Origin IGS: acaaatattatgacataaaaaatctatatttgcaaccataaaattctttttttgggcaatacctcttacaatttatacgtaatacagactgttttaatcggtacttgtacaaagataaaaaaaagactataattcacacttataattgcaataagggagataaatt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aatttatctcccttattgcaattataagtgtgaattatagtcttttttttatctttgtacaagtaccgattaaaacagtctgtattacgtataaattgtaagaggtattgcccaaaaaaagaattttatggttgcaaatatagattttttatgtcataatatttgt Mask Tandem Repeat Region ================================================ acaaatattatgacataaaaaatctatatttgcaaccataaaattctttttttgggcaatacctcttacaatttatacgtaatacagactgttttaatcggtacttgtacaaagataaaaaaaagactataattcacacttataattgcaataagggagataaatt Find is-nt database================================================ Query_seq: TDE0019:TDE0020|TDE0019:TDE0020:formate--tetrahydrofolate ligase:glycyl-tRNA synthetase:<-->:25420..25585 166 acaaatattatgacataaaaaatctatatttgcaaccataaaattctttttttgggcaatacctcttacaatttatacgtaatacagactgttttaatcggtacttgtacaaagataaaaaaaagactataattcacacttataattgcaataagggagataaatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE0019:TDE0020|TDE0019:TDE0020:formate--tetrahydrofolate ligase:glycyl-tRNA synthetase:<-->:25420..25585 166 acaaatattatgacataaaaaatctatatttgcaaccataaaattctttttttgggcaatacctcttacaatttatacgtaatacagactgttttaatcggtacttgtacaaagataaaaaaaagactataattcacacttataattgcaataagggagataaatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE0019:TDE0020|TDE0019:TDE0020:formate--tetrahydrofolate ligase:glycyl-tRNA synthetase:<-->:25420..25585 166 acaaatattatgacataaaaaatctatatttgcaaccataaaattctttttttgggcaatacctcttacaatttatacgtaatacagactgttttaatcggtacttgtacaaagataaaaaaaagactataattcacacttataattgcaataagggagataaatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 acaaatattatgacataaaaaatctatatttgcaaccataaaattctttttttgggcaatacctcttacaatttatacgtaatacagactgttttaatcggtacttgtacaaagataaaaaaaagactataattcacacttataattgcaataagggagataaatt Predict ORF larger than 30AA ================================================ Protein_Len: 36 Strand: + Start: 22 End: 129 ..................... M Y I C N H K I L F L G N T S Y N L Y V I Q T V L I G T C T K I K K R L ..................................... Protein_Len: 30 Strand: + Start: 75 End: 164 .......................................................................... M R N T D C F N R Y L Y K D K K K T I I H T Y N C N K G D K .. Protein_Len: 31 Strand: - Start: 69 End: 161 .................................................................... L K Y T I C V T K I P V Q V F I F F L S Y N V S I I A I L S M ..... Protein_Len: 41 Strand: - Start: 11 End: 133 .......... S M F F R Y K C G Y F E K K P C Y R K C N I R L V S Q K L R Y K Y L S L F F V I M ................................. acaaatattatgacataaaaaatctatatttgcaaccataaaattctttttttgggcaatacctcttacaatttatacgtaatacagactgttttaatcggtacttgtacaaagataaaaaaaagactataattcacacttataattgcaataagggagataaatt 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: 86 Start: 7 End: 36 ......GTTGCAAATATAGATTTTTTATGTCATAAT.................................................................................................................................. PromScan Matrix: RpoD-17 Strand: + Score: 82 Start: 104 End: 133 .......................................................................................................CTTGTACAAAGATAAAAAAAAGACTATAAT................................. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ acaaatattatgacataaaaaatctatatttgcaaccataaaattctttttttgggcaatacctcttacaatttatacgtaatacagactgttttaatcggtacttgtacaaagataaaaaaaagactataattcacacttataattgcaataagggagataaatt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE0019:TDE0020|TDE0019:TDE0020:formate--tetrahydrofolate ligase:glycyl-tRNA synthetase:<-->:25420..25585 166 acaaatattatgacataaaaaatctatatttgcaaccataaaattctttttttgggcaatacctcttacaatttatacgtaatacagactgttttaatcggtacttgtacaaagataaaaaaaagactataattcacacttataattgcaataagggagataaatt Intra-Species Hit: Count: 1 Min: 1 Max: 166 Len: 166 Subject: NC_002967_TDE0019_TDE0020|formate--tetrahydrofolate ligase:glycyl-tRNA synthetase|NEGATIVE:POSITIVE|[25420,25585]|166 HSP 1 e-value: 1.0E-62 bit: 240.0 Len: 166 Query Start:1 Query End:166 Subject Strand: POSITIVE Subject Start: 1 Subject End: 166 acaaatattatgacataaaaaatctatatttgcaaccataaaattcnnnnnnngggcaatacctcttacaatttatacgtaatacagactgttttaatcggtacttgtacaaagatnnnnnnnngactataattcacacttataattgcaataagggagataaatt acaaatattatgacataaaaaatctatatttgcaaccataaaattctttttttgggcaatacctcttacaatttatacgtaatacagactgttttaatcggtacttgtacaaagataaaaaaaagactataattcacacttataattgcaataagggagataaatt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ ACAAAUAUUAUGACAUAAAAAAUCUAUAUUUGCAACCAUAAAAUUCUUUUUUUGGGCAAUACCUCUUACAAUUUAUACGUAAUACAGACUGUUUUAAUCGGUACUUGUACAAAGAUAAAAAAAAGACUAUAAUUCACACUUAUAAUUGCAAUAAGGGAGAUAAAUU ......................(((....((((((.........(((((((((((......))...............(((......((((.......)))).....))).......))))))))).(((((.......))))).))))))....)))........ (-18.60) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAUUUAUCUCCCUUAUUGCAAUUAUAAGUGUGAAUUAUAGUCUUUUUUUUAUCUUUGUACAAGUACCGAUUAAAACAGUCUGUAUUACGUAUAAAUUGUAAGAGGUAUUGCCCAAAAAAAGAAUUUUAUGGUUGCAAAUAUAGAUUUUUUAUGUCAUAAUAUUUGU ...............(((((((((((((............(((((((((....(((((((.(((((.((((.....)))).)))))..)))))))..((((......))))..)))))))))..))))))))))))).....(((.......)))........... (-27.14) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 780 100 51 191 142 NC_002967:TDE0019|5end_formate--tetrahydrofolate_ligase_25329..25559_NEGATIVE 239 90 43 60 17 NC_002967:TDE2578|5end_hypothetical_protein_2603154..2603384_NEGATIVE 236 57 12 88 39 NC_002967:TDE0063|5end_hypothetical_protein_69714..69944_POSITIVE 216 117 71 225 174 NC_002967:TDE1533|5end_hypothetical_protein_1577114..1577344_POSITIVE 214 109 61 150 96 NC_002967:TDE0267|5end_HAM1_protein_299108..299338_NEGATIVE 213 68 31 65 26 NC_002967:TDE2668|5end_serine_hydroxymethyltransferase_2706066..2706296_NEGATIVE 213 105 62 148 100 NC_002967:TDE2305|5end_hypothetical_protein_2343652..2343882_POSITIVE 213 63 29 123 75 NC_002967:TDE0780|5end_ribosomal_protein_S14_812364..812594_POSITIVE 209 68 23 47 11 NC_002967:TDE0601|5end_malonyl_CoA-acyl_carrier_protein_transacylase,_putative_639811..640041_NEGATIVE 