Origin IGS: gaagtgaatagtgagttgtgctgaaaacccaattcttccactctccttgccaatagacatggcaaggagagtgagggtataatacaaggaacccccgaaagccacggctttcggggggttgcttttatcagagcttccgccggtctcttttcctcgtcggaatgggtggccgggaaaaatgc .........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 gcatttttcccggccacccattccgacgaggaaaagagaccggcggaagctctgataaaagcaaccccccgaaagccgtggctttcgggggttccttgtattataccctcactctccttgccatgtctattggcaaggagagtggaagaattgggttttcagcacaactcactattcacttc Mask Tandem Repeat Region ================================================ gaagtgaatagtgagttgtgctgaaaacccaattcttccactctccttgccaatagacatggcaaggagagtgagggtataatacaaggaacccccgaaagccacggctttcggggggttgcttttatcagagcttccgccggtctcttttcctcgtcggaatgggtggccgggaaaaatgc Find is-nt database================================================ Query_seq: PG0045:PG0046|PG0045:PG0046:heat shock protein 90:phosphatidate cytidylyltransferase:-><-:56254..56435 182 gaagtgaatagtgagttgtgctgaaaacccaattcttccactctccttgccaatagacatggcaaggagagtgagggtataatacaaggaacccccgaaagccacggctttcggggggttgcttttatcagagcttccgccggtctcttttcctcgtcggaatgggtggccgggaaaaatgc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG0045:PG0046|PG0045:PG0046:heat shock protein 90:phosphatidate cytidylyltransferase:-><-:56254..56435 182 gaagtgaatagtgagttgtgctgaaaacccaattcttccactctccttgccaatagacatggcaaggagagtgagggtataatacaaggaacccccgaaagccacggctttcggggggttgcttttatcagagcttccgccggtctcttttcctcgtcggaatgggtggccgggaaaaatgc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG0045:PG0046|PG0045:PG0046:heat shock protein 90:phosphatidate cytidylyltransferase:-><-:56254..56435 182 gaagtgaatagtgagttgtgctgaaaacccaattcttccactctccttgccaatagacatggcaaggagagtgagggtataatacaaggaacccccgaaagccacggctttcggggggttgcttttatcagagcttccgccggtctcttttcctcgtcggaatgggtggccgggaaaaatgc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gaagtgaatagtgagttgtgctgaaaacccaattcttccactctccttgccaatagacatggcaaggagagtgagggtataatacaaggaacccccgaaagccacggctttcggggggttgcttttatcagagcttccgccggtctcttttcctcgtcggaatgggtggccgggaaaaatgc Predict ORF larger than 30AA ================================================ Protein_Len: 34 Strand: + Start: 79 End: 180 .............................................................................. M I Q G T P E S H G F R G V A F I R A S A G L F S S S E W V A G K N .. Protein_Len: 43 Strand: - Start: 3 End: 131 .. T F L S N H Q F G L E E V R R A L L C P L S L S P I I C P V G S L W P K R P T A K I M ................................................... Protein_Len: 60 Strand: - Start: 1 End: 180 F H I T L Q A S F G I R G S E K G I S M A L L T L T Y Y L S G G F A V A K P P N S K D S S G G T E K G R R F P H G P F M .. gaagtgaatagtgagttgtgctgaaaacccaattcttccactctccttgccaatagacatggcaaggagagtgagggtataatacaaggaacccccgaaagccacggctttcggggggttgcttttatcagagcttccgccggtctcttttcctcgtcggaatgggtggccgggaaaaatgc 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================================================ gaagtgaatagtgagttgtgctgaaaacccaattcttccactctccttgccaatagacatggcaaggagagtgagggtataatacaaggaacccccgaaagccacggctttcggggggttgcttttatcagagcttccgccggtctcttttcctcgtcggaatgggtggccgggaaaaatgc Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 75 HP_score: -10.2 Tail_Score: -3.36823 Start: 33 End: 79 Full_Region: gggttccttgtatta taccctcactctccttgcca tgtctat tggcaaggagagtggaagaa ttgggttttcagcac ................................taccctcactctccttgccatgtctattggcaaggagagtggaagaa....................................................................................................... TransTerm Strand: + Conf: 84 HP_score: -15.0 Tail_Score: -2.78384 Start: 35 End: 77 Full_Region: GCTGAAAACCCAATT CTTCCACTCTCCTTGCCA ATAGACA TGGCAAGGAGAGTGAGGG TATAATACAAGGAAC ..................................CTTCCACTCTCCTTGCCAATAGACATGGCAAGGAGAGTGAGGG......................................................................................................... TransTerm Strand: + Conf: 100 HP_score: -13.7 Tail_Score: -4.386 Start: 88 End: 122 Full_Region: GAGGGTATAATACAA GGAACCCCCGAAAGC CACG GCTTTCGGGGGGTTGC TTTTATCAGAGCTTC .......................................................................................GGAACCCCCGAAAGCCACGGCTTTCGGGGGGTTGC............................................................ TransTerm Strand: - Conf: 90 HP_score: -13.7 Tail_Score: -3.75824 Start: 88 End: 122 Full_Region: gaagctctgataaaa gcaaccccccgaaagc cgtg gctttcgggggttcc ttgtattataccctc .......................................................................................gcaaccccccgaaagccgtggctttcgggggttcc............................................................ TransTerm Strand: + Conf: 100 HP_score: -15.6 Tail_Score: -3.75115 Start: 91 End: 118 Full_Region: GGTATAATACAAGGA ACCCCCGAAAGC CACG GCTTTCGGGGGG TTGCTTTTATCAGAG ..........................................................................................ACCCCCGAAAGCCACGGCTTTCGGGGGG................................................................ TransTerm Strand: - Conf: 100 HP_score: -19.1 Tail_Score: -3.56569 Start: 92 End: 117 Full_Region: tctgataaaagcaac cccccgaaagc cgtg gctttcggggg ttccttgtattatac ...........................................................................................cccccgaaagccgtggctttcggggg................................................................. Find igs database================================================ Query_seq: PG0045:PG0046|PG0045:PG0046:heat shock protein 90:phosphatidate cytidylyltransferase:-><-:56254..56435 182 gaagtgaatagtgagttgtgctgaaaacccaattcttccactctccttgccaatagacatggcaaggagagtgagggtataatacaaggaacccccgaaagccacggctttcggggggttgcttttatcagagcttccgccggtctcttttcctcgtcggaatgggtggccgggaaaaatgc Intra-Species Hit: Count: 1 Min: 1 Max: 182 Len: 182 Subject: NC_002950_PG0045_PG0046|heat shock protein 90:phosphatidate cytidylyltransferase|POSITIVE:NEGATIVE|[56254,56435]|182 HSP 1 e-value: 5.0E-99 bit: 361.0 Len: 182 Query Start:1 Query End:182 Subject Strand: POSITIVE Subject Start: 1 Subject End: 182 gaagtgaatagtgagttgtgctgaaaacccaattcttccactctccttgccaatagacatggcaaggagagtgagggtataatacaaggaacccccgaaagccacggctttcggggggttgcttttatcagagcttccgccggtctcttttcctcgtcggaatgggtggccgggaaaaatgc gaagtgaatagtgagttgtgctgaaaacccaattcttccactctccttgccaatagacatggcaaggagagtgagggtataatacaaggaacccccgaaagccacggctttcggggggttgcttttatcagagcttccgccggtctcttttcctcgtcggaatgggtggccgggaaaaatgc Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAAGUGAAUAGUGAGUUGUGCUGAAAACCCAAUUCUUCCACUCUCCUUGCCAAUAGACAUGGCAAGGAGAGUGAGGGUAUAAUACAAGGAACCCCCGAAAGCCACGGCUUUCGGGGGGUUGCUUUUAUCAGAGCUUCCGCCGGUCUCUUUUCCUCGUCGGAAUGGGUGGCCGGGAAAAAUGC ...........((.(((((((((((.......)))...((((((((((((((.......))))))))))))))..)))))))).)).(((.(((((((((((....)))))))))))...((((......)))).))).(((((((((.((((.....)))).))).))))))......... (-79.40) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GCAUUUUUCCCGGCCACCCAUUCCGACGAGGAAAAGAGACCGGCGGAAGCUCUGAUAAAAGCAACCCCCCGAAAGCCGUGGCUUUCGGGGGUUCCUUGUAUUAUACCCUCACUCUCCUUGCCAUGUCUAUUGGCAAGGAGAGUGGAAGAAUUGGGUUUUCAGCACAACUCACUAUUCACUUC ...........((..((((((((..((((((((........(((....)))..............(((((((((((....))))))))))))))))))).........(((((((((((((((.......)))))))))))))))..))).)))))..))