Origin IGS: ctgtgcgcttcctgctgtacttaggtcccgctgtaatactctcgtttgcgcatgggctgatgagatgcccagtacaactgcaaaggttaaaaataaaagttttttcatatttgtgaaaatttaagttaatgttccgtatttggttattacggcattatttaacacgtttttttatctttattttgaggtaacaatatatttcttagtatattgttgtaaattctttgctcctctctttagatagtactgtattgaatacaaaattacagaattattttgaaaacaccacctcgtggttgtaaaaattcattaaaaagtttaaagaaccatttttgatatatcttcgtagggatttccctattgcaaaatagagaaaaagaatttcaacagtttgttatattctctaattttgcggtattgaaaagattataaacataaaaagttacgatt .........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.........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aatcgtaactttttatgtttataatcttttcaataccgcaaaattagagaatataacaaactgttgaaattctttttctctattttgcaatagggaaatccctacgaagatatatcaaaaatggttctttaaactttttaatgaatttttacaaccacgaggtggtgttttcaaaataattctgtaattttgtattcaatacagtactatctaaagagaggagcaaagaatttacaacaatatactaagaaatatattgttacctcaaaataaagataaaaaaacgtgttaaataatgccgtaataaccaaatacggaacattaacttaaattttcacaaatatgaaaaaacttttatttttaacctttgcagttgtactgggcatctcatcagcccatgcgcaaacgagagtattacagcgggacctaagtacagcaggaagcgcacag Mask Tandem Repeat Region ================================================ ctgtgcgcttcctgctgtacttaggtcccgctgtaatactctcgtttgcgcatgggctgatgagatgcccagtacaactgcaaaggttaaaaataaaagttttttcatatttgtgaaaatttaagttaatgttccgtatttggttattacggcattatttaacacgtttttttatctttattttgaggtaacaatatatttcttagtatattgttgtaaattctttgctcctctctttagatagtactgtattgaatacaaaattacagaattattttgaaaacaccacctcgtggttgtaaaaattcattaaaaagtttaaagaaccatttttgatatatcttcgtagggatttccctattgcaaaatagagaaaaagaatttcaacagtttgttatattctctaattttgcggtattgaaaagattataaacataaaaagttacgatt Find is-nt database================================================ Query_seq: PI0947:PI0948|PI0947:PI0948:conserved hypothetical protein:hypothetical protein:->->:880770..881219 450 ctgtgcgcttcctgctgtacttaggtcccgctgtaatactctcgtttgcgcatgggctgatgagatgcccagtacaactgcaaaggttaaaaataaaagttttttcatatttgtgaaaatttaagttaatgttccgtatttggttattacggcattatttaacacgtttttttatctttattttgaggtaacaatatatttcttagtatattgttgtaaattctttgctcctctctttagatagtactgtattgaatacaaaattacagaattattttgaaaacaccacctcgtggttgtaaaaattcattaaaaagtttaaagaaccatttttgatatatcttcgtagggatttccctattgcaaaatagagaaaaagaatttcaacagtttgttatattctctaattttgcggtattgaaaagattataaacataaaaagttacgatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI0947:PI0948|PI0947:PI0948:conserved hypothetical protein:hypothetical protein:->->:880770..881219 450 ctgtgcgcttcctgctgtacttaggtcccgctgtaatactctcgtttgcgcatgggctgatgagatgcccagtacaactgcaaaggttaaaaataaaagttttttcatatttgtgaaaatttaagttaatgttccgtatttggttattacggcattatttaacacgtttttttatctttattttgaggtaacaatatatttcttagtatattgttgtaaattctttgctcctctctttagatagtactgtattgaatacaaaattacagaattattttgaaaacaccacctcgtggttgtaaaaattcattaaaaagtttaaagaaccatttttgatatatcttcgtagggatttccctattgcaaaatagagaaaaagaatttcaacagtttgttatattctctaattttgcggtattgaaaagattataaacataaaaagttacgatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI0947:PI0948|PI0947:PI0948:conserved hypothetical protein:hypothetical protein:->->:880770..881219 450 