Origin IGS: tcggcttaaggatttgcgggctgactaagatgtctgatatagttattataacccgctttccggcggatttcaacgttttgggggagatttttaatgggtaatttcttaaattatcaattaattcagcgcttccacttcttctttggaaaggccggtcattgtacaaatttctgcaatcgggtaattatgcatacgcatcagctttgccgtttcaagctttgtttggtatgaaccttcggaaaagccttgttcaatacctttttatcataaaattaatttttatgcataacatcttttagcttgaatagatttttgatttttgttagaatagaggcctt .........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 aaggcctctattctaacaaaaatcaaaaatctattcaagctaaaagatgttatgcataaaaattaattttatgataaaaaggtattgaacaaggcttttccgaaggttcataccaaacaaagcttgaaacggcaaagctgatgcgtatgcataattacccgattgcagaaatttgtacaatgaccggcctttccaaagaagaagtggaagcgctgaattaattgataatttaagaaattacccattaaaaatctcccccaaaacgttgaaatccgccggaaagcgggttataataactatatcagacatcttagtcagcccgcaaatccttaagccga Mask Tandem Repeat Region ================================================ tcggcttaaggatttgcgggctgactaagatgtctgatatagttattataacccgctttccggcggatttcaacgttttgggggagatttttaatgggtaatttcttaaattatcaattaattcagcgcttccacttcttctttggaaaggccggtcattgtacaaatttctgcaatcgggtaattatgcatacgcatcagctttgccgtttcaagctttgtttggtatgaaccttcggaaaagccttgttcaatacctttttatcataaaattaatttttatgcataacatcttttagcttgaatagatttttgatttttgttagaatagaggcctt Find is-nt database================================================ Query_seq: TDE2715:TDE2716|TDE2715:TDE2716:hypothetical protein:HAD-superfamily hydrolase, subfamily IA:->->:2772997..2773334 338 tcggcttaaggatttgcgggctgactaagatgtctgatatagttattataacccgctttccggcggatttcaacgttttgggggagatttttaatgggtaatttcttaaattatcaattaattcagcgcttccacttcttctttggaaaggccggtcattgtacaaatttctgcaatcgggtaattatgcatacgcatcagctttgccgtttcaagctttgtttggtatgaaccttcggaaaagccttgttcaatacctttttatcataaaattaatttttatgcataacatcttttagcttgaatagatttttgatttttgttagaatagaggcctt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE2715:TDE2716|TDE2715:TDE2716:hypothetical protein:HAD-superfamily hydrolase, subfamily IA:->->:2772997..2773334 338 tcggcttaaggatttgcgggctgactaagatgtctgatatagttattataacccgctttccggcggatttcaacgttttgggggagatttttaatgggtaatttcttaaattatcaattaattcagcgcttccacttcttctttggaaaggccggtcattgtacaaatttctgcaatcgggtaattatgcatacgcatcagctttgccgtttcaagctttgtttggtatgaaccttcggaaaagccttgttcaatacctttttatcataaaattaatttttatgcataacatcttttagcttgaatagatttttgatttttgttagaatagaggcctt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 1 Min: 124 Max: 261 Len: 138 Subject: gi|42526487|ref|NP_971585.1| hypothetical protein TDE0975 [Treponema denticola ATCC 35405] HSP 1 e-value: 2.0E-7 bit: 50.8 Len: 138 Query Start:124 Query End:261 Subject Strand: null Subject Start: 247 Subject End: 292 ........................................................................................................................... K G I E Q G F S E G S Y Q T K L E T A K L M R M H N Y P I A E I C T M T G L S K E E V E A L ............................................................................. ........................................................................................................................... E G I E Q G I A D G V Y K K A L E T A K L M R Y E N L G I D L I S K V T G L S V E E I K A L ............................................................................. Find nr database================================================ Query_seq: TDE2715:TDE2716|TDE2715:TDE2716:hypothetical protein:HAD-superfamily hydrolase, subfamily IA:->->:2772997..2773334 338 tcggcttaaggatttgcgggctgactaagatgtctgatatagttattataacccgctttccggcggatttcaacgttttgggggagatttttaatgggtaatttcttaaattatcaattaattnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnttatcataaaattaatttttatgcataacatcttttagcttgaatagatttttgatttttgttagaatagaggcctt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tcggcttaaggatttgcgggctgactaagatgtctgatatagttattataacccgctttccggcggatttcaacgttttgggggagatttttaatgggtaatttcttaaattatcaattaattnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnttatcataaaattaatttttatgcataacatcttttagcttgaatagatttttgatttttgttagaatagaggcctt