AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0964710

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0964710 MtrunA17_Chr6g0485481 60.000 120 47 1 23 141 1 120 4.45e-47 149
Msa0964710 MtrunA17_Chr6g0485491 55.263 76 34 0 65 140 4 79 1.05e-23 90.1
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 45 sgRNAs with CRISPR-Local

Find 110 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CATGCTGACCATATAATATT+TGG 0.148969 6_3:+91637088 None:intergenic
AAGATGAAAATATTGATTAT+TGG 0.166905 6_3:-91637638 Msa0964710:CDS
GACTGACTCTTCATCCCTTT+TGG 0.233722 6_3:+91637203 None:intergenic
ACTATTAAAGCTCTCTTTGT+AGG 0.282700 6_3:+91637744 None:intergenic
AGAGTCAGTCAAAGGTTCTT+TGG 0.292750 6_3:-91637190 Msa0964710:three_prime_UTR
AGTATCACCTGGCTTTGATA+TGG 0.372210 6_3:+91637539 None:intergenic
GAGTCAGTCAAAGGTTCTTT+GGG 0.376370 6_3:-91637189 Msa0964710:three_prime_UTR
AATTCATCATGCGTTATTCC+AGG 0.382392 6_3:+91637123 None:intergenic
CAAAGGATCCAAATATTATA+TGG 0.383489 6_3:-91637096 Msa0964710:three_prime_UTR
TTCTATTCACATCTTCCAAA+AGG 0.390556 6_3:-91637218 Msa0964710:three_prime_UTR
TCTTGACGCCGTCAGCCATT+TGG 0.395579 6_3:+91637303 None:intergenic
GCCAATGGAACTCCTTTACT+TGG 0.433502 6_3:-91637453 Msa0964710:intron
TTCATGATTGATGCTTGTTA+CGG 0.446394 6_3:-91637275 Msa0964710:CDS
CTCATCAGTGGCACAAAGGT+CGG 0.466093 6_3:+91637050 None:intergenic
TCATCAGTGGCACAAAGGTC+GGG 0.493995 6_3:+91637051 None:intergenic
ATTGATGCTTGTTACGGAGG+GGG 0.497851 6_3:-91637269 Msa0964710:CDS
TGATTGATGCTTGTTACGGA+GGG 0.498805 6_3:-91637271 Msa0964710:CDS
AGTTACCTTGTTGCAGCCAA+TGG 0.499386 6_3:-91637468 Msa0964710:CDS
TCTATTCACATCTTCCAAAA+GGG 0.515999 6_3:-91637217 Msa0964710:three_prime_UTR
TTGAGGAAGTTACCAAGTAA+AGG 0.533780 6_3:+91637441 None:intergenic
ACCAAGTAAAGGAGTTCCAT+TGG 0.537259 6_3:+91637452 None:intergenic
TTAATTACCATATCAAAGCC+AGG 0.542624 6_3:-91637546 Msa0964710:CDS
GACAGAAACGATGGAGGACC+TGG 0.548548 6_3:-91637612 Msa0964710:CDS
ATGATTGATGCTTGTTACGG+AGG 0.558998 6_3:-91637272 Msa0964710:CDS
ATGTGAATAGAACAACTTTG+TGG 0.564614 6_3:+91637229 None:intergenic
CAAATATTATATGGTCAGCA+TGG 0.570578 6_3:-91637087 Msa0964710:three_prime_UTR
GTGGCACAAAGGTCGGGTAG+TGG 0.571496 6_3:+91637057 None:intergenic
CGCATGATGAATTGATACAA+AGG 0.574943 6_3:-91637113 Msa0964710:three_prime_UTR
GATTGATGCTTGTTACGGAG+GGG 0.576750 6_3:-91637270 Msa0964710:CDS
AAAAGTTTGCTAATAAATCG+TGG 0.578152 6_3:-91637666 Msa0964710:CDS
ATTCATCATGCGTTATTCCA+GGG 0.587040 6_3:+91637124 None:intergenic
TCGGAATATGTATTGAGTGT+AGG 0.587606 6_3:+91637702 None:intergenic
TAGAATCAAGTTAAGAGAGT+GGG 0.593682 6_3:-91637003 Msa0964710:three_prime_UTR
AGGGATGAAGAGTCAGTCAA+AGG 0.601689 6_3:-91637198 Msa0964710:three_prime_UTR
