AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene040859

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene040859.t1 MTR_1g035640 49.612 129 65 0 2 130 163 291 4.52e-35 127
MS.gene040859.t1 MTR_1g035620 45.198 177 69 6 1 152 160 333 7.97e-33 120
MS.gene040859.t1 MTR_1g035570 40.260 154 88 2 1 152 167 318 4.69e-32 118
MS.gene040859.t1 MTR_1g050845 44.444 162 66 4 15 152 159 320 5.44e-30 114
MS.gene040859.t1 MTR_6g061070 45.588 136 67 3 3 131 199 334 1.71e-29 112
MS.gene040859.t1 MTR_1g035490 44.000 125 62 1 1 125 86 202 1.66e-28 107
MS.gene040859.t1 MTR_5g044670 40.179 112 64 2 22 132 207 316 1.40e-20 86.3
MS.gene040859.t1 MTR_8g103940 40.336 119 61 5 10 125 226 337 3.68e-14 68.9
MS.gene040859.t1 MTR_8g103940 32.787 122 74 3 5 120 377 496 1.12e-11 61.6
MS.gene040859.t1 MTR_1g035540 48.485 66 32 1 85 150 32 95 2.74e-13 63.2
MS.gene040859.t1 MTR_1g108780 35.897 117 65 5 10 123 185 294 3.32e-12 63.2
MS.gene040859.t1 MTR_1g108780 29.839 124 80 2 4 121 338 460 4.30e-11 60.1
MS.gene040859.t1 MTR_1g035460 29.412 102 66 1 22 123 196 291 9.35e-12 62.0
MS.gene040859.t1 MTR_1g034240 26.144 153 97 4 2 141 269 418 1.90e-11 61.2
MS.gene040859.t1 MTR_3g098790 32.039 103 65 3 22 119 197 299 2.22e-11 60.8
MS.gene040859.t1 MTR_4g068320 29.412 102 70 1 32 133 303 402 4.59e-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 25 sgRNAs with CRISPR-Local

