Origin IGS: tgataagatttaaaggttgggagcactgaatgaatgtattagctaaaagataaatttctctccccccttattttattcgtgttcttccgaacacaagaagagaataagggagggggattttctta .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 taagaaaatccccctcccttattctcttcttgtgttcggaagaacacgaataaaataaggggggagagaaatttatcttttagctaatacattcattcagtgctcccaacctttaaatcttatca Mask Tandem Repeat Region ================================================ tgataagatttaaaggttgggagcactgaatgaatgtattagctaaaagataaatttctctccccccttattttattcgtgttcttccgaacacaagaagagaataagggagggggattttctta Find is-nt database================================================ Query_seq: TF1136:TF1137|TF1136:TF1137:glycosyltransferase:asparaginyl-tRNA synthetase (asparagine--tRNA ligase):->->:1212458..1212582 125 tgataagatttaaaggttgggagcactgaatgaatgtattagctaaaagataaatttctctccccccttattttattcgtgttcttccgaacacaagaagagaataagggagggggattttctta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF1136:TF1137|TF1136:TF1137:glycosyltransferase:asparaginyl-tRNA synthetase (asparagine--tRNA ligase):->->:1212458..1212582 125 tgataagatttaaaggttgggagcactgaatgaatgtattagctaaaagataaatttctctccccccttattttattcgtgttcttccgaacacaagaagagaataagggagggggattttctta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF1136:TF1137|TF1136:TF1137:glycosyltransferase:asparaginyl-tRNA synthetase (asparagine--tRNA ligase):->->:1212458..1212582 125 tgataagatttaaaggttgggagcactgaatgaatgtattagctaaaagataaatttctctccccccttattttattcgtgttcttccgaacacaagaagagaataagggagggggattttctta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tgataagatttaaaggttgggagcactgaatgaatgtattagctaaaagataaatttctctccccccttattttattcgtgttcttccgaacacaagaagagaataagggagggggattttctta Predict ORF larger than 30AA ================================================ tgataagatttaaaggttgggagcactgaatgaatgtattagctaaaagataaatttctctccccccttattttattcgtgttcttccgaacacaagaagagaataagggagggggattttctta 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================================================ tgataagatttaaaggttgggagcactgaatgaatgtattagctaaaagataaatttctctccccccttattttattcgtgttcttccgaacacaagaagagaataagggagggggattttctta Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TF1136:TF1137|TF1136:TF1137:glycosyltransferase:asparaginyl-tRNA synthetase (asparagine--tRNA ligase):->->:1212458..1212582 125 tgataagatttaaaggttgggagcactgaatgaatgtattagctaaaagataaatttctctccccccttattttattcgtgttcttccgaacacaagaagagaataagggagggggattttctta Intra-Species Hit: Count: 1 Min: 1 Max: 125 Len: 125 Subject: tfor_TF1136_TF1137|glycosyltransferase:asparaginyl-tRNA synthetase (asparagine--tRNA ligase)|POSITIVE:POSITIVE|[1212458,1212582]|125 HSP 1 e-value: 4.0E-65 bit: 248.0 Len: 125 Query Start:1 Query End:125 Subject Strand: POSITIVE Subject Start: 1 Subject End: 125 tgataagatttaaaggttgggagcactgaatgaatgtattagctaaaagataaatttctctccccccttattttattcgtgttcttccgaacacaagaagagaataagggagggggattttctta tgataagatttaaaggttgggagcactgaatgaatgtattagctaaaagataaatttctctccccccttattttattcgtgttcttccgaacacaagaagagaataagggagggggattttctta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGAUAAGAUUUAAAGGUUGGGAGCACUGAAUGAAUGUAUUAGCUAAAAGAUAAAUUUCUCUCCCCCCUUAUUUUAUUCGUGUUCUUCCGAACACAAGAAGAGAAUAAGGGAGGGGGAUUUUCUUA ...(((((......((((((..(((.........))).))))))..............((((((((((((((((.(((((((((....))))))..))).)))))))))).))))))...))))) (-36.70) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAGAAAAUCCCCCUCCCUUAUUCUCUUCUUGUGUUCGGAAGAACACGAAUAAAAUAAGGGGGGAGAGAAAUUUAUCUUUUAGCUAAUACAUUCAUUCAGUGCUCCCAACCUUUAAAUCUUAUCA (((((...(((.(((((((((((......((((((((....))))))))....))))))))))).).))............(((.................))).............)))))