Origin IGS: ttttgtaaacactttgaggctataaaatctttaggtaaagatttatccataaaactaaagacccgcttttgcgggtctttttttatctgcgcacaccgaaaacaacttataccctatactaaataagaatttatatgtaaaatataagagctgtattttaaggcagcgaaggagctaaat .........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 atttagctccttcgctgccttaaaatacagctcttatattttacatataaattcttatttagtatagggtataagttgttttcggtgtgcgcagataaaaaaagacccgcaaaagcgggtctttagttttatggataaatctttacctaaagattttatagcctcaaagtgtttacaaaa Mask Tandem Repeat Region ================================================ ttttgtaaacactttgaggctataaaatctttaggtaaagatttatccataaaactaaagacccgcttttgcgggtctttttttatctgcgcacaccgaaaacaacttataccctatactaaataagaatttatatgtaaaatataagagctgtattttaaggcagcgaaggagctaaat Find is-nt database================================================ Query_seq: TDE0095:TDE0096|TDE0095:TDE0096:hypothetical protein:NADH oxidase:->->:112683..112862 180 ttttgtaaacactttgaggctataaaatctttaggtaaagatttatccataaaactaaagacccgcttttgcgggtctttttttatctgcgcacaccgaaaacaacttataccctatactaaataagaatttatatgtaaaatataagagctgtattttaaggcagcgaaggagctaaat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE0095:TDE0096|TDE0095:TDE0096:hypothetical protein:NADH oxidase:->->:112683..112862 180 ttttgtaaacactttgaggctataaaatctttaggtaaagatttatccataaaactaaagacccgcttttgcgggtctttttttatctgcgcacaccgaaaacaacttataccctatactaaataagaatttatatgtaaaatataagagctgtattttaaggcagcgaaggagctaaat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE0095:TDE0096|TDE0095:TDE0096:hypothetical protein:NADH oxidase:->->:112683..112862 180 ttttgtaaacactttgaggctataaaatctttaggtaaagatttatccataaaactaaagacccgcttttgcgggtctttttttatctgcgcacaccgaaaacaacttataccctatactaaataagaatttatatgtaaaatataagagctgtattttaaggcagcgaaggagctaaat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ttttgtaaacactttgaggctataaaatctttaggtaaagatttatccataaaactaaagacccgcttttgcgggtctttttttatctgcgcacaccgaaaacaacttataccctatactaaataagaatttatatgtaaaatataagagctgtattttaaggcagcgaaggagctaaat Predict ORF larger than 30AA ================================================ Protein_Len: 34 Strand: + Start: 22 End: 123 ..................... M K S L G K D L S I K L K T R F C G S F F I C A H R K Q L I P Y T K ......................................................... Protein_Len: 33 Strand: - Start: 58 End: 156 ......................................................... L G A K A P R K K D A C V S F L K Y G I S F L F K Y T F Y L L Q M ........................ Protein_Len: 36 Strand: - Start: 3 End: 110 .. Q L C K S A I F D K P L S K D M F S F V R K Q P D K K I Q A C R F C S M ...................................................................... ttttgtaaacactttgaggctataaaatctttaggtaaagatttatccataaaactaaagacccgcttttgcgggtctttttttatctgcgcacaccgaaaacaacttataccctatactaaataagaatttatatgtaaaatataagagctgtattttaaggcagcgaaggagctaaat 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================================================ ttttgtaaacactttgaggctataaaatctttaggtaaagatttatccataaaactaaagacccgcttttgcgggtctttttttatctgcgcacaccgaaaacaacttataccctatactaaataagaatttatatgtaaaatataagagctgtattttaaggcagcgaaggagctaaat Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 85 HP_score: -8.4 Tail_Score: -4.431 Start: 55 End: 82 Full_Region: ggtgtgcgcagataa aaaaagacccgc aaaa gcgggtctttag ttttatggataaatc ......................................................aaaaagacccgcaaaagcgggtctttag.................................................................................................. TransTerm Strand: + Conf: 100 HP_score: -12.7 Tail_Score: -5.71712 Start: 60 End: 77 Full_Region: ATCCATAAAACTAAA GACCCGC TTTT GCGGGTC TTTTTTTATCTGCGC ...........................................................GACCCGCTTTTGCGGGTC....................................................................................................... TransTerm Strand: - Conf: 100 HP_score: -12.7 Tail_Score: -4.27483 Start: 60 End: 77 Full_Region: gcgcagataaaaaaa gacccgc aaaa gcgggtc tttagttttatggat ...........................................................gacccgcaaaagcgggtc....................................................................................................... Find igs database================================================ Query_seq: TDE0095:TDE0096|TDE0095:TDE0096:hypothetical protein:NADH oxidase:->->:112683..112862 180 ttttgtaaacactttgaggctataaaatctttaggtaaagatttatccataaaactaaagacccgcttttgcgggtctttttttatctgcgcacaccgaaaacaacttataccctatactaaataagaatttatatgtaaaatataagagctgtattttaaggcagcgaaggagctaaat Intra-Species Hit: Count: 1 Min: 1 Max: 180 Len: 180 Subject: NC_002967_TDE0095_TDE0096|hypothetical protein:NADH oxidase|POSITIVE:POSITIVE|[112683,112862]|180 HSP 1 e-value: 3.0E-85 bit: 315.0 Len: 180 Query Start:1 Query End:180 Subject Strand: POSITIVE Subject Start: 1 Subject End: 180 ttttgtaaacactttgaggctataaaatctttaggtaaagatttatccataaaactaaagacccgcttttgcgggtcnnnnnnnatctgcgcacaccgaaaacaacttataccctatactaaataagaatttatatgtaaaatataagagctgtattttaaggcagcgaaggagctaaat ttttgtaaacactttgaggctataaaatctttaggtaaagatttatccataaaactaaagacccgcttttgcgggtctttttttatctgcgcacaccgaaaacaacttataccctatactaaataagaatttatatgtaaaatataagagctgtattttaaggcagcgaaggagctaaat Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUUGUAAACACUUUGAGGCUAUAAAAUCUUUAGGUAAAGAUUUAUCCAUAAAACUAAAGACCCGCUUUUGCGGGUCUUUUUUUAUCUGCGCACACCGAAAACAACUUAUACCCUAUACUAAAUAAGAAUUUAUAUGUAAAAUAUAAGAGCUGUAUUUUAAGGCAGCGAAGGAGCUAAAU ...........(((((..(((.(((((((..((((((((((................(((((((((....))))))))))))))))))).((.............(((((............)))))..(((((((.....))))))).)).).)))))).)))..)))))......... (-38.69) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUUUAGCUCCUUCGCUGCCUUAAAAUACAGCUCUUAUAUUUUACAUAUAAAUUCUUAUUUAGUAUAGGGUAUAAGUUGUUUUCGGUGUGCGCAGAUAAAAAAAGACCCGCAAAAGCGGGUCUUUAGUUUUAUGGAUAAAUCUUUACCUAAAGAUUUUAUAGCCUCAAAGUGUUUACAAAA ...((((......)))).........((((((..(((((((((....(((((....)))))...))))))))))))))).....(((.((((..((((((((((((((((....))))))))))..))))))((..((((((((....)))))))).....)).....)))).))).... (-43.50) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 295 98 59 204 166 NC_002967:TDE1348|5end_TPR_domain_protein_1388333..1388563_POSITIVE 282 98 63 193 158 NC_002967:TDE1266|5end_phosphoribosylaminoimidazole_synthetase_1301588..1301818_NEGATIVE 280 101 63 168 136 NC_002967:TDE1207|5end_DNA_processing_protein_DprA,_putative_1239236..1239466_POSITIVE 274 99 63 227 195 NC_002967:TDE2551|5end_hypothetical_protein_2577282..2577512_NEGATIVE 273 76 32 197 151 NC_002967:TDE0406|5end_hypothetical_protein_457230..457460_POSITIVE 266 98 63 178 126 NC_002967:TDE2744|5end_type_I_restriction-modification_system,_S_subunit_2799853..2800083_NEGATIVE 260 