Origin IGS: gagcctgttagtataacaaaccttgtagaggagccgatgaggcgaagggcttttgtggctcgtcgcattcattcggctcctttttcatccatcgaagagagtt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aactctcttcgatggatgaaaaaggagccgaatgaatgcgacgagccacaaaagcccttcgcctcatcggctcctctacaaggtttgttatactaacaggctc Mask Tandem Repeat Region ================================================ gagcctgttagtataacaaaccttgtagaggagccgatgaggcgaagggcttttgtggctcgtcgcattcattcggctcctttttcatccatcgaagagagtt Find is-nt database================================================ Query_seq: PG1078:PG1079|PG1078:PG1079:electron transfer flavoprotein, alpha subunit:enoyl-CoA hydratase/isomerase family protein:->->:1146586..1146688 103 gagcctgttagtataacaaaccttgtagaggagccgatgaggcgaagggcttttgtggctcgtcgcattcattcggctcctttttcatccatcgaagagagtt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG1078:PG1079|PG1078:PG1079:electron transfer flavoprotein, alpha subunit:enoyl-CoA hydratase/isomerase family protein:->->:1146586..1146688 103 gagcctgttagtataacaaaccttgtagaggagccgatgaggcgaagggcttttgtggctcgtcgcattcattcggctcctttttcatccatcgaagagagtt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG1078:PG1079|PG1078:PG1079:electron transfer flavoprotein, alpha subunit:enoyl-CoA hydratase/isomerase family protein:->->:1146586..1146688 103 gagcctgttagtataacaaaccttgtagaggagccgatgaggcgaagggcttttgtggctcgtcgcattcattcggctcctttttcatccatcgaagagagtt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gagcctgttagtataacaaaccttgtagaggagccgatgaggcgaagggcttttgtggctcgtcgcattcattcggctcctttttcatccatcgaagagagtt Predict ORF larger than 30AA ================================================ Protein_Len: 30 Strand: + Start: 13 End: 102 ............ M T N L V E E P M R R R A F V A R R I H S A P F S S I E E S . gagcctgttagtataacaaaccttgtagaggagccgatgaggcgaagggcttttgtggctcgtcgcattcattcggctcctttttcatccatcgaagagagtt 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================================================ gagcctgttagtataacaaaccttgtagaggagccgatgaggcgaagggcttttgtggctcgtcgcattcattcggctcctttttcatccatcgaagagagtt Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 100 HP_score: -12.0 Tail_Score: -4.7497 Start: 30 End: 80 Full_Region: AACAAACCTTGTAGA GGAGCCGATGAGGCGAAGGGCT TTTGT GGCTCGTCGCATTCATTCGGCTCC TTTTTCATCCATCGA .............................GGAGCCGATGAGGCGAAGGGCTTTTGTGGCTCGTCGCATTCATTCGGCTCC....................... Find igs database================================================ Query_seq: PG1078:PG1079|PG1078:PG1079:electron transfer flavoprotein, alpha subunit:enoyl-CoA hydratase/isomerase family protein:->->:1146586..1146688 103 gagcctgttagtataacaaaccttgtagaggagccgatgaggcgaagggcttttgtggctcgtcgcattcattcggctcctttttcatccatcgaagagagtt Intra-Species Hit: Count: 1 Min: 1 Max: 103 Len: 103 Subject: NC_002950_PG1078_PG1079|electron transfer flavoprotein, alpha subunit:enoyl-CoA hydratase/isomerase family protein|POSITIVE:POSITIVE|[1146586,1146688]|103 HSP 1 e-value: 4.0E-52 bit: 204.0 Len: 103 Query Start:1 Query End:103 Subject Strand: POSITIVE Subject Start: 1 Subject End: 103 gagcctgttagtataacaaaccttgtagaggagccgatgaggcgaagggcttttgtggctcgtcgcattcattcggctcctttttcatccatcgaagagagtt gagcctgttagtataacaaaccttgtagaggagccgatgaggcgaagggcttttgtggctcgtcgcattcattcggctcctttttcatccatcgaagagagtt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAGCCUGUUAGUAUAACAAACCUUGUAGAGGAGCCGAUGAGGCGAAGGGCUUUUGUGGCUCGUCGCAUUCAUUCGGCUCCUUUUUCAUCCAUCGAAGAGAGUU (((..(((((...)))))...)))...((((((((((((((((((.(((((.....))))).)))).)))).))))))))))((((.((....)).))))... (-36.70) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AACUCUCUUCGAUGGAUGAAAAAGGAGCCGAAUGAAUGCGACGAGCCACAAAAGCCCUUCGCCUCAUCGGCUCCUCUACAAGGUUUGUUAUACUAACAGGCUC ...(((((.....))).))...(((((((((.(((..((((.(.((.......)).).)))).))))))))))))......