AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene052301

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene052301.t1 MTR_1g087870 82.915 199 34 0 1 199 31 229 6.66e-124 350
MS.gene052301.t1 MTR_7g110090 43.814 194 104 1 2 195 84 272 3.17e-57 182
MS.gene052301.t1 MTR_3g452180 43.850 187 100 1 9 195 7 188 4.28e-56 176
MS.gene052301.t1 MTR_4g032560 40.513 195 111 1 1 195 112 301 5.71e-51 166
MS.gene052301.t1 MTR_4g032580 40.513 195 111 1 1 195 112 301 1.64e-50 165
MS.gene052301.t1 MTR_2g100360 44.000 175 98 0 1 175 83 257 4.79e-50 163
MS.gene052301.t1 MTR_3g070250 39.896 193 116 0 1 193 88 280 9.51e-50 163
MS.gene052301.t1 MTR_3g048970 42.268 194 110 2 1 193 83 275 1.25e-49 162
MS.gene052301.t1 MTR_1g084880 42.268 194 110 2 1 193 83 275 3.24e-49 161
MS.gene052301.t1 MTR_1g105780 41.026 195 110 1 1 195 84 273 1.02e-44 149
MS.gene052301.t1 MTR_1g105765 41.026 195 110 1 1 195 84 273 1.05e-44 149
MS.gene052301.t1 MTR_4g121040 39.053 169 98 1 21 189 7 170 6.42e-40 135
MS.gene052301.t1 MTR_1g047540 39.683 189 94 3 2 190 84 252 2.26e-38 137
MS.gene052301.t1 MTR_2g038740 42.138 159 92 0 1 159 83 241 3.87e-38 139
MS.gene052301.t1 MTR_1g069260 37.912 182 96 3 24 193 111 287 1.89e-36 129
MS.gene052301.t1 MTR_4g062370 38.068 176 104 2 1 176 87 257 6.10e-36 133
MS.gene052301.t1 MTR_3g449750 40.426 141 82 2 13 152 31 170 1.25e-32 116
MS.gene052301.t1 MTR_5g094740 36.129 155 90 1 39 193 673 818 1.51e-28 112
MS.gene052301.t1 MTR_3g085990 34.031 191 84 2 1 191 84 232 2.51e-28 106
MS.gene052301.t1 MTR_1g019580 40.164 122 70 1 77 195 9 130 1.42e-26 99.0
MS.gene052301.t1 MTR_4g081330 64.516 62 22 0 113 174 1084 1145 9.13e-26 104
MS.gene052301.t1 MTR_8g042540 48.235 85 44 0 111 195 3 87 3.51e-25 94.0
MS.gene052301.t1 MTR_5g066660 32.105 190 97 3 1 190 83 240 7.16e-25 98.2
MS.gene052301.t1 MTR_8g042540 48.780 82 42 0 114 195 18 99 1.40e-24 92.8
MS.gene052301.t1 MTR_4g117740 32.857 140 60 2 1 140 94 199 1.33e-22 90.5
MS.gene052301.t1 MTR_0521s0010 37.008 127 78 2 14 139 76 201 1.20e-21 89.0
MS.gene052301.t1 MTR_2g016390 38.235 102 63 0 78 179 593 694 4.21e-19 85.1
MS.gene052301.t1 MTR_6g465600 29.381 194 126 2 2 191 90 276 7.28e-19 82.8
MS.gene052301.t1 MTR_5g075200 40.000 100 55 2 1 100 96 190 1.13e-17 77.8
MS.gene052301.t1 MTR_1g052720 27.041 196 128 4 2 192 87 272 7.13e-17 77.4
MS.gene052301.t1 MTR_1g037600 36.842 95 60 0 78 172 60 154 2.02e-16 75.5
MS.gene052301.t1 MTR_4g057880 47.692 65 34 0 129 193 7 71 1.67e-15 68.6
MS.gene052301.t1 MTR_0091s0090 27.461 193 120 6 2 192 6 180 3.78e-15 72.0
MS.gene052301.t1 MTR_0152s0060 38.636 88 53 1 92 179 221 307 1.32e-14 71.6
MS.gene052301.t1 MTR_6g016445 42.373 59 34 0 115 173 10 68 1.48e-12 61.6
MS.gene052301.t1 MTR_1g045920 76.190 42 10 0 1 42 42 83 6.60e-12 63.2
MS.gene052301.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 4.2:+33076684 MS.gene052301:CDS
