Origin IGS: aagatttctttcctcccctataacccctcctatcttcaaaagaaccgcttagggctctgccctaagaacccgcattgttacataatttctagcttactttttagtcgagatgacaataaaagttttgggttaaatttaaaaattaagctagtcagaagtaatgcgttattattaaagcattaaaaaattctttaagtcctttgtgttccttgcggttaaattagtt .........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 aactaatttaaccgcaaggaacacaaaggacttaaagaattttttaatgctttaataataacgcattacttctgactagcttaatttttaaatttaacccaaaacttttattgtcatctcgactaaaaagtaagctagaaattatgtaacaatgcgggttcttagggcagagccctaagcggttcttttgaagataggaggggttataggggaggaaagaaatctt Mask Tandem Repeat Region ================================================ aagatttctttcctcccctataacccctcctatcttcaaaagaaccgcttagggctctgccctaagaacccgcattgttacataatttctagcttactttttagtcgagatgacaataaaagttttgggttaaatttaaaaattaagctagtcagaagtaatgcgttattattaaagcattaaaaaattctttaagtcctttgtgttccttgcggttaaattagtt Find is-nt database================================================ Query_seq: TDE1008:TDE1009|TDE1008:TDE1009:flagellar protein, putative:methyl-accepting chemotaxis protein:-><-:1032867..1033092 226 aagatttctttcctcccctataacccctcctatcttcaaaagaaccgcttagggctctgccctaagaacccgcattgttacataatttctagcttactttttagtcgagatgacaataaaagttttgggttaaatttaaaaattaagctagtcagaagtaatgcgttattattaaagcattaaaaaattctttaagtcctttgtgttccttgcggttaaattagtt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE1008:TDE1009|TDE1008:TDE1009:flagellar protein, putative:methyl-accepting chemotaxis protein:-><-:1032867..1033092 226 aagatttctttcctcccctataacccctcctatcttcaaaagaaccgcttagggctctgccctaagaacccgcattgttacataatttctagcttactttttagtcgagatgacaataaaagttttgggttaaatttaaaaattaagctagtcagaagtaatgcgttattattaaagcattaaaaaattctttaagtcctttgtgttccttgcggttaaattagtt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE1008:TDE1009|TDE1008:TDE1009:flagellar protein, putative:methyl-accepting chemotaxis protein:-><-:1032867..1033092 226 aagatttctttcctcccctataacccctcctatcttcaaaagaaccgcttagggctctgccctaagaacccgcattgttacataatttctagcttactttttagtcgagatgacaataaaagttttgggttaaatttaaaaattaagctagtcagaagtaatgcgttattattaaagcattaaaaaattctttaagtcctttgtgttccttgcggttaaattagtt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aagatttctttcctcccctataacccctcctatcttcaaaagaaccgcttagggctctgccctaagaacccgcattgttacataatttctagcttactttttagtcgagatgacaataaaagttttgggttaaatttaaaaattaagctagtcagaagtaatgcgttattattaaagcattaaaaaattctttaagtcctttgtgttccttgcggttaaattagtt Predict ORF larger than 30AA ================================================ Protein_Len: 59 Strand: + Start: 4 End: 180 ... M S F L P Y N P S Y L Q K N R L G L C P K N P H C Y I I S S L L F S R D D N K S F G L N L K I K L V R S N A L L L K H .............................................. aagatttctttcctcccctataacccctcctatcttcaaaagaaccgcttagggctctgccctaagaacccgcattgttacataatttctagcttactttttagtcgagatgacaataaaagttttgggttaaatttaaaaattaagctagtcagaagtaatgcgttattattaaagcattaaaaaattctttaagtcctttgtgttccttgcggttaaattagtt Predict Promoter with matrix: RpoD-15 score > 80================================================ Predict Promoter with matrix: RpoD-16 score > 80================================================ Predict Promoter with matrix: RpoD-17 score > 