...................... (-74.30) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 440 160 112 65 16 NC_002950:PG2046|5end_hypothetical_protein_2144349..2144579_POSITIVE 432 143 108 47 2 NC_002950:PG1774|5end_transcription-repair_coupling_factor_1864547..1864777_NEGATIVE 426 174 132 216 173 NC_002950:PG0165|5end_heat_shock_protein_15_187807..188037_NEGATIVE 423 178 131 167 107 NC_002950:PG0145|5end_hypothetical_protein_167831..168061_POSITIVE 415 133 92 126 69 NC_002950:PG0938|5end_calcium-transporting_ATPase_1000385..1000615_NEGATIVE 414 173 134 197 162 NC_002950:PG2154|5end_hypothetical_protein_2260945..2261175_NEGATIVE 414 146 102 178 134 NC_002950:PG1938|5end_50S_ribosomal_protein_L3_2024753..2024983_NEGATIVE 411 150 101 224 154 NC_002950:PG0264|5end_glycosyl_transferase,_group_2_family_protein_296975..297205_POSITIVE 408 147 102 176 129 NC_002950:PG1760|5end_ABC_transporter,_ATP-binding_protein_1846507..1846737_POSITIVE 408 175 132 63 15 NC_002950:PG1459|5end_hypothetical_protein_1539769..1539999_NEGATIVE 405 175 132 220 172 NC_002950:PG1634|5end_hypothetical_protein_1715148..1715378_NEGATIVE 401 175 133 227 182 NC_002950:PG0221|5end_hypothetical_protein_255834..256064_NEGATIVE 398 149 103 203 146 NC_002950:PG1078|5end_electron_transfer_flavoprotein,_alpha_subunit_1145438..1145668_POSITIVE 396 147 105 48 4 NC_002950:PG2125|5end_transcriptional_regulator,_AraC_family_2232254..2232484_NEGATIVE 396 139 94 222 176 NC_002950:PG0665|5end_beta-galactosidase_711827..712057_POSITIVE 395 147 108 185 142 NC_002950:PG1285|5end_glucosamine-6-phosphate_deaminase_1362894..1363124_POSITIVE 393 175 133 51 3 NC_002950:PG0128|5end_hypothetical_protein_149594..149824_POSITIVE 390 145 101 231 176 NC_002950:PG2101|5end_hypothetical_protein_2211273..2211503_NEGATIVE 390 173 132 168 112 NC_002950:PG1226|5end_peptidyl-prolyl_cis-trans_isomerase,_cyclophilin-type_1303264..1303494_POSITIVE 382 147 101 61 10 NC_002950:PG1487|5end_hypothetical_protein_1561468..1561698_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 511 78 32 59 13 NC_002950:PG0045|3end_heat_shock_protein_90_56193..56343_POSITIVE 465 177 131 86 32 NC_002950:PG0332|3end_transcription_termination_factor_Rho_367675..367825_POSITIVE 454 136 93 70 17 NC_002950:PG0343|3end_methionine_gamma-lyase_377181..377331_NEGATIVE 441 144 101 108 68 NC_002950:PG1972|3end_hemagglutinin_protein_HagB_2061203..2061353_POSITIVE 437 144 101 108 70 NC_002950:PG1975|3end_hemagglutinin_protein_HagC_2064350..2064500_POSITIVE 429 149 105 138 83 NC_002950:PG0020|3end_transcriptional_regulator,_MarR_family_24166..24316_POSITIVE 411 148 109 57 14 NC_002950:PG0461|3end_ISPg7,_transposase_503439..503589_NEGATIVE 406 142 101 146 98 NC_002950:PG0377|3end_30S_ribosomal_protein_S2_407845..407995_POSITIVE 405 159 111 127 77 NC_002950:PG0443|3end_hemagglutinin-related_protein_483147..483297_POSITIVE 405 142 101 148 97 NC_002950:PG0361|3end_hypothetical_protein_395481..395631_POSITIVE 402 175 132 109 67 NC_002950:PG2031|3end_hypothetical_protein_2130871..2131021_POSITIVE 401 175 133 148 103 NC_002950:PG0222|3end_DNA-binding_protein,_histone-like_family_255913..256063_NEGATIVE 398 133 92 101 45 NC_002950:PG1244|3end_ISPg1,_transposase_1320699..1320849_POSITIVE 398 133 92 101 45 NC_002950:PG0549|3end_ISPg1,_transposase_605987..606137_NEGATIVE 398 133 92 101 45 NC_002950:PG0460|3end_ISPg1,_transposase_503102..503252_POSITIVE 397 129 94 50 10 NC_002950:PG1788|3end_cysteine_peptidase,_putative_1877327..1877477_POSITIVE 397 169 127 141 90 NC_002950:PG1497|3end_DNA-binding_protein,_histone-like_family_1574635..1574785_POSITIVE 394 173 134 146 105 NC_002950:PG0047|3end_cell_division_protein_FtsH,_putative_57229..57379_NEGATIVE 390 145 101 80 25 NC_002950:PG2102|3end_immunoreactive_61_kDa_antigen_PG91_2211424..2211574_NEGATIVE 379 138 93 102 35 NC_002950:PG1498|3end_hypothetical_protein_1575650..1575800_POSITIVE