AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1031620


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1031620 MtrunA17_Chr7g0253181 86.842 190 2 1 1 167 166 355 2.90e-116 333
Msa1031620 MtrunA17_Chr6g0461551 31.765 85 57 1 83 166 302 386 4.39e-11 60.1
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1031620 AT1G64770.1 55.263 190 59 3 1 166 161 348 4.87e-64 200
Msa1031620 AT1G64770.2 48.800 125 39 2 1 102 161 283 1.45e-28 107
Msa1031620 AT1G64770.3 47.656 128 42 2 1 105 161 286 2.35e-28 108
Msa1031620 AT1G55370.2 31.897 116 67 1 50 165 250 353 1.19e-13 67.8

Find 39 sgRNAs with CRISPR-Local

Find 126 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AAAAGCCTTTGTTCTTTCTT+TGG 0.192458 7_1:+66358851 None:intergenic
CTCTTCTCTTAAATCTAAAA+TGG 0.228276 7_1:+66359102 None:intergenic
ATAGCATTGGTTAGAGTAAC+AGG 0.282402 7_1:+66359131 None:intergenic
CACTGGTCCTGCTTCAATAT+TGG 0.282753 7_1:-66358423 Msa1031620:CDS
CATGAACCTGGCTTCAATTC+AGG 0.299182 7_1:+66358939 None:intergenic
AAAGCCTTTGTTCTTTCTTT+GGG 0.310843 7_1:+66358852 None:intergenic
GGTTCCATGTCAGACAAATA+TGG 0.314864 7_1:-66358464 Msa1031620:CDS
TTGGTTAGAGTAACAGGTTT+TGG 0.328743 7_1:+66359137 None:intergenic
TTATTCTCAAGGAGAGTAAT+AGG 0.341075 7_1:+66358900 None:intergenic
AGAGGTGGTGCGGCAATTAA+AGG 0.342398 7_1:-66359083 Msa1031620:intron
TCTCAAAGGTTGATTTCATT+TGG 0.368709 7_1:-66358969 Msa1031620:CDS
AAAATATGAAATCATTGATC+AGG 0.416361 7_1:-66358811 Msa1031620:intron
TTCTACAGGGTGATAAGAAT+GGG 0.419592 7_1:-66358515 Msa1031620:CDS
TTTCTACAGGGTGATAAGAA+TGG 0.440970 7_1:-66358516 Msa1031620:CDS
TATTTGTCTGACATGGAACC+AGG 0.462459 7_1:+66358467 None:intergenic
GCCTTTGTTCTTTCTTTGGG+AGG 0.467470 7_1:+66358855 None:intergenic
CTGAATTGAAGCCAGGTTCA+TGG 0.470856 7_1:-66358938 Msa1031620:CDS
GGTGATAAGAATGGGATTTG+AGG 0.481567 7_1:-66358507 Msa1031620:CDS
GAGCCTGTGACTGTGAATCC+TGG 0.502873 7_1:-66358401 Msa1031620:CDS
CCTTGTTGAGTCCATGAACC+TGG 0.507008 7_1:+66358927 None:intergenic
GATATTTACGTGTCAAGCCC+TGG 0.509482 7_1:-66358485 Msa1031620:CDS
GCTCCTCTGAATTCTTCACC+AGG 0.521135 7_1:+66358383 None:intergenic
GTTCCATGTCAGACAAATAT+GGG 0.524034 7_1:-66358463 Msa1031620:CDS
TGAAATCAACCTTTGAGACT+CGG 0.532325 7_1:+66358974 None:intergenic
AAAATGGCTTAATATAGCAT+TGG 0.535095 7_1:+66359118 None:intergenic
CCTCCCATATTTGTCTGACA+TGG 0.538146 7_1:+66358460 None:intergenic
