Origin IGS: taatttcccctgtgctatatatggcgccggaaacgggcgccatattttttatatctcactgtgaaacttgaagacaacataaaatgaggaaaaatctgattacaaccgcgatttaaagttatttttaagtaaaatattcttacatttacgataaataggattatccatgcactggttattcctggcattaactatagtgggaggagtcttcggttcatcaatgttaaaaattaagtagcggttttgtccgtgctttttattttttgtctattgcgctgcgctaaaaaatattctgctcggcactgtatatgctatttggactggcataggtttggcaccacttgagcagagttttacattatttggtgtctacttgtcgatttcttcgaatgctattatacgactaccgctgcgtcgtatttcagcactggtttggcgtatttttcatgtgtggcatgagaaacttcttgctgttctgctttttctttccttctatgctaaactagcgcgcaatttttccgtatttttgactatttttaagcagtt .........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.........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.........1.........2.........3.........4.........5.........6.........7.........8.........9 aactgcttaaaaatagtcaaaaatacggaaaaattgcgcgctagtttagcatagaaggaaagaaaaagcagaacagcaagaagtttctcatgccacacatgaaaaatacgccaaaccagtgctgaaatacgacgcagcggtagtcgtataatagcattcgaagaaatcgacaagtagacaccaaataatgtaaaactctgctcaagtggtgccaaacctatgccagtccaaatagcatatacagtgccgagcagaatattttttagcgcagcgcaatagacaaaaaataaaaagcacggacaaaaccgctacttaatttttaacattgatgaaccgaagactcctcccactatagttaatgccaggaataaccagtgcatggataatcctatttatcgtaaatgtaagaatattttacttaaaaataactttaaatcgcggttgtaatcagatttttcctcattttatgttgtcttcaagtttcacagtgagatataaaaaatatggcgcccgtttccggcgccatatatagcacaggggaaatta Mask Tandem Repeat Region ================================================ taatttcccctgtgctatatatggcgccggaaacgggcgccatattttttatatctcactgtgaaacttgaagacaacataaaatgaggaaaaatctgattacaaccgcgatttaaagttatttttaagtaaaatattcttacatttacgataaataggattatccatgcactggttattcctggcattaactatagtgggaggagtcttcggttcatcaatgttaaaaattaagtagcggttttgtccgtgctttttattttttgtctattgcgctgcgctaaaaaatattctgctcggcactgtatatgctatttggactggcataggtttggcaccacttgagcagagttttacattatttggtgtctacttgtcgatttcttcgaatgctattatacgactaccgctgcgtcgtatttcagcactggtttggcgtatttttcatgtgtggcatgagaaacttcttgctgttctgctttttctttccttctatgctaaactagcgcgcaatttttccgtatttttgactatttttaagcagtt Find is-nt database================================================ Query_seq: AA01614:AA01615|AA01614:AA01615:D-isomer specific 2-hydroxyacid dehydrogenase family protein:lipoprotein releasing system transmembrane:->->:1090780..1091325 546 taatttcccctgtgctatatatggcgccggaaacgggcgccatattttttatatctcactgtgaaacttgaagacaacataaaatgaggaaaaatctgattacaaccgcgatttaaagttatttttaagtaaaatattcttacatttacgataaataggattatccatgcactggttattcctggcattaactatagtgggaggagtcttcggttcatcaatgttaaaaattaagtagcggttttgtccgtgctttttattttttgtctattgcgctgcgctaaaaaatattctgctcggcactgtatatgctatttggactggcataggtttggcaccacttgagcagagttttacattatttggtgtctacttgtcgatttcttcgaatgctattatacgactaccgctgcgtcgtatttcagcactggtttggcgtatttttcatgtgtggcatgagaaacttcttgctgttctgctttttctttccttctatgctaaactagcgcgcaatttttccgtatttttgactatttttaagcagtt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: AA01614:AA01615|AA01614:AA01615:D-isomer specific 2-hydroxyacid dehydrogenase family protein:lipoprotein releasing system transmembrane:->->:1090780..1091325 546 taatttcccctgtgctatatatggcgccggaaacgggcgccatattttttatatctcactgtgaaacttgaagacaacataaaatgaggaaaaatctgattacaaccgcgatttaaagttatttttaagtaaaatattcttacatttacgataaataggattatccatgcactggttattcctggcattaactatagtgggaggagtcttcggttcatcaatgttaaaaattaagtagcggttttgtccgtgctttttattttttgtctattgcgctgcgctaaaaaatattctgctcggcactgtatatgctatttggactggcataggtttggcaccacttgagcagagttttacattatttggtgtctacttgtcgatttcttcgaatgctattatacgactaccgctgcgtcgtatttcagcactggtttggcgtatttttcatgtgtggcatgagaaacttcttgctgttctgctttttctttccttctatgctaaactagcgcgcaatttttccgtatttttgactatttttaagcagtt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: