AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0871410

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 17 sgRNAs with CRISPR-Local

Find 146 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TCACTAAACTATTTATGATT+AGG 0.312535 6_1:-6289757 None:intergenic
CAAAATCGGCGTCTGTGTTA+TGG 0.324560 6_1:+6288549 Msa0871410:CDS
AGCACTTGACTCTTGTGTTT+AGG 0.349441 6_1:+6289589 Msa0871410:CDS
TGGTCAGGAGGGTTTATTGC+AGG 0.380165 6_1:+6289548 Msa0871410:CDS
TGTTCCTCGACAGCCCAAAA+AGG 0.401614 6_1:-6289695 None:intergenic
TTTATTGCAGGAACAACAAT+TGG 0.416798 6_1:+6289560 Msa0871410:CDS
AAAGTGAATGCTGATTTGTA+AGG 0.460390 6_1:+6289615 Msa0871410:three_prime_UTR
ATTACAGAGAAAATCAAAAT+CGG 0.462826 6_1:+6288535 Msa0871410:CDS
TGTTCTATATACAGAATGCT+TGG 0.465819 6_1:+6289528 Msa0871410:intron
TATATACAGAATGCTTGGTC+AGG 0.512151 6_1:+6289533 Msa0871410:intron
ATTGCAGGAACAACAATTGG+TGG 0.518923 6_1:+6289563 Msa0871410:CDS
TACAGAATGCTTGGTCAGGA+GGG 0.542715 6_1:+6289537 Msa0871410:intron
CGTCTGTGTTATGGAAAAGA+AGG 0.546814 6_1:+6288558 Msa0871410:CDS
GAAAATCACTCAAATGGTAG+AGG 0.550063 6_1:-6289823 None:intergenic
ATACAGAATGCTTGGTCAGG+AGG 0.578478 6_1:+6289536 Msa0871410:intron
GAAGGTGAAATGTGGCTCCG+AGG 0.672348 6_1:+6288576 Msa0871410:CDS
ATGGAAAAGAAGGTGAAATG+TGG 0.709851 6_1:+6288568 Msa0871410:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TAAAATATAACTATATCTAT+AGG - chr6_1:6288702-6288721 None:intergenic 10.0%
!! TAAAATATAACTATATCTAT+AGG - chr6_1:6288702-6288721 None:intergenic 10.0%
!! TTGAATGAAAAAAATTCATA+CGG + chr6_1:6288934-6288953 Msa0871410:intron 15.0%
!! TTGAATGAAAAAAATTCATA+CGG + chr6_1:6288934-6288953 Msa0871410:intron 15.0%
!! ATTACAGAGAAAATCAAAAT+CGG + chr6_1:6288535-6288554 Msa0871410:CDS 20.0%
!! TGAATGAAAAAAATTCATAC+GGG + chr6_1:6288935-6288954 Msa0871410:intron 20.0%
!!! TATAACTTTTTAAGAATGCT+AGG - chr6_1:6289062-6289081 None:intergenic 20.0%
!! GTATATAGAACAAAGAAAAA+TGG - chr6_1:6289520-6289539 None:intergenic 20.0%
!! TCACTAAACTATTTATGATT+AGG - chr6_1:6289760-6289779 None:intergenic 20.0%
!! ATTACAGAGAAAATCAAAAT+CGG + chr6_1:6288535-6288554 Msa0871410:CDS 20.0%
!! TGAATGAAAAAAATTCATAC+GGG + chr6_1:6288935-6288954 Msa0871410:intron 20.0%
!!! TATAACTTTTTAAGAATGCT+AGG - chr6_1:6289062-6289081 None:intergenic 20.0%
!! GTATATAGAACAAAGAAAAA+TGG - chr6_1:6289520-6289539 None:intergenic 20.0%
!! TCACTAAACTATTTATGATT+AGG - chr6_1:6289760-6289779 None:intergenic 20.0%
!!! TTTCTGGTTTTTGCATTTTT+CGG + chr6_1:6288667-6288686 Msa0871410:intron 25.0%
! TGTATCATTGTTGAGTTTAA+AGG + chr6_1:6288734-6288753 Msa0871410:intron 25.0%
! AACTATGAAATATGACCTTT+AGG - chr6_1:6289161-6289180 None:intergenic 25.0%
! GCAAGTTACTTAATTGATAA+AGG - chr6_1:6289214-6289233 None:intergenic 25.0%
