 134 93 NC_002967:TDE1918|5end_hypothetical_protein_1938344..1938574_NEGATIVE 219 89 69 148 124 NC_002967:TDE2094|5end_hypothetical_protein_2121319..2121549_NEGATIVE 216 108 62 64 12 NC_002967:TDE2778|5end_PspC_domain_protein_2829604..2829834_NEGATIVE 216 79 52 28 4 NC_002967:TDE1972|5end_hypothetical_protein_1987224..1987454_NEGATIVE 207 90 44 189 154 NC_002967:TDE2353|5end_flagellar_hook-associated_protein_2389129..2389359_POSITIVE 205 117 75 95 55 NC_002967:TDE1782|5end_hypothetical_protein_1823417..1823647_NEGATIVE 205 109 63 217 161 NC_002967:TDE0083|5end_GTP-binding_protein_EngA_95684..95914_NEGATIVE 200 89 46 47 1 NC_002967:TDE0112|5end_hypothetical_protein_132044..132274_POSITIVE 193 91 54 50 19 NC_002967:TDE2432|5end_treponemal_membrane_protein,_putative_2461414..2461644_POSITIVE 187 91 53 210 176 NC_002967:TDE2514|5end_serine/threonine_protein_phosphatase_family_protein_2540532..2540762_NEGATIVE 187 39 2 123 81 NC_002967:TDE1448|5end_glutamate_racemase,_putative_1493535..1493765_POSITIVE 184 110 71 179 143 NC_002967:TDE0382|5end_hypothetical_protein_434393..434623_POSITIVE 182 102 61 86 53 NC_002967:TDE1063|5end_methionyl-tRNA_synthetase_1090507..1090737_POSITIVE 181 87 49 219 160 NC_002967:TDE0595|5end_hypothetical_protein_634972..635202_NEGATIVE 181 103 63 154 114 NC_002967:TDE0461|5end_hypothetical_protein_515863..516093_POSITIVE 179 110 70 210 157 NC_002967:TDE0768|5end_50S_ribosomal_protein_L4_806996..807226_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 243 79 31 150 98 NC_002967:TDE1972|3end_hypothetical_protein_1987102..1987252_NEGATIVE 228 94 71 61 40 NC_002967:TDE1982|3end_hypothetical_protein_1992511..1992661_NEGATIVE 226 89 56 132 88 NC_002967:TDE2570|3end_ribonuclease_HI_2597937..2598087_POSITIVE 218 89 54 139 104 NC_002967:TDE2767|3end_flagellar_protein-related_protein_2820896..2821046_NEGATIVE 214 87 49 145 106 NC_002967:TDE1652|3end_ABC_transporter,_ATP-binding/permease_protein_1698857..1699007_NEGATIVE 205 117 75 74 34 NC_002967:TDE1783|3end_hypothetical_protein_1823438..1823588_NEGATIVE 193 84 44 122 85 NC_002967:TDE0111|3end_hypothetical_protein_132114..132264_POSITIVE 187 39 2 96 54 NC_002967:TDE1447|3end_tRNA_delta(2)-isopentenylpyrophosphate_transferase_1493588..1493738_POSITIVE 186 88 61 91 54 NC_002967:TDE0439|3end_hypothetical_protein_495104..495254_NEGATIVE 185 79 48 41 9 NC_002967:TDE2411|3end_glycogen_phosphorylase_2437234..2437384_NEGATIVE 185 119 74 71 24 NC_002967:TDE1002|3end_hypothetical_protein_1028445..1028595_NEGATIVE 183 89 47 140 83 NC_002967:TDE0399|3end_zinc_carboxypeptidase_family_protein_450845..450995_POSITIVE 179 118 71 66 18 NC_002967:TDE2173|3end_hypothetical_protein_2202737..2202887_NEGATIVE 179 118 71 151 103 NC_002967:TDE2172|3end_hypothetical_protein_2202652..2202802_NEGATIVE 178 87 42 128 89 NC_002967:TDE2205|3end_enoate_reductase,_putative_2242575..2242725_NEGATIVE 176 105 71 71 38 NC_002967:TDE0784|3end_ribosomal_protein_S5_814492..814642_POSITIVE 173 102 61 140 106 NC_002967:TDE0145|3end_thiamine_ABC_transporter,_ATP-binding_protein_167412..167562_POSITIVE 172 89 71 37 14 NC_002967:TDE2393|3end_hypothetical_protein_2422588..2422738_POSITIVE 172 89 71 98 75 NC_002967:TDE1902|3end_hypothetical_protein_1922377..1922527_NEGATIVE 171 85 58 59 22 NC_002967:TDE1323|3end_hypothetical_protein_1360968..1361118_POSITIVE