AA01614:AA01615|AA01614:AA01615:D-isomer specific 2-hydroxyacid dehydrogenase family protein:lipoprotein releasing system transmembrane:->->:1090780..1091325 546 taatttcccctgtgctatatatggcgccggaaacgggcgccatattttttatatctcactgtgaaacttgaagacaacataaaatgaggaaaaatctgattacaaccgcgatttaaagttatttttaagtaaaatattcttacatttacgataaataggattatccatgcactggttattcctggcattaactatagtgggaggagtcttcggttcatcaatgttaaaaattaagtagcggttttgtccgtgctttttattttttgtctattgcgctgcgctaaaaaatattctgctcggcactgtatatgctatttggactggcataggtttggcaccacttgagcagagttttacattatttggtgtctacttgtcgatttcttcgaatgctattatacgactaccgctgcgtcgtatttcagcactggtttggcgtatttttcatgtgtggcatgagaaacttcttgctgttctgctttttctttccttctatgctaaactagcgcgcaatttttccgtatttttgactatttttaagcagtt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 taatttcccctgtgctatatatggcgccggaaacgggcgccatattttttatatctcactgtgaaacttgaagacaacataaaatgaggaaaaatctgattacaaccgcgatttaaagttatttttaagtaaaatattcttacatttacgataaataggattatccatgcactggttattcctggcattaactatagtgggaggagtcttcggttcatcaatgttaaaaattaagtagcggttttgtccgtgctttttattttttgtctattgcgctgcgctaaaaaatattctgctcggcactgtatatgctatttggactggcataggtttggcaccacttgagcagagttttacattatttggtgtctacttgtcgatttcttcgaatgctattatacgactaccgctgcgtcgtatttcagcactggtttggcgtatttttcatgtgtggcatgagaaacttcttgctgttctgctttttctttccttctatgctaaactagcgcgcaatttttccgtatttttgactatttttaagcagtt Predict ORF larger than 30AA ================================================ Protein_Len: 32 Strand: + Start: 136 End: 231 ....................................................................................................................................... M L T F T I N R I I H A L V I P G I N Y S G R S L R F I N V K N ........................................................................................................................................................................................................................................................................................................................... Protein_Len: 33 Strand: + Start: 244 End: 342 ................................................................................................................................................................................................................................................... M S V L F I F C L L R C A K K Y S A R H C I C Y L D W H R F G T T ............................................................................................................................................................................................................ Protein_Len: 33 Strand: + Start: 358 End: 456 ..................................................................................................................................................................................................................................................................................................................................................................... M I W C L L V D F F E C Y Y T T T A A S Y F S T G L A Y F S C V A .......................................................................................... Protein_Len: 54 Strand: + Start: 342 End: 503 ..................................................................................................................................................................................................................................................................................................................................................... M