Origin IGS: tgtaccgttgttcaatgctccccaaaatagtccttttgctgttttctcctttaacgtttgctctgccattctaccgttgttttcgtgcaaaaacgcacttattcgttcaactta .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 taagttgaacgaataagtgcgtttttgcacgaaaacaacggtagaatggcagagcaaacgttaaaggagaaaacagcaaaaggactattttggggagcattgaacaacggtaca Mask Tandem Repeat Region ================================================ tgtaccgttgttcaatgctccccaaaatagtccttttgctgttttctcctttaacgtttgctctgccattctaccgttgttttcgtgcaaaaacgcacttattcgttcaactta Find is-nt database================================================ Query_seq: PI1855:PI1856|PI1855:PI1856:lipopolysaccharide biosynthesis protein:nicotinate-nucleotide adenylyltransferase:->->:1803229..1803342 114 tgtaccgttgttcaatgctccccaaaatagtccttttgctgttttctcctttaacgtttgctctgccattctaccgttgttttcgtgcaaaaacgcacttattcgttcaactta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI1855:PI1856|PI1855:PI1856:lipopolysaccharide biosynthesis protein:nicotinate-nucleotide adenylyltransferase:->->:1803229..1803342 114 tgtaccgttgttcaatgctccccaaaatagtccttttgctgttttctcctttaacgtttgctctgccattctaccgttgttttcgtgcaaaaacgcacttattcgttcaactta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI1855:PI1856|PI1855:PI1856:lipopolysaccharide biosynthesis protein:nicotinate-nucleotide adenylyltransferase:->->:1803229..1803342 114 tgtaccgttgttcaatgctccccaaaatagtccttttgctgttttctcctttaacgtttgctctgccattctaccgttgttttcgtgcaaaaacgcacttattcgttcaactta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tgtaccgttgttcaatgctccccaaaatagtccttttgctgttttctcctttaacgtttgctctgccattctaccgttgttttcgtgcaaaaacgcacttattcgttcaactta Predict ORF larger than 30AA ================================================ Protein_Len: 35 Strand: + Start: 8 End: 112 ....... M F N A P Q N S P F A V F S F N V C S A I L P L F S C K N A L I R S T .. Protein_Len: 33 Strand: + Start: 15 End: 113 .............. M L P K I V L L L F S P L T F A L P F Y R C F R A K T H L F V Q L . Protein_Len: 34 Strand: - Start: 1 End: 102 T G N N L A G W F L G K A T K E K L T Q E A M R G N N E H L F A S M ............ tgtaccgttgttcaatgctccccaaaatagtccttttgctgttttctcctttaacgtttgctctgccattctaccgttgttttcgtgcaaaaacgcacttattcgttcaactta 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================================================ tgtaccgttgttcaatgctccccaaaatagtccttttgctgttttctcctttaacgtttgctctgccattctaccgttgttttcgtgcaaaaacgcacttattcgttcaactta Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PI1855:PI1856|PI1855:PI1856:lipopolysaccharide biosynthesis protein:nicotinate-nucleotide adenylyltransferase:->->:1803229..1803342 114 tgtaccgttgttcaatgctccccaaaatagtccttttgctgttttctcctttaacgtttgctctgccattctaccgttgttttcgtgcaaaaacgcacttattcgttcaactta Intra-Species Hit: Count: 1 Min: 1 Max: 114 Len: 114 Subject: pint_PI1855_PI1856|lipopolysaccharide biosynthesis protein:nicotinate-nucleotide adenylyltransferase|POSITIVE:POSITIVE|[1803229, 1803342]|114 HSP 1 e-value: 1.0E-58 bit: 226.0 Len: 114 Query Start:1 Query End:114 Subject Strand: POSITIVE Subject Start: 1 Subject End: 114 tgtaccgttgttcaatgctccccaaaatagtccttttgctgttttctcctttaacgtttgctctgccattctaccgttgttttcgtgcaaaaacgcacttattcgttcaactta tgtaccgttgttcaatgctccccaaaatagtccttttgctgttttctcctttaacgtttgctctgccattctaccgttgttttcgtgcaaaaacgcacttattcgttcaactta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGUACCGUUGUUCAAUGCUCCCCAAAAUAGUCCUUUUGCUGUUUUCUCCUUUAACGUUUGCUCUGCCAUUCUACCGUUGUUUUCGUGCAAAAACGCACUUAUUCGUUCAACUUA ......((((..(..........((((((((......))))))))......(((((..................))))).....((((......))))......)..))))... (-14.37) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAGUUGAACGAAUAAGUGCGUUUUUGCACGAAAACAACGGUAGAAUGGCAGAGCAAACGUUAAAGGAGAAAACAGCAAAAGGACUAUUUUGGGGAGCAUUGAACAACGGUACA ...