Origin IGS: attatcttctccttaaaaattagatttttgtgctttttaagcaccttaagcagacagggggtcagcttttgaagcctgactgcttaacttctttcggaaatatccgaaagtttgtt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aacaaactttcggatatttccgaaagaagttaagcagtcaggcttcaaaagctgaccccctgtctgcttaaggtgcttaaaaagcacaaaaatctaatttttaaggagaagataat Mask Tandem Repeat Region ================================================ attatcttctccttaaaaattagatttttgtgctttttaagcaccttaagcagacagggggtcagcttttgaagcctgactgcttaacttctttcggaaatatccgaaagtttgtt Find is-nt database================================================ Query_seq: TDE2422:TDE2423|TDE2422:TDE2423:ribosomal protein L7/L12:ribosomal protein L10:<-<-:2453391..2453506 116 attatcttctccttaaaaattagatttttgtgctttttaagcaccttaagcagacagggggtcagcttttgaagcctgactgcttaacttctttcggaaatatccgaaagtttgtt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE2422:TDE2423|TDE2422:TDE2423:ribosomal protein L7/L12:ribosomal protein L10:<-<-:2453391..2453506 116 attatcttctccttaaaaattagatttttgtgctttttaagcaccttaagcagacagggggtcagcttttgaagcctgactgcttaacttctttcggaaatatccgaaagtttgtt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE2422:TDE2423|TDE2422:TDE2423:ribosomal protein L7/L12:ribosomal protein L10:<-<-:2453391..2453506 116 attatcttctccttaaaaattagatttttgtgctttttaagcaccttaagcagacagggggtcagcttttgaagcctgactgcttaacttctttcggaaatatccgaaagtttgtt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 attatcttctccttaaaaattagatttttgtgctttttaagcaccttaagcagacagggggtcagcttttgaagcctgactgcttaacttctttcggaaatatccgaaagtttgtt Predict ORF larger than 30AA ================================================ Protein_Len: 31 Strand: + Start: 24 End: 116 ....................... M F V L F K H L K Q T G G Q L L K P D C L T S F G N I R K F V attatcttctccttaaaaattagatttttgtgctttttaagcaccttaagcagacagggggtcagcttttgaagcctgactgcttaacttctttcggaaatatccgaaagtttgtt 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================================================ attatcttctccttaaaaattagatttttgtgctttttaagcaccttaagcagacagggggtcagcttttgaagcctgactgcttaacttctttcggaaatatccgaaagtttgtt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE2422:TDE2423|TDE2422:TDE2423:ribosomal protein L7/L12:ribosomal protein L10:<-<-:2453391..2453506 116 attatcttctccttaaaaattagatttttgtgctttttaagcaccttaagcagacagggggtcagcttttgaagcctgactgcttaacttctttcggaaatatccgaaagtttgtt Intra-Species Hit: Count: 1 Min: 1 Max: 116 Len: 116 Subject: NC_002967_TDE2422_TDE2423|ribosomal protein L7/L12:ribosomal protein L10|NEGATIVE:NEGATIVE|[2453391,2453506]|116 HSP 1 e-value: 8.0E-60 bit: 230.0 Len: 116 Query Start:1 Query End:116 Subject Strand: POSITIVE Subject Start: 1 Subject End: 116 attatcttctccttaaaaattagatttttgtgctttttaagcaccttaagcagacagggggtcagcttttgaagcctgactgcttaacttctttcggaaatatccgaaagtttgtt attatcttctccttaaaaattagatttttgtgctttttaagcaccttaagcagacagggggtcagcttttgaagcctgactgcttaacttctttcggaaatatccgaaagtttgtt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUUAUCUUCUCCUUAAAAAUUAGAUUUUUGUGCUUUUUAAGCACCUUAAGCAGACAGGGGGUCAGCUUUUGAAGCCUGACUGCUUAACUUCUUUCGGAAAUAUCCGAAAGUUUGUU .............................(((((.....))))).((((((((.((((...((((...))))..)))).))))))))...((((((((....))))))))...... (-31.60) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AACAAACUUUCGGAUAUUUCCGAAAGAAGUUAAGCAGUCAGGCUUCAAAAGCUGACCCCCUGUCUGCUUAAGGUGCUUAAAAAGCACAAAAAUCUAAUUUUUAAGGAGAAGAUAAU ......((((((((....))))))))...((((((((.((((..(((.....)))...)))).)))))))).(((((.....)))))....((((..(((....)))..))))