AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar ZhongmuNo.1 / MsG0280009461.01

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsG0280009461.01.T01 MTR_2g063620 97.345 113 3 0 32 144 587 699 1.27e-76 247
MsG0280009461.01.T01 MTR_2g063813 66.935 124 36 3 21 144 628 746 2.63e-47 163
MsG0280009461.01.T01 MTR_6g091960 66.129 124 37 3 21 144 643 761 7.72e-46 159
MsG0280009461.01.T01 MTR_8g447090 58.400 125 50 2 21 144 628 751 4.32e-42 149
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsG0280009461.01.T01 AT1G79350 51.961 102 48 1 44 144 690 791 5.51e-30 114

Find 32 sgRNAs with CRISPR-Local

Find 82 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TCAAGAACAAAATCGCTAAT+TGG 0.308205 2:+52386032 None:intergenic
GATTCTTCTGATTCTGATTA+CGG 0.316476 2:-52386765 MsG0280009461.01.T01:CDS
GCACCACTTTCATTCCCTTC+TGG 0.345854 2:+52386741 None:intergenic
TCCAGGAGGGAGATAGTTTA+CGG 0.350048 2:+52385977 None:intergenic
AGTTCAATTATATCTGTTCC+AGG 0.401402 2:+52385960 None:intergenic
CTTGGATGATATTATTGATC+AGG 0.402590 2:-52385675 MsG0280009461.01.T01:CDS
TTGTTTGATGCAGCTGCCTC+TGG 0.403542 2:-52386271 MsG0280009461.01.T01:intron
ATCTTCCGACTCTGATTATG+AGG 0.447746 2:-52386242 MsG0280009461.01.T01:CDS
TAATCAGAATCAGAAGAATC+AGG 0.450903 2:+52386768 None:intergenic
TGAATGATTTATTTCACCAT+TGG 0.458465 2:-52386812 MsG0280009461.01.T01:CDS
ATATCATCCAAGGGATTGTT+CGG 0.473416 2:+52385686 None:intergenic
AGATCTTCCGAACAATCCCT+TGG 0.484001 2:-52385693 MsG0280009461.01.T01:CDS
ACCGTAAACTATCTCCCTCC+TGG 0.508924 2:-52385978 MsG0280009461.01.T01:CDS
ATATAATTGAACTCCAGAAA+AGG 0.522669 2:-52385950 MsG0280009461.01.T01:intron
CTGATCAATAATATCATCCA+AGG 0.535452 2:+52385676 None:intergenic
GATTCTGATTACGGACCAGA+AGG 0.557557 2:-52386756 MsG0280009461.01.T01:CDS
ATACGCTCATCACTCATGCT+TGG 0.557677 2:-52386060 MsG0280009461.01.T01:CDS
TTTCAGAAATGTGAAATATG+TGG 0.578026 2:-52386217 MsG0280009461.01.T01:CDS
AGAACAAAATCGCTAATTGG+TGG 0.579439 2:+52386035 None:intergenic
AGGCAGCTGCATCAAGCCAA+TGG 0.602321 2:+52386796 None:intergenic
GTCGGAAGATTCAAGACCAG+AGG 0.602868 2:+52386255 None:intergenic
AAACTCCTCATAATCAGAGT+CGG 0.607035 2:+52386237 None:intergenic
GGACCAGAAGGGAATGAAAG+TGG 0.615699 2:-52386744 MsG0280009461.01.T01:intron
TGAAATATGTGGCACTGAAG+AGG 0.621053 2:-52386206 MsG0280009461.01.T01:intron
CAATTATATCTGTTCCAGGA+GGG 0.621228 2:+52385964 None:intergenic
ATCAGAAGAATCAGGAACAG+AGG 0.624321 2:+52386776 None:intergenic
TGATCAATAATATCATCCAA+GGG 0.637584 2:+52385677 None:intergenic
CTGTAGGTATGACACAGCCA+TGG 0.645637 2:-52385753 MsG0280009461.01.T01:intron
TCAATTATATCTGTTCCAGG+AGG 0.669015 2:+52385963 None:intergenic
ATGGGCATGTGATTTGTGCA+AGG 0.690665 2:-52386006 MsG0280009461.01.T01:CDS
ATTCTGATTACGGACCAGAA+GGG 0.702463 2:-52386755 MsG0280009461.01.T01:CDS
TTGTTGCAGTGTTCCCACTG+TGG 0.723683 2:-52386086 MsG0280009461.01.T01:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! AAGTTCTTTTAAAATATTAA+TGG - Chr2:52386120-52386139 MsG0280009461.01.T01:intron 10.0%
!!! TTGGATAATTTTTTTTAATT+TGG - Chr2:52386552-52386571 MsG0280009461.01.T01:intron 10.0%
!!! TTTGATAATTTGTTTTAATT+TGG - Chr2:52386610-52386629 MsG0280009461.01.T01:intron 10.0%
!! TAAAAAAAAAAAATTGCCTT+TGG - Chr2:52385935-52385954 MsG0280009461.01.T01:intron 15.0%
!!! AGGCAATTTTTTTTTTTTAA+TGG + Chr2:52385934-52385953 None:intergenic 15.0%
!! AACAAAACAGAATAACAAAA+AGG + Chr2:52385975-52385994 None:intergenic 20.0%
!! ACAAAACAGAATAACAAAAA+GGG + Chr2:52385974-52385993 None:intergenic 20.0%
!! GGTAAAATACTAAAATCAAA+TGG + Chr2:52386179-52386198 None:intergenic 20.0%
