Origin IGS: aaattaacttccttacgattatactataactcgagcttttacgcaatatttttctaaaattatattctaaaattaagatatatttactaatgatgattttattcccattctaacggctggtttatattacttttttttgttatactgatcgacgaggagatatgcggtttataaaaaaccgcttgaacttttttgaggagaagaag .........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 cttcttctcctcaaaaaagttcaagcggttttttataaaccgcatatctcctcgtcgatcagtataacaaaaaaaagtaatataaaccagccgttagaatgggaataaaatcatcattagtaaatatatcttaattttagaatataattttagaaaaatattgcgtaaaagctcgagttatagtataatcgtaaggaagttaattt Mask Tandem Repeat Region ================================================ aaattaacttccttacgattatactataactcgagcttttacgcaatatttttctaaaattatattctaaaattaagatatatttactaatgatgattttattcccattctaacggctggtttatattacttttttttgttatactgatcgacgaggagatatgcggtttataaaaaaccgcttgaacttttttgaggagaagaag Find is-nt database================================================ Query_seq: TDE0183:TDE0184|TDE0183:TDE0184:ABC transporter, permease protein:ABC transporter, ATP-binding protein:<-->:218682..218887 206 aaattaacttccttacgattatactataactcgagcttttacgcaatatttttctaaaattatattctaaaattaagatatatttactaatgatgattttattcccattctaacggctggtttatattacttttttttgttatactgatcgacgaggagatatgcggtttataaaaaaccgcttgaacttttttgaggagaagaag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE0183:TDE0184|TDE0183:TDE0184:ABC transporter, permease protein:ABC transporter, ATP-binding protein:<-->:218682..218887 206 aaattaacttccttacgattatactataactcgagcttttacgcaatatttttctaaaattatattctaaaattaagatatatttactaatgatgattttattcccattctaacggctggtttatattacttttttttgttatactgatcgacgaggagatatgcggtttataaaaaaccgcttgaacttttttgaggagaagaag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE0183:TDE0184|TDE0183:TDE0184:ABC transporter, permease protein:ABC transporter, ATP-binding protein:<-->:218682..218887 206 aaattaacttccttacgattatactataactcgagcttttacgcaatatttttctaaaattatattctaaaattaagatatatttactaatgatgattttattcccattctaacggctggtttatattacttttttttgttatactgatcgacgaggagatatgcggtttataaaaaaccgcttgaacttttttgaggagaagaag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aaattaacttccttacgattatactataactcgagcttttacgcaatatttttctaaaattatattctaaaattaagatatatttactaatgatgattttattcccattctaacggctggtttatattacttttttttgttatactgatcgacgaggagatatgcggtttataaaaaaccgcttgaacttttttgaggagaagaag Predict ORF larger than 30AA ================================================ Protein_Len: 30 Strand: + Start: 117 End: 206 .................................................................................................................... M V Y I T F F C Y T D R R G D M R F I K N R L N F F E E K K Protein_Len: 32 Strand: - Start: 2 End: 97 . I L K R V I I S Y S S S K R L I K R F N Y E L I L I Y K S I I M ............................................................................................................. aaattaacttccttacgattatactataactcgagcttttacgcaatatttttctaaaattatattctaaaattaagatatatttactaatgatgattttattcccattctaacggctggtttatattacttttttttgttatactgatcgacgaggagatatgcggtttataaaaaaccgcttgaacttttttgaggagaagaag 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: 84 Start: 18 End: 47 .................ATTGCGTAAAAGCTCGAGTTATAGTATAAT............................................................................................