Origin IGS: aaatattatcctttaataaaaccatattatactactatttattccgaaaagcaatctgtttcttctaaagtctccgaagacaaagattttgtatcgatagatgttgtatccatagattgacatcttcatataaaaagcctatactcactcttgcatcccgaattgcgttagacgcacgcaaaaggagaggagtt .........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 aactcctctccttttgcgtgcgtctaacgcaattcgggatgcaagagtgagtataggctttttatatgaagatgtcaatctatggatacaacatctatcgatacaaaatctttgtcttcggagactttagaagaaacagattgcttttcggaataaatagtagtataatatggttttattaaaggataatattt Mask Tandem Repeat Region ================================================ aaatattatcctttaataaaaccatattatactactatttattccgaaaagcaatctgtttcttctaaagtctccgaagacaannnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnngacatcttcatataaaaagcctatactcactcttgcatcccgaattgcgttagacgcacgcaaaaggagaggagtt Find is-nt database================================================ Query_seq: TDE0360:TDE0361|TDE0360:TDE0361:ABC transporter, ATP-binding/permease protein:transporter, putative:<-->:405935..406128 194 aaatattatcctttaataaaaccatattatactactatttattccgaaaagcaatctgtttcttctaaagtctccgaagacaaagattttgtatcgatagatgttgtatccatagattgacatcttcatataaaaagcctatactcactcttgcatcccgaattgcgttagacgcacgcaaaaggagaggagtt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE0360:TDE0361|TDE0360:TDE0361:ABC transporter, ATP-binding/permease protein:transporter, putative:<-->:405935..406128 194 aaatattatcctttaataaaaccatattatactactatttattccgaaaagcaatctgtttcttctaaagtctccgaagacaaagattttgtatcgatagatgttgtatccatagattgacatcttcatataaaaagcctatactcactcttgcatcccgaattgcgttagacgcacgcaaaaggagaggagtt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE0360:TDE0361|TDE0360:TDE0361:ABC transporter, ATP-binding/permease protein:transporter, putative:<-->:405935..406128 194 aaatattatcctttaataaaaccatattatactactatttattccgaaaagcaatctgtttcttctaaagtctccgaagacaaagattttgtatcgatagatgttgtatccatagattgacatcttcatataaaaagcctatactcactcttgcatcccgaattgcgttagacgcacgcaaaaggagaggagtt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aaatattatcctttaataaaaccatattatactactatttattccgaaaagcaatctgtttcttctaaagtctccgaagacaaagattttgtatcgatagatgttgtatccatagattgacatcttcatataaaaagcctatactcactcttgcatcccgaattgcgttagacgcacgcaaaaggagaggagtt Predict ORF larger than 30AA ================================================ Protein_Len: 34 Strand: + Start: 16 End: 117 ............... M K P Y Y T T I Y S E K Q S V S S K V S E D K D F V S I D V V S I D ............................................................................. Protein_Len: 34 Strand: + Start: 93 End: 194 ............................................................................................ M D R C C I H R L T S S Y K K P I L T L A S R I A L D A R K R R G V Protein_Len: 38 Strand: - Start: 68 End: 181 ................................................................... L R R L C L N Q I S L H Q I W L N V D E Y L F G I S V R A D R I A N S A R M ............. Protein_Len: 38 Strand: - Start: 16 End: 129 ............... Y F W I I S S N I G F L L R N R R F D G F V F I K Y R Y I N Y G Y I S M K M ................................................................. aaatattatcctttaataaaaccatattatactactatttattccgaaaagcaatctgtttcttctaaagtctccgaagacaaagattttgtatcgatagatgttgtatccatagattgacatcttcatataaaaagcctatactcactcttgcatcccgaattgcgttagacgcacgcaaaaggagaggagtt 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: 87 Start: 116 End: 145 ...................................................................................................................ATTGACATCTTCATATAAAAAGCCTATACT................................................. PromScan Matrix: RpoD-17 Strand: - Score: 83 Start: 26 End: 55 .........................ATTGCTTTTCGGAATAAATAGTAGTATAAT........................................................................