... (-32.23) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 326 89 41 115 60 tfor:TF0328|5end_conserved_hypothetical_protein_354182..354412_POSITIVE 296 92 54 155 115 tfor:TF0120|5end_hexouronate_transporter_131307..131537_POSITIVE 283 119 72 113 76 tfor:TF1141|5end_conserved_hypothetical_protein_1217972..1218202_POSITIVE 279 102 61 91 49 tfor:TF1762|5end_hypothetical_protein_1899320..1899550_POSITIVE 279 102 61 76 34 tfor:TF1761|5end_hypothetical_protein_1899305..1899535_POSITIVE 272 117 76 184 149 tfor:TF2794|5end_possible_transcriptional_regulator_2979938..2980168_POSITIVE 260 117 76 127 75 tfor:TF3027|5end_zinc_metalloprotease_3250223..3250453_POSITIVE 258 116 79 140 105 tfor:TF2747|5end_heat_shock_protein,_HSP90_family_2928279..2928509_POSITIVE 258 89 60 202 164 tfor:TF2253|5end_conjugative_transposon_protein,_TraG_2424950..2425180_POSITIVE 256 86 48 124 86 tfor:TF0200|5end_2-nitropropane_dioxygenase_225061..225291_POSITIVE 255 117 74 142 92 tfor:TF1592|5end_hypothetical_protein_1708325..1708555_POSITIVE 255 117 74 142 92 tfor:TF1590|5end_hypothetical_protein_1705811..1706041_POSITIVE 254 119 80 68 19 tfor:TF2994|5end_hypothetical_protein_3210605..3210835_POSITIVE 252 116 89 86 55 tfor:TF1650|5end_integrase_1760039..1760269_POSITIVE 251 116 77 129 99 tfor:TF3114|5end_hypothetical_protein_3349134..3349364_POSITIVE 251 116 77 109 79 tfor:TF3113|5end_hypothetical_protein_3349114..3349344_POSITIVE 251 90 54 51 12 tfor:TF1455|5end_conserved_hypothetical_protein_1540688..1540918_POSITIVE 249 116 78 213 153 tfor:TF1638|5end_conserved_hypothetical_protein_1747359..1747589_POSITIVE 244 95 60 66 28 tfor:TF2336|5end_conserved_hypothetical_protein_2496169..2496399_POSITIVE 244 115 76 180 149 tfor:TF0605|5end_conserved_hypothetical_protein_636051..636281_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 312 97 56 51 11 tfor:TF2687|3end_iron-regulated_ABC-type_transporter_membrane_component_2864962..2865112_POSITIVE 296 92 54 102 62 tfor:TF0119|3end_gluconate_aldolase_131334..131484_POSITIVE 279 102 61 104 62 tfor:TF1760|3end_guanosine-3',5'-bis(diphosphate)_3'-pyrophosphohydrolase_1899413..1899563_POSITIVE 275 117 75 115 74 tfor:TF1204|3end_possible_metal-dependent_membrane_protease_1287461..1287611_POSITIVE 272 117 76 54 19 tfor:TF2793|3end_possible_L-lysine_2,3-aminomutase_2979888..2980038_POSITIVE 262 89 51 60 20 tfor:TF2744|3end_methionyl-tRNA_formyltransferase_2927378..2927528_POSITIVE 260 117 76 78 26 tfor:TF3026|3end_conserved_hypothetical_protein_3250254..3250404_POSITIVE 252 116 89 86 55 tfor:TF1649|3end_hypothetical_protein_1760119..1760269_POSITIVE 251 119 77 99 34 tfor:TF1713|3end_hypothetical_protein_1833716..1833866_POSITIVE 251 117 89 32 7 tfor:TF1136|3end_glycosyltransferase_1212397..1212547_POSITIVE 250 37 15 79 58 tfor:TF2922|3end_surface_antigen_BspA_3121538..3121688_POSITIVE 250 118 77 129 89 tfor:TF2895|3end_hypothetical_protein_3084192..3084342_POSITIVE 242 119 78 87 44 tfor:TF2368|3end_uridine_phosphorylase_2534618..2534768_POSITIVE 242 117 77 96 51 tfor:TF0712|3end_TPR-repeat-containing_protein_763512..763662_POSITIVE 241 118 72 92 45 tfor:TF1819|3end_cation_efflux_system_AcrB/AcrD/AcrF_family;_ABC_transporter,_ATP-binding/permease_component_1963443..1963593_POSITIVE 241 119 88 56 15 tfor:TF1026|3end_beta-N-acetylglucosaminidase;_beta_lactamase_1085639..1085789_POSITIVE 241 119 80 141 94 tfor:TF0016|3end_hypothetical_protein_10581..10731_POSITIVE 240 116 87 27 1 tfor:TF2746|3end_hypothetical_protein_2928246..2928396_POSITIVE 240 118 77 87 37 tfor:TF0431|3end_hypothetical_protein_452470..452620_POSITIVE 240 118 77 120 70 tfor:TF0430|3end_hypothetical_protein_452503..452653_POSITIVE