Origin IGS: ctcaataaaacatgttgttgggttagttccttattgtgatcattttcgctgttttcgtgctgtgtatctgtgcgctattcgcaaaaaagccacttcggtcgcttcttattgcagaccggaagtggctccgagtttattattggggaaacgcctgcctcaaagga .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tcctttgaggcaggcgtttccccaataataaactcggagccacttccggtctgcaataagaagcgaccgaagtggcttttttgcgaatagcgcacagatacacagcacgaaaacagcgaaaatgatcacaataaggaactaacccaacaacatgttttattgag Mask Tandem Repeat Region ================================================ ctcaataaaacatgttgttgggttagttccttattgtgatcattttcgctgttttcgtgctgtgtatctgtgcgctattcgcaaaaaagccacttcggtcgcttcttattgcagaccggaagtggctccgagtttattattggggaaacgcctgcctcaaagga Find is-nt database================================================ Query_seq: PG0245:PG0246|PG0245:PG0246:universal stress protein family:hypothetical protein:<-<-:280976..281139 164 ctcaataaaacatgttgttgggttagttccttattgtgatcattttcgctgttttcgtgctgtgtatctgtgcgctattcgcaaaaaagccacttcggtcgcttcttattgcagaccggaagtggctccgagtttattattggggaaacgcctgcctcaaagga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG0245:PG0246|PG0245:PG0246:universal stress protein family:hypothetical protein:<-<-:280976..281139 164 ctcaataaaacatgttgttgggttagttccttattgtgatcattttcgctgttttcgtgctgtgtatctgtgcgctattcgcaaaaaagccacttcggtcgcttcttattgcagaccggaagtggctccgagtttattattggggaaacgcctgcctcaaagga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG0245:PG0246|PG0245:PG0246:universal stress protein family:hypothetical protein:<-<-:280976..281139 164 ctcaataaaacatgttgttgggttagttccttattgtgatcattttcgctgttttcgtgctgtgtatctgtgcgctattcgcaaaaaagccacttcggtcgcttcttattgcagaccggaagtggctccgagtttattattggggaaacgcctgcctcaaagga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ctcaataaaacatgttgttgggttagttccttattgtgatcattttcgctgttttcgtgctgtgtatctgtgcgctattcgcaaaaaagccacttcggtcgcttcttattgcagaccggaagtggctccgagtttattattggggaaacgcctgcctcaaagga Predict ORF larger than 30AA ================================================ Protein_Len: 38 Strand: + Start: 49 End: 162 ................................................ M F S C C V S V R Y S Q K S H F G R F L L Q T G S G S E F I I G E T P A S K .. Protein_Len: 53 Strand: + Start: 5 End: 163 .... M K H V V G L V P Y C D H F R C F R A V Y L C A I R K K A T S V A S Y C R P E V A P S L L L G K R L P Q R . Protein_Len: 44 Strand: + Start: 33 End: 164 ................................ M V I I F A V F V L C I C A L F A K K P L R S L L I A D R K W L R V Y Y W G N A C L K G ctcaataaaacatgttgttgggttagttccttattgtgatcattttcgctgttttcgtgctgtgtatctgtgcgctattcgcaaaaaagccacttcggtcgcttcttattgcagaccggaagtggctccgagtttattattggggaaacgcctgcctcaaagga 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================================================ ctcaataaaacatgttgttgggttagttccttattgtgatcattttcgctgttttcgtgctgtgtatctgtgcgctattcgcaaaaaagccacttcggtcgcttcttattgcagaccggaagtggctccgagtttattattggggaaacgcctgcctcaaagga Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 100 HP_score: -8.6 