Origin IGS: tccgttctgtttaatatttaatcttttaaatctgttttttcttttatgcagggtgcaaaattagacttataattttaatctcgcaaatataaaacatccaataaacaataattttcgctataaaacacttgtttattccgattttatctgtttctttgcggcgtgaaaggagtgattatacttccgaacgtacttaacaatcggtttttatctctgtcagcgattgatgatttatttttcattgttttgaacttccggttttcttgcacttttcattagtaacgatcgagtatttttaattttatatttt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aaaatataaaattaaaaatactcgatcgttactaatgaaaagtgcaagaaaaccggaagttcaaaacaatgaaaaataaatcatcaatcgctgacagagataaaaaccgattgttaagtacgttcggaagtataatcactcctttcacgccgcaaagaaacagataaaatcggaataaacaagtgttttatagcgaaaattattgtttattggatgttttatatttgcgagattaaaattataagtctaattttgcaccctgcataaaagaaaaaacagatttaaaagattaaatattaaacagaacgga Mask Tandem Repeat Region ================================================ tccgttctgtttaatatttaatcttttaaatctgttttttcttttatgcagggtgcaaaattagacttataattttaatctcgcaaatataaaacatccaataaacaataattttcgctataaaacacttgtttattccgattttatctgtttctttgcggcgtgaaaggagtgattatacttccgaacgtacttaacaatcggtttttatctctgtcagcgattgatgatttatttttcattgttttgaacttccggttttcttgcacttttcattagtaacgatcgagtatttttaattttatatttt Find is-nt database================================================ Query_seq: TF2510:TF2511|TF2510:TF2511:trigger factor, peptidyl prolyl cis-trans isomerase:RNA binding protein:->->:2689740..2690049 310 tccgttctgtttaatatttaatcttttaaatctgttttttcttttatgcagggtgcaaaattagacttataattttaatctcgcaaatataaaacatccaataaacaataattttcgctataaaacacttgtttattccgattttatctgtttctttgcggcgtgaaaggagtgattatacttccgaacgtacttaacaatcggtttttatctctgtcagcgattgatgatttatttttcattgttttgaacttccggttttcttgcacttttcattagtaacgatcgagtatttttaattttatatttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF2510:TF2511|TF2510:TF2511:trigger factor, peptidyl prolyl cis-trans isomerase:RNA binding protein:->->:2689740..2690049 310 tccgttctgtttaatatttaatcttttaaatctgttttttcttttatgcagggtgcaaaattagacttataattttaatctcgcaaatataaaacatccaataaacaataattttcgctataaaacacttgtttattccgattttatctgtttctttgcggcgtgaaaggagtgattatacttccgaacgtacttaacaatcggtttttatctctgtcagcgattgatgatttatttttcattgttttgaacttccggttttcttgcacttttcattagtaacgatcgagtatttttaattttatatttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF2510:TF2511|TF2510:TF2511:trigger factor, peptidyl prolyl cis-trans isomerase:RNA binding protein:->->:2689740..2690049 310 tccgttctgtttaatatttaatcttttaaatctgttttttcttttatgcagggtgcaaaattagacttataattttaatctcgcaaatataaaacatccaataaacaataattttcgctataaaacacttgtttattccgattttatctgtttctttgcggcgtgaaaggagtgattatacttccgaacgtacttaacaatcggtttttatctctgtcagcgattgatgatttatttttcattgttttgaacttccggttttcttgcacttttcattagtaacgatcgagtatttttaattttatatttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tccgttctgtttaatatttaatcttttaaatctgttttttcttttatgcagggtgcaaaattagacttataattttaatctcgcaaatataaaacatccaataaacaataattttcgctataaaacacttgtttattccgattttatctgtttctttgcggcgtgaaaggagtgattatacttccgaacgtacttaacaatcggtttttatctctgtcagcgattgatgatttatttttcattgttttgaacttccggttttcttgcacttttcattagtaacgatcgagtatttttaattttatatttt Predict ORF larger than 30AA ================================================ Protein_Len: 43 Strand: + Start: 148 End: 276 ................................................................................................................................................... M F L C G V K G V I I L P N V L N N R F L S L S A I D D L F F I V L N F R F S C T F H .................................. Protein_Len: 41 Strand: - Start: 147 End: 269 .................................................................................................................................................. R N R Q P T F P T I I S G F T S L L R N K D R D A I S S K N K M T K F K R N E Q M ......................................... Protein_Len: 32 Strand: - Start: 47 End: 142 .............................................. A P H L I L S I I