AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene20798

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene20798.t1 MTR_1g087200 98.734 158 2 0 1 158 1 158 1.66e-114 321
MS.gene20798.t1 MTR_1g083950 52.597 154 67 3 6 158 9 157 7.02e-56 173
MS.gene20798.t1 MTR_1g088640 39.375 160 91 4 2 158 7 163 8.12e-33 114
MS.gene20798.t1 MTR_1g088640 39.873 158 90 4 2 158 7 160 1.64e-31 111
MS.gene20798.t1 MTR_1g054750 34.706 170 95 5 2 158 17 183 1.64e-30 109
MS.gene20798.t1 MTR_1g054765 36.471 170 87 5 7 158 4 170 1.67e-29 106
MS.gene20798.t1 MTR_7g108830 41.026 156 87 4 5 158 6 158 4.98e-27 99.8
MS.gene20798.t1 MTR_8g058620 41.026 156 87 4 5 158 6 158 4.98e-27 99.8
MS.gene20798.t1 MTR_5g065980 35.185 162 91 4 8 156 10 170 1.03e-26 99.4
MS.gene20798.t1 MTR_5g065980 35.185 162 89 4 8 156 10 168 1.24e-26 99.0
MS.gene20798.t1 MTR_5g077130 36.774 155 84 5 10 156 9 157 1.58e-21 85.5
MS.gene20798.t1 MTR_5g077130 36.538 156 84 6 10 156 9 158 2.43e-20 82.4
MS.gene20798.t1 MTR_2g089350 32.738 168 89 6 6 158 25 183 2.48e-20 84.0
MS.gene20798.t1 MTR_1g088620 58.462 65 25 1 94 158 220 282 4.37e-18 79.0
MS.gene20798.t1 MTR_4g019800 33.129 163 91 6 4 156 3 157 3.10e-17 74.3
MS.gene20798.t1 MTR_6g006190 27.168 173 100 4 1 157 1 163 9.42e-17 73.6
MS.gene20798.t1 MTR_2g034200 28.481 158 101 3 6 156 5 157 3.67e-16 71.6
MS.gene20798.t1 MTR_4g064933 35.404 161 88 5 6 157 5 158 1.12e-15 70.5
MS.gene20798.t1 MTR_5g065980 32.394 142 80 4 8 136 10 148 1.51e-15 70.9
MS.gene20798.t1 MTR_7g065770 29.091 165 95 4 4 156 3 157 2.60e-13 64.3
MS.gene20798.t1 MTR_6g006190 39.683 63 38 0 95 157 77 139 3.18e-12 60.8
MS.gene20798.t1 MTR_1717s0010 28.571 161 89 5 6 143 42 199 1.27e-11 60.8
MS.gene20798.t1 MTR_1527s0010 28.571 161 89 5 6 143 42 199 1.27e-11 60.8
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene20798.t1 AT3G62550 61.146 157 58 3 2 157 3 157 5.33e-64 193
MS.gene20798.t1 AT3G11930 36.970 165 89 4 6 158 33 194 3.38e-29 106
MS.gene20798.t1 AT3G11930 36.747 166 89 4 6 158 33 195 4.59e-29 105
MS.gene20798.t1 AT3G11930 36.527 167 89 4 6 158 33 196 6.35e-29 105
MS.gene20798.t1 AT2G47710 39.869 153 86 4 8 158 10 158 1.06e-27 101
MS.gene20798.t1 AT3G58450 35.802 162 90 5 8 158 32 190 3.17e-27 101
MS.gene20798.t1 AT1G09740 37.975 158 86 4 8 156 10 164 8.72e-27 99.4
MS.gene20798.t1 AT1G09740 37.975 158 86 4 8 156 10 164 8.72e-27 99.4
MS.gene20798.t1 AT3G58450 36.076 158 88 4 8 158 32 183 9.82e-27 100
