AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0485780


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0485780 MtrunA17_Chr4g0002051 50.286 175 85 1 1 173 142 316 1.51e-54 175
Msa0485780 MtrunA17_Chr8g0381471 48.837 172 86 1 4 173 1 172 1.19e-53 168
Msa0485780 MtrunA17_Chr2g0287671 35.862 145 81 5 12 152 272 408 8.68e-22 91.3
Msa0485780 MtrunA17_Chr8g0361701 32.061 131 81 3 1 130 119 242 6.02e-16 73.2
Msa0485780 MtrunA17_Chr8g0349191 31.818 110 72 2 75 181 1 110 3.34e-12 60.5
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 38 sgRNAs with CRISPR-Local

Find 102 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CCTTGACGTCCCAAACCTTT+TGG 0.174160 3_4:+3587479 None:intergenic
AACTGTTTCATTTGCCAAAA+TGG 0.193914 3_4:+3587939 None:intergenic
CATAAGCAAGATTTCATTAA+AGG 0.220107 3_4:-3587121 Msa0485780:CDS
TTTGATGTTGGCAAAGTCTT+TGG 0.263575 3_4:-3587146 Msa0485780:CDS
TGTCGTGGAATTCACCATTT+TGG 0.264921 3_4:-3587953 Msa0485780:CDS
GTTGTTTCAGGCTATGTTTA+TGG 0.272519 3_4:-3587582 Msa0485780:intron
TAGGAATGATTGTGCGGTTT+GGG 0.307093 3_4:-3587373 Msa0485780:CDS
AATAGTCACCCCAAAAGGTT+TGG 0.336042 3_4:-3587489 Msa0485780:CDS
TCATCTACACTGGTTCCTTT+TGG 0.345121 3_4:-3587771 Msa0485780:CDS
GTGCGGTTTGGGTAATTAAC+TGG 0.355704 3_4:-3587362 Msa0485780:CDS
GTTTATGGAGGAGTTCTTGA+TGG 0.373775 3_4:-3587567 Msa0485780:CDS
CGTGAAGCACCGACGAACTT+TGG 0.382229 3_4:+3587705 None:intergenic
TTAGGAATGATTGTGCGGTT+TGG 0.432957 3_4:-3587374 Msa0485780:intron
CAGTGTAGATGATCATATAT+TGG 0.446763 3_4:+3587782 None:intergenic
TTTAAAATAGTCACCCCAAA+AGG 0.463204 3_4:-3587494 Msa0485780:CDS
CAAAGTTCGTCGGTGCTTCA+CGG 0.486634 3_4:-3587704 Msa0485780:CDS
TTGATGGATCCATCTTTCCA+TGG 0.492954 3_4:-3587551 Msa0485780:CDS
ATAGTCACCCCAAAAGGTTT+GGG 0.495339 3_4:-3587488 Msa0485780:CDS
AAATCTCTCTTGTCGTTGAA+AGG 0.515792 3_4:+3587166 None:intergenic
GGTTTGGGACGTCAAGGGGA+TGG 0.517176 3_4:-3587473 Msa0485780:CDS
GAATCAGTGCCATGGAAAGA+TGG 0.518164 3_4:+3587542 None:intergenic
TCACAAAGTCAATAACCAAA+AGG 0.520836 3_4:+3587756 None:intergenic
ATGATGCAACGTGGAGAGAA+TGG 0.542299 3_4:-3587339 Msa0485780:CDS
GTTTCAGGCTATGTTTATGG+AGG 0.543768 3_4:-3587579 Msa0485780:intron
CCAAAAGGTTTGGGACGTCA+AGG 0.551652 3_4:-3587479 Msa0485780:CDS
CAAAAGGTTTGGGACGTCAA+GGG 0.561039 3_4:-3587478 Msa0485780:CDS
GTTCGTCGGTGCTTCACGGA+AGG 0.563242 3_4:-3587700 Msa0485780:CDS
AAAAGGTTTGGGACGTCAAG+GGG 0.574712 3_4:-3587477 Msa0485780:CDS
CATTAAAGGATATGATTCAG+AGG 0.576591 3_4:-3587107 Msa0485780:CDS
TTTAGCGATATGTGCTGTCG+TGG 0.583539 3_4:-3587968 None:intergenic
