AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar ZhongmuNo.1 / MsG0680033488.01

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsG0680033488.01.T01 MTR_5g077900 52.991 117 2 1 19 82 109 225 9.29e-31 107
MsG0680033488.01.T01 MTR_0002s1270 52.991 117 2 1 19 82 283 399 4.05e-30 109
MsG0680033488.01.T01 MTR_0057s0200 83.333 54 9 0 30 83 6 59 1.59e-26 92.4
MsG0680033488.01.T01 MTR_7g046380 50.000 106 0 1 19 71 291 396 3.27e-24 94.0
MsG0680033488.01.T01 MTR_4g066320 74.000 50 12 1 35 83 72 121 4.25e-20 77.8
MsG0680033488.01.T01 MTR_3g028430 52.941 68 17 2 16 83 7 59 7.79e-16 65.5
MsG0680033488.01.T01 MTR_2g086200 63.830 47 17 0 35 81 186 232 6.03e-14 64.3
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 74 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AATGATGAAATTAGCCTCAT+TGG 0.333544 6:+66422912 None:intergenic
GACAACTAAACTATTGTCCT+TGG 0.409668 6:+66421856 None:intergenic
ATTTCATCATTGAAACCTAT+AGG 0.411287 6:-66422900 MsG0680033488.01.T01:CDS
TCTTGACTTGTATAACGCTT+AGG 0.431501 6:-66421608 None:intergenic
CTGCTAATATTACTAAGTCT+TGG 0.472781 6:-66421808 MsG0680033488.01.T01:CDS
TCATCTTCAGTTAATGTCGT+TGG 0.484681 6:+66421667 None:intergenic
GTTAATAATTATTTGTCCCA+AGG 0.509187 6:-66421873 MsG0680033488.01.T01:CDS
ACAACTAAACTATTGTCCTT+GGG 0.519949 6:+66421857 None:intergenic
GTATGATTTGCGAAACTCAT+GGG 0.537054 6:-66421641 MsG0680033488.01.T01:CDS
CCTATAGGACACTTCGTGAC+GGG 0.543807 6:-66422885 MsG0680033488.01.T01:intron
TGTATGATTTGCGAAACTCA+TGG 0.560022 6:-66421642 MsG0680033488.01.T01:CDS
CCCGTCACGAAGTGTCCTAT+AGG 0.580159 6:+66422885 None:intergenic
TCTACGTGTGCAGAGGACAC+TGG 0.601997 6:-66421898 MsG0680033488.01.T01:intron
TAATATTACTAAGTCTTGGA+TGG 0.604101 6:-66421804 MsG0680033488.01.T01:CDS
ACCTATAGGACACTTCGTGA+CGG 0.611426 6:-66422886 MsG0680033488.01.T01:CDS
TATTACTAAGTCTTGGATGG+AGG 0.643493 6:-66421801 MsG0680033488.01.T01:intron
GCTATAACAGGGAACCAATG+AGG 0.662397 6:-66422926 None:intergenic
TGATATCTAGCATTGAACAA+AGG 0.686838 6:+66421834 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TATATTTACTTAAATAGATA+TGG + Chr6:66422548-66422567 None:intergenic 10.0%
!! AATAAGGATATGTTTATATT+TGG + Chr6:66422791-66422810 None:intergenic 15.0%
!! ATTCTTTATAATTTACTACA+TGG - Chr6:66421800-66421819 MsG0680033488.01.T01:intron 15.0%
!! TAATTGCAATAGTTAAAATA+TGG + Chr6:66421931-66421950 None:intergenic 15.0%
!! ATAATTAAAGTGATTGAAAG+AGG + Chr6:66421767-66421786 None:intergenic 20.0%
!! TAATTAAAGTGATTGAAAGA+GGG + Chr6:66421766-66421785 None:intergenic 20.0%
!!! GATGAATTGTAAAAACATTT+TGG - Chr6:66422187-66422206 MsG0680033488.01.T01:intron 20.0%
!!! TGGTTTTATTAATTTACTAC+AGG - Chr6:66421820-66421839 MsG0680033488.01.T01:CDS 20.0%
! AATTAAAGTGATTGAAAGAG+GGG + Chr6:66421765-66421784 None:intergenic 25.0%
! ACGTAGAAGAACAATTATTA+AGG + Chr6:66422614-66422633 None:intergenic 25.0%
! ATCATCTATGATAACAAAGA+TGG - Chr6:66421716-66421735 MsG0680033488.01.T01:intron 25.0%
! ATTTCATCATTGAAACCTAT+AGG - Chr6:66421625-66421644 MsG0680033488.01.T01:CDS 25.0%
! GTTAATAATTATTTGTCCCA+AGG - Chr6:66422652-66422671 MsG0680033488.01.T01:intron 25.0%
