Origin IGS: aatgataaggggttcttctatttatgatcgattttgtggaacaaaagtacgaaacaaagcggacttttcctcctaaaacactcgatgctgcgtgggggtaataccctaaaagcaaaggccttgcacatttgcggaaagtcctatgaagaaaacaggtctttgacccgattgggactttacggagattacgtagtgtaagagactctgtgatttgactgcatgcagtctgtttccatcatccgacggctctgccgtcgtatagcagttctcagaccaaaaacgcatggggcatggggcgagaaaacgtggcgcgggatttttttcgttttggttcgggaatgaaaaatttctcgcgcgtaaacgaagtaatttacgcgcctaaatctcgcagaatacgcgccgcaattccatcgattgcagtgcgtaaaat .........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 attttacgcactgcaatcgatggaattgcggcgcgtattctgcgagatttaggcgcgtaaattacttcgtttacgcgcgagaaatttttcattcccgaaccaaaacgaaaaaaatcccgcgccacgttttctcgccccatgccccatgcgtttttggtctgagaactgctatacgacggcagagccgtcggatgatggaaacagactgcatgcagtcaaatcacagagtctcttacactacgtaatctccgtaaagtcccaatcgggtcaaagacctgttttcttcataggactttccgcaaatgtgcaaggcctttgcttttagggtattacccccacgcagcatcgagtgttttaggaggaaaagtccgctttgtttcgtacttttgttccacaaaatcgatcataaatagaagaaccccttatcatt Mask Tandem Repeat Region ================================================ aatgataaggggttcttctatttatgatcgattttgtggaacaaaagtacgaaacaaagcggacttttcctcctaaaacactcgatgctgcgtgggggtaataccctaaaagcaaaggccttgcacatttgcggaaagtcctatgaagaaaacaggtctttgacccgattgggactttacggagattacgtagtgtaagagactctgtgatttgactgcatgcagtctgtttccatcatccgacggctctgccgtcgtatagcagttctcagaccaaaaacgcatggggcatggggcgagaaaacgtggcgcgggatttttttcgttttggttcgggaatgaaaaatttctcgcgcgtaaacgaagtaatttacgcgcctaaatctcgcagaatacgcgccgcaattccatcgattgcagtgcgtaaaat Find is-nt database================================================ Query_seq: PG0153:PG0155|PG0153:PG0155:aspartyl-tRNA synthetase:riboflavin biosynthesis protein RibD:<-<-:177521..177950 430 aatgataaggggttcttctatttatgatcgattttgtggaacaaaagtacgaaacaaagcggacttttcctcctaaaacactcgatgctgcgtgggggtaataccctaaaagcaaaggccttgcacatttgcggaaagtcctatgaagaaaacaggtctttgacccgattgggactttacggagattacgtagtgtaagagactctgtgatttgactgcatgcagtctgtttccatcatccgacggctctgccgtcgtatagcagttctcagaccaaaaacgcatggggcatggggcgagaaaacgtggcgcgggatttttttcgttttggttcgggaatgaaaaatttctcgcgcgtaaacgaagtaatttacgcgcctaaatctcgcagaatacgcgccgcaattccatcgattgcagtgcgtaaaat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG0153:PG0155|PG0153:PG0155:aspartyl-tRNA synthetase:riboflavin biosynthesis protein RibD:<-<-:177521..177950 430 aatgataaggggttcttctatttatgatcgattttgtggaacaaaagtacgaaacaaagcggacttttcctcctaaaacactcgatgctgcgtgggggtaataccctaaaagcaaaggccttgcacatttgcggaaagtcctatgaagaaaacaggtctttgacccgattgggactttacggagattacgtagtgtaagagactctgtgatttgactgcatgcagtctgtttccatcatccgacggctctgccgtcgtatagcagttctcagaccaaaaacgcatggggcatggggcgagaaaacgtggcgcgggatttttttcgttttggttcgggaatgaaaaatttctcgcgcgtaaacgaagtaatttacgcgcctaaatctcgcagaatacgcgccgcaattccatcgattgcagtgcgtaaaat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG0153:PG0155|PG0153:PG0155:aspartyl-tRNA synthetase:riboflavin biosynthesis protein RibD:<-<-:177521..177950 430 aatgataaggggttcttctatttatgatcgattttgtggaacaaaagtacgaaacaaagcggacttttcctcctaaaacactcgatgctgcgtgggggtaataccctaaaagcaaaggccttgcacatttgcggaaagtcctatgaagaaaacaggtctttgacccgattgggactttacggagattacgtagtgtaagagactctgtgatttgactgcatgcagtctgtttccatcatccgacggctctgccgtcgtatagcagttctcagaccaaaaacgcatggggcatggggcgagaaaacgtggcgcgggatttttttcgttttggttcgggaatgaaaaatttctcgcgcgtaaacgaagtaatttacgcgcctaaatctcgcagaatacgcgccgcaattccatcgattgcagtgcgtaaaat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aatgataaggggttcttctatttatgatcgattttgtggaacaaaagtacgaaacaaagcggacttttcctcctaaaacactcgatgctgcgtgggggtaataccctaaaagcaaaggccttgcacatttgcggaaagtcctatgaagaaaacaggtctttgacccgattgggactttacggagattacgtagtgtaagagactctgtgatttgactgcatgcagtctgtttccatcatccgacggctctgccgtcgtatagcagttctcagaccaaaaacgcatggggcatggggcgagaaaacgtggcgcgggatttttttcgttttggttcgggaatgaaaaatttctcgcgcgtaaacgaagtaatttacgcgcctaaatctcgcagaatacgcgccgcaattccatcgattgcagtgcgtaaaat