Origin IGS: taaagagccgcataaggctttcattaccccacgggcaaggtgcaagaacctcgttcgtggggtatttcgtgaatatgcgaaagccgccttggcagagagtgccaaggcggctttgtttacgtttttatactttgtacaccatcttttcagttctcgaaacaaaacagtggacatggcaatgaaagatattgtca .........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 tgacaatatctttcattgccatgtccactgttttgtttcgagaactgaaaagatggtgtacaaagtataaaaacgtaaacaaagccgccttggcactctctgccaaggcggctttcgcatattcacgaaataccccacgaacgaggttcttgcaccttgcccgtggggtaatgaaagccttatgcggctcttta Mask Tandem Repeat Region ================================================ taaagagccgcataaggctttcattaccccacgggcaaggtgcaagaacctcgttcgtggggtatttcgtgaatatgcgaaagccgccttggcagagagtgccaaggcggctttgtttacgtttttatactttgtacaccatcttttcagttctcgaaacaaaacagtggacatggcaatgaaagatattgtca Find is-nt database================================================ Query_seq: PI1223:PI1224|PI1223:PI1224:conserved hypothetical protein:sensor histidine kinase and response regulator:->->:1144520..1144713 194 taaagagccgcataaggctttcattaccccacgggcaaggtgcaagaacctcgttcgtggggtatttcgtgaatatgcgaaagccgccttggcagagagtgccaaggcggctttgtttacgtttttatactttgtacaccatcttttcagttctcgaaacaaaacagtggacatggcaatgaaagatattgtca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI1223:PI1224|PI1223:PI1224:conserved hypothetical protein:sensor histidine kinase and response regulator:->->:1144520..1144713 194 taaagagccgcataaggctttcattaccccacgggcaaggtgcaagaacctcgttcgtggggtatttcgtgaatatgcgaaagccgccttggcagagagtgccaaggcggctttgtttacgtttttatactttgtacaccatcttttcagttctcgaaacaaaacagtggacatggcaatgaaagatattgtca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI1223:PI1224|PI1223:PI1224:conserved hypothetical protein:sensor histidine kinase and response regulator:->->:1144520..1144713 194 taaagagccgcataaggctttcattaccccacgggcaaggtgcaagaacctcgttcgtggggtatttcgtgaatatgcgaaagccgccttggcagagagtgccaaggcggctttgtttacgtttttatactttgtacaccatcttttcagttctcgaaacaaaacagtggacatggcaatgaaagatattgtca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 taaagagccgcataaggctttcattaccccacgggcaaggtgcaagaacctcgttcgtggggtatttcgtgaatatgcgaaagccgccttggcagagagtgccaaggcggctttgtttacgtttttatactttgtacaccatcttttcagttctcgaaacaaaacagtggacatggcaatgaaagatattgtca Predict ORF larger than 30AA ================================================ Protein_Len: 56 Strand: + Start: 12 End: 179 ........... M R L S L P H G Q G A R T S F V G Y F V N M R K P P W Q R V P R R L C L R F Y T L Y T I F S V L E T K Q W T W Q ............... Protein_Len: 40 Strand: + Start: 73 End: 192 ........................................................................ M C E S R L G R E C Q G G F V Y V F I L C T P S F Q F S K Q N S G H G N E R Y C .. Protein_Len: 57 Strand: + Start: 23 End: 193 ...................... M T P R A R C K N L V R G V F R E Y A K A A L A E S A K A A L F T F L Y F V H H L F S S R N K T V D M A M K D I V . Protein_Len: 60 Strand: - Start: 1 End: 189 C L A K M V G R A L H L F R T R P T N R S Y A F A A K A S L A L A A K N V N K Y K T C W R K L E R F L V T S M A I F S M ..... taaagagccgcataaggctttcattaccccacgggcaaggtgcaagaacctcgttcgtggggtatttcgtgaatatgcgaaagccgccttggcagagagtgccaaggcggctttgtttacgtttttatactttgtacaccatcttttcagttctcgaaacaaaacagtggacatggcaatgaaagatattgtca 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================================================ taaagagccgcataaggctttcattaccccacgggcaaggtgcaagaacctcgttcgtggggtatttcgtgaatatgcgaaagccgccttggcagagagtgccaaggcggctttgtttacgtttttatactttgtacaccatcttttcagttctcgaaacaaaacagtggacatggcaatgaaagatattgtca Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 100 HP_score: -15.1 Tail_Score: -3.78022 Start: 25 End: 