Origin IGS: gctatttctcagatgaaacgaatacttccaatagtcgcattcctttctctcttccttgcccttgctttgcctgcgaaagcgcaacgagctatggggaagacggccgaccgttcgcta .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tagcgaacggtcggccgtcttccccatagctcgttgcgctttcgcaggcaaagcaagggcaaggaagagagaaaggaatgcgactattggaagtattcgtttcatctgagaaatagc Mask Tandem Repeat Region ================================================ gctatttctcagatgaaacgaatacttccaatagtcgcattcctttctctcttccttgcccttgctttgcctgcgaaagcgcaacgagctatggggaagacggccgaccgttcgcta Find is-nt database================================================ Query_seq: PG0025:PG0026|PG0025:PG0026:fumarylacetoacetate hydrolase family protein:hypothetical protein:->->:29257..29373 117 gctatttctcagatgaaacgaatacttccaatagtcgcattcctttctctcttccttgcccttgctttgcctgcgaaagcgcaacgagctatggggaagacggccgaccgttcgcta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG0025:PG0026|PG0025:PG0026:fumarylacetoacetate hydrolase family protein:hypothetical protein:->->:29257..29373 117 gctatttctcagatgaaacgaatacttccaatagtcgcattcctttctctcttccttgcccttgctttgcctgcgaaagcgcaacgagctatggggaagacggccgaccgttcgcta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG0025:PG0026|PG0025:PG0026:fumarylacetoacetate hydrolase family protein:hypothetical protein:->->:29257..29373 117 gctatttctcagatgaaacgaatacttccaatagtcgcattcctttctctcttccttgcccttgctttgcctgcgaaagcgcaacgagctatggggaagacggccgaccgttcgcta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gctatttctcagatgaaacgaatacttccaatagtcgcattcctttctctcttccttgcccttgctttgcctgcgaaagcgcaacgagctatggggaagacggccgaccgttcgcta Predict ORF larger than 30AA ================================================ Protein_Len: 38 Strand: + Start: 4 End: 117 ... M S Q M K R I L P I V A F L S L F L A L A L P A K A Q R A M G K T A D R S L gctatttctcagatgaaacgaatacttccaatagtcgcattcctttctctcttccttgcccttgctttgcctgcgaaagcgcaacgagctatggggaagacggccgaccgttcgcta 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================================================ gctatttctcagatgaaacgaatacttccaatagtcgcattcctttctctcttccttgcccttgctttgcctgcgaaagcgcaacgagctatggggaagacggccgaccgttcgcta Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PG0025:PG0026|PG0025:PG0026:fumarylacetoacetate hydrolase family protein:hypothetical protein:->->:29257..29373 117 gctatttctcagatgaaacgaatacttccaatagtcgcattcctttctctcttccttgcccttgctttgcctgcgaaagcgcaacgagctatggggaagacggccgaccgttcgcta Intra-Species Hit: Count: 1 Min: 1 Max: 117 Len: 117 Subject: NC_002950_PG0025_PG0026|fumarylacetoacetate hydrolase family protein:hypothetical protein|POSITIVE:POSITIVE|[29257,29373]|117 HSP 1 e-value: 2.0E-60 bit: 232.0 Len: 117 Query Start:1 Query End:117 Subject Strand: POSITIVE Subject Start: 1 Subject End: 117 gctatttctcagatgaaacgaatacttccaatagtcgcattcctttctctcttccttgcccttgctttgcctgcgaaagcgcaacgagctatggggaagacggccgaccgttcgcta gctatttctcagatgaaacgaatacttccaatagtcgcattcctttctctcttccttgcccttgctttgcctgcgaaagcgcaacgagctatggggaagacggccgaccgttcgcta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GCUAUUUCUCAGAUGAAACGAAUACUUCCAAUAGUCGCAUUCCUUUCUCUCUUCCUUGCCCUUGCUUUGCCUGCGAAAGCGCAACGAGCUAUGGGGAAGACGGCCGACCGUUCGCUA ((........(((.((((.(((((((......)))...)))).)))))))....(((.(((..(((((((..((....)))))..))))...))).)))((((....))))..)).. (-28.50) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAGCGAACGGUCGGCCGUCUUCCCCAUAGCUCGUUGCGCUUUCGCAGGCAAAGCAAGGGCAAGGAAGAGAGAAAGGAAUGCGACUAUUGGAAGUAUUCGUUUCAUCUGAGAAAUAGC ..((......((((...((((((.....((((.(((((((......)))...))))))))..))))))..((((.((((((..(.....)..)))))).))))..))))