AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1450090


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 33 sgRNAs with CRISPR-Local

Find 122 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CTGCAACTCAATTGAAATTA+TGG 0.134418 tig0032786:+7529 Msa1450090:CDS
AAGACTCGGGGACGTCTTTA+TGG 0.233436 tig0032786:+7570 Msa1450090:CDS
CATAATTTCAATTGAGTTGC+AGG 0.269649 tig0032786:-7528 Msa1450090:intergenic
TCTTGAGCAGGAAACATATA+AGG 0.323244 tig0032786:+7461 Msa1450090:CDS
TGATAAGAGCACACAGGATT+TGG 0.348341 tig0032786:+7771 Msa1450090:CDS
TGCAACTCAATTGAAATTAT+GGG 0.353224 tig0032786:+7530 Msa1450090:CDS
TCTTTATGGTACTGGTGATA+TGG 0.360936 tig0032786:+7584 Msa1450090:CDS
GGAGATACAACTGAAGGAAT+TGG 0.373917 tig0032786:+7792 Msa1450090:CDS
ATGGAGAAGGCATCTGATAA+TGG 0.413051 tig0032786:+7489 Msa1450090:CDS
AATTATGGGCTGAATCAGTT+GGG 0.435146 tig0032786:+7544 Msa1450090:CDS
AAATTATGGGCTGAATCAGT+TGG 0.456563 tig0032786:+7543 Msa1450090:CDS
ACGGTGTCAGCCAACCTTGA+TGG 0.458588 tig0032786:-7830 Msa1450090:intergenic
CGGGGACGTCTTTATGGTAC+TGG 0.462779 tig0032786:+7576 Msa1450090:CDS
GGAAACATATAAGGAGAAGA+TGG 0.470179 tig0032786:+7470 Msa1450090:CDS
ATGGTAAAGCGCTACAAGCC+AGG 0.510350 tig0032786:+7603 Msa1450090:CDS
ATCAGTTGGGGAAAAGACTC+GGG 0.520712 tig0032786:+7557 Msa1450090:CDS
AGTTGCAGGATCAACCTCCT+TGG 0.527395 tig0032786:-7514 Msa1450090:intergenic
AATCAGTTGGGGAAAAGACT+CGG 0.529570 tig0032786:+7556 Msa1450090:CDS
TGAGAGTGTTGCTTCCATCA+AGG 0.578124 tig0032786:+7816 Msa1450090:CDS
GTAGAGAGCAAATGCAGCAG+AGG 0.591348 tig0032786:+7711 Msa1450090:intron
GCATACAAAAGCATTACAGA+TGG 0.613088 tig0032786:+8245 Msa1450090:CDS
TGATGCTCGAGTTGCACGTG+AGG 0.614438 tig0032786:+7735 Msa1450090:CDS
CTTTAAGCTTCAAATACCCA+CGG 0.616421 tig0032786:-8223 Msa1450090:intergenic
CATTATTGAAGGCTTACCGT+GGG 0.621659 tig0032786:+8207 Msa1450090:CDS
GGCATCTGATAATGGAACCA+AGG 0.625874 tig0032786:+7497 Msa1450090:CDS
TGCACGTGAGGAATGTCGCA+AGG 0.626178 tig0032786:+7747 Msa1450090:CDS
ATATAAGGAGAAGATGGAGA+AGG 0.633981 tig0032786:+7476 Msa1450090:CDS
ACATTATTGAAGGCTTACCG+TGG 0.637699 tig0032786:+8206 Msa1450090:CDS
ATTATGGGCTGAATCAGTTG+GGG 0.658835 tig0032786:+7545 Msa1450090:CDS
GGATTTGGAGATACAACTGA+AGG 0.659048 tig0032786:+7786 Msa1450090:CDS
TCAGTTGGGGAAAAGACTCG+GGG 0.699015 tig0032786:+7558 Msa1450090:CDS
CAAGGCTGATAAGAGCACAC+AGG 0.714892 tig0032786:+7765 Msa1450090:CDS
ATCTGATAATGGAACCAAGG+AGG 0.721491 tig0032786:+7500 Msa1450090:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TATATTAATGTATATTTCAT+TGG + tig0032786:8005-8024 Msa1450090:intron 10.0%