207 94 54 202 163 NC_002967:TDE2320|5end_RNA_polymerase_sigma-24_factor,_putative_2356951..2357181_NEGATIVE 203 110 62 149 100 NC_002967:TDE2768|5end_flagellar_hook_protein_2822510..2822740_NEGATIVE 201 108 63 150 98 NC_002967:TDE0988|5end_oligopeptide/dipeptide_ABC_transporter,_peptide-binding_protein_1015082..1015312_POSITIVE 198 36 5 135 104 NC_002967:TDE1936|5end_hypothetical_protein_1953086..1953316_POSITIVE 198 36 5 43 12 NC_002967:TDE1935|5end_hypothetical_protein_1952994..1953224_POSITIVE 198 103 65 156 120 NC_002967:TDE1173|5end_site-specific_recombinase,_phage_integrase_family_1202321..1202551_NEGATIVE 198 79 32 188 139 NC_002967:TDE0777|5end_50S_ribosomal_protein_L14_811109..811339_POSITIVE 198 109 70 52 1 NC_002967:TDE0657|5end_ABC_transporter,_ATP-binding_protein_692765..692995_POSITIVE 196 106 62 144 99 NC_002967:TDE1996|5end_hypothetical_protein_2014243..2014473_POSITIVE 196 109 63 66 10 NC_002967:TDE1607|5end_MutT/nudix_family_protein_1657531..1657761_NEGATIVE 196 160 112 52 4 NC_002967:TDE1053|5end_lipoprotein,_putative_1080726..1080956_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 213 105 62 151 103 NC_002967:TDE2304|3end_hypothetical_protein_2343735..2343885_POSITIVE 213 109 64 146 99 NC_002967:TDE2258|3end_surface_antigen_BspA,_putative_2295334..2295484_NEGATIVE 213 63 29 111 63 NC_002967:TDE0779|3end_ribosomal_protein_L5_812432..812582_POSITIVE 212 70 28 115 67 NC_002967:TDE1322|3end_hypothetical_protein_1360020..1360170_NEGATIVE 203 110 62 136 87 NC_002967:TDE2769|3end_flagellar_hook_assembly_protein_2822523..2822673_NEGATIVE 201 108 63 65 13 NC_002967:TDE0987|3end_oligopeptide/dipeptide_ABC_transporter,_ATP-binding_protein_1015077..1015227_POSITIVE 198 36 5 135 104 NC_002967:TDE1935|3end_hypothetical_protein_1953166..1953316_POSITIVE 196 56 26 42 13 NC_002967:TDE2533|3end_hypothetical_protein_2560240..2560390_POSITIVE 196 106 62 65 20 NC_002967:TDE1995|3end_magnesium_chelatase_family_protein_2014244..2014394_POSITIVE 195 108 62 43 1 NC_002967:TDE0142|3end_hypothetical_protein_163979..164129_NEGATIVE 193 90 47 79 35 NC_002967:TDE0042|3end_phosphate_acetyltransferase_49763..49913_POSITIVE 190 70 27 122 80 NC_002967:TDE1889|3end_branched-chain_amino_acid_transport_system_II_carrier_protein_1909500..1909650_NEGATIVE 190 116 78 91 55 NC_002967:TDE1568|3end_hypothetical_protein_1619827..1619977_POSITIVE 190 101 61 149 98 NC_002967:TDE1098|3end_hypothetical_protein_1132770..1132920_NEGATIVE 190 106 63 88 47 NC_002967:TDE0026|3end_TraB_family_protein_31826..31976_NEGATIVE 189 79 47 111 76 NC_002967:TDE1573|3end_DNA-damage-inducible_protein_J,_putative_1621541..1621691_NEGATIVE 187 66 26 61 18 NC_002967:TDE0844|3end_pyruvate_phosphate_dikinase,_putative_867773..867923_POSITIVE 186 92 54 86 49 NC_002967:TDE1753|3end_UDP-glucose_4-epimerase_1805521..1805671_NEGATIVE 184 109 63 63 15 NC_002967:TDE0858|3end_hypothetical_protein_880170..880320_POSITIVE 183 100 52 47 9 NC_002967:TDE2343|3end_phosphatidate_cytidylyltransferase_2380383..2380533_NEGATIVE