Origin IGS: tgagatggctgaaaatagcgagaaatagcgcctttgtaaggatgcctccggaagtctccgcgaagctcgctaagccttccgtcgatgcacggaagtctccgcgcggttcattaagatttccgacaacggacggaagtctccgcaaaactcgctaagcctttcgtcgatgcacggaagtctccgcgcaactcgctaagccttccgtcg .........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 cgacggaaggcttagcgagttgcgcggagacttccgtgcatcgacgaaaggcttagcgagttttgcggagacttccgtccgttgtcggaaatcttaatgaaccgcgcggagacttccgtgcatcgacggaaggcttagcgagcttcgcggagacttccggaggcatccttacaaaggcgctatttctcgctattttcagccatctca Mask Tandem Repeat Region ================================================ tgagatggctgaaaatagcgagaaatagcgcctttgtaaggatgcctcnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn Find is-nt database================================================ Query_seq: TF0279:TF0280|TF0279:TF0280:conserved hypothetical protein:hypothetical protein:->->:308740..308946 207 tgagatggctgaaaatagcgagaaatagcgcctttgtaaggatgcctccggaagtctccgcgaagctcgctaagccttccgtcgatgcacggaagtctccgcgcggttcattaagatttccgacaacggacggaagtctccgcaaaactcgctaagcctttcgtcgatgcacggaagtctccgcgcaactcgctaagccttccgtcg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF0279:TF0280|TF0279:TF0280:conserved hypothetical protein:hypothetical protein:->->:308740..308946 207 tgagatggctgaaaatagcgagaaatagcgcctttgtaaggatgcctccggaagtctccgcgaagctcgctaagccttccgtcgatgcacggaagtctccgcgcggttcattaagatttccgacaacggacggaagtctccgcaaaactcgctaagcctttcgtcgatgcacggaagtctccgcgcaactcgctaagccttccgtcg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF0279:TF0280|TF0279:TF0280:conserved hypothetical protein:hypothetical protein:->->:308740..308946 207 tgagatggctgaaaatagcgagaaatagcgcctttgtaaggatgcctccggaagtctccgcgaagctcgctaagccttccgtcgatgcacggaagtctccgcgcggttcattaagatttccgacaacggacggaagtctccgcaaaactcgctaagcctttcgtcgatgcacggaagtctccgcgcaactcgctaagccttccgtcg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tgagatggctgaaaatagcgagaaatagcgcctttgtaaggatgcctccggaagtctccgcgaagctcgctaagccttccgtcgatgcacggaagtctccgcgcggttcattaagatttccgacaacggacggaagtctccgcaaaactcgctaagcctttcgtcgatgcacggaagtctccgcgcaactcgctaagccttccgtcg Predict ORF larger than 30AA ================================================ Protein_Len: 48 Strand: + Start: 9 End: 152 ........ M K I A R N S A F V R M P P E V S A K L A K P S V D A R K S P R G S L R F P T T D G S L R K T R ....................................................... Protein_Len: 32 Strand: - Start: 73 End: 168 ........................................................................ A K R R H V S T E A R N M L I E S L P R F D G C F E S L R E D M ....................................... Protein_Len: 48 Strand: - Start: 2 End: 145 . L H S F I A L F L A K T L I G G S T E A F S A L G E T S A R F D G R P E N L N G V V S P L R R M .............................................................. tgagatggctgaaaatagcgagaaatagcgcctttgtaaggatgcctccggaagtctccgcgaagctcgctaagccttccgtcgatgcacggaagtctccgcgcggttcattaagatttccgacaacggacggaagtctccgcaaaactcgctaagcctttcgtcgatgcacggaagtctccgcgcaactcgctaagccttccgtcg 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================================================ tgagatggctgaaaatagcgagaaatagcgcctttgtaaggatgcctccggaagtctccgcgaagctcgctaagccttccgtcgatgcacggaagtctccgcgcggttcattaagatttccgacaacggacggaagtctccgcaaaactcgctaagcctttcgtcgatgcacggaagtctccgcgcaactcgctaagccttccgtcg Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 