Origin IGS: tttttaactctccgtttatttctttccttccatttcggtcagagcttcgtaggctatttggttacaataagaatattataataggcaaaatttgtgttgtcaattatttttcttgccctcttttactcttttaaaaatagagttatactaaaatataggcttttgtttttaaagaatgagttttttactctgtgcccctttttaagaacattagtcacttttatactaataggagaagagt .........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 actcttctcctattagtataaaagtgactaatgttcttaaaaaggggcacagagtaaaaaactcattctttaaaaacaaaagcctatattttagtataactctatttttaaaagagtaaaagagggcaagaaaaataattgacaacacaaattttgcctattataatattcttattgtaaccaaatagcctacgaagctctgaccgaaatggaaggaaagaaataaacggagagttaaaaa Mask Tandem Repeat Region ================================================ tttttaactctccgtttatttctttccttccatttcggtcagagcttcgtaggctatttggttacaataagaatattataataggcaaaatttgtgttgtcaattatttttcttgccctcttttactcttttaaaaatagagttatactaaaatataggcttttgtttttaaagaatgagttttttactctgtgcccctttttaagaacattagtcacttttatactaataggagaagagt Find is-nt database================================================ Query_seq: TDE0433:TDE0434|TDE0433:TDE0434:hypothetical protein:rubrerythrin:<-->:488808..489048 241 tttttaactctccgtttatttctttccttccatttcggtcagagcttcgtaggctatttggttacaataagaatattataataggcaaaatttgtgttgtcaattatttttcttgccctcttttactcttttaaaaatagagttatactaaaatataggcttttgtttttaaagaatgagttttttactctgtgcccctttttaagaacattagtcacttttatactaataggagaagagt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE0433:TDE0434|TDE0433:TDE0434:hypothetical protein:rubrerythrin:<-->:488808..489048 241 tttttaactctccgtttatttctttccttccatttcggtcagagcttcgtaggctatttggttacaataagaatattataataggcaaaatttgtgttgtcaattatttttcttgccctcttttactcttttaaaaatagagttatactaaaatataggcttttgtttttaaagaatgagttttttactctgtgcccctttttaagaacattagtcacttttatactaataggagaagagt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE0433:TDE0434|TDE0433:TDE0434:hypothetical protein:rubrerythrin:<-->:488808..489048 241 tttttaactctccgtttatttctttccttccatttcggtcagagcttcgtaggctatttggttacaataagaatattataataggcaaaatttgtgttgtcaattatttttcttgccctcttttactcttttaaaaatagagttatactaaaatataggcttttgtttttaaagaatgagttttttactctgtgcccctttttaagaacattagtcacttttatactaataggagaagagt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tttttaactctccgtttatttctttccttccatttcggtcagagcttcgtaggctatttggttacaataagaatattataataggcaaaatttgtgttgtcaattatttttcttgccctcttttactcttttaaaaatagagttatactaaaatataggcttttgtttttaaagaatgagttttttactctgtgcccctttttaagaacattagtcacttttatactaataggagaagagt Predict ORF larger than 30AA ================================================ Protein_Len: 38 Strand: + Start: 18 End: 131 ................. M S F L P F R S E L R R L F G Y N K N I I I G K I C V V N Y F S C P L L L F .............................................................................................................. Protein_Len: 49 Strand: + Start: 94 End: 240 ............................................................................................. M L S I I F L A L F Y S F K N R V I L K Y R L L F L K N E F F T L C P F L R T L V T F I L I G E E . Protein_Len: 35 Strand: - Start: 126 End: 230 ............................................................................................................................. E K L F L T I S F Y L S K N K F F S N K V R H G K K L V N T V K I S M ........... tttttaactctccgtttatttctttccttccatttcggtcagagcttcgtaggctatttggttacaataagaatattataataggcaaaatttgtgttgtcaattatttttcttgccctcttttactcttttaaaaatagagttatactaaaatataggcttttgtttttaaagaatgagttttttactctgtgcccctttttaagaacattagtcacttttatactaataggagaagagt 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: 92 Start: 75 End: 104 ..........................................................................ATTGACAACACAAATTTTGCCTATTATAAT......................................................................