Origin IGS: aacttaagactttttaagtaaaacaaaaggctgttccccataagggacctcccacaaggggctcccatacgggcggacagcctttttactgtaaagaacctttttttaaactatacggaacctctaaaaaccaatcgagtttttagagattccctatc .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 gatagggaatctctaaaaactcgattggtttttagaggttccgtatagtttaaaaaaaggttctttacagtaaaaaggctgtccgcccgtatgggagccccttgtgggaggtcccttatggggaacagccttttgttttacttaaaaagtcttaagtt Mask Tandem Repeat Region ================================================ aacttaagactttttaagtaaaacaaaaggctgttccccataagggacctcccacaaggggctcccatacgggcggacagcctttttactgtaaagaacctttttttaaactatacggaacctctaaaaaccaatcgagtttttagagattccctatc Find is-nt database================================================ Query_seq: TDE2028:TDE2029|TDE2028:TDE2029:OmpA family protein:hydrolase, TatD family:-><-:2057080..2057237 158 aacttaagactttttaagtaaaacaaaaggctgttccccataagggacctcccacaaggggctcccatacgggcggacagcctttttactgtaaagaacctttttttaaactatacggaacctctaaaaaccaatcgagtttttagagattccctatc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE2028:TDE2029|TDE2028:TDE2029:OmpA family protein:hydrolase, TatD family:-><-:2057080..2057237 158 aacttaagactttttaagtaaaacaaaaggctgttccccataagggacctcccacaaggggctcccatacgggcggacagcctttttactgtaaagaacctttttttaaactatacggaacctctaaaaaccaatcgagtttttagagattccctatc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE2028:TDE2029|TDE2028:TDE2029:OmpA family protein:hydrolase, TatD family:-><-:2057080..2057237 158 aacttaagactttttaagtaaaacaaaaggctgttccccataagggacctcccacaaggggctcccatacgggcggacagcctttttactgtaaagaacctttttttaaactatacggaacctctaaaaaccaatcgagtttttagagattccctatc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aacttaagactttttaagtaaaacaaaaggctgttccccataagggacctcccacaaggggctcccatacgggcggacagcctttttactgtaaagaacctttttttaaactatacggaacctctaaaaaccaatcgagtttttagagattccctatc Predict ORF larger than 30AA ================================================ Protein_Len: 42 Strand: + Start: 31 End: 156 .............................. M F P I R D L P Q G A P I R A D S L F T V K N L F L N Y T E P L K T N R V F R D S L .. aacttaagactttttaagtaaaacaaaaggctgttccccataagggacctcccacaaggggctcccatacgggcggacagcctttttactgtaaagaacctttttttaaactatacggaacctctaaaaaccaatcgagtttttagagattccctatc 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================================================ aacttaagactttttaagtaaaacaaaaggctgttccccataagggacctcccacaaggggctcccatacgggcggacagcctttttactgtaaagaacctttttttaaactatacggaacctctaaaaaccaatcgagtttttagagattccctatc Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 100 HP_score: -14.6 Tail_Score: -4.8048 Start: 29 End: 82 Full_Region: TTAAGTAAAACAAAA GGCTGTTCCCCATAAGGGACCTCC CACAA GGGGCTCCCATACGGGCGGACAGCC TTTTTACTGTAAAGA ............................GGCTGTTCCCCATAAGGGACCTCCCACAAGGGGCTCCCATACGGGCGGACAGCC............................................................................ TransTerm Strand: - Conf: 100 HP_score: -13.2 Tail_Score: -5.18643 Start: 29 End: 82 Full_Region: tctttacagtaaaaa ggctgtccgcccgtatgggagcccc ttgt gggaggtcccttatggggaacagcc ttttgttttacttaa ............................ggctgtccgcccgtatgggagccccttgtgggaggtcccttatggggaacagcc............................................................................ Find igs database================================================ Query_seq: TDE2028:TDE2029|TDE2028:TDE2029:OmpA family protein:hydrolase, TatD family:-><-:2057080..2057237 158 aacttaagactttttaagtaaaacaaaaggctgttccccataagggacctcccacaaggggctcccatacgggcggacagcctttttactgtaaagaacctttttttaaactatacggaacctctaaaaaccaatcgagtttttagagattccctatc Intra-Species Hit: Count: 1 Min: 1 Max: 158 Len: 158 Subject: NC_002967_TDE2028_TDE2029|OmpA family protein:hydrolase, TatD family|POSITIVE:NEGATIVE|[2057080,2057237]|158 HSP 1 e-value: 3.0E-72 bit: 272.0 Len: 158 Query Start:1 Query End:158 Subject Strand: POSITIVE Subject Start: 1 Subject End: 158 aacttaagactttttaagtaaaacaaaaggctgttccccataagggacctcccacaaggggctcccatacgggcggacagcctttttactgtaaagaaccnnnnnnnaaactatacggaacctctaaaaaccaatcgagtttttagagattccctatc aacttaagactttttaagtaaaacaaaaggctgttccccataagggacctcccacaaggggctcccatacgggcggacagcctttttactgtaaagaacctttttttaaactatacggaacctctaaaaaccaatcgagtttttagagattccctatc Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AACUUAAGACUUUUUAAGUAAAACAAAAGGCUGUUCCCCAUAAGGGACCUCCCACAAGGGGCUCCCAUACGGGCGGACAGCCUUUUUACUGUAAAGAACCUUUUUUUAAACUAUACGGAACCUCUAAAAACCAAUCGAGUUUUUAGAGAUUCCCUAUC .........((((...(((((((....((((((((((((.((.((((.((((.....)))).)))).)).))).))))))))))))))))..))))....................((((.(((((((((((....).)))))))))).))))..... (-56.40) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAUAGGGAAUCUCUAAAAACUCGAUUGGUUUUUAGAGGUUCCGUAUAGUUUAAAAAAAGGUUCUUUACAGUAAAAAGGCUGUCCGCCCGUAUGGGAGCCCCUUGUGGGAGGUCCCUUAUGGGGAACAGCCUUUUGUUUUACUUAAAAAGUCUUAAGUU .(((.((((((((((((((((.....)))))))))))))))).)))..........(((..(.((((.((((((((((((((.(.((((((.((((.((((....))).).)))).))))))).)))))))....))))))))))).)..)))..... (-67.20) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 410 80 31 64 1 NC_002967:TDE2028|5end_OmpA_family_protein_2052923..2053153_POSITIVE 352 148 116 103 74 NC_002967:TDE0629|5end_chaperone_protein_DnaJ_662587..662817_POSITIVE 341 76 31 160 107 NC_002967:TDE2103|5end_glycosyl_transferase,_group_2_family_protein_2128393..2128623_NEGATIVE 331 76 37 201 156 NC_002967:TDE1060|5end_hypothetical_protein_1086519..1086749_POSITIVE 326 87 43 109 64 NC_002967:TDE1644|5end_methionyl-tRNA_formyltransferase_1695546..1695776_NEGATIVE 324 64 22 119 74 NC_002967:TDE2786|5end_DNA_polymerase_III_subunit_alpha_2842672..2842902_NEGATIVE 324 77 37 140 108 NC_002967:TDE0573|5end_hypothetical_protein_604681..604911_POSITIVE 323 69 27 212 166 NC_002967:TDE1261|5end_choline/carnitine/betaine_transporter_family_protein_1295593..1295823_POSITIVE 322 77 31 218 173 NC_002967:TDE0945|5end_hypothetical_protein_967128..967358_POSITIVE 318 81 44 157 