47 HP_score: -2.8 Tail_Score: -3.3907 Start: 65 End: 106 Full_Region: GGAAGTCTCCGCGAA GCTCGCTAAGCCTTCCGT CGATGC ACGGAAGTCTCCGCGCGG TTCATTAAGATTTCC ................................................................GCTCGCTAAGCCTTCCGTCGATGCACGGAAGTCTCCGCGCGG..................................................................................................... TransTerm Strand: + Conf: 49 HP_score: -6.3 Tail_Score: -2.6296 Start: 66 End: 105 Full_Region: GAAGTCTCCGCGAAG CTCGCTAAGCCTTCCGT CGATGC ACGGAAGTCTCCGCGCG GTTCATTAAGATTTC .................................................................CTCGCTAAGCCTTCCGTCGATGCACGGAAGTCTCCGCGCG...................................................................................................... Find igs database================================================ Query_seq: TF0279:TF0280|TF0279:TF0280:conserved hypothetical protein:hypothetical protein:->->:308740..308946 207 tgagatggctgaaaatagcgagaaatagcgcctttgtaaggatgcctccggaagtctccgcgaagctcgctaagccttccgtcgatgcacggaagtctccgcgcggttcattaagatttccgacaacggacggaagtctccgcaaaactcgctaagcctttcgtcgatgcacggaagtctccgcgcaactcgctaagccttccgtcg Intra-Species Hit: Count: 1 Min: 1 Max: 207 Len: 207 Subject: tfor_TF0279_TF0280|conserved hypothetical protein:hypothetical protein|POSITIVE:POSITIVE|[308740,308946]|207 HSP 1 e-value: 1.0E-114 bit: 410.0 Len: 207 Query Start:1 Query End:207 Subject Strand: POSITIVE Subject Start: 1 Subject End: 207 tgagatggctgaaaatagcgagaaatagcgcctttgtaaggatgcctccggaagtctccgcgaagctcgctaagccttccgtcgatgcacggaagtctccgcgcggttcattaagatttccgacaacggacggaagtctccgcaaaactcgctaagcctttcgtcgatgcacggaagtctccgcgcaactcgctaagccttccgtcg tgagatggctgaaaatagcgagaaatagcgcctttgtaaggatgcctccggaagtctccgcgaagctcgctaagccttccgtcgatgcacggaagtctccgcgcggttcattaagatttccgacaacggacggaagtctccgcaaaactcgctaagcctttcgtcgatgcacggaagtctccgcgcaactcgctaagccttccgtcg Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGAGAUGGCUGAAAAUAGCGAGAAAUAGCGCCUUUGUAAGGAUGCCUCCGGAAGUCUCCGCGAAGCUCGCUAAGCCUUCCGUCGAUGCACGGAAGUCUCCGCGCGGUUCAUUAAGAUUUCCGACAACGGACGGAAGUCUCCGCAAAACUCGCUAAGCCUUUCGUCGAUGCACGGAAGUCUCCGCGCAACUCGCUAAGCCUUCCGUCG ...(((((..(....(((((((...(((((.((((((..((((..(....)..))))..))))))..)))))...(((((((......))))))).....((((((.......(((((((((.((.((.(((((((.((..((.......))..)).))))))))).))..)))))))))))))))..)))))))...)..))))). (-77.41) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CGACGGAAGGCUUAGCGAGUUGCGCGGAGACUUCCGUGCAUCGACGAAAGGCUUAGCGAGUUUUGCGGAGACUUCCGUCCGUUGUCGGAAAUCUUAAUGAACCGCGCGGAGACUUCCGUGCAUCGACGGAAGGCUUAGCGAGCUUCGCGGAGACUUCCGGAGGCAUCCUUACAAAGGCGCUAUUUCUCGCUAUUUUCAGCCAUCUCA ....(((.(((((((((((.(((((((......)))))))....((.(((.(((.(((((.(((((.(((.((((((((...((((((((.((((..((.....))..)))).))))).)))..)))))))).))).))))).))))).))).))).))..(((..(((.....))).)))