Origin IGS: agtttactcccataataacacgatgttttgtgcaaagcacaaaactcgaagacaaacagcgaggcagaatttctgccgaactgtttatcacacctcccataaaatcattttaacatatttccagataaaatactacaatttataaaatttt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aaaattttataaattgtagtattttatctggaaatatgttaaaatgattttatgggaggtgtgataaacagttcggcagaaattctgcctcgctgtttgtcttcgagttttgtgctttgcacaaaacatcgtgttattatgggagtaaact Mask Tandem Repeat Region ================================================ agtttactcccataataacacgatgttttgtgcaaagcacaaaactcgaagacaaacagcgaggcagaatttctgccgaactgtttatcacacctcccataaaatcattttaacatatttccagataaaatactacaatttataaaatttt Find is-nt database================================================ Query_seq: TDE0466:TDE0467|TDE0466:TDE0467:hypothetical protein:hypothetical protein:<-<-:518945..519095 151 agtttactcccataataacacgatgttttgtgcaaagcacaaaactcgaagacaaacagcgaggcagaatttctgccgaactgtttatcacacctcccataaaatcattttaacatatttccagataaaatactacaatttataaaatttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE0466:TDE0467|TDE0466:TDE0467:hypothetical protein:hypothetical protein:<-<-:518945..519095 151 agtttactcccataataacacgatgttttgtgcaaagcacaaaactcgaagacaaacagcgaggcagaatttctgccgaactgtttatcacacctcccataaaatcattttaacatatttccagataaaatactacaatttataaaatttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE0466:TDE0467|TDE0466:TDE0467:hypothetical protein:hypothetical protein:<-<-:518945..519095 151 agtttactcccataataacacgatgttttgtgcaaagcacaaaactcgaagacaaacagcgaggcagaatttctgccgaactgtttatcacacctcccataaaatcattttaacatatttccagataaaatactacaatttataaaatttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 agtttactcccataataacacgatgttttgtgcaaagcacaaaactcgaagacaaacagcgaggcagaatttctgccgaactgtttatcacacctcccataaaatcattttaacatatttccagataaaatactacaatttataaaatttt Predict ORF larger than 30AA ================================================ Protein_Len: 33 Strand: + Start: 12 End: 110 ........... M I T R C F V Q S T K L E D K Q R G R I S A E L F I T P P I K S F ......................................... Protein_Len: 40 Strand: + Start: 23 End: 142 ...................... M F C A K H K T R R Q T A R Q N F C R T V Y H T S H K I I L T Y F Q I K Y Y N L ......... Protein_Len: 33 Strand: - Start: 2 End: 100 . N V G M I V R H K T C L V F S S S L C R P L I E A S S N I V G G M ................................................... agtttactcccataataacacgatgttttgtgcaaagcacaaaactcgaagacaaacagcgaggcagaatttctgccgaactgtttatcacacctcccataaaatcattttaacatatttccagataaaatactacaatttataaaatttt 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================================================ agtttactcccataataacacgatgttttgtgcaaagcacaaaactcgaagacaaacagcgaggcagaatttctgccgaactgtttatcacacctcccataaaatcattttaacatatttccagataaaatactacaatttataaaatttt Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 70 HP_score: -7.4 Tail_Score: -3.79906 Start: 19 End: 50 Full_Region: gcctcgctgtttgtc ttcgagttttgtgc ttt gcacaaaacatcgtg ttattatgggagtaa ..................ttcgagttttgtgctttgcacaaaacatcgtg..................................................................................................... TransTerm Strand: - Conf: 90 HP_score: -12.2 Tail_Score: -3.48378 Start: 21 End: 48 Full_Region: ctcgctgtttgtctt cgagttttgtgc