Origin IGS: cgcattatagtatagcacattacgtcaaaatatcaagtttctttttcctttttttacaaatatatcaaattttttatcaaaattcttgcctttatcaaagaatattattaaaaaaaataagaatttgcttgtaaaatacggatttttacagtactttatatgt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 acatataaagtactgtaaaaatccgtattttacaagcaaattcttattttttttaataatattctttgataaaggcaagaattttgataaaaaatttgatatatttgtaaaaaaaggaaaaagaaacttgatattttgacgtaatgtgctatactataatgcg Mask Tandem Repeat Region ================================================ cgcattatagtatagcacattacgtcaaaatatcaagtttctttttcctttttttacaaatatatcaaattttttatcaaaattcttgcctttatcaaagaatattattaaaaaaaataagaatttgcttgtaaaatacggatttttacagtactttatatgt Find is-nt database================================================ Query_seq: TDE2122:TDE2123|TDE2122:TDE2123:DHH superfamily protein:hypothetical protein:<-->:2156001..2156163 163 cgcattatagtatagcacattacgtcaaaatatcaagtttctttttcctttttttacaaatatatcaaattttttatcaaaattcttgcctttatcaaagaatattattaaaaaaaataagaatttgcttgtaaaatacggatttttacagtactttatatgt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE2122:TDE2123|TDE2122:TDE2123:DHH superfamily protein:hypothetical protein:<-->:2156001..2156163 163 cgcattatagtatagcacattacgtcaaaatatcaagtttctttttcctttttttacaaatatatcaaattttttatcaaaattcttgcctttatcaaagaatattattaaaaaaaataagaatttgcttgtaaaatacggatttttacagtactttatatgt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE2122:TDE2123|TDE2122:TDE2123:DHH superfamily protein:hypothetical protein:<-->:2156001..2156163 163 cgcattatagtatagcacattacgtcaaaatatcaagtttctttttcctttttttacaaatatatcaaattttttatcaaaattcttgcctttatcaaagaatattattaaaaaaaataagaatttgcttgtaaaatacggatttttacagtactttatatgt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 cgcattatagtatagcacattacgtcaaaatatcaagtttctttttcctttttttacaaatatatcaaattttttatcaaaattcttgcctttatcaaagaatattattaaaaaaaataagaatttgcttgtaaaatacggatttttacagtactttatatgt Predict ORF larger than 30AA ================================================ Protein_Len: 30 Strand: + Start: 19 End: 108 .................. M T S K Y Q V S F S F F Y K Y I K F F I K I L A F I K E Y Y ....................................................... Protein_Len: 40 Strand: + Start: 12 End: 131 ........... M A H Y V K I S S F F F L F L Q I Y Q I F Y Q N S C L Y Q R I L L K K I R I C L ................................ Protein_Len: 44 Strand: + Start: 32 End: 163 ............................... M K F L F P F F T N I S N F L S K F L P L S K N I I K K N K N L L V K Y G F L Q Y F I C Protein_Len: 44 Strand: - Start: 28 End: 159 ........................... F I L N R K G K K V F I D F K K D F N K G K D F F I I L F F L F K S T F Y P N K C Y K M .... cgcattatagtatagcacattacgtcaaaatatcaagtttctttttcctttttttacaaatatatcaaattttttatcaaaattcttgcctttatcaaagaatattattaaaaaaaataagaatttgcttgtaaaatacggatttttacagtactttatatgt 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: 81 Start: 107 End: 136 ..........................................................................................................TTTTACAAGCAAATTCTTATTTTTTTTAAT........................