Origin IGS: taataattggggtttgtgttgaattgtgcgtagataaaaaaacacggagcagtccccgaaagagcttcgcgtgaaaaggaaatgtcaaggcctgcatggattttctgtcttaaacgcatgctcgtggcacaattagaattatctttgagggatactattaatgtataatctcttatagattaattttcagtcgattgaagtgaagaatgttatctttgtgcatggcacaaagtaagtatattcatagatcataaaatgtgacagttttgctctatcacattccccatagaaggggcggatttattggggagaaatgaaaaaaaaacgggatgaaccttttaattggttctcccgcttttatcatttaatcgataaatagtgtgctgcaggcatctgctttta .........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 taaaagcagatgcctgcagcacactatttatcgattaaatgataaaagcgggagaaccaattaaaaggttcatcccgtttttttttcatttctccccaataaatccgccccttctatggggaatgtgatagagcaaaactgtcacattttatgatctatgaatatacttactttgtgccatgcacaaagataacattcttcacttcaatcgactgaaaattaatctataagagattatacattaatagtatccctcaaagataattctaattgtgccacgagcatgcgtttaagacagaaaatccatgcaggccttgacatttccttttcacgcgaagctctttcggggactgctccgtgtttttttatctacgcacaattcaacacaaaccccaattatta Mask Tandem Repeat Region ================================================ taataattggggtttgtgttgaattgtgcgtagataaaaaaacacggagcagtccccgaaagagcttcgcgtgaaaaggaaatgtcaaggcctgcatggattttctgtcttaaacgcatgctcgtggcacaattagaattatctttgagggatactattaatgtataatctcttatagattaattttcagtcgattgaagtgaagaatgttatctttgtgcatggcacaaagtaagtatattcatagatcataaaatgtgacagttttgctctatcacattccccatagaaggggcggatttattggggagaaatgaaaaaaaaacgggatgaaccttttaattggttctcccgcttttatcatttaatcgataaatagtgtgctgcaggcatctgctttta Find is-nt database================================================ Query_seq: TF0392:TF0394|TF0392:TF0394:hypothetical protein:oxaloacetate decarboxylase, alpha subunit (pyruvate carboxylase, C-terminal domain):->->:413006..413407 402 taataattggggtttgtgttgaattgtgcgtagataaaaaaacacggagcagtccccgaaagagcttcgcgtgaaaaggaaatgtcaaggcctgcatggattttctgtcttaaacgcatgctcgtggcacaattagaattatctttgagggatactattaatgtataatctcttatagattaattttcagtcgattgaagtgaagaatgttatctttgtgcatggcacaaagtaagtatattcatagatcataaaatgtgacagttttgctctatcacattccccatagaaggggcggatttattggggagaaatgaaaaaaaaacgggatgaaccttttaattggttctcccgcttttatcatttaatcgataaatagtgtgctgcaggcatctgctttta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF0392:TF0394|TF0392:TF0394:hypothetical protein:oxaloacetate decarboxylase, alpha subunit (pyruvate carboxylase, C-terminal domain):->->:413006..413407 402 taataattggggtttgtgttgaattgtgcgtagataaaaaaacacggagcagtccccgaaagagcttcgcgtgaaaaggaaatgtcaaggcctgcatggattttctgtcttaaacgcatgctcgtggcacaattagaattatctttgagggatactattaatgtataatctcttatagattaattttcagtcgattgaagtgaagaatgttatctttgtgcatggcacaaagtaagtatattcatagatcataaaatgtgacagttttgctctatcacattccccatagaaggggcggatttattggggagaaatgaaaaaaaaacgggatgaaccttttaattggttctcccgcttttatcatttaatcgataaatagtgtgctgcaggcatctgctttta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF0392:TF0394|TF0392:TF0394:hypothetical protein:oxaloacetate decarboxylase, alpha subunit (pyruvate carboxylase, C-terminal domain):->->:413006..413407 402 taataattggggtttgtgttgaattgtgcgtagataaaaaaacacggagcagtccccgaaagagcttcgcgtgaaaaggaaatgtcaaggcctgcatggattttctgtcttaaacgcatgctcgtggcacaattagaattatctttgagggatactattaatgtataatctcttatagattaattttcagtcgattgaagtgaagaatgttatctttgtgcatggcacaaagtaagtatattcatagatcataaaatgtgacagttttgctctatcacattccccatagaaggggcggatttattggggagaaatgaaaaaaaaacgggatgaaccttttaattggttctcccgcttttatcatttaatcgataaatagtgtgctgcaggcatctgctttta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 