AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0293850

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0293850 MtrunA17_Chr2g0315201 98.611 72 1 0 1 72 1 72 4.65e-48 155
Msa0293850 MtrunA17_Chr1g0154651 66.667 81 26 1 6 86 14 93 4.57e-30 107
Msa0293850 MtrunA17_Chr2g0315211 94.444 72 4 0 1 72 1 72 2.05e-28 104
Msa0293850 MtrunA17_Chr3g0141401 77.143 70 16 0 3 72 12 81 1.39e-23 91.7
Msa0293850 MtrunA17_Chr5g0403631 74.157 89 22 1 3 91 6 93 1.51e-22 89.0
Msa0293850 MtrunA17_Chr5g0408851 61.404 57 22 0 17 73 61 117 1.45e-18 79.0
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0293850 AT1G78700.1 91.667 72 6 0 1 72 1 72 4.68e-28 103
Msa0293850 AT4G18890.1 90.278 72 7 0 1 72 1 72 1.25e-26 99.4
Msa0293850 AT1G19350.5 73.973 73 19 0 6 78 22 94 8.25e-25 95.5
Msa0293850 AT1G19350.1 73.973 73 19 0 6 78 22 94 8.25e-25 95.5
Msa0293850 AT1G19350.6 73.973 73 19 0 6 78 22 94 8.25e-25 95.5
Msa0293850 AT1G19350.4 73.973 73 19 0 6 78 22 94 8.25e-25 95.5
Msa0293850 AT3G50750.1 83.582 67 11 0 6 72 14 80 1.44e-24 94.0
Msa0293850 AT1G19350.3 73.973 73 19 0 6 78 44 116 1.67e-24 94.7
Msa0293850 AT4G36780.1 81.159 69 13 0 6 74 16 84 1.86e-24 93.2
Msa0293850 AT1G75080.2 72.603 73 20 0 6 78 23 95 1.14e-22 89.7
Msa0293850 AT1G75080.1 72.603 73 20 0 6 78 23 95 1.14e-22 89.7
Msa0293850 AT5G45300.1 61.290 62 22 1 17 78 97 156 5.03e-19 80.5
Msa0293850 AT5G45300.2 61.290 62 22 1 17 78 97 156 5.55e-19 80.5
Msa0293850 AT5G45300.3 61.290 62 22 1 17 78 111 170 6.12e-19 80.5
Msa0293850 AT2G45880.1 55.000 60 27 0 11 70 74 133 1.31e-15 70.9

Find 41 sgRNAs with CRISPR-Local

Find 116 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TGGGGTGTAGTTAGTATATT+TGG 0.217831 2_3:+45354965 None:intergenic
GTTGATGTTAATGAGGATTA+TGG 0.283185 2_3:-45354167 Msa0293850:CDS
AGTATATTTGGAAATGGATT+TGG 0.293195 2_3:+45354977 None:intergenic
TCATTGTTATCACAATGTTT+AGG 0.355738 2_3:+45354726 None:intergenic
AATCCAAAGGTTGCATTTAG+TGG 0.362338 2_3:+45354197 None:intergenic
TTCTCTGGTTTGAGAATGTA+TGG 0.389954 2_3:-45354762 Msa0293850:CDS
GTAGTTAGTATATTTGGAAA+TGG 0.397691 2_3:+45354971 None:intergenic
ATGCCACTAAATGCAACCTT+TGG 0.398006 2_3:-45354200 Msa0293850:CDS
AGAAAAGAATTGAACTTTGA+AGG 0.412503 2_3:+45354910 None:intergenic
GAACTTTGAAGGAGAGAAAG+AGG 0.424311 2_3:+45354921 None:intergenic
TCAAAAGGGTGTTCACGAAA+TGG 0.427164 2_3:+45354887 None:intergenic
CATTGAGAGTAACTCTCAAA+AGG 0.443094 2_3:+45354872 None:intergenic
