Origin IGS: agcgagaagtataccaaaagatgggatggcttgcaattgcttatcaagcaaaagcatcttcatcatgtgagcgtctcatagctatgacgtatttacggtatacataatcgatatacataatcgataaattattttttaaattttactatctattacaaacaatttctataataattatgaaagggggaaatttttcttccttttaaataatttttatgagaggtaaaaa .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tttttacctctcataaaaattatttaaaaggaagaaaaatttccccctttcataattattatagaaattgtttgtaatagatagtaaaatttaaaaaataatttatcgattatgtatatcgattatgtataccgtaaatacgtcatagctatgagacgctcacatgatgaagatgcttttgcttgataagcaattgcaagccatcccatcttttggtatacttctcgct Mask Tandem Repeat Region ================================================ agcgagaagtataccaaaagatgggatggcttgcaattgcttatcaagcaaaagcatcttcatcatgtgagcgtctcatagctatgacgtatttacggnnnnnnnnnnnnnnnnnnnnnnnnnnnnaattattttttaaattttactatctattacaaacaatttctataataattatgaaagggggaaatttttcttccttttaaataatttttatgagaggtaaaaa Find is-nt database================================================ Query_seq: TDE0006:TDE0007|TDE0006:TDE0007:Snf2 family protein:hypothetical protein:<-->:9785..10013 229 agcgagaagtataccaaaagatgggatggcttgcaattgcttatcaagcaaaagcatcttcatcatgtgagcgtctcatagctatgacgtatttacggtatacataatcgatatacataatcgataaattattttttaaattttactatctattacaaacaatttctataataattatgaaagggggaaatttttcttccttttaaataatttttatgagaggtaaaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE0006:TDE0007|TDE0006:TDE0007:Snf2 family protein:hypothetical protein:<-->:9785..10013 229 agcgagaagtataccaaaagatgggatggcttgcaattgcttatcaagcaaaagcatcttcatcatgtgagcgtctcatagctatgacgtatttacggtatacataatcgatatacataatcgataaattattttttaaattttactatctattacaaacaatttctataataattatgaaagggggaaatttttcttccttttaaataatttttatgagaggtaaaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE0006:TDE0007|TDE0006:TDE0007:Snf2 family protein:hypothetical protein:<-->:9785..10013 229 agcgagaagtataccaaaagatgggatggcttgcaattgcttatcaagcaaaagcatcttcatcatgtgagcgtctcatagctatgacgtatttacggtatacataatcgatatacataatcgataaattattttttaaattttactatctattacaaacaatttctataataattatgaaagggggaaatttttcttccttttaaataatttttatgagaggtaaaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 agcgagaagtataccaaaagatgggatggcttgcaattgcttatcaagcaaaagcatcttcatcatgtgagcgtctcatagctatgacgtatttacggtatacataatcgatatacataatcgataaattattttttaaattttactatctattacaaacaatttctataataattatgaaagggggaaatttttcttccttttaaataatttttatgagaggtaaaaa Predict ORF larger than 30AA ================================================ Protein_Len: 31 Strand: + Start: 111 End: 203 .............................................................................................................. M Y I I D K L F F K F Y Y L L Q T I S I I I M K G G N F S S F .......................... agcgagaagtataccaaaagatgggatggcttgcaattgcttatcaagcaaaagcatcttcatcatgtgagcgtctcatagctatgacgtatttacggtatacataatcgatatacataatcgataaattattttttaaattttactatctattacaaacaatttctataataattatgaaagggggaaatttttcttccttttaaataatttttatgagaggtaaaaa 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: 84 Start: 8 End: 37 .......ATTGCAAGCCATCCCATCTTTTGGTATACT................................................................................................................................................................................................ PromScan Matrix: RpoD-17 Strand: - Score: 81 Start: 140 End: 169 ...........................................................................................................................................ATAGAAATTGTTTGTAATAGATAGTAAAAT............................................................ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ agcgagaagtataccaaaagatgggatggcttgcaattgcttatcaagcaaaagcatcttcatcatgtgagcgtctcatagctatgacgtatttacggtatacataatcgatatacataatcgataaattattttttaaattttactatctattacaaacaatttctataataattatgaaagggggaaatttttcttccttttaaataatttttatgagaggtaaaaa Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE0006:TDE0007|TDE0006:TDE0007:Snf2 family protein:hypothetical protein:<-->:9785..10013 229 agcgagaagtataccaaaagatgggatggcttgcaattgcttatcaagcaaaagcatcttcatcatgtgagcgtctcatagctatgacgtatttacggtatacataatcgatatacataatcgataaattattttttaaattttactatctattacaaacaatttctataataattatgaaagggggaaatttttcttccttttaaataatttttatgagaggtaaaaa Intra-Species Hit: Count: 1 Min: 1 Max: 229 Len: 229 Subject: NC_002967_TDE0006_TDE0007|Snf2 family protein:hypothetical protein|NEGATIVE:POSITIVE|[9785,10013]|229 HSP 1 e-value: 1.0E-127 bit: 454.0 Len: 229 Query Start:1 Query End:229 Subject Strand: POSITIVE Subject Start: 1 Subject End: 229 agcgagaagtataccaaaagatgggatggcttgcaattgcttatcaagcaaaagcatcttcatcatgtgagcgtctcatagctatgacgtatttacggtatacataatcgatatacataatcgataaattattttttaaattttactatctattacaaacaatttctataataattatgaaagggggaaatttttcttccttttaaataatttttatgagaggtaaaaa agcgagaagtataccaaaagatgggatggcttgcaattgcttatcaagcaaaagcatcttcatcatgtgagcgtctcatagctatgacgtatttacggtatacataatcgatatacataatcgataaattattttttaaattttactatctattacaaacaatttctataataattatgaaagggggaaatttttcttccttttaaataatttttatgagaggtaaaaa Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGCGAGAAGUAUACCAAAAGAUGGGAUGGCUUGCAAUUGCUUAUCAAGCAAAAGCAUCUUCAUCAUGUGAGCGUCUCAUAGCUAUGACGUAUUUACGGUAUACAUAAUCGAUAUACAUAAUCGAUAAAUUAUUUUUUAAAUUUUACUAUCUAUUACAAACAAUUUCUAUAAUAAUUAUGAAAGGGGGAAAUUUUUCUUCCUUUUAAAUAAUUUUUAUGAGAGGUAAAAA ((..(((.(((((((....(((((((((.(((....(((((.....)))))))))))).)))))......(((((..........)))))......)))))))...((((((.......))))))...............)))..))..............((((((((((.(((((((((((((((((....)))))))))))..)))))).)))).))))))..... (-54.60) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUUUACCUCUCAUAAAAAUUAUUUAAAAGGAAGAAAAAUUUCCCCCUUUCAUAAUUAUUAUAGAAAUUGUUUGUAAUAGAUAGUAAAAUUUAAAAAAUAAUUUAUCGAUUAUGUAUAUCGAUUAUGUAUACCGUAAAUACGUCAUAGCUAUGAGACGCUCACAUGAUGAAGAUGCUUUUGCUUGAUAAGCAAUUGCAAGCCAUCCCAUCUUUUGGUAUACUUCUCGCU ................(((((((((.(((((..(((....)))..))))).....((((((((((.....))))))))))...............))))))))).(((((.......)))))....((((((((......(((((((((........)))...)))))).(((((.....(((((.(((....)))))))).....)))))..))))))))........ (-44.00) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 914 50 1 141 92 NC_002967:TDE0006|5end_Snf2_family_protein_9694..9924_NEGATIVE 610 189 141 215 167 NC_002967:TDE0670|5end_ATP-dependent_protease_La_707938..708168_POSITIVE 537 210 161 216 167 NC_002967:TDE0861|5end_tyrosyl-tRNA_synthetase_883098..883328_NEGATIVE 467 190 141 226 177 NC_002967:TDE0164|5end_hypothetical_protein_193998..194228_NEGATIVE 444 210 163 142 96 NC_002967:TDE1692|5end_hypothetical_protein_1748293..1748523_POSITIVE 401 220 171 76 26 NC_002967:TDE2099|5end_hypothetical_protein_2125027..2125257_POSITIVE 