Origin IGS: taggaaaaaaaaggaaagaaaaccactgtattgacagttctatgcaattccgaaggaaatgtttcttttggaattaaatatgctttggtttgtgcaaatactaagctaaaaatgtgtaact .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 agttacacatttttagcttagtatttgcacaaaccaaagcatatttaattccaaaagaaacatttccttcggaattgcatagaactgtcaatacagtggttttctttccttttttttccta Mask Tandem Repeat Region ================================================ taggaaaaaaaaggaaagaaaaccactgtattgacagttctatgcaattccgaaggaaatgtttcttttggaattaaatatgctttggtttgtgcaaatactaagctaaaaatgtgtaact Find is-nt database================================================ Query_seq: PI1513:PI1514|PI1513:PI1514:conserved hypothetical protein:tRNA nucleotidyltransferase/poly(A) polymerase:->->:1432563..1432683 121 taggaaaaaaaaggaaagaaaaccactgtattgacagttctatgcaattccgaaggaaatgtttcttttggaattaaatatgctttggtttgtgcaaatactaagctaaaaatgtgtaact Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI1513:PI1514|PI1513:PI1514:conserved hypothetical protein:tRNA nucleotidyltransferase/poly(A) polymerase:->->:1432563..1432683 121 taggaaaaaaaaggaaagaaaaccactgtattgacagttctatgcaattccgaaggaaatgtttcttttggaattaaatatgctttggtttgtgcaaatactaagctaaaaatgtgtaact Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI1513:PI1514|PI1513:PI1514:conserved hypothetical protein:tRNA nucleotidyltransferase/poly(A) polymerase:->->:1432563..1432683 121 taggaaaaaaaaggaaagaaaaccactgtattgacagttctatgcaattccgaaggaaatgtttcttttggaattaaatatgctttggtttgtgcaaatactaagctaaaaatgtgtaact Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 taggaaaaaaaaggaaagaaaaccactgtattgacagttctatgcaattccgaaggaaatgtttcttttggaattaaatatgctttggtttgtgcaaatactaagctaaaaatgtgtaact Predict ORF larger than 30AA ================================================ Protein_Len: 30 Strand: + Start: 31 End: 120 .............................. M T V L C N S E G N V S F G I K Y A L V C A N T K L K M C N . Protein_Len: 37 Strand: - Start: 3 End: 113 .. S F F P F F V V T N V T R H L E S P F T E K P I L Y A K T Q A F V L S F M ........ taggaaaaaaaaggaaagaaaaccactgtattgacagttctatgcaattccgaaggaaatgtttcttttggaattaaatatgctttggtttgtgcaaatactaagctaaaaatgtgtaact 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================================================ taggaaaaaaaaggaaagaaaaccactgtattgacagttctatgcaattccgaaggaaatgtttcttttggaattaaatatgctttggtttgtgcaaatactaagctaaaaatgtgtaact Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PI1513:PI1514|PI1513:PI1514:conserved hypothetical protein:tRNA nucleotidyltransferase/poly(A) polymerase:->->:1432563..1432683 121 taggaaaaaaaaggaaagaaaaccactgtattgacagttctatgcaattccgaaggaaatgtttcttttggaattaaatatgctttggtttgtgcaaatactaagctaaaaatgtgtaact Intra-Species Hit: Count: 1 Min: 13 Max: 121 Len: 109 Subject: pint_PI1513_PI1514|conserved hypothetical protein:tRNA nucleotidyltransferase/poly(A) polymerase|POSITIVE:POSITIVE|[1432563,1432683]|121 HSP 1 e-value: 1.0E-55 bit: 216.0 Len: 109 Query Start:13 Query End:121 Subject Strand: POSITIVE Subject Start: 13 Subject End: 121 ............ggaaagaaaaccactgtattgacagttctatgcaattccgaaggaaatgtttcttttggaattaaatatgctttggtttgtgcaaatactaagctaaaaatgtgtaact ............ggaaagaaaaccactgtattgacagttctatgcaattccgaaggaaatgtttcttttggaattaaatatgctttggtttgtgcaaatactaagctaaaaatgtgtaact Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GGAAAGAAAACCACUGUAUUGACAGUUCUAUGCAAUUCCGAAGGAAAUGUUUCUUUUGGAAUUAAAUAUGCUUUGGUUUGUGCAAAUACUAAGCUAAAAAUGUGUAACU ....(((.....(((((....))))))))....(((((((((((((....)))))))))))))..((((..(((((((((((....))).)))))))).))))...... (-23.80) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGUUACACAUUUUUAGCUUAGUAUUUGCACAAACCAAAGCAUAUUUAAUUCCAAAAGAAACAUUUCCUUCGGAAUUGCAUAGAACUGUCAAUACAGUGGUUUUCUUUCC ...............((.........))..(((((......(((.(((((((.((.