Origin IGS: taaaaaaaaggatttttttttcatattatttaaaattagtattgttggaggttgtctctcgtgagagaggcggcctctttttttctgcctgagtactacgatcaatgaggaggggtcttctgcgtagcaaccgttcgtgtatcagctatcaaagagtcctcgttgcaaacaaccggaaaaaggtaaaaaaaagttatctttgccgtttgaaaaaaagaagaag .........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 cttcttctttttttcaaacggcaaagataacttttttttacctttttccggttgtttgcaacgaggactctttgatagctgatacacgaacggttgctacgcagaagacccctcctcattgatcgtagtactcaggcagaaaaaaagaggccgcctctctcacgagagacaacctccaacaatactaattttaaataatatgaaaaaaaaatcctttttttta Mask Tandem Repeat Region ================================================ taaaaaaaaggatttttttttcatattatttaaaattagtattgttggaggttgtctctcgtgagagaggcggcctctttttttctgcctgagtactacgatcaatgaggaggggtcttctgcgtagcaaccgttcgtgtatcagctatcaaagagtcctcgttgcaaacaaccggaaaaaggtaaaaaaaagttatctttgccgtttgaaaaaaagaagaag Find is-nt database================================================ Query_seq: TF0428:TF0429|TF0428:TF0429:methylmalonyl-CoA mutase, beta subunit:ABC transporter, ATP-binding protein:->->:450094..450316 223 taaaaaaaaggatttttttttcatattatttaaaattagtattgttggaggttgtctctcgtgagagaggcggcctctttttttctgcctgagtactacgatcaatgaggaggggtcttctgcgtagcaaccgttcgtgtatcagctatcaaagagtcctcgttgcaaacaaccggaaaaaggtaaaaaaaagttatctttgccgtttgaaaaaaagaagaag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF0428:TF0429|TF0428:TF0429:methylmalonyl-CoA mutase, beta subunit:ABC transporter, ATP-binding protein:->->:450094..450316 223 taaaaaaaaggatttttttttcatattatttaaaattagtattgttggaggttgtctctcgtgagagaggcggcctctttttttctgcctgagtactacgatcaatgaggaggggtcttctgcgtagcaaccgttcgtgtatcagctatcaaagagtcctcgttgcaaacaaccggaaaaaggtaaaaaaaagttatctttgccgtttgaaaaaaagaagaag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF0428:TF0429|TF0428:TF0429:methylmalonyl-CoA mutase, beta subunit:ABC transporter, ATP-binding protein:->->:450094..450316 223 taaaaaaaaggatttttttttcatattatttaaaattagtattgttggaggttgtctctcgtgagagaggcggcctctttttttctgcctgagtactacgatcaatgaggaggggtcttctgcgtagcaaccgttcgtgtatcagctatcaaagagtcctcgttgcaaacaaccggaaaaaggtaaaaaaaagttatctttgccgtttgaaaaaaagaagaag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 taaaaaaaaggatttttttttcatattatttaaaattagtattgttggaggttgtctctcgtgagagaggcggcctctttttttctgcctgagtactacgatcaatgaggaggggtcttctgcgtagcaaccgttcgtgtatcagctatcaaagagtcctcgttgcaaacaaccggaaaaaggtaaaaaaaagttatctttgccgtttgaaaaaaagaagaag Predict ORF larger than 30AA ================================================ Protein_Len: 39 Strand: + Start: 105 End: 221 ........................................................................................................ M R R G L L R S N R S C I S Y Q R V L V A N N R K K V K K S Y L C R L K K R R .. Protein_Len: 31 Strand: - Start: 105 End: 197 ........................................................................................................ H P P T K Q T A V T R T D A I L S D E N C V V P F L Y F F T M .......................... Protein_Len: 39 Strand: - Start: 29 End: 145 ............................ K F N T N N S T T E R S L P P R K K E A Q T S R D I L L P R R R L L R E H I M .............................................................................. Protein_Len: 35 Strand: - Start: 1 End: 105 L F F S K K K M N N L I L I T P P Q R E H S L R G R K K Q R L V V I M ...................................................................................................................... taaaaaaaaggatttttttttcatattatttaaaattagtattgttggaggttgtctctcgtgagagaggcggcctctttttttctgcctgagtactacgatcaatgaggaggggtcttctgcgtagcaaccgttcgtgtatcagctatcaaagagtcctcgttgcaaacaaccggaaaaaggtaaaaaaaagttatctttgccgtttgaaaaaaagaagaag 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================================================ taaaaaaaaggatttttttttcatattatttaaaattagtattgttggaggttgtctctcgtgagagaggcggcctctttttttctgcctgagtactacgatcaatgaggaggggtcttctgcgtagcaaccgttcgtgtatcagctatcaaagagtcctcgttgcaaacaaccggaaaaaggtaaaaaaaagttatctttgccgtttgaaaaaaagaagaag Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 100 HP_score: -12.9 Tail_Score: -5.64274 Start: 48 End: 77 Full_Region: AAATTAGTATTGTTG GAGGTTGTCTCTC GTGA GAGAGGCGGCCTC TTTTTTTCTGCCTGA ...............................................GAGGTTGTCTCTCGTGAGAGAGGCGGCCTC.................................................................................................................................................. Find igs database================================================ Query_seq: TF0428:TF0429|TF0428:TF0429:methylmalonyl-CoA mutase, beta subunit:ABC transporter, ATP-binding protein:->->:450094..450316 223 taaaaaaaaggatttttttttcatattatttaaaattagtattgttggaggttgtctctcgtgagagaggcggcctctttttttctgcctgagtactacgatcaatgaggaggggtcttctgcgtagcaaccgttcgtgtatcagctatcaaagagtcctcgttgcaaacaaccggaaaaaggtaaaaaaaagttatctttgccgtttgaaaaaaagaagaag Intra-Species Hit: Count: 1 Min: 22 Max: 209 Len: 188 Subject: tfor_TF0428_TF0429|methylmalonyl-CoA mutase, beta subunit:ABC transporter, ATP-binding protein|POSITIVE:POSITIVE|[450094,450316]|223 HSP 1 e-value: 1.0E-75 bit: 283.0 Len: 188 Query Start:22 Query End:209 Subject Strand: POSITIVE Subject Start: 22 Subject End: 209 .....................catattatttaaaattagtattgttggaggttgtctctcgtgagagaggcggcctcnnnnnnnctgcctgagtactacgatcaatgaggaggggtcttctgcgtagcaaccgttcgtgtatcagctatcaaagagtcctcgttgcaaacaaccggaaaaaggtnnnnnnnngttatctttgccgtttg.............. .....................catattatttaaaattagtattgttggaggttgtctctcgtgagagaggcggcctctttttttctgcctgagtactacgatcaatgaggaggggtcttctgcgtagcaaccgttcgtgtatcagctatcaaagagtcctcgttgcaaacaaccggaaaaaggtaaaaaaaagttatctttgccgtttg.............. Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CAUAUUAUUUAAAAUUAGUAUUGUUGGAGGUUGUCUCUCGUGAGAGAGGCGGCCUCUUUUUUUCUGCCUGAGUACUACGAUCAAUGAGGAGGGGUCUUCUGCGUAGCAACCGUUCGUGUAUCAGCUAUCAAAGAGUCCUCGUUGCAAACAACCGGAAAAAGGUAAAAAAAAGUUAUCUUUGCCGUUUG ...............(((((((((.((((((((((((((....))))))))))))))........))...)))))))........((.(((((.((((.((.(((((................))))))))))).))))).)).....(((.(((..((((((((.......)))))))).))).))) (-55.79) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CAAACGGCAAAGAUAACUUUUUUUUACCUUUUUCCGGUUGUUUGCAACGAGGACUCUUUGAUAGCUGAUACACGAACGGUUGCUACGCAGAAGACCCCUCCUCAUUGAUCGUAGUACUCAGGCAGAAAAAAAGAGGCCGCCUCUCUCACGAGAGACAACCUCCAACAAUACUAAUUUUAAAUAAUAUG ((((((((...((...................))..))))))))....((((..(((((..((((....((.(....))).))))....)))))..))))....((((...(((((.((.....))......((((..(.(((((....))))).)..))))......)))))...))))........ (-34.21) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 387 125 88 77 36 tfor:TF0828|5end_hypothetical_protein_887090..887320_POSITIVE 378 112 86 175 144 tfor:TF0050|5end_hypothetical_protein_55059..55289_POSITIVE 372 89 44 54 1 tfor:TF3026|5end_conserved_hypothetical_protein_3249137..3249367_POSITIVE 364 55 17 54 8 tfor:TF1003|5end_conserved_hypothetical_protein;_possible_secreted_glycosylhydrolase_1058177..1058407_POSITIVE 362 125 88 77 35 tfor:TF2746|5end_hypothetical_protein_2927996..2928226_POSITIVE 357 63 26 152 117 tfor:TF0198|5end_transposase_related_sequence_221054..221284_POSITIVE 347 118 77 49 2 tfor:TF2308|5end_conserved_hypothetical_protein_2466932..2467162_POSITIVE 347 83 46 36 2 tfor:TF2047|5end_hypothetical_protein_2210057..2210287_POSITIVE 343 89 42 179 132 tfor:TF2692|5end_3-deoxy-7-phosphoheptulonate_synthase_2867330..2867560_POSITIVE 339 63 26 171 122 tfor:TF1027|5end_hypothetical_protein_1085641..1085871_POSITIVE 338 69 26 153 108 tfor:TF0392|5end_hypothetical_protein_412335..412565_POSITIVE 338 69 26 102 57 tfor:TF0393|5end_conserved_hypothetical_protein_412284..412514_POSITIVE 333 70 22 62 15 tfor:TF3136|5end_Na+-translocating_NADH-quinone_reductase,_subunit_F_3369994..3370224_POSITIVE 333 125 86 84 42 tfor:TF1842|5end_hypothetical_protein_1992571..1992801_POSITIVE 333 138 91 89 51 tfor:TF0122|5end_hypothetical_protein_133162..133392_POSITIVE 329 66 26 170 121 tfor:TF2790|5end_prismane_protein,_hybrid-cluster_protein_2973397..2973627_POSITIVE 328 130 90 193 147 tfor:TF1011|5end_cell_division_protein;_rod_shape-determining_protein_1066647..1066877_POSITIVE 327 55 18 139 88 tfor:TF2754|5end_hypothetical_protein_2940446..2940676_POSITIVE 327 79 31 146 106 tfor:TF0224|5end_N-acetylglucosamine-6-phosphate_deacetylase_250268..250498_POSITIVE 326 70 28 65 16 tfor:TF2026|5end_hypothetical_protein_2182659..2182889_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 388 97 53 84 31 tfor:TF0369|3end_hypothetical_protein_386186..386336_POSITIVE 387 80 31 86 34 tfor:TF2768|3end_ferredoxin_oxidoreductase,_beta_subunit_2955169..2955319_POSITIVE 367 69 21 106 46 tfor:TF1942|3end_conserved_hypothetical_protein_2090646..2090796_POSITIVE 366 80 36 48 8 tfor:TF2046|3end_polyribonucleotide_nucleotidyltransferase_2210152..2210302_POSITIVE 357 63 26 55 20 tfor:TF0196|3end_conserved_hypothetical_protein_221037..221187_POSITIVE 351 59 27 140 109 tfor:TF2047|3end_hypothetical_protein_2210298..2210448_POSITIVE 342 56 26 43 14 tfor:TF0428|3end_methylmalonyl-CoA_mutase,_beta_subunit_450033..450183_POSITIVE 339 63 26 89 40 tfor:TF1026|3end_beta-N-acetylglucosaminidase;_beta_lactamase_1085639..1085789_POSITIVE 333 70 22 62 15 tfor:TF3135|3end_hypothetical_protein_3370074..3370224_POSITIVE 333 138 91 64 26 tfor:TF0121|3end_hypothetical_protein_133217..133367_POSITIVE 329 66 26 58 9 tfor:TF2789|3end_enoyl-[acyl-carrier-protein]_reductase_2973365..2973515_POSITIVE 327 55 18 61 10 tfor:TF2753|3end_zinc_protease_2940448..2940598_POSITIVE 327 79 31 108 68 tfor:TF0223|3end_conserved_hypothetical_protein_250310..250460_POSITIVE 325 139 94 134 75 tfor:TF2221|3end_CTn_excision_protein_2394229..2394379_POSITIVE 324 116 71 53 1 tfor:TF1489|3end_argininosuccinate_lyase_1590318..1590468_POSITIVE 319 55 20 149 115 tfor:TF2458|3end_ribosome-binding_factor_A_2635645..2635795_POSITIVE 318 67 25 81 45 tfor:TF2009|3end_octaprenyl-diphosphate_synthase_ispB_2163245..2163395_POSITIVE 317 61 26 58 11 tfor:TF2490|3end_4-hydroxyphenylacetate-3-hydroxylase/4-hydroxybut_yryl_dehydratase_2666755..2666905_POSITIVE 317 80 37 68 25 tfor:TF1275|3end_transcription-repair_coupling_factor_1361290..1361440_POSITIVE 315 140 91 149 94 tfor:TF2133|3end_aspartate-semialdehyde_dehydrogenase_2311362..2311512_POSITIVE