Origin IGS: aacttttgcaaatatgcgggcatctgcgttgtcgcttaacaaaaaacagtcctcgacgtacaataagtacgcctgcgggtgttttttgtacgctcctagcatctacctcgcctatttgcaaaaggcttcttttaaaaaggatgtgttaat .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 attaacacatcctttttaaaagaagccttttgcaaataggcgaggtagatgctaggagcgtacaaaaaacacccgcaggcgtacttattgtacgtcgaggactgttttttgttaagcgacaacgcagatgcccgcatatttgcaaaagtt Mask Tandem Repeat Region ================================================ aacttttgcaaatatgcgggcatctgcgttgtcgcttaacaaaaaacagtcctcgacgtacaataagtacgcctgcgggtgttttttgtacgctcctagcatctacctcgcctatttgcaaaaggcttcttttaaaaaggatgtgttaat Find is-nt database================================================ Query_seq: TDE2009:TDE2010|TDE2009:TDE2010:hypothetical protein:hypothetical protein:->->:2031308..2031457 150 aacttttgcaaatatgcgggcatctgcgttgtcgcttaacaaaaaacagtcctcgacgtacaataagtacgcctgcgggtgttttttgtacgctcctagcatctacctcgcctatttgcaaaaggcttcttttaaaaaggatgtgttaat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE2009:TDE2010|TDE2009:TDE2010:hypothetical protein:hypothetical protein:->->:2031308..2031457 150 aacttttgcaaatatgcgggcatctgcgttgtcgcttaacaaaaaacagtcctcgacgtacaataagtacgcctgcgggtgttttttgtacgctcctagcatctacctcgcctatttgcaaaaggcttcttttaaaaaggatgtgttaat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE2009:TDE2010|TDE2009:TDE2010:hypothetical protein:hypothetical protein:->->:2031308..2031457 150 aacttttgcaaatatgcgggcatctgcgttgtcgcttaacaaaaaacagtcctcgacgtacaataagtacgcctgcgggtgttttttgtacgctcctagcatctacctcgcctatttgcaaaaggcttcttttaaaaaggatgtgttaat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aacttttgcaaatatgcgggcatctgcgttgtcgcttaacaaaaaacagtcctcgacgtacaataagtacgcctgcgggtgttttttgtacgctcctagcatctacctcgcctatttgcaaaaggcttcttttaaaaaggatgtgttaat Predict ORF larger than 30AA ================================================ Protein_Len: 45 Strand: + Start: 14 End: 148 ............. M R A S A L S L N K K Q S S T Y N K Y A C G C F L Y A P S I Y L A Y L Q K A S F K K D V L .. Protein_Len: 48 Strand: + Start: 6 End: 146 ..... M Q I C G H L R C R L T K N S P R R T I S T P A G V F C T L L A S T S P I C K R L L L K R M C * .... Protein_Len: 47 Strand: - Start: 2 End: 142 . S K C I H P C R R Q R K V F F L G R R V I L V G A P T K Q V S R A D V E G I Q L L S R K F L M ........ Protein_Len: 34 Strand: - Start: 1 End: 102 V K A F I R A D A N D S L L F C D E V Y L L Y A Q P H K K Y A G L M ................................................ aacttttgcaaatatgcgggcatctgcgttgtcgcttaacaaaaaacagtcctcgacgtacaataagtacgcctgcgggtgttttttgtacgctcctagcatctacctcgcctatttgcaaaaggcttcttttaaaaaggatgtgttaat 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: 35 End: 64 ..................................CTTAACAAAAAACAGTCCTCGACGTACAAT...................