AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene52541

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene52541.t1 MTR_3g006010 90.435 115 11 0 1 115 1 115 6.51e-58 185
MS.gene52541.t1 MTR_3g006105 74.227 97 24 1 1 96 1 97 1.49e-44 143
MS.gene52541.t1 MTR_3g006105 37.838 111 39 1 4 114 95 175 5.39e-13 62.4
MS.gene52541.t1 MTR_3g006125 76.289 97 22 1 1 96 82 178 6.95e-41 136
MS.gene52541.t1 MTR_3g006125 41.071 112 36 1 4 115 176 257 4.59e-17 74.3
MS.gene52541.t1 MTR_3g006185 75.000 96 24 0 1 96 1 96 1.05e-39 130
MS.gene52541.t1 MTR_3g006185 41.071 112 36 1 4 115 94 175 1.85e-17 73.9
MS.gene52541.t1 MTR_3g006150 61.798 89 30 1 1 89 1 85 3.19e-31 108
MS.gene52541.t1 MTR_3g006150 46.575 73 39 0 2 74 84 156 6.35e-14 64.3
MS.gene52541.t1 MTR_3g006065 59.551 89 32 1 1 89 1 85 3.91e-28 101
MS.gene52541.t1 MTR_3g006065 46.575 73 39 0 2 74 84 156 5.15e-14 65.1
MS.gene52541.t1 MTR_1g104940 50.000 90 42 2 3 91 7 94 7.37e-23 86.3
MS.gene52541.t1 MTR_1g104960 52.564 78 36 1 6 83 11 87 7.96e-19 77.4
MS.gene52541.t1 MTR_1g104960 42.857 77 43 1 7 83 98 173 1.46e-13 63.5
MS.gene52541.t1 MTR_8g062700 52.564 78 36 1 4 81 38 114 7.65e-18 78.2
MS.gene52541.t1 MTR_8g062700 52.564 78 36 1 4 81 38 114 7.80e-18 78.2
MS.gene52541.t1 MTR_5g036670 53.333 75 34 1 4 78 39 112 5.24e-17 75.5
MS.gene52541.t1 MTR_1g105010 40.230 87 51 1 4 90 12 97 5.00e-16 68.6
MS.gene52541.t1 MTR_1g105955 49.296 71 35 1 6 76 93 162 7.39e-16 69.7
MS.gene52541.t1 MTR_1g105955 38.961 77 46 1 5 81 13 88 3.69e-11 57.4
MS.gene52541.t1 MTR_1g104937 45.349 86 44 2 6 91 10 92 7.65e-16 68.2
MS.gene52541.t1 MTR_1g104980 44.444 90 48 2 11 100 73 160 1.48e-15 68.9
MS.gene52541.t1 MTR_1g104980 48.214 56 29 0 23 78 13 68 1.43e-11 58.5
MS.gene52541.t1 MTR_7g013380 42.857 77 43 1 8 83 185 261 2.34e-15 70.1
MS.gene52541.t1 MTR_7g013380 37.079 89 55 1 8 95 99 187 2.07e-13 64.7
MS.gene52541.t1 MTR_7g013380 48.214 56 29 0 24 79 30 85 9.29e-12 60.5
MS.gene52541.t1 MTR_6g008970 45.679 81 43 1 4 84 59 138 2.97e-15 70.5
MS.gene52541.t1 MTR_1g105960 46.341 82 42 2 9 90 2 81 8.10e-15 65.5
MS.gene52541.t1 MTR_8g062350 46.753 77 40 1 2 78 8 83 7.17e-14 65.1
MS.gene52541.t1 MTR_2g097830 39.583 96 53 2 6 101 68 158 8.06e-14 64.3
MS.gene52541.t1 MTR_4g133470 39.583 96 53 2 6 101 10 100 3.11e-13 63.9
MS.gene52541.t1 MTR_4g133300 39.583 96 53 2 6 101 10 100 3.17e-13 63.9
MS.gene52541.t1 MTR_3g006000 44.156 77 41 2 5 80 4 79 4.59e-13 60.1
MS.gene52541.t1 MTR_6g008995 41.250 80 46 1 2 81 31 109 2.48e-12 62.4
