sp|Q9C642|DCL_ARATH ----> Protein DCL homolog, chloroplastic

Intron 1 GTAAAAGTCT ... ATTTCAGCAG

Sample	Retention score (%)	Exon junction reads	5'ss reads	3'ss reads
A1	61.04	30	76	18
A2	63.27	18	35	27
A3	86.3	5	44	19
A4	56.25	7	11	7
A5	66.67	1	2	2
A6	52.5	19	5	37
A7	58.78	27	38	39
A8	63.38	26	34	56
A9	52.17	33	29	43
A10	67.01	16	35	30

>TRINITY_DN42819_c0_g1_i1 from sample A9 / Example spliced isoform

AAACAGATGGTTGGATTTGCTCAATGGCTGGCAAGGAAGCATCCAAATGTCAAACAACTATCCAGTTATCTGTCTGGGAGGAATCCACAAAGACAGACTCACAAACAGATGGTTGGGAGGCATCGTCAAAGCCAGACTCACAATCAGATGGTTGGGTTTCCTCGATAGCCAAGAAGGAAGCATCCAAATGTCAAAGGAGT
ATTCAGTTATCTGGTTGGGAGGCATCCACAAAGCCAGACTCACAAACAGATGGTTGGGTTTCCTCGATATCCAAGAAGGAAGCATCCAAATGTCAAAGGAGTATTCAGTTATCTGGTTGGGAGGCATCCACAAAGCCAGACTCACAAACAGATGGTTGGGTTTGCTCAAAGGCTGACAAGAAAGCAACCAAAAATGCAAG
GAGTATTCAGTTATCTGGTTGGGAGGCATCCACTGGTTGGAACTTAAGTGCAGATATCGCGGGGTGCGTGTCAAAATGTGGAGAGAATCCATGGGACAGCAATTGGAAACATGATGAAGTTAGAAATTTGTTTAGTTCGGACTCAAACTTGAGGCCTAAAGGGAAAAGGCATTGCACAGTTGGTTGGACAAAAATTGACA
GTTACAGTATGTCAAGGGAAGATGAATGGAAATGCTCCGAAGAAGAAAAAGGTTGGAAAACTGGATTGCAAGAGGATTATATCACAAATATATCAGGTTGGAATTCAAATGTAGAAACAGCAGGTGAAAAAGATTGTAGTGGTGGTTTGCAAGGTAATGCAATTCCTAATATGTCAAAGAGTAAGGACTTGAATAGCGCC
TTTGCTAGTAAGAAAAGCGCTAGGGAAACTGGTAAGACACAGTTTAAGACTGCAAACTCACCACATTGGAAATCAAACAGGGAAACTAGAGGCAAAAACGATTATACTTATTTGAACAATCATTGTTCAGAAAGAATACATCAACAAGAGATGACAGGAATGCATGATAATCAGCACAGTCACTTTAAATCAACATTACC
TAGATTCCAAAAGACTACTGCTTTTGAAGGGAAAGGGAGTAAGGGACTTCAGAAAAACTTGGAAGGCAATGATATGGAGATTAAGTGCAGACCTGAAGAAAGTGGATTGAAGAAAGATCCATCTCTTCCTCCTGGGTTTTCTTTCCAAGAGGACAGTTCCCCAGGAAGGAAATTTTCATTCCAACAAAATGGAAAGAAAA
ATACCGGTTGGCCTTCCAGTACTGATATTCTAACAAATTCTAGTTTGGGGAACTGTGCAAAGGAAGAAAGTGAACATAAATCGTCTTTTTCTGATGTAACGGTATCTGATAACAGCTTCAAATTTAAAAAGACTCGTGCAAACCCAGTACCTCTTGGAAAAACAAGATCATTTAGCAAAATCCAGACAGAAGCACATGCT
AGAAATACTTTTCAGGAGGTAGAACTGGATCAAAAGATAGGCAAAGATTCACAAGCTACCGGGTGGGGTGTGGATTGGCAAGCAGAGGTTCAAGAAATAAGTTCAACCAGACAACAGCCTATCATTCAAAGTATGTCTGTTGAGACTAGCACTCGAGATACACTAAGTAAAGTTATAACAATGGTGATAGACTACGGCCT
GAACATGAAAGGGAAATTCTTGAAAAGGTTCTCATTCACCATCCAGAAGCCGAAGGAAAGATGGGATGTGGTGTTGATTTCATAATGGTGGACAGTCACTCAGTGTTTAATTCAAGCAGATGCTTTTACATTGTTAGGAAAGATGGAACGAAAATAGATTTCTCGTATTTGAAGTGTTTAAAGGGACTTATTGAAAAGAA
ATTTCCAGATTCTGCAAAGGCCTTCATAGAAAAATATCTGTCACAGAGGAAATAGGAGTAGAGATAACAAAACAGGCCTTTCGGAGTTTGAGAAGCAGAGGTCGGATTCCTCCGCTATCCGAAATATCAGAGAACATTCATACTATCACACCTTATTTGCATATCACAAGTACTTTGTTATTATCATATATATATATATG
ATGATAGATATTATATGATGGATATTATATGATAGATATTATCATATATATATATATATATGATGGATAGATATTATATGGCTTCCATGTTTCAGTCATAAGAGAGTCTTTAGGGAAAGCTCATTTTAAGGTTTACATGTTCATAGCAGAAGAGATTTGAAATTTAATCTCTTTGTAATTTTTATTATTATATTTTTACA
TGTTCATAGCAGAAGAG

