Origin IGS: aacctatctgttgtgtttatagagagcttttgcgccgttatggtgcggttggatttcgctcccaataatgaaatcgtattgttgtttattatttttctctattctctgtta .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 taacagagaatagagaaaaataataaacaacaatacgatttcattattgggagcgaaatccaaccgcaccataacggcgcaaaagctctctataaacacaacagataggtt Mask Tandem Repeat Region ================================================ aacctatctgttgtgtttatagagagcttttgcgccgttatggtgcggttggatttcgctcccaataatgaaatcgtattgttgtttattatttttctctattctctgtta Find is-nt database================================================ Query_seq: PI2027:PI2028|PI2027:PI2028:arginine decarboxylase:shikimate kinase:->->:1982191..1982301 111 aacctatctgttgtgtttatagagagcttttgcgccgttatggtgcggttggatttcgctcccaataatgaaatcgtattgttgtttattatttttctctattctctgtta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI2027:PI2028|PI2027:PI2028:arginine decarboxylase:shikimate kinase:->->:1982191..1982301 111 aacctatctgttgtgtttatagagagcttttgcgccgttatggtgcggttggatttcgctcccaataatgaaatcgtattgttgtttattatttttctctattctctgtta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI2027:PI2028|PI2027:PI2028:arginine decarboxylase:shikimate kinase:->->:1982191..1982301 111 aacctatctgttgtgtttatagagagcttttgcgccgttatggtgcggttggatttcgctcccaataatgaaatcgtattgttgtttattatttttctctattctctgtta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aacctatctgttgtgtttatagagagcttttgcgccgttatggtgcggttggatttcgctcccaataatgaaatcgtattgttgtttattatttttctctattctctgtta Predict ORF larger than 30AA ================================================ Protein_Len: 33 Strand: + Start: 13 End: 111 ............ M F I E S F C A V M V R L D F A P N N E I V L L F I I F L Y S L L Protein_Len: 32 Strand: - Start: 7 End: 102 ...... R N H K Y L A K A G N H H P Q I E S G I I F D Y Q Q K N N K E M ......... Protein_Len: 30 Strand: - Start: 3 End: 92 .. R D T T N I S L K Q A T I T R N S K A G L L S I T N N N I M ................... aacctatctgttgtgtttatagagagcttttgcgccgttatggtgcggttggatttcgctcccaataatgaaatcgtattgttgtttattatttttctctattctctgtta 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================================================ aacctatctgttgtgtttatagagagcttttgcgccgttatggtgcggttggatttcgctcccaataatgaaatcgtattgttgtttattatttttctctattctctgtta Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PI2027:PI2028|PI2027:PI2028:arginine decarboxylase:shikimate kinase:->->:1982191..1982301 111 aacctatctgttgtgtttatagagagcttttgcgccgttatggtgcggttggatttcgctcccaataatgaaatcgtattgttgtttattatttttctctattctctgtta Intra-Species Hit: Count: 1 Min: 1 Max: 111 Len: 111 Subject: pint_PI2027_PI2028|arginine decarboxylase:shikimate kinase|POSITIVE:POSITIVE|[1982191,1982301]|111 HSP 1 e-value: 7.0E-57 bit: 220.0 Len: 111 Query Start:1 Query End:111 Subject Strand: POSITIVE Subject Start: 1 Subject End: 111 aacctatctgttgtgtttatagagagcttttgcgccgttatggtgcggttggatttcgctcccaataatgaaatcgtattgttgtttattatttttctctattctctgtta aacctatctgttgtgtttatagagagcttttgcgccgttatggtgcggttggatttcgctcccaataatgaaatcgtattgttgtttattatttttctctattctctgtta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AACCUAUCUGUUGUGUUUAUAGAGAGCUUUUGCGCCGUUAUGGUGCGGUUGGAUUUCGCUCCCAAUAAUGAAAUCGUAUUGUUGUUUAUUAUUUUUCUCUAUUCUCUGUUA ..............(...(((((((.(..(((((((.....)))))))..)...........((((((((......))))))))...........)))))))...)..... (-20.60) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAACAGAGAAUAGAGAAAAAUAAUAAACAACAAUACGAUUUCAUUAUUGGGAGCGAAAUCCAACCGCACCAUAACGGCGCAAAAGCUCUCUAUAAACACAACAGAUAGGUU .........(((((((...................((.(..((....))..).))..........((.((.....)).))