AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene035730

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene035730.t1 MTR_1g087870 82.915 199 34 0 1 199 31 229 5.35e-124 350
MS.gene035730.t1 MTR_7g110090 43.814 194 104 1 2 195 84 272 3.35e-57 181
MS.gene035730.t1 MTR_3g452180 43.850 187 100 1 9 195 7 188 3.83e-56 176
MS.gene035730.t1 MTR_4g032560 40.513 195 111 1 1 195 112 301 5.59e-51 166
MS.gene035730.t1 MTR_4g032580 40.513 195 111 1 1 195 112 301 1.63e-50 165
MS.gene035730.t1 MTR_2g100360 44.000 175 98 0 1 175 83 257 4.58e-50 163
MS.gene035730.t1 MTR_3g070250 39.896 193 116 0 1 193 88 280 8.18e-50 163
MS.gene035730.t1 MTR_3g048970 42.268 194 110 2 1 193 83 275 1.31e-49 162
MS.gene035730.t1 MTR_1g084880 42.268 194 110 2 1 193 83 275 3.14e-49 161
MS.gene035730.t1 MTR_1g105780 41.026 195 110 1 1 195 84 273 1.12e-44 149
MS.gene035730.t1 MTR_1g105765 41.026 195 110 1 1 195 84 273 1.15e-44 149
MS.gene035730.t1 MTR_4g121040 39.053 169 98 1 21 189 7 170 7.24e-40 135
MS.gene035730.t1 MTR_1g047540 39.683 189 94 3 2 190 84 252 2.34e-38 137
MS.gene035730.t1 MTR_2g038740 42.138 159 92 0 1 159 83 241 3.68e-38 139
MS.gene035730.t1 MTR_1g069260 37.912 182 96 3 24 193 111 287 1.83e-36 129
MS.gene035730.t1 MTR_4g062370 38.068 176 104 2 1 176 87 257 6.41e-36 133
MS.gene035730.t1 MTR_3g449750 40.426 141 82 2 13 152 31 170 1.31e-32 115
MS.gene035730.t1 MTR_5g094740 36.129 155 90 1 39 193 673 818 1.49e-28 112
MS.gene035730.t1 MTR_3g085990 34.031 191 84 2 1 191 84 232 2.38e-28 106
MS.gene035730.t1 MTR_1g019580 40.164 122 70 1 77 195 9 130 1.45e-26 99.0
MS.gene035730.t1 MTR_4g081330 64.516 62 22 0 113 174 1084 1145 9.13e-26 104
MS.gene035730.t1 MTR_8g042540 48.235 85 44 0 111 195 3 87 3.51e-25 94.0
MS.gene035730.t1 MTR_5g066660 32.105 190 97 3 1 190 83 240 7.16e-25 98.2
MS.gene035730.t1 MTR_8g042540 48.780 82 42 0 114 195 18 99 1.35e-24 92.8
MS.gene035730.t1 MTR_4g117740 32.857 140 60 2 1 140 94 199 1.32e-22 90.5
MS.gene035730.t1 MTR_0521s0010 37.008 127 78 2 14 139 76 201 1.16e-21 89.0
MS.gene035730.t1 MTR_2g016390 38.235 102 63 0 78 179 593 694 3.90e-19 85.1
MS.gene035730.t1 MTR_6g465600 29.381 194 126 2 2 191 90 276 7.58e-19 82.8
MS.gene035730.t1 MTR_5g075200 40.000 100 55 2 1 100 96 190 1.12e-17 77.8
MS.gene035730.t1 MTR_1g052720 27.041 196 128 4 2 192 87 272 7.20e-17 77.4
