Origin IGS: aggtttattgtaacacaagtttttaaatttgacaaaggggctccaaacatgtaagttttcgaaaatcaaaaatccaaagatttaaaagactagacttttttgataaaatatgataaaattatttggttgctgtgattacatttttactaaatcacagacctggtttagtct .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 agactaaaccaggtctgtgatttagtaaaaatgtaatcacagcaaccaaataattttatcatattttatcaaaaaagtctagtcttttaaatctttggatttttgattttcgaaaacttacatgtttggagcccctttgtcaaatttaaaaacttgtgttacaataaacct Mask Tandem Repeat Region ================================================ aggtttattgtaacacaagtttttaaatttgacaaaggggctccaaacatgtaagttttcgaaaatcaaaaatccaaagatttaaaagactagacttttttgataaaatatgataaaattatttggttgctgtgattacatttttactaaatcacagacctggtttagtct Find is-nt database================================================ Query_seq: TDE2579:TDE2580|TDE2579:TDE2580:ATP-dependent DNA helicase RecG:GGDEF domain protein:<-->:2605415..2605585 171 aggtttattgtaacacaagtttttaaatttgacaaaggggctccaaacatgtaagttttcgaaaatcaaaaatccaaagatttaaaagactagacttttttgataaaatatgataaaattatttggttgctgtgattacatttttactaaatcacagacctggtttagtct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE2579:TDE2580|TDE2579:TDE2580:ATP-dependent DNA helicase RecG:GGDEF domain protein:<-->:2605415..2605585 171 aggtttattgtaacacaagtttttaaatttgacaaaggggctccaaacatgtaagttttcgaaaatcaaaaatccaaagatttaaaagactagacttttttgataaaatatgataaaattatttggttgctgtgattacatttttactaaatcacagacctggtttagtct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE2579:TDE2580|TDE2579:TDE2580:ATP-dependent DNA helicase RecG:GGDEF domain protein:<-->:2605415..2605585 171 aggtttattgtaacacaagtttttaaatttgacaaaggggctccaaacatgtaagttttcgaaaatcaaaaatccaaagatttaaaagactagacttttttgataaaatatgataaaattatttggttgctgtgattacatttttactaaatcacagacctggtttagtct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aggtttattgtaacacaagtttttaaatttgacaaaggggctccaaacatgtaagttttcgaaaatcaaaaatccaaagatttaaaagactagacttttttgataaaatatgataaaattatttggttgctgtgattacatttttactaaatcacagacctggtttagtct Predict ORF larger than 30AA ================================================ aggtttattgtaacacaagtttttaaatttgacaaaggggctccaaacatgtaagttttcgaaaatcaaaaatccaaagatttaaaagactagacttttttgataaaatatgataaaattatttggttgctgtgattacatttttactaaatcacagacctggtttagtct 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: 90 Start: 7 End: 36 ......TTTGTCAAATTTAAAAACTTGTGTTACAAT....................................................................................................................................... PromScan Matrix: RpoD-17 Strand: + Score: 82 Start: 80 End: 109 ...............................................................................ATTTAAAAGACTAGACTTTTTTGATAAAAT.............................................................. PromScan Matrix: RpoD-17 Strand: + Score: 82 Start: 90 End: 119 .........................................................................................CTAGACTTTTTTGATAAAATATGATAAAAT.................................................... PromScan Matrix: RpoD-17 Strand: + Score: 81 Start: 28 End: 57 ...........................TTTGACAAAGGGGCTCCAAACATGTAAGTT.................................................................................................................. