Origin IGS: ctgataacagactttgcttgctcttcttgacgcgcttcgcgtgctttcttctgcattttgcttttgttgctcataatgatattattttacgtgagaagttttgttccttctcgcaggttattatatataataaggtgaaaatcggtttttcagctccaccttttcta .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tagaaaaggtggagctgaaaaaccgattttcaccttattatatataataacctgcgagaaggaacaaaacttctcacgtaaaataatatcattatgagcaacaaaagcaaaatgcagaagaaagcacgcgaagcgcgtcaagaagagcaagcaaagtctgttatcag Mask Tandem Repeat Region ================================================ ctgataacagactttgcttgctcttcttgacgcgcttcgcgtgctttcttctgcattttgcttttgttgctcataatgatattattttacgtgagaagttttgttccttctcgcaggttattatatataataaggtgaaaatcggtttttcagctccaccttttcta Find is-nt database================================================ Query_seq: PI0058:PI0059|PI0058:PI0059:conserved hypothetical protein:peptide chain release factor RF-2:->->:57105..57271 167 ctgataacagactttgcttgctcttcttgacgcgcttcgcgtgctttcttctgcattttgcttttgttgctcataatgatattattttacgtgagaagttttgttccttctcgcaggttattatatataataaggtgaaaatcggtttttcagctccaccttttcta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI0058:PI0059|PI0058:PI0059:conserved hypothetical protein:peptide chain release factor RF-2:->->:57105..57271 167 ctgataacagactttgcttgctcttcttgacgcgcttcgcgtgctttcttctgcattttgcttttgttgctcataatgatattattttacgtgagaagttttgttccttctcgcaggttattatatataataaggtgaaaatcggtttttcagctccaccttttcta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI0058:PI0059|PI0058:PI0059:conserved hypothetical protein:peptide chain release factor RF-2:->->:57105..57271 167 ctgataacagactttgcttgctcttcttgacgcgcttcgcgtgctttcttctgcattttgcttttgttgctcataatgatattattttacgtgagaagttttgttccttctcgcaggttattatatataataaggtgaaaatcggtttttcagctccaccttttcta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ctgataacagactttgcttgctcttcttgacgcgcttcgcgtgctttcttctgcattttgcttttgttgctcataatgatattattttacgtgagaagttttgttccttctcgcaggttattatatataataaggtgaaaatcggtttttcagctccaccttttcta Predict ORF larger than 30AA ================================================ Protein_Len: 50 Strand: + Start: 18 End: 167 ................. M L F L T R F A C F L L H F A F V A H N D I I L R E K F C S F S Q V I I Y N K V K I G F S A P P F L ctgataacagactttgcttgctcttcttgacgcgcttcgcgtgctttcttctgcattttgcttttgttgctcataatgatattattttacgtgagaagttttgttccttctcgcaggttattatatataataaggtgaaaatcggtttttcagctccaccttttcta 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================================================ ctgataacagactttgcttgctcttcttgacgcgcttcgcgtgctttcttctgcattttgcttttgttgctcataatgatattattttacgtgagaagttttgttccttctcgcaggttattatatataataaggtgaaaatcggtttttcagctccaccttttcta Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PI0058:PI0059|PI0058:PI0059:conserved hypothetical protein:peptide chain release factor RF-2:->->:57105..57271 167 ctgataacagactttgcttgctcttcttgacgcgcttcgcgtgctttcttctgcattttgcttttgttgctcataatgatattattttacgtgagaagttttgttccttctcgcaggttattatatataataaggtgaaaatcggtttttcagctccaccttttcta Intra-Species Hit: Count: 1 Min: 1 Max: 167 Len: 167 Subject: pint_PI0058_PI0059|conserved hypothetical protein:peptide chain release factor RF-2|POSITIVE:POSITIVE|[57105,57271]|167 HSP 1 e-value: 4.0E-90 bit: 331.0 Len: 167 Query Start:1 Query End:167 Subject Strand: POSITIVE Subject Start: 1 Subject End: 167 ctgataacagactttgcttgctcttcttgacgcgcttcgcgtgctttcttctgcattttgcttttgttgctcataatgatattattttacgtgagaagttttgttccttctcgcaggttattatatataataaggtgaaaatcggtttttcagctccaccttttcta ctgataacagactttgcttgctcttcttgacgcgcttcgcgtgctttcttctgcattttgcttttgttgctcataatgatattattttacgtgagaagttttgttccttctcgcaggttattatatataataaggtgaaaatcggtttttcagctccaccttttcta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CUGAUAACAGACUUUGCUUGCUCUUCUUGACGCGCUUCGCGUGCUUUCUUCUGCAUUUUGCUUUUGUUGCUCAUAAUGAUAUUAUUUUACGUGAGAAGUUUUGUUCCUUCUCGCAGGUUAUUAUAUAUAAUAAGGUGAAAAUCGGUUUUUCAGCUCCACCUUUUCUA .((((((((((....((.(((.........(((((...))))).........)))....)).))))))).))).................((((((((........)))))))).((((((((....))))).(.((((((.....)))))).)...)))....... (-32.57) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAGAAAAGGUGGAGCUGAAAAACCGAUUUUCACCUUAUUAUAUAUAAUAACCUGCGAGAAGGAACAAAACUUCUCACGUAAAAUAAUAUCAUUAUGAGCAACAAAAGCAAAAUGCAGAAGAAAGCACGCGAAGCGCGUCAAGAAGAGCAAGCAAAGUCUGUUAUCAG .....