AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene031526

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene031526.t1 MTR_4g081420 98.955 287 2 1 1 286 151 437 0.0 578
MS.gene031526.t1 MTR_2g010860 53.147 286 124 6 4 285 97 376 1.63e-90 273
MS.gene031526.t1 MTR_2g010870 54.348 276 112 5 22 285 82 355 7.36e-90 271
MS.gene031526.t1 MTR_3g072920 51.240 242 104 7 49 283 214 448 4.31e-71 226
MS.gene031526.t1 MTR_1g024980 50.840 238 104 3 49 283 171 398 3.99e-70 222
MS.gene031526.t1 MTR_3g463270 44.167 240 117 8 54 283 154 386 1.56e-55 184
MS.gene031526.t1 MTR_5g012220 37.736 212 103 8 76 285 105 289 2.31e-29 113
MS.gene031526.t1 MTR_5g094440 32.864 213 129 5 73 283 68 268 3.37e-27 107
MS.gene031526.t1 MTR_4g101450 35.096 208 99 6 79 283 98 272 3.69e-27 107
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene031526.t1 AT5G54630 71.382 304 65 7 1 285 171 471 6.96e-143 410
MS.gene031526.t1 AT4G27240 75.969 258 59 3 31 285 173 430 6.46e-137 394
MS.gene031526.t1 AT4G27240 74.783 230 55 3 31 257 173 402 5.84e-116 340
MS.gene031526.t1 AT1G11490 50.199 251 111 5 44 285 119 364 8.26e-73 228
MS.gene031526.t1 AT1G11490 50.199 251 111 5 44 285 119 364 8.26e-73 228
MS.gene031526.t1 AT1G75710 46.484 256 110 5 54 285 206 458 2.00e-61 201
MS.gene031526.t1 AT2G29660 41.245 257 126 7 46 283 120 370 1.27e-48 166
MS.gene031526.t1 AT1G62520 38.863 211 96 7 77 285 100 279 5.71e-30 114
MS.gene031526.t1 AT4G22560 38.140 215 87 9 73 283 89 261 1.49e-28 110
MS.gene031526.t1 AT4G12450 32.719 217 97 7 77 283 97 274 1.19e-22 95.1

Find 49 sgRNAs with CRISPR-Local

Find 88 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TCAAACTGGATTTGATTCTT+TGG 0.236240 4.2:-28111671 MS.gene031526:CDS
CTTGGCAGTTACTGAACTTT+TGG 0.259869 4.2:-28112193 MS.gene031526:intron
GACGCCTAGGATGTTTCTTC+TGG 0.313874 4.2:+28112001 None:intergenic
ACCACAGTAGCTTGTTCTCT+TGG 0.380190 4.2:-28111943 MS.gene031526:CDS
TCTCTTGAAACAGATTCTAA+TGG 0.386384 4.2:-28112710 MS.gene031526:CDS
GCTTGTTCTCTTGGTCTCAA+TGG 0.401559 4.2:-28111934 MS.gene031526:CDS
AAAATATTTACCAGCATGCT+TGG 0.405089 4.2:+28112613 None:intergenic
AAGGAGTTGAAAGGTGGAAT+AGG 0.409316 4.2:-28111841 MS.gene031526:CDS
GTTGTGTTTGTAGAATCATT+AGG 0.411461 4.2:-28111882 MS.gene031526:CDS
TAATTGCTGGTAGGGTTCAT+AGG 0.416479 4.2:-28111723 MS.gene031526:CDS
