Origin IGS: tttgtaattcctgataggtaatgagtaagccgcttattcgtgcggagggtttaataccccgacgcttgcgtcggggttgttgattacccatttttaatttttaacccttctttaaaaaaagtttaaacttttttcctatgacaaatgtcatatttaaactccaaaaaatatgacaattttcagttttaaaattccaaaaaaaaggtataattatctataaaagatatcggaggaagtt .........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 aacttcctccgatatcttttatagataattataccttttttttggaattttaaaactgaaaattgtcatattttttggagtttaaatatgacatttgtcataggaaaaaagtttaaactttttttaaagaagggttaaaaattaaaaatgggtaatcaacaaccccgacgcaagcgtcggggtattaaaccctccgcacgaataagcggcttactcattacctatcaggaattacaaa Mask Tandem Repeat Region ================================================ tttgtaattcctgataggtaatgagtaagccgcttattcgtgcggagggtttaataccccgacgcttgcgtcggggttgttgattacccatttttaatttttaacccttctttaaaaaaagtttaaacttttttcctatgacaaatgtcatatttaaactccaaaaaatatgacaattttcagttttaaaattccaaaaaaaaggtataattatctataaaagatatcggaggaagtt Find is-nt database================================================ Query_seq: TDE0693:TDE0694|TDE0693:TDE0694:phosphomethylpyrimidine kinase:ABC transporter, ATP-binding protein:->->:730892..731129 238 tttgtaattcctgataggtaatgagtaagccgcttattcgtgcggagggtttaataccccgacgcttgcgtcggggttgttgattacccatttttaatttttaacccttctttaaaaaaagtttaaacttttttcctatgacaaatgtcatatttaaactccaaaaaatatgacaattttcagttttaaaattccaaaaaaaaggtataattatctataaaagatatcggaggaagtt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE0693:TDE0694|TDE0693:TDE0694:phosphomethylpyrimidine kinase:ABC transporter, ATP-binding protein:->->:730892..731129 238 tttgtaattcctgataggtaatgagtaagccgcttattcgtgcggagggtttaataccccgacgcttgcgtcggggttgttgattacccatttttaatttttaacccttctttaaaaaaagtttaaacttttttcctatgacaaatgtcatatttaaactccaaaaaatatgacaattttcagttttaaaattccaaaaaaaaggtataattatctataaaagatatcggaggaagtt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE0693:TDE0694|TDE0693:TDE0694:phosphomethylpyrimidine kinase:ABC transporter, ATP-binding protein:->->:730892..731129 238 tttgtaattcctgataggtaatgagtaagccgcttattcgtgcggagggtttaataccccgacgcttgcgtcggggttgttgattacccatttttaatttttaacccttctttaaaaaaagtttaaacttttttcctatgacaaatgtcatatttaaactccaaaaaatatgacaattttcagttttaaaattccaaaaaaaaggtataattatctataaaagatatcggaggaagtt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tttgtaattcctgataggtaatgagtaagccgcttattcgtgcggagggtttaataccccgacgcttgcgtcggggttgttgattacccatttttaatttttaacccttctttaaaaaaagtttaaacttttttcctatgacaaatgtcatatttaaactccaaaaaatatgacaattttcagttttaaaattccaaaaaaaaggtataattatctataaaagatatcggaggaagtt Predict ORF larger than 30AA ================================================ Protein_Len: 37 Strand: - Start: 104 End: 214 ....................................................................................................... G K K L F L K F K K G I V F T M N L S W F I H C N E T K F N W F F P I I M ........................ Protein_Len: 30 Strand: - Start: 2 End: 91 . Q L E Q Y T I L L G S I R A S P K I G R R K R R P Q Q N G M ................................................................................................................................................... tttgtaattcctgataggtaatgagtaagccgcttattcgtgcggagggtttaataccccgacgcttgcgtcggggttgttgattacccatttttaatttttaacccttctttaaaaaaagtttaaacttttttcctatgacaaatgtcatatttaaactccaaaaaatatgacaattttcagttttaaaattccaaaaaaaaggtataattatctataaaagatatcggaggaagtt 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================================================ tttgtaattcctgataggtaatgagtaagccgcttattcgtgcggagggtttaataccccgacgcttgcgtcggggttgttgattacccatttttaatttttaacccttctttaaaaaaagtttaaacttttttcctatgacaaatgtcatatttaaactccaaaaaatatgacaattttcagttttaaaattccaaaaaaaaggtataattatctataaaagatatcggaggaagtt Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 100 HP_score: -15.0 Tail_Score: -3.81414 Start: 57 End: 76 Full_Region: GCGGAGGGTTTAATA