......))))))).................. (-16.70) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 372 63 21 56 6 pint:PI0262|5end_conserved_hypothetical_protein_254685..254915_POSITIVE 359 50 4 172 116 pint:PI1822|5end_ABC_transporter,_ATP-binding_/_permease_1761452..1761682_POSITIVE 353 60 26 87 50 pint:PI1711|5end_ABC_transporter,_ATP-binding_protein_1627597..1627827_POSITIVE 352 69 22 92 42 pint:PI0789|5end_NAD-utilizing_dehydrogenase_726728..726958_POSITIVE 346 59 22 96 56 pint:PI1928|5end_conserved_hypothetical_protein_1871996..1872226_POSITIVE 342 85 41 167 117 pint:PI0260|5end_conjugative_transposon_protein,_TraJ_253023..253253_POSITIVE 331 53 13 227 180 pint:PI1684|5end_dimethyladenosine_transferase_1601073..1601303_POSITIVE 331 48 3 73 22 pint:PI0740|5end_hypothetical_protein_672112..672342_POSITIVE 330 62 26 59 13 pint:PI1625|5end_conserved_hypothetical_protein;_possible_phage_transposase_1549316..1549546_POSITIVE 330 62 26 59 13 pint:PI0332|5end_conserved_hypothetical_protein_312600..312830_POSITIVE 322 60 11 106 58 pint:PI2022|5end_hypothetical_protein_1978631..1978861_POSITIVE 322 60 11 60 12 pint:PI2023|5end_hypothetical_protein_1978585..1978815_POSITIVE 322 60 23 187 145 pint:PI1985|5end_hypothetical_protein_1940291..1940521_POSITIVE 322 60 23 80 38 pint:PI1984|5end_MutT/nudix_family_protein_1940184..1940414_POSITIVE 317 80 31 102 69 pint:PI0768|5end_conserved_hypothetical_protein;_possible_acetyltransferase_704072..704302_POSITIVE 317 67 22 67 21 pint:PI0715|5end_hypothetical_protein_652311..652541_POSITIVE 316 48 6 71 22 pint:PI0635|5end_dephospho-CoA_kinase_580954..581184_POSITIVE 314 60 21 56 17 pint:PI1187|5end_conserved_hypothetical_protein_1106692..1106922_POSITIVE 308 46 2 75 24 pint:PI2126|5end_conserved_hypothetical_protein_2074907..2075137_POSITIVE 308 60 13 146 103 pint:PI0867|5end_hypothetical_protein_803859..804089_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 372 63 21 56 6 pint:PI0261|3end_conjugative_transposon_protein,_TraK_254765..254915_POSITIVE 352 69 22 73 23 pint:PI0788|3end_3-methyladenine_DNA_glycosylase_(DNA-3-methyladenine_glycosylase_I)_726789..726939_POSITIVE 351 46 4 151 101 pint:PI1821|3end_possible_thioredoxin_family_protein_1761517..1761667_POSITIVE 346 59 22 66 26 pint:PI1927|3end_hypothetical_protein_1872046..1872196_POSITIVE 342 85 41 107 57 pint:PI0259|3end_conserved_protein_found_in_conjugation,_TraI_253043..253193_POSITIVE 339 70 24 144 84 pint:PI1143|3end_hypothetical_protein_1070504..1070654_POSITIVE 336 58 18 103 69 pint:PI0189|3end_integrase_180437..180587_POSITIVE 325 59 12 146 91 pint:PI2019|3end_elongation_factor_P_1976774..1976924_POSITIVE 314 60 21 56 17 pint:PI1186|3end_conserved_hypothetical_protein_1106772..1106922_POSITIVE 312 47 5 97 51 pint:PI1916|3end_conserved_hypothetical_protein_1860740..1860890_POSITIVE 308 46 2 67 16 pint:PI2125|3end_D-tyrosyl-tRNA(Tyr)_deacylase_2074979..2075129_POSITIVE 305 53 14 47 6 pint:PI0739|3end_conserved_hypothetical_protein_672161..672311_POSITIVE 304 50 9 111 57 pint:PI1691|3end_hypothetical_protein_1605736..1605886_POSITIVE 303 48 8 41 1 pint:PI0653|3end_hypothetical_protein_596236..596386_POSITIVE 302 87 42 128 78 pint:PI0066|3end_ABC_transport_system,_ATP-binding_component_66089..66239_POSITIVE 300 60 21 114 69 pint:PI0369|3end_hypothetical_protein_340409..340559_POSITIVE 299 61 31 132 92 pint:PI0595|3end_conserved_hypothetical_protein_546406..546556_POSITIVE 294 55 12 131 90 pint:PI2053|3end_conserved_hypothetical_protein;_possible_outer_membrane_receptor_protein_2012876..2013026_POSITIVE 292 60 36 112 86 pint:PI1934|3end_hypothetical_protein_1882601..1882751_POSITIVE 290 67 23 123 72 pint:PI2132|3end_hypothetical_protein_2081139..2081289_POSITIVE