Origin IGS: taaggttgtacataggttatttccgaaagagcctgccggacgccatagccgagcaggctcttgtttttttgggggagggcgtcttcgtgtctgaattttcaaaacgctcctattcacattcacaaggtcgtatcttgcgagatgaggtgtaatgtccgatggaacagcgttattttta .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 taaaaataacgctgttccatcggacattacacctcatctcgcaagatacgaccttgtgaatgtgaataggagcgttttgaaaattcagacacgaagacgccctcccccaaaaaaacaagagcctgctcggctatggcgtccggcaggctctttcggaaataacctatgtacaacctta Mask Tandem Repeat Region ================================================ taaggttgtacataggttatttccgaaagagcctgccggacgccatagccgagcaggctcttgtttttttgggggagggcgtcttcgtgtctgaattttcaaaacgctcctattcacattcacaaggtcgtatcttgcgagatgaggtgtaatgtccgatggaacagcgttattttta Find is-nt database================================================ Query_seq: TF2646:TF2647|TF2646:TF2647:conserved hypothetical protein:transcriptional regulator, possible arylsulfatase regulator:->->:2816758..2816935 178 taaggttgtacataggttatttccgaaagagcctgccggacgccatagccgagcaggctcttgtttttttgggggagggcgtcttcgtgtctgaattttcaaaacgctcctattcacattcacaaggtcgtatcttgcgagatgaggtgtaatgtccgatggaacagcgttattttta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF2646:TF2647|TF2646:TF2647:conserved hypothetical protein:transcriptional regulator, possible arylsulfatase regulator:->->:2816758..2816935 178 taaggttgtacataggttatttccgaaagagcctgccggacgccatagccgagcaggctcttgtttttttgggggagggcgtcttcgtgtctgaattttcaaaacgctcctattcacattcacaaggtcgtatcttgcgagatgaggtgtaatgtccgatggaacagcgttattttta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF2646:TF2647|TF2646:TF2647:conserved hypothetical protein:transcriptional regulator, possible arylsulfatase regulator:->->:2816758..2816935 178 taaggttgtacataggttatttccgaaagagcctgccggacgccatagccgagcaggctcttgtttttttgggggagggcgtcttcgtgtctgaattttcaaaacgctcctattcacattcacaaggtcgtatcttgcgagatgaggtgtaatgtccgatggaacagcgttattttta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 taaggttgtacataggttatttccgaaagagcctgccggacgccatagccgagcaggctcttgtttttttgggggagggcgtcttcgtgtctgaattttcaaaacgctcctattcacattcacaaggtcgtatcttgcgagatgaggtgtaatgtccgatggaacagcgttattttta Predict ORF larger than 30AA ================================================ Protein_Len: 48 Strand: + Start: 6 End: 149 ..... M Y I G Y F R K S L P D A I A E Q A L V F L G E G V F V S E F S K R S Y S H S Q G R I L R D E V ............................. Protein_Len: 39 Strand: + Start: 61 End: 177 ............................................................ M F F W G R A S S C L N F Q N A P I H I H K V V S C E M R C N V R W N S V I F . Protein_Len: 51 Strand: - Start: 1 End: 153 L T T C L N N G F S G A P R W L R A P E Q K K P P P R R R T Q I K L V S R N V N V L D Y R A L H P T M ......................... taaggttgtacataggttatttccgaaagagcctgccggacgccatagccgagcaggctcttgtttttttgggggagggcgtcttcgtgtctgaattttcaaaacgctcctattcacattcacaaggtcgtatcttgcgagatgaggtgtaatgtccgatggaacagcgttattttta 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================================================ taaggttgtacataggttatttccgaaagagcctgccggacgccatagccgagcaggctcttgtttttttgggggagggcgtcttcgtgtctgaattttcaaaacgctcctattcacattcacaaggtcgtatcttgcgagatgaggtgtaatgtccgatggaacagcgttattttta Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 95 HP_score: -7.8 Tail_Score: -5.40072 Start: 26 End: 63 Full_Region: CATAGGTTATTTCCG AAAGAGCCTGCCGG ACGCCATAG CCGAGCAGGCTCTTG