AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1168580


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 156 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TGTACAACTAGTGGCATAAA+TGG 0.276171 7_4:-61271904 Msa1168580:CDS
TGCTTACACGAAAAGGGTTC+TGG 0.324747 7_4:-61271203 Msa1168580:CDS
ACTACATTCAACACATCTAA+TGG 0.405290 7_4:+61272192 None:intergenic
AGATGTTTGCTTACACGAAA+AGG 0.412363 7_4:-61271210 Msa1168580:CDS
CGAAAAGGGTTCTGGATTGT+CGG 0.442985 7_4:-61271195 Msa1168580:CDS
TGTGAAATGTTTCTTCTTGA+AGG 0.457821 7_4:-61271046 Msa1168580:CDS
GATGTTTGCTTACACGAAAA+GGG 0.458466 7_4:-61271209 Msa1168580:CDS
GATGTTTGTGTACATGCAAA+GGG 0.475084 7_4:-61271160 Msa1168580:CDS
GTGAAATGTTTCTTCTTGAA+GGG 0.492918 7_4:-61271045 Msa1168580:CDS
AGATGTTTGTGTACATGCAA+AGG 0.512617 7_4:-61271161 Msa1168580:CDS
TCTTGTGTATATTCTAAATG+AGG 0.516413 7_4:-61272148 Msa1168580:CDS
GAATACTATAGTCTTCCTAC+TGG 0.533058 7_4:-61271074 Msa1168580:CDS
GTTGAATGTAGTTCGCCTCA+AGG 0.596310 7_4:-61272181 Msa1168580:CDS
TTCAACTGAAGAAGATCAGA+GGG 0.602091 7_4:-61271137 Msa1168580:CDS
ATGTACAAGTGTACAACTAG+TGG 0.638951 7_4:-61271913 Msa1168580:intron
GTTCAACTGAAGAAGATCAG+AGG 0.645723 7_4:-61271138 Msa1168580:CDS
ACATTTCACATACAACCAGT+AGG 0.664111 7_4:+61271059 None:intergenic
GGACATCATCTACAAGAACA+AGG 0.666572 7_4:-61271883 Msa1168580:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TTTATTTCATTGTTGTTAAA+TGG - chr7_4:61271667-61271686 Msa1168580:intron 15.0%
!!! ATATTTTGTTATAACATCAA+TGG - chr7_4:61271919-61271938 Msa1168580:intron 15.0%
!!! TATTTTGTTATAACATCAAT+GGG - chr7_4:61271920-61271939 Msa1168580:intron 15.0%
!!! TTTATTTCATTGTTGTTAAA+TGG - chr7_4:61271667-61271686 Msa1168580:intron 15.0%
!!! ATATTTTGTTATAACATCAA+TGG - chr7_4:61271919-61271938 Msa1168580:intron 15.0%
!!! TATTTTGTTATAACATCAAT+GGG - chr7_4:61271920-61271939 Msa1168580:intron 15.0%
!!! TTCAAGTTGATAACAAAATT+AGG - chr7_4:61271585-61271604 Msa1168580:intron 20.0%
!!! TCAAGTTGATAACAAAATTA+GGG - chr7_4:61271586-61271605 Msa1168580:intron 20.0%
!! AAATTAGGGATATATATTCT+AGG - chr7_4:61271600-61271619 Msa1168580:intron 20.0%
!!! TTCAAGTTGATAACAAAATT+AGG - chr7_4:61271585-61271604 Msa1168580:intron 20.0%
!!! TCAAGTTGATAACAAAATTA+GGG - chr7_4:61271586-61271605 Msa1168580:intron 20.0%
!! AAATTAGGGATATATATTCT+AGG - chr7_4:61271600-61271619 Msa1168580:intron 20.0%
! TCTTGTGTATATTCTAAATG+AGG - chr7_4:61271068-61271087 Msa1168580:CDS 25.0%
