Origin IGS: gctcttcttttttgtcgcccgcaaaaatacggaattgttaaatcatccccaaatttgcatttcacgctccataagcctatctttatgccctcaaccgaatgttcc .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 ggaacattcggttgagggcataaagataggcttatggagcgtgaaatgcaaatttggggatgatttaacaattccgtatttttgcgggcgacaaaaaagaagagc Mask Tandem Repeat Region ================================================ gctcttcttttttgtcgcccgcaaaaatacggaattgttaaatcatccccaaatttgcatttcacgctccataagcctatctttatgccctcaaccgaatgttcc Find is-nt database================================================ Query_seq: TF2835:TF2834|TF2835:TF2834:stationary-phase survival protein SurE:cardiolipin synthase:->->:3026021..3026125 105 gctcttcttttttgtcgcccgcaaaaatacggaattgttaaatcatccccaaatttgcatttcacgctccataagcctatctttatgccctcaaccgaatgttcc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF2835:TF2834|TF2835:TF2834:stationary-phase survival protein SurE:cardiolipin synthase:->->:3026021..3026125 105 gctcttcttttttgtcgcccgcaaaaatacggaattgttaaatcatccccaaatttgcatttcacgctccataagcctatctttatgccctcaaccgaatgttcc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF2835:TF2834|TF2835:TF2834:stationary-phase survival protein SurE:cardiolipin synthase:->->:3026021..3026125 105 gctcttcttttttgtcgcccgcaaaaatacggaattgttaaatcatccccaaatttgcatttcacgctccataagcctatctttatgccctcaaccgaatgttcc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gctcttcttttttgtcgcccgcaaaaatacggaattgttaaatcatccccaaatttgcatttcacgctccataagcctatctttatgccctcaaccgaatgttcc Predict ORF larger than 30AA ================================================ gctcttcttttttgtcgcccgcaaaaatacggaattgttaaatcatccccaaatttgcatttcacgctccataagcctatctttatgccctcaaccgaatgttcc 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================================================ gctcttcttttttgtcgcccgcaaaaatacggaattgttaaatcatccccaaatttgcatttcacgctccataagcctatctttatgccctcaaccgaatgttcc Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TF2835:TF2834|TF2835:TF2834:stationary-phase survival protein SurE:cardiolipin synthase:->->:3026021..3026125 105 gctcttcttttttgtcgcccgcaaaaatacggaattgttaaatcatccccaaatttgcatttcacgctccataagcctatctttatgccctcaaccgaatgttcc Intra-Species Hit: Count: 1 Min: 1 Max: 105 Len: 105 Subject: tfor_TF2835_TF2834|stationary-phase survival protein SurE:cardiolipin synthase|POSITIVE:POSITIVE|[3026021,3026125]|105 HSP 1 e-value: 3.0E-53 bit: 208.0 Len: 105 Query Start:1 Query End:105 Subject Strand: POSITIVE Subject Start: 1 Subject End: 105 gctcttcttttttgtcgcccgcaaaaatacggaattgttaaatcatccccaaatttgcatttcacgctccataagcctatctttatgccctcaaccgaatgttcc gctcttcttttttgtcgcccgcaaaaatacggaattgttaaatcatccccaaatttgcatttcacgctccataagcctatctttatgccctcaaccgaatgttcc Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GCUCUUCUUUUUUGUCGCCCGCAAAAAUACGGAAUUGUUAAAUCAUCCCCAAAUUUGCAUUUCACGCUCCAUAAGCCUAUCUUUAUGCCCUCAACCGAAUGUUCC ........(((((((.....)))))))..(((....((.((((((..........)).)))).))....((((((......)))))).......)))........ ( -9.20) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GGAACAUUCGGUUGAGGGCAUAAAGAUAGGCUUAUGGAGCGUGAAAUGCAAAUUUGGGGAUGAUUUAACAAUUCCGUAUUUUUGCGGGCGACAAAAAAGAAGAGC ......(((..((..(.((.......((.((((...)))).))...((((((..((.(((............))).))..)))))).))..)..))