Origin IGS: atttccccctaaataattactagaattattatatcaaaaagaggcagattttgcaattgaaaaaaagaaaaacataaagcaggaatctttaaccttattatggagttataatagaacctaaaaatgcttt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aaagcatttttaggttctattataactccataataaggttaaagattcctgctttatgtttttctttttttcaattgcaaaatctgcctctttttgatataataattctagtaattatttagggggaaat Mask Tandem Repeat Region ================================================ atttccccctaaataattactagaattattatatcaaaaagaggcagattttgcaattgaaaaaaagaaaaacataaagcaggaatctttaaccttattatggagttataatagaacctaaaaatgcttt Find is-nt database================================================ Query_seq: TDE2406:TDE2407|TDE2406:TDE2407:TldD/PmbA family protein:amidophosphoribosyltransferase:<-<-:2433604..2433733 130 atttccccctaaataattactagaattattatatcaaaaagaggcagattttgcaattgaaaaaaagaaaaacataaagcaggaatctttaaccttattatggagttataatagaacctaaaaatgcttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE2406:TDE2407|TDE2406:TDE2407:TldD/PmbA family protein:amidophosphoribosyltransferase:<-<-:2433604..2433733 130 atttccccctaaataattactagaattattatatcaaaaagaggcagattttgcaattgaaaaaaagaaaaacataaagcaggaatctttaaccttattatggagttataatagaacctaaaaatgcttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE2406:TDE2407|TDE2406:TDE2407:TldD/PmbA family protein:amidophosphoribosyltransferase:<-<-:2433604..2433733 130 atttccccctaaataattactagaattattatatcaaaaagaggcagattttgcaattgaaaaaaagaaaaacataaagcaggaatctttaaccttattatggagttataatagaacctaaaaatgcttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 atttccccctaaataattactagaattattatatcaaaaagaggcagattttgcaattgaaaaaaagaaaaacataaagcaggaatctttaaccttattatggagttataatagaacctaaaaatgcttt Predict ORF larger than 30AA ================================================ Protein_Len: 38 Strand: - Start: 12 End: 125 ........... I I V L I I I D F L P L N Q L Q F F S F C L A P I K L R I I S N Y Y F R F M ..... atttccccctaaataattactagaattattatatcaaaaagaggcagattttgcaattgaaaaaaagaaaaacataaagcaggaatctttaaccttattatggagttataatagaacctaaaaatgcttt 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: 91 Start: 28 End: 57 ...........................ATTGCAAAATCTGCCTCTTTTTGATATAAT......................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ atttccccctaaataattactagaattattatatcaaaaagaggcagattttgcaattgaaaaaaagaaaaacataaagcaggaatctttaaccttattatggagttataatagaacctaaaaatgcttt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE2406:TDE2407|TDE2406:TDE2407:TldD/PmbA family protein:amidophosphoribosyltransferase:<-<-:2433604..2433733 130 atttccccctaaataattactagaattattatatcaaaaagaggcagattttgcaattgaaaaaaagaaaaacataaagcaggaatctttaaccttattatggagttataatagaacctaaaaatgcttt Intra-Species Hit: Count: 1 Min: 1 Max: 130 Len: 130 Subject: NC_002967_TDE2406_TDE2407|TldD/PmbA family protein:amidophosphoribosyltransferase|NEGATIVE:NEGATIV E|[2433604,2433733]|130 HSP 1 e-value: 9.0E-26 bit: 117.0 Len: 59 Query Start:1 Query End:59 Subject Strand: POSITIVE Subject Start: 1 Subject End: 59 atttccccctaaataattactagaattattatatcaaaaagaggcagattttgcaattg....................................................................... atttccccctaaataattactagaattattatatcaaaaagaggcagattttgcaattg....................................................................... HSP 2 e-value: 4.0E-25 bit: 115.0 Len: 58 Query Start:73 Query End:130 Subject Strand: POSITIVE Subject Start: 73 Subject End: 130 ........................................................................cataaagcaggaatctttaaccttattatggagttataatagaacctaaaaatgcttt ........................................................................cataaagcaggaatctttaaccttattatggagttataatagaacctaaaaatgcttt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUUUCCCCCUAAAUAAUUACUAGAAUUAUUAUAUCAAAAAGAGGCAGAUUUUGCAAUUGAAAAAAAGAAAAACAUAAAGCAGGAAUCUUUAACCUUAUUAUGGAGUUAUAAUAGAACCUAAAAAUGCUUU ...........(((((((.....)))))))..........((((((..((((((........................)))))).(((.((((((......)).))))....))).........)))))) (-12.46) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAGCAUUUUUAGGUUCUAUUAUAACUCCAUAAUAAGGUUAAAGAUUCCUGCUUUAUGUUUUUCUUUUUUUCAAUUGCAAAAUCUGCCUCUUUUUGAUAUAAUAAUUCUAGUAAUUAUUUAGGGGGAAAU (((((((((((((.