Origin IGS: agaatctccgtgatgttactctggtatgtaaataaaatatgagggaatactaacattacgataggtgaaagtcaaggagaggggaaatttcttctttgaaatggaggtggttaataggatatggaaaataatttatcttaaatacggcttcatctgacttggcaatttatcgataaaaggttataatcttaaatctctaaggttttatatacagaacaaattatgtttatgaaccttaaaaaaactatagtaggcagaaaaagcatgtagaggccgatatggtaccccattctttaaaatggagcatttttgccgctgcaccgctttttttgttcaaataggaggttaagt .........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.........1.........2.........3.........4.........5.........6.........7.........8.........9 acttaacctcctatttgaacaaaaaaagcggtgcagcggcaaaaatgctccattttaaagaatggggtaccatatcggcctctacatgctttttctgcctactatagtttttttaaggttcataaacataatttgttctgtatataaaaccttagagatttaagattataaccttttatcgataaattgccaagtcagatgaagccgtatttaagataaattattttccatatcctattaaccacctccatttcaaagaagaaatttcccctctccttgactttcacctatcgtaatgttagtattccctcatattttatttacataccagagtaacatcacggagattct Mask Tandem Repeat Region ================================================ agaatctccgtgatgttactctggtatgtaaataaaatatgagggaatactaacattacgataggtgaaagtcaaggagaggggaaatttcttctttgaaatggaggtggttaataggatatggaaaataatttatcttaaatacggcttcatctgacttggcaatttatcgataaaaggttataatcttaaatctctaaggttttatatacagaacaaattatgtttatgaaccttaaaaaaactatagtaggcagaaaaagcatgtagaggccgatatggtaccccattctttaaaatggagcatttttgccgctgcaccgctttttttgttcaaataggaggttaagt Find is-nt database================================================ Query_seq: TDE0751:TDE0752|TDE0751:TDE0752:magnesium chelatase, subunit D/I family:hypothetical protein:<-->:791142..791492 351 agaatctccgtgatgttactctggtatgtaaataaaatatgagggaatactaacattacgataggtgaaagtcaaggagaggggaaatttcttctttgaaatggaggtggttaataggatatggaaaataatttatcttaaatacggcttcatctgacttggcaatttatcgataaaaggttataatcttaaatctctaaggttttatatacagaacaaattatgtttatgaaccttaaaaaaactatagtaggcagaaaaagcatgtagaggccgatatggtaccccattctttaaaatggagcatttttgccgctgcaccgctttttttgttcaaataggaggttaagt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE0751:TDE0752|TDE0751:TDE0752:magnesium chelatase, subunit D/I family:hypothetical protein:<-->:791142..791492 351 agaatctccgtgatgttactctggtatgtaaataaaatatgagggaatactaacattacgataggtgaaagtcaaggagaggggaaatttcttctttgaaatggaggtggttaataggatatggaaaataatttatcttaaatacggcttcatctgacttggcaatttatcgataaaaggttataatcttaaatctctaaggttttatatacagaacaaattatgtttatgaaccttaaaaaaactatagtaggcagaaaaagcatgtagaggccgatatggtaccccattctttaaaatggagcatttttgccgctgcaccgctttttttgttcaaataggaggttaagt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE0751:TDE0752|TDE0751:TDE0752:magnesium chelatase, subunit D/I family:hypothetical protein:<-->:791142..791492 351 agaatctccgtgatgttactctggtatgtaaataaaatatgagggaatactaacattacgataggtgaaagtcaaggagaggggaaatttcttctttgaaatggaggtggttaataggatatggaaaataatttatcttaaatacggcttcatctgacttggcaatttatcgataaaaggttataatcttaaatctctaaggttttatatacagaacaaattatgtttatgaaccttaaaaaaactatagtaggcagaaaaagcatgtagaggccgatatggtaccccattctttaaaatggagcatttttgccgctgcaccgctttttttgttcaaataggaggttaagt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 agaatctccgtgatgttactctggtatgtaaataaaatatgagggaatactaacattacgataggtgaaagtcaaggagaggggaaatttcttctttgaaatggaggtggttaataggatatggaaaataatttatcttaaatacggcttcatctgacttggcaatttatcgataaaaggttataatcttaaatctctaaggttttatatacagaacaaattatgtttatgaaccttaaaaaaactatagtaggcagaaaaagcatgtagaggccgatatggtaccccattctttaaaatggagcatttttgccgctgcaccgctttttttgttcaaataggaggttaagt Predict ORF larger than 30AA ================================================ Protein_Len: 30 Strand: + Start: 65 End: 154 ................................................................ M K V K E R G N F F F E M E V V N R I W K I I Y L K Y G F I ..................................................................................................................................................................................................... Protein_Len: 30 Strand: - Start: 248 End: 337 ....................................................................................................................................................................................................................................................... L L C F F C T S A S I T G W E K F H L M K A A A G S K K N M .............. Protein_Len: 38 Strand: - Start: 208 End: 321 ............................................................................................................................................................................................................... I C F L N H K H V K F F S Y Y A S F A H L P R Y P V G N K L I S C K Q R Q M .............................. Protein_Len: 33 Strand: - Start: 192 End: 290 ............................................................................................................................................................................................... I E L T K Y V S C I I N I F R L F V I T P L F L M Y L G I H Y G M ............................................................. Protein_Len: 36 Strand: - Start: 59 End: 166 .......................................................... S L H F D L L P S I E E K F H L H N I P Y P F Y N I K F V A E D S K A M ......................................................................................................................................................................................... Protein_Len: 38 Strand: - Start: 19 End: 132 .................. E P I Y I F Y S P I S V N R Y T F T L S L P F K K K S I S T T L L I H F I M ........................................................................................................................................................................................................................... agaatctccgtgatgttactctggtatgtaaataaaatatgagggaatactaacattacgataggtgaaagtcaaggagaggggaaatttcttctttgaaatggaggtggttaataggatatggaaaataatttatcttaaatacggcttcatctgacttggcaatttatcgataaaaggttataatcttaaatctctaaggttttatatacagaacaaattatgtttatgaaccttaaaaaaactatagtaggcagaaaaagcatgtagaggccgatatggtaccccattctttaaaatggagcatttttgccgctgcaccgctttttttgttcaaataggaggttaagt 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: 158 End: 187 .............................................................................................................................................................CTTGGCAATTTATCGATAAAAGGTTATAAT.................................................................................................................................................................... PromScan Matrix: RpoD-17 Strand: - Score: 84 Start: 47 End: 76 ..............................................CTTGACTTTCACCTATCGTAATGTTAGTAT................................................................................................................................................................................................................