Origin IGS: aatgtgaattttattaacattgatttcgcaaagtaatgtattttcctgcaaaaaagcaaaatcagcatatagacatcatatagacaatatatcaaataagtgttaaaagaaagggcataatctatgaaaatcattatctttgttgcaaaaacggcttacc .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 ggtaagccgtttttgcaacaaagataatgattttcatagattatgccctttcttttaacacttatttgatatattgtctatatgatgtctatatgctgattttgcttttttgcaggaaaatacattactttgcgaaatcaatgttaataaaattcacatt Mask Tandem Repeat Region ================================================ aatgtgaattttattaacattgatttcgcaaagtaatgtattttcctgcaaaaaagcaaaatcagcatatagacatcatatagacaatatatcaaataagtgttaaaagaaagggcataatctatgaaaatcattatctttgttgcaaaaacggcttacc Find is-nt database================================================ Query_seq: PI1344:PI1345|PI1344:PI1345:hypothetical protein:conserved hypothetical protein; possible TPR-repeat-containing protein:->->:1259165..1259324 160 aatgtgaattttattaacattgatttcgcaaagtaatgtattttcctgcaaaaaagcaaaatcagcatatagacatcatatagacaatatatcaaataagtgttaaaagaaagggcataatctatgaaaatcattatctttgttgcaaaaacggcttacc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI1344:PI1345|PI1344:PI1345:hypothetical protein:conserved hypothetical protein; possible TPR-repeat-containing protein:->->:1259165..1259324 160 aatgtgaattttattaacattgatttcgcaaagtaatgtattttcctgcaaaaaagcaaaatcagcatatagacatcatatagacaatatatcaaataagtgttaaaagaaagggcataatctatgaaaatcattatctttgttgcaaaaacggcttacc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI1344:PI1345|PI1344:PI1345:hypothetical protein:conserved hypothetical protein; possible TPR-repeat-containing protein:->->:1259165..1259324 160 aatgtgaattttattaacattgatttcgcaaagtaatgtattttcctgcaaaaaagcaaaatcagcatatagacatcatatagacaatatatcaaataagtgttaaaagaaagggcataatctatgaaaatcattatctttgttgcaaaaacggcttacc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aatgtgaattttattaacattgatttcgcaaagtaatgtattttcctgcaaaaaagcaaaatcagcatatagacatcatatagacaatatatcaaataagtgttaaaagaaagggcataatctatgaaaatcattatctttgttgcaaaaacggcttacc Predict ORF larger than 30AA ================================================ Protein_Len: 32 Strand: + Start: 8 End: 103 ....... M L L T L I S Q S N V F S C K K A K S A Y R H H I D N I S N K C ......................................................... Protein_Len: 45 Strand: - Start: 3 End: 137 .. T F K I L M S K A F Y H I K R C F L L I L M Y V D Y L C Y I L Y T N F S L A Y D I F I M M ....................... aatgtgaattttattaacattgatttcgcaaagtaatgtattttcctgcaaaaaagcaaaatcagcatatagacatcatatagacaatatatcaaataagtgttaaaagaaagggcataatctatgaaaatcattatctttgttgcaaaaacggcttacc 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: 81 Start: 80 End: 109 ...............................................................................ATAGACAATATATCAAATAAGTGTTAAAAG................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ aatgtgaattttattaacattgatttcgcaaagtaatgtattttcctgcaaaaaagcaaaatcagcatatagacatcatatagacaatatatcaaataagtgttaaaagaaagggcataatctatgaaaatcattatctttgttgcaaaaacggcttacc Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PI1344:PI1345|PI1344:PI1345:hypothetical protein:conserved hypothetical protein; possible TPR-repeat-containing protein:->->:1259165..1259324 160 aatgtgaattttattaacattgatttcgcaaagtaatgtattttcctgcaaaaaagcaaaatcagcatatagacatcatatagacaatatatcaaataagtgttaaaagaaagggcataatctatgaaaatcattatctttgttgcaaaaacggcttacc Intra-Species Hit: Count: 1 Min: 1 Max: 160 Len: 160 Subject: pint_PI1344_PI1345|hypothetical protein:conserved hypothetical protein; possible TPR-repeat-containing protein|POSITIVE:POSITIVE|[1259165,1259324]|160 HSP 1 e-value: 6.0E-86 bit: 317.0 Len: 160 Query Start:1 Query End:160 Subject Strand: POSITIVE Subject Start: 1 Subject End: 160 aatgtgaattttattaacattgatttcgcaaagtaatgtattttcctgcaaaaaagcaaaatcagcatatagacatcatatagacaatatatcaaataagtgttaaaagaaagggcataatctatgaaaatcattatctttgttgcaaaaacggcttacc aatgtgaattttattaacattgatttcgcaaagtaatgtattttcctgcaaaaaagcaaaatcagcatatagacatcatatagacaatatatcaaataagtgttaaaagaaagggcataatctatgaaaatcattatctttgttgcaaaaacggcttacc Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAUGUGAAUUUUAUUAACAUUGAUUUCGCAAAGUAAUGUAUUUUCCUGCAAAAAAGCAAAAUCAGCAUAUAGACAUCAUAUAGACAAUAUAUCAAAUAAGUGUUAAAAGAAAGGGCAUAAUCUAUGAAAAUCAUUAUCUUUGUUGCAAAAACGGCUUACC (((((...........)))))......(((((((((((.((((((.(((......)))