AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0905880


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 18 sgRNAs with CRISPR-Local

Find 138 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CATTATTGAGAAAATGAATA+TGG 0.327958 6_2:+4306999 None:intergenic
CAATTGATCAAGGGCACATC+AGG 0.413224 6_2:+4305279 None:intergenic
ATAGTTGCAGAGCCATGATA+TGG 0.424217 6_2:-4305328 Msa0905880:intron
CACATCAGGTTGAGGCATCA+TGG 0.457305 6_2:+4305293 None:intergenic
ATTGTGAGCTCAATTGATCA+AGG 0.472161 6_2:+4305269 None:intergenic
AATTCAAATTATTTGCTCAA+AGG 0.504194 6_2:-4306867 Msa0905880:intron
GCAGCAAAAGCAATAACAAA+TGG 0.505702 6_2:-4306174 Msa0905880:intron
GGTTTGAATCATTCATATGT+TGG 0.508347 6_2:-4306196 Msa0905880:CDS
TTTACAATTGCAGGAGCCAT+GGG 0.512510 6_2:-4306217 Msa0905880:intron
TGATTTGATTGCAGCTACAT+TGG 0.518236 6_2:-4306963 Msa0905880:five_prime_UTR
GATAATCTTCTTCCATATCA+TGG 0.524522 6_2:+4305316 None:intergenic
ACATCAGGTTGAGGCATCAT+GGG 0.542727 6_2:+4305294 None:intergenic
TTGTGAGCTCAATTGATCAA+GGG 0.568312 6_2:+4305270 None:intergenic
ATTAATATGATGACAAGGGA+TGG 0.568971 6_2:-4307065 Msa0905880:five_prime_UTR
ATCAAGGGCACATCAGGTTG+AGG 0.588858 6_2:+4305285 None:intergenic
ATATGAATGATTCAAACCCA+TGG 0.620215 6_2:+4306201 None:intergenic
GGGGTATTAATATGATGACA+AGG 0.628650 6_2:-4307070 Msa0905880:five_prime_UTR
GGGTATTAATATGATGACAA+GGG 0.647434 6_2:-4307069 Msa0905880:five_prime_UTR

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! ATGTTTTGATTTCTTTAAAA+TGG - chr6_2:4305340-4305359 Msa0905880:intron 15.0%
!!! TGTTTTGATTTCTTTAAAAT+GGG - chr6_2:4305341-4305360 Msa0905880:intron 15.0%
!! GTTCATGTTTATAATTTATA+TGG - chr6_2:4306979-4306998 Msa0905880:five_prime_UTR 15.0%
!!! ATGTTTTGATTTCTTTAAAA+TGG - chr6_2:4305340-4305359 Msa0905880:intron 15.0%
!!! TGTTTTGATTTCTTTAAAAT+GGG - chr6_2:4305341-4305360 Msa0905880:intron 15.0%
!! GTTCATGTTTATAATTTATA+TGG - chr6_2:4306979-4306998 Msa0905880:five_prime_UTR 15.0%
!!! GTTTTGATTTCTTTAAAATG+GGG - chr6_2:4305342-4305361 Msa0905880:intron 20.0%
!!! TTTTGATTTCTTTAAAATGG+GGG - chr6_2:4305343-4305362 Msa0905880:intron 20.0%
!! CATTATTGAGAAAATGAATA+TGG + chr6_2:4305436-4305455 None:intergenic 20.0%
!! AATTCAAATTATTTGCTCAA+AGG - chr6_2:4305565-4305584 Msa0905880:intron 20.0%
!!! CTTTCTTAATTTGTCTATAT+AGG - chr6_2:4305600-4305619 Msa0905880:intron 20.0%
!!! GCTTCTTTTTTTTTTGTAAA+AGG - chr6_2:4305873-4305892 Msa0905880:intron 20.0%
!!! CTATTGATTTTGTAATCTTA+TGG - chr6_2:4306033-4306052 Msa0905880:intron 20.0%
!! AATTTCATTTGATAAACACA+TGG - chr6_2:4306167-4306186 Msa0905880:intron 20.0%
!! AACATTTCATCTATACAATT+AGG + chr6_2:4306480-4306499 None:intergenic 20.0%
