Origin IGS: agtttattttgtatatgaaataaaagaatgttgtctcaacgacaaatatacggcttttttcgttgatgaatatattccgtcatttttttgtagaaaagtgaaaaatccattcctgttttcttcctttt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aaaaggaagaaaacaggaatggatttttcacttttctacaaaaaaatgacggaatatattcatcaacgaaaaaagccgtatatttgtcgttgagacaacattcttttatttcatatacaaaataaact Mask Tandem Repeat Region ================================================ agtttattttgtatatgaaataaaagaatgttgtctcaacgacaaatatacggcttttttcgttgatgaatatattccgtcatttttttgtagaaaagtgaaaaatccattcctgttttcttcctttt Find is-nt database================================================ Query_seq: TF0246:TF0247|TF0246:TF0247:saccharopine dehydrogenase:conserved hypothetical protein:->->:277591..277718 128 agtttattttgtatatgaaataaaagaatgttgtctcaacgacaaatatacggcttttttcgttgatgaatatattccgtcatttttttgtagaaaagtgaaaaatccattcctgttttcttcctttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF0246:TF0247|TF0246:TF0247:saccharopine dehydrogenase:conserved hypothetical protein:->->:277591..277718 128 agtttattttgtatatgaaataaaagaatgttgtctcaacgacaaatatacggcttttttcgttgatgaatatattccgtcatttttttgtagaaaagtgaaaaatccattcctgttttcttcctttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF0246:TF0247|TF0246:TF0247:saccharopine dehydrogenase:conserved hypothetical protein:->->:277591..277718 128 agtttattttgtatatgaaataaaagaatgttgtctcaacgacaaatatacggcttttttcgttgatgaatatattccgtcatttttttgtagaaaagtgaaaaatccattcctgttttcttcctttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 agtttattttgtatatgaaataaaagaatgttgtctcaacgacaaatatacggcttttttcgttgatgaatatattccgtcatttttttgtagaaaagtgaaaaatccattcctgttttcttcctttt Predict ORF larger than 30AA ================================================ Protein_Len: 36 Strand: + Start: 20 End: 127 ................... M K E C C L N D K Y T A F F V D E Y I P S F F C R K V K N P F L F S S F . agtttattttgtatatgaaataaaagaatgttgtctcaacgacaaatatacggcttttttcgttgatgaatatattccgtcatttttttgtagaaaagtgaaaaatccattcctgttttcttcctttt 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================================================ agtttattttgtatatgaaataaaagaatgttgtctcaacgacaaatatacggcttttttcgttgatgaatatattccgtcatttttttgtagaaaagtgaaaaatccattcctgttttcttcctttt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TF0246:TF0247|TF0246:TF0247:saccharopine dehydrogenase:conserved hypothetical protein:->->:277591..277718 128 agtttattttgtatatgaaataaaagaatgttgtctcaacgacaaatatacggcttttttcgttgatgaatatattccgtcatttttttgtagaaaagtgaaaaatccattcctgttttcttcctttt Intra-Species Hit: Count: 1 Min: 1 Max: 128 Len: 128 Subject: tfor_TF0246_TF0247|saccharopine dehydrogenase:conserved hypothetical protein|POSITIVE:POSITIVE|[277591,277718]|128 HSP 1 e-value: 2.0E-54 bit: 212.0 Len: 128 Query Start:1 Query End:128 Subject Strand: POSITIVE Subject Start: 1 Subject End: 128 agtttattttgtatatgaaataaaagaatgttgtctcaacgacaaatatacggcttttttcgttgatgaatatattccgtcannnnnnngtagaaaagtgaaaaatccattcctgttttcttcctttt agtttattttgtatatgaaataaaagaatgttgtctcaacgacaaatatacggcttttttcgttgatgaatatattccgtcatttttttgtagaaaagtgaaaaatccattcctgttttcttcctttt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGUUUAUUUUGUAUAUGAAAUAAAAGAAUGUUGUCUCAACGACAAAUAUACGGCUUUUUUCGUUGAUGAAUAUAUUCCGUCAUUUUUUUGUAGAAAAGUGAAAAAUCCAUUCCUGUUUUCUUCCUUUU ..((((((((......)))))))).((((((..(((((((((.(((.........))).))))))).))..))))))..(((((((((....)))))))))........................... (-22.10) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAAGGAAGAAAACAGGAAUGGAUUUUUCACUUUUCUACAAAAAAAUGACGGAAUAUAUUCAUCAACGAAAAAAGCCGUAUAUUUGUCGUUGAGACAACAUUCUUUUAUUUCAUAUACAAAAUAAACU (((((((((((..((....))..)))))).)))))........((((((.(((((....((.(((((((..(((........))).)))))))))....))))).))))))