Origin IGS: taattattgctgaaaaactcgttgaatataagtctttaaaagactaattcaaataatcttatcgccaaatctattagttcccaagtacttttcaaaaacataatctatagttacatctttttcaaaataatgacgtagcatttttactctttcttcatagggtattcctccgatatcagtccattttctagggaaacctaattcttcttcaatatcatcgaatgatttcccgcctgctgtgatgatatatacaaaatattctacaggatcaatgatgtggccaaaggttttaaagcaatcactaataagcta .........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.........1.........2.........3.........4.........5.........6.........7.........8.........9 tagcttattagtgattgctttaaaacctttggccacatcattgatcctgtagaatattttgtatatatcatcacagcaggcgggaaatcattcgatgatattgaagaagaattaggtttccctagaaaatggactgatatcggaggaataccctatgaagaaagagtaaaaatgctacgtcattattttgaaaaagatgtaactatagattatgtttttgaaaagtacttgggaactaatagatttggcgataagattatttgaattagtcttttaaagacttatattcaacgagtttttcagcaataatta Mask Tandem Repeat Region ================================================ taattattgctgaaaaactcgttgaatataagtctttaaaagactaattcaaataatcttatcgccaaatctattagttcccaagtacttttcaaaaacataatctatagttacatctttttcaaaataatgacgtagcatttttactctttcttcatagggtattcctccgatatcagtccattttctagggaaacctaattcttcttcaatatcatcgaatgatttcccgcctgctgtgatgatatatacaaaatattctacaggatcaatgatgtggccaaaggttttaaagcaatcactaataagcta Find is-nt database================================================ Query_seq: TF1640:TF1641|TF1640:TF1641:DNA mismatch endonuclease vsr:hypothetical protein:->->:1748653..1748964 312 taattattgctgaaaaactcgttgaatataagtctttaaaagactaattcaaataatcttatcgccaaatctattagttcccaagtacttttcaaaaacataatctatagttacatctttttcaaaataatgacgtagcatttttactctttcttcatagggtattcctccgatatcagtccattttctagggaaacctaattcttcttcaatatcatcgaatgatttcccgcctgctgtgatgatatatacaaaatattctacaggatcaatgatgtggccaaaggttttaaagcaatcactaataagcta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF1640:TF1641|TF1640:TF1641:DNA mismatch endonuclease vsr:hypothetical protein:->->:1748653..1748964 312 taattattgctgaaaaactcgttgaatataagtctttaaaagactaattcaaataatcttatcgccaaatctattagttcccaagtacttttcaaaaacataatctatagttacatctttttcaaaataatgacgtagcatttttactctttcttcatagggtattcctccgatatcagtccattttctagggaaacctaattcttcttcaatatcatcgaatgatttcccgcctgctgtgatgatatatacaaaatattctacaggatcaatgatgtggccaaaggttttaaagcaatcactaataagcta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF1640:TF1641|TF1640:TF1641:DNA mismatch endonuclease vsr:hypothetical protein:->->:1748653..1748964 312 taattattgctgaaaaactcgttgaatataagtctttaaaagactaattcaaataatcttatcgccaaatctattagttcccaagtacttttcaaaaacataatctatagttacatctttttcaaaataatgacgtagcatttttactctttcttcatagggtattcctccgatatcagtccattttctagggaaacctaattcttcttcaatatcatcgaatgatttcccgcctgctgtgatgatatatacaaaatattctacaggatcaatgatgtggccaaaggttttaaagcaatcactaataagcta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 taattattgctgaaaaactcgttgaatataagtctttaaaagactaattcaaataatcttatcgccaaatctattagttcccaagtacttttcaaaaacataatctatagttacatctttttcaaaataatgacgtagcatttttactctttcttcatagggtattcctccgatatcagtccattttctagggaaacctaattcttcttcaatatcatcgaatgatttcccgcctgctgtgatgatatatacaaaatattctacaggatcaatgatgtggccaaaggttttaaagcaatcactaataagcta Predict ORF larger than 30AA ================================================ Protein_Len: 49 Strand: + Start: 164 End: 310 ................................................................................................................................................................... M P P I S V H F L G K P N S S S I S S N D F P P A V M I Y T K Y S T G S M M W P K V L K Q S L I S .. Protein_Len: 60 Strand: - Start: 52 End: 306 ................................................... Y H R L M K V R E E Y P I G G I D T W K R P F G L E E E I D D F S K G G A T I I Y V F Y E V P D I I H G F T K F C D S M ...... taattattgctgaaaaactcgttgaatataagtctttaaaagactaattcaaataatcttatcgccaaatctattagttcccaagtacttttcaaaaacataatctatagttacatctttttcaaaataatgacgtagcatttttactctttcttcatagggtattcctccgatatcagtccattttctagggaaacctaattcttcttcaatatcatcgaatgatttcccgcctgctgtgatgatatatacaaaatattctacaggatcaatgatgtggccaaaggttttaaagcaatcactaataagcta 