Origin IGS: actttctccataatggttagtggatagtttaattggtgatatgtgaattttccacattacttatgttatcacaaacaccgcagttttacaagagaatatacacggaaatcaatttttgaaaaatgatactacaattgaatttgttctatctatgtttttagaaaaatagaacactttctaacatttttctcatattttcagttttaaaatctgtgaaaatggcaaaaattgatttccctgtagggaggattatttaagtgacaaataataagatttatgctaaaatatcccgatataaattttaaagacaaaacaaatttagtaagggatttattat .........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.........1.........2.........3.........4.........5.........6.........7.........8.........9 ataataaatcccttactaaatttgttttgtctttaaaatttatatcgggatattttagcataaatcttattatttgtcacttaaataatcctccctacagggaaatcaatttttgccattttcacagattttaaaactgaaaatatgagaaaaatgttagaaagtgttctatttttctaaaaacatagatagaacaaattcaattgtagtatcatttttcaaaaattgatttccgtgtatattctcttgtaaaactgcggtgtttgtgataacataagtaatgtggaaaattcacatatcaccaattaaactatccactaaccattatggagaaagt Mask Tandem Repeat Region ================================================ actttctccataatggttagtggatagtttaattggtgatatgtgaattttccacattacttatgttatcacaaacaccgcagttttacaagagaatatacacggaaatcaatttttgaaaaatgatactacaattgaatttgttctatctatgtttttagaaaaatagaacactttctaacatttttctcatattttcagttttaaaatctgtgaaaatggcaaaaattgatttccctgtagggaggattatttaagtgacaaataataagatttatgctaaaatatcccgatataaattttaaagacaaaacaaatttagtaagggatttattat Find is-nt database================================================ Query_seq: TDE0156:TDE0157|TDE0156:TDE0157:adenylate/guanylate cyclase catalytic domain protein:KHG/KDPG family aldolase/carbohydrate kinase, PfkB family:<-->:183662..183998 337 actttctccataatggttagtggatagtttaattggtgatatgtgaattttccacattacttatgttatcacaaacaccgcagttttacaagagaatatacacggaaatcaatttttgaaaaatgatactacaattgaatttgttctatctatgtttttagaaaaatagaacactttctaacatttttctcatattttcagttttaaaatctgtgaaaatggcaaaaattgatttccctgtagggaggattatttaagtgacaaataataagatttatgctaaaatatcccgatataaattttaaagacaaaacaaatttagtaagggatttattat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE0156:TDE0157|TDE0156:TDE0157:adenylate/guanylate cyclase catalytic domain protein:KHG/KDPG family aldolase/carbohydrate kinase, PfkB family:<-->:183662..183998 337 actttctccataatggttagtggatagtttaattggtgatatgtgaattttccacattacttatgttatcacaaacaccgcagttttacaagagaatatacacggaaatcaatttttgaaaaatgatactacaattgaatttgttctatctatgtttttagaaaaatagaacactttctaacatttttctcatattttcagttttaaaatctgtgaaaatggcaaaaattgatttccctgtagggaggattatttaagtgacaaataataagatttatgctaaaatatcccgatataaattttaaagacaaaacaaatttagtaagggatttattat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE0156:TDE0157|TDE0156:TDE0157:adenylate/guanylate cyclase catalytic domain protein:KHG/KDPG family aldolase/carbohydrate kinase, PfkB family:<-->:183662..183998 337 actttctccataatggttagtggatagtttaattggtgatatgtgaattttccacattacttatgttatcacaaacaccgcagttttacaagagaatatacacggaaatcaatttttgaaaaatgatactacaattgaatttgttctatctatgtttttagaaaaatagaacactttctaacatttttctcatattttcagttttaaaatctgtgaaaatggcaaaaattgatttccctgtagggaggattatttaagtgacaaataataagatttatgctaaaatatcccgatataaattttaaagacaaaacaaatttagtaagggatttattat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 actttctccataatggttagtggatagtttaattggtgatatgtgaattttccacattacttatgttatcacaaacaccgcagttttacaagagaatatacacggaaatcaatttttgaaaaatgatactacaattgaatttgttctatctatgtttttagaaaaatagaacactttctaacatttttctcatattttcagttttaaaatctgtgaaaatggcaaaaattgatttccctgtagggaggattatttaagtgacaaataataagatttatgctaaaatatcccgatataaattttaaagacaaaacaaatttagtaagggatttattat