Origin IGS: taagatcggataggagggaggaatagctcctcctttctttccgtcggaggtgggcgctttgtgtgtttattccgtcagcgctttccaaagcggttcgtccggtacgggcgcgacgatannnnnttaattaattaannnnnttaatcggtcgtttcgataccgg .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 ccggtatcgaaacgaccgattaannnnnttaattaattaannnnntatcgtcgcgcccgtaccggacgaaccgctttggaaagcgctgacggaataaacacacaaagcgcccacctccgacggaaagaaaggaggagctattcctccctcctatccgatctta Mask Tandem Repeat Region ================================================ taagatcggataggagggaggaatagctcctcctttctttccgtcggaggtgggcgctttgtgtgtttattccgtcagcgctttccaaagcggttcgtccggtacgggcgcgacgatannnnnttaattaattaannnnnttaatcggtcgtttcgataccgg Find is-nt database================================================ Query_seq: TF3165:TF0001|TF3165:TF0001:thiol:disulfide interchange protein, thioredoxin family protein:hypothetical protein:->->:biojavax:join:[1..23,3405404..3405543] 163 taagatcggataggagggaggaatagctcctcctttctttccgtcggaggtgggcgctttgtgtgtttattccgtcagcgctttccaaagcggttcgtccggtacgggcgcgacgatannnnnttaattaattaannnnnttaatcggtcgtttcgataccgg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF3165:TF0001|TF3165:TF0001:thiol:disulfide interchange protein, thioredoxin family protein:hypothetical protein:->->:biojavax:join:[1..23,3405404..3405543] 163 taagatcggataggagggaggaatagctcctcctttctttccgtcggaggtgggcgctttgtgtgtttattccgtcagcgctttccaaagcggttcgtccggtacgggcgcgacgatannnnnttaattaattaannnnnttaatcggtcgtttcgataccgg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF3165:TF0001|TF3165:TF0001:thiol:disulfide interchange protein, thioredoxin family protein:hypothetical protein:->->:biojavax:join:[1..23,3405404..3405543] 163 taagatcggataggagggaggaatagctcctcctttctttccgtcggaggtgggcgctttgtgtgtttattccgtcagcgctttccaaagcggttcgtccggtacgggcgcgacgatannnnnttaattaattaannnnnttaatcggtcgtttcgataccgg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 taagatcggataggagggaggaatagctcctcctttctttccgtcggaggtgggcgctttgtgtgtttattccgtcagcgctttccaaagcggttcgtccggtacgggcgcgacgatannnnnttaattaattaannnnnttaatcggtcgtttcgataccgg Predict ORF larger than 30AA ================================================ Protein_Len: 34 Strand: + Start: 23 End: 124 ...................... M A P P F F P S E V G A L C V Y S V S A F Q S G S S G T G A T I X X ....................................... Protein_Len: 41 Strand: + Start: 10 End: 132 ......... M G G R N S S S F L S V G G G R F V C L F R Q R F P K R F V R Y G R D D X X L I N ............................... taagatcggataggagggaggaatagctcctcctttctttccgtcggaggtgggcgctttgtgtgtttattccgtcagcgctttccaaagcggttcgtccggtacgggcgcgacgatannnnnttaattaattaannnnnttaatcggtcgtttcgataccgg 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================================================ taagatcggataggagggaggaatagctcctcctttctttccgtcggaggtgggcgctttgtgtgtttattccgtcagcgctttccaaagcggttcgtccggtacgggcgcgacgatannnnnttaattaattaannnnnttaatcggtcgtttcgataccgg Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TF3165:TF0001|TF3165:TF0001:thiol:disulfide interchange protein, thioredoxin family protein:hypothetical protein:->->:biojavax:join:[1..23,3405404..3405543] 163 taagatcggataggagggaggaatagctcctcctttctttccgtcggaggtgggcgctttgtgtgtttattccgtcagcgctttccaaagcggttcgtccggtacgggcgcgacgatannnnnttaattaattaannnnnttaatcggtcgtttcgataccgg Intra-Species Hit: Count: 1 Min: 1 Max: 163 Len: 163 Subject: tfor_TF3165_TF0001|thiol:disulfide interchange protein, thioredoxin family protein:hypothetical protein|POSITIVE:POSITIVE|3405404, 23 {([3405404,3405543]), ([1,23])} (circular)|163 HSP 1 e-value: 8.0E-70 bit: 264.0 Len: 163 Query Start:1 Query End:163 Subject Strand: POSITIVE Subject Start: 1 Subject End: 163 taagatcggataggagggaggaatagctcctcctttctttccgtcggaggtgggcgctttgtgtgtttattccgtcagcgctttccaaagcggttcgtccggtacgggcgcgacgatannnnnttaattaattaannnnnttaatcggtcgtttcgataccgg taagatcggataggagggaggaatagctcctcctttctttccgtcggaggtgggcgctttgtgtgtttattccgtcagcgctttccaaagcggttcgtccggtacgggcgcgacgatannnnnttaattaattaannnnnttaatcggtcgtttcgataccgg Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAGAUCGGAUAGGAGGGAGGAAUAGCUCCUCCUUUCUUUCCGUCGGAGGUGGGCGCUUUGUGUGUUUAUUCCGUCAGCGCUUUCCAAAGCGGUUCGUCCGGUACGGGCGCGACGAUANNNNNUUAAUUAAUUAANNNNNUUAAUCGGUCGUUUCGAUACCGG ......((((.(((((((((((.....))))))))))).)))).