MS.gene52541.t1 MTR_1g091047 48.649 74 35 3 1 72 1 73 4.03e-12 57.4
MS.gene52541.t1 MTR_1g109550 40.000 70 40 1 8 77 16 83 2.95e-11 57.0
MS.gene52541.t1 MTR_1g104950 42.857 70 39 1 32 100 1 70 3.74e-11 55.1
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene52541.t1 AT1G70060 50.000 84 38 2 4 87 10 89 1.66e-17 77.0
MS.gene52541.t1 AT1G70060 50.000 84 38 2 4 87 10 89 1.66e-17 77.0
MS.gene52541.t1 AT5G15025 47.059 85 40 2 4 88 43 122 1.16e-16 70.5
MS.gene52541.t1 AT1G24190 48.000 75 38 1 4 78 10 83 2.91e-16 73.6
MS.gene52541.t1 AT1G24190 48.000 75 38 1 4 78 10 83 3.30e-16 73.6
MS.gene52541.t1 AT1G24190 48.000 75 38 1 4 78 10 83 3.36e-16 73.6
MS.gene52541.t1 AT3G01320 46.988 83 42 2 2 84 51 131 2.83e-15 70.9
MS.gene52541.t1 AT3G01320 46.988 83 42 2 2 84 51 131 3.27e-15 70.5
MS.gene52541.t1 AT1G59890 49.296 71 35 1 8 78 45 114 2.67e-14 68.2
MS.gene52541.t1 AT1G59890 49.296 71 35 1 8 78 45 114 2.75e-14 67.8
MS.gene52541.t1 AT1G59890 49.296 71 35 1 8 78 45 114 2.77e-14 67.8
MS.gene52541.t1 AT1G59890 49.296 71 35 1 8 78 45 114 2.91e-14 67.8
MS.gene52541.t1 AT5G15020 46.667 75 39 1 4 78 48 121 3.11e-14 67.8
MS.gene52541.t1 AT5G15020 46.667 75 39 1 4 78 48 121 3.36e-14 67.8
MS.gene52541.t1 AT1G24200 48.611 72 36 1 5 76 11 81 1.72e-13 63.9
MS.gene52541.t1 AT1G70030 43.750 80 44 1 2 81 16 94 3.14e-13 61.6
MS.gene52541.t1 AT1G70030 44.156 77 42 1 2 78 16 91 9.25e-13 60.8
MS.gene52541.t1 AT1G10450 47.887 71 36 1 8 78 33 102 1.10e-12 63.5
MS.gene52541.t1 AT1G10450 47.887 71 36 1 8 78 33 102 1.10e-12 63.5
MS.gene52541.t1 AT1G10450 47.887 71 36 1 8 78 84 153 1.20e-12 63.2
MS.gene52541.t1 AT1G70030 43.750 80 44 1 2 81 5 83 1.45e-12 60.8
MS.gene52541.t1 AT1G24230 42.857 70 40 0 4 73 10 79 3.55e-12 61.2
MS.gene52541.t1 AT4G12020 39.286 84 48 2 1 84 301 381 1.63e-11 60.1
MS.gene52541.t1 AT4G12020 39.286 84 48 2 1 84 301 381 1.77e-11 60.1
MS.gene52541.t1 AT4G12020 39.286 84 48 2 1 84 301 381 1.77e-11 60.1
MS.gene52541.t1 AT4G12020 39.286 84 48 2 1 84 301 381 1.79e-11 60.1
MS.gene52541.t1 AT4G12020 39.286 84 48 2 1 84 301 381 1.80e-11 60.1
MS.gene52541.t1 AT4G12020 39.286 84 48 2 1 84 301 381 1.80e-11 60.1
MS.gene52541.t1 AT4G12020 39.286 84 48 2 1 84 234 314 1.86e-11 60.1
MS.gene52541.t1 AT4G12020 39.286 84 48 2 1 84 301 381 1.86e-11 60.1
MS.gene52541.t1 AT4G12020 39.286 84 48 2 1 84 301 381 1.88e-11 60.1
MS.gene52541.t1 AT4G12020 39.286 84 48 2 1 84 301 381 1.91e-11 59.7
MS.gene52541.t1 AT4G12020 39.286 84 48 2 1 84 301 381 1.91e-11 59.7
MS.gene52541.t1 AT1G27220 43.056 72 40 1 5 76 11 81 7.84e-11 56.6