ctgtgcgcttcctgctgtacttaggtcccgctgtaatactctcgtttgcgcatgggctgatgagatgcccagtacaactgcaaaggttaaaaataaaagttttttcatatttgtgaaaatttaagttaatgttccgtatttggttattacggcattatttaacacgtttttttatctttattttgaggtaacaatatatttcttagtatattgttgtaaattctttgctcctctctttagatagtactgtattgaatacaaaattacagaattattttgaaaacaccacctcgtggttgtaaaaattcattaaaaagtttaaagaaccatttttgatatatcttcgtagggatttccctattgcaaaatagagaaaaagaatttcaacagtttgttatattctctaattttgcggtattgaaaagattataaacataaaaagttacgatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ctgtgcgcttcctgctgtacttaggtcccgctgtaatactctcgtttgcgcatgggctgatgagatgcccagtacaactgcaaaggttaaaaataaaagttttttcatatttgtgaaaatttaagttaatgttccgtatttggttattacggcattatttaacacgtttttttatctttattttgaggtaacaatatatttcttagtatattgttgtaaattctttgctcctctctttagatagtactgtattgaatacaaaattacagaattattttgaaaacaccacctcgtggttgtaaaaattcattaaaaagtttaaagaaccatttttgatatatcttcgtagggatttccctattgcaaaatagagaaaaagaatttcaacagtttgttatattctctaattttgcggtattgaaaagattataaacataaaaagttacgatt Predict ORF larger than 30AA ================================================ Protein_Len: 37 Strand: + Start: 3 End: 113 .. M R F L L Y L G P A V I L S F A H G L M R C P V Q L Q R L K I K V F S Y L ................................................................................................................................................................................................................................................................................................................................................. Protein_Len: 34 Strand: + Start: 140 End: 241 ........................................................................................................................................... M V I T A L F N T F F Y L Y F E V T I Y F L V Y C C K F F A P L F R ................................................................................................................................................................................................................. Protein_Len: 30 Strand: + Start: 210 End: 299 ................................................................................................................................................................................................................. M V V N S L L L S L D S T V L N T K L Q N Y F E N T T S W L ....................................................................................................................................................... Protein_Len: 30 Strand: + Start: 340 End: 429 ................................................................................................................................................................................................................................................................................................................................................... M F V G I S L L Q N R E K E F Q Q F V I F S N F A V L K R L ..................... Protein_Len: 36 Strand: - Start: 275 End: 382 .................................................................................................................................................................................................................................................................................. K S F V V E H N Y F N M L F N L S G N K I Y R R L S K G I A F Y L F L M .................................................................... Protein_Len: 42 Strand: - Start: 181 End: 306 .................................................................................................................................................................................... K S T V I Y K K T Y Q Q L N K A G R K L Y Y Q I S Y L I V S N N Q F C W R T T T F M ................................................................................................................................................ Protein_Len: 46 Strand: - Start: 2 End: 139 . T R K R S Y K P G A T I S E N A C P S I L H G T C S C L N F I F T K E Y K H F N L N I N R M ....................................................................................................................................................................................................................................................................................................................... Protein_Len: 40 Strand: - Start: 1 End: 120 Q A S G A T S L D R Q L V R T Q A H A S S I G L V V A F T L F L L K K M N T F M .......................................................................................................................................................................................................................................................................................................................................... ctgtgcgcttcctgctgtacttaggtcccgctgtaatactctcgtttgcgcatgggctgatgagatgcccagtacaactgcaaaggttaaaaataaaagttttttcatatttgtgaaaatttaagttaatgttccgtatttggttattacggcattatttaacacgtttttttatctttattttgaggtaacaatatatttcttagtatattgttgtaaattctttgctcctctctttagatagtactgtattgaatacaaaattacagaattattttgaaaacaccacctcgtggttgtaaaaattcattaaaaagtttaaagaaccatttttgatatatcttcgtagggatttccctattgcaaaatagagaaaaagaatttcaacagtttgttatattctctaattttgcggtattgaaaagattataaacataaaaagttacgatt 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================================================ ctgtgcgcttcctgctgtacttaggtcccgctgtaatactctcgtttgcgcatgggctgatgagatgcccagtacaactgcaaaggttaaaaataaaagttttttcatatttgtgaaaatttaagttaatgttccgtatttggttattacggcattatttaacacgtttttttatctttattttgaggtaacaatatatttcttagtatattgttgtaaattctttgctcctctctttagatagtactgtattgaatacaaaattacagaattattttgaaaacaccacctcgtggttgtaaaaattcattaaaaagtttaaagaaccatttttgatatatcttcgtagggatttccctattgcaaaatagagaaaaagaatttcaacagtttgttatattctctaattttgcggtattgaaaagattataaacataaaaagttacgatt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PI0947:PI0948|PI0947:PI0948:conserved hypothetical protein:hypothetical protein:->->:880770..881219 450 ctgtgcgcttcctgctgtacttaggtcccgctgtaatactctcgtttgcgcatgggctgatgagatgcccagtacaactgcaaaggttaaaaataaaagttttttcatatttgtgaaaatttaagttaatgttccgtatttggttattacggcattatttaacacgtttttttatctttattttgaggtaacaatatatttcttagtatattgttgtaaattctttgctcctctctttagatagtactgtattgaatacaaaattacagaattattttgaaaacaccacctcgtggttgtaaaaattcattaaaaagtttaaagaaccatttttgatatatcttcgtagggatttccctattgcaaaatagagaaaaagaatttcaacagtttgttatattctctaattttgcggtattgaaaagattataaacataaaaagttacgatt Intra-Species Hit: Count: 1 Min: 1 Max: 450 Len: 450 Subject: pint_PI0947_PI0948|conserved hypothetical protein:hypothetical protein|POSITIVE:POSITIVE|[880770,881219]|450 HSP 1 e-value: 0.0 bit: 850.0 Len: 450 Query Start:1 Query End:450 Subject Strand: POSITIVE Subject Start: 1 Subject End: 450 