TCACCAGGATTCACAGTCAC+AGG 0.541793 7_1:+66358398 None:intergenic
GCTGAGCCTGAATTGAAGCC+AGG 0.546842 7_1:-66358945 Msa1031620:CDS
TTTAGATTTAAGAGAAGAGG+TGG 0.556422 7_1:-66359098 Msa1031620:CDS
ACAGGCTCCAATATTGAAGC+AGG 0.556496 7_1:+66358416 None:intergenic
CAATGAAAACCGAGTCTCAA+AGG 0.560884 7_1:-66358983 Msa1031620:CDS
CTCTACTCATCTTATTCTCA+AGG 0.565176 7_1:+66358889 None:intergenic
CCAGGTTCATGGACTCAACA+AGG 0.611546 7_1:-66358927 Msa1031620:CDS
CATGTCAGACAAATATGGGA+GGG 0.662782 7_1:-66358459 Msa1031620:CDS
ACCTCCCAAAGAAAGAACAA+AGG 0.664272 7_1:-66358856 Msa1031620:CDS
ATTTAAGAGAAGAGGTGGTG+CGG 0.665156 7_1:-66359093 Msa1031620:CDS
CCATGTCAGACAAATATGGG+AGG 0.669410 7_1:-66358460 Msa1031620:CDS
AATCCTGGTGAAGAATTCAG+AGG 0.670082 7_1:-66358386 Msa1031620:CDS
ATTTGTCTGACATGGAACCA+GGG 0.675047 7_1:+66358468 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AAAAAAACTATTCTATAAAA+AGG + chr7_1:66358964-66358983 None:intergenic 10.0%
!! AAAAAAACTATTCTATAAAA+AGG + chr7_1:66358964-66358983 None:intergenic 10.0%
!!! TCAATGATTTCATATTTTGA+AGG + chr7_1:66358709-66358728 None:intergenic 20.0%
!! AAAATATGAAATCATTGATC+AGG - chr7_1:66358711-66358730 Msa1031620:intron 20.0%
!!! ATAGTTTTTTTCTTTCTTTC+AGG - chr7_1:66358973-66358992 Msa1031620:CDS 20.0%
!!! TAGTTTTTTTCTTTCTTTCA+GGG - chr7_1:66358974-66358993 Msa1031620:CDS 20.0%
!!! TCAATGATTTCATATTTTGA+AGG + chr7_1:66358709-66358728 None:intergenic 20.0%
!! AAAATATGAAATCATTGATC+AGG - chr7_1:66358711-66358730 Msa1031620:intron 20.0%
!!! ATAGTTTTTTTCTTTCTTTC+AGG - chr7_1:66358973-66358992 Msa1031620:CDS 20.0%
!!! TAGTTTTTTTCTTTCTTTCA+GGG - chr7_1:66358974-66358993 Msa1031620:CDS 20.0%
! AAAATGGCTTAATATAGCAT+TGG + chr7_1:66358407-66358426 None:intergenic 25.0%
! CTCTTCTCTTAAATCTAAAA+TGG + chr7_1:66358423-66358442 None:intergenic 25.0%
!! CATTTTAGATTTAAGAGAAG+AGG - chr7_1:66358421-66358440 Msa1031620:CDS 25.0%
!!! ATGATTTCATATTTTGAAGG+CGG + chr7_1:66358706-66358725 None:intergenic 25.0%
!! CATATAAGATGATTTGTGAT+TGG - chr7_1:66358815-66358834 Msa1031620:CDS 25.0%
! CATGAAAAATTCCAAATGTT+TGG + chr7_1:66358922-66358941 None:intergenic 25.0%
! AAAATGGCTTAATATAGCAT+TGG + chr7_1:66358407-66358426 None:intergenic 25.0%
! CTCTTCTCTTAAATCTAAAA+TGG + chr7_1:66358423-66358442 None:intergenic 25.0%
!! CATTTTAGATTTAAGAGAAG+AGG - chr7_1:66358421-66358440 Msa1031620:CDS 25.0%
!!! ATGATTTCATATTTTGAAGG+CGG + chr7_1:66358706-66358725 None:intergenic 25.0%