>TRINITY_DN42819_c0_g1_i2 from sample A9 / Example unspliced isoform:

AAACAGATGGTTGGATTTGCTCAATGGCTGGCAAGGAAGCATCCAAATGTCAAACAACTATCCAGTTATCTGTCTGGGAGGAATCCACAAAGACAGACTCACAAACAGATGGTTGGGAGGCATCGTCAAAGCCAGACTCACAATCAGATGGTTGGGTTTCCTCGATAGCCAAGAAGGAAGCATCCAAATGTCAAAGGAGT
ATTCAGTTATCTGGTTGGGAGGCATCCACAAAGCCAGACTCACAAACAGATGGTTGGGTTTCCTCGATATCCAAGAAGGAAGCATCCAAATGTCAAAGGAGTATTCAGTTATCTGGTTGGGAGGCATCCACAAAGCCAGACTCACAAACAGATGGTTGGGTTTGCTCAAAGGCTGACAAGAAAGCAACCAAAAATGCAAG
GAGTATTCAGTTATCTGGTTGGGAGGCATCCACTGGTTGGAACTTAAGTGCAGATATCGCGGGGTGCGTGTCAAAATGTGGAGAGAATCCATGGGACAGCAATTGGAAACATGATGAAGTTAGAAATTTGTTTAGTTCGGACTCAAACTTGAGGCCTAAAGGGAAAAGGCATTGCACAGTTGGTTGGACAAAAATTGACA
GTTACAGTATGTCAAGGGAAGATGAATGGAAATGCTCCGAAGAAGAAAAAGGTTGGAAAACTGGATTGCAAGAGGATTATATCACAAATATATCAGGTTGGAATTCAAATGTAGAAACAGCAGGTGAAAAAGATTGTAGTGGTGGTTTGCAAGGTAATGCAATTCCTAATATGTCAAAGAGTAAGGACTTGAATAGCGCC
TTTGCTAGTAAGAAAAGCGCTAGGGAAACTGGTAAGACACAGTTTAAGACTGCAAACTCACCACATTGGAAATCAAACAGGGAAACTAGAGGCAAAAACGATTATACTTATTTGAACAATCATTGTTCAGAAAGAATACATCAACAAGAGATGACAGGAATGCATGATAATCAGCACAGTCACTTTAAATCAACATTACC
TAGATTCCAAAAGACTACTGCTTTTGAAGGGAAAGGGAGTAAGGGACTTCAGAAAAACTTGGAAGGCAATGATATGGAGATTAAGTGCAGACCTGAAGAAAGTGGATTGAAGAAAGATCCATCTCTTCCTCCTGGGTTTTCTTTCCAAGAGGACAGTTCCCCAGGAAGGAAATTTTCATTCCAACAAAATGGAAAGAAAA
ATACCGGTTGGCCTTCCAGTACTGATATTCTAACAAATTCTAGTTTGGGGAACTGTGCAAAGGAAGAAAGTGAACATAAATCGTCTTTTTCTGATGTAACGGTATCTGATAACAGCTTCAAATTTAAAAAGACTCGTGCAAACCCAGTACCTCTTGGAAAAACAAGATCATTTAGCAAAATCCAGACAGAAGCACATGCT
AGAAATACTTTTCAGGAGGTAGAACTGGATCAAAAGATAGGCAAAGATTCACAAGCTACCGGGTGGGGTGTGGATTGGCAAGCAGAGGTTCAAGAAATAAGTTCAACCAGACAACAGCCTATCATTCAAAGTATGTCTGTTGAGACTAGCACTCGAGATACACTAAGTAAAGgtaaaagtctaactgcaaacataagctg
