AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene41664

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene41664.t1 MTR_3g098790 88.000 100 12 0 36 135 213 312 2.49e-61 191
MS.gene41664.t1 MTR_7g050580 65.421 107 37 0 36 142 204 310 4.02e-46 152
MS.gene41664.t1 MTR_7g050560 57.944 107 44 1 36 142 205 310 3.78e-39 134
MS.gene41664.t1 MTR_7g050590 61.386 101 38 1 36 135 193 293 1.20e-37 130
MS.gene41664.t1 MTR_7g050710 60.784 102 38 1 36 135 219 320 1.26e-37 130
MS.gene41664.t1 MTR_7g050720 60.440 91 32 4 38 124 227 317 2.77e-27 103
MS.gene41664.t1 MTR_4g068320 36.667 120 64 4 20 139 296 403 2.50e-15 72.0
MS.gene41664.t1 MTR_1g034240 36.508 126 66 4 20 141 300 415 8.06e-15 70.5
MS.gene41664.t1 MTR_1g035460 36.364 110 55 3 18 122 188 287 3.34e-14 68.6
MS.gene41664.t1 MTR_1g108780 37.234 94 48 3 37 129 214 297 4.45e-12 62.8
MS.gene41664.t1 MTR_8g103940 43.678 87 38 3 37 122 255 331 3.17e-11 60.1
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 26 sgRNAs with CRISPR-Local