S R V L H Y L V S T C R F L R M L L Y D Y R C V V F Q H W F G V F F M C G M R N F L L F C F F F P S M L N ........................................... Protein_Len: 60 Strand: + Start: 290 End: 544 ................................................................................................................................................................................................................................................................................................. M L L G T V Y A I W T G I G L A P L E Q S F T L F G V Y L S I S S N A I I R L P L R R I S A L V W R I F H V W H E K L L .. Protein_Len: 43 Strand: - Start: 103 End: 231 ...................................................................................................... L R S K F N N K L L I N K C K R Y I P N D M C Q N N R A N V I T P P T K P E D I N F M ........................................................................................................................................................................................................................................................................................................................... Protein_Len: 57 Strand: - Start: 18 End: 188 ................. I H R R F R A G Y K K Y R V T F S S S L M F H P F I Q N C G R N L T I K L Y F I R V N V I F L I I W A S T I G P M ...................................................................................................................................................................................................................................................................................................................................................................... taatttcccctgtgctatatatggcgccggaaacgggcgccatattttttatatctcactgtgaaacttgaagacaacataaaatgaggaaaaatctgattacaaccgcgatttaaagttatttttaagtaaaatattcttacatttacgataaataggattatccatgcactggttattcctggcattaactatagtgggaggagtcttcggttcatcaatgttaaaaattaagtagcggttttgtccgtgctttttattttttgtctattgcgctgcgctaaaaaatattctgctcggcactgtatatgctatttggactggcataggtttggcaccacttgagcagagttttacattatttggtgtctacttgtcgatttcttcgaatgctattatacgactaccgctgcgtcgtatttcagcactggtttggcgtatttttcatgtgtggcatgagaaacttcttgctgttctgctttttctttccttctatgctaaactagcgcgcaatttttccgtatttttgactatttttaagcagtt 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================================================ PromScan Matrix: RpoN Strand: + Score: 82 Start: 321 End: 337 ................................................................................................................................................................................................................................................................................................................................CTGGCATAGGTTTGGCA................................................................................................................................................................................................................. taatttcccctgtgctatatatggcgccggaaacgggcgccatattttttatatctcactgtgaaacttgaagacaacataaaatgaggaaaaatctgattacaaccgcgatttaaagttatttttaagtaaaatattcttacatttacgataaataggattatccatgcactggttattcctggcattaactatagtgggaggagtcttcggttcatcaatgttaaaaattaagtagcggttttgtccgtgctttttattttttgtctattgcgctgcgctaaaaaatattctgctcggcactgtatatgctatttggactggcataggtttggcaccacttgagcagagttttacattatttggtgtctacttgtcgatttcttcgaatgctattatacgactaccgctgcgtcgtatttcagcactggtttggcgtatttttcatgtgtggcatgagaaacttcttgctgttctgctttttctttccttctatgctaaactagcgcgcaatttttccgtatttttgactatttttaagcagtt Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 90 HP_score: -12.5 Tail_Score: -2.87132 Start: 22 End: 42 Full_Region: gagatataaaaaata tggcgcccg ttt ccggcgcca tatatagcacagggg .....................tggcgcccgtttccggcgcca........................