Origin IGS: taagcacagctaaaatagccaaagtgctatcaagaataacgcccatcttgccattcaacagcaagatgggcgttttgcgtatgccttgtggcgaacgtgagttggtgtaagaattatgcaggtatattatttataagatactttaatatgcctataatcaaaaagaagtgcagtatcttcgactaattcttacaccaaactcacgttattttgtgagcgaaaagaaggctataa .........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 ttatagccttcttttcgctcacaaaataacgtgagtttggtgtaagaattagtcgaagatactgcacttctttttgattataggcatattaaagtatcttataaataatatacctgcataattcttacaccaactcacgttcgccacaaggcatacgcaaaacgcccatcttgctgttgaatggcaagatgggcgttattcttgatagcactttggctattttagctgtgctta Mask Tandem Repeat Region ================================================ taagcacagctaaaatagccaaagtgctatcaagaataacgcccatcttgccattcaacagcaagatgggcgttttgcgtatgccttgtggcgaacgtgagttggtgtaagaattatgcaggtatattatttataagatactttaatatgcctataatcaaaaagaagtgcagtatcttcgactaattcttacaccaaactcacgttattttgtgagcgaaaagaaggctataa Find is-nt database================================================ Query_seq: PI0927:PI0928|PI0927:PI0928:transglutaminase-related protein:hypothetical protein:->->:859757..859990 234 taagcacagctaaaatagccaaagtgctatcaagaataacgcccatcttgccattcaacagcaagatgggcgttttgcgtatgccttgtggcgaacgtgagttggtgtaagaattatgcaggtatattatttataagatactttaatatgcctataatcaaaaagaagtgcagtatcttcgactaattcttacaccaaactcacgttattttgtgagcgaaaagaaggctataa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI0927:PI0928|PI0927:PI0928:transglutaminase-related protein:hypothetical protein:->->:859757..859990 234 taagcacagctaaaatagccaaagtgctatcaagaataacgcccatcttgccattcaacagcaagatgggcgttttgcgtatgccttgtggcgaacgtgagttggtgtaagaattatgcaggtatattatttataagatactttaatatgcctataatcaaaaagaagtgcagtatcttcgactaattcttacaccaaactcacgttattttgtgagcgaaaagaaggctataa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI0927:PI0928|PI0927:PI0928:transglutaminase-related protein:hypothetical protein:->->:859757..859990 234 taagcacagctaaaatagccaaagtgctatcaagaataacgcccatcttgccattcaacagcaagatgggcgttttgcgtatgccttgtggcgaacgtgagttggtgtaagaattatgcaggtatattatttataagatactttaatatgcctataatcaaaaagaagtgcagtatcttcgactaattcttacaccaaactcacgttattttgtgagcgaaaagaaggctataa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 taagcacagctaaaatagccaaagtgctatcaagaataacgcccatcttgccattcaacagcaagatgggcgttttgcgtatgccttgtggcgaacgtgagttggtgtaagaattatgcaggtatattatttataagatactttaatatgcctataatcaaaaagaagtgcagtatcttcgactaattcttacaccaaactcacgttattttgtgagcgaaaagaaggctataa Predict ORF larger than 30AA ================================================ Protein_Len: 31 Strand: + Start: 15 End: 107 .............. M A K V L S R I T P I L P F N S K M G V L R M P C G E R E L V ............................................................................................................................... Protein_Len: 32 Strand: + Start: 88 End: 183 ....................................................................................... M A N V S W C K N Y A G I L F I R Y F N M P I I K K K C S I F D ................................................... Protein_Len: 43 Strand: - Start: 2 End: 130 . L V A L I A L T S D L I V G M K G N L L L I P T K R I G Q P S R S N T Y S N H L Y I M ........................................................................................................ taagcacagctaaaatagccaaagtgctatcaagaataacgcccatcttgccattcaacagcaagatgggcgttttgcgtatgccttgtggcgaacgtgagttggtgtaagaattatgcaggtatattatttataagatactttaatatgcctataatcaaaaagaagtgcagtatcttcgactaattcttacaccaaactcacgttattttgtgagcgaaaagaaggctataa 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: 84 Start: 129 End: 158 ................................................................................................................................ATTTATAAGATACTTTAATATGCCTATAAT............................................................................ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ taagcacagctaaaatagccaaagtgctatcaagaataacgcccatcttgccattcaacagcaagatgggcgttttgcgtatgccttgtggcgaacgtgagttggtgtaagaattatgcaggtatattatttataagatactttaatatgcctataatcaaaaagaagtgcagtatcttcgactaattcttacaccaaactcacgttattttgtgagcgaaaagaaggctataa Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 100 HP_score: -15.0 Tail_Score: -4.24606 Start: 40 End: 72 Full_Region: TGCTATCAAGAATAA CGCCCATCTTGC CATTCAACA GCAAGATGGGCG TTTTGCGTATGCCTT .......................................CGCCCATCTTGCCATTCAACAGCAAGATGGGCG.................................................................................................................................................................. TransTerm Strand: - Conf: 100 HP_score: -19.3 Tail_Score: -3.99374 Start: 40 End: 72 Full_Region: aaggcatacgcaaaa cgcccatcttgctgt tga atggcaagatgggcg ttattcttgatagca .......................................cgcccatcttgctgttgaatggcaagatgggcg.................................................................................................................................................................. Find igs database================================================ Query_seq: PI0927:PI0928|PI0927:PI0928:transglutaminase-related protein:hypothetical protein:->->:859757..859990 234 taagcacagctaaaatagccaaagtgctatcaagaataacgcccatcttgccattcaacagcaagatgggcgttttgcgtatgccttgtggcgaacgtgagttggtgtaagaattatgcaggtatattatttataagatactttaatatgcctataatcaaaaagaagtgcagtatcttcgactaattcttacaccaaactcacgttattttgtgagcgaaaagaaggctataa Intra-Species Hit: Count: 1 Min: 1 Max: 234 Len: 234 Subject: pint_PI0927_PI0928|transglutaminase-related protein:hypothetical protein|POSITIVE:POSITIVE|[859757,859990]|234 HSP 1 e-value: 1.0E-130 bit: 464.0 Len: 234 Query Start:1 Query End:234 Subject Strand: POSITIVE Subject Start: 1 Subject End: 234 taagcacagctaaaatagccaaagtgctatcaagaataacgcccatcttgccattcaacagcaagatgggcgttttgcgtatgccttgtggcgaacgtgagttggtgtaagaattatgcaggtatattatttataagatactttaatatgcctataatcaaaaagaagtgcagtatcttcgactaattcttacaccaaactcacgttattttgtgagcgaaaagaaggctataa taagcacagctaaaatagccaaagtgctatcaagaataacgcccatcttgccattcaacagcaagatgggcgttttgcgtatgccttgtggcgaacgtgagttggtgtaagaattatgcaggtatattatttataagatactttaatatgcctataatcaaaaagaagtgcagtatcttcgactaattcttacaccaaactcacgttattttgtgagcgaaaagaaggctataa Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAGCACAGCUAAAAUAGCCAAAGUGCUAUCAAGAAUAACGCCCAUCUUGCCAUUCAACAGCAAGAUGGGCGUUUUGCGUAUGCCUUGUGGCGAACGUGAGUUGGUGUAAGAAUUAUGCAGGUAUAUUAUUUAUAAGAUACUUUAAUAUGCCUAUAAUCAAAAAGAAGUGCAGUAUCUUCGACUAAUUCUUACACCAAACUCACGUUAUUUUGUGAGCGAAAAGAAGGCUAUAA ..(((...)))...((((((....((((..(((((..((((((((((((((.........))))))))))))))........(((....))).(((((((((((((((((((((((...((((((((((..............))))))))))...........((((........))))...))))))))))))).)))))))))).)))))..)))).......)))))).. (-87.04) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUAUAGCCUUCUUUUCGCUCACAAAAUAACGUGAGUUUGGUGUAAGAAUUAGUCGAAGAUACUGCACUUCUUUUUGAUUAUAGGCAUAUUAAAGUAUCUUAUAAAUAAUAUACCUGCAUAAUUCUUACACCAACUCACGUUCGCCACAAGGCAUACGCAAAACGCCCAUCUUGCUGUUGAAUGGCAAGAUGGGCGUUAUUCUUGAUAGCACUUUGGCUAUUUUAGCUGUGCUUA .((((((.........((.........((((((((((.(((((((((((((...((((........)))).......(((((((.((((....)))))))))))..............))))))))))))))))))))))).(((....)))....))..(((((((((((((((((...)))))))))))))))))......((((((......))))))