AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene54304

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene54304.t1 MTR_2g016020 97.619 168 4 0 1 168 1 168 2.55e-120 336
MS.gene54304.t1 MTR_2g077940 35.928 167 88 4 8 161 11 171 2.81e-27 100
MS.gene54304.t1 MTR_2g077960 36.025 161 90 4 8 161 11 165 4.50e-27 100
MS.gene54304.t1 MTR_3g087540 34.091 132 79 5 28 155 25 152 6.91e-22 86.7
MS.gene54304.t1 MTR_3g073990 32.911 158 102 2 1 157 1 155 1.28e-21 86.3
MS.gene54304.t1 MTR_0390s0010 35.032 157 92 2 8 161 11 160 2.86e-19 80.1
MS.gene54304.t1 MTR_0786s0020 34.395 157 93 2 8 161 11 160 2.01e-18 77.8
MS.gene54304.t1 MTR_2g450190 33.758 157 91 3 8 161 11 157 3.47e-16 72.0
MS.gene54304.t1 MTR_0390s0040 33.758 157 91 3 8 161 11 157 3.47e-16 72.0
MS.gene54304.t1 MTR_2g077080 31.915 141 87 2 23 161 31 164 4.76e-14 66.2
MS.gene54304.t1 MTR_1678s0010 28.082 146 95 5 28 168 38 178 1.37e-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
MS.gene54304.t1 AT1G29140 49.412 170 80 4 1 164 1 170 2.26e-50 159
MS.gene54304.t1 AT5G45880 53.571 140 63 2 27 164 34 173 8.99e-50 158
MS.gene54304.t1 AT4G18596 47.953 171 82 4 1 164 1 171 1.16e-49 158
MS.gene54304.t1 AT4G18596 47.953 171 82 4 1 164 47 217 6.37e-49 157
MS.gene54304.t1 AT4G08685 39.241 158 89 5 8 162 6 159 1.88e-31 111
MS.gene54304.t1 AT5G10130 37.349 166 94 3 1 162 1 160 6.64e-28 102
MS.gene54304.t1 AT1G78040 32.143 168 103 5 1 162 1 163 4.30e-21 85.1
MS.gene54304.t1 AT1G78040 32.143 168 103 5 1 162 1 163 4.30e-21 85.1
MS.gene54304.t1 AT1G78040 32.143 168 103 5 1 162 1 163 4.30e-21 85.1