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................ TransTerm Strand: - Conf: 49 HP_score: -2.8 Tail_Score: -3.5812 Start: 158 End: 182 Full_Region: ctatagttaatgcca ggaataacca gtgca tggataatcc tatttatcgtaaatg .............................................................................................................................................................ggaataaccagtgcatggataatcc............................................................................................................................................................................................................................................................................................................................................................................ TransTerm Strand: + Conf: 49 HP_score: -2.6 Tail_Score: -3.56836 Start: 399 End: 419 Full_Region: CTTCGAATGCTATTA TACGAC TACCGCTGC GTCGTA TTTCAGCACTGGTTT ..............................................................................................................................................................................................................................................................................................................................................................................................................TACGACTACCGCTGCGTCGTA............................................................................................................................... Find igs database================================================ Query_seq: AA01614:AA01615|AA01614:AA01615:D-isomer specific 2-hydroxyacid dehydrogenase family protein:lipoprotein releasing system transmembrane:->->:1090780..1091325 546 taatttcccctgtgctatatatggcgccggaaacgggcgccatattttttatatctcactgtgaaacttgaagacaacataaaatgaggaaaaatctgattacaaccgcgatttaaagttatttttaagtaaaatattcttacatttacgataaataggattatccatgcactggttattcctggcattaactatagtgggaggagtcttcggttcatcaatgttaaaaattaagtagcggttttgtccgtgctttttattttttgtctattgcgctgcgctaaaaaatattctgctcggcactgtatatgctatttggactggcataggtttggcaccacttgagcagagttttacattatttggtgtctacttgtcgatttcttcgaatgctattatacgactaccgctgcgtcgtatttcagcactggtttggcgtatttttcatgtgtggcatgagaaacttcttgctgttctgctttttctttccttctatgctaaactagcgcgcaatttttccgtatttttgactatttttaagcagtt Intra-Species Hit: Count: 1 Min: 1 Max: 546 Len: 546 Subject: aact_AA01614_AA01615|D-isomer specific 2-hydroxyacid dehydrogenase family protein:lipoprotein releasing system transmembrane|POSITIVE:POSITIVE|[1090780,1091325]|546 HSP 1 e-value: 0.0 bit: 1011.0 Len: 546 Query Start:1 Query End:546 Subject Strand: POSITIVE Subject Start: 1 Subject End: 546 taatttcccctgtgctatatatggcgccggaaacgggcgccatattttttatatctcactgtgaaacttgaagacaacataaaatgaggaaaaatctgattacaaccgcgatttaaagttatttttaagtaaaatattcttacatttacgataaataggattatccatgcactggttattcctggcattaactatagtgggaggagtcttcggttcatcaatgttaaaaattaagtagcggttttgtccgtgcnnnnnnnnnnnngtctattgcgctgcgctaaaaaatattctgctcggcactgtatatgctatttggactggcataggtttggcaccacttgagcagagttttacattatttggtgtctacttgtcgatttcttcgaatgctattatacgactaccgctgcgtcgtatttcagcactggtttggcgtatttttcatgtgtggcatgagaaacttcttgctgttctgctttttctttccttctatgctaaactagcgcgcaatttttccgtatttttgactatttttaagcagtt