Origin IGS: ggaaatcaaccgcaagggccgctaatagcgcaaagagatttatgtgtcttaccctttaccgattaaaatttatatgctattatatatcttgtgaattttatgtaaacattt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aaatgtttacataaaattcacaagatatataatagcatataaattttaatcggtaaagggtaagacacataaatctctttgcgctattagcggcccttgcggttgatttcc Mask Tandem Repeat Region ================================================ ggaaatcaaccgcaagggccgctaatagcgcaaagagatttatgtgtcttaccctttaccgattaaaatttatatgctattatatatcttgtgaattttatgtaaacattt Find is-nt database================================================ Query_seq: TDE1287:TDE1288|TDE1287:TDE1288:transcription-repair coupling factor:CAAX amino terminal protease family protein:->->:1326346..1326456 111 ggaaatcaaccgcaagggccgctaatagcgcaaagagatttatgtgtcttaccctttaccgattaaaatttatatgctattatatatcttgtgaattttatgtaaacattt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE1287:TDE1288|TDE1287:TDE1288:transcription-repair coupling factor:CAAX amino terminal protease family protein:->->:1326346..1326456 111 ggaaatcaaccgcaagggccgctaatagcgcaaagagatttatgtgtcttaccctttaccgattaaaatttatatgctattatatatcttgtgaattttatgtaaacattt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE1287:TDE1288|TDE1287:TDE1288:transcription-repair coupling factor:CAAX amino terminal protease family protein:->->:1326346..1326456 111 ggaaatcaaccgcaagggccgctaatagcgcaaagagatttatgtgtcttaccctttaccgattaaaatttatatgctattatatatcttgtgaattttatgtaaacattt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ggaaatcaaccgcaagggccgctaatagcgcaaagagatttatgtgtcttaccctttaccgattaaaatttatatgctattatatatcttgtgaattttatgtaaacattt Predict ORF larger than 30AA ================================================ ggaaatcaaccgcaagggccgctaatagcgcaaagagatttatgtgtcttaccctttaccgattaaaatttatatgctattatatatcttgtgaattttatgtaaacattt 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: 83 Start: 54 End: 83 .....................................................CTTTACCGATTAAAATTTATATGCTATTAT............................ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ ggaaatcaaccgcaagggccgctaatagcgcaaagagatttatgtgtcttaccctttaccgattaaaatttatatgctattatatatcttgtgaattttatgtaaacattt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE1287:TDE1288|TDE1287:TDE1288:transcription-repair coupling factor:CAAX amino terminal protease family protein:->->:1326346..1326456 111 ggaaatcaaccgcaagggccgctaatagcgcaaagagatttatgtgtcttaccctttaccgattaaaatttatatgctattatatatcttgtgaattttatgtaaacattt Intra-Species Hit: Count: 1 Min: 1 Max: 111 Len: 111 Subject: NC_002967_TDE1287_TDE1288|transcription-repair coupling factor:CAAX amino terminal protease family protein|POSITIVE:POSITIVE|[1326346,1326456]|111 HSP 1 e-value: 7.0E-57 bit: 220.0 Len: 111 Query Start:1 Query End:111 Subject Strand: POSITIVE Subject Start: 1 Subject End: 111 ggaaatcaaccgcaagggccgctaatagcgcaaagagatttatgtgtcttaccctttaccgattaaaatttatatgctattatatatcttgtgaattttatgtaaacattt ggaaatcaaccgcaagggccgctaatagcgcaaagagatttatgtgtcttaccctttaccgattaaaatttatatgctattatatatcttgtgaattttatgtaaacattt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GGAAAUCAACCGCAAGGGCCGCUAAUAGCGCAAAGAGAUUUAUGUGUCUUACCCUUUACCGAUUAAAAUUUAUAUGCUAUUAUAUAUCUUGUGAAUUUUAUGUAAACAUUU ((.......((....))..(((.....)))....(((((......)))))..)).((((....(((((((((((...............))))))))))).))))...... (-17.56) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAUGUUUACAUAAAAUUCACAAGAUAUAUAAUAGCAUAUAAAUUUUAAUCGGUAAAGGGUAAGACACAUAAAUCUCUUUGCGCUAUUAGCGGCCCUUGCGGUUGAUUUCC ..(((((...(((....((....))..)))...))))).......(((((((...((((((.(((........))).....(((.....))))))))).)))))))