ctgtgcgcttcctgctgtacttaggtcccgctgtaatactctcgtttgcgcatgggctgatgagatgcccagtacaactgcaaaggttaaaaataaaagttttttcatatttgtgaaaatttaagttaatgttccgtatttggttattacggcattatttaacacgnnnnnnnatctttattttgaggtaacaatatatttcttagtatattgttgtaaattctttgctcctctctttagatagtactgtattgaatacaaaattacagaattattttgaaaacaccacctcgtggttgtaaaaattcattaaaaagtttaaagaaccatttttgatatatcttcgtagggatttccctattgcaaaatagagaaaaagaatttcaacagtttgttatattctctaattttgcggtattgaaaagattataaacataaaaagttacgatt ctgtgcgcttcctgctgtacttaggtcccgctgtaatactctcgtttgcgcatgggctgatgagatgcccagtacaactgcaaaggttaaaaataaaagttttttcatatttgtgaaaatttaagttaatgttccgtatttggttattacggcattatttaacacgtttttttatctttattttgaggtaacaatatatttcttagtatattgttgtaaattctttgctcctctctttagatagtactgtattgaatacaaaattacagaattattttgaaaacaccacctcgtggttgtaaaaattcattaaaaagtttaaagaaccatttttgatatatcttcgtagggatttccctattgcaaaatagagaaaaagaatttcaacagtttgttatattctctaattttgcggtattgaaaagattataaacataaaaagttacgatt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CUGUGCGCUUCCUGCUGUACUUAGGUCCCGCUGUAAUACUCUCGUUUGCGCAUGGGCUGAUGAGAUGCCCAGUACAACUGCAAAGGUUAAAAAUAAAAGUUUUUUCAUAUUUGUGAAAAUUUAAGUUAAUGUUCCGUAUUUGGUUAUUACGGCAUUAUUUAACACGUUUUUUUAUCUUUAUUUUGAGGUAACAAUAUAUUUCUUAGUAUAUUGUUGUAAAUUCUUUGCUCCUCUCUUUAGAUAGUACUGUAUUGAAUACAAAAUUACAGAAUUAUUUUGAAAACACCACCUCGUGGUUGUAAAAAUUCAUUAAAAAGUUUAAAGAACCAUUUUUGAUAUAUCUUCGUAGGGAUUUCCCUAUUGCAAAAUAGAGAAAAAGAAUUUCAACAGUUUGUUAUAUUCUCUAAUUUUGCGGUAUUGAAAAGAUUAUAAACAUAAAAAGUUACGAUU ..((((((.....)).))))...((((..(((((((((.(((((((.((......)).))))))).(((.(((((..((....))...........((((((((.((....)).)))))))).............))))).))))))))))))......((((..(((((((...((((.(..((((.((((((((((((....)))))))))))).......(((((.....((...(((((((.(((((.............))))).))))))).))....(((((...))))).)))))..))))..).))))...)))))))..((((..((((......((((((....)))))).(((((((((((((...(((((.....)))))......)))))).))))))).))))..)))).................)))).)))) (-97.82) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAUCGUAACUUUUUAUGUUUAUAAUCUUUUCAAUACCGCAAAAUUAGAGAAUAUAACAAACUGUUGAAAUUCUUUUUCUCUAUUUUGCAAUAGGGAAAUCCCUACGAAGAUAUAUCAAAAAUGGUUCUUUAAACUUUUUAAUGAAUUUUUACAACCACGAGGUGGUGUUUUCAAAAUAAUUCUGUAAUUUUGUAUUCAAUACAGUACUAUCUAAAGAGAGGAGCAAAGAAUUUACAACAAUAUACUAAGAAAUAUAUUGUUACCUCAAAAUAAAGAUAAAAAAACGUGUUAAAUAAUGCCGUAAUAACCAAAUACGGAACAUUAACUUAAAUUUUCACAAAUAUGAAAAAACUUUUAUUUUUAACCUUUGCAGUUGUACUGGGCAUCUCAUCAGCCCAUGCGCAAACGAGAGUAUUACAGCGGGACCUAAGUACAGCAGGAAGCGCACAG ..((((.........((..((((.(((((........(((((((.((((((..((((.....)))).........)))))))))))))..(((((....))))).))))))))).))..((..((((.((((.....)))).))))..))......)))).(((.(((((((.......((((........(((((......))))).......))))....((((((.......(((((((((........))))))))).........(((((((((((......(((((......(((((.........)))))....))))).....((((((......))))))...)))))))))))..)))))).((((((((((((.........))))...(((..((....))......))).......)))))))).)))))))))).. (-90.96) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 397 71 32 45 2 pint:PI0079|5end_hypothetical_protein_78565..78795_POSITIVE 394 57 11 183 117 pint:PI0636|5end_hypothetical_protein_582032..582262_POSITIVE 355 69 25 53 2 pint:PI0036|5end_glutathione_peroxidase_38598..38828_POSITIVE 350 58 15 181 143 pint:PI1665|5end_thymidylate_synthase_1578086..1578316_POSITIVE 337 65 25 85 36 pint:PI1066|5end_dihydrofolate_reductase_983427..983657_POSITIVE 335 69 23 