Origin IGS: ctcacgcctacctttgcatcgttttaataaaaagaataacgaatttattatgtaaacaaagatgaatgaactgtgactgaaaacccggagaaaagtcgggaagacggagctaagataaagaaaaacagtccatgcaaaaaaaaacagccgatttatttgttgcgtcagaataaaatcatttactttgcacgagtgtaaaaaaatgataaagatgcgaccataagacgctgaaaatattttgcaaaacttgcagaccgattattagacccggttaaatctggaaaattcaacaagggagtctgagaataatttgtcgaagcatgtgatgcaccctgcataaggggcatggactgtgcttttacttattcagactccaaggttttccagaaccgaaccgggtgaatagcagaagttgggacgtgtccctctcttttttgcctttcggtcacagttcaaaacaaaacaaacaat .........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.........1.........2.........3.........4.........5.........6.........7.........8.........9 attgtttgttttgttttgaactgtgaccgaaaggcaaaaaagagagggacacgtcccaacttctgctattcacccggttcggttctggaaaaccttggagtctgaataagtaaaagcacagtccatgccccttatgcagggtgcatcacatgcttcgacaaattattctcagactcccttgttgaattttccagatttaaccgggtctaataatcggtctgcaagttttgcaaaatattttcagcgtcttatggtcgcatctttatcatttttttacactcgtgcaaagtaaatgattttattctgacgcaacaaataaatcggctgtttttttttgcatggactgtttttctttatcttagctccgtcttcccgacttttctccgggttttcagtcacagttcattcatctttgtttacataataaattcgttattctttttattaaaacgatgcaaaggtaggcgtgag Mask Tandem Repeat Region ================================================ ctcacgcctacctttgcatcgttttaataaaaagaataacgaatttattatgtaaacaaagatgaatgaactgtgactgaaaacccggagaaaagtcgggaagacggagctaagataaagaaaaacagtccatgcaaaaaaaaacagccgatttatttgttgcgtcagaataaaatcatttactttgcacgagtgtaaaaaaatgataaagatgcgaccataagacgctgaaaatattttgcaaaacttgcagaccgattattagacccggttaaatctggaaaattcaacaagggagtctgagaataatttgtcgaagcatgtgatgcaccctgcataaggggcatggactgtgcttttacttattcagactccaaggttttccagaaccgaaccgggtgaatagcagaagttgggacgtgtccctctcttttttgcctttcggtcacagttcaaaacaaaacaaacaat Find is-nt database================================================ Query_seq: TF1343:TF1344|TF1343:TF1344:hypothetical protein:conserved hypothetical protein:->->:1424920..1425390 471 ctcacgcctacctttgcatcgttttaataaaaagaataacgaatttattatgtaaacaaagatgaatgaactgtgactgaaaacccggagaaaagtcgggaagacggagctaagataaagaaaaacagtccatgcaaaaaaaaacagccgatttatttgttgcgtcagaataaaatcatttactttgcacgagtgtaaaaaaatgataaagatgcgaccataagacgctgaaaatattttgcaaaacttgcagaccgattattagacccggttaaatctggaaaattcaacaagggagtctgagaataatttgtcgaagcatgtgatgcaccctgcataaggggcatggactgtgcttttacttattcagactccaaggttttccagaaccgaaccgggtgaatagcagaagttgggacgtgtccctctcttttttgcctttcggtcacagttcaaaacaaaacaaacaat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF1343:TF1344|TF1343:TF1344:hypothetical protein:conserved hypothetical protein:->->:1424920..1425390 471 ctcacgcctacctttgcatcgttttaataaaaagaataacgaatttattatgtaaacaaagatgaatgaactgtgactgaaaacccggagaaaagtcgggaagacggagctaagataaagaaaaacagtccatgcaaaaaaaaacagccgatttatttgttgcgtcagaataaaatcatttactttgcacgagtgtaaaaaaatgataaagatgcgaccataagacgctgaaaatattttgcaaaacttgcagaccgattattagacccggttaaatctggaaaattcaacaagggagtctgagaataatttgtcgaagcatgtgatgcaccctgcataaggggcatggactgtgcttttacttattcagactccaaggttttccagaaccgaaccgggtgaatagcagaagttgggacgtgtccctctcttttttgcctttcggtcacagttcaaaacaaaacaaacaat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF1343:TF1344|TF1343:TF1344:hypothetical protein:conserved hypothetical protein:->->:1424920..1425390 471 