TGATGTTAGCTCTGGATTTC+TGG 0.165668 4.2:+33076487 MS.gene052301:CDS
CTTCTCAATTTCAAACTTCA+TGG 0.267710 4.2:-33076351 None:intergenic
TGATGGAATGAGAGGATTTC+GGG 0.294439 4.2:-33076416 None:intergenic
TCTCAAACTCAAACAACTAT+TGG 0.300126 4.2:-33076849 None:intergenic
TTTACTGGTAATGGTCAGTT+TGG 0.323884 4.2:+33076272 MS.gene052301:CDS
ACGTTTCACTTCAATGTAGA+TGG 0.346590 4.2:-33076826 None:intergenic
ATGATGGAATGAGAGGATTT+CGG 0.364690 4.2:-33076417 None:intergenic
TTCATGGGAGGTATAAATAA+AGG 0.396538 4.2:-33076335 None:intergenic
GTGCCATCGTTTGTTTATCA+AGG 0.414248 4.2:+33076380 MS.gene052301:CDS
TTACTGGTAATGGTCAGTTT+GGG 0.414794 4.2:+33076273 MS.gene052301:CDS
ACTATCGTCATGGTGTTTAC+TGG 0.438683 4.2:+33076257 MS.gene052301:CDS
GAGAGGATTTCGGGTGTGAC+TGG 0.444509 4.2:-33076407 None:intergenic
ACTGGATATGATGTTAGCTC+TGG 0.447476 4.2:+33076479 MS.gene052301:CDS
GCATCACAATATTTGGAACT+AGG 0.455508 4.2:+33076691 MS.gene052301:CDS
TTCTCAATTTCAAACTTCAT+GGG 0.459280 4.2:-33076350 None:intergenic
GGACTATGTGACGTGACAAT+TGG 0.459653 4.2:+33076615 MS.gene052301:CDS
AGCTTGGAGGAGGGTGGAAA+AGG 0.464293 4.2:+33076730 MS.gene052301:CDS
GTCATGGTGTTTACTGGTAA+TGG 0.491948 4.2:+33076263 MS.gene052301:CDS
TGGAGGAGGGTGGAAAAGGA+TGG 0.500308 4.2:+33076734 MS.gene052301:CDS
GAAGGTGTCGTGGTCAAGGT+TGG 0.513832 4.2:+33076777 MS.gene052301:CDS
CCACACCACCACATCAAGCT+TGG 0.515731 4.2:+33076714 MS.gene052301:CDS
GAAAATTGATCTCATCATGA+TGG 0.516547 4.2:-33076433 None:intergenic
CTCCTCCAAGCTTGATGTGG+TGG 0.531491 4.2:-33076719 None:intergenic
CACCACATCAAGCTTGGAGG+AGG 0.534818 4.2:+33076720 MS.gene052301:CDS
AACGCACATTGTAAAAGTCT+CGG 0.537561 4.2:-33076226 None:intergenic
ACCCTCCTCCAAGCTTGATG+TGG 0.545430 4.2:-33076722 None:intergenic
TGAAGAAGGTGTCGTGGTCA+AGG 0.545787 4.2:+33076773 MS.gene052301:CDS
CCAAGCTTGATGTGGTGGTG+TGG 0.547240 4.2:-33076714 None:intergenic
CACCACCACATCAAGCTTGG+AGG 0.557816 4.2:+33076717 MS.gene052301:CDS
GTCATGGTGGAAAGGATAAG+TGG 0.571095 4.2:+33076170 None:intergenic
TTGCAGATGCTTATTTACAA+AGG 0.583138 4.2:+33076594 MS.gene052301:intron
AGTTTGATGTCATGGTGGAA+AGG 0.589089 4.2:+33076162 None:intergenic
TCTCATCATGATGGAATGAG+AGG 0.601577 4.2:-33076424 None:intergenic
TCAATTTCAAACTTCATGGG+AGG 0.602862 4.2:-33076347 None:intergenic
ACATCAAGCTTGGAGGAGGG+TGG 0.613250 4.2:+33076724 MS.gene052301:CDS
AAGGTTGGATTTCGACACGC+TGG 0.618883 4.2:+33076792 MS.gene052301:CDS
TTGACGATTGTGGGAACAAG+TGG 0.630425 4.2:+33076664 MS.gene052301:CDS
ACCACATCAAGCTTGGAGGA+GGG 0.639220 4.2:+33076721 MS.gene052301:CDS
GCTGCGCGGAGACTTGAAGA+AGG 0.643869 4.2:+33076759 MS.gene052301:CDS
TTTAGGCGGAACTATCGTCA+TGG 0.647378 4.2:+33076247 MS.gene052301:CDS
ATTAACGTACTTGATCGAGC+AGG 0.652929 4.2:+33076296 MS.gene052301:CDS
ATGGGAGGTATAAATAAAGG+AGG 0.660218 4.2:-33076332 None:intergenic
