Origin IGS: taaaacatcaaaccttacggattttgcctgttcgtaggtgttaatattatgctgtatcgaaaaaagagtaaattataaaaaatttgtgacgaatttatgtgactaatttgattgatagttttttatacttaaactaattattctacaaatttaacaaaattgatattttgacccttgactttaagtttttttgtttgatatatttatagtatgaaaaagaattgcataaaagcagcactctttgttatggtatttttaagaggtttatttctttttgctcaagaaacgaatgaggagcctaag .........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 cttaggctcctcattcgtttcttgagcaaaaagaaataaacctcttaaaaataccataacaaagagtgctgcttttatgcaattctttttcatactataaatatatcaaacaaaaaaacttaaagtcaagggtcaaaatatcaattttgttaaatttgtagaataattagtttaagtataaaaaactatcaatcaaattagtcacataaattcgtcacaaattttttataatttactcttttttcgatacagcataatattaacacctacgaacaggcaaaatccgtaaggtttgatgtttta Mask Tandem Repeat Region ================================================ taaaacatcaaaccttacggattttgcctgttcgtaggtgttaatattatgctgtatcgaaaaaagagtaaattataaaaaatttgtgacgaatttatgtgactaatttgattgatagttttttatacttaaactaattattctacaaatttaacaaaattgatattttgacccttgactttaagtttttttgtttgatatatttatagtatgaaaaagaattgcataaaagcagcactctttgttatggtatttttaagaggtttatttctttttgctcaagaaacgaatgaggagcctaag Find is-nt database================================================ Query_seq: TDE0831:TDE0832|TDE0831:TDE0832:hypothetical protein:hypothetical protein:<-->:852386..852688 303 taaaacatcaaaccttacggattttgcctgttcgtaggtgttaatattatgctgtatcgaaaaaagagtaaattataaaaaatttgtgacgaatttatgtgactaatttgattgatagttttttatacttaaactaattattctacaaatttaacaaaattgatattttgacccttgactttaagtttttttgtttgatatatttatagtatgaaaaagaattgcataaaagcagcactctttgttatggtatttttaagaggtttatttctttttgctcaagaaacgaatgaggagcctaag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE0831:TDE0832|TDE0831:TDE0832:hypothetical protein:hypothetical protein:<-->:852386..852688 303 taaaacatcaaaccttacggattttgcctgttcgtaggtgttaatattatgctgtatcgaaaaaagagtaaattataaaaaatttgtgacgaatttatgtgactaatttgattgatagttttttatacttaaactaattattctacaaatttaacaaaattgatattttgacccttgactttaagtttttttgtttgatatatttatagtatgaaaaagaattgcataaaagcagcactctttgttatggtatttttaagaggtttatttctttttgctcaagaaacgaatgaggagcctaag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE0831:TDE0832|TDE0831:TDE0832:hypothetical protein:hypothetical protein:<-->:852386..852688 303 taaaacatcaaaccttacggattttgcctgttcgtaggtgttaatattatgctgtatcgaaaaaagagtaaattataaaaaatttgtgacgaatttatgtgactaatttgattgatagttttttatacttaaactaattattctacaaatttaacaaaattgatattttgacccttgactttaagtttttttgtttgatatatttatagtatgaaaaagaattgcataaaagcagcactctttgttatggtatttttaagaggtttatttctttttgctcaagaaacgaatgaggagcctaag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 taaaacatcaaaccttacggattttgcctgttcgtaggtgttaatattatgctgtatcgaaaaaagagtaaattataaaaaatttgtgacgaatttatgtgactaatttgattgatagttttttatacttaaactaattattctacaaatttaacaaaattgatattttgacccttgactttaagtttttttgtttgatatatttatagtatgaaaaagaattgcataaaagcagcactctttgttatggtatttttaagaggtttatttctttttgctcaagaaacgaatgaggagcctaag Predict ORF larger than 30AA ================================================ Protein_Len: 34 Strand: + Start: 202 End: 303 ......................................................................................................................................................................................................... M Y S M K K N C I K A A L F V M V F L R G L F L F A Q E T N E E P K Protein_Len: 31 Strand: - Start: 146 End: 238 ................................................................................................................................................. L N L L I S I K V R S K L N K Q K I Y K Y Y S F S N C L L L M ................................................................. Protein_Len: 33 Strand: - Start: 18 End: 116 ................. P N Q R N T P T L I I S Y R F F L L N Y F I Q S S N I H S I Q N M ........................................................................................................................................................................................... taaaacatcaaaccttacggattttgcctgttcgtaggtgttaatattatgctgtatcgaaaaaagagtaaattataaaaaatttgtgacgaatttatgtgactaatttgattgatagttttttatacttaaactaattattctacaaatttaacaaaattgatattttgacccttgactttaagtttttttgtttgatatatttatagtatgaaaaagaattgcataaaagcagcactctttgttatggtatttttaagaggtttatttctttttgctcaagaaacgaatgaggagcctaag Predict Promoter with matrix: RpoD-15 score > 80================================================ Predict Promoter with matrix: RpoD-16 score > 80================================================ Predict Promoter with matrix: RpoD-17 score > 80================================================ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ taaaacatcaaaccttacggattttgcctgttcgtaggtgttaatattatgctgtatcgaaaaaagagtaaattataaaaaatttgtgacgaatttatgtgactaatttgattgatagttttttatacttaaactaattattctacaaatttaacaaaattgatattttgacccttgactttaagtttttttgtttgatatatttatagtatgaaaaagaattgcataaaagcagcactctttgttatggtatttttaagaggtttatttctttttgctcaagaaacgaatgaggagcctaag Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE0831:TDE0832|TDE0831:TDE0832:hypothetical protein:hypothetical protein:<-->:852386..852688 303 taaaacatcaaaccttacggattttgcctgttcgtaggtgttaatattatgctgtatcgaaaaaagagtaaattataaaaaatttgtgacgaatttatgtgactaatttgattgatagttttttatacttaaactaattattctacaaatttaacaaaattgatattttgacccttgactttaagtttttttgtttgatatatttatagtatgaaaaagaattgcataaaagcagcactctttgttatggtatttttaagaggtttatttctttttgctcaagaaacgaatgaggagcctaag Intra-Species Hit: Count: 1 Min: 1 Max: 303 Len: 303 Subject: NC_002967_TDE0831_TDE0832|hypothetical protein:hypothetical protein|NEGATIVE:POSITIVE|[852386,852688]|303 HSP 1 e-value: 1.0E-158 bit: 559.0 Len: 303 Query Start:1 Query End:303 Subject Strand: POSITIVE Subject Start: 1 Subject End: 303 taaaacatcaaaccttacggattttgcctgttcgtaggtgttaatattatgctgtatcgaaaaaagagtaaattataaaaaatttgtgacgaatttatgtgactaatttgattgatagttttttatacttaaactaattattctacaaatttaacaaaattgatattttgacccttgactttaagnnnnnnngtttgatatatttatagtatgaaaaagaattgcataaaagcagcactctttgttatggtatttttaagaggtttatttctttttgctcaagaaacgaatgaggagcctaag taaaacatcaaaccttacggattttgcctgttcgtaggtgttaatattatgctgtatcgaaaaaagagtaaattataaaaaatttgtgacgaatttatgtgactaatttgattgatagttttttatacttaaactaattattctacaaatttaacaaaattgatattttgacccttgactttaagtttttttgtttgatatatttatagtatgaaaaagaattgcataaaagcagcactctttgttatggtatttttaagaggtttatttctttttgctcaagaaacgaatgaggagcctaag Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAAACAUCAAACCUUACGGAUUUUGCCUGUUCGUAGGUGUUAAUAUUAUGCUGUAUCGAAAAAAGAGUAAAUUAUAAAAAAUUUGUGACGAAUUUAUGUGACUAAUUUGAUUGAUAGUUUUUUAUACUUAAACUAAUUAUUCUACAAAUUUAACAAAAUUGAUAUUUUGACCCUUGACUUUAAGUUUUUUUGUUUGAUAUAUUUAUAGUAUGAAAAAGAAUUGCAUAAAAGCAGCACUCUUUGUUAUGGUAUUUUUAAGAGGUUUAUUUCUUUUUGCUCAAGAAACGAAUGAGGAGCCUAAG ..........((((((((((((.......))))))))).)))......((((((((......(((((((..((((....(((((.((.(((......))).)).)))))...))))..(((((((((((.........((((..(((((.....((((((....))))))...((((....))))....)))))..)))).......)))))))))))...((((......)))).)))))))..)))))))).......((((((..((((((((.....))))).)))....))))))... (-53.19) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CUUAGGCUCCUCAUUCGUUUCUUGAGCAAAAAGAAAUAAACCUCUUAAAAAUACCAUAACAAAGAGUGCUGCUUUUAUGCAAUUCUUUUUCAUACUAUAAAUAUAUCAAACAAAAAAACUUAAAGUCAAGGGUCAAAAUAUCAAUUUUGUUAAAUUUGUAGAAUAAUUAGUUUAAGUAUAAAAAACUAUCAAUCAAAUUAGUCACAUAAAUUCGUCACAAAUUUUUUAUAAUUUACUCUUUUUUCGAUACAGCAUAAUAUUAACACCUACGAACAGGCAAAAUCCGUAAGGUUUGAUGUUUUA ....(((.(((.....(((((((.......))))))).......................(((((((..(((......))))))))))........................................)))))).((((((((.(((((((...(((((((......((((((.........))))))......(((((.((.((........)).)).)))))..........................................)))))))..))))))).((....))