Find 21 sgRNAs with CRISPR-Local

Find 22 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GTCTCAAAATTAAATCTTCA+TGG 0.305008 3.4:+1557969 None:intergenic
CTCTCCCTTGATGATGCATT+AGG 0.309761 3.4:-1558133 MS.gene52541:CDS
TCAGCATTAAAATGTAAGTT+TGG 0.340713 3.4:-1558103 MS.gene52541:CDS
TCTCCCTTGATGATGCATTA+GGG 0.364954 3.4:-1558132 MS.gene52541:CDS
ATTAAGAGTGTACGAGTTGT+TGG 0.382597 3.4:-1557996 MS.gene52541:CDS
GTAAGTTTGGATATGAGAAA+AGG 0.430304 3.4:-1558090 MS.gene52541:CDS
TAAGTTTGGATATGAGAAAA+GGG 0.432227 3.4:-1558089 MS.gene52541:CDS
AGTTTGATTTCATATTTAGT+TGG 0.445957 3.4:+1557932 None:intergenic
TTCATATTTAGTTGGCAAGA+AGG 0.469109 3.4:+1557940 None:intergenic
ATATGAAATCAAACTTCCAT+TGG 0.479714 3.4:-1557924 MS.gene52541:CDS
ACAAATTATGAAGGATTACA+AGG 0.516015 3.4:-1558047 MS.gene52541:CDS
AATCACACCTTCAGTTCAGC+TGG 0.522086 3.4:-1557828 MS.gene52541:CDS
GGCTGAAAGAATTGATGCTA+GGG 0.536935 3.4:-1558026 MS.gene52541:CDS
AGGCTGAAAGAATTGATGCT+AGG 0.540522 3.4:-1558027 MS.gene52541:CDS
TTAACCCTAATGCATCATCA+AGG 0.572182 3.4:+1558128 None:intergenic
CCAGTGTCCAGCTGAACTGA+AGG 0.581775 3.4:+1557821 None:intergenic
CCTTCAGTTCAGCTGGACAC+TGG 0.584057 3.4:-1557821 MS.gene52541:CDS
TCATCGTCATCACGATCCAA+TGG 0.590882 3.4:+1557908 None:intergenic
TAACCCTAATGCATCATCAA+GGG 0.615763 3.4:+1558129 None:intergenic
AGAGTGTACGAGTTGTTGGA+CGG 0.625456 3.4:-1557992 MS.gene52541:CDS
GACGATGATGAAGAACAAGA+TGG 0.708057 3.4:-1557893 MS.gene52541:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! AGTTTGATTTCATATTTAGT+TGG + chr3.4:1558030-1558049 None:intergenic 20.0%
!!! ATCTTTTCTACAAATTATGA+AGG - chr3.4:1557903-1557922 MS.gene52541:CDS 20.0%
! ACAAATTATGAAGGATTACA+AGG - chr3.4:1557912-1557931 MS.gene52541:CDS 25.0%
! ATATGAAATCAAACTTCCAT+TGG - chr3.4:1558035-1558054 MS.gene52541:CDS 25.0%
! GTCTCAAAATTAAATCTTCA+TGG + chr3.4:1557993-1558012 None:intergenic 25.0%
! TAAGTTTGGATATGAGAAAA+GGG - chr3.4:1557870-1557889 MS.gene52541:CDS 25.0%
! TCAGCATTAAAATGTAAGTT+TGG - chr3.4:1557856-1557875 MS.gene52541:CDS 25.0%
GTAAGTTTGGATATGAGAAA+AGG - chr3.4:1557869-1557888 MS.gene52541:CDS 30.0%
TTCATATTTAGTTGGCAAGA+AGG + chr3.4:1558022-1558041 None:intergenic 30.0%
TAACCCTAATGCATCATCAA+GGG + chr3.4:1557833-1557852 None:intergenic 35.0%
TTAACCCTAATGCATCATCA+AGG + chr3.4:1557834-1557853 None:intergenic 35.0%
! ATTAAGAGTGTACGAGTTGT+TGG - chr3.4:1557963-1557982 MS.gene52541:CDS 35.0%
AGGCTGAAAGAATTGATGCT+AGG - chr3.4:1557932-1557951 MS.gene52541:CDS 40.0%
GACGATGATGAAGAACAAGA+TGG - chr3.4:1558066-1558085 MS.gene52541:CDS 40.0%
GGCTGAAAGAATTGATGCTA+GGG - chr3.4:1557933-1557952 MS.gene52541:CDS 40.0%
!! TCTCCCTTGATGATGCATTA+GGG - chr3.4:1557827-1557846 MS.gene52541:CDS 40.0%
AATCACACCTTCAGTTCAGC+TGG - chr3.4:1558131-1558150 MS.gene52541:CDS 45.0%
AGAGTGTACGAGTTGTTGGA+CGG - chr3.4:1557967-1557986 MS.gene52541:CDS 45.0%
TCATCGTCATCACGATCCAA+TGG + chr3.4:1558054-1558073 None:intergenic 45.0%
!! CTCTCCCTTGATGATGCATT+AGG - chr3.4:1557826-1557845 MS.gene52541:CDS 45.0%
CCAGTGTCCAGCTGAACTGA+AGG + chr3.4:1558141-1558160 None:intergenic 55.0%
CCTTCAGTTCAGCTGGACAC+TGG - chr3.4:1558138-1558157 MS.gene52541:CDS 55.0%