! TAATATTACTAAGTCTTGGA+TGG - Chr6:66422721-66422740 MsG0680033488.01.T01:intron 25.0%
! TAGTACTAAAACTAAAGTTC+AGG - Chr6:66422472-66422491 MsG0680033488.01.T01:intron 25.0%
! TATATTAACCTACACATTGT+AGG - Chr6:66422824-66422843 MsG0680033488.01.T01:intron 25.0%
!!! AAATAACTTGATGGTAGTTT+TGG - Chr6:66421689-66421708 MsG0680033488.01.T01:intron 25.0%
!!! GTTTTAGTACTATGATCTTT+TGG + Chr6:66422464-66422483 None:intergenic 25.0%
!!! TTGTAAAAACATTTTGGTTC+AGG - Chr6:66422193-66422212 MsG0680033488.01.T01:intron 25.0%
AAGTCCTCAAAATAACTTGA+TGG - Chr6:66421680-66421699 MsG0680033488.01.T01:CDS 30.0%
ACAACTAAACTATTGTCCTT+GGG + Chr6:66422671-66422690 None:intergenic 30.0%
ATTGAATACCTACAATGTGT+AGG + Chr6:66422835-66422854 None:intergenic 30.0%
CTGCTAATATTACTAAGTCT+TGG - Chr6:66422717-66422736 MsG0680033488.01.T01:intron 30.0%
GAGAAGAAAAACTAGCAAAA+TGG + Chr6:66422022-66422041 None:intergenic 30.0%
TGTATTAGCCATCATAATAC+AGG + Chr6:66422108-66422127 None:intergenic 30.0%
! AATGATGAAATTAGCCTCAT+TGG + Chr6:66421616-66421635 None:intergenic 30.0%
! TGATATCTAGCATTGAACAA+AGG + Chr6:66422694-66422713 None:intergenic 30.0%
!! ACTACCATCAAGTTATTTTG+AGG + Chr6:66421687-66421706 None:intergenic 30.0%
!!! AAAAACATTTTGGTTCAGGT+TGG - Chr6:66422197-66422216 MsG0680033488.01.T01:intron 30.0%
GACAACTAAACTATTGTCCT+TGG + Chr6:66422672-66422691 None:intergenic 35.0%
TATTACTAAGTCTTGGATGG+AGG - Chr6:66422724-66422743 MsG0680033488.01.T01:intron 35.0%
TCATCCTTCCTGTATTATGA+TGG - Chr6:66422097-66422116 MsG0680033488.01.T01:intron 35.0%
TCATCTTCAGTTAATGTCGT+TGG + Chr6:66422861-66422880 None:intergenic 35.0%
TTAGCCATCATAATACAGGA+AGG + Chr6:66422104-66422123 None:intergenic 35.0%
TTCAGGAACACATACAAACT+AGG - Chr6:66422489-66422508 MsG0680033488.01.T01:intron 35.0%
! GTATGATTTGCGAAACTCAT+GGG - Chr6:66422884-66422903 MsG0680033488.01.T01:intron 35.0%
! TGTATGATTTGCGAAACTCA+TGG - Chr6:66422883-66422902 MsG0680033488.01.T01:intron 35.0%
!! CTTGACTTGTATAACGCTTA+GGG - Chr6:66422918-66422937 MsG0680033488.01.T01:CDS 35.0%
!! TCTTGACTTGTATAACGCTT+AGG - Chr6:66422917-66422936 MsG0680033488.01.T01:CDS 35.0%
!!! GTTACAGGTTGATTGTTTTG+AGG - Chr6:66422413-66422432 MsG0680033488.01.T01:intron 35.0%
CCAGTTAGCCATCATAATAC+AGG + Chr6:66422244-66422263 None:intergenic 40.0%
CCTGTATTATGATGGCTAAC+TGG - Chr6:66422241-66422260 MsG0680033488.01.T01:intron 40.0%
!! ATTTTGAGGACTTGATCTGC+AGG + Chr6:66421673-66421692 None:intergenic 40.0%
!! TTTTGAGGACTTGATCTGCA+GGG + Chr6:66421672-66421691 None:intergenic 40.0%
!!! AGCAGTTTTGGGAGGTTTTT+TGG - Chr6:66422389-66422408 MsG0680033488.01.T01:intron 40.0%
!!! AGGTTGATTGTTTTGAGGCT+CGG - Chr6:66422418-66422437 MsG0680033488.01.T01:intron 40.0%
!!! ATTGTTTTGAGGCTCGGATA+TGG - Chr6:66422424-66422443 MsG0680033488.01.T01:intron 40.0%
!!! CAGTTTTGGGAGGTTTTTTG+GGG - Chr6:66422391-66422410 MsG0680033488.01.T01:intron 40.0%
!!! GCAGTTTTGGGAGGTTTTTT+GGG - Chr6:66422390-66422409 MsG0680033488.01.T01:intron 40.0%
ACCTATAGGACACTTCGTGA+CGG - Chr6:66421639-66421658 MsG0680033488.01.T01:CDS 45.0%
TTGTTCTTCTACGTGTGCAG+AGG - Chr6:66422620-66422639 MsG0680033488.01.T01:intron 45.0%