Tail_Score: -5.03314 Start: 89 End: 126 Full_Region: aataataaactcgga gccacttccggtctgc aataagaa gcgaccgaagtggc ttttttgcgaatagc ........................................................................................gccacttccggtctgcaataagaagcgaccgaagtggc...................................... Find igs database================================================ Query_seq: PG0245:PG0246|PG0245:PG0246:universal stress protein family:hypothetical protein:<-<-:280976..281139 164 ctcaataaaacatgttgttgggttagttccttattgtgatcattttcgctgttttcgtgctgtgtatctgtgcgctattcgcaaaaaagccacttcggtcgcttcttattgcagaccggaagtggctccgagtttattattggggaaacgcctgcctcaaagga Intra-Species Hit: Count: 1 Min: 1 Max: 164 Len: 164 Subject: NC_002950_PG0245_PG0246|universal stress protein family:hypothetical protein|NEGATIVE:NEGATIVE|[280976,281139]|164 HSP 1 e-value: 3.0E-88 bit: 325.0 Len: 164 Query Start:1 Query End:164 Subject Strand: POSITIVE Subject Start: 1 Subject End: 164 ctcaataaaacatgttgttgggttagttccttattgtgatcattttcgctgttttcgtgctgtgtatctgtgcgctattcgcaaaaaagccacttcggtcgcttcttattgcagaccggaagtggctccgagtttattattggggaaacgcctgcctcaaagga ctcaataaaacatgttgttgggttagttccttattgtgatcattttcgctgttttcgtgctgtgtatctgtgcgctattcgcaaaaaagccacttcggtcgcttcttattgcagaccggaagtggctccgagtttattattggggaaacgcctgcctcaaagga Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CUCAAUAAAACAUGUUGUUGGGUUAGUUCCUUAUUGUGAUCAUUUUCGCUGUUUUCGUGCUGUGUAUCUGUGCGCUAUUCGCAAAAAAGCCACUUCGGUCGCUUCUUAUUGCAGACCGGAAGUGGCUCCGAGUUUAUUAUUGGGGAAACGCCUGCCUCAAAGGA ((((((((......)))))))).....(((((...((((......)))).......(.((.((((.((..((((.....))))....(((((((((((((((........)).)))).)))))))))((((........)))).)).))))..)))...))))) (-48.30) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UCCUUUGAGGCAGGCGUUUCCCCAAUAAUAAACUCGGAGCCACUUCCGGUCUGCAAUAAGAAGCGACCGAAGUGGCUUUUUUGCGAAUAGCGCACAGAUACACAGCACGAAAACAGCGAAAAUGAUCACAAUAAGGAACUAACCCAACAACAUGUUUUAUUGAG ..(..(((((((.((.((((...............(((((((((((.((((.((........)))))))))))))))))..((((.....))))..............))))...)).................((.......)).......)))))))..).. (-39.10) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 1024 130 81 221 172 NC_002950:PG0245|5end_universal_stress_protein_family_280885..281115_NEGATIVE 402 82 46 74 37 NC_002950:PG1398|5end_hypothetical_protein_1480694..1480924_POSITIVE 399 130 88 57 26 NC_002950:PG1992|5end_glucose-inhibited_division_protein_A_2081410..2081640_POSITIVE 396 137 92 215 167 NC_002950:PG0009|5end_ISPg5_transposase_Orf1_8466..8696_NEGATIVE 393 90 43 58 7 NC_002950:PG1119|5end_flavodoxin,_putative_1194843..1195073_POSITIVE 383 130 94 39 2 NC_002950:PG0441|5end_hypothetical_protein_478734..478964_POSITIVE 378 155 111 231 185 NC_002950:PG0120|5end_UDP-N-acetylglucosamine_2-epimerase_143004..143234_POSITIVE 376 76 33 57 7 NC_002950:PG1854|5end_5-formyltetrahydrofolate_cyclo-ligase_family_protein_1953882..1954112_NEGATIVE 365 130 89 68 24 