AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0137330

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0137330 MtrunA17_Chr1g0209391 90.196 153 14 1 1 153 497 648 2.05e-87 268
Msa0137330 MtrunA17_Chr1g0209361 56.954 151 59 3 2 149 541 688 5.83e-44 153
Msa0137330 MtrunA17_Chr1g0209381 53.901 141 57 2 4 144 528 660 7.28e-41 144
Msa0137330 MtrunA17_Chr1g0209431 51.007 149 65 4 1 149 535 675 2.71e-39 140
Msa0137330 MtrunA17_Chr5g0423061 56.383 94 39 1 1 94 510 601 5.06e-30 114
Msa0137330 MtrunA17_Chr7g0251121 41.007 139 64 2 1 139 564 684 4.90e-28 108
Msa0137330 MtrunA17_Chr6g0483931 59.259 81 33 0 1 81 566 646 5.52e-28 108
Msa0137330 MtrunA17_Chr8g0376061 58.025 81 34 0 1 81 533 613 9.76e-27 104
Msa0137330 MtrunA17_Chr6g0467631 54.023 87 39 1 1 87 547 632 7.24e-26 102
Msa0137330 MtrunA17_Chr6g0467601 52.874 87 40 1 1 87 351 436 9.96e-25 98.6
Msa0137330 MtrunA17_Chr6g0483731 45.882 85 44 1 1 85 268 350 7.02e-18 79.0
Msa0137330 MtrunA17_Chr5g0415451 41.975 81 47 0 1 81 639 719 1.11e-14 70.1
Msa0137330 MtrunA17_Chr8g0374031 38.835 103 59 1 1 103 533 631 2.01e-14 69.3
Msa0137330 MtrunA17_Chr6g0483781 44.118 68 38 0 15 82 160 227 2.11e-12 62.4
Msa0137330 MtrunA17_Chr6g0483831 39.506 81 48 1 2 82 187 266 3.40e-12 62.4
Msa0137330 MtrunA17_Chr6g0483841 40.278 72 43 0 11 82 156 227 6.25e-12 61.6
Msa0137330 MtrunA17_Chr6g0483771 39.506 81 48 1 2 82 187 266 8.51e-12 61.2
Msa0137330 MtrunA17_Chr5g0403051 38.947 95 54 1 1 95 527 617 2.86e-11 60.5
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0137330 AT1G25390.1 43.333 150 70 3 2 149 490 626 5.82e-30 114
Msa0137330 AT1G25390.2 43.333 150 70 3 2 149 490 626 5.82e-30 114
Msa0137330 AT1G66880.1 41.667 144 67 5 3 145 1166 1293 3.12e-26 103
Msa0137330 AT1G18390.2 41.135 141 56 4 1 141 541 654 6.33e-26 102
Msa0137330 AT1G18390.1 41.135 141 56 4 1 141 535 648 7.51e-26 102
Msa0137330 AT1G66880.2 41.667 144 67 5 3 145 787 914 1.36e-25 102
Msa0137330 AT1G66880.3 40.972 144 68 5 3 145 545 672 2.69e-25 100
Msa0137330 AT5G38210.1 47.826 92 48 0 3 94 557 648 4.52e-23 94.7
Msa0137330 AT5G38210.2 53.247 77 36 0 3 79 569 645 1.01e-22 93.6
Msa0137330 AT5G38210.3 47.826 92 48 0 3 94 551 642 1.75e-22 92.8
Msa0137330 AT2G23450.2 43.038 79 45 0 1 79 545 623 1.24e-12 64.7
Msa0137330 AT2G23450.1 43.038 79 45 0 1 79 545 623 1.24e-12 64.7
Msa0137330 AT5G66790.1 36.842 76 48 0 4 79 518 593 3.87e-11 60.5