MS.gene20798.t1 AT1G68300 35.714 154 90 3 6 156 10 157 4.20e-26 97.4
MS.gene20798.t1 AT1G11360 35.802 162 93 4 5 158 37 195 8.51e-24 93.6
MS.gene20798.t1 AT1G11360 35.802 162 93 4 5 158 37 195 8.51e-24 93.6
MS.gene20798.t1 AT1G11360 35.802 162 93 4 5 158 37 195 8.51e-24 93.6
MS.gene20798.t1 AT1G11360 35.802 162 93 4 5 158 37 195 8.51e-24 93.6
MS.gene20798.t1 AT3G11930 31.771 192 89 5 6 158 33 221 4.84e-23 91.3
MS.gene20798.t1 AT5G14680 26.506 166 110 3 1 157 1 163 2.71e-18 77.4
MS.gene20798.t1 AT3G01520 28.000 175 96 5 1 157 1 163 2.21e-17 75.1
MS.gene20798.t1 AT3G03270 30.357 168 89 4 4 156 3 157 1.17e-15 70.1
MS.gene20798.t1 AT3G53990 27.215 158 107 2 4 156 3 157 3.88e-15 68.9
MS.gene20798.t1 AT3G17020 29.518 166 98 4 2 156 3 160 8.91e-15 68.2

Find 27 sgRNAs with CRISPR-Local

Find 62 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CACAATTACAACTGGGCATT+TGG 0.240443 1.2:-65524983 None:intergenic
CAAAGTATCAATTGTATCAT+TGG 0.275490 1.2:-65524532 None:intergenic
AAAGAGAGAGCGGAAGATTA+TGG 0.304990 1.2:+65523748 MS.gene20798:CDS
CAATGATACAATTGATACTT+TGG 0.330035 1.2:+65524533 MS.gene20798:CDS
TGTTGTTAGTGTCAGCAATA+AGG 0.334363 1.2:-65523826 None:intergenic
GGTTGCTTCACAATTACAAC+TGG 0.349891 1.2:-65524991 None:intergenic
CCAATTTGTAGGGCACTACT+TGG 0.389332 1.2:+65524931 MS.gene20798:intron
AGAGCATGTATGCACTTTCC+TGG 0.390396 1.2:+65523792 MS.gene20798:CDS
ACCTTCTGCTGTCTACTCAT+TGG 0.404228 1.2:+65523880 MS.gene20798:CDS
GGTAGCAGTTGATGAGAGTG+AGG 0.430921 1.2:+65523769 MS.gene20798:CDS
ATAGAGAAAGTAGTTGGTAC+TGG 0.447004 1.2:+65524740 MS.gene20798:CDS
GTCTACTCATTGGATTCTGC+AGG 0.448519 1.2:+65523890 MS.gene20798:CDS
GCAACGCAGCAAAGAAACTA+GGG 0.514798 1.2:+65524783 MS.gene20798:CDS
TGCAACGCAGCAAAGAAACT+AGG 0.519057 1.2:+65524782 MS.gene20798:CDS
ACCTTAGTCATGGGAAGTCA+TGG 0.528245 1.2:+65524812 MS.gene20798:CDS
GCCATGACTTCCCATGACTA+AGG 0.537843 1.2:-65524813 None:intergenic
GTCATGGGAAGTCATGGCTA+TGG 0.540428 1.2:+65524818 MS.gene20798:CDS
ATAAATATAGAGAAAGTAGT+TGG 0.543839 1.2:+65524734 MS.gene20798:CDS
TCCAATGAGTAGACAGCAGA+AGG 0.550516 1.2:-65523881 None:intergenic
AGGGGCTGATACCTTAGTCA+TGG 0.560207 1.2:+65524802 MS.gene20798:CDS
ATGGCTATGGATTCATCAAG+AGG 0.623962 1.2:+65524831 MS.gene20798:CDS
GGGGCTGATACCTTAGTCAT+GGG 0.624939 1.2:+65524803 MS.gene20798:CDS
AATAAGGTTACTGATAGACC+AGG 0.625419 1.2:-65523810 None:intergenic
AATGAGTAGACAGCAGAAGG+TGG 0.668557 1.2:-65523878 None:intergenic
ACAAAATGGAAAAGAGAGAG+CGG 0.669276 1.2:+65523738 None:intergenic
