Origin IGS: ataggctaaaggtctgtttgccatagttttatattaagtgctccttgtaggttaatccttcagaggttaggagcgtatgccctctgtcggcattctgtgttttatcactactgcaaaggtataaaatcaatcgttagaatgcaagaaaacagtcgactaattttcaaaaatactcgactgattttcaaaaacagtcgactgatttgttgttggcatatagcatagctatcatagactgtaattgccacaagtactataaacggacttagtcgttgcaattataacttttgtttctccta .........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 taggagaaacaaaagttataattgcaacgactaagtccgtttatagtacttgtggcaattacagtctatgatagctatgctatatgccaacaacaaatcagtcgactgtttttgaaaatcagtcgagtatttttgaaaattagtcgactgttttcttgcattctaacgattgattttatacctttgcagtagtgataaaacacagaatgccgacagagggcatacgctcctaacctctgaaggattaacctacaaggagcacttaatataaaactatggcaaacagacctttagcctat Mask Tandem Repeat Region ================================================ ataggctaaaggtctgtttgccatagttttatattaagtgctccttgtaggttaatccttcagaggttaggagcgtatgccctctgtcggcattctgtgttttatcactactgcaaaggtataaaatcaatcgttagaatgcaagnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnngttgttggcatatagcatagctatcatagactgtaattgccacaagtactataaacggacttagtcgttgcaattataacttttgtttctccta Find is-nt database================================================ Query_seq: PI1012:PI1013|PI1012:PI1013:DNA-binding protein, histone-like family:probable transcriptional regulator:->->:933605..933903 299 ataggctaaaggtctgtttgccatagttttatattaagtgctccttgtaggttaatccttcagaggttaggagcgtatgccctctgtcggcattctgtgttttatcactactgcaaaggtataaaatcaatcgttagaatgcaagaaaacagtcgactaattttcaaaaatactcgactgattttcaaaaacagtcgactgatttgttgttggcatatagcatagctatcatagactgtaattgccacaagtactataaacggacttagtcgttgcaattataacttttgtttctccta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI1012:PI1013|PI1012:PI1013:DNA-binding protein, histone-like family:probable transcriptional regulator:->->:933605..933903 299 ataggctaaaggtctgtttgccatagttttatattaagtgctccttgtaggttaatccttcagaggttaggagcgtatgccctctgtcggcattctgtgttttatcactactgcaaaggtataaaatcaatcgttagaatgcaagaaaacagtcgactaattttcaaaaatactcgactgattttcaaaaacagtcgactgatttgttgttggcatatagcatagctatcatagactgtaattgccacaagtactataaacggacttagtcgttgcaattataacttttgtttctccta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI1012:PI1013|PI1012:PI1013:DNA-binding protein, histone-like family:probable transcriptional regulator:->->:933605..933903 299 ataggctaaaggtctgtttgccatagttttatattaagtgctccttgtaggttaatccttcagaggttaggagcgtatgccctctgtcggcattctgtgttttatcactactgcaaaggtataaaatcaatcgttagaatgcaagaaaacagtcgactaattttcaaaaatactcgactgattttcaaaaacagtcgactgatttgttgttggcatatagcatagctatcatagactgtaattgccacaagtactataaacggacttagtcgttgcaattataacttttgtttctccta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ataggctaaaggtctgtttgccatagttttatattaagtgctccttgtaggttaatccttcagaggttaggagcgtatgccctctgtcggcattctgtgttttatcactactgcaaaggtataaaatcaatcgttagaatgcaagaaaacagtcgactaattttcaaaaatactcgactgattttcaaaaacagtcgactgatttgttgttggcatatagcatagctatcatagactgtaattgccacaagtactataaacggacttagtcgttgcaattataacttttgtttctccta Predict ORF larger than 30AA ================================================ Protein_Len: 60 Strand: + Start: 31 End: 222 .............................. M L S A P C R L I L Q R L G A Y A L C R H S V F Y H Y C K G I K S I V R M Q E N S R L I F K N T R L I F K N S R L I C