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ aaatattatcctttaataaaaccatattatactactatttattccgaaaagcaatctgtttcttctaaagtctccgaagacaaagattttgtatcgatagatgttgtatccatagattgacatcttcatataaaaagcctatactcactcttgcatcccgaattgcgttagacgcacgcaaaaggagaggagtt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE0360:TDE0361|TDE0360:TDE0361:ABC transporter, ATP-binding/permease protein:transporter, putative:<-->:405935..406128 194 aaatattatcctttaataaaaccatattatactactatttattccgaaaagcaatctgtttcttctaaagtctccgaagacaaagattttgtatcgatagatgttgtatccatagattgacatcttcatataaaaagcctatactcactcttgcatcccgaattgcgttagacgcacgcaaaaggagaggagtt Intra-Species Hit: Count: 1 Min: 1 Max: 194 Len: 194 Subject: NC_002967_TDE0360_TDE0361|ABC transporter, ATP-binding/permease protein:transporter, putative|NEGATIVE:POSITIVE|[405935,406128]|194 HSP 1 e-value: 1.0E-106 bit: 385.0 Len: 194 Query Start:1 Query End:194 Subject Strand: POSITIVE Subject Start: 1 Subject End: 194 aaatattatcctttaataaaaccatattatactactatttattccgaaaagcaatctgtttcttctaaagtctccgaagacaaagattttgtatcgatagatgttgtatccatagattgacatcttcatataaaaagcctatactcactcttgcatcccgaattgcgttagacgcacgcaaaaggagaggagtt aaatattatcctttaataaaaccatattatactactatttattccgaaaagcaatctgtttcttctaaagtctccgaagacaaagattttgtatcgatagatgttgtatccatagattgacatcttcatataaaaagcctatactcactcttgcatcccgaattgcgttagacgcacgcaaaaggagaggagtt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAUAUUAUCCUUUAAUAAAACCAUAUUAUACUACUAUUUAUUCCGAAAAGCAAUCUGUUUCUUCUAAAGUCUCCGAAGACAAAGAUUUUGUAUCGAUAGAUGUUGUAUCCAUAGAUUGACAUCUUCAUAUAAAAAGCCUAUACUCACUCUUGCAUCCCGAAUUGCGUUAGACGCACGCAAAAGGAGAGGAGUU ...(((((.....)))))......................(((((.....((.((((...(((((..........)))))...))))(((((((.((.((((((((.(((....))))))))))))))))))))..)).....(((.((.((((.........((((.....)))).)))).))))).))))). (-34.90) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AACUCCUCUCCUUUUGCGUGCGUCUAACGCAAUUCGGGAUGCAAGAGUGAGUAUAGGCUUUUUAUAUGAAGAUGUCAAUCUAUGGAUACAACAUCUAUCGAUACAAAAUCUUUGUCUUCGGAGACUUUAGAAGAAACAGAUUGCUUUUCGGAAUAAAUAGUAGUAUAAUAUGGUUUUAUUAAAGGAUAAUAUUU ...(((((((((((((((((((.....))))........)))))))).)))...(((((..((((((..((((((..(((....)))...)))))).((((.....(((((...((((((....)....)))))...))))).....))))...........))))))...)))))......))))........ (-42.30) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 820 100 51 191 142 NC_002967:TDE0360|5end_ABC_transporter,_ATP-binding/permease_protein_405844..406074_NEGATIVE 307 180 134 219 165 NC_002967:TDE0350|5end_MATE_efflux_family_protein_393572..393802_POSITIVE 305 170 123 217 170 NC_002967:TDE0091|5end_RNA_polymerase_sigma-24_factor,_putative_109732..109962_NEGATIVE 295 180 136 56 13 NC_002967:TDE0908|5end_ABC_transporter,_ATP-binding/permease_protein_925254..925484_POSITIVE 288 96 51 189 136 NC_002967:TDE1543|5end_conserved_hypothetical_protein_TIGR00247_1586068..1586298_POSITIVE 285 180 133 58 17 