Origin IGS: gattgttttattttagaagtggcaaagatagggatttttggctgttttgcgtaatttttgtgagaattattcgaccagaatgttttcaaaacacgtaatcctccgcacagtcgacattacagagttttttccatatagtctgctttctcaaatgcgcttttgagcgtaacccacttttttctcgtgctgcttccggtcgtcttttaagggggataagccgactgacgaccctta .........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 taagggtcgtcagtcggcttatcccccttaaaagacgaccggaagcagcacgagaaaaaagtgggttacgctcaaaagcgcatttgagaaagcagactatatggaaaaaactctgtaatgtcgactgtgcggaggattacgtgttttgaaaacattctggtcgaataattctcacaaaaattacgcaaaacagccaaaaatccctatctttgccacttctaaaataaaacaatc Mask Tandem Repeat Region ================================================ gattgttttattttagaagtggcaaagatagggatttttggctgttttgcgtaatttttgtgagaattattcgaccagaatgttttcaaaacacgtaatcctccgcacagtcgacattacagagttttttccatatagtctgctttctcaaatgcgcttttgagcgtaacccacttttttctcgtgctgcttccggtcgtcttttaagggggataagccgactgacgaccctta Find is-nt database================================================ Query_seq: TF0434:TF0435|TF0434:TF0435:CTP synthetase (UTP ammonia ligase):DNA mismatch repair protein:->->:457088..457321 234 gattgttttattttagaagtggcaaagatagggatttttggctgttttgcgtaatttttgtgagaattattcgaccagaatgttttcaaaacacgtaatcctccgcacagtcgacattacagagttttttccatatagtctgctttctcaaatgcgcttttgagcgtaacccacttttttctcgtgctgcttccggtcgtcttttaagggggataagccgactgacgaccctta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF0434:TF0435|TF0434:TF0435:CTP synthetase (UTP ammonia ligase):DNA mismatch repair protein:->->:457088..457321 234 gattgttttattttagaagtggcaaagatagggatttttggctgttttgcgtaatttttgtgagaattattcgaccagaatgttttcaaaacacgtaatcctccgcacagtcgacattacagagttttttccatatagtctgctttctcaaatgcgcttttgagcgtaacccacttttttctcgtgctgcttccggtcgtcttttaagggggataagccgactgacgaccctta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF0434:TF0435|TF0434:TF0435:CTP synthetase (UTP ammonia ligase):DNA mismatch repair protein:->->:457088..457321 234 gattgttttattttagaagtggcaaagatagggatttttggctgttttgcgtaatttttgtgagaattattcgaccagaatgttttcaaaacacgtaatcctccgcacagtcgacattacagagttttttccatatagtctgctttctcaaatgcgcttttgagcgtaacccacttttttctcgtgctgcttccggtcgtcttttaagggggataagccgactgacgaccctta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gattgttttattttagaagtggcaaagatagggatttttggctgttttgcgtaatttttgtgagaattattcgaccagaatgttttcaaaacacgtaatcctccgcacagtcgacattacagagttttttccatatagtctgctttctcaaatgcgcttttgagcgtaacccacttttttctcgtgctgcttccggtcgtcttttaagggggataagccgactgacgaccctta Predict ORF larger than 30AA ================================================ Protein_Len: 31 Strand: + Start: 3 End: 95 .. M F Y F R S G K D R D F W L F C V I F V R I I R P E C F Q N T ........................................................................................................................................... Protein_Len: 41 Strand: + Start: 38 End: 160 ..................................... M A V L R N F C E N Y S T R M F S K H V I L R T V D I T E F F P Y S L L S Q M R F .......................................................................... Protein_Len: 33 Strand: + Start: 135 End: 233 ...................................................................................................................................... M V C F L K C A F E R N P L F S R A A S G R L L R G I S R L T T L . Protein_Len: 42 Strand: - Start: 89 End: 214 ........................................................................................ F V Y D E A C D V N C L K K W I T Q K R L H A K S R L G S K E R A A E P R R K L P M .................... Protein_Len: 36 Strand: - Start: 3 End: 110 .. Q K I K S T A F I P I K P Q K A Y N K H S N N S W F T K L V R L G G C M ............................................................................................................................ gattgttttattttagaagtggcaaagatagggatttttggctgttttgcgtaatttttgtgagaattattcgaccagaatgttttcaaaacacgtaatcctccgcacagtcgacattacagagttttttccatatagtctgctttctcaaatgcgcttttgagcgtaacccacttttttctcgtgctgcttccggtcgtcttttaagggggataagccgactgacgaccctta 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: 82 Start: 110 End: 139 .............................................................................................................GTCGACATTACAGAGTTTTTTCCATATAGT............................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ gattgttttattttagaagtggcaaagatagggatttttggctgttttgcgtaatttttgtgagaattattcgaccagaatgttttcaaaacacgtaatcctccgcacagtcgacattacagagttttttccatatagtctgctttctcaaatgcgcttttgagcgtaacccacttttttctcgtgctgcttccggtcgtcttttaagggggataagccgactgacgaccctta Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TF0434:TF0435|TF0434:TF0435:CTP synthetase (UTP ammonia ligase):DNA mismatch repair protein:->->:457088..457321 234 gattgttttattttagaagtggcaaagatagggatttttggctgttttgcgtaatttttgtgagaattattcgaccagaatgttttcaaaacacgtaatcctccgcacagtcgacattacagagttttttccatatagtctgctttctcaaatgcgcttttgagcgtaacccacttttttctcgtgctgcttccggtcgtcttttaagggggataagccgactgacgaccctta Intra-Species Hit: Count: 1 Min: 1 Max: 234 Len: 234 Subject: tfor_TF0434_TF0435|CTP synthetase (UTP ammonia ligase):DNA mismatch repair protein|POSITIVE:POSITIVE|[457088,457321]|234 HSP 1 e-value: 1.0E-130 bit: 464.0 Len: 234 Query Start:1 Query End:234 Subject Strand: POSITIVE Subject Start: 1 Subject End: 234 gattgttttattttagaagtggcaaagatagggatttttggctgttttgcgtaatttttgtgagaattattcgaccagaatgttttcaaaacacgtaatcctccgcacagtcgacattacagagttttttccatatagtctgctttctcaaatgcgcttttgagcgtaacccacttttttctcgtgctgcttccggtcgtcttttaagggggataagccgactgacgaccctta gattgttttattttagaagtggcaaagatagggatttttggctgttttgcgtaatttttgtgagaattattcgaccagaatgttttcaaaacacgtaatcctccgcacagtcgacattacagagttttttccatatagtctgctttctcaaatgcgcttttgagcgtaacccacttttttctcgtgctgcttccggtcgtcttttaagggggataagccgactgacgaccctta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAUUGUUUUAUUUUAGAAGUGGCAAAGAUAGGGAUUUUUGGCUGUUUUGCGUAAUUUUUGUGAGAAUUAUUCGACCAGAAUGUUUUCAAAACACGUAAUCCUCCGCACAGUCGACAUUACAGAGUUUUUUCCAUAUAGUCUGCUUUCUCAAAUGCGCUUUUGAGCGUAACCCACUUUUUUCUCGUGCUGCUUCCGGUCGUCUUUUAAGGGGGAUAAGCCGACUGACGACCCUUA ...............((((..(((.(((..((((...((((((((.((((((........(((((((.((((.....)))))))))))....))))))........)))))))).....((((.(...........).))))...))))...((((((....))))))...........)))..)))..)))).(((((((.....((..((.....))..))))))))).... (-57.30) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAGGGUCGUCAGUCGGCUUAUCCCCCUUAAAAGACGACCGGAAGCAGCACGAGAAAAAAGUGGGUUACGCUCAAAAGCGCAUUUGAGAAAGCAGACUAUAUGGAAAAAACUCUGUAAUGUCGACUGUGCGGAGGAUUACGUGUUUUGAAAACAUUCUGGUCGAAUAAUUCUCACAAAAAUUACGCAAAACAGCCAAAAAUCCCUAUCUUUGCCACUUCUAAAAUAAAACAAUC ....(((((((((..((.....))..)).....))))))).((((..(((.((((....((.(((((..(((.....(((((.((((.(..(((((...............)))))..).)))).))))).((((((((..((....(((....)))....))..))))))))..................)))....))))))).)))))))..))))