Origin IGS: ctttgaagtattatatgtttattgtttaattatcaaatgtataagtttcaaaggcagaacgatagaacgtctacccacttcgaggcgcaaaggtacttaaattttgcctaactacataatatatagagataaaaaaaacatttttaagaattagccttacttatcatctctgttgccaaccgtaggcagacaaggctgcaagacagcaaaaagcctcgaagaacatcaacgttctccgaggctcgcaagttatggata .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tatccataacttgcgagcctcggagaacgttgatgttcttcgaggctttttgctgtcttgcagccttgtctgcctacggttggcaacagagatgataagtaaggctaattcttaaaaatgttttttttatctctatatattatgtagttaggcaaaatttaagtacctttgcgcctcgaagtgggtagacgttctatcgttctgcctttgaaacttatacatttgataattaaacaataaacatataatacttcaaag Mask Tandem Repeat Region ================================================ ctttgaagtattatatgtttattgtttaattatcaaatgtataagtttcaaaggcagaacgatagaacgtctacccacttcgaggcgcaaaggtacttaaattttgcctaactacataatatatagagataaaaaaaacatttttaagaattagccttacttatcatctctgttgccaaccgtaggcagacaaggctgcaagacagcaaaaagcctcgaagaacatcaacgttctccgaggctcgcaagttatggata Find is-nt database================================================ Query_seq: PI1729:PI1730|PI1729:PI1730:FKBP-type peptidyl-prolyl cis-trans isomerase, trigger factor:hypothetical protein:->->:1649996..1650253 258 ctttgaagtattatatgtttattgtttaattatcaaatgtataagtttcaaaggcagaacgatagaacgtctacccacttcgaggcgcaaaggtacttaaattttgcctaactacataatatatagagataaaaaaaacatttttaagaattagccttacttatcatctctgttgccaaccgtaggcagacaaggctgcaagacagcaaaaagcctcgaagaacatcaacgttctccgaggctcgcaagttatggata Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI1729:PI1730|PI1729:PI1730:FKBP-type peptidyl-prolyl cis-trans isomerase, trigger factor:hypothetical protein:->->:1649996..1650253 258 ctttgaagtattatatgtttattgtttaattatcaaatgtataagtttcaaaggcagaacgatagaacgtctacccacttcgaggcgcaaaggtacttaaattttgcctaactacataatatatagagataaaaaaaacatttttaagaattagccttacttatcatctctgttgccaaccgtaggcagacaaggctgcaagacagcaaaaagcctcgaagaacatcaacgttctccgaggctcgcaagttatggata Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI1729:PI1730|PI1729:PI1730:FKBP-type peptidyl-prolyl cis-trans isomerase, trigger factor:hypothetical protein:->->:1649996..1650253 258 ctttgaagtattatatgtttattgtttaattatcaaatgtataagtttcaaaggcagaacgatagaacgtctacccacttcgaggcgcaaaggtacttaaattttgcctaactacataatatatagagataaaaaaaacatttttaagaattagccttacttatcatctctgttgccaaccgtaggcagacaaggctgcaagacagcaaaaagcctcgaagaacatcaacgttctccgaggctcgcaagttatggata Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ctttgaagtattatatgtttattgtttaattatcaaatgtataagtttcaaaggcagaacgatagaacgtctacccacttcgaggcgcaaaggtacttaaattttgcctaactacataatatatagagataaaaaaaacatttttaagaattagccttacttatcatctctgttgccaaccgtaggcagacaaggctgcaagacagcaaaaagcctcgaagaacatcaacgttctccgaggctcgcaagttatggata Predict ORF larger than 30AA ================================================ Protein_Len: 33 Strand: + Start: 10 End: 108 ......... M I C L L F N Y Q M Y K F Q R Q N D R T S T H F E A Q R Y L N F A ...................................................................................................................................................... Protein_Len: 32 Strand: + Start: 163 End: 258 .................................................................................................................................................................. M I S V A N R R Q T R L Q D S K K P R R T S T F S E A R K L W I Protein_Len: 37 Strand: - Start: 147 End: 257 .................................................................................................................................................. S N A K S I M E T A L R L C V L S C S L L F G R L V D V N E S A R L N H M . ctttgaagtattatatgtttattgtttaattatcaaatgtataagtttcaaaggcagaacgatagaacgtctacccacttcgaggcgcaaaggtacttaaattttgcctaactacataatatatagagataaaaaaaacatttttaagaattagccttacttatcatctctgttgccaaccgtaggcagacaaggctgcaagacagcaaaaagcctcgaagaacatcaacgttctccgaggctcgcaagttatggata 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================================================ ctttgaagtattatatgtttattgtttaattatcaaatgtataagtttcaaaggcagaacgatagaacgtctacccacttcgaggcgcaaaggtacttaaattttgcctaactacataatatatagagataaaaaaaacatttttaagaattagccttacttatcatctctgttgccaaccgtaggcagacaaggctgcaagacagcaaaaagcctcgaagaacatcaacgttctccgaggctcgcaagttatggata Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 42 HP_score: -2.4 Tail_Score: -3.11966 Start: 130 End: 146 Full_Region: agtaaggctaattct taaaaa tgttt ttttta tctctatatattatg .................................................................................................................................taaaaatgtttttttta................................................................................................................ Find igs database================================================ Query_seq: PI1729:PI1730|PI1729:PI1730:FKBP-type peptidyl-prolyl cis-trans isomerase, trigger factor:hypothetical protein:->->:1649996..1650253 258 ctttgaagtattatatgtttattgtttaattatcaaatgtataagtttcaaaggcagaacgatagaacgtctacccacttcgaggcgcaaaggtacttaaattttgcctaactacataatatatagagataaaaaaaacatttttaagaattagccttacttatcatctctgttgccaaccgtaggcagacaaggctgcaagacagcaaaaagcctcgaagaacatcaacgttctccgaggctcgcaagttatggata Intra-Species Hit: Count: 1 Min: 1 Max: 258 Len: 258 Subject: pint_PI1729_PI1730|FKBP-type peptidyl-prolyl cis-trans isomerase, trigger factor:hypothetical protein|POSITIVE:POSITIVE|[1649996,1650253]|258 HSP 1 e-value: 1.0E-130 bit: 464.0 Len: 258 Query Start:1 Query End:258 Subject Strand: POSITIVE Subject Start: 1 Subject End: 258 ctttgaagtattatatgtttattgtttaattatcaaatgtataagtttcaaaggcagaacgatagaacgtctacccacttcgaggcgcaaaggtacttaaattttgcctaactacataatatatagagatnnnnnnnncatttttaagaattagccttacttatcatctctgttgccaaccgtaggcagacaaggctgcaagacagcaaaaagcctcgaagaacatcaacgttctccgaggctcgcaagttatggata ctttgaagtattatatgtttattgtttaattatcaaatgtataagtttcaaaggcagaacgatagaacgtctacccacttcgaggcgcaaaggtacttaaattttgcctaactacataatatatagagataaaaaaaacatttttaagaattagccttacttatcatctctgttgccaaccgtaggcagacaaggctgcaagacagcaaaaagcctcgaagaacatcaacgttctccgaggctcgcaagttatggata Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CUUUGAAGUAUUAUAUGUUUAUUGUUUAAUUAUCAAAUGUAUAAGUUUCAAAGGCAGAACGAUAGAACGUCUACCCACUUCGAGGCGCAAAGGUACUUAAAUUUUGCCUAACUACAUAAUAUAUAGAGAUAAAAAAAACAUUUUUAAGAAUUAGCCUUACUUAUCAUCUCUGUUGCCAACCGUAGGCAGACAAGGCUGCAAGACAGCAAAAAGCCUCGAAGAACAUCAACGUUCUCCGAGGCUCGCAAGUUAUGGAUA (((((((...((((((((((..((......))..))))))))))..)))))))..........(((((((.......(((((((((................((((((((............((((((((..((((....))))((((.......))))......)))))))).........))))))))....((((.....)))).....))))))))).......)))))))(((..(((....)))..)))... (-60.74) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAUCCAUAACUUGCGAGCCUCGGAGAACGUUGAUGUUCUUCGAGGCUUUUUGCUGUCUUGCAGCCUUGUCUGCCUACGGUUGGCAACAGAGAUGAUAAGUAAGGCUAAUUCUUAAAAAUGUUUUUUUUAUCUCUAUAUAUUAUGUAGUUAGGCAAAAUUUAAGUACCUUUGCGCCUCGAAGUGGGUAGACGUUCUAUCGUUCUGCCUUUGAAACUUAUACAUUUGAUAAUUAAACAAUAAACAUAUAAUACUUCAAAG ....((.(((....(((((((((((((((....)))))))))))))))...((((.....))))...((((((((((....(((...((((((((.....(((((..............)))))..)))))))).........(((.(((((.....))))).)))......))).....))))))))))........))).)).(((((((..(((((..((((............))))..)))))