AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene73808

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene73808.t1 MTR_4g079930 97.727 176 4 0 1 176 1 176 6.74e-130 361
MS.gene73808.t1 MTR_2g092950 83.832 167 23 3 10 176 5 167 3.19e-98 281
MS.gene73808.t1 MTR_2g016110 76.471 153 36 0 21 173 27 179 3.01e-86 251
MS.gene73808.t1 MTR_2g076400 80.405 148 29 0 27 174 31 178 3.45e-85 248
MS.gene73808.t1 MTR_5g072510 65.972 144 47 1 14 157 24 165 6.31e-73 219
MS.gene73808.t1 MTR_4g094428 71.756 131 37 0 27 157 44 174 1.05e-71 216
MS.gene73808.t1 MTR_1g442860 74.400 125 32 0 29 153 65 189 5.75e-70 211
MS.gene73808.t1 MTR_8g086350 82.540 126 22 0 27 152 29 154 6.57e-70 210
MS.gene73808.t1 MTR_1g075990 72.794 136 37 0 22 157 46 181 7.90e-66 200
MS.gene73808.t1 MTR_3g031830 63.924 158 43 1 14 157 13 170 6.38e-64 196
MS.gene73808.t1 MTR_7g115700 62.162 148 51 3 27 171 25 170 1.01e-63 194
MS.gene73808.t1 MTR_7g097030 74.615 130 33 0 28 157 63 192 4.92e-63 193
MS.gene73808.t1 MTR_1g069825 74.419 129 33 0 29 157 52 180 2.26e-62 192
MS.gene73808.t1 MTR_1g080210 66.434 143 48 0 29 171 40 182 2.64e-58 180
MS.gene73808.t1 MTR_1g114020 66.667 45 15 0 28 72 70 114 1.03e-14 68.6
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene73808.t1 AT2G42610 84.615 143 20 2 10 152 8 148 2.98e-88 256
MS.gene73808.t1 AT2G42610 84.615 143 20 2 10 152 8 148 2.98e-88 256
MS.gene73808.t1 AT1G07090 65.385 156 54 0 2 157 4 159 1.11e-76 228
MS.gene73808.t1 AT1G78815 76.378 127 30 0 26 152 37 163 3.08e-75 224
MS.gene73808.t1 AT4G18610 80.159 126 24 1 28 152 36 161 1.14e-74 222
MS.gene73808.t1 AT1G16910 68.531 143 45 0 23 165 17 159 3.98e-72 215
MS.gene73808.t1 AT5G58500 70.992 131 37 1 28 157 18 148 2.38e-70 211
MS.gene73808.t1 AT3G23290 76.378 127 30 0 27 153 46 172 5.74e-64 195
MS.gene73808.t1 AT2G31160 73.643 129 34 0 29 157 54 182 1.07e-63 195
MS.gene73808.t1 AT5G28490 65.806 155 52 1 9 163 6 159 1.46e-63 194
MS.gene73808.t1 AT3G04510 71.212 132 38 0 29 160 33 164 8.56e-63 192

