Origin IGS: agccctgtcctgccccgttggtcttcggcacaaaaaagatcggcagtctatagccgtggcttatttatgagccgctatcggctgtagtctgcctttctttttctctattatcttttcgaagtagtgtgagtcgttcccgctcgaatcggcaatccaaagaatatagcaagact .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 agtcttgctatattctttggattgccgattcgagcgggaacgactcacactacttcgaaaagataatagagaaaaagaaaggcagactacagccgatagcggctcataaataagccacggctatagactgccgatcttttttgtgccgaagaccaacggggcaggacagggct Mask Tandem Repeat Region ================================================ agccctgtcctgccccgttggtcttcggcacaaaaaagatcggcagtctatagccgtggcttatttatgagccgctatcggctgtagtctgcctttctttttctctattatcttttcgaagtagtgtgagtcgttcccgctcgaatcggcaatccaaagaatatagcaagact Find is-nt database================================================ Query_seq: PG0951:PG0952|PG0951:PG0952:phosphoribosylaminoimidazole carboxylase, PurE protein:4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase:->->:1010889..1011061 173 agccctgtcctgccccgttggtcttcggcacaaaaaagatcggcagtctatagccgtggcttatttatgagccgctatcggctgtagtctgcctttctttttctctattatcttttcgaagtagtgtgagtcgttcccgctcgaatcggcaatccaaagaatatagcaagact Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG0951:PG0952|PG0951:PG0952:phosphoribosylaminoimidazole carboxylase, PurE protein:4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase:->->:1010889..1011061 173 agccctgtcctgccccgttggtcttcggcacaaaaaagatcggcagtctatagccgtggcttatttatgagccgctatcggctgtagtctgcctttctttttctctattatcttttcgaagtagtgtgagtcgttcccgctcgaatcggcaatccaaagaatatagcaagact Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG0951:PG0952|PG0951:PG0952:phosphoribosylaminoimidazole carboxylase, PurE protein:4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase:->->:1010889..1011061 173 agccctgtcctgccccgttggtcttcggcacaaaaaagatcggcagtctatagccgtggcttatttatgagccgctatcggctgtagtctgcctttctttttctctattatcttttcgaagtagtgtgagtcgttcccgctcgaatcggcaatccaaagaatatagcaagact Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 agccctgtcctgccccgttggtcttcggcacaaaaaagatcggcagtctatagccgtggcttatttatgagccgctatcggctgtagtctgcctttctttttctctattatcttttcgaagtagtgtgagtcgttcccgctcgaatcggcaatccaaagaatatagcaagact Predict ORF larger than 30AA ================================================ Protein_Len: 37 Strand: + Start: 63 End: 173 .............................................................. M Y E P L S A V V C L S F S L L S F R S S V S R S R S N R Q S K E Y S K T Protein_Len: 34 Strand: - Start: 68 End: 169 ................................................................... S G S D A T T Q R E K E R N D K R L L T L R E R E F R C D L S Y L M .... Protein_Len: 33 Strand: - Start: 64 End: 162 ............................................................... K H A A I P Q L R G K K K E I I K E F Y H S D N G S S D A I W L M ........... agccctgtcctgccccgttggtcttcggcacaaaaaagatcggcagtctatagccgtggcttatttatgagccgctatcggctgtagtctgcctttctttttctctattatcttttcgaagtagtgtgagtcgttcccgctcgaatcggcaatccaaagaatatagcaagact 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================================================ agccctgtcctgccccgttggtcttcggcacaaaaaagatcggcagtctatagccgtggcttatttatgagccgctatcggctgtagtctgcctttctttttctctattatcttttcgaagtagtgtgagtcgttcccgctcgaatcggcaatccaaagaatatagcaagact Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 86 HP_score: -6.7 Tail_Score: -5.02777 Start: 42 End: 93 Full_Region: GGCACAAAAAAGATC GGCAGTCTATAGCCGTGGC TTATTTATGAGCC GCTATCGGCTGTAGTCTGCC TTTCTTTTTCTCTAT .........................................GGCAGTCTATAGCCGTGGCTTATTTATGAGCCGCTATCGGCTGTAGTCTGCC................................................................................ Find igs database================================================ Query_seq: PG0951:PG0952|PG0951:PG0952:phosphoribosylaminoimidazole carboxylase, PurE protein:4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase:->->:1010889..1011061 173 agccctgtcctgccccgttggtcttcggcacaaaaaagatcggcagtctatagccgtggcttatttatgagccgctatcggctgtagtctgcctttctttttctctattatcttttcgaagtagtgtgagtcgttcccgctcgaatcggcaatccaaagaatatagcaagact Intra-Species Hit: Count: 1 Min: 1 Max: 173 Len: 173 Subject: NC_002950_PG0951_PG0952|phosphoribosylaminoimidazole carboxylase, PurE protein:4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase|POSITIVE:POSITIVE|[1010889,1011061]|173 HSP 1 e-value: 1.0E-93 bit: 343.0 Len: 173 Query Start:1 Query End:173 Subject Strand: POSITIVE Subject Start: 1 Subject End: 173 agccctgtcctgccccgttggtcttcggcacaaaaaagatcggcagtctatagccgtggcttatttatgagccgctatcggctgtagtctgcctttctttttctctattatcttttcgaagtagtgtgagtcgttcccgctcgaatcggcaatccaaagaatatagcaagact agccctgtcctgccccgttggtcttcggcacaaaaaagatcggcagtctatagccgtggcttatttatgagccgctatcggctgtagtctgcctttctttttctctattatcttttcgaagtagtgtgagtcgttcccgctcgaatcggcaatccaaagaatatagcaagact Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGCCCUGUCCUGCCCCGUUGGUCUUCGGCACAAAAAAGAUCGGCAGUCUAUAGCCGUGGCUUAUUUAUGAGCCGCUAUCGGCUGUAGUCUGCCUUUCUUUUUCUCUAUUAUCUUUUCGAAGUAGUGUGAGUCGUUCCCGCUCGAAUCGGCAAUCCAAAGAAUAUAGCAAGACU ......(((.(((...((((((..(((((...(((((((..(((((.((((((((((((((((....))))))))....)))))))).)))))..)))))))((((((((.(((....)))))))).)))........)).)))))))))..((....)).....))).))). (-58.80) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGUCUUGCUAUAUUCUUUGGAUUGCCGAUUCGAGCGGGAACGACUCACACUACUUCGAAAAGAUAAUAGAGAAAAAGAAAGGCAGACUACAGCCGAUAGCGGCUCAUAAAUAAGCCACGGCUAUAGACUGCCGAUCUUUUUUGUGCCGAAGACCAACGGGGCAGGACAGGGCU .((((((((....(((((((...........(((((....)).)))...(((..((.....))...))).((((((((..(((((.(((.(((((.....((((........)))).))))).))).)))))..))))))))...))))))).......))))))))...... (-58.90) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 423 60 12 59 17 NC_002950:PG0802|5end_alpha_keto_acid_dehydrogenase_complex,_E3_component,_lipoamide_dehydrogenase_859722..859952_NEGATIVE 408 89 41 101 47 NC_002950:PG0753|5end_protease_798301..798531_POSITIVE 403 57 11 58 5 NC_002950:PG0228|5end_DdaH_family_protein_264950..265180_NEGATIVE 381 170 130 220 164 NC_002950:PG1659|5end_hypothetical_protein_1743747..1743977_NEGATIVE 379 50 1 71 2 NC_002950:PG0434|5end_hypothetical_protein_472513..472743_NEGATIVE 372 83 41 66 7 NC_002950:PG2065|5end_conserved_hypothetical_protein_TIGR00048_2161000..2161230_POSITIVE 370 109 61 181 135 NC_002950:PG1252|5end_hypothetical_protein_1329584..1329814_NEGATIVE 365 151 111 49 3 NC_002950:PG0790|5end_GTP-binding_protein_Obg_842583..842813_NEGATIVE 