!!! CTGATTTGTAAGGTTTTAAA+CGG + chr6_1:6289625-6289644 Msa0871410:three_prime_UTR 25.0%
!!! TGATTTGTAAGGTTTTAAAC+GGG + chr6_1:6289626-6289645 Msa0871410:three_prime_UTR 25.0%
!!! AACTTGGTTTTTTCCTTTTT+GGG + chr6_1:6289682-6289701 Msa0871410:three_prime_UTR 25.0%
!!! GAGGAACAAGTATATTTTTT+AGG + chr6_1:6289710-6289729 Msa0871410:three_prime_UTR 25.0%
!!! TTTCTGGTTTTTGCATTTTT+CGG + chr6_1:6288667-6288686 Msa0871410:intron 25.0%
! TGTATCATTGTTGAGTTTAA+AGG + chr6_1:6288734-6288753 Msa0871410:intron 25.0%
! AACTATGAAATATGACCTTT+AGG - chr6_1:6289161-6289180 None:intergenic 25.0%
! GCAAGTTACTTAATTGATAA+AGG - chr6_1:6289214-6289233 None:intergenic 25.0%
!!! CTGATTTGTAAGGTTTTAAA+CGG + chr6_1:6289625-6289644 Msa0871410:three_prime_UTR 25.0%
!!! TGATTTGTAAGGTTTTAAAC+GGG + chr6_1:6289626-6289645 Msa0871410:three_prime_UTR 25.0%
!!! AACTTGGTTTTTTCCTTTTT+GGG + chr6_1:6289682-6289701 Msa0871410:three_prime_UTR 25.0%
!!! GAGGAACAAGTATATTTTTT+AGG + chr6_1:6289710-6289729 Msa0871410:three_prime_UTR 25.0%
CATTGTTGAGTTTAAAGGAT+TGG + chr6_1:6288739-6288758 Msa0871410:intron 30.0%
! GGGTCACACAAATTTTATAT+GGG + chr6_1:6288955-6288974 Msa0871410:intron 30.0%
CTTTCAACACACTTTATCAT+CGG - chr6_1:6289015-6289034 None:intergenic 30.0%
!! AAATATGACCTTTAGGTTGA+TGG - chr6_1:6289154-6289173 None:intergenic 30.0%
TGTTCTATATACAGAATGCT+TGG + chr6_1:6289528-6289547 Msa0871410:intron 30.0%
TTTATTGCAGGAACAACAAT+TGG + chr6_1:6289560-6289579 Msa0871410:CDS 30.0%
!! AAAGTGAATGCTGATTTGTA+AGG + chr6_1:6289615-6289634 Msa0871410:three_prime_UTR 30.0%
CAAAAAGGAAAAAACCAAGT+TGG - chr6_1:6289683-6289702 None:intergenic 30.0%
!!! CAACTTGGTTTTTTCCTTTT+TGG + chr6_1:6289681-6289700 Msa0871410:three_prime_UTR 30.0%
CATTGTTGAGTTTAAAGGAT+TGG + chr6_1:6288739-6288758 Msa0871410:intron 30.0%
! GGGTCACACAAATTTTATAT+GGG + chr6_1:6288955-6288974 Msa0871410:intron 30.0%
CTTTCAACACACTTTATCAT+CGG - chr6_1:6289015-6289034 None:intergenic 30.0%
!! AAATATGACCTTTAGGTTGA+TGG - chr6_1:6289154-6289173 None:intergenic 30.0%
TGTTCTATATACAGAATGCT+TGG + chr6_1:6289528-6289547 Msa0871410:intron 30.0%
TTTATTGCAGGAACAACAAT+TGG + chr6_1:6289560-6289579 Msa0871410:CDS 30.0%
!! AAAGTGAATGCTGATTTGTA+AGG + chr6_1:6289615-6289634 Msa0871410:three_prime_UTR 30.0%
CAAAAAGGAAAAAACCAAGT+TGG - chr6_1:6289683-6289702 None:intergenic 30.0%
!!! CAACTTGGTTTTTTCCTTTT+TGG + chr6_1:6289681-6289700 Msa0871410:three_prime_UTR 30.0%
ATGGAAAAGAAGGTGAAATG+TGG + chr6_1:6288568-6288587 Msa0871410:CDS 35.0%
GAGTTTAAAGGATTGGATCT+CGG + chr6_1:6288746-6288765 Msa0871410:intron 35.0%
! CGGGTCACACAAATTTTATA+TGG + chr6_1:6288954-6288973 Msa0871410:intron 35.0%
TATCCAAACCATCAACCTAA+AGG + chr6_1:6289143-6289162 Msa0871410:intron 35.0%