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ aaattaacttccttacgattatactataactcgagcttttacgcaatatttttctaaaattatattctaaaattaagatatatttactaatgatgattttattcccattctaacggctggtttatattacttttttttgttatactgatcgacgaggagatatgcggtttataaaaaaccgcttgaacttttttgaggagaagaag Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE0183:TDE0184|TDE0183:TDE0184:ABC transporter, permease protein:ABC transporter, ATP-binding protein:<-->:218682..218887 206 aaattaacttccttacgattatactataactcgagcttttacgcaatatttttctaaaattatattctaaaattaagatatatttactaatgatgattttattcccattctaacggctggtttatattacttttttttgttatactgatcgacgaggagatatgcggtttataaaaaaccgcttgaacttttttgaggagaagaag Intra-Species Hit: Count: 1 Min: 1 Max: 206 Len: 206 Subject: NC_002967_TDE0183_TDE0184|ABC transporter, permease protein:ABC transporter, ATP-binding protein|NEGATIVE:POSITIVE|[218682,218887]|206 HSP 1 e-value: 6.0E-99 bit: 361.0 Len: 206 Query Start:1 Query End:206 Subject Strand: POSITIVE Subject Start: 1 Subject End: 206 aaattaacttccttacgattatactataactcgagcttttacgcaatatttttctaaaattatattctaaaattaagatatatttactaatgatgattttattcccattctaacggctggtttatattacnnnnnnnngttatactgatcgacgaggagatatgcggtttataaaaaaccgcttgaacttttttgaggagaagaag aaattaacttccttacgattatactataactcgagcttttacgcaatatttttctaaaattatattctaaaattaagatatatttactaatgatgattttattcccattctaacggctggtttatattacttttttttgttatactgatcgacgaggagatatgcggtttataaaaaaccgcttgaacttttttgaggagaagaag Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAUUAACUUCCUUACGAUUAUACUAUAACUCGAGCUUUUACGCAAUAUUUUUCUAAAAUUAUAUUCUAAAAUUAAGAUAUAUUUACUAAUGAUGAUUUUAUUCCCAUUCUAACGGCUGGUUUAUAUUACUUUUUUUUGUUAUACUGAUCGACGAGGAGAUAUGCGGUUUAUAAAAAACCGCUUGAACUUUUUUGAGGAGAAGAAG ........((((((.((((((...((((((....((......))..........(((((((((......((((........)))).......)))))))))...(((..(....)..)))..................)))))).))))))..))))))....(((((((.....))))))).....((((((....))))))... (-34.72) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CUUCUUCUCCUCAAAAAAGUUCAAGCGGUUUUUUAUAAACCGCAUAUCUCCUCGUCGAUCAGUAUAACAAAAAAAAGUAAUAUAAACCAGCCGUUAGAAUGGGAAUAAAAUCAUCAUUAGUAAAUAUAUCUUAAUUUUAGAAUAUAAUUUUAGAAAAAUAUUGCGUAAAAGCUCGAGUUAUAGUAUAAUCGUAAGGAAGUUAAUUU ........................(((((((.....))))))).....((((...((((.(.((((((........(((((((...(((..(....)..)))................................(((((((((...)))))))))..)))))))((....))....)))))).)...))))..))))......... (-30.60) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 749 50 1 141 92 NC_002967:TDE0183|5end_ABC_transporter,_permease_protein_218591..218821_NEGATIVE 327 199 156 151 104 NC_002967:TDE1326|5end_hypothetical_protein_1361661..1361891_POSITIVE 310 55 11 67 29 NC_002967:TDE0452|5end_hypothetical_protein_510143..510373_NEGATIVE 256 156 111 193 150 NC_002967:TDE0620|5end_hypothetical_protein_652478..652708_POSITIVE 250 196 153 203 158 NC_002967:TDE1081|5end_hypothetical_protein_1112639..1112869_POSITIVE 249 199 153 192 132 NC_002967:TDE2010|5end_hypothetical_protein_2031318..2031548_POSITIVE 249 183 145 222 183 NC_002967:TDE0600|5end_hypothetical_protein_638777..639007_NEGATIVE 248 200 151 189 135 NC_002967:TDE1613|5end_hypothetical_protein_1661625..1661855_POSITIVE 244 184 144 193 160 