AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene068588

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene068588.t1 MTR_5g031830 91.156 147 13 0 1 147 1 147 3.89e-94 280
MS.gene068588.t1 MTR_5g031860 89.116 147 16 0 1 147 1 147 8.96e-93 276
MS.gene068588.t1 MTR_5g031840 82.014 139 24 1 10 147 3 141 1.36e-78 240
MS.gene068588.t1 MTR_3g479490 38.776 147 71 6 12 147 6 144 4.12e-18 80.1
MS.gene068588.t1 MTR_3g479620 36.301 146 82 6 9 147 3 144 6.26e-18 76.3
MS.gene068588.t1 MTR_5g464760 34.615 156 88 5 1 147 1 151 2.12e-17 77.8
MS.gene068588.t1 MTR_3g479520 34.932 146 86 4 8 147 11 153 1.82e-16 75.5
MS.gene068588.t1 MTR_4g094220 33.803 142 77 6 7 137 2 137 1.38e-15 72.8
MS.gene068588.t1 MTR_3g079480 32.903 155 71 5 11 147 20 159 7.79e-15 70.5
MS.gene068588.t1 MTR_0036s0220 33.775 151 82 7 8 147 8 151 1.02e-14 70.5
MS.gene068588.t1 MTR_3g479470 34.868 152 72 7 11 147 12 151 1.86e-13 66.6
MS.gene068588.t1 MTR_2g008210 34.965 143 81 6 11 147 10 146 3.32e-13 65.9
MS.gene068588.t1 MTR_5g464810 33.758 157 74 7 8 147 8 151 3.76e-13 65.9
MS.gene068588.t1 MTR_5g064240 33.758 157 74 7 8 147 8 151 3.76e-13 65.9
MS.gene068588.t1 MTR_7g013220 32.667 150 83 5 11 147 4 148 7.63e-13 65.1
MS.gene068588.t1 MTR_6g014220 43.284 67 36 1 11 77 9 73 5.66e-12 62.4
MS.gene068588.t1 MTR_6g013440 40.845 71 40 1 7 77 6 74 7.15e-12 62.0
MS.gene068588.t1 MTR_6g014020 40.000 70 40 1 8 77 6 73 1.12e-11 61.6
MS.gene068588.t1 MTR_6g014270 54.348 46 21 0 9 54 4 49 1.29e-11 61.2
MS.gene068588.t1 MTR_0475s0020 54.545 44 20 0 11 54 9 52 1.48e-11 60.1
MS.gene068588.t1 MTR_3g008010 54.348 46 21 0 9 54 7 52 2.12e-11 60.8
MS.gene068588.t1 MTR_8g059425 55.319 47 21 0 8 54 6 52 2.23e-11 60.8
MS.gene068588.t1 MTR_0288s0020 54.545 44 20 0 11 54 9 52 2.48e-11 60.5
MS.gene068588.t1 MTR_6g014040 31.333 150 86 6 11 147 9 154 2.65e-11 60.5
MS.gene068588.t1 MTR_6g014290 54.545 44 20 0 11 54 9 52 3.50e-11 60.1
MS.gene068588.t1 MTR_6g014170 54.545 44 20 0 11 54 9 52 6.26e-11 59.3
MS.gene068588.t1 MTR_6g014187 39.437 71 41 1 7 77 5 73 7.65e-11 59.3
MS.gene068588.t1 MTR_7g013200 32.639 144 80 5 11 147 4 137 8.98e-11 58.9
MS.gene068588.t1 MTR_6g014186 38.806 67 39 1 11 77 6 70 9.70e-11 58.9
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene068588.t1 AT1G22380 35.570 149 81 6 8 147 9 151 9.03e-20 84.7
MS.gene068588.t1 AT1G22370 36.986 146 77 6 11 147 12 151 4.67e-17 77.0
MS.gene068588.t1 AT1G22340 34.014 147 80 6 11 147 12 151 1.48e-15 72.8
MS.gene068588.t1 AT3G02100 33.333 153 85 5 6 147 7 153 6.34e-15 70.9
MS.gene068588.t1 AT1G22360 31.333 150 78 4 12 147 10 148 2.21e-14 69.3
MS.gene068588.t1 AT1G22360 31.333 150 78 4 12 147 10 148 2.52e-14 69.3
MS.gene068588.t1 AT1G22400 27.815 151 84 4 11 147 12 151 1.28e-13 67.4
MS.gene068588.t1 AT1G78270 44.776 67 35 2 11 77 12 76 5.46e-12 62.4