AAAGACCACGAAAAACGATA+CGG - chr6_1:6289186-6289205 None:intergenic 35.0%
ATTCTCTCCAGTGCTAATTT+AGG + chr6_1:6289312-6289331 Msa0871410:intron 35.0%
! TAGAAGTGTAGCATAACTTG+AGG + chr6_1:6289429-6289448 Msa0871410:intron 35.0%
! AGAAGTGTAGCATAACTTGA+GGG + chr6_1:6289430-6289449 Msa0871410:intron 35.0%
CAAGTGGTTCATGCAAAAAA+TGG - chr6_1:6289457-6289476 None:intergenic 35.0%
TATATACAGAATGCTTGGTC+AGG + chr6_1:6289533-6289552 Msa0871410:intron 35.0%
!!! GTGTTGCATCATGCTTTTTT+AGG + chr6_1:6289657-6289676 Msa0871410:three_prime_UTR 35.0%
ATGGAAAAGAAGGTGAAATG+TGG + chr6_1:6288568-6288587 Msa0871410:CDS 35.0%
GAGTTTAAAGGATTGGATCT+CGG + chr6_1:6288746-6288765 Msa0871410:intron 35.0%
! CGGGTCACACAAATTTTATA+TGG + chr6_1:6288954-6288973 Msa0871410:intron 35.0%
TATCCAAACCATCAACCTAA+AGG + chr6_1:6289143-6289162 Msa0871410:intron 35.0%
AAAGACCACGAAAAACGATA+CGG - chr6_1:6289186-6289205 None:intergenic 35.0%
ATTCTCTCCAGTGCTAATTT+AGG + chr6_1:6289312-6289331 Msa0871410:intron 35.0%
! TAGAAGTGTAGCATAACTTG+AGG + chr6_1:6289429-6289448 Msa0871410:intron 35.0%
! AGAAGTGTAGCATAACTTGA+GGG + chr6_1:6289430-6289449 Msa0871410:intron 35.0%
CAAGTGGTTCATGCAAAAAA+TGG - chr6_1:6289457-6289476 None:intergenic 35.0%
TATATACAGAATGCTTGGTC+AGG + chr6_1:6289533-6289552 Msa0871410:intron 35.0%
!!! GTGTTGCATCATGCTTTTTT+AGG + chr6_1:6289657-6289676 Msa0871410:three_prime_UTR 35.0%
CGTCTGTGTTATGGAAAAGA+AGG + chr6_1:6288558-6288577 Msa0871410:CDS 40.0%
! TCTCTCTGCTTCTTCTTTTC+TGG + chr6_1:6288651-6288670 Msa0871410:intron 40.0%
!! TGACCTTTAGGTTGATGGTT+TGG - chr6_1:6289149-6289168 None:intergenic 40.0%
!! GTTTTCCGTATCGTTTTTCG+TGG + chr6_1:6289178-6289197 Msa0871410:intron 40.0%
TCTCCAGTGCTAATTTAGGT+GGG + chr6_1:6289316-6289335 Msa0871410:intron 40.0%
TAACCCACCTAAATTAGCAC+TGG - chr6_1:6289322-6289341 None:intergenic 40.0%
ATTGCAGGAACAACAATTGG+TGG + chr6_1:6289563-6289582 Msa0871410:CDS 40.0%
AGCACTTGACTCTTGTGTTT+AGG + chr6_1:6289589-6289608 Msa0871410:CDS 40.0%
!!! AGGTTTTAAACGGGTAGTGT+TGG + chr6_1:6289635-6289654 Msa0871410:three_prime_UTR 40.0%
!!! CATGCTTTTTTAGGCCAACT+TGG + chr6_1:6289666-6289685 Msa0871410:three_prime_UTR 40.0%
CGTCTGTGTTATGGAAAAGA+AGG + chr6_1:6288558-6288577 Msa0871410:CDS 40.0%
! TCTCTCTGCTTCTTCTTTTC+TGG + chr6_1:6288651-6288670 Msa0871410:intron 40.0%
!! TGACCTTTAGGTTGATGGTT+TGG - chr6_1:6289149-6289168 None:intergenic 40.0%
!! GTTTTCCGTATCGTTTTTCG+TGG + chr6_1:6289178-6289197 Msa0871410:intron 40.0%
TCTCCAGTGCTAATTTAGGT+GGG + chr6_1:6289316-6289335 Msa0871410:intron 40.0%
TAACCCACCTAAATTAGCAC+TGG - chr6_1:6289322-6289341 None:intergenic 40.0%
ATTGCAGGAACAACAATTGG+TGG + chr6_1:6289563-6289582 Msa0871410:CDS 40.0%
