Origin IGS: tacttctgcattaccttcgcttaccacacgtacttcccgtgcatggatttgttcattcacacggtactgtaacttcattttgtcattcttcattcaactatattaaagttttattttttgttattaaacggctgcaaagatacggcttttacaatgattagccaaatttttagtattatttttatcttcaattcattgatagaaagccactttttgctatttcgccatattttacaccaatattatcctaaagtctta .........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 taagactttaggataatattggtgtaaaatatggcgaaatagcaaaaagtggctttctatcaatgaattgaagataaaaataatactaaaaatttggctaatcattgtaaaagccgtatctttgcagccgtttaataacaaaaaataaaactttaatatagttgaatgaagaatgacaaaatgaagttacagtaccgtgtgaatgaacaaatccatgcacgggaagtacgtgtggtaagcgaaggtaatgcagaagta Mask Tandem Repeat Region ================================================ tacttctgcattaccttcgcttaccacacgtacttcccgtgcatggatttgttcattcacacggtactgtaacttcattttgtcattcttcattcaactatattaaagttttattttttgttattaaacggctgcaaagatacggcttttacaatgattagccaaatttttagtattatttttatcttcaattcattgatagaaagccactttttgctatttcgccatattttacaccaatattatcctaaagtctta Find is-nt database================================================ Query_seq: PI1146:PI1147|PI1146:PI1147:translation initiation factor IF3:conserved hypothetical protein:->->:1073564..1073821 258 tacttctgcattaccttcgcttaccacacgtacttcccgtgcatggatttgttcattcacacggtactgtaacttcattttgtcattcttcattcaactatattaaagttttattttttgttattaaacggctgcaaagatacggcttttacaatgattagccaaatttttagtattatttttatcttcaattcattgatagaaagccactttttgctatttcgccatattttacaccaatattatcctaaagtctta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI1146:PI1147|PI1146:PI1147:translation initiation factor IF3:conserved hypothetical protein:->->:1073564..1073821 258 tacttctgcattaccttcgcttaccacacgtacttcccgtgcatggatttgttcattcacacggtactgtaacttcattttgtcattcttcattcaactatattaaagttttattttttgttattaaacggctgcaaagatacggcttttacaatgattagccaaatttttagtattatttttatcttcaattcattgatagaaagccactttttgctatttcgccatattttacaccaatattatcctaaagtctta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI1146:PI1147|PI1146:PI1147:translation initiation factor IF3:conserved hypothetical protein:->->:1073564..1073821 258 tacttctgcattaccttcgcttaccacacgtacttcccgtgcatggatttgttcattcacacggtactgtaacttcattttgtcattcttcattcaactatattaaagttttattttttgttattaaacggctgcaaagatacggcttttacaatgattagccaaatttttagtattatttttatcttcaattcattgatagaaagccactttttgctatttcgccatattttacaccaatattatcctaaagtctta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tacttctgcattaccttcgcttaccacacgtacttcccgtgcatggatttgttcattcacacggtactgtaacttcattttgtcattcttcattcaactatattaaagttttattttttgttattaaacggctgcaaagatacggcttttacaatgattagccaaatttttagtattatttttatcttcaattcattgatagaaagccactttttgctatttcgccatattttacaccaatattatcctaaagtctta Predict ORF larger than 30AA ================================================ Protein_Len: 51 Strand: + Start: 6 End: 158 ..... M H Y L R L P H V L P V H G F V H S H G T V T S F C H S S F N Y I K V L F F V I K R L Q R Y G F Y N D .................................................................................................... Protein_Len: 58 Strand: + Start: 85 End: 258 .................................................................................... M L H S T I L K F Y F L L L N G C K D T A F T M I S Q I F S I I F I F N S L I E S H F L L F R H I L H Q Y Y P K V L Protein_Len: 39 Strand: - Start: 114 End: 230 ................................................................................................................. K K N N F P Q L S V A K V I I L W I K L I I K I K L E N I S L W K K S N R W M ............................ Protein_Len: 31 Strand: - Start: 1 End: 93 V E A N G E S V V R V E R A H I Q E N V R Y Q L K M K D N K M ..................................................................................................................................................................... tacttctgcattaccttcgcttaccacacgtacttcccgtgcatggatttgttcattcacacggtactgtaacttcattttgtcattcttcattcaactatattaaagttttattttttgttattaaacggctgcaaagatacggcttttacaatgattagccaaatttttagtattatttttatcttcaattcattgatagaaagccactttttgctatttcgccatattttacaccaatattatcctaaagtctta 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================================================ tacttctgcattaccttcgcttaccacacgtacttcccgtgcatggatttgttcattcacacggtactgtaacttcattttgtcattcttcattcaactatattaaagttttattttttgttattaaacggctgcaaagatacggcttttacaatgattagccaaatttttagtattatttttatcttcaattcattgatagaaagccactttttgctatttcgccatattttacaccaatattatcctaaagtctta Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PI1146:PI1147|PI1146:PI1147:translation initiation factor IF3:conserved hypothetical protein:->->:1073564..1073821 258 tacttctgcattaccttcgcttaccacacgtacttcccgtgcatggatttgttcattcacacggtactgtaacttcattttgtcattcttcattcaactatattaaagttttattttttgttattaaacggctgcaaagatacggcttttacaatgattagccaaatttttagtattatttttatcttcaattcattgatagaaagccactttttgctatttcgccatattttacaccaatattatcctaaagtctta Intra-Species Hit: Count: 1 Min: 1 Max: 258 Len: 258 Subject: pint_PI1146_PI1147|translation initiation factor IF3:conserved hypothetical protein|POSITIVE:POSITIVE|[1073564,1073821]|258 HSP 1 e-value: 1.0E-144 bit: 511.0 Len: 258 Query Start:1 Query End:258 Subject Strand: POSITIVE Subject Start: 1 Subject End: 258 tacttctgcattaccttcgcttaccacacgtacttcccgtgcatggatttgttcattcacacggtactgtaacttcattttgtcattcttcattcaactatattaaagttttattttttgttattaaacggctgcaaagatacggcttttacaatgattagccaaatttttagtattatttttatcttcaattcattgatagaaagccactttttgctatttcgccatattttacaccaatattatcctaaagtctta tacttctgcattaccttcgcttaccacacgtacttcccgtgcatggatttgttcattcacacggtactgtaacttcattttgtcattcttcattcaactatattaaagttttattttttgttattaaacggctgcaaagatacggcttttacaatgattagccaaatttttagtattatttttatcttcaattcattgatagaaagccactttttgctatttcgccatattttacaccaatattatcctaaagtctta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UACUUCUGCAUUACCUUCGCUUACCACACGUACUUCCCGUGCAUGGAUUUGUUCAUUCACACGGUACUGUAACUUCAUUUUGUCAUUCUUCAUUCAACUAUAUUAAAGUUUUAUUUUUUGUUAUUAAACGGCUGCAAAGAUACGGCUUUUACAAUGAUUAGCCAAAUUUUUAGUAUUAUUUUUAUCUUCAAUUCAUUGAUAGAAAGCCACUUUUUGCUAUUUCGCCAUAUUUUACACCAAUAUUAUCCUAAAGUCUUA .((((.((((.((((......(((.....)))......(((.(((((....))))).)))..)))).))))..........................................................(((.(((((((...(((((((.((((((...................................))))))...)))))))..)))))))......)))........................)))).... (-34.65) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAGACUUUAGGAUAAUAUUGGUGUAAAAUAUGGCGAAAUAGCAAAAAGUGGCUUUCUAUCAAUGAAUUGAAGAUAAAAAUAAUACUAAAAAUUUGGCUAAUCAUUGUAAAAGCCGUAUCUUUGCAGCCGUUUAAUAACAAAAAAUAAAACUUUAAUAUAGUUGAAUGAAGAAUGACAAAAUGAAGUUACAGUACCGUGUGAAUGAACAAAUCCAUGCACGGGAAGUACGUGUGGUAAGCGAAGGUAAUGCAGAAGUA ....(((((.(.((......(.(((((((((((((......((((....(((((.(((.((((....))))))).....................)))))....))))....))))))).)))))).)((((((...(((........(((((((.....(((...........)))....)))))))......((((((..(((........)))))))))........)))..))))))