Origin IGS: catatttgtatacatttttccattctccgcttgctttatattctaggatatgatatacttttgcaagttgtgagggctaaaatgttttatcaaaaatacggtagtcaaatttttagaaacacaaaaaacaaacaactttcttcctatatatatatatatatatatatatatatatatataaccgcaaaccggcagtttatttaaacattccaataatttttatttcacatacaactgactatactcaagcaaaggagaaccttt .........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 aaaggttctcctttgcttgagtatagtcagttgtatgtgaaataaaaattattggaatgtttaaataaactgccggtttgcggttatatatatatatatatatatatatatatatatataggaagaaagttgtttgttttttgtgtttctaaaaatttgactaccgtatttttgataaaacattttagccctcacaacttgcaaaagtatatcatatcctagaatataaagcaagcggagaatggaaaaatgtatacaaatatg Mask Tandem Repeat Region ================================================ catatttgtatacatttttccattctccgcttgctttatattctaggatatgatatacttttgcaagttgtgagggctaaaatgttttatcaaaaatacggtagtcaaatttttagaaacacaaaaaacaaacaactttcttccnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnaccgcaaaccggcagtttatttaaacattccaataatttttatttcacatacaactgactatactcaagcaaaggagaaccttt Find is-nt database================================================ Query_seq: TDE2230:TDE2231|TDE2230:TDE2231:hypothetical protein:internalin-related protein:->->:2269514..2269777 264 catatttgtatacatttttccattctccgcttgctttatattctaggatatgatatacttttgcaagttgtgagggctaaaatgttttatcaaaaatacggtagtcaaatttttagaaacacaaaaaacaaacaactttcttcctatatatatatatatatatatatatatatatatataaccgcaaaccggcagtttatttaaacattccaataatttttatttcacatacaactgactatactcaagcaaaggagaaccttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE2230:TDE2231|TDE2230:TDE2231:hypothetical protein:internalin-related protein:->->:2269514..2269777 264 catatttgtatacatttttccattctccgcttgctttatattctaggatatgatatacttttgcaagttgtgagggctaaaatgttttatcaaaaatacggtagtcaaatttttagaaacacaaaaaacaaacaactttcttcctatatatatatatatatatatatatatatatatataaccgcaaaccggcagtttatttaaacattccaataatttttatttcacatacaactgactatactcaagcaaaggagaaccttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE2230:TDE2231|TDE2230:TDE2231:hypothetical protein:internalin-related protein:->->:2269514..2269777 264 catatttgtatacatttttccattctccgcttgctttatattctaggatatgatatacttttgcaagttgtgagggctaaaatgttttatcaaaaatacggtagtcaaatttttagaaacacaaaaaacaaacaactttcttcctatatatatatatatatatatatatatatatatataaccgcaaaccggcagtttatttaaacattccaataatttttatttcacatacaactgactatactcaagcaaaggagaaccttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 catatttgtatacatttttccattctccgcttgctttatattctaggatatgatatacttttgcaagttgtgagggctaaaatgttttatcaaaaatacggtagtcaaatttttagaaacacaaaaaacaaacaactttcttcctatatatatatatatatatatatatatatatatataaccgcaaaccggcagtttatttaaacattccaataatttttatttcacatacaactgactatactcaagcaaaggagaaccttt Predict ORF larger than 30AA ================================================ Protein_Len: 30 Strand: + Start: 89 End: 178 ........................................................................................ M K N T V V K F L E T Q K T N N F L P I Y I Y I Y I Y I Y I ...................................................................................... Protein_Len: 60 Strand: + Start: 4 End: 201 ... M C I H F S I L R L L Y I L G Y D I L L Q V V R A K M F Y Q K Y G S Q I F R N T K N K Q L S S Y I Y I Y I Y I Y I Y I T ............................................................... Protein_Len: 38 Strand: + Start: 150 End: 263 ..................................................................................................................................................... M