Origin IGS: tttactgtttatattcttttttattattcttcaaagactatcgggatgaggcccggttgtcgtttgtctgcgatgcaaagatggggtgaaaaggatgcgtttgtttccaatttcccagcatcgcgaaaaaaaaggaagtgattacgaaaaaagagcggtcttggggttgcttcgtgaggcttagattgaattgtaacggtttgaaccataaaagatagagaaataagcataactggcggatttttcaggcaaaggcgaaaaaaacatcggtaaagacgaaaaagaggctgttcatcgtcccttccattttagaaaaacgggcgaaatattttcatatctttgcaaacaaagaaatatcgtc .........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.........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 gacgatatttctttgtttgcaaagatatgaaaatatttcgcccgtttttctaaaatggaagggacgatgaacagcctctttttcgtctttaccgatgtttttttcgcctttgcctgaaaaatccgccagttatgcttatttctctatcttttatggttcaaaccgttacaattcaatctaagcctcacgaagcaaccccaagaccgctcttttttcgtaatcacttccttttttttcgcgatgctgggaaattggaaacaaacgcatccttttcaccccatctttgcatcgcagacaaacgacaaccgggcctcatcccgatagtctttgaagaataataaaaaagaatataaacagtaaa Mask Tandem Repeat Region ================================================ tttactgtttatattcttttttattattcttcaaagactatcgggatgaggcccggttgtcgtttgtctgcgatgcaaagatggggtgaaaaggatgcgtttgtttccaatttcccagcatcgcgaaaaaaaaggaagtgattacgaaaaaagagcggtcttggggttgcttcgtgaggcttagattgaattgtaacggtttgaaccataaaagatagagaaataagcataactggcggatttttcaggcaaaggcgaaaaaaacatcggtaaagacgaaaaagaggctgttcatcgtcccttccattttagaaaaacgggcgaaatattttcatatctttgcaaacaaagaaatatcgtc Find is-nt database================================================ Query_seq: TF3043:TF3044|TF3043:TF3044:conserved hypothetical protein:two-component system sensor kinase:->->:3272470..3272830 361 tttactgtttatattcttttttattattcttcaaagactatcgggatgaggcccggttgtcgtttgtctgcgatgcaaagatggggtgaaaaggatgcgtttgtttccaatttcccagcatcgcgaaaaaaaaggaagtgattacgaaaaaagagcggtcttggggttgcttcgtgaggcttagattgaattgtaacggtttgaaccataaaagatagagaaataagcataactggcggatttttcaggcaaaggcgaaaaaaacatcggtaaagacgaaaaagaggctgttcatcgtcccttccattttagaaaaacgggcgaaatattttcatatctttgcaaacaaagaaatatcgtc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF3043:TF3044|TF3043:TF3044:conserved hypothetical protein:two-component system sensor kinase:->->:3272470..3272830 361 tttactgtttatattcttttttattattcttcaaagactatcgggatgaggcccggttgtcgtttgtctgcgatgcaaagatggggtgaaaaggatgcgtttgtttccaatttcccagcatcgcgaaaaaaaaggaagtgattacgaaaaaagagcggtcttggggttgcttcgtgaggcttagattgaattgtaacggtttgaaccataaaagatagagaaataagcataactggcggatttttcaggcaaaggcgaaaaaaacatcggtaaagacgaaaaagaggctgttcatcgtcccttccattttagaaaaacgggcgaaatattttcatatctttgcaaacaaagaaatatcgtc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF3043:TF3044|TF3043:TF3044:conserved hypothetical protein:two-component system sensor kinase:->->:3272470..3272830 361 tttactgtttatattcttttttattattcttcaaagactatcgggatgaggcccggttgtcgtttgtctgcgatgcaaagatggggtgaaaaggatgcgtttgtttccaatttcccagcatcgcgaaaaaaaaggaagtgattacgaaaaaagagcggtcttggggttgcttcgtgaggcttagattgaattgtaacggtttgaaccataaaagatagagaaataagcataactggcggatttttcaggcaaaggcgaaaaaaacatcggtaaagacgaaaaagaggctgttcatcgtcccttccattttagaaaaacgggcgaaatattttcatatctttgcaaacaaagaaatatcgtc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tttactgtttatattcttttttattattcttcaaagactatcgggatgaggcccggttgtcgtttgtctgcgatgcaaagatggggtgaaaaggatgcgtttgtttccaatttcccagcatcgcgaaaaaaaaggaagtgattacgaaaaaagagcggtcttggggttgcttcgtgaggcttagattgaattgtaacggtttgaaccataaaagatagagaaataagcataactggcggatttttcaggcaaaggcgaaaaaaacatcggtaaagacgaaaaagaggctgttcatcgtcccttccattttagaaaaacgggcgaaatattttcatatctttgcaaacaaagaaatatcgtc Predict ORF larger than 30AA ================================================ Protein_Len: 42 Strand: + Start: 13 End: 138 ............ M L F Y Y S S K T I G M R P G C R L S A M Q R W G E K D A F V S N F P A S R K K R K ............................................................................................................................................................................................................................... Protein_Len: 38 Strand: + Start: 68 End: 181 ................................................................... M R C K D G V K R M R L F P I S Q H R E K K G S D Y E K R A V L G L L R E A .................................................................................................................................................................................... Protein_Len: 32 Strand: + Start: 120 End: 215 ....................................................................................................................... M A K K K E V I T K K E R S W G C F V R L R L N C N G L N H K R .................................................................................................................................................. Protein_Len: 40 Strand: + Start: 240 End: 359 ............................................................................................................................................................................................................................................... M F Q A K A K K T S V K T K K R L F I V P S I L E K R A K Y F H I F A N K E I S .. Protein_Len: 43 Strand: + Start: 233 End: 361 ........................................................................................................................................................................................................................................ M A D F S G K G E K N I G K D E K E A V H R P F H F R K T G E I F S Y L C K Q R N I V Protein_Len: 60 Strand: - Start: 41 End: 241 ........................................ N T Q S A F I P H F P H T Q K W N G L M A F F F S T I V F F S R D Q P Q K T L S L N F Q L P K F W L L Y L F L C L Q R M ........................................................................................................................ Protein_Len: 60 Strand: - Start: 27 End: 248 .......................... A I C L H P S F S A N T E L K G A D R F F L F H N R F F L P R P T A E H P K S Q I T V T Q V M F S L S I L M V P P N K M ................................................................................................................. tttactgtttatattcttttttattattcttcaaagactatcgggatgaggcccggttgtcgtttgtctgcgatgcaaagatggggtgaaaaggatgcgtttgtttccaatttcccagcatcgcgaaaaaaaaggaagtgattacgaaaaaagagcggtcttggggttgcttcgtgaggcttagattgaattgtaacggtttgaaccataaaagatagagaaataagcataactggcggatttttcaggcaaaggcgaaaaaaacatcggtaaagacgaaaaagaggctgttcatcgtcccttccattttagaaaaacgggcgaaatattttcatatctttgcaaacaaagaaatatcgtc 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================================================ tttactgtttatattcttttttattattcttcaaagactatcgggatgaggcccggttgtcgtttgtctgcgatgcaaagatggggtgaaaaggatgcgtttgtttccaatttcccagcatcgcgaaaaaaaaggaagtgattacgaaaaaagagcggtcttggggttgcttcgtgaggcttagattgaattgtaacggtttgaaccataaaagatagagaaataagcataactggcggatttttcaggcaaaggcgaaaaaaacatcggtaaagacgaaaaagaggctgttcatcgtcccttccattttagaaaaacgggcgaaatattttcatatctttgcaaacaaagaaatatcgtc Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 56 HP_score: -3.3 Tail_Score: -4.05033 Start: 35 End: 62 Full_Region: TTTATTATTCTTCAA AGACTATCGGG ATGAGG CCCGGTTGTCG TTTGTCTGCGATGCA ..................................AGACTATCGGGATGAGGCCCGGTTGTCG........................................................................................................................................................................................................................................................................................................... TransTerm Strand: + Conf: 59 HP_score: -6.8 Tail_Score: -3.02698 Start: 36 End: 61 Full_Region: TTATTATTCTTCAAA GACTATCGGG ATGAGG CCCGGTTGTC GTTTGTCTGCGATGC ...................................GACTATCGGGATGAGGCCCGGTTGTC............................................................................................................................................................................................................................................................................................................ TransTerm