Origin IGS: gggcttatcatacacaaaaaacatggtctatggaagtagcggttattaattagtaatgaatccaataatccattactccacggtaaacctatccttagcggtgtcctgtcacggacggcaaaaaaaacgtcataagtcttgcgagtttggcgaagacaaactcggtatgaaaattgcacacggaggtgcaattcccataccgacacgcgatgtttgccgtaaggcagacatcctgcccgcttttggcttaaccgcacaggatgtgcggtggttccacgcgtgcgatgttttaggcggaaagc .........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 gctttccgcctaaaacatcgcacgcgtggaaccaccgcacatcctgtgcggttaagccaaaagcgggcaggatgtctgccttacggcaaacatcgcgtgtcggtatgggaattgcacctccgtgtgcaattttcataccgagtttgtcttcgccaaactcgcaagacttatgacgttttttttgccgtccgtgacaggacaccgctaaggataggtttaccgtggagtaatggattattggattcattactaattaataaccgctacttccatagaccatgttttttgtgtatgataagccc Mask Tandem Repeat Region ================================================ gggcttatcatacacaaaaaacatggtctatggaagtagcggttattaattagtaatgaatccaataatccattactccacggtaaacctatccttagcggtgtcctgtcacggacggcaaaaaaaacgtcataagtcttgcgagtttggcgaagacaaactcggtatgaaaattgcacacggaggtgcaattcccataccgacacgcgatgtttgccgtaaggcagacatcctgcccgcttttggcttaaccgcacaggatgtgcggtggttccacgcgtgcgatgttttaggcggaaagc Find is-nt database================================================ Query_seq: TDE2713:TDE2714|TDE2713:TDE2714:RNA methyltransferase, TrmH family:hypothetical protein:<-<-:2770415..2770716 302 gggcttatcatacacaaaaaacatggtctatggaagtagcggttattaattagtaatgaatccaataatccattactccacggtaaacctatccttagcggtgtcctgtcacggacggcaaaaaaaacgtcataagtcttgcgagtttggcgaagacaaactcggtatgaaaattgcacacggaggtgcaattcccataccgacacgcgatgtttgccgtaaggcagacatcctgcccgcttttggcttaaccgcacaggatgtgcggtggttccacgcgtgcgatgttttaggcggaaagc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE2713:TDE2714|TDE2713:TDE2714:RNA methyltransferase, TrmH family:hypothetical protein:<-<-:2770415..2770716 302 gggcttatcatacacaaaaaacatggtctatggaagtagcggttattaattagtaatgaatccaataatccattactccacggtaaacctatccttagcggtgtcctgtcacggacggcaaaaaaaacgtcataagtcttgcgagtttggcgaagacaaactcggtatgaaaattgcacacggaggtgcaattcccataccgacacgcgatgtttgccgtaaggcagacatcctgcccgcttttggcttaaccgcacaggatgtgcggtggttccacgcgtgcgatgttttaggcggaaagc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE2713:TDE2714|TDE2713:TDE2714:RNA methyltransferase, TrmH family:hypothetical protein:<-<-:2770415..2770716 302 gggcttatcatacacaaaaaacatggtctatggaagtagcggttattaattagtaatgaatccaataatccattactccacggtaaacctatccttagcggtgtcctgtcacggacggcaaaaaaaacgtcataagtcttgcgagtttggcgaagacaaactcggtatgaaaattgcacacggaggtgcaattcccataccgacacgcgatgtttgccgtaaggcagacatcctgcccgcttttggcttaaccgcacaggatgtgcggtggttccacgcgtgcgatgttttaggcggaaagc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gggcttatcatacacaaaaaacatggtctatggaagtagcggttattaattagtaatgaatccaataatccattactccacggtaaacctatccttagcggtgtcctgtcacggacggcaaaaaaaacgtcataagtcttgcgagtttggcgaagacaaactcggtatgaaaattgcacacggaggtgcaattcccataccgacacgcgatgtttgccgtaaggcagacatcctgcccgcttttggcttaaccgcacaggatgtgcggtggttccacgcgtgcgatgttttaggcggaaagc Predict ORF larger than 30AA ================================================ Protein_Len: 60 Strand: + Start: 56 End: 301 ....................................................... M N P I I H Y S T V N L S L A V S C H G R Q K K R H K S C E F G E D K L G M K I A H G G A I P I P T R D V C R K A D I L . Protein_Len: 