Origin IGS: ctccttgacatatcgctttaaaaacatacggaaacgttcaggacgactgaatgcacgccccattaaaagcaagtatttgccgaaaattgtcagccaattgaatataagcattgttgtttgtttatctatgcagatgcaaaagtaaccaaaatccgctaaaaaactgcaatataaaccattgttttaatcaatatcaatgatattagcatttattttacta .........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 tagtaaaataaatgctaatatcattgatattgattaaaacaatggtttatattgcagttttttagcggattttggttacttttgcatctgcatagataaacaaacaacaatgcttatattcaattggctgacaattttcggcaaatacttgcttttaatggggcgtgcattcagtcgtcctgaacgtttccgtatgtttttaaagcgatatgtcaaggag Mask Tandem Repeat Region ================================================ ctccttgacatatcgctttaaaaacatacggaaacgttcaggacgactgaatgcacgccccattaaaagcaagtatttgccgaaaattgtcagccaattgaatataagcattgttgtttgtttatctatgcagatgcaaaagtaaccaaaatccgctaaaaaactgcaatataaaccattgttttaatcaatatcaatgatattagcatttattttacta Find is-nt database================================================ Query_seq: PI1710:PI1712|PI1710:PI1712:ABC-type permease component:hypothetical protein:->->:1627417..1627636 220 ctccttgacatatcgctttaaaaacatacggaaacgttcaggacgactgaatgcacgccccattaaaagcaagtatttgccgaaaattgtcagccaattgaatataagcattgttgtttgtttatctatgcagatgcaaaagtaaccaaaatccgctaaaaaactgcaatataaaccattgttttaatcaatatcaatgatattagcatttattttacta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI1710:PI1712|PI1710:PI1712:ABC-type permease component:hypothetical protein:->->:1627417..1627636 220 ctccttgacatatcgctttaaaaacatacggaaacgttcaggacgactgaatgcacgccccattaaaagcaagtatttgccgaaaattgtcagccaattgaatataagcattgttgtttgtttatctatgcagatgcaaaagtaaccaaaatccgctaaaaaactgcaatataaaccattgttttaatcaatatcaatgatattagcatttattttacta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI1710:PI1712|PI1710:PI1712:ABC-type permease component:hypothetical protein:->->:1627417..1627636 220 ctccttgacatatcgctttaaaaacatacggaaacgttcaggacgactgaatgcacgccccattaaaagcaagtatttgccgaaaattgtcagccaattgaatataagcattgttgtttgtttatctatgcagatgcaaaagtaaccaaaatccgctaaaaaactgcaatataaaccattgttttaatcaatatcaatgatattagcatttattttacta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ctccttgacatatcgctttaaaaacatacggaaacgttcaggacgactgaatgcacgccccattaaaagcaagtatttgccgaaaattgtcagccaattgaatataagcattgttgtttgtttatctatgcagatgcaaaagtaaccaaaatccgctaaaaaactgcaatataaaccattgttttaatcaatatcaatgatattagcatttattttacta Predict ORF larger than 30AA ================================================ Protein_Len: 46 Strand: + Start: 5 End: 142 .... M T Y R F K N I R K R S G R L N A R P I K S K Y L P K I V S Q L N I S I V V C L S M Q M Q K .............................................................................. Protein_Len: 45 Strand: - Start: 1 End: 135 E K V Y R K L F M R F R E P R S F A R G M L L L Y K G F I T L W N F I L M T T Q K D I C M ..................................................................................... ctccttgacatatcgctttaaaaacatacggaaacgttcaggacgactgaatgcacgccccattaaaagcaagtatttgccgaaaattgtcagccaattgaatataagcattgttgtttgtttatctatgcagatgcaaaagtaaccaaaatccgctaaaaaactgcaatataaaccattgttttaatcaatatcaatgatattagcatttattttacta 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================================================ ctccttgacatatcgctttaaaaacatacggaaacgttcaggacgactgaatgcacgccccattaaaagcaagtatttgccgaaaattgtcagccaattgaatataagcattgttgtttgtttatctatgcagatgcaaaagtaaccaaaatccgctaaaaaactgcaatataaaccattgttttaatcaatatcaatgatattagcatttattttacta Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 52 HP_score: -3.1 Tail_Score: -3.81473 Start: 35 End: 53 Full_Region: ttttaatggggcgtg cattcag tcgtc ctgaacg tttccgtatgttttt ..................................cattcagtcgtcctgaacg....................................................................................................................................................................... Find igs database================================================ Query_seq: PI1710:PI1712|PI1710:PI1712:ABC-type permease component:hypothetical protein:->->:1627417..1627636 220 ctccttgacatatcgctttaaaaacatacggaaacgttcaggacgactgaatgcacgccccattaaaagcaagtatttgccgaaaattgtcagccaattgaatataagcattgttgtttgtttatctatgcagatgcaaaagtaaccaaaatccgctaaaaaactgcaatataaaccattgttttaatcaatatcaatgatattagcatttattttacta Intra-Species Hit: Count: 1 Min: 1 Max: 220 Len: 220 Subject: pint_PI1710_PI1712|ABC-type permease component:hypothetical protein|POSITIVE:POSITIVE|[1627417,1627636]|220 HSP 1 e-value: 1.0E-121 bit: 436.0 Len: 220 Query Start:1 Query End:220 Subject Strand: POSITIVE Subject Start: 1 Subject End: 220 ctccttgacatatcgctttaaaaacatacggaaacgttcaggacgactgaatgcacgccccattaaaagcaagtatttgccgaaaattgtcagccaattgaatataagcattgttgtttgtttatctatgcagatgcaaaagtaaccaaaatccgctaaaaaactgcaatataaaccattgttttaatcaatatcaatgatattagcatttattttacta ctccttgacatatcgctttaaaaacatacggaaacgttcaggacgactgaatgcacgccccattaaaagcaagtatttgccgaaaattgtcagccaattgaatataagcattgttgtttgtttatctatgcagatgcaaaagtaaccaaaatccgctaaaaaactgcaatataaaccattgttttaatcaatatcaatgatattagcatttattttacta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CUCCUUGACAUAUCGCUUUAAAAACAUACGGAAACGUUCAGGACGACUGAAUGCACGCCCCAUUAAAAGCAAGUAUUUGCCGAAAAUUGUCAGCCAAUUGAAUAUAAGCAUUGUUGUUUGUUUAUCUAUGCAGAUGCAAAAGUAACCAAAAUCCGCUAAAAAACUGCAAUAUAAACCAUUGUUUUAAUCAAUAUCAAUGAUAUUAGCAUUUAUUUUACUA ..............(((((........(((....)))((((.....))))...............)))))..((((((((....(((((.....)))))((..(((((((....)))))))...))...))))))))...(((((...((((..(((((......(((((.......)))))....((((.......)))).)))))))))...))))). (-35.80) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAGUAAAAUAAAUGCUAAUAUCAUUGAUAUUGAUUAAAACAAUGGUUUAUAUUGCAGUUUUUUAGCGGAUUUUGGUUACUUUUGCAUCUGCAUAGAUAAACAAACAACAAUGCUUAUAUUCAAUUGGCUGACAAUUUUCGGCAAAUACUUGCUUUUAAUGGGGCGUGCAUUCAGUCGUCCUGAACGUUUCCGUAUGUUUUUAAAGCGAUAUGUCAAGGAG (((((.......)))))...((.(((((((..............((((((..(((((.......(((((...........)))))..)))))...)))))).........................(((((......)))))......(((((((....((((((.((.....))))))))((((((......))))))..))))))).))))))).)). (-40.80) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 322 60 14 150 102 pint:PI0566|5end_enoyl-[acyl-carrier-protein]_reductase_511832..512062_POSITIVE 296 46 2 53 9 pint:PI0508|5end_possible_cell_filamentation_protein_466463..466693_POSITIVE 291 85 41 151 111 pint:PI0052|5end_hypothetical_protein_52312..52542_POSITIVE 284 58 11 183 141 pint:PI0850|5end_conserved_hypothetical_protein_783231..783461_POSITIVE 284 58 11 145 103 pint:PI0849|5end_hypothetical_protein_783193..783423_POSITIVE 278 62 30 196 144 