taataattggggtttgtgttgaattgtgcgtagataaaaaaacacggagcagtccccgaaagagcttcgcgtgaaaaggaaatgtcaaggcctgcatggattttctgtcttaaacgcatgctcgtggcacaattagaattatctttgagggatactattaatgtataatctcttatagattaattttcagtcgattgaagtgaagaatgttatctttgtgcatggcacaaagtaagtatattcatagatcataaaatgtgacagttttgctctatcacattccccatagaaggggcggatttattggggagaaatgaaaaaaaaacgggatgaaccttttaattggttctcccgcttttatcatttaatcgataaatagtgtgctgcaggcatctgctttta Predict ORF larger than 30AA ================================================ Protein_Len: 44 Strand: + Start: 34 End: 165 ................................. M K K H G A V P E R A S R E K E M S R P A W I F C L K R M L V A Q L E L S L R D T I N V ............................................................................................................................................................................................................................................. Protein_Len: 37 Strand: - Start: 190 End: 300 ............................................................................................................................................................................................. D I S T F F T I K T C P V F Y T Y E Y I M F H S L K A R D C E G Y F P R M ...................................................................................................... Protein_Len: 58 Strand: - Start: 3 End: 176 .. Y N P N T N F Q A Y I F F C P A T G S L A E R S F S I D L G A H I K Q R L R M S T A C N S N D K L S V I L T Y D R M .................................................................................................................................................................................................................................. Protein_Len: 32 Strand: - Start: 2 End: 97 . I I P T Q T S N H T S L F V R L L G R F L K A H F P F T L A Q M ................................................................................................................................................................................................................................................................................................................. taataattggggtttgtgttgaattgtgcgtagataaaaaaacacggagcagtccccgaaagagcttcgcgtgaaaaggaaatgtcaaggcctgcatggattttctgtcttaaacgcatgctcgtggcacaattagaattatctttgagggatactattaatgtataatctcttatagattaattttcagtcgattgaagtgaagaatgttatctttgtgcatggcacaaagtaagtatattcatagatcataaaatgtgacagttttgctctatcacattccccatagaaggggcggatttattggggagaaatgaaaaaaaaacgggatgaaccttttaattggttctcccgcttttatcatttaatcgataaatagtgtgctgcaggcatctgctttta 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================================================ taataattggggtttgtgttgaattgtgcgtagataaaaaaacacggagcagtccccgaaagagcttcgcgtgaaaaggaaatgtcaaggcctgcatggattttctgtcttaaacgcatgctcgtggcacaattagaattatctttgagggatactattaatgtataatctcttatagattaattttcagtcgattgaagtgaagaatgttatctttgtgcatggcacaaagtaagtatattcatagatcataaaatgtgacagttttgctctatcacattccccatagaaggggcggatttattggggagaaatgaaaaaaaaacgggatgaaccttttaattggttctcccgcttttatcatttaatcgataaatagtgtgctgcaggcatctgctttta Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 73 HP_score: -5.9 Tail_Score: -4.50122 Start: 45 End: 58 Full_Region: cacgcgaagctcttt cgggg actg ctccg tgtttttttatctac ............................................cggggactgctccg........................................................................................................................................................................................................................................................................................................................................................ TransTerm