Origin IGS: tcttactccgcctcctgttattctgtatatattaaatatatacagaataacaatctttgtcaagagggaaattgaaaaaagatacattttaatataaaaatttaaagttacttaaagacaaaaatcttgacatttttaataatgtttgtcataatctaccttaaagt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 actttaaggtagattatgacaaacattattaaaaatgtcaagatttttgtctttaagtaactttaaatttttatattaaaatgtatcttttttcaatttccctcttgacaaagattgttattctgtatatatttaatatatacagaataacaggaggcggagtaaga Mask Tandem Repeat Region ================================================ tcttactccgcctcctgttattctgtatatattaaatatatacagaataacaatctttgtcaagagggaaattgaaaaaagatacattttaatataaaaatttaaagttacttaaagacaaaaatcttgacatttttaataatgtttgtcataatctaccttaaagt Find is-nt database================================================ Query_seq: TDE2650:TDE2651|TDE2650:TDE2651:transcriptional regulator, putative:ABC transporter, ATP-binding protein:<-->:2689122..2689288 167 tcttactccgcctcctgttattctgtatatattaaatatatacagaataacaatctttgtcaagagggaaattgaaaaaagatacattttaatataaaaatttaaagttacttaaagacaaaaatcttgacatttttaataatgtttgtcataatctaccttaaagt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE2650:TDE2651|TDE2650:TDE2651:transcriptional regulator, putative:ABC transporter, ATP-binding protein:<-->:2689122..2689288 167 tcttactccgcctcctgttattctgtatatattaaatatatacagaataacaatctttgtcaagagggaaattgaaaaaagatacattttaatataaaaatttaaagttacttaaagacaaaaatcttgacatttttaataatgtttgtcataatctaccttaaagt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE2650:TDE2651|TDE2650:TDE2651:transcriptional regulator, putative:ABC transporter, ATP-binding protein:<-->:2689122..2689288 167 tcttactccgcctcctgttattctgtatatattaaatatatacagaataacaatctttgtcaagagggaaattgaaaaaagatacattttaatataaaaatttaaagttacttaaagacaaaaatcttgacatttttaataatgtttgtcataatctaccttaaagt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tcttactccgcctcctgttattctgtatatattaaatatatacagaataacaatctttgtcaagagggaaattgaaaaaagatacattttaatataaaaatttaaagttacttaaagacaaaaatcttgacatttttaataatgtttgtcataatctaccttaaagt Predict ORF larger than 30AA ================================================ Protein_Len: 31 Strand: - Start: 1 End: 93 R V G G G T I R Y I N F I Y L I V I K T L L S I S F L Y M K M .......................................................................... tcttactccgcctcctgttattctgtatatattaaatatatacagaataacaatctttgtcaagagggaaattgaaaaaagatacattttaatataaaaatttaaagttacttaaagacaaaaatcttgacatttttaataatgtttgtcataatctaccttaaagt 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: 91 Start: 126 End: 155 .............................................................................................................................CTTGACATTTTTAATAATGTTTGTCATAAT............ PromScan Matrix: RpoD-17 Strand: - Score: 89 Start: 35 End: 64 ..................................CTTGACAAAGATTGTTATTCTGTATATATT....................................