Strand: - Conf: 54 HP_score: -4.6 Tail_Score: -3.56092 Start: 36 End: 61 Full_Region: gcatcgcagacaaac gacaaccggg cctcat cccgatagtc tttgaagaataataa ...................................gacaaccgggcctcatcccgatagtc............................................................................................................................................................................................................................................................................................................ Find igs database================================================ Query_seq: TF3043:TF3044|TF3043:TF3044:conserved hypothetical protein:two-component system sensor kinase:->->:3272470..3272830 361 tttactgtttatattcttttttattattcttcaaagactatcgggatgaggcccggttgtcgtttgtctgcgatgcaaagatggggtgaaaaggatgcgtttgtttccaatttcccagcatcgcgaaaaaaaaggaagtgattacgaaaaaagagcggtcttggggttgcttcgtgaggcttagattgaattgtaacggtttgaaccataaaagatagagaaataagcataactggcggatttttcaggcaaaggcgaaaaaaacatcggtaaagacgaaaaagaggctgttcatcgtcccttccattttagaaaaacgggcgaaatattttcatatctttgcaaacaaagaaatatcgtc Intra-Species Hit: Count: 1 Min: 1 Max: 361 Len: 361 Subject: tfor_TF3043_TF3044|conserved hypothetical protein:two-component system sensor kinase|POSITIVE:POSITIVE|[3272470,3272830]|361 HSP 1 e-value: 1.0E-178 bit: 626.0 Len: 361 Query Start:1 Query End:361 Subject Strand: POSITIVE Subject Start: 1 Subject End: 361 tttactgtttatattcttttttattattcttcaaagactatcgggatgaggcccggttgtcgtttgtctgcgatgcaaagatggggtgaaaaggatgcgtttgtttccaatttcccagcatcgcgnnnnnnnnggaagtgattacgaaaaaagagcggtcttggggttgcttcgtgaggcttagattgaattgtaacggtttgaaccataaaagatagagaaataagcataactggcggatttttcaggcaaaggcgnnnnnnncatcggtaaagacgaaaaagaggctgttcatcgtcccttccattttagaaaaacgggcgaaatattttcatatctttgcaaacaaagaaatatcgtc tttactgtttatattcttttttattattcttcaaagactatcgggatgaggcccggttgtcgtttgtctgcgatgcaaagatggggtgaaaaggatgcgtttgtttccaatttcccagcatcgcgaaaaaaaaggaagtgattacgaaaaaagagcggtcttggggttgcttcgtgaggcttagattgaattgtaacggtttgaaccataaaagatagagaaataagcataactggcggatttttcaggcaaaggcgaaaaaaacatcggtaaagacgaaaaagaggctgttcatcgtcccttccattttagaaaaacgggcgaaatattttcatatctttgcaaacaaagaaatatcgtc Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUACUGUUUAUAUUCUUUUUUAUUAUUCUUCAAAGACUAUCGGGAUGAGGCCCGGUUGUCGUUUGUCUGCGAUGCAAAGAUGGGGUGAAAAGGAUGCGUUUGUUUCCAAUUUCCCAGCAUCGCGAAAAAAAAGGAAGUGAUUACGAAAAAAGAGCGGUCUUGGGGUUGCUUCGUGAGGCUUAGAUUGAAUUGUAACGGUUUGAACCAUAAAAGAUAGAGAAAUAAGCAUAACUGGCGGAUUUUUCAGGCAAAGGCGAAAAAAACAUCGGUAAAGACGAAAAAGAGGCUGUUCAUCGUCCCUUCCAUUUUAGAAAAACGGGCGAAAUAUUUUCAUAUCUUUGCAAACAAAGAAAUAUCGUC ........((((.(((((((((.........(((((((.((((((......)))))).))).))))..((((((((.....(((((......(((.((....)).)))....)))))))))))))..))))))))).))))....(((((..((((((((((...(((..(((((..((.((((((((........)))))))).))..........(((((((..((.......))..)))))))........)))))...))).(((.......)))....)))))))))).((((((.(((.......)))....))))))....)))))...((((((....))))))......... (-94.30) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GACGAUAUUUCUUUGUUUGCAAAGAUAUGAAAAUAUUUCGCCCGUUUUUCUAAAAUGGAAGGGACGAUGAACAGCCUCUUUUUCGUCUUUACCGAUGUUUUUUUCGCCUUUGCCUGAAAAAUCCGCCAGUUAUGCUUAUUUCUCUAUCUUUUAUGGUUCAAACCGUUACAAUUCAAUCUAAGCCUCACGAAGCAACCCCAAGACCGCUCUUUUUUCGUAAUCACUUCCUUUUUUUUCGCGAUGCUGGGAAAUUGGAAACAAACGCAUCCUUUUCACCCCAUCUUUGCAUCGCAGACAAACGACAACCGGGCCUCAUCCCGAUAGUCUUUGAAGAAUAAUAAAAAAGAAUAUAAACAGUAAA (((((.......))))).((((((....(((((((((....((((((.....)))))).((((((((.((......))....))))))))...))))))))).....))))))(((........((..((...(((((..............(((((....)))))............)))))...))...))..............((((((((..((.((...............(((((((((((.((..(((..(....)..)))..))...)))).....)))))))...((((.(((...((((......))))