AGCACTTGACTCTTGTGTTT+AGG + chr6_1:6289589-6289608 Msa0871410:CDS 40.0%
!!! AGGTTTTAAACGGGTAGTGT+TGG + chr6_1:6289635-6289654 Msa0871410:three_prime_UTR 40.0%
!!! CATGCTTTTTTAGGCCAACT+TGG + chr6_1:6289666-6289685 Msa0871410:three_prime_UTR 40.0%
CAAAATCGGCGTCTGTGTTA+TGG + chr6_1:6288549-6288568 Msa0871410:CDS 45.0%
CGCAAAGAAAGAGAGAACCT+CGG - chr6_1:6288596-6288615 None:intergenic 45.0%
!! TTGACCTGGTGGTATTGACT+TGG + chr6_1:6289251-6289270 Msa0871410:intron 45.0%
!! TGACCTGGTGGTATTGACTT+GGG + chr6_1:6289252-6289271 Msa0871410:intron 45.0%
!! GTGGTATTGACTTGGGATCT+GGG + chr6_1:6289259-6289278 Msa0871410:intron 45.0%
GAATCGAACCTGAAATCTCG+AGG - chr6_1:6289296-6289315 None:intergenic 45.0%
CTCTCCAGTGCTAATTTAGG+TGG + chr6_1:6289315-6289334 Msa0871410:intron 45.0%
TGCATGAACCACTTGCTCAT+TGG + chr6_1:6289462-6289481 Msa0871410:intron 45.0%
! ACCACTTGCTCATTGGTTGA+TGG + chr6_1:6289469-6289488 Msa0871410:intron 45.0%
ACCATCAACCAATGAGCAAG+TGG - chr6_1:6289473-6289492 None:intergenic 45.0%
ATACAGAATGCTTGGTCAGG+AGG + chr6_1:6289536-6289555 Msa0871410:intron 45.0%
TACAGAATGCTTGGTCAGGA+GGG + chr6_1:6289537-6289556 Msa0871410:intron 45.0%
!! TTTTCCTTTTTGGGCTGTCG+AGG + chr6_1:6289691-6289710 Msa0871410:three_prime_UTR 45.0%
CAAAATCGGCGTCTGTGTTA+TGG + chr6_1:6288549-6288568 Msa0871410:CDS 45.0%
CGCAAAGAAAGAGAGAACCT+CGG - chr6_1:6288596-6288615 None:intergenic 45.0%
!! TTGACCTGGTGGTATTGACT+TGG + chr6_1:6289251-6289270 Msa0871410:intron 45.0%
!! TGACCTGGTGGTATTGACTT+GGG + chr6_1:6289252-6289271 Msa0871410:intron 45.0%
!! GTGGTATTGACTTGGGATCT+GGG + chr6_1:6289259-6289278 Msa0871410:intron 45.0%
GAATCGAACCTGAAATCTCG+AGG - chr6_1:6289296-6289315 None:intergenic 45.0%
CTCTCCAGTGCTAATTTAGG+TGG + chr6_1:6289315-6289334 Msa0871410:intron 45.0%
TGCATGAACCACTTGCTCAT+TGG + chr6_1:6289462-6289481 Msa0871410:intron 45.0%
! ACCACTTGCTCATTGGTTGA+TGG + chr6_1:6289469-6289488 Msa0871410:intron 45.0%
ACCATCAACCAATGAGCAAG+TGG - chr6_1:6289473-6289492 None:intergenic 45.0%
ATACAGAATGCTTGGTCAGG+AGG + chr6_1:6289536-6289555 Msa0871410:intron 45.0%
TACAGAATGCTTGGTCAGGA+GGG + chr6_1:6289537-6289556 Msa0871410:intron 45.0%
!! TTTTCCTTTTTGGGCTGTCG+AGG + chr6_1:6289691-6289710 Msa0871410:three_prime_UTR 45.0%
! TAACTTGCCGCGAAACCCAT+TGG + chr6_1:6289226-6289245 Msa0871410:intron 50.0%
AACTTGCCGCGAAACCCATT+GGG + chr6_1:6289227-6289246 Msa0871410:intron 50.0%
GATCCCAAGTCAATACCACC+AGG - chr6_1:6289258-6289277 None:intergenic 50.0%
!! GGTGGTATTGACTTGGGATC+TGG + chr6_1:6289258-6289277 Msa0871410:intron 50.0%
TCGAACCTGAAATCTCGAGG+AGG - chr6_1:6289293-6289312 None:intergenic 50.0%
TGGTCAGGAGGGTTTATTGC+AGG + chr6_1:6289548-6289567 Msa0871410:CDS 50.0%
TGTTCCTCGACAGCCCAAAA+AGG - chr6_1:6289698-6289717 None:intergenic 50.0%
