AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene025421

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene025421.t1 MTR_1g087870 82.915 199 34 0 1 199 31 229 6.66e-124 350
MS.gene025421.t1 MTR_7g110090 43.814 194 104 1 2 195 84 272 3.17e-57 182
MS.gene025421.t1 MTR_3g452180 43.850 187 100 1 9 195 7 188 4.28e-56 176
MS.gene025421.t1 MTR_4g032560 40.513 195 111 1 1 195 112 301 5.71e-51 166
MS.gene025421.t1 MTR_4g032580 40.513 195 111 1 1 195 112 301 1.64e-50 165
MS.gene025421.t1 MTR_2g100360 44.000 175 98 0 1 175 83 257 4.79e-50 163
MS.gene025421.t1 MTR_3g070250 39.896 193 116 0 1 193 88 280 9.51e-50 163
MS.gene025421.t1 MTR_3g048970 42.268 194 110 2 1 193 83 275 1.25e-49 162
MS.gene025421.t1 MTR_1g084880 42.268 194 110 2 1 193 83 275 3.24e-49 161
MS.gene025421.t1 MTR_1g105780 41.026 195 110 1 1 195 84 273 1.02e-44 149
MS.gene025421.t1 MTR_1g105765 41.026 195 110 1 1 195 84 273 1.05e-44 149
MS.gene025421.t1 MTR_4g121040 39.053 169 98 1 21 189 7 170 6.42e-40 135
MS.gene025421.t1 MTR_1g047540 39.683 189 94 3 2 190 84 252 2.26e-38 137
MS.gene025421.t1 MTR_2g038740 42.138 159 92 0 1 159 83 241 3.87e-38 139
MS.gene025421.t1 MTR_1g069260 37.912 182 96 3 24 193 111 287 1.89e-36 129
MS.gene025421.t1 MTR_4g062370 38.068 176 104 2 1 176 87 257 6.10e-36 133
MS.gene025421.t1 MTR_3g449750 40.426 141 82 2 13 152 31 170 1.25e-32 116
MS.gene025421.t1 MTR_5g094740 36.129 155 90 1 39 193 673 818 1.51e-28 112
MS.gene025421.t1 MTR_3g085990 34.031 191 84 2 1 191 84 232 2.51e-28 106
MS.gene025421.t1 MTR_1g019580 40.164 122 70 1 77 195 9 130 1.42e-26 99.0
MS.gene025421.t1 MTR_4g081330 64.516 62 22 0 113 174 1084 1145 9.13e-26 104
MS.gene025421.t1 MTR_8g042540 48.235 85 44 0 111 195 3 87 3.51e-25 94.0
MS.gene025421.t1 MTR_5g066660 32.105 190 97 3 1 190 83 240 7.16e-25 98.2
MS.gene025421.t1 MTR_8g042540 48.780 82 42 0 114 195 18 99 1.40e-24 92.8
MS.gene025421.t1 MTR_4g117740 32.857 140 60 2 1 140 94 199 1.33e-22 90.5
MS.gene025421.t1 MTR_0521s0010 37.008 127 78 2 14 139 76 201 1.20e-21 89.0
MS.gene025421.t1 MTR_2g016390 38.235 102 63 0 78 179 593 694 4.21e-19 85.1
MS.gene025421.t1 MTR_6g465600 29.381 194 126 2 2 191 90 276 7.28e-19 82.8
MS.gene025421.t1 MTR_5g075200 40.000 100 55 2 1 100 96 190 1.13e-17 77.8
MS.gene025421.t1 MTR_1g052720 27.041 196 128 4 2 192 87 272 7.13e-17 77.4
