Origin IGS: cgctgcttgcaaggccttcagtttgccttcagcagggttttgtgcttcttctttagtcatatattaattaatctattttatcttgtaatttaaaccttttattagcaaacg .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 cgtttgctaataaaaggtttaaattacaagataaaatagattaattaatatatgactaaagaagaagcacaaaaccctgctgaaggcaaactgaaggccttgcaagcagcg Mask Tandem Repeat Region ================================================ cgctgcttgcaaggccttcagtttgccttcagcagggttttgtgcttcttctttagtcatatattaattaatctattttatcttgtaatttaaaccttttattagcaaacg Find is-nt database================================================ Query_seq: PI0553:PI0554|PI0553:PI0554:recombination protein:hypothetical protein:->->:504444..504554 111 cgctgcttgcaaggccttcagtttgccttcagcagggttttgtgcttcttctttagtcatatattaattaatctattttatcttgtaatttaaaccttttattagcaaacg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI0553:PI0554|PI0553:PI0554:recombination protein:hypothetical protein:->->:504444..504554 111 cgctgcttgcaaggccttcagtttgccttcagcagggttttgtgcttcttctttagtcatatattaattaatctattttatcttgtaatttaaaccttttattagcaaacg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI0553:PI0554|PI0553:PI0554:recombination protein:hypothetical protein:->->:504444..504554 111 cgctgcttgcaaggccttcagtttgccttcagcagggttttgtgcttcttctttagtcatatattaattaatctattttatcttgtaatttaaaccttttattagcaaacg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 cgctgcttgcaaggccttcagtttgccttcagcagggttttgtgcttcttctttagtcatatattaattaatctattttatcttgtaatttaaaccttttattagcaaacg Predict ORF larger than 30AA ================================================ cgctgcttgcaaggccttcagtttgccttcagcagggttttgtgcttcttctttagtcatatattaattaatctattttatcttgtaatttaaaccttttattagcaaacg 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================================================ cgctgcttgcaaggccttcagtttgccttcagcagggttttgtgcttcttctttagtcatatattaattaatctattttatcttgtaatttaaaccttttattagcaaacg Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PI0553:PI0554|PI0553:PI0554:recombination protein:hypothetical protein:->->:504444..504554 111 cgctgcttgcaaggccttcagtttgccttcagcagggttttgtgcttcttctttagtcatatattaattaatctattttatcttgtaatttaaaccttttattagcaaacg Intra-Species Hit: Count: 1 Min: 1 Max: 111 Len: 111 Subject: pint_PI0553_PI0554|recombination protein:hypothetical protein|POSITIVE:POSITIVE|[504444,504554]|111 HSP 1 e-value: 7.0E-57 bit: 220.0 Len: 111 Query Start:1 Query End:111 Subject Strand: POSITIVE Subject Start: 1 Subject End: 111 cgctgcttgcaaggccttcagtttgccttcagcagggttttgtgcttcttctttagtcatatattaattaatctattttatcttgtaatttaaaccttttattagcaaacg cgctgcttgcaaggccttcagtttgccttcagcagggttttgtgcttcttctttagtcatatattaattaatctattttatcttgtaatttaaaccttttattagcaaacg Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CGCUGCUUGCAAGGCCUUCAGUUUGCCUUCAGCAGGGUUUUGUGCUUCUUCUUUAGUCAUAUAUUAAUUAAUCUAUUUUAUCUUGUAAUUUAAACCUUUUAUUAGCAAACG .((((((.(.(((((.........))))))))).((((((..(((........(((................))).........)))....))))))......)))..... (-15.72) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CGUUUGCUAAUAAAAGGUUUAAAUUACAAGAUAAAAUAGAUUAAUUAAUAUAUGACUAAAGAAGAAGCACAAAACCCUGCUGAAGGCAAACUGAAGGCCUUGCAAGCAGCG .((((((..........................................................((((........)))).