Origin IGS: taagtaaagtaaatagcaacatcaaacacttctgaatggttcttaaaacttaagttttggaatgtcagacagttccgaatgatttttaaaagcagagttcctaaacgaccagataattcagaatactttgcaattcctaaatatttaagcataaaaagagcagctaaaacacgttagctgctcttttctatgcttgccaccgcttagcggaagctatctttcaatta .........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 taattgaaagatagcttccgctaagcggtggcaagcatagaaaagagcagctaacgtgttttagctgctctttttatgcttaaatatttaggaattgcaaagtattctgaattatctggtcgtttaggaactctgcttttaaaaatcattcggaactgtctgacattccaaaacttaagttttaagaaccattcagaagtgtttgatgttgctatttactttactta Mask Tandem Repeat Region ================================================ taagtaaagtaaatagcaacatcaaacacttctgaatggttcttaaaacttaagttttggaatgtcagacagttccgaatgatttttaaaagcagagttcctaaacgaccagataattcagaatactttgcaattcctaaatatttaagcataaaaagagcagctaaaacacgttagctgctcttttctatgcttgccaccgcttagcggaagctatctttcaatta Find is-nt database================================================ Query_seq: PI0414:PI0415|PI0414:PI0415:hypothetical protein:malate dehydrogenase:->->:385271..385497 227 taagtaaagtaaatagcaacatcaaacacttctgaatggttcttaaaacttaagttttggaatgtcagacagttccgaatgatttttaaaagcagagttcctaaacgaccagataattcagaatactttgcaattcctaaatatttaagcataaaaagagcagctaaaacacgttagctgctcttttctatgcttgccaccgcttagcggaagctatctttcaatta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI0414:PI0415|PI0414:PI0415:hypothetical protein:malate dehydrogenase:->->:385271..385497 227 taagtaaagtaaatagcaacatcaaacacttctgaatggttcttaaaacttaagttttggaatgtcagacagttccgaatgatttttaaaagcagagttcctaaacgaccagataattcagaatactttgcaattcctaaatatttaagcataaaaagagcagctaaaacacgttagctgctcttttctatgcttgccaccgcttagcggaagctatctttcaatta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI0414:PI0415|PI0414:PI0415:hypothetical protein:malate dehydrogenase:->->:385271..385497 227 taagtaaagtaaatagcaacatcaaacacttctgaatggttcttaaaacttaagttttggaatgtcagacagttccgaatgatttttaaaagcagagttcctaaacgaccagataattcagaatactttgcaattcctaaatatttaagcataaaaagagcagctaaaacacgttagctgctcttttctatgcttgccaccgcttagcggaagctatctttcaatta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 taagtaaagtaaatagcaacatcaaacacttctgaatggttcttaaaacttaagttttggaatgtcagacagttccgaatgatttttaaaagcagagttcctaaacgaccagataattcagaatactttgcaattcctaaatatttaagcataaaaagagcagctaaaacacgttagctgctcttttctatgcttgccaccgcttagcggaagctatctttcaatta Predict ORF larger than 30AA ================================================ Protein_Len: 54 Strand: + Start: 13 End: 174 ............ M A T S N T S E W F L K L K F W N V R Q F R M I F K S R V P K R P D N S E Y F A I P K Y L S I K R A A K T R ..................................................... Protein_Len: 50 Strand: - Start: 3 End: 152 .. T F Y I A V D F V E S H N K F S L N Q F T L C N R I I K L L L T G L R G S L E S Y K A I G L Y K L M ........................................................................... taagtaaagtaaatagcaacatcaaacacttctgaatggttcttaaaacttaagttttggaatgtcagacagttccgaatgatttttaaaagcagagttcctaaacgaccagataattcagaatactttgcaattcctaaatatttaagcataaaaagagcagctaaaacacgttagctgctcttttctatgcttgccaccgcttagcggaagctatctttcaatta 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================================================ taagtaaagtaaatagcaacatcaaacacttctgaatggttcttaaaacttaagttttggaatgtcagacagttccgaatgatttttaaaagcagagttcctaaacgaccagataattcagaatactttgcaattcctaaatatttaagcataaaaagagcagctaaaacacgttagctgctcttttctatgcttgccaccgcttagcggaagctatctttcaatta Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 