Origin IGS: agtttcaccttataagactatagacaaggcttttccgaaaaggttgcaatagaaagaaaatgaaaaatatggtagaattcagtttgattttaaaggatgcttattttaaagaattttt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aaaaattctttaaaataagcatcctttaaaatcaaactgaattctaccatatttttcattttctttctattgcaaccttttcggaaaagccttgtctatagtcttataaggtgaaact Mask Tandem Repeat Region ================================================ agtttcaccttataagactatagacaaggcttttccgaaaaggttgcaatagaaagaaaatgaaaaatatggtagaattcagtttgattttaaaggatgcttattttaaagaattttt Find is-nt database================================================ Query_seq: TDE0040:TDE0041|TDE0040:TDE0041:AMP-binding protein:birA bifunctional protein:<-->:47519..47636 118 agtttcaccttataagactatagacaaggcttttccgaaaaggttgcaatagaaagaaaatgaaaaatatggtagaattcagtttgattttaaaggatgcttattttaaagaattttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE0040:TDE0041|TDE0040:TDE0041:AMP-binding protein:birA bifunctional protein:<-->:47519..47636 118 agtttcaccttataagactatagacaaggcttttccgaaaaggttgcaatagaaagaaaatgaaaaatatggtagaattcagtttgattttaaaggatgcttattttaaagaattttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE0040:TDE0041|TDE0040:TDE0041:AMP-binding protein:birA bifunctional protein:<-->:47519..47636 118 agtttcaccttataagactatagacaaggcttttccgaaaaggttgcaatagaaagaaaatgaaaaatatggtagaattcagtttgattttaaaggatgcttattttaaagaattttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 agtttcaccttataagactatagacaaggcttttccgaaaaggttgcaatagaaagaaaatgaaaaatatggtagaattcagtttgattttaaaggatgcttattttaaagaattttt Predict ORF larger than 30AA ================================================ agtttcaccttataagactatagacaaggcttttccgaaaaggttgcaatagaaagaaaatgaaaaatatggtagaattcagtttgattttaaaggatgcttattttaaagaattttt 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: 81 Start: 49 End: 78 ................................................ATAGAAAGAAAATGAAAAATATGGTAGAAT........................................ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ agtttcaccttataagactatagacaaggcttttccgaaaaggttgcaatagaaagaaaatgaaaaatatggtagaattcagtttgattttaaaggatgcttattttaaagaattttt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE0040:TDE0041|TDE0040:TDE0041:AMP-binding protein:birA bifunctional protein:<-->:47519..47636 118 agtttcaccttataagactatagacaaggcttttccgaaaaggttgcaatagaaagaaaatgaaaaatatggtagaattcagtttgattttaaaggatgcttattttaaagaattttt Intra-Species Hit: Count: 1 Min: 1 Max: 118 Len: 118 Subject: NC_002967_TDE0040_TDE0041|AMP-binding protein:birA bifunctional protein|NEGATIVE:POSITIVE|[47519,47636]|118 HSP 1 e-value: 5.0E-61 bit: 234.0 Len: 118 Query Start:1 Query End:118 Subject Strand: POSITIVE Subject Start: 1 Subject End: 118 agtttcaccttataagactatagacaaggcttttccgaaaaggttgcaatagaaagaaaatgaaaaatatggtagaattcagtttgattttaaaggatgcttattttaaagaattttt agtttcaccttataagactatagacaaggcttttccgaaaaggttgcaatagaaagaaaatgaaaaatatggtagaattcagtttgattttaaaggatgcttattttaaagaattttt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGUUUCACCUUAUAAGACUAUAGACAAGGCUUUUCCGAAAAGGUUGCAAUAGAAAGAAAAUGAAAAAUAUGGUAGAAUUCAGUUUGAUUUUAAAGGAUGCUUAUUUUAAAGAAUUUUU .......((((......((((.(....(((((((....))))))).).))))....(((((.(((....(((......))).))).))))).))))...................... (-12.20) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAAAUUCUUUAAAAUAAGCAUCCUUUAAAAUCAAACUGAAUUCUACCAUAUUUUUCAUUUUCUUUCUAUUGCAACCUUUUCGGAAAAGCCUUGUCUAUAGUCUUAUAAGGUGAAACU .....................................................(((((((((....((((.((((.((((.....))))..))))..))))