C ............................................................................. Protein_Len: 56 Strand: - Start: 111 End: 278 .............................................................................................................. Q L P I F D I T L I C S F L R S I K L F V R S I K L F L R S I Q Q Q C I A Y S D Y V T I A V L V I F P S L R Q M ..................... Protein_Len: 33 Strand: - Start: 32 End: 130 ............................... I L H E K Y T L G E S T L L T H G R D A N Q T K D S S C L Y L I M ......................................................................................................................................................................... ataggctaaaggtctgtttgccatagttttatattaagtgctccttgtaggttaatccttcagaggttaggagcgtatgccctctgtcggcattctgtgttttatcactactgcaaaggtataaaatcaatcgttagaatgcaagaaaacagtcgactaattttcaaaaatactcgactgattttcaaaaacagtcgactgatttgttgttggcatatagcatagctatcatagactgtaattgccacaagtactataaacggacttagtcgttgcaattataacttttgtttctccta Predict Promoter with matrix: RpoD-15 score > 80================================================ Predict Promoter with matrix: RpoD-16 score > 80================================================ Predict Promoter with matrix: RpoD-17 score > 80================================================ PromScan Matrix: RpoD-17 Strand: - Score: 84 Start: 160 End: 189 ...............................................................................................................................................................TTTGAAAATCAGTCGAGTATTTTTGAAAAT.............................................................................................................. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ ataggctaaaggtctgtttgccatagttttatattaagtgctccttgtaggttaatccttcagaggttaggagcgtatgccctctgtcggcattctgtgttttatcactactgcaaaggtataaaatcaatcgttagaatgcaagaaaacagtcgactaattttcaaaaatactcgactgattttcaaaaacagtcgactgatttgttgttggcatatagcatagctatcatagactgtaattgccacaagtactataaacggacttagtcgttgcaattataacttttgtttctccta Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 95 HP_score: -8.4 Tail_Score: -4.73635 Start: 150 End: 180 Full_Region: actgtttttgaaaat cagtcgagtatttt tga aaattagtcgactg ttttcttgcattcta .....................................................................................................................................................cagtcgagtatttttgaaaattagtcgactg....................................................................................................................... TransTerm Strand: - Conf: 76 HP_score: -10.1 Tail_Score: -2.94823 Start: 174 End: 198 Full_Region: ccaacaacaaatcag tcgactgtttt tga aaatcagtcga gtatttttgaaaatt .............................................................................................................................................................................tcgactgtttttgaaaatcagtcga..................................................................................................... Find igs database================================================ Query_seq: PI1012:PI1013|PI1012:PI1013:DNA-binding protein, histone-like family:probable transcriptional regulator:->->:933605..933903 