Find 22 sgRNAs with CRISPR-Local

Find 27 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GAAAATAAGTTGCATTATTT+TGG 0.129986 5.1:+21810932 MS.gene068588:CDS
ACTGATTTGGCTGCTGAGTT+TGG 0.266869 5.1:+21810978 MS.gene068588:CDS
GAGGAGAAGCATCCTGGATT+TGG 0.312050 5.1:+21810834 MS.gene068588:CDS
CTGATTTGGCTGCTGAGTTT+GGG 0.334780 5.1:+21810979 MS.gene068588:CDS
TGGTGATCTTGCTACTGATT+TGG 0.352180 5.1:+21810965 MS.gene068588:CDS
CACAGTGAGGAGAAGCATCC+TGG 0.364154 5.1:+21810828 MS.gene068588:CDS
ATGGTCTTGAATTGTAGCTT+AGG 0.425350 5.1:-21810795 None:intergenic
AGCTCAGCTAGCTTTAGCAT+TGG 0.453685 5.1:-21810669 None:intergenic
AGCATCCTGGATTTGGAGAA+AGG 0.475413 5.1:+21810841 MS.gene068588:CDS
GGATTTACATGGCCTTGTGC+TGG 0.486767 5.1:-21810648 None:intergenic
TGGTCTTGAATTGTAGCTTA+GGG 0.493157 5.1:-21810794 None:intergenic
GCTTTAGCATTGGATTTACA+TGG 0.505828 5.1:-21810659 None:intergenic
GCTATCCTTTCTCCAAATCC+AGG 0.521331 5.1:-21810846 None:intergenic
ACATGGCCTTGTGCTGGACA+TGG 0.534043 5.1:-21810642 None:intergenic
TGAAACTAATGAGACGGTTG+TGG 0.551286 5.1:-21810740 None:intergenic
CATGGGAAGATTAGCAAATG+TGG 0.557319 5.1:-21810624 None:intergenic
CTCACTGTGAAAATCAGAGA+TGG 0.579959 5.1:-21810814 None:intergenic
CATGGCCTTGTGCTGGACAT+GGG 0.589394 5.1:-21810641 None:intergenic
ACAATAATATCTTTCAACAA+AGG 0.592002 5.1:-21810903 None:intergenic
TATCATTGAAACTAATGAGA+CGG 0.592738 5.1:-21810746 None:intergenic
ATCTTCCCATGTCCAGCACA+AGG 0.604045 5.1:+21810636 MS.gene068588:CDS
TGTGGATGTACTCAGTGTTG+AGG 0.692218 5.1:-21810722 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! ACAATAATATCTTTCAACAA+AGG - chr5.1:21810906-21810925 None:intergenic 20.0%
!!! ATTATTTTGGATGGAATATT+TGG + chr5.1:21810945-21810964 MS.gene068588:CDS 20.0%
!!! GAAAATAAGTTGCATTATTT+TGG + chr5.1:21810932-21810951 MS.gene068588:CDS 20.0%
! TATCATTGAAACTAATGAGA+CGG - chr5.1:21810749-21810768 None:intergenic 25.0%
!! ATTTTATCACTGAGTTTGTA+TGG + chr5.1:21810876-21810895 MS.gene068588:CDS 25.0%
!!! ATAAGTTGCATTATTTTGGA+TGG + chr5.1:21810936-21810955 MS.gene068588:CDS 25.0%
! ATGGTCTTGAATTGTAGCTT+AGG - chr5.1:21810798-21810817 None:intergenic 35.0%
! GCTTTAGCATTGGATTTACA+TGG - chr5.1:21810662-21810681 None:intergenic 35.0%
! TGGTCTTGAATTGTAGCTTA+GGG - chr5.1:21810797-21810816 None:intergenic 35.0%
! TGTGGAGAAGATTTTTCCTT+AGG - chr5.1:21810609-21810628 None:intergenic 35.0%
CATGGGAAGATTAGCAAATG+TGG - chr5.1:21810627-21810646 None:intergenic 40.0%
CTCACTGTGAAAATCAGAGA+TGG - chr5.1:21810817-21810836 None:intergenic 40.0%
TGAAACTAATGAGACGGTTG+TGG - chr5.1:21810743-21810762 None:intergenic 40.0%
! CATCTCTGATTTTCACAGTG+AGG + chr5.1:21810815-21810834 MS.gene068588:CDS 40.0%
! TGGTGATCTTGCTACTGATT+TGG + chr5.1:21810965-21810984 MS.gene068588:CDS 40.0%
AGCATCCTGGATTTGGAGAA+AGG + chr5.1:21810841-21810860 MS.gene068588:CDS 45.0%
GCTATCCTTTCTCCAAATCC+AGG - chr5.1:21810849-21810868 None:intergenic 45.0%
TGTGGATGTACTCAGTGTTG+AGG - chr5.1:21810725-21810744 None:intergenic 45.0%
!! ACTGATTTGGCTGCTGAGTT+TGG + chr5.1:21810978-21810997 MS.gene068588:CDS 45.0%
!! AGCTCAGCTAGCTTTAGCAT+TGG - chr5.1:21810672-21810691 None:intergenic 45.0%
!! CTGATTTGGCTGCTGAGTTT+GGG + chr5.1:21810979-21810998 MS.gene068588:CDS 45.0%
ATCTTCCCATGTCCAGCACA+AGG + chr5.1:21810636-21810655 MS.gene068588:CDS 50.0%
!! GAGGAGAAGCATCCTGGATT+TGG + chr5.1:21810834-21810853 MS.gene068588:CDS 50.0%
!! GGATTTACATGGCCTTGTGC+TGG - chr5.1:21810651-21810670 None:intergenic 50.0%
!! ACATGGCCTTGTGCTGGACA+TGG - chr5.1:21810645-21810664 None:intergenic 55.0%
!! CACAGTGAGGAGAAGCATCC+TGG + chr5.1:21810828-21810847 MS.gene068588:CDS 55.0%
!! CATGGCCTTGTGCTGGACAT+GGG - chr5.1:21810644-21810663 None:intergenic 55.0%