taatttcccctgtgctatatatggcgccggaaacgggcgccatattttttatatctcactgtgaaacttgaagacaacataaaatgaggaaaaatctgattacaaccgcgatttaaagttatttttaagtaaaatattcttacatttacgataaataggattatccatgcactggttattcctggcattaactatagtgggaggagtcttcggttcatcaatgttaaaaattaagtagcggttttgtccgtgctttttattttttgtctattgcgctgcgctaaaaaatattctgctcggcactgtatatgctatttggactggcataggtttggcaccacttgagcagagttttacattatttggtgtctacttgtcgatttcttcgaatgctattatacgactaccgctgcgtcgtatttcagcactggtttggcgtatttttcatgtgtggcatgagaaacttcttgctgttctgctttttctttccttctatgctaaactagcgcgcaatttttccgtatttttgactatttttaagcagtt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAUUUCCCCUGUGCUAUAUAUGGCGCCGGAAACGGGCGCCAUAUUUUUUAUAUCUCACUGUGAAACUUGAAGACAACAUAAAAUGAGGAAAAAUCUGAUUACAACCGCGAUUUAAAGUUAUUUUUAAGUAAAAUAUUCUUACAUUUACGAUAAAUAGGAUUAUCCAUGCACUGGUUAUUCCUGGCAUUAACUAUAGUGGGAGGAGUCUUCGGUUCAUCAAUGUUAAAAAUUAAGUAGCGGUUUUGUCCGUGCUUUUUAUUUUUUGUCUAUUGCGCUGCGCUAAAAAAUAUUCUGCUCGGCACUGUAUAUGCUAUUUGGACUGGCAUAGGUUUGGCACCACUUGAGCAGAGUUUUACAUUAUUUGGUGUCUACUUGUCGAUUUCUUCGAAUGCUAUUAUACGACUACCGCUGCGUCGUAUUUCAGCACUGGUUUGGCGUAUUUUUCAUGUGUGGCAUGAGAAACUUCUUGCUGUUCUGCUUUUUCUUUCCUUCUAUGCUAAACUAGCGCGCAAUUUUUCCGUAUUUUUGACUAUUUUUAAGCAGUU ..........((((....(((((((((((....).))))))))))....))))....((((.....((((((((......((((((.((((((....(((...((((((.((((((...((((((.....)))))).....(((((...(((((......))))).(((.(((((..((((((..(((((....)))))..))))))..))))).))).)))))......)))))).))))))..))).....................(((((((.((((((((.((((((((((((((.......(((((((.......)))))))(((.....)))..))))))))))).....))).)))))))).......((((.....))))..(((...(((((((.........)))))))...))).(((((((((((((.((((((((.....)))))))).......((......))..............))))))))))))).))))))))))))).))))))......)))))))))))). (-143.40) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AACUGCUUAAAAAUAGUCAAAAAUACGGAAAAAUUGCGCGCUAGUUUAGCAUAGAAGGAAAGAAAAAGCAGAACAGCAAGAAGUUUCUCAUGCCACACAUGAAAAAUACGCCAAACCAGUGCUGAAAUACGACGCAGCGGUAGUCGUAUAAUAGCAUUCGAAGAAAUCGACAAGUAGACACCAAAUAAUGUAAAACUCUGCUCAAGUGGUGCCAAACCUAUGCCAGUCCAAAUAGCAUAUACAGUGCCGAGCAGAAUAUUUUUUAGCGCAGCGCAAUAGACAAAAAAUAAAAAGCACGGACAAAACCGCUACUUAAUUUUUAACAUUGAUGAACCGAAGACUCCUCCCACUAUAGUUAAUGCCAGGAAUAACCAGUGCAUGGAUAAUCCUAUUUAUCGUAAAUGUAAGAAUAUUUUACUUAAAAAUAACUUUAAAUCGCGGUUGUAAUCAGAUUUUUCCUCAUUUUAUGUUGUCUUCAAGUUUCACAGUGAGAUAUAAAAAAUAUGGCGCCCGUUUCCGGCGCCAUAUAUAGCACAGGGGAAAUUA ..(((((((((((..(((....((((((....(((((((((((.((((((((....((.........((......)).....((((.(((((.....))))).))))........)).)))))))).)).).))).)))))..))))))........((((.....))))......))).................(((((((....((..(......(((((...........)))))....)..)))))))))....))))))).))))......((((((...((((((......((...((((((......(((((((.((((.((((......((((...........))))......((((.((.(((.....))).)).)))).....)))).))))))))))).......(((((......)))))...))))))....)).((....))....)))))).))))))...((((((.(.(((...((((.....(((((((((.......))))))))))))).))).)