Origin IGS: gtgttacctctcattgttgatattagtatgaaagtacataaatgtcaagtctaaaatttgattgaacttgatgattgaacttgataattgacaatgaatgatttatattgtagaatacgaaatgtgaaaaatctatgtaaaacttgtggataagtaggg .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 ccctacttatccacaagttttacatagatttttcacatttcgtattctacaatataaatcattcattgtcaattatcaagttcaatcatcaagttcaatcaaattttagacttgacatttatgtactttcatactaatatcaacaatgagaggtaacac Mask Tandem Repeat Region ================================================ gtgttacctctcattgttgatattagtatgaaagtacataaatgtcaagtctaaaattnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnncaatgaatgatttatattgtagaatacgaaatgtgaaaaatctatgtaaaacttgtggataagtaggg Find is-nt database================================================ Query_seq: TDE2191:TDE2192|TDE2191:TDE2192:pyrimidine-nucleoside phosphorylase:threonine synthase:<-->:2227742..2227900 159 gtgttacctctcattgttgatattagtatgaaagtacataaatgtcaagtctaaaatttgattgaacttgatgattgaacttgataattgacaatgaatgatttatattgtagaatacgaaatgtgaaaaatctatgtaaaacttgtggataagtaggg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE2191:TDE2192|TDE2191:TDE2192:pyrimidine-nucleoside phosphorylase:threonine synthase:<-->:2227742..2227900 159 gtgttacctctcattgttgatattagtatgaaagtacataaatgtcaagtctaaaatttgattgaacttgatgattgaacttgataattgacaatgaatgatttatattgtagaatacgaaatgtgaaaaatctatgtaaaacttgtggataagtaggg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE2191:TDE2192|TDE2191:TDE2192:pyrimidine-nucleoside phosphorylase:threonine synthase:<-->:2227742..2227900 159 gtgttacctctcattgttgatattagtatgaaagtacataaatgtcaagtctaaaatttgattgaacttgatgattgaacttgataattgacaatgaatgatttatattgtagaatacgaaatgtgaaaaatctatgtaaaacttgtggataagtaggg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gtgttacctctcattgttgatattagtatgaaagtacataaatgtcaagtctaaaatttgattgaacttgatgattgaacttgataattgacaatgaatgatttatattgtagaatacgaaatgtgaaaaatctatgtaaaacttgtggataagtaggg Predict ORF larger than 30AA ================================================ Protein_Len: 42 Strand: - Start: 26 End: 151 ......................... Y S L V Y I D L R F N S Q V Q H N F K I I S L S H N I N Y F V F H S F D I Y F K H M ........ Protein_Len: 32 Strand: - Start: 7 End: 102 ...... R E N N I N T H F Y M F T L D L I Q N F K I I S S S L Q C H I M ......................................................... gtgttacctctcattgttgatattagtatgaaagtacataaatgtcaagtctaaaatttgattgaacttgatgattgaacttgataattgacaatgaatgatttatattgtagaatacgaaatgtgaaaaatctatgtaaaacttgtggataagtaggg 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: 90 Start: 87 End: 116 ......................................................................................ATTGACAATGAATGATTTATATTGTAGAAT........................................... PromScan Matrix: RpoD-17 Strand: - Score: 88 Start: 20 End: 49 ...................CTTGACATTTATGTACTTTCATACTAATAT.............................................................................................................. PromScan Matrix: RpoD-17 Strand: + Score: 85 Start: 80 End: 109 ...............................................................................CTTGATAATTGACAATGAATGATTTATATT.................................................. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ gtgttacctctcattgttgatattagtatgaaagtacataaatgtcaagtctaaaatttgattgaacttgatgattgaacttgataattgacaatgaatgatttatattgtagaatacgaaatgtgaaaaatctatgtaaaacttgtggataagtaggg Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE2191:TDE2192|TDE2191:TDE2192:pyrimidine-nucleoside phosphorylase:threonine synthase:<-->:2227742..2227900 159 gtgttacctctcattgttgatattagtatgaaagtacataaatgtcaagtctaaaatttgattgaacttgatgattgaacttgataattgacaatgaatgatttatattgtagaatacgaaatgtgaaaaatctatgtaaaacttgtggataagtaggg Intra-Species Hit: Count: 1 Min: 1 Max: 159 Len: 159 Subject: NC_002967_TDE2191_TDE2192|pyrimidine-nucleoside phosphorylase:threonine synthase|NEGATIVE:POSITIVE|[2227742,2227900]|159 HSP 1 e-value: 2.0E-85 bit: 315.0 Len: 159 Query Start:1 Query End:159 Subject Strand: POSITIVE Subject Start: 1 Subject End: 159 gtgttacctctcattgttgatattagtatgaaagtacataaatgtcaagtctaaaatttgattgaacttgatgattgaacttgataattgacaatgaatgatttatattgtagaatacgaaatgtgaaaaatctatgtaaaacttgtggataagtaggg gtgttacctctcattgttgatattagtatgaaagtacataaatgtcaagtctaaaatttgattgaacttgatgattgaacttgataattgacaatgaatgatttatattgtagaatacgaaatgtgaaaaatctatgtaaaacttgtggataagtaggg Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GUGUUACCUCUCAUUGUUGAUAUUAGUAUGAAAGUACAUAAAUGUCAAGUCUAAAAUUUGAUUGAACUUGAUGAUUGAACUUGAUAAUUGACAAUGAAUGAUUUAUAUUGUAGAAUACGAAAUGUGAAAAAUCUAUGUAAAACUUGUGGAUAAGUAGGG ......(((.(((((((..((....((((....)))).....((((((((.(((...(..(......)..)...))).))))))))))..)))))))....((((((((...........))))))))..(((((((.......)))))))....))). (-30.30) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CCCUACUUAUCCACAAGUUUUACAUAGAUUUUUCACAUUUCGUAUUCUACAAUAUAAAUCAUUCAUUGUCAAUUAUCAAGUUCAAUCAUCAAGUUCAAUCAAAUUUUAGACUUGACAUUUAUGUACUUUCAUACUAAUAUCAACAAUGAGAGGUAACAC ................(((.(((((((((.......((((.(((....(((((...........)))))....))).)))).......((((((..((.......))..)))))).)))))))))(((((((.............)))))))..))).. (-17.32) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 761 50 1 141 92 NC_002967:TDE2191|5end_pyrimidine-nucleoside_phosphorylase_2227651..2227881_NEGATIVE 235 89 43 168 121 NC_002967:TDE2307|5end_seryl-tRNA_synthetase_2345503..2345733_NEGATIVE 226 29 1 34 9 NC_002967:TDE0357|5end_hypothetical_protein_400743..400973_NEGATIVE 215 100 61 70 35 NC_002967:TDE0129|5end_PyrBI_protein_150299..150529_NEGATIVE 209 112 72 111 72 NC_002967:TDE1726|5end_polyA_polymerase_family_protein_1779546..1779776_POSITIVE 200 47 6 142 95 NC_002967:TDE1270|5end_hypothetical_protein_1305011..1305241_NEGATIVE 195 34 4 129 94 NC_002967:TDE0435|5end_ATP-dependent_DNA_helicase,_RecQ_family_491261..491491_NEGATIVE 185 48 10 119 87 NC_002967:TDE2122|5end_DHH_superfamily_protein_2155910..2156140_NEGATIVE 180 50 1 134 93 NC_002967:TDE0909|5end_type_II_DNA_modification_methyltransferase_M.TdeIII_927166..927396_POSITIVE 