AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar ZhongmuNo.1 / MsG0380013988.01


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsG0380013988.01.T02 MTR_4g051410 93.827 81 5 0 1 81 130 210 3.44e-48 152
MsG0380013988.01.T02 MTR_0002s0790 67.901 81 26 0 1 81 155 235 4.60e-35 119
MsG0380013988.01.T02 MTR_8g038470 75.000 72 11 1 1 72 107 171 6.72e-28 99.8
MsG0380013988.01.T05 MTR_4g051410 90.196 51 5 0 1 51 160 210 1.23e-26 95.5
MsG0380013988.01.T05 MTR_0002s0790 68.627 51 16 0 1 51 185 235 1.75e-20 80.1
MsG0380013988.01.T04 MTR_4g051410 91.803 61 5 0 1 61 150 210 8.03e-34 114
MsG0380013988.01.T04 MTR_0002s0790 63.934 61 22 0 1 61 175 235 3.38e-23 87.8
MsG0380013988.01.T04 MTR_8g038470 66.667 51 10 1 1 51 127 170 2.10e-14 63.9
MsG0380013988.01.T03 MTR_4g051410 93.056 72 5 0 1 72 139 210 3.36e-41 134
MsG0380013988.01.T03 MTR_0002s0790 65.278 72 25 0 1 72 164 235 1.84e-28 102
MsG0380013988.01.T03 MTR_8g038470 71.429 63 11 1 1 63 116 171 2.98e-21 82.4
MsG0380013988.01.T06 MTR_4g051410 84.615 39 6 0 6 44 172 210 9.68e-18 72.4
MsG0380013988.01.T06 MTR_0002s0790 65.789 38 13 0 7 44 198 235 3.16e-14 63.5
MsG0380013988.01.T01 MTR_4g051410 94.382 89 5 0 1 89 122 210 5.42e-54 167
MsG0380013988.01.T01 MTR_0002s0790 68.539 89 28 0 1 89 147 235 8.29e-39 129
MsG0380013988.01.T01 MTR_8g038470 77.500 80 11 1 1 80 99 171 1.31e-33 114
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsG0380013988.01.T02 ATCG00800 88.889 81 9 0 1 81 134 214 1.98e-47 150
MsG0380013988.01.T05 ATCG00800 92.157 51 4 0 1 51 164 214 3.35e-28 99.8
MsG0380013988.01.T04 ATCG00800 90.164 61 6 0 1 61 154 214 1.79e-34 116
MsG0380013988.01.T03 ATCG00800 88.889 72 8 0 1 72 143 214 9.77e-41 132
MsG0380013988.01.T06 ATCG00800 87.179 39 5 0 6 44 176 214 9.58e-21 80.1
MsG0380013988.01.T01 ATCG00800 89.888 89 9 0 1 89 126 214 4.09e-53 165