Find 37 sgRNAs with CRISPR-Local

Find 42 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AGTCAGATAACGATGTTAAA+AGG 0.259871 1_3:+69738873 Msa0137330:CDS
CTAAGTCCGTGACAGATAAA+TGG 0.268636 1_3:+69739149 Msa0137330:CDS
GCCCTCAATGGATGAGGTTT+TGG 0.323285 1_3:+69738955 Msa0137330:CDS
TCAGTGTTTGCAACGGGATA+AGG 0.375219 1_3:+69738925 Msa0137330:CDS
CATTTATCTGTCACGGACTT+AGG 0.383164 1_3:-69739148 None:intergenic
GGGAGCGGGAGGGATGAGTT+TGG 0.414095 1_3:+69739001 Msa0137330:CDS
GAGCTGGTGGATCCTTCCCT+TGG 0.430370 1_3:+69738845 Msa0137330:CDS
AGTTTCATCTCAACGTGATC+GGG 0.475815 1_3:-69739097 None:intergenic
GGATTGATAGTGGGAGCGGG+AGG 0.483904 1_3:+69738990 Msa0137330:CDS
GTGCTTAAGAGGATTGATAG+TGG 0.489788 1_3:+69738980 Msa0137330:CDS
CAGTTTCATCTCAACGTGAT+CGG 0.492259 1_3:-69739098 None:intergenic
TAAGTCCGTGACAGATAAAT+GGG 0.494420 1_3:+69739150 Msa0137330:CDS
AATAGTTTCGATAGCAGAGT+TGG 0.512039 1_3:+69738898 Msa0137330:CDS
GATTGATAGTGGGAGCGGGA+GGG 0.516926 1_3:+69738991 Msa0137330:CDS
TAAGGAATTGAGGCCCTCAA+TGG 0.519644 1_3:+69738943 Msa0137330:CDS
AGTTGATATGAGCAGAGATA+AGG 0.527760 1_3:+69738766 Msa0137330:CDS
TCCAAAACCTCATCCATTGA+GGG 0.532645 1_3:-69738956 None:intergenic
ATCCAAAACCTCATCCATTG+AGG 0.537748 1_3:-69738957 None:intergenic
TCTCTGCTCATATCAACTGC+TGG 0.544298 1_3:-69738761 None:intergenic
ACTTGGCAAATTTAGCCGTA+AGG 0.550481 1_3:+69738798 Msa0137330:CDS
TGCTTAAGAGGATTGATAGT+GGG 0.553372 1_3:+69738981 Msa0137330:CDS
ATTGAGGCCCTCAATGGATG+AGG 0.560196 1_3:+69738949 Msa0137330:CDS
AAGAGGATTGATAGTGGGAG+CGG 0.562809 1_3:+69738986 Msa0137330:CDS
GGGAAGGATCCACCAGCTCA+TGG 0.564106 1_3:-69738841 None:intergenic
GGATGAGTTTGGACATGTAG+AGG 0.568660 1_3:+69739012 Msa0137330:CDS
ACTATCCCATTTATCTGTCA+CGG 0.571266 1_3:-69739155 None:intergenic
AGAGGATTGATAGTGGGAGC+GGG 0.578226 1_3:+69738987 Msa0137330:CDS
TGCAACGGGATAAGGAATTG+AGG 0.581438 1_3:+69738933 Msa0137330:CDS
CGTTATCTGACTCAAAGCCA+AGG 0.598356 1_3:-69738862 None:intergenic
GTAGAGGAAGTAATAGCTTG+TGG 0.600381 1_3:+69739028 Msa0137330:CDS
AAGTAAAATCCATGAGCTGG+TGG 0.601099 1_3:+69738832 Msa0137330:CDS
TCTGTCACGGACTTAGGAGA+AGG 0.608500 1_3:-69739142 None:intergenic
AGATAAGGATGAGATAGACT+TGG 0.608833 1_3:+69738781 Msa0137330:CDS
TCTGACTCAAAGCCAAGGGA+AGG 0.635280 1_3:-69738857 None:intergenic
TCGACTACTTCTAATGTCAG+TGG 0.653823 1_3:+69739181 Msa0137330:CDS
GTTATCTGACTCAAAGCCAA+GGG 0.661526 1_3:-69738861 None:intergenic
ACGTGATCGGGTGAAGACAG+TGG 0.664220 1_3:-69739085 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! ACTTTTTTGAATCTTCCTTA+CGG - chr1_3:69738816-69738835 None:intergenic 25.0%
AAAAAGTAAAATCCATGAGC+TGG + chr1_3:69738829-69738848 Msa0137330:CDS 30.0%
AGTCAGATAACGATGTTAAA+AGG + chr1_3:69738873-69738892 Msa0137330:CDS 30.0%
! AGTTGATATGAGCAGAGATA+AGG + chr1_3:69738766-69738785 Msa0137330:CDS 35.0%
AGATAAGGATGAGATAGACT+TGG + chr1_3:69738781-69738800 Msa0137330:CDS 35.0%
AATAGTTTCGATAGCAGAGT+TGG + chr1_3:69738898-69738917 Msa0137330:CDS 35.0%
! TGCTTAAGAGGATTGATAGT+GGG + chr1_3:69738981-69739000 Msa0137330:CDS 35.0%