ttt gcacaaaacatcg tgttattatgggagt ....................cgagttttgtgctttgcacaaaacatcg....................................................................................................... TransTerm Strand: - Conf: 70 HP_score: -8.6 Tail_Score: -3.16437 Start: 53 End: 87 Full_Region: ttatgggaggtgtga taaacagttcggcaga aat tctgcctcgctgtttg tcttcgagttttgtg ....................................................taaacagttcggcagaaattctgcctcgctgtttg................................................................ TransTerm Strand: - Conf: 76 HP_score: -7.2 Tail_Score: -4.22041 Start: 57 End: 83 Full_Region: gggaggtgtgataaa cagttcggcaga aat tctgcctcgctg tttgtcttcgagttt ........................................................cagttcggcagaaattctgcctcgctg.................................................................... Find igs database================================================ Query_seq: TDE0466:TDE0467|TDE0466:TDE0467:hypothetical protein:hypothetical protein:<-<-:518945..519095 151 agtttactcccataataacacgatgttttgtgcaaagcacaaaactcgaagacaaacagcgaggcagaatttctgccgaactgtttatcacacctcccataaaatcattttaacatatttccagataaaatactacaatttataaaatttt Intra-Species Hit: Count: 1 Min: 1 Max: 151 Len: 151 Subject: NC_002967_TDE0466_TDE0467|hypothetical protein:hypothetical protein|NEGATIVE:NEGATIVE|[518945,519095]|151 HSP 1 e-value: 1.0E-80 bit: 299.0 Len: 151 Query Start:1 Query End:151 Subject Strand: POSITIVE Subject Start: 1 Subject End: 151 agtttactcccataataacacgatgttttgtgcaaagcacaaaactcgaagacaaacagcgaggcagaatttctgccgaactgtttatcacacctcccataaaatcattttaacatatttccagataaaatactacaatttataaaatttt agtttactcccataataacacgatgttttgtgcaaagcacaaaactcgaagacaaacagcgaggcagaatttctgccgaactgtttatcacacctcccataaaatcattttaacatatttccagataaaatactacaatttataaaatttt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGUUUACUCCCAUAAUAACACGAUGUUUUGUGCAAAGCACAAAACUCGAAGACAAACAGCGAGGCAGAAUUUCUGCCGAACUGUUUAUCACACCUCCCAUAAAAUCAUUUUAACAUAUUUCCAGAUAAAAUACUACAAUUUAUAAAAUUUU ..((((.((....((((...(((.(((((((((...))))))))))))..((.((((((...(((((.....)))))...)))))).))..........................))))....))))))...................... (-31.30) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAAUUUUAUAAAUUGUAGUAUUUUAUCUGGAAAUAUGUUAAAAUGAUUUUAUGGGAGGUGUGAUAAACAGUUCGGCAGAAAUUCUGCCUCGCUGUUUGUCUUCGAGUUUUGUGCUUUGCACAAAACAUCGUGUUAUUAUGGGAGUAAACU .....(((((........(((((((.....)))))))......(((((..(((((..((...((((((((((..(((((.....)))))..)))))))))).))..(((((((((...))))))))).)))))..)))))....))))).. (-41.30) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 963 100 51 191 142 NC_002967:TDE0466|5end_hypothetical_protein_518854..519084_NEGATIVE 713 97 54 154 111 NC_002967:TDE1655|5end_hypothetical_protein_1704958..1705188_POSITIVE 700 70 21 231 182 NC_002967:TDE0064|5end_diphosphate--fructose-6-phosphate_1-phosphotransferase_72651..72881_NEGATIVE 691 97 54 197 154 NC_002967:TDE2497|5end_hypothetical_protein_2522083..2522313_NEGATIVE 691 97 54 198 155 NC_002967:TDE2224|5end_hypothetical_protein_2264743..2264973_POSITIVE 691 97 54 97 54 NC_002967:TDE2223|5end_hypothetical_protein_2264642..2264872_POSITIVE 690 79 31 130 82 NC_002967:TDE1325|5end_hypothetical_protein_1361721..1361951_NEGATIVE 