AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0307740

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0307740 MtrunA17_Chr5g0426511 51.351 148 43 7 1 123 1 144 1.43e-23 88.6
Msa0307740 MtrunA17_Chr2g0279541 61.290 124 15 5 1 123 1 92 4.65e-22 83.2
Msa0307740 MtrunA17_Chr4g0049911 46.789 109 40 3 1 100 1 100 1.66e-15 67.8
Msa0307740 MtrunA17_Chr4g0049921 52.885 104 41 3 1 100 1 100 4.19e-15 66.6
Msa0307740 MtrunA17_Chr4g0049951 45.872 109 41 3 1 100 1 100 8.59e-15 65.9
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0307740 AT5G09520.1 36.290 124 65 6 2 112 5 127 1.24e-11 58.2

Find 40 sgRNAs with CRISPR-Local

Find 43 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TTTGGAAGTGTTGGTGTAGT+TGG 0.341757 2_4:+879147 None:intergenic
TTTGGCAATGTTGGGATTGT+AGG 0.346130 2_4:+879054 None:intergenic
ATAGATGGCTGAGTAGGTTT+TGG 0.351476 2_4:+879036 None:intergenic
GGGATTGTAGTAGGAATGTT+TGG 0.366842 2_4:+878958 None:intergenic
GGGAATGTTGGCATAGTGAT+TGG 0.393983 2_4:+878937 None:intergenic
TGAGGCAATGTTGGAATTGT+TGG 0.400561 2_4:+879096 None:intergenic
TGTGGAATAGTTGGAATTGT+AGG 0.403230 2_4:+879000 None:intergenic
TGAAGGTGGTGGAGAAAAGA+AGG 0.426869 2_4:+878915 None:intergenic
AATGTTGGCAATGTTGGTTT+TGG 0.454379 2_4:+879129 None:intergenic
GGGATAGTACTAGGAATAGA+TGG 0.460146 2_4:+879021 None:intergenic
TGCTAAAATGAAGGAACTAT+AGG 0.465331 2_4:+879242 None:intergenic
TGCTATTTCCTTCTCAAACA+TGG 0.466175 2_4:-879211 Msa0307740:CDS
AAGAAGATTGCGAGCTGCTA+GGG 0.477055 2_4:+879182 None:intergenic
GGTGGCAATGTTGGCAATGT+TGG 0.477572 2_4:+879123 None:intergenic
ACATTTCCTTGAGGCAATGT+TGG 0.483996 2_4:+879087 None:intergenic
GGAATGTTGGCATAGTGATT+GGG 0.491312 2_4:+878938 None:intergenic
ATAGTGATTGGGATTGTAGT+AGG 0.509782 2_4:+878949 None:intergenic
GGAGAAAAGAAGGGGAATGT+TGG 0.509998 2_4:+878925 None:intergenic
AATGAAAATTGCTAAAATGA+AGG 0.510394 2_4:+879233 None:intergenic
AGAGTGAACTGTGGAATAGT+TGG 0.512404 2_4:+878991 None:intergenic
GAAGGTGGTGGAGAAAAGAA+GGG 0.525536 2_4:+878916 None:intergenic
GAAGAAGATTGCGAGCTGCT+AGG 0.529340 2_4:+879181 None:intergenic
GTGGAATAGTTGGAATTGTA+GGG 0.531662 2_4:+879001 None:intergenic
GTTGGAATTGTTGGCAAAGG+TGG 0.537047 2_4:+879105 None:intergenic
CTAGGAATAGATGGCTGAGT+AGG 0.540861 2_4:+879030 None:intergenic
GTAGTAGGAATGTTTGGAAG+TGG 0.541956 2_4:+878964 None:intergenic
GTTGGCAAAGGTGGCAATGT+TGG 0.545513 2_4:+879114 None:intergenic
GGAATTGTAGGGATAGTACT+AGG 0.546673 2_4:+879012 None:intergenic