GATTGTGTTAATGATTACCC+TGG 0.604085 6_3:-91637141 Msa0964710:three_prime_UTR
CATGGTAACTATCAACAAAG+AGG 0.608307 6_3:-91637495 Msa0964710:CDS
ATAGAATCAAGTTAAGAGAG+TGG 0.627109 6_3:-91637004 Msa0964710:three_prime_UTR
ATGGTAACTATCAACAAAGA+GGG 0.636257 6_3:-91637494 Msa0964710:CDS
GAGTTCCATTGGCTGCAACA+AGG 0.637602 6_3:+91637463 None:intergenic
ACACTCAATACATATTCCGA+TGG 0.646069 6_3:-91637699 Msa0964710:CDS
GTGTTAGACCAAATGGCTGA+CGG 0.654978 6_3:-91637311 Msa0964710:CDS
TATTGGCAAGACAGAAACGA+TGG 0.655578 6_3:-91637621 Msa0964710:CDS
TCAGCATCAATAAGGAAACC+AGG 0.656233 6_3:+91637594 None:intergenic
TTATCTCATCAGTGGCACAA+AGG 0.659996 6_3:+91637046 None:intergenic
TGGCAAGACAGAAACGATGG+AGG 0.703781 6_3:-91637618 Msa0964710:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! AAGATGAAAATATTGATTAT+TGG - chr6_3:91637087-91637106 Msa0964710:three_prime_UTR 15.0%
!!! AAGATGAAAATATTGATTAT+TGG - chr6_3:91637087-91637106 Msa0964710:three_prime_UTR 15.0%
!!! AAAAGTTTGCTAATAAATCG+TGG - chr6_3:91637059-91637078 Msa0964710:three_prime_UTR 25.0%
!! TGAAAAAATAAAGTATCACC+TGG + chr6_3:91637200-91637219 None:intergenic 25.0%
!!! ACTTTATTTTTTCACTTCAG+TGG - chr6_3:91637206-91637225 Msa0964710:three_prime_UTR 25.0%
!!! TAAAAAAGTGTTAGACCAAA+TGG - chr6_3:91637407-91637426 Msa0964710:intron 25.0%
! CAAAGGATCCAAATATTATA+TGG - chr6_3:91637629-91637648 Msa0964710:CDS 25.0%
!!! AGAATTTTTTATCTCATCAG+TGG + chr6_3:91637690-91637709 None:intergenic 25.0%
!!! AAAAGTTTGCTAATAAATCG+TGG - chr6_3:91637059-91637078 Msa0964710:three_prime_UTR 25.0%
!! TGAAAAAATAAAGTATCACC+TGG + chr6_3:91637200-91637219 None:intergenic 25.0%
!!! ACTTTATTTTTTCACTTCAG+TGG - chr6_3:91637206-91637225 Msa0964710:three_prime_UTR 25.0%
!!! TAAAAAAGTGTTAGACCAAA+TGG - chr6_3:91637407-91637426 Msa0964710:intron 25.0%
! CAAAGGATCCAAATATTATA+TGG - chr6_3:91637629-91637648 Msa0964710:CDS 25.0%
!!! AGAATTTTTTATCTCATCAG+TGG + chr6_3:91637690-91637709 None:intergenic 25.0%
ACTATTAAAGCTCTCTTTGT+AGG + chr6_3:91636984-91637003 None:intergenic 30.0%
! GTATTTTGTCAGCATCAATA+AGG + chr6_3:91637142-91637161 None:intergenic 30.0%
TTAATTACCATATCAAAGCC+AGG - chr6_3:91637179-91637198 Msa0964710:three_prime_UTR 30.0%
ATGGTAACTATCAACAAAGA+GGG - chr6_3:91637231-91637250 Msa0964710:three_prime_UTR 30.0%
TATTTGTGATTCTCAATGCA+TGG - chr6_3:91637335-91637354 Msa0964710:intron 30.0%
! TTCATGATTGATGCTTGTTA+CGG - chr6_3:91637450-91637469 Msa0964710:intron 30.0%
ATGTGAATAGAACAACTTTG+TGG + chr6_3:91637499-91637518 None:intergenic 30.0%
TTCTATTCACATCTTCCAAA+AGG - chr6_3:91637507-91637526 Msa0964710:CDS 30.0%
TCTATTCACATCTTCCAAAA+GGG - chr6_3:91637508-91637527 Msa0964710:CDS 30.0%