33 Strand: - Start: 133 End: 231 .................................................................................................................................... L D Q S N P S S L S P I F I A C P P A I G M G V R S T Q R L A S M ....................................................................... Protein_Len: 38 Strand: - Start: 98 End: 211 ................................................................................................. R H G T V S P L F F T M L R A L K A F V F E T H F N C V S T C N G Y R C A M ........................................................................................... Protein_Len: 60 Strand: - Start: 3 End: 257 .. W P L G I R L P T R D R V A F F V D Y T K R T Q R L C V R Y S F Q V R L H L E W V S V R H K G Y P L C G A R K Q S L R M ............................................. gggcttatcatacacaaaaaacatggtctatggaagtagcggttattaattagtaatgaatccaataatccattactccacggtaaacctatccttagcggtgtcctgtcacggacggcaaaaaaaacgtcataagtcttgcgagtttggcgaagacaaactcggtatgaaaattgcacacggaggtgcaattcccataccgacacgcgatgtttgccgtaaggcagacatcctgcccgcttttggcttaaccgcacaggatgtgcggtggttccacgcgtgcgatgttttaggcggaaagc 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================================================ gggcttatcatacacaaaaaacatggtctatggaagtagcggttattaattagtaatgaatccaataatccattactccacggtaaacctatccttagcggtgtcctgtcacggacggcaaaaaaaacgtcataagtcttgcgagtttggcgaagacaaactcggtatgaaaattgcacacggaggtgcaattcccataccgacacgcgatgtttgccgtaaggcagacatcctgcccgcttttggcttaaccgcacaggatgtgcggtggttccacgcgtgcgatgttttaggcggaaagc Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 100 HP_score: -14.1 Tail_Score: -4.1891 Start: 161 End: 204 Full_Region: cggcaaacatcgcgt gtcggtatgggaattgcac ctccgt gtgcaattttcataccgag tttgtcttcgccaaa ................................................................................................................................................................gtcggtatgggaattgcacctccgtgtgcaattttcataccgag.................................................................................................. TransTerm Strand: - Conf: 100 HP_score: -17.6 Tail_Score: -3.11024 Start: 162 End: 203 Full_Region: ggcaaacatcgcgtg tcggtatgggaattgcac ctccgt gtgcaattttcataccga gtttgtcttcgccaa .................................................................................................................................................................tcggtatgggaattgcacctccgtgtgcaattttcataccga................................................................................................... TransTerm Strand: + Conf: 78 HP_score: -12.3 Tail_Score: -2.71364 Start: 252 End: 268 Full_Region: CCGCTTTTGGCTTAA CCGCACA GGA TGTGCGG TGGTTCCACGCGTGC ...........................................................................................................................................................................................................................................................CCGCACAGGATGTGCGG.................................. Find igs database================================================ Query_seq: TDE2713:TDE2714|TDE2713:TDE2714:RNA methyltransferase, TrmH family:hypothetical protein:<-<-:2770415..2770716 