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ agaatctccgtgatgttactctggtatgtaaataaaatatgagggaatactaacattacgataggtgaaagtcaaggagaggggaaatttcttctttgaaatggaggtggttaataggatatggaaaataatttatcttaaatacggcttcatctgacttggcaatttatcgataaaaggttataatcttaaatctctaaggttttatatacagaacaaattatgtttatgaaccttaaaaaaactatagtaggcagaaaaagcatgtagaggccgatatggtaccccattctttaaaatggagcatttttgccgctgcaccgctttttttgttcaaataggaggttaagt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE0751:TDE0752|TDE0751:TDE0752:magnesium chelatase, subunit D/I family:hypothetical protein:<-->:791142..791492 351 agaatctccgtgatgttactctggtatgtaaataaaatatgagggaatactaacattacgataggtgaaagtcaaggagaggggaaatttcttctttgaaatggaggtggttaataggatatggaaaataatttatcttaaatacggcttcatctgacttggcaatttatcgataaaaggttataatcttaaatctctaaggttttatatacagaacaaattatgtttatgaaccttaaaaaaactatagtaggcagaaaaagcatgtagaggccgatatggtaccccattctttaaaatggagcatttttgccgctgcaccgctttttttgttcaaataggaggttaagt Intra-Species Hit: Count: 1 Min: 1 Max: 351 Len: 351 Subject: NC_002967_TDE0751_TDE0752|magnesium chelatase, subunit D/I family:hypothetical protein|NEGATIVE:POSITIVE|[791142,791492]|351 HSP 1 e-value: 1.0E-174 bit: 613.0 Len: 351 Query Start:1 Query End:351 Subject Strand: POSITIVE Subject Start: 1 Subject End: 351 agaatctccgtgatgttactctggtatgtaaataaaatatgagggaatactaacattacgataggtgaaagtcaaggagaggggaaatttcttctttgaaatggaggtggttaataggatatggaaaataatttatcttaaatacggcttcatctgacttggcaatttatcgataaaaggttataatcttaaatctctaaggttttatatacagaacaaattatgtttatgaaccttnnnnnnnctatagtaggcagaaaaagcatgtagaggccgatatggtaccccattctttaaaatggagcatttttgccgctgcaccgcnnnnnnngttcaaataggaggttaagt agaatctccgtgatgttactctggtatgtaaataaaatatgagggaatactaacattacgataggtgaaagtcaaggagaggggaaatttcttctttgaaatggaggtggttaataggatatggaaaataatttatcttaaatacggcttcatctgacttggcaatttatcgataaaaggttataatcttaaatctctaaggttttatatacagaacaaattatgtttatgaaccttaaaaaaactatagtaggcagaaaaagcatgtagaggccgatatggtaccccattctttaaaatggagcatttttgccgctgcaccgctttttttgttcaaataggaggttaagt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGAAUCUCCGUGAUGUUACUCUGGUAUGUAAAUAAAAUAUGAGGGAAUACUAACAUUACGAUAGGUGAAAGUCAAGGAGAGGGGAAAUUUCUUCUUUGAAAUGGAGGUGGUUAAUAGGAUAUGGAAAAUAAUUUAUCUUAAAUACGGCUUCAUCUGACUUGGCAAUUUAUCGAUAAAAGGUUAUAAUCUUAAAUCUCUAAGGUUUUAUAUACAGAACAAAUUAUGUUUAUGAACCUUAAAAAAACUAUAGUAGGCAGAAAAAGCAUGUAGAGGCCGAUAUGGUACCCCAUUCUUUAAAAUGGAGCAUUUUUGCCGCUGCACCGCUUUUUUUGUUCAAAUAGGAGGUUAAGU ..(((((((.(((...((((.((((..(((.(((((((...(((((............((((((((..((((((.(((((((((....)))))))))......(((((.((...(((((((............)))))))...)).)))))...))))))....))))))))....(((((....)))))...)))))...))))))).))).(((((.....)))))...............)))).)))).(((((((((((.(((((.(((.((.(((.(...(((((......)))))).))).)).))).)))))..))))))))))))))....))))))).... (-93.40) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ ACUUAACCUCCUAUUUGAACAAAAAAAGCGGUGCAGCGGCAAAAAUGCUCCAUUUUAAAGAAUGGGGUACCAUAUCGGCCUCUACAUGCUUUUUCUGCCUACUAUAGUUUUUUUAAGGUUCAUAAACAUAAUUUGUUCUGUAUAUAAAACCUUAGAGAUUUAAGAUUAUAACCUUUUAUCGAUAAAUUGCCAAGUCAGAUGAAGCCGUAUUUAAGAUAAAUUAUUUUCCAUAUCCUAUUAACCACCUCCAUUUCAAAGAAGAAAUUUCCCCUCUCCUUGACUUUCACCUAUCGUAAUGUUAGUAUUCCCUCAUAUUUUAUUUACAUACCAGAGUAACAUCACGGAGAUUCU ........((...((((((((.((((((((.((.((.(((.....((((((((((....))))))))))........))).)).)))))))))).))......((((..(((((((((((.(((.(((.((....)).))).)))..))))))))))).....((..((((...((((((..(((((.((....((....))....))))))).))))))))))..))......)))).............))))))...)).........(((((.(((............((((....(((((......)))))....)))).(((....)))