MS.gene025421.t1 MTR_1g037600 36.842 95 60 0 78 172 60 154 2.02e-16 75.5
MS.gene025421.t1 MTR_4g057880 47.692 65 34 0 129 193 7 71 1.67e-15 68.6
MS.gene025421.t1 MTR_0091s0090 27.461 193 120 6 2 192 6 180 3.78e-15 72.0
MS.gene025421.t1 MTR_0152s0060 38.636 88 53 1 92 179 221 307 1.32e-14 71.6
MS.gene025421.t1 MTR_6g016445 42.373 59 34 0 115 173 10 68 1.48e-12 61.6
MS.gene025421.t1 MTR_1g045920 76.190 42 10 0 1 42 42 83 6.60e-12 63.2
MS.gene025421.t1 MTR_1g054585 30.172 116 61 1 78 193 11 106 1.25e-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

Find 46 sgRNAs with CRISPR-Local

Find 51 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TGGAATTGCATCACAATATT+TGG 0.142675 2.2:-41553055 MS.gene025421:CDS
TGATGTTAGCTCTGGATTTC+TGG 0.165668 2.2:-41553252 MS.gene025421:intron
CTTCTCAATTTCAAACTTCA+TGG 0.267710 2.2:+41553388 None:intergenic
TGATGGAATGAGAGGATTTC+GGG 0.294439 2.2:+41553323 None:intergenic
TCTCAAACTCAAACAACTAT+TGG 0.300126 2.2:+41552890 None:intergenic
TTTACTGGTAATGGTCAGTT+TGG 0.323884 2.2:-41553467 MS.gene025421:CDS
ACGTTTCACTTCAATGTAGA+TGG 0.346590 2.2:+41552913 None:intergenic
ATGATGGAATGAGAGGATTT+CGG 0.364690 2.2:+41553322 None:intergenic
TTCATGGGAGGTATAAATAA+AGG 0.396538 2.2:+41553404 None:intergenic
GTGCCATCGTTTGTTTATCA+AGG 0.414248 2.2:-41553359 MS.gene025421:CDS
TTACTGGTAATGGTCAGTTT+GGG 0.414794 2.2:-41553466 MS.gene025421:CDS
ACTATCGTCATGGTGTTTAC+TGG 0.438683 2.2:-41553482 MS.gene025421:CDS
GAGAGGATTTCGGGTGTGAC+TGG 0.444509 2.2:+41553332 None:intergenic
ACTGGATATGATGTTAGCTC+TGG 0.447476 2.2:-41553260 MS.gene025421:CDS
GCATCACAATATTTGGAACT+AGG 0.455508 2.2:-41553048 MS.gene025421:CDS
TTCTCAATTTCAAACTTCAT+GGG 0.459280 2.2:+41553389 None:intergenic
GGACTATGTGACGTGACAAT+TGG 0.459653 2.2:-41553124 MS.gene025421:CDS
AGCTTGGAGGAGGGTGGAAA+AGG 0.464293 2.2:-41553009 MS.gene025421:CDS
GTCATGGTGTTTACTGGTAA+TGG 0.491948 2.2:-41553476 MS.gene025421:CDS
TGGAGGAGGGTGGAAAAGGA+TGG 0.500308 2.2:-41553005 MS.gene025421:CDS
GAAGGTGTCGTGGTCAAGGT+TGG 0.513832 2.2:-41552962 MS.gene025421:CDS
CCACACCACCACATCAAGCT+TGG 0.515731 2.2:-41553025 MS.gene025421:CDS
GAAAATTGATCTCATCATGA+TGG 0.516547 2.2:+41553306 None:intergenic
CTCCTCCAAGCTTGATGTGG+TGG 0.531491 2.2:+41553020 None:intergenic
CACCACATCAAGCTTGGAGG+AGG 0.534818 2.2:-41553019 MS.gene025421:CDS
