Origin IGS: ttcgccatatttttgttttgtactgtctattggtgttgcaccgtgtctcatttgtccagtatctcggtatatacgcgaggggctggagggttggcgagctgcgtgcggtacaaataaggtacaagaatgagcgaaagaaaggctccgaatgatgcctaacgaacagaaagggcaaaaagaaaggcgctcataatgaacgccttttcgatatttggtgatatatgattatcggttgtaatcagaaa .........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 tttctgattacaaccgataatcatatatcaccaaatatcgaaaaggcgttcattatgagcgcctttctttttgccctttctgttcgttaggcatcattcggagcctttctttcgctcattcttgtaccttatttgtaccgcacgcagctcgccaaccctccagcccctcgcgtatataccgagatactggacaaatgagacacggtgcaacaccaatagacagtacaaaacaaaaatatggcgaa Mask Tandem Repeat Region ================================================ ttcgccatatttttgttttgtactgtctattggtgttgcaccgtgtctcatttgtccagtatctcggtatatacgcgaggggctggagggttggcgagctgcgtgcggtacaaataaggtacaagaatgagcgaaagaaaggctccgaatgatgcctaacgaacagaaagggcaaaaagaaaggcgctcataatgaacgccttttcgatatttggtgatatatgattatcggttgtaatcagaaa Find is-nt database================================================ Query_seq: PG0875:PG0876|PG0875:PG0876:mobilizable transposon, tnpA protein:tRNA modification GTPase:<-<-:939095..939339 245 ttcgccatatttttgttttgtactgtctattggtgttgcaccgtgtctcatttgtccagtatctcggtatatacgcgaggggctggagggttggcgagctgcgtgcggtacaaataaggtacaagaatgagcgaaagaaaggctccgaatgatgcctaacgaacagaaagggcaaaaagaaaggcgctcataatgaacgccttttcgatatttggtgatatatgattatcggttgtaatcagaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG0875:PG0876|PG0875:PG0876:mobilizable transposon, tnpA protein:tRNA modification GTPase:<-<-:939095..939339 245 ttcgccatatttttgttttgtactgtctattggtgttgcaccgtgtctcatttgtccagtatctcggtatatacgcgaggggctggagggttggcgagctgcgtgcggtacaaataaggtacaagaatgagcgaaagaaaggctccgaatgatgcctaacgaacagaaagggcaaaaagaaaggcgctcataatgaacgccttttcgatatttggtgatatatgattatcggttgtaatcagaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG0875:PG0876|PG0875:PG0876:mobilizable transposon, tnpA protein:tRNA modification GTPase:<-<-:939095..939339 245 ttcgccatatttttgttttgtactgtctattggtgttgcaccgtgtctcatttgtccagtatctcggtatatacgcgaggggctggagggttggcgagctgcgtgcggtacaaataaggtacaagaatgagcgaaagaaaggctccgaatgatgcctaacgaacagaaagggcaaaaagaaaggcgctcataatgaacgccttttcgatatttggtgatatatgattatcggttgtaatcagaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ttcgccatatttttgttttgtactgtctattggtgttgcaccgtgtctcatttgtccagtatctcggtatatacgcgaggggctggagggttggcgagctgcgtgcggtacaaataaggtacaagaatgagcgaaagaaaggctccgaatgatgcctaacgaacagaaagggcaaaaagaaaggcgctcataatgaacgccttttcgatatttggtgatatatgattatcggttgtaatcagaaa Predict ORF larger than 30AA ================================================ Protein_Len: 36 Strand: + Start: 7 End: 114 ...... M F L F C T V Y W C C T V S H L S S I S V Y T R G A G G L A S C V R Y K ................................................................................................................................... Protein_Len: 35 Strand: + Start: 23 End: 127 ...................... M S I G V A P C L I C P V S R Y I R E G L E G W R A A C G T N K V Q E ...................................................................................................................... Protein_Len: 47 Strand: + Start: 9 End: 149 ........ M F V L Y C L L V L H R V S F V Q Y L G I Y A R G W R V G E L R A V Q I R Y K N E R K K G S E ................................................................................................ Protein_Len: 58 Strand: - Start: 2 End: 175 . R W I K T K Y Q R N T N C R T E N T W Y R P I Y A L P Q L T P S S R A T C I L Y L F S R F F P E S H H R V F L F P M ...................................................................... Protein_Len: 60 Strand: - Start: 1 End: 219 G H R M Q G T D R Y I R S P S S P Q R A A H P V F L T C S H A F S L S R I I G L S C F P C F S L R E Y H V G K R Y K T M .......................... ttcgccatatttttgttttgtactgtctattggtgttgcaccgtgtctcatttgtccagtatctcggtatatacgcgaggggctggagggttggcgagctgcgtgcggtacaaataaggtacaagaatgagcgaaagaaaggctccgaatgatgcctaacgaacagaaagggcaaaaagaaaggcgctcataatgaacgccttttcgatatttggtgatatatgattatcggttgtaatcagaaa 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================================================ ttcgccatatttttgttttgtactgtctattggtgttgcaccgtgtctcatttgtccagtatctcggtatatacgcgaggggctggagggttggcgagctgcgtgcggtacaaataaggtacaagaatgagcgaaagaaaggctccgaatgatgcctaacgaacagaaagggcaaaaagaaaggcgctcataatgaacgccttttcgatatttggtgatatatgattatcggttgtaatcagaaa Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 100 HP_score: -11.0 Tail_Score: -4.88293 Start: 183 End: 201 Full_Region: accaaatatcgaaaa ggcgttca tta tgagcgcc tttctttttgccctt ......................................................................................................................................................................................ggcgttcattatgagcgcc............................................ Find igs database================================================ Query_seq: PG0875:PG0876|PG0875:PG0876:mobilizable transposon, tnpA protein:tRNA modification GTPase:<-<-:939095..939339 245 ttcgccatatttttgttttgtactgtctattggtgttgcaccgtgtctcatttgtccagtatctcggtatatacgcgaggggctggagggttggcgagctgcgtgcggtacaaataaggtacaagaatgagcgaaagaaaggctccgaatgatgcctaacgaacagaaagggcaaaaagaaaggcgctcataatgaacgccttttcgatatttggtgatatatgattatcggttgtaatcagaaa Intra-Species Hit: Count: 1 Min: 1 Max: 245 Len: 245 Subject: NC_002950_PG0875_PG0876|mobilizable transposon, tnpA protein:tRNA modification GTPase|NEGATIVE:NEGATIVE|[939095,939339]|245 HSP 1 e-value: 1.0E-136 bit: 486.0 Len: 245 Query Start:1 Query End:245 Subject Strand: POSITIVE Subject Start: 1 Subject End: 245 ttcgccatatttttgttttgtactgtctattggtgttgcaccgtgtctcatttgtccagtatctcggtatatacgcgaggggctggagggttggcgagctgcgtgcggtacaaataaggtacaagaatgagcgaaagaaaggctccgaatgatgcctaacgaacagaaagggcaaaaagaaaggcgctcataatgaacgccttttcgatatttggtgatatatgattatcggttgtaatcagaaa ttcgccatatttttgttttgtactgtctattggtgttgcaccgtgtctcatttgtccagtatctcggtatatacgcgaggggctggagggttggcgagctgcgtgcggtacaaataaggtacaagaatgagcgaaagaaaggctccgaatgatgcctaacgaacagaaagggcaaaaagaaaggcgctcataatgaacgccttttcgatatttggtgatatatgattatcggttgtaatcagaaa Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUCGCCAUAUUUUUGUUUUGUACUGUCUAUUGGUGUUGCACCGUGUCUCAUUUGUCCAGUAUCUCGGUAUAUACGCGAGGGGCUGGAGGGUUGGCGAGCUGCGUGCGGUACAAAUAAGGUACAAGAAUGAGCGAAAGAAAGGCUCCGAAUGAUGCCUAACGAACAGAAAGGGCAAAAAGAAAGGCGCUCAUAAUGAACGCCUUUUCGAUAUUUGGUGAUAUAUGAUUAUCGGUUGUAAUCAGAAA ((((((((.......(((((((((...((((.(((..((((((..(((((.((.((((((..((((((....)).))))..)))))).)).))).))..)).))))..))).)))).)))))))))))).))))).......(.(((((((.(((((............)))))....((((((((.((.....)).))))))))...))))))).).....(((((((.....))))))).... (-76.21) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUCUGAUUACAACCGAUAAUCAUAUAUCACCAAAUAUCGAAAAGGCGUUCAUUAUGAGCGCCUUUCUUUUUGCCCUUUCUGUUCGUUAGGCAUCAUUCGGAGCCUUUCUUUCGCUCAUUCUUGUACCUUAUUUGUACCGCACGCAGCUCGCCAACCCUCCAGCCCCUCGCGUAUAUACCGAGAUACUGGACAAAUGAGACACGGUGCAACACCAAUAGACAGUACAAAACAAAAAUAUGGCGAA ....(((((((....).))))))....((.(((........((((((((((.....))))))))))..(((((..((.((((((.((...(((((.....((((.........))))..........((((((((....((.....))..........(((((...((((.((....))))))...)))))))))))))....)))))...)).)))))).))..)))))