! TTTCTCAAACCTTGTAATTT+GGG + chr7_4:61271175-61271194 None:intergenic 25.0%
! ATTTCTCAAACCTTGTAATT+TGG + chr7_4:61271176-61271195 None:intergenic 25.0%
!!! TTTTTAGAAAGTGTTCATTC+AGG - chr7_4:61271407-61271426 Msa1168580:intron 25.0%
!! ATTTCATTGTTGTTAAATGG+CGG - chr7_4:61271670-61271689 Msa1168580:intron 25.0%
! TCTTGTGTATATTCTAAATG+AGG - chr7_4:61271068-61271087 Msa1168580:CDS 25.0%
! TTTCTCAAACCTTGTAATTT+GGG + chr7_4:61271175-61271194 None:intergenic 25.0%
! ATTTCTCAAACCTTGTAATT+TGG + chr7_4:61271176-61271195 None:intergenic 25.0%
!!! TTTTTAGAAAGTGTTCATTC+AGG - chr7_4:61271407-61271426 Msa1168580:intron 25.0%
!! ATTTCATTGTTGTTAAATGG+CGG - chr7_4:61271670-61271689 Msa1168580:intron 25.0%
ACTACATTCAACACATCTAA+TGG + chr7_4:61271027-61271046 None:intergenic 30.0%
CGACAAACAAAAATGCTATA+GGG + chr7_4:61271264-61271283 None:intergenic 30.0%
!! CCTATAGCATTTTTGTTTGT+CGG - chr7_4:61271262-61271281 Msa1168580:intron 30.0%
TATGTATAGAATCATCTTGC+AGG - chr7_4:61271498-61271517 Msa1168580:intron 30.0%
ATGTATAGAATCATCTTGCA+GGG - chr7_4:61271499-61271518 Msa1168580:intron 30.0%
CAACAATGAATTTCAACACT+TGG + chr7_4:61271635-61271654 None:intergenic 30.0%
! GTGTTTATATGGTGTACTTT+TGG - chr7_4:61271786-61271805 Msa1168580:intron 30.0%
TAGTAATCAGAGTCAAAACT+TGG - chr7_4:61271867-61271886 Msa1168580:CDS 30.0%
TTTCCTTTAACTCATAGCTT+TGG - chr7_4:61271962-61271981 Msa1168580:intron 30.0%
TTCCTTTAACTCATAGCTTT+GGG - chr7_4:61271963-61271982 Msa1168580:intron 30.0%
TGTGAAATGTTTCTTCTTGA+AGG - chr7_4:61272170-61272189 Msa1168580:CDS 30.0%
GTGAAATGTTTCTTCTTGAA+GGG - chr7_4:61272171-61272190 Msa1168580:CDS 30.0%
ACTACATTCAACACATCTAA+TGG + chr7_4:61271027-61271046 None:intergenic 30.0%
CGACAAACAAAAATGCTATA+GGG + chr7_4:61271264-61271283 None:intergenic 30.0%
!! CCTATAGCATTTTTGTTTGT+CGG - chr7_4:61271262-61271281 Msa1168580:intron 30.0%
TATGTATAGAATCATCTTGC+AGG - chr7_4:61271498-61271517 Msa1168580:intron 30.0%
ATGTATAGAATCATCTTGCA+GGG - chr7_4:61271499-61271518 Msa1168580:intron 30.0%
CAACAATGAATTTCAACACT+TGG + chr7_4:61271635-61271654 None:intergenic 30.0%
! GTGTTTATATGGTGTACTTT+TGG - chr7_4:61271786-61271805 Msa1168580:intron 30.0%
TAGTAATCAGAGTCAAAACT+TGG - chr7_4:61271867-61271886 Msa1168580:CDS 30.0%
TTTCCTTTAACTCATAGCTT+TGG - chr7_4:61271962-61271981 Msa1168580:intron 30.0%
TTCCTTTAACTCATAGCTTT+GGG - chr7_4:61271963-61271982 Msa1168580:intron 30.0%
TGTGAAATGTTTCTTCTTGA+AGG - chr7_4:61272170-61272189 Msa1168580:CDS 30.0%
