Origin IGS: taattcacagttattattcaccactttaatccaaagtaaaaatgaaaagaacagttttagccatcgccctgatgctgggcgcagtctgtgccaacgcacaggaaacgacttcaagcggagacctctatcaggggctgacccgcaaaatcacctttgagcgg .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 ccgctcaaaggtgattttgcgggtcagcccctgatagaggtctccgcttgaagtcgtttcctgtgcgttggcacagactgcgcccagcatcagggcgatggctaaaactgttcttttcatttttactttggattaaagtggtgaataataactgtgaatta Mask Tandem Repeat Region ================================================ taattcacagttattattcaccactttaatccaaagtaaaaatgaaaagaacagttttagccatcgccctgatgctgggcgcagtctgtgccaacgcacaggaaacgacttcaagcggagacctctatcaggggctgacccgcaaaatcacctttgagcgg Find is-nt database================================================ Query_seq: PI0263:PI0264|PI0263:PI0264:conjugative transposon protein, TraM:transfer region-related protein, TraN:->->:256473..256633 161 taattcacagttattattcaccactttaatccaaagtaaaaatgaaaagaacagttttagccatcgccctgatgctgggcgcagtctgtgccaacgcacaggaaacgacttcaagcggagacctctatcaggggctgacccgcaaaatcacctttgagcgg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI0263:PI0264|PI0263:PI0264:conjugative transposon protein, TraM:transfer region-related protein, TraN:->->:256473..256633 161 taattcacagttattattcaccactttaatccaaagtaaaaatgaaaagaacagttttagccatcgccctgatgctgggcgcagtctgtgccaacgcacaggaaacgacttcaagcggagacctctatcaggggctgacccgcaaaatcacctttgagcgg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI0263:PI0264|PI0263:PI0264:conjugative transposon protein, TraM:transfer region-related protein, TraN:->->:256473..256633 161 taattcacagttattattcaccactttaatccaaagtaaaaatgaaaagaacagttttagccatcgccctgatgctgggcgcagtctgtgccaacgcacaggaaacgacttcaagcggagacctctatcaggggctgacccgcaaaatcacctttgagcgg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 taattcacagttattattcaccactttaatccaaagtaaaaatgaaaagaacagttttagccatcgccctgatgctgggcgcagtctgtgccaacgcacaggaaacgacttcaagcggagacctctatcaggggctgacccgcaaaatcacctttgagcgg Predict ORF larger than 30AA ================================================ Protein_Len: 42 Strand: + Start: 29 End: 154 ............................ M Q S K N E K N S F S H R P D A G R S L C Q R T G N D F K R R P L S G A D P Q N H L ....... Protein_Len: 40 Strand: + Start: 42 End: 161 ......................................... M K R T V L A I A L M L G A V C A N A Q E T T S S G D L Y Q G L T R K I T F E R Protein_Len: 38 Strand: - Start: 1 End: 114 L E C N N N V V K I W L L F S F F L K L W R G S A P R L R H W R V P F S K M ............................................... taattcacagttattattcaccactttaatccaaagtaaaaatgaaaagaacagttttagccatcgccctgatgctgggcgcagtctgtgccaacgcacaggaaacgacttcaagcggagacctctatcaggggctgacccgcaaaatcacctttgagcgg 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================================================ taattcacagttattattcaccactttaatccaaagtaaaaatgaaaagaacagttttagccatcgccctgatgctgggcgcagtctgtgccaacgcacaggaaacgacttcaagcggagacctctatcaggggctgacccgcaaaatcacctttgagcgg Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PI0263:PI0264|PI0263:PI0264:conjugative transposon protein, TraM:transfer region-related protein, TraN:->->:256473..256633 161 taattcacagttattattcaccactttaatccaaagtaaaaatgaaaagaacagttttagccatcgccctgatgctgggcgcagtctgtgccaacgcacaggaaacgacttcaagcggagacctctatcaggggctgacccgcaaaatcacctttgagcgg Intra-Species Hit: Count: 1 Min: 1 Max: 161 Len: 161 Subject: pint_PI0263_PI0264|conjugative transposon protein, TraM:transfer region-related protein, TraN|POSITIVE:POSITIVE|[256473,256633]|161 HSP 1 e-value: 2.0E-86 bit: 319.0 Len: 161 Query Start:1 Query End:161 Subject Strand: POSITIVE Subject Start: 1 Subject End: 161 taattcacagttattattcaccactttaatccaaagtaaaaatgaaaagaacagttttagccatcgccctgatgctgggcgcagtctgtgccaacgcacaggaaacgacttcaagcggagacctctatcaggggctgacccgcaaaatcacctttgagcgg taattcacagttattattcaccactttaatccaaagtaaaaatgaaaagaacagttttagccatcgccctgatgctgggcgcagtctgtgccaacgcacaggaaacgacttcaagcggagacctctatcaggggctgacccgcaaaatcacctttgagcgg Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAUUCACAGUUAUUAUUCACCACUUUAAUCCAAAGUAAAAAUGAAAAGAACAGUUUUAGCCAUCGCCCUGAUGCUGGGCGCAGUCUGUGCCAACGCACAGGAAACGACUUCAAGCGGAGACCUCUAUCAGGGGCUGACCCGCAAAAUCACCUUUGAGCGG .........(((....((((..(((((.....))))).....))))...)))....((((((.....(((((((..((.((...(((((((....)))))))...)).