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ tcttactccgcctcctgttattctgtatatattaaatatatacagaataacaatctttgtcaagagggaaattgaaaaaagatacattttaatataaaaatttaaagttacttaaagacaaaaatcttgacatttttaataatgtttgtcataatctaccttaaagt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE2650:TDE2651|TDE2650:TDE2651:transcriptional regulator, putative:ABC transporter, ATP-binding protein:<-->:2689122..2689288 167 tcttactccgcctcctgttattctgtatatattaaatatatacagaataacaatctttgtcaagagggaaattgaaaaaagatacattttaatataaaaatttaaagttacttaaagacaaaaatcttgacatttttaataatgtttgtcataatctaccttaaagt Intra-Species Hit: Count: 1 Min: 1 Max: 167 Len: 167 Subject: NC_002967_TDE2650_TDE2651|transcriptional regulator, putative:ABC transporter, ATP-binding protein|NEGATIVE:POSITIVE|[2689122,2689288]|167 HSP 1 e-value: 5.0E-31 bit: 135.0 Len: 68 Query Start:1 Query End:68 Subject Strand: POSITIVE Subject Start: 1 Subject End: 68 tcttactccgcctcctgttattctgtatatattaaatatatacagaataacaatctttgtcaagaggg................................................................................................... tcttactccgcctcctgttattctgtatatattaaatatatacagaataacaatctttgtcaagaggg................................................................................................... HSP 2 e-value: 2.0E-15 bit: 83.8 Len: 42 Query Start:126 Query End:167 Subject Strand: POSITIVE Subject Start: 126 Subject End: 167 .............................................................................................................................cttgacatttttaataatgtttgtcataatctaccttaaagt .............................................................................................................................cttgacatttttaataatgtttgtcataatctaccttaaagt HSP 3 e-value: 4.0E-10 bit: 65.9 Len: 37 Query Start:16 Query End:52 Subject Strand: NEGATIVE Subject Start: 16 Subject End: 52 ...............tgttattctgtatatattaaatatatacagaataaca................................................................................................................... ...............tgttattctgtatatatttaatatatacagaataaca................................................................................................................... Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UCUUACUCCGCCUCCUGUUAUUCUGUAUAUAUUAAAUAUAUACAGAAUAACAAUCUUUGUCAAGAGGGAAAUUGAAAAAAGAUACAUUUUAAUAUAAAAAUUUAAAGUUACUUAAAGACAAAAAUCUUGACAUUUUUAAUAAUGUUUGUCAUAAUCUACCUUAAAGU ......(((......(((((((((((((((((...))))))))))))))))).((((....)))).)))..........((((..(((((((.........)))))))........((((........((((((......))))))))))...)))).......... (-30.60) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ ACUUUAAGGUAGAUUAUGACAAACAUUAUUAAAAAUGUCAAGAUUUUUGUCUUUAAGUAACUUUAAAUUUUUAUAUUAAAAUGUAUCUUUUUUCAAUUUCCCUCUUGACAAAGAUUGUUAUUCUGUAUAUAUUUAAUAUAUACAGAAUAACAGGAGGCGGAGUAAGA ..((((((((...(((.((((((((((......)))))........)))))..)))...))))))))............................((((((((((..........(((((((((((((((((...)))))))))))))))))))))).))))).... (-37.40) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 760 50 1 141 92 NC_002967:TDE2650|5end_transcriptional_regulator,_putative_2689031..2689261_NEGATIVE 264 27 2 114 83 NC_002967:TDE1151|5end_hypothetical_protein_1188534..1188764_NEGATIVE 253 109 61 78 27 NC_002967:TDE1135|5end_hypothetical_protein_1165542..1165772_NEGATIVE 248 27 5 195 170 NC_002967:TDE2390|5end_hypothetical_protein_2420558..2420788_NEGATIVE 232 33 7 149 121 NC_002967:TDE1310|5end_modulator_of_DNA_gyrase_family_protein_1345962..1346192_POSITIVE 230 72 41 182 155 NC_002967:TDE2006|5end_hypothetical_protein_2024421..2024651_POSITIVE 225 48 1 143 81 NC_002967:TDE1460|5end_hypothetical_protein_1511091..1511321_NEGATIVE 225 24 7 156 139 NC_002967:TDE1222|5end_iron-dependent_transcriptional_regulator_1256709..1256939_NEGATIVE 