Origin IGS: tagcttcctcctatttttaagaccaagaaaaccttagtcaaagctattataatcttaccattgaataaccgaattttcaagtttttatttacttttttccatatttatgttacagtaccggacatataagtattcgttggaggatttt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aaaatcctccaacgaatacttatatgtccggtactgtaacataaatatggaaaaaagtaaataaaaacttgaaaattcggttattcaatggtaagattataatagctttgactaaggttttcttggtcttaaaaataggaggaagcta Mask Tandem Repeat Region ================================================ tagcttcctcctatttttaagaccaagaaaaccttagtcaaagctattataatcttaccattgaataaccgaattttcaagtttttatttacttttttccatatttatgttacagtaccggacatataagtattcgttggaggatttt Find is-nt database================================================ Query_seq: TDE2336:TDE2337|TDE2336:TDE2337:sodium/dicarboxylate symporter family protein:aminopeptidase:<-->:2373287..2373434 148 tagcttcctcctatttttaagaccaagaaaaccttagtcaaagctattataatcttaccattgaataaccgaattttcaagtttttatttacttttttccatatttatgttacagtaccggacatataagtattcgttggaggatttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE2336:TDE2337|TDE2336:TDE2337:sodium/dicarboxylate symporter family protein:aminopeptidase:<-->:2373287..2373434 148 tagcttcctcctatttttaagaccaagaaaaccttagtcaaagctattataatcttaccattgaataaccgaattttcaagtttttatttacttttttccatatttatgttacagtaccggacatataagtattcgttggaggatttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE2336:TDE2337|TDE2336:TDE2337:sodium/dicarboxylate symporter family protein:aminopeptidase:<-->:2373287..2373434 148 tagcttcctcctatttttaagaccaagaaaaccttagtcaaagctattataatcttaccattgaataaccgaattttcaagtttttatttacttttttccatatttatgttacagtaccggacatataagtattcgttggaggatttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tagcttcctcctatttttaagaccaagaaaaccttagtcaaagctattataatcttaccattgaataaccgaattttcaagtttttatttacttttttccatatttatgttacagtaccggacatataagtattcgttggaggatttt Predict ORF larger than 30AA ================================================ Protein_Len: 38 Strand: + Start: 13 End: 126 ............ M F K T K K T L V K A I I I L P L N N R I F K F L F T F F H I Y V T V P D I ...................... Protein_Len: 34 Strand: - Start: 3 End: 104 .. S G G I K L V L F V K T L A I I I K G N F L R I K L N K N V K K W M ............................................ tagcttcctcctatttttaagaccaagaaaaccttagtcaaagctattataatcttaccattgaataaccgaattttcaagtttttatttacttttttccatatttatgttacagtaccggacatataagtattcgttggaggatttt Predict Promoter with matrix: RpoD-15 score > 80================================================ Predict Promoter with matrix: RpoD-16 score > 80================================================ Predict Promoter with matrix: RpoD-17 score > 80================================================ PromScan Matrix: RpoD-17 Strand: - Score: 87 Start: 52 End: 81 ...................................................CTTGAAAATTCGGTTATTCAATGGTAAGAT................................................................... PromScan Matrix: RpoD-17 Strand: + Score: 82 Start: 87 End: 116 ......................................................................................ATTTACTTTTTTCCATATTTATGTTACAGT................................ PromScan Matrix: RpoD-17 Strand: - Score: 81 Start: 13 End: 42 ............TTTGACTAAGGTTTTCTTGGTCTTAAAAAT.......................................