MS.gene035730.t1 MTR_1g037600 36.842 95 60 0 78 172 60 154 2.06e-16 75.5
MS.gene035730.t1 MTR_4g057880 47.692 65 34 0 129 193 7 71 1.50e-15 68.9
MS.gene035730.t1 MTR_0091s0090 27.461 193 120 6 2 192 6 180 3.97e-15 72.0
MS.gene035730.t1 MTR_0152s0060 38.636 88 53 1 92 179 221 307 1.33e-14 71.6
MS.gene035730.t1 MTR_6g016445 42.373 59 34 0 115 173 10 68 1.47e-12 61.6
MS.gene035730.t1 MTR_1g045920 76.190 42 10 0 1 42 42 83 6.87e-12 63.2
MS.gene035730.t1 MTR_1g054585 30.172 116 61 1 78 193 11 106 1.16e-11 59.7
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 47 sgRNAs with CRISPR-Local

Find 52 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TGGAATTGCATCACAATATT+TGG 0.142675 3.2:-47034620 MS.gene035730:CDS
TGATGTTAGCTCTGGATTTC+TGG 0.165668 3.2:-47034817 MS.gene035730:intron
TTTACTGGTAATGGTCAATT+TGG 0.176931 3.2:-47035032 MS.gene035730:CDS
CTTCTCAATTTCAAACTTCA+TGG 0.267710 3.2:+47034953 None:intergenic
TGATGGAATGATAGGATTTC+GGG 0.277789 3.2:+47034888 None:intergenic
ATGATGGAATGATAGGATTT+CGG 0.326681 3.2:+47034887 None:intergenic
ACGTTTCACTTCAATGTAGA+TGG 0.373124 3.2:+47034478 None:intergenic
TCTCATCATGATGGAATGAT+AGG 0.390247 3.2:+47034880 None:intergenic
TTCATGGGAGGTATAAATAA+AGG 0.396538 3.2:+47034969 None:intergenic
GTGCCATCGTTTGTTTATCA+AGG 0.414248 3.2:-47034924 MS.gene035730:CDS
GATAGGATTTCGGGTGTGAC+TGG 0.428403 3.2:+47034897 None:intergenic
ACTATCGTCATGGTGTTTAC+TGG 0.438683 3.2:-47035047 MS.gene035730:CDS
TTACTGGTAATGGTCAATTT+GGG 0.440998 3.2:-47035031 MS.gene035730:CDS
ACTGGATATGATGTTAGCTC+TGG 0.447476 3.2:-47034825 MS.gene035730:CDS
GCATCACAATATTTGGAACT+AGG 0.455508 3.2:-47034613 MS.gene035730:CDS
TCTCAAACTCAAACAACTAC+TGG 0.458362 3.2:+47034455 None:intergenic
TTCTCAATTTCAAACTTCAT+GGG 0.459280 3.2:+47034954 None:intergenic
GGACTATGTGACGTGACAAT+TGG 0.459653 3.2:-47034689 MS.gene035730:CDS
AGCTTGGAGGAGGGTGGAAA+AGG 0.464293 3.2:-47034574 MS.gene035730:CDS
AAGGTGTCGTGGTCAAGGTT+GGG 0.484660 3.2:-47034526 MS.gene035730:CDS
GTCATGGTGTTTACTGGTAA+TGG 0.491948 3.2:-47035041 MS.gene035730:CDS
GAAGGTGTCGTGGTCAAGGT+TGG 0.496737 3.2:-47034527 MS.gene035730:CDS
TGGAGGAGGGTGGAAAAGGA+TGG 0.500308 3.2:-47034570 MS.gene035730:CDS
CCACACCACCACATCAAGCT+TGG 0.515731 3.2:-47034590 MS.gene035730:CDS
GAAAATTGATCTCATCATGA+TGG 0.516547 3.2:+47034871 None:intergenic