223 26 6 53 34 NC_002967:TDE1150|5end_hypothetical_protein_1188243..1188473_NEGATIVE 220 76 34 169 126 NC_002967:TDE0155|5end_adenylate/guanylate_cyclase_catalytic_domain_protein_180154..180384_NEGATIVE 211 90 56 231 198 NC_002967:TDE1552|5end_hypothetical_protein_1595759..1595989_POSITIVE 208 26 1 206 172 NC_002967:TDE2676|5end_threonine_synthase_2714285..2714515_POSITIVE 208 18 7 73 62 NC_002967:TDE1974|5end_UDP-N-acetylglucosamine--N-acetylmuramyl-_(pentapeptide)_pyrophosphoryl-undecaprenol_N-acetylglucosamine_transferase_1988910..1989140_NEGATIVE 207 27 7 181 159 NC_002967:TDE1004|5end_flagellar_filament_core_protein_1030136..1030366_NEGATIVE 205 31 2 231 196 NC_002967:TDE0732|5end_hypothetical_protein_772730..772960_NEGATIVE 202 34 5 220 192 NC_002967:TDE1412|5end_sodium/hydrogen_exchanger_family_protein_1453462..1453692_POSITIVE 200 69 25 154 110 NC_002967:TDE1277|5end_Fe-hydrogenase_large_subunit_family_protein_1310681..1310911_POSITIVE 197 64 21 138 98 NC_002967:TDE1281|5end_hypothetical_protein_1316500..1316730_POSITIVE 195 34 1 93 62 NC_002967:TDE1547|5end_ribonuclease_HII_1591124..1591354_POSITIVE 191 23 7 42 26 NC_002967:TDE2762|5end_flagellar_motor_switch_protein_FliY_2817744..2817974_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 264 27 2 121 90 NC_002967:TDE1152|3end_head-to-tail_joining_protein,_putative_1188527..1188677_NEGATIVE 253 109 61 77 26 NC_002967:TDE1136|3end_M23/M37_peptidase_domain_protein_1165543..1165693_NEGATIVE 232 33 7 149 121 NC_002967:TDE1309|3end_modulator_of_DNA_gyrase_family_protein_1346042..1346192_POSITIVE 230 72 41 91 64 NC_002967:TDE2005|3end_hypothetical_protein_2024410..2024560_POSITIVE 225 24 7 130 113 NC_002967:TDE1223|3end_zinc_ABC_transporter,_permease_protein_1256735..1256885_NEGATIVE 223 26 6 28 9 NC_002967:TDE1151|3end_hypothetical_protein_1188268..1188418_NEGATIVE 215 26 3 85 54 NC_002967:TDE0908|3end_ABC_transporter,_ATP-binding/permease_protein_927085..927235_POSITIVE 208 46 6 105 69 NC_002967:TDE2260|3end_hypothetical_protein_2297573..2297723_POSITIVE 195 34 1 93 62 NC_002967:TDE1546|3end_hypothetical_protein_1591204..1591354_POSITIVE 195 47 4 75 22 NC_002967:TDE0146|3end_amidohydrolase_family_protein_167435..167585_NEGATIVE 194 81 54 43 15 NC_002967:TDE1928|3end_hypothetical_protein_1946583..1946733_POSITIVE 191 23 7 49 33 NC_002967:TDE2763|3end_flagellar_motor_switch_protein_2817737..2817887_NEGATIVE 189 18 6 116 103 NC_002967:TDE1725|3end_hypothetical_protein_1778393..1778543_NEGATIVE 187 19 6 61 49 NC_002967:TDE1426|3end_aminotransferase,_DegT/DnrJ/EryC1/StrS_family_1469805..1469955_POSITIVE 186 28 6 137 108 NC_002967:TDE0133|3end_transcriptional_regulator,_GntR_family_153202..153352_POSITIVE 185 26 4 114 94 NC_002967:TDE1069|3end_oligopeptide/dipeptide_ABC_transporter,_permease_protein_1096683..1096833_NEGATIVE 185 46 2 54 1 NC_002967:TDE0954|3end_branched-chain_amino_acid_ABC_transporter,_permease_protein_978840..978990_POSITIVE 185 37 2 44 3 NC_002967:TDE0737|3end_hypothetical_protein_775408..775558_NEGATIVE 183 70 25 70 26 NC_002967:TDE1634|3end_hypothetical_protein_1682785..1682935_NEGATIVE 182 28 7 119 97 NC_002967:TDE2406|3end_TldD/PmbA_family_protein_2432047..2432197_NEGATIVE