Origin IGS: tcgccgacccgatccgtatagaataagaacctccgtgctaagagaaatttatcgtacggaggtatgctttttggcggaaatatatttactttgggatagaagagtagacccataaggagcttgaatacgatgcgatcgtatccgaagggcatgcgaaatatagatcgggaaaggtgcccgtattctttggttttgcgagcttcttttttgactttcccgtggagtttttcccctgatgtatggccgaagaggaagcattcgtgcctcttcagggcatagggacaaaatttttaagaatacaattatcagatttatcaca .........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 tgtgataaatctgataattgtattcttaaaaattttgtccctatgccctgaagaggcacgaatgcttcctcttcggccatacatcaggggaaaaactccacgggaaagtcaaaaaagaagctcgcaaaaccaaagaatacgggcacctttcccgatctatatttcgcatgcccttcggatacgatcgcatcgtattcaagctccttatgggtctactcttctatcccaaagtaaatatatttccgccaaaaagcatacctccgtacgataaatttctcttagcacggaggttcttattctatacggatcgggtcggcga Mask Tandem Repeat Region ================================================ tcgccgacccgatccgtatagaataagaacctccgtgctaagagaaatttatcgtacggaggtatgctttttggcggaaatatatttactttgggatagaagagtagacccataaggagcttgaatacgatgcgatcgtatccgaagggcatgcgaaatatagatcgggaaaggtgcccgtattctttggttttgcgagcttcttttttgactttcccgtggagtttttcccctgatgtatggccgaagaggaagcattcgtgcctcttcagggcatagggacaaaatttttaagaatacaattatcagatttatcaca Find is-nt database================================================ Query_seq: PG1170:PG1171|PG1170:PG1171:SerB family protein:oxidoreductase, putative:->->:1250176..1250494 319 tcgccgacccgatccgtatagaataagaacctccgtgctaagagaaatttatcgtacggaggtatgctttttggcggaaatatatttactttgggatagaagagtagacccataaggagcttgaatacgatgcgatcgtatccgaagggcatgcgaaatatagatcgggaaaggtgcccgtattctttggttttgcgagcttcttttttgactttcccgtggagtttttcccctgatgtatggccgaagaggaagcattcgtgcctcttcagggcatagggacaaaatttttaagaatacaattatcagatttatcaca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG1170:PG1171|PG1170:PG1171:SerB family protein:oxidoreductase, putative:->->:1250176..1250494 319 tcgccgacccgatccgtatagaataagaacctccgtgctaagagaaatttatcgtacggaggtatgctttttggcggaaatatatttactttgggatagaagagtagacccataaggagcttgaatacgatgcgatcgtatccgaagggcatgcgaaatatagatcgggaaaggtgcccgtattctttggttttgcgagcttcttttttgactttcccgtggagtttttcccctgatgtatggccgaagaggaagcattcgtgcctcttcagggcatagggacaaaatttttaagaatacaattatcagatttatcaca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG1170:PG1171|PG1170:PG1171:SerB family protein:oxidoreductase, putative:->->:1250176..1250494 319 tcgccgacccgatccgtatagaataagaacctccgtgctaagagaaatttatcgtacggaggtatgctttttggcggaaatatatttactttgggatagaagagtagacccataaggagcttgaatacgatgcgatcgtatccgaagggcatgcgaaatatagatcgggaaaggtgcccgtattctttggttttgcgagcttcttttttgactttcccgtggagtttttcccctgatgtatggccgaagaggaagcattcgtgcctcttcagggcatagggacaaaatttttaagaatacaattatcagatttatcaca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tcgccgacccgatccgtatagaataagaacctccgtgctaagagaaatttatcgtacggaggtatgctttttggcggaaatatatttactttgggatagaagagtagacccataaggagcttgaatacgatgcgatcgtatccgaagggcatgcgaaatatagatcgggaaaggtgcccgtattctttggttttgcgagcttcttttttgactttcccgtggagtttttcccctgatgtatggccgaagaggaagcattcgtgcctcttcagggcatagggacaaaatttttaagaatacaattatcagatttatcaca Predict ORF larger than 30AA ================================================ Protein_Len: 30 Strand: + Start: 23 