Origin IGS: aatatttctcaatagttcaaggtttttattcttaaaaaaattttattttttaagttccgctttgctttgggaaaaggtttttgaatgtgtaacttccgttggcttgacaaaaattataattttaactattatattagtgtaaaataagacccttgatatatgatgataatgttacctatatgtgcattatctcaaataacttggtttaattacaatcgaactattaagatataaaaattttgcttataattttatttaaagggggagaaaa .........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.........1.........2.........3.........4.........5.........6.........7.........8.........9 ttttctccccctttaaataaaattataagcaaaatttttatatcttaatagttcgattgtaattaaaccaagttatttgagataatgcacatataggtaacattatcatcatatatcaagggtcttattttacactaatataatagttaaaattataatttttgtcaagccaacggaagttacacattcaaaaaccttttcccaaagcaaagcggaacttaaaaaataaaatttttttaagaataaaaaccttgaactattgagaaatatt Mask Tandem Repeat Region ================================================ aatatttctcaatagttcaaggtttttattcttaaaaaaattttattttttaagttccgctttgctttgggaaaaggtttttgaatgtgtaacttccgttggcttgacaaaaattataattttaactattatattagtgtaaaataagacccttgatatatgatgataatgttacctatatgtgcattatctcaaataacttggtttaattacaatcgaactattaagatataaaaattttgcttataattttatttaaagggggagaaaa Find is-nt database================================================ Query_seq: TDE0585:TDE0586|TDE0585:TDE0586:hypothetical protein:hypothetical protein:<-->:625115..625385 271 aatatttctcaatagttcaaggtttttattcttaaaaaaattttattttttaagttccgctttgctttgggaaaaggtttttgaatgtgtaacttccgttggcttgacaaaaattataattttaactattatattagtgtaaaataagacccttgatatatgatgataatgttacctatatgtgcattatctcaaataacttggtttaattacaatcgaactattaagatataaaaattttgcttataattttatttaaagggggagaaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE0585:TDE0586|TDE0585:TDE0586:hypothetical protein:hypothetical protein:<-->:625115..625385 271 aatatttctcaatagttcaaggtttttattcttaaaaaaattttattttttaagttccgctttgctttgggaaaaggtttttgaatgtgtaacttccgttggcttgacaaaaattataattttaactattatattagtgtaaaataagacccttgatatatgatgataatgttacctatatgtgcattatctcaaataacttggtttaattacaatcgaactattaagatataaaaattttgcttataattttatttaaagggggagaaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE0585:TDE0586|TDE0585:TDE0586:hypothetical protein:hypothetical protein:<-->:625115..625385 271 aatatttctcaatagttcaaggtttttattcttaaaaaaattttattttttaagttccgctttgctttgggaaaaggtttttgaatgtgtaacttccgttggcttgacaaaaattataattttaactattatattagtgtaaaataagacccttgatatatgatgataatgttacctatatgtgcattatctcaaataacttggtttaattacaatcgaactattaagatataaaaattttgcttataattttatttaaagggggagaaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aatatttctcaatagttcaaggtttttattcttaaaaaaattttattttttaagttccgctttgctttgggaaaaggtttttgaatgtgtaacttccgttggcttgacaaaaattataattttaactattatattagtgtaaaataagacccttgatatatgatgataatgttacctatatgtgcattatctcaaataacttggtttaattacaatcgaactattaagatataaaaattttgcttataattttatttaaagggggagaaaa Predict ORF larger than 30AA ================================================ Protein_Len: 46 Strand: + Start: 2 End: 139 . M F L N S S R F L F L K K F Y F L S S A L L W E K V F E C V T S V G L T K I I I L T I I L V .................................................................................................................................... Protein_Len: 38 Strand: - Start: 46 End: 159 ............................................. K K L E A K S Q S F T K S H T V E T P K V F I I I K V I I N T Y F L V R S M ................................................................................................................ Protein_Len: 33 Strand: - Start: 12 End: 110 ........... Y N L T K I R L F I K N K L N R K A K P F P K Q I H L K R Q S S M ................................................................................................................................................................. aatatttctcaatagttcaaggtttttattcttaaaaaaattttattttttaagttccgctttgctttgggaaaaggtttttgaatgtgtaacttccgttggcttgacaaaaattataattttaactattatattagtgtaaaataagacccttgatatatgatgataatgttacctatatgtgcattatctcaaataacttggtttaattacaatcgaactattaagatataaaaattttgcttataattttatttaaagggggagaaaa 