TAAGTCCGTGACAGATAAAT+GGG + chr1_3:69739150-69739169 Msa0137330:CDS 35.0%
ACTATCCCATTTATCTGTCA+CGG - chr1_3:69739158-69739177 None:intergenic 35.0%
ACTTGGCAAATTTAGCCGTA+AGG + chr1_3:69738798-69738817 Msa0137330:CDS 40.0%
AAGTAAAATCCATGAGCTGG+TGG + chr1_3:69738832-69738851 Msa0137330:CDS 40.0%
GTTATCTGACTCAAAGCCAA+GGG - chr1_3:69738864-69738883 None:intergenic 40.0%
! TGGCTTTTCAGTGTTTGCAA+CGG + chr1_3:69738918-69738937 Msa0137330:CDS 40.0%
TCCAAAACCTCATCCATTGA+GGG - chr1_3:69738959-69738978 None:intergenic 40.0%
ATCCAAAACCTCATCCATTG+AGG - chr1_3:69738960-69738979 None:intergenic 40.0%
!!! AGGTTTTGGATGTGCTTAAG+AGG + chr1_3:69738969-69738988 Msa0137330:CDS 40.0%
GTGCTTAAGAGGATTGATAG+TGG + chr1_3:69738980-69738999 Msa0137330:CDS 40.0%
GTAGAGGAAGTAATAGCTTG+TGG + chr1_3:69739028-69739047 Msa0137330:CDS 40.0%
AGTTTCATCTCAACGTGATC+GGG - chr1_3:69739100-69739119 None:intergenic 40.0%
CAGTTTCATCTCAACGTGAT+CGG - chr1_3:69739101-69739120 None:intergenic 40.0%
CATTTATCTGTCACGGACTT+AGG - chr1_3:69739151-69739170 None:intergenic 40.0%
CTAAGTCCGTGACAGATAAA+TGG + chr1_3:69739149-69739168 Msa0137330:CDS 40.0%
TCGACTACTTCTAATGTCAG+TGG + chr1_3:69739181-69739200 Msa0137330:CDS 40.0%
TCTCTGCTCATATCAACTGC+TGG - chr1_3:69738764-69738783 None:intergenic 45.0%
CGTTATCTGACTCAAAGCCA+AGG - chr1_3:69738865-69738884 None:intergenic 45.0%
! GGCTTTTCAGTGTTTGCAAC+GGG + chr1_3:69738919-69738938 Msa0137330:CDS 45.0%
TCAGTGTTTGCAACGGGATA+AGG + chr1_3:69738925-69738944 Msa0137330:CDS 45.0%
TGCAACGGGATAAGGAATTG+AGG + chr1_3:69738933-69738952 Msa0137330:CDS 45.0%
TAAGGAATTGAGGCCCTCAA+TGG + chr1_3:69738943-69738962 Msa0137330:CDS 45.0%
!! AAGAGGATTGATAGTGGGAG+CGG + chr1_3:69738986-69739005 Msa0137330:CDS 45.0%
GGATGAGTTTGGACATGTAG+AGG + chr1_3:69739012-69739031 Msa0137330:CDS 45.0%
TCTGACTCAAAGCCAAGGGA+AGG - chr1_3:69738860-69738879 None:intergenic 50.0%
ATTGAGGCCCTCAATGGATG+AGG + chr1_3:69738949-69738968 Msa0137330:CDS 50.0%
! GCCCTCAATGGATGAGGTTT+TGG + chr1_3:69738955-69738974 Msa0137330:CDS 50.0%
!! AGAGGATTGATAGTGGGAGC+GGG + chr1_3:69738987-69739006 Msa0137330:CDS 50.0%
TCTGTCACGGACTTAGGAGA+AGG - chr1_3:69739145-69739164 None:intergenic 50.0%
!! GATTGATAGTGGGAGCGGGA+GGG + chr1_3:69738991-69739010 Msa0137330:CDS 55.0%
ACGTGATCGGGTGAAGACAG+TGG - chr1_3:69739088-69739107 None:intergenic 55.0%
GGGAAGGATCCACCAGCTCA+TGG - chr1_3:69738844-69738863 None:intergenic 60.0%
! GAGCTGGTGGATCCTTCCCT+TGG + chr1_3:69738845-69738864 Msa0137330:CDS 60.0%
!! GGATTGATAGTGGGAGCGGG+AGG + chr1_3:69738990-69739009 Msa0137330:CDS 60.0%
GGGAGCGGGAGGGATGAGTT+TGG + chr1_3:69739001-69739020 Msa0137330:CDS 65.0%
Chromosome Type Strat End Strand Name
chr1_3 gene 69738758 69739219 69738758 ID=Msa0137330;Name=Msa0137330
chr1_3 mRNA 69738758 69739219 69738758 ID=Msa0137330-mRNA-1;Parent=Msa0137330;Name=Msa0137330-mRNA-1;_AED=0.48;_eAED=0.48;_QI=0|-1|0|1|-1|1|1|0|153
chr1_3 exon 69738758 69739219 69738758 ID=Msa0137330-mRNA-1:exon:24155;Parent=Msa0137330-mRNA-1
chr1_3 CDS 69738758 69739219 69738758 ID=Msa0137330-mRNA-1:cds;Parent=Msa0137330-mRNA-1
Gene Sequence