64 Full_Region: GCATAAGGCTTTCAT TACCCCACGGGCAAGGT GCAAGA ACCTCGTTCGTGGGGTA TTTCGTGAATATGCG ........................TACCCCACGGGCAAGGTGCAAGAACCTCGTTCGTGGGGTA.................................................................................................................................. TransTerm Strand: + Conf: 100 HP_score: -9.4 Tail_Score: -5.06735 Start: 72 End: 121 Full_Region: GTGGGGTATTTCGTG AATATGCGAAAGCCGCCTTGGCA GAGAG TGCCAAGGCGGCTTTGTTTACG TTTTTATACTTTGTA .......................................................................AATATGCGAAAGCCGCCTTGGCAGAGAGTGCCAAGGCGGCTTTGTTTACG......................................................................... TransTerm Strand: + Conf: 100 HP_score: -20.4 Tail_Score: -4.57205 Start: 83 End: 111 Full_Region: CGTGAATATGCGAAA GCCGCCTTGGCA GAGAG TGCCAAGGCGGC TTTGTTTACGTTTTT ..................................................................................GCCGCCTTGGCAGAGAGTGCCAAGGCGGC................................................................................... TransTerm Strand: - Conf: 100 HP_score: -20.4 Tail_Score: -3.66803 Start: 83 End: 111 Full_Region: aaaaacgtaaacaaa gccgccttggca ctctc tgccaaggcggc tttcgcatattcacg ..................................................................................gccgccttggcactctctgccaaggcggc................................................................................... Find igs database================================================ Query_seq: PI1223:PI1224|PI1223:PI1224:conserved hypothetical protein:sensor histidine kinase and response regulator:->->:1144520..1144713 194 taaagagccgcataaggctttcattaccccacgggcaaggtgcaagaacctcgttcgtggggtatttcgtgaatatgcgaaagccgccttggcagagagtgccaaggcggctttgtttacgtttttatactttgtacaccatcttttcagttctcgaaacaaaacagtggacatggcaatgaaagatattgtca Intra-Species Hit: Count: 1 Min: 1 Max: 194 Len: 194 Subject: pint_PI1223_PI1224|conserved hypothetical protein:sensor histidine kinase and response regulator|POSITIVE:POSITIVE|[1144520,1144713]|194 HSP 1 e-value: 1.0E-106 bit: 385.0 Len: 194 Query Start:1 Query End:194 Subject Strand: POSITIVE Subject Start: 1 Subject End: 194 taaagagccgcataaggctttcattaccccacgggcaaggtgcaagaacctcgttcgtggggtatttcgtgaatatgcgaaagccgccttggcagagagtgccaaggcggctttgtttacgtttttatactttgtacaccatcttttcagttctcgaaacaaaacagtggacatggcaatgaaagatattgtca taaagagccgcataaggctttcattaccccacgggcaaggtgcaagaacctcgttcgtggggtatttcgtgaatatgcgaaagccgccttggcagagagtgccaaggcggctttgtttacgtttttatactttgtacaccatcttttcagttctcgaaacaaaacagtggacatggcaatgaaagatattgtca Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAAGAGCCGCAUAAGGCUUUCAUUACCCCACGGGCAAGGUGCAAGAACCUCGUUCGUGGGGUAUUUCGUGAAUAUGCGAAAGCCGCCUUGGCAGAGAGUGCCAAGGCGGCUUUGUUUACGUUUUUAUACUUUGUACACCAUCUUUUCAGUUCUCGAAACAAAACAGUGGACAUGGCAAUGAAAGAUAUUGUCA ...((((((......))))))...((((((((((((.((((......)))).))))))))))))...((((((((.....((((((((((((((.....))))))))))))))))))))))...........(((.(((.....((((.......)))).......))).))).(((((((.....))))))). (-76.20) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGACAAUAUCUUUCAUUGCCAUGUCCACUGUUUUGUUUCGAGAACUGAAAAGAUGGUGUACAAAGUAUAAAAACGUAAACAAAGCCGCCUUGGCACUCUCUGCCAAGGCGGCUUUCGCAUAUUCACGAAAUACCCCACGAACGAGGUUCUUGCACCUUGCCCGUGGGGUAAUGAAAGCCUUAUGCGGCUCUUUA ......(((.(((...(((..(((.(((((((...(((((.....))))).))))))).)))..)))...))).)))...(((((((((((((((.....)))))))))))))))((((((.........(((((((((..((((((......))))))..)))))))))..........))))))........ (-71.21) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 539 125 81 172 132 pint:PI1230|5end_probable_metallo-beta-lactamase_family_protein_1151840..1152070_POSITIVE 470 70 25 194 146 pint:PI1227|5end_conserved_hypothetical_protein;_possible_DNA-binding_protein,_histone-like_family_1148448..1148678_POSITIVE 378 122 83 178 141 pint:PI1564|5end_surface_antigen_BspA_1483455..1483685_POSITIVE 376 109 61 95 54 pint:PI2022|5end_hypothetical_protein_1978631..1978861_POSITIVE 376 109 61 49 8 pint:PI2023|5end_hypothetical_protein_1978585..1978815_POSITIVE 376 117 77 190 156 pint:PI0667|5end_hypothetical_protein_610113..610343_POSITIVE 369 109 69 157 122 pint:PI1371|5end_hypothetical_protein_1292359..1292589_POSITIVE 369 109 69 81 46 pint:PI0659|5end_hypothetical_protein_603203..603433_POSITIVE 365 50 5 171 121 pint:PI1547|5end_hypothetical_protein_1465808..1466038_POSITIVE 365 115 78 45 7 pint:PI0858|5end_carbamyl_phosphate_synthase,_large_subunit_790093..790323_POSITIVE 361 111 77 59 27 pint:PI0265|5end_conjugative_transposon_protein,_TraO_257296..257526_POSITIVE 356 121 83 56 3 pint:PI1634|5end_conserved_hypothetical_protein_1553179..1553409_POSITIVE 356 109 75 222 190 pint:PI0991|5end_conserved_hypothetical_protein_915309..915539_POSITIVE 356 121 83 56 3 pint:PI0340|5end_conserved_hypothetical_protein_316095..316325_POSITIVE 355 80 32 176 114 pint:PI0094|5end_protoporphyrinogen_oxidase_89571..89801_POSITIVE 355 80 32 102 40 pint:PI0091|5end_hypothetical_protein_89497..89727_POSITIVE 347 70 28 161 114 pint:PI1864|5end_chromate_transport_protein_1810318..1810548_POSITIVE 346 112 76 67 25 pint:PI1729|5end_FKBP-type_peptidyl-prolyl_cis-trans_isomerase,_trigger_factor_1648416..1648646_POSITIVE 344 127 82 74 29 pint:PI1778|5end_UDP-N-acetylglucosamine_1-carboxyvinyltransferase_1710009..1710239_POSITIVE 344 110 76 203 169 pint:PI0088|5end_S-adenosylmethionine_synthetase_86663..86893_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 568 127 82 69 29 pint:PI1431|3end_conserved_hypothetical_protein_1352809..1352959_POSITIVE 482 64 25 66 27 pint:PI1223|3end_conserved_hypothetical_protein_1144459..1144609_POSITIVE 475 117 81 80 46 pint:PI1499|3end_hypothetical_protein_1420180..1420330_POSITIVE 361 111 77 54 22 pint:PI0264|3end_transfer_region-related_protein,_TraN_257371..257521_POSITIVE 353 116 77 81 43 pint:PI0005|3end_hypothetical_protein_7450..7600_POSITIVE 345 123 81 148 101 pint:PI0948|3end_hypothetical_protein_881978..882128_POSITIVE 344 127 82 66 21 pint:PI1777|3end_conserved_hypothetical_protein_1710081..1710231_POSITIVE 340 122 84 81 37 pint:PI0539|3end_hypothetical_protein_493728..493878_POSITIVE 336 118 87 41 9 pint:PI0222|3end_conserved_hypothetical_protein_218442..218592_POSITIVE 332 118 76 100 51 pint:PI1892|3end_UDP-N-acetylmuramoylalanine--D-glutamate_ligase_1835547..1835697_POSITIVE 331 130 83 47 1 pint:PI1787|3end_conserved_hypothetical_protein_1719165..1719315_POSITIVE 330 116 78 119 66 pint:PI1722|3end_possible_peptidyl-prolyl_cis-trans_isomerase_1640995..1641145_POSITIVE 326 58 11 65 25 pint:PI1023|3end_hypothetical_protein_940195..940345_POSITIVE 325 120 78 69 19 pint:PI0187|3end_hypothetical_protein_178211..178361_POSITIVE 323 70 27 140 98 pint:PI1437|3end_hypothetical_protein_1356407..1356557_POSITIVE 320 99 52 110 65 pint:PI1440|3end_conserved_hypothetical_protein_1363009..1363159_POSITIVE 320 79 31 145 97 pint:PI0784|3end_possible_amidase_enhancer_precursor_723303..723453_POSITIVE 319 66 27 148 120 pint:PI0407|3end_tryptophanyl-tRNA_synthetase_(tryptophan--tRNA_ligase)_374147..374297_POSITIVE 313 96 52 66 12 pint:PI1647|3end_hypothetical_protein_1562531..1562681_POSITIVE 313 96 52 66 12 pint:PI0353|3end_hypothetical_protein_325337..325487_POSITIVE