AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar ZhongmuNo.1 / MsG0580029594.01


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsG0580029594.01.T01 MTR_5g089030 92.157 102 5 1 6 107 22 120 2.96e-62 185
MsG0580029594.01.T01 MTR_5g089030 88.785 107 9 1 1 107 10 113 3.40e-62 185
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsG0580029594.01.T01 AT5G12240 50.667 75 34 3 34 106 41 114 1.41e-15 67.0

Find 31 sgRNAs with CRISPR-Local

Find 97 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CCAAACTAACAGATTCATTT+TGG 0.150883 5:+99074386 MsG0580029594.01.T01:intron
ATTGACAACTGTTAAATTTC+AGG 0.175941 5:+99074018 None:intergenic
TTTAGATGTTGCTCGAAAAT+TGG 0.248254 5:+99075710 MsG0580029594.01.T01:CDS
AAAGTCAGAGGCTGCTAAAA+AGG 0.332380 5:+99074417 MsG0580029594.01.T01:CDS
TGCTTGTAACTCTGCATCTT+AGG 0.351202 5:-99075742 None:intergenic
AGATCCAGGTGTTAATTGTC+TGG 0.439476 5:-99074062 None:intergenic
TCCAATACAATCCCTAGTCT+TGG 0.443977 5:-99075867 None:intergenic
GATTTGTCTCAATAATTACA+TGG 0.452406 5:-99076001 None:intergenic
TTAACACCTGGATCTGGATC+TGG 0.464092 5:+99074070 MsG0580029594.01.T01:CDS
AGACAATTAACACCTGGATC+TGG 0.479178 5:+99074064 MsG0580029594.01.T01:CDS
TCCAAGACTAGGGATTGTAT+TGG 0.504722 5:+99075866 MsG0580029594.01.T01:three_prime_UTR
GCAGATCCAGATCCAGATCC+AGG 0.505288 5:-99074076 None:intergenic
TGCATGGAATGAAAAGGATA+AGG 0.508203 5:+99074203 MsG0580029594.01.T01:CDS
TATCACTGCAGCTAAATGAA+TGG 0.519982 5:+99074175 MsG0580029594.01.T01:intron
TTGAGTAGTAAAGTTGGTGT+GGG 0.522255 5:+99075841 MsG0580029594.01.T01:three_prime_UTR
TATAATGTATAATGCAAATG+TGG 0.522293 5:+99075894 MsG0580029594.01.T01:three_prime_UTR
ATCTGGATCTGCACAGGAAG+AGG 0.529978 5:+99074087 MsG0580029594.01.T01:CDS
ATCTGGATCTGGATCTGCAC+AGG 0.538020 5:+99074081 MsG0580029594.01.T01:CDS
TTTGAGTAGTAAAGTTGGTG+TGG 0.541565 5:+99075840 MsG0580029594.01.T01:three_prime_UTR
GCATGATGCATGGAATGAAA+AGG 0.553411 5:+99074197 MsG0580029594.01.T01:CDS
TGGTGTGGGAATCCAAGACT+AGG 0.561188 5:+99075855 MsG0580029594.01.T01:three_prime_UTR
ATTTGTCTCAATAATTACAT+GGG 0.617097 5:-99076000 None:intergenic
TTGGAACAAGCTAAAGTCAG+AGG 0.617833 5:+99074405 MsG0580029594.01.T01:CDS
ACAGGTTGGTACAGAAGAAG+CGG 0.620709 5:+99075282 MsG0580029594.01.T01:intron
GGTGTGGGAATCCAAGACTA+GGG 0.626844 5:+99075856 MsG0580029594.01.T01:three_prime_UTR
TAAATGAATGGCATGATGCA+TGG 0.637004 5:+99074187 MsG0580029594.01.T01:CDS
ATAATGTATAATGCAAATGT+GGG 0.638049 5:+99075895 MsG0580029594.01.T01:three_prime_UTR
TCATCCAGACAATTAACACC+TGG 0.646730 5:+99074058 MsG0580029594.01.T01:CDS