(((((.(((((((.....))))))))))))....(((((....)))))......((((((((((.((((((((......((((....))))........))).))))))))).)))))) (-56.94) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CCGGUAUCGAAACGACCGAUUAANNNNNUUAAUUAAUUAANNNNNUAUCGUCGCGCCCGUACCGGACGAACCGCUUUGGAAAGCGCUGACGGAAUAAACACACAAAGCGCCCACCUCCGACGGAAAGAAAGGAGGAGCUAUUCCUCCCUCCUAUCCGAUCUUA (((((((.(...((((.(((........((((....))))......)))))))...).)))))))..........(((((..(((((....(........)....))))).....)))))((((.((...(((((((...)))))))...)).))))...... (-40.14) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 459 118 72 59 14 tfor:TF0038|5end_conserved_hypothetical_protein_39907..40137_POSITIVE 448 80 32 51 13 tfor:TF2876|5end_cytosine_deaminase_3065144..3065374_POSITIVE 435 116 72 206 158 tfor:TF0971|5end_conserved_hypothetical_protein_1021355..1021585_POSITIVE 423 109 63 206 153 tfor:TF1850|5end_Na+/H+-exchanging_protein_1998542..1998772_POSITIVE 416 57 12 155 94 tfor:TF3158|5end_inner_membrane_protein_3393729..3393959_POSITIVE 401 104 63 48 2 tfor:TF1600|5end_uroporphyrinogen-III_synthase_1713964..1714194_POSITIVE 399 115 76 157 114 tfor:TF1948|5end_conserved_hypothetical_protein_2095942..2096172_POSITIVE 398 115 73 164 117 tfor:TF2079|5end_permease_2245585..2245815_POSITIVE 397 89 43 76 29 tfor:TF0606|5end_signal_peptidase_II_636816..637046_POSITIVE 396 115 72 59 10 tfor:TF0496|5end_conserved_hypothetical_protein_522332..522562_POSITIVE 391 115 72 103 42 tfor:TF3145|5end_conserved_hypothetical_protein;_possible_GTP_cyclohydrolase_I_family_3381254..3381484_POSITIVE 391 50 3 161 102 tfor:TF1327|5end_L-fucose_permease_1405790..1406020_POSITIVE 390 54 17 178 131 tfor:TF1481|5end_ABC_transporter,_ATP-binding_protein_1574783..1575013_POSITIVE 390 79 33 182 136 tfor:TF0028|5end_hypothetical_protein_24249..24479_POSITIVE 387 115 73 197 155 tfor:TF0140|5end_exodeoxyribonuclease_VII,_small_subunit_148203..148433_POSITIVE 385 115 73 207 158 tfor:TF1782|5end_conserved_hypothetical_protein_1922003..1922233_POSITIVE 384 81 41 223 168 tfor:TF2248|5end_transfer_region-related_protein,_TraB_2422551..2422781_POSITIVE 384 110 63 216 164 tfor:TF1300|5end_conserved_hypothetical_protein_1382389..1382619_POSITIVE 384 116 77 51 12 tfor:TF1196|5end_acetyl-coenzyme_A_synthetase_1279064..1279294_POSITIVE 383 115 72 220 174 tfor:TF2667|5end_hypothetical_protein_2842395..2842625_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 468 115 71 101 46 tfor:TF2640|3end_hypothetical_protein_2809533..2809683_POSITIVE 459 118 72 63 18 tfor:TF0037|3end_sialic_acid-specific_9-O-acetylesterase_39991..40141_POSITIVE 453 110 62 141 90 tfor:TF2653|3end_hypothetical_protein_2822460..2822610_POSITIVE 448 80 32 51 13 tfor:TF2874|3end_conserved_hypothetical_protein_3065224..3065374_POSITIVE 436 43 7 84 48 tfor:TF3165|3end_thiol:disulfide_interchange_protein,_thioredoxin_family_protein_3405343..3405493_POSITIVE 424 118 71 75 12 tfor:TF0989|3end_conserved_hypothetical_protein_1045227..1045377_POSITIVE 416 57 12 133 72 tfor:TF3157|3end_sodium/solute_symporter_3393787..3393937_POSITIVE 406 115 72 132 71 tfor:TF0685|3end_hypothetical_protein_731132..731282_POSITIVE 401 104 63 58 12 tfor:TF1599|3end_ribonuclease_P_protein_component_1714054..1714204_POSITIVE 397 89 43 63 16 tfor:TF0605|3end_conserved_hypothetical_protein_636883..637033_POSITIVE 390 79 33 52 6 tfor:TF0027|3end_conserved_hypothetical_protein_24199..24349_POSITIVE 385 116 72 137 89 tfor:TF2855|3end_ATPase,_AAA_family_3042011..3042161_POSITIVE 381 115 71 135 70 tfor:TF2556|3end_conserved_hypothetical_protein_2737095..2737245_POSITIVE 380 86 41 101 66 tfor:TF2846|3end_cobyric_acid_synthase_3036469..3036619_POSITIVE 380 118 71 82 28 tfor:TF2659|3end_conserved_hypothetical_protein_2833055..2833205_POSITIVE 380 118 73 76 23 tfor:TF2012|3end_conserved_hypothetical_protein_2168720..2168870_POSITIVE 377 112 71 41 6 tfor:TF2266|3end_transfer_region-related_protein,_TraQ_2434949..2435099_POSITIVE 369 117 72 72 35 tfor:TF2808|3end_bacterial_sugar_transferase_2999909..3000059_POSITIVE 369 116 72 126 79 tfor:TF0145|3end_glutamine_synthetase_154718..154868_POSITIVE 369 115 72 141 94 tfor:TF0061|3end_hypothetical_protein_65006..65156_POSITIVE