Origin IGS: aatggcgcaaaattataaaaaaacttccatttgcgaaagaaaacccttgataaggtttgctgtattgtgccgaatatattgttttattgcaaccaagatggtgctgtttcgcttattttcttctatcagtgaatggttctggtgctttttttagcctttaacttcttgcttgtttgtatgtgtttatggttacaaaatgttaatctgtattctgaaaaccactgacgtatatctgcaatacttatctaaaagcgttccttttgacactgaaaagtagcgaaatgacagtgtttataggcttttgtaagtgtaaaattgcttcaatataatttttttattctaactaaataagtacctttgcaccaataaatttacactt .........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.........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aagtgtaaatttattggtgcaaaggtacttatttagttagaataaaaaaattatattgaagcaattttacacttacaaaagcctataaacactgtcatttcgctacttttcagtgtcaaaaggaacgcttttagataagtattgcagatatacgtcagtggttttcagaatacagattaacattttgtaaccataaacacatacaaacaagcaagaagttaaaggctaaaaaaagcaccagaaccattcactgatagaagaaaataagcgaaacagcaccatcttggttgcaataaaacaatatattcggcacaatacagcaaaccttatcaagggttttctttcgcaaatggaagtttttttataattttgcgccatt Mask Tandem Repeat Region ================================================ aatggcgcaaaattataaaaaaacttccatttgcgaaagaaaacccttgataaggtttgctgtattgtgccgaatatattgttttattgcaaccaagatggtgctgtttcgcttattttcttctatcagtgaatggttctggtgctttttttagcctttaacttcttgcttgtttgtatgtgtttatggttacaaaatgttaatctgtattctgaaaaccactgacgtatatctgcaatacttatctaaaagcgttccttttgacactgaaaagtagcgaaatgacagtgtttataggcttttgtaagtgtaaaattgcttcaatataatttttttattctaactaaataagtacctttgcaccaataaatttacactt Find is-nt database================================================ Query_seq: PI0646:PI0647|PI0646:PI0647:hypothetical protein:potassium uptake protein:->->:587266..587644 379 aatggcgcaaaattataaaaaaacttccatttgcgaaagaaaacccttgataaggtttgctgtattgtgccgaatatattgttttattgcaaccaagatggtgctgtttcgcttattttcttctatcagtgaatggttctggtgctttttttagcctttaacttcttgcttgtttgtatgtgtttatggttacaaaatgttaatctgtattctgaaaaccactgacgtatatctgcaatacttatctaaaagcgttccttttgacactgaaaagtagcgaaatgacagtgtttataggcttttgtaagtgtaaaattgcttcaatataatttttttattctaactaaataagtacctttgcaccaataaatttacactt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI0646:PI0647|PI0646:PI0647:hypothetical protein:potassium uptake protein:->->:587266..587644 379 aatggcgcaaaattataaaaaaacttccatttgcgaaagaaaacccttgataaggtttgctgtattgtgccgaatatattgttttattgcaaccaagatggtgctgtttcgcttattttcttctatcagtgaatggttctggtgctttttttagcctttaacttcttgcttgtttgtatgtgtttatggttacaaaatgttaatctgtattctgaaaaccactgacgtatatctgcaatacttatctaaaagcgttccttttgacactgaaaagtagcgaaatgacagtgtttataggcttttgtaagtgtaaaattgcttcaatataatttttttattctaactaaataagtacctttgcaccaataaatttacactt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI0646:PI0647|PI0646:PI0647:hypothetical protein:potassium uptake protein:->->:587266..587644 379 aatggcgcaaaattataaaaaaacttccatttgcgaaagaaaacccttgataaggtttgctgtattgtgccgaatatattgttttattgcaaccaagatggtgctgtttcgcttattttcttctatcagtgaatggttctggtgctttttttagcctttaacttcttgcttgtttgtatgtgtttatggttacaaaatgttaatctgtattctgaaaaccactgacgtatatctgcaatacttatctaaaagcgttccttttgacactgaaaagtagcgaaatgacagtgtttataggcttttgtaagtgtaaaattgcttcaatataatttttttattctaactaaataagtacctttgcaccaataaatttacactt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aatggcgcaaaattataaaaaaacttccatttgcgaaagaaaacccttgataaggtttgctgtattgtgccgaatatattgttttattgcaaccaagatggtgctgtttcgcttattttcttctatcagtgaatggttctggtgctttttttagcctttaacttcttgcttgtttgtatgtgtttatggttacaaaatgttaatctgtattctgaaaaccactgacgtatatctgcaatacttatctaaaagcgttccttttgacactgaaaagtagcgaaatgacagtgtttataggcttttgtaagtgtaaaattgcttcaatataatttttttattctaactaaataagtacctttgcaccaataaatttacactt Predict ORF larger than 30AA ================================================ Protein_Len: 33 Strand: + Start: 31 End: 129 .............................. M R K K T L D K V C C I V P N I L F Y C N Q D G A V S L I F F Y Q .......................................................................................................................................................................................................................................................... Protein_Len: 50 Strand: + Start: 2 End: 151 . M A Q N Y K K T S I C E R K P L I R F A V L C R I Y C F I A T K M V L F R L F S S I S E W F W C F F .................................................................................................................................................................................................................................... Protein_Len: 34 Strand: + Start: 57 End: 158 ........................................................ M L Y C A E Y I V L L Q P R W C C F A Y F L L S V N G S G A F F S L ............................................................................................................................................................................................................................. Protein_Len: 30 Strand: + Start: 133 End: 222 .................................................................................................................................... M V L V L F L A F N F L L V C M C L W L Q N V N L Y S E N H ............................................................................................................................................................. Protein_Len: 35 Strand: + Start: 170 End: 274 ......................................................................................................................................................................... M F V C V Y G Y K M L I C I L K T T D V Y L Q Y L S K S V P F D T E K ......................................................................................................... Protein_Len: 35 Strand: + Start: 222 End: 326 ............................................................................................................................................................................................................................. M T Y I C N T Y L K A F L L T L K S S E M T V F I G F C K C K I A S I ..................................................... Protein_Len: 32 Strand: - Start: 193 End: 288 ................................................................................................................................................................................................ L I N I Q I R F V V S T Y R C Y K D L L T G K S V S F Y R F S M ........................................................................................... Protein_Len: 39 Strand: - Start: 129 End: 245 ................................................................................................................................ H I T R T S K K A K L K K S T Q I H K H N C F T L R Y E S F W Q R I D A I S M ...................................................................................................................................... Protein_Len: 38 Strand: - Start: 16 End: 129 ............... L F V E M Q S L F G K I L N A T N H R I Y Q K I A V L I T S N R K N E E I M .......................................................................................................................................................................................................................................................... aatggcgcaaaattataaaaaaacttccatttgcgaaagaaaacccttgataaggtttgctgtattgtgccgaatatattgttttattgcaaccaagatggtgctgtttcgcttattttcttctatcagtgaatggttctggtgctttttttagcctttaacttcttgcttgtttgtatgtgtttatggttacaaaatgttaatctgtattctgaaaaccactgacgtatatctgcaatacttatctaaaagcgttccttttgacactgaaaagtagcgaaatgacagtgtttataggcttttgtaagtgtaaaattgcttcaatataatttttttattctaactaaataagtacctttgcaccaataaatttacactt Predict Promoter with matrix: RpoD-15 score > 80================================================ Predict Promoter with matrix: RpoD-16 score > 80================================================ Predict Promoter with matrix: RpoD-17 score > 80================================================ PromScan Matrix: RpoD-17 Strand: + Score: 82 Start: 301 End: 330 ............................................................................................................................................................................................................................................................................................................TTTGTAAGTGTAAAATTGCTTCAATATAAT................................................. PromScan Matrix: RpoD-17 Strand: - Score: 81 Start: 64 End: 93 ...............................................................GTTGCAATAAAACAATATATTCGGCACAAT.............................................................................................................................................................................................................................................................................................. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ aatggcgcaaaattataaaaaaacttccatttgcgaaagaaaacccttgataaggtttgctgtattgtgccgaatatattgttttattgcaaccaagatggtgctgtttcgcttattttcttctatcagtgaatggttctggtgctttttttagcctttaacttcttgcttgtttgtatgtgtttatggttacaaaatgttaatctgtattctgaaaaccactgacgtatatctgcaatacttatctaaaagcgttccttttgacactgaaaagtagcgaaatgacagtgtttataggcttttgtaagtgtaaaattgcttcaatataatttttttattctaactaaataagtacctttgcaccaataaatttacactt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PI0646:PI0647|PI0646:PI0647:hypothetical protein:potassium uptake protein:->->:587266..587644 379 aatggcgcaaaattataaaaaaacttccatttgcgaaagaaaacccttgataaggtttgctgtattgtgccgaatatattgttttattgcaaccaagatggtgctgtttcgcttattttcttctatcagtgaatggttctggtgctttttttagcctttaacttcttgcttgtttgtatgtgtttatggttacaaaatgttaatctgtattctgaaaaccactgacgtatatctgcaatacttatctaaaagcgttccttttgacactgaaaagtagcgaaatgacagtgtttataggcttttgtaagtgtaaaattgcttcaatataatttttttattctaactaaataagtacctttgcaccaataaatttacactt Intra-Species Hit: Count: 1 Min: 1 Max: 379 Len: 379 Subject: pint_PI0646_PI0647|hypothetical protein:potassium uptake protein|POSITIVE:POSITIVE|[587266,587644]|379 HSP 1 e-value: 1.0E-178 bit: 626.0 Len: 379 Query Start:1 Query End:379 Subject Strand: POSITIVE Subject Start: 1 Subject End: 379 aatggcgcaaaattatnnnnnnncttccatttgcgaaagaaaacccttgataaggtttgctgtattgtgccgaatatattgttttattgcaaccaagatggtgctgtttcgcttattttcttctatcagtgaatggttctggtgcnnnnnnnagcctttaacttcttgcttgtttgtatgtgtttatggttacaaaatgttaatctgtattctgaaaaccactgacgtatatctgcaatacttatctaaaagcgttccttttgacactgaaaagtagcgaaatgacagtgtttataggcttttgtaagtgtaaaattgcttcaatataannnnnnnattctaactaaataagtacctttgcaccaataaatttacactt aatggcgcaaaattataaaaaaacttccatttgcgaaagaaaacccttgataaggtttgctgtattgtgccgaatatattgttttattgcaaccaagatggtgctgtttcgcttattttcttctatcagtgaatggttctggtgctttttttagcctttaacttcttgcttgtttgtatgtgtttatggttacaaaatgttaatctgtattctgaaaaccactgacgtatatctgcaatacttatctaaaagcgttccttttgacactgaaaagtagcgaaatgacagtgtttataggcttttgtaagtgtaaaattgcttcaatataatttttttattctaactaaataagtacctttgcaccaataaatttacactt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAUGGCGCAAAAUUAUAAAAAAACUUCCAUUUGCGAAAGAAAACCCUUGAUAAGGUUUGCUGUAUUGUGCCGAAUAUAUUGUUUUAUUGCAACCAAGAUGGUGCUGUUUCGCUUAUUUUCUUCUAUCAGUGAAUGGUUCUGGUGCUUUUUUUAGCCUUUAACUUCUUGCUUGUUUGUAUGUGUUUAUGGUUACAAAAUGUUAAUCUGUAUUCUGAAAACCACUGACGUAUAUCUGCAAUACUUAUCUAAAAGCGUUCCUUUUGACACUGAAAAGUAGCGAAAUGACAGUGUUUAUAGGCUUUUGUAAGUGUAAAAUUGCUUCAAUAUAAUUUUUUUAUUCUAACUAAAUAAGUACCUUUGCACCAAUAAAUUUACACUU ..(((.(((((...(((((((((....((((((((((((.(((((........)))))(((((...(..(((......((((......))))......)))..).((((((((.(((((......((((((...((((..((.(((......)))))..))))......((((..(((((((((..(((((.((.((((........)))).))..)))))..)))))))))..))))........((((((.....)))))).))))))))))))))))))).))))).........))))))))))))....((((...))))....)))))))))....(((.....)))...))))).))).............. (-76.70) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAGUGUAAAUUUAUUGGUGCAAAGGUACUUAUUUAGUUAGAAUAAAAAAAUUAUAUUGAAGCAAUUUUACACUUACAAAAGCCUAUAAACACUGUCAUUUCGCUACUUUUCAGUGUCAAAAGGAACGCUUUUAGAUAAGUAUUGCAGAUAUACGUCAGUGGUUUUCAGAAUACAGAUUAACAUUUUGUAACCAUAAACACAUACAAACAAGCAAGAAGUUAAAGGCUAAAAAAAGCACCAGAACCAUUCACUGAUAGAAGAAAAUAAGCGAAACAGCACCAUCUUGGUUGCAAUAAAACAAUAUAUUCGGCACAAUACAGCAAACCUUAUCAAGGGUUUUCUUUCGCAAAUGGAAGUUUUUUUAUAAUUUUGCGCCAUU ..............((((((((((..(((.....)))....(((((((((((.((((...((..................(((..............(((((((..(((((.(((((....(.((..(((......)))..)).).)))))..((((((((..(((..........(((((.