GTTGCTTCACAATTACAACT+GGG 0.683814 1.2:-65524990 None:intergenic
CAACGCAGCAAAGAAACTAG+GGG 0.702473 1.2:+65524784 MS.gene20798:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! ATTAAGTTTTATTAGTAAAA+AGG - chr1.2:65524060-65524079 None:intergenic 10.0%
!! ATGTTTATTGAATACTAATT+TGG + chr1.2:65524479-65524498 MS.gene20798:intron 15.0%
!! TAAAACATTAAACACATAAT+TGG + chr1.2:65523939-65523958 MS.gene20798:intron 15.0%
!!! AAACTAATATTTTTGTTGAT+AGG + chr1.2:65524081-65524100 MS.gene20798:intron 15.0%
!!! ATGTGTTTAATGTTTTAATA+AGG - chr1.2:65523936-65523955 None:intergenic 15.0%
!!! TTTTAGAATATACAAAATGA+TGG + chr1.2:65524888-65524907 MS.gene20798:intron 15.0%
!! ATAAATATAGAGAAAGTAGT+TGG + chr1.2:65524734-65524753 MS.gene20798:CDS 20.0%
!! TATGTAATTACTATTACTCT+TGG + chr1.2:65524444-65524463 MS.gene20798:intron 20.0%
!!! GACTTGGTATTATTATTTAT+AGG + chr1.2:65524414-65524433 MS.gene20798:intron 20.0%
!!! TAGGTTTTGATATATATATG+AGG + chr1.2:65524012-65524031 MS.gene20798:intron 20.0%
!!! TGGTAGTAATATATTTTACA+GGG + chr1.2:65524499-65524518 MS.gene20798:intron 20.0%
!!! TTGGTAGTAATATATTTTAC+AGG + chr1.2:65524498-65524517 MS.gene20798:intron 20.0%
! AAAGTGAAAAAAAATTGAGC+TGG - chr1.2:65524650-65524669 None:intergenic 25.0%
! CAATGATACAATTGATACTT+TGG + chr1.2:65524533-65524552 MS.gene20798:CDS 25.0%
!! ACAAATAAGTTGTTGTTGTT+TGG - chr1.2:65524363-65524382 None:intergenic 25.0%
!! CAAAGTATCAATTGTATCAT+TGG - chr1.2:65524535-65524554 None:intergenic 25.0%
!! GATGGTATAACTAACTTTTA+TGG + chr1.2:65524906-65524925 MS.gene20798:intron 25.0%
!! TAAGTCAATATATGTTGACT+TGG + chr1.2:65524398-65524417 MS.gene20798:intron 25.0%
!!! ACTTATTTCTGGAGATTATT+GGG - chr1.2:65523981-65524000 None:intergenic 25.0%
!!! CTTATTTTATAAGCTCTTCA+AGG - chr1.2:65524294-65524313 None:intergenic 25.0%
AAATAAGTGAGGCATGAAAT+AGG + chr1.2:65523993-65524012 MS.gene20798:intron 30.0%
ACTCATAGACATGTTATGAA+CGG + chr1.2:65524323-65524342 MS.gene20798:intron 30.0%
ATAATCTCCAGAAATAAGTG+AGG + chr1.2:65523982-65524001 MS.gene20798:intron 30.0%
!! ACACATAATTGGTCTTATTC+AGG + chr1.2:65523950-65523969 MS.gene20798:intron 30.0%
!! CACTTATTTCTGGAGATTAT+TGG - chr1.2:65523982-65524001 None:intergenic 30.0%
!! TAATTGGTCTTATTCAGGAT+CGG + chr1.2:65523955-65523974 MS.gene20798:intron 30.0%
!! TTTTATGGTGCCAATTTGTA+GGG + chr1.2:65524921-65524940 MS.gene20798:intron 30.0%
AATAAGGTTACTGATAGACC+AGG - chr1.2:65523813-65523832 None:intergenic 35.0%
GTTGCTTCACAATTACAACT+GGG - chr1.2:65524993-65525012 None:intergenic 35.0%