682 80 31 172 123 NC_002967:TDE1298|5end_cyclic_nucleotide_binding_domain_protein_1335315..1335545_NEGATIVE 675 80 31 169 120 NC_002967:TDE1236|5end_triosephosphate_isomerase_1269486..1269716_POSITIVE 675 80 31 59 10 NC_002967:TDE1235|5end_hypothetical_protein_1269376..1269606_POSITIVE 658 80 31 168 118 NC_002967:TDE1849|5end_hypothetical_protein_1878123..1878353_NEGATIVE 626 97 54 175 132 NC_002967:TDE2394|5end_hypothetical_protein_2422612..2422842_NEGATIVE 625 69 22 231 184 NC_002967:TDE1324|5end_hypothetical_protein_1361610..1361840_NEGATIVE 623 90 41 66 16 NC_002967:TDE1972|5end_hypothetical_protein_1987224..1987454_NEGATIVE 607 90 41 90 40 NC_002967:TDE0692|5end_hypothetical_protein_729712..729942_POSITIVE 605 97 54 136 93 NC_002967:TDE1334|5end_hypothetical_protein_1370144..1370374_POSITIVE 602 100 54 164 116 NC_002967:TDE2666|5end_hydrolase,_carbon-nitrogen_family_2704394..2704624_NEGATIVE 595 98 54 203 159 NC_002967:TDE0870|5end_phosphatase/nucleotidase_892698..892928_POSITIVE 588 90 46 150 106 NC_002967:TDE2131|5end_cobalamin_biosynthesis_protein_CbiM,_putative_2162683..2162913_NEGATIVE 588 97 54 118 75 NC_002967:TDE1694|5end_hypothetical_protein_1749366..1749596_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 795 89 42 61 14 NC_002967:TDE2396|3end_putative_inner_membrane_protein_translocase_component_YidC_2423650..2423800_NEGATIVE 730 80 31 70 21 NC_002967:TDE0065|3end_hypothetical_protein_72822..72972_NEGATIVE 691 97 54 86 43 NC_002967:TDE2498|3end_metallo-beta-lactamase_family_protein_2522194..2522344_NEGATIVE 691 97 54 77 34 NC_002967:TDE2222|3end_hypothetical_protein_2264702..2264852_POSITIVE 691 97 54 80 37 NC_002967:TDE1901|3end_ABC_transporter,_ATP-binding_protein_1922319..1922469_POSITIVE 690 79 31 62 14 NC_002967:TDE1327|3end_hypothetical_protein_1361789..1361939_NEGATIVE 682 80 31 70 21 NC_002967:TDE1299|3end_hypothetical_protein_1335417..1335567_NEGATIVE 669 80 31 73 23 NC_002967:TDE0591|3end_acetyl-CoA_carboxylase,_biotin_carboxylase_630033..630183_NEGATIVE 658 80 31 64 14 NC_002967:TDE1850|3end_ABC_transporter,_permease_protein,_putative_1878227..1878377_NEGATIVE 624 70 21 150 101 NC_002967:TDE1235|3end_hypothetical_protein_1269557..1269707_POSITIVE 623 90 41 51 1 NC_002967:TDE1973|3end_CvpA_family_protein_1987239..1987389_NEGATIVE 620 89 41 82 33 NC_002967:TDE0743|3end_thioredoxin_reductase_779751..779901_POSITIVE 617 97 55 43 1 NC_002967:TDE2395|3end_Jag_protein,_putative_2422744..2422894_NEGATIVE 605 97 54 60 17 NC_002967:TDE1333|3end_hflC_protein,_putative_1370148..1370298_POSITIVE 604 89 42 75 28 NC_002967:TDE1916|3end_glycerol_kinase_1933277..1933427_NEGATIVE 595 98 54 87 43 NC_002967:TDE0869|3end_hypothetical_protein_892662..892812_POSITIVE 588 90 46 77 33 NC_002967:TDE2132|3end_cobalt_ABC_transporter,_ATP-binding_protein,_putative_2162756..2162906_NEGATIVE 568 89 41 73 24 NC_002967:TDE2485|3end_hypothetical_protein_2507903..2508053_NEGATIVE 563 97 54 87 44 NC_002967:TDE1209|3end_site-specific_recombinase,_phage_integrase_family_1243342..1243492_POSITIVE 537 79 31 57 9 NC_002967:TDE2398|3end_conserved_hypothetical_protein_TIGR00278_2425586..2425736_NEGATIVE