!! CATATAAGATGATTTGTGAT+TGG - chr7_1:66358815-66358834 Msa1031620:CDS 25.0%
! CATGAAAAATTCCAAATGTT+TGG + chr7_1:66358922-66358941 None:intergenic 25.0%
TTTAGATTTAAGAGAAGAGG+TGG - chr7_1:66358424-66358443 Msa1031620:CDS 30.0%
ATGGAGTCAAGATTTGAAAA+GGG + chr7_1:66358513-66358532 None:intergenic 30.0%
! TCTCAAAGGTTGATTTCATT+TGG - chr7_1:66358553-66358572 Msa1031620:intron 30.0%
TTATTCTCAAGGAGAGTAAT+AGG + chr7_1:66358625-66358644 None:intergenic 30.0%
AAAGCCTTTGTTCTTTCTTT+GGG + chr7_1:66358673-66358692 None:intergenic 30.0%
AAAAGCCTTTGTTCTTTCTT+TGG + chr7_1:66358674-66358693 None:intergenic 30.0%
AAATCGTTCCAGAACTTAAT+CGG + chr7_1:66358882-66358901 None:intergenic 30.0%
AAAAGGCTTCACTCAATAAT+TGG + chr7_1:66358947-66358966 None:intergenic 30.0%
TTTAGATTTAAGAGAAGAGG+TGG - chr7_1:66358424-66358443 Msa1031620:CDS 30.0%
ATGGAGTCAAGATTTGAAAA+GGG + chr7_1:66358513-66358532 None:intergenic 30.0%
! TCTCAAAGGTTGATTTCATT+TGG - chr7_1:66358553-66358572 Msa1031620:intron 30.0%
TTATTCTCAAGGAGAGTAAT+AGG + chr7_1:66358625-66358644 None:intergenic 30.0%
AAAGCCTTTGTTCTTTCTTT+GGG + chr7_1:66358673-66358692 None:intergenic 30.0%
AAAAGCCTTTGTTCTTTCTT+TGG + chr7_1:66358674-66358693 None:intergenic 30.0%
AAATCGTTCCAGAACTTAAT+CGG + chr7_1:66358882-66358901 None:intergenic 30.0%
AAAAGGCTTCACTCAATAAT+TGG + chr7_1:66358947-66358966 None:intergenic 30.0%
! TTGGTTAGAGTAACAGGTTT+TGG + chr7_1:66358388-66358407 None:intergenic 35.0%
!! ATAGCATTGGTTAGAGTAAC+AGG + chr7_1:66358394-66358413 None:intergenic 35.0%
TGGAGTCAAGATTTGAAAAG+GGG + chr7_1:66358512-66358531 None:intergenic 35.0%
GATGGAGTCAAGATTTGAAA+AGG + chr7_1:66358514-66358533 None:intergenic 35.0%
!! TGAAATCAACCTTTGAGACT+CGG + chr7_1:66358551-66358570 None:intergenic 35.0%
CTCTACTCATCTTATTCTCA+AGG + chr7_1:66358636-66358655 None:intergenic 35.0%
!! TTCTGGAACGATTTACATTG+TGG - chr7_1:66358888-66358907 Msa1031620:CDS 35.0%
TTTCTACAGGGTGATAAGAA+TGG - chr7_1:66359006-66359025 Msa1031620:intron 35.0%
TTCTACAGGGTGATAAGAAT+GGG - chr7_1:66359007-66359026 Msa1031620:intron 35.0%
GTTCCATGTCAGACAAATAT+GGG - chr7_1:66359059-66359078 Msa1031620:intron 35.0%
! TTGGTTAGAGTAACAGGTTT+TGG + chr7_1:66358388-66358407 None:intergenic 35.0%
!! ATAGCATTGGTTAGAGTAAC+AGG + chr7_1:66358394-66358413 None:intergenic 35.0%
TGGAGTCAAGATTTGAAAAG+GGG + chr7_1:66358512-66358531 None:intergenic 35.0%
GATGGAGTCAAGATTTGAAA+AGG + chr7_1:66358514-66358533 None:intergenic 35.0%
