Karen Mungall wrote... Here are the reads that potentially form the RF121/trim37 breakpoint in NBL06 (HS1794) >SOLEXA5_1:6:29:1278:1122 CAAGTGATCCTCCCACCTCAGCCTCCCAAGAATCAAAGAATATTTTTTAAAAAAACAACAAAAAGAGAGATATAG >SOLEXA7_1:6:17:889:1280 CTCTTTTTGTTGTTTTTTTAAAAAATATTCTTTGATTCTTGGGAGGCTGAGGTGGGAGGATCACTTGAGCTTGGG Shaun Jackman wrote... >NBL06-RNF121-TRIM37 CCCAAGCTCAAGTGATCCTCCCACCTCAGCCTCCCAAGAATCAAAGAATATTTTTTAAAAAAACAACAAAAAGAGAGATATAG $ exonerate --bestn 1 --showalignment 0 RNF121-TRIM37.fa k40/HS1794-contigs.fa vulgar: NBL06-RNF121-TRIM37 0 83 + 2124 1 84 + 415 M 83 83 $ grep -wA1 2124 k40/HS1794-contigs.fa >2124 101 453 TCCCAAGCTCAAGTGATCCTCCCACCTCAGCCTCCCAAGAATCAAAGAATATTTTTTAAAAAAACAACAAAAAGAGAGATATAGAGAGGAAAGAGCGGCTA $ grep -w ^2124 k40/HS1794-4.adj 2124 101 453 ; 3525- ; 7479- $ MergeContigs --only-merged -k40 k40/HS1794-4.fa - -o RNF121-TRIM37.fa <k40:7479-,2124+,3525-7479- 133 910 2124+,3525- TCCCAAGCTCAAGTGATCCTCCCACCTCAGCCTCCCAAGAATCAAAGAATATTTTTTAAAAAAACAACAAAAAGAGAGATATAGAGAGGAAAGAGCGGCTAGTTTCCTGGCATTCTATAGCAAACTAAGAAAG $ gmap -dHG18 -K0 -x25 -n0 RNF121-TRIM37.fa >k40:7479-,2124+,3525- 270 3493 7479-,2124+,3525- Paths (2): *** Possible chimera with breakpoint at 176..177 Path 1: query 1..176 (176 bp) => genome 17:54,427,144..54,427,319 (176 bp) cDNA direction: indeterminate Genomic pos: HG18:2,544,384,651..2,544,384,826 (+ strand) Accessions: 17:54,427,144..54,427,319 (out of 78774742 bp) Number of exons: 1 Coverage: 65.2 (query length: 270 bp) Trimmed coverage: 65.2 (trimmed length: 270 bp, trimmed region: 1..270) Percent identity: 100.0 (176 matches, 0 mismatches, 0 indels, 0 unknowns) Translation: 2..175 (58 aa) Amino acid changes: Path 2: query 177..270 (94 bp) => genome 11:71,370,149..71,370,053 (-97 bp) cDNA direction: indeterminate Genomic pos: HG18:1,884,848,004..1,884,847,908 (- strand) Accessions: 11:71,370,053..71,370,149 (out of 134452384 bp) Number of exons: 1 Coverage: 34.8 (query length: 270 bp) Trimmed coverage: 34.8 (trimmed length: 270 bp, trimmed region: 1..270) Percent identity: 95.9 (93 matches, 1 mismatches, 3 indels, 0 unknowns) Non-intron gaps: 0 openings, 0 bases in cdna; 1 openings, 3 bases in genome Translation: 179..265 (29 aa) Amino acid changes: delKKNNNKKRDIERKERLVSWHSIAN*6* [193] Alignments: Alignment for path 1: +17:54427144-54427319 (1-176) 100% 0 . : . : . : . : . : aa.g 1 A S Q S T G I T G M S H C A R P Y +17:54427144 AGCCTCCCAAAGTACTGGGATTACAGGCATGAGCCACTGTGCCCGGCCAT |||||||||||||||||||||||||||||||||||||||||||||||||| 1 AGCCTCCCAAAGTACTGGGATTACAGGCATGAGCCACTGTGCCCGGCCAT aa.c 1 A S Q S T G I T G M S H C A R P Y 50 . : . : . : . : . : aa.g 18 I F F F L R Q C L T L S R R L K +17:54427194 ACATTTTCTTTTTTTTGAGACAGTGTCTCACTCTGTCACGCAGGCTGAAG |||||||||||||||||||||||||||||||||||||||||||||||||| 51 ACATTTTCTTTTTTTTGAGACAGTGTCTCACTCTGTCACGCAGGCTGAAG aa.c 18 I F F F L R Q C L T L S R R L K 100 . : . : . : . : . : aa.g 34 C S S T I L A H C N L Y L P S S S +17:54427244 TGCAGTAGCACGATTTTGGCTCACTGCAACCTCTACCTCCCAAGCTCAAG |||||||||||||||||||||||||||||||||||||||||||||||||| 101 TGCAGTAGCACGATTTTGGCTCACTGCAACCTCTACCTCCCAAGCTCAAG aa.c 34 C S S T I L A H C N L Y L P S S S 150 . : . : . aa.g 51 D P P T S A S Q +17:54427294 TGATCCTCCCACCTCAGCCTCCCAAG |||||||||||||||||||||||||| 151 TGATCCTCCCACCTCAGCCTCCCAAG aa.c 51 D P P T S A S Q Alignment for path 2: -11:71370149-71370053 (177-270) 95% 0 . : . : . : . : . : aa.g 1 S K N I F K K N N N K K R D I E -11:71370149 AATCAAAGAATATTTTTAAAAAAAACAACAACAAAAAGAGAGATATAGAG ||||||||||||||||| |||||||||||||---|||||||||||||||| 177 AATCAAAGAATATTTTTTAAAAAAACAACAA AAAGAGAGATATAGAG aa.c 1 S K N I F * 50 . : . : . : . : . aa.g 17 R K E R L V S W H S I A N * -11:71370099 AGGAAAGAGCGGCTAGTTTCCTGGCATTCTATAGCAAACTAAGAAAG ||||||||||||||||||||||||||||||||||||||||||||||| 224 AGGAAAGAGCGGCTAGTTTCCTGGCATTCTATAGCAAACTAAGAAAG