tcttgtttcaaatatttctgatgaggatacaacaacaaatagacatagcagtgtaaatgaaacaaaggataaggtgatagatttattaaaaagtgaacattctgatggtttggaaccatactcagagtccattgtaaaacctggttgggagggatgtaataacgaaaaaattgtttctgaaagctatgctgttaggtctt
tgagcactgataatttggccagtccaacctgcggtggattttcggaaggagagcatgataaatgcgatagatctatttctgatcatagccacacattcaagccaacaggtgcaaacatagtcccattaggaagaaagttatatagaagagcccagctagaagaatatgatagaaatactatacaggaatcgatacaggat
caagcagtaatgaaagtgatgcaactgaaggaaaggcttttagattgtcctgtggaagaaactaggagcaggggacctgatggggaatataagcatgcagaatttgacattcaaaatacatcaagtttggaaaaagaaaccattcctagtggaaattgtcacaagtcaagaacatcaggagaggatatagtcacacctag
caattgcaacatggaaacagaagaaaatttcgggttgactgtaaaacagggacaagattcagatgggtggaatcaaagaccagagacaataaccgcaggaactggattgagaggatggcataacgaacatgtcacctatgacagcaaaacaccaataaaatcaggttgggaagtagagaatgagaataatccagttgaaa
agtgcacgaaaaaaggtatggaatatggaaggaccagcaaaggtgaaggccgtatttcttcattgtggtctaagaaaaaggataaggtgcatcgggactacaaaaatcatactgcgagaaaatgttctcccagatcatgtaacactagaagatctgtagaacaaaccagtaatggttctcccaaattgcaggggattttt
caagaaatcaatcctttactccattcagtgagaacaattcttcatttcagcagTTATAACAATGGTGATAGACTACGGCCTGAACATGAAAGGGAAATTCTTGAAAAGGTTCTCATTCACCATCCAGAAGCCGAAGGAAAGATGGGATGTGGTGTTGATTTCATAATGGTGGACAGTCACTCAGTGTTTAATTCAAGCAG
ATGCTTTTACATTGTTAGGAAAGATGGAACGAAAATAGATTTCTCGTATTTGAAGTGTTTAAAGGGACTTATTGAAAAGAAATTTCCAGATTCTGCAAAGGCCTTCATAGAAAAATATCTGTCACAGAGGAAATAGGAGTAGAGATAACAAAACAGGCCTTTCGGAGTTTGAGAAGCAGAGGTCGGATTCCTCCGCTATC
CGAAATATCAGAGAACATTCATACTATCACACCTTATTTGCATATCAGAGAACATTCATATGATATCACAAGTACTTTGTTATTATCATATATATATATATGATGATAGATATTATATGATGGATATTATATGATAGATATTATCATATATATATATATATATGATGGATAGATATTATATGGCTTCCATGTTTCAGTCA
TAAGAGAGTCTTTAGGGAAAGCTCATTTTAAGGTTTACATGTTCATAGCAGAAGAGATTTGAAATTTAATCTCTTTGTAATTTTTATTATTATATTTTTACATGTTCATAGCAGAAGAG

