Origin IGS: tccccggagtttgtcaaaacatgttatccgaacctcccgcccttatcaagtagaattttttacctctccgaagaaaaaacgagcttttttttgctatctttgcggcgacttcataaaaaaacaaaaaaaattgggaacag .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 ctgttcccaattttttttgtttttttatgaagtcgccgcaaagatagcaaaaaaaagctcgttttttcttcggagaggtaaaaaattctacttgataagggcgggaggttcggataacatgttttgacaaactccgggga Mask Tandem Repeat Region ================================================ tccccggagtttgtcaaaacatgttatccgaacctcccgcccttatcaagtagaattttttacctctccgaagaaaaaacgagcttttttttgctatctttgcggcgacttcataaaaaaacaaaaaaaattgggaacag Find is-nt database================================================ Query_seq: TF2395:TF2396|TF2395:TF2396:conserved hypothetical protein:dimethyladenosine transferase:->->:2567725..2567864 140 tccccggagtttgtcaaaacatgttatccgaacctcccgcccttatcaagtagaattttttacctctccgaagaaaaaacgagcttttttttgctatctttgcggcgacttcataaaaaaacaaaaaaaattgggaacag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF2395:TF2396|TF2395:TF2396:conserved hypothetical protein:dimethyladenosine transferase:->->:2567725..2567864 140 tccccggagtttgtcaaaacatgttatccgaacctcccgcccttatcaagtagaattttttacctctccgaagaaaaaacgagcttttttttgctatctttgcggcgacttcataaaaaaacaaaaaaaattgggaacag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF2395:TF2396|TF2395:TF2396:conserved hypothetical protein:dimethyladenosine transferase:->->:2567725..2567864 140 tccccggagtttgtcaaaacatgttatccgaacctcccgcccttatcaagtagaattttttacctctccgaagaaaaaacgagcttttttttgctatctttgcggcgacttcataaaaaaacaaaaaaaattgggaacag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tccccggagtttgtcaaaacatgttatccgaacctcccgcccttatcaagtagaattttttacctctccgaagaaaaaacgagcttttttttgctatctttgcggcgacttcataaaaaaacaaaaaaaattgggaacag Predict ORF larger than 30AA ================================================ Protein_Len: 43 Strand: + Start: 11 End: 139 .......... M S K H V I R T S R P Y Q V E F F T S P K K K R A F F C Y L C G D F I K K Q K K L G T . Protein_Len: 36 Strand: - Start: 17 End: 124 ................ F M N D S G G A R I L Y F K K G R R L F F S S K K A I K A A V E Y F F M ................ tccccggagtttgtcaaaacatgttatccgaacctcccgcccttatcaagtagaattttttacctctccgaagaaaaaacgagcttttttttgctatctttgcggcgacttcataaaaaaacaaaaaaaattgggaacag 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: 21 End: 50 ....................CTTGATAAGGGCGGGAGGTTCGGATAACAT.......................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ tccccggagtttgtcaaaacatgttatccgaacctcccgcccttatcaagtagaattttttacctctccgaagaaaaaacgagcttttttttgctatctttgcggcgacttcataaaaaaacaaaaaaaattgggaacag Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TF2395:TF2396|TF2395:TF2396:conserved hypothetical protein:dimethyladenosine transferase:->->:2567725..2567864 140 tccccggagtttgtcaaaacatgttatccgaacctcccgcccttatcaagtagaattttttacctctccgaagaaaaaacgagcttttttttgctatctttgcggcgacttcataaaaaaacaaaaaaaattgggaacag Intra-Species Hit: Count: 1 Min: 1 Max: 114 Len: 114 Subject: tfor_TF2395_TF2396|conserved hypothetical protein:dimethyladenosine transferase|POSITIVE:POSITIVE|[2567725,2567864]|140 HSP 1 e-value: 3.0E-44 bit: 178.0 Len: 114 Query Start:1 Query End:114 Subject Strand: POSITIVE Subject Start: 1 Subject End: 114 tccccggagtttgtcaaaacatgttatccgaacctcccgcccttatcaagtagaattttttacctctccgaagaaaaaacgagcnnnnnnnngctatctttgcggcgacttcat.......................... tccccggagtttgtcaaaacatgttatccgaacctcccgcccttatcaagtagaattttttacctctccgaagaaaaaacgagcttttttttgctatctttgcggcgacttcat.......................... Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UCCCCGGAGUUUGUCAAAACAUGUUAUCCGAACCUCCCGCCCUUAUCAAGUAGAAUUUUUUACCUCUCCGAAGAAAAAACGAGCUUUUUUUUGCUAUCUUUGCGGCGACUUCAU ....((((...(((....))).....)))).......((((........(((((....))))).....((((((.......(((........))).)))))).))))