K I E C I Y F M W Y V I I K A I F C K N I G M ........................................................................................................................................................................ tccgttctgtttaatatttaatcttttaaatctgttttttcttttatgcagggtgcaaaattagacttataattttaatctcgcaaatataaaacatccaataaacaataattttcgctataaaacacttgtttattccgattttatctgtttctttgcggcgtgaaaggagtgattatacttccgaacgtacttaacaatcggtttttatctctgtcagcgattgatgatttatttttcattgttttgaacttccggttttcttgcacttttcattagtaacgatcgagtatttttaattttatatttt 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================================================ tccgttctgtttaatatttaatcttttaaatctgttttttcttttatgcagggtgcaaaattagacttataattttaatctcgcaaatataaaacatccaataaacaataattttcgctataaaacacttgtttattccgattttatctgtttctttgcggcgtgaaaggagtgattatacttccgaacgtacttaacaatcggtttttatctctgtcagcgattgatgatttatttttcattgttttgaacttccggttttcttgcacttttcattagtaacgatcgagtatttttaattttatatttt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TF2510:TF2511|TF2510:TF2511:trigger factor, peptidyl prolyl cis-trans isomerase:RNA binding protein:->->:2689740..2690049 310 tccgttctgtttaatatttaatcttttaaatctgttttttcttttatgcagggtgcaaaattagacttataattttaatctcgcaaatataaaacatccaataaacaataattttcgctataaaacacttgtttattccgattttatctgtttctttgcggcgtgaaaggagtgattatacttccgaacgtacttaacaatcggtttttatctctgtcagcgattgatgatttatttttcattgttttgaacttccggttttcttgcacttttcattagtaacgatcgagtatttttaattttatatttt Intra-Species Hit: Count: 1 Min: 1 Max: 310 Len: 310 Subject: tfor_TF2510_TF2511|trigger factor, peptidyl prolyl cis-trans isomerase:RNA binding protein|POSITIVE:POSITIVE|[2689740,2690049]|310 HSP 1 e-value: 1.0E-175 bit: 615.0 Len: 310 Query Start:1 Query End:310 Subject Strand: POSITIVE Subject Start: 1 Subject End: 310 tccgttctgtttaatatttaatcttttaaatctgttttttcttttatgcagggtgcaaaattagacttataattttaatctcgcaaatataaaacatccaataaacaataattttcgctataaaacacttgtttattccgattttatctgtttctttgcggcgtgaaaggagtgattatacttccgaacgtacttaacaatcggtttttatctctgtcagcgattgatgatttatttttcattgttttgaacttccggttttcttgcacttttcattagtaacgatcgagtatttttaattttatatttt tccgttctgtttaatatttaatcttttaaatctgttttttcttttatgcagggtgcaaaattagacttataattttaatctcgcaaatataaaacatccaataaacaataattttcgctataaaacacttgtttattccgattttatctgtttctttgcggcgtgaaaggagtgattatacttccgaacgtacttaacaatcggtttttatctctgtcagcgattgatgatttatttttcattgttttgaacttccggttttcttgcacttttcattagtaacgatcgagtatttttaattttatatttt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UCCGUUCUGUUUAAUAUUUAAUCUUUUAAAUCUGUUUUUUCUUUUAUGCAGGGUGCAAAAUUAGACUUAUAAUUUUAAUCUCGCAAAUAUAAAACAUCCAAUAAACAAUAAUUUUCGCUAUAAAACACUUGUUUAUUCCGAUUUUAUCUGUUUCUUUGCGGCGUGAAAGGAGUGAUUAUACUUCCGAACGUACUUAACAAUCGGUUUUUAUCUCUGUCAGCGAUUGAUGAUUUAUUUUUCAUUGUUUUGAACUUCCGGUUUUCUUGCACUUUUCAUUAGUAACGAUCGAGUAUUUUUAAUUUUAUAUUUU ............((((((..(((.....((((.....((((((((((((.((((..(((((((......))))))).))))((((((...............(((((((((...(((..(((((.(....))))))..)))..)))).))))).)))))))))))))))))).)))).((((...(((.((.(.....((((((...(((((...(((...))).))))).......((((......))))...)))))).....).))..)))...))))..)))..))))))................ (-45.59) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAAUAUAAAAUUAAAAAUACUCGAUCGUUACUAAUGAAAAGUGCAAGAAAACCGGAAGUUCAAAACAAUGAAAAAUAAAUCAUCAAUCGCUGACAGAGAUAAAAACCGAUUGUUAAGUACGUUCGGAAGUAUAAUCACUCCUUUCACGCCGCAAAGAAACAGAUAAAAUCGGAAUAAACAAGUGUUUUAUAGCGAAAAUUAUUGUUUAUUGGAUGUUUUAUAUUUGCGAGAUUAAAAUUAUAAGUCUAAUUUUGCACCCUGCAUAAAAGAAAAAACAGAUUUAAAAGAUUAAAUAUUAAACAGAACGGA .........................(((((.((.(((....((((((((..........((((......)))).....((((.......(((((..(((.......((((.(((.....))).))))..(......).)))...))).))(((((((((((((((...)))..(((((((((..(((((......)))))..)))))))))...))))))...)))))).))))................))))))))....)))..............