Origin IGS: ttttattctccgttatgcctttattcgtgcggagggtttaataccccgacgctctgcgtcgtaacaaagggtattaaagccgactgcaacctccttatgagaacaacataccccgatg .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 catcggggtatgttgttctcataaggaggttgcagtcggctttaataccctttgttacgacgcagagcgtcggggtattaaaccctccgcacgaataaaggcataacggagaataaaa Mask Tandem Repeat Region ================================================ ttttattctccgttatgcctttattcgtgcggagggtttaataccccgacgctctgcgtcgtaacaaagggtattaaagccgactgcaacctccttatgagaacaacataccccgatg Find is-nt database================================================ Query_seq: TDE1470:TDE1471|TDE1470:TDE1471:hypothetical protein:hypothetical protein:<-<-:1518117..1518234 118 ttttattctccgttatgcctttattcgtgcggagggtttaataccccgacgctctgcgtcgtaacaaagggtattaaagccgactgcaacctccttatgagaacaacataccccgatg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE1470:TDE1471|TDE1470:TDE1471:hypothetical protein:hypothetical protein:<-<-:1518117..1518234 118 ttttattctccgttatgcctttattcgtgcggagggtttaataccccgacgctctgcgtcgtaacaaagggtattaaagccgactgcaacctccttatgagaacaacataccccgatg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE1470:TDE1471|TDE1470:TDE1471:hypothetical protein:hypothetical protein:<-<-:1518117..1518234 118 ttttattctccgttatgcctttattcgtgcggagggtttaataccccgacgctctgcgtcgtaacaaagggtattaaagccgactgcaacctccttatgagaacaacataccccgatg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ttttattctccgttatgcctttattcgtgcggagggtttaataccccgacgctctgcgtcgtaacaaagggtattaaagccgactgcaacctccttatgagaacaacataccccgatg Predict ORF larger than 30AA ================================================ Protein_Len: 34 Strand: - Start: 16 End: 117 ............... A K I R A S P K I G R R E A D Y C L T N F G V A V E K H S C C V G M . ttttattctccgttatgcctttattcgtgcggagggtttaataccccgacgctctgcgtcgtaacaaagggtattaaagccgactgcaacctccttatgagaacaacataccccgatg 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================================================ ttttattctccgttatgcctttattcgtgcggagggtttaataccccgacgctctgcgtcgtaacaaagggtattaaagccgactgcaacctccttatgagaacaacataccccgatg Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE1470:TDE1471|TDE1470:TDE1471:hypothetical protein:hypothetical protein:<-<-:1518117..1518234 118 ttttattctccgttatgcctttattcgtgcggagggtttaataccccgacgctctgcgtcgtaacaaagggtattaaagccgactgcaacctccttatgagaacaacataccccgatg Intra-Species Hit: Count: 1 Min: 1 Max: 118 Len: 118 Subject: NC_002967_TDE1470_TDE1471|hypothetical protein:hypothetical protein|NEGATIVE:NEGATIVE|[1518117,1518234]|118 HSP 1 e-value: 5.0E-61 bit: 234.0 Len: 118 Query Start:1 Query End:118 Subject Strand: POSITIVE Subject Start: 1 Subject End: 118 ttttattctccgttatgcctttattcgtgcggagggtttaataccccgacgctctgcgtcgtaacaaagggtattaaagccgactgcaacctccttatgagaacaacataccccgatg ttttattctccgttatgcctttattcgtgcggagggtttaataccccgacgctctgcgtcgtaacaaagggtattaaagccgactgcaacctccttatgagaacaacataccccgatg Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUUAUUCUCCGUUAUGCCUUUAUUCGUGCGGAGGGUUUAAUACCCCGACGCUCUGCGUCGUAACAAAGGGUAUUAAAGCCGACUGCAACCUCCUUAUGAGAACAACAUACCCCGAUG ..........((.((((......((((((.(((((..(((((((((((((((...)))))).......))))))))).((.....))..))))).)))))).....))))...))... (-32.71) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CAUCGGGGUAUGUUGUUCUCAUAAGGAGGUUGCAGUCGGCUUUAAUACCCUUUGUUACGACGCAGAGCGUCGGGGUAUUAAACCCUCCGCACGAAUAAAGGCAUAACGGAGAAUAAAA ............((((((((....(((((..((.....)).(((((((((.......((((((...)))))))))))))))..)))))((.(.......)))