TGCACAGGAAGAGGTAGTTG+TGG 0.651343 5:+99074096 MsG0580029594.01.T01:CDS
GACATTGCAACTAACTGTTG+AGG 0.652421 5:-99075957 None:intergenic
AATCAAGGAATCAACAAACA+TGG 0.667146 5:+99074234 MsG0580029594.01.T01:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AATAAATGAAATAAAATTGA+TGG + Chr5:99075589-99075608 MsG0580029594.01.T01:intron 10.0%
!!! ATAAAACAATAAAAGATTTT+TGG - Chr5:99075665-99075684 None:intergenic 10.0%
!!! TTTATTTCATTTATTTTTTC+TGG - Chr5:99075584-99075603 None:intergenic 10.0%
!!! TTTTATTGTTTTATTTCTTT+AGG + Chr5:99075671-99075690 MsG0580029594.01.T01:intron 10.0%
!! AAATGTAAAAAAAGTAAACA+AGG - Chr5:99074561-99074580 None:intergenic 15.0%
!! AATGTAAAAAAAGTAAACAA+GGG - Chr5:99074560-99074579 None:intergenic 15.0%
!! CTTGTTCTTAATTATTAAAA+TGG + Chr5:99074498-99074517 MsG0580029594.01.T01:intron 15.0%
!!! AAATGAACATTTTGTTTTTT+AGG + Chr5:99075454-99075473 MsG0580029594.01.T01:intron 15.0%
!!! AATGAACATTTTGTTTTTTA+GGG + Chr5:99075455-99075474 MsG0580029594.01.T01:intron 15.0%
!!! CATTTTAATAATTAAGAACA+AGG - Chr5:99074500-99074519 None:intergenic 15.0%
!! AAAATCAAAGTAATTCAAAC+TGG - Chr5:99074738-99074757 None:intergenic 20.0%
!! AAATCAAAGTAATTCAAACT+GGG - Chr5:99074737-99074756 None:intergenic 20.0%
!! ACGTTTAAATGATTATCATT+TGG + Chr5:99075348-99075367 MsG0580029594.01.T01:intron 20.0%
!! ATAATGTATAATGCAAATGT+GGG + Chr5:99075895-99075914 MsG0580029594.01.T01:three_prime_UTR 20.0%
!! ATAATTAAGAACAAGGATAA+TGG - Chr5:99074493-99074512 None:intergenic 20.0%
!! ATTTATAGAAAGTAGTTTCT+TGG + Chr5:99075409-99075428 MsG0580029594.01.T01:intron 20.0%
!! ATTTGTCTCAATAATTACAT+GGG - Chr5:99076003-99076022 None:intergenic 20.0%
!! CGTTTAAATGATTATCATTT+GGG + Chr5:99075349-99075368 MsG0580029594.01.T01:intron 20.0%
!! TATAATGTATAATGCAAATG+TGG + Chr5:99075894-99075913 MsG0580029594.01.T01:three_prime_UTR 20.0%
!! TTGAAAGTTTCATTTAATGA+TGG + Chr5:99074938-99074957 MsG0580029594.01.T01:intron 20.0%
!!! ATGAACATTTTGTTTTTTAG+GGG + Chr5:99075456-99075475 MsG0580029594.01.T01:intron 20.0%
!!! TTATTTTTTCTGGAATTTCA+TGG - Chr5:99075574-99075593 None:intergenic 20.0%
!!! TTGATGATTTTGTAAAGATA+GGG + Chr5:99074970-99074989 MsG0580029594.01.T01:intron 20.0%
! AACATAGCACATGTTTATAT+TGG + Chr5:99074521-99074540 MsG0580029594.01.T01:intron 25.0%
! ATTGGTTATAATGTTTCAAC+AGG + Chr5:99075264-99075283 MsG0580029594.01.T01:intron 25.0%
! GATTTGTCTCAATAATTACA+TGG - Chr5:99076004-99076023 None:intergenic 25.0%
!! AAAATGAATCTGTTAGTTTG+GGG - Chr5:99074387-99074406 None:intergenic 25.0%