Find 43 sgRNAs with CRISPR-Local

Find 50 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CTTCGTTACTTGGACCAATT+TGG 0.191736 4.4:-31352550 MS.gene73808:CDS
GGAAGCTTAGATGCTCTTAT+TGG 0.259171 4.4:-31352439 MS.gene73808:CDS
AGAAGAGATTGGAACACTTT+TGG 0.305989 4.4:-31352643 MS.gene73808:CDS
GTTCCATTCGTGTCTACCTT+AGG 0.324117 4.4:-31352354 MS.gene73808:CDS
ATGCTCTTATTGGAAGGTTA+AGG 0.327795 4.4:-31352429 MS.gene73808:CDS
TCAAGAAAATTGAATATTGC+TGG 0.334695 4.4:+31352237 None:intergenic
GTACAAGGTGCAGGTGGTTC+TGG 0.337886 4.4:+31352484 None:intergenic
CTAGCAAAAGGATTAGTATC+AGG 0.342280 4.4:+31352379 None:intergenic
TGCTCTTATTGGAAGGTTAA+GGG 0.358240 4.4:-31352428 MS.gene73808:CDS
TTGTCCTCTTAGACAAGCTT+GGG 0.372306 4.4:-31352461 MS.gene73808:CDS
TTTAGATTTCCTTCGTTACT+TGG 0.382958 4.4:-31352560 MS.gene73808:CDS
CTTCCCCAAGCTTGTCTAAG+AGG 0.435738 4.4:+31352457 None:intergenic
AATCACAAAAGAGAAGAGAT+TGG 0.447023 4.4:-31352654 MS.gene73808:CDS
AGGGCTGCTTATGAAGAAAA+TGG 0.451783 4.4:-31352409 MS.gene73808:CDS
CTTGTCCTCTTAGACAAGCT+TGG 0.466135 4.4:-31352462 MS.gene73808:CDS
TTCCATTCGTGTCTACCTTA+GGG 0.466186 4.4:-31352353 MS.gene73808:CDS
AAATTGAATATTGCTGGAGC+TGG 0.466512 4.4:+31352243 None:intergenic
TTGCACTGTGAAAGTGGAAC+TGG 0.487945 4.4:+31352595 None:intergenic
AAAACTAAGGTTCATTTACA+AGG 0.499878 4.4:-31352526 MS.gene73808:CDS
GCTAAGTGTCGCTACGGGAG+TGG 0.514607 4.4:+31352684 None:intergenic
CGAATGGAACCACTAGCAAA+AGG 0.517835 4.4:+31352367 None:intergenic
GAAAAGCACAAGTCAAAGCA+AGG 0.536094 4.4:-31352278 MS.gene73808:CDS
GATTAGAGAGTCTCAAGCTA+AGG 0.539311 4.4:-31352329 MS.gene73808:CDS
GCTTAGATGCTCTTATTGGA+AGG 0.540733 4.4:-31352435 MS.gene73808:CDS
AAAAGCACAAGTCAAAGCAA+GGG 0.546373 4.4:-31352277 MS.gene73808:CDS
TAGCAAAAGGATTAGTATCA+GGG 0.547090 4.4:+31352380 None:intergenic
ATAGCGGCTAAGTGTCGCTA+CGG 0.563998 4.4:+31352678 None:intergenic
TTGCTATTGCACTGTGAAAG+TGG 0.566505 4.4:+31352589 None:intergenic
AGAGGACAAGTACAAGGTGC+AGG 0.577150 4.4:+31352475 None:intergenic
CTCCCTAAGGTAGACACGAA+TGG 0.577313 4.4:+31352351 None:intergenic
GAGTCTCAAGCTAAGGCTAG+AGG 0.578787 4.4:-31352322 MS.gene73808:CDS
GAGACTCTCTAATCTCCCTA+AGG 0.589359 4.4:+31352338 None:intergenic
TGTCTAAGAGGACAAGTACA+AGG 0.604570 4.4:+31352469 None:intergenic
TAGCGGCTAAGTGTCGCTAC+GGG 0.605733 4.4:+31352679 None:intergenic
CAAATTGGTCCAAGTAACGA+AGG 0.614807 4.4:+31352551 None:intergenic
CACTGTGAAAGTGGAACTGG+TGG 0.616068 4.4:+31352598 None:intergenic
CACAAGAAAATGTCTACTAG+TGG 0.633092 4.4:-31352754 None:intergenic
CTGCTTATGAAGAAAATGGT+GGG 0.645013 4.4:-31352405 MS.gene73808:CDS
AGCAAAAGGATTAGTATCAG+GGG 0.648452 4.4:+31352381 None:intergenic
TGTCCTCTTAGACAAGCTTG+GGG 0.649148 4.4:-31352460 MS.gene73808:CDS
GCTGCTTATGAAGAAAATGG+TGG 0.659838 4.4:-31352406 MS.gene73808:CDS
AACGAAGGAAATCTAAAACA+TGG 0.665632 4.4:+31352566 None:intergenic
GGACAAGTACAAGGTGCAGG+TGG 0.672826 4.4:+31352478 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
! AAAACTAAGGTTCATTTACA+AGG - chr4.4:31352456-31352475 MS.gene73808:CDS 25.0%
! TCAAGAAAATTGAATATTGC+TGG + chr4.4:31352748-31352767 None:intergenic 25.0%
!! CTTTTCTTTTTCTTCTTGTA+TGG + chr4.4:31352690-31352709 None:intergenic 25.0%
!! TTACAAGGTTGTATGTTTTA+TGG - chr4.4:31352471-31352490 MS.gene73808:CDS 25.0%
AATCACAAAAGAGAAGAGAT+TGG - chr4.4:31352328-31352347 MS.gene73808:CDS 30.0%
TTTAGATTTCCTTCGTTACT+TGG - chr4.4:31352422-31352441 MS.gene73808:CDS 30.0%