80================================================ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ aagatttctttcctcccctataacccctcctatcttcaaaagaaccgcttagggctctgccctaagaacccgcattgttacataatttctagcttactttttagtcgagatgacaataaaagttttgggttaaatttaaaaattaagctagtcagaagtaatgcgttattattaaagcattaaaaaattctttaagtcctttgtgttccttgcggttaaattagtt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE1008:TDE1009|TDE1008:TDE1009:flagellar protein, putative:methyl-accepting chemotaxis protein:-><-:1032867..1033092 226 aagatttctttcctcccctataacccctcctatcttcaaaagaaccgcttagggctctgccctaagaacccgcattgttacataatttctagcttactttttagtcgagatgacaataaaagttttgggttaaatttaaaaattaagctagtcagaagtaatgcgttattattaaagcattaaaaaattctttaagtcctttgtgttccttgcggttaaattagtt Intra-Species Hit: Count: 1 Min: 1 Max: 226 Len: 226 Subject: NC_002967_TDE1008_TDE1009|flagellar protein, putative:methyl-accepting chemotaxis protein|POSITIVE:NEGATIVE|[1032867,1033092]|226 HSP 1 e-value: 1.0E-125 bit: 448.0 Len: 226 Query Start:1 Query End:226 Subject Strand: POSITIVE Subject Start: 1 Subject End: 226 aagatttctttcctcccctataacccctcctatcttcaaaagaaccgcttagggctctgccctaagaacccgcattgttacataatttctagcttactttttagtcgagatgacaataaaagttttgggttaaatttaaaaattaagctagtcagaagtaatgcgttattattaaagcattaaaaaattctttaagtcctttgtgttccttgcggttaaattagtt aagatttctttcctcccctataacccctcctatcttcaaaagaaccgcttagggctctgccctaagaacccgcattgttacataatttctagcttactttttagtcgagatgacaataaaagttttgggttaaatttaaaaattaagctagtcagaagtaatgcgttattattaaagcattaaaaaattctttaagtcctttgtgttccttgcggttaaattagtt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAGAUUUCUUUCCUCCCCUAUAACCCCUCCUAUCUUCAAAAGAACCGCUUAGGGCUCUGCCCUAAGAACCCGCAUUGUUACAUAAUUUCUAGCUUACUUUUUAGUCGAGAUGACAAUAAAAGUUUUGGGUUAAAUUUAAAAAUUAAGCUAGUCAGAAGUAAUGCGUUAUUAUUAAAGCAUUAAAAAAUUCUUUAAGUCCUUUGUGUUCCUUGCGGUUAAAUUAGUU .....((((((...........................))))))...((((((((...))))))))...(((((..(..((((((...((((((((.(((((((....(((..(((........))).)))....))))))).))))))))..((((.((((((.(((....))).)))))).....)))).........))))))..).)))))........... (-47.23) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AACUAAUUUAACCGCAAGGAACACAAAGGACUUAAAGAAUUUUUUAAUGCUUUAAUAAUAACGCAUUACUUCUGACUAGCUUAAUUUUUAAAUUUAACCCAAAACUUUUAUUGUCAUCUCGACUAAAAAGUAAGCUAGAAAUUAUGUAACAAUGCGGGUUCUUAGGGCAGAGCCCUAAGCGGUUCUUUUGAAGAUAGGAGGGGUUAUAGGGGAGGAAAGAAAUCUU ...........((....))...............((((.((((((..(.(((((.((((..(...(((((((...((((((((.((((((......................(((.....))))))))).)))))))).................(..((((((((((...)))))))).))..)....)))).)))..)..))))))))).)..)))))).)))) (-46.64) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 1018 60 11 225 176 NC_002967:TDE2097|5end_hypothetical_protein_2124741..2124971_NEGATIVE 666 60 11 204 155 NC_002967:TDE1982|5end_hypothetical_protein_1992984..1993214_NEGATIVE 598 57 11 231 184 NC_002967:TDE2024|5end_hypothetical_protein_2051021..2051251_NEGATIVE 564 70 25 214 166 NC_002967:TDE2142|5end_methyl-accepting_chemotaxis_protein_2175769..2175999_POSITIVE 444 220 174 207 154 NC_002967:TDE2436|5end_hypothetical_protein_2466602..2466832_POSITIVE 418 70 27 191 135 NC_002967:TDE0619|5end_methyl-accepting_chemotaxis_protein_650318..650548_POSITIVE 401 60 13 214 168 