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: 97 End: 126 ................................................................................................TTTGAAAAAGATGTAACTATAGATTATGTT.......................................................................................................................................................................................... PromScan Matrix: RpoD-17 Strand: - Score: 81 Start: 56 End: 85 .......................................................CTTGGGAACTAATAGATTTGGCGATAAGAT................................................................................................................................................................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ taattattgctgaaaaactcgttgaatataagtctttaaaagactaattcaaataatcttatcgccaaatctattagttcccaagtacttttcaaaaacataatctatagttacatctttttcaaaataatgacgtagcatttttactctttcttcatagggtattcctccgatatcagtccattttctagggaaacctaattcttcttcaatatcatcgaatgatttcccgcctgctgtgatgatatatacaaaatattctacaggatcaatgatgtggccaaaggttttaaagcaatcactaataagcta Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TF1640:TF1641|TF1640:TF1641:DNA mismatch endonuclease vsr:hypothetical protein:->->:1748653..1748964 312 taattattgctgaaaaactcgttgaatataagtctttaaaagactaattcaaataatcttatcgccaaatctattagttcccaagtacttttcaaaaacataatctatagttacatctttttcaaaataatgacgtagcatttttactctttcttcatagggtattcctccgatatcagtccattttctagggaaacctaattcttcttcaatatcatcgaatgatttcccgcctgctgtgatgatatatacaaaatattctacaggatcaatgatgtggccaaaggttttaaagcaatcactaataagcta Intra-Species Hit: Count: 1 Min: 1 Max: 312 Len: 312 Subject: tfor_TF1640_TF1641|DNA mismatch endonuclease vsr:hypothetical protein|POSITIVE:POSITIVE|[1748653,1748964]|312 HSP 1 e-value: 1.0E-176 bit: 618.0 Len: 312 Query Start:1 Query End:312 Subject Strand: POSITIVE Subject Start: 1 Subject End: 312 taattattgctgaaaaactcgttgaatataagtctttaaaagactaattcaaataatcttatcgccaaatctattagttcccaagtacttttcaaaaacataatctatagttacatctttttcaaaataatgacgtagcatttttactctttcttcatagggtattcctccgatatcagtccattttctagggaaacctaattcttcttcaatatcatcgaatgatttcccgcctgctgtgatgatatatacaaaatattctacaggatcaatgatgtggccaaaggttttaaagcaatcactaataagcta taattattgctgaaaaactcgttgaatataagtctttaaaagactaattcaaataatcttatcgccaaatctattagttcccaagtacttttcaaaaacataatctatagttacatctttttcaaaataatgacgtagcatttttactctttcttcatagggtattcctccgatatcagtccattttctagggaaacctaattcttcttcaatatcatcgaatgatttcccgcctgctgtgatgatatatacaaaatattctacaggatcaatgatgtggccaaaggttttaaagcaatcactaataagcta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAUUAUUGCUGAAAAACUCGUUGAAUAUAAGUCUUUAAAAGACUAAUUCAAAUAAUCUUAUCGCCAAAUCUAUUAGUUCCCAAGUACUUUUCAAAAACAUAAUCUAUAGUUACAUCUUUUUCAAAAUAAUGACGUAGCAUUUUUACUCUUUCUUCAUAGGGUAUUCCUCCGAUAUCAGUCCAUUUUCUAGGGAAACCUAAUUCUUCUUCAAUAUCAUCGAAUGAUUUCCCGCCUGCUGUGAUGAUAUAUACAAAAUAUUCUACAGGAUCAAUGAUGUGGCCAAAGGUUUUAAAGCAAUCACUAAUAAGCUA .....((((((..((((((..((((((...(((((.....))))).))))))...........((((.(((.(((.(.(((............................(((((.((..............)).)))))..................(((((((((......((((((...(((......((((((....((((...............))))..)))))).......))).))))))......)))))))))..))).))))))).))))....))))))..))))))............. (-54.42) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAGCUUAUUAGUGAUUGCUUUAAAACCUUUGGCCACAUCAUUGAUCCUGUAGAAUAUUUUGUAUAUAUCAUCACAGCAGGCGGGAAAUCAUUCGAUGAUAUUGAAGAAGAAUUAGGUUUCCCUAGAAAAUGGACUGAUAUCGGAGGAAUACCCUAUGAAGAAAGAGUAAAAAUGCUACGUCAUUAUUUUGAAAAAGAUGUAACUAUAGAUUAUGUUUUUGAAAAGUACUUGGGAACUAAUAGAUUUGGCGAUAAGAUUAUUUGAAUUAGUCUUUUAAAGACUUAUAUUCAACGAGUUUUUCAGCAAUAAUUA ........((((.((((((..(((((.....((((.(((..(((((.(((((..((((((....((((((((.((......((((((((((((...............))))..)))))))).......)))).))))))....)))))).........((...((((....))))...))..((((((....))))))...)))))))))).(((((..(.......)..))))).....))).))))...........((((((.(((((.....)))))...))))))...)))))