TGTTGTTAGTGTCAGCAATA+AGG - chr1.2:65523829-65523848 None:intergenic 35.0%
TTGATAGGCCTTAAACGATA+GGG + chr1.2:65524096-65524115 MS.gene20798:intron 35.0%
TTGTTCATCATAACAAGTCG+CGG - chr1.2:65524144-65524163 None:intergenic 35.0%
TTTCATGCCTCACTTATTTC+TGG - chr1.2:65523992-65524011 None:intergenic 35.0%
! ATAGAGAAAGTAGTTGGTAC+TGG + chr1.2:65524740-65524759 MS.gene20798:CDS 35.0%
!! CTTTTATGGTGCCAATTTGT+AGG + chr1.2:65524920-65524939 MS.gene20798:intron 35.0%
AAAGAGAGAGCGGAAGATTA+TGG + chr1.2:65523748-65523767 MS.gene20798:CDS 40.0%
ATGGCTATGGATTCATCAAG+AGG + chr1.2:65524831-65524850 MS.gene20798:CDS 40.0%
CACAATTACAACTGGGCATT+TGG - chr1.2:65524986-65525005 None:intergenic 40.0%
CACTAAAGCCCTATCGTTTA+AGG - chr1.2:65524107-65524126 None:intergenic 40.0%
GGTTGCTTCACAATTACAAC+TGG - chr1.2:65524994-65525013 None:intergenic 40.0%
! CTTAAACGATAGGGCTTTAG+TGG + chr1.2:65524105-65524124 MS.gene20798:intron 40.0%
! GTCTTTTTGTCTGCAATACG+AGG + chr1.2:65524034-65524053 MS.gene20798:intron 40.0%
! GTTGATAGGCCTTAAACGAT+AGG + chr1.2:65524095-65524114 MS.gene20798:intron 40.0%
AATGAGTAGACAGCAGAAGG+TGG - chr1.2:65523881-65523900 None:intergenic 45.0%
ACCTTAGTCATGGGAAGTCA+TGG + chr1.2:65524812-65524831 MS.gene20798:CDS 45.0%
ACCTTCTGCTGTCTACTCAT+TGG + chr1.2:65523880-65523899 MS.gene20798:CDS 45.0%
AGAGCATGTATGCACTTTCC+TGG + chr1.2:65523792-65523811 MS.gene20798:CDS 45.0%
CAACGCAGCAAAGAAACTAG+GGG + chr1.2:65524784-65524803 MS.gene20798:CDS 45.0%
CCAAGTAGTGCCCTACAAAT+TGG - chr1.2:65524934-65524953 None:intergenic 45.0%
GCAACGCAGCAAAGAAACTA+GGG + chr1.2:65524783-65524802 MS.gene20798:CDS 45.0%
GTCTACTCATTGGATTCTGC+AGG + chr1.2:65523890-65523909 MS.gene20798:CDS 45.0%
TCCAATGAGTAGACAGCAGA+AGG - chr1.2:65523884-65523903 None:intergenic 45.0%
TGCAACGCAGCAAAGAAACT+AGG + chr1.2:65524782-65524801 MS.gene20798:CDS 45.0%
! CCAATTTGTAGGGCACTACT+TGG + chr1.2:65524931-65524950 MS.gene20798:intron 45.0%
! GCTTTAGTGGCCTTACCTTT+AGG + chr1.2:65524118-65524137 MS.gene20798:intron 45.0%
AGGGGCTGATACCTTAGTCA+TGG + chr1.2:65524802-65524821 MS.gene20798:CDS 50.0%
CATAACAAGTCGCGGCCTAA+AGG - chr1.2:65524136-65524155 None:intergenic 50.0%
GCCATGACTTCCCATGACTA+AGG - chr1.2:65524816-65524835 None:intergenic 50.0%
GGGGCTGATACCTTAGTCAT+GGG + chr1.2:65524803-65524822 MS.gene20798:CDS 50.0%
GTCATGGGAAGTCATGGCTA+TGG + chr1.2:65524818-65524837 MS.gene20798:CDS 50.0%
!! GGTAGCAGTTGATGAGAGTG+AGG + chr1.2:65523769-65523788 MS.gene20798:CDS 50.0%