TTTGGAAATGGATTTGGAGG+TGG 0.455823 2_3:+45354983 None:intergenic
TTACGATAAGTTGTTCCATC+AGG 0.461183 2_3:+45354660 None:intergenic
AAATGCAACCTTTGGATTGA+CGG 0.466530 2_3:-45354192 Msa0293850:CDS
ATAGCTGCTAAGATCTTCTC+TGG 0.470421 2_3:-45354777 Msa0293850:CDS
AAAGCTCTTTGTAATGAAGC+TGG 0.472686 2_3:-45354696 Msa0293850:CDS
AGGTGGAGGGTGATCTTTGT+CGG 0.480030 2_3:+45355000 None:intergenic
GGAAATGGATTTGGAGGTGG+AGG 0.484848 2_3:+45354986 None:intergenic
GACGGTAGTTGATGTTAATG+AGG 0.487517 2_3:-45354174 Msa0293850:CDS
ATATTTGGAAATGGATTTGG+AGG 0.490012 2_3:+45354980 None:intergenic
TGTAATGAAAATAAAGGAAA+GGG 0.490496 2_3:+45355051 None:intergenic
AGGAGAGAAAGAGGGAGGTG+TGG 0.492949 2_3:+45354930 None:intergenic
TTCTCTCTCTCCTTCCATGT+TGG 0.499958 2_3:+45354831 None:intergenic
AGGTGTGGAAGTAGAAGAAG+TGG 0.501319 2_3:+45354945 None:intergenic
AAAGTGTGTAATGAAAATAA+AGG 0.508090 2_3:+45355045 None:intergenic
GAGTTACTCTCAATGACATC+TGG 0.509973 2_3:-45354864 Msa0293850:exon
AACTTTGAAGGAGAGAAAGA+GGG 0.529635 2_3:+45354922 None:intergenic
GGTTGGTCTGTTGAACCTGA+TGG 0.545542 2_3:-45354675 Msa0293850:CDS
ATTGAGAGTAACTCTCAAAA+GGG 0.547709 2_3:+45354873 None:intergenic
CTCTTTGTAATGAAGCTGGT+TGG 0.548313 2_3:-45354692 Msa0293850:CDS
GTGTAATGAAAATAAAGGAA+AGG 0.558624 2_3:+45355050 None:intergenic
GGTGTGGAAGTAGAAGAAGT+GGG 0.575717 2_3:+45354946 None:intergenic
TTTGAAGGAGAGAAAGAGGG+AGG 0.577067 2_3:+45354925 None:intergenic
GAAATGGATTTGGAGGTGGA+GGG 0.584278 2_3:+45354987 None:intergenic
TGATGGAACAACTTATCGTA+AGG 0.588204 2_3:-45354658 Msa0293850:intron
GTGTGGAAGTAGAAGAAGTG+GGG 0.600322 2_3:+45354947 None:intergenic
ATCAACTACCGTCAATCCAA+AGG 0.603498 2_3:+45354184 None:intergenic
CTGGTACAAGACTACCAACA+TGG 0.603713 2_3:-45354845 Msa0293850:CDS
AGGAGAGAGAGAACAACAAG+AGG 0.604704 2_3:-45354821 Msa0293850:CDS
TACAAGACTACCAACATGGA+AGG 0.634618 2_3:-45354841 Msa0293850:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! GATATTATAATATAATTTGA+TGG - chr2_3:45354720-45354739 Msa0293850:CDS 10.0%
!! GATATTATAATATAATTTGA+TGG - chr2_3:45354720-45354739 Msa0293850:CDS 10.0%
!! GATATTATAATATGATTTGA+CGG - chr2_3:45354801-45354820 Msa0293850:CDS 15.0%
!! GATATTATAATATGATTTGA+CGG - chr2_3:45354801-45354820 Msa0293850:CDS 15.0%
!! TGTAATGAAAATAAAGGAAA+GGG + chr2_3:45354172-45354191 None:intergenic 20.0%
!! AAAGTGTGTAATGAAAATAA+AGG + chr2_3:45354178-45354197 None:intergenic 20.0%
!! TTCTTTGCATTATTACATTA+TGG - chr2_3:45354591-45354610 Msa0293850:intron 20.0%