CGACAAGAGAGATTTGATGT+TGG 0.587936 3_4:-3587158 Msa0485780:CDS
CATAGTTTGAATCAGTGCCA+TGG 0.596462 3_4:+3587534 None:intergenic
ATTTATGGGAAATGCTGATG+TGG 0.609698 3_4:-3587904 Msa0485780:CDS
AAATGCTGATGTGGTTTCAA+AGG 0.609916 3_4:-3587895 Msa0485780:intron
CAATATATGATCATCTACAC+TGG 0.632704 3_4:-3587781 Msa0485780:CDS
TTATGCAAACAGGTGGACGA+AGG 0.671354 3_4:-3587226 Msa0485780:intron
TGACTCGTACCAAAGTTCGT+CGG 0.721179 3_4:-3587714 Msa0485780:CDS
ATTAACTGGATGATGCAACG+TGG 0.737445 3_4:-3587348 Msa0485780:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TAATGATTAAATTTTGTTTT+AGG - chr3_4:3587670-3587689 Msa0485780:intron 10.0%
!!! TAATGATTAAATTTTGTTTT+AGG - chr3_4:3587670-3587689 Msa0485780:intron 10.0%
!! TCTAATTAAATAATACATAG+TGG + chr3_4:3587626-3587645 None:intergenic 15.0%
!! TCTAATTAAATAATACATAG+TGG + chr3_4:3587626-3587645 None:intergenic 15.0%
!! TTCTACCAAAAAGAATTTAT+GGG - chr3_4:3587144-3587163 Msa0485780:CDS 20.0%
!! GATATCAAGTATCAAAAAAT+TGG - chr3_4:3587384-3587403 Msa0485780:intron 20.0%
!!! TGCAATTTCATTACATTTTA+TGG - chr3_4:3587786-3587805 Msa0485780:CDS 20.0%
!! TTCTACCAAAAAGAATTTAT+GGG - chr3_4:3587144-3587163 Msa0485780:CDS 20.0%
!! GATATCAAGTATCAAAAAAT+TGG - chr3_4:3587384-3587403 Msa0485780:intron 20.0%
!!! TGCAATTTCATTACATTTTA+TGG - chr3_4:3587786-3587805 Msa0485780:CDS 20.0%
! GTTCTACCAAAAAGAATTTA+TGG - chr3_4:3587143-3587162 Msa0485780:CDS 25.0%
!! CATTTCCCATAAATTCTTTT+TGG + chr3_4:3587152-3587171 None:intergenic 25.0%
! CATAAGCAAGATTTCATTAA+AGG - chr3_4:3587941-3587960 Msa0485780:CDS 25.0%
! GTTCTACCAAAAAGAATTTA+TGG - chr3_4:3587143-3587162 Msa0485780:CDS 25.0%
!! CATTTCCCATAAATTCTTTT+TGG + chr3_4:3587152-3587171 None:intergenic 25.0%
! CATAAGCAAGATTTCATTAA+AGG - chr3_4:3587941-3587960 Msa0485780:CDS 25.0%
AACTGTTTCATTTGCCAAAA+TGG + chr3_4:3587126-3587145 None:intergenic 30.0%
CAGTGTAGATGATCATATAT+TGG + chr3_4:3587283-3587302 None:intergenic 30.0%
CAATATATGATCATCTACAC+TGG - chr3_4:3587281-3587300 Msa0485780:intron 30.0%
TCACAAAGTCAATAACCAAA+AGG + chr3_4:3587309-3587328 None:intergenic 30.0%
!! CAAATTTCAAGTGTTGTTTC+AGG - chr3_4:3587468-3587487 Msa0485780:intron 30.0%
! TTTAAAATAGTCACCCCAAA+AGG - chr3_4:3587568-3587587 Msa0485780:CDS 30.0%
!!! TTGTTTTAGGAATGATTGTG+CGG - chr3_4:3587683-3587702 Msa0485780:CDS 30.0%
TTTAGCCAAATTATGCAAAC+AGG - chr3_4:3587826-3587845 Msa0485780:intron 30.0%
CATTAAAGGATATGATTCAG+AGG - chr3_4:3587955-3587974 Msa0485780:CDS 30.0%
AACTGTTTCATTTGCCAAAA+TGG + chr3_4:3587126-3587145 None:intergenic 30.0%