!! ATATTAATGTATATTTCATT+GGG + tig0032786:8006-8025 Msa1450090:intron 10.0%
!! TATATTAATGTATATTTCAT+TGG + tig0032786:8005-8024 Msa1450090:intron 10.0%
!! ATATTAATGTATATTTCATT+GGG + tig0032786:8006-8025 Msa1450090:intron 10.0%
!! TTGTTTATGTTAAAATCCAT+TGG + tig0032786:8057-8076 Msa1450090:intron 20.0%
!! TTGTTTATGTTAAAATCCAT+TGG + tig0032786:8057-8076 Msa1450090:intron 20.0%
! TGCAACTCAATTGAAATTAT+GGG + tig0032786:7530-7549 Msa1450090:CDS 25.0%
! AATAACTTTCATAACTCCAA+TGG - tig0032786:8076-8095 Msa1450090:intergenic 25.0%
!!! AGCTTTTGTTGATTACTTAA+AGG + tig0032786:8114-8133 Msa1450090:intron 25.0%
! TGAAACAAAAGAATCATCAA+TGG + tig0032786:8143-8162 Msa1450090:intron 25.0%
! GGAAAAAGAAACATTATTGA+AGG + tig0032786:8196-8215 Msa1450090:intron 25.0%
! TGCAACTCAATTGAAATTAT+GGG + tig0032786:7530-7549 Msa1450090:CDS 25.0%
! AATAACTTTCATAACTCCAA+TGG - tig0032786:8076-8095 Msa1450090:intergenic 25.0%
!!! AGCTTTTGTTGATTACTTAA+AGG + tig0032786:8114-8133 Msa1450090:intron 25.0%
! TGAAACAAAAGAATCATCAA+TGG + tig0032786:8143-8162 Msa1450090:intron 25.0%
! GGAAAAAGAAACATTATTGA+AGG + tig0032786:8196-8215 Msa1450090:intron 25.0%
! CATAATTTCAATTGAGTTGC+AGG - tig0032786:7531-7550 Msa1450090:intergenic 30.0%
CTGCAACTCAATTGAAATTA+TGG + tig0032786:7529-7548 Msa1450090:CDS 30.0%
GTCTTCAATAAAACATAGTG+CGG - tig0032786:7948-7967 Msa1450090:intergenic 30.0%
ATATTTCATTGGGAGAATTG+TGG + tig0032786:8016-8035 Msa1450090:intron 30.0%
TATTGTGTATTCTTGCATAC+AGG + tig0032786:8175-8194 Msa1450090:intron 30.0%
! CATAATTTCAATTGAGTTGC+AGG - tig0032786:7531-7550 Msa1450090:intergenic 30.0%
CTGCAACTCAATTGAAATTA+TGG + tig0032786:7529-7548 Msa1450090:CDS 30.0%
GTCTTCAATAAAACATAGTG+CGG - tig0032786:7948-7967 Msa1450090:intergenic 30.0%
ATATTTCATTGGGAGAATTG+TGG + tig0032786:8016-8035 Msa1450090:intron 30.0%
TATTGTGTATTCTTGCATAC+AGG + tig0032786:8175-8194 Msa1450090:intron 30.0%
! TGTATGTTTTTCTCTTGAGC+AGG + tig0032786:7449-7468 Msa1450090:CDS 35.0%
TCTTGAGCAGGAAACATATA+AGG + tig0032786:7461-7480 Msa1450090:CDS 35.0%
GGAAACATATAAGGAGAAGA+TGG + tig0032786:7470-7489 Msa1450090:CDS 35.0%
ATATAAGGAGAAGATGGAGA+AGG + tig0032786:7476-7495 Msa1450090:CDS 35.0%
! AAATTATGGGCTGAATCAGT+TGG + tig0032786:7543-7562 Msa1450090:CDS 35.0%
! AATTATGGGCTGAATCAGTT+GGG + tig0032786:7544-7563 Msa1450090:CDS 35.0%
!! TCTTTATGGTACTGGTGATA+TGG + tig0032786:7584-7603 Msa1450090:CDS 35.0%
TCAGAGTCATCATCATAGTT+AGG - tig0032786:7862-7881 Msa1450090:intergenic 35.0%
CTTTAAGCTTCAAATACCCA+CGG - tig0032786:8226-8245 Msa1450090:intergenic 35.0%