Find 58 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CTTTCCAAGTTCATATATTC+AGG 0.253552 3.4:+88738623 MS.gene41664:CDS
ATTGAGTAGCTTCTTTCATT+TGG 0.267478 3.4:-88738773 None:intergenic
TTGTTGTGGGAACCAGAAAA+AGG 0.303294 3.4:+88737693 MS.gene41664:CDS
AGATGCGGTGCTGGTTTAAT+AGG 0.331444 3.4:+88737654 None:intergenic
ATCCTGATTCGGTACTTTGC+AGG 0.347997 3.4:-88738484 None:intergenic
TTGAGTAGCTTCTTTCATTT+GGG 0.352726 3.4:-88738772 None:intergenic
AAGTGTCAAATGGCAGAGTT+TGG 0.384047 3.4:+88738461 MS.gene41664:CDS
GGCCTGCAAAGTACCGAATC+AGG 0.422243 3.4:+88738482 MS.gene41664:CDS
CCCACAACAATTTGCGTCGT+TGG 0.438163 3.4:-88737680 None:intergenic
ACCCGTAGCAGATGCGGTGC+TGG 0.473649 3.4:+88737645 None:intergenic
GAAGACAATAACTTGAAAGT+TGG 0.499244 3.4:+88738559 MS.gene41664:CDS
TCTCCCTGAATATATGAACT+TGG 0.502600 3.4:-88738627 None:intergenic
ACCAACGACGCAAATTGTTG+TGG 0.517247 3.4:+88737679 MS.gene41664:CDS
CAGACTATACCGTCTATGTT+CGG 0.532014 3.4:+88738391 MS.gene41664:intron
CCAACGACGCAAATTGTTGT+GGG 0.534350 3.4:+88737680 MS.gene41664:CDS
GGACTAAGATTTGAACTCTC+AGG 0.534942 3.4:+88738517 MS.gene41664:CDS
TTTCCAAGTTCATATATTCA+GGG 0.536079 3.4:+88738624 MS.gene41664:CDS
CTGTGTAGGACATCCTGATT+CGG 0.552002 3.4:-88738495 None:intergenic
GATTTGAACTCTCAGGTGGA+TGG 0.563558 3.4:+88738524 MS.gene41664:CDS
TTTAATTTGAATAAGAAGCG+AGG 0.603085 3.4:+88738424 MS.gene41664:CDS
CTAAGATTTGAACTCTCAGG+TGG 0.618080 3.4:+88738520 MS.gene41664:CDS
ATCGCACCATCGTTTCATGT+TGG 0.636487 3.4:+88737741 MS.gene41664:CDS
TTCAAATCTTAGTCCTGTGT+AGG 0.640354 3.4:-88738509 None:intergenic
TGTCTCTTACCGAACATAGA+CGG 0.669663 3.4:-88738400 None:intergenic
CGAATCAGGATGTCCTACAC+AGG 0.677734 3.4:+88738496 MS.gene41664:CDS
GATGTACCAACATGAAACGA+TGG 0.688052 3.4:-88737747 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TTTATTTAAATTTTTTTAAT+GGG - chr3.4:88738091-88738110 None:intergenic 0.0%
!!! TTTTATTTAAATTTTTTTAA+TGG - chr3.4:88738092-88738111 None:intergenic 0.0%
!! AAATATATCTAATTAATAAG+AGG - chr3.4:88737880-88737899 None:intergenic 10.0%
!! CATATCAAAGTAAGATTAAT+TGG + chr3.4:88738677-88738696 MS.gene41664:intron 20.0%
!! TTTCGAAAAATTCGAAAAAA+GGG + chr3.4:88737784-88737803 MS.gene41664:intron 20.0%
! GTTTCGAAAAATTCGAAAAA+AGG + chr3.4:88737783-88737802 MS.gene41664:intron 25.0%
! TCTGTTATAATCTACCATTA+TGG - chr3.4:88737847-88737866 None:intergenic 25.0%
! TTCGAAAAATTCGAAAAAAG+GGG + chr3.4:88737785-88737804 MS.gene41664:intron 25.0%
! TTTCCAAGTTCATATATTCA+GGG + chr3.4:88738624-88738643 MS.gene41664:CDS 25.0%
!!! ATTCATTTTCAAGTGTCAAA+TGG + chr3.4:88738451-88738470 MS.gene41664:CDS 25.0%
!!! TTTAATTTGAATAAGAAGCG+AGG + chr3.4:88738424-88738443 MS.gene41664:CDS 25.0%
ATTGAGTAGCTTCTTTCATT+TGG - chr3.4:88738776-88738795 None:intergenic 30.0%
CTTTCCAAGTTCATATATTC+AGG + chr3.4:88738623-88738642 MS.gene41664:CDS 30.0%
GAAGACAATAACTTGAAAGT+TGG + chr3.4:88738559-88738578 MS.gene41664:CDS 30.0%
TCGAAAAATTCGAAAAAAGG+GGG + chr3.4:88737786-88737805 MS.gene41664:intron 30.0%
TTGAGTAGCTTCTTTCATTT+GGG - chr3.4:88738775-88738794 None:intergenic 30.0%
AATAAAATGTATCCCGTGCT+TGG + chr3.4:88738105-88738124 MS.gene41664:intron 35.0%
