Origin IGS: aaaaactcctttatataagtttctttttctttataataatactttaaagtctcggacatgtcaatgctgaaaaaaactttgtaaaatctgcttaatcaatctcttcttgccaaatttcccgttttttggtatactcacccctcct .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aggaggggtgagtataccaaaaaacgggaaatttggcaagaagagattgattaagcagattttacaaagtttttttcagcattgacatgtccgagactttaaagtattattataaagaaaaagaaacttatataaaggagttttt Mask Tandem Repeat Region ================================================ aaaaactcctttatataagtttctttttctttataataatactttaaagtctcggacatgtcaatgctgaaaaaaactttgtaaaatctgcttaatcaatctcttcttgccaaatttcccgttttttggtatactcacccctcct Find is-nt database================================================ Query_seq: TDE0902:TDE0903|TDE0902:TDE0903:hypothetical protein:ATP-dependent DNA helicase PcrA:<-->:920223..920367 145 aaaaactcctttatataagtttctttttctttataataatactttaaagtctcggacatgtcaatgctgaaaaaaactttgtaaaatctgcttaatcaatctcttcttgccaaatttcccgttttttggtatactcacccctcct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE0902:TDE0903|TDE0902:TDE0903:hypothetical protein:ATP-dependent DNA helicase PcrA:<-->:920223..920367 145 aaaaactcctttatataagtttctttttctttataataatactttaaagtctcggacatgtcaatgctgaaaaaaactttgtaaaatctgcttaatcaatctcttcttgccaaatttcccgttttttggtatactcacccctcct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE0902:TDE0903|TDE0902:TDE0903:hypothetical protein:ATP-dependent DNA helicase PcrA:<-->:920223..920367 145 aaaaactcctttatataagtttctttttctttataataatactttaaagtctcggacatgtcaatgctgaaaaaaactttgtaaaatctgcttaatcaatctcttcttgccaaatttcccgttttttggtatactcacccctcct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aaaaactcctttatataagtttctttttctttataataatactttaaagtctcggacatgtcaatgctgaaaaaaactttgtaaaatctgcttaatcaatctcttcttgccaaatttcccgttttttggtatactcacccctcct Predict ORF larger than 30AA ================================================ aaaaactcctttatataagtttctttttctttataataatactttaaagtctcggacatgtcaatgctgaaaaaaactttgtaaaatctgcttaatcaatctcttcttgccaaatttcccgttttttggtatactcacccctcct 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: 90 Start: 106 End: 135 .........................................................................................................CTTGCCAAATTTCCCGTTTTTTGGTATACT.......... PromScan Matrix: RpoD-17 Strand: - Score: 89 Start: 36 End: 65 ...................................ATTGACATGTCCGAGACTTTAAAGTATTAT................................................................................ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ aaaaactcctttatataagtttctttttctttataataatactttaaagtctcggacatgtcaatgctgaaaaaaactttgtaaaatctgcttaatcaatctcttcttgccaaatttcccgttttttggtatactcacccctcct Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE0902:TDE0903|TDE0902:TDE0903:hypothetical protein:ATP-dependent DNA helicase PcrA:<-->:920223..920367 145 aaaaactcctttatataagtttctttttctttataataatactttaaagtctcggacatgtcaatgctgaaaaaaactttgtaaaatctgcttaatcaatctcttcttgccaaatttcccgttttttggtatactcacccctcct Intra-Species Hit: Count: 1 Min: 1 Max: 145 Len: 145 Subject: NC_002967_TDE0902_TDE0903|hypothetical protein:ATP-dependent DNA helicase PcrA|NEGATIVE:POSITIVE|[920223,920367]|145 HSP 1 e-value: 2.0E-64 bit: 246.0 Len: 145 Query Start:1 Query End:145 Subject Strand: POSITIVE Subject Start: 1 Subject End: 145 aaaaactcctttatataagtttctttttctttataataatactttaaagtctcggacatgtcaatgctgnnnnnnnctttgtaaaatctgcttaatcaatctcttcttgccaaatttcccgttttttggtatactcacccctcct aaaaactcctttatataagtttctttttctttataataatactttaaagtctcggacatgtcaatgctgaaaaaaactttgtaaaatctgcttaatcaatctcttcttgccaaatttcccgttttttggtatactcacccctcct Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAAACUCCUUUAUAUAAGUUUCUUUUUCUUUAUAAUAAUACUUUAAAGUCUCGGACAUGUCAAUGCUGAAAAAAACUUUGUAAAAUCUGCUUAAUCAAUCUCUUCUUGCCAAAUUUCCCGUUUUUUGGUAUACUCACCCCUCCU .........((((((.((((((......(((((...........)))))..((((.(((....)))))))...))))))))))))......................(((((((..........))))))).............. (-16.20) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGGAGGGGUGAGUAUACCAAAAAACGGGAAAUUUGGCAAGAAGAGAUUGAUUAAGCAGAUUUUACAAAGUUUUUUUCAGCAUUGACAUGUCCGAGACUUUAAAGUAUUAUUAUAAAGAAAAAGAAACUUAUAUAAAGGAGUUUUU .(((.(.((.(((.....(((((((..((((((((.