CTCCTCCAAGCTTGATGTGG+TGG 0.531491 3.2:+47034585 None:intergenic
CACCACATCAAGCTTGGAGG+AGG 0.534818 3.2:-47034584 MS.gene035730:CDS
AACGCACATTGTAAAAGTCT+CGG 0.537561 3.2:+47035078 None:intergenic
ACCCTCCTCCAAGCTTGATG+TGG 0.545430 3.2:+47034582 None:intergenic
TGAAGAAGGTGTCGTGGTCA+AGG 0.545787 3.2:-47034531 MS.gene035730:CDS
CCAAGCTTGATGTGGTGGTG+TGG 0.547240 3.2:+47034590 None:intergenic
CACCACCACATCAAGCTTGG+AGG 0.557816 3.2:-47034587 MS.gene035730:CDS
GTCATGGTGGAAAGGATAAG+TGG 0.571095 3.2:-47035134 MS.gene035730:CDS
AAGGTTGGGTTTCGACACGC+TGG 0.587337 3.2:-47034512 MS.gene035730:CDS
AGTTTGATGTCATGGTGGAA+AGG 0.589089 3.2:-47035142 None:intergenic
TCAATTTCAAACTTCATGGG+AGG 0.602862 3.2:+47034957 None:intergenic
TTGCAGATGCTAATTTACAA+AGG 0.604896 3.2:-47034710 MS.gene035730:intron
ACATCAAGCTTGGAGGAGGG+TGG 0.613250 3.2:-47034580 MS.gene035730:CDS
TTGACGATTGTGGGAACAAG+TGG 0.630425 3.2:-47034640 MS.gene035730:CDS
ACCACATCAAGCTTGGAGGA+GGG 0.639220 3.2:-47034583 MS.gene035730:CDS
GCTGCGCGGAGACTTGAAGA+AGG 0.643869 3.2:-47034545 MS.gene035730:CDS
TTTAGGCGGAACTATCGTCA+TGG 0.647378 3.2:-47035057 MS.gene035730:CDS
ATTAACGTACTTGATCGAGC+AGG 0.652929 3.2:-47035008 MS.gene035730:CDS
ATGGGAGGTATAAATAAAGG+AGG 0.660218 3.2:+47034972 None:intergenic
GAGACTTGAAGAAGGTGTCG+TGG 0.672602 3.2:-47034537 MS.gene035730:CDS
ACACCTTGATAAACAAACGA+TGG 0.679749 3.2:+47034921 None:intergenic
GGAAAAGGATGGTTGCTGCG+CGG 0.715685 3.2:-47034559 MS.gene035730:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
! TTCTCAATTTCAAACTTCAT+GGG + chr3.2:47034643-47034662 None:intergenic 25.0%
CTTCTCAATTTCAAACTTCA+TGG + chr3.2:47034644-47034663 None:intergenic 30.0%
GAAAATTGATCTCATCATGA+TGG + chr3.2:47034726-47034745 None:intergenic 30.0%
TGGAATTGCATCACAATATT+TGG - chr3.2:47034974-47034993 MS.gene035730:CDS 30.0%
TTGCAGATGCTAATTTACAA+AGG - chr3.2:47034884-47034903 MS.gene035730:CDS 30.0%
! AGATCAATTTTCAGATAAGC+TGG - chr3.2:47034734-47034753 MS.gene035730:intron 30.0%
! ATGATGGAATGATAGGATTT+CGG + chr3.2:47034710-47034729 None:intergenic 30.0%
! GATCAATTTTCAGATAAGCT+GGG - chr3.2:47034735-47034754 MS.gene035730:intron 30.0%
! TTCATGGGAGGTATAAATAA+AGG + chr3.2:47034628-47034647 None:intergenic 30.0%
!! TTACTGGTAATGGTCAATTT+GGG - chr3.2:47034563-47034582 MS.gene035730:CDS 30.0%
!! TTTACTGGTAATGGTCAATT+TGG - chr3.2:47034562-47034581 MS.gene035730:CDS 30.0%
