Origin IGS: taagtttctatcgttactccgtactattgcaatcttaacaaaaaagcctctgcaccgaacgtgcagaggctttttgctgaatgtgaacggctctttggtgccgtttttctgcttccgtcaggttta .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 taaacctgacggaagcagaaaaacggcaccaaagagccgttcacattcagcaaaaagcctctgcacgttcggtgcagaggcttttttgttaagattgcaatagtacggagtaacgatagaaactta Mask Tandem Repeat Region ================================================ taagtttctatcgttactccgtactattgcaatcttaacaaaaaagcctctgcaccgaacgtgcagaggctttttgctgaatgtgaacggctctttggtgccgtttttctgcttccgtcaggttta Find is-nt database================================================ Query_seq: PI0653:PI0654|PI0653:PI0654:hypothetical protein:K+-dependent Na+/Ca+ exchanger related-protein:->->:596297..596422 126 taagtttctatcgttactccgtactattgcaatcttaacaaaaaagcctctgcaccgaacgtgcagaggctttttgctgaatgtgaacggctctttggtgccgtttttctgcttccgtcaggttta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI0653:PI0654|PI0653:PI0654:hypothetical protein:K+-dependent Na+/Ca+ exchanger related-protein:->->:596297..596422 126 taagtttctatcgttactccgtactattgcaatcttaacaaaaaagcctctgcaccgaacgtgcagaggctttttgctgaatgtgaacggctctttggtgccgtttttctgcttccgtcaggttta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI0653:PI0654|PI0653:PI0654:hypothetical protein:K+-dependent Na+/Ca+ exchanger related-protein:->->:596297..596422 126 taagtttctatcgttactccgtactattgcaatcttaacaaaaaagcctctgcaccgaacgtgcagaggctttttgctgaatgtgaacggctctttggtgccgtttttctgcttccgtcaggttta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 taagtttctatcgttactccgtactattgcaatcttaacaaaaaagcctctgcaccgaacgtgcagaggctttttgctgaatgtgaacggctctttggtgccgtttttctgcttccgtcaggttta Predict ORF larger than 30AA ================================================ Protein_Len: 33 Strand: + Start: 26 End: 124 ......................... M A I L T K K P L H R T C R G F L L N V N G S L V P F F C F R Q V .. Protein_Len: 39 Strand: + Start: 10 End: 126 ......... M V T P Y Y C N L N K K A S A P N V Q R L F A E C E R L F G A V F L L P S G L taagtttctatcgttactccgtactattgcaatcttaacaaaaaagcctctgcaccgaacgtgcagaggctttttgctgaatgtgaacggctctttggtgccgtttttctgcttccgtcaggttta 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================================================ taagtttctatcgttactccgtactattgcaatcttaacaaaaaagcctctgcaccgaacgtgcagaggctttttgctgaatgtgaacggctctttggtgccgtttttctgcttccgtcaggttta Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 100 HP_score: -15.8 Tail_Score: -4.76041 Start: 46 End: 70 Full_Region: AATCTTAACAAAAAA GCCTCTGCAC CGAAC GTGCAGAGGC TTTTTGCTGAATGTG .............................................GCCTCTGCACCGAACGTGCAGAGGC........................................................ TransTerm Strand: - Conf: 100 HP_score: -15.8 Tail_Score: -5.4756 Start: 46 End: 70 Full_Region: cacattcagcaaaaa gcctctgcac gttcg gtgcagaggc ttttttgttaagatt .............................................gcctctgcacgttcggtgcagaggc........................................................ TransTerm Strand: + Conf: 81 HP_score: -6.0 Tail_Score: -4.98857 Start: 88 End: 103 Full_Region: TTTGCTGAATGTGAA CGGCTC TTTG GTGCCG TTTTTCTGCTTCCGT .......................................................................................CGGCTCTTTGGTGCCG....................... Find igs database================================================ Query_seq: PI0653:PI0654|PI0653:PI0654:hypothetical protein:K+-dependent Na+/Ca+ exchanger related-protein:->->:596297..596422 126 taagtttctatcgttactccgtactattgcaatcttaacaaaaaagcctctgcaccgaacgtgcagaggctttttgctgaatgtgaacggctctttggtgccgtttttctgcttccgtcaggttta Intra-Species Hit: Count: 1 Min: 1 Max: 126 Len: 126 Subject: pint_PI0653_PI0654|hypothetical protein:K+-dependent Na+/Ca+ exchanger related-protein|POSITIVE:POSITIVE|[596297,596422]|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 taagtttctatcgttactccgtactattgcaatcttaacaaaaaagcctctgcaccgaacgtgcagaggctttttgctgaatgtgaacggctctttggtgccgtttttctgcttccgtcaggttta taagtttctatcgttactccgtactattgcaatcttaacaaaaaagcctctgcaccgaacgtgcagaggctttttgctgaatgtgaacggctctttggtgccgtttttctgcttccgtcaggttta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAGUUUCUAUCGUUACUCCGUACUAUUGCAAUCUUAACAAAAAAGCCUCUGCACCGAACGUGCAGAGGCUUUUUGCUGAAUGUGAACGGCUCUUUGGUGCCGUUUUUCUGCUUCCGUCAGGUUUA ......