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: 90 Start: 103 End: 132 ......................................................................................................CTTGACAAAAATTATAATTTTAACTATTAT........................................................................................................................................... PromScan Matrix: RpoD-17 Strand: - Score: 81 Start: 113 End: 142 ................................................................................................................TTACACTAATATAATAGTTAAAATTATAAT................................................................................................................................. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ aatatttctcaatagttcaaggtttttattcttaaaaaaattttattttttaagttccgctttgctttgggaaaaggtttttgaatgtgtaacttccgttggcttgacaaaaattataattttaactattatattagtgtaaaataagacccttgatatatgatgataatgttacctatatgtgcattatctcaaataacttggtttaattacaatcgaactattaagatataaaaattttgcttataattttatttaaagggggagaaaa Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE0585:TDE0586|TDE0585:TDE0586:hypothetical protein:hypothetical protein:<-->:625115..625385 271 aatatttctcaatagttcaaggtttttattcttaaaaaaattttattttttaagttccgctttgctttgggaaaaggtttttgaatgtgtaacttccgttggcttgacaaaaattataattttaactattatattagtgtaaaataagacccttgatatatgatgataatgttacctatatgtgcattatctcaaataacttggtttaattacaatcgaactattaagatataaaaattttgcttataattttatttaaagggggagaaaa Intra-Species Hit: Count: 1 Min: 1 Max: 271 Len: 271 Subject: NC_002967_TDE0585_TDE0586|hypothetical protein:hypothetical protein|NEGATIVE:POSITIVE|[625115,625385]|271 HSP 1 e-value: 1.0E-139 bit: 496.0 Len: 271 Query Start:1 Query End:271 Subject Strand: POSITIVE Subject Start: 1 Subject End: 271 aatatttctcaatagttcaaggtttttattcttnnnnnnnttttattttttaagttccgctttgctttgggaaaaggtttttgaatgtgtaacttccgttggcttgacaaaaattataattttaactattatattagtgtaaaataagacccttgatatatgatgataatgttacctatatgtgcattatctcaaataacttggtttaattacaatcgaactattaagatataaaaattttgcttataattttatttaaagggggagaaaa aatatttctcaatagttcaaggtttttattcttaaaaaaattttattttttaagttccgctttgctttgggaaaaggtttttgaatgtgtaacttccgttggcttgacaaaaattataattttaactattatattagtgtaaaataagacccttgatatatgatgataatgttacctatatgtgcattatctcaaataacttggtttaattacaatcgaactattaagatataaaaattttgcttataattttatttaaagggggagaaaa Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAUAUUUCUCAAUAGUUCAAGGUUUUUAUUCUUAAAAAAAUUUUAUUUUUUAAGUUCCGCUUUGCUUUGGGAAAAGGUUUUUGAAUGUGUAACUUCCGUUGGCUUGACAAAAAUUAUAAUUUUAACUAUUAUAUUAGUGUAAAAUAAGACCCUUGAUAUAUGAUGAUAAUGUUACCUAUAUGUGCAUUAUCUCAAAUAACUUGGUUUAAUUACAAUCGAACUAUUAAGAUAUAAAAAUUUUGCUUAUAAUUUUAUUUAAAGGGGGAGAAAA ....((((((.......((((((((((((((((((.......((((..((((((..((..(((.(....).))).))..))))))...)))).....(((.(.(((............((((((((((......)))).)))))).(((((...(.(((.(((.((((((((.((......))))))))))))).))).)..))))).....))).).)))..)))))).))))))))))))(((.(((......))).)))..)))))). (-49.10) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUUCUCCCCCUUUAAAUAAAAUUAUAAGCAAAAUUUUUAUAUCUUAAUAGUUCGAUUGUAAUUAAACCAAGUUAUUUGAGAUAAUGCACAUAUAGGUAACAUUAUCAUCAUAUAUCAAGGGUCUUAUUUUACACUAAUAUAAUAGUUAAAAUUAUAAUUUUUGUCAAGCCAACGGAAGUUACACAUUCAAAAACCUUUUCCCAAAGCAAAGCGGAACUUAAAAAAUAAAAUUUUUUUAAGAAUAAAAACCUUGAACUAUUGAGAAAUAUU ......................................(((.((((((((((((((...........((..(.(((.((((((((((.((......))..))))))).))).))).)..(((....((((((.((((......)))))))))).....((((((.......(((....))).......))))))......)))..........))..(((((((((......)))))))))