! AACGAAGGAAATCTAAAACA+TGG + chr4.4:31352419-31352438 None:intergenic 30.0%
! TAGCAAAAGGATTAGTATCA+GGG + chr4.4:31352605-31352624 None:intergenic 30.0%
! TTCTCTTTTGTGATTCATAG+CGG + chr4.4:31352323-31352342 None:intergenic 30.0%
!! GAACCTTAGTTTTTCCAAAT+TGG + chr4.4:31352449-31352468 None:intergenic 30.0%
AAATTGAATATTGCTGGAGC+TGG + chr4.4:31352742-31352761 None:intergenic 35.0%
ATGCTCTTATTGGAAGGTTA+AGG - chr4.4:31352553-31352572 MS.gene73808:CDS 35.0%
CTGCTTATGAAGAAAATGGT+GGG - chr4.4:31352577-31352596 MS.gene73808:CDS 35.0%
GGACCAATTTGGAAAAACTA+AGG - chr4.4:31352443-31352462 MS.gene73808:CDS 35.0%
TGCTCTTATTGGAAGGTTAA+GGG - chr4.4:31352554-31352573 MS.gene73808:CDS 35.0%
! AAAAGCACAAGTCAAAGCAA+GGG - chr4.4:31352705-31352724 MS.gene73808:CDS 35.0%
! ACTAGTGGTAGCAATTTTCA+TGG - chr4.4:31352243-31352262 MS.gene73808:CDS 35.0%
! AGAAGAGATTGGAACACTTT+TGG - chr4.4:31352339-31352358 MS.gene73808:CDS 35.0%
! AGCAAAAGGATTAGTATCAG+GGG + chr4.4:31352604-31352623 None:intergenic 35.0%
! CAATTTTCATGGCAAGAATC+TGG - chr4.4:31352254-31352273 MS.gene73808:CDS 35.0%
! CTAGCAAAAGGATTAGTATC+AGG + chr4.4:31352606-31352625 None:intergenic 35.0%
! GATACTAATCCTTTTGCTAG+TGG - chr4.4:31352606-31352625 MS.gene73808:CDS 35.0%
AGGGCTGCTTATGAAGAAAA+TGG - chr4.4:31352573-31352592 MS.gene73808:CDS 40.0%
CAAATTGGTCCAAGTAACGA+AGG + chr4.4:31352434-31352453 None:intergenic 40.0%
CTTCGTTACTTGGACCAATT+TGG - chr4.4:31352432-31352451 MS.gene73808:CDS 40.0%
GATTAGAGAGTCTCAAGCTA+AGG - chr4.4:31352653-31352672 MS.gene73808:CDS 40.0%
GCTGCTTATGAAGAAAATGG+TGG - chr4.4:31352576-31352595 MS.gene73808:CDS 40.0%
GCTTAGATGCTCTTATTGGA+AGG - chr4.4:31352547-31352566 MS.gene73808:CDS 40.0%
GGAAGCTTAGATGCTCTTAT+TGG - chr4.4:31352543-31352562 MS.gene73808:CDS 40.0%
TGTCTAAGAGGACAAGTACA+AGG + chr4.4:31352516-31352535 None:intergenic 40.0%
TTCCATTCGTGTCTACCTTA+GGG - chr4.4:31352629-31352648 MS.gene73808:CDS 40.0%
TTGTCCTCTTAGACAAGCTT+GGG - chr4.4:31352521-31352540 MS.gene73808:CDS 40.0%
! GAAAAGCACAAGTCAAAGCA+AGG - chr4.4:31352704-31352723 MS.gene73808:CDS 40.0%
! TTGCTATTGCACTGTGAAAG+TGG + chr4.4:31352396-31352415 None:intergenic 40.0%
CGAATGGAACCACTAGCAAA+AGG + chr4.4:31352618-31352637 None:intergenic 45.0%
CTTGTCCTCTTAGACAAGCT+TGG - chr4.4:31352520-31352539 MS.gene73808:CDS 45.0%
GAGACTCTCTAATCTCCCTA+AGG + chr4.4:31352647-31352666 None:intergenic 45.0%
GTTCCATTCGTGTCTACCTT+AGG - chr4.4:31352628-31352647 MS.gene73808:CDS 45.0%
TGTCCTCTTAGACAAGCTTG+GGG - chr4.4:31352522-31352541 MS.gene73808:CDS 45.0%
TTGCACTGTGAAAGTGGAAC+TGG + chr4.4:31352390-31352409 None:intergenic 45.0%
AGAGGACAAGTACAAGGTGC+AGG + chr4.4:31352510-31352529 None:intergenic 50.0%
CACTGTGAAAGTGGAACTGG+TGG + chr4.4:31352387-31352406 None:intergenic 50.0%
CTCCCTAAGGTAGACACGAA+TGG + chr4.4:31352634-31352653 None:intergenic 50.0%
CTTCCCCAAGCTTGTCTAAG+AGG + chr4.4:31352528-31352547 None:intergenic 50.0%
GAGTCTCAAGCTAAGGCTAG+AGG - chr4.4:31352660-31352679 MS.gene73808:CDS 50.0%
! ATAGCGGCTAAGTGTCGCTA+CGG + chr4.4:31352307-31352326 None:intergenic 50.0%
GGACAAGTACAAGGTGCAGG+TGG + chr4.4:31352507-31352526 None:intergenic 55.0%
GTACAAGGTGCAGGTGGTTC+TGG + chr4.4:31352501-31352520 None:intergenic 55.0%
! TAGCGGCTAAGTGTCGCTAC+GGG + chr4.4:31352306-31352325 None:intergenic 55.0%
! GCTAAGTGTCGCTACGGGAG+TGG + chr4.4:31352301-31352320 None:intergenic 60.0%


