Origin IGS: tgatgcgctcgccggccttaaactcgatcgagtccaaggtcgtttttgtggtccgtgtttccggaccctttaggcccattgatgatttgaatatttttcacacctcgttttttacccaaatatgctatctttgtcgttcttcaacgcacaaaagtagtgcttttttttcgagattctcaac .........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 gttgagaatctcgaaaaaaaagcactacttttgtgcgttgaagaacgacaaagatagcatatttgggtaaaaaacgaggtgtgaaaaatattcaaatcatcaatgggcctaaagggtccggaaacacggaccacaaaaacgaccttggactcgatcgagtttaaggccggcgagcgcatca Mask Tandem Repeat Region ================================================ tgatgcgctcgccggccttaaactcgatcgagtccaaggtcgtttttgtggtccgtgtttccggaccctttaggcccattgatgatttgaatatttttcacacctcgttttttacccaaatatgctatctttgtcgttcttcaacgcacaaaagtagtgcttttttttcgagattctcaac Find is-nt database================================================ Query_seq: TF2392:TF2394|TF2392:TF2394:alpha-galactosidase:integrase/recombinase XerD:->->:2565567..2565747 181 tgatgcgctcgccggccttaaactcgatcgagtccaaggtcgtttttgtggtccgtgtttccggaccctttaggcccattgatgatttgaatatttttcacacctcgttttttacccaaatatgctatctttgtcgttcttcaacgcacaaaagtagtgcttttttttcgagattctcaac Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF2392:TF2394|TF2392:TF2394:alpha-galactosidase:integrase/recombinase XerD:->->:2565567..2565747 181 tgatgcgctcgccggccttaaactcgatcgagtccaaggtcgtttttgtggtccgtgtttccggaccctttaggcccattgatgatttgaatatttttcacacctcgttttttacccaaatatgctatctttgtcgttcttcaacgcacaaaagtagtgcttttttttcgagattctcaac Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF2392:TF2394|TF2392:TF2394:alpha-galactosidase:integrase/recombinase XerD:->->:2565567..2565747 181 tgatgcgctcgccggccttaaactcgatcgagtccaaggtcgtttttgtggtccgtgtttccggaccctttaggcccattgatgatttgaatatttttcacacctcgttttttacccaaatatgctatctttgtcgttcttcaacgcacaaaagtagtgcttttttttcgagattctcaac Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tgatgcgctcgccggccttaaactcgatcgagtccaaggtcgtttttgtggtccgtgtttccggaccctttaggcccattgatgatttgaatatttttcacacctcgttttttacccaaatatgctatctttgtcgttcttcaacgcacaaaagtagtgcttttttttcgagattctcaac Predict ORF larger than 30AA ================================================ Protein_Len: 59 Strand: + Start: 3 End: 179 .. M R S P A L N S I E S K V V F V V R V S G P F R P I D D L N I F H T S F F T Q I C Y L C R S S T H K S S A F F S R F S .. Protein_Len: 30 Strand: + Start: 91 End: 180 .......................................................................................... M F F T P R F L P K Y A I F V V L Q R T K V V L F F R D S Q . Protein_Len: 36 Strand: - Start: 21 End: 128 .................... V R D L G L D N K H D T N G S G K P G N I I Q I N K V G R K K G L Y A M ..................................................... Protein_Len: 31 Strand: - Start: 2 End: 94 . I R E G A K F E I S D L T T K T T R T E P G K L G M S S K F M ....................................................................................... tgatgcgctcgccggccttaaactcgatcgagtccaaggtcgtttttgtggtccgtgtttccggaccctttaggcccattgatgatttgaatatttttcacacctcgttttttacccaaatatgctatctttgtcgttcttcaacgcacaaaagtagtgcttttttttcgagattctcaac 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================================================ tgatgcgctcgccggccttaaactcgatcgagtccaaggtcgtttttgtggtccgtgtttccggaccctttaggcccattgatgatttgaatatttttcacacctcgttttttacccaaatatgctatctttgtcgttcttcaacgcacaaaagtagtgcttttttttcgagattctcaac Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 100 HP_score: -4.2 Tail_Score: -5.77853 Start: 146 End: 160 Full_Region: TTGTCGTTCTTCAAC GCACAA AAG TAGTGC TTTTTTTTCGAGATT .................................................................................................................................................GCACAAAAGTAGTGC..................... Find igs database================================================ Query_seq: TF2392:TF2394|TF2392:TF2394:alpha-galactosidase:integrase/recombinase XerD:->->:2565567..2565747 181 tgatgcgctcgccggccttaaactcgatcgagtccaaggtcgtttttgtggtccgtgtttccggaccctttaggcccattgatgatttgaatatttttcacacctcgttttttacccaaatatgctatctttgtcgttcttcaacgcacaaaagtagtgcttttttttcgagattctcaac Intra-Species Hit: Count: 1 Min: 1 Max: 160 Len: 160 Subject: tfor_TF2392_TF2394|alpha-galactosidase:integrase/recombinase XerD|POSITIVE:POSITIVE|[2565567,2565747]|181 HSP 1 e-value: 7.0E-86 bit: 317.0 Len: 160 Query Start:1 Query End:160 Subject Strand: POSITIVE Subject Start: 1 Subject End: 160 tgatgcgctcgccggccttaaactcgatcgagtccaaggtcgtttttgtggtccgtgtttccggaccctttaggcccattgatgatttgaatatttttcacacctcgttttttacccaaatatgctatctttgtcgttcttcaacgcacaaaagtagtgc..................... tgatgcgctcgccggccttaaactcgatcgagtccaaggtcgtttttgtggtccgtgtttccggaccctttaggcccattgatgatttgaatatttttcacacctcgttttttacccaaatatgctatctttgtcgttcttcaacgcacaaaagtagtgc..................... Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGAUGCGCUCGCCGGCCUUAAACUCGAUCGAGUCCAAGGUCGUUUUUGUGGUCCGUGUUUCCGGACCCUUUAGGCCCAUUGAUGAUUUGAAUAUUUUUCACACCUCGUUUUUUACCCAAAUAUGCUAUCUUUGUCGUUCUUCAACGCACAAAAGUAGUGC .((((.(((...(((((((..((((....))))..))))))).......((((((......)))))).....))).))))(((((..((((.....))))....)))))..............((((..(((((((((....)))).)))))..)))).. (-42.30) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GCACUACUUUUGUGCGUUGAAGAACGACAAAGAUAGCAUAUUUGGGUAAAAAACGAGGUGUGAAAAAUAUUCAAAUCAUCAAUGGGCCUAAAGGGUCCGGAAACACGGACCACAAAAACGACCUUGGACUCGAUCGAGUUUAAGGCCGGCGAGCGCAUCA ((.((..((((((.((((....))))))))))...((...(((((((.......(((((.((((.....)))).))).)).....))))))).((((((......)))))).......((.((((((((((....)))))))))).)))).)).)).... (-48.50) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 427 50 2 198 146 tfor:TF2025|5end_hypothetical_protein_2181933..2182163_POSITIVE 400 58 13 79 25 tfor:TF1797|5end_SNF_family_transporter_1937136..1937366_POSITIVE 382 50 2 61 9 tfor:TF2835|5end_stationary-phase_survival_protein_SurE_3025113..3025343_POSITIVE 376 48 5 198 152 tfor:TF2673|5end_conserved_hypothetical_protein_2846987..2847217_POSITIVE 363 65 23 100 50 tfor:TF2231|5end_DNA_methylase,_site-specific_DNA-methyltransferase_(adenine-specific)_2400307..2400537_POSITIVE 360 60 11 142 82 tfor:TF2345|5end_dGTP_triphosphohydrolase_2508372..2508602_POSITIVE 358 58 11 75 23 tfor:TF2893|5end_conserved_hypothetical_protein;_possible_phosphoesterase_3080766..3080996_POSITIVE 356 