Origin IGS: aaggtaattgatattctaacataaatttggtataatgtcgataacagaggttttatatttgaatacccctgtagaaacggattgaatttgccgatactcactatgtgtatttattttttgtagaaaatgttgttttttgtttgacaaataatgttttttacaatataatacaacacagagtttgaaacgaaacaaaaggagttataa .........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 ttataactccttttgtttcgtttcaaactctgtgttgtattatattgtaaaaaacattatttgtcaaacaaaaaacaacattttctacaaaaaataaatacacatagtgagtatcggcaaattcaatccgtttctacaggggtattcaaatataaaacctctgttatcgacattataccaaatttatgttagaatatcaattacctt Mask Tandem Repeat Region ================================================ aaggtaattgatattctaacataaatttggtataatgtcgataacagaggttttatatttgaatacccctgtagaaacggattgaatttgccgatactcactatgtgtatttattttttgtagaaaatgttgttttttgtttgacaaataatgttttttacaatataatacaacacagagtttgaaacgaaacaaaaggagttataa Find is-nt database================================================ Query_seq: TDE1407:TDE1408|TDE1407:TDE1408:hypothetical protein:flagellar filament outer layer protein FlaA, putative:<-->:1450762..1450968 207 aaggtaattgatattctaacataaatttggtataatgtcgataacagaggttttatatttgaatacccctgtagaaacggattgaatttgccgatactcactatgtgtatttattttttgtagaaaatgttgttttttgtttgacaaataatgttttttacaatataatacaacacagagtttgaaacgaaacaaaaggagttataa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE1407:TDE1408|TDE1407:TDE1408:hypothetical protein:flagellar filament outer layer protein FlaA, putative:<-->:1450762..1450968 207 aaggtaattgatattctaacataaatttggtataatgtcgataacagaggttttatatttgaatacccctgtagaaacggattgaatttgccgatactcactatgtgtatttattttttgtagaaaatgttgttttttgtttgacaaataatgttttttacaatataatacaacacagagtttgaaacgaaacaaaaggagttataa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE1407:TDE1408|TDE1407:TDE1408:hypothetical protein:flagellar filament outer layer protein FlaA, putative:<-->:1450762..1450968 207 aaggtaattgatattctaacataaatttggtataatgtcgataacagaggttttatatttgaatacccctgtagaaacggattgaatttgccgatactcactatgtgtatttattttttgtagaaaatgttgttttttgtttgacaaataatgttttttacaatataatacaacacagagtttgaaacgaaacaaaaggagttataa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aaggtaattgatattctaacataaatttggtataatgtcgataacagaggttttatatttgaatacccctgtagaaacggattgaatttgccgatactcactatgtgtatttattttttgtagaaaatgttgttttttgtttgacaaataatgttttttacaatataatacaacacagagtttgaaacgaaacaaaaggagttataa Predict ORF larger than 30AA ================================================ Protein_Len: 32 Strand: + Start: 25 End: 120 ........................ M W Y N V D N R G F I F E Y P C R N G L N L P I L T M C I Y F L ....................................................................................... Protein_Len: 34 Strand: + Start: 81 End: 182 ................................................................................ M E F A D T H Y V Y L F F V E N V V F C L T N N V F Y N I I Q H R V ......................... Protein_Len: 59 Strand: - Start: 19 End: 195 .................. C L N P I I D I V S T K Y K F V G T S V S Q I Q R Y E S H T N I K Q L F H Q K K N S L Y H K K C Y L V V C L K F R F M ............ Protein_Len: 36 Strand: - Start: 3 End: 110 .. T I S I R V Y I Q Y L T S L L P K I N S Y G Q L F P N F K G I S V I H M ................................................................................................. aaggtaattgatattctaacataaatttggtataatgtcgataacagaggttttatatttgaatacccctgtagaaacggattgaatttgccgatactcactatgtgtatttattttttgtagaaaatgttgttttttgtttgacaaataatgttttttacaatataatacaacacagagtttgaaacgaaacaaaaggagttataa Predict Promoter with matrix: RpoD-15 score > 80================================================ Predict Promoter with matrix: RpoD-16 score > 80================================================ Predict Promoter with matrix: RpoD-17 score > 80================================================ PromScan Matrix: RpoD-17 Strand: + Score: 94 Start: 140 End: 169 ...........................................................................................................................................TTTGACAAATAATGTTTTTTACAATATAAT...................................... PromScan Matrix: RpoD-17 Strand: + Score: 90 Start: 7 End: 36 ......ATTGATATTCTAACATAAATTTGGTATAAT........................................................................................................................................................................... PromScan Matrix: RpoD-17 Strand: - Score: 87 Start: 13 End: 42 ............ATCGACATTATACCAAATTTATGTTAGAAT..................................................................................................