GTGAAATGTTTCTTCTTGAA+GGG - chr7_4:61272171-61272190 Msa1168580:CDS 30.0%
!!! CAAGAACTATTTTAGCCTTG+AGG + chr7_4:61271053-61271072 None:intergenic 35.0%
! TGATTTTTCTCCATGCAACA+TGG - chr7_4:61271211-61271230 Msa1168580:CDS 35.0%
ACATAAAACTCCATGTTGCA+TGG + chr7_4:61271224-61271243 None:intergenic 35.0%
CCGACAAACAAAAATGCTAT+AGG + chr7_4:61271265-61271284 None:intergenic 35.0%
ATGTACAAGTGTACAACTAG+TGG - chr7_4:61271303-61271322 Msa1168580:intron 35.0%
TGTACAACTAGTGGCATAAA+TGG - chr7_4:61271312-61271331 Msa1168580:intron 35.0%
CTTTGACAGAATTTGACTGA+TGG - chr7_4:61271556-61271575 Msa1168580:intron 35.0%
! TCCTTTAACTCATAGCTTTG+GGG - chr7_4:61271964-61271983 Msa1168580:intron 35.0%
AGATGTTTGCTTACACGAAA+AGG - chr7_4:61272006-61272025 Msa1168580:intron 35.0%
GATGTTTGCTTACACGAAAA+GGG - chr7_4:61272007-61272026 Msa1168580:intron 35.0%
AGATGTTTGTGTACATGCAA+AGG - chr7_4:61272055-61272074 Msa1168580:intron 35.0%
GATGTTTGTGTACATGCAAA+GGG - chr7_4:61272056-61272075 Msa1168580:intron 35.0%
TTCAACTGAAGAAGATCAGA+GGG - chr7_4:61272079-61272098 Msa1168580:intron 35.0%
GAATACTATAGTCTTCCTAC+TGG - chr7_4:61272142-61272161 Msa1168580:CDS 35.0%
ACATTTCACATACAACCAGT+AGG + chr7_4:61272160-61272179 None:intergenic 35.0%
!!! CAAGAACTATTTTAGCCTTG+AGG + chr7_4:61271053-61271072 None:intergenic 35.0%
! TGATTTTTCTCCATGCAACA+TGG - chr7_4:61271211-61271230 Msa1168580:CDS 35.0%
ACATAAAACTCCATGTTGCA+TGG + chr7_4:61271224-61271243 None:intergenic 35.0%
CCGACAAACAAAAATGCTAT+AGG + chr7_4:61271265-61271284 None:intergenic 35.0%
ATGTACAAGTGTACAACTAG+TGG - chr7_4:61271303-61271322 Msa1168580:intron 35.0%
TGTACAACTAGTGGCATAAA+TGG - chr7_4:61271312-61271331 Msa1168580:intron 35.0%
CTTTGACAGAATTTGACTGA+TGG - chr7_4:61271556-61271575 Msa1168580:intron 35.0%
! TCCTTTAACTCATAGCTTTG+GGG - chr7_4:61271964-61271983 Msa1168580:intron 35.0%
AGATGTTTGCTTACACGAAA+AGG - chr7_4:61272006-61272025 Msa1168580:intron 35.0%
GATGTTTGCTTACACGAAAA+GGG - chr7_4:61272007-61272026 Msa1168580:intron 35.0%
AGATGTTTGTGTACATGCAA+AGG - chr7_4:61272055-61272074 Msa1168580:intron 35.0%
GATGTTTGTGTACATGCAAA+GGG - chr7_4:61272056-61272075 Msa1168580:intron 35.0%
TTCAACTGAAGAAGATCAGA+GGG - chr7_4:61272079-61272098 Msa1168580:intron 35.0%
GAATACTATAGTCTTCCTAC+TGG - chr7_4:61272142-61272161 Msa1168580:CDS 35.0%
ACATTTCACATACAACCAGT+AGG + chr7_4:61272160-61272179 None:intergenic 35.0%
AAATAGCGCACACAATGTGT+TGG - chr7_4:61271125-61271144 Msa1168580:CDS 40.0%
GTCTGTAGTCCCAAATTACA+AGG - chr7_4:61271163-61271182 Msa1168580:CDS 40.0%
