Origin IGS: cacggggcaaaggtaaaaaaaactgaagtactatccttaatttttggatcgatttattcagctccggcgtatctgctcttaaaccgaatgatccggacgattgcagatcgcagatacatgataatacgctgcaaacacacggaaacacgacaggtttttatatttccggcataggatatcctgctttttgtctaattttgtacgctcaattgatacatcata .........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 tatgatgtatcaattgagcgtacaaaattagacaaaaagcaggatatcctatgccggaaatataaaaacctgtcgtgtttccgtgtgtttgcagcgtattatcatgtatctgcgatctgcaatcgtccggatcattcggtttaagagcagatacgccggagctgaataaatcgatccaaaaattaaggatagtacttcagttttttttacctttgccccgtg Mask Tandem Repeat Region ================================================ cacggggcaaaggtaaaaaaaactgaagtactatccttaatttttggatcgatttattcagctccggcgtatctgctcttaaaccgaatgatccggacgattgcagatcgcagatacatgataatacgctgcaaacacacggaaacacgacaggtttttatatttccggcataggatatcctgctttttgtctaattttgtacgctcaattgatacatcata Find is-nt database================================================ Query_seq: TF0435:TF0436|TF0435:TF0436:DNA mismatch repair protein:conserved hyothetical protein:->->:459125..459346 222 cacggggcaaaggtaaaaaaaactgaagtactatccttaatttttggatcgatttattcagctccggcgtatctgctcttaaaccgaatgatccggacgattgcagatcgcagatacatgataatacgctgcaaacacacggaaacacgacaggtttttatatttccggcataggatatcctgctttttgtctaattttgtacgctcaattgatacatcata Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF0435:TF0436|TF0435:TF0436:DNA mismatch repair protein:conserved hyothetical protein:->->:459125..459346 222 cacggggcaaaggtaaaaaaaactgaagtactatccttaatttttggatcgatttattcagctccggcgtatctgctcttaaaccgaatgatccggacgattgcagatcgcagatacatgataatacgctgcaaacacacggaaacacgacaggtttttatatttccggcataggatatcctgctttttgtctaattttgtacgctcaattgatacatcata Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF0435:TF0436|TF0435:TF0436:DNA mismatch repair protein:conserved hyothetical protein:->->:459125..459346 222 cacggggcaaaggtaaaaaaaactgaagtactatccttaatttttggatcgatttattcagctccggcgtatctgctcttaaaccgaatgatccggacgattgcagatcgcagatacatgataatacgctgcaaacacacggaaacacgacaggtttttatatttccggcataggatatcctgctttttgtctaattttgtacgctcaattgatacatcata Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 cacggggcaaaggtaaaaaaaactgaagtactatccttaatttttggatcgatttattcagctccggcgtatctgctcttaaaccgaatgatccggacgattgcagatcgcagatacatgataatacgctgcaaacacacggaaacacgacaggtttttatatttccggcataggatatcctgctttttgtctaattttgtacgctcaattgatacatcata Predict ORF larger than 30AA ================================================ Protein_Len: 44 Strand: + Start: 40 End: 171 ....................................... M F G S I Y S A P A Y L L L N R M I R T I A D R R Y M I I R C K H T E T R Q V F I F P A ................................................... Protein_Len: 60 Strand: + Start: 33 End: 221 ................................ M L N F W I D L F S S G V S A L K P N D P D D C R S Q I H D N T L Q T H G N T T G F Y I S G I G Y P A F C L I L Y A Q L . Protein_Len: 43 Strand: - Start: 82 End: 210 ................................................................................. V S H D P R N C I A S V H Y Y A A F V R F C S L N K Y K R C L I D Q K K D L K T R E M ............ Protein_Len: 41 Strand: - Start: 57 End: 179 ........................................................ E A G A Y R S K F R I I R V I A S R L Y M I I R Q L C V S V R C T K I N G A Y S M ........................................... Protein_Len: 49 Strand: - Start: 2 End: 148 . R P L P L F F Q L V I R L K Q I S K N L E P T D A R L G F S G S S Q L D C I C S L V S C V C P F M .......................................................................... cacggggcaaaggtaaaaaaaactgaagtactatccttaatttttggatcgatttattcagctccggcgtatctgctcttaaaccgaatgatccggacgattgcagatcgcagatacatgataatacgctgcaaacacacggaaacacgacaggtttttatatttccggcataggatatcctgctttttgtctaattttgtacgctcaattgatacatcata 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================================================ cacggggcaaaggtaaaaaaaactgaagtactatccttaatttttggatcgatttattcagctccggcgtatctgctcttaaaccgaatgatccggacgattgcagatcgcagatacatgataatacgctgcaaacacacggaaacacgacaggtttttatatttccggcataggatatcctgctttttgtctaattttgtacgctcaattgatacatcata Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TF0435:TF0436|TF0435:TF0436:DNA mismatch repair protein:conserved hyothetical protein:->->:459125..459346 222 cacggggcaaaggtaaaaaaaactgaagtactatccttaatttttggatcgatttattcagctccggcgtatctgctcttaaaccgaatgatccggacgattgcagatcgcagatacatgataatacgctgcaaacacacggaaacacgacaggtttttatatttccggcataggatatcctgctttttgtctaattttgtacgctcaattgatacatcata Intra-Species Hit: Count: 1 Min: 23 Max: 222 Len: 200 Subject: tfor_TF0435_TF0436|DNA mismatch repair protein:conserved hyothetical protein|POSITIVE:POSITIVE|[459125,459346]|222 HSP 1 e-value: 1.0E-109 bit: 396.0 Len: 200 Query Start:23 Query End:222 Subject Strand: POSITIVE Subject Start: 23 Subject End: 222 ......................ctgaagtactatccttaatttttggatcgatttattcagctccggcgtatctgctcttaaaccgaatgatccggacgattgcagatcgcagatacatgataatacgctgcaaacacacggaaacacgacaggtttttatatttccggcataggatatcctgctttttgtctaattttgtacgctcaattgatacatcata ......................ctgaagtactatccttaatttttggatcgatttattcagctccggcgtatctgctcttaaaccgaatgatccggacgattgcagatcgcagatacatgataatacgctgcaaacacacggaaacacgacaggtttttatatttccggcataggatatcctgctttttgtctaattttgtacgctcaattgatacatcata Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CUGAAGUACUAUCCUUAAUUUUUGGAUCGAUUUAUUCAGCUCCGGCGUAUCUGCUCUUAAACCGAAUGAUCCGGACGAUUGCAGAUCGCAGAUACAUGAUAAUACGCUGCAAACACACGGAAACACGACAGGUUUUUAUAUUUCCGGCAUAGGAUAUCCUGCUUUUUGUCUAAUUUUGUACGCUCAAUUGAUACAUCAUA .(((.(((..((((.........))))(((((...(((......(((.((((((.......(((.......)))......))))))))).......)))......((((((((.....(....)..((((((..........(((......)))..........))))))....)))))).))..))))).))).))).. (-39.49) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAUGAUGUAUCAAUUGAGCGUACAAAAUUAGACAAAAAGCAGGAUAUCCUAUGCCGGAAAUAUAAAAACCUGUCGUGUUUCCGUGUGUUUGCAGCGUAUUAUCAUGUAUCUGCGAUCUGCAAUCGUCCGGAUCAUUCGGUUUAAGAGCAGAUACGCCGGAGCUGAAUAAAUCGAUCCAAAAAUUAAGGAUAGUACUUCAG ..............((((.((((...............((((........(((((((((((((...........))))))))).))))((((((.((((......)))))))))).))))....((((((((((((((((((....((......))