Origin IGS: taaaaccaaagtttatgttatgagcatataagattgctcataacatagaattatttaaggatttttaatattgtcggggaagtcccgattaattaaacatttataattt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aaattataaatgtttaattaatcgggacttccccgacaatattaaaaatccttaaataattctatgttatgagcaatcttatatgctcataacataaactttggtttta Mask Tandem Repeat Region ================================================ taaaaccaaagtttatgttatgagcatataagattgctcataacatagaattatttaaggatttttaatattgtcggggaagtcccgattaattaaacatttataattt Find is-nt database================================================ Query_seq: PI0473:PI0474|PI0473:PI0474:30S ribosomal protein S14:30S ribosomal protein S8:->->:439074..439182 109 taaaaccaaagtttatgttatgagcatataagattgctcataacatagaattatttaaggatttttaatattgtcggggaagtcccgattaattaaacatttataattt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI0473:PI0474|PI0473:PI0474:30S ribosomal protein S14:30S ribosomal protein S8:->->:439074..439182 109 taaaaccaaagtttatgttatgagcatataagattgctcataacatagaattatttaaggatttttaatattgtcggggaagtcccgattaattaaacatttataattt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI0473:PI0474|PI0473:PI0474:30S ribosomal protein S14:30S ribosomal protein S8:->->:439074..439182 109 taaaaccaaagtttatgttatgagcatataagattgctcataacatagaattatttaaggatttttaatattgtcggggaagtcccgattaattaaacatttataattt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 taaaaccaaagtttatgttatgagcatataagattgctcataacatagaattatttaaggatttttaatattgtcggggaagtcccgattaattaaacatttataattt Predict ORF larger than 30AA ================================================ taaaaccaaagtttatgttatgagcatataagattgctcataacatagaattatttaaggatttttaatattgtcggggaagtcccgattaattaaacatttataattt 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================================================ taaaaccaaagtttatgttatgagcatataagattgctcataacatagaattatttaaggatttttaatattgtcggggaagtcccgattaattaaacatttataattt Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 70 HP_score: -7.8 Tail_Score: -3.36581 Start: 74 End: 88 Full_Region: GGATTTTTAATATTG TCGGGG AAG TCCCGA TTAATTAAACATTTA .........................................................................TCGGGGAAGTCCCGA..................... Find igs database================================================ Query_seq: PI0473:PI0474|PI0473:PI0474:30S ribosomal protein S14:30S ribosomal protein S8:->->:439074..439182 109 taaaaccaaagtttatgttatgagcatataagattgctcataacatagaattatttaaggatttttaatattgtcggggaagtcccgattaattaaacatttataattt Intra-Species Hit: Count: 1 Min: 1 Max: 109 Len: 109 Subject: pint_PI0473_PI0474|30S ribosomal protein S14:30S ribosomal protein S8|POSITIVE:POSITIVE|[439074,439182]|109 HSP 1 e-value: 1.0E-55 bit: 216.0 Len: 109 Query Start:1 Query End:109 Subject Strand: POSITIVE Subject Start: 1 Subject End: 109 taaaaccaaagtttatgttatgagcatataagattgctcataacatagaattatttaaggatttttaatattgtcggggaagtcccgattaattaaacatttataattt taaaaccaaagtttatgttatgagcatataagattgctcataacatagaattatttaaggatttttaatattgtcggggaagtcccgattaattaaacatttataattt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAAACCAAAGUUUAUGUUAUGAGCAUAUAAGAUUGCUCAUAACAUAGAAUUAUUUAAGGAUUUUUAAUAUUGUCGGGGAAGUCCCGAUUAAUUAAACAUUUAUAAUUU ...........(((((((((((((((........))))))))))))))).....(((..(((.((((((...((((((.....))))))..)))))).)))..)))... (-32.70) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAUUAUAAAUGUUUAAUUAAUCGGGACUUCCCCGACAAUAUUAAAAAUCCUUAAAUAAUUCUAUGUUAUGAGCAAUCUUAUAUGCUCAUAACAUAAACUUUGGUUUUA ............((((((...(((((.....)))))....))))))................(((((((((((((........)))))))))))))