Origin IGS: ttcgggcaatactgtaattatatctattctcatattgtaagtacaaagttaccaatatttccaataaaaggtacaagcattaagttttttttgtaactttgcaggcaaattctaatgcaaatttaaaatactt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aagtattttaaatttgcattagaatttgcctgcaaagttacaaaaaaaacttaatgcttgtaccttttattggaaatattggtaactttgtacttacaatatgagaatagatataattacagtattgcccgaa Mask Tandem Repeat Region ================================================ ttcgggcaatactgtaattatatctattctcatattgtaagtacaaagttaccaatatttccaataaaaggtacaagcattaagttttttttgtaactttgcaggcaaattctaatgcaaatttaaaatactt Find is-nt database================================================ Query_seq: PI1242:PI1243|PI1242:PI1243:tRNA (guanine-N1-)-methyltransferase:conserved hypothetical protein:->->:1167941..1168073 133 ttcgggcaatactgtaattatatctattctcatattgtaagtacaaagttaccaatatttccaataaaaggtacaagcattaagttttttttgtaactttgcaggcaaattctaatgcaaatttaaaatactt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI1242:PI1243|PI1242:PI1243:tRNA (guanine-N1-)-methyltransferase:conserved hypothetical protein:->->:1167941..1168073 133 ttcgggcaatactgtaattatatctattctcatattgtaagtacaaagttaccaatatttccaataaaaggtacaagcattaagttttttttgtaactttgcaggcaaattctaatgcaaatttaaaatactt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI1242:PI1243|PI1242:PI1243:tRNA (guanine-N1-)-methyltransferase:conserved hypothetical protein:->->:1167941..1168073 133 ttcgggcaatactgtaattatatctattctcatattgtaagtacaaagttaccaatatttccaataaaaggtacaagcattaagttttttttgtaactttgcaggcaaattctaatgcaaatttaaaatactt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ttcgggcaatactgtaattatatctattctcatattgtaagtacaaagttaccaatatttccaataaaaggtacaagcattaagttttttttgtaactttgcaggcaaattctaatgcaaatttaaaatactt Predict ORF larger than 30AA ================================================ Protein_Len: 30 Strand: - Start: 33 End: 122 ................................ I T L V F N G I N G I F P V L M L N K K Y S Q L C I R I C M ........... ttcgggcaatactgtaattatatctattctcatattgtaagtacaaagttaccaatatttccaataaaaggtacaagcattaagttttttttgtaactttgcaggcaaattctaatgcaaatttaaaatactt 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================================================ ttcgggcaatactgtaattatatctattctcatattgtaagtacaaagttaccaatatttccaataaaaggtacaagcattaagttttttttgtaactttgcaggcaaattctaatgcaaatttaaaatactt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PI1242:PI1243|PI1242:PI1243:tRNA (guanine-N1-)-methyltransferase:conserved hypothetical protein:->->:1167941..1168073 133 ttcgggcaatactgtaattatatctattctcatattgtaagtacaaagttaccaatatttccaataaaaggtacaagcattaagttttttttgtaactttgcaggcaaattctaatgcaaatttaaaatactt Intra-Species Hit: Count: 1 Min: 1 Max: 133 Len: 133 Subject: pint_PI1242_PI1243|tRNA (guanine-N1-)-methyltransferase:conserved hypothetical protein|POSITIVE:POSITIVE|[1167941,1168073]|133 HSP 1 e-value: 1.0E-55 bit: 216.0 Len: 133 Query Start:1 Query End:133 Subject Strand: POSITIVE Subject Start: 1 Subject End: 133 ttcgggcaatactgtaattatatctattctcatattgtaagtacaaagttaccaatatttccaataaaaggtacaagcattaagnnnnnnnngtaactttgcaggcaaattctaatgcaaatttaaaatactt ttcgggcaatactgtaattatatctattctcatattgtaagtacaaagttaccaatatttccaataaaaggtacaagcattaagttttttttgtaactttgcaggcaaattctaatgcaaatttaaaatactt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUCGGGCAAUACUGUAAUUAUAUCUAUUCUCAUAUUGUAAGUACAAAGUUACCAAUAUUUCCAAUAAAAGGUACAAGCAUUAAGUUUUUUUUGUAACUUUGCAGGCAAAUUCUAAUGCAAAUUUAAAAUACUU ....((.(((..((((.(((((.............))))).))))..))).)).......................((((((.(..(((((((((....)))))).)))..)))))))............... (-16.12) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAGUAUUUUAAAUUUGCAUUAGAAUUUGCCUGCAAAGUUACAAAAAAAACUUAAUGCUUGUACCUUUUAUUGGAAAUAUUGGUAACUUUGUACUUACAAUAUGAGAAUAGAUAUAAUUACAGUAUUGCCCGAA ...........((((.((.(((((..(((..((((((((........)))))..)))..)))..))))).)).))))...(((((..(((((.(((...(((....)))