Origin IGS: tagaaatgaatgctattctcgaacaagacgtagagcaattcgcccttcgcttcgccttaaaagacgaactgcggggaaagacggttgccgtaacaggggcgacaggactgctcggagcgtgt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 acacgctccgagcagtcctgtcgcccctgttacggcaaccgtctttccccgcagttcgtcttttaaggcgaagcgaagggcgaattgctctacgtcttgttcgagaatagcattcatttcta Mask Tandem Repeat Region ================================================ tagaaatgaatgctattctcgaacaagacgtagagcaattcgcccttcgcttcgccttaaaagacgaactgcggggaaagacggttgccgtaacaggggcgacaggactgctcggagcgtgt Find is-nt database================================================ Query_seq: PI1783:PI1784|PI1783:PI1784:possible 4-diphosphocytidyl-2c-methyl-D-erythritol synthase:possible dTDP-glucose 4,6-dehydratase, NAD-dependent epimerase/dehydratase family:->->:1716219..1716340 122 tagaaatgaatgctattctcgaacaagacgtagagcaattcgcccttcgcttcgccttaaaagacgaactgcggggaaagacggttgccgtaacaggggcgacaggactgctcggagcgtgt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI1783:PI1784|PI1783:PI1784:possible 4-diphosphocytidyl-2c-methyl-D-erythritol synthase:possible dTDP-glucose 4,6-dehydratase, NAD-dependent epimerase/dehydratase family:->->:1716219..1716340 122 tagaaatgaatgctattctcgaacaagacgtagagcaattcgcccttcgcttcgccttaaaagacgaactgcggggaaagacggttgccgtaacaggggcgacaggactgctcggagcgtgt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI1783:PI1784|PI1783:PI1784:possible 4-diphosphocytidyl-2c-methyl-D-erythritol synthase:possible dTDP-glucose 4,6-dehydratase, NAD-dependent epimerase/dehydratase family:->->:1716219..1716340 122 tagaaatgaatgctattctcgaacaagacgtagagcaattcgcccttcgcttcgccttaaaagacgaactgcggggaaagacggttgccgtaacaggggcgacaggactgctcggagcgtgt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tagaaatgaatgctattctcgaacaagacgtagagcaattcgcccttcgcttcgccttaaaagacgaactgcggggaaagacggttgccgtaacaggggcgacaggactgctcggagcgtgt Predict ORF larger than 30AA ================================================ Protein_Len: 39 Strand: + Start: 6 End: 122 ..... M N A I L E Q D V E Q F A L R F A L K D E L R G K T V A V T G A T G L L G A C Protein_Len: 30 Strand: - Start: 16 End: 105 ............... E R V L R L A I R G E S R R L L R V A P F S P Q R L L P S M ................. tagaaatgaatgctattctcgaacaagacgtagagcaattcgcccttcgcttcgccttaaaagacgaactgcggggaaagacggttgccgtaacaggggcgacaggactgctcggagcgtgt 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================================================ tagaaatgaatgctattctcgaacaagacgtagagcaattcgcccttcgcttcgccttaaaagacgaactgcggggaaagacggttgccgtaacaggggcgacaggactgctcggagcgtgt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PI1783:PI1784|PI1783:PI1784:possible 4-diphosphocytidyl-2c-methyl-D-erythritol synthase:possible dTDP-glucose 4,6-dehydratase, NAD-dependent epimerase/dehydratase family:->->:1716219..1716340 122 tagaaatgaatgctattctcgaacaagacgtagagcaattcgcccttcgcttcgccttaaaagacgaactgcggggaaagacggttgccgtaacaggggcgacaggactgctcggagcgtgt Intra-Species Hit: Count: 1 Min: 1 Max: 122 Len: 122 Subject: pint_PI1783_PI1784|possible 4-diphosphocytidyl-2c-methyl-D-erythritol synthase:possible dTDP-glucose 4,6-dehydratase, NAD-dependent epimerase/dehydratase family|POSITIVE:POSITIVE|[1716219,1716340]|122 HSP 1 e-value: 2.0E-63 bit: 242.0 Len: 122 Query Start:1 Query End:122 Subject Strand: POSITIVE Subject Start: 1 Subject End: 122 tagaaatgaatgctattctcgaacaagacgtagagcaattcgcccttcgcttcgccttaaaagacgaactgcggggaaagacggttgccgtaacaggggcgacaggactgctcggagcgtgt tagaaatgaatgctattctcgaacaagacgtagagcaattcgcccttcgcttcgccttaaaagacgaactgcggggaaagacggttgccgtaacaggggcgacaggactgctcggagcgtgt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAGAAAUGAAUGCUAUUCUCGAACAAGACGUAGAGCAAUUCGCCCUUCGCUUCGCCUUAAAAGACGAACUGCGGGGAAAGACGGUUGCCGUAACAGGGGCGACAGGACUGCUCGGAGCGUGU .........(((((..(((......)))....(((((.(((.((((.((.((((.((....)).)))).)).)))).......((((((........)))))).))).)))))..))))).. (-34.20) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ ACACGCUCCGAGCAGUCCUGUCGCCCCUGUUACGGCAACCGUCUUUCCCCGCAGUUCGUCUUUUAAGGCGAAGCGAAGGGCGAAUUGCUCUACGUCUUGUUCGAGAAUAGCAUUCAUUUCUA ....