NC_002967:TDE2773|5end_hypothetical_protein_2825963..2826193_NEGATIVE 235 150 105 118 70 NC_002967:TDE1137|5end_hypothetical_protein_1166749..1166979_NEGATIVE 232 169 129 211 173 NC_002967:TDE2778|5end_PspC_domain_protein_2829604..2829834_NEGATIVE 231 160 114 175 127 NC_002967:TDE2127|5end_vapC_protein,_putative_2159763..2159993_POSITIVE 228 185 155 185 159 NC_002967:TDE2214|5end_hypothetical_protein_2253050..2253280_POSITIVE 228 170 128 123 79 NC_002967:TDE1409|5end_flagellar_filament_outer_layer_protein_FlaA,_putative_1451561..1451791_POSITIVE 227 187 141 207 153 NC_002967:TDE1241|5end_HD_domain_protein_1272269..1272499_POSITIVE 225 186 156 74 46 NC_002967:TDE1913|5end_hypothetical_protein_1929810..1930040_POSITIVE 225 199 154 208 158 NC_002967:TDE1356|5end_lipoprotein,_putative_1396669..1396899_NEGATIVE 225 40 6 134 95 NC_002967:TDE0923|5end_ABC_transporter,_ATP-binding/permease_protein_945731..945961_NEGATIVE 224 158 114 105 67 NC_002967:TDE2306|5end_hypothetical_protein_2344251..2344481_NEGATIVE 224 188 148 46 12 NC_002967:TDE2055|5end_hemin-binding_protein_B_2083769..2083999_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 310 55 11 67 29 NC_002967:TDE0453|3end_hypothetical_protein_510143..510293_NEGATIVE 256 156 111 123 80 NC_002967:TDE0619|3end_methyl-accepting_chemotaxis_protein_652488..652638_POSITIVE 238 186 156 63 30 NC_002967:TDE1012|3end_tex_protein,_putative_1043926..1044076_POSITIVE 237 165 130 33 3 NC_002967:TDE0375|3end_ABC_transporter,_ATP-binding_protein_429197..429347_NEGATIVE 236 123 96 120 88 NC_002967:TDE1718|3end_GMP_synthase_1773811..1773961_POSITIVE 231 195 154 106 79 NC_002967:TDE0456|3end_pyridoxine_biosynthesis_protein_512536..512686_NEGATIVE 230 182 145 70 26 NC_002967:TDE1038|3end_hypothetical_protein_1065405..1065555_NEGATIVE 230 160 114 144 80 NC_002967:TDE0113|3end_Tpl_protein_133609..133759_POSITIVE 229 129 83 48 3 NC_002967:TDE2750|3end_GTP-binding_protein_HflX,_truncation_2807288..2807438_POSITIVE 228 170 128 101 57 NC_002967:TDE1408|3end_flagellar_filament_outer_layer_protein_FlaA,_putative_1451619..1451769_POSITIVE 225 186 156 72 44 NC_002967:TDE1912|3end_redox-sensing_transcriptional_repressor_Rex_1929888..1930038_POSITIVE 225 40 6 114 75 NC_002967:TDE0924|3end_ABC_transporter,_ATP-binding/permease_protein_945751..945901_NEGATIVE 224 158 114 121 83 NC_002967:TDE2307|3end_seryl-tRNA_synthetase_2344235..2344385_NEGATIVE 224 182 144 52 21 NC_002967:TDE0837|3end_Na(+)-translocating_NADH-quinone_reductase,_B_subunit_856093..856243_NEGATIVE 224 185 145 49 4 NC_002967:TDE0143|3end_thiamine_ABC_transporter,_thiamine-binding_protein_165103..165253_POSITIVE 222 190 145 89 34 NC_002967:TDE2226|3end_ABC_transporter,_substrate-binding_protein,_putative_2266412..2266562_POSITIVE 221 198 151 102 52 NC_002967:TDE1496|3end_chromosome_partition_protein_SmC,_putative_1543307..1543457_POSITIVE 220 198 151 118 75 NC_002967:TDE0915|3end_hypothetical_protein_933147..933297_NEGATIVE 219 54 12 90 34 NC_002967:TDE1622|3end_hypothetical_protein_1670820..1670970_NEGATIVE 218 196 163 99 60 NC_002967:TDE0682|3end_preprotein_translocase,_YajC_subunit_720665..720815_NEGATIVE