Origin IGS: tagccatcgttcgtgaatgaggagagtgagaaacgaagaacgaaaagtgaaatatgcgtttatttgcgtcatttgcgttactcgcgttcgaatcgaacatcgcaattcgtaattcgacattcgtaattcattctta .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 taagaatgaattacgaatgtcgaattacgaattgcgatgttcgattcgaacgcgagtaacgcaaatgacgcaaataaacgcatatttcacttttcgttcttcgtttctcactctcctcattcacgaacgatggcta Mask Tandem Repeat Region ================================================ tagccatcgttcgtgaatgaggagagtgagaaacgaagaacgaaaagtgaaatatgcgtttatttgcgtcatttgcgttactcgcgttcgaatcgaacatcgcaattcgtaattcgacattcgtaattcattctta Find is-nt database================================================ Query_seq: TF2013:TF2014|TF2013:TF2014:polysaccharide deacetylase:dipeptidyl aminopeptidase IV:->->:2169402..2169537 136 tagccatcgttcgtgaatgaggagagtgagaaacgaagaacgaaaagtgaaatatgcgtttatttgcgtcatttgcgttactcgcgttcgaatcgaacatcgcaattcgtaattcgacattcgtaattcattctta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF2013:TF2014|TF2013:TF2014:polysaccharide deacetylase:dipeptidyl aminopeptidase IV:->->:2169402..2169537 136 tagccatcgttcgtgaatgaggagagtgagaaacgaagaacgaaaagtgaaatatgcgtttatttgcgtcatttgcgttactcgcgttcgaatcgaacatcgcaattcgtaattcgacattcgtaattcattctta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF2013:TF2014|TF2013:TF2014:polysaccharide deacetylase:dipeptidyl aminopeptidase IV:->->:2169402..2169537 136 tagccatcgttcgtgaatgaggagagtgagaaacgaagaacgaaaagtgaaatatgcgtttatttgcgtcatttgcgttactcgcgttcgaatcgaacatcgcaattcgtaattcgacattcgtaattcattctta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tagccatcgttcgtgaatgaggagagtgagaaacgaagaacgaaaagtgaaatatgcgtttatttgcgtcatttgcgttactcgcgttcgaatcgaacatcgcaattcgtaattcgacattcgtaattcattctta Predict ORF larger than 30AA ================================================ Protein_Len: 31 Strand: + Start: 17 End: 109 ................ M R R V R N E E R K V K Y A F I C V I C V T R V R I E H R N S ........................... Protein_Len: 37 Strand: + Start: 13 End: 123 ............ M N E E S E K R R T K S E I C V Y L R H L R Y S R S N R T S Q F V I R H S ............. Protein_Len: 42 Strand: - Start: 2 End: 127 . A M T R S H P S H S V F F S F H F I R K N A D N A N S A N S D F M A I R L E V N T M ......... Protein_Len: 40 Strand: - Start: 1 End: 120 L W R E H I L L T L F S S R F T F Y A N I Q T M Q T V R T R I S C R L E Y N S M ................ tagccatcgttcgtgaatgaggagagtgagaaacgaagaacgaaaagtgaaatatgcgtttatttgcgtcatttgcgttactcgcgttcgaatcgaacatcgcaattcgtaattcgacattcgtaattcattctta 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================================================ tagccatcgttcgtgaatgaggagagtgagaaacgaagaacgaaaagtgaaatatgcgtttatttgcgtcatttgcgttactcgcgttcgaatcgaacatcgcaattcgtaattcgacattcgtaattcattctta Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TF2013:TF2014|TF2013:TF2014:polysaccharide deacetylase:dipeptidyl aminopeptidase IV:->->:2169402..2169537 136 tagccatcgttcgtgaatgaggagagtgagaaacgaagaacgaaaagtgaaatatgcgtttatttgcgtcatttgcgttactcgcgttcgaatcgaacatcgcaattcgtaattcgacattcgtaattcattctta Intra-Species Hit: Count: 1 Min: 1 Max: 136 Len: 136 Subject: tfor_TF2013_TF2014|polysaccharide deacetylase:dipeptidyl aminopeptidase IV|POSITIVE:POSITIVE|[2169402,2169537]|136 HSP 1 e-value: 1.0E-71 bit: 270.0 Len: 136 Query Start:1 Query End:136 Subject Strand: POSITIVE Subject Start: 1 Subject End: 136 tagccatcgttcgtgaatgaggagagtgagaaacgaagaacgaaaagtgaaatatgcgtttatttgcgtcatttgcgttactcgcgttcgaatcgaacatcgcaattcgtaattcgacattcgtaattcattctta tagccatcgttcgtgaatgaggagagtgagaaacgaagaacgaaaagtgaaatatgcgtttatttgcgtcatttgcgttactcgcgttcgaatcgaacatcgcaattcgtaattcgacattcgtaattcattctta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAGCCAUCGUUCGUGAAUGAGGAGAGUGAGAAACGAAGAACGAAAAGUGAAAUAUGCGUUUAUUUGCGUCAUUUGCGUUACUCGCGUUCGAAUCGAACAUCGCAAUUCGUAAUUCGACAUUCGUAAUUCAUUCUUA ......(((((....))))).(((((((((..((((((((((...(((((...((((((......))).))).....)))))..)))))...(((((...((.....))...)))))..)))))