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ tagcttcctcctatttttaagaccaagaaaaccttagtcaaagctattataatcttaccattgaataaccgaattttcaagtttttatttacttttttccatatttatgttacagtaccggacatataagtattcgttggaggatttt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE2336:TDE2337|TDE2336:TDE2337:sodium/dicarboxylate symporter family protein:aminopeptidase:<-->:2373287..2373434 148 tagcttcctcctatttttaagaccaagaaaaccttagtcaaagctattataatcttaccattgaataaccgaattttcaagtttttatttacttttttccatatttatgttacagtaccggacatataagtattcgttggaggatttt Intra-Species Hit: Count: 1 Min: 1 Max: 148 Len: 148 Subject: NC_002967_TDE2336_TDE2337|sodium/dicarboxylate symporter family protein:aminopeptidase|NEGATIVE:POSITIVE|[2373287, 2373434]|148 HSP 1 e-value: 5.0E-34 bit: 145.0 Len: 73 Query Start:1 Query End:73 Subject Strand: POSITIVE Subject Start: 1 Subject End: 73 tagcttcctcctatttttaagaccaagaaaaccttagtcaaagctattataatcttaccattgaataaccgaa........................................................................... tagcttcctcctatttttaagaccaagaaaaccttagtcaaagctattataatcttaccattgaataaccgaa........................................................................... HSP 2 e-value: 2.0E-20 bit: 99.6 Len: 50 Query Start:99 Query End:148 Subject Strand: POSITIVE Subject Start: 99 Subject End: 148 ..................................................................................................ccatatttatgttacagtaccggacatataagtattcgttggaggatttt ..................................................................................................ccatatttatgttacagtaccggacatataagtattcgttggaggatttt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAGCUUCCUCCUAUUUUUAAGACCAAGAAAACCUUAGUCAAAGCUAUUAUAAUCUUACCAUUGAAUAACCGAAUUUUCAAGUUUUUAUUUACUUUUUUCCAUAUUUAUGUUACAGUACCGGACAUAUAAGUAUUCGUUGGAGGAUUUU ((((((.....((....)).(((.(((.....))).))).))))))....((((((.(((.((((((...(((.....((((........))))..)))......((((((.........))))))....)))))).))))))))).. (-21.30) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAAUCCUCCAACGAAUACUUAUAUGUCCGGUACUGUAACAUAAAUAUGGAAAAAAGUAAAUAAAAACUUGAAAAUUCGGUUAUUCAAUGGUAAGAUUAUAAUAGCUUUGACUAAGGUUUUCUUGGUCUUAAAAAUAGGAGGAAGCUA ....((((((.........(((((.(((...((((((...((((...((((...((((........)))).....)))).))))...)))))).)))))))).......(((((((.....))))))).........))))))..... (-27.40) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 791 50 1 141 92 NC_002967:TDE2336|5end_sodium/dicarboxylate_symporter_family_protein_2373196..2373426_NEGATIVE 289 49 6 142 96 NC_002967:TDE0004|5end_hypothetical_protein_4243..4473_POSITIVE 241 44 3 64 24 NC_002967:TDE0169|5end_methyl-accepting_chemotaxis_domain_protein_198792..199022_NEGATIVE 232 70 21 55 11 NC_002967:TDE2207|5end_hypothetical_protein_2246634..2246864_NEGATIVE 230 104 61 43 6 NC_002967:TDE2781|5end_ABC_transporter,_ATP-binding/permease_protein_2832468..2832698_NEGATIVE 216 97 56 57 22 NC_002967:TDE1855|5end_hypothetical_protein_1882846..1883076_POSITIVE 213 35 1 189 160 NC_002967:TDE2002|5end_hypothetical_protein_2022195..2022425_NEGATIVE 213 39 1 129 94 NC_002967:TDE1089|5end_hypothetical_protein_1120944..1121174_NEGATIVE 