!! TGAAATCAACCTTTGAGACT+CGG + chr7_1:66358551-66358570 None:intergenic 35.0%
CTCTACTCATCTTATTCTCA+AGG + chr7_1:66358636-66358655 None:intergenic 35.0%
!! TTCTGGAACGATTTACATTG+TGG - chr7_1:66358888-66358907 Msa1031620:CDS 35.0%
TTTCTACAGGGTGATAAGAA+TGG - chr7_1:66359006-66359025 Msa1031620:intron 35.0%
TTCTACAGGGTGATAAGAAT+GGG - chr7_1:66359007-66359026 Msa1031620:intron 35.0%
GTTCCATGTCAGACAAATAT+GGG - chr7_1:66359059-66359078 Msa1031620:intron 35.0%
ATTTAAGAGAAGAGGTGGTG+CGG - chr7_1:66358429-66358448 Msa1031620:CDS 40.0%
ATTTGAAAAGGGGAAGCAAG+AGG + chr7_1:66358502-66358521 None:intergenic 40.0%
! TCGGTTTTCATTGCTTCTGA+TGG + chr7_1:66358532-66358551 None:intergenic 40.0%
CAATGAAAACCGAGTCTCAA+AGG - chr7_1:66358539-66358558 Msa1031620:intron 40.0%
ACCTCCCAAAGAAAGAACAA+AGG - chr7_1:66358666-66358685 Msa1031620:intron 40.0%
!! TATGCGTACCGATTAAGTTC+TGG - chr7_1:66358871-66358890 Msa1031620:CDS 40.0%
GGTGATAAGAATGGGATTTG+AGG - chr7_1:66359015-66359034 Msa1031620:intron 40.0%
ATTTGTCTGACATGGAACCA+GGG + chr7_1:66359057-66359076 None:intergenic 40.0%
TATTTGTCTGACATGGAACC+AGG + chr7_1:66359058-66359077 None:intergenic 40.0%
GGTTCCATGTCAGACAAATA+TGG - chr7_1:66359058-66359077 Msa1031620:intron 40.0%
CATGTCAGACAAATATGGGA+GGG - chr7_1:66359063-66359082 Msa1031620:intron 40.0%
! AGGGACTATTTTGTATGCAC+TGG - chr7_1:66359082-66359101 Msa1031620:intron 40.0%
AATCCTGGTGAAGAATTCAG+AGG - chr7_1:66359136-66359155 Msa1031620:CDS 40.0%
ATTTAAGAGAAGAGGTGGTG+CGG - chr7_1:66358429-66358448 Msa1031620:CDS 40.0%
ATTTGAAAAGGGGAAGCAAG+AGG + chr7_1:66358502-66358521 None:intergenic 40.0%
! TCGGTTTTCATTGCTTCTGA+TGG + chr7_1:66358532-66358551 None:intergenic 40.0%
CAATGAAAACCGAGTCTCAA+AGG - chr7_1:66358539-66358558 Msa1031620:intron 40.0%
ACCTCCCAAAGAAAGAACAA+AGG - chr7_1:66358666-66358685 Msa1031620:intron 40.0%
!! TATGCGTACCGATTAAGTTC+TGG - chr7_1:66358871-66358890 Msa1031620:CDS 40.0%
GGTGATAAGAATGGGATTTG+AGG - chr7_1:66359015-66359034 Msa1031620:intron 40.0%
ATTTGTCTGACATGGAACCA+GGG + chr7_1:66359057-66359076 None:intergenic 40.0%
TATTTGTCTGACATGGAACC+AGG + chr7_1:66359058-66359077 None:intergenic 40.0%
GGTTCCATGTCAGACAAATA+TGG - chr7_1:66359058-66359077 Msa1031620:intron 40.0%
CATGTCAGACAAATATGGGA+GGG - chr7_1:66359063-66359082 Msa1031620:intron 40.0%
! AGGGACTATTTTGTATGCAC+TGG - chr7_1:66359082-66359101 Msa1031620:intron 40.0%
