Origin IGS: ttcacaaacgcttcaatcgaggcgtttttttgctttctgttctccgcctttggcggaatattggcgggtggtaatcctactctgtatgggtatgtatttgatagtaatatagaaatagccccattcggattggcgtgtagtctcgattgacattatcttaataatggagtacaaaagacaagagtattcacaagaatgataatttggataacagctaaggagaatttgat .........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 atcaaattctccttagctgttatccaaattatcattcttgtgaatactcttgtcttttgtactccattattaagataatgtcaatcgagactacacgccaatccgaatggggctatttctatattactatcaaatacatacccatacagagtaggattaccacccgccaatattccgccaaaggcggagaacagaaagcaaaaaaacgcctcgattgaagcgtttgtgaa Mask Tandem Repeat Region ================================================ ttcacaaacgcttcaatcgaggcgtttttttgctttctgttctccgcctttggcggaatattggcgggtggtaatcctactctgtatgggtatgtatttgatagtaatatagaaatagccccattcggattggcgtgtagtctcgattgacattatcttaataatggagtacaaaagacaagagtattcacaagaatgataatttggataacagctaaggagaatttgat Find is-nt database================================================ Query_seq: TDE0562:TDE0563|TDE0562:TDE0563:hypothetical protein:hypothetical protein:->->:595642..595871 230 ttcacaaacgcttcaatcgaggcgtttttttgctttctgttctccgcctttggcggaatattggcgggtggtaatcctactctgtatgggtatgtatttgatagtaatatagaaatagccccattcggattggcgtgtagtctcgattgacattatcttaataatggagtacaaaagacaagagtattcacaagaatgataatttggataacagctaaggagaatttgat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE0562:TDE0563|TDE0562:TDE0563:hypothetical protein:hypothetical protein:->->:595642..595871 230 ttcacaaacgcttcaatcgaggcgtttttttgctttctgttctccgcctttggcggaatattggcgggtggtaatcctactctgtatgggtatgtatttgatagtaatatagaaatagccccattcggattggcgtgtagtctcgattgacattatcttaataatggagtacaaaagacaagagtattcacaagaatgataatttggataacagctaaggagaatttgat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE0562:TDE0563|TDE0562:TDE0563:hypothetical protein:hypothetical protein:->->:595642..595871 230 ttcacaaacgcttcaatcgaggcgtttttttgctttctgttctccgcctttggcggaatattggcgggtggtaatcctactctgtatgggtatgtatttgatagtaatatagaaatagccccattcggattggcgtgtagtctcgattgacattatcttaataatggagtacaaaagacaagagtattcacaagaatgataatttggataacagctaaggagaatttgat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ttcacaaacgcttcaatcgaggcgtttttttgctttctgttctccgcctttggcggaatattggcgggtggtaatcctactctgtatgggtatgtatttgatagtaatatagaaatagccccattcggattggcgtgtagtctcgattgacattatcttaataatggagtacaaaagacaagagtattcacaagaatgataatttggataacagctaaggagaatttgat Predict ORF larger than 30AA ================================================ Protein_Len: 44 Strand: + Start: 16 End: 147 ............... M E A F F C F L F S A F G G I L A G G N P T L Y G Y V F D S N I E I A P F G L A C S L D ................................................................................... Protein_Len: 60 Strand: - Start: 16 End: 225 ............... G K A S Y Q R T T I R S Q I P I Y K I T I Y F Y G W E S Q R T T E I S M I K I I S Y L L C S Y E C S H Y N P Y C S L L M ..... Protein_Len: 38 Strand: - Start: 3 End: 116 .. V F A E I S A N K Q K R N E A K P P I N A P P L G V R Y P Y T N S L L I S M .................................................................................................................. ttcacaaacgcttcaatcgaggcgtttttttgctttctgttctccgcctttggcggaatattggcgggtggtaatcctactctgtatgggtatgtatttgatagtaatatagaaatagccccattcggattggcgtgtagtctcgattgacattatcttaataatggagtacaaaagacaagagtattcacaagaatgataatttggataacagctaaggagaatttgat 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: 82 Start: 146 End: 175 .................................................................................................................................................ATTGACATTATCTTAATAATGGAGTACAAA....................