Origin IGS: tatatttttggcattgaaaacctcaaattcatcctatcaaataaaagaatcctaataaactcattcgaaatgggattaatttctttatctttgcattatatttattatcttttagtacctgtaaag .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 ctttacaggtactaaaagataataaatataatgcaaagataaagaaattaatcccatttcgaatgagtttattaggattcttttatttgataggatgaatttgaggttttcaatgccaaaaatata Mask Tandem Repeat Region ================================================ tatatttttggcattgaaaacctcaaattcatcctatcaaataaaagaatcctaataaactcattcgaaatgggattaatttctttatctttgcattatatttattatcttttagtacctgtaaag Find is-nt database================================================ Query_seq: PG1435:PG1436|PG1435:PG1436:integrase:ATPase, putative:->->:1521670..1521795 126 tatatttttggcattgaaaacctcaaattcatcctatcaaataaaagaatcctaataaactcattcgaaatgggattaatttctttatctttgcattatatttattatcttttagtacctgtaaag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG1435:PG1436|PG1435:PG1436:integrase:ATPase, putative:->->:1521670..1521795 126 tatatttttggcattgaaaacctcaaattcatcctatcaaataaaagaatcctaataaactcattcgaaatgggattaatttctttatctttgcattatatttattatcttttagtacctgtaaag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG1435:PG1436|PG1435:PG1436:integrase:ATPase, putative:->->:1521670..1521795 126 tatatttttggcattgaaaacctcaaattcatcctatcaaataaaagaatcctaataaactcattcgaaatgggattaatttctttatctttgcattatatttattatcttttagtacctgtaaag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tatatttttggcattgaaaacctcaaattcatcctatcaaataaaagaatcctaataaactcattcgaaatgggattaatttctttatctttgcattatatttattatcttttagtacctgtaaag Predict ORF larger than 30AA ================================================ Protein_Len: 41 Strand: + Start: 4 End: 126 ... M F G I E N L K F I L S N K R I L I N S F E M G L I S L S L H Y I Y Y L L V P V K tatatttttggcattgaaaacctcaaattcatcctatcaaataaaagaatcctaataaactcattcgaaatgggattaatttctttatctttgcattatatttattatcttttagtacctgtaaag 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================================================ tatatttttggcattgaaaacctcaaattcatcctatcaaataaaagaatcctaataaactcattcgaaatgggattaatttctttatctttgcattatatttattatcttttagtacctgtaaag Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PG1435:PG1436|PG1435:PG1436:integrase:ATPase, putative:->->:1521670..1521795 126 tatatttttggcattgaaaacctcaaattcatcctatcaaataaaagaatcctaataaactcattcgaaatgggattaatttctttatctttgcattatatttattatcttttagtacctgtaaag Intra-Species Hit: Count: 1 Min: 1 Max: 126 Len: 126 Subject: NC_002950_PG1435_PG1436|integrase:ATPase, putative|POSITIVE:POSITIVE|[1521670,1521795]|126 HSP 1 e-value: 9.0E-66 bit: 250.0 Len: 126 Query Start:1 Query End:126 Subject Strand: POSITIVE Subject Start: 1 Subject End: 126 tatatttttggcattgaaaacctcaaattcatcctatcaaataaaagaatcctaataaactcattcgaaatgggattaatttctttatctttgcattatatttattatcttttagtacctgtaaag tatatttttggcattgaaaacctcaaattcatcctatcaaataaaagaatcctaataaactcattcgaaatgggattaatttctttatctttgcattatatttattatcttttagtacctgtaaag Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAUAUUUUUGGCAUUGAAAACCUCAAAUUCAUCCUAUCAAAUAAAAGAAUCCUAAUAAACUCAUUCGAAAUGGGAUUAAUUUCUUUAUCUUUGCAUUAUAUUUAUUAUCUUUUAGUACCUGUAAAG ..........(((..((.......(((((.(((((((.........((((............))))...))))))).))))).....))..))).(((((..(((((.....)))))..))))).. (-12.80) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CUUUACAGGUACUAAAAGAUAAUAAAUAUAAUGCAAAGAUAAAGAAAUUAAUCCCAUUUCGAAUGAGUUUAUUAGGAUUCUUUUAUUUGAUAGGAUGAAUUUGAGGUUUUCAAUGCCAAAAAUAUA .......((((....(((((..(((((..............((....)).((((....(((((((((..............)))))))))..))))..)))))..)))))...))))