ctcacgcctacctttgcatcgttttaataaaaagaataacgaatttattatgtaaacaaagatgaatgaactgtgactgaaaacccggagaaaagtcgggaagacggagctaagataaagaaaaacagtccatgcaaaaaaaaacagccgatttatttgttgcgtcagaataaaatcatttactttgcacgagtgtaaaaaaatgataaagatgcgaccataagacgctgaaaatattttgcaaaacttgcagaccgattattagacccggttaaatctggaaaattcaacaagggagtctgagaataatttgtcgaagcatgtgatgcaccctgcataaggggcatggactgtgcttttacttattcagactccaaggttttccagaaccgaaccgggtgaatagcagaagttgggacgtgtccctctcttttttgcctttcggtcacagttcaaaacaaaacaaacaat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ctcacgcctacctttgcatcgttttaataaaaagaataacgaatttattatgtaaacaaagatgaatgaactgtgactgaaaacccggagaaaagtcgggaagacggagctaagataaagaaaaacagtccatgcaaaaaaaaacagccgatttatttgttgcgtcagaataaaatcatttactttgcacgagtgtaaaaaaatgataaagatgcgaccataagacgctgaaaatattttgcaaaacttgcagaccgattattagacccggttaaatctggaaaattcaacaagggagtctgagaataatttgtcgaagcatgtgatgcaccctgcataaggggcatggactgtgcttttacttattcagactccaaggttttccagaaccgaaccgggtgaatagcagaagttgggacgtgtccctctcttttttgcctttcggtcacagttcaaaacaaaacaaacaat Predict ORF larger than 30AA ================================================ Protein_Len: 41 Strand: + Start: 73 End: 195 ........................................................................ M T E N P E K S R E D G A K I K K N S P C K K K Q P I Y L L R Q N K I I Y F A R V .................................................................................................................................................................................................................................................................................... Protein_Len: 46 Strand: + Start: 333 End: 470 ............................................................................................................................................................................................................................................................................................................................................ M H K G H G L C F Y L F R L Q G F P E P N R V N S R S W D V S L S F L P F G H S S K Q N K Q . Protein_Len: 34 Strand: - Start: 370 End: 471 ................................................................................................................................................................................................................................................................................................................................................................................. V G L N E L V S G P S Y C F N P R T G R K K A K R D C N L V F C V M Protein_Len: 34 Strand: - Start: 265 End: 366 ........................................................................................................................................................................................................................................................................ V R N F R S F E V L S D S F L K D F C T I C G A Y P A H V T S K S M ......................................................................................................... Protein_Len: 55 Strand: - Start: 183 End: 347 ...................................................................................................................................................................................... K A R T Y F F S L S A V M L R Q F Y K A F S A S R N N S G T L D P F N L L P T Q S Y N T S A H S A G Q M L P M ............................................................................................................................ Protein_Len: 34 Strand: - Start: 51 End: 152 .................................................. T F L S S H V T V S F G S F L R S S P A L I F F F L G H L F F C G M ............................................................................................................................................................................................................................................................................................................................... Protein_Len: 60 Strand: - Start: 1 End: 237 F I F S S H S F V R L F T P F V S S L Y L F V T W A F F F L R N I Q Q T L I F D N V K C S H L F I I F I R G Y S A S F M .......................................................................................................................................................................................................................................... ctcacgcctacctttgcatcgttttaataaaaagaataacgaatttattatgtaaacaaagatgaatgaactgtgactgaaaacccggagaaaagtcgggaagacggagctaagataaagaaaaacagtccatgcaaaaaaaaacagccgatttatttgttgcgtcagaataaaatcatttactttgcacgagtgtaaaaaaatgataaagatgcgaccataagacgctgaaaatattttgcaaaacttgcagaccgattattagacccggttaaatctggaaaattcaacaagggagtctgagaataatttgtcgaagcatgtgatgcaccctgcataaggggcatggactgtgcttttacttattcagactccaaggttttccagaaccgaaccgggtgaatagcagaagttgggacgtgtccctctcttttttgcctttcggtcacagttcaaaacaaaacaaacaat 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================================================ ctcacgcctacctttgcatcgttttaataaaaagaataacgaatttattatgtaaacaaagatgaatgaactgtgactgaaaacccggagaaaagtcgggaagacggagctaagataaagaaaaacagtccatgcaaaaaaaaacagccgatttatttgttgcgtcagaataaaatcatttactttgcacgagtgtaaaaaaatgataaagatgcgaccataagacgctgaaaatattttgcaaaacttgcagaccgattattagacccggttaaatctggaaaattcaacaagggagtctgagaataatttgtcgaagcatgtgatgcaccctgcataaggggcatggactgtgcttttacttattcagactccaaggttttccagaaccgaaccgggtgaatagcagaagttgggacgtgtccctctcttttttgcctttcggtcacagttcaaaacaaaacaaacaat Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TF1343:TF1344|TF1343:TF1344:hypothetical protein:conserved hypothetical protein:->->:1424920..1425390 471 ctcacgcctacctttgcatcgttttaataaaaagaataacgaatttattatgtaaacaaagatgaatgaactgtgactgaaaacccggagaaaagtcgggaagacggagctaagataaagaaaaacagtccatgcaaaaaaaaacagccgatttatttgttgcgtcagaataaaatcatttactttgcacgagtgtaaaaaaatgataaagatgcgaccataagacgctgaaaatattttgcaaaacttgcagaccgattattagacccggttaaatctggaaaattcaacaagggagtctgagaataatttgtcgaagcatgtgatgcaccctgcataaggggcatggactgtgcttttacttattcagactccaaggttttccagaaccgaaccgggtgaatagcagaagttgggacgtgtccctctcttttttgcctttcggtcacagttcaaaacaaaacaaacaat Intra-Species Hit: Count: 1 Min: 1 Max: 471 Len: 471 Subject: tfor_TF1343_TF1344|hypothetical protein:conserved hypothetical protein|POSITIVE:POSITIVE|[1424920,1425390]|471 HSP 1 e-value: 0.0 bit: 839.0 Len: 471 Query Start:1 Query End:471 Subject Strand: POSITIVE Subject Start: 1 Subject End: 471 ctcacgcctacctttgcatcgttttaataaaaagaataacgaatttattatgtaaacaaagatgaatgaactgtgactgaaaacccggagaaaagtcgggaagacggagctaagataaagaaaaacagtccatgcnnnnnnnnncagccgatttatttgttgcgtcagaataaaatcatttactttgcacgagtgtnnnnnnntgataaagatgcgaccataagacgctgaaaatattttgcaaaacttgcagaccgattattagacccggttaaatctggaaaattcaacaagggagtctgagaataatttgtcgaagcatgtgatgcaccctgcataaggggcatggactgtgcttttacttattcagactccaaggttttccagaaccgaaccgggtgaatagcagaagttgggacgtgtccctctcttttttgcctttcggtcacagttcaaaacaaaacaaacaat