Intron 2 GCATCCACAA ... TGGTTGGGAG

Sample	Retention score (%)	Exon junction reads	5'ss reads	3'ss reads
A1	49.37	40	39	39
A2	34.6	69	47	26
A3	37.21	27	18	14
A4	21.88	25	8	6
A5	45.83	13	11	11
A6	60	1	1	2
A7	44	7	5	6
A8	40	3	2	2
A9	41.18	5	5	2
A10	41.18	10	7	7

>TRINITY_DN109262_c0_g3_i6 from sample A4 / Example spliced isoform

TTGGGAGGCATCTACAAAGCCAGGCTCAAACACAGATGGTTGGGAGGCATTGACAAAGCTAGGCTCACAAATAGAAGGTTGGGAGGCATCTACAAAGCCAGGCTCAAACACAGATGGTTGGGAGGCATTGACAAATCTAGATTCACAAACAAAAGGTTGGGTTTTCCCAGTGGCTGACAAGAAGGCATCCAAATGTCAAA
CAACTATTCAGTTATCTGTCTGGGAGGAATCCACAAAGACAGACTCACAAACAGATGGTTGGGAGGCATCGTCAAAGCCAGACTCACAATCAGATGGTTGGGTTTCCTCGATAGCCAAGAAGGAAGCATCCAAATGTCAAAGGAGTATTCAGTTATCTGGTTGGGAGGCATCCACAAAGCCAGACTCACAAACAGATGGT
TGGGTTTCCTCGATATCCAAGAAGGAAGCATCCAAATGTCAAAGGAGTATTCAGTTATCTGGTTGGGAGGCATCCACAAAGCCAGACTCACAAACAGATGGTTGGGTTTGCTCAAAGGCTGACAAGAAAGCAACCAAAAATGCAAGGAGTATTCAGTTATCTGGTTGGGAGGCATCCACTGGTTGGAACTTAAGTGCAGA
TATCGCGGGGTGCGTGTCAAAATGTGGAGAGAATCCATGGGACAGCAATTGGAAACATGATGAAGTTAGAAATTTGTTTAGTTGGGACTCAAACTTGAGGCCTAAAGGGAAAAGGCATTGCACAGTTGGTTGGACAAAAATTGACAGTTACAGTATGTCGAGGGAAGATGAATGGAAATGCTCCGAAGAAGAAAAAGGTT
GGAAAACTGGATTGCAAGAGGATTATATCACAAATATATCAGGTTGGAATTCAAATGTAGAAACAGCAGGTGAAAAAGATTGTAGTGGTGGTTTGCAAGGTAATGCAATTCCTAATATGTCAAAGAGTAAGGACTTGAATAGCGCCTTTGCTAGTAAGAAAAGCGCTAGGGAAACTGGTAAGACACAGTTTAAGACTGCA