92 62 60 35 NC_002967:TDE0793|5end_hypothetical_protein_818910..819140_POSITIVE 256 99 64 194 153 NC_002967:TDE0771|5end_ribosomal_protein_S19_808795..809025_POSITIVE 252 76 34 67 25 NC_002967:TDE1676|5end_ribosomal_protein_S18_1729642..1729872_NEGATIVE 250 99 63 73 22 NC_002967:TDE1896|5end_phosphoribosylaminoimidazolecarboxamide_formyltransferase/IMP_cyclohydrolase_1917505..1917735_NEGATIVE 249 99 57 147 104 NC_002967:TDE1924|5end_hypothetical_protein_1941886..1942116_NEGATIVE 249 103 65 188 148 NC_002967:TDE0211|5end_ABC_transporter,_permease_protein,_cysTW_family_247286..247516_NEGATIVE 248 90 61 196 168 NC_002967:TDE2764|5end_flagellar_protein_2819331..2819561_NEGATIVE 247 109 62 209 160 NC_002967:TDE1463|5end_hypothetical_protein_1513072..1513302_NEGATIVE 246 79 37 82 38 NC_002967:TDE2731|5end_TIM-barrel_protein,_putative,_NifR3_family_2787372..2787602_POSITIVE 246 99 63 175 147 NC_002967:TDE2009|5end_hypothetical_protein_2030382..2030612_POSITIVE 246 176 136 99 64 NC_002967:TDE1476|5end_hypothetical_protein_1522177..1522407_POSITIVE 244 104 62 155 104 NC_002967:TDE2631|5end_peptide_ABC_transporter,_permease_protein,_putative_2671829..2672059_POSITIVE 241 98 66 197 171 NC_002967:TDE2499|5end_hypothetical_protein_2523952..2524182_NEGATIVE 241 99 63 41 1 NC_002967:TDE2306|5end_hypothetical_protein_2344251..2344481_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 350 86 49 42 5 NC_002967:TDE0095|3end_hypothetical_protein_112622..112772_POSITIVE 281 80 36 74 29 NC_002967:TDE1483|3end_hypothetical_protein_1529067..1529217_POSITIVE 275 98 61 109 60 NC_002967:TDE0157|3end_KHG/KDPG_family_aldolase/carbohydrate_kinase,_PfkB_family_185711..185861_POSITIVE 274 98 63 144 107 NC_002967:TDE2552|3end_ABC_transporter,_ATP-binding/permease_protein_2577370..2577520_NEGATIVE 273 76 32 68 22 NC_002967:TDE0405|3end_major_outer_sheath_protein_457181..457331_POSITIVE 266 98 63 150 98 NC_002967:TDE2745|3end_fic_family_protein_2799881..2800031_NEGATIVE 260 99 57 57 13 NC_002967:TDE2307|3end_seryl-tRNA_synthetase_2344235..2344385_NEGATIVE 260 88 62 98 68 NC_002967:TDE0794|3end_hypothetical_protein_819224..819374_NEGATIVE 260 92 62 76 51 NC_002967:TDE0792|3end_ribosomal_protein_L17_819006..819156_POSITIVE 257 97 57 151 110 NC_002967:TDE2306|3end_hypothetical_protein_2344138..2344288_NEGATIVE 254 76 31 85 40 NC_002967:TDE0109|3end_phenylalanyl-tRNA_synthetase_alpha_subunit_128833..128983_NEGATIVE 250 99 63 53 2 NC_002967:TDE1897|3end_phosphoribosylglycinamide_formyltransferase_1917525..1917675_NEGATIVE 250 174 148 86 59 NC_002967:TDE0165|3end_hypothetical_protein_195056..195206_POSITIVE 248 92 63 150 119 NC_002967:TDE1267|3end_phosphoribosylamine--glycine_ligase_1301627..1301777_NEGATIVE 248 76 33 76 30 NC_002967:TDE0900|3end_ABC_transporter,_ATP-binding_protein_918692..918842_POSITIVE 246 79 37 69 25 NC_002967:TDE2730|3end_hydrolase,_TatD_family_2787439..2787589_POSITIVE 246 99 63 128 100 NC_002967:TDE2008|3end_ABC_transporter,_ATP-binding/permease_protein_2030415..2030565_POSITIVE 242 174 144 41 10 NC_002967:TDE0090|3end_hypothetical_protein_108544..108694_NEGATIVE 241 97 57 103 68 NC_002967:TDE1674|3end_hypothetical_protein_1728232..1728382_NEGATIVE 239 108 63 70 29 NC_002967:TDE2269|3end_hypothetical_protein_2304931..2305081_NEGATIVE