Predict ORF larger than 30AA ================================================ Protein_Len: 54 Strand: + Start: 67 End: 228 .................................................................. M S T F W G R F L M G N F L N Y Q L I Q R F H F F F G K A G H C T N F C N R V I M H T H Q L C R F K L C L V .............................................................................................................. Protein_Len: 32 Strand: + Start: 191 End: 286 .............................................................................................................................................................................................. M R I S F A V S S F V W Y E P S E K P C S I P F Y H K I N F Y A .................................................... Protein_Len: 60 Strand: + Start: 117 End: 296 .................................................................................................................... M N S A L P L L L W K G R S L Y K F L Q S G N Y A Y A S A L P F Q A L F G M N L R K S L V Q Y L F I I K L I F M H N I F .......................................... Protein_Len: 45 Strand: - Start: 121 End: 255 ........................................................................................................................ N L A E V E E K S L G T M T C I E A I P Y N H M R M L K A T E L K T Q Y S G E S F G Q E M ................................................................................... Protein_Len: 55 Strand: - Start: 2 End: 166 . P K L I Q P S V L I D S I T I I V R K G A S K L T K P S I K L P Y N R L N D I L E A S G S R R Q F P R D N Y M ............................................................................................................................................................................ tcggcttaaggatttgcgggctgactaagatgtctgatatagttattataacccgctttccggcggatttcaacgttttgggggagatttttaatgggtaatttcttaaattatcaattaattnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnttatcataaaattaatttttatgcataacatcttttagcttgaatagatttttgatttttgttagaatagaggcctt 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: 89 Start: 45 End: 74 ............................................GTTGAAATCCGCCGGAAAGCGGGTTATAAT........................................................................................................................................................................................................................................................................ PromScan Matrix: RpoD-17 Strand: + Score: 86 Start: 300 End: 329 ...........................................................................................................................................................................................................................................................................................................CTTGAATAGATTTTTGATTTTTGTTAGAAT......... PromScan Matrix: RpoD-17 Strand: + Score: 81 Start: 20 End: 49 ...................GCTGACTAAGATGTCTGATATAGTTATTAT................................................................................................................................................................................................................................................................................................. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ tcggcttaaggatttgcgggctgactaagatgtctgatatagttattataacccgctttccggcggatttcaacgttttgggggagatttttaatgggtaatttcttaaattatcaattaattnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnttatcataaaattaatttttatgcataacatcttttagcttgaatagatttttgatttttgttagaatagaggcctt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE2715:TDE2716|TDE2715:TDE2716:hypothetical protein:HAD-superfamily hydrolase, subfamily IA:->->:2772997..2773334 338 tcggcttaaggatttgcgggctgactaagatgtctgatatagttattataacccgctttccggcggatttcaacgttttgggggagatttttaatgggtaatttcttaaattatcaattaattnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnttatcataaaattaatttttatgcataacatcttttagcttgaatagatttttgatttttgttagaatagaggcctt Intra-Species Hit: Count: 1 Min: 1 Max: 338 Len: 338 Subject: NC_002967_TDE2715_TDE2716|hypothetical protein:HAD-superfamily hydrolase, subfamily IA|POSITIVE:POSITIVE|[2772997,2773334]|338 HSP 1 e-value: 2.0E-63 bit: 244.0 Len: 123 Query Start:1 Query End:123 Subject Strand: POSITIVE Subject Start: 1 Subject End: 123 tcggcttaaggatttgcgggctgactaagatgtctgatatagttattataacccgctttccggcggatttcaacgttttgggggagatttttaatgggtaatttcttaaattatcaattaatt....................................................................................................................................................................................................................... tcggcttaaggatttgcgggctgactaagatgtctgatatagttattataacccgctttccggcggatttcaacgttttgggggagatttttaatgggtaatttcttaaattatcaattaatt....................................................................................................................................................................................................................... HSP 2 e-value: 5.0E-36 bit: 153.0 Len: 77 Query Start:262 Query End:338 Subject Strand: POSITIVE Subject Start: 262 Subject End: 338 .....................................................................................................................................................................................................................................................................ttatcataaaattaatttttatgcataacatcttttagcttgaatagatttttgatttttgttagaatagaggcctt .....................................................................................................................................................................................................................................................................ttatcataaaattaatttttatgcataacatcttttagcttgaatagatttttgatttttgttagaatagaggcctt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UCGGCUUAAGGAUUUGCGGGCUGACUAAGAUGUCUGAUAUAGUUAUUAUAACCCGCUUUCCGGCGGAUUUCAACGUUUUGGGGGAGAUUUUUAAUGGGUAAUUUCUUAAAUUAUCAAUUAAUUCAGCGCUUCCACUUCUUCUUUGGAAAGGCCGGUCAUUGUACAAAUUUCUGCAAUCGGGUAAUUAUGCAUACGCAUCAGCUUUGCCGUUUCAAGCUUUGUUUGGUAUGAACCUUCGGAAAAGCCUUGUUCAAUACCUUUUUAUCAUAAAAUUAAUUUUUAUGCAUAACAUCUUUUAGCUUGAAUAGAUUUUUGAUUUUUGUUAGAAUAGAGGCCUU ((.(((...(((...(((((..(((......))).((((....))))....)))))..)))))).)).(((((.(....(((((((....(((((.(((((((.....))))))).))))).......))))).))....).))))).(((((.........(((((..((...((((.(((((..((((....)))).....)))))..((((((((......(((((((((....((.....))..)))).)))))...(((((((((((.....))))))).))))........))))))))..))))...))..))))).........))))). (-83.27) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAGGCCUCUAUUCUAACAAAAAUCAAAAAUCUAUUCAAGCUAAAAGAUGUUAUGCAUAAAAAUUAAUUUUAUGAUAAAAAGGUAUUGAACAAGGCUUUUCCGAAGGUUCAUACCAAACAAAGCUUGAAACGGCAAAGCUGAUGCGUAUGCAUAAUUACCCGAUUGCAGAAAUUUGUACAAUGACCGGCCUUUCCAAAGAAGAAGUGGAAGCGCUGAAUUAAUUGAUAAUUUAAGAAAUUACCCAUUAAAAAUCUCCCCCAAAACGUUGAAAUCCGCCGGAAAGCGGGUUAUAAUAACUAUAUCAGACAUCUUAGUCAGCCCGCAAAUCCUUAAGCCGA ..(((..........(((((..((...((((..((((((((........((((.(((((((.....)))))))))))...(((((.((((..((.....))....)))))))))......))))))))...(((..((....))...)))..........))))...))..))))).(((((..((((.((((((.........)))))).))))..(((((.(.(((((.....))))).).)))))...............))))).........(((..((((((((((.....))))...(((......))).))))))...)))