AACTCACCACATTGGAAATCAAACAGGGAAACTAGAGGCAAAAACGATTATACTTATTTGAACAATCATTGTTCAGAAAGAATACATCAACAAGAGATGACAGGAATGCATGATAATCAGCACAGTCACTTTAAATCAACATTACCTAGATTCCAAAAGACTACTGCTTTTGAAGGGAAAGGGAGTAAGGGACTTCAGAA
AAACTTGGAAGGCAATGATATGGAGATTAAGTGCAGACCTGAAGAAAGTGGATTGAAGAAAGATCCATCTCTTCCTCCTGGGTTTTCTTTCCAAGAGGACAGTTCCCCAGGAAGGAAATTTTCATTCCAACAAAATGGAAAGAAAAATACCGGTTGGCCTTCCAGTACTGATATTCTAACAAATTCTAGTTTGGGGAACT
GTGCAAAGGAAGAAAGTGAACATAAATCGTCTTTTTCTGATGTCACGGTATCTGATAACAGCTTCAAATTTAAAAAGACTCGTGCAAACCCAGTACCTCTTGGAAAAACAAGATCATTTAGCAAAATCCAGACAGAAGCACATGCTAGAAATACTTTTCAGGAGGTAGAACTGGATCAAAAGATAGGCAAAGATTCACAA
GCTACCGGGTGGGGTGTGGATTGGCAAGCAGAGGTTCAAGAAATAAGTTCAACCAGACAACAGCCTATCATTCAAAGTATGTCTGTTGAGACTAGCACTCGAGATACACTAAGTAAAGGTAAAAGTCTAACTGCAAACATAAGCTGTCTTGTTTCAAATATTTCTGATGAGGATACAACAACAAATAGACATAGCAGTGT
AAATGAAACAAAGGATAAGGTGATAGATTTATTAAAAAGTGAACATTCTGATGGTTTGGAACCATACTCAGAGTCCATTGTAAAACCTGGTTGGGAGGGATGTAATAACGAAAAAATTGTTTCTGAAAGCTATGCTGTTAGGTCTTTGAGCACTGATAATTTGGCCAGTCCAACCTGGGGTGGATTTTCGGAAGGAGAGC
ATGATAAATGCGATAGATCTATTTCTGATCGTAGCCACACATTCAAGCCAACAGGTGCAAACATAGTCCCATTAGGAAGAAAGTTATATAGAAGAGCCCAGCTAGAAGAATATGATAGAAATACTATACAGGAATCGATACAGGATCAAGCAGTAATGAAAGTGATGCAACTGAAGGAAAGGCTTTTAGATTGTCCTGTG
GAAGAAACTAGGAGCAGGGGACCTGATGGGGAATATAAGCATGCAGAATTTGACATTCAAAATACATCAAGTTTGGAAAAAGAAACCATTCCTAGTGGAAATTGTCACAAGTCAAGAACATCAGGAGAGGATATAGTCACACCTAGCAATTGCAACATGGAAACAGAAGAAAATTTCGGGTTGACTGTAAAAC