..)))))). (-116.10) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 389 205 165 87 47 aact:AA01370|5end_rod_shape-determining_protein_925436..925666_POSITIVE 366 41 3 230 188 aact:AA02146|5end_iron(III)_ABC_transporter,_ATP-binding_protein_1468828..1469058_POSITIVE 364 48 3 160 108 aact:AA01335|5end_primosomal_protein_N'_901993..902223_POSITIVE 363 337 293 91 42 aact:AA02536|5end_conserved_hypothetical_protein_1764854..1765084_POSITIVE 359 439 398 86 43 aact:AA02563|5end_transketolase_C-terminal_section_1785239..1785469_POSITIVE 355 447 406 45 3 aact:AA02774|5end_collagenase_prtC_homolog,_possible_protease_1936870..1937100_POSITIVE 353 48 2 88 47 aact:AA01750|5end_MTA/SAH_nucleosidase_[Includes:_5'-methylthioadenosine_nucleosidase;_S-adenosylhomocysteine_nucleosidase]_1183750..1183980_POSITIVE 350 519 471 209 149 aact:AA01961|5end_lipid_A_export_ATP-binding/permease_protein_msbA_1324405..1324635_POSITIVE 349 44 8 67 33 aact:AA01866|5end_thiamin_ABC_transporter,_permease_protein_1253313..1253543_POSITIVE 347 41 9 206 160 aact:AA01408|5end_conserved_hypothetical_protein_950191..950421_POSITIVE 343 430 384 172 123 aact:AA02715|5end_paraquat-inducible_protein_pqiB_homolog_1897053..1897283_POSITIVE 342 41 11 46 18 aact:AA01519.1|5end_conserved_hypothetical_protein_1022466..1022696_POSITIVE 342 49 7 100 48 aact:AA00804|5end_fumarate_reductase_flavoprotein_subunit_A_549770..550000_POSITIVE 339 528 481 157 95 aact:AA02993|5end_6-phosphofructokinase_2091766..2091996_POSITIVE 336 39 9 219 192 aact:AA02158|5end_TonB-dependent_outer_membrane_receptor_1476155..1476385_POSITIVE 336 460 411 198 133 aact:AA00533|5end_conserved_hypothetical_protein_365323..365553_POSITIVE 335 41 14 70 35 aact:AA02616|5end_transcriptional_regulator_1823684..1823914_POSITIVE 335 443 401 57 7 aact:AA00729|5end_possible_hemolysin_(TlyC-like)_500204..500434_POSITIVE 335 438 405 181 139 aact:AA00327|5end_conserved_hypothetical_protein_222339..222569_POSITIVE 333 283 242 81 42 aact:AA02599|5end_outer_membrane_protein,_Slp_family_1810083..1810313_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 401 319 272 83 35 aact:AA00534|3end_hypothetical_protein_365594..365744_POSITIVE 389 205 165 84 44 aact:AA01369|3end_rod_shape-determining_protein_925513..925663_POSITIVE 353 48 2 68 27 aact:AA01748|3end_thiol:disulfide_interchange_protein_1183810..1183960_POSITIVE 345 337 293 59 8 aact:AA01021|3end_hypothetical_protein_714276..714426_POSITIVE 342 41 11 39 11 aact:AA01519|3end_conserved_hypothetical_protein_1022539..1022689_POSITIVE 340 41 7 150 96 aact:AA00221|3end_NADP-specific_glutamate_dehydrogenase_153865..154015_POSITIVE 331 241 206 37 3 aact:AA02144|3end_iron_(III)_ABC_transporter,_permease_protein_1468679..1468829_POSITIVE 330 45 19 72 46 aact:AA01614|3end_D-isomer_specific_2-hydroxyacid_dehydrogenase_family_protein_1090719..1090869_POSITIVE 327 437 391 86 25 aact:AA01291|3end_excinuclease_ABC_subunit_A_876001..876151_POSITIVE 319 448 406 131 98 aact:AA01124.1|3end_biopolymer_transport_protein_D_772752..772902_POSITIVE 319 448 406 130 97 aact:AA01125|3end_hypothetical_protein_772751..772901_POSITIVE 317 440 408 51 26 aact:AA00969|3end_conserved_hypothetical_protein_(possible_NADH_pyrophosphatase)_676206..676356_POSITIVE 316 336 291 95 33 aact:AA00530|3end_hypothetical_protein_362668..362818_POSITIVE 315 438 396 145 102 aact:AA01167|3end_glucose-6-phosphate_1-dehydrogenase_801067..801217_POSITIVE 313 337 291 76 28 aact:AA02204|3end_hypothetical_protein_1501262..1501412_POSITIVE 311 336 293 63 14 aact:AA02454|3end_ATP-dependent_helicase_1694433..1694583_POSITIVE 311 305 270 51 22 aact:AA00910|3end_hypothetical_protein_627260..627410_POSITIVE 307 269 237 114 82 aact:AA02727|3end_hypothetical_protein_1909925..1910075_POSITIVE 307 438 392 114 64 aact:AA02037|3end_hypothetical_protein_1387052..1387202_POSITIVE 306 340 291 79 22 aact:AA01987|3end_hypothetical_protein_1350620..1350770_POSITIVE