Origin IGS: agggagtcccgccgggagtttttgataaacaacgagcgtccccgctcctaccagccctaaaaaaatgataatcaatacacctatcttccaataatttttctccataaagtatattatagcacataaatgaaaaaattgtcaaaggacaagtgtcaaacggtgagctcattccataattt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aaattatggaatgagctcaccgtttgacacttgtcctttgacaattttttcatttatgtgctataatatactttatggagaaaaattattggaagataggtgtattgattatcatttttttagggctggtaggagcggggacgctcgttgtttatcaaaaactcccggcgggactccct Mask Tandem Repeat Region ================================================ agggagtcccgccgggagtttttgataaacaacgagcgtccccgctcctaccagccctaaaaaaatgataatcaatacacctatcttccaataatttttctccataaagtatattatagcacataaatgaaaaaattgtcaaaggacaagtgtcaaacggtgagctcattccataattt Find is-nt database================================================ Query_seq: TDE2102:TDE2103|TDE2102:TDE2103:hypothetical protein:glycosyl transferase, group 2 family protein:<-<-:2127438..2127616 179 agggagtcccgccgggagtttttgataaacaacgagcgtccccgctcctaccagccctaaaaaaatgataatcaatacacctatcttccaataatttttctccataaagtatattatagcacataaatgaaaaaattgtcaaaggacaagtgtcaaacggtgagctcattccataattt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE2102:TDE2103|TDE2102:TDE2103:hypothetical protein:glycosyl transferase, group 2 family protein:<-<-:2127438..2127616 179 agggagtcccgccgggagtttttgataaacaacgagcgtccccgctcctaccagccctaaaaaaatgataatcaatacacctatcttccaataatttttctccataaagtatattatagcacataaatgaaaaaattgtcaaaggacaagtgtcaaacggtgagctcattccataattt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE2102:TDE2103|TDE2102:TDE2103:hypothetical protein:glycosyl transferase, group 2 family protein:<-<-:2127438..2127616 179 agggagtcccgccgggagtttttgataaacaacgagcgtccccgctcctaccagccctaaaaaaatgataatcaatacacctatcttccaataatttttctccataaagtatattatagcacataaatgaaaaaattgtcaaaggacaagtgtcaaacggtgagctcattccataattt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 agggagtcccgccgggagtttttgataaacaacgagcgtccccgctcctaccagccctaaaaaaatgataatcaatacacctatcttccaataatttttctccataaagtatattatagcacataaatgaaaaaattgtcaaaggacaagtgtcaaacggtgagctcattccataattt Predict ORF larger than 30AA ================================================ Protein_Len: 56 Strand: - Start: 2 End: 169 . P T G G P T K S L C R A D G S R G A R F F H Y D I C R D E L L K E G Y L I N Y C M F S F I T L P C T D F P S S M .......... Protein_Len: 39 Strand: - Start: 1 End: 117 P L G A P L K Q Y V V L T G A G V L G L F I I I L V G I K W Y N K E M F Y I M .............................................................. agggagtcccgccgggagtttttgataaacaacgagcgtccccgctcctaccagccctaaaaaaatgataatcaatacacctatcttccaataatttttctccataaagtatattatagcacataaatgaaaaaattgtcaaaggacaagtgtcaaacggtgagctcattccataattt 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================================================ agggagtcccgccgggagtttttgataaacaacgagcgtccccgctcctaccagccctaaaaaaatgataatcaatacacctatcttccaataatttttctccataaagtatattatagcacataaatgaaaaaattgtcaaaggacaagtgtcaaacggtgagctcattccataattt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE2102:TDE2103|TDE2102:TDE2103:hypothetical protein:glycosyl transferase, group 2 family protein:<-<-:2127438..2127616 179 agggagtcccgccgggagtttttgataaacaacgagcgtccccgctcctaccagccctaaaaaaatgataatcaatacacctatcttccaataatttttctccataaagtatattatagcacataaatgaaaaaattgtcaaaggacaagtgtcaaacggtgagctcattccataattt Intra-Species Hit: Count: 1 Min: 1 Max: 179 Len: 179 Subject: NC_002967_TDE2102_TDE2103|hypothetical protein:glycosyl transferase, group 2 family protein|NEGATIVE:NEGATIVE|[2127438,2127616]|179 HSP 1 e-value: 1.0E-84 bit: 313.0 Len: 179 Query Start:1 Query End:179 Subject Strand: POSITIVE Subject Start: 1 Subject End: 179 agggagtcccgccgggagtttttgataaacaacgagcgtccccgctcctaccagccctnnnnnnntgataatcaatacacctatcttccaataatttttctccataaagtatattatagcacataaatgaaaaaattgtcaaaggacaagtgtcaaacggtgagctcattccataattt agggagtcccgccgggagtttttgataaacaacgagcgtccccgctcctaccagccctaaaaaaatgataatcaatacacctatcttccaataatttttctccataaagtatattatagcacataaatgaaaaaattgtcaaaggacaagtgtcaaacggtgagctcattccataattt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGGGAGUCCCGCCGGGAGUUUUUGAUAAACAACGAGCGUCCCCGCUCCUACCAGCCCUAAAAAAAUGAUAAUCAAUACACCUAUCUUCCAAUAAUUUUUCUCCAUAAAGUAUAUUAUAGCACAUAAAUGAAAAAAUUGUCAAAGGACAAGUGUCAAACGGUGAGCUCAUUCCAUAAUUU .((((((..(((((...(((..(((((.((...(((((....)))))...................