AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar ZhongmuNo.1 / MsG0480019812.01


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsG0480019812.01.T02 MTR_4g039540 96.875 64 2 0 1 64 55 118 3.63e-43 135
MsG0480019812.01.T01 MTR_4g039540 94.017 117 6 1 3 118 2 118 3.45e-80 231
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsG0480019812.01.T02 AT3G52070 74.359 39 9 1 18 55 66 104 2.29e-13 59.7
MsG0480019812.01.T02 AT3G52070 74.359 39 9 1 18 55 66 104 3.69e-13 59.3
MsG0480019812.01.T01 AT3G52070 43.333 90 39 3 32 109 15 104 2.87e-13 61.6
MsG0480019812.01.T01 AT3G52070 43.333 90 39 3 32 109 15 104 4.19e-13 61.2

Find 25 sgRNAs with CRISPR-Local

Find 28 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GCCACTCTTGGTATAGAATT+AGG 0.267818 4:-27745246 MsG0480019812.01.T01:CDS
CTTCTACCTTGGCAAGATAA+TGG 0.344639 4:+27745211 None:intergenic
GTCCACAACAAAAGGGTGAT+TGG 0.404912 4:-27745042 MsG0480019812.01.T01:CDS
GTATAGAATTAGGACCCCTT+TGG 0.412469 4:-27745236 MsG0480019812.01.T01:CDS
AATAAGCACATACTAACTTC+TGG 0.421785 4:+27744969 None:intergenic
GAATTTAAGTCCACAACAAA+AGG 0.428735 4:-27745050 MsG0480019812.01.T01:CDS
AACTACCATACATGTACATT+AGG 0.446681 4:+27744929 None:intergenic
ATAAGCACATACTAACTTCT+GGG 0.459372 4:+27744970 None:intergenic
AAATTCTTCATCTCTTGTTG+TGG 0.464351 4:+27745067 None:intergenic
TAGTATGTGCTTATTGTGCT+TGG 0.469587 4:-27744961 MsG0480019812.01.T01:CDS
CACTCACCATTAGCCACTCT+TGG 0.472156 4:-27745258 MsG0480019812.01.T01:CDS
AAGAAAGACATAGGAGGAAG+AGG 0.481981 4:-27745157 MsG0480019812.01.T01:CDS
AGATGCATGGTCTTCTACCT+TGG 0.492293 4:+27745200 None:intergenic
TCTATACCAAGAGTGGCTAA+TGG 0.502607 4:+27745252 None:intergenic
CTATGCCTAATGTACATGTA+TGG 0.513001 4:-27744934 MsG0480019812.01.T01:CDS
GGCAAGATAATGGAACCAAA+GGG 0.513637 4:+27745221 None:intergenic
TTGAGAAGCTAATTGGGAAG+AGG 0.524139 4:-27745090 MsG0480019812.01.T01:CDS
TTGGTTCCATTATCTTGCCA+AGG 0.539176 4:-27745217 MsG0480019812.01.T01:CDS
CATGAAGAAAAGAAAGACAT+AGG 0.556728 4:-27745166 MsG0480019812.01.T01:CDS
TGGCAAGATAATGGAACCAA+AGG 0.571857 4:+27745220 None:intergenic
TCCTAATTCTATACCAAGAG+TGG 0.590163 4:+27745245 None:intergenic
AATTTAAGTCCACAACAAAA+GGG 0.599106 4:-27745049 MsG0480019812.01.T01:CDS
TGATTGGAGTTAGAGATGCA+TGG 0.614307 4:+27745187 None:intergenic
GAAGAAAAGAAAGACATAGG+AGG 0.619275 4:-27745163 MsG0480019812.01.T01:CDS
GCAAGATAATGGAACCAAAG+GGG 0.711481 4:+27745222 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
! AATTTAAGTCCACAACAAAA+GGG - Chr4:27745147-27745166 MsG0480019812.01.T01:CDS 25.0%
!!! AATGATTTTGAGAAGCTAAT+TGG - Chr4:27745099-27745118 MsG0480019812.01.T01:CDS 25.0%
!!! ATGATTTTGAGAAGCTAATT+GGG - Chr4:27745100-27745119 MsG0480019812.01.T01:CDS 25.0%
AAATTCTTCATCTCTTGTTG+TGG + Chr4:27745132-27745151 None:intergenic 30.0%
AATAAGCACATACTAACTTC+TGG + Chr4:27745230-27745249 None:intergenic 30.0%
ATAAGCACATACTAACTTCT+GGG + Chr4:27745229-27745248 None:intergenic 30.0%
CATGAAGAAAAGAAAGACAT+AGG - Chr4:27745030-27745049 MsG0480019812.01.T01:CDS 30.0%
GAATTTAAGTCCACAACAAA+AGG - Chr4:27745146-27745165 MsG0480019812.01.T01:CDS 30.0%
! GTCTTTCTTTTCTTCATGAT+TGG + Chr4:27745028-27745047 None:intergenic 30.0%
CTATGCCTAATGTACATGTA+TGG - Chr4:27745262-27745281 MsG0480019812.01.T01:CDS 35.0%
GAAGAAAAGAAAGACATAGG+AGG - Chr4:27745033-27745052 MsG0480019812.01.T01:CDS 35.0%
TAGTATGTGCTTATTGTGCT+TGG - Chr4:27745235-27745254 MsG0480019812.01.T01:CDS 35.0%
TCCTAATTCTATACCAAGAG+TGG + Chr4:27744954-27744973 None:intergenic 35.0%
AAGAAAGACATAGGAGGAAG+AGG - Chr4:27745039-27745058 MsG0480019812.01.T01:CDS 40.0%
CTTCTACCTTGGCAAGATAA+TGG + Chr4:27744988-27745007 None:intergenic 40.0%
GCCACTCTTGGTATAGAATT+AGG - Chr4:27744950-27744969 MsG0480019812.01.T01:CDS 40.0%
GTATAGAATTAGGACCCCTT+TGG - Chr4:27744960-27744979 MsG0480019812.01.T01:CDS 40.0%
TCTATACCAAGAGTGGCTAA+TGG + Chr4:27744947-27744966 None:intergenic 40.0%
TGATTGGAGTTAGAGATGCA+TGG + Chr4:27745012-27745031 None:intergenic 40.0%
TTGAGAAGCTAATTGGGAAG+AGG - Chr4:27745106-27745125 MsG0480019812.01.T01:CDS 40.0%
TTGGTTCCATTATCTTGCCA+AGG - Chr4:27744979-27744998 MsG0480019812.01.T01:CDS 40.0%
! TTCCAATCACCCTTTTGTTG+TGG + Chr4:27745159-27745178 None:intergenic 40.0%
!! GCAAGATAATGGAACCAAAG+GGG + Chr4:27744977-27744996 None:intergenic 40.0%
!! GGCAAGATAATGGAACCAAA+GGG + Chr4:27744978-27744997 None:intergenic 40.0%
!! TGGCAAGATAATGGAACCAA+AGG + Chr4:27744979-27744998 None:intergenic 40.0%
AGATGCATGGTCTTCTACCT+TGG + Chr4:27744999-27745018 None:intergenic 45.0%
GTCCACAACAAAAGGGTGAT+TGG - Chr4:27745154-27745173 MsG0480019812.01.T01:CDS 45.0%
CACTCACCATTAGCCACTCT+TGG - Chr4:27744938-27744957 MsG0480019812.01.T01:CDS 50.0%
Chromosome Type Strat End Strand Name
Chr4 gene 27744931 27745287 27744931 ID=MsG0480019812.01;Name=MsG0480019812.01
Chr4 mRNA 27744931 27745287 27744931 ID=MsG0480019812.01.T01;Parent=MsG0480019812.01;Name=MsG0480019812.01.T01;_AED=0.50;_eAED=0.50;_QI=0|-1|0|1|-1|0|1|0|118
Chr4 exon 27744931 27745287 27744931 ID=MsG0480019812.01.T01:exon:2451;Parent=MsG0480019812.01.T01
Chr4 CDS 27744931 27745287 27744931 ID=MsG0480019812.01.T01:cds;Parent=MsG0480019812.01.T01
Chr4 mRNA 27744931 27745125 27744931 ID=MsG0480019812.01.T02;Parent=MsG0480019812.01;Name=MsG0480019812.01.T02;_AED=0.50;_eAED=0.50;_QI=0|-1|0|1|-1|0|1|0|64
Chr4 exon 27744931 27745125 27744931 ID=MsG0480019812.01.T02:exon:2452;Parent=MsG0480019812.01.T02
Chr4 CDS 27744931 27745125 27744931 ID=MsG0480019812.01.T02:cds;Parent=MsG0480019812.01.T02
Gene Sequence