........))).)). (-62.90) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 1147 110 61 201 152 NC_002950:PG0875|5end_mobilizable_transposon,_tnpA_protein_939004..939234_NEGATIVE 450 107 61 226 172 NC_002950:PG1875|5end_hemolysin_1970621..1970851_NEGATIVE 439 110 65 218 156 NC_002950:PG0305|5end_electron_transport_complex,_RnfABCDGE_type,_D_subunit_340906..341136_POSITIVE 427 110 61 71 12 NC_002950:PG0522|5end_tRNA_delta(2)-isopentenylpyrophosphate_transferase_566901..567131_NEGATIVE 425 109 74 55 10 NC_002950:PG0585|5end_YqeY_family_protein_643272..643502_POSITIVE 411 108 80 27 4 NC_002950:PG1552|5end_TonB-dependent_receptor_HmuR_1628881..1629111_POSITIVE 410 109 63 231 168 NC_002950:PG0986|5end_hypothetical_protein_1047426..1047656_POSITIVE 405 106 63 210 159 NC_002950:PG0364|5end_hypothetical_protein_399615..399845_NEGATIVE 400 107 75 73 24 NC_002950:PG2102|5end_immunoreactive_61_kDa_antigen_PG91_2213046..2213276_NEGATIVE 385 110 64 58 1 NC_002950:PG1285|5end_glucosamine-6-phosphate_deaminase_1362894..1363124_POSITIVE 380 99 53 207 153 NC_002950:PG0413|5end_hypothetical_protein_451781..452011_NEGATIVE 379 106 62 82 38 NC_002950:PG0884|5end_hypothetical_protein_946479..946709_POSITIVE 376 110 61 78 28 NC_002950:PG0228|5end_DdaH_family_protein_264950..265180_NEGATIVE 372 108 62 224 169 NC_002950:PG0594|5end_RNA_polymerase_sigma-70_factor_652048..652278_POSITIVE 369 106 62 86 16 NC_002950:PG0524|5end_hypothetical_protein_568599..568829_POSITIVE 367 80 31 164 123 NC_002950:PG1300|5end_hypothetical_protein_1379069..1379299_NEGATIVE 365 108 62 191 146 NC_002950:PG1999|5end_hypothetical_protein_2088821..2089051_NEGATIVE 365 109 61 183 119 NC_002950:PG0560|5end_hypothetical_protein_617423..617653_POSITIVE 364 134 94 54 4 NC_002950:PG0751|5end_porT_protein_797578..797808_NEGATIVE 361 110 75 50 15 NC_002950:PG0328|5end_imidazolonepropionase_363426..363656_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 427 110 61 74 15 NC_002950:PG0523|3end_inositol-5-monophosphate_dehydrogenase_566898..567048_NEGATIVE 383 110 63 51 1 NC_002950:PG0752|3end_uracil_phosphoribosyltransferase_798397..798547_POSITIVE 379 106 62 85 41 NC_002950:PG0883|3end_hypothetical_protein_946562..946712_POSITIVE 369 110 61 109 56 NC_002950:PG1808|3end_guanosine-3',5'-bis(diphosphate)_3'-pyrophosphohydrolase_1902955..1903105_NEGATIVE 368 105 62 134 82 NC_002950:PG1364|3end_1-deoxy-D-xylulose_5-phosphate_reductoisomerase_1444388..1444538_NEGATIVE 367 80 31 127 86 NC_002950:PG1301|3end_hypothetical_protein_1379106..1379256_NEGATIVE 363 108 61 110 51 NC_002950:PG1943|3end_hypothetical_protein_2028974..2029124_NEGATIVE 360 120 80 72 34 NC_002950:PG2028|3end_ebsC_protein_2126616..2126766_POSITIVE 360 108 61 103 35 NC_002950:PG0412|3end_DNA_mismatch_repair_protein_MutL_449584..449734_NEGATIVE 359 107 62 150 88 NC_002950:PG1351|3end_hypothetical_protein_1432238..1432388_NEGATIVE 358 108 64 130 84 NC_002950:PG1040|3end_transcriptional_regulator,_putative_1107485..1107635_NEGATIVE 354 108 64 139 82 NC_002950:PG0684|3end_ABC_transporter,_permease_protein,_putative_740103..740253_POSITIVE 353 120 74 66 20 NC_002950:PG0399|3end_lipoprotein,_putative_435707..435857_NEGATIVE 347 110 63 118 47 NC_002950:PG0223|3end_exonuclease_257119..257269_NEGATIVE 346 100 56 149 109 NC_002950:PG0877|3end_hypothetical_protein_940838..940988_NEGATIVE 346 110 74 138 99 NC_002950:PG0534|3end_hypothetical_protein_585805..585955_POSITIVE 345 103 64 149 107 NC_002950:PG0574|3end_hypothetical_protein_629571..629721_POSITIVE 344 108 61 85 39 NC_002950:PG1213|3end_ribonuclease_H_1293163..1293313_POSITIVE 343 108 64 65 4 NC_002950:PG1777|3end_hypothetical_protein_1867105..1867255_POSITIVE 341 111 75 128 80 NC_002950:PG1648|3end_RelA/SpoT_family_protein_1730082..1730232_POSITIVE