............. (-26.70) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 274 88 73 75 60 pint:PI2074|5end_conserved_hypothetical_protein_2033660..2033890_POSITIVE 267 86 51 132 94 pint:PI0442|5end_50S_ribosomal_protein_L1_411644..411874_POSITIVE 206 90 53 172 130 pint:PI1238|5end_single-strand_DNA-specific_exonuclease_1161637..1161867_POSITIVE 202 80 34 87 44 pint:PI0030|5end_transcriptional_regulator,_AsnC_family_34509..34739_POSITIVE 200 89 73 74 50 pint:PI1468|5end_conserved_hypothetical_protein;_probable_TPR_domain_protein_1393900..1394130_POSITIVE 198 49 5 99 54 pint:PI0796|5end_competence_protein_733324..733554_POSITIVE 196 80 33 85 33 pint:PI0395|5end_Na+-driven_multidrug_efflux_pump_360388..360618_POSITIVE 190 58 14 188 136 pint:PI1696|5end_conserved_hypothetical_protein_1610544..1610774_POSITIVE 188 100 68 66 27 pint:PI1453|5end_probable_thiamine_pyrophosphokinase_1375982..1376212_POSITIVE 186 47 15 69 31 pint:PI1698|5end_subtilisin-like_serine_protease_1613830..1614060_POSITIVE 185 80 31 54 9 pint:PI1664|5end_conserved_hypothetical_protein_1577285..1577515_POSITIVE 185 80 31 54 9 pint:PI0370|5end_conserved_hypothetical_protein_340453..340683_POSITIVE 184 88 74 57 39 pint:PI1767|5end_fructokinase,_pfkB_family_1694285..1694515_POSITIVE 183 80 35 48 10 pint:PI0345|5end_conserved_hypothetical_protein_319485..319715_POSITIVE 182 87 47 122 81 pint:PI1511|5end_hypothetical_protein_1429580..1429810_POSITIVE 182 87 47 71 30 pint:PI1512|5end_hypothetical_protein_1429529..1429759_POSITIVE 182 83 41 211 169 pint:PI0438|5end_elongation_factor_Tu_409037..409267_POSITIVE 180 59 15 108 57 pint:PI1958|5end_hypothetical_protein_1916582..1916812_POSITIVE 180 60 16 77 31 pint:PI1775|5end_hypothetical_protein_1707255..1707485_POSITIVE 180 87 69 29 13 pint:PI0367|5end_hypothetical_protein_337884..338114_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 339 49 12 79 42 pint:PI0473|3end_30S_ribosomal_protein_S14_439013..439163_POSITIVE 267 86 51 107 69 pint:PI0441|3end_50S_ribosomal_protein_L11_411699..411849_POSITIVE 210 91 73 151 132 pint:PI1560|3end_integrase_1478265..1478415_POSITIVE 207 50 1 119 74 pint:PI1938|3end_hypothetical_protein_1895638..1895788_POSITIVE 194 79 35 59 17 pint:PI0948|3end_hypothetical_protein_881978..882128_POSITIVE 188 100 68 66 27 pint:PI1452|3end_possible_nicotinamide_mononucleotide_transporter_1376062..1376212_POSITIVE 188 82 51 111 72 pint:PI0970|3end_hypothetical_protein_897654..897804_POSITIVE 186 47 15 48 10 pint:PI1697|3end_conserved_hypothetical_protein_1613889..1614039_POSITIVE 184 88 74 42 24 pint:PI1766|3end_sugar_transporter,_possible_glucose/galactose_transporter_1694350..1694500_POSITIVE 183 88 74 72 53 pint:PI2107|3end_hypothetical_protein_2060023..2060173_POSITIVE 178 89 45 135 81 pint:PI1908|3end_transcriptional_regulator,_AraC_family_1853204..1853354_POSITIVE 176 87 64 127 102 pint:PI0630|3end_peptidyl-tRNA_hydrolase_(aminoacyl-tRNA_hydrolase)_577694..577844_POSITIVE 176 40 5 109 78 pint:PI0377|3end_DNA_primase/mobilizable_transposon,_excision_protein_347823..347973_POSITIVE 173 89 59 58 28 pint:PI0265|3end_conjugative_transposon_protein,_TraO_257957..258107_POSITIVE 172 43 16 38 13 pint:PI1411|3end_conserved_hypothetical_protein_1332254..1332404_POSITIVE 172 89 69 85 56 pint:PI0795|3end_hypothetical_protein_731253..731403_POSITIVE 171 48 12 48 10 pint:PI1010|3end_conserved_hypothetical_protein_932195..932345_POSITIVE 165 98 54 56 5 pint:PI1107|3end_conserved_hypothetical_protein_1031536..1031686_POSITIVE 163 29 8 116 94 pint:PI1305|3end_conserved_hypothetical_protein_1219732..1219882_POSITIVE 162 40 10 112 80 pint:PI1642|3end_conserved_hypothetical_protein_1560439..1560589_POSITIVE