Strand: + Conf: 48 HP_score: -3.8 Tail_Score: -3.12283 Start: 166 End: 182 Full_Region: GATACTATTAATGTA TAATCT CTTAT AGATTA ATTTTCAGTCGATTG .....................................................................................................................................................................TAATCTCTTATAGATTA............................................................................................................................................................................................................................ TransTerm Strand: - Conf: 45 HP_score: -3.8 Tail_Score: -2.58272 Start: 166 End: 182 Full_Region: caatcgactgaaaat taatct ataag agatta tacattaatagtatc .....................................................................................................................................................................taatctataagagatta............................................................................................................................................................................................................................ TransTerm Strand: - Conf: 66 HP_score: -4.2 Tail_Score: -4.53163 Start: 257 End: 279 Full_Region: cccttctatggggaa tgtgatag agcaaaa ctgtcaca ttttatgatctatga ................................................................................................................................................................................................................................................................tgtgatagagcaaaactgtcaca........................................................................................................................... TransTerm Strand: + Conf: 64 HP_score: -3.3 Tail_Score: -4.63172 Start: 325 End: 355 Full_Region: AGAAATGAAAAAAAA ACGGGATGAACC TTTTAATT GGTTCTCCCGC TTTTATCATTTAATC ....................................................................................................................................................................................................................................................................................................................................ACGGGATGAACCTTTTAATTGGTTCTCCCGC............................................... TransTerm Strand: - Conf: 100 HP_score: -6.8 Tail_Score: -6.28631 Start: 326 End: 354 Full_Region: attaaatgataaaag cgggagaacc aattaaaa ggttcatcccg tttttttttcatttc .....................................................................................................................................................................................................................................................................................................................................cgggagaaccaattaaaaggttcatcccg................................................ Find igs database================================================ Query_seq: TF0392:TF0394|TF0392:TF0394:hypothetical protein:oxaloacetate decarboxylase, alpha subunit (pyruvate carboxylase, C-terminal domain):->->:413006..413407 402 taataattggggtttgtgttgaattgtgcgtagataaaaaaacacggagcagtccccgaaagagcttcgcgtgaaaaggaaatgtcaaggcctgcatggattttctgtcttaaacgcatgctcgtggcacaattagaattatctttgagggatactattaatgtataatctcttatagattaattttcagtcgattgaagtgaagaatgttatctttgtgcatggcacaaagtaagtatattcatagatcataaaatgtgacagttttgctctatcacattccccatagaaggggcggatttattggggagaaatgaaaaaaaaacgggatgaaccttttaattggttctcccgcttttatcatttaatcgataaatagtgtgctgcaggcatctgctttta Intra-Species Hit: Count: 1 Min: 1 Max: 402 Len: 402 Subject: tfor_TF0392_TF0394|hypothetical protein:oxaloacetate decarboxylase, alpha subunit (pyruvate carboxylase, C-terminal domain)|POSITIVE:POSITIVE|[413006,413407]|402 HSP 1 e-value: 0.0 bit: 702.0 Len: 402 Query Start:1 Query End:402 Subject Strand: POSITIVE Subject Start: 1 Subject End: 402 taataattggggtttgtgttgaattgtgcgtagatnnnnnnncacggagcagtccccgaaagagcttcgcgtgaaaaggaaatgtcaaggcctgcatggattttctgtcttaaacgcatgctcgtggcacaattagaattatctttgagggatactattaatgtataatctcttatagattaattttcagtcgattgaagtgaagaatgttatctttgtgcatggcacaaagtaagtatattcatagatcataaaatgtgacagttttgctctatcacattccccatagaaggggcggatttattggggagaaatgnnnnnnnnncgggatgaaccttttaattggttctcccgcttttatcatttaatcgataaatagtgtgctgcaggcatctgctttta taataattggggtttgtgttgaattgtgcgtagataaaaaaacacggagcagtccccgaaagagcttcgcgtgaaaaggaaatgtcaaggcctgcatggattttctgtcttaaacgcatgctcgtggcacaattagaattatctttgagggatactattaatgtataatctcttatagattaattttcagtcgattgaagtgaagaatgttatctttgtgcatggcacaaagtaagtatattcatagatcataaaatgtgacagttttgctctatcacattccccatagaaggggcggatttattggggagaaatgaaaaaaaaacgggatgaaccttttaattggttctcccgcttttatcatttaatcgataaatagtgtgctgcaggcatctgctttta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAUAAUUGGGGUUUGUGUUGAAUUGUGCGUAGAUAAAAAAACACGGAGCAGUCCCCGAAAGAGCUUCGCGUGAAAAGGAAAUGUCAAGGCCUGCAUGGAUUUUCUGUCUUAAACGCAUGCUCGUGGCACAAUUAGAAUUAUCUUUGAGGGAUACUAUUAAUGUAUAAUCUCUUAUAGAUUAAUUUUCAGUCGAUUGAAGUGAAGAAUGUUAUCUUUGUGCAUGGCACAAAGUAAGUAUAUUCAUAGAUCAUAAAAUGUGACAGUUUUGCUCUAUCACAUUCCCCAUAGAAGGGGCGGAUUUAUUGGGGAGAAAUGAAAAAAAAACGGGAUGAACCUUUUAAUUGGUUCUCCCGCUUUUAUCAUUUAAUCGAUAAAUAGUGUGCUGCAGGCAUCUGCUUUUA ......((((((((((((((...((((......))))...)))))))).....))))))((((((...((((.....(((((.(((...(....)...)))))))).......)))).(((..(..(((((...((((((((((.((((((((..(((....)))..)))))))).))).)))))))..((((((((((.(((.((((((...((((((((...)))))))).....)))))).....((((...((((((.((.......)).))))))((((((..(((........)))..))))))...))))...((((.(((((.(((((........)))))))))).)))).)))))))))))))......)))))..)..)))...)))))). (-120.00) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAAAGCAGAUGCCUGCAGCACACUAUUUAUCGAUUAAAUGAUAAAAGCGGGAGAACCAAUUAAAAGGUUCAUCCCGUUUUUUUUUCAUUUCUCCCCAAUAAAUCCGCCCCUUCUAUGGGGAAUGUGAUAGAGCAAAACUGUCACAUUUUAUGAUCUAUGAAUAUACUUACUUUGUGCCAUGCACAAAGAUAACAUUCUUCACUUCAAUCGACUGAAAAUUAAUCUAUAAGAGAUUAUACAUUAAUAGUAUCCCUCAAAGAUAAUUCUAAUUGUGCCACGAGCAUGCGUUUAAGACAGAAAAUCCAUGCAGGCCUUGACAUUUCCUUUUCACGCGAAGCUCUUUCGGGGACUGCUCCGUGUUUUUUUAUCUACGCACAAUUCAACACAAACCCCAAUUAUUA .....((((....)))).(((((.(((((((.((((((((((.(((((((((((((((........))))).))))))))))...))))).................((((......)))).(((((((((.......)))))))))....))))).)))))))......((((((((...)))))))).......((((...((((......)))).((((((.(((((....))))).))))))...........))))..........)))))...(((..(((((...(((..(((((..(((((((.((((((......((((......)))).....)))))).))))...)))..))))).))))))))