GGACATCATCTACAAGAACA+AGG - chr7_4:61271333-61271352 Msa1168580:intron 40.0%
! TACCAACATCTTTTGCCGAA+AGG - chr7_4:61271460-61271479 Msa1168580:intron 40.0%
CAGCAAACAAAGAAGCCTTT+CGG + chr7_4:61271478-61271497 None:intergenic 40.0%
ACCATATAAACACGCCATTG+TGG + chr7_4:61271779-61271798 None:intergenic 40.0%
AACTAAACCAGTGTTGTCGA+TGG + chr7_4:61271826-61271845 None:intergenic 40.0%
AAACTTGGATGCTCTCTGTT+TGG - chr7_4:61271882-61271901 Msa1168580:CDS 40.0%
TCCCCAAAGCTATGAGTTAA+AGG + chr7_4:61271968-61271987 None:intergenic 40.0%
GTTCAACTGAAGAAGATCAG+AGG - chr7_4:61272078-61272097 Msa1168580:intron 40.0%
AAATAGCGCACACAATGTGT+TGG - chr7_4:61271125-61271144 Msa1168580:CDS 40.0%
GTCTGTAGTCCCAAATTACA+AGG - chr7_4:61271163-61271182 Msa1168580:CDS 40.0%
GGACATCATCTACAAGAACA+AGG - chr7_4:61271333-61271352 Msa1168580:intron 40.0%
! TACCAACATCTTTTGCCGAA+AGG - chr7_4:61271460-61271479 Msa1168580:intron 40.0%
CAGCAAACAAAGAAGCCTTT+CGG + chr7_4:61271478-61271497 None:intergenic 40.0%
ACCATATAAACACGCCATTG+TGG + chr7_4:61271779-61271798 None:intergenic 40.0%
AACTAAACCAGTGTTGTCGA+TGG + chr7_4:61271826-61271845 None:intergenic 40.0%
AAACTTGGATGCTCTCTGTT+TGG - chr7_4:61271882-61271901 Msa1168580:CDS 40.0%
TCCCCAAAGCTATGAGTTAA+AGG + chr7_4:61271968-61271987 None:intergenic 40.0%
GTTCAACTGAAGAAGATCAG+AGG - chr7_4:61272078-61272097 Msa1168580:intron 40.0%
GTTGAATGTAGTTCGCCTCA+AGG - chr7_4:61271035-61271054 Msa1168580:CDS 45.0%
! GCACACAATGTGTTGGTGAA+TGG - chr7_4:61271132-61271151 Msa1168580:CDS 45.0%
AGCCTTTCGGCAAAAGATGT+TGG + chr7_4:61271465-61271484 None:intergenic 45.0%
! TTGTTGTTAAATGGCGGCCA+AGG - chr7_4:61271676-61271695 Msa1168580:intron 45.0%
TGACAGTTCCCACATGCAAT+TGG - chr7_4:61271720-61271739 Msa1168580:intron 45.0%
GCCACAATGGCGTGTTTATA+TGG - chr7_4:61271775-61271794 Msa1168580:intron 45.0%
TAAACCAGTGTTGTCGATGG+CGG + chr7_4:61271823-61271842 None:intergenic 45.0%
!! CTCATAGCTTTGGGGATTGT+CGG - chr7_4:61271972-61271991 Msa1168580:intron 45.0%
TGCTTACACGAAAAGGGTTC+TGG - chr7_4:61272013-61272032 Msa1168580:intron 45.0%
!! CGAAAAGGGTTCTGGATTGT+CGG - chr7_4:61272021-61272040 Msa1168580:intron 45.0%
GTTGAATGTAGTTCGCCTCA+AGG - chr7_4:61271035-61271054 Msa1168580:CDS 45.0%
! GCACACAATGTGTTGGTGAA+TGG - chr7_4:61271132-61271151 Msa1168580:CDS 45.0%
AGCCTTTCGGCAAAAGATGT+TGG + chr7_4:61271465-61271484 None:intergenic 45.0%
! TTGTTGTTAAATGGCGGCCA+AGG - chr7_4:61271676-61271695 Msa1168580:intron 45.0%