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ cgcattatagtatagcacattacgtcaaaatatcaagtttctttttcctttttttacaaatatatcaaattttttatcaaaattcttgcctttatcaaagaatattattaaaaaaaataagaatttgcttgtaaaatacggatttttacagtactttatatgt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE2122:TDE2123|TDE2122:TDE2123:DHH superfamily protein:hypothetical protein:<-->:2156001..2156163 163 cgcattatagtatagcacattacgtcaaaatatcaagtttctttttcctttttttacaaatatatcaaattttttatcaaaattcttgcctttatcaaagaatattattaaaaaaaataagaatttgcttgtaaaatacggatttttacagtactttatatgt Intra-Species Hit: Count: 1 Min: 1 Max: 163 Len: 163 Subject: NC_002967_TDE2122_TDE2123|DHH superfamily protein:hypothetical protein|NEGATIVE:POSITIVE|[2156001,2156163]|163 HSP 1 e-value: 1.0E-40 bit: 167.0 Len: 108 Query Start:56 Query End:163 Subject Strand: POSITIVE Subject Start: 56 Subject End: 163 .......................................................acaaatatatcaaattttttatcaaaattcttgcctttatcaaagaatattattnnnnnnnntaagaatttgcttgtaaaatacggatttttacagtactttatatgt .......................................................acaaatatatcaaattttttatcaaaattcttgcctttatcaaagaatattattaaaaaaaataagaatttgcttgtaaaatacggatttttacagtactttatatgt HSP 2 e-value: 6.0E-15 bit: 81.8 Len: 41 Query Start:1 Query End:41 Subject Strand: POSITIVE Subject Start: 1 Subject End: 41 cgcattatagtatagcacattacgtcaaaatatcaagtttc.......................................................................................................................... cgcattatagtatagcacattacgtcaaaatatcaagtttc.......................................................................................................................... Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CGCAUUAUAGUAUAGCACAUUACGUCAAAAUAUCAAGUUUCUUUUUCCUUUUUUUACAAAUAUAUCAAAUUUUUUAUCAAAAUUCUUGCCUUUAUCAAAGAAUAUUAUUAAAAAAAAUAAGAAUUUGCUUGUAAAAUACGGAUUUUUACAGUACUUUAUAUGU .((((...(((((.(.((.....)))...................(((...((((((((.((..((...(((((((..((.((((((..........)))))).))..))))))).....))...)).))))))))...)))........)))))....)))) (-17.60) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ ACAUAUAAAGUACUGUAAAAAUCCGUAUUUUACAAGCAAAUUCUUAUUUUUUUUAAUAAUAUUCUUUGAUAAAGGCAAGAAUUUUGAUAAAAAAUUUGAUAUAUUUGUAAAAAAAGGAAAAAGAAACUUGAUAUUUUGACGUAAUGUGCUAUACUAUAAUGCG ........(((((........(((...(((((((((.....((..(((((((((((....((((((.(.......))))))).)))).)))))))..))....)))))))))...))).......(((..(....)..).))...)))))............. (-21.00) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 762 50 1 141 92 NC_002967:TDE2122|5end_DHH_superfamily_protein_2155910..2156140_NEGATIVE 250 67 21 231 187 NC_002967:TDE2022|5end_YD_repeat_protein_2049222..2049452_NEGATIVE 223 49 4 197 147 NC_002967:TDE2637|5end_hypothetical_protein_2677316..2677546_NEGATIVE 219 130 88 79 45 NC_002967:TDE0993|5end_lipoprotein,_putative_1020415..1020645_NEGATIVE 209 47 2 84 39 NC_002967:TDE1023|5end_methylaspartate_mutase_subunit_S_1055123..1055353_POSITIVE 208 59 14 197 157 NC_002967:TDE2024|5end_hypothetical_protein_2051021..2051251_NEGATIVE 207 54 16 193 156 NC_002967:TDE1306|5end_hypothetical_protein_1340874..1341104_NEGATIVE 207 155 117 158 109 NC_002967:TDE0437|5end_PBS_lyase_HEAT-like_repeat_domain_protein_493605..493835_NEGATIVE 206 90 41 49 4 