AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene064331

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 32 sgRNAs with CRISPR-Local

Find 50 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CCCAAGAGCATGTGTGTATT+TGG 0.245539 6.2:+87318639 None:intergenic
CATTTGCAACCTTCACCTTC+AGG 0.298861 6.2:+87318548 None:intergenic
AACAGCTTGAAGCATGTTCC+TGG 0.350575 6.2:-87319435 None:intergenic
AACTTGACATGCTTGTTCTC+TGG 0.352143 6.2:+87318679 None:intergenic
GCCAAATACACACATGCTCT+TGG 0.365981 6.2:-87318640 MS.gene064331:CDS
ATCCATTTGTGCTGAATTCA+TGG 0.400960 6.2:-87318714 MS.gene064331:CDS
GCCCATGAATTCAGCACAAA+TGG 0.408653 6.2:+87318712 None:intergenic
ACTTGACATGCTTGTTCTCT+GGG 0.413856 6.2:+87318680 None:intergenic
CTTGTTCTCTGGGAATGTCT+TGG 0.426261 6.2:+87318690 None:intergenic
AACAAGAAGAGCAAACCTCT+TGG 0.455187 6.2:+87318576 None:intergenic
CCAAATACACACATGCTCTT+GGG 0.477554 6.2:-87318639 MS.gene064331:CDS
CTTGATGATTTCTTCAGCAC+CGG 0.493646 6.2:+87318498 None:intergenic
GACCTCAGCGACAAAGGTCT+CGG 0.528430 6.2:-87318607 MS.gene064331:CDS
GGAGGAGAATACACCATCTC+CGG 0.528627 6.2:-87318517 MS.gene064331:CDS
TCAGAAGAGCTGAAAGGAAA+GGG 0.536940 6.2:-87319399 MS.gene064331:CDS
GATTTCTTCAGCACCGGAGA+TGG 0.540136 6.2:+87318504 None:intergenic
TCTGATCTCTCAATGAAGCC+AGG 0.542391 6.2:+87319417 None:intergenic
CATGTCAAGTTCCTTGCTGA+TGG 0.542780 6.2:-87318667 MS.gene064331:CDS
GAGCTTGACCTCAGCGACAA+AGG 0.549694 6.2:-87318613 MS.gene064331:CDS
ATACACACATGCTCTTGGGT+TGG 0.558587 6.2:-87318635 MS.gene064331:CDS
AAGGTTGCAAATGTTGAAGA+AGG 0.566267 6.2:-87318538 MS.gene064331:CDS
TCTTCTTGTTGAAGACCTGA+AGG 0.568574 6.2:-87318563 MS.gene064331:CDS
ATCAGAAGAGCTGAAAGGAA+AGG 0.571012 6.2:-87319400 MS.gene064331:CDS
GTTGCAAATGTTGAAGAAGG+AGG 0.581974 6.2:-87318535 MS.gene064331:CDS
TGCCGAGACCTTTGTCGCTG+AGG 0.592538 6.2:+87318605 None:intergenic
CGGTGCTGAAGAAATCATCA+AGG 0.594261 6.2:-87318497 MS.gene064331:CDS
TCCATTTGTGCTGAATTCAT+GGG 0.611814 6.2:-87318713 MS.gene064331:CDS
GAGAGATCAGAAGAGCTGAA+AGG 0.621848 6.2:-87319405 MS.gene064331:CDS
TGTTGAAGACCTGAAGGTGA+AGG 0.633342 6.2:-87318557 MS.gene064331:CDS
GTCTCGGCATTCGCTCCAAG+AGG 0.644758 6.2:-87318591 MS.gene064331:CDS
GATGAAATCATCTGCATCAG+TGG 0.655212 6.2:-87319372 MS.gene064331:intron
ATTTGGCAGAGCCATCAGCA+AGG 0.708029 6.2:+87318656 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TGAATGTATTTTTTATAATG+TGG - chr6.2:87318848-87318867 MS.gene064331:intron 15.0%
! AATTACAAAGCTTGAAATCT+AGG + chr6.2:87318989-87319008 None:intergenic 25.0%
! ATCTATGAATGCTTCAAAAT+TGG - chr6.2:87318701-87318720 MS.gene064331:CDS 25.0%
! TCTATGAATGCTTCAAAATT+GGG - chr6.2:87318702-87318721 MS.gene064331:CDS 25.0%
AAATTCAGATTGCCTGTAAT+CGG + chr6.2:87319068-87319087 None:intergenic 30.0%
AGAAAAGCTGCATTAAAATC+TGG - chr6.2:87319025-87319044 MS.gene064331:intron 30.0%
CAACATCATAAGTATAGAAC+AGG + chr6.2:87319112-87319131 None:intergenic 30.0%
CTATGAATGCTTCAAAATTG+GGG - chr6.2:87318703-87318722 MS.gene064331:CDS 30.0%
CTGTTCTATACTTATGATGT+TGG - chr6.2:87319110-87319129 MS.gene064331:intron 30.0%
TGATTCAATGTCTTGCTAAA+TGG - chr6.2:87318807-87318826 MS.gene064331:intron 30.0%