299 ataggctaaaggtctgtttgccatagttttatattaagtgctccttgtaggttaatccttcagaggttaggagcgtatgccctctgtcggcattctgtgttttatcactactgcaaaggtataaaatcaatcgttagaatgcaagaaaacagtcgactaattttcaaaaatactcgactgattttcaaaaacagtcgactgatttgttgttggcatatagcatagctatcatagactgtaattgccacaagtactataaacggacttagtcgttgcaattataacttttgtttctccta Intra-Species Hit: Count: 1 Min: 1 Max: 299 Len: 299 Subject: pint_PI1012_PI1013|DNA-binding protein, histone-like family:probable transcriptional regulator|POSITIVE:POSITIVE|[933605,933903]|299 HSP 1 e-value: 1.0E-168 bit: 593.0 Len: 299 Query Start:1 Query End:299 Subject Strand: POSITIVE Subject Start: 1 Subject End: 299 ataggctaaaggtctgtttgccatagttttatattaagtgctccttgtaggttaatccttcagaggttaggagcgtatgccctctgtcggcattctgtgttttatcactactgcaaaggtataaaatcaatcgttagaatgcaagaaaacagtcgactaattttcaaaaatactcgactgattttcaaaaacagtcgactgatttgttgttggcatatagcatagctatcatagactgtaattgccacaagtactataaacggacttagtcgttgcaattataacttttgtttctccta ataggctaaaggtctgtttgccatagttttatattaagtgctccttgtaggttaatccttcagaggttaggagcgtatgccctctgtcggcattctgtgttttatcactactgcaaaggtataaaatcaatcgttagaatgcaagaaaacagtcgactaattttcaaaaatactcgactgattttcaaaaacagtcgactgatttgttgttggcatatagcatagctatcatagactgtaattgccacaagtactataaacggacttagtcgttgcaattataacttttgtttctccta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUAGGCUAAAGGUCUGUUUGCCAUAGUUUUAUAUUAAGUGCUCCUUGUAGGUUAAUCCUUCAGAGGUUAGGAGCGUAUGCCCUCUGUCGGCAUUCUGUGUUUUAUCACUACUGCAAAGGUAUAAAAUCAAUCGUUAGAAUGCAAGAAAACAGUCGACUAAUUUUCAAAAAUACUCGACUGAUUUUCAAAAACAGUCGACUGAUUUGUUGUUGGCAUAUAGCAUAGCUAUCAUAGACUGUAAUUGCCACAAGUACUAUAAACGGACUUAGUCGUUGCAAUUAUAACUUUUGUUUCUCCUA ...(((((..((((((((((..(((......)))..((((((...(((.(((........((((((.((........)).))))))...((((((((((((((((.(((........))))))))).)).....))))))))..((((((((((((...((((....))))..))))))).)))))....((((((...((((..(((((..((.....))))))).))))..))))))....)))))))))))).)))))))))))))))............................ (-70.80) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAGGAGAAACAAAAGUUAUAAUUGCAACGACUAAGUCCGUUUAUAGUACUUGUGGCAAUUACAGUCUAUGAUAGCUAUGCUAUAUGCCAACAACAAAUCAGUCGACUGUUUUUGAAAAUCAGUCGAGUAUUUUUGAAAAUUAGUCGACUGUUUUCUUGCAUUCUAACGAUUGAUUUUAUACCUUUGCAGUAGUGAUAAAACACAGAAUGCCGACAGAGGGCAUACGCUCCUAACCUCUGAAGGAUUAACCUACAAGGAGCACUUAAUAUAAAACUAUGGCAAACAGACCUUUAGCCUAU ((((..(((.....(((((((.(((((((........))))....))).))))))).......((((...(((((...))))).(((((.(((.(((.((((((((((((((..((((((......).)))))..)))).)))))))))).))).)))((.((....)).)).((((((((((((((.((((((......)))....))).).))))))......((((((......((.(((.....))).))))))))......)))))))...)))))...)))).)))..)))). (-73.40) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 422 200 151 183 134 pint:PI1491|5end_conserved_hypothetical_protein_1409410..1409640_POSITIVE 367 106 63 134 77 pint:PI0844|5end_cytidine/deoxycytidylate_deaminase_(dCMP_deaminase)_777793..778023_POSITIVE 345 99 64 192 149 pint:PI0080|5end_hypothetical_protein_79047..79277_POSITIVE 343 95 56 143 87 pint:PI0331|5end_hypothetical_protein_311656..311886_POSITIVE 335 99 63 42 2 pint:PI0058|5end_conserved_hypothetical_protein_56398..56628_POSITIVE 317 114 73 222 174 pint:PI1205|5end_hypothetical_protein_1127047..1127277_POSITIVE 