Origin IGS: cgttatttttttaatttatactccggcaataccggcaacgttattattgaatcggtcaaaggtacgaatattttcagcataatgaccataacataccgacgatttgtccgctcatcggcagaaagcaggtcataccgcggacgaacaacaaccttaaccttctcctca .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tgaggagaaggttaaggttgttgttcgtccgcggtatgacctgctttctgccgatgagcggacaaatcgtcggtatgttatggtcattatgctgaaaatattcgtacctttgaccgattcaataataacgttgccggtattgccggagtataaattaaaaaaataacg Mask Tandem Repeat Region ================================================ cgttatttttttaatttatactccggcaataccggcaacgttattattgaatcggtcaaaggtacgaatattttcagcataatgaccataacataccgacgatttgtccgctcatcggcagaaagcaggtcataccgcggacgaacaacaaccttaaccttctcctca Find is-nt database================================================ Query_seq: TF2086:TF2087|TF2086:TF2087:transglutaminase-related protein:conserved hypothetical protein:->->:2256828..2256995 168 cgttatttttttaatttatactccggcaataccggcaacgttattattgaatcggtcaaaggtacgaatattttcagcataatgaccataacataccgacgatttgtccgctcatcggcagaaagcaggtcataccgcggacgaacaacaaccttaaccttctcctca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF2086:TF2087|TF2086:TF2087:transglutaminase-related protein:conserved hypothetical protein:->->:2256828..2256995 168 cgttatttttttaatttatactccggcaataccggcaacgttattattgaatcggtcaaaggtacgaatattttcagcataatgaccataacataccgacgatttgtccgctcatcggcagaaagcaggtcataccgcggacgaacaacaaccttaaccttctcctca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF2086:TF2087|TF2086:TF2087:transglutaminase-related protein:conserved hypothetical protein:->->:2256828..2256995 168 cgttatttttttaatttatactccggcaataccggcaacgttattattgaatcggtcaaaggtacgaatattttcagcataatgaccataacataccgacgatttgtccgctcatcggcagaaagcaggtcataccgcggacgaacaacaaccttaaccttctcctca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 cgttatttttttaatttatactccggcaataccggcaacgttattattgaatcggtcaaaggtacgaatattttcagcataatgaccataacataccgacgatttgtccgctcatcggcagaaagcaggtcataccgcggacgaacaacaaccttaaccttctcctca Predict ORF larger than 30AA ================================================ Protein_Len: 39 Strand: + Start: 51 End: 167 .................................................. M G Q R Y E Y F Q H N D H N I P T I C P L I G R K Q V I P R T N N N L N L L L . Protein_Len: 42 Strand: + Start: 43 End: 168 .......................................... M I E S V K G T N I F S I M T I T Y R R F V R S S A E S R S Y R G R T T T L T F S S Protein_Len: 42 Strand: - Start: 6 End: 128 ..... * K K L K Y E P L V P L T I I S D T L P V F I K L M I V M V Y R R N T R E D A S L M ........................................ cgttatttttttaatttatactccggcaataccggcaacgttattattgaatcggtcaaaggtacgaatattttcagcataatgaccataacataccgacgatttgtccgctcatcggcagaaagcaggtcataccgcggacgaacaacaaccttaaccttctcctca 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================================================ cgttatttttttaatttatactccggcaataccggcaacgttattattgaatcggtcaaaggtacgaatattttcagcataatgaccataacataccgacgatttgtccgctcatcggcagaaagcaggtcataccgcggacgaacaacaaccttaaccttctcctca Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 45 HP_score: -2.3 Tail_Score: -3.31133 Start: 94 End: 120 Full_Region: gtatgacctgctttc tgccgatga gcggacaaa tcgtcggta tgttatggtcattat .............................................................................................tgccgatgagcggacaaatcgtcggta................................................ TransTerm Strand: - Conf: 44 HP_score: -2.7 Tail_Score: -3.21438 Start: 96 End: 118 Full_Region: atgacctgctttctg ccgatga gcggacaaa tcgtcgg tatgttatggtcatt ...............................................................................................ccgatgagcggacaaatcgtcgg.................................................. Find igs database================================================ Query_seq: TF2086:TF2087|TF2086:TF2087:transglutaminase-related protein:conserved hypothetical protein:->->:2256828..2256995 168 cgttatttttttaatttatactccggcaataccggcaacgttattattgaatcggtcaaaggtacgaatattttcagcataatgaccataacataccgacgatttgtccgctcatcggcagaaagcaggtcataccgcggacgaacaacaaccttaaccttctcctca Intra-Species Hit: Count: 1 Min: 13 Max: 168 Len: 156 Subject: tfor_TF2086_TF2087|transglutaminase-related protein:conserved hypothetical protein|POSITIVE:POSITIVE|[2256828,2256995]|168 HSP 1 e-value: 2.0E-83 bit: 309.0 Len: 156 Query Start:13 Query End:168 Subject Strand: POSITIVE Subject Start: 13 Subject End: 168 ............aatttatactccggcaataccggcaacgttattattgaatcggtcaaaggtacgaatattttcagcataatgaccataacataccgacgatttgtccgctcatcggcagaaagcaggtcataccgcggacgaacaacaaccttaaccttctcctca ............aatttatactccggcaataccggcaacgttattattgaatcggtcaaaggtacgaatattttcagcataatgaccataacataccgacgatttgtccgctcatcggcagaaagcaggtcataccgcggacgaacaacaaccttaaccttctcctca Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAUUUAUACUCCGGCAAUACCGGCAACGUUAUUAUUGAAUCGGUCAAAGGUACGAAUAUUUUCAGCAUAAUGACCAUAACAUACCGACGAUUUGUCCGCUCAUCGGCAGAAAGCAGGUCAUACCGCGGACGAACAACAACCUUAACCUUCUCCUCA ..........((((.....))))....((((...(((....(((((...((..(((....))).))....))))).............(.(((((((((......((.....)).((.....))))))))))))..)))...)))).......... (-30.70) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGAGGAGAAGGUUAAGGUUGUUGUUCGUCCGCGGUAUGACCUGCUUUCUGCCGAUGAGCGGACAAAUCGUCGGUAUGUUAUGGUCAUUAUGCUGAAAAUAUUCGUACCUUUGACCGAUUCAAUAAUAACGUUGCCGGUAUUGCCGGAGUAUAAAUU ...(((...(((((((((((.......((.(((..((((((.((....(((((((((.........))))))))).))...))))))..))).)).......)).))).))))))..))).......((....((((.....)))).))....... (-44.84) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 421 131 93 40 1 tfor:TF2809|5end_conserved_hypothetical_protein;_possible_translation_factor_(SUA5)_2999832..3000062_POSITIVE 406 129 83 112 65 tfor:TF0947|5end_extracellular_protease_990627..990857_POSITIVE 399 129 84 79 30 tfor:TF1933|5end_methionyl-tRNA_synthetase_2079675..2079905_POSITIVE 392 128 81 227 162 tfor:TF2307|5end_two-component_system_sensor_histidine_kinase/response_2462618..2462848_POSITIVE 391 140 97 59 2 tfor:TF2831|5end_ABC_transporter,_permease_component_3021317..3021547_POSITIVE 385 129 83 135 84 tfor:TF2820|5end_argininosuccinate_synthetase_3009876..3010106_POSITIVE 375 128 90 157 107 tfor:TF0303|5end_conserved_hypothetical_protein_328331..328561_POSITIVE 375 132 97 44 1 tfor:TF0013|5end_conserved_hypothetical_protein;_possible_TPR-repeat-containing_protein_6414..6644_POSITIVE 368 129 81 219 