Origin IGS: acatgctccatccttttttattctataatgcagtataggccattcatctattttttgtcaattatccaccacagaaattacttttttgattcctcctataattcaatgcttgttgtatatttttatctaaatataccgagtaaagattctttacggcaatgccgaataaggtacgggagaacatg .........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 catgttctcccgtaccttattcggcattgccgtaaagaatctttactcggtatatttagataaaaatatacaacaagcattgaattataggaggaatcaaaaaagtaatttctgtggtggataattgacaaaaaatagatgaatggcctatactgcattatagaataaaaaaggatggagcatgt Mask Tandem Repeat Region ================================================ acatgctccatccttttttattctataatgcagtataggccattcatctattttttgtcaattatccaccacagaaattacttttttgattcctcctataattcaatgcttgttgtatatttttatctaaatataccgagtaaagattctttacggcaatgccgaataaggtacgggagaacatg Find is-nt database================================================ Query_seq: TDE1660:TDE1661|TDE1660:TDE1661:leucine Rich Repeat domain protein:hypothetical protein:<-->:1715357..1715541 185 acatgctccatccttttttattctataatgcagtataggccattcatctattttttgtcaattatccaccacagaaattacttttttgattcctcctataattcaatgcttgttgtatatttttatctaaatataccgagtaaagattctttacggcaatgccgaataaggtacgggagaacatg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE1660:TDE1661|TDE1660:TDE1661:leucine Rich Repeat domain protein:hypothetical protein:<-->:1715357..1715541 185 acatgctccatccttttttattctataatgcagtataggccattcatctattttttgtcaattatccaccacagaaattacttttttgattcctcctataattcaatgcttgttgtatatttttatctaaatataccgagtaaagattctttacggcaatgccgaataaggtacgggagaacatg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE1660:TDE1661|TDE1660:TDE1661:leucine Rich Repeat domain protein:hypothetical protein:<-->:1715357..1715541 185 acatgctccatccttttttattctataatgcagtataggccattcatctattttttgtcaattatccaccacagaaattacttttttgattcctcctataattcaatgcttgttgtatatttttatctaaatataccgagtaaagattctttacggcaatgccgaataaggtacgggagaacatg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 acatgctccatccttttttattctataatgcagtataggccattcatctattttttgtcaattatccaccacagaaattacttttttgattcctcctataattcaatgcttgttgtatatttttatctaaatataccgagtaaagattctttacggcaatgccgaataaggtacgggagaacatg Predict ORF larger than 30AA ================================================ Protein_Len: 31 Strand: + Start: 35 End: 127 .................................. M G H S S I F C Q L S T T E I T F L I P P I I Q C L L Y I F I .......................................................... Protein_Len: 58 Strand: + Start: 10 End: 183 ......... M L F Y S I M Q Y R P F I Y F L S I I H H R N Y F F D S S Y N S M L V V Y F Y L N I P S K D S L R Q C R I R Y G R T .. Protein_Len: 40 Strand: - Start: 65 End: 184 ................................................................ G G C F N S K Q N R R Y N L A Q Q I N K D L Y V S Y L N K V A I G F L T R S F M . acatgctccatccttttttattctataatgcagtataggccattcatctattttttgtcaattatccaccacagaaattacttttttgattcctcctataattcaatgcttgttgtatatttttatctaaatataccgagtaaagattctttacggcaatgccgaataaggtacgggagaacatg 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================================================ acatgctccatccttttttattctataatgcagtataggccattcatctattttttgtcaattatccaccacagaaattacttttttgattcctcctataattcaatgcttgttgtatatttttatctaaatataccgagtaaagattctttacggcaatgccgaataaggtacgggagaacatg Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE1660:TDE1661|TDE1660:TDE1661:leucine Rich Repeat domain protein:hypothetical protein:<-->:1715357..1715541 185 acatgctccatccttttttattctataatgcagtataggccattcatctattttttgtcaattatccaccacagaaattacttttttgattcctcctataattcaatgcttgttgtatatttttatctaaatataccgagtaaagattctttacggcaatgccgaataaggtacgggagaacatg Intra-Species Hit: Count: 1 Min: 1 Max: 185 Len: 185 Subject: NC_002967_TDE1660_TDE1661|leucine Rich Repeat domain protein:hypothetical protein|NEGATIVE:POSITIVE|[1715357,1715541]|185 HSP 1 e-value: 1.0E-101 bit: 367.0 Len: 185 Query Start:1 Query End:185 Subject Strand: POSITIVE Subject Start: 1 Subject End: 185 acatgctccatccttttttattctataatgcagtataggccattcatctattttttgtcaattatccaccacagaaattacttttttgattcctcctataattcaatgcttgttgtatatttttatctaaatataccgagtaaagattctttacggcaatgccgaataaggtacgggagaacatg acatgctccatccttttttattctataatgcagtataggccattcatctattttttgtcaattatccaccacagaaattacttttttgattcctcctataattcaatgcttgttgtatatttttatctaaatataccgagtaaagattctttacggcaatgccgaataaggtacgggagaacatg Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ ACAUGCUCCAUCCUUUUUUAUUCUAUAAUGCAGUAUAGGCCAUUCAUCUAUUUUUUGUCAAUUAUCCACCACAGAAAUUACUUUUUUGAUUCCUCCUAUAAUUCAAUGCUUGUUGUAUAUUUUUAUCUAAAUAUACCGAGUAAAGAUUCUUUACGGCAAUGCCGAAUAAGGUACGGGAGAACAUG .((((((((..((((((((((((......(((.((((((....(((.....(((((((............))))))).........))).....))))))......))).....((((((((......)))))))).))))))))).......((((...))))....)))....))))..)))) (-36.34) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CAUGUUCUCCCGUACCUUAUUCGGCAUUGCCGUAAAGAAUCUUUACUCGGUAUAUUUAGAUAAAAAUAUACAACAAGCAUUGAAUUAUAGGAGGAAUCAAAAAAGUAAUUUCUGUGGUGGAUAAUUGACAAAAAAUAGAUGAAUGGCCUAUACUGCAUUAUAGAAUAAAAAAGGAUGGAGCAUGU ((((((((.((.....((((((.....(((.(((.((..(.((((.((.((((((((......))))))))..(((..(((..((((((((((....(......)...)))))))))).)))..)))..........)))))).)..)).))).))).....))))))....))..)))))))). (-37.50) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 829 50 1 141 92 NC_002967:TDE1660|5end_leucine_Rich_Repeat_domain_protein_1715266..1715496_NEGATIVE 283 177 137 44 4 NC_002967:TDE1737|5end_hypothetical_protein_1790133..1790363_POSITIVE 281 180 135 216 168 NC_002967:TDE1448|5end_glutamate_racemase,_putative_1493535..1493765_POSITIVE 273 180 147 216 173 NC_002967:TDE1864|5end_crossover_junction_endodeoxyribonuclease_RuvC_1889108..1889338_NEGATIVE 263 177 136 200 160 NC_002967:TDE2697|5end_3-oxo-5-alpha-steroid_4-dehydrogenase_family_protein_2740260..2740490_POSITIVE 262 178 133 52 22 NC_002967:TDE2645|5end_hypothetical_protein_2684972..2685202_POSITIVE 256 178 134 56 18 NC_002967:TDE1399|5end_prolipoprotein_diacylglyceryl_transferase_1439393..1439623_POSITIVE 251 179 152 78 51 NC_002967:TDE2639|5end_oligoendopeptidase_F_2678120..2678350_POSITIVE 251 176 132 214 168 NC_002967:TDE1547|5end_ribonuclease_HII_1591124..1591354_POSITIVE 249 180 135 41 2 