..))))))))).....))))).........)))).)))))))). (-47.40) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 422 80 38 171 136 tfor:TF1898|5end_RNA_polymerase_ECF-type_sigma_factor_2052115..2052345_POSITIVE 397 49 1 175 131 tfor:TF2181|5end_conserved_hypothetical_protein_2353870..2354100_POSITIVE 391 80 35 156 97 tfor:TF3125|5end_recombination/repair_protein_3359808..3360038_POSITIVE 382 85 41 111 73 tfor:TF0253|5end_conserved_hypothetical_protein_283707..283937_POSITIVE 371 89 41 52 16 tfor:TF2267|5end_lysozyme-related_protein_2434869..2435099_POSITIVE 369 90 42 76 23 tfor:TF2296|5end_hypothetical_protein_2448892..2449122_POSITIVE 369 76 34 164 129 tfor:TF0765|5end_conserved_hypothetical_protein_811302..811532_POSITIVE 367 90 43 112 64 tfor:TF0600|5end_oxidoreductase/dehydrogenase_630083..630313_POSITIVE 360 88 41 221 168 tfor:TF2196|5end_hypothetical_protein_2371678..2371908_POSITIVE 359 80 36 80 37 tfor:TF2304|5end_OmpA_family_protein_2459320..2459550_POSITIVE 358 100 53 70 19 tfor:TF0906|5end_conserved_hypothetical_protein_949675..949905_POSITIVE 350 120 71 199 139 tfor:TF3039|5end_ABC_transporter,_ATP-binding_protein_3265731..3265961_POSITIVE 346 120 71 85 44 tfor:TF1198|5end_conserved_hypothetical_protein_1281464..1281694_POSITIVE 346 76 36 136 78 tfor:TF0187|5end_ferredoxin_202151..202381_POSITIVE 345 89 41 227 183 tfor:TF1622|5end_conserved_hypothetical_protein_1736393..1736623_POSITIVE 344 90 41 121 71 tfor:TF2883|5end_peptidyl-prolyl_cis-trans_isomerase_3074321..3074551_POSITIVE 344 88 41 72 17 tfor:TF2560|5end_30S_ribosomal_protein_S3_2737897..2738127_POSITIVE 344 79 36 73 28 tfor:TF1494|5end_cobinamide_kinase/cobinamide_phosphate_guanylyltransferase_1594016..1594246_POSITIVE 337 89 43 185 132 tfor:TF2849|5end_histidinol-phosphate_transaminase_3037288..3037518_POSITIVE 334 168 124 162 119 tfor:TF2657|5end_conserved_hypothetical_protein_2829729..2829959_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 422 80 38 83 48 tfor:TF1897|3end_conserved_hypothetical_protein;_possible_aminopeptidase_2052107..2052257_POSITIVE 391 80 35 151 92 tfor:TF3124|3end_dTDP-glucose_4,6-dehydratase_3359883..3360033_POSITIVE 382 85 41 83 45 tfor:TF0252|3end_hypothetical_protein_283759..283909_POSITIVE 371 89 41 52 16 tfor:TF2266|3end_transfer_region-related_protein,_TraQ_2434949..2435099_POSITIVE 367 90 43 79 31 tfor:TF0599|3end_hypothetical_protein_630130..630280_POSITIVE 344 90 41 121 71 tfor:TF2882|3end_conserved_hypothetical_protein_3074401..3074551_POSITIVE 344 88 41 62 7 tfor:TF2558|3end_50S_ribosomal_protein_L22_2737967..2738117_POSITIVE 344 88 44 49 13 tfor:TF0822|3end_hypothetical_protein_880764..880914_POSITIVE 341 79 39 43 1 tfor:TF1493|3end_thioredoxin_family_protein_1594066..1594216_POSITIVE 327 74 34 151 118 tfor:TF0764|3end_conserved_hypothetical_protein;_possible_exopolyphosphatase-related_protein_811371..811521_POSITIVE 325 110 61 75 22 tfor:TF0795|3end_hypothetical_protein_853199..853349_POSITIVE 324 55 11 82 29 tfor:TF1513|3end_hypothetical_protein_1625450..1625600_POSITIVE 324 75 36 133 96 tfor:TF0535|3end_surface_antigen_BspA_561701..561851_POSITIVE 323 89 43 52 7 tfor:TF1040|3end_dihydroorotate_dehydrogenase,_electron_transfer_subunit_1102118..1102268_POSITIVE 321 85 41 92 47 tfor:TF2636|3end_glutaminase_2807099..2807249_POSITIVE 320 109 63 62 8 tfor:TF0782|3end_ThiJ/PfpI_family_protein_836592..836742_POSITIVE 319 110 63 97 45 tfor:TF0098|3end_permease_109280..109430_POSITIVE 318 110 62 104 44 tfor:TF1761|3end_hypothetical_protein_1899579..1899729_POSITIVE 318 120 71 84 33 tfor:TF1743|3end_conserved_hypothetical_protein_1877909..1878059_POSITIVE 316 89 42 135 76 tfor:TF2392|3end_alpha-galactosidase_2565506..2565656_POSITIVE