116 NC_002967:TDE2725|5end_cyclic_nucleotide_binding_domain/GGDEF_domain_protein_2783208..2783438_NEGATIVE 317 74 32 174 118 NC_002967:TDE0570|5end_hypothetical_protein_600169..600399_POSITIVE 315 58 11 112 55 NC_002967:TDE2742|5end_site-specific_recombinase,_phage_integrase_family_2797659..2797889_NEGATIVE 313 66 29 108 52 NC_002967:TDE1892|5end_hypothetical_protein_1912065..1912295_POSITIVE 311 82 44 73 30 NC_002967:TDE1112|5end_adenylate_kinase_1146918..1147148_POSITIVE 308 66 31 30 1 NC_002967:TDE2286|5end_MazG_family_protein_2323354..2323584_POSITIVE 305 79 34 231 188 NC_002967:TDE0575|5end_aspartyl/glutamyl-tRNA_amidotransferase_subunit_B_607733..607963_NEGATIVE 304 88 51 45 1 NC_002967:TDE0522|5end_hypothetical_protein_568499..568729_POSITIVE 302 86 57 152 128 NC_002967:TDE0143|5end_thiamine_ABC_transporter,_thiamine-binding_protein_164013..164243_POSITIVE 300 83 44 131 84 NC_002967:TDE0132|5end_hypothetical_protein_152046..152276_POSITIVE 299 73 31 116 67 NC_002967:TDE1612|5end_phosphoribosyl_transferase_domain_protein_1660549..1660779_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 399 90 44 74 25 NC_002967:TDE2028|3end_OmpA_family_protein_2057019..2057169_POSITIVE 373 80 35 59 1 NC_002967:TDE2027|3end_hypothetical_protein_2052998..2053148_POSITIVE 368 86 41 140 94 NC_002967:TDE0731|3end_hypothetical_protein_770691..770841_NEGATIVE 352 148 116 65 36 NC_002967:TDE0628|3end_molecular_chaperone_DnaK_662629..662779_POSITIVE 326 87 43 112 67 NC_002967:TDE1645|3end_polypeptide_deformylase_1695543..1695693_NEGATIVE 326 91 57 61 21 NC_002967:TDE0977|3end_hypothetical_protein_1001640..1001790_POSITIVE 324 77 37 113 81 NC_002967:TDE0572|3end_hypothetical_protein_604734..604884_POSITIVE 322 77 31 47 2 NC_002967:TDE0944|3end_hypothetical_protein_967037..967187_POSITIVE 320 82 49 45 2 NC_002967:TDE2403|3end_metallo-beta-lactamase_family_protein_2428641..2428791_NEGATIVE 317 74 32 87 31 NC_002967:TDE0569|3end_hypothetical_protein_600162..600312_POSITIVE 311 65 28 106 50 NC_002967:TDE1914|3end_Holliday_junction_DNA_helicase_RuvB_1930889..1931039_NEGATIVE 310 88 43 136 85 NC_002967:TDE0833|3end_lipoprotein,_putative_854097..854247_POSITIVE 310 76 40 151 111 NC_002967:TDE0451|3end_arginine_deiminase_509965..510115_POSITIVE 307 87 49 138 96 NC_002967:TDE1173|3end_site-specific_recombinase,_phage_integrase_family_1201257..1201407_NEGATIVE 305 150 108 85 45 NC_002967:TDE1264|3end_hypothetical_protein_1298152..1298302_NEGATIVE 302 86 57 124 100 NC_002967:TDE0141|3end_hypothetical_protein_164065..164215_POSITIVE 301 63 29 76 49 NC_002967:TDE0870|3end_phosphatase/nucleotidase_894676..894826_POSITIVE 300 95 51 79 33 NC_002967:TDE2673|3end_hypothetical_protein_2711670..2711820_NEGATIVE 300 92 54 94 57 NC_002967:TDE0658|3end_ABC_transporter,_permease_protein_695679..695829_POSITIVE 300 83 44 106 59 NC_002967:TDE0131|3end_hypothetical_protein_152101..152251_POSITIVE