AACGCACATTGTAAAAGTCT+CGG 0.537561 2.2:+41553513 None:intergenic
ACCCTCCTCCAAGCTTGATG+TGG 0.545430 2.2:+41553017 None:intergenic
TGAAGAAGGTGTCGTGGTCA+AGG 0.545787 2.2:-41552966 MS.gene025421:CDS
CCAAGCTTGATGTGGTGGTG+TGG 0.547240 2.2:+41553025 None:intergenic
CACCACCACATCAAGCTTGG+AGG 0.557816 2.2:-41553022 MS.gene025421:CDS
GTCATGGTGGAAAGGATAAG+TGG 0.571095 2.2:-41553569 MS.gene025421:CDS
TTGCAGATGCTTATTTACAA+AGG 0.583138 2.2:-41553145 MS.gene025421:intron
AGTTTGATGTCATGGTGGAA+AGG 0.589089 2.2:-41553577 None:intergenic
TCTCATCATGATGGAATGAG+AGG 0.601577 2.2:+41553315 None:intergenic
TCAATTTCAAACTTCATGGG+AGG 0.602862 2.2:+41553392 None:intergenic
ACATCAAGCTTGGAGGAGGG+TGG 0.613250 2.2:-41553015 MS.gene025421:CDS
AAGGTTGGATTTCGACACGC+TGG 0.618883 2.2:-41552947 MS.gene025421:CDS
TTGACGATTGTGGGAACAAG+TGG 0.630425 2.2:-41553075 MS.gene025421:CDS
ACCACATCAAGCTTGGAGGA+GGG 0.639220 2.2:-41553018 MS.gene025421:CDS
GCTGCGCGGAGACTTGAAGA+AGG 0.643869 2.2:-41552980 MS.gene025421:CDS
TTTAGGCGGAACTATCGTCA+TGG 0.647378 2.2:-41553492 MS.gene025421:CDS
ATTAACGTACTTGATCGAGC+AGG 0.652929 2.2:-41553443 MS.gene025421:CDS
ATGGGAGGTATAAATAAAGG+AGG 0.660218 2.2:+41553407 None:intergenic
GAGACTTGAAGAAGGTGTCG+TGG 0.672602 2.2:-41552972 MS.gene025421:CDS
ACACCTTGATAAACAAACGA+TGG 0.686570 2.2:+41553356 None:intergenic
GGAAAAGGATGGTTGCTGCG+CGG 0.715685 2.2:-41552994 MS.gene025421:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
! TTCTCAATTTCAAACTTCAT+GGG + chr2.2:41553078-41553097 None:intergenic 25.0%
CTTCTCAATTTCAAACTTCA+TGG + chr2.2:41553079-41553098 None:intergenic 30.0%
GAAAATTGATCTCATCATGA+TGG + chr2.2:41553161-41553180 None:intergenic 30.0%
TGGAATTGCATCACAATATT+TGG - chr2.2:41553409-41553428 MS.gene025421:CDS 30.0%
TTGCAGATGCTTATTTACAA+AGG - chr2.2:41553319-41553338 MS.gene025421:CDS 30.0%
! AGATCAATTTTCAGATAAGC+TGG - chr2.2:41553169-41553188 MS.gene025421:intron 30.0%
! GATCAATTTTCAGATAAGCT+GGG - chr2.2:41553170-41553189 MS.gene025421:intron 30.0%
! TTCATGGGAGGTATAAATAA+AGG + chr2.2:41553063-41553082 None:intergenic 30.0%
!!! GGAGTTGTTTTTTTAACAAC+TGG - chr2.2:41552916-41552935 MS.gene025421:CDS 30.0%
AACGCACATTGTAAAAGTCT+CGG + chr2.2:41552954-41552973 None:intergenic 35.0%
ACACCTTGATAAACAAACGA+TGG + chr2.2:41553111-41553130 None:intergenic 35.0%