...))).))))).... (-58.92) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 889 110 61 201 152 NC_002967:TDE0751|5end_magnesium_chelatase,_subunit_D/I_family_791051..791281_NEGATIVE 323 343 303 56 11 NC_002967:TDE1397|5end_flagellar_synthesis_regulator_FleN,_putative_1436014..1436244_POSITIVE 319 95 53 172 122 NC_002967:TDE1146|5end_hypothetical_protein_1185414..1185644_NEGATIVE 312 305 265 216 174 NC_002967:TDE1909|5end_conserved_hypothetical_protein_TIGR00159_1926872..1927102_NEGATIVE 308 337 299 182 131 NC_002967:TDE1556|5end_hypothetical_protein_1598787..1599017_POSITIVE 295 309 264 210 169 NC_002967:TDE2490|5end_primosomal_protein_N'_2514685..2514915_NEGATIVE 295 329 283 139 85 NC_002967:TDE1260|5end_cholinephosphate_cytidylyltransferase/choline_kinase_1294028..1294258_POSITIVE 295 330 286 165 100 NC_002967:TDE1254|5end_Smr_domain_protein_1288411..1288641_POSITIVE 284 317 274 177 137 NC_002967:TDE0857|5end_lipoprotein,_putative_878313..878543_POSITIVE 280 329 282 182 140 NC_002967:TDE1935|5end_hypothetical_protein_1952994..1953224_POSITIVE 278 345 301 76 26 NC_002967:TDE2728|5end_hypothetical_protein_2785607..2785837_POSITIVE 278 327 281 189 129 NC_002967:TDE0371|5end_hypothetical_protein_422687..422917_POSITIVE 276 322 296 168 135 NC_002967:TDE2232|5end_iron_compound_ABC_transporter,_ATP-binding_protein,_putative_2271285..2271515_NEGATIVE 273 118 76 169 114 NC_002967:TDE0778|5end_ribosomal_protein_L24_811487..811717_POSITIVE 270 283 245 137 95 NC_002967:TDE2326|5end_cobyric_acid_synthase_CobQ,_putative_2361087..2361317_POSITIVE 270 330 286 204 166 NC_002967:TDE0016|5end_ATPase,_AAA_family_20457..20687_POSITIVE 269 319 284 135 96 NC_002967:TDE1588|5end_tryptophanyl-tRNA_synthetase_1635813..1636043_POSITIVE 268 314 274 55 4 NC_002967:TDE2510|5end_ABC_transporter,_ATP-binding/permease_protein_2534182..2534412_POSITIVE 268 337 300 118 73 NC_002967:TDE0854|5end_regulatory_protein_RecX_875813..876043_POSITIVE 268 110 65 229 182 NC_002967:TDE0347|5end_methyl-accepting_chemotaxis_protein_DmcA_390239..390469_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 764 330 284 91 45 NC_002967:TDE0746|3end_iron_compound_ABC_transporter,_ATP-binding_protein,_putative_780931..781081_NEGATIVE 323 343 303 89 44 NC_002967:TDE1396|3end_hypothetical_protein_1436127..1436277_POSITIVE 319 95 53 57 7 NC_002967:TDE1147|3end_hypothetical_protein_1185529..1185679_NEGATIVE 295 330 286 147 82 NC_002967:TDE1253|3end_hypothetical_protein_1288473..1288623_POSITIVE 290 325 290 83 50 NC_002967:TDE0320|3end_CBS_domain_protein_352480..352630_NEGATIVE 285 350 301 89 31 NC_002967:TDE0824|3end_lipoprotein,_putative_845226..845376_NEGATIVE 278 327 281 92 32 NC_002967:TDE0711|3end_hypothetical_protein_745690..745840_NEGATIVE 277 293 253 119 71 NC_002967:TDE1770|3end_hypothetical_protein_1814468..1814618_POSITIVE 274 331 296 86 48 NC_002967:TDE2049|3end_bacterial_extracellular_solute-binding_proteins,_family_5_2079537..2079687_POSITIVE 273 319 273 132 72 NC_002967:TDE0741|3end_hypothetical_protein_776185..776335_NEGATIVE 270 283 245 147 105 NC_002967:TDE2325|3end_hypothetical_protein_2361177..2361327_POSITIVE 269 319 284 127 88 NC_002967:TDE1587|3end_aspartyl-tRNA_synthetase_1635885..1636035_POSITIVE 266 319 271 66 12 NC_002967:TDE2100|3end_hypothetical_protein_2125572..2125722_POSITIVE 265 318 271 113 65 NC_002967:TDE2310|3end_hypothetical_protein_2348256..2348406_POSITIVE 265 348 305 113 58 NC_002967:TDE2093|3end_hypothetical_protein_2120470..2120620_NEGATIVE 265 318 271 143 106 NC_002967:TDE0503|3end_hypothetical_protein_556580..556730_NEGATIVE 264 289 245 139 91 NC_002967:TDE2239|3end_hypothetical_protein_2276554..2276704_NEGATIVE 262 320 271 59 10 NC_002967:TDE2234|3end_iron_compound_ABC_transporter,_periplasmic_iron_compound-binding_protein,_putative_2272310..2272460_NEGATIVE 262 293 252 78 23 NC_002967:TDE2082|3end_hypothetical_protein_2112489..2112639_NEGATIVE 262 335 298 113 79 NC_002967:TDE1353|3end_rod_shape-determining_protein_RodA_1394931..1395081_POSITIVE