380 189 141 204 157 NC_002967:TDE1990|5end_ATP-dependent_helicase,_DinG_family_2008496..2008726_NEGATIVE 379 183 141 231 189 NC_002967:TDE2718|5end_magnesium_transporter_2775910..2776140_NEGATIVE 378 199 151 190 141 NC_002967:TDE0402|5end_hypothetical_protein_454352..454582_NEGATIVE 319 64 24 101 54 NC_002967:TDE1563|5end_hypothetical_protein_1615693..1615923_POSITIVE 302 99 54 202 153 NC_002967:TDE2731|5end_TIM-barrel_protein,_putative,_NifR3_family_2787372..2787602_POSITIVE 295 98 52 143 90 NC_002967:TDE1926|5end_hypothetical_protein_1942495..1942725_POSITIVE 292 77 36 100 62 NC_002967:TDE1655|5end_hypothetical_protein_1704958..1705188_POSITIVE 289 50 8 148 102 NC_002967:TDE0903|5end_ATP-dependent_DNA_helicase_PcrA_920228..920458_POSITIVE 289 70 21 77 19 NC_002967:TDE0432|5end_TPR_domain_protein,_truncation_488193..488423_NEGATIVE 285 67 21 48 12 NC_002967:TDE1989|5end_acyltransferase_family_protein_2006343..2006573_NEGATIVE 279 165 138 231 204 NC_002967:TDE2706|5end_hypothetical_protein_2753793..2754023_NEGATIVE 277 205 161 140 96 NC_002967:TDE2136|5end_hypothetical_protein_2165659..2165889_NEGATIVE 276 114 71 228 173 NC_002967:TDE2235|5end_methylaspartate_ammonia-lyase_2274588..2274818_NEGATIVE 272 50 2 69 17 NC_002967:TDE2406|5end_TldD/PmbA_family_protein_2433513..2433743_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 380 189 141 66 19 NC_002967:TDE1991|3end_hypothetical_protein_2008634..2008784_NEGATIVE 267 48 1 147 104 NC_002967:TDE2496|3end_methyl-accepting_chemotaxis_protein_2521170..2521320_NEGATIVE 260 83 41 118 64 NC_002967:TDE1633|3end_citrate_lyase_acyl_carrier_protein_1682428..1682578_NEGATIVE 258 75 33 149 106 NC_002967:TDE1925|3end_peptidyl-prolyl_cis-trans_isomerase,_FKBP-type_1942605..1942755_POSITIVE 258 47 2 76 31 NC_002967:TDE0446|3end_fibronectin_type_III_domain_protein_502848..502998_POSITIVE 255 50 1 132 83 NC_002967:TDE2570|3end_ribonuclease_HI_2597937..2598087_POSITIVE 253 77 33 47 5 NC_002967:TDE0960|3end_neuB_family_protein_983595..983745_POSITIVE 248 69 21 115 54 NC_002967:TDE0693|3end_phosphomethylpyrimidine_kinase_730831..730981_POSITIVE 246 50 1 55 14 NC_002967:TDE2690|3end_hypothetical_protein_2728743..2728893_NEGATIVE 243 97 54 57 8 NC_002967:TDE2162|3end_NOL1/NOP2/sun_family_protein_2195560..2195710_POSITIVE 243 50 1 51 2 NC_002967:TDE1803|3end_hypothetical_protein_1838395..1838545_NEGATIVE 242 98 53 75 35 NC_002967:TDE1589|3end_purine-binding_chemotaxis_protein_1637590..1637740_POSITIVE 240 100 53 45 1 NC_002967:TDE0286|3end_ABC_transporter,_ATP-binding_protein_315768..315918_NEGATIVE 239 49 1 128 78 NC_002967:TDE2722|3end_carhohydrate_kinase,_FGGY_family_2779666..2779816_NEGATIVE 235 50 2 52 7 NC_002967:TDE2583|3end_hypothetical_protein_2616500..2616650_POSITIVE 233 100 53 86 35 NC_002967:TDE2123|3end_hypothetical_protein_2156409..2156559_POSITIVE 229 77 37 45 2 NC_002967:TDE2696|3end_TPR_domain_protein_2739098..2739248_NEGATIVE 228 98 63 46 3 NC_002967:TDE1821|3end_hypothetical_protein_1854815..1854965_NEGATIVE 228 91 54 145 107 NC_002967:TDE0602|3end_3-oxoacyl-(acyl-carrier-protein)_synthase_III_639836..639986_NEGATIVE 225 110 62 145 97 NC_002967:TDE0035|3end_acetyltransferase,_GNAT_family_41580..41730_NEGATIVE