Origin IGS: ttttacctccgcaatcagcggagataggatagcattaaagaagatgtttttcaatagggcttttgaaaataggcgggcaattactgcgtcgttacacaaaagcgaatgctcaacgtacaggaagtacgcctacgctttattttcgactatctctttgcacctgctccgactatttgcaaaagaactgtcagtactgcgttactccacaaaaaacagtattcgacgtacaggaagtacgcctacgctttattttcggctatctccttgcatctactctgcctatttgcaaaagtactgtcagtgctgcgttactccacaaaaaacagtcctcaacgtatactcgatacgcatgcgtccgccacggatggcggtgggt .........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.........1.........2.........3.........4.........5.........6.........7.........8.........9 acccaccgccatccgtggcggacgcatgcgtatcgagtatacgttgaggactgttttttgtggagtaacgcagcactgacagtacttttgcaaataggcagagtagatgcaaggagatagccgaaaataaagcgtaggcgtacttcctgtacgtcgaatactgttttttgtggagtaacgcagtactgacagttcttttgcaaatagtcggagcaggtgcaaagagatagtcgaaaataaagcgtaggcgtacttcctgtacgttgagcattcgcttttgtgtaacgacgcagtaattgcccgcctattttcaaaagccctattgaaaaacatcttctttaatgctatcctatctccgctgattgcggaggtaaaa Mask Tandem Repeat Region ================================================ ttttacctccgcaatcagcggagataggatagcattaaagaagatgtttttcaatagggcttttgaaaataggcgggcaattactgcgtcgttacacaaaagcgaatgnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnntactcgatacgcatgcgtccgccacggatggcggtgggt Find is-nt database================================================ Query_seq: TDE0048:TDE0049|TDE0048:TDE0049:hypothetical protein:hypothetical protein:<-<-:57913..58288 376 ttttacctccgcaatcagcggagataggatagcattaaagaagatgtttttcaatagggcttttgaaaataggcgggcaattactgcgtcgttacacaaaagcgaatgctcaacgtacaggaagtacgcctacgctttattttcgactatctctttgcacctgctccgactatttgcaaaagaactgtcagtactgcgttactccacaaaaaacagtattcgacgtacaggaagtacgcctacgctttattttcggctatctccttgcatctactctgcctatttgcaaaagtactgtcagtgctgcgttactccacaaaaaacagtcctcaacgtatactcgatacgcatgcgtccgccacggatggcggtgggt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE0048:TDE0049|TDE0048:TDE0049:hypothetical protein:hypothetical protein:<-<-:57913..58288 376 ttttacctccgcaatcagcggagataggatagcattaaagaagatgtttttcaatagggcttttgaaaataggcgggcaattactgcgtcgttacacaaaagcgaatgctcaacgtacaggaagtacgcctacgctttattttcgactatctctttgcacctgctccgactatttgcaaaagaactgtcagtactgcgttactccacaaaaaacagtattcgacgtacaggaagtacgcctacgctttattttcggctatctccttgcatctactctgcctatttgcaaaagtactgtcagtgctgcgttactccacaaaaaacagtcctcaacgtatactcgatacgcatgcgtccgccacggatggcggtgggt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE0048:TDE0049|TDE0048:TDE0049:hypothetical protein:hypothetical protein:<-<-:57913..58288 376 ttttacctccgcaatcagcggagataggatagcattaaagaagatgtttttcaatagggcttttgaaaataggcgggcaattactgcgtcgttacacaaaagcgaatgctcaacgtacaggaagtacgcctacgctttattttcgactatctctttgcacctgctccgactatttgcaaaagaactgtcagtactgcgttactccacaaaaaacagtattcgacgtacaggaagtacgcctacgctttattttcggctatctccttgcatctactctgcctatttgcaaaagtactgtcagtgctgcgttactccacaaaaaacagtcctcaacgtatactcgatacgcatgcgtccgccacggatggcggtgggt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ttttacctccgcaatcagcggagataggatagcattaaagaagatgtttttcaatagggcttttgaaaataggcgggcaattactgcgtcgttacacaaaagcgaatgctcaacgtacaggaagtacgcctacgctttattttcgactatctctttgcacctgctccgactatttgcaaaagaactgtcagtactgcgttactccacaaaaaacagtattcgacgtacaggaagtacgcctacgctttattttcggctatctccttgcatctactctgcctatttgcaaaagtactgtcagtgctgcgttactccacaaaaaacagtcctcaacgtatactcgatacgcatgcgtccgccacggatggcggtgggt