CATGCTGACCATATAATATT+TGG + chr6_3:91637640-91637659 None:intergenic 30.0%
CAAATATTATATGGTCAGCA+TGG - chr6_3:91637638-91637657 Msa0964710:CDS 30.0%
ATAGAATCAAGTTAAGAGAG+TGG - chr6_3:91637721-91637740 Msa0964710:CDS 30.0%
TAGAATCAAGTTAAGAGAGT+GGG - chr6_3:91637722-91637741 Msa0964710:CDS 30.0%
ACTATTAAAGCTCTCTTTGT+AGG + chr6_3:91636984-91637003 None:intergenic 30.0%
! GTATTTTGTCAGCATCAATA+AGG + chr6_3:91637142-91637161 None:intergenic 30.0%
TTAATTACCATATCAAAGCC+AGG - chr6_3:91637179-91637198 Msa0964710:three_prime_UTR 30.0%
ATGGTAACTATCAACAAAGA+GGG - chr6_3:91637231-91637250 Msa0964710:three_prime_UTR 30.0%
TATTTGTGATTCTCAATGCA+TGG - chr6_3:91637335-91637354 Msa0964710:intron 30.0%
! TTCATGATTGATGCTTGTTA+CGG - chr6_3:91637450-91637469 Msa0964710:intron 30.0%
ATGTGAATAGAACAACTTTG+TGG + chr6_3:91637499-91637518 None:intergenic 30.0%
TTCTATTCACATCTTCCAAA+AGG - chr6_3:91637507-91637526 Msa0964710:CDS 30.0%
TCTATTCACATCTTCCAAAA+GGG - chr6_3:91637508-91637527 Msa0964710:CDS 30.0%
CATGCTGACCATATAATATT+TGG + chr6_3:91637640-91637659 None:intergenic 30.0%
CAAATATTATATGGTCAGCA+TGG - chr6_3:91637638-91637657 Msa0964710:CDS 30.0%
ATAGAATCAAGTTAAGAGAG+TGG - chr6_3:91637721-91637740 Msa0964710:CDS 30.0%
TAGAATCAAGTTAAGAGAGT+GGG - chr6_3:91637722-91637741 Msa0964710:CDS 30.0%
TCGGAATATGTATTGAGTGT+AGG + chr6_3:91637026-91637045 None:intergenic 35.0%
ACACTCAATACATATTCCGA+TGG - chr6_3:91637026-91637045 Msa0964710:three_prime_UTR 35.0%
! ACTTTTTATCTTCGCACCAT+CGG + chr6_3:91637045-91637064 None:intergenic 35.0%
!!! TTTTTTCACTTCAGTGGACA+TGG - chr6_3:91637212-91637231 Msa0964710:three_prime_UTR 35.0%
CATGGTAACTATCAACAAAG+AGG - chr6_3:91637230-91637249 Msa0964710:three_prime_UTR 35.0%
TTGAGGAAGTTACCAAGTAA+AGG + chr6_3:91637287-91637306 None:intergenic 35.0%
TATTAGCATGAGATGTGTTG+AGG + chr6_3:91637304-91637323 None:intergenic 35.0%
GATTGTGTTAATGATTACCC+TGG - chr6_3:91637584-91637603 Msa0964710:CDS 35.0%
ATTCATCATGCGTTATTCCA+GGG + chr6_3:91637604-91637623 None:intergenic 35.0%
AATTCATCATGCGTTATTCC+AGG + chr6_3:91637605-91637624 None:intergenic 35.0%
CGCATGATGAATTGATACAA+AGG - chr6_3:91637612-91637631 Msa0964710:CDS 35.0%
TCGGAATATGTATTGAGTGT+AGG + chr6_3:91637026-91637045 None:intergenic 35.0%
ACACTCAATACATATTCCGA+TGG - chr6_3:91637026-91637045 Msa0964710:three_prime_UTR 35.0%
! ACTTTTTATCTTCGCACCAT+CGG + chr6_3:91637045-91637064 None:intergenic 35.0%
!!! TTTTTTCACTTCAGTGGACA+TGG - chr6_3:91637212-91637231 Msa0964710:three_prime_UTR 35.0%
CATGGTAACTATCAACAAAG+AGG - chr6_3:91637230-91637249 Msa0964710:three_prime_UTR 35.0%
TTGAGGAAGTTACCAAGTAA+AGG + chr6_3:91637287-91637306 None:intergenic 35.0%
TATTAGCATGAGATGTGTTG+AGG + chr6_3:91637304-91637323 None:intergenic 35.0%