!! GCATACAAAAGCATTACAGA+TGG + tig0032786:8245-8264 Msa1450090:CDS 35.0%
! TGTATGTTTTTCTCTTGAGC+AGG + tig0032786:7449-7468 Msa1450090:CDS 35.0%
TCTTGAGCAGGAAACATATA+AGG + tig0032786:7461-7480 Msa1450090:CDS 35.0%
GGAAACATATAAGGAGAAGA+TGG + tig0032786:7470-7489 Msa1450090:CDS 35.0%
ATATAAGGAGAAGATGGAGA+AGG + tig0032786:7476-7495 Msa1450090:CDS 35.0%
! AAATTATGGGCTGAATCAGT+TGG + tig0032786:7543-7562 Msa1450090:CDS 35.0%
! AATTATGGGCTGAATCAGTT+GGG + tig0032786:7544-7563 Msa1450090:CDS 35.0%
!! TCTTTATGGTACTGGTGATA+TGG + tig0032786:7584-7603 Msa1450090:CDS 35.0%
TCAGAGTCATCATCATAGTT+AGG - tig0032786:7862-7881 Msa1450090:intergenic 35.0%
CTTTAAGCTTCAAATACCCA+CGG - tig0032786:8226-8245 Msa1450090:intergenic 35.0%
!! GCATACAAAAGCATTACAGA+TGG + tig0032786:8245-8264 Msa1450090:CDS 35.0%
!! ATGGAGAAGGCATCTGATAA+TGG + tig0032786:7489-7508 Msa1450090:CDS 40.0%
!! ATCTGATAATGGAACCAAGG+AGG + tig0032786:7500-7519 Msa1450090:CDS 40.0%
! ATTATGGGCTGAATCAGTTG+GGG + tig0032786:7545-7564 Msa1450090:CDS 40.0%
AATCAGTTGGGGAAAAGACT+CGG + tig0032786:7556-7575 Msa1450090:CDS 40.0%
GCAGAAACATGGCTACTATA+TGG - tig0032786:7663-7682 Msa1450090:intergenic 40.0%
! TATAGTAGCCATGTTTCTGC+CGG + tig0032786:7663-7682 Msa1450090:intron 40.0%
! TGATAAGAGCACACAGGATT+TGG + tig0032786:7771-7790 Msa1450090:CDS 40.0%
GGATTTGGAGATACAACTGA+AGG + tig0032786:7786-7805 Msa1450090:CDS 40.0%
GGAGATACAACTGAAGGAAT+TGG + tig0032786:7792-7811 Msa1450090:CDS 40.0%
CATCATAGTTAGGATAGCGA+CGG - tig0032786:7852-7871 Msa1450090:intergenic 40.0%
ACATTATTGAAGGCTTACCG+TGG + tig0032786:8206-8225 Msa1450090:CDS 40.0%
CATTATTGAAGGCTTACCGT+GGG + tig0032786:8207-8226 Msa1450090:CDS 40.0%
!! ATGGAGAAGGCATCTGATAA+TGG + tig0032786:7489-7508 Msa1450090:CDS 40.0%
!! ATCTGATAATGGAACCAAGG+AGG + tig0032786:7500-7519 Msa1450090:CDS 40.0%
! ATTATGGGCTGAATCAGTTG+GGG + tig0032786:7545-7564 Msa1450090:CDS 40.0%
AATCAGTTGGGGAAAAGACT+CGG + tig0032786:7556-7575 Msa1450090:CDS 40.0%
GCAGAAACATGGCTACTATA+TGG - tig0032786:7663-7682 Msa1450090:intergenic 40.0%
! TATAGTAGCCATGTTTCTGC+CGG + tig0032786:7663-7682 Msa1450090:intron 40.0%
! TGATAAGAGCACACAGGATT+TGG + tig0032786:7771-7790 Msa1450090:CDS 40.0%
GGATTTGGAGATACAACTGA+AGG + tig0032786:7786-7805 Msa1450090:CDS 40.0%
GGAGATACAACTGAAGGAAT+TGG + tig0032786:7792-7811 Msa1450090:CDS 40.0%
CATCATAGTTAGGATAGCGA+CGG - tig0032786:7852-7871 Msa1450090:intergenic 40.0%
ACATTATTGAAGGCTTACCG+TGG + tig0032786:8206-8225 Msa1450090:CDS 40.0%
CATTATTGAAGGCTTACCGT+GGG + tig0032786:8207-8226 Msa1450090:CDS 40.0%
!! GGCATCTGATAATGGAACCA+AGG + tig0032786:7497-7516 Msa1450090:CDS 45.0%