! TAACTTGCCGCGAAACCCAT+TGG + chr6_1:6289226-6289245 Msa0871410:intron 50.0%
AACTTGCCGCGAAACCCATT+GGG + chr6_1:6289227-6289246 Msa0871410:intron 50.0%
GATCCCAAGTCAATACCACC+AGG - chr6_1:6289258-6289277 None:intergenic 50.0%
!! GGTGGTATTGACTTGGGATC+TGG + chr6_1:6289258-6289277 Msa0871410:intron 50.0%
TCGAACCTGAAATCTCGAGG+AGG - chr6_1:6289293-6289312 None:intergenic 50.0%
TGGTCAGGAGGGTTTATTGC+AGG + chr6_1:6289548-6289567 Msa0871410:CDS 50.0%
TGTTCCTCGACAGCCCAAAA+AGG - chr6_1:6289698-6289717 None:intergenic 50.0%
GAAGGTGAAATGTGGCTCCG+AGG + chr6_1:6288576-6288595 Msa0871410:CDS 55.0%
ACTTGCCGCGAAACCCATTG+GGG + chr6_1:6289228-6289247 Msa0871410:intron 55.0%
! GTCAACCCCAATGGGTTTCG+CGG - chr6_1:6289236-6289255 None:intergenic 55.0%
GAAACCCATTGGGGTTGACC+TGG + chr6_1:6289237-6289256 Msa0871410:intron 55.0%
ACCACCAGGTCAACCCCAAT+GGG - chr6_1:6289244-6289263 None:intergenic 55.0%
TACCACCAGGTCAACCCCAA+TGG - chr6_1:6289245-6289264 None:intergenic 55.0%
GTGCTCCTCCTCGAGATTTC+AGG + chr6_1:6289285-6289304 Msa0871410:intron 55.0%
GAAGGTGAAATGTGGCTCCG+AGG + chr6_1:6288576-6288595 Msa0871410:CDS 55.0%
ACTTGCCGCGAAACCCATTG+GGG + chr6_1:6289228-6289247 Msa0871410:intron 55.0%
! GTCAACCCCAATGGGTTTCG+CGG - chr6_1:6289236-6289255 None:intergenic 55.0%
GAAACCCATTGGGGTTGACC+TGG + chr6_1:6289237-6289256 Msa0871410:intron 55.0%
ACCACCAGGTCAACCCCAAT+GGG - chr6_1:6289244-6289263 None:intergenic 55.0%
TACCACCAGGTCAACCCCAA+TGG - chr6_1:6289245-6289264 None:intergenic 55.0%
GTGCTCCTCCTCGAGATTTC+AGG + chr6_1:6289285-6289304 Msa0871410:intron 55.0%
ACCCATTGGGGTTGACCTGG+TGG + chr6_1:6289240-6289259 Msa0871410:intron 60.0%
ACCCATTGGGGTTGACCTGG+TGG + chr6_1:6289240-6289259 Msa0871410:intron 60.0%
Chromosome Type Strat End Strand Name
chr6_1 gene 6288526 6289832 6288526 ID=Msa0871410;Name=Msa0871410
chr6_1 mRNA 6288526 6289832 6288526 ID=Msa0871410-mRNA-1;Parent=Msa0871410;Name=Msa0871410-mRNA-1;_AED=0.47;_eAED=0.47;_QI=0|0|0.5|1|1|1|2|222|46
chr6_1 exon 6288526 6288597 6288526 ID=Msa0871410-mRNA-1:exon:2005;Parent=Msa0871410-mRNA-1
chr6_1 exon 6289542 6289832 6289542 ID=Msa0871410-mRNA-1:exon:2006;Parent=Msa0871410-mRNA-1
chr6_1 CDS 6288526 6288597 6288526 ID=Msa0871410-mRNA-1:cds;Parent=Msa0871410-mRNA-1
chr6_1 CDS 6289542 6289610 6289542 ID=Msa0871410-mRNA-1:cds;Parent=Msa0871410-mRNA-1
chr6_1 three_prime_UTR 6289611 6289832 6289611 ID=Msa0871410-mRNA-1:three_prime_utr;Parent=Msa0871410-mRNA-1
Gene Sequence

>Msa0871410

ATGGAGAAGATTACAGAGAAAATCAAAATCGGCGTCTGTGTTATGGAAAAGAAGGTGAAATGTGGCTCCGAGAATGCTTGGTCAGGAGGGTTTATTGCAGGAACAACAATTGGTGGATTAGCACTTGACTCTTGTGTTTAG
Protein sequence

>Msa0871410

MEKITEKIKIGVCVMEKKVKCGSENAWSGGFIAGTTIGGLALDSCV*