Origin IGS: taaagaaatagagtatagaaacatataatcaaagaattaagggcaacgaaacgaatgtttcgttgcccttgtcgttgtgtttgctttattttgtatagtttta .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 taaaactatacaaaataaagcaaacacaacgacaagggcaacgaaacattcgtttcgttgcccttaattctttgattatatgtttctatactctatttcttta Mask Tandem Repeat Region ================================================ taaagaaatagagtatagaaacatataatcaaagaattaagggcaacgaaacgaatgtttcgttgcccttgtcgttgtgtttgctttattttgtatagtttta Find is-nt database================================================ Query_seq: PI0623:PI0625|PI0623:PI0625:hypothetical protein:possible membrane transport protein:->->:573141..573243 103 taaagaaatagagtatagaaacatataatcaaagaattaagggcaacgaaacgaatgtttcgttgcccttgtcgttgtgtttgctttattttgtatagtttta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI0623:PI0625|PI0623:PI0625:hypothetical protein:possible membrane transport protein:->->:573141..573243 103 taaagaaatagagtatagaaacatataatcaaagaattaagggcaacgaaacgaatgtttcgttgcccttgtcgttgtgtttgctttattttgtatagtttta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI0623:PI0625|PI0623:PI0625:hypothetical protein:possible membrane transport protein:->->:573141..573243 103 taaagaaatagagtatagaaacatataatcaaagaattaagggcaacgaaacgaatgtttcgttgcccttgtcgttgtgtttgctttattttgtatagtttta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 taaagaaatagagtatagaaacatataatcaaagaattaagggcaacgaaacgaatgtttcgttgcccttgtcgttgtgtttgctttattttgtatagtttta Predict ORF larger than 30AA ================================================ taaagaaatagagtatagaaacatataatcaaagaattaagggcaacgaaacgaatgtttcgttgcccttgtcgttgtgtttgctttattttgtatagtttta 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================================================ taaagaaatagagtatagaaacatataatcaaagaattaagggcaacgaaacgaatgtttcgttgcccttgtcgttgtgtttgctttattttgtatagtttta Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 90 HP_score: -10.9 Tail_Score: -3.73447 Start: 30 End: 77 Full_Region: ATAGAAACATATAAT CAAAGAATTAAGGGCAACGAAAC GAAT GTTTCGTTGCCCTTGTCGTTG TGTTTGCTTTATTTT .............................CAAAGAATTAAGGGCAACGAAACGAATGTTTCGTTGCCCTTGTCGTTG.......................... TransTerm Strand: + Conf: 81 HP_score: -7.9 Tail_Score: -4.33487 Start: 30 End: 79 Full_Region: ATAGAAACATATAAT CAAAGAATTAAGGGCAACGAAAC GAAT GTTTCGTTGCCCTTGTCGTTGTG TTTGCTTTATTTTGT .............................CAAAGAATTAAGGGCAACGAAACGAATGTTTCGTTGCCCTTGTCGTTGTG........................ TransTerm Strand: + Conf: 82 HP_score: -8.6 Tail_Score: -3.94482 Start: 35 End: 74 Full_Region: AACATATAATCAAAG AATTAAGGGCAACGAAAC GAAT GTTTCGTTGCCCTTGTCG TTGTGTTTGCTTTAT ..................................AATTAAGGGCAACGAAACGAATGTTTCGTTGCCCTTGTCG............................. TransTerm Strand: - Conf: 100 HP_score: -13.4 Tail_Score: -4.13903 Start: 37 End: 72 Full_Region: aaagcaaacacaacg acaagggcaacgaaac attc gtttcgttgcccttaa ttctttgattatatg ....................................acaagggcaacgaaacattcgtttcgttgcccttaa............................... TransTerm Strand: + Conf: 100 HP_score: -19.1 Tail_Score: -3.00731 Start: 38 End: 71 Full_Region: ATATAATCAAAGAAT TAAGGGCAACGAAAC GAAT GTTTCGTTGCCCTTG TCGTTGTGTTTGCTT .....................................TAAGGGCAACGAAACGAATGTTTCGTTGCCCTTG................................ TransTerm Strand: - Conf: 100 HP_score: -18.6 Tail_Score: -3.65446 Start: 41 End: 68 Full_Region: caaacacaacgacaa gggcaacgaaac attc gtttcgttgccc ttaattctttgatta ........................................gggcaacgaaacattcgtttcgttgccc................................... Find igs database================================================ Query_seq: PI0623:PI0625|PI0623:PI0625:hypothetical protein:possible membrane transport protein:->->:573141..573243 103 taaagaaatagagtatagaaacatataatcaaagaattaagggcaacgaaacgaatgtttcgttgcccttgtcgttgtgtttgctttattttgtatagtttta Intra-Species Hit: Count: 1 Min: 1 Max: 103 Len: 103 Subject: pint_PI0623_PI0625|hypothetical protein:possible membrane transport protein|POSITIVE:POSITIVE|[573141,573243]|103 HSP 1 e-value: 4.0E-52 bit: 204.0 Len: 103 Query Start:1 Query End:103 Subject Strand: POSITIVE Subject Start: 1 Subject End: 103 taaagaaatagagtatagaaacatataatcaaagaattaagggcaacgaaacgaatgtttcgttgcccttgtcgttgtgtttgctttattttgtatagtttta taaagaaatagagtatagaaacatataatcaaagaattaagggcaacgaaacgaatgtttcgttgcccttgtcgttgtgtttgctttattttgtatagtttta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAAGAAAUAGAGUAUAGAAACAUAUAAUCAAAGAAUUAAGGGCAACGAAACGAAUGUUUCGUUGCCCUUGUCGUUGUGUUUGCUUUAUUUUGUAUAGUUUUA ....