90 24 pint:PI0736|5end_transcriptional_regulator,_TetR_family_670580..670810_POSITIVE 333 59 14 158 110 pint:PI0758|5end_hypothetical_protein_690247..690477_POSITIVE 329 60 11 160 102 pint:PI2074|5end_conserved_hypothetical_protein_2033660..2033890_POSITIVE 329 70 21 49 6 pint:PI1925|5end_conserved_hypothetical_protein_1866387..1866617_POSITIVE 327 68 25 52 9 pint:PI2158|5end_glycosyl_transferase,_group_2_family_protein_2104392..2104622_POSITIVE 325 75 31 206 142 pint:PI0956|5end_conserved_hypothetical_protein_886077..886307_POSITIVE 323 70 42 172 144 pint:PI0275|5end_hypothetical_protein_263138..263368_POSITIVE 319 68 24 96 58 pint:PI1415|5end_cation_transporting_ATPase/E1-E2_ATPase_1333939..1334169_POSITIVE 319 68 24 70 32 pint:PI1414|5end_conserved_hypothetical_protein_1333913..1334143_POSITIVE 315 59 12 64 13 pint:PI2160|5end_hypothetical_protein_2107270..2107500_POSITIVE 313 87 44 221 168 pint:PI0171|5end_hypothetical_protein_163850..164080_POSITIVE 312 70 25 133 78 pint:PI1639|5end_conserved_hypothetical_protein_1556725..1556955_POSITIVE 311 40 2 97 67 pint:PI0489|5end_probable_cardiolipin_synthetase_447610..447840_POSITIVE 309 59 11 180 121 pint:PI0355|5end_probable__N-acetylmuramoyl-L-alanine_amidase_326157..326387_POSITIVE 308 60 12 81 36 pint:PI0263|5end_conjugative_transposon_protein,_TraM_255256..255486_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 350 58 15 105 67 pint:PI1664|3end_conserved_hypothetical_protein_1578090..1578240_POSITIVE 329 70 21 77 34 pint:PI1924|3end_cytidine_deaminase_1866495..1866645_POSITIVE 328 58 11 59 5 pint:PI1634|3end_conserved_hypothetical_protein_1553819..1553969_POSITIVE 325 75 31 133 69 pint:PI0955|3end_conserved_hypothetical_protein_886084..886234_POSITIVE 323 70 42 141 113 pint:PI0274|3end_conserved_hypothetical_protein_263187..263337_POSITIVE 315 59 12 85 34 pint:PI2159|3end_immunoreactive_84_kDa_antigen_PG93_2107371..2107521_POSITIVE 309 70 24 150 115 pint:PI0654|3end_K+-dependent_Na+/Ca+_exchanger_related-protein_597223..597373_POSITIVE 307 59 11 55 5 pint:PI1136|3end_conserved_hypothetical_protein_1062541..1062691_POSITIVE 307 49 1 150 99 pint:PI0456|3end_30S_ribosomal_protein_S12_429219..429369_POSITIVE 304 87 43 136 97 pint:PI0788|3end_3-methyladenine_DNA_glycosylase_(DNA-3-methyladenine_glycosylase_I)_726789..726939_POSITIVE 303 73 44 42 9 pint:PI1413|3end_hypothetical_protein_1333959..1334109_POSITIVE 300 69 25 88 44 pint:PI0683|3end_hypothetical_protein_619797..619947_POSITIVE 299 60 11 144 104 pint:PI2041|3end_conserved_hypothetical_protein_1994660..1994810_POSITIVE 297 49 2 62 13 pint:PI0616|3end_electron_transfer_flavoprotein,_beta-subunit_566440..566590_POSITIVE 297 72 33 151 107 pint:PI0516|3end_ferredoxin,_4Fe-4S_476108..476258_POSITIVE 295 50 1 136 89 pint:PI0528|3end_hypothetical_protein_483122..483272_POSITIVE 293 58 11 131 82 pint:PI0998|3end_possible_flavin_reductase_domain_protein_923336..923486_POSITIVE 287 79 33 117 71 pint:PI0056|3end_conserved_hypothetical_protein;_possible_DNA_uptake_protein_55907..56057_POSITIVE 286 48 1 57 8 pint:PI0379|3end_conserved_hypothetical_protein_350239..350389_POSITIVE 285 57 17 69 28 pint:PI1149|3end_30S_ribosomal_protein_S18_1075757..1075907_POSITIVE