Find 41 sgRNAs with CRISPR-Local

Find 57 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TTGAGAACCTCACCACATTT+AGG 0.300765 2.3:+69410059 None:intergenic
CGGTCAATCTGGTGATGAAT+TGG 0.316647 2.3:+69410746 None:intergenic
GTGGAATGCAAAGAAGAAAA+TGG 0.335509 2.3:-69410329 MS.gene54304:CDS
AGAGGGCTAGCAGCACGAAC+TGG 0.354642 2.3:+69410107 None:intergenic
CCTGAACGCTTCTTTGTAGA+AGG 0.366196 2.3:-69410796 MS.gene54304:CDS
AAATACAGTGTGGAGATAGA+TGG 0.398924 2.3:-69410263 MS.gene54304:CDS
GTTCGTGCTGCTAGCCCTCT+TGG 0.402448 2.3:-69410104 MS.gene54304:CDS
TAGGTAGACGCTCTTTCTTA+AGG 0.405456 2.3:+69410078 None:intergenic
TGATCCTAGCAGCTTGTTGT+AGG 0.405713 2.3:+69410159 None:intergenic
TTCAATGAACTCGGTCAATC+TGG 0.407937 2.3:+69410735 None:intergenic
TACAAAGAAGCGTTCAGGCT+TGG 0.439377 2.3:+69410801 None:intergenic
GAACTTGGAATTAATGAAGA+TGG 0.440677 2.3:-69410035 MS.gene54304:CDS
ACCTCTGAGCAATCTTTCCT+TGG 0.443518 2.3:+69410197 None:intergenic
GAAGCAACAACAGATAAATC+AGG 0.454577 2.3:-69410287 MS.gene54304:CDS
TAATGAAGATGGAACTGAAA+AGG 0.471543 2.3:-69410024 MS.gene54304:CDS
CCTTCTACAAAGAAGCGTTC+AGG 0.474728 2.3:+69410796 None:intergenic
GGAATAAGCCGCACCTAAGA+AGG 0.479861 2.3:+69410822 None:intergenic
GAGGGCTAGCAGCACGAACT+GGG 0.491624 2.3:+69410108 None:intergenic
AGATTGACCGAGTTCATTGA+AGG 0.500832 2.3:-69410733 MS.gene54304:intron
GGTGAGGTTCTCAAAGAACT+TGG 0.517638 2.3:-69410050 MS.gene54304:CDS
GGTCAATCTGGTGATGAATT+GGG 0.518245 2.3:+69410747 None:intergenic
CTTCACATGTTTCATCCTCA+TGG 0.533134 2.3:+69410237 None:intergenic
TTATTCTTTGCAAGAGTCCA+AGG 0.534437 2.3:-69410214 MS.gene54304:CDS
AAAAGCAAAGGGTGAAGACA+AGG 0.570670 2.3:+69410848 None:intergenic
TGAAGGTGCAACGGTGCGTG+TGG 0.602260 2.3:-69410348 MS.gene54304:intron
CTTTCTTAAGGAAACCAAGA+GGG 0.608256 2.3:+69410090 None:intergenic
ATCAGTGTCACAAACAACAA+TGG 0.613848 2.3:-69410140 MS.gene54304:CDS
AAGCAAAGGGTGAAGACAAG+GGG 0.617019 2.3:+69410850 None:intergenic
CTCACCTACAACAAGCTGCT+AGG 0.622703 2.3:-69410163 MS.gene54304:CDS
TGAAGATGGAACTGAAAAGG+AGG 0.627791 2.3:-69410021 MS.gene54304:CDS
GTACGTACCTTCAATGAACT+CGG 0.638216 2.3:+69410726 None:intergenic
AAAGAGCGTCTACCTAAATG+TGG 0.642536 2.3:-69410071 MS.gene54304:CDS
AGGGCTAGCAGCACGAACTG+GGG 0.655258 2.3:+69410109 None:intergenic
TATATGTAATGAAGGTGCAA+CGG 0.656510 2.3:-69410357 MS.gene54304:intron
AAAGCAAAGGGTGAAGACAA+GGG 0.660463 2.3:+69410849 None:intergenic
GCGTCTACCTAAATGTGGTG+AGG 0.675591 2.3:-69410066 MS.gene54304:CDS
TCTTTCTTAAGGAAACCAAG+AGG 0.685975 2.3:+69410089 None:intergenic
TAAATCAGGAAAATACAGTG+TGG 0.693438 2.3:-69410273 MS.gene54304:CDS
TCCAAGGAAAGATTGCTCAG+AGG 0.698789 2.3:-69410198 MS.gene54304:CDS
AGCAAAGGGTGAAGACAAGG+GGG 0.721824 2.3:+69410851 None:intergenic
GGAGATAGATGGAGACCATG+AGG 0.745188 2.3:-69410252 MS.gene54304:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! ATAATCTGAATTTTACTTTT+AGG + chr2.3:69410367-69410386 None:intergenic 15.0%
!!! GACATAAATAATAATTTTTG+TGG - chr2.3:69410501-69410520 MS.gene54304:intron 15.0%
! ACACATTTATTACTAAGAAG+CGG - chr2.3:69410427-69410446 MS.gene54304:intron 25.0%
! TAAGAAGGATAAAAAGCAAA+GGG + chr2.3:69410050-69410069 None:intergenic 25.0%
!!! TTTTACTTTTAGGTATTACG+AGG + chr2.3:69410357-69410376 None:intergenic 25.0%
CTAAGAAGGATAAAAAGCAA+AGG + chr2.3:69410051-69410070 None:intergenic 30.0%
GAACTTGGAATTAATGAAGA+TGG - chr2.3:69410849-69410868 MS.gene54304:CDS 30.0%
TAAATCAGGAAAATACAGTG+TGG - chr2.3:69410611-69410630 MS.gene54304:intron 30.0%
TAATGAAGATGGAACTGAAA+AGG - chr2.3:69410860-69410879 MS.gene54304:CDS 30.0%
TTGCACCTTCATTACATATA+TGG + chr2.3:69410527-69410546 None:intergenic 30.0%