(((((((((.((......))..)))))))))...............((((((((((........))))))......................((.......)).....))))..((.((((.((...((((.((.....))))..))...)).)))).)).. (-30.30) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 346 54 16 78 33 pint:PI1633|5end_hypothetical_protein_1552504..1552734_POSITIVE 346 70 25 161 102 pint:PI1619|5end_two-component_system_response_regulator_1543210..1543440_POSITIVE 339 54 19 152 119 pint:PI0092|5end_regulatory_protein_RecX_89080..89310_POSITIVE 334 70 27 40 4 pint:PI0205|5end_deoxyuridine_5'-triphosphate_nucleotidohydrolase_197581..197811_POSITIVE 333 70 29 55 6 pint:PI1625|5end_conserved_hypothetical_protein;_possible_phage_transposase_1549316..1549546_POSITIVE 333 70 29 55 6 pint:PI0332|5end_conserved_hypothetical_protein_312600..312830_POSITIVE 331 71 31 127 79 pint:PI1711|5end_ABC_transporter,_ATP-binding_protein_1627597..1627827_POSITIVE 326 45 1 155 91 pint:PI0528|5end_hypothetical_protein_482791..483021_POSITIVE 320 44 8 196 157 pint:PI1781|5end_membrane-associated_zinc_metalloprotease_1713074..1713304_POSITIVE 320 48 1 74 28 pint:PI0473|5end_30S_ribosomal_protein_S14_438634..438864_POSITIVE 313 54 16 51 1 pint:PI1634|5end_conserved_hypothetical_protein_1553179..1553409_POSITIVE 313 54 16 51 1 pint:PI0340|5end_conserved_hypothetical_protein_316095..316325_POSITIVE 312 70 21 166 98 pint:PI1516|5end_multidrug_resistance_protein;_HlyD_family_secretion_protein_1434381..1434611_POSITIVE 310 65 21 69 23 pint:PI1631|5end_hypothetical_protein_1552424..1552654_POSITIVE 310 70 35 81 46 pint:PI1363|5end_hypothetical_protein_1281666..1281896_POSITIVE 309 73 33 164 123 pint:PI0848|5end_glycosyl_transferase,_group_2_family_protein_782247..782477_POSITIVE 305 80 32 228 181 pint:PI0751|5end_conserved_hypothetical_protein_680623..680853_POSITIVE 303 70 25 55 7 pint:PI1430|5end_subtilisin-like_serine_proteinase_1349598..1349828_POSITIVE 303 42 13 58 22 pint:PI1347|5end_DNA_damage-inducible_protein_1261130..1261360_POSITIVE 302 56 11 109 61 pint:PI1632|5end_hypothetical_protein_1552819..1553049_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 337 60 15 148 95 pint:PI1227|3end_conserved_hypothetical_protein;_possible_DNA-binding_protein,_histone-like_family_1148974..1149124_POSITIVE 320 44 8 139 100 pint:PI1780|3end_1-deoxy-D-xylulose_5-phosphate_reductoisomerase_1713097..1713247_POSITIVE 320 48 1 65 19 pint:PI0472|3end_50S_ribosomal_protein_L5_438705..438855_POSITIVE 310 65 21 59 13 pint:PI1630|3end_hypothetical_protein_1552494..1552644_POSITIVE 310 70 35 148 113 pint:PI1362|3end_60Kd_inner_membrane_protein_1281813..1281963_POSITIVE 309 73 33 69 28 pint:PI0847|3end_thiamine_biosynthesis_lipoprotein,_ApbE_782232..782382_POSITIVE 308 75 36 112 66 pint:PI2010|3end_ABC_transporter,_permease_component_1970242..1970392_POSITIVE 305 53 19 151 119 pint:PI0090|3end_amidophosphoribosyltransferase_89160..89310_POSITIVE 303 60 11 147 90 pint:PI0835|3end_conserved_hypothetical_protein;_possible_protein-export_membrane_protein_771859..772009_POSITIVE 301 43 9 115 72 pint:PI2132|3end_hypothetical_protein_2081139..2081289_POSITIVE 296 70 34 138 92 pint:PI0969|3end_30S_ribosomal_protein_S16_897261..897411_POSITIVE 295 57 16 135 98 pint:PI1651|3end_hypothetical_protein_1564512..1564662_POSITIVE 293 72 32 62 3 pint:PI0849|3end_hypothetical_protein_783542..783692_POSITIVE 293 54 14 115 74 pint:PI0734|3end_ABC_transporter,_ATP-binding_/_permease_668760..668910_POSITIVE 291 40 7 142 108 pint:PI0750|3end_zinc_protease_680633..680783_POSITIVE 290 68 32 99 53 pint:PI2125|3end_D-tyrosyl-tRNA(Tyr)_deacylase_2074979..2075129_POSITIVE 290 60 12 145 85 pint:PI1768|3end_conserved_hypothetical_protein_1696639..1696789_POSITIVE 289 68 21 124 73 pint:PI0674|3end_conserved_hypothetical_protein_616154..616304_POSITIVE 286 74 32 128 97 pint:PI2085|3end_conserved_hypothetical_protein_2041803..2041953_POSITIVE 286 80 33 144 97 pint:PI1527|3end_immunoreactive_46_kDa_antigen_PG99_1449520..1449670_POSITIVE