ctcacgcctacctttgcatcgttttaataaaaagaataacgaatttattatgtaaacaaagatgaatgaactgtgactgaaaacccggagaaaagtcgggaagacggagctaagataaagaaaaacagtccatgcaaaaaaaaacagccgatttatttgttgcgtcagaataaaatcatttactttgcacgagtgtaaaaaaatgataaagatgcgaccataagacgctgaaaatattttgcaaaacttgcagaccgattattagacccggttaaatctggaaaattcaacaagggagtctgagaataatttgtcgaagcatgtgatgcaccctgcataaggggcatggactgtgcttttacttattcagactccaaggttttccagaaccgaaccgggtgaatagcagaagttgggacgtgtccctctcttttttgcctttcggtcacagttcaaaacaaaacaaacaat Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CUCACGCCUACCUUUGCAUCGUUUUAAUAAAAAGAAUAACGAAUUUAUUAUGUAAACAAAGAUGAAUGAACUGUGACUGAAAACCCGGAGAAAAGUCGGGAAGACGGAGCUAAGAUAAAGAAAAACAGUCCAUGCAAAAAAAAACAGCCGAUUUAUUUGUUGCGUCAGAAUAAAAUCAUUUACUUUGCACGAGUGUAAAAAAAUGAUAAAGAUGCGACCAUAAGACGCUGAAAAUAUUUUGCAAAACUUGCAGACCGAUUAUUAGACCCGGUUAAAUCUGGAAAAUUCAACAAGGGAGUCUGAGAAUAAUUUGUCGAAGCAUGUGAUGCACCCUGCAUAAGGGGCAUGGACUGUGCUUUUACUUAUUCAGACUCCAAGGUUUUCCAGAACCGAACCGGGUGAAUAGCAGAAGUUGGGACGUGUCCCUCUCUUUUUUGCCUUUCGGUCACAGUUCAAAACAAAACAAACAAU ............((((..(((((((.........(((((.....))))).........))))))).(((((((((((((((.((((((.....((((((......(((.((...............))))).(((((((.....((((.(.(((((..((((((((........(((((((..((((((....)))))).)))))))...)))))))).))))).)))))......)))))))...........))))))........((((....(((((((((((.......(((((((((..((((...((.(((((((.(.((((.((((.....)))))))).)...))))))).)))))))))))))))..)))))))))))))))..)))))).....(((((((..((((....)))).....)))))))..)))))))))))))))...))))......... (-141.33) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUUGUUUGUUUUGUUUUGAACUGUGACCGAAAGGCAAAAAAGAGAGGGACACGUCCCAACUUCUGCUAUUCACCCGGUUCGGUUCUGGAAAACCUUGGAGUCUGAAUAAGUAAAAGCACAGUCCAUGCCCCUUAUGCAGGGUGCAUCACAUGCUUCGACAAAUUAUUCUCAGACUCCCUUGUUGAAUUUUCCAGAUUUAACCGGGUCUAAUAAUCGGUCUGCAAGUUUUGCAAAAUAUUUUCAGCGUCUUAUGGUCGCAUCUUUAUCAUUUUUUUACACUCGUGCAAAGUAAAUGAUUUUAUUCUGACGCAACAAAUAAAUCGGCUGUUUUUUUUUGCAUGGACUGUUUUUCUUUAUCUUAGCUCCGUCUUCCCGACUUUUCUCCGGGUUUUCAGUCACAGUUCAUUCAUCUUUGUUUACAUAAUAAAUUCGUUAUUCUUUUUAUUAAAACGAUGCAAAGGUAGGCGUGAG ...(((((...((...(((((((((((.(((.((((...(((...((((....))))..))).))))....((((((...((((..((((.((...((((.(((((((((.((((..(((((((((((.......((((..((((..((.(((...(((..((((((...((((((....((((((((.....)))))))).))))))))))))..))).))).))..))))...(((((...(((((..((((..........(((((((((((.((....)).)))).))))))).))))...)))))...)))))......))))........))))))))))))))).))))).)))))))))).)))).)))).....)))))).))).)))))))))))..)).((((((.....(((((((............))))))).......)))))).)))))..... (-128.26) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 438 440 394 231 190 tfor:TF3149|5end_conserved_hypothetical_protein_3384424..3384654_POSITIVE 383 428 387 75 29 tfor:TF2039|5end_possible_cell-cycle_regulation_histidine_triad_(HIT)_protein_2199318..2199548_POSITIVE 378 420 374 110 48 tfor:TF1735|5end_dehydrogenase,_possible_NADH-dependent_dehydrogenase_1860127..1860357_POSITIVE 343 357 312 200 143 tfor:TF0444|5end_Na+-translocating_NADH-quinone_oxidoreductase,_subunit_5_465869..466099_POSITIVE 334 437 391 71 29 tfor:TF0766|5end_hypothetical_protein_811934..812164_POSITIVE 330 439 394 68 30 