AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene66370

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene66370.t1 MTR_6g005210 96.226 53 2 0 1 53 187 239 2.44e-30 111
MS.gene66370.t1 MTR_4g097810 77.358 53 12 0 1 53 7 59 1.84e-24 88.2
MS.gene66370.t1 MTR_1g028230 87.500 48 6 0 6 53 91 138 6.84e-24 90.9
MS.gene66370.t1 MTR_6g090470 46.875 64 34 0 3 66 172 235 1.56e-14 67.0
MS.gene66370.t1 MTR_4g125800 54.167 48 22 0 3 50 120 167 1.51e-13 63.9
MS.gene66370.t1 MTR_4g125800 54.167 48 22 0 3 50 173 220 1.82e-13 63.9
MS.gene66370.t1 MTR_4g125800 54.167 48 22 0 3 50 196 243 1.89e-13 63.9
MS.gene66370.t1 MTR_2g040510 50.000 48 24 0 3 50 173 220 6.11e-13 62.4
MS.gene66370.t1 MTR_6g071280 59.524 42 16 1 3 44 161 201 6.14e-11 57.0
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene66370.t1 AT5G40440 84.906 53 8 0 1 53 104 156 3.48e-27 102
MS.gene66370.t1 AT5G40440 84.906 53 8 0 1 53 186 238 5.42e-27 102
MS.gene66370.t1 AT5G40440 84.906 53 8 0 1 53 186 238 5.42e-27 102
MS.gene66370.t1 AT5G40440 84.906 53 8 0 1 53 168 220 4.06e-26 100
MS.gene66370.t1 AT5G40440 84.906 53 8 0 1 53 168 220 4.06e-26 100
MS.gene66370.t1 AT5G40440 84.906 53 8 0 1 53 168 220 4.06e-26 100
MS.gene66370.t1 AT4G29810 50.943 53 26 0 1 53 180 232 6.07e-15 68.2
MS.gene66370.t1 AT4G29810 50.943 53 26 0 1 53 171 223 6.61e-15 68.2
MS.gene66370.t1 AT4G29810 50.943 53 26 0 1 53 180 232 6.77e-15 68.2
MS.gene66370.t1 AT5G56580 53.846 52 24 0 3 54 174 225 2.24e-14 66.6
MS.gene66370.t1 AT4G26070 59.524 42 17 0 3 44 158 199 2.85e-12 60.8
MS.gene66370.t1 AT4G26070 59.524 42 17 0 3 44 170 211 2.91e-12 60.8
MS.gene66370.t1 AT4G26070 59.524 42 17 0 3 44 171 212 3.10e-12 60.5
MS.gene66370.t1 AT4G26070 59.524 42 17 0 3 44 171 212 3.10e-12 60.5
MS.gene66370.t1 AT4G26070 59.524 42 17 0 3 44 171 212 3.14e-12 60.5
MS.gene66370.t1 AT1G73500 64.286 42 14 1 3 44 149 189 3.51e-11 57.4
MS.gene66370.t1 AT1G18350 57.143 49 20 1 3 51 147 194 4.51e-11 57.4