Predict ORF larger than 30AA ================================================ Protein_Len: 55 Strand: + Start: 31 End: 195 .............................. M L W N K S T K Q S G L F L L K H S M L R G G N T L K A K A L H I C G K S Y E E N R S L T R L G L Y G D Y V V ........................................................................................................................................................................................................................................... Protein_Len: 40 Strand: + Start: 220 End: 339 ........................................................................................................................................................................................................................... M Q S V S I I R R L C R R I A V L R P K T H G A W G E K T W R G I F F V L V R E ........................................................................................... Protein_Len: 32 Strand: + Start: 284 End: 379 ........................................................................................................................................................................................................................................................................................... M G H G A R K R G A G F F S F W F G N E K F L A R K R S N L R A ................................................... Protein_Len: 60 Strand: + Start: 216 End: 428 ....................................................................................................................................................................................................................... M H A V C F H H P T A L P S Y S S S Q T K N A W G M G R E N V A R D F F R F G S G M K N F S R V N E V I Y A P K S R R I .. Protein_Len: 33 Strand: - Start: 272 End: 370 ............................................................................................................................................................................................................................................................................... V L F A H P M P R S F T A R S K K R K P E P I F F K E R T F S T M ............................................................ Protein_Len: 53 Strand: - Start: 189 End: 347 ............................................................................................................................................................................................ T T Y S V R H N S Q M C D T E M M R R S Q R R I A T R L G F V C P A H P S F V H R P I K K T K T R S H F M ................................................................................... Protein_Len: 59 Strand: - Start: 109 End: 285 ............................................................................................................ F C L G Q V N A S L G I F F V P R Q G S Q S K V S I V Y H L L S Q S K V A H L R N G D D S P E A T T Y C N E S W F R M ................................................................................................................................................. Protein_Len: 36 Strand: - Start: 21 End: 128 .................... K H D I K H F L L V F C L P S K R R F C E I S R P P L V R F A F A K C M .............................................................................................................................................................................................................................................................................................................. Protein_Len: 