Chromosome Type Strat End Strand Name
chr4.4 gene 31352237 31352767 31352237 ID=MS.gene73808
chr4.4 mRNA 31352237 31352767 31352237 ID=MS.gene73808.t1;Parent=MS.gene73808
chr4.4 exon 31352237 31352767 31352237 ID=MS.gene73808.t1.exon1;Parent=MS.gene73808.t1
chr4.4 CDS 31352237 31352767 31352237 ID=cds.MS.gene73808.t1;Parent=MS.gene73808.t1
Gene Sequence

>MS.gene73808

ATGTCTACTAGTGGTAGCAATTTTCATGGCAAGAATCTGGAACAAGAATCATCATCAACAACCACTCCCGTAGCGACACTTAGCCGCTATGAATCACAAAAGAGAAGAGATTGGAACACTTTTGGTCAATACTTGAACAACATGAGACCACCAGTTCCACTTTCACAGTGCAATAGCAACCATGTTTTAGATTTCCTTCGTTACTTGGACCAATTTGGAAAAACTAAGGTTCATTTACAAGGTTGTATGTTTTATGGACAACCAGAACCACCTGCACCTTGTACTTGTCCTCTTAGACAAGCTTGGGGAAGCTTAGATGCTCTTATTGGAAGGTTAAGGGCTGCTTATGAAGAAAATGGTGGGTCCCCTGATACTAATCCTTTTGCTAGTGGTTCCATTCGTGTCTACCTTAGGGAGATTAGAGAGTCTCAAGCTAAGGCTAGAGGTATACCATACAAGAAGAAAAAGAAAAGCACAAGTCAAAGCAAGGGAAGTGAAGAATCCAGCTCCAGCAATATTCAATTTTCTTGA
Protein sequence

>MS.gene73808.t1

MSTSGSNFHGKNLEQESSSTTTPVATLSRYESQKRRDWNTFGQYLNNMRPPVPLSQCNSNHVLDFLRYLDQFGKTKVHLQGCMFYGQPEPPAPCTCPLRQAWGSLDALIGRLRAAYEENGGSPDTNPFASGSIRVYLREIRESQAKARGIPYKKKKKSTSQSKGSEESSSSNIQFS