......)) (-31.60) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 420 107 65 69 28 NC_002950:PG1848|5end_RNA_methyltransferase,_TrmH_family_1947382..1947612_NEGATIVE 408 105 68 119 77 NC_002950:PG0447|5end_hypothetical_protein_487278..487508_POSITIVE 394 100 53 184 133 NC_002950:PG0583|5end_cell_division_protein_FtsA_640425..640655_POSITIVE 391 100 56 106 54 NC_002950:PG2162|5end_lipid_A_disaccharide_synthase_2268764..2268994_NEGATIVE 388 106 61 194 142 NC_002950:PG2107|5end_thiamine_biosynthesis_protein_ThiH_2216658..2216888_NEGATIVE 382 110 61 185 122 NC_002950:PG1196|5end_hypothetical_protein_1275127..1275357_POSITIVE 380 108 64 62 6 NC_002950:PG1595|5end_ribulose-phosphate_3-epimerase_1674250..1674480_NEGATIVE 380 110 62 188 139 NC_002950:PG0158|5end_competence_protein_F-related_protein_180175..180405_POSITIVE 379 108 61 197 148 NC_002950:PG0701|5end_cobinamide_kinase/cobinamide_phosphate_guanylyltransferase_756511..756741_POSITIVE 373 107 61 64 16 NC_002950:PG1495|5end_DNA_topoisomerase_III_1571243..1571473_POSITIVE 361 71 35 84 37 NC_002950:PG0930|5end_hypothetical_protein_987542..987772_NEGATIVE 361 100 52 210 141 NC_002950:PG0899|5end_cytochrome_d_ubiquinol_oxidase,_subunit_II_964660..964890_NEGATIVE 357 80 31 70 18 NC_002950:PG1252|5end_hypothetical_protein_1329584..1329814_NEGATIVE 355 109 64 81 42 NC_002950:PG0172|5end_exonuclease_193493..193723_POSITIVE 354 97 51 48 4 NC_002950:PG0425|5end_esterase,_putative_463989..464219_NEGATIVE 353 110 61 198 154 NC_002950:PG0271|5end_single-stranded_binding_protein_303842..304072_POSITIVE 351 110 68 36 2 NC_002950:PG1992|5end_glucose-inhibited_division_protein_A_2081410..2081640_POSITIVE 349 110 61 66 27 NC_002950:PG0210|5end_precorrin-6x_reductase/cobalamin_biosynthetic_protein_CbiD_245969..246199_NEGATIVE 348 110 62 162 117 NC_002950:PG0677|5end_saccharopine_dehydrogenase_727653..727883_POSITIVE 345 90 42 231 172 NC_002950:PG2173|5end_outer_membrane_lipoprotein_Omp28_2280813..2281043_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 448 110 62 103 51 NC_002950:PG1972|3end_hemagglutinin_protein_HagB_2061203..2061353_POSITIVE 420 107 65 72 31 NC_002950:PG1849|3end_DNA_repair_protein_RecN_1947379..1947529_NEGATIVE 417 100 58 81 34 NC_002950:PG0340|3end_hypothetical_protein_376436..376586_POSITIVE 410 108 64 150 90 NC_002950:PG0333|3end_hypothetical_protein_368811..368961_POSITIVE 408 105 68 147 105 NC_002950:PG0446|3end_thiF_protein_487386..487536_POSITIVE 398 88 41 126 63 NC_002950:PG0322|3end_serine/threonine_transporter_356966..357116_POSITIVE 394 100 53 135 84 NC_002950:PG0582|3end_cell_division_protein_FtsQ,_putative_640456..640606_POSITIVE 392 109 61 148 97 NC_002950:PG1690|3end_Sua5/YciO/YrdC/YwlC_family_protein_1775171..1775321_NEGATIVE 391 100 56 69 17 NC_002950:PG2163|3end_acid_phosphatase_2268801..2268951_NEGATIVE 384 110 62 103 45 NC_002950:PG1975|3end_hemagglutinin_protein_HagC_2064350..2064500_POSITIVE 372 72 31 91 47 NC_002950:PG0945|3end_ABC_transporter,_permease_protein,_putative_1005104..1005254_NEGATIVE 367 110 61 82 43 NC_002950:PG0130|3end_phosphoglyceromutase_151922..152072_NEGATIVE 364 110 61 147 78 NC_002950:PG0143|3end_hydrolase,_carbon-nitrogen_family_165747..165897_NEGATIVE 362 109 61 109 49 NC_002950:PG0320|3end_hypothetical_protein_354577..354727_POSITIVE 359 110 62 54 4 NC_002950:PG1133|3end_hypothetical_protein_1214103..1214253_POSITIVE 358 106 62 134 87 NC_002950:PG0932|3end_DNA_polymerase_III,_delta_prime_subunit,_putative_989833..989983_POSITIVE 357 80 31 57 5 NC_002950:PG1253|3end_DNA_ligase,_NAD-dependent_1329597..1329747_NEGATIVE 355 109 64 84 45 NC_002950:PG0171|3end_5'-nucleotidase_family_protein_193576..193726_POSITIVE 353 110 61 147 103 NC_002950:PG0270|3end_redox-sensitive_transcriptional_activator_OxyR_303871..304021_POSITIVE 349 110 61 69 30 NC_002950:PG0211|3end_cobalamin_biosynthesis_protein_CbiG/precorrin-4_C11-methyltransferase_245966..246116_NEGATIVE