Origin IGS: gcagcaaagatagggacttgtttgtgaacgggaagatcatccgctgtaaaaatcgtataaagataaaaacggcgctgtctctgaagtgggagcagcgccgttcgattgtatatca .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tgatatacaatcgaacggcgctgctcccacttcagagacagcgccgtttttatctttatacgatttttacagcggatgatcttcccgttcacaaacaagtccctatctttgctgc Mask Tandem Repeat Region ================================================ gcagcaaagatagggacttgtttgtgaacgggaagatcatccgctgtaaaaatcgtataaagataaaaacggcgctgtctctgaagtgggagcagcgccgttcgattgtatatca Find is-nt database================================================ Query_seq: TF2125:TF2126|TF2125:TF2126:conserved hypothetical protein:S-adenosylhomocysteine hydrolase:->->:2302526..2302640 115 gcagcaaagatagggacttgtttgtgaacgggaagatcatccgctgtaaaaatcgtataaagataaaaacggcgctgtctctgaagtgggagcagcgccgttcgattgtatatca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF2125:TF2126|TF2125:TF2126:conserved hypothetical protein:S-adenosylhomocysteine hydrolase:->->:2302526..2302640 115 gcagcaaagatagggacttgtttgtgaacgggaagatcatccgctgtaaaaatcgtataaagataaaaacggcgctgtctctgaagtgggagcagcgccgttcgattgtatatca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF2125:TF2126|TF2125:TF2126:conserved hypothetical protein:S-adenosylhomocysteine hydrolase:->->:2302526..2302640 115 gcagcaaagatagggacttgtttgtgaacgggaagatcatccgctgtaaaaatcgtataaagataaaaacggcgctgtctctgaagtgggagcagcgccgttcgattgtatatca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gcagcaaagatagggacttgtttgtgaacgggaagatcatccgctgtaaaaatcgtataaagataaaaacggcgctgtctctgaagtgggagcagcgccgttcgattgtatatca Predict ORF larger than 30AA ================================================ Protein_Len: 32 Strand: + Start: 18 End: 113 ................. M F V N G K I I R C K N R I K I K T A L S L K W E Q R R S I V Y .. Protein_Len: 37 Strand: - Start: 3 End: 113 .. A F I P V Q K H V P L D D A T F I T Y L Y F R R Q R Q L P L L A T R N Y M .. Protein_Len: 35 Strand: - Start: 2 End: 106 . L L S L S K N T F P F I M R Q L F R I F I F V A S D R F H S C R R E M ......... gcagcaaagatagggacttgtttgtgaacgggaagatcatccgctgtaaaaatcgtataaagataaaaacggcgctgtctctgaagtgggagcagcgccgttcgattgtatatca 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================================================ gcagcaaagatagggacttgtttgtgaacgggaagatcatccgctgtaaaaatcgtataaagataaaaacggcgctgtctctgaagtgggagcagcgccgttcgattgtatatca Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TF2125:TF2126|TF2125:TF2126:conserved hypothetical protein:S-adenosylhomocysteine hydrolase:->->:2302526..2302640 115 gcagcaaagatagggacttgtttgtgaacgggaagatcatccgctgtaaaaatcgtataaagataaaaacggcgctgtctctgaagtgggagcagcgccgttcgattgtatatca Intra-Species Hit: Count: 1 Min: 1 Max: 115 Len: 115 Subject: tfor_TF2125_TF2126|conserved hypothetical protein:S-adenosylhomocysteine hydrolase|POSITIVE:POSITIVE|[2302526,2302640]|115 HSP 1 e-value: 3.0E-59 bit: 228.0 Len: 115 Query Start:1 Query End:115 Subject Strand: POSITIVE Subject Start: 1 Subject End: 115 gcagcaaagatagggacttgtttgtgaacgggaagatcatccgctgtaaaaatcgtataaagataaaaacggcgctgtctctgaagtgggagcagcgccgttcgattgtatatca gcagcaaagatagggacttgtttgtgaacgggaagatcatccgctgtaaaaatcgtataaagataaaaacggcgctgtctctgaagtgggagcagcgccgttcgattgtatatca Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GCAGCAAAGAUAGGGACUUGUUUGUGAACGGGAAGAUCAUCCGCUGUAAAAAUCGUAUAAAGAUAAAAACGGCGCUGUCUCUGAAGUGGGAGCAGCGCCGUUCGAUUGUAUAUCA (((((...(((.((..((((((....))))))....))))).)))))...(((((............((((((((((.((((......)))))))))))))))))))........ (-35.30) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGAUAUACAAUCGAACGGCGCUGCUCCCACUUCAGAGACAGCGCCGUUUUUAUCUUUAUACGAUUUUUACAGCGGAUGAUCUUCCCGUUCACAAACAAGUCCCUAUCUUUGCUGC .((((.......((((((((((((((........))).))))))))))).))))...............(((((((.(((......(((....)))