((((..........(((..((((((.((.......))))))))..)))..((....(((.........)))..(((((......)))))....))......))))...... (-15.60) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 338 99 53 83 28 pint:PI0545|5end_sugar_kinase_496411..496641_POSITIVE 331 70 21 216 161 pint:PI0559|5end_conserved_hypothetical_protein_507668..507898_POSITIVE 330 98 60 170 134 pint:PI0753|5end_hypothetical_protein_683391..683621_POSITIVE 329 49 1 148 92 pint:PI0530|5end_possible_membrane-fusion_protein_483772..484002_POSITIVE 327 100 55 174 124 pint:PI0723|5end_conserved_hypothetical_protein_656043..656273_POSITIVE 310 89 41 86 32 pint:PI0916|5end_hypothetical_protein_845617..845847_POSITIVE 309 77 33 185 144 pint:PI2084|5end_hypothetical_protein_2040387..2040617_POSITIVE 309 77 33 122 81 pint:PI2083|5end_hypothetical_protein_2040324..2040554_POSITIVE 303 80 32 55 7 pint:PI0602|5end_conserved_hypothetical_protein_549099..549329_POSITIVE 300 100 54 54 11 pint:PI0338|5end_hypothetical_protein_315337..315567_POSITIVE 299 98 54 192 151 pint:PI2155|5end_hypothetical_protein_2100664..2100894_POSITIVE 297 100 54 137 94 pint:PI1633|5end_hypothetical_protein_1552504..1552734_POSITIVE 297 100 54 57 14 pint:PI1631|5end_hypothetical_protein_1552424..1552654_POSITIVE 297 90 44 126 72 pint:PI0581|5end_conserved_hypothetical_protein_525055..525285_POSITIVE 293 42 6 126 89 pint:PI0756|5end_50S_ribosomal_protein_L7/L12_687146..687376_POSITIVE 288 108 61 64 12 pint:PI2017|5end_conserved_hypothetical_protein_1974862..1975092_POSITIVE 287 66 25 138 103 pint:PI1824|5end_ThiJ/PfpI_family_protein_1764479..1764709_POSITIVE 286 110 69 228 189 pint:PI0720|5end_conserved_hypothetical_protein_653949..654179_POSITIVE 282 67 30 214 183 pint:PI0117|5end_ribonuclease_HI_110731..110961_POSITIVE 282 76 34 64 15 pint:PI0052|5end_hypothetical_protein_52312..52542_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 346 68 22 78 36 pint:PI0683|3end_hypothetical_protein_619797..619947_POSITIVE 342 80 37 109 62 pint:PI0652|3end_conserved_hypothetical_protein_595792..595942_POSITIVE 297 100 54 47 4 pint:PI1630|3end_hypothetical_protein_1552494..1552644_POSITIVE 288 108 61 55 3 pint:PI2016|3end_ribosomal_large_subunit_pseudouridine_synthase_D_1974933..1975083_POSITIVE 285 68 29 118 75 pint:PI0327|3end_hypothetical_protein_309107..309257_POSITIVE 277 85 44 118 81 pint:PI1746|3end_hypothetical_protein_1667606..1667756_POSITIVE 275 97 56 133 98 pint:PI1651|3end_hypothetical_protein_1564512..1564662_POSITIVE 268 77 37 150 121 pint:PI0147|3end_HIT_family_protein_141308..141458_POSITIVE 262 43 10 42 8 pint:PI1824|3end_ThiJ/PfpI_family_protein_1765005..1765155_POSITIVE 262 97 55 51 8 pint:PI1097|3end_acetyltransferase,_GNAT_family_1021999..1022149_POSITIVE 261 80 36 137 99 pint:PI1847|3end_conserved_hypothetical_protein;_possible_integral_membrane_protein_1793849..1793999_POSITIVE 261 78 31 147 94 pint:PI0332|3end_conserved_hypothetical_protein_313552..313702_POSITIVE 260 97 54 140 92 pint:PI1768|3end_conserved_hypothetical_protein_1696639..1696789_POSITIVE 260 88 55 130 85 pint:PI0843|3end_carboxyl-terminal_protease_777862..778012_POSITIVE 258 95 54 80 32 pint:PI2093|3end_hypothetical_protein_2049440..2049590_POSITIVE 257 86 55 75 34 pint:PI1812|3end_possible_alpha-amylase_1752854..1753004_POSITIVE 257 76 38 134 98 pint:PI0838|3end_DNA_replication_and_repair_protein_773927..774077_POSITIVE 255 106 74 57 17 pint:PI2096|3end_conserved_hypothetical_protein;_possible_phosphoesterase_2050884..2051034_POSITIVE 255 96 55 61 9 pint:PI1381|3end_conserved_hypothetical_protein_1303676..1303826_POSITIVE 255 89 42 84 33 pint:PI0958|3end_G:T/U_mismatch-specific_DNA_glycosylase_890569..890719_POSITIVE