Predict ORF larger than 30AA ================================================ Protein_Len: 40 Strand: + Start: 47 End: 166 .............................................. M F H I T Y V I T N T A V L Q E N I H G N Q F L K N D T T I E F V L S M F L E K ........................................................................................................................................................................... Protein_Len: 35 Strand: - Start: 207 End: 311 .............................................................................................................................................................................................................. F R H F H C F N I E R Y P P N N L H C I I L N I S F Y G S I F K L S M .......................... Protein_Len: 31 Strand: - Start: 161 End: 253 ................................................................................................................................................................ F F L V S E L M K R M N E T K F D T F I A F I S K G T P L I M .................................................................................... actttctccataatggttagtggatagtttaattggtgatatgtgaattttccacattacttatgttatcacaaacaccgcagttttacaagagaatatacacggaaatcaatttttgaaaaatgatactacaattgaatttgttctatctatgtttttagaaaaatagaacactttctaacatttttctcatattttcagttttaaaatctgtgaaaatggcaaaaattgatttccctgtagggaggattatttaagtgacaaataataagatttatgctaaaatatcccgatataaattttaaagacaaaacaaatttagtaagggatttattat 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: 86 Start: 257 End: 286 ................................................................................................................................................................................................................................................................AGTGACAAATAATAAGATTTATGCTAAAAT................................................... PromScan Matrix: RpoD-17 Strand: - Score: 84 Start: 63 End: 92 ..............................................................CTTGTAAAACTGCGGTGTTTGTGATAACAT..................................................................................................................................................................................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ actttctccataatggttagtggatagtttaattggtgatatgtgaattttccacattacttatgttatcacaaacaccgcagttttacaagagaatatacacggaaatcaatttttgaaaaatgatactacaattgaatttgttctatctatgtttttagaaaaatagaacactttctaacatttttctcatattttcagttttaaaatctgtgaaaatggcaaaaattgatttccctgtagggaggattatttaagtgacaaataataagatttatgctaaaatatcccgatataaattttaaagacaaaacaaatttagtaagggatttattat Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE0156:TDE0157|TDE0156:TDE0157:adenylate/guanylate cyclase catalytic domain protein:KHG/KDPG family aldolase/carbohydrate kinase, PfkB family:<-->:183662..183998 337 actttctccataatggttagtggatagtttaattggtgatatgtgaattttccacattacttatgttatcacaaacaccgcagttttacaagagaatatacacggaaatcaatttttgaaaaatgatactacaattgaatttgttctatctatgtttttagaaaaatagaacactttctaacatttttctcatattttcagttttaaaatctgtgaaaatggcaaaaattgatttccctgtagggaggattatttaagtgacaaataataagatttatgctaaaatatcccgatataaattttaaagacaaaacaaatttagtaagggatttattat