302 gggcttatcatacacaaaaaacatggtctatggaagtagcggttattaattagtaatgaatccaataatccattactccacggtaaacctatccttagcggtgtcctgtcacggacggcaaaaaaaacgtcataagtcttgcgagtttggcgaagacaaactcggtatgaaaattgcacacggaggtgcaattcccataccgacacgcgatgtttgccgtaaggcagacatcctgcccgcttttggcttaaccgcacaggatgtgcggtggttccacgcgtgcgatgttttaggcggaaagc Intra-Species Hit: Count: 1 Min: 1 Max: 302 Len: 302 Subject: NC_002967_TDE2713_TDE2714|RNA methyltransferase, TrmH family:hypothetical protein|NEGATIVE:NEGATIVE|[2770415,2770716]|302 HSP 1 e-value: 1.0E-156 bit: 551.0 Len: 302 Query Start:1 Query End:302 Subject Strand: POSITIVE Subject Start: 1 Subject End: 302 gggcttatcatacacaaaaaacatggtctatggaagtagcggttattaattagtaatgaatccaataatccattactccacggtaaacctatccttagcggtgtcctgtcacggacggcnnnnnnnncgtcataagtcttgcgagtttggcgaagacaaactcggtatgaaaattgcacacggaggtgcaattcccataccgacacgcgatgtttgccgtaaggcagacatcctgcccgcttttggcttaaccgcacaggatgtgcggtggttccacgcgtgcgatgttttaggcggaaagc gggcttatcatacacaaaaaacatggtctatggaagtagcggttattaattagtaatgaatccaataatccattactccacggtaaacctatccttagcggtgtcctgtcacggacggcaaaaaaaacgtcataagtcttgcgagtttggcgaagacaaactcggtatgaaaattgcacacggaggtgcaattcccataccgacacgcgatgtttgccgtaaggcagacatcctgcccgcttttggcttaaccgcacaggatgtgcggtggttccacgcgtgcgatgttttaggcggaaagc Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GGGCUUAUCAUACACAAAAAACAUGGUCUAUGGAAGUAGCGGUUAUUAAUUAGUAAUGAAUCCAAUAAUCCAUUACUCCACGGUAAACCUAUCCUUAGCGGUGUCCUGUCACGGACGGCAAAAAAAACGUCAUAAGUCUUGCGAGUUUGGCGAAGACAAACUCGGUAUGAAAAUUGCACACGGAGGUGCAAUUCCCAUACCGACACGCGAUGUUUGCCGUAAGGCAGACAUCCUGCCCGCUUUUGGCUUAACCGCACAGGAUGUGCGGUGGUUCCACGCGUGCGAUGUUUUAGGCGGAAAGC ..((((..................((((..((((.((((.(((((((..(((....)))....))))).)).))))))))..)...)))..(((.....(.(((((......))))).)....((((((((....(((((((.......)).)))))....((((((((..((((((((......))))))))..))))))))(((((((((((((((....))))))))))...........(((....(((((((.....)))))))....))).))))).))))))))....))))))) (-101.70) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GCUUUCCGCCUAAAACAUCGCACGCGUGGAACCACCGCACAUCCUGUGCGGUUAAGCCAAAAGCGGGCAGGAUGUCUGCCUUACGGCAAACAUCGCGUGUCGGUAUGGGAAUUGCACCUCCGUGUGCAAUUUUCAUACCGAGUUUGUCUUCGCCAAACUCGCAAGACUUAUGACGUUUUUUUUGCCGUCCGUGACAGGACACCGCUAAGGAUAGGUUUACCGUGGAGUAAUGGAUUAUUGGAUUCAUUACUAAUUAAUAACCGCUACUUCCAUAGACCAUGUUUUUUGUGUAUGAUAAGCCC (((((((((..(((((((.((.(((.(((....(((((((.....)))))))....)))...))).)).((.(((((.((..((((((((.(..((((.((((((((..((((((((......))))))))..))))))))....(((((.((.......))))))).....))))..).))))))))..).)...))))))).(((.(((..((((........(((((((((((....))))))))))).......))))......))).)))...)))))))..)))...)).)))).. (-108.96) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 1033 120 71 211 162 NC_002967:TDE2713|5end_RNA_methyltransferase,_TrmH_family_2770324..2770554_NEGATIVE 593 297 251 138 91 NC_002967:TDE2134|5end_hypothetical_protein_2164447..2164677_POSITIVE 494 276 232 166 121 NC_002967:TDE2237|5end_hypothetical_protein_2276402..2276632_NEGATIVE 492 298 251 227 179 NC_002967:TDE0976|5end_hypothetical_protein_1000026..1000256_POSITIVE 440 229 181 222 170 NC_002967:TDE2093|5end_hypothetical_protein_2121003..2121233_NEGATIVE 439 296 251 111 66 NC_002967:TDE2548|5end_hypothetical_protein_2573198..2573428_NEGATIVE 