Origin IGS: taaaagcaatgaagcacagataatagaaggtgaaaaaagaagtcgaaaactatcgtggttttcgactttttttgtatgtttgcataataatttaagaattt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aaattcttaaattattatgcaaacatacaaaaaaagtcgaaaaccacgatagttttcgacttcttttttcaccttctattatctgtgcttcattgctttta Mask Tandem Repeat Region ================================================ taaaagcaatgaagcacagataatagaaggtgaaaaaagaagtcgaaaactatcgtggttttcgactttttttgtatgtttgcataataatttaagaattt Find is-nt database================================================ Query_seq: PI0873:PI0874|PI0873:PI0874:conserved hypothetical protein; possible permease:conserved hypothetical protein:->->:809017..809117 101 taaaagcaatgaagcacagataatagaaggtgaaaaaagaagtcgaaaactatcgtggttttcgactttttttgtatgtttgcataataatttaagaattt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI0873:PI0874|PI0873:PI0874:conserved hypothetical protein; possible permease:conserved hypothetical protein:->->:809017..809117 101 taaaagcaatgaagcacagataatagaaggtgaaaaaagaagtcgaaaactatcgtggttttcgactttttttgtatgtttgcataataatttaagaattt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI0873:PI0874|PI0873:PI0874:conserved hypothetical protein; possible permease:conserved hypothetical protein:->->:809017..809117 101 taaaagcaatgaagcacagataatagaaggtgaaaaaagaagtcgaaaactatcgtggttttcgactttttttgtatgtttgcataataatttaagaattt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 taaaagcaatgaagcacagataatagaaggtgaaaaaagaagtcgaaaactatcgtggttttcgactttttttgtatgtttgcataataatttaagaattt Predict ORF larger than 30AA ================================================ Protein_Len: 33 Strand: - Start: 1 End: 99 L L L S A C I I S P S F L L R F S D H N E V K K T H K C L L K L M .. taaaagcaatgaagcacagataatagaaggtgaaaaaagaagtcgaaaactatcgtggttttcgactttttttgtatgtttgcataataatttaagaattt 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================================================ taaaagcaatgaagcacagataatagaaggtgaaaaaagaagtcgaaaactatcgtggttttcgactttttttgtatgtttgcataataatttaagaattt Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 100 HP_score: -12.3 Tail_Score: -5.82281 Start: 42 End: 66 Full_Region: AAGGTGAAAAAAGAA GTCGAAAACTA TCG TGGTTTTCGAC TTTTTTTGTATGTTT .........................................GTCGAAAACTATCGTGGTTTTCGAC................................... Find igs database================================================ Query_seq: PI0873:PI0874|PI0873:PI0874:conserved hypothetical protein; possible permease:conserved hypothetical protein:->->:809017..809117 101 taaaagcaatgaagcacagataatagaaggtgaaaaaagaagtcgaaaactatcgtggttttcgactttttttgtatgtttgcataataatttaagaattt Intra-Species Hit: Count: 1 Min: 1 Max: 101 Len: 101 Subject: pint_PI0873_PI0874|conserved hypothetical protein; possible permease:conserved hypothetical protein|POSITIVE:POSITIVE|[809017,809117]|101 HSP 1 e-value: 2.0E-38 bit: 159.0 Len: 101 Query Start:1 Query End:101 Subject Strand: POSITIVE Subject Start: 1 Subject End: 101 taaaagcaatgaagcacagataatagaaggtgaaaaaagaagtcgaaaactatcgtggttttcgacnnnnnnngtatgtttgcataataatttaagaattt taaaagcaatgaagcacagataatagaaggtgaaaaaagaagtcgaaaactatcgtggttttcgactttttttgtatgtttgcataataatttaagaattt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAAAGCAAUGAAGCACAGAUAAUAGAAGGUGAAAAAAGAAGUCGAAAACUAUCGUGGUUUUCGACUUUUUUUGUAUGUUUGCAUAAUAAUUUAAGAAUUU .....((((.....(((............)))..(((((((((((((((((.....)))))))))))))))))......)))).................. (-23.70) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAUUCUUAAAUUAUUAUGCAAACAUACAAAAAAAGUCGAAAACCACGAUAGUUUUCGACUUCUUUUUUCACCUUCUAUUAUCUGUGCUUCAUUGCUUUUA ..................((((......((((.(((((((((((.......))))))))))).))))..(((............))).....))))