Predict ORF larger than 30AA ================================================ Protein_Len: 60 Strand: + Start: 54 End: 374 ..................................................... M G L L K I G G Q L L R R Y T K A N A Q R T G S T P T L Y F R L S L C T C S D Y L Q K N C Q Y C V T P Q K T V F D V Q E .. Protein_Len: 60 Strand: + Start: 106 End: 375 ......................................................................................................... M L N V Q E V R L R F I F D Y L F A P A P T I C K R T V S T A L L H K K Q Y S T Y R K Y A Y A L F S A I S L H L L C L F . Protein_Len: 60 Strand: + Start: 14 End: 376 ............. M S G D R I A L K K M F F N R A F E N R R A I T A S L H K S E C S T Y R K Y A Y A L F S T I S L H L L R L F A K E L S V Protein_Len: 40 Strand: - Start: 1 End: 120 K V E A I L P S L I A N F F I N K L L A K S F L R A I V A D N C L L S H E V Y M ................................................................................................................................................................................................................................................................ ttttacctccgcaatcagcggagataggatagcattaaagaagatgtttttcaatagggcttttgaaaataggcgggcaattactgcgtcgttacacaaaagcgaatgctcaacgtacaggaagtacgcctacgctttattttcgactatctctttgcacctgctccgactatttgcaaaagaactgtcagtactgcgttactccacaaaaaacagtattcgacgtacaggaagtacgcctacgctttattttcggctatctccttgcatctactctgcctatttgcaaaagtactgtcagtgctgcgttactccacaaaaaacagtcctcaacgtatactcgatacgcatgcgtccgccacggatggcggtgggt 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: 26 End: 55 .........................ATTGAAAAACATCTTCTTTAATGCTATCCT................................................................................................................................................................................................................................................................................................................................. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ ttttacctccgcaatcagcggagataggatagcattaaagaagatgtttttcaatagggcttttgaaaataggcgggcaattactgcgtcgttacacaaaagcgaatgctcaacgtacaggaagtacgcctacgctttattttcgactatctctttgcacctgctccgactatttgcaaaagaactgtcagtactgcgttactccacaaaaaacagtattcgacgtacaggaagtacgcctacgctttattttcggctatctccttgcatctactctgcctatttgcaaaagtactgtcagtgctgcgttactccacaaaaaacagtcctcaacgtatactcgatacgcatgcgtccgccacggatggcggtgggt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE0048:TDE0049|TDE0048:TDE0049:hypothetical protein:hypothetical protein:<-<-:57913..58288 376 ttttacctccgcaatcagcggagataggatagcattaaagaagatgtttttcaatagggcttttgaaaataggcgggcaattactgcgtcgttacacaaaagcgaatgctcaacgtacaggaagtacgcctacgctttattttcgactatctctttgcacctgctccgactatttgcaaaagaactgtcagtactgcgttactccacaaaaaacagtattcgacgtacaggaagtacgcctacgctttattttcggctatctccttgcatctactctgcctatttgcaaaagtactgtcagtgctgcgttactccacaaaaaacagtcctcaacgtatactcgatacgcatgcgtccgccacggatggcggtgggt Intra-Species Hit: Count: 1 Min: 1 Max: 376 Len: 376 Subject: NC_002967_TDE0048_TDE0049|hypothetical protein:hypothetical protein|NEGATIVE:NEGATIVE|[57913,58288]|376 HSP 1 e-value: 0.0 