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ aacttttgcaaatatgcgggcatctgcgttgtcgcttaacaaaaaacagtcctcgacgtacaataagtacgcctgcgggtgttttttgtacgctcctagcatctacctcgcctatttgcaaaaggcttcttttaaaaaggatgtgttaat Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 44 HP_score: -4.1 Tail_Score: -2.51438 Start: 51 End: 78 Full_Region: gcgtacaaaaaacac ccgcaggcgtac ttatt gtacgtcgagg actgttttttgttaa ..................................................ccgcaggcgtacttattgtacgtcgagg........................................................................ TransTerm Strand: + Conf: 77 HP_score: -3.6 Tail_Score: -5.26316 Start: 70 End: 81 Full_Region: GACGTACAATAAGTA CGCC TGCG GGTG TTTTTTGTACGCTCC .....................................................................CGCCTGCGGGTG..................................................................... Find igs database================================================ Query_seq: TDE2009:TDE2010|TDE2009:TDE2010:hypothetical protein:hypothetical protein:->->:2031308..2031457 150 aacttttgcaaatatgcgggcatctgcgttgtcgcttaacaaaaaacagtcctcgacgtacaataagtacgcctgcgggtgttttttgtacgctcctagcatctacctcgcctatttgcaaaaggcttcttttaaaaaggatgtgttaat Intra-Species Hit: Count: 1 Min: 1 Max: 150 Len: 150 Subject: NC_002967_TDE2009_TDE2010|hypothetical protein:hypothetical protein|POSITIVE:POSITIVE|[2031308,2031457]|150 HSP 1 e-value: 5.0E-80 bit: 297.0 Len: 150 Query Start:1 Query End:150 Subject Strand: POSITIVE Subject Start: 1 Subject End: 150 aacttttgcaaatatgcgggcatctgcgttgtcgcttaacaaaaaacagtcctcgacgtacaataagtacgcctgcgggtgttttttgtacgctcctagcatctacctcgcctatttgcaaaaggcttcttttaaaaaggatgtgttaat aacttttgcaaatatgcgggcatctgcgttgtcgcttaacaaaaaacagtcctcgacgtacaataagtacgcctgcgggtgttttttgtacgctcctagcatctacctcgcctatttgcaaaaggcttcttttaaaaaggatgtgttaat Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AACUUUUGCAAAUAUGCGGGCAUCUGCGUUGUCGCUUAACAAAAAACAGUCCUCGACGUACAAUAAGUACGCCUGCGGGUGUUUUUUGUACGCUCCUAGCAUCUACCUCGCCUAUUUGCAAAAGGCUUCUUUUAAAAAGGAUGUGUUAAU ..((((((((((((.(((((....(((...(..((...((((((((((.(((.((.(((((.....)))))..)).)))))))))))))..))..)..))).....))))).))))))))))))...(((((....)))))......... (-47.70) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUUAACACAUCCUUUUUAAAAGAAGCCUUUUGCAAAUAGGCGAGGUAGAUGCUAGGAGCGUACAAAAAACACCCGCAGGCGUACUUAUUGUACGUCGAGGACUGUUUUUUGUUAAGCGACAACGCAGAUGCCCGCAUAUUUGCAAAAGUU ..........................((((((((((((.(((.((((..(((..(..((..((((((((((.((...(((((((.....)))))))..))..))))))))))...))..)...)))..))))))).)))))))))))).. (-57.10) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 683 77 34 105 62 NC_002967:TDE1847|5end_hypothetical_protein_1875664..1875894_POSITIVE 598 60 11 207 156 NC_002967:TDE0569|5end_hypothetical_protein_599636..599866_POSITIVE 535 60 11 173 124 NC_002967:TDE0976|5end_hypothetical_protein_1000026..1000256_POSITIVE 442 77 31 225 179 NC_002967:TDE0048|5end_hypothetical_protein_57822..58052_NEGATIVE 419 60 16 146 105 NC_002967:TDE1566|5end_hypothetical_protein_1617822..1618052_POSITIVE 354 45 4 151 110 NC_002967:TDE0819|5end_ABC_transporter,_ATP-binding/permease_protein_843385..843615_NEGATIVE 328 40 5 221 184 NC_002967:TDE0573|5end_hypothetical_protein_604681..604911_POSITIVE 327 120 71 151 114 NC_002967:TDE0279|5end_hypothetical_protein_309782..310012_NEGATIVE 