NC_002967:TDE0902|5end_hypothetical_protein_920132..920362_NEGATIVE 246 178 136 58 22 NC_002967:TDE2028|5end_OmpA_family_protein_2052923..2053153_POSITIVE 245 176 137 51 10 NC_002967:TDE2131|5end_cobalamin_biosynthesis_protein_CbiM,_putative_2162683..2162913_NEGATIVE 245 49 2 180 125 NC_002967:TDE1401|5end_DedA_family_protein_1442365..1442595_POSITIVE 243 165 129 184 149 NC_002967:TDE2000|5end_ABC_transporter,_ATP-binding/permease_protein,_HlyB_family_2017859..2018089_POSITIVE 241 180 136 69 7 NC_002967:TDE2280|5end_transglycosylase,_SLT_family_2317358..2317588_NEGATIVE 241 157 113 148 106 NC_002967:TDE0286|5end_ABC_transporter,_ATP-binding_protein_317378..317608_NEGATIVE 239 48 5 157 116 NC_002967:TDE2347|5end_30S_ribosomal_protein_S2_2384378..2384608_NEGATIVE 239 180 136 73 36 NC_002967:TDE0436|5end_Recombination_protein_O_492133..492363_NEGATIVE 236 170 128 172 136 NC_002967:TDE0208|5end_glycerate_kinase_242982..243212_POSITIVE 235 173 136 144 104 NC_002967:TDE1127|5end_TPR_domain_protein_1158278..1158508_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 262 178 133 59 29 NC_002967:TDE2644|3end_pyridine_nucleotide-disulphide_oxidoreductase_family_protein_2685059..2685209_POSITIVE 261 180 154 35 5 NC_002967:TDE1949|3end_ABC_transporter,_ATP-binding_protein_1964544..1964694_NEGATIVE 261 178 132 59 13 NC_002967:TDE0823|3end_(3R)-hydroxymyristoyl-(acyl-carrier-protein)_dehydratase,_putative_845252..845402_POSITIVE 256 178 134 41 3 NC_002967:TDE1398|3end_hypothetical_protein_1439458..1439608_POSITIVE 251 179 152 77 50 NC_002967:TDE2638|3end_hypothetical_protein_2678199..2678349_POSITIVE 246 178 136 53 17 NC_002967:TDE2027|3end_hypothetical_protein_2052998..2053148_POSITIVE 243 165 129 41 6 NC_002967:TDE1999|3end_DNA_polymerase_III_domain_protein_2017796..2017946_POSITIVE 241 178 134 116 46 NC_002967:TDE0845|3end_conserved_hypothetical_protein_TIGR00266_868549..868699_POSITIVE 241 157 113 151 109 NC_002967:TDE0287|3end_ABC_transporter,_ATP-binding_protein,_putative_317375..317525_NEGATIVE 239 180 136 70 33 NC_002967:TDE0437|3end_PBS_lyase_HEAT-like_repeat_domain_protein_492136..492286_NEGATIVE 236 170 128 147 111 NC_002967:TDE0207|3end_permease,_GntP_family_243037..243187_POSITIVE 235 173 136 151 111 NC_002967:TDE1126|3end_TPR_domain_protein_1158365..1158515_POSITIVE 233 179 136 115 73 NC_002967:TDE2269|3end_hypothetical_protein_2304931..2305081_NEGATIVE 233 176 143 69 38 NC_002967:TDE1593|3end_Fe-hydrogenase_1641209..1641359_NEGATIVE 228 176 136 131 98 NC_002967:TDE2063|3end_ferrous_iron_transport_protein_B_2088430..2088580_NEGATIVE 227 179 136 115 73 NC_002967:TDE2515|3end_hypothetical_protein_2540972..2541122_NEGATIVE 227 180 143 37 4 NC_002967:TDE1524|3end_hypothetical_protein_1570464..1570614_POSITIVE 227 179 136 115 73 NC_002967:TDE0945|3end_hypothetical_protein_968320..968470_POSITIVE 226 50 1 63 21 NC_002967:TDE2307|3end_seryl-tRNA_synthetase_2344235..2344385_NEGATIVE 225 176 136 125 71 NC_002967:TDE2058|3end_hypothetical_protein_2085354..2085504_NEGATIVE