GATTGTGTTAATGATTACCC+TGG - chr6_3:91637584-91637603 Msa0964710:CDS 35.0%
ATTCATCATGCGTTATTCCA+GGG + chr6_3:91637604-91637623 None:intergenic 35.0%
AATTCATCATGCGTTATTCC+AGG + chr6_3:91637605-91637624 None:intergenic 35.0%
CGCATGATGAATTGATACAA+AGG - chr6_3:91637612-91637631 Msa0964710:CDS 35.0%
TATTGGCAAGACAGAAACGA+TGG - chr6_3:91637104-91637123 Msa0964710:three_prime_UTR 40.0%
TCAGCATCAATAAGGAAACC+AGG + chr6_3:91637134-91637153 None:intergenic 40.0%
!! AGTATCACCTGGCTTTGATA+TGG + chr6_3:91637189-91637208 None:intergenic 40.0%
ACCAAGTAAAGGAGTTCCAT+TGG + chr6_3:91637276-91637295 None:intergenic 40.0%
! ATGATTGATGCTTGTTACGG+AGG - chr6_3:91637453-91637472 Msa0964710:intron 40.0%
! TGATTGATGCTTGTTACGGA+GGG - chr6_3:91637454-91637473 Msa0964710:CDS 40.0%
AGAGTCAGTCAAAGGTTCTT+TGG - chr6_3:91637535-91637554 Msa0964710:CDS 40.0%
GAGTCAGTCAAAGGTTCTTT+GGG - chr6_3:91637536-91637555 Msa0964710:CDS 40.0%
TTATCTCATCAGTGGCACAA+AGG + chr6_3:91637682-91637701 None:intergenic 40.0%
TATTGGCAAGACAGAAACGA+TGG - chr6_3:91637104-91637123 Msa0964710:three_prime_UTR 40.0%
TCAGCATCAATAAGGAAACC+AGG + chr6_3:91637134-91637153 None:intergenic 40.0%
!! AGTATCACCTGGCTTTGATA+TGG + chr6_3:91637189-91637208 None:intergenic 40.0%
ACCAAGTAAAGGAGTTCCAT+TGG + chr6_3:91637276-91637295 None:intergenic 40.0%
! ATGATTGATGCTTGTTACGG+AGG - chr6_3:91637453-91637472 Msa0964710:intron 40.0%
! TGATTGATGCTTGTTACGGA+GGG - chr6_3:91637454-91637473 Msa0964710:CDS 40.0%
AGAGTCAGTCAAAGGTTCTT+TGG - chr6_3:91637535-91637554 Msa0964710:CDS 40.0%
GAGTCAGTCAAAGGTTCTTT+GGG - chr6_3:91637536-91637555 Msa0964710:CDS 40.0%
TTATCTCATCAGTGGCACAA+AGG + chr6_3:91637682-91637701 None:intergenic 40.0%
AGTTACCTTGTTGCAGCCAA+TGG - chr6_3:91637257-91637276 Msa0964710:CDS 45.0%
GCCAATGGAACTCCTTTACT+TGG - chr6_3:91637272-91637291 Msa0964710:CDS 45.0%
! ATTTGCTACGTGACTTGTGC+AGG - chr6_3:91637375-91637394 Msa0964710:intron 45.0%
GTGTTAGACCAAATGGCTGA+CGG - chr6_3:91637414-91637433 Msa0964710:intron 45.0%
! GATTGATGCTTGTTACGGAG+GGG - chr6_3:91637455-91637474 Msa0964710:CDS 45.0%
! ATTGATGCTTGTTACGGAGG+GGG - chr6_3:91637456-91637475 Msa0964710:CDS 45.0%
!! GACTGACTCTTCATCCCTTT+TGG + chr6_3:91637525-91637544 None:intergenic 45.0%
AGGGATGAAGAGTCAGTCAA+AGG - chr6_3:91637527-91637546 Msa0964710:CDS 45.0%
AGTTACCTTGTTGCAGCCAA+TGG - chr6_3:91637257-91637276 Msa0964710:CDS 45.0%
GCCAATGGAACTCCTTTACT+TGG - chr6_3:91637272-91637291 Msa0964710:CDS 45.0%
! ATTTGCTACGTGACTTGTGC+AGG - chr6_3:91637375-91637394 Msa0964710:intron 45.0%
GTGTTAGACCAAATGGCTGA+CGG - chr6_3:91637414-91637433 Msa0964710:intron 45.0%
! GATTGATGCTTGTTACGGAG+GGG - chr6_3:91637455-91637474 Msa0964710:CDS 45.0%