(((((((((((....((((((........((..(((((((((((((((....)))))))))))))))))..)))))))))))))))))........... (-34.20) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAAACUAUACAAAAUAAAGCAAACACAACGACAAGGGCAACGAAACAUUCGUUUCGUUGCCCUUAAUUCUUUGAUUAUAUGUUUCUAUACUCUAUUUCUUUA ..................((.((((((((.((.((((((((((((((....))))))))))))))...)).)))......)))))))................ (-25.50) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 425 71 41 214 184 pint:PI0623|5end_hypothetical_protein_572167..572397_POSITIVE 317 86 52 37 1 pint:PI1382|5end_hypothetical_protein_1303608..1303838_POSITIVE 315 84 48 217 180 pint:PI0281|5end_conserved_hypothetical_protein_266309..266539_POSITIVE 314 86 42 228 176 pint:PI0784|5end_possible_amidase_enhancer_precursor_721892..722122_POSITIVE 302 87 41 113 67 pint:PI2085|5end_conserved_hypothetical_protein_2041100..2041330_POSITIVE 292 100 52 168 129 pint:PI1670|5end_hypothetical_protein_1583725..1583955_POSITIVE 290 94 57 108 62 pint:PI1633|5end_hypothetical_protein_1552504..1552734_POSITIVE 290 79 39 164 125 pint:PI0897|5end_ferredoxin,_4Fe-4S_828227..828457_POSITIVE 289 96 51 209 159 pint:PI0366|5end_conserved_hypothetical_protein_336765..336995_POSITIVE 286 80 41 41 1 pint:PI0577|5end_conserved_hypothetical_protein_521811..522041_POSITIVE 280 87 41 229 180 pint:PI1621|5end_hypothetical_protein_1545424..1545654_POSITIVE 280 84 42 71 18 pint:PI0658|5end_conserved_hypothetical_protein_602187..602417_POSITIVE 279 99 59 37 6 pint:PI0962|5end_phosphoglycerate_mutase_892101..892331_POSITIVE 279 74 37 199 149 pint:PI0953|5end_hypothetical_protein_885119..885349_POSITIVE 277 79 39 219 170 pint:PI0323|5end_hypothetical_protein_305349..305579_POSITIVE 274 100 51 179 125 pint:PI1134|5end_ABC_transporter,_ATP-binding_protein_1060374..1060604_POSITIVE 273 77 33 131 86 pint:PI0213|5end_conserved_hypothetical_protein_207065..207295_POSITIVE 272 81 42 46 4 pint:PI2018|5end_50S_ribosomal_protein_L34_1975757..1975987_POSITIVE 271 96 52 145 101 pint:PI2175|5end_RNA_polymerase_sigma-54_2115007..2115237_POSITIVE 271 90 42 77 26 pint:PI0531|5end_ABC_transporter,_ATP-binding_protein;_possible_gliding_motility_related_484696..484926_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 458 90 41 84 23 pint:PI0623|3end_hypothetical_protein_573080..573230_POSITIVE 437 90 41 79 24 pint:PI0622|3end_hypothetical_protein_572087..572237_POSITIVE 415 78 34 62 18 pint:PI0620|3end_hypothetical_protein_570630..570780_POSITIVE 310 90 42 92 36 pint:PI2166|3end_hypothetical_protein_2112073..2112223_POSITIVE 306 99 55 51 6 pint:PI1706|3end_GTP-binding_protein_1623668..1623818_POSITIVE 295 80 31 128 76 pint:PI2018|3end_50S_ribosomal_protein_L34_1975989..1976139_POSITIVE 290 79 39 133 94 pint:PI0896|3end_2-oxoglutarate_oxidoreductase,_alpha_subunit_828276..828426_POSITIVE 282 80 39 73 32 pint:PI0447|3end_DNA-directed_RNA_polymerase,_beta'_subunit_421755..421905_POSITIVE 277 78 35 57 5 pint:PI0683|3end_hypothetical_protein_619797..619947_POSITIVE 276 85 41 129 78 pint:PI1855|3end_lipopolysaccharide_biosynthesis_protein_1803168..1803318_POSITIVE 276 77 33 115 74 pint:PI1227|3end_conserved_hypothetical_protein;_possible_DNA-binding_protein,_histone-like_family_1148974..1149124_POSITIVE 274 100 51 129 75 pint:PI1133|3end_GrpE_protein_1060404..1060554_POSITIVE 272 80 39 68 22 pint:PI0932|3end_conserved_hypothetical_protein;_possible_hemin_receptor_865364..865514_POSITIVE 271 90 42 58 7 pint:PI0530|3end_possible_membrane-fusion_protein_484757..484907_POSITIVE 267 96 56 88 51 pint:PI0190|3end_3-dehydroquinate_dehydratase_II_181126..181276_POSITIVE 266 84 41 114 66 pint:PI0843|3end_carboxyl-terminal_protease_777862..778012_POSITIVE 266 95 61 63 28 pint:PI0616|3end_electron_transfer_flavoprotein,_beta-subunit_566440..566590_POSITIVE 264 78 31 65 10 pint:PI0647|3end_potassium_uptake_protein_589276..589426_POSITIVE 263 85 41 137 69 pint:PI0583|3end_hypothetical_protein_526276..526426_POSITIVE 261 86 41 96 39 pint:PI1740|3end_DedA_family_protein_1662316..1662466_POSITIVE