GTTGGGATTGTAGGCAAAGG+TGG 0.549782 2_4:+879063 None:intergenic
GTAGGAATGTTTGGAAGTGG+TGG 0.557881 2_4:+878967 None:intergenic
GAAGGAACTATAGGAGGCCA+TGG 0.565486 2_4:+879251 None:intergenic
TAAAATGAAGGAACTATAGG+AGG 0.579978 2_4:+879245 None:intergenic
GGTAATGTCCATGTTTGAGA+AGG 0.594515 2_4:+879203 None:intergenic
TTGACACGAACTTCAAGGAG+TGG 0.601056 2_4:+878888 None:intergenic
ACAATTCCAACATTGCCTCA+AGG 0.633830 2_4:-879093 Msa0307740:CDS
AAGGTGGTGGAGAAAAGAAG+GGG 0.639486 2_4:+878917 None:intergenic
AATGTTGGAATTGTTGGCAA+AGG 0.641702 2_4:+879102 None:intergenic
AGTGGTGGAAGAGTGAACTG+TGG 0.689745 2_4:+878982 None:intergenic
AATGTTGGGATTGTAGGCAA+AGG 0.702377 2_4:+879060 None:intergenic
AAAGGTGGAACATTTCCTTG+AGG 0.706888 2_4:+879078 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AATGAAAATTGCTAAAATGA+AGG + chr2_4:878919-878938 None:intergenic 20.0%
TAAAATGAAGGAACTATAGG+AGG + chr2_4:878907-878926 None:intergenic 30.0%
TGCTAAAATGAAGGAACTAT+AGG + chr2_4:878910-878929 None:intergenic 30.0%
!! TGCTATTTCCTTCTCAAACA+TGG - chr2_4:878938-878957 Msa0307740:CDS 35.0%
!!! AATGTTGGTTTTGGAAGTGT+TGG + chr2_4:879014-879033 None:intergenic 35.0%
!!! AATGTTGGCAATGTTGGTTT+TGG + chr2_4:879023-879042 None:intergenic 35.0%
AATGTTGGAATTGTTGGCAA+AGG + chr2_4:879050-879069 None:intergenic 35.0%
GTGGAATAGTTGGAATTGTA+GGG + chr2_4:879151-879170 None:intergenic 35.0%
TGTGGAATAGTTGGAATTGT+AGG + chr2_4:879152-879171 None:intergenic 35.0%
ATAGTGATTGGGATTGTAGT+AGG + chr2_4:879203-879222 None:intergenic 35.0%
GGTAATGTCCATGTTTGAGA+AGG + chr2_4:878949-878968 None:intergenic 40.0%
!! TTTGGAAGTGTTGGTGTAGT+TGG + chr2_4:879005-879024 None:intergenic 40.0%
TGAGGCAATGTTGGAATTGT+TGG + chr2_4:879056-879075 None:intergenic 40.0%
ACAATTCCAACATTGCCTCA+AGG - chr2_4:879056-879075 Msa0307740:CDS 40.0%
ACATTTCCTTGAGGCAATGT+TGG + chr2_4:879065-879084 None:intergenic 40.0%
AAAGGTGGAACATTTCCTTG+AGG + chr2_4:879074-879093 None:intergenic 40.0%
AATGTTGGGATTGTAGGCAA+AGG + chr2_4:879092-879111 None:intergenic 40.0%
TTTGGCAATGTTGGGATTGT+AGG + chr2_4:879098-879117 None:intergenic 40.0%
!! GAGTAGGTTTTGGCAATGTT+GGG + chr2_4:879106-879125 None:intergenic 40.0%
!! TGAGTAGGTTTTGGCAATGT+TGG + chr2_4:879107-879126 None:intergenic 40.0%
! ATAGATGGCTGAGTAGGTTT+TGG + chr2_4:879116-879135 None:intergenic 40.0%
GGGATAGTACTAGGAATAGA+TGG + chr2_4:879131-879150 None:intergenic 40.0%
GGAATTGTAGGGATAGTACT+AGG + chr2_4:879140-879159 None:intergenic 40.0%
