AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0626880

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0626880 MtrunA17_Chr4g0003091 91.146 192 3 3 1 190 1 180 2.62e-119 335
Msa0626880 MtrunA17_Chr2g0282361 35.450 189 81 10 16 184 83 250 8.69e-14 67.8
Msa0626880 MtrunA17_Chr2g0317321 36.598 194 92 8 16 190 65 246 2.85e-13 66.2
Msa0626880 MtrunA17_Chr4g0047141 34.021 194 86 8 16 187 61 234 7.92e-11 59.3
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0626880 AT1G80450.1 41.709 199 55 7 11 189 10 167 3.93e-31 112
Msa0626880 AT1G28280.1 35.938 192 88 10 16 184 57 236 6.85e-14 68.2
Msa0626880 AT1G28280.2 35.938 192 88 10 16 184 57 236 7.76e-14 68.2
Msa0626880 AT5G08480.2 34.054 185 86 5 11 186 12 169 2.71e-13 65.1
Msa0626880 AT5G08480.3 34.054 185 86 5 11 186 12 169 2.71e-13 65.1
Msa0626880 AT3G15300.1 33.161 193 89 8 16 184 37 213 1.04e-11 62.0
Msa0626880 AT2G33780.1 32.065 184 98 8 16 189 36 202 1.07e-11 61.6
Msa0626880 AT5G53830.1 34.634 205 92 11 16 188 49 243 4.80e-11 60.5

