AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene059800

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene059800.t1 MTR_2g079120 98.936 94 1 0 6 99 153 246 9.11e-60 183
MS.gene059800.t1 MTR_2g013950 59.596 99 27 3 8 94 155 252 4.82e-25 94.7
MS.gene059800.t1 MTR_4g088695 56.044 91 28 3 16 94 143 233 1.20e-23 90.9
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene059800.t1 AT5G53830 69.663 89 20 4 11 92 151 239 1.90e-32 113
MS.gene059800.t1 AT1G28280 68.132 91 24 2 8 95 151 239 1.69e-31 110
MS.gene059800.t1 AT1G28280 67.778 90 24 2 8 94 151 238 6.10e-31 109
MS.gene059800.t1 AT3G15300 65.591 93 18 4 11 95 130 216 4.85e-30 106
MS.gene059800.t1 AT2G33780 48.780 82 30 2 19 90 113 192 1.51e-17 73.9

Find 20 sgRNAs with CRISPR-Local

Find 53 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GATAAATCTTCACCTTCATT+AGG 0.311360 2.4:+19071295 MS.gene059800:CDS
GCATCTCTTGGTGTAGTAAT+AGG 0.315866 2.4:-19071376 None:intergenic
GAAGGTGAAGATTTATCAAA+AGG 0.403207 2.4:-19071289 None:intergenic
TCATCATTCAATGGTGTGAC+AGG 0.420771 2.4:-19071265 None:intergenic
TCTGATGAGTTTCCTAATGA+AGG 0.454202 2.4:-19071307 None:intergenic
GAAGGAAAATCAAGCAAGCT+TGG 0.463885 2.4:-19071229 None:intergenic
AGTTGTGGCTCTGCATCTCT+TGG 0.480249 2.4:-19071388 None:intergenic
TCAAAAGGGTCATCATTCAA+TGG 0.482624 2.4:-19071274 None:intergenic
GACAAAGCAATTGCTGAAAG+AGG 0.510604 2.4:+19071334 MS.gene059800:CDS
CTTGGTGTAGTAATAGGAGA+GGG 0.527748 2.4:-19071370 None:intergenic
AAGGTGAAGATTTATCAAAA+GGG 0.535615 2.4:-19071288 None:intergenic
GAATTTGATTGTGAAACTCT+AGG 0.540707 2.4:-19071436 None:intergenic
GGTGAAGAAAGAGGAAACAA+AGG 0.573082 2.4:-19071415 None:intergenic
GGAAACAAAGGAAGAAGTTG+TGG 0.576455 2.4:-19071403 None:intergenic
GAAACTCTAGGTGAAGAAAG+AGG 0.626680 2.4:-19071424 None:intergenic
CATCATTCAATGGTGTGACA+GGG 0.632245 2.4:-19071264 None:intergenic
TCTTGGTGTAGTAATAGGAG+AGG 0.640047 2.4:-19071371 None:intergenic
ACAGGGCTAAGAGCAAGAGA+AGG 0.663065 2.4:-19071247 None:intergenic
TTCATTAGGAAACTCATCAG+AGG 0.664188 2.4:+19071309 MS.gene059800:CDS
TTGGTGTAGTAATAGGAGAG+GGG 0.712277 2.4:-19071369 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
! AAGGTGAAGATTTATCAAAA+GGG - chr2.4:19071291-19071310 None:intergenic 25.0%
! TTGGAATTCTGTGAAAAATT+TGG - chr2.4:19071172-19071191 None:intergenic 25.0%
!! AATTTGAAACCTTGTTTCTT+TGG - chr2.4:19071094-19071113 None:intergenic 25.0%
!! TTAAAGTTTCTTGTTTGTTG+AGG - chr2.4:19071049-19071068 None:intergenic 25.0%
!!! ATTTCTTGTTGTTGTTTTCT+TGG - chr2.4:19071202-19071221 None:intergenic 25.0%
ATAAGGATTTGAATCAGATC+TGG - chr2.4:19070891-19070910 None:intergenic 30.0%
CAAGTAGTTCAAATGTTAAC+TGG + chr2.4:19070950-19070969 MS.gene059800:intron 30.0%
CTGTGAAAAATTTGGCATAA+GGG - chr2.4:19071164-19071183 None:intergenic 30.0%
GAAGGTGAAGATTTATCAAA+AGG - chr2.4:19071292-19071311 None:intergenic 30.0%
GAATTTGATTGTGAAACTCT+AGG - chr2.4:19071439-19071458 None:intergenic 30.0%
GATAAATCTTCACCTTCATT+AGG + chr2.4:19071295-19071314 MS.gene059800:CDS 30.0%
TAAGGATTTGAATCAGATCT+GGG - chr2.4:19070890-19070909 None:intergenic 30.0%