((.((((((......)))))))).)))))))....))))))..((((..((((...((((..(((.....)))......))))...(((((((.....))))))).))))..)))) (-16.20) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 750 120 71 211 162 NC_002967:TDE2406|5end_TldD/PmbA_family_protein_2433513..2433743_NEGATIVE 224 44 5 130 98 NC_002967:TDE0005|5end_L-threonine_aldolase,_low-specificity_6040..6270_NEGATIVE 214 120 79 215 178 NC_002967:TDE1063|5end_methionyl-tRNA_synthetase_1090507..1090737_POSITIVE 204 128 81 139 91 NC_002967:TDE2168|5end_hypothetical_protein_2201003..2201233_NEGATIVE 203 85 43 48 8 NC_002967:TDE1126|5end_TPR_domain_protein_1157545..1157775_POSITIVE 201 89 42 85 23 NC_002967:TDE2254|5end_hypothetical_protein_2291642..2291872_NEGATIVE 200 96 59 79 40 NC_002967:TDE2316|5end_hypothetical_protein_2353080..2353310_POSITIVE 197 105 68 178 141 NC_002967:TDE1194|5end_hypothetical_protein_1224973..1225203_POSITIVE 196 130 88 136 95 NC_002967:TDE2300|5end_trypsin_domain/PDZ_domain_protein_2341434..2341664_NEGATIVE 192 103 78 176 141 NC_002967:TDE2428|5end_ribosomal_protein_L33_2456292..2456522_NEGATIVE 190 103 73 39 10 NC_002967:TDE1316|5end_hypothetical_protein_1354741..1354971_POSITIVE 186 60 31 154 119 NC_002967:TDE0780|5end_ribosomal_protein_S14_812364..812594_POSITIVE 185 88 41 49 2 NC_002967:TDE2533|5end_hypothetical_protein_2558964..2559194_POSITIVE 185 59 39 28 4 NC_002967:TDE2163|5end_hypothetical_protein_2196213..2196443_NEGATIVE 183 119 80 168 132 NC_002967:TDE1649|5end_hypothetical_protein_1697437..1697667_NEGATIVE 183 70 40 228 199 NC_002967:TDE0061|5end_fic_family_protein_68944..69174_NEGATIVE 182 109 62 182 130 NC_002967:TDE1685|5end_GGDEF_domain_protein_1740315..1740545_NEGATIVE 182 118 78 196 158 NC_002967:TDE0172|5end_undecaprenyl_pyrophosphate_phosphatase_203136..203366_POSITIVE 180 87 49 65 37 NC_002967:TDE2016|5end_hypothetical_protein_2038894..2039124_NEGATIVE 180 48 2 54 13 NC_002967:TDE1335|5end_alginate_O-acetylation_protein,_putative_1370816..1371046_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 224 44 5 60 28 NC_002967:TDE0006|3end_Snf2_family_protein_6110..6260_NEGATIVE 200 96 59 98 59 NC_002967:TDE2315|3end_conserved_hypothetical_protein_TIGR00044_2353179..2353329_POSITIVE 199 51 22 73 39 NC_002967:TDE1593|3end_Fe-hydrogenase_1641209..1641359_NEGATIVE 190 103 73 51 22 NC_002967:TDE1315|3end_hypothetical_protein_1354833..1354983_POSITIVE 188 110 63 74 31 NC_002967:TDE2267|3end_HRDC_domain_protein_2303982..2304132_NEGATIVE 186 116 74 54 8 NC_002967:TDE1376|3end_hypothetical_protein_1419079..1419229_POSITIVE 186 60 31 142 107 NC_002967:TDE0779|3end_ribosomal_protein_L5_812432..812582_POSITIVE 184 115 73 119 78 NC_002967:TDE1233|3end_hypothetical_protein_1267609..1267759_POSITIVE 182 109 62 83 31 NC_002967:TDE1686|3end_3-phosphoshikimate_1-carboxyvinyltransferase_1740414..1740564_NEGATIVE 182 118 78 117 79 NC_002967:TDE0171|3end_nuclease_SbcCD,_C_subunit,_putative_203137..203287_POSITIVE 180 96 58 90 41 NC_002967:TDE1011|3end_hypothetical_protein_1041402..1041552_POSITIVE 180 54 22 46 12 NC_002967:TDE0357|3end_hypothetical_protein_400108..400258_NEGATIVE 179 80 35 89 48 NC_002967:TDE2489|3end_peptide_chain_release_factor_1_2511391..2511541_NEGATIVE 179 102 61 50 7 NC_002967:TDE1409|3end_flagellar_filament_outer_layer_protein_FlaA,_putative_1452381..1452531_POSITIVE 175 119 73 56 3 NC_002967:TDE2487|3end_acetyltransferase,_GNAT_family_2510393..2510543_POSITIVE 172 128 82 65 11 NC_002967:TDE1957|3end_hypothetical_protein_1972233..1972383_POSITIVE 172 130 94 90 54 NC_002967:TDE0641|3end_UDP-N-acetylglucosamine_1-carboxyvinyltransferase_677002..677152_NEGATIVE 171 59 41 55 33 NC_002967:TDE2396|3end_putative_inner_membrane_protein_translocase_component_YidC_2423650..2423800_NEGATIVE 171 80 34 66 20 NC_002967:TDE0085|3end_ATP-dependent_DNA_helicase,_UvrD/Rep_family_97596..97746_NEGATIVE 170 120 97 88 60 NC_002967:TDE1763|3end_hypothetical_protein_1810876..1811026_NEGATIVE