Origin IGS: aaatactccttttttatgctttatatacactattatataacatatttgaaaaaaaatcatcaactttaaataaaaactctttacattatgcaaaatatgtttataattatataatagtgatatatattgtaattaacaaaattgctaaaagtaaggagagttagga .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tcctaactctccttacttttagcaattttgttaattacaatatatatcactattatataattataaacatattttgcataatgtaaagagtttttatttaaagttgatgattttttttcaaatatgttatataatagtgtatataaagcataaaaaaggagtattt Mask Tandem Repeat Region ================================================ aaatactccttttttatgctttatatacactattatataacatatttgaaaaaaaatcatcaactttaaataaaaactctttacattatgcaaaatatgtttataattatataatagtgatatatattgtaattaacaaaattgctaaaagtaaggagagttagga Find is-nt database================================================ Query_seq: TDE0841:TDE0842|TDE0841:TDE0842:hypothetical protein:cytoplasmic filament protein A:<-->:861689..861854 166 aaatactccttttttatgctttatatacactattatataacatatttgaaaaaaaatcatcaactttaaataaaaactctttacattatgcaaaatatgtttataattatataatagtgatatatattgtaattaacaaaattgctaaaagtaaggagagttagga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE0841:TDE0842|TDE0841:TDE0842:hypothetical protein:cytoplasmic filament protein A:<-->:861689..861854 166 aaatactccttttttatgctttatatacactattatataacatatttgaaaaaaaatcatcaactttaaataaaaactctttacattatgcaaaatatgtttataattatataatagtgatatatattgtaattaacaaaattgctaaaagtaaggagagttagga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE0841:TDE0842|TDE0841:TDE0842:hypothetical protein:cytoplasmic filament protein A:<-->:861689..861854 166 aaatactccttttttatgctttatatacactattatataacatatttgaaaaaaaatcatcaactttaaataaaaactctttacattatgcaaaatatgtttataattatataatagtgatatatattgtaattaacaaaattgctaaaagtaaggagagttagga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aaatactccttttttatgctttatatacactattatataacatatttgaaaaaaaatcatcaactttaaataaaaactctttacattatgcaaaatatgtttataattatataatagtgatatatattgtaattaacaaaattgctaaaagtaaggagagttagga Predict ORF larger than 30AA ================================================ Protein_Len: 54 Strand: + Start: 3 End: 161 .. M L L F Y A L Y T L L Y N I F E K K S S T L N K N S L H Y A K Y V Y N Y I I V I Y I V I N K I A K S K E S * ..... Protein_Len: 41 Strand: - Start: 1 End: 123 F V G K K H K I Y V I I Y C I Q F F I M L K L Y F S K V N H L I H K Y N Y L L S M ........................................... aaatactccttttttatgctttatatacactattatataacatatttgaaaaaaaatcatcaactttaaataaaaactctttacattatgcaaaatatgtttataattatataatagtgatatatattgtaattaacaaaattgctaaaagtaaggagagttagga 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: 83 Start: 111 End: 140 ..............................................................................................................TTTGTTAATTACAATATATATCACTATTAT.......................... PromScan Matrix: RpoD-17 Strand: - Score: 82 Start: 32 End: 61 ...............................GATGATTTTTTTTCAAATATGTTATATAAT......................................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ aaatactccttttttatgctttatatacactattatataacatatttgaaaaaaaatcatcaactttaaataaaaactctttacattatgcaaaatatgtttataattatataatagtgatatatattgtaattaacaaaattgctaaaagtaaggagagttagga Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE0841:TDE0842|TDE0841:TDE0842:hypothetical protein:cytoplasmic filament protein A:<-->:861689..861854 166 aaatactccttttttatgctttatatacactattatataacatatttgaaaaaaaatcatcaactttaaataaaaactctttacattatgcaaaatatgtttataattatataatagtgatatatattgtaattaacaaaattgctaaaagtaaggagagttagga Intra-Species Hit: Count: 1 Min: 1 Max: 166 Len: 166 Subject: NC_002967_TDE0841_TDE0842|hypothetical protein:cytoplasmic filament protein A|NEGATIVE:POSITIVE|[861689,861854]|166 HSP 1 e-value: 4.0E-75 bit: 281.0 Len: 166 Query Start:1 Query End:166 Subject Strand: POSITIVE Subject Start: 1 Subject End: 166 aaatactccttttttatgctttatatacactattatataacatatttgnnnnnnnntcatcaactttaaataaaaactctttacattatgcaaaatatgtttataattatataatagtgatatatattgtaattaacaaaattgctaaaagtaaggagagttagga aaatactccttttttatgctttatatacactattatataacatatttgaaaaaaaatcatcaactttaaataaaaactctttacattatgcaaaatatgtttataattatataatagtgatatatattgtaattaacaaaattgctaaaagtaaggagagttagga Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAUACUCCUUUUUUAUGCUUUAUAUACACUAUUAUAUAACAUAUUUGAAAAAAAAUCAUCAACUUUAAAUAAAAACUCUUUACAUUAUGCAAAAUAUGUUUAUAAUUAUAUAAUAGUGAUAUAUAUUGUAAUUAACAAAAUUGCUAAAAGUAAGGAGAGUUAGGA .(((.((((((((((......(((((((((((((((((((..