ACTGGATTTGATTCTTTGGC+TGG 0.418812 4.2:-28111667 MS.gene031526:CDS
CAAGAAATGGCATCTCAAAC+TGG 0.425597 4.2:-28111685 MS.gene031526:CDS
GTGGTGTTCATTCAAGTAAT+AGG 0.426313 4.2:-28112736 MS.gene031526:CDS
AAAAGAAAAGGTGATTTCCT+TGG 0.433309 4.2:+28112788 None:intergenic
ACTTGAAAACATTCAAGAAA+TGG 0.445655 4.2:-28111698 MS.gene031526:CDS
GTGGTGAACAGTTTAACAAA+TGG 0.446542 4.2:-28112661 MS.gene031526:CDS
TAATGAACCTTCACTTAGAA+AGG 0.446634 4.2:-28111764 MS.gene031526:CDS
GATTCTTTGGCTGGTAAAGT+AGG 0.457682 4.2:-28111658 MS.gene031526:CDS
GTTGAAGAAGTCCTAAAAGA+AGG 0.458747 4.2:+28112815 None:intergenic
ATGCAGAGTAATTGCTGGTA+GGG 0.484307 4.2:-28111731 MS.gene031526:CDS
TACCAGCATGCTTGGAGAGA+TGG 0.491155 4.2:+28112621 None:intergenic
ATAGTATGCAGAGTAATTGC+TGG 0.496317 4.2:-28111736 MS.gene031526:CDS
TGGTGAACAGTTTAACAAAT+GGG 0.498621 4.2:-28112660 MS.gene031526:CDS
GACCCTTCTGACAAAAGAAA+AGG 0.499545 4.2:+28112776 None:intergenic
ATCAATGCCTTTCTAAGTGA+AGG 0.505745 4.2:+28111757 None:intergenic
CATCCTAGGCGTCTAGCTGA+TGG 0.519157 4.2:-28111991 MS.gene031526:CDS
CACCATCTCTCCAAGCATGC+TGG 0.523843 4.2:-28112623 MS.gene031526:intron
AAACAAGGAAGAAGAGCTCT+AGG 0.526190 4.2:+28111598 None:intergenic
AAATTATATGCAGGACAAGC+TGG 0.530091 4.2:-28112143 MS.gene031526:CDS
AGGTCTTTATTCAAACATTG+AGG 0.530157 4.2:-28111638 MS.gene031526:CDS
AGATTCATCAAGGAAAATAG+TGG 0.534245 4.2:-28112166 MS.gene031526:CDS
AGAAAAGGTGATTTCCTTGG+AGG 0.540659 4.2:+28112791 None:intergenic
CACAACATCTACAAGTGGAA+GGG 0.551250 4.2:-28111812 MS.gene031526:CDS
GGACTTCTTCAACTCCTCCA+AGG 0.558541 4.2:-28112805 MS.gene031526:CDS
TATGCAGAGTAATTGCTGGT+AGG 0.562940 4.2:-28111732 MS.gene031526:CDS
TTTCCATCAGCTAGACGCCT+AGG 0.564002 4.2:+28111988 None:intergenic
TCACAACATCTACAAGTGGA+AGG 0.571126 4.2:-28111813 MS.gene031526:CDS
AAATAGTGGAAATTATATGC+AGG 0.573880 4.2:-28112152 MS.gene031526:CDS
TTGAAGAAGTCCTAAAAGAA+GGG 0.580726 4.2:+28112816 None:intergenic
TCTGCTAAGAAGGAGTTGAA+AGG 0.586835 4.2:-28111850 MS.gene031526:CDS
AACTCCAGAAGAAACATCCT+AGG 0.587019 4.2:-28112005 MS.gene031526:CDS
ATTTGAAGAGTACAGAGAGA+TGG 0.595060 4.2:-28112046 MS.gene031526:CDS
GTTTGTAGAATCATTAGGAG+TGG 0.602627 4.2:-28111877 MS.gene031526:CDS
TTGCAAATTACCACAAAACA+AGG 0.607767 4.2:+28111583 None:intergenic
GCTAAGAAGGAGTTGAAAGG+TGG 0.609494 4.2:-28111847 MS.gene031526:CDS
CTCTCTCTATTCTGCCACAG+TGG 0.632803 4.2:+28112106 None:intergenic