TTTTTTTGGGGGAGG .........................AAAGAGCCTGCCGGACGCCATAGCCGAGCAGGCTCTTG................................................................................................................... TransTerm Strand: + Conf: 100 HP_score: -9.5 Tail_Score: -4.79949 Start: 29 End: 60 Full_Region: AGGTTATTTCCGAAA GAGCCTGCCGG ACGCCATAG CCGAGCAGGCTC TTGTTTTTTTGGGGG ............................GAGCCTGCCGGACGCCATAGCCGAGCAGGCTC...................................................................................................................... TransTerm Strand: - Conf: 77 HP_score: -10.1 Tail_Score: -3.55563 Start: 29 End: 60 Full_Region: cccccaaaaaaacaa gagcctgctcggc tatggc gtccggcaggctc tttcggaaataacct ............................gagcctgctcggctatggcgtccggcaggctc...................................................................................................................... Find igs database================================================ Query_seq: TF2646:TF2647|TF2646:TF2647:conserved hypothetical protein:transcriptional regulator, possible arylsulfatase regulator:->->:2816758..2816935 178 taaggttgtacataggttatttccgaaagagcctgccggacgccatagccgagcaggctcttgtttttttgggggagggcgtcttcgtgtctgaattttcaaaacgctcctattcacattcacaaggtcgtatcttgcgagatgaggtgtaatgtccgatggaacagcgttattttta Intra-Species Hit: Count: 1 Min: 1 Max: 178 Len: 178 Subject: tfor_TF2646_TF2647|conserved hypothetical protein:transcriptional regulator, possible arylsulfatase regulator|POSITIVE:POSITIVE|[2816758,2816935]|178 HSP 1 e-value: 4.0E-84 bit: 311.0 Len: 178 Query Start:1 Query End:178 Subject Strand: POSITIVE Subject Start: 1 Subject End: 178 taaggttgtacataggttatttccgaaagagcctgccggacgccatagccgagcaggctcttgnnnnnnngggggagggcgtcttcgtgtctgaattttcaaaacgctcctattcacattcacaaggtcgtatcttgcgagatgaggtgtaatgtccgatggaacagcgttattttta taaggttgtacataggttatttccgaaagagcctgccggacgccatagccgagcaggctcttgtttttttgggggagggcgtcttcgtgtctgaattttcaaaacgctcctattcacattcacaaggtcgtatcttgcgagatgaggtgtaatgtccgatggaacagcgttattttta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAGGUUGUACAUAGGUUAUUUCCGAAAGAGCCUGCCGGACGCCAUAGCCGAGCAGGCUCUUGUUUUUUUGGGGGAGGGCGUCUUCGUGUCUGAAUUUUCAAAACGCUCCUAUUCACAUUCACAAGGUCGUAUCUUGCGAGAUGAGGUGUAAUGUCCGAUGGAACAGCGUUAUUUUUA (((.(((((.(((.((.((((.((..(((((((((((((.(......)))).))))))))))....(((((.((((..(((.(((.(((..(((((...............)))))....))).))).))).)))).)))))...))...)))).)).)))..))))).)))...... (-56.56) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAAAAUAACGCUGUUCCAUCGGACAUUACACCUCAUCUCGCAAGAUACGACCUUGUGAAUGUGAAUAGGAGCGUUUUGAAAAUUCAGACACGAAGACGCCCUCCCCCAAAAAAACAAGAGCCUGCUCGGCUAUGGCGUCCGGCAGGCUCUUUCGGAAAUAACCUAUGUACAACCUUA ..............((((...((..........((((.(((((((.......)))))))..))))..(((.(((((((...............))))))))))...))........(((((((((((.(((......))).)))))))))))..)))).................... (-48.16) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 472 80 31 60 6 tfor:TF2848|5end_cobalamin_biosynthesis_protein_3036368..3036598_POSITIVE 445 80 31 169 99 tfor:TF2831|5end_ABC_transporter,_permease_component_3021317..3021547_POSITIVE 433 79 32 71 8 tfor:TF1589|5end_surface_antigen_BspA_1703189..1703419_POSITIVE 414 73 35 211 172 tfor:TF2160|5end_magnesium_chelatase,_subunit_I_2335974..2336204_POSITIVE 413 76 32 231 180 tfor:TF0620|5end_phosphoribosylaminoimidazole-succinocarboxamide_synthase_654711..654941_POSITIVE 