!!! GGAGTTGTTTTTTTAACAAC+TGG - chr3.2:47034481-47034500 MS.gene035730:CDS 30.0%
AACGCACATTGTAAAAGTCT+CGG + chr3.2:47034519-47034538 None:intergenic 35.0%
ACACCTTGATAAACAAACGA+TGG + chr3.2:47034676-47034695 None:intergenic 35.0%
ACGTTTCACTTCAATGTAGA+TGG + chr3.2:47035119-47035138 None:intergenic 35.0%
TCAATTTCAAACTTCATGGG+AGG + chr3.2:47034640-47034659 None:intergenic 35.0%
TGATGGAATGATAGGATTTC+GGG + chr3.2:47034709-47034728 None:intergenic 35.0%
! ATGGGAGGTATAAATAAAGG+AGG + chr3.2:47034625-47034644 None:intergenic 35.0%
! GACTTTTACAATGTGCGTTT+AGG - chr3.2:47034520-47034539 MS.gene035730:CDS 35.0%
! GCATCACAATATTTGGAACT+AGG - chr3.2:47034981-47035000 MS.gene035730:CDS 35.0%
! TCTCATCATGATGGAATGAT+AGG + chr3.2:47034717-47034736 None:intergenic 35.0%
! TGATTTTGCTTGACGATTGT+GGG - chr3.2:47034945-47034964 MS.gene035730:CDS 35.0%
! TTGATTTTGCTTGACGATTG+TGG - chr3.2:47034944-47034963 MS.gene035730:CDS 35.0%
! TTTTACAATGTGCGTTTAGG+CGG - chr3.2:47034523-47034542 MS.gene035730:CDS 35.0%
ACTATCGTCATGGTGTTTAC+TGG - chr3.2:47034547-47034566 MS.gene035730:CDS 40.0%
ACTGGATATGATGTTAGCTC+TGG - chr3.2:47034769-47034788 MS.gene035730:intron 40.0%
ATTAACGTACTTGATCGAGC+AGG - chr3.2:47034586-47034605 MS.gene035730:CDS 40.0%
GTCATGGTGTTTACTGGTAA+TGG - chr3.2:47034553-47034572 MS.gene035730:CDS 40.0%
GTGCCATCGTTTGTTTATCA+AGG - chr3.2:47034670-47034689 MS.gene035730:CDS 40.0%
!! TGATGTTAGCTCTGGATTTC+TGG - chr3.2:47034777-47034796 MS.gene035730:intron 40.0%
GGACTATGTGACGTGACAAT+TGG - chr3.2:47034905-47034924 MS.gene035730:CDS 45.0%
TTGACGATTGTGGGAACAAG+TGG - chr3.2:47034954-47034973 MS.gene035730:CDS 45.0%
TTTAGGCGGAACTATCGTCA+TGG - chr3.2:47034537-47034556 MS.gene035730:CDS 45.0%
!! AGCTGGGAAAAAGTGTTGAC+TGG - chr3.2:47034751-47034770 MS.gene035730:intron 45.0%
ACCACATCAAGCTTGGAGGA+GGG - chr3.2:47035011-47035030 MS.gene035730:CDS 50.0%
! GATAGGATTTCGGGTGTGAC+TGG + chr3.2:47034700-47034719 None:intergenic 50.0%
!! AAGGTGTCGTGGTCAAGGTT+GGG - chr3.2:47035068-47035087 MS.gene035730:CDS 50.0%
!! GAGACTTGAAGAAGGTGTCG+TGG - chr3.2:47035057-47035076 MS.gene035730:CDS 50.0%
!! TGAAGAAGGTGTCGTGGTCA+AGG - chr3.2:47035063-47035082 MS.gene035730:CDS 50.0%
AAGGTTGGGTTTCGACACGC+TGG - chr3.2:47035082-47035101 MS.gene035730:CDS 55.0%
ACATCAAGCTTGGAGGAGGG+TGG - chr3.2:47035014-47035033 MS.gene035730:CDS 55.0%