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ tttttaactctccgtttatttctttccttccatttcggtcagagcttcgtaggctatttggttacaataagaatattataataggcaaaatttgtgttgtcaattatttttcttgccctcttttactcttttaaaaatagagttatactaaaatataggcttttgtttttaaagaatgagttttttactctgtgcccctttttaagaacattagtcacttttatactaataggagaagagt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE0433:TDE0434|TDE0433:TDE0434:hypothetical protein:rubrerythrin:<-->:488808..489048 241 tttttaactctccgtttatttctttccttccatttcggtcagagcttcgtaggctatttggttacaataagaatattataataggcaaaatttgtgttgtcaattatttttcttgccctcttttactcttttaaaaatagagttatactaaaatataggcttttgtttttaaagaatgagttttttactctgtgcccctttttaagaacattagtcacttttatactaataggagaagagt Intra-Species Hit: Count: 1 Min: 1 Max: 241 Len: 241 Subject: NC_002967_TDE0433_TDE0434|hypothetical protein:rubrerythrin|NEGATIVE:POSITIVE|[488808, 489048]|241 HSP 1 e-value: 1.0E-134 bit: 478.0 Len: 241 Query Start:1 Query End:241 Subject Strand: POSITIVE Subject Start: 1 Subject End: 241 tttttaactctccgtttatttctttccttccatttcggtcagagcttcgtaggctatttggttacaataagaatattataataggcaaaatttgtgttgtcaattatttttcttgccctcttttactcttttaaaaatagagttatactaaaatataggcttttgtttttaaagaatgagttttttactctgtgcccctttttaagaacattagtcacttttatactaataggagaagagt tttttaactctccgtttatttctttccttccatttcggtcagagcttcgtaggctatttggttacaataagaatattataataggcaaaatttgtgttgtcaattatttttcttgccctcttttactcttttaaaaatagagttatactaaaatataggcttttgtttttaaagaatgagttttttactctgtgcccctttttaagaacattagtcacttttatactaataggagaagagt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUUUAACUCUCCGUUUAUUUCUUUCCUUCCAUUUCGGUCAGAGCUUCGUAGGCUAUUUGGUUACAAUAAGAAUAUUAUAAUAGGCAAAAUUUGUGUUGUCAAUUAUUUUUCUUGCCCUCUUUUACUCUUUUAAAAAUAGAGUUAUACUAAAAUAUAGGCUUUUGUUUUUAAAGAAUGAGUUUUUUACUCUGUGCCCCUUUUUAAGAACAUUAGUCACUUUUAUACUAAUAGGAGAAGAGU ........(((((..................((((..((.((((....((((.(.....).))))..((((((....(((((.(((((........))))).)))))..))))))..))))...(((((.........)))))...))..))))...((((..((((((((((((..((((.....))))........))))))))))))..))))...............)))))..... (-45.00) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ ACUCUUCUCCUAUUAGUAUAAAAGUGACUAAUGUUCUUAAAAAGGGGCACAGAGUAAAAAACUCAUUCUUUAAAAACAAAAGCCUAUAUUUUAGUAUAACUCUAUUUUUAAAAGAGUAAAAGAGGGCAAGAAAAAUAAUUGACAACACAAAUUUUGCCUAUUAUAAUAUUCUUAUUGUAACCAAAUAGCCUACGAAGCUCUGACCGAAAUGGAAGGAAAGAAAUAAACGGAGAGUUAAAAA (((((((...(((((((.........)))))))(((((.((((.((((...((((.....))))....(((......))).))))...))))........((((((((....(((((......((((((((....................)))))))).((((((((....))))))))................)))))....))))))))....)))))......)))))))...... (-43.65) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 893 60 11 151 102 NC_002967:TDE0433|5end_hypothetical_protein_488717..488947_NEGATIVE 732 50 1 141 92 NC_002967:TDE0429|5end_hypothetical_protein_485423..485653_NEGATIVE 362 66 26 49 6 NC_002967:TDE0859|5end_hypothetical_protein_880100..880330_POSITIVE 300 54 14 120 82 NC_002967:TDE1948|5end_ABC_transporter,_permease_protein_1964551..1964781_NEGATIVE 289 61 28 144 119 NC_002967:TDE2310|5end_hypothetical_protein_2348042..2348272_POSITIVE 288 48 1 61 16 