Origin IGS: taatacattcgacaccttatttaaagtgccaagcataggcattatatgtcgcatttttccttatagaaccattgaaaggcgtttttgattagggtttatcagctataaaaaatttgagagcgttcaaccgaacgctctcaaccaacacaaaaactaaactagacttaactaaaagttttcgctctatttatctcaaacagtaacgaaacatagcgcaaagatacgataaaataattataaaatcgtacttttatgcagtattttctcttttttcagaaaaatgtta .........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.........1.........2.........3.........4.........5.........6.........7.........8.........9 taacatttttctgaaaaaagagaaaatactgcataaaagtacgattttataattattttatcgtatctttgcgctatgtttcgttactgtttgagataaatagagcgaaaacttttagttaagtctagtttagtttttgtgttggttgagagcgttcggttgaacgctctcaaattttttatagctgataaaccctaatcaaaaacgcctttcaatggttctataaggaaaaatgcgacatataatgcctatgcttggcactttaaataaggtgtcgaatgtatta Mask Tandem Repeat Region ================================================ taatacattcgacaccttatttaaagtgccaagcataggcattatatgtcgcatttttccttatagaaccattgaaaggcgtttttgattagggtttatcagctataaaaaatttgagagcgttcaaccgaacgctctcaaccaacacaaaaactaaactagacttaactaaaagttttcgctctatttatctcaaacagtaacgaaacatagcgcaaagatacgataaaataattataaaatcgtacttttatgcagtattttctcttttttcagaaaaatgtta Find is-nt database================================================ Query_seq: PI0665:PI0666|PI0665:PI0666:dihydroorotate dehydrogenase:chorismate synthase:->->:608860..609145 286 taatacattcgacaccttatttaaagtgccaagcataggcattatatgtcgcatttttccttatagaaccattgaaaggcgtttttgattagggtttatcagctataaaaaatttgagagcgttcaaccgaacgctctcaaccaacacaaaaactaaactagacttaactaaaagttttcgctctatttatctcaaacagtaacgaaacatagcgcaaagatacgataaaataattataaaatcgtacttttatgcagtattttctcttttttcagaaaaatgtta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI0665:PI0666|PI0665:PI0666:dihydroorotate dehydrogenase:chorismate synthase:->->:608860..609145 286 taatacattcgacaccttatttaaagtgccaagcataggcattatatgtcgcatttttccttatagaaccattgaaaggcgtttttgattagggtttatcagctataaaaaatttgagagcgttcaaccgaacgctctcaaccaacacaaaaactaaactagacttaactaaaagttttcgctctatttatctcaaacagtaacgaaacatagcgcaaagatacgataaaataattataaaatcgtacttttatgcagtattttctcttttttcagaaaaatgtta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI0665:PI0666|PI0665:PI0666:dihydroorotate dehydrogenase:chorismate synthase:->->:608860..609145 286 taatacattcgacaccttatttaaagtgccaagcataggcattatatgtcgcatttttccttatagaaccattgaaaggcgtttttgattagggtttatcagctataaaaaatttgagagcgttcaaccgaacgctctcaaccaacacaaaaactaaactagacttaactaaaagttttcgctctatttatctcaaacagtaacgaaacatagcgcaaagatacgataaaataattataaaatcgtacttttatgcagtattttctcttttttcagaaaaatgtta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 taatacattcgacaccttatttaaagtgccaagcataggcattatatgtcgcatttttccttatagaaccattgaaaggcgtttttgattagggtttatcagctataaaaaatttgagagcgttcaaccgaacgctctcaaccaacacaaaaactaaactagacttaactaaaagttttcgctctatttatctcaaacagtaacgaaacatagcgcaaagatacgataaaataattataaaatcgtacttttatgcagtattttctcttttttcagaaaaatgtta Predict ORF larger than 30AA ================================================ Protein_Len: 32 Strand: + Start: 105 End: 200 ........................................................................................................ M K N L R A F N R T L S T N T K T K L D L T K S F R S I Y L K Q ...................................................................................... Protein_Len: 32 Strand: - Start: 92 End: 187 ........................................................................................... P K D A I F F K L A N L R V S E V L V F V L S S K V L L K R E M ................................................................................................... taatacattcgacaccttatttaaagtgccaagcataggcattatatgtcgcatttttccttatagaaccattgaaaggcgtttttgattagggtttatcagctataaaaaatttgagagcgttcaaccgaacgctctcaaccaacacaaaaactaaactagacttaactaaaagttttcgctctatttatctcaaacagtaacgaaacatagcgcaaagatacgataaaataattataaaatcgtacttttatgcagtattttctcttttttcagaaaaatgtta 