....))).)))))..))))).... (-21.90) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 259 109 75 187 146 pint:PI1742|5end_SpoOJ_regulator_protein_1664826..1665056_POSITIVE 251 102 69 159 123 pint:PI1051|5end_hypothetical_protein_970053..970283_POSITIVE 232 108 66 36 1 pint:PI1555|5end_conserved_hypothetical_protein_1470577..1470807_POSITIVE 227 109 85 193 168 pint:PI0396|5end_possible_tetracycline_resistance_element_mobilization_regulatory_protein,_C-terminal_fragment_361993..362223_POSITIVE 226 109 61 163 101 pint:PI0692|5end_iron_compound_ABC_transporter,_permease_protein_627350..627580_POSITIVE 214 70 21 212 161 pint:PI1638|5end_conserved_hypothetical_protein_1555337..1555567_POSITIVE 214 121 83 197 166 pint:PI1033|5end_ATP-dependent_RNA_helicase,_DEAD/DEAH_box_family_950297..950527_POSITIVE 212 106 67 154 103 pint:PI2146|5end_prolipoprotein_diacylglyceryl_transferase_2092402..2092632_POSITIVE 212 42 3 100 61 pint:PI2125|5end_D-tyrosyl-tRNA(Tyr)_deacylase_2074450..2074680_POSITIVE 209 107 70 101 47 pint:PI1472|5end_hypothetical_protein_1395671..1395901_POSITIVE 209 106 61 85 44 pint:PI0090|5end_amidophosphoribosyltransferase_88379..88609_POSITIVE 207 105 69 84 55 pint:PI1058|5end_possible_FHA_domain_protein_977577..977807_POSITIVE 198 47 3 184 134 pint:PI1451|5end_outer_membrane_receptor_proteins,_tonB_dependent_(possibly_iron_transport_related)_1372931..1373161_POSITIVE 198 118 73 190 148 pint:PI0832|5end_sigma-54-dependent_transcriptional_regulator_768834..769064_POSITIVE 196 88 43 167 108 pint:PI0148|5end_mannose-1-phosphate_guanylyltransferase_141423..141653_POSITIVE 196 105 67 43 1 pint:PI0056|5end_conserved_hypothetical_protein;_possible_DNA_uptake_protein_54967..55197_POSITIVE 194 104 61 89 41 pint:PI0980|5end_conserved_hypothetical_protein_905703..905933_POSITIVE 193 106 61 72 27 pint:PI1551|5end_HesA/MoeB/ThiF_family_protein_1467787..1468017_POSITIVE 193 107 83 145 122 pint:PI0846|5end_transcription_regulator,_CRP_family_780435..780665_POSITIVE 192 106 70 80 38 pint:PI2078|5end_hypothetical_protein_2036053..2036283_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 226 109 61 49 2 pint:PI0690|3end_uracil_permease_627316..627466_POSITIVE 222 109 61 52 5 pint:PI1267|3end_probable_integrase_1186475..1186625_POSITIVE 218 111 74 137 97 pint:PI1575|3end_LemA_protein_1501852..1502002_POSITIVE 214 70 21 79 28 pint:PI1637|3end_hypothetical_protein_1555284..1555434_POSITIVE 212 42 3 66 27 pint:PI2124|3end_excinuclease_ABC,_subunit_C_2074496..2074646_POSITIVE 203 118 76 144 103 pint:PI0642|3end_thioredoxin_family_protein_585582..585732_POSITIVE 199 108 61 62 11 pint:PI0809|3end_hypothetical_protein_747108..747258_POSITIVE 198 47 3 64 14 pint:PI1450|3end_hypothetical_protein_1372891..1373041_POSITIVE 196 105 67 120 78 pint:PI0053|3end_hypothetical_protein_55124..55274_POSITIVE 193 107 83 69 46 pint:PI0845|3end_peptidyl-dipeptidase_780439..780589_POSITIVE 191 90 41 99 46 pint:PI1873|3end_hypothetical_protein_1818419..1818569_POSITIVE 191 119 92 58 27 pint:PI0561|3end_hypothetical_protein_509136..509286_POSITIVE 190 105 68 41 5 pint:PI2030|3end_hypothetical_protein_1986127..1986277_POSITIVE 190 106 75 81 49 pint:PI0296|3end_hypothetical_protein_277824..277974_POSITIVE 189 120 71 130 73 pint:PI1247|3end_conserved_hypothetical_protein_1173182..1173332_POSITIVE 183 109 82 135 110 pint:PI1384|3end_conserved_hypothetical_protein_1306174..1306324_POSITIVE 183 119 97 127 106 pint:PI0434|3end_possible_beta-lactamase_406890..407040_POSITIVE 182 107 72 72 45 pint:PI1238|3end_single-strand_DNA-specific_exonuclease_1163438..1163588_POSITIVE 182 121 93 46 16 pint:PI0660|3end_conserved_hypothetical_protein_603997..604147_POSITIVE 182 119 89 143 113 pint:PI0110|3end_ABC_transport_system,_ATP-binding_protein_107920..108070_POSITIVE