......... (-14.04) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 235 96 63 32 2 NC_002950:PG0180|5end_lipoprotein,_putative_203055..203285_POSITIVE 221 35 9 38 13 NC_002950:PG0162|5end_RNA_polymerase_sigma-70_factor,_ECF_subfamily_185086..185316_NEGATIVE 203 100 51 133 75 NC_002950:PG0109|5end_hypothetical_protein_131331..131561_POSITIVE 202 95 58 54 17 NC_002950:PG1602|5end_hypothetical_protein_1682144..1682374_NEGATIVE 202 103 65 168 134 NC_002950:PG1521|5end_O-succinylbenzoic_acid--CoA_ligase_1599103..1599333_NEGATIVE 195 97 60 173 143 NC_002950:PG1417|5end_fumarate_hydratase_class_I,_anaerobic_1501295..1501525_POSITIVE 195 95 66 144 120 NC_002950:PG0003|5end_hypothetical_protein_2938..3168_NEGATIVE 192 79 46 63 37 NC_002950:PG1762|5end_protein-export_membrane_protein_SecD/protein-export_membrane_protein_SecF_1847988..1848218_POSITIVE 190 35 6 214 192 NC_002950:PG1842|5end_acetyltransferase,_GNAT_family_1938241..1938471_POSITIVE 186 35 2 180 151 NC_002950:PG1841|5end_hypothetical_protein_1937310..1937540_POSITIVE 184 96 59 91 56 NC_002950:PG1067|5end_hypothetical_protein_1134219..1134449_POSITIVE 182 89 44 200 155 NC_002950:PG1945|5end_hypothetical_protein_2031697..2031927_POSITIVE 182 113 74 106 65 NC_002950:PG0986|5end_hypothetical_protein_1047426..1047656_POSITIVE 179 93 51 125 82 NC_002950:PG1202|5end_hypothetical_protein_1283014..1283244_NEGATIVE 178 94 60 226 196 NC_002950:PG1554|5end_hypothetical_protein_1635264..1635494_POSITIVE 178 36 9 49 21 NC_002950:PG1297|5end_ribosomal_protein_S1_1375831..1376061_POSITIVE 178 38 3 133 98 NC_002950:PG0607|5end_hypothetical_protein_662552..662782_POSITIVE 177 39 7 220 189 NC_002950:PG0976|5end_phosphoribosylaminoimidazole-succinocarboxamide_synthase_1038326..1038556_POSITIVE 176 116 71 186 146 NC_002950:PG1493|5end_hypothetical_protein_1566783..1567013_POSITIVE 173 94 66 221 188 NC_002950:PG0174|5end_pyridine_nucleotide-disulphide_oxidoreductase_family_protein_197628..197858_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 203 100 51 111 53 NC_002950:PG0108|3end_UDP-N-acetyl-D-mannosaminuronic_acid_dehydrogenase_131389..131539_POSITIVE 193 97 58 95 60 NC_002950:PG1964|3end_bacterial_sugar_transferase_2054396..2054546_POSITIVE 193 110 62 76 23 NC_002950:PG0545|3end_hypothetical_protein_600228..600378_POSITIVE 186 35 2 85 56 NC_002950:PG1840|3end_hypothetical_protein_1937295..1937445_POSITIVE 184 96 59 37 2 NC_002950:PG1066|3end_butyrate-acetoacetate_CoA-transferase,_subunit_A_1134245..1134395_POSITIVE 182 113 74 116 75 NC_002950:PG0985|3end_RNA_polymerase_sigma-70_factor,_ECF_subfamily_1047516..1047666_POSITIVE 176 93 58 124 93 NC_002950:PG0721|3end_NLP/P60_family_protein_774535..774685_POSITIVE 171 94 64 56 30 NC_002950:PG1783|3end_glycosyl_transferase,_group_2_family_protein_1872658..1872808_POSITIVE 169 97 61 70 32 NC_002950:PG0896|3end_beta-galactosidase_960382..960532_POSITIVE 169 73 38 90 53 NC_002950:PG0556|3end_hypothetical_protein_614260..614410_POSITIVE 166 95 64 47 18 NC_002950:PG0844|3end_hypothetical_protein_905461..905611_POSITIVE 164 95 55 109 69 NC_002950:PG2055|3end_dihydroorotate_dehydrogenase_2152080..2152230_NEGATIVE 163 99 60 94 51 NC_002950:PG0066|3end_hypothetical_protein_81264..81414_NEGATIVE 161 93 63 89 63 NC_002950:PG0582|3end_cell_division_protein_FtsQ,_putative_640456..640606_POSITIVE 159 53 11 85 45 NC_002950:PG0580|3end_N-acetylglucosaminyl_transferase_638316..638466_POSITIVE 158 35 9 105 77 NC_002950:PG1490|3end_TraG_family_protein_1565504..1565654_POSITIVE 156 39 11 134 106 NC_002950:PG1010|3end_ABC_transporter,_ATP-binding_protein_1068509..1068659_NEGATIVE 155 33 11 151 134 NC_002950:PG2202|3end_Holliday_junction_resolvase-like_protein_2309517..2309667_NEGATIVE 154 23 4 77 56 NC_002950:PG1701|3end_glutamine_amidotransferase,_class_II/dipeptidase_1786145..1786295_NEGATIVE 153 110 66 119 66 NC_002950:PG2042|3end_thioredoxin_family_protein_2140099..2140249_NEGATIVE