317 114 73 152 104 pint:PI1207|5end_hypothtical_protein_1126977..1127207_POSITIVE 314 89 43 138 91 pint:PI0167|5end_hypothetical_protein_163164..163394_POSITIVE 309 88 42 195 139 pint:PI0249|5end_conserved_hypothetical_protein_246572..246802_POSITIVE 308 50 3 76 27 pint:PI1123|5end_conserved_hypothetical_protein_1048011..1048241_POSITIVE 308 90 41 162 109 pint:PI0213|5end_conserved_hypothetical_protein_207065..207295_POSITIVE 307 92 59 169 130 pint:PI0502|5end_conserved_hypothetical_protein;_possible_helicase_461798..462028_POSITIVE 306 95 58 143 101 pint:PI1672|5end_conserved_hypothetical_protein;_possible_DNA-binding_protein,_histone-like_family_1587027..1587257_POSITIVE 305 99 51 136 85 pint:PI0118|5end_hypothetical_protein_111321..111551_POSITIVE 304 100 56 213 159 pint:PI2076|5end_hypothetical_protein_2035403..2035633_POSITIVE 303 120 71 163 120 pint:PI1536|5end_hypothetical_protein_1455555..1455785_POSITIVE 302 100 58 219 174 pint:PI1637|5end_hypothetical_protein_1554500..1554730_POSITIVE 300 90 41 219 177 pint:PI1818|5end_hypothetical_protein_1756891..1757121_POSITIVE 297 90 48 188 134 pint:PI0866|5end_hypothetical_protein_803776..804006_POSITIVE 295 110 61 90 28 pint:PI0663|5end_possible_transcriptional_regulator_605999..606229_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 367 106 63 123 66 pint:PI0843|3end_carboxyl-terminal_protease_777862..778012_POSITIVE 335 100 59 105 63 pint:PI0421|3end_hypothetical_protein_387774..387924_POSITIVE 335 99 63 76 36 pint:PI0057|3end_conserved_hypothetical_protein_56512..56662_POSITIVE 306 95 58 62 20 pint:PI1670|3end_hypothetical_protein_1587026..1587176_POSITIVE 304 100 56 85 31 pint:PI2075|3end_conserved_hypothetical_protein_2035355..2035505_POSITIVE 300 91 62 141 110 pint:PI0306|3end_conserved_hypothetical_protein_289828..289978_POSITIVE 300 119 73 55 2 pint:PI0052|3end_hypothetical_protein_52715..52865_POSITIVE 297 100 57 64 7 pint:PI0358|3end_hypothetical_protein_328105..328255_POSITIVE 296 260 212 115 74 pint:PI1414|3end_conserved_hypothetical_protein_1334436..1334586_POSITIVE 293 99 57 49 2 pint:PI0117|3end_ribonuclease_HI_111314..111464_POSITIVE 291 109 63 97 44 pint:PI0798|3end_malonyl_CoA-acyl_carrier_protein_transacylase_736975..737125_POSITIVE 291 98 55 147 90 pint:PI0352|3end_hypothetical_protein_325934..326084_POSITIVE 288 119 73 107 55 pint:PI1651|3end_hypothetical_protein_1564512..1564662_POSITIVE 288 99 56 48 9 pint:PI0257|3end_conjugative_transposon_protein,_TraF_249802..249952_POSITIVE 285 108 61 140 82 pint:PI1857|3end_guanylate_kinase_1804396..1804546_POSITIVE 283 119 71 138 82 pint:PI0425|3end_hypothetical_protein_389722..389872_POSITIVE 279 222 192 49 15 pint:PI0752|3end_conserved_hypothetical_protein_683467..683617_POSITIVE 276 240 193 141 90 pint:PI0943|3end_conserved_hypothetical_protein_875991..876141_POSITIVE 276 99 60 130 88 pint:PI0600|3end_bifunctional_purine_biosynthesis_protein,_5-aminoimidazole-4-carboxamide_ribonucleotide(AICAR)_transformylase/IMP_cyclohydrolase_548797..548947_POSITIVE 276 269 222 37 3 pint:PI0355|3end_probable__N-acetylmuramoyl-L-alanine_amidase_326698..326848_POSITIVE