Origin IGS: taagtttcgttttcgctgaaacaatatatacgcatacgatttctacaaagttcgtatcgtaataaacaataaaaacggagaagttcaagtttaaacttctccgttttttatttatacttgtttgtcaatctgctta .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 taagcagattgacaaacaagtataaataaaaaacggagaagtttaaacttgaacttctccgtttttattgtttattacgatacgaactttgtagaaatcgtatgcgtatatattgtttcagcgaaaacgaaactta Mask Tandem Repeat Region ================================================ taagtttcgttttcgctgaaacaatatatacgcatacgatttctacaaagttcgtatcgtaataaacaataaaaacggagaagttcaagtttaaacttctccgttttttatttatacttgtttgtcaatctgctta Find is-nt database================================================ Query_seq: PI1234:PI1235|PI1234:PI1235:valyl-tRNA synthetase (valine--tRNA ligase):60 kDa chaperonin, groEL, cpn60:->->:1157190..1157325 136 taagtttcgttttcgctgaaacaatatatacgcatacgatttctacaaagttcgtatcgtaataaacaataaaaacggagaagttcaagtttaaacttctccgttttttatttatacttgtttgtcaatctgctta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI1234:PI1235|PI1234:PI1235:valyl-tRNA synthetase (valine--tRNA ligase):60 kDa chaperonin, groEL, cpn60:->->:1157190..1157325 136 taagtttcgttttcgctgaaacaatatatacgcatacgatttctacaaagttcgtatcgtaataaacaataaaaacggagaagttcaagtttaaacttctccgttttttatttatacttgtttgtcaatctgctta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI1234:PI1235|PI1234:PI1235:valyl-tRNA synthetase (valine--tRNA ligase):60 kDa chaperonin, groEL, cpn60:->->:1157190..1157325 136 taagtttcgttttcgctgaaacaatatatacgcatacgatttctacaaagttcgtatcgtaataaacaataaaaacggagaagttcaagtttaaacttctccgttttttatttatacttgtttgtcaatctgctta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 taagtttcgttttcgctgaaacaatatatacgcatacgatttctacaaagttcgtatcgtaataaacaataaaaacggagaagttcaagtttaaacttctccgttttttatttatacttgtttgtcaatctgctta Predict ORF larger than 30AA ================================================ Protein_Len: 38 Strand: - Start: 2 End: 115 . L K T K A S V I Y V C V I E V F N T D Y Y V I F V S F N L N L S R R K K N M ..................... taagtttcgttttcgctgaaacaatatatacgcatacgatttctacaaagttcgtatcgtaataaacaataaaaacggagaagttcaagtttaaacttctccgttttttatttatacttgtttgtcaatctgctta 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: 83 Start: 89 End: 118 ........................................................................................GTTTAAACTTCTCCGTTTTTTATTTATACT.................. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ taagtttcgttttcgctgaaacaatatatacgcatacgatttctacaaagttcgtatcgtaataaacaataaaaacggagaagttcaagtttaaacttctccgttttttatttatacttgtttgtcaatctgctta Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 100 HP_score: -11.4 Tail_Score: -5.73978 Start: 76 End: 103 Full_Region: AATAAACAATAAAAA CGGAGAAGTTCA AGTT TAAACTTCTCCG TTTTTTATTTATACT ...........................................................................CGGAGAAGTTCAAGTTTAAACTTCTCCG................................. TransTerm Strand: - Conf: 100 HP_score: -13.6 Tail_Score: -5.44198 Start: 76 End: 103 Full_Region: agtataaataaaaaa cggagaagttta aact tgaacttctccg tttttattgtttatt ...........................................................................cggagaagtttaaacttgaacttctccg................................. Find igs database================================================ Query_seq: PI1234:PI1235|PI1234:PI1235:valyl-tRNA synthetase (valine--tRNA ligase):60 kDa chaperonin, groEL, cpn60:->->:1157190..1157325 136 taagtttcgttttcgctgaaacaatatatacgcatacgatttctacaaagttcgtatcgtaataaacaataaaaacggagaagttcaagtttaaacttctccgttttttatttatacttgtttgtcaatctgctta Intra-Species Hit: Count: 1 Min: 1 Max: 136 Len: 136 Subject: pint_PI1234_PI1235|valyl-tRNA synthetase (valine--tRNA ligase):60 kDa chaperonin, groEL, cpn60|POSITIVE:POSITIVE|[1157190,1157325]|136 HSP 1 e-value: 1.0E-71 bit: 270.0 Len: 136 Query Start:1 Query End:136 Subject Strand: POSITIVE Subject Start: 1 Subject End: 136 taagtttcgttttcgctgaaacaatatatacgcatacgatttctacaaagttcgtatcgtaataaacaataaaaacggagaagttcaagtttaaacttctccgttttttatttatacttgtttgtcaatctgctta taagtttcgttttcgctgaaacaatatatacgcatacgatttctacaaagttcgtatcgtaataaacaataaaaacggagaagttcaagtttaaacttctccgttttttatttatacttgtttgtcaatctgctta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAGUUUCGUUUUCGCUGAAACAAUAUAUACGCAUACGAUUUCUACAAAGUUCGUAUCGUAAUAAACAAUAAAAACGGAGAAGUUCAAGUUUAAACUUCUCCGUUUUUUAUUUAUACUUGUUUGUCAAUCUGCUUA ...