((((((......................)))))).)))))..(((......)))....)))....))))))))....)))))..)))))))..(((((.....)).))).................))).......((.(((((((....))))))).))...)).))))..)))))))))))..)))))))))).. (-73.95) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 296 169 133 169 135 pint:PI0767|5end_possible_TonB-dependent_receptor_701915..702145_POSITIVE 289 279 250 144 120 pint:PI2139|5end_cysteinyl-tRNA_synthetase_2085266..2085496_POSITIVE 286 267 221 185 133 pint:PI0639|5end_small_heat_shock_protein_582678..582908_POSITIVE 283 78 34 44 2 pint:PI2087|5end_dihydropicolinate_reductase_2043423..2043653_POSITIVE 283 189 142 167 114 pint:PI0528|5end_hypothetical_protein_482791..483021_POSITIVE 281 318 280 225 187 pint:PI0677|5end_hypothetical_protein_616513..616743_POSITIVE 277 113 77 227 197 pint:PI0838|5end_DNA_replication_and_repair_protein_772699..772929_POSITIVE 276 299 251 185 139 pint:PI0735|5end_ABC_transporter,_ATP-binding_/_permease_668793..669023_POSITIVE 275 145 103 63 21 pint:PI0468|5end_50S_ribosomal_protein_L29_436905..437135_POSITIVE 274 149 102 198 148 pint:PI1216|5end_probable_phosphohydrolase_1134814..1135044_POSITIVE 272 138 92 200 144 pint:PI0435|5end_30S_ribosomal_protein_S21_406997..407227_POSITIVE 271 145 102 222 172 pint:PI0580|5end_Holliday_junction_DNA_helicase_524178..524408_POSITIVE 269 306 263 52 8 pint:PI0049|5end_outer_membrane_receptor_protein_(iron_transport)_48605..48835_POSITIVE 267 300 252 74 23 pint:PI0258|5end_conjugative_transposon_protein,_TraG_249722..249952_POSITIVE 264 198 153 57 19 pint:PI0619|5end_hypothetical_protein_569364..569594_POSITIVE 263 151 111 230 177 pint:PI0138|5end_hypothetical_protein_131082..131312_POSITIVE 262 170 123 58 1 pint:PI1715|5end_conserved_hypothetical_protein;_possible_DNA-binding_protein,_histone-like_family_1631639..1631869_POSITIVE 262 175 132 163 117 pint:PI1619|5end_two-component_system_response_regulator_1543210..1543440_POSITIVE 262 99 54 108 60 pint:PI0431|5end_Xaa-Pro_aminopeptidase_403064..403294_POSITIVE 256 145 102 180 141 pint:PI0764|5end_permease_697962..698192_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 296 169 133 150 116 pint:PI0766|3end_conserved_hypothetical_protein_701976..702126_POSITIVE 287 170 121 137 86 pint:PI1021|3end_conserved_hypothetical_protein;_possible_methyltransferase_939634..939784_POSITIVE 287 139 92 97 48 pint:PI0183|3end_hypothetical_protein_174810..174960_POSITIVE 284 73 33 107 71 pint:PI0056|3end_conserved_hypothetical_protein;_possible_DNA_uptake_protein_55907..56057_POSITIVE 277 113 77 129 99 pint:PI0837|3end_conserved_hypothetical_protein_772681..772831_POSITIVE 277 190 141 88 38 pint:PI0145|3end_secDF_export_membrane_protein_139724..139874_POSITIVE 276 299 251 72 26 pint:PI0734|3end_ABC_transporter,_ATP-binding_/_permease_668760..668910_POSITIVE 275 145 103 54 12 pint:PI0467|3end_50S_ribosomal_protein_L16_436976..437126_POSITIVE 272 300 251 108 57 pint:PI1879|3end_uracil_phosphoribosyltransferase_1821245..1821395_POSITIVE 272 199 151 146 94 pint:PI0294|3end_conserved_hypothetical_protein_276806..276956_POSITIVE 267 300 252 74 23 pint:PI0257|3end_conjugative_transposon_protein,_TraF_249802..249952_POSITIVE 264 119 85 46 7 pint:PI2036|3end_hypothetical_protein_1989516..1989666_POSITIVE 262 99 54 65 17 pint:PI0430|3end_periplasmic_protease;_MdsD_protein_403101..403251_POSITIVE 257 170 123 95 43 pint:PI1187|3end_conserved_hypothetical_protein_1107245..1107395_POSITIVE 256 145 102 140 101 pint:PI0763|3end_thymidine_kinase_698002..698152_POSITIVE 254 322 293 138 108 pint:PI2037|3end_TIM-barrel_protein,_NifR3_family_1990369..1990519_POSITIVE 252 150 102 122 73 pint:PI1713|3end_ABC_transporter,_ATP-binding_protein_1630192..1630342_POSITIVE 252 189 141 71 7 pint:PI1168|3end_hypothetical_protein_1089922..1090072_POSITIVE 252 62 32 140 113 pint:PI0100|3end_LPS_biosynthesis_protein_(lipopolysaccharide_biosynthesis_protein)_96726..96876_POSITIVE 249 175 136 37 1 pint:PI1617|3end_hypothetical_protein_1543164..1543314_POSITIVE