End: 112 ...................... M R T S V L R E I Y R T E V C F L A E I Y L L W D R R V D P ............................................................................................................................................................................................................... Protein_Len: 33 Strand: + Start: 135 End: 233 ...................................................................................................................................... M V S E G H A K Y R S G K V P V F F G F A S F F F D F P V E F F P ...................................................................................... Protein_Len: 55 Strand: + Start: 112 End: 276 ............................................................................................................... M R S L N T M R S Y P K G M R N I D R E R C P Y S L V L R A S F L T F P W S F S P D V W P K R K H S C L F R A ........................................... Protein_Len: 51 Strand: - Start: 89 End: 241 ........................................................................................ K P I S S Y V W L S S S Y S A I T D S P C A F Y L D P F T G T N K P K A L K K K S K G T S N K G Q H M .............................................................................. Protein_Len: 60 Strand: - Start: 52 End: 318 ................................................... I R L A H S I Y I P F P A R I R Q N Q S S R K Q S E R P T K G R I Y P R L P L M R A E E P C L S L I K L F V I I L N I M . Protein_Len: 60 Strand: - Start: 3 End: 272 .. P Y F L L G M L L K F V I R D Y G F P M R F I S R S L H G Y E K T K R A E K K V K G H L K E G S T H G F L F C E H R K M ............................................... tcgccgacccgatccgtatagaataagaacctccgtgctaagagaaatttatcgtacggaggtatgctttttggcggaaatatatttactttgggatagaagagtagacccataaggagcttgaatacgatgcgatcgtatccgaagggcatgcgaaatatagatcgggaaaggtgcccgtattctttggttttgcgagcttcttttttgactttcccgtggagtttttcccctgatgtatggccgaagaggaagcattcgtgcctcttcagggcatagggacaaaatttttaagaatacaattatcagatttatcaca 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================================================ tcgccgacccgatccgtatagaataagaacctccgtgctaagagaaatttatcgtacggaggtatgctttttggcggaaatatatttactttgggatagaagagtagacccataaggagcttgaatacgatgcgatcgtatccgaagggcatgcgaaatatagatcgggaaaggtgcccgtattctttggttttgcgagcttcttttttgactttcccgtggagtttttcccctgatgtatggccgaagaggaagcattcgtgcctcttcagggcatagggacaaaatttttaagaatacaattatcagatttatcaca Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PG1170:PG1171|PG1170:PG1171:SerB family protein:oxidoreductase, putative:->->:1250176..1250494 319 tcgccgacccgatccgtatagaataagaacctccgtgctaagagaaatttatcgtacggaggtatgctttttggcggaaatatatttactttgggatagaagagtagacccataaggagcttgaatacgatgcgatcgtatccgaagggcatgcgaaatatagatcgggaaaggtgcccgtattctttggttttgcgagcttcttttttgactttcccgtggagtttttcccctgatgtatggccgaagaggaagcattcgtgcctcttcagggcatagggacaaaatttttaagaatacaattatcagatttatcaca Intra-Species Hit: Count: 1 Min: 1 Max: 319 Len: 319 Subject: NC_002950_PG1170_PG1171|SerB family