363 93 55 37 2 NC_002950:PG1599|5end_hypothetical_protein_1679087..1679317_POSITIVE 359 90 41 212 168 NC_002950:PG2222|5end_acyltransferase,_HtrB/MsbB_family_2336757..2336987_POSITIVE 357 69 22 216 173 NC_002950:PG1434|5end_2-C-methyl-D-erythritol_4-phosphate_cytidylyltransferase_1519022..1519252_POSITIVE 355 60 23 185 149 NC_002950:PG2081|5end_biotin_synthetase_2181661..2181891_NEGATIVE 353 86 41 186 138 NC_002950:PG1250|5end_hypothetical_protein_1327846..1328076_NEGATIVE 351 55 13 203 152 NC_002950:PG1852|5end_exonuclease_1951973..1952203_NEGATIVE 347 45 4 149 107 NC_002950:PG2120|5end_metallo-beta-lactamase_superfamily_protein_2228492..2228722_NEGATIVE 343 89 47 141 98 NC_002950:PG1790|5end_hypothetical_protein_1880954..1881184_NEGATIVE 343 89 41 177 128 NC_002950:PG0576|5end_UDP-N-acetylmuramoylalanyl-D-glutamate--2,_6-diaminopimelate_ligase_631719..631949_POSITIVE 341 60 14 60 13 NC_002950:PG0834|5end_hypothetical_protein_893260..893490_NEGATIVE 340 83 41 186 143 NC_002950:PG1638|5end_thioredoxin_family_protein_1719650..1719880_NEGATIVE 340 59 11 194 138 NC_002950:PG1173|5end_YkgG_family_protein_1252435..1252665_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 488 100 51 56 5 NC_002950:PG0951|3end_phosphoribosylaminoimidazole_carboxylase,_PurE_protein_1010828..1010978_POSITIVE 423 60 12 54 12 NC_002950:PG0803|3end_glucosamine-6-phosphate_deaminase_859727..859877_NEGATIVE 408 89 41 117 63 NC_002950:PG0752|3end_uracil_phosphoribosyltransferase_798397..798547_POSITIVE 392 120 71 117 53 NC_002950:PG1162|3end_ATP:cob(I)alamin_adenosyltransferase,_putative_1241473..1241623_NEGATIVE 373 100 53 147 86 NC_002950:PG0605|3end_hypothetical_protein_661165..661315_NEGATIVE 363 93 55 40 5 NC_002950:PG1598|3end_lipoprotein_signal_peptidase,_putative_1679170..1679320_POSITIVE 363 87 42 67 3 NC_002950:PG0334|3end_glycosyl_transferase,_group_2_family_protein_368792..368942_NEGATIVE 356 42 3 70 31 NC_002950:PG1253|3end_DNA_ligase,_NAD-dependent_1329597..1329747_NEGATIVE 356 86 43 151 106 NC_002950:PG0592|3end_50S_ribosomal_protein_L31_650225..650375_POSITIVE 347 45 4 96 54 NC_002950:PG2121|3end_L-asparaginase_2228545..2228695_NEGATIVE 345 151 118 39 1 NC_002950:PG0791|3end_adenylate_kinase_842593..842743_NEGATIVE 343 89 47 144 101 NC_002950:PG1791|3end_hypothetical_protein_1880951..1881101_NEGATIVE 342 58 14 135 82 NC_002950:PG1638|3end_thioredoxin_family_protein_1718664..1718814_NEGATIVE 340 97 56 102 51 NC_002950:PG1761|3end_acetyltransferase,_GNAT_family_1847739..1847889_POSITIVE 340 83 41 60 17 NC_002950:PG1639|3end_hypothetical_protein_1719776..1719926_NEGATIVE 338 48 6 53 7 NC_002950:PG0648|3end_iron_compound_ABC_transporter,_periplasmic_iron_compound-binding_protein,_putative_700110..700260_NEGATIVE 334 81 41 72 22 NC_002950:PG1724|3end_O-sialoglycoprotein_endopeptidase_1814846..1814996_POSITIVE 331 156 111 57 5 NC_002950:PG1649|3end_hypothetical_protein_1730030..1730180_NEGATIVE 329 154 117 42 1 NC_002950:PG1682|3end_glycosyl_transferase,_group_1_family_protein_1769727..1769877_POSITIVE 326 48 4 98 54 NC_002950:PG1972|3end_hemagglutinin_protein_HagB_2061203..2061353_POSITIVE