435 229 181 203 152 NC_002967:TDE1514|5end_permease_domain_protein_1560652..1560882_POSITIVE 429 299 251 69 20 NC_002967:TDE1923|5end_hypothetical_protein_1941692..1941922_NEGATIVE 412 297 265 199 167 NC_002967:TDE2143|5end_penicillin-binding_protein_2178107..2178337_POSITIVE 401 296 251 134 91 NC_002967:TDE2338|5end_hypothetical_protein_2374719..2374949_NEGATIVE 392 229 187 144 102 NC_002967:TDE2497|5end_hypothetical_protein_2522083..2522313_NEGATIVE 392 229 187 122 80 NC_002967:TDE2394|5end_hypothetical_protein_2422612..2422842_NEGATIVE 392 229 187 205 163 NC_002967:TDE1903|5end_hypothetical_protein_1922417..1922647_POSITIVE 392 229 187 65 23 NC_002967:TDE1694|5end_hypothetical_protein_1749366..1749596_NEGATIVE 392 229 187 205 163 NC_002967:TDE1693|5end_hypothetical_protein_1749226..1749456_NEGATIVE 392 229 187 205 163 NC_002967:TDE0641|5end_UDP-N-acetylglucosamine_1-carboxyvinyltransferase_678282..678512_NEGATIVE 391 270 224 61 2 NC_002967:TDE2517|5end_DNA_repair_protein_RadA_2543842..2544072_NEGATIVE 389 284 247 132 87 NC_002967:TDE1890|5end_hypothetical_protein_1911012..1911242_POSITIVE 381 279 232 186 134 NC_002967:TDE1803|5end_hypothetical_protein_1839270..1839500_NEGATIVE 379 229 181 205 153 NC_002967:TDE1915|5end_alcohol_dehydrogenase,_iron-containing_1933103..1933333_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 538 299 252 116 63 NC_002967:TDE1934|3end_hypothetical_protein_1952804..1952954_POSITIVE 525 297 264 33 1 NC_002967:TDE2735|3end_surface_antigen,_putative_2791616..2791766_POSITIVE 440 229 181 148 96 NC_002967:TDE2094|3end_hypothetical_protein_2121077..2121227_NEGATIVE 429 299 251 87 38 NC_002967:TDE1924|3end_hypothetical_protein_1941674..1941824_NEGATIVE 416 260 215 78 16 NC_002967:TDE1843|3end_hypothetical_protein_1872199..1872349_NEGATIVE 396 247 207 50 9 NC_002967:TDE2419|3end_hypothetical_protein_2444023..2444173_NEGATIVE 383 270 223 79 16 NC_002967:TDE2736|3end_hypothetical_protein_2791702..2791852_NEGATIVE 372 260 215 69 7 NC_002967:TDE1812|3end_hypothetical_protein_1847580..1847730_NEGATIVE 371 260 216 61 1 NC_002967:TDE1840|3end_hypothetical_protein_1871324..1871474_NEGATIVE 371 279 232 88 38 NC_002967:TDE1837|3end_hypothetical_protein_1869542..1869692_NEGATIVE 371 279 232 80 30 NC_002967:TDE1787|3end_hypothetical_protein_1826378..1826528_NEGATIVE 368 270 224 62 11 NC_002967:TDE2104|3end_hypothetical_protein_2128525..2128675_NEGATIVE 365 263 222 134 95 NC_002967:TDE0142|3end_hypothetical_protein_163979..164129_NEGATIVE 363 260 215 64 3 NC_002967:TDE1810|3end_hypothetical_protein_1845924..1846074_NEGATIVE 360 260 215 67 6 NC_002967:TDE1776|3end_hypothetical_protein_1818414..1818564_NEGATIVE 359 248 205 151 103 NC_002967:TDE2051|3end_hypothetical_protein_2079990..2080140_NEGATIVE 358 236 197 38 1 NC_002967:TDE2498|3end_metallo-beta-lactamase_family_protein_2522194..2522344_NEGATIVE 356 236 207 34 7 NC_002967:TDE2020|3end_YD_repeat_protein_2040734..2040884_NEGATIVE 356 236 207 32 5 NC_002967:TDE1901|3end_ABC_transporter,_ATP-binding_protein_1922319..1922469_POSITIVE 351 278 232 80 31 NC_002967:TDE1800|3end_hypothetical_protein_1837427..1837577_NEGATIVE