324 110 71 196 152 NC_002967:TDE2197|5end_hypothetical_protein_2232848..2233078_NEGATIVE 319 127 81 201 135 NC_002967:TDE0166|5end_hypothetical_protein_195871..196101_NEGATIVE 314 50 1 177 135 NC_002967:TDE1816|5end_hypothetical_protein_1851673..1851903_NEGATIVE 314 98 51 138 76 NC_002967:TDE1334|5end_hypothetical_protein_1370144..1370374_POSITIVE 312 119 71 57 5 NC_002967:TDE2346|5end_elongation_factor_Ts_2383429..2383659_NEGATIVE 309 120 72 50 2 NC_002967:TDE2003|5end_internalin-related_protein_2022277..2022507_POSITIVE 307 100 53 191 146 NC_002967:TDE2415|5end_hypothetical_protein_2442345..2442575_NEGATIVE 301 97 51 95 42 NC_002967:TDE0709|5end_bifunctional_methionine_sulfoxide_reductase_A/B_protein_745434..745664_NEGATIVE 297 120 72 56 3 NC_002967:TDE1072|5end_lipoprotein,_putative_1100741..1100971_POSITIVE 297 60 15 53 1 NC_002967:TDE0339|5end_transcriptional_regulator,_TetR_family_377871..378101_POSITIVE 295 128 82 152 102 NC_002967:TDE1825|5end_hypothetical_protein_1858344..1858574_NEGATIVE 294 129 91 176 140 NC_002967:TDE2714|5end_hypothetical_protein_2772618..2772848_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 454 78 31 83 36 NC_002967:TDE1847|3end_hypothetical_protein_1875845..1875995_POSITIVE 412 80 33 80 21 NC_002967:TDE0049|3end_hypothetical_protein_58199..58349_NEGATIVE 365 120 71 77 27 NC_002967:TDE0977|3end_hypothetical_protein_1001640..1001790_POSITIVE 365 111 71 84 43 NC_002967:TDE0975|3end_hypothetical_protein_999879..1000029_POSITIVE 338 128 92 42 2 NC_002967:TDE0820|3end_transcriptional_regulator,_TetR_family_843714..843864_NEGATIVE 328 127 86 48 4 NC_002967:TDE0740|3end_hypothetical_protein_776204..776354_POSITIVE 327 120 71 38 1 NC_002967:TDE0280|3end_PIN_domain_protein_309895..310045_NEGATIVE 325 95 51 99 52 NC_002967:TDE0794|3end_hypothetical_protein_819224..819374_NEGATIVE 324 110 71 142 98 NC_002967:TDE2198|3end_pyruvate-ferredoxin_oxidoreductase_2232902..2233052_NEGATIVE 323 120 71 141 100 NC_002967:TDE1753|3end_UDP-glucose_4-epimerase_1805521..1805671_NEGATIVE 318 38 4 89 55 NC_002967:TDE2548|3end_hypothetical_protein_2573064..2573214_NEGATIVE 314 50 1 84 42 NC_002967:TDE1817|3end_hypothetical_protein_1851766..1851916_NEGATIVE 309 120 73 128 77 NC_002967:TDE0142|3end_hypothetical_protein_163979..164129_NEGATIVE 294 100 51 150 95 NC_002967:TDE2310|3end_hypothetical_protein_2348256..2348406_POSITIVE 290 78 33 70 23 NC_002967:TDE1323|3end_hypothetical_protein_1360968..1361118_POSITIVE 286 92 59 34 1 NC_002967:TDE2009|3end_hypothetical_protein_2031247..2031397_POSITIVE 286 119 73 49 1 NC_002967:TDE1808|3end_hypothetical_protein_1844084..1844234_NEGATIVE 286 128 83 90 34 NC_002967:TDE0135|3end_pyridine_nucleotide-disulphide_oxidoreductase_family_protein_156377..156527_POSITIVE 285 120 75 142 97 NC_002967:TDE2631|3end_peptide_ABC_transporter,_permease_protein,_putative_2672733..2672883_POSITIVE 282 114 71 56 8 NC_002967:TDE0295|3end_DNA_gyrase,_A_subunit_324220..324370_NEGATIVE