155 tfor:TF2932|5end_capsule_biosynthesis_protein_3135514..3135744_POSITIVE 364 126 84 208 153 tfor:TF2879|5end_tRNA_(guanine-N-1)-methyltransferase_3068254..3068484_POSITIVE 364 127 85 52 5 tfor:TF0826|5end_primosomal_protein_N'_883751..883981_POSITIVE 364 130 88 115 57 tfor:TF0062|5end_conserved_hypothetical_protein_64916..65146_POSITIVE 358 128 85 56 19 tfor:TF2801|5end_outer_membrane_protein,_TonB_dependent_receptor_2986285..2986515_POSITIVE 358 130 84 63 17 tfor:TF2267|5end_lysozyme-related_protein_2434869..2435099_POSITIVE 356 129 82 87 26 tfor:TF2445|5end_protoporphyrinogen_oxidase_2621457..2621687_POSITIVE 353 129 83 222 160 tfor:TF1859|5end_aspartate_carbamoyltransferase,_regulatory_subunit_2015711..2015941_POSITIVE 352 129 85 75 19 tfor:TF2457|5end_ABC_transporter,_permease_component,_zinc-binding_protein_2633147..2633377_POSITIVE 352 127 88 171 118 tfor:TF2145|5end_conserved_hypothetical_protein;_possible_rhodanese-domain_protein_2319764..2319994_POSITIVE 351 127 84 228 174 tfor:TF1261|5end_GrpE-related_chaperonin;_HSP-70_cofactor_1346504..1346734_POSITIVE 348 130 81 212 163 tfor:TF0713|5end_polypeptide_deformylase;_formylmethionine_deformylase;_763440..763670_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 406 129 83 103 56 tfor:TF0946|3end_iron(III)_ABC_transporter,_periplasmic_iron-binding_protein_990698..990848_POSITIVE 399 129 84 79 30 tfor:TF1932|3end_pigmentation_and_extracellular_proteinase_regulator_2079755..2079905_POSITIVE 391 140 97 81 24 tfor:TF2830|3end_ABC_transporter,_ATP-binding_protein_3021419..3021569_POSITIVE 385 129 83 135 84 tfor:TF2819|3end_N-acetyl-gamma-glutamylphosphate_reductase_3009956..3010106_POSITIVE 364 127 85 71 24 tfor:TF0825|3end_hypothetical_protein_883850..884000_POSITIVE 364 130 88 125 67 tfor:TF0061|3end_hypothetical_protein_65006..65156_POSITIVE 362 131 96 37 1 tfor:TF2808|3end_bacterial_sugar_transferase_2999909..3000059_POSITIVE 358 130 84 63 17 tfor:TF2266|3end_transfer_region-related_protein,_TraQ_2434949..2435099_POSITIVE 356 129 82 99 38 tfor:TF2444|3end_regulatory_protein_RecX_2621549..2621699_POSITIVE 345 127 83 142 96 tfor:TF2515|3end_outer_membrane_protein,_TonB_dependent_receptor_2694865..2695015_POSITIVE 337 128 83 72 14 tfor:TF2846|3end_cobyric_acid_synthase_3036469..3036619_POSITIVE 329 46 2 136 93 tfor:TF0380|3end_conserved_hypothetical_protein_401633..401783_POSITIVE 327 148 106 75 10 tfor:TF2275|3end_conserved_hypothetical_protein_2438300..2438450_POSITIVE 326 127 81 133 90 tfor:TF2618|3end_integral_membrane_protein,_possible_zinc_transporter_2796113..2796263_POSITIVE 325 128 88 127 87 tfor:TF0528|3end_two-component_system_sensor_histidine_kinase_554779..554929_POSITIVE 324 128 97 37 7 tfor:TF2800|3end_anti-sigma_factor_2986346..2986496_POSITIVE 319 130 86 151 109 tfor:TF3087|3end_conserved_hypothetical_protein_3322582..3322732_POSITIVE 318 129 86 56 1 tfor:TF2456|3end_ABC_transporter,_ATP-binding_protein_2633208..2633358_POSITIVE 318 127 89 136 84 tfor:TF2133|3end_aspartate-semialdehyde_dehydrogenase_2311362..2311512_POSITIVE 316 118 74 42 10 tfor:TF3093|3end_30S_ribosomal_protein_S2_3326181..3326331_POSITIVE