ACCAAGAGAACAAGCTACTG+TGG 0.672385 4.2:+28111942 None:intergenic
ACTGTTACTTGTCACAAATG+TGG 0.687396 4.2:-28112680 MS.gene031526:CDS
TTAAAGTCAGAAAACCACTG+TGG 0.819817 4.2:-28112120 MS.gene031526:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! ATTTTATTTTCAAAATATCT+AGG - chr4.2:28112029-28112048 MS.gene031526:CDS 10.0%
!!! TTTTTATTAAAAATTCTTCT+TGG - chr4.2:28111814-28111833 MS.gene031526:CDS 10.0%
!! CAAACAATTCTAAATTAAAA+AGG + chr4.2:28111996-28112015 None:intergenic 15.0%
!!! ATTTTGAAAATAAAATCTGT+TGG + chr4.2:28112025-28112044 None:intergenic 15.0%
!!! TATGCTATAGAATTTTTTTA+TGG - chr4.2:28111896-28111915 MS.gene031526:CDS 15.0%
!! AATTCTAAATTAAAAAGGCA+TGG + chr4.2:28111991-28112010 None:intergenic 20.0%
! AATACTAGGATAAAGTAGAT+TGG + chr4.2:28112081-28112100 None:intergenic 25.0%
! ACTTGAAAACATTCAAGAAA+TGG - chr4.2:28112708-28112727 MS.gene031526:CDS 25.0%
! TGTTCAATGTTCAAAATACT+AGG + chr4.2:28112095-28112114 None:intergenic 25.0%
! TTTGTGGTCAGAAAAATATT+TGG + chr4.2:28111851-28111870 None:intergenic 25.0%
!! AAATAGTGGAAATTATATGC+AGG - chr4.2:28112254-28112273 MS.gene031526:intron 25.0%
!! ATTACTTTAACCCTTCTTTT+AGG - chr4.2:28111580-28111599 MS.gene031526:CDS 25.0%
!! TAAAAATTCTTCTTGGCTTT+AGG - chr4.2:28111821-28111840 MS.gene031526:CDS 25.0%
!!! AAATCCACACTTTTTGAATT+TGG - chr4.2:28111940-28111959 MS.gene031526:CDS 25.0%
!!! AATCCACACTTTTTGAATTT+GGG - chr4.2:28111941-28111960 MS.gene031526:CDS 25.0%
!!! AGAAAAATTTGTTTTTCCCT+TGG - chr4.2:28112195-28112214 MS.gene031526:intron 25.0%
!!! ATTTCTTGAATGTTTTCAAG+TGG + chr4.2:28112709-28112728 None:intergenic 25.0%
!!! CTAAAGTTTTTTGCATATTG+TGG + chr4.2:28112336-28112355 None:intergenic 25.0%
!!! GCTATAGAATTTTTTTATGG+TGG - chr4.2:28111899-28111918 MS.gene031526:CDS 25.0%
AAAAGAAAAGGTGATTTCCT+TGG + chr4.2:28111621-28111640 None:intergenic 30.0%
AAAATATTTACCAGCATGCT+TGG + chr4.2:28111796-28111815 None:intergenic 30.0%
AGATTCATCAAGGAAAATAG+TGG - chr4.2:28112240-28112259 MS.gene031526:intron 30.0%
AGCATATCAGATAAAGACTA+TGG + chr4.2:28111882-28111901 None:intergenic 30.0%
AGGATAAAGTAGATTGGAAA+AGG + chr4.2:28112075-28112094 None:intergenic 30.0%
AGGTCTTTATTCAAACATTG+AGG - chr4.2:28112768-28112787 MS.gene031526:CDS 30.0%
GGATAAAGTAGATTGGAAAA+GGG + chr4.2:28112074-28112093 None:intergenic 30.0%