...)))))))..)).))..)))))))).......))).... (-69.37) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 451 109 61 166 113 tfor:TF2245|5end_conserved_hypothetical_protein_2420654..2420884_POSITIVE 444 90 41 160 117 tfor:TF2579|5end_30S_ribosomal_protein_S4_2747202..2747432_POSITIVE 442 89 42 202 148 tfor:TF1948|5end_conserved_hypothetical_protein_2095942..2096172_POSITIVE 419 88 42 83 32 tfor:TF1938|5end_hypothetical_protein_2085717..2085947_POSITIVE 419 88 41 206 154 tfor:TF0931|5end_superfamily_II_DNA/RNA_helicase,_SNF2_family_970031..970261_POSITIVE 418 86 50 43 3 tfor:TF1985|5end_surface_antigen_BspA_2135659..2135889_POSITIVE 415 88 41 54 10 tfor:TF1767|5end_3-dehydroquinate_synthase_1905492..1905722_POSITIVE 410 89 41 65 13 tfor:TF2296|5end_hypothetical_protein_2448892..2449122_POSITIVE 404 126 81 60 22 tfor:TF0027|5end_conserved_hypothetical_protein_22866..23096_POSITIVE 396 89 41 89 28 tfor:TF2759|5end_xylose_repressor,_ROK_family_2943568..2943798_POSITIVE 392 199 156 50 8 tfor:TF0847|5end_hypothetical_protein_897633..897863_POSITIVE 387 88 42 70 7 tfor:TF0457|5end_beta-glucanase_precursor_474099..474329_POSITIVE 386 88 41 190 134 tfor:TF1036|5end_iron(III)_ABC_transporter,_permease_component_1097160..1097390_POSITIVE 383 69 29 88 49 tfor:TF1061|5end_glycosyltransferase_1130264..1130494_POSITIVE 381 98 51 231 190 tfor:TF0366|5end_hypothetical_protein_383564..383794_POSITIVE 381 98 51 231 190 tfor:TF0362|5end_hypothetical_protein_379952..380182_POSITIVE 381 98 51 164 123 tfor:TF0350|5end_hypothetical_protein_370794..371024_POSITIVE 380 89 41 70 4 tfor:TF3114|5end_hypothetical_protein_3349134..3349364_POSITIVE 378 96 61 178 142 tfor:TF0801|5end_transport_permease_858586..858816_POSITIVE 374 90 44 222 171 tfor:TF2037|5end_conserved_hypothetical_protein;_possible_anaerobic_ribonucleoside-triphosphate_reductase_2196754..2196984_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 419 88 41 60 8 tfor:TF0930|3end_conserved_hypothetical_protein;_possible_prophage_protein_969965..970115_POSITIVE 415 88 41 47 3 tfor:TF1766|3end_alanyl-tRNA_synthetase_1905565..1905715_POSITIVE 406 89 41 148 95 tfor:TF2477|3end_phosphatase_2654965..2655115_POSITIVE 394 90 43 42 1 tfor:TF2578|3end_30S_ribosomal_protein_S11_2747164..2747314_POSITIVE 386 100 51 72 4 tfor:TF0181|3end_ATP-dependent_DNA_helicase_194863..195013_POSITIVE 383 69 29 61 22 tfor:TF1059|3end_possible_xanthan_lyase_1130317..1130467_POSITIVE 370 90 42 101 45 tfor:TF1461|3end_DNA-damage-inducible_protein_F_1552253..1552403_POSITIVE 367 89 50 48 7 tfor:TF2205|3end_conserved_hypothetical_protein;_possible_transcriptional_regulator_2380010..2380160_POSITIVE 365 84 42 66 13 tfor:TF2237|3end_two-component_system_response_regulator_involved_in_CTn_2413893..2414043_POSITIVE 356 88 42 70 22 tfor:TF2593|3end_amino_acid_transport_protein_2764242..2764392_POSITIVE 356 305 267 121 74 tfor:TF1689|3end_conserved_hypothetical_protein_1806614..1806764_POSITIVE 356 88 44 63 1 tfor:TF0456|3end_conserved_hypothetical_protein_474172..474322_POSITIVE 352 88 41 65 19 tfor:TF0616|3end_conserved_hypothetical_protein_650658..650808_POSITIVE 351 85 42 107 64 tfor:TF0251|3end_conserved_hypothetical_protein;_possible_exporter_283529..283679_POSITIVE 350 88 41 63 4 tfor:TF1400|3end_polysaccharide_biosynthesis_protein;_membrane_protein_1476573..1476723_POSITIVE 349 88 43 143 93 tfor:TF2774|3end_2-amino-4-hydroxy-6-hydroxymethyldihydropteridine_pyrophosphokinase_2959719..2959869_POSITIVE 347 88 41 58 2 tfor:TF1917|3end_hypothetical_protein_2070244..2070394_POSITIVE 342 90 42 60 11 tfor:TF2521|3end_TPR-repeat-containing_protein_2701598..2701748_POSITIVE 339 89 42 77 12 tfor:TF2846|3end_cobyric_acid_synthase_3036469..3036619_POSITIVE 338 86 44 142 85 tfor:TF1775|3end_oxidoreductase,_Gfo/Idh/MocA_family_1914618..1914768_POSITIVE