Origin IGS: attgtttattttcgtttttttattgttttctctatagtctcttgtccggacaaaaaaaatgccagacccttcatgtccgacattttgtctgtctgcttatacgcaacgccgatcgtgcttca .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tgaagcacgatcggcgttgcgtataagcagacagacaaaatgtcggacatgaagggtctggcattttttttgtccggacaagagactatagagaaaacaataaaaaaacgaaaataaacaat Mask Tandem Repeat Region ================================================ attgtttattttcgtttttttattgttttctctatagtctcttgtccggacaaaaaaaatgccagacccttcatgtccgacattttgtctgtctgcttatacgcaacgccgatcgtgcttca Find is-nt database================================================ Query_seq: TF2747:TF2748|TF2747:TF2748:heat shock protein, HSP90 family:ATP-dependent Clp protease:->->:2930477..2930598 122 attgtttattttcgtttttttattgttttctctatagtctcttgtccggacaaaaaaaatgccagacccttcatgtccgacattttgtctgtctgcttatacgcaacgccgatcgtgcttca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF2747:TF2748|TF2747:TF2748:heat shock protein, HSP90 family:ATP-dependent Clp protease:->->:2930477..2930598 122 attgtttattttcgtttttttattgttttctctatagtctcttgtccggacaaaaaaaatgccagacccttcatgtccgacattttgtctgtctgcttatacgcaacgccgatcgtgcttca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF2747:TF2748|TF2747:TF2748:heat shock protein, HSP90 family:ATP-dependent Clp protease:->->:2930477..2930598 122 attgtttattttcgtttttttattgttttctctatagtctcttgtccggacaaaaaaaatgccagacccttcatgtccgacattttgtctgtctgcttatacgcaacgccgatcgtgcttca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 attgtttattttcgtttttttattgttttctctatagtctcttgtccggacaaaaaaaatgccagacccttcatgtccgacattttgtctgtctgcttatacgcaacgccgatcgtgcttca Predict ORF larger than 30AA ================================================ Protein_Len: 40 Strand: + Start: 1 End: 120 M V Y F R F F I V F S I V S C P D K K N A R P F M S D I L S V C L Y A T P I V L .. Protein_Len: 35 Strand: - Start: 9 End: 113 ........ K R K K I T K E I T E Q G S L F F A L G K M D S M K D T Q K Y A V G M ......... attgtttattttcgtttttttattgttttctctatagtctcttgtccggacaaaaaaaatgccagacccttcatgtccgacattttgtctgtctgcttatacgcaacgccgatcgtgcttca 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================================================ attgtttattttcgtttttttattgttttctctatagtctcttgtccggacaaaaaaaatgccagacccttcatgtccgacattttgtctgtctgcttatacgcaacgccgatcgtgcttca Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 88 HP_score: -3.4 Tail_Score: -5.93809 Start: 60 End: 82 Full_Region: agcagacagacaaaa tgtcggac atgaagg gtctggca ttttttttgtccgga ...........................................................tgtcggacatgaagggtctggca........................................ Find igs database================================================ Query_seq: TF2747:TF2748|TF2747:TF2748:heat shock protein, HSP90 family:ATP-dependent Clp protease:->->:2930477..2930598 122 attgtttattttcgtttttttattgttttctctatagtctcttgtccggacaaaaaaaatgccagacccttcatgtccgacattttgtctgtctgcttatacgcaacgccgatcgtgcttca Intra-Species Hit: Count: 1 Min: 22 Max: 122 Len: 101 Subject: tfor_TF2747_TF2748|heat shock protein, HSP90 family:ATP-dependent Clp protease|POSITIVE:POSITIVE|[2930477,2930598]|122 HSP 1 e-value: 2.0E-36 bit: 153.0 Len: 101 Query Start:22 Query End:122 Subject Strand: POSITIVE Subject Start: 22 Subject End: 122 .....................attgttttctctatagtctcttgtccggacnnnnnnnntgccagacccttcatgtccgacattttgtctgtctgcttatacgcaacgccgatcgtgcttca .....................attgttttctctatagtctcttgtccggacaaaaaaaatgccagacccttcatgtccgacattttgtctgtctgcttatacgcaacgccgatcgtgcttca Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUUGUUUUCUCUAUAGUCUCUUGUCCGGACAAAAAAAAUGCCAGACCCUUCAUGUCCGACAUUUUGUCUGUCUGCUUAUACGCAACGCCGAUCGUGCUUCA .........................((((((...((((((.(.(((.......))).).))))))...)))))).......(((.((.....))))).... (-15.90) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGAAGCACGAUCGGCGUUGCGUAUAAGCAGACAGACAAAAUGUCGGACAUGAAGGGUCUGGCAUUUUUUUUGUCCGGACAAGAGACUAUAGAGAAAACAAU ....(((((.....)).))).......(.((((((.((((((((((((.......)))))))))))).)))))).)