!!! TAGTACTCAATTTTTTTTGT+TGG - chr6_2:4306558-4306577 Msa0905880:intron 20.0%
!! AAGAAATATGTAAATCACAA+AGG - chr6_2:4306660-4306679 Msa0905880:intron 20.0%
!! AGAAATATGTAAATCACAAA+GGG - chr6_2:4306661-4306680 Msa0905880:intron 20.0%
!!! GTTTTGATTTCTTTAAAATG+GGG - chr6_2:4305342-4305361 Msa0905880:intron 20.0%
!!! TTTTGATTTCTTTAAAATGG+GGG - chr6_2:4305343-4305362 Msa0905880:intron 20.0%
!! CATTATTGAGAAAATGAATA+TGG + chr6_2:4305436-4305455 None:intergenic 20.0%
!! AATTCAAATTATTTGCTCAA+AGG - chr6_2:4305565-4305584 Msa0905880:intron 20.0%
!!! CTTTCTTAATTTGTCTATAT+AGG - chr6_2:4305600-4305619 Msa0905880:intron 20.0%
!!! GCTTCTTTTTTTTTTGTAAA+AGG - chr6_2:4305873-4305892 Msa0905880:intron 20.0%
!!! CTATTGATTTTGTAATCTTA+TGG - chr6_2:4306033-4306052 Msa0905880:intron 20.0%
!! AATTTCATTTGATAAACACA+TGG - chr6_2:4306167-4306186 Msa0905880:intron 20.0%
!! AACATTTCATCTATACAATT+AGG + chr6_2:4306480-4306499 None:intergenic 20.0%
!!! TAGTACTCAATTTTTTTTGT+TGG - chr6_2:4306558-4306577 Msa0905880:intron 20.0%
!! AAGAAATATGTAAATCACAA+AGG - chr6_2:4306660-4306679 Msa0905880:intron 20.0%
!! AGAAATATGTAAATCACAAA+GGG - chr6_2:4306661-4306680 Msa0905880:intron 20.0%
! TCTATATGAATCATATTTGC+AGG - chr6_2:4305779-4305798 Msa0905880:intron 25.0%
! TAAAAGGATATCTCATGAAT+TGG - chr6_2:4305889-4305908 Msa0905880:intron 25.0%
! AAAAGGATATCTCATGAATT+GGG - chr6_2:4305890-4305909 Msa0905880:intron 25.0%
!! GTTTTTCTCTATTACTTTGT+AGG - chr6_2:4305925-4305944 Msa0905880:intron 25.0%
! CAAATGGTAAGTATTTCTTA+TGG - chr6_2:4306274-4306293 Msa0905880:intron 25.0%
! ATCTATACAATTAGGTTTCA+TGG + chr6_2:4306472-4306491 None:intergenic 25.0%
! GCGTGTTTGTAATTAAATAA+CGG - chr6_2:4306520-4306539 Msa0905880:intron 25.0%
!!! TTTCTTTTAAAAACCTCCAT+AGG + chr6_2:4306646-4306665 None:intergenic 25.0%
! TATCTGAATCATAGTTTAGA+AGG + chr6_2:4306866-4306885 None:intergenic 25.0%
!! GTGATTATTGTTGTTCTTAT+AGG - chr6_2:4306895-4306914 Msa0905880:CDS 25.0%
! TCTATATGAATCATATTTGC+AGG - chr6_2:4305779-4305798 Msa0905880:intron 25.0%
! TAAAAGGATATCTCATGAAT+TGG - chr6_2:4305889-4305908 Msa0905880:intron 25.0%
! AAAAGGATATCTCATGAATT+GGG - chr6_2:4305890-4305909 Msa0905880:intron 25.0%
!! GTTTTTCTCTATTACTTTGT+AGG - chr6_2:4305925-4305944 Msa0905880:intron 25.0%
! CAAATGGTAAGTATTTCTTA+TGG - chr6_2:4306274-4306293 Msa0905880:intron 25.0%
! ATCTATACAATTAGGTTTCA+TGG + chr6_2:4306472-4306491 None:intergenic 25.0%
! GCGTGTTTGTAATTAAATAA+CGG - chr6_2:4306520-4306539 Msa0905880:intron 25.0%
!!! TTTCTTTTAAAAACCTCCAT+AGG + chr6_2:4306646-4306665 None:intergenic 25.0%
! TATCTGAATCATAGTTTAGA+AGG + chr6_2:4306866-4306885 None:intergenic 25.0%
!! GTGATTATTGTTGTTCTTAT+AGG - chr6_2:4306895-4306914 Msa0905880:CDS 25.0%