!!! ATTTTTGTTGATTCAAGATA+TGG + Chr2:52386638-52386657 None:intergenic 20.0%
!!! TTTTGATTTCTAACTTTTTG+TGG + Chr2:52386664-52386683 None:intergenic 20.0%
! ATATAATTGAACTCCAGAAA+AGG - Chr2:52386521-52386540 MsG0280009461.01.T01:intron 25.0%
! TGAATGATTTATTTCACCAT+TGG - Chr2:52385659-52385678 MsG0280009461.01.T01:CDS 25.0%
! TGATCAATAATATCATCCAA+GGG + Chr2:52386797-52386816 None:intergenic 25.0%
! TTTCAGAAATGTGAAATATG+TGG - Chr2:52386254-52386273 MsG0280009461.01.T01:CDS 25.0%
!!! TTTTTTTTAATTTGGCACTC+TGG - Chr2:52386560-52386579 MsG0280009461.01.T01:intron 25.0%
AGTTCAATTATATCTGTTCC+AGG + Chr2:52386514-52386533 None:intergenic 30.0%
ATATGTGAATCCTACACATA+TGG + Chr2:52386341-52386360 None:intergenic 30.0%
CTGATCAATAATATCATCCA+AGG + Chr2:52386798-52386817 None:intergenic 30.0%
CTTGGATGATATTATTGATC+AGG - Chr2:52386796-52386815 MsG0280009461.01.T01:CDS 30.0%
GATTCTTCTGATTCTGATTA+CGG - Chr2:52385706-52385725 MsG0280009461.01.T01:CDS 30.0%
TAATCAGAATCAGAAGAATC+AGG + Chr2:52385706-52385725 None:intergenic 30.0%
TCAAGAACAAAATCGCTAAT+TGG + Chr2:52386442-52386461 None:intergenic 30.0%
! AATTAGCGATTTTGTTCTTG+AGG - Chr2:52386441-52386460 MsG0280009461.01.T01:intron 30.0%
! ACAGTGATGAATATTTTCGT+GGG - Chr2:52386691-52386710 MsG0280009461.01.T01:intron 30.0%
! ATATTTTTCTGTGCAGGAAA+GGG - Chr2:52386357-52386376 MsG0280009461.01.T01:intron 30.0%
! ATTCACATATTTTTCTGTGC+AGG - Chr2:52386351-52386370 MsG0280009461.01.T01:intron 30.0%
! TATATTTTTCTTGCACTCCA+TGG + Chr2:52386738-52386757 None:intergenic 30.0%
! TCCAGAAAAGGTTTAAAACT+TGG - Chr2:52386533-52386552 MsG0280009461.01.T01:intron 30.0%
! TTTTGTACAAAAGTTGCCTT+GGG - Chr2:52385792-52385811 MsG0280009461.01.T01:intron 30.0%
!!! TCCAAGTTTTAAACCTTTTC+TGG + Chr2:52386537-52386556 None:intergenic 30.0%
AAACTCCTCATAATCAGAGT+CGG + Chr2:52386237-52386256 None:intergenic 35.0%
AGAACAAAATCGCTAATTGG+TGG + Chr2:52386439-52386458 None:intergenic 35.0%
ATATCATCCAAGGGATTGTT+CGG + Chr2:52386788-52386807 None:intergenic 35.0%
CAATTATATCTGTTCCAGGA+GGG + Chr2:52386510-52386529 None:intergenic 35.0%
TCAATTATATCTGTTCCAGG+AGG + Chr2:52386511-52386530 None:intergenic 35.0%
TTTGTACAAAAGTTGCCTTG+GGG - Chr2:52385793-52385812 MsG0280009461.01.T01:intron 35.0%
! CATATTTTTCTGTGCAGGAA+AGG - Chr2:52386356-52386375 MsG0280009461.01.T01:intron 35.0%
! CGATTTTGTTCTTGAGGAAT+GGG - Chr2:52386447-52386466 MsG0280009461.01.T01:intron 35.0%
! CTTTTGTACAAAAGTTGCCT+TGG - Chr2:52385791-52385810 MsG0280009461.01.T01:intron 35.0%
! GACAGTGATGAATATTTTCG+TGG - Chr2:52386690-52386709 MsG0280009461.01.T01:intron 35.0%
! GGGTGAAATTCTTTTACCAA+AGG + Chr2:52385954-52385973 None:intergenic 35.0%
!! TCACATGCTTGTTATTGTGA+CGG - Chr2:52386027-52386046 MsG0280009461.01.T01:CDS 35.0%
!!! ATATTAGTTTTCTCCTTGCC+AGG + Chr2:52385888-52385907 None:intergenic 35.0%
AATCCTACACATATGGCATC+AGG + Chr2:52386334-52386353 None:intergenic 40.0%
ATCAGAAGAATCAGGAACAG+AGG + Chr2:52385698-52385717 None:intergenic 40.0%
ATCCTACACATATGGCATCA+GGG + Chr2:52386333-52386352 None:intergenic 40.0%
ATCTTCCGACTCTGATTATG+AGG - Chr2:52386229-52386248 MsG0280009461.01.T01:CDS 40.0%
ATTCTGATTACGGACCAGAA+GGG - Chr2:52385716-52385735 MsG0280009461.01.T01:CDS 40.0%
CTAAGGGATTAAAGGAGTTG+AGG - Chr2:52385841-52385860 MsG0280009461.01.T01:intron 40.0%
GAGTTGAGGAGTTAAAAGTC+AGG - Chr2:52385855-52385874 MsG0280009461.01.T01:intron 40.0%
GGTTTGAGCTAAGGGATTAA+AGG - Chr2:52385833-52385852 MsG0280009461.01.T01:intron 40.0%
TAAAAGTCAGGTTCAAGTCC+TGG - Chr2:52385867-52385886 MsG0280009461.01.T01:intron 40.0%