..... (-16.00) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 412 50 8 158 114 NC_002967:TDE0944|5end_hypothetical_protein_966247..966477_POSITIVE 345 35 8 134 108 NC_002967:TDE2480|5end_heat_shock_protein_90_2505288..2505518_NEGATIVE 335 45 8 202 166 NC_002967:TDE0162|5end_hypothetical_protein_187898..188128_POSITIVE 329 45 8 200 159 NC_002967:TDE0975|5end_hypothetical_protein_998921..999151_POSITIVE 313 50 8 168 124 NC_002967:TDE0977|5end_hypothetical_protein_1000415..1000645_POSITIVE 307 41 8 226 194 NC_002967:TDE0438|5end_queuine_tRNA-ribosyltransferase_494811..495041_NEGATIVE 303 37 9 54 23 NC_002967:TDE0139|5end_hypothetical_protein_162583..162813_NEGATIVE 298 50 1 230 179 NC_002967:TDE1345|5end_DNA_primase_1383439..1383669_POSITIVE 289 41 1 200 158 NC_002967:TDE2435|5end_hypothetical_protein_2466462..2466692_NEGATIVE 285 60 14 89 44 NC_002967:TDE2739|5end_hypothetical_protein_2794673..2794903_POSITIVE 281 60 16 208 157 NC_002967:TDE1018|5end_hypothetical_protein_1049227..1049457_POSITIVE 279 38 11 141 116 NC_002967:TDE1251|5end_batB_protein,_putative_1285448..1285678_POSITIVE 278 50 8 169 125 NC_002967:TDE0597|5end_hypothetical_protein_637212..637442_NEGATIVE 269 38 3 36 2 NC_002967:TDE2160|5end_hypothetical_protein_2193968..2194198_NEGATIVE 267 47 8 165 118 NC_002967:TDE2734|5end_hypothetical_protein_2789071..2789301_POSITIVE 267 44 5 41 3 NC_002967:TDE0908|5end_ABC_transporter,_ATP-binding/permease_protein_925254..925484_POSITIVE 260 47 8 173 127 NC_002967:TDE2315|5end_conserved_hypothetical_protein_TIGR00044_2352272..2352502_POSITIVE 259 49 1 192 150 NC_002967:TDE2605|5end_phosphoglycerate_mutase_family_protein_2645818..2646048_POSITIVE 258 31 9 33 14 NC_002967:TDE2715|5end_hypothetical_protein_2772668..2772898_POSITIVE 257 38 1 216 165 NC_002967:TDE1354|5end_hypothetical_protein_1394886..1395116_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 412 50 8 103 59 NC_002967:TDE0943|3end_hypothetical_protein_966272..966422_POSITIVE 372 47 8 69 26 NC_002967:TDE2261|3end_hypothetical_protein_2297915..2298065_NEGATIVE 345 35 8 70 44 NC_002967:TDE2481|3end_hypothetical_protein_2505352..2505502_NEGATIVE 329 45 8 74 33 NC_002967:TDE0974|3end_hypothetical_protein_998875..999025_POSITIVE 298 50 1 61 10 NC_002967:TDE1344|3end_hypothetical_protein_1383350..1383500_POSITIVE 287 60 14 141 95 NC_002967:TDE1848|3end_hypothetical_protein_1875897..1876047_NEGATIVE 281 60 16 112 61 NC_002967:TDE1017|3end_exodeoxyribonuclease_VII,_large_subunit_1049211..1049361_POSITIVE 279 38 11 144 119 NC_002967:TDE1250|3end_batA_protein,_putative_1285531..1285681_POSITIVE 273 46 1 105 56 NC_002967:TDE2593|3end_sigma-54-binding_protein_2628963..2629113_POSITIVE 269 38 3 131 97 NC_002967:TDE2160|3end_hypothetical_protein_2193873..2194023_NEGATIVE 267 47 8 140 93 NC_002967:TDE2733|3end_hypothetical_protein_2789126..2789276_POSITIVE 262 33 3 32 9 NC_002967:TDE1013|3end_hemerythrin-related_protein_1043977..1044127_NEGATIVE 249 49 12 112 69 NC_002967:TDE1231|3end_hypothetical_protein_1263479..1263629_NEGATIVE 246 32 10 53 25 NC_002967:TDE0837|3end_Na(+)-translocating_NADH-quinone_reductase,_B_subunit_856093..856243_NEGATIVE 245 52 12 48 10 NC_002967:TDE0835|3end_NADH-ubiquinone_oxidoreductase_854867..855017_NEGATIVE 243 57 12 136 78 NC_002967:TDE0982|3end_dihydroorotate_dehydrogenase/oxidoreductase,_FAD-binding_1008332..1008482_POSITIVE 242 60 12 76 30 NC_002967:TDE2661|3end_hypothetical_protein_2697524..2697674_NEGATIVE 242 60 16 106 68 NC_002967:TDE1364|3end_valyl-tRNA_synthetase_1407572..1407722_POSITIVE 242 49 13 132 92 NC_002967:TDE0572|3end_hypothetical_protein_604734..604884_POSITIVE 241 54 18 85 48 NC_002967:TDE2735|3end_surface_antigen,_putative_2791616..2791766_POSITIVE