Origin IGS: caatgtagagcaggcgatgcctttccgcaagtctttcgctcctttttcggtgagggcgaaccgttgttgaagatattttatcataatcttgtgtcctttctgtttaggttta .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 taaacctaaacagaaaggacacaagattatgataaaatatcttcaacaacggttcgccctcaccgaaaaaggagcgaaagacttgcggaaaggcatcgcctgctctacattg Mask Tandem Repeat Region ================================================ caatgtagagcaggcgatgcctttccgcaagtctttcgctcctttttcggtgagggcgaaccgttgttgaagatattttatcataatcttgtgtcctttctgtttaggttta Find is-nt database================================================ Query_seq: PI0734:PI0735|PI0734:PI0735:ABC transporter, ATP-binding / permease:ABC transporter, ATP-binding / permease:->->:668821..668932 112 caatgtagagcaggcgatgcctttccgcaagtctttcgctcctttttcggtgagggcgaaccgttgttgaagatattttatcataatcttgtgtcctttctgtttaggttta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI0734:PI0735|PI0734:PI0735:ABC transporter, ATP-binding / permease:ABC transporter, ATP-binding / permease:->->:668821..668932 112 caatgtagagcaggcgatgcctttccgcaagtctttcgctcctttttcggtgagggcgaaccgttgttgaagatattttatcataatcttgtgtcctttctgtttaggttta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI0734:PI0735|PI0734:PI0735:ABC transporter, ATP-binding / permease:ABC transporter, ATP-binding / permease:->->:668821..668932 112 caatgtagagcaggcgatgcctttccgcaagtctttcgctcctttttcggtgagggcgaaccgttgttgaagatattttatcataatcttgtgtcctttctgtttaggttta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 caatgtagagcaggcgatgcctttccgcaagtctttcgctcctttttcggtgagggcgaaccgttgttgaagatattttatcataatcttgtgtcctttctgtttaggttta Predict ORF larger than 30AA ================================================ caatgtagagcaggcgatgcctttccgcaagtctttcgctcctttttcggtgagggcgaaccgttgttgaagatattttatcataatcttgtgtcctttctgtttaggttta 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================================================ caatgtagagcaggcgatgcctttccgcaagtctttcgctcctttttcggtgagggcgaaccgttgttgaagatattttatcataatcttgtgtcctttctgtttaggttta Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PI0734:PI0735|PI0734:PI0735:ABC transporter, ATP-binding / permease:ABC transporter, ATP-binding / permease:->->:668821..668932 112 caatgtagagcaggcgatgcctttccgcaagtctttcgctcctttttcggtgagggcgaaccgttgttgaagatattttatcataatcttgtgtcctttctgtttaggttta Intra-Species Hit: Count: 1 Min: 1 Max: 112 Len: 112 Subject: pint_PI0734_PI0735|ABC transporter, ATP-binding / permease:ABC transporter, ATP-binding / permease|POSITIVE:POSITIVE|[668821,668932]|112 HSP 1 e-value: 2.0E-57 bit: 222.0 Len: 112 Query Start:1 Query End:112 Subject Strand: POSITIVE Subject Start: 1 Subject End: 112 caatgtagagcaggcgatgcctttccgcaagtctttcgctcctttttcggtgagggcgaaccgttgttgaagatattttatcataatcttgtgtcctttctgtttaggttta caatgtagagcaggcgatgcctttccgcaagtctttcgctcctttttcggtgagggcgaaccgttgttgaagatattttatcataatcttgtgtcctttctgtttaggttta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CAAUGUAGAGCAGGCGAUGCCUUUCCGCAAGUCUUUCGCUCCUUUUUCGGUGAGGGCGAACCGUUGUUGAAGAUAUUUUAUCAUAAUCUUGUGUCCUUUCUGUUUAGGUUUA ...((..(((.((((...)))))))..))...........(((....(((.(((((((....(((((.((.((....)).)))))))....))))))).)))...))).... (-24.70) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAACCUAAACAGAAAGGACACAAGAUUAUGAUAAAAUAUCUUCAACAACGGUUCGCCCUCACCGAAAAAGGAGCGAAAGACUUGCGGAAAGGCAUCGCCUGCUCUACAUUG ...........(((.(((.(..(((((.((......)))))))............(((....(((...(((...(....).))).)))...)))...))))..)))