!! TGTAATGAAAATAAAGGAAA+GGG + chr2_3:45354172-45354191 None:intergenic 20.0%
!! AAAGTGTGTAATGAAAATAA+AGG + chr2_3:45354178-45354197 None:intergenic 20.0%
!! TTCTTTGCATTATTACATTA+TGG - chr2_3:45354591-45354610 Msa0293850:intron 20.0%
! GTGTAATGAAAATAAAGGAA+AGG + chr2_3:45354173-45354192 None:intergenic 25.0%
!! AGTATATTTGGAAATGGATT+TGG + chr2_3:45354246-45354265 None:intergenic 25.0%
! GTAGTTAGTATATTTGGAAA+TGG + chr2_3:45354252-45354271 None:intergenic 25.0%
! AGAAAAGAATTGAACTTTGA+AGG + chr2_3:45354313-45354332 None:intergenic 25.0%
! TCATTGTTATCACAATGTTT+AGG + chr2_3:45354497-45354516 None:intergenic 25.0%
! TAGTTTCAAAAATATCTAGG+TGG + chr2_3:45354770-45354789 None:intergenic 25.0%
!!! GGTTAGTTTCAAAAATATCT+AGG + chr2_3:45354773-45354792 None:intergenic 25.0%
!! TGTAAAAAGTTTTACACAGT+CGG - chr2_3:45354831-45354850 Msa0293850:CDS 25.0%
!!! GAAACCATCAATGTTTTAAA+AGG - chr2_3:45354945-45354964 Msa0293850:five_prime_UTR 25.0%
! GTGTAATGAAAATAAAGGAA+AGG + chr2_3:45354173-45354192 None:intergenic 25.0%
!! AGTATATTTGGAAATGGATT+TGG + chr2_3:45354246-45354265 None:intergenic 25.0%
! GTAGTTAGTATATTTGGAAA+TGG + chr2_3:45354252-45354271 None:intergenic 25.0%
! AGAAAAGAATTGAACTTTGA+AGG + chr2_3:45354313-45354332 None:intergenic 25.0%
! TCATTGTTATCACAATGTTT+AGG + chr2_3:45354497-45354516 None:intergenic 25.0%
! TAGTTTCAAAAATATCTAGG+TGG + chr2_3:45354770-45354789 None:intergenic 25.0%
!!! GGTTAGTTTCAAAAATATCT+AGG + chr2_3:45354773-45354792 None:intergenic 25.0%
!! TGTAAAAAGTTTTACACAGT+CGG - chr2_3:45354831-45354850 Msa0293850:CDS 25.0%
!!! GAAACCATCAATGTTTTAAA+AGG - chr2_3:45354945-45354964 Msa0293850:five_prime_UTR 25.0%
! ATATTTGGAAATGGATTTGG+AGG + chr2_3:45354243-45354262 None:intergenic 30.0%
ATTGAGAGTAACTCTCAAAA+GGG + chr2_3:45354350-45354369 None:intergenic 30.0%
!!! ACCATCAATGTTTTAAAAGG+TGG - chr2_3:45354948-45354967 Msa0293850:five_prime_UTR 30.0%
!!! ACCACCTTTTAAAACATTGA+TGG + chr2_3:45354952-45354971 None:intergenic 30.0%
!!! AATGTTTTAAAAGGTGGTTG+TGG - chr2_3:45354954-45354973 Msa0293850:five_prime_UTR 30.0%
GTTGATGTTAATGAGGATTA+TGG - chr2_3:45355053-45355072 Msa0293850:five_prime_UTR 30.0%
! ATATTTGGAAATGGATTTGG+AGG + chr2_3:45354243-45354262 None:intergenic 30.0%
ATTGAGAGTAACTCTCAAAA+GGG + chr2_3:45354350-45354369 None:intergenic 30.0%
!!! ACCATCAATGTTTTAAAAGG+TGG - chr2_3:45354948-45354967 Msa0293850:five_prime_UTR 30.0%
!!! ACCACCTTTTAAAACATTGA+TGG + chr2_3:45354952-45354971 None:intergenic 30.0%
