Origin IGS: ttatgttgttacaacatttaattaggtgcaaagttacgaaaagaaaggaatataaagcatttttctctttattatttctattctgtacgcaataattggaaattccta .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 taggaatttccaattattgcgtacagaatagaaataataaagagaaaaatgctttatattcctttcttttcgtaactttgcacctaattaaatgttgtaacaacataa Mask Tandem Repeat Region ================================================ ttatgttgttacaacatttaattaggtgcaaagttacgaaaagaaaggaatataaagcatttttctctttattatttctattctgtacgcaataattggaaattccta Find is-nt database================================================ Query_seq: PI0523:PI0524|PI0523:PI0524:hypothetical protein:meso-diaminopimelate D-dehydrogenase:->->:479905..480012 108 ttatgttgttacaacatttaattaggtgcaaagttacgaaaagaaaggaatataaagcatttttctctttattatttctattctgtacgcaataattggaaattccta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI0523:PI0524|PI0523:PI0524:hypothetical protein:meso-diaminopimelate D-dehydrogenase:->->:479905..480012 108 ttatgttgttacaacatttaattaggtgcaaagttacgaaaagaaaggaatataaagcatttttctctttattatttctattctgtacgcaataattggaaattccta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI0523:PI0524|PI0523:PI0524:hypothetical protein:meso-diaminopimelate D-dehydrogenase:->->:479905..480012 108 ttatgttgttacaacatttaattaggtgcaaagttacgaaaagaaaggaatataaagcatttttctctttattatttctattctgtacgcaataattggaaattccta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ttatgttgttacaacatttaattaggtgcaaagttacgaaaagaaaggaatataaagcatttttctctttattatttctattctgtacgcaataattggaaattccta Predict ORF larger than 30AA ================================================ Protein_Len: 30 Strand: + Start: 3 End: 92 .. M L L Q H L I R C K V T K R K E Y K A F F S L L F L F C T Q ................ Protein_Len: 34 Strand: - Start: 2 End: 103 . I N N C C K I L H L T V F L F S Y L A N K E K N N R N Q V C Y N S M ..... ttatgttgttacaacatttaattaggtgcaaagttacgaaaagaaaggaatataaagcatttttctctttattatttctattctgtacgcaataattggaaattccta 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================================================ ttatgttgttacaacatttaattaggtgcaaagttacgaaaagaaaggaatataaagcatttttctctttattatttctattctgtacgcaataattggaaattccta Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PI0523:PI0524|PI0523:PI0524:hypothetical protein:meso-diaminopimelate D-dehydrogenase:->->:479905..480012 108 ttatgttgttacaacatttaattaggtgcaaagttacgaaaagaaaggaatataaagcatttttctctttattatttctattctgtacgcaataattggaaattccta Intra-Species Hit: Count: 1 Min: 1 Max: 108 Len: 108 Subject: pint_PI0523_PI0524|hypothetical protein:meso-diaminopimelate D-dehydrogenase|POSITIVE:POSITIVE|[479905,480012]|108 HSP 1 e-value: 4.0E-55 bit: 214.0 Len: 108 Query Start:1 Query End:108 Subject Strand: POSITIVE Subject Start: 1 Subject End: 108 ttatgttgttacaacatttaattaggtgcaaagttacgaaaagaaaggaatataaagcatttttctctttattatttctattctgtacgcaataattggaaattccta ttatgttgttacaacatttaattaggtgcaaagttacgaaaagaaaggaatataaagcatttttctctttattatttctattctgtacgcaataattggaaattccta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUAUGUUGUUACAACAUUUAAUUAGGUGCAAAGUUACGAAAAGAAAGGAAUAUAAAGCAUUUUUCUCUUUAUUAUUUCUAUUCUGUACGCAAUAAUUGGAAAUUCCUA ..((((((...)))))).....((((.....(((((((...((((((((((((((((.........))))).))))))).))))...))...))))).......)))) (-14.90) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAGGAAUUUCCAAUUAUUGCGUACAGAAUAGAAAUAAUAAAGAGAAAAAUGCUUUAUAUUCCUUUCUUUUCGUAACUUUGCACCUAAUUAAAUGUUGUAACAACAUAA ((((......(((...(((((...((((..(((...((((((.........)))))).)))..))))...)))))..)))..)))).....