...)))))).... (-83.90) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 481 229 181 198 142 pint:PI0286|5end_ISPg3-related_transposase_271833..272063_POSITIVE 407 130 85 146 102 pint:PI1500|5end_hypothetical_protein_1420626..1420856_POSITIVE 397 207 162 188 143 pint:PI1380|5end_conserved_hypothetical_protein_1302587..1302817_POSITIVE 393 137 91 192 144 pint:PI0312|5end_hypothetical_protein_294591..294821_POSITIVE 387 88 42 42 2 pint:PI0265|5end_conjugative_transposon_protein,_TraO_257296..257526_POSITIVE 365 100 56 51 3 pint:PI1490|5end_GTP_cyclohydrolase_I_1408571..1408801_POSITIVE 361 107 61 175 131 pint:PI0094|5end_protoporphyrinogen_oxidase_89571..89801_POSITIVE 361 107 61 101 57 pint:PI0091|5end_hypothetical_protein_89497..89727_POSITIVE 358 93 56 68 36 pint:PI0635|5end_dephospho-CoA_kinase_580954..581184_POSITIVE 358 80 38 147 105 pint:PI0213|5end_conserved_hypothetical_protein_207065..207295_POSITIVE 350 99 59 223 181 pint:PI1228|5end_conserved_hypothetical_protein_1149045..1149275_POSITIVE 350 90 41 68 15 pint:PI0314|5end_conserved_hypothetical_protein_295552..295782_POSITIVE 349 98 51 198 154 pint:PI2034|5end_conserved_hypothetical_protein_1987573..1987803_POSITIVE 342 98 57 157 121 pint:PI1640|5end_hypothetical_protein_1558062..1558292_POSITIVE 341 88 43 221 169 pint:PI1493|5end_conserved_hypothetical_protein_1412268..1412498_POSITIVE 339 77 31 208 159 pint:PI0269|5end_conserved_hypothetical_protein_259835..260065_POSITIVE 337 100 51 63 18 pint:PI0519|5end_5'-nucleotidase/2',3'-cyclic_phosphodiesterase_477953..478183_POSITIVE 335 80 40 62 13 pint:PI0806|5end_heavy_metal_efflux_pump_743679..743909_POSITIVE 334 109 66 123 81 pint:PI0260|5end_conjugative_transposon_protein,_TraJ_253023..253253_POSITIVE 330 94 53 53 7 pint:PI2013|5end_hypothetical_protein_1972329..1972559_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 468 74 38 53 17 pint:PI0927|3end_transglutaminase-related_protein_859696..859846_POSITIVE 360 108 69 140 96 pint:PI1715|3end_conserved_hypothetical_protein;_possible_DNA-binding_protein,_histone-like_family_1632324..1632474_POSITIVE 356 104 61 54 8 pint:PI0212|3end_surface_protein/internalin-related_protein_207022..207172_POSITIVE 350 99 59 72 30 pint:PI1227|3end_conserved_hypothetical_protein;_possible_DNA-binding_protein,_histone-like_family_1148974..1149124_POSITIVE 342 98 57 148 112 pint:PI1639|3end_conserved_hypothetical_protein_1558133..1558283_POSITIVE 340 88 45 37 1 pint:PI0264|3end_transfer_region-related_protein,_TraN_257371..257521_POSITIVE 339 99 51 124 68 pint:PI1378|3end_GTP-binding_protein_lepA_1301651..1301801_POSITIVE 339 77 31 83 34 pint:PI0268|3end_lysozyme-related_protein_259790..259940_POSITIVE 335 80 40 110 61 pint:PI0805|3end_conserved_hypothetical_protein_743807..743957_POSITIVE 334 109 61 123 75 pint:PI2041|3end_conserved_hypothetical_protein_1994660..1994810_POSITIVE 334 109 66 63 21 pint:PI0259|3end_conserved_protein_found_in_conjugation,_TraI_253043..253193_POSITIVE 327 86 42 61 13 pint:PI0814|3end_conserved_hypothetical_protein_754426..754576_POSITIVE 324 106 67 40 4 pint:PI0923|3end_6-phosphofructokinase_855051..855201_POSITIVE 322 106 61 147 87 pint:PI1607|3end_ABC-related_lipoprotein_releasing_system,_ATP-binding_protein_1535834..1535984_POSITIVE 312 108 61 143 85 pint:PI1302|3end_hypothetical_protein_1215167..1215317_POSITIVE 312 102 64 41 6 pint:PI0261|3end_conjugative_transposon_protein,_TraK_254765..254915_POSITIVE 309 96 61 67 38 pint:PI1647|3end_hypothetical_protein_1562531..1562681_POSITIVE 309 96 61 67 38 pint:PI0353|3end_hypothetical_protein_325337..325487_POSITIVE 309 84 41 74 31 pint:PI0220|3end_conserved_hypothetical_protein_212341..212491_POSITIVE 306 96 53 65 11 pint:PI2012|3end_hypothetical_protein_1971555..1971705_POSITIVE