TCTGTGAAAAATTTGGCATA+AGG - chr2.4:19071165-19071184 None:intergenic 30.0%
TTGAACTACTTGTTTGAAAG+TGG - chr2.4:19070942-19070961 None:intergenic 30.0%
! TTGTTTTCTTGGTGAGAAAT+TGG - chr2.4:19071191-19071210 None:intergenic 30.0%
AAAACAGCACCAAAGAAACA+AGG + chr2.4:19071082-19071101 MS.gene059800:intron 35.0%
AAGGATTTGAATCAGATCTG+GGG - chr2.4:19070889-19070908 None:intergenic 35.0%
AATTTGGATTCCATTGCTGT+TGG - chr2.4:19070837-19070856 None:intergenic 35.0%
TCAAAAGGGTCATCATTCAA+TGG - chr2.4:19071277-19071296 None:intergenic 35.0%
TCTGATGAGTTTCCTAATGA+AGG - chr2.4:19071310-19071329 None:intergenic 35.0%
TGAACAAAGGTTGTTGGATA+AGG - chr2.4:19070908-19070927 None:intergenic 35.0%
TTCATTAGGAAACTCATCAG+AGG + chr2.4:19071309-19071328 MS.gene059800:CDS 35.0%
!! CAGTTGCTTACATTGCTTTT+TGG - chr2.4:19070797-19070816 None:intergenic 35.0%
!!! GTTGTTGGTTTTGTTGTTGT+TGG - chr2.4:19071001-19071020 None:intergenic 35.0%
!!! TGTTGGTTTGGTTTTGTTGT+TGG - chr2.4:19071016-19071035 None:intergenic 35.0%
!!! TTCTTTGGTGCTGTTTTGAT+TGG - chr2.4:19071079-19071098 None:intergenic 35.0%
AGTAGCAATTCCAACAGCAA+TGG + chr2.4:19070824-19070843 MS.gene059800:intron 40.0%
CATCATTCAATGGTGTGACA+GGG - chr2.4:19071267-19071286 None:intergenic 40.0%
GAAACTCTAGGTGAAGAAAG+AGG - chr2.4:19071427-19071446 None:intergenic 40.0%
GAAGGAAAATCAAGCAAGCT+TGG - chr2.4:19071232-19071251 None:intergenic 40.0%
GACAAAGCAATTGCTGAAAG+AGG + chr2.4:19071334-19071353 MS.gene059800:CDS 40.0%
GGAAACAAAGGAAGAAGTTG+TGG - chr2.4:19071406-19071425 None:intergenic 40.0%
GGTGAAGAAAGAGGAAACAA+AGG - chr2.4:19071418-19071437 None:intergenic 40.0%
TCAGCTTGAACAAAGGTTGT+TGG - chr2.4:19070914-19070933 None:intergenic 40.0%
TCATCATTCAATGGTGTGAC+AGG - chr2.4:19071268-19071287 None:intergenic 40.0%
TTGGTGTAGTAATAGGAGAG+GGG - chr2.4:19071372-19071391 None:intergenic 40.0%
! CTTGGTGTAGTAATAGGAGA+GGG - chr2.4:19071373-19071392 None:intergenic 40.0%
! GCATCTCTTGGTGTAGTAAT+AGG - chr2.4:19071379-19071398 None:intergenic 40.0%
! GTTGAGGTAGATCTTGTTGT+TGG - chr2.4:19071033-19071052 None:intergenic 40.0%
! TCAGATCTGGGGATTGTTTT+TGG - chr2.4:19070878-19070897 None:intergenic 40.0%
! TCTTGGTGTAGTAATAGGAG+AGG - chr2.4:19071374-19071393 None:intergenic 40.0%
!! GGTAGATCTTGTTGTTGGTT+TGG - chr2.4:19071028-19071047 None:intergenic 40.0%
!! TGTTGTTGAGGTTGTTTCTG+AGG - chr2.4:19070978-19070997 None:intergenic 40.0%
!! TGTTGTTGTTGGTGTTGTTG+AGG - chr2.4:19070990-19071009 None:intergenic 40.0%
!!! ATTGTTTTTGGAGTGAGAGG+TGG - chr2.4:19070866-19070885 None:intergenic 40.0%
!!! TTGGTGCTGTTTTGATTGGT+GGG - chr2.4:19071075-19071094 None:intergenic 40.0%
!!! TTTGGTGCTGTTTTGATTGG+TGG - chr2.4:19071076-19071095 None:intergenic 40.0%
GGTTGTGTCAGCTTGAACAA+AGG - chr2.4:19070921-19070940 None:intergenic 45.0%
! TGAGAGGTGGTGTTGGAATT+TGG - chr2.4:19070853-19070872 None:intergenic 45.0%
!!! GGGATTGTTTTTGGAGTGAG+AGG - chr2.4:19070869-19070888 None:intergenic 45.0%
ACAGGGCTAAGAGCAAGAGA+AGG - chr2.4:19071250-19071269 None:intergenic 50.0%
! AGTTGTGGCTCTGCATCTCT+TGG - chr2.4:19071391-19071410 None:intergenic 50.0%
! TTTGGAGTGAGAGGTGGTGT+TGG - chr2.4:19070860-19070879 None:intergenic 50.0%