ATCAGTTGGGGAAAAGACTC+GGG + tig0032786:7557-7576 Msa1450090:CDS 45.0%
TGGAGATACATGCGATTGCT+GGG - tig0032786:7643-7662 Msa1450090:intergenic 45.0%
ATGGAGATACATGCGATTGC+TGG - tig0032786:7644-7663 Msa1450090:intergenic 45.0%
! ATAGTAGCCATGTTTCTGCC+GGG + tig0032786:7664-7683 Msa1450090:intron 45.0%
!! TGAGAGTGTTGCTTCCATCA+AGG + tig0032786:7816-7835 Msa1450090:CDS 45.0%
!! AGTGTTGCTTCCATCAAGGT+TGG + tig0032786:7820-7839 Msa1450090:intron 45.0%
GCTATCAACAGAGTCAGCAT+CGG - tig0032786:7887-7906 Msa1450090:intergenic 45.0%
!! TGACTCTGTTGATAGCGTAG+AGG + tig0032786:7891-7910 Msa1450090:intron 45.0%
!! GGCATCTGATAATGGAACCA+AGG + tig0032786:7497-7516 Msa1450090:CDS 45.0%
ATCAGTTGGGGAAAAGACTC+GGG + tig0032786:7557-7576 Msa1450090:CDS 45.0%
TGGAGATACATGCGATTGCT+GGG - tig0032786:7643-7662 Msa1450090:intergenic 45.0%
ATGGAGATACATGCGATTGC+TGG - tig0032786:7644-7663 Msa1450090:intergenic 45.0%
! ATAGTAGCCATGTTTCTGCC+GGG + tig0032786:7664-7683 Msa1450090:intron 45.0%
!! TGAGAGTGTTGCTTCCATCA+AGG + tig0032786:7816-7835 Msa1450090:CDS 45.0%
!! AGTGTTGCTTCCATCAAGGT+TGG + tig0032786:7820-7839 Msa1450090:intron 45.0%
GCTATCAACAGAGTCAGCAT+CGG - tig0032786:7887-7906 Msa1450090:intergenic 45.0%
!! TGACTCTGTTGATAGCGTAG+AGG + tig0032786:7891-7910 Msa1450090:intron 45.0%
AGTTGCAGGATCAACCTCCT+TGG - tig0032786:7517-7536 Msa1450090:intergenic 50.0%
TCAGTTGGGGAAAAGACTCG+GGG + tig0032786:7558-7577 Msa1450090:CDS 50.0%
AAGACTCGGGGACGTCTTTA+TGG + tig0032786:7570-7589 Msa1450090:CDS 50.0%
! ATGGTAAAGCGCTACAAGCC+AGG + tig0032786:7603-7622 Msa1450090:CDS 50.0%
TACATGCGATTGCTGGGTCA+GGG - tig0032786:7637-7656 Msa1450090:intergenic 50.0%
ATACATGCGATTGCTGGGTC+AGG - tig0032786:7638-7657 Msa1450090:intergenic 50.0%
GTAGAGAGCAAATGCAGCAG+AGG + tig0032786:7711-7730 Msa1450090:intron 50.0%
! CAAGGCTGATAAGAGCACAC+AGG + tig0032786:7765-7784 Msa1450090:CDS 50.0%
AGTTGCAGGATCAACCTCCT+TGG - tig0032786:7517-7536 Msa1450090:intergenic 50.0%
TCAGTTGGGGAAAAGACTCG+GGG + tig0032786:7558-7577 Msa1450090:CDS 50.0%
AAGACTCGGGGACGTCTTTA+TGG + tig0032786:7570-7589 Msa1450090:CDS 50.0%
! ATGGTAAAGCGCTACAAGCC+AGG + tig0032786:7603-7622 Msa1450090:CDS 50.0%
TACATGCGATTGCTGGGTCA+GGG - tig0032786:7637-7656 Msa1450090:intergenic 50.0%
ATACATGCGATTGCTGGGTC+AGG - tig0032786:7638-7657 Msa1450090:intergenic 50.0%
GTAGAGAGCAAATGCAGCAG+AGG + tig0032786:7711-7730 Msa1450090:intron 50.0%
! CAAGGCTGATAAGAGCACAC+AGG + tig0032786:7765-7784 Msa1450090:CDS 50.0%
CGGGGACGTCTTTATGGTAC+TGG + tig0032786:7576-7595 Msa1450090:CDS 55.0%
CAGCAATCCCGGCAGAAACA+TGG - tig0032786:7674-7693 Msa1450090:intergenic 55.0%