NC_002967:TDE1141|5end_tail_fiber_domain_protein_1171443..1171673_NEGATIVE 282 130 86 177 129 NC_002967:TDE0343|5end_hydrolase,_alpha/beta_fold_family_385365..385595_NEGATIVE 281 63 25 84 39 NC_002967:TDE1287|5end_transcription-repair_coupling_factor_1322738..1322968_POSITIVE 281 55 12 128 88 NC_002967:TDE0837|5end_Na(+)-translocating_NADH-quinone_reductase,_B_subunit_857109..857339_NEGATIVE 280 52 14 152 113 NC_002967:TDE1877|5end_conserved_hypothetical_protein_TIGR00046_1898433..1898663_NEGATIVE 270 50 1 102 42 NC_002967:TDE2427|5end_preprotein_translocase,_SecE_subunit_2455982..2456212_NEGATIVE 269 60 11 78 11 NC_002967:TDE1338|5end_4-diphosphocytidyl-2C-methyl-D-erythritol_kinase_1374889..1375119_POSITIVE 267 79 37 136 83 NC_002967:TDE2168|5end_hypothetical_protein_2201003..2201233_NEGATIVE 267 55 16 111 60 NC_002967:TDE1844|5end_DNA_integrase_1874204..1874434_NEGATIVE 266 48 1 193 140 NC_002967:TDE0741|5end_hypothetical_protein_778158..778388_NEGATIVE 265 49 9 187 134 NC_002967:TDE1978|5end_hypothetical_protein_1991758..1991988_NEGATIVE 265 56 14 76 36 NC_002967:TDE0729|5end_hypothetical_protein_769124..769354_NEGATIVE 263 50 9 70 24 NC_002967:TDE2770|5end_flagellar_hook-length_control_protein_FliK_2824417..2824647_NEGATIVE 263 50 1 121 75 NC_002967:TDE1855|5end_hypothetical_protein_1882846..1883076_POSITIVE 262 54 13 95 45 NC_002967:TDE2035|5end_glucose-1-phosphate_adenylyltransferase_2062801..2063031_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 732 50 1 125 76 NC_002967:TDE0430|3end_TPR_domain_protein_485439..485589_NEGATIVE 437 60 15 132 90 NC_002967:TDE0432|3end_TPR_domain_protein,_truncation_487720..487870_NEGATIVE 347 60 27 132 99 NC_002967:TDE0428|3end_TPR_domain_protein_484453..484603_NEGATIVE 301 55 12 67 17 NC_002967:TDE2402|3end_radical_SAM_domain_protein_2428664..2428814_POSITIVE 300 54 14 127 89 NC_002967:TDE1949|3end_ABC_transporter,_ATP-binding_protein_1964544..1964694_NEGATIVE 281 63 25 83 38 NC_002967:TDE1286|3end_TPR_domain_protein_1322817..1322967_POSITIVE 281 55 12 128 88 NC_002967:TDE0838|3end_Na(+)-translocating_NADH-quinone_reductase,_A_subunit_857109..857259_NEGATIVE 280 63 21 145 104 NC_002967:TDE0880|3end_nicotinate-nucleotide-dimethylbenzimidazole_phosphoribosyltransferase_901136..901286_POSITIVE 270 55 14 42 1 NC_002967:TDE1142|3end_phage_minor_structural_protein,_putative_1171468..1171618_NEGATIVE 262 63 22 147 89 NC_002967:TDE1718|3end_GMP_synthase_1773811..1773961_POSITIVE 261 58 11 142 83 NC_002967:TDE1293|3end_TldD/PmbA_family_protein_1330621..1330771_NEGATIVE 261 51 12 136 97 NC_002967:TDE0133|3end_transcriptional_regulator,_GntR_family_153202..153352_POSITIVE 260 56 11 140 87 NC_002967:TDE1073|3end_oligopeptide/dipeptide_ABC_transporter,_permease_protein_1104635..1104785_POSITIVE 256 63 29 64 33 NC_002967:TDE2302|3end_HD_domain_protein_2343135..2343285_POSITIVE 252 52 11 61 14 NC_002967:TDE1881|3end_methyltransferase,_putative_1903631..1903781_POSITIVE 249 54 13 98 62 NC_002967:TDE2027|3end_hypothetical_protein_2052998..2053148_POSITIVE 248 54 11 136 80 NC_002967:TDE0083|3end_GTP-binding_protein_EngA_94254..94404_NEGATIVE 246 63 21 147 95 NC_002967:TDE1310|3end_modulator_of_DNA_gyrase_family_protein_1347340..1347490_POSITIVE 245 54 12 135 87 NC_002967:TDE1736|3end_ferredoxin,_2(4Fe-4S)_1790158..1790308_POSITIVE 245 66 31 39 1 NC_002967:TDE0858|3end_hypothetical_protein_880170..880320_POSITIVE