................. (-20.90) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 307 88 50 88 54 tfor:TF2492|5end_NifU-related_protein_2666683..2666913_POSITIVE 296 93 51 163 119 tfor:TF2407|5end_glycosyltransferase_2581574..2581804_POSITIVE 268 100 51 228 182 tfor:TF1529|5end_hypothetical_protein_1634300..1634530_POSITIVE 256 68 25 199 163 tfor:TF1515|5end_hypothetical_protein_1625307..1625537_POSITIVE 255 80 31 225 167 tfor:TF0492|5end_outer_membrane_protein,_TonB_dependent_receptor_514060..514290_POSITIVE 255 80 31 225 167 tfor:TF0482|5end_outer_membrane_receptor_500729..500959_POSITIVE 248 99 51 92 31 tfor:TF2439|5end_conserved_hypothetical_protein_2616380..2616610_POSITIVE 238 120 72 156 104 tfor:TF0309|5end_conserved_hypothetical_protein_334174..334404_POSITIVE 237 79 40 144 105 tfor:TF1906|5end_conserved_hypothetical_protein_2060955..2061185_POSITIVE 235 86 47 194 157 tfor:TF2555|5end_50S_ribosomal_protein_L2_2736326..2736556_POSITIVE 235 79 32 107 56 tfor:TF1539|5end_conserved_hypothetical_protein_1644067..1644297_POSITIVE 235 82 43 135 89 tfor:TF1264|5end_possible_transposase_1351290..1351520_POSITIVE 234 93 51 93 56 tfor:TF0207|5end_conserved_hypothetical_protein_233105..233335_POSITIVE 233 83 41 170 127 tfor:TF1916|5end_conserved_hypothetical_protein;_possible_ATPase_2068530..2068760_POSITIVE 232 80 35 198 161 tfor:TF3051|5end_conserved_hypothetical_protein_3277649..3277879_POSITIVE 231 68 32 83 48 tfor:TF2032|5end_outer_membrane_protein,_TonB_dependent_receptor_2188269..2188499_POSITIVE 228 63 29 59 24 tfor:TF0465|5end_cobalamin_biosynthesis_protein_482028..482258_POSITIVE 226 90 49 72 21 tfor:TF2870|5end_hypothetical_protein_3062002..3062232_POSITIVE 226 80 34 66 23 tfor:TF0442|5end_Na+-transporting_NADH:ubiquinone_oxidoreductase,_subunit_4_465270..465500_POSITIVE 226 90 44 173 121 tfor:TF0387|5end_hypothetical_protein_407612..407842_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 307 88 50 80 46 tfor:TF2490|3end_4-hydroxyphenylacetate-3-hydroxylase/4-hydroxybut_yryl_dehydratase_2666755..2666905_POSITIVE 246 70 25 54 2 tfor:TF0789|3end_preprotein_translocase,_secDF_family_843670..843820_POSITIVE 235 79 32 92 41 tfor:TF1538|3end_conserved_hypothetical_protein_1644132..1644282_POSITIVE 235 82 43 100 54 tfor:TF1263|3end_DNA-mismatch_repair_protein_1351335..1351485_POSITIVE 234 62 24 51 3 tfor:TF0681|3end_sugar_kinase,_PfkB_family_724209..724359_POSITIVE 233 83 41 49 6 tfor:TF1915|3end_NAD-dependent_protein_deacetylase,_SIR2_family_2068489..2068639_POSITIVE 231 68 32 80 45 tfor:TF2031|3end_conserved_hypothetical_protein_2188346..2188496_POSITIVE 228 63 29 59 24 tfor:TF0464|3end_precorrin_methylase_482108..482258_POSITIVE 226 90 44 60 8 tfor:TF0386|3end_transcriptional_regulator,_possible_LuxR_family_407579..407729_POSITIVE 225 118 74 144 81 tfor:TF2052|3end_acetyl_transferase_2217165..2217315_POSITIVE 223 94 51 97 48 tfor:TF1314|3end_conserved_hypothetical_protein_1390302..1390452_POSITIVE 221 115 75 47 4 tfor:TF3116|3end_conserved_hypothetical_protein_3352413..3352563_POSITIVE 221 59 26 78 44 tfor:TF2881|3end_conserved_hypothetical_protein_3072380..3072530_POSITIVE 219 80 32 128 74 tfor:TF2221|3end_CTn_excision_protein_2394229..2394379_POSITIVE 219 80 31 61 17 tfor:TF0726|3end_ABC_transporter,_permease_component_779258..779408_POSITIVE 217 44 17 126 100 tfor:TF2820|3end_argininosuccinate_synthetase_3011200..3011350_POSITIVE 217 80 38 150 103 tfor:TF2058|3end_possible_ATP-dependent_DNA_helicase_2223798..2223948_POSITIVE 216 99 52 60 2 tfor:TF0192|3end_hypothetical_protein_207984..208134_POSITIVE 214 81 51 53 15 tfor:TF2978|3end_conserved_hypothetical_protein_3190862..3191012_POSITIVE 214 82 50 104 74 tfor:TF0467|3end_acetyltransferase-related_protein_486543..486693_POSITIVE