Origin IGS: atcaaataaaagcgtaatactgcatttttgaagtgcaatattacgctttttttagcaaacaagcaagtttattttctaaaaagatgcttattgttactctttacatacgtcaatta .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 taattgacgtatgtaaagagtaacaataagcatctttttagaaaataaacttgcttgtttgctaaaaaaagcgtaatattgcacttcaaaaatgcagtattacgcttttatttgat Mask Tandem Repeat Region ================================================ atcaaataaaagcgtaatactgcatttttgaagtgcaatattacgctttttttagcaaacaagcaagtttattttctaaaaagatgcttattgttactctttacatacgtcaatta Find is-nt database================================================ Query_seq: PI1323:PI1324|PI1323:PI1324:conserved hypothetical protein:conserved hypothetical protein:->->:1242544..1242659 116 atcaaataaaagcgtaatactgcatttttgaagtgcaatattacgctttttttagcaaacaagcaagtttattttctaaaaagatgcttattgttactctttacatacgtcaatta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI1323:PI1324|PI1323:PI1324:conserved hypothetical protein:conserved hypothetical protein:->->:1242544..1242659 116 atcaaataaaagcgtaatactgcatttttgaagtgcaatattacgctttttttagcaaacaagcaagtttattttctaaaaagatgcttattgttactctttacatacgtcaatta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI1323:PI1324|PI1323:PI1324:conserved hypothetical protein:conserved hypothetical protein:->->:1242544..1242659 116 atcaaataaaagcgtaatactgcatttttgaagtgcaatattacgctttttttagcaaacaagcaagtttattttctaaaaagatgcttattgttactctttacatacgtcaatta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 atcaaataaaagcgtaatactgcatttttgaagtgcaatattacgctttttttagcaaacaagcaagtttattttctaaaaagatgcttattgttactctttacatacgtcaatta Predict ORF larger than 30AA ================================================ Protein_Len: 31 Strand: + Start: 24 End: 116 ....................... M F E V Q Y Y A F F S K Q A S L F S K K M L I V T L Y I R Q L atcaaataaaagcgtaatactgcatttttgaagtgcaatattacgctttttttagcaaacaagcaagtttattttctaaaaagatgcttattgttactctttacatacgtcaatta 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================================================ atcaaataaaagcgtaatactgcatttttgaagtgcaatattacgctttttttagcaaacaagcaagtttattttctaaaaagatgcttattgttactctttacatacgtcaatta Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PI1323:PI1324|PI1323:PI1324:conserved hypothetical protein:conserved hypothetical protein:->->:1242544..1242659 116 atcaaataaaagcgtaatactgcatttttgaagtgcaatattacgctttttttagcaaacaagcaagtttattttctaaaaagatgcttattgttactctttacatacgtcaatta Intra-Species Hit: Count: 1 Min: 1 Max: 116 Len: 116 Subject: pint_PI1323_PI1324|conserved hypothetical protein:conserved hypothetical protein|POSITIVE:POSITIVE|[1242544,1242659]|116 HSP 1 e-value: 3.0E-47 bit: 188.0 Len: 116 Query Start:1 Query End:116 Subject Strand: POSITIVE Subject Start: 1 Subject End: 116 atcaaataaaagcgtaatactgcatttttgaagtgcaatattacgcnnnnnnnagcaaacaagcaagtttattttctaaaaagatgcttattgttactctttacatacgtcaatta atcaaataaaagcgtaatactgcatttttgaagtgcaatattacgctttttttagcaaacaagcaagtttattttctaaaaagatgcttattgttactctttacatacgtcaatta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUCAAAUAAAAGCGUAAUACUGCAUUUUUGAAGUGCAAUAUUACGCUUUUUUUAGCAAACAAGCAAGUUUAUUUUCUAAAAAGAUGCUUAUUGUUACUCUUUACAUACGUCAAUUA .......((((((((((((.((((((.....)))))).))))))))))))..((((((..(((((..((((.....))))....))))).)))))).................... (-26.70) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAUUGACGUAUGUAAAGAGUAACAAUAAGCAUCUUUUUAGAAAAUAAACUUGCUUGUUUGCUAAAAAAAGCGUAAUAUUGCACUUCAAAAAUGCAGUAUUACGCUUUUAUUUGAU ..................(((((..(((((((....((((.....))))..))))))))))))...(((((((((((((((((.........)))))))))))))))))