TGCCATCTGTGCAGCAATCC+CGG - tig0032786:7685-7704 Msa1450090:intergenic 55.0%
! TGATGCTCGAGTTGCACGTG+AGG + tig0032786:7735-7754 Msa1450090:CDS 55.0%
TGCACGTGAGGAATGTCGCA+AGG + tig0032786:7747-7766 Msa1450090:CDS 55.0%
! ACGGTGTCAGCCAACCTTGA+TGG - tig0032786:7833-7852 Msa1450090:intergenic 55.0%
CGGGGACGTCTTTATGGTAC+TGG + tig0032786:7576-7595 Msa1450090:CDS 55.0%
CAGCAATCCCGGCAGAAACA+TGG - tig0032786:7674-7693 Msa1450090:intergenic 55.0%
TGCCATCTGTGCAGCAATCC+CGG - tig0032786:7685-7704 Msa1450090:intergenic 55.0%
! TGATGCTCGAGTTGCACGTG+AGG + tig0032786:7735-7754 Msa1450090:CDS 55.0%
TGCACGTGAGGAATGTCGCA+AGG + tig0032786:7747-7766 Msa1450090:CDS 55.0%
! ACGGTGTCAGCCAACCTTGA+TGG - tig0032786:7833-7852 Msa1450090:intergenic 55.0%
TGGGTCAGGGAGGATACACC+TGG - tig0032786:7624-7643 Msa1450090:intergenic 60.0%
ATGCGATTGCTGGGTCAGGG+AGG - tig0032786:7634-7653 Msa1450090:intergenic 60.0%
TGCCGGGATTGCTGCACAGA+TGG + tig0032786:7680-7699 Msa1450090:intron 60.0%
TGGGTCAGGGAGGATACACC+TGG - tig0032786:7624-7643 Msa1450090:intergenic 60.0%
ATGCGATTGCTGGGTCAGGG+AGG - tig0032786:7634-7653 Msa1450090:intergenic 60.0%
TGCCGGGATTGCTGCACAGA+TGG + tig0032786:7680-7699 Msa1450090:intron 60.0%
Chromosome Type Strat End Strand Name
tig0032786 gene 7441 8271 7441 ID=Msa1450090;Name=Msa1450090
tig0032786 mRNA 7441 8271 7441 ID=Msa1450090-mRNA-1;Parent=Msa1450090;Name=Msa1450090-mRNA-1;_AED=0.57;_eAED=0.75;_QI=0|0|0|0.66|1|1|3|0|127
tig0032786 exon 7441 7626 7441 ID=Msa1450090-mRNA-1:exon:17274;Parent=Msa1450090-mRNA-1
tig0032786 exon 7715 7837 7715 ID=Msa1450090-mRNA-1:exon:17275;Parent=Msa1450090-mRNA-1
tig0032786 exon 8197 8271 8197 ID=Msa1450090-mRNA-1:exon:17276;Parent=Msa1450090-mRNA-1
tig0032786 CDS 7441 7626 7441 ID=Msa1450090-mRNA-1:cds;Parent=Msa1450090-mRNA-1
tig0032786 CDS 7715 7837 7715 ID=Msa1450090-mRNA-1:cds;Parent=Msa1450090-mRNA-1
tig0032786 CDS 8197 8271 8197 ID=Msa1450090-mRNA-1:cds;Parent=Msa1450090-mRNA-1
Gene Sequence

>Msa1450090

ATGCAATATGTATGTTTTTCTCTTGAGCAGGAAACATATAAGGAGAAGATGGAGAAGGCATCTGATAATGGAACCAAGGAGGTTGATCCTGCAACTCAATTGAAATTATGGGCTGAATCAGTTGGGGAAAAGACTCGGGGACGTCTTTATGGTACTGGTGATATGGTAAAGCGCTACAAGCCAGGTAGAGCAAATGCAGCAGAGGATGATGCTCGAGTTGCACGTGAGGAATGTCGCAAGGCTGATAAGAGCACACAGGATTTGGAGATACAACTGAAGGAATTGGCTGAGAGTGTTGCTTCCATCAAGGAAAAAGAAACATTATTGAAGGCTTACCGTGGGTATTTGAAGCTTAAAGCATACAAAAGCATTACAGATGGCTAA

Protein sequence

>Msa1450090

MQYVCFSLEQETYKEKMEKASDNGTKEVDPATQLKLWAESVGEKTRGRLYGTGDMVKRYKPGRANAAEDDARVAREECRKADKSTQDLEIQLKELAESVASIKEKETLLKAYRGYLKLKAYKSITDG*