Origin IGS: ccctaactcccttataatttatagtatatatactattgtacacatagtcaagaattatgaagcttttctaagaaaaaaacgaaacactataatttccttattttaaaggtcaagaatcgaatttaactacaaggaaggctaagaccgcaattttttatgcagtcttagctgaatttacctttgcggtttaattttat .........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 ataaaattaaaccgcaaaggtaaattcagctaagactgcataaaaaattgcggtcttagccttccttgtagttaaattcgattcttgacctttaaaataaggaaattatagtgtttcgtttttttcttagaaaagcttcataattcttgactatgtgtacaatagtatatatactataaattataagggagttaggg Mask Tandem Repeat Region ================================================ ccctaactcccttataatttatagtatatatactattgtacacatagtcaagaattatgaagcttttctaagaaaaaaacgaaacactataatttccttattttaaaggtcaagaatcgaatttaactacaaggaaggctaagaccgcaattttttatgcagtcttagctgaatttacctttgcggtttaattttat Find is-nt database================================================ Query_seq: TDE1635:TDE1636|TDE1635:TDE1636:hypothetical protein:surface antigen, putative:<-<-:1683410..1683606 197 ccctaactcccttataatttatagtatatatactattgtacacatagtcaagaattatgaagcttttctaagaaaaaaacgaaacactataatttccttattttaaaggtcaagaatcgaatttaactacaaggaaggctaagaccgcaattttttatgcagtcttagctgaatttacctttgcggtttaattttat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE1635:TDE1636|TDE1635:TDE1636:hypothetical protein:surface antigen, putative:<-<-:1683410..1683606 197 ccctaactcccttataatttatagtatatatactattgtacacatagtcaagaattatgaagcttttctaagaaaaaaacgaaacactataatttccttattttaaaggtcaagaatcgaatttaactacaaggaaggctaagaccgcaattttttatgcagtcttagctgaatttacctttgcggtttaattttat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE1635:TDE1636|TDE1635:TDE1636:hypothetical protein:surface antigen, putative:<-<-:1683410..1683606 197 ccctaactcccttataatttatagtatatatactattgtacacatagtcaagaattatgaagcttttctaagaaaaaaacgaaacactataatttccttattttaaaggtcaagaatcgaatttaactacaaggaaggctaagaccgcaattttttatgcagtcttagctgaatttacctttgcggtttaattttat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ccctaactcccttataatttatagtatatatactattgtacacatagtcaagaattatgaagcttttctaagaaaaaaacgaaacactataatttccttattttaaaggtcaagaatcgaatttaactacaaggaaggctaagaccgcaattttttatgcagtcttagctgaatttacctttgcggtttaattttat Predict ORF larger than 30AA ================================================ Protein_Len: 30 Strand: + Start: 14 End: 103 ............. M I Y S I Y T I V H I V K N Y E A F L R K K R N T I I S L F .............................................................................................. ccctaactcccttataatttatagtatatatactattgtacacatagtcaagaattatgaagcttttctaagaaaaaaacgaaacactataatttccttattttaaaggtcaagaatcgaatttaactacaaggaaggctaagaccgcaattttttatgcagtcttagctgaatttacctttgcggtttaattttat 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: 83 Start: 23 End: 52 ......................CTTGACTATGTGTACAATAGTATATATACT................................................................................................................................................. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ ccctaactcccttataatttatagtatatatactattgtacacatagtcaagaattatgaagcttttctaagaaaaaaacgaaacactataatttccttattttaaaggtcaagaatcgaatttaactacaaggaaggctaagaccgcaattttttatgcagtcttagctgaatttacctttgcggtttaattttat Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 68 HP_score: -7.5 Tail_Score: -3.5002 Start: 137 End: 170 Full_Region: cgcaaaggtaaattc agctaagactgca taaaaaat tgcggtcttagcc ttccttgtagttaaa ........................................................................................................................................agctaagactgcataaaaaattgcggtcttagcc........................... TransTerm Strand: - Conf: 82 HP_score: -11.0 Tail_Score: -2.6953 Start: 138 End: 169 Full_Region: gcaaaggtaaattca gctaagactgca taaaaaat tgcggtcttagc cttccttgtagttaa .........................................................................................................................................gctaagactgcataaaaaattgcggtcttagc............................ Find igs database================================================ Query_seq: TDE1635:TDE1636|TDE1635:TDE1636:hypothetical protein:surface antigen, putative:<-<-:1683410..1683606 197 ccctaactcccttataatttatagtatatatactattgtacacatagtcaagaattatgaagcttttctaagaaaaaaacgaaacactataatttccttattttaaaggtcaagaatcgaatttaactacaaggaaggctaagaccgcaattttttatgcagtcttagctgaatttacctttgcggtttaattttat Intra-Species Hit: Count: 1 Min: 1 Max: 197 Len: 197 Subject: NC_002967_TDE1635_TDE1636|hypothetical protein:surface antigen, putative|NEGATIVE:NEGATIVE|[1683410,1683606]|197 HSP 1 e-value: 2.0E-95 bit: 349.0 Len: 197 Query Start:1 Query End:197 Subject Strand: POSITIVE Subject Start: 1 Subject End: 197 ccctaactcccttataatttatagtatatatactattgtacacatagtcaagaattatgaagcttttctaagnnnnnnncgaaacactataatttccttattttaaaggtcaagaatcgaatttaactacaaggaaggctaagaccgcaattttttatgcagtcttagctgaatttacctttgcggtttaattttat ccctaactcccttataatttatagtatatatactattgtacacatagtcaagaattatgaagcttttctaagaaaaaaacgaaacactataatttccttattttaaaggtcaagaatcgaatttaactacaaggaaggctaagaccgcaattttttatgcagtcttagctgaatttacctttgcggtttaattttat Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CCCUAACUCCCUUAUAAUUUAUAGUAUAUAUACUAUUGUACACAUAGUCAAGAAUUAUGAAGCUUUUCUAAGAAAAAAACGAAACACUAUAAUUUCCUUAUUUUAAAGGUCAAGAAUCGAAUUUAACUACAAGGAAGGCUAAGACCGCAAUUUUUUAUGCAGUCUUAGCUGAAUUUACCUUUGCGGUUUAAUUUUAU ..........(((.....(((((((.....(((....)))..((((((.....))))))..........................)))))))...((((......))))..)))....(((((.(((..(((((..(((((((((.(((........))).)))))))))........)))))..))).)))))... (-34.30) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUAAAAUUAAACCGCAAAGGUAAAUUCAGCUAAGACUGCAUAAAAAAUUGCGGUCUUAGCCUUCCUUGUAGUUAAAUUCGAUUCUUGACCUUUAAAAUAAGGAAAUUAUAGUGUUUCGUUUUUUUCUUAGAAAAGCUUCAUAAUUCUUGACUAUGUGUACAAUAGUAUAUAUACUAUAAAUUAUAAGGGAGUUAGGG ..........(((.....))).......((((((((((((........))))))))))))(((((((((((((...............((((......))))....((((((.....(((((((.....)))))))................((((((((....)))))))))))))))))))))))))))...... (-50.90) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 758 140 91 231 182 NC_002967:TDE1635|5end_hypothetical_protein_1683319..1683549_NEGATIVE 437 50 3 141 94 NC_002967:TDE2106|5end_hypothetical_protein_2131740..2131970_NEGATIVE 314 170 127 178 126 NC_002967:TDE0986|5end_oligopeptide/dipeptide_ABC_transporter,_ATP-binding_protein_1013061..1013291_POSITIVE 296 148 113 189 151 NC_002967:TDE0162|5end_hypothetical_protein_187898..188128_POSITIVE 278 50 1 75 17 NC_002967:TDE0035|5end_acetyltransferase,_GNAT_family_42020..42250_NEGATIVE 275 188 143 111 51 NC_002967:TDE2645|5end_hypothetical_protein_2684972..2685202_POSITIVE 264 147 101 177 115 NC_002967:TDE2061|5end_hypothetical_protein_2087792..2088022_NEGATIVE 264 188 141 195 153 