CAGTGTAGATGATCATATAT+TGG + chr3_4:3587283-3587302 None:intergenic 30.0%
CAATATATGATCATCTACAC+TGG - chr3_4:3587281-3587300 Msa0485780:intron 30.0%
TCACAAAGTCAATAACCAAA+AGG + chr3_4:3587309-3587328 None:intergenic 30.0%
!! CAAATTTCAAGTGTTGTTTC+AGG - chr3_4:3587468-3587487 Msa0485780:intron 30.0%
! TTTAAAATAGTCACCCCAAA+AGG - chr3_4:3587568-3587587 Msa0485780:CDS 30.0%
!!! TTGTTTTAGGAATGATTGTG+CGG - chr3_4:3587683-3587702 Msa0485780:CDS 30.0%
TTTAGCCAAATTATGCAAAC+AGG - chr3_4:3587826-3587845 Msa0485780:intron 30.0%
CATTAAAGGATATGATTCAG+AGG - chr3_4:3587955-3587974 Msa0485780:CDS 30.0%
ATTTATGGGAAATGCTGATG+TGG - chr3_4:3587158-3587177 Msa0485780:CDS 35.0%
AAATGCTGATGTGGTTTCAA+AGG - chr3_4:3587167-3587186 Msa0485780:CDS 35.0%
! GTTGTTTCAGGCTATGTTTA+TGG - chr3_4:3587480-3587499 Msa0485780:CDS 35.0%
AAATCTCTCTTGTCGTTGAA+AGG + chr3_4:3587899-3587918 None:intergenic 35.0%
TTTGATGTTGGCAAAGTCTT+TGG - chr3_4:3587916-3587935 Msa0485780:CDS 35.0%
ATTTATGGGAAATGCTGATG+TGG - chr3_4:3587158-3587177 Msa0485780:CDS 35.0%
AAATGCTGATGTGGTTTCAA+AGG - chr3_4:3587167-3587186 Msa0485780:CDS 35.0%
! GTTGTTTCAGGCTATGTTTA+TGG - chr3_4:3587480-3587499 Msa0485780:CDS 35.0%
AAATCTCTCTTGTCGTTGAA+AGG + chr3_4:3587899-3587918 None:intergenic 35.0%
TTTGATGTTGGCAAAGTCTT+TGG - chr3_4:3587916-3587935 Msa0485780:CDS 35.0%
! TGTCGTGGAATTCACCATTT+TGG - chr3_4:3587109-3587128 Msa0485780:CDS 40.0%
!!! TCATCTACACTGGTTCCTTT+TGG - chr3_4:3587291-3587310 Msa0485780:intron 40.0%
GTTTCAGGCTATGTTTATGG+AGG - chr3_4:3587483-3587502 Msa0485780:CDS 40.0%
GTTTATGGAGGAGTTCTTGA+TGG - chr3_4:3587495-3587514 Msa0485780:CDS 40.0%
! TTGATGGATCCATCTTTCCA+TGG - chr3_4:3587511-3587530 Msa0485780:CDS 40.0%
CATAGTTTGAATCAGTGCCA+TGG + chr3_4:3587531-3587550 None:intergenic 40.0%
AATAGTCACCCCAAAAGGTT+TGG - chr3_4:3587573-3587592 Msa0485780:CDS 40.0%
ATAGTCACCCCAAAAGGTTT+GGG - chr3_4:3587574-3587593 Msa0485780:CDS 40.0%
TTAGGAATGATTGTGCGGTT+TGG - chr3_4:3587688-3587707 Msa0485780:CDS 40.0%
TAGGAATGATTGTGCGGTTT+GGG - chr3_4:3587689-3587708 Msa0485780:CDS 40.0%
ATTAACTGGATGATGCAACG+TGG - chr3_4:3587714-3587733 Msa0485780:CDS 40.0%
AGCCAAATTATGCAAACAGG+TGG - chr3_4:3587829-3587848 Msa0485780:intron 40.0%
GTCCACCTGTTTGCATAATT+TGG + chr3_4:3587834-3587853 None:intergenic 40.0%
CGACAAGAGAGATTTGATGT+TGG - chr3_4:3587904-3587923 Msa0485780:CDS 40.0%
! TGTCGTGGAATTCACCATTT+TGG - chr3_4:3587109-3587128 Msa0485780:CDS 40.0%
!!! TCATCTACACTGGTTCCTTT+TGG - chr3_4:3587291-3587310 Msa0485780:intron 40.0%