((((....)))).))..))))))))))))).((((..((......))..)))) (-38.70) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CCGCUCAAAGGUGAUUUUGCGGGUCAGCCCCUGAUAGAGGUCUCCGCUUGAAGUCGUUUCCUGUGCGUUGGCACAGACUGCGCCCAGCAUCAGGGCGAUGGCUAAAACUGUUCUUUUCAUUUUUACUUUGGAUUAAAGUGGUGAAUAAUAACUGUGAAUUA ....((((.((.((((((.((((......))))...)))))).))..))))(((((((((((((((...(((.(.....).)))..))).))))).)))))))...((.(((...(((((...(((((((...))))))))))))....))).))...... (-43.20) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 406 109 62 158 89 pint:PI1439|5end_hypothetical_protein_1360009..1360239_POSITIVE 401 90 47 46 1 pint:PI0536|5end_hypothetical_protein_492163..492393_POSITIVE 394 109 61 89 25 pint:PI1468|5end_conserved_hypothetical_protein;_probable_TPR_domain_protein_1393900..1394130_POSITIVE 373 97 51 227 177 pint:PI0431|5end_Xaa-Pro_aminopeptidase_403064..403294_POSITIVE 369 98 59 91 39 pint:PI1909|5end_DNA_gyrase,_B_subunit_1853223..1853453_POSITIVE 369 100 51 75 18 pint:PI1364|5end_dipeptidyl_peptidase_IV_1281862..1282092_POSITIVE 368 117 72 103 50 pint:PI1650|5end_N-acetylmuramoyl-L-alanine_amidase_1563195..1563425_POSITIVE 367 129 83 220 167 pint:PI0093|5end_riboflavin_biosynthesis_protein_90489..90719_POSITIVE 364 108 64 219 172 pint:PI0766|5end_conserved_hypothetical_protein_700781..701011_POSITIVE 362 140 91 71 11 pint:PI0895|5end_2-oxoglutarate_oxidoreductase,_beta_subunit,_possible_ketoisovalerate_oxidoreductase,__vorA_826347..826577_POSITIVE 361 97 52 81 25 pint:PI0128|5end_dipeptidase,_pathogenicity_island-encoded_protein_D_120532..120762_POSITIVE 360 98 51 169 111 pint:PI0683|5end_hypothetical_protein_619292..619522_POSITIVE 359 120 71 77 23 pint:PI0516|5end_ferredoxin,_4Fe-4S_475864..476094_POSITIVE 355 100 59 79 32 pint:PI0567|5end_hypothetical_protein_512781..513011_POSITIVE 352 117 72 181 118 pint:PI0701|5end_hypothetical_protein_638356..638586_POSITIVE 344 109 61 107 52 pint:PI1745|5end_conserved_hypothetical_protein_1666615..1666845_POSITIVE 344 118 71 70 16 pint:PI0265|5end_conjugative_transposon_protein,_TraO_257296..257526_POSITIVE 344 117 74 135 86 pint:PI0108|5end_L-lactate_permease_104892..105122_POSITIVE 342 108 61 90 38 pint:PI2017|5end_conserved_hypothetical_protein_1974862..1975092_POSITIVE 341 92 54 108 63 pint:PI0688|5end_hypothetical_protein_625458..625688_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 400 98 53 147 99 pint:PI1239|3end_possible_peptidase_C1-like_family_(aminopeptidase_C)_1164780..1164930_POSITIVE 389 98 54 141 95 pint:PI1794|3end_conserved_hypothetical_protein_1726696..1726846_POSITIVE 383 109 61 141 96 pint:PI1547|3end_hypothetical_protein_1466226..1466376_POSITIVE 370 120 73 142 106 pint:PI0160|3end_conserved_hypothetical_protein_153268..153418_POSITIVE 363 107 65 142 95 pint:PI1973|3end_conserved_hypothetical_protein_1931171..1931321_POSITIVE 346 87 48 102 69 pint:PI1408|3end_glucose-1-phosphate_thymidylyltransferase_1329761..1329911_POSITIVE 346 120 83 151 109 pint:PI0094|3end_protoporphyrinogen_oxidase_90511..90661_POSITIVE 345 117 74 55 1 pint:PI2044|3end_hypothetical_protein_1997351..1997501_POSITIVE 342 108 61 81 29 pint:PI2016|3end_ribosomal_large_subunit_pseudouridine_synthase_D_1974933..1975083_POSITIVE 341 104 66 48 1 pint:PI1815|3end_polyphosphate-selective_porin_O_1754510..1754660_POSITIVE 340 91 53 148 109 pint:PI0835|3end_conserved_hypothetical_protein;_possible_protein-export_membrane_protein_771859..772009_POSITIVE 335 116 73 149 102 pint:PI1752|3end_conserved_hypothetical_protein_1681270..1681420_POSITIVE 334 97 52 62 23 pint:PI0654|3end_K+-dependent_Na+/Ca+_exchanger_related-protein_597223..597373_POSITIVE 334 118 73 124 74 pint:PI0598|3end_hypothetical_protein_547233..547383_POSITIVE 331 89 52 141 102 pint:PI0906|3end_hypothetical_protein_836008..836158_POSITIVE 329 108 63 60 18 pint:PI0206|3end_TPR-repeat-containing_protein_199856..200006_POSITIVE 327 97 52 143 102 pint:PI1574|3end_conserved_hypothetical_protein_1501226..1501376_POSITIVE 324 90 41 148 90 pint:PI2018|3end_50S_ribosomal_protein_L34_1975989..1976139_POSITIVE 324 110 64 64 6 pint:PI0091|3end_hypothetical_protein_89774..89924_POSITIVE 321 100 60 55 9 pint:PI1363|3end_hypothetical_protein_1281922..1282072_POSITIVE