...))))))) (-67.74) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 393 220 173 194 149 pint:PI1822|5end_ABC_transporter,_ATP-binding_/_permease_1761452..1761682_POSITIVE 356 218 180 87 46 pint:PI0245|5end_possible_mobilization_protein_242946..243176_POSITIVE 353 207 168 201 166 pint:PI0554|5end_hypothetical_protein_504415..504645_POSITIVE 353 207 163 88 39 pint:PI0207|5end_conserved_hypothetical_protein_199797..200027_POSITIVE 352 199 151 88 43 pint:PI0870|5end_branched-chain_amino_acid_aminotransferase_805933..806163_POSITIVE 351 209 165 118 79 pint:PI0564|5end_hypothetical_protein_511537..511767_POSITIVE 351 209 165 60 21 pint:PI0565|5end_hypothetical_protein_511479..511709_POSITIVE 349 208 164 197 134 pint:PI0733|5end_membrane_protein;_predicted_exporter_664389..664619_POSITIVE 344 89 48 171 125 pint:PI0592|5end_DNA_mismatch_repair_protein_540795..541025_POSITIVE 344 97 51 153 100 pint:PI0307|5end_RNA_polymerase_sigma-70_factor,_ECF_subfamily_290042..290272_POSITIVE 338 223 181 77 38 pint:PI0681|5end_hypothetical_protein_619000..619230_POSITIVE 338 223 181 49 10 pint:PI0682|5end_hypothetical_protein_618972..619202_POSITIVE 333 197 152 179 129 pint:PI0530|5end_possible_membrane-fusion_protein_483772..484002_POSITIVE 328 87 43 127 79 pint:PI2020|5end_glycosyl_transferase,_group_2_family_protein_1976866..1977096_POSITIVE 327 200 151 181 137 pint:PI1476|5end_acyl-CoA_synthase/O-succinylbenzoic_acid-CoA_ligase_1397699..1397929_POSITIVE 326 202 166 79 28 pint:PI1935|5end_possible__internalin-related_protein_1883324..1883554_POSITIVE 325 221 186 46 14 pint:PI1729|5end_FKBP-type_peptidyl-prolyl_cis-trans_isomerase,_trigger_factor_1648416..1648646_POSITIVE 325 213 171 143 105 pint:PI0906|5end_hypothetical_protein_835653..835883_POSITIVE 320 207 172 54 18 pint:PI0774|5end_phosphoserine_aminotransferase_(phosphoserine_transaminase)_709497..709727_POSITIVE 318 198 153 180 121 pint:PI2137|5end_RNA_methylase_SpoU_family_2083173..2083403_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 353 207 168 89 54 pint:PI0553|3end_recombination_protein_504383..504533_POSITIVE 353 207 163 67 18 pint:PI0206|3end_TPR-repeat-containing_protein_199856..200006_POSITIVE 349 208 164 95 32 pint:PI0732|3end_conserved_hypothetical_protein_664367..664517_POSITIVE 333 197 152 68 18 pint:PI0529|3end_hypothetical_protein_483741..483891_POSITIVE 322 197 153 50 1 pint:PI0527|3end_outer_membrane_efflux_protein_483723..483873_POSITIVE 315 210 165 61 25 pint:PI1010|3end_conserved_hypothetical_protein_932195..932345_POSITIVE 300 213 172 69 30 pint:PI0072|3end_conserved_hypothetical_protein_70992..71142_POSITIVE 297 243 204 46 12 pint:PI0653|3end_hypothetical_protein_596236..596386_POSITIVE 293 200 154 140 93 pint:PI0087|3end_conserved_hypothetical_protein_86733..86883_POSITIVE 292 89 52 84 39 pint:PI0603|3end_3-dehydroquinate_synthase_550841..550991_POSITIVE 286 204 168 90 53 pint:PI0684|3end_coproporphyrinogen_III_oxidase_620507..620657_POSITIVE 285 219 177 99 40 pint:PI1789|3end_hypothetical_protein_1719037..1719187_POSITIVE 285 209 171 46 2 pint:PI1643|3end_conserved_hypothetical_protein_1562029..1562179_POSITIVE 283 249 206 101 57 pint:PI0183|3end_hypothetical_protein_174810..174960_POSITIVE 282 208 170 39 7 pint:PI0355|3end_probable__N-acetylmuramoyl-L-alanine_amidase_326698..326848_POSITIVE 281 210 164 134 79 pint:PI0428|3end_hypothetical_protein_396321..396471_POSITIVE 280 81 41 94 57 pint:PI1742|3end_SpoOJ_regulator_protein_1665670..1665820_POSITIVE 279 92 51 150 114 pint:PI0918|3end_Fe-S_oxidoreductase,_family_2_849236..849386_POSITIVE 278 226 183 48 6 pint:PI1544|3end_hypothetical_protein_1463679..1463829_POSITIVE 277 239 192 126 68 pint:PI0721|3end_hypothetical_protein_654982..655132_POSITIVE