Find 44 sgRNAs with CRISPR-Local

Find 60 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TTGGTGGAGGACGGTGGGCT+TGG 0.256659 4_3:-6907991 None:intergenic
GAGGACGGTGGGCTTGGGCT+TGG 0.257828 4_3:-6907985 None:intergenic
CAACATGCGAAGTGTTATTA+TGG 0.268568 4_3:+6908177 Msa0626880:CDS
TCATGTTATTGTTGTTGTTT+TGG 0.291134 4_3:-6908123 None:intergenic
AGGACGGTGGGCTTGGGCTT+GGG 0.306796 4_3:-6907984 None:intergenic
TAATATTCCAATGGTGAAAC+TGG 0.334222 4_3:-6908205 None:intergenic
TGGTGGAGGACGGTGGGCTT+GGG 0.338898 4_3:-6907990 None:intergenic
TTGTGTTTGGTTGTGTTGTT+AGG 0.343814 4_3:-6907847 None:intergenic
GGTTCCATGGTGGTTGTTGT+TGG 0.392587 4_3:-6908010 None:intergenic
TCCATGGTGGTTGTTGTTGG+TGG 0.405900 4_3:-6908007 None:intergenic
GCTTGTACAAAGGTTGTGTT+TGG 0.409951 4_3:-6907860 None:intergenic
ACAACTTGTCGGAAATTTGA+TGG 0.417823 4_3:-6907887 None:intergenic
TAAGAATGAGATTGAGAGGA+AGG 0.425929 4_3:-6908370 None:intergenic
GCGTTCGTGGAGTTTGAAGT+TGG 0.435488 4_3:-6908053 None:intergenic
CGTTCGTGGAGTTTGAAGTT+GGG 0.446220 4_3:-6908052 None:intergenic
TGGTTGTTGTTGGTGGAGGA+CGG 0.455302 4_3:-6908000 None:intergenic
TAAGCCCATTGGTGGTTCCA+TGG 0.464436 4_3:-6908023 None:intergenic
ACCATGCATTCACCAACATA+TGG 0.465787 4_3:+6907818 None:intergenic
GGCTTCACCAGTTTCACCAT+TGG 0.477870 4_3:+6908198 Msa0626880:CDS
TGTTGTTGGTGGAGGACGGT+GGG 0.481918 4_3:-6907996 None:intergenic
AAAACTCCAACTCAACGTTT+CGG 0.499017 4_3:+6908084 Msa0626880:CDS
AGACGAGAAGGGAGTGTGAG+TGG 0.503781 4_3:-6907956 None:intergenic
TGATGGGTCTTGTGATGCTC+CGG 0.504118 4_3:-6907921 None:intergenic
ATGGTGGTTGTTGTTGGTGG+AGG 0.515633 4_3:-6908004 None:intergenic
AACCACCATGGAACCACCAA+TGG 0.516253 4_3:+6908018 Msa0626880:CDS
AATTTAAGAATGAGATTGAG+AGG 0.526049 4_3:-6908374 None:intergenic
ACCACCATGGAACCACCAAT+GGG 0.535319 4_3:+6908019 Msa0626880:CDS
GTTTGGTTGTGTTGTTAGGT+CGG 0.535973 4_3:-6907843 None:intergenic
GCTTGGGCTGTTAGACGAGA+AGG 0.539771 4_3:-6907968 None:intergenic
TTGTTGTTGGTGGAGGACGG+TGG 0.540140 4_3:-6907997 None:intergenic
TGATGGGTCTGCTTGTACAA+AGG 0.550070 4_3:-6907870 None:intergenic
GGACTATAGTAATATTCCAA+TGG 0.550459 4_3:-6908214 None:intergenic
CAACTTGTCGGAAATTTGAT+GGG 0.562610 4_3:-6907886 None:intergenic
TGTTGAGAAGCTCTAGGAGA+GGG 0.563092 4_3:-6908307 None:intergenic
TGAGAGGAAGGAGAATGCAA+AGG 0.574115 4_3:-6908358 None:intergenic
GGTTGTTGTTGAGAAGCTCT+AGG 0.576546 4_3:-6908313 None:intergenic
GTTAGGTCGGATCCATATGT+TGG 0.606638 4_3:-6907830 None:intergenic
AAAAGAGGTAAAAGTTCAGG+TGG 0.608567 4_3:-6908334 None:intergenic
TCCATATGTTGGTGAATGCA+TGG 0.614670 4_3:-6907819 None:intergenic
CTTGGGCTGTTAGACGAGAA+GGG 0.624849 4_3:-6907967 None:intergenic
TTGTTGAGAAGCTCTAGGAG+AGG 0.644100 4_3:-6908308 None:intergenic
TCCACCAACAACAACCACCA+TGG 0.648779 4_3:+6908006 Msa0626880:CDS
GCCCATTGGTGGTTCCATGG+TGG 0.657294 4_3:-6908020 None:intergenic
GTTGAGAAGCTCTAGGAGAG+GGG 0.657383 4_3:-6908306 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TCATGTTATTGTTGTTGTTT+TGG - chr4_3:6908126-6908145 None:intergenic 25.0%
!! TCTTTTTCTTCATTTTCATG+TGG - chr4_3:6908247-6908266 None:intergenic 25.0%
!! TTAGTTTTTGGACAACTTGT+CGG - chr4_3:6907901-6907920 None:intergenic 30.0%
!!! TTGTTGTTTTGGAACATCAT+GGG - chr4_3:6908115-6908134 None:intergenic 30.0%
TAATATTCCAATGGTGAAAC+TGG - chr4_3:6908208-6908227 None:intergenic 30.0%
GGACTATAGTAATATTCCAA+TGG - chr4_3:6908217-6908236 None:intergenic 30.0%
! TCATTTTCATGTGGTGATTT+TGG - chr4_3:6908238-6908257 None:intergenic 30.0%
GAAAAAGTGATAGCTGAAAA+AGG + chr4_3:6908271-6908290 Msa0626880:CDS 30.0%
! TTGTGTTTGGTTGTGTTGTT+AGG - chr4_3:6907850-6907869 None:intergenic 35.0%
CAACTTGTCGGAAATTTGAT+GGG - chr4_3:6907889-6907908 None:intergenic 35.0%
ACAACTTGTCGGAAATTTGA+TGG - chr4_3:6907890-6907909 None:intergenic 35.0%
CAAGTTGTCCAAAAACTAAC+CGG + chr4_3:6907902-6907921 Msa0626880:CDS 35.0%
!!! TTGGGTTTTTTTAAGCCCAT+TGG - chr4_3:6908037-6908056 None:intergenic 35.0%