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ aggtttattgtaacacaagtttttaaatttgacaaaggggctccaaacatgtaagttttcgaaaatcaaaaatccaaagatttaaaagactagacttttttgataaaatatgataaaattatttggttgctgtgattacatttttactaaatcacagacctggtttagtct Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE2579:TDE2580|TDE2579:TDE2580:ATP-dependent DNA helicase RecG:GGDEF domain protein:<-->:2605415..2605585 171 aggtttattgtaacacaagtttttaaatttgacaaaggggctccaaacatgtaagttttcgaaaatcaaaaatccaaagatttaaaagactagacttttttgataaaatatgataaaattatttggttgctgtgattacatttttactaaatcacagacctggtttagtct Intra-Species Hit: Count: 1 Min: 1 Max: 171 Len: 171 Subject: NC_002967_TDE2579_TDE2580|ATP-dependent DNA helicase RecG:GGDEF domain protein|NEGATIVE:POSITIVE|[2605415,2605585]|171 HSP 1 e-value: 2.0E-92 bit: 339.0 Len: 171 Query Start:1 Query End:171 Subject Strand: POSITIVE Subject Start: 1 Subject End: 171 aggtttattgtaacacaagtttttaaatttgacaaaggggctccaaacatgtaagttttcgaaaatcaaaaatccaaagatttaaaagactagacttttttgataaaatatgataaaattatttggttgctgtgattacatttttactaaatcacagacctggtttagtct aggtttattgtaacacaagtttttaaatttgacaaaggggctccaaacatgtaagttttcgaaaatcaaaaatccaaagatttaaaagactagacttttttgataaaatatgataaaattatttggttgctgtgattacatttttactaaatcacagacctggtttagtct Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGGUUUAUUGUAACACAAGUUUUUAAAUUUGACAAAGGGGCUCCAAACAUGUAAGUUUUCGAAAAUCAAAAAUCCAAAGAUUUAAAAGACUAGACUUUUUUGAUAAAAUAUGAUAAAAUUAUUUGGUUGCUGUGAUUACAUUUUUACUAAAUCACAGACCUGGUUUAGUCU .(((((.(((.(((.((((((....)))))).....((....))..........)))..))))))))..(((((....)))))...((((((((((.........(((((.........)))))(((..((((((((............))))))))))).)))))))))) (-28.40) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGACUAAACCAGGUCUGUGAUUUAGUAAAAAUGUAAUCACAGCAACCAAAUAAUUUUAUCAUAUUUUAUCAAAAAAGUCUAGUCUUUUAAAUCUUUGGAUUUUUGAUUUUCGAAAACUUACAUGUUUGGAGCCCCUUUGUCAAAUUUAAAAACUUGUGUUACAAUAAACCU ......((((((((((((((((............))))))))...(((((((...............(((((((..((((((............)))))))))))))...............)))))))......................))))).)))........... (-25.91) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 808 80 31 171 122 NC_002967:TDE2579|5end_ATP-dependent_DNA_helicase_RecG_2605324..2605554_NEGATIVE 234 62 28 215 181 NC_002967:TDE1000|5end_3-hydroxyacid_dehydrogenase_family_protein_1026763..1026993_POSITIVE 228 170 122 160 105 NC_002967:TDE2694|5end_hypothetical_protein_2736301..2736531_NEGATIVE 209 80 32 57 15 NC_002967:TDE0870|5end_phosphatase/nucleotidase_892698..892928_POSITIVE 207 138 108 33 8 NC_002967:TDE2693|5end_ankyrin_repeat_protein_2731133..2731363_POSITIVE 207 164 121 147 104 NC_002967:TDE0118|5end_hypothetical_protein_137047..137277_NEGATIVE 200 44 1 190 137 NC_002967:TDE1688|5end_hypothetical_protein_1745791..1746021_NEGATIVE 198 50 2 216 164 NC_002967:TDE0765|5end_translation_elongation_factor_Tu_804732..804962_POSITIVE 196 67 30 226 