TTGTACAAAAGTTGCCTTGG+GGG - Chr2:52385794-52385813 MsG0280009461.01.T01:intron 40.0%
! ATGAGCGTATTTTCCACAGT+GGG + Chr2:52386401-52386420 None:intergenic 40.0%
! GCGATTTTGTTCTTGAGGAA+TGG - Chr2:52386446-52386465 MsG0280009461.01.T01:intron 40.0%
! TATTTTCGTGGGATTGCTGT+AGG - Chr2:52386702-52386721 MsG0280009461.01.T01:intron 40.0%
! TGAAATATGTGGCACTGAAG+AGG - Chr2:52386265-52386284 MsG0280009461.01.T01:intron 40.0%
!! AACTCAACTGGTTTGAGCTA+AGG - Chr2:52385824-52385843 MsG0280009461.01.T01:intron 40.0%
!! ACTCAACTGGTTTGAGCTAA+GGG - Chr2:52385825-52385844 MsG0280009461.01.T01:intron 40.0%
!! TTCTCATGCTTGCTATTGTG+AGG - Chr2:52386061-52386080 MsG0280009461.01.T01:CDS 40.0%
AGATCTTCCGAACAATCCCT+TGG - Chr2:52386778-52386797 MsG0280009461.01.T01:CDS 45.0%
ATACGCTCATCACTCATGCT+TGG - Chr2:52386411-52386430 MsG0280009461.01.T01:intron 45.0%
GATTCTGATTACGGACCAGA+AGG - Chr2:52385715-52385734 MsG0280009461.01.T01:CDS 45.0%
TCCAGGAGGGAGATAGTTTA+CGG + Chr2:52386497-52386516 None:intergenic 45.0%
TGTACAAAAGTTGCCTTGGG+GGG - Chr2:52385795-52385814 MsG0280009461.01.T01:intron 45.0%
! ATGGGCATGTGATTTGTGCA+AGG - Chr2:52386465-52386484 MsG0280009461.01.T01:intron 45.0%
! GATGAGCGTATTTTCCACAG+TGG + Chr2:52386402-52386421 None:intergenic 45.0%
AAAAGTTGCCTTGGGGGGTT+GGG - Chr2:52385800-52385819 MsG0280009461.01.T01:intron 50.0%
ACCGTAAACTATCTCCCTCC+TGG - Chr2:52386493-52386512 MsG0280009461.01.T01:intron 50.0%
CTGTAGGTATGACACAGCCA+TGG - Chr2:52386718-52386737 MsG0280009461.01.T01:intron 50.0%
GAGGCAGCTGCATCAAACAA+TGG + Chr2:52386200-52386219 None:intergenic 50.0%
GCACCACTTTCATTCCCTTC+TGG + Chr2:52385733-52385752 None:intergenic 50.0%
GGACCAGAAGGGAATGAAAG+TGG - Chr2:52385727-52385746 MsG0280009461.01.T01:CDS 50.0%
GTCGGAAGATTCAAGACCAG+AGG + Chr2:52386219-52386238 None:intergenic 50.0%
TGCCCTGATGCCATATGTGT+AGG - Chr2:52386328-52386347 MsG0280009461.01.T01:intron 50.0%
TTGTTGCAGTGTTCCCACTG+TGG - Chr2:52386385-52386404 MsG0280009461.01.T01:intron 50.0%
TTGTTTGATGCAGCTGCCTC+TGG - Chr2:52386200-52386219 MsG0280009461.01.T01:intron 50.0%
AGGCAGCTGCATCAAGCCAA+TGG + Chr2:52385678-52385697 None:intergenic 55.0%
CAAAAGTTGCCTTGGGGGGT+TGG - Chr2:52385799-52385818 MsG0280009461.01.T01:intron 55.0%
GTCAGGTTCAAGTCCTGGCA+AGG - Chr2:52385872-52385891 MsG0280009461.01.T01:intron 55.0%
TTGAGTTACCCAACCCCCCA+AGG + Chr2:52385811-52385830 None:intergenic 55.0%
GGGGGGTTGGGTAACTCAAC+TGG - Chr2:52385812-52385831 MsG0280009461.01.T01:intron 60.0%
Chromosome Type Strat End Strand Name
Chr2 gene 52385658 52386835 52385658 ID=MsG0280009461.01;Name=MsG0280009461.01
Chr2 mRNA 52385658 52386835 52385658 ID=MsG0280009461.01.T01;Parent=MsG0280009461.01;Name=MsG0280009461.01.T01;_AED=0.50;_eAED=0.55;_QI=0|0|0|1|1|1|4|0|148
Chr2 exon 52386745 52386835 52386745 ID=MsG0280009461.01.T01:exon:24157;Parent=MsG0280009461.01.T01
Chr2 exon 52386207 52386280 52386207 ID=MsG0280009461.01.T01:exon:24156;Parent=MsG0280009461.01.T01
Chr2 exon 52385951 52386120 52385951 ID=MsG0280009461.01.T01:exon:24155;Parent=MsG0280009461.01.T01
Chr2 exon 52385658 52385769 52385658 ID=MsG0280009461.01.T01:exon:24154;Parent=MsG0280009461.01.T01
Chr2 CDS 52386745 52386835 52386745 ID=MsG0280009461.01.T01:cds;Parent=MsG0280009461.01.T01
Chr2 CDS 52386207 52386280 52386207 ID=MsG0280009461.01.T01:cds;Parent=MsG0280009461.01.T01
Chr2 CDS 52385951 52386120 52385951 ID=MsG0280009461.01.T01:cds;Parent=MsG0280009461.01.T01
Chr2 CDS 52385658 52385769 52385658 ID=MsG0280009461.01.T01:cds;Parent=MsG0280009461.01.T01
Gene Sequence