....... (-18.40) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUGAAGUCGCCGCAAAGAUAGCAAAAAAAAGCUCGUUUUUUCUUCGGAGAGGUAAAAAAUUCUACUUGAUAAGGGCGGGAGGUUCGGAUAACAUGUUUUGACAAACUCCGGGGA .............(((((((((........))).))))))(((((((((..........(((..(((.....)))..))).(((..(((.....)))..)))...))))))))) (-21.60) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 332 48 4 164 130 tfor:TF2922|5end_surface_antigen_BspA_3119122..3119352_POSITIVE 310 40 2 50 10 tfor:TF2014|5end_dipeptidyl_aminopeptidase_IV_2169398..2169628_POSITIVE 310 106 61 49 3 tfor:TF0100|5end_conserved_hypothetical_protein_111135..111365_POSITIVE 303 43 1 99 45 tfor:TF2772|5end_tRNA_pseudouridine_synthase_B_2957383..2957613_POSITIVE 303 40 1 202 148 tfor:TF0160|5end_conserved_hypothetical_protein;_possible_Fic_family_protein_170327..170557_POSITIVE 297 51 19 219 180 tfor:TF3029|5end_membrane_peptidase_3252803..3253033_POSITIVE 295 70 27 227 175 tfor:TF1000|5end_sec-independent_protein_translocase_1053241..1053471_POSITIVE 293 107 63 159 99 tfor:TF2566|5end_50S_ribosomal_protein_L5_2740303..2740533_POSITIVE 291 49 2 205 137 tfor:TF0136|5end_transposase_element_145627..145857_POSITIVE 291 49 2 120 52 tfor:TF0134|5end_transposase_element_145542..145772_POSITIVE 289 103 62 51 9 tfor:TF0168|5end_hypothetical_protein_178160..178390_POSITIVE 285 66 21 197 138 tfor:TF2295|5end_hypothetical_protein_2448164..2448394_POSITIVE 285 46 2 76 37 tfor:TF1516|5end_transposase_fragment_1626407..1626637_POSITIVE 284 40 5 61 18 tfor:TF3111|5end_hypothetical_protein_3346601..3346831_POSITIVE 283 42 3 107 73 tfor:TF2246|5end_hypothetical_protein_2421288..2421518_POSITIVE 282 43 5 111 67 tfor:TF0467|5end_acetyltransferase-related_protein_485936..486166_POSITIVE 280 70 26 169 120 tfor:TF0254|5end_hypothetical_protein_285260..285490_POSITIVE 278 42 5 68 15 tfor:TF2793|5end_possible_L-lysine_2,3-aminomutase_2977661..2977891_POSITIVE 278 107 65 59 22 tfor:TF0629|5end_hypothetical_protein_665230..665460_POSITIVE 277 49 2 214 165 tfor:TF1170|5end_conserved_hypothetical_protein_1251862..1252092_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 303 43 1 84 30 tfor:TF2771|3end_undecaprenol_kinase,_bacitracin_resistance_protein_2957448..2957598_POSITIVE 289 103 62 45 3 tfor:TF0167|3end_conserved_hypothetical_protein_178234..178384_POSITIVE 286 107 64 60 17 tfor:TF0073|3end_possible_dTDP-glucose_4,6-dehydratase,_NAD-dependent_epimerase/dehydratase_family_82051..82201_POSITIVE 282 43 5 67 23 tfor:TF0466|3end_amidophosphoribosyltransferase_485972..486122_POSITIVE 281 43 9 149 110 tfor:TF1824|3end_ABC_transporter,_ATP-binding_protein_1973510..1973660_POSITIVE 278 107 65 42 5 tfor:TF0628|3end_conserved_hypothetical_protein_665293..665443_POSITIVE 276 42 2 54 9 tfor:TF2631|3end_conserved_hypothetical_protein_2802088..2802238_POSITIVE 276 44 5 134 77 tfor:TF0948|3end_50S_ribosomal_protein_L34_993918..994068_POSITIVE 274 109 67 132 92 tfor:TF0934|3end_hypothetical_protein_975207..975357_POSITIVE 265 42 5 151 109 tfor:TF2996|3end_hypothetical_protein_3211121..3211271_POSITIVE 263 104 63 150 99 tfor:TF2565|3end_50S_ribosomal_protein_L24_2740383..2740533_POSITIVE 263 42 3 103 57 tfor:TF0238|3end_outer_membrane_protein_268957..269107_POSITIVE 262 42 2 54 10 tfor:TF2978|3end_conserved_hypothetical_protein_3190862..3191012_POSITIVE 261 107 63 50 13 tfor:TF2646|3end_conserved_hypothetical_protein_2816697..2816847_POSITIVE 261 44 2 137 100 tfor:TF1274|3end_hypothetical_protein_1357895..1358045_POSITIVE 259 40 5 73 36 tfor:TF2430|3end_hypothetical_protein_2613204..2613354_POSITIVE 259 44 5 149 102 tfor:TF1000|3end_sec-independent_protein_translocase_1054169..1054319_POSITIVE 258 69 28 57 14 tfor:TF2127|3end_hypothetical_protein_2304306..2304456_POSITIVE 257 47 1 100 43 tfor:TF3133|3end_conserved_hypothetical_protein_3369913..3370063_POSITIVE 256 108 61 124 69 tfor:TF2547|3end_hypothetical_protein_2730947..2731097_POSITIVE