Y I Y I Y I Y I Y N R K P A V Y L N I P I I F I S H T T D Y T Q A K E N L . Protein_Len: 56 Strand: - Start: 46 End: 213 ............................................. S I I Y K Q L N H P S F H K I L F V T T L N K S V C F V F L K R G I Y I Y I Y I Y I Y I Y G C V P L K N L C E M ................................................... catatttgtatacatttttccattctccgcttgctttatattctaggatatgatatacttttgcaagttgtgagggctaaaatgttttatcaaaaatacggtagtcaaatttttagaaacacaaaaaacaaacaactttcttcctatatatatatatatatatatatatatatatatataaccgcaaaccggcagtttatttaaacattccaataatttttatttcacatacaactgactatactcaagcaaaggagaaccttt 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: 30 End: 59 .............................CTTGCTTTATATTCTAGGATATGATATACT............................................................................................................................................................................................................. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ catatttgtatacatttttccattctccgcttgctttatattctaggatatgatatacttttgcaagttgtgagggctaaaatgttttatcaaaaatacggtagtcaaatttttagaaacacaaaaaacaaacaactttcttcctatatatatatatatatatatatatatatatatataaccgcaaaccggcagtttatttaaacattccaataatttttatttcacatacaactgactatactcaagcaaaggagaaccttt Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 74 HP_score: -8.8 Tail_Score: -2.98823 Start: 145 End: 172 Full_Region: AAACAACTTTCTTCC TATATATATATA TATA TATATATATATA TATATATAACCGCAA ................................................................................................................................................TATATATATATATATATATATATATATA............................................................................................ TransTerm Strand: + Conf: 76 HP_score: -9.7 Tail_Score: -2.87132 Start: 145 End: 174 Full_Region: AAACAACTTTCTTCC TATATATATATAT ATAT ATATATATATATA TATATAACCGCAAAC ................................................................................................................................................TATATATATATATATATATATATATATATA.......................................................................................... TransTerm Strand: - Conf: 76 HP_score: -9.7 Tail_Score: -2.87132 Start: 151 End: 180 Full_Region: ctgccggtttgcggt tatatatatatat atat atatatatatata tatataggaagaaag ......................................................................................................................................................tatatatatatatatatatatatatatata.................................................................................... TransTerm Strand: - Conf: 74 HP_score: -8.8 Tail_Score: -2.98823 Start: 153 End: 180 Full_Region: ctgccggtttgcggt tatatatatata tata tatatatatata tatatataggaagaa ........................................................................................................................................................tatatatatatatatatatatatatata.................................................................................... Find igs database================================================ Query_seq: TDE2230:TDE2231|TDE2230:TDE2231:hypothetical protein:internalin-related protein:->->:2269514..2269777 264 catatttgtatacatttttccattctccgcttgctttatattctaggatatgatatacttttgcaagttgtgagggctaaaatgttttatcaaaaatacggtagtcaaatttttagaaacacaaaaaacaaacaactttcttcctatatatatatatatatatatatatatatatatataaccgcaaaccggcagtttatttaaacattccaataatttttatttcacatacaactgactatactcaagcaaaggagaaccttt