GGGTATTAATATGATGACAA+GGG - chr6_2:4305363-4305382 Msa0905880:intron 30.0%
ATTAATATGATGACAAGGGA+TGG - chr6_2:4305367-4305386 Msa0905880:intron 30.0%
!!! GACTTTTTTGTCGTTTGTTT+TGG - chr6_2:4305517-4305536 Msa0905880:intron 30.0%
! ATTATTTGCTCAAAGGTATG+TGG - chr6_2:4305572-4305591 Msa0905880:intron 30.0%
TTATGATCATGAGATGTTTG+AGG - chr6_2:4305631-4305650 Msa0905880:intron 30.0%
GGCTTATCTTCATAACTTTA+TGG - chr6_2:4305851-4305870 Msa0905880:intron 30.0%
ATATGAATGATTCAAACCCA+TGG + chr6_2:4306234-4306253 None:intergenic 30.0%
GGTTTGAATCATTCATATGT+TGG - chr6_2:4306236-4306255 Msa0905880:intron 30.0%
AGTAACATAGATCAAGTGTT+TGG - chr6_2:4306332-4306351 Msa0905880:intron 30.0%
GCAAAGAAATCATTGAAGTT+AGG + chr6_2:4306400-4306419 None:intergenic 30.0%
! AGTCTTTTACCATACAACAT+GGG + chr6_2:4306770-4306789 None:intergenic 30.0%
! AAGTCTTTTACCATACAACA+TGG + chr6_2:4306771-4306790 None:intergenic 30.0%
ATGTTGTATGGTAAAAGACT+TGG - chr6_2:4306770-4306789 Msa0905880:intron 30.0%
TGTTGTATGGTAAAAGACTT+GGG - chr6_2:4306771-4306790 Msa0905880:intron 30.0%
GATAATCTTCTTCCATATCA+TGG + chr6_2:4307119-4307138 None:intergenic 30.0%
GGGTATTAATATGATGACAA+GGG - chr6_2:4305363-4305382 Msa0905880:intron 30.0%
ATTAATATGATGACAAGGGA+TGG - chr6_2:4305367-4305386 Msa0905880:intron 30.0%
!!! GACTTTTTTGTCGTTTGTTT+TGG - chr6_2:4305517-4305536 Msa0905880:intron 30.0%
! ATTATTTGCTCAAAGGTATG+TGG - chr6_2:4305572-4305591 Msa0905880:intron 30.0%
TTATGATCATGAGATGTTTG+AGG - chr6_2:4305631-4305650 Msa0905880:intron 30.0%
GGCTTATCTTCATAACTTTA+TGG - chr6_2:4305851-4305870 Msa0905880:intron 30.0%
ATATGAATGATTCAAACCCA+TGG + chr6_2:4306234-4306253 None:intergenic 30.0%
GGTTTGAATCATTCATATGT+TGG - chr6_2:4306236-4306255 Msa0905880:intron 30.0%
AGTAACATAGATCAAGTGTT+TGG - chr6_2:4306332-4306351 Msa0905880:intron 30.0%
GCAAAGAAATCATTGAAGTT+AGG + chr6_2:4306400-4306419 None:intergenic 30.0%
! AGTCTTTTACCATACAACAT+GGG + chr6_2:4306770-4306789 None:intergenic 30.0%
! AAGTCTTTTACCATACAACA+TGG + chr6_2:4306771-4306790 None:intergenic 30.0%
ATGTTGTATGGTAAAAGACT+TGG - chr6_2:4306770-4306789 Msa0905880:intron 30.0%
TGTTGTATGGTAAAAGACTT+GGG - chr6_2:4306771-4306790 Msa0905880:intron 30.0%
GATAATCTTCTTCCATATCA+TGG + chr6_2:4307119-4307138 None:intergenic 30.0%
! GGGGTATTAATATGATGACA+AGG - chr6_2:4305362-4305381 Msa0905880:intron 35.0%
TGATTTGATTGCAGCTACAT+TGG - chr6_2:4305469-4305488 Msa0905880:intron 35.0%
GTCTCAATCTGAAAAACAGA+TGG - chr6_2:4305658-4305677 Msa0905880:intron 35.0%
GAGCTTACTAAACCTGAATT+AGG - chr6_2:4305962-4305981 Msa0905880:intron 35.0%
!!! TAGTTTTGAGAACGCTCTTA+TGG - chr6_2:4306058-4306077 Msa0905880:intron 35.0%
! CAACTGCATTTTACAATTGC+AGG - chr6_2:4306206-4306225 Msa0905880:CDS 35.0%
