Origin IGS: ttgttgttttaatagcggacgcaaaattacgactttacgctggaaaaacaatcgtgcatgctatgaatatctgttttttttcgtgtatttttgcaaggttttaaagg .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 cctttaaaaccttgcaaaaatacacgaaaaaaaacagatattcatagcatgcacgattgtttttccagcgtaaagtcgtaattttgcgtccgctattaaaacaacaa Mask Tandem Repeat Region ================================================ ttgttgttttaatagcggacgcaaaattacgactttacgctggaaaaacaatcgtgcatgctatgaatatctgttttttttcgtgtatttttgcaaggttttaaagg Find is-nt database================================================ Query_seq: TF2977:TF2978|TF2977:TF2978:candidate b-glycosyltransferase, Glycosyltransferase Family 2 protein:conserved hypothetical protein:->->:3186109..3186215 107 ttgttgttttaatagcggacgcaaaattacgactttacgctggaaaaacaatcgtgcatgctatgaatatctgttttttttcgtgtatttttgcaaggttttaaagg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF2977:TF2978|TF2977:TF2978:candidate b-glycosyltransferase, Glycosyltransferase Family 2 protein:conserved hypothetical protein:->->:3186109..3186215 107 ttgttgttttaatagcggacgcaaaattacgactttacgctggaaaaacaatcgtgcatgctatgaatatctgttttttttcgtgtatttttgcaaggttttaaagg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF2977:TF2978|TF2977:TF2978:candidate b-glycosyltransferase, Glycosyltransferase Family 2 protein:conserved hypothetical protein:->->:3186109..3186215 107 ttgttgttttaatagcggacgcaaaattacgactttacgctggaaaaacaatcgtgcatgctatgaatatctgttttttttcgtgtatttttgcaaggttttaaagg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ttgttgttttaatagcggacgcaaaattacgactttacgctggaaaaacaatcgtgcatgctatgaatatctgttttttttcgtgtatttttgcaaggttttaaagg Predict ORF larger than 30AA ================================================ Protein_Len: 30 Strand: + Start: 12 End: 101 ........... M A D A K L R L Y A G K T I V H A M N I C F F S C I F A R F ...... ttgttgttttaatagcggacgcaaaattacgactttacgctggaaaaacaatcgtgcatgctatgaatatctgttttttttcgtgtatttttgcaaggttttaaagg 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================================================ ttgttgttttaatagcggacgcaaaattacgactttacgctggaaaaacaatcgtgcatgctatgaatatctgttttttttcgtgtatttttgcaaggttttaaagg Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TF2977:TF2978|TF2977:TF2978:candidate b-glycosyltransferase, Glycosyltransferase Family 2 protein:conserved hypothetical protein:->->:3186109..3186215 107 ttgttgttttaatagcggacgcaaaattacgactttacgctggaaaaacaatcgtgcatgctatgaatatctgttttttttcgtgtatttttgcaaggttttaaagg Intra-Species Hit: Count: 1 Min: 1 Max: 107 Len: 107 Subject: tfor_TF2977_TF2978|candidate b-glycosyltransferase, Glycosyltransferase Family 2 protein:conserved hypothetical protein|POSITIVE:POSITIVE|[3186109,3186215]|107 HSP 1 e-value: 3.0E-40 bit: 165.0 Len: 107 Query Start:1 Query End:107 Subject Strand: POSITIVE Subject Start: 1 Subject End: 107 ttgttgttttaatagcggacgcaaaattacgactttacgctggaaaaacaatcgtgcatgctatgaatatctgnnnnnnnncgtgtatttttgcaaggttttaaagg ttgttgttttaatagcggacgcaaaattacgactttacgctggaaaaacaatcgtgcatgctatgaatatctgttttttttcgtgtatttttgcaaggttttaaagg Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUGUUGUUUUAAUAGCGGACGCAAAAUUACGACUUUACGCUGGAAAAACAAUCGUGCAUGCUAUGAAUAUCUGUUUUUUUUCGUGUAUUUUUGCAAGGUUUUAAAGG ..((((((((..(((((....................)))))..))))))))......(((...((((((.((........)).))))))..)))............ (-17.75) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CCUUUAAAACCUUGCAAAAAUACACGAAAAAAAACAGAUAUUCAUAGCAUGCACGAUUGUUUUUCCAGCGUAAAGUCGUAAUUUUGCGUCCGCUAUUAAAACAACAA ............((((.................................))))...(((((((...((((....(.((((....)))).)))))...)))))))