(((.......)))......)))))))).....))))))).....))).)).).)))....(((((.(((...))).)))))....((((((((........)))))))) (-19.90) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 835 140 91 231 182 NC_002967:TDE0902|5end_hypothetical_protein_920132..920362_NEGATIVE 539 80 31 167 117 NC_002967:TDE2419|5end_hypothetical_protein_2444769..2444999_NEGATIVE 286 130 87 55 6 NC_002967:TDE1405|5end_phosphoribosylformylglycinamidine_synthetase_I_1448674..1448904_NEGATIVE 267 140 91 219 167 NC_002967:TDE1659|5end_alanyl-tRNA_synthetase_1710633..1710863_NEGATIVE 264 123 85 123 80 NC_002967:TDE0777|5end_50S_ribosomal_protein_L14_811109..811339_POSITIVE 260 70 36 167 134 NC_002967:TDE1953|5end_transcriptional_regulator,_TetR_family_1969671..1969901_NEGATIVE 256 130 81 206 132 NC_002967:TDE2004|5end_hypothetical_protein_2023622..2023852_POSITIVE 254 140 102 101 51 NC_002967:TDE1114|5end_transcriptional_regulator,_TetR_family_1148905..1149135_NEGATIVE 254 120 73 172 130 NC_002967:TDE0343|5end_hydrolase,_alpha/beta_fold_family_385365..385595_NEGATIVE 252 136 96 231 186 NC_002967:TDE0509|5end_hypothetical_protein_560373..560603_NEGATIVE 247 70 22 162 113 NC_002967:TDE1413|5end_cytidylyltransferase/phosphoenolpyruvate_phosphomutase,_putative_1455510..1455740_POSITIVE 240 130 87 121 68 NC_002967:TDE0201|5end_hypothetical_protein_235363..235593_POSITIVE 238 120 77 188 146 NC_002967:TDE1598|5end_ABC_transporter,_ATP-binding_protein_1648910..1649140_NEGATIVE 238 131 93 119 79 NC_002967:TDE1394|5end_hypothetical_protein_1433084..1433314_POSITIVE 233 140 92 117 61 NC_002967:TDE0402|5end_hypothetical_protein_454352..454582_NEGATIVE 227 130 85 107 62 NC_002967:TDE2425|5end_50S_ribosomal_protein_L11_2455150..2455380_NEGATIVE 227 133 103 47 11 NC_002967:TDE0589|5end_acetyl-CoA_carboxylase,_carboxyl_transferase,_alpha_subunit_629044..629274_NEGATIVE 226 139 102 101 66 NC_002967:TDE2207|5end_hypothetical_protein_2246634..2246864_NEGATIVE 226 123 86 199 157 NC_002967:TDE1074|5end_oligopeptide/dipeptide_ABC_transporter,_permease_protein_1104555..1104785_POSITIVE 221 110 62 107 45 NC_002967:TDE1168|5end_hypothetical_protein_1199482..1199712_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 286 130 87 52 3 NC_002967:TDE1406|3end_hypothetical_protein_1448677..1448827_NEGATIVE 276 110 62 59 10 NC_002967:TDE0098|3end_hypothetical_protein_114842..114992_NEGATIVE 267 140 91 142 90 NC_002967:TDE1660|3end_leucine_Rich_Repeat_domain_protein_1710710..1710860_NEGATIVE 266 107 62 110 60 NC_002967:TDE2009|3end_hypothetical_protein_2031247..2031397_POSITIVE 264 123 85 104 61 NC_002967:TDE0776|3end_ribosomal_protein_S17_811170..811320_POSITIVE 256 130 81 135 61 NC_002967:TDE2003|3end_internalin-related_protein_2023631..2023781_POSITIVE 241 136 102 126 102 NC_002967:TDE1725|3end_hypothetical_protein_1778393..1778543_NEGATIVE 238 131 93 122 82 NC_002967:TDE1393|3end_hypothetical_protein_1433167..1433317_POSITIVE 237 127 89 110 79 NC_002967:TDE0241|3end_hypothetical_protein_274701..274851_NEGATIVE 224 132 102 88 48 NC_002967:TDE1585|3end_hypothetical_protein_1632932..1633082_NEGATIVE 223 140 107 49 15 NC_002967:TDE2074|3end_radical_SAM_enzyme,_Cfr_family_2101537..2101687_POSITIVE 221 110 62 110 48 NC_002967:TDE1169|3end_phage_DNA-binding_protein,_excisionase_family_1199479..1199629_NEGATIVE 214 111 74 144 107 NC_002967:TDE0041|3end_birA_bifunctional_protein_48635..48785_POSITIVE 213 128 95 131 100 NC_002967:TDE0896|3end_ABC_transporter,_ATP-binding/permease_protein_914193..914343_POSITIVE 213 129 87 72 32 NC_002967:TDE0533|3end_hypothetical_protein_576577..576727_POSITIVE 209 89 48 92 43 NC_002967:TDE2480|3end_heat_shock_protein_90_2503366..2503516_NEGATIVE 209 62 21 129 81 NC_002967:TDE1371|3end_RNB-like_family_protein_1413298..1413448_NEGATIVE 207 139 102 127 77 NC_002967:TDE1070|3end_oligopeptide/dipeptide_ABC_transporter,_permease_protein_1097700..1097850_NEGATIVE 205 136 91 136 90 NC_002967:TDE0593|3end_internalin-related_protein_632041..632191_NEGATIVE 205 130 86 143 102 NC_002967:TDE0014|3end_hypothetical_protein_19487..19637_POSITIVE