211 48 9 59 10 NC_002967:TDE1456|5end_GGDEF_domain_protein_1504739..1504969_NEGATIVE 206 45 2 231 186 NC_002967:TDE1485|5end_hypothetical_protein_1529697..1529927_POSITIVE 203 41 2 176 130 NC_002967:TDE2662|5end_lipoprotein,_putative_2698650..2698880_NEGATIVE 203 60 19 90 45 NC_002967:TDE2341|5end_membrane-associated_zinc_metalloprotease,_putative_2379218..2379448_NEGATIVE 201 123 89 35 1 NC_002967:TDE0856|5end_L-fuculose_phosphate_aldolase,_putative_877111..877341_POSITIVE 201 27 2 40 18 NC_002967:TDE0370|5end_UDP-N-acetylmuramoylalanine--D-glutamate_ligase_421084..421314_POSITIVE 200 37 1 217 186 NC_002967:TDE2097|5end_hypothetical_protein_2124741..2124971_NEGATIVE 200 130 95 183 139 NC_002967:TDE0156|5end_adenylate/guanylate_cyclase_catalytic_domain_protein_183571..183801_NEGATIVE 198 140 92 149 99 NC_002967:TDE1589|5end_purine-binding_chemotaxis_protein_1637004..1637234_POSITIVE 198 45 3 175 131 NC_002967:TDE1492|5end_chemotaxis_protein_CheW_1537231..1537461_POSITIVE 195 47 8 129 99 NC_002967:TDE0457|5end_hypothetical_protein_513525..513755_POSITIVE 194 45 2 41 2 NC_002967:TDE2192|5end_threonine_synthase_2227761..2227991_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 289 49 6 101 55 NC_002967:TDE0003|3end_hypothetical_protein_4282..4432_POSITIVE 222 78 32 142 87 NC_002967:TDE2435|3end_hypothetical_protein_2465866..2466016_NEGATIVE 213 128 100 138 104 NC_002967:TDE0269|3end_hypothetical_protein_300196..300346_NEGATIVE 211 48 9 59 10 NC_002967:TDE1457|3end_hypothetical_protein_1504739..1504889_NEGATIVE 209 45 2 74 19 NC_002967:TDE0464|3end_NifU_domain_protein_517948..518098_NEGATIVE 203 60 19 70 25 NC_002967:TDE2342|3end_1-deoxy-D-xylulose_5-phosphate_reductoisomerase_2379238..2379388_NEGATIVE 194 50 3 94 27 NC_002967:TDE1293|3end_TldD/PmbA_family_protein_1330621..1330771_NEGATIVE 193 140 117 143 124 NC_002967:TDE2597|3end_ribulose-phosphate_3-epimerase_2632036..2632186_NEGATIVE 192 140 91 149 96 NC_002967:TDE1657|3end_transcription_antitermination_protein_NusB_1707230..1707380_NEGATIVE 192 129 84 70 22 NC_002967:TDE0581|3end_transglutaminase-like_domain_protein_620416..620566_POSITIVE 191 86 42 125 89 NC_002967:TDE2076|3end_hypothetical_protein_2104530..2104680_NEGATIVE 190 64 25 98 53 NC_002967:TDE1010|3end_excinuclease_ABC,_A_subunit_1038171..1038321_POSITIVE 190 119 74 91 42 NC_002967:TDE0677|3end_hypothetical_protein_716051..716201_POSITIVE 188 48 8 51 6 NC_002967:TDE2302|3end_HD_domain_protein_2343135..2343285_POSITIVE 188 94 51 75 31 NC_002967:TDE0398|3end_oligopeptide/dipeptide_ABC_transporter,_periplasmic_peptide-binding_protein_449436..449586_POSITIVE 187 36 8 40 12 NC_002967:TDE1527|3end_hypothetical_protein_1571795..1571945_POSITIVE 186 86 41 127 88 NC_002967:TDE0008|3end_copper-translocating_P-type_ATPase_13646..13796_POSITIVE 185 45 5 122 85 NC_002967:TDE2683|3end_sigma_factor_WhiG_2723367..2723517_NEGATIVE 185 38 4 110 83 NC_002967:TDE1632|3end_citrate_lyase,_beta_subunit_1681569..1681719_NEGATIVE 184 139 92 122 76 NC_002967:TDE2747|3end_type_I_restriction-modification_system,_R_subunit_2802138..2802288_NEGATIVE