60 Strand: - Start: 2 End: 211 . K T S C F Y S V F R V K G G L V S S A A H P Y Y G L L L P R A C K R F T R H L F C T K S G I P V K R L N R L T L S E T M ........................................................................................................................................................................................................................... aatgataaggggttcttctatttatgatcgattttgtggaacaaaagtacgaaacaaagcggacttttcctcctaaaacactcgatgctgcgtgggggtaataccctaaaagcaaaggccttgcacatttgcggaaagtcctatgaagaaaacaggtctttgacccgattgggactttacggagattacgtagtgtaagagactctgtgatttgactgcatgcagtctgtttccatcatccgacggctctgccgtcgtatagcagttctcagaccaaaaacgcatggggcatggggcgagaaaacgtggcgcgggatttttttcgttttggttcgggaatgaaaaatttctcgcgcgtaaacgaagtaatttacgcgcctaaatctcgcagaatacgcgccgcaattccatcgattgcagtgcgtaaaat 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================================================ aatgataaggggttcttctatttatgatcgattttgtggaacaaaagtacgaaacaaagcggacttttcctcctaaaacactcgatgctgcgtgggggtaataccctaaaagcaaaggccttgcacatttgcggaaagtcctatgaagaaaacaggtctttgacccgattgggactttacggagattacgtagtgtaagagactctgtgatttgactgcatgcagtctgtttccatcatccgacggctctgccgtcgtatagcagttctcagaccaaaaacgcatggggcatggggcgagaaaacgtggcgcgggatttttttcgttttggttcgggaatgaaaaatttctcgcgcgtaaacgaagtaatttacgcgcctaaatctcgcagaatacgcgccgcaattccatcgattgcagtgcgtaaaat Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 82 HP_score: -7.8 Tail_Score: -4.71426 Start: 153 End: 167 Full_Region: ccgtaaagtcccaat cgggtc aaa gacctg ttttcttcataggac ........................................................................................................................................................cgggtcaaagacctg....................................................................................................................................................................................................................................................................... TransTerm Strand: - Conf: 73 HP_score: -4.2 Tail_Score: -4.8048 Start: 281 End: 295 Full_Region: gccacgttttctcgc cccatg ccc catgcg tttttggtctgagaa ........................................................................................................................................................................................................................................................................................cccatgccccatgcg....................................................................................................................................... TransTerm Strand: - Conf: 51 HP_score: -3.3 Tail_Score: -3.5125 Start: 348 End: 383 Full_Region: gcgtattctgcgaga tttaggcgcgtaaat tacttc gtttacgcgcgagaa atttttcattcccga ...........................................................................................................................................................................................................................................................................................................................................................tttaggcgcgtaaattacttcgtttacgcgcgagaa............................................... Find igs database================================================ Query_seq: PG0153:PG0155|PG0153:PG0155:aspartyl-tRNA synthetase:riboflavin biosynthesis protein RibD:<-<-:177521..177950 430 