Chromosome Type Strat End Strand Name
chr5.1 gene 21810594 21811037 21810594 ID=MS.gene068588
chr5.1 mRNA 21810594 21811037 21810594 ID=MS.gene068588.t1;Parent=MS.gene068588
chr5.1 exon 21810594 21811037 21810594 ID=MS.gene068588.t1.exon1;Parent=MS.gene068588.t1
chr5.1 CDS 21810594 21811037 21810594 ID=cds.MS.gene068588.t1;Parent=MS.gene068588.t1
Gene Sequence

>MS.gene068588

ATGGAAACACAGCCTAAGGAAAAATCTTCTCCACATTTGCTAATCTTCCCATGTCCAGCACAAGGCCATGTAAATCCAATGCTAAAGCTAGCTGAGCTTCTTGCAATTCAAAATCTCAACATAACTTTCCTCAACACTGAGTACATCCACAACCGTCTCATTAGTTTCAATGATAATATTCAATCTCTTTCAGAATGTTACCCTAAGCTACAATTCAAGACCATCTCTGATTTTCACAGTGAGGAGAAGCATCCTGGATTTGGAGAAAGGATAGCAGATGTAATTTTATCACTGAGTTTGTATGGTAAGCCTTTGTTGAAAGATATTATTGTGTCTGAGAAAATAAGTTGCATTATTTTGGATGGAATATTTGGTGATCTTGCTACTGATTTGGCTGCTGAGTTTGGGATACAATTGATTCATTTTCGTACTGTTAGTGCTTAG
Protein sequence

>MS.gene068588.t1

METQPKEKSSPHLLIFPCPAQGHVNPMLKLAELLAIQNLNITFLNTEYIHNRLISFNDNIQSLSECYPKLQFKTISDFHSEEKHPGFGERIADVILSLSLYGKPLLKDIIVSEKISCIILDGIFGDLATDLAAEFGIQLIHFRTVSA