..)))))).)))) (-63.88) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 311 244 216 37 10 tfor:TF2527|5end_RNA_polymerase_ECF-type_sigma_factor_2710097..2710327_POSITIVE 288 241 217 136 105 tfor:TF1623|5end_5-formyltetrahydrofolate_cyclo-ligase_1736698..1736928_POSITIVE 288 244 212 78 48 tfor:TF0024|5end_conserved_hypothetical_protein;_possible_ATPase_20191..20421_POSITIVE 286 200 159 191 147 tfor:TF0238|5end_outer_membrane_protein_266871..267101_POSITIVE 278 180 138 60 15 tfor:TF3052|5end_conserved_hypothetical_protein_3278323..3278553_POSITIVE 278 171 134 211 177 tfor:TF2344|5end_ATP/GTP_binding_protein_2507422..2507652_POSITIVE 278 189 148 66 36 tfor:TF1856|5end_conserved_hypothetical_protein_2009969..2010199_POSITIVE 276 220 171 193 147 tfor:TF2583|5end_possible_ABC_transporter,__permease_component_2750206..2750436_POSITIVE 271 242 212 47 15 tfor:TF0461|5end_ATP:cob(I)alamin_adenosyltransferase_476990..477220_POSITIVE 269 242 204 130 97 tfor:TF2039|5end_possible_cell-cycle_regulation_histidine_triad_(HIT)_protein_2199318..2199548_POSITIVE 269 279 231 98 38 tfor:TF1649|5end_hypothetical_protein_1759638..1759868_POSITIVE 269 241 209 50 18 tfor:TF0389|5end_conserved_hypothetical_protein;_possible_integral_membrane_protein_408774..409004_POSITIVE 262 240 191 213 168 tfor:TF2951|5end_O-succinylbenzoic_acid--CoA_ligase_3158496..3158726_POSITIVE 262 209 169 51 8 tfor:TF2501|5end_DNA_mismatch_repair_protein_2676280..2676510_POSITIVE 261 172 132 49 9 tfor:TF2566|5end_50S_ribosomal_protein_L5_2740303..2740533_POSITIVE 260 246 213 199 158 tfor:TF1315|5end_purine_nucleoside_phosphorylase_1390236..1390466_POSITIVE 258 199 153 60 14 tfor:TF2599|5end_alpha-amylase_family_protein_2771883..2772113_POSITIVE 256 193 161 127 94 tfor:TF2230|5end_CTn_excision_protein_2399799..2400029_POSITIVE 256 229 182 147 89 tfor:TF1787|5end_conserved_hypothetical_protein_1926377..1926607_POSITIVE 255 199 158 165 126 tfor:TF0837|5end_possible_transposase_fragment_889820..890050_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 288 241 217 121 90 tfor:TF1622|3end_conserved_hypothetical_protein_1736763..1736913_POSITIVE 288 244 212 40 10 tfor:TF0023|3end_possible_response_element_in_two_component_regulation_20233..20383_POSITIVE 271 242 212 47 15 tfor:TF0460|3end_hypothetical_protein_477070..477220_POSITIVE 269 241 209 42 10 tfor:TF0388|3end_conserved_hypothetical_protein;_possible_integral_membrane_protein_408846..408996_POSITIVE 261 172 132 49 9 tfor:TF2565|3end_50S_ribosomal_protein_L24_2740383..2740533_POSITIVE 258 199 153 48 2 tfor:TF2598|3end_conserved_hypothetical_protein_2771951..2772101_POSITIVE 256 229 182 115 57 tfor:TF1786|3end_hypothetical_protein_1926425..1926575_POSITIVE 253 196 151 61 17 tfor:TF2305|3end_S-adenosylmethionine:tRNA_ribosyltransferase-isomerase_2462693..2462843_POSITIVE 253 182 142 96 52 tfor:TF1951|3end_xanthosine_triphosphate_pyrophosphatase,_Ham1-like_protein_2101447..2101597_POSITIVE 247 277 231 73 30 tfor:TF2425|3end_hypothetical_protein_2603530..2603680_POSITIVE 246 177 131 94 38 tfor:TF2654|3end_arginyl-tRNA_synthetase_2824559..2824709_POSITIVE 245 198 151 111 65 tfor:TF0975|3end_hypothetical_protein_1024361..1024511_POSITIVE 243 245 204 114 75 tfor:TF1254|3end_conserved_hypothetical_protein;_possible_transcriptional_regulator_1336705..1336855_POSITIVE 243 172 147 110 86 tfor:TF0533|3end_hypothetical_protein_559519..559669_POSITIVE 242 243 204 96 58 tfor:TF2600|3end_ribose-phosphate_pyrophosphokinase_2774709..2774859_POSITIVE 242 188 154 127 95 tfor:TF0948|3end_50S_ribosomal_protein_L34_993918..994068_POSITIVE 241 246 201 138 90 tfor:TF3115|3end_possible_sugar_kinase_3352025..3352175_POSITIVE 240 192 152 59 25 tfor:TF3118|3end_conserved_hypothetical_protein_3352824..3352974_POSITIVE 239 193 153 39 1 tfor:TF1847|3end_hypothetical_protein_1997666..1997816_POSITIVE 238 200 152 65 11 tfor:TF2985|3end_glycosyltransferase_protein_3201646..3201796_POSITIVE