AATCCTGGTGAAGAATTCAG+AGG - chr7_1:66359136-66359155 Msa1031620:CDS 40.0%
CATGAACCTGGCTTCAATTC+AGG + chr7_1:66358586-66358605 None:intergenic 45.0%
CTGAATTGAAGCCAGGTTCA+TGG - chr7_1:66358584-66358603 Msa1031620:intron 45.0%
GCCTTTGTTCTTTCTTTGGG+AGG + chr7_1:66358670-66358689 None:intergenic 45.0%
TGGACACGTGACCAAACATT+TGG - chr7_1:66358908-66358927 Msa1031620:CDS 45.0%
! AGGGACGTGAGATTTTCTAC+AGG - chr7_1:66358993-66359012 Msa1031620:intron 45.0%
! GGGACGTGAGATTTTCTACA+GGG - chr7_1:66358994-66359013 Msa1031620:intron 45.0%
GATATTTACGTGTCAAGCCC+TGG - chr7_1:66359037-66359056 Msa1031620:intron 45.0%
CCTCCCATATTTGTCTGACA+TGG + chr7_1:66359065-66359084 None:intergenic 45.0%
CCATGTCAGACAAATATGGG+AGG - chr7_1:66359062-66359081 Msa1031620:intron 45.0%
CACTGGTCCTGCTTCAATAT+TGG - chr7_1:66359099-66359118 Msa1031620:CDS 45.0%
ACAGGCTCCAATATTGAAGC+AGG + chr7_1:66359109-66359128 None:intergenic 45.0%
CATGAACCTGGCTTCAATTC+AGG + chr7_1:66358586-66358605 None:intergenic 45.0%
CTGAATTGAAGCCAGGTTCA+TGG - chr7_1:66358584-66358603 Msa1031620:intron 45.0%
GCCTTTGTTCTTTCTTTGGG+AGG + chr7_1:66358670-66358689 None:intergenic 45.0%
TGGACACGTGACCAAACATT+TGG - chr7_1:66358908-66358927 Msa1031620:CDS 45.0%
! AGGGACGTGAGATTTTCTAC+AGG - chr7_1:66358993-66359012 Msa1031620:intron 45.0%
! GGGACGTGAGATTTTCTACA+GGG - chr7_1:66358994-66359013 Msa1031620:intron 45.0%
GATATTTACGTGTCAAGCCC+TGG - chr7_1:66359037-66359056 Msa1031620:intron 45.0%
CCTCCCATATTTGTCTGACA+TGG + chr7_1:66359065-66359084 None:intergenic 45.0%
CCATGTCAGACAAATATGGG+AGG - chr7_1:66359062-66359081 Msa1031620:intron 45.0%
CACTGGTCCTGCTTCAATAT+TGG - chr7_1:66359099-66359118 Msa1031620:CDS 45.0%
ACAGGCTCCAATATTGAAGC+AGG + chr7_1:66359109-66359128 None:intergenic 45.0%
AGAGGTGGTGCGGCAATTAA+AGG - chr7_1:66358439-66358458 Msa1031620:CDS 50.0%
TGAGCACTAGCAGTATGAGC+AGG + chr7_1:66358473-66358492 None:intergenic 50.0%
GAAAAGGGGAAGCAAGAGGA+GGG + chr7_1:66358498-66358517 None:intergenic 50.0%
TGAAAAGGGGAAGCAAGAGG+AGG + chr7_1:66358499-66358518 None:intergenic 50.0%
CCTTGTTGAGTCCATGAACC+TGG + chr7_1:66358598-66358617 None:intergenic 50.0%
CCAGGTTCATGGACTCAACA+AGG - chr7_1:66358595-66358614 Msa1031620:intron 50.0%
TCACCAGGATTCACAGTCAC+AGG + chr7_1:66359127-66359146 None:intergenic 50.0%
GCTCCTCTGAATTCTTCACC+AGG + chr7_1:66359142-66359161 None:intergenic 50.0%
AGAGGTGGTGCGGCAATTAA+AGG - chr7_1:66358439-66358458 Msa1031620:CDS 50.0%