(((..(((((((....((((((.....((((...)))).......(((..(((((((....))))))))))..)))))))))))))....((((....))))..)))........... (-37.10) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 491 120 71 119 63 pint:PI0668|5end_peptidyl-prolyl_cis-trans_isomerase_SlyD,_FKBP-type_(peptidylprolyl_isomerase)_610216..610446_POSITIVE 400 120 71 185 126 pint:PI2170|5end_RNA_polymerase_sigma-70_factor,_ECF_subfamily_2112238..2112468_POSITIVE 396 119 76 114 68 pint:PI1884|5end_conserved_hypothetical_protein_1826883..1827113_POSITIVE 393 119 71 59 9 pint:PI0734|5end_ABC_transporter,_ATP-binding_/_permease_667052..667282_POSITIVE 393 118 83 50 4 pint:PI0224|5end_conserved_hypothetical_protein_220541..220771_POSITIVE 384 120 71 165 113 pint:PI0094|5end_protoporphyrinogen_oxidase_89571..89801_POSITIVE 384 120 71 91 39 pint:PI0091|5end_hypothetical_protein_89497..89727_POSITIVE 375 119 71 60 6 pint:PI0705|5end_conserved_hypothetical_protein;_possible_lipoprotein_641274..641504_POSITIVE 373 119 71 225 168 pint:PI0258|5end_conjugative_transposon_protein,_TraG_249722..249952_POSITIVE 366 117 71 91 56 pint:PI1271|5end_transcriptional_regulator,__AraC/XylS_family_1190755..1190985_POSITIVE 366 119 72 231 172 pint:PI0244|5end_possible_mobilization_protein_C_240752..240982_POSITIVE 364 120 73 140 86 pint:PI0930|5end_alpha-L-fucosidase_precursor_860977..861207_POSITIVE 364 119 71 38 1 pint:PI0726|5end_hypothetical_protein_659042..659272_POSITIVE 361 108 61 162 115 pint:PI1564|5end_surface_antigen_BspA_1483455..1483685_POSITIVE 357 107 63 56 12 pint:PI1895|5end_penicillin-binding_protein_2_1838460..1838690_POSITIVE 356 120 71 64 12 pint:PI0262|5end_conserved_hypothetical_protein_254685..254915_POSITIVE 355 118 71 42 2 pint:PI0843|5end_carboxyl-terminal_protease_776145..776375_POSITIVE 353 90 41 83 30 pint:PI1636|5end_hypothetical_protein_1554246..1554476_POSITIVE 353 119 79 47 3 pint:PI0063|5end_transcriptional_regulator,_GntR_family_63181..63411_POSITIVE 352 117 71 70 26 pint:PI0699|5end_conserved_hypothetical_protein_636647..636877_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 391 120 71 92 37 pint:PI1892|3end_UDP-N-acetylmuramoylalanine--D-glutamate_ligase_1835547..1835697_POSITIVE 375 119 71 70 16 pint:PI0704|3end_conserved_hypothetical_protein_641364..641514_POSITIVE 366 117 71 85 50 pint:PI1270|3end_probable_dipeptidyl_peptidase_1190829..1190979_POSITIVE 366 119 72 137 78 pint:PI0243|3end_hypothetical_protein_240738..240888_POSITIVE 365 120 72 143 99 pint:PI0720|3end_conserved_hypothetical_protein_654460..654610_POSITIVE 365 107 63 116 57 pint:PI0684|3end_coproporphyrinogen_III_oxidase_620507..620657_POSITIVE 365 120 73 90 44 pint:PI0654|3end_K+-dependent_Na+/Ca+_exchanger_related-protein_597223..597373_POSITIVE 364 120 73 131 77 pint:PI0929|3end_copper_homeostasis_protein_861048..861198_POSITIVE 356 120 71 64 12 pint:PI0261|3end_conjugative_transposon_protein,_TraK_254765..254915_POSITIVE 353 90 41 63 10 pint:PI1635|3end_hypothetical_protein_1554306..1554456_POSITIVE 352 117 71 54 10 pint:PI0698|3end_conserved_hypothetical_protein_636711..636861_POSITIVE 345 120 71 146 93 pint:PI0965|3end_hypothetical_protein_894392..894542_POSITIVE 342 106 65 60 25 pint:PI2158|3end_glycosyl_transferase,_group_2_family_protein_2105347..2105497_POSITIVE 341 106 68 151 112 pint:PI0667|3end_hypothetical_protein_610477..610627_POSITIVE 341 118 71 123 72 pint:PI0157|3end_hypothetical_protein_151387..151537_POSITIVE 336 74 33 81 25 pint:PI1807|3end_hypothetical_protein_1742481..1742631_POSITIVE 334 120 71 144 101 pint:PI1230|3end_probable_metallo-beta-lactamase_family_protein_1152729..1152879_POSITIVE 334 119 80 74 23 pint:PI0418|3end_hypothetical_protein_386856..387006_POSITIVE 331 89 41 78 33 pint:PI0734|3end_ABC_transporter,_ATP-binding_/_permease_668760..668910_POSITIVE 329 116 71 143 85 pint:PI2117|3end_fumarate_reductase/succinate_dehydrogenase_flavoprotein_subunit,_C-terminal_2066684..2066834_POSITIVE