......)).).))))). (-45.15) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 337 49 1 212 168 pint:PI0610|5end_conserved_hypothetical_protein_557403..557633_POSITIVE 310 68 24 86 40 pint:PI1871|5end_glycosyl_transferase,_group_1_family_protein_1815788..1816018_POSITIVE 306 47 3 164 113 pint:PI1207|5end_hypothtical_protein_1126977..1127207_POSITIVE 287 47 3 135 81 pint:PI0785|5end_hypothetical_protein_723744..723974_POSITIVE 287 47 1 85 25 pint:PI0126|5end_conserved_hypothetical_protein_117925..118155_POSITIVE 280 41 3 227 183 pint:PI1205|5end_hypothetical_protein_1127047..1127277_POSITIVE 280 50 5 185 136 pint:PI0730|5end_hypothetical_protein_661685..661915_POSITIVE 280 47 2 76 35 pint:PI0263|5end_conjugative_transposon_protein,_TraM_255256..255486_POSITIVE 280 151 114 136 101 pint:PI0070|5end_conserved_hypothetical_protein_67653..67883_POSITIVE 279 46 5 216 163 pint:PI0537|5end_alanyl-tRNA_synthetase_(alanine--tRNA_ligase)_489756..489986_POSITIVE 278 41 1 158 119 pint:PI1241|5end_probable_phosphoesterase_1166365..1166595_POSITIVE 277 66 25 50 4 pint:PI1724|5end_inosine-5'-monophosphate_dehydrogenase_1641075..1641305_POSITIVE 275 84 41 70 13 pint:PI2135|5end_conserved_hypothetical_protein_2082754..2082984_POSITIVE 269 39 4 105 68 pint:PI1789|5end_hypothetical_protein_1718727..1718957_POSITIVE 265 90 41 179 124 pint:PI0265|5end_conjugative_transposon_protein,_TraO_257296..257526_POSITIVE 264 146 114 213 178 pint:PI1772|5end_pullulanase_1702257..1702487_POSITIVE 264 43 2 59 21 pint:PI1173|5end_transcription_regulatory_protein,_LacI_family_1095051..1095281_POSITIVE 263 58 18 75 33 pint:PI0336|5end_hypothetical_protein_314499..314729_POSITIVE 262 46 3 189 138 pint:PI0380|5end_conserved_hypothetical_protein_350162..350392_POSITIVE 260 49 14 65 22 pint:PI0355|5end_probable__N-acetylmuramoyl-L-alanine_amidase_326157..326387_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 351 153 111 117 74 pint:PI0761|3end_hypothetical_protein_696348..696498_POSITIVE 321 149 126 51 28 pint:PI0437|3end_conserved_hypothetical_protein;_possible_ribosomal_subunit_interface_protein_408543..408693_POSITIVE 315 49 15 69 21 pint:PI1649|3end_hypothetical_protein_1563441..1563591_POSITIVE 275 84 41 76 19 pint:PI2136|3end_hypothetical_protein_2082840..2082990_POSITIVE 267 85 41 79 38 pint:PI0857|3end_hypothetical_protein_790986..791136_POSITIVE 267 43 3 127 79 pint:PI0358|3end_hypothetical_protein_328105..328255_POSITIVE 264 146 114 150 115 pint:PI1771|3end_alpha-glucosidase_1702274..1702424_POSITIVE 263 70 24 129 81 pint:PI1009|3end_cytochrome_c_nitrite_reductase,_large_subunit_930840..930990_POSITIVE 260 49 14 69 26 pint:PI0354|3end_hypothetical_protein_326241..326391_POSITIVE 259 90 41 65 17 pint:PI1526|3end_hypothetical_protein_1447695..1447845_POSITIVE 259 60 11 57 10 pint:PI0355|3end_probable__N-acetylmuramoyl-L-alanine_amidase_326698..326848_POSITIVE 258 45 5 145 107 pint:PI0356|3end_hypothetical_protein_327288..327438_POSITIVE 255 47 2 143 95 pint:PI0734|3end_ABC_transporter,_ATP-binding_/_permease_668760..668910_POSITIVE 254 101 68 42 10 pint:PI1776|3end_probable_peptidase_of_the_M22_family_(inactive?_chaperone?))_1709425..1709575_POSITIVE 252 69 24 74 32 pint:PI1807|3end_hypothetical_protein_1742481..1742631_POSITIVE 252 150 110 122 76 pint:PI0990|3end_GDP-mannose_4,6-dehydratase_915054..915204_POSITIVE 246 50 5 82 23 pint:PI0187|3end_hypothetical_protein_178211..178361_POSITIVE 243 20 3 143 126 pint:PI1651|3end_hypothetical_protein_1564512..1564662_POSITIVE 243 49 3 87 29 pint:PI0951|3end_hypothetical_protein_885448..885598_POSITIVE 242 46 9 135 94 pint:PI2099|3end_D-alanyl-D-alanine_dipeptidase_2053277..2053427_POSITIVE