ACCCTCCTCCAAGCTTGATG+TGG + chr3.2:47035015-47035034 None:intergenic 55.0%
AGCTTGGAGGAGGGTGGAAA+AGG - chr3.2:47035020-47035039 MS.gene035730:CDS 55.0%
CACCACATCAAGCTTGGAGG+AGG - chr3.2:47035010-47035029 MS.gene035730:CDS 55.0%
CACCACCACATCAAGCTTGG+AGG - chr3.2:47035007-47035026 MS.gene035730:CDS 55.0%
CCACACCACCACATCAAGCT+TGG - chr3.2:47035004-47035023 MS.gene035730:CDS 55.0%
CTCCTCCAAGCTTGATGTGG+TGG + chr3.2:47035012-47035031 None:intergenic 55.0%
GGAAAAGGATGGTTGCTGCG+CGG - chr3.2:47035035-47035054 MS.gene035730:CDS 55.0%
TGGAGGAGGGTGGAAAAGGA+TGG - chr3.2:47035024-47035043 MS.gene035730:CDS 55.0%
! CCAAGCTTGATGTGGTGGTG+TGG + chr3.2:47035007-47035026 None:intergenic 55.0%
!! GAAGGTGTCGTGGTCAAGGT+TGG - chr3.2:47035067-47035086 MS.gene035730:CDS 55.0%
GCTGCGCGGAGACTTGAAGA+AGG - chr3.2:47035049-47035068 MS.gene035730:CDS 60.0%


Chromosome Type Strat End Strand Name
chr3.2 gene 47034463 47035153 47034463 ID=MS.gene035730
chr3.2 mRNA 47034463 47035153 47034463 ID=MS.gene035730.t1;Parent=MS.gene035730
chr3.2 exon 47034818 47035153 47034818 ID=MS.gene035730.t1.exon1;Parent=MS.gene035730.t1
chr3.2 CDS 47034818 47035153 47034818 ID=cds.MS.gene035730.t1;Parent=MS.gene035730.t1
chr3.2 exon 47034463 47034726 47034463 ID=MS.gene035730.t1.exon2;Parent=MS.gene035730.t1
chr3.2 CDS 47034463 47034726 47034463 ID=cds.MS.gene035730.t1;Parent=MS.gene035730.t1
Gene Sequence

>MS.gene035730

ATGGTGGAAAGGATAAGTGGAGTTGTTTTTTTAACAACTGGATTCAATGCGATCCGAGACTTTTACAATGTGCGTTTAGGCGGAACTATCGTCATGGTGTTTACTGGTAATGGTCAATTTGGGATTAACGTACTTGATCGAGCAGGACGTGTTGTTGATCCTCCTTTATTTATACCTCCCATGAAGTTTGAAATTGAGAAGACAATTGTGCCATCGTTTGTTTATCAAGGTGTTCCAGTCACACCCGAAATCCTATCATTCCATCATGATGAGATCAATTTTCAGATAAGCTGGGAAAAAGTGTTGACTGGATATGATGTTAGCTCTGGATTTCTGGTATAAGTTTGATGTATTAGTATTGCTCACATAAACAGTTATTTTTAGCATATATACATTTGTTTGTATTAACACATCTTGATGTTTGCAGATGCTAATTTACAAAGGACTATGTGACGTGACAATTGGCAAGAAGACAACTTCATTGATTTTGCTTGACGATTGTGGGAACAAGTGGAATTGCATCACAATATTTGGAACTAGGCCACACCACCACATCAAGCTTGGAGGAGGGTGGAAAAGGATGGTTGCTGCGCGGAGACTTGAAGAAGGTGTCGTGGTCAAGGTTGGGTTTCGACACGCTGGAAAGAACGATACCATCTACATTGAAGTGAAACGTCCAGTAGTTGTTTGA
Protein sequence

>MS.gene035730.t1

MVERISGVVFLTTGFNAIRDFYNVRLGGTIVMVFTGNGQFGINVLDRAGRVVDPPLFIPPMKFEIEKTIVPSFVYQGVPVTPEILSFHHDEINFQISWEKVLTGYDVSSGFLMLIYKGLCDVTIGKKTTSLILLDDCGNKWNCITIFGTRPHHHIKLGGGWKRMVAARRLEEGVVVKVGFRHAGKNDTIYIEVKRPVVV