100 HP_score: -16.9 Tail_Score: -3.24021 Start: 149 End: 193 Full_Region: gctaagcggtggcaa gcatagaaaagagcagctaa cgtgtt ttagctgctctttttatgc ttaaatatttaggaa ....................................................................................................................................................gcatagaaaagagcagctaacgtgttttagctgctctttttatgc.................................. TransTerm Strand: - Conf: 100 HP_score: -12.0 Tail_Score: -4.98857 Start: 158 End: 183 Full_Region: ggcaagcatagaaaa gagcagctaa cgtgtt ttagctgctc tttttatgcttaaat .............................................................................................................................................................gagcagctaacgtgttttagctgctc............................................ Find igs database================================================ Query_seq: PI0414:PI0415|PI0414:PI0415:hypothetical protein:malate dehydrogenase:->->:385271..385497 227 taagtaaagtaaatagcaacatcaaacacttctgaatggttcttaaaacttaagttttggaatgtcagacagttccgaatgatttttaaaagcagagttcctaaacgaccagataattcagaatactttgcaattcctaaatatttaagcataaaaagagcagctaaaacacgttagctgctcttttctatgcttgccaccgcttagcggaagctatctttcaatta Intra-Species Hit: Count: 1 Min: 1 Max: 227 Len: 227 Subject: pint_PI0414_PI0415|hypothetical protein:malate dehydrogenase|POSITIVE:POSITIVE|[385271,385497]|227 HSP 1 e-value: 1.0E-126 bit: 450.0 Len: 227 Query Start:1 Query End:227 Subject Strand: POSITIVE Subject Start: 1 Subject End: 227 taagtaaagtaaatagcaacatcaaacacttctgaatggttcttaaaacttaagttttggaatgtcagacagttccgaatgatttttaaaagcagagttcctaaacgaccagataattcagaatactttgcaattcctaaatatttaagcataaaaagagcagctaaaacacgttagctgctcttttctatgcttgccaccgcttagcggaagctatctttcaatta taagtaaagtaaatagcaacatcaaacacttctgaatggttcttaaaacttaagttttggaatgtcagacagttccgaatgatttttaaaagcagagttcctaaacgaccagataattcagaatactttgcaattcctaaatatttaagcataaaaagagcagctaaaacacgttagctgctcttttctatgcttgccaccgcttagcggaagctatctttcaatta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAGUAAAGUAAAUAGCAACAUCAAACACUUCUGAAUGGUUCUUAAAACUUAAGUUUUGGAAUGUCAGACAGUUCCGAAUGAUUUUUAAAAGCAGAGUUCCUAAACGACCAGAUAAUUCAGAAUACUUUGCAAUUCCUAAAUAUUUAAGCAUAAAAAGAGCAGCUAAAACACGUUAGCUGCUCUUUUCUAUGCUUGCCACCGCUUAGCGGAAGCUAUCUUUCAAUUA ...((((((((..................((((((((.(((.((((((.(((...((((((((........))))))))))).)))))).)))...(((....))).........))))))))))))))))..............((((((((((((((((((((((......)))))))))))))).))))))))........((((....))))........... (-60.26) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAUUGAAAGAUAGCUUCCGCUAAGCGGUGGCAAGCAUAGAAAAGAGCAGCUAACGUGUUUUAGCUGCUCUUUUUAUGCUUAAAUAUUUAGGAAUUGCAAAGUAUUCUGAAUUAUCUGGUCGUUUAGGAACUCUGCUUUUAAAAAUCAUUCGGAACUGUCUGACAUUCCAAAACUUAAGUUUUAAGAACCAUUCAGAAGUGUUUGAUGUUGCUAUUUACUUUACUUA ........(((((((..((((...))))...(((((((.(((((((((((((((......)))))))))))))))...((((((.(((((((....(((.(((.((((((((.........))))))))))).)))...............((((.((.....))))))....)))))))))))))