Intra-Species Hit: Count: 1 Min: 1 Max: 337 Len: 337 Subject: NC_002967_TDE0156_TDE0157|adenylate/guanylate cyclase catalytic domain protein:KHG/KDPG family aldolase/carbohydrate kinase, PfkB family|NEGATIVE:POSITIVE|[183662,183998]|337 HSP 1 e-value: 0.0 bit: 668.0 Len: 337 Query Start:1 Query End:337 Subject Strand: POSITIVE Subject Start: 1 Subject End: 337 actttctccataatggttagtggatagtttaattggtgatatgtgaattttccacattacttatgttatcacaaacaccgcagttttacaagagaatatacacggaaatcaatttttgaaaaatgatactacaattgaatttgttctatctatgtttttagaaaaatagaacactttctaacatttttctcatattttcagttttaaaatctgtgaaaatggcaaaaattgatttccctgtagggaggattatttaagtgacaaataataagatttatgctaaaatatcccgatataaattttaaagacaaaacaaatttagtaagggatttattat actttctccataatggttagtggatagtttaattggtgatatgtgaattttccacattacttatgttatcacaaacaccgcagttttacaagagaatatacacggaaatcaatttttgaaaaatgatactacaattgaatttgttctatctatgtttttagaaaaatagaacactttctaacatttttctcatattttcagttttaaaatctgtgaaaatggcaaaaattgatttccctgtagggaggattatttaagtgacaaataataagatttatgctaaaatatcccgatataaattttaaagacaaaacaaatttagtaagggatttattat Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ ACUUUCUCCAUAAUGGUUAGUGGAUAGUUUAAUUGGUGAUAUGUGAAUUUUCCACAUUACUUAUGUUAUCACAAACACCGCAGUUUUACAAGAGAAUAUACACGGAAAUCAAUUUUUGAAAAAUGAUACUACAAUUGAAUUUGUUCUAUCUAUGUUUUUAGAAAAAUAGAACACUUUCUAACAUUUUUCUCAUAUUUUCAGUUUUAAAAUCUGUGAAAAUGGCAAAAAUUGAUUUCCCUGUAGGGAGGAUUAUUUAAGUGACAAAUAAUAAGAUUUAUGCUAAAAUAUCCCGAUAUAAAUUUUAAAGACAAAACAAAUUUAGUAAGGGAUUUAUUAU ...((((((.....(((...(((((((..((...(((((..((((.......)))))))))))..))))).))...)))...................((((.(((((((((((((((..................(((..(((((((((((......))))....)))))))..)))...(((((((..((.(((((.......))))).)).))))))).))))))))))))))).)))).))))))...............(((((((...............(((((....(((((((............)))))))....)))))))))))) (-68.06) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUAAUAAAUCCCUUACUAAAUUUGUUUUGUCUUUAAAAUUUAUAUCGGGAUAUUUUAGCAUAAAUCUUAUUAUUUGUCACUUAAAUAAUCCUCCCUACAGGGAAAUCAAUUUUUGCCAUUUUCACAGAUUUUAAAACUGAAAAUAUGAGAAAAAUGUUAGAAAGUGUUCUAUUUUUCUAAAAACAUAGAUAGAACAAAUUCAAUUGUAGUAUCAUUUUUCAAAAAUUGAUUUCCGUGUAUAUUCUCUUGUAAAACUGCGGUGUUUGUGAUAACAUAAGUAAUGUGGAAAAUUCACAUAUCACCAAUUAAACUAUCCACUAACCAUUAUGGAGAAAGU .......(((((....(((((((............)))))))....))))).................((((((((.....)))))))).((((.((((.(((((((((((((((...(((((.((.(((((.......))))).)).)))))......(((..((((((((((............))))))))))..)))..................))))))))))))))).))))...................((((..(((((...((((.....))))......)))))...)))).........................))))..... (-68.70) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 799 110 61 201 152 NC_002967:TDE0156|5end_adenylate/guanylate_cyclase_catalytic_domain_protein_183571..183801_NEGATIVE 252 119 77 161 126 NC_002967:TDE1938|5end_hypothetical_protein_1953640..1953870_POSITIVE 247 90 44 205 155 NC_002967:TDE1737|5end_hypothetical_protein_1790133..1790363_POSITIVE 237 265 221 222 169 NC_002967:TDE2445|5end_DNA-binding_protein_2474282..2474512_POSITIVE 217 255 230 159 127 NC_002967:TDE2545|5end_hypothetical_protein_2571814..2572044_NEGATIVE 216 118 72 74 22 NC_002967:TDE1849|5end_hypothetical_protein_1878123..1878353_NEGATIVE 