Origin IGS: tttataagcctttcattattttataaataatatattatataatgaatttggatctttattcaatacggtttgtttatgcgttttgtttattcgaatcctatctttcatttatccattcctcctcatctggtacttcctaaaattttttgttataatgatgct .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 agcatcattataacaaaaaattttaggaagtaccagatgaggaggaatggataaatgaaagataggattcgaataaacaaaacgcataaacaaaccgtattgaataaagatccaaattcattatataatatattatttataaaataatgaaaggcttataaa Mask Tandem Repeat Region ================================================ tttataagcctttcattattttataaataatatattatataatgaatttggatctttattcaatacggtttgtttatgcgttttgtttattcgaatcctatctttcatttatccattcctcctcatctggtacttcctaaaattttttgttataatgatgct Find is-nt database================================================ Query_seq: TDE0369:TDE0370|TDE0369:TDE0370:type I restriction-modification system, M subunit:UDP-N-acetylmuramoylalanine--D-glutamate ligase:<-->:421062..421223 162 tttataagcctttcattattttataaataatatattatataatgaatttggatctttattcaatacggtttgtttatgcgttttgtttattcgaatcctatctttcatttatccattcctcctcatctggtacttcctaaaattttttgttataatgatgct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE0369:TDE0370|TDE0369:TDE0370:type I restriction-modification system, M subunit:UDP-N-acetylmuramoylalanine--D-glutamate ligase:<-->:421062..421223 162 tttataagcctttcattattttataaataatatattatataatgaatttggatctttattcaatacggtttgtttatgcgttttgtttattcgaatcctatctttcatttatccattcctcctcatctggtacttcctaaaattttttgttataatgatgct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE0369:TDE0370|TDE0369:TDE0370:type I restriction-modification system, M subunit:UDP-N-acetylmuramoylalanine--D-glutamate ligase:<-->:421062..421223 162 tttataagcctttcattattttataaataatatattatataatgaatttggatctttattcaatacggtttgtttatgcgttttgtttattcgaatcctatctttcatttatccattcctcctcatctggtacttcctaaaattttttgttataatgatgct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tttataagcctttcattattttataaataatatattatataatgaatttggatctttattcaatacggtttgtttatgcgttttgtttattcgaatcctatctttcatttatccattcctcctcatctggtacttcctaaaattttttgttataatgatgct Predict ORF larger than 30AA ================================================ Protein_Len: 37 Strand: + Start: 27 End: 137 .......................... M I Y Y I M N L D L Y S I R F V Y A F C L F E S Y L S F I H S S S S G T S ......................... Protein_Len: 46 Strand: + Start: 23 End: 160 ...................... M N N I L Y N E F G S L F N T V C L C V L F I R I L S F I Y P F L L I W Y F L K F F V I M M .. Protein_Len: 39 Strand: + Start: 46 End: 162 ............................................. M W I F I Q Y G L F M R F V Y S N P I F H L S I P P H L V L P K I F C Y N D A Protein_Len: 30 Strand: - Start: 19 End: 108 .................. K I F L I N Y L S N P D K N L V T Q K H T K N I R I R D K M ...................................................... tttataagcctttcattattttataaataatatattatataatgaatttggatctttattcaatacggtttgtttatgcgttttgtttattcgaatcctatctttcatttatccattcctcctcatctggtacttcctaaaattttttgttataatgatgct 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================================================ tttataagcctttcattattttataaataatatattatataatgaatttggatctttattcaatacggtttgtttatgcgttttgtttattcgaatcctatctttcatttatccattcctcctcatctggtacttcctaaaattttttgttataatgatgct Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE0369:TDE0370|TDE0369:TDE0370:type I restriction-modification system, M subunit:UDP-N-acetylmuramoylalanine--D-glutamate ligase:<-->:421062..421223 162 tttataagcctttcattattttataaataatatattatataatgaatttggatctttattcaatacggtttgtttatgcgttttgtttattcgaatcctatctttcatttatccattcctcctcatctggtacttcctaaaattttttgttataatgatgct Intra-Species Hit: Count: 1 Min: 1 Max: 162 Len: 162 Subject: NC_002967_TDE0369_TDE0370|type I restriction-modification system, M subunit:UDP-N-acetylmuramoylalanine--D-glutamate ligase|NEGATIVE:POSITIVE|[421062,421223]|162 HSP 1 e-value: 4.0E-87 bit: 321.0 Len: 162 Query Start:1 Query End:162 Subject Strand: POSITIVE Subject Start: 1 Subject End: 162 tttataagcctttcattattttataaataatatattatataatgaatttggatctttattcaatacggtttgtttatgcgttttgtttattcgaatcctatctttcatttatccattcctcctcatctggtacttcctaaaattttttgttataatgatgct tttataagcctttcattattttataaataatatattatataatgaatttggatctttattcaatacggtttgtttatgcgttttgtttattcgaatcctatctttcatttatccattcctcctcatctggtacttcctaaaattttttgttataatgatgct Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUAUAAGCCUUUCAUUAUUUUAUAAAUAAUAUAUUAUAUAAUGAAUUUGGAUCUUUAUUCAAUACGGUUUGUUUAUGCGUUUUGUUUAUUCGAAUCCUAUCUUUCAUUUAUCCAUUCCUCCUCAUCUGGUACUUCCUAAAAUUUUUUGUUAUAAUGAUGCU ......(((...(((((((...(((((.(((.................