ACGTTTCACTTCAATGTAGA+TGG + chr2.2:41553554-41553573 None:intergenic 35.0%
TCAATTTCAAACTTCATGGG+AGG + chr2.2:41553075-41553094 None:intergenic 35.0%
! ATGATGGAATGAGAGGATTT+CGG + chr2.2:41553145-41553164 None:intergenic 35.0%
! ATGGGAGGTATAAATAAAGG+AGG + chr2.2:41553060-41553079 None:intergenic 35.0%
! GACTTTTACAATGTGCGTTT+AGG - chr2.2:41552955-41552974 MS.gene025421:CDS 35.0%
! GCATCACAATATTTGGAACT+AGG - chr2.2:41553416-41553435 MS.gene025421:CDS 35.0%
! TGATTTTGCTTGACGATTGT+GGG - chr2.2:41553380-41553399 MS.gene025421:CDS 35.0%
! TTGATTTTGCTTGACGATTG+TGG - chr2.2:41553379-41553398 MS.gene025421:CDS 35.0%
! TTTTACAATGTGCGTTTAGG+CGG - chr2.2:41552958-41552977 MS.gene025421:CDS 35.0%
!! TTACTGGTAATGGTCAGTTT+GGG - chr2.2:41552998-41553017 MS.gene025421:CDS 35.0%
!! TTTACTGGTAATGGTCAGTT+TGG - chr2.2:41552997-41553016 MS.gene025421:CDS 35.0%
ACTATCGTCATGGTGTTTAC+TGG - chr2.2:41552982-41553001 MS.gene025421:CDS 40.0%
ACTGGATATGATGTTAGCTC+TGG - chr2.2:41553204-41553223 MS.gene025421:intron 40.0%
ATTAACGTACTTGATCGAGC+AGG - chr2.2:41553021-41553040 MS.gene025421:CDS 40.0%
GTCATGGTGTTTACTGGTAA+TGG - chr2.2:41552988-41553007 MS.gene025421:CDS 40.0%
GTGCCATCGTTTGTTTATCA+AGG - chr2.2:41553105-41553124 MS.gene025421:CDS 40.0%
TGATGGAATGAGAGGATTTC+GGG + chr2.2:41553144-41553163 None:intergenic 40.0%
! TCTCATCATGATGGAATGAG+AGG + chr2.2:41553152-41553171 None:intergenic 40.0%
!! TGATGTTAGCTCTGGATTTC+TGG - chr2.2:41553212-41553231 MS.gene025421:intron 40.0%
GGACTATGTGACGTGACAAT+TGG - chr2.2:41553340-41553359 MS.gene025421:CDS 45.0%
TTGACGATTGTGGGAACAAG+TGG - chr2.2:41553389-41553408 MS.gene025421:CDS 45.0%
TTTAGGCGGAACTATCGTCA+TGG - chr2.2:41552972-41552991 MS.gene025421:CDS 45.0%
!! AGCTGGGAAAAAGTGTTGAC+TGG - chr2.2:41553186-41553205 MS.gene025421:intron 45.0%
AAGGTTGGATTTCGACACGC+TGG - chr2.2:41553517-41553536 MS.gene025421:CDS 50.0%
ACCACATCAAGCTTGGAGGA+GGG - chr2.2:41553446-41553465 MS.gene025421:CDS 50.0%
!! GAGACTTGAAGAAGGTGTCG+TGG - chr2.2:41553492-41553511 MS.gene025421:CDS 50.0%
!! TGAAGAAGGTGTCGTGGTCA+AGG - chr2.2:41553498-41553517 MS.gene025421:CDS 50.0%
ACATCAAGCTTGGAGGAGGG+TGG - chr2.2:41553449-41553468 MS.gene025421:CDS 55.0%
ACCCTCCTCCAAGCTTGATG+TGG + chr2.2:41553450-41553469 None:intergenic 55.0%
AGCTTGGAGGAGGGTGGAAA+AGG - chr2.2:41553455-41553474 MS.gene025421:CDS 55.0%