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ ttcacaaacgcttcaatcgaggcgtttttttgctttctgttctccgcctttggcggaatattggcgggtggtaatcctactctgtatgggtatgtatttgatagtaatatagaaatagccccattcggattggcgtgtagtctcgattgacattatcttaataatggagtacaaaagacaagagtattcacaagaatgataatttggataacagctaaggagaatttgat Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 42 HP_score: -2.2 Tail_Score: -2.94622 Start: 66 End: 82 Full_Region: TGGCGGAATATTGGC GGGTGG TAATC CTACTC TGTATGGGTATGTAT .................................................................GGGTGGTAATCCTACTC.................................................................................................................................................... Find igs database================================================ Query_seq: TDE0562:TDE0563|TDE0562:TDE0563:hypothetical protein:hypothetical protein:->->:595642..595871 230 ttcacaaacgcttcaatcgaggcgtttttttgctttctgttctccgcctttggcggaatattggcgggtggtaatcctactctgtatgggtatgtatttgatagtaatatagaaatagccccattcggattggcgtgtagtctcgattgacattatcttaataatggagtacaaaagacaagagtattcacaagaatgataatttggataacagctaaggagaatttgat Intra-Species Hit: Count: 1 Min: 1 Max: 230 Len: 230 Subject: NC_002967_TDE0562_TDE0563|hypothetical protein:hypothetical protein|POSITIVE:POSITIVE|[595642,595871]|230 HSP 1 e-value: 1.0E-115 bit: 414.0 Len: 230 Query Start:1 Query End:230 Subject Strand: POSITIVE Subject Start: 1 Subject End: 230 ttcacaaacgcttcaatcgaggcgnnnnnnngctttctgttctccgcctttggcggaatattggcgggtggtaatcctactctgtatgggtatgtatttgatagtaatatagaaatagccccattcggattggcgtgtagtctcgattgacattatcttaataatggagtacaaaagacaagagtattcacaagaatgataatttggataacagctaaggagaatttgat ttcacaaacgcttcaatcgaggcgtttttttgctttctgttctccgcctttggcggaatattggcgggtggtaatcctactctgtatgggtatgtatttgatagtaatatagaaatagccccattcggattggcgtgtagtctcgattgacattatcttaataatggagtacaaaagacaagagtattcacaagaatgataatttggataacagctaaggagaatttgat Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUCACAAACGCUUCAAUCGAGGCGUUUUUUUGCUUUCUGUUCUCCGCCUUUGGCGGAAUAUUGGCGGGUGGUAAUCCUACUCUGUAUGGGUAUGUAUUUGAUAGUAAUAUAGAAAUAGCCCCAUUCGGAUUGGCGUGUAGUCUCGAUUGACAUUAUCUUAAUAAUGGAGUACAAAAGACAAGAGUAUUCACAAGAAUGAUAAUUUGGAUAACAGCUAAGGAGAAUUUGAU .....(((((((((....)))))))))..(((((.((((((.((((((...)))))).....)))))).)))))((((..((((.(((((..(((.((((.((....)))))).)))..))))).)))).((((.(((.((((.(((((.(((..((((.......((((((...........))))))..))))))).))))).)))).)))))))))))......... (-61.60) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUCAAAUUCUCCUUAGCUGUUAUCCAAAUUAUCAUUCUUGUGAAUACUCUUGUCUUUUGUACUCCAUUAUUAAGAUAAUGUCAAUCGAGACUACACGCCAAUCCGAAUGGGGCUAUUUCUAUAUUACUAUCAAAUACAUACCCAUACAGAGUAGGAUUACCACCCGCCAAUAUUCCGCCAAAGGCGGAGAACAGAAAGCAAAAAAACGCCUCGAUUGAAGCGUUUGUGAA .(((...........(((((.((((......((((....)))).((((((.((((((((.....((((((....)))))).)))..)))))...............(((((..(((((..(((....))).)))))....)))))..)))))))))).))............(((((((...))))))).......)))....((((((.