>MsG0280009461.01.T01

CTGAATGATTTATTTCACCATTGGCTTGATGCAGCTGCCTCTGTTCCTGATTCTTCTGATTCTGATTACGGACCAGAAGGGAATGAAAGTGCTGCCTCTGGTCTTGAATCTTCCGACTCTGATTATGAGGAGTTTCAGAAATGTGAAATATGTGGCACTGAAGAGGAAAGGGAAAACTTGTTGCAGTGTTCCCACTGTGGAAAATACGCTCATCACTCATGCTTGGTGCCACCAATTAGCGATTTTGTTCTTGAGGAATGGGCATGTGATTTGTGCAAGGATACAACCGTAAACTATCTCCCTCCTGGAACAGATATAATTGAACTCCAGAAAAGGTATGACACAGCCATGGAGTGCAAGAAAAATATATTAGAGATGATTTGTGCTTTAGATCTTCCGAACAATCCCTTGGATGATATTATTGATCAGGTAATGATCATTCATTGA
Protein sequence

>MsG0280009461.01.T01

LNDLFHHWLDAAASVPDSSDSDYGPEGNESAASGLESSDSDYEEFQKCEICGTEEERENLLQCSHCGKYAHHSCLVPPISDFVLEEWACDLCKDTTVNYLPPGTDIIELQKRYDTAMECKKNILEMICALDLPNNPLDDIIDQVMIIH*