aatgataaggggttcttctatttatgatcgattttgtggaacaaaagtacgaaacaaagcggacttttcctcctaaaacactcgatgctgcgtgggggtaataccctaaaagcaaaggccttgcacatttgcggaaagtcctatgaagaaaacaggtctttgacccgattgggactttacggagattacgtagtgtaagagactctgtgatttgactgcatgcagtctgtttccatcatccgacggctctgccgtcgtatagcagttctcagaccaaaaacgcatggggcatggggcgagaaaacgtggcgcgggatttttttcgttttggttcgggaatgaaaaatttctcgcgcgtaaacgaagtaatttacgcgcctaaatctcgcagaatacgcgccgcaattccatcgattgcagtgcgtaaaat Intra-Species Hit: Count: 1 Min: 1 Max: 430 Len: 430 Subject: NC_002950_PG0153_PG0155|aspartyl-tRNA synthetase:riboflavin biosynthesis protein RibD|NEGATIVE:NEGATIVE|[177521,177950]|430 HSP 1 e-value: 0.0 bit: 811.0 Len: 430 Query Start:1 Query End:430 Subject Strand: POSITIVE Subject Start: 1 Subject End: 430 aatgataaggggttcttctatttatgatcgattttgtggaacaaaagtacgaaacaaagcggacttttcctcctaaaacactcgatgctgcgtgggggtaataccctaaaagcaaaggccttgcacatttgcggaaagtcctatgaagaaaacaggtctttgacccgattgggactttacggagattacgtagtgtaagagactctgtgatttgactgcatgcagtctgtttccatcatccgacggctctgccgtcgtatagcagttctcagaccaaaaacgcatggggcatggggcgagaaaacgtggcgcgggannnnnnncgttttggttcgggaatgaaaaatttctcgcgcgtaaacgaagtaatttacgcgcctaaatctcgcagaatacgcgccgcaattccatcgattgcagtgcgtaaaat aatgataaggggttcttctatttatgatcgattttgtggaacaaaagtacgaaacaaagcggacttttcctcctaaaacactcgatgctgcgtgggggtaataccctaaaagcaaaggccttgcacatttgcggaaagtcctatgaagaaaacaggtctttgacccgattgggactttacggagattacgtagtgtaagagactctgtgatttgactgcatgcagtctgtttccatcatccgacggctctgccgtcgtatagcagttctcagaccaaaaacgcatggggcatggggcgagaaaacgtggcgcgggatttttttcgttttggttcgggaatgaaaaatttctcgcgcgtaaacgaagtaatttacgcgcctaaatctcgcagaatacgcgccgcaattccatcgattgcagtgcgtaaaat Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAUGAUAAGGGGUUCUUCUAUUUAUGAUCGAUUUUGUGGAACAAAAGUACGAAACAAAGCGGACUUUUCCUCCUAAAACACUCGAUGCUGCGUGGGGGUAAUACCCUAAAAGCAAAGGCCUUGCACAUUUGCGGAAAGUCCUAUGAAGAAAACAGGUCUUUGACCCGAUUGGGACUUUACGGAGAUUACGUAGUGUAAGAGACUCUGUGAUUUGACUGCAUGCAGUCUGUUUCCAUCAUCCGACGGCUCUGCCGUCGUAUAGCAGUUCUCAGACCAAAAACGCAUGGGGCAUGGGGCGAGAAAACGUGGCGCGGGAUUUUUUUCGUUUUGGUUCGGGAAUGAAAAAUUUCUCGCGCGUAAACGAAGUAAUUUACGCGCCUAAAUCUCGCAGAAUACGCGCCGCAAUUCCAUCGAUUGCAGUGCGUAAAAU ..((.(((((................((((((((((.(((..((((((.((........)).))))))..))))))))...)))))(((...(((((......)))))..))).....)))))))..((((((((..((((((((.........(((((..((...(((.(..((.((((((((.((((.....))))....))))))))...(((((....))))).))..).)))...(((((((...))))))).........))..))))).......))))))))...(((((......(((.((((((((..(((((((((((......)))))))))))..))))))))....)))..(((...))).)))))...)).)))))).(((((((.((((((.....)))))).))))))).... (-143.49) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUUUUACGCACUGCAAUCGAUGGAAUUGCGGCGCGUAUUCUGCGAGAUUUAGGCGCGUAAAUUACUUCGUUUACGCGCGAGAAAUUUUUCAUUCCCGAACCAAAACGAAAAAAAUCCCGCGCCACGUUUUCUCGCCCCAUGCCCCAUGCGUUUUUGGUCUGAGAACUGCUAUACGACGGCAGAGCCGUCGGAUGAUGGAAACAGACUGCAUGCAGUCAAAUCACAGAGUCUCUUACACUACGUAAUCUCCGUAAAGUCCCAAUCGGGUCAAAGACCUGUUUUCUUCAUAGGACUUUCCGCAAAUGUGCAAGGCCUUUGCUUUUAGGGUAUUACCCCCACGCAGCAUCGAGUGUUUUAGGAGGAAAAGUCCGCUUUGUUUCGUACUUUUGUUCCACAAAAUCGAUCAUAAAUAGAAGAACCCCUUAUCAUU ....(((((.((((((((....).))))))).)))))....(((.(((((..((((((((((......))))))))))..(((....))).....................))))).))).....((((((..(((..((((.....))))....)))..)))))).......(((((((...)))))))(((((.((.....(((((....))))).....((((.((((.......((((.......))))..(.(((....))).)..)))))))).((((((..(((.((((.(((....))).))))))).(((.....(((.....)))....)))..(((((.(((....((((.((((((.((........)).)))))).)))))))...)))))........)))))).)).)))))