protein:oxidoreductase, putative|POSITIVE:POSITIVE|[1250176,1250494]|319 HSP 1 e-value: 1.0E-180 bit: 632.0 Len: 319 Query Start:1 Query End:319 Subject Strand: POSITIVE Subject Start: 1 Subject End: 319 tcgccgacccgatccgtatagaataagaacctccgtgctaagagaaatttatcgtacggaggtatgctttttggcggaaatatatttactttgggatagaagagtagacccataaggagcttgaatacgatgcgatcgtatccgaagggcatgcgaaatatagatcgggaaaggtgcccgtattctttggttttgcgagcttcttttttgactttcccgtggagtttttcccctgatgtatggccgaagaggaagcattcgtgcctcttcagggcatagggacaaaatttttaagaatacaattatcagatttatcaca tcgccgacccgatccgtatagaataagaacctccgtgctaagagaaatttatcgtacggaggtatgctttttggcggaaatatatttactttgggatagaagagtagacccataaggagcttgaatacgatgcgatcgtatccgaagggcatgcgaaatatagatcgggaaaggtgcccgtattctttggttttgcgagcttcttttttgactttcccgtggagtttttcccctgatgtatggccgaagaggaagcattcgtgcctcttcagggcatagggacaaaatttttaagaatacaattatcagatttatcaca Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UCGCCGACCCGAUCCGUAUAGAAUAAGAACCUCCGUGCUAAGAGAAAUUUAUCGUACGGAGGUAUGCUUUUUGGCGGAAAUAUAUUUACUUUGGGAUAGAAGAGUAGACCCAUAAGGAGCUUGAAUACGAUGCGAUCGUAUCCGAAGGGCAUGCGAAAUAUAGAUCGGGAAAGGUGCCCGUAUUCUUUGGUUUUGCGAGCUUCUUUUUUGACUUUCCCGUGGAGUUUUUCCCCUGAUGUAUGGCCGAAGAGGAAGCAUUCGUGCCUCUUCAGGGCAUAGGGACAAAAUUUUUAAGAAUACAAUUAUCAGAUUUAUCACA .((((..((((((((((((.........((((((((((..(((....)))...))))))))))..((((((((..((.......((((((((........))))))))))..))))))))....)))))......((((((((....)).))))))......)))))))...))))...((((((((.((((((((..((((((((((((.((.((..(.((((...)))))..)).....)).))))))))))))....((((((.....))))))...).)))))))...))))))))................... (-100.21) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGUGAUAAAUCUGAUAAUUGUAUUCUUAAAAAUUUUGUCCCUAUGCCCUGAAGAGGCACGAAUGCUUCCUCUUCGGCCAUACAUCAGGGGAAAAACUCCACGGGAAAGUCAAAAAAGAAGCUCGCAAAACCAAAGAAUACGGGCACCUUUCCCGAUCUAUAUUUCGCAUGCCCUUCGGAUACGAUCGCAUCGUAUUCAAGCUCCUUAUGGGUCUACUCUUCUAUCCCAAAGUAAAUAUAUUUCCGCCAAAAAGCAUACCUCCGUACGAUAAAUUUCUCUUAGCACGGAGGUUCUUAUUCUAUACGGAUCGGGUCGGCGA ................................((((..(((((((..(((((((((...........))))))))).....))).))))..)))).....((((((((((......)).(((((...............)))))..)))))))).........((((..((((...(((((((((...)))))))))......(((.((((.............)))))))..........((((...........((((((((.(...............).))))))))............))))..))))..)))) (-77.74) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 375 277 242 41 1 NC_002950:PG0346|5end_GTP-binding_protein_380659..380889_POSITIVE 373 280 231 201 131 NC_002950:PG0756|5end_hypothetical_protein_805673..805903_NEGATIVE 364 180 131 57 8 NC_002950:PG0271|5end_single-stranded_binding_protein_303842..304072_POSITIVE 357 168 128 211 169 NC_002950:PG1927|5end_50S_ribosomal_protein_L24_2019557..2019787_NEGATIVE 356 281 242 55 9 NC_002950:PG2214|5end_hypothetical_protein_2326575..2326805_NEGATIVE 356 180 131 123 73 NC_002950:PG0651|5end_HDIG_domain_protein_703622..703852_NEGATIVE 355 279 233 192 134 NC_002950:PG1022|5end_hypothetical_protein_1083537..1083767_POSITIVE 353 280 232 205 152 NC_002950:PG1779|5end_hypothetical_protein_1867924..1868154_POSITIVE 352 269 225 138 83 