(((((.........(((.((((((..((.((.....)).))..)))))).))).........))))).....((......))...........))).))))).))))))).))) (-20.07) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGCAUCAUUAUAACAAAAAAUUUUAGGAAGUACCAGAUGAGGAGGAAUGGAUAAAUGAAAGAUAGGAUUCGAAUAAACAAAACGCAUAAACAAACCGUAUUGAAUAAAGAUCCAAAUUCAUUAUAUAAUAUAUUAUUUAUAAAAUAAUGAAAGGCUUAUAAA (((.(((((((..............((.....))..((((.(((...(((((........((......)).......(((.(((...........))).))).......)))))..))).))))...................)))))))...)))...... (-18.10) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 863 140 91 231 182 NC_002967:TDE0369|5end_type_I_restriction-modification_system,_M_subunit_420971..421201_NEGATIVE 319 136 101 128 84 NC_002967:TDE1527|5end_hypothetical_protein_1570804..1571034_POSITIVE 289 159 111 128 65 NC_002967:TDE1261|5end_choline/carnitine/betaine_transporter_family_protein_1295593..1295823_POSITIVE 284 137 91 114 69 NC_002967:TDE2420|5end_DNA-directed_RNA_polymerase_beta'_subunit_2449234..2449464_NEGATIVE 274 116 73 107 59 NC_002967:TDE2779|5end_hypothetical_protein_2830425..2830655_NEGATIVE 269 129 84 39 2 NC_002967:TDE2515|5end_hypothetical_protein_2542057..2542287_NEGATIVE 265 133 92 106 66 NC_002967:TDE2740|5end_type_I_restriction-modification_system,_S_subunit,_truncation_2795202..2795432_POSITIVE 263 100 51 128 79 NC_002967:TDE0016|5end_ATPase,_AAA_family_20457..20687_POSITIVE 259 108 66 198 150 NC_002967:TDE1135|5end_hypothetical_protein_1165542..1165772_NEGATIVE 259 128 87 191 144 NC_002967:TDE0416|5end_bacteriocin-type_signal_domain_protein_468939..469169_POSITIVE 258 135 91 123 78 NC_002967:TDE1292|5end_TldD/PmbA_family_protein_1330621..1330851_NEGATIVE 257 140 99 126 83 NC_002967:TDE1207|5end_DNA_processing_protein_DprA,_putative_1239236..1239466_POSITIVE 252 140 98 113 67 NC_002967:TDE0264|5end_ribbon-helix-helix_protein,_CopG_family_297287..297517_NEGATIVE 251 130 91 114 76 NC_002967:TDE2456|5end_hypothetical_protein_2484573..2484803_NEGATIVE 250 150 105 196 159 NC_002967:TDE0424|5end_bacteriocin-type_signal_domain_protein_477870..478100_POSITIVE 243 75 33 164 120 NC_002967:TDE1989|5end_acyltransferase_family_protein_2006343..2006573_NEGATIVE 242 105 66 189 139 NC_002967:TDE1945|5end_hypothetical_protein_1961445..1961675_NEGATIVE 239 123 81 103 56 NC_002967:TDE0772|5end_50S_ribosomal_protein_L22_809084..809314_POSITIVE 236 160 113 118 58 NC_002967:TDE1513|5end_hypothetical_protein_1560484..1560714_POSITIVE 234 138 95 130 78 NC_002967:TDE1310|5end_modulator_of_DNA_gyrase_family_protein_1345962..1346192_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 319 136 101 131 87 NC_002967:TDE1526|3end_hypothetical_protein_1570887..1571037_POSITIVE 289 159 111 131 68 NC_002967:TDE1260|3end_cholinephosphate_cytidylyltransferase/choline_kinase_1295676..1295826_POSITIVE 284 137 91 89 44 NC_002967:TDE2421|3end_DNA-directed_RNA_polymerase_beta_subunit_2449259..2449409_NEGATIVE 266 126 83 137 87 NC_002967:TDE0406|3end_hypothetical_protein_458929..459079_POSITIVE 263 100 51 135 86 NC_002967:TDE0015|3end_lipoprotein,_putative_20544..20694_POSITIVE 258 135 91 123 78 NC_002967:TDE1293|3end_TldD/PmbA_family_protein_1330621..1330771_NEGATIVE 257 140 99 122 79 NC_002967:TDE1206|3end_TPR_domain_protein_1239312..1239462_POSITIVE 243 75 33 140 96 NC_002967:TDE1990|3end_ATP-dependent_helicase,_DinG_family_2006367..2006517_NEGATIVE 240 100 64 73 32 NC_002967:TDE0977|3end_hypothetical_protein_1001640..1001790_POSITIVE 239 123 81 92 45 NC_002967:TDE0771|3end_ribosomal_protein_S19_809153..809303_POSITIVE 236 160 113 105 45 NC_002967:TDE1512|3end_hypothetical_protein_1560551..1560701_POSITIVE 235 110 69 131 90 NC_002967:TDE1502|3end_chorismate_mutase_1551377..1551527_POSITIVE 234 138 95 130 78 NC_002967:TDE1309|3end_modulator_of_DNA_gyrase_family_protein_1346042..1346192_POSITIVE 234 138 97 134 94 NC_002967:TDE1280|3end_hypothetical_protein_1315750..1315900_NEGATIVE 232 146 115 92 55 NC_002967:TDE1916|3end_glycerol_kinase_1933277..1933427_NEGATIVE 232 89 48 76 29 NC_002967:TDE0588|3end_histidine_ammonia-lyase_628053..628203_POSITIVE 232 134 92 112 65 NC_002967:TDE0078|3end_glycine_reductase_complex_selenoprotein_GrdB1_88745..88895_NEGATIVE 230 106 66 117 78 NC_002967:TDE1152|3end_head-to-tail_joining_protein,_putative_1188527..1188677_NEGATIVE 229 104 66 148 117 NC_002967:TDE1870|3end_CAAX_amino_terminal_protease_family_protein_1892656..1892806_NEGATIVE 229 158 118 107 79 NC_002967:TDE1253|3end_hypothetical_protein_1288473..1288623_POSITIVE