... (-123.70) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 992 130 81 221 172 NC_002950:PG0153|5end_aspartyl-tRNA_synthetase_177430..177660_NEGATIVE 682 350 301 141 91 NC_002950:PG0132|5end_hypothetical_protein_152879..153109_POSITIVE 672 349 301 153 104 NC_002950:PG2063|5end_hypothetical_protein_2160596..2160826_NEGATIVE 528 357 312 50 6 NC_002950:PG0080|5end_hypothetical_protein_93832..94062_NEGATIVE 481 334 291 88 46 NC_002950:PG0007|5end_hypothetical_protein_6913..7143_NEGATIVE 463 400 351 130 81 NC_002950:PG1617|5end_hypothetical_protein_1697755..1697985_NEGATIVE 445 340 297 72 30 NC_002950:PG1980|5end_hypothetical_protein_2067930..2068160_NEGATIVE 444 340 297 50 9 NC_002950:PG1799|5end_hypothetical_protein_1894499..1894729_POSITIVE 431 330 284 217 169 NC_002950:PG0638|5end_tetraacyldisaccharide_4'-kinase_691183..691413_NEGATIVE 415 259 218 123 64 NC_002950:PG1255|5end_recombination_protein_RecR_1332751..1332981_NEGATIVE 406 257 216 215 172 NC_002950:PG1003|5end_hypothetical_protein_1059232..1059462_POSITIVE 399 255 211 228 185 NC_002950:PG0888|5end_hypothetical_protein_949910..950140_POSITIVE 375 338 301 163 126 NC_002950:PG0081|5end_hypothetical_protein_93805..94035_POSITIVE 374 290 246 55 6 NC_002950:PG0228|5end_DdaH_family_protein_264950..265180_NEGATIVE 372 420 373 131 86 NC_002950:PG0438|5end_hypothetical_protein_476884..477114_POSITIVE 367 282 241 69 29 NC_002950:PG0441|5end_hypothetical_protein_478734..478964_POSITIVE 367 300 251 206 142 NC_002950:PG0113|5end_hypothetical_protein_135925..136155_POSITIVE 364 316 278 180 129 NC_002950:PG2159|5end_protoporphyrinogen_oxidase_2264397..2264627_POSITIVE 364 270 221 183 138 NC_002950:PG1069|5end_alcohol_dehydrogenase,_zinc-containing,_putative_1135499..1135729_POSITIVE 360 327 281 136 85 NC_002950:PG2225|5end_hypothetical_protein_2339440..2339670_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 417 337 291 150 107 NC_002950:PG0401|3end_hypothetical_protein_437765..437915_NEGATIVE 415 259 218 126 67 NC_002950:PG1256|3end_ribonuclease,_Rne/Rng_family_1332748..1332898_NEGATIVE 414 330 284 149 95 NC_002950:PG0028|3end_2C-methyl-D-erythritol_2,4-cyclodiphosphate_synthase_34431..34581_POSITIVE 412 365 321 143 99 NC_002950:PG1718|3end_hypothetical_protein_1806532..1806682_NEGATIVE 406 257 216 140 97 NC_002950:PG1002|3end_hypothetical_protein_1059237..1059387_POSITIVE 404 314 282 142 107 NC_002950:PG0932|3end_DNA_polymerase_III,_delta_prime_subunit,_putative_989833..989983_POSITIVE 403 413 374 118 79 NC_002950:PG0732|3end_hypothetical_protein_783018..783168_POSITIVE 399 257 212 85 37 NC_002950:PG0086|3end_ATP-dependent_RNA_helicase,_DEAD/DEAH_box_family_100545..100695_NEGATIVE 394 379 333 49 2 NC_002950:PG0542|3end_hypothetical_protein_595377..595527_NEGATIVE 376 421 384 36 6 NC_002950:PG1943|3end_hypothetical_protein_2028974..2029124_NEGATIVE 370 316 290 149 124 NC_002950:PG2212|3end_hypothetical_protein_2324483..2324633_NEGATIVE 367 282 241 65 25 NC_002950:PG0439|3end_hypothetical_protein_478810..478960_POSITIVE 364 315 278 150 105 NC_002950:PG1097|3end_Mur_ligase_domain_protein/alanine_racemase_1165508..1165658_POSITIVE 364 270 221 141 96 NC_002950:PG1068|3end_hypothetical_protein_1135537..1135687_POSITIVE 360 327 281 116 65 NC_002950:PG2224|3end_hypothetical_protein_2339500..2339650_POSITIVE 359 250 205 134 84 NC_002950:PG2001|3end_signal_peptidase_I_2089458..2089608_NEGATIVE 359 317 274 117 72 NC_002950:PG1366|3end_UDP-N-acetylglucosamine_1-carboxyvinyltransferase_1446076..1446226_NEGATIVE 358 257 214 130 89 NC_002950:PG0443|3end_hemagglutinin-related_protein_483147..483297_POSITIVE 358 310 262 78 18 NC_002950:PG0277|3end_ISPg2,_transposase_310066..310216_POSITIVE 357 314 280 78 42 NC_002950:PG0725|3end_hydrolase,_haloacid_dehalogenase-like_family_777966..778116_POSITIVE