((((((.......))))))......((((.((((((...((....)).))))))))))((((((((.(((((((((((((((........))))))))))))))).........))))))))........... (-34.70) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAGCAGAUUGACAAACAAGUAUAAAUAAAAAACGGAGAAGUUUAAACUUGAACUUCUCCGUUUUUAUUGUUUAUUACGAUACGAACUUUGUAGAAAUCGUAUGCGUAUAUAUUGUUUCAGCGAAAACGAAACUUA ...((.((..(((((......((((((((((((((((((((((((....))))))))))))))))..))))))))((((((((((.((....))...)))))).))))....))))))).)).............. (-37.20) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 284 34 2 61 31 pint:PI0630|5end_peptidyl-tRNA_hydrolase_(aminoacyl-tRNA_hydrolase)_577045..577275_POSITIVE 254 103 75 62 30 pint:PI0223|5end_topoisomerase_IA_218377..218607_POSITIVE 239 126 95 125 93 pint:PI0943|5end_conserved_hypothetical_protein_875153..875383_POSITIVE 239 126 95 40 8 pint:PI0944|5end_hypothetical_protein_875068..875298_POSITIVE 227 58 14 178 133 pint:PI0350|5end_conserved_hypothetical_protein_323757..323987_POSITIVE 222 59 11 58 10 pint:PI1354|5end_UDP-N-acetylglucosamine_2-epimerase_1270900..1271130_POSITIVE 221 60 15 115 54 pint:PI0549|5end_hypothetical_protein_500504..500734_POSITIVE 216 58 12 64 22 pint:PI1201|5end_peptidyl-arginine_deiminase_1116598..1116828_POSITIVE 208 47 4 163 117 pint:PI2155|5end_hypothetical_protein_2100664..2100894_POSITIVE 206 106 74 180 149 pint:PI1917|5end_uracil-DNA_glycosylase_1860797..1861027_POSITIVE 205 119 72 178 123 pint:PI2018|5end_50S_ribosomal_protein_L34_1975757..1975987_POSITIVE 203 122 101 155 134 pint:PI0984|5end_hypothetical_protein_909936..910166_POSITIVE 202 105 61 150 101 pint:PI0981|5end_outer_membrane_protein,_TonB_dependent_receptor_906968..907198_POSITIVE 201 127 81 156 118 pint:PI1482|5end_hypothetical_protein_1404179..1404409_POSITIVE 200 62 32 42 14 pint:PI1766|5end_sugar_transporter,_possible_glucose/galactose_transporter_1693119..1693349_POSITIVE 200 56 13 74 42 pint:PI0096|5end_glycerol-3-phosphate_cytidylyltransferase_91885..92115_POSITIVE 199 120 73 155 106 pint:PI1499|5end_hypothetical_protein_1419960..1420190_POSITIVE 199 60 17 137 104 pint:PI1068|5end_nucleolar_protein,_Sun_(Fmu)_family_protein;_tRNA/rRNA_cytosine-C5-methylase_984743..984973_POSITIVE 198 61 30 229 198 pint:PI1537|5end_predicted_TPR-repeat-containing_protein_1455764..1455994_POSITIVE 198 38 5 38 2 pint:PI0121|5end_outer_membrane_protein,_ompH_family_112625..112855_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 284 34 2 58 28 pint:PI0629|3end_heat_shock_protein_15_577122..577272_POSITIVE 254 103 75 47 15 pint:PI0222|3end_conserved_hypothetical_protein_218442..218592_POSITIVE 239 126 95 141 109 pint:PI0944|3end_hypothetical_protein_875249..875399_POSITIVE 227 58 14 143 98 pint:PI0349|3end_hypothetical_protein_323802..323952_POSITIVE 224 60 13 82 29 pint:PI0238|3end_two-component_system_response_regulator_237826..237976_POSITIVE 221 60 15 102 41 pint:PI0548|3end_possible_acetylxylan_esterase_500571..500721_POSITIVE 211 55 15 47 9 pint:PI0943|3end_conserved_hypothetical_protein_875991..876141_POSITIVE 210 69 29 128 80 pint:PI0023|3end_internalin-related_protein_28070..28220_POSITIVE 206 106 74 43 12 pint:PI1916|3end_conserved_hypothetical_protein_1860740..1860890_POSITIVE 205 119 72 59 4 pint:PI2017|3end_conserved_hypothetical_protein_1975718..1975868_POSITIVE 203 122 101 130 109 pint:PI0983|3end_hypothetical_protein_909991..910141_POSITIVE 203 90 44 67 19 pint:PI0494|3end_hypothetical_protein_455170..455320_POSITIVE 202 105 61 123 74 pint:PI0980|3end_conserved_hypothetical_protein_907021..907171_POSITIVE 201 127 81 129 91 pint:PI1481|3end_hypothetical_protein_1404232..1404382_POSITIVE 199 120 73 103 54 pint:PI1498|3end_probable_membrane_associated_lipoprotein_1419988..1420138_POSITIVE 199 60 17 125 92 pint:PI1067|3end_thymidylate_synthase_984811..984961_POSITIVE 198 89 53 102 68 pint:PI0101|3end_lauroyl/myristoyl_acyltransferase_97753..97903_POSITIVE 196 60 14 71 23 pint:PI2166|3end_hypothetical_protein_2112073..2112223_POSITIVE 196 122 83 77 34 pint:PI1549|3end_conserved_hypothetical_protein_1467382..1467532_POSITIVE 195 39 6 139 102 pint:PI0796|3end_competence_protein_734954..735104_POSITIVE