!!! AATGTTTTAAAAGGTGGTTG+TGG - chr2_3:45354954-45354973 Msa0293850:five_prime_UTR 30.0%
GTTGATGTTAATGAGGATTA+TGG - chr2_3:45355053-45355072 Msa0293850:five_prime_UTR 30.0%
AAAGGAAAGGGAAAAAGTGA+AGG + chr2_3:45354160-45354179 None:intergenic 35.0%
TGGGGTGTAGTTAGTATATT+TGG + chr2_3:45354258-45354277 None:intergenic 35.0%
! AACTTTGAAGGAGAGAAAGA+GGG + chr2_3:45354301-45354320 None:intergenic 35.0%
CATTGAGAGTAACTCTCAAA+AGG + chr2_3:45354351-45354370 None:intergenic 35.0%
! TTCTCTGGTTTGAGAATGTA+TGG - chr2_3:45354458-45354477 Msa0293850:intron 35.0%
AAAGCTCTTTGTAATGAAGC+TGG - chr2_3:45354524-45354543 Msa0293850:intron 35.0%
TTACGATAAGTTGTTCCATC+AGG + chr2_3:45354563-45354582 None:intergenic 35.0%
TGATGGAACAACTTATCGTA+AGG - chr2_3:45354562-45354581 Msa0293850:intron 35.0%
TTAAAAGGTGGTTGTGGTAA+TGG - chr2_3:45354960-45354979 Msa0293850:five_prime_UTR 35.0%
AATCCAAAGGTTGCATTTAG+TGG + chr2_3:45355026-45355045 None:intergenic 35.0%
AAATGCAACCTTTGGATTGA+CGG - chr2_3:45355028-45355047 Msa0293850:five_prime_UTR 35.0%
AAAGGAAAGGGAAAAAGTGA+AGG + chr2_3:45354160-45354179 None:intergenic 35.0%
TGGGGTGTAGTTAGTATATT+TGG + chr2_3:45354258-45354277 None:intergenic 35.0%
! AACTTTGAAGGAGAGAAAGA+GGG + chr2_3:45354301-45354320 None:intergenic 35.0%
CATTGAGAGTAACTCTCAAA+AGG + chr2_3:45354351-45354370 None:intergenic 35.0%
! TTCTCTGGTTTGAGAATGTA+TGG - chr2_3:45354458-45354477 Msa0293850:intron 35.0%
AAAGCTCTTTGTAATGAAGC+TGG - chr2_3:45354524-45354543 Msa0293850:intron 35.0%
TTACGATAAGTTGTTCCATC+AGG + chr2_3:45354563-45354582 None:intergenic 35.0%
TGATGGAACAACTTATCGTA+AGG - chr2_3:45354562-45354581 Msa0293850:intron 35.0%
TTAAAAGGTGGTTGTGGTAA+TGG - chr2_3:45354960-45354979 Msa0293850:five_prime_UTR 35.0%
AATCCAAAGGTTGCATTTAG+TGG + chr2_3:45355026-45355045 None:intergenic 35.0%
AAATGCAACCTTTGGATTGA+CGG - chr2_3:45355028-45355047 Msa0293850:five_prime_UTR 35.0%
! TTTGGAAATGGATTTGGAGG+TGG + chr2_3:45354240-45354259 None:intergenic 40.0%
! GAACTTTGAAGGAGAGAAAG+AGG + chr2_3:45354302-45354321 None:intergenic 40.0%
!! TCAAAAGGGTGTTCACGAAA+TGG + chr2_3:45354336-45354355 None:intergenic 40.0%
GAGTTACTCTCAATGACATC+TGG - chr2_3:45354356-45354375 Msa0293850:intron 40.0%
TACAAGACTACCAACATGGA+AGG - chr2_3:45354379-45354398 Msa0293850:intron 40.0%
ATAGCTGCTAAGATCTTCTC+TGG - chr2_3:45354443-45354462 Msa0293850:intron 40.0%
CTCTTTGTAATGAAGCTGGT+TGG - chr2_3:45354528-45354547 Msa0293850:intron 40.0%