>MsG0480019812.01.T02

ATGTTGAATGATTTTGAGAAGCTAATTGGGAAGAGGCCACAACAAGAGATGAAGAATTTAAGTCCACAACAAAAGGGTGATTGGAAAGACTTGTTTCTAATGAGTATTTCTTTTGCTGTTTATGTGTACATATCCCAGAAGTTAGTATGTGCTTATTGTGCTTGGACTTCTATGCCTAATGTACATGTATGGTAG

>MsG0480019812.01.T01

ATGGCATCACTCACCATTAGCCACTCTTGGTATAGAATTAGGACCCCTTTGGTTCCATTATCTTGCCAAGGTAGAAGACCATGCATCTCTAACTCCAATCATGAAGAAAAGAAAGACATAGGAGGAAGAGGAGCAAAGAGATCATTGTTGAAATTGAAAGTAATGTTGAATGATTTTGAGAAGCTAATTGGGAAGAGGCCACAACAAGAGATGAAGAATTTAAGTCCACAACAAAAGGGTGATTGGAAAGACTTGTTTCTAATGAGTATTTCTTTTGCTGTTTATGTGTACATATCCCAGAAGTTAGTATGTGCTTATTGTGCTTGGACTTCTATGCCTAATGTACATGTATGGTAG

Protein sequence

>MsG0480019812.01.T02

MLNDFEKLIGKRPQQEMKNLSPQQKGDWKDLFLMSISFAVYVYISQKLVCAYCAWTSMPNVHVW*

>MsG0480019812.01.T01

MASLTISHSWYRIRTPLVPLSCQGRRPCISNSNHEEKKDIGGRGAKRSLLKLKVMLNDFEKLIGKRPQQEMKNLSPQQKGDWKDLFLMSISFAVYVYISQKLVCAYCAWTSMPNVHVW*