! TATATGTAATGAAGGTGCAA+CGG - chr2.3:69410527-69410546 MS.gene54304:intron 30.0%
!!! CTTTGCTTTTTATCCTTCTT+AGG - chr2.3:69410049-69410068 MS.gene54304:CDS 30.0%
AAATACAGTGTGGAGATAGA+TGG - chr2.3:69410621-69410640 MS.gene54304:intron 35.0%
ACACGATACATATTTGACAC+CGG + chr2.3:69410238-69410257 None:intergenic 35.0%
ATATATGTGACAGTGTGTGT+TGG + chr2.3:69410267-69410286 None:intergenic 35.0%
ATCAGTGTCACAAACAACAA+TGG - chr2.3:69410744-69410763 MS.gene54304:CDS 35.0%
CTTTCTTAAGGAAACCAAGA+GGG + chr2.3:69410797-69410816 None:intergenic 35.0%
GAAGCAACAACAGATAAATC+AGG - chr2.3:69410597-69410616 MS.gene54304:intron 35.0%
GTGGAATGCAAAGAAGAAAA+TGG - chr2.3:69410555-69410574 MS.gene54304:intron 35.0%
TCTTTCTTAAGGAAACCAAG+AGG + chr2.3:69410798-69410817 None:intergenic 35.0%
TGTGGCCATATATGTAATGA+AGG - chr2.3:69410519-69410538 MS.gene54304:intron 35.0%
TTATTCTTTGCAAGAGTCCA+AGG - chr2.3:69410670-69410689 MS.gene54304:intron 35.0%
! CTTTTTATCCTTCTTAGGTG+CGG - chr2.3:69410054-69410073 MS.gene54304:CDS 35.0%
AAAAGCAAAGGGTGAAGACA+AGG + chr2.3:69410039-69410058 None:intergenic 40.0%
AAAGCAAAGGGTGAAGACAA+GGG + chr2.3:69410038-69410057 None:intergenic 40.0%
AGATTGACCGAGTTCATTGA+AGG - chr2.3:69410151-69410170 MS.gene54304:CDS 40.0%
CTTCACATGTTTCATCCTCA+TGG + chr2.3:69410650-69410669 None:intergenic 40.0%
GCAAGACATTCGATATGCTA+AGG + chr2.3:69410476-69410495 None:intergenic 40.0%
GTACGTACCTTCAATGAACT+CGG + chr2.3:69410161-69410180 None:intergenic 40.0%
TAGGTAGACGCTCTTTCTTA+AGG + chr2.3:69410809-69410828 None:intergenic 40.0%
TATACTCCTCGAATTATGCG+TGG - chr2.3:69410211-69410230 MS.gene54304:CDS 40.0%
TGAAGATGGAACTGAAAAGG+AGG - chr2.3:69410863-69410882 MS.gene54304:CDS 40.0%
TTCAATGAACTCGGTCAATC+TGG + chr2.3:69410152-69410171 None:intergenic 40.0%
TTGAGAACCTCACCACATTT+AGG + chr2.3:69410828-69410847 None:intergenic 40.0%
! GGTCAATCTGGTGATGAATT+GGG + chr2.3:69410140-69410159 None:intergenic 40.0%
!! AAAGAGCGTCTACCTAAATG+TGG - chr2.3:69410813-69410832 MS.gene54304:CDS 40.0%
AAGCAAAGGGTGAAGACAAG+GGG + chr2.3:69410037-69410056 None:intergenic 45.0%
ACCTCTGAGCAATCTTTCCT+TGG + chr2.3:69410690-69410709 None:intergenic 45.0%
CCTGAACGCTTCTTTGTAGA+AGG - chr2.3:69410088-69410107 MS.gene54304:CDS 45.0%
GGTGAGGTTCTCAAAGAACT+TGG - chr2.3:69410834-69410853 MS.gene54304:CDS 45.0%
TCCAAGGAAAGATTGCTCAG+AGG - chr2.3:69410686-69410705 MS.gene54304:intron 45.0%
! CGGTCAATCTGGTGATGAAT+TGG + chr2.3:69410141-69410160 None:intergenic 45.0%
!! CCTTCTACAAAGAAGCGTTC+AGG + chr2.3:69410091-69410110 None:intergenic 45.0%
!! TACAAAGAAGCGTTCAGGCT+TGG + chr2.3:69410086-69410105 None:intergenic 45.0%
!! TGATCCTAGCAGCTTGTTGT+AGG + chr2.3:69410728-69410747 None:intergenic 45.0%
AGCAAAGGGTGAAGACAAGG+GGG + chr2.3:69410036-69410055 None:intergenic 50.0%
CTCACCTACAACAAGCTGCT+AGG - chr2.3:69410721-69410740 MS.gene54304:intron 50.0%
GCGTCTACCTAAATGTGGTG+AGG - chr2.3:69410818-69410837 MS.gene54304:CDS 50.0%
GGAATAAGCCGCACCTAAGA+AGG + chr2.3:69410065-69410084 None:intergenic 50.0%
GGAGATAGATGGAGACCATG+AGG - chr2.3:69410632-69410651 MS.gene54304:intron 50.0%
TCCTCGAATTATGCGTGGTC+CGG - chr2.3:69410216-69410235 MS.gene54304:CDS 50.0%
ACCGGACCACGCATAATTCG+AGG + chr2.3:69410220-69410239 None:intergenic 55.0%
! AGAGGGCTAGCAGCACGAAC+TGG + chr2.3:69410780-69410799 None:intergenic 60.0%
! AGGGCTAGCAGCACGAACTG+GGG + chr2.3:69410778-69410797 None:intergenic 60.0%
! GAGGGCTAGCAGCACGAACT+GGG + chr2.3:69410779-69410798 None:intergenic 60.0%
! GTTCGTGCTGCTAGCCCTCT+TGG - chr2.3:69410780-69410799 MS.gene54304:CDS 60.0%
! TGAAGGTGCAACGGTGCGTG+TGG - chr2.3:69410536-69410555 MS.gene54304:intron 60.0%