............... (-51.06) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 504 229 182 98 45 tfor:TF1469|5end_2-methylthioadenine_synthetase_1561293..1561523_POSITIVE 386 230 184 160 118 tfor:TF0206|5end_conserved_hypothetical_protein_232218..232448_POSITIVE 385 228 181 226 178 tfor:TF1848|5end_conserved_hypothetical_protein_1997589..1997819_POSITIVE 384 220 174 85 42 tfor:TF0886|5end_conjugative_transposon_protein_fragment_937914..938144_POSITIVE 369 205 178 36 2 tfor:TF1174|5end_ABC_transporter,_permease_component_1256584..1256814_POSITIVE 368 230 183 152 95 tfor:TF1599|5end_ribonuclease_P_protein_component_1713564..1713794_POSITIVE 363 205 166 96 55 tfor:TF2979|5end_possible_outer_membrane__protein_3190778..3191008_POSITIVE 363 229 184 222 185 tfor:TF2682|5end_N_utilization_substance_protein_A_2856308..2856538_POSITIVE 361 228 183 201 153 tfor:TF1449|5end_RNA_polymerase_sigma_factor,_RpoD_1533124..1533354_POSITIVE 359 230 182 147 95 tfor:TF1970|5end_oxaloacetate_decarboxylase,_beta_subunit_2116804..2117034_POSITIVE 359 230 183 61 9 tfor:TF1759|5end_membrane-bound_lytic_murein_transglycosylase_D_precursor_1895472..1895702_POSITIVE 350 190 142 73 16 tfor:TF2759|5end_xylose_repressor,_ROK_family_2943568..2943798_POSITIVE 346 230 182 62 15 tfor:TF3068|5end_flavodoxin_A_3292812..3293042_POSITIVE 346 199 154 71 24 tfor:TF0951|5end_D-alanine--D-alanine_ligase_995718..995948_POSITIVE 345 227 181 231 168 tfor:TF2037|5end_conserved_hypothetical_protein;_possible_anaerobic_ribonucleoside-triphosphate_reductase_2196754..2196984_POSITIVE 343 198 152 81 36 tfor:TF1963|5end_hypothetical_protein_2113359..2113589_POSITIVE 341 65 21 169 128 tfor:TF2518|5end_ATP-dependent_DNA_helicase_2695541..2695771_POSITIVE 341 200 154 171 124 tfor:TF2161|5end_conserved_hypothetical_protein_2336972..2337202_POSITIVE 341 229 182 67 3 tfor:TF0961|5end_translation_initiation_inhibitor,_endoribonuclease_activity_1010445..1010675_POSITIVE 339 228 188 56 21 tfor:TF1281|5end_2-dehydro-3-deoxyphosphooctonate_aldolase_(3-deoxy-D-manno-2-octulosonate-8-phosphate_synthase)_(KDO-8-phosphate_synthetase)_(KDO_8-P_synthase)_1365604..1365834_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 386 230 184 151 109 tfor:TF0205|3end_exsB_protein_232289..232439_POSITIVE 384 220 174 146 103 tfor:TF0885|3end_conjugative_transposon_protein_fragment_938055..938205_POSITIVE 363 205 166 100 59 tfor:TF2978|3end_conserved_hypothetical_protein_3190862..3191012_POSITIVE 362 228 181 110 52 tfor:TF2640|3end_hypothetical_protein_2809533..2809683_POSITIVE 362 230 181 57 3 tfor:TF2230|3end_CTn_excision_protein_2400394..2400544_POSITIVE 359 230 183 53 1 tfor:TF1758|3end_conserved_hypothetical_protein_1895544..1895694_POSITIVE 355 220 181 140 101 tfor:TF2442|3end_heat_shock_protein_60_2620271..2620421_POSITIVE 351 227 190 85 46 tfor:TF1588|3end_hypothetical_protein_1702560..1702710_POSITIVE 346 199 154 50 3 tfor:TF0950|3end_ribosomal_large_subunit_pseudouridine_synthase_D_(pseudouridylate_synthase)_(uracil_hydrolyase)_995777..995927_POSITIVE 342 229 190 63 22 tfor:TF1592|3end_hypothetical_protein_1708557..1708707_POSITIVE 337 223 182 85 54 tfor:TF0982|3end_conserved_hypothetical_protein_1039474..1039624_POSITIVE 335 230 183 99 46 tfor:TF0679|3end_hypothetical_protein_721489..721639_POSITIVE 334 225 181 81 35 tfor:TF2462|3end_hypothetical_protein_2642076..2642226_POSITIVE 332 229 184 59 6 tfor:TF1169|3end_lipoprotein_ABC_transporter,_permease_component_1251573..1251723_POSITIVE 331 229 181 80 35 tfor:TF1719|3end_ribonuclease_R_1843668..1843818_POSITIVE 330 230 183 47 1 tfor:TF3067|3end_conserved_hypothetical_protein_3292877..3293027_POSITIVE 330 205 162 151 107 tfor:TF1205|3end_beta-glucanase/beta-glucan_synthetase;_endoglucanase_related_1288580..1288730_POSITIVE 329 230 181 112 67 tfor:TF3006|3end_response_regulator,_transcriptional_regulator_RprY_3227162..3227312_POSITIVE 324 219 174 51 13 tfor:TF0463|3end_precorrin-6Y_C5,15-methyltransferase_480291..480441_POSITIVE 323 198 152 112 54 tfor:TF1087|3end_ISPg4_transposase_1158225..1158375_POSITIVE