GTTGTGTTTGTAGAATCATT+AGG - chr4.2:28112524-28112543 MS.gene031526:intron 30.0%
TAATGAACCTTCACTTAGAA+AGG - chr4.2:28112642-28112661 MS.gene031526:CDS 30.0%
TCAAACTGGATTTGATTCTT+TGG - chr4.2:28112735-28112754 MS.gene031526:CDS 30.0%
TCTCTTGAAACAGATTCTAA+TGG - chr4.2:28111696-28111715 MS.gene031526:CDS 30.0%
TGGTGAACAGTTTAACAAAT+GGG - chr4.2:28111746-28111765 MS.gene031526:CDS 30.0%
TTGAAGAAGTCCTAAAAGAA+GGG + chr4.2:28111593-28111612 None:intergenic 30.0%
TTGCAAATTACCACAAAACA+AGG + chr4.2:28112826-28112845 None:intergenic 30.0%
! AATGAACTTTTACGGTTCTA+TGG - chr4.2:28112439-28112458 MS.gene031526:intron 30.0%
! CTGATGGAAATGAACTTTTA+CGG - chr4.2:28112431-28112450 MS.gene031526:intron 30.0%
! TTTTCTGACCACAAACTTTT+TGG - chr4.2:28111856-28111875 MS.gene031526:CDS 30.0%
!! CAGAATAGAGAGAGTTTTAA+AGG - chr4.2:28112309-28112328 MS.gene031526:intron 30.0%
AAAAGTTCAGTAACTGCCAA+GGG + chr4.2:28112214-28112233 None:intergenic 35.0%
AAATTATATGCAGGACAAGC+TGG - chr4.2:28112263-28112282 MS.gene031526:intron 35.0%
AGTCCCAAATTCAAAAAGTG+TGG + chr4.2:28111947-28111966 None:intergenic 35.0%
ATAGTATGCAGAGTAATTGC+TGG - chr4.2:28112670-28112689 MS.gene031526:CDS 35.0%
ATCAATGCCTTTCTAAGTGA+AGG + chr4.2:28112652-28112671 None:intergenic 35.0%
GTGGTGAACAGTTTAACAAA+TGG - chr4.2:28111745-28111764 MS.gene031526:CDS 35.0%
GTGGTGTTCATTCAAGTAAT+AGG - chr4.2:28111670-28111689 MS.gene031526:CDS 35.0%
GTTGAAGAAGTCCTAAAAGA+AGG + chr4.2:28111594-28111613 None:intergenic 35.0%
GTTTGTAGAATCATTAGGAG+TGG - chr4.2:28112529-28112548 MS.gene031526:intron 35.0%
TTAAAGTCAGAAAACCACTG+TGG - chr4.2:28112286-28112305 MS.gene031526:intron 35.0%
! ACTGTTACTTGTCACAAATG+TGG - chr4.2:28111726-28111745 MS.gene031526:CDS 35.0%
! ATTTGAAGAGTACAGAGAGA+TGG - chr4.2:28112360-28112379 MS.gene031526:intron 35.0%
! CACCTTTTCTTTTGTCAGAA+GGG - chr4.2:28111628-28111647 MS.gene031526:CDS 35.0%
! GTTTTCACAACATCTACAAG+TGG - chr4.2:28112589-28112608 MS.gene031526:intron 35.0%
! TCACCTTTTCTTTTGTCAGA+AGG - chr4.2:28111627-28111646 MS.gene031526:CDS 35.0%
!! TTTTGGAAGGAGATTCATCA+AGG - chr4.2:28112230-28112249 MS.gene031526:intron 35.0%
AAACAAGGAAGAAGAGCTCT+AGG + chr4.2:28112811-28112830 None:intergenic 40.0%
AACTCCAGAAGAAACATCCT+AGG - chr4.2:28112401-28112420 MS.gene031526:intron 40.0%
AAGGAGTTGAAAGGTGGAAT+AGG - chr4.2:28112565-28112584 MS.gene031526:intron 40.0%