pint:PI2010|5end_ABC_transporter,_permease_component_1968936..1969166_POSITIVE 273 62 26 75 33 pint:PI1720|5end_conserved_hypothetical_protein_1636146..1636376_POSITIVE 271 62 24 225 175 pint:PI1314|5end_hypothetical_protein_1231188..1231418_POSITIVE 268 80 31 110 43 pint:PI0324|5end_conserved_hypothetical_protein_303735..303965_POSITIVE 267 60 14 175 127 pint:PI0709|5end_possible_IS1249-related_transposase_646467..646697_POSITIVE 265 80 44 217 182 pint:PI1980|5end_conserved_hypothetical_protein_1937470..1937700_POSITIVE 264 70 28 56 3 pint:PI1951|5end_ABC_transporter,_ATP-binding_protein_1905823..1906053_POSITIVE 264 79 39 228 197 pint:PI0408|5end_hypothetical_protein_374154..374384_POSITIVE 263 61 25 41 6 pint:PI0355|5end_probable__N-acetylmuramoyl-L-alanine_amidase_326157..326387_POSITIVE 259 72 36 100 67 pint:PI1892|5end_UDP-N-acetylmuramoylalanine--D-glutamate_ligase_1834217..1834447_POSITIVE 258 95 52 231 184 pint:PI0830|5end_conserved_hypothetical_protein_766576..766806_POSITIVE 256 70 27 116 81 pint:PI2037|5end_TIM-barrel_protein,_NifR3_family_1989372..1989602_POSITIVE 256 144 108 210 167 pint:PI1053|5end_conserved_hypothetical_protein_972533..972763_POSITIVE 256 45 3 182 128 pint:PI0883|5end_para-aminobenzoate_synthase_component_I_816131..816361_POSITIVE 256 137 92 81 37 pint:PI0096|5end_glycerol-3-phosphate_cytidylyltransferase_91885..92115_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 309 60 13 137 96 pint:PI0800|3end_alanyl-tRNA_synthetase_(alanine--tRNA_ligase)_739331..739481_POSITIVE 296 46 2 57 13 pint:PI0507|3end_transcriptional_regulator_466547..466697_POSITIVE 284 58 11 107 65 pint:PI0848|3end_glycosyl_transferase,_group_2_family_protein_783235..783385_POSITIVE 273 62 26 56 14 pint:PI1719|3end_conserved_hypothetical_protein_1636207..1636357_POSITIVE 268 56 21 74 34 pint:PI2167|3end_hypothetical_protein_2111891..2112041_POSITIVE 268 80 31 107 40 pint:PI0322|3end_hypothetical_protein_303812..303962_POSITIVE 264 79 39 141 110 pint:PI0407|3end_tryptophanyl-tRNA_synthetase_(tryptophan--tRNA_ligase)_374147..374297_POSITIVE 263 61 25 45 10 pint:PI0354|3end_hypothetical_protein_326241..326391_POSITIVE 258 95 52 114 67 pint:PI0829|3end_nucleotidyl_transferase_family;_possible_mannose-1-phosphate_guanyltransferase_766539..766689_POSITIVE 254 37 2 145 116 pint:PI0935|3end_collagenase,_protease_868320..868470_POSITIVE 254 79 34 145 82 pint:PI0722|3end_RNA_polymerase_sigma-70_factor_655413..655563_POSITIVE 253 100 55 145 103 pint:PI0857|3end_hypothetical_protein_790986..791136_POSITIVE 253 80 31 121 64 pint:PI0422|3end_conserved_hypothetical_protein_388025..388175_POSITIVE 248 80 40 49 14 pint:PI1652|3end_hypothetical_protein_1565235..1565385_POSITIVE 247 62 22 58 19 pint:PI0938|3end_hypothetical_protein_869541..869691_POSITIVE 245 60 12 74 34 pint:PI0634|3end_conserved_hypothetical_protein_581121..581271_POSITIVE 244 62 28 35 3 pint:PI0937|3end_hypothetical_protein_869518..869668_POSITIVE 243 70 29 59 19 pint:PI1049|3end_hypothetical_protein_967341..967491_POSITIVE 242 65 28 63 18 pint:PI1681|3end_Mg2+/Co2+_transporter_1598129..1598279_POSITIVE 242 181 145 129 98 pint:PI0584|3end_hypothetical_protein_527656..527806_POSITIVE