......................... (-25.40) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 424 100 51 196 143 tfor:TF2259|5end_transfer_region-related_protein,_TraK_2429577..2429807_POSITIVE 373 100 54 230 182 tfor:TF1782|5end_conserved_hypothetical_protein_1922003..1922233_POSITIVE 347 90 43 225 174 tfor:TF0452|5end_conserved_hypothetical_protein,_endonuclease/exonuclease/phosphatase_family_470972..471202_POSITIVE 344 97 53 198 144 tfor:TF0145|5end_glutamine_synthetase_152446..152676_POSITIVE 342 97 56 209 161 tfor:TF2904|5end_ATP-dependent__helicase,_possible_UvrD/REP_helicase_domain_protein_3098903..3099133_POSITIVE 336 100 53 81 35 tfor:TF1537|5end_hypothetical_protein_1642906..1643136_POSITIVE 330 97 56 87 36 tfor:TF2108|5end_hypothetical_protein_2277385..2277615_POSITIVE 329 97 54 207 174 tfor:TF2931|5end_3-deoxy-D-manno-2-octulosonic_acid_(Kdo_transferase)_3134275..3134505_POSITIVE 327 88 42 230 180 tfor:TF1157|5end_glutamate_synthase,_small_subunit_1238012..1238242_POSITIVE 326 97 53 45 4 tfor:TF1189|5end_outer_membrane_protein,_TonB_dependent_receptor_1270586..1270816_POSITIVE 319 90 41 137 79 tfor:TF3127|5end_acetyltransferase,_possible_GNAT_family_3361627..3361857_POSITIVE 319 99 51 107 61 tfor:TF2853|5end_2-C-methyl-D-erythritol_2,4-cyclodiphosphate_synthase_3040172..3040402_POSITIVE 318 98 55 54 9 tfor:TF2249|5end_transfer_region-related_protein,_TraC_2422988..2423218_POSITIVE 315 97 51 225 165 tfor:TF2307|5end_two-component_system_sensor_histidine_kinase/response_2462618..2462848_POSITIVE 315 98 52 188 145 tfor:TF2161|5end_conserved_hypothetical_protein_2336972..2337202_POSITIVE 313 90 43 199 146 tfor:TF2790|5end_prismane_protein,_hybrid-cluster_protein_2973397..2973627_POSITIVE 313 90 41 222 170 tfor:TF0331|5end_hypothetical_protein_359074..359304_POSITIVE 313 90 41 168 116 tfor:TF0333|5end_hypothetical_protein_359020..359250_POSITIVE 312 75 39 66 23 tfor:TF1710|5end_possible_cell_filamentation_protein_1829679..1829909_POSITIVE 312 97 52 186 133 tfor:TF0344|5end_hypothetical_protein_366722..366952_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 389 100 51 149 108 tfor:TF2257|3end_transfer_region-related_protein,_TraJ_2429622..2429772_POSITIVE 330 97 56 58 7 tfor:TF2107|3end_hypothetical_protein_2277436..2277586_POSITIVE 319 90 41 115 57 tfor:TF3126|3end_glycosyltransferase,_group_2_family_3361685..3361835_POSITIVE 319 99 51 76 30 tfor:TF2852|3end_conserved_hypothetical_protein_3040221..3040371_POSITIVE 318 98 55 54 9 tfor:TF2248|3end_transfer_region-related_protein,_TraB_2423068..2423218_POSITIVE 314 90 41 106 44 tfor:TF1983|3end_conserved_hypothetical_protein_2135000..2135150_POSITIVE 313 100 51 108 45 tfor:TF2850|3end_endoribonuclease_L-PSP_3038871..3039021_POSITIVE 313 90 43 87 34 tfor:TF2789|3end_enoyl-[acyl-carrier-protein]_reductase_2973365..2973515_POSITIVE 312 99 57 89 50 tfor:TF0145|3end_glutamine_synthetase_154718..154868_POSITIVE 311 90 45 142 90 tfor:TF1186|3end_hypothetical_protein_1269815..1269965_POSITIVE 306 90 45 105 57 tfor:TF0307|3end_conserved_hypothetical_protein_333750..333900_POSITIVE 300 90 42 145 97 tfor:TF1405|3end_conserved_hypothetical_protein_1481819..1481969_POSITIVE 298 99 51 150 89 tfor:TF1729|3end_aspartokinase_1854718..1854868_POSITIVE 298 100 56 73 29 tfor:TF0252|3end_hypothetical_protein_283759..283909_POSITIVE 294 90 41 50 2 tfor:TF0804|3end_possible_phosphatidylglycerophosphate_synthase_862899..863049_POSITIVE 291 100 66 31 3 tfor:TF0037|3end_sialic_acid-specific_9-O-acetylesterase_39991..40141_POSITIVE 290 97 55 94 43 tfor:TF0203|3end_PhoH-like_protein_230660..230810_POSITIVE 289 97 51 119 73 tfor:TF2774|3end_2-amino-4-hydroxy-6-hydroxymethyldihydropteridine_pyrophosphokinase_2959719..2959869_POSITIVE 287 95 60 54 4 tfor:TF0084|3end_possible_membrane-fusion_protein_91597..91747_POSITIVE 284 89 41 53 7 tfor:TF2266|3end_transfer_region-related_protein,_TraQ_2434949..2435099_POSITIVE