bit: 745.0 Len: 376 Query Start:1 Query End:376 Subject Strand: POSITIVE Subject Start: 1 Subject End: 376 ttttacctccgcaatcagcggagataggatagcattaaagaagatgtttttcaatagggcttttgaaaataggcgggcaattactgcgtcgttacacaaaagcgaatgctcaacgtacaggaagtacgcctacgctttattttcgactatctctttgcacctgctccgactatttgcaaaagaactgtcagtactgcgttactccacaaaaaacagtattcgacgtacaggaagtacgcctacgctttattttcggctatctccttgcatctactctgcctatttgcaaaagtactgtcagtgctgcgttactccacaaaaaacagtcctcaacgtatactcgatacgcatgcgtccgccacggatggcggtgggt ttttacctccgcaatcagcggagataggatagcattaaagaagatgtttttcaatagggcttttgaaaataggcgggcaattactgcgtcgttacacaaaagcgaatgctcaacgtacaggaagtacgcctacgctttattttcgactatctctttgcacctgctccgactatttgcaaaagaactgtcagtactgcgttactccacaaaaaacagtattcgacgtacaggaagtacgcctacgctttattttcggctatctccttgcatctactctgcctatttgcaaaagtactgtcagtgctgcgttactccacaaaaaacagtcctcaacgtatactcgatacgcatgcgtccgccacggatggcggtgggt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUUACCUCCGCAAUCAGCGGAGAUAGGAUAGCAUUAAAGAAGAUGUUUUUCAAUAGGGCUUUUGAAAAUAGGCGGGCAAUUACUGCGUCGUUACACAAAAGCGAAUGCUCAACGUACAGGAAGUACGCCUACGCUUUAUUUUCGACUAUCUCUUUGCACCUGCUCCGACUAUUUGCAAAAGAACUGUCAGUACUGCGUUACUCCACAAAAAACAGUAUUCGACGUACAGGAAGUACGCCUACGCUUUAUUUUCGGCUAUCUCCUUGCAUCUACUCUGCCUAUUUGCAAAAGUACUGUCAGUGCUGCGUUACUCCACAAAAAACAGUCCUCAACGUAUACUCGAUACGCAUGCGUCCGCCACGGAUGGCGGUGGGU (((((.((((((.....)))))).)))))..((((....((.(((((((((..((((..((((((.((((((.((((((.....(((((((.......((((((...((.....((((.....))))))...)))))).....)))).........)))..))).))).)))))).))))))..))))((((((((.((......)).....((((((((.((.(((.((((..((.(((..............)))))..))))))).)).....(((......)))..))))))))))))))))............))))))).)).))..(((((.....))))).))))..((((((....))))))..... (-99.54) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ ACCCACCGCCAUCCGUGGCGGACGCAUGCGUAUCGAGUAUACGUUGAGGACUGUUUUUUGUGGAGUAACGCAGCACUGACAGUACUUUUGCAAAUAGGCAGAGUAGAUGCAAGGAGAUAGCCGAAAAUAAAGCGUAGGCGUACUUCCUGUACGUCGAAUACUGUUUUUUGUGGAGUAACGCAGUACUGACAGUUCUUUUGCAAAUAGUCGGAGCAGGUGCAAAGAGAUAGUCGAAAAUAAAGCGUAGGCGUACUUCCUGUACGUUGAGCAUUCGCUUUUGUGUAACGACGCAGUAAUUGCCCGCCUAUUUUCAAAAGCCCUAUUGAAAAACAUCUUCUUUAAUGCUAUCCUAUCUCCGCUGAUUGCGGAGGUAAAA .....((((((....))))))..((((((((((.....)))))).(((((.(((((((((.((...(((.(((.((((....((((.(..((((.((((((.((.((((..(((((.(((((..............))).)).)))))...))))..)).))))))))))..)))))...)))).)))...)))((((((.((((((.(((.((((.(((..................((((((..(((((((.....))))))).......)))))).((((....)))).))).))))))).)))))).)))))).))...))))))))))))))....)))).....(((((((((.....)))))))))... (-120.04) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 988 120 71 211 162 NC_002967:TDE0048|5end_hypothetical_protein_57822..58052_NEGATIVE 713 370 321 121 72 NC_002967:TDE1847|5end_hypothetical_protein_1875664..1875894_POSITIVE 459 117 72 146 104 NC_002967:TDE1566|5end_hypothetical_protein_1617822..1618052_POSITIVE 397 179 131 142 95 NC_002967:TDE0518|5end_hypothetical_protein_565263..565493_NEGATIVE 374 349 302 217 171 NC_002967:TDE0569|5end_hypothetical_protein_599636..599866_POSITIVE 371 240 194 184 140 NC_002967:TDE0976|5end_hypothetical_protein_1000026..1000256_POSITIVE 334 316 275 219 184 NC_002967:TDE0573|5end_hypothetical_protein_604681..604911_POSITIVE 