...))).................... (-97.70) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 379 310 264 51 11 tfor:TF1842|5end_hypothetical_protein_1992571..1992801_POSITIVE 377 310 267 43 1 tfor:TF2762|5end_conserved_hypothetical_protein_2945857..2946087_POSITIVE 361 100 51 212 152 tfor:TF2852|5end_conserved_hypothetical_protein_3038966..3039196_POSITIVE 360 108 61 227 173 tfor:TF2521|5end_TPR-repeat-containing_protein_2699737..2699967_POSITIVE 359 309 264 145 107 tfor:TF3107|5end_hypothetical_protein_3338459..3338689_POSITIVE 359 309 264 41 3 tfor:TF3106|5end_hypothetical_protein_3338355..3338585_POSITIVE 356 300 264 180 147 tfor:TF2818|5end_acetylornithine_aminotransferase_3007739..3007969_POSITIVE 354 109 64 58 8 tfor:TF0701|5end_Fe-S-cluster_redox_enzyme_743799..744029_POSITIVE 350 99 52 136 83 tfor:TF3070|5end_conserved_hypothetical_protein_3294380..3294610_POSITIVE 350 129 83 210 166 tfor:TF2371|5end_conserved_hypothetical_protein_2536974..2537204_POSITIVE 350 89 52 43 1 tfor:TF0233|5end_DNA_polymerase_III_gamma/tau_subunit_259355..259585_POSITIVE 346 309 264 193 154 tfor:TF1840|5end_transposase_1990221..1990451_POSITIVE 336 336 291 112 69 tfor:TF2363|5end_conserved_hypothetical_protein_2529271..2529501_POSITIVE 334 130 87 206 162 tfor:TF0543|5end_glycine_cleavage_system_p-protein_572251..572481_POSITIVE 332 309 265 41 7 tfor:TF2745|5end_hypothetical_protein_2927562..2927792_POSITIVE 331 90 43 80 28 tfor:TF1776|5end_urocanate_hydratase_1914660..1914890_POSITIVE 328 95 53 89 34 tfor:TF2038|5end_hypothetical_protein_2198978..2199208_POSITIVE 326 129 88 231 181 tfor:TF1157|5end_glutamate_synthase,_small_subunit_1238012..1238242_POSITIVE 324 399 352 214 173 tfor:TF0529|5end_transposase_554776..555006_POSITIVE 324 128 82 58 3 tfor:TF0084|5end_possible_membrane-fusion_protein_90585..90815_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 355 309 264 108 73 tfor:TF0370|3end_hypothetical_protein_386317..386467_POSITIVE 350 99 52 89 36 tfor:TF3069|3end_hypothetical_protein_3294413..3294563_POSITIVE 350 309 264 88 54 tfor:TF0821|3end_hypothetical_protein_880195..880345_POSITIVE 349 309 264 67 28 tfor:TF0828|3end_hypothetical_protein_887508..887658_POSITIVE 343 309 264 81 46 tfor:TF2651|3end_hypothetical_protein_2822014..2822164_POSITIVE 325 98 51 100 55 tfor:TF0885|3end_conjugative_transposon_protein_fragment_938055..938205_POSITIVE 324 399 352 137 96 tfor:TF0528|3end_two-component_system_sensor_histidine_kinase_554779..554929_POSITIVE 322 70 21 64 20 tfor:TF0548|3end_TPR-repeat-containing_protein_581417..581567_POSITIVE 319 94 56 73 22 tfor:TF2974|3end_conserved_hypothetical_protein;_possible_hydrolase_3182439..3182589_POSITIVE 318 130 82 135 72 tfor:TF2343|3end_ribosome_recycling_factor_2507502..2507652_POSITIVE 315 109 64 46 1 tfor:TF2221|3end_CTn_excision_protein_2394229..2394379_POSITIVE 314 87 42 75 37 tfor:TF2266|3end_transfer_region-related_protein,_TraQ_2434949..2435099_POSITIVE 312 100 55 61 26 tfor:TF2994|3end_hypothetical_protein_3210849..3210999_POSITIVE 309 100 53 64 17 tfor:TF2874|3end_conserved_hypothetical_protein_3065224..3065374_POSITIVE 308 90 45 127 83 tfor:TF2954|3end_outer_membrane_protein,_TonB_dependent_receptor_3162121..3162271_POSITIVE 307 130 82 97 44 tfor:TF2204|3end_conserved_hypothetical_protein_2379122..2379272_POSITIVE 303 89 56 39 5 tfor:TF0232|3end_conserved_hypothetical_protein_259431..259581_POSITIVE 300 309 262 146 112 tfor:TF2816|3end_hypothetical_protein_3007184..3007334_POSITIVE 299 108 61 131 77 tfor:TF0520|3end_tetraacyldisaccharide_4'-kinase_545929..546079_POSITIVE 299 35 7 57 20 tfor:TF0353|3end_transposase_element_372543..372693_POSITIVE