Origin IGS: tgataacaggtttggcatagccggaacgtaccatcttcataaatggcctccggaagtgaagaaatcgatatcggatgaatgaaaaaactgaaccgatgcgtaccattatctgaaaaaaagagcctatctttgtcagaccttctgccaattttactgggcggagaaaaaagaaataaatacacaataaagcataatatcatttctgatt .........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 aatcagaaatgatattatgctttattgtgtatttatttcttttttctccgcccagtaaaattggcagaaggtctgacaaagataggctctttttttcagataatggtacgcatcggttcagttttttcattcatccgatatcgatttcttcacttccggaggccatttatgaagatggtacgttccggctatgccaaacctgttatca Mask Tandem Repeat Region ================================================ tgataacaggtttggcatagccggaacgtaccatcttcataaatggcctccggaagtgaagaaatcgatatcggatgaatgaaaaaactgaaccgatgcgtaccattatctgaaaaaaagagcctatctttgtcagaccttctgccaattttactgggcggagaaaaaagaaataaatacacaataaagcataatatcatttctgatt Find is-nt database================================================ Query_seq: TF3143:TF3144|TF3143:TF3144:conserved hypothetical protein; possible membrane protein:phosphomannomutase/phosphoglucomutase:->->:3379288..3379495 208 tgataacaggtttggcatagccggaacgtaccatcttcataaatggcctccggaagtgaagaaatcgatatcggatgaatgaaaaaactgaaccgatgcgtaccattatctgaaaaaaagagcctatctttgtcagaccttctgccaattttactgggcggagaaaaaagaaataaatacacaataaagcataatatcatttctgatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF3143:TF3144|TF3143:TF3144:conserved hypothetical protein; possible membrane protein:phosphomannomutase/phosphoglucomutase:->->:3379288..3379495 208 tgataacaggtttggcatagccggaacgtaccatcttcataaatggcctccggaagtgaagaaatcgatatcggatgaatgaaaaaactgaaccgatgcgtaccattatctgaaaaaaagagcctatctttgtcagaccttctgccaattttactgggcggagaaaaaagaaataaatacacaataaagcataatatcatttctgatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF3143:TF3144|TF3143:TF3144:conserved hypothetical protein; possible membrane protein:phosphomannomutase/phosphoglucomutase:->->:3379288..3379495 208 tgataacaggtttggcatagccggaacgtaccatcttcataaatggcctccggaagtgaagaaatcgatatcggatgaatgaaaaaactgaaccgatgcgtaccattatctgaaaaaaagagcctatctttgtcagaccttctgccaattttactgggcggagaaaaaagaaataaatacacaataaagcataatatcatttctgatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tgataacaggtttggcatagccggaacgtaccatcttcataaatggcctccggaagtgaagaaatcgatatcggatgaatgaaaaaactgaaccgatgcgtaccattatctgaaaaaaagagcctatctttgtcagaccttctgccaattttactgggcggagaaaaaagaaataaatacacaataaagcataatatcatttctgatt Predict ORF larger than 30AA ================================================ Protein_Len: 43 Strand: + Start: 79 End: 207 .............................................................................. M K K L N R C V P L S E K K S L S L S D L L P I L L G G E K R N K Y T I K H N I I S D . Protein_Len: 60 Strand: - Start: 3 End: 200 .. R F T G D E Y I A E P L S S I S I P H I F F S F R H T G N D S F F L R D K D S R R G I K S P P S F L F L Y V I F C L I M ........ Protein_Len: 60 Strand: - Start: 2 End: 184 . V P K A Y G S R V M K M F P R R F H L F R Y R I F S F V S G I R V M I Q F F S G I K T L G E A L K V P R L F F F Y I C M ........................ tgataacaggtttggcatagccggaacgtaccatcttcataaatggcctccggaagtgaagaaatcgatatcggatgaatgaaaaaactgaaccgatgcgtaccattatctgaaaaaaagagcctatctttgtcagaccttctgccaattttactgggcggagaaaaaagaaataaatacacaataaagcataatatcatttctgatt 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================================================ tgataacaggtttggcatagccggaacgtaccatcttcataaatggcctccggaagtgaagaaatcgatatcggatgaatgaaaaaactgaaccgatgcgtaccattatctgaaaaaaagagcctatctttgtcagaccttctgccaattttactgggcggagaaaaaagaaataaatacacaataaagcataatatcatttctgatt Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 71 HP_score: -6.0 Tail_Score: -4.25104 Start: 130 End: 148 Full_Region: AAAAAGAGCCTATCT TTGTCAGA CCT TCTGCCAA TTTTACTGGGCGGAG .................................................................................................................................TTGTCAGACCTTCTGCCAA............................................................ Find igs database================================================ Query_seq: TF3143:TF3144|TF3143:TF3144:conserved hypothetical protein; possible membrane protein:phosphomannomutase/phosphoglucomutase:->->:3379288..3379495 208 tgataacaggtttggcatagccggaacgtaccatcttcataaatggcctccggaagtgaagaaatcgatatcggatgaatgaaaaaactgaaccgatgcgtaccattatctgaaaaaaagagcctatctttgtcagaccttctgccaattttactgggcggagaaaaaagaaataaatacacaataaagcataatatcatttctgatt Intra-Species Hit: Count: 1 Min: 1 Max: 208 Len: 208 Subject: tfor_TF3143_TF3144|conserved hypothetical protein; possible membrane protein:phosphomannomutase/phosphoglucomutase|POSITIVE:P OSITIVE|[3379288,3379495]|208 HSP 1 e-value: 1.0E-102 bit: 371.0 Len: 208 Query Start:1 Query End:208 Subject Strand: POSITIVE Subject Start: 1 Subject End: 208 tgataacaggtttggcatagccggaacgtaccatcttcataaatggcctccggaagtgaagaaatcgatatcggatgaatgaaaaaactgaaccgatgcgtaccattatctgnnnnnnngagcctatctttgtcagaccttctgccaattttactgggcggagaaaaaagaaataaatacacaataaagcataatatcatttctgatt tgataacaggtttggcatagccggaacgtaccatcttcataaatggcctccggaagtgaagaaatcgatatcggatgaatgaaaaaactgaaccgatgcgtaccattatctgaaaaaaagagcctatctttgtcagaccttctgccaattttactgggcggagaaaaaagaaataaatacacaataaagcataatatcatttctgatt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGAUAACAGGUUUGGCAUAGCCGGAACGUACCAUCUUCAUAAAUGGCCUCCGGAAGUGAAGAAAUCGAUAUCGGAUGAAUGAAAAAACUGAACCGAUGCGUACCAUUAUCUGAAAAAAAGAGCCUAUCUUUGUCAGACCUUCUGCCAAUUUUACUGGGCGGAGAAAAAAGAAAUAAAUACACAAUAAAGCAUAAUAUCAUUUCUGAUU (((((...((((..((((..(((((.....((((........))))..)))))..)))......(((....))).............)..)))).((((.........(((((...(((((.....))))).)))))..(((((((..........))))))).........................))))..)))))......... (-45.50) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAUCAGAAAUGAUAUUAUGCUUUAUUGUGUAUUUAUUUCUUUUUUCUCCGCCCAGUAAAAUUGGCAGAAGGUCUGACAAAGAUAGGCUCUUUUUUUCAGAUAAUGGUACGCAUCGGUUCAGUUUUUUCAUUCAUCCGAUAUCGAUUUCUUCACUUCCGGAGGCCAUUUAUGAAGAUGGUACGUUCCGGCUAUGCCAAACCUGUUAUCA ....((((((((...(((((......))))).)))))))).....................((((((...((((((.(((((.....)))))...))))))..(((((...(((((...(((......)))...)))))................(((((((((((((....)))))))...))))))...)))))...))))))... (-45.30) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 389 57 12 195 142 tfor:TF0404|5end_conserved_hypothetical_protein_423432..423662_POSITIVE 355 114 71 73 32 tfor:TF2677|5end_aspartate_transaminase_2850809..2851039_POSITIVE 334 136 92 191 127 tfor:TF3105|5end_hypothetical_protein_3338068..3338298_POSITIVE 330 60 11 128 63 tfor:TF0813|5end_glycosyl_hydrolase,_secreted_870677..870907_POSITIVE 328 159 121 150 102 tfor:TF1955|5end_amino_acid_exporter,_possible_threonine_efflux_protein_2106952..2107182_POSITIVE 327 89 44 72 24 tfor:TF1422|5end_GLCNAC_transferase_(UDP-N-acetylglucosamine-N-acetylmuramyl-(pentapeptide)-pyr_ophosphoryl-undecaprenol_N-acetylglucosamine_transferase)_1504841..1505071_POSITIVE 318 100 51 137 83 