AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene023891

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene023891.t1 MTR_7g077650 72.727 198 45 3 1 190 99 295 6.66e-92 273
MS.gene023891.t1 MTR_7g077620 69.588 194 53 3 2 190 101 293 1.01e-87 263
MS.gene023891.t1 MTR_7g077660 70.619 194 50 4 2 190 99 290 5.20e-86 258
MS.gene023891.t1 MTR_7g076110 51.042 192 84 5 6 188 38 228 4.49e-56 179
MS.gene023891.t1 MTR_7g076100 54.430 158 64 4 39 190 66 221 5.67e-47 155
MS.gene023891.t1 MTR_7g076130 57.265 117 46 2 71 184 27 142 2.19e-38 129
MS.gene023891.t1 MTR_5g038260 42.000 200 92 7 6 188 96 288 3.27e-36 130
MS.gene023891.t1 MTR_1g108740 43.011 186 93 7 6 188 97 272 4.90e-36 129
MS.gene023891.t1 MTR_5g082770 41.969 193 83 5 6 184 90 267 3.04e-33 120
MS.gene023891.t1 MTR_5g038230 39.500 200 71 7 6 188 94 260 1.13e-32 120
MS.gene023891.t1 MTR_1g064570 34.498 229 95 9 2 188 90 305 2.11e-22 93.2
MS.gene023891.t1 MTR_5g082780 32.990 194 88 7 15 190 1 170 9.80e-22 89.0
MS.gene023891.t1 MTR_1g016150 48.193 83 39 3 6 85 106 187 5.19e-16 73.6
MS.gene023891.t1 MTR_6g023955 42.857 98 52 3 41 137 73 167 1.40e-11 61.2
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 27 sgRNAs with CRISPR-Local