CACCACATCAAGCTTGGAGG+AGG - chr2.2:41553445-41553464 MS.gene025421:CDS 55.0%
CACCACCACATCAAGCTTGG+AGG - chr2.2:41553442-41553461 MS.gene025421:CDS 55.0%
CCACACCACCACATCAAGCT+TGG - chr2.2:41553439-41553458 MS.gene025421:CDS 55.0%
CTCCTCCAAGCTTGATGTGG+TGG + chr2.2:41553447-41553466 None:intergenic 55.0%
GGAAAAGGATGGTTGCTGCG+CGG - chr2.2:41553470-41553489 MS.gene025421:CDS 55.0%
TGGAGGAGGGTGGAAAAGGA+TGG - chr2.2:41553459-41553478 MS.gene025421:CDS 55.0%
! CCAAGCTTGATGTGGTGGTG+TGG + chr2.2:41553442-41553461 None:intergenic 55.0%
! GAGAGGATTTCGGGTGTGAC+TGG + chr2.2:41553135-41553154 None:intergenic 55.0%
!! GAAGGTGTCGTGGTCAAGGT+TGG - chr2.2:41553502-41553521 MS.gene025421:CDS 55.0%
GCTGCGCGGAGACTTGAAGA+AGG - chr2.2:41553484-41553503 MS.gene025421:CDS 60.0%


Chromosome Type Strat End Strand Name
chr2.2 gene 41552898 41553588 41552898 ID=MS.gene025421
chr2.2 mRNA 41552898 41553588 41552898 ID=MS.gene025421.t1;Parent=MS.gene025421
chr2.2 exon 41553253 41553588 41553253 ID=MS.gene025421.t1.exon1;Parent=MS.gene025421.t1
chr2.2 CDS 41553253 41553588 41553253 ID=cds.MS.gene025421.t1;Parent=MS.gene025421.t1
chr2.2 exon 41552898 41553161 41552898 ID=MS.gene025421.t1.exon2;Parent=MS.gene025421.t1
chr2.2 CDS 41552898 41553161 41552898 ID=cds.MS.gene025421.t1;Parent=MS.gene025421.t1
Gene Sequence

>MS.gene025421

ATGGTGGAAAGGATAAGTGGAGTTGTTTTTTTAACAACTGGATTCAATGCGATCCGAGACTTTTACAATGTGCGTTTAGGCGGAACTATCGTCATGGTGTTTACTGGTAATGGTCAGTTTGGGATTAACGTACTTGATCGAGCAGGACGTGTTGTTGATCCTCCTTTATTTATACCTCCCATGAAGTTTGAAATTGAGAAGACAATTGTGCCATCGTTTGTTTATCAAGGTGTGCCAGTCACACCCGAAATCCTCTCATTCCATCATGATGAGATCAATTTTCAGATAAGCTGGGAAAAAGTGTTGACTGGATATGATGTTAGCTCTGGATTTCTGGTATAAGTTTGATGTATTAGTATTGCTCACATAAACAGTTACTTTTAGCATATATACATTTGTTTGTATTAACACATCTTGATGTTTGCAGATGCTTATTTACAAAGGACTATGTGACGTGACAATTGGCAAGAAGACAACTTCATTGATTTTGCTTGACGATTGTGGGAACAAGTGGAATTGCATCACAATATTTGGAACTAGGCCACACCACCACATCAAGCTTGGAGGAGGGTGGAAAAGGATGGTTGCTGCGCGGAGACTTGAAGAAGGTGTCGTGGTCAAGGTTGGATTTCGACACGCTGGAAAGAACGATACCATCTACATTGAAGTGAAACGTCCAATAGTTGTTTGA
Protein sequence

>MS.gene025421.t1

MVERISGVVFLTTGFNAIRDFYNVRLGGTIVMVFTGNGQFGINVLDRAGRVVDPPLFIPPMKFEIEKTIVPSFVYQGVPVTPEILSFHHDEINFQISWEKVLTGYDVSSGFLMLIYKGLCDVTIGKKTTSLILLDDCGNKWNCITIFGTRPHHHIKLGGGWKRMVAARRLEEGVVVKVGFRHAGKNDTIYIEVKRPIVV