Intra-Species Hit: Count: 1 Min: 1 Max: 264 Len: 264 Subject: NC_002967_TDE2230_TDE2231|hypothetical protein:internalin-related protein|POSITIVE:POSITIVE|[2269514,2269777]|264 HSP 1 e-value: 4.0E-76 bit: 285.0 Len: 144 Query Start:1 Query End:144 Subject Strand: POSITIVE Subject Start: 1 Subject End: 144 catatttgtatacatttttccattctccgcttgctttatattctaggatatgatatacttttgcaagttgtgagggctaaaatgttttatcaaaaatacggtagtcaaatttttagaaacacaaaaaacaaacaactttcttcc........................................................................................................................ catatttgtatacatttttccattctccgcttgctttatattctaggatatgatatacttttgcaagttgtgagggctaaaatgttttatcaaaaatacggtagtcaaatttttagaaacacaaaaaacaaacaactttcttcc........................................................................................................................ HSP 2 e-value: 2.0E-40 bit: 167.0 Len: 84 Query Start:181 Query End:264 Subject Strand: POSITIVE Subject Start: 181 Subject End: 264 ....................................................................................................................................................................................accgcaaaccggcagtttatttaaacattccaataatttttatttcacatacaactgactatactcaagcaaaggagaaccttt ....................................................................................................................................................................................accgcaaaccggcagtttatttaaacattccaataatttttatttcacatacaactgactatactcaagcaaaggagaaccttt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CAUAUUUGUAUACAUUUUUCCAUUCUCCGCUUGCUUUAUAUUCUAGGAUAUGAUAUACUUUUGCAAGUUGUGAGGGCUAAAAUGUUUUAUCAAAAAUACGGUAGUCAAAUUUUUAGAAACACAAAAAACAAACAACUUUCUUCCUAUAUAUAUAUAUAUAUAUAUAUAUAUAUAUAUAUAACCGCAAACCGGCAGUUUAUUUAAACAUUCCAAUAAUUUUUAUUUCACAUACAACUGACUAUACUCAAGCAAAGGAGAACCUUU ......................((((((..((((((((((.((.((..((((.......(((((.((((((...(((((...((((((....))))))...)))))...(((((........)))))....)))))).......((((((((((((((((....))))))))))))))))...)))))..((..((((....))))...))................))))...)))).))))...)))))).))))))..... (-50.30) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAGGUUCUCCUUUGCUUGAGUAUAGUCAGUUGUAUGUGAAAUAAAAAUUAUUGGAAUGUUUAAAUAAACUGCCGGUUUGCGGUUAUAUAUAUAUAUAUAUAUAUAUAUAUAUAUAUAUAGGAAGAAAGUUGUUUGUUUUUUGUGUUUCUAAAAAUUUGACUACCGUAUUUUUGAUAAAACAUUUUAGCCCUCACAACUUGCAAAAGUAUAUCAUAUCCUAGAAUAUAAAGCAAGCGGAGAAUGGAAAAAUGUAUACAAAUAUG ....(((((((...(((((..((((.((....(.((((((.(((......(((((...((((....))))..)))))((((..(((((((((((((((((....))))))))))))))))).....(((((((..(((....((((((.(((((((.((.....)).)))))))...))))))...)))....)))))))))))...))).)))))).)..)).))))...))))))))))))..................... (-57.20) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 288 197 180 69 52 NC_002967:TDE2713|5end_RNA_methyltransferase,_TrmH_family_2770324..2770554_NEGATIVE 274 70 23 150 96 NC_002967:TDE1296|5end_ribosomal_subunit_interface_protein,_putative_1333754..1333984_NEGATIVE 271 100 53 82 33 NC_002967:TDE0860|5end_ribosomal_small_subunit_pseudouridine_synthase_A_881023..881253_POSITIVE 257 47 6 214 171 NC_002967:TDE2139|5end_hypothetical_protein_2172032..2172262_POSITIVE 253 78 33 231 173 NC_002967:TDE2355|5end_carbon_storage_regulator_2390838..2391068_POSITIVE 