NC_002967:TDE1288|5end_CAAX_amino_terminal_protease_family_protein_1326317..1326547_POSITIVE 262 189 142 81 37 NC_002967:TDE2636|5end_hypothetical_protein_2676070..2676300_POSITIVE 262 134 92 147 104 NC_002967:TDE0591|5end_acetyl-CoA_carboxylase,_biotin_carboxylase_631352..631582_NEGATIVE 260 187 145 211 174 NC_002967:TDE2527|5end_hypothetical_protein_2556219..2556449_NEGATIVE 260 186 141 225 173 NC_002967:TDE0005|5end_L-threonine_aldolase,_low-specificity_6040..6270_NEGATIVE 259 169 123 71 21 NC_002967:TDE1444|5end_metallo-beta-lactamase_family_protein_1491004..1491234_NEGATIVE 257 171 136 102 65 NC_002967:TDE0904|5end_hypothetical_protein_922406..922636_NEGATIVE 255 179 132 89 41 NC_002967:TDE0737|5end_hypothetical_protein_775674..775904_NEGATIVE 253 168 128 207 173 NC_002967:TDE0532|5end_TPR_domain_protein_575570..575800_POSITIVE 251 149 108 53 3 NC_002967:TDE1125|5end_TPR_domain_protein_1157557..1157787_NEGATIVE 245 171 132 39 2 NC_002967:TDE1651|5end_BioY_family_protein_1698732..1698962_NEGATIVE 244 189 144 157 115 NC_002967:TDE2633|5end_hypothetical_protein_2674359..2674589_POSITIVE 244 188 142 132 95 NC_002967:TDE2516|5end_hypothetical_protein_2542021..2542251_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 437 50 3 122 75 NC_002967:TDE2107|3end_dihydroorotase,_putative_2131759..2131909_NEGATIVE 321 189 141 113 64 NC_002967:TDE2712|3end_hypothetical_protein_2769615..2769765_POSITIVE 321 169 131 60 18 NC_002967:TDE2300|3end_trypsin_domain/PDZ_domain_protein_2339953..2340103_NEGATIVE 314 170 127 91 39 NC_002967:TDE0985|3end_oligopeptide/dipeptide_ABC_transporter,_periplasmic_peptide-binding_protein,_putative_1013054..1013204_POSITIVE 280 179 136 138 99 NC_002967:TDE2104|3end_hypothetical_protein_2128525..2128675_NEGATIVE 275 188 143 118 58 NC_002967:TDE2644|3end_pyridine_nucleotide-disulphide_oxidoreductase_family_protein_2685059..2685209_POSITIVE 264 188 141 83 41 NC_002967:TDE1287|3end_transcription-repair_coupling_factor_1326285..1326435_POSITIVE 262 134 92 136 93 NC_002967:TDE0592|3end_acetyl-CoA_carboxylase,_biotin_carboxyl_carrier_protein_631363..631513_NEGATIVE 255 179 132 89 41 NC_002967:TDE0738|3end_hypothetical_protein_775674..775824_NEGATIVE 244 189 144 142 100 NC_002967:TDE2632|3end_peptide_ABC_transporter,_ATP-binding_protein,_putative_2674424..2674574_POSITIVE 243 187 145 86 36 NC_002967:TDE0142|3end_hypothetical_protein_163979..164129_NEGATIVE 242 173 132 99 59 NC_002967:TDE0478|3end_cyclic_nucleotide_binding_domain_protein_535013..535163_POSITIVE 241 189 144 137 87 NC_002967:TDE0741|3end_hypothetical_protein_776185..776335_NEGATIVE 241 186 142 132 73 NC_002967:TDE0601|3end_malonyl_CoA-acyl_carrier_protein_transacylase,_putative_638834..638984_NEGATIVE 240 187 145 81 48 NC_002967:TDE2548|3end_hypothetical_protein_2573064..2573214_NEGATIVE 235 167 131 72 34 NC_002967:TDE1673|3end_ATP-dependent_protease_ATP-binding_subunit_1728205..1728355_POSITIVE 232 186 147 136 95 NC_002967:TDE0273|3end_ABC_transporter,_ATP-binding/permease_protein_302867..303017_NEGATIVE 230 156 112 73 6 NC_002967:TDE2013|3end_hypothetical_protein_2034359..2034509_NEGATIVE 229 178 133 46 4 NC_002967:TDE0817|3end_histidine_kinase-related_ATPase,_putative_839959..840109_POSITIVE 224 189 149 80 41 NC_002967:TDE2741|3end_hypothetical_protein_2796722..2796872_POSITIVE