....... (-30.30) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 253 96 53 191 153 pint:PI0168|5end_methionyl-tRNA_synthetase_(methionine--tRNA_ligase)_161181..161411_POSITIVE 253 96 53 96 58 pint:PI0166|5end_hypothetical_protein_161086..161316_POSITIVE 238 56 13 108 60 pint:PI1514|5end_tRNA_nucleotidyltransferase/poly(A)_polymerase_1432544..1432774_POSITIVE 230 69 22 179 133 pint:PI0715|5end_hypothetical_protein_652311..652541_POSITIVE 226 90 44 75 39 pint:PI0729|5end_integrase_661428..661658_POSITIVE 221 53 12 162 133 pint:PI1254|5end_probable_glucokinase_1175634..1175864_POSITIVE 221 53 12 44 15 pint:PI1253|5end_hypothetical_protein_1175516..1175746_POSITIVE 221 56 11 56 8 pint:PI0011|5end_conserved_hypothetical_protein_12142..12372_POSITIVE 220 59 11 65 22 pint:PI2153|5end_hypothetical_protein_2099392..2099622_POSITIVE 220 59 11 65 22 pint:PI1567|5end_hypothetical_protein_1489229..1489459_POSITIVE 220 59 11 207 164 pint:PI1486|5end_alginate_O-acetylation_protein_1405507..1405737_POSITIVE 220 59 11 191 148 pint:PI0788|5end_3-methyladenine_DNA_glycosylase_(DNA-3-methyladenine_glycosylase_I)_726152..726382_POSITIVE 219 50 12 214 171 pint:PI0159|5end_hypothetical_protein_151273..151503_POSITIVE 219 50 12 126 83 pint:PI0157|5end_hypothetical_protein_151185..151415_POSITIVE 218 47 11 74 49 pint:PI1382|5end_hypothetical_protein_1303608..1303838_POSITIVE 218 57 12 136 88 pint:PI0406|5end_hypothetical_protein_372734..372964_POSITIVE 216 70 22 206 157 pint:PI0771|5end_conserved_hypothetical_protein_706524..706754_POSITIVE 215 59 12 114 66 pint:PI0851|5end_hypothetical_protein_784310..784540_POSITIVE 215 59 12 114 66 pint:PI0841|5end_hypothetical_protein_775406..775636_POSITIVE 215 59 12 59 6 pint:PI0200|5end_hypothetical_protein_191545..191775_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 399 50 8 83 41 pint:PI1323|3end_conserved_hypothetical_protein_1242483..1242633_POSITIVE 264 47 13 39 7 pint:PI0634|3end_conserved_hypothetical_protein_581121..581271_POSITIVE 226 90 44 75 39 pint:PI0728|3end_integrase_661508..661658_POSITIVE 221 59 11 133 76 pint:PI1748|3end_guanosine-3',5'-bis(diphosphate)_3'-pyrophosphohydrolase/possible_(p)ppgpp_synthetase_II_1670922..1671072_POSITIVE 221 53 12 139 110 pint:PI1253|3end_hypothetical_protein_1175691..1175841_POSITIVE 218 47 11 62 37 pint:PI1381|3end_conserved_hypothetical_protein_1303676..1303826_POSITIVE 218 57 12 67 19 pint:PI0405|3end_hypothetical_protein_372745..372895_POSITIVE 210 59 18 108 59 pint:PI0098|3end_conserved_hypothetical_protein_(possible_glycosyl/glycerophosphate_transferase)_95532..95682_POSITIVE 209 59 12 147 99 pint:PI0689|3end_hypothetical_protein_625877..626027_POSITIVE 206 56 22 49 10 pint:PI1762|3end_ISPg3-related_transposase_1685645..1685795_POSITIVE 203 49 7 113 77 pint:PI0819|3end_hypothetical_protein_759919..760069_POSITIVE 199 59 12 147 99 pint:PI1814|3end_hypothetical_protein_1753233..1753383_POSITIVE 199 47 9 67 27 pint:PI0349|3end_hypothetical_protein_323802..323952_POSITIVE 198 52 11 125 95 pint:PI1402|3end_3-deoxy-7-phosphoheptulonate_synthase_1323980..1324130_POSITIVE 198 48 9 39 2 pint:PI1358|3end_phospho-N-acetylmuramoyl-pentapeptide-transferase__1275516..1275666_POSITIVE 198 49 18 122 89 pint:PI1011|3end_cytochrome_c_biogenesis_protein_CycY_932989..933139_POSITIVE 198 47 12 51 13 pint:PI0530|3end_possible_membrane-fusion_protein_484757..484907_POSITIVE 198 73 43 124 98 pint:PI0434|3end_possible_beta-lactamase_406890..407040_POSITIVE 197 59 11 151 108 pint:PI1922|3end_hypothetical_protein_1865454..1865604_POSITIVE 197 59 11 147 104 pint:PI1340|3end_hypothetical_protein_1256872..1257022_POSITIVE