((....)).)))))).))). (-44.30) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 376 90 41 215 181 NC_002967:TDE0945|5end_hypothetical_protein_967128..967358_POSITIVE 354 68 21 49 1 NC_002967:TDE2494|5end_hypothetical_protein_2518497..2518727_POSITIVE 352 66 23 230 185 NC_002967:TDE1011|5end_hypothetical_protein_1038101..1038331_POSITIVE 351 88 41 46 3 NC_002967:TDE0828|5end_glucose-inhibited_division_protein_A_850169..850399_NEGATIVE 347 68 31 218 177 NC_002967:TDE2139|5end_hypothetical_protein_2172032..2172262_POSITIVE 343 48 6 48 1 NC_002967:TDE1139|5end_hypothetical_protein_1168615..1168845_NEGATIVE 340 72 32 127 95 NC_002967:TDE1847|5end_hypothetical_protein_1875664..1875894_POSITIVE 333 68 21 180 133 NC_002967:TDE0628|5end_molecular_chaperone_DnaK_660609..660839_POSITIVE 331 90 41 172 123 NC_002967:TDE1516|5end_ABC_transporter,_ATP-binding_protein,_putative_1563127..1563357_POSITIVE 331 78 39 228 193 NC_002967:TDE0766|5end_30S_ribosomal_protein_S10_805984..806214_POSITIVE 328 65 32 89 56 NC_002967:TDE1878|5end_hydrolase,_haloacid_dehalogenase-like_family_1900745..1900975_NEGATIVE 326 70 44 230 206 NC_002967:TDE1095|5end_alanine_racemase_1129826..1130056_POSITIVE 325 69 21 185 136 NC_002967:TDE0644|5end_ABC_transporter,_ATP-binding_protein_680576..680806_NEGATIVE 324 48 10 183 141 NC_002967:TDE0774|5end_50S_ribosomal_protein_L16_810165..810395_POSITIVE 322 90 41 153 100 NC_002967:TDE0833|5end_lipoprotein,_putative_852992..853222_POSITIVE 319 70 21 61 20 NC_002967:TDE0838|5end_Na(+)-translocating_NADH-quinone_reductase,_A_subunit_858551..858781_NEGATIVE 318 65 21 165 117 NC_002967:TDE2537|5end_hypothetical_protein_2563266..2563496_POSITIVE 317 69 22 199 149 NC_002967:TDE0279|5end_hypothetical_protein_309782..310012_NEGATIVE 316 56 12 189 137 NC_002967:TDE1818|5end_hypothetical_protein_1853791..1854021_NEGATIVE 315 180 131 174 123 NC_002967:TDE0450|5end_hypothetical_protein_508529..508759_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 404 87 44 59 22 NC_002967:TDE1094|3end_hypothetical_protein_1129722..1129872_POSITIVE 383 70 22 145 80 NC_002967:TDE1847|3end_hypothetical_protein_1875845..1875995_POSITIVE 376 90 41 44 10 NC_002967:TDE0944|3end_hypothetical_protein_967037..967187_POSITIVE 333 76 31 89 38 NC_002967:TDE2719|3end_hypothetical_protein_2777015..2777165_POSITIVE 331 90 41 144 95 NC_002967:TDE1515|3end_permease_domain_protein_1563179..1563329_POSITIVE 330 82 43 149 104 NC_002967:TDE1740|3end_hypothetical_protein_1792630..1792780_NEGATIVE 317 69 22 86 36 NC_002967:TDE0280|3end_PIN_domain_protein_309895..310045_NEGATIVE 314 69 21 83 11 NC_002967:TDE1406|3end_hypothetical_protein_1448677..1448827_NEGATIVE 311 54 11 136 90 NC_002967:TDE1450|3end_MutS2_family_protein_1497856..1498006_POSITIVE 310 67 21 131 57 NC_002967:TDE0598|3end_3-oxoacyl-(acyl-carrier-protein)_reductase_637358..637508_NEGATIVE 309 65 31 147 114 NC_002967:TDE2725|3end_cyclic_nucleotide_binding_domain/GGDEF_domain_protein_2782240..2782390_NEGATIVE 308 72 42 29 2 NC_002967:TDE1739|3end_femAB_family_protein_1792657..1792807_POSITIVE 307 159 116 140 92 NC_002967:TDE2751|3end_hypothetical_protein_2809194..2809344_POSITIVE 307 54 11 116 79 NC_002967:TDE2527|3end_hypothetical_protein_2555449..2555599_NEGATIVE 304 70 23 60 12 NC_002967:TDE1831|3end_hypothetical_protein_1864415..1864565_NEGATIVE 304 70 23 60 12 NC_002967:TDE1797|3end_hypothetical_protein_1835655..1835805_NEGATIVE 303 78 37 79 36 NC_002967:TDE2343|3end_phosphatidate_cytidylyltransferase_2380383..2380533_NEGATIVE 303 70 21 137 83 NC_002967:TDE0835|3end_NADH-ubiquinone_oxidoreductase_854867..855017_NEGATIVE 301 59 11 82 42 NC_002967:TDE2269|3end_hypothetical_protein_2304931..2305081_NEGATIVE 301 68 28 55 20 NC_002967:TDE2163|3end_hypothetical_protein_2195533..2195683_NEGATIVE