..........(((((....(((((.....))))).......(((((.........)))))..)))))))))))))))).)))))).((.......))..... (-20.20) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GGUAAGCCGUUUUUGCAACAAAGAUAAUGAUUUUCAUAGAUUAUGCCCUUUCUUUUAACACUUAUUUGAUAUAUUGUCUAUAUGAUGUCUAUAUGCUGAUUUUGCUUUUUUGCAGGAAAAUACAUUACUUUGCGAAAUCAAUGUUAAUAAAAUUCACAUU ((....))..((((((((...((.(((((((((((..((((((.((...........(((.((((..(((.....)))...)))))))......))))))))(((......))).)))))).)))))))))))))))..(((((.(((...))).))))) (-21.53) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 236 157 112 192 156 pint:PI1344|5end_hypothetical_protein_1258551..1258781_POSITIVE 235 66 21 68 19 pint:PI0530|5end_possible_membrane-fusion_protein_483772..484002_POSITIVE 230 160 111 155 106 pint:PI0735|5end_ABC_transporter,_ATP-binding_/_permease_668793..669023_POSITIVE 219 89 45 80 38 pint:PI0723|5end_conserved_hypothetical_protein_656043..656273_POSITIVE 219 65 24 208 163 pint:PI0059|5end_peptide_chain_release_factor_RF-2_57132..57362_POSITIVE 209 160 113 170 114 pint:PI1296|5end_glycosyltransferase_1208820..1209050_POSITIVE 209 69 27 105 58 pint:PI0644|5end_dnaJ_protein_585704..585934_POSITIVE 207 147 111 74 41 pint:PI0954|5end_hypothetical_protein_885567..885797_POSITIVE 207 160 112 159 112 pint:PI0668|5end_peptidyl-prolyl_cis-trans_isomerase_SlyD,_FKBP-type_(peptidylprolyl_isomerase)_610216..610446_POSITIVE 207 160 112 56 9 pint:PI0667|5end_hypothetical_protein_610113..610343_POSITIVE 206 58 11 175 130 pint:PI1969|5end_hypothetical_protein_1925496..1925726_POSITIVE 204 66 27 146 104 pint:PI0606|5end_naphthoate_synthase_552956..553186_POSITIVE 203 159 123 174 140 pint:PI0829|5end_nucleotidyl_transferase_family;_possible_mannose-1-phosphate_guanyltransferase_765665..765895_POSITIVE 203 120 75 192 153 pint:PI0664|5end_dihydroorotate_dehydrogenase,_electron_transfer_subunit_606891..607121_POSITIVE 203 49 25 146 122 pint:PI0230|5end_hypothetical_protein_228590..228820_POSITIVE 202 58 16 44 5 pint:PI1039|5end_conserved_hypothetical_protein_957721..957951_POSITIVE 201 155 111 61 23 pint:PI1774|5end_hypothetical_protein_1706184..1706414_POSITIVE 199 160 111 125 78 pint:PI1381|5end_conserved_hypothetical_protein_1303060..1303290_POSITIVE 199 149 112 117 78 pint:PI0868|5end_exodeoxyribonuclease_VII,_large_subunit_804201..804431_POSITIVE 198 123 95 188 154 pint:PI1954|5end_translation_initiation_factor_IF-2_1908784..1909014_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 236 157 112 100 64 pint:PI1343|3end_conserved_hypothetical_protein_1258539..1258689_POSITIVE 214 70 28 46 5 pint:PI1728|3end_ATP-dependent_Clp_protease,_proteolytic_subunit_1647658..1647808_POSITIVE 209 160 113 120 64 pint:PI1295|3end_hypothetical_protein_1208850..1209000_POSITIVE 204 66 27 136 94 pint:PI0605|3end_chloromuconate_cycloisomerase_553026..553176_POSITIVE 203 76 31 116 86 pint:PI1146|3end_translation_initiation_factor_IF3_1073503..1073653_POSITIVE 203 159 123 124 90 pint:PI0828|3end_GMP_synthase_(glutamine_amidotransferase)_765695..765845_POSITIVE 198 58 28 75 43 pint:PI0199|3end_phosphate_acetyltransferase_190923..191073_POSITIVE 195 154 135 77 54 pint:PI1244|3end_hypothetical_protein_1169176..1169326_POSITIVE 194 129 82 117 71 pint:PI1644|3end_hypothetical_protein_1561030..1561180_POSITIVE 194 89 45 72 23 pint:PI0949|3end_endonuclease_883279..883429_POSITIVE 194 159 115 128 93 pint:PI0094|3end_protoporphyrinogen_oxidase_90511..90661_POSITIVE 193 146 111 48 21 pint:PI0623|3end_hypothetical_protein_573080..573230_POSITIVE 192 155 112 86 45 pint:PI1302|3end_hypothetical_protein_1215167..1215317_POSITIVE 190 155 111 123 82 pint:PI1921|3end_conserved_hypothetical_protein_1865100..1865250_POSITIVE 190 74 32 147 102 pint:PI0518|3end_5'-nucleotidase_precursor_477959..478109_POSITIVE 187 80 31 85 41 pint:PI1061|3end_conserved_hypothetical_protein_980073..980223_POSITIVE 185 146 107 116 76 pint:PI1227|3end_conserved_hypothetical_protein;_possible_DNA-binding_protein,_histone-like_family_1148974..1149124_POSITIVE 185 77 40 79 37 pint:PI0891|3end_transketolase_822905..823055_POSITIVE 185 146 109 119 94 pint:PI0523|3end_hypothetical_protein_479844..479994_POSITIVE 182 51 19 149 118 pint:PI0404|3end_integrase_372526..372676_POSITIVE