GAGACTTGAAGAAGGTGTCG+TGG 0.672602 4.2:+33076767 MS.gene052301:CDS
ACACCTTGATAAACAAACGA+TGG 0.686570 4.2:-33076383 None:intergenic
GGAAAAGGATGGTTGCTGCG+CGG 0.715685 4.2:+33076745 MS.gene052301:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
! TTCTCAATTTCAAACTTCAT+GGG - chr4.2:33076353-33076372 None:intergenic 25.0%
CTTCTCAATTTCAAACTTCA+TGG - chr4.2:33076354-33076373 None:intergenic 30.0%
GAAAATTGATCTCATCATGA+TGG - chr4.2:33076436-33076455 None:intergenic 30.0%
TGGAATTGCATCACAATATT+TGG + chr4.2:33076684-33076703 MS.gene052301:CDS 30.0%
TTGCAGATGCTTATTTACAA+AGG + chr4.2:33076594-33076613 MS.gene052301:intron 30.0%
! AGATCAATTTTCAGATAAGC+TGG + chr4.2:33076444-33076463 MS.gene052301:CDS 30.0%
! GATCAATTTTCAGATAAGCT+GGG + chr4.2:33076445-33076464 MS.gene052301:CDS 30.0%
! TTCATGGGAGGTATAAATAA+AGG - chr4.2:33076338-33076357 None:intergenic 30.0%
!!! GGAGTTGTTTTTTTAACAAC+TGG + chr4.2:33076191-33076210 MS.gene052301:CDS 30.0%
AACGCACATTGTAAAAGTCT+CGG - chr4.2:33076229-33076248 None:intergenic 35.0%
ACACCTTGATAAACAAACGA+TGG - chr4.2:33076386-33076405 None:intergenic 35.0%
ACGTTTCACTTCAATGTAGA+TGG - chr4.2:33076829-33076848 None:intergenic 35.0%
TCAATTTCAAACTTCATGGG+AGG - chr4.2:33076350-33076369 None:intergenic 35.0%
! ATGATGGAATGAGAGGATTT+CGG - chr4.2:33076420-33076439 None:intergenic 35.0%
! ATGGGAGGTATAAATAAAGG+AGG - chr4.2:33076335-33076354 None:intergenic 35.0%
! GACTTTTACAATGTGCGTTT+AGG + chr4.2:33076230-33076249 MS.gene052301:CDS 35.0%
! GCATCACAATATTTGGAACT+AGG + chr4.2:33076691-33076710 MS.gene052301:CDS 35.0%
! TGATTTTGCTTGACGATTGT+GGG + chr4.2:33076655-33076674 MS.gene052301:CDS 35.0%
! TTGATTTTGCTTGACGATTG+TGG + chr4.2:33076654-33076673 MS.gene052301:CDS 35.0%
! TTTTACAATGTGCGTTTAGG+CGG + chr4.2:33076233-33076252 MS.gene052301:CDS 35.0%
!! TTACTGGTAATGGTCAGTTT+GGG + chr4.2:33076273-33076292 MS.gene052301:CDS 35.0%
!! TTTACTGGTAATGGTCAGTT+TGG + chr4.2:33076272-33076291 MS.gene052301:CDS 35.0%
ACTATCGTCATGGTGTTTAC+TGG + chr4.2:33076257-33076276 MS.gene052301:CDS 40.0%
ACTGGATATGATGTTAGCTC+TGG + chr4.2:33076479-33076498 MS.gene052301:CDS 40.0%
ATTAACGTACTTGATCGAGC+AGG + chr4.2:33076296-33076315 MS.gene052301:CDS 40.0%
GTCATGGTGTTTACTGGTAA+TGG + chr4.2:33076263-33076282 MS.gene052301:CDS 40.0%
GTGCCATCGTTTGTTTATCA+AGG + chr4.2:33076380-33076399 MS.gene052301:CDS 40.0%
TGATGGAATGAGAGGATTTC+GGG - chr4.2:33076419-33076438 None:intergenic 40.0%
! TCTCATCATGATGGAATGAG+AGG - chr4.2:33076427-33076446 None:intergenic 40.0%
!! TGATGTTAGCTCTGGATTTC+TGG + chr4.2:33076487-33076506 MS.gene052301:CDS 40.0%
GGACTATGTGACGTGACAAT+TGG + chr4.2:33076615-33076634 MS.gene052301:CDS 45.0%
TTGACGATTGTGGGAACAAG+TGG + chr4.2:33076664-33076683 MS.gene052301:CDS 45.0%
TTTAGGCGGAACTATCGTCA+TGG + chr4.2:33076247-33076266 MS.gene052301:CDS 45.0%
!! AGCTGGGAAAAAGTGTTGAC+TGG + chr4.2:33076461-33076480 MS.gene052301:CDS 45.0%