!!! TGAGTTGGAGTTTTTTAGAG+CGG - chr4_3:6908078-6908097 None:intergenic 35.0%
AAAACTCCAACTCAACGTTT+CGG + chr4_3:6908084-6908103 Msa0626880:CDS 35.0%
!!! GTTGTTGTTTTGGAACATCA+TGG - chr4_3:6908116-6908135 None:intergenic 35.0%
! CAACATGCGAAGTGTTATTA+TGG + chr4_3:6908177-6908196 Msa0626880:CDS 35.0%
AAAAGAGGTAAAAGTTCAGG+TGG - chr4_3:6908337-6908356 None:intergenic 35.0%
GGAAAAAGAGGTAAAAGTTC+AGG - chr4_3:6908340-6908359 None:intergenic 35.0%
TAAGAATGAGATTGAGAGGA+AGG - chr4_3:6908373-6908392 None:intergenic 35.0%
! GTTTGGTTGTGTTGTTAGGT+CGG - chr4_3:6907846-6907865 None:intergenic 40.0%
GCTTGTACAAAGGTTGTGTT+TGG - chr4_3:6907863-6907882 None:intergenic 40.0%
! GAGTGTGAGTGGAAGTTTTT+GGG - chr4_3:6907948-6907967 None:intergenic 40.0%
!!! GGTTTTTTTAAGCCCATTGG+TGG - chr4_3:6908034-6908053 None:intergenic 40.0%
! GATTTTCCGAAACGTTGAGT+TGG - chr4_3:6908093-6908112 None:intergenic 40.0%
GGAGAATGCAAAGGAAAAAG+AGG - chr4_3:6908352-6908371 None:intergenic 40.0%
GTTAGGTCGGATCCATATGT+TGG - chr4_3:6907833-6907852 None:intergenic 45.0%
! TGATGGGTCTGCTTGTACAA+AGG - chr4_3:6907873-6907892 None:intergenic 45.0%
!!! GTGATGCTCCGGTTAGTTTT+TGG - chr4_3:6907913-6907932 None:intergenic 45.0%
!! GTGGAAGTTTTTGGGCTGAT+GGG - chr4_3:6907940-6907959 None:intergenic 45.0%
!! AGTGGAAGTTTTTGGGCTGA+TGG - chr4_3:6907941-6907960 None:intergenic 45.0%
! GGAGTGTGAGTGGAAGTTTT+TGG - chr4_3:6907949-6907968 None:intergenic 45.0%
! CGTTCGTGGAGTTTGAAGTT+GGG - chr4_3:6908055-6908074 None:intergenic 45.0%
!! TGTTGAGAAGCTCTAGGAGA+GGG - chr4_3:6908310-6908329 None:intergenic 45.0%
!! TTGTTGAGAAGCTCTAGGAG+AGG - chr4_3:6908311-6908330 None:intergenic 45.0%
! GGTTGTTGTTGAGAAGCTCT+AGG - chr4_3:6908316-6908335 None:intergenic 45.0%
TGAGAGGAAGGAGAATGCAA+AGG - chr4_3:6908361-6908380 None:intergenic 45.0%
! TGATGGGTCTTGTGATGCTC+CGG - chr4_3:6907924-6907943 None:intergenic 50.0%
CTTGGGCTGTTAGACGAGAA+GGG - chr4_3:6907970-6907989 None:intergenic 50.0%
! TGGTTGTTGTTGGTGGAGGA+CGG - chr4_3:6908003-6908022 None:intergenic 50.0%
! ATGGTGGTTGTTGTTGGTGG+AGG - chr4_3:6908007-6908026 None:intergenic 50.0%
TCCACCAACAACAACCACCA+TGG + chr4_3:6908006-6908025 Msa0626880:CDS 50.0%
! TCCATGGTGGTTGTTGTTGG+TGG - chr4_3:6908010-6908029 None:intergenic 50.0%
GGTTCCATGGTGGTTGTTGT+TGG - chr4_3:6908013-6908032 None:intergenic 50.0%
AACCACCATGGAACCACCAA+TGG + chr4_3:6908018-6908037 Msa0626880:CDS 50.0%
ACCACCATGGAACCACCAAT+GGG + chr4_3:6908019-6908038 Msa0626880:CDS 50.0%
! TAAGCCCATTGGTGGTTCCA+TGG - chr4_3:6908026-6908045 None:intergenic 50.0%
! GCGTTCGTGGAGTTTGAAGT+TGG - chr4_3:6908056-6908075 None:intergenic 50.0%
!!! GTTTTTTAGAGCGGCGTTCG+TGG - chr4_3:6908069-6908088 None:intergenic 50.0%
GGCTTCACCAGTTTCACCAT+TGG + chr4_3:6908198-6908217 Msa0626880:CDS 50.0%
!! GTTGAGAAGCTCTAGGAGAG+GGG - chr4_3:6908309-6908328 None:intergenic 50.0%
! AGACGAGAAGGGAGTGTGAG+TGG - chr4_3:6907959-6907978 None:intergenic 55.0%
GCTTGGGCTGTTAGACGAGA+AGG - chr4_3:6907971-6907990 None:intergenic 55.0%
! TGTTGTTGGTGGAGGACGGT+GGG - chr4_3:6907999-6908018 None:intergenic 55.0%
! TTGTTGTTGGTGGAGGACGG+TGG - chr4_3:6908000-6908019 None:intergenic 55.0%
! GCCCATTGGTGGTTCCATGG+TGG - chr4_3:6908023-6908042 None:intergenic 60.0%
! AGGACGGTGGGCTTGGGCTT+GGG - chr4_3:6907987-6908006 None:intergenic 65.0%
! TGGTGGAGGACGGTGGGCTT+GGG - chr4_3:6907993-6908012 None:intergenic 65.0%
! TTGGTGGAGGACGGTGGGCT+TGG - chr4_3:6907994-6908013 None:intergenic 65.0%
! GAGGACGGTGGGCTTGGGCT+TGG - chr4_3:6907988-6908007 None:intergenic 70.0%
Chromosome Type Strat End Strand Name
chr4_3 gene 6907821 6908393 6907821 ID=Msa0626880;Name=Msa0626880
chr4_3 mRNA 6907821 6908393 6907821 ID=Msa0626880-mRNA-1;Parent=Msa0626880;Name=Msa0626880-mRNA-1;_AED=0.00;_eAED=0.04;_QI=0|-1|0|1|-1|1|1|0|190
chr4_3 exon 6907821 6908393 6907821 ID=Msa0626880-mRNA-1:exon:1985;Parent=Msa0626880-mRNA-1
chr4_3 CDS 6907821 6908393 6907821 ID=Msa0626880-mRNA-1:cds;Parent=Msa0626880-mRNA-1
Gene Sequence