NC_002950:PG1173|5end_YkgG_family_protein_1252435..1252665_POSITIVE 348 256 217 231 190 NC_002950:PG0635|5end_ribosomal_protein_L11_methyltransferase_687773..688003_NEGATIVE 347 260 211 223 171 NC_002950:PG2173|5end_outer_membrane_lipoprotein_Omp28_2280813..2281043_NEGATIVE 347 219 171 159 109 NC_002950:PG1949|5end_malate_dehydrogenase_2039188..2039418_NEGATIVE 347 273 231 205 156 NC_002950:PG1829|5end_long-chain-fatty-acid--CoA_ligase,_putative_1922980..1923210_NEGATIVE 347 222 181 187 134 NC_002950:PG0594|5end_RNA_polymerase_sigma-70_factor_652048..652278_POSITIVE 346 280 232 231 185 NC_002950:PG1682|5end_glycosyl_transferase,_group_1_family_protein_1768385..1768615_POSITIVE 344 270 221 156 96 NC_002950:PG1035|5end_hypothetical_protein_1096875..1097105_POSITIVE 341 273 233 228 184 NC_002950:PG1484|5end_hypothetical_protein_1559979..1560209_NEGATIVE 339 220 174 45 6 NC_002950:PG2060|5end_thymidylate_synthase_2157573..2157803_POSITIVE 337 66 32 198 167 NC_002950:PG1887|5end_rhodanese-like_domain_protein_1984565..1984795_POSITIVE 332 200 154 196 152 NC_002950:PG2199|5end_ABC_transporter,_ATP-binding_protein,_putative_2306723..2306953_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 373 280 231 151 81 NC_002950:PG0757|3end_hypothetical_protein_805723..805873_NEGATIVE 353 280 232 123 70 NC_002950:PG1778|3end_hypothetical_protein_1867922..1868072_POSITIVE 343 275 231 97 57 NC_002950:PG0605|3end_hypothetical_protein_661165..661315_NEGATIVE 340 180 131 138 83 NC_002950:PG0445|3end_peptidase_T_486549..486699_POSITIVE 332 275 233 107 46 NC_002950:PG2159|3end_protoporphyrinogen_oxidase_2265874..2266024_POSITIVE 332 205 162 59 8 NC_002950:PG1579|3end_ATPase,_MoxR_family_1657568..1657718_POSITIVE 332 266 224 48 1 NC_002950:PG0340|3end_hypothetical_protein_376436..376586_POSITIVE 330 280 231 148 98 NC_002950:PG0674|3end_indolepyruvate_ferredoxin_oxidoreductase,_beta_subunit_724209..724359_NEGATIVE 329 275 231 99 28 NC_002950:PG0378|3end_elongation_factor_Ts_408808..408958_POSITIVE 328 260 217 77 22 NC_002950:PG0752|3end_uracil_phosphoribosyltransferase_798397..798547_POSITIVE 328 203 165 115 78 NC_002950:PG0522|3end_tRNA_delta(2)-isopentenylpyrophosphate_transferase_565993..566143_NEGATIVE 326 180 131 131 80 NC_002950:PG0896|3end_beta-galactosidase_960382..960532_POSITIVE 325 63 29 62 28 NC_002950:PG1170|3end_SerB_family_protein_1250115..1250265_POSITIVE 325 260 214 148 94 NC_002950:PG1012|3end_tRNA-i(6)A37_modification_enzyme_MiaB_1070089..1070239_NEGATIVE 320 190 143 137 92 NC_002950:PG0558|3end_purine_nucleoside_phosphorylase_615510..615660_NEGATIVE 319 79 31 88 32 NC_002950:PG0767|3end_4-alpha-glucanotransferase_818557..818707_NEGATIVE 318 180 131 110 44 NC_002950:PG2003|3end_deoxyguanosinetriphosphate_triphosphohydrolase_2091648..2091798_NEGATIVE 317 169 121 79 30 NC_002950:PG2027|3end_hypothetical_protein_2126098..2126248_POSITIVE 315 284 246 118 78 NC_002950:PG1793|3end_1,4-alpha-glucan_branching_enzyme_1886008..1886158_POSITIVE 313 210 162 67 19 NC_002950:PG0471|3end_hypothetical_protein_513432..513582_POSITIVE