!! ATAAGTAATTAATATTAATA+AGG + Chr6:66422807-66422826 None:intergenic 5.0%
AAAACAGCAGCACAGCAGCA+AGG + Chr6:66422273-66422292 None:intergenic 50.0%
AACCTCCCAAAACTGCTGCT+AGG + Chr6:66422386-66422405 None:intergenic 50.0%
AGGACTTGATCTGCAGGGAA+TGG + Chr6:66421667-66421686 None:intergenic 50.0%
CCTATAGGACACTTCGTGAC+GGG - Chr6:66421640-66421659 MsG0680033488.01.T01:CDS 50.0%
! CCAGTCCTAGCAGCAGTTTT+GGG - Chr6:66422378-66422397 MsG0680033488.01.T01:intron 50.0%
! TTTTCCTGTCCCAGCAGTGT+TGG - Chr6:66422289-66422308 MsG0680033488.01.T01:intron 50.0%
!!! GGGAGGTTTTTTGGGGTTAC+AGG - Chr6:66422398-66422417 MsG0680033488.01.T01:intron 50.0%
CCCAAAACTGCTGCTAGGAC+TGG + Chr6:66422381-66422400 None:intergenic 55.0%
TCTACGTGTGCAGAGGACAC+TGG - Chr6:66422627-66422646 MsG0680033488.01.T01:intron 55.0%
! CCCGTCACGAAGTGTCCTAT+AGG + Chr6:66421643-66421662 None:intergenic 55.0%
! GCCAGTCCTAGCAGCAGTTT+TGG - Chr6:66422377-66422396 MsG0680033488.01.T01:intron 55.0%
!!! GTCCTAGCAGCAGTTTTGGG+AGG - Chr6:66422381-66422400 MsG0680033488.01.T01:intron 55.0%
CAGATAGCAGCACCAGCTGC+TGG + Chr6:66422356-66422375 None:intergenic 60.0%
CAGGCGAGACCAACACTGCT+GGG + Chr6:66422301-66422320 None:intergenic 60.0%
GAGACCAACACTGCTGGGAC+AGG + Chr6:66422296-66422315 None:intergenic 60.0%
TGCTGTCCTGCTGTCTGCAC+AGG - Chr6:66422329-66422348 MsG0680033488.01.T01:intron 60.0%
!! CAGCAGTGTTGGTCTCGCCT+GGG - Chr6:66422300-66422319 MsG0680033488.01.T01:intron 60.0%
CCAGGCGAGACCAACACTGC+TGG + Chr6:66422302-66422321 None:intergenic 65.0%
GCAGGACAGCAAAGCTGCCC+AGG + Chr6:66422320-66422339 None:intergenic 65.0%
GCTGGACCTGTGCAGACAGC+AGG + Chr6:66422338-66422357 None:intergenic 65.0%
GTCTGCACAGGTCCAGCAGC+TGG - Chr6:66422341-66422360 MsG0680033488.01.T01:intron 65.0%
!! CCAGCAGTGTTGGTCTCGCC+TGG - Chr6:66422299-66422318 MsG0680033488.01.T01:intron 65.0%
Chromosome Type Strat End Strand Name
Chr6 gene 66421609 66422938 66421609 ID=MsG0680033488.01;Name=MsG0680033488.01
Chr6 mRNA 66421609 66422938 66421609 ID=MsG0680033488.01.T01;Parent=MsG0680033488.01;Name=MsG0680033488.01.T01;_AED=0.37;_eAED=0.37;_QI=0|0|0|0.66|0|0|3|0|83
Chr6 exon 66422886 66422938 66422886 ID=MsG0680033488.01.T01:exon:3467;Parent=MsG0680033488.01.T01
Chr6 exon 66421802 66421907 66421802 ID=MsG0680033488.01.T01:exon:3468;Parent=MsG0680033488.01.T01
Chr6 exon 66421609 66421701 66421609 ID=MsG0680033488.01.T01:exon:3469;Parent=MsG0680033488.01.T01
Chr6 CDS 66422886 66422938 66422886 ID=MsG0680033488.01.T01:cds;Parent=MsG0680033488.01.T01
Chr6 CDS 66421802 66421907 66421802 ID=MsG0680033488.01.T01:cds;Parent=MsG0680033488.01.T01
Chr6 CDS 66421609 66421701 66421609 ID=MsG0680033488.01.T01:cds;Parent=MsG0680033488.01.T01
Gene Sequence

>MsG0680033488.01.T01

GGAACCAATGAGGCTAATTTCATCATTGAAACCTATAGGACACTTCGTGACGGAGGACACTGGCAGTTAATAATTATTTGTCCCAAGGACAATAGTTTAGTTGTCCTTTGTTCAATGCTAGATATCATCTCTGCTAATATTACTAAGTCTTGGATGGAGGTATTCAATGATCCAACGACATTAACTGAAGATGACTTGTATGATTTGCGAAACTCATGGGCAACTTGTTTTCTTGACTTGTATAACGCTTAG
Protein sequence

>MsG0680033488.01.T01

GTNEANFIIETYRTLRDGGHWQLIIICPKDNSLVVLCSMLDIISANITKSWMEVFNDPTTLTEDDLYDLRNSWATCFLDLYNA*