Find 23 sgRNAs with CRISPR-Local

Find 37 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TATACAGTTCGAACTATTTA+TGG 0.120735 3:-48581434 MsG0380013988.01.T01:CDS
ATAAATTCTGCAAGAATATT+AGG 0.153378 3:+48581866 None:intergenic
CGAACTATTTATGGGGTATT+AGG 0.214307 3:-48581425 MsG0380013988.01.T01:CDS
TAAAGAATAGAATTTCGTTT+AGG 0.349086 3:-48581832 MsG0380013988.01.T01:CDS
AGCTATTGAATTAGCTGAAC+AGG 0.363850 3:-48581795 MsG0380013988.01.T01:CDS
ATACAGTTCGAACTATTTAT+GGG 0.369096 3:-48581433 MsG0380013988.01.T01:CDS
GGGTATTAGGAATCAAAGTT+TGG 0.387551 3:-48581412 MsG0380013988.01.T01:CDS
TAAATTCTGCAAGAATATTA+GGG 0.426926 3:+48581867 None:intergenic
ATAAATAGTTCGAACTGTAT+AGG 0.427068 3:+48581436 None:intergenic
GGAGTTCAAGTACAAATTGC+GGG 0.442137 3:-48581761 MsG0380013988.01.T01:CDS
ATTCTTGCAGAATTTATAGC+TGG 0.468432 3:-48581860 MsG0380013988.01.T01:CDS
AAGAAATTGCACGTGTCGAA+TGG 0.483791 3:-48581724 MsG0380013988.01.T01:CDS
GCTGAACAGGCAGGTACAAA+AGG 0.497837 3:-48581782 MsG0380013988.01.T01:CDS
GAAATTGCACGTGTCTCGAA+TGG 0.543788 3:-48581514 MsG0380013988.01.T01:intron
CAAATTGCGGGACGTATCGA+CGG 0.567491 3:-48581749 MsG0380013988.01.T01:CDS
CGAATGGATTAGAGAAGGTA+GGG 0.570902 3:-48581498 MsG0380013988.01.T01:intron
TCGAATGGATTAGAGAAGGT+AGG 0.586825 3:-48581499 MsG0380013988.01.T01:intron
TTTAGCTCGAATGGTTGTAG+AGG 0.594421 3:+48581473 None:intergenic
ATTGAATTAGCTGAACAGGC+AGG 0.608696 3:-48581791 MsG0380013988.01.T01:CDS
CGTGTCGAATGGATTAGAGA+AGG 0.634314 3:-48581713 MsG0380013988.01.T01:intron
TACAGTTCGAACTATTTATG+GGG 0.637128 3:-48581432 MsG0380013988.01.T01:CDS
AGGAGTTCAAGTACAAATTG+CGG 0.647406 3:-48581762 MsG0380013988.01.T01:CDS
TGTCTCGAATGGATTAGAGA+AGG 0.652115 3:-48581503 MsG0380013988.01.T01:intron