TGAGCACTAGCAGTATGAGC+AGG + chr7_1:66358473-66358492 None:intergenic 50.0%
GAAAAGGGGAAGCAAGAGGA+GGG + chr7_1:66358498-66358517 None:intergenic 50.0%
TGAAAAGGGGAAGCAAGAGG+AGG + chr7_1:66358499-66358518 None:intergenic 50.0%
CCTTGTTGAGTCCATGAACC+TGG + chr7_1:66358598-66358617 None:intergenic 50.0%
CCAGGTTCATGGACTCAACA+AGG - chr7_1:66358595-66358614 Msa1031620:intron 50.0%
TCACCAGGATTCACAGTCAC+AGG + chr7_1:66359127-66359146 None:intergenic 50.0%
GCTCCTCTGAATTCTTCACC+AGG + chr7_1:66359142-66359161 None:intergenic 50.0%
GCTGAGCCTGAATTGAAGCC+AGG - chr7_1:66358577-66358596 Msa1031620:intron 55.0%
GAGCCTGTGACTGTGAATCC+TGG - chr7_1:66359121-66359140 Msa1031620:CDS 55.0%
GCTGAGCCTGAATTGAAGCC+AGG - chr7_1:66358577-66358596 Msa1031620:intron 55.0%
GAGCCTGTGACTGTGAATCC+TGG - chr7_1:66359121-66359140 Msa1031620:CDS 55.0%
Chromosome Type Strat End Strand Name
chr7_1 gene 66358352 66359192 66358352 ID=Msa1031620;Name=Msa1031620
chr7_1 mRNA 66358352 66359192 66358352 ID=Msa1031620-mRNA-1;Parent=Msa1031620;Name=Msa1031620-mRNA-1;_AED=0.14;_eAED=0.14;_QI=0|0|0|1|1|1|3|0|167
chr7_1 exon 66359084 66359192 66359084 ID=Msa1031620-mRNA-1:exon:14914;Parent=Msa1031620-mRNA-1
chr7_1 exon 66358812 66359008 66358812 ID=Msa1031620-mRNA-1:exon:14913;Parent=Msa1031620-mRNA-1
chr7_1 exon 66358352 66358549 66358352 ID=Msa1031620-mRNA-1:exon:14912;Parent=Msa1031620-mRNA-1
chr7_1 CDS 66359084 66359192 66359084 ID=Msa1031620-mRNA-1:cds;Parent=Msa1031620-mRNA-1
chr7_1 CDS 66358812 66359008 66358812 ID=Msa1031620-mRNA-1:cds;Parent=Msa1031620-mRNA-1
chr7_1 CDS 66358352 66358549 66358352 ID=Msa1031620-mRNA-1:cds;Parent=Msa1031620-mRNA-1
Gene Sequence

>Msa1031620

ATGGCAACAGCAGTTATAGTTAAGAACAAATCTCCAAAACCTGTTACTCTAACCAATGCTATATTAAGCCATTTTAGATTTAAGAGAAGAGGTGGTGCGGCAATTAAAGAAGCAATGAAAACCGAGTCTCAAAGGTTGATTTCATTTGGTGCTGAGCCTGAATTGAAGCCAGGTTCATGGACTCAACAAGGTGTTCCTATTACTCTCCTTGAGAATAAGATGAGTAGAGTTTTTGCTGCACCTCCCAAAGAAAGAACAAAGGCTTTTTATAACACACCGCCTTCAAAATATGAAATCATTGATCAGGGACGTGAGATTTTCTACAGGGTGATAAGAATGGGATTTGAGGATATTTACGTGTCAAGCCCTGGTTCCATGTCAGACAAATATGGGAGGGACTATTTTGTATGCACTGGTCCTGCTTCAATATTGGAGCCTGTGACTGTGAATCCTGGTGAAGAATTCAGAGGAGCACAAGTTATTGAGCATGATAATCTCTCATAA

Protein sequence

>Msa1031620

MATAVIVKNKSPKPVTLTNAILSHFRFKRRGGAAIKEAMKTESQRLISFGAEPELKPGSWTQQGVPITLLENKMSRVFAAPPKERTKAFYNTPPSKYEIIDQGREIFYRVIRMGFEDIYVSSPGSMSDKYGRDYFVCTGPASILEPVTVNPGEEFRGAQVIEHDNLS*