Origin IGS: taaacttcatccctttttttgatgtatcttcgcacacgtcaaaattacccgttatgaattattttacagattacgcatcgccggtcggcatgttacgcatcgtgaaaacggtcgagggattacggccatcaaatacgtcaggaacgagcatgtt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aacatgctcgttcctgacgtatttgatggccgtaatccctcgaccgttttcacgatgcgtaacatgccgaccggcgatgcgtaatctgtaaaataattcataacgggtaattttgacgtgtgcgaagatacatcaaaaaaagggatgaagttta Mask Tandem Repeat Region ================================================ taaacttcatccctttttttgatgtatcttcgcacacgtcaaaattacccgttatgaattattttacagattacgcatcgccggtcggcatgttacgcatcgtgaaaacggtcgagggattacggccatcaaatacgtcaggaacgagcatgtt Find is-nt database================================================ Query_seq: TF1179:TF1181|TF1179:TF1181:two-component sensor histidine kinase:methylated-DNA--[protein]-cysteine S-methyltransferase:->->:1267508..1267661 154 taaacttcatccctttttttgatgtatcttcgcacacgtcaaaattacccgttatgaattattttacagattacgcatcgccggtcggcatgttacgcatcgtgaaaacggtcgagggattacggccatcaaatacgtcaggaacgagcatgtt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF1179:TF1181|TF1179:TF1181:two-component sensor histidine kinase:methylated-DNA--[protein]-cysteine S-methyltransferase:->->:1267508..1267661 154 taaacttcatccctttttttgatgtatcttcgcacacgtcaaaattacccgttatgaattattttacagattacgcatcgccggtcggcatgttacgcatcgtgaaaacggtcgagggattacggccatcaaatacgtcaggaacgagcatgtt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF1179:TF1181|TF1179:TF1181:two-component sensor histidine kinase:methylated-DNA--[protein]-cysteine S-methyltransferase:->->:1267508..1267661 154 taaacttcatccctttttttgatgtatcttcgcacacgtcaaaattacccgttatgaattattttacagattacgcatcgccggtcggcatgttacgcatcgtgaaaacggtcgagggattacggccatcaaatacgtcaggaacgagcatgtt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 taaacttcatccctttttttgatgtatcttcgcacacgtcaaaattacccgttatgaattattttacagattacgcatcgccggtcggcatgttacgcatcgtgaaaacggtcgagggattacggccatcaaatacgtcaggaacgagcatgtt Predict ORF larger than 30AA ================================================ Protein_Len: 48 Strand: + Start: 9 End: 152 ........ M P F F D V S S H T S K L P V M N Y F T D Y A S P V G M L R I V K T V E G L R P S N T S G T S M .. Protein_Len: 43 Strand: + Start: 26 End: 154 ......................... M F A H V K I T R Y E L F Y R L R I A G R H V T H R E N G R G I T A I K Y V R N E H V taaacttcatccctttttttgatgtatcttcgcacacgtcaaaattacccgttatgaattattttacagattacgcatcgccggtcggcatgttacgcatcgtgaaaacggtcgagggattacggccatcaaatacgtcaggaacgagcatgtt 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================================================ taaacttcatccctttttttgatgtatcttcgcacacgtcaaaattacccgttatgaattattttacagattacgcatcgccggtcggcatgttacgcatcgtgaaaacggtcgagggattacggccatcaaatacgtcaggaacgagcatgtt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TF1179:TF1181|TF1179:TF1181:two-component sensor histidine kinase:methylated-DNA--[protein]-cysteine S-methyltransferase:->->:1267508..1267661 154 taaacttcatccctttttttgatgtatcttcgcacacgtcaaaattacccgttatgaattattttacagattacgcatcgccggtcggcatgttacgcatcgtgaaaacggtcgagggattacggccatcaaatacgtcaggaacgagcatgtt Intra-Species Hit: Count: 1 Min: 21 Max: 154 Len: 134 Subject: tfor_TF1179_TF1181|two-component sensor histidine kinase:methylated-DNA--[protein]-cysteine S-methyltransferase|POSITIVE:POSITIVE|[1267508, 1267661]|154 HSP 1 e-value: 2.0E-70 bit: 266.0 Len: 134 Query Start:21 Query End:154 Subject Strand: POSITIVE Subject Start: 21 Subject End: 154 ....................gatgtatcttcgcacacgtcaaaattacccgttatgaattattttacagattacgcatcgccggtcggcatgttacgcatcgtgaaaacggtcgagggattacggccatcaaatacgtcaggaacgagcatgtt ....................gatgtatcttcgcacacgtcaaaattacccgttatgaattattttacagattacgcatcgccggtcggcatgttacgcatcgtgaaaacggtcgagggattacggccatcaaatacgtcaggaacgagcatgtt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAUGUAUCUUCGCACACGUCAAAAUUACCCGUUAUGAAUUAUUUUACAGAUUACGCAUCGCCGGUCGGCAUGUUACGCAUCGUGAAAACGGUCGAGGGAUUACGGCCAUCAAAUACGUCAGGAACGAGCAUGUU (((((..........))))).........((((.(((..(((((....(((.....)))...(((((..((.(..((.(((((....)))))))..).))..)))))...)))))..)))..))))........ (-27.20) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AACAUGCUCGUUCCUGACGUAUUUGAUGGCCGUAAUCCCUCGACCGUUUUCACGAUGCGUAACAUGCCGACCGGCGAUGCGUAAUCUGUAAAAUAAUUCAUAACGGGUAAUUUUGACGUGUGCGAAGAUACAUC ....((((((((..(((..((((((((((.((........)).))))).....((((((((...((((....)))).))))).)))....)))))..))).))))))))........((((......))))... (-29.00) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 437 98 55 217 180 tfor:TF0094|5end_alpha-glucosidase_103561..103791_POSITIVE 434 110 62 209 155 tfor:TF0975|5end_hypothetical_protein_1023994..1024224_POSITIVE 425 100 53 72 25 tfor:TF2218|5end_two-component_system_response_regulator_2390162..2390392_POSITIVE 421 110 62 79 22 tfor:TF0064|5end_conserved_hypothetical_protein_68419..68649_POSITIVE 403 98 52 137 101 tfor:TF1292|5end_sensor_histidine_protein_kinase_1372567..1372797_POSITIVE 401 109 61 114 56 tfor:TF2016|5end_hypothetical_protein_2172948..2173178_POSITIVE 396 109 62 179 125 tfor:TF0302|5end_FKBP-type_peptidyl-prolyl_cis-trans_isomerase_328641..328871_POSITIVE 395 99 55 98 31 tfor:TF1464|5end_conserved_hypothetical_protein_1553467..1553697_POSITIVE 395 108 62 86 27 tfor:TF0700|5end_possible_lipoprotein_742649..742879_POSITIVE 389 99 58 216 168 tfor:TF0597|5end_hypothetical_protein_628788..629018_POSITIVE 384 110 62 187 125 tfor:TF0152|5end_RNA_polymerase_ECF-type_sigma_factor_162021..162251_POSITIVE 383 99 55 107 58 tfor:TF1975|5end_uridylate_kinase_2121536..2121766_POSITIVE 382 106 61 49 11 tfor:TF0150|5end_peptidyl-arginyl_deiminase_160077..160307_POSITIVE 380 99 51 180 127 tfor:TF1688|5end_conserved_hypothetical_protein;_possible_periplasmic_protein_1803354..1803584_POSITIVE 379 98 53 59 21 tfor:TF3022|5end_chorismate_synthase_3246136..3246366_POSITIVE 378 106 61 114 66 tfor:TF1240|5end_conserved_hypothetical_protein_1324304..1324534_POSITIVE 372 94 55 162 121 tfor:TF1042|5end_possible_surface_antigen_with_leucine-rich_repeat_1102957..1103187_POSITIVE 370 100 54 68 4 tfor:TF0090|5end_conserved_hypothetical_protein_96285..96515_POSITIVE 366 90 46 62 22 tfor:TF2243|5end_possible_mobilization_protein_2417384..2417614_POSITIVE 366 110 63 174 140 tfor:TF0374|5end_glycerophosphoryl_diester_phosphodiesterase_392527..392757_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 421 110 62 70 13 tfor:TF0063|3end_conserved_hypothetical_protein_68490..68640_POSITIVE 403 98 52 137 101 tfor:TF1291|3end_response_regulator_(fimR__protein)_1372647..1372797_POSITIVE 401 109 61 106 48 tfor:TF2015|3end_N6-adenine-specific_DNA_methylase_2173020..2173170_POSITIVE 395 108 62 102 43 tfor:TF0699|3end_pyridoxal_phosphate_biosynthetic_protein_742745..742895_POSITIVE 382 106 61 49 11 tfor:TF0148|3end_conserved_hypothetical_protein_160157..160307_POSITIVE 372 94 55 145 104 tfor:TF1041|3end_dihydroorotate_dehydrogenase,_catalytic_subunit_1103020..1103170_POSITIVE 372 98 55 105 63 tfor:TF0685|3end_hypothetical_protein_731132..731282_POSITIVE 368 100 51 73 13 tfor:TF2092|3end_ribonuclease_III_2261823..2261973_POSITIVE 366 110 62 69 12 tfor:TF0062|3end_conserved_hypothetical_protein_66180..66330_POSITIVE 364 99 53 83 46 tfor:TF3107|3end_hypothetical_protein_3338736..3338886_POSITIVE 363 98 54 63 2 tfor:TF2808|3end_bacterial_sugar_transferase_2999909..3000059_POSITIVE 363 99 54 102 47 tfor:TF2527|3end_RNA_polymerase_ECF-type_sigma_factor_2710749..2710899_POSITIVE 356 97 57 77 26 tfor:TF1479|3end_ABC_transporter,_permease_component_1573592..1573742_POSITIVE 355 99 54 81 40 tfor:TF2847|3end_hypothetical_protein_3034985..3035135_POSITIVE 350 95 54 59 23 tfor:TF1426|3end_N-acetylymuramoylalanyl-D-glutamate-2,6-diaminopi_melate_ligase_1511413..1511563_POSITIVE 348 95 58 55 13 tfor:TF0214|3end_DNA_recombination_and_repair_protein,_RecN_241571..241721_POSITIVE 346 109 63 103 47 tfor:TF1596|3end_hypothetical_protein_1712723..1712873_POSITIVE 345 98 53 74 18 tfor:TF2846|3end_cobyric_acid_synthase_3036469..3036619_POSITIVE 343 105 61 61 19 tfor:TF1247|3end_alanyl-tRNA_synthetase_(alanine--tRNA_ligase)_1330928..1331078_POSITIVE 342 110 62 148 96 tfor:TF3143|3end_conserved_hypothetical_protein;_possible_membrane_protein_3379227..3379377_POSITIVE