TGACAGTTCCCACATGCAAT+TGG - chr7_4:61271720-61271739 Msa1168580:intron 45.0%
GCCACAATGGCGTGTTTATA+TGG - chr7_4:61271775-61271794 Msa1168580:intron 45.0%
TAAACCAGTGTTGTCGATGG+CGG + chr7_4:61271823-61271842 None:intergenic 45.0%
!! CTCATAGCTTTGGGGATTGT+CGG - chr7_4:61271972-61271991 Msa1168580:intron 45.0%
TGCTTACACGAAAAGGGTTC+TGG - chr7_4:61272013-61272032 Msa1168580:intron 45.0%
!! CGAAAAGGGTTCTGGATTGT+CGG - chr7_4:61272021-61272040 Msa1168580:intron 45.0%
TTGTTAAATGGCGGCCAAGG+TGG - chr7_4:61271679-61271698 Msa1168580:intron 50.0%
TCCACCACACTATTCCACCT+TGG + chr7_4:61271696-61271715 None:intergenic 50.0%
CAGTTCCCACATGCAATTGG+TGG - chr7_4:61271723-61271742 Msa1168580:intron 50.0%
TTCCCACATGCAATTGGTGG+AGG - chr7_4:61271726-61271745 Msa1168580:intron 50.0%
TCCCACATGCAATTGGTGGA+GGG - chr7_4:61271727-61271746 Msa1168580:intron 50.0%
TCCCTCCACCAATTGCATGT+GGG + chr7_4:61271731-61271750 None:intergenic 50.0%
ATCCCTCCACCAATTGCATG+TGG + chr7_4:61271732-61271751 None:intergenic 50.0%
AACACGCCATTGTGGCCTAT+GGG + chr7_4:61271771-61271790 None:intergenic 50.0%
AAACACGCCATTGTGGCCTA+TGG + chr7_4:61271772-61271791 None:intergenic 50.0%
CTTGGATGCTCTCTGTTTGG+TGG - chr7_4:61271885-61271904 Msa1168580:CDS 50.0%
TTGTTAAATGGCGGCCAAGG+TGG - chr7_4:61271679-61271698 Msa1168580:intron 50.0%
TCCACCACACTATTCCACCT+TGG + chr7_4:61271696-61271715 None:intergenic 50.0%
CAGTTCCCACATGCAATTGG+TGG - chr7_4:61271723-61271742 Msa1168580:intron 50.0%
TTCCCACATGCAATTGGTGG+AGG - chr7_4:61271726-61271745 Msa1168580:intron 50.0%
TCCCACATGCAATTGGTGGA+GGG - chr7_4:61271727-61271746 Msa1168580:intron 50.0%
TCCCTCCACCAATTGCATGT+GGG + chr7_4:61271731-61271750 None:intergenic 50.0%
ATCCCTCCACCAATTGCATG+TGG + chr7_4:61271732-61271751 None:intergenic 50.0%
AACACGCCATTGTGGCCTAT+GGG + chr7_4:61271771-61271790 None:intergenic 50.0%
AAACACGCCATTGTGGCCTA+TGG + chr7_4:61271772-61271791 None:intergenic 50.0%
CTTGGATGCTCTCTGTTTGG+TGG - chr7_4:61271885-61271904 Msa1168580:CDS 50.0%
GCCAAGGTGGAATAGTGTGG+TGG - chr7_4:61271692-61271711 Msa1168580:intron 55.0%
!! TGTCGATGGCGGATGGTGAA+AGG + chr7_4:61271812-61271831 None:intergenic 55.0%
GCCAAGGTGGAATAGTGTGG+TGG - chr7_4:61271692-61271711 Msa1168580:intron 55.0%
!! TGTCGATGGCGGATGGTGAA+AGG + chr7_4:61271812-61271831 None:intergenic 55.0%
GCGGCCAAGGTGGAATAGTG+TGG - chr7_4:61271689-61271708 Msa1168580:intron 60.0%
TGGTGGAGGGATGCCTGCAA+TGG - chr7_4:61271740-61271759 Msa1168580:intron 60.0%