..))))))))). (-33.90) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAGAAUGAAUUACGAAUGUCGAAUUACGAAUUGCGAUGUUCGAUUCGAACGCGAGUAACGCAAAUGACGCAAAUAAACGCAUAUUUCACUUUUCGUUCUUCGUUUCUCACUCUCCUCAUUCACGAACGAUGGCUA ...((((((....((((((((((((.....))).)))))))))....(((.(((((.((((.((((((.((........)).....))).))).)))).)))))))).........)))))).............. (-26.90) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 477 90 41 224 175 tfor:TF1841|5end_hypothetical_protein_1991936..1992166_POSITIVE 448 100 55 102 53 tfor:TF1184|5end_hypothetical_protein_1269004..1269234_POSITIVE 440 90 47 55 11 tfor:TF2652|5end_hypothetical_protein_2821803..2822033_POSITIVE 427 96 55 226 179 tfor:TF1844|5end_hypothetical_protein_1996389..1996619_POSITIVE 423 99 55 137 87 tfor:TF3105|5end_hypothetical_protein_3338068..3338298_POSITIVE 423 50 1 119 64 tfor:TF1173|5end_ABC_transporter,_permease_component_1255444..1255674_POSITIVE 410 48 7 140 99 tfor:TF2779|5end_fucose_permease_2964566..2964796_POSITIVE 410 50 8 211 167 tfor:TF1588|5end_hypothetical_protein_1702268..1702498_POSITIVE 403 107 61 166 116 tfor:TF2816|5end_hypothetical_protein_3006925..3007155_POSITIVE 383 50 1 129 72 tfor:TF1589|5end_surface_antigen_BspA_1703189..1703419_POSITIVE 382 57 13 136 87 tfor:TF1172|5end_ABC_transporter,_permease_component_1252806..1253036_POSITIVE 377 57 18 127 92 tfor:TF0359|5end_conserved_hypothetical_protein_376943..377173_POSITIVE 370 100 55 136 87 tfor:TF1187|5end_hypothetical_protein_1269625..1269855_POSITIVE 370 100 55 79 30 tfor:TF1186|5end_hypothetical_protein_1269568..1269798_POSITIVE 367 69 21 145 102 tfor:TF0347|5end_possible_serine_protease_367542..367772_POSITIVE 358 102 61 36 2 tfor:TF0373|5end_conserved_hypothetical_protein,_yngK-related_391038..391268_POSITIVE 357 69 21 143 93 tfor:TF2167|5end_hypothetical_protein_2342586..2342816_POSITIVE 331 48 1 120 72 tfor:TF1591|5end_surface_antigen_BspA_1706387..1706617_POSITIVE 329 89 41 165 119 tfor:TF0307|5end_conserved_hypothetical_protein_332783..333013_POSITIVE 327 57 18 127 92 tfor:TF0351|5end_hypothetical_protein_370922..371152_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 475 90 55 128 93 tfor:TF1841|3end_hypothetical_protein_1992267..1992417_POSITIVE 369 100 55 68 20 tfor:TF2823|3end_TPR-containing_protein_3014337..3014487_POSITIVE 358 102 61 36 2 tfor:TF0372|3end_transcriptional_regulator_391118..391268_POSITIVE 356 57 14 49 1 tfor:TF1170|3end_conserved_hypothetical_protein_1252799..1252949_POSITIVE 329 89 41 51 5 tfor:TF0306|3end_transglutaminase-like_enzyme/cysteine_protease_332749..332899_POSITIVE 316 110 61 64 4 tfor:TF2659|3end_conserved_hypothetical_protein_2833055..2833205_POSITIVE 315 36 3 72 38 tfor:TF3155|3end_glycosyltransferase,_group_2_family_protein_3391444..3391594_POSITIVE 315 124 81 91 56 tfor:TF2430|3end_hypothetical_protein_2613204..2613354_POSITIVE 314 88 47 44 8 tfor:TF0078|3end_aminopeptidase_C,_peptidase_C1-like_family_85802..85952_POSITIVE 313 104 62 124 82 tfor:TF1291|3end_response_regulator_(fimR__protein)_1372647..1372797_POSITIVE 312 102 64 149 118 tfor:TF1245|3end_LemA_protein_1329462..1329612_POSITIVE 309 56 21 82 47 tfor:TF1783|3end_conserved_hypothetical_protein_1923865..1924015_POSITIVE 306 109 62 151 93 tfor:TF1104|3end_hypothetical_protein_1172194..1172344_POSITIVE 301 40 7 69 27 tfor:TF1985|3end_surface_antigen_BspA_2136905..2137055_POSITIVE 300 100 57 43 1 tfor:TF2816|3end_hypothetical_protein_3007184..3007334_POSITIVE 299 109 63 148 97 tfor:TF1184|3end_hypothetical_protein_1269311..1269461_POSITIVE 299 109 63 148 97 tfor:TF1183|3end_hypothetical_protein_1268728..1268878_POSITIVE 297 85 57 145 119 tfor:TF1276|3end_acyl-CoA_dehydrogenase_(short_chain_coenzyme_A_dehydrogenase)_1363080..1363230_POSITIVE 296 42 1 143 105 tfor:TF2852|3end_conserved_hypothetical_protein_3040221..3040371_POSITIVE 295 44 7 49 15 tfor:TF2365|3end_conserved_hypothetical_protein_2531280..2531430_POSITIVE