Chromosome Type Strat End Strand Name
chr3.4 gene 1557817 1558164 1557817 ID=MS.gene52541
chr3.4 mRNA 1557817 1558164 1557817 ID=MS.gene52541.t1;Parent=MS.gene52541
chr3.4 exon 1557817 1558164 1557817 ID=MS.gene52541.t1.exon1;Parent=MS.gene52541.t1
chr3.4 CDS 1557817 1558164 1557817 ID=cds.MS.gene52541.t1;Parent=MS.gene52541.t1
Gene Sequence

>MS.gene52541

ATGAAGAATCTCTCCCTTGATGATGCATTAGGGTTAATCTCAGCATTAAAATGTAAGTTTGGATATGAGAAAAGGGAAAAATATGAATCTTTTCTACAAATTATGAAGGATTACAAGGCTGAAAGAATTGATGCTAGGGTTGTCAAATTAAGAGTGTACGAGTTGTTGGACGGCCATGAAGATTTAATTTTGAGACTCAACACCTTCTTGCCAACTAAATATGAAATCAAACTTCCATTGGATCGTGATGACGATGATGAAGAACAAGATGGTCGAATGACAAAGACAAATATCAAAGTGCTAAAGAAATATCGAATCACACCTTCAGTTCAGCTGGACACTGGTTAG
Protein sequence

>MS.gene52541.t1

MKNLSLDDALGLISALKCKFGYEKREKYESFLQIMKDYKAERIDARVVKLRVYELLDGHEDLILRLNTFLPTKYEIKLPLDRDDDDEEQDGRMTKTNIKVLKKYRITPSVQLDTG