Find 37 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AGGAGGATTGTTTAGCTTTA+AGG 0.194494 7.1:+26060652 None:intergenic
AAAGAGCAAGCCAATCATTT+TGG 0.202770 7.1:-26060766 MS.gene023891:CDS
TCGAGAGGTGGCAGACTAAT+AGG 0.314526 7.1:+26060884 None:intergenic
GGAGGAATACTACACTTAAA+AGG 0.326804 7.1:+26060905 None:intergenic
ACCTCTCGAATCTCTCAAAA+AGG 0.330053 7.1:-26060870 MS.gene023891:CDS
CCATCATAACAACGTAGTTT+TGG 0.331154 7.1:+26060563 None:intergenic
CCATGGTTGGCTTGCATTGG+TGG 0.397590 7.1:-26060957 MS.gene023891:CDS
CCAAAACTACGTTGTTATGA+TGG 0.407066 7.1:-26060563 MS.gene023891:CDS
ACTAGCCATCTTCTCATAGT+AGG 0.443005 7.1:+26060601 None:intergenic
TGAGAAGATGCTTAATCGAC+AGG 0.454104 7.1:-26060496 MS.gene023891:CDS
TAGCCATGGTTGGCTTGCAT+TGG 0.461010 7.1:-26060960 MS.gene023891:CDS
CTACACGAATCCAAAATGAT+TGG 0.482901 7.1:+26060756 None:intergenic
TAATCACTTGGATTTGTCAT+GGG 0.490766 7.1:+26060830 None:intergenic
AATCATTGACCGGAGACATA+TGG 0.521122 7.1:-26060523 MS.gene023891:CDS
AATGATTTCACAAAATAAGC+AGG 0.533478 7.1:+26060539 None:intergenic
ATAATCACTTGGATTTGTCA+TGG 0.537229 7.1:+26060829 None:intergenic
TGTCATGGGGTCAGCAGACA+AGG 0.556574 7.1:+26060844 None:intergenic
TCTCATCAACCATATGTCTC+CGG 0.558876 7.1:+26060514 None:intergenic
GACAAATCCAAGTGATTATG+TGG 0.574598 7.1:-26060825 MS.gene023891:CDS
ATTGGAACTGAATGCTAGAG+TGG 0.576030 7.1:-26060447 MS.gene023891:CDS
CGATCAATTGAGTCATCAGA+AGG 0.588157 7.1:+26060632 None:intergenic
GTTTAGCTTTAAGGATACAA+TGG 0.589562 7.1:+26060661 None:intergenic
GCTGCAACCACATAATCACT+TGG 0.591162 7.1:+26060818 None:intergenic
AATCACTTGGATTTGTCATG+GGG 0.596697 7.1:+26060831 None:intergenic
TCAATTGAGTCATCAGAAGG+AGG 0.655171 7.1:+26060635 None:intergenic
CCACCAATGCAAGCCAACCA+TGG 0.665097 7.1:+26060957 None:intergenic
AGAGGTGGCAGACTAATAGG+AGG 0.669617 7.1:+26060887 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! ACTAATGTTGTATTTTATAA+AGG - chr7.1:26060697-26060716 MS.gene023891:CDS 15.0%
! AATGATTTCACAAAATAAGC+AGG + chr7.1:26060874-26060893 None:intergenic 25.0%
!! TATTTTGTGAAATCATTGAC+CGG - chr7.1:26060877-26060896 MS.gene023891:CDS 25.0%
!! TGTTGTATTTTATAAAGGCT+TGG - chr7.1:26060702-26060721 MS.gene023891:CDS 25.0%
ATAATCACTTGGATTTGTCA+TGG + chr7.1:26060584-26060603 None:intergenic 30.0%
TAATCACTTGGATTTGTCAT+GGG + chr7.1:26060583-26060602 None:intergenic 30.0%
! CAAAATGCACGTTTTCAAAT+TGG - chr7.1:26060945-26060964 MS.gene023891:CDS 30.0%
! TTTTTCCTACTATGAGAAGA+TGG - chr7.1:26060804-26060823 MS.gene023891:CDS 30.0%
!! GTTTAGCTTTAAGGATACAA+TGG + chr7.1:26060752-26060771 None:intergenic 30.0%
!!! CGTAGTTTTGGAATCATATA+TGG + chr7.1:26060838-26060857 None:intergenic 30.0%
AATCACTTGGATTTGTCATG+GGG + chr7.1:26060582-26060601 None:intergenic 35.0%
CCAAAACTACGTTGTTATGA+TGG - chr7.1:26060847-26060866 MS.gene023891:CDS 35.0%
CTACACGAATCCAAAATGAT+TGG + chr7.1:26060657-26060676 None:intergenic 35.0%
GACAAATCCAAGTGATTATG+TGG - chr7.1:26060585-26060604 MS.gene023891:CDS 35.0%
GGAGGAATACTACACTTAAA+AGG + chr7.1:26060508-26060527 None:intergenic 35.0%
! AAAGAGCAAGCCAATCATTT+TGG - chr7.1:26060644-26060663 MS.gene023891:CDS 35.0%
! CCATCATAACAACGTAGTTT+TGG + chr7.1:26060850-26060869 None:intergenic 35.0%
!! AGGAGGATTGTTTAGCTTTA+AGG + chr7.1:26060761-26060780 None:intergenic 35.0%
AATCATTGACCGGAGACATA+TGG - chr7.1:26060887-26060906 MS.gene023891:CDS 40.0%
ACCTCTCGAATCTCTCAAAA+AGG - chr7.1:26060540-26060559 MS.gene023891:CDS 40.0%
ACTAGCCATCTTCTCATAGT+AGG + chr7.1:26060812-26060831 None:intergenic 40.0%
ATTGGAACTGAATGCTAGAG+TGG - chr7.1:26060963-26060982 MS.gene023891:CDS 40.0%
CGATCAATTGAGTCATCAGA+AGG + chr7.1:26060781-26060800 None:intergenic 40.0%
TCAATTGAGTCATCAGAAGG+AGG + chr7.1:26060778-26060797 None:intergenic 40.0%
TCTCATCAACCATATGTCTC+CGG + chr7.1:26060899-26060918 None:intergenic 40.0%
TGAGAAGATGCTTAATCGAC+AGG - chr7.1:26060914-26060933 MS.gene023891:CDS 40.0%
!! ACCTTTTTGAGAGATTCGAG+AGG + chr7.1:26060544-26060563 None:intergenic 40.0%
!! TTTTTGAGAGATTCGAGAGG+TGG + chr7.1:26060541-26060560 None:intergenic 40.0%
GCTGCAACCACATAATCACT+TGG + chr7.1:26060595-26060614 None:intergenic 45.0%
!!! TTGTTTTTGGGCTGTAGCCA+TGG - chr7.1:26060436-26060455 MS.gene023891:CDS 45.0%
AGAGGTGGCAGACTAATAGG+AGG + chr7.1:26060526-26060545 None:intergenic 50.0%
TCGAGAGGTGGCAGACTAAT+AGG + chr7.1:26060529-26060548 None:intergenic 50.0%
! TTTTGGGCTGTAGCCATGGT+TGG - chr7.1:26060440-26060459 MS.gene023891:CDS 50.0%
!! TAGCCATGGTTGGCTTGCAT+TGG - chr7.1:26060450-26060469 MS.gene023891:CDS 50.0%
CCACCAATGCAAGCCAACCA+TGG + chr7.1:26060456-26060475 None:intergenic 55.0%
TGTCATGGGGTCAGCAGACA+AGG + chr7.1:26060569-26060588 None:intergenic 55.0%
!! CCATGGTTGGCTTGCATTGG+TGG - chr7.1:26060453-26060472 MS.gene023891:CDS 55.0%