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! ATAAATTCTGCAAGAATATT+AGG + Chr3:48581420-48581439 None:intergenic 20.0%
!! TAAAGAATAGAATTTCGTTT+AGG - Chr3:48581451-48581470 MsG0380013988.01.T01:CDS 20.0%
!! TAAATTCTGCAAGAATATTA+GGG + Chr3:48581419-48581438 None:intergenic 20.0%
! AATTCCTTGCAAGAATATTA+GGG + Chr3:48581622-48581641 None:intergenic 25.0%
! ATAAATAGTTCGAACTGTAT+AGG + Chr3:48581850-48581869 None:intergenic 25.0%
! ATACAGTTCGAACTATTTAT+GGG - Chr3:48581850-48581869 MsG0380013988.01.T01:CDS 25.0%
! TAATTCCTTGCAAGAATATT+AGG + Chr3:48581623-48581642 None:intergenic 25.0%
! TATACAGTTCGAACTATTTA+TGG - Chr3:48581849-48581868 MsG0380013988.01.T01:CDS 25.0%
!!! TAATCAATTTTTAGCTCGAA+TGG + Chr3:48581822-48581841 None:intergenic 25.0%
ATTCTTGCAGAATTTATAGC+TGG - Chr3:48581423-48581442 MsG0380013988.01.T01:CDS 30.0%
TACAGTTCGAACTATTTATG+GGG - Chr3:48581851-48581870 MsG0380013988.01.T01:CDS 30.0%
AAGGAGTTCAAGTACAATTG+CGG - Chr3:48581728-48581747 MsG0380013988.01.T01:CDS 35.0%
AGCTATTGAATTAGCTGAAC+AGG - Chr3:48581488-48581507 MsG0380013988.01.T01:intron 35.0%
AGGAGTTCAAGTACAAATTG+CGG - Chr3:48581521-48581540 MsG0380013988.01.T01:intron 35.0%
GGGTATTAGGAATCAAAGTT+TGG - Chr3:48581871-48581890 MsG0380013988.01.T07:CDS 35.0%
TAAAGACTCGAACTTCGTTT+AGG - Chr3:48581657-48581676 MsG0380013988.01.T01:intron 35.0%
TCTTGCAAGGAATTATAGTG+CGG - Chr3:48581628-48581647 MsG0380013988.01.T01:intron 35.0%
! CGAACTATTTATGGGGTATT+AGG - Chr3:48581858-48581877 MsG0380013988.01.T01:CDS 35.0%
AAGAAATTGCACGTGTCGAA+TGG - Chr3:48581559-48581578 MsG0380013988.01.T01:intron 40.0%
AGGAGTTCAAGTACAATTGC+GGG - Chr3:48581729-48581748 MsG0380013988.01.T01:CDS 40.0%
ATTGAATTAGCTGAACAGGC+AGG - Chr3:48581492-48581511 MsG0380013988.01.T01:intron 40.0%
CTTGCAAGGAATTATAGTGC+GGG - Chr3:48581629-48581648 MsG0380013988.01.T01:intron 40.0%
GGAGTTCAAGTACAAATTGC+GGG - Chr3:48581522-48581541 MsG0380013988.01.T01:intron 40.0%
TTGAATTAGCTGAACAGGCA+GGG - Chr3:48581493-48581512 MsG0380013988.01.T01:intron 40.0%
! TTTAGCTCGAATGGTTGTAG+AGG + Chr3:48581813-48581832 None:intergenic 40.0%
!! CGAATGGATTAGAGAAGGTA+GGG - Chr3:48581575-48581594 MsG0380013988.01.T01:intron 40.0%
!! TCGAATGGATTAGAGAAGGT+AGG - Chr3:48581574-48581593 MsG0380013988.01.T01:intron 40.0%
!! TGTCTCGAATGGATTAGAGA+AGG - Chr3:48581780-48581799 MsG0380013988.01.T01:CDS 40.0%
AGGGTCGCTATTGTTTGTAG+AGG + Chr3:48581603-48581622 None:intergenic 45.0%
GAAATTGCACGTGTCTCGAA+TGG - Chr3:48581769-48581788 MsG0380013988.01.T01:CDS 45.0%
GCGACCCTAATATTCTTGCA+AGG - Chr3:48581412-48581431 MsG0380013988.01.T01:CDS 45.0%
!! CGTGTCGAATGGATTAGAGA+AGG - Chr3:48581570-48581589 MsG0380013988.01.T01:intron 45.0%
ACAATTGCGGGACGTATCGA+CGG - Chr3:48581741-48581760 MsG0380013988.01.T01:CDS 50.0%
CAAATTGCGGGACGTATCGA+CGG - Chr3:48581534-48581553 MsG0380013988.01.T01:intron 50.0%
GAACAGGCAGGGTTGACAAA+AGG - Chr3:48581709-48581728 MsG0380013988.01.T01:intron 50.0%
GCTGAACAGGCAGGTACAAA+AGG - Chr3:48581501-48581520 MsG0380013988.01.T01:intron 50.0%
! GCGGGACGTATCGACGGAAA+AGG - Chr3:48581540-48581559 MsG0380013988.01.T01:intron 60.0%
Chromosome Type Strat End Strand Name
Chr3 gene 48581403 48581902 48581403 ID=MsG0380013988.01;Name=MsG0380013988.01