>TRINITY_DN109262_c0_g3_i2 from sample A4 / Example unspliced isoform:

TTGGGAGGCATCTACAAAGCCAGGCTCAAACACAGATGGTTGGGAGGCATTGACAAAGCTAGGCTCACAAATAGAAGGTTGGGAGGCATCTACAAAGCCAGGCTCAAACACAGATGGTTGGGAGGCATTGACAAATCTAGATTCACAAACAAAAGGTTGGGTTTTCCCAGTGGCTGACAAGAAGGCATCCAAATGTCAAA
CAACTATTCAGTTATCTGGTTGGGAGgcatccacaaaggcaaacacgcaaacagatggttgggagGCATCCACAAAGCCAGACTCACAAACAGATGGTTGGGAGGCATCGTCAAAGCCAGACTCACAATCAGATGGTTGGGTTTCCTCGATAGCCAAGAAGGAAGCATCCAAATGTCAAAGGAGTATTCAGTTATCTGGT
TGGGAGGCATCCACAAAGCCAGACTCACAAACAGATGGTTGGGTTTCCTCGATATCCAAGAAGGAAGCATCCAAATGTCAAAGGAGTATTCAGTTATCTGGTTGGGAGGCATCCACAAAGCCAGACTCACAAACAGATGGTTGGGTTTGCTCAAAGGCTGACAAGAAAGCAACCAAAAATGCAAGGAGTATTCAGTTATC
TGGTTGGGAGGCATCCACTGGTTGGAACTTAAGTGCAGATATCGCGGGGTGCGTGTCAAAATGTGGAGAGAATCCATGGGACAGCAATTGGAAACATGATGAAGTTAGAAATTTGTTTAGTTGGGACTCAAACTTGAGGCCTAAAGGGAAAAGGCATTGCACAGTTGGTTGGACAAAAATTGACAGTTACAGTATGTCGA
GGGAAGATGAATGGAAATGCTCCGAAGAAGAAAAAGGTTGGAAAACTGGATTGCAAGAGGATTATATCACAAATATATCAGGTTGGAATTCAAATGTAGAAACAGCAGGTGAAAAAGATTGTAGTGGTGGTTTGCAAGGTAATGCAATTCCTAATATGTCAAAGAGTAAGGACTTGAATAGCGCCTTTGCTAGTAAGAAA
AGCGCTAGGGAAACTGGTAAGACACAGTTTAAGACTGCAAACTCACCACATTGGAAATCAAACAGGGAAACTAGAGGCAAAAACGATTATACTTATTTGAACAATCATTGTTCAGAAAGAATACATCAACAAGAGATGACAGGAATGCATGATAATCAGCACAGTCACTTTAAATCAACATTACCTAGATTCCAAAAGAC
TACTGCTTTTGAAGGGAAAGGGAGTAAGGGACTTCAGAAAAACTTGGAAGGCAATGATATGGAGATTAAGTGCAGACCTGAAGAAAGTGGATTGAAGAAAGATCCATCTCTTCCTCCTGGGTTTTCTTTCCAAGAGGACAGTTCCCCAGGAAGGAAATTTTCATTCCAACAAAATGGAAAGAAAAATACCGGTTGGCCTT
CCAGTACTGATATTCTAACAAATTCTAGTTTGGGGAACTGTGCAAAGGAAGAAAGTGAACATAAATCGTCTTTTTCTGATGTCACGGTATCTGATAACAGCTTCAAATTTAAAAAGACTCGTGCAAACCCAGTACCTCTTGGAAAAACAAGATCATTTAGCAAAATCCAGACAGAAGCACATGCTAGAAATACTTTTCAG
GAGGTAGAACTGGATCAAAAGATAGGCAAAGATTCACAAGCTACCGGGTGGGGTGTGGATTGGCAAGCAGAGGTTCAAGAAATAAGTTCAACCAGACAACAGCCTATCATTCAAAGTATGTCTGTTGAGACTAGCACTCGAGATACACTAAGTAAAGGTAAAAGTCTAACTGCAAACATAAGCTGTCTTGTTTCAAATAT
TTCTGATGAGGATACAACAACAAATAGACATAGCAGTGTAAATGAAACAAAGGATAAGGTGATAGATTTATTAAAAAGTGAACATTCTGATGGTTTGGAACCATACTCAGAGTCCATTGTAAAACCTGGTTGGGAGGGATGTAATAACGAAAAAATTGTTTCTGAAAGCTATGCTGTTAGGTCTTTGAGCACTGATAATT
TGGCCAGTCCAACCTGGGGTGGATTTTCGGAAGGAGAGCATGATAAATGCGATAGATCTATTTCTGATCGTAGCCACACATTCAAGCCAACAGGTGCAAACATAGTCCCATTAGGAAGAAAGTTATATAGAAGAGCCCAGCTAGAAGAATATGATAGAAATACTATACAGGAATCGATACAGGATCAAGCAGTAATGAAA
GTGATGCAACTGAAGGAAAGGCTTTTAGATTGTCCTGTGGAAGAAACTAGGAGCAGGGGACCTGATGGGGAATATAAGCATGCAGAATTTGACATTCAAAATACATCAAGTTTGGAAAAAGAAACCATTCCTAGTGGAAATTGTCACAAGTCAAGAACATCAGGAGAGGATATAGTCACACCTAGCAATTGCAACATGGA
AACAGAAGAAAATTTCGGGTTGACTGTAAAAC