NC_002967:TDE0474|5end_hypothetical_protein_530740..530970_POSITIVE 205 74 33 128 88 NC_002967:TDE2585|5end_methyl-accepting_chemotaxis_domain/unknown_domain_protein_2620303..2620533_NEGATIVE 203 128 82 156 109 NC_002967:TDE2084|5end_RNA_methyltransferase,_TrmH_family_2113394..2113624_POSITIVE 200 80 33 108 63 NC_002967:TDE2668|5end_serine_hydroxymethyltransferase_2706066..2706296_NEGATIVE 195 49 2 51 7 NC_002967:TDE1107|5end_transcription_elongation_factor_NusA_1142377..1142607_NEGATIVE 193 130 81 131 85 NC_002967:TDE2723|5end_phosphoribosylpyrophosphate_synthetase_2782127..2782357_NEGATIVE 193 156 124 115 81 NC_002967:TDE1922|5end_hypothetical_protein_1941485..1941715_NEGATIVE 190 96 51 67 13 NC_002967:TDE0132|5end_hypothetical_protein_152046..152276_POSITIVE 189 146 107 68 20 NC_002967:TDE2264|5end_ABC_transporter,_ATP-binding/permease_protein_2302033..2302263_NEGATIVE 188 75 33 130 88 NC_002967:TDE1342|5end_hypothetical_protein_1378442..1378672_POSITIVE 188 153 112 170 135 NC_002967:TDE1059|5end_hypothetical_protein_1086605..1086835_NEGATIVE 187 43 1 217 179 NC_002967:TDE0586|5end_hypothetical_protein_625246..625476_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 208 59 14 143 103 NC_002967:TDE2025|3end_hypothetical_protein_2051075..2051225_NEGATIVE 207 155 117 91 42 NC_002967:TDE0438|3end_queuine_tRNA-ribosyltransferase_493672..493822_NEGATIVE 200 52 23 85 59 NC_002967:TDE2420|3end_DNA-directed_RNA_polymerase_beta'_subunit_2444960..2445110_NEGATIVE 193 156 124 87 53 NC_002967:TDE1923|3end_hypothetical_protein_1941513..1941663_NEGATIVE 188 75 33 133 91 NC_002967:TDE1341|3end_hypothetical_protein_1378525..1378675_POSITIVE 188 93 62 32 4 NC_002967:TDE0473|3end_heavy_metal_translocating_P-type_ATPase_530800..530950_POSITIVE 186 66 26 116 76 NC_002967:TDE1201|3end_cell_cycle_protein,_FtsW/RodA/SpoVE_family_1234262..1234412_POSITIVE 184 70 24 130 84 NC_002967:TDE1594|3end_pyridine_nucleotide-disulphide_oxidoreductase_family_protein_1642993..1643143_NEGATIVE 183 52 11 92 47 NC_002967:TDE2241|3end_glycosyl_transferase,_group_2_family_protein_2278506..2278656_NEGATIVE 183 41 12 99 77 NC_002967:TDE1568|3end_hypothetical_protein_1619827..1619977_POSITIVE 178 49 1 103 57 NC_002967:TDE1329|3end_ATPase,_AAA_family_1365346..1365496_POSITIVE 177 158 112 68 23 NC_002967:TDE1727|3end_hypothetical_protein_1780774..1780924_NEGATIVE 176 50 9 72 13 NC_002967:TDE1597|3end_transporter,_putative_1646695..1646845_NEGATIVE 174 69 24 68 12 NC_002967:TDE1111|3end_transporter,_putative_1146939..1147089_POSITIVE 173 50 5 145 91 NC_002967:TDE1823|3end_hypothetical_protein_1856601..1856751_NEGATIVE 169 151 129 86 62 NC_002967:TDE2591|3end_rhodanese-like_domain_protein_2627009..2627159_POSITIVE 168 32 2 42 17 NC_002967:TDE2397|3end_hypothetical_protein_2425433..2425583_NEGATIVE 168 42 2 91 51 NC_002967:TDE1743|3end_chromate_transport_protein_1797940..1798090_NEGATIVE 167 108 70 85 47 NC_002967:TDE1608|3end_hypothetical_protein_1658369..1658519_POSITIVE 165 55 30 108 81 NC_002967:TDE1169|3end_phage_DNA-binding_protein,_excisionase_family_1199479..1199629_NEGATIVE