NC_002950:PG0676|5end_oxidoreductase,_short_chain_dehydrogenase/reductase_family_727275..727505_NEGATIVE 361 128 88 207 163 NC_002950:PG0986|5end_hypothetical_protein_1047426..1047656_POSITIVE 357 135 93 79 25 NC_002950:PG1040|5end_transcriptional_regulator,_putative_1107949..1108179_NEGATIVE 354 129 89 146 109 NC_002950:PG0809|5end_hypothetical_protein_872014..872244_NEGATIVE 352 120 71 213 163 NC_002950:PG2107|5end_thiamine_biosynthesis_protein_ThiH_2216658..2216888_NEGATIVE 343 84 46 162 127 NC_002950:PG0583|5end_cell_division_protein_FtsA_640425..640655_POSITIVE 342 150 101 72 22 NC_002950:PG1975|5end_hemagglutinin_protein_HagC_2063218..2063448_POSITIVE 339 135 91 199 137 NC_002950:PG1035|5end_hypothetical_protein_1096875..1097105_POSITIVE 339 118 73 187 131 NC_002950:PG0242|5end_conserved_hypothetical_protein_TIGR00096_278960..279190_NEGATIVE 338 100 55 186 144 NC_002950:PG1050|5end_hypothetical_protein_1117272..1117502_POSITIVE 333 158 111 230 190 NC_002950:PG0447|5end_hypothetical_protein_487278..487508_POSITIVE 332 130 90 131 93 NC_002950:PG1861|5end_hypothetical_protein_1960057..1960287_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 399 75 44 151 114 NC_002950:PG1556|3end_hypothetical_protein_1637001..1637151_POSITIVE 396 130 87 146 99 NC_002950:PG1484|3end_hypothetical_protein_1559275..1559425_NEGATIVE 393 158 111 147 101 NC_002950:PG0199|3end_TatD_family_protein_237424..237574_NEGATIVE 376 76 33 97 47 NC_002950:PG1855|3end_carboxyl-terminal_protease_1953842..1953992_NEGATIVE 370 130 88 86 44 NC_002950:PG0605|3end_hypothetical_protein_661165..661315_NEGATIVE 367 159 111 101 38 NC_002950:PG2044|3end_hypothetical_protein_2144165..2144315_POSITIVE 357 135 93 58 4 NC_002950:PG1041|3end_K+-dependent_Na+/Ca+_exchanger_related-protein_1107970..1108120_NEGATIVE 343 84 46 113 78 NC_002950:PG0582|3end_cell_division_protein_FtsQ,_putative_640456..640606_POSITIVE 333 99 52 49 5 NC_002950:PG0698|3end_lipoprotein,_putative_752373..752523_NEGATIVE 332 130 90 118 80 NC_002950:PG1862|3end_hypothetical_protein_1960070..1960220_NEGATIVE 327 130 97 35 1 NC_002950:PG0439|3end_hypothetical_protein_478810..478960_POSITIVE 326 117 71 74 34 NC_002950:PG0507|3end_hypothetical_protein_548190..548340_POSITIVE 325 129 81 108 52 NC_002950:PG1389|3end_DNA-binding_protein,_histone-like_family_1470870..1471020_NEGATIVE 322 133 92 145 102 NC_002950:PG1185|3end_hypothetical_protein_1266892..1267042_NEGATIVE 319 119 72 146 107 NC_002950:PG0758|3end_peptidyl-dipeptidase_Dcp_806467..806617_NEGATIVE 319 125 81 59 14 NC_002950:PG0433|3end_tetrapyrrole_methylase_family_protein_470683..470833_NEGATIVE 318 158 117 57 9 NC_002950:PG2172|3end_hypothetical_protein_2279191..2279341_NEGATIVE 317 157 117 68 25 NC_002950:PG1593|3end_shikimate_kinase_1672143..1672293_POSITIVE 317 119 72 149 105 NC_002950:PG0378|3end_elongation_factor_Ts_408808..408958_POSITIVE 316 129 88 132 96 NC_002950:PG0361|3end_hypothetical_protein_395481..395631_POSITIVE