ATGCCACTAAATGCAACCTT+TGG - chr2_3:45355020-45355039 Msa0293850:five_prime_UTR 40.0%
ATCAACTACCGTCAATCCAA+AGG + chr2_3:45355039-45355058 None:intergenic 40.0%
! GACGGTAGTTGATGTTAATG+AGG - chr2_3:45355046-45355065 Msa0293850:five_prime_UTR 40.0%
! TTTGGAAATGGATTTGGAGG+TGG + chr2_3:45354240-45354259 None:intergenic 40.0%
! GAACTTTGAAGGAGAGAAAG+AGG + chr2_3:45354302-45354321 None:intergenic 40.0%
!! TCAAAAGGGTGTTCACGAAA+TGG + chr2_3:45354336-45354355 None:intergenic 40.0%
GAGTTACTCTCAATGACATC+TGG - chr2_3:45354356-45354375 Msa0293850:intron 40.0%
TACAAGACTACCAACATGGA+AGG - chr2_3:45354379-45354398 Msa0293850:intron 40.0%
ATAGCTGCTAAGATCTTCTC+TGG - chr2_3:45354443-45354462 Msa0293850:intron 40.0%
CTCTTTGTAATGAAGCTGGT+TGG - chr2_3:45354528-45354547 Msa0293850:intron 40.0%
ATGCCACTAAATGCAACCTT+TGG - chr2_3:45355020-45355039 Msa0293850:five_prime_UTR 40.0%
ATCAACTACCGTCAATCCAA+AGG + chr2_3:45355039-45355058 None:intergenic 40.0%
! GACGGTAGTTGATGTTAATG+AGG - chr2_3:45355046-45355065 Msa0293850:five_prime_UTR 40.0%
CGGAAAAATGAGAGAGTGAG+AGG + chr2_3:45354203-45354222 None:intergenic 45.0%
! GAAATGGATTTGGAGGTGGA+GGG + chr2_3:45354236-45354255 None:intergenic 45.0%
GTGTGGAAGTAGAAGAAGTG+GGG + chr2_3:45354276-45354295 None:intergenic 45.0%
GGTGTGGAAGTAGAAGAAGT+GGG + chr2_3:45354277-45354296 None:intergenic 45.0%
AGGTGTGGAAGTAGAAGAAG+TGG + chr2_3:45354278-45354297 None:intergenic 45.0%
TTTGAAGGAGAGAAAGAGGG+AGG + chr2_3:45354298-45354317 None:intergenic 45.0%
CTGGTACAAGACTACCAACA+TGG - chr2_3:45354375-45354394 Msa0293850:intron 45.0%
TTCTCTCTCTCCTTCCATGT+TGG + chr2_3:45354392-45354411 None:intergenic 45.0%
AGGAGAGAGAGAACAACAAG+AGG - chr2_3:45354399-45354418 Msa0293850:intron 45.0%
!! TTGTGGTAATGGTTGTGGCT+CGG - chr2_3:45354971-45354990 Msa0293850:five_prime_UTR 45.0%
CGGAAAAATGAGAGAGTGAG+AGG + chr2_3:45354203-45354222 None:intergenic 45.0%
! GAAATGGATTTGGAGGTGGA+GGG + chr2_3:45354236-45354255 None:intergenic 45.0%
GTGTGGAAGTAGAAGAAGTG+GGG + chr2_3:45354276-45354295 None:intergenic 45.0%
GGTGTGGAAGTAGAAGAAGT+GGG + chr2_3:45354277-45354296 None:intergenic 45.0%
AGGTGTGGAAGTAGAAGAAG+TGG + chr2_3:45354278-45354297 None:intergenic 45.0%
TTTGAAGGAGAGAAAGAGGG+AGG + chr2_3:45354298-45354317 None:intergenic 45.0%
CTGGTACAAGACTACCAACA+TGG - chr2_3:45354375-45354394 Msa0293850:intron 45.0%
TTCTCTCTCTCCTTCCATGT+TGG + chr2_3:45354392-45354411 None:intergenic 45.0%