!! AAAGAAGTCTTTCATTGATT+AGG + Chr5:99075487-99075506 MsG0580029594.01.T01:intron 25.0%
!! ATTTTGTTACAACAATCAAC+TGG + Chr5:99074323-99074342 MsG0580029594.01.T01:intron 25.0%
!! CAAAATGAATCTGTTAGTTT+GGG - Chr5:99074388-99074407 None:intergenic 25.0%
!! CATTCTTTCATAGAAAGTAT+TGG + Chr5:99075372-99075391 MsG0580029594.01.T01:intron 25.0%
!! GATGTATTTGTTGAACAATA+AGG - Chr5:99074272-99074291 None:intergenic 25.0%
!! TGATGATTTTGTAAAGATAG+GGG + Chr5:99074971-99074990 MsG0580029594.01.T01:intron 25.0%
!!! GTTGATGATTTTGTAAAGAT+AGG + Chr5:99074969-99074988 MsG0580029594.01.T01:intron 25.0%
AAAGTAATTCAAACTGGGTT+TGG - Chr5:99074732-99074751 None:intergenic 30.0%
AAATTGTCACACGCATAAAT+AGG + Chr5:99075103-99075122 MsG0580029594.01.T01:intron 30.0%
AATCAAGGAATCAACAAACA+TGG + Chr5:99074234-99074253 MsG0580029594.01.T01:CDS 30.0%
AATTGTCACACGCATAAATA+GGG + Chr5:99075104-99075123 MsG0580029594.01.T01:intron 30.0%
ATAAAAATTCTTGTCCCATC+TGG + Chr5:99074825-99074844 MsG0580029594.01.T01:intron 30.0%
ATTTATGCGTGTGACAATTT+AGG - Chr5:99075103-99075122 None:intergenic 30.0%
CCAAAATGAATCTGTTAGTT+TGG - Chr5:99074389-99074408 None:intergenic 30.0%
GCTTTAACCTTAAAAGTTTG+AGG + Chr5:99074611-99074630 MsG0580029594.01.T01:intron 30.0%
GTATGCATGTAAAAATAAGC+AGG - Chr5:99074456-99074475 None:intergenic 30.0%
GTTATAATGTTTCAACAGGT+TGG + Chr5:99075268-99075287 MsG0580029594.01.T01:intron 30.0%
TCTCTTTATCATGTTTGTGA+AGG + Chr5:99075067-99075086 MsG0580029594.01.T01:intron 30.0%
TTTAGATGTTGCTCGAAAAT+TGG + Chr5:99075710-99075729 MsG0580029594.01.T01:CDS 30.0%
! CCAAACTAACAGATTCATTT+TGG + Chr5:99074386-99074405 MsG0580029594.01.T01:intron 30.0%
! TAATCAGCCTCAAACTTTTA+AGG - Chr5:99074621-99074640 None:intergenic 30.0%
!! GACATTTTGAGTAGTAAAGT+TGG + Chr5:99075835-99075854 MsG0580029594.01.T01:three_prime_UTR 30.0%
!! GATAAGGATTTTGAGAATCA+AGG + Chr5:99074219-99074238 MsG0580029594.01.T01:CDS 30.0%
!!! ATTTTTTTCACATGCCAGAT+GGG - Chr5:99074842-99074861 None:intergenic 30.0%
AGGGATAAAAGAAAGTGAGA+GGG + Chr5:99075123-99075142 MsG0580029594.01.T01:intron 35.0%
TAAATGAATGGCATGATGCA+TGG + Chr5:99074187-99074206 MsG0580029594.01.T01:CDS 35.0%
TAGGGATAAAAGAAAGTGAG+AGG + Chr5:99075122-99075141 MsG0580029594.01.T01:intron 35.0%
TATCACTGCAGCTAAATGAA+TGG + Chr5:99074175-99074194 MsG0580029594.01.T01:intron 35.0%
TGCATGGAATGAAAAGGATA+AGG + Chr5:99074203-99074222 MsG0580029594.01.T01:CDS 35.0%
!! TTGAGTAGTAAAGTTGGTGT+GGG + Chr5:99075841-99075860 MsG0580029594.01.T01:three_prime_UTR 35.0%
!! TTTGAGTAGTAAAGTTGGTG+TGG + Chr5:99075840-99075859 MsG0580029594.01.T01:three_prime_UTR 35.0%
