Origin IGS: ctcatgaacttaaaacgtggcaaaggtagttattttttattgtaggaaaaaacgcgatggactctgttataacaaggttttatctgcgtccgaaaatctcctgcagtttctcttccaacccacgtccgttgatatcggcatacgccacccgcccatcgggatcgatcagatagacggtcggaatccatgctttaaatacgtttcacta .........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 tagtgaaacgtatttaaagcatggattccgaccgtctatctgatcgatcccgatgggcgggtggcgtatgccgatatcaacggacgtgggttggaagagaaactgcaggagattttcggacgcagataaaaccttgttataacagagtccatcgcgttttttcctacaataaaaaataactacctttgccacgttttaagttcatgag Mask Tandem Repeat Region ================================================ ctcatgaacttaaaacgtggcaaaggtagttattttttattgtaggaaaaaacgcgatggactctgttataacaaggttttatctgcgtccgaaaatctcctgcagtttctcttccaacccacgtccgttgatatcggcatacgccacccgcccatcgggatcgatcagatagacggtcggaatccatgctttaaatacgtttcacta Find is-nt database================================================ Query_seq: TF1242:TF1243|TF1242:TF1243:3-methyl-2-oxobutanoate hydroxymethyltransferase:periplasmic protease:->->:1327175..1327382 208 ctcatgaacttaaaacgtggcaaaggtagttattttttattgtaggaaaaaacgcgatggactctgttataacaaggttttatctgcgtccgaaaatctcctgcagtttctcttccaacccacgtccgttgatatcggcatacgccacccgcccatcgggatcgatcagatagacggtcggaatccatgctttaaatacgtttcacta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF1242:TF1243|TF1242:TF1243:3-methyl-2-oxobutanoate hydroxymethyltransferase:periplasmic protease:->->:1327175..1327382 208 ctcatgaacttaaaacgtggcaaaggtagttattttttattgtaggaaaaaacgcgatggactctgttataacaaggttttatctgcgtccgaaaatctcctgcagtttctcttccaacccacgtccgttgatatcggcatacgccacccgcccatcgggatcgatcagatagacggtcggaatccatgctttaaatacgtttcacta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF1242:TF1243|TF1242:TF1243:3-methyl-2-oxobutanoate hydroxymethyltransferase:periplasmic protease:->->:1327175..1327382 208 ctcatgaacttaaaacgtggcaaaggtagttattttttattgtaggaaaaaacgcgatggactctgttataacaaggttttatctgcgtccgaaaatctcctgcagtttctcttccaacccacgtccgttgatatcggcatacgccacccgcccatcgggatcgatcagatagacggtcggaatccatgctttaaatacgtttcacta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ctcatgaacttaaaacgtggcaaaggtagttattttttattgtaggaaaaaacgcgatggactctgttataacaaggttttatctgcgtccgaaaatctcctgcagtttctcttccaacccacgtccgttgatatcggcatacgccacccgcccatcgggatcgatcagatagacggtcggaatccatgctttaaatacgtttcacta Predict ORF larger than 30AA ================================================ Protein_Len: 44 Strand: + Start: 39 End: 170 ...................................... M V G K N A M D S V I T R F Y L R P K I S C S F S S N P R P L I S A Y A T R P S G S I R ...................................... Protein_Len: 60 Strand: + Start: 17 End: 208 ................ M A K V V I F Y C R K K R D G L C Y N K V L S A S E N L L Q F L F Q P T S V D I G I R H P P I G I D Q I D G R N P C F K Protein_Len: 34 Strand: - Start: 83 End: 184 .................................................................................. R R G F I E Q L K E E L G R G N I D A Y A V R G D P D I L Y V T P M ........................ Protein_Len: 31 Strand: - Start: 70 End: 162 ..................................................................... L L T K D A D S F R R C N R K W G V D T S I P M R W G G M P M .............................................. Protein_Len: 52 Strand: - Start: 33 End: 188 ................................ K K N Y S F V R H V R N Y C P K I Q T R F D G A T E R G V W T R Q Y R C V G G A W R S R D S L R D S D M .................... ctcatgaacttaaaacgtggcaaaggtagttattttttattgtaggaaaaaacgcgatggactctgttataacaaggttttatctgcgtccgaaaatctcctgcagtttctcttccaacccacgtccgttgatatcggcatacgccacccgcccatcgggatcgatcagatagacggtcggaatccatgctttaaatacgtttcacta 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================================================ ctcatgaacttaaaacgtggcaaaggtagttattttttattgtaggaaaaaacgcgatggactctgttataacaaggttttatctgcgtccgaaaatctcctgcagtttctcttccaacccacgtccgttgatatcggcatacgccacccgcccatcgggatcgatcagatagacggtcggaatccatgctttaaatacgtttcacta Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TF1242:TF1243|TF1242:TF1243:3-methyl-2-oxobutanoate hydroxymethyltransferase:periplasmic protease:->->:1327175..1327382 208 ctcatgaacttaaaacgtggcaaaggtagttattttttattgtaggaaaaaacgcgatggactctgttataacaaggttttatctgcgtccgaaaatctcctgcagtttctcttccaacccacgtccgttgatatcggcatacgccacccgcccatcgggatcgatcagatagacggtcggaatccatgctttaaatacgtttcacta Intra-Species Hit: Count: 1 Min: 1 Max: 208 Len: 208 Subject: tfor_TF1242_TF1243|3-methyl-2-oxobutanoate hydroxymethyltransferase:periplasmic protease|POSITIVE:POSITIVE|[1327175,1327382]|208 HSP 1 e-value: 1.0E-114 bit: 412.0 Len: 208 Query Start:1 Query End:208 Subject Strand: POSITIVE Subject Start: 1 Subject End: 208 ctcatgaacttaaaacgtggcaaaggtagttattttttattgtaggaaaaaacgcgatggactctgttataacaaggttttatctgcgtccgaaaatctcctgcagtttctcttccaacccacgtccgttgatatcggcatacgccacccgcccatcgggatcgatcagatagacggtcggaatccatgctttaaatacgtttcacta ctcatgaacttaaaacgtggcaaaggtagttattttttattgtaggaaaaaacgcgatggactctgttataacaaggttttatctgcgtccgaaaatctcctgcagtttctcttccaacccacgtccgttgatatcggcatacgccacccgcccatcgggatcgatcagatagacggtcggaatccatgctttaaatacgtttcacta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CUCAUGAACUUAAAACGUGGCAAAGGUAGUUAUUUUUUAUUGUAGGAAAAAACGCGAUGGACUCUGUUAUAACAAGGUUUUAUCUGCGUCCGAAAAUCUCCUGCAGUUUCUCUUCCAACCCACGUCCGUUGAUAUCGGCAUACGCCACCCGCCCAUCGGGAUCGAUCAGAUAGACGGUCGGAAUCCAUGCUUUAAAUACGUUUCACUA ............(((((((...((((((..........(((((((((....(((((((((((..(((....)))..).)))))).)))).........))))))))).....((((.(((...(((..(((((...(((....))).((((.....))))....)))))...)))))).))))....))))))...)))))))..... (-52.42) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAGUGAAACGUAUUUAAAGCAUGGAUUCCGACCGUCUAUCUGAUCGAUCCCGAUGGGCGGGUGGCGUAUGCCGAUAUCAACGGACGUGGGUUGGAAGAGAAACUGCAGGAGAUUUUCGGACGCAGAUAAAACCUUGUUAUAACAGAGUCCAUCGCGUUUUUUCCUACAAUAAAAAAUAACUACCUUUGCCACGUUUUAAGUUCAUGAG ..((((.....(((((((((.(((.((((..(((((((((.(.......).)))))))))..(((.(((((((.......))).)))).))))))).......((.((((((.....((((((.(((...((.((((....)))).))..))))))))))))))).))....................))).)))))))))))))... (-51.80) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 489 180 136 159 106 tfor:TF2079|5end_permease_2245585..2245815_POSITIVE 451 168 122 188 148 tfor:TF1224|5end_hypothetical_protein_1311203..1311433_POSITIVE 420 170 122 185 138 tfor:TF2781|5end_hypothetical_protein_2965822..2966052_POSITIVE 415 187 145 193 148 tfor:TF2758|5end_hypothetical_protein_2942392..2942622_POSITIVE 405 170 123 90 40 tfor:TF1484|5end_penicillin_binding_protein_1579559..1579789_POSITIVE 404 60 13 153 104 tfor:TF2906|5end_phosphatidylserine_decarboxylase_3102182..3102412_POSITIVE 404 164 123 55 6 tfor:TF2893|5end_conserved_hypothetical_protein;_possible_phosphoesterase_3080766..3080996_POSITIVE 400 190 144 