TGGAGGGATGCCTGCAATGG+CGG - chr7_4:61271743-61271762 Msa1168580:intron 60.0%
!! CCAGTGTTGTCGATGGCGGA+TGG + chr7_4:61271819-61271838 None:intergenic 60.0%
CCATCCGCCATCGACAACAC+TGG - chr7_4:61271816-61271835 Msa1168580:intron 60.0%
GCGGCCAAGGTGGAATAGTG+TGG - chr7_4:61271689-61271708 Msa1168580:intron 60.0%
TGGTGGAGGGATGCCTGCAA+TGG - chr7_4:61271740-61271759 Msa1168580:intron 60.0%
TGGAGGGATGCCTGCAATGG+CGG - chr7_4:61271743-61271762 Msa1168580:intron 60.0%
!! CCAGTGTTGTCGATGGCGGA+TGG + chr7_4:61271819-61271838 None:intergenic 60.0%
CCATCCGCCATCGACAACAC+TGG - chr7_4:61271816-61271835 Msa1168580:intron 60.0%
! CCTATGGGCACCGCCATTGC+AGG + chr7_4:61271756-61271775 None:intergenic 65.0%
CCTGCAATGGCGGTGCCCAT+AGG - chr7_4:61271753-61271772 Msa1168580:intron 65.0%
GCGGTGCCCATAGGCCACAA+TGG - chr7_4:61271762-61271781 Msa1168580:intron 65.0%
! CCTATGGGCACCGCCATTGC+AGG + chr7_4:61271756-61271775 None:intergenic 65.0%
CCTGCAATGGCGGTGCCCAT+AGG - chr7_4:61271753-61271772 Msa1168580:intron 65.0%
GCGGTGCCCATAGGCCACAA+TGG - chr7_4:61271762-61271781 Msa1168580:intron 65.0%
Chromosome Type Strat End Strand Name
chr7_4 gene 61271021 61272217 61271021 ID=Msa1168580;Name=Msa1168580
chr7_4 mRNA 61271021 61272217 61271021 ID=Msa1168580-mRNA-1;Parent=Msa1168580;Name=Msa1168580-mRNA-1;_AED=0.88;_eAED=0.88;_QI=0|0|0|0.33|1|1|3|0|123
chr7_4 exon 61272137 61272217 61272137 ID=Msa1168580-mRNA-1:exon:19373;Parent=Msa1168580-mRNA-1
chr7_4 exon 61271846 61271926 61271846 ID=Msa1168580-mRNA-1:exon:19372;Parent=Msa1168580-mRNA-1
chr7_4 exon 61271021 61271230 61271021 ID=Msa1168580-mRNA-1:exon:19371;Parent=Msa1168580-mRNA-1
chr7_4 CDS 61272137 61272217 61272137 ID=Msa1168580-mRNA-1:cds;Parent=Msa1168580-mRNA-1
chr7_4 CDS 61271846 61271926 61271846 ID=Msa1168580-mRNA-1:cds;Parent=Msa1168580-mRNA-1
chr7_4 CDS 61271021 61271230 61271021 ID=Msa1168580-mRNA-1:cds;Parent=Msa1168580-mRNA-1
Gene Sequence

>Msa1168580

ATGCCATTAGATGTGTTGAATGTAGTTCGCCTCAAGGCTAAAATAGTTCTTGTGTATATTCTAAATGAGGATGCTTCATATTGTACAACTAGTGGCATAAATGGACATCATCTACAAGAACAAGGAAATGCACTTGAATCTGCAAGAACTTGCAAAATTGTTATGTTTGCTTACACGAAAAGGGTTCTGGATTGTCGGTTTTCATGTATAGATGTTTGTGTACATGCAAAGGGTTCAACTGAAGAAGATCAGAGGGATATAAACAGTGTGCAAATGAATCTTGATTTCAGTTTAATGAATACTATAGTCTTCCTACTGGTTGTATGTGAAATGTTTCTTCTTGAAGGGATAAATGTAGTATACTATTATTAA

Protein sequence

>Msa1168580

MPLDVLNVVRLKAKIVLVYILNEDASYCTTSGINGHHLQEQGNALESARTCKIVMFAYTKRVLDCRFSCIDVCVHAKGSTEEDQRDINSVQMNLDFSLMNTIVFLLVVCEMFLLEGINVVYYY*