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================================================ taatacattcgacaccttatttaaagtgccaagcataggcattatatgtcgcatttttccttatagaaccattgaaaggcgtttttgattagggtttatcagctataaaaaatttgagagcgttcaaccgaacgctctcaaccaacacaaaaactaaactagacttaactaaaagttttcgctctatttatctcaaacagtaacgaaacatagcgcaaagatacgataaaataattataaaatcgtacttttatgcagtattttctcttttttcagaaaaatgtta Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 100 HP_score: -13.7 Tail_Score: -5.28778 Start: 113 End: 142 Full_Region: ttagtttttgtgttg gttgagagcgttc ggtt gaacgctctcaaa ttttttatagctgat ................................................................................................................gttgagagcgttcggttgaacgctctcaaa................................................................................................................................................ TransTerm Strand: - Conf: 100 HP_score: -17.2 Tail_Score: -3.76182 Start: 114 End: 141 Full_Region: tagtttttgtgttgg ttgagagcgttc ggtt gaacgctctcaa attttttatagctga .................................................................................................................ttgagagcgttcggttgaacgctctcaa................................................................................................................................................. Find igs database================================================ Query_seq: PI0665:PI0666|PI0665:PI0666:dihydroorotate dehydrogenase:chorismate synthase:->->:608860..609145 286 taatacattcgacaccttatttaaagtgccaagcataggcattatatgtcgcatttttccttatagaaccattgaaaggcgtttttgattagggtttatcagctataaaaaatttgagagcgttcaaccgaacgctctcaaccaacacaaaaactaaactagacttaactaaaagttttcgctctatttatctcaaacagtaacgaaacatagcgcaaagatacgataaaataattataaaatcgtacttttatgcagtattttctcttttttcagaaaaatgtta Intra-Species Hit: Count: 1 Min: 1 Max: 286 Len: 286 Subject: pint_PI0665_PI0666|dihydroorotate dehydrogenase:chorismate synthase|POSITIVE:POSITIVE|[608860,609145]|286 HSP 1 e-value: 1.0E-161 bit: 567.0 Len: 286 Query Start:1 Query End:286 Subject Strand: POSITIVE Subject Start: 1 Subject End: 286 taatacattcgacaccttatttaaagtgccaagcataggcattatatgtcgcatttttccttatagaaccattgaaaggcgtttttgattagggtttatcagctataaaaaatttgagagcgttcaaccgaacgctctcaaccaacacaaaaactaaactagacttaactaaaagttttcgctctatttatctcaaacagtaacgaaacatagcgcaaagatacgataaaataattataaaatcgtacttttatgcagtattttctcttttttcagaaaaatgtta taatacattcgacaccttatttaaagtgccaagcataggcattatatgtcgcatttttccttatagaaccattgaaaggcgtttttgattagggtttatcagctataaaaaatttgagagcgttcaaccgaacgctctcaaccaacacaaaaactaaactagacttaactaaaagttttcgctctatttatctcaaacagtaacgaaacatagcgcaaagatacgataaaataattataaaatcgtacttttatgcagtattttctcttttttcagaaaaatgtta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAUACAUUCGACACCUUAUUUAAAGUGCCAAGCAUAGGCAUUAUAUGUCGCAUUUUUCCUUAUAGAACCAUUGAAAGGCGUUUUUGAUUAGGGUUUAUCAGCUAUAAAAAAUUUGAGAGCGUUCAACCGAACGCUCUCAACCAACACAAAAACUAAACUAGACUUAACUAAAAGUUUUCGCUCUAUUUAUCUCAAACAGUAACGAAACAUAGCGCAAAGAUACGAUAAAAUAAUUAUAAAAUCGUACUUUUAUGCAGUAUUUUCUCUUUUUUCAGAAAAAUGUUA .........(((((.......((.((((((.......)))))).)))))))((((((((.............((((((.((((.(((.((..(((..((.(((..........((((((((((((....))))))))))))...................((((((......))))))..)))..))..)))..)).))).)))).......(((.((((.((((((..............)))))).)))).))).............))))))))))))))... (-56.36) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAACAUUUUUCUGAAAAAAGAGAAAAUACUGCAUAAAAGUACGAUUUUAUAAUUAUUUUAUCGUAUCUUUGCGCUAUGUUUCGUUACUGUUUGAGAUAAAUAGAGCGAAAACUUUUAGUUAAGUCUAGUUUAGUUUUUGUGUUGGUUGAGAGCGUUCGGUUGAACGCUCUCAAAUUUUUUAUAGCUGAUAAACCCUAAUCAAAAACGCCUUUCAAUGGUUCUAUAAGGAAAAAUGCGACAUAUAAUGCCUAUGCUUGGCACUUUAAAUAAGGUGUCGAAUGUAUUA ......((((((......))))))(((((.(((((...(((((((...((....))...)))))))....(((.(((((.((((..(((((((...))))))).(((((((((.((((......))))