>Msa0137330

ATGCCAGCAGTTGATATGAGCAGAGATAAGGATGAGATAGACTTGGCAAATTTAGCCGTAAGGAAGATTCAAAAAAGTAAAATCCATGAGCTGGTGGATCCTTCCCTTGGCTTTGAGTCAGATAACGATGTTAAAAGGAAAATAGTTTCGATAGCAGAGTTGGCTTTTCAGTGTTTGCAACGGGATAAGGAATTGAGGCCCTCAATGGATGAGGTTTTGGATGTGCTTAAGAGGATTGATAGTGGGAGCGGGAGGGATGAGTTTGGACATGTAGAGGAAGTAATAGCTTGTGGAGCAGTGATGTCGAGTATCAATGTACGTTCAATGCCACTGTCTTCACCCGATCACGTTGAGATGAAACTGTTGAAGAATAAGAAGTTAACACCTTCTCCTAAGTCCGTGACAGATAAATGGGATAGTGAATCGACTACTTCTAATGTCAGTGGTCAATCAGCGAGCTGA
Protein sequence

>Msa0137330

MPAVDMSRDKDEIDLANLAVRKIQKSKIHELVDPSLGFESDNDVKRKIVSIAELAFQCLQRDKELRPSMDEVLDVLKRIDSGSGRDEFGHVEEVIACGAVMSSINVRSMPLSSPDHVEMKLLKNKKLTPSPKSVTDKWDSESTTSNVSGQSAS*