Origin IGS: aaaatctccttaaagttttatttatttaaccgtaaaggccgacattttatcatttatacaggcagagtgtctatcccttataaaaatccatttttaagcatc .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 gatgcttaaaaatggatttttataagggatagacactctgcctgtataaatgataaaatgtcggcctttacggttaaataaataaaactttaaggagatttt Mask Tandem Repeat Region ================================================ aaaatctccttaaagttttatttatttaaccgtaaaggccgacattttatcatttatacaggcagagtgtctatcccttataaaaatccatttttaagcatc Find is-nt database================================================ Query_seq: TDE0592:TDE0593|TDE0592:TDE0593:acetyl-CoA carboxylase, biotin carboxyl carrier protein:internalin-related protein:<-<-:632029..632130 102 aaaatctccttaaagttttatttatttaaccgtaaaggccgacattttatcatttatacaggcagagtgtctatcccttataaaaatccatttttaagcatc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE0592:TDE0593|TDE0592:TDE0593:acetyl-CoA carboxylase, biotin carboxyl carrier protein:internalin-related protein:<-<-:632029..632130 102 aaaatctccttaaagttttatttatttaaccgtaaaggccgacattttatcatttatacaggcagagtgtctatcccttataaaaatccatttttaagcatc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE0592:TDE0593|TDE0592:TDE0593:acetyl-CoA carboxylase, biotin carboxyl carrier protein:internalin-related protein:<-<-:632029..632130 102 aaaatctccttaaagttttatttatttaaccgtaaaggccgacattttatcatttatacaggcagagtgtctatcccttataaaaatccatttttaagcatc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aaaatctccttaaagttttatttatttaaccgtaaaggccgacattttatcatttatacaggcagagtgtctatcccttataaaaatccatttttaagcatc Predict ORF larger than 30AA ================================================ Protein_Len: 33 Strand: + Start: 4 End: 102 ... M S L K F Y L F N R K G R H F I I Y T G R V S I P Y K N P F L S I aaaatctccttaaagttttatttatttaaccgtaaaggccgacattttatcatttatacaggcagagtgtctatcccttataaaaatccatttttaagcatc 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================================================ aaaatctccttaaagttttatttatttaaccgtaaaggccgacattttatcatttatacaggcagagtgtctatcccttataaaaatccatttttaagcatc Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE0592:TDE0593|TDE0592:TDE0593:acetyl-CoA carboxylase, biotin carboxyl carrier protein:internalin-related protein:<-<-:632029..632130 102 aaaatctccttaaagttttatttatttaaccgtaaaggccgacattttatcatttatacaggcagagtgtctatcccttataaaaatccatttttaagcatc Intra-Species Hit: Count: 1 Min: 1 Max: 102 Len: 102 Subject: NC_002967_TDE0592_TDE0593|acetyl-CoA carboxylase, biotin carboxyl carrier protein:internalin-related protein|NEGATIVE:NEGATIVE|[632029,632130]|102 HSP 1 e-value: 2.0E-51 bit: 202.0 Len: 102 Query Start:1 Query End:102 Subject Strand: POSITIVE Subject Start: 1 Subject End: 102 aaaatctccttaaagttttatttatttaaccgtaaaggccgacattttatcatttatacaggcagagtgtctatcccttataaaaatccatttttaagcatc aaaatctccttaaagttttatttatttaaccgtaaaggccgacattttatcatttatacaggcagagtgtctatcccttataaaaatccatttttaagcatc Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAAUCUCCUUAAAGUUUUAUUUAUUUAACCGUAAAGGCCGACAUUUUAUCAUUUAUACAGGCAGAGUGUCUAUCCCUUAUAAAAAUCCAUUUUUAAGCAUC ........(((((((....((((......((.....))..((((((((..(.........)..))))))))............))))....))))))).... (-11.80) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAUGCUUAAAAAUGGAUUUUUAUAAGGGAUAGACACUCUGCCUGUAUAAAUGAUAAAAUGUCGGCCUUUACGGUUAAAUAAAUAAAACUUUAAGGAGAUUUU ..(.((((((........((((((.(((.(((.....)))))).))))))............((((.....)))).............)))))).)