CCCCGACG CTTG CGTCGGGG TTGTTGATTACCCAT ........................................................CCCCGACGCTTGCGTCGGGG.................................................................................................................................................................. TransTerm Strand: - Conf: 100 HP_score: -15.0 Tail_Score: -3.03124 Start: 57 End: 76 Full_Region: atgggtaatcaacaa ccccgacg caag cgtcgggg tattaaaccctccgc ........................................................ccccgacgcaagcgtcgggg.................................................................................................................................................................. TransTerm Strand: + Conf: 49 HP_score: -2.4 Tail_Score: -3.72302 Start: 111 End: 127 Full_Region: AATTTTTAACCCTTC TTTAAA AAAAG TTTAAA CTTTTTTCCTATGAC ..............................................................................................................TTTAAAAAAAGTTTAAA............................................................................................................... TransTerm Strand: - Conf: 56 HP_score: -3.8 Tail_Score: -3.96148 Start: 146 End: 175 Full_Region: tttaaaactgaaaat tgtcatattt tttggagttt aaatatgaca tttgtcataggaaaa .................................................................................................................................................tgtcatattttttggagtttaaatatgaca............................................................... Find igs database================================================ Query_seq: TDE0693:TDE0694|TDE0693:TDE0694:phosphomethylpyrimidine kinase:ABC transporter, ATP-binding protein:->->:730892..731129 238 tttgtaattcctgataggtaatgagtaagccgcttattcgtgcggagggtttaataccccgacgcttgcgtcggggttgttgattacccatttttaatttttaacccttctttaaaaaaagtttaaacttttttcctatgacaaatgtcatatttaaactccaaaaaatatgacaattttcagttttaaaattccaaaaaaaaggtataattatctataaaagatatcggaggaagtt Intra-Species Hit: Count: 1 Min: 1 Max: 238 Len: 238 Subject: NC_002967_TDE0693_TDE0694|phosphomethylpyrimidine kinase:ABC transporter, ATP-binding protein|POSITIVE:POSITIVE|[730892,731129]|238 HSP 1 e-value: 1.0E-105 bit: 383.0 Len: 238 Query Start:1 Query End:238 Subject Strand: POSITIVE Subject Start: 1 Subject End: 238 tttgtaattcctgataggtaatgagtaagccgcttattcgtgcggagggtttaataccccgacgcttgcgtcggggttgttgattacccatttttaatttttaacccttctttnnnnnnngtttaaacttttttcctatgacaaatgtcatatttaaactccaaaaaatatgacaattttcagttttaaaattccnnnnnnnnggtataattatctataaaagatatcggaggaagtt tttgtaattcctgataggtaatgagtaagccgcttattcgtgcggagggtttaataccccgacgcttgcgtcggggttgttgattacccatttttaatttttaacccttctttaaaaaaagtttaaacttttttcctatgacaaatgtcatatttaaactccaaaaaatatgacaattttcagttttaaaattccaaaaaaaaggtataattatctataaaagatatcggaggaagtt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUGUAAUUCCUGAUAGGUAAUGAGUAAGCCGCUUAUUCGUGCGGAGGGUUUAAUACCCCGACGCUUGCGUCGGGGUUGUUGAUUACCCAUUUUUAAUUUUUAACCCUUCUUUAAAAAAAGUUUAAACUUUUUUCCUAUGACAAAUGUCAUAUUUAAACUCCAAAAAAUAUGACAAUUUUCAGUUUUAAAAUUCCAAAAAAAAGGUAUAAUUAUCUAUAAAAGAUAUCGGAGGAAGUU .......(((((.(((((((((.......((((........)))).((((((((((((((((((....)))))))).))))))..))))................((((.(((.((((((((....))))))))....(((.((.((((((((((..........)))))))))).)).)))...............))).))))....)))))))))....(....)..)))))... (-60.70) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AACUUCCUCCGAUAUCUUUUAUAGAUAAUUAUACCUUUUUUUUGGAAUUUUAAAACUGAAAAUUGUCAUAUUUUUUGGAGUUUAAAUAUGACAUUUGUCAUAGGAAAAAAGUUUAAACUUUUUUUAAAGAAGGGUUAAAAAUUAAAAAUGGGUAAUCAACAACCCCGACGCAAGCGUCGGGGUAUUAAACCCUCCGCACGAAUAAGCGGCUUACUCAUUACCUAUCAGGAAUUACAAA ...(((((..((((...........(((((..((((((((((..............(((....((((((((((..........))))))))))....)))...(((((((((....)))))))))))))))))))....)))))..(((((((((......(((((((((....)))))))))..........