GCAGCAAAAGCAATAACAAA+TGG - chr6_2:4306258-4306277 Msa0905880:intron 35.0%
AAGTGTAGCATATAGTGAAG+CGG - chr6_2:4306697-4306716 Msa0905880:intron 35.0%
CAGATCAGTTTCATATTCAG+TGG + chr6_2:4306940-4306959 None:intergenic 35.0%
! GGGGTATTAATATGATGACA+AGG - chr6_2:4305362-4305381 Msa0905880:intron 35.0%
TGATTTGATTGCAGCTACAT+TGG - chr6_2:4305469-4305488 Msa0905880:intron 35.0%
GTCTCAATCTGAAAAACAGA+TGG - chr6_2:4305658-4305677 Msa0905880:intron 35.0%
GAGCTTACTAAACCTGAATT+AGG - chr6_2:4305962-4305981 Msa0905880:intron 35.0%
!!! TAGTTTTGAGAACGCTCTTA+TGG - chr6_2:4306058-4306077 Msa0905880:intron 35.0%
! CAACTGCATTTTACAATTGC+AGG - chr6_2:4306206-4306225 Msa0905880:CDS 35.0%
GCAGCAAAAGCAATAACAAA+TGG - chr6_2:4306258-4306277 Msa0905880:intron 35.0%
AAGTGTAGCATATAGTGAAG+CGG - chr6_2:4306697-4306716 Msa0905880:intron 35.0%
CAGATCAGTTTCATATTCAG+TGG + chr6_2:4306940-4306959 None:intergenic 35.0%
!! GTGCTTTGTTTGAAGTGTAG+TGG - chr6_2:4305830-4305849 Msa0905880:intron 40.0%
GCGTTCACAAAACCTAATTC+AGG + chr6_2:4305977-4305996 None:intergenic 40.0%
! TTTTGTGAACGCTCATGTAG+AGG - chr6_2:4305985-4306004 Msa0905880:intron 40.0%
! TTTTACAATTGCAGGAGCCA+TGG - chr6_2:4306214-4306233 Msa0905880:intron 40.0%
TTTACAATTGCAGGAGCCAT+GGG - chr6_2:4306215-4306234 Msa0905880:intron 40.0%
ACGTTTGTGAACACAACCTA+TGG - chr6_2:4306627-4306646 Msa0905880:intron 40.0%
TTTGTGAACACAACCTATGG+AGG - chr6_2:4306630-4306649 Msa0905880:intron 40.0%
GTTAAGAGTCCCATGTTGTA+TGG - chr6_2:4306758-4306777 Msa0905880:intron 40.0%
CATGTTTGCAGGGAACAATA+AGG + chr6_2:4307026-4307045 None:intergenic 40.0%
ACCAAATCTGCATGTTTGCA+GGG + chr6_2:4307036-4307055 None:intergenic 40.0%
!! CAAACATGCAGATTTGGTGT+TGG - chr6_2:4307038-4307057 Msa0905880:five_prime_UTR 40.0%
ATAGTTGCAGAGCCATGATA+TGG - chr6_2:4307104-4307123 Msa0905880:five_prime_UTR 40.0%
!! GTGCTTTGTTTGAAGTGTAG+TGG - chr6_2:4305830-4305849 Msa0905880:intron 40.0%
GCGTTCACAAAACCTAATTC+AGG + chr6_2:4305977-4305996 None:intergenic 40.0%
! TTTTGTGAACGCTCATGTAG+AGG - chr6_2:4305985-4306004 Msa0905880:intron 40.0%
! TTTTACAATTGCAGGAGCCA+TGG - chr6_2:4306214-4306233 Msa0905880:intron 40.0%
TTTACAATTGCAGGAGCCAT+GGG - chr6_2:4306215-4306234 Msa0905880:intron 40.0%
ACGTTTGTGAACACAACCTA+TGG - chr6_2:4306627-4306646 Msa0905880:intron 40.0%
TTTGTGAACACAACCTATGG+AGG - chr6_2:4306630-4306649 Msa0905880:intron 40.0%
GTTAAGAGTCCCATGTTGTA+TGG - chr6_2:4306758-4306777 Msa0905880:intron 40.0%
CATGTTTGCAGGGAACAATA+AGG + chr6_2:4307026-4307045 None:intergenic 40.0%
ACCAAATCTGCATGTTTGCA+GGG + chr6_2:4307036-4307055 None:intergenic 40.0%
!! CAAACATGCAGATTTGGTGT+TGG - chr6_2:4307038-4307057 Msa0905880:five_prime_UTR 40.0%
ATAGTTGCAGAGCCATGATA+TGG - chr6_2:4307104-4307123 Msa0905880:five_prime_UTR 40.0%