>Msa0626880

ATGCATTCACCAACATATGGATCCGACCTAACAACACAACCAAACACAACCTTTGTACAAGCAGACCCATCAAATTTCCGACAAGTTGTCCAAAAACTAACCGGAGCATCACAAGACCCATCAGCCCAAAAACTTCCACTCACACTCCCTTCTCGTCTAACAGCCCAAGCCCAAGCCCACCGTCCTCCACCAACAACAACCACCATGGAACCACCAATGGGCTTAAAAAAACCCAACTTCAAACTCCACGAACGCCGCTCTAAAAAACTCCAACTCAACGTTTCGGAAAATCCCATGATGTTCCAAAACAACAACAATAACATGATGATGATGTTAATGAATAGTAACAACAACAACAACATGCGAAGTGTTATTATGGCTTCACCAGTTTCACCATTGGAATATTACTATAGTCCAAAATCACCACATGAAAATGAAGAAAAAGAAGAAGAAAAAGTGATAGCTGAAAAAGGTTTCTATTTGCACCCCTCTCCTAGAGCTTCTCAACAACAACCACCTGAACTTTTACCTCTTTTTCCTTTGCATTCTCCTTCCTCTCAATCTCATTCTTAA
Protein sequence

>Msa0626880

MHSPTYGSDLTTQPNTTFVQADPSNFRQVVQKLTGASQDPSAQKLPLTLPSRLTAQAQAHRPPPTTTTMEPPMGLKKPNFKLHERRSKKLQLNVSENPMMFQNNNNNMMMMLMNSNNNNNMRSVIMASPVSPLEYYYSPKSPHENEEKEEEKVIAEKGFYLHPSPRASQQQPPELLPLFPLHSPSSQSHS*