ACTGGATTTGATTCTTTGGC+TGG - chr4.2:28112739-28112758 MS.gene031526:CDS 40.0%
AGAAAAGGTGATTTCCTTGG+AGG + chr4.2:28111618-28111637 None:intergenic 40.0%
ATGCAGAGTAATTGCTGGTA+GGG - chr4.2:28112675-28112694 MS.gene031526:CDS 40.0%
CAAAAGTTCAGTAACTGCCA+AGG + chr4.2:28112215-28112234 None:intergenic 40.0%
CAAGAAATGGCATCTCAAAC+TGG - chr4.2:28112721-28112740 MS.gene031526:CDS 40.0%
CACAACATCTACAAGTGGAA+GGG - chr4.2:28112594-28112613 MS.gene031526:intron 40.0%
GACCCTTCTGACAAAAGAAA+AGG + chr4.2:28111633-28111652 None:intergenic 40.0%
GACTATGGCCAAAAAGTTTG+TGG + chr4.2:28111867-28111886 None:intergenic 40.0%
GATTCTTTGGCTGGTAAAGT+AGG - chr4.2:28112748-28112767 MS.gene031526:CDS 40.0%
TAATTGCTGGTAGGGTTCAT+AGG - chr4.2:28112683-28112702 MS.gene031526:CDS 40.0%
TATGCAGAGTAATTGCTGGT+AGG - chr4.2:28112674-28112693 MS.gene031526:CDS 40.0%
TCACAACATCTACAAGTGGA+AGG - chr4.2:28112593-28112612 MS.gene031526:intron 40.0%
TCTGCTAAGAAGGAGTTGAA+AGG - chr4.2:28112556-28112575 MS.gene031526:intron 40.0%
! CTTGGCAGTTACTGAACTTT+TGG - chr4.2:28112213-28112232 MS.gene031526:intron 40.0%
! CTTTTGTCAGAAGGGTCTAA+TGG - chr4.2:28111636-28111655 MS.gene031526:CDS 40.0%
! GAAGGGTCTAATGGTTTTCA+TGG - chr4.2:28111645-28111664 MS.gene031526:CDS 40.0%
! GAGTGGTTTTTCTGCTAAGA+AGG - chr4.2:28112546-28112565 MS.gene031526:intron 40.0%
! GCAGTTACTGAACTTTTGGA+AGG - chr4.2:28112217-28112236 MS.gene031526:intron 40.0%
! TCTAATGGTTTTCATGGTGG+TGG - chr4.2:28111651-28111670 MS.gene031526:CDS 40.0%
!!! AGCTCTTCTTCCTTGTTTTG+TGG - chr4.2:28112813-28112832 MS.gene031526:CDS 40.0%
ACCAAGAGAACAAGCTACTG+TGG + chr4.2:28112467-28112486 None:intergenic 45.0%
GCTAAGAAGGAGTTGAAAGG+TGG - chr4.2:28112559-28112578 MS.gene031526:intron 45.0%
GCTTGTTCTCTTGGTCTCAA+TGG - chr4.2:28112472-28112491 MS.gene031526:intron 45.0%
! GGGTCTAATGGTTTTCATGG+TGG - chr4.2:28111648-28111667 MS.gene031526:CDS 45.0%
!! ACCACAGTAGCTTGTTCTCT+TGG - chr4.2:28112463-28112482 MS.gene031526:intron 45.0%
CTCTCTCTATTCTGCCACAG+TGG + chr4.2:28112303-28112322 None:intergenic 50.0%
GACGCCTAGGATGTTTCTTC+TGG + chr4.2:28112408-28112427 None:intergenic 50.0%
GGACTTCTTCAACTCCTCCA+AGG - chr4.2:28111601-28111620 MS.gene031526:CDS 50.0%
TACCAGCATGCTTGGAGAGA+TGG + chr4.2:28111788-28111807 None:intergenic 50.0%
TTTCCATCAGCTAGACGCCT+AGG + chr4.2:28112421-28112440 None:intergenic 50.0%