AGATGCATTCTACGTGTCGA+AGG - chr6_2:4306828-4306847 Msa0905880:intron 45.0%
TCCCTGCAAACATGCAGATT+TGG - chr6_2:4307032-4307051 Msa0905880:five_prime_UTR 45.0%
CACCAAATCTGCATGTTTGC+AGG + chr6_2:4307037-4307056 None:intergenic 45.0%
ACGCATAACTTCGCAACTGA+TGG + chr6_2:4307068-4307087 None:intergenic 45.0%
TCAGTTGCGAAGTTATGCGT+TGG - chr6_2:4307068-4307087 Msa0905880:five_prime_UTR 45.0%
!! ACATCAGGTTGAGGCATCAT+GGG + chr6_2:4307141-4307160 None:intergenic 45.0%
AGATGCATTCTACGTGTCGA+AGG - chr6_2:4306828-4306847 Msa0905880:intron 45.0%
TCCCTGCAAACATGCAGATT+TGG - chr6_2:4307032-4307051 Msa0905880:five_prime_UTR 45.0%
CACCAAATCTGCATGTTTGC+AGG + chr6_2:4307037-4307056 None:intergenic 45.0%
ACGCATAACTTCGCAACTGA+TGG + chr6_2:4307068-4307087 None:intergenic 45.0%
TCAGTTGCGAAGTTATGCGT+TGG - chr6_2:4307068-4307087 Msa0905880:five_prime_UTR 45.0%
!! ACATCAGGTTGAGGCATCAT+GGG + chr6_2:4307141-4307160 None:intergenic 45.0%
!! CACATCAGGTTGAGGCATCA+TGG + chr6_2:4307142-4307161 None:intergenic 50.0%
! ATCAAGGGCACATCAGGTTG+AGG + chr6_2:4307150-4307169 None:intergenic 50.0%
!! CACATCAGGTTGAGGCATCA+TGG + chr6_2:4307142-4307161 None:intergenic 50.0%
! ATCAAGGGCACATCAGGTTG+AGG + chr6_2:4307150-4307169 None:intergenic 50.0%
Chromosome Type Strat End Strand Name
chr6_2 gene 4305281 4307173 4305281 ID=Msa0905880;Name=Msa0905880
chr6_2 mRNA 4305281 4307173 4305281 ID=Msa0905880-mRNA-1;Parent=Msa0905880;Name=Msa0905880-mRNA-1;_AED=0.35;_eAED=0.45;_QI=215|0|0.5|1|0.33|0.5|4|0|70
chr6_2 exon 4305281 4305340 4305281 ID=Msa0905880-mRNA-1:exon:1275;Parent=Msa0905880-mRNA-1
chr6_2 exon 4305376 4305382 4305376 ID=Msa0905880-mRNA-1:exon:1274;Parent=Msa0905880-mRNA-1
chr6_2 exon 4306175 4306226 4306175 ID=Msa0905880-mRNA-1:exon:1273;Parent=Msa0905880-mRNA-1
chr6_2 exon 4306868 4307173 4306868 ID=Msa0905880-mRNA-1:exon:1272;Parent=Msa0905880-mRNA-1
chr6_2 five_prime_UTR 4306959 4307173 4306959 ID=Msa0905880-mRNA-1:five_prime_utr;Parent=Msa0905880-mRNA-1
chr6_2 CDS 4306868 4306958 4306868 ID=Msa0905880-mRNA-1:cds;Parent=Msa0905880-mRNA-1
chr6_2 CDS 4306175 4306226 4306175 ID=Msa0905880-mRNA-1:cds;Parent=Msa0905880-mRNA-1
chr6_2 CDS 4305376 4305382 4305376 ID=Msa0905880-mRNA-1:cds;Parent=Msa0905880-mRNA-1
chr6_2 CDS 4305281 4305340 4305281 ID=Msa0905880-mRNA-1:cds;Parent=Msa0905880-mRNA-1
Gene Sequence

>Msa0905880

ATGTATATATATAATTTTCTTGACTTTTTTGTCGTTTGTTTTGGTTCAACTGACGAAAATTGCAAGTTGAATTCAAATTATTTGCTCAAAGGAGCCATGGGTTTGAATCATTCATATGTTGGCAGCAAAAGCAATAACAAATGTTGCGAAAGCCATGATATGGAAGAAGATTATCCCATGATGCCTCAACCTGATGTGCCCTTGATCAAT

Protein sequence

>Msa0905880

MYIYNFLDFFVVCFGSTDENCKLNSNYLLKGAMGLNHSYVGSKSNNKCCESHDMEEDYPMMPQPDVPLIN