Origin IGS: gcattatactcctaaattcgaggcattttagcataaaaaaggggcttggtcaaggaatggagaaaattcaactatctgcaaaccggaaaagtgcacctagccgtagcataaaataaaaaaacagattaccgagcattcccgacaatctgttttttaaaaattcttatagtaaat .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 atttactataagaatttttaaaaaacagattgtcgggaatgctcggtaatctgtttttttattttatgctacggctaggtgcacttttccggtttgcagatagttgaattttctccattccttgaccaagccccttttttatgctaaaatgcctcgaatttaggagtataatgc Mask Tandem Repeat Region ================================================ gcattatactcctaaattcgaggcattttagcataaaaaaggggcttggtcaaggaatggagaaaattcaactatctgcaaaccggaaaagtgcacctagccgtagcataaaataaaaaaacagattaccgagcattcccgacaatctgttttttaaaaattcttatagtaaat Find is-nt database================================================ Query_seq: TDE0295:TDE0296|TDE0295:TDE0296:DNA gyrase, A subunit:formiminotransferase, putative:<-<-:326758..326931 174 gcattatactcctaaattcgaggcattttagcataaaaaaggggcttggtcaaggaatggagaaaattcaactatctgcaaaccggaaaagtgcacctagccgtagcataaaataaaaaaacagattaccgagcattcccgacaatctgttttttaaaaattcttatagtaaat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE0295:TDE0296|TDE0295:TDE0296:DNA gyrase, A subunit:formiminotransferase, putative:<-<-:326758..326931 174 gcattatactcctaaattcgaggcattttagcataaaaaaggggcttggtcaaggaatggagaaaattcaactatctgcaaaccggaaaagtgcacctagccgtagcataaaataaaaaaacagattaccgagcattcccgacaatctgttttttaaaaattcttatagtaaat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE0295:TDE0296|TDE0295:TDE0296:DNA gyrase, A subunit:formiminotransferase, putative:<-<-:326758..326931 174 gcattatactcctaaattcgaggcattttagcataaaaaaggggcttggtcaaggaatggagaaaattcaactatctgcaaaccggaaaagtgcacctagccgtagcataaaataaaaaaacagattaccgagcattcccgacaatctgttttttaaaaattcttatagtaaat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gcattatactcctaaattcgaggcattttagcataaaaaaggggcttggtcaaggaatggagaaaattcaactatctgcaaaccggaaaagtgcacctagccgtagcataaaataaaaaaacagattaccgagcattcccgacaatctgttttttaaaaattcttatagtaaat Predict ORF larger than 30AA ================================================ Protein_Len: 37 Strand: + Start: 3 End: 113 .. M I L L N S R H F S I K K G L G Q G M E K I Q L S A N R K S A P S R S I K ............................................................. gcattatactcctaaattcgaggcattttagcataaaaaaggggcttggtcaaggaatggagaaaattcaactatctgcaaaccggaaaagtgcacctagccgtagcataaaataaaaaaacagattaccgagcattcccgacaatctgttttttaaaaattcttatagtaaat 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: 89 Start: 25 End: 54 ........................CTTGACCAAGCCCCTTTTTTATGCTAAAAT........................................................................................................................ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ gcattatactcctaaattcgaggcattttagcataaaaaaggggcttggtcaaggaatggagaaaattcaactatctgcaaaccggaaaagtgcacctagccgtagcataaaataaaaaaacagattaccgagcattcccgacaatctgttttttaaaaattcttatagtaaat Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 70 HP_score: -2.6 Tail_Score: -5.06103 Start: 122 End: 149 Full_Region: CATAAAATAAAAAAA CAGATTACCGAG CATT CCCGACAATCTG TTTTTTAAAAATTCT .........................................................................................................................CAGATTACCGAGCATTCCCGACAATCTG......................... Find igs database================================================ Query_seq: TDE0295:TDE0296|TDE0295:TDE0296:DNA gyrase, A subunit:formiminotransferase, putative:<-<-:326758..326931 174 gcattatactcctaaattcgaggcattttagcataaaaaaggggcttggtcaaggaatggagaaaattcaactatctgcaaaccggaaaagtgcacctagccgtagcataaaataaaaaaacagattaccgagcattcccgacaatctgttttttaaaaattcttatagtaaat Intra-Species Hit: Count: 1 Min: 1 Max: 174 Len: 174 Subject: NC_002967_TDE0295_TDE0296|DNA gyrase, A subunit:formiminotransferase, putative|NEGATIVE:NEGATIVE|[326758,326931]|174 HSP 1 e-value: 1.0E-81 bit: 303.0 Len: 174 Query Start:1 Query End:174 Subject Strand: POSITIVE Subject Start: 1 Subject End: 174 gcattatactcctaaattcgaggcattttagcataaaaaaggggcttggtcaaggaatggagaaaattcaactatctgcaaaccggaaaagtgcacctagccgtagcataaaatnnnnnnncagattaccgagcattcccgacaatctgttttttaaaaattcttatagtaaat gcattatactcctaaattcgaggcattttagcataaaaaaggggcttggtcaaggaatggagaaaattcaactatctgcaaaccggaaaagtgcacctagccgtagcataaaataaaaaaacagattaccgagcattcccgacaatctgttttttaaaaattcttatagtaaat Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GCAUUAUACUCCUAAAUUCGAGGCAUUUUAGCAUAAAAAAGGGGCUUGGUCAAGGAAUGGAGAAAAUUCAACUAUCUGCAAACCGGAAAAGUGCACCUAGCCGUAGCAUAAAAUAAAAAAACAGAUUACCGAGCAUUCCCGACAAUCUGUUUUUUAAAAAUUCUUAUAGUAAAU ((......(((........)))....................((((.(((((..((((.......)))).....((((.....))))....)).))).))))...))........((((((((((((..((........))..))))))))))))................... (-31.00) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUUUACUAUAAGAAUUUUUAAAAAACAGAUUGUCGGGAAUGCUCGGUAAUCUGUUUUUUUAUUUUAUGCUACGGCUAGGUGCACUUUUCCGGUUUGCAGAUAGUUGAAUUUUCUCCAUUCCUUGACCAAGCCCCUUUUUUAUGCUAAAAUGCCUCGAAUUUAGGAGUAUAAUGC .((((.((((((((.....((((((((((((..((((....))))..)))))))))))).............((((.(((.((.......((..((.(((...........))).))..)).))))).))))...)))))))).))))((((..(.......)..))))..... (-37.90) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 908 90 41 181 132 NC_002967:TDE0295|5end_DNA_gyrase,_A_subunit_326667..326897_NEGATIVE 309 49 1 149 88 NC_002967:TDE1963|5end_selenocysteine-specific_translation_elongation_factor_1975289..1975519_POSITIVE 309 71 32 187 154 NC_002967:TDE0487|5end_ABC_transporter,_ATP-binding_protein_544413..544643_NEGATIVE 294 66 22 142 93 NC_002967:TDE1375|5end_pantetheine-phosphate_adenylyltransferase_1418081..1418311_POSITIVE 286 58 21 164 120 NC_002967:TDE1993|5end_aspartate_ammonia-lyase,_putative_2012308..2012538_NEGATIVE 265 79 37 179 142 NC_002967:TDE2260|5end_hypothetical_protein_2297338..2297568_POSITIVE 265 88 41 149 92 NC_002967:TDE1964|5end_Na/Pi_cotransporter_family_protein_1978780..1979010_NEGATIVE 265 115 73 90 49 NC_002967:TDE0003|5end_hypothetical_protein_3483..3713_POSITIVE 257 62 21 51 12 