!!! CATTTTTTTCACATGCCAGA+TGG - Chr5:99074843-99074862 None:intergenic 35.0%
AAAGTCAGAGGCTGCTAAAA+AGG + Chr5:99074417-99074436 MsG0580029594.01.T01:CDS 40.0%
AATCATTACATGTTTCCCCC+AGG + Chr5:99076020-99076039 MsG0580029594.01.T01:three_prime_UTR 40.0%
AGACAATTAACACCTGGATC+TGG + Chr5:99074064-99074083 MsG0580029594.01.T01:CDS 40.0%
AGATCCAGGTGTTAATTGTC+TGG - Chr5:99074065-99074084 None:intergenic 40.0%
GACATTGCAACTAACTGTTG+AGG - Chr5:99075960-99075979 None:intergenic 40.0%
GCATGATGCATGGAATGAAA+AGG + Chr5:99074197-99074216 MsG0580029594.01.T01:CDS 40.0%
GGGATAAAAGAAAGTGAGAG+GGG + Chr5:99075124-99075143 MsG0580029594.01.T01:intron 40.0%
GGTTTCAAAGGAAAGGACTA+AGG - Chr5:99074887-99074906 None:intergenic 40.0%
TAGAATGACACTACGCTCAT+TGG + Chr5:99075246-99075265 MsG0580029594.01.T01:intron 40.0%
TCATCCAGACAATTAACACC+TGG + Chr5:99074058-99074077 MsG0580029594.01.T01:CDS 40.0%
TCCAAGACTAGGGATTGTAT+TGG + Chr5:99075866-99075885 MsG0580029594.01.T01:three_prime_UTR 40.0%
TCCAATACAATCCCTAGTCT+TGG - Chr5:99075870-99075889 None:intergenic 40.0%
TGCTTGTAACTCTGCATCTT+AGG - Chr5:99075745-99075764 None:intergenic 40.0%
TTCAAAGGAAAGGACTAAGG+AGG - Chr5:99074884-99074903 None:intergenic 40.0%
TTGGAACAAGCTAAAGTCAG+AGG + Chr5:99074405-99074424 MsG0580029594.01.T01:CDS 40.0%
! AGAAGCGGAAAGATTTTGCA+AGG + Chr5:99075297-99075316 MsG0580029594.01.T01:CDS 40.0%
! ATAGGGGAGATTGTTGTTGT+AGG + Chr5:99074987-99075006 MsG0580029594.01.T01:intron 40.0%
! CTAGGGTGTTATAACTGTGA+TGG + Chr5:99075162-99075181 MsG0580029594.01.T01:intron 40.0%
AAACCAAGTCTACTGGTCAC+TGG - Chr5:99074908-99074927 None:intergenic 45.0%
AAACCAGTGACCAGTAGACT+TGG + Chr5:99074902-99074921 MsG0580029594.01.T01:intron 45.0%
TGCATGCAAACCAAGTCTAC+TGG - Chr5:99074915-99074934 None:intergenic 45.0%
TTAACACCTGGATCTGGATC+TGG + Chr5:99074070-99074089 MsG0580029594.01.T01:CDS 45.0%
!! ACAGGTTGGTACAGAAGAAG+CGG + Chr5:99075282-99075301 MsG0580029594.01.T01:intron 45.0%
!! CTACTGGTCACTGGTTTCAA+AGG - Chr5:99074899-99074918 None:intergenic 45.0%
!! GGTCACTGGTTTCAAAGGAA+AGG - Chr5:99074894-99074913 None:intergenic 45.0%
AGGAAAGGACTAAGGAGGCA+AGG - Chr5:99074879-99074898 None:intergenic 50.0%
ATCTGGATCTGCACAGGAAG+AGG + Chr5:99074087-99074106 MsG0580029594.01.T01:CDS 50.0%
ATCTGGATCTGGATCTGCAC+AGG + Chr5:99074081-99074100 MsG0580029594.01.T01:CDS 50.0%
GGTACATGTGTGTTGGGCTA+GGG + Chr5:99075145-99075164 MsG0580029594.01.T01:intron 50.0%
GGTGTGGGAATCCAAGACTA+GGG + Chr5:99075856-99075875 MsG0580029594.01.T01:three_prime_UTR 50.0%