((((((((..............))))))))..........((((.((.....))))))......))))))))))))).))))))..((((((.....))))))..)))).)))))).))).... (-29.24) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UCCUAACUCUCCUUACUUUUAGCAAUUUUGUUAAUUACAAUAUAUAUCACUAUUAUAUAAUUAUAAACAUAUUUUGCAUAAUGUAAAGAGUUUUUAUUUAAAGUUGAUGAUUUUUUUUCAAAUAUGUUAUAUAAUAGUGUAUAUAAAGCAUAAAAAAGGAGUAUUU ........((((((..(((((((....((((.....))))((((((.((((((((((((((.(((((.((.((((((.....)))))).)).)))))......((((.((....)).))))....))))))))))))))))))))..)).)))))))))))..... (-33.90) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 638 50 1 141 92 NC_002967:TDE0841|5end_hypothetical_protein_861598..861828_NEGATIVE 212 100 51 140 82 NC_002967:TDE1568|5end_hypothetical_protein_1619544..1619774_POSITIVE 204 43 5 148 100 NC_002967:TDE0497|5end_hypothetical_protein_551880..552110_NEGATIVE 192 130 88 110 70 NC_002967:TDE2049|5end_bacterial_extracellular_solute-binding_proteins,_family_5_2077865..2078095_POSITIVE 185 159 111 230 175 NC_002967:TDE1582|5end_glycogen_synthase_1631759..1631989_NEGATIVE 179 49 6 153 99 NC_002967:TDE1072|5end_lipoprotein,_putative_1100741..1100971_POSITIVE 175 147 118 143 112 NC_002967:TDE1090|5end_threonyl-tRNA_synthetase_1121106..1121336_POSITIVE 173 160 137 141 117 NC_002967:TDE1713|5end_hypothetical_protein_1768468..1768698_NEGATIVE 171 158 121 44 17 NC_002967:TDE0995|5end_hypothetical_protein_1022576..1022806_NEGATIVE 167 31 3 118 90 NC_002967:TDE2365|5end_high-affinity_branched-chain_amino_acid_ABC_transporter,_permease_protein_2399949..2400179_NEGATIVE 165 44 5 129 91 NC_002967:TDE2446|5end_malate_dehydrogenase_2476249..2476479_NEGATIVE 160 59 12 137 80 NC_002967:TDE0071|5end_peptidase,_U32_family_78602..78832_POSITIVE 159 45 6 139 98 NC_002967:TDE0096|5end_NADH_oxidase_112723..112953_POSITIVE 158 44 1 139 95 NC_002967:TDE2293|5end_hypothetical_protein_2332570..2332800_NEGATIVE 157 151 124 190 163 NC_002967:TDE0053|5end_flagellar_biosynthetic_protein_FliR_61593..61823_POSITIVE 156 25 6 58 40 NC_002967:TDE1751|5end_ribosomal_protein_L21_1804142..1804372_NEGATIVE 155 36 6 63 27 NC_002967:TDE0778|5end_ribosomal_protein_L24_811487..811717_POSITIVE 153 47 3 152 107 NC_002967:TDE2638|5end_hypothetical_protein_2677493..2677723_POSITIVE 152 43 2 130 95 NC_002967:TDE1483|5end_hypothetical_protein_1528763..1528993_POSITIVE 150 129 82 132 87 NC_002967:TDE2729|5end_hypothetical_protein_2786457..2786687_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 212 100 51 107 49 NC_002967:TDE1567|3end_hypothetical_protein_1619591..1619741_POSITIVE 204 43 5 102 54 NC_002967:TDE0498|3end_hypothetical_protein_551926..552076_NEGATIVE 192 130 88 59 19 NC_002967:TDE2048|3end_hypothetical_protein_2077894..2078044_POSITIVE 173 160 137 126 102 NC_002967:TDE1714|3end_N-acetylmuramoyl-L-alanine_amidase,_family_3_1768483..1768633_NEGATIVE 167 31 3 108 80 NC_002967:TDE2366|3end_high-affinity_branched-chain_amino_acid_ABC_transporter,_permease_protein_2399959..2400109_NEGATIVE 166 160 141 135 113 NC_002967:TDE2755|3end_hypothetical_protein_2811941..2812091_POSITIVE 166 50 3 109 53 NC_002967:TDE1193|3end_hypothetical_protein_1219526..1219676_NEGATIVE 165 44 5 58 20 NC_002967:TDE2447|3end_shikimate_kinase_2476320..2476470_NEGATIVE 163 38 6 61 33 NC_002967:TDE0026|3end_TraB_family_protein_31826..31976_NEGATIVE 160 59 12 75 18 NC_002967:TDE0070|3end_RNA_polymerase_sigma-70_factor,_region_2_family_78620..78770_POSITIVE 158 44 1 100 56 NC_002967:TDE2294|3end_hydrolase,_haloacid_dehalogenase-like_family_2332609..2332759_NEGATIVE 155 36 6 53 17 NC_002967:TDE0777|3end_50S_ribosomal_protein_L14_811557..811707_POSITIVE 152 126 85 83 42 NC_002967:TDE1524|3end_hypothetical_protein_1570464..1570614_POSITIVE 149 31 3 79 53 NC_002967:TDE0579|3end_hypothetical_protein_609898..610048_NEGATIVE 147 119 86 125 91 NC_002967:TDE2223|3end_hypothetical_protein_2264826..2264976_POSITIVE 147 31 6 66 40 NC_002967:TDE2177|3end_hypothetical_protein_2206300..2206450_NEGATIVE 146 49 1 121 73 NC_002967:TDE2696|3end_TPR_domain_protein_2739098..2739248_NEGATIVE 146 46 6 62 11 NC_002967:TDE1329|3end_ATPase,_AAA_family_1365346..1365496_POSITIVE 143 160 114 80 26 NC_002967:TDE1899|3end_hypothetical_protein_1920942..1921092_NEGATIVE 143 148 101 70 17 NC_002967:TDE1566|3end_hypothetical_protein_1618984..1619134_POSITIVE