! GCTTGTTACTTGATTCTATA+TGG - chr6.2:87318725-87318744 MS.gene064331:intron 30.0%
! TTACTAATGTTACCGATTAC+AGG - chr6.2:87319053-87319072 MS.gene064331:intron 30.0%
AAGGTTGCAAATGTTGAAGA+AGG - chr6.2:87319381-87319400 MS.gene064331:CDS 35.0%
ATCCATTTGTGCTGAATTCA+TGG - chr6.2:87319205-87319224 MS.gene064331:intron 35.0%
TAACACATTGTATTCGCCAA+TGG + chr6.2:87318894-87318913 None:intergenic 35.0%
TCCATTTGTGCTGAATTCAT+GGG - chr6.2:87319206-87319225 MS.gene064331:intron 35.0%
TGTCTTGCTAAATGGTGATA+TGG - chr6.2:87318815-87318834 MS.gene064331:intron 35.0%
AACAAGAAGAGCAAACCTCT+TGG + chr6.2:87319346-87319365 None:intergenic 40.0%
AACTTGACATGCTTGTTCTC+TGG + chr6.2:87319243-87319262 None:intergenic 40.0%
ACTTGACATGCTTGTTCTCT+GGG + chr6.2:87319242-87319261 None:intergenic 40.0%
ATCAGAAGAGCTGAAAGGAA+AGG - chr6.2:87318519-87318538 MS.gene064331:CDS 40.0%
CCAAATACACACATGCTCTT+GGG - chr6.2:87319280-87319299 MS.gene064331:intron 40.0%
GATGAAATCATCTGCATCAG+TGG - chr6.2:87318547-87318566 MS.gene064331:CDS 40.0%
GCTTGAAATCTAGGCAATCT+AGG + chr6.2:87318980-87318999 None:intergenic 40.0%
GTTGCAAATGTTGAAGAAGG+AGG - chr6.2:87319384-87319403 MS.gene064331:CDS 40.0%
TCAGAAGAGCTGAAAGGAAA+GGG - chr6.2:87318520-87318539 MS.gene064331:CDS 40.0%
TCTTCTTGTTGAAGACCTGA+AGG - chr6.2:87319356-87319375 MS.gene064331:intron 40.0%
TTTGTCACATCGATACCTGT+TGG - chr6.2:87318939-87318958 MS.gene064331:intron 40.0%
! AACTGAAAGCTTTGTGCCAT+TGG - chr6.2:87318875-87318894 MS.gene064331:intron 40.0%
! CTTGATGATTTCTTCAGCAC+CGG + chr6.2:87319424-87319443 None:intergenic 40.0%
ATACACACATGCTCTTGGGT+TGG - chr6.2:87319284-87319303 MS.gene064331:intron 45.0%
CATGTCAAGTTCCTTGCTGA+TGG - chr6.2:87319252-87319271 MS.gene064331:intron 45.0%
CATTTGCAACCTTCACCTTC+AGG + chr6.2:87319374-87319393 None:intergenic 45.0%
GAGAGATCAGAAGAGCTGAA+AGG - chr6.2:87318514-87318533 MS.gene064331:CDS 45.0%
GATACCTGTTGGATCGAGAT+TGG - chr6.2:87318950-87318969 MS.gene064331:intron 45.0%
GCCAAATACACACATGCTCT+TGG - chr6.2:87319279-87319298 MS.gene064331:intron 45.0%
GCCCATGAATTCAGCACAAA+TGG + chr6.2:87319210-87319229 None:intergenic 45.0%
TCTGATCTCTCAATGAAGCC+AGG + chr6.2:87318505-87318524 None:intergenic 45.0%
TGTTGAAGACCTGAAGGTGA+AGG - chr6.2:87319362-87319381 MS.gene064331:intron 45.0%
! CCCAAGAGCATGTGTGTATT+TGG + chr6.2:87319283-87319302 None:intergenic 45.0%
! CGGTGCTGAAGAAATCATCA+AGG - chr6.2:87319422-87319441 MS.gene064331:CDS 45.0%
! CTTGTTCTCTGGGAATGTCT+TGG + chr6.2:87319232-87319251 None:intergenic 45.0%
ATTTGGCAGAGCCATCAGCA+AGG + chr6.2:87319266-87319285 None:intergenic 50.0%
CAGTCCAATCTCGATCCAAC+AGG + chr6.2:87318957-87318976 None:intergenic 50.0%
GGAGGAGAATACACCATCTC+CGG - chr6.2:87319402-87319421 MS.gene064331:CDS 50.0%
! GATTTCTTCAGCACCGGAGA+TGG + chr6.2:87319418-87319437 None:intergenic 50.0%
GACCTCAGCGACAAAGGTCT+CGG - chr6.2:87319312-87319331 MS.gene064331:intron 55.0%
GAGCTTGACCTCAGCGACAA+AGG - chr6.2:87319306-87319325 MS.gene064331:intron 55.0%
GTCTCGGCATTCGCTCCAAG+AGG - chr6.2:87319328-87319347 MS.gene064331:intron 60.0%
TGCCGAGACCTTTGTCGCTG+AGG + chr6.2:87319317-87319336 None:intergenic 60.0%