... (-11.41) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 300 97 52 73 23 tfor:TF2313|5end_SAM-dependent_methyltransferase_2472423..2472653_POSITIVE 294 79 37 227 188 tfor:TF0228|5end_probable_integral_outer_membrane_protein_253851..254081_POSITIVE 281 98 51 221 177 tfor:TF2466|5end_pyruvate_kinase_2644385..2644615_POSITIVE 276 78 38 81 29 tfor:TF2367|5end_delta-1-pyrroline-5-carboxylate_dehydrogenase_2532002..2532232_POSITIVE 276 56 16 162 125 tfor:TF0203|5end_PhoH-like_protein_229255..229485_POSITIVE 273 58 16 43 6 tfor:TF0426|5end_conserved_hypothetical_protein_444728..444958_POSITIVE 268 75 33 186 141 tfor:TF1754|5end_conserved_hypothetical_protein_1890937..1891167_POSITIVE 267 56 14 155 106 tfor:TF0998|5end_[acyl-carrier-protein]_S-malonyltransferase_1052019..1052249_POSITIVE 264 56 17 141 103 tfor:TF1295|5end_conserved_hypothetical_protein_1375854..1376084_POSITIVE 263 55 15 82 48 tfor:TF1577|5end_hypothetical_protein_1685960..1686190_POSITIVE 261 60 20 44 14 tfor:TF1965|5end_conserved_hypothetical_protein_2114313..2114543_POSITIVE 258 99 53 78 35 tfor:TF2759|5end_xylose_repressor,_ROK_family_2943568..2943798_POSITIVE 258 70 21 120 63 tfor:TF0186|5end_ribonucleotide_reductase,_alpha_subunit_199198..199428_POSITIVE 256 60 14 106 65 tfor:TF3070|5end_conserved_hypothetical_protein_3294380..3294610_POSITIVE 256 69 30 45 16 tfor:TF0064|5end_conserved_hypothetical_protein_68419..68649_POSITIVE 254 60 15 88 39 tfor:TF0227|5end_transcriptional_regulator,_Crp/Fnr_family_252820..253050_POSITIVE 249 99 53 161 111 tfor:TF0690|5end_preprotein_translocase_subunit_735243..735473_POSITIVE 248 58 14 175 142 tfor:TF0152|5end_RNA_polymerase_ECF-type_sigma_factor_162021..162251_POSITIVE 247 57 16 180 140 tfor:TF2372|5end_acyl-(acyl-carrier-protein)-UDP-N-acetylglucosami_ne_acyltransferase_2537558..2537788_POSITIVE 245 98 51 218 161 tfor:TF3139|5end_Na+-translocating_NADH-quinone_reductase,_subunit_C_3372581..3372811_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 300 97 52 92 42 tfor:TF2312|3end_conserved_hypothetical_protein;_possible_glycosyl_transferase_2472522..2472672_POSITIVE 294 79 37 143 104 tfor:TF0226|3end_hypothetical_protein_253847..253997_POSITIVE 267 56 14 147 98 tfor:TF0997|3end_conserved_hypothetical_protein_1052091..1052241_POSITIVE 264 56 17 131 93 tfor:TF1293|3end_ATPase,_possible_AAA_superfamily_1375924..1376074_POSITIVE 263 62 33 150 117 tfor:TF1753|3end_topoisomerase_IV_subunit_A_1890993..1891143_POSITIVE 261 60 20 31 1 tfor:TF1964|3end_MotA/TolQ/ExbB_proton_channel_family_2114380..2114530_POSITIVE 258 70 21 98 41 tfor:TF0185|3end_4-alpha-glucanotransferase_(amylomaltase)_199256..199406_POSITIVE 256 60 14 59 18 tfor:TF3069|3end_hypothetical_protein_3294413..3294563_POSITIVE 256 69 30 36 7 tfor:TF0063|3end_conserved_hypothetical_protein_68490..68640_POSITIVE 254 100 55 62 27 tfor:TF2165|3end_hypothetical_protein_2341922..2342072_POSITIVE 248 58 14 146 113 tfor:TF0151|3end_hydrolase/beta-alanine_synthase_162072..162222_POSITIVE 245 60 11 129 84 tfor:TF2086|3end_transglutaminase-related_protein_2256767..2256917_POSITIVE 244 65 21 145 95 tfor:TF1571|3end_conserved_hypothetical_protein_1681032..1681182_POSITIVE 235 91 53 151 104 tfor:TF2638|3end_cation_transport_protein_2809051..2809201_POSITIVE 234 79 34 57 6 tfor:TF2110|3end_transposase_2280526..2280676_POSITIVE 233 76 38 32 4 tfor:TF0645|3end_hypothetical_protein_689139..689289_POSITIVE 232 60 11 148 114 tfor:TF1269|3end_acetyltransferase_1355180..1355330_POSITIVE 230 58 14 146 104 tfor:TF2213|3end_glycyl-tRNA_synthetase_2386940..2387090_POSITIVE 230 56 15 92 51 tfor:TF1323|3end_metallo-beta-lactamase_superfamily_protein_1403533..1403683_POSITIVE 229 60 14 71 17 tfor:TF2847|3end_hypothetical_protein_3034985..3035135_POSITIVE