Origin IGS: atacaagctcctaaaaaaatatccgcccaattccgggagtcggaaagggctttttgacatagtctaatttttaatgtaagcaaaaactctaacgcaatgaagctttaggcagctgcttacattaaaattc .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 gaattttaatgtaagcagctgcctaaagcttcattgcgttagagtttttgcttacattaaaaattagactatgtcaaaaagccctttccgactcccggaattgggcggatatttttttaggagcttgtat Mask Tandem Repeat Region ================================================ atacaagctcctaaaaaaatatccgcccaattccgggagtcggaaagggctttttgacatagtctaatttttaatgtaagcaaaaactctaacgcaatgaagctttaggcagctgcttacattaaaattc Find is-nt database================================================ Query_seq: TDE1675:TDE1676|TDE1675:TDE1676:ribosomal protein L9:ribosomal protein S18:<-<-:1729333..1729462 130 atacaagctcctaaaaaaatatccgcccaattccgggagtcggaaagggctttttgacatagtctaatttttaatgtaagcaaaaactctaacgcaatgaagctttaggcagctgcttacattaaaattc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE1675:TDE1676|TDE1675:TDE1676:ribosomal protein L9:ribosomal protein S18:<-<-:1729333..1729462 130 atacaagctcctaaaaaaatatccgcccaattccgggagtcggaaagggctttttgacatagtctaatttttaatgtaagcaaaaactctaacgcaatgaagctttaggcagctgcttacattaaaattc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE1675:TDE1676|TDE1675:TDE1676:ribosomal protein L9:ribosomal protein S18:<-<-:1729333..1729462 130 atacaagctcctaaaaaaatatccgcccaattccgggagtcggaaagggctttttgacatagtctaatttttaatgtaagcaaaaactctaacgcaatgaagctttaggcagctgcttacattaaaattc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 atacaagctcctaaaaaaatatccgcccaattccgggagtcggaaagggctttttgacatagtctaatttttaatgtaagcaaaaactctaacgcaatgaagctttaggcagctgcttacattaaaattc Predict ORF larger than 30AA ================================================ Protein_Len: 32 Strand: - Start: 3 End: 98 .. C A G L F I D A W N R S D S L A K Q C L R I K L T L L F E L A M ................................ atacaagctcctaaaaaaatatccgcccaattccgggagtcggaaagggctttttgacatagtctaatttttaatgtaagcaaaaactctaacgcaatgaagctttaggcagctgcttacattaaaattc 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================================================ atacaagctcctaaaaaaatatccgcccaattccgggagtcggaaagggctttttgacatagtctaatttttaatgtaagcaaaaactctaacgcaatgaagctttaggcagctgcttacattaaaattc Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE1675:TDE1676|TDE1675:TDE1676:ribosomal protein L9:ribosomal protein S18:<-<-:1729333..1729462 130 atacaagctcctaaaaaaatatccgcccaattccgggagtcggaaagggctttttgacatagtctaatttttaatgtaagcaaaaactctaacgcaatgaagctttaggcagctgcttacattaaaattc Intra-Species Hit: Count: 1 Min: 20 Max: 130 Len: 111 Subject: NC_002967_TDE1675_TDE1676|ribosomal protein L9:ribosomal protein S18|NEGATIVE:NEGATIVE|[1729333,1729462]|130 HSP 1 e-value: 9.0E-57 bit: 220.0 Len: 111 Query Start:20 Query End:130 Subject Strand: POSITIVE Subject Start: 20 Subject End: 130 ...................tatccgcccaattccgggagtcggaaagggctttttgacatagtctaatttttaatgtaagcaaaaactctaacgcaatgaagctttaggcagctgcttacattaaaattc ...................tatccgcccaattccgggagtcggaaagggctttttgacatagtctaatttttaatgtaagcaaaaactctaacgcaatgaagctttaggcagctgcttacattaaaattc Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAUCCGCCCAAUUCCGGGAGUCGGAAAGGGCUUUUUGACAUAGUCUAAUUUUUAAUGUAAGCAAAAACUCUAACGCAAUGAAGCUUUAGGCAGCUGCUUACAUUAAAAUUC .....((((..(((((.....))))).)))).....(((...)))....((((((((((((((.....(((((.((......)).)))))....))))))))))))))... (-33.30) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAAUUUUAAUGUAAGCAGCUGCCUAAAGCUUCAUUGCGUUAGAGUUUUUGCUUACAUUAAAAAUUAGACUAUGUCAAAAAGCCCUUUCCGACUCCCGGAAUUGGGCGGAUA ...(((((((((((((((..((((((.((......)).)))).))..))))))))))))))).........((((.....((((.(((((.....)))))