((((((...)))))).. (-15.70) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 278 66 25 155 113 pint:PI0704|5end_conserved_hypothetical_protein_640247..640477_POSITIVE 265 62 27 211 179 pint:PI2175|5end_RNA_polymerase_sigma-54_2115007..2115237_POSITIVE 232 66 25 191 145 pint:PI2019|5end_elongation_factor_P_1976131..1976361_POSITIVE 219 89 41 123 82 pint:PI1501|5end_GTP-binding_elongation_factor_family_protein_TypA/BipA_1421424..1421654_POSITIVE 213 70 24 72 1 pint:PI0090|5end_amidophosphoribosyltransferase_88379..88609_POSITIVE 208 91 56 210 182 pint:PI0073|5end_dihydropteroate_synthase_70956..71186_POSITIVE 206 49 15 222 186 pint:PI2139|5end_cysteinyl-tRNA_synthetase_2085266..2085496_POSITIVE 204 39 25 189 175 pint:PI0522|5end_50S_ribosomal_protein_L19_479004..479234_POSITIVE 204 39 25 71 57 pint:PI0521|5end_hypothetical_protein_478886..479116_POSITIVE 196 38 11 169 142 pint:PI0435|5end_30S_ribosomal_protein_S21_406997..407227_POSITIVE 194 49 24 221 192 pint:PI1075|5end_pyruvate_phosphate_dikinase_995828..996058_POSITIVE 193 46 1 173 130 pint:PI0740|5end_hypothetical_protein_672112..672342_POSITIVE 191 68 25 194 151 pint:PI1954|5end_translation_initiation_factor_IF-2_1908784..1909014_POSITIVE 188 44 6 38 6 pint:PI0102|5end_hypothetical_protein_97856..98086_POSITIVE 187 59 25 165 119 pint:PI0865|5end_possible_phosphoglycerol_transferase_801637..801867_POSITIVE 187 43 6 180 150 pint:PI0781|5end_UDP-glucose/GDP-mannose_dehydrogenase_family;_probable__UDP-glucose_6-dehydrogenase_719260..719490_POSITIVE 186 85 57 58 27 pint:PI1585|5end_ampG_permease_1512900..1513130_POSITIVE 186 89 56 167 131 pint:PI0818|5end_alpha-amylase_758185..758415_POSITIVE 185 66 24 138 84 pint:PI1064|5end_hypothetical_protein_983071..983301_POSITIVE 183 70 28 166 127 pint:PI1833|5end_bacterioferritin_comigratory_protein_1773957..1774187_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 265 62 27 93 61 pint:PI2174|3end_hypothetical_protein_2114969..2115119_POSITIVE 204 39 25 56 42 pint:PI0520|3end_hypothetical_protein_478951..479101_POSITIVE 194 83 46 42 10 pint:PI1610|3end_Na+/H+_anti-porter_1538002..1538152_POSITIVE 193 46 1 142 99 pint:PI0739|3end_conserved_hypothetical_protein_672161..672311_POSITIVE 187 70 26 53 13 pint:PI1811|3end_conserved_hypothetical_protein_1750629..1750779_POSITIVE 186 85 57 36 5 pint:PI1584|3end_A/G-specific_adenine_glycosylase_1512958..1513108_POSITIVE 186 89 56 111 75 pint:PI0817|3end_glycosyl_transferase,_group_1_family_protein_758209..758359_POSITIVE 185 66 24 86 32 pint:PI1063|3end_excinuclease_ABC,_subunit_B_983099..983249_POSITIVE 184 69 27 44 9 pint:PI0823|3end_glyceraldehyde_3-phosphate_dehydrogenase,_type_I_763138..763288_POSITIVE 183 90 47 85 35 pint:PI1839|3end_hypothetical_protein_1782500..1782650_POSITIVE 181 97 57 131 86 pint:PI1744|3end_chromosome_partitioning_protein_1666620..1666770_POSITIVE 180 40 26 24 10 pint:PI1702|3end_hypothetical_protein_1620867..1621017_POSITIVE 179 48 5 122 81 pint:PI0728|3end_integrase_661508..661658_POSITIVE 178 50 24 150 125 pint:PI0792|3end_conserved_hypothetical_protein_729627..729777_POSITIVE 177 38 6 126 85 pint:PI2064|3end_conserved_hypothetical_protein;_possible_type_I_restriction-modification_system,_S_subunit_2026991..2027141_POSITIVE 177 87 57 121 92 pint:PI0332|3end_conserved_hypothetical_protein_313552..313702_POSITIVE 176 61 24 86 42 pint:PI1414|3end_conserved_hypothetical_protein_1334436..1334586_POSITIVE 174 69 28 151 113 pint:PI1832|3end_conserved_hypothetical_protein_1774023..1774173_POSITIVE 172 42 1 131 88 pint:PI0111|3end_hypothetical_protein_108265..108415_POSITIVE 172 42 1 78 35 pint:PI0112|3end_hypothetical_protein_108212..108362_POSITIVE