GTTTCAGGCTATGTTTATGG+AGG - chr3_4:3587483-3587502 Msa0485780:CDS 40.0%
GTTTATGGAGGAGTTCTTGA+TGG - chr3_4:3587495-3587514 Msa0485780:CDS 40.0%
! TTGATGGATCCATCTTTCCA+TGG - chr3_4:3587511-3587530 Msa0485780:CDS 40.0%
CATAGTTTGAATCAGTGCCA+TGG + chr3_4:3587531-3587550 None:intergenic 40.0%
AATAGTCACCCCAAAAGGTT+TGG - chr3_4:3587573-3587592 Msa0485780:CDS 40.0%
ATAGTCACCCCAAAAGGTTT+GGG - chr3_4:3587574-3587593 Msa0485780:CDS 40.0%
TTAGGAATGATTGTGCGGTT+TGG - chr3_4:3587688-3587707 Msa0485780:CDS 40.0%
TAGGAATGATTGTGCGGTTT+GGG - chr3_4:3587689-3587708 Msa0485780:CDS 40.0%
ATTAACTGGATGATGCAACG+TGG - chr3_4:3587714-3587733 Msa0485780:CDS 40.0%
AGCCAAATTATGCAAACAGG+TGG - chr3_4:3587829-3587848 Msa0485780:intron 40.0%
GTCCACCTGTTTGCATAATT+TGG + chr3_4:3587834-3587853 None:intergenic 40.0%
CGACAAGAGAGATTTGATGT+TGG - chr3_4:3587904-3587923 Msa0485780:CDS 40.0%
TGACTCGTACCAAAGTTCGT+CGG - chr3_4:3587348-3587367 Msa0485780:CDS 45.0%
GAATCAGTGCCATGGAAAGA+TGG + chr3_4:3587523-3587542 None:intergenic 45.0%
! TTGACGTCCCAAACCTTTTG+GGG + chr3_4:3587584-3587603 None:intergenic 45.0%
! CTTGACGTCCCAAACCTTTT+GGG + chr3_4:3587585-3587604 None:intergenic 45.0%
! CAAAAGGTTTGGGACGTCAA+GGG - chr3_4:3587584-3587603 Msa0485780:intron 45.0%
! AAAAGGTTTGGGACGTCAAG+GGG - chr3_4:3587585-3587604 Msa0485780:intron 45.0%
! GTGCGGTTTGGGTAATTAAC+TGG - chr3_4:3587700-3587719 Msa0485780:CDS 45.0%
ATGATGCAACGTGGAGAGAA+TGG - chr3_4:3587723-3587742 Msa0485780:CDS 45.0%
TTATGCAAACAGGTGGACGA+AGG - chr3_4:3587836-3587855 Msa0485780:intron 45.0%
TGACTCGTACCAAAGTTCGT+CGG - chr3_4:3587348-3587367 Msa0485780:CDS 45.0%
GAATCAGTGCCATGGAAAGA+TGG + chr3_4:3587523-3587542 None:intergenic 45.0%
! TTGACGTCCCAAACCTTTTG+GGG + chr3_4:3587584-3587603 None:intergenic 45.0%
! CTTGACGTCCCAAACCTTTT+GGG + chr3_4:3587585-3587604 None:intergenic 45.0%
! CAAAAGGTTTGGGACGTCAA+GGG - chr3_4:3587584-3587603 Msa0485780:intron 45.0%
! AAAAGGTTTGGGACGTCAAG+GGG - chr3_4:3587585-3587604 Msa0485780:intron 45.0%
! GTGCGGTTTGGGTAATTAAC+TGG - chr3_4:3587700-3587719 Msa0485780:CDS 45.0%
ATGATGCAACGTGGAGAGAA+TGG - chr3_4:3587723-3587742 Msa0485780:CDS 45.0%
TTATGCAAACAGGTGGACGA+AGG - chr3_4:3587836-3587855 Msa0485780:intron 45.0%
! CAAAGTTCGTCGGTGCTTCA+CGG - chr3_4:3587358-3587377 Msa0485780:CDS 50.0%
! CCTTGACGTCCCAAACCTTT+TGG + chr3_4:3587586-3587605 None:intergenic 50.0%
! CCAAAAGGTTTGGGACGTCA+AGG - chr3_4:3587583-3587602 Msa0485780:intron 50.0%
! CAAAGTTCGTCGGTGCTTCA+CGG - chr3_4:3587358-3587377 Msa0485780:CDS 50.0%
! CCTTGACGTCCCAAACCTTT+TGG + chr3_4:3587586-3587605 None:intergenic 50.0%