..)))))))).. (-38.20) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 859 60 11 151 102 NC_002967:TDE0831|5end_hypothetical_protein_852295..852525_NEGATIVE 599 57 14 148 105 NC_002967:TDE1922|5end_hypothetical_protein_1941485..1941715_NEGATIVE 290 42 13 80 44 NC_002967:TDE0591|5end_acetyl-CoA_carboxylase,_biotin_carboxylase_631352..631582_NEGATIVE 265 55 13 69 25 NC_002967:TDE2769|5end_flagellar_hook_assembly_protein_2823032..2823262_NEGATIVE 259 65 25 77 39 NC_002967:TDE0329|5end_CRISPR-associated_protein_Cas2_365942..366172_POSITIVE 256 56 11 180 124 NC_002967:TDE1138|5end_hypothetical_protein_1167555..1167785_NEGATIVE 252 198 161 208 166 NC_002967:TDE0605|5end_hypothetical_protein_643215..643445_NEGATIVE 250 41 6 200 168 NC_002967:TDE1400|5end_NAD(+)_synthetase_1440402..1440632_POSITIVE 247 128 85 141 100 NC_002967:TDE0476|5end_hypothetical_protein_532914..533144_NEGATIVE 245 41 10 58 25 NC_002967:TDE1427|5end_glycosyl_transferase,_group_1_family_protein_1469713..1469943_POSITIVE 244 280 233 77 29 NC_002967:TDE2079|5end_sigma-54_dependent_transcriptional_regulator,_putative_2109035..2109265_NEGATIVE 238 53 13 76 35 NC_002967:TDE2353|5end_flagellar_hook-associated_protein_2389129..2389359_POSITIVE 237 209 171 93 57 NC_002967:TDE1938|5end_hypothetical_protein_1953640..1953870_POSITIVE 236 59 18 206 157 NC_002967:TDE2622|5end_ABC_transporter,_ATP-binding_protein_2663590..2663820_NEGATIVE 236 43 18 212 186 NC_002967:TDE1129|5end_lipoprotein,_putative_1161730..1161960_POSITIVE 236 55 17 169 132 NC_002967:TDE0280|5end_PIN_domain_protein_310296..310526_NEGATIVE 235 264 231 227 190 NC_002967:TDE0884|5end_tRNA_(guanine-N(1)-)-methyltransferase_902221..902451_POSITIVE 234 54 16 56 28 NC_002967:TDE0204|5end_glutamyl-tRNA_synthetase_236968..237198_POSITIVE 234 297 260 44 9 NC_002967:TDE0126|5end_hypothetical_protein_145637..145867_NEGATIVE 232 299 261 47 2 NC_002967:TDE0423|5end_hypothetical_protein_476601..476831_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 599 57 14 120 77 NC_002967:TDE1923|3end_hypothetical_protein_1941513..1941663_NEGATIVE 290 42 13 69 33 NC_002967:TDE0592|3end_acetyl-CoA_carboxylase,_biotin_carboxyl_carrier_protein_631363..631513_NEGATIVE 271 53 18 151 117 NC_002967:TDE2423|3end_ribosomal_protein_L10_2453417..2453567_NEGATIVE 267 257 214 54 16 NC_002967:TDE1051|3end_hypothetical_protein_1078212..1078362_NEGATIVE 266 60 27 61 25 NC_002967:TDE2110|3end_orotidine_5'-phosphate_decarboxylase_2136311..2136461_POSITIVE 265 55 13 57 13 NC_002967:TDE2770|3end_flagellar_hook-length_control_protein_FliK_2823044..2823194_NEGATIVE 259 65 25 72 34 NC_002967:TDE0328|3end_CRISPR-associated_protein_Cas1_366017..366167_POSITIVE 247 34 6 131 105 NC_002967:TDE2268|3end_hypothetical_protein_2304822..2304972_NEGATIVE 247 128 85 85 44 NC_002967:TDE0477|3end_hypothetical_protein_532970..533120_NEGATIVE 245 59 12 81 16 NC_002967:TDE2734|3end_hypothetical_protein_2789861..2790011_POSITIVE 245 41 10 70 37 NC_002967:TDE1426|3end_aminotransferase,_DegT/DnrJ/EryC1/StrS_family_1469805..1469955_POSITIVE 245 52 13 65 34 NC_002967:TDE0823|3end_(3R)-hydroxymyristoyl-(acyl-carrier-protein)_dehydratase,_putative_845252..845402_POSITIVE 244 280 233 63 15 NC_002967:TDE2080|3end_cytidylate_kinase/ribosomal_protein_S1_2109049..2109199_NEGATIVE 242 300 257 91 53 NC_002967:TDE1650|3end_ABC_transporter,_ATP-binding_protein_1697377..1697527_NEGATIVE 238 53 13 53 12 NC_002967:TDE2352|3end_flagellar_hook-associated_protein_2389186..2389336_POSITIVE 234 54 16 66 38 NC_002967:TDE0203|3end_hypothetical_protein_237058..237208_POSITIVE 230 279 232 133 86 NC_002967:TDE0440|3end_DNA-binding_protein_496306..496456_POSITIVE 224 48 6 137 100 NC_002967:TDE2088|3end_C4_zinc_finger_domain_protein,_DksA/TraR_family_2116183..2116333_POSITIVE 224 300 258 55 10 NC_002967:TDE1463|3end_hypothetical_protein_1512206..1512356_NEGATIVE 224 60 21 58 21 NC_002967:TDE0513|3end_hypothetical_protein_561519..561669_NEGATIVE