TCTCCCTGAATATATGAACT+TGG - chr3.4:88738630-88738649 None:intergenic 35.0%
TGGGAAAATTCTGCATAAAG+TGG - chr3.4:88738756-88738775 None:intergenic 35.0%
TTCAAATCTTAGTCCTGTGT+AGG - chr3.4:88738512-88738531 None:intergenic 35.0%
! CATTTGCCTTTTCTTTTGCT+TGG + chr3.4:88738368-88738387 MS.gene41664:intron 35.0%
!! CTCACTATTTTAAGCAGAGT+TGG + chr3.4:88737956-88737975 MS.gene41664:intron 35.0%
AAATTCGAAAAAAGGGGGTG+AGG + chr3.4:88737791-88737810 MS.gene41664:intron 40.0%
AAGTGTCAAATGGCAGAGTT+TGG + chr3.4:88738461-88738480 MS.gene41664:CDS 40.0%
AGTCTGCCAAGCAAAAGAAA+AGG - chr3.4:88738377-88738396 None:intergenic 40.0%
CAGACTATACCGTCTATGTT+CGG + chr3.4:88738391-88738410 MS.gene41664:intron 40.0%
CTAAGATTTGAACTCTCAGG+TGG + chr3.4:88738520-88738539 MS.gene41664:CDS 40.0%
GATGTACCAACATGAAACGA+TGG - chr3.4:88737750-88737769 None:intergenic 40.0%
GGACTAAGATTTGAACTCTC+AGG + chr3.4:88738517-88738536 MS.gene41664:CDS 40.0%
TGTCTCTTACCGAACATAGA+CGG - chr3.4:88738403-88738422 None:intergenic 40.0%
TGTTGTGGGAACCAGAAAAA+GGG + chr3.4:88737694-88737713 MS.gene41664:CDS 40.0%
TTGTTGTGGGAACCAGAAAA+AGG + chr3.4:88737693-88737712 MS.gene41664:CDS 40.0%
! GCGGAAGATTTCTAAAGAGA+GGG + chr3.4:88737816-88737835 MS.gene41664:intron 40.0%
!! TGGTACATCGTAAGTGTTGA+AGG + chr3.4:88737761-88737780 MS.gene41664:intron 40.0%
ACCAACGACGCAAATTGTTG+TGG + chr3.4:88737679-88737698 MS.gene41664:CDS 45.0%
ATCGCACCATCGTTTCATGT+TGG + chr3.4:88737741-88737760 MS.gene41664:CDS 45.0%
CCAACGACGCAAATTGTTGT+GGG + chr3.4:88737680-88737699 MS.gene41664:CDS 45.0%
CTGTGTAGGACATCCTGATT+CGG - chr3.4:88738498-88738517 None:intergenic 45.0%
GATTTGAACTCTCAGGTGGA+TGG + chr3.4:88738524-88738543 MS.gene41664:CDS 45.0%
! GGCGGAAGATTTCTAAAGAG+AGG + chr3.4:88737815-88737834 MS.gene41664:intron 45.0%
!! ATCCTGATTCGGTACTTTGC+AGG - chr3.4:88738487-88738506 None:intergenic 45.0%
!!! TTATTTAAATTTTTTTAATG+GGG - chr3.4:88738090-88738109 None:intergenic 5.0%
AAGAGAGGGCAGAGCCATAA+TGG + chr3.4:88737830-88737849 MS.gene41664:intron 50.0%
AATGTATCCCGTGCTTGGCA+CGG + chr3.4:88738110-88738129 MS.gene41664:intron 50.0%
CCCACAACAATTTGCGTCGT+TGG - chr3.4:88737683-88737702 None:intergenic 50.0%
CGAATCAGGATGTCCTACAC+AGG + chr3.4:88738496-88738515 MS.gene41664:CDS 50.0%
TGTGGGAACCAGAAAAAGGG+CGG + chr3.4:88737697-88737716 MS.gene41664:CDS 50.0%
TTCGAAAAAAGGGGGTGAGG+TGG + chr3.4:88737794-88737813 MS.gene41664:intron 50.0%
ATGTATCCCGTGCTTGGCAC+GGG + chr3.4:88738111-88738130 MS.gene41664:intron 55.0%
GAAAAAAGGGGGTGAGGTGG+CGG + chr3.4:88737797-88737816 MS.gene41664:intron 55.0%
GAACCAGAAAAAGGGCGGTG+CGG + chr3.4:88737702-88737721 MS.gene41664:CDS 55.0%
!! GGCCTGCAAAGTACCGAATC+AGG + chr3.4:88738482-88738501 MS.gene41664:CDS 55.0%
CAGAAAAAGGGCGGTGCGGA+GGG + chr3.4:88737706-88737725 MS.gene41664:CDS 60.0%
TGTATCCCGTGCTTGGCACG+GGG + chr3.4:88738112-88738131 MS.gene41664:intron 60.0%
CCAGAAAAAGGGCGGTGCGG+AGG + chr3.4:88737705-88737724 MS.gene41664:CDS 65.0%
GTAACGCCCCGTGCCAAGCA+CGG - chr3.4:88738121-88738140 None:intergenic 65.0%
TAACGCCCCGTGCCAAGCAC+GGG - chr3.4:88738120-88738139 None:intergenic 65.0%
! CCTCCGCACCGCCCTTTTTC+TGG - chr3.4:88737708-88737727 None:intergenic 65.0%