..)))).)))) (-40.60) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 946 50 1 160 111 NC_002967:TDE1675|5end_ribosomal_protein_L9_1729242..1729472_NEGATIVE 334 40 4 59 18 NC_002967:TDE0046|5end_formiminotransferase-cyclodeaminase_family_protein_55849..56079_NEGATIVE 320 47 4 75 31 NC_002967:TDE2535|5end_pyruvate_kinase_2560892..2561122_POSITIVE 311 43 3 93 56 NC_002967:TDE2035|5end_glucose-1-phosphate_adenylyltransferase_2062801..2063031_POSITIVE 306 45 9 199 152 NC_002967:TDE1540|5end_hypothetical_protein_1584422..1584652_POSITIVE 283 44 3 72 38 NC_002967:TDE2119|5end_glycine_reductase_complex_selenoprotein_GrdB2_2152693..2152923_NEGATIVE 275 45 4 157 108 NC_002967:TDE2751|5end_hypothetical_protein_2807570..2807800_POSITIVE 269 45 3 148 100 NC_002967:TDE0143|5end_thiamine_ABC_transporter,_thiamine-binding_protein_164013..164243_POSITIVE 266 46 4 195 152 NC_002967:TDE0043|5end_TPR_domain_protein_49688..49918_POSITIVE 265 42 1 154 111 NC_002967:TDE1047|5end_30S_ribosomal_protein_S12_1074097..1074327_POSITIVE 264 45 2 174 127 NC_002967:TDE0987|5end_oligopeptide/dipeptide_ABC_transporter,_ATP-binding_protein_1014041..1014271_POSITIVE 263 49 4 117 70 NC_002967:TDE1137|5end_hypothetical_protein_1166749..1166979_NEGATIVE 262 45 6 37 1 NC_002967:TDE0861|5end_tyrosyl-tRNA_synthetase_883098..883328_NEGATIVE 261 36 4 38 17 NC_002967:TDE0573|5end_hypothetical_protein_604681..604911_POSITIVE 255 41 3 49 14 NC_002967:TDE2654|5end_macrolide_efflux_protein,_putative_2691675..2691905_POSITIVE 254 32 3 231 198 NC_002967:TDE2431|5end_bacteriocin_ABC_transporter,_ATP-binding/permease_protein,_putative_2461449..2461679_NEGATIVE 254 45 5 46 10 NC_002967:TDE1737|5end_hypothetical_protein_1790133..1790363_POSITIVE 254 99 59 41 1 NC_002967:TDE1512|5end_hypothetical_protein_1559203..1559433_POSITIVE 253 37 4 57 21 NC_002967:TDE2571|5end_hypothetical_protein_2598152..2598382_NEGATIVE 253 47 5 191 150 NC_002967:TDE2158|5end_ABC_transporter,_ATP-binding_protein_2191664..2191894_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 298 46 3 63 14 NC_002967:TDE2028|3end_OmpA_family_protein_2057019..2057169_POSITIVE 289 45 1 148 100 NC_002967:TDE0930|3end_hypothetical_protein_952843..952993_NEGATIVE 283 44 3 60 26 NC_002967:TDE2120|3end_glycine_reductase_complex_proprotein_GrdE2_2152705..2152855_NEGATIVE 282 36 4 50 12 NC_002967:TDE1928|3end_hypothetical_protein_1946583..1946733_POSITIVE 282 33 5 84 47 NC_002967:TDE0793|3end_hypothetical_protein_819205..819355_POSITIVE 269 45 3 120 72 NC_002967:TDE0141|3end_hypothetical_protein_164065..164215_POSITIVE 265 42 1 53 10 NC_002967:TDE1046|3end_hypothetical_protein_1074076..1074226_POSITIVE 264 39 6 141 115 NC_002967:TDE2504|3end_O-sialoglycoprotein_endopeptidase_2530097..2530247_POSITIVE 262 34 6 78 56 NC_002967:TDE0603|3end_hypothetical_protein_641885..642035_POSITIVE 261 45 4 108 44 NC_002967:TDE0824|3end_lipoprotein,_putative_845226..845376_NEGATIVE 260 46 8 121 90 NC_002967:TDE1614|3end_hypothetical_protein_1662295..1662445_NEGATIVE 260 23 3 134 113 NC_002967:TDE1054|3end_methyl-accepting_chemotaxis_protein_1082998..1083148_POSITIVE 255 41 3 38 3 NC_002967:TDE2653|3end_hypothetical_protein_2691744..2691894_POSITIVE 253 37 4 64 28 NC_002967:TDE2572|3end_CDP-diacylglycerol--glycerol-3-phosphate_3-phosphatidyltransferase_2598145..2598295_NEGATIVE 251 55 15 46 16 NC_002967:TDE2301|3end_FlhB_domain_protein_2341852..2342002_POSITIVE 251 33 3 39 13 NC_002967:TDE0769|3end_ribosomal_protein_L23_807998..808148_POSITIVE 250 47 6 71 33 NC_002967:TDE2569|3end_3-deoxy-7-phosphoheptulonate_synthase_2597458..2597608_POSITIVE 250 43 5 81 44 NC_002967:TDE2205|3end_enoate_reductase,_putative_2242575..2242725_NEGATIVE 247 46 3 81 38 NC_002967:TDE0635|3end_hypothetical_protein_670578..670728_POSITIVE 247 45 15 89 55 NC_002967:TDE0478|3end_cyclic_nucleotide_binding_domain_protein_535013..535163_POSITIVE