Chromosome Type Strat End Strand Name
chr7.1 gene 26060430 26061002 26060430 ID=MS.gene023891
chr7.1 mRNA 26060430 26061002 26060430 ID=MS.gene023891.t1;Parent=MS.gene023891
chr7.1 exon 26060430 26061002 26060430 ID=MS.gene023891.t1.exon1;Parent=MS.gene023891.t1
chr7.1 CDS 26060430 26061002 26060430 ID=cds.MS.gene023891.t1;Parent=MS.gene023891.t1
Gene Sequence

>MS.gene023891

ATGAAATTGTTTTTGGGCTGTAGCCATGGTTGGCTTGCATTGGTGGATGATAACGATGTCATTACTCTAGTGAATCCTTTTAAGTGTAGTATTCCTCCTATTAGTCTGCCACCTCTCGAATCTCTCAAAAAGGTTACCTTGTCTGCTGACCCCATGACAAATCCAAGTGATTATGTGGTTGCAGCAATTCACAAGTTTGTTTATCTCGCTTTCAAAAGAGCAAGCCAATCATTTTGGATTCGTGTAGACACAAATGAATTTTTTTTCACTAATGTTGTATTTTATAAAGGCTTGGTATTTGCTGATAGCAACAGAGACACCATTGTATCCTTAAAGCTAAACAATCCTCCTTCTGATGACTCAATTGATCGTAATTTTTCCTACTATGAGAAGATGGCTAGTACTCCATATATGATTCCAAAACTACGTTGTTATGATGGACCTGCTTATTTTGTGAAATCATTGACCGGAGACATATGGTTGATGAGAAGATGCTTAATCGACAGGTTTTCTATCAAAATGCACGTTTTCAAATTGGAACTGAATGCTAGAGTGGAAAACTTGAACAAATGA
Protein sequence

>MS.gene023891.t1

MKLFLGCSHGWLALVDDNDVITLVNPFKCSIPPISLPPLESLKKVTLSADPMTNPSDYVVAAIHKFVYLAFKRASQSFWIRVDTNEFFFTNVVFYKGLVFADSNRDTIVSLKLNNPPSDDSIDRNFSYYEKMASTPYMIPKLRCYDGPAYFVKSLTGDIWLMRRCLIDRFSIKMHVFKLELNARVENLNK