(((((.........))))))))))).... (-15.00) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 417 50 1 105 58 pint:PI0342|5end_hypothetical_protein_317556..317786_POSITIVE 417 50 1 54 7 pint:PI0343|5end_hypothetical_protein_317505..317735_POSITIVE 365 49 3 203 156 pint:PI0796|5end_competence_protein_733324..733554_POSITIVE 353 37 2 190 151 pint:PI1731|5end_formate--tetrahydrofolate_ligase_1650122..1650352_POSITIVE 353 37 2 182 143 pint:PI1730|5end_hypothetical_protein_1650114..1650344_POSITIVE 350 50 1 188 123 pint:PI1769|5end_hypothetical_protein_1696507..1696737_POSITIVE 347 64 22 192 134 pint:PI1777|5end_conserved_hypothetical_protein_1709402..1709632_POSITIVE 341 50 3 115 50 pint:PI1647|5end_hypothetical_protein_1561564..1561794_POSITIVE 341 58 15 209 152 pint:PI0117|5end_ribonuclease_HI_110731..110961_POSITIVE 337 48 5 202 165 pint:PI0970|5end_hypothetical_protein_897254..897484_POSITIVE 337 50 1 122 78 pint:PI0528|5end_hypothetical_protein_482791..483021_POSITIVE 334 49 2 160 104 pint:PI0819|5end_hypothetical_protein_759414..759644_POSITIVE 324 47 1 65 1 pint:PI0496|5end_heat_shock_protein_hsp70_(chaperone_protein_dnaK)_456632..456862_POSITIVE 323 49 3 221 166 pint:PI1310|5end_LysM_domain_protein_1227262..1227492_POSITIVE 322 48 2 171 110 pint:PI2045|5end_hypothetical_protein_1998494..1998724_POSITIVE 321 45 1 133 79 pint:PI0128|5end_dipeptidase,_pathogenicity_island-encoded_protein_D_120532..120762_POSITIVE 308 42 1 225 179 pint:PI2123|5end_adenine_phosphoribosyltransferase_2071711..2071941_POSITIVE 308 45 1 196 148 pint:PI0561|5end_hypothetical_protein_508952..509182_POSITIVE 306 45 1 81 24 pint:PI0867|5end_hypothetical_protein_803859..804089_POSITIVE 302 46 1 169 116 pint:PI0539|5end_hypothetical_protein_493406..493636_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 417 50 1 84 37 pint:PI0341|3end_conserved_hypothetical_protein_317615..317765_POSITIVE 379 50 1 84 37 pint:PI1636|3end_hypothetical_protein_1554823..1554973_POSITIVE 361 47 1 79 35 pint:PI1608|3end_possible_Na+/H+_anti-porter_1536300..1536450_POSITIVE 347 64 22 135 77 pint:PI1776|3end_probable_peptidase_of_the_M22_family_(inactive?_chaperone?))_1709425..1709575_POSITIVE 337 48 5 129 92 pint:PI0969|3end_30S_ribosomal_protein_S16_897261..897411_POSITIVE 336 45 1 151 111 pint:PI1227|3end_conserved_hypothetical_protein;_possible_DNA-binding_protein,_histone-like_family_1148974..1149124_POSITIVE 315 50 1 84 22 pint:PI1706|3end_GTP-binding_protein_1623668..1623818_POSITIVE 310 46 15 151 110 pint:PI0116|3end_conserved_hypothetical_protein_110769..110919_POSITIVE 308 45 1 74 26 pint:PI0560|3end_hypothetical_protein_508910..509060_POSITIVE 306 45 1 135 78 pint:PI0866|3end_hypothetical_protein_803993..804143_POSITIVE 306 47 1 119 66 pint:PI0343|3end_hypothetical_protein_317920..318070_POSITIVE 305 41 1 103 58 pint:PI2072|3end_possible_ISmav2-related_transposase_2031470..2031620_POSITIVE 304 50 2 113 72 pint:PI1651|3end_hypothetical_protein_1564512..1564662_POSITIVE 304 48 4 135 76 pint:PI0487|3end_50S_ribosomal_protein_L17_446703..446853_POSITIVE 301 50 6 99 51 pint:PI0331|3end_hypothetical_protein_312575..312725_POSITIVE 301 50 6 69 21 pint:PI0330|3end_hypothetical_protein_312545..312695_POSITIVE 297 48 2 145 81 pint:PI1623|3end_hypothetical_protein_1549261..1549411_POSITIVE 295 43 2 70 24 pint:PI1506|3end_S-adenosylmethionine:tRNA_ribosyltransferase-isomerase_(queuine_synthetase)_1426562..1426712_POSITIVE 294 54 12 58 18 pint:PI1652|3end_hypothetical_protein_1565235..1565385_POSITIVE 288 50 1 109 48 pint:PI0838|3end_DNA_replication_and_repair_protein_773927..774077_POSITIVE