....))))))).....)))).))).. (-80.40) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 462 109 61 204 153 tfor:TF0971|5end_conserved_hypothetical_protein_1021355..1021585_POSITIVE 456 88 43 57 1 tfor:TF0553|5end_Bacteroides_aerotolerance_protein,_BatD_584462..584692_POSITIVE 432 185 142 109 61 tfor:TF0688|5end_membrane-associated_protein,_possible_sulfatase_family_732760..732990_POSITIVE 429 90 44 206 165 tfor:TF0543|5end_glycine_cleavage_system_p-protein_572251..572481_POSITIVE 425 110 61 220 164 tfor:TF2259|5end_transfer_region-related_protein,_TraK_2429577..2429807_POSITIVE 422 87 41 204 166 tfor:TF0655|5end_outer_membrane_protein_699947..700177_POSITIVE 421 90 43 67 10 tfor:TF1602|5end_L-aspartate_oxidase_1715579..1715809_POSITIVE 420 88 41 200 147 tfor:TF1329|5end_glucose-1-phosphate_thymidyltransferase_1408578..1408808_POSITIVE 418 109 61 117 53 tfor:TF0600|5end_oxidoreductase/dehydrogenase_630083..630313_POSITIVE 417 109 61 213 172 tfor:TF2224|5end_CTn_excision_protein_2394592..2394822_POSITIVE 413 110 64 164 120 tfor:TF2782|5end_conserved_hypothetical_protein_2966455..2966685_POSITIVE 411 107 61 231 186 tfor:TF1929|5end_conserved_hypothetical_protein_2076049..2076279_POSITIVE 408 110 65 190 150 tfor:TF1909|5end_cobalamin_(5`-phosphate)_synthase_2063207..2063437_POSITIVE 405 107 65 67 12 tfor:TF2128|5end_3-oxoacyl-(acyl-carrier_protein)_synthase_2304258..2304488_POSITIVE 403 198 151 216 165 tfor:TF0004|5end_conserved_hypothetical_protein_1736..1966_POSITIVE 402 179 131 51 4 tfor:TF0464|5end_precorrin_methylase_480211..480441_POSITIVE 399 97 53 196 138 tfor:TF3141|5end_NADH:_ubiquinone_oxidoreductase,_subunit_A_3374667..3374897_POSITIVE 399 90 43 206 149 tfor:TF1845|5end_hypothetical_protein_1996620..1996850_POSITIVE 399 87 43 71 27 tfor:TF0414|5end_N-ethylammeline_chlorohydrolase_431789..432019_POSITIVE 399 110 61 217 168 tfor:TF0289|5end_conserved_hypothetical_protein_318015..318245_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 418 109 61 84 20 tfor:TF0599|3end_hypothetical_protein_630130..630280_POSITIVE 402 106 64 147 111 tfor:TF2780|3end_hypothetical_protein_2966526..2966676_POSITIVE 402 179 131 51 4 tfor:TF0463|3end_precorrin-6Y_C5,15-methyltransferase_480291..480441_POSITIVE 399 84 41 89 54 tfor:TF2556|3end_conserved_hypothetical_protein_2737095..2737245_POSITIVE 399 87 43 71 27 tfor:TF0413|3end_succinyl-diaminopimelate_desuccinylase_431869..432019_POSITIVE 395 88 42 94 41 tfor:TF1295|3end_conserved_hypothetical_protein_1377256..1377406_POSITIVE 393 101 62 76 33 tfor:TF2515|3end_outer_membrane_protein,_TonB_dependent_receptor_2694865..2695015_POSITIVE 393 138 91 67 19 tfor:TF1160|3end_MutT/nudix_family_protein_1241008..1241158_POSITIVE 389 84 41 94 37 tfor:TF0744|3end_DNA_polymerase_III_subunit,_gamma/tau_792308..792458_POSITIVE 387 85 44 134 77 tfor:TF2730|3end_thiol:disulfide_interchange_protein_2910946..2911096_POSITIVE 376 88 49 49 4 tfor:TF0788|3end_protein-export_membrane_protein_841370..841520_POSITIVE 375 110 61 133 79 tfor:TF2735|3end_hypothetical_protein_2917928..2918078_POSITIVE 372 88 46 151 105 tfor:TF2745|3end_hypothetical_protein_2927947..2928097_POSITIVE 372 89 43 48 2 tfor:TF0279|3end_conserved_hypothetical_protein_308679..308829_POSITIVE 369 88 43 52 9 tfor:TF1382|3end_hypothetical_protein_1457777..1457927_POSITIVE 369 88 43 48 5 tfor:TF1383|3end_hypothetical_protein_1457773..1457923_POSITIVE 367 200 151 143 86 tfor:TF3106|3end_hypothetical_protein_3338608..3338758_POSITIVE 367 108 65 83 32 tfor:TF0825|3end_hypothetical_protein_883850..884000_POSITIVE 367 76 31 149 82 tfor:TF0291|3end_triose-phosphate_isomerase_320131..320281_POSITIVE 366 199 157 59 9 tfor:TF2012|3end_conserved_hypothetical_protein_2168720..2168870_POSITIVE