... (-37.00) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 991 90 41 181 132 NC_002967:TDE2422|5end_ribosomal_protein_L7/L12_2453300..2453530_NEGATIVE 353 97 59 48 8 NC_002967:TDE2268|5end_hypothetical_protein_2304959..2305189_NEGATIVE 332 95 51 67 22 NC_002967:TDE1892|5end_hypothetical_protein_1912065..1912295_POSITIVE 311 97 56 202 154 NC_002967:TDE2593|5end_sigma-54-binding_protein_2627747..2627977_POSITIVE 305 94 53 187 152 NC_002967:TDE1470|5end_hypothetical_protein_1518026..1518256_NEGATIVE 303 79 32 212 145 NC_002967:TDE1214|5end_flagellar_basal_body_protein_1246307..1246537_POSITIVE 291 90 41 229 165 NC_002967:TDE0783|5end_ribosomal_protein_L18_813520..813750_POSITIVE 289 90 41 141 103 NC_002967:TDE1781|5end_hypothetical_protein_1823260..1823490_NEGATIVE 283 96 55 143 109 NC_002967:TDE1803|5end_hypothetical_protein_1839270..1839500_NEGATIVE 282 65 23 118 73 NC_002967:TDE1325|5end_hypothetical_protein_1361721..1361951_NEGATIVE 282 65 23 229 184 NC_002967:TDE1324|5end_hypothetical_protein_1361610..1361840_NEGATIVE 281 90 41 201 159 NC_002967:TDE1056|5end_hypothetical_protein_1085210..1085440_POSITIVE 279 110 64 40 1 NC_002967:TDE1248|5end_hypothetical_protein_1282596..1282826_POSITIVE 277 97 58 54 2 NC_002967:TDE0973|5end_DNA_repair_protein_RadC_998617..998847_NEGATIVE 274 100 58 228 177 NC_002967:TDE2393|5end_hypothetical_protein_2422398..2422628_POSITIVE 274 86 50 51 12 NC_002967:TDE0135|5end_pyridine_nucleotide-disulphide_oxidoreductase_family_protein_154927..155157_POSITIVE 273 85 41 190 119 NC_002967:TDE1199|5end_cell_division_protein_FtsL,_putative_1231341..1231571_POSITIVE 272 79 39 222 180 NC_002967:TDE1261|5end_choline/carnitine/betaine_transporter_family_protein_1295593..1295823_POSITIVE 272 65 23 158 113 NC_002967:TDE0466|5end_hypothetical_protein_518854..519084_NEGATIVE 269 97 56 52 15 NC_002967:TDE0872|5end_recA_protein_894841..895071_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 354 105 61 147 90 NC_002967:TDE2527|3end_hypothetical_protein_2555449..2555599_NEGATIVE 353 97 59 76 36 NC_002967:TDE2269|3end_hypothetical_protein_2304931..2305081_NEGATIVE 311 97 56 107 59 NC_002967:TDE2592|3end_DbpA_RNA_binding_domain_protein_2627732..2627882_POSITIVE 305 94 53 68 33 NC_002967:TDE1471|3end_hypothetical_protein_1518145..1518295_NEGATIVE 304 78 38 51 9 NC_002967:TDE2075|3end_GGDEF_domain/EAL_domain_protein_2101504..2101654_NEGATIVE 303 84 41 147 102 NC_002967:TDE1892|3end_hypothetical_protein_1912237..1912387_POSITIVE 292 84 41 48 7 NC_002967:TDE2763|3end_flagellar_motor_switch_protein_2817737..2817887_NEGATIVE 289 90 41 97 59 NC_002967:TDE1782|3end_hypothetical_protein_1823304..1823454_NEGATIVE 288 71 32 146 106 NC_002967:TDE1624|3end_glycine_dehydrogenase_subunit_2_1672071..1672221_NEGATIVE 287 87 49 82 34 NC_002967:TDE2641|3end_Fic_family_protein_2682068..2682218_POSITIVE 282 65 23 50 5 NC_002967:TDE1327|3end_hypothetical_protein_1361789..1361939_NEGATIVE 279 98 56 61 18 NC_002967:TDE1803|3end_hypothetical_protein_1838395..1838545_NEGATIVE 276 83 44 43 5 NC_002967:TDE2714|3end_hypothetical_protein_2770627..2770777_NEGATIVE 276 90 48 46 2 NC_002967:TDE1093|3end_hypothetical_protein_1128158..1128308_POSITIVE 275 85 42 73 30 NC_002967:TDE2100|3end_hypothetical_protein_2125572..2125722_POSITIVE 274 85 43 84 39 NC_002967:TDE0238|3end_thioredoxin,_selenocysteine-containing_271783..271933_POSITIVE 274 86 50 54 15 NC_002967:TDE0134|3end_oxidoreductase,_FAD-dependent_155010..155160_POSITIVE 268 98 58 40 1 NC_002967:TDE2312|3end_hypothetical_protein_2349049..2349199_POSITIVE 265 82 41 124 75 NC_002967:TDE0977|3end_hypothetical_protein_1001640..1001790_POSITIVE 262 84 44 58 24 NC_002967:TDE2068|3end_antigen,_putative_2096595..2096745_POSITIVE