Find 34 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TCAAAGGGATTGCAAGCATT+AGG 0.348097 1.2:-18473863 MS.gene040859:CDS
CAAAGGGATTGCAAGCATTA+GGG 0.352259 1.2:-18473862 MS.gene040859:CDS
AAAACTTGGATTCTTATCAT+TGG 0.358112 1.2:+18474041 None:intergenic
TATTCTCTTGAAAACTTACT+TGG 0.379463 1.2:+18473897 None:intergenic
GTCAATTTAAGTTCAAAACT+TGG 0.433190 1.2:+18474027 None:intergenic
TGCGTAATAGTTAATCATAC+CGG 0.440953 1.2:+18473451 None:intergenic
GGCTTGATTCCTCTCTAGCT+CGG 0.457584 1.2:+18473667 None:intergenic
AATACTTGAACGAGTTCAAA+GGG 0.491876 1.2:-18473878 MS.gene040859:CDS
CAAAGGAGGCATGACTAAGA+AGG 0.500047 1.2:-18474103 None:intergenic
CTTTGAGAATTCCTTGTACC+CGG 0.517220 1.2:-18473470 MS.gene040859:CDS
AGTTAATCATACCGGGTACA+AGG 0.518064 1.2:+18473459 None:intergenic
TTTAGAAGTTTCTAATGTGA+GGG 0.522348 1.2:-18473512 MS.gene040859:CDS
GTTCTATTGTGAATGGTGGT+TGG 0.525249 1.2:-18473785 MS.gene040859:CDS
GCTTGATTCCTCTCTAGCTC+GGG 0.531379 1.2:+18473668 None:intergenic
GGGTTGATGAAGATAGAACT+TGG 0.534209 1.2:-18473842 MS.gene040859:CDS
TTCTATTTCCCGAGCTAGAG+AGG 0.537691 1.2:-18473676 MS.gene040859:CDS
TGATGAAGATAGAACTTGGA+AGG 0.543162 1.2:-18473838 MS.gene040859:CDS
ATAGAAATATTAAAAGAAAG+AGG 0.543614 1.2:+18473693 None:intergenic
ATTTAGAAGTTTCTAATGTG+AGG 0.550511 1.2:-18473513 MS.gene040859:CDS
GAATACTTGAACGAGTTCAA+AGG 0.559537 1.2:-18473879 MS.gene040859:CDS
AACAGAAGTTCTATTGTGAA+TGG 0.573160 1.2:-18473792 MS.gene040859:CDS
GCGTAATAGTTAATCATACC+GGG 0.602108 1.2:+18473452 None:intergenic
TGGTTGGAATTTATTTACCA+AGG 0.603797 1.2:-18473769 MS.gene040859:CDS
AGAAGTTCTATTGTGAATGG+TGG 0.647616 1.2:-18473789 MS.gene040859:CDS
AAGGAAAATAACTTGCAAGT+CGG 0.656533 1.2:-18473750 MS.gene040859:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! ATAGAAATATTAAAAGAAAG+AGG + chr1.2:18473868-18473887 None:intergenic 15.0%
!!! TTTGAAAATGTCTATTATTT+TGG - chr1.2:18473593-18473612 MS.gene040859:intron 15.0%
!! TGTTTGTTTATTAAAGTTTG+TGG - chr1.2:18473951-18473970 MS.gene040859:intron 20.0%
!!! AACTTACAAATAATTTTCCT+TGG + chr1.2:18473569-18473588 None:intergenic 20.0%
!!! ACTTACAAATAATTTTCCTT+GGG + chr1.2:18473568-18473587 None:intergenic 20.0%
!!! TATTAAAGTTTGTGGTTTTT+TGG - chr1.2:18473959-18473978 MS.gene040859:intron 20.0%
! AAAACTTGGATTCTTATCAT+TGG + chr1.2:18473520-18473539 None:intergenic 25.0%
! AAACTTCTAAATCTGTAGAA+GGG + chr1.2:18474037-18474056 None:intergenic 25.0%
! ATTTAGAAGTTTCTAATGTG+AGG - chr1.2:18474045-18474064 MS.gene040859:CDS 25.0%
! TATTCTCTTGAAAACTTACT+TGG + chr1.2:18473664-18473683 None:intergenic 25.0%
! TTTAGAAGTTTCTAATGTGA+GGG - chr1.2:18474046-18474065 MS.gene040859:CDS 25.0%
!! GTCAATTTAAGTTCAAAACT+TGG + chr1.2:18473534-18473553 None:intergenic 25.0%
!!! AAGTAACCTTGCAATTTTTT+AGG + chr1.2:18473916-18473935 None:intergenic 25.0%
!!! AGTAACCTTGCAATTTTTTA+GGG + chr1.2:18473915-18473934 None:intergenic 25.0%
AACAGAAGTTCTATTGTGAA+TGG - chr1.2:18473766-18473785 MS.gene040859:CDS 30.0%
AATACTTGAACGAGTTCAAA+GGG - chr1.2:18473680-18473699 MS.gene040859:CDS 30.0%
GAAACTTCTAAATCTGTAGA+AGG + chr1.2:18474038-18474057 None:intergenic 30.0%
GTATTCTCTGTTTCAATTCA+TGG + chr1.2:18473642-18473661 None:intergenic 30.0%
TGGTTGGAATTTATTTACCA+AGG - chr1.2:18473789-18473808 MS.gene040859:CDS 30.0%
! AAGGAAAATAACTTGCAAGT+CGG - chr1.2:18473808-18473827 MS.gene040859:CDS 30.0%
AGAAGTTCTATTGTGAATGG+TGG - chr1.2:18473769-18473788 MS.gene040859:CDS 35.0%
GAATACTTGAACGAGTTCAA+AGG - chr1.2:18473679-18473698 MS.gene040859:CDS 35.0%
TCAAGCCCTAAAAAATTGCA+AGG - chr1.2:18473907-18473926 MS.gene040859:intron 35.0%
TGATGAAGATAGAACTTGGA+AGG - chr1.2:18473720-18473739 MS.gene040859:CDS 35.0%
! TTGACACAATTTTATGCCCA+AGG - chr1.2:18473549-18473568 MS.gene040859:intron 35.0%
!! GACTTGCAAGTTATTTTCCT+TGG + chr1.2:18473809-18473828 None:intergenic 35.0%
CAAAGGGATTGCAAGCATTA+GGG - chr1.2:18473696-18473715 MS.gene040859:CDS 40.0%
GTTCTATTGTGAATGGTGGT+TGG - chr1.2:18473773-18473792 MS.gene040859:CDS 40.0%
TCAAAGGGATTGCAAGCATT+AGG - chr1.2:18473695-18473714 MS.gene040859:CDS 40.0%
! CTTTGAGAATTCCTTGTACC+CGG - chr1.2:18474088-18474107 MS.gene040859:CDS 40.0%
!! GGGTTGATGAAGATAGAACT+TGG - chr1.2:18473716-18473735 MS.gene040859:CDS 40.0%
TTCTATTTCCCGAGCTAGAG+AGG - chr1.2:18473882-18473901 MS.gene040859:CDS 45.0%
GGCTTGATTCCTCTCTAGCT+CGG + chr1.2:18473894-18473913 None:intergenic 50.0%
! GCTTGATTCCTCTCTAGCTC+GGG + chr1.2:18473893-18473912 None:intergenic 50.0%


