Origin IGS: gggaaagtttctcctcttcaacttcaaatttgtttatctatattgactaatattatagcatttttttcgatatttttctactgtcatatttctctactcacta .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tagtgagtagagaaatatgacagtagaaaaatatcgaaaaaaatgctataatattagtcaatatagataaacaaatttgaagttgaagaggagaaactttccc Mask Tandem Repeat Region ================================================ gggaaagtttctcctcttcaacttcaaatttgtttatctatattgactaatattatagcatttttttcgatatttttctactgtcatatttctctactcacta Find is-nt database================================================ Query_seq: TDE2174:TDE2175|TDE2174:TDE2175:hypothetical protein:hypothetical protein:<-<-:2204125..2204227 103 gggaaagtttctcctcttcaacttcaaatttgtttatctatattgactaatattatagcatttttttcgatatttttctactgtcatatttctctactcacta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE2174:TDE2175|TDE2174:TDE2175:hypothetical protein:hypothetical protein:<-<-:2204125..2204227 103 gggaaagtttctcctcttcaacttcaaatttgtttatctatattgactaatattatagcatttttttcgatatttttctactgtcatatttctctactcacta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE2174:TDE2175|TDE2174:TDE2175:hypothetical protein:hypothetical protein:<-<-:2204125..2204227 103 gggaaagtttctcctcttcaacttcaaatttgtttatctatattgactaatattatagcatttttttcgatatttttctactgtcatatttctctactcacta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gggaaagtttctcctcttcaacttcaaatttgtttatctatattgactaatattatagcatttttttcgatatttttctactgtcatatttctctactcacta Predict ORF larger than 30AA ================================================ gggaaagtttctcctcttcaacttcaaatttgtttatctatattgactaatattatagcatttttttcgatatttttctactgtcatatttctctactcacta 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: 85 Start: 52 End: 81 ...................................................GTAGAAAAATATCGAAAAAAATGCTATAAT...................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ gggaaagtttctcctcttcaacttcaaatttgtttatctatattgactaatattatagcatttttttcgatatttttctactgtcatatttctctactcacta Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE2174:TDE2175|TDE2174:TDE2175:hypothetical protein:hypothetical protein:<-<-:2204125..2204227 103 gggaaagtttctcctcttcaacttcaaatttgtttatctatattgactaatattatagcatttttttcgatatttttctactgtcatatttctctactcacta Intra-Species Hit: Count: 1 Min: 1 Max: 103 Len: 103 Subject: NC_002967_TDE2174_TDE2175|hypothetical protein:hypothetical protein|NEGATIVE:NEGATIVE|[2204125,2204227]|103 HSP 1 e-value: 1.0E-39 bit: 163.0 Len: 103 Query Start:1 Query End:103 Subject Strand: POSITIVE Subject Start: 1 Subject End: 103 gggaaagtttctcctcttcaacttcaaatttgtttatctatattgactaatattatagcannnnnnncgatatttttctactgtcatatttctctactcacta gggaaagtttctcctcttcaacttcaaatttgtttatctatattgactaatattatagcatttttttcgatatttttctactgtcatatttctctactcacta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GGGAAAGUUUCUCCUCUUCAACUUCAAAUUUGUUUAUCUAUAUUGACUAAUAUUAUAGCAUUUUUUUCGAUAUUUUUCUACUGUCAUAUUUCUCUACUCACUA ((((((...................(((..((((.....(((((....)))))...))))..)))...((((.........))))...))))))......... ( -7.70) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAGUGAGUAGAGAAAUAUGACAGUAGAAAAAUAUCGAAAAAAAUGCUAUAAUAUUAGUCAAUAUAGAUAAACAAAUUUGAAGUUGAAGAGGAGAAACUUUCCC .............(((((...((((..................))))...)))))..(((((.(((((......)))))..)))))...