195 NC_002967:TDE2355|5end_carbon_storage_regulator_2390838..2391068_POSITIVE 196 68 21 227 170 NC_002967:TDE0015|5end_lipoprotein,_putative_19427..19657_POSITIVE 192 162 121 225 179 NC_002967:TDE1958|5end_surface_protein,_putative_1973685..1973915_NEGATIVE 191 148 119 138 108 NC_002967:TDE1661|5end_hypothetical_protein_1715402..1715632_POSITIVE 189 75 38 217 180 NC_002967:TDE0711|5end_hypothetical_protein_746181..746411_NEGATIVE 189 49 35 227 212 NC_002967:TDE0069|5end_conserved_hypothetical_protein_TIGR00238_76551..76781_POSITIVE 188 170 125 215 169 NC_002967:TDE1956|5end_hypothetical_protein_1971114..1971344_POSITIVE 188 80 34 94 43 NC_002967:TDE1358|5end_hypothetical_protein_1397732..1397962_POSITIVE 187 75 47 145 119 NC_002967:TDE0738|5end_hypothetical_protein_775934..776164_NEGATIVE 186 48 17 74 45 NC_002967:TDE2248|5end_HesA/MoeB/ThiF_family_protein_2287478..2287708_NEGATIVE 185 67 39 73 45 NC_002967:TDE2466|5end_hypothetical_protein_2489860..2490090_NEGATIVE 184 80 35 72 9 NC_002967:TDE0849|5end_hypothetical_protein_871599..871829_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 251 44 1 126 80 NC_002967:TDE2667|3end_hypothetical_protein_2704579..2704729_POSITIVE 228 170 122 87 32 NC_002967:TDE2695|3end_transcript_cleavage_factor/unknown_domain_fusion_protein_2736374..2736524_NEGATIVE 210 166 121 137 93 NC_002967:TDE0496|3end_DNA-binding_protein,_putative_550971..551121_NEGATIVE 207 164 121 136 93 NC_002967:TDE0119|3end_flagellar_protein_FliS_137058..137208_NEGATIVE 198 44 8 141 101 NC_002967:TDE0999|3end_formate/nitrite_transporter_1026786..1026936_POSITIVE 192 162 121 105 59 NC_002967:TDE1959|3end_hypothetical_protein_1973805..1973955_NEGATIVE 188 80 34 112 61 NC_002967:TDE1357|3end_aldose_1-epimerase_1397830..1397980_POSITIVE 186 48 17 54 25 NC_002967:TDE2249|3end_phospho-N-acetylmuramoyl-pentapeptide-_transferase_2287498..2287648_NEGATIVE 185 67 39 52 24 NC_002967:TDE2467|3end_hypothetical_protein_2489881..2490031_NEGATIVE 182 59 27 40 4 NC_002967:TDE1982|3end_hypothetical_protein_1992511..1992661_NEGATIVE 182 58 16 92 43 NC_002967:TDE1026|3end_acyl_carrier_protein_1057618..1057768_POSITIVE 182 149 111 148 107 NC_002967:TDE0514|3end_hypothetical_protein_562420..562570_NEGATIVE 181 75 34 57 21 NC_002967:TDE2553|3end_lysyl-tRNA_synthetase_2579047..2579197_NEGATIVE 180 62 32 31 9 NC_002967:TDE2629|3end_peptide_ABC_transporter,_periplasmic_peptide-binding_protein,_putative_2670962..2671112_POSITIVE 180 62 35 129 100 NC_002967:TDE0779|3end_ribosomal_protein_L5_812432..812582_POSITIVE 179 76 33 86 41 NC_002967:TDE2313|3end_hypothetical_protein_2349506..2349656_NEGATIVE 179 62 33 45 8 NC_002967:TDE1463|3end_hypothetical_protein_1512206..1512356_NEGATIVE 179 115 80 147 110 NC_002967:TDE0995|3end_hypothetical_protein_1022442..1022592_NEGATIVE 179 70 26 114 65 NC_002967:TDE0284|3end_hypothetical_protein_312826..312976_NEGATIVE 177 162 125 138 107 NC_002967:TDE1383|3end_hypothetical_protein_1422851..1423001_POSITIVE