Chr3 mRNA 48581403 48581882 48581403 ID=MsG0380013988.01.T01;Parent=MsG0380013988.01;Name=MsG0380013988.01.T01;_AED=0.50;_eAED=0.50;_QI=0|0|0|1|0|0|2|0|89
Chr3 exon 48581714 48581882 48581714 ID=MsG0380013988.01.T01:exon:9397;Parent=MsG0380013988.01.T01
Chr3 CDS 48581714 48581882 48581714 ID=MsG0380013988.01.T01:cds;Parent=MsG0380013988.01.T01
Chr3 CDS 48581403 48581503 48581403 ID=MsG0380013988.01.T01:cds;Parent=MsG0380013988.01.T01
Chr3 mRNA 48581403 48581858 48581403 ID=MsG0380013988.01.T02;Parent=MsG0380013988.01;Name=MsG0380013988.01.T02;_AED=0.50;_eAED=0.50;_QI=0|0|0|1|0|0|2|0|81
Chr3 exon 48581714 48581858 48581714 ID=MsG0380013988.01.T02:exon:9399;Parent=MsG0380013988.01.T02
Chr3 CDS 48581714 48581858 48581714 ID=MsG0380013988.01.T02:cds;Parent=MsG0380013988.01.T02
Chr3 CDS 48581403 48581503 48581403 ID=MsG0380013988.01.T02:cds;Parent=MsG0380013988.01.T02
Chr3 mRNA 48581403 48581831 48581403 ID=MsG0380013988.01.T03;Parent=MsG0380013988.01;Name=MsG0380013988.01.T03;_AED=0.50;_eAED=0.50;_QI=0|0|0|1|0|0|2|0|72
Chr3 exon 48581714 48581831 48581714 ID=MsG0380013988.01.T03:exon:9400;Parent=MsG0380013988.01.T03
Chr3 CDS 48581714 48581831 48581714 ID=MsG0380013988.01.T03:cds;Parent=MsG0380013988.01.T03
Chr3 CDS 48581403 48581503 48581403 ID=MsG0380013988.01.T03:cds;Parent=MsG0380013988.01.T03
Chr3 mRNA 48581403 48581798 48581403 ID=MsG0380013988.01.T04;Parent=MsG0380013988.01;Name=MsG0380013988.01.T04;_AED=0.50;_eAED=0.50;_QI=0|0|0|1|0|0|2|0|61
Chr3 exon 48581714 48581798 48581714 ID=MsG0380013988.01.T04:exon:9401;Parent=MsG0380013988.01.T04
Chr3 CDS 48581714 48581798 48581714 ID=MsG0380013988.01.T04:cds;Parent=MsG0380013988.01.T04
Chr3 CDS 48581403 48581503 48581403 ID=MsG0380013988.01.T04:cds;Parent=MsG0380013988.01.T04
Chr3 mRNA 48581403 48581768 48581403 ID=MsG0380013988.01.T05;Parent=MsG0380013988.01;Name=MsG0380013988.01.T05;_AED=0.50;_eAED=0.50;_QI=0|0|0|1|0|0|2|0|51
Chr3 exon 48581714 48581768 48581714 ID=MsG0380013988.01.T05:exon:9402;Parent=MsG0380013988.01.T05
Chr3 CDS 48581714 48581768 48581714 ID=MsG0380013988.01.T05:cds;Parent=MsG0380013988.01.T05
Chr3 CDS 48581403 48581503 48581403 ID=MsG0380013988.01.T05:cds;Parent=MsG0380013988.01.T05
Chr3 mRNA 48581403 48581537 48581403 ID=MsG0380013988.01.T06;Parent=MsG0380013988.01;Name=MsG0380013988.01.T06;_AED=0.50;_eAED=0.50;_QI=0|-1|0|1|-1|0|1|0|44
Chr3 exon 48581403 48581537 48581403 ID=MsG0380013988.01.T06:exon:9403;Parent=MsG0380013988.01.T06
Chr3 CDS 48581403 48581537 48581403 ID=MsG0380013988.01.T06:cds;Parent=MsG0380013988.01.T06
Chr3 mRNA 48581864 48581902 48581864 ID=MsG0380013988.01.T07;Parent=MsG0380013988.01;Name=MsG0380013988.01.T07;_AED=0.50;_eAED=0.50;_QI=0|-1|0|1|-1|0|1|0|12
Chr3 exon 48581864 48581902 48581864 ID=MsG0380013988.01.T07:exon:9404;Parent=MsG0380013988.01.T07
Chr3 CDS 48581864 48581902 48581864 ID=MsG0380013988.01.T07:cds;Parent=MsG0380013988.01.T07
Chr3 mRNA 48581426 48581437 48581426 ID=MsG0380013988.01.T08;Parent=MsG0380013988.01;Name=MsG0380013988.01.T08;_AED=0.50;_eAED=0.50;_QI=0|-1|0|1|-1|0|1|0|3
Chr3 exon 48581426 48581437 48581426 ID=MsG0380013988.01.T08:exon:9405;Parent=MsG0380013988.01.T08
Chr3 CDS 48581426 48581437 48581426 ID=MsG0380013988.01.T08:cds;Parent=MsG0380013988.01.T08
Gene Sequence