CACCATCTCTCCAAGCATGC+TGG - chr4.2:28111783-28111802 MS.gene031526:CDS 55.0%
CATCCTAGGCGTCTAGCTGA+TGG - chr4.2:28112415-28112434 MS.gene031526:intron 55.0%


Chromosome Type Strat End Strand Name
chr4.2 gene 28111576 28112852 28111576 ID=MS.gene031526
chr4.2 mRNA 28111576 28112852 28111576 ID=MS.gene031526.t1;Parent=MS.gene031526
chr4.2 exon 28112624 28112852 28112624 ID=MS.gene031526.t1.exon1;Parent=MS.gene031526.t1
chr4.2 CDS 28112624 28112852 28112624 ID=cds.MS.gene031526.t1;Parent=MS.gene031526.t1
chr4.2 exon 28111576 28112207 28111576 ID=MS.gene031526.t1.exon2;Parent=MS.gene031526.t1
chr4.2 CDS 28111576 28112207 28111576 ID=cds.MS.gene031526.t1;Parent=MS.gene031526.t1
Gene Sequence

>MS.gene031526

ATGCATTACTTTAACCCTTCTTTTAGGACTTCTTCAACTCCTCCAAGGAAATCACCTTTTCTTTTGTCAGAAGGGTCTAATGGTTTTCATGGTGGTGGTGTTCATTCAAGTAATAGGATGTCTCTTGAAACAGATTCTAATGGTTCTTCAACTGTTACTTGTCACAAATGTGGTGAACAGTTTAACAAATGGGAAGCTGCTGAAGCTCACCATCTCTCCAAGCATGCTGGTAAATATTTTTTTATTAAAAATTCTTCTTGGCTTTAGGTTATCCAAATATTTTTCTGACCACAAACTTTTTGGCCATAGTCTTTATCTGATATGCTATAGAATTTTTTTATGGTGGTGTGACAAATCTTACAATAAATCCACACTTTTTGAATTTGGGACTGTAAAGCTGATTTTGCTTTTTCCATGCCTTTTTAATTTAGAATTGTTTGTATTCTCCAACAGATTTTATTTTCAAAATATCTAGGATAAATAAAAGTACTATCTCCCTTTTCCAATCTACTTTATCCTAGTATTTTGAACATTGAACAATAGTGTATCAAAGAACAATAGAGATTTGTTCAAGTTTGTTGTTATGACATTTTGAGTTTCATAAATTTTGAATTTTAAGAGAAAAATTTGTTTTTCCCTTGGCAGTTACTGAACTTTTGGAAGGAGATTCATCAAGGAAAATAGTGGAAATTATATGCAGGACAAGCTGGTTAAAGTCAGAAAACCACTGTGGCAGAATAGAGAGAGTTTTAAAGGTCCACAATATGCAAAAAACTTTAGCTAGATTTGAAGAGTACAGAGAGATGGTAAAAATCAAAGCAAGTAAACTCCAGAAGAAACATCCTAGGCGTCTAGCTGATGGAAATGAACTTTTACGGTTCTATGGAACCACAGTAGCTTGTTCTCTTGGTCTCAATGGCTCTTCAAGTCTTTGTTTATCAGAAAAATGTTGTGTTTGTAGAATCATTAGGAGTGGTTTTTCTGCTAAGAAGGAGTTGAAAGGTGGAATAGGTGTTTTCACAACATCTACAAGTGGAAGGGCTTTTGAATCTATAGAAATTTTTGATAATGAACCTTCACTTAGAAAGGCATTGATAGTATGCAGAGTAATTGCTGGTAGGGTTCATAGGCCACTTGAAAACATTCAAGAAATGGCATCTCAAACTGGATTTGATTCTTTGGCTGGTAAAGTAGGTCTTTATTCAAACATTGAGGAGCTTTATTTGCTCAATCCTAGAGCTCTTCTTCCTTGTTTTGTGGTAATTTGCAAATCATGA
Protein sequence

>MS.gene031526.t1

MHYFNPSFRTSSTPPRKSPFLLSEGSNGFHGGGVHSSNRMSLETDSNGSSTVTCHKCGEQFNKWEAAEAHHLSKHAVTELLEGDSSRKIVEIICRTSWLKSENHCGRIERVLKVHNMQKTLARFEEYREMVKIKASKLQKKHPRRLADGNELLRFYGTTVACSLGLNGSSSLCLSEKCCVCRIIRSGFSAKKELKGGIGVFTTSTSGRAFESIEIFDNEPSLRKALIVCRVIAGRVHRPLENIQEMASQTGFDSLAGKVGLYSNIEELYLLNPRALLPCFVVICKS