NC_002967:TDE0169|5end_methyl-accepting_chemotaxis_domain_protein_198792..199022_NEGATIVE 280 190 146 106 56 NC_002967:TDE1824|5end_hypothetical_protein_1857011..1857241_POSITIVE 278 180 135 231 181 NC_002967:TDE2494|5end_hypothetical_protein_2518497..2518727_POSITIVE 271 89 44 59 16 NC_002967:TDE2762|5end_flagellar_motor_switch_protein_FliY_2817744..2817974_NEGATIVE 271 81 43 40 3 NC_002967:TDE0049|5end_hypothetical_protein_59089..59319_NEGATIVE 261 81 43 40 3 NC_002967:TDE1691|5end_hypothetical_protein_1748273..1748503_NEGATIVE 260 170 121 63 16 NC_002967:TDE2457|5end_hypothetical_protein_2485570..2485800_NEGATIVE 258 190 148 228 194 NC_002967:TDE0854|5end_regulatory_protein_RecX_875813..876043_POSITIVE 258 85 44 220 188 NC_002967:TDE0833|5end_lipoprotein,_putative_852992..853222_POSITIVE 253 86 43 55 6 NC_002967:TDE2761|5end_hypothetical_protein_2816537..2816767_NEGATIVE 253 168 122 184 149 NC_002967:TDE0828|5end_glucose-inhibited_division_protein_A_850169..850399_NEGATIVE 253 190 142 85 35 NC_002967:TDE0603|5end_hypothetical_protein_640888..641118_POSITIVE 252 186 144 203 134 NC_002967:TDE0957|5end_glycerophosphoryl_diester_phosphodiesterase_family_protein_980252..980482_POSITIVE 251 190 159 223 195 NC_002967:TDE2322|5end_flagellar_protein_FliL-related_protein_2357810..2358040_NEGATIVE 251 86 49 205 152 NC_002967:TDE1261|5end_choline/carnitine/betaine_transporter_family_protein_1295593..1295823_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 299 175 138 36 1 NC_002967:TDE0210|3end_cob(I)yrinic_acid_a,c-diamide_adenosyltransferase_246146..246296_POSITIVE 288 186 148 60 14 NC_002967:TDE2308|3end_hypothetical_protein_2346313..2346463_POSITIVE 281 176 135 57 8 NC_002967:TDE1323|3end_hypothetical_protein_1360968..1361118_POSITIVE 271 89 44 66 23 NC_002967:TDE2763|3end_flagellar_motor_switch_protein_2817737..2817887_NEGATIVE 254 178 133 139 104 NC_002967:TDE0339|3end_transcriptional_regulator,_TetR_family_378568..378718_POSITIVE 250 179 137 60 13 NC_002967:TDE1770|3end_hypothetical_protein_1814468..1814618_POSITIVE 250 186 141 45 4 NC_002967:TDE0907|3end_hypothetical_protein_925320..925470_POSITIVE 246 75 51 123 95 NC_002967:TDE0866|3end_hypothetical_protein_888629..888779_POSITIVE 246 190 143 87 27 NC_002967:TDE0098|3end_hypothetical_protein_114842..114992_NEGATIVE 245 75 33 132 92 NC_002967:TDE2527|3end_hypothetical_protein_2555449..2555599_NEGATIVE 244 188 142 148 92 NC_002967:TDE0772|3end_50S_ribosomal_protein_L22_809520..809670_POSITIVE 243 175 138 69 33 NC_002967:TDE1059|3end_hypothetical_protein_1086498..1086648_NEGATIVE 240 75 45 140 108 NC_002967:TDE1542|3end_hypothetical_protein_1586128..1586278_POSITIVE 240 177 137 98 66 NC_002967:TDE0908|3end_ABC_transporter,_ATP-binding/permease_protein_927085..927235_POSITIVE 239 80 35 109 55 NC_002967:TDE1865|3end_peptidase,_M16_family_1889141..1889291_NEGATIVE 238 190 161 134 93 NC_002967:TDE2733|3end_hypothetical_protein_2789126..2789276_POSITIVE 236 178 134 124 86 NC_002967:TDE2714|3end_hypothetical_protein_2770627..2770777_NEGATIVE 236 178 136 54 11 NC_002967:TDE2196|3end_hypothetical_protein_2231883..2232033_NEGATIVE 236 185 145 45 3 NC_002967:TDE2169|3end_hypothetical_protein_2201509..2201659_POSITIVE 236 177 134 137 86 NC_002967:TDE0824|3end_lipoprotein,_putative_845226..845376_NEGATIVE