....))).. (-72.40) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 453 86 44 140 98 NC_002967:TDE2733|5end_hypothetical_protein_2788573..2788803_POSITIVE 410 246 206 220 180 NC_002967:TDE0733|5end_hypothetical_protein_774096..774326_NEGATIVE 357 240 195 210 156 NC_002967:TDE2311|5end_hypothetical_protein_2348238..2348468_POSITIVE 354 235 194 85 44 NC_002967:TDE1638|5end_dephospho-CoA_kinase,_putative_1688882..1689112_POSITIVE 345 75 32 187 138 NC_002967:TDE1590|5end_aminotransferase,_DegT/DnrJ/EryC1/StrS_family_1637516..1637746_POSITIVE 339 179 135 110 58 NC_002967:TDE2751|5end_hypothetical_protein_2807570..2807800_POSITIVE 332 240 194 103 55 NC_002967:TDE2629|5end_peptide_ABC_transporter,_periplasmic_peptide-binding_protein,_putative_2669329..2669559_POSITIVE 329 190 148 226 189 NC_002967:TDE0572|5end_hypothetical_protein_603494..603724_POSITIVE 327 250 203 186 134 NC_002967:TDE0041|5end_birA_bifunctional_protein_47497..47727_POSITIVE 309 217 173 198 155 NC_002967:TDE2390|5end_hypothetical_protein_2420558..2420788_NEGATIVE 308 240 194 58 11 NC_002967:TDE2786|5end_DNA_polymerase_III_subunit_alpha_2842672..2842902_NEGATIVE 308 210 166 58 2 NC_002967:TDE2418|5end_hypothetical_protein_2443833..2444063_NEGATIVE 306 225 189 46 1 NC_002967:TDE1568|5end_hypothetical_protein_1619544..1619774_POSITIVE 305 248 203 199 159 NC_002967:TDE2657|5end_precorrin-2_C20-methyltransferase,_putative_2693822..2694052_POSITIVE 305 217 178 33 1 NC_002967:TDE2461|5end_selenide,_water_dikinase_(selenocysteine-containing)_2488260..2488490_NEGATIVE 303 239 194 61 11 NC_002967:TDE2746|5end_type_I_restriction-modification_system,_M_subunit_2802135..2802365_NEGATIVE 301 66 28 195 158 NC_002967:TDE0406|5end_hypothetical_protein_457230..457460_POSITIVE 297 220 171 79 28 NC_002967:TDE2010|5end_hypothetical_protein_2031318..2031548_POSITIVE 295 229 181 52 5 NC_002967:TDE1927|5end_phenylalanyl-tRNA_synthetase_beta_subunit_1943984..1944214_POSITIVE 294 218 173 74 21 NC_002967:TDE0356|5end_hypothetical_protein_400088..400318_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 670 170 127 143 100 NC_002967:TDE2097|3end_hypothetical_protein_2124478..2124628_NEGATIVE 496 180 136 150 106 NC_002967:TDE1904|3end_hypothetical_protein_1923197..1923347_NEGATIVE 453 86 44 107 65 NC_002967:TDE2732|3end_hypothetical_protein_2788620..2788770_POSITIVE 415 180 136 150 106 NC_002967:TDE0007|3end_hypothetical_protein_10808..10958_POSITIVE 384 165 127 101 62 NC_002967:TDE1978|3end_hypothetical_protein_1991501..1991651_NEGATIVE 381 180 135 150 106 NC_002967:TDE2707|3end_hypothetical_protein_2754929..2755079_POSITIVE 374 163 136 137 106 NC_002967:TDE1938|3end_hypothetical_protein_1954586..1954736_POSITIVE 370 179 133 149 103 NC_002967:TDE0049|3end_hypothetical_protein_58199..58349_NEGATIVE 358 180 131 150 100 NC_002967:TDE2711|3end_hypothetical_protein_2768991..2769141_POSITIVE 357 240 195 148 94 NC_002967:TDE2310|3end_hypothetical_protein_2348256..2348406_POSITIVE 357 100 53 72 25 NC_002967:TDE0940|3end_hypothetical_protein_963635..963785_POSITIVE 354 235 194 85 44 NC_002967:TDE1637|3end_DNA_polymerase_I_1688962..1689112_POSITIVE 329 190 148 149 112 NC_002967:TDE0571|3end_hypothetical_protein_603497..603647_POSITIVE 328 259 213 75 23 NC_002967:TDE0693|3end_phosphomethylpyrimidine_kinase_730831..730981_POSITIVE 321 240 192 141 92 NC_002967:TDE2527|3end_hypothetical_protein_2555449..2555599_NEGATIVE 304 249 201 144 94 NC_002967:TDE0016|3end_ATPase,_AAA_family_21862..22012_POSITIVE 303 239 194 58 8 NC_002967:TDE2747|3end_type_I_restriction-modification_system,_R_subunit_2802138..2802288_NEGATIVE 301 66 28 66 29 NC_002967:TDE0405|3end_major_outer_sheath_protein_457181..457331_POSITIVE 299 34 4 150 110 NC_002967:TDE2195|3end_RNA_pseudouridylate_synthase_family_protein_2231911..2232061_POSITIVE 298 237 195 45 7 NC_002967:TDE2682|3end_hypothetical_protein_2721388..2721538_NEGATIVE