333 307 263 166 112 NC_002967:TDE2714|5end_hypothetical_protein_2772618..2772848_NEGATIVE 331 130 84 64 17 NC_002967:TDE1408|5end_flagellar_filament_outer_layer_protein_FlaA,_putative_1450829..1451059_POSITIVE 330 268 224 50 6 NC_002967:TDE1337|5end_hypothetical_protein_1374806..1375036_NEGATIVE 329 280 236 120 68 NC_002967:TDE0674|5end_hypothetical_protein_713161..713391_POSITIVE 328 370 325 216 171 NC_002967:TDE0766|5end_30S_ribosomal_protein_S10_805984..806214_POSITIVE 327 165 130 159 124 NC_002967:TDE0358|5end_cinnamoyl_ester_hydrolase_401638..401868_NEGATIVE 322 229 181 86 24 NC_002967:TDE1096|5end_hydroxymethylbutenyl_pyrophosphate_reductase_1130989..1131219_POSITIVE 322 316 274 82 46 NC_002967:TDE0472|5end_hypothetical_protein_528376..528606_POSITIVE 315 280 240 161 121 NC_002967:TDE0865|5end_hypothetical_protein_887127..887357_POSITIVE 313 97 52 87 40 NC_002967:TDE1657|5end_transcription_antitermination_protein_NusB_1707640..1707870_NEGATIVE 313 293 251 222 180 NC_002967:TDE0036|5end_hypothetical_protein_42527..42757_NEGATIVE 305 269 224 183 126 NC_002967:TDE2405|5end_hypothetical_protein_2432050..2432280_NEGATIVE 302 280 233 85 45 NC_002967:TDE0544|5end_hypothetical_protein_583854..584084_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 357 370 326 57 19 NC_002967:TDE2516|3end_hypothetical_protein_2542193..2542343_POSITIVE 339 295 251 50 2 NC_002967:TDE0919|3end_hypothetical_protein_939125..939275_POSITIVE 338 280 234 72 29 NC_002967:TDE2312|3end_hypothetical_protein_2349049..2349199_POSITIVE 328 370 325 151 106 NC_002967:TDE0765|3end_translation_elongation_factor_Tu_805999..806149_POSITIVE 325 368 326 112 51 NC_002967:TDE0977|3end_hypothetical_protein_1001640..1001790_POSITIVE 322 295 251 84 42 NC_002967:TDE0519|3end_hypothetical_protein_565438..565588_NEGATIVE 321 309 266 130 80 NC_002967:TDE0869|3end_hypothetical_protein_892662..892812_POSITIVE 319 49 8 71 34 NC_002967:TDE0562|3end_hypothetical_protein_595581..595731_POSITIVE 316 205 162 99 52 NC_002967:TDE0156|3end_adenylate/guanylate_cyclase_catalytic_domain_protein_180344..180494_NEGATIVE 315 280 240 131 91 NC_002967:TDE0864|3end_phosphohexose_mutase_family_protein_887177..887327_POSITIVE 315 168 127 109 63 NC_002967:TDE0157|3end_KHG/KDPG_family_aldolase/carbohydrate_kinase,_PfkB_family_185711..185861_POSITIVE 313 97 52 72 25 NC_002967:TDE1658|3end_basic_membrane_protein,_putative_1707655..1707805_NEGATIVE 306 370 324 121 68 NC_002967:TDE2622|3end_ABC_transporter,_ATP-binding_protein_2662178..2662328_NEGATIVE 306 368 322 47 8 NC_002967:TDE2429|3end_hypothetical_protein_2456628..2456778_NEGATIVE 303 229 182 62 1 NC_002967:TDE1095|3end_alanine_racemase_1131045..1131195_POSITIVE 300 310 262 148 99 NC_002967:TDE0787|3end_preprotein_translocase_SecY_816464..816614_POSITIVE 299 315 276 35 3 NC_002967:TDE2100|3end_hypothetical_protein_2125572..2125722_POSITIVE 290 279 238 144 98 NC_002967:TDE2198|3end_pyruvate-ferredoxin_oxidoreductase_2232902..2233052_NEGATIVE 289 370 335 53 17 NC_002967:TDE1924|3end_hypothetical_protein_1941674..1941824_NEGATIVE 288 269 225 102 43 NC_002967:TDE2262|3end_peptidase,_U32_family_2298033..2298183_NEGATIVE