..))).... (-17.70) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 310 49 7 107 63 tfor:TF1742|5end_TPR_repeat-containing_protein_1873129..1873359_POSITIVE 297 90 47 196 148 tfor:TF2523|5end_NAD(P)H-flavin_oxidoreductase_2702114..2702344_POSITIVE 287 97 61 34 1 tfor:TF2265|5end_transfer_region-related_protein,_TraP;_DNA_primase_involved_in_conjugation_2433474..2433704_POSITIVE 285 90 54 174 138 tfor:TF0739|5end_hypothetical_protein_789448..789678_POSITIVE 285 90 54 174 138 tfor:TF0734|5end_hypothetical_protein_786244..786474_POSITIVE 284 70 30 64 17 tfor:TF2423|5end_papain_family_cysteine_protease_2601608..2601838_POSITIVE 281 90 46 106 59 tfor:TF0679|5end_hypothetical_protein_721155..721385_POSITIVE 281 90 46 54 7 tfor:TF0678|5end_hypothetical_protein_721103..721333_POSITIVE 280 88 45 183 143 tfor:TF2941|5end_50S_ribosomal_protein_L1_3141828..3142058_POSITIVE 279 90 44 152 113 tfor:TF2375|5end_conserved_hypothetical_protein_2540953..2541183_POSITIVE 275 60 15 89 44 tfor:TF1292|5end_sensor_histidine_protein_kinase_1372567..1372797_POSITIVE 267 60 14 76 25 tfor:TF3111|5end_hypothetical_protein_3346601..3346831_POSITIVE 267 50 1 190 135 tfor:TF2810|5end_conserved_hypothetical_protein_3000583..3000813_POSITIVE 267 32 3 44 15 tfor:TF2229|5end_CTn_excision_protein;_DNA_topoisomerase_IA_2397536..2397766_POSITIVE 258 89 44 54 13 tfor:TF1221|5end_conserved_hypothetical_protein_1307723..1307953_POSITIVE 253 48 1 208 153 tfor:TF1948|5end_conserved_hypothetical_protein_2095942..2096172_POSITIVE 252 98 61 206 170 tfor:TF2249|5end_transfer_region-related_protein,_TraC_2422988..2423218_POSITIVE 252 90 46 113 67 tfor:TF0538|5end_hypothetical_protein_566891..567121_POSITIVE 252 90 46 106 60 tfor:TF0539|5end_hypothetical_protein_566884..567114_POSITIVE 251 98 66 134 104 tfor:TF0662|5end_hypothetical_protein_708316..708546_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 297 90 47 131 83 tfor:TF2522|3end_deoxyuridine_5'-triphosphate_nucleotidohydrolase_(dUTPase)_2702129..2702279_POSITIVE 287 39 8 150 118 tfor:TF0709|3end_preprotein_translocase,_subunit_SecA_757241..757391_POSITIVE 284 70 30 53 6 tfor:TF2422|3end_hypothetical_protein_2601677..2601827_POSITIVE 283 58 14 85 42 tfor:TF2366|3end_conserved_hypothetical_protein_2531892..2532042_POSITIVE 275 60 15 89 44 tfor:TF1291|3end_response_regulator_(fimR__protein)_1372647..1372797_POSITIVE 265 69 29 41 2 tfor:TF0370|3end_hypothetical_protein_386317..386467_POSITIVE 262 34 1 55 23 tfor:TF3053|3end_conserved_hypothetical_protein_3278889..3279039_POSITIVE 258 89 44 48 7 tfor:TF1220|3end_conserved_hypothetical_protein_1307797..1307947_POSITIVE 252 90 42 84 29 tfor:TF0877|3end_ISPg2-related_(PGIS2-related)_transposase_931817..931967_POSITIVE 249 98 58 100 59 tfor:TF3159|3end_conserved_hypothetical_protein;_possible_transcriptional_regulator_3395611..3395761_POSITIVE 248 70 27 150 106 tfor:TF2996|3end_hypothetical_protein_3211121..3211271_POSITIVE 246 97 55 128 88 tfor:TF2442|3end_heat_shock_protein_60_2620271..2620421_POSITIVE 243 49 11 102 70 tfor:TF2891|3end_lipoprotein_3079381..3079531_POSITIVE 243 88 49 79 40 tfor:TF1638|3end_conserved_hypothetical_protein_1747732..1747882_POSITIVE 241 32 2 50 13 tfor:TF1927|3end_RNA_polymerase_sigma-70_factor,_ECF_subfamily_2075602..2075752_POSITIVE 240 90 43 48 2 tfor:TF3043|3end_conserved_hypothetical_protein_3272409..3272559_POSITIVE 238 90 46 145 98 tfor:TF0752|3end_nucleotide-binding_protein;_MAF-like_protein_801713..801863_POSITIVE 234 50 1 104 40 tfor:TF2518|3end_ATP-dependent_DNA_helicase_2697711..2697861_POSITIVE 232 90 48 115 81 tfor:TF2654|3end_arginyl-tRNA_synthetase_2824559..2824709_POSITIVE 231 50 1 48 3 tfor:TF1588|3end_hypothetical_protein_1702560..1702710_POSITIVE