tfor:TF2657|5end_conserved_hypothetical_protein_2829729..2829959_POSITIVE 329 356 313 69 28 tfor:TF0094|5end_alpha-glucosidase_103561..103791_POSITIVE 324 360 311 216 150 tfor:TF2129|5end_possible_3-oxoacyl-(acyl-carrier-protein)_synthase_2305464..2305694_POSITIVE 324 369 321 60 15 tfor:TF1835|5end_possible_dihydroxy-acid_dehydratase_1984201..1984431_POSITIVE 323 356 311 65 9 tfor:TF1293|5end_ATPase,_possible_AAA_superfamily_1374579..1374809_POSITIVE 321 350 301 182 120 tfor:TF1276|5end_acyl-CoA_dehydrogenase_(short_chain_coenzyme_A_dehydrogenase)_1361297..1361527_POSITIVE 320 430 388 69 27 tfor:TF1484|5end_penicillin_binding_protein_1579559..1579789_POSITIVE 319 360 311 181 121 tfor:TF1183|5end_hypothetical_protein_1268391..1268621_POSITIVE 318 447 406 90 46 tfor:TF2969|5end_hypothetical_protein_3177933..3178163_POSITIVE 318 408 366 191 137 tfor:TF0379|5end_conserved_hypothetical_protein,_nif3_family_399458..399688_POSITIVE 317 350 312 66 24 tfor:TF0400|5end_conserved_hypothetical_protein_421524..421754_POSITIVE 316 420 373 127 73 tfor:TF0253|5end_conserved_hypothetical_protein_283707..283937_POSITIVE 316 356 312 101 50 tfor:TF0187|5end_ferredoxin_202151..202381_POSITIVE 314 358 314 226 172 tfor:TF2560|5end_30S_ribosomal_protein_S3_2737897..2738127_POSITIVE 313 357 311 168 119 tfor:TF3062|5end_conserved_hypothetical_protein_3286140..3286370_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 334 437 391 71 29 tfor:TF0765|3end_conserved_hypothetical_protein_812014..812164_POSITIVE 330 439 394 81 43 tfor:TF2656|3end_valyl-tRNA_synthetase_2829822..2829972_POSITIVE 330 346 302 123 77 tfor:TF0998|3end_[acyl-carrier-protein]_S-malonyltransferase_1052977..1053127_POSITIVE 329 438 391 62 21 tfor:TF1762|3end_hypothetical_protein_1899648..1899798_POSITIVE 329 356 313 46 5 tfor:TF0093|3end_outer_membrane_protein,_TonB_dependent_receptor_103618..103768_POSITIVE 326 429 390 148 99 tfor:TF0467|3end_acetyltransferase-related_protein_486543..486693_POSITIVE 324 369 321 90 45 tfor:TF1834|3end_3-isopropylmalate_dehydrogenase_1984311..1984461_POSITIVE 321 350 301 95 33 tfor:TF1275|3end_transcription-repair_coupling_factor_1361290..1361440_POSITIVE 318 447 406 77 33 tfor:TF2967|3end_hypothetical_protein_3178000..3178150_POSITIVE 317 350 312 55 13 tfor:TF0401|3end_hypothetical_protein_421593..421743_POSITIVE 316 420 373 99 45 tfor:TF0252|3end_hypothetical_protein_283759..283909_POSITIVE 313 360 315 65 20 tfor:TF1972|3end_conserved_hypothetical_protein_2119415..2119565_POSITIVE 313 343 301 140 92 tfor:TF0070|3end_possible_regulatory_element_77735..77885_POSITIVE 311 354 316 130 84 tfor:TF3121|3end_nicotinate_phosphoribosyltransferase_3356124..3356274_POSITIVE 311 440 391 102 51 tfor:TF2330|3end_conserved_hypothetical_protein_2491109..2491259_POSITIVE 311 355 311 66 32 tfor:TF2148|3end_conserved_hypothetical_protein_2322189..2322339_POSITIVE 311 455 414 95 57 tfor:TF1262|3end_PDZ_domain_protein_1348831..1348981_POSITIVE 310 440 395 55 20 tfor:TF2651|3end_hypothetical_protein_2822014..2822164_POSITIVE 307 356 312 42 4 tfor:TF0496|3end_conserved_hypothetical_protein_523869..524019_POSITIVE 307 357 314 134 98 tfor:TF0477|3end_dipeptide/tripeptide_permease,_POT_family_(proton-dependent_oligopeptide_transport_family)_497085..497235_POSITIVE