......))))))))).. ( -8.90) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 832 50 1 141 92 NC_002967:TDE0040|5end_AMP-binding_protein_47428..47658_NEGATIVE 280 108 61 136 76 NC_002967:TDE1457|5end_hypothetical_protein_1506262..1506492_NEGATIVE 265 64 24 69 12 NC_002967:TDE1987|5end_hypothetical_protein_2002312..2002542_POSITIVE 263 57 18 83 44 NC_002967:TDE1989|5end_acyltransferase_family_protein_2006343..2006573_NEGATIVE 263 66 30 66 26 NC_002967:TDE0642|5end_hypothetical_protein_679164..679394_NEGATIVE 259 58 14 182 137 NC_002967:TDE1509|5end_lipoprotein_releasing_system,_ATP-binding_protein,_putative_1556389..1556619_POSITIVE 258 62 23 222 178 NC_002967:TDE2716|5end_HAD-superfamily_hydrolase,_subfamily_IA_2773195..2773425_POSITIVE 241 47 2 168 114 NC_002967:TDE1486|5end_hypothetical_protein_1530299..1530529_POSITIVE 241 50 4 229 183 NC_002967:TDE0706|5end_adenine-specific_DNA_modification_methyltransferase_740420..740650_POSITIVE 232 62 28 56 20 NC_002967:TDE1737|5end_hypothetical_protein_1790133..1790363_POSITIVE 230 46 12 50 3 NC_002967:TDE2701|5end_hypothetical_protein_2745689..2745919_POSITIVE 230 48 8 202 164 NC_002967:TDE1413|5end_cytidylyltransferase/phosphoenolpyruvate_phosphomutase,_putative_1455510..1455740_POSITIVE 226 47 1 209 155 NC_002967:TDE1708|5end_apolipoprotein_N-acyltransferase_1764822..1765052_NEGATIVE 225 37 4 139 97 NC_002967:TDE2352|5end_flagellar_hook-associated_protein_2387235..2387465_POSITIVE 225 64 24 218 170 NC_002967:TDE0502|5end_ankyrin_repeat_protein_556558..556788_NEGATIVE 224 60 17 175 138 NC_002967:TDE0566|5end_hypothetical_protein_597185..597415_POSITIVE 222 47 22 28 2 NC_002967:TDE0880|5end_nicotinate-nucleotide-dimethylbenzimidazole_phosphoribosyltransferase_899974..900204_POSITIVE 217 59 11 160 114 NC_002967:TDE2300|5end_trypsin_domain/PDZ_domain_protein_2341434..2341664_NEGATIVE 215 36 1 121 92 NC_002967:TDE2212|5end_galactokinase_2252681..2252911_NEGATIVE 214 109 66 225 177 NC_002967:TDE0457|5end_hypothetical_protein_513525..513755_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 280 108 61 139 79 NC_002967:TDE1458|3end_hypothetical_protein_1506259..1506409_NEGATIVE 263 57 18 59 20 NC_002967:TDE1990|3end_ATP-dependent_helicase,_DinG_family_2006367..2006517_NEGATIVE 239 44 1 125 73 NC_002967:TDE1117|3end_hypothetical_protein_1149871..1150021_POSITIVE 230 46 12 142 95 NC_002967:TDE2701|3end_hypothetical_protein_2745861..2746011_POSITIVE 230 46 12 49 2 NC_002967:TDE2700|3end_citrate_carrier_protein,_CCS_family_2745768..2745918_POSITIVE 229 68 23 57 26 NC_002967:TDE1907|3end_holo-(acyl-carrier-protein)_synthase_1924726..1924876_NEGATIVE 225 37 4 128 86 NC_002967:TDE2351|3end_hypothetical_protein_2387304..2387454_POSITIVE 225 46 5 105 67 NC_002967:TDE1667|3end_translation_initiation_factor_IF-2B_subunit_alpha_1719993..1720143_NEGATIVE 224 60 17 140 103 NC_002967:TDE0565|3end_hypothetical_protein_597230..597380_POSITIVE 222 47 22 31 5 NC_002967:TDE0879|3end_hypothetical_protein_900057..900207_POSITIVE 218 43 1 76 38 NC_002967:TDE2558|3end_ABC_transporter,_ATP-binding/permease_protein_2583729..2583879_NEGATIVE 212 48 13 54 17 NC_002967:TDE1967|3end_hypothetical_protein_1982533..1982683_POSITIVE 212 55 22 63 35 NC_002967:TDE1612|3end_phosphoribosyl_transferase_domain_protein_1661690..1661840_POSITIVE 212 44 10 136 104 NC_002967:TDE0487|3end_ABC_transporter,_ATP-binding_protein_543628..543778_NEGATIVE 206 46 1 78 35 NC_002967:TDE2437|3end_cyclic_nucleotide_binding_domain_protein_2467418..2467568_NEGATIVE 202 80 34 66 17 NC_002967:TDE2698|3end_hypothetical_protein_2742775..2742925_POSITIVE 199 33 1 128 87 NC_002967:TDE0111|3end_hypothetical_protein_132114..132264_POSITIVE 197 48 7 139 95 NC_002967:TDE1538|3end_DNA_ligase,_NAD-dependent_1583585..1583735_POSITIVE 196 74 31 58 14 NC_002967:TDE2461|3end_selenide,_water_dikinase_(selenocysteine-containing)_2487196..2487346_NEGATIVE 196 37 14 140 119 NC_002967:TDE1508|3end_hypothetical_protein_1556451..1556601_POSITIVE