175 122 tfor:TF0719|5end_hypothetical_protein_769798..770028_POSITIVE 398 165 123 228 181 tfor:TF0543|5end_glycine_cleavage_system_p-protein_572251..572481_POSITIVE 397 159 113 199 136 tfor:TF2259|5end_transfer_region-related_protein,_TraK_2429577..2429807_POSITIVE 397 159 115 62 15 tfor:TF1797|5end_SNF_family_transporter_1937136..1937366_POSITIVE 396 170 123 200 151 tfor:TF0606|5end_signal_peptidase_II_636816..637046_POSITIVE 391 169 123 219 162 tfor:TF1925|5end_hypothetical_protein_2074458..2074688_POSITIVE 391 169 123 176 119 tfor:TF1926|5end_hypothetical_protein_2074415..2074645_POSITIVE 390 188 144 65 9 tfor:TF0414|5end_N-ethylammeline_chlorohydrolase_431789..432019_POSITIVE 385 160 112 68 16 tfor:TF2832|5end_possible_proton/sodium:glutamate_symporter_protein_3022660..3022890_POSITIVE 385 189 143 214 156 tfor:TF2265|5end_transfer_region-related_protein,_TraP;_DNA_primase_involved_in_conjugation_2433474..2433704_POSITIVE 384 159 112 195 146 tfor:TF0971|5end_conserved_hypothetical_protein_1021355..1021585_POSITIVE 383 190 144 70 9 tfor:TF0777|5end_1,4-dihydroxy-2-naphthoate_octaprenyltransferase_826098..826328_POSITIVE 380 189 143 231 184 tfor:TF1315|5end_purine_nucleoside_phosphorylase_1390236..1390466_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 440 182 143 130 75 tfor:TF2556|3end_conserved_hypothetical_protein_2737095..2737245_POSITIVE 415 187 145 56 11 tfor:TF2757|3end_hypothetical_protein_2942335..2942485_POSITIVE 404 60 13 95 46 tfor:TF2904|3end_ATP-dependent__helicase,_possible_UvrD/REP_helicase_domain_protein_3102204..3102354_POSITIVE 397 159 115 62 15 tfor:TF1796|3end_ABC_transporter,_ATP-binding_protein_1937216..1937366_POSITIVE 390 188 144 65 9 tfor:TF0413|3end_succinyl-diaminopimelate_desuccinylase_431869..432019_POSITIVE 388 160 111 73 17 tfor:TF2340|3end_hypothetical_protein_2500915..2501065_POSITIVE 383 190 144 65 4 tfor:TF0776|3end_ABC_transporter,_permease_component_826173..826323_POSITIVE 378 185 143 63 11 tfor:TF1426|3end_N-acetylymuramoylalanyl-D-glutamate-2,6-diaminopi_melate_ligase_1511413..1511563_POSITIVE 377 164 123 57 1 tfor:TF2428|3end_conserved_hypothetical_protein_2610525..2610675_POSITIVE 377 179 131 87 23 tfor:TF0022|3end_two-component_system_sensor_histidine_kinase_19522..19672_POSITIVE 376 159 112 81 36 tfor:TF1326|3end_hypothetical_protein_1404100..1404250_POSITIVE 375 159 111 125 80 tfor:TF2660|3end_hypothetical_protein_2833540..2833690_POSITIVE 375 186 142 51 4 tfor:TF2124|3end_conserved_hypothetical_protein;_possible_TonB_dependent_receptor_2302191..2302341_POSITIVE 373 160 128 136 103 tfor:TF1349|3end_conserved_hypothetical_protein;_possible_prophage_maintanence_or_virulance_related_1429685..1429835_POSITIVE 371 176 134 123 72 tfor:TF3159|3end_conserved_hypothetical_protein;_possible_transcriptional_regulator_3395611..3395761_POSITIVE 358 150 103 150 96 tfor:TF2257|3end_transfer_region-related_protein,_TraJ_2429622..2429772_POSITIVE 356 180 132 100 42 tfor:TF0982|3end_conserved_hypothetical_protein_1039474..1039624_POSITIVE 355 180 131 111 64 tfor:TF1775|3end_oxidoreductase,_Gfo/Idh/MocA_family_1914618..1914768_POSITIVE 355 179 135 72 18 tfor:TF0212|3end_DNA/pantothenate_metabolism_flavoprotein_239001..239151_POSITIVE 354 190 143 151 92 tfor:TF0833|3end_conserved_hypothetical_protein_889052..889202_POSITIVE