(((((...))))). ( -7.07) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 751 50 1 141 92 NC_002967:TDE2174|5end_hypothetical_protein_2204034..2204264_NEGATIVE 245 44 11 120 93 NC_002967:TDE1826|5end_hypothetical_protein_1859781..1860011_NEGATIVE 231 99 73 35 5 NC_002967:TDE0500|5end_hypothetical_protein_553686..553916_NEGATIVE 231 99 73 224 194 NC_002967:TDE0499|5end_hypothetical_protein_553497..553727_NEGATIVE 214 96 55 101 56 NC_002967:TDE2161|5end_acetyltransferase,_GNAT_family_2194090..2194320_POSITIVE 210 100 53 205 169 NC_002967:TDE1209|5end_site-specific_recombinase,_phage_integrase_family_1242345..1242575_POSITIVE 209 100 56 127 86 NC_002967:TDE1906|5end_hypothetical_protein_1923883..1924113_POSITIVE 206 96 51 60 1 NC_002967:TDE0170|5end_nuclease_SbcCD,_D_subunit,_putative_198789..199019_POSITIVE 202 48 5 124 90 NC_002967:TDE2411|5end_glycogen_phosphorylase_2439687..2439917_NEGATIVE 200 95 58 185 152 NC_002967:TDE1134|5end_hypothetical_protein_1165187..1165417_NEGATIVE 199 39 1 80 38 NC_002967:TDE2087|5end_translation_initiation_factor_IF-1_2115686..2115916_NEGATIVE 198 99 58 65 16 NC_002967:TDE2172|5end_hypothetical_protein_2202768..2202998_NEGATIVE 196 47 1 97 40 NC_002967:TDE2742|5end_site-specific_recombinase,_phage_integrase_family_2797659..2797889_NEGATIVE 196 46 8 36 3 NC_002967:TDE1516|5end_ABC_transporter,_ATP-binding_protein,_putative_1563127..1563357_POSITIVE 195 39 1 174 137 NC_002967:TDE0229|5end_ATPase_family_protein_262746..262976_NEGATIVE 193 48 9 138 97 NC_002967:TDE2456|5end_hypothetical_protein_2484573..2484803_NEGATIVE 190 100 67 44 9 NC_002967:TDE2622|5end_ABC_transporter,_ATP-binding_protein_2663590..2663820_NEGATIVE 190 39 2 210 169 NC_002967:TDE2344|5end_undecaprenyl_diphosphate_synthase_2381945..2382175_NEGATIVE 188 59 14 188 136 NC_002967:TDE1563|5end_hypothetical_protein_1615693..1615923_POSITIVE 187 41 1 215 182 NC_002967:TDE0028|5end_ABC_transporter,_ATP-binding_protein,_HlyB_family_35930..36160_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 222 96 73 149 127 NC_002967:TDE0500|3end_hypothetical_protein_553564..553714_NEGATIVE 219 38 3 145 98 NC_002967:TDE1603|3end_ABC_transporter,_ATP-binding_protein_1653411..1653561_NEGATIVE 198 99 58 96 47 NC_002967:TDE2173|3end_hypothetical_protein_2202737..2202887_NEGATIVE 195 39 1 121 84 NC_002967:TDE0230|3end_DNA_replication_and_repair_protein_RecF_262799..262949_NEGATIVE 193 79 31 112 72 NC_002967:TDE0403|3end_hypothetical_protein_455367..455517_POSITIVE 190 100 67 50 15 NC_002967:TDE2623|3end_hypothetical_protein_2663584..2663734_NEGATIVE 188 59 14 60 8 NC_002967:TDE1562|3end_hypothetical_protein_1615645..1615795_POSITIVE 188 50 1 148 98 NC_002967:TDE0374|3end_glycosyl_transferase,_group_1_family_protein_427914..428064_NEGATIVE 186 47 5 112 66 NC_002967:TDE2188|3end_hypothetical_protein_2221574..2221724_NEGATIVE 185 100 58 148 102 NC_002967:TDE0499|3end_hypothetical_protein_552517..552667_NEGATIVE 184 48 6 100 54 NC_002967:TDE2779|3end_hypothetical_protein_2829628..2829778_NEGATIVE 184 100 72 97 71 NC_002967:TDE2644|3end_pyridine_nucleotide-disulphide_oxidoreductase_family_protein_2685059..2685209_POSITIVE 182 88 42 67 20 NC_002967:TDE0899|3end_ABC_transporter,_permease_protein,_putative_917277..917427_POSITIVE 181 96 60 109 68 NC_002967:TDE1805|3end_radical_SAM_domain_protein_1842035..1842185_NEGATIVE 181 70 22 107 60 NC_002967:TDE1546|3end_hypothetical_protein_1591204..1591354_POSITIVE 180 98 55 109 59 NC_002967:TDE0767|3end_ribosomal_protein_L3_807061..807211_POSITIVE 177 48 16 145 112 NC_002967:TDE0418|3end_lipoprotein,_putative_470893..471043_POSITIVE 176 88 56 147 114 NC_002967:TDE1629|3end_dihydrolipoamide_dehydrogenase_1677153..1677303_NEGATIVE 175 98 57 95 42 NC_002967:TDE2359|3end_DAK2_domain_protein_2394153..2394303_NEGATIVE 175 81 58 42 14 NC_002967:TDE1950|3end_membrane_lipoprotein_TmpC,_putative_1966191..1966341_NEGATIVE