..........)))))))))))))).))).. (-46.94) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 837 100 51 191 142 NC_002967:TDE0585|5end_hypothetical_protein_625024..625254_NEGATIVE 299 100 51 92 40 NC_002967:TDE1104|5end_tRNA_pseudouridine_synthase_B_1137786..1138016_NEGATIVE 281 108 69 176 137 NC_002967:TDE1358|5end_hypothetical_protein_1397732..1397962_POSITIVE 279 99 53 43 3 NC_002967:TDE1308|5end_transketolase_1342463..1342693_POSITIVE 274 90 41 211 166 NC_002967:TDE1374|5end_hypothetical_protein_1417998..1418228_NEGATIVE 272 100 53 227 183 NC_002967:TDE2701|5end_hypothetical_protein_2745689..2745919_POSITIVE 267 106 61 227 178 NC_002967:TDE0854|5end_regulatory_protein_RecX_875813..876043_POSITIVE 261 108 62 70 18 NC_002967:TDE2327|5end_ATP-dependent_Clp_protease,_ATP-binding_subunit_ClpB_2364627..2364857_NEGATIVE 261 100 58 51 6 NC_002967:TDE0783|5end_ribosomal_protein_L18_813520..813750_POSITIVE 261 87 44 173 115 NC_002967:TDE0595|5end_hypothetical_protein_634972..635202_NEGATIVE 260 104 63 157 117 NC_002967:TDE2550|5end_hypothetical_protein_2576215..2576445_NEGATIVE 258 97 53 194 155 NC_002967:TDE0169|5end_methyl-accepting_chemotaxis_domain_protein_198792..199022_NEGATIVE 254 102 69 53 17 NC_002967:TDE0435|5end_ATP-dependent_DNA_helicase,_RecQ_family_491261..491491_NEGATIVE 252 98 53 134 95 NC_002967:TDE1066|5end_hypothetical_protein_1094544..1094774_NEGATIVE 248 98 52 102 59 NC_002967:TDE2102|5end_hypothetical_protein_2127347..2127577_NEGATIVE 248 83 43 213 179 NC_002967:TDE1070|5end_oligopeptide/dipeptide_ABC_transporter,_permease_protein_1098725..1098955_NEGATIVE 248 83 53 52 18 NC_002967:TDE1027|5end_ribonuclease_III_1057562..1057792_POSITIVE 247 106 61 60 6 NC_002967:TDE1405|5end_phosphoribosylformylglycinamidine_synthetase_I_1448674..1448904_NEGATIVE 246 96 52 64 22 NC_002967:TDE2406|5end_TldD/PmbA_family_protein_2433513..2433743_NEGATIVE 245 98 52 146 106 NC_002967:TDE1924|5end_hypothetical_protein_1941886..1942116_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 299 100 51 77 25 NC_002967:TDE1105|3end_ribosome-binding_factor_A_1137801..1137951_NEGATIVE 269 102 73 45 11 NC_002967:TDE0635|3end_hypothetical_protein_670578..670728_POSITIVE 261 91 55 75 29 NC_002967:TDE0919|3end_hypothetical_protein_939125..939275_POSITIVE 252 98 53 134 95 NC_002967:TDE1067|3end_oligopeptide/dipeptide_ABC_transporter,_ATP-binding_protein_1094544..1094694_NEGATIVE 248 83 43 125 91 NC_002967:TDE1071|3end_peptide_ABC_transporter,_peptide-binding_protein_OppA_1098813..1098963_NEGATIVE 247 106 61 57 3 NC_002967:TDE1406|3end_hypothetical_protein_1448677..1448827_NEGATIVE 243 108 61 68 24 NC_002967:TDE2269|3end_hypothetical_protein_2304931..2305081_NEGATIVE 238 107 61 151 101 NC_002967:TDE1856|3end_radical_SAM_domain_protein_1883956..1884106_POSITIVE 236 105 63 77 28 NC_002967:TDE2139|3end_hypothetical_protein_2172897..2173047_POSITIVE 236 97 58 66 22 NC_002967:TDE1471|3end_hypothetical_protein_1518145..1518295_NEGATIVE 234 60 15 150 111 NC_002967:TDE2244|3end_hypothetical_protein_2284320..2284470_POSITIVE 234 110 88 57 32 NC_002967:TDE0277|3end_hypothetical_protein_308109..308259_NEGATIVE 231 105 87 120 100 NC_002967:TDE2041|3end_lipoprotein_releasing_system,_permease_protein,_putative_2070214..2070364_NEGATIVE 230 100 54 91 24 NC_002967:TDE2021|3end_hypothetical_protein_2044157..2044307_NEGATIVE 227 105 63 101 58 NC_002967:TDE2645|3end_hypothetical_protein_2685444..2685594_POSITIVE 226 103 61 64 24 NC_002967:TDE0469|3end_hypothetical_protein_521270..521420_NEGATIVE 224 100 54 57 2 NC_002967:TDE1549|3end_recombination_protein_RecR_1592807..1592957_POSITIVE 224 98 60 145 97 NC_002967:TDE0618|3end_hypothetical_protein_650242..650392_NEGATIVE 223 105 64 54 11 NC_002967:TDE2460|3end_aminotransferase,_class_V_2487229..2487379_POSITIVE 221 100 70 40 9 NC_002967:TDE0782|3end_50S_ribosomal_protein_L6_813589..813739_POSITIVE