NC_002967:TDE2735|5end_surface_antigen,_putative_2790154..2790384_POSITIVE 392 36 5 167 139 NC_002967:TDE0741|5end_hypothetical_protein_778158..778388_NEGATIVE 348 49 5 208 164 NC_002967:TDE2259|5end_hypothetical_protein_2297237..2297467_NEGATIVE 347 70 24 191 133 NC_002967:TDE0957|5end_glycerophosphoryl_diester_phosphodiesterase_family_protein_980252..980482_POSITIVE 337 58 11 125 71 NC_002967:TDE2265|5end_hypothetical_protein_2302165..2302395_POSITIVE 322 220 181 74 34 NC_002967:TDE1059|5end_hypothetical_protein_1086605..1086835_NEGATIVE 318 57 11 103 50 NC_002967:TDE0402|5end_hypothetical_protein_454352..454582_NEGATIVE 318 57 11 225 172 NC_002967:TDE0401|5end_adenylate/guanylate_cyclase_catalytic_domain_protein_454230..454460_NEGATIVE 307 73 33 113 57 NC_002967:TDE1198|5end_S-adenosyl-methyltransferase_MraW_1230392..1230622_POSITIVE 304 90 44 220 178 NC_002967:TDE0767|5end_ribosomal_protein_L3_806355..806585_POSITIVE 301 76 31 222 168 NC_002967:TDE2550|5end_hypothetical_protein_2576215..2576445_NEGATIVE 299 66 27 54 4 NC_002967:TDE0928|5end_phosphonate_ABC_transporter,_ATP-binding_protein,_putative_951640..951870_NEGATIVE 295 74 31 203 165 NC_002967:TDE1314|5end_penicillin-binding_protein_1351174..1351404_POSITIVE 293 76 32 72 28 NC_002967:TDE2736|5end_hypothetical_protein_2791812..2792042_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 575 79 46 34 1 NC_002967:TDE2098|3end_hypothetical_protein_2124951..2125101_NEGATIVE 532 56 11 79 38 NC_002967:TDE0664|3end_OmpA_family_protein_699728..699878_POSITIVE 422 32 1 151 122 NC_002967:TDE2025|3end_hypothetical_protein_2051075..2051225_NEGATIVE 364 60 13 118 67 NC_002967:TDE1564|3end_hypothetical_protein_1616704..1616854_POSITIVE 353 88 46 76 29 NC_002967:TDE1981|3end_hypothetical_protein_1992437..1992587_POSITIVE 335 215 187 117 86 NC_002967:TDE0974|3end_hypothetical_protein_998875..999025_POSITIVE 325 217 187 114 81 NC_002967:TDE2261|3end_hypothetical_protein_2297915..2298065_NEGATIVE 321 80 31 121 58 NC_002967:TDE1914|3end_Holliday_junction_DNA_helicase_RuvB_1930889..1931039_NEGATIVE 307 73 33 107 51 NC_002967:TDE1197|3end_conserved_hypothetical_protein_TIGR00242_1230466..1230616_POSITIVE 302 90 44 72 28 NC_002967:TDE2269|3end_hypothetical_protein_2304931..2305081_NEGATIVE 299 66 26 77 31 NC_002967:TDE1499|3end_adenylosuccinate_lyase,_putative_1546788..1546938_POSITIVE 296 49 9 150 110 NC_002967:TDE0569|3end_hypothetical_protein_600162..600312_POSITIVE 284 215 187 37 7 NC_002967:TDE2731|3end_TIM-barrel_protein,_putative,_NifR3_family_2788453..2788603_POSITIVE 284 49 5 58 23 NC_002967:TDE1059|3end_hypothetical_protein_1086498..1086648_NEGATIVE 283 72 32 43 1 NC_002967:TDE2711|3end_hypothetical_protein_2768991..2769141_POSITIVE 281 74 35 138 100 NC_002967:TDE0859|3end_hypothetical_protein_881106..881256_POSITIVE 273 73 45 58 31 NC_002967:TDE2238|3end_hypothetical_protein_2276545..2276695_POSITIVE 272 76 34 149 103 NC_002967:TDE0618|3end_hypothetical_protein_650242..650392_NEGATIVE 270 54 15 96 55 NC_002967:TDE1131|3end_hypothetical_protein_1163531..1163681_POSITIVE 268 74 32 67 32 NC_002967:TDE2481|3end_hypothetical_protein_2505352..2505502_NEGATIVE