((((........)))).)))))))))...)))))))))....... (-63.20) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 885 80 34 154 107 NC_002967:TDE0538|5end_hypothetical_protein_580066..580296_POSITIVE 813 77 34 165 115 NC_002967:TDE0371|5end_hypothetical_protein_422687..422917_POSITIVE 786 73 32 152 108 NC_002967:TDE1470|5end_hypothetical_protein_1518026..1518256_NEGATIVE 698 73 34 150 110 NC_002967:TDE0167|5end_ABC_transporter,_ATP-binding_protein_196574..196804_NEGATIVE 673 100 54 192 147 NC_002967:TDE0509|5end_hypothetical_protein_560373..560603_NEGATIVE 532 80 32 119 65 NC_002967:TDE0830|5end_hypothetical_protein_852025..852255_NEGATIVE 519 95 56 95 56 NC_002967:TDE2690|5end_hypothetical_protein_2728898..2729128_NEGATIVE 511 77 32 163 122 NC_002967:TDE0017|5end_hypothetical_protein_22936..23166_NEGATIVE 503 63 21 231 182 NC_002967:TDE0712|5end_hypothetical_protein_746963..747193_NEGATIVE 463 82 42 193 151 NC_002967:TDE1194|5end_hypothetical_protein_1224973..1225203_POSITIVE 459 82 41 121 82 NC_002967:TDE2691|5end_hypothetical_protein_2728838..2729068_POSITIVE 436 70 25 227 165 NC_002967:TDE0238|5end_thioredoxin,_selenocysteine-containing_271380..271610_POSITIVE 420 82 51 162 128 NC_002967:TDE0580|5end_hypothetical_protein_615338..615568_POSITIVE 385 87 58 31 1 NC_002967:TDE0613|5end_hypothetical_protein_647966..648196_NEGATIVE 378 80 36 226 169 NC_002967:TDE2516|5end_hypothetical_protein_2542021..2542251_POSITIVE 362 88 55 163 132 NC_002967:TDE0713|5end_transcription_antitermination_protein,_NusG_family_747109..747339_POSITIVE 358 79 32 222 164 NC_002967:TDE1355|5end_hypothetical_protein_1395109..1395339_POSITIVE 357 77 32 51 3 NC_002967:TDE0745|5end_glycine_reductase_complex_selenoprotein_GrdA_780287..780517_POSITIVE 348 77 51 148 122 NC_002967:TDE1051|5end_hypothetical_protein_1078496..1078726_NEGATIVE 343 75 36 209 166 NC_002967:TDE0738|5end_hypothetical_protein_775934..776164_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 885 80 34 86 39 NC_002967:TDE0537|3end_hypothetical_protein_580078..580228_POSITIVE 842 80 34 77 30 NC_002967:TDE0202|3end_hypothetical_protein_235870..236020_NEGATIVE 813 77 34 68 18 NC_002967:TDE0711|3end_hypothetical_protein_745690..745840_NEGATIVE 783 77 34 89 39 NC_002967:TDE0133|3end_transcriptional_regulator,_GntR_family_153202..153352_POSITIVE 780 77 34 141 91 NC_002967:TDE2458|3end_hypothetical_protein_2485849..2485999_POSITIVE 698 73 34 57 17 NC_002967:TDE0168|3end_transcriptional_regulator,_GntR_family_196667..196817_NEGATIVE 654 98 54 150 107 NC_002967:TDE0510|3end_hypothetical_protein_560413..560563_NEGATIVE 638 73 42 33 1 NC_002967:TDE1471|3end_hypothetical_protein_1518145..1518295_NEGATIVE 579 90 41 61 1 NC_002967:TDE2139|3end_hypothetical_protein_2172897..2173047_POSITIVE 557 89 41 133 80 NC_002967:TDE2459|3end_hypothetical_protein_2485764..2485914_NEGATIVE 556 89 47 44 2 NC_002967:TDE0693|3end_phosphomethylpyrimidine_kinase_730831..730981_POSITIVE 527 89 41 98 45 NC_002967:TDE0710|3end_hypothetical_protein_745667..745817_POSITIVE 507 82 41 51 12 NC_002967:TDE0831|3end_hypothetical_protein_852095..852245_NEGATIVE 478 89 41 75 22 NC_002967:TDE2499|3end_hypothetical_protein_2523191..2523341_NEGATIVE 459 82 41 51 12 NC_002967:TDE2689|3end_hypothetical_protein_2728848..2728998_POSITIVE 457 89 43 51 4 NC_002967:TDE0333|3end_MATE_efflux_family_protein_373083..373233_POSITIVE 443 62 34 151 123 NC_002967:TDE2690|3end_hypothetical_protein_2728743..2728893_NEGATIVE 430 85 59 61 33 NC_002967:TDE0370|3end_UDP-N-acetylmuramoylalanine--D-glutamate_ligase_422594..422744_POSITIVE 425 88 54 35 2 NC_002967:TDE0018|3end_LysM_domain_protein_23073..23223_NEGATIVE 407 89 53 41 1 NC_002967:TDE2140|3end_protease_II_2173083..2173233_NEGATIVE