215 99 51 149 99 NC_002967:TDE0948|5end_hypothetical_protein_971837..972067_NEGATIVE 214 189 143 208 164 NC_002967:TDE2539|5end_hypothetical_protein_2565158..2565388_NEGATIVE 214 248 202 231 171 NC_002967:TDE1230|5end_hypothetical_protein_1263066..1263296_POSITIVE 214 50 5 151 107 NC_002967:TDE0231|5end_DNA_polymerase_III,_beta_subunit_264993..265223_NEGATIVE 212 248 212 220 185 NC_002967:TDE2081|5end_hypothetical_protein_2111529..2111759_POSITIVE 211 80 33 109 63 NC_002967:TDE2733|5end_hypothetical_protein_2788573..2788803_POSITIVE 211 105 78 93 64 NC_002967:TDE0016|5end_ATPase,_AAA_family_20457..20687_POSITIVE 210 248 210 72 36 NC_002967:TDE0317|5end_hypothetical_protein_350656..350886_POSITIVE 209 248 209 205 168 NC_002967:TDE2258|5end_surface_antigen_BspA,_putative_2296401..2296631_NEGATIVE 208 263 242 149 126 NC_002967:TDE1731|5end_hypothetical_protein_1786935..1787165_NEGATIVE 207 106 73 170 147 NC_002967:TDE1574|5end_hypothetical_protein_1621800..1622030_POSITIVE 207 249 207 171 129 NC_002967:TDE0556|5end_hypothetical_protein_592092..592322_NEGATIVE 206 55 14 195 153 NC_002967:TDE2745|5end_fic_family_protein_2800696..2800926_NEGATIVE 206 97 61 131 79 NC_002967:TDE2644|5end_pyridine_nucleotide-disulphide_oxidoreductase_family_protein_2683651..2683881_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 266 104 61 112 60 NC_002967:TDE0142|3end_hypothetical_protein_163979..164129_NEGATIVE 247 90 44 150 100 NC_002967:TDE1736|3end_ferredoxin,_2(4Fe-4S)_1790158..1790308_POSITIVE 232 249 210 50 4 NC_002967:TDE1459|3end_hypothetical_protein_1507772..1507922_NEGATIVE 217 255 230 96 64 NC_002967:TDE2546|3end_hypothetical_protein_2571877..2572027_NEGATIVE 216 117 79 36 3 NC_002967:TDE0975|3end_hypothetical_protein_999879..1000029_POSITIVE 213 260 221 62 15 NC_002967:TDE0434|3end_rubrerythrin_489564..489714_POSITIVE 211 80 33 76 30 NC_002967:TDE2732|3end_hypothetical_protein_2788620..2788770_POSITIVE 211 105 78 100 71 NC_002967:TDE0015|3end_lipoprotein,_putative_20544..20694_POSITIVE 209 248 209 79 42 NC_002967:TDE2259|3end_hypothetical_protein_2296527..2296677_NEGATIVE 207 249 207 117 75 NC_002967:TDE0557|3end_hypothetical_protein_592146..592296_NEGATIVE 206 97 61 134 82 NC_002967:TDE2643|3end_oxidoreductase,_FAD-dependent_2683734..2683884_POSITIVE 205 264 221 61 11 NC_002967:TDE0488|3end_lipoprotein,_putative_545145..545295_POSITIVE 203 220 172 149 109 NC_002967:TDE1208|3end_DNA_topoisomerase_I_1242432..1242582_POSITIVE 203 59 12 127 81 NC_002967:TDE0817|3end_histidine_kinase-related_ATPase,_putative_839959..840109_POSITIVE 200 85 46 128 86 NC_002967:TDE2742|3end_site-specific_recombinase,_phage_integrase_family_2796850..2797000_NEGATIVE 200 248 209 53 14 NC_002967:TDE1069|3end_oligopeptide/dipeptide_ABC_transporter,_permease_protein_1096683..1096833_NEGATIVE 199 118 78 72 32 NC_002967:TDE2661|3end_hypothetical_protein_2697524..2697674_NEGATIVE 198 80 33 124 79 NC_002967:TDE2424|3end_50S_ribosomal_protein_L1_2454037..2454187_NEGATIVE 198 224 182 131 92 NC_002967:TDE1389|3end_hypothetical_protein_1429775..1429925_POSITIVE 196 151 114 130 94 NC_002967:TDE0149|3end_DNA-binding_response_regulator_170506..170656_POSITIVE