...))))))))).....((((((((((((....)))))))))))).((((((((((.((((........)))).....(((.......))).))))))))))....)))).))))).))).)))))((((((((((....))))))))))..))))). (-72.60) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 299 149 101 78 18 pint:PI0953|5end_hypothetical_protein_885119..885349_POSITIVE 276 140 93 229 170 pint:PI0492|5end_hypothetical_protein_451701..451931_POSITIVE 273 96 54 77 33 pint:PI1832|5end_conserved_hypothetical_protein_1773161..1773391_POSITIVE 266 139 93 190 146 pint:PI2115|5end_hypothetical_protein_2064966..2065196_POSITIVE 263 56 12 75 27 pint:PI2094|5end_hypothetical_protein_2049540..2049770_POSITIVE 256 45 10 91 58 pint:PI0260|5end_conjugative_transposon_protein,_TraJ_253023..253253_POSITIVE 255 104 69 69 27 pint:PI0530|5end_possible_membrane-fusion_protein_483772..484002_POSITIVE 252 61 26 108 73 pint:PI1003|5end_conserved_hypothetical_protein_924694..924924_POSITIVE 251 89 47 128 82 pint:PI1531|5end_biotin--acetyl-CoA-carboxylase_ligase_1450839..1451069_POSITIVE 247 60 12 122 66 pint:PI0698|5end_conserved_hypothetical_protein_635372..635602_POSITIVE 244 41 6 160 127 pint:PI1453|5end_probable_thiamine_pyrophosphokinase_1375982..1376212_POSITIVE 244 64 27 96 43 pint:PI0770|5end_hypothetical_protein_706170..706400_POSITIVE 242 150 114 192 138 pint:PI2028|5end_shikimate_kinase_1982162..1982392_POSITIVE 241 165 123 56 7 pint:PI1089|5end_conserved_hypothetical_protein_1012875..1013105_POSITIVE 238 100 51 68 27 pint:PI1585|5end_ampG_permease_1512900..1513130_POSITIVE 237 52 11 230 194 pint:PI2034|5end_conserved_hypothetical_protein_1987573..1987803_POSITIVE 237 80 38 164 115 pint:PI1924|5end_cytidine_deaminase_1865897..1866127_POSITIVE 236 80 31 128 68 pint:PI0823|5end_glyceraldehyde_3-phosphate_dehydrogenase,_type_I_762042..762272_POSITIVE 235 100 58 131 87 pint:PI1602|5end_conserved_hypothetical_protein;_possible_internalin-related_protein_1531025..1531255_POSITIVE 234 41 1 211 176 pint:PI1509|5end_conserved_hypothetical_protein_1428103..1428333_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 251 89 47 117 71 pint:PI1530|3end_conserved_hypothetical_protein_1450908..1451058_POSITIVE 251 60 13 81 36 pint:PI0138|3end_hypothetical_protein_131365..131515_POSITIVE 249 139 91 43 1 pint:PI1807|3end_hypothetical_protein_1742481..1742631_POSITIVE 242 150 114 80 26 pint:PI2027|3end_arginine_decarboxylase_1982130..1982280_POSITIVE 238 100 51 46 5 pint:PI1584|3end_A/G-specific_adenine_glycosylase_1512958..1513108_POSITIVE 237 80 38 99 50 pint:PI1923|3end_conserved_hypothetical_protein_1865912..1866062_POSITIVE 237 57 26 47 7 pint:PI0374|3end_MbpB_protein_345727..345877_POSITIVE 236 33 6 34 2 pint:PI0421|3end_hypothetical_protein_387774..387924_POSITIVE 234 50 2 78 19 pint:PI0360|3end_conserved_hypothetical_protein_333472..333622_POSITIVE 227 228 182 85 38 pint:PI1426|3end_flavodoxin_1345446..1345596_POSITIVE 227 61 25 36 1 pint:PI0717|3end_conserved_hypothetical_protein_653120..653270_POSITIVE 221 61 26 69 35 pint:PI0199|3end_phosphate_acetyltransferase_190923..191073_POSITIVE 219 100 51 99 54 pint:PI1733|3end_hypothetical_protein_1652437..1652587_POSITIVE 218 53 13 100 53 pint:PI0865|3end_possible_phosphoglycerol_transferase_803684..803834_POSITIVE 218 53 11 129 93 pint:PI0202|3end_DNA_helicase_195189..195339_POSITIVE 216 152 112 89 53 pint:PI0788|3end_3-methyladenine_DNA_glycosylase_(DNA-3-methyladenine_glycosylase_I)_726789..726939_POSITIVE 215 50 5 123 79 pint:PI0998|3end_possible_flavin_reductase_domain_protein_923336..923486_POSITIVE 214 96 55 58 20 pint:PI1547|3end_hypothetical_protein_1466226..1466376_POSITIVE 213 60 14 142 98 pint:PI1462|3end_hypothetical_protein_1385383..1385533_POSITIVE 213 61 34 131 107 pint:PI0750|3end_zinc_protease_680633..680783_POSITIVE