Chromosome Type Strat End Strand Name
chr6.2 gene 87318489 87319452 87318489 ID=MS.gene064331
chr6.2 mRNA 87318489 87319452 87318489 ID=MS.gene064331.t1;Parent=MS.gene064331
chr6.2 exon 87319373 87319452 87319373 ID=MS.gene064331.t1.exon1;Parent=MS.gene064331.t1
chr6.2 CDS 87319373 87319452 87319373 ID=cds.MS.gene064331.t1;Parent=MS.gene064331.t1
chr6.2 exon 87318489 87318742 87318489 ID=MS.gene064331.t1.exon2;Parent=MS.gene064331.t1
chr6.2 CDS 87318489 87318742 87318489 ID=cds.MS.gene064331.t1;Parent=MS.gene064331.t1
Gene Sequence

>MS.gene064331

CTTGAAGCATGTTCCTGGCTTCATTGAGAGATCAGAAGAGCTGAAAGGAAAGGGTGTTGATGAAATCATCTGCATCAGTGGTAAAGTTTCTAGTCATATATCATGATTTTGCTGTCTATAATGATTCTTTTGTTGCTGATTGTGTTGTTTATTGACAAATATTATATGTACACGTAATTCTTAGTTTTTACAACTTTCATGTTCAATTCAATATCTATGAATGCTTCAAAATTGGGGCTTGTTACTTGATTCTATATGGCTTGTTACTTGATTTTTGTAGTTTATCTAATAATTTAGATTGAACGTGTCTTAGATTTTTGATTCAATGTCTTGCTAAATGGTGATATGGATAGAACTATTGAATGTATTTTTTATAATGTGGATCTAACTGAAAGCTTTGTGCCATTGGCGAATACAATGTGTTAACATCAAAGAATTCACATTCACACATTTGTCACATCGATACCTGTTGGATCGAGATTGGACTGCCTAGATTGCCTAGATTTCAAGCTTTGTAATTTAGTTTTTTAAAATGAAGAAAAGCTGCATTAAAATCTGGACTGTTTACTAATGTTACCGATTACAGGCAATCTGAATTTGCTAACATAATAACATGAATGCCTGTTCTATACTTATGATGTTGGTGATCAAATTGTCGAAGATAAATTGTCTATTATGCGACTAACTTGTTATTGTCTTTGATTTTGTAGTCAATGATCCATTTGTGCTGAATTCATGGGCCAAGACATTCCCAGAGAACAAGCATGTCAAGTTCCTTGCTGATGGCTCTGCCAAATACACACATGCTCTTGGGTTGGAGCTTGACCTCAGCGACAAAGGTCTCGGCATTCGCTCCAAGAGGTTTGCTCTTCTTGTTGAAGACCTGAAGGTGAAGGTTGCAAATGTTGAAGAAGGAGGAGAATACACCATCTCCGGTGCTGAAGAAATCATCAAGGCTCTTTGA
Protein sequence

>MS.gene064331.t1

LEACSWLHUEIRRAERKGCUUNHLHQCQUSICAEFMGQDIPREQACQVPCUWLCQIHTCSWVGAUPQRQRSRHSLQEVCSSCURPEGEGCKCURRRRIHHLRCURNHQGSL