Chromosome Type Strat End Strand Name
chr3.4 gene 88737656 88738797 88737656 ID=MS.gene41664
chr3.4 mRNA 88737656 88738797 88737656 ID=MS.gene41664.t1;Parent=MS.gene41664
chr3.4 exon 88737656 88737769 88737656 ID=MS.gene41664.t1.exon1;Parent=MS.gene41664.t1
chr3.4 CDS 88737656 88737769 88737656 ID=cds.MS.gene41664.t1;Parent=MS.gene41664.t1
chr3.4 exon 88738394 88738685 88738394 ID=MS.gene41664.t1.exon2;Parent=MS.gene41664.t1
chr3.4 CDS 88738394 88738685 88738394 ID=cds.MS.gene41664.t1;Parent=MS.gene41664.t1
chr3.4 exon 88738766 88738797 88738766 ID=MS.gene41664.t1.exon3;Parent=MS.gene41664.t1
chr3.4 CDS 88738766 88738797 88738766 ID=cds.MS.gene41664.t1;Parent=MS.gene41664.t1
Gene Sequence

>MS.gene41664

ATGCGGTGCTGGTTTAATAGGAAACCAACGACGCAAATTGTTGTGGGAACCAGAAAAAGGGCGGTGCGGAGGGACGACGCTACTCATCGCACCATCGTTTCATGTTGGTACATCGTAAGTGTTGAAGGTTTCGAAAAATTCGAAAAAAGGGGGTGAGGTGGCGGAAGATTTCTAAAGAGAGGGCAGAGCCATAATGGTAGATTATAACAGAGTTAATCACACCTCTTATTAATTAGATATATTTTAGTATTTAGTAATTATTTATAGTATTTTTATATTTTAAGCATAGTTGTACTTTTTCTCACTATTTTAAGCAGAGTTGGCATGTCTCAATTTTAAATATGAAGATAAAGTACTACATAATATCAAAATTCTAAATGAAATCAAACTAAAAAGTCAAATAATATCTAAAAAACTTATTTATGTGTAAACCCCATTAAAAAAATTTAAATAAAATGTATCCCGTGCTTGGCACGGGGCGTTACACTAGTACAATAACATGTCAGTGTTTTACAAAGTTATTCAATCAGATGTCACAACATAGATGTTTATTGAAATAGTATAAGAAATAATGTAACTAAATGACATCTTCATAAAATATGATTAGAAAACTATGTAAAAAATGTATACTGTTCAGTGTCAATACACAGTCATTAAACTCATTTACATAACTGCACTTTTCAACAAGAAGTTTTTGTATTTTATTCTTTAACATTTGCCTTTTCTTTTGCTTGGCAGACTATACCGTCTATGTTCGGTAAGAGACACTTTAATTTGAATAAGAAGCGAGGAGATATTCATTTTCAAGTGTCAAATGGCAGAGTTTGGCCTGCAAAGTACCGAATCAGGATGTCCTACACAGGACTAAGATTTGAACTCTCAGGTGGATGGAAGACATTCGCAGAAGACAATAACTTGAAAGTTGGTGATGCTTGCAACTTTGAGCTCATTCTTAGTACTAATATGACTTTCCAAGTTCATATATTCAGGGAGACAGATAAAGACAACGCAGATTGTTTAACATATCAAAGTAAGATTAATTGGTGTTTAATTTTCTTTTCAAATCTTTTTCTCATATGACAAATAAATTTATTCTTCCACTTTATGCAGAATTTTCCCAAATGAAAGAAGCTACTCAATGA
Protein sequence

>MS.gene41664.t1

MRCWFNRKPTTQIVVGTRKRAVRRDDATHRTIVSCWYITIPSMFGKRHFNLNKKRGDIHFQVSNGRVWPAKYRIRMSYTGLRFELSGGWKTFAEDNNLKVGDACNFELILSTNMTFQVHIFRETDKDNADCLTYQKFSQMKEATQ