(((((((((...))))))))). (-32.10) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 434 80 31 77 18 NC_002950:PG0145|5end_hypothetical_protein_167831..168061_POSITIVE 428 80 33 195 151 NC_002950:PG0677|5end_saccharopine_dehydrogenase_727653..727883_POSITIVE 403 70 25 229 185 NC_002950:PG1639|5end_hypothetical_protein_1719919..1720149_NEGATIVE 398 79 36 105 61 NC_002950:PG2098|5end_hypothetical_protein_2206635..2206865_NEGATIVE 395 80 31 98 48 NC_002950:PG0326|5end_hypothetical_protein_360974..361204_NEGATIVE 392 80 34 185 134 NC_002950:PG0882|5end_hypothetical_protein_944195..944425_POSITIVE 391 80 32 69 15 NC_002950:PG1738|5end_hypothetical_protein_1825131..1825361_NEGATIVE 389 79 31 209 164 NC_002950:PG0961|5end_hypothetical_protein_1022272..1022502_NEGATIVE 387 77 31 156 114 NC_002950:PG1655|5end_hypothetical_protein_1737095..1737325_POSITIVE 386 80 33 225 171 NC_002950:PG1226|5end_peptidyl-prolyl_cis-trans_isomerase,_cyclophilin-type_1303264..1303494_POSITIVE 381 78 33 63 17 NC_002950:PG0380|5end_excinuclease_ABC_subunit_B_409102..409332_POSITIVE 376 66 21 206 149 NC_002950:PG0740|5end_NLP/P60_family_protein_787836..788066_POSITIVE 371 77 34 145 95 NC_002950:PG1815|5end_3-deoxy-manno-octulosonate_cytidylyltransferase_1911433..1911663_NEGATIVE 367 89 41 52 4 NC_002950:PG2163|5end_acid_phosphatase_2269571..2269801_NEGATIVE 367 66 21 190 128 NC_002950:PG1633|5end_galactokinase_1713385..1713615_POSITIVE 366 77 31 223 178 NC_002950:PG0215|5end_hypothetical_protein_251460..251690_POSITIVE 366 80 33 99 49 NC_002950:PG0212|5end_precorrin-6Y_C5,15-methyltransferase,_decarboxylating_249065..249295_NEGATIVE 362 77 34 224 182 NC_002950:PG2204|5end_hypothetical_protein_2310381..2310611_POSITIVE 362 70 23 225 169 NC_002950:PG1484|5end_hypothetical_protein_1559979..1560209_NEGATIVE 361 80 31 200 153 NC_002950:PG2107|5end_thiamine_biosynthesis_protein_ThiH_2216658..2216888_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 434 66 21 61 1 NC_002950:PG1739|3end_hypothetical_protein_1825128..1825278_NEGATIVE 413 80 31 61 12 NC_002950:PG1078|3end_electron_transfer_flavoprotein,_alpha_subunit_1146525..1146675_POSITIVE 398 79 36 91 47 NC_002950:PG2099|3end_ATP-dependent_RNA_helicase,_DEAD/DEAH_box_family_2206649..2206799_NEGATIVE 392 80 34 75 24 NC_002950:PG0881|3end_recombinase_A_944165..944315_POSITIVE 389 80 31 135 87 NC_002950:PG1218|3end_hypothetical_protein_1296475..1296625_POSITIVE 387 77 31 142 100 NC_002950:PG1654|3end_D-alanyl-D-alanine_dipeptidase_1737161..1737311_POSITIVE 386 89 44 76 26 NC_002950:PG0726|3end_lipoprotein,_putative_778003..778153_NEGATIVE 384 66 28 141 106 NC_002950:PG0962|3end_prolyl-tRNA_synthetase_1022327..1022477_NEGATIVE 373 79 34 99 59 NC_002950:PG0605|3end_hypothetical_protein_661165..661315_NEGATIVE 371 77 34 148 98 NC_002950:PG1816|3end_NAD(P)H_dehydrogenase,_quinone_family,_putative_1911430..1911580_NEGATIVE 367 89 41 55 7 NC_002950:PG2164|3end_peptidyl-prolyl_cis-trans_isomerase,_FKBP-type_2269568..2269718_NEGATIVE 367 66 21 140 78 NC_002950:PG1632|3end_aldose_1-epimerase_1713415..1713565_POSITIVE 366 80 33 106 56 NC_002950:PG0213|3end_precorrin-3_methylase/precorrin-8X_methylmutase_249058..249208_NEGATIVE 365 70 27 47 6 NC_002950:PG0085|3end_alpha-galactosidase_100556..100706_POSITIVE 363 62 21 128 78 NC_002950:PG1252|3end_hypothetical_protein_1328349..1328499_NEGATIVE 362 76 33 68 12 NC_002950:PG2145|3end_polysaccharide_deacetylase_2253938..2254088_POSITIVE 361 80 32 80 27 NC_002950:PG0523|3end_inositol-5-monophosphate_dehydrogenase_566898..567048_NEGATIVE 359 64 21 102 48 NC_002950:PG2188|3end_diaminopimelate_decarboxylase_2294633..2294783_NEGATIVE 357 70 21 59 7 NC_002950:PG0639|3end_signal_peptide_peptidase_SppA,_67K_type_691213..691363_NEGATIVE 355 80 33 142 100 NC_002950:PG0767|3end_4-alpha-glucanotransferase_818557..818707_NEGATIVE