Chromosome Type Strat End Strand Name
chr2.4 gene 19070785 19071462 19070785 ID=MS.gene059800
chr2.4 mRNA 19070785 19071462 19070785 ID=MS.gene059800.t1;Parent=MS.gene059800
chr2.4 exon 19070785 19070805 19070785 ID=MS.gene059800.t1.exon1;Parent=MS.gene059800.t1
chr2.4 CDS 19070785 19070805 19070785 ID=cds.MS.gene059800.t1;Parent=MS.gene059800.t1
chr2.4 exon 19071184 19071462 19071184 ID=MS.gene059800.t1.exon2;Parent=MS.gene059800.t1
chr2.4 CDS 19071184 19071462 19071184 ID=cds.MS.gene059800.t1;Parent=MS.gene059800.t1
Gene Sequence

>MS.gene059800

ATGAACTCACCAAAAAGCAATGTAAGCAACTGCATGAGTAGTAGCAATTCCAACAGCAATGGAATCCAAATTCCAACACCACCTCTCACTCCAAAAACAATCCCCAGATCTGATTCAAATCCTTATCCAACAACCTTTGTTCAAGCTGACACAACCACTTTCAAACAAGTAGTTCAAATGTTAACTGGTTCCTCAGAAACAACCTCAACAACACCAACAACAACAAAACCAACAACAAAACCAAACCAACAACAAGATCTACCTCAACAAACAAGAAACTTTAACATCCCACCAATCAAAACAGCACCAAAGAAACAAGGTTTCAAATTATATGAAAGAAGAAACAGTCTCAAAAACAGTGTTCTTATGCTGAACACCCTTATGCCAAATTTTTCACAGAATTCCAATTTCTCACCAAGAAAACAACAACAAGAAATTCTCTCTCCAAGCTTGCTTGATTTTCCTTCTCTTGCTCTTAGCCCTGTCACACCATTGAATGATGACCCTTTTGATAAATCTTCACCTTCATTAGGAAACTCATCAGAGGAAGACAAAGCAATTGCTGAAAGAGGTTACTATTTGCACCCCTCTCCTATTACTACACCAAGAGATGCAGAGCCACAACTTCTTCCTTTGTTTCCTCTTTCTTCACCTAGAGTTTCACAATCAAATTCTTGA
Protein sequence

>MS.gene059800.t1

MNSPKSNNSNFSPRKQQQEILSPSLLDFPSLALSPVTPLNDDPFDKSSPSLGNSSEEDKAIAERGYYLHPSPITTPRDAEPQLLPLFPLSSPRVSQSNS