NC_002967:TDE2326|5end_cobyric_acid_synthase_CobQ,_putative_2361087..2361317_POSITIVE 252 99 52 170 133 NC_002967:TDE2232|5end_iron_compound_ABC_transporter,_ATP-binding_protein,_putative_2271285..2271515_NEGATIVE 247 59 11 150 100 NC_002967:TDE2346|5end_elongation_factor_Ts_2383429..2383659_NEGATIVE 246 85 43 49 8 NC_002967:TDE2728|5end_hypothetical_protein_2785607..2785837_POSITIVE 246 110 64 219 152 NC_002967:TDE1211|5end_ATP-dependent_protease_ATP-binding_subunit_1243865..1244095_POSITIVE 245 64 30 138 106 NC_002967:TDE2503|5end_hypothetical_protein_2527827..2528057_POSITIVE 245 47 9 135 99 NC_002967:TDE0005|5end_L-threonine_aldolase,_low-specificity_6040..6270_NEGATIVE 243 85 43 110 68 NC_002967:TDE2751|5end_hypothetical_protein_2807570..2807800_POSITIVE 243 50 9 44 1 NC_002967:TDE0437|5end_PBS_lyase_HEAT-like_repeat_domain_protein_493605..493835_NEGATIVE 242 60 28 33 3 NC_002967:TDE1257|5end_hypothetical_protein_1290878..1291108_POSITIVE 239 127 85 88 42 NC_002967:TDE1951|5end_ribonuclease_Z_1968329..1968559_NEGATIVE 237 53 17 227 196 NC_002967:TDE0971|5end_arginyl-tRNA_synthetase_995179..995409_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 286 58 21 130 86 NC_002967:TDE1994|3end_hypothetical_protein_2012342..2012492_NEGATIVE 265 115 73 67 26 NC_002967:TDE0002|3end_DNA_gyrase,_B_subunit_3540..3690_POSITIVE 264 53 11 56 18 NC_002967:TDE0479|3end_hydroxylamine_reductase_535029..535179_NEGATIVE 263 61 21 72 34 NC_002967:TDE2473|3end_30S_ribosomal_protein_S21_2496587..2496737_POSITIVE 259 88 41 112 50 NC_002967:TDE2104|3end_hypothetical_protein_2128525..2128675_NEGATIVE 257 80 40 46 9 NC_002967:TDE2375|3end_hypothetical_protein_2406344..2406494_NEGATIVE 257 62 21 61 22 NC_002967:TDE2325|3end_hypothetical_protein_2361177..2361327_POSITIVE 256 56 20 64 27 NC_002967:TDE2075|3end_GGDEF_domain/EAL_domain_protein_2101504..2101654_NEGATIVE 254 106 68 42 1 NC_002967:TDE0740|3end_hypothetical_protein_776204..776354_POSITIVE 250 87 41 66 3 NC_002967:TDE0099|3end_adenine-specific_DNA_modification_methyltransferase_117014..117164_POSITIVE 247 59 11 76 26 NC_002967:TDE2347|3end_30S_ribosomal_protein_S2_2383503..2383653_NEGATIVE 246 87 43 41 1 NC_002967:TDE1433|3end_glycosyl_transferase,_group_2_family_protein_1478302..1478452_POSITIVE 245 64 30 75 43 NC_002967:TDE2502|3end_sensor_histidine_kinase/response_regulator_2527844..2527994_POSITIVE 245 55 11 71 21 NC_002967:TDE1913|3end_hypothetical_protein_1930897..1931047_POSITIVE 245 47 9 65 29 NC_002967:TDE0006|3end_Snf2_family_protein_6110..6260_NEGATIVE 244 118 82 151 115 NC_002967:TDE2760|3end_flagellar_biosynthesis_protein_2815066..2815216_NEGATIVE 241 49 2 94 31 NC_002967:TDE0297|3end_hypothetical_protein_327796..327946_NEGATIVE 237 138 91 57 11 NC_002967:TDE0242|3end_hypothetical_protein_275314..275464_NEGATIVE 236 61 21 63 23 NC_002967:TDE2082|3end_hypothetical_protein_2112489..2112639_NEGATIVE 236 107 73 151 123 NC_002967:TDE0949|3end_enolase_973391..973541_POSITIVE