252 45 10 95 61 NC_002967:TDE1196|5end_hypothetical_protein_1229937..1230167_NEGATIVE 252 88 45 211 163 NC_002967:TDE0944|5end_hypothetical_protein_966247..966477_POSITIVE 249 224 182 105 61 NC_002967:TDE1897|5end_phosphoribosylglycinamide_formyltransferase_1918109..1918339_NEGATIVE 244 77 32 55 11 NC_002967:TDE0574|5end_surface_protein,_putative_604925..605155_POSITIVE 243 49 5 123 72 NC_002967:TDE1274|5end_oligopeptide/dipeptide_ABC_transporter,_permease_protein_1309560..1309790_NEGATIVE 241 87 42 179 127 NC_002967:TDE0178|5end_methyl-accepting_chemotaxis_protein_212628..212858_NEGATIVE 240 51 21 99 64 NC_002967:TDE1459|5end_hypothetical_protein_1508707..1508937_NEGATIVE 240 64 24 53 20 NC_002967:TDE1027|5end_ribonuclease_III_1057562..1057792_POSITIVE 236 48 5 170 120 NC_002967:TDE1684|5end_adenine_phosphoribosyltransferase_1737327..1737557_NEGATIVE 236 47 7 126 83 NC_002967:TDE0654|5end_peptidase,_M20/M25/M40_family_689606..689836_POSITIVE 233 92 56 90 47 NC_002967:TDE1209|5end_site-specific_recombinase,_phage_integrase_family_1242345..1242575_POSITIVE 232 69 26 170 122 NC_002967:TDE2021|5end_hypothetical_protein_2044759..2044989_NEGATIVE 232 62 25 99 52 NC_002967:TDE0847|5end_hypothetical_protein_870894..871124_POSITIVE 232 38 1 114 65 NC_002967:TDE0787|5end_preprotein_translocase_SecY_815068..815298_POSITIVE 232 78 31 146 92 NC_002967:TDE0185|5end_ABC_transporter,_ATP-binding_protein,_HlyB_family_220498..220728_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 271 100 53 85 36 NC_002967:TDE0859|3end_hypothetical_protein_881106..881256_POSITIVE 249 224 182 92 48 NC_002967:TDE1898|3end_translocase_1918122..1918272_NEGATIVE 243 49 5 113 62 NC_002967:TDE1275|3end_oligopeptide/dipeptide_ABC_transporter,_permease_protein_1309570..1309720_NEGATIVE 240 51 21 99 64 NC_002967:TDE1460|3end_hypothetical_protein_1508707..1508857_NEGATIVE 236 48 5 145 95 NC_002967:TDE1685|3end_GGDEF_domain_protein_1737352..1737502_NEGATIVE 236 47 7 114 71 NC_002967:TDE0653|3end_hypothetical_protein_689674..689824_POSITIVE 233 92 56 97 54 NC_002967:TDE1208|3end_DNA_topoisomerase_I_1242432..1242582_POSITIVE 232 38 1 100 51 NC_002967:TDE0786|3end_ribosomal_protein_L15_815134..815284_POSITIVE 231 70 23 145 96 NC_002967:TDE0109|3end_phenylalanyl-tRNA_synthetase_alpha_subunit_128833..128983_NEGATIVE 230 88 44 71 24 NC_002967:TDE2753|3end_LysM_domain/M23/M37_peptidase_domain_protein_2809558..2809708_NEGATIVE 226 78 60 151 131 NC_002967:TDE2163|3end_hypothetical_protein_2195533..2195683_NEGATIVE 226 70 23 127 82 NC_002967:TDE1122|3end_anti-anti-sigma_factor_1153373..1153523_NEGATIVE 225 47 13 122 92 NC_002967:TDE1526|3end_hypothetical_protein_1570887..1571037_POSITIVE 223 77 32 135 104 NC_002967:TDE0660|3end_transcriptional_regulator,_putative_696279..696429_NEGATIVE 222 104 66 53 16 NC_002967:TDE0593|3end_internalin-related_protein_632041..632191_NEGATIVE 221 49 1 114 64 NC_002967:TDE1457|3end_hypothetical_protein_1504739..1504889_NEGATIVE 220 77 46 141 111 NC_002967:TDE1856|3end_radical_SAM_domain_protein_1883956..1884106_POSITIVE 219 38 3 107 66 NC_002967:TDE1683|3end_V-type_ATP_synthase_subunit_A_1734845..1734995_NEGATIVE 218 212 177 128 92 NC_002967:TDE1446|3end_hypothetical_protein_1492679..1492829_POSITIVE 215 53 12 55 6 NC_002967:TDE2230|3end_hypothetical_protein_2269453..2269603_POSITIVE