179 113 75 136 93 NC_002967:TDE1940|5end_hypothetical_protein_1956508..1956738_NEGATIVE 179 70 37 112 80 NC_002967:TDE1799|5end_hypothetical_protein_1837264..1837494_NEGATIVE 178 46 9 189 153 NC_002967:TDE0514|5end_hypothetical_protein_562743..562973_NEGATIVE 178 77 43 231 191 NC_002967:TDE0356|5end_hypothetical_protein_400088..400318_NEGATIVE 177 70 23 202 148 NC_002967:TDE2715|5end_hypothetical_protein_2772668..2772898_POSITIVE 177 148 118 228 187 NC_002967:TDE1024|5end_conserved_hypothetical_protein_TIGR01319_1055575..1055805_POSITIVE 177 79 31 97 46 NC_002967:TDE0877|5end_hypothetical_protein_898589..898819_POSITIVE 174 48 1 134 94 NC_002967:TDE0430|5end_TPR_domain_protein_486455..486685_NEGATIVE 173 89 56 137 106 NC_002967:TDE0816|5end_peptidase,_M20/M25/M40_family_838564..838794_NEGATIVE 173 47 8 168 133 NC_002967:TDE0631|5end_sigma_factor_regulatory_protein,_putative_665295..665525_POSITIVE 171 37 5 125 96 NC_002967:TDE2432|5end_treponemal_membrane_protein,_putative_2461414..2461644_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 209 71 33 79 30 NC_002967:TDE0670|3end_ATP-dependent_protease_La_710393..710543_POSITIVE 205 49 7 125 76 NC_002967:TDE0828|3end_glucose-inhibited_division_protein_A_848283..848433_NEGATIVE 203 149 112 64 24 NC_002967:TDE0708|3end_nitroreductase_family_protein_744495..744645_POSITIVE 200 47 6 124 77 NC_002967:TDE1271|3end_oligopeptide/dipeptide_ABC_transporter,_ATP-binding_protein_1305029..1305179_NEGATIVE 196 48 1 78 26 NC_002967:TDE2517|3end_DNA_repair_protein_RadA_2542454..2542604_NEGATIVE 196 47 1 74 24 NC_002967:TDE0745|3end_glycine_reductase_complex_selenoprotein_GrdA_780840..780990_POSITIVE 195 34 4 66 31 NC_002967:TDE0436|3end_Recombination_protein_O_491324..491474_NEGATIVE 190 79 34 114 64 NC_002967:TDE2210|3end_hypothetical_protein_2249394..2249544_NEGATIVE 185 50 3 71 15 NC_002967:TDE2750|3end_GTP-binding_protein_HflX,_truncation_2807288..2807438_POSITIVE 184 150 103 62 15 NC_002967:TDE0709|3end_bifunctional_methionine_sulfoxide_reductase_A/B_protein_744481..744631_NEGATIVE 179 113 75 139 96 NC_002967:TDE1941|3end_hypothetical_protein_1956505..1956655_NEGATIVE 177 52 24 70 42 NC_002967:TDE1356|3end_lipoprotein,_putative_1395674..1395824_NEGATIVE 174 30 9 145 126 NC_002967:TDE0515|3end_hypothetical_protein_562770..562920_NEGATIVE 174 48 1 119 79 NC_002967:TDE0431|3end_LysM_domain_protein_486470..486620_NEGATIVE 172 126 89 114 77 NC_002967:TDE2494|3end_hypothetical_protein_2518714..2518864_POSITIVE 166 150 110 65 28 NC_002967:TDE0322|3end_regulatory_protein,_P-II_family_355106..355256_NEGATIVE 164 52 12 47 14 NC_002967:TDE2671|3end_hypothetical_protein_2708143..2708293_NEGATIVE 162 79 31 124 63 NC_002967:TDE1174|3end_hypothetical_protein_1202651..1202801_NEGATIVE 161 73 32 84 47 NC_002967:TDE2072|3end_hypothetical_protein_2099195..2099345_POSITIVE 161 132 95 75 31 NC_002967:TDE1280|3end_hypothetical_protein_1315750..1315900_NEGATIVE