AAGGTTGGATTTCGACACGC+TGG + chr4.2:33076792-33076811 MS.gene052301:CDS 50.0%
ACCACATCAAGCTTGGAGGA+GGG + chr4.2:33076721-33076740 MS.gene052301:CDS 50.0%
!! GAGACTTGAAGAAGGTGTCG+TGG + chr4.2:33076767-33076786 MS.gene052301:CDS 50.0%
!! TGAAGAAGGTGTCGTGGTCA+AGG + chr4.2:33076773-33076792 MS.gene052301:CDS 50.0%
ACATCAAGCTTGGAGGAGGG+TGG + chr4.2:33076724-33076743 MS.gene052301:CDS 55.0%
ACCCTCCTCCAAGCTTGATG+TGG - chr4.2:33076725-33076744 None:intergenic 55.0%
AGCTTGGAGGAGGGTGGAAA+AGG + chr4.2:33076730-33076749 MS.gene052301:CDS 55.0%
CACCACATCAAGCTTGGAGG+AGG + chr4.2:33076720-33076739 MS.gene052301:CDS 55.0%
CACCACCACATCAAGCTTGG+AGG + chr4.2:33076717-33076736 MS.gene052301:CDS 55.0%
CCACACCACCACATCAAGCT+TGG + chr4.2:33076714-33076733 MS.gene052301:CDS 55.0%
CTCCTCCAAGCTTGATGTGG+TGG - chr4.2:33076722-33076741 None:intergenic 55.0%
GGAAAAGGATGGTTGCTGCG+CGG + chr4.2:33076745-33076764 MS.gene052301:CDS 55.0%
TGGAGGAGGGTGGAAAAGGA+TGG + chr4.2:33076734-33076753 MS.gene052301:CDS 55.0%
! CCAAGCTTGATGTGGTGGTG+TGG - chr4.2:33076717-33076736 None:intergenic 55.0%
! GAGAGGATTTCGGGTGTGAC+TGG - chr4.2:33076410-33076429 None:intergenic 55.0%
!! GAAGGTGTCGTGGTCAAGGT+TGG + chr4.2:33076777-33076796 MS.gene052301:CDS 55.0%
GCTGCGCGGAGACTTGAAGA+AGG + chr4.2:33076759-33076778 MS.gene052301:CDS 60.0%


Chromosome Type Strat End Strand Name
chr4.2 gene 33076173 33076863 33076173 ID=MS.gene052301
chr4.2 mRNA 33076173 33076863 33076173 ID=MS.gene052301.t1;Parent=MS.gene052301
chr4.2 exon 33076173 33076508 33076173 ID=MS.gene052301.t1.exon1;Parent=MS.gene052301.t1
chr4.2 CDS 33076173 33076508 33076173 ID=cds.MS.gene052301.t1;Parent=MS.gene052301.t1
chr4.2 exon 33076600 33076863 33076600 ID=MS.gene052301.t1.exon2;Parent=MS.gene052301.t1
chr4.2 CDS 33076600 33076863 33076600 ID=cds.MS.gene052301.t1;Parent=MS.gene052301.t1
Gene Sequence

>MS.gene052301

ATGGTGGAAAGGATAAGTGGAGTTGTTTTTTTAACAACTGGATTCAATGCGATCCGAGACTTTTACAATGTGCGTTTAGGCGGAACTATCGTCATGGTGTTTACTGGTAATGGTCAGTTTGGGATTAACGTACTTGATCGAGCAGGACGTGTTGTTGATCCTCCTTTATTTATACCTCCCATGAAGTTTGAAATTGAGAAGACAATTGTGCCATCGTTTGTTTATCAAGGTGTGCCAGTCACACCCGAAATCCTCTCATTCCATCATGATGAGATCAATTTTCAGATAAGCTGGGAAAAAGTGTTGACTGGATATGATGTTAGCTCTGGATTTCTGGTATAAGTTTGATGTATTAGTATTGCTCACATAAACAGTTACTTTTAGCATATATACATTTGTTTGTATTAACACATCTTGATGTTTGCAGATGCTTATTTACAAAGGACTATGTGACGTGACAATTGGCAAGAAGACAACTTCATTGATTTTGCTTGACGATTGTGGGAACAAGTGGAATTGCATCACAATATTTGGAACTAGGCCACACCACCACATCAAGCTTGGAGGAGGGTGGAAAAGGATGGTTGCTGCGCGGAGACTTGAAGAAGGTGTCGTGGTCAAGGTTGGATTTCGACACGCTGGAAAGAACGATACCATCTACATTGAAGTGAAACGTCCAATAGTTGTTTGA
Protein sequence

>MS.gene052301.t1

MVERISGVVFLTTGFNAIRDFYNVRLGGTIVMVFTGNGQFGINVLDRAGRVVDPPLFIPPMKFEIEKTIVPSFVYQGVPVTPEILSFHHDEINFQISWEKVLTGYDVSSGFLMLIYKGLCDVTIGKKTTSLILLDDCGNKWNCITIFGTRPHHHIKLGGGWKRMVAARRLEEGVVVKVGFRHAGKNDTIYIEVKRPIVV