AGGAGAGAGAGAACAACAAG+AGG - chr2_3:45354399-45354418 Msa0293850:intron 45.0%
!! TTGTGGTAATGGTTGTGGCT+CGG - chr2_3:45354971-45354990 Msa0293850:five_prime_UTR 45.0%
!!! ATATTATAATATCATTTTAT+AGG + chr2_3:45354713-45354732 None:intergenic 5.0%
!!! ATATTATAATATCATTTTAT+AGG + chr2_3:45354713-45354732 None:intergenic 5.0%
!!! ATATTATAATATCATTTTAT+AGG + chr2_3:45354713-45354732 None:intergenic 5.0%
!!! ATATTATAATATCATTTTAT+AGG + chr2_3:45354713-45354732 None:intergenic 5.0%
AGGTGGAGGGTGATCTTTGT+CGG + chr2_3:45354223-45354242 None:intergenic 50.0%
! GGAAATGGATTTGGAGGTGG+AGG + chr2_3:45354237-45354256 None:intergenic 50.0%
!! GGTTGGTCTGTTGAACCTGA+TGG - chr2_3:45354545-45354564 Msa0293850:intron 50.0%
!! GGTGGTTGTGGTAATGGTTG+TGG - chr2_3:45354966-45354985 Msa0293850:five_prime_UTR 50.0%
AGGTGGAGGGTGATCTTTGT+CGG + chr2_3:45354223-45354242 None:intergenic 50.0%
! GGAAATGGATTTGGAGGTGG+AGG + chr2_3:45354237-45354256 None:intergenic 50.0%
!! GGTTGGTCTGTTGAACCTGA+TGG - chr2_3:45354545-45354564 Msa0293850:intron 50.0%
!! GGTGGTTGTGGTAATGGTTG+TGG - chr2_3:45354966-45354985 Msa0293850:five_prime_UTR 50.0%
AGGAGAGAAAGAGGGAGGTG+TGG + chr2_3:45354293-45354312 None:intergenic 55.0%
AGGAGAGAAAGAGGGAGGTG+TGG + chr2_3:45354293-45354312 None:intergenic 55.0%
Chromosome Type Strat End Strand Name
chr2_3 gene 45354157 45355085 45354157 ID=Msa0293850;Name=Msa0293850
chr2_3 mRNA 45354157 45355085 45354157 ID=Msa0293850-mRNA-1;Parent=Msa0293850;Name=Msa0293850-mRNA-1;_AED=0.52;_eAED=0.52;_QI=211|0|0.5|0.5|1|1|2|0|97
chr2_3 exon 45354157 45354234 45354157 ID=Msa0293850-mRNA-1:exon:14177;Parent=Msa0293850-mRNA-1
chr2_3 exon 45354659 45355085 45354659 ID=Msa0293850-mRNA-1:exon:14176;Parent=Msa0293850-mRNA-1
chr2_3 five_prime_UTR 45354875 45355085 45354875 ID=Msa0293850-mRNA-1:five_prime_utr;Parent=Msa0293850-mRNA-1
chr2_3 CDS 45354659 45354874 45354659 ID=Msa0293850-mRNA-1:cds;Parent=Msa0293850-mRNA-1
chr2_3 CDS 45354157 45354234 45354157 ID=Msa0293850-mRNA-1:cds;Parent=Msa0293850-mRNA-1
Gene Sequence

>Msa0293850

ATGACATCTGGTACAAGACTACCAACATGGAAGGAGAGAGAGAACAACAAGAGGAGAGAGAGAAGAAGAAGAGCTATAGCTGCTAAGATCTTCTCTGGTTTGAGAATGTATGGTAACTTTAGATTACCTAAACATTGTGATAACAATGAAGTTCTTAAAGCTCTTTGTAATGAAGCTGGTTGGTCTGTTGAACCTGATGGAACAACTTATCGTAAGTGTTACAGTCAAATGCCACTAAATGCAACCTTTGGATTGACGGTAGTTGATGTTAATGAGGATTATGGTCGAATGTGA
Protein sequence

>Msa0293850

MTSGTRLPTWKERENNKRRERRRRAIAAKIFSGLRMYGNFRLPKHCDNNEVLKALCNEAGWSVEPDGTTYRKCYSQMPLNATFGLTVVDVNEDYGRM*