Chromosome Type Strat End Strand Name
chr1.2 gene 18473465 18474115 18473465 ID=MS.gene040859
chr1.2 mRNA 18473465 18474115 18473465 ID=MS.gene040859.t1;Parent=MS.gene040859
chr1.2 exon 18473999 18474115 18473999 ID=MS.gene040859.t1.exon1;Parent=MS.gene040859.t1
chr1.2 CDS 18473999 18474115 18473999 ID=cds.MS.gene040859.t1;Parent=MS.gene040859.t1
chr1.2 exon 18473652 18473925 18473652 ID=MS.gene040859.t1.exon2;Parent=MS.gene040859.t1
chr1.2 CDS 18473652 18473925 18473652 ID=cds.MS.gene040859.t1;Parent=MS.gene040859.t1
chr1.2 exon 18473465 18473535 18473465 ID=MS.gene040859.t1.exon3;Parent=MS.gene040859.t1
chr1.2 CDS 18473465 18473535 18473465 ID=cds.MS.gene040859.t1;Parent=MS.gene040859.t1
Gene Sequence

>MS.gene040859

ATGACTAAGAAGGCTAAGAAATGTTCAATAACTGAAGCAAATACTAAGAAATCCAATGATAAGAATCCAAGTTTTGAACTTAAATTGACACAATTTTATGCCCAAGGAAAATTATTTGTAAGTTTACTTTTGAAAATGTCTATTATTTTGGCTTTAATTAATATCTCTAATAAACCATGAATTGAAACAGAGAATACCAAGTAAGTTTTCAAGAGAATACTTGAACGAGTTCAAAGGGATTGCAAGCATTAGGGTTGATGAAGATAGAACTTGGAAGGTGAATGTGAAGTTTGATTATGCAAACAGAAGTTCTATTGTGAATGGTGGTTGGAATTTATTTACCAAGGAAAATAACTTGCAAGTCGGCGATGTGTGTAAATTTGAGATGACTCGATCTGAGCCTCTTTCTTTTAATATTTCTATTTCCCGAGCTAGAGAGGAATCAAGCCCTAAAAAATTGCAAGGTTACTTTCTTTCTTCATTATTTGTTTGTTTATTAAAGTTTGTGGTTTTTTGGTCATTGATGTTTGATTAACATTTATCAATCAGTTTTTCACTAACTTCTTAATCCCTTCTACAGATTTAGAAGTTTCTAATGTGAGGGAACATAACACATTTGAGCTCTTTGAGAATTCCTTGTACCCGGTATGA
Protein sequence

>MS.gene040859.t1

MTKKAKKCSITEANTKKSNDKNPSFELKLTQFYAQGKLFRIPSKFSREYLNEFKGIASIRVDEDRTWKVNVKFDYANRSSIVNGGWNLFTKENNLQVGDVCKFEMTRSEPLSFNISISRAREESSPKKLQDLEVSNVREHNTFELFENSLYPV