((((...........)))).......................)).))))).))).......(((.....(((((....)))))...)))..))))).))))...))....... (-30.80) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAUUAUGGAAUGAGCUCACCGUUUGACACUUGUCCUUUGACAAUUUUUUCAUUUAUGUGCUAUAAUAUACUUUAUGGAGAAAAAUUAUUGGAAGAUAGGUGUAUUGAUUAUCAUUUUUUUAGGGCUGGUAGGAGCGGGGACGCUCGUUGUUUAUCAAAAACUCCCGGCGGGACUCCCU .......((...((((((.(((....(((((((((.((..(.((((((((..........((((((......)))))).)))))))).)..)).))))))))).((((((((((.(((....))).))))).(((((....))))).......))))).......))).))).))))). (-45.80) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 1081 50 1 141 92 NC_002967:TDE2102|5end_hypothetical_protein_2127347..2127577_NEGATIVE 973 60 11 76 27 NC_002967:TDE2240|5end_hypothetical_protein_2278422..2278652_NEGATIVE 390 45 1 89 39 NC_002967:TDE1926|5end_hypothetical_protein_1942495..1942725_POSITIVE 323 48 2 199 157 NC_002967:TDE2583|5end_hypothetical_protein_2616322..2616552_POSITIVE 322 56 11 72 23 NC_002967:TDE1505|5end_hypothetical_protein_1553614..1553844_POSITIVE 320 46 2 189 145 NC_002967:TDE1391|5end_NQR2/RnfD/RnfE_family_protein_1430975..1431205_POSITIVE 320 41 2 50 8 NC_002967:TDE0934|5end_chaperonin,_10_kDa_959661..959891_NEGATIVE 315 57 11 170 108 NC_002967:TDE2268|5end_hypothetical_protein_2304959..2305189_NEGATIVE 314 88 42 101 54 NC_002967:TDE1629|5end_dihydrolipoamide_dehydrogenase_1678514..1678744_NEGATIVE 312 60 31 31 5 NC_002967:TDE2684|5end_hypothetical_protein_2724848..2725078_NEGATIVE 310 58 11 128 66 NC_002967:TDE2604|5end_hypothetical_protein_2645774..2646004_NEGATIVE 307 44 1 184 131 NC_002967:TDE2044|5end_lipoprotein,_putative_2074616..2074846_NEGATIVE 304 49 1 103 39 NC_002967:TDE0682|5end_preprotein_translocase,_YajC_subunit_721078..721308_NEGATIVE 302 51 13 46 1 NC_002967:TDE1582|5end_glycogen_synthase_1631759..1631989_NEGATIVE 299 49 8 147 107 NC_002967:TDE2491|5end_DNA_polymerase_domain_protein_2515499..2515729_NEGATIVE 298 48 3 102 47 NC_002967:TDE1249|5end_hypothetical_protein_1283525..1283755_POSITIVE 294 39 2 159 116 NC_002967:TDE2725|5end_cyclic_nucleotide_binding_domain/GGDEF_domain_protein_2783208..2783438_NEGATIVE 291 58 17 87 36 NC_002967:TDE0690|5end_tRNA_(5-methylaminomethyl-2-thiouridylate)-methyltransferase_726898..727128_POSITIVE 287 49 1 230 175 NC_002967:TDE2701|5end_hypothetical_protein_2745689..2745919_POSITIVE 287 46 9 166 132 NC_002967:TDE0250|5end_sodium-dependent_transporter,_putative_284635..284865_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 675 120 71 52 3 NC_002967:TDE2241|3end_glycosyl_transferase,_group_2_family_protein_2278506..2278656_NEGATIVE 390 45 1 119 69 NC_002967:TDE1925|3end_peptidyl-prolyl_cis-trans_isomerase,_FKBP-type_1942605..1942755_POSITIVE 350 80 33 98 54 NC_002967:TDE2260|3end_hypothetical_protein_2297573..2297723_POSITIVE 320 41 2 50 8 NC_002967:TDE0935|3end_hypothetical_protein_959661..959811_NEGATIVE 308 59 11 139 79 NC_002967:TDE0142|3end_hypothetical_protein_163979..164129_NEGATIVE 299 49 8 137 97 NC_002967:TDE2492|3end_hypothetical_protein_2515509..2515659_NEGATIVE 298 48 3 117 62 NC_002967:TDE1248|3end_hypothetical_protein_1283620..1283770_POSITIVE 291 58 17 81 30 NC_002967:TDE0689|3end_5-methylthioribose_kinase_726972..727122_POSITIVE 290 49 3 70 22 NC_002967:TDE2269|3end_hypothetical_protein_2304931..2305081_NEGATIVE 288 49 2 73 23 NC_002967:TDE1131|3end_hypothetical_protein_1163531..1163681_POSITIVE 287 46 9 84 50 NC_002967:TDE0251|3end_tryptophanase_284717..284867_NEGATIVE 279 49 3 82 20 NC_002967:TDE2715|3end_hypothetical_protein_2772936..2773086_POSITIVE 278 56 11 84 40 NC_002967:TDE0607|3end_ParA_family_ATPase_644125..644275_NEGATIVE 274 48 1 138 94 NC_002967:TDE0977|3end_hypothetical_protein_1001640..1001790_POSITIVE 272 49 1 89 43 NC_002967:TDE2226|3end_ABC_transporter,_substrate-binding_protein,_putative_2266412..2266562_POSITIVE 271 54 11 87 41 NC_002967:TDE1533|3end_hypothetical_protein_1578657..1578807_POSITIVE 268 49 1 110 69 NC_002967:TDE1913|3end_hypothetical_protein_1930897..1931047_POSITIVE 265 49 1 143 96 NC_002967:TDE0872|3end_recA_protein_896165..896315_POSITIVE 262 56 11 66 2 NC_002967:TDE2682|3end_hypothetical_protein_2721388..2721538_NEGATIVE 260 50 1 88 21 NC_002967:TDE1911|3end_hypothetical_protein_1928943..1929093_NEGATIVE