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ aaggtaattgatattctaacataaatttggtataatgtcgataacagaggttttatatttgaatacccctgtagaaacggattgaatttgccgatactcactatgtgtatttattttttgtagaaaatgttgttttttgtttgacaaataatgttttttacaatataatacaacacagagtttgaaacgaaacaaaaggagttataa Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 47 HP_score: -3.0 Tail_Score: -3.34233 Start: 45 End: 71 Full_Region: ttcaatccgtttcta caggggtatt caaatat aaaacctctg ttatcgacattatac ............................................caggggtattcaaatataaaacctctg........................................................................................................................................ Find igs database================================================ Query_seq: TDE1407:TDE1408|TDE1407:TDE1408:hypothetical protein:flagellar filament outer layer protein FlaA, putative:<-->:1450762..1450968 207 aaggtaattgatattctaacataaatttggtataatgtcgataacagaggttttatatttgaatacccctgtagaaacggattgaatttgccgatactcactatgtgtatttattttttgtagaaaatgttgttttttgtttgacaaataatgttttttacaatataatacaacacagagtttgaaacgaaacaaaaggagttataa Intra-Species Hit: Count: 1 Min: 1 Max: 207 Len: 207 Subject: NC_002967_TDE1407_TDE1408|hypothetical protein:flagellar filament outer layer protein FlaA, putative|NEGATIVE:POSITIVE|[1450762,1450968]|207 HSP 1 e-value: 8.0E-52 bit: 204.0 Len: 103 Query Start:1 Query End:103 Subject Strand: POSITIVE Subject Start: 1 Subject End: 103 aaggtaattgatattctaacataaatttggtataatgtcgataacagaggttttatatttgaatacccctgtagaaacggattgaatttgccgatactcacta........................................................................................................ aaggtaattgatattctaacataaatttggtataatgtcgataacagaggttttatatttgaatacccctgtagaaacggattgaatttgccgatactcacta........................................................................................................ HSP 2 e-value: 6.0E-19 bit: 95.6 Len: 48 Query Start:160 Query End:207 Subject Strand: POSITIVE Subject Start: 160 Subject End: 207 ...............................................................................................................................................................acaatataatacaacacagagtttgaaacgaaacaaaaggagttataa ...............................................................................................................................................................acaatataatacaacacagagtttgaaacgaaacaaaaggagttataa Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAGGUAAUUGAUAUUCUAACAUAAAUUUGGUAUAAUGUCGAUAACAGAGGUUUUAUAUUUGAAUACCCCUGUAGAAACGGAUUGAAUUUGCCGAUACUCACUAUGUGUAUUUAUUUUUUGUAGAAAAUGUUGUUUUUUGUUUGACAAAUAAUGUUUUUUACAAUAUAAUACAACACAGAGUUUGAAACGAAACAAAAGGAGUUAUAA ..(((((((((((((.((.((......)).)).))))))))..((((.(((((((....)))).))).))))...............)))))...((((.((.(((((...((((..((((((((((((((((((.((....)).))))))))))))))))))...))))..)))))..((((......))))...))))))..... (-43.30) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUAUAACUCCUUUUGUUUCGUUUCAAACUCUGUGUUGUAUUAUAUUGUAAAAAACAUUAUUUGUCAAACAAAAAACAACAUUUUCUACAAAAAAUAAAUACACAUAGUGAGUAUCGGCAAAUUCAAUCCGUUUCUACAGGGGUAUUCAAAUAUAAAACCUCUGUUAUCGACAUUAUACCAAAUUUAUGUUAGAAUAUCAAUUACCUU ...((((....(((((..((...(..(((.(((((..((((...(((((.((((.....((((.....))))........)))).)))))..))))...))))).)))..)...)))))))........(((...((((((((.............))))))))....)))................))))................ (-28.04) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 877 110 61 201 152 NC_002967:TDE1407|5end_hypothetical_protein_1450671..1450901_NEGATIVE 264 81 45 177 132 NC_002967:TDE1310|5end_modulator_of_DNA_gyrase_family_protein_1345962..1346192_POSITIVE 258 105 66 69 22 NC_002967:TDE1039|5end_riboflavin_biosynthesis_protein,_putative_1067072..1067302_POSITIVE 252 100 69 202 161 NC_002967:TDE1904|5end_hypothetical_protein_1923613..1923843_NEGATIVE 248 104 66 134 98 NC_002967:TDE1093|5end_hypothetical_protein_1127374..1127604_POSITIVE 234 95 66 193 161 NC_002967:TDE1651|5end_BioY_family_protein_1698732..1698962_NEGATIVE 233 93 58 159 128 NC_002967:TDE2410|5end_hemolysin_2437247..2437477_NEGATIVE 232 109 74 218 183 NC_002967:TDE1671|5end_trigger_factor_1724912..1725142_POSITIVE 231 80 36 176 136 NC_002967:TDE0423|5end_hypothetical_protein_476601..476831_POSITIVE 226 80 33 218 170 NC_002967:TDE1047|5end_30S_ribosomal_protein_S12_1074097..1074327_POSITIVE 225 80 34 158 118 NC_002967:TDE2012|5end_hypothetical_protein_2034351..2034581_NEGATIVE 225 140 91 224 160 NC_002967:TDE1580|5end_hypothetical_protein_1629726..1629956_NEGATIVE 222 105 66 171 130 NC_002967:TDE2340|5end_FMN-binding_domain_protein_2377855..2378085_NEGATIVE 221 108 78 64 34 NC_002967:TDE0708|5end_nitroreductase_family_protein_743900..744130_POSITIVE 220 104 68 91 54 NC_002967:TDE1896|5end_phosphoribosylaminoimidazolecarboxamide_formyltransferase/IMP_cyclohydrolase_1917505..1917735_NEGATIVE 215 130 84 126 78 NC_002967:TDE1132|5end_chorismate_synthase_1163415..1163645_POSITIVE 215 110 67 213 160 NC_002967:TDE0633|5end_D-alanyl-D-alanine_carboxypeptidase,_putative_667778..668008_POSITIVE 215 93 51 210 161 NC_002967:TDE0088|5end_Trk_system_potassium_uptake_protein_TrkH_105347..105577_POSITIVE 214 52 20 161 134 NC_002967:TDE0639|5end_oligopeptide/dipeptide_ABC_transporter,_permease_protein_674394..674624_NEGATIVE 213 118 75 99 65 NC_002967:TDE1493|5end_chemotaxis_protein_CheX_1538590..1538820_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 256 93 66 109 76 NC_002967:TDE1533|3end_hypothetical_protein_1578657..1578807_POSITIVE 252 100 69 93 52 NC_002967:TDE1905|3end_hypothetical_protein_1923722..1923872_NEGATIVE 240 110 68 58 2 NC_002967:TDE0818|3end_ABC_transporter,_ATP-binding/permease_protein_839926..840076_NEGATIVE 234 95 66 68 36 NC_002967:TDE1652|3end_ABC_transporter,_ATP-binding/permease_protein_1698857..1699007_NEGATIVE 231 80 36 105 65 NC_002967:TDE0422|3end_bacteriocin-type_signal_domain_protein_476610..476760_POSITIVE 230 119 78 148 107 NC_002967:TDE2783|3end_methyl-accepting_chemotaxis_protein_2836607..2836757_POSITIVE 226 80 33 117 69 NC_002967:TDE1046|3end_hypothetical_protein_1074076..1074226_POSITIVE 225 80 34 150 110 NC_002967:TDE2013|3end_hypothetical_protein_2034359..2034509_NEGATIVE 220 104 68 71 34 NC_002967:TDE1897|3end_phosphoribosylglycinamide_formyltransferase_1917525..1917675_NEGATIVE 219 94 66 38 5 NC_002967:TDE0794|3end_hypothetical_protein_819224..819374_NEGATIVE 218 93 63 82 52 NC_002967:TDE0361|3end_transporter,_putative_407442..407592_POSITIVE 217 96 64 42 8 NC_002967:TDE0128|3end_HAMP_domain/GGDEF_domain/EAL_domain_protein_148725..148875_POSITIVE 214 67 27 46 9 NC_002967:TDE1539|3end_hypothetical_protein_1584190..1584340_POSITIVE 213 80 39 61 14 NC_002967:TDE2205|3end_enoate_reductase,_putative_2242575..2242725_NEGATIVE 213 118 75 74 40 NC_002967:TDE1492|3end_chemotaxis_protein_CheW_1538645..1538795_POSITIVE 208 80 35 35 1 NC_002967:TDE2663|3end_isoleucyl-tRNA_synthetase_2698616..2698766_NEGATIVE 208 72 31 134 92 NC_002967:TDE1005|3end_hypothetical_protein_1030495..1030645_POSITIVE 206 80 36 46 3 NC_002967:TDE1810|3end_hypothetical_protein_1845924..1846074_NEGATIVE 202 96 56 127 92 NC_002967:TDE0565|3end_hypothetical_protein_597230..597380_POSITIVE 202 102 66 43 7 NC_002967:TDE0548|3end_hypothetical_protein_586882..587032_NEGATIVE