Find 11 sgRNAs with CRISPR-Local

Find 21 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GAGCCGAAAATTACTGATTT+TGG 0.210770 6.1:-78813617 MS.gene66370:CDS
ATTTACTTGTAAACCTCAAA+GGG 0.420841 6.1:-78813640 MS.gene66370:CDS
GAAGTGCAATTTCTATCTAT+AGG 0.434795 6.1:+78813420 None:intergenic
AGGTTTACAAGTAAATTAGC+AGG 0.487423 6.1:+78813647 None:intergenic
AATTTACTTGTAAACCTCAA+AGG 0.501450 6.1:-78813641 MS.gene66370:CDS
CATAGAGAATTCAGTTGCAA+TGG 0.563989 6.1:-78813582 MS.gene66370:intron
ACGTAGGAGCTTCTGAAACA+TGG 0.573800 6.1:+78813825 None:intergenic
GCTCAACAAGATCCTCAATA+CGG 0.592189 6.1:+78813382 None:intergenic
AGATGAGCAAGTCCGTATTG+AGG 0.604364 6.1:-78813394 MS.gene66370:CDS
AAGGGTCTAAGTTATCTGCA+CGG 0.655190 6.1:-78813701 MS.gene66370:CDS
TTTACTTGTAAACCTCAAAG+GGG 0.694553 6.1:-78813639 MS.gene66370:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! GTTTTTTTAATCTTTTTGAA+GGG - chr6.1:78813481-78813500 MS.gene66370:intron 15.0%
!!! ATACCAAAATCAGTAATTTT+CGG + chr6.1:78813589-78813608 None:intergenic 20.0%
!!! GGTTTTTTTAATCTTTTTGA+AGG - chr6.1:78813480-78813499 MS.gene66370:intron 20.0%
! AATTTACTTGTAAACCTCAA+AGG - chr6.1:78813559-78813578 MS.gene66370:intron 25.0%
! ATTTACTTGTAAACCTCAAA+GGG - chr6.1:78813560-78813579 MS.gene66370:intron 25.0%
AGGTTTACAAGTAAATTAGC+AGG + chr6.1:78813556-78813575 None:intergenic 30.0%
ATTGAGATATGCTACTAACT+TGG - chr6.1:78813455-78813474 MS.gene66370:CDS 30.0%
GAAGTGCAATTTCTATCTAT+AGG + chr6.1:78813783-78813802 None:intergenic 30.0%
TTTACTTGTAAACCTCAAAG+GGG - chr6.1:78813561-78813580 MS.gene66370:intron 30.0%
!! ACTGATTTTGGTATTAGTGT+TGG - chr6.1:78813595-78813614 MS.gene66370:CDS 30.0%
AACAAAGTGTGGAAGCAAAT+CGG + chr6.1:78813684-78813703 None:intergenic 35.0%
AATATATGCTCCTTACACGT+AGG + chr6.1:78813394-78813413 None:intergenic 35.0%
AGATATGCTACTAACTTGGT+TGG - chr6.1:78813459-78813478 MS.gene66370:CDS 35.0%
CATAGAGAATTCAGTTGCAA+TGG - chr6.1:78813618-78813637 MS.gene66370:CDS 35.0%
!!! GAGCCGAAAATTACTGATTT+TGG - chr6.1:78813583-78813602 MS.gene66370:CDS 35.0%
AAGGGTCTAAGTTATCTGCA+CGG - chr6.1:78813499-78813518 MS.gene66370:intron 40.0%
GCTCAACAAGATCCTCAATA+CGG + chr6.1:78813821-78813840 None:intergenic 40.0%
TCAGTCAAGCAAACAAAGTG+TGG + chr6.1:78813695-78813714 None:intergenic 40.0%
AGATGAGCAAGTCCGTATTG+AGG - chr6.1:78813806-78813825 MS.gene66370:intron 45.0%
TTCAGAAGCTCCTACGTGTA+AGG - chr6.1:78813381-78813400 MS.gene66370:CDS 45.0%
! TAATTTTCGGCTCCCCTTTG+AGG + chr6.1:78813576-78813595 None:intergenic 45.0%


Chromosome Type Strat End Strand Name
chr6.1 gene 78813377 78813845 78813377 ID=MS.gene66370
chr6.1 mRNA 78813377 78813845 78813377 ID=MS.gene66370.t1;Parent=MS.gene66370
chr6.1 exon 78813825 78813845 78813825 ID=MS.gene66370.t1.exon1;Parent=MS.gene66370.t1
chr6.1 CDS 78813825 78813845 78813825 ID=cds.MS.gene66370.t1;Parent=MS.gene66370.t1
chr6.1 exon 78813583 78813720 78813583 ID=MS.gene66370.t1.exon2;Parent=MS.gene66370.t1
chr6.1 CDS 78813583 78813720 78813583 ID=cds.MS.gene66370.t1;Parent=MS.gene66370.t1
chr6.1 exon 78813377 78813478 78813377 ID=MS.gene66370.t1.exon3;Parent=MS.gene66370.t1
chr6.1 CDS 78813377 78813478 78813377 ID=cds.MS.gene66370.t1;Parent=MS.gene66370.t1
Gene Sequence

>MS.gene66370

ATGTTTCAGAAGCTCCTACGTGTAAGGAGCATATATTCTTACTTTTCATTTTAAATTTTCATTACTGAAACATTGTGAATTGAGATATGCTACTAACTTGGTTGGTTTTTTTAATCTTTTTGAAGGGTCTAAGTTATCTGCACGGAGTCAGATATTTAGTTCACAGAGACATAAAGCCTGCTAATTTACTTGTAAACCTCAAAGGGGAGCCGAAAATTACTGATTTTGGTATTAGTGTTGGCATAGAGAATTCAGTTGCAATGGTCAGTCACATTTTGTTGCTGTCATGCTTTGCTTCAACATACCGATTTGCTTCCACACTTTGTTTGCTTGACTGATGTGTATGAATTGTGTTTGAATTGTTTAGAAATGTTTGAATTGTGTATGTTTGAATTGTTTTGCTCCTATAGATAGAAATTGCACTTCAAAAGATGAGCAAGTCCGTATTGAGGATCTTGTTGAGCTGTGA
Protein sequence

>MS.gene66370.t1

MFQKLLRGLSYLHGVRYLVHRDIKPANLLVNLKGEPKITDFGISVGIENSVAMKCLNCVCLNCFAPIDRNCTSKDEQVRIEDLVEL