(((....))).)).))))))).)))..(((((....))))))))))....... (-15.60) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 283 55 15 211 167 pint:PI1818|5end_hypothetical_protein_1756891..1757121_POSITIVE 268 60 16 129 88 pint:PI0936|5end_conserved_hypothetical_protein_868329..868559_POSITIVE 267 83 41 108 71 pint:PI0256|5end_conjugative_transposon_protein,_TraE_249044..249274_POSITIVE 251 84 43 58 17 pint:PI1564|5end_surface_antigen_BspA_1483455..1483685_POSITIVE 251 90 42 130 81 pint:PI0732|5end_conserved_hypothetical_protein_663598..663828_POSITIVE 245 50 12 182 137 pint:PI1288|5end_hypothetical_protein_1202333..1202563_POSITIVE 245 59 13 212 156 pint:PI0603|5end_3-dehydroquinate_synthase_549718..549948_POSITIVE 239 50 1 216 174 pint:PI0641|5end_conserved_hypothetical_protein_583791..584021_POSITIVE 234 58 13 175 107 pint:PI2170|5end_RNA_polymerase_sigma-70_factor,_ECF_subfamily_2112238..2112468_POSITIVE 234 76 39 151 114 pint:PI1584|5end_A/G-specific_adenine_glycosylase_1511898..1512128_POSITIVE 230 59 13 66 29 pint:PI0749|5end_hypothetical_protein_677234..677464_POSITIVE 228 40 9 210 181 pint:PI0693|5end_periplasmic_iron_binding_protein,_ABC_transporter_628387..628617_POSITIVE 227 60 11 63 17 pint:PI0219|5end_conserved_hypothetical_protein_211412..211642_POSITIVE 223 89 53 43 3 pint:PI0874|5end_conserved_hypothetical_protein_808978..809208_POSITIVE 221 63 21 96 50 pint:PI1139|5end_endopeptidase,_endothelin-converting_enzyme_1065216..1065446_POSITIVE 216 55 15 169 128 pint:PI1307|5end_possible_Fe-S_oxidoreductase_1222517..1222747_POSITIVE 213 59 14 191 138 pint:PI1489|5end_exodeoxyribonuclease_III_1407758..1407988_POSITIVE 213 59 14 57 4 pint:PI1487|5end_hypothetical_protein_1407624..1407854_POSITIVE 209 58 14 66 25 pint:PI1845|5end_hypothetical_protein_1791457..1791687_POSITIVE 209 50 9 64 27 pint:PI0178|5end_2-oxoglutarate_synthase,_subunit_korA_169524..169754_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 299 63 34 45 16 pint:PI1513|3end_conserved_hypothetical_protein_1432502..1432652_POSITIVE 275 55 19 150 109 pint:PI0935|3end_collagenase,_protease_868320..868470_POSITIVE 251 90 42 125 76 pint:PI0731|3end_conserved_hypothetical_protein_663673..663823_POSITIVE 240 59 25 45 7 pint:PI0602|3end_conserved_hypothetical_protein_549631..549781_POSITIVE 239 58 12 51 8 pint:PI2129|3end_octaprenyl-diphosphate_synthase_2077721..2077871_POSITIVE 235 49 5 83 35 pint:PI0606|3end_naphthoate_synthase_553917..554067_POSITIVE 232 57 14 83 28 pint:PI0111|3end_hypothetical_protein_108265..108415_POSITIVE 228 40 9 112 83 pint:PI0691|3end_hypothetical_protein_628369..628519_POSITIVE 226 81 43 143 106 pint:PI0451|3end_serine_proteases,__S51_group_425127..425277_POSITIVE 219 59 24 127 82 pint:PI1194|3end_DnaJ_protein_(Hsp-40)_1113124..1113274_POSITIVE 209 83 42 93 46 pint:PI2145|3end_hypothetical_protein_2092649..2092799_POSITIVE 209 50 9 43 6 pint:PI0177|3end_2-oxoglutarate_synthase,_subunit_korB_169583..169733_POSITIVE 208 83 43 119 75 pint:PI1773|3end_alpha-amylase_(neopullulanase)_1706107..1706257_POSITIVE 207 43 9 151 105 pint:PI1128|3end_probable_yrdC_domain_protein,_translation_factor_(SUA5)_1055055..1055205_POSITIVE 207 54 14 151 119 pint:PI0361|3end_hypothetical_protein_333426..333576_POSITIVE 205 59 11 120 60 pint:PI0743|3end_hypothetical_protein_673026..673176_POSITIVE 205 49 11 147 94 pint:PI0203|3end_conserved_hypothetical_protein_196064..196214_POSITIVE 204 59 21 48 1 pint:PI1527|3end_immunoreactive_46_kDa_antigen_PG99_1449520..1449670_POSITIVE 204 46 1 150 104 pint:PI1238|3end_single-strand_DNA-specific_exonuclease_1163438..1163588_POSITIVE 204 60 12 64 15 pint:PI0508|3end_possible_cell_filamentation_protein_467436..467586_POSITIVE