........)))))))))). (-29.64) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 443 110 70 220 174 tfor:TF2775|5end_conserved_hypothetical_protein;_possible_mucoidy_inhibitor-related_protein_2959668..2959898_POSITIVE 402 108 69 61 24 tfor:TF1797|5end_SNF_family_transporter_1937136..1937366_POSITIVE 396 99 53 47 4 tfor:TF0970|5end_2-keto-3-deoxygluconate_kinase_1020396..1020626_POSITIVE 389 108 69 47 1 tfor:TF1464|5end_conserved_hypothetical_protein_1553467..1553697_POSITIVE 386 106 71 227 190 tfor:TF2849|5end_histidinol-phosphate_transaminase_3037288..3037518_POSITIVE 377 109 61 83 13 tfor:TF0001|5end_hypothetical_protein_-116..114_POSITIVE 373 104 70 50 15 tfor:TF0888|5end_transfer_region-related_protein,_TraN_938392..938622_POSITIVE 369 100 62 228 182 tfor:TF0587|5end_outer_membrane_protein_618319..618549_POSITIVE 365 108 70 206 164 tfor:TF2255|5end_transfer_region-related_protein,_TraH_2427504..2427734_POSITIVE 365 105 62 191 137 tfor:TF1909|5end_cobalamin_(5`-phosphate)_synthase_2063207..2063437_POSITIVE 363 102 67 143 93 tfor:TF0607|5end_DnaK_suppressor_protein_637441..637671_POSITIVE 362 108 70 180 131 tfor:TF1329|5end_glucose-1-phosphate_thymidyltransferase_1408578..1408808_POSITIVE 361 100 52 213 168 tfor:TF2693|5end_possible_aminotransferase_2868435..2868665_POSITIVE 356 105 70 61 18 tfor:TF2267|5end_lysozyme-related_protein_2434869..2435099_POSITIVE 352 104 69 69 11 tfor:TF2038|5end_hypothetical_protein_2198978..2199208_POSITIVE 348 105 70 227 185 tfor:TF0016|5end_hypothetical_protein_10292..10522_POSITIVE 345 107 69 83 29 tfor:TF1401|5end_Holliday_junction_DNA_helicase_1476502..1476732_POSITIVE 341 105 69 215 171 tfor:TF2224|5end_CTn_excision_protein_2394592..2394822_POSITIVE 341 106 69 92 55 tfor:TF1509|5end_possible_acylaminoacyl-peptidase_1617538..1617768_POSITIVE 338 105 68 61 18 tfor:TF0464|5end_precorrin_methylase_480211..480441_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 402 108 69 61 24 tfor:TF1796|3end_ABC_transporter,_ATP-binding_protein_1937216..1937366_POSITIVE 365 98 63 39 1 tfor:TF0309|3end_conserved_hypothetical_protein_334775..334925_POSITIVE 363 102 67 126 76 tfor:TF0606|3end_signal_peptidase_II_637504..637654_POSITIVE 356 105 70 61 18 tfor:TF2266|3end_transfer_region-related_protein,_TraQ_2434949..2435099_POSITIVE 345 107 69 74 20 tfor:TF1400|3end_polysaccharide_biosynthesis_protein;_membrane_protein_1476573..1476723_POSITIVE 338 105 68 61 18 tfor:TF0463|3end_precorrin-6Y_C5,15-methyltransferase_480291..480441_POSITIVE 334 109 61 101 43 tfor:TF0679|3end_hypothetical_protein_721489..721639_POSITIVE 332 109 70 136 97 tfor:TF1947|3end_conserved_hypothetical_protein_2096023..2096173_POSITIVE 332 100 70 145 99 tfor:TF1848|3end_conserved_hypothetical_protein_1997944..1998094_POSITIVE 329 106 70 151 111 tfor:TF2253|3end_conjugative_transposon_protein,_TraG_2427531..2427681_POSITIVE 327 102 70 57 23 tfor:TF2874|3end_conserved_hypothetical_protein_3065224..3065374_POSITIVE 324 109 69 117 68 tfor:TF2774|3end_2-amino-4-hydroxy-6-hydroxymethyldihydropteridine_pyrophosphokinase_2959719..2959869_POSITIVE 323 105 65 99 39 tfor:TF3038|3end_conserved_hypothetical_protein_3265799..3265949_POSITIVE 323 110 65 75 25 tfor:TF0841|3end_NADH_dehydrogenase/NAD(P)H_nitroreductase_893048..893198_POSITIVE 322 109 71 42 1 tfor:TF2244|3end_possible_mobilization_protein_2420752..2420902_POSITIVE 321 105 69 56 16 tfor:TF1491|3end_mannosyltransferase_1592087..1592237_POSITIVE 320 100 54 53 7 tfor:TF1468|3end_beta-galactosidase_1561251..1561401_POSITIVE 315 100 51 148 95 tfor:TF1234|3end_rhamnulose-1-phosphate_aldolase_1319761..1319911_POSITIVE 312 94 51 145 99 tfor:TF2979|3end_possible_outer_membrane__protein_3193164..3193314_POSITIVE 312 108 70 55 5 tfor:TF2230|3end_CTn_excision_protein_2400394..2400544_POSITIVE