...... (-13.90) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 881 80 31 171 122 NC_002967:TDE0592|5end_acetyl-CoA_carboxylase,_biotin_carboxyl_carrier_protein_631938..632168_NEGATIVE 334 65 23 184 144 NC_002967:TDE1580|5end_hypothetical_protein_1629726..1629956_NEGATIVE 281 79 31 42 3 NC_002967:TDE0522|5end_hypothetical_protein_568499..568729_POSITIVE 268 58 29 59 29 NC_002967:TDE0176|5end_hypothetical_protein_209798..210028_NEGATIVE 266 80 36 211 170 NC_002967:TDE0448|5end_deoxyribose-phosphate_aldolase_505796..506026_POSITIVE 252 70 30 150 106 NC_002967:TDE0443|5end_hypothetical_protein_497938..498168_POSITIVE 248 78 31 127 73 NC_002967:TDE1330|5end_conserved_hypothetical_protein_TIGR00244_1365379..1365609_POSITIVE 241 80 31 143 101 NC_002967:TDE1356|5end_lipoprotein,_putative_1396669..1396899_NEGATIVE 239 100 53 95 38 NC_002967:TDE1495|5end_hypothetical_protein_1540216..1540446_NEGATIVE 239 46 3 143 95 NC_002967:TDE0748|5end_iron_compound_ABC_transporter,_periplasmic_iron_compound-binding_protein,_putative_784288..784518_NEGATIVE 238 41 2 139 95 NC_002967:TDE2258|5end_surface_antigen_BspA,_putative_2296401..2296631_NEGATIVE 238 77 31 228 176 NC_002967:TDE2061|5end_hypothetical_protein_2087792..2088022_NEGATIVE 238 45 6 138 97 NC_002967:TDE0671|5end_PIN_domain_protein_710621..710851_POSITIVE 236 76 37 81 35 NC_002967:TDE2151|5end_hypothetical_protein_2188807..2189037_NEGATIVE 233 64 30 69 39 NC_002967:TDE0857|5end_lipoprotein,_putative_878313..878543_POSITIVE 229 79 39 149 101 NC_002967:TDE1750|5end_hypothetical_protein_1803825..1804055_NEGATIVE 227 80 37 71 26 NC_002967:TDE1737|5end_hypothetical_protein_1790133..1790363_POSITIVE 225 75 31 58 16 NC_002967:TDE2576|5end_RNA_pseudouridylate_synthase_family_protein_2601672..2601902_POSITIVE 224 42 6 136 103 NC_002967:TDE2333|5end_sanA_protein,_putative_2368551..2368781_NEGATIVE 224 80 37 48 2 NC_002967:TDE0591|5end_acetyl-CoA_carboxylase,_biotin_carboxylase_631352..631582_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 291 70 30 53 12 NC_002967:TDE0005|3end_L-threonine_aldolase,_low-specificity_4985..5135_NEGATIVE 268 58 29 66 36 NC_002967:TDE0177|3end_hypothetical_protein_209791..209941_NEGATIVE 266 80 36 151 110 NC_002967:TDE0447|3end_TPR_domain_protein_505816..505966_POSITIVE 250 42 15 73 45 NC_002967:TDE1013|3end_hemerythrin-related_protein_1043977..1044127_NEGATIVE 236 76 37 84 38 NC_002967:TDE2152|3end_hypothetical_protein_2188804..2188954_NEGATIVE 233 64 30 54 24 NC_002967:TDE0856|3end_L-fuculose_phosphate_aldolase,_putative_878378..878528_POSITIVE 230 79 37 132 95 NC_002967:TDE0833|3end_lipoprotein,_putative_854097..854247_POSITIVE 229 79 39 143 95 NC_002967:TDE1751|3end_ribosomal_protein_L21_1803831..1803981_NEGATIVE 226 47 6 56 9 NC_002967:TDE2673|3end_hypothetical_protein_2711670..2711820_NEGATIVE 225 78 35 51 6 NC_002967:TDE0039|3end_ISTde1,_transposase_44489..44639_NEGATIVE 221 79 31 85 32 NC_002967:TDE0143|3end_thiamine_ABC_transporter,_thiamine-binding_protein_165103..165253_POSITIVE 219 79 32 110 60 NC_002967:TDE1117|3end_hypothetical_protein_1149871..1150021_POSITIVE 219 42 7 143 102 NC_002967:TDE0638|3end_oligopeptide/dipeptide_ABC_transporter,_permease_protein_672488..672638_NEGATIVE 218 73 35 76 30 NC_002967:TDE1093|3end_hypothetical_protein_1128158..1128308_POSITIVE 218 87 52 38 9 NC_002967:TDE0830|3end_hypothetical_protein_851609..851759_NEGATIVE 217 64 30 68 40 NC_002967:TDE1998|3end_phosphohexose_mutase_family_protein_2017143..2017293_POSITIVE 216 75 31 64 23 NC_002967:TDE2734|3end_hypothetical_protein_2789861..2790011_POSITIVE 213 42 3 144 97 NC_002967:TDE0976|3end_hypothetical_protein_1000498..1000648_POSITIVE 212 74 31 63 12 NC_002967:TDE1887|3end_TPR_domain_protein_1908492..1908642_NEGATIVE 212 66 32 150 118 NC_002967:TDE1379|3end_hypothetical_protein_1420014..1420164_NEGATIVE