..... (-15.80) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 296 55 11 70 23 pint:PI0608|5end_isochorismate_synthase_555487..555717_POSITIVE 263 57 11 156 116 pint:PI2171|5end_conserved_hypothetical_protein_2112735..2112965_POSITIVE 262 47 6 118 72 pint:PI1607|5end_ABC-related_lipoprotein_releasing_system,_ATP-binding_protein_1535125..1535355_POSITIVE 262 47 6 92 46 pint:PI1606|5end_conserved_hypothetical_protein_1535099..1535329_POSITIVE 259 80 34 159 115 pint:PI1672|5end_conserved_hypothetical_protein;_possible_DNA-binding_protein,_histone-like_family_1587027..1587257_POSITIVE 248 49 1 119 72 pint:PI1951|5end_ABC_transporter,_ATP-binding_protein_1905823..1906053_POSITIVE 242 69 38 153 121 pint:PI0607|5end_2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxy_lic_acid_synthase/2-oxoglutarate_decarboxylase_553801..554031_POSITIVE 234 84 42 173 129 pint:PI0002|5end_conserved_hypothetical_protein_2972..3202_POSITIVE 232 58 11 60 26 pint:PI1384|5end_conserved_hypothetical_protein_1305171..1305401_POSITIVE 227 60 11 133 80 pint:PI0859|5end_carbamoyl-phosphate_synthase,_small_subunit_793317..793547_POSITIVE 225 64 22 117 79 pint:PI1198|5end_acetyltransferase_1114582..1114812_POSITIVE 223 59 13 127 80 pint:PI1992|5end_hypothetical_protein_1946427..1946657_POSITIVE 223 80 37 176 122 pint:PI1495|5end_conserved_hypothetical_protein_1414432..1414662_POSITIVE 223 56 14 195 146 pint:PI0937|5end_hypothetical_protein_869235..869465_POSITIVE 222 70 26 161 114 pint:PI1923|5end_conserved_hypothetical_protein_1865560..1865790_POSITIVE 221 55 12 131 93 pint:PI0282|5end_hypothetical_protein_266540..266770_POSITIVE 218 60 14 106 48 pint:PI1481|5end_hypothetical_protein_1404036..1404266_POSITIVE 217 96 55 180 128 pint:PI0444|5end_50S_ribosomal_protein_L7/L12_412933..413163_POSITIVE 217 96 55 173 121 pint:PI0445|5end_conserved_hypothetical_protein_412926..413156_POSITIVE 216 55 13 138 93 pint:PI1884|5end_conserved_hypothetical_protein_1826883..1827113_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 406 73 35 56 18 pint:PI0873|3end_conserved_hypothetical_protein;_possible_permease_808956..809106_POSITIVE 296 55 11 51 4 pint:PI0607|3end_2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxy_lic_acid_synthase/2-oxoglutarate_decarboxylase_555548..555698_POSITIVE 263 57 11 129 89 pint:PI2170|3end_RNA_polymerase_sigma-70_factor,_ECF_subfamily_2112788..2112938_POSITIVE 262 47 6 91 45 pint:PI1605|3end_conserved_hypothetical_protein_1535178..1535328_POSITIVE 259 80 34 78 34 pint:PI1670|3end_hypothetical_protein_1587026..1587176_POSITIVE 257 46 6 128 77 pint:PI1736|3end_topoisomerase_IV,_subunit_A_1657090..1657240_POSITIVE 248 49 1 104 57 pint:PI1950|3end_iron-regulated_membrane_permease_1905888..1906038_POSITIVE 227 60 11 130 77 pint:PI0858|3end_carbamyl_phosphate_synthase,_large_subunit_793394..793544_POSITIVE 221 55 12 115 77 pint:PI0281|3end_conserved_hypothetical_protein_266604..266754_POSITIVE 219 50 5 132 87 pint:PI0557|3end_conserved_hypothetical_protein_506884..507034_POSITIVE 218 60 14 85 27 pint:PI1480|3end_xanthine/uracil_permease_family_protein_1404095..1404245_POSITIVE 218 97 53 113 57 pint:PI0544|3end_hypoxanthine-guanine_phosphoribosyltransferase_(hypoxanthine_phosphoribosyltransferase)_496261..496411_POSITIVE 217 84 41 65 14 pint:PI0685|3end_elongation_factor_G_623048..623198_POSITIVE 217 96 55 117 65 pint:PI0443|3end_50S_ribosomal_protein_L10_412950..413100_POSITIVE 216 62 35 147 113 pint:PI1271|3end_transcriptional_regulator,__AraC/XylS_family_1191284..1191434_POSITIVE 214 83 41 61 19 pint:PI0147|3end_HIT_family_protein_141308..141458_POSITIVE 211 32 3 99 69 pint:PI1560|3end_integrase_1478265..1478415_POSITIVE 209 46 5 67 32 pint:PI1492|3end_triosephosphate_isomerase_1412310..1412460_POSITIVE 208 57 14 146 100 pint:PI1046|3end_hypothetical_protein_966081..966231_POSITIVE 205 68 36 140 109 pint:PI0359|3end_hypothetical_protein_328835..328985_POSITIVE