CAAGTCGCGGCCTAAAGGTA+AGG - chr1.2:65524131-65524150 None:intergenic 55.0%


Chromosome Type Strat End Strand Name
chr1.2 gene 65523743 65525017 65523743 ID=MS.gene20798
chr1.2 mRNA 65523743 65525017 65523743 ID=MS.gene20798.t1;Parent=MS.gene20798
chr1.2 exon 65523743 65523911 65523743 ID=MS.gene20798.t1.exon1;Parent=MS.gene20798.t1
chr1.2 CDS 65523743 65523911 65523743 ID=cds.MS.gene20798.t1;Parent=MS.gene20798.t1
chr1.2 exon 65524520 65524632 65524520 ID=MS.gene20798.t1.exon2;Parent=MS.gene20798.t1
chr1.2 CDS 65524520 65524632 65524520 ID=cds.MS.gene20798.t1;Parent=MS.gene20798.t1
chr1.2 exon 65524734 65524852 65524734 ID=MS.gene20798.t1.exon3;Parent=MS.gene20798.t1
chr1.2 CDS 65524734 65524852 65524734 ID=cds.MS.gene20798.t1;Parent=MS.gene20798.t1
chr1.2 exon 65524942 65525017 65524942 ID=MS.gene20798.t1.exon4;Parent=MS.gene20798.t1
chr1.2 CDS 65524942 65525017 65524942 ID=cds.MS.gene20798.t1;Parent=MS.gene20798.t1
Gene Sequence

>MS.gene20798

ATGGAAAAGAGAGAGCGGAAGATTATGGTAGCAGTTGATGAGAGTGAGGAGAGCATGTATGCACTTTCCTGGTCTATCAGTAACCTTATTGCTGACACTAACAACAATAACAAGCTTGTGCTTCTCTATGTCAAGCCACCTTCTGCTGTCTACTCATTGGATTCTGCAGGTTAATTTCTTCACACTCACTCCTTATTAAAACATTAAACACATAATTGGTCTTATTCAGGATCGGCCCAATAATCTCCAGAAATAAGTGAGGCATGAAATAGGTTTTGATATATATATGAGGTCTTTTTGTCTGCAATACGAGGCCTTTTTACTAATAAAACTTAATAAAACTAATATTTTTGTTGATAGGCCTTAAACGATAGGGCTTTAGTGGCCTTACCTTTAGGCCGCGACTTGTTATGATGAACAACTTAATTAAAAGCTTATTGAATAAACTTTTAATATATAAGTGCTCATGTAAAAGTAATTTTCATAACAAAAATATAAAATAAAGATTAACTGTTTTCATATAAATTATAAGTTGATTTTATAAGCTACCTTGAAGAGCTTATAAAATAAGTTAAAAACAACTCATAGACATGTTATGAACGGTTTCATTAGTTCTTCCAAACAACAACAACTTATTTGTCTAGATAAACTCAAATAAGTCAATATATGTTGACTTGGTATTATTATTTATAGGATATTATTATGTAATTACTATTACTCTTGGCTTTTGAGTAACATGTTTATTGAATACTAATTTGGTAGTAATATATTTTACAGGGTATATTTTTTCCAATGATACAATTGATACTTTGGAAAACTATAGTTCACAGTTAGCTAAATCAGTAATGAAAAGAGCTGAAGCTATTTACAGAAACTTTGACGATGCAGATGTAAGTCAACTCATCCAGCTCAATTTTTTTTCACTTTTTTTTTTTAAAAAAAAATCTTCAATTTTTAGTTGTTGACTCTGAATTTGAGATTTTATTTACAGATAAATATAGAGAAAGTAGTTGGTACTGGAGATGCTAAGAATGTTATATGCAACGCAGCAAAGAAACTAGGGGCTGATACCTTAGTCATGGGAAGTCATGGCTATGGATTCATCAAGAGGTAATTAACATTAACATATATAGTCTTTAGTTATTTTTTAGAATATACAAAATGATGGTATAACTAACTTTTATGGTGCCAATTTGTAGGGCACTACTTGGAAGTGTAAGTGATTACTGTGTCAAGAATGCCAAATGCCCAGTTGTAATTGTGAAGCAACCATAG
Protein sequence

>MS.gene20798.t1

MEKRERKIMVAVDESEESMYALSWSISNLIADTNNNNKLVLLYVKPPSAVYSLDSAGYIFSNDTIDTLENYSSQLAKSVMKRAEAIYRNFDDADINIEKVVGTGDAKNVICNAAKKLGADTLVMGSHGYGFIKRALLGSVSDYCVKNAKCPVVIVKQP