(((..((...........................(((((((((((((((.....)))))))))))))))((.(((...(((((((.(....).)))))))))).))...))..))).... (-38.70) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAACCUGACGGAAGCAGAAAAACGGCACCAAAGAGCCGUUCACAUUCAGCAAAAAGCCUCUGCACGUUCGGUGCAGAGGCUUUUUUGUUAAGAUUGCAAUAGUACGGAGUAACGAUAGAAACUUA ...(((((((....((((...((((((........)))))).......((((((((((((((((((.....)))))))))).))))))))....))))....)).))).))............... (-42.10) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 561 78 32 191 143 pint:PI1588|5end_DNA_polymerase_III,_epsilon_chain_1516302..1516532_POSITIVE 355 85 42 94 53 pint:PI0870|5end_branched-chain_amino_acid_aminotransferase_805933..806163_POSITIVE 352 110 61 65 3 pint:PI0729|5end_integrase_661428..661658_POSITIVE 349 118 71 145 91 pint:PI0260|5end_conjugative_transposon_protein,_TraJ_253023..253253_POSITIVE 341 119 82 58 23 pint:PI1634|5end_conserved_hypothetical_protein_1553179..1553409_POSITIVE 341 119 82 58 23 pint:PI0340|5end_conserved_hypothetical_protein_316095..316325_POSITIVE 341 119 71 138 94 pint:PI0273|5end_hypothetical_protein_262956..263186_POSITIVE 341 90 46 189 147 pint:PI0248|5end_protein_associated_with_conjugate_transformation/chromosome_partioning_246139..246369_POSITIVE 327 90 45 213 168 pint:PI0609|5end_conserved_hypothetical_protein_556519..556749_POSITIVE 324 96 51 208 165 pint:PI1870|5end_hypothetical_protein_1815302..1815532_POSITIVE 324 85 45 213 160 pint:PI0737|5end_hypothetical_protein_671182..671412_POSITIVE 323 109 61 166 115 pint:PI1980|5end_conserved_hypothetical_protein_1937470..1937700_POSITIVE 323 100 52 120 59 pint:PI1671|5end_hypothetical_protein_1586397..1586627_POSITIVE 323 104 64 64 22 pint:PI0037|5end_hypothetical_protein_39354..39584_POSITIVE 320 91 52 55 5 pint:PI1736|5end_topoisomerase_IV,_subunit_A_1654254..1654484_POSITIVE 315 88 44 114 65 pint:PI0052|5end_hypothetical_protein_52312..52542_POSITIVE 314 90 44 129 79 pint:PI0715|5end_hypothetical_protein_652311..652541_POSITIVE 313 90 47 195 151 pint:PI2028|5end_shikimate_kinase_1982162..1982392_POSITIVE 313 96 55 115 66 pint:PI0263|5end_conjugative_transposon_protein,_TraM_255256..255486_POSITIVE 312 117 73 75 29 pint:PI2042|5end_cation-transporting_ATPase_1994175..1994405_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 561 78 32 75 27 pint:PI1587|3end_conserved_hypothetical_protein;_possible_permease_1516266..1516416_POSITIVE 502 90 41 72 16 pint:PI0653|3end_hypothetical_protein_596236..596386_POSITIVE 352 110 61 65 3 pint:PI0728|3end_integrase_661508..661658_POSITIVE 349 118 71 85 31 pint:PI0259|3end_conserved_protein_found_in_conjugation,_TraI_253043..253193_POSITIVE 341 119 71 45 1 pint:PI0272|3end_conserved_hypothetical_protein_262943..263093_POSITIVE 334 118 71 80 18 pint:PI2117|3end_fumarate_reductase/succinate_dehydrogenase_flavoprotein_subunit,_C-terminal_2066684..2066834_POSITIVE 329 116 84 81 50 pint:PI0327|3end_hypothetical_protein_309107..309257_POSITIVE 320 103 61 118 70 pint:PI1227|3end_conserved_hypothetical_protein;_possible_DNA-binding_protein,_histone-like_family_1148974..1149124_POSITIVE 319 83 46 118 80 pint:PI1065|3end_hypothetical_protein_983650..983800_POSITIVE 317 98 51 81 24 pint:PI1367|3end_redox-sensitive_transcriptional_activator,__OxyR_1287863..1288013_POSITIVE 313 90 47 83 39 pint:PI2027|3end_arginine_decarboxylase_1982130..1982280_POSITIVE 312 110 68 65 19 pint:PI1527|3end_immunoreactive_46_kDa_antigen_PG99_1449520..1449670_POSITIVE 310 100 52 142 85 pint:PI2037|3end_TIM-barrel_protein,_NifR3_family_1990369..1990519_POSITIVE 308 118 92 129 102 pint:PI2067|3end_hypothetical_protein_2028337..2028487_POSITIVE 308 108 62 137 85 pint:PI0200|3end_hypothetical_protein_191735..191885_POSITIVE 307 118 77 88 41 pint:PI1734|3end_possible_carboxyl-terminal_protease-related_protein_1653829..1653979_POSITIVE 306 96 51 113 70 pint:PI0905|3end_hypothetical_protein_834697..834847_POSITIVE 306 96 51 91 48 pint:PI0560|3end_hypothetical_protein_508910..509060_POSITIVE 300 84 44 112 62 pint:PI0195|3end_epimerase/reductase_188202..188352_POSITIVE 299 109 62 137 99 pint:PI2132|3end_hypothetical_protein_2081139..2081289_POSITIVE