! ATTGATGCTTGTTACGGAGG+GGG - chr6_3:91637456-91637475 Msa0964710:CDS 45.0%
!! GACTGACTCTTCATCCCTTT+TGG + chr6_3:91637525-91637544 None:intergenic 45.0%
AGGGATGAAGAGTCAGTCAA+AGG - chr6_3:91637527-91637546 Msa0964710:CDS 45.0%
TGGCAAGACAGAAACGATGG+AGG - chr6_3:91637107-91637126 Msa0964710:three_prime_UTR 50.0%
! GAGTTCCATTGGCTGCAACA+AGG + chr6_3:91637265-91637284 None:intergenic 50.0%
TCATCAGTGGCACAAAGGTC+GGG + chr6_3:91637677-91637696 None:intergenic 50.0%
CTCATCAGTGGCACAAAGGT+CGG + chr6_3:91637678-91637697 None:intergenic 50.0%
TGGCAAGACAGAAACGATGG+AGG - chr6_3:91637107-91637126 Msa0964710:three_prime_UTR 50.0%
! GAGTTCCATTGGCTGCAACA+AGG + chr6_3:91637265-91637284 None:intergenic 50.0%
TCATCAGTGGCACAAAGGTC+GGG + chr6_3:91637677-91637696 None:intergenic 50.0%
CTCATCAGTGGCACAAAGGT+CGG + chr6_3:91637678-91637697 None:intergenic 50.0%
GACAGAAACGATGGAGGACC+TGG - chr6_3:91637113-91637132 Msa0964710:three_prime_UTR 55.0%
TCTTGACGCCGTCAGCCATT+TGG + chr6_3:91637425-91637444 None:intergenic 55.0%
GACAGAAACGATGGAGGACC+TGG - chr6_3:91637113-91637132 Msa0964710:three_prime_UTR 55.0%
TCTTGACGCCGTCAGCCATT+TGG + chr6_3:91637425-91637444 None:intergenic 55.0%
GTGGCACAAAGGTCGGGTAG+TGG + chr6_3:91637671-91637690 None:intergenic 60.0%
GTGGCACAAAGGTCGGGTAG+TGG + chr6_3:91637671-91637690 None:intergenic 60.0%
Chromosome Type Strat End Strand Name
chr6_3 gene 91636963 91637784 91636963 ID=Msa0964710;Name=Msa0964710
chr6_3 mRNA 91636963 91637784 91636963 ID=Msa0964710-mRNA-1;Parent=Msa0964710;Name=Msa0964710-mRNA-1;_AED=0.11;_eAED=0.11;_QI=0|1|0.5|1|1|1|2|293|141
chr6_3 exon 91636963 91637350 91636963 ID=Msa0964710-mRNA-1:exon:16603;Parent=Msa0964710-mRNA-1
chr6_3 exon 91637454 91637784 91637454 ID=Msa0964710-mRNA-1:exon:16602;Parent=Msa0964710-mRNA-1
chr6_3 CDS 91637454 91637784 91637454 ID=Msa0964710-mRNA-1:cds;Parent=Msa0964710-mRNA-1
chr6_3 CDS 91637256 91637350 91637256 ID=Msa0964710-mRNA-1:cds;Parent=Msa0964710-mRNA-1
chr6_3 three_prime_UTR 91636963 91637255 91636963 ID=Msa0964710-mRNA-1:three_prime_utr;Parent=Msa0964710-mRNA-1
Gene Sequence

>Msa0964710

TTGTACAGCAATAATTCTCCTACAAAGAGAGCTTTAATAGTCAATTTACAATTTCGAGAACCTACACTCAATACATATTCCGATGGTGCGAAGATAAAAAGTTTGCTAATAAATCGTGGATTTAAAGATGAAAATATTGATTATTGGCAAGACAGAAACGATGGAGGACCTGGTTTCCTTATTGATGCTGACAAAATACGTAATAGATTACATGATTTAATTACCATATCAAAGCCAGGTGATACTTTATTTTTTCACTTCAGTGGACATGGTAACTATCAACAAAGAGGGAGAAGTTACCTTGTTGCAGCCAATGGAACTCCTTTACTTGGTTGTGAATTTAAAAAAGTGTTAGACCAAATGGCTGACGGCGTCAAGATAATTTTCATGATTGATGCTTGTTACGGAGGGGGTTTATTGAACTAG
Protein sequence

>Msa0964710

LYSNNSPTKRALIVNLQFREPTLNTYSDGAKIKSLLINRGFKDENIDYWQDRNDGGPGFLIDADKIRNRLHDLITISKPGDTLFFHFSGHGNYQQRGRSYLVAANGTPLLGCEFKKVLDQMADGVKIIFMIDACYGGGLLN*