tfor:TF0372|5end_transcriptional_regulator_390538..390768_POSITIVE 314 69 21 85 29 tfor:TF0376|5end_conserved_hypothetical_protein_394303..394533_POSITIVE 313 59 13 66 27 tfor:TF2343|5end_ribosome_recycling_factor_2506862..2507092_POSITIVE 313 100 52 85 28 tfor:TF1036|5end_iron(III)_ABC_transporter,_permease_component_1097160..1097390_POSITIVE 313 54 14 104 42 tfor:TF0253|5end_conserved_hypothetical_protein_283707..283937_POSITIVE 308 59 13 64 26 tfor:TF0248|5end_hypothetical_protein_278249..278479_POSITIVE 302 67 21 53 3 tfor:TF0585|5end_conserved_hypothetical_protein_614782..615012_POSITIVE 301 59 16 73 22 tfor:TF2322|5end_conserved_hypothetical_protein;_possible_lipoprotein_2482743..2482973_POSITIVE 301 161 121 59 29 tfor:TF2252|5end_transfer_region-related_protein,_TraF_2424621..2424851_POSITIVE 299 59 11 77 8 tfor:TF2893|5end_conserved_hypothetical_protein;_possible_phosphoesterase_3080766..3080996_POSITIVE 299 53 11 229 175 tfor:TF0954|5end_2-hydroxyhepta-2,4-diene-1,7-dioate_isomerase,_fumarylacetoacetate_hydrolase_family_998584..998814_POSITIVE 297 75 32 107 59 tfor:TF3160|5end_conserved_hypothetical_protein_3395531..3395761_POSITIVE 296 77 32 82 34 tfor:TF1580|5end_conserved_hypothetical_protein;_possible_fibronectin_domain_containing_protein_1687187..1687417_POSITIVE 295 59 12 111 47 tfor:TF1721|5end_2,3-bisphosphoglycerate-independent_phosphoglycerate_mutase_1844374..1844604_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 330 60 11 95 30 tfor:TF0811|3end_conserved_hypothetical_protein;_posible_sugar_phosphate_isomerase_870724..870874_POSITIVE 328 159 121 58 10 tfor:TF1954|3end_long-chain-fatty-acid--CoA_ligase_2106940..2107090_POSITIVE 327 89 44 72 24 tfor:TF1421|3end_UDP-N-acetylmuramate--alanine_ligase_1504921..1505071_POSITIVE 313 100 52 85 28 tfor:TF1035|3end_iron(III)_ABC_transporter,_periplasmic-binding_protein_1097240..1097390_POSITIVE 313 54 14 76 14 tfor:TF0252|3end_hypothetical_protein_283759..283909_POSITIVE 308 59 13 83 45 tfor:TF0247|3end_conserved_hypothetical_protein_278348..278498_POSITIVE 305 55 13 145 101 tfor:TF2617|3end_conserved_hypothetical_protein_2795172..2795322_POSITIVE 301 161 121 45 15 tfor:TF2251|3end_conjugative_transposon_protein,_TraE_2424687..2424837_POSITIVE 297 75 32 107 59 tfor:TF3159|3end_conserved_hypothetical_protein;_possible_transcriptional_regulator_3395611..3395761_POSITIVE 296 77 32 89 41 tfor:TF1579|3end_hypothetical_protein_1687274..1687424_POSITIVE 293 70 21 71 20 tfor:TF3124|3end_dTDP-glucose_4,6-dehydratase_3359883..3360033_POSITIVE 290 160 119 142 103 tfor:TF2189|3end_conserved_hypothetical_protein_2364884..2365034_POSITIVE 290 88 43 67 3 tfor:TF0699|3end_pyridoxal_phosphate_biosynthetic_protein_742745..742895_POSITIVE 289 50 2 99 46 tfor:TF2344|3end_ATP/GTP_binding_protein_2508434..2508584_POSITIVE 286 75 35 58 7 tfor:TF2170|3end_hypothetical_protein_2345070..2345220_POSITIVE 278 82 45 99 61 tfor:TF2917|3end_conserved_hypothetical_protein_3114161..3114311_POSITIVE 278 100 51 117 69 tfor:TF2509|3end_ATP-dependent_clp_protease,_proteolytic_subunit_2688304..2688454_POSITIVE 278 77 35 85 38 tfor:TF1686|3end_alginate_O-acetylation_protein_1802068..1802218_POSITIVE 276 58 15 50 11 tfor:TF2379|3end_phosphoribosylformylglycinamidine_cyclo-ligase_(AIR_synthase)_2545092..2545242_POSITIVE 275 135 99 57 25 tfor:TF1434|3end_transketolase_1519595..1519745_POSITIVE