412 89 41 160 89 tfor:TF2389|5end_conserved_hypothetical_protein_2558795..2559025_POSITIVE 401 90 41 221 179 tfor:TF1681|5end_dTDP-4-keto-L-rhamnose_reductase_1794904..1795134_POSITIVE 393 58 14 145 94 tfor:TF3108|5end_glutamine-hydrolyzing_carbamoyl-phosphate_synthase,_large_subunit_3338732..3338962_POSITIVE 389 71 31 80 32 tfor:TF2446|5end_riboflavin-specific_deaminase_2622370..2622600_POSITIVE 388 90 41 102 48 tfor:TF0842|5end_long-chain-fatty-acid--CoA_ligase_893053..893283_POSITIVE 387 80 32 68 8 tfor:TF1591|5end_surface_antigen_BspA_1706387..1706617_POSITIVE 387 58 15 51 5 tfor:TF0946|5end_iron(III)_ABC_transporter,_periplasmic_iron-binding_protein_989482..989712_POSITIVE 383 80 32 64 14 tfor:TF0396|5end_conserved_hypothetical_protein_417018..417248_POSITIVE 379 83 41 230 185 tfor:TF2655|5end_DNA_topoisomerase_I_2824543..2824773_POSITIVE 378 79 32 138 77 tfor:TF0600|5end_oxidoreductase/dehydrogenase_630083..630313_POSITIVE 377 63 24 67 7 tfor:TF2850|5end_endoribonuclease_L-PSP_3038417..3038647_POSITIVE 377 60 18 45 8 tfor:TF0298|5end_dipeptidase_323127..323357_POSITIVE 376 58 11 156 112 tfor:TF1947|5end_conserved_hypothetical_protein_2095521..2095751_POSITIVE 376 79 31 121 56 tfor:TF0583|5end_possible_gliding_motility-related_protein_613189..613419_POSITIVE 375 87 42 219 175 tfor:TF2246|5end_hypothetical_protein_2421288..2421518_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 472 80 31 81 27 tfor:TF2846|3end_cobyric_acid_synthase_3036469..3036619_POSITIVE 450 80 35 102 64 tfor:TF0880|3end_conserved_hypothetical_protein_934371..934521_POSITIVE 418 62 27 64 29 tfor:TF2646|3end_conserved_hypothetical_protein_2816697..2816847_POSITIVE 393 58 14 69 18 tfor:TF3107|3end_hypothetical_protein_3338736..3338886_POSITIVE 378 79 32 105 44 tfor:TF0599|3end_hypothetical_protein_630130..630280_POSITIVE 376 79 31 115 50 tfor:TF0582|3end_hemolysin-related_protein,_with_CBS_domains;_possible_gliding-motility_related_protein_613263..613413_POSITIVE 375 87 42 142 98 tfor:TF2245|3end_conserved_hypothetical_protein_2421291..2421441_POSITIVE 374 89 45 108 62 tfor:TF3006|3end_response_regulator,_transcriptional_regulator_RprY_3227162..3227312_POSITIVE 368 59 22 149 110 tfor:TF0141|3end_exodeoxyribonuclease_VII,_large_subunit_149830..149980_POSITIVE 367 73 33 66 35 tfor:TF2251|3end_conjugative_transposon_protein,_TraE_2424687..2424837_POSITIVE 365 66 21 58 20 tfor:TF2874|3end_conserved_hypothetical_protein_3065224..3065374_POSITIVE 360 80 36 50 6 tfor:TF2434|3end_conserved_hypothetical_protein_2614363..2614513_POSITIVE 355 89 47 141 94 tfor:TF0528|3end_two-component_system_sensor_histidine_kinase_554779..554929_POSITIVE 354 79 34 141 106 tfor:TF2979|3end_possible_outer_membrane__protein_3193164..3193314_POSITIVE 354 57 15 53 7 tfor:TF1298|3end_possible_membrane_protein_1381197..1381347_POSITIVE 354 80 31 100 49 tfor:TF0175|3end_hypothetical_protein_185907..186057_POSITIVE 352 84 41 146 99 tfor:TF2442|3end_heat_shock_protein_60_2620271..2620421_POSITIVE 351 55 15 137 86 tfor:TF2831|3end_ABC_transporter,_permease_component_3022671..3022821_POSITIVE 351 80 31 72 14 tfor:TF1599|3end_ribonuclease_P_protein_component_1714054..1714204_POSITIVE 349 64 22 64 13 tfor:TF1255|3end_conserved_hypothetical_protein_1338151..1338301_POSITIVE