TGCACAGGAAGAGGTAGTTG+TGG + Chr5:99074096-99074115 MsG0580029594.01.T01:CDS 50.0%
TGGTGTGGGAATCCAAGACT+AGG + Chr5:99075855-99075874 MsG0580029594.01.T01:three_prime_UTR 50.0%
TTACATGTTTCCCCCAGGTG+TGG + Chr5:99076025-99076044 MsG0580029594.01.T01:three_prime_UTR 50.0%
! CTGTGATGGTGATGTTGCAG+AGG + Chr5:99075176-99075195 MsG0580029594.01.T01:intron 50.0%
! GAGAGGGGTACATGTGTGTT+GGG + Chr5:99075139-99075158 MsG0580029594.01.T01:intron 50.0%
! TGAGAGGGGTACATGTGTGT+TGG + Chr5:99075138-99075157 MsG0580029594.01.T01:intron 50.0%
GCAGATCCAGATCCAGATCC+AGG - Chr5:99074079-99074098 None:intergenic 55.0%
GGGTACATGTGTGTTGGGCT+AGG + Chr5:99075144-99075163 MsG0580029594.01.T01:intron 55.0%
Chromosome Type Strat End Strand Name
Chr5 gene 99074019 99076053 99074019 ID=MsG0580029594.01;Name=MsG0580029594.01
Chr5 mRNA 99074019 99076053 99074019 ID=MsG0580029594.01.T01;Parent=MsG0580029594.01;Name=MsG0580029594.01.T01;_AED=0.49;_eAED=0.51;_QI=0|0.75|0.8|1|0|0|5|307|107
Chr5 exon 99074019 99074117 99074019 ID=MsG0580029594.01.T01:exon:26073;Parent=MsG0580029594.01.T01
Chr5 exon 99074186 99074255 99074186 ID=MsG0580029594.01.T01:exon:26074;Parent=MsG0580029594.01.T01
Chr5 exon 99074398 99074438 99074398 ID=MsG0580029594.01.T01:exon:26075;Parent=MsG0580029594.01.T01
Chr5 exon 99075286 99075345 99075286 ID=MsG0580029594.01.T01:exon:26076;Parent=MsG0580029594.01.T01
Chr5 exon 99075693 99076053 99075693 ID=MsG0580029594.01.T01:exon:26077;Parent=MsG0580029594.01.T01
Chr5 CDS 99074019 99074117 99074019 ID=MsG0580029594.01.T01:cds;Parent=MsG0580029594.01.T01
Chr5 CDS 99074186 99074255 99074186 ID=MsG0580029594.01.T01:cds;Parent=MsG0580029594.01.T01
Chr5 CDS 99074398 99074438 99074398 ID=MsG0580029594.01.T01:cds;Parent=MsG0580029594.01.T01
Chr5 CDS 99075286 99075345 99075286 ID=MsG0580029594.01.T01:cds;Parent=MsG0580029594.01.T01
Chr5 CDS 99075693 99075746 99075693 ID=MsG0580029594.01.T01:cds;Parent=MsG0580029594.01.T01
Chr5 three_prime_UTR 99075747 99076053 99075747 ID=MsG0580029594.01.T01:three_prime_utr;Parent=MsG0580029594.01.T01
Gene Sequence

>MsG0580029594.01.T01

TTGACAACTGTTAAATTTCAGGAAGAATCATCATCATCATCATCCAGACAATTAACACCTGGATCTGGATCTGGATCTGCACAGGAAGAGGTAGTTGTGCTAAATGAATGGCATGATGCATGGAATGAAAAGGATAAGGATTTTGAGAATCAAGGAATCAACAAACATGATTCATTTTGGAACAAGCTAAAGTCAGAGGCTGCTAAAAAGGTTGGTACAGAAGAAGCGGAAAGATTTTGCAAGGCGTTTCAACAAATTCATAAGAGACTAGTCAATGAAGAGTTAAGTTTAGATGTTGCTCGAAAATTGGTAAACTCATCCTAA

Protein sequence

>MsG0580029594.01.T01

LTTVKFQEESSSSSSRQLTPGSGSGSAQEEVVVLNEWHDAWNEKDKDFENQGINKHDSFWNKLKSEAAKKVGTEEAERFCKAFQQIHKRLVNEELSLDVARKLVNSS*