((((((....)))))).......))))))). (-43.40) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 322 177 132 137 87 tfor:TF0466|5end_amidophosphoribosyltransferase_483994..484224_POSITIVE 321 188 142 125 71 tfor:TF0324|5end_conserved_hypothetical_protein_351228..351458_POSITIVE 320 173 134 100 55 tfor:TF1934|5end_hypothetical_protein_2083787..2084017_POSITIVE 317 190 146 165 112 tfor:TF2900|5end_conserved_hypothetical_protein_3088252..3088482_POSITIVE 317 188 148 200 160 tfor:TF0902|5end_methyltransferase_947237..947467_POSITIVE 306 295 254 51 7 tfor:TF1639|5end_conserved_hypothetical_protein_1747652..1747882_POSITIVE 306 196 153 52 10 tfor:TF1528|5end_malate_dehydrogenase_1633287..1633517_POSITIVE 302 189 144 137 95 tfor:TF1545|5end_conserved_hypothetical_protein_1651134..1651364_POSITIVE 289 190 147 178 136 tfor:TF1468|5end_beta-galactosidase_1557785..1558015_POSITIVE 286 256 211 105 59 tfor:TF0814|5end_conserved_hypothetical_protein_872546..872776_POSITIVE 283 175 138 175 145 tfor:TF1354|5end_TonB_protein_1433274..1433504_POSITIVE 282 198 158 64 12 tfor:TF0091|5end_outer_membrane_protein_97701..97931_POSITIVE 281 225 192 193 165 tfor:TF0931|5end_superfamily_II_DNA/RNA_helicase,_SNF2_family_970031..970261_POSITIVE 278 193 152 220 170 tfor:TF2484|5end_hypothetical_protein_2660005..2660235_POSITIVE 277 178 139 214 169 tfor:TF0630|5end_hypothetical_protein_666287..666517_POSITIVE 276 273 239 92 58 tfor:TF2215|5end_conserved_hypothetical_protein_2387501..2387731_POSITIVE 275 219 173 126 85 tfor:TF2856|5end_conserved_hypothetical_protein;_possible_TPR-repeat-containing_protein_3042118..3042348_POSITIVE 275 175 139 63 22 tfor:TF2582|5end_ABC_transporter,_ATP-binding_protein_2749433..2749663_POSITIVE 275 190 142 225 168 tfor:TF2549|5end_30S_ribosomal_protein_S7_2731711..2731941_POSITIVE 274 188 141 195 137 tfor:TF0275|5end_outer_membrane_protein_300884..301114_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 320 173 134 114 69 tfor:TF1935|3end_ATP-dependent_RNA_helicase,_DEAD/DEAH-related_helicase_2083881..2084031_POSITIVE 306 295 254 51 7 tfor:TF1638|3end_conserved_hypothetical_protein_1747732..1747882_POSITIVE 302 189 144 137 95 tfor:TF1544|3end_possible_transcriptional_regulator_1651214..1651364_POSITIVE 295 230 181 148 100 tfor:TF2386|3end_beta-galactosidase_2554449..2554599_POSITIVE 293 175 148 143 116 tfor:TF0901|3end_conserved_hypothetical_protein_947273..947423_POSITIVE 289 190 147 150 108 tfor:TF1467|3end_conserved_hypothetical_protein_1557837..1557987_POSITIVE 286 256 211 86 40 tfor:TF0812|3end_conserved_hypothetical_protein_872607..872757_POSITIVE 281 225 192 47 19 tfor:TF0930|3end_conserved_hypothetical_protein;_possible_prophage_protein_969965..970115_POSITIVE 278 267 225 142 101 tfor:TF2134|3end_conserved_hypothetical_protein_2310187..2310337_POSITIVE 276 273 239 75 41 tfor:TF2214|3end_peptidyl-prolyl_cis-trans_isomerase_2387564..2387714_POSITIVE 275 190 142 138 81 tfor:TF2548|3end_30S_ribosomal_protein_S12_2731704..2731854_POSITIVE 275 258 211 146 96 tfor:TF0922|3end_MATE_efflux_family_protein_961086..961236_POSITIVE 270 224 181 137 102 tfor:TF0429|3end_ABC_transporter,_ATP-binding_protein_452227..452377_POSITIVE 268 177 136 125 78 tfor:TF1767|3end_3-dehydroquinate_synthase_1906624..1906774_POSITIVE 264 68 30 57 10 tfor:TF1472|3end_acyl-ACP_thioesterase_1566337..1566487_POSITIVE 264 190 141 102 50 tfor:TF0283|3end_possible_nicotinamide_mononucleotide_transporter_312074..312224_POSITIVE 263 162 128 149 121 tfor:TF2721|3end_conserved_hypothetical_protein_2896956..2897106_POSITIVE 262 176 132 95 43 tfor:TF2010|3end_hypothetical_protein_2163811..2163961_POSITIVE 259 193 151 85 34 tfor:TF2315|3end_thioesterase_2474498..2474648_POSITIVE 259 170 129 76 27 tfor:TF1740|3end_hypothetical_protein_1869192..1869342_POSITIVE