AGAGTGAACTGTGGAATAGT+TGG + chr2_4:879161-879180 None:intergenic 40.0%
GTAGTAGGAATGTTTGGAAG+TGG + chr2_4:879188-879207 None:intergenic 40.0%
GGGATTGTAGTAGGAATGTT+TGG + chr2_4:879194-879213 None:intergenic 40.0%
GGAATGTTGGCATAGTGATT+GGG + chr2_4:879214-879233 None:intergenic 40.0%
AAGAAGATTGCGAGCTGCTA+GGG + chr2_4:878970-878989 None:intergenic 45.0%
GTTGGAATTGTTGGCAAAGG+TGG + chr2_4:879047-879066 None:intergenic 45.0%
CTAGGAATAGATGGCTGAGT+AGG + chr2_4:879122-879141 None:intergenic 45.0%
GTAGGAATGTTTGGAAGTGG+TGG + chr2_4:879185-879204 None:intergenic 45.0%
GGGAATGTTGGCATAGTGAT+TGG + chr2_4:879215-879234 None:intergenic 45.0%
GGAGAAAAGAAGGGGAATGT+TGG + chr2_4:879227-879246 None:intergenic 45.0%
!! AAGGTGGTGGAGAAAAGAAG+GGG + chr2_4:879235-879254 None:intergenic 45.0%
!! GAAGGTGGTGGAGAAAAGAA+GGG + chr2_4:879236-879255 None:intergenic 45.0%
!! TGAAGGTGGTGGAGAAAAGA+AGG + chr2_4:879237-879256 None:intergenic 45.0%
!! CAAGGAGTGGTTTTTGAAGG+TGG + chr2_4:879251-879270 None:intergenic 45.0%
GAAGAAGATTGCGAGCTGCT+AGG + chr2_4:878971-878990 None:intergenic 50.0%
GGTGGCAATGTTGGCAATGT+TGG + chr2_4:879029-879048 None:intergenic 50.0%
GTTGGCAAAGGTGGCAATGT+TGG + chr2_4:879038-879057 None:intergenic 50.0%
GTTGGGATTGTAGGCAAAGG+TGG + chr2_4:879089-879108 None:intergenic 50.0%
! AGTGGTGGAAGAGTGAACTG+TGG + chr2_4:879170-879189 None:intergenic 50.0%
!! GGAGTGGTTTTTGAAGGTGG+TGG + chr2_4:879248-879267 None:intergenic 50.0%
Chromosome Type Strat End Strand Name
chr2_4 gene 878900 879271 878900 ID=Msa0307740;Name=Msa0307740
chr2_4 mRNA 878900 879271 878900 ID=Msa0307740-mRNA-1;Parent=Msa0307740;Name=Msa0307740-mRNA-1;_AED=0.00;_eAED=0.10;_QI=0|-1|0|1|-1|1|1|0|123
chr2_4 exon 878900 879271 878900 ID=Msa0307740-mRNA-1:exon:330;Parent=Msa0307740-mRNA-1
chr2_4 CDS 878900 879271 878900 ID=Msa0307740-mRNA-1:cds;Parent=Msa0307740-mRNA-1
Gene Sequence

>Msa0307740

ATGGCCTCCTATAGTTCCTTCATTTTAGCAATTTTCATTGCTATTTCCTTCTCAAACATGGACATTACCCTAGCAGCTCGCAATCTTCTTCAGACAACAAATCCAACTACACCAACACTTCCAAAACCAACATTGCCAACATTGCCACCTTTGCCAACAATTCCAACATTGCCTCAAGGAAATGTTCCACCTTTGCCTACAATCCCAACATTGCCAAAACCTACTCAGCCATCTATTCCTAGTACTATCCCTACAATTCCAACTATTCCACAGTTCACTCTTCCACCACTTCCAAACATTCCTACTACAATCCCAATCACTATGCCAACATTCCCCTTCTTTTCTCCACCACCTTCAAAAACCACTCCTTGA
Protein sequence

>Msa0307740

MASYSSFILAIFIAISFSNMDITLAARNLLQTTNPTTPTLPKPTLPTLPPLPTIPTLPQGNVPPLPTIPTLPKPTQPSIPSTIPTIPTIPQFTLPPLPNIPTTIPITMPTFPFFSPPPSKTTP*