>MsG0380013988.01.T07

ATGCTTATAGCGACCCTAATATTCTTGCAGAATTTATAG

>MsG0380013988.01.T08

ATGGGGTATTAG

>MsG0380013988.01.T02

CAATTAAAGAATAGAATTTCGTTTAGGAAAGCAATCAAAAAAGCTATTGAATTAGCTGAACAGGCAGGTACAAAAGGAGTTCAAGTACAAATTGCGGGACGTATCGACGGAAAAGAAATTGCACGTGTCGAATGGATTAGAGAAGGTAGGGTTCCTCTACAACCATTCGAGCTAAAAATTGATTATTGTTCCTATACAGTTCGAACTATTTATGGGGTATTAGGAATCAAAGTTTGGATATTTTAA

>MsG0380013988.01.T05

ATTGCGGGACGTATCGACGGAAAAGAAATTGCACGTGTCGAATGGATTAGAGAAGGTAGGGTTCCTCTACAACCATTCGAGCTAAAAATTGATTATTGTTCCTATACAGTTCGAACTATTTATGGGGTATTAGGAATCAAAGTTTGGATATTTTAA

>MsG0380013988.01.T04

CAGGCAGGTACAAAAGGAGTTCAAGTACAAATTGCGGGACGTATCGACGGAAAAGAAATTGCACGTGTCGAATGGATTAGAGAAGGTAGGGTTCCTCTACAACCATTCGAGCTAAAAATTGATTATTGTTCCTATACAGTTCGAACTATTTATGGGGTATTAGGAATCAAAGTTTGGATATTTTAA

>MsG0380013988.01.T03

AAAGCAATCAAAAAAGCTATTGAATTAGCTGAACAGGCAGGTACAAAAGGAGTTCAAGTACAAATTGCGGGACGTATCGACGGAAAAGAAATTGCACGTGTCGAATGGATTAGAGAAGGTAGGGTTCCTCTACAACCATTCGAGCTAAAAATTGATTATTGTTCCTATACAGTTCGAACTATTTATGGGGTATTAGGAATCAAAGTTTGGATATTTTAA

>MsG0380013988.01.T06

GGAAATTGCACGTGTCTCGAATGGATTAGAGAAGGTAGGGTTCCTCTACAACCATTCGAGCTAAAAATTGATTATTGTTCCTATACAGTTCGAACTATTTATGGGGTATTAGGAATCAAAGTTTGGATATTTTAA

>MsG0380013988.01.T01

ATTCTTGCAGAATTTATAGCTGGACAATTAAAGAATAGAATTTCGTTTAGGAAAGCAATCAAAAAAGCTATTGAATTAGCTGAACAGGCAGGTACAAAAGGAGTTCAAGTACAAATTGCGGGACGTATCGACGGAAAAGAAATTGCACGTGTCGAATGGATTAGAGAAGGTAGGGTTCCTCTACAACCATTCGAGCTAAAAATTGATTATTGTTCCTATACAGTTCGAACTATTTATGGGGTATTAGGAATCAAAGTTTGGATATTTTAA

Protein sequence

>MsG0380013988.01.T07

MLIATLIFLQNL*

>MsG0380013988.01.T08

MGY*

>MsG0380013988.01.T02

QLKNRISFRKAIKKAIELAEQAGTKGVQVQIAGRIDGKEIARVEWIREGRVPLQPFELKIDYCSYTVRTIYGVLGIKVWIF*

>MsG0380013988.01.T05

IAGRIDGKEIARVEWIREGRVPLQPFELKIDYCSYTVRTIYGVLGIKVWIF*

>MsG0380013988.01.T04

QAGTKGVQVQIAGRIDGKEIARVEWIREGRVPLQPFELKIDYCSYTVRTIYGVLGIKVWIF*

>MsG0380013988.01.T03

KAIKKAIELAEQAGTKGVQVQIAGRIDGKEIARVEWIREGRVPLQPFELKIDYCSYTVRTIYGVLGIKVWIF*

>MsG0380013988.01.T06

GNCTCLEWIREGRVPLQPFELKIDYCSYTVRTIYGVLGIKVWIF*

>MsG0380013988.01.T01

ILAEFIAGQLKNRISFRKAIKKAIELAEQAGTKGVQVQIAGRIDGKEIARVEWIREGRVPLQPFELKIDYCSYTVRTIYGVLGIKVWIF*