85 41 78 40 tfor:TF1841|5end_hypothetical_protein_1991936..1992166_POSITIVE 354 50 7 104 37 tfor:TF0582|5end_hemolysin-related_protein,_with_CBS_domains;_possible_gliding-motility_related_protein_611885..612115_POSITIVE 351 49 1 231 184 tfor:TF1467|5end_conserved_hypothetical_protein_1557011..1557241_POSITIVE 350 76 31 56 3 tfor:TF2221|5end_CTn_excision_protein_2393790..2394020_POSITIVE 349 56 11 57 14 tfor:TF1308|5end_50S_ribosomal_protein_L28_1387224..1387454_POSITIVE 347 47 3 154 114 tfor:TF2257|5end_transfer_region-related_protein,_TraJ_2428541..2428771_POSITIVE 345 68 24 218 161 tfor:TF2186|5end_outer_membrane_protein_2360291..2360521_POSITIVE 345 49 5 58 1 tfor:TF0083|5end_outer_membrane_efflux_protein_89289..89519_POSITIVE 342 70 23 136 87 tfor:TF2771|5end_undecaprenol_kinase,_bacitracin_resistance_protein_2956559..2956789_POSITIVE 341 50 1 182 129 tfor:TF0250|5end_glycosyltransferase_Family_2_protein_279176..279406_POSITIVE 340 47 2 69 25 tfor:TF2704|5end_ribonuclease_HII_2876242..2876472_POSITIVE 340 55 12 57 11 tfor:TF2573|5end_50S_ribosomal_protein_L15_2743310..2743540_POSITIVE 338 41 5 48 13 tfor:TF0462|5end_possible_cobalamin_biosynthesis_precorrin-3_methylase_477600..477830_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 400 58 13 79 25 tfor:TF1796|3end_ABC_transporter,_ATP-binding_protein_1937216..1937366_POSITIVE 393 58 13 88 49 tfor:TF2392|3end_alpha-galactosidase_2565506..2565656_POSITIVE 376 48 5 145 99 tfor:TF2672|3end_lipoic_acid_synthetase_2847014..2847164_POSITIVE 363 65 23 107 57 tfor:TF2230|3end_CTn_excision_protein_2400394..2400544_POSITIVE 360 60 11 124 64 tfor:TF2344|3end_ATP/GTP_binding_protein_2508434..2508584_POSITIVE 354 50 7 71 4 tfor:TF0581|3end_single_stranded_DNA-binding_protein_611932..612082_POSITIVE 350 42 1 135 89 tfor:TF2602|3end_tRNA-(5-methylaminomethyl-2-thiouridylate)_methyltransferase_2776500..2776650_POSITIVE 348 50 3 51 2 tfor:TF2833|3end_lipid_A_disaccharide_synthase_3025183..3025333_POSITIVE 347 47 3 147 107 tfor:TF2256|3end_transfer_region-related_protein,_TraI_2428614..2428764_POSITIVE 342 70 23 136 87 tfor:TF2770|3end_conserved_hypothetical_protein_2956639..2956789_POSITIVE 340 47 2 64 20 tfor:TF2703|3end_conserved_hypothetical_protein_2876317..2876467_POSITIVE 336 38 2 151 112 tfor:TF2024|3end_conserved_hypothetical_protein_2181979..2182129_POSITIVE 335 65 23 52 8 tfor:TF1929|3end_conserved_hypothetical_protein_2076614..2076764_POSITIVE 335 48 5 69 19 tfor:TF0525|3end_conserved_hypothetical_protein_549584..549734_POSITIVE 333 39 6 82 38 tfor:TF0431|3end_hypothetical_protein_452470..452620_POSITIVE 333 39 6 115 71 tfor:TF0430|3end_hypothetical_protein_452503..452653_POSITIVE 326 160 114 59 3 tfor:TF1801|3end_conserved_hypothetical_protein;_possible_TPR-repeat-containing_protein_1945669..1945819_POSITIVE 324 50 1 62 1 tfor:TF2088|3end_heptosyltransferase_protein_2258725..2258875_POSITIVE 322 58 11 104 47 tfor:TF2483|3end_hypothetical_protein_2660022..2660172_POSITIVE 319 74 31 147 112 tfor:TF1722|3end_conserved_hypothetical_protein_1848471..1848621_POSITIVE