Chromosome Type Strat End Strand Name
chr2.3 gene 69410016 69410890 69410016 ID=MS.gene54304
chr2.3 mRNA 69410016 69410890 69410016 ID=MS.gene54304.t1;Parent=MS.gene54304
chr2.3 exon 69410734 69410890 69410734 ID=MS.gene54304.t1.exon1;Parent=MS.gene54304.t1
chr2.3 CDS 69410734 69410890 69410734 ID=cds.MS.gene54304.t1;Parent=MS.gene54304.t1
chr2.3 exon 69410016 69410365 69410016 ID=MS.gene54304.t1.exon2;Parent=MS.gene54304.t1
chr2.3 CDS 69410016 69410365 69410016 ID=cds.MS.gene54304.t1;Parent=MS.gene54304.t1
Gene Sequence

>MS.gene54304

ATGGCAAAGTCTACAATCCCCCTTGTCTTCACCCTTTGCTTTTTATCCTTCTTAGGTGCGGCTTATTCCAAGCCTGAACGCTTCTTTGTAGAAGGTGTTGTTTACTGTGACACATGTCGCACCCAATTCATCACCAGATTGACCGAGTTCATTGAAGGTACGTACATATTTTTTAATGTGAATCTATGAAGCACATATACTCCTCGAATTATGCGTGGTCCGGTGTCAAATATGTATCGTGTCTGACACCAACACACACTGTCACATATATGTCATTTTCTTAAATCATTATCGATGTTCACATGTCATGTCATGTCGTGTCTAGTGTATAGTCTGTGCCTCGTAATACCTAAAAGTAAAATTCAGATTATTGATTTTTATTTTTTTAAAGAGTCTAACGATGAAACTCACACACATTTATTACTAAGAAGCGGAGAATTAAGAGTTCTAACTCGTGCCTTAGCATATCGAATGTCTTGCAACTTGACATAAATAATAATTTTTGTGGCCATATATGTAATGAAGGTGCAACGGTGCGTGTGGAATGCAAAGAAGAAAATGGAACATTGACATTCAACAAAGAAGCAACAACAGATAAATCAGGAAAATACAGTGTGGAGATAGATGGAGACCATGAGGATGAAACATGTGAAGTTATTCTTTGCAAGAGTCCAAGGAAAGATTGCTCAGAGGTTGACTCAGAAGCTCACCTACAACAAGCTGCTAGGATCAGTGTCACAAACAACAATGGAATTGTGTCCCCAGTTCGTGCTGCTAGCCCTCTTGGTTTCCTTAAGAAAGAGCGTCTACCTAAATGTGGTGAGGTTCTCAAAGAACTTGGAATTAATGAAGATGGAACTGAAAAGGAGGACTAG
Protein sequence

>MS.gene54304.t1

MAKSTIPLVFTLCFLSFLGAAYSKPERFFVEGVVYCDTCRTQFITRLTEFIEGATVRVECKEENGTLTFNKEATTDKSGKYSVEIDGDHEDETCEVILCKSPRKDCSEVDSEAHLQQAARISVTNNNGIVSPVRAASPLGFLKKERLPKCGEVLKELGINEDGTEKED