! CCAAAAGGTTTGGGACGTCA+AGG - chr3_4:3587583-3587602 Msa0485780:intron 50.0%
!! CGTGAAGCACCGACGAACTT+TGG + chr3_4:3587360-3587379 None:intergenic 55.0%
!! CGTGAAGCACCGACGAACTT+TGG + chr3_4:3587360-3587379 None:intergenic 55.0%
! GTTCGTCGGTGCTTCACGGA+AGG - chr3_4:3587362-3587381 Msa0485780:CDS 60.0%
! GGTTTGGGACGTCAAGGGGA+TGG - chr3_4:3587589-3587608 Msa0485780:intron 60.0%
! GTTCGTCGGTGCTTCACGGA+AGG - chr3_4:3587362-3587381 Msa0485780:CDS 60.0%
! GGTTTGGGACGTCAAGGGGA+TGG - chr3_4:3587589-3587608 Msa0485780:intron 60.0%
Chromosome Type Strat End Strand Name
chr3_4 gene 3587099 3587985 3587099 ID=Msa0485780;Name=Msa0485780
chr3_4 mRNA 3587099 3587985 3587099 ID=Msa0485780-mRNA-1;Parent=Msa0485780;Name=Msa0485780-mRNA-1;_AED=0.19;_eAED=0.19;_QI=0|0|0|0.8|0.5|0.8|5|0|184
chr3_4 exon 3587896 3587985 3587896 ID=Msa0485780-mRNA-1:exon:1328;Parent=Msa0485780-mRNA-1
chr3_4 exon 3587679 3587813 3587679 ID=Msa0485780-mRNA-1:exon:1327;Parent=Msa0485780-mRNA-1
chr3_4 exon 3587470 3587594 3587470 ID=Msa0485780-mRNA-1:exon:1326;Parent=Msa0485780-mRNA-1
chr3_4 exon 3587326 3587392 3587326 ID=Msa0485780-mRNA-1:exon:1325;Parent=Msa0485780-mRNA-1
chr3_4 exon 3587099 3587236 3587099 ID=Msa0485780-mRNA-1:exon:1324;Parent=Msa0485780-mRNA-1
chr3_4 CDS 3587896 3587985 3587896 ID=Msa0485780-mRNA-1:cds;Parent=Msa0485780-mRNA-1
chr3_4 CDS 3587679 3587813 3587679 ID=Msa0485780-mRNA-1:cds;Parent=Msa0485780-mRNA-1
chr3_4 CDS 3587470 3587594 3587470 ID=Msa0485780-mRNA-1:cds;Parent=Msa0485780-mRNA-1
chr3_4 CDS 3587326 3587392 3587326 ID=Msa0485780-mRNA-1:cds;Parent=Msa0485780-mRNA-1
chr3_4 CDS 3587099 3587236 3587099 ID=Msa0485780-mRNA-1:cds;Parent=Msa0485780-mRNA-1
Gene Sequence

>Msa0485780

CGATATGTGCTGTCGTGGAATTCACCATTTTGGCAAATGAAACAGTTCTACCAAAAAGAATTTATGGGAAATGCTGATGTGGTTTCAAAGATCTTTTTACCAATATATGATCATCTACACTGGTTCCTTTTGGTTATTGACTTTGTGAGAAAAGAATTAGTATATCTTGACTCGTACCAAAGTTCGTCGGTGCTTCACGGAAGGATATCAAGTATCAAAAAATTGGCTATGTTTATGGAGGAGTTCTTGATGGATCCATCTTTCCATGGCACTGATTCAAACTATGACTATAAAATAACAAAGTTTAAAATAGTCACCCCAAAAGGTTTGGGACGTCAAGGGGATGGATCGAATGATTGTGCGGTTTGGGTAATTAACTGGATGATGCAACGTGGAGAGAATGGATACAAGATTGAAGTGGACGAAGGATCGAGACTAAAAATTGCACTACAATTGACACTGCATCCTTTCAACGACAAGAGAGATTTGATGTTGGCAAAGTCTTTGGAACATAAGCAAGATTTCATTAAAGGATATGATTCAGAGGTGTACTGA

Protein sequence

>Msa0485780

RYVLSWNSPFWQMKQFYQKEFMGNADVVSKIFLPIYDHLHWFLLVIDFVRKELVYLDSYQSSSVLHGRISSIKKLAMFMEEFLMDPSFHGTDSNYDYKITKFKIVTPKGLGRQGDGSNDCAVWVINWMMQRGENGYKIEVDEGSRLKIALQLTLHPFNDKRDLMLAKSLEHKQDFIKGYDSEVY*