......)))))))).. (-34.71) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 1028 60 11 151 102 NC_002967:TDE1470|5end_hypothetical_protein_1518026..1518256_NEGATIVE 984 89 41 178 130 NC_002967:TDE0167|5end_ABC_transporter,_ATP-binding_protein_196574..196804_NEGATIVE 884 90 41 183 135 NC_002967:TDE0371|5end_hypothetical_protein_422687..422917_POSITIVE 799 100 54 47 1 NC_002967:TDE2690|5end_hypothetical_protein_2728898..2729128_NEGATIVE 728 58 11 143 96 NC_002967:TDE0538|5end_hypothetical_protein_580066..580296_POSITIVE 508 50 17 231 193 NC_002967:TDE0712|5end_hypothetical_protein_746963..747193_NEGATIVE 481 88 41 178 139 NC_002967:TDE0017|5end_hypothetical_protein_22936..23166_NEGATIVE 422 58 20 227 182 NC_002967:TDE0238|5end_thioredoxin,_selenocysteine-containing_271380..271610_POSITIVE 403 88 42 169 132 NC_002967:TDE0713|5end_transcription_antitermination_protein,_NusG_family_747109..747339_POSITIVE 371 58 11 201 153 NC_002967:TDE2583|5end_hypothetical_protein_2616322..2616552_POSITIVE 363 88 47 197 164 NC_002967:TDE0830|5end_hypothetical_protein_852025..852255_NEGATIVE 356 60 16 46 2 NC_002967:TDE0745|5end_glycine_reductase_complex_selenoprotein_GrdA_780287..780517_POSITIVE 349 61 36 166 137 NC_002967:TDE0509|5end_hypothetical_protein_560373..560603_NEGATIVE 338 58 18 208 165 NC_002967:TDE0741|5end_hypothetical_protein_778158..778388_NEGATIVE 333 61 28 231 191 NC_002967:TDE1051|5end_hypothetical_protein_1078496..1078726_NEGATIVE 332 60 23 214 169 NC_002967:TDE2516|5end_hypothetical_protein_2542021..2542251_POSITIVE 331 88 47 197 164 NC_002967:TDE2691|5end_hypothetical_protein_2728838..2729068_POSITIVE 327 59 11 218 168 NC_002967:TDE1027|5end_ribonuclease_III_1057562..1057792_POSITIVE 326 89 46 57 15 NC_002967:TDE1072|5end_lipoprotein,_putative_1100741..1100971_POSITIVE 323 55 11 185 140 NC_002967:TDE2399|5end_ribonuclease_P_protein_component_2426160..2426390_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 984 89 41 85 37 NC_002967:TDE0168|3end_transcriptional_regulator,_GntR_family_196667..196817_NEGATIVE 884 90 41 86 38 NC_002967:TDE0711|3end_hypothetical_protein_745690..745840_NEGATIVE 868 70 21 139 91 NC_002967:TDE2458|3end_hypothetical_protein_2485849..2485999_POSITIVE 850 70 21 87 39 NC_002967:TDE0133|3end_transcriptional_regulator,_GntR_family_153202..153352_POSITIVE 728 58 11 75 28 NC_002967:TDE0537|3end_hypothetical_protein_580078..580228_POSITIVE 703 60 17 69 23 NC_002967:TDE0202|3end_hypothetical_protein_235870..236020_NEGATIVE 481 88 41 41 2 NC_002967:TDE0018|3end_LysM_domain_protein_23073..23223_NEGATIVE 479 88 43 63 12 NC_002967:TDE2429|3end_hypothetical_protein_2456628..2456778_NEGATIVE 452 49 20 151 122 NC_002967:TDE2690|3end_hypothetical_protein_2728743..2728893_NEGATIVE 447 110 81 30 1 NC_002967:TDE0370|3end_UDP-N-acetylmuramoylalanine--D-glutamate_ligase_422594..422744_POSITIVE 399 88 43 50 14 NC_002967:TDE0693|3end_phosphomethylpyrimidine_kinase_730831..730981_POSITIVE 365 61 28 120 80 NC_002967:TDE2459|3end_hypothetical_protein_2485764..2485914_NEGATIVE 363 88 47 127 94 NC_002967:TDE0831|3end_hypothetical_protein_852095..852245_NEGATIVE 349 61 36 126 97 NC_002967:TDE0510|3end_hypothetical_protein_560413..560563_NEGATIVE 344 61 28 38 1 NC_002967:TDE2139|3end_hypothetical_protein_2172897..2173047_POSITIVE 344 86 43 63 13 NC_002967:TDE1500|3end_hypothetical_protein_1546763..1546913_NEGATIVE 343 60 11 84 34 NC_002967:TDE0210|3end_cob(I)yrinic_acid_a,c-diamide_adenosyltransferase_246146..246296_POSITIVE 341 70 25 54 3 NC_002967:TDE1839|3end_hypothetical_protein_1870391..1870541_NEGATIVE 333 61 28 85 45 NC_002967:TDE0710|3end_hypothetical_protein_745667..745817_POSITIVE 331 88 47 127 94 NC_002967:TDE2689|3end_hypothetical_protein_2728848..2728998_POSITIVE