............))))))).....))))))).......... (-61.00) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 382 218 178 74 34 pint:PI0212|5end_surface_protein/internalin-related_protein_204417..204647_POSITIVE 379 219 177 72 21 pint:PI1550|5end_conserved_hypothetical_protein_1467360..1467590_POSITIVE 332 210 170 165 123 pint:PI0733|5end_membrane_protein;_predicted_exporter_664389..664619_POSITIVE 331 219 172 167 124 pint:PI0333|5end_hypothetical_protein_313478..313708_POSITIVE 323 218 171 89 34 pint:PI0729|5end_integrase_661428..661658_POSITIVE 322 220 171 75 20 pint:PI0146|5end_transcription_elongation_factor_140338..140568_POSITIVE 321 210 161 123 69 pint:PI0121|5end_outer_membrane_protein,_ompH_family_112625..112855_POSITIVE 319 219 171 109 70 pint:PI0185|5end_conserved_hypothetical_protein_176992..177222_POSITIVE 301 220 171 172 113 pint:PI0701|5end_hypothetical_protein_638356..638586_POSITIVE 299 214 184 44 1 pint:PI2159|5end_immunoreactive_84_kDa_antigen_PG93_2105267..2105497_POSITIVE 298 215 172 172 125 pint:PI1822|5end_ABC_transporter,_ATP-binding_/_permease_1761452..1761682_POSITIVE 296 219 172 154 114 pint:PI1575|5end_LemA_protein_1501143..1501373_POSITIVE 296 216 171 169 127 pint:PI0541|5end_GTP-binding_protein,_GTP1/OBG_family_493760..493990_POSITIVE 296 219 177 57 15 pint:PI0010|5end_conserved_hypothetical_protein_10628..10858_POSITIVE 295 215 171 180 127 pint:PI0869|5end_possible_exodeoxyribonuclease_VII_(small_subunit)_805518..805748_POSITIVE 295 217 173 67 27 pint:PI0229|5end_hypothetical_protein_228146..228376_POSITIVE 289 215 179 230 182 pint:PI1769|5end_hypothetical_protein_1696507..1696737_POSITIVE 287 220 174 208 158 pint:PI2176|5end_conserved_hypothetical_protein_2116484..2116714_POSITIVE 287 214 172 70 18 pint:PI1829|5end_hypothetical_protein_1769255..1769485_POSITIVE 287 213 172 50 14 pint:PI1636|5end_hypothetical_protein_1554246..1554476_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 332 210 170 63 21 pint:PI0732|3end_conserved_hypothetical_protein_664367..664517_POSITIVE 323 218 171 89 34 pint:PI0728|3end_integrase_661508..661658_POSITIVE 321 209 162 132 83 pint:PI0456|3end_30S_ribosomal_protein_S12_429219..429369_POSITIVE 321 210 161 115 61 pint:PI0120|3end_glutamate_racemase_112697..112847_POSITIVE 308 214 171 119 76 pint:PI0377|3end_DNA_primase/mobilizable_transposon,_excision_protein_347823..347973_POSITIVE 301 220 171 149 90 pint:PI0700|3end_UDP-glucose_4-epimerase_638413..638563_POSITIVE 299 214 184 44 1 pint:PI2158|3end_glycosyl_transferase,_group_2_family_protein_2105347..2105497_POSITIVE 297 185 149 54 9 pint:PI0618|3end_acyl-CoA_dehydrogenase_family_protein_569213..569363_POSITIVE 296 220 171 117 54 pint:PI0759|3end_hypothetical_protein_693998..694148_POSITIVE 296 216 171 57 15 pint:PI0539|3end_hypothetical_protein_493728..493878_POSITIVE 295 217 173 45 5 pint:PI0228|3end_outer_membrane_cobalamin_receptor_protein_228204..228354_POSITIVE 294 218 173 151 93 pint:PI2085|3end_conserved_hypothetical_protein_2041803..2041953_POSITIVE 290 208 171 150 105 pint:PI0868|3end_exodeoxyribonuclease_VII,_large_subunit_805576..805726_POSITIVE 287 203 161 132 79 pint:PI1651|3end_hypothetical_protein_1564512..1564662_POSITIVE 287 216 172 66 14 pint:PI0681|3end_hypothetical_protein_619256..619406_POSITIVE 287 214 171 139 84 pint:PI0378|3end_conserved_hypothetical_protein;_possible_helicase_349539..349689_POSITIVE 287 208 166 149 96 pint:PI0163|3end_conserved_hypothetical_protein_158410..158560_POSITIVE 286 209 162 150 99 pint:PI1821|3end_possible_thioredoxin_family_protein_1761517..1761667_POSITIVE 285 214 172 84 45 pint:PI0704|3end_conserved_hypothetical_protein_641364..641514_POSITIVE 280 220 172 131 69 pint:PI1356|3end_hypothetical_protein_1273340..1273490_POSITIVE