...... (-18.90) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 410 57 13 222 173 pint:PI1205|5end_hypothetical_protein_1127047..1127277_POSITIVE 410 57 13 152 103 pint:PI1207|5end_hypothtical_protein_1126977..1127207_POSITIVE 385 57 11 66 22 pint:PI0358|5end_hypothetical_protein_327561..327791_POSITIVE 370 50 4 65 13 pint:PI1653|5end_hypothetical_protein_1565158..1565388_POSITIVE 368 60 13 231 169 pint:PI1157|5end_hypothetical_protein_1081704..1081934_POSITIVE 356 60 13 175 125 pint:PI1784|5end_possible_dTDP-glucose_4,6-dehydratase,_NAD-dependent_epimerase/dehydratase_family_1716201..1716431_POSITIVE 349 58 11 171 98 pint:PI0248|5end_protein_associated_with_conjugate_transformation/chromosome_partioning_246139..246369_POSITIVE 348 58 11 103 58 pint:PI0744|5end_DNA_primase/mobilizable_transposon,_excision_protein_674171..674401_POSITIVE 345 60 11 128 70 pint:PI2100|5end_conserved_hypothetical_protein_2053351..2053581_POSITIVE 340 57 14 188 144 pint:PI0285|5end_succinyltransferase_protein_270097..270327_POSITIVE 339 59 12 145 94 pint:PI1543|5end_hypothetical_protein_1462773..1463003_POSITIVE 337 69 21 189 139 pint:PI0626|5end_penicillin-binding_protein,_D-alanyl-D-alanine_carboxypeptidase_574305..574535_POSITIVE 337 69 21 87 37 pint:PI0624|5end_hypothetical_protein_574203..574433_POSITIVE 337 67 31 203 165 pint:PI0431|5end_Xaa-Pro_aminopeptidase_403064..403294_POSITIVE 335 58 13 129 81 pint:PI0645|5end_hypothetical_protein_586419..586649_POSITIVE 335 58 13 108 60 pint:PI0643|5end_hypothetical_protein_586398..586628_POSITIVE 334 60 11 209 163 pint:PI0632|5end_NusB_family_protein_(N_utilization_substance_protein_B)_578476..578706_POSITIVE 332 69 26 56 8 pint:PI1389|5end_transcriptional_regulator,_LuxR_family_1310039..1310269_POSITIVE 327 66 25 44 2 pint:PI1640|5end_hypothetical_protein_1558062..1558292_POSITIVE 326 76 34 226 186 pint:PI1494|5end_conserved_hypothetical_protein_1413046..1413276_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 370 50 4 62 10 pint:PI1652|3end_hypothetical_protein_1565235..1565385_POSITIVE 356 60 13 52 2 pint:PI1783|3end_possible_4-diphosphocytidyl-2c-methyl-D-erythritol_synthase_1716158..1716308_POSITIVE 356 58 15 133 89 pint:PI0513|3end_ion_transporter_472371..472521_POSITIVE 341 58 13 57 14 pint:PI1649|3end_hypothetical_protein_1563441..1563591_POSITIVE 334 60 11 53 7 pint:PI0631|3end_50S_ribosomal_protein_L25/general_stress_protein_578400..578550_POSITIVE 312 40 4 67 30 pint:PI1738|3end_FKBP-type_peptidyl-prolyl_cis-trans_isomerase_1660112..1660262_POSITIVE 312 47 8 60 10 pint:PI0261|3end_conjugative_transposon_protein,_TraK_254765..254915_POSITIVE 310 60 16 128 70 pint:PI0817|3end_glycosyl_transferase,_group_1_family_protein_758209..758359_POSITIVE 310 66 21 144 102 pint:PI0420|3end_hypothetical_protein_386828..386978_POSITIVE 310 66 21 46 4 pint:PI0417|3end_hypothetical_protein_386730..386880_POSITIVE 307 83 46 109 72 pint:PI1448|3end_hypothetical_protein_1371832..1371982_POSITIVE 306 59 13 62 14 pint:PI0091|3end_hypothetical_protein_89774..89924_POSITIVE 305 58 11 76 15 pint:PI0951|3end_hypothetical_protein_885448..885598_POSITIVE 304 67 26 69 37 pint:PI1001|3end_hypothetical_protein_923922..924072_POSITIVE 302 59 13 86 52 pint:PI1741|3end_lipid-A-disaccharide_synthase_1663856..1664006_POSITIVE 298 64 21 53 6 pint:PI2039|3end_hypothetical_protein_1992991..1993141_POSITIVE 298 57 